The deal.II Homepage

From: heltai Date: Thu, 14 Nov 2013 16:20:41 +0000 (+0000) Subject: Merged from trunk. X-Git-Url: https://gitweb.dealii.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=57969a9ca79cd4d9cf5a2efae7345e920b2fa1a8;p=dealii-svn.git Merged from trunk. git-svn-id: https://svn.dealii.org/branches/branch_manifold_id@31657 0785d39b-7218-0410-832d-ea1e28bc413d --- diff --git a/deal.II/LICENSE b/deal.II/LICENSE index 8b89d07dc6..4ef81d521a 100644 --- a/deal.II/LICENSE +++ b/deal.II/LICENSE @@ -12,10 +12,10 @@ License as published by the Free Software Foundation; either version The full text of the GNU Lesser General Public version 2.1 is quoted below. -The subdirectory "bundled/" is not licensed by the deal.II authors. PLEASE -NOTE THAT THE SOFTWARE THERE IS COPYRIGHTED BY OTHERS THAN THE deal.II -AUTHORS, but is included by permission. For details, consult the stated -licenses there. +The subdirectories "bundled/" and "contrib/" contain third party software. +PLEASE NOTE THAT THE SOFTWARE THERE IS COPYRIGHTED BY OTHERS THAN THE +deal.II AUTHORS, but is included by permission. For details, consult the +stated licenses there. ---------------------------------------------------------------------- diff --git a/deal.II/README b/deal.II/README index 3d878e4de0..c88147149a 100644 --- a/deal.II/README +++ b/deal.II/README @@ -13,6 +13,7 @@ For the impatient: $ cd build $ cmake -DCMAKE_INSTALL_PREFIX=/path/where/deal.II/should/be/intalled/to .. $ make install (alternatively $ make -j install) + $ make test A detailed ReadME can be found at ./doc/readme.html and ./doc/users/cmake.html or at http://www.dealii.org/. diff --git a/deal.II/cmake/checks/check_03_compiler_bugs.cmake b/deal.II/cmake/checks/check_03_compiler_bugs.cmake index f2cc702cb0..a31f9f4824 100644 --- a/deal.II/cmake/checks/check_03_compiler_bugs.cmake +++ b/deal.II/cmake/checks/check_03_compiler_bugs.cmake @@ -314,15 +314,42 @@ CHECK_CXX_COMPILER_BUG( " DEAL_II_ICC_NUMERICLIMITS_BUG) -IF(DEAL_II_ICC_NUMERICLIMITS_BUG) +# +# icc-14.0.0 has an astonishing bug [1] where it hits an internal compiler +# error when run in C++11 mode with libstdc++-4.7 (from gcc). +# +# We just disable C++11 mode in this case +# +# [1] http://software.intel.com/en-us/forums/topic/472385 +# +# - Matthias Maier, 2013 +# +CHECK_CXX_COMPILER_BUG( + " + #include + template void foo() + { + std::vector data(100); + } + int main() + { + foo(); + } + " + DEAL_II_ICC_LIBSTDCPP47CXX11_BUG) + + +IF( DEAL_II_ICC_NUMERICLIMITS_BUG OR + DEAL_II_ICC_LIBSTDCPP47CXX11_BUG ) MESSAGE(STATUS - "DEAL_II_ICC_NUMERICLIMITS_BUG found, disabling c++11 support" + "Intel C++11 bug found, disabling C++11 support" ) STRIP_FLAG(CMAKE_CXX_FLAGS "${DEAL_II_CXX11_FLAG}") SET(DEAL_II_CAN_USE_CXX1X FALSE) SET(DEAL_II_USE_CXX11 FALSE) ENDIF() + # # gcc-4.8.1 has some problems with the constexpr "vertices_per_cell" in the # definition of alternating_form_at_vertices. diff --git a/deal.II/cmake/config/CMakeLists.txt b/deal.II/cmake/config/CMakeLists.txt index 8f21d7981e..d6b3bb2a89 100644 --- a/deal.II/cmake/config/CMakeLists.txt +++ b/deal.II/cmake/config/CMakeLists.txt @@ -173,7 +173,6 @@ CONFIGURE_FILE( ${CMAKE_CURRENT_BINARY_DIR}/${DEAL_II_PROJECT_CONFIG_NAME}ConfigVersion.cmake @ONLY ) - INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/${DEAL_II_PROJECT_CONFIG_NAME}Config.cmake ${CMAKE_CURRENT_BINARY_DIR}/${DEAL_II_PROJECT_CONFIG_NAME}ConfigVersion.cmake @@ -219,6 +218,7 @@ IF(DEAL_II_COMPONENT_COMPAT_FILES) # FOREACH(build ${DEAL_II_BUILD_TYPES}) + TO_STRING_AND_ADD_PREFIX(MAKEFILE_DEFINITIONS_${build} "-D" ${DEAL_II_USER_DEFINITIONS} @@ -228,14 +228,16 @@ IF(DEAL_II_COMPONENT_COMPAT_FILES) # # Ideally, DEAL_II_EXTERNAL_LIBRARIES should just contain a list of # full library paths. Nevertheless, filter out all elements that are - # not a full path starting with "/". + # not a full path starting with "/" or that happen to be a "framework" + # - we won't deal with that in Make.global_options. # + SET(_libs) FOREACH(_lib ${DEAL_II_EXTERNAL_LIBRARIES_${build}} ${DEAL_II_EXTERNAL_LIBRARIES} ) - IF(_lib MATCHES "^\\s*/") + IF(_lib MATCHES "^\\s*\\/" AND NOT _lib MATCHES "\\.framework$") LIST(APPEND _libs "${_lib}") ENDIF() ENDFOREACH() @@ -245,8 +247,6 @@ IF(DEAL_II_COMPONENT_COMPAT_FILES) ${_libs} ) - MESSAGE("\n\nDEBUG:") - SET(_paths) FOREACH(_lib $(D)/${DEAL_II_LIBRARY_RELDIR}/${CONFIG_LIBRARY_${build}} @@ -257,36 +257,48 @@ IF(DEAL_II_COMPONENT_COMPAT_FILES) # # Strip leading and trailing whitespace # - MESSAGE("--> \"${_lib}\"") STRING(STRIP "${_lib}" _lib) - MESSAGE(" stripped: \"${_lib}\"") - IF(_lib MATCHES "^(/|\\$\$D\$)") - # Full path: /path/to/libfoo.so: + IF(_lib MATCHES "^\\/.*\\.framework$") + # + # We have a MacOSX framework + # + # TODO: What do? + # + + ELSEIF(_lib MATCHES "^(\\/|\\$\$D\$)") + # + # Full path: /path/to/libfoo.(so|dylib|etc): + # # Extract library paths: GET_FILENAME_COMPONENT(_path ${_lib} PATH) LIST(APPEND _paths ${_path}) - MESSAGE(" appended: \"${_lib}\"") LIST(APPEND MAKEFILE_LIBS_${build} ${_lib}) - ELSEIF(_lib MATCHES "^-") - # Library is of the form "-lflag", don't touch it: - MESSAGE(" appended: \"${_lib}\"") + ELSEIF(_lib MATCHES "^-l") + # + # Library is of the form "-lfoo": + # LIST(APPEND MAKEFILE_LIBS_${build} ${_lib}) - ELSEIF(NOT "${_lib}" STREQUAL "") - # Well in this case we just assume that we have to append an "-l" - # Note: This won't cover case where a relative library name, such as - # libfoo.so, libfoo.dylib, etc. is specified... - MESSAGE(" appended: \"-l${_lib}\"") + ELSEIF(NOT _lib MATCHES "^\\s*$" AND NOT _lib MATCHES "\\.so(\\.[0-9]+)*$") + # + # Well in this case we just assume that we have to append a "-l" + # + LIST(APPEND MAKEFILE_LIBS_${build} "-l${_lib}") + ELSE() + # + # For now, ignore the rest. + # + # TODO: What do? + # ENDIF() - ENDFOREACH() -# MESSAGE(FATAL_ERROR "bailout") + ENDFOREACH() # # And build up an rpath: diff --git a/deal.II/cmake/configure/configure_1_lapack.cmake b/deal.II/cmake/configure/configure_1_lapack.cmake index 7c64e0dbe9..ede31c24ba 100644 --- a/deal.II/cmake/configure/configure_1_lapack.cmake +++ b/deal.II/cmake/configure/configure_1_lapack.cmake @@ -79,12 +79,8 @@ MACRO(RESET_LAPACK_FUNCTIONS_CACHE) ENDMACRO() - MACRO(FEATURE_LAPACK_CONFIGURE_EXTERNAL) - - ADD_FLAGS(DEAL_II_LINKER_FLAGS "${LAPACK_LINKER_FLAGS}") - DEAL_II_APPEND_LIBRARIES(${LAPACK_LIBRARIES}) - + REGISTER_FEATURE(LAPACK) CHECK_FOR_LAPACK_FUNCTIONS() ENDMACRO() diff --git a/deal.II/cmake/configure/configure_1_mpi.cmake b/deal.II/cmake/configure/configure_1_mpi.cmake index cd92d2707c..647ea4a81c 100644 --- a/deal.II/cmake/configure/configure_1_mpi.cmake +++ b/deal.II/cmake/configure/configure_1_mpi.cmake @@ -143,14 +143,12 @@ ENDMACRO() MACRO(FEATURE_MPI_CONFIGURE_EXTERNAL) - ADD_FLAGS(CMAKE_CXX_FLAGS "${MPI_CXX_COMPILE_FLAGS}") - ADD_FLAGS(DEAL_II_LINKER_FLAGS "${MPI_CXX_LINK_FLAGS}") - - DEAL_II_APPEND_LIBRARIES(${MPI_CXX_LIBRARIES}) - INCLUDE_DIRECTORIES(${MPI_CXX_INCLUDE_PATH}) - + # # The user has to know the location of the mpi headers as well: - LIST(APPEND DEAL_II_USER_INCLUDE_DIRS ${MPI_CXX_INCLUDE_PATH}) + # + SET(MPI_CXX_ADD_TO_USER_INCLUDE_DIRS TRUE) + + REGISTER_FEATURE(MPI_CXX) ENDMACRO() diff --git a/deal.II/cmake/configure/configure_1_threads.cmake b/deal.II/cmake/configure/configure_1_threads.cmake index 52e16e0ab8..da49c2eb24 100644 --- a/deal.II/cmake/configure/configure_1_threads.cmake +++ b/deal.II/cmake/configure/configure_1_threads.cmake @@ -151,9 +151,8 @@ ENDMACRO() MACRO(FEATURE_THREADS_CONFIGURE_EXTERNAL) - INCLUDE_DIRECTORIES(${TBB_INCLUDE_DIR}) - DEAL_II_APPEND_LIBRARIES(${TBB_LIBRARIES}) + REGISTER_FEATURE(TBB) IF(CMAKE_BUILD_TYPE MATCHES "Debug") IF(TBB_WITH_DEBUG_LIB) @@ -161,7 +160,6 @@ MACRO(FEATURE_THREADS_CONFIGURE_EXTERNAL) "TBB_USE_DEBUG=1" "TBB_DO_ASSERT=1" ) ENDIF() - ENDIF() # @@ -217,7 +215,7 @@ MACRO(FEATURE_THREADS_CONFIGURE_BUNDLED) FIND_LIBRARY(dl_LIBRARY NAMES dl) MARK_AS_ADVANCED(dl_LIBRARY) IF(NOT dl_LIBRARY MATCHES "-NOTFOUND") - DEAL_II_APPEND_LIBRARIES(${dl_LIBRARY}) + LIST(APPEND DEAL_II_EXTERNAL_LIBRARIES ${dl_LIBRARY}) ENDIF() INCLUDE_DIRECTORIES(${TBB_FOLDER}/include) diff --git a/deal.II/cmake/configure/configure_2_trilinos.cmake b/deal.II/cmake/configure/configure_2_trilinos.cmake index 6693073042..0060efb50b 100644 --- a/deal.II/cmake/configure/configure_2_trilinos.cmake +++ b/deal.II/cmake/configure/configure_2_trilinos.cmake @@ -195,12 +195,8 @@ ENDMACRO() MACRO(FEATURE_TRILINOS_CONFIGURE_EXTERNAL) - INCLUDE_DIRECTORIES(${TRILINOS_INCLUDE_DIRS}) - - # The user has to know the location of the trilinos headers as well: - LIST(APPEND DEAL_II_USER_INCLUDE_DIRS ${TRILINOS_INCLUDE_DIRS}) - - DEAL_II_APPEND_LIBRARIES(${TRILINOS_LIBRARIES}) + SET(TRILINOS_ADD_TO_USER_INCLUDE_DIRS TRUE) + REGISTER_FEATURE(TRILINOS) SET(DEAL_II_EXPAND_TRILINOS_VECTOR "TrilinosWrappers::Vector") SET(DEAL_II_EXPAND_TRILINOS_BLOCKVECTOR "TrilinosWrappers::BlockVector") diff --git a/deal.II/cmake/configure/configure_3_petsc.cmake b/deal.II/cmake/configure/configure_3_petsc.cmake index c1c71a4a83..3627e7c49c 100644 --- a/deal.II/cmake/configure/configure_3_petsc.cmake +++ b/deal.II/cmake/configure/configure_3_petsc.cmake @@ -114,10 +114,8 @@ ENDMACRO() MACRO(FEATURE_PETSC_CONFIGURE_EXTERNAL) INCLUDE_DIRECTORIES(${PETSC_INCLUDE_DIRS}) - # The user has to know the location of the petsc headers as well: - LIST(APPEND DEAL_II_USER_INCLUDE_DIRS ${PETSC_INCLUDE_DIRS}) - - DEAL_II_APPEND_LIBRARIES(${PETSC_LIBRARIES}) + SET(PETSC_ADD_TO_USER_INCLUDE_DIRS TRUE) + REGISTER_FEATURE(PETSC) # # Disable a bunch of warnings when compiling with petsc: diff --git a/deal.II/cmake/configure/configure_boost.cmake b/deal.II/cmake/configure/configure_boost.cmake index b6ed7c3b2c..9571fe9b0e 100644 --- a/deal.II/cmake/configure/configure_boost.cmake +++ b/deal.II/cmake/configure/configure_boost.cmake @@ -74,21 +74,33 @@ MACRO(FEATURE_BOOST_FIND_EXTERNAL var) MARK_AS_ADVANCED(Boost_DIR) - SET(BOOST_VERSION_MAJOR "${Boost_MAJOR_VERSION}") - SET(BOOST_VERSION_MINOR "${Boost_MINOR_VERSION}") - SET(BOOST_VERSION_SUBMINOR "${Boost_SUBMINOR_VERSION}") - SET(BOOST_VERSION - "${BOOST_VERSION_MAJOR}.${BOOST_VERSION_MINOR}.${BOOST_VERSION_SUBMINOR}" - ) - IF( Boost_SERIALIZATION_FOUND AND Boost_SYSTEM_FOUND AND - (NOT DEAL_II_WITH_THREADS OR Boost_THREAD_FOUND) - ) + (NOT DEAL_II_WITH_THREADS OR Boost_THREAD_FOUND) ) + + SET(BOOST_VERSION_MAJOR "${Boost_MAJOR_VERSION}") + SET(BOOST_VERSION_MINOR "${Boost_MINOR_VERSION}") + SET(BOOST_VERSION_SUBMINOR "${Boost_SUBMINOR_VERSION}") + SET(BOOST_VERSION + "${BOOST_VERSION_MAJOR}.${BOOST_VERSION_MINOR}.${BOOST_VERSION_SUBMINOR}" + ) + + # + # Remove "pthread" from Boost_LIBRARIES. Threading, if necessary, is + # already set up via configure_1_threads.cmake. + # + LIST(REMOVE_ITEM Boost_LIBRARIES "pthread") + + SET(BOOST_INCLUDE_DIRS ${Boost_INCLUDE_DIRS}) + SET(BOOST_LIBRARIES ${Boost_LIBRARIES}) + MARK_AS_ADVANCED(BOOST_DIR) + SET(${var} TRUE) + ELSE() + SET(BOOST_DIR "" CACHE PATH "An optional hint to a boost directory" ) @@ -96,21 +108,10 @@ MACRO(FEATURE_BOOST_FIND_EXTERNAL var) ENDMACRO() -MACRO(FEATURE_BOOST_CONFIGURE_EXTERNAL) - INCLUDE_DIRECTORIES (${Boost_INCLUDE_DIRS}) - - # The user has to know the location of the boost headers as well: - LIST(APPEND DEAL_II_USER_INCLUDE_DIRS ${Boost_INCLUDE_DIRS}) - - # - # Remove "pthread" from Boost_LIBRARIES. Threading, if necessary, is - # already set up via configure_1_threads.cmake. - # - LIST(REMOVE_ITEM Boost_LIBRARIES "pthread") - - DEAL_II_APPEND_LIBRARIES(${Boost_LIBRARIES}) - -ENDMACRO() +# +# The user has to know the location of the boost headers as well: +# +SET(BOOST_ADD_TO_USER_INCLUDE_DIRS TRUE) MACRO(FEATURE_BOOST_CONFIGURE_BUNDLED) diff --git a/deal.II/cmake/configure/configure_hdf5.cmake b/deal.II/cmake/configure/configure_hdf5.cmake index a5a40a255a..81e71ceffa 100644 --- a/deal.II/cmake/configure/configure_hdf5.cmake +++ b/deal.II/cmake/configure/configure_hdf5.cmake @@ -47,14 +47,10 @@ MACRO(FEATURE_HDF5_FIND_EXTERNAL var) ENDMACRO() -MACRO(FEATURE_HDF5_CONFIGURE_EXTERNAL) - INCLUDE_DIRECTORIES(${HDF5_INCLUDE_DIRS}) - - # The user has to know the location of the HDF5 headers as well: - LIST(APPEND DEAL_II_USER_INCLUDE_DIRS ${HDF5_INCLUDE_DIRS}) - - DEAL_II_APPEND_LIBRARIES(${HDF5_LIBRARIES}) -ENDMACRO() +# +# The user has to know the location of the hdf5 headers as well: +# +SET(HDF5_ADD_TO_USER_INCLUDE_DIRS TRUE) CONFIGURE_FEATURE(HDF5) diff --git a/deal.II/cmake/configure/configure_mumps.cmake b/deal.II/cmake/configure/configure_mumps.cmake index 0739098602..4022f98026 100644 --- a/deal.II/cmake/configure/configure_mumps.cmake +++ b/deal.II/cmake/configure/configure_mumps.cmake @@ -20,13 +20,11 @@ SET(FEATURE_MUMPS_DEPENDS DEAL_II_WITH_MPI DEAL_II_WITH_LAPACK) -MACRO(FEATURE_MUMPS_CONFIGURE_EXTERNAL) - INCLUDE_DIRECTORIES(${MUMPS_INCLUDE_DIRS}) - # The user has to know the location of the MUMPS headers as well: - LIST(APPEND DEAL_II_USER_INCLUDE_DIRS ${MUMPS_INCLUDE_DIRS}) +# +# The user has to know the location of the MUMPS headers as well: +# +SET(MUMPS_ADD_TO_USER_INCLUDE_DIRS TRUE) - DEAL_II_APPEND_LIBRARIES(${MUMPS_LIBRARIES}) -ENDMACRO() CONFIGURE_FEATURE(MUMPS) diff --git a/deal.II/cmake/configure/configure_p4est.cmake b/deal.II/cmake/configure/configure_p4est.cmake index de91ef6ea1..4055c0f30c 100644 --- a/deal.II/cmake/configure/configure_p4est.cmake +++ b/deal.II/cmake/configure/configure_p4est.cmake @@ -75,13 +75,10 @@ MACRO(FEATURE_P4EST_FIND_EXTERNAL var) ENDMACRO() -MACRO(FEATURE_P4EST_CONFIGURE_EXTERNAL) - INCLUDE_DIRECTORIES(${P4EST_INCLUDE_DIRS}) - - # The user has to know the location of the P4EST headers as well: - LIST(APPEND DEAL_II_USER_INCLUDE_DIRS ${P4EST_INCLUDE_DIRS}) +# +# The user has to know the location of the P4est headers as well: +# +SET(P4EST_ADD_TO_USER_INCLUDE_DIRS TRUE) - DEAL_II_APPEND_LIBRARIES(${P4EST_LIBRARIES}) -ENDMACRO() CONFIGURE_FEATURE(P4EST) diff --git a/deal.II/cmake/configure/configure_slepc.cmake b/deal.II/cmake/configure/configure_slepc.cmake index bf5415a0ff..fdb87649d0 100644 --- a/deal.II/cmake/configure/configure_slepc.cmake +++ b/deal.II/cmake/configure/configure_slepc.cmake @@ -57,14 +57,11 @@ MACRO(FEATURE_SLEPC_FIND_EXTERNAL var) ENDIF() ENDMACRO() -MACRO(FEATURE_SLEPC_CONFIGURE_EXTERNAL) - INCLUDE_DIRECTORIES(${SLEPC_INCLUDE_DIRS}) - # The user has to know the location of the SLEPC headers as well: - LIST(APPEND DEAL_II_USER_INCLUDE_DIRS ${SLEPC_INCLUDE_DIRS}) - - DEAL_II_APPEND_LIBRARIES(${SLEPC_LIBRARIES}) -ENDMACRO() +# +# The user has to know the location of the SLEPC headers as well: +# +SET(SLEPC_ADD_TO_USER_INCLUDE_DIRS TRUE) MACRO(FEATURE_SLEPC_ERROR_MESSAGE) diff --git a/deal.II/cmake/macros/macro_configure_feature.cmake b/deal.II/cmake/macros/macro_configure_feature.cmake index 0ffbf4fb10..4a35b260fd 100644 --- a/deal.II/cmake/macros/macro_configure_feature.cmake +++ b/deal.II/cmake/macros/macro_configure_feature.cmake @@ -134,22 +134,6 @@ MACRO(FEATURE_FIND_EXTERNAL _feature _var) ENDMACRO() -# -# Default macro for basic external setup: -# -MACRO(FEATURE_CONFIGURE_EXTERNAL _feature) - IF(DEFINED ${_feature}_INCLUDE_DIRS) - INCLUDE_DIRECTORIES(${${_feature}_INCLUDE_DIRS}) - ENDIF() - IF(DEFINED ${_feature}_LIBRARIES) - DEAL_II_APPEND_LIBRARIES(${${_feature}_LIBRARIES}) - ENDIF() - IF(DEFINED ${_feature}_LINKER_FLAGS) - ADD_FLAGS(DEAL_II_LINKER_FLAGS "${${_feature}_LINKER_FLAGS}") - ENDIF() -ENDMACRO() - - ######################################################################## # # # CONFIGURE_FEATURE: # @@ -249,7 +233,7 @@ MACRO(CONFIGURE_FEATURE _feature) IF(COMMAND FEATURE_${_feature}_CONFIGURE_EXTERNAL) RUN_COMMAND("FEATURE_${_feature}_CONFIGURE_EXTERNAL()") ELSE() - FEATURE_CONFIGURE_EXTERNAL(${_feature}) + REGISTER_FEATURE(${_feature}) ENDIF() MESSAGE(STATUS "DEAL_II_WITH_${_feature} successfully set up with external dependencies.") diff --git a/deal.II/cmake/macros/macro_deal_ii_append_libraries.cmake b/deal.II/cmake/macros/macro_deal_ii_append_libraries.cmake deleted file mode 100644 index de291d39b6..0000000000 --- a/deal.II/cmake/macros/macro_deal_ii_append_libraries.cmake +++ /dev/null @@ -1,47 +0,0 @@ -## --------------------------------------------------------------------- -## $Id$ -## -## Copyright (C) 2013 by the deal.II authors -## -## This file is part of the deal.II library. -## -## The deal.II library is free software; you can use it, redistribute -## it, and/or modify it under the terms of the GNU Lesser General -## Public License as published by the Free Software Foundation; either -## version 2.1 of the License, or (at your option) any later version. -## The full text of the license can be found in the file LICENSE at -## the top level of the deal.II distribution. -## -## --------------------------------------------------------------------- - -# -# A small macro to add libraries to -# DEAL_II_EXTERNAL_LIBRARIES -# DEAL_II_EXTERNAL_LIBRARIES_DEBUG -# DEAL_II_EXTERNAL_LIBRARIES_RELEASE -# depending on the "optmized", "debug" or "general" keyword -# -# Usage: -# DEAL_II_APPEND_LIBRARIES() -# - -MACRO(DEAL_II_APPEND_LIBRARIES) - - SET(_toggle "general") - FOREACH(_tmp ${ARGN}) - IF( "${_tmp}" STREQUAL "debug" OR - "${_tmp}" STREQUAL "optimized" OR - "${_tmp}" STREQUAL "general" ) - SET(_toggle "${_tmp}") - ELSE() - IF("${_toggle}" STREQUAL "general") - LIST(APPEND DEAL_II_EXTERNAL_LIBRARIES ${_tmp}) - ELSEIF("${_toggle}" STREQUAL "debug") - LIST(APPEND DEAL_II_EXTERNAL_LIBRARIES_DEBUG ${_tmp}) - ELSEIF("${_toggle}" STREQUAL "optimized") - LIST(APPEND DEAL_II_EXTERNAL_LIBRARIES_RELEASE ${_tmp}) - ENDIF() - ENDIF() - ENDFOREACH() - -ENDMACRO() diff --git a/deal.II/cmake/macros/macro_deal_ii_invoke_autopilot.cmake b/deal.II/cmake/macros/macro_deal_ii_invoke_autopilot.cmake index 38c93daec9..29867f93f8 100644 --- a/deal.II/cmake/macros/macro_deal_ii_invoke_autopilot.cmake +++ b/deal.II/cmake/macros/macro_deal_ii_invoke_autopilot.cmake @@ -152,7 +152,7 @@ ${_switch_targets}# # $ make edit_cache - to change (cached) configuration variables # and rerun the configure and generate phases of CMake # -# $ make strip_comments - strip the source files in this +# $ make strip_comments - to strip the source files in this # directory off the documentation comments # $ make clean - to remove the generated executable as well as # all intermediate compilation files diff --git a/deal.II/cmake/macros/macro_pickup_tests.cmake b/deal.II/cmake/macros/macro_pickup_tests.cmake index 2b0ace6afb..1e840dee4a 100644 --- a/deal.II/cmake/macros/macro_pickup_tests.cmake +++ b/deal.II/cmake/macros/macro_pickup_tests.cmake @@ -74,12 +74,12 @@ MACRO(DEAL_II_PICKUP_TESTS) SET(_define_test FALSE) ENDIF() ELSE() - MESSAGE(WARNING " + MESSAGE(FATAL_ERROR " Invalid feature constraint \"${_match}\" in file \"${_comparison}\": -The feature \"DEAL_II_${_feature}\" does not exist. Test dropped.\n" +The feature \"DEAL_II_${_feature}\" does not exist.\n" ) - SET(_define_test FALSE) + #SET(_define_test FALSE) ENDIF() ENDFOREACH() diff --git a/deal.II/cmake/macros/macro_register_feature.cmake b/deal.II/cmake/macros/macro_register_feature.cmake new file mode 100644 index 0000000000..a4408fe8d9 --- /dev/null +++ b/deal.II/cmake/macros/macro_register_feature.cmake @@ -0,0 +1,99 @@ +## --------------------------------------------------------------------- +## $Id$ +## +## Copyright (C) 2013 by the deal.II authors +## +## This file is part of the deal.II library. +## +## The deal.II library is free software; you can use it, redistribute +## it, and/or modify it under the terms of the GNU Lesser General +## Public License as published by the Free Software Foundation; either +## version 2.1 of the License, or (at your option) any later version. +## The full text of the license can be found in the file LICENSE at +## the top level of the deal.II distribution. +## +## --------------------------------------------------------------------- + +# +# This macro is used for the feature configuration in deal.II +# +# Usage: +# REGISTER_FEATURE(feature) +# +# This macro will +# +# - add ${feature}_INCLUDE_DIRS and ${feature}_INCLUDE_PATH +# to the list of (internal) include +# directories +# - and if ${feature}_ADD_TO_USER_INCLUDE_DIRS is defined also to +# DEAL_II_USER_INCLUDE_DIRS +# +# - add ${feature}_LINKER_FLAGS and ${feature}_LINK_FLAGS to +# DEAL_II_LINKER_FLAGS +# +# - add ${feature}_CXX_FLAGS and ${feature}_COMPILE_FLAGS to +# CMAKE_CXX_FLAGS +# +# - add ${feature}_LIBRARIES to the list of deal.II libraries depending +# on general, optimized or debug keyword +# + + +MACRO(REGISTER_FEATURE _feature) + MESSAGE(STATUS "Register enabled external feature ${_feature}:") + + # variables for include directories: + FOREACH(_var ${_feature}_INCLUDE_DIRS ${_feature}_INCLUDE_PATH) + IF(DEFINED ${_var}) + MESSAGE(STATUS " ${_var}") + INCLUDE_DIRECTORIES(${${_var}}) + IF(${_feature}_ADD_TO_USER_INCLUDE_DIRS) + LIST(APPEND DEAL_II_USER_INCLUDE_DIRS ${${_var}}) + ENDIF() + ENDIF() + ENDFOREACH() + + # variables for linker flags: + FOREACH(_var ${_feature}_LINKER_FLAGS ${_feature}_LINK_FLAGS) + IF(DEFINED ${_var}) + MESSAGE(STATUS " ${_var}") + ADD_FLAGS(DEAL_II_LINKER_FLAGS "${${_var}}") + ENDIF() + ENDFOREACH() + + # variables for compiler flags: + FOREACH(_var ${_feature}_CXX_FLAGS ${_feature}_COMPILE_FLAGS) + IF(DEFINED ${_var}) + MESSAGE(STATUS " ${_var}") + ADD_FLAGS(CMAKE_CXX_FLAGS "${${_var}}") + ENDIF() + ENDFOREACH() + + IF(DEFINED ${_feature}_LIBRARIES) + MESSAGE(STATUS " ${_feature}_LIBRARIES") + # + # Add ${_feature}_LIBRARIES to + # DEAL_II_EXTERNAL_LIBRARIES + # DEAL_II_EXTERNAL_LIBRARIES_DEBUG + # DEAL_II_EXTERNAL_LIBRARIES_RELEASE + # depending on the "optmized", "debug" or "general" keyword + # + SET(_toggle "general") + FOREACH(_tmp ${${_feature}_LIBRARIES}) + IF( "${_tmp}" STREQUAL "debug" OR + "${_tmp}" STREQUAL "optimized" OR + "${_tmp}" STREQUAL "general" ) + SET(_toggle "${_tmp}") + ELSE() + IF("${_toggle}" STREQUAL "general") + LIST(APPEND DEAL_II_EXTERNAL_LIBRARIES ${_tmp}) + ELSEIF("${_toggle}" STREQUAL "debug") + LIST(APPEND DEAL_II_EXTERNAL_LIBRARIES_DEBUG ${_tmp}) + ELSEIF("${_toggle}" STREQUAL "optimized") + LIST(APPEND DEAL_II_EXTERNAL_LIBRARIES_RELEASE ${_tmp}) + ENDIF() + ENDIF() + ENDFOREACH() + ENDIF() + +ENDMACRO() diff --git a/deal.II/cmake/modules/FindDEALII_LAPACK.cmake b/deal.II/cmake/modules/FindDEALII_LAPACK.cmake index be470cec36..84b6a37d3f 100644 --- a/deal.II/cmake/modules/FindDEALII_LAPACK.cmake +++ b/deal.II/cmake/modules/FindDEALII_LAPACK.cmake @@ -114,6 +114,14 @@ IF(LAPACK_FOUND) ENDFOREACH() SWITCH_LIBRARY_PREFERENCE() + # + # Filter out spurious "FALSE" in the library lists: + # + IF(DEFINED BLAS_LIBRARIES) + LIST(REMOVE_ITEM BLAS_LIBRARIES "FALSE") + ENDIF() + LIST(REMOVE_ITEM LAPACK_LIBRARIES "FALSE") + MARK_AS_ADVANCED( BLAS_DIR LAPACK_DIR @@ -130,14 +138,10 @@ ELSE() ) # - # If we couldn't find LAPACK, clean up the library variables: + # Clean up the library variables in case we couldn't find the libraries + # to avoid spurious inclusions of "-NOTFOUND" or "FALSE": # - - IF("${BLAS_LIBRARIES}" STREQUAL "FALSE") - SET(BLAS_LIBRARIES "") - ENDIF() - IF("${LAPACK_LIBRARIES}" STREQUAL "FALSE") - SET(LAPACK_LIBRARIES "") - ENDIF() + SET(BLAS_LIBRARIES) + SET(LAPACK_LIBRARIES) ENDIF() diff --git a/deal.II/cmake/modules/FindHDF5.cmake b/deal.II/cmake/modules/FindHDF5.cmake index fec6194dbe..66417e3c33 100644 --- a/deal.II/cmake/modules/FindHDF5.cmake +++ b/deal.II/cmake/modules/FindHDF5.cmake @@ -49,7 +49,7 @@ FIND_LIBRARY(HDF5_HL_LIBRARY NAMES hdf5_hl lib${LIB_SUFFIX} lib64 lib ) -FIND_FILE(HDF5_PUBCONF H5pubconf.h +FIND_FILE(HDF5_PUBCONF NAMES H5pubconf.h H5pubconf-64.h HINTS ${HDF5_INCLUDE_DIR} ${HDF5_DIR} diff --git a/deal.II/cmake/modules/FindPETSC.cmake b/deal.II/cmake/modules/FindPETSC.cmake index 3bd673927c..1a4f3122c4 100644 --- a/deal.II/cmake/modules/FindPETSC.cmake +++ b/deal.II/cmake/modules/FindPETSC.cmake @@ -29,6 +29,7 @@ # PETSC_VERSION_PATCH # PETSC_WITH_MPIUNI # PETSC_WITH_64BIT_INDICES +# PETSC_WITH_COMPLEX # INCLUDE(FindPackageHandleStandardArgs) @@ -207,6 +208,17 @@ IF(PETSC_FOUND) SET(PETSC_WITH_64BIT_INDICES TRUE) ENDIF() + # + # Is petsc compiled with support for COMPLEX numbers? + # + FILE(STRINGS "${PETSC_PETSCCONF_H}" PETSC_COMPLEX_STRING + REGEX "#define.*PETSC_USE_COMPLEX 1") + IF("${PETSC_COMPLEX_STRING}" STREQUAL "") + SET(PETSC_WITH_COMPLEX FALSE) + ELSE() + SET(PETSC_WITH_COMPLEX TRUE) + ENDIF() + FILE(STRINGS "${PETSC_PETSCVERSION_H}" PETSC_VERSION_MAJOR_STRING REGEX "#define.*PETSC_VERSION_MAJOR") STRING(REGEX REPLACE "^.*PETSC_VERSION_MAJOR.*([0-9]+).*" "\\1" diff --git a/deal.II/cmake/setup_finalize.cmake b/deal.II/cmake/setup_finalize.cmake index 1b3849d7a4..cb01181acf 100644 --- a/deal.II/cmake/setup_finalize.cmake +++ b/deal.II/cmake/setup_finalize.cmake @@ -124,10 +124,15 @@ _both( # ${CMAKE_CXX_COMPILER} " ) -_detailed( -"# CMAKE_GENERATOR: ${CMAKE_GENERATOR} -" - ) + +IF(CMAKE_C_COMPILER_WORKS) + _detailed("# CMAKE_C_COMPILER: ${CMAKE_C_COMPILER}\n") +ENDIF() +IF(CMAKE_Fortran_COMPILER_WORKS) + _detailed("# CMAKE_Fortran_COMPILER: ${CMAKE_Fortran_COMPILER}\n") +ENDIF() +_detailed("# CMAKE_GENERATOR: ${CMAKE_GENERATOR}\n") + IF(CMAKE_CROSSCOMPILING) _both( "#\n# CROSSCOMPILING!\n" @@ -226,7 +231,7 @@ FOREACH(_var ${_features}) IF( # MPI: _var2 MATCHES "^${_feature}_CXX_(COMPILER|COMPILE_FLAGS|LINK_FLAGS|LIBRARIES|INCLUDE_PATH)$" OR # Boost: - ( _feature MATCHES "BOOST" AND _var2 MATCHES "^Boost_(LIBRARIES|INCLUDE_DIRS)$" ) OR + ( _feature MATCHES "BOOST" AND _var2 MATCHES "^BOOST_(LIBRARIES|INCLUDE_DIRS)$" ) OR # TBB: ( _feature MATCHES "THREADS" AND _var2 MATCHES "^TBB_(LIBRARIES|INCLUDE_DIRS)$" ) OR # Generic: diff --git a/deal.II/contrib/mesh_conversion/README.txt b/deal.II/contrib/mesh_conversion/README.txt index ef00b074b1..10dfeb0360 100644 --- a/deal.II/contrib/mesh_conversion/README.txt +++ b/deal.II/contrib/mesh_conversion/README.txt @@ -54,3 +54,13 @@ Copyright: ---------- This program is distributed under the GNU GPL v2.0 copyright. Details can be found at: http://www.gnu.org/licenses/gpl-2.0.html + +This copyright is extended to the example mesh files distributed with this program, namely +./mesh/2d/2d_test.* +./mesh/2d/quad.* +./mesh/3d/CC.* +./mesh/3d/CC_cubit_new.* +./mesh/3d/CC_cubit_old.* +./mesh/3d/test_cube_1.* +./mesh/3d/test_cube_pave_1.* +./mesh/3d/test_cube_two_materials.* \ No newline at end of file diff --git a/deal.II/contrib/mesh_conversion/mesh/2d/2d_test.cub b/deal.II/contrib/mesh_conversion/mesh/2d/2d_test.cub old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/2d/2d_test.inp b/deal.II/contrib/mesh_conversion/mesh/2d/2d_test.inp old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/2d/2d_test.ucd b/deal.II/contrib/mesh_conversion/mesh/2d/2d_test.ucd old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/2d/quad.cub b/deal.II/contrib/mesh_conversion/mesh/2d/quad.cub old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/2d/quad.inp b/deal.II/contrib/mesh_conversion/mesh/2d/quad.inp old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/2d/quad.ucd b/deal.II/contrib/mesh_conversion/mesh/2d/quad.ucd old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/3d/CC.cub b/deal.II/contrib/mesh_conversion/mesh/3d/CC.cub old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/3d/CC_cubit_new.inp b/deal.II/contrib/mesh_conversion/mesh/3d/CC_cubit_new.inp old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/3d/CC_cubit_new.ucd b/deal.II/contrib/mesh_conversion/mesh/3d/CC_cubit_new.ucd old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/3d/CC_cubit_old.inp b/deal.II/contrib/mesh_conversion/mesh/3d/CC_cubit_old.inp old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/3d/CC_cubit_old.ucd b/deal.II/contrib/mesh_conversion/mesh/3d/CC_cubit_old.ucd old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_1.cub b/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_1.cub old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_1.inp b/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_1.inp old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_1.ucd b/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_1.ucd old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_pave_1.cub b/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_pave_1.cub old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_pave_1.inp b/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_pave_1.inp old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_pave_1.ucd b/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_pave_1.ucd old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_two_materials.cub b/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_two_materials.cub old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_two_materials.inp b/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_two_materials.inp old mode 100755 new mode 100644 diff --git a/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_two_materials.ucd b/deal.II/contrib/mesh_conversion/mesh/3d/test_cube_two_materials.ucd old mode 100755 new mode 100644 diff --git a/deal.II/doc/README.doc b/deal.II/doc/README.doc index c2b56533b9..b3b1fd0c96 100644 --- a/deal.II/doc/README.doc +++ b/deal.II/doc/README.doc @@ -1,13 +1,9 @@ This folder contains the html documentation of deal.II -With the exception of the content under publications/* and reports/* the -documentation is covered by the same license as the deal.II library itself, -namely LGPL-2.1+. +The documentation is generally covered by the same license as the deal.II +library itself, namely LGPL-2.1+. -Unclear license status: +Exceptions: - external-libraries/p4est-setup.sh - doxygen/doxygen.sty - doxygen/options.dox.in - reports/* + external-libraries/p4est-setup.sh - coming from the p4est project, GPL-2+ diff --git a/deal.II/doc/doxygen/doxygen.sty b/deal.II/doc/doxygen/doxygen.sty deleted file mode 100644 index 948092592f..0000000000 --- a/deal.II/doc/doxygen/doxygen.sty +++ /dev/null @@ -1,63 +0,0 @@ -\NeedsTeXFormat{LaTeX2e} -\ProvidesPackage{doxygen} -\RequirePackage{calc} -\RequirePackage{array} -\pagestyle{fancyplain} -\newcommand{\clearemptydoublepage}{\newpage{\pagestyle{empty}\cleardoublepage}} -\renewcommand{\chaptermark}[1]{\markboth{#1}{}} -\renewcommand{\sectionmark}[1]{\markright{\thesection\ #1}} -\lhead[\fancyplain{}{\bfseries\thepage}] - {\fancyplain{}{\bfseries\rightmark}} -\rhead[\fancyplain{}{\bfseries\leftmark}] - {\fancyplain{}{\bfseries\thepage}} -\rfoot[\fancyplain{}{\bfseries\scriptsize Generated on Wed Jan 11 21:30:49 2006 by doxygen\lfoot[]{\fancyplain{}{\bfseries\scriptsize Generated on Wed Jan 11 21:30:49 2006 by doxygen}} -\cfoot{} -\newenvironment{CompactList} -{\begin{list}{}{ - \setlength{\leftmargin}{0.5cm} - \setlength{\itemsep}{0pt} - \setlength{\parsep}{0pt} - \setlength{\topsep}{0pt} - \renewcommand{\makelabel}{}}} -{\end{list}} -\newenvironment{CompactItemize} -{ - \begin{itemize} - \setlength{\itemsep}{-3pt} - \setlength{\parsep}{0pt} - \setlength{\topsep}{0pt} - \setlength{\partopsep}{0pt} -} -{\end{itemize}} -\newcommand{\PBS}[1]{\let\temp=\\#1\let\\=\temp} -\newlength{\tmplength} -\newenvironment{TabularC}[1] -{ -\setlength{\tmplength} - {\linewidth/(#1)-\tabcolsep*2-\arrayrulewidth*(#1+1)/(#1)} - \par\begin{tabular*}{\linewidth} - {*{#1}{|>{\PBS\raggedright\hspace{0pt}}p{\the\tmplength}}|} -} -{\end{tabular*}\par} -\newcommand{\entrylabel}[1]{ - {\parbox[b]{\labelwidth-4pt}{\makebox[0pt][l]{\textbf{#1}}\\}}} -\newenvironment{Desc} -{\begin{list}{} - { - \settowidth{\labelwidth}{40pt} - \setlength{\leftmargin}{\labelwidth} - \setlength{\parsep}{0pt} - \setlength{\itemsep}{-4pt} - \renewcommand{\makelabel}{\entrylabel} - } -} -{\end{list}} -\newenvironment{Indent} - {\begin{list}{}{\setlength{\leftmargin}{0.5cm}} - \item[]\ignorespaces} - {\unskip\end{list}} -\setlength{\parindent}{0cm} -\setlength{\parskip}{0.2cm} -\addtocounter{secnumdepth}{1} -\sloppy -\usepackage[T1]{fontenc} diff --git a/deal.II/doc/doxygen/options.dox.in b/deal.II/doc/doxygen/options.dox.in index e30740fbdd..da03da80a6 100644 --- a/deal.II/doc/doxygen/options.dox.in +++ b/deal.II/doc/doxygen/options.dox.in @@ -1,996 +1,140 @@ -# Doxyfile 1.3.6 - -# This file describes the settings to be used by the documentation system -# doxygen (www.doxygen.org) for a project -# -# All text after a hash (#) is considered a comment and will be ignored -# The format is: -# TAG = value [value, ...] -# For lists items can also be appended using: -# TAG += value [value, ...] -# Values that contain spaces should be placed between quotes (" ") - -#--------------------------------------------------------------------------- -# Project related configuration options -#--------------------------------------------------------------------------- - -# The PROJECT_NAME tag is a single word (or a sequence of words surrounded -# by quotes) that should identify the project. +# This file contains project-specific configurations for the +# deal.II documentation. PROJECT_NAME = "The deal.II library" - -# The PROJECT_NUMBER tag can be used to enter a project or revision number. -# This could be handy for archiving the generated documentation or -# if some version control system is used. - PROJECT_NUMBER = "Reference documentation for deal.II version @DEAL_II_PACKAGE_VERSION@" - -# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) -# base path where the generated documentation will be put. -# If a relative path is entered, it will be relative to the location -# where doxygen was started. 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CREATE_SUBDIRS = NO +SHORT_NAMES = NO +CASE_SENSE_NAMES = YES -# The OUTPUT_LANGUAGE tag is used to specify the language in which all -# documentation generated by doxygen is written. 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Doxygen will then generate output that is more tailored for Java. -# For instance, namespaces will be presented as packages, qualified scopes -# will look different, etc. - -OPTIMIZE_OUTPUT_JAVA = NO - -# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want to -# include (a tag file for) the STL sources as input, then you should -# set this tag to YES in order to let doxygen match functions declarations and -# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. -# func(std::string) {}). This also make the inheritance and collaboration -# diagrams that involve STL classes more complete and accurate. - -BUILTIN_STL_SUPPORT = NO - -# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC -# tag is set to YES, then doxygen will reuse the documentation of the first -# member in the group (if any) for the other members of the group. By default -# all members of a group must be documented explicitly. - -DISTRIBUTE_GROUP_DOC = NO - -# Set the SUBGROUPING tag to YES (the default) to allow class member groups of -# the same type (for instance a group of public functions) to be put as a -# subgroup of that type (e.g. under the Public Functions section). Set it to -# NO to prevent subgrouping. Alternatively, this can be done per class using -# the \nosubgrouping command. +BUILTIN_STL_SUPPORT = YES -SUBGROUPING = YES #--------------------------------------------------------------------------- # Build related configuration options #--------------------------------------------------------------------------- -# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in -# documentation are documented, even if no documentation was available. -# Private class members and static file members will be hidden unless -# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES - EXTRACT_ALL = NO - -# If the EXTRACT_PRIVATE tag is set to YES all private members of a class -# will be included in the documentation. - EXTRACT_PRIVATE = YES - -# If the EXTRACT_STATIC tag is set to YES all static members of a file -# will be included in the documentation. - EXTRACT_STATIC = YES - -# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) -# defined locally in source files will be included in the documentation. -# If set to NO only classes defined in header files are included. - EXTRACT_LOCAL_CLASSES = YES - -# This flag is only useful for Objective-C code. When set to YES local -# methods, which are defined in the implementation section but not in -# the interface are included in the documentation. -# If set to NO (the default) only methods in the interface are included. - -EXTRACT_LOCAL_METHODS = NO - -# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all -# undocumented members of documented classes, files or namespaces. -# If set to NO (the default) these members will be included in the -# various overviews, but no documentation section is generated. -# This option has no effect if EXTRACT_ALL is enabled. - -HIDE_UNDOC_MEMBERS = YES - -# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all -# undocumented classes that are normally visible in the class hierarchy. -# If set to NO (the default) these classes will be included in the various -# overviews. This option has no effect if EXTRACT_ALL is enabled. - -HIDE_UNDOC_CLASSES = YES - -# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all -# friend (class|struct|union) declarations. -# If set to NO (the default) these declarations will be included in the -# documentation. - -HIDE_FRIEND_COMPOUNDS = NO - -# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any -# documentation blocks found inside the body of a function. -# If set to NO (the default) these blocks will be appended to the -# function's detailed documentation block. - -HIDE_IN_BODY_DOCS = NO - -# The INTERNAL_DOCS tag determines if documentation -# that is typed after a \internal command is included. If the tag is set -# to NO (the default) then the documentation will be excluded. -# Set it to YES to include the internal documentation. - -INTERNAL_DOCS = NO - -# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate -# file names in lower-case letters. If set to YES upper-case letters are also -# allowed. This is useful if you have classes or files whose names only differ -# in case and if your file system supports case sensitive file names. Windows -# and Mac users are advised to set this option to NO. - -CASE_SENSE_NAMES = YES - -# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen -# will show members with their full class and namespace scopes in the -# documentation. If set to YES the scope will be hidden. - -HIDE_SCOPE_NAMES = NO - -# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen -# will put a list of the files that are included by a file in the documentation -# of that file. - -SHOW_INCLUDE_FILES = NO - -# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] -# is inserted in the documentation for inline members. - -INLINE_INFO = YES - -# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen -# will sort the (detailed) documentation of file and class members -# alphabetically by member name. If set to NO the members will appear in -# declaration order. - +HIDE_UNDOC_MEMBERS = NO +HIDE_UNDOC_CLASSES = NO SORT_MEMBER_DOCS = NO - -# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the -# brief documentation of file, namespace and class members alphabetically -# by member name. If set to NO (the default) the members will appear in -# declaration order. - SORT_BRIEF_DOCS = NO - -# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be -# sorted by fully-qualified names, including namespaces. If set to -# NO (the default), the class list will be sorted only by class name, -# not including the namespace part. -# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. -# Note: This option applies only to the class list, not to the -# alphabetical list. - SORT_BY_SCOPE_NAME = NO - -# The GENERATE_TODOLIST tag can be used to enable (YES) or -# disable (NO) the todo list. This list is created by putting \todo -# commands in the documentation. - GENERATE_TODOLIST = YES - -# The GENERATE_TESTLIST tag can be used to enable (YES) or -# disable (NO) the test list. This list is created by putting \test -# commands in the documentation. - -GENERATE_TESTLIST = YES - -# The GENERATE_BUGLIST tag can be used to enable (YES) or -# disable (NO) the bug list. This list is created by putting \bug -# commands in the documentation. - -GENERATE_BUGLIST = YES - -# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or -# disable (NO) the deprecated list. This list is created by putting -# \deprecated commands in the documentation. - GENERATE_DEPRECATEDLIST= YES - -# The ENABLED_SECTIONS tag can be used to enable conditional -# documentation sections, marked by \if sectionname ... \endif. - -ENABLED_SECTIONS = YES - -# The MAX_INITIALIZER_LINES tag determines the maximum number of lines -# the initial value of a variable or define consists of for it to appear in -# the documentation. If the initializer consists of more lines than specified -# here it will be hidden. Use a value of 0 to hide initializers completely. -# The appearance of the initializer of individual variables and defines in the -# documentation can be controlled using \showinitializer or \hideinitializer -# command in the documentation regardless of this setting. - -MAX_INITIALIZER_LINES = 30 - -# Set the SHOW_USED_FILES tag to NO to disable the list of files generated -# at the bottom of the documentation of classes and structs. If set to YES the -# list will mention the files that were used to generate the documentation. - SHOW_USED_FILES = YES -# The FILE_VERSION_FILTER tag can be used to specify a program or script that -# doxygen should invoke to get the current version for each file (typically from the -# version control system). Doxygen will invoke the program by executing (via -# popen()) the command

, where is the value of -# the FILE_VERSION_FILTER tag, and is the name of an input file -# provided by doxygen. Whatever the program writes to standard output -# is used as the file version. See the manual for examples. - -FILE_VERSION_FILTER = - #--------------------------------------------------------------------------- # configuration options related to warning and progress messages #--------------------------------------------------------------------------- -# The QUIET tag can be used to turn on/off the messages that are generated -# by doxygen. Possible values are YES and NO. If left blank NO is used. - QUIET = YES - -# The WARNINGS tag can be used to turn on/off the warning messages that are -# generated by doxygen. Possible values are YES and NO. If left blank -# NO is used. - WARNINGS = YES - -# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings -# for undocumented members. If EXTRACT_ALL is set to YES then this flag will -# automatically be disabled. - WARN_IF_UNDOCUMENTED = YES - -# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for -# potential errors in the documentation, such as not documenting some -# parameters in a documented function, or documenting parameters that -# don't exist or using markup commands wrongly. - WARN_IF_DOC_ERROR = YES -# This WARN_NO_PARAMDOC option can be abled to get warnings for -# functions that are documented, but have no documentation for their parameters -# or return value. If set to NO (the default) doxygen will only warn about -# wrong or incomplete parameter documentation, but not about the absence of -# documentation. - -WARN_NO_PARAMDOC = NO - -# The WARN_FORMAT tag determines the format of the warning messages that -# doxygen can produce. The string should contain the $file, $line, and $text -# tags, which will be replaced by the file and line number from which the -# warning originated and the warning text. Optionally the format may contain -# $version, which will be replaced by the version of the file (if it could -# be obtained via FILE_VERSION_FILTER) - -WARN_FORMAT = "$file:$line: $text " - -# The WARN_LOGFILE tag can be used to specify a file to which warning -# and error messages should be written. If left blank the output is written -# to stderr. - -WARN_LOGFILE = - #--------------------------------------------------------------------------- # configuration options related to the input files #--------------------------------------------------------------------------- -# The INPUT tag can be used to specify the files and/or directories that contain -# documented source files. You may enter file names like "myfile.cpp" or -# directories like "/usr/src/myproject". Separate the files or directories -# with spaces. - INPUT = - -# If the value of the INPUT tag contains directories, you can use the -# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp -# and *.h) to filter out the source-files in the directories. If left -# blank the following patterns are tested: -# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx -# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py - -FILE_PATTERNS = - -# The RECURSIVE tag can be used to turn specify whether or not subdirectories -# should be searched for input files as well. Possible values are YES and NO. -# If left blank NO is used. - -RECURSIVE = NO - -# The EXCLUDE tag can be used to specify files and/or directories that should -# excluded from the INPUT source files. This way you can easily exclude a -# subdirectory from a directory tree whose root is specified with the INPUT tag. - -EXCLUDE = - -# The EXCLUDE_SYMLINKS tag can be used select whether or not files or -# directories that are symbolic links (a Unix filesystem feature) are excluded -# from the input. - -EXCLUDE_SYMLINKS = NO - -# If the value of the INPUT tag contains directories, you can use the -# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude -# certain files from those directories. Note that the wildcards are matched -# against the file with absolute path, so to exclude all test directories -# for example use the pattern */test/* - EXCLUDE_PATTERNS = *.templates.h - -# The EXAMPLE_PATH tag can be used to specify one or more files or -# directories that contain example code fragments that are included (see -# the \include command). - EXAMPLE_PATH = @CMAKE_BINARY_DIR@/doc/doxygen/tutorial \ @CMAKE_SOURCE_DIR@/examples/doxygen - -# If the value of the EXAMPLE_PATH tag contains directories, you can use the -# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp -# and *.h) to filter out the source-files in the directories. If left -# blank all files are included. - -EXAMPLE_PATTERNS = - -# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be -# searched for input files to be used with the \include or \dontinclude -# commands irrespective of the value of the RECURSIVE tag. -# Possible values are YES and NO. If left blank NO is used. - EXAMPLE_RECURSIVE = NO - -# The IMAGE_PATH tag can be used to specify one or more files or -# directories that contain image that are included in the documentation (see -# the \image command). This is overwritten in deal.dox - IMAGE_PATH = - -# The INPUT_FILTER tag can be used to specify a program that doxygen should -# invoke to filter for each input file. Doxygen will invoke the filter program -# by executing (via popen()) the command

, where -# is the value of the INPUT_FILTER tag, and is the name of an -# input file. Doxygen will then use the output that the filter program writes -# to standard output. If FILTER_PATTERNS is specified, this tag will be -# ignored. - INPUT_FILTER = ${CMAKE_SOURCE_DIR}/doc/doxygen/scripts/filter - -# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern -# basis. Doxygen will compare the file name with each pattern and apply the -# filter if there is a match. The filters are a list of the form: -# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further -# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER -# is applied to all files. - -FILTER_PATTERNS = - -# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using -# INPUT_FILTER) will be used to filter the input files when producing source -# files to browse (i.e. when SOURCE_BROWSER is set to YES). - FILTER_SOURCE_FILES = YES #--------------------------------------------------------------------------- # configuration options related to source browsing #--------------------------------------------------------------------------- -# If the SOURCE_BROWSER tag is set to YES then a list of source files will -# be generated. Documented entities will be cross-referenced with these sources. -# Note: To get rid of all source code in the generated output, make sure also -# VERBATIM_HEADERS is set to NO. If you have enabled CALL_GRAPH or CALLER_GRAPH -# then you must also enable this option. If you don't then doxygen will produce -# a warning and turn it on anyway - SOURCE_BROWSER = YES - -# Setting the INLINE_SOURCES tag to YES will include the body -# of functions and classes directly in the documentation. - INLINE_SOURCES = NO - -# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct -# doxygen to hide any special comment blocks from generated source code -# fragments. Normal C and C++ comments will always remain visible. - STRIP_CODE_COMMENTS = YES - -# If the REFERENCED_BY_RELATION tag is set to YES (the default) -# then for each documented function all documented -# functions referencing it will be listed. - -REFERENCED_BY_RELATION = YES - -# If the REFERENCES_RELATION tag is set to YES (the default) -# then for each documented function all documented entities -# called/used by that function will be listed. - -REFERENCES_RELATION = YES - -# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) -# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from -# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will -# link to the source code. Otherwise they will link to the documentstion. - -REFERENCES_LINK_SOURCE = YES - -# If the USE_HTAGS tag is set to YES then the references to source code -# will point to the HTML generated by the htags(1) tool instead of doxygen -# built-in source browser. The htags tool is part of GNU's global source -# tagging system (see http://www.gnu.org/software/global/global.html). You -# will need version 4.8.6 or higher. - USE_HTAGS = NO - -# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen -# will generate a verbatim copy of the header file for each class for -# which an include is specified. Set to NO to disable this. - VERBATIM_HEADERS = NO #--------------------------------------------------------------------------- # configuration options related to the alphabetical class index #--------------------------------------------------------------------------- -# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index -# of all compounds will be generated. Enable this if the project -# contains a lot of classes, structs, unions or interfaces. - ALPHABETICAL_INDEX = YES - -# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then -# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns -# in which this list will be split (can be a number in the range [1..20]) - COLS_IN_ALPHA_INDEX = 3 -# In case all classes in a project start with a common prefix, all -# classes will be put under the same header in the alphabetical index. -# The IGNORE_PREFIX tag can be used to specify one or more prefixes that -# should be ignored while generating the index headers. - -IGNORE_PREFIX = - #--------------------------------------------------------------------------- # configuration options related to the HTML output #--------------------------------------------------------------------------- -# If the GENERATE_HTML tag is set to YES (the default) Doxygen will -# generate HTML output. - GENERATE_HTML = YES - -# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. -# If a relative path is entered the value of OUTPUT_DIRECTORY will be -# put in front of it. If left blank `html' will be used as the default path. - HTML_OUTPUT = deal.II - -# The HTML_FILE_EXTENSION tag can be used to specify the file extension for -# each generated HTML page (for example: .htm,.php,.asp). If it is left blank -# doxygen will generate files with .html extension. - HTML_FILE_EXTENSION = .html - -# The HTML_HEADER tag can be used to specify a personal HTML header for -# each generated HTML page. If it is left blank doxygen will generate a -# standard header. - HTML_HEADER = header.html - -# The HTML_FOOTER tag can be used to specify a personal HTML footer for -# each generated HTML page. If it is left blank doxygen will generate a -# standard footer. - HTML_FOOTER = footer.html -# The HTML_STYLESHEET tag can be used to specify a user-defined cascading -# style sheet that is used by each HTML page. It can be used to -# fine-tune the look of the HTML output. If the tag is left blank doxygen -# will generate a default style sheet. Note that doxygen will try to copy -# the style sheet file to the HTML output directory, so don't put your own -# stylesheet in the HTML output directory as well, or it will be erased! - -HTML_STYLESHEET = - -# If the GENERATE_HTMLHELP tag is set to YES, additional index files -# will be generated that can be used as input for tools like the -# Microsoft HTML help workshop to generate a compressed HTML help file (.chm) -# of the generated HTML documentation. - -GENERATE_HTMLHELP = NO - -# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can -# be used to specify the file name of the resulting .chm file. You -# can add a path in front of the file if the result should not be -# written to the html output directory. - -CHM_FILE = - -# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can -# be used to specify the location (absolute path including file name) of -# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run -# the HTML help compiler on the generated index.hhp. - -HHC_LOCATION = - -# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag -# controls if a separate .chi index file is generated (YES) or that -# it should be included in the master .chm file (NO). - -GENERATE_CHI = NO - -# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag -# controls whether a binary table of contents is generated (YES) or a -# normal table of contents (NO) in the .chm file. - -BINARY_TOC = NO - -# The TOC_EXPAND flag can be set to YES to add extra items for group members -# to the contents of the HTML help documentation and to the tree view. - -TOC_EXPAND = NO - -# The DISABLE_INDEX tag can be used to turn on/off the condensed index at -# top of each HTML page. The value NO (the default) enables the index and -# the value YES disables it. - -DISABLE_INDEX = NO - -# This tag can be used to set the number of enum values (range [1..20]) -# that doxygen will group on one line in the generated HTML documentation. - -ENUM_VALUES_PER_LINE = 4 - -# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be -# generated containing a tree-like index structure (just like the one that -# is generated for HTML Help). For this to work a browser that supports -# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, -# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are -# probably better off using the HTML help feature. - -GENERATE_TREEVIEW = NO - -# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be -# used to set the initial width (in pixels) of the frame in which the tree -# is shown. - -TREEVIEW_WIDTH = 250 - #--------------------------------------------------------------------------- # configuration options related to the LaTeX output #--------------------------------------------------------------------------- -# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will -# generate Latex output. - +# don't generate latex output -- it's simply too big! GENERATE_LATEX = NO -# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. -# If a relative path is entered the value of OUTPUT_DIRECTORY will be -# put in front of it. If left blank `latex' will be used as the default path. - -LATEX_OUTPUT = LaTeX/deal.II - -# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be -# invoked. If left blank `latex' will be used as the default command name. - -LATEX_CMD_NAME = latex - -# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to -# generate index for LaTeX. If left blank `makeindex' will be used as the -# default command name. - -MAKEINDEX_CMD_NAME = makeindex - -# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact -# LaTeX documents. This may be useful for small projects and may help to -# save some trees in general. - -COMPACT_LATEX = NO - -# The PAPER_TYPE tag can be used to set the paper type that is used -# by the printer. Possible values are: a4, a4wide, letter, legal and -# executive. If left blank a4wide will be used. - +# but set a few flags for when processing formulas embedded +# in the documentation. PAPER_TYPE = a4wide - -# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX -# packages that should be included in the LaTeX output. - EXTRA_PACKAGES = amsmath amsfonts - -# The LATEX_HEADER tag can be used to specify a personal LaTeX header for -# the generated latex document. The header should contain everything until -# the first chapter. If it is left blank doxygen will generate a -# standard header. Notice: only use this tag if you know what you are doing! - -LATEX_HEADER = - -# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated -# is prepared for conversion to pdf (using ps2pdf). The pdf file will -# contain links (just like the HTML output) instead of page references -# This makes the output suitable for online browsing using a pdf viewer. - -PDF_HYPERLINKS = NO - -# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of -# plain latex in the generated Makefile. Set this option to YES to get a -# higher quality PDF documentation. - -USE_PDFLATEX = NO - -# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. -# command to the generated LaTeX files. This will instruct LaTeX to keep -# running if errors occur, instead of asking the user for help. -# This option is also used when generating formulas in HTML. - LATEX_BATCHMODE = YES -# If LATEX_HIDE_INDICES is set to YES then doxygen will not -# include the index chapters (such as File Index, Compound Index, etc.) -# in the output. - -LATEX_HIDE_INDICES = NO - #--------------------------------------------------------------------------- -# configuration options related to the RTF output +# Other output formats #--------------------------------------------------------------------------- -# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output -# The RTF output is optimized for Word 97 and may not look very pretty with -# other RTF readers or editors. - GENERATE_RTF = NO - -# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. -# If a relative path is entered the value of OUTPUT_DIRECTORY will be -# put in front of it. If left blank `rtf' will be used as the default path. - -RTF_OUTPUT = rtf - -# If the COMPACT_RTF tag is set to YES Doxygen generates more compact -# RTF documents. This may be useful for small projects and may help to -# save some trees in general. - -COMPACT_RTF = NO - -# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated -# will contain hyperlink fields. The RTF file will -# contain links (just like the HTML output) instead of page references. -# This makes the output suitable for online browsing using WORD or other -# programs which support those fields. -# Note: wordpad (write) and others do not support links. - -RTF_HYPERLINKS = NO - -# Load stylesheet definitions from file. Syntax is similar to doxygen's -# config file, i.e. a series of assignments. You only have to provide -# replacements, missing definitions are set to their default value. - -RTF_STYLESHEET_FILE = - -# Set optional variables used in the generation of an rtf document. -# Syntax is similar to doxygen's config file. - -RTF_EXTENSIONS_FILE = - -#--------------------------------------------------------------------------- -# configuration options related to the man page output -#--------------------------------------------------------------------------- - -# If the GENERATE_MAN tag is set to YES (the default) Doxygen will -# generate man pages - GENERATE_MAN = NO - -# The MAN_OUTPUT tag is used to specify where the man pages will be put. -# If a relative path is entered the value of OUTPUT_DIRECTORY will be -# put in front of it. If left blank `man' will be used as the default path. - -MAN_OUTPUT = man - -# The MAN_EXTENSION tag determines the extension that is added to -# the generated man pages (default is the subroutine's section .3) - -MAN_EXTENSION = .3 - -# If the MAN_LINKS tag is set to YES and Doxygen generates man output, -# then it will generate one additional man file for each entity -# documented in the real man page(s). These additional files -# only source the real man page, but without them the man command -# would be unable to find the correct page. The default is NO. - -MAN_LINKS = NO - -#--------------------------------------------------------------------------- -# configuration options related to the XML output -#--------------------------------------------------------------------------- - -# If the GENERATE_XML tag is set to YES Doxygen will -# generate an XML file that captures the structure of -# the code including all documentation. - GENERATE_XML = NO - -# The XML_OUTPUT tag is used to specify where the XML pages will be put. -# If a relative path is entered the value of OUTPUT_DIRECTORY will be -# put in front of it. If left blank `xml' will be used as the default path. - -XML_OUTPUT = xml - -# The XML_SCHEMA tag can be used to specify an XML schema, -# which can be used by a validating XML parser to check the -# syntax of the XML files. - -XML_SCHEMA = - -# The XML_DTD tag can be used to specify an XML DTD, -# which can be used by a validating XML parser to check the -# syntax of the XML files. - -XML_DTD = - -# If the XML_PROGRAMLISTING tag is set to YES Doxygen will -# dump the program listings (including syntax highlighting -# and cross-referencing information) to the XML output. Note that -# enabling this will significantly increase the size of the XML output. - -XML_PROGRAMLISTING = YES - -#--------------------------------------------------------------------------- -# configuration options for the AutoGen Definitions output -#--------------------------------------------------------------------------- - -# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will -# generate an AutoGen Definitions (see autogen.sf.net) file -# that captures the structure of the code including all -# documentation. Note that this feature is still experimental -# and incomplete at the moment. - GENERATE_AUTOGEN_DEF = NO - -#--------------------------------------------------------------------------- -# configuration options related to the Perl module output -#--------------------------------------------------------------------------- - -# If the GENERATE_PERLMOD tag is set to YES Doxygen will -# generate a Perl module file that captures the structure of -# the code including all documentation. Note that this -# feature is still experimental and incomplete at the -# moment. - GENERATE_PERLMOD = NO -# If the PERLMOD_LATEX tag is set to YES Doxygen will generate -# the necessary Makefile rules, Perl scripts and LaTeX code to be able -# to generate PDF and DVI output from the Perl module output. - -PERLMOD_LATEX = NO - -# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be -# nicely formatted so it can be parsed by a human reader. This is useful -# if you want to understand what is going on. On the other hand, if this -# tag is set to NO the size of the Perl module output will be much smaller -# and Perl will parse it just the same. - -PERLMOD_PRETTY = YES - -# The names of the make variables in the generated doxyrules.make file -# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. -# This is useful so different doxyrules.make files included by the same -# Makefile don't overwrite each other's variables. - -PERLMOD_MAKEVAR_PREFIX = - #--------------------------------------------------------------------------- # Configuration options related to the preprocessor #--------------------------------------------------------------------------- -# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will -# evaluate all C-preprocessor directives found in the sources and include -# files. - ENABLE_PREPROCESSING = YES - -# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro -# names in the source code. If set to NO (the default) only conditional -# compilation will be performed. Macro expansion can be done in a controlled -# way by setting EXPAND_ONLY_PREDEF to YES. - MACRO_EXPANSION = YES - -# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES -# then the macro expansion is limited to the macros specified with the -# PREDEFINED and EXPAND_AS_DEFINED tags. - EXPAND_ONLY_PREDEF = YES - -# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files -# in the INCLUDE_PATH (see below) will be search if a #include is found. - SEARCH_INCLUDES = YES - -# The INCLUDE_PATH tag can be used to specify one or more directories that -# contain include files that are not input files but should be processed by -# the preprocessor. - INCLUDE_PATH = @CMAKE_SOURCE_DIR@/include/deal.II - -# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard -# patterns (like *.h and *.hpp) to filter out the header-files in the -# directories. If left blank, the patterns specified with FILE_PATTERNS will -# be used. - INCLUDE_FILE_PATTERNS = -# The PREDEFINED tag can be used to specify one or more macro names that -# are defined before the preprocessor is started (similar to the -D option of -# gcc). The argument of the tag is a list of macros of the form: name -# or name=definition (no spaces). If the definition and the = are -# omitted =1 is assumed. To prevent a macro definition from being -# undefined via #undef or recursively expanded use the := operator -# instead of the = operator. - -# [deal.II] Set MT flags so that the corresponding documentation will always -# be visible, irrespective of whether MT is actually switched on or not. Do -# the same for a bunch of other external packages as well. Also, define a -# variable DOXYGEN in order to mask out inline functions - +# set a few variables that help us generate documentation for +# things like the PETSc and Trilinos wrappers, even if they were +# not configured PREDEFINED = DOXYGEN=1 \ DEBUG=1 \ DEAL_II_WITH_PETSC=1 \ @@ -1004,227 +148,52 @@ PREDEFINED = DOXYGEN=1 \ DEAL_II_WITH_P4EST=1 \ DEAL_II_WITH_MPI=1 -# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then -# this tag can be used to specify a list of macro names that should be expanded. -# The macro definition that is found in the sources will be used. -# Use the PREDEFINED tag if you want to use a different macro definition. - +# do not expand exception declarations EXPAND_AS_DEFINED = DeclException0 \ DeclException1 \ DeclException2 \ DeclException3 \ DeclException4 \ DeclException5 - -# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then -# doxygen's preprocessor will remove all function-like macros that are alone -# on a line, have an all uppercase name, and do not end with a semicolon. Such -# function macros are typically used for boiler-plate code, and will confuse -# the parser if not removed. - SKIP_FUNCTION_MACROS = YES #--------------------------------------------------------------------------- # Configuration::additions related to external references #--------------------------------------------------------------------------- -# The TAGFILES option can be used to specify one or more tagfiles. -# Optionally an initial location of the external documentation -# can be added for each tagfile. The format of a tag file without -# this location is as follows: -# TAGFILES = file1 file2 ... -# Adding location for the tag files is done as follows: -# TAGFILES = file1=loc1 "file2 = loc2" ... -# where "loc1" and "loc2" can be relative or absolute paths or -# URLs. If a location is present for each tag, the installdox tool -# does not have to be run to correct the links. -# Note that each tag file must have a unique name -# (where the name does NOT include the path) -# If a tag file is not located in the directory in which doxygen -# is run, you must also specify the path to the tagfile here. - -TAGFILES = - -# When a file name is specified after GENERATE_TAGFILE, doxygen will create -# a tag file that is based on the input files it reads. - GENERATE_TAGFILE = deal.tag - -# If the ALLEXTERNALS tag is set to YES all external classes will be listed -# in the class index. If set to NO only the inherited external classes -# will be listed. - ALLEXTERNALS = NO - -# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed -# in the modules index. If set to NO, only the current project's groups will -# be listed. - EXTERNAL_GROUPS = YES - -# The PERL_PATH should be the absolute path and name of the perl script -# interpreter (i.e. the result of `which perl'). - PERL_PATH = /usr/bin/perl #--------------------------------------------------------------------------- # Configuration options related to the dot tool #--------------------------------------------------------------------------- -# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will -# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base -# or super classes. Setting the tag to NO turns the diagrams off. Note that -# this option is superseded by the HAVE_DOT option below. This is only a -# fallback. 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This -# makes dot run faster, but since only newer versions of dot (>1.8.10) -# support this, this feature is disabled by default. - -DOT_MULTI_TARGETS = NO - -# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will -# generate a legend page explaining the meaning of the various boxes and -# arrows in the dot generated graphs. - GENERATE_LEGEND = YES -# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will -# remove the intermediate dot files that are used to generate -# the various graphs. - DOT_CLEANUP = YES #--------------------------------------------------------------------------- # Configuration::additions related to the search engine #--------------------------------------------------------------------------- -# The SEARCHENGINE tag specifies whether or not a search engine should be -# used. If set to NO the values of all tags below this one will be ignored. - SEARCHENGINE = YES SERVER_BASED_SEARCH = NO diff --git a/deal.II/doc/news/changes.h b/deal.II/doc/news/changes.h index b4eab15de5..b5997b9a33 100644 --- a/deal.II/doc/news/changes.h +++ b/deal.II/doc/news/changes.h @@ -94,6 +94,14 @@ inconvenience this causes.

New: introduced "make test" that runs a minimal set of tests. We + encourage every user to run this, especially if they run in to problems. + The tests are automatically picked depending on the configuration and + will be shipped with every release. +
+ (Timo Heister, Matthias Maier, 2013/11/08) +
Changed: It is now possible to restore a parallel Triangulation (and solutions) with a different number of processors it was saved with using Triangulation::save() and Triangulation::load(). @@ -203,6 +211,19 @@ inconvenience this causes.
Specific improvements
1. Fixed: The CellData class now has a default constructor that + sets the material and boundary indicators to zero. This fixes certain + internal errors with the Intel ICC compiler. +
  + (Wolfgang Bangerth, 2013/11/13) +
2. New: There is now a framework for coloring graphs, with functions + in namespace GraphColoring. +
  + (Bruno Turcksin, Martin Kronbichler, 2013/11/06) +
3. Fixed: the DerivativeApproximation class was not working correctly when used with parallel vectors. diff --git a/deal.II/doc/news/news.html b/deal.II/doc/news/news.html index 143f96af29..b2eabc101b 100644 --- a/deal.II/doc/news/news.html +++ b/deal.II/doc/news/news.html @@ -36,6 +36,17 @@
  +
  + 2013/11/01: step-42 solves an elasto-plastic contact problem +
  +
  + step-42, written by Jörg Frohne, Timo Heister and Wolfgang + Bangerth, shows how to solve an elasto-plastic contact problem. + The program is an extension of step-41 to a much more complex + equation (nonlinear elasto-plasticity) and also demonstrates + how to compute solutions for such problems in parallel. +
  +
  2013/10/01: step-51 implements an HDG method
  diff --git a/deal.II/doc/readme.html b/deal.II/doc/readme.html index 2709045d84..571859682d 100644 --- a/deal.II/doc/readme.html +++ b/deal.II/doc/readme.html @@ -220,12 +220,13 @@ cd build cmake -DCMAKE_INSTALL_PREFIX=/path/to/install/dir ../deal.II make install + make test
  - These steps compile, link and install the deal.II library. The - whole process should take between a few minutes and an hour, depending - on your machine. + These steps compile, link, install the deal.II library, and run a few + consistency checks. The whole process should take between a few minutes + and an hour, depending on your machine.
  
  @@ -370,7 +371,7 @@ paths. However, this behavior can be changed using command line switches to the initial call to cmake. A detailed description - can be found here: Detailed build system description. + can be found here: Detailed build system description.
  
  @@ -534,7 +535,7 @@ for deal.II being able to use them). For details on how to set up deal.II with a non standard BLAS/LAPACK implementation, see the - advanced + advanced setup section in the CMake ReadME.
  @@ -775,7 +776,9 @@ The deal.II cmake system allows far greater control over what exactly is configured or built than just the outline above. If you want to learn more about this, take a look - here. + here. You might also be interested in + CMake for user projects or + build system internals.
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16:34:54 - -% Copyright (C) 1997 American Mathematical Society. All Rights Reserved. - -11 dict begin -/FontInfo 7 dict dup begin -/version (1.0) readonly def -/Notice (Copyright (C) 1997 American Mathematical Society. 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All Rights Reserved. - -11 dict begin -/FontInfo 7 dict dup begin -/version (1.100) readonly def -/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def -/FullName (CMMI7) readonly def -/FamilyName (Computer Modern) readonly def -/Weight (Medium) readonly def -/ItalicAngle -14.04 def -/isFixedPitch false def -end readonly def -/FontName /CMMI7 def -/PaintType 0 def -/FontType 1 def -/FontMatrix [0.001 0 0 0.001 0 0] readonly def -/Encoding 256 array -0 1 255 {1 index exch /.notdef put} for -dup 59 /comma put -dup 75 /K put -dup 78 /N put -dup 84 /T put -dup 97 /a put -dup 98 /b put -dup 99 /c put -dup 103 /g put -dup 104 /h put -dup 105 /i put -dup 106 /j put -dup 107 /k put -dup 108 /l put -dup 111 /o put -dup 113 /q put -readonly def -/FontBBox{0 -250 1171 750}readonly def -/UniqueXX 5087382 def -currentdict end -currentfile eexec -80347982ab3942d930e069a70d0d48311d725e830d1c76fba12e12486e989c98 -74c2b527f0925722787027f44470d484262c360cdfdddf3657533a57bb16f730 -48bfbbfcb73a650484015441fdc837add94ac8fbd2022e3ec8f115d4b4bb7b7f -15388f22cc6198efe768bd9fceb3446ee4a8dc27d6cd152485384ef5f59381ff 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All Rights Reserved. - -11 dict begin -/FontInfo 7 dict dup begin -/version (1.0) readonly def -/Notice (Copyright (C) 1997 American Mathematical Society. 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All Rights Reserved. - -11 dict begin -/FontInfo 7 dict dup begin -/version (1.00B) readonly def -/Notice (Copyright (C) 1997 American Mathematical Society. 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All Rights Reserved. - -11 dict begin -/FontInfo 7 dict dup begin -/version (1.00B) readonly def -/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def -/FullName (CMTT10) readonly def -/FamilyName (Computer Modern) readonly def -/Weight (Medium) readonly def -/ItalicAngle 0 def -/isFixedPitch true def -end readonly def -/FontName /CMTT10 def -/PaintType 0 def -/FontType 1 def -/FontMatrix [0.001 0 0 0.001 0 0] readonly def -/Encoding 256 array -0 1 255 {1 index exch /.notdef put} for -dup 33 /exclam put -dup 38 /ampersand put -dup 40 /parenleft put -dup 41 /parenright put -dup 42 /asterisk put -dup 43 /plus put -dup 44 /comma put -dup 45 /hyphen put -dup 46 /period put -dup 47 /slash put -dup 48 /zero put -dup 49 /one put -dup 50 /two put -dup 58 /colon put -dup 59 /semicolon put -dup 60 /less put -dup 61 /equal put -dup 62 /greater put -dup 63 /question put -dup 68 /D put -dup 69 /E put -dup 70 /F put -dup 71 /G put -dup 72 /H put -dup 73 /I put -dup 74 /J put -dup 77 /M put -dup 81 /Q put -dup 84 /T put -dup 85 /U put -dup 86 /V put -dup 87 /W put -dup 91 /bracketleft put -dup 93 /bracketright put 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All Rights Reserved. - -11 dict begin -/FontInfo 7 dict dup begin -/version (1.00B) readonly def -/Notice (Copyright (C) 1997 American Mathematical Society. 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All Rights Reserved. - -11 dict begin -/FontInfo 7 dict dup begin -/version (1.0) readonly def -/Notice (Copyright (C) 1997 American Mathematical Society. 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Fn($)24 b(=)f($\()p -Fk(\025)c Fn(+)f Fk(\026)p Fn($)p Fj(r)h(\001)g Fa(u)p -Fk(;)14 b Fj(r)k(\001)h Fa(v)q Fn(\))1958 1311 y Fi(\012)2028 -1286 y Fn(+)2111 1207 y Fg(X)2152 1386 y Fh(k)2244 1286 -y Fn($)q Fk(\026)p Fj(r)p Fk(u)2444 1298 y Fh(k)2484 -1286 y Fk(;)14 b Fj(r)p Fk(v)2630 1298 y Fh(k)2671 1286 -y Fn($)2704 1311 y Fi(\012)2769 1286 y Fk(;)330 1499 -y Fn(or)27 b(as)g(a)g(sum)h(o)n(v)n(er)d(comp)r(onen)n(ts:)828 -1685 y Fk(a)p Fn($)p Fa(u)p Fk(;)14 b Fa(v)q Fn($)24 -b(=)1189 1606 y Fg(X)1210 1785 y Fh(k)q(;l)1322 1685 -y Fn($)q(\()p Fk(\025)19 b Fn(+)f Fk(\026)p Fn($)p -Fk(@)1663 1697 y Fh(l)1689 1685 y Fk(u)1737 1697 y Fh(l)1762 -1685 y Fk(;)c(@)1843 1697 y Fh(k)1884 1685 y Fk(v)1924 -1697 y Fh(k)1965 1685 y Fn(\))1997 1710 y Fi(\012)2067 -1685 y Fn(+)2150 1606 y Fg(X)2171 1785 y Fh(k)q(;l)2284 -1685 y Fn($)p Fk(\026@)2410 1697 y Fh(l)2436 1685 y -Fk(u)2484 1697 y Fh(k)2524 1685 y Fk(;)g(@)2605 1697 -y Fh(l)2630 1685 y Fk(v)2670 1697 y Fh(k)2711 1685 y -Fn($)2744 1710 y Fi(\012)2809 1685 y Fk(:)455 1951 y -Fn(When)25 b(assem)n(bling)g(matrices,)g(it)h(is)f(adv)-5 -b(an)n(tageous)23 b(to)i(write)h(the)f(w)n(eak)g(form)g($i.e.)36 -b(after)330 2050 y(in)n(tegration)g(b)n(y)h(parts$)f(as)h(a)g(kind)g -(of)g(op)r(erator.)64 b(This)37 b(is)g(since)g(matrix)f(elemen)n(ts)h -(after)330 2150 y(discretization)27 b(are)f(de\014ned)i(as)1519 -2325 y Fk(A)1581 2337 y Fh(ij)1662 2325 y Fn(=)23 b Fk(a)p -Fn($)p Fk(')1880 2337 y Fh(j)1916 2325 y Fk(;)14 b(')2007 -2337 y Fh(i)2034 2325 y Fn($)2066 2337 y Fi(\012)2118 -2325 y Fk(;)330 2499 y Fn(where)27 b Fk(')624 2511 y -Fh(i)652 2499 y Fk(;)14 b(')743 2511 y Fh(j)805 2499 -y Fn(are)26 b(t)n(w)n(o)h(v)n(ector-v)-5 b(alued)26 b(trial)g -(functions,)i(and)f(it)h(w)n(ould)f(b)r(e)g(nice)h(if)f(w)n(e)g(could) -330 2599 y(write)33 b(the)g(bilinear)g(form)f Fk(a)p -Fn($)p Fj(\001)p Fk(;)14 b Fj(\001)p Fn($)34 b(as)e(a)g(kind)i(of)f -(scalar)e(pro)r(duct)i($)p Fk(')2546 2611 y Fh(i)2574 -2599 y Fk(;)14 b(Q')2731 2611 y Fh(j)2766 2599 y Fn($,)35 -b(where)d Fk(Q)h Fn(is)f(a)330 2699 y(di\013eren)n(tial)25 -b(op)r(erator.)34 b(This)25 b(is)g(trivial)f(if)i(w)n(e)e(tak)n(e)h -Fk(Q)f Fn(as)h(the)g(op)r(erator)e(of)i(the)h(strong)d(form,)330 -2798 y Fk(Q)g Fn(=)f Fj(\000r)p Fn($)p Fk(\025)11 b -Fn(+)g Fk(\026)p Fn($)p Fj(r)g(\001)g(\000)p Fn($)p -Fj(r)g(\001)g Fk(\026)p Fj(r)p Fn($,)28 b(but)c(w)n(e)g(w)n(an)n(ted)f -(to)h(do)g(this)g(for)g(the)g(w)n(eak)f(form.)35 b(F)-7 -b(or)24 b(this,)330 2898 y(w)n(e)33 b(in)n(tro)r(duce)h(some)f -(notation)g(that)h(is)g(used)g(in)g(quan)n(tum)g(\014eld)g(theory:)48 -b(for)33 b(di\013eren)n(tial)330 2998 y(op)r(erators,)i(w)n(e)h -(indicate)f(b)n(y)g(an)g(arro)n(w)f(placed)h(atop)g(of)g(it)h(whether)f -(it)h(shall)f(act)h(on)f(the)330 3109 y(ob)5 b(ject)26 -b(to)h(the)g(left)g(or)f(to)h(the)g(righ)n(t)f(of)g(it.)37 -b(Th)n(us,)27 b Fk(')2006 3052 y Fj( )-65 b(\000)2013 -3109 y(r)24 b(\001)2145 3052 y(\000)-65 b(!)2152 3109 -y(r)7 b Fk( )26 b Fn(=)d($)p Fj(r)p Fk(')p 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Fn(+)1451 1491 y Fj( )g(\000)1469 1549 y Fk(@)1534 -1561 y Fi(2)1572 1491 y Fj(\000)g(!)1589 1549 y Fk(@)1655 -1561 y Fi(2)1692 1549 y Fn($)409 b(0)g Fj(\000)2649 -1491 y( )-65 b(\000)2665 1549 y Fk(@)2731 1561 y Fi(1)1357 -1667 y Fn(0)408 b Fk(\027)5 b Fn($)1885 1609 y Fj( )-65 -b(\000)1903 1667 y Fk(@)1969 1679 y Fi(1)2006 1609 y -Fj(\000)g(!)2023 1667 y Fk(@)2089 1679 y Fi(1)2145 1667 -y Fn(+)2228 1609 y Fj( )g(\000)2245 1667 y Fk(@)2311 -1679 y Fi(2)2348 1609 y Fj(\000)g(!)2365 1667 y Fk(@)2431 -1679 y Fi(2)2468 1667 y Fn($)84 b Fj(\000)2649 1609 -y( )-65 b(\000)2665 1667 y Fk(@)2731 1679 y Fi(2)1317 -1727 y Fj(\000)g(!)1335 1785 y Fk(@)1400 1797 y Fi(1)2094 -1727 y Fj(\000)g(!)2111 1785 y Fk(@)2177 1797 y Fi(2)2655 -1785 y Fn(0)2769 1467 y Fg(1)2769 1613 y(C)2769 1666 -y(A)2855 1658 y Fk(:)330 1936 y Fn(Again,)22 b(it)g(is)g(clear)e(from)h -(this)h(form)f(that)h(w)n(e)f(could)g(ha)n(v)n(e)f(made)i(the)g(op)r -(erator)d(symmetric)i(b)n(y)330 2035 y(m)n(ultiplying)i(the)g(last)g 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Fn(The)j(simple)g(case)f(in)h(assem)n(bling)e(v) -n(ector-v)-5 b(alued)37 b(problems)h(is)h(when)g(the)g($also)f(v)n -(ector-)330 3048 y(v)-5 b(alued$)31 b(shap)r(e)g(functions)g(are)e(c)n -(hosen)h(suc)n(h)h(that)g(only)f(one)g(comp)r(onen)n(t)h(in)g(the)g(v)n -(ector)e(is)330 3148 y(nonzero.)38 b(This)29 b(is)f(usually)h(the)f -(case,)g(if)i(w)n(e)e(c)n(ho)r(ose)f(the)i(shap)r(e)f(functions)h(to)g -(b)r(e)g(the)g(outer)330 3247 y(pro)r(duct)34 b(of)g(scalar)e(shap)r(e) -i(functions,)i(suc)n(h)d(as)g(indep)r(enden)n(t)i(bilinear)f(ansatz)f -(spaces)g(for)330 3347 y(eac)n(h)27 b(comp)r(onen)n(t)g(of)h(a)f -(\014nite)h(elemen)n(t)g(space.)455 3446 y(In)f(this)h(case,)f(eac)n(h) -g(shap)r(e)g(function)h(\010)1724 3458 y Fh(i)1780 3446 -y Fn(has)f(the)h(represen)n(tation)1194 3601 y(\010)1254 -3613 y Fh(i)1281 3601 y Fn($)p Fa(x)p Fn($)c(=)f($0)p -Fk(;)14 b(:)g(:)g(:)f(;)h Fn(0)p Fk(;)g(')1898 3613 y -Fh(i)1926 3601 y Fn(\()p Fa(x)p Fn($)p Fk(;)g Fn(0)p -Fk(;)g(:)g(:)g(:)f(;)h Fn(0\))2377 3559 y Fh(T)2443 3601 -y Fk(;)330 3756 y Fn(where)27 b(\010)630 3768 y Fh(i)686 -3756 y Fn(is)g(the)h(v)n(ector-v)-5 b(alued)26 b(shap)r(e)i(function,)g -(and)f Fk(')2219 3768 y Fh(i)2275 3756 y Fn(its)h(only)f(non-zero)f -(comp)r(onen)n(t.)330 3856 y(Let)34 b(us)f(denote)g(b)n(y)h -Fk(c)p Fn($)p Fk(i)p Fn($)f(the)h(index)g(of)f(this)h(non-zero)d -(comp)r(onen)n(t,)k(then)f(\010)2853 3868 y Fh(i)2914 -3856 y Fn(can)f(also)g(b)r(e)330 3955 y(written)28 b(as)1425 -4110 y($\010)1517 4122 y Fh(i)1545 4110 y Fn(\()p Fa(x)p -Fn($\))1692 4135 y Fh(l)1740 4110 y Fn(=)23 b Fk(')1882 -4122 y Fh(i)1910 4110 y Fn($)p Fa(x)p Fn($)p Fk(\016)2061 -4125 y Fh(c)p Fi($)p Fh(i)p Fi($)p Fh(;l)2212 4110 -y Fk(;)330 4265 y Fn(with)28 b(the)g(Kronec)n(k)n(er)d(delta)i -(function)i Fk(\016)1627 4277 y Fh(j)s(k)1698 4265 y -Fn(.)455 4365 y(With)f(this)g(simple)g(form,)f(the)h(cell)g(matrix)f -(on)g(cell)h Fk(K)33 b Fn(has)27 b(a)g(simple)h(form:)751 -4519 y Fk(A)813 4485 y Fh(K)813 4540 y(ij)900 4519 y -Fn(=)22 b Fk(a)1031 4531 y Fh(K)1095 4519 y Fn($\010)1187 -4531 y Fh(i)1215 4519 y Fk(;)14 b Fn(\010)1312 4531 y -Fh(j)1347 4519 y Fn($)23 b(=)g($\010)1582 4531 y Fh(i)1633 -4519 y Fj(j)g Fk(Q)g Fj(j)g Fn(\010)1874 4531 y Fh(j)1909 -4519 y Fn($)1941 4547 y Fh(K)2028 4519 y Fn(=)2116 4452 -y Fg(\000)2154 4519 y Fk(')2208 4531 y Fh(i)2259 4519 -y Fj(j)g Fk(Q)2371 4534 y Fh(c)p Fi($)p Fh(i)p Fi($)p -Fh(;c)p Fi($)p Fh(j)s Fi($)2635 4519 y Fj(j)g Fk(')2735 -4531 y Fh(j)2771 4452 y Fg(\001)2809 4553 y Fh(K)2886 -4519 y Fk(:)330 4674 y Fn(Th)n(us,)35 b(in)e(assem)n(bling)f(the)i(lo)r -(cal)f(cell)g(matrices,)h(w)n(e)f(only)g(ha)n(v)n(e)f(to)h(determine)h -(the)g(single)330 4774 y(comp)r(onen)n(ts)d(in)h(whic)n(h)g(the)g(t)n -(w)n(o)f(shap)r(e)h(functions)g(are)e(non-zero,)i(and)f(pic)n(k)h(one)f -(elemen)n(t)330 4873 y(from)h(the)g(matrix)g Fk(Q)f Fn(to)h(assem)n -(ble)f(eac)n(h)g(en)n(try)h(of)g(the)g(cell)g(matrix)g(with)g(the)g -(help)h(of)f(the)330 4973 y(v)-5 b(alues)29 b(of)f(the)i(functions)f -Fk(')1232 4985 y Fh(i)1289 4973 y Fn(at)g(the)g(quadrature)e(p)r(oin)n -(ts.)41 b(Here,)29 b(it)g(comes)g(handy)f(that)h(w)n(e)330 -5073 y(ha)n(v)n(e)k(written)i(the)f(op)r(erator)f(as)h(a)g(matrix)g(op) -r(erator)e Fk(Q)p Fn(,)k(since)e(this)h(mak)n(es)e(it)i(v)n(ery)e -(clear)330 5172 y(ho)n(w)27 b(shap)r(e)g(functions)h -Fk(i)f Fn(and)g Fk(j)32 b Fn(couple:)37 b(if)28 b Fk(Q)1810 -5187 y Fh(c)p Fi($)p Fh(i)p Fi($)p Fh(;c)p Fi($)p -Fh(j)s Fi($)2078 5172 y Fn(is)g(zero,)e(then)i(they)g(do)f(not)g -(couple)g(at)330 5272 y(all)j(for)g(this)h(op)r(erator.)45 -b(Otherwise,)30 b(it)h(is)g(easily)f(visible)g(whic)n(h)h(deriv)-5 -b(ativ)n(e)30 b(acts)g(on)g(whic)n(h)330 5372 y(shap)r(e)d(function)i -(for)e(this)h(com)n(bination)e(of)i(shap)r(e)f(functions.)455 -5471 y(In)21 b Fm(deal.II)p Fn(,)d(these)j(t)n(w)n(o)g(actions)f(men)n -(tioned)h(ab)r(o)n(v)n(e)f($getting)h(the)h(non-zero)d(comp)r(onen)n -(t)330 5571 y(of)29 b(a)f(shap)r(e)h(function,)h(and)f(the)g(v)-5 -b(alue)29 b(of)g(this)g(comp)r(onen)n(t)g(at)g(a)f(giv)n(en)g -(quadrature)g(p)r(oin)n(t$)330 5670 y(are)f(done)g(as)g(follo)n(ws:) -1809 5919 y(7)p eop -%%Page: 8 8 -8 7 bop 455 390 a Fj(\017)41 b Fl(Determining)27 b(the)g(non-zer)l(o)f -(c)l(omp)l(onent:)41 b Fn(Giv)n(en)25 b(the)g(shap)r(e)f(function)h -(with)g(n)n(um)n(b)r(er)538 490 y Fk(i)30 b Fn($i.e.)48 -b(its)31 b(index)g(lo)r(cal)f(to)h(the)h(degrees)d(of)i(freedom)g(on)f -(the)i(presen)n(t)e(cell$,)i(its)f(only)538 589 y(non-zero)25 -b(comp)r(onen)n(t)j(is)f(obtained)h(b)n(y)f(the)h(function)g(call)625 -789 y Fm(const)41 b(unsigned)g(int)h(nonzero_componen)o(t_)o(i)755 -888 y(=)i(fe.system_to_co)o(mpo)o(ne)o(nt_)o(in)o(de)o(x$i)o($.)o -(fir)o(st)o(;)538 1088 y Fn(The)20 b Fm(FiniteElement::sy)o(st)o(em)p -1628 1088 27 4 v 25 w(to)p 1741 1088 V 31 w(component)p -2168 1088 V 27 w(index)f Fn(returns)h(a)g(pair)g(of)h(n)n(um)n(b)r(ers) -538 1187 y(for)38 b(eac)n(h)g(index)h(0)i Fj(\024)g Fk(i)h(<)f(N)1542 -1199 y Fh(K)1606 1187 y Fn(,)g(the)f(\014rst)e(of)h(whic)n(h)g(denotes) -f(the)h(only)g(non-zero)538 1287 y(comp)r(onen)n(t)21 -b(of)g(the)g(shap)r(e)h(function)f Fk(i)p Fn(.)35 b(Since)21 -b(for)g(the)h(case)e(describ)r(ed)h(in)h(this)f(section,)538 -1386 y(the)f(individual)g(comp)r(onen)n(ts)g(of)g(the)g(v)n(ector-v)-5 -b(alued)18 b(\014nite)j(elemen)n(t)f(are)f(indep)r(enden)n(t,)538 -1486 y(w)n(e)35 b(consider)g(eac)n(h)h(comp)r(onen)n(t)g(as)f(a)h(set)g -(of)g(scalar)e(shap)r(e)i(functions;)41 b(the)c(second)538 -1586 y(n)n(um)n(b)r(er)d(of)h(the)g(pair)g(returned)f(b)n(y)h(the)g -(function)g(then)h(denotes)f(the)g(index)g(of)g(the)538 -1685 y(shap)r(e)18 b(function)i Fk(')1133 1697 y Fh(i)1180 -1685 y Fn(within)g(the)f(shap)r(e)g(functions)h(corresp)r(onding)d(to)i -(this)g(comp)r(onen)n(t.)538 1818 y(If,)40 b(for)e(example,)i(our)d -(\014nite)h(elemen)n(t)g(in)g(use)g(is)f(a)h Fk(Q)2352 -1788 y Fi(2)2389 1818 y Fk(=Q)2497 1788 y Fi(2)2533 1818 -y Fk(=Q)2641 1788 y Fi(1)2715 1818 y Fn(com)n(bination)f($for)538 -1918 y(example)30 b(for)h(2d)g(\015o)n(w)g(computations:)44 -b(bi-quadratic)30 b(ansatz)h(functions)g(for)g(the)h(v)n(e-)538 -2017 y(lo)r(cities,)25 b(bi-linear)g(for)g(the)h(pressure$,)f(then)h -(w)n(e)f(ha)n(v)n(e)f(a)h(total)g(of)h(22)e(shap)r(e)i(functions)538 -2117 y($9+9+4$.)34 b(F)-7 b(or)25 b(eac)n(h)f(0)f Fj(\024)g -Fk(i)f(<)h Fn(22,)i(the)g(\014rst)h(part)e(of)i(the)f(pair)g(returned)g -(b)n(y)g(the)h(func-)538 2217 y(tion)31 b(describ)r(ed)f(ab)r(o)n(v)n -(e,)h Fk(c)p Fn($)p Fk(i)p Fn($,)h(ma)n(y)e(then)i(either)e(b)r(e)i -(0,)f(1,)h(or)e(2,)h(denoting)g(the)g(three)538 2316 -y(p)r(ossible)i(comp)r(onen)n(ts)h(of)g(the)h(\014nite)g(elemen)n(t.)57 -b(If)35 b Fk(c)p Fn($)p Fk(i)p Fn($)f(is)g(either)g(0)g(or)f(1,)j -(then)f(the)538 2416 y(comp)r(onen)n(t)30 b(to)h(whic)n(h)g(the)h(shap) -r(e)f(function)h Fk(i)e Fn(b)r(elongs)h(is)g(a)g(bi-quadratic)f(one,)h -(and)538 2516 y(the)24 b(second)f(index)i(is)f(b)r(et)n(w)n(een)g(0)f -(and)h(8)g($inclusiv)n(e$)g(as)f(the)i Fk(Q)2550 2485 -y Fi(2)2611 2516 y Fn(elemen)n(t)f(has)g(9)f(shap)r(e)538 -2615 y(functions.)37 b(If)28 b Fk(c)p Fn($)p Fk(i)p -Fn($)23 b(==)f(2,)27 b(then)i(the)e(second)g(part)h(is)f(b)r(et)n(w)n -(een)h(0)f(and)g(3)g($inclusiv)n(e$.)455 2781 y Fj(\017)41 -b Fl(Getting)f(the)g(value)h(of)f Fk(')1380 2793 y Fh(i)1408 -2781 y Fn($)p Fa(x)1490 2793 y Fh(q)1528 2781 y Fn($)p -Fl(:)65 b Fn(Since)39 b(only)f(one)h(comp)r(onen)n(t)g(of)f(\010)2836 -2793 y Fh(i)2903 2781 y Fn(is)h(non-zero,)538 2881 y(w)n(e)30 -b(can)h(use)f(the)i(same)e(function)h(as)g(b)r(efore,)g(i.e.)47 -b Fm(FEValues::shape)p 2851 2881 V 25 w(value$i,q$)p -Fn(,)538 2980 y(whic)n(h)36 b(in)h(the)g(scalar)e(case)h(returned)h -(the)g(v)-5 b(alue)36 b(of)h(shap)r(e)f(function)i Fk(i)e -Fn(at)h(quadra-)538 3080 y(ture)23 b(p)r(oin)n(t)g Fk(q)s -Fn(.)35 b(Lik)n(ewise,)24 b(the)f Fm(FEValues::shape)p -2176 3080 V 25 w(grad$i,q$)d Fn(function)j(returns)g(the)538 -3180 y(gradien)n(t)j(of)i(this)f(particular)g(comp)r(onen)n(t.)538 -3313 y(In)h(other)f(w)n(ords,)g(whether)h(the)h(\014nite)f(elemen)n(t)g -(is)g(scalar)f(or)g(not,)h(the)h(t)n(w)n(o)e(indicated)538 -3412 y(functions)22 b(return)f(v)-5 b(alue)21 b(and)h(gradien)n(t)e(of) -i(the)g(only)f(non-zero)f(comp)r(onen)n(t)h(of)h(a)f(shap)r(e)538 -3512 y(function.)36 b(If)23 b(the)h(\014nite)f(elemen)n(t)h(is)f -(scalar,)f(then)i(it)f(is)h(of)f(course)f(clear)g(whic)n(h)h(comp)r(o-) -538 3611 y(nen)n(t)k(this)g(is)f($since)h(there)g Fk(c)p -Fn(\()p Fk(i)p Fn($)c(==)f(0)k(for)h(all)f(v)-5 b(alid)27 -b(indices)g Fk(i)p Fn(\),)g(in)g(the)g(v)n(ector-v)-5 -b(alued)538 3711 y(case,)26 b(it)i(is)g(comp)r(onen)n(t)f -Fk(c)p Fn($)p Fk(i)p Fn($.)330 3943 y Fb(5.1)112 b(The)38 -b(elastic)g(equations)330 4097 y Fn(With)29 b(this,)g(and)g(the)f -(de\014nition)h(of)g(the)f(\\bi-directional")f(op)r(erator)g -Fk(Q)h Fn(in)g(Section)h(4.1,)f(the)330 4196 y(lo)r(cal)d(matrix)g -(assem)n(bly)f(function)j(for)e(the)g(elastic)h(equations)e(w)n(ould)h -(then)h(read)f(as)g(follo)n(ws:)417 4362 y Fm(for)43 -b(\(unsigned)c(int)k(i=0;)f(i)22 b Fn(class.)330 2416 y Fb(5.2)112 -b(The)38 b(Stok)m(es)g(equations)330 2569 y Fn(F)-7 b(or)27 -b(the)i(Stok)n(es)e(equation,)h(things)f(are)g(sligh)n(tly)h(more)f -(complicated)h(since)g(the)g(three)g(com-)330 2669 y(p)r(onen)n(ts)23 -b(denote)g(di\013eren)n(t)g(quan)n(tities,)h(and)f(the)g(op)r(erator)f -Fk(Q)h Fn(do)r(es)f(not)i(ha)n(v)n(e)d(suc)n(h)i(a)g(simple)330 -2768 y(form,)29 b(but)g(the)h(case)e(is)h(still)g(simple)g(enough.)40 -b(W)-7 b(e)29 b(presen)n(t)g(its)g(generalization)e(to)h(an)h(arbi-)330 -2868 y(trary)c(n)n(um)n(b)r(er)g(of)h(space)f(dimensions,)h(i.e.)36 -b(assume)25 b(that)h(there)g(are)f Fm(dim)f Fn(v)n(elo)r(cit)n(y)h(v)-5 -b(ariables)330 2968 y(and)27 b(one)h(scalar)e(pressure:)417 -3134 y Fm(for)43 b(\(unsigned)c(int)k(i=0;)f(i quadrature_formula; - FEValues<2> fe_values (fe, quadrature_formula, - UpdateFlags(update_values | - update_gradients | - update_JxW_values)); -\end{verbatim} -In practice, you may want to use a different set of fields to be updated on -each cell. For example if you do not need the values of shape functions on a -cell, you may omit \texttt{update\_values} from the list. Also note that by -default a bi- or tri-linear (depending on space dimension) mapping between -unit and real cell is used. Other mappings are possible, for example quadratic -ones, or a mapping that makes use of the fact that in many cases cells are -actually rectangular, rather than arbitrary quadrilaterals; in order to use -them, another constructor of the \texttt{FEValues} class can be used, which -takes a mapping object as first argument, before the other arguments listed -above. - -Next we define abbreviations for the values of $N_K$ and $N_q$: -\begin{verbatim} - const unsigned int - dofs_per_cell = fe.dofs_per_cell, - n_q_points = quadrature_formula.n_quadrature_points; -\end{verbatim} -Then have an object to store the matrix $\hat A^K$, which is of size -$N_K\times N_K$: -\begin{verbatim} - FullMatrix cell_matrix (dofs_per_cell, dofs_per_cell); -\end{verbatim} -And an object representing the set of global indices of degrees of freedom, -previously denoted by $I_K$, that have support on the present cell, i.e. those -degrees of freedom local to the present cell: -\begin{verbatim} - std::vector local_dof_indices (dofs_per_cell); -\end{verbatim} -The next step is then to loop over all cells: -\begin{verbatim} - typename DoFHandler::active_cell_iterator - cell = dof_handler.begin_active(), - endc = dof_handler.end(); - for (; cell!=endc; ++cell) - { -\end{verbatim} -On each cell, first tell the \texttt{FEValues} object to compute the values of -the various fields for this particular cell, and do not forget to reset the -local matrix $\hat A^K$ to zero before adding it up: -\begin{verbatim} - fe_values.reinit (cell); - cell_matrix.clear (); -\end{verbatim} -Now comes the main part, assembling the local matrix $\hat A^K$. It consists -of a loop over all indices $0\le i,j \le N_K$ and all quadrature points $0\le -q\le N_q$, and summing up the contributions. As this is what we will discuss -in detail later on, we only denote it here by an ellipse: -\begin{verbatim} - for (unsigned int i=0; iget_dof_indices (local_dof_indices); - - for (unsigned int i=0; i}, which -represents a tensor of rank 1 in \texttt{dim} space dimensions. - -Assembling matrices for scalar problems is also shown from a practical -perspective in many of the example programs of \texttt{deal.II}, where it is -also demonstrated how to do this for the right hand side vectors. Thus, scalar -problems are not too interesting, and we now turn to vector-valued problems. - - - -\section{Vector-valued problems} - -Since we need some problems at which we will explain assembling the matrix for -the vector-valued case, we now briefly introduce two simple equations. The -first are the Lam\'e equations of elasticity, which are taken for the symmetric -case, then we briefly introduce the Stokes equations as a nonsymmetric problem. - -\subsection{The elastic equations} -\label{sec:elastic} - -As first example for the methods we are going to discuss for vector-valued -problems, we consider the elastic Lam\'e equations for isotropic materials, -which read in strong form: -$$ - - - \nabla (\lambda+\mu) (\div \vec u) - - - (\nabla \cdot \mu \nabla) \vec u - = - \vec f. -$$ -These equations describe the three-dimensional deformation $\vec u$ of an -elastic body under a body force $\vec f$. The respective bilinear form -associated with this operator is then -$$ - a(\vec u, \vec v) = - \left( - (\lambda+\mu) \div \vec u, \div \vec v - \right)_\Omega - + - \sum_k - \left( - \mu \nabla u_k, \nabla v_k - \right)_\Omega, -$$ -or as a sum over components: -$$ - a(\vec u, \vec v) = - \sum_{k,l} - \left( - (\lambda+\mu) \partial_l u_l, \partial_k v_k - \right)_\Omega - + - \sum_{k,l} - \left( - \mu \partial_l u_k, \partial_l v_k - \right)_\Omega. -$$ - -When assembling matrices, it is advantageous to write the weak form -(i.e. after integration by parts) as a kind of operator. This is since matrix -elements after discretization are defined as -\begin{gather*} - A_{ij} = a(\varphi_j,\varphi_i)_\Omega, -\end{gather*} -where $\varphi_i,\varphi_j$ are two vector-valued trial functions, and it -would be nice if we could write the bilinear form $a(\cdot,\cdot)$ as a kind -of scalar product $(\varphi_i, Q \varphi_j)$, where $Q$ is a differential -operator. This is trivial if we take $Q$ as the operator of the strong form, -$Q=-\nabla (\lambda+\mu) \div - (\nabla \cdot \mu \nabla)$, but we wanted to -do this for the weak form. For this, we introduce some notation that is used -in quantum field theory: for differential operators, we indicate by an arrow -placed atop of it whether it shall act on the object to the left or to the -right of it. Thus, -$\varphi \overleftarrow\nabla \cdot \overrightarrow\nabla \psi -=(\nabla\varphi)\cdot(\nabla\psi)$. With this, a simple computation shows -that -\begin{multline*} - a(\vec u,\vec v) - = - (\lambda+\mu) - \left( - \begin{pmatrix} - u_1 \\ u_2 - \end{pmatrix} - \mid - \begin{pmatrix} - \leftpartial_1 \rightpartial_1 & - \leftpartial_1 \rightpartial_2 \\ - \leftpartial_2 \rightpartial_1 & - \leftpartial_2 \rightpartial_2 - \end{pmatrix} - \mid - \begin{pmatrix} - v_1 \\ v_2 - \end{pmatrix} - \right)_\Omega - \\ - + - \mu - \left( - \begin{pmatrix} - u_1 \\ u_2 - \end{pmatrix} - \mid - \left( - \leftpartial_1 \rightpartial_1 + - \leftpartial_2 \rightpartial_2 - \right) - \begin{pmatrix} - 1 & 0 \\ - 0 & 1 - \end{pmatrix} - \mid - \begin{pmatrix} - v_1 \\ v_2 - \end{pmatrix} - \right)_\Omega. -\end{multline*} -The sought operator $Q$ is then -\begin{gather*} - Q - = - (\lambda+\mu) - \begin{pmatrix} - \leftpartial_1 \rightpartial_1 & - \leftpartial_1 \rightpartial_2 \\ - \leftpartial_2 \rightpartial_1 & - \leftpartial_2 \rightpartial_2 - \end{pmatrix} - + - \mu - \begin{pmatrix} - \leftpartial_1 \rightpartial_1 + - \leftpartial_2 \rightpartial_2 & 0 \\ - 0 & \leftpartial_1 \rightpartial_1 + - \leftpartial_2 \rightpartial_2 - \end{pmatrix}, -\end{gather*} -and $a(\vec u,\vec v)=(\vec u | Q | \vec v)$. We demonstrate the fact that $Q$ -acts to both sides by placing it in the middle of the scalar product, just as -in the bra-ket notation of quantum physics. - -The advantages of this formulation will become clear when discussing -assembling matrices below. For now, we remark that the symmetry of the weak -form is equally apparent from the form of $Q$ as well as from the initial -definition of $a(\cdot,\cdot)$. - - - -\subsection{The Stokes equations} -\label{sec:stokes} - -For a nonsymmetric problem, we take the Stokes equations: -\begin{align*} - -\Delta \vec u + \nabla p &= 0, - \\ - \text{div } \vec u &= 0. -\end{align*} -We denote by $\vec w=\{\vec u,p\}$ the entire solution vector. In the weak -form, the above equations read -\begin{gather*} - a(\vec u,p; \vec v, q) - = - \nu(\nabla \vec u_1, \nabla \vec v_1) - +\nu(\nabla \vec u_2, \nabla \vec v_2) - - (p, \nabla\cdot \vec v) - + (\nabla\cdot\vec u, q). -\end{gather*} -Since we integrated the gradient term in the first equation by parts, but not -the divergence term in the second equation, the problem is now -nonsymmetric. If we would have liked, we could have made the problem symmetric -again by multiplying the entire second equation by $-1$, but we don't want to -do that for now for illustrational purposes. - -Again, we introduce the operator $Q$ for this problem, which after some -computations turns out to be -\begin{gather*} - Q - = - \begin{pmatrix} - \nu(\leftpartial_1 \rightpartial_1 + - \leftpartial_2 \rightpartial_2) & 0 & -\leftpartial_1 \\ - 0 & \nu(\leftpartial_1 \rightpartial_1 + - \leftpartial_2 \rightpartial_2) & -\leftpartial_2 \\ - \rightpartial_1 & \rightpartial_2 & 0 - \end{pmatrix}. -\end{gather*} -Again, it is clear from this form that we could have made the operator -symmetric by multiplying the last row by $-1$. Note when checking the symmetry -of $Q$ that taking the transpose of such an operator means reverting the -directions of the arrows over the operators, and exchanging their order. -For example, using the first term, these two steps are -$\leftpartial_1 \rightpartial_1 \rightarrow \rightpartial_1 \leftpartial_1 -\rightarrow \leftpartial_1 \rightpartial_1$. - - -\section{Assembling vector-valued problems: The simple case} - -The simple case in assembling vector-valued problems is when the (also -vector-valued) shape functions are chosen such that only one component in the -vector is nonzero. This is usually the case, if we choose the shape functions -to be the outer product of scalar shape functions, such as independent -bilinear ansatz spaces for each component of a finite element space. - -In this case, each shape function $\Phi_i$ has the representation -\begin{gather*} - \Phi_i(\vec x) = - \left( 0, \dots, 0, \varphi_i(\vec x), 0, \ldots, 0\right)^T, -\end{gather*} -where $\Phi_i$ is the vector-valued shape function, and $\varphi_i$ its -only non-zero component. Let us denote by $c(i)$ the index of this non-zero -component, then $\Phi_i$ can also be written as -\begin{gather*} - \left(\Phi_i(\vec x)\right)_l - = - \varphi_i(\vec x) \delta_{c(i),l}, -\end{gather*} -with the Kronecker delta function $\delta_{jk}$. - -With this simple form, the cell matrix on cell $K$ has a simple form: -\begin{gather*} - A^K_{ij} - = - a_K(\Phi_i,\Phi_j) - = - \left(\Phi_i \mid Q \mid \Phi_j \right)_K - = - \left(\varphi_i \mid Q_{c(i),c(j)} \mid \varphi_j \right)_K. -\end{gather*} -Thus, in assembling the local cell matrices, we only have to determine the -single components in which the two shape functions are non-zero, and -pick one element from the matrix $Q$ to assemble each entry of the cell -matrix with the help of the values of the functions $\varphi_i$ at the -quadrature points. Here, it comes handy that we have written the operator as a -matrix operator $Q$, since this makes it very clear how shape functions $i$ -and $j$ couple: if $Q_{c(i),c(j)}$ is zero, then they do not couple at all for -this operator. Otherwise, it is easily visible which derivative acts on which -shape function for this combination of shape functions. - -In \texttt{deal.II}, these two actions mentioned above (getting the non-zero -component of a shape function, and the value of this component at a given -quadrature point) are done as follows: -\begin{itemize} -\item \textit{Determining the non-zero component:} Given the shape function - with number $i$ (i.e. its index local to the degrees of freedom on the - present cell), its only non-zero component is obtained by the function call -\begin{verbatim} - const unsigned int nonzero_component_i - = fe.system_to_component_index(i).first; -\end{verbatim} - The \texttt{FiniteElement::system\_to\_component\_index} returns a pair of - numbers for each index $0\le i < N_K$, the first of which denotes the only - non-zero component of the shape function $i$. Since for the case described - in this section, the individual components of the vector-valued finite - element are independent, we consider each component as a set of scalar shape - functions; the second number of the pair returned by the function then - denotes the index of the shape function $\varphi_i$ within the shape - functions corresponding to this component. - - If, for example, our finite element in use is a $Q^2/Q^2/Q^1$ combination - (for example for 2d flow computations: bi-quadratic ansatz functions for the - velocities, bi-linear for the pressure), then we have a total of 22 shape - functions (9+9+4). For each $0\le i < 22$, the first part of the pair - returned by the function described above, $c(i)$, may then either be 0, 1, - or 2, denoting the three possible components of the finite element. If - $c(i)$ is either 0 or 1, then the component to which the shape function $i$ - belongs is a bi-quadratic one, and the second index is between $0$ and $8$ - (inclusive) as the $Q^2$ element has 9 shape functions. If $c(i)==2$, then - the second part is between 0 and 3 (inclusive). - -\item \textit{Getting the value of $\varphi_i(\vec x_q)$:} Since only one - component of $\Phi_i$ is non-zero, we can use the same function as before, - i.e. \texttt{FEValues::shape\_value(i,q)}, which in the scalar case returned - the value of shape function $i$ at quadrature point $q$. Likewise, the - \texttt{FEValues::shape\_grad(i,q)} function returns the gradient of this - particular component. - - In other words, whether the finite element is scalar or not, the two - indicated functions return value and gradient of the only non-zero component - of a shape function. If the finite element is scalar, then it is of course - clear which component this is (since there $c(i)==0$ for all valid indices - $i$), in the vector-valued case, it is component $c(i)$. -\end{itemize} - - -\subsection{The elastic equations} -\label{sec:elastic-simple} - -With this, and the definition of the ``bi-directional'' operator $Q$ in -Section~\ref{sec:elastic}, the local matrix assembly function for the elastic -equations would then read as follows: -\begin{verbatim} - for (unsigned int i=0; i} class. - - -\subsection{The Stokes equations} -\label{sec:stokes-simple} - -For the Stokes equation, things are slightly more complicated since the three -components denote different quantities, and the operator $Q$ does not have -such a simple form, but the case is still simple enough. We present its -generalization to an arbitrary number of space dimensions, i.e. assume that -there are \texttt{dim} velocity variables and one scalar pressure: -\begin{verbatim} - for (unsigned int i=0; i) dup sw pop 2 div neg 0 rm col0 sh gr -/Times-Roman-iso ff 300.00 scf sf -1200 1800 m -gs 1 -1 sc (CellAccessor<1>) dup sw pop 2 div neg 0 rm col0 sh gr -/Times-Roman-iso ff 300.00 scf sf -2400 3000 m -gs 1 -1 sc (DoFObjectAccessor<1,1>) dup sw pop 2 div neg 0 rm col0 sh gr -/Times-Roman-iso ff 300.00 scf sf -2400 4200 m -gs 1 -1 sc (DoFCellAccessor<1>) dup sw pop 2 div neg 0 rm col0 sh gr -$F2psEnd -rs diff --git a/deal.II/doc/reports/class-hierarchies/1d-dof.fig b/deal.II/doc/reports/class-hierarchies/1d-dof.fig deleted file mode 100644 index 6d1e056206..0000000000 --- a/deal.II/doc/reports/class-hierarchies/1d-dof.fig +++ /dev/null @@ -1,28 +0,0 @@ -#FIG 3.2 -Landscape -Center -Inches -Letter -100.00 -Single -0 -1200 2 -2 4 0 1 0 7 0 0 -1 0.000 0 0 7 0 0 5 - 6000 1875 6000 1500 3600 1500 3600 1875 6000 1875 -2 1 0 2 0 7 0 0 -1 0.000 0 0 -1 0 0 2 - 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7725 1875 7725 1500 5325 1500 5325 1875 7725 1875 -4 1 0 0 0 0 20 0.0000 4 195 1995 6525 1800 DoFAccessor<3>\001 --6 -6 225 750 3225 1125 -2 4 0 1 0 7 0 0 -1 0.000 0 0 7 0 0 5 - 3225 1125 225 1125 225 750 3225 750 3225 1125 -4 1 0 0 0 0 20 0.0000 4 255 2925 1725 1050 TriaObjectAccessor<1,3>\001 --6 -6 2025 1200 5025 1575 -2 4 0 1 0 7 0 0 -1 0.000 0 0 7 0 0 5 - 5025 1575 2025 1575 2025 1200 5025 1200 5025 1575 -4 1 0 0 0 0 20 0.0000 4 255 2925 3525 1500 TriaObjectAccessor<1,3>\001 --6 -6 7950 975 10050 1350 -6 7950 975 10050 1350 -6 7950 975 10050 1350 -2 4 0 1 0 7 0 0 -1 0.000 0 0 7 0 0 5 - 10050 1350 10050 975 7950 975 7950 1350 10050 1350 --6 --6 -4 1 0 0 0 0 20 0.0000 4 195 1950 9000 1275 CellAccessor<3>\001 --6 -2 4 0 1 0 7 0 0 -1 0.000 0 0 7 0 0 5 - 6800 3075 3700 3075 3700 2700 6800 2700 6800 3075 -2 4 0 1 0 7 0 0 -1 0.000 0 0 7 0 0 5 - 3575 3075 475 3075 475 2700 3575 2700 3575 3075 -2 4 0 1 0 7 0 0 -1 0.000 0 0 7 0 0 5 - 9975 3075 6875 3075 6875 2700 9975 2700 9975 3075 -2 4 0 1 0 7 0 0 -1 0.000 0 0 7 0 0 5 - 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3350 3075 275 3075 275 2700 3350 2700 3350 3075 -2 4 0 1 0 7 0 0 -1 0.000 0 0 7 0 0 5 - 6575 3075 3375 3075 3375 2700 6575 2700 6575 3075 -2 4 0 1 0 7 0 0 -1 0.000 0 0 7 0 0 5 - 9825 3075 6625 3075 6625 2700 9825 2700 9825 3075 -2 4 0 1 0 7 0 0 -1 0.000 0 0 7 0 0 5 - 6300 1875 6300 1500 3900 1500 3900 1875 6300 1875 -2 1 0 2 0 7 0 0 -1 0.000 0 0 -1 0 0 2 - 5100 1875 1800 2700 -2 1 0 2 0 7 0 0 -1 0.000 0 0 -1 0 0 2 - 5100 1875 8200 2700 -2 1 0 2 0 7 0 0 -1 0.000 0 0 -1 0 0 2 - 8250 3075 8250 3900 -2 4 0 1 0 7 0 0 -1 0.000 0 0 7 0 0 5 - 9300 4275 9300 3900 7200 3900 7200 4275 9300 4275 -2 1 0 2 0 7 100 0 -1 0.000 0 0 -1 0 0 2 - 5100 1875 5100 2700 -4 1 0 0 0 0 20 0.0000 4 255 2925 1800 3000 TriaObjectAccessor<1,3>\001 -4 1 0 0 0 0 20 0.0000 4 255 2925 8250 3000 TriaObjectAccessor<3,3>\001 -4 1 0 0 0 0 20 0.0000 4 195 1980 5100 1800 TriaAccessor<3>\001 -4 1 0 0 0 0 20 0.0000 4 195 1950 8250 4200 CellAccessor<3>\001 -4 1 0 0 0 0 20 0.0000 4 255 2925 5025 3000 TriaObjectAccessor<2,3>\001 -4 1 0 0 0 0 25 0.0000 4 345 7590 4800 600 Class Hierarchy for the 3-dimensional Case, Part 1\001 diff --git a/deal.II/doc/reports/class-hierarchies/3d-tria.jpg b/deal.II/doc/reports/class-hierarchies/3d-tria.jpg deleted file mode 100644 index 6aa0d0b821..0000000000 Binary files a/deal.II/doc/reports/class-hierarchies/3d-tria.jpg and /dev/null differ diff --git a/deal.II/doc/reports/class-hierarchies/index.html b/deal.II/doc/reports/class-hierarchies/index.html deleted file mode 100644 index f2c3ac547e..0000000000 --- a/deal.II/doc/reports/class-hierarchies/index.html +++ /dev/null @@ -1,996 +0,0 @@ - - - - - The deal.II Homepage - - - - - - -
  -Description of the C++ class hierarchy for the -accessor classes -
  - - -
  - Wolfgang Bangerth, 1998, 1999, 2000 -
  - - -
  -The class hierarchy of the accessor classes used to retrieve and store -data in the triangulation and degree of freedom handler objects is one -of the more complicated parts of the library. It makes heavy use of -class templates with integers as template parameters as well as of -explicit specialization of classes and member functions. Therefore, -it is not so easy to see the connections and inheritance relations -within this part of the class tree; this document tries to shed a bit -of light onto this. -
  - -
  -Furthermore, it lists the member functions that can be queried to -obtain information from an iterator. -
  - - -Table of contents -
  -
  What iterators and accessors - are -
  The triangulation - accessor hierarchy -
  Typedefs of the - Triangulation class to iterators and accessors -
  Functions offered by - triangulation accessors -
  The degree of freedom - accessor hierarchy -
  Typedefs of the - DoFHandler class to iterators and accessors -
  Functions offered by - degree of freedom accessors -
  - - - -
  -What iterators and accessors are -
  - -
  -When using adative finite elements, the data structures often are -extremely complex, requiring multiply indirected access and complex -relationships between the different places where data is stored. The -traditional way to handle this is to put all data which belongs -together somehow into a structure or object; however, sometimes this -can not be done efficiently, leading to either higher memory -consumption (when you have to store many small data pieces and because -you have to store a lot of pointers to other objects) or higher coding -requirements (when you want to follow all those pointers to the object -you desire). -
  - -
  -Therefore, we took over a concept which was already used in the C++ -standard template library, namely iterators and accessors. An accessor -is an object that looks like if it had all the information stored but -really only delegates the access to the right places; in fact, within -this library, accessor store almost no information but know where to -get everything from the complex and nested data structures the -triangulation object offers. They have a simple interface which allows -to extract any desired information from the triangulation and -therefore makes access much easier and safer in three ways: first it -performs range and parameter checking when in debugging mode; second, -it encapsulates the access to the real data from the user, hiding the -true data structures and thus allowing them without changing the user -programs as well as those parts of the library which only act through -accessors; and third by reducing the coding errors because of reduced -complexity, since the chains of indirect access are replaces by simple -commands. -
  - -
  -Iterators are a related concept: while accessors act as if they were -structures with data contained in them, iterators act as if they were -pointers pointing to accessors. You can dereference them using the --> and * operators as with any other pointer, but they have more -functionality. Essentially, they have overloaded ++ and -- operators, -which allow the next or previous object pointed to to be just about -anywhere in memory. A good introductory example are the iterators of -the STL list<T> class, which act on a linked list -as if it were a contiguous array. The iterators in this library go -even a step further: they do not point to different objects but rather -tell the associated accessor object which data to look at -next. -
  - -
  -Additionally, there are different versions of the iterators which -behave differently when being incremented or decremented: while -raw iterators let the associated accessor point to any of the -objects it is made for, normal iterators always point to -objects which are in use. Usually, you will not want to see cells or -lines which are there but are unused by the triangulation (these cells -are somewhat like holes in the arrays of the triangulation; such -things happen when unrefining a cell, the freed memory is then kept -for a while because of better efficiency), so you will almost never -want to use raw iterators; they are mostly there for internal use in -the library. Normal iterators are almost like raw iterators, but -whenever you call the ++ or -- operator, the look at what they are -pointing at and skip all unused elements by increasing or decreasing -the pointer as often as necessary to reach the next used object. -
  - -
  -Finally, there are active iterators, which are the most -important ones. They are like normal iterators but only point to -active cells or lines. By active we mean that they have no children; -in the context in which this library is used, this is equivalent to -the fact that we do computations on these cells, lines or -whatever. Active iterators are normal iterators which skip over all -non-active cells, lines, etc when being incremented or decremented. -
  - - - - -
  -The triangulation accessor hierarchy -
  - -
  -The triangulation accessors are used to retrieve and store data in the -triangulation. There exist accessors for lines in one and higher -dimensions, accessors for quads in two and higher dimensions, and so -on. The general naming scheme is as follows: -
  -
  TriaAccessor<dim> is a general base class - which is of not much interest. -
  TriaObjectAccessor<objectdim,spacedim> denotes - an accessor for an object with dimension - objectdim in a spacedim dimensional - space. It is derived from TriaAccessor<spacedim>. -
  CellAccessor<dim> presents the special - properties that a cell has. It is therefore derived from - TriaObjectAccessor<spacedimdim,spacedim>. -
  -
  - -
  -Their inheritance trees in the different space dimensions therefore -look like this: -
  - -
  - - - - -
  - -
  - - - - -
  - -
  - - - - -
  - -
  - -
  -Some of the data is only useful if an object is a cell. For example, -neighborship is only accessible for cells, while faces (e.g. lines in -2D) can't access their neighbors (neither the adjacent cells, nor the -other faces it touches). Therefore, the CellAccessor classes are -derived from whatever object a cell is in the respective dimension, -i.e. from lines in 1D, from quads in 2D, and so on. -
  - - - - -
  -Typedefs of the Triangulation class to iterators and accessors -
  - -
  -The Triangulation<1> class declares the following data -types which involve accessors: -
  - typedef TriaRawIterator <1,CellAccessor<1> > raw_line_iterator; - typedef TriaIterator <1,CellAccessor<1> > line_iterator; - typedef TriaActiveIterator<1,CellAccessor<1> > active_line_iterator; - - typedef raw_line_iterator raw_cell_iterator; - typedef line_iterator cell_iterator; - typedef active_line_iterator active_cell_iterator; -
  -Since lines are cells in one space dimension, all line iterators are -cell iterators as well. -
  - -
  -In two space dimensions, the following types are declared by the -Triangulation<2> class: -
  - typedef TriaRawIterator <2,TriaObjectAccessor<1, 2> > raw_line_iterator; - typedef TriaIterator <2,TriaObjectAccessor<1, 2> > line_iterator; - typedef TriaActiveIterator<2,TriaObjectAccessor<1, 2> > active_line_iterator; - - typedef TriaRawIterator <2,CellAccessor<2> > raw_quad_iterator; - typedef TriaIterator <2,CellAccessor<2> > quad_iterator; - typedef TriaActiveIterator<2,CellAccessor<2> > active_quad_iterator; - - typedef raw_quad_iterator raw_cell_iterator; - typedef quad_iterator cell_iterator; - typedef active_quad_iterator active_cell_iterator; - - typedef raw_line_iterator raw_face_iterator; - typedef line_iterator face_iterator; - typedef active_line_iterator active_face_iterator; -
  -Since in this space dimension, quads are cells and lines are the faces -of cells, the appropriate face and cell iterators are declared in -terms of the underlying accessor types. -
  - - -
  -In three space dimensions, the following types are declared by the -Triangulation<3> class: -
  - typedef TriaRawIterator <3,TriaObjectAccessor<1, 3> > raw_line_iterator; - typedef TriaIterator <3,TriaObjectAccessor<1, 3> > line_iterator; - typedef TriaActiveIterator<3,TriaObjectAccessor<1, 3> > active_line_iterator; - - typedef TriaRawIterator <3,TriaObjectAccessor<2, 3> > raw_quad_iterator; - typedef TriaIterator <3,TriaObjectAccessor<2, 3> > quad_iterator; - typedef TriaActiveIterator<3,TriaObjectAccessor<2, 3> > active_quad_iterator; - - typedef TriaRawIterator <3,CellAccessor<3> > raw_hex_iterator; - typedef TriaIterator <3,CellAccessor<3> > hex_iterator; - typedef TriaActiveIterator<3,CellAccessor<3> > active_hex_iterator; - - typedef raw_hex_iterator raw_cell_iterator; - typedef hex_iterator cell_iterator; - typedef active_hex_iterator active_cell_iterator; - - typedef raw_quad_iterator raw_face_iterator; - typedef quad_iterator face_iterator; - typedef active_quad_iterator active_face_iterator; -
  -Since in this space dimension, hexes are cells and quads are the faces -of cells, the appropriate face and cell iterators are declared in -terms of the underlying accessor types. -
  - - - - -
  Functions offered by triangulation accessors
  - -
  -We briefly state a short list of the functions offered by the -triangulation accessors. For a more complete discussion of these -functions, please refer to the online -API -documentation of the `grid' classes. These functions can be -accessed by iterator->function() if iterator -is a cell-, face-, hex-, quad-, or line-iterator. Some functions are -not available for all iterator types, which is noted for the -individual entries. -
  - -
  -
  - level () -
  - -
  - Return the hierarchical refinement level on - which this object lives. -
  - - -
  - index () -
  - -
  - Return the index within the hierarchical refinement level on - which this object lives. -
  - - -
  - get_triangulation () -
  - -
  - Return a reference to the triangulation to which this object belongs. -
  - - -
  - vertex_index (vertex_number) -
  - -
  - Return the global index of one of the vertices of this object. -
  - - -
  - vertex (vertex_number) -
  - -
  - Return the position of the respective vertex in space. -
  - - -
  - used () -
  - -
  - Return whether the object is used. The return value is - true for all iterators that are either normal iterators - or active iterators, only raw iterators can return - false. Since raw iterators are only used in the - interiors of the library, you will not usually need this function. -
  - - -
  - set_used () / clear_used () -
  - -
  - Set or clear the flag that describes whether the object is used by - the triangulation. Only for internal use. -
  - - -
  - user_flag_set () -
  - -
  - Return whether the user flag is set. -
  - - -
  - set_user_flag () / clear_user_flag () -
  - -
  - Set or clear the flag that might be used by a user to indicate that - something should happen with this object. -
  - - -
  - recursively_set_user_flag () / recursively_clear_user_flag () -
  - -
  - Set or clear the user flag for this cell and all its descendants. -
  - - -
  - user_pointer () -
  - -
  - Query the pointer belonging to this object which may be used by - the user to store additional information with this object. -
  - - -
  - set_user_pointer () / clear_user_pointer () -
  - -
  - Set or clear a pointer belonging to this object which may be used by - the user to store additional information with this object. -
  - - -
  - child (child_number) -
  - -
  - Return an iterator to one of the children of this object. -
  - - -
  - child_index (child_number) -
  - -
  - Return the index of the child within the next finer level of the - triangulation. -
  - - -
  - set_children (index), clear_children () -
  - -
  - Only for internal use. -
  - - -
  - has_children () -
  - -
  - Return whether an object has children, i.e. whether it is further - refined. If it has children, then it is not active. -
  - - -
  - max_refinement_depth () -
  - -
  - Return how often this cell or one of its children is refined. -
  - - -
  - boundary_indicator -
  - -
  - Return the number of the boundary at which this object lies, if the - object has a dimension less than the space dimension. -
  - - -
  - set_boundary_indicator (boundary_id) -
  - -
  - Set the number of the boundary to which this object belongs. -
  - - -
  - at_boundary () -
  - -
  - Return whether this object is at the boundary (if the dimension of - the object is less than the space dimension), or one of its faces is - at the boundary for cells. -
  - - -
  - has_boundary_lines () -
  - -
  - Return whether one of the lines bounding this cell is at the - boundary. For 1d and 2d this is equivalent to at_boundary, - in 3d, there are cases where bounding lines of a hex are at the - boundary, while the faces are in the interior. (Only for cell - iterators.) -
  - - -
  - diameter () -
  - -
  - Return the diameter of the object. -
  - - -
  - center () -
  - -
  - Return the coordinates of the center of the object. -
  - - -
  - barycenter () -
  - -
  - Return the coordinates of the barycenter of the object. -
  - - -
  - measure () -
  - -
  - Return the length, area, or volume of an object, depending on the - dimension of the object. -
  - - -
  - point_inside (point) -
  - -
  - Return whether the given point is inside this cell, or rather the - (bi-, tri-)linearly mapped image of the unit cell with the vertices - of this cell. (Only for cell iterators.) -
  - - -
  - number_of_children () -
  - -
  - Accumulated number of children and their children. -
  - - -
  - line (line_number) -
  - -
  - Return an iterator to one of the bounding lines of this object. (Only - for iterators to quadrilaterals and hexahedra.) -
  - - -
  - line_index (line_number) -
  - -
  - Return the index of one of the bounding lines of this object. The - level index is the same as that of the present object. (Only - for iterators to quadrilaterals and hexahedra.) -
  - - -
  - quad (quad_number) -
  - -
  - Return an iterator to one of the bounding quadrilaterals of this - object. (Only for iterators to hexahedra.) -
  - - -
  - line_index (line_number) -
  - -
  - Return the index of one of the bounding quadrilaterals of this - object. The level index is the same as that of the present - object. (Only for iterators to hexahedra.) -
  - - -
  - neighbor (neighbor_number) -
  - -
  - Return iterator to one of the neighbors. (Only for cell iterators.) -
  - - -
  - neighbor_index (neighbor_number) / neighbor_level (neighbor_number) -
  - -
  - Return number and level of one of the neighbors. (Only for cell - iterators.) -
  - - -
  - set_neighbor () -
  - -
  - Set a neighbor. Only for internal use. (Only for cell iterators.) -
  - - -
  - neighbor_of_neighbor (neighbor_number) -
  - -
  - Return the how-manyth neighbor the present cell is of the neighbor - specified by the argument. (Only for cell iterators.) -
  - - -
  - at_boundary (face_number) -
  - -
  - Return whether this cell's given face is at the boundary. (Only for - cell iterators.) -
  - - -
  - refine_flag_set () -
  - -
  - Return whether the refinement flag is set or not for the present - cell. (Only for cell iterators.) -
  - - -
  - set_refine_flag () / clear_refine_flag () -
  - -
  - Set/clear the flag indicating refinement. (Only for cell iterators.) -
  - - -
  - coarsen_flag_set () -
  - -
  - Query whether the flag indicating coarsening is set for this - object. (Only for cell iterators.) -
  - - -
  - set_coarsen_flag () / claer_coarsen_flag () -
  - -
  - Set/clear the flag indicating coarsening. (Only for cell iterators.) -
  - - -
  - face (face_number) -
  - -
  - Return an iterator to one of the faces of this cell, if dimension is - greater than one. (Only for cell iterators.) -
  - - -
  - material_id () -
  - -
  - Return the material number of this cell. (Only for cell iterators.) -
  - - -
  - set_material_id (id) -
  - -
  - Set the material number of this cell. (Only for cell iterators.) -
  - - -
  - active () -
  - -
  - Return whether this cell is active, i.e. has no children. (Only for - cell iterators.) -
  -
  - - - - -
  -The degree of freedom accessor hierarchy -
  - -
  -The DoFAccessor classes provide access to the degree of freedom -information associated with cells, lines, etc. The inheritance -relationship is much the same as for the triangulation accessor -classes, as can be seen from the following pictures. - -
  - - - - -
  - - -
  - - - - -
  - - -
  - - - - -
  - -
  - -
  -The main difference to the triangulation accessor hierarchy is that we -want the DoF accessors to provide the information about the degrees of -freedom, but for convenience also that of the triangulation. This way, -we can get all the information from one object rather than needing two -which work in parallel, and the class hierarchy shown above does -exactly this. -
  - -
  -For the named reason, it is necessary to derive the -DoFObjectAccessor<1,dim> from the -TriaObjectAccessor<1,dim> class of the -triangulation accessor hierarchy, as well as the -DoFObjectAccessor<2,dim> from the -TriaObjectAccessor<2,dim>. However, we would also -like to include the functionality added by the CellAccessor class; -this is done through some template magic: when in one space dimension, -the DoFObjectAccessor<1,1> is derived from -CellAccessor<1>, while when in higher dimensions, it is derived -from DoFObjectAccessor<1,dim>; the same applies for -the DoFObjectAccessor<2,dim> class. Note that this -way, CellAccessor is always a base class to DoFCellAccessor and the -inheritance lattice is dimension dependant; the exact way of achieving -this is complicated but not of interest here. -
  - - - -
  -Typedefs of the DoFHandler class to iterators and accessors -
  - -
  -The typedefs done by the DoFHandler class are much alike those done by -the Triangulation class. They could be summarized as follows: -
  - -
  -For one space dimension: -
  - typedef TriaRawIterator <1,DoFCellAccessor<1> > raw_line_iterator; - typedef TriaIterator <1,DoFCellAccessor<1> > line_iterator; - typedef TriaActiveIterator<1,DoFCellAccessor<1> > active_line_iterator; - - typedef raw_line_iterator raw_cell_iterator; - typedef line_iterator cell_iterator; - typedef active_line_iterator active_cell_iterator; -
  -Since lines are cells in one space dimension, all line iterators are -cell iterators as well. -
  - -
  -For two space dimensions: -
  - typedef TriaRawIterator <2,DoFObjectAccessor<1, 2> > raw_line_iterator; - typedef TriaIterator <2,DoFObjectAccessor<1, 2> > line_iterator; - typedef TriaActiveIterator<2,DoFObjectAccessor<1, 2> > active_line_iterator; - - typedef TriaRawIterator <2,DoFCellAccessor<2> > raw_quad_iterator; - typedef TriaIterator <2,DoFCellAccessor<2> > quad_iterator; - typedef TriaActiveIterator<2,DoFCellAccessor<2> > active_quad_iterator; - - typedef raw_quad_iterator raw_cell_iterator; - typedef quad_iterator cell_iterator; - typedef active_quad_iterator active_cell_iterator; - - typedef raw_line_iterator raw_face_iterator; - typedef line_iterator face_iterator; - typedef active_line_iterator active_face_iterator; -
  -
  - -
  -For three space dimensions: -
  - typedef TriaRawIterator <3,DoFObjectAccessor<1, 3> > raw_line_iterator; - typedef TriaIterator <3,DoFObjectAccessor<1, 3> > line_iterator; - typedef TriaActiveIterator<3,DoFObjectAccessor<1, 3> > active_line_iterator; - - typedef TriaRawIterator <3,DoFObjectAccessor<2, 3> > raw_quad_iterator; - typedef TriaIterator <3,DoFObjectAccessor<2, 3> > quad_iterator; - typedef TriaActiveIterator<3,DoFObjectAccessor<2, 3> > active_quad_iterator; - - typedef TriaRawIterator <3,DoFCellAccessor<3> > raw_hex_iterator; - typedef TriaIterator <3,DoFCellAccessor<3> > hex_iterator; - typedef TriaActiveIterator<3,DoFCellAccessor<3> > active_hex_iterator; - - typedef raw_hex_iterator raw_cell_iterator; - typedef hex_iterator cell_iterator; - typedef active_hex_iterator active_cell_iterator; - - typedef raw_quad_iterator raw_face_iterator; - typedef quad_iterator face_iterator; - typedef active_quad_iterator active_face_iterator; -
  -
  - - - - -
  Functions offered by degree of freedom accessors
  - -
  -Since degree of freedom accessors are derived from triangulation -accessors, they inherit the functionality of these accessors, but add -some of their own. We only list the additional functionality -below. For a full reference, including data types of parameters and -return values, please refer to the general -API -documentation of the `DoF' classes. -
  - - -
  -
  - dof_index (dof_number) -
  - -
  - Return the global index of one of the DoFs on this object. -
  - - -
  - set_dof_index (dof_number, index) -
  - -
  - Set the index of a DoF. Only for internal use. -
  - - -
  - vertex_dof_index (vertex_number, dof_number) -
  - -
  - Return the index of one of the DoFs on one of the vertices of this - object. -
  - - -
  - set_vertex_dof_index (...) -
  - -
  - Set the vertex DoF index. Only for internal use. -
  - - -
  - get_dof_indices (vector_of_indices) -
  - -
  - Return a vector of the indices of the DoFs on this object. -
  - - -
  - get_dof_values (global_values, local_values) -
  - -
  - Extract and return the values of the DoFs on this object from a data - vector defined on all DoFs. -
  - - -
  - set_dof_values (local_values, global_values) -
  - -
  - Reverse operation: take values of DoFs on this object, and set them - into a global data vector. -
  - - -
  - distribute_local_to_global (local_source, global_destination) -
  - -
  - Add the elements of local_source, defining values of the degrees of - freedom on this object, to the elements of the global data - vector. The two parameters may be either vectors or matrices. -
  - - -
  - get_interpolated_dof_values (global_values, local_interpolation) -
  - -
  - Interpolate the global field to this cell. If this cell is active, - then this is the restriction of the global field to this cell, - but when this cell is not active then it is the interpolation of the - restriction of the field to the child cells and the interpolation to - the present one. (For cell iterators only.) -
  - - -
  - set_dof_values_by_interpolation (local_values, global_interpolation) -
  - -
  - Inverse operation: interpolate the local values to the children (if - this cell is not active) and set the respective values in the global - vector. (For cell iterators only.) -
  -
  - - -
  - -
  -Wolfgang Bangerth, 1998, 1999, 2000 -
  -
  
  - - - - - - - diff --git a/deal.II/doc/reports/codimension-one/desimone-heltai-manigrasso.pdf b/deal.II/doc/reports/codimension-one/desimone-heltai-manigrasso.pdf deleted file mode 100644 index d64a5e5bc0..0000000000 Binary files a/deal.II/doc/reports/codimension-one/desimone-heltai-manigrasso.pdf and /dev/null differ diff --git a/deal.II/doc/reports/index.html b/deal.II/doc/reports/index.html index f7ca37206e..9a2246b474 100644 --- a/deal.II/doc/reports/index.html +++ b/deal.II/doc/reports/index.html @@ -24,7 +24,7 @@
  
  A brief report about the classes involved in the - iterators and accessors used to access cells in the triangulations and the data thereon, such as their geometry, the number of the @@ -35,7 +35,7 @@
  
  - A brief report on mapping functions of higher polynomial degrees (by Ralf Hartmann). These allow the realisation of higher order boundary approximations. This report @@ -45,37 +45,30 @@
  A report on - assembling matrices (by Wolfgang Bangerth). This report looks in particular at how matrices are assembled for vector-valued problems, and how things change if vector-valued finite elements are used for which the shape functions have more than one non-zero vector component, such as Nedelec or - Raviart-Thomas elements. There are printable - versions of the report - in postscript and - PDF format. + Raviart-Thomas elements.
  
  A very detailed report on - Nedelec elements (by Anna Schneebeli, University of Basel, Switzerland). It explains the construction and application of Nedelec edge elements for H-curl spaces, as used, for example, in the numerical solution of the Maxwell equations. It also gives numerical results obtained with deal.II. - There is also a postscript version of the report.
  
  A report on the - codimension one capabilities of the library (by Antonio DeSimone, Luca Heltai and Cataldo Manigrasso, SISSA, Trieste, Italy). 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  -In modified form taken from -
  -
  -Ralf Hartmann -
  -Adaptive Finite Element Methods for the Compressible Euler Equations -
  -PhD thesis, University of Heidelberg, 2002. -
  - - -
  -
  -Higher order Boundary approximation - -
  -
  -Introduction: In many numerical applications the domain - - - $\Omega\subset\mathbb R^d$ , - $d\geq 2$ -is not a polygonal domain but includes -curved boundaries. For these cases the boundary cannot be represented -exactly by the discretised boundary. Approximating the boundary by a -piecewise linear boundary interpolation, i.e. by a polygonal boundary, -may in some applications not be sufficient. In these cases a higher -order boundary approximation, for example by piecewise quadratic or -cubic boundary interpolation, must be employed. In the finite element -framework this higher order boundary approximation is realized by -mapping the reference element $\hat K$ -to the element - - - $K=\sigma_K(\hat K)$ -in real space, whereas on cells K at the -boundary, i.e. - - $\partial K\cap\Gamma=\emptyset$ , -the mappings - $\sigma_K$ -are given by polynomial functions of higher degree. - -
  -Elements with general mapping functions $\sigma_K$ . We begin -by first introducing some notation. Let $K\in T_h$ -be a cell of the -triangulation T_h with - - $K=\sigma_K(\hat K)$ , -where $\sigma_K$ is a smooth bijective mapping of the reference element (unit square) - $\hat K$ -to the element K in real space, see Figure -1. -
  -
     - - - -
  Figure: -Mapping $\sigma$ -of reference element $\hat K$ -to the element K in real space.
  -
  - - - $\includegraphics[scale=0.3]{figures/m1.ps}$
  -
  -
  -
  -In the following and for the sake of simplicity we suppress the letter -K in the subscript and write $\sigma$ -instead of $\sigma_K$ . - -
  -Mapping functions of higher polynomial degree. A mapping -function $\sigma$ , -that maps the reference element $\hat K$ -to an -arbitrary quadrilateral cell K with straight boundaries, can in -general be represented by a bilinear function, i.e. by a -Q₁-mapping. For the case that the cell K includes curved -boundaries it might be necessary to employ polynomial mapping -functions of higher degree. - -
  -Given a degree p>0, a cell $K\in T_h$ , -and (p+1)^d mapping -support points $p_i\in K$ , - - - $i=0,\ldots,(p+1)^d-1$ , -we define a -Q_p-mapping - - $\sigma\in [Q_p]^d$ -as follows -
  -
  - - - - - - -
  $\begin{displaymath} -\sigma(\hat x)=\sum_{i=0}^{(p+1)^d-1}p_i\phi_i(\hat x). -\end{displaymath}$ -(1)
  -
  -
  -Here, $\phi_i$ , - - - $i=0,\ldots,(p+1)^d-1$ -denote the Lagrange interpolation -basis functions, that satisfy -
  -
  - - - - $\begin{displaymath}\phi_i(\hat p_j)=\delta_{ij}, \quad i,j=0,\ldots,(p+1)^d-1, -\end{displaymath}$ -
  -
  -
  -where $\hat p_i$ , - - - $i=0,\ldots,(p+1)^d-1$ -denote the Lagrange support -points on the unit cell $\hat K$ . -The definition of $\sigma$ (1) ensures that each of the unit support points - $\hat p_i$ -is mapped onto the corresponding mapping support points -p_i, i.e. -
  -
  - - - - - - -
  $\begin{displaymath} -\sigma(\hat p_i)=p_i, \quad i=0,\ldots,(p+1)^d-1 -\end{displaymath}$ -(2)
  -
  -
  -Analogous to Lagrange finite elements the unit Lagrange support points - $\hat p_i$ -are equidistantly distributed on $\hat K$ -based on a tensor -product mesh. In the following we only consider the two-dimensional -case, d=2. For that case, Figure 2 -shows the distributions of the unit support points $\hat p_i$ , - - - $i=0,\ldots,(p+1)^2-1$ -for degrees - - $p=1,\ldots ,4$ . -
  -
     - - - -
  Figure: -Unit support points $\hat p_i$ , - - - $0\leq i<(p+1)^2$ , -for degrees - - $p=1,\ldots ,4$ .
  -
  - - - $\includegraphics*[width=2.750cm]{../../../phd/figures/boundary_approximation/mapping/unit_points_q1_n.eps}$ - - - $\includegraphics*[width=2.750cm]{../../../phd/figures/boundary_approximation/mapping/unit_points_q2_n.eps}$ - - - $\includegraphics*[width=2.750cm]{../../../phd/figures/boundary_approximation/mapping/unit_points_q3_n.eps}$ - - - $\includegraphics*[width=2.750cm]{../../../phd/figures/boundary_approximation/mapping/unit_points_q4_n.eps}$
  -
  -
  -Let the ordering and numbering of the unit support points be as -follows: first the corners, then the points on the edges and finally -the inner support points, see also Figure -2. Thus the first 4p points are placed -on the boundary - - $\partial\hat K$ -of the reference cell, i.e. -
  -
  - - - - $\begin{displaymath}\hat p_k\in\partial\hat K, \quad k=0,\ldots,4p-1. -\end{displaymath}$ -
  -
  -
  -According to (2) these points are mapped to the -mapping support points p_k, - - $k=0,\ldots,4p-1$ -that are chosen to be -placed on the boundary of the real cell in approximatively equal -distances, i.e. -
  -
  - - - - $\begin{displaymath}p_k\in\partial K, \quad k=0,\ldots,4p-1. -\end{displaymath}$ -
  -
  -
  -While the support points p_k, - - $k=0,\ldots,4p-1$ -on the boundary are -given by the boundary description of the real cell K, the inner - mapping support points -
  -
  - - - - $\begin{displaymath}p_i\in K\setminus\partial K, \quad i=4p,\ldots,(p+1)^2-1 -\end{displaymath}$ -
  -
  -
  -are not uniquely determined. Numerical tests show that it is not a -trivial task to define the positions of the inner mapping support -points appropriately. If they are not chosen appropriately the -resulting mapping $\sigma$ -for a cell K may degenerate, i.e. the -mapping $\sigma$ -for some cell K may not be bijective. - -
  -Computation of inner support points by smooth transformation. -In the following we will define the positions of the inner mapping -support points so that the mapping does - in all practical cases - not -degenerate. To this end, we employ an approach for the mapping of the -support points, that is in the style of the smooth transformations -that is used to transform structured triangulations to match complex -boundary discriptions. In the following, again for notational -convenience, we consider only the two-dimensional case. - -
  -The smooth transformation mentioned above is based on solutions to the -Laplace equation that is solved on the reference cell $\hat K$ . -Discrete boundary conditions are imposed that are given by the -coordinates of the mapping support points p_k, - - $k=0,\ldots,4p-1$ , -on -the boundary of the cell K in real space. - -
  -To be more explicite we define a Laplace problem on the unit -cell $\hat K$ -
  -
  - - - - - - -
  $\begin{displaymath} -\begin{array}{rcll} --\hat\Delta \sigma_l(\hat x)&=&0, \quad... -...l \hat K}(\hat x), \quad &\hat x\in \partial\hat K, -\end{array}\end{displaymath}$ -(3)
  -
  -
  -for each component $\sigma_l$ , -l=1,2, of the Q_p mapping - $\sigma$ . -Here, the discrete boundary function - - $g\in [Q_p]^2$ -is -given by -
  -
  - - - - - - -
  $\begin{displaymath} -g_l(\hat x)=\sum_{i=0}^{4p-1}(p_i)_l\phi_i(\hat x), \quad l=1,\ldots,d -\end{displaymath}$ -(4)
  -
  -
  -where (p_i)_l denotes the lth component of the support point p_i, -and $\phi_i$ -the corresponding Lagrangian interpolation basis -function. We recall that the numbering of the mapping support points -involves - - $p_k\in\partial K$ -for - - $k=0,\ldots,4p-1$ . -Substituting -
  -
  - - - - - - -
  $\begin{displaymath} -\tilde \sigma_l:=\sigma_l-g_l, \quad l=1,2, -\end{displaymath}$ -(5)
  -
  -
  -into the Laplace problem (3) yields the -zero boundary value problem, -
  -
  - - - - - - -
  $\begin{displaymath} -\begin{array}{rcll} --\hat\Delta \tilde\sigma_l(\hat x)&=&\h... -...gma_l(\hat x)&=&0, \quad &\hat x\in \partial\hat K, -\end{array}\end{displaymath}$ -(6)
  -
  -
  -that is equivalent to the following variational formulation -
  -
  - - - - $\begin{displaymath}\tilde\sigma_l\in H^1_0(\hat K):\qquad -(\hat\nabla \tilde\si... -...\hat\nabla \phi)_{\hat K} \quad \forall \phi\in H^1_0(\hat K). \end{displaymath}$ -
  -
  -
  -Discretisation of this problem -
  -
  - - - - $\begin{displaymath}\tilde\sigma_l\in Q_p(\hat K):\qquad -(\hat\nabla \tilde\sigm... -...bla \phi_{4p+i})_{\hat K} \quad \forall i=0,\ldots, (p-1)^2-1, \end{displaymath}$ -
  -
  -
  -and recalling definitions (1), (5) and (4) gives -
  -
  - - - - - - -
  $\begin{displaymath} -\sum_{j=1}^{(p-1)^2}S_{ij}(p_{4p+j})_l=-\sum_{k=0}^{4p-1}T_{ik}(p_k)_l, \quad i=0, \ldots, (p-1)^2-1, -\end{displaymath}$ -(7)
  -
  -
  -with the matrices - - $S_{ij}\in\mathbb R^{(p-1)^2\times(p-1)^2}$ -and - - $T_{ik}\in\mathbb R^{(p-1)^2\times 4p}$ -given by -
  -
  - - - - $\begin{displaymath}S_{ij}=(\hat\nabla \phi_{4p+i}, \hat\nabla \phi_{4p+j})_{\hat K}, \quad i,j=0,\ldots,(p-1)^2-1, -\end{displaymath}$ -
  -
  -
  -and -
  -
  - - - - $\begin{displaymath}T_{ik}=(\hat\nabla \phi_{4p+i}, \hat\nabla \phi_k)_{\hat K}, \quad i=0,\ldots,(p-1)^2-1,\quad k=0,\ldots,4p-1. -\end{displaymath}$ -
  -
  -
  -The solutions to problem (7) for l=1,2 are -
  -
  - - - - $\begin{displaymath}(p_{4p+j})_l=-\sum_{i=0}^{(p-1)^2-1}\sum_{k=0}^{4p-1}S^{-1}_{ji}T_{ik}(p_k)_l, \quad j=0,\ldots,(p-1)^2-1, -\end{displaymath}$ -
  -
  -
  -that may be written in compact form: -
  -
  - - - - - - -
  $\begin{displaymath} -p_{4p+j}=\sum_{k=0}^{4p-1}c_{jk}p_k, \quad j=0,\ldots,(p-1)^2-1, -\end{displaymath}$ -(8)
  -
  -
  -where c_jk represents the coefficient -
  -
  - - - - - - -
  $\begin{displaymath} -c_{jk}=-\sum_{i=0}^{(p-1)^2-1}S^{-1}_{ji}T_{ik}. -\end{displaymath}$ -(9)
  -
  -
  -of the linear combination (8), that -represents the dependency of the jth inner mapping support point -p_4p+j on the support points p_k, - - $k=0,\ldots,4p-1$ , -that are -placed on the boundary of the cell K. For a fixed degree p, these -coefficients c_jk are the same for the mapping of all cells -K in real space because the c_jk depend only on the reference -element $\hat K$ . -Therefore the coefficients c_jk can be -precomputed and result in following linear combinations: - -
  -For p=2 the linear combination turns out to be -
  -
  - - - - $\begin{displaymath}p_8=\tfrac{1}{16}\sum_{k=0}^3p_k+\tfrac{3}{16}\sum_{k=4}^7p_k, -\end{displaymath}$ -
  -
  -
  -see also Figure 3, left. -
  -
     - - - -
  Figure 3: -Left: Coefficients c_8,k for Q₂ mapping. Right: Coefficients c_12,k for Q₃ mapping.
  -
  - - - $\includegraphics*[scale=0.4]{figures/m2.ps}$
  -
  -
  -For the case that p=3, Figure 3, right, shows the coefficients c_12,k of the linear combination for the inner mapping support point p₁₂. The coefficents for the points p₁₃, p₁₄ and p₁₅ can be obtain by rotation of the coefficients. - -
  -Implementation in deal.II. The coefficients c_jk, see -(9), are represented in the MappingQ -class by the laplace_on_quad_vector as follows -
  -
  - - - - $\begin{displaymath}\mbox{\textit{laplace\_on\_quad\_vector}[j][k]}=c_{jk} -\end{displaymath}$ -
  -
  -
  -These coefficients are the same for the mapping of all cells -K in real space because the c_jk depend only on the reference -element $\hat K$ . -Hence for a given degree p the -laplace_on_quad_vector can be filled by the constructor of -the MappingQ class. This is done by calling the -MappingQ::set_laplace_on_quad_vector function that -includes the coefficients hardcoded for p=2 and p=3 in d=2 dimensions, and a routine for computing the coefficients according to -(9) for all other cases. The mapping support -points $p_i\in K$ , - - - $i=0,\ldots,(p+1)^d-1$ -are computed once for each -MappingQ object by the -MappingQ::compute_support_points_laplace that is invoked -by the virtual compute_mapping_support_points function of -the base Mapping class. In -MappingQ::compute_support_points_laplace, first the 4p points on the boundary of the cell are computed (by calling -MappingQ::add_line_support_points), then by calling -MappingQ::apply_laplace_vector the remaining (p-1)² inner mapping supports points are computed, where -MappingQ::apply_laplace_vector just performs the linear -combination given in (8). -
  - -
  -Ralf Hartmann -
  2001-09-03 -
  - - diff --git a/deal.II/doc/reports/nedelec/nedelec.pdf b/deal.II/doc/reports/nedelec/nedelec.pdf deleted file mode 100644 index 1ed9f2effa..0000000000 Binary files a/deal.II/doc/reports/nedelec/nedelec.pdf and /dev/null differ diff --git a/deal.II/doc/reports/nedelec/nedelec.ps b/deal.II/doc/reports/nedelec/nedelec.ps deleted file mode 100644 index 3baeec4a23..0000000000 --- a/deal.II/doc/reports/nedelec/nedelec.ps +++ /dev/null @@ -1,7851 +0,0 @@ -%!PS-Adobe-2.0 -%%Creator: dvips(k) 5.86 Copyright 1999 Radical Eye Software -%%Title: main.dvi -%%Pages: 23 -%%PageOrder: Ascend -%%BoundingBox: 0 0 596 842 -%%DocumentFonts: Helvetica -%%EndComments -%DVIPSWebPage: (www.radicaleye.com) -%DVIPSCommandLine: dvips main -o nedelec.ps -%DVIPSParameters: dpi=600, compressed -%DVIPSSource: TeX output 2003.05.02:0909 -%%BeginProcSet: texc.pro -%! -/TeXDict 300 dict def TeXDict begin/N{def}def/B{bind def}N/S{exch}N/X{S -N}B/A{dup}B/TR{translate}N/isls false N/vsize 11 72 mul N/hsize 8.5 72 -mul 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image} bdef -/tMatrix matrix def -/MakeOval {newpath tMatrix currentmatrix pop translate scale -0 0 1 0 360 arc tMatrix setmatrix} bdef -/FO {MakeOval stroke} bdef -/PO {MakeOval fill} bdef -/PD {currentlinecap 1 cap 3 1 roll 2 copy mt lineto stroke - cap PDlw -1 eq not {PDlw w /PDlw -1 def} if} def -/FA {newpath tMatrix currentmatrix pop translate scale - 0 0 1 5 -2 roll arc tMatrix setmatrix stroke} bdef -/PA {newpath tMatrix currentmatrix pop translate 0 0 moveto scale - 0 0 1 5 -2 roll arc closepath tMatrix setmatrix fill} bdef -/FAn {newpath tMatrix currentmatrix pop translate scale - 0 0 1 5 -2 roll arcn tMatrix setmatrix stroke} bdef -/PAn {newpath tMatrix currentmatrix pop translate 0 0 moveto scale - 0 0 1 5 -2 roll arcn closepath tMatrix setmatrix fill} bdef -/vradius 0 def /hradius 0 def /lry 0 def -/lrx 0 def /uly 0 def /ulx 0 def /rad 0 def -/MRR {/vradius xdef /hradius xdef /lry xdef /lrx xdef /uly xdef - /ulx xdef newpath tMatrix currentmatrix pop ulx hradius add uly - vradius add translate hradius vradius scale 0 0 1 180 270 arc - tMatrix setmatrix lrx hradius sub uly vradius add translate - hradius vradius scale 0 0 1 270 360 arc tMatrix setmatrix - lrx hradius sub lry vradius sub translate hradius vradius scale - 0 0 1 0 90 arc tMatrix setmatrix ulx hradius add lry vradius sub - translate hradius vradius scale 0 0 1 90 180 arc tMatrix setmatrix - closepath} bdef -/FRR {MRR stroke } bdef -/PRR {MRR fill } bdef -/MlrRR {/lry xdef /lrx xdef /uly xdef /ulx xdef /rad lry uly sub 2 div def - newpath tMatrix currentmatrix pop ulx rad add uly rad add translate - rad rad scale 0 0 1 90 270 arc tMatrix setmatrix lrx rad sub lry rad - sub translate rad rad scale 0 0 1 270 90 arc tMatrix setmatrix - closepath} bdef -/FlrRR {MlrRR stroke } bdef -/PlrRR {MlrRR fill } bdef -/MtbRR {/lry xdef /lrx xdef /uly xdef /ulx xdef /rad lrx ulx sub 2 div def - newpath tMatrix currentmatrix pop ulx rad add uly rad add translate - rad rad scale 0 0 1 180 360 arc tMatrix 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@setspecial -%%BeginDocument: example2_errors.eps -%!PS-Adobe-2.0 EPSF-1.2 -%%Creator: MATLAB, The Mathworks, Inc. -%%Title: pix.eps -%%CreationDate: 08/26/2002 11:52:50 -%%DocumentNeededFonts: Helvetica -%%DocumentProcessColors: Cyan Magenta Yellow Black -%%Pages: 1 -%%BoundingBox: 52 194 549 605 -%%EndComments - -%%BeginProlog -% MathWorks dictionary -/MathWorks 160 dict begin -% definition operators -/bdef {bind def} bind def -/ldef {load def} bind def -/xdef {exch def} bdef -/xstore {exch store} bdef -% operator abbreviations -/c /clip ldef -/cc /concat ldef -/cp /closepath ldef -/gr /grestore ldef -/gs /gsave ldef -/mt /moveto ldef -/np /newpath ldef -/cm /currentmatrix ldef -/sm /setmatrix ldef -/rm /rmoveto ldef -/rl /rlineto ldef -/s /show ldef -/sc {setcmykcolor} bdef -/sr /setrgbcolor ldef -/sg /setgray ldef -/w /setlinewidth ldef -/j /setlinejoin ldef -/cap /setlinecap ldef -/rc {rectclip} bdef -/rf {rectfill} bdef -% page state control -/pgsv () def -/bpage {/pgsv save def} bdef -/epage {pgsv restore} bdef -/bplot /gsave ldef -/eplot {stroke grestore} bdef -% orientation switch -/portraitMode 0 def /landscapeMode 1 def /rotateMode 2 def -% coordinate system mappings -/dpi2point 0 def -% font control -/FontSize 0 def -/FMS {/FontSize xstore findfont [FontSize 0 0 FontSize neg 0 0] - makefont setfont} bdef -/reencode {exch dup where {pop load} {pop StandardEncoding} ifelse - exch dup 3 1 roll findfont dup length dict begin - { 1 index /FID ne {def}{pop pop} ifelse } forall - /Encoding exch def currentdict end definefont pop} bdef -/isroman {findfont /CharStrings get /Agrave known} bdef -/FMSR {3 1 roll 1 index dup isroman {reencode} {pop pop} ifelse - exch FMS} bdef -/csm {1 dpi2point div -1 dpi2point div scale neg translate - dup landscapeMode eq {pop -90 rotate} - {rotateMode eq {90 rotate} if} ifelse} bdef -% line types: solid, dotted, dashed, dotdash -/SO { [] 0 setdash } bdef -/DO { [.5 dpi2point mul 4 dpi2point mul] 0 setdash } bdef -/DA { [6 dpi2point mul] 0 setdash } bdef -/DD { [.5 dpi2point mul 4 dpi2point mul 6 dpi2point mul 4 - dpi2point mul] 0 setdash } bdef -% macros for lines and objects -/L {lineto stroke} bdef -/MP {3 1 roll moveto 1 sub {rlineto} repeat} bdef -/AP {{rlineto} repeat} bdef -/PDlw -1 def -/W {/PDlw currentlinewidth def setlinewidth} def -/PP {closepath eofill} bdef -/DP {closepath stroke} bdef -/MR {4 -2 roll moveto dup 0 exch rlineto exch 0 rlineto - neg 0 exch rlineto closepath} bdef -/FR {MR stroke} bdef -/PR {MR fill} bdef -/L1i {{currentfile picstr readhexstring pop} image} bdef -/tMatrix matrix def -/MakeOval {newpath tMatrix currentmatrix pop translate scale -0 0 1 0 360 arc tMatrix setmatrix} bdef -/FO {MakeOval stroke} bdef -/PO {MakeOval fill} bdef -/PD {currentlinecap 1 cap 3 1 roll 2 copy mt lineto stroke - cap PDlw -1 eq not {PDlw w /PDlw -1 def} if} def -/FA {newpath tMatrix currentmatrix pop translate scale - 0 0 1 5 -2 roll arc tMatrix setmatrix stroke} bdef -/PA {newpath tMatrix currentmatrix pop translate 0 0 moveto scale - 0 0 1 5 -2 roll arc closepath tMatrix setmatrix fill} bdef -/FAn {newpath tMatrix currentmatrix pop translate scale - 0 0 1 5 -2 roll arcn tMatrix setmatrix stroke} bdef -/PAn {newpath tMatrix currentmatrix pop translate 0 0 moveto scale - 0 0 1 5 -2 roll arcn closepath tMatrix setmatrix fill} bdef -/vradius 0 def /hradius 0 def /lry 0 def -/lrx 0 def /uly 0 def /ulx 0 def /rad 0 def -/MRR {/vradius xdef /hradius xdef /lry xdef /lrx xdef /uly xdef - /ulx xdef newpath tMatrix currentmatrix pop ulx hradius add uly - vradius add translate hradius vradius scale 0 0 1 180 270 arc - tMatrix setmatrix lrx hradius sub uly vradius add translate - hradius vradius scale 0 0 1 270 360 arc tMatrix setmatrix - lrx hradius sub lry vradius sub translate hradius vradius scale - 0 0 1 0 90 arc tMatrix setmatrix ulx hradius add lry vradius sub - translate hradius vradius scale 0 0 1 90 180 arc tMatrix setmatrix - closepath} bdef -/FRR {MRR stroke } bdef -/PRR {MRR fill } bdef -/MlrRR {/lry xdef /lrx xdef /uly xdef /ulx xdef /rad lry uly sub 2 div def - newpath tMatrix currentmatrix pop ulx rad add uly rad add translate - rad rad scale 0 0 1 90 270 arc tMatrix setmatrix lrx rad sub lry rad - sub translate rad rad scale 0 0 1 270 90 arc tMatrix setmatrix - closepath} bdef -/FlrRR {MlrRR stroke } bdef -/PlrRR {MlrRR fill } bdef -/MtbRR {/lry xdef /lrx xdef /uly xdef /ulx xdef /rad lrx ulx sub 2 div def - newpath tMatrix currentmatrix pop ulx rad add uly rad add translate - rad rad scale 0 0 1 180 360 arc tMatrix setmatrix lrx rad sub lry rad - sub translate rad rad scale 0 0 1 0 180 arc tMatrix setmatrix - closepath} bdef -/FtbRR {MtbRR stroke } bdef -/PtbRR {MtbRR fill } bdef -/stri 6 array def /dtri 6 array def -/smat 6 array def /dmat 6 array def -/tmat1 6 array def /tmat2 6 array def /dif 3 array def -/asub {/ind2 exch def /ind1 exch def dup dup - ind1 get exch ind2 get sub exch } bdef -/tri_to_matrix { - 2 0 asub 3 1 asub 4 0 asub 5 1 asub - dup 0 get exch 1 get 7 -1 roll astore } bdef -/compute_transform { - dmat dtri tri_to_matrix tmat1 invertmatrix - smat stri tri_to_matrix tmat2 concatmatrix } bdef -/ds {stri astore pop} bdef -/dt {dtri astore pop} bdef -/db {2 copy /cols xdef /rows xdef mul dup string - currentfile exch readhexstring pop - /bmap xdef pop pop} bdef -/it {gs np dtri aload pop moveto lineto lineto cp c - cols rows 8 compute_transform - {bmap} image gr}bdef -/il {newpath moveto lineto stroke}bdef -currentdict end def -%%EndProlog - -%%BeginSetup -MathWorks begin - -0 cap - -end -%%EndSetup - -%%Page: 1 1 -%%BeginPageSetup -%%PageBoundingBox: 52 194 549 605 -MathWorks begin -bpage -%%EndPageSetup - -%%BeginObject: obj1 -bplot - -/dpi2point 12 def -portraitMode 0204 7344 csm - - 424 80 5969 4933 MR c np -92 dict begin %Colortable dictionary -/c0 { 0 0 0 sr} bdef -/c1 { 1 1 1 sr} bdef -/c2 { 1 0 0 sr} bdef -/c3 { 0 1 0 sr} bdef -/c4 { 0 0 1 sr} bdef -/c5 { 1 1 0 sr} bdef -/c6 { 1 0 1 sr} bdef -/c7 { 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MP stroke -5183 1093 PD --5 1 5 1 909 3908 3 MP stroke --25 5 25 5 948 3703 3 MP stroke --45 10 45 10 991 3497 3 MP stroke --58 12 58 13 1017 3293 3 MP stroke --71 15 71 16 1045 3089 3 MP stroke --78 17 78 17 1058 2886 3 MP stroke --85 19 85 18 1071 2684 3 MP stroke --85 18 85 18 1071 2483 3 MP stroke --81 18 81 18 1065 2282 3 MP stroke --78 16 78 17 1056 2082 3 MP stroke --68 15 68 14 1037 1883 3 MP stroke --57 13 57 12 1014 1684 3 MP stroke --40 9 40 9 982 1486 3 MP stroke --22 5 22 5 944 1289 3 MP stroke -899 1093 PD -8 17 9 -17 1196 3877 3 MP stroke --18 19 31 -8 1248 3676 3 MP stroke --33 24 49 -7 1280 3466 3 MP stroke --52 26 65 -1 1316 3266 3 MP stroke --60 30 76 -1 1335 3058 3 MP stroke --71 31 85 3 1357 2859 3 MP stroke --74 33 90 2 1363 2653 3 MP stroke --78 32 92 5 1370 2454 3 MP stroke --76 34 92 3 1367 2250 3 MP stroke --71 31 85 3 1355 2053 3 MP stroke --62 30 77 0 1338 1852 3 MP stroke --50 27 64 -2 1313 1654 3 MP stroke --34 24 49 -6 1282 1456 3 MP stroke --15 20 30 -10 1243 1259 3 MP stroke -7 15 8 -15 1197 1063 3 MP stroke -15 30 15 -30 1496 3849 3 MP stroke --11 32 38 -21 1546 3648 3 MP stroke --26 38 56 -20 1579 3438 3 MP stroke --45 40 72 -14 1615 3238 3 MP stroke --58 42 85 -11 1642 3034 3 MP stroke --65 44 92 -10 1656 2831 3 MP stroke --70 45 98 -9 1668 2629 3 MP stroke --71 45 99 -8 1669 2427 3 MP stroke --69 45 96 -10 1664 2227 3 MP stroke --64 44 91 -10 1655 2026 3 MP stroke --55 42 83 -12 1636 1827 3 MP stroke --43 39 70 -14 1613 1628 3 MP stroke --28 37 56 -19 1581 1431 3 MP stroke --9 32 36 -22 1543 1233 3 MP stroke -13 27 14 -27 1497 1038 3 MP stroke -19 38 20 -38 1797 3831 3 MP stroke --1 43 39 -34 1839 3626 3 MP stroke --22 47 60 -29 1881 3420 3 MP stroke --36 50 74 -26 1909 3216 3 MP stroke --49 53 87 -23 1937 3012 3 MP stroke --60 53 97 -19 1957 2812 3 MP stroke --63 56 101 -20 1965 2607 3 MP stroke --67 56 104 -19 1970 2408 3 MP stroke --65 56 103 -20 1967 2205 3 MP stroke --59 54 96 -20 1956 2006 3 MP stroke --51 53 88 -23 1939 1806 3 MP stroke --38 50 76 -26 1914 1608 3 MP stroke --22 47 60 -29 1882 1410 3 MP stroke --4 43 41 -33 1843 1213 3 MP stroke -18 38 19 -38 1798 1017 3 MP stroke -23 47 24 -47 2099 3813 3 MP stroke --1 50 46 -40 2149 3612 3 MP stroke --17 56 64 -38 2183 3403 3 MP stroke --35 58 80 -33 2218 3202 3 MP stroke --48 60 93 -30 2244 2998 3 MP stroke --56 63 101 -29 2259 2795 3 MP stroke --61 64 106 -27 2271 2592 3 MP stroke --62 63 108 -27 2272 2391 3 MP stroke --60 64 105 -28 2268 2190 3 MP stroke --55 62 101 -28 2258 1989 3 MP stroke --47 61 93 -31 2240 1790 3 MP stroke --34 58 80 -33 2216 1591 3 MP stroke --18 54 64 -36 2184 1394 3 MP stroke -0 51 46 -41 2146 1196 3 MP stroke -22 45 23 -45 2100 1002 3 MP stroke -26 52 26 -52 2403 3805 3 MP stroke -5 56 47 -47 2445 3599 3 MP stroke --16 60 67 -43 2487 3394 3 MP stroke --30 63 81 -39 2516 3189 3 MP stroke --43 66 95 -36 2542 2985 3 MP stroke --53 67 104 -33 2562 2784 3 MP stroke --57 69 108 -33 2571 2580 3 MP stroke --59 69 110 -32 2576 2379 3 MP stroke --57 70 109 -34 2572 2178 3 MP stroke --52 69 104 -35 2561 1978 3 MP stroke --43 66 94 -36 2544 1778 3 MP stroke --31 64 82 -39 2518 1580 3 MP stroke --15 60 67 -42 2487 1382 3 MP stroke -4 56 47 -46 2447 1185 3 MP stroke -25 51 26 -51 2403 989 3 MP stroke -28 56 28 -56 2707 3796 3 MP stroke -4 59 50 -49 2756 3594 3 MP stroke --14 64 69 -46 2791 3385 3 MP stroke --31 66 85 -41 2825 3183 3 MP stroke --41 70 96 -41 2847 2978 3 MP stroke --50 71 105 -37 2866 2776 3 MP stroke --55 73 111 -37 2875 2573 3 MP stroke --57 73 112 -36 2880 2372 3 MP stroke --56 73 111 -37 2876 2171 3 MP stroke --50 71 105 -38 2866 1971 3 MP stroke --42 69 96 -39 2848 1772 3 MP stroke --30 67 85 -42 2824 1572 3 MP stroke --14 63 68 -45 2792 1376 3 MP stroke -5 60 51 -50 2754 1177 3 MP stroke -27 53 27 -53 2708 983 3 MP stroke -28 56 28 -56 3013 3796 3 MP stroke -7 60 49 -51 3056 3590 3 MP stroke --13 65 69 -47 3097 3385 3 MP stroke --28 68 84 -43 3127 3180 3 MP stroke --41 70 97 -40 3153 2976 3 MP stroke --49 73 105 -39 3170 2773 3 MP stroke --55 74 111 -38 3181 2571 3 MP stroke --57 74 113 -37 3185 2369 3 MP stroke --55 74 111 -38 3181 2169 3 MP stroke --49 72 105 -39 3170 1969 3 MP stroke --41 71 97 -41 3153 1769 3 MP stroke --28 68 84 -44 3127 1571 3 MP stroke --13 65 69 -47 3097 1373 3 MP stroke -7 60 49 -51 3056 1176 3 MP stroke -28 55 28 -55 3013 979 3 MP stroke -27 54 27 -54 3320 3800 3 MP stroke -4 60 51 -50 3367 3591 3 MP stroke --14 63 68 -45 3404 3388 3 MP stroke --30 68 85 -43 3436 3182 3 MP stroke --42 69 96 -39 3460 2979 3 MP stroke --50 72 105 -38 3478 2775 3 MP stroke --56 72 111 -36 3488 2573 3 MP stroke --57 73 112 -36 3492 2372 3 MP stroke --55 73 111 -37 3487 2170 3 MP stroke --51 71 106 -37 3478 1971 3 MP stroke --42 70 97 -40 3459 1770 3 MP stroke --31 67 85 -42 3437 1574 3 MP stroke --13 64 69 -46 3403 1373 3 MP stroke -3 59 51 -48 3368 1179 3 MP stroke -28 55 28 -55 3319 979 3 MP stroke -26 51 26 -51 3627 3806 3 MP stroke -4 56 48 -47 3671 3600 3 MP stroke --15 60 67 -42 3711 3394 3 MP stroke --31 63 83 -39 3742 3190 3 MP stroke --44 67 95 -37 3768 2986 3 MP stroke --52 68 103 -34 3786 2782 3 MP stroke --57 69 109 -33 3796 2580 3 MP stroke --59 69 110 -32 3800 2379 3 MP stroke --56 70 108 -34 3795 2178 3 MP stroke --53 67 104 -33 3786 1979 3 MP stroke --43 66 94 -36 3767 1778 3 MP stroke --29 64 81 -40 3740 1580 3 MP stroke --16 60 67 -43 3711 1382 3 MP stroke -5 56 47 -47 3669 1185 3 MP stroke -26 52 26 -52 3627 988 3 MP stroke -23 45 22 -45 3937 3818 3 MP stroke -0 50 46 -40 3983 3610 3 MP stroke --19 54 64 -36 4021 3406 3 MP stroke --35 58 81 -33 4052 3201 3 MP stroke --46 60 92 -30 4077 2997 3 MP stroke --55 62 101 -28 4094 2794 3 MP stroke --60 63 106 -27 4104 2592 3 MP stroke --62 63 107 -27 4109 2391 3 MP stroke --62 63 107 -27 4107 2190 3 MP stroke --55 62 101 -28 4095 1990 3 MP stroke --48 60 94 -29 4080 1790 3 MP stroke --36 57 81 -32 4054 1592 3 MP stroke --18 56 65 -38 4019 1391 3 MP stroke --2 50 47 -40 3985 1198 3 MP stroke -24 48 24 -48 3935 997 3 MP stroke -19 37 19 -37 4246 3833 3 MP stroke --3 42 41 -32 4291 3627 3 MP stroke --23 47 60 -29 4331 3422 3 MP stroke --38 50 76 -25 4362 3217 3 MP stroke --50 52 88 -22 4387 3013 3 MP stroke --59 54 97 -20 4404 2811 3 MP stroke --64 56 102 -19 4416 2607 3 MP stroke --66 56 103 -19 4419 2408 3 MP stroke --64 56 102 -20 4413 2205 3 MP stroke --60 54 96 -20 4406 2008 3 MP stroke --50 53 88 -23 4385 1805 3 MP stroke --36 50 74 -26 4358 1607 3 MP stroke --22 47 61 -30 4329 1409 3 MP stroke --1 43 40 -34 4287 1212 3 MP stroke -19 39 19 -39 4246 1015 3 MP stroke -14 27 13 -27 4558 3855 3 MP stroke --9 33 37 -23 4603 3648 3 MP stroke --28 37 55 -18 4642 3442 3 MP stroke --43 40 71 -15 4673 3238 3 MP stroke --55 42 82 -12 4697 3034 3 MP stroke --64 44 92 -10 4715 2831 3 MP stroke --68 45 95 -9 4725 2629 3 MP stroke --71 45 98 -8 4730 2427 3 MP stroke --71 45 98 -8 4729 2226 3 MP stroke --64 44 91 -10 4717 2027 3 MP stroke --58 43 85 -12 4703 1827 3 MP stroke --44 40 71 -15 4676 1629 3 MP stroke --26 38 55 -20 4640 1426 3 MP stroke --11 32 38 -22 4607 1234 3 MP stroke -15 30 15 -30 4556 1032 3 MP stroke -8 15 7 -15 4870 3880 3 MP stroke --15 20 30 -10 4915 3673 3 MP stroke --34 24 49 -6 4954 3468 3 MP stroke --50 27 64 -2 4986 3264 3 MP stroke --62 30 77 0 5011 3059 3 MP stroke --71 31 85 2 5028 2858 3 MP stroke --77 33 92 3 5040 2653 3 MP stroke --77 32 91 5 5043 2454 3 MP stroke --75 33 90 3 5036 2250 3 MP stroke --72 31 86 3 5029 2054 3 MP stroke --60 30 76 -1 5008 1851 3 MP stroke --52 26 65 0 4989 1656 3 MP stroke --33 25 49 -7 4952 1454 3 MP stroke --18 19 31 -8 4920 1262 3 MP stroke -8 16 8 -16 4869 1060 3 MP stroke -5183 3909 PD --22 5 22 5 5229 3703 3 MP stroke --41 9 41 9 5266 3498 3 MP stroke --56 12 56 13 5299 3293 3 MP stroke --68 14 68 15 5322 3090 3 MP stroke --78 17 78 16 5341 2887 3 MP stroke --82 18 82 18 5349 2684 3 MP stroke --84 18 84 18 5356 2483 3 MP stroke --84 18 84 19 5356 2281 3 MP stroke --79 17 79 17 5342 2082 3 MP stroke --72 16 72 15 5329 1882 3 MP stroke --58 13 58 12 5302 1684 3 MP stroke --46 10 46 10 5275 1485 3 MP stroke --25 5 25 5 5233 1289 3 MP stroke -5183 1093 PD -gr - -%%IncludeResource: font Helvetica -/Helvetica /ISOLatin1Encoding 168 FMSR - -2300 208 mt -(Vector-field plot of FE-solution E) s -%%IncludeResource: font Helvetica -/Helvetica /ISOLatin1Encoding 132 FMSR - -4779 292 mt -(h) s -%%IncludeResource: font Helvetica -/Helvetica /ISOLatin1Encoding 120 FMSR - -3546 4902 mt -(x) s - 573 2532 mt -90 rotate -(y) s -90 rotate - -end - -eplot -%%EndObject - -epage -end - -showpage - -%%Trailer -%%EOF - -%%EndDocument - @endspecial 758 2326 a Fk(Figure)30 b(4:)41 b(V)-8 b(ector-\014eld)32 -b(plot)d(of)i(the)f(FE-solution)g(of)g(example)h($31$.)872 -4824 y @beginspecial 55 @llx 201 @lly 549 @urx 611 @ury -2692 @rwi 1984 @rhi @setspecial -%%BeginDocument: field2.eps -%!PS-Adobe-2.0 EPSF-1.2 -%%Creator: MATLAB, The Mathworks, Inc. -%%Title: pix.eps -%%CreationDate: 08/26/2002 11:55:05 -%%DocumentNeededFonts: Helvetica -%%DocumentProcessColors: Cyan Magenta Yellow Black -%%Pages: 1 -%%BoundingBox: 55 201 549 611 -%%EndComments - -%%BeginProlog -% MathWorks dictionary -/MathWorks 160 dict begin -% definition operators -/bdef {bind def} bind def -/ldef {load def} bind def -/xdef {exch def} bdef -/xstore {exch store} bdef -% operator abbreviations -/c /clip ldef -/cc /concat ldef -/cp /closepath ldef -/gr /grestore ldef -/gs /gsave ldef -/mt /moveto ldef -/np /newpath ldef -/cm /currentmatrix ldef -/sm /setmatrix ldef -/rm /rmoveto ldef -/rl /rlineto ldef -/s /show ldef -/sc {setcmykcolor} bdef -/sr /setrgbcolor ldef -/sg /setgray ldef -/w /setlinewidth ldef -/j /setlinejoin ldef -/cap /setlinecap ldef -/rc {rectclip} bdef -/rf {rectfill} bdef -% page state control -/pgsv () def -/bpage {/pgsv save def} bdef -/epage {pgsv restore} bdef -/bplot /gsave ldef -/eplot {stroke grestore} bdef -% orientation switch -/portraitMode 0 def /landscapeMode 1 def /rotateMode 2 def -% coordinate system mappings -/dpi2point 0 def -% font control -/FontSize 0 def -/FMS {/FontSize xstore findfont [FontSize 0 0 FontSize neg 0 0] - makefont setfont} bdef -/reencode {exch dup where {pop load} {pop StandardEncoding} ifelse - exch dup 3 1 roll findfont dup length dict begin - { 1 index /FID ne {def}{pop pop} ifelse } forall - /Encoding exch def currentdict end definefont pop} bdef -/isroman {findfont /CharStrings get /Agrave known} bdef -/FMSR {3 1 roll 1 index dup isroman {reencode} {pop pop} ifelse - exch FMS} bdef -/csm {1 dpi2point div -1 dpi2point div scale neg translate - dup landscapeMode eq {pop -90 rotate} - {rotateMode eq {90 rotate} if} ifelse} bdef -% line types: solid, dotted, dashed, dotdash -/SO { [] 0 setdash } bdef -/DO { [.5 dpi2point mul 4 dpi2point mul] 0 setdash } bdef -/DA { [6 dpi2point mul] 0 setdash } bdef -/DD { [.5 dpi2point mul 4 dpi2point mul 6 dpi2point mul 4 - dpi2point mul] 0 setdash } bdef -% macros for lines and objects -/L {lineto stroke} bdef -/MP {3 1 roll moveto 1 sub {rlineto} repeat} bdef -/AP {{rlineto} repeat} bdef -/PDlw -1 def -/W {/PDlw currentlinewidth def setlinewidth} def -/PP {closepath eofill} bdef -/DP {closepath stroke} bdef -/MR {4 -2 roll moveto dup 0 exch rlineto exch 0 rlineto - neg 0 exch rlineto closepath} bdef -/FR {MR stroke} bdef -/PR {MR fill} bdef -/L1i {{currentfile picstr readhexstring pop} image} bdef -/tMatrix matrix def -/MakeOval {newpath tMatrix currentmatrix pop translate scale -0 0 1 0 360 arc tMatrix setmatrix} bdef -/FO {MakeOval stroke} bdef -/PO {MakeOval fill} bdef -/PD {currentlinecap 1 cap 3 1 roll 2 copy mt lineto stroke - cap PDlw -1 eq not {PDlw w /PDlw -1 def} if} def -/FA {newpath tMatrix currentmatrix pop translate scale - 0 0 1 5 -2 roll arc tMatrix setmatrix stroke} bdef -/PA {newpath tMatrix currentmatrix pop translate 0 0 moveto scale - 0 0 1 5 -2 roll arc closepath tMatrix setmatrix fill} bdef -/FAn {newpath tMatrix currentmatrix pop translate scale - 0 0 1 5 -2 roll arcn tMatrix setmatrix stroke} bdef -/PAn {newpath tMatrix currentmatrix pop translate 0 0 moveto scale - 0 0 1 5 -2 roll arcn closepath tMatrix setmatrix fill} bdef -/vradius 0 def /hradius 0 def /lry 0 def -/lrx 0 def /uly 0 def /ulx 0 def /rad 0 def -/MRR {/vradius xdef /hradius xdef /lry xdef /lrx xdef /uly xdef - /ulx xdef newpath tMatrix currentmatrix pop ulx hradius add uly - vradius add translate hradius vradius scale 0 0 1 180 270 arc - tMatrix setmatrix lrx hradius sub uly vradius add translate - hradius vradius scale 0 0 1 270 360 arc tMatrix setmatrix - lrx hradius sub lry vradius sub translate hradius vradius scale - 0 0 1 0 90 arc tMatrix setmatrix ulx hradius add lry vradius sub - translate hradius vradius scale 0 0 1 90 180 arc tMatrix setmatrix - closepath} bdef -/FRR {MRR stroke } bdef -/PRR {MRR fill } bdef -/MlrRR {/lry xdef /lrx xdef /uly xdef /ulx xdef /rad lry uly sub 2 div def - newpath tMatrix currentmatrix pop ulx rad add uly rad add translate - rad rad scale 0 0 1 90 270 arc tMatrix setmatrix lrx rad sub lry rad - sub translate rad rad scale 0 0 1 270 90 arc tMatrix setmatrix - closepath} bdef -/FlrRR {MlrRR stroke } bdef -/PlrRR {MlrRR fill } bdef -/MtbRR {/lry xdef /lrx xdef /uly xdef /ulx xdef /rad lrx ulx sub 2 div def - newpath tMatrix currentmatrix pop ulx rad add uly rad add translate - rad rad scale 0 0 1 180 360 arc tMatrix setmatrix lrx rad sub lry rad - sub translate rad rad scale 0 0 1 0 180 arc tMatrix setmatrix - closepath} bdef -/FtbRR {MtbRR stroke } bdef -/PtbRR {MtbRR fill } bdef -/stri 6 array def /dtri 6 array def -/smat 6 array def /dmat 6 array def -/tmat1 6 array def /tmat2 6 array def /dif 3 array def -/asub {/ind2 exch def /ind1 exch def dup dup - ind1 get exch ind2 get sub exch } bdef -/tri_to_matrix { - 2 0 asub 3 1 asub 4 0 asub 5 1 asub - dup 0 get exch 1 get 7 -1 roll astore } bdef -/compute_transform { - dmat dtri tri_to_matrix tmat1 invertmatrix - smat stri tri_to_matrix tmat2 concatmatrix } bdef 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MP stroke --81 173 4852 2300 2 MP stroke --145 114 4852 2099 2 MP stroke --181 47 4852 1897 2 MP stroke --181 -46 4852 1696 2 MP stroke --145 -114 4852 1495 2 MP stroke --80 -174 4852 1294 2 MP stroke -0 -192 4852 1093 2 MP stroke -0 -106 5107 3909 2 MP stroke -122 -96 5107 3708 2 MP stroke -220 -63 5107 3507 2 MP stroke -274 -26 5107 3306 2 MP stroke -274 26 5107 3105 2 MP stroke -220 64 5107 2903 2 MP stroke -122 96 5107 2702 2 MP stroke -0 106 5107 2501 2 MP stroke --122 96 5107 2300 2 MP stroke --220 63 5107 2099 2 MP stroke --274 26 5107 1897 2 MP stroke --274 -25 5107 1696 2 MP stroke --220 -63 5107 1495 2 MP stroke --122 -96 5107 1294 2 MP stroke -0 -107 5107 1093 2 MP stroke -5362 3909 PD -135 0 5362 3708 2 MP stroke -243 0 5362 3507 2 MP stroke -303 0 5362 3306 2 MP stroke -303 0 5362 3105 2 MP stroke -243 0 5362 2903 2 MP stroke -135 0 5362 2702 2 MP stroke -5362 2501 PD --135 0 5362 2300 2 MP stroke --243 0 5362 2099 2 MP stroke --303 0 5362 1897 2 MP stroke --303 0 5362 1696 2 MP stroke --243 0 5362 1495 2 MP stroke --135 0 5362 1294 2 MP stroke -5362 1093 PD -1791 3909 PD --45 12 45 11 1881 3697 3 MP stroke --80 21 80 21 1954 3486 3 MP stroke --100 26 100 26 1994 3280 3 MP stroke --100 26 100 26 1994 3079 3 MP stroke --80 21 80 20 1954 2883 3 MP stroke --45 12 45 11 1881 2691 3 MP stroke -1791 2501 PD -45 -12 -45 -11 1701 2311 3 MP stroke -80 -21 -80 -20 1628 2119 3 MP stroke -100 -26 -100 -26 1588 1923 3 MP stroke -100 -26 -100 -26 1588 1722 3 MP stroke -80 -21 -80 -21 1628 1516 3 MP stroke -45 -12 -45 -11 1701 1305 3 MP stroke -1791 1093 PD --14 -35 -15 35 2061 3981 3 MP stroke --53 -21 27 42 2141 3762 3 MP stroke --81 -2 64 40 2202 3530 3 MP stroke --94 15 87 32 2233 3299 3 MP stroke --87 32 94 15 2226 3064 3 MP stroke --64 40 81 -2 2185 2842 3 MP stroke --27 42 53 -21 2115 2627 3 MP stroke -15 35 14 -35 2032 2430 3 MP stroke -54 21 -27 -42 1951 2246 3 MP stroke -82 2 -64 -40 1890 2075 3 MP stroke -94 -15 -87 -33 1859 1904 3 MP stroke -87 -32 -94 -15 1866 1737 3 MP stroke -64 -39 -82 2 1908 1556 3 MP stroke -27 -42 -54 21 1978 1369 3 MP stroke --14 -35 -15 35 2061 1164 3 MP stroke --26 -63 -27 63 2328 4038 3 MP stroke --50 -51 2 65 2379 3817 3 MP stroke --63 -25 32 50 2414 3571 3 MP stroke --66 0 53 31 2429 3321 3 MP stroke --53 31 66 0 2416 3058 3 MP stroke --32 50 63 -25 2383 2814 3 MP stroke --3 64 51 -50 2331 2579 3 MP stroke -27 64 26 -64 2275 2373 3 MP stroke -50 51 -2 -65 2223 2191 3 MP stroke -64 26 -32 -50 2188 2034 3 MP stroke -67 0 -54 -31 2174 1882 3 MP stroke -53 -31 -66 0 2187 1743 3 MP stroke -32 -50 -64 25 2220 1584 3 MP stroke -3 -64 -50 50 2271 1417 3 MP stroke --26 -63 -27 63 2328 1221 3 MP stroke --33 -79 -33 79 2589 4069 3 MP stroke --41 -68 -19 74 2608 3850 3 MP stroke --39 -42 -1 52 2616 3597 3 MP stroke --32 -13 16 26 2614 3338 3 MP stroke --16 26 32 -13 2598 3059 3 MP stroke -1 52 39 -42 2576 2803 3 MP stroke -19 74 40 -69 2549 2555 3 MP stroke -33 79 33 -79 2523 2341 3 MP stroke -41 68 19 -74 2504 2158 3 MP stroke -39 42 0 -52 2497 2008 3 MP stroke -32 13 -16 -26 2499 1865 3 MP stroke -16 -25 -32 13 2515 1741 3 MP stroke -0 -52 -39 41 2536 1596 3 MP stroke --19 -74 -40 69 2564 1441 3 MP stroke --33 -79 -33 79 2589 1253 3 MP stroke --33 -79 -33 79 2844 4069 3 MP stroke --19 -74 -41 68 2819 3856 3 MP stroke -0 -53 -39 42 2791 3608 3 MP stroke -16 -26 -32 13 2770 3351 3 MP stroke -32 13 -16 -26 2754 3072 3 MP stroke -39 42 0 -52 2752 2813 3 MP stroke -40 69 19 -74 2760 2560 3 MP stroke -33 79 33 -79 2778 2341 3 MP stroke -19 74 41 -68 2803 2152 3 MP stroke -1 52 39 -42 2831 1998 3 MP stroke --16 26 32 -13 2853 1852 3 MP stroke --32 -12 16 25 2869 1729 3 MP stroke --39 -42 -1 52 2871 1586 3 MP stroke --40 -68 -19 74 2863 1436 3 MP stroke --33 -79 -33 79 2844 1253 3 MP stroke --26 -63 -27 63 3093 4038 3 MP stroke -2 -65 -50 51 3036 3831 3 MP stroke -32 -50 -63 25 2985 3596 3 MP stroke -53 -31 -66 -1 2952 3353 3 MP stroke -66 0 -53 -31 2939 3089 3 MP stroke -63 25 -32 -50 2954 2839 3 MP 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50 -3 -64 4009 3599 3 MP stroke -63 25 -32 -50 3974 3443 3 MP stroke -66 0 -53 -31 3959 3290 3 MP stroke -53 -31 -66 0 3972 3151 3 MP stroke -32 -51 -63 26 4005 2992 3 MP stroke -3 -65 -51 51 4057 2825 3 MP stroke --27 -64 -26 64 4113 2629 3 MP stroke --51 -50 3 64 4164 2409 3 MP stroke --63 -25 32 50 4199 2163 3 MP stroke --66 0 53 31 4214 1913 3 MP stroke --53 31 66 1 4201 1649 3 MP stroke --32 50 63 -25 4168 1406 3 MP stroke --2 65 50 -51 4117 1171 3 MP stroke -26 63 27 -63 4060 964 3 MP stroke -33 79 33 -79 4309 3749 3 MP stroke -40 68 19 -74 4290 3566 3 MP stroke -39 42 1 -52 4282 3416 3 MP stroke -32 12 -16 -25 4284 3273 3 MP stroke -16 -26 -32 13 4300 3150 3 MP stroke --1 -52 -39 42 4322 3004 3 MP stroke --19 -74 -41 68 4350 2850 3 MP stroke --33 -79 -33 79 4375 2661 3 MP stroke --40 -69 -19 74 4393 2442 3 MP stroke --39 -42 0 52 4401 2189 3 MP stroke --32 -13 16 26 4399 1930 3 MP stroke --16 26 32 -13 4383 1651 3 MP stroke -0 53 39 -42 4362 1394 3 MP stroke -19 74 41 -68 4334 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Fh(\000)p Fp(1)1623 4774 y Fz(curl)14 -b Fx(u)p Fz($)k(+)g Fx(i!)s(\033)s(u)k Fz(=)h Fx(F)95 -b Fz(in)83 b(\012)14 b Fx(;)1948 4899 y(u)k Fs(^)h Fx(n)k -Fz(=)g(0)82 b(on)h Fx(@)5 b Fz(\012)14 b Fx(:)3814 4837 -y Fz($37$)28 5082 y(Although)23 b(problem)g($37$)h(is)f(complex-v) --5 b(alued,)24 b(\014nding)f(a)g(\014nite)i(elemen)n(t)e(metho)r(d)h -(to)g(appro)n(ximate)e($37$)h(basically)f(b)r(oils)28 -5182 y(do)n(wn)27 b(to)g(\014nding)h(a)f(\014nite)h(elemen)n(t)g(metho) -r(d)g(for)f(the)h(real)f(v)-5 b(alued)27 b(mo)r(del)h(problem)f($1$.) -1949 5719 y Fk(23)p eop -%%Trailer -end -userdict /end-hook known{end-hook}if -%%EOF diff --git a/deal.II/doc/reports/new-threads/index.html b/deal.II/doc/reports/new-threads/index.html deleted file mode 100644 index b146117901..0000000000 --- a/deal.II/doc/reports/new-threads/index.html +++ /dev/null @@ -1,1059 +0,0 @@ - -
  -A short description of the new threading scheme -
  - - -
  - Wolfgang Bangerth, May 2003 -
  - - -
  -Since the first deal.II report on -multithreading was written in 2000 (see the list of deal.II -publications), -we have put in place a new -implementation of the threading scheme (the first release to contain it is -4.0). The new scheme can do all that you could do before, so the report is in a -sense still valid, but it describes a syntax that is no more used. We will here -briefly describe this syntax as well as some considerations that guided us -while implementing it. For general questions on multithreading, how programs -that use it must look like, and for pitfalls to watch out for, please still -refer to the report mentioned above. -
  - -
  -We note that since this report was written, there has been another -incarnation of support for multicore machines, namely by using the -Threading Building Blocks and tasks. The documentation module on -parallel computing, available through the modules page of the deal.II -manual, explains this new direction in more detail. -
  - - -
  1. Rationale and Introduction
  - - -
  -POSIX and other thread libraries only allow functions as thread entry -points that satisfy the signature -
  - void * (*) (void *) -
  -and starting threads involves a clumsy syntax. Thread entry points -with another signature need to be "wrapped", i.e. their arguments need -to be stored in a structure, and we need a function with above -signature that can be used to "unpack" the arguments and call the -desired function. This basically forces us to have one such structure -and entry function for each function signature that we want to start a -thread with. -
  - -
  -The first incarnations of the threading scheme in deal.II already got a long -way towards making this simpler, by hiding the thread entry points, the packing -and unpacking behind a layer of carefully crafted templates. It allowed you to -call (almost) any function with arbitrary argument lists on a new thread, -except that functions that returned values were not allowed. Implementing such -a template scheme is not simple, since, besides simplicity to use, it has to -take care of the lifetimes of objects that need to be synchronised across -threads, and in particular since templates do not allow for functions with -arbitrary numbers of arguments - they need to be repeated for every number of -arguments, which makes implementation tedious. Nevertheless, the old scheme was -very much usable. -
  - -
  -However, the old scheme had a number of shortcomings: -
  -
  The implementation did not allow for functions returning - anything but void. We want to be able to call everything - on a new thread that can also be called on the present one.
  -
  Thread objects could not be copied. Rather, thread ids were put into a -thread manager object that took care of it, but handling single, or even -detached threads was not too convenient.
  -
  The general syntax for calling a function on a new thread was a - little clumsy and not intuitive.
  -
  -
  - -
  -Regarding the last point, note that any other function is called by -
  - f(arg1, arg2); - obj.f(arg1, arg2); -
  -Ideally, the following syntax for starting any function on a new -thread would be nice: -- spawn f(arg1, arg2); - spawn obj.f(arg1,arg2); - -This syntax is not possible in C++, but the following syntax is, -making it relatively clear what the intent of the statement is: -- spawn (f)(arg1, arg2); - spawn (obj, &Class::f)(arg1,arg2); - -This is the syntax we will want to achieve (except for the fact that the -spawn function is in a namespace Threads, just like -all other entities described here). -
  - -
  -This text will discuss the details that are needed to implement -this syntax, as well as the following points: -
  -
  Overloading spawn() so as to take unbound functions and member -functions, whether virtual or static. Of course, every call needs to be type -safe, i.e. the exact - same conversions of arguments need to be performed as in a usual call (except - for two additional copies that are necessary).
  -
  spawn() needs to return a value that allows us to identify, -and join a thread. The syntax for this will be -- Thread<> t = spawn(f)(arg1, arg2); - t.join (); - - If we don't save the return value of spawn(), as in the examples - above, then we have just created a detached thread.
  -
  Return values: if f() returns a value, say, an integer, then -we want to be able to retrieve it once the thread has finished: -- Thread<int> t = spawn (f)(1., 1.); - t.join (); - int i = t.return_value (); - - This requires some care when functions return references, but some - template magic will save us. Another special case are functions that - return void.
  -
  Thread groups: if threads are created inside a loop, we will want to - put all of them into a ThreadGroup object, and wait for them - collectively, rather than one-by-one.
  -
  -
  - -
  -Basically, the syntax above is all you need to know. It is as simple as -that. The rest of this text, in comparison is very much of technical nature. I -took most of it from a technical discussion I had with the author of the -threading scheme in boost, William Kempf. It describes the way the threading -scheme is implemented, the meaning of the various classes, etc. It probably -doesn't give you much insight how to use it, but should explain in -reasonable detail how it works. For more examples of use, take a look -at a number of the example programs in deal.II, or at some places in the -library itself. -
  - - -
  -This paper is divided into the following parts: -
  -
  This introduction
  -
  Entities (functions, classes) that are used by both and that - describe the newly created thread
  -
  Entities that are used on the calling thread
  -
  Entities that are used to create a thread
  -
  Tool classes
  -
  Open problems
  -
  Further suggestions
  -
  -We will present the main parts of the code in the text. The implementation is -in the library; all entities that -are not to be used by the user are placed into a namespace -internal, those to be used are in a namespace -Threads. The implementation uses Boost's shared_ptr. Some parts of -the implementation parallel the -boost::function library, but they are small and taylored to the -particular purpose at hand; in particular, they make heavy use of the -boost::tuple library. We note that the code has in some places already evolved -a little bit beyond the state of this paper, but the main ideas are all to be -found still. -
  - - - -
  2. Entities that describe threads
  - - -
  -Each thread that has been created is described by exactly one object -of type thread_description<RT>, where RT here and in the -sequel will always denote the return type of the function being called -on a new thread. The thread_description class is split into an -operating system dependent base class, and an independent derived -class. The base class is responsible for abstracting the OS -interface to the functions creating, joining, killing, and signalling -threads. For POSIX threads, this class looks as follows: -
  - -- struct thread_description_base { - private: - pthread_t pt; - mutable volatile bool was_joined; - mutable boost::mutex join_mutex; - mutable boost::condition join_condition; - - public: - thread_description_base () : was_joined (false) {}; - virtual ~thread_description_base () { /* ... */ }; - - void create (void * (*p) (void *), void *d) { - pthread_create (&pt, 0, p, d); - }; - - void join () const { - if (was_joined) - return; - boost::mutex::scoped_lock lock(join_mutex); - if (!was_joined) - pthread_join (pt, 0); - was_joined = true; - }; - }; - - -
  -join() can be called more than once and uses Schmidt's thread-safe -double-checking pattern for speed. There could be additional functions -kill() or send_signal(), but these are not presently -implemented. -
  - -
  -In the destructor, we need to make sure that a thread is joined at -least once in its lifetime, or if not that it is being detached -(otherwise, we create the thread equivalent of a zombie process, which -will lead to a resource leak in the operating system). This is a -little tricky, since the destructor might be called while the thread -is still running; comments in the code explain how we work around -this. -
  - -
  -The thread_description<RT> class is derived from this base -class: -
  - template <typename RT> - struct thread_description : public thread_description_base - { - return_value<RT> ret_val; - }; -
  -
  - -
  -Its only purpose is to provide a place of storage for the return -value of the function being called on the new thread. Since functions -might return references or just nothing at all, the return_value -template is used. It is described below in the section on Tool -Classes. The return value will be set on exit of the function being -called. -
  - -
  -As mentioned, there is exactly one thread_description<RT> -object per created thread. It is accessed using boost::shared_ptr -objects, and references are held from each Thread<RT> object -for this thread as -well as from a wrapper function on the new thread. The object is thus -deleted, when all Thread<RT> objects for this thread have gone out of -scope (or point to different threads) and the thread itself has -finished; this is the appropriate time. -
  - - - -
  3. Entities that are used on the calling thread
  - - -
  -On the calling thread, we basically use the Thread<RT> -class, ThreadGroup<RT> class, and spawn -function. The Thread<RT> class has the following -implementation: -
  - -- template <typename RT = void> - class Thread { - public: - Thread () {}; - Thread (const boost::shared_ptr<thread_description<RT> > &td) - : thread_description (td) {}; - - void join () const { thread_description->join (); }; - - RT return_value () { - join (); - return thread_description->ret_val.get(); - }; - - bool operator == (const thread &t) { - return thread_description == t.thread_description; - }; - - private: - boost::shared_ptr<thread_description<RT> > thread_description; - }; - - -
  -Copy constructor and operator= are generated automatically by the -compiler. Note that asking for the return_value automatically waits -for the thread to finish, and that for this it is helpful that we can -call join() more than once on the thread description object. The -return_value() function also makes use of the fact that if RT=void, -then the return construct is still valid. Furthermore, since this is -the most common case, the template argument of the thread class has a -default of void. -
  - -
  -The ThreadGroup class is a container distributing calls to its -member functions to all its elements. Elements are added using -operator+=, and they are stored using a -std::vector. (A std::set would be more appropriate, -but then we would have to have operator< for -Thread<RT> objects.) It has the same default value for the -template argument: -
  - -- template <typename RT = void> - class ThreadGroup - { - public: - ThreadGroup & operator += (const Thread<RT> &t) { - threads.push_back (t); - return *this; - }; - - void join_all () const { - for (typename std::vector<Thread<RT> >::const_iterator - t=threads.begin(); t!=threads.end(); ++t) - t->join (); - }; - - private: - std::vector<Thread<RT> > threads; - }; - - -
  -Since objects of type Thread<RT> are freely copyable, there -is no need -to provide an index operator for ThreadGroup; if you need to index -its elements (for example to get at the return value), use -std::vector<Thread<RT> >. -
  - -
  -Finally, there are overloads of the spawn template, for unbound -functions, as well as const and non-const member -functions. We only show them for unary member functions: -
  - template <typename RT, typename C, typename Arg1> - mem_fun_encapsulator<RT,C,boost::tuple<Arg1> > - spawn (C &c, RT (C::*fun_ptr)(Arg1)) { - return mem_fun_encapsulator<RT, C, boost::tuple<Arg1> > (c,fun_ptr); - } - - template <typename RT, typename C, typename Arg1> - mem_fun_encapsulator<RT,const C,boost::tuple<Arg1> > - spawn (const C &c, RT (C::*fun_ptr)(Arg1) const) { - return mem_fun_encapsulator<RT, const C, boost::tuple<Arg1> > (c,fun_ptr); - } -
  -
  - -
  -Note that we need two overloaded versions, for const and -non-const -member functions. Both create an intermediate object (in the -internal -namespace) that will accept arguments in place of the function being -called on the new thread, make sure a new thread is created, copy the -arguments to the new thread's stack, and only then return. The exact -mechanism is described in the next section. -
  - -
  -In the implementation, we have to repeat the functions above for -binary, ternary, ... member functions, and also for unbound member -functions. One would really like to have something also for objects other than -pointers to (member-)functions that provide an -operator(). However, this doesn't seem to be possible if -operator() returns something other than void or takes -arguments. This -would need some kind of typeof-operator which is not standard C++. See the -discussion in the Open Problems section. -
  - - -
  4. Entities that are used to create a thread
  - - -
  -In this section, we describe the gory details of copying arguments -from the stack of the old thread to the stack of the new one. These -details are not necessary to use the spawn() functions, -so are probably boring and may be skipped. -
  - -
  -The basic idea is the following: spawn() returns an object and provides -it with the address of the function to be called, and in the case of a -member function with the address of an object. mem_fun_encapsulator -looks like this: -
  - -- template <typename RT, typename C, typename ArgList, - int length = boost::tuples::length<ArgList>::value> - class mem_fun_encapsulator; - - template <typename RT, typename C, typename ArgList> - class mem_fun_encapsulator<RT,C,ArgList,1> { - typedef typename mem_fun_ptr<RT,C,ArgList>::type MemFunPtr; - - public: - mem_fun_encapsulator (C &c, MemFunPtr mem_fun_ptr) - : c (c), mem_fun_ptr(mem_fun_ptr) {}; - - Thread<RT> - operator() (typename boost::tuples::element<0,ArgList>::type arg1) { - return mem_fun_wrapper<RT,C,ArgList> (mem_fun_ptr, c, - boost::tie(arg1)).fire_up (); - }; - - private: - C &c; - MemFunPtr mem_fun_ptr; - }; - - -
  -(Note how the default value specification of the last template -argument automatically redirects uses with three template parameters -to the correct four-parameter specialization, even though the general -template is never used.) -
  - -
  -The constructor stores the two addresses. If one calls -
  - spawn(obj, &C::f) (42); -
  -the next thing that is invoked is the operator() of this class. It -takes the argument(s), creates a temporary with the two addresses and -a reference to the argument (that's what boost::tie) does, and calls -fire_up() on this temporary. fire_up has all the information, and does -the work. Note that we will not pass references to the individual -arguments, but bind them all together with boost::tie, so that we need -not have different versions of the mem_fun_wrapper class for different -numbers of arguments. (However, we need a separate partial -specialization of the mem_fun_encapsulator class for each number of -function arguments.) The tie_args template is used to make a version -of the ArgList type with all reference types; it is described below. -
  - -
  -The next question, of course, is how mem_fun_wrapper looks like. Let -us first consider the base class that it has in common with -fun_wrapper, the wrapping class for non-member function objects: -
  - template <typename RT, typename EntryPointClass> - struct wrapper_base { - Thread<RT> fire_up () { - thread_descriptor - = DescriptionPointer(new typename thread_description<RT>()); - - boost::mutex::scoped_lock lock (mutex); - thread_descriptor->create (&EntryPointClass::entry_point, - (void *)this); - condition.wait (lock); - - return thread_descriptor; - } - - protected: - typedef boost::shared_ptr<thread_description<RT> > - DescriptionPointer; - - DescriptionPointer thread_descriptor; - - mutable boost::mutex mutex; - mutable boost::condition condition; - }; -
  -
  -fire_up is the only real function; it creates a thread descriptor -object, and calls it with a pointer to the present object, and the address of -the starting point is EntryPointClass::entry_point, where -EntryPoint is the name of a class that implements this thread -starting function and is passed as a template argument to -wrapper_base. -Before it starts the new thread, it acquires a mutex and -afterwards wait until a condition is signalled before it finishes by -using the thread descriptor object to generate a Thread<RT> -object. -
  - -
  -The magic happens in the derived class: -
  - template <typename RT, class C, typename ArgList> - struct mem_fun_wrapper - : public wrapper_base<RT, mem_fun_wrapper<RT,C,ArgList> > - { - typedef typename mem_fun_ptr<RT,C,ArgList>::type MemFunPtr; - typedef typename tie_args<ArgList>::type ArgReferences; - mem_fun_wrapper (MemFunPtr mem_fun_ptr, - C &c, - const ArgReferences &args) - : c (c), - mem_fun_ptr (mem_fun_ptr), - args (args) {}; - private: - mem_fun_wrapper (); - mem_fun_wrapper (const mem_fun_wrapper &); - - C &c; - MemFunPtr mem_fun_ptr; - ArgReferences args; - - static void * entry_point (void *arg) - { - const wrapper_base<RT> *w - = reinterpret_cast<const wrapper_base<RT>*> (arg); - const mem_fun_wrapper *wrapper - = static_cast<const mem_fun_wrapper*> (w); - MemFunPtr mem_fun_ptr = wrapper->mem_fun_ptr; - C &c = wrapper->c; - ArgList args = wrapper->args; - - boost::shared_ptr<thread_description<RT> > - thread_descriptor = wrapper->thread_descriptor; - - { - boost::mutex::scoped_lock lock (wrapper->mutex); - wrapper->condition.notify_one (); - } - - call (mem_fun_ptr, c, args, thread_descriptor->ret_val); - - return 0; - }; - }; -
  -
  - -
  -Note in particular, how this class passes itself as second template parameter -to the base class, enabling the latter to call the -mem_fun_wrapper::entry_point function as entry point to the new -thread. When the fire_up function in the base -class is called, it creates a new thread that starts inside this -function, and the argument given to it is the address of the -wrapper_base object. The first thing the entry_point function does, is -to cast back this address to the real object's type (it knows the real -type of the object, since the address of this function has been handed -down through the template magic), then copies the address of -the object to work with and the address of the member function to be -called from the stack of the old thread to the stack of this new -thread. It then also copies the arguments, which so far have been held -only as references, but copies them by value. Next, it gets the -address of the return thread descriptor, and with it the address of -the return value (the shared_ptr will also make sure that the object -lives long enough). The part in braces signals the condition to the -old thread, which hangs in the fire_up function: the arguments have -been copied, and the old thread can go on, eventually also destroying -objects that have been copied by value. Finally, it calls the -requested function with the proper arguments through a generic -interface (described in the section on tools) and sets the return -value of the thread. -
  - - -
  5. Tool classes
  - - -
  -In the implementation above, some tool classes have been used. These -are briefly described here. -
  - -
  a) The return_value<T> class template
  - -
  -This class stores a value of type T if T is not a -reference or void. It offers get() and -set() functions that get and set the value. If T is a -reference type, then set() is obviously not possible since -references cannot be rebound after construction time. The class therefore -stores a pointer, and set() sets the pointer to the object the -reference references. get() then returns the reference again. If -T is void, then the class is empty and there is only -a get() function that returns void. -
  - -- template <typename RT> struct return_value - { - private: - RT value; - public: - RT get () const { return value; } - void set (RT v) { value = v; } - }; - - template <typename RT> struct return_value<RT &> - { - private: - RT * value; - public: - RT & get () const { return *value; } - void set (RT & v) { value = &v; } - }; - - template <> struct return_value<void> { - static void get () {}; - }; - - - -b) The call function templates - - -The call function templates take a function pointer, an argument list -tuple, and the address of the return value object, and call the -function with these arguments. Since we have to unpack the argument -list, we have to dispatch to different functions, depending on the -number of arguments, in the usual way: - - -- template <int> struct int2type; - - template <typename RT, typename PFun, typename ArgList> - static void call (PFun fun_ptr, - ArgList &arg_list, - return_value<RT> &ret_val) - { - Caller<RT>::do_call (fun_ptr, arg_list, ret_val, - int2type<boost::tuples::length<ArgList>::value>()); - }; - - - -The Caller class has the following member functions: - - - template <typename RT> struct Caller - { - template <typename PFun, typename ArgList> - static void do_call (PFun fun_ptr, - ArgList &arg_list, - return_value<RT> &ret_val, - const int2type<1> &) - { ret_val.set ((*fun_ptr) (arg_list.template get<0>())); }; - - // likewise for int2type<0>, int2type<2>, ... - }; - - - - - -There is a specialization Caller<void> that does not set a return -value, and for each call and do_call function there is a second -function for member function pointers that takes an object as -additional argument. - - - -c) mem_fun_ptr - - -In order to form a pointer to member function for both cases of const -and non-const member functions, we need a simple tool: - - template <typename RT, class C, typename ArgList, - int length = boost::tuples::length<ArgList>::value> - struct mem_fun_ptr_helper; - - template <typename RT, class C, typename ArgList> - struct mem_fun_ptr_helper<RT, C, ArgList, 1> - { - typedef RT (C::*type) (typename boost::tuples::element<0,ArgList>::type); - }; - - template <typename RT, class C, typename ArgList> - struct mem_fun_ptr_helper<RT, const C, ArgList, 1> - { - typedef RT (C::*type) (typename boost::tuples::element<0,ArgList>::type) const; - }; - - template <typename RT, class C, typename ArgList> - struct mem_fun_ptr - { - typedef typename mem_fun_ptr_helper<RT,C,ArgList>::type type; - }; - - - - -Note that if the second template argument is a const C, then we mark -the member function const. The two templates for mem_fun_ptr_helper -have to be repeated for every number of arguments that we have in -mind. Note also that the specification of the default argument in the -declaration of the general template of mem_fun_ptr_helper saves us -from recomputing it in mem_fun_ptr. - - - - -d) add_reference for tuples - - -The following classes add references to the elements of a tuple, thus -providing the type equivalent of the return value of the boost::tie -functions. There are probably ways inside boost's tuples library to do -this, but I couldn't locate this. - - template <int N, typename Tuple> - struct add_reference_to_Nth - { - typedef typename boost::tuples::element<N,Tuple>::type ArgType; - typedef typename boost::add_reference<ArgType>::type type; - }; - - template <typename Tuple, int = boost::tuples::length<Tuple>::value> - struct tie_args_helper; - - template <typename Tuple> - struct tie_args_helper<Tuple,1> - { - typedef - boost::tuple<typename add_reference_to_Nth<0,Tuple>::type> - type; - }; - - template <typename Tuple> - struct tie_args - { - typedef typename tie_args_helper<Tuple>::type type; - }; - - - -The tie_args_helper class is repeated for every number of elements we -want to use. - - - - -6. Open Problems - - -a) A variable lifetime problem - -The only unsolved semantic problem I am aware of at present is the -following: if we have a function - - void f(const int &i); - -then this function can be called as -- f(1); - -i.e. the compiler creates a temporary and passes its address to -f(). When invoking f() on a new thread, however, as in -- spawn (f)(1); - -then it is only guaranteed that the call to spawn() does not return -before the new thread is started and has copied the arguments to -f(). However, the argument is only the reference to the temporary, not -its value. f() will thus likely observe corrupted values for its -argument. On the other hand, copying the value is no option either, of -course. Since to the author's best knowledge the language does not -provide means to avoid taking the address of a temporary, there is -presently no way to avoid this problem. Suggestions for healing it are -very welcome. - - - -b) Forwarding of operator() - -Above, we have not defined an overload of spawn for functor-like -objects, even though that would be desirable. One way to do so would be - - template <typename C> - mem_fun_encapsulator<void,C,boost::tuple<> > - spawn (C &c) { - return spawn (c, &C::operator()); - } - -This only works if operator() satisfies the signature -- struct C { void operator() (); }; - - - -We could add another overload if operator() is -const. However, what one -would like is an overload for more general signatures. Unfortunately, -this requires that we can infer type and number of arguments and -return type of operator() at the time we declare the return type of -above overload of spawn(). I have not found a way to infer this -information just by using the template parameter C -- it just seems -not possible. What would work if it were supported by compilers is a -kind of typeof-operator: - - template <typename C> - typeof(spawn(c,&C::operator())) // ** - spawn (C &c) { - return spawn (c, &C::operator()); - } - - - -When seeing the declaration, the compiler would automatically check -which version of the overloaded spawn() function it would call, and -correspondingly take the return type. gcc does support the typeof -keyword, but even present CVS snapshots generate an internal compiler -error on this construct. - - -c) Using a memory based scheme rather than condition variables - -The scheme using mutices and condition variables to synchronise -calling and called thread seems expensive. A simpler approach would be -to replace it by letting the creating thread generate an object on the -heap that holds copies of the arguments (instead of references as -presently), spawn the new thread and just go on without any -synchronisation. - - - -The calling thread would then not have to copy the arguments onto its -local stack and signal to the calling thread. It would only have to -delete the memory after the call to the user-supplied function -returns. Apart from replacing ArgReferences by -ArgList in some places, -the scheme would basically just replace *_encapsulator::operator(), -fire_up, and thread_entry_point: - - -- thread<RT> - operator() (typename boost::tuples::element<0,ArgList>::type arg1) { - return (new mem_fun_wrapper<RT,C,ArgList> (mem_fun_ptr, c, - boost::tie(arg1)))->fire_up (); - }; - - thread<RT> fire_up () { - thread_descriptor - = DescriptionPointer(new typename detail::thread_description<RT>()); - - thread_descriptor->create (entry_point, (void *)this); - // no synchronisation here - return thread_descriptor; - } - - static void * entry_point (void *arg) { - wrapper_base<RT> *w = reinterpret_cast<wrapper_base<RT>*> (arg); - fun_wrapper *wrapper = static_cast<fun_wrapper*> (w); - // no copying here; no synchronisation necessary - detail::call (wrapper->fun_ptr, wrapper->args, - wrapper->thread_descriptor->ret_val); - // delete memory - delete wrapper; - return 0; - } - - - -The perceived simplicity without using mutices and condition variable -might be deceptive, however, since memory allocation and deallocation -requires locking and unlocking mutices as well, and is generally not a -cheap operation. - - - -However, the main problem is that I get spurious segmentation faults -with this on my Linux box. These always happen inside the memory -allocation and deallocation functions in the C++ and C language -support libraries. I believe that these are not bugs in the -application, but in the language runtime. However, my motivation to -debug multithreading problems in the libc is very limited; for -reference, valgrind 1.94 does not show accesses to uninitialized or -already freed memory portions, even for runs that eventually crash -later on. - - - -7. Alternative Suggestions - - - -Here are some additional suggestions for discussion: - - -a) Conversions between return values - - -If f() is a function returning an integer, then the following is -legal: - - double d = f(arg1, arg2); - -The question, then, would be: do we want to allow conversions between -Thread<double> and Thread<int> objects? -And do we want to allow a -conversion from Thread<T> to Thread<void> -(i.e.: casting away the return value)? - - - -Since one can still assign the return value of the thread to a double, - - double d = thread.return_value(); - -the only real merit in allowing conversions is in putting threads with -different return value types into a ThreadGroup: -- double f1 (); - int f2 (); - - ThreadTroup<double> tg; - tg += spawn(f1)(); - tg += spawn(f2)(); // convert Thread<int> to Thread<double> - tg.join_all (); - - - -Being able to do this is probably only syntactic sugar, except for the -case where we are not interested in the return values of all threads, -i.e. the conversion Thread<T> -> Thread<void> seems -like the only one that is really worth it. - - - -I have made some initial experiments with implementing general -conversions. The main problem is that we need to allow conversion -chains: - - thread<double> t1 = spawn (f)(arg1, arg2); - thread<int> t2 = t1; - thread<double> t3 = t2; - - - -If f() returns 1.5, then t3.return_value() needs to -return 1.0. I believe that such conversions could be implemented, by adding the -types in the chain into a boost::tuple of growing length, and writing -a function that converts a value of the first type of this tuple to -the second, to the third, ..., to the last type in the tuple. However, -a plethora of internal compiler errors has scared me off doing more -experiments in this direction. - - - -b) Conversions between class types I - - -When you have a class hierarchy like - - struct B { void f(); }; - struct D : public B {}; - -then calling -- spawn (D(), &B::f); - -fails for gcc (but succeeds with Intel's icc). Presumably, gcc is -right: template arguments must match exactly, and D() is of type -D, while &B::f leads to a class type of -B. There is no function template for spawn for which this call can -match without a derived-to-base conversion. We could now change the template -- template <typename RT, typename C, typename Arg1> - mem_fun_encapsulator<RT,C,boost::tuple<Arg1> > - spawn (C &c, RT (C::*fun_ptr)(Arg1)) { - return mem_fun_encapsulator<RT, C, boost::tuple<Arg1> > (c,fun_ptr); - } - -into -- template <typename RT, typename A, typename C, typename Arg1> - mem_fun_encapsulator<RT,C,boost::tuple<Arg1> > - spawn (A &a, RT (C::*fun_ptr)(Arg1)) { - return mem_fun_encapsulator<RT, C, boost::tuple<Arg1> > (a,fun_ptr); - } - -i.e. introduce another class template A for the type of the -object. Since the arguments of the constructor to the -mem_fun_encapsulator object are known, the compiler would perform a -derived-to-base conversion for object a if necessary. I don't know -whether this is desirable, in particular since also other conversions -could happen here that one would not want (in the extreme case -generating a temporary).. - - - -c) Conversions between class types II - - -When one writes - - spawn (this, &X::f) - -one gets an error that "'this' is not convertible to type X&". One has -to write *this instead. It would be simple to have another set of -overloads of spawn() that accepts a pointer instead of a reference, -and simply forwards to the existing function. This is just for the -lazy people, probably, but it is a common case. - - - -d) Catching exceptions - - -When a function on a new thread throws an exception, it only -propagates up to one of the two entry_point() functions, then vanishes -into the run-time system and kills the program. Ideally, we would have -a way to pass it over to the main thread. This, however, would need -some support from the language. Basically, we would need two -operations: - -clone an exception without knowing its type; we could then in the - entry_point function catch it and stack it somewhere, just like we - do for the return value -back on the main thread, the Thread::join() function must raise this - stored exception if there was one, again without knowing its type. - -Given how exceptions are implemented usually, the machinery for these -operations is probably there, but is not exported to the user through -the run-time environment. Thus, an implementation of such ideas has to -wait for changes in the language specification. - - - - - - -Wolfgang Bangerth, 2003 - - - - - - - - - diff --git a/deal.II/examples/README.example b/deal.II/examples/README.example new file mode 100644 index 0000000000..1f4f838258 --- /dev/null +++ b/deal.II/examples/README.example @@ -0,0 +1,4 @@ +This folder contains example programs for deal.II + +They are distributed under the same license as the deal.II library itself, +namely LGPL-2.1+. diff --git a/deal.II/examples/step-25/doc/animate.sh b/deal.II/examples/step-25/doc/animate.sh index 31807c2625..c3a7cf9fb0 100755 --- a/deal.II/examples/step-25/doc/animate.sh +++ b/deal.II/examples/step-25/doc/animate.sh @@ -1,4 +1,24 @@ #!/bin/sh +## --------------------------------------------------------------------- +## $Id$ +## +## Copyright (C) 2006 - 2013 by the deal.II authors +## +## This file is part of the deal.II library. +## +## The deal.II library is free software; you can use it, redistribute +## it, and/or modify it under the terms of the GNU Lesser General +## Public License as published by the Free Software Foundation; either +## version 2.1 of the License, or (at your option) any later version. +## The full text of the license can be found in the file LICENSE at +## the top level of the deal.II distribution. +## +## --------------------------------------------------------------------- + +# +# Author: Ivan Christov, Wolfgang Bangerth, Texas A&M University, 2006 +# + dim=1 tstep=0 tstepinc=20 @@ -35,4 +55,4 @@ done gnuplot -persist $batchfile # use ImageMagick to create an animated gif from the PNG files -convert -delay 0 -loop 0 "solution-"$dim"d-*.png" "solution-"$dim"d.gif" \ No newline at end of file +convert -delay 0 -loop 0 "solution-"$dim"d-*.png" "solution-"$dim"d.gif" diff --git a/deal.II/examples/step-42/step-42.cc b/deal.II/examples/step-42/step-42.cc index 29a165bd59..f4b600317f 100644 --- a/deal.II/examples/step-42/step-42.cc +++ b/deal.II/examples/step-42/step-42.cc @@ -1820,8 +1820,8 @@ namespace Step42 break; } - old_solution = solution; solution = tmp_vector; + old_solution = solution; } old_active_set = active_set; diff --git a/deal.II/include/deal.II/base/graph_coloring.h b/deal.II/include/deal.II/base/graph_coloring.h index 64f39e54ae..5de886009b 100644 --- a/deal.II/include/deal.II/base/graph_coloring.h +++ b/deal.II/include/deal.II/base/graph_coloring.h @@ -20,6 +20,7 @@ #include +#include #include #include #include @@ -31,344 +32,482 @@ DEAL_II_NAMESPACE_OPEN -/// This namespace contains the functions necessary to color a graph. -namespace graph_coloring { - - /** - * Create the partitioning using a simplified version of the Cuthill-McKee - * algorithm (Breadth First Search algorithm). - */ - template - std::vector > create_partitioning(Iterator const &begin, - typename identity::type const &end, - std_cxx1x::function (Iterator const &)> - const &get_conflict_indices) +/** + * A namespace containing functions that can color graphs. + */ +namespace GraphColoring +{ + namespace internal { - std::vector > partitioning(1,std::vector (1,begin)); - // Number of iterators. - unsigned int n_iterators(0); - // Create a map from conflict indices to iterators - boost::unordered_map > indices_to_iterators; - for (Iterator it=begin; it!=end; ++it) + /** + * Create a partitioning of the given range of iterators using a simplified + * version of the Cuthill-McKee algorithm (Breadth First Search algorithm). + * The function creates partitions that contain "zones" of iterators + * where the first partition contains the first iterator, the second + * zone contains all those iterators that have conflicts with the single + * element in the first zone, the third zone contains those iterators that + * have conflicts with the iterators of the second zone and have not previously + * been assigned to a zone, etc. If the iterators represent cells, then this + * generates partitions that are like onion shells around the very first + * cell. Note that elements in each zone may conflict with other elements in + * the same zone. + * + * The question whether two iterators conflict is determined by a user-provided + * function. The meaning of this function is discussed in the documentation of + * the GraphColoring::make_graph_coloring() function. + * + * @param[in] begin The first element of a range of iterators for which a + * partitioning is sought. + * @param[in] end The element past the end of the range of iterators. + * @param[in] get_conflict_indices A user defined function object returning + * a set of indicators that are descriptive of what represents a + * conflict. See above for a more thorough discussion. + * @return A set of sets of iterators (where sets are represented by + * std::vector for efficiency). Each element of the outermost set + * corresponds to the iterators pointing to objects that are in the + * same partition (i.e., the same zone). + * + * @author Martin Kronbichler, Bruno Turcksin + */ + template + std::vector > + create_partitioning(const Iterator &begin, + const typename identity::type &end, + const std_cxx1x::function (const Iterator &)> &get_conflict_indices) { - std::vector conflict_indices = get_conflict_indices(it); - const unsigned int n_conflict_indices(conflict_indices.size()); - for (unsigned int i=0; i used_it; - used_it.insert(begin); - while (used_it.size()!=n_iterators) - { - typename std::vector::iterator vector_it(partitioning.back().begin()); - typename std::vector::iterator vector_end(partitioning.back().end()); - std::vector new_zone; - for (; vector_it!=vector_end; ++vector_it) - { - std::vector conflict_indices = get_conflict_indices(*vector_it); - const unsigned int n_conflict_indices(conflict_indices.size()); - for (unsigned int i=0; i > indices_to_iterators; + for (Iterator it=begin; it!=end; ++it) { - std::vector iterator_vector(indices_to_iterators[conflict_indices[i]]); - for (unsigned int j=0; j conflict_indices = get_conflict_indices(it); + const unsigned int n_conflict_indices = conflict_indices.size(); + for (unsigned int i=0; i > zones(1,std::vector (1,begin)); + std::set used_it; + used_it.insert(begin); + while (used_it.size()!=n_iterators) + { + // loop over the elements of the previous zone. for each element of + // the previous zone, get the conflict indices and from there get + // those iterators that are conflicting with the current element + typename std::vector::iterator previous_zone_it(zones.back().begin()); + typename std::vector::iterator previous_zone_end(zones.back().end()); + std::vector new_zone; + for (; previous_zone_it!=previous_zone_end; ++previous_zone_it) { - new_zone.push_back(iterator_vector[j]); - used_it.insert(iterator_vector[j]); + std::vector conflict_indices = get_conflict_indices(*previous_zone_it); + const unsigned int n_conflict_indices(conflict_indices.size()); + for (unsigned int i=0; i &conflicting_elements + = indices_to_iterators[conflict_indices[i]]; + for (unsigned int j=0; j (1,it)); + used_it.insert(it); + break; + } } - } - // If there are iterators in the new zone, then the zone is added to the - // partition. Otherwise, the graph is disconnected and we need to find - // an iterator on the other part of the graph. - if (new_zone.size()!=0) - partitioning.push_back(new_zone); - else - for (Iterator it=begin; it!=end; ++it) - if (used_it.count(it)==0) - { - partitioning.push_back(std::vector (1,it)); - break; - } - } - return partitioning; - } + return zones; + } - /** - * This function uses DSATUR (Degree SATURation) to color one zone of the - * partition. DSATUR works as follows: - * -# Arrange the vertices by decreasing order of degrees. - * -# Color a vertex of maximal degree with color 1. - * -# Choose a vertex with a maximal saturation degree. If there is equality, - * choose any vertex of maximal degree in the uncolored subgraph. - * -# Color the chosen vertex with the least possible (lowest numbered) color. - * -# If all the vertices are colored, stop. Otherwise, return to 3. - */ - template - std::vector > make_dsatur_coloring(std::vector &partition, - std_cxx1x::function (Iterator const &)> - const &get_conflict_indices) - { - std::vector > partition_coloring; - // Number of zones composing the partitioning. - const unsigned int partition_size(partition.size()); - std::vector sorted_vertices(partition_size); - std::vector degrees(partition_size); - std::vector > conflict_indices(partition_size); - std::vector > graph(partition_size); - - // Get the conflict indices associated to each iterator. The conflict_indices have to be sorted so - // set_intersection can be used later. - for (unsigned int i=0; i + void + make_dsatur_coloring(std::vector &partition, + const std_cxx1x::function (const Iterator &)> &get_conflict_indices, + std::vector > &partition_coloring) { - conflict_indices[i] = get_conflict_indices(partition[i]); - std::sort(conflict_indices[i].begin(),conflict_indices[i].end()); - } - - // Compute the degree of each vertex of the graph using the - // intersection of the conflict indices. - std::vector conflict_indices_intersection; - std::vector::iterator intersection_it; - for (unsigned int i=0; i sorted_vertices(partition_size); + std::vector degrees(partition_size); + std::vector > conflict_indices(partition_size); + std::vector > graph(partition_size); + + // Get the conflict indices associated to each iterator. The conflict_indices have to be sorted so + // set_intersection can be used later. + for (unsigned int i=0; i::iterator degrees_it; - for (unsigned int i=0; i > colors_used; - for (unsigned int i=0; i conflict_indices_intersection; + std::vector::iterator intersection_it; + for (unsigned int i=0; i::iterator degrees_it; + for (unsigned int i=0; i (1, - partition[current_vertex])); - boost::unordered_set tmp; - tmp.insert(current_vertex); - colors_used.push_back(tmp); - } - } - return partition_coloring; - } + // Color the graph. + std::vector > colors_used; + for (unsigned int i=0; i (1, + partition[current_vertex])); + boost::unordered_set tmp; + tmp.insert(current_vertex); + colors_used.push_back(tmp); + } + } + } - /** - * Given a partition-coloring graph, gather the colors together. All the - * colors on even (resp. odd) partition can be executed simultaneously. This - * function tries to create colors of similar number of elements. - */ - template - std::vector > - gather_colors(std::vector > > const &partition_coloring) - { - std::vector > coloring; - - // Count the number of iterators in each color. - const unsigned int partition_size(partition_coloring.size()); - std::vector > colors_counter(partition_size); - for (unsigned int i=0; i + std::vector > + gather_colors(const std::vector > > &partition_coloring) { - const unsigned int n_colors(partition_coloring[i].size()); - colors_counter[i].resize(n_colors); - for (unsigned int j=0; j > coloring; - // Find the partition with the largest number of colors for the even partition. - unsigned int i_color(0); - unsigned int max_even_n_colors(0); - const unsigned int colors_size(colors_counter.size()); - for (unsigned int i=0; i > colors_counter(partition_size); + for (unsigned int i=0; i used_k; - for (unsigned int j=0; j::iterator it; - it = std::max_element(colors_counter[i].begin(),colors_counter[i].end()); - unsigned int min_iterators(-1); - unsigned int pos(0); - // Find the color of coloring with the least number of colors among - // the colors that have not been used yet. - for (unsigned int k=0; k used_k; + for (unsigned int j=0; j::iterator it; + it = std::max_element(colors_counter[i].begin(),colors_counter[i].end()); + unsigned int min_iterators(-1); + unsigned int pos(0); + // Find the color of coloring with the least number of colors among + // the colors that have not been used yet. + for (unsigned int k=0; k used_k; - for (unsigned int j=0; j1) { - // Find the color in the current partition with the largest number of - // iterators. - std::vector::iterator it; - it = std::max_element(colors_counter[i].begin(),colors_counter[i].end()); - unsigned int min_iterators(-1); - unsigned int pos(0); - // Find the color of coloring with the least number of colors among - // the colors that have not been used yet. - for (unsigned int k=0; k used_k; + for (unsigned int j=0; j::iterator it; + it = std::max_element(colors_counter[i].begin(),colors_counter[i].end()); + unsigned int min_iterators(-1); + unsigned int pos(0); + // Find the color of coloring with the least number of colors among + // the colors that have not been used yet. + for (unsigned int k=0; kall degrees of + * freedom for which anything is written into the matrix or right hand side. + * In other words, if the writing happens through a function like + * ConstraintMatrix::copy_local_to_global(), then the set of conflict indices + * must actually contain not only the degrees of freedom on the current + * cell, but also those they are linked to by constraints such as hanging + * nodes. + * + * In other situations, the conflict indicator sets may represent + * something different altogether -- it is up to the caller of this function + * to describe what it means for two iterators to conflict. Given this, + * computing conflict graph edges can be done significantly more cheaply + * than with ${\cal O}(N^2)$ operations. + * + * In any case, the result of the function will be so that iterators whose + * conflict indicator sets have overlap will not be assigned to the same + * color. + * + * @param[in] begin The first element of a range of iterators for which a + * coloring is sought. + * @param[in] end The element past the end of the range of iterators. + * @param[in] get_conflict_indices A user defined function object returning + * a set of indicators that are descriptive of what represents a + * conflict. See above for a more thorough discussion. + * @return A set of sets of iterators (where sets are represented by + * std::vector for efficiency). Each element of the outermost set + * corresponds to the iterators pointing to objects that are in the + * same partition (have the same color) and consequently do not + * conflict. The elements of different sets may conflict. + * + * @author Martin Kronbichler, Bruno Turcksin */ template - std::vector > - make_graph_coloring(Iterator const &begin,typename identity::type const &end, - std_cxx1x::function (Iterator const &)> - const &get_conflict_indices) + std::vector > + make_graph_coloring(const Iterator &begin, + const typename identity::type &end, + const std_cxx1x::function (const typename identity::type &)> &get_conflict_indices) { + Assert (begin != end, ExcMessage ("GraphColoring is not prepared to deal with empty ranges!")); + // Create the partitioning. - std::vector > partitioning = create_partitioning(begin,end, - get_conflict_indices); + std::vector > + partitioning = internal::create_partitioning (begin, + end, + get_conflict_indices); // Color the iterators within each partition. + // Run the coloring algorithm on each zone in parallel const unsigned int partitioning_size(partitioning.size()); - std::vector > > partition_coloring( - partitioning_size); - for (unsigned int i=0; i > > + partition_coloring(partitioning_size); - // Gather the colors together. - std::vector > coloring = gather_colors(partition_coloring); - - return coloring; + Threads::TaskGroup<> tasks; + for (unsigned int i=0; i, + partitioning[i], + get_conflict_indices, + partition_coloring[i]); + tasks.join_all(); + + // Gather the colors together. + return internal::gather_colors(partition_coloring); } } // End graph_coloring namespace diff --git a/deal.II/include/deal.II/base/parameter_handler.h b/deal.II/include/deal.II/base/parameter_handler.h index 0e6acd4ed0..2e1ce3b072 100644 --- a/deal.II/include/deal.II/base/parameter_handler.h +++ b/deal.II/include/deal.II/base/parameter_handler.h @@ -34,7 +34,6 @@ DEAL_II_NAMESPACE_OPEN //TODO: Allow long input lines to be broken by appending a backslash character -//TODO: Provide an "include" command for parameter files // public classes; to be declared below diff --git a/deal.II/include/deal.II/base/thread_management.h b/deal.II/include/deal.II/base/thread_management.h index a0d4418cfe..ab3cde9387 100644 --- a/deal.II/include/deal.II/base/thread_management.h +++ b/deal.II/include/deal.II/base/thread_management.h @@ -1279,50 +1279,14 @@ namespace Threads * While we have only one of these * objects per thread, several * Threads::Thread objects may refer to - * this descriptor. - * - * Note, however, that since this - * object holds the location - * where we store the return - * value of the thread, the - * object has to live at least as - * long as the thread - * executes. This means that even - * if all Threads::Thread objects - * that referred to this - * descriptor (through a - * std::shared_ptr) have gone out - * of scope, we must still hold - * on to the object. We do this - * by having the descriptor keep - * a pointer to itself and reset - * it to zero once it is done -- - * effectively keeping the use - * pointer above zero as long as - * work is going on. - * - * To enable the current class to - * obtain a shared_ptr from - * itself, we derive from the - * class - * std::enable_shared_from_this. + * this descriptor. If all Thread + * objects go out of scope the + * ThreadDescriptor will detach from + * the thread before being destructed. */ template - struct ThreadDescriptor : public std_cxx1x::enable_shared_from_this > + struct ThreadDescriptor { - /** - * A pointer to the current - * object, kept nonzero as - * long as the thread is - * executing to avoid - * destroying the current - * object while we are still - * expecting to write - * something into the return - * value location. - */ - std_cxx1x::shared_ptr > self; - /** * An object that represents the * thread started. @@ -1333,8 +1297,14 @@ namespace Threads * An object that will hold the value * returned by the function called on * the thread. + * + * The return value is stored + * in a shared_ptr because we might + * abandon the the ThreadDescriptor. + * This makes sure the object stays + * alive until the thread exits. */ - return_value ret_val; + std_cxx1x::shared_ptr > ret_val; /** * A bool variable that is initially @@ -1405,41 +1375,24 @@ namespace Threads thread_is_active (false) {} + ~ThreadDescriptor () + { + if (!thread_is_active) + return; + thread.detach(); + thread_is_active = false; + } /** * Start the thread and let * it put its return value * into the ret_val object. - * - * Note that we cannot - * already do this in the - * constructor of this class: - * we will call - * enable_shared_from_this::shared_from_this - * which requires that there - * is already a shared_ptr - * that owns this object; - * however, at the time of - * creation, there can of - * course be no shared_ptr - * that owns the object -- it - * is, after all, just being - * created and can not - * already have been handed - * off to a shared_ptr; as a - * consequence, we first - * create the object, give it - * to a shared_ptr, and then - * call shared_from_this. */ void start (const std_cxx1x::function &function) { - // set the self pointer - // and then start the - // thread - self = this->shared_from_this (); thread_is_active = true; - thread = std_cxx1x::thread (thread_entry_point, function, this); + ret_val.reset(new return_value()); + thread = std_cxx1x::thread (thread_entry_point, function, ret_val); } @@ -1472,7 +1425,7 @@ namespace Threads */ static void thread_entry_point (const std_cxx1x::function function, - ThreadDescriptor *descriptor) + std_cxx1x::shared_ptr > ret_val) { // call the function // in question. since an @@ -1489,7 +1442,7 @@ namespace Threads internal::register_thread (); try { - call (function, descriptor->ret_val); + call (function, *ret_val); } catch (const std::exception &exc) { @@ -1500,24 +1453,6 @@ namespace Threads internal::handle_unknown_exception (); } internal::deregister_thread (); - - // once we are done, - // we can release our - // hold on the thread - // descriptor - // object. if all - // Threads::Thread - // objects that - // pointed here - // should have gone - // out of scope - // already, then this - // will trigger - // destruction of the - // descriptor object - Assert (descriptor->self.use_count () > 0, - ExcInternalError()); - descriptor->self.reset (); } }; @@ -1542,7 +1477,7 @@ namespace Threads * returned by the function called on * the thread. */ - return_value ret_val; + std_cxx1x::shared_ptr > ret_val; /** * Start the thread and @@ -1551,7 +1486,8 @@ namespace Threads */ void start (const std_cxx1x::function &function) { - call (function, ret_val); + ret_val.reset(new return_value()); + call (function, *ret_val); } /** @@ -1615,15 +1551,7 @@ namespace Threads thread_descriptor (new internal::ThreadDescriptor()) { // in a second step, start - // the thread. this needs - // to be done in two steps - // because inside the start - // function we call - // enable_shared_from_this::shared_from_this - // which requires that - // there is already a - // shared_ptr that owns the - // object + // the thread. thread_descriptor->start (function); } @@ -1671,7 +1599,7 @@ namespace Threads RT return_value () { join (); - return thread_descriptor->ret_val.get(); + return thread_descriptor->ret_val->get(); } /** @@ -1712,29 +1640,6 @@ namespace Threads * sure that that object lives * as long as there is at least * one subscriber to it. - * - * Note that since the - * descriptor holds the - * location where the return - * value is stored, even if all - * Threads::Thread objects that - * point to the descriptor go - * out of scope, we must make - * sure that the descriptor is - * not yet destroyed. Rather, - * the descriptor must be - * destroyed when the last - * Threads::Thread object that - * points to it goes out of - * scope or whenever the thread - * is finished, whatever - * happens later. We do this by - * having the descriptor keep a - * pointer to itself and reset - * it to zero once it is done - * -- effectively keeping the use - * pointer above zero as long - * as work is going on. */ std_cxx1x::shared_ptr > thread_descriptor; }; diff --git a/deal.II/include/deal.II/base/work_stream.h b/deal.II/include/deal.II/base/work_stream.h index a029e9b0c5..330afcf1ce 100644 --- a/deal.II/include/deal.II/base/work_stream.h +++ b/deal.II/include/deal.II/base/work_stream.h @@ -146,87 +146,240 @@ namespace WorkStream // and that is available also as a fall-back whenever via boost or similar /** - * A class that creates a sequence of items from a range of iterators. + * A namespace for the implementation of details of the WorkStream pattern + * and function. This namespace holds classes that deal with the second + * implementation described in the paper by Turcksin, Kronbichler and + * Bangerth. + * + * Even though this implementation is slower than the third implementation + * discussed in that paper, we need to keep it around for two reasons: + * (i) a user may not give us a graph coloring, (ii) we want to use + * this implementation for colors that are just too small. */ - template - class IteratorRangeToItemStream : public tbb::filter + namespace Implementation2 { - public: /** - * A data type that we use to identify items to be worked on. This is - * the structure that is passed around between the different parts of - * the WorkStream implementation to identify what needs to be done by - * the various stages of the pipeline. + * A class that creates a sequence of items from a range of iterators. */ - struct ItemType + template + class IteratorRangeToItemStream : public tbb::filter { + public: /** - * A structure that contains a pointer to a scratch data object along - * with a flag that indicates whether this object is currently in use. + * A data type that we use to identify items to be worked on. This is + * the structure that is passed around between the different parts of + * the WorkStream implementation to identify what needs to be done by + * the various stages of the pipeline. */ - struct ScratchDataObject + struct ItemType { - std_cxx1x::shared_ptr scratch_data; - bool currently_in_use; - /** - * Default constructor. + * A structure that contains a pointer to a scratch data object along + * with a flag that indicates whether this object is currently in use. */ - ScratchDataObject () - : - currently_in_use (false) - {} - - ScratchDataObject (ScratchData *p, - const bool in_use) - : - scratch_data (p), - currently_in_use (in_use) - {} - -//TODO: when we push back an object to the list of scratch objects, in -// Worker::operator(), we first create an object and then copy -// it to the end of this list. this involves having two objects + struct ScratchDataObject + { + std_cxx1x::shared_ptr scratch_data; + bool currently_in_use; + + /** + * Default constructor. + */ + ScratchDataObject () + : + currently_in_use (false) + {} + + ScratchDataObject (ScratchData *p, + const bool in_use) + : + scratch_data (p), + currently_in_use (in_use) + {} + +//TODO: when we push back an object to the list of scratch objects, in +// Worker::operator(), we first create an object and then copy +// it to the end of this list. this involves having two objects // of the current type having pointers to it, each with their own // currently_in_use flag. there is probably little harm in this because // the original one goes out of scope right away again, but it's // certainly awkward. one way to avoid this would be to use unique_ptr // but we'd need to figure out a way to use it in non-C++11 mode - ScratchDataObject (const ScratchDataObject &o) + ScratchDataObject (const ScratchDataObject &o) + : + scratch_data (o.scratch_data), + currently_in_use (o.currently_in_use) + {} + }; + + + /** + * Typedef to a list of scratch data objects. The rationale for this + * list is provided in the variables that use these lists. + */ + typedef std::list ScratchDataList; + + /** + * A list of iterators that need to be worked on. Only the first + * n_items are relevant. + */ + std::vector work_items; + + /** + * The CopyData objects that the Worker part of the pipeline + * fills for each work item. Again, only the first n_items + * elements are what we care about. + */ + std::vector copy_datas; + + /** + * Number of items identified by the work_items array that the + * Worker and Copier pipeline stage need to work on. The maximum + * value of this variable will be chunk_size. + */ + unsigned int n_items; + + /** + * Pointer to a thread local variable identifying the scratch data objects + * this thread will use. The initial implementation of this + * class using thread local variables provided only a single + * scratch object per thread. This doesn't work, because + * the worker functions may start tasks itself and then call + * Threads::TaskGroup::join_all() or a similar function, which the + * TBB scheduler may use to run something else on the current + * thread -- for example another instance of the worker function. + * Consequently, there would be two instances of the worker + * function that use the same scratch object if we only + * provided a single scratch object per thread. The solution is + * to provide a list of scratch objects for each thread, together + * with a flag indicating whether this scratch object is currently + * used. If a thread needs a scratch object, it walks this list + * until it finds an unused object, or, if there is none, creates one + * itself. Note that we need not use synchronization primitives + * for this process since the lists are thread-local and + * we are guaranteed that only a single thread accesses them as long + * as we have no yield point in between the accesses to the list. + * + * The pointers to scratch objects stored in each of these lists must + * be so that they are deleted on all threads when the thread + * local object is destroyed. This is achieved by using shared_ptr. + * + * Note that when a worker needs to create a scratch object, it allocates + * it using sample_scratch_data to copy from. This has + * the advantage of a first-touch initialization, i.e., the + * memory for the scratch data object is allocated and initialized + * by the same thread that will later use it. + */ + Threads::ThreadLocalStorage *scratch_data; + + /** + * Pointer to a sample scratch data object, to be used to initialize + * the scratch data objects created for each individual thread. + */ + const ScratchData *sample_scratch_data; + + + /** + * Default constructor. + * Initialize everything that doesn't have a default constructor + * itself. + */ + ItemType () : - scratch_data (o.scratch_data), - currently_in_use (o.currently_in_use) + n_items (0), + scratch_data (0), + sample_scratch_data (0) {} }; /** - * Typedef to a list of scratch data objects. The rationale for this - * list is provided in the variables that use these lists. + * Constructor. Take an iterator range, the size of a buffer that can + * hold items, and the sample additional data object that will be passed + * to each worker and copier function invokation. */ - typedef std::list ScratchDataList; + IteratorRangeToItemStream (const Iterator &begin, + const Iterator &end, + const unsigned int buffer_size, + const unsigned int chunk_size, + const ScratchData &sample_scratch_data, + const CopyData &sample_copy_data) + : + tbb::filter (/*is_serial=*/true), + remaining_iterator_range (begin, end), + ring_buffer (buffer_size), + sample_scratch_data (sample_scratch_data), + n_emitted_items (0), + chunk_size (chunk_size) + { + // initialize the elements of the ring buffer + for (unsigned int element=0; element work_items; + virtual void *operator () (void *) + { + // store the current + // position of the pointer + ItemType *current_item + = &ring_buffer[n_emitted_items % ring_buffer.size()]; + + // initialize the next item. it may + // consist of at most chunk_size + // elements + current_item->n_items = 0; + while ((remaining_iterator_range.first != + remaining_iterator_range.second) + && + (current_item->n_items < chunk_size)) + { + current_item->work_items[current_item->n_items] + = remaining_iterator_range.first; + + ++remaining_iterator_range.first; + ++current_item->n_items; + } + + if (current_item->n_items == 0) + // there were no items + // left. terminate the pipeline + return 0; + else + { + ++n_emitted_items; + return current_item; + } + } + private: /** - * The CopyData objects that the Worker part of the pipeline - * fills for each work item. Again, only the first n_items - * elements are what we care about. + * The interval of iterators still to + * be worked on. This range will shrink + * over time. */ - std::vector copy_datas; + std::pair remaining_iterator_range; /** - * Number of items identified by the work_items array that the - * Worker and Copier pipeline stage need to work on. The maximum - * value of this variable will be chunk_size. + * A ring buffer that will store items. */ - unsigned int n_items; + std::vector ring_buffer; /** * Pointer to a thread local variable identifying the scratch data objects @@ -259,492 +412,741 @@ namespace WorkStream * memory for the scratch data object is allocated and initialized * by the same thread that will later use it. */ - Threads::ThreadLocalStorage *scratch_data; + Threads::ThreadLocalStorage thread_local_scratch; /** - * Pointer to a sample scratch data object, to be used to initialize - * the scratch data objects created for each individual thread. + * A reference to a sample scratch data that will be used to + * initialize the thread-local pointers to a scratch data object + * each of the worker tasks uses. */ - const ScratchData *sample_scratch_data; + const ScratchData &sample_scratch_data; + /** + * Counter for the number of emitted + * items. Each item may consist of up + * to chunk_size iterator elements. + */ + unsigned int n_emitted_items; /** - * Default constructor. - * Initialize everything that doesn't have a default constructor - * itself. + * Number of elements of the + * iterator range that each + * thread should work on + * sequentially; a large number + * makes sure that each thread + * gets a significant amount of + * work before the next task + * switch happens, whereas a + * small number is better for + * load balancing. */ - ItemType () - : - n_items (0), - scratch_data (0), - sample_scratch_data (0) - {} + const unsigned int chunk_size; + + /** + * Initialize the pointers and vector + * elements in the specified entry of + * the ring buffer. + */ + void init_buffer_elements (const unsigned int element, + const CopyData &sample_copy_data) + { + Assert (ring_buffer[element].n_items == 0, + ExcInternalError()); + + ring_buffer[element].work_items + .resize (chunk_size, remaining_iterator_range.second); + ring_buffer[element].scratch_data + = &thread_local_scratch; + ring_buffer[element].sample_scratch_data + = &sample_scratch_data; + ring_buffer[element].copy_datas + .resize (chunk_size, sample_copy_data); + } }; + /** - * Constructor. Take an iterator range, the size of a buffer that can - * hold items, and the sample additional data object that will be passed - * to each worker and copier function invokation. + * A class that manages calling the + * worker function on a number of + * parallel threads. Note that it is, in + * the TBB notation, a filter that can + * run in parallel. */ - IteratorRangeToItemStream (const Iterator &begin, - const Iterator &end, - const unsigned int buffer_size, - const unsigned int chunk_size, - const ScratchData &sample_scratch_data, - const CopyData &sample_copy_data) - : - tbb::filter (/*is_serial=*/true), - remaining_iterator_range (new std::pair (begin, end)), - ring_buffer (buffer_size), - sample_scratch_data (sample_scratch_data), - color(false), - n_emitted_items (0), - chunk_size (chunk_size) + template + class Worker : public tbb::filter { - // initialize the elements of the ring buffer - for (unsigned int element=0; element &worker) + : + tbb::filter (/* is_serial= */ false), + worker (worker) + {} + + + /** + * Work on an item. + */ + void *operator () (void *item) { - Assert (ring_buffer[element].n_items == 0, - ExcInternalError()); - - ring_buffer[element].work_items.resize (chunk_size, - remaining_iterator_range->second); - ring_buffer[element].scratch_data = &thread_local_scratch; - ring_buffer[element].sample_scratch_data = &sample_scratch_data; - ring_buffer[element].copy_datas.resize (chunk_size, - sample_copy_data); + // first unpack the current item + typedef + typename IteratorRangeToItemStream::ItemType + ItemType; + + ItemType *current_item = static_cast (item); + + // we need to find an unused scratch data object in the list that + // corresponds to the current thread and then mark it as used. if + // we can't find one, create one + // + // as discussed in the discussion of the documentation of the + // IteratorRangeToItemStream::scratch_data variable, there is no + // need to synchronize access to this variable using a mutex + // as long as we have no yield-point in between. this means that + // we can't take an iterator into the list now and expect it to + // still be valid after calling the worker, but we at least do + // not have to lock the following section + ScratchData *scratch_data = 0; + { + typename ItemType::ScratchDataList & + scratch_data_list = current_item->scratch_data->get(); + + // see if there is an unused object. if so, grab it and mark + // it as used + for (typename ItemType::ScratchDataList::iterator + p = scratch_data_list.begin(); + p != scratch_data_list.end(); ++p) + if (p->currently_in_use == false) + { + scratch_data = p->scratch_data.get(); + p->currently_in_use = true; + break; + } + + // if no object was found, create one and mark it as used + if (scratch_data == 0) + { + scratch_data = new ScratchData(*current_item->sample_scratch_data); + + typename ItemType::ScratchDataList::value_type + new_scratch_object (scratch_data, true); + scratch_data_list.push_back (new_scratch_object); + } + } + + // then call the worker function on each element of the chunk we were + // given. since these worker functions are called on separate threads, + // nothing good can happen if they throw an exception and we are best + // off catching it and showing an error message + for (unsigned int i=0; in_items; ++i) + { + try + { + if (worker) + worker (current_item->work_items[i], + *scratch_data, + current_item->copy_datas[i]); + } + catch (const std::exception &exc) + { + Threads::internal::handle_std_exception (exc); + } + catch (...) + { + Threads::internal::handle_unknown_exception (); + } + } + + // finally mark the scratch object as unused again. as above, there + // is no need to lock anything here since the object we work on + // is thread-local + { + typename ItemType::ScratchDataList & + scratch_data_list = current_item->scratch_data->get(); + + for (typename ItemType::ScratchDataList::iterator p = + scratch_data_list.begin(); p != scratch_data_list.end(); + ++p) + if (p->scratch_data.get() == scratch_data) + { + Assert(p->currently_in_use == true, ExcInternalError()); + p->currently_in_use = false; + } + } + + + + // then return the original pointer + // to the now modified object + return item; } - } - IteratorRangeToItemStream (const typename std::vector::iterator &begin, - const typename std::vector::iterator &end, - const unsigned int buffer_size, - const unsigned int chunk_size, - const ScratchData &sample_scratch_data, - const CopyData &sample_copy_data) - : - tbb::filter (/*is_serial=*/true), - color_remaining_iterator_range (new std::pair::iterator, - typename std::vector::iterator> (begin,end)), - ring_buffer (buffer_size), - sample_scratch_data (sample_scratch_data), - color(true), - n_emitted_items (0), - chunk_size (chunk_size) + + private: + /** + * Pointer to the function + * that does the assembling + * on the sequence of cells. + */ + const std_cxx1x::function worker; + }; + + + + /** + * A class that manages calling the + * copier function. Note that it is, in + * the TBB notation, a filter that runs + * sequentially, ensuring that all items + * are copied in the same order in which + * they are created. + */ + template + class Copier : public tbb::filter { - for (unsigned int element=0; element &copier) + : + tbb::filter (/*is_serial=*/true), + copier (copier) + {} + + + /** + * Work on a single item. + */ + void *operator () (void *item) { - Assert (ring_buffer[element].n_items == 0, - ExcInternalError()); - - // work_items is templated on iterator. Therefore, the resize must - // be done given *(color_remaining_iterator_range->firts) because - // iterator may not have a default constructor and - // *(color_remaining_iterator_range->second) is invalid. - ring_buffer[element].work_items.resize (chunk_size, - *(color_remaining_iterator_range->first)); - ring_buffer[element].scratch_data = &thread_local_scratch; - ring_buffer[element].sample_scratch_data = &sample_scratch_data; - ring_buffer[element].copy_datas.resize (chunk_size, - sample_copy_data); + // first unpack the current item + typedef + typename IteratorRangeToItemStream::ItemType + ItemType; + + ItemType *current_item = static_cast (item); + + // initiate copying data. for the same reasons as in the worker class + // above, catch exceptions rather than letting it propagate into + // unknown territories + for (unsigned int i=0; in_items; ++i) + { + try + { + if (copier) + copier (current_item->copy_datas[i]); + } + catch (const std::exception &exc) + { + Threads::internal::handle_std_exception (exc); + } + catch (...) + { + Threads::internal::handle_unknown_exception (); + } + } + + + // return an invalid item since we are at the end of the + // pipeline + return 0; } - } + + private: + /** + * Pointer to the function that does the copying of data. + */ + const std_cxx1x::function copier; + }; + + } + + + /** + * A namespace for the implementation of details of the WorkStream pattern + * and function. This namespace holds classes that deal with the third + * implementation described in the paper by Turcksin, Kronbichler and + * Bangerth. + */ + namespace Implementation3 + { /** - * Create a item and return a - * pointer to it. + * A class that creates a sequence of items from a range of iterators. */ - virtual void *operator () (void *) + template + class IteratorRangeToItemStream : public tbb::filter { - // store the current - // position of the pointer - ItemType *current_item - = &ring_buffer[n_emitted_items % ring_buffer.size()]; - - // initialize the next item. it may - // consist of at most chunk_size - // elements - current_item->n_items = 0; - if (color==false) - while ((remaining_iterator_range->first != - remaining_iterator_range->second) - && - (current_item->n_items < chunk_size)) + public: + /** + * A data type that we use to identify items to be worked on. This is + * the structure that is passed around between the different parts of + * the WorkStream implementation to identify what needs to be done by + * the various stages of the pipeline. + */ + struct ItemType + { + /** + * A structure that contains a pointer to scratch and copy data objects along + * with a flag that indicates whether this object is currently in use. + */ + struct ScratchAndCopyDataObjects { - current_item->work_items[current_item->n_items] - = remaining_iterator_range->first; + std_cxx1x::shared_ptr scratch_data; + std_cxx1x::shared_ptr copy_data; + bool currently_in_use; + + /** + * Default constructor. + */ + ScratchAndCopyDataObjects () + : + currently_in_use (false) + {} + + ScratchAndCopyDataObjects (ScratchData *p, + CopyData *q, + const bool in_use) + : + scratch_data (p), + copy_data (q), + currently_in_use (in_use) + {} + +//TODO: when we push back an object to the list of scratch objects, in +// Worker::operator(), we first create an object and then copy +// it to the end of this list. this involves having two objects +// of the current type having pointers to it, each with their own +// currently_in_use flag. there is probably little harm in this because +// the original one goes out of scope right away again, but it's +// certainly awkward. one way to avoid this would be to use unique_ptr +// but we'd need to figure out a way to use it in non-C++11 mode + ScratchAndCopyDataObjects (const ScratchAndCopyDataObjects &o) + : + scratch_data (o.scratch_data), + copy_data (o.copy_data), + currently_in_use (o.currently_in_use) + {} + }; - ++remaining_iterator_range->first; - ++current_item->n_items; - } - else - while ((color_remaining_iterator_range->first != - color_remaining_iterator_range->second) - && - (current_item->n_items < chunk_size)) - { - current_item->work_items[current_item->n_items] - = *(color_remaining_iterator_range->first); - ++color_remaining_iterator_range->first; - ++current_item->n_items; - } + /** + * Typedef to a list of scratch data objects. The rationale for this + * list is provided in the variables that use these lists. + */ + typedef std::list ScratchAndCopyDataList; - if (current_item->n_items == 0) - // there were no items - // left. terminate the pipeline - return 0; - else + /** + * A list of iterators that need to be worked on. Only the first + * n_items are relevant. + */ + std::vector work_items; + + /** + * Number of items identified by the work_items array that the + * Worker and Copier pipeline stage need to work on. The maximum + * value of this variable will be chunk_size. + */ + unsigned int n_items; + + /** + * Pointer to a thread local variable identifying the scratch + * and copy data objects this thread will use. The same considerations + * apply as documented in the Implementation2::IteratorRangeToItemStream + * class as well as in the paper by Turcksin, Kronbichler and Bangerth. + */ + Threads::ThreadLocalStorage *scratch_and_copy_data; + + /** + * Pointer to a sample scratch data object, to be used to initialize + * the scratch data objects created for each individual thread. + */ + const ScratchData *sample_scratch_data; + + /** + * Pointer to a sample copy data object. + */ + const CopyData *sample_copy_data; + + /** + * Flag is true if the buffer is used and false if the buffer can be + * used. + */ + bool currently_in_use; + + /** + * Default constructor. + * Initialize everything that doesn't have a default constructor + * itself. + */ + ItemType () + : + n_items (0), + sample_scratch_data (0), + sample_copy_data (0), + currently_in_use (false) + {} + }; + + + /** + * Constructor. Take range of iterators into an array of the kind of object we + * want to loop over, the size of a buffer that can + * hold items, and the sample additional data object that will be passed + * to each worker and copier function invokation. + */ + IteratorRangeToItemStream (const typename std::vector::const_iterator &begin, + const typename std::vector::const_iterator &end, + const unsigned int buffer_size, + const unsigned int chunk_size, + const ScratchData &sample_scratch_data, + const CopyData &sample_copy_data) + : + tbb::filter (/*is_serial=*/true), + remaining_iterator_range (begin, end), + item_buffer (buffer_size), + sample_scratch_data (sample_scratch_data), + sample_copy_data (sample_copy_data), + chunk_size (chunk_size) { - ++n_emitted_items; - return current_item; + Assert (begin != end, ExcMessage ("This class is not prepared to deal with empty ranges!")); + // initialize the elements of the item_buffer + for (unsigned int element=0; element > remaining_iterator_range; - /** - * When graph coloring is used the iterators to be worked on are given - * in a vector defined by a pair of iterators. - */ - std_cxx1x::shared_ptr::iterator, - typename std::vector::iterator> > - color_remaining_iterator_range; + /** + * Create an item and return a + * pointer to it. + */ + virtual void *operator () (void *) + { + // find first unused item. we know that there must be one + // because we have set the maximal number of tokens in flight + // and have set the ring buffer to have exactly this size. so + // if this function is called, we know that less than the + // maximal number of items in currently in flight + ItemType *current_item = 0; + for (unsigned int i=0; in_items = 0; + while ((remaining_iterator_range.first != + remaining_iterator_range.second) + && + (current_item->n_items < chunk_size)) + { + // initialize the iterators to work on with the elements + // of the vector that remaining_iterator_range + // points into + current_item->work_items[current_item->n_items] + = *remaining_iterator_range.first; + + ++remaining_iterator_range.first; + ++current_item->n_items; + } + + if (current_item->n_items == 0) + // there were no items + // left. terminate the pipeline + return 0; + else + return current_item; + } - /** - * A ring buffer that will store items. - */ - std::vector ring_buffer; + private: + /** + * The interval of iterators still to + * be worked on. This range will shrink + * over time. + */ + std::pair::const_iterator,typename std::vector::const_iterator> remaining_iterator_range; - /** - * Pointer to a thread local variable identifying the scratch data objects - * this thread will use. The initial implementation of this - * class using thread local variables provided only a single - * scratch object per thread. This doesn't work, because - * the worker functions may start tasks itself and then call - * Threads::TaskGroup::join_all() or a similar function, which the - * TBB scheduler may use to run something else on the current - * thread -- for example another instance of the worker function. - * Consequently, there would be two instances of the worker - * function that use the same scratch object if we only - * provided a single scratch object per thread. The solution is - * to provide a list of scratch objects for each thread, together - * with a flag indicating whether this scratch object is currently - * used. If a thread needs a scratch object, it walks this list - * until it finds an unused object, or, if there is none, creates one - * itself. Note that we need not use synchronization primitives - * for this process since the lists are thread-local and - * we are guaranteed that only a single thread accesses them as long - * as we have no yield point in between the accesses to the list. - * - * The pointers to scratch objects stored in each of these lists must - * be so that they are deleted on all threads when the thread - * local object is destroyed. This is achieved by using shared_ptr. - * - * Note that when a worker needs to create a scratch object, it allocates - * it using sample_scratch_data to copy from. This has - * the advantage of a first-touch initialization, i.e., the - * memory for the scratch data object is allocated and initialized - * by the same thread that will later use it. - */ - Threads::ThreadLocalStorage thread_local_scratch; + /** + * A ring buffer that will store items. + */ + std::vector item_buffer; - /** - * A reference to a sample scratch data that will be used to - * initialize the thread-local pointers to a scratch data object - * each of the worker tasks uses. - */ - const ScratchData &sample_scratch_data; + /** + * Pointer to a thread local variable identifying the scratch and + * copy data objects each thread will use. The same is true as + * discussed for the implementation in the + * Implementation2::IteratorRangeToItemStream class and the paper + * by Turcksin, Kronbichler and Bangerth. + */ + Threads::ThreadLocalStorage thread_local_scratch_and_copy; - /** - * This flag is used to know if graph coloring is used or not. - */ - bool color; + /** + * A reference to a sample scratch data that will be used to + * initialize the thread-local pointers to a scratch data object + * each of the worker tasks uses. + */ + const ScratchData &sample_scratch_data; + + /** + * A reference to a sample scratch data that will be used to + * initialize the thread-local pointers to a scratch data object + * each of the worker tasks uses. + */ + const CopyData &sample_copy_data; + + /** + * Number of elements of the + * iterator range that each + * thread should work on + * sequentially; a large number + * makes sure that each thread + * gets a significant amount of + * work before the next task + * switch happens, whereas a + * small number is better for + * load balancing. + */ + const unsigned int chunk_size; + + /** + * Initialize the pointers and vector + * elements in the specified entry of + * the item_buffer. + */ + void init_buffer_elements (const unsigned int element) + { + Assert (item_buffer[element].n_items == 0, + ExcInternalError()); + + item_buffer[element].work_items + .resize (chunk_size, remaining_iterator_range.second); + item_buffer[element].scratch_and_copy_data + = &thread_local_scratch_and_copy; + item_buffer[element].sample_scratch_data + = &sample_scratch_data; + item_buffer[element].sample_copy_data + = &sample_copy_data; + } + }; - /** - * Counter for the number of emitted - * items. Each item may consist of up - * to chunk_size iterator elements. - */ - unsigned int n_emitted_items; - /** - * Number of elements of the - * iterator range that each - * thread should work on - * sequentially; a large number - * makes sure that each thread - * gets a significant amount of - * work before the next task - * switch happens, whereas a - * small number is better for - * load balancing. - */ - const unsigned int chunk_size; /** - * Initialize the pointers and vector - * elements in the specified entry of - * the ring buffer. + * A class that manages calling the + * worker function on a number of + * parallel threads. Note that it is, in + * the TBB notation, a filter that can + * run in parallel. */ - void init_buffer_elements (const unsigned int element, - const CopyData &sample_copy_data) + template + class WorkerAndCopier : public tbb::filter { - Assert (ring_buffer[element].n_items == 0, - ExcInternalError()); - - ring_buffer[element].work_items - .resize (chunk_size, remaining_iterator_range->second); - ring_buffer[element].scratch_data - = &thread_local_scratch; - ring_buffer[element].sample_scratch_data - = &sample_scratch_data; - ring_buffer[element].copy_datas - .resize (chunk_size, sample_copy_data); - } - }; + public: + /** + * Constructor. Takes a + * reference to the object on + * which we will operate as + * well as a pointer to the + * function that will do the + * assembly. + */ + WorkerAndCopier (const std_cxx1x::function &worker, + const std_cxx1x::function &copier) + : + tbb::filter (/* is_serial= */ false), + worker (worker), + copier (copier) + {} + + /** + * Work on an item. + */ + void *operator () (void *item) + { + // first unpack the current item + typedef + typename IteratorRangeToItemStream::ItemType + ItemType; + + ItemType *current_item = static_cast (item); + + // we need to find an unused scratch and corresponding copy + // data object in the list that + // corresponds to the current thread and then mark it as used. if + // we can't find one, create one + // + // as discussed in the discussion of the documentation of the + // IteratorRangeToItemStream::scratch_data variable, there is no + // need to synchronize access to this variable using a mutex + // as long as we have no yield-point in between. this means that + // we can't take an iterator into the list now and expect it to + // still be valid after calling the worker, but we at least do + // not have to lock the following section + ScratchData *scratch_data = 0; + CopyData *copy_data = 0; + { + typename ItemType::ScratchAndCopyDataList & + scratch_and_copy_data_list = current_item->scratch_and_copy_data->get(); + + // see if there is an unused object. if so, grab it and mark + // it as used + for (typename ItemType::ScratchAndCopyDataList::iterator + p = scratch_and_copy_data_list.begin(); + p != scratch_and_copy_data_list.end(); ++p) + if (p->currently_in_use == false) + { + scratch_data = p->scratch_data.get(); + copy_data = p->copy_data.get(); + p->currently_in_use = true; + break; + } + + // if no element in the list was found, create one and mark it as used + if (scratch_data == 0) + { + Assert (copy_data==0, ExcInternalError()); + scratch_data = new ScratchData(*current_item->sample_scratch_data); + copy_data = new CopyData(*current_item->sample_copy_data); + + typename ItemType::ScratchAndCopyDataList::value_type + new_scratch_object (scratch_data, copy_data, true); + scratch_and_copy_data_list.push_back (new_scratch_object); + } + } + // then call the worker and copier function on each element of the chunk we were + // given. since these functions are called on separate threads, + // nothing good can happen if they throw an exception and we are best + // off catching it and showing an error message + for (unsigned int i=0; in_items; ++i) + { + try + { + if (worker) + worker (current_item->work_items[i], + *scratch_data, + *copy_data); + if (copier) + copier (*copy_data); + } + catch (const std::exception &exc) + { + Threads::internal::handle_std_exception (exc); + } + catch (...) + { + Threads::internal::handle_unknown_exception (); + } + } + + // finally mark the scratch object as unused again. as above, there + // is no need to lock anything here since the object we work on + // is thread-local + { + typename ItemType::ScratchAndCopyDataList & + scratch_and_copy_data_list = current_item->scratch_and_copy_data->get(); + + for (typename ItemType::ScratchAndCopyDataList::iterator p = + scratch_and_copy_data_list.begin(); p != scratch_and_copy_data_list.end(); + ++p) + if (p->scratch_data.get() == scratch_data) + { + Assert(p->currently_in_use == true, ExcInternalError()); + p->currently_in_use = false; + } + } - /** - * A class that manages calling the - * worker function on a number of - * parallel threads. Note that it is, in - * the TBB notation, a filter that can - * run in parallel. - */ - template - class Worker : public tbb::filter - { - public: - /** - * Constructor. Takes a - * reference to the object on - * which we will operate as - * well as a pointer to the - * function that will do the - * assembly. - */ - Worker (const std_cxx1x::function &worker) - : - tbb::filter (/* is_serial= */ false), - worker (worker) - {} - - - /** - * Work on an item. - */ - void *operator () (void *item) - { - // first unpack the current item - typedef - typename IteratorRangeToItemStream::ItemType - ItemType; - - ItemType *current_item = static_cast (item); - - // we need to find an unused scratch data object in the list that - // corresponds to the current thread and then mark it as used. if - // we can't find one, create one - // - // as discussed in the discussion of the documentation of the - // IteratorRangeToItemStream::scratch_data variable, there is no - // need to synchronize access to this variable using a mutex - // as long as we have no yield-point in between. this means that - // we can't take an iterator into the list now and expect it to - // still be valid after calling the worker, but we at least do - // not have to lock the following section - ScratchData *scratch_data = 0; - { - typename ItemType::ScratchDataList & - scratch_data_list = current_item->scratch_data->get(); - - // see if there is an unused object. if so, grab it and mark - // it as used - for (typename ItemType::ScratchDataList::iterator - p = scratch_data_list.begin(); - p != scratch_data_list.end(); ++p) - if (p->currently_in_use == false) - { - scratch_data = p->scratch_data.get(); - p->currently_in_use = true; - break; - } - - // if no object was found, create one and mark it as used - if (scratch_data == 0) - { - scratch_data = new ScratchData(*current_item->sample_scratch_data); - - typename ItemType::ScratchDataList::value_type - new_scratch_object (scratch_data, true); - scratch_data_list.push_back (new_scratch_object); - } - } - - // then call the worker function on each element of the chunk we were - // given. since these worker functions are called on separate threads, - // nothing good can happen if they throw an exception and we are best - // off catching it and showing an error message - for (unsigned int i=0; in_items; ++i) - { - try - { - if (worker) - worker (current_item->work_items[i], - *scratch_data, - current_item->copy_datas[i]); - } - catch (const std::exception &exc) - { - Threads::internal::handle_std_exception (exc); - } - catch (...) - { - Threads::internal::handle_unknown_exception (); - } - } - - // finally mark the scratch object as unused again. as above, there - // is no need to lock anything here since the object we work on - // is thread-local - { - typename ItemType::ScratchDataList & - scratch_data_list = current_item->scratch_data->get(); - - for (typename ItemType::ScratchDataList::iterator p = - scratch_data_list.begin(); p != scratch_data_list.end(); - ++p) - if (p->scratch_data.get() == scratch_data) - { - Assert(p->currently_in_use == true, ExcInternalError()); - p->currently_in_use = false; - } - } - - - - // then return the original pointer - // to the now modified object - return item; - } - - - private: - /** - * Pointer to the function - * that does the assembling - * on the sequence of cells. - */ - const std_cxx1x::function worker; - }; + // mark current item as usable again + current_item->currently_in_use = false; + // return an invalid item since we are at the end of the + // pipeline + return 0; + } - /** - * A class that manages calling the - * copier function. Note that it is, in - * the TBB notation, a filter that runs - * sequentially, ensuring that all items - * are copied in the same order in which - * they are created. - */ - template - class Copier : public tbb::filter - { - public: - /** - * Constructor. Takes a - * reference to the object on - * which we will operate as - * well as a pointer to the - * function that will do the - * copying from the - * additional data object to - * the global matrix or - * similar. - */ - Copier (const std_cxx1x::function &copier,bool is_serial) - : - tbb::filter (is_serial), - copier (copier) - {} - - - /** - * Work on a single item. - */ - void *operator () (void *item) - { - // first unpack the current item - typedef - typename IteratorRangeToItemStream::ItemType - ItemType; - - ItemType *current_item = static_cast (item); - - // initiate copying data. for the same reasons as in the worker class - // above, catch exceptions rather than letting it propagate into - // unknown territories - for (unsigned int i=0; in_items; ++i) - { - try - { - if (copier) - copier (current_item->copy_datas[i]); - } - catch (const std::exception &exc) - { - Threads::internal::handle_std_exception (exc); - } - catch (...) - { - Threads::internal::handle_unknown_exception (); - } - } - - - // return an invalid item since we are at the end of the - // pipeline - return 0; - } - - - private: - /** - * Pointer to the function that does the copying of data. - */ - const std_cxx1x::function copier; - }; + private: + /** + * Pointer to the function + * that does the assembling + * on the sequence of cells. + */ + const std_cxx1x::function worker; + /** + * Pointer to the function that does the copying from + * local contribution to global object. + */ + const std_cxx1x::function copier; + }; + } } - #endif // DEAL_II_WITH_THREADS /** - * This is the main function of the WorkStream concept, doing work as - * described in the introduction to this namespace. + * This is one of two main functions of the WorkStream concept, doing work as + * described in the introduction to this namespace. It corresponds to + * implementation 2 of the paper by Turcksin, Kronbichler and Bangerth. * - * This is the function that can be used for worker and copier objects that + * This function that can be used for worker and copier objects that * are either pointers to non-member functions or objects that allow to be * called with an operator(), for example objects created by std::bind. * @@ -776,8 +1178,8 @@ namespace WorkStream typename Iterator, typename ScratchData, typename CopyData> - void - run (const Iterator &begin, + void + run (const Iterator &begin, const typename identity::type &end, Worker worker, Copier copier, @@ -813,29 +1215,29 @@ namespace WorkStream { // need to check if the function is not the zero function. To // check zero-ness, create a C++ function out of it and check that - if (static_cast& >(worker)) - worker (i, scratch_data, copy_data); - if (static_cast& > - (copier)) - copier (copy_data); + if (static_cast& >(worker)) + worker (i, scratch_data, copy_data); + if (static_cast& > + (copier)) + copier (copy_data); } } #ifdef DEAL_II_WITH_THREADS else // have TBB and use more than one thread { // create the three stages of the pipeline - internal::IteratorRangeToItemStream + internal::Implementation2::IteratorRangeToItemStream iterator_range_to_item_stream (begin, end, - queue_length, - chunk_size, - sample_scratch_data, - sample_copy_data); + queue_length, + chunk_size, + sample_scratch_data, + sample_copy_data); - internal::Worker worker_filter (worker); - internal::Copier copier_filter (copier,true); + internal::Implementation2::Worker worker_filter (worker); + internal::Implementation2::Copier copier_filter (copier); // now create a pipeline from these stages tbb::pipeline assembly_line; @@ -852,34 +1254,28 @@ namespace WorkStream } - /** - * This is the main function of the WorkStream concept, doing work as - * described in the introduction to this namespace. + * This is one of two main functions of the WorkStream concept, doing work as + * described in the introduction to this namespace. It corresponds to + * implementation 3 of the paper by Turcksin, Kronbichler and Bangerth. + * As such, it takes not a range of iterators described by a begin + * and end iterator, but a "colored" graph of iterators where each + * color represents cells for which writing the cell contributions into + * the global object does not conflict (in other words, these cells + * are not neighbors). Each "color" is represented by std::vectors of cells. + * The first argument to this function, a set of sets of cells (which are + * represent as a vector of vectors, for efficiency), is typically + * constructed by calling GraphColoring::make_graph_coloring(). * - * This is the function that can be used for worker and copier objects that + * This function that can be used for worker and copier objects that * are either pointers to non-member functions or objects that allow to be * called with an operator(), for example objects created by std::bind. * - * The argument passed as @p end must be convertible to the same type as @p - * begin, but doesn't have to be of the same type itself. This allows to - * write code like WorkStream().run(dof_handler.begin_active(), - * dof_handler.end(), ... where the first is of type - * DoFHandler::active_cell_iterator whereas the second is of type - * DoFHandler::raw_cell_iterator. - * * The two data types ScratchData and CopyData need to * have a working copy constructor. ScratchData is only used in the * worker function, while CopyData is the object passed * from the worker to the copier. * - * The @p get_conflict_indices argument, is a function that given an - * iterator computes the conflict indices necessary for the - * graph_coloring. Graph coloring is necessary to be able to copy the data - * in parallel. If the number of elements in some colors is less than @p - * chunk_size time multithread_info.n_threads(), these elements are - * aggregated and copied serially. - * * The @p queue_length argument indicates the number of items that can be * live at any given time. Each item consists of @p chunk_size elements of * the input stream that will be worked on by the worker and copier @@ -896,15 +1292,12 @@ namespace WorkStream typename Iterator, typename ScratchData, typename CopyData> - void - run (const Iterator &begin, - const typename identity::type &end, + void + run (const std::vector > &colored_iterators, Worker worker, Copier copier, const ScratchData &sample_scratch_data, const CopyData &sample_copy_data, - const std_cxx1x::function (const Iterator &)> - &get_conflict_indices, const unsigned int queue_length = 2*multithread_info.n_threads(), const unsigned int chunk_size = 8) { @@ -916,171 +1309,73 @@ namespace WorkStream ExcMessage ("The chunk_size must be at least one.")); (void)chunk_size; // removes -Wunused-parameter warning in optimized mode - // if no work then skip. (only use - // operator!= for iterators since we may - // not have an equality comparison - // operator) - if (!(begin != end)) - return; - // we want to use TBB if we have support and if it is not disabled at // runtime: - #ifdef DEAL_II_WITH_THREADS - if (multithread_info.n_threads()==1) - #endif - { - // need to copy the sample since it is - // marked const - ScratchData scratch_data = sample_scratch_data; - CopyData copy_data = sample_copy_data; - - for (Iterator i=begin; i!=end; ++i) - { - if (static_cast& >(worker)) - worker (i, scratch_data, copy_data); - if (static_cast& > - (copier)) - copier (copy_data); - } - } #ifdef DEAL_II_WITH_THREADS - else - { - // color the graph - std::vector > coloring = graph_coloring::make_graph_coloring( - begin,end,get_conflict_indices); - - // colors that do not have cells, i.e., less than chunk_size times - // multithread_info.n_threads(), are gathered and the copier is - // called serially. - const unsigned int serial_limit(chunk_size*multithread_info.n_threads()); - std::vector serial_copying; - - for (unsigned int color=0; color - iterator_range_to_item_stream (coloring[color].begin(), coloring[color].end(), - queue_length, - chunk_size, - sample_scratch_data, - sample_copy_data); - - internal::Worker worker_filter (worker); - internal::Copier copier_filter (copier,false); - - // now create a pipeline from - // these stages - tbb::pipeline assembly_line; - assembly_line.add_filter (iterator_range_to_item_stream); - assembly_line.add_filter (worker_filter); - assembly_line.add_filter (copier_filter); - - // and run it - assembly_line.run (queue_length); - - assembly_line.clear (); - } - } - - // use the serial copier for all the colors that do not have enough cells - if (serial_copying.size()!=0) - { - internal::IteratorRangeToItemStream - iterator_range_to_item_stream (serial_copying.begin(), serial_copying.end(), - queue_length, - chunk_size, - sample_scratch_data, - sample_copy_data); - - internal::Worker worker_filter (worker); - internal::Copier copier_filter (copier,true); - - tbb::pipeline assembly_line; - assembly_line.add_filter (iterator_range_to_item_stream); - assembly_line.add_filter (worker_filter); - assembly_line.add_filter (copier_filter); - - // and run it - assembly_line.run (queue_length); - - assembly_line.clear (); - } - } + if (multithread_info.n_threads()==1) #endif - } - - + { + // need to copy the sample since it is marked const + ScratchData scratch_data = sample_scratch_data; + CopyData copy_data = sample_copy_data; - /** - * This is the main function of the WorkStream concept, doing work as - * described in the introduction to this namespace. - * - * This is the function that can be used for worker and copier functions - * that are member functions of a class. - * - * The argument passed as @p end must be convertible to the same type as @p - * begin, but doesn't have to be of the same type itself. This allows to - * write code like WorkStream().run(dof_handler.begin_active(), - * dof_handler.end(), ... where the first is of type - * DoFHandler::active_cell_iterator whereas the second is of type - * DoFHandler::raw_cell_iterator. - * - * The @p queue_length argument indicates the number of items that can be - * live at any given time. Each item consists of @p chunk_size elements of - * the input stream that will be worked on by the worker and copier - * functions one after the other on the same thread. - * - * @note If your data objects are large, or their constructors are - * expensive, it is helpful to keep in mind that queue_length - * copies of the ScratchData object and - * queue_length*chunk_size copies of the CopyData object - * are generated. - */ - template - void - run (const Iterator &begin, - const typename identity::type &end, - MainClass &main_object, - void (MainClass::*worker) (const Iterator &, - ScratchData &, - CopyData &), - void (MainClass::*copier) (const CopyData &), - const ScratchData &sample_scratch_data, - const CopyData &sample_copy_data, - const unsigned int queue_length = 2*multithread_info.n_threads(), - const unsigned int chunk_size = 8) - { - // forward to the other function - run (begin, end, - std_cxx1x::bind (worker, - std_cxx1x::ref (main_object), - std_cxx1x::_1, std_cxx1x::_2, std_cxx1x::_3), - std_cxx1x::bind (copier, - std_cxx1x::ref (main_object), - std_cxx1x::_1), - sample_scratch_data, - sample_copy_data, - queue_length, - chunk_size); + for (unsigned int color=0; color::const_iterator p = colored_iterators[color].begin(); + p != colored_iterators[color].end(); ++p) + { + // need to check if the function is not the zero function. To + // check zero-ness, create a C++ function out of it and check that + if (static_cast& >(worker)) + worker (*p, scratch_data, copy_data); + if (static_cast& >(copier)) + copier (copy_data); + } + } +#ifdef DEAL_II_WITH_THREADS + else // have TBB and use more than one thread + { + // loop over the various colors of what we're given + for (unsigned int color=0; color 0) + { + // create the three stages of the pipeline + internal::Implementation3::IteratorRangeToItemStream + iterator_range_to_item_stream (colored_iterators[color].begin(), + colored_iterators[color].end(), + queue_length, + chunk_size, + sample_scratch_data, + sample_copy_data); + + + internal::Implementation3::WorkerAndCopier + worker_and_copier_filter (worker, copier); + + // now create a pipeline from these stages + tbb::pipeline assembly_line; + assembly_line.add_filter (iterator_range_to_item_stream); + assembly_line.add_filter (worker_and_copier_filter); + + // and run it + assembly_line.run (queue_length); + + assembly_line.clear (); + } + } +#endif } + /** - * This is the main function of the WorkStream concept, doing work as - * described in the introduction to this namespace. + * This is a variant of one of the two main functions of the WorkStream + * concept, doing work as described in the introduction to this namespace. + * It corresponds to implementation 2 of the paper by Turcksin, Kronbichler + * and Bangerth. * * This is the function that can be used for worker and copier functions * that are member functions of a class. @@ -1092,13 +1387,6 @@ namespace WorkStream * DoFHandler::active_cell_iterator whereas the second is of type * DoFHandler::raw_cell_iterator. * - * The @p get_conflict_indices argument, is a function that given an - * iterator computes the conflict indices necessary for the - * graph_coloring. Graph coloring is necessary to be able to copy the data - * in parallel. If the number of elements in some colors is less than @p - * chunk_size time multithread_info.n_threads(), these elements are - * aggregated and copied serially. - * * The @p queue_length argument indicates the number of items that can be * live at any given time. Each item consists of @p chunk_size elements of * the input stream that will be worked on by the worker and copier @@ -1124,7 +1412,6 @@ namespace WorkStream void (MainClass::*copier) (const CopyData &), const ScratchData &sample_scratch_data, const CopyData &sample_copy_data, - std::vector (MainClass::*get_conflict_indices)(const Iterator &), const unsigned int queue_length = 2*multithread_info.n_threads(), const unsigned int chunk_size = 8) { @@ -1138,8 +1425,6 @@ namespace WorkStream std_cxx1x::_1), sample_scratch_data, sample_copy_data, - std_cxx1x::bind(get_conflict_indices, - std_cxx1x::ref (main_object)), queue_length, chunk_size); } diff --git a/deal.II/include/deal.II/dofs/dof_renumbering.h b/deal.II/include/deal.II/dofs/dof_renumbering.h index c52ddaafd9..9484864df3 100644 --- a/deal.II/include/deal.II/dofs/dof_renumbering.h +++ b/deal.II/include/deal.II/dofs/dof_renumbering.h @@ -120,7 +120,7 @@ DEAL_II_NAMESPACE_OPEN * results. However, after all there is no algorithm that * accomplishes this within reasonable time. There are situations * where the lack of optimality even leads to worse results than with - * the original, crude, levelwise numering scheme; one of these + * the original, crude, levelwise numbering scheme; one of these * examples is a mesh of four cells of which always those cells are * refined which are neighbors to the center (you may call this mesh a * `zoom in' mesh). In one such example the bandwidth was increased by @@ -345,7 +345,7 @@ DEAL_II_NAMESPACE_OPEN * after DoFHandler::distribute_dofs. The minimum degree algorithm does not * attempt to minimize the bandwidth of a matrix but to minimize the amount * of fill-in a LU decomposition would produce, i.e. the number of places in - * the matrix that would be occupied by elements of an LU decompisition that + * the matrix that would be occupied by elements of an LU decomposition that * are not already occupied by elements of the original matrix. The resulting * sparsity pattern obviously has an entirely different structure than the * ones produced by algorithms trying to minimize the bandwidth. @@ -428,14 +428,11 @@ namespace DoFRenumbering /** - * Point based comparator for downstream - * directions: it returns @p true if the - * second point is downstream of the first - * one with respect to the direction given - * to the constructor. If the points are - * the same with respect to the downstream - * direction, the point with the lower DoF - * number is considered smaller. + * Point based comparator for downstream directions: it returns @p true if + * the second point is downstream of the first one with respect to the + * direction given to the constructor. If the points are the same with + * respect to the downstream direction, the point with the lower DoF number + * is considered smaller. */ template struct ComparePointwiseDownstream @@ -465,48 +462,29 @@ namespace DoFRenumbering }; /** - * A namespace for the - * implementation of some - * renumbering algorithms based - * on algorithms implemented in - * the Boost Graph Library (BGL) - * by Jeremy Siek and others. + * A namespace for the implementation of some renumbering algorithms based + * on algorithms implemented in the Boost Graph Library (BGL) by Jeremy Siek + * and others. * - * While often slighty slower to - * compute, the algorithms using - * BOOST often lead to matrices - * with smaller bandwidths and - * sparse ILUs based on this - * numbering are therefore more - * efficient. + * While often slightly slower to compute, the algorithms using BOOST often + * lead to matrices with smaller bandwidths and sparse ILUs based on this + * numbering are therefore more efficient. * - * For a comparison of these - * algorithms with the ones - * defined in DoFRenumbering, see - * the comparison section in the - * documentation of the + * For a comparison of these algorithms with the ones defined in + * DoFRenumbering, see the comparison section in the documentation of the * DoFRenumbering namespace. */ namespace boost { /** - * Renumber the degrees of - * freedom according to the - * Cuthill-McKee method, - * eventually using the reverse - * numbering scheme. + * Renumber the degrees of freedom according to the Cuthill-McKee method, + * eventually using the reverse numbering scheme. * - * See the general - * documentation of the - * parent class for details - * on the different methods. + * See the general documentation of the parent class for details on the + * different methods. * - * As an example of the - * results of this algorithm, - * take a look at the - * comparison of various - * algorithms in the - * documentation of the + * As an example of the results of this algorithm, take a look at the + * comparison of various algorithms in the documentation of the * DoFRenumbering namespace. */ template @@ -516,13 +494,9 @@ namespace DoFRenumbering const bool use_constraints = false); /** - * Computes the renumbering - * vector needed by the - * Cuthill_McKee() function. Does - * not perform the renumbering on - * the DoFHandler dofs but - * returns the renumbering - * vector. + * Computes the renumbering vector needed by the Cuthill_McKee() + * function. Does not perform the renumbering on the DoFHandler dofs but + * returns the renumbering vector. */ template void @@ -532,29 +506,16 @@ namespace DoFRenumbering const bool use_constraints = false); /** - * Renumber the degrees of - * freedom based on the BOOST - * implementation of the King - * algorithm. This often - * results in slightly larger - * (by a few percent) - * bandwidths than the - * Cuthill-McKee algorithm, - * but sparse ILUs are often - * slightly (also by a few - * percent) better - * preconditioners. + * Renumber the degrees of freedom based on the BOOST implementation of + * the King algorithm. This often results in slightly larger (by a few + * percent) bandwidths than the Cuthill-McKee algorithm, but sparse ILUs + * are often slightly (also by a few percent) better preconditioners. * - * As an example of the - * results of this algorithm, - * take a look at the - * comparison of various - * algorithms in the - * documentation of the + * As an example of the results of this algorithm, take a look at the + * comparison of various algorithms in the documentation of the * DoFRenumbering namespace. * - * This algorithm is used in - * step-22. + * This algorithm is used in step-22. */ template void @@ -563,11 +524,8 @@ namespace DoFRenumbering const bool use_constraints = false); /** - * Compute the renumbering - * for the King algorithm but - * do not actually renumber - * the degrees of freedom in - * the DoF handler argument. + * Compute the renumbering for the King algorithm but do not actually + * renumber the degrees of freedom in the DoF handler argument. */ template void @@ -577,28 +535,14 @@ namespace DoFRenumbering const bool use_constraints = false); /** - * Renumber the degrees of - * freedom based on the BOOST - * implementation of the - * minimum degree - * algorithm. Unlike the - * Cuthill-McKee algorithm, - * this algorithm does not - * attempt to minimize the - * bandwidth of a matrix but - * to minimize the amount of - * fill-in when doing an LU - * decomposition. It may - * sometimes yield better - * ILUs because of this - * property. + * Renumber the degrees of freedom based on the BOOST implementation of + * the minimum degree algorithm. Unlike the Cuthill-McKee algorithm, this + * algorithm does not attempt to minimize the bandwidth of a matrix but to + * minimize the amount of fill-in when doing an LU decomposition. It may + * sometimes yield better ILUs because of this property. * - * As an example of the - * results of this algorithm, - * take a look at the - * comparison of various - * algorithms in the - * documentation of the + * As an example of the results of this algorithm, take a look at the + * comparison of various algorithms in the documentation of the * DoFRenumbering namespace. */ template @@ -608,12 +552,8 @@ namespace DoFRenumbering const bool use_constraints = false); /** - * Compute the renumbering - * for the minimum degree - * algorithm but do not - * actually renumber the - * degrees of freedom in the - * DoF handler argument. + * Compute the renumbering for the minimum degree algorithm but do not + * actually renumber the degrees of freedom in the DoF handler argument. */ template void @@ -624,21 +564,14 @@ namespace DoFRenumbering } /** - * Renumber the degrees of - * freedom according to the - * Cuthill-McKee method, - * eventually using the reverse - * numbering scheme. + * Renumber the degrees of freedom according to the Cuthill-McKee method, + * eventually using the reverse numbering scheme. * - * See the general documentation - * of this class for details on - * the different methods. + * See the general documentation of this class for details on the different + * methods. * - * As an example of the results - * of this algorithm, take a look - * at the comparison of various - * algorithms in the - * documentation of the + * As an example of the results of this algorithm, take a look at the + * comparison of various algorithms in the documentation of the * DoFRenumbering namespace. */ template @@ -649,13 +582,9 @@ namespace DoFRenumbering const std::vector &starting_indices = std::vector()); /** - * Computes the renumbering - * vector needed by the - * Cuthill_McKee() function. Does - * not perform the renumbering on - * the DoFHandler dofs but - * returns the renumbering - * vector. + * Computes the renumbering vector needed by the Cuthill_McKee() + * function. Does not perform the renumbering on the DoFHandler dofs but + * returns the renumbering vector. */ template void @@ -666,27 +595,17 @@ namespace DoFRenumbering const std::vector &starting_indices = std::vector()); /** - * Renumber the degrees of - * freedom according to the - * Cuthill-McKee method, - * eventually using the reverse - * numbering scheme, in this case - * for a multigrid numbering of - * degrees of freedom. + * Renumber the degrees of freedom according to the Cuthill-McKee method, + * eventually using the reverse numbering scheme, in this case for a + * multigrid numbering of degrees of freedom. * - * You can give a triangulation - * level to which this function - * is to be applied. Since with - * a level-wise numbering there - * are no hanging nodes, no - * constraints can be used, so - * the respective parameter of - * the previous function is - * ommitted. + * You can give a triangulation level to which this function is to be + * applied. Since with a level-wise numbering there are no hanging nodes, + * no constraints can be used, so the respective parameter of the previous + * function is omitted. * - * See the general documentation - * of this class for details on - * the different methods. + * See the general documentation of this class for details on the different + * methods. */ template void @@ -701,67 +620,34 @@ namespace DoFRenumbering */ /** - * Sort the degrees of freedom by - * vector component. The - * numbering within each - * component is not touched, so a - * degree of freedom with index - * $i$, belonging to some - * component, and another degree - * of freedom with index $j$ - * belonging to the same - * component will be assigned new - * indices $n(i)$ and $n(j)$ with - * $n(i)n(j)$ if $i>j$. + * Sort the degrees of freedom by vector component. The numbering within + * each component is not touched, so a degree of freedom with index $i$, + * belonging to some component, and another degree of freedom with index $j$ + * belonging to the same component will be assigned new indices $n(i)$ and + * $n(j)$ with $n(i)n(j)$ if $i>j$. * - * You can specify that the - * components are ordered in a - * different way than suggested - * by the FESystem object you - * use. To this end, set up the - * vector @p target_component - * such that the entry at index - * @p i denotes the number of the - * target component for dofs with - * component @p i in the - * FESystem. Naming the same - * target component more than once is - * possible and results in a - * blocking of several components - * into one. This is discussed in - * step-22. If you - * omit this argument, the same - * order as given by the finite - * element is used. + * You can specify that the components are ordered in a different way than + * suggested by the FESystem object you use. To this end, set up the vector + * @p target_component such that the entry at index @p i denotes the number + * of the target component for dofs with component @p i in the + * FESystem. Naming the same target component more than once is possible and + * results in a blocking of several components into one. This is discussed + * in step-22. If you omit this argument, the same order as given by the + * finite element is used. * - * If one of the base finite - * elements from which the global - * finite element under - * consideration here, is a - * non-primitive one, i.e. its - * shape functions have more than - * one non-zero component, then - * it is not possible to - * associate these degrees of - * freedom with a single vector - * component. In this case, they - * are associated with the first - * vector component to which they - * belong. + * If one of the base finite elements from which the global finite element + * under consideration here, is a non-primitive one, i.e. its shape + * functions have more than one non-zero component, then it is not possible + * to associate these degrees of freedom with a single vector component. In + * this case, they are associated with the first vector component to which + * they belong. * - * For finite elements with only - * one component, or a single - * non-primitive base element, - * this function is the identity - * operation. + * For finite elements with only one component, or a single non-primitive + * base element, this function is the identity operation. * - * @note A similar function, which - * renumbered all levels existed - * for MGDoFHandler. This function - * was deleted. Thus, you have to - * call the level function for each - * level now. + * @note A similar function, which renumbered all levels existed for + * MGDoFHandler. This function was deleted. Thus, you have to call the level + * function for each level now. */ template void @@ -771,9 +657,8 @@ namespace DoFRenumbering /** - * Sort the degrees of freedom by - * component. It does the same - * thing as the above function. + * Sort the degrees of freedom by component. It does the same thing as the + * above function. */ template void @@ -781,14 +666,10 @@ namespace DoFRenumbering const std::vector &target_component = std::vector ()); /** - * Sort the degrees of freedom by - * component. It does the same - * thing as the above function, - * only that it does this for one - * single level of a multi-level - * discretization. The - * non-multigrid part of the - * MGDoFHandler is not touched. + * Sort the degrees of freedom by component. It does the same thing as the + * above function, only that it does this for one single level of a + * multi-level discretization. The non-multigrid part of the MGDoFHandler is + * not touched. */ template void @@ -798,14 +679,9 @@ namespace DoFRenumbering /** - * Sort the degrees of freedom by - * component. It does the same - * thing as the previous - * functions, but more: it - * renumbers not only every level - * of the multigrid part, but - * also the global, - * i.e. non-multigrid components. + * Sort the degrees of freedom by component. It does the same thing as the + * previous functions, but more: it renumbers not only every level of the + * multigrid part, but also the global, i.e. non-multigrid components. */ template void @@ -813,13 +689,9 @@ namespace DoFRenumbering const std::vector &target_component = std::vector()); /** - * Computes the renumbering - * vector needed by the - * component_wise() - * functions. Does not perform - * the renumbering on the - * DoFHandler dofs but returns - * the renumbering vector. + * Computes the renumbering vector needed by the component_wise() + * functions. Does not perform the renumbering on the DoFHandler dofs but + * returns the renumbering vector. */ template types::global_dof_index @@ -839,19 +711,11 @@ namespace DoFRenumbering */ /** - * Sort the degrees of freedom by - * vector block. The - * numbering within each - * block is not touched, so a - * degree of freedom with index - * $i$, belonging to some - * block, and another degree - * of freedom with index $j$ - * belonging to the same - * block will be assigned new - * indices $n(i)$ and $n(j)$ with - * $n(i)n(j)$ if $i>j$. + * Sort the degrees of freedom by vector block. The numbering within each + * block is not touched, so a degree of freedom with index $i$, belonging to + * some block, and another degree of freedom with index $j$ belonging to the + * same block will be assigned new indices $n(i)$ and $n(j)$ with + * $n(i)n(j)$ if $i>j$. */ template void @@ -859,41 +723,29 @@ namespace DoFRenumbering /** - * Sort the degrees of freedom by - * block. It does the same - * thing as the above function. - * - * This function only succeeds if each of - * the elements in the hp::FECollection - * attached to the hp::DoFHandler argument - * has exactly the same number of blocks - * (see @ref GlossBlock "the glossary" for - * more information). Note that this is not - * always given: while the hp::FECollection - * class ensures that all of its elements - * have the same number of vector - * components, they need not have the same - * number of blocks. At the same time, this - * function here needs to match individual - * blocks across elements and therefore - * requires that elements have the same - * number of blocks and that subsequent - * blocks in one element have the same - * meaning as in another element. + * Sort the degrees of freedom by block. It does the same thing as the above + * function. + * + * This function only succeeds if each of the elements in the + * hp::FECollection attached to the hp::DoFHandler argument has exactly the + * same number of blocks (see @ref GlossBlock "the glossary" for more + * information). Note that this is not always given: while the + * hp::FECollection class ensures that all of its elements have the same + * number of vector components, they need not have the same number of + * blocks. At the same time, this function here needs to match individual + * blocks across elements and therefore requires that elements have the same + * number of blocks and that subsequent blocks in one element have the same + * meaning as in another element. */ template void block_wise (hp::DoFHandler &dof_handler); /** - * Sort the degrees of freedom by - * block. It does the same - * thing as the above function, - * only that it does this for one - * single level of a multi-level - * discretization. The - * non-multigrid part of the - * MGDoFHandler is not touched. + * Sort the degrees of freedom by block. It does the same thing as the above + * function, only that it does this for one single level of a multi-level + * discretization. The non-multigrid part of the MGDoFHandler is not + * touched. */ template void @@ -902,27 +754,18 @@ namespace DoFRenumbering /** - * Sort the degrees of freedom by - * block. It does the same - * thing as the previous - * functions, but more: it - * renumbers not only every level - * of the multigrid part, but - * also the global, - * i.e. non-multigrid components. + * Sort the degrees of freedom by block. It does the same thing as the + * previous functions, but more: it renumbers not only every level of the + * multigrid part, but also the global, i.e. non-multigrid components. */ template void block_wise (MGDoFHandler &dof_handler); /** - * Computes the renumbering - * vector needed by the - * block_wise() - * functions. Does not perform - * the renumbering on the - * DoFHandler dofs but returns - * the renumbering vector. + * Computes the renumbering vector needed by the block_wise() + * functions. Does not perform the renumbering on the DoFHandler dofs but + * returns the renumbering vector. */ template types::global_dof_index @@ -940,10 +783,9 @@ namespace DoFRenumbering */ /** - * Renumber the degrees cell by cell in hierarchical order - * (also known as z-order). The main usage is that this - * guarantees the same ordering independent of the - * number of processors involved in a parallel + * Renumber the degrees cell by cell in hierarchical order (also known as + * z-order). The main usage is that this guarantees the same ordering + * independent of the number of processors involved in a parallel * distributed computation. */ template @@ -951,16 +793,11 @@ namespace DoFRenumbering hierarchical (DoFHandler &dof_handler); /** - * Cell-wise renumbering. This function takes - * the ordered set of cells in - * cell_order, and makes - * sure that all degrees of - * freedom in a cell with higher - * index are behind all degrees - * of freedom of a cell with - * lower index. The order inside - * a cell block will be the same - * as before this renumbering. + * Cell-wise renumbering. This function takes the ordered set of cells in + * cell_order, and makes sure that all degrees of freedom in a cell + * with higher index are behind all degrees of freedom of a cell with lower + * index. The order inside a cell block will be the same as before this + * renumbering. */ template void @@ -968,13 +805,9 @@ namespace DoFRenumbering const std::vector &cell_order); /** - * Computes the renumbering - * vector needed by the - * cell_wise() function. Does - * not perform the renumbering on - * the DoFHandler dofs but - * returns the renumbering - * vector. + * Computes the renumbering vector needed by the cell_wise() function. Does + * not perform the renumbering on the DoFHandler dofs but returns the + * renumbering vector. */ template void @@ -984,9 +817,8 @@ namespace DoFRenumbering const std::vector &cell_order); /** - * Cell-wise renumbering on one - * level. See the other function - * with the same name. + * Cell-wise renumbering on one level. See the other function with the same + * name. */ template void @@ -995,13 +827,9 @@ namespace DoFRenumbering const std::vector &cell_order); /** - * Computes the renumbering - * vector needed by the - * cell_wise() level renumbering function. Does - * not perform the renumbering on - * the DoFHandler dofs but - * returns the renumbering - * vector. + * Computes the renumbering vector needed by the cell_wise() level + * renumbering function. Does not perform the renumbering on the DoFHandler + * dofs but returns the renumbering vector. */ template void @@ -1021,47 +849,29 @@ namespace DoFRenumbering */ /** - * Downstream numbering with respect to a - * constant flow direction. If the - * additional argument @p - * dof_wise_renumbering is set to @p false, - * the numbering is performed cell-wise, - * otherwise it is performed based on the + * Downstream numbering with respect to a constant flow direction. If the + * additional argument @p dof_wise_renumbering is set to @p false, the + * numbering is performed cell-wise, otherwise it is performed based on the * location of the support points. * - * The cells are sorted such that - * the centers of higher numbers - * are further downstream with - * respect to the constant vector - * @p direction than the centers - * of lower numbers. Even if this - * yields a downstream numbering - * with respect to the flux on - * the edges for fairly general - * grids, this might not be - * guaranteed for all meshes. + * The cells are sorted such that the centers of higher numbers are further + * downstream with respect to the constant vector @p direction than the + * centers of lower numbers. Even if this yields a downstream numbering with + * respect to the flux on the edges for fairly general grids, this might not + * be guaranteed for all meshes. * - * If the @p dof_wise_renumbering argument - * is set to @p false, this function - * produces a downstream ordering of the - * mesh cells and calls - * cell_wise(). Therefore, the output only - * makes sense for Discontinuous Galerkin - * Finite Elements (all degrees of freedom - * have to be associated with the interior - * of the cell in that case) in that case. + * If the @p dof_wise_renumbering argument is set to @p false, this function + * produces a downstream ordering of the mesh cells and calls + * cell_wise(). Therefore, the output only makes sense for Discontinuous + * Galerkin Finite Elements (all degrees of freedom have to be associated + * with the interior of the cell in that case) in that case. * - * If @p dof_wise_renumbering is set to @p - * true, the degrees of freedom are - * renumbered based on the support point - * location of the individual degrees of - * freedom (obviously, the finite element - * needs to define support points for this - * to work). The numbering of points with - * the same position in downstream location - * (e.g. those parallel to the flow - * direction, or several dofs within a - * FESystem) will be unaffected. + * If @p dof_wise_renumbering is set to @p true, the degrees of freedom are + * renumbered based on the support point location of the individual degrees + * of freedom (obviously, the finite element needs to define support points + * for this to work). The numbering of points with the same position in + * downstream location (e.g. those parallel to the flow direction, or + * several dofs within a FESystem) will be unaffected. */ template void @@ -1071,11 +881,8 @@ namespace DoFRenumbering /** - * Cell-wise downstream numbering - * with respect to a constant - * flow direction on one - * level. See the other function - * with the same name. + * Cell-wise downstream numbering with respect to a constant flow direction + * on one level. See the other function with the same name. */ template void @@ -1085,12 +892,11 @@ namespace DoFRenumbering const bool dof_wise_renumbering = false); /** - * This function does the downstream numbering for the individual - * levels of a multigrid hierarchy, but not for the global degrees - * of freedom. + * This function does the downstream numbering for the individual levels of + * a multigrid hierarchy, but not for the global degrees of freedom. * - * @deprecated Call downstream() function that takes a level - * argument for each of the levels of the multigrid hierarchy. + * @deprecated Call downstream() function that takes a level argument for + * each of the levels of the multigrid hierarchy. */ template void @@ -1134,13 +940,9 @@ namespace DoFRenumbering } /** - * Computes the renumbering - * vector needed by the - * downstream() function. Does - * not perform the renumbering on - * the DoFHandler dofs but - * returns the renumbering - * vector. + * Computes the renumbering vector needed by the downstream() function. Does + * not perform the renumbering on the DoFHandler dofs but returns the + * renumbering vector. */ template void @@ -1151,13 +953,9 @@ namespace DoFRenumbering const bool dof_wise_renumbering); /** - * Computes the renumbering - * vector needed by the - * downstream() function. Does - * not perform the renumbering on - * the DoFHandler dofs but - * returns the renumbering - * vector. + * Computes the renumbering vector needed by the downstream() function. Does + * not perform the renumbering on the DoFHandler dofs but returns the + * renumbering vector. */ template void @@ -1171,16 +969,10 @@ namespace DoFRenumbering /** * Cell-wise clockwise numbering. * - * This function produces a - * (counter)clockwise ordering of - * the mesh cells with respect to - * the hub @p center and calls - * cell_wise(). Therefore, it - * only works with Discontinuous - * Galerkin Finite Elements, - * i.e. all degrees of freedom - * have to be associated with the - * interior of the cell. + * This function produces a (counter)clockwise ordering of the mesh cells + * with respect to the hub @p center and calls cell_wise(). Therefore, it + * only works with Discontinuous Galerkin Finite Elements, i.e. all degrees + * of freedom have to be associated with the interior of the cell. */ template void @@ -1189,9 +981,8 @@ namespace DoFRenumbering const bool counter = false); /** - * Cell-wise clockwise numbering - * on one level. See the other - * function with the same name. + * Cell-wise clockwise numbering on one level. See the other function with + * the same name. */ template void @@ -1201,13 +992,9 @@ namespace DoFRenumbering const bool counter = false); /** - * Computes the renumbering - * vector needed by the - * clockwise_dg() functions. Does - * not perform the renumbering on - * the DoFHandler dofs but - * returns the renumbering - * vector. + * Computes the renumbering vector needed by the clockwise_dg() + * functions. Does not perform the renumbering on the DoFHandler dofs but + * returns the renumbering vector. */ template void @@ -1226,22 +1013,13 @@ namespace DoFRenumbering */ /** - * Sort those degrees of freedom - * which are tagged with @p true - * in the @p selected_dofs array - * to the back of the DoF - * numbers. The sorting is - * stable, i.e. the relative - * order within the tagged - * degrees of freedom is - * preserved, as is the relative - * order within the untagged - * ones. + * Sort those degrees of freedom which are tagged with @p true in the @p + * selected_dofs array to the back of the DoF numbers. The sorting is + * stable, i.e. the relative order within the tagged degrees of freedom is + * preserved, as is the relative order within the untagged ones. * - * @pre The @p selected_dofs - * array must have as many elements as - * the @p dof_handler has degrees of - * freedom. + * @pre The @p selected_dofs array must have as many elements as the @p + * dof_handler has degrees of freedom. */ template void @@ -1249,14 +1027,14 @@ namespace DoFRenumbering const std::vector &selected_dofs); /** - * Sort those degrees of freedom which are tagged with @p true in - * the @p selected_dofs array on the level @p level to the back of - * the DoF numbers. The sorting is stable, i.e. the relative order - * within the tagged degrees of freedom is preserved, as is the - * relative order within the untagged ones. + * Sort those degrees of freedom which are tagged with @p true in the @p + * selected_dofs array on the level @p level to the back of the DoF + * numbers. The sorting is stable, i.e. the relative order within the tagged + * degrees of freedom is preserved, as is the relative order within the + * untagged ones. * - * @pre The @p selected_dofs array must have as many elements as the - * @p dof_handler has degrees of freedom on the given level. + * @pre The @p selected_dofs array must have as many elements as the @p + * dof_handler has degrees of freedom on the given level. */ template void @@ -1265,18 +1043,12 @@ namespace DoFRenumbering const unsigned int level); /** - * Computes the renumbering - * vector needed by the - * sort_selected_dofs_back() - * function. Does not perform the - * renumbering on the DoFHandler - * dofs but returns the - * renumbering vector. + * Computes the renumbering vector needed by the sort_selected_dofs_back() + * function. Does not perform the renumbering on the DoFHandler dofs but + * returns the renumbering vector. * - * @pre The @p selected_dofs - * array must have as many elements as - * the @p dof_handler has degrees of - * freedom. + * @pre The @p selected_dofs array must have as many elements as the @p + * dof_handler has degrees of freedom. */ template void @@ -1285,19 +1057,12 @@ namespace DoFRenumbering const std::vector &selected_dofs); /** - * Computes the renumbering - * vector on each level - * needed by the - * sort_selected_dofs_back() - * function. Does not perform the - * renumbering on the MGDoFHandler - * dofs but returns the - * renumbering vector. + * Computes the renumbering vector on each level needed by the + * sort_selected_dofs_back() function. Does not perform the renumbering on + * the MGDoFHandler dofs but returns the renumbering vector. * - * @pre The @p selected_dofs - * array must have as many elements as - * the @p dof_handler has degrees of - * freedom on the given level. + * @pre The @p selected_dofs array must have as many elements as the @p + * dof_handler has degrees of freedom on the given level. */ template void @@ -1307,19 +1072,15 @@ namespace DoFRenumbering const unsigned int level); /** - * Renumber the degrees of - * freedom in a random way. + * Renumber the degrees of freedom in a random way. */ template void random (DH &dof_handler); /** - * Computes the renumbering - * vector needed by the random() - * function. Does not perform the - * renumbering on the DoFHandler - * dofs but returns the + * Computes the renumbering vector needed by the random() function. Does not + * perform the renumbering on the DoFHandler dofs but returns the * renumbering vector. */ template @@ -1337,38 +1098,21 @@ namespace DoFRenumbering */ /** - * Renumber the degrees of - * freedom such that they are - * associated with the subdomain - * id of the cells they are - * living on, i.e. first all - * degrees of freedom that belong - * to cells with subdomain zero, - * then all with subdomain one, - * etc. This is useful when doing - * parallel computations after - * assigning subdomain ids using - * a partitioner (see the - * GridTools::partition_triangulation - * function for this). + * Renumber the degrees of freedom such that they are associated with the + * subdomain id of the cells they are living on, i.e. first all degrees of + * freedom that belong to cells with subdomain zero, then all with subdomain + * one, etc. This is useful when doing parallel computations after assigning + * subdomain ids using a partitioner (see the + * GridTools::partition_triangulation function for this). * - * Note that degrees of freedom - * associated with faces, edges, - * and vertices may be associated - * with multiple subdomains if - * they are sitting on partition - * boundaries. It would therefore - * be undefined with which - * subdomain they have to be - * associated. For this, we use - * what we get from the - * DoFTools::get_subdomain_association - * function. + * Note that degrees of freedom associated with faces, edges, and vertices + * may be associated with multiple subdomains if they are sitting on + * partition boundaries. It would therefore be undefined with which + * subdomain they have to be associated. For this, we use what we get from + * the DoFTools::get_subdomain_association function. * - * The algorithm is stable, i.e. if - * two dofs i,j have i and belong - * to the same subdomain, then they - * will be in this order also after + * The algorithm is stable, i.e. if two dofs i,j have i and + * belong to the same subdomain, then they will be in this order also after * reordering. */ template @@ -1376,13 +1120,9 @@ namespace DoFRenumbering subdomain_wise (DH &dof_handler); /** - * Computes the renumbering - * vector needed by the - * subdomain_wise() - * function. Does not perform the - * renumbering on the @p - * DoFHandler dofs but returns - * the renumbering vector. + * Computes the renumbering vector needed by the subdomain_wise() + * function. Does not perform the renumbering on the @p DoFHandler dofs but + * returns the renumbering vector. */ template void diff --git a/deal.II/include/deal.II/grid/tria.h b/deal.II/include/deal.II/grid/tria.h index 315e325a41..a15b9b0e26 100644 --- a/deal.II/include/deal.II/grid/tria.h +++ b/deal.II/include/deal.II/grid/tria.h @@ -128,16 +128,18 @@ struct CellData types::boundary_id boundary_id; types::material_id material_id; }; - /** - * Manifold identificator of this - * object. This identificator - * should be used to identify the - * manifold to which this object - * belongs, and from which this - * object will collect information - * on how to add points upon - * refinement.*/ + /** + * Manifold identificator of this object. This identificator should + * be used to identify the manifold to which this object belongs, + * and from which this object will collect information on how to add + * points upon refinement.*/ types::manifold_id manifold_id; + + /** + * Default constructor. Sets the vertex indices to invalid values and the boundary or material + * id the default value (zero). + */ + CellData (); }; @@ -3323,6 +3325,19 @@ private: #ifndef DOXYGEN + +template +inline +CellData::CellData () +{ + for (unsigned int i=0; i::vertices_per_cell; ++i) + vertices[i] = numbers::invalid_unsigned_int; + + material_id = 0; +} + + + namespace internal { namespace Triangulation diff --git a/deal.II/include/deal.II/lac/block_sparse_matrix.h b/deal.II/include/deal.II/lac/block_sparse_matrix.h index e5f91ad22b..75d3c5811e 100644 --- a/deal.II/include/deal.II/lac/block_sparse_matrix.h +++ b/deal.II/include/deal.II/lac/block_sparse_matrix.h @@ -186,8 +186,11 @@ public: * sparsity patterns of the * parameter. * - * The elements of the matrix are - * set to zero by this function. + * You have to make sure that the lifetime of the sparsity structure is at + * least as long as that of this matrix or as long as reinit(const + * SparsityPattern &) is not called with a new sparsity structure. + * + * The elements of the matrix are set to zero by this function. */ virtual void reinit (const BlockSparsityPattern &sparsity); //@} diff --git a/deal.II/include/deal.II/lac/sparse_matrix.h b/deal.II/include/deal.II/lac/sparse_matrix.h index 79b71911ac..6f9519ae27 100644 --- a/deal.II/include/deal.II/lac/sparse_matrix.h +++ b/deal.II/include/deal.II/lac/sparse_matrix.h @@ -453,6 +453,10 @@ namespace SparseMatrixIterators } +/** + * @} + */ + //TODO: Add multithreading to the other vmult functions. @@ -1492,7 +1496,9 @@ public: * elements in a row are written in ascending column order. */ template - void print (STREAM &out, bool across=false, bool diagonal_first=true) const; + void print (STREAM &out, + const bool across = false, + const bool diagonal_first = true) const; /** * Print the matrix in the usual format, i.e. as a matrix and not as a list @@ -1653,10 +1659,6 @@ private: template friend class SparseMatrixIterators::Accessor; }; -/** - * @} - */ - #ifndef DOXYGEN /*---------------------- Inline functions -----------------------------------*/ @@ -2474,13 +2476,15 @@ SparseMatrix::end (const size_type r) template template inline -void SparseMatrix::print (STREAM &out, bool across, bool diagonal_first) const +void SparseMatrix::print (STREAM &out, + const bool across, + const bool diagonal_first) const { Assert (cols != 0, ExcNotInitialized()); Assert (val != 0, ExcNotInitialized()); bool hanging_diagonal = false; - number diagonal; + number diagonal = number(); for (size_type i=0; irows; ++i) { diff --git a/deal.II/source/CMakeLists.txt b/deal.II/source/CMakeLists.txt index c221f854c6..cabda8f8fd 100644 --- a/deal.II/source/CMakeLists.txt +++ b/deal.II/source/CMakeLists.txt @@ -49,6 +49,9 @@ ADD_SUBDIRECTORY(integrators) ADD_SUBDIRECTORY(matrix_free) ADD_SUBDIRECTORY(meshworker) +# A custom target to build the library: +ADD_CUSTOM_TARGET(build_library) + FOREACH(build ${DEAL_II_BUILD_TYPES}) STRING(TOLOWER ${build} build_lowercase) @@ -64,6 +67,7 @@ FOREACH(build ${DEAL_II_BUILD_TYPES}) ${deal_ii_objects_${build_lowercase}} ) + ADD_DEPENDENCIES(build_library ${DEAL_II_BASE_NAME}${DEAL_II_${_build}_SUFFIX}) ADD_DEPENDENCIES(library ${DEAL_II_BASE_NAME}${DEAL_II_${_build}_SUFFIX}) SET_TARGET_PROPERTIES(${DEAL_II_BASE_NAME}${DEAL_II_${build}_SUFFIX} diff --git a/deal.II/source/base/data_out_base.cc b/deal.II/source/base/data_out_base.cc index f1e611fc5d..b000b1435e 100644 --- a/deal.II/source/base/data_out_base.cc +++ b/deal.II/source/base/data_out_base.cc @@ -5629,6 +5629,16 @@ void DataOutBase::write_vtu_main (const std::vector > &patch AssertThrow (out, ExcIO()); } +template <> +void DataOutBase::write_svg<1,1> (const std::vector > &patches, + const std::vector &data_names, + const std::vector > &vector_data_ranges, + const SvgFlags &flags, + std::ostream &out) +{ + AssertThrow (false, ExcNotImplemented()); +} + template void DataOutBase::write_svg (const std::vector > &patches, @@ -5648,9 +5658,7 @@ void DataOutBase::write_svg (const std::vector > &patches, if (flags.margin) margin_in_percent = 5; -// determine the bounding box in the model space - double x_min, y_min, z_min; - double x_max, y_max, z_max; + // determine the bounding box in the model space double x_dimension, y_dimension, z_dimension; typename std::vector >::const_iterator patch = patches.begin(); @@ -5672,12 +5680,12 @@ void DataOutBase::write_svg (const std::vector > &patches, patch->data.n_rows() == 0, ExcIndexRange (flags.height_vector, 0, patch->data.n_rows())); - x_min = projected_point[0]; - x_max = x_min; - y_min = projected_point[1]; - y_max = y_min; - z_min = patch->data.n_rows() != 0 ? patch->data(flags.height_vector,0) : 0; - z_max = z_min; + double x_min = projected_point[0]; + double x_max = x_min; + double y_min = projected_point[1]; + double y_max = y_min; + double z_min = patch->data.n_rows() != 0 ? patch->data(flags.height_vector,0) : 0; + double z_max = z_min; // iterate over the patches for (; patch != patches.end(); ++patch) @@ -5757,9 +5765,9 @@ void DataOutBase::write_svg (const std::vector > &patches, camera_focus = .5 * z_dimension; - Point<3> camera_position_temp(true); - Point<3> camera_direction_temp(true); - Point<3> camera_horizontal_temp(true); + Point<3> camera_position_temp; + Point<3> camera_direction_temp; + Point<3> camera_horizontal_temp; const float angle_factor = 3.14159265 / 180.; diff --git a/deal.II/source/base/data_out_base.inst.in b/deal.II/source/base/data_out_base.inst.in index 96cc2fea22..28547f6d17 100644 --- a/deal.II/source/base/data_out_base.inst.in +++ b/deal.II/source/base/data_out_base.inst.in @@ -111,6 +111,8 @@ for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension : SPACE_DIMENSIONS const std::vector > &vector_data_ranges, const TecplotFlags &flags, std::ostream &out); + +#if deal_II_space_dimension >1 template void DataOutBase::write_svg (const std::vector > &patches, @@ -118,6 +120,7 @@ for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension : SPACE_DIMENSIONS const std::vector > &vector_data_ranges, const SvgFlags &flags, std::ostream &out); +#endif template void DataOutBase::write_deal_II_intermediate (const std::vector > &patches, diff --git a/deal.II/source/base/multithread_info.cc b/deal.II/source/base/multithread_info.cc index 6ea0b132a6..a3a92163de 100644 --- a/deal.II/source/base/multithread_info.cc +++ b/deal.II/source/base/multithread_info.cc @@ -26,8 +26,11 @@ # include #endif -#ifdef DEAL_II_WITH_THREADS +#if defined(__FreeBSD__) +# include +#endif +#ifdef DEAL_II_WITH_THREADS # include # include #endif diff --git a/deal.II/source/dofs/dof_renumbering.inst.in b/deal.II/source/dofs/dof_renumbering.inst.in index c8c1115558..d35eeb5dcd 100644 --- a/deal.II/source/dofs/dof_renumbering.inst.in +++ b/deal.II/source/dofs/dof_renumbering.inst.in @@ -204,7 +204,7 @@ namespace DoFRenumbering template void downstream > - (DoFHandler&, const Point&, + (DoFHandler&, const Point::space_dimension>&, const bool); template void @@ -240,13 +240,13 @@ namespace DoFRenumbering template void downstream > (hp::DoFHandler&, - const Point&, + const Point::space_dimension>&, const bool); template void downstream > (MGDoFHandler&, - const Point&, + const Point::space_dimension>&, const bool); template void @@ -281,7 +281,8 @@ namespace DoFRenumbering template void downstream - (DoFHandler&, const unsigned int, + (DoFHandler&, + const unsigned int, const Point&, const bool); diff --git a/deal.II/source/dummy.cc b/deal.II/source/dummy.cc index f7cb351468..dc760cd36b 100644 --- a/deal.II/source/dummy.cc +++ b/deal.II/source/dummy.cc @@ -21,5 +21,5 @@ * the generated Xcode project. */ -const int _global_symbol_42 = 42; +const int global_symbol_42 = 42; diff --git a/deal.II/source/lac/trilinos_sparse_matrix.cc b/deal.II/source/lac/trilinos_sparse_matrix.cc index dddb391a86..8423493505 100644 --- a/deal.II/source/lac/trilinos_sparse_matrix.cc +++ b/deal.II/source/lac/trilinos_sparse_matrix.cc @@ -1040,6 +1040,9 @@ namespace TrilinosWrappers const VectorBase &V, const bool transpose_left) { +#ifdef DEAL_II_USE_LARGE_INDEX_TYPE + Assert(false,ExcNotImplemented()) +#endif const bool use_vector = (V.size() == inputright.m() ? true : false); if (transpose_left == false) { @@ -1254,6 +1257,9 @@ namespace TrilinosWrappers const SparseMatrix &B, const VectorBase &V) const { +#ifdef DEAL_II_USE_LARGE_INDEX_TYPE + Assert(false,ExcNotImplemented()) +#endif internals::perform_mmult (*this, B, C, V, false); } @@ -1264,6 +1270,9 @@ namespace TrilinosWrappers const SparseMatrix &B, const VectorBase &V) const { +#ifdef DEAL_II_USE_LARGE_INDEX_TYPE + Assert(false,ExcNotImplemented()) +#endif internals::perform_mmult (*this, B, C, V, true); } diff --git a/deal.II/tests/CMakeLists.txt b/deal.II/tests/CMakeLists.txt index 23449544a1..d594c3c3d4 100644 --- a/deal.II/tests/CMakeLists.txt +++ b/deal.II/tests/CMakeLists.txt @@ -105,8 +105,8 @@ FOREACH(_category ${_categories}) ) ADD_DEPENDENCIES(setup_tests setup_tests_${_category}) - # depend on a valid build directory: - ADD_DEPENDENCIES(setup_tests_${_category} setup_build_dir) + # depend on a compiled library: + ADD_DEPENDENCIES(setup_tests_${_category} build_library) ADD_CUSTOM_TARGET(regen_tests_${_category} COMMAND [ ! -d ${_category} ] || ${CMAKE_COMMAND} diff --git a/deal.II/tests/mesh_converter/meshes/README.txt b/deal.II/tests/mesh_converter/meshes/README.txt new file mode 100644 index 0000000000..9bc70cb14b --- /dev/null +++ b/deal.II/tests/mesh_converter/meshes/README.txt @@ -0,0 +1,66 @@ +==================================================== +MESH CONVERSION TOOL +v. 1.2 + +Use: Convert an ABAQUS .inp file to an AVS UCD file. + +Author: Jean-Paul Pelteret + jppelteret.uct@gmail.com + modified by: Timo Heister, heister@clemson.edu +=================================================== + + +This tool is intended to support converting ABAQUS .inp files into a +format that deal.II can read. To use this tool, you need to configure +deal.II using the "-DDEAL_II_COMPONENT_MESH_CONVERTER=ON" argument +when calling 'cmake'. The resulting executable will then be placed in +the installation directory. + + + +Cubit features captured by ABAQUS .inp files: +--------------------------------------------- +1. Multiple material-id's can be defined in the mesh. This is done by specifying blocksets in the pre-processor. +2. Arbitrary surface boundaries can be defined in the mesh. This is done by specifying sidesets in the pre-processor. In particular, boundaries are not confined to just surfaces (in 3d) - individual element faces can be added to the sideset as well. This is useful when a boundary condition is to be applied on a complex shape boundary that is difficult to define using "surfaces" alone. Similar can be done in 2d. + +How to use: +----------- +1. It is necessary to save the mesh as an Abaqus input file .inp. In Cubit, this is done as follows: +1.1. Go to "Analysis setup mode" by clicking on the disc icon in the toolbar on the right. +1.2. Select "Export Mesh" under "Operation" by clicking on the necessary icon in the toolbar on the right. +1.3. Select an output file. I have found that in Cubit version 11.0 and 12.0 that it is necessary to click on the browse button and type it in the dialogue that pops up. +1.4. Select the dimension to output in. +1.5. Tick the overwrite box. +1.6. If using Cubit v12.0 onwards, uncheck the box "Export using Cubit ID's". The conversion process will encounter errors if box if left checked. +1.7. Click apply. + +2. Converting the mesh +IMPORTANT NOTE: From v12.0 onwards, the format of the Abaqus file that Cubit outputted changed. This has been accounted for but an requires a flag to be passed to the conversion program. + I describe outputs from before v12.0 as "Abaqus OLD" and v12.0 an on (up to v12.1 at this point) as "Abaqus NEW". +2.1. Compile the program using 'make' or another suitable tool +2.2. Run the program with the following command line arguments: + './convert_mesh /path/to/input_file.inp /path/to/output_file.ucd' + + The first input argument is the spatial dimension of the input file, the second is the path to the read-in Abaqus .inp file, and the third is the name of the file to which you wish to write the output AVS .ucd file to. + An example of the correct program usage is: +e.g. './convert_mesh 3 mesh/3d/test_in.inp mesh/3d/test_out.ucd' + + +Notes: +------ +1. A few example / test meshes are provided in the directory "mesh". The .inp files that have been generated are all of the Abaqus OLD format except for one - CC.cub has been converted into both the "new" and "old" formats and both subsequently converted into deal.II readable meshes. + +Copyright: +---------- +This program is distributed under the GNU GPL v2.0 copyright. Details can be found at: +http://www.gnu.org/licenses/gpl-2.0.html + +This copyright is extended to the example mesh files distributed with this program, namely +./mesh/2d/2d_test.* +./mesh/2d/quad.* +./mesh/3d/CC.* +./mesh/3d/CC_cubit_new.* +./mesh/3d/CC_cubit_old.* +./mesh/3d/test_cube_1.* +./mesh/3d/test_cube_pave_1.* +./mesh/3d/test_cube_two_materials.* diff --git a/deal.II/tests/quick_tests/CMakeLists.txt b/deal.II/tests/quick_tests/CMakeLists.txt index 57ef944d87..727911cb15 100644 --- a/deal.II/tests/quick_tests/CMakeLists.txt +++ b/deal.II/tests/quick_tests/CMakeLists.txt @@ -85,11 +85,21 @@ IF (DEAL_II_WITH_P4EST) make_quicktest("p4est" ${_mybuild} 10) ENDIF() +# Test petsc +IF (DEAL_II_WITH_PETSC) + make_quicktest("step-petsc" ${_mybuild} "") +ENDIF() + +# Test slepc +IF (DEAL_II_WITH_PETSC AND DEAL_II_WITH_SLEPC) + make_quicktest("step-slepc" ${_mybuild} "") +ENDIF() # A custom test target: ADD_CUSTOM_TARGET(test COMMAND ${CMAKE_CTEST_COMMAND} --force-new-ctest-process WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) +ADD_DEPENDENCIES(test build_library) MESSAGE(STATUS "Setup quick_tests in ${_mybuild} mode - Done") diff --git a/deal.II/tests/quick_tests/step-petsc.cc b/deal.II/tests/quick_tests/step-petsc.cc new file mode 100644 index 0000000000..9290f55a11 --- /dev/null +++ b/deal.II/tests/quick_tests/step-petsc.cc @@ -0,0 +1,220 @@ +/* --------------------------------------------------------------------- + * $Id: step-petsc.cc $ + * + * Copyright (C) 2013 by the deal.II authors + * + * This file is part of the deal.II library. + * + * The deal.II library is free software; you can use it, redistribute + * it, and/or modify it under the terms of the GNU Lesser General + * Public License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * The full text of the license can be found in the file LICENSE at + * the top level of the deal.II distribution. + * + * --------------------------------------------------------------------- + */ + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include + +using namespace dealii; + +// Test that deal.II is working with PETSc by solving the Laplace's +// problem in 2d. +class LaplaceProblem +{ +public: + LaplaceProblem (); + void run (); + +private: + void setup_system (); + void assemble_system (); + void solve (); + + Triangulation<2> triangulation; + FE_Q<2> fe; + DoFHandler<2> dof_handler; + + PETScWrappers::SparseMatrix A; + PETScWrappers::Vector b, x; + ConstraintMatrix constraints; + + TableHandler output_table; +}; + +LaplaceProblem::LaplaceProblem () + : + fe (1), + dof_handler (triangulation) +{} + +void LaplaceProblem::setup_system () +{ + dof_handler.distribute_dofs (fe); + + constraints.clear (); + DoFTools::make_zero_boundary_constraints (dof_handler, constraints); + constraints.close (); + + A.reinit (dof_handler.n_dofs(), dof_handler.n_dofs(), + dof_handler.max_couplings_between_dofs()); + b.reinit (dof_handler.n_dofs()); + x.reinit (dof_handler.n_dofs()); + + // some output + output_table.add_value ("cells", triangulation.n_active_cells()); + output_table.add_value ("dofs", dof_handler.n_dofs()); +} + +void LaplaceProblem::assemble_system () +{ + QGauss<2> quadrature_formula(2); + + FEValues<2> fe_values (fe, quadrature_formula, + update_values | + update_gradients | + update_quadrature_points | + update_JxW_values); + + const unsigned int dofs_per_cell = fe.dofs_per_cell; + const unsigned int n_q_points = quadrature_formula.size(); + + FullMatrix cell_A (dofs_per_cell, dofs_per_cell); + Vector cell_b (dofs_per_cell); + + std::vector local_dof_indices (dofs_per_cell); + + typename DoFHandler<2>::active_cell_iterator + cell = dof_handler.begin_active (), + endc = dof_handler.end (); + + for (; cell!=endc; ++cell) + { + fe_values.reinit (cell); + cell_A = 0; + cell_b = 0; + + for (unsigned int q_point=0; q_pointget_dof_indices (local_dof_indices); + + constraints.distribute_local_to_global (cell_A, local_dof_indices, A); + constraints.distribute_local_to_global (cell_b, local_dof_indices, b); + } + + A.compress (VectorOperation::add); + b.compress (VectorOperation::add); +} + +void LaplaceProblem::solve () +{ + SolverControl solver_control (1e03, 1e-03); + PETScWrappers::SolverCG cg_solver (solver_control); + PETScWrappers::PreconditionBlockJacobi preconditioner (A); + cg_solver.solve (A, x, b, preconditioner); + + // some output + // ? +} + +void LaplaceProblem::run () +{ + GridGenerator::hyper_cube (triangulation, -1, 1); + + for (unsigned int c=0; c<5; ++c) + { + triangulation.refine_global (1); + setup_system (); + assemble_system (); + solve (); + } + + // finialise output + output_table.write_text (std::cout); + deallog << std::endl; +} + + +int main (int argc, char **argv) +{ + try + { + dealii::Utilities::MPI::MPI_InitFinalize mpi_initialization (argc, argv, 1); + { + deallog.depth_console (0); + LaplaceProblem problem; + problem.run (); + deallog << "OK" << std::endl; + } + } + + catch (std::exception &exc) + { + std::cerr << std::endl << std::endl + << "----------------------------------------------------" + << std::endl; + std::cerr << "Exception on processing: " << std::endl + << exc.what() << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + + return 1; + } + catch (...) + { + std::cerr << std::endl << std::endl + << "----------------------------------------------------" + << std::endl; + std::cerr << "Unknown exception!" << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + return 1; + } + + return 0; +} diff --git a/deal.II/tests/quick_tests/step-slepc.cc b/deal.II/tests/quick_tests/step-slepc.cc new file mode 100644 index 0000000000..e0818b475e --- /dev/null +++ b/deal.II/tests/quick_tests/step-slepc.cc @@ -0,0 +1,239 @@ +/* --------------------------------------------------------------------- + * $Id$ + * + * Copyright (C) 2013 by the deal.II authors + * + * This file is part of the deal.II library. + * + * The deal.II library is free software; you can use it, redistribute + * it, and/or modify it under the terms of the GNU Lesser General + * Public License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * The full text of the license can be found in the file LICENSE at + * the top level of the deal.II distribution. + * + * --------------------------------------------------------------------- + */ + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include + +using namespace dealii; + +// Test that deal.II is working with SLEPc by solving the Laplace's +// eigenspectrum problem in 2d. +class LaplaceEigenspectrumProblem +{ +public: + LaplaceEigenspectrumProblem (); + void run (); + +private: + void setup_system (); + void assemble_system (); + void solve (); + + Triangulation<2> triangulation; + FE_Q<2> fe; + DoFHandler<2> dof_handler; + + PETScWrappers::SparseMatrix A, B; + std::vector x; + std::vector lambda; + ConstraintMatrix constraints; + + TableHandler output_table; +}; + +LaplaceEigenspectrumProblem::LaplaceEigenspectrumProblem () + : + fe (1), + dof_handler (triangulation) +{} + +void LaplaceEigenspectrumProblem::setup_system () +{ + dof_handler.distribute_dofs (fe); + + constraints.clear (); + DoFTools::make_zero_boundary_constraints (dof_handler, constraints); + constraints.close (); + + A.reinit (dof_handler.n_dofs(), dof_handler.n_dofs(), + dof_handler.max_couplings_between_dofs()); + B.reinit (dof_handler.n_dofs(), dof_handler.n_dofs(), + dof_handler.max_couplings_between_dofs()); + + x.resize (1); + x[0].reinit (dof_handler.n_dofs ()); + lambda.resize (1); + lambda[0] = 0.; + + // some output + output_table.add_value ("cells", triangulation.n_active_cells()); + output_table.add_value ("dofs", dof_handler.n_dofs()); +} + +void LaplaceEigenspectrumProblem::assemble_system () +{ + QGauss<2> quadrature_formula(2); + + FEValues<2> fe_values (fe, quadrature_formula, + update_values | + update_gradients | + update_quadrature_points | + update_JxW_values); + + const unsigned int dofs_per_cell = fe.dofs_per_cell; + const unsigned int n_q_points = quadrature_formula.size(); + + FullMatrix cell_A (dofs_per_cell, dofs_per_cell); + FullMatrix cell_B (dofs_per_cell, dofs_per_cell); + + std::vector local_dof_indices (dofs_per_cell); + + typename DoFHandler<2>::active_cell_iterator + cell = dof_handler.begin_active (), + endc = dof_handler.end (); + + for (; cell!=endc; ++cell) + { + fe_values.reinit (cell); + cell_A = 0; + cell_B = 0; + + for (unsigned int q_point=0; q_pointget_dof_indices (local_dof_indices); + + constraints.distribute_local_to_global (cell_A, local_dof_indices, A); + constraints.distribute_local_to_global (cell_B, local_dof_indices, B); + } + + A.compress (VectorOperation::add); + B.compress (VectorOperation::add); +} + +void LaplaceEigenspectrumProblem::solve () +{ + SolverControl solver_control (1000, 1e-03); + SLEPcWrappers::SolverArnoldi eigensolver (solver_control); + eigensolver.set_which_eigenpairs (EPS_SMALLEST_REAL); + eigensolver.solve (A, B, lambda, x, x.size()); + + // some output + output_table.add_value ("lambda", lambda[0]); + output_table.add_value ("error", std::fabs(2.-lambda[0])); +} + +void LaplaceEigenspectrumProblem::run () +{ + const double radius = dealii::numbers::PI/2.; + GridGenerator::hyper_cube (triangulation, -radius, radius); + + // set the old eigenvalue to a silly number. + double old_lambda = 1000; + + for (unsigned int c=0; c<5; ++c) + { + // obtain numerical result + triangulation.refine_global (1); + setup_system (); + assemble_system (); + solve (); + + // check energy convergence with previous result + AssertThrow (lambda[0]

Specific improvements

-Description of the C++ class hierarchy for the -accessor classes -

-What iterators and accessors are -

-The triangulation accessor hierarchy -

-Typedefs of the Triangulation class to iterators and accessors -

Functions offered by triangulation accessors

-The degree of freedom accessor hierarchy -

-Typedefs of the DoFHandler class to iterators and accessors -

Functions offered by degree of freedom accessors

-A short description of the new threading scheme -

1. Rationale and Introduction

2. Entities that describe threads

3. Entities that are used on the calling thread

4. Entities that are used to create a thread

5. Tool classes

a) The `return_value<T>` class template

b) The `call` function templates

c) `mem_fun_ptr`

d) `add_reference` for tuples

6. Open Problems

a) A variable lifetime problem

b) Forwarding of `operator()`

c) Using a memory based scheme rather than condition variables

7. Alternative Suggestions

a) Conversions between return values

b) Conversions between class types I

c) Conversions between class types II

d) Catching exceptions