From a430dd20bed58742f8e130f4a7c71e28d599e430 Mon Sep 17 00:00:00 2001 From: heltai Date: Wed, 4 Dec 2013 23:21:50 +0000 Subject: [PATCH] Merged from trunk. git-svn-id: https://svn.dealii.org/branches/branch_manifold_id@31889 0785d39b-7218-0410-832d-ea1e28bc413d --- deal.II/CMakeLists.txt | 8 +- deal.II/bundled/CMakeLists.txt | 60 +- deal.II/bundled/setup_bundled.cmake | 74 + deal.II/cmake/config/CMakeLists.txt | 4 + .../macro_deal_ii_invoke_autopilot.cmake | 83 +- deal.II/cmake/macros/macro_pickup_tests.cmake | 4 - deal.II/cmake/scripts/CMakeLists.txt | 52 +- deal.II/cmake/scripts/report_features.cc.in | 175 -- deal.II/cmake/scripts/run_testsuite.cmake | 1 - deal.II/cmake/setup_cached_variables.cmake | 13 + deal.II/cmake/setup_compiler_flags.cmake | 6 +- deal.II/cmake/setup_custom_targets.cmake | 107 +- deal.II/cmake/setup_finalize.cmake | 8 +- deal.II/cmake/setup_testsubproject.cmake | 4 +- deal.II/cmake/setup_testsuite.cmake | 3 +- deal.II/contrib/CMakeLists.txt | 4 + .../contrib/mesh_conversion/CMakeLists.txt | 12 +- deal.II/contrib/parameter_gui/CMakeLists.txt | 18 +- deal.II/contrib/utilities/build_test | 128 -- deal.II/doc/CMakeLists.txt | 11 +- deal.II/doc/documentation.html | 2 +- deal.II/doc/doxygen/CMakeLists.txt | 9 +- .../doc/doxygen/headers/coding_conventions.h | 6 +- deal.II/doc/doxygen/headers/main.h | 7 +- deal.II/doc/doxygen/headers/tutorial.h | 28 - deal.II/doc/doxygen/scripts/make_toc.pl | 32 - .../{mod_footer.pl => mod_footer.pl.in} | 2 +- .../{mod_header.pl => mod_header.pl.in} | 0 deal.II/doc/doxygen/scripts/steps.pl | 20 +- deal.II/doc/doxygen/stylesheet.css | 15 + deal.II/doc/doxygen/tutorial/CMakeLists.txt | 72 +- deal.II/doc/doxygen/tutorial/index.html | 29 - deal.II/doc/doxygen/tutorial/navbar.html | 121 -- deal.II/doc/doxygen/tutorial/title.html | 26 - deal.II/doc/doxygen/tutorial/toc-list.html | 330 ---- deal.II/doc/doxygen/tutorial/toc-topics.html | 640 ------- deal.II/doc/doxygen/tutorial/toc.html.in | 94 - deal.II/doc/doxygen/tutorial/tutorial.h.in | 959 ++++++++++ deal.II/doc/navbar.html | 2 +- deal.II/doc/news/changes.h | 31 + deal.II/doc/publications/index.html | 74 +- deal.II/doc/readme.html | 4 +- deal.II/doc/screen.css | 14 - deal.II/doc/users/cmake.html | 39 +- deal.II/doc/users/cmakelists.html | 1 - deal.II/doc/users/navbar.html | 2 +- deal.II/doc/users/toc.html | 2 +- deal.II/examples/CMakeLists.txt | 4 + deal.II/examples/step-18/step-18.cc | 11 + deal.II/examples/step-25/doc/intro.dox | 2 +- deal.II/examples/step-36/doc/intro.dox | 2 +- deal.II/examples/step-36/doc/tooltip | 2 +- deal.II/examples/step-37/doc/tooltip | 2 +- deal.II/examples/step-41/doc/intro.dox | 2 +- deal.II/examples/step-42/doc/intro.dox | 2 +- deal.II/examples/step-42/doc/results.dox | 2 +- deal.II/examples/step-48/doc/tooltip | 2 +- .../include/deal.II/base/function_parser.h | 4 +- .../include/deal.II/base/parsed_function.h | 7 +- deal.II/include/deal.II/distributed/tria.h | 9 +- deal.II/include/deal.II/fe/fe.h | 27 +- deal.II/include/deal.II/grid/grid_tools.h | 23 +- .../include/deal.II/lac/constraint_matrix.h | 1699 +++++++---------- .../deal.II/lac/constraint_matrix.templates.h | 957 +++++----- deal.II/include/deal.II/lac/parallel_vector.h | 8 +- deal.II/include/deal.II/lac/pointer_matrix.h | 2 +- .../deal.II/numerics/vector_tools.templates.h | 218 +-- deal.II/source/CMakeLists.txt | 4 + deal.II/source/grid/grid_tools.cc | 80 +- deal.II/source/grid/grid_tools.inst.in | 45 + 70 files changed, 2724 insertions(+), 3726 deletions(-) create mode 100644 deal.II/bundled/setup_bundled.cmake delete mode 100644 deal.II/cmake/scripts/report_features.cc.in delete mode 100755 deal.II/contrib/utilities/build_test delete mode 100644 deal.II/doc/doxygen/headers/tutorial.h delete mode 100644 deal.II/doc/doxygen/scripts/make_toc.pl rename deal.II/doc/doxygen/scripts/{mod_footer.pl => mod_footer.pl.in} (91%) rename deal.II/doc/doxygen/scripts/{mod_header.pl => mod_header.pl.in} (100%) delete mode 100644 deal.II/doc/doxygen/tutorial/index.html delete mode 100644 deal.II/doc/doxygen/tutorial/navbar.html delete mode 100644 deal.II/doc/doxygen/tutorial/title.html delete mode 100644 deal.II/doc/doxygen/tutorial/toc-list.html delete mode 100644 deal.II/doc/doxygen/tutorial/toc-topics.html delete mode 100644 deal.II/doc/doxygen/tutorial/toc.html.in create mode 100644 deal.II/doc/doxygen/tutorial/tutorial.h.in diff --git a/deal.II/CMakeLists.txt b/deal.II/CMakeLists.txt index 4caaebe4c8..8ae7818a1e 100644 --- a/deal.II/CMakeLists.txt +++ b/deal.II/CMakeLists.txt @@ -88,7 +88,13 @@ INCLUDE(setup_compiler_flags) # Include information about bundled libraries: # IF(DEAL_II_HAVE_BUNDLED_DIRECTORY) - INCLUDE(bundled/CMakeLists.txt) + FILE(GLOB _check_files "bundled/*.cmake") + LIST(SORT _check_files) + FOREACH(_file ${_check_files}) + MESSAGE(STATUS "") + MESSAGE(STATUS "Include ${_file}") + INCLUDE(${_file}) + ENDFOREACH() ENDIF() # diff --git a/deal.II/bundled/CMakeLists.txt b/deal.II/bundled/CMakeLists.txt index ff7abbe921..30e62c7d3f 100644 --- a/deal.II/bundled/CMakeLists.txt +++ b/deal.II/bundled/CMakeLists.txt @@ -15,19 +15,11 @@ ## --------------------------------------------------------------------- # -# Export information about bundled library locations and do the actual -# setup of compilation targets and installation here: +# Compile and install enabled bundled features: # +MESSAGE(STATUS "Setup bundled features") -# -# Boost C++ libraries -# -SET(FEATURE_BOOST_HAVE_BUNDLED TRUE) -OPTION(DEAL_II_FORCE_BUNDLED_BOOST - "Always use the bundled boost library instead of an external one." - OFF) -SET(BOOST_FOLDER "${CMAKE_SOURCE_DIR}/bundled/boost-1.49.0") IF(FEATURE_BOOST_BUNDLED_CONFIGURED) INSTALL(DIRECTORY ${BOOST_FOLDER}/include/boost @@ -35,13 +27,14 @@ IF(FEATURE_BOOST_BUNDLED_CONFIGURED) COMPONENT library PATTERN ".svn" EXCLUDE ) + FILE(APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/deal_ii_source_includes "${BOOST_FOLDER}/include\n" ) ADD_SUBDIRECTORY(${BOOST_FOLDER}/libs/serialization/src) - IF( DEAL_II_WITH_THREADS AND NOT DEAL_II_USE_CXX11) + IF(DEAL_II_WITH_THREADS AND NOT DEAL_II_USE_CXX11) # # If the C++ compiler doesn't completely support the C++11 standard # (and consequently we can't use std::thread, std::mutex, etc), then @@ -54,36 +47,11 @@ IF(FEATURE_BOOST_BUNDLED_CONFIGURED) ENDIF() -# -# FunctionParser project: -# -SET(FEATURE_FUNCTIONPARSER_HAVE_BUNDLED TRUE) -OPTION(DEAL_II_FORCE_BUNDLED_FUNCTIONPARSER - "Always use the bundled functionparser library instead of an external one." - OFF) -SET(FUNCTIONPARSER_FOLDER "${CMAKE_SOURCE_DIR}/bundled/functionparser/") - IF(FEATURE_FUNCTIONPARSER_BUNDLED_CONFIGURED) ADD_SUBDIRECTORY(${FUNCTIONPARSER_FOLDER}) ENDIF() -# -# Threading Building Blocks library -# -IF(NOT CMAKE_SYSTEM_NAME MATCHES "CYGWIN" - AND NOT CMAKE_SYSTEM_NAME MATCHES "Windows") - # - # Cygwin is unsupported by tbb, Windows due to the way we compile tbb... - # - SET(FEATURE_THREADS_HAVE_BUNDLED TRUE) - OPTION(DEAL_II_FORCE_BUNDLED_THREADS - "Always use the bundled tbb library instead of an external one." - OFF) - SET(TBB_FOLDER "${CMAKE_SOURCE_DIR}/bundled/tbb41_20130401oss") -ENDIF() - - IF(FEATURE_THREADS_BUNDLED_CONFIGURED) INSTALL(DIRECTORY ${TBB_FOLDER}/include/tbb DESTINATION ${DEAL_II_INCLUDE_RELDIR}/deal.II/bundled @@ -91,6 +59,7 @@ IF(FEATURE_THREADS_BUNDLED_CONFIGURED) FILES_MATCHING PATTERN "*.h" PATTERN ".svn" EXCLUDE ) + FILE(APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/deal_ii_source_includes "${TBB_FOLDER}/include\n" ) @@ -99,25 +68,10 @@ IF(FEATURE_THREADS_BUNDLED_CONFIGURED) ENDIF() -# -# UMFPACK, AMD and UFCONFIG: -# -SET(FEATURE_UMFPACK_HAVE_BUNDLED TRUE) -SET(UMFPACK_FOLDER "${CMAKE_SOURCE_DIR}/bundled/umfpack") -OPTION(DEAL_II_FORCE_BUNDLED_UMFPACK - "Always use the bundled umfpack library instead of an external one." - OFF) - -# -# Resolve a cache invalidation problem by searching for these flags -# unconditionally. They're used for compiling the sources in -# ${UMFPACK_FOLDER}/UMFPACK/Source depending on cached variables. -# -ENABLE_IF_SUPPORTED(_dummy "-Wno-sign-compare") -ENABLE_IF_SUPPORTED(_dummy "-Wno-write-strings") - IF(FEATURE_UMFPACK_BUNDLED_CONFIGURED) ADD_SUBDIRECTORY(${UMFPACK_FOLDER}/UMFPACK/Source) ADD_SUBDIRECTORY(${UMFPACK_FOLDER}/AMD/Source) ENDIF() + +MESSAGE(STATUS "Setup bundled features - Done") diff --git a/deal.II/bundled/setup_bundled.cmake b/deal.II/bundled/setup_bundled.cmake new file mode 100644 index 0000000000..42e1a592b8 --- /dev/null +++ b/deal.II/bundled/setup_bundled.cmake @@ -0,0 +1,74 @@ +## --------------------------------------------------------------------- +## $Id$ +## +## 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. +## +## --------------------------------------------------------------------- + +# +# Export information about bundled library locations and do the actual +# setup of compilation targets and installation here: +# + +# +# Boost C++ libraries +# + +SET(FEATURE_BOOST_HAVE_BUNDLED TRUE) + +OPTION(DEAL_II_FORCE_BUNDLED_BOOST + "Always use the bundled boost library instead of an external one." + OFF) + +SET(BOOST_FOLDER "${CMAKE_SOURCE_DIR}/bundled/boost-1.49.0") + +# +# FunctionParser project: +# + +SET(FEATURE_FUNCTIONPARSER_HAVE_BUNDLED TRUE) + +OPTION(DEAL_II_FORCE_BUNDLED_FUNCTIONPARSER + "Always use the bundled functionparser library instead of an external one." + OFF) + +SET(FUNCTIONPARSER_FOLDER "${CMAKE_SOURCE_DIR}/bundled/functionparser/") + +# +# Threading Building Blocks library +# + +IF( NOT CMAKE_SYSTEM_NAME MATCHES "CYGWIN" + AND NOT CMAKE_SYSTEM_NAME MATCHES "Windows" ) + # + # Cygwin is unsupported by tbb, Windows due to the way we compile tbb... + # + SET(FEATURE_THREADS_HAVE_BUNDLED TRUE) + + OPTION(DEAL_II_FORCE_BUNDLED_THREADS + "Always use the bundled tbb library instead of an external one." + OFF) + + SET(TBB_FOLDER "${CMAKE_SOURCE_DIR}/bundled/tbb41_20130401oss") +ENDIF() + +# +# UMFPACK, AMD and UFCONFIG: +# + +SET(FEATURE_UMFPACK_HAVE_BUNDLED TRUE) + +OPTION(DEAL_II_FORCE_BUNDLED_UMFPACK + "Always use the bundled umfpack library instead of an external one." + OFF) + +SET(UMFPACK_FOLDER "${CMAKE_SOURCE_DIR}/bundled/umfpack") diff --git a/deal.II/cmake/config/CMakeLists.txt b/deal.II/cmake/config/CMakeLists.txt index d6b3bb2a89..e499bafbee 100644 --- a/deal.II/cmake/config/CMakeLists.txt +++ b/deal.II/cmake/config/CMakeLists.txt @@ -26,6 +26,8 @@ # two distinct set ups. # +MESSAGE(STATUS "Setup project configuration") + # # Read in auxiliary include directories for the build directory # configuration: @@ -377,3 +379,5 @@ IF(DEAL_II_COMPONENT_COMPAT_FILES) COMPONENT compat_files ) ENDIF() + +MESSAGE(STATUS "Setup project configuration - Done") 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 c0207506c9..e8c8bd63a2 100644 --- a/deal.II/cmake/macros/macro_deal_ii_invoke_autopilot.cmake +++ b/deal.II/cmake/macros/macro_deal_ii_invoke_autopilot.cmake @@ -38,6 +38,17 @@ MACRO(DEAL_II_INVOKE_AUTOPILOT) + # Generator specific values: + IF(CMAKE_GENERATOR MATCHES "Ninja") + # + # Ninja doesn't like a redifinition of the "help" target, so use "info" + # in this case... + # + SET(_make_command "$ ninja") + ELSE() + SET(_make_command " $ make") + ENDIF() + # Define and setup a compilation target: ADD_EXECUTABLE(${TARGET} ${TARGET_SRC}) DEAL_II_SETUP_TARGET(${TARGET}) @@ -84,7 +95,7 @@ MACRO(DEAL_II_INVOKE_AUTOPILOT) COMMENT "Run ${TARGET} with ${CMAKE_BUILD_TYPE} configuration" ) SET(_run_targets - "# $ make run - to (compile, link and) run the program\n" + "# ${_make_command} run - to (compile, link and) run the program\n" ) ENDIF() @@ -122,7 +133,7 @@ MACRO(DEAL_II_INVOKE_AUTOPILOT) ENDIF() SET(_run_targets - "${_run_targets}#\n# $ make sign - to sign the executable with the supplied OSX developer key\n" + "${_run_targets}#\n# ${_make_command} sign - to sign the executable with the supplied OSX developer key\n" ) ENDIF() @@ -143,8 +154,8 @@ MACRO(DEAL_II_INVOKE_AUTOPILOT) # switch between them: IF(${DEAL_II_BUILD_TYPE} MATCHES "DebugRelease") SET(_switch_targets -"# $ make debug - to switch the build type to \"Debug\" -# $ make release - to switch the build type to \"Release\"\n" +"# ${_make_command} debug - to switch the build type to 'Debug' +# ${_make_command} release - to switch the build type to 'Release'\n" ) ENDIF() @@ -175,50 +186,78 @@ MACRO(DEAL_II_INVOKE_AUTOPILOT) ) ENDIF() + # Print out some usage information to file: FILE(WRITE ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/print_usage.cmake "MESSAGE( \"### # -# Successfully set up project ${TARGET} with ${DEAL_II_PACKAGE_NAME}-${DEAL_II_PACKAGE_VERSION} found at +# Project ${TARGET} set up with ${DEAL_II_PACKAGE_NAME}-${DEAL_II_PACKAGE_VERSION} found at # ${DEAL_II_PATH} # -# CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE} +# CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE} # # You can now run -# $ make - to compile and link the program +# ${_make_command} - to compile and link the program ${_run_targets}# ${_switch_targets}# -# $ make edit_cache - to change (cached) configuration variables -# and rerun the configure and generate phases of CMake -# -# $ 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 -# $ make runclean - to remove all output generated by the program -# $ make distclean - to clean the directory from _all_ generated -# files (includes clean, runclean and the removal -# of the generated build system) +") + IF(NOT CMAKE_GENERATOR MATCHES "Ninja") + FILE(APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/print_usage.cmake +"# ${_make_command} edit_cache - to change (cached) configuration variables +# and rerun the configure and generate phases of CMake # -# $ make help - to view this message again +") + ENDIF() + FILE(APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/print_usage.cmake +"# ${_make_command} strip_comments - to strip the source files in this +# directory off the documentation comments +# ${_make_command} clean - to remove the generated executable as well as +# all intermediate compilation files +# ${_make_command} runclean - to remove all output generated by the program +# ${_make_command} distclean - to clean the directory from _all_ generated +# files (includes clean, runclean and the removal +# of the generated build system) # +" + ) + IF(CMAKE_GENERATOR MATCHES "Ninja") + FILE(APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/print_usage.cmake +"# $ ninja info - to view this message again +" + ) + ELSE() + FILE(APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/print_usage.cmake +"# $ make help - to view this message again +" ) + ENDIF() + FILE(APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/print_usage.cmake +"# # Have a nice day! # ###\")" - ) + ) # A custom target to print the message: - ADD_CUSTOM_TARGET(help + ADD_CUSTOM_TARGET(info COMMAND ${CMAKE_COMMAND} -P ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/print_usage.cmake ) + IF(NOT CMAKE_GENERATOR MATCHES "Ninja") + ADD_CUSTOM_TARGET(help + COMMAND ${CMAKE_COMMAND} -P ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/print_usage.cmake + ) + ENDIF() # Print this message once: IF(NOT USAGE_PRINTED) INCLUDE(${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/print_usage.cmake) SET(USAGE_PRINTED TRUE CACHE INTERNAL "") ELSE() - MESSAGE(STATUS "Run $ make help to print a detailed help message") + IF(CMAKE_GENERATOR MATCHES "Ninja") + MESSAGE(STATUS "Run $ ninja info to print a detailed help message") + ELSE() + MESSAGE(STATUS "Run $ make help to print a detailed help message") + ENDIF() ENDIF() ENDMACRO() diff --git a/deal.II/cmake/macros/macro_pickup_tests.cmake b/deal.II/cmake/macros/macro_pickup_tests.cmake index 69a3950b97..4c702545f3 100644 --- a/deal.II/cmake/macros/macro_pickup_tests.cmake +++ b/deal.II/cmake/macros/macro_pickup_tests.cmake @@ -20,10 +20,6 @@ # If TEST_PICKUP_REGEX is set, only tests matching the regex will be # processed. # -# If TEST_OVERRIDE_LOCATION is set, a comparison file category/test.output -# will be substituted by ${TEST_OVERRIDE_LOCATION}/category/test.output if -# the latter exists. -# # Usage: # DEAL_II_PICKUP_TESTS() # diff --git a/deal.II/cmake/scripts/CMakeLists.txt b/deal.II/cmake/scripts/CMakeLists.txt index 82e0bb4eff..8c38f883de 100644 --- a/deal.II/cmake/scripts/CMakeLists.txt +++ b/deal.II/cmake/scripts/CMakeLists.txt @@ -20,67 +20,25 @@ SET_TARGET_PROPERTIES(expand_instantiations_exe ) IF(DEAL_II_COMPONENT_COMPAT_FILES) + MESSAGE(STATUS "Setup compat_files") # - # Build and install the old dependency_resolution and report_features - # executables: + # Also build and install the old dependency_resolution executable: # - INCLUDE_DIRECTORIES( - BEFORE # Ensure deal.II include directories come first - # - # Reverse order due to BEFORE: - # - ${CMAKE_SOURCE_DIR}/include/ - ${CMAKE_BINARY_DIR}/include/ - ) - ADD_EXECUTABLE(make_dependencies make_dependencies.cc) - IF(BUILD_SHARED_LIBS) - SET(_shared_libs "true") - ELSE() - SET(_shared_libs "false") - ENDIF() - CONFIGURE_FILE( - ${CMAKE_CURRENT_SOURCE_DIR}/report_features.cc.in - ${CMAKE_CURRENT_BINARY_DIR}/report_features.cc - ) - - ADD_EXECUTABLE(report_features - ${CMAKE_CURRENT_BINARY_DIR}/report_features.cc - ) - - # - # Link report_features in the same way as the library/final executable: - # - TARGET_LINK_LIBRARIES(report_features ${DEAL_II_EXTERNAL_LIBRARIES}) - SET_TARGET_PROPERTIES(report_features - PROPERTIES - LINK_FLAGS "${DEAL_II_LINKER_FLAGS}" - COMPILE_DEFINITIONS "${DEAL_II_DEFINITIONS}" - ) - IF(DEAL_II_STATIC_EXECUTABLE) - SET_PROPERTY(TARGET report_features PROPERTY - LINK_SEARCH_END_STATIC TRUE - ) - ENDIF() - - IF(NOT CMAKE_CROSSCOMPILING) - ADD_CUSTOM_TARGET(run_report_features COMMAND report_features) - ENDIF() - ADD_DEPENDENCIES(compat_files expand_instantiations_exe make_dependencies - report_features ) - SET_TARGET_PROPERTIES(expand_instantiations_exe make_dependencies report_features + SET_TARGET_PROPERTIES(expand_instantiations_exe make_dependencies PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/${DEAL_II_COMMON_RELDIR}/scripts ) - INSTALL(TARGETS expand_instantiations_exe make_dependencies report_features + INSTALL(TARGETS expand_instantiations_exe make_dependencies DESTINATION ${DEAL_II_COMMON_RELDIR}/scripts COMPONENT compat_files ) + MESSAGE(STATUS "Setup compat_files - Done") ENDIF() diff --git a/deal.II/cmake/scripts/report_features.cc.in b/deal.II/cmake/scripts/report_features.cc.in deleted file mode 100644 index 457d226e04..0000000000 --- a/deal.II/cmake/scripts/report_features.cc.in +++ /dev/null @@ -1,175 +0,0 @@ -// --------------------------------------------------------------------- -// $Id$ -// -// Copyright (C) 2010 - 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 - -#ifdef DEAL_II_WITH_UMFPACK -extern "C" { -#include -} -#endif - -#if defined(DEAL_II_WITH_MPI) -#include -#endif - -#ifdef DEAL_II_WITH_TRILINOS -# include -#endif - -#ifdef DEAL_II_WITH_MUMPS -# include -# include -#endif - -#ifdef DEAL_II_WITH_PETSC -# include -#endif - -#ifdef DEAL_II_WITH_SLEPC -# include -#endif - -// Output configuration options from config.h. -// The format of each line is -// -// deal-feature: FEATURE=value -// -// no spaces in any token! - -int main() -{ - std::cout << "dealii-feature: target=" - << "@CMAKE_SYSTEM_NAME@" << std::endl; - std::cout << "dealii-feature: compiler=" - << "@CMAKE_CXX_COMPILER_ID@@CMAKE_CXX_COMPILER_VERSION@" - << std::endl; - if(${_shared_libs}) - std::cout << "dealii-feature: shared_libs=yes" << std::endl; - else - std::cout << "dealii-feature: shared_libs=no" << std::endl; - -#ifdef DEAL_II_WITH_ARPACK - std::cout << "dealii-feature: ARPACK=yes" << std::endl; -#endif - -std::cout << "dealii-feature: BOOST=" - << BOOST_VERSION / 100000 << "." - << BOOST_VERSION / 100 % 1000 - << std::endl; - -#ifdef DEAL_II_WITH_FUNCTIONPARSER - std::cout << "dealii-feature: parser=yes" << std::endl; -#else - std::cout << "dealii-feature: parser=no" << std::endl; -#endif - -#ifdef DEAL_II_WITH_HDF5 - std::cout << "dealii-feature: HDF5=yes" << std::endl; -#endif - -#ifdef DEAL_II_WITH_LAPACK - std::cout << "dealii-feature: BLAS=yes" << std::endl; - std::cout << "dealii-feature: LAPACK=yes" << std::endl; -#endif - -#ifdef DEAL_II_WITH_METIS - std::cout << "dealii-feature: METIS=yes" << std::endl; -#endif - -#if defined(DEAL_II_WITH_MPI) -# ifdef OMPI_MAJOR_VERSION - std::cout << "dealii-feature: MPI=OpenMPI-" - << OMPI_MAJOR_VERSION << '.' - << OMPI_MINOR_VERSION << '.' - << OMPI_RELEASE_VERSION << std::endl; -# else - std::cout << "dealii-feature: MPI=" - << MPI_VERSION << '.' - << MPI_SUBVERSION << std::endl; -# endif -#endif - -#ifdef DEAL_II_WITH_MUMPS - std::cout << "dealii-feature: MUMPS=yes" << std::endl; -#endif - -#ifdef DEAL_II_WITH_P4EST - std::cout << "dealii-feature: P4est=yes" << std::endl; -#endif - -#ifdef DEAL_II_WITH_PETSC - std::cout << "dealii-feature: PETSc=" - << PETSC_VERSION_MAJOR << '.' - << PETSC_VERSION_MINOR << '.' - << PETSC_VERSION_SUBMINOR << "-p" - << PETSC_VERSION_PATCH << std::endl; -#endif - -#ifdef DEAL_II_WITH_SLEPC - std::cout << "dealii-feature: SLEPc=" - << SLEPC_VERSION_MAJOR << '.' - << SLEPC_VERSION_MINOR << '.' - << SLEPC_VERSION_SUBMINOR << "-p" - << SLEPC_VERSION_PATCH << std::endl; -#endif - -#ifdef DEAL_II_WITH_NETCDF - std::cout << "dealii-feature: NetCDF=yes" << std::endl; -#endif - -#ifdef DEAL_II_WITH_TECPLOT - std::cout << "dealii-feature: Tecplot=yes" << std::endl; -#endif - -#ifdef DEAL_II_WITH_THREADS - std::cout << "dealii-feature: multithreading=yes" << std::endl; -#else - std::cout << "dealii-feature: multithreading=no" << std::endl; -#endif - -#ifdef DEAL_II_WITH_TRILINOS -# ifdef TRILINOS_VERSION_STRING - std::cout << "dealii-feature: Trilinos=" << TRILINOS_VERSION_STRING << std::endl; -# else - const unsigned int trilinos_subminor = TRILINOS_MAJOR_MINOR_VERSION % 100; - const unsigned int trilinos_minor = (TRILINOS_MAJOR_MINOR_VERSION/100) % 100; - std::cout << "dealii-feature: Trilinos=" - << TRILINOS_MAJOR_VERSION << '.' - << trilinos_minor << '.' - << trilinos_subminor << std::endl; -# endif -#endif - -#ifdef DEAL_II_WITH_UMFPACK - std::cout << "dealii-feature: UMFPACK=" - << UMFPACK_MAIN_VERSION << '.' - << UMFPACK_SUB_VERSION << '.' - << UMFPACK_SUBSUB_VERSION << std::endl; -#endif - -#ifdef DEAL_II_WITH_ZLIB - std::cout << "dealii-feature: LibZ=yes" << std::endl; -#endif - -#ifdef DEAL_II_WITH_64BIT_INDICES - std::cout << "dealii-feature: 64bit_indices=yes" <): +# The following targets are available (invoke by $ ${_make_command} ): # -# all - compiles the library and all enabled components -# clean - removes all generated files -# install - installs into CMAKE_INSTALL_PREFIX -# help - prints a list of valid top level targets -# info - prints this help message +# all - compile the library and all enabled components +# clean - remove all generated files +# install - install into CMAKE_INSTALL_PREFIX +") + +IF(CMAKE_GENERATOR MATCHES "Ninja") + FILE(APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/print_info.cmake +"# info - print this help message +# help - print a list of valid top level targets +# +") +ELSE() + FILE(APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/print_info.cmake +"# help - print this help message in the toplevel directory, +# otherwise print a list of targets (in subdirectories) # -# edit_cache - runs ccmake for changing (cached) configuration variables +") +ENDIF() + +FILE(APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/print_info.cmake +"# edit_cache - run ccmake for changing (cached) configuration variables # and reruns the configure and generate phases of CMake -# rebuild_cache - reruns the configure and generate phases of CMake +# rebuild_cache - rerun the configure and generate phases of CMake # -# compat_files - builds and installs the 'compat_files' component -# documentation - builds and installs the 'documentation' component -# examples - builds and installs the 'examples' component -# library - builds and installs the 'library' component -# mesh_converter - builds and installs the 'mesh_converter' component -# parameter_gui - builds and installs the 'parameter_gui' component +# compat_files - ${_description_string} component 'compat_files' +# documentation - ${_description_string} component 'documentation' +# examples - ${_description_string} component 'examples' +# library - ${_description_string} component 'library' +# mesh_converter - ${_description_string} component 'mesh_converter' +# parameter_gui - ${_description_string} component 'parameter_gui' # -# test - runs a minimal set of tests +# test - run a minimal set of tests # -# setup_tests - sets up the testsuite subprojects +# setup_tests - set up the testsuite subprojects # regen_tests - rerun configure stage in every testsuite subprojects -# clean_tests - runs the 'clean' target in every testsuite subproject -# prune_tests - removes all testsuite subprojects +# clean_tests - run the 'clean' target in every testsuite subproject +# prune_tests - remove all testsuite subprojects # ###\")" ) + ADD_CUSTOM_TARGET(info COMMAND ${CMAKE_COMMAND} -P ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/print_info.cmake ) +IF(NOT CMAKE_GENERATOR MATCHES "Ninja") + ADD_CUSTOM_TARGET(help + COMMAND ${CMAKE_COMMAND} -P ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/print_info.cmake + ) +ENDIF() diff --git a/deal.II/cmake/setup_finalize.cmake b/deal.II/cmake/setup_finalize.cmake index cb01181acf..45ed9f36a5 100644 --- a/deal.II/cmake/setup_finalize.cmake +++ b/deal.II/cmake/setup_finalize.cmake @@ -274,8 +274,14 @@ ENDFOREACH() _summary( "#\n# Detailed information (compiler flags, feature configuration) can be found in detailed.log -#\n# Run $ make info to print a help message with a list of top level targets\n" +#\n# Run $ " ) +IF(CMAKE_GENERATOR MATCHES "Ninja") + _summary("ninja info") +ELSE() +_summary("make help") +ENDIF() +_summary(" to print a help message with a list of top level targets\n") _both("#\n###") diff --git a/deal.II/cmake/setup_testsubproject.cmake b/deal.II/cmake/setup_testsubproject.cmake index e40a167517..b1bd6bf6ee 100644 --- a/deal.II/cmake/setup_testsubproject.cmake +++ b/deal.II/cmake/setup_testsubproject.cmake @@ -29,7 +29,6 @@ # environment or command line: # # TEST_DIFF -# TEST_OVERRIDE_LOCATION # TEST_PICKUP_REGEX # TEST_TIME_LIMIT # @@ -51,14 +50,13 @@ FOREACH(_var TEST_DIFF TEST_TIME_LIMIT TEST_PICKUP_REGEX - TEST_OVERRIDE_LOCATION ) # Environment wins: IF(DEFINED ENV{${_var}}) SET(${_var} $ENV{${_var}}) ENDIF() IF(NOT "${_var}" STREQUAL "") - SET(${_var} "${${_var}}" CACHE STRING "") + SET(${_var} "${${_var}}" CACHE STRING "" FORCE) ENDIF() ENDFOREACH() diff --git a/deal.II/cmake/setup_testsuite.cmake b/deal.II/cmake/setup_testsuite.cmake index 9dc9756a74..98580373d0 100644 --- a/deal.II/cmake/setup_testsuite.cmake +++ b/deal.II/cmake/setup_testsuite.cmake @@ -91,8 +91,7 @@ SET(_options) LIST(APPEND _options -DDEAL_II_SOURCE_DIR=${CMAKE_SOURCE_DIR}) LIST(APPEND _options -DDEAL_II_BINARY_DIR=${CMAKE_BINARY_DIR}) FOREACH(_var - DIFF_DIR NUMDIFF_DIR TEST_DIFF TEST_OVERRIDE_LOCATION TEST_PICKUP_REGEX - TEST_TIME_LIMIT + DIFF_DIR NUMDIFF_DIR TEST_DIFF TEST_PICKUP_REGEX TEST_TIME_LIMIT ) # always undefine: LIST(APPEND _options "-U${_var}") diff --git a/deal.II/contrib/CMakeLists.txt b/deal.II/contrib/CMakeLists.txt index 6e92950efa..0be39e772a 100644 --- a/deal.II/contrib/CMakeLists.txt +++ b/deal.II/contrib/CMakeLists.txt @@ -15,10 +15,14 @@ ## --------------------------------------------------------------------- IF(DEAL_II_COMPONENT_MESH_CONVERTER) + MESSAGE(STATUS "Setup mesh_converter") ADD_SUBDIRECTORY(mesh_conversion) + MESSAGE(STATUS "Setup mesh_converter - Done") ENDIF() IF(DEAL_II_COMPONENT_PARAMETER_GUI) + MESSAGE(STATUS "Setup parameter_gui") ADD_SUBDIRECTORY(parameter_gui) + MESSAGE(STATUS "Setup parameter_gui - Done") ENDIF() diff --git a/deal.II/contrib/mesh_conversion/CMakeLists.txt b/deal.II/contrib/mesh_conversion/CMakeLists.txt index 387797f3e1..6a0f4d5693 100644 --- a/deal.II/contrib/mesh_conversion/CMakeLists.txt +++ b/deal.II/contrib/mesh_conversion/CMakeLists.txt @@ -17,20 +17,22 @@ CMAKE_MINIMUM_REQUIRED(VERSION 2.8) #PROJECT(mesh_converter) +IF("${DEAL_II_EXECUTABLE_RELDIR}" STREQUAL "") + SET(DEAL_II_EXECUTABLE_RELDIR "bin") +ENDIF() + ADD_EXECUTABLE(mesh_converter_exe Main.cc MeshConversion.cc ) SET_TARGET_PROPERTIES(mesh_converter_exe - PROPERTIES OUTPUT_NAME mesh_converter + PROPERTIES + OUTPUT_NAME mesh_converter + RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/${DEAL_II_EXECUTABLE_RELDIR}" ) ADD_DEPENDENCIES(mesh_converter mesh_converter_exe) -IF("${DEAL_II_EXECUTABLE_RELDIR}" STREQUAL "") - SET(DEAL_II_EXECUTABLE_RELDIR "bin") -ENDIF() - INSTALL(TARGETS mesh_converter_exe RUNTIME DESTINATION ${DEAL_II_EXECUTABLE_RELDIR} COMPONENT mesh_converter diff --git a/deal.II/contrib/parameter_gui/CMakeLists.txt b/deal.II/contrib/parameter_gui/CMakeLists.txt index b0350b59e0..8c7687b23d 100644 --- a/deal.II/contrib/parameter_gui/CMakeLists.txt +++ b/deal.II/contrib/parameter_gui/CMakeLists.txt @@ -17,6 +17,10 @@ CMAKE_MINIMUM_REQUIRED(VERSION 2.8) #PROJECT(parameter_gui) +IF("${DEAL_II_EXECUTABLE_RELDIR}" STREQUAL "") + SET(DEAL_II_EXECUTABLE_RELDIR "bin") +ENDIF() + FIND_PACKAGE(Qt4 REQUIRED QtCore QtGui QtXml) MARK_AS_ADVANCED(QT_QMAKE_EXECUTABLE) @@ -46,21 +50,21 @@ ADD_EXECUTABLE(parameter_gui_exe ${SOURCE_MOC} ${SOURCE_RCC} ) -SET_TARGET_PROPERTIES(parameter_gui_exe PROPERTIES OUTPUT_NAME parameter_gui) +SET_TARGET_PROPERTIES(parameter_gui_exe + PROPERTIES + OUTPUT_NAME parameter_gui + RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/${DEAL_II_EXECUTABLE_RELDIR}" + ) TARGET_LINK_LIBRARIES(parameter_gui_exe ${QT_LIBRARIES}) ADD_DEPENDENCIES(parameter_gui parameter_gui_exe) -IF("${DEAL_II_EXECUTABLE_RELDIR}" STREQUAL "") - SET(DEAL_II_EXECUTABLE_RELDIR "bin") -ENDIF() - INSTALL(TARGETS parameter_gui_exe RUNTIME DESTINATION ${DEAL_II_EXECUTABLE_RELDIR} COMPONENT parameter_gui ) EXPORT(TARGETS parameter_gui_exe - FILE ${CMAKE_BINARY_DIR}/${DEAL_II_PROJECT_CONFIG_RELDIR}/${DEAL_II_PROJECT_CONFIG_NAME}Targets.cmake + FILE + ${CMAKE_BINARY_DIR}/${DEAL_II_PROJECT_CONFIG_RELDIR}/${DEAL_II_PROJECT_CONFIG_NAME}Targets.cmake APPEND ) - diff --git a/deal.II/contrib/utilities/build_test b/deal.II/contrib/utilities/build_test deleted file mode 100755 index 49893db116..0000000000 --- a/deal.II/contrib/utilities/build_test +++ /dev/null @@ -1,128 +0,0 @@ -#!/usr/bin/make -f -## --------------------------------------------------------------------- -## $Id$ -## -## Copyright (C) 2012 - 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 build_test for deal.II -# -# Usage: Invoke this script either in a source directory or with $SOURCEDIR -# set -# -# The following environment variables may be set: -# -# SOURCEDIR - the source directory to use (if not invoked in a source -# directory) -# CONFIGFILE - A cmake configuration file for the build test -# LOGDIR - directory for the log file -# LOGFILE - the logfile to use, defaults to -# $LOGDIR/$CONFIGFILE..log -# -# CMAKE - the cmake executable to use -# SVN - svn info command to use -# TMPDIR - defaults to "/tmp" -# CLEAN_TMPDIR - defaults to "true" -# RUN_EXAMPLES - defaults to "true" -# - -# -# Specify default values: -# -SOURCEDIR=$(CURDIR) -LOGDIR=$(PWD) -TMPDIR?=/tmp -CMAKE=cmake -SVN=svn info $(SOURCEDIR) - -branch:=$(shell $(SVN) | perl -ne 'print "$$1" if m/svn\.dealii\.org.*\/(.+?)\/deal.II/;') -revision:=$(shell $(SVN) | perl -ne 'print "$$_" if s/Last Changed Rev: //;') - -date:= $(shell date +%s) -random:=$(shell echo "$$RANDOM") -testdir:= "$(TMPDIR)"/deal-build-test.$(date)-$(random) -builddir:= $(testdir)/build -installdir:= $(testdir)/install -LOGFILE=$(LOGDIR)/$(firstword $(branch) unknown_branch).$(firstword $(notdir $(CONFIGFILE)) no_configuration).$(date).log -CLEAN_TMPDIR=true -RUN_EXAMPLES=true - -PIPEnTRAP:= >>$(LOGFILE) 2>&1 || (if ${CLEAN_TMPDIR}; then rm -rf $(testdir); fi; false) - -.PHONY: main -main: - @if test ! -f $(SOURCEDIR)/CMakeLists.txt; then echo "ERROR: $(SOURCEDIR) doesn't seem to be a top-level source directory"; false; fi - mkdir -p $(LOGDIR) - mkdir -p $(builddir) - mkdir -p $(installdir) - @echo "AUTOMATED DEAL.II BUILD TEST" | tee $(LOGFILE) - @echo "BEGIN HEADER `date -u '+%Y-%m-%d %T'`" | tee -a $(LOGFILE) - @echo "dealii-feature: branch=$(branch)" | tee -a $(LOGFILE) - @echo "dealii-feature: revision=$(revision)" | tee -a $(LOGFILE) - @echo "dealii-feature: user=$(USER)" | tee -a $(LOGFILE) - @echo "dealii-feature: host=`hostname`" | tee -a $(LOGFILE) - @echo "dealii-feature: configuration=`basename \"$(CONFIGFILE)\"`" | tee -a $(LOGFILE) - @echo END HEADER `date -u '+%Y-%m-%d %T'`\n | tee -a $(LOGFILE) - @echo "BEGIN CONFIGURE OUTPUT `date -u '+%Y-%m-%d %T'`" | tee -a $(LOGFILE) - cd $(builddir) && $(CMAKE) -C "$(CONFIGFILE)" -DCMAKE_INSTALL_PREFIX=$(installdir) $(SOURCEDIR) $(PIPEnTRAP) - @echo "END CONFIGURE OUTPUT `date -u '+%Y-%m-%d %T'`" | tee -a $(LOGFILE) - @echo "BEGIN REPORT FEATURES `date -u '+%Y-%m-%d %T'`" | tee -a $(LOGFILE) - cd $(builddir) && make $(MAKEOPTS) run_report_features $(PIPEnTRAP) - @echo "END REPORT FEATURES `date -u '+%Y-%m-%d %T'`" | tee -a $(LOGFILE) - @echo "BEGIN BUILD INSTALL OUTPUT `date -u '+%Y-%m-%d %T'`" | tee -a $(LOGFILE) - cd $(builddir) && make $(MAKEOPTS) install $(PIPEnTRAP) - @echo "END BUILD INSTALL OUTPUT `date -u '+%Y-%m-%d %T'`" | tee -a $(LOGFILE) - @echo "BEGIN BUILD EXAMPLES OUTPUT `date -u '+%Y-%m-%d %T'`" | tee -a $(LOGFILE) - cd $(installdir)/examples && make -f $(SOURCEDIR)/contrib/utilities/build_test DEAL_II_DIR=$(installdir) build_examples $(PIPEnTRAP) - @echo "END BUILD EXAMPLES OUTPUT `date -u '+%Y-%m-%d %T'`" | tee -a $(LOGFILE) - @echo "BEGIN RUN EXAMPLES OUTPUT `date -u '+%Y-%m-%d %T'`" | tee -a $(LOGFILE) - cd $(installdir)/examples && make -f $(SOURCEDIR)/contrib/utilities/build_test run_examples $(PIPEnTRAP) - @echo "END RUN EXAMPLES OUTPUT `date -u '+%Y-%m-%d %T'`" | tee -a $(LOGFILE) - @echo "BUILD TEST SUCCESSFUL `date -u '+%Y-%m-%d %T'`" | tee -a $(LOGFILE) - if ${CLEAN_TMPDIR}; then rm -rf $(testdir); fi - - -# -# Recipes used for testing the example steps -# - -steps:= $(wildcard step-*) - -%/%: - -cd $(@D) && $(CMAKE) . >/dev/null 2>&1 - cd $(@D) && if [ -f Makefile ]; then make; fi - -.PHONY: build_examples -build_examples: $(steps:%=%/%) - - -# Run a minimalistic set of steps in debug configuration: -runsteps_debug:= step-1 step-2 step-3 step-4 step-5 step-6 step-47 - -# Run all configuration independent steps in release configuration: -runsteps_release= step-1 step-2 step-3 step-4 step-5 step-6 step-7 step-8 step-9 step-10 step-11 step-12 step-13 step-14 step-16 step-20 step-23 step-25 step-26 step-27 step-28 step-30 step-38 step-39 step-44 step-45 step-47 step-48 step-49 -# step-15 step-21 step-24 - - -%/OK_DEBUG: - cd $(@D) && $(CMAKE) -DCMAKE_BUILD_TYPE=Debug . >/dev/null 2>&1 - cd $(@D) && if $(RUN_EXAMPLES); then make run; fi && touch OK_DEBUG - -%/OK_RELEASE: - cd $(@D) && $(CMAKE) -DCMAKE_BUILD_TYPE=Release . >/dev/null 2>&1 - cd $(@D) && if $(RUN_EXAMPLES); then make run; fi && touch OK_RELEASE - -.PHONY: run_examples -run_examples: $(runsteps_debug:%=%/OK_DEBUG) $(runsteps_release:%=%/OK_RELEASE) - diff --git a/deal.II/doc/CMakeLists.txt b/deal.II/doc/CMakeLists.txt index ff3bc2d970..c4ec069aff 100644 --- a/deal.II/doc/CMakeLists.txt +++ b/deal.II/doc/CMakeLists.txt @@ -14,14 +14,13 @@ ## ## --------------------------------------------------------------------- - - - # # Set up all necessary bits for the documentation # IF(DEAL_II_COMPONENT_DOCUMENTATION) + MESSAGE(STATUS "Setup documentation") + # # Required packages for the document generation: # @@ -46,10 +45,6 @@ IF(DEAL_II_COMPONENT_DOCUMENTATION) # Generate the source documentation via doxygen: # ADD_SUBDIRECTORY(doxygen) - - # - # A custom target with the same name as the component: - # ADD_DEPENDENCIES(documentation doxygen) # @@ -73,6 +68,8 @@ IF(DEAL_II_COMPONENT_DOCUMENTATION) COMPONENT documentation ) + MESSAGE(STATUS "Setup documentation - Done") + ENDIF(DEAL_II_COMPONENT_DOCUMENTATION) # diff --git a/deal.II/doc/documentation.html b/deal.II/doc/documentation.html index 564bf7288b..0a40acc0ae 100644 --- a/deal.II/doc/documentation.html +++ b/deal.II/doc/documentation.html @@ -29,7 +29,7 @@ installation instructions
  • CMake documentation
  • CMake in user projects
    • -
  • Tutorial
    • +
  • Tutorial
  • Manual
  • Wolfgang's lectures
  • Technical reports
    • diff --git a/deal.II/doc/doxygen/CMakeLists.txt b/deal.II/doc/doxygen/CMakeLists.txt index 84e4226d20..17fd2d2b1f 100644 --- a/deal.II/doc/doxygen/CMakeLists.txt +++ b/deal.II/doc/doxygen/CMakeLists.txt @@ -54,12 +54,12 @@ CONFIGURE_FILE( ) CONFIGURE_FILE( - ${CMAKE_CURRENT_SOURCE_DIR}/scripts/mod_header.pl + ${CMAKE_CURRENT_SOURCE_DIR}/scripts/mod_header.pl.in ${CMAKE_CURRENT_BINARY_DIR}/scripts/mod_header.pl ) CONFIGURE_FILE( - ${CMAKE_CURRENT_SOURCE_DIR}/scripts/mod_footer.pl + ${CMAKE_CURRENT_SOURCE_DIR}/scripts/mod_footer.pl.in ${CMAKE_CURRENT_BINARY_DIR}/scripts/mod_footer.pl ) @@ -88,8 +88,10 @@ file(GLOB _doxygen_input ${CMAKE_SOURCE_DIR}/contrib/parameter_gui/main.cpp ${CMAKE_SOURCE_DIR}/doc/news/*.h ${CMAKE_SOURCE_DIR}/include/deal.II/**/*.h - + ) +LIST(APPEND _doxygen_input ${CMAKE_BINARY_DIR}/include/deal.II/base/config.h + ${CMAKE_CURRENT_BINARY_DIR}/tutorial/tutorial.h ) FOREACH(_step ${DEAL_II_STEPS}) GET_FILENAME_COMPONENT(_step "${_step}" NAME) @@ -139,7 +141,6 @@ ADD_CUSTOM_TARGET(doxygen ALL DEPENDS ${CMAKE_BINARY_DIR}/doxygen.log ) - INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/deal.tag ${CMAKE_CURRENT_SOURCE_DIR}/stylesheet.css diff --git a/deal.II/doc/doxygen/headers/coding_conventions.h b/deal.II/doc/doxygen/headers/coding_conventions.h index f6fff10ef5..bb73ab74ab 100644 --- a/deal.II/doc/doxygen/headers/coding_conventions.h +++ b/deal.II/doc/doxygen/headers/coding_conventions.h @@ -141,7 +141,7 @@ we list here: 
         Vector &
     operator += (Vector       &lhs,
-                 const Vector &rhs) {
+                 const Vector &rhs)
     {
       for (unsigned int i=0; i
     Vector &
     operator += (Vector       &lhs,
-                 const Vector &rhs) {
+                 const Vector &rhs)
     {
       Assert (lhs.size() == rhs.size(),
               ExcDimensionMismatch (lhs.size(), rhs.size());
@@ -210,7 +210,7 @@ we list here:
   follows:
   
   
    -    double norm (const Vector &v) {
+    double norm (const Vector &v)
     {
       double s = 0;
       for (unsigned int i=0; itutorial programs on the use of this
- * library.
+ * documentation. Documentation on other aspects, such as the build
+ * system, can be found elsewhere. In addition, there are
+ * Tutorial programs on the use of the library.
  *
  * Many of the classes in the deal.II library can be grouped into modules (see
  * the Modules page or the corresponding entry in
diff --git a/deal.II/doc/doxygen/headers/tutorial.h b/deal.II/doc/doxygen/headers/tutorial.h
deleted file mode 100644
index 0cb94932d6..0000000000
--- a/deal.II/doc/doxygen/headers/tutorial.h
+++ /dev/null
@@ -1,28 +0,0 @@
-// ---------------------------------------------------------------------
-// $Id$
-//
-// Copyright (C) 2005 - 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.
-//
-// ---------------------------------------------------------------------
-
-
-/**
- * @page Tutorial Tutorial programs
- *
- * The tutorial is a separate part of the documentation for deal.II. It
- * consists of a collection of small programs, each more or less built atop
- * previous ones. They demonstrate various aspects of the library. A more
- * detailed overview can be found on this
- * page that also includes short summaries of what each of the tutorial
- * programs are supposed to demonstrate, as well as a list of the programs
- * sorted by topic.
- */
diff --git a/deal.II/doc/doxygen/scripts/make_toc.pl b/deal.II/doc/doxygen/scripts/make_toc.pl
deleted file mode 100644
index 1b1fbfe84c..0000000000
--- a/deal.II/doc/doxygen/scripts/make_toc.pl
+++ /dev/null
@@ -1,32 +0,0 @@
-## ---------------------------------------------------------------------
-## $Id$
-##
-## 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.
-##
-## ---------------------------------------------------------------------
-
-$/ = undef;
-
-# Read source for web page
-open TOC, ";
-close TOC;
-
-# Read generated map file
-open MAP, ";
-close MAP;
-
-# Insert contents of map file for @@MAP@@
-$toc =~ s/\@\@MAP\@\@/$map/;
-
-print $toc;
diff --git a/deal.II/doc/doxygen/scripts/mod_footer.pl b/deal.II/doc/doxygen/scripts/mod_footer.pl.in
similarity index 91%
rename from deal.II/doc/doxygen/scripts/mod_footer.pl
rename to deal.II/doc/doxygen/scripts/mod_footer.pl.in
index 149545d707..ab562cbd71 100644
--- a/deal.II/doc/doxygen/scripts/mod_footer.pl
+++ b/deal.II/doc/doxygen/scripts/mod_footer.pl.in
@@ -3,7 +3,7 @@ use Sys::Hostname;
 my $host = hostname;
 
 my $hosting = << 'EOT'
-   Hosting provided by
+  Hosting provided by 
 IWR
 Universität Heidelberg
 EOT
diff --git a/deal.II/doc/doxygen/scripts/mod_header.pl b/deal.II/doc/doxygen/scripts/mod_header.pl.in
similarity index 100%
rename from deal.II/doc/doxygen/scripts/mod_header.pl
rename to deal.II/doc/doxygen/scripts/mod_header.pl.in
diff --git a/deal.II/doc/doxygen/scripts/steps.pl b/deal.II/doc/doxygen/scripts/steps.pl
index 7384b1e7f2..72e0e50a28 100644
--- a/deal.II/doc/doxygen/scripts/steps.pl
+++ b/deal.II/doc/doxygen/scripts/steps.pl
@@ -16,6 +16,16 @@
 
 use strict;
 
+my $tutorial_file = shift;
+open TUTORIAL, "<$tutorial_file";
+
+# Print the first part of tutorial.h.in
+while (my $line = )
+{
+  last if($line =~ m/\@\@MAP\@\@/);
+  print $line;
+}
+
 # List of additional node attributes to highlight purpose and state of the example
 my %style = (
  "basic"          => ',height=.8,width=.8,shape="octagon",fillcolor="green"',
@@ -26,9 +36,7 @@ my %style = (
  "unfinished"     => ',height=.25,width=.25,style="dashed"'
     );
 
-
 # Print a preamble setting common attributes
-
 print << 'EOT'
 digraph StepsMap
 {
@@ -65,7 +73,7 @@ foreach $step (@ARGV)
     close TF;
     chop $tooltip;
 
-    printf "Step$number [label=\"$number\", URL=\"../deal.II/step_$number.html\", tooltip=\"$tooltip\"";
+    printf "Step$number [label=\"$number\", URL=\"\\ref step_$number\", tooltip=\"$tooltip\"";
 
 
     # read first line of 'kind' file
@@ -106,3 +114,9 @@ foreach $step (@ARGV)
 
 print "}\n";
 
+# Print the rest of tutorial.h.in
+while (my $line = )
+{
+  print $line;
+}
+close TUTORIAL;
diff --git a/deal.II/doc/doxygen/stylesheet.css b/deal.II/doc/doxygen/stylesheet.css
index 5ac8648c74..7002ba8acd 100644
--- a/deal.II/doc/doxygen/stylesheet.css
+++ b/deal.II/doc/doxygen/stylesheet.css
@@ -4,3 +4,18 @@
     background-color: #0000ff;
     color: #80ff00;
 }
+
+table.tutorial {
+    color: black;
+    border: 1px solid #aaa;
+    background-color: #f9f9f9;
+    padding: 5px;
+    font-size: 95%;
+}
+div.tutorial {
+    color: black;
+    border: 1px solid #aaa;
+    background-color: #f9f9f9;
+    padding: 50px;
+    font-size: 95%;
+}
diff --git a/deal.II/doc/doxygen/tutorial/CMakeLists.txt b/deal.II/doc/doxygen/tutorial/CMakeLists.txt
index acb617e981..6af4da8c98 100644
--- a/deal.II/doc/doxygen/tutorial/CMakeLists.txt
+++ b/deal.II/doc/doxygen/tutorial/CMakeLists.txt
@@ -16,69 +16,34 @@
 
 
 #
-# Prepare steps.png and steps.cmapx:
+# Prepare tutorial.h:
 #
+
 ADD_CUSTOM_COMMAND(
-  OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/steps.dot
+  OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/tutorial.h
   COMMAND ${PERL_EXECUTABLE}
   ARGS
     ${CMAKE_SOURCE_DIR}/doc/doxygen/scripts/steps.pl
+    ${CMAKE_CURRENT_SOURCE_DIR}/tutorial.h.in
     ${DEAL_II_STEPS}
-    > ${CMAKE_CURRENT_BINARY_DIR}/steps.dot
-  )
-ADD_CUSTOM_COMMAND(
-  OUTPUT
-    ${CMAKE_CURRENT_BINARY_DIR}/steps.png
-    ${CMAKE_CURRENT_BINARY_DIR}/steps.cmapx
-  COMMAND ${DOXYGEN_DOT_EXECUTABLE}
-  ARGS
-    -Tpng -o ${CMAKE_CURRENT_BINARY_DIR}/steps.png
-    -Tcmapx -o ${CMAKE_CURRENT_BINARY_DIR}/steps.cmapx
-    ${CMAKE_CURRENT_BINARY_DIR}/steps.dot
+    > ${CMAKE_CURRENT_BINARY_DIR}/tutorial.h
   DEPENDS
-    ${CMAKE_CURRENT_BINARY_DIR}/steps.dot
+    ${DEAL_II_STEPS}
+    ${CMAKE_CURRENT_SOURCE_DIR}/tutorial.h.in
   )
 
-
-#
-# Prepare toc.html:
-#
-CONFIGURE_FILE(
-  ${CMAKE_CURRENT_SOURCE_DIR}/toc.html.in
-  ${CMAKE_CURRENT_BINARY_DIR}/toc.html.in
-  COPYONLY
-  )
-ADD_CUSTOM_COMMAND(
-  OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/toc.html
-  COMMAND ${PERL_EXECUTABLE}
-  ARGS
-    ${CMAKE_SOURCE_DIR}/doc/doxygen/scripts/make_toc.pl
-    > ${CMAKE_CURRENT_BINARY_DIR}/toc.html
-  WORKING_DIRECTORY
-    ${CMAKE_CURRENT_BINARY_DIR}
-  DEPENDS
-    ${CMAKE_CURRENT_BINARY_DIR}/toc.html.in
-    ${CMAKE_CURRENT_BINARY_DIR}/steps.cmapx
-  )
-
-
-#
-# TODO:
-# Are toc-list.html and toc-topics.html really generated by hand?
-#
-
-
 #
 # A target for the preparation of all the stuff happening in here...
 #
+
 ADD_CUSTOM_TARGET(tutorial
-  DEPENDS
-    ${CMAKE_CURRENT_BINARY_DIR}/toc.html
+  DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/tutorial.h
   )
 
 #
 # Prepare the steps for documentation generation
 #
+
 FOREACH(_step ${DEAL_II_STEPS})
   GET_FILENAME_COMPONENT(_step "${_step}" NAME)
 
@@ -118,20 +83,3 @@ FOREACH(_step ${DEAL_II_STEPS})
     )
   ADD_DEPENDENCIES(tutorial tutorial_${_step})
 ENDFOREACH()
-
-#
-# Install all bits:
-#
-
-INSTALL(FILES
-  index.html
-  navbar.html
-  title.html
-  toc-list.html
-  toc-topics.html
-  ${CMAKE_CURRENT_BINARY_DIR}/steps.png
-  ${CMAKE_CURRENT_BINARY_DIR}/toc.html
-  DESTINATION ${DEAL_II_DOCHTML_RELDIR}/doxygen/tutorial
-  COMPONENT documentation
-  )
-
diff --git a/deal.II/doc/doxygen/tutorial/index.html b/deal.II/doc/doxygen/tutorial/index.html
deleted file mode 100644
index a6c308ae7b..0000000000
--- a/deal.II/doc/doxygen/tutorial/index.html
+++ /dev/null
@@ -1,29 +0,0 @@
-
-
-
-
-Step-by-Step Examples
-    
-    
-    
-
-
-
-  
-  
-
-
-
-<h1>The deal.II Tutorial</h1>
-Your browser does not seem to understand frames. A version of this
-tutorial that does not use frames can be found 
-<a href="toc.html">here</a>.
-
-
-
-
-
-
-
-
diff --git a/deal.II/doc/doxygen/tutorial/navbar.html b/deal.II/doc/doxygen/tutorial/navbar.html
deleted file mode 100644
index b88c2c9818..0000000000
--- a/deal.II/doc/doxygen/tutorial/navbar.html
+++ /dev/null
@@ -1,121 +0,0 @@
-
-
-
-Step-by-Step Examples
-  
-  
-  
-  
-  
-
-
-
-
-	
    
-	  Overview
-	
    
-	
    
-	  Connections between programs
-	
    
-	
    
-	  Programs by number
-	
    
-	
    
-	  Programs by topic
-	
    
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-	
    
-	  Programs by number:
-	
    
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-	  1 
-	  2 
-	  3
    
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-	  6
    
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-	  45 
-	  46
    
-
-	  48 
-	  49 
-	  51
-	
    
-
-	
    
-
-    
    
-      Back to the deal.II homepage
-    
    
-
-
-    
    
-
-    
    
-      Comments on the tutorial
-    
    
-
-
-
-
-
-
-
-
-
-
diff --git a/deal.II/doc/doxygen/tutorial/title.html b/deal.II/doc/doxygen/tutorial/title.html
deleted file mode 100644
index d5cfc51d59..0000000000
--- a/deal.II/doc/doxygen/tutorial/title.html
+++ /dev/null
@@ -1,26 +0,0 @@
-
-
-
-Step-by-Step Examples
-  
-  
-  
-  
-  
-  
-
-
-
-
-  
    
-    
     The deal.II tutorial - Step-by-step examples
    
-  
    
-
-
-
-
-
-
-
-
diff --git a/deal.II/doc/doxygen/tutorial/toc-list.html b/deal.II/doc/doxygen/tutorial/toc-list.html
deleted file mode 100644
index c93510dfdf..0000000000
--- a/deal.II/doc/doxygen/tutorial/toc-list.html
+++ /dev/null
@@ -1,330 +0,0 @@
-
-
-
-Step-by-Step
-  
-  
-  
-  
-
-
-
-
-
-
    Tutorial programs listed by number
    
-
-
-  
-      
-      
-
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-      
-      
-
    Step-1 Creating a grid. A simple way to write it to a file.
-      
    Step-2 Associate degrees of freedom to
-      each vertex and compute the resulting sparsity pattern of
-      matrices. Show that renumbering reduces the bandwidth of
-      matrices significantly, i.e. clusters nonzero entries around the
-      diagonal.
-      
    Step-3 Actually solve Laplace's
-      problem. Object-orientation. Assembling matrices and
-      vectors. Boundary values.
-      
    Step-4 This example is programmed in a
-      way that it is independent of the dimension for which we want to
-      solve Laplace's equation; we will solve the equation in 2D and
-      3D, although the program is exactly the same. Non-constant right
-      hand side function. Non-homogeneous boundary values.
-      
    Step-5 Computations on successively
-      refined grids. Reading a grid from disk. Some optimizations.
-      Using assertions. Non-constant coefficient in
-      the elliptic operator (yielding the extended Poisson
-      equation). Preconditioning the CG solver for the
-      linear system of equations.
-      
    Step-6 Adaptive local
-      refinement. Handling of hanging nodes. Higher order elements.
-      Catching exceptions in the “main” function.
-      
    Step-7 Helmholtz
-      equation. Non-homogeneous Neumann boundary conditions and
-      boundary integrals. Verification of correctness of computed
-      solutions. Computing the error between exact and numerical
-      solution and output of the data in tables. Using counted pointers.
-      
    Step-8 The elasticity equations will be
-      solved instead of Laplace's equation. The solution is
-      vector-valued and the equations form a system with as many
-      equations as the dimension of the space in which it is posed.
-      
    Step-9 Linear advection equation, assembling
-      the system of equations in parallel using multi-threading,
-      implementing a refinement criterion based on a finite difference
-      approximation of the gradient.
-
-  
    Step-10 Higher order mappings. Do not
-      solve equations, but rather compute the value of pi to high
-      accuracy.
-      
    Step-11 Solving a Laplace problem with
-      higher order mappings. Using strange constraints and
-      intermediate representations of sparsity patterns.
-      
    Step-12 Discontinuous Galerkin methods for linear advection problems.
-      
    Step-13 Software design questions and
-      how to write a modular, extensible finite element program.
-      
    Step-14 Duality based error estimators,
-      more strategies to write a modular, extensible finite element
-      program.
-      
    Step-15 A nonlinear elliptic problem: The minimal surface equation.
-	Newton's method. Transferring a solution across mesh refinement.
-      
    Step-16 Multigrid preconditioning of the Laplace equation on adaptive
-      meshes.
-      
    Step-17 Using PETSc for linear algebra; running
-      in parallel on clusters of computers linked together by MPI.
-      
    Step-18 A time dependent problem; using a much
-      simplified version of implementing elasticity; moving meshes; handling
-      large scale output of parallel programs.
-      
    Step-19 Input parameter file handling. Merging
-      output of a parallel program.
-      
    Step-20 Mixed finite elements. Using block
-      matrices and block vectors to define more complicated solvers and
-      preconditioners working on the Schur complement.
-      
    Step-21 The time dependent two-phase flow in
-      porous media. Extensions of mixed Laplace discretizations. More
-      complicated block solvers. Simple time stepping.
-      
    Step-22 Solving the Stokes equations of slow fluid flow on adaptive
-      meshes. More on Schur complement solvers. Advanced use of the
-      ConstraintMatrix class.
-      
    Step-23 Finally a "real" time dependent problem, the wave equation.
-      
    Step-24 A variant of step-23 with absorbing
-      boundary conditions, and extracting practically useful data.
-      
    Step-25 The sine-Gordon
-      soliton equation, which is a nonlinear variant of the time
-      dependent wave equation covered in step-23 and step-24.
-      
    Step-27 hp finite element methods  
    Step-28 Multiple grids for solving a multigroup diffusion equation
-      in nuclear physics simulating a nuclear reactor core  
    Step-29 Solving a complex-valued Helmholtz equation. Sparse direct
-      solvers. Dealing with parameter files.  
    Step-30 Anisotropic refinement for DG finite element methods.
-      
    Step-31 Time-dependent Stokes flow driven by temperature
-      differences in a fluid. Adaptive meshes that change between time
-      steps.
-      
    Step-32 A massively parallel solver for time-dependent Stokes flow driven
-      by temperature differences in a fluid. Adapting methods for real-world
-      equations.
-      
    Step-33 A nonlinear hyperbolic conservation law: The Euler equations of
-      compressible gas dynamics.
-      
    Step-34 Boundary element methods (BEM) of low order: Exterior irrotational
-      flow. The ParsedFunction class.
-      
    Step-35 A projection solver for the Navier–Stokes equations.
-      
    Step-36 Using SLEPc for linear algebra; solving an eigenspectrum
-      problem. The Schrödinger wave equation.
-      
    Step-37 Solving a Poisson problem with a multilevel preconditioner without
-	explicitly storing the matrix (a matrix-free method).
-      
    Step-38Solving the Laplace-Beltrami equation on curved manifolds embedded
-      in higher dimensional spaces.
-      
    Step-39 Solving Poisson's equation once more, this time with the
-      interior penalty method, one of the discontinous Galerkin
-      methods developed for this problem. Error estimator, adaptive
-      meshes, and multigrid preconditioner, all using the MeshWorker
-      framework.
-      
    Step-40 Techniques for the massively parallel solution of the Laplace
-	equation (up to 10,000s of processors).
-      
    Step-41 Solving the obstacle problem, a variational inequality.
-      
    Step-42 A solver for an elasto-plastic contact problem, running on
-	parallel machines.
-      
    Step-43 Advanced techniques for the simulation of porous media flow.
-      
    Step-44 Finite strain hyperelasticity based on a three-field formulation.
-      
    Step-45 Periodic boundary conditions.
-      
    Step-46 Coupling different kinds of equations in different parts of the domain.
-      
    Step-48 Explicit time stepping for the Sine–Gordon equation based on
-	a diagonal mass matrix. Efficient implementation of (nonlinear) finite
-	element operators.
-      
    Step-49 Advanced mesh creation and manipulation techniques.
-      
    Step-51 Solving the convection-diffusion equation with a hyrbidizable
-      discontinuous Galerkin method using face elements.
-      
    
-
-
-
-
    
-
    
-The deal.II group
    
-
-
diff --git a/deal.II/doc/doxygen/tutorial/toc-topics.html b/deal.II/doc/doxygen/tutorial/toc-topics.html
deleted file mode 100644
index 54e69bbb93..0000000000
--- a/deal.II/doc/doxygen/tutorial/toc-topics.html
+++ /dev/null
@@ -1,640 +0,0 @@
-
-
-
-Step-by-Step
-  
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-
    Tutorial programs grouped by topics
    
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    Basic techniquesStep-1 Creating a grid. A simple way to write it to a file
-    
    Step-2 Degrees of freedom
-    
    Step-3 Solve the Laplace equation
-    
    Step-4 Dimension independent programming, non-zero data
-    
    Step-5 Computing on uniformly refined meshes
-    
    Step-6 Adaptivity
-    
    Step-7 Evaluating errors
-    
    Step-15 Nonlinear problems, Newton's method
-    

    Advanced techniques
-      Step-9,
-      Step-28,
-      Step-32,
-      Step-44,
-      Step-48,
-      Step-51
-     Multithreading
-    
    
-      Step-20,
-      Step-21,
-      Step-22,
-      Step-31,
-      Step-32,
-      Step-43,
-      Step-44
-     Block solvers and preconditioners
-    
    
-      Step-31,
-      Step-32,
-      Step-33,
-      Step-41,
-      Step-42,
-      Step-43
-     Using Trilinos
-    
    
-      Step-17,
-      Step-18,
-      Step-19,
-      Step-40
-     Parallelization via PETSc and MPI
-    
    
-      Step-32,
-      Step-42
-     Parallelization via Trilinos and MPI
-    
    
-      Step-32,
-      Step-40,
-      Step-42
-     Parallelization on very large numbers of processors
-    
    
-      Step-19,
-      Step-28,
-      Step-29,
-      Step-32,
-      Step-33,
-      Step-34,
-      Step-35,
-      Step-36,
-      Step-42,
-      Step-44
-     Input parameter handling
-    
    
-      Step-10,
-      Step-11,
-      Step-32
-     Higher order mappings
-    
    
-      Step-6,
-      Step-9,
-      Step-14,
-      Step-39
-     Error indicators and estimators
-    
    
-      Step-15,
-      Step-28,
-      Step-31,
-      Step-32,
-      Step-33,
-      Step-40,
-      Step-42,
-      Step-43
-     Transferring solutions across mesh refinement
-    
    
-      Step-12,
-      Step-21,
-      Step-39,
-      Step-46,
-      Step-51
-     Discontinuous Galerkin methods
-    
    
-      Step-27,
-      Step-46
-     hp finite elements
-    
    Step-30 Anisotropic refinement for DG finite element methods
-    
    
-      Step-16,
-      Step-31,
-      Step-32,
-      Step-39,
-      Step-41,
-      Step-42,
-      Step-43
-     Multilevel preconditioners
-    
    Step-33 Computing Jacobians from residuals, automatic differentiation
-    
    
-      Step-32,
-      Step-34,
-      Step-38
-     Boundary element methods, curved manifolds
-    
    
-      Step-45
-     Periodic boundary conditions
-    
    
-      Step-37,
-      Step-48
-     Matrix-free methods
-    
    
-      Step-49
-     Advanced meshes
-    

    Linear solver issuesStep-3 Conjugate Gradient solver
-    
    Step-5 Preconditioned CG solver
-    
    Step-9 BiCGStab
-    
    
-      Step-16,
-      Step-31,
-      Step-32,
-      Step-37,
-      Step-39,
-      Step-41,
-      Step-42,
-      Step-43
-     Multilevel preconditioners
-    
    
-      Step-17,
-      Step-18,
-      Step-32,
-      Step-40,
-      Step-42
-     Parallel solvers
-    
    
-      Step-20,
-      Step-21,
-      Step-22,
-      Step-31,
-      Step-32,
-      Step-43
-     Block and Schur complement solvers
-    
    Step-35 Decoupled projection solvers
-    
    
-      Step-33,
-      Step-41,
-      Step-42,
-      Step-44
-     Linear Newton systems from nonlinear equations
-    
    Step-36 Eigenvalue solvers
-    

    Other equations
-      Step-7,
-      Step-29
-     Helmholtz equation
-    
    
-      Step-8,
-      Step-42,
-      Step-46
-     Elasticity and elasto-plasticity equations
-    
    
-      Step-15
-     Minimal surface equation
-    
    
-      Step-18,
-      Step-44
-     Quasi-static elasticity equations
-    
    Step-9,
-        Step-21,
-	Step-31,
-        Step-32,
-        Step-43,
-        Step-51
-     Transport (advection) equations
-    
    Step-33 The nonlinear hyperbolic Euler system of compressible gas dynamics
-    
    
-      Step-20,
-      Step-21,
-      Step-43
-     Mixed Laplace, Darcy, Porous media
-    
    
-      Step-22,
-      Step-31,
-      Step-32,
-      Step-35,
-      Step-46
-     Stokes and incompressible Navier-Stokes flow
-    
    
-      Step-23,
-      Step-24,
-      Step-25,
-      Step-48
-     The wave equation, in linear and nonlinear variants
-    
    Step-28 A multigroup diffusion problem in neutron transport
-    
    Step-34 Irrotational flow
-    
    Step-36 An eigenspectrum problem
-  
    
-      Step-41,
-      Step-42
-     The obstacle problem, a variational inequality
-  
    Step-46 Coupling different equations in different parts of the domain
-  

    Vector problems
-      Step-8,
-      Step-42
-     Elasticity and elasto-plasticity equations
-    
    Step-20 Mixed Laplace
-    
    Step-21,
-        Step-43
-     Mixed Laplace plus an advection equation
-    
    Step-22,
-        Step-31,
-        Step-32,
-        Step-35 Incompressible Stokes and Navier-Stokes flow
-    
    Step-29 A complex-valued Helmholtz problem
-    
    Step-33 The Euler equations of compressible gas dynamics
-    
    Step-46 Coupling different equations in different parts of the domain
-  
    Time-dependent problems
-     Step-18,
-     Step-44
-     Quasi-static elasticity
-    
    Step-21,
-        Step-43
-     Porous media flow
-    
    Step-23,
-        Step-24,
-        Step-25,
-        Step-48
-     The wave equation, in linear and nonlinear variants
-    
    Step-31,
-        Step-32
-     Time dependent Stokes flow driven by buoyancy
-    
    Step-33 The Euler equations of compressible gas dynamics
-    
    
-
-
-
    
-
    
-The deal.II group
    
-
-
diff --git a/deal.II/doc/doxygen/tutorial/toc.html.in b/deal.II/doc/doxygen/tutorial/toc.html.in
deleted file mode 100644
index 279556c734..0000000000
--- a/deal.II/doc/doxygen/tutorial/toc.html.in
+++ /dev/null
@@ -1,94 +0,0 @@
-
-
-
-Step-by-Step
-  
-  
-  
-  
-
-
-
-
-
-
-
    Overview
    
-
-
    New to deal.II? You might want to start with tutorial Step-1 and work your way up to Step-5.
-At that point you can explore what features you are interested in and look at the large collection
-of programs listed below.
-
    
-
-
    
-The deal.II tutorial contains a collection of
-programs, each more
-or less built atop of previous ones, which demonstrate various
-aspects of the library. Each such example has the following structure:
-
      
-  
    1.  Introduction: What the program does, including
-       the mathematical model, and
-       what programming techniques are new.
-  
    2.  The commented program: An extensively documented listing of the
-       source code.
-  
    3.  Results: The output of the program, with comments and
-       interpretation.
-  
    4.  The plain program: The source code stripped of
-       all comments.
-
    
-
    
-
-
    
-You can browse the available tutorial programs
-
      
-  
    1.  as a graph (see below) that shows how tutorial programs build upon each other.
-  
    2.  as a list that provides a short
-    synopsis of each program.
-  
    3.  or grouped by topic.
-
    
-Some of the programs also jointly form
-the geodynamics
-  demonstration suite.
-
    
-
-
    
-The programs are in the examples/ directory of your local deal.II
-installation. After compiling the library itself, if you go into one of the
-tutorial directories, you can compile
-the program by typing make, and run it
-using make run. The latter command also compiles the program
-if that has not already been done. The Makefiles in the different
-directories are based on the small program Makefile template described
-in this section.
-
    
-
-
-
-
    Connections between tutorial programs
    
-
-The following graph shows the connections between tutorial programs and
-how they build on each other.
-Click on any of the boxes to go to one of the programs. If you hover
-your mouse pointer over a box, a brief description of the program
-should appear.
-
-
    
-
-@@MAP@@
-
    
-
-
    
-Legend:
-Green octagons: programs that show basic techniques;
-Orange boxes: advanced techniques;
-Yellow: applications in fluid dynamics;
-Light blue: applications in solid mechanics;
-Dark blue boxes: time dependent problems.
-
    
-
-
-
    
-
    
-The deal.II group
    
-
-
diff --git a/deal.II/doc/doxygen/tutorial/tutorial.h.in b/deal.II/doc/doxygen/tutorial/tutorial.h.in
new file mode 100644
index 0000000000..d7495be2a8
--- /dev/null
+++ b/deal.II/doc/doxygen/tutorial/tutorial.h.in
@@ -0,0 +1,959 @@
+// ---------------------------------------------------------------------
+// $Id$
+//
+// Copyright (C) 2005 - 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.
+//
+// ---------------------------------------------------------------------
+
+
+/**
+ * @page Tutorial Tutorial programs
+ *
+ * New to deal.II? You might want to start with tutorial Step-1 and work
+ * your way up to Step-5. At that point you can explore what features you
+ * are interested in and look at the large collection of programs listed
+ * below.
+ *
+ * The deal.II tutorial contains a collection of programs, each more or
+ * less built atop of previous ones, which demonstrate various aspects of
+ * the library. Each such example has the following structure:
+ * 
      
+ *   
    1.  Introduction: What the program does, including
+ *        the mathematical model, and
+ *        what programming techniques are new.
+ *   
    2.  The commented program: An extensively documented listing of the
+ *        source code.
+ *   
    3.  Results: The output of the program, with comments and
+ *        interpretation.
+ *   
    4.  The plain program: The source code stripped of
+ *        all comments.
+ * 
    
+ * You can browse the available tutorial programs
+ * 
      
+ *   
    1.  as a graph that shows how tutorial programs build upon each other.
+ *   
    2.  as a list that provides a short
+ *     synopsis of each program.
+ *   
    3.  or grouped by topic.
+ * 
    
+ * Some of the programs also jointly form
+ * the geodynamics
+ * demonstration suite.
+ *
+ * The programs are in the examples/ directory of your local
+ * deal.II installation. After compiling the library itself, if you go into
+ * one of the tutorial directories, you can configure the program by typing
+ * cmake ., build it via make and run it using
+ * make run. The latter command also compiles the program if
+ * that has not already been done. The CMakefiles.txt files in the
+ * different directories are based on the small program Makefile template
+ * described in this
+ * section.
+ *
+ * 
+ * 
    Connections between tutorial programs
    
+ *
+ * The following graph shows the connections between tutorial programs and
+ * how they build on each other.
+ * Click on any of the boxes to go to one of the programs. If you hover
+ * your mouse pointer over a box, a brief description of the program
+ * should appear.
+ * @dot
+@@MAP@@
+ * @enddot
+ *
+ * Legend:
    
+ * Green octagons: programs that show basic techniques;
    
+ * Orange boxes: advanced techniques;
    
+ * Yellow: applications in fluid dynamics;
    
+ * Light blue: applications in solid mechanics;
    
+ * Dark blue boxes: time dependent problems.
+ *
+ * 
+ * 
    Tutorial programs listed by number
    
+ *
+ * 
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ *
+ *   
+ *       
+ *       
+ * 
    Step-1 Creating a grid. A simple way to write it to a file.
+ *       
    Step-2 Associate degrees of freedom to
+ *       each vertex and compute the resulting sparsity pattern of
+ *       matrices. Show that renumbering reduces the bandwidth of
+ *       matrices significantly, i.e. clusters nonzero entries around the
+ *       diagonal.
+ *       
    Step-3 Actually solve Laplace's
+ *       problem. Object-orientation. Assembling matrices and
+ *       vectors. Boundary values.
+ *       
    Step-4 This example is programmed in a
+ *       way that it is independent of the dimension for which we want to
+ *       solve Laplace's equation; we will solve the equation in 2D and
+ *       3D, although the program is exactly the same. Non-constant right
+ *       hand side function. Non-homogeneous boundary values.
+ *       
    Step-5 Computations on successively
+ *       refined grids. Reading a grid from disk. Some optimizations.
+ *       Using assertions. Non-constant coefficient in
+ *       the elliptic operator (yielding the extended Poisson
+ *       equation). Preconditioning the CG solver for the
+ *       linear system of equations.
+ *       
    Step-6 Adaptive local
+ *       refinement. Handling of hanging nodes. Higher order elements.
+ *       Catching exceptions in the main; function.
+ *       
    Step-7 Helmholtz
+ *       equation. Non-homogeneous Neumann boundary conditions and
+ *       boundary integrals. Verification of correctness of computed
+ *       solutions. Computing the error between exact and numerical
+ *       solution and output of the data in tables. Using counted pointers.
+ *       
    Step-8 The elasticity equations will be
+ *       solved instead of Laplace's equation. The solution is
+ *       vector-valued and the equations form a system with as many
+ *       equations as the dimension of the space in which it is posed.
+ *       
    Step-9 Linear advection equation, assembling
+ *       the system of equations in parallel using multi-threading,
+ *       implementing a refinement criterion based on a finite difference
+ *       approximation of the gradient.
+ *
+ *   
    Step-10 Higher order mappings. Do not
+ *       solve equations, but rather compute the value of pi to high
+ *       accuracy.
+ *       
    Step-11 Solving a Laplace problem with
+ *       higher order mappings. Using strange constraints and
+ *       intermediate representations of sparsity patterns.
+ *       
    Step-12 Discontinuous Galerkin methods for linear advection problems.
+ *       
    Step-13 Software design questions and
+ *       how to write a modular, extensible finite element program.
+ *       
    Step-14 Duality based error estimators,
+ *       more strategies to write a modular, extensible finite element
+ *       program.
+ *       
    Step-15 A nonlinear elliptic problem: The minimal surface equation.
+ *       Newton's method. Transferring a solution across mesh refinement.
+ *       
    Step-16 Multigrid preconditioning of the Laplace equation on adaptive
+ *       meshes.
+ *       
    Step-17 Using PETSc for linear algebra; running
+ *       in parallel on clusters of computers linked together by MPI.
+ *       
    Step-18 A time dependent problem; using a much
+ *       simplified version of implementing elasticity; moving meshes; handling
+ *       large scale output of parallel programs.
+ *       
    Step-19 Input parameter file handling. Merging
+ *       output of a parallel program.
+ *       
    Step-20 Mixed finite elements. Using block
+ *       matrices and block vectors to define more complicated solvers and
+ *       preconditioners working on the Schur complement.
+ *       
    Step-21 The time dependent two-phase flow in
+ *       porous media. Extensions of mixed Laplace discretizations. More
+ *       complicated block solvers. Simple time stepping.
+ *       
    Step-22 Solving the Stokes equations of slow fluid flow on adaptive
+ *       meshes. More on Schur complement solvers. Advanced use of the
+ *       ConstraintMatrix class.
+ *       
    Step-23 Finally a "real" time dependent problem, the wave equation.
+ *       
    Step-24 A variant of step-23 with absorbing
+ *       boundary conditions, and extracting practically useful data.
+ *       
    Step-25 The sine-Gordon
+ *       soliton equation, which is a nonlinear variant of the time
+ *       dependent wave equation covered in step-23 and step-24.
+ *       
    Step-27 hp finite element methods  
    Step-28 Multiple grids for solving a multigroup diffusion equation
+ *       in nuclear physics simulating a nuclear reactor core  
    Step-29 Solving a complex-valued Helmholtz equation. Sparse direct
+ *       solvers. Dealing with parameter files.  
    Step-30 Anisotropic refinement for DG finite element methods.
+ *       
    Step-31 Time-dependent Stokes flow driven by temperature
+ *       differences in a fluid. Adaptive meshes that change between time
+ *       steps.
+ *       
    Step-32 A massively parallel solver for time-dependent Stokes flow driven
+ *       by temperature differences in a fluid. Adapting methods for real-world
+ *       equations.
+ *       
    Step-33 A nonlinear hyperbolic conservation law: The Euler equations of
+ *       compressible gas dynamics.
+ *       
    Step-34 Boundary element methods (BEM) of low order: Exterior irrotational
+ *       flow. The ParsedFunction class.
+ *       
    Step-35 A projection solver for the Navier–Stokes equations.
+ *       
    Step-36 Using SLEPc for linear algebra; solving an eigenspectrum
+ *       problem. The Schrödinger wave equation.
+ *       
    Step-37 Solving a Poisson problem with a multilevel preconditioner without
+ *       explicitly storing the matrix (a matrix-free method).
+ *       
    Step-38Solving the Laplace-Beltrami equation on curved manifolds embedded
+ *       in higher dimensional spaces.
+ *       
    Step-39 Solving Poisson's equation once more, this time with the
+ *       interior penalty method, one of the discontinous Galerkin
+ *       methods developed for this problem. Error estimator, adaptive
+ *       meshes, and multigrid preconditioner, all using the MeshWorker
+ *       framework.
+ *       
    Step-40 Techniques for the massively parallel solution of the Laplace
+ *       equation (up to 10,000s of processors).
+ *       
    Step-41 Solving the obstacle problem, a variational inequality.
+ *       
    Step-42 A solver for an elasto-plastic contact problem, running on
+ *       parallel machines.
+ *       
    Step-43 Advanced techniques for the simulation of porous media flow.
+ *       
    Step-44 Finite strain hyperelasticity based on a three-field formulation.
+ *       
    Step-45 Periodic boundary conditions.
+ *       
    Step-46 Coupling different kinds of equations in different parts of the domain.
+ *       
    Step-48 Explicit time stepping for the Sine–Gordon equation based on
+ *       a diagonal mass matrix. Efficient implementation of (nonlinear) finite
+ *       element operators.
+ *       
    Step-49 Advanced mesh creation and manipulation techniques.
+ *       
    Step-51 Solving the convection-diffusion equation with a hyrbidizable
+ *       discontinuous Galerkin method using face elements.
+ *       
    
+ *
+ * 
+ * 
    Tutorial programs grouped by topics
    
+ *
+ * 
    Basic techniques
    
+ * 
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ * 
     Creating a grid. A simple way to write it to a file
+ *     Step-1
     Degrees of freedom
+ *     Step-2
     Solve the Laplace equation
+ *     Step-3
     Dimension independent programming, non-zero data
+ *     Step-4
     Computing on uniformly refined meshes
+ *     Step-5
     Adaptivity
+ *     Step-6
     Evaluating errors
+ *     Step-7
     Nonlinear problems, Newton's method
+ *     Step-15
    
+ * 
    Advanced techniques
    
+ * 
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ * 
     Multithreading
+ *     
+ *       Step-9,
+ *       Step-28,
+ *       Step-32,
+ *       Step-44,
+ *       Step-48,
+ *       Step-51
+ *     
     Block solvers and preconditioners
+ *     
+ *       Step-20,
+ *       Step-21,
+ *       Step-22,
+ *       Step-31,
+ *       Step-32,
+ *       Step-43,
+ *       Step-44
+ *     
     Using Trilinos
+ *     
+ *       Step-31,
+ *       Step-32,
+ *       Step-33,
+ *       Step-41,
+ *       Step-42,
+ *       Step-43
+ *     
     Parallelization via PETSc and MPI
+ *     
+ *       Step-17,
+ *       Step-18,
+ *       Step-19,
+ *       Step-40
+ *     
     Parallelization via Trilinos and MPI
+ *     
+ *       Step-32,
+ *       Step-42
+ *     
     Parallelization on very large numbers of processors
+ *     
+ *       Step-32,
+ *       Step-40,
+ *       Step-42
+ *     
     Input parameter handling
+ *     
+ *       Step-19,
+ *       Step-28,
+ *       Step-29,
+ *       Step-32,
+ *       Step-33,
+ *       Step-34,
+ *       Step-35,
+ *       Step-36,
+ *       Step-42,
+ *       Step-44
+ *     
     Higher order mappings
+ *     
+ *       Step-10,
+ *       Step-11,
+ *       Step-32
+ *     
     Error indicators and estimators
+ *     
+ *       Step-6,
+ *       Step-9,
+ *       Step-14,
+ *       Step-39
+ *     
     Transferring solutions across mesh refinement
+ *     
+ *       Step-15,
+ *       Step-28,
+ *       Step-31,
+ *       Step-32,
+ *       Step-33,
+ *       Step-40,
+ *       Step-42,
+ *       Step-43
+ *     
     Discontinuous Galerkin methods
+ *     
+ *       Step-12,
+ *       Step-21,
+ *       Step-39,
+ *       Step-46,
+ *       Step-51
+ *     
     hp finite elements
+ *     
+ *       Step-27,
+ *       Step-46
+ *     
     Anisotropic refinement for DG finite element methods
+ *     Step-30
     Multilevel preconditioners
+ *     
+ *       Step-16,
+ *       Step-31,
+ *       Step-32,
+ *       Step-39,
+ *       Step-41,
+ *       Step-42,
+ *       Step-43
+ *     
     Computing Jacobians from residuals, automatic differentiation
+ *     Step-33
     Boundary element methods, curved manifolds
+ *     
+ *       Step-32,
+ *       Step-34,
+ *       Step-38
+ *     
     Periodic boundary conditions
+ *     
+ *       Step-45
+ *     
     Matrix-free methods
+ *     
+ *       Step-37,
+ *       Step-48
+ *     
     Advanced meshes
+ *     
+ *       Step-49
+ *     
    
+ * 
    Linear solvers
    
+ * 
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ * 
     Conjugate Gradient solver
+ *     Step-3
     Preconditioned CG solver
+ *     Step-5
     BiCGStab
+ *     Step-9
     Multilevel preconditioners
+ *     
+ *       Step-16,
+ *       Step-31,
+ *       Step-32,
+ *       Step-37,
+ *       Step-39,
+ *       Step-41,
+ *       Step-42,
+ *       Step-43
+ *     
     Parallel solvers
+ *     
+ *       Step-17,
+ *       Step-18,
+ *       Step-32,
+ *       Step-40,
+ *       Step-42
+ *     
     Block and Schur complement solvers
+ *     
+ *       Step-20,
+ *       Step-21,
+ *       Step-22,
+ *       Step-31,
+ *       Step-32,
+ *       Step-43
+ *     
     Decoupled projection solvers
+ *     Step-35
     Linear Newton systems from nonlinear equations
+ *     
+ *       Step-33,
+ *       Step-41,
+ *       Step-42,
+ *       Step-44
+ *     
     Eigenvalue solvers
+ *     Step-36
    
+ * 
    Other equations
    
+ * 
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ * 
     Helmholtz equation
+ *     
+ *       Step-7,
+ *       Step-29
+ *     
     Elasticity and elasto-plasticity equations
+ *     
+ *       Step-8,
+ *       Step-42,
+ *       Step-46
+ *     
     Minimal surface equation
+ *     
+ *       Step-15
+ *     
     Quasi-static elasticity equations
+ *     
+ *       Step-18,
+ *       Step-44
+ *     
     Transport (advection) equations
+ *     Step-9,
+ *         Step-21,
+ *         Step-31,
+ *         Step-32,
+ *         Step-43,
+ *         Step-51
+ *     
     The nonlinear hyperbolic Euler system of compressible gas dynamics
+ *     Step-33
     Mixed Laplace, Darcy, Porous media
+ *     
+ *       Step-20,
+ *       Step-21,
+ *       Step-43
+ *     
     Stokes and incompressible Navier-Stokes flow
+ *     
+ *       Step-22,
+ *       Step-31,
+ *       Step-32,
+ *       Step-35,
+ *       Step-46
+ *     
     The wave equation, in linear and nonlinear variants
+ *     
+ *       Step-23,
+ *       Step-24,
+ *       Step-25,
+ *       Step-48
+ *     
     A multigroup diffusion problem in neutron transport
+ *     Step-28
     Irrotational flow
+ *     Step-34
     An eigenspectrum problem
+ *     Step-36
     The obstacle problem, a variational inequality
+ *     
+ *       Step-41,
+ *       Step-42
+ *     
     Coupling different equations in different parts of the domain
+ *     Step-46
    
+ * 
    Vector problems
    
+ * 
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *   
+ *
+ * 
     Elasticity and elasto-plasticity equations
+ *     
+ *       Step-8,
+ *       Step-42
+ *     
     Mixed Laplace
+ *     Step-20
     Mixed Laplace plus an advection equation
+ *     Step-21,
+ *         Step-43
+ *     
     Incompressible Stokes and Navier-Stokes flow
+ *     Step-22,
+ *         Step-31,
+ *         Step-32,
+ *         Step-35
     A complex-valued Helmholtz problem
+ *     Step-29
     The Euler equations of compressible gas dynamics
+ *     Step-33
     Coupling different equations in different parts of the domain
+ *     Step-46
    
+ * 
    Time dependent problems
    
+ * 
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ *
+ *   
+ *     
+ *     
+ *   
+ * 
     Quasi-static elasticity
+ *     
+ *      Step-18,
+ *      Step-44
+ *     
     Porous media flow
+ *     Step-21,
+ *         Step-43
+ *     
     The wave equation, in linear and nonlinear variants
+ *     Step-23,
+ *         Step-24,
+ *         Step-25,
+ *         Step-48
+ *     
     Time dependent Stokes flow driven by buoyancy
+ *     Step-31,
+ *         Step-32
+ *     
     The Euler equations of compressible gas dynamics
+ *     Step-33
    
+ */
diff --git a/deal.II/doc/navbar.html b/deal.II/doc/navbar.html
index 9fe716955d..af84e94087 100644
--- a/deal.II/doc/navbar.html
+++ b/deal.II/doc/navbar.html
@@ -27,7 +27,7 @@
 
     Doxygen and Lectures
     
    
-      Tutorial
    
+      Tutorial
    
       Manual
    
       Wolfgang's lectures
    
diff --git a/deal.II/doc/news/changes.h b/deal.II/doc/news/changes.h
index 4101eeb4bc..93c0ecd3a3 100644
--- a/deal.II/doc/news/changes.h
+++ b/deal.II/doc/news/changes.h
@@ -40,6 +40,12 @@ inconvenience this causes.
 
    
 
 
      
+  
    1.  Removed: With the switch of the testsuite to CMake, the old report_features
+  and build test facilities are removed.
+  
      
+  (Matthias Maier, 2013/12/03)
+  
      2. 
+
   
    2. 
   Changed: The kinds of template arguments for the VectorTools::interpolate
   function taking a Mapping as first argument has changed. This was done to
@@ -107,6 +113,16 @@ inconvenience this causes.
 
 
 
        
+  
      1.  Improved: The build system now supports usage of the library
+  out of the build directory without prior installation. This is done by
+  exporting an additional project configuration just for the build directory.
+  Furthermore, a bunch of convenience targets get now defined that just build
+  individual components (such as just the documentation or the libraries), and
+  if CMAKE_INSTALL_PREFIX is set, also install that specific component.
+  
        
+  (Matthias Maier, Luca Heltai, 2013/12/03)
+  
        2. 
+
   
      2.  Fixed: Missing instantiations of SparseDirectMUMPS have been added.
   
        
   (Timo Heister, 2013/11/25)
@@ -230,6 +246,21 @@ inconvenience this causes.
 
        Specific improvements
        
 
 
          
+  
        1.  Fixed: Several functions in namespace GridTools were not instantiated
+  for parallel::distributed::Triangulation objects. This is now fixed.
+  
          
+  (Denis Davydov, Wolfgang Bangerth, 2013/12/01)
+  
          2. 
+
+  
        2.  Improved: The methods ConstraintMatrix::distribute_local_to_global
+  now use scratch data that is private to each thread instead of allocating
+  it for every cell anew. This gives better performance, in particular in
+  parallel, of these operations, while maintaining thread-safety (when
+  accessing non-overlapping rows, no race condition can exist).
+  
          
+  (Martin Kronbichler, 2013/12/03)
+  
          3. 
+
   
        3.  Improved: When attempting operations such as FEValues::get_function_values()
   or FEValues::shape_value(), the FEValues object needs to know that what these
   functions return has been computed previously. What is computed is specified
diff --git a/deal.II/doc/publications/index.html b/deal.II/doc/publications/index.html
index bd0feb08cb..65522db8e5 100644
--- a/deal.II/doc/publications/index.html
+++ b/deal.II/doc/publications/index.html
@@ -250,6 +250,23 @@
 	
          4. 
       
 
+
+
+       
+      
          Publications in 2014
          
+
+      
+      
            
+	
          1.  T. Wick, G. Singh, M.F. Wheeler
+ 	  
            
+	  Pressurized-Fracture propagation using a phase-field approach coupled to a reservoir simulator
+	  
+	  
            
+	  SPE 168597-MS, SPE HFTC Proc. 2014.
+        
            2. 
+	
          
+
+
        
       
          Publications in 2013
          
 
@@ -505,6 +522,23 @@
 	  Journal of Elasticity, in press, 2013.
 	
 
+	
        4.  S. Frei, T. Richter, T. Wick
+	  
          
+          Eulerian Techniques for Fluid-Structure Interactions - Part
+          I: Modeling and Simulation
+          
+	  
          
+	  ENUMATH Proc., submitted Nov 2013.
+	
          5. 
+
+	
        5.  S. Frei, T. Richter, T. Wick
+	  
          
+          Eulerian Techniques for Fluid-Structure Interactions - Part II: Applications
+          
+	  
          
+	  ENUMATH Proc., submitted Nov 2013.
+	
          6. 
+
 	
        6.  A. Geringer, B. Lenhof, S. Diebels
 	  
          
           Macroscopic modeling of foams: an order-parameter
@@ -608,14 +642,21 @@
 	  PhD thesis, University of Siegen, Germany, 2013.
 	
          7. 
 
+	
        7.  K. Kumar, T. van Noorden, M. F. Wheeler, T. Wick
+	  
          
+          An ALE-based method for reaction-induced boundary movement towards clogging
+          
+	  
          
+	  ENUMATH Proc., submitted Nov 2013.
+	
          8. 
+
 	
        8.  K. Kumar, M.F. Wheeler, T. Wick
  	  
          
-	  Reactive flow in a thin channel
-and reaction-induced boundary movement in
-a monolithic ALE framework
+	  Reactive flow reaction-induced boundary movement in
+	    a thin channel
 	  
 	  
          
-	  submitted to SISC, 2013.
+	  SIAM J. Sci. Comput. 35(6), pp. B1235-B1266, 2013
         
          9. 
 
 	
        9.  B. Lenhof, A. Geringer, S. Diebels
@@ -679,12 +720,29 @@ a monolithic ALE framework
 	  pp. 41-46, 2013.
 	
          10. 
 
+	
        10.  T. Richter, T. Wick
+ 	  
          
+	  Solid growth and clogging in fluid-structure interaction computed in ALE and fully Eulerian coordinates
+	  
+	  
          
+	  submitted Oct 2013 (peer-reviewed journal)
+        
          11. 
+
+	
        11.  T. Richter, T. Wick
+ 	  
          
+	  On time discretizations of fluid-structure interactions
+	  
+	  
          
+	  submitted Oct 2013 (book proceedings)
+        
          12. 
+
+
 	
        12.  T. Richter, T. Wick
  	  
          
 	  Optimal Control and Parameter Estimation for Stationary Fluid-Structure Interaction Problems
 	  
 	  
          
-	  SISC, accepted in May, 2013.
+	  SIAM J. Sci. Comput., accepted in May, 2013.
         
          13. 
 
 	
        13.  S. Roy, L. Heltai, D. Drapaca, F. Costanzo
@@ -773,6 +831,8 @@ a monolithic ALE framework
 	  ARMA Conference in San Francisco, Jun 23-26, 2013.
         
          14. 
 
+
+
 	
        14.  J. Weinbub, K. Rupp, S. Selberherr
  	  
          
 	  ViennaX: a parallel plugin execution framework for
@@ -789,7 +849,7 @@ a monolithic ALE framework
   and Mesh Adaptivity
 	  
 	  
          
-	  Comp. Mech., DOI: 10.1007/s00466-013-0890-3, 2013.
+	  Computational Mechanics, DOI: 10.1007/s00466-013-0890-3, 2013.
         
          15. 
 
 	
        15.  T. Wick
@@ -798,7 +858,7 @@ a monolithic ALE framework
   methods for fluid-structure interaction computations
 	  
 	  
          
-	  Comp. Mech., DOI: 10.1007/s00466-013-0866-3, 2013.
+	  Computational Mechanics, DOI: 10.1007/s00466-013-0866-3, 2013.
         
          16. 
 
 	
        16.  T. Wick
diff --git a/deal.II/doc/readme.html b/deal.II/doc/readme.html
index 5ea8cc3d06..f4c41181f3 100644
--- a/deal.II/doc/readme.html
+++ b/deal.II/doc/readme.html
@@ -318,7 +318,7 @@
       At this point, you have generated everything necessary to write
       programs based on deal.II. If you are new to
       deal.II, you may want to continue with the
-      tutorial.
+      tutorial.
     
          
 
     
@@ -349,7 +349,7 @@
       install both this readme, other installation instructions, as well as the
       manual that documents
       all functions and classes as well as
-      the  tutorial
+      the  tutorial
       of well-documented example programs (the "steps").
     
          
 
diff --git a/deal.II/doc/screen.css b/deal.II/doc/screen.css
index 2abc65f177..b13ec87ed6 100644
--- a/deal.II/doc/screen.css
+++ b/deal.II/doc/screen.css
@@ -254,20 +254,6 @@ pre.sample {
 }
     
 table.navbar { }
-table.tutorial {
-    color: black;
-    border: 1px solid #aaa;
-    background-color: #f9f9f9;
-    padding: 5px;
-    font-size: 95%;
-}
-div.tutorial {
-    color: black;
-    border: 1px solid #aaa;
-    background-color: #f9f9f9;
-    padding: 50px;
-    font-size: 95%;
-}
 
 strong.red { color: #ff0000; }
 code.program { color: #700000; }
diff --git a/deal.II/doc/users/cmake.html b/deal.II/doc/users/cmake.html
index 7a571607ef..1f2d695a10 100644
--- a/deal.II/doc/users/cmake.html
+++ b/deal.II/doc/users/cmake.html
@@ -206,34 +206,35 @@ cmake -DDEAL_II_WITH_MPI=ON <...>
     
          Primary build targets
          
 
     
           The current list of primary build targets can be queried via
-    make info:
+    make help:
 
           ###
 #
 #  The following targets are available (invoke via $ make <target>):
 #
-#    all            - compiles the library and all enabled components
-#    clean          - removes all generated files
-#    install        - installs into CMAKE_INSTALL_PREFIX
-#    help           - prints a list of valid top level targets
-#    info           - prints this help message
+#    all            - compile the library and all enabled components
+#    clean          - remove all generated files
+#    install        - install into CMAKE_INSTALL_PREFIX
+#    help           - print this help message in the toplevel directory,
+#                     otherwise print a list of targets (in subdirectories)
 #
-#    edit_cache     - runs ccmake for changing (cached) configuration variables
+#    edit_cache     - run ccmake for changing (cached) configuration variables
 #                     and reruns the configure and generate phases of CMake
-#    rebuild_cache  - reruns the configure and generate phases of CMake
+#    rebuild_cache  - rerun the configure and generate phases of CMake
 #
-#    compat_files   - builds and installs the 'compat_files' component
-#    documentation  - builds and installs the 'documentation' component
-#    examples       - builds and installs the 'examples' component
-#    library        - builds and installs the 'library' component
-#    mesh_converter - builds and installs the 'mesh_converter' component
-#    parameter_gui  - builds and installs the 'parameter_gui' component
+#    compat_files   - build and install component 'compat_files'
+#    documentation  - build and install component 'documentation'
+#    examples       - build and install component 'examples'
+#    library        - build and install component 'library'
+#    mesh_converter - build and install component 'mesh_converter'
+#    parameter_gui  - build and install component 'parameter_gui'
 #
-#    test           - runs a minimal set of tests
+#    test           - run a minimal set of tests
 #
-#    setup_test     - sets up the testsuite subprojects
-#    clean_test     - runs the 'clean' target in every testsuite subproject
-#    prune_test     - removes all testsuite subprojects
+#    setup_tests    - set up the testsuite subprojects
+#    regen_tests    - rerun configure stage in every testsuite subprojects
+#    clean_tests    - run the 'clean' target in every testsuite subproject
+#    prune_tests    - remove all testsuite subprojects
 #
 ###
 
          
@@ -273,7 +274,7 @@ cmake -DDEAL_II_WITH_MPI=ON <...>
 #
 #  Detailed information (compiler flags, feature configuration) can be found in detailed.log
 #
-#  Run  $ make info  to print a help message with a list of top level targets
+#  Run  $ make help  to print a help message with a list of top level targets
 #
 ###
 
    
diff --git a/deal.II/doc/users/cmakelists.html b/deal.II/doc/users/cmakelists.html
index 19d5686899..e6a45736ff 100644
--- a/deal.II/doc/users/cmakelists.html
+++ b/deal.II/doc/users/cmakelists.html
@@ -822,7 +822,6 @@ ${CMAKE_INSTALL_PREFIX}/
     common/Make.global_options
     common/scripts/expand_instantiations
     common/scripts/make_dependencies
-    common/scripts/report_features
    Therefore, it should be sufficient to set D in the old diff --git a/deal.II/doc/users/navbar.html b/deal.II/doc/users/navbar.html index 8b55b4c263..411bf6cf72 100644 --- a/deal.II/doc/users/navbar.html +++ b/deal.II/doc/users/navbar.html @@ -40,7 +40,7 @@ Doxygen

    - Tutorial
    + Tutorial
    Manual
    Wolfgang's lectures
    diff --git a/deal.II/doc/users/toc.html b/deal.II/doc/users/toc.html index 417b838e03..1d43275fab 100644 --- a/deal.II/doc/users/toc.html +++ b/deal.II/doc/users/toc.html @@ -63,7 +63,7 @@ available:

    Tutorials

    - The tutorial is for new users of the library. It explains the basic elements of finite element programs based on the library, and provides small example diff --git a/deal.II/examples/CMakeLists.txt b/deal.II/examples/CMakeLists.txt index 3655a42bf1..45f41856a9 100644 --- a/deal.II/examples/CMakeLists.txt +++ b/deal.II/examples/CMakeLists.txt @@ -15,6 +15,8 @@ ## --------------------------------------------------------------------- IF(DEAL_II_COMPONENT_EXAMPLES) + MESSAGE(STATUS "Setup examples") + INSTALL(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/ DESTINATION ${DEAL_II_EXAMPLES_RELDIR} COMPONENT examples @@ -42,4 +44,6 @@ IF(DEAL_II_COMPONENT_EXAMPLES) PATTERN "untitled.geo" # step-49 PATTERN "untitled.msh" # step-49 ) + + MESSAGE(STATUS "Setup examples - Done") ENDIF() diff --git a/deal.II/examples/step-18/step-18.cc b/deal.II/examples/step-18/step-18.cc index 0bd852c572..283419e941 100644 --- a/deal.II/examples/step-18/step-18.cc +++ b/deal.II/examples/step-18/step-18.cc @@ -1718,6 +1718,17 @@ namespace Step18 // to the vertex we consider at present, as they may or may not be ordered // in the same order. // + // This inconvenience could be avoided if finite elements have support + // points on vertices (which the one here has; for the concept of support + // points, see @ref GlossSupport "support points"). For such a case, one + // could construct a custom quadrature rule using + // FiniteElement::get_unit_support_points(). The first + // GeometryInfo@::vertices_per_cell*fe.dofs_per_vertex + // quadrature points will then correspond to the vertices of the cell and + // are ordered consistent with cell-@>vertex(i), taking into + // account that support points for vector elements will be duplicated + // fe.dofs_per_vertex times. + // // Another point worth explaining about this short function is the way in // which the triangulation class exports information about its vertices: // through the Triangulation::n_vertices function, it diff --git a/deal.II/examples/step-25/doc/intro.dox b/deal.II/examples/step-25/doc/intro.dox index 41a133cc8c..e06d36fc27 100644 --- a/deal.II/examples/step-25/doc/intro.dox +++ b/deal.II/examples/step-25/doc/intro.dox @@ -11,7 +11,7 @@ extensively. Rather facetiously, the sine-Gordon equation's moniker is a pun on the so-called Klein-Gordon equation, which is a relativistic version of -the Schrödinger equation for particles with non-zero mass. The resemblance is not just +the Schrödinger equation for particles with non-zero mass. The resemblance is not just superficial, the sine-Gordon equation has been shown to model some unified-field phenomena such as interaction of subatomic particles (see, e.g., Perring & Skyrme in Nuclear Physics 31) and the diff --git a/deal.II/examples/step-36/doc/intro.dox b/deal.II/examples/step-36/doc/intro.dox index c5e4aecf00..f0eb3867cb 100644 --- a/deal.II/examples/step-36/doc/intro.dox +++ b/deal.II/examples/step-36/doc/intro.dox @@ -53,7 +53,7 @@ for linear algebra contents.

    Introduction

    The basic equation of stationary quantum mechanics is the -Schrödinger equation which models the motion of particles in an +Schrödinger equation which models the motion of particles in an external potential $V(\mathbf x)$. The particle is described by a wave function $\Psi(\mathbf x)$ that satisfies a relation of the (nondimensionalized) form diff --git a/deal.II/examples/step-36/doc/tooltip b/deal.II/examples/step-36/doc/tooltip index 3a5f92e61a..1e1a5da68b 100644 --- a/deal.II/examples/step-36/doc/tooltip +++ b/deal.II/examples/step-36/doc/tooltip @@ -1 +1 @@ -Finding eigenvalues of the Schrödinger equation. +Finding eigenvalues of the Schrödinger equation. diff --git a/deal.II/examples/step-37/doc/tooltip b/deal.II/examples/step-37/doc/tooltip index 65cc3a07fc..83658ea2c4 100644 --- a/deal.II/examples/step-37/doc/tooltip +++ b/deal.II/examples/step-37/doc/tooltip @@ -1 +1 @@ -Matrix-free methods. Multigrid. Cell-based finite element operator. +Matrix-free methods. Multigrid. Fast assembly techniques. diff --git a/deal.II/examples/step-41/doc/intro.dox b/deal.II/examples/step-41/doc/intro.dox index 84afbba1f6..62e8876b0b 100644 --- a/deal.II/examples/step-41/doc/intro.dox +++ b/deal.II/examples/step-41/doc/intro.dox @@ -1,6 +1,6 @@
    -This program was contributed by Jörg Frohne (University of Siegen, +This program was contributed by Jörg Frohne (University of Siegen, Germany) while on a long-term visit to Texas A&M University.
    This material is based upon work partly supported by ThyssenKrupp Steel Europe. diff --git a/deal.II/examples/step-42/doc/intro.dox b/deal.II/examples/step-42/doc/intro.dox index e9dbabb604..27ce612c59 100644 --- a/deal.II/examples/step-42/doc/intro.dox +++ b/deal.II/examples/step-42/doc/intro.dox @@ -1,6 +1,6 @@
    -This program was contributed by Jörg Frohne (University of Siegen, +This program was contributed by Jörg Frohne (University of Siegen, Germany) while on a long-term visit to Texas A&M University, with significant contributions by Timo Heister and Wolfgang Bangerth.
    diff --git a/deal.II/examples/step-42/doc/results.dox b/deal.II/examples/step-42/doc/results.dox index 59158fd480..73911f11fe 100644 --- a/deal.II/examples/step-42/doc/results.dox +++ b/deal.II/examples/step-42/doc/results.dox @@ -199,7 +199,7 @@ situations are concerned:
    • Extend the program from a static to a quasi-static situation, perhaps by choosing a backward-Euler-scheme for the time discretization. Some theoretical -results can be found in the PhD thesis by Jörg Frohne, FEM-Simulation +results can be found in the PhD thesis by Jörg Frohne, FEM-Simulation der Umformtechnik metallischer Oberflächen im Mikrokosmos, University of Siegen, Germany, 2011. diff --git a/deal.II/examples/step-48/doc/tooltip b/deal.II/examples/step-48/doc/tooltip index b7f08a32cc..ffe23aeb00 100644 --- a/deal.II/examples/step-48/doc/tooltip +++ b/deal.II/examples/step-48/doc/tooltip @@ -1 +1 @@ -Parallelization via MPI. The wave equation, in linear and nonlinear variants. Mass lumping. Cell-based finite element operator. +Parallelization via MPI. The wave equation, in linear and nonlinear variants. Mass lumping. Fast assembly techniques. diff --git a/deal.II/include/deal.II/base/function_parser.h b/deal.II/include/deal.II/base/function_parser.h index 0fff67c271..77858606fc 100644 --- a/deal.II/include/deal.II/base/function_parser.h +++ b/deal.II/include/deal.II/base/function_parser.h @@ -508,8 +508,8 @@ public: /** * Return all components of a - * vector-valued function at a - * given point. + * vector-valued function at the + * given point @p p. * * values shall have the * right size beforehand, diff --git a/deal.II/include/deal.II/base/parsed_function.h b/deal.II/include/deal.II/base/parsed_function.h index 408ec9ae17..90a3202b50 100644 --- a/deal.II/include/deal.II/base/parsed_function.h +++ b/deal.II/include/deal.II/base/parsed_function.h @@ -221,8 +221,9 @@ namespace Functions void parse_parameters(ParameterHandler &prm); /** - * Get one value at the given - * point. + * Return all components of a + * vector-valued function at the + * given point @p p. */ virtual void vector_value (const Point &p, Vector &values) const; @@ -258,7 +259,7 @@ namespace Functions * The object with which we do * computations. */ - FunctionParser function_object; + FunctionParse function_object; }; } diff --git a/deal.II/include/deal.II/distributed/tria.h b/deal.II/include/deal.II/distributed/tria.h index a4c0526529..1bfe32cd5a 100644 --- a/deal.II/include/deal.II/distributed/tria.h +++ b/deal.II/include/deal.II/distributed/tria.h @@ -706,17 +706,20 @@ namespace parallel /** - * Join faces in the p4est forest due to periodic boundary conditions. + * Join faces in the p4est forest for periodic boundary conditions. As a + * result, each pair of faces will differ by at most one refinement level + * and ghost neighbors will be available across these faces. * * The vector can be filled by the function * GridTools::collect_periodic_faces. * * @todo At the moment just default orientation is implemented. * - * @note Before this function can be used the triangulation has to be + * @note Before this function can be used the Triangulation has to be * initialized and must not be refined. * Calling this function more than once is possible, but not recommended: - * The function destroys and rebuilds the p4est forest each time it is called. + * The function destroys and rebuilds the p4est forest each time it is + * called. */ void add_periodicity diff --git a/deal.II/include/deal.II/fe/fe.h b/deal.II/include/deal.II/fe/fe.h index 31fb8c8cb7..40b4c742c5 100644 --- a/deal.II/include/deal.II/fe/fe.h +++ b/deal.II/include/deal.II/fe/fe.h @@ -114,12 +114,12 @@ namespace hp * FEValues fe_values (mapping, fe, dummy_quadrature, * update_quadrature_points); * fe_values.reinit (cell); - * Point& mapped_point = fe_values.quadrature_point (i); + * Point mapped_point = fe_values.quadrature_point (i); * @endcode * * Alternatively, the points can be transformed one-by-one: * @code - * const vector >& unit_points = + * const vector > &unit_points = * fe.get_unit_support_points(); * * Point mapped_point = @@ -129,6 +129,13 @@ namespace hp * If the mapping of all support points is needed, the first variant should * be preferred for efficiency. * + * @note Finite elements' implementation of the get_unit_support_points() + * returns these points in the same order as shape functions. As a consequence, + * the quadrature points accessed above are also ordered in this way. The + * order of shape functions is typically documented in the class documentation + * of the various finite element classes. + * + * *

      Notes on the implementation of derived classes

      * * The following sections list the information to be provided by @@ -1315,7 +1322,7 @@ public: /** * Return the support points of the trial functions on the unit cell, if the - * derived finite element defines some. Finite elements that allow some + * derived finite element defines them. Finite elements that allow some * kind of interpolation operation usually have support points. On the other * hand, elements that define their degrees of freedom by, for example, * moments on faces, or as derivatives, don't have support points. In that @@ -1327,6 +1334,20 @@ public: * function. * * See the class documentation for details on support points. + * + * @note Finite elements' implementation of this function + * returns these points in the same order as shape functions. The + * order of shape functions is typically documented in the class documentation + * of the various finite element classes. In particular, shape functions (and + * consequently the mapped quadrature points discussed in the class documentation + * of this class) will then traverse first those shape functions + * located on vertices, then on lines, then on quads, etc. + * + * @note If this element implements support points, then it will return one + * such point per shape function. Since multiple shape functions may be defined + * at the same location, the support points returned here may be duplicated. An + * example would be an element of the kind FESystem(FE_Q(1),3) + * for which each support point would appear three times in the returned array. */ const std::vector > & get_unit_support_points () const; diff --git a/deal.II/include/deal.II/grid/grid_tools.h b/deal.II/include/deal.II/grid/grid_tools.h index 61ce67c53d..29cefdfe52 100644 --- a/deal.II/include/deal.II/grid/grid_tools.h +++ b/deal.II/include/deal.II/grid/grid_tools.h @@ -1065,8 +1065,8 @@ namespace GridTools /** - * This function will collect periodic face pairs on the highest (i.e. - * coarsest) mesh level. + * This function will collect periodic face pairs on the + * coarsest mesh level of the given @p container (a Triangulation or DoFHandler). * * Define a 'first' boundary as all boundary faces having boundary_id * @p b_id1 and a 'second' boundary consisting of all faces belonging @@ -1095,14 +1095,14 @@ namespace GridTools * * @author Daniel Arndt, Matthias Maier, 2013 */ - template - std::vector > + template + std::vector > collect_periodic_faces - (const DH &dof_handler, + (const CONTAINER &container, const types::boundary_id b_id1, const types::boundary_id b_id2, const int direction, - const dealii::Tensor<1,DH::space_dimension> &offset = dealii::Tensor<1,DH::space_dimension>()); + const dealii::Tensor<1,CONTAINER::space_dimension> &offset = dealii::Tensor<1,CONTAINER::space_dimension>()); /** @@ -1116,8 +1116,7 @@ namespace GridTools * face with local face index 2*dimension+1 and boundary * indicator @p b_id. * - * This function will collect periodic face pairs on the highest (i.e. - * coarsest) mesh level. + * This function will collect periodic face pairs on the coarsest mesh level. * * @note This version of collect_periodic_face_pairs will not work on * meshes with cells not in @ref GlossFaceOrientation @@ -1125,13 +1124,13 @@ namespace GridTools * * @author Daniel Arndt, Matthias Maier, 2013 */ - template - std::vector > + template + std::vector > collect_periodic_faces - (const DH &dof_handler, + (const CONTAINER &container, const types::boundary_id b_id, const int direction, - const dealii::Tensor<1,DH::space_dimension> &offset = dealii::Tensor<1,DH::space_dimension>()); + const dealii::Tensor<1,CONTAINER::space_dimension> &offset = dealii::Tensor<1,CONTAINER::space_dimension>()); /** diff --git a/deal.II/include/deal.II/lac/constraint_matrix.h b/deal.II/include/deal.II/lac/constraint_matrix.h index 7020842c8a..e6cecd0ceb 100644 --- a/deal.II/include/deal.II/lac/constraint_matrix.h +++ b/deal.II/include/deal.II/lac/constraint_matrix.h @@ -23,6 +23,7 @@ #include #include #include +#include #include @@ -150,58 +151,40 @@ public: typedef types::global_dof_index size_type; /** - * An enum that describes what should - * happen if the two ConstraintMatrix - * objects involved in a call to the - * merge() function happen to have - * constraints on the same degrees of - * freedom. + * An enum that describes what should happen if the two ConstraintMatrix + * objects involved in a call to the merge() function happen to have + * constraints on the same degrees of freedom. */ enum MergeConflictBehavior { /** - * Throw an exception if the two - * objects concerned have - * conflicting constraints on the - * same degree of freedom. + * Throw an exception if the two objects concerned have conflicting + * constraints on the same degree of freedom. */ no_conflicts_allowed, /** - * In an operation - * cm1.merge(cm2), if - * cm1 and - * cm2 have - * constraints on the same degree - * of freedom, take the one from - * cm1. + * In an operation cm1.merge(cm2), if cm1 and + * cm2 have constraints on the same degree of freedom, take + * the one from cm1. */ left_object_wins, /** - * In an operation - * cm1.merge(cm2), if - * cm1 and - * cm2 have - * constraints on the same degree - * of freedom, take the one from - * cm2. + * In an operation cm1.merge(cm2), if cm1 and + * cm2 have constraints on the same degree of freedom, take + * the one from cm2. */ right_object_wins }; /** - * Constructor. The supplied IndexSet - * defines which indices might be - * constrained inside this - * ConstraintMatrix. In a calculation - * with a - * parallel::distributed::DoFHandler one - * should use locally_relevant_dofs. The - * IndexSet allows the ConstraintMatrix - * to safe memory. Otherwise internal - * data structures for all possible - * indices will be created. + * Constructor. The supplied IndexSet defines which indices might be + * constrained inside this ConstraintMatrix. In a calculation with a + * parallel::distributed::DoFHandler one should use + * locally_relevant_dofs. The IndexSet allows the ConstraintMatrix to safe + * memory. Otherwise internal data structures for all possible indices will + * be created. */ ConstraintMatrix (const IndexSet &local_constraints = IndexSet()); @@ -211,25 +194,18 @@ public: ConstraintMatrix (const ConstraintMatrix &constraint_matrix); /** - * Reinit the ConstraintMatrix object and - * supply an IndexSet with lines that may - * be constrained. This function is only - * relevant in the distributed case to - * supply a different IndexSet. Otherwise - * this routine is equivalent to calling - * clear(). See the constructor for - * details. + * Reinit the ConstraintMatrix object and supply an IndexSet with lines that + * may be constrained. This function is only relevant in the distributed + * case to supply a different IndexSet. Otherwise this routine is equivalent + * to calling clear(). See the constructor for details. */ void reinit (const IndexSet &local_constraints = IndexSet()); /** - * Determines if we can store a - * constraint for the given @p - * line_index. This routine only matters - * in the distributed case and checks if - * the IndexSet allows storage of this - * line. Always returns true if not in - * the distributed case. + * Determines if we can store a constraint for the given @p line_index. This + * routine only matters in the distributed case and checks if the IndexSet + * allows storage of this line. Always returns true if not in the + * distributed case. */ bool can_store_line (const size_type line_index) const; @@ -242,39 +218,23 @@ public: const IndexSet & get_local_lines() const; /** - * This function copies the content of @p - * constraints_in with DoFs that are - * element of the IndexSet @p - * filter. Elements that are not present - * in the IndexSet are ignored. All DoFs - * will be transformed to local index - * space of the filter, both the - * constrained DoFs and the other DoFs - * these entries are constrained to. The - * local index space of the filter is a - * contiguous numbering of all (global) - * DoFs that are elements in the - * filter. - * - * If, for example, the filter represents - * the range [10,20), and the - * constraint matrix @p constraints_in - * includes the global indices - * {7,13,14}, the indices - * {3,4} are added to the - * calling constraint matrix (since 13 - * and 14 are elements in the filter and - * element 13 is the fourth element in - * the index, and 14 is the fifth). - * - * This function provides an easy way to - * create a ConstraintMatrix for certain - * vector components in a vector-valued - * problem from a full ConstraintMatrix, - * i.e. extracting a diagonal subblock - * from a larger ConstraintMatrix. The - * block is specified by the IndexSet - * argument. + * This function copies the content of @p constraints_in with DoFs that are + * element of the IndexSet @p filter. Elements that are not present in the + * IndexSet are ignored. All DoFs will be transformed to local index space + * of the filter, both the constrained DoFs and the other DoFs these entries + * are constrained to. The local index space of the filter is a contiguous + * numbering of all (global) DoFs that are elements in the filter. + * + * If, for example, the filter represents the range [10,20), and + * the constraint matrix @p constraints_in includes the global indices + * {7,13,14}, the indices {3,4} are added to the calling + * constraint matrix (since 13 and 14 are elements in the filter and element + * 13 is the fourth element in the index, and 14 is the fifth). + * + * This function provides an easy way to create a ConstraintMatrix for + * certain vector components in a vector-valued problem from a full + * ConstraintMatrix, i.e. extracting a diagonal subblock from a larger + * ConstraintMatrix. The block is specified by the IndexSet argument. */ void add_selected_constraints (const ConstraintMatrix &constraints_in, const IndexSet &filter); @@ -285,220 +245,147 @@ public: */ /** - * Add a new line to the matrix. If the - * line already exists, then the function - * simply returns without doing anything. + * Add a new line to the matrix. If the line already exists, then the + * function simply returns without doing anything. */ void add_line (const size_type line); /** - * Call the first add_line() function for - * every index i for which - * lines[i] is true. - * - * This function essentially exists to - * allow adding several constraints of - * the form xi=0 all at once, where - * the set of indices i for which these - * constraints should be added are given - * by the argument of this function. On - * the other hand, just as if the - * single-argument add_line() function - * were called repeatedly, the - * constraints can later be modified to - * include linear dependencies using the - * add_entry() function as well as - * inhomogeneities using + * Call the first add_line() function for every index i for + * which lines[i] is true. + * + * This function essentially exists to allow adding several constraints of + * the form xi=0 all at once, where the set of indices + * i for which these constraints should be added are given by the + * argument of this function. On the other hand, just as if the + * single-argument add_line() function were called repeatedly, the + * constraints can later be modified to include linear dependencies using + * the add_entry() function as well as inhomogeneities using * set_inhomogeneity(). */ void add_lines (const std::vector &lines); /** - * Call the first add_line() function for - * every index i that + * Call the first add_line() function for every index i that * appears in the argument. * - * This function essentially exists to - * allow adding several constraints of - * the form xi=0 all at once, where - * the set of indices i for which these - * constraints should be added are given - * by the argument of this function. On - * the other hand, just as if the - * single-argument add_line() function - * were called repeatedly, the - * constraints can later be modified to - * include linear dependencies using the - * add_entry() function as well as - * inhomogeneities using + * This function essentially exists to allow adding several constraints of + * the form xi=0 all at once, where the set of indices + * i for which these constraints should be added are given by the + * argument of this function. On the other hand, just as if the + * single-argument add_line() function were called repeatedly, the + * constraints can later be modified to include linear dependencies using + * the add_entry() function as well as inhomogeneities using * set_inhomogeneity(). */ void add_lines (const std::set &lines); /** - * Call the first add_line() function for - * every index i that + * Call the first add_line() function for every index i that * appears in the argument. * - * This function essentially exists to - * allow adding several constraints of - * the form xi=0 all at once, where - * the set of indices i for which these - * constraints should be added are given - * by the argument of this function. On - * the other hand, just as if the - * single-argument add_line() function - * were called repeatedly, the - * constraints can later be modified to - * include linear dependencies using the - * add_entry() function as well as - * inhomogeneities using + * This function essentially exists to allow adding several constraints of + * the form xi=0 all at once, where the set of indices + * i for which these constraints should be added are given by the + * argument of this function. On the other hand, just as if the + * single-argument add_line() function were called repeatedly, the + * constraints can later be modified to include linear dependencies using + * the add_entry() function as well as inhomogeneities using * set_inhomogeneity(). */ void add_lines (const IndexSet &lines); /** - * Add an entry to a given - * line. The list of lines is - * searched from the back to the - * front, so clever programming - * would add a new line (which is - * pushed to the back) and - * immediately afterwards fill - * the entries of that line. This - * way, no expensive searching is - * needed. - * - * If an entry with the same - * indices as the one this - * function call denotes already - * exists, then this function - * simply returns provided that - * the value of the entry is the - * same. Thus, it does no harm to - * enter a constraint twice. + * Add an entry to a given line. The list of lines is searched from the back + * to the front, so clever programming would add a new line (which is pushed + * to the back) and immediately afterwards fill the entries of that + * line. This way, no expensive searching is needed. + * + * If an entry with the same indices as the one this function call denotes + * already exists, then this function simply returns provided that the value + * of the entry is the same. Thus, it does no harm to enter a constraint + * twice. */ void add_entry (const size_type line, const size_type column, const double value); /** - * Add a whole series of entries, - * denoted by pairs of column indices - * and values, to a line of - * constraints. This function is - * equivalent to calling the preceding - * function several times, but is - * faster. + * Add a whole series of entries, denoted by pairs of column indices and + * values, to a line of constraints. This function is equivalent to calling + * the preceding function several times, but is faster. */ void add_entries (const size_type line, const std::vector > &col_val_pairs); /** - * Set an imhomogeneity to the - * constraint line i, according - * to the discussion in the general - * class description. + * Set an imhomogeneity to the constraint line i, according to the + * discussion in the general class description. * - * @note the line needs to be added with - * one of the add_line() calls first. + * @note the line needs to be added with one of the add_line() calls first. */ void set_inhomogeneity (const size_type line, const double value); /** - * Close the filling of entries. Since - * the lines of a matrix of this type - * are usually filled in an arbitrary - * order and since we do not want to - * use associative constainers to store - * the lines, we need to sort the lines - * and within the lines the columns - * before usage of the matrix. This is - * done through this function. - * - * Also, zero entries are discarded, - * since they are not needed. - * - * After closing, no more entries are - * accepted. If the object was already - * closed, then this function returns - * immediately. - * - * This function also resolves chains - * of constraints. For example, degree - * of freedom 13 may be constrained to - * u13=u3/2+u7/2 while degree of - * freedom 7 is itself constrained as - * u7=u2/2+u4/2. Then, the - * resolution will be that - * u13=u3/2+u2/4+u4/4. Note, - * however, that cycles in this graph - * of constraints are not allowed, - * i.e. for example u4 may not be - * constrained, directly or indirectly, - * to u13 again. + * Close the filling of entries. Since the lines of a matrix of this type + * are usually filled in an arbitrary order and since we do not want to use + * associative constainers to store the lines, we need to sort the lines and + * within the lines the columns before usage of the matrix. This is done + * through this function. + * + * Also, zero entries are discarded, since they are not needed. + * + * After closing, no more entries are accepted. If the object was already + * closed, then this function returns immediately. + * + * This function also resolves chains of constraints. For example, degree of + * freedom 13 may be constrained to $u_{13} = \frac{u_3}{2} + \frac{u_7}{2}$ + * while degree of freedom 7 is itself constrained as $u_{7} = \frac{u_2}{2} + * + \frac{u_4}{2}$. Then, the resolution will be that $u_{13} = + * \frac{u_3}{2} + \frac{u_2}{4} + \frac{u_4}{4}$. Note, however, that + * cycles in this graph of constraints are not allowed, i.e. for example + * $u_4$ may not be constrained, directly or indirectly, to $u_{13}$ again. */ void close (); /** - * Merge the constraints represented by - * the object given as argument into - * the constraints represented by this - * object. Both objects may or may not - * be closed (by having their function - * close() called before). If this - * object was closed before, then it - * will be closed afterwards as - * well. Note, however, that if the - * other argument is closed, then - * merging may be significantly faster. - * - * Using the default value of the second - * arguments, the constraints in each of - * the two objects (the old one - * represented by this object and the - * argument) may not refer to the same - * degree of freedom, i.e. a degree of - * freedom that is constrained in one - * object may not be constrained in the - * second. If this is nevertheless the - * case, an exception is thrown. However, - * this behavior can be changed by - * providing a different value for the - * second argument. + * Merge the constraints represented by the object given as argument into + * the constraints represented by this object. Both objects may or may not + * be closed (by having their function close() called before). If this + * object was closed before, then it will be closed afterwards as + * well. Note, however, that if the other argument is closed, then merging + * may be significantly faster. + * + * Using the default value of the second arguments, the constraints in each + * of the two objects (the old one represented by this object and the + * argument) may not refer to the same degree of freedom, i.e. a degree of + * freedom that is constrained in one object may not be constrained in the + * second. If this is nevertheless the case, an exception is + * thrown. However, this behavior can be changed by providing a different + * value for the second argument. */ void merge (const ConstraintMatrix &other_constraints, const MergeConflictBehavior merge_conflict_behavior = no_conflicts_allowed); /** - * Shift all entries of this matrix - * down @p offset rows and over @p - * offset columns. + * Shift all entries of this matrix down @p offset rows and over @p offset + * columns. * - * This function is useful if you are - * building block matrices, where all - * blocks are built by the same - * DoFHandler object, i.e. the matrix - * size is larger than the number of - * degrees of freedom. Since several - * matrix rows and columns correspond - * to the same degrees of freedom, - * you'd generate several constraint - * objects, then shift them, and - * finally merge() them together - * again. + * This function is useful if you are building block matrices, where all + * blocks are built by the same DoFHandler object, i.e. the matrix size is + * larger than the number of degrees of freedom. Since several matrix rows + * and columns correspond to the same degrees of freedom, you'd generate + * several constraint objects, then shift them, and finally merge() them + * together again. */ void shift (const size_type offset); /** - * Clear all entries of this - * matrix. Reset the flag determining - * whether new entries are accepted or - * not. + * Clear all entries of this matrix. Reset the flag determining whether new + * entries are accepted or not. * - * This function may be called also on - * objects which are empty or already + * This function may be called also on objects which are empty or already * cleared. */ void clear (); @@ -514,51 +401,37 @@ public: */ /** - * Return number of constraints stored in - * this matrix. + * Return number of constraints stored in this matrix. */ size_type n_constraints () const; /** - * Return whether the degree of freedom - * with number @p index is a + * Return whether the degree of freedom with number @p index is a * constrained one. * - * Note that if close() was called - * before, then this function is - * significantly faster, since then the - * constrained degrees of freedom are - * sorted and we can do a binary - * search, while before close() was - * called, we have to perform a linear - * search through all entries. + * Note that if close() was called before, then this function is + * significantly faster, since then the constrained degrees of freedom are + * sorted and we can do a binary search, while before close() was called, we + * have to perform a linear search through all entries. */ bool is_constrained (const size_type index) const; /** - * Return whether the dof is - * constrained, and whether it is - * constrained to only one other degree - * of freedom with weight one. The - * function therefore returns whether - * the degree of freedom would simply - * be eliminated in favor of exactly - * one other degree of freedom. - * - * The function returns @p false if - * either the degree of freedom is not - * constrained at all, or if it is - * constrained to more than one other - * degree of freedom, or if it is - * constrained to only one degree of - * freedom but with a weight different - * from one. + * Return whether the dof is constrained, and whether it is constrained to + * only one other degree of freedom with weight one. The function therefore + * returns whether the degree of freedom would simply be eliminated in favor + * of exactly one other degree of freedom. + * + * The function returns @p false if either the degree of freedom is not + * constrained at all, or if it is constrained to more than one other degree + * of freedom, or if it is constrained to only one degree of freedom but + * with a weight different from one. */ bool is_identity_constrained (const size_type index) const; /** - * Return whether the two given degrees of freedom are linked by an - * equality constraint that either constrains index1 to be so that + * Return whether the two given degrees of freedom are linked by an equality + * constraint that either constrains index1 to be so that * index1=index2 or constrains index2 so that * index2=index1. */ @@ -566,105 +439,78 @@ public: const size_type index2) const; /** - * Return the maximum number of other - * dofs that one dof is constrained - * to. For example, in 2d a hanging - * node is constrained only to its two - * neighbors, so the returned value - * would be 2. However, for higher - * order elements and/or higher - * dimensions, or other types of - * constraints, this number is no more - * obvious. + * Return the maximum number of other dofs that one dof is constrained + * to. For example, in 2d a hanging node is constrained only to its two + * neighbors, so the returned value would be 2. However, for higher order + * elements and/or higher dimensions, or other types of constraints, this + * number is no more obvious. * - * The name indicates that within the - * system matrix, references to a - * constrained node are indirected to - * the nodes it is constrained to. + * The name indicates that within the system matrix, references to a + * constrained node are indirected to the nodes it is constrained to. */ size_type max_constraint_indirections () const; /** - * Returns true in case the - * dof is constrained and there is a - * non-trivial inhomogeneous valeus set - * to the dof. + * Returns true in case the dof is constrained and there is a + * non-trivial inhomogeneous valeus set to the dof. */ bool is_inhomogeneously_constrained (const size_type index) const; /** - * Returns false if all - * constraints in the ConstraintMatrix - * are homogeneous ones, and - * true if there is at least - * one inhomogeneity. + * Returns false if all constraints in the ConstraintMatrix are + * homogeneous ones, and true if there is at least one + * inhomogeneity. */ bool has_inhomogeneities () const; /** - * Returns a pointer to the the vector of - * entries if a line is constrained, and a - * zero pointer in case the dof is not - * constrained. + * Returns a pointer to the the vector of entries if a line is constrained, + * and a zero pointer in case the dof is not constrained. */ const std::vector > * get_constraint_entries (const size_type line) const; /** - * Returns the value of the inhomogeneity - * stored in the constrained dof @p - * line. Unconstrained dofs also return a - * zero value. + * Returns the value of the inhomogeneity stored in the constrained dof @p + * line. Unconstrained dofs also return a zero value. */ double get_inhomogeneity (const size_type line) const; /** - * Print the constraint lines. Mainly - * for debugging purposes. + * Print the constraint lines. Mainly for debugging purposes. * - * This function writes out all entries - * in the constraint matrix lines with - * their value in the form row col - * : value. Unconstrained lines - * containing only one identity entry - * are not stored in this object and - * are not printed. + * This function writes out all entries in the constraint matrix lines with + * their value in the form row col : value. Unconstrained lines + * containing only one identity entry are not stored in this object and are + * not printed. */ void print (std::ostream &) const; /** - * Write the graph of constraints in - * 'dot' format. 'dot' is a program - * that can take a list of nodes and - * produce a graphical representation - * of the graph of constrained degrees - * of freedom and the degrees of - * freedom they are constrained to. + * Write the graph of constraints in 'dot' format. 'dot' is a program that + * can take a list of nodes and produce a graphical representation of the + * graph of constrained degrees of freedom and the degrees of freedom they + * are constrained to. * - * The output of this function can be - * used as input to the 'dot' program - * that can convert the graph into a - * graphical representation in - * postscript, png, xfig, and a number - * of other formats. + * The output of this function can be used as input to the 'dot' program + * that can convert the graph into a graphical representation in postscript, + * png, xfig, and a number of other formats. * - * This function exists mostly for - * debugging purposes. + * This function exists mostly for debugging purposes. */ void write_dot (std::ostream &) const; /** - * Determine an estimate for the memory - * consumption (in bytes) of this + * Determine an estimate for the memory consumption (in bytes) of this * object. */ std::size_t memory_consumption () const; /** * Add the constraint indices associated to the indices in the given vector. - * After a call to this function, the indices vector contains the - * initial elements and all the associated constrained indices. This - * function sorts the elements and suppresses duplicates. + * After a call to this function, the indices vector contains the initial + * elements and all the associated constrained indices. This function sorts + * the elements and suppresses duplicates. */ void resolve_indices(std::vector &indices) const; @@ -678,150 +524,100 @@ public: */ /** - * Condense a given sparsity - * pattern. This function assumes the - * uncondensed matrix struct to be - * compressed and the one to be filled - * to be empty. The condensed structure - * is compressed afterwards. + * Condense a given sparsity pattern. This function assumes the uncondensed + * matrix struct to be compressed and the one to be filled to be empty. The + * condensed structure is compressed afterwards. * - * The constraint matrix object must be - * closed to call this function. + * The constraint matrix object must be closed to call this function. * - * @note The hanging nodes are - * completely eliminated from the - * linear system referring to - * condensed. Therefore, the - * dimension of condensed is - * the dimension of - * uncondensed minus the - * number of constrained degrees of - * freedom. + * @note The hanging nodes are completely eliminated from the linear system + * referring to condensed. Therefore, the dimension of + * condensed is the dimension of uncondensed minus the + * number of constrained degrees of freedom. */ void condense (const SparsityPattern &uncondensed, SparsityPattern &condensed) const; /** - * This function does much the same as - * the above one, except that it - * condenses the matrix struct - * 'in-place'. It does not remove - * nonzero entries from the matrix but - * adds those needed for the process of - * distribution of the constrained - * degrees of freedom. + * This function does much the same as the above one, except that it + * condenses the matrix struct 'in-place'. It does not remove nonzero + * entries from the matrix but adds those needed for the process of + * distribution of the constrained degrees of freedom. * - * Since this function adds new nonzero - * entries to the sparsity pattern, the - * argument must not be - * compressed. However the constraint - * matrix must be closed. The matrix - * struct is compressed at the end of - * the function. + * Since this function adds new nonzero entries to the sparsity pattern, the + * argument must not be compressed. However the constraint matrix must be + * closed. The matrix struct is compressed at the end of the function. */ void condense (SparsityPattern &sparsity) const; /** - * Same function as above, but - * condenses square block sparsity - * patterns. + * Same function as above, but condenses square block sparsity patterns. */ void condense (BlockSparsityPattern &sparsity) const; /** - * Same function as above, but - * condenses square compressed sparsity + * Same function as above, but condenses square compressed sparsity * patterns. * - * Given the data structure used by - * CompressedSparsityPattern, this - * function becomes quadratic in the - * number of degrees of freedom for - * large problems and can dominate - * setting up linear systems when - * several hundred thousand or millions - * of unknowns are involved and for - * problems with many nonzero elements - * per row (for example for - * vector-valued problems or hp finite - * elements). In this case, it is - * advisable to use the - * CompressedSetSparsityPattern class - * instead, see for example @ref - * step_27 "step-27", or to use the - * CompressedSimpleSparsityPattern - * class, see for example @ref step_31 - * "step-31". + * Given the data structure used by CompressedSparsityPattern, this function + * becomes quadratic in the number of degrees of freedom for large problems + * and can dominate setting up linear systems when several hundred thousand + * or millions of unknowns are involved and for problems with many nonzero + * elements per row (for example for vector-valued problems or hp finite + * elements). In this case, it is advisable to use the + * CompressedSetSparsityPattern class instead, see for example @ref step_27 + * "step-27", or to use the CompressedSimpleSparsityPattern class, see for + * example @ref step_31 "step-31". */ void condense (CompressedSparsityPattern &sparsity) const; /** - * Same function as above, but - * condenses compressed sparsity - * patterns, which are based on the - * std::set container. + * Same function as above, but condenses compressed sparsity patterns, which + * are based on the std::set container. */ void condense (CompressedSetSparsityPattern &sparsity) const; /** - * Same function as above, but - * condenses compressed sparsity - * patterns, which are based on the - * ''simple'' aproach. + * Same function as above, but condenses compressed sparsity patterns, which + * are based on the ''simple'' aproach. */ void condense (CompressedSimpleSparsityPattern &sparsity) const; /** - * Same function as above, but - * condenses square compressed sparsity + * Same function as above, but condenses square compressed sparsity * patterns. * - * Given the data structure used by - * BlockCompressedSparsityPattern, this - * function becomes quadratic in the - * number of degrees of freedom for - * large problems and can dominate - * setting up linear systems when - * several hundred thousand or millions - * of unknowns are involved and for - * problems with many nonzero elements - * per row (for example for - * vector-valued problems or hp finite - * elements). In this case, it is - * advisable to use the - * BlockCompressedSetSparsityPattern - * class instead, see for example @ref - * step_27 "step-27" and @ref step_31 - * "step-31". + * Given the data structure used by BlockCompressedSparsityPattern, this + * function becomes quadratic in the number of degrees of freedom for large + * problems and can dominate setting up linear systems when several hundred + * thousand or millions of unknowns are involved and for problems with many + * nonzero elements per row (for example for vector-valued problems or hp + * finite elements). In this case, it is advisable to use the + * BlockCompressedSetSparsityPattern class instead, see for example @ref + * step_27 "step-27" and @ref step_31 "step-31". */ void condense (BlockCompressedSparsityPattern &sparsity) const; /** - * Same function as above, but - * condenses square compressed sparsity + * Same function as above, but condenses square compressed sparsity * patterns. */ void condense (BlockCompressedSetSparsityPattern &sparsity) const; /** - * Same function as above, but - * condenses square compressed sparsity + * Same function as above, but condenses square compressed sparsity * patterns. */ void condense (BlockCompressedSimpleSparsityPattern &sparsity) const; /** - * Condense a given matrix. The - * associated matrix struct should be - * condensed and compressed. It is the - * user's responsibility to guarantee - * that all entries in the @p condensed - * matrix be zero! + * Condense a given matrix. The associated matrix struct should be condensed + * and compressed. It is the user's responsibility to guarantee that all + * entries in the @p condensed matrix be zero! * - * The constraint matrix object must be - * closed to call this function. + * The constraint matrix object must be closed to call this function. * * @deprecated The functions converting an uncondensed matrix into * its condensed form are deprecated. Use the functions doing the @@ -832,42 +628,30 @@ public: SparseMatrix &condensed) const DEAL_II_DEPRECATED; /** - * This function does much the same as - * the above one, except that it - * condenses the matrix 'in-place'. See - * the general documentation of this + * This function does much the same as the above one, except that it + * condenses the matrix 'in-place'. See the general documentation of this * class for more detailed information. */ template void condense (SparseMatrix &matrix) const; /** - * Same function as above, but - * condenses square block sparse - * matrices. + * Same function as above, but condenses square block sparse matrices. */ template void condense (BlockSparseMatrix &matrix) const; /** - * Condense the given vector @p - * uncondensed into @p condensed. It is - * the user's responsibility to - * guarantee that all entries of @p - * condensed be zero. Note that this - * function does not take any - * inhomogeneity into account and - * throws an exception in case there - * are any inhomogeneities. Use - * the function using both a matrix and - * vector for that case. - * - * The @p VectorType may be a - * Vector, Vector, - * BlockVector<...>, a PETSc - * or Trilinos vector wrapper class, or - * any other type having the same - * interface. + * Condense the given vector @p uncondensed into @p condensed. It is the + * user's responsibility to guarantee that all entries of @p condensed be + * zero. Note that this function does not take any inhomogeneity into + * account and throws an exception in case there are any + * inhomogeneities. Use the function using both a matrix and vector for that + * case. + * + * The @p VectorType may be a Vector, Vector, + * BlockVector<...>, a PETSc or Trilinos vector wrapper class, or + * any other type having the same interface. * * @deprecated The functions converting an uncondensed matrix into * its condensed form are deprecated. Use the functions doing the @@ -878,36 +662,25 @@ public: VectorType &condensed) const DEAL_II_DEPRECATED; /** - * Condense the given vector - * in-place. The @p VectorType may be a - * Vector, Vector, - * BlockVector<...>, a PETSc - * or Trilinos vector wrapper class, or - * any other type having the same - * interface. Note that this function - * does not take any inhomogeneity into - * account and throws an exception in - * case there are any - * inhomogeneities. Use the function - * using both a matrix and vector for - * that case. + * Condense the given vector in-place. The @p VectorType may be a + * Vector, Vector, BlockVector<...>, a PETSc or + * Trilinos vector wrapper class, or any other type having the same + * interface. Note that this function does not take any inhomogeneity into + * account and throws an exception in case there are any + * inhomogeneities. Use the function using both a matrix and vector for that + * case. */ template void condense (VectorType &vec) const; /** - * Condense a given matrix and a given - * vector. The associated matrix struct - * should be condensed and - * compressed. It is the user's - * responsibility to guarantee that all - * entries in the @p condensed matrix - * and vector be zero! This function is - * the appropriate choice for applying - * inhomogeneous constraints. + * Condense a given matrix and a given vector. The associated matrix struct + * should be condensed and compressed. It is the user's responsibility to + * guarantee that all entries in the @p condensed matrix and vector be zero! + * This function is the appropriate choice for applying inhomogeneous + * constraints. * - * The constraint matrix object must be - * closed to call this function. + * The constraint matrix object must be closed to call this function. * * @deprecated The functions converting an uncondensed matrix into * its condensed form are deprecated. Use the functions doing the @@ -920,36 +693,27 @@ public: VectorType &condensed_vector) const DEAL_II_DEPRECATED; /** - * This function does much the same as - * the above one, except that it - * condenses matrix and vector - * 'in-place'. See the general - * documentation of this class for more - * detailed information. + * This function does much the same as the above one, except that it + * condenses matrix and vector 'in-place'. See the general documentation of + * this class for more detailed information. */ template void condense (SparseMatrix &matrix, VectorType &vector) const; /** - * Same function as above, but - * condenses square block sparse - * matrices and vectors. + * Same function as above, but condenses square block sparse matrices and + * vectors. */ template void condense (BlockSparseMatrix &matrix, BlockVectorType &vector) const; /** - * Sets the values of all constrained - * DoFs in a vector to zero. - * The @p VectorType may be a - * Vector, Vector, - * BlockVector<...>, a - * PETSc or Trilinos vector - * wrapper class, or any other - * type having the same - * interface. + * Sets the values of all constrained DoFs in a vector to zero. The @p + * VectorType may be a Vector, Vector, + * BlockVector<...>, a PETSc or Trilinos vector wrapper class, or + * any other type having the same interface. */ template void set_zero (VectorType &vec) const; @@ -964,59 +728,40 @@ public: */ /** - * This function takes a vector of - * local contributions (@p - * local_vector) corresponding to the - * degrees of freedom indices given in - * @p local_dof_indices and distributes - * them to the global vector. In most - * cases, these local contributions - * will be the result of an integration - * over a cell or face of a - * cell. However, as long as @p - * local_vector and @p - * local_dof_indices have the same - * number of elements, this function is - * happy with whatever it is - * given. - * - * In contrast to the similar function - * in the DoFAccessor class, this - * function also takes care of - * constraints, i.e. if one of the - * elements of @p local_dof_indices - * belongs to a constrained node, then - * rather than writing the - * corresponding element of @p - * local_vector into @p global_vector, - * the element is distributed to the - * entries in the global vector to - * which this particular degree of - * freedom is constrained. - * - * Thus, by using this function to - * distribute local contributions to the - * global object, one saves the call to - * the condense function after the - * vectors and matrices are fully - * assembled. On the other hand, by - * consequence, the function does not - * only write into the entries enumerated - * by the @p local_dof_indices array, but - * also (possibly) others as necessary. - * - * Note that this function will apply all - * constraints as if they were - * homogeneous. For correctly setting - * inhomogeneous constraints, use the - * similar function with a matrix - * argument or the function with both - * matrix and vector arguments. - * - * @note This function is not - * thread-safe, so you will need to make - * sure that only one process at a time - * calls this function. + * This function takes a vector of local contributions (@p local_vector) + * corresponding to the degrees of freedom indices given in @p + * local_dof_indices and distributes them to the global vector. In most + * cases, these local contributions will be the result of an integration + * over a cell or face of a cell. However, as long as @p local_vector and @p + * local_dof_indices have the same number of elements, this function is + * happy with whatever it is given. + * + * In contrast to the similar function in the DoFAccessor class, this + * function also takes care of constraints, i.e. if one of the elements of + * @p local_dof_indices belongs to a constrained node, then rather than + * writing the corresponding element of @p local_vector into @p + * global_vector, the element is distributed to the entries in the global + * vector to which this particular degree of freedom is constrained. + * + * Thus, by using this function to distribute local contributions to the + * global object, one saves the call to the condense function after the + * vectors and matrices are fully assembled. On the other hand, by + * consequence, the function does not only write into the entries enumerated + * by the @p local_dof_indices array, but also (possibly) others as + * necessary. + * + * Note that this function will apply all constraints as if they were + * homogeneous. For correctly setting inhomogeneous constraints, use the + * similar function with a matrix argument or the function with both matrix + * and vector arguments. + * + * @note This function in itself is thread-safe, i.e., it works properly + * also when several threads call it simultaneously. However, the function + * call is only thread-safe if the underlying global vector allows + * for simultaneous access and the access is not to rows with the same + * global index at the same time. This needs to be made sure from the + * caller's site. There is no locking mechanism inside this method to + * prevent data races. */ template void @@ -1025,75 +770,47 @@ public: OutVector &global_vector) const; /** - * This function takes a vector of - * local contributions (@p - * local_vector) corresponding to the - * degrees of freedom indices given in - * @p local_dof_indices and distributes - * them to the global vector. In most - * cases, these local contributions - * will be the result of an integration - * over a cell or face of a - * cell. However, as long as @p - * local_vector and @p - * local_dof_indices have the same - * number of elements, this function is - * happy with whatever it is - * given. - * - * In contrast to the similar function in - * the DoFAccessor class, this function - * also takes care of constraints, - * i.e. if one of the elements of @p - * local_dof_indices belongs to a - * constrained node, then rather than - * writing the corresponding element of - * @p local_vector into @p global_vector, - * the element is distributed to the - * entries in the global vector to which - * this particular degree of freedom is - * constrained. - * - * Thus, by using this function to - * distribute local contributions to the - * global object, one saves the call to - * the condense function after the - * vectors and matrices are fully - * assembled. On the other hand, by - * consequence, the function does not - * only write into the entries enumerated - * by the @p local_dof_indices array, but - * also (possibly) others as - * necessary. This includes writing into - * diagonal elements of the matrix if the - * corresponding degree of freedom is - * constrained. + * This function takes a vector of local contributions (@p local_vector) + * corresponding to the degrees of freedom indices given in @p + * local_dof_indices and distributes them to the global vector. In most + * cases, these local contributions will be the result of an integration + * over a cell or face of a cell. However, as long as @p local_vector and @p + * local_dof_indices have the same number of elements, this function is + * happy with whatever it is given. * - * The fourth argument - * local_matrix is intended to - * be used in case one wants to apply - * inhomogeneous constraints on the - * vector only. Such a situation could be - * where one wants to assemble of a right - * hand side vector on a problem with - * inhomogeneous constraints, but the - * global matrix has been assembled - * previously. A typical example of this - * is a time stepping algorithm where the - * stiffness matrix is assembled once, - * and the right hand side updated every - * time step. Note that, however, the - * entries in the columns of the local - * matrix have to be exactly the same as - * those that have been written into the - * global matrix. Otherwise, this - * function will not be able to correctly - * handle inhomogeneities. - * - * @note This function is not - * thread-safe, so you will need to make - * sure that only one process at a time - * calls this function. + * In contrast to the similar function in the DoFAccessor class, this + * function also takes care of constraints, i.e. if one of the elements of + * @p local_dof_indices belongs to a constrained node, then rather than + * writing the corresponding element of @p local_vector into @p + * global_vector, the element is distributed to the entries in the global + * vector to which this particular degree of freedom is constrained. + * + * Thus, by using this function to distribute local contributions to the + * global object, one saves the call to the condense function after the + * vectors and matrices are fully assembled. On the other hand, by + * consequence, the function does not only write into the entries enumerated + * by the @p local_dof_indices array, but also (possibly) others as + * necessary. This includes writing into diagonal elements of the matrix if + * the corresponding degree of freedom is constrained. + * + * The fourth argument local_matrix is intended to be used in case + * one wants to apply inhomogeneous constraints on the vector only. Such a + * situation could be where one wants to assemble of a right hand side + * vector on a problem with inhomogeneous constraints, but the global matrix + * has been assembled previously. A typical example of this is a time + * stepping algorithm where the stiffness matrix is assembled once, and the + * right hand side updated every time step. Note that, however, the entries + * in the columns of the local matrix have to be exactly the same as those + * that have been written into the global matrix. Otherwise, this function + * will not be able to correctly handle inhomogeneities. + * + * @note This function in itself is thread-safe, i.e., it works properly + * also when several threads call it simultaneously. However, the function + * call is only thread-safe if the underlying global vector allows + * for simultaneous access and the access is not to rows with the same + * global index at the same time. This needs to be made sure from the + * caller's site. There is no locking mechanism inside this method to + * prevent data races. */ template void @@ -1103,8 +820,7 @@ public: const FullMatrix &local_matrix) const; /** - * Enter a single value into a - * result vector, obeying constraints. + * Enter a single value into a result vector, obeying constraints. */ template void @@ -1113,45 +829,32 @@ public: VectorType &global_vector) const; /** - * This function takes a pointer to a - * vector of local contributions (@p - * local_vector) corresponding to the - * degrees of freedom indices given in - * @p local_dof_indices and distributes - * them to the global vector. In most - * cases, these local contributions - * will be the result of an integration - * over a cell or face of a - * cell. However, as long as the - * entries in @p local_dof_indices - * indicate reasonable global vector - * entries, this function is happy with - * whatever it is given. - * - * If one of the elements of @p - * local_dof_indices belongs to a - * constrained node, then rather than - * writing the corresponding element of - * @p local_vector into @p - * global_vector, the element is - * distributed to the entries in the - * global vector to which this - * particular degree of freedom is - * constrained. - * - * Thus, by using this function to - * distribute local contributions to - * the global object, one saves the - * call to the condense function after - * the vectors and matrices are fully - * assembled. Note that this function - * completely ignores inhomogeneous - * constraints. - * - * @note This function is not - * thread-safe, so you will need to - * make sure that only one process at a - * time calls this function. + * This function takes a pointer to a vector of local contributions (@p + * local_vector) corresponding to the degrees of freedom indices given in @p + * local_dof_indices and distributes them to the global vector. In most + * cases, these local contributions will be the result of an integration + * over a cell or face of a cell. However, as long as the entries in @p + * local_dof_indices indicate reasonable global vector entries, this + * function is happy with whatever it is given. + * + * If one of the elements of @p local_dof_indices belongs to a constrained + * node, then rather than writing the corresponding element of @p + * local_vector into @p global_vector, the element is distributed to the + * entries in the global vector to which this particular degree of freedom + * is constrained. + * + * Thus, by using this function to distribute local contributions to the + * global object, one saves the call to the condense function after the + * vectors and matrices are fully assembled. Note that this function + * completely ignores inhomogeneous constraints. + * + * @note This function in itself is thread-safe, i.e., it works properly + * also when several threads call it simultaneously. However, the function + * call is only thread-safe if the underlying global vector allows + * for simultaneous access and the access is not to rows with the same + * global index at the same time. This needs to be made sure from the + * caller's site. There is no locking mechanism inside this method to + * prevent data races. */ template @@ -1162,71 +865,45 @@ public: VectorType &global_vector) const; /** - * This function takes a matrix of - * local contributions (@p - * local_matrix) corresponding to the - * degrees of freedom indices given in - * @p local_dof_indices and distributes - * them to the global matrix. In most - * cases, these local contributions - * will be the result of an integration - * over a cell or face of a - * cell. However, as long as @p - * local_matrix and @p - * local_dof_indices have the same - * number of elements, this function is + * This function takes a matrix of local contributions (@p local_matrix) + * corresponding to the degrees of freedom indices given in @p + * local_dof_indices and distributes them to the global matrix. In most + * cases, these local contributions will be the result of an integration + * over a cell or face of a cell. However, as long as @p local_matrix and @p + * local_dof_indices have the same number of elements, this function is * happy with whatever it is given. * - * In contrast to the similar function - * in the DoFAccessor class, this - * function also takes care of - * constraints, i.e. if one of the - * elements of @p local_dof_indices - * belongs to a constrained node, then - * rather than writing the - * corresponding element of @p - * local_matrix into @p global_matrix, - * the element is distributed to the - * entries in the global matrix to - * which this particular degree of - * freedom is constrained. - * - * With this scheme, we never write - * into rows or columns of constrained - * degrees of freedom. In order to make - * sure that the resulting matrix can - * still be inverted, we need to do - * something with the diagonal elements - * corresponding to constrained - * nodes. Thus, if a degree of freedom - * in @p local_dof_indices is - * constrained, we distribute the - * corresponding entries in the matrix, - * but also add the absolute value of - * the diagonal entry of the local - * matrix to the corresponding entry in - * the global matrix. Since the exact - * value of the diagonal element is not - * important (the value of the - * respective degree of freedom will be - * overwritten by the distribute() call - * later on anyway), this guarantees - * that the diagonal entry is always - * non-zero, positive, and of the same - * order of magnitude as the other + * In contrast to the similar function in the DoFAccessor class, this + * function also takes care of constraints, i.e. if one of the elements of + * @p local_dof_indices belongs to a constrained node, then rather than + * writing the corresponding element of @p local_matrix into @p + * global_matrix, the element is distributed to the entries in the global + * matrix to which this particular degree of freedom is constrained. + * + * With this scheme, we never write into rows or columns of constrained + * degrees of freedom. In order to make sure that the resulting matrix can + * still be inverted, we need to do something with the diagonal elements + * corresponding to constrained nodes. Thus, if a degree of freedom in @p + * local_dof_indices is constrained, we distribute the corresponding entries + * in the matrix, but also add the absolute value of the diagonal entry of + * the local matrix to the corresponding entry in the global matrix. Since + * the exact value of the diagonal element is not important (the value of + * the respective degree of freedom will be overwritten by the distribute() + * call later on anyway), this guarantees that the diagonal entry is always + * non-zero, positive, and of the same order of magnitude as the other * entries of the matrix. * - * Thus, by using this function to - * distribute local contributions to - * the global object, one saves the - * call to the condense function after - * the vectors and matrices are fully - * assembled. + * Thus, by using this function to distribute local contributions to the + * global object, one saves the call to the condense function after the + * vectors and matrices are fully assembled. * - * @note This function is not - * thread-safe, so you will need to - * make sure that only one process at a - * time calls this function. + * @note This function in itself is thread-safe, i.e., it works properly + * also when several threads call it simultaneously. However, the function + * call is only thread-safe if the underlying global matrix allows + * for simultaneous access and the access is not to rows with the same + * global index at the same time. This needs to be made sure from the + * caller's site. There is no locking mechanism inside this method to + * prevent data races. */ template void @@ -1235,9 +912,7 @@ public: MatrixType &global_matrix) const; /** - * Does the same as the function - * above but can treat non - * quadratic matrices. + * Does the same as the function above but can treat non quadratic matrices. */ template void @@ -1247,22 +922,19 @@ public: MatrixType &global_matrix) const; /** - * This function simultaneously - * writes elements into matrix - * and vector, according to the - * constraints specified by the - * calling ConstraintMatrix. This - * function can correctly handle - * inhomogeneous constraints as - * well. For the parameter - * use_inhomogeneities_for_rhs - * see the documentation in @ref - * constraints module. + * This function simultaneously writes elements into matrix and vector, + * according to the constraints specified by the calling + * ConstraintMatrix. This function can correctly handle inhomogeneous + * constraints as well. For the parameter use_inhomogeneities_for_rhs see + * the documentation in @ref constraints module. * - * @note This function is not - * thread-safe, so you will need to - * make sure that only one process at a - * time calls this function. + * @note This function in itself is thread-safe, i.e., it works properly + * also when several threads call it simultaneously. However, the function + * call is only thread-safe if the underlying global matrix and vector allow + * for simultaneous access and the access is not to rows with the same + * global index at the same time. This needs to be made sure from the + * caller's site. There is no locking mechanism inside this method to + * prevent data races. */ template void @@ -1274,97 +946,67 @@ public: bool use_inhomogeneities_for_rhs = false) const; /** - * Do a similar operation as the - * distribute_local_to_global() function - * that distributes writing entries into - * a matrix for constrained degrees of - * freedom, except that here we don't - * write into a matrix but only allocate + * Do a similar operation as the distribute_local_to_global() function that + * distributes writing entries into a matrix for constrained degrees of + * freedom, except that here we don't write into a matrix but only allocate * sparsity pattern entries. * - * As explained in the - * @ref hp_paper "hp paper" - * and in step-27, - * first allocating a sparsity pattern - * and later coming back and allocating - * additional entries for those matrix - * entries that will be written to due to - * the elimination of constrained degrees - * of freedom (using - * ConstraintMatrix::condense() ), can be - * a very expensive procedure. It is - * cheaper to allocate these entries - * right away without having to do a - * second pass over the sparsity pattern - * object. This function does exactly + * As explained in the @ref hp_paper "hp paper" and in step-27, first + * allocating a sparsity pattern and later coming back and allocating + * additional entries for those matrix entries that will be written to due + * to the elimination of constrained degrees of freedom (using + * ConstraintMatrix::condense() ), can be a very expensive procedure. It is + * cheaper to allocate these entries right away without having to do a + * second pass over the sparsity pattern object. This function does exactly * that. * - * Because the function only allocates - * entries in a sparsity pattern, all it - * needs to know are the degrees of - * freedom that couple to each - * other. Unlike the previous function, - * no actual values are written, so the - * second input argument is not necessary - * here. - * - * The third argument to this function, - * keep_constrained_entries determines - * whether the function shall allocate - * entries in the sparsity pattern at - * all for entries that will later be - * set to zero upon condensation of the - * matrix. These entries are necessary - * if the matrix is built - * unconstrained, and only later - * condensed. They are not necessary if - * the matrix is built using the - * distribute_local_to_global() - * function of this class which - * distributes entries right away when - * copying a local matrix into a global - * object. The default of this argument - * is true, meaning to allocate the few - * entries that may later be set to - * zero. - * - * By default, the function adds - * entries for all pairs of indices - * given in the first argument to the - * sparsity pattern (unless - * keep_constrained_entries is - * false). However, sometimes one would - * like to only add a subset of all of - * these pairs. In that case, the last - * argument can be used which specifies - * a boolean mask which of the pairs of - * indices should be considered. If the - * mask is false for a pair of indices, - * then no entry will be added to the - * sparsity pattern for this pair, - * irrespective of whether one or both - * of the indices correspond to - * constrained degrees of freedom. - * - * This function is not typically called - * from user code, but is used in the - * DoFTools::make_sparsity_pattern() - * function when passed a constraint + * Because the function only allocates entries in a sparsity pattern, all it + * needs to know are the degrees of freedom that couple to each + * other. Unlike the previous function, no actual values are written, so the + * second input argument is not necessary here. + * + * The third argument to this function, keep_constrained_entries determines + * whether the function shall allocate entries in the sparsity pattern at + * all for entries that will later be set to zero upon condensation of the + * matrix. These entries are necessary if the matrix is built unconstrained, + * and only later condensed. They are not necessary if the matrix is built + * using the distribute_local_to_global() function of this class which + * distributes entries right away when copying a local matrix into a global + * object. The default of this argument is true, meaning to allocate the few + * entries that may later be set to zero. + * + * By default, the function adds entries for all pairs of indices given in + * the first argument to the sparsity pattern (unless + * keep_constrained_entries is false). However, sometimes one would like to + * only add a subset of all of these pairs. In that case, the last argument + * can be used which specifies a boolean mask which of the pairs of indices + * should be considered. If the mask is false for a pair of indices, then no + * entry will be added to the sparsity pattern for this pair, irrespective + * of whether one or both of the indices correspond to constrained degrees + * of freedom. + * + * This function is not typically called from user code, but is used in the + * DoFTools::make_sparsity_pattern() function when passed a constraint * matrix object. + * + * @note This function in itself is thread-safe, i.e., it works properly + * also when several threads call it simultaneously. However, the function + * call is only thread-safe if the underlying global sparsity pattern allows + * for simultaneous access and the access is not to rows with the same + * global index at the same time. This needs to be made sure from the + * caller's site. There is no locking mechanism inside this method to + * prevent data races. */ template void add_entries_local_to_global (const std::vector &local_dof_indices, SparsityType &sparsity_pattern, const bool keep_constrained_entries = true, - const Table<2,bool> &dof_mask = default_empty_table) const; + const Table<2,bool> &dof_mask = default_empty_table) const; /** - * Similar to the other function, - * but for non-quadratic sparsity - * patterns. + * Similar to the other function, but for non-quadratic sparsity patterns. */ - template void add_entries_local_to_global (const std::vector &row_indices, @@ -1374,38 +1016,23 @@ public: const Table<2,bool> &dof_mask = default_empty_table) const; /** - * This function imports values from a - * global vector (@p global_vector) by - * applying the constraints to a vector - * of local values, expressed in - * iterator format. In most cases, the - * local values will be identified by - * the local dof values on a - * cell. However, as long as the - * entries in @p local_dof_indices - * indicate reasonable global vector - * entries, this function is happy with - * whatever it is given. - * - * If one of the elements of @p - * local_dof_indices belongs to a - * constrained node, then rather than - * writing the corresponding element of - * @p global_vector into @p - * local_vector, the constraints are - * resolved as the respective - * distribute function does, i.e., the - * local entry is constructed from the - * global entries to which this - * particular degree of freedom is + * This function imports values from a global vector (@p global_vector) by + * applying the constraints to a vector of local values, expressed in + * iterator format. In most cases, the local values will be identified by + * the local dof values on a cell. However, as long as the entries in @p + * local_dof_indices indicate reasonable global vector entries, this + * function is happy with whatever it is given. + * + * If one of the elements of @p local_dof_indices belongs to a constrained + * node, then rather than writing the corresponding element of @p + * global_vector into @p local_vector, the constraints are resolved as the + * respective distribute function does, i.e., the local entry is constructed + * from the global entries to which this particular degree of freedom is * constrained. * - * In contrast to the similar function - * get_dof_values in the DoFAccessor - * class, this function does not need - * the constrained values to be - * correctly set (i.e., distribute to - * be called). + * In contrast to the similar function get_dof_values in the DoFAccessor + * class, this function does not need the constrained values to be correctly + * set (i.e., distribute to be called). */ template @@ -1425,41 +1052,29 @@ public: */ /** - * Re-distribute the elements of the - * vector @p condensed to @p - * uncondensed. It is the user's - * responsibility to guarantee that all + * Re-distribute the elements of the vector @p condensed to @p + * uncondensed. It is the user's responsibility to guarantee that all * entries of @p uncondensed be zero! * - * This function undoes the action of - * @p condense somehow, but it should - * be noted that it is not the inverse - * of @p condense. + * This function undoes the action of @p condense somehow, but it should be + * noted that it is not the inverse of @p condense. * - * The @p VectorType may be a - * Vector, Vector, - * BlockVector<...>, a PETSc - * or Trilinos vector wrapper class, or - * any other type having the same - * interface. + * The @p VectorType may be a Vector, Vector, + * BlockVector<...>, a PETSc or Trilinos vector wrapper class, or + * any other type having the same interface. */ template void distribute (const VectorType &condensed, VectorType &uncondensed) const; /** - * Re-distribute the elements of the - * vector in-place. The @p VectorType - * may be a Vector, - * Vector, - * BlockVector<...>, a PETSc - * or Trilinos vector wrapper class, or - * any other type having the same + * Re-distribute the elements of the vector in-place. The @p VectorType may + * be a Vector, Vector, BlockVector<...>, a PETSc or + * Trilinos vector wrapper class, or any other type having the same * interface. * - * Note that if called with a - * TrilinosWrappers::MPI::Vector it may - * not contain ghost elements. + * Note that if called with a TrilinosWrappers::MPI::Vector it may not + * contain ghost elements. */ template void distribute (VectorType &vec) const; @@ -1563,35 +1178,27 @@ public: private: /** - * This class represents one line of a - * constraint matrix. + * This class represents one line of a constraint matrix. */ struct ConstraintLine { /** - * A data type in which we store the list - * of entries that make up the homogenous - * part of a constraint. + * A data type in which we store the list of entries that make up the + * homogenous part of a constraint. */ typedef std::vector > Entries; /** - * Number of this line. Since only - * very few lines are stored, we - * can not assume a specific order - * and have to store the line - * number explicitly. + * Number of this line. Since only very few lines are stored, we can not + * assume a specific order and have to store the line number explicitly. */ size_type line; /** - * Row numbers and values of the - * entries in this line. + * Row numbers and values of the entries in this line. * - * For the reason why we use a - * vector instead of a map and the - * consequences thereof, the same - * applies as what is said for + * For the reason why we use a vector instead of a map and the + * consequences thereof, the same applies as what is said for * ConstraintMatrix::lines. */ Entries entries; @@ -1602,159 +1209,177 @@ private: double inhomogeneity; /** - * This operator is a bit weird and - * unintuitive: it compares the - * line numbers of two lines. We - * need this to sort the lines; in - * fact we could do this using a - * comparison predicate. However, - * this way, it is easier, albeit - * unintuitive since two lines - * really have no god-given order + * This operator is a bit weird and unintuitive: it compares the line + * numbers of two lines. We need this to sort the lines; in fact we could + * do this using a comparison predicate. However, this way, it is easier, + * albeit unintuitive since two lines really have no god-given order * relation. */ bool operator < (const ConstraintLine &) const; /** - * This operator is likewise weird: - * it checks whether the line - * indices of the two operands are - * equal, irrespective of the fact - * that the contents of the line - * may be different. + * This operator is likewise weird: it checks whether the line indices of + * the two operands are equal, irrespective of the fact that the contents + * of the line may be different. */ bool operator == (const ConstraintLine &) const; /** - * Determine an estimate for the - * memory consumption (in bytes) of - * this object. + * Determine an estimate for the memory consumption (in bytes) of this + * object. */ std::size_t memory_consumption () const; }; /** - * Store the lines of the matrix. - * Entries are usually appended in an - * arbitrary order and insertion into a - * vector is done best at the end, so - * the order is unspecified after all - * entries are inserted. Sorting of the - * entries takes place when calling the - * close() function. + * Store the lines of the matrix. Entries are usually appended in an + * arbitrary order and insertion into a vector is done best at the end, so + * the order is unspecified after all entries are inserted. Sorting of the + * entries takes place when calling the close() function. * - * We could, instead of using a vector, - * use an associative array, like a map - * to store the lines. This, however, - * would mean a much more fractioned - * heap since it allocates many small - * objects, and would additionally make - * usage of this matrix much slower. + * We could, instead of using a vector, use an associative array, like a map + * to store the lines. This, however, would mean a much more fractioned heap + * since it allocates many small objects, and would additionally make usage + * of this matrix much slower. */ std::vector lines; /** - * A list of size_type that - * contains the position of the - * ConstraintLine of a constrained degree - * of freedom, or - * numbers::invalid_size_type if the - * degree of freedom is not - * constrained. The - * numbers::invalid_size_type - * return value returns thus whether - * there is a constraint line for a given - * degree of freedom index. Note that - * this class has no notion of how many - * degrees of freedom there really are, - * so if we check whether there is a - * constraint line for a given degree of - * freedom, then this vector may actually - * be shorter than the index of the DoF - * we check for. - * - * This field exists since when adding a - * new constraint line we have to figure - * out whether it already - * exists. Previously, we would simply - * walk the unsorted list of constraint - * lines until we either hit the end or - * found it. This algorithm is O(N) if N - * is the number of constraints, which - * makes it O(N^2) when inserting all - * constraints. For large problems with - * many constraints, this could easily - * take 5-10 per cent of the total run - * time. With this field, we can save - * this time since we find any constraint - * in O(1) time or get to know that it a - * certain degree of freedom is not + * A list of size_type that contains the position of the ConstraintLine of a + * constrained degree of freedom, or numbers::invalid_size_type if the + * degree of freedom is not constrained. The numbers::invalid_size_type + * return value returns thus whether there is a constraint line for a given + * degree of freedom index. Note that this class has no notion of how many + * degrees of freedom there really are, so if we check whether there is a + * constraint line for a given degree of freedom, then this vector may + * actually be shorter than the index of the DoF we check for. + * + * This field exists since when adding a new constraint line we have to + * figure out whether it already exists. Previously, we would simply walk + * the unsorted list of constraint lines until we either hit the end or + * found it. This algorithm is O(N) if N is the number of constraints, which + * makes it O(N^2) when inserting all constraints. For large problems with + * many constraints, this could easily take 5-10 per cent of the total run + * time. With this field, we can save this time since we find any constraint + * in O(1) time or get to know that it a certain degree of freedom is not * constrained. * - * To make things worse, traversing the - * list of existing constraints requires - * reads from many different places in - * memory. Thus, in large 3d - * applications, the add_line() function - * showed up very prominently in the - * overall compute time, mainly because - * it generated a lot of cache - * misses. This should also be fixed by - * using the O(1) algorithm to access the - * fields of this array. - * - * The field is useful in a number of - * other contexts as well, e.g. when one - * needs random access to the constraints - * as in all the functions that apply - * constraints on the fly while add cell - * contributions into vectors and + * To make things worse, traversing the list of existing constraints + * requires reads from many different places in memory. Thus, in large 3d + * applications, the add_line() function showed up very prominently in the + * overall compute time, mainly because it generated a lot of cache + * misses. This should also be fixed by using the O(1) algorithm to access + * the fields of this array. + * + * The field is useful in a number of other contexts as well, e.g. when one + * needs random access to the constraints as in all the functions that apply + * constraints on the fly while add cell contributions into vectors and * matrices. */ std::vector lines_cache; /** - * This IndexSet is used to limit the - * lines to save in the ContraintMatrix - * to a subset. This is necessary, - * because the lines_cache vector would - * become too big in a distributed - * calculation. + * This IndexSet is used to limit the lines to save in the ConstraintMatrix + * to a subset. This is necessary, because the lines_cache vector would + * become too big in a distributed calculation. */ IndexSet local_lines; /** - * Store whether the arrays are sorted. - * If so, no new entries can be added. + * Store whether the arrays are sorted. If so, no new entries can be added. */ bool sorted; /** - * Internal function to calculate the - * index of line @p line in the vector + * Scratch data that is used during calls to distribute_local_to_global and + * add_entries_local_to_global. In order to avoid frequent memory + * allocation, we keep the data alive from one call to the next. + */ + struct ScratchData + { + /** + * Constructor, does nothing. + */ + ScratchData () : + in_use (false) + {} + + /** + * Copy constructor, does nothing + */ + ScratchData (const ScratchData &) : + in_use (false) + {} + + /** + * Stores whether the data is currently in use. + */ + bool in_use; + + /** + * Temporary array for column indices + */ + std::vector columns; + + /** + * Temporary array for column values + */ + std::vector values; + + /** + * Temporary array for block start indices + */ + std::vector block_starts; + + /** + * Temporary array for vector indices + */ + std::vector vector_indices; + + /** + * Data array for reorder row/column indices. Use a shared ptr to + * global_rows to avoid defining in the .h file + */ + std_cxx1x::shared_ptr global_rows; + + /** + * Data array for reorder row/column indices. Use a shared ptr to + * global_rows to avoid defining in the .h file + */ + std_cxx1x::shared_ptr global_columns; + }; + + /** + * Here comes the actual data structure for the scratch data. It is made + * mutable since it is modified in a const function. Since only one thread + * can access it at a time, no conflicting access can occur. For this to be + * valid, we need to make sure that no call within + * distribute_local_to_global is made that by itself can spawn + * tasks. Otherwise, we might end up in a situation where several threads + * fight for the data. + */ + mutable Threads::ThreadLocalStorage scratch_data; + + /** + * Internal function to calculate the index of line @p line in the vector * lines_cache using local_lines. */ size_type calculate_line_index (const size_type line) const; /** - * Return @p true if the weight of an - * entry (the second element of the - * pair) equals zero. This function is - * used to delete entries with zero - * weight. + * Return @p true if the weight of an entry (the second element of the pair) + * equals zero. This function is used to delete entries with zero weight. */ static bool check_zero_weight (const std::pair &p); /** - * Dummy table that serves as default - * argument for function + * Dummy table that serves as default argument for function * add_entries_local_to_global(). */ static const Table<2,bool> default_empty_table; /** - * This function actually implements - * the local_to_global function for + * This function actually implements the local_to_global function for * standard (non-block) matrices. */ template @@ -1768,9 +1393,8 @@ private: internal::bool2type) const; /** - * This function actually implements - * the local_to_global function for - * block matrices. + * This function actually implements the local_to_global function for block + * matrices. */ template void @@ -1783,8 +1407,7 @@ private: internal::bool2type) const; /** - * This function actually implements - * the local_to_global function for + * This function actually implements the local_to_global function for * standard (non-block) sparsity types. */ template @@ -1796,9 +1419,8 @@ private: internal::bool2type) const; /** - * This function actually implements - * the local_to_global function for - * block sparsity types. + * This function actually implements the local_to_global function for block + * sparsity types. */ template void @@ -1809,27 +1431,21 @@ private: internal::bool2type) const; /** - * Internal helper function for - * distribute_local_to_global function. + * Internal helper function for distribute_local_to_global function. * - * Creates a list of affected global rows - * for distribution, including the local - * rows where the entries come from. The - * list is sorted according to the global - * row indices. + * Creates a list of affected global rows for distribution, including the + * local rows where the entries come from. The list is sorted according to + * the global row indices. */ void make_sorted_row_list (const std::vector &local_dof_indices, internals::GlobalRowsFromLocal &global_rows) const; /** - * Internal helper function for - * add_entries_local_to_global function. + * Internal helper function for add_entries_local_to_global function. * - * Creates a list of affected rows for - * distribution without any additional - * information, otherwise similar to the - * other make_sorted_row_list() + * Creates a list of affected rows for distribution without any additional + * information, otherwise similar to the other make_sorted_row_list() * function. */ void @@ -1837,8 +1453,7 @@ private: std::vector &active_dofs) const; /** - * Internal helper function for - * distribute_local_to_global function. + * Internal helper function for distribute_local_to_global function. */ double resolve_vector_entry (const size_type i, @@ -1857,7 +1472,8 @@ ConstraintMatrix::ConstraintMatrix (const IndexSet &local_constraints) : lines (), local_lines (local_constraints), - sorted (false) + sorted (false), + scratch_data (ScratchData()) { // make sure the IndexSet is compressed. Otherwise this can lead to crashes // that are hard to find (only happen in release mode). @@ -1874,7 +1490,8 @@ ConstraintMatrix::ConstraintMatrix (const ConstraintMatrix &constraint_matrix) lines (constraint_matrix.lines), lines_cache (constraint_matrix.lines_cache), local_lines (constraint_matrix.local_lines), - sorted (constraint_matrix.sorted) + sorted (constraint_matrix.sorted), + scratch_data (ScratchData()) {} @@ -1884,34 +1501,25 @@ ConstraintMatrix::add_line (const size_type line) { Assert (sorted==false, ExcMatrixIsClosed()); - // the following can happen when we - // compute with distributed meshes - // and dof handlers and we - // constrain a degree of freedom - // whose number we don't have - // locally. if we don't abort here - // the program will try to allocate - // several terabytes of memory to - // resize the various arrays below - // :-) + // the following can happen when we compute with distributed meshes and dof + // handlers and we constrain a degree of freedom whose number we don't have + // locally. if we don't abort here the program will try to allocate several + // terabytes of memory to resize the various arrays below :-) Assert (line != numbers::invalid_size_type, ExcInternalError()); const size_type line_index = calculate_line_index (line); - // check whether line already exists; it - // may, in which case we can just quit + // check whether line already exists; it may, in which case we can just quit if (is_constrained(line)) return; - // if necessary enlarge vector of - // existing entries for cache + // if necessary enlarge vector of existing entries for cache if (line_index >= lines_cache.size()) lines_cache.resize (std::max(2*static_cast(lines_cache.size()), line_index+1), numbers::invalid_size_type); - // push a new line to the end of the - // list + // push a new line to the end of the list lines.push_back (ConstraintLine()); lines.back().line = line; lines.back().inhomogeneity = 0.; @@ -1930,14 +1538,11 @@ ConstraintMatrix::add_entry (const size_type line, Assert (line != column, ExcMessage ("Can't constrain a degree of freedom to itself")); - // if in debug mode, check whether an - // entry for this column already - // exists and if it's the same as - // the one entered at present + // if in debug mode, check whether an entry for this column already exists + // and if it's the same as the one entered at present // - // in any case: exit the function if an - // entry for this column already exists, - // since we don't want to enter it twice + // in any case: exit the function if an entry for this column already + // exists, since we don't want to enter it twice Assert (lines_cache[calculate_line_index(line)] != numbers::invalid_size_type, ExcInternalError()); ConstraintLine *line_ptr = &lines[lines_cache[calculate_line_index(line)]]; @@ -1998,8 +1603,7 @@ inline bool ConstraintMatrix::is_inhomogeneously_constrained (const size_type index) const { - // check whether the entry is - // constrained. could use is_constrained, but + // check whether the entry is constrained. could use is_constrained, but // that means computing the line index twice const size_type line_index = calculate_line_index(index); if (line_index >= lines_cache.size() || @@ -2018,8 +1622,7 @@ inline const std::vector > * ConstraintMatrix::get_constraint_entries (const size_type line) const { - // check whether the entry is - // constrained. could use is_constrained, but + // check whether the entry is constrained. could use is_constrained, but // that means computing the line index twice const size_type line_index = calculate_line_index(line); if (line_index >= lines_cache.size() || @@ -2035,8 +1638,7 @@ inline double ConstraintMatrix::get_inhomogeneity (const size_type line) const { - // check whether the entry is - // constrained. could use is_constrained, but + // check whether the entry is constrained. could use is_constrained, but // that means computing the line index twice const size_type line_index = calculate_line_index(line); if (line_index >= lines_cache.size() || @@ -2182,8 +1784,7 @@ distribute_local_to_global (const FullMatrix &local_matrix, const std::vector &local_dof_indices, MatrixType &global_matrix) const { - // create a dummy and hand on to the - // function actually implementing this + // create a dummy and hand on to the function actually implementing this // feature in the cm.templates.h file. Vector dummy(0); distribute_local_to_global (local_matrix, dummy, local_dof_indices, @@ -2204,10 +1805,8 @@ distribute_local_to_global (const FullMatrix &local_matrix, VectorType &global_vector, bool use_inhomogeneities_for_rhs) const { - // enter the internal function with the - // respective block information set, the - // actual implementation follows in the - // cm.templates.h file. + // enter the internal function with the respective block information set, + // the actual implementation follows in the cm.templates.h file. distribute_local_to_global (local_matrix, local_vector, local_dof_indices, global_matrix, global_vector, use_inhomogeneities_for_rhs, internal::bool2type::value>()); @@ -2224,10 +1823,8 @@ add_entries_local_to_global (const std::vector &local_dof_indices, const bool keep_constrained_entries, const Table<2,bool> &dof_mask) const { - // enter the internal function with the - // respective block information set, the - // actual implementation follows in the - // cm.templates.h file. + // enter the internal function with the respective block information set, + // the actual implementation follows in the cm.templates.h file. add_entries_local_to_global (local_dof_indices, sparsity_pattern, keep_constrained_entries, dof_mask, internal::bool2type::value>()); diff --git a/deal.II/include/deal.II/lac/constraint_matrix.templates.h b/deal.II/include/deal.II/lac/constraint_matrix.templates.h index 4a1ce1888c..d2e4dce533 100644 --- a/deal.II/include/deal.II/lac/constraint_matrix.templates.h +++ b/deal.II/include/deal.II/lac/constraint_matrix.templates.h @@ -1197,39 +1197,26 @@ ConstraintMatrix::distribute (VectorType &vec) const -// Some helper definitions for the -// local_to_global functions. +// Some helper definitions for the local_to_global functions. namespace internals { typedef types::global_dof_index size_type; - // this struct contains all the information - // we need to store about each of the - // global entries (global_row): are they - // obtained directly by some local entry - // (local_row) or some constraints - // (constraint_position). This is not - // directly used in the user code, but - // accessed via the - // GlobalRowsFromLocal. + // this struct contains all the information we need to store about each of + // the global entries (global_row): are they obtained directly by some local + // entry (local_row) or some constraints (constraint_position). This is not + // directly used in the user code, but accessed via the GlobalRowsFromLocal. // - // The actions performed here correspond to - // reshaping the constraint information - // from global degrees of freedom to local - // ones (i.e., cell-related DoFs), and also - // transforming the constraint information - // from compressed row storage (each local - // dof that is constrained has a list of - // constraint entries associated to it) - // into compressed column storage based on - // the cell-related DoFs (we have a list of - // global degrees of freedom, and to each - // we have a list of local rows where the - // entries come from). To increase the - // speed, we additionally store whether an - // entry is generated directly from the - // local degrees of freedom or whether it - // comes from a constraint. + // The actions performed here correspond to reshaping the constraint + // information from global degrees of freedom to local ones (i.e., + // cell-related DoFs), and also transforming the constraint information from + // compressed row storage (each local dof that is constrained has a list of + // constraint entries associated to it) into compressed column storage based + // on the cell-related DoFs (we have a list of global degrees of freedom, + // and to each we have a list of local rows where the entries come from). To + // increase the speed, we additionally store whether an entry is generated + // directly from the local degrees of freedom or whether it comes from a + // constraint. struct Distributing { Distributing (const size_type global_row = numbers::invalid_size_type, @@ -1266,8 +1253,7 @@ namespace internals { global_row = in.global_row; local_row = in.local_row; - // the constraints pointer should not - // contain any data here. + // the constraints pointer should not contain any data here. Assert (constraint_position == numbers::invalid_size_type, ExcInternalError()); @@ -1281,86 +1267,61 @@ namespace internals - // this is a cache for constraints that - // are encountered on a local level. + // this is a cache for constraints that are encountered on a local level. // The functionality is similar to - // std::vector - // > >, but tuned so that frequent memory - // allocation for each entry is - // avoided. This is not directly used in - // the user code, but accessed via the - // GlobalRowsFromLocal. + // std::vector > >, but tuned so that + // frequent memory allocation for each entry is avoided. The data is put + // into a std::vector > and the row length is kept + // fixed at row_length. Both the number of rows and the row length can + // change is this structure is filled. In that case, the data is + // rearranged. This is not directly used in the user code, but accessed via + // the GlobalRowsFromLocal. struct DataCache { DataCache () : - element_size (0), - data (0), - n_used_elements(0) + row_length (8) {} - ~DataCache() - { - delete [] data; - data = 0; - } - void reinit () { - Assert (element_size == 0, ExcInternalError()); - element_size = 6; - data = new std::pair [20*6]; - individual_size.resize(20); - n_used_elements = 0; + individual_size.resize(0); + data.resize(0); } - size_type element_size; - - std::pair *data; - - std::vector individual_size; - - size_type n_used_elements; - size_type insert_new_index (const std::pair &pair) { - if (element_size == 0) - reinit(); - if (n_used_elements == individual_size.size()) - { - std::pair *new_data = - new std::pair [2*individual_size.size()*element_size]; - memcpy (new_data, data, individual_size.size()*element_size* - sizeof(std::pair)); - delete [] data; - data = new_data; - individual_size.resize (2*individual_size.size(), 0); - } - size_type index = n_used_elements; - data[index*element_size] = pair; + Assert(row_length > 0, ExcInternalError()); + const unsigned int index = individual_size.size(); + individual_size.push_back(1); + data.resize(individual_size.size()*row_length); + data[index*row_length] = pair; individual_size[index] = 1; - ++n_used_elements; return index; } void append_index (const size_type index, const std::pair &pair) { - AssertIndexRange (index, n_used_elements); - const size_type my_size = individual_size[index]; - if (my_size == element_size) + AssertIndexRange (index, individual_size.size()); + const size_type my_length = individual_size[index]; + if (my_length == row_length) { - std::pair *new_data = - new std::pair [2*individual_size.size()*element_size]; - for (size_type i=0; i)); - delete [] data; - data = new_data; - element_size *= 2; + AssertDimension(data.size(), individual_size.size()*row_length); + // no space left in this row, need to double row_length and + // rearrange the data items + data.resize(2*data.size()); + for (size_type i=individual_size.size(); i>0; ) + { + --i; + std::memmove(&data[i*row_length*2], &data[i*row_length], + individual_size[i]* + sizeof(std::pair)); + } + row_length *= 2; } - data[index*element_size+my_size] = pair; - individual_size[index]++; + data[index*row_length+my_length] = pair; + individual_size[index] = my_length + 1; } size_type @@ -1372,60 +1333,61 @@ namespace internals const std::pair * get_entry (const size_type index) const { - return &data[index*element_size]; + return &data[index*row_length]; } + + size_type row_length; + + std::vector > data; + + std::vector individual_size; }; - // collects all the global rows from a - // local contribution (cell) and their - // origin (direct/constraint). this is - // basically a vector consisting of - // "Distributing" structs using access via - // the DataCache. Provides some + // collects all the global rows from a local contribution (cell) and their + // origin (direct/constraint). this is basically a vector consisting of + // "Distributing" structs using access via the DataCache. Provides some // specialized sort and insert functions. // - // in case there are no constraints, this is - // basically a list of pairs with - // the first index being the global index and - // the second index the local index. The list - // is sorted with respect to the global index. + // in case there are no constraints, this is basically a list of pairs + // with the first index being the global index and the second + // index the local index. The list is sorted with respect to the global + // index. // - // in case there are constraints, a global dof - // might get a contribution also because it - // gets data from a constrained dof. This - // means that a global dof might also have - // indirect contributions from a local dof via - // a constraint, besides the direct ones. + // in case there are constraints, a global dof might get a contribution also + // because it gets data from a constrained dof. This means that a global dof + // might also have indirect contributions from a local dof via a constraint, + // besides the direct ones. // - // The actions performed here correspond to - // reshaping the constraint information - // from global degrees of freedom to local - // ones (i.e., cell-related DoFs), and also - // transforming the constraint information - // from compressed row storage (each local - // dof that is constrained has a list of - // constraint entries associated to it) - // into compressed column storage based on - // the cell-related DoFs (we have a list of - // global degrees of freedom, and to each - // we have a list of local rows where the - // entries come from). To increase the - // speed, we additionally store whether an - // entry is generated directly from the - // local degrees of freedom or whether it - // comes from a constraint. + // The actions performed here correspond to reshaping the constraint + // information from global degrees of freedom to local ones (i.e., + // cell-related DoFs), and also transforming the constraint information from + // compressed row storage (each local dof that is constrained has a list of + // constraint entries associated to it) into compressed column storage based + // on the cell-related DoFs (we have a list of global degrees of freedom, + // and to each we have a list of local rows where the entries come from). To + // increase the speed, we additionally store whether an entry is generated + // directly from the local degrees of freedom or whether it comes from a + // constraint. class GlobalRowsFromLocal { public: - GlobalRowsFromLocal (const size_type n_local_rows) + GlobalRowsFromLocal () : - total_row_indices (n_local_rows), - n_active_rows (n_local_rows), + n_active_rows (0), n_inhomogeneous_rows (0) {} + void reinit (const size_type n_local_rows) + { + total_row_indices.resize(n_local_rows); + for (unsigned int i=0; i total_row_indices; private: - // holds the actual data from - // the constraints + // holds the actual data from the constraints DataCache data_cache; - // how many rows there are, - // constraints disregarded + // how many rows there are, constraints disregarded size_type n_active_rows; - // the number of rows with - // inhomogeneous constraints + // the number of rows with inhomogeneous constraints size_type n_inhomogeneous_rows; }; - // a function that appends an additional - // row to the list of values, or appends a - // value to an already existing - // row. Similar functionality as for - // std::map, but - // here done for a - // std::vector, much faster - // for short lists as we have them here + // a function that appends an additional row to the list of values, or + // appends a value to an already existing row. Similar functionality as for + // std::map, but here done for a + // std::vector, much faster for short lists as we have them + // here inline void GlobalRowsFromLocal::insert_index (const size_type global_row, @@ -1632,8 +1562,7 @@ namespace internals Distributing row_value (global_row); std::pair constraint (local_row, constraint_value); - // check whether the list was really - // sorted before entering here + // check whether the list was really sorted before entering here for (size_type i=1; iconstraint_position, constraint); } - // this sort algorithm sorts - // std::vector, but does not - // take the constraints into account. this - // means that in case that constraints are - // already inserted, this function does not - // work as expected. Use shellsort, which - // is very fast in case the indices are - // already sorted (which is the usual case - // with DG elements), and not too slow in - // other cases + // this sort algorithm sorts std::vector, but does not take + // the constraints into account. this means that in case that constraints + // are already inserted, this function does not work as expected. Use + // shellsort, which is very fast in case the indices are already sorted + // (which is the usual case with DG elements), and not too slow in other + // cases inline void GlobalRowsFromLocal::sort () @@ -1671,12 +1596,10 @@ namespace internals size_type i, j, j2, temp, templ, istep; size_type step; - // check whether the - // constraints are really empty. + // check whether the constraints are really empty. const size_type length = size(); - // make sure that we are in the - // range of the vector + // make sure that we are in the range of the vector AssertIndexRange (length, total_row_indices.size()+1); for (size_type i=0; i inline void @@ -1746,9 +1664,9 @@ namespace internals block_starts[i] = first_block - global_rows.total_row_indices.begin(); block_indices = first_block; } + block_starts[num_blocks] = n_active_rows; - // transform row indices to block-local - // index space + // transform row indices to block-local index space for (size_type i=block_starts[1]; i instead of - // GlobalRowsFromLocal. Used in functions - // for sparsity patterns. + // same as before, but for std::vector instead of + // GlobalRowsFromLocal. Used in functions for sparsity patterns. template inline void @@ -1785,9 +1701,9 @@ namespace internals block_starts[i] = first_block - row_indices.begin(); col_indices = first_block; } + block_starts[num_blocks] = row_indices.size(); - // transform row indices to local index - // space + // transform row indices to local index space for (size_type i=block_starts[1]; i inline void @@ -1874,12 +1782,9 @@ namespace internals AssertIndexRange (column_end-1, global_cols.size()); const size_type loc_row = global_rows.local_row(i); - // fast function if there are no indirect - // references to any of the local rows at - // all on this set of dofs (saves a lot - // of checks). the only check we actually - // need to perform is whether the matrix - // element is zero. + // fast function if there are no indirect references to any of the local + // rows at all on this set of dofs (saves a lot of checks). the only check + // we actually need to perform is whether the matrix element is zero. if (global_rows.have_indirect_rows() == false && global_cols.have_indirect_rows() == false) { @@ -1899,8 +1804,7 @@ namespace internals } } - // more difficult part when there are - // indirect references and when we need + // more difficult part when there are indirect references and when we need // to do some more checks. else { @@ -1909,8 +1813,8 @@ namespace internals double col_val = resolve_matrix_entry (global_rows, global_cols, i, j, loc_row, local_matrix); - // if we got some nontrivial value, - // append it to the array of values. + // if we got some nontrivial value, append it to the array of + // values. if (col_val != 0.) { *val_ptr++ = static_cast (col_val); @@ -1922,8 +1826,8 @@ namespace internals - // specialized function that can write into - // the row of a SparseMatrix. + // specialized function that can write into the row of a + // SparseMatrix. namespace dealiiSparseMatrix { template @@ -1945,11 +1849,9 @@ namespace internals } - // similar as before, now with shortcut for - // deal.II sparse matrices. this lets us - // avoid using extra arrays, and does all the - // operations just in place, i.e., in the - // respective matrix row + // similar as before, now with shortcut for deal.II sparse matrices. this + // lets us avoid using extra arrays, and does all the operations just in + // place, i.e., in the respective matrix row template inline void @@ -1976,11 +1878,9 @@ namespace internals matrix_values = sparse_matrix->begin(row); const bool optimize_diagonal = sparsity.n_rows() == sparsity.n_cols(); - // distinguish three cases about what can - // happen for checking whether the diagonal is - // the first element of the row. this avoids - // if statements at the innermost loop - // positions + // distinguish three cases about what can happen for checking whether the + // diagonal is the first element of the row. this avoids if statements at + // the innermost loop positions if (!optimize_diagonal) // case 1: no diagonal optimization in matrix { @@ -2059,8 +1959,7 @@ namespace internals } } } - // case 3: can't say - need to check inside - // the loop + // case 3: can't say - need to check inside the loop else if (global_rows.have_indirect_rows() == false) { ++matrix_values; // jump over diagonal element @@ -2098,10 +1997,8 @@ namespace internals - // Same function to resolve all entries that - // will be added to the given global row - // global_rows[i] as before, now for sparsity - // pattern + // Same function to resolve all entries that will be added to the given + // global row global_rows[i] as before, now for sparsity pattern inline void resolve_matrix_row (const GlobalRowsFromLocal &global_rows, @@ -2116,9 +2013,8 @@ namespace internals const size_type loc_row = global_rows.local_row(i); - // fast function if there are no indirect - // references to any of the local rows at - // all on this set of dofs + // fast function if there are no indirect references to any of the local + // rows at all on this set of dofs if (global_rows.have_indirect_rows() == false) { Assert(loc_row < dof_mask.n_rows(), @@ -2134,9 +2030,8 @@ namespace internals } } - // slower functions when there are - // indirect references and when we need - // to do some more checks. + // slower functions when there are indirect references and when we need to + // do some more checks. else { for (size_type j=column_start; j inline void set_matrix_diagonals (const internals::GlobalRowsFromLocal &global_rows, @@ -2236,12 +2117,10 @@ add_this_index: std::fabs(local_matrix(local_row,local_row)) : average_diagonal); global_matrix.add(global_row, global_row, new_diagonal); - // if the use_inhomogeneities_for_rhs flag is - // set to true, the inhomogeneities are used - // to create the global vector. instead of - // fill in a zero in the ith components with an - // inhomogeneity, we set those to: - // inhomogeneity(i)*global_matrix (i,i). + // if the use_inhomogeneities_for_rhs flag is set to true, the + // inhomogeneities are used to create the global vector. instead + // of fill in a zero in the ith components with an inhomogeneity, + // we set those to: inhomogeneity(i)*global_matrix (i,i). if (use_inhomogeneities_for_rhs == true) global_vector(global_row) += constraints.get_inhomogeneity(global_row) * new_diagonal; } @@ -2250,26 +2129,21 @@ add_this_index: - // similar function as the one above for - // setting matrix diagonals, but now doing - // that for sparsity patterns when setting - // them up using - // add_entries_local_to_global. In case we - // keep constrained entries, add all the rows - // and columns related to the constrained dof, - // otherwise just add the diagonal + // similar function as the one above for setting matrix diagonals, but now + // doing that for sparsity patterns when setting them up using + // add_entries_local_to_global. In case we keep constrained entries, add all + // the rows and columns related to the constrained dof, otherwise just add + // the diagonal template inline void set_sparsity_diagonals (const internals::GlobalRowsFromLocal &global_rows, - const std::vector &local_dof_indices, + const std::vector &local_dof_indices, const Table<2,bool> &dof_mask, const bool keep_constrained_entries, SparsityType &sparsity_pattern) { - // if we got constraints, need to add - // the diagonal element and, if the - // user requested so, also the rest of - // the entries in rows and columns + // if we got constraints, need to add the diagonal element and, if the + // user requested so, also the rest of the entries in rows and columns // that have been left out above if (global_rows.n_constraints() > 0) { @@ -2290,8 +2164,7 @@ add_this_index: } } else - // don't keep constrained entries - just - // add the diagonal. + // don't keep constrained entries - just add the diagonal. sparsity_pattern.add(global_row,global_row); } } @@ -2309,57 +2182,42 @@ add_this_index: // are related to it. void ConstraintMatrix:: -make_sorted_row_list (const std::vector &local_dof_indices, - internals::GlobalRowsFromLocal &global_rows) const +make_sorted_row_list (const std::vector &local_dof_indices, + internals::GlobalRowsFromLocal &global_rows) const { const size_type n_local_dofs = local_dof_indices.size(); AssertDimension (n_local_dofs, global_rows.size()); - // when distributing the local data to - // the global matrix, we can quite - // cheaply sort the indices (obviously, - // this introduces the need for - // allocating some memory on the way, but - // we need to do this only for rows, - // whereas the distribution process - // itself goes over rows and - // columns). This has the advantage that - // when writing into the global matrix, - // we can make use of the sortedness. - - // so the first step is to create a - // sorted list of all row values that are - // possible. these values are either the - // rows from unconstrained dofs, or some - // indices introduced by dofs constrained - // to a combination of some other - // dofs. regarding the data type, choose - // an STL vector of a pair of unsigned - // ints (for global columns) and internal - // data (containing local columns + - // possible jumps from - // constraints). Choosing an STL map or - // anything else M.K. knows of would be - // much more expensive here! - - // cache whether we have to resolve any - // indirect rows generated from resolving - // constrained dofs. + // when distributing the local data to the global matrix, we can quite + // cheaply sort the indices (obviously, this introduces the need for + // allocating some memory on the way, but we need to do this only for rows, + // whereas the distribution process itself goes over rows and columns). This + // has the advantage that when writing into the global matrix, we can make + // use of the sortedness. + + // so the first step is to create a sorted list of all row values that are + // possible. these values are either the rows from unconstrained dofs, or + // some indices introduced by dofs constrained to a combination of some + // other dofs. regarding the data type, choose an STL vector of a pair of + // unsigned ints (for global columns) and internal data (containing local + // columns + possible jumps from constraints). Choosing an STL map or + // anything else M.K. knows of would be much more expensive here! + + // cache whether we have to resolve any indirect rows generated from + // resolving constrained dofs. size_type added_rows = 0; - // first add the indices in an unsorted - // way and only keep track of the - // constraints that appear. They are - // resolved in a second step. + // first add the indices in an unsorted way and only keep track of the + // constraints that appear. They are resolved in a second step. for (size_type i = 0; i &local_dof_indices, -// Same function as before, but now do -// only extract the global indices -// that come from the local ones -// without storing their origin. Used -// for sparsity pattern generation. +// Same function as before, but now do only extract the global indices that +// come from the local ones without storing their origin. Used for sparsity +// pattern generation. inline void ConstraintMatrix:: @@ -2413,8 +2269,7 @@ make_sorted_row_list (const std::vector &local_dof_indices, { const size_type local_row = active_dofs.back(); - // remove constrained entry since we - // are going to resolve it in place + // remove constrained entry since we are going to resolve it in place active_dofs.pop_back(); const size_type global_row = local_dof_indices[local_row]; const ConstraintLine &position = @@ -2425,9 +2280,8 @@ make_sorted_row_list (const std::vector &local_dof_indices, if (active_dofs[active_dofs.size()-i] < new_index) active_dofs.insert(active_dofs.end()-i+1,new_index); - // make binary search to find where to - // put the new index in order to keep - // the list sorted + // make binary search to find where to put the new index in order to + // keep the list sorted else { std::vector::iterator it = @@ -2443,8 +2297,7 @@ make_sorted_row_list (const std::vector &local_dof_indices, -// Resolve the constraints from the vector and -// apply inhomogeneities. +// Resolve the constraints from the vector and apply inhomogeneities. inline double ConstraintMatrix:: @@ -2457,10 +2310,9 @@ resolve_vector_entry (const size_type i, const size_type loc_row = global_rows.local_row(i); const size_type n_inhomogeneous_rows = global_rows.n_inhomogeneities(); double val = 0; - // has a direct contribution from some local - // entry. If we have inhomogeneous - // constraints, compute the contribution of - // the inhomogeneity in the current row. + // has a direct contribution from some local entry. If we have inhomogeneous + // constraints, compute the contribution of the inhomogeneity in the current + // row. if (loc_row != numbers::invalid_size_type) { val = local_vector(loc_row); @@ -2488,9 +2340,8 @@ resolve_vector_entry (const size_type i, } -// internal implementation for -// distribute_local_to_global for -// standard (non-block) matrices +// internal implementation for distribute_local_to_global for standard +// (non-block) matrices template void ConstraintMatrix::distribute_local_to_global ( @@ -2502,9 +2353,8 @@ ConstraintMatrix::distribute_local_to_global ( bool use_inhomogeneities_for_rhs, internal::bool2type) const { - // check whether we work on real vectors - // or we just used a dummy when calling - // the other function above. + // check whether we work on real vectors or we just used a dummy when + // calling the other function above. const bool use_vectors = (local_vector.size() == 0 && global_vector.size() == 0) ? false : true; typedef typename MatrixType::value_type number; @@ -2522,62 +2372,76 @@ ConstraintMatrix::distribute_local_to_global ( Assert (lines.empty() || sorted == true, ExcMatrixNotClosed()); const size_type n_local_dofs = local_dof_indices.size(); - internals::GlobalRowsFromLocal global_rows (n_local_dofs); + + ScratchData &my_scratch_data = scratch_data.get(); + Assert(my_scratch_data.in_use == false, + ExcMessage("Access to thread-local scratch data tried, but it is already " + "in use")); + // TODO: might want to have a scoped variable for in_use here and in the + // methods below + my_scratch_data.in_use = true; + + if (my_scratch_data.global_rows.get() == 0) + my_scratch_data.global_rows.reset(new internals::GlobalRowsFromLocal()); + internals::GlobalRowsFromLocal &global_rows = *my_scratch_data.global_rows; + global_rows.reinit(n_local_dofs); make_sorted_row_list (local_dof_indices, global_rows); const size_type n_actual_dofs = global_rows.size(); - // create arrays for the column data - // (indices and values) that will then be - // written into the matrix. Shortcut for - // deal.II sparse matrix - std::vector cols; - std::vector vals; + // create arrays for the column data (indices and values) that will then be + // written into the matrix. Shortcut for deal.II sparse matrix. We can use + // the scratch data if we have a double matrix. Otherwise, we need to create + // an array in any case since we cannot know about the actual data type in + // the ConstraintMatrix class (unless we do cast). This involves a little + // bit of logic to determine the type of the matrix value. + std::vector & cols = my_scratch_data.columns; + std::vector & vals = my_scratch_data.values; + std::vector values_non_double; SparseMatrix *sparse_matrix = dynamic_cast *>(&global_matrix); if (use_dealii_matrix == false) { cols.resize (n_actual_dofs); - vals.resize (n_actual_dofs); + if (types_are_equal::value == false) + values_non_double.resize(n_actual_dofs); + else + vals.resize (n_actual_dofs); } else Assert (sparse_matrix != 0, ExcInternalError()); - // now do the actual job. go through all - // the global rows that we will touch and - // call resolve_matrix_row for each of - // those. + // now do the actual job. go through all the global rows that we will touch + // and call resolve_matrix_row for each of those. for (size_type i=0; i::value ? + reinterpret_cast(&vals[0]) : &values_non_double[0]; internals::resolve_matrix_row (global_rows, global_rows, i, 0, n_actual_dofs, local_matrix, col_ptr, val_ptr); const size_type n_values = col_ptr - &cols[0]; - Assert (n_values == (size_type)(val_ptr - &vals[0]), - ExcInternalError()); if (n_values > 0) - global_matrix.add(row, n_values, &cols[0], &vals[0], false, true); + global_matrix.add(row, n_values, &cols[0], val_ptr-n_values, false, + true); } else internals::resolve_matrix_row (global_rows, i, 0, n_actual_dofs, local_matrix, sparse_matrix); - // now to the vectors. besides doing the - // same job as we did above (i.e., - // distribute the content of the local - // vector into the global one), need to - // account for inhomogeneities here: thie - // corresponds to eliminating the - // respective column in the local matrix - // with value on the right hand side. + // now to the vectors. besides doing the same job as we did above (i.e., + // distribute the content of the local vector into the global one), need + // to account for inhomogeneities here: thie corresponds to eliminating + // the respective column in the local matrix with value on the right + // hand side. if (use_vectors == true) { const double val = resolve_vector_entry (i, global_rows, @@ -2593,6 +2457,7 @@ ConstraintMatrix::distribute_local_to_global ( internals::set_matrix_diagonals (global_rows, local_dof_indices, local_matrix, *this, global_matrix, global_vector, use_inhomogeneities_for_rhs); + my_scratch_data.in_use = false; } @@ -2613,46 +2478,62 @@ ConstraintMatrix::distribute_local_to_global ( const size_type n_local_row_dofs = row_indices.size(); const size_type n_local_col_dofs = col_indices.size(); - internals::GlobalRowsFromLocal global_rows (n_local_row_dofs); - internals::GlobalRowsFromLocal global_cols (n_local_col_dofs); + + ScratchData &my_scratch_data = scratch_data.get(); + Assert(my_scratch_data.in_use == false, + ExcMessage("Access to thread-local scratch data tried, but it is already " + "in use")); + my_scratch_data.in_use = true; + + if (my_scratch_data.global_rows.get() == 0) + my_scratch_data.global_rows.reset(new internals::GlobalRowsFromLocal()); + if (my_scratch_data.global_columns.get() == 0) + my_scratch_data.global_columns.reset(new internals::GlobalRowsFromLocal()); + internals::GlobalRowsFromLocal &global_rows = *my_scratch_data.global_rows; + global_rows.reinit(n_local_row_dofs); + internals::GlobalRowsFromLocal &global_cols = *my_scratch_data.global_columns; + global_cols.reinit(n_local_col_dofs); make_sorted_row_list (row_indices, global_rows); make_sorted_row_list (col_indices, global_cols); const size_type n_actual_row_dofs = global_rows.size(); const size_type n_actual_col_dofs = global_cols.size(); - // create arrays for the column data - // (indices and values) that will then be - // written into the matrix. Shortcut for - // deal.II sparse matrix - std::vector cols (n_actual_col_dofs); - std::vector vals (n_actual_col_dofs); + // create arrays for the column data (indices and values) that will then be + // written into the matrix. Shortcut for deal.II sparse matrix + std::vector & cols = my_scratch_data.columns; + std::vector & vals = my_scratch_data.values; + std::vector values_non_double; + cols.resize(n_actual_col_dofs); + if (types_are_equal::value == true) + vals.resize(n_actual_col_dofs); + else + values_non_double.resize(n_actual_col_dofs); // now do the actual job. for (size_type i=0; i::value ? + reinterpret_cast(&vals[0]) : &values_non_double[0]; internals::resolve_matrix_row (global_rows, global_cols, i, 0, n_actual_col_dofs, local_matrix, col_ptr, val_ptr); const size_type n_values = col_ptr - &cols[0]; - Assert (n_values == (size_type)(val_ptr - &vals[0]), - ExcInternalError()); if (n_values > 0) - global_matrix.add(row, n_values, &cols[0], &vals[0], false, true); + global_matrix.add(row, n_values, &cols[0], val_ptr-n_values, + false, true); } + + my_scratch_data.in_use = false; } -// similar function as above, but now -// specialized for block matrices. See -// the other function for additional -// comments. +// similar function as above, but now specialized for block matrices. See the +// other function for additional comments. template void ConstraintMatrix:: @@ -2682,12 +2563,22 @@ distribute_local_to_global (const FullMatrix &local_matrix, } Assert (sorted == true, ExcMatrixNotClosed()); + ScratchData &my_scratch_data = scratch_data.get(); + Assert(my_scratch_data.in_use == false, + ExcMessage("Access to thread-local scratch data tried, but it is already " + "in use")); + my_scratch_data.in_use = true; + const size_type n_local_dofs = local_dof_indices.size(); - internals::GlobalRowsFromLocal global_rows (n_local_dofs); + if (my_scratch_data.global_rows.get() == 0) + my_scratch_data.global_rows.reset(new internals::GlobalRowsFromLocal()); + internals::GlobalRowsFromLocal &global_rows = *my_scratch_data.global_rows; + global_rows.reinit(n_local_dofs); + make_sorted_row_list (local_dof_indices, global_rows); const size_type n_actual_dofs = global_rows.size(); - std::vector global_indices; + std::vector &global_indices = my_scratch_data.vector_indices; if (use_vectors == true) { global_indices.resize(n_actual_dofs); @@ -2695,25 +2586,27 @@ distribute_local_to_global (const FullMatrix &local_matrix, global_indices[i] = global_rows.global_row(i); } - // additional construct that also takes - // care of block indices. + // additional construct that also takes care of block indices. const size_type num_blocks = global_matrix.n_block_rows(); - std::vector block_starts(num_blocks+1, n_actual_dofs); + std::vector &block_starts = my_scratch_data.block_starts; + block_starts.resize(num_blocks+1); internals::make_block_starts (global_matrix, global_rows, block_starts); - std::vector cols; - std::vector vals; + std::vector & cols = my_scratch_data.columns; + std::vector & vals = my_scratch_data.values; + std::vector values_non_double; if (use_dealii_matrix == false) { cols.resize (n_actual_dofs); - vals.resize (n_actual_dofs); + if (types_are_equal::value == true) + vals.resize(n_actual_dofs); + else + values_non_double.resize(n_actual_dofs); } - // the basic difference to the non-block - // variant from now onwards is that we go - // through the blocks of the matrix - // separately, which allows us to set the - // block entries individually + // the basic difference to the non-block variant from now onwards is that we + // go through the blocks of the matrix separately, which allows us to set + // the block entries individually for (size_type block=0; block &local_matrix, if (use_dealii_matrix == false) { size_type *col_ptr = &cols[0]; - number *val_ptr = &vals[0]; + number *val_ptr = types_are_equal::value ? + reinterpret_cast(&vals[0]) : &values_non_double[0]; internals::resolve_matrix_row (global_rows, global_rows, i, start_block, end_block, local_matrix, col_ptr, val_ptr); const size_type n_values = col_ptr - &cols[0]; - Assert (n_values == (size_type )(val_ptr - &vals[0]), - ExcInternalError()); if (n_values > 0) global_matrix.block(block, block_col).add(row, n_values, - &cols[0], &vals[0], + &cols[0], + val_ptr-n_values, false, true); } else @@ -2768,6 +2661,8 @@ distribute_local_to_global (const FullMatrix &local_matrix, internals::set_matrix_diagonals (global_rows, local_dof_indices, local_matrix, *this, global_matrix, global_vector, use_inhomogeneities_for_rhs); + + my_scratch_data.in_use = false; } @@ -2791,35 +2686,34 @@ add_entries_local_to_global (const std::vector &local_dof_indices, AssertDimension (dof_mask.n_cols(), n_local_dofs); } - // if the dof mask is not active, all we - // have to do is to add some indices in a - // matrix format. To do this, we first - // create an array of all the indices - // that are to be added. these indices - // are the local dof indices plus some - // indices that come from constraints. + ScratchData &my_scratch_data = scratch_data.get(); + Assert(my_scratch_data.in_use == false, + ExcMessage("Access to thread-local scratch data tried, but it is already " + "in use")); + my_scratch_data.in_use = true; + + // if the dof mask is not active, all we have to do is to add some indices + // in a matrix format. To do this, we first create an array of all the + // indices that are to be added. these indices are the local dof indices + // plus some indices that come from constraints. if (dof_mask_is_active == false) { - std::vector actual_dof_indices (n_local_dofs); + std::vector & actual_dof_indices = my_scratch_data.columns; + actual_dof_indices.resize(n_local_dofs); make_sorted_row_list (local_dof_indices, actual_dof_indices); const size_type n_actual_dofs = actual_dof_indices.size(); - // now add the indices we collected above - // to the sparsity pattern. Very easy - // here - just add the same array to all - // the rows... + // now add the indices we collected above to the sparsity pattern. Very + // easy here - just add the same array to all the rows... for (size_type i=0; i &local_dof_indices, sparsity_pattern.add (local_dof_indices[i], local_dof_indices[i]); } + my_scratch_data.in_use = false; return; } - // complicated case: we need to filter - // out some indices. then the function - // gets similar to the function for - // distributing matrix entries, see there + // complicated case: we need to filter out some indices. then the function + // gets similar to the function for distributing matrix entries, see there // for additional comments. - internals::GlobalRowsFromLocal global_rows (n_local_dofs); + if (my_scratch_data.global_rows.get() == 0) + my_scratch_data.global_rows.reset(new internals::GlobalRowsFromLocal()); + internals::GlobalRowsFromLocal &global_rows = *my_scratch_data.global_rows; + global_rows.reinit(n_local_dofs); make_sorted_row_list (local_dof_indices, global_rows); const size_type n_actual_dofs = global_rows.size(); - // create arrays for the column indices - // that will then be written into the + // create arrays for the column indices that will then be written into the // sparsity pattern. - std::vector cols (n_actual_dofs); + std::vector & cols = my_scratch_data.columns; + cols.resize(n_actual_dofs); for (size_type i=0; i &local_dof_indices, internals::resolve_matrix_row (global_rows, i, 0, n_actual_dofs, dof_mask, col_ptr); - // finally, write all the information - // that accumulated under the given - // process into the global matrix row and - // into the vector + // finally, write all the information that accumulated under the given + // process into the global matrix row and into the vector if (col_ptr != cols.begin()) sparsity_pattern.add_entries(row, cols.begin(), col_ptr, true); @@ -2869,6 +2763,7 @@ add_entries_local_to_global (const std::vector &local_dof_indices, internals::set_sparsity_diagonals (global_rows, local_dof_indices, dof_mask, keep_constrained_entries, sparsity_pattern); + my_scratch_data.in_use = false; } @@ -2879,9 +2774,9 @@ void ConstraintMatrix:: add_entries_local_to_global (const std::vector &row_indices, const std::vector &col_indices, - SparsityType &sparsity_pattern, - const bool keep_constrained_entries, - const Table<2,bool> &dof_mask) const + SparsityType &sparsity_pattern, + const bool keep_constrained_entries, + const Table<2,bool> &dof_mask) const { const size_type n_local_rows = row_indices.size(); const size_type n_local_cols = col_indices.size(); @@ -2889,13 +2784,10 @@ add_entries_local_to_global (const std::vector &row_indices, if (dof_mask.n_rows() == n_local_rows && dof_mask.n_cols() == n_local_cols) dof_mask_is_active = true; - // if the dof mask is not active, all we - // have to do is to add some indices in a - // matrix format. To do this, we first - // create an array of all the indices - // that are to be added. these indices - // are the local dof indices plus some - // indices that come from constraints. + // if the dof mask is not active, all we have to do is to add some indices + // in a matrix format. To do this, we first create an array of all the + // indices that are to be added. these indices are the local dof indices + // plus some indices that come from constraints. if (dof_mask_is_active == false) { std::vector actual_row_indices (n_local_rows); @@ -2904,10 +2796,8 @@ add_entries_local_to_global (const std::vector &row_indices, make_sorted_row_list (col_indices, actual_col_indices); const size_type n_actual_rows = actual_row_indices.size(); - // now add the indices we collected above - // to the sparsity pattern. Very easy - // here - just add the same array to all - // the rows... + // now add the indices we collected above to the sparsity pattern. Very + // easy here - just add the same array to all the rows... for (size_type i=0; i &row_indices, return; } - // if constrained entries should be - // kept, need to add rows and columns - // of those to the sparsity pattern + // if constrained entries should be kept, need to add rows and columns of + // those to the sparsity pattern if (keep_constrained_entries == true) { for (size_type i=0; i &local_dof_indices, const Table<2,bool> &dof_mask, internal::bool2type ) const { - // just as the other - // add_entries_local_to_global function, - // but now specialized for block - // matrices. + // just as the other add_entries_local_to_global function, but now + // specialized for block matrices. Assert (sparsity_pattern.n_rows() == sparsity_pattern.n_cols(), ExcNotQuadratic()); Assert (sparsity_pattern.n_block_rows() == sparsity_pattern.n_block_cols(), ExcNotQuadratic()); @@ -2959,6 +2846,12 @@ add_entries_local_to_global (const std::vector &local_dof_indices, const size_type n_local_dofs = local_dof_indices.size(); const size_type num_blocks = sparsity_pattern.n_block_rows(); + ScratchData &my_scratch_data = scratch_data.get(); + Assert(my_scratch_data.in_use == false, + ExcMessage("Access to thread-local scratch data tried, but it is already " + "in use")); + my_scratch_data.in_use = true; + bool dof_mask_is_active = false; if (dof_mask.n_rows() == n_local_dofs) { @@ -2968,13 +2861,14 @@ add_entries_local_to_global (const std::vector &local_dof_indices, if (dof_mask_is_active == false) { - std::vector actual_dof_indices (n_local_dofs); + std::vector & actual_dof_indices = my_scratch_data.columns; + actual_dof_indices.resize(n_local_dofs); make_sorted_row_list (local_dof_indices, actual_dof_indices); const size_type n_actual_dofs = actual_dof_indices.size(); - // additional construct that also takes - // care of block indices. - std::vector block_starts(num_blocks+1, n_actual_dofs); + // additional construct that also takes care of block indices. + std::vector &block_starts = my_scratch_data.block_starts; + block_starts.resize(num_blocks+1); internals::make_block_starts (sparsity_pattern, actual_dof_indices, block_starts); @@ -3014,28 +2908,29 @@ add_entries_local_to_global (const std::vector &local_dof_indices, sparsity_pattern.add (local_dof_indices[i], local_dof_indices[i]); } + my_scratch_data.in_use = false; return; } - // difficult case with dof_mask, similar - // to the distribute_local_to_global + // difficult case with dof_mask, similar to the distribute_local_to_global // function for block matrices - internals::GlobalRowsFromLocal global_rows (n_local_dofs); + if (my_scratch_data.global_rows.get() == 0) + my_scratch_data.global_rows.reset(new internals::GlobalRowsFromLocal()); + internals::GlobalRowsFromLocal &global_rows = *my_scratch_data.global_rows; + global_rows.reinit(n_local_dofs); make_sorted_row_list (local_dof_indices, global_rows); const size_type n_actual_dofs = global_rows.size(); - // additional construct that also takes - // care of block indices. - std::vector block_starts(num_blocks+1, n_actual_dofs); - internals::make_block_starts(sparsity_pattern, global_rows, - block_starts); + // additional construct that also takes care of block indices. + std::vector & block_starts = my_scratch_data.block_starts; + block_starts.resize(num_blocks+1); + internals::make_block_starts(sparsity_pattern, global_rows, block_starts); - std::vector cols (n_actual_dofs); + std::vector &cols = my_scratch_data.columns; + cols.resize(n_actual_dofs); - // the basic difference to the - // non-block variant from now onwards - // is that we go through the blocks - // of the matrix separately. + // the basic difference to the non-block variant from now onwards is that we + // go through the blocks of the matrix separately. for (size_type block=0; block &local_dof_indices, internals::set_sparsity_diagonals (global_rows, local_dof_indices, dof_mask, keep_constrained_entries, sparsity_pattern); + my_scratch_data.in_use = false; } DEAL_II_NAMESPACE_CLOSE #endif - diff --git a/deal.II/include/deal.II/lac/parallel_vector.h b/deal.II/include/deal.II/lac/parallel_vector.h index c568a4aba7..fbc865798f 100644 --- a/deal.II/include/deal.II/lac/parallel_vector.h +++ b/deal.II/include/deal.II/lac/parallel_vector.h @@ -1185,11 +1185,9 @@ namespace parallel { Assert (c.partitioner.get() != 0, ExcNotInitialized()); - // check whether the two vectors use the same - // parallel partitioner. if not, check if all - // local ranges are the same (that way, we can - // exchange data between different parallel - // layouts) + // check whether the two vectors use the same parallel partitioner. if + // not, check if all local ranges are the same (that way, we can + // exchange data between different parallel layouts) if (partitioner.get() == 0) reinit (c, true); else if (partitioner.get() != c.partitioner.get()) diff --git a/deal.II/include/deal.II/lac/pointer_matrix.h b/deal.II/include/deal.II/lac/pointer_matrix.h index 9235de13b0..6c0d5ca692 100644 --- a/deal.II/include/deal.II/lac/pointer_matrix.h +++ b/deal.II/include/deal.II/lac/pointer_matrix.h @@ -398,7 +398,7 @@ private: * product (#vmult()) and scalar multiplication (#Tvmult()) functions * of the Vector class. * - * @author Guidl Kanschat, 2006 + * @author Guido Kanschat, 2006 */ template class PointerMatrixVector : public PointerMatrixBase > diff --git a/deal.II/include/deal.II/numerics/vector_tools.templates.h b/deal.II/include/deal.II/numerics/vector_tools.templates.h index e814f047db..5462558aff 100644 --- a/deal.II/include/deal.II/numerics/vector_tools.templates.h +++ b/deal.II/include/deal.II/numerics/vector_tools.templates.h @@ -1579,8 +1579,7 @@ namespace VectorTools "element.")); - // if for whatever reason we were - // passed an empty map, return + // if for whatever reason we were passed an empty map, return // immediately if (function_map.size() == 0) return; @@ -1603,78 +1602,48 @@ namespace VectorTools std::vector > dof_locations; dof_locations.reserve (DoFTools::max_dofs_per_face(dof)); - // array to store the values of - // the boundary function at the - // boundary points. have two arrays - // for scalar and vector functions - // to use the more efficient one - // respectively + // array to store the values of the boundary function at the boundary + // points. have two arrays for scalar and vector functions to use the + // more efficient one respectively std::vector dof_values_scalar; std::vector > dof_values_system; dof_values_scalar.reserve (DoFTools::max_dofs_per_face (dof)); dof_values_system.reserve (DoFTools::max_dofs_per_face (dof)); - // before we start with the loop - // over all cells create an - // hp::FEValues object that holds - // the interpolation points of all - // finite elements that may ever be - // in use + // before we start with the loop over all cells create an hp::FEValues + // object that holds the interpolation points of all finite elements + // that may ever be in use dealii::hp::FECollection finite_elements (dof.get_fe()); dealii::hp::QCollection q_collection; for (unsigned int f=0; f &fe = finite_elements[f]; - // generate a quadrature rule - // on the face from the unit - // support points. this will be - // used to obtain the - // quadrature points on the + // generate a quadrature rule on the face from the unit support + // points. this will be used to obtain the quadrature points on the // real cell's face // - // to do this, we check whether - // the FE has support points on - // the face at all: + // to do this, we check whether the FE has support points on the + // face at all: if (fe.has_face_support_points()) q_collection.push_back (Quadrature(fe.get_unit_face_support_points())); else { - // if not, then we should - // try a more clever - // way. the idea is that a - // finite element may not - // offer support points for - // all its shape functions, - // but maybe only some. if - // it offers support points - // for the components we - // are interested in in - // this function, then - // that's fine. if not, the - // function we call in the - // finite element will - // raise an exception. the - // support points for the - // other shape functions - // are left uninitialized - // (well, initialized by - // the default - // constructor), since we + // if not, then we should try a more clever way. the idea is + // that a finite element may not offer support points for all + // its shape functions, but maybe only some. if it offers + // support points for the components we are interested in in + // this function, then that's fine. if not, the function we call + // in the finite element will raise an exception. the support + // points for the other shape functions are left uninitialized + // (well, initialized by the default constructor), since we // don't need them anyway. // - // As a detour, we must - // make sure we only query - // face_system_to_component_index - // if the index corresponds - // to a primitive shape - // function. since we know - // that all the components - // we are interested in are - // primitive (by the above - // check), we can safely - // put such a check in - // front + // As a detour, we must make sure we only query + // face_system_to_component_index if the index corresponds to a + // primitive shape function. since we know that all the + // components we are interested in are primitive (by the above + // check), we can safely put such a check in front std::vector > unit_support_points (fe.dofs_per_face); for (unsigned int i=0; i(unit_support_points)); } } - // now that we have a q_collection - // object with all the right - // quadrature points, create an - // hp::FEFaceValues object that we - // can use to evaluate the boundary - // values at + // now that we have a q_collection object with all the right quadrature + // points, create an hp::FEFaceValues object that we can use to evaluate + // the boundary values at dealii::hp::MappingCollection mapping_collection (mapping); dealii::hp::FEFaceValues x_fe_values (mapping_collection, finite_elements, q_collection, update_quadrature_points); @@ -1705,15 +1671,11 @@ namespace VectorTools { const FiniteElement &fe = cell->get_fe(); - // we can presently deal only with - // primitive elements for boundary - // values. this does not preclude - // us using non-primitive elements - // in components that we aren't - // interested in, however. make - // sure that all shape functions - // that are non-zero for the - // components we are interested in, + // we can presently deal only with primitive elements for + // boundary values. this does not preclude us using + // non-primitive elements in components that we aren't + // interested in, however. make sure that all shape functions + // that are non-zero for the components we are interested in, // are in fact primitive for (unsigned int i=0; iget_fe().dofs_per_cell; ++i) { @@ -1732,15 +1694,9 @@ namespace VectorTools const typename DH::face_iterator face = cell->face(face_no); const types::boundary_id boundary_component = face->boundary_indicator(); - // see if this face is - // part of the - // boundaries for which - // we are supposed to - // do something, and - // also see if the - // finite element in - // use here has DoFs on - // the face at all + // see if this face is part of the boundaries for which we are + // supposed to do something, and also see if the finite element + // in use here has DoFs on the face at all if ((function_map.find(boundary_component) != function_map.end()) && (cell->get_fe().dofs_per_face > 0)) @@ -1750,9 +1706,8 @@ namespace VectorTools const dealii::FEFaceValues &fe_values = x_fe_values.get_present_fe_values(); - // get indices, physical location and - // boundary values of dofs on this - // face + // get indices, physical location and boundary values of + // dofs on this face face_dofs.resize (fe.dofs_per_face); face->get_dof_indices (face_dofs, cell->active_fe_index()); const std::vector > &dof_locations @@ -1760,12 +1715,8 @@ namespace VectorTools if (fe_is_system) { - // resize - // array. avoid - // construction of a - // memory allocating - // temporary if - // possible + // resize array. avoid construction of a memory + // allocating temporary if possible if (dof_values_system.size() < fe.dofs_per_face) dof_values_system.resize (fe.dofs_per_face, dealii::Vector(fe.n_components())); @@ -1775,17 +1726,10 @@ namespace VectorTools function_map.find(boundary_component)->second ->vector_value_list (dof_locations, dof_values_system); - // enter those dofs - // into the list that - // match the - // component - // signature. avoid - // the usual - // complication that - // we can't just use - // *_system_to_component_index - // for non-primitive - // FEs + // enter those dofs into the list that match the + // component signature. avoid the usual complication + // that we can't just use *_system_to_component_index + // for non-primitive FEs for (unsigned int i=0; isecond ->value_list (dof_locations, dof_values_scalar, 0); diff --git a/deal.II/source/CMakeLists.txt b/deal.II/source/CMakeLists.txt index cabda8f8fd..dd6de69d3e 100644 --- a/deal.II/source/CMakeLists.txt +++ b/deal.II/source/CMakeLists.txt @@ -14,6 +14,8 @@ ## ## --------------------------------------------------------------------- +MESSAGE(STATUS "Setup library") + # # Compile the deal.II library # @@ -114,3 +116,5 @@ INSTALL(EXPORT ${DEAL_II_PROJECT_CONFIG_NAME}Targets DESTINATION ${DEAL_II_PROJECT_CONFIG_RELDIR} COMPONENT library ) + +MESSAGE(STATUS "Setup library - Done") diff --git a/deal.II/source/grid/grid_tools.cc b/deal.II/source/grid/grid_tools.cc index 7cd43ae0fb..f62d935d63 100644 --- a/deal.II/source/grid/grid_tools.cc +++ b/deal.II/source/grid/grid_tools.cc @@ -59,6 +59,13 @@ namespace GridTools return tria; } + template + const Triangulation & + get_tria(const parallel::distributed::Triangulation &tria) + { + return tria; + } + template class Container, int spacedim> const Triangulation & get_tria(const Container &container) @@ -74,6 +81,13 @@ namespace GridTools return tria; } + template + Triangulation & + get_tria(parallel::distributed::Triangulation &tria) + { + return tria; + } + template class Container, int spacedim> const Triangulation & get_tria(Container &container) @@ -862,8 +876,10 @@ next_cell: find_active_cell_around_point (const Container &container, const Point &p) { - return find_active_cell_around_point(StaticMappingQ1::mapping, - container, p).first; + return + find_active_cell_around_point + (StaticMappingQ1::mapping, + container, p).first; } @@ -1417,8 +1433,8 @@ next_cell: have_same_coarse_mesh (const Container &mesh_1, const Container &mesh_2) { - return have_same_coarse_mesh (mesh_1.get_tria(), - mesh_2.get_tria()); + return have_same_coarse_mesh (get_tria(mesh_1), + get_tria(mesh_2)); } @@ -2401,42 +2417,42 @@ next_cell: - template - std::vector > + template + std::vector > collect_periodic_faces - (const DH &dof_handler, + (const CONTAINER &container, const types::boundary_id b_id1, const types::boundary_id b_id2, const int direction, - const dealii::Tensor<1,DH::space_dimension> &offset) + const dealii::Tensor<1,CONTAINER::space_dimension> &offset) { - static const int dim = DH::dimension; - static const int space_dim = DH::space_dimension; + static const int dim = CONTAINER::dimension; + static const int space_dim = CONTAINER::space_dimension; Assert (0<=direction && direction > pairs1; - std::set > pairs2; + std::set > pairs1; + std::set > pairs2; - for (typename DH::cell_iterator cell = dof_handler.begin(0); - cell != dof_handler.end(0); ++cell) + for (typename CONTAINER::cell_iterator cell = container.begin(0); + cell != container.end(0); ++cell) { for (unsigned int i = 0; i < GeometryInfo::faces_per_cell; ++i) { - const typename DH::face_iterator face = cell->face(i); + const typename CONTAINER::face_iterator face = cell->face(i); if (face->at_boundary() && face->boundary_indicator() == b_id1) { - const std::pair pair1 + const std::pair pair1 = std::make_pair(cell, i); pairs1.insert(pair1); } if (face->at_boundary() && face->boundary_indicator() == b_id2) { - const std::pair pair2 + const std::pair pair2 = std::make_pair(cell, i); pairs2.insert(pair2); } @@ -2452,15 +2468,15 @@ next_cell: - template - std::vector > - collect_periodic_faces (const DH &dof_handler, + template + std::vector > + collect_periodic_faces (const CONTAINER &container, const types::boundary_id b_id, const int direction, - const dealii::Tensor<1,DH::space_dimension> &offset) + const dealii::Tensor<1,CONTAINER::space_dimension> &offset) { - static const int dim = DH::dimension; - static const int space_dim = DH::space_dimension; + static const int dim = CONTAINER::dimension; + static const int space_dim = CONTAINER::space_dimension; Assert (0<=direction && direction > pairs1; - std::set > pairs2; + std::set > pairs1; + std::set > pairs2; - for (typename DH::cell_iterator cell = dof_handler.begin(0); - cell != dof_handler.end(0); ++cell) + for (typename CONTAINER::cell_iterator cell = container.begin(0); + cell != container.end(0); ++cell) { - const typename DH::face_iterator face_1 = cell->face(2*direction); - const typename DH::face_iterator face_2 = cell->face(2*direction+1); + const typename CONTAINER::face_iterator face_1 = cell->face(2*direction); + const typename CONTAINER::face_iterator face_2 = cell->face(2*direction+1); if (face_1->at_boundary() && face_1->boundary_indicator() == b_id) { - const std::pair pair1 + const std::pair pair1 = std::make_pair(cell, 2*direction); pairs1.insert(pair1); } if (face_2->at_boundary() && face_2->boundary_indicator() == b_id) { - const std::pair pair2 + const std::pair pair2 = std::make_pair(cell, 2*direction+1); pairs2.insert(pair2); } @@ -2499,7 +2515,7 @@ next_cell: // and call match_periodic_face_pairs that does the actual matching: - typedef std::vector > + typedef std::vector > FaceVector; FaceVector matching = match_periodic_face_pairs(pairs1, pairs2, diff --git a/deal.II/source/grid/grid_tools.inst.in b/deal.II/source/grid/grid_tools.inst.in index 3d1076e57a..6e827d7111 100644 --- a/deal.II/source/grid/grid_tools.inst.in +++ b/deal.II/source/grid/grid_tools.inst.in @@ -69,6 +69,51 @@ for (X : TRIANGULATION_AND_DOFHANDLERS; deal_II_dimension : DIMENSIONS ; deal_II } +// now also instantiate these functions for parallel::distributed::Triangulation +for (deal_II_dimension : DIMENSIONS ; deal_II_space_dimension : SPACE_DIMENSIONS) +{ + +#if deal_II_dimension <= deal_II_space_dimension + namespace GridTools \{ + + template + unsigned int + find_closest_vertex (const parallel::distributed::Triangulation &, + const Point &); + + template + std::vector::active_cell_iterator> + find_cells_adjacent_to_vertex(const parallel::distributed::Triangulation &, + const unsigned int); + template + parallel::distributed::Triangulation::active_cell_iterator + find_active_cell_around_point (const parallel::distributed::Triangulation &, + const Point &p); + + template + std::pair::active_cell_iterator, Point > + find_active_cell_around_point (const Mapping &, + const parallel::distributed::Triangulation &, + const Point &); + + template + std::list::cell_iterator, parallel::distributed::Triangulation::cell_iterator> > + get_finest_common_cells (const parallel::distributed::Triangulation &mesh_1, + const parallel::distributed::Triangulation &mesh_2); + + + template + bool + have_same_coarse_mesh (const parallel::distributed::Triangulation &mesh_1, + const parallel::distributed::Triangulation &mesh_2); + + \} + + #endif +} + + + for (deal_II_space_dimension : SPACE_DIMENSIONS) { -- 2.39.5