diff --git a/AMDiS/CMakeLists.txt b/AMDiS/CMakeLists.txt
index b0a3da6ceb0ed87c13b4e146da634d8645f8aea6..15cb4acfafc663b394420715d68140412daaed9e 100644
--- a/AMDiS/CMakeLists.txt
+++ b/AMDiS/CMakeLists.txt
@@ -1,547 +1,12 @@
-project(AMDIS)
-
-cmake_minimum_required(VERSION 2.6)
-cmake_policy(SET CMP0017 OLD)
-if(POLICY CMP0042)
- cmake_policy(SET CMP0042 NEW)
-endif()
-if(POLICY CMP0054)
- cmake_policy(SET CMP0054 NEW)
-endif()
-
-SET(LIB_DIR ${AMDIS_SOURCE_DIR}/lib)
-SET(SOURCE_DIR ${AMDIS_SOURCE_DIR}/src)
-
-#TODO: use the cmake build type
-SET(MTL_INCLUDE_DIR ${LIB_DIR}/mtl4/ CACHE PATH "mtl4 directory")
-
-# set global compile_definitions for all target, depending on build-type
-set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS
- $<$<CONFIG:Debug>:DEBUG=1>
- $<$<CONFIG:Release>:DEBUG=0>)
-
-# find_package(Subversion QUIET)
-# if(Subversion_FOUND)
-# Subversion_WC_INFO(${CMAKE_CURRENT_SOURCE_DIR} svn_info)
-# #message("svn-rev: ${svn_info_WC_REVISION}")
-# set(AMDIS_SUB_MINOR "${svn_info_WC_REVISION}")
-# endif()
-set(CurrentRevision "0.9")
-if(NOT AMDIS_MAJOR)
- set(AMDIS_MAJOR "0")
-endif()
-if(NOT AMDIS_MINOR)
- set(AMDIS_MINOR "9")
-endif()
-list(APPEND COMPILEFLAGS "-DAMDIS_VERSION=${CurrentRevision}")
-
-#define the build type, empty can be everything and nothing
-if(CMAKE_BUILD_TYPE STREQUAL "")
- set(CMAKE_BUILD_TYPE "Release")
-endif()
-
-if(CMAKE_CXX_COMPILER MATCHES ".*icpc")
- Message("Compiler: Intel")
- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -diag-disable 654 -diag-disable 858")
-endif()
-
-
-SET(ENABLE_PARALLEL_DOMAIN "OFF" CACHE STRING "use parallel domain decomposition. please set to one of: PMTL, PETSC, OFF" )
-option(ENABLE_CXX11 "Enable C++11 compiler features" false)
-option(ENABLE_SEQ_PETSC "Use sequential PETSc solvers" false)
-option(ENABLE_UMFPACK "Use of UMFPACK solver" false)
-option(ENABLE_HYPRE "Use HYPRE AMG solver" false)
-option(ENABLE_PNG "use png reader/writer" false)
-option(ENABLE_BDDCML "Use of BDDCML library" false)
-mark_as_advanced(ENABLE_BDDCML)
-option(ENABLE_EXTENSIONS "Use extensions" false)
-option(ENABLE_OPENMP "Use OpenMP" false)
-option(ENABLE_COMPRESSION "Use output compression" false)
-option(ENABLE_OUTPUT "AMDiS output printing, disable only for debugging!" true)
-mark_as_advanced(ENABLE_OUTPUT)
-
-
-find_package(Boost 1.44 REQUIRED)
-if (Boost_FOUND)
- list(APPEND AMDIS_INCLUDE_DIRS ${Boost_INCLUDE_DIR})
- message("boost lib-dirs: ${Boost_LIBRARY_DIRS}")
- message("use the boost dir: ${Boost_INCLUDE_DIR}")
- #if (WIN32)
- #message("the windows find_boost does not set the boost library paths, please set it")
- #SET(Boost_LIBRARY_DIRS CACHE PATH "The directory containing the boost libraries")
- #endif (WIN32)
- list(APPEND AMDIS_LINK_DIRS ${Boost_LIBRARY_DIRS})
-endif (Boost_FOUND)
-
-
-SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
- ${SOURCE_DIR}/AdaptInfo.cc
- ${SOURCE_DIR}/AdaptInstationary.cc
- ${SOURCE_DIR}/AdaptStationary.cc
- ${SOURCE_DIR}/AMDiS.cc
- ${SOURCE_DIR}/Assembler.cc
- ${SOURCE_DIR}/BasisFunction.cc
- ${SOURCE_DIR}/Boundary.cc
- ${SOURCE_DIR}/BoundaryManager.cc
- ${SOURCE_DIR}/BoundaryObject.cc
- ${SOURCE_DIR}/Bubble.cc
- ${SOURCE_DIR}/Cholesky.cc
- ${SOURCE_DIR}/CoarseningManager.cc
- ${SOURCE_DIR}/CoarseningManager1d.cc
- ${SOURCE_DIR}/CoarseningManager2d.cc
- ${SOURCE_DIR}/CoarseningManager3d.cc
- ${SOURCE_DIR}/ComponentTraverseInfo.cc
- ${SOURCE_DIR}/CouplingIterationInterface.cc
- ${SOURCE_DIR}/CreatorMap.cc
- ${SOURCE_DIR}/DOFAdmin.cc
- ${SOURCE_DIR}/DOFIndexed.cc
- ${SOURCE_DIR}/DOFMatrix.cc
- ${SOURCE_DIR}/DOFVector.cc
- ${SOURCE_DIR}/Debug.cc
- ${SOURCE_DIR}/DirichletBC.cc
- ${SOURCE_DIR}/DualTraverse.cc
- ${SOURCE_DIR}/ElInfo.cc
- ${SOURCE_DIR}/ElInfo1d.cc
- ${SOURCE_DIR}/ElInfo2d.cc
- ${SOURCE_DIR}/ElInfo3d.cc
- ${SOURCE_DIR}/ElInfoStack.cc
- ${SOURCE_DIR}/Element.cc
- ${SOURCE_DIR}/ElementData.cc
- ${SOURCE_DIR}/ElementDofIterator.cc
- ${SOURCE_DIR}/ElementRegion_ED.cc
- ${SOURCE_DIR}/FiniteElemSpace.cc
- ${SOURCE_DIR}/FirstOrderAssembler.cc
- ${SOURCE_DIR}/FirstOrderTerm.cc
- ${SOURCE_DIR}/FixVec.cc
- ${SOURCE_DIR}/Global.cc
- ${SOURCE_DIR}/GlobalDOFNumbering.cc
- ${SOURCE_DIR}/GlobalElementNumbering.cc
- ${SOURCE_DIR}/Initfile.cc
- ${SOURCE_DIR}/Lagrange.cc
- ${SOURCE_DIR}/LeafData.cc
- ${SOURCE_DIR}/Line.cc
- ${SOURCE_DIR}/MacroElement.cc
- ${SOURCE_DIR}/Marker.cc
- ${SOURCE_DIR}/MatrixVector.cc
- ${SOURCE_DIR}/Mesh.cc
- ${SOURCE_DIR}/MeshStructure.cc
- ${SOURCE_DIR}/Operator.cc
- ${SOURCE_DIR}/OperatorTerm.cc
- ${SOURCE_DIR}/Parametric.cc
- ${SOURCE_DIR}/PeriodicBC.cc
- ${SOURCE_DIR}/ProblemInstat.cc
- ${SOURCE_DIR}/ProblemInterpol.cc
- ${SOURCE_DIR}/ProblemStat.cc
- ${SOURCE_DIR}/ProblemStatDbg.cc
- ${SOURCE_DIR}/Projection.cc
- ${SOURCE_DIR}/QPInfo.cc
- ${SOURCE_DIR}/QPsiPhi.cc
- ${SOURCE_DIR}/Quadrature.cc
- ${SOURCE_DIR}/RCNeighbourList.cc
- ${SOURCE_DIR}/Recovery.cc
- ${SOURCE_DIR}/RefinementManager.cc
- ${SOURCE_DIR}/RefinementManager1d.cc
- ${SOURCE_DIR}/RefinementManager2d.cc
- ${SOURCE_DIR}/RefinementManager3d.cc
- ${SOURCE_DIR}/RobinBC.cc
- ${SOURCE_DIR}/ScalableQuadrature.cc
- ${SOURCE_DIR}/SecondOrderAssembler.cc
- ${SOURCE_DIR}/SecondOrderTerm.cc
- ${SOURCE_DIR}/Serializer.cc
- ${SOURCE_DIR}/StandardProblemIteration.cc
- ${SOURCE_DIR}/SubAssembler.cc
- ${SOURCE_DIR}/SubElInfo.cc
- ${SOURCE_DIR}/SubQuadrature.cc
- ${SOURCE_DIR}/SurfaceQuadrature.cc
- ${SOURCE_DIR}/SurfaceRegion_ED.cc
- ${SOURCE_DIR}/SystemVector.cc
- ${SOURCE_DIR}/Tetrahedron.cc
- ${SOURCE_DIR}/Timer.cc
- ${SOURCE_DIR}/Traverse.cc
- ${SOURCE_DIR}/Triangle.cc
- ${SOURCE_DIR}/VertexVector.cc
- ${SOURCE_DIR}/ZeroOrderAssembler.cc
- ${SOURCE_DIR}/ZeroOrderTerm.cc
- ${SOURCE_DIR}/est/Estimator.cc
- ${SOURCE_DIR}/est/RecoveryEstimator.cc
- ${SOURCE_DIR}/est/ResidualEstimator.cc
- ${SOURCE_DIR}/est/SimpleResidualEstimator.cc
- ${SOURCE_DIR}/io/ArhReader.cc
- ${SOURCE_DIR}/io/detail/ArhReader.cc
- ${SOURCE_DIR}/io/Arh2Reader.cc
- ${SOURCE_DIR}/io/Arh2Writer.cc
- ${SOURCE_DIR}/io/Arh3Reader.cc
- ${SOURCE_DIR}/io/Arh3Writer.cc
- ${SOURCE_DIR}/io/detail/Arh2Reader.cc
- ${SOURCE_DIR}/io/detail/ArhWriter.cc
- ${SOURCE_DIR}/io/detail/Arh2Writer.cc
- ${SOURCE_DIR}/io/detail/Arh3Reader.cc
- ${SOURCE_DIR}/io/detail/Arh3Writer.cc
- ${SOURCE_DIR}/io/DofWriter.cc
- ${SOURCE_DIR}/io/ElementFileWriter.cc
- ${SOURCE_DIR}/io/FileWriterInterface.cc
- ${SOURCE_DIR}/io/FileWriter.cc
- ${SOURCE_DIR}/io/GNUPlotWriter.cc
- ${SOURCE_DIR}/io/MacroInfo.cc
- ${SOURCE_DIR}/io/MacroReader.cc
- ${SOURCE_DIR}/io/MacroWriter.cc
- ${SOURCE_DIR}/io/PngReader.cc
- ${SOURCE_DIR}/io/PngWriter.cc
- ${SOURCE_DIR}/io/PovrayWriter.cc
- ${SOURCE_DIR}/io/Spreadsheet.cc
- ${SOURCE_DIR}/io/ValueReader.cc
- ${SOURCE_DIR}/io/ValueWriter.cc
- ${SOURCE_DIR}/io/VtkWriter.cc
- ${SOURCE_DIR}/io/VtkVectorWriter.cc
- ${SOURCE_DIR}/io/detail/VtkWriter.cc
- ${SOURCE_DIR}/nonlin/ProblemNonLin.cc
- ${SOURCE_DIR}/solver/SolverMatrix.cc
- ${SOURCE_DIR}/time/RosenbrockAdaptInstationary.cc
- ${SOURCE_DIR}/time/RosenbrockMethod.cc
- ${SOURCE_DIR}/time/RosenbrockStationary.cc
- )
-
-
-include(cmake/enable_cxx11.cmake)
-include(cmake/enable_parallel_domain.cmake)
-include(cmake/enable_seq_petsc.cmake)
-include(cmake/enable_umfpack.cmake)
-include(cmake/enable_hypre.cmake)
-include(cmake/enable_png.cmake)
-include(cmake/enable_bddcml.cmake)
-include(cmake/enable_extensions.cmake)
-include(cmake/enable_openmp.cmake)
-
-if(ENABLE_COMPRESSION)
- list(APPEND COMPILEFLAGS "-DHAVE_COMPRESSION=1")
-endif(ENABLE_COMPRESSION)
-
-if(NOT ENABLE_OUTPUT)
- message(WARNING "AMDiS cout output disabled!")
- list(APPEND COMPILEFLAGS "-DSUPPRESS_OUTPUT")
-endif(NOT ENABLE_OUTPUT)
-
-if(ENABLE_MARMOT)
- Message("please set marmotcc manually")
-endif(ENABLE_MARMOT)
-
-
-# composite fem includes
-SET(COMPOSITE_SOURCE_DIR ${SOURCE_DIR}/compositeFEM)
-SET(COMPOSITE_FEM_SRC ${COMPOSITE_SOURCE_DIR}/CFE_Integration.cc
- ${COMPOSITE_SOURCE_DIR}/CFE_NormAndErrorFcts.cc
- ${COMPOSITE_SOURCE_DIR}/CompositeFEMMethods.cc
- ${COMPOSITE_SOURCE_DIR}/CompositeFEMOperator.cc
- ${COMPOSITE_SOURCE_DIR}/LevelSetAdaptMesh.cc
- ${COMPOSITE_SOURCE_DIR}/PenaltyOperator.cc
- ${COMPOSITE_SOURCE_DIR}/ElementLevelSet.cc
- ${COMPOSITE_SOURCE_DIR}/SubPolytope.cc
- ${COMPOSITE_SOURCE_DIR}/SubElementAssembler.cc )
-
-# reinit includes
-set(REINIT_SOURCE_DIR ${SOURCE_DIR}/reinit)
-file(GLOB REINIT_SRC ${REINIT_SOURCE_DIR}/*.cc)
-list(APPEND AMDIS_INCLUDE_DIRS ${REINIT_SOURCE_DIR})
-
-# muparser includes
-set(MUPARSER_SOURCE_DIR ${AMDIS_SOURCE_DIR}/lib/muparser_v134)
-file(GLOB MUPARSER_SRC ${MUPARSER_SOURCE_DIR}/src/*.cpp)
-list(APPEND AMDIS_INCLUDE_DIRS ${MUPARSER_SOURCE_DIR}/include)
-
-# mtl4 includes
-list(APPEND AMDIS_INCLUDE_DIRS ${MTL_INCLUDE_DIR})
-list(APPEND AMDIS_INCLUDE_DIRS ${SOURCE_DIR})
-
-
-include_directories(${AMDIS_INCLUDE_DIRS})
-
-if(WIN32)
- add_library(amdis STATIC ${AMDIS_SRC} ${PARALLEL_DOMAIN_AMDIS_SRC})
- add_library(compositeFEM STATIC ${COMPOSITE_FEM_SRC})
- add_library(reinit STATIC ${REINIT_SRC})
- add_library(muparser STATIC ${MUPARSER_SRC})
-else()
- add_library(amdis SHARED ${AMDIS_SRC} ${PARALLEL_DOMAIN_AMDIS_SRC})
- add_library(compositeFEM SHARED ${COMPOSITE_FEM_SRC})
- add_library(reinit SHARED ${REINIT_SRC})
- add_library(muparser SHARED ${MUPARSER_SRC})
-endif()
-
-
-list(APPEND AMDIS_LIBS amdis ${Boost_LIBRARIES})
-
-# some special treatements for Windows systems
-# --------------------------------------------
-if(WIN32)
- list(APPEND COMPILEFLAGS "-D_SCL_SECURE_NO_WARNINGS" "-D_CRT_SECURE_NO_WARNINGS")
-endif(WIN32)
-
-# some special treatements for MacOS Systems
-# ------------------------------------------
-if(CMAKE_SYSTEM_NAME MATCHES Darwin)
- if(CMAKE_COMPILER_IS_GNUCXX OR ${CMAKE_CXX_COMPILER_ID} STREQUAL Clang)
- SET(CMAKE_SHARED_LIBRARY_CREATE_C_FLAGS "${CMAKE_SHARED_LIBRARY_CREATE_C_FLAGS} -flat_namespace -single_module -undefined dynamic_lookup")
- SET(CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS "${CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS} -flat_namespace -single_module -undefined dynamic_lookup")
-
- set(CMAKE_C_LINK_FLAGS "${CMAKE_C_LINK_FLAGS} -bind_at_load -m64")
- set(CMAKE_CXX_LINK_FLAGS "${CMAKE_CXX_LINK_FLAGS} -bind_at_load -m64")
- endif()
-endif()
-
-
-message("compileflags: ${COMPILEFLAGS}")
-add_definitions(${COMPILEFLAGS})
-
-#dont change this destination. the GUI depends on it to guess the buildsystem
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/*.h")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/)
-list(APPEND deb_add_dirs "include/amdis")
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/config/*.h*")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/config/)
-list(APPEND deb_add_dirs "include/amdis/config")
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/*.hh")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/)
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/*.hpp")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/)
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/parallel/*.h")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/parallel/)
-list(APPEND deb_add_dirs "include/amdis/parallel")
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/nonlin/*.h")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/nonlin/)
-list(APPEND deb_add_dirs "include/amdis/nonlin")
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/est/*.h")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/est/)
-list(APPEND deb_add_dirs "include/amdis/est")
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/expressions/*.h*")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/expressions/)
-list(APPEND deb_add_dirs "include/amdis/expressions")
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/operations/*.h*")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/operations/)
-list(APPEND deb_add_dirs "include/amdis/operations")
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/traits/*.h*")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/traits/)
-list(APPEND deb_add_dirs "include/amdis/traits")
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/utility/*.h*")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/utility/)
-list(APPEND deb_add_dirs "include/amdis/utility")
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/time/*.h")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/time/)
-list(APPEND deb_add_dirs "include/amdis/time")
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/traits/*.h*")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/traits/)
-list(APPEND deb_add_dirs "include/amdis/traits")
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/solver/*.h")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/solver)
-list(APPEND deb_add_dirs "include/amdis/solver")
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/solver/*.hh")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/solver)
-list(APPEND deb_add_dirs "include/amdis/solver")
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/solver/details/*.h")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/solver/details)
-list(APPEND deb_add_dirs "include/amdis/solver/details")
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/solver/itl/*.hpp")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/solver/itl)
-list(APPEND deb_add_dirs "include/amdis/solver/itl")
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/solver/details/*.h")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/solver/details)
-list(APPEND deb_add_dirs "include/amdis/solver/details")
-
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/io/*.h")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/io)
-list(APPEND deb_add_dirs "include/amdis/io")
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/io/*.hh")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/io)
-
-FILE(GLOB HEADERS "${SOURCE_DIR}/io/detail/*h")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/io/detail)
-list(APPEND deb_add_dirs "include/amdis/io/detail")
-
-FILE(GLOB HEADERS "${REINIT_SOURCE_DIR}/*.h")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/reinit)
-list(APPEND deb_add_dirs "include/amdis/reinit")
-
-FILE(GLOB HEADERS "${COMPOSITE_SOURCE_DIR}/*.h")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/compositeFEM)
-list(APPEND deb_add_dirs "include/amdis/compositeFEM")
-
-FILE(GLOB HEADERS "${MUPARSER_SOURCE_DIR}/include/*.h")
-INSTALL(FILES ${HEADERS}
- DESTINATION include/amdis/muparser)
-list(APPEND deb_add_dirs "include/amdis/muparser")
-
-list(APPEND deb_add_dirs "lib/amdis")
-install(TARGETS amdis compositeFEM reinit muparser
- DESTINATION lib/amdis/ )
-
-configure_file(${AMDIS_SOURCE_DIR}/cmake/AMDISConfig.cmake.in
- ${AMDIS_BINARY_DIR}/AMDISConfig.cmake
- @ONLY
- )
-
-INSTALL(FILES ${AMDIS_BINARY_DIR}/AMDISConfig.cmake
- DESTINATION share/amdis/)
-list(APPEND deb_add_dirs "share/amdis/")
-
-FILE(GLOB CMAKE_FILES "${AMDIS_SOURCE_DIR}/cmake/*.cmake")
-INSTALL(FILES ${CMAKE_FILES}
- DESTINATION share/amdis/)
-
-#install mtl
-INSTALL(DIRECTORY ${AMDIS_SOURCE_DIR}/lib/mtl4/
- DESTINATION include/amdis/mtl4/
- FILES_MATCHING PATTERN "*.hpp"
- PATTERN ".svn" EXCLUDE
- PATTERN ".svn/*" EXCLUDE
- PATTERN "mtl4/libs" EXCLUDE
- PATTERN "mtl4/extern" EXCLUDE
- )
-FILE(GLOB_RECURSE mtl4_files
- RELATIVE ${AMDIS_SOURCE_DIR}/lib/mtl4/boost/
- ${AMDIS_SOURCE_DIR}/lib/mtl4/boost/*.hpp)
-foreach(mtl4_file in ${mtl4_files})
- get_filename_component(mtl4File_path ${mtl4_file} PATH)
- list(APPEND deb_add_dirs "include/amdis/mtl4/boost/${mtl4File_path}")
-endforeach(mtl4_file)
-
-#install documentation
-FILE(GLOB DOCS "${AMDIS_SOURCE_DIR}/doc/*.pdf")
-INSTALL(FILES ${DOCS} DESTINATION share/amdis/doc)
-list(APPEND deb_add_dirs "share/amdis/doc")
-
-list(REMOVE_DUPLICATES deb_add_dirs)
-
-ENABLE_TESTING()
-INCLUDE(CTest)
-INCLUDE(Dart)
-if(NOT CTEST_MODEL)
- set(CTEST_MODEL "Experimental")
-endif()
-if( NOT N_TEST_PROC)
- set(N_TEST_PROC "8")
-endif()
-configure_file(cmake/myMake.sh.in myMake.sh @ONLY)
-configure_file(cmake/CTestScript.cmake.in CTestScript.cmake @ONLY)
-
-
-# PACKAGES
-# ========================================================
-set(CPACK_PACKAGE_NAME "AMDIS")
-set(CPACK_PACKAGE_CONTACT "Andreas.Naumann@tu-dresden.de")
-set(CPACK_PACKAGE_VERSION "${CurrentRevision}")
-set(CPACK_GENERATOR "RPM" "DEB" "TGZ")
-set(CPACK_INSTALL_PREFIX "/usr/")
-set(CPACK_RESOURCE_FILE_LICENSE "${AMDIS_SOURCE_DIR}/license.opensource.txt")
-
-# library depends on boost, but boost libraries have version-number in name on some systems.
-# so we have to find a workaround to enforce allowed boost versions
-set(boost_ver ${Boost_MINOR_VERSION})
-math(EXPR boost_ver_start "${Boost_MINOR_VERSION}+1")
-math(EXPR boost_ver_stop "${Boost_MINOR_VERSION}+10")
-
-set(boost_depends "libboost${Boost_MAJOR_VERSION}.${boost_ver}-dev (>= ${Boost_MAJOR_VERSION}.${boost_ver})")
-set(boost_iostreams_depends "libboost-iostreams${Boost_MAJOR_VERSION}.${boost_ver}-dev (>= ${Boost_MAJOR_VERSION}.${boost_ver})")
-set(boost_system_depends "libboost-system${Boost_MAJOR_VERSION}.${boost_ver}-dev (>= ${Boost_MAJOR_VERSION}.${boost_ver})")
-set(boost_filesystem_depends "libboost-filesystem${Boost_MAJOR_VERSION}.${boost_ver}-dev (>= ${Boost_MAJOR_VERSION}.${boost_ver})")
-
-foreach(boost_ver RANGE ${boost_ver_start} ${boost_ver_stop})
- set(boost_depends "${boost_depends} | libboost${Boost_MAJOR_VERSION}.${boost_ver}-dev (>= ${Boost_MAJOR_VERSION}.${boost_ver})")
- set(boost_iostreams_depends "${boost_iostreams_depends} | libboost-iostreams${Boost_MAJOR_VERSION}.${boost_ver}-dev (>= ${Boost_MAJOR_VERSION}.${boost_ver})")
- set(boost_system_depends "${boost_system_depends} | libboost-system${Boost_MAJOR_VERSION}.${boost_ver}-dev (>= ${Boost_MAJOR_VERSION}.${boost_ver})")
- set(boost_filesystem_depends "${boost_filesystem_depends} | libboost-filesystem${Boost_MAJOR_VERSION}.${boost_ver}-dev (>= ${Boost_MAJOR_VERSION}.${boost_ver})")
-endforeach(boost_ver)
-
-configure_file(${AMDIS_SOURCE_DIR}/cmake/preinst.in
- ${AMDIS_BINARY_DIR}/preinst
- @ONLY)
-
-configure_file(${AMDIS_SOURCE_DIR}/cmake/postrm.in
- ${AMDIS_BINARY_DIR}/postrm
- @ONLY)
-
-#----Test if clang setup works----------------------------------------------------------------------
-set(COMPILER_VERSION "")
-if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
- exec_program(${CMAKE_C_COMPILER} ARGS "-v" OUTPUT_VARIABLE _clang_version_info)
- string(REGEX REPLACE "^.*[ ]([0-9]+)\\.[0-9].*$" "\\1" CLANG_MAJOR "${_clang_version_info}")
- string(REGEX REPLACE "^.*[ ][0-9]+\\.([0-9]).*$" "\\1" CLANG_MINOR "${_clang_version_info}")
- set(COMPILER_VERSION "clang ${CLANG_MAJOR}.${CLANG_MINOR}")
-endif()
-
-#---Obtain the major and minor version of the GNU compiler-------------------------------------------
-if (CMAKE_COMPILER_IS_GNUCXX)
- exec_program(${CMAKE_C_COMPILER} ARGS "-dumpversion" OUTPUT_VARIABLE _gcc_version_info)
- string(REGEX REPLACE "^([0-9]+).*$" "\\1" GCC_MAJOR ${_gcc_version_info})
- string(REGEX REPLACE "^[0-9]+\\.([0-9]+).*$" "\\1" GCC_MINOR ${_gcc_version_info})
- string(REGEX REPLACE "^[0-9]+\\.[0-9]+\\.([0-9]+).*$" "\\1" GCC_PATCH ${_gcc_version_info})
-
- if(GCC_PATCH MATCHES "\\.+")
- set(GCC_PATCH "")
- endif()
- if(GCC_MINOR MATCHES "\\.+")
- set(GCC_MINOR "")
- endif()
- if(GCC_MAJOR MATCHES "\\.+")
- set(GCC_MAJOR "")
- endif()
- set(COMPILER_VERSION "gcc ${_gcc_version_info}")
-endif()
-
-set(CPACK_RPM_PACKAGE_REQUIRES "boost-devel >= ${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}, ${RPM_DEPEND_STR}")
-set(CPACK_DEBIAN_PACKAGE_DEPENDS "${boost_depends},\\n ${boost_iostreams_depends},\\n ${boost_system_depends},\\n ${boost_filesystem_depends}")
-set(CPACK_DEBIAN_PACKAGE_DESCRIPTION "AMDiS (Adaptive Multi-Dimensional Simulations) - a C++ library to solve partial differential equations using adaptive finite elements. The main features of AMDiS are:
- .
- - full adaptive meshes in 1D, 2D and 3D
- - adaptive time stepping strategies for time dependent equations
- - uses high performance Krylov subspace solvers from MTL4 and the direct solvers UMFPACK and Intel's Pardiso
- - parallelization of the overall finite element method with excelent scaling up to several thounds of processors
- - uses PETSc for solving parallel distributed linear systems
- - easy to use interface, no additional effort to run code in parallel!
- .
- The library is compiled with ${COMPILER_VERSION} and compiled/linked with boost ${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION}.")
-
-set(CPACK_DEBIAN_PACKAGE_CONTROL_EXTRA "${AMDIS_BINARY_DIR}/preinst" "${AMDIS_BINARY_DIR}/postrm")
-
-include(CPack)
+cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
+project(AMDiS)
+
+if (USE_NEW_CMAKE AND ${CMAKE_VERSION} VERSION_GREATER "3.0")
+ # Experimental implementation of new CMakeLists.txt
+ # Can be selected by calling cmake -DUSE_NEW_CMAKE=ON .
+ # Use only if you know what you are doing :-)
+ include(${AMDiS_SOURCE_DIR}/cmake3/CMakeLists_3.0.txt)
+else ()
+ # By defualt the classical CMakeLists file ist used
+ include(${AMDiS_SOURCE_DIR}/cmake/CMakeLists_2.8.txt)
+endif ()
diff --git a/AMDiS/cmake/CMakeLists_2.8.txt b/AMDiS/cmake/CMakeLists_2.8.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43444ccc422af3c4b3b3ac15c5700b3afb87cbf0
--- /dev/null
+++ b/AMDiS/cmake/CMakeLists_2.8.txt
@@ -0,0 +1,548 @@
+cmake_minimum_required(VERSION 2.8.10)
+project(AMDIS)
+cmake_policy(SET CMP0017 OLD)
+if(POLICY CMP0042)
+ cmake_policy(SET CMP0042 NEW)
+endif()
+if(POLICY CMP0054)
+ cmake_policy(SET CMP0054 NEW)
+endif()
+
+SET(LIB_DIR ${AMDIS_SOURCE_DIR}/lib)
+SET(SOURCE_DIR ${AMDIS_SOURCE_DIR}/src)
+
+#TODO: use the cmake build type
+SET(MTL_INCLUDE_DIR ${LIB_DIR}/mtl4/ CACHE PATH "mtl4 directory")
+
+# set global compile_definitions for all target, depending on build-type
+set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS
+ $<$<CONFIG:Debug>:DEBUG=1>
+ $<$<CONFIG:Release>:DEBUG=0>)
+
+# find_package(Subversion QUIET)
+# if(Subversion_FOUND)
+# Subversion_WC_INFO(${CMAKE_CURRENT_SOURCE_DIR} svn_info)
+# #message("svn-rev: ${svn_info_WC_REVISION}")
+# set(AMDIS_SUB_MINOR "${svn_info_WC_REVISION}")
+# endif()
+set(CurrentRevision "0.9")
+if(NOT AMDIS_MAJOR)
+ set(AMDIS_MAJOR "0")
+endif()
+if(NOT AMDIS_MINOR)
+ set(AMDIS_MINOR "9")
+endif()
+list(APPEND COMPILEFLAGS "-DAMDIS_VERSION=${CurrentRevision}")
+
+#define the build type, empty can be everything and nothing
+if(CMAKE_BUILD_TYPE STREQUAL "")
+ set(CMAKE_BUILD_TYPE "Release")
+endif()
+
+if(CMAKE_CXX_COMPILER MATCHES ".*icpc")
+ Message("Compiler: Intel")
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -diag-disable 654 -diag-disable 858")
+endif()
+
+
+SET(ENABLE_PARALLEL_DOMAIN "OFF" CACHE STRING "use parallel domain decomposition. please set to one of: PMTL, PETSC, OFF" )
+option(ENABLE_CXX11 "Enable C++11 compiler features" false)
+option(ENABLE_SEQ_PETSC "Use sequential PETSc solvers" false)
+option(ENABLE_UMFPACK "Use of UMFPACK solver" false)
+option(ENABLE_HYPRE "Use HYPRE AMG solver" false)
+option(ENABLE_PNG "use png reader/writer" false)
+option(ENABLE_BDDCML "Use of BDDCML library" false)
+mark_as_advanced(ENABLE_BDDCML)
+option(ENABLE_EXTENSIONS "Use extensions" false)
+option(ENABLE_OPENMP "Use OpenMP" false)
+option(ENABLE_COMPRESSION "Use output compression" false)
+option(ENABLE_OUTPUT "AMDiS output printing, disable only for debugging!" true)
+mark_as_advanced(ENABLE_OUTPUT)
+
+
+find_package(Boost 1.44 REQUIRED)
+if (Boost_FOUND)
+ list(APPEND AMDIS_INCLUDE_DIRS ${Boost_INCLUDE_DIR})
+ message("boost lib-dirs: ${Boost_LIBRARY_DIRS}")
+ message("use the boost dir: ${Boost_INCLUDE_DIR}")
+ #if (WIN32)
+ #message("the windows find_boost does not set the boost library paths, please set it")
+ #SET(Boost_LIBRARY_DIRS CACHE PATH "The directory containing the boost libraries")
+ #endif (WIN32)
+ list(APPEND AMDIS_LINK_DIRS ${Boost_LIBRARY_DIRS})
+endif (Boost_FOUND)
+
+
+SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
+ ${SOURCE_DIR}/AdaptInfo.cc
+ ${SOURCE_DIR}/AdaptInstationary.cc
+ ${SOURCE_DIR}/AdaptStationary.cc
+ ${SOURCE_DIR}/AMDiS.cc
+ ${SOURCE_DIR}/Assembler.cc
+ ${SOURCE_DIR}/BasisFunction.cc
+ ${SOURCE_DIR}/Boundary.cc
+ ${SOURCE_DIR}/BoundaryManager.cc
+ ${SOURCE_DIR}/BoundaryObject.cc
+ ${SOURCE_DIR}/Bubble.cc
+ ${SOURCE_DIR}/Cholesky.cc
+ ${SOURCE_DIR}/CoarseningManager.cc
+ ${SOURCE_DIR}/CoarseningManager1d.cc
+ ${SOURCE_DIR}/CoarseningManager2d.cc
+ ${SOURCE_DIR}/CoarseningManager3d.cc
+ ${SOURCE_DIR}/ComponentTraverseInfo.cc
+ ${SOURCE_DIR}/CouplingIterationInterface.cc
+ ${SOURCE_DIR}/CreatorMap.cc
+ ${SOURCE_DIR}/DOFAdmin.cc
+ ${SOURCE_DIR}/DOFIndexed.cc
+ ${SOURCE_DIR}/DOFMatrix.cc
+ ${SOURCE_DIR}/DOFVector.cc
+ ${SOURCE_DIR}/Debug.cc
+ ${SOURCE_DIR}/DirichletBC.cc
+ ${SOURCE_DIR}/DualTraverse.cc
+ ${SOURCE_DIR}/ElInfo.cc
+ ${SOURCE_DIR}/ElInfo1d.cc
+ ${SOURCE_DIR}/ElInfo2d.cc
+ ${SOURCE_DIR}/ElInfo3d.cc
+ ${SOURCE_DIR}/ElInfoStack.cc
+ ${SOURCE_DIR}/Element.cc
+ ${SOURCE_DIR}/ElementData.cc
+ ${SOURCE_DIR}/ElementDofIterator.cc
+ ${SOURCE_DIR}/ElementRegion_ED.cc
+ ${SOURCE_DIR}/FiniteElemSpace.cc
+ ${SOURCE_DIR}/FirstOrderAssembler.cc
+ ${SOURCE_DIR}/FirstOrderTerm.cc
+ ${SOURCE_DIR}/FixVec.cc
+ ${SOURCE_DIR}/Global.cc
+ ${SOURCE_DIR}/GlobalDOFNumbering.cc
+ ${SOURCE_DIR}/GlobalElementNumbering.cc
+ ${SOURCE_DIR}/Initfile.cc
+ ${SOURCE_DIR}/Lagrange.cc
+ ${SOURCE_DIR}/LeafData.cc
+ ${SOURCE_DIR}/Line.cc
+ ${SOURCE_DIR}/MacroElement.cc
+ ${SOURCE_DIR}/Marker.cc
+ ${SOURCE_DIR}/MatrixVector.cc
+ ${SOURCE_DIR}/Mesh.cc
+ ${SOURCE_DIR}/MeshStructure.cc
+ ${SOURCE_DIR}/Operator.cc
+ ${SOURCE_DIR}/OperatorTerm.cc
+ ${SOURCE_DIR}/Parametric.cc
+ ${SOURCE_DIR}/PeriodicBC.cc
+ ${SOURCE_DIR}/ProblemInstat.cc
+ ${SOURCE_DIR}/ProblemInterpol.cc
+ ${SOURCE_DIR}/ProblemStat.cc
+ ${SOURCE_DIR}/ProblemStatDbg.cc
+ ${SOURCE_DIR}/Projection.cc
+ ${SOURCE_DIR}/QPInfo.cc
+ ${SOURCE_DIR}/QPsiPhi.cc
+ ${SOURCE_DIR}/Quadrature.cc
+ ${SOURCE_DIR}/RCNeighbourList.cc
+ ${SOURCE_DIR}/Recovery.cc
+ ${SOURCE_DIR}/RefinementManager.cc
+ ${SOURCE_DIR}/RefinementManager1d.cc
+ ${SOURCE_DIR}/RefinementManager2d.cc
+ ${SOURCE_DIR}/RefinementManager3d.cc
+ ${SOURCE_DIR}/RobinBC.cc
+ ${SOURCE_DIR}/ScalableQuadrature.cc
+ ${SOURCE_DIR}/SecondOrderAssembler.cc
+ ${SOURCE_DIR}/SecondOrderTerm.cc
+ ${SOURCE_DIR}/Serializer.cc
+ ${SOURCE_DIR}/StandardProblemIteration.cc
+ ${SOURCE_DIR}/SubAssembler.cc
+ ${SOURCE_DIR}/SubElInfo.cc
+ ${SOURCE_DIR}/SubQuadrature.cc
+ ${SOURCE_DIR}/SurfaceQuadrature.cc
+ ${SOURCE_DIR}/SurfaceRegion_ED.cc
+ ${SOURCE_DIR}/SystemVector.cc
+ ${SOURCE_DIR}/Tetrahedron.cc
+ ${SOURCE_DIR}/Timer.cc
+ ${SOURCE_DIR}/Traverse.cc
+ ${SOURCE_DIR}/Triangle.cc
+ ${SOURCE_DIR}/VertexVector.cc
+ ${SOURCE_DIR}/ZeroOrderAssembler.cc
+ ${SOURCE_DIR}/ZeroOrderTerm.cc
+ ${SOURCE_DIR}/est/Estimator.cc
+ ${SOURCE_DIR}/est/RecoveryEstimator.cc
+ ${SOURCE_DIR}/est/ResidualEstimator.cc
+ ${SOURCE_DIR}/est/SimpleResidualEstimator.cc
+ ${SOURCE_DIR}/io/ArhReader.cc
+ ${SOURCE_DIR}/io/detail/ArhReader.cc
+ ${SOURCE_DIR}/io/Arh2Reader.cc
+ ${SOURCE_DIR}/io/Arh2Writer.cc
+ ${SOURCE_DIR}/io/Arh3Reader.cc
+ ${SOURCE_DIR}/io/Arh3Writer.cc
+ ${SOURCE_DIR}/io/detail/Arh2Reader.cc
+ ${SOURCE_DIR}/io/detail/ArhWriter.cc
+ ${SOURCE_DIR}/io/detail/Arh2Writer.cc
+ ${SOURCE_DIR}/io/detail/Arh3Reader.cc
+ ${SOURCE_DIR}/io/detail/Arh3Writer.cc
+ ${SOURCE_DIR}/io/DofWriter.cc
+ ${SOURCE_DIR}/io/ElementFileWriter.cc
+ ${SOURCE_DIR}/io/FileWriterInterface.cc
+ ${SOURCE_DIR}/io/FileWriter.cc
+ ${SOURCE_DIR}/io/GNUPlotWriter.cc
+ ${SOURCE_DIR}/io/MacroInfo.cc
+ ${SOURCE_DIR}/io/MacroReader.cc
+ ${SOURCE_DIR}/io/MacroWriter.cc
+ ${SOURCE_DIR}/io/PngReader.cc
+ ${SOURCE_DIR}/io/PngWriter.cc
+ ${SOURCE_DIR}/io/PovrayWriter.cc
+ ${SOURCE_DIR}/io/Spreadsheet.cc
+ ${SOURCE_DIR}/io/ValueReader.cc
+ ${SOURCE_DIR}/io/ValueWriter.cc
+ ${SOURCE_DIR}/io/VtkWriter.cc
+ ${SOURCE_DIR}/io/VtkVectorWriter.cc
+ ${SOURCE_DIR}/io/detail/VtkWriter.cc
+ ${SOURCE_DIR}/nonlin/ProblemNonLin.cc
+ ${SOURCE_DIR}/solver/SolverMatrix.cc
+ ${SOURCE_DIR}/time/RosenbrockAdaptInstationary.cc
+ ${SOURCE_DIR}/time/RosenbrockMethod.cc
+ ${SOURCE_DIR}/time/RosenbrockStationary.cc
+ )
+
+
+include(cmake/enable_cxx11.cmake)
+include(cmake/enable_parallel_domain.cmake)
+include(cmake/enable_seq_petsc.cmake)
+include(cmake/enable_umfpack.cmake)
+include(cmake/enable_hypre.cmake)
+include(cmake/enable_png.cmake)
+include(cmake/enable_bddcml.cmake)
+include(cmake/enable_extensions.cmake)
+include(cmake/enable_openmp.cmake)
+
+if(ENABLE_COMPRESSION)
+ list(APPEND COMPILEFLAGS "-DHAVE_COMPRESSION=1")
+endif(ENABLE_COMPRESSION)
+
+if(NOT ENABLE_OUTPUT)
+ message(WARNING "AMDiS cout output disabled!")
+ list(APPEND COMPILEFLAGS "-DSUPPRESS_OUTPUT")
+endif(NOT ENABLE_OUTPUT)
+
+if(ENABLE_MARMOT)
+ Message("please set marmotcc manually")
+endif(ENABLE_MARMOT)
+
+# TODO: make composidte-fem and reinit a subproject
+# add_subdirectory(${SOURCE_DIR}/compositeFEM [binarydir])
+
+# composite fem includes
+SET(COMPOSITE_SOURCE_DIR ${SOURCE_DIR}/compositeFEM)
+SET(COMPOSITE_FEM_SRC ${COMPOSITE_SOURCE_DIR}/CFE_Integration.cc
+ ${COMPOSITE_SOURCE_DIR}/CFE_NormAndErrorFcts.cc
+ ${COMPOSITE_SOURCE_DIR}/CompositeFEMMethods.cc
+ ${COMPOSITE_SOURCE_DIR}/CompositeFEMOperator.cc
+ ${COMPOSITE_SOURCE_DIR}/LevelSetAdaptMesh.cc
+ ${COMPOSITE_SOURCE_DIR}/PenaltyOperator.cc
+ ${COMPOSITE_SOURCE_DIR}/ElementLevelSet.cc
+ ${COMPOSITE_SOURCE_DIR}/SubPolytope.cc
+ ${COMPOSITE_SOURCE_DIR}/SubElementAssembler.cc )
+
+# reinit includes
+set(REINIT_SOURCE_DIR ${SOURCE_DIR}/reinit)
+file(GLOB REINIT_SRC ${REINIT_SOURCE_DIR}/*.cc)
+list(APPEND AMDIS_INCLUDE_DIRS ${REINIT_SOURCE_DIR})
+
+# muparser includes
+set(MUPARSER_SOURCE_DIR ${AMDIS_SOURCE_DIR}/lib/muparser_v134)
+file(GLOB MUPARSER_SRC ${MUPARSER_SOURCE_DIR}/src/*.cpp)
+list(APPEND AMDIS_INCLUDE_DIRS ${MUPARSER_SOURCE_DIR}/include)
+
+# mtl4 includes
+list(APPEND AMDIS_INCLUDE_DIRS ${MTL_INCLUDE_DIR})
+list(APPEND AMDIS_INCLUDE_DIRS ${SOURCE_DIR})
+
+
+include_directories(${AMDIS_INCLUDE_DIRS})
+
+if(WIN32)
+ add_library(amdis STATIC ${AMDIS_SRC} ${PARALLEL_DOMAIN_AMDIS_SRC})
+ add_library(compositeFEM STATIC ${COMPOSITE_FEM_SRC})
+ add_library(reinit STATIC ${REINIT_SRC})
+ add_library(muparser STATIC ${MUPARSER_SRC})
+else()
+ add_library(amdis SHARED ${AMDIS_SRC} ${PARALLEL_DOMAIN_AMDIS_SRC})
+ add_library(compositeFEM SHARED ${COMPOSITE_FEM_SRC})
+ add_library(reinit SHARED ${REINIT_SRC})
+ add_library(muparser SHARED ${MUPARSER_SRC})
+endif()
+
+
+list(APPEND AMDIS_LIBS amdis ${Boost_LIBRARIES})
+
+# some special treatements for Windows systems
+# --------------------------------------------
+if(WIN32)
+ list(APPEND COMPILEFLAGS "-D_SCL_SECURE_NO_WARNINGS" "-D_CRT_SECURE_NO_WARNINGS")
+endif(WIN32)
+
+# some special treatements for MacOS Systems
+# ------------------------------------------
+if(CMAKE_SYSTEM_NAME MATCHES Darwin)
+ if(CMAKE_COMPILER_IS_GNUCXX OR ${CMAKE_CXX_COMPILER_ID} STREQUAL Clang)
+ SET(CMAKE_SHARED_LIBRARY_CREATE_C_FLAGS "${CMAKE_SHARED_LIBRARY_CREATE_C_FLAGS} -flat_namespace -single_module -undefined dynamic_lookup")
+ SET(CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS "${CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS} -flat_namespace -single_module -undefined dynamic_lookup")
+
+ set(CMAKE_C_LINK_FLAGS "${CMAKE_C_LINK_FLAGS} -bind_at_load -m64")
+ set(CMAKE_CXX_LINK_FLAGS "${CMAKE_CXX_LINK_FLAGS} -bind_at_load -m64")
+ endif()
+endif()
+
+
+message("compileflags: ${COMPILEFLAGS}")
+add_definitions(${COMPILEFLAGS})
+
+#dont change this destination. the GUI depends on it to guess the buildsystem
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/*.h")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/)
+list(APPEND deb_add_dirs "include/amdis")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/config/*.h*")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/config/)
+list(APPEND deb_add_dirs "include/amdis/config")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/*.hh")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/)
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/*.hpp")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/)
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/parallel/*.h")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/parallel/)
+list(APPEND deb_add_dirs "include/amdis/parallel")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/nonlin/*.h")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/nonlin/)
+list(APPEND deb_add_dirs "include/amdis/nonlin")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/est/*.h")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/est/)
+list(APPEND deb_add_dirs "include/amdis/est")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/expressions/*.h*")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/expressions/)
+list(APPEND deb_add_dirs "include/amdis/expressions")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/operations/*.h*")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/operations/)
+list(APPEND deb_add_dirs "include/amdis/operations")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/traits/*.h*")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/traits/)
+list(APPEND deb_add_dirs "include/amdis/traits")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/utility/*.h*")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/utility/)
+list(APPEND deb_add_dirs "include/amdis/utility")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/time/*.h")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/time/)
+list(APPEND deb_add_dirs "include/amdis/time")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/traits/*.h*")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/traits/)
+list(APPEND deb_add_dirs "include/amdis/traits")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/solver/*.h")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/solver)
+list(APPEND deb_add_dirs "include/amdis/solver")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/solver/*.hh")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/solver)
+list(APPEND deb_add_dirs "include/amdis/solver")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/solver/details/*.h")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/solver/details)
+list(APPEND deb_add_dirs "include/amdis/solver/details")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/solver/itl/*.hpp")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/solver/itl)
+list(APPEND deb_add_dirs "include/amdis/solver/itl")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/solver/details/*.h")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/solver/details)
+list(APPEND deb_add_dirs "include/amdis/solver/details")
+
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/io/*.h")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/io)
+list(APPEND deb_add_dirs "include/amdis/io")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/io/*.hh")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/io)
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/io/detail/*h")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/io/detail)
+list(APPEND deb_add_dirs "include/amdis/io/detail")
+
+FILE(GLOB HEADERS "${REINIT_SOURCE_DIR}/*.h")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/reinit)
+list(APPEND deb_add_dirs "include/amdis/reinit")
+
+FILE(GLOB HEADERS "${COMPOSITE_SOURCE_DIR}/*.h")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/compositeFEM)
+list(APPEND deb_add_dirs "include/amdis/compositeFEM")
+
+FILE(GLOB HEADERS "${MUPARSER_SOURCE_DIR}/include/*.h")
+INSTALL(FILES ${HEADERS}
+ DESTINATION include/amdis/muparser)
+list(APPEND deb_add_dirs "include/amdis/muparser")
+
+list(APPEND deb_add_dirs "lib/amdis")
+install(TARGETS amdis compositeFEM reinit muparser
+ DESTINATION lib/amdis/ )
+
+configure_file(${AMDIS_SOURCE_DIR}/cmake/AMDISConfig.cmake.in
+ ${AMDIS_BINARY_DIR}/AMDISConfig.cmake
+ @ONLY
+ )
+
+INSTALL(FILES ${AMDIS_BINARY_DIR}/AMDISConfig.cmake
+ DESTINATION share/amdis/)
+list(APPEND deb_add_dirs "share/amdis/")
+
+FILE(GLOB CMAKE_FILES "${AMDIS_SOURCE_DIR}/cmake/*.cmake")
+INSTALL(FILES ${CMAKE_FILES}
+ DESTINATION share/amdis/)
+
+#install mtl
+INSTALL(DIRECTORY ${AMDIS_SOURCE_DIR}/lib/mtl4/
+ DESTINATION include/amdis/mtl4/
+ FILES_MATCHING PATTERN "*.hpp"
+ PATTERN ".svn" EXCLUDE
+ PATTERN ".svn/*" EXCLUDE
+ PATTERN "mtl4/libs" EXCLUDE
+ PATTERN "mtl4/extern" EXCLUDE
+ )
+FILE(GLOB_RECURSE mtl4_files
+ RELATIVE ${AMDIS_SOURCE_DIR}/lib/mtl4/boost/
+ ${AMDIS_SOURCE_DIR}/lib/mtl4/boost/*.hpp)
+foreach(mtl4_file in ${mtl4_files})
+ get_filename_component(mtl4File_path ${mtl4_file} PATH)
+ list(APPEND deb_add_dirs "include/amdis/mtl4/boost/${mtl4File_path}")
+endforeach(mtl4_file)
+
+#install documentation
+FILE(GLOB DOCS "${AMDIS_SOURCE_DIR}/doc/*.pdf")
+INSTALL(FILES ${DOCS} DESTINATION share/amdis/doc)
+list(APPEND deb_add_dirs "share/amdis/doc")
+
+list(REMOVE_DUPLICATES deb_add_dirs)
+
+ENABLE_TESTING()
+INCLUDE(CTest)
+INCLUDE(Dart)
+if(NOT CTEST_MODEL)
+ set(CTEST_MODEL "Experimental")
+endif()
+if( NOT N_TEST_PROC)
+ set(N_TEST_PROC "8")
+endif()
+configure_file(cmake/myMake.sh.in myMake.sh @ONLY)
+configure_file(cmake/CTestScript.cmake.in CTestScript.cmake @ONLY)
+
+
+# PACKAGES
+# ========================================================
+set(CPACK_PACKAGE_NAME "AMDIS")
+set(CPACK_PACKAGE_CONTACT "Andreas.Naumann@tu-dresden.de")
+set(CPACK_PACKAGE_VERSION "${CurrentRevision}")
+set(CPACK_GENERATOR "RPM" "DEB" "TGZ")
+set(CPACK_INSTALL_PREFIX "/usr/")
+set(CPACK_RESOURCE_FILE_LICENSE "${AMDIS_SOURCE_DIR}/license.opensource.txt")
+
+# library depends on boost, but boost libraries have version-number in name on some systems.
+# so we have to find a workaround to enforce allowed boost versions
+set(boost_ver ${Boost_MINOR_VERSION})
+math(EXPR boost_ver_start "${Boost_MINOR_VERSION}+1")
+math(EXPR boost_ver_stop "${Boost_MINOR_VERSION}+10")
+
+set(boost_depends "libboost${Boost_MAJOR_VERSION}.${boost_ver}-dev (>= ${Boost_MAJOR_VERSION}.${boost_ver})")
+set(boost_iostreams_depends "libboost-iostreams${Boost_MAJOR_VERSION}.${boost_ver}-dev (>= ${Boost_MAJOR_VERSION}.${boost_ver})")
+set(boost_system_depends "libboost-system${Boost_MAJOR_VERSION}.${boost_ver}-dev (>= ${Boost_MAJOR_VERSION}.${boost_ver})")
+set(boost_filesystem_depends "libboost-filesystem${Boost_MAJOR_VERSION}.${boost_ver}-dev (>= ${Boost_MAJOR_VERSION}.${boost_ver})")
+
+foreach(boost_ver RANGE ${boost_ver_start} ${boost_ver_stop})
+ set(boost_depends "${boost_depends} | libboost${Boost_MAJOR_VERSION}.${boost_ver}-dev (>= ${Boost_MAJOR_VERSION}.${boost_ver})")
+ set(boost_iostreams_depends "${boost_iostreams_depends} | libboost-iostreams${Boost_MAJOR_VERSION}.${boost_ver}-dev (>= ${Boost_MAJOR_VERSION}.${boost_ver})")
+ set(boost_system_depends "${boost_system_depends} | libboost-system${Boost_MAJOR_VERSION}.${boost_ver}-dev (>= ${Boost_MAJOR_VERSION}.${boost_ver})")
+ set(boost_filesystem_depends "${boost_filesystem_depends} | libboost-filesystem${Boost_MAJOR_VERSION}.${boost_ver}-dev (>= ${Boost_MAJOR_VERSION}.${boost_ver})")
+endforeach(boost_ver)
+
+configure_file(${AMDIS_SOURCE_DIR}/cmake/preinst.in
+ ${AMDIS_BINARY_DIR}/preinst
+ @ONLY)
+
+configure_file(${AMDIS_SOURCE_DIR}/cmake/postrm.in
+ ${AMDIS_BINARY_DIR}/postrm
+ @ONLY)
+
+#----Test if clang setup works----------------------------------------------------------------------
+set(COMPILER_VERSION "")
+if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+ exec_program(${CMAKE_C_COMPILER} ARGS "-v" OUTPUT_VARIABLE _clang_version_info)
+ string(REGEX REPLACE "^.*[ ]([0-9]+)\\.[0-9].*$" "\\1" CLANG_MAJOR "${_clang_version_info}")
+ string(REGEX REPLACE "^.*[ ][0-9]+\\.([0-9]).*$" "\\1" CLANG_MINOR "${_clang_version_info}")
+ set(COMPILER_VERSION "clang ${CLANG_MAJOR}.${CLANG_MINOR}")
+endif()
+
+#---Obtain the major and minor version of the GNU compiler-------------------------------------------
+if (CMAKE_COMPILER_IS_GNUCXX)
+ exec_program(${CMAKE_C_COMPILER} ARGS "-dumpversion" OUTPUT_VARIABLE _gcc_version_info)
+ string(REGEX REPLACE "^([0-9]+).*$" "\\1" GCC_MAJOR ${_gcc_version_info})
+ string(REGEX REPLACE "^[0-9]+\\.([0-9]+).*$" "\\1" GCC_MINOR ${_gcc_version_info})
+ string(REGEX REPLACE "^[0-9]+\\.[0-9]+\\.([0-9]+).*$" "\\1" GCC_PATCH ${_gcc_version_info})
+
+ if(GCC_PATCH MATCHES "\\.+")
+ set(GCC_PATCH "")
+ endif()
+ if(GCC_MINOR MATCHES "\\.+")
+ set(GCC_MINOR "")
+ endif()
+ if(GCC_MAJOR MATCHES "\\.+")
+ set(GCC_MAJOR "")
+ endif()
+ set(COMPILER_VERSION "gcc ${_gcc_version_info}")
+endif()
+
+set(CPACK_RPM_PACKAGE_REQUIRES "boost-devel >= ${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}, ${RPM_DEPEND_STR}")
+set(CPACK_DEBIAN_PACKAGE_DEPENDS "${boost_depends},\\n ${boost_iostreams_depends},\\n ${boost_system_depends},\\n ${boost_filesystem_depends}")
+set(CPACK_DEBIAN_PACKAGE_DESCRIPTION "AMDiS (Adaptive Multi-Dimensional Simulations) - a C++ library to solve partial differential equations using adaptive finite elements. The main features of AMDiS are:
+ .
+ - full adaptive meshes in 1D, 2D and 3D
+ - adaptive time stepping strategies for time dependent equations
+ - uses high performance Krylov subspace solvers from MTL4 and the direct solvers UMFPACK and Intel's Pardiso
+ - parallelization of the overall finite element method with excelent scaling up to several thounds of processors
+ - uses PETSc for solving parallel distributed linear systems
+ - easy to use interface, no additional effort to run code in parallel!
+ .
+ The library is compiled with ${COMPILER_VERSION} and compiled/linked with boost ${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION}.")
+
+set(CPACK_DEBIAN_PACKAGE_CONTROL_EXTRA "${AMDIS_BINARY_DIR}/preinst" "${AMDIS_BINARY_DIR}/postrm")
+
+include(CPack)
diff --git a/AMDiS/cmake/PETScConfig.cmake b/AMDiS/cmake/PETScConfig.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..a082857accf24d41b2516c24778f71088cc532b5
--- /dev/null
+++ b/AMDiS/cmake/PETScConfig.cmake
@@ -0,0 +1,251 @@
+# - Try to find PETSc
+# Once done this will define
+# source: https://github.com/jedbrown/cmake-modules/blob/master/FindPETSc.cmake
+#
+# PETSC_FOUND - system has PETSc
+# PETSC_INCLUDES - the PETSc include directories
+# PETSC_LIBRARIES - Link these to use PETSc
+# PETSC_COMPILER - Compiler used by PETSc, helpful to find a compatible MPI
+# PETSC_DEFINITIONS - Compiler switches for using PETSc
+# PETSC_MPIEXEC - Executable for running MPI programs
+# PETSC_VERSION - Version string (MAJOR.MINOR.SUBMINOR)
+#
+# Hack: PETSC_VERSION currently decides on the version based on the
+# layout. Otherwise we need to run C code to determine the version.
+#
+# Setting these changes the behavior of the search
+# PETSC_DIR - directory in which PETSc resides
+# PETSC_ARCH - build architecture
+#
+# Redistribution and use is allowed according to the terms of the BSD license.
+# For details see the accompanying COPYING-CMAKE-SCRIPTS file.
+#
+
+function (petsc_get_version)
+ if (EXISTS "${PETSC_DIR}/include/petscversion.h")
+ file (STRINGS "${PETSC_DIR}/include/petscversion.h" vstrings REGEX "#define PETSC_VERSION_(RELEASE|MAJOR|MINOR|SUBMINOR|PATCH) ")
+ foreach (line ${vstrings})
+ string (REGEX REPLACE " +" ";" fields ${line}) # break line into three fields (the first is always "#define")
+ list (GET fields 1 var)
+ list (GET fields 2 val)
+ set (${var} ${val} PARENT_SCOPE)
+ set (${var} ${val}) # Also in local scope so we have access below
+ endforeach ()
+ if (PETSC_VERSION_RELEASE)
+ set (PETSC_VERSION "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}p${PETSC_VERSION_PATCH}" PARENT_SCOPE)
+ else ()
+ # make dev version compare higher than any patch level of a released version
+ set (PETSC_VERSION "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}.99" PARENT_SCOPE)
+ endif ()
+ else ()
+ message (SEND_ERROR "PETSC_DIR can not be used, ${PETSC_DIR}/include/petscversion.h does not exist")
+ endif ()
+endfunction ()
+
+find_path (PETSC_DIR include/petsc.h
+ HINTS ENV PETSC_DIR
+ PATHS
+ /usr/lib/petscdir/3.1 /usr/lib/petscdir/3.0.0 /usr/lib/petscdir/2.3.3 /usr/lib/petscdir/2.3.2 # Debian
+ $ENV{HOME}/petsc
+ DOC "PETSc Directory")
+
+if (PETSC_DIR AND NOT PETSC_ARCH)
+ set (_petsc_arches
+ $ENV{PETSC_ARCH} # If set, use environment variable first
+ linux-gnu-c-debug linux-gnu-c-opt # Debian defaults
+ x86_64-unknown-linux-gnu i386-unknown-linux-gnu)
+ set (petscconf "NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
+ foreach (arch ${_petsc_arches})
+ if (NOT PETSC_ARCH)
+ find_path (petscconf petscconf.h
+ HINTS ${PETSC_DIR}
+ PATH_SUFFIXES ${arch}/include bmake/${arch}
+ NO_DEFAULT_PATH)
+ if (petscconf)
+ set (PETSC_ARCH "${arch}" CACHE STRING "PETSc build architecture")
+ endif (petscconf)
+ endif (NOT PETSC_ARCH)
+ endforeach (arch)
+ set (petscconf "NOTFOUND" CACHE INTERNAL "Scratch variable" FORCE)
+endif (PETSC_DIR AND NOT PETSC_ARCH)
+
+set (petsc_slaves LIBRARIES_SYS LIBRARIES_VEC LIBRARIES_MAT LIBRARIES_DM LIBRARIES_KSP LIBRARIES_SNES LIBRARIES_TS
+ INCLUDE_DIR INCLUDE_CONF)
+include (cmake/FindPackageMultipass.cmake)
+find_package_multipass (PETSc petsc_config_current
+ STATES DIR ARCH
+ DEPENDENTS INCLUDES LIBRARIES COMPILER MPIEXEC ${petsc_slaves})
+
+# Determine whether the PETSc layout is old-style (through 2.3.3) or
+# new-style (>= 3.0.0)
+if (EXISTS "${PETSC_DIR}/${PETSC_ARCH}/include/petscconf.h") # > 2.3.3
+ set (petsc_conf_rules "${PETSC_DIR}/conf/rules")
+ set (petsc_conf_variables "${PETSC_DIR}/conf/variables")
+elseif (EXISTS "${PETSC_DIR}/bmake/${PETSC_ARCH}/petscconf.h") # <= 2.3.3
+ set (petsc_conf_rules "${PETSC_DIR}/bmake/common/rules")
+ set (petsc_conf_variables "${PETSC_DIR}/bmake/common/variables")
+elseif (PETSC_DIR)
+ message (SEND_ERROR "The pair PETSC_DIR=${PETSC_DIR} PETSC_ARCH=${PETSC_ARCH} do not specify a valid PETSc installation")
+else ()
+ message (FATAL_ERROR "PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH.")
+endif ()
+petsc_get_version()
+
+if (petsc_conf_rules AND petsc_conf_variables AND NOT petsc_config_current)
+ # Put variables into environment since they are needed to get
+ # configuration (petscvariables) in the PETSc makefile
+ set (ENV{PETSC_DIR} "${PETSC_DIR}")
+ set (ENV{PETSC_ARCH} "${PETSC_ARCH}")
+
+ # A temporary makefile to probe the PETSc configuration
+ set (petsc_config_makefile "${PROJECT_BINARY_DIR}/Makefile.petsc")
+ file (WRITE "${petsc_config_makefile}"
+"## This file was autogenerated by FindPETSc.cmake
+# PETSC_DIR = ${PETSC_DIR}
+# PETSC_ARCH = ${PETSC_ARCH}
+include ${petsc_conf_rules}
+include ${petsc_conf_variables}
+show :
+ -@echo -n \${\${VARIABLE}}
+")
+
+ macro (PETSC_GET_VARIABLE name var)
+ set (${var} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
+ execute_process (COMMAND ${CMAKE_MAKE_PROGRAM} --no-print-directory -f ${petsc_config_makefile} show VARIABLE=${name}
+ OUTPUT_VARIABLE ${var}
+ RESULT_VARIABLE petsc_return)
+ endmacro (PETSC_GET_VARIABLE)
+ petsc_get_variable (PETSC_LIB_DIR petsc_lib_dir)
+ petsc_get_variable (PETSC_EXTERNAL_LIB_BASIC petsc_libs_external)
+ petsc_get_variable (PETSC_CCPPFLAGS petsc_cpp_line)
+ petsc_get_variable (PETSC_INCLUDE petsc_include)
+ petsc_get_variable (PCC petsc_cc)
+ petsc_get_variable (MPIEXEC petsc_mpiexec)
+ # We are done with the temporary Makefile, calling PETSC_GET_VARIABLE after this point is invalid!
+ file (REMOVE ${petsc_config_makefile})
+
+ include (cmake/ResolveCompilerPaths.cmake)
+ # Extract include paths and libraries from compile command line
+ resolve_includes (petsc_includes_all "${petsc_cpp_line}")
+
+ message (STATUS "petsc_lib_dir ${petsc_lib_dir}")
+
+ macro (PETSC_FIND_LIBRARY suffix name)
+ set (PETSC_LIBRARY_${suffix} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE) # Clear any stale value, if we got here, we need to find it again
+ find_library (PETSC_LIBRARY_${suffix} NAMES ${name} HINTS ${petsc_lib_dir} NO_DEFAULT_PATH)
+ set (PETSC_LIBRARIES_${suffix} "${PETSC_LIBRARY_${suffix}}")
+ mark_as_advanced (PETSC_LIBRARY_${suffix})
+ endmacro (PETSC_FIND_LIBRARY suffix name)
+
+ # Look for petscvec first, if it doesn't exist, we must be using single-library
+ petsc_find_library (VEC petscvec)
+ if (PETSC_LIBRARY_VEC)
+ petsc_find_library (SYS "petscsys;petsc") # libpetscsys is called libpetsc prior to 3.1 (when single-library was introduced)
+ petsc_find_library (MAT petscmat)
+ petsc_find_library (DM petscdm)
+ petsc_find_library (KSP petscksp)
+ petsc_find_library (SNES petscsnes)
+ petsc_find_library (TS petscts)
+ macro (PETSC_JOIN libs deps)
+ list (APPEND PETSC_LIBRARIES_${libs} ${PETSC_LIBRARIES_${deps}})
+ endmacro (PETSC_JOIN libs deps)
+ petsc_join (VEC SYS)
+ petsc_join (MAT VEC)
+ petsc_join (DM MAT)
+ petsc_join (KSP DM)
+ petsc_join (SNES KSP)
+ petsc_join (TS SNES)
+ petsc_join (ALL TS)
+ else ()
+ set (PETSC_LIBRARY_VEC "NOTFOUND" CACHE INTERNAL "Cleared" FORCE) # There is no libpetscvec
+ petsc_find_library (SINGLE petsc)
+ foreach (pkg SYS VEC MAT DM KSP SNES TS ALL)
+ set (PETSC_LIBRARIES_${pkg} "${PETSC_LIBRARY_SINGLE}")
+ endforeach ()
+ endif ()
+ if (PETSC_LIBRARY_TS)
+ message (STATUS "Recognized PETSc install with separate libraries for each package")
+ else ()
+ message (STATUS "Recognized PETSc install with single library for all packages")
+ endif ()
+
+ include (CheckCSourceRuns)
+ macro (PETSC_TEST_RUNS includes libraries runs)
+ multipass_c_source_runs ("${includes}" "${libraries}" "
+static const char help[] = \"PETSc test program.\";
+#include \"petscts.h\"
+int main(int argc,char *argv[]) {
+ PetscErrorCode ierr;
+ TS ts;
+
+ ierr = PetscInitialize(&argc,&argv,0,help);CHKERRQ(ierr);
+ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
+ ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
+ ierr = TSDestroy(ts);CHKERRQ(ierr);
+ ierr = PetscFinalize();CHKERRQ(ierr);
+ return 0;
+}
+" ${runs})
+ if (${${runs}})
+ set (PETSC_EXECUTABLE_RUNS "YES" CACHE BOOL
+ "Can the system successfully run a PETSc executable? This variable can be manually set to \"YES\" to force CMake to accept a given PETSc configuration, but this will almost always result in a broken build. If you change PETSC_DIR, PETSC_ARCH, or PETSC_CURRENT you would have to reset this variable." FORCE)
+ endif (${${runs}})
+ endmacro (PETSC_TEST_RUNS)
+
+ find_path (PETSC_INCLUDE_DIR petscts.h HINTS "${PETSC_DIR}" PATH_SUFFIXES include NO_DEFAULT_PATH)
+ find_path (PETSC_INCLUDE_CONF petscconf.h HINTS "${PETSC_DIR}" PATH_SUFFIXES "${PETSC_ARCH}/include" "bmake/${PETSC_ARCH}" NO_DEFAULT_PATH)
+ mark_as_advanced (PETSC_INCLUDE_DIR PETSC_INCLUDE_CONF)
+ set (petsc_includes_minimal ${PETSC_INCLUDE_CONF} ${PETSC_INCLUDE_DIR})
+
+ petsc_test_runs ("${petsc_includes_minimal}" "${PETSC_LIBRARIES_TS}" petsc_works_minimal)
+ if (petsc_works_minimal)
+ message (STATUS "Minimal PETSc includes and libraries work. This probably means we are building with shared libs.")
+ set (petsc_includes_needed "${petsc_includes_minimal}")
+ else (petsc_works_minimal) # Minimal includes fail, see if just adding full includes fixes it
+ petsc_test_runs ("${petsc_includes_all}" "${PETSC_LIBRARIES_TS}" petsc_works_allincludes)
+ if (petsc_works_allincludes) # It does, we just need all the includes (
+ message (STATUS "PETSc requires extra include paths, but links correctly with only interface libraries. This is an unexpected configuration (but it seems to work fine).")
+ set (petsc_includes_needed ${petsc_includes_all})
+ else (petsc_works_allincludes) # We are going to need to link the external libs explicitly
+ resolve_libraries (petsc_libraries_external "${petsc_libs_external}")
+ foreach (pkg SYS VEC MAT DM KSP SNES TS ALL)
+ list (APPEND PETSC_LIBRARIES_${pkg} ${petsc_libraries_external})
+ endforeach (pkg)
+ petsc_test_runs ("${petsc_includes_minimal}" "${PETSC_LIBRARIES_TS}" petsc_works_alllibraries)
+ if (petsc_works_alllibraries)
+ message (STATUS "PETSc only need minimal includes, but requires explicit linking to all dependencies. This is expected when PETSc is built with static libraries.")
+ set (petsc_includes_needed ${petsc_includes_minimal})
+ else (petsc_works_alllibraries)
+ # It looks like we really need everything, should have listened to Matt
+ set (petsc_includes_needed ${petsc_includes_all})
+ petsc_test_runs ("${petsc_includes_all}" "${PETSC_LIBRARIES_TS}" petsc_works_all)
+ if (petsc_works_all) # We fail anyways
+ message (STATUS "PETSc requires extra include paths and explicit linking to all dependencies. This probably means you have static libraries and something unexpected in PETSc headers.")
+ else (petsc_works_all) # We fail anyways
+ message (STATUS "PETSc could not be used, maybe the install is broken.")
+ endif (petsc_works_all)
+ endif (petsc_works_alllibraries)
+ endif (petsc_works_allincludes)
+ endif (petsc_works_minimal)
+
+ # We do an out-of-source build so __FILE__ will be an absolute path, hence __INSDIR__ is superfluous
+ if (${PETSC_VERSION} VERSION_LESS 3.1)
+ set (PETSC_DEFINITIONS "-D__SDIR__=\"\"" CACHE STRING "PETSc definitions" FORCE)
+ else ()
+ set (PETSC_DEFINITIONS "-D__INSDIR__=" CACHE STRING "PETSc definitions" FORCE)
+ endif ()
+ # Sometimes this can be used to assist FindMPI.cmake
+ set (PETSC_MPIEXEC ${petsc_mpiexec} CACHE FILEPATH "Executable for running PETSc MPI programs" FORCE)
+ set (PETSC_INCLUDES ${petsc_includes_needed} CACHE STRING "PETSc include path" FORCE)
+ set (PETSC_LIBRARIES ${PETSC_LIBRARIES_ALL} CACHE STRING "PETSc libraries" FORCE)
+ set (PETSC_COMPILER ${petsc_cc} CACHE FILEPATH "PETSc compiler" FORCE)
+ # Note that we have forced values for all these choices. If you
+ # change these, you are telling the system to trust you that they
+ # work. It is likely that you will end up with a broken build.
+ mark_as_advanced (PETSC_INCLUDES PETSC_LIBRARIES PETSC_COMPILER PETSC_DEFINITIONS PETSC_MPIEXEC PETSC_EXECUTABLE_RUNS)
+endif ()
+
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (PETSc
+ "PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH."
+ PETSC_INCLUDES PETSC_LIBRARIES PETSC_EXECUTABLE_RUNS)
diff --git a/AMDiS/cmake/enable_extensions.cmake b/AMDiS/cmake/enable_extensions.cmake
index ef6f09be43c955789ee92141f026d229ed2ad75c..16d9d077e654b8e8cf3ceb213b792194af945796 100644
--- a/AMDiS/cmake/enable_extensions.cmake
+++ b/AMDiS/cmake/enable_extensions.cmake
@@ -1,4 +1,7 @@
+# TODO: make extensions a subproject
+# add_subdirectory(${SOURCE_DIR}/compositeFEM [binarydir])
+
if (ENABLE_EXTENSIONS)
option(ENABLE_BASE_PROBLEMS "Use base_problems" true)
find_path(EXTENSIONS_DIR NAMES Helpers.h
diff --git a/AMDiS/cmake/enable_parallel_domain.cmake b/AMDiS/cmake/enable_parallel_domain.cmake
index 7d1b0705efec545b35cd7176c6a0dbd7de2df831..562ff0ac649e7c0f4bf73a6ccc6714b2aec554b5 100644
--- a/AMDiS/cmake/enable_parallel_domain.cmake
+++ b/AMDiS/cmake/enable_parallel_domain.cmake
@@ -108,7 +108,7 @@ if (ENABLE_PARALLEL_DOMAIN)
message(SEND_ERROR "Set the domain-decomposition version correctly.")
endif()
- INSTALL(FILES ResolveCompilerPaths.cmake FindPackageMultipass.cmake FindPETSc.cmake
+ INSTALL(FILES cmake/ResolveCompilerPaths.cmake cmake/FindPackageMultipass.cmake cmake/FindPETSc.cmake
DESTINATION share/amdis/)
if(USE_PETSC_DEV)
list(APPEND COMPILEFLAGS "-DHAVE_PETSC_DEV")
diff --git a/AMDiS/cmake3/AMDISConfig.cmake.in b/AMDiS/cmake3/AMDISConfig.cmake.in
new file mode 100644
index 0000000000000000000000000000000000000000..58ce23b3470e64e771c7e95de38b569dcb23c12e
--- /dev/null
+++ b/AMDiS/cmake3/AMDISConfig.cmake.in
@@ -0,0 +1,199 @@
+# This configuration file is shipped with the great FEM-Toolbox AMDiS.
+# It simplifies the configure of different amdis-versions.
+#
+# In order to compile an amdis-project and link against the amdis
+# (and subsequent) libraries simply add 'AMDiS' to the target_link_libraries
+# of your executable target. All include-paths and additional libraries are
+# automatically added.
+#
+# For a fast start, you use this package in the following way
+# simply look for it, possibly set the AMDiS directory
+#
+# find_package(AMDiS REQUIRED)
+# add_executable(yourTarget <yourSources>)
+# target_link_libraries(yourTarget AMDiS)
+#
+
+if (${CMAKE_VERSION} VERSION_LESS "3.0")
+ message(FATAL_ERROR "The Configuration file was created for CMake version >= 3.0")
+endif ()
+
+list(APPEND CMAKE_MODULE_PATH ${AMDIS_DIR})
+
+set(AMDIS_NEED_ZOLTAN @ENABLE_ZOLTAN@)
+set(AMDIS_NEED_CXX11 @ENABLE_CXX11@)
+set(AMDIS_NEED_UMFPACK @ENABLE_UMFPACK@)
+set(AMDIS_HAS_PARALLEL_DOMAIN @ENABLE_PARALLEL_DOMAIN@)
+set(AMDIS_NEED_COMPRESSION @ENABLE_COMPRESSION@)
+
+
+add_library(amdis_base INTERFACE)
+add_library(AMDiS ALIAS amdis_base)
+
+target_compile_definitions(amdis_base INTERFACE
+ $<$<CONFIG:Debug>:DEBUG=1>
+ $<$<CONFIG:Release>:DEBUG=0>)
+
+if (AMDIS_NEED_CXX11)
+ target_compile_features(amdis_base INTERFACE
+ cxx_alias_templates
+ cxx_auto_type
+ cxx_lambdas
+ cxx_override
+ cxx_range_for
+ cxx_static_assert
+ cxx_variadic_templates)
+ target_compile_definitions(amdis_base INTERFACE HAS_CXX11=1)
+else ()
+ target_compile_definitions(amdis_base INTERFACE HAS_CXX11=0)
+endif (AMDIS_NEED_CXX11)
+
+
+# try to detect the AMDiS include directory
+# -------------------------------------------
+find_file(_AMDIS_H AMDiS.h PATHS ${AMDIS_DIR}/../../include/amdis/)
+if (_AMDIS_H)
+ get_filename_component(AMDIS_INCLUDE_DIR ${_AMDIS_H} PATH CACHE)
+ target_include_directories(amdis_base INTERFACE ${AMDIS_INCLUDE_DIR})
+ target_include_directories(amdis_base INTERFACE ${AMDIS_INCLUDE_DIR}/mtl4)
+else ()
+ message(ERROR "Could not detect the AMDiS include directory. Please set the variable AMDIS_INCLUDE_DIR to the directory containing the AMDiS headers.")
+endif ()
+unset(_AMDIS_H CACHE)
+
+
+# AMDiS base libraries
+# --------------------
+find_library(_AMDIS_LIB amdis PATHS ${AMDIS_DIR}/../../lib/amdis/)
+if (_AMDIS_LIB)
+ target_link_libraries(amdis_base INTERFACE ${_AMDIS_LIB})
+else ()
+ message(ERROR "Could not detect the AMDiS library. Please set the variable _AMDIS_LIB to the AMDiS library.")
+endif ()
+unset(_AMDIS_LIB CACHE)
+
+
+# Boost libraries
+# ---------------
+set(BOOST_LIBS_REQUIRED system iostreams filesystem program_options date_time)
+if (WIN32)
+ list(APPEND BOOST_LIBS_REQUIRED zlib)
+ if (AMDIS_NEED_COMPRESSION)
+ list(APPEND BOOST_LIBS_REQUIRED bzip2)
+ endif ()
+endif ()
+
+set(BOOST_VERSION "1.48")
+find_package(Boost ${BOOST_VERSION} REQUIRED ${BOOST_LIBS_REQUIRED})
+
+if (Boost_FOUND)
+ target_include_directories(amdis_base INTERFACE ${Boost_INCLUDE_DIR})
+ target_link_libraries(amdis_base INTERFACE ${Boost_LIBRARIES})
+else ()
+ message(ERROR "Boost libraries not found")
+endif(Boost_FOUND)
+
+
+# umfpack library
+# --------------------
+if (AMDIS_NEED_UMFPACK)
+ set(AMDIS_UMFPACK_INCLUDE_DIR @UMFPACK_INCLUDE_DIRS@)
+ set(AMDIS_UMFPACK_LIB_DIR ${AMDIS_UMFPACK_INCLUDE_DIR}/../lib)
+ find_file(UMFPACK_H umfpack.h HINTS ${AMDIS_UMFPACK_INCLUDE_DIR})
+ find_library(UMFPACK_LIBRARY umfpack HINTS ${AMDIS_UMFPACK_LIB_DIR})
+ if (UMFPACK_H AND UMFPACK_LIBRARY)
+ get_filename_component(UMFPACK_INCLUDE_DIRS ${UMFPACK_H} PATH)
+ target_include_directories(amdis_base INTERFACE ${UMFPACK_INCLUDE_DIRS})
+
+ find_library(AMD_LIBRARY amd HINTS ${AMDIS_UMFPACK_LIB_DIR})
+ find_library(BLAS_LIBRARY blas HINTS ${AMDIS_UMFPACK_LIB_DIR})
+ if (AMD_LIBRARY AND BLAS_LIBRARY)
+ target_link_libraries(amdis_base INTERFACE
+ ${UMFPACK_LIBRARY}
+ ${AMD_LIBRARY}
+ ${BLAS_LIBRARY})
+ # TODO: add test whether umfpack is configured successfully
+ endif()
+ else()
+ message(FATAL_ERROR "Could not find the UMFPACK library")
+ endif()
+endif (AMDIS_NEED_UMFPACK)
+
+
+# Parallel amdis
+# --------------
+if (AMDIS_HAS_PARALLEL_DOMAIN)
+ find_package(MPI REQUIRED)
+ if (MPI_FOUND)
+ target_include_directories(amdis_base INTERFACE ${MPI_INCLUDE_PATH})
+ target_compile_options(amdis_base INTERFACE ${MPI_COMPILE_FLAGS})
+ target_link_libraries(amdis_base INTERFACE ${MPI_LIBRARIES})
+ endif (MPI_FOUND)
+
+ set(PETSC_EXECUTABLE_RUNS ON)
+ set(AMDIS_PETSC_DIR @PETSC_DIR@)
+ include(find_petsc)
+ if (PETSc_FOUND)
+ target_include_directories(amdis_base INTERFACE ${PETSC_INCLUDES})
+ target_link_libraries(amdis_base INTERFACE
+ ${PETSC_LIBRARY_SYS}
+ ${PETSC_LIBRARIES})
+ else()
+ message(FATAL_ERROR "Could not find PETSc!")
+ endif (PETSc_FOUND)
+
+ find_library(_AMDIS_PARALLEL_LIB amdis_parallel PATHS ${AMDIS_DIR}/../../lib/amdis/)
+ if (_AMDIS_PARALLEL_LIB)
+ target_link_libraries(amdis_base INTERFACE ${_AMDIS_PARALLEL_LIB})
+ else ()
+ message(ERROR "Could not detect the AMDiS::parallel library. Please set the variable _AMDIS_PARALLEL_LIB to this library.")
+ endif ()
+ unset(_AMDIS_PARALLEL_LIB CACHE)
+endif (AMDIS_HAS_PARALLEL_DOMAIN)
+
+
+# reinit library
+# --------------
+find_library(_REINIT_LIB amdis_reinit PATHS ${AMDIS_DIR}/../../lib/amdis/)
+if (_REINIT_LIB)
+ target_include_directories(amdis_base INTERFACE ${Boost_INCLUDE_DIR}/reinit)
+ target_link_libraries(amdis_base INTERFACE ${_REINIT_LIB})
+else ()
+ message(ERROR "Reinit library not found")
+endif ()
+unset(_REINIT_LIB CACHE)
+
+
+# compositeFEM library
+# --------------------
+find_library(_COMPOSITE_FEM_LIB amdis_compositeFEM PATHS ${AMDIS_DIR}/../../lib/amdis/)
+if (_COMPOSITE_FEM_LIB)
+ target_include_directories(amdis_base INTERFACE ${Boost_INCLUDE_DIR}/compositeFEM)
+ target_link_libraries(amdis_base INTERFACE ${_COMPOSITE_FEM_LIB})
+else ()
+ message(ERROR "CompositeFEM library not found")
+endif ()
+unset(_COMPOSITE_FEM_LIB CACHE)
+
+
+# muparser library
+# --------------------
+find_library(_MUPARSER_LIB muparser PATHS ${AMDIS_DIR}/../../lib/amdis/)
+if (_MUPARSER_LIB)
+ target_include_directories(amdis_base INTERFACE ${Boost_INCLUDE_DIR}/muparser)
+ target_link_libraries(amdis_base INTERFACE ${_MUPARSER_LIB})
+else ()
+ message(ERROR "MuParser library not found")
+endif ()
+unset(_MUPARSER_LIB CACHE)
+
+# Zoltan library
+# --------------
+if (AMDIS_NEED_ZOLTAN)
+ find_library(ZOLTAN_LIB zoltan HINTS ENV LIBRARY_PATH DOC "Full path to the zoltan library")
+ if (ZOLTAN_LIB)
+ target_link_libraries(amdis_base INTERFACE ${ZOLTAN_LIB})
+ else()
+ message(FATAL_ERROR "Could not find zoltan library!")
+ endif()
+endif ()
diff --git a/AMDiS/cmake3/CMakeLists_3.0.txt b/AMDiS/cmake3/CMakeLists_3.0.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1431a75a9d241f6b74df343e29e541b3529cd865
--- /dev/null
+++ b/AMDiS/cmake3/CMakeLists_3.0.txt
@@ -0,0 +1,219 @@
+cmake_minimum_required(VERSION 3.2 FATAL_ERROR)
+project(AMDiS VERSION 0.9 LANGUAGES CXX)
+
+set(BASE_DIR ${AMDiS_SOURCE_DIR})
+set(SOURCE_DIR ${BASE_DIR}/src)
+list(APPEND CMAKE_MODULE_PATH ${BASE_DIR}/cmake3)
+
+option(BUILD_SHARED_LIBS "Build all libraries as shared or static, default: shared" true)
+option(ENABLE_CXX11 "Enable C++11 compiler features" false)
+option(ENABLE_PARALLEL_DOMAIN "Use parallel domain decomposition" false)
+option(ENABLE_UMFPACK "Use of UMFPACK solver" false)
+option(ENABLE_COMPRESSION "Use output compression" false)
+
+
+add_library(amdis_base INTERFACE)
+add_library(AMDiS::base ALIAS amdis_base)
+
+target_include_directories(amdis_base INTERFACE ${SOURCE_DIR})
+target_compile_definitions(amdis_base INTERFACE
+ $<$<CONFIG:Debug>:DEBUG=1>
+ $<$<CONFIG:Release>:DEBUG=0>)
+
+if (ENABLE_CXX11)
+ target_compile_features(amdis_base INTERFACE
+ cxx_alias_templates
+ cxx_auto_type
+ cxx_lambdas
+ cxx_override
+ cxx_range_for
+ cxx_static_assert
+ cxx_variadic_templates)
+ target_compile_definitions(amdis_base INTERFACE HAS_CXX11=1)
+else ()
+ target_compile_definitions(amdis_base INTERFACE HAS_CXX11=0)
+endif (ENABLE_CXX11)
+
+# ------------------------------------------------------------------------------
+
+include(find_mtl4) # -> target mtl4
+include(find_boost) # -> target boost
+
+# ------------------------------------------------------------------------------
+
+add_library(amdis
+ ${SOURCE_DIR}/AdaptBase.cc
+ ${SOURCE_DIR}/AdaptInfo.cc
+ ${SOURCE_DIR}/AdaptInstationary.cc
+ ${SOURCE_DIR}/AdaptStationary.cc
+ ${SOURCE_DIR}/AMDiS.cc
+ ${SOURCE_DIR}/Assembler.cc
+ ${SOURCE_DIR}/BasisFunction.cc
+ ${SOURCE_DIR}/Boundary.cc
+ ${SOURCE_DIR}/BoundaryManager.cc
+ ${SOURCE_DIR}/BoundaryObject.cc
+ ${SOURCE_DIR}/Bubble.cc
+ ${SOURCE_DIR}/Cholesky.cc
+ ${SOURCE_DIR}/CoarseningManager.cc
+ ${SOURCE_DIR}/CoarseningManager1d.cc
+ ${SOURCE_DIR}/CoarseningManager2d.cc
+ ${SOURCE_DIR}/CoarseningManager3d.cc
+ ${SOURCE_DIR}/ComponentTraverseInfo.cc
+ ${SOURCE_DIR}/CouplingIterationInterface.cc
+ ${SOURCE_DIR}/CreatorMap.cc
+ ${SOURCE_DIR}/DOFAdmin.cc
+ ${SOURCE_DIR}/DOFIndexed.cc
+ ${SOURCE_DIR}/DOFMatrix.cc
+ ${SOURCE_DIR}/DOFVector.cc
+ ${SOURCE_DIR}/Debug.cc
+ ${SOURCE_DIR}/DirichletBC.cc
+ ${SOURCE_DIR}/DualTraverse.cc
+ ${SOURCE_DIR}/ElInfo.cc
+ ${SOURCE_DIR}/ElInfo1d.cc
+ ${SOURCE_DIR}/ElInfo2d.cc
+ ${SOURCE_DIR}/ElInfo3d.cc
+ ${SOURCE_DIR}/ElInfoStack.cc
+ ${SOURCE_DIR}/Element.cc
+ ${SOURCE_DIR}/ElementData.cc
+ ${SOURCE_DIR}/ElementDofIterator.cc
+ ${SOURCE_DIR}/ElementRegion_ED.cc
+ ${SOURCE_DIR}/FiniteElemSpace.cc
+ ${SOURCE_DIR}/FirstOrderAssembler.cc
+ ${SOURCE_DIR}/FirstOrderTerm.cc
+ ${SOURCE_DIR}/FixVec.cc
+ ${SOURCE_DIR}/Global.cc
+ ${SOURCE_DIR}/GlobalDOFNumbering.cc
+ ${SOURCE_DIR}/GlobalElementNumbering.cc
+ ${SOURCE_DIR}/Initfile.cc
+ ${SOURCE_DIR}/Lagrange.cc
+ ${SOURCE_DIR}/LeafData.cc
+ ${SOURCE_DIR}/Line.cc
+ ${SOURCE_DIR}/MacroElement.cc
+ ${SOURCE_DIR}/Marker.cc
+ ${SOURCE_DIR}/MatrixVector.cc
+ ${SOURCE_DIR}/Mesh.cc
+ ${SOURCE_DIR}/MeshStructure.cc
+ ${SOURCE_DIR}/Operator.cc
+ ${SOURCE_DIR}/OperatorTerm.cc
+ ${SOURCE_DIR}/Parametric.cc
+ ${SOURCE_DIR}/PeriodicBC.cc
+ ${SOURCE_DIR}/ProblemInstat.cc
+ ${SOURCE_DIR}/ProblemInterpol.cc
+ ${SOURCE_DIR}/ProblemStat.cc
+ ${SOURCE_DIR}/ProblemStatDbg.cc
+ ${SOURCE_DIR}/Projection.cc
+ ${SOURCE_DIR}/QPInfo.cc
+ ${SOURCE_DIR}/QPsiPhi.cc
+ ${SOURCE_DIR}/Quadrature.cc
+ ${SOURCE_DIR}/RCNeighbourList.cc
+ ${SOURCE_DIR}/Recovery.cc
+ ${SOURCE_DIR}/RefinementManager.cc
+ ${SOURCE_DIR}/RefinementManager1d.cc
+ ${SOURCE_DIR}/RefinementManager2d.cc
+ ${SOURCE_DIR}/RefinementManager3d.cc
+ ${SOURCE_DIR}/RobinBC.cc
+ ${SOURCE_DIR}/ScalableQuadrature.cc
+ ${SOURCE_DIR}/SecondOrderAssembler.cc
+ ${SOURCE_DIR}/SecondOrderTerm.cc
+ ${SOURCE_DIR}/Serializer.cc
+ ${SOURCE_DIR}/StandardProblemIteration.cc
+ ${SOURCE_DIR}/SubAssembler.cc
+ ${SOURCE_DIR}/SubElInfo.cc
+ ${SOURCE_DIR}/SubQuadrature.cc
+ ${SOURCE_DIR}/SurfaceQuadrature.cc
+ ${SOURCE_DIR}/SurfaceRegion_ED.cc
+ ${SOURCE_DIR}/SystemVector.cc
+ ${SOURCE_DIR}/Tetrahedron.cc
+ ${SOURCE_DIR}/Timer.cc
+ ${SOURCE_DIR}/Traverse.cc
+ ${SOURCE_DIR}/Triangle.cc
+ ${SOURCE_DIR}/VertexVector.cc
+ ${SOURCE_DIR}/ZeroOrderAssembler.cc
+ ${SOURCE_DIR}/ZeroOrderTerm.cc
+ ${SOURCE_DIR}/est/Estimator.cc
+ ${SOURCE_DIR}/est/RecoveryEstimator.cc
+ ${SOURCE_DIR}/est/ResidualEstimator.cc
+ ${SOURCE_DIR}/est/SimpleResidualEstimator.cc
+ ${SOURCE_DIR}/io/ArhReader.cc
+ ${SOURCE_DIR}/io/detail/ArhReader.cc
+ ${SOURCE_DIR}/io/Arh2Reader.cc
+ ${SOURCE_DIR}/io/Arh2Writer.cc
+ ${SOURCE_DIR}/io/Arh3Reader.cc
+ ${SOURCE_DIR}/io/Arh3Writer.cc
+ ${SOURCE_DIR}/io/detail/Arh2Reader.cc
+ ${SOURCE_DIR}/io/detail/ArhWriter.cc
+ ${SOURCE_DIR}/io/detail/Arh2Writer.cc
+ ${SOURCE_DIR}/io/detail/Arh3Reader.cc
+ ${SOURCE_DIR}/io/detail/Arh3Writer.cc
+ ${SOURCE_DIR}/io/DofWriter.cc
+ ${SOURCE_DIR}/io/ElementFileWriter.cc
+ ${SOURCE_DIR}/io/FileWriterInterface.cc
+ ${SOURCE_DIR}/io/FileWriter.cc
+ ${SOURCE_DIR}/io/GNUPlotWriter.cc
+ ${SOURCE_DIR}/io/MacroInfo.cc
+ ${SOURCE_DIR}/io/MacroReader.cc
+ ${SOURCE_DIR}/io/MacroWriter.cc
+ ${SOURCE_DIR}/io/PngReader.cc
+ ${SOURCE_DIR}/io/PngWriter.cc
+ ${SOURCE_DIR}/io/PovrayWriter.cc
+ ${SOURCE_DIR}/io/Spreadsheet.cc
+ ${SOURCE_DIR}/io/ValueReader.cc
+ ${SOURCE_DIR}/io/ValueWriter.cc
+ ${SOURCE_DIR}/io/VtkWriter.cc
+ ${SOURCE_DIR}/io/VtkVectorWriter.cc
+ ${SOURCE_DIR}/io/detail/VtkWriter.cc
+ ${SOURCE_DIR}/nonlin/ProblemNonLin.cc
+ ${SOURCE_DIR}/solver/SolverMatrix.cc
+ ${SOURCE_DIR}/time/RosenbrockAdaptInstationary.cc
+ ${SOURCE_DIR}/time/RosenbrockMethod.cc
+ ${SOURCE_DIR}/time/RosenbrockStationary.cc
+ )
+
+if (ENABLE_COMPRESSION)
+ target_compile_definitions(amdis PRIVATE HAVE_COMPRESSION=1)
+endif (ENABLE_COMPRESSION)
+
+include(amdis_parallel) # -> target AMDiS::parallel
+include(amdis_reinit) # -> target AMDiS::reinit
+include(amdis_compositeFEM) # -> target AMDiS::compositeFEM
+include(muparser) # -> target muparser
+
+
+if (MSVC)
+ target_compile_definitions(amdis PRIVATE
+ _SCL_SECURE_NO_WARNINGS
+ _CRT_SECURE_NO_WARNINGS)
+endif (MSVC)
+
+target_link_libraries(amdis AMDiS::base AMDiS::reinit AMDiS::compositeFEM muparser)
+if (ENABLE_PARALLEL_DOMAIN)
+ target_link_libraries(amdis AMDiS::parallel)
+endif (ENABLE_PARALLEL_DOMAIN)
+
+
+# specify how to install this target:
+# -----------------------------------
+
+set(INSTALL_SUBDIRS . config nonlin est expressions operations traits
+ utility time solver solver/details solver/itl io io/detail)
+
+foreach (SUBDIR ${INSTALL_SUBDIRS})
+ file(GLOB HEADERS "${SOURCE_DIR}/${SUBDIR}/*.h*")
+ install(FILES ${HEADERS} DESTINATION include/amdis/${SUBDIR}/)
+endforeach ()
+
+install(TARGETS amdis DESTINATION lib/amdis/ )
+
+# generate configuration file:
+# ----------------------------
+
+configure_file(${BASE_DIR}/cmake3/AMDISConfig.cmake.in
+ ${AMDiS_BINARY_DIR}/AMDISConfig.cmake
+ @ONLY
+)
+
+install(FILES ${AMDiS_BINARY_DIR}/AMDISConfig.cmake DESTINATION share/amdis/)
+
+# file(GLOB CMAKE_FILES "${BASE_DIR}/cmake3/*.cmake")
+# install(FILES ${CMAKE_FILES} DESTINATION share/amdis/)
+
diff --git a/AMDiS/cmake3/FindPackageMultipass.cmake b/AMDiS/cmake3/FindPackageMultipass.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..7199e026db92465e81d2e730a4720a722fce4ff4
--- /dev/null
+++ b/AMDiS/cmake3/FindPackageMultipass.cmake
@@ -0,0 +1,91 @@
+# PackageMultipass - this module defines two macros
+#
+# FIND_PACKAGE_MULTIPASS (Name CURRENT
+# STATES VAR0 VAR1 ...
+# DEPENDENTS DEP0 DEP1 ...)
+#
+# This function creates a cache entry <UPPERCASED-Name>_CURRENT which
+# the user can set to "NO" to trigger a reconfiguration of the package.
+# The first time this function is called, the values of
+# <UPPERCASED-Name>_VAR0, ... are saved. If <UPPERCASED-Name>_CURRENT
+# is false or if any STATE has changed since the last time
+# FIND_PACKAGE_MULTIPASS() was called, then CURRENT will be set to "NO",
+# otherwise CURRENT will be "YES". IF not CURRENT, then
+# <UPPERCASED-Name>_DEP0, ... will be FORCED to NOTFOUND.
+# Example:
+# find_path (FOO_DIR include/foo.h)
+# FIND_PACKAGE_MULTIPASS (Foo foo_current
+# STATES DIR
+# DEPENDENTS INCLUDES LIBRARIES)
+# if (NOT foo_current)
+# # Make temporary files, run programs, etc, to determine FOO_INCLUDES and FOO_LIBRARIES
+# endif (NOT foo_current)
+#
+# MULTIPASS_C_SOURCE_RUNS (Name INCLUDES LIBRARIES SOURCE RUNS)
+# Always runs the given test, use this when you need to re-run tests
+# because parent variables have made old cache entries stale.
+
+macro (FIND_PACKAGE_MULTIPASS _name _current)
+ string (TOUPPER ${_name} _NAME)
+ set (_args ${ARGV})
+ list (REMOVE_AT _args 0 1)
+
+ set (_states_current "YES")
+ list (GET _args 0 _cmd)
+ if (_cmd STREQUAL "STATES")
+ list (REMOVE_AT _args 0)
+ list (GET _args 0 _state)
+ while (_state AND NOT _state STREQUAL "DEPENDENTS")
+ # The name of the stored value for the given state
+ set (_stored_var PACKAGE_MULTIPASS_${_NAME}_${_state})
+ if (NOT "${${_stored_var}}" STREQUAL "${${_NAME}_${_state}}")
+ set (_states_current "NO")
+ endif (NOT "${${_stored_var}}" STREQUAL "${${_NAME}_${_state}}")
+ set (${_stored_var} "${${_NAME}_${_state}}" CACHE INTERNAL "Stored state for ${_name}." FORCE)
+ list (REMOVE_AT _args 0)
+ list (GET _args 0 _state)
+ endwhile (_state AND NOT _state STREQUAL "DEPENDENTS")
+ endif (_cmd STREQUAL "STATES")
+
+ set (_stored ${_NAME}_CURRENT)
+ if (NOT ${_stored})
+ set (${_stored} "YES" CACHE BOOL "Is the configuration for ${_name} current? Set to \"NO\" to reconfigure." FORCE)
+ set (_states_current "NO")
+ endif (NOT ${_stored})
+
+ set (${_current} ${_states_current})
+ if (NOT ${_current} AND PACKAGE_MULTIPASS_${_name}_CALLED)
+ message (STATUS "Clearing ${_name} dependent variables")
+ # Clear all the dependent variables so that the module can reset them
+ list (GET _args 0 _cmd)
+ if (_cmd STREQUAL "DEPENDENTS")
+ list (REMOVE_AT _args 0)
+ foreach (dep ${_args})
+ set (${_NAME}_${dep} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
+ endforeach (dep)
+ endif (_cmd STREQUAL "DEPENDENTS")
+ set (${_NAME}_FOUND "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
+ endif ()
+ set (PACKAGE_MULTIPASS_${name}_CALLED YES CACHE INTERNAL "Private" FORCE)
+endmacro (FIND_PACKAGE_MULTIPASS)
+
+
+macro (MULTIPASS_C_SOURCE_RUNS includes libraries source runs)
+ include (CheckCSourceRuns)
+ # This is a ridiculous hack. CHECK_C_SOURCE_* thinks that if the
+ # *name* of the return variable doesn't change, then the test does
+ # not need to be re-run. We keep an internal count which we
+ # increment to guarantee that every test name is unique. If we've
+ # gotten here, then the configuration has changed enough that the
+ # test *needs* to be rerun.
+ if (NOT MULTIPASS_TEST_COUNT)
+ set (MULTIPASS_TEST_COUNT 00)
+ endif (NOT MULTIPASS_TEST_COUNT)
+ math (EXPR _tmp "${MULTIPASS_TEST_COUNT} + 1") # Why can't I add to a cache variable?
+ set (MULTIPASS_TEST_COUNT ${_tmp} CACHE INTERNAL "Unique test ID")
+ set (testname MULTIPASS_TEST_${MULTIPASS_TEST_COUNT}_${runs})
+ set (CMAKE_REQUIRED_INCLUDES ${includes})
+ set (CMAKE_REQUIRED_LIBRARIES ${libraries})
+ check_c_source_runs ("${source}" ${testname})
+ set (${runs} "${${testname}}")
+endmacro (MULTIPASS_C_SOURCE_RUNS)
diff --git a/AMDiS/cmake3/ResolveCompilerPaths.cmake b/AMDiS/cmake3/ResolveCompilerPaths.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..b398025e95518511f4e06ba218dcef386a4e8eaa
--- /dev/null
+++ b/AMDiS/cmake3/ResolveCompilerPaths.cmake
@@ -0,0 +1,93 @@
+# ResolveCompilerPaths - this module defines two macros
+#
+# RESOLVE_LIBRARIES (XXX_LIBRARIES LINK_LINE)
+# This macro is intended to be used by FindXXX.cmake modules.
+# It parses a compiler link line and resolves all libraries
+# (-lfoo) using the library path contexts (-L/path) in scope.
+# The result in XXX_LIBRARIES is the list of fully resolved libs.
+# Example:
+#
+# RESOLVE_LIBRARIES (FOO_LIBRARIES "-L/A -la -L/B -lb -lc -ld")
+#
+# will be resolved to
+#
+# FOO_LIBRARIES:STRING="/A/liba.so;/B/libb.so;/A/libc.so;/usr/lib/libd.so"
+#
+# if the filesystem looks like
+#
+# /A: liba.so libc.so
+# /B: liba.so libb.so
+# /usr/lib: liba.so libb.so libc.so libd.so
+#
+# and /usr/lib is a system directory.
+#
+# Note: If RESOLVE_LIBRARIES() resolves a link line differently from
+# the native linker, there is a bug in this macro (please report it).
+#
+# RESOLVE_INCLUDES (XXX_INCLUDES INCLUDE_LINE)
+# This macro is intended to be used by FindXXX.cmake modules.
+# It parses a compile line and resolves all includes
+# (-I/path/to/include) to a list of directories. Other flags are ignored.
+# Example:
+#
+# RESOLVE_INCLUDES (FOO_INCLUDES "-I/A -DBAR='\"irrelevant -I/string here\"' -I/B")
+#
+# will be resolved to
+#
+# FOO_INCLUDES:STRING="/A;/B"
+#
+# assuming both directories exist.
+# Note: as currently implemented, the -I/string will be picked up mistakenly (cry, cry)
+
+macro (RESOLVE_LIBRARIES LIBS LINK_LINE)
+ string (REGEX MATCHALL "((-L|-l|-Wl)([^\" ]+|\"[^\"]+\")|/[^\" ]+(a|so|dll))" _all_tokens "${LINK_LINE}")
+ set (_libs_found)
+ set (_directory_list)
+ foreach (token ${_all_tokens})
+ if (token MATCHES "-L([^\" ]+|\"[^\"]+\")")
+ # If it's a library path, add it to the list
+ string (REGEX REPLACE "^-L" "" token ${token})
+ string (REGEX REPLACE "//" "/" token ${token})
+ list (APPEND _directory_list ${token})
+ elseif (token MATCHES "^(-l([^\" ]+|\"[^\"]+\")|/[^\" ]+(a|so|dll))")
+ # It's a library, resolve the path by looking in the list and then (by default) in system directories
+ string (REGEX REPLACE "^-l" "" token ${token})
+ set (_root)
+ if (token MATCHES "^/") # We have an absolute path, add root to the search path
+ set (_root "/")
+ endif (token MATCHES "^/")
+ set (_lib "NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
+ find_library (_lib ${token} HINTS ${_directory_list} ${_root})
+ if (_lib)
+ string (REPLACE "//" "/" _lib ${_lib})
+ list (APPEND _libs_found ${_lib})
+ else (_lib)
+ message (STATUS "Unable to find library ${token}")
+ endif (_lib)
+ endif (token MATCHES "-L([^\" ]+|\"[^\"]+\")")
+ endforeach (token)
+ set (_lib "NOTFOUND" CACHE INTERNAL "Scratch variable" FORCE)
+ # only the LAST occurence of each library is required since there should be no circular dependencies
+ if (_libs_found)
+ list (REVERSE _libs_found)
+ list (REMOVE_DUPLICATES _libs_found)
+ list (REVERSE _libs_found)
+ endif (_libs_found)
+ set (${LIBS} "${_libs_found}")
+endmacro (RESOLVE_LIBRARIES)
+
+macro (RESOLVE_INCLUDES INCS COMPILE_LINE)
+ string (REGEX MATCHALL "-I([^\" ]+|\"[^\"]+\")" _all_tokens "${COMPILE_LINE}")
+ set (_incs_found)
+ foreach (token ${_all_tokens})
+ string (REGEX REPLACE "^-I" "" token ${token})
+ string (REGEX REPLACE "//" "/" token ${token})
+ if (EXISTS ${token})
+ list (APPEND _incs_found ${token})
+ else (EXISTS ${token})
+ message (STATUS "Include directory ${token} does not exist")
+ endif (EXISTS ${token})
+ endforeach (token)
+ list (REMOVE_DUPLICATES _incs_found)
+ set (${INCS} "${_incs_found}")
+endmacro (RESOLVE_INCLUDES)
diff --git a/AMDiS/cmake3/amdis_compositeFEM.cmake b/AMDiS/cmake3/amdis_compositeFEM.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..33a6e3406e96415521f30fa9be0f1e357582c201
--- /dev/null
+++ b/AMDiS/cmake3/amdis_compositeFEM.cmake
@@ -0,0 +1,26 @@
+# specify the target and requirements for the composite fem library
+
+SET(COMPOSITE_SOURCE_DIR ${SOURCE_DIR}/compositeFEM)
+add_library(amdis_compositeFEM
+ ${COMPOSITE_SOURCE_DIR}/CFE_Integration.cc
+ ${COMPOSITE_SOURCE_DIR}/CFE_NormAndErrorFcts.cc
+ ${COMPOSITE_SOURCE_DIR}/CompositeFEMMethods.cc
+ ${COMPOSITE_SOURCE_DIR}/CompositeFEMOperator.cc
+ ${COMPOSITE_SOURCE_DIR}/LevelSetAdaptMesh.cc
+ ${COMPOSITE_SOURCE_DIR}/PenaltyOperator.cc
+ ${COMPOSITE_SOURCE_DIR}/ElementLevelSet.cc
+ ${COMPOSITE_SOURCE_DIR}/SubPolytope.cc
+ ${COMPOSITE_SOURCE_DIR}/SubElementAssembler.cc)
+add_library(AMDiS::compositeFEM ALIAS amdis_compositeFEM)
+
+target_compile_definitions(amdis_compositeFEM PUBLIC
+ HAVE_COMPOSITE_FEM=1)
+target_include_directories(amdis_compositeFEM PRIVATE ${COMPOSITE_SOURCE_DIR})
+target_link_libraries(amdis_compositeFEM amdis_base)
+
+# specify how to install this target:
+# -----------------------------------
+
+file(GLOB COMPOSITE_HEADERS "${COMPOSITE_SOURCE_DIR}/*.h*")
+install(FILES ${COMPOSITE_HEADERS} DESTINATION include/amdis/compositeFEM)
+install(TARGETS amdis_compositeFEM DESTINATION lib/amdis/ )
\ No newline at end of file
diff --git a/AMDiS/cmake3/amdis_parallel.cmake b/AMDiS/cmake3/amdis_parallel.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..60c9a588901420847bcd09112c2c79bf9fa19467
--- /dev/null
+++ b/AMDiS/cmake3/amdis_parallel.cmake
@@ -0,0 +1,112 @@
+if (ENABLE_PARALLEL_DOMAIN)
+ option(ENABLE_ZOLTAN "Add support for the Parallel Partitioning suite Zoltan" false)
+ option(ENABLE_PARALLEL_SOLVERS "Add some problem dependent solver, e.g. Feti, Navier-Stokes and Cahn-Hilliard" false)
+
+ add_library(amdis_parallel
+ ${SOURCE_DIR}/parallel/BddcMlSolver.cc
+ ${SOURCE_DIR}/parallel/DofComm.cc
+ ${SOURCE_DIR}/parallel/CheckerPartitioner.cc
+ ${SOURCE_DIR}/parallel/ElementObjectDatabase.cc
+ ${SOURCE_DIR}/parallel/InteriorBoundary.cc
+ ${SOURCE_DIR}/parallel/MeshDistributor.cc
+ ${SOURCE_DIR}/parallel/MeshLevelData.cc
+ ${SOURCE_DIR}/parallel/MeshManipulation.cc
+ ${SOURCE_DIR}/parallel/MeshPartitioner.cc
+ ${SOURCE_DIR}/parallel/MpiHelper.cc
+ ${SOURCE_DIR}/parallel/ParallelDebug.cc
+ ${SOURCE_DIR}/parallel/ParallelDofMapping.cc
+ ${SOURCE_DIR}/parallel/ParallelProblemStat.cc
+ ${SOURCE_DIR}/parallel/ParallelSolver.cc
+ ${SOURCE_DIR}/parallel/PeriodicMap.cc
+ ${SOURCE_DIR}/parallel/ParMetisPartitioner.cc
+ ${SOURCE_DIR}/parallel/StdMpi.cc
+ ${SOURCE_DIR}/parallel/ZoltanPartitioner.cc
+ )
+ add_library(AMDiS::parallel ALIAS amdis_parallel)
+
+ target_compile_definitions(amdis_parallel PUBLIC
+ HAVE_PARALLEL_DOMAIN_AMDIS=1)
+ target_link_libraries(amdis_parallel amdis_base)
+
+ # MPI is required
+ find_package(MPI REQUIRED)
+ if (MPI_FOUND)
+ target_include_directories(amdis_parallel PUBLIC
+ ${MPI_INCLUDE_PATH})
+ target_compile_options(amdis_parallel PUBLIC
+ ${MPI_COMPILE_FLAGS})
+ endif (MPI_FOUND)
+
+ # PETSc library is required
+ set(PETSC_EXECUTABLE_RUNS ON)
+ include(find_petsc)
+ if (PETSc_FOUND)
+ target_include_directories(amdis_parallel PUBLIC
+ ${PETSC_DIR}/include
+ ${PETSC_DIR}/${PETSC_ARCH}/include)
+
+ # parmetis is required
+ find_file(PARMETIS_HEADER_FILE "parmetis.h" HINTS ${PETSC_DIR}/include )
+ if (PARMETIS_HEADER_FILE)
+ get_filename_component(PARMETIS_INCLUDE_PATH "${PARMETIS_HEADER_FILE}" PATH CACHE)
+ target_include_directories(amdis_parallel PUBLIC ${PARMETIS_INCLUDE_PATH})
+ else()
+ message(FATAL_ERROR "Could not find ParMetis header file 'parmetis.h'!")
+ endif (PARMETIS_HEADER_FILE)
+
+ # add support for the zoltan library
+ if (ENABLE_ZOLTAN)
+ find_file(ZOLTAN_HEADER_FILE "zoltan_cpp.h" HINTS ${PETSC_DIR}/include)
+ if (ZOLTAN_HEADER_FILE)
+ get_filename_component(ZOLTAN_HEADER_DIR "${ZOLTAN_HEADER_FILE}" PATH CACHE)
+ target_include_directories(amdis_parallel PRIVATE ${ZOLTAN_HEADER_DIR})
+ target_compile_definitions(amdis_parallel PRIVATE HAVE_ZOLTAN=1)
+ else()
+ message(FATAL_ERROR "Could not find Zoltan include file 'zoltan_cpp.h'!")
+ endif(ZOLTAN_HEADER_FILE)
+ endif (ENABLE_ZOLTAN)
+
+ # add some more source-files that need petsc
+ target_sources(amdis_parallel PRIVATE
+ ${SOURCE_DIR}/parallel/MatrixNnzStructure.cc
+ ${SOURCE_DIR}/parallel/ParallelCoarseSpaceSolver.cc
+ ${SOURCE_DIR}/parallel/PetscHelper.cc
+ ${SOURCE_DIR}/parallel/PetscSolver.cc
+ ${SOURCE_DIR}/parallel/PetscSolverGlobalMatrix.cc
+ ${SOURCE_DIR}/parallel/PetscSolverGlobalBlockMatrix.cc
+ ${SOURCE_DIR}/solver/PetscTypes.cc
+ )
+
+ if (ENABLE_PARALLEL_SOLVERS)
+ target_sources(amdis_parallel PRIVATE
+ ${SOURCE_DIR}/parallel/PetscSolverFeti.cc
+ ${SOURCE_DIR}/parallel/PetscSolverFetiDebug.cc
+ ${SOURCE_DIR}/parallel/PetscSolverFetiMonitor.cc
+ ${SOURCE_DIR}/parallel/PetscSolverFetiOperators.cc
+ ${SOURCE_DIR}/parallel/PetscSolverFetiTimings.cc
+ ${SOURCE_DIR}/parallel/PetscSolverNavierStokes.cc
+ ${SOURCE_DIR}/parallel/PetscSolverNSCH.cc
+ ${SOURCE_DIR}/parallel/PetscSolverCahnHilliard2.cc
+ ${SOURCE_DIR}/parallel/PetscSolverCahnHilliard.cc
+ ${SOURCE_DIR}/parallel/PetscSolverSchur.cc
+ )
+ endif (ENABLE_PARALLEL_SOLVERS)
+
+ target_compile_definitions(amdis_parallel PUBLIC
+ HAVE_PARALLEL_PETSC=1
+ PETSC_VERSION=${PETSC_VERSION})
+ endif (PETSc_FOUND)
+
+ # specify how to install this target:
+ # -----------------------------------
+
+ file(GLOB AMDIS_PARALLEL_HEADERS "${SOURCE_DIR}/parallel/*.h")
+ install(FILES ${AMDIS_PARALLEL_HEADERS} DESTINATION include/amdis/parallel/)
+ install(TARGETS amdis_parallel DESTINATION lib/amdis/ )
+
+ install(FILES
+ ${BASE_DIR}/cmake3/ResolveCompilerPaths.cmake
+ ${BASE_DIR}/cmake3/FindPackageMultipass.cmake
+ ${BASE_DIR}/cmake3/find_petsc.cmake
+ DESTINATION share/amdis/)
+endif (ENABLE_PARALLEL_DOMAIN)
diff --git a/AMDiS/cmake3/amdis_reinit.cmake b/AMDiS/cmake3/amdis_reinit.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..862cb62abc90800781f6d864d5d6ac240f4f3848
--- /dev/null
+++ b/AMDiS/cmake3/amdis_reinit.cmake
@@ -0,0 +1,19 @@
+# specify the target and requirements for the reinit library
+
+SET(COMPOSITE_SOURCE_DIR ${SOURCE_DIR}/reinit)
+set(REINIT_SOURCE_DIR ${SOURCE_DIR}/reinit)
+file(GLOB REINIT_SRC ${REINIT_SOURCE_DIR}/*.cc)
+add_library(amdis_reinit ${REINIT_SRC})
+add_library(AMDiS::reinit ALIAS amdis_reinit)
+
+target_compile_definitions(amdis_reinit PUBLIC
+ HAVE_REINIT=1)
+target_include_directories(amdis_reinit PRIVATE ${REINIT_SOURCE_DIR})
+target_link_libraries(amdis_reinit amdis_base)
+
+# specify how to install this target:
+# -----------------------------------
+
+file(GLOB RINIT_HEADERS "${REINIT_SOURCE_DIR}/*.h*")
+install(FILES ${RINIT_HEADERS} DESTINATION include/amdis/reinit)
+install(TARGETS amdis_reinit DESTINATION lib/amdis/ )
\ No newline at end of file
diff --git a/AMDiS/cmake3/find_boost.cmake b/AMDiS/cmake3/find_boost.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..19eb347e2cf982810eb1fd38005497f7eb5d8d4d
--- /dev/null
+++ b/AMDiS/cmake3/find_boost.cmake
@@ -0,0 +1,7 @@
+find_package(Boost 1.44 REQUIRED)
+if (Boost_FOUND)
+ add_library(boost INTERFACE)
+ target_include_directories(boost INTERFACE ${Boost_INCLUDE_DIR})
+
+ target_link_libraries(amdis_base INTERFACE boost)
+endif (Boost_FOUND)
diff --git a/AMDiS/cmake3/find_mtl4.cmake b/AMDiS/cmake3/find_mtl4.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..bf5b4867926874fd325a7ea9f16905ae45ce26b9
--- /dev/null
+++ b/AMDiS/cmake3/find_mtl4.cmake
@@ -0,0 +1,48 @@
+find_package(MTL REQUIRED HINTS ${BASE_DIR}/lib/mtl4)
+# hide options of MTL4 and use the AMDiS replacement
+mark_as_advanced(ENABLE_CXX_ELEVEN)
+mark_as_advanced(ENABLE_SHORT_ELE_PROD)
+mark_as_advanced(ENABLE_VAMPIR)
+if (MTL_FOUND)
+ add_library(mtl4 INTERFACE)
+
+ target_include_directories(mtl4 INTERFACE
+ $<BUILD_INTERFACE:${MTL_INCLUDE_DIRS}>
+ $<INSTALL_INTERFACE:include/amdis/mtl4>)
+
+ if (ENABLE_CXX11)
+ string (REPLACE "-std=c++0x" "" MTL_CXX_DEFINITIONS "${MTL_CXX_DEFINITIONS}")
+ string (REPLACE "-std=c++11" "" MTL_CXX_DEFINITIONS "${MTL_CXX_DEFINITIONS}")
+ string (REPLACE "-std=gnu++0x" "" MTL_CXX_DEFINITIONS "${MTL_CXX_DEFINITIONS}")
+ string (REPLACE "-std=gnu++11" "" MTL_CXX_DEFINITIONS "${MTL_CXX_DEFINITIONS}")
+ target_compile_features(mtl4 INTERFACE
+ cxx_rvalue_references
+ cxx_auto_type
+ cxx_range_for
+ cxx_generalized_initializers
+ cxx_static_assert
+ cxx_defaulted_functions)
+ set(ENABLE_CXX_ELEVEN true)
+ else ()
+ set(ENABLE_CXX_ELEVEN false)
+ endif ()
+
+ if (ENABLE_UMFPACK)
+ target_compile_definitions(mtl4 INTERFACE HAVE_UMFPACK=1)
+ endif (ENABLE_UMFPACK)
+
+ target_compile_options(mtl4 INTERFACE ${MTL_CXX_DEFINITIONS})
+ target_link_libraries(mtl4 INTERFACE ${MTL_LIBRARIES})
+
+ # specify how to install this target:
+ # -----------------------------------
+ install(DIRECTORY ${MTL_DIR}/
+ DESTINATION include/amdis/mtl4/
+ FILES_MATCHING PATTERN "*.hpp"
+ PATTERN ".svn" EXCLUDE
+ PATTERN ".svn/*" EXCLUDE
+ PATTERN "mtl4/libs" EXCLUDE
+ PATTERN "mtl4/extern" EXCLUDE)
+
+ target_link_libraries(amdis_base INTERFACE mtl4)
+endif (MTL_FOUND)
diff --git a/AMDiS/cmake3/find_petsc.cmake b/AMDiS/cmake3/find_petsc.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..9b1683844459df05971a43ca0215dbb6d7bc5e29
--- /dev/null
+++ b/AMDiS/cmake3/find_petsc.cmake
@@ -0,0 +1,248 @@
+# - Try to find PETSc
+# Once done this will define
+# source: https://github.com/jedbrown/cmake-modules/blob/master/FindPETSc.cmake
+#
+# PETSC_FOUND - system has PETSc
+# PETSC_INCLUDES - the PETSc include directories
+# PETSC_LIBRARIES - Link these to use PETSc
+# PETSC_COMPILER - Compiler used by PETSc, helpful to find a compatible MPI
+# PETSC_DEFINITIONS - Compiler switches for using PETSc
+# PETSC_MPIEXEC - Executable for running MPI programs
+# PETSC_VERSION - Version string (MAJOR.MINOR.SUBMINOR)
+#
+# Hack: PETSC_VERSION currently decides on the version based on the
+# layout. Otherwise we need to run C code to determine the version.
+#
+# Setting these changes the behavior of the search
+# PETSC_DIR - directory in which PETSc resides
+# PETSC_ARCH - build architecture
+#
+# Redistribution and use is allowed according to the terms of the BSD license.
+# For details see the accompanying COPYING-CMAKE-SCRIPTS file.
+#
+
+function (petsc_get_version)
+ if (EXISTS "${PETSC_DIR}/include/petscversion.h")
+ file (STRINGS "${PETSC_DIR}/include/petscversion.h" vstrings REGEX "#define PETSC_VERSION_(RELEASE|MAJOR|MINOR|SUBMINOR|PATCH) ")
+ foreach (line ${vstrings})
+ string (REGEX REPLACE " +" ";" fields ${line}) # break line into three fields (the first is always "#define")
+ list (GET fields 1 var)
+ list (GET fields 2 val)
+ set (${var} ${val} PARENT_SCOPE)
+ set (${var} ${val}) # Also in local scope so we have access below
+ endforeach ()
+ if (PETSC_VERSION_RELEASE)
+ set (PETSC_VERSION "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}p${PETSC_VERSION_PATCH}" PARENT_SCOPE)
+ else ()
+ # make dev version compare higher than any patch level of a released version
+ set (PETSC_VERSION "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}.99" PARENT_SCOPE)
+ endif ()
+ else ()
+ message (SEND_ERROR "PETSC_DIR can not be used, ${PETSC_DIR}/include/petscversion.h does not exist")
+ endif ()
+endfunction ()
+
+find_path (PETSC_DIR include/petsc.h
+ HINTS ${AMDIS_PETSC_DIR} $ENV{HOME}/petsc ENV PETSC_DIR
+ DOC "PETSc Directory")
+
+if (PETSC_DIR AND NOT PETSC_ARCH)
+ set (_petsc_arches
+ $ENV{PETSC_ARCH} # If set, use environment variable first
+ linux-gnu-c-debug linux-gnu-c-opt # Debian defaults
+ x86_64-unknown-linux-gnu i386-unknown-linux-gnu)
+ set (petscconf "NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
+ foreach (arch ${_petsc_arches})
+ if (NOT PETSC_ARCH)
+ find_path (petscconf petscconf.h
+ HINTS ${PETSC_DIR}
+ PATH_SUFFIXES ${arch}/include bmake/${arch}
+ NO_DEFAULT_PATH)
+ if (petscconf)
+ set (PETSC_ARCH "${arch}" CACHE STRING "PETSc build architecture")
+ endif (petscconf)
+ endif (NOT PETSC_ARCH)
+ endforeach (arch)
+ set (petscconf "NOTFOUND" CACHE INTERNAL "Scratch variable" FORCE)
+endif (PETSC_DIR AND NOT PETSC_ARCH)
+
+set (petsc_slaves LIBRARIES_SYS LIBRARIES_VEC LIBRARIES_MAT LIBRARIES_DM LIBRARIES_KSP LIBRARIES_SNES LIBRARIES_TS
+ INCLUDE_DIR INCLUDE_CONF)
+include (FindPackageMultipass)
+find_package_multipass (PETSc petsc_config_current
+ STATES DIR ARCH
+ DEPENDENTS INCLUDES LIBRARIES COMPILER MPIEXEC ${petsc_slaves})
+
+# Determine whether the PETSc layout is old-style (through 2.3.3) or
+# new-style (>= 3.0.0)
+if (EXISTS "${PETSC_DIR}/${PETSC_ARCH}/include/petscconf.h") # > 2.3.3
+ set (petsc_conf_rules "${PETSC_DIR}/conf/rules")
+ set (petsc_conf_variables "${PETSC_DIR}/conf/variables")
+elseif (EXISTS "${PETSC_DIR}/bmake/${PETSC_ARCH}/petscconf.h") # <= 2.3.3
+ set (petsc_conf_rules "${PETSC_DIR}/bmake/common/rules")
+ set (petsc_conf_variables "${PETSC_DIR}/bmake/common/variables")
+elseif (PETSC_DIR)
+ message (SEND_ERROR "The pair PETSC_DIR=${PETSC_DIR} PETSC_ARCH=${PETSC_ARCH} do not specify a valid PETSc installation")
+else ()
+ message (FATAL_ERROR "PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH.")
+endif ()
+petsc_get_version()
+
+if (petsc_conf_rules AND petsc_conf_variables AND NOT petsc_config_current)
+ # Put variables into environment since they are needed to get
+ # configuration (petscvariables) in the PETSc makefile
+ set (ENV{PETSC_DIR} "${PETSC_DIR}")
+ set (ENV{PETSC_ARCH} "${PETSC_ARCH}")
+
+ # A temporary makefile to probe the PETSc configuration
+ set (petsc_config_makefile "${PROJECT_BINARY_DIR}/Makefile.petsc")
+ file (WRITE "${petsc_config_makefile}"
+"## This file was autogenerated by FindPETSc.cmake
+# PETSC_DIR = ${PETSC_DIR}
+# PETSC_ARCH = ${PETSC_ARCH}
+include ${petsc_conf_rules}
+include ${petsc_conf_variables}
+show :
+ -@echo -n \${\${VARIABLE}}
+")
+
+ macro (PETSC_GET_VARIABLE name var)
+ set (${var} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
+ execute_process (COMMAND ${CMAKE_MAKE_PROGRAM} --no-print-directory -f ${petsc_config_makefile} show VARIABLE=${name}
+ OUTPUT_VARIABLE ${var}
+ RESULT_VARIABLE petsc_return)
+ endmacro (PETSC_GET_VARIABLE)
+ petsc_get_variable (PETSC_LIB_DIR petsc_lib_dir)
+ petsc_get_variable (PETSC_EXTERNAL_LIB_BASIC petsc_libs_external)
+ petsc_get_variable (PETSC_CCPPFLAGS petsc_cpp_line)
+ petsc_get_variable (PETSC_INCLUDE petsc_include)
+ petsc_get_variable (PCC petsc_cc)
+ petsc_get_variable (MPIEXEC petsc_mpiexec)
+ # We are done with the temporary Makefile, calling PETSC_GET_VARIABLE after this point is invalid!
+ file (REMOVE ${petsc_config_makefile})
+
+ include (ResolveCompilerPaths)
+ # Extract include paths and libraries from compile command line
+ resolve_includes (petsc_includes_all "${petsc_cpp_line}")
+
+ message (STATUS "petsc_lib_dir ${petsc_lib_dir}")
+
+ macro (PETSC_FIND_LIBRARY suffix name)
+ set (PETSC_LIBRARY_${suffix} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE) # Clear any stale value, if we got here, we need to find it again
+ find_library (PETSC_LIBRARY_${suffix} NAMES ${name} HINTS ${petsc_lib_dir} NO_DEFAULT_PATH)
+ set (PETSC_LIBRARIES_${suffix} "${PETSC_LIBRARY_${suffix}}")
+ mark_as_advanced (PETSC_LIBRARY_${suffix})
+ endmacro (PETSC_FIND_LIBRARY suffix name)
+
+ # Look for petscvec first, if it doesn't exist, we must be using single-library
+ petsc_find_library (VEC petscvec)
+ if (PETSC_LIBRARY_VEC)
+ petsc_find_library (SYS "petscsys;petsc") # libpetscsys is called libpetsc prior to 3.1 (when single-library was introduced)
+ petsc_find_library (MAT petscmat)
+ petsc_find_library (DM petscdm)
+ petsc_find_library (KSP petscksp)
+ petsc_find_library (SNES petscsnes)
+ petsc_find_library (TS petscts)
+ macro (PETSC_JOIN libs deps)
+ list (APPEND PETSC_LIBRARIES_${libs} ${PETSC_LIBRARIES_${deps}})
+ endmacro (PETSC_JOIN libs deps)
+ petsc_join (VEC SYS)
+ petsc_join (MAT VEC)
+ petsc_join (DM MAT)
+ petsc_join (KSP DM)
+ petsc_join (SNES KSP)
+ petsc_join (TS SNES)
+ petsc_join (ALL TS)
+ else ()
+ set (PETSC_LIBRARY_VEC "NOTFOUND" CACHE INTERNAL "Cleared" FORCE) # There is no libpetscvec
+ petsc_find_library (SINGLE petsc)
+ foreach (pkg SYS VEC MAT DM KSP SNES TS ALL)
+ set (PETSC_LIBRARIES_${pkg} "${PETSC_LIBRARY_SINGLE}")
+ endforeach ()
+ endif ()
+ if (PETSC_LIBRARY_TS)
+ message (STATUS "Recognized PETSc install with separate libraries for each package")
+ else ()
+ message (STATUS "Recognized PETSc install with single library for all packages")
+ endif ()
+
+ include (CheckCSourceRuns)
+ macro (PETSC_TEST_RUNS includes libraries runs)
+ multipass_c_source_runs ("${includes}" "${libraries}" "
+static const char help[] = \"PETSc test program.\";
+#include \"petscts.h\"
+int main(int argc,char *argv[]) {
+ PetscErrorCode ierr;
+ TS ts;
+
+ ierr = PetscInitialize(&argc,&argv,0,help);CHKERRQ(ierr);
+ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
+ ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
+ ierr = TSDestroy(ts);CHKERRQ(ierr);
+ ierr = PetscFinalize();CHKERRQ(ierr);
+ return 0;
+}
+" ${runs})
+ if (${${runs}})
+ set (PETSC_EXECUTABLE_RUNS "YES" CACHE BOOL
+ "Can the system successfully run a PETSc executable? This variable can be manually set to \"YES\" to force CMake to accept a given PETSc configuration, but this will almost always result in a broken build. If you change PETSC_DIR, PETSC_ARCH, or PETSC_CURRENT you would have to reset this variable." FORCE)
+ endif (${${runs}})
+ endmacro (PETSC_TEST_RUNS)
+
+ find_path (PETSC_INCLUDE_DIR petscts.h HINTS "${PETSC_DIR}" PATH_SUFFIXES include NO_DEFAULT_PATH)
+ find_path (PETSC_INCLUDE_CONF petscconf.h HINTS "${PETSC_DIR}" PATH_SUFFIXES "${PETSC_ARCH}/include" "bmake/${PETSC_ARCH}" NO_DEFAULT_PATH)
+ mark_as_advanced (PETSC_INCLUDE_DIR PETSC_INCLUDE_CONF)
+ set (petsc_includes_minimal ${PETSC_INCLUDE_CONF} ${PETSC_INCLUDE_DIR})
+
+ petsc_test_runs ("${petsc_includes_minimal}" "${PETSC_LIBRARIES_TS}" petsc_works_minimal)
+ if (petsc_works_minimal)
+ message (STATUS "Minimal PETSc includes and libraries work. This probably means we are building with shared libs.")
+ set (petsc_includes_needed "${petsc_includes_minimal}")
+ else (petsc_works_minimal) # Minimal includes fail, see if just adding full includes fixes it
+ petsc_test_runs ("${petsc_includes_all}" "${PETSC_LIBRARIES_TS}" petsc_works_allincludes)
+ if (petsc_works_allincludes) # It does, we just need all the includes (
+ message (STATUS "PETSc requires extra include paths, but links correctly with only interface libraries. This is an unexpected configuration (but it seems to work fine).")
+ set (petsc_includes_needed ${petsc_includes_all})
+ else (petsc_works_allincludes) # We are going to need to link the external libs explicitly
+ resolve_libraries (petsc_libraries_external "${petsc_libs_external}")
+ foreach (pkg SYS VEC MAT DM KSP SNES TS ALL)
+ list (APPEND PETSC_LIBRARIES_${pkg} ${petsc_libraries_external})
+ endforeach (pkg)
+ petsc_test_runs ("${petsc_includes_minimal}" "${PETSC_LIBRARIES_TS}" petsc_works_alllibraries)
+ if (petsc_works_alllibraries)
+ message (STATUS "PETSc only need minimal includes, but requires explicit linking to all dependencies. This is expected when PETSc is built with static libraries.")
+ set (petsc_includes_needed ${petsc_includes_minimal})
+ else (petsc_works_alllibraries)
+ # It looks like we really need everything, should have listened to Matt
+ set (petsc_includes_needed ${petsc_includes_all})
+ petsc_test_runs ("${petsc_includes_all}" "${PETSC_LIBRARIES_TS}" petsc_works_all)
+ if (petsc_works_all) # We fail anyways
+ message (STATUS "PETSc requires extra include paths and explicit linking to all dependencies. This probably means you have static libraries and something unexpected in PETSc headers.")
+ else (petsc_works_all) # We fail anyways
+ message (STATUS "PETSc could not be used, maybe the install is broken.")
+ endif (petsc_works_all)
+ endif (petsc_works_alllibraries)
+ endif (petsc_works_allincludes)
+ endif (petsc_works_minimal)
+
+ # We do an out-of-source build so __FILE__ will be an absolute path, hence __INSDIR__ is superfluous
+ if (${PETSC_VERSION} VERSION_LESS 3.1)
+ set (PETSC_DEFINITIONS "-D__SDIR__=\"\"" CACHE STRING "PETSc definitions" FORCE)
+ else ()
+ set (PETSC_DEFINITIONS "-D__INSDIR__=" CACHE STRING "PETSc definitions" FORCE)
+ endif ()
+ # Sometimes this can be used to assist FindMPI.cmake
+ set (PETSC_MPIEXEC ${petsc_mpiexec} CACHE FILEPATH "Executable for running PETSc MPI programs" FORCE)
+ set (PETSC_INCLUDES ${petsc_includes_needed} CACHE STRING "PETSc include path" FORCE)
+ set (PETSC_LIBRARIES ${PETSC_LIBRARIES_ALL} CACHE STRING "PETSc libraries" FORCE)
+ set (PETSC_COMPILER ${petsc_cc} CACHE FILEPATH "PETSc compiler" FORCE)
+ # Note that we have forced values for all these choices. If you
+ # change these, you are telling the system to trust you that they
+ # work. It is likely that you will end up with a broken build.
+ mark_as_advanced (PETSC_INCLUDES PETSC_LIBRARIES PETSC_COMPILER PETSC_DEFINITIONS PETSC_MPIEXEC PETSC_EXECUTABLE_RUNS)
+endif ()
+
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (PETSc
+ "PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH."
+ PETSC_INCLUDES PETSC_LIBRARIES PETSC_EXECUTABLE_RUNS)
diff --git a/AMDiS/cmake3/muparser.cmake b/AMDiS/cmake3/muparser.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..b6751cb62902df57d4583626fd9cf450cf02229c
--- /dev/null
+++ b/AMDiS/cmake3/muparser.cmake
@@ -0,0 +1,32 @@
+# specify the target and requirements for the muparser library
+
+set(MUPARSER_SOURCE_DIR ${BASE_DIR}/lib/muparser_v134/src)
+set(MUPARSER_INCLUDE_DIR ${BASE_DIR}/lib/muparser_v134/include)
+add_library(muparser
+ ${MUPARSER_SOURCE_DIR}/muParser.cpp
+ ${MUPARSER_SOURCE_DIR}/muParserBase.cpp
+ ${MUPARSER_SOURCE_DIR}/muParserBytecode.cpp
+ ${MUPARSER_SOURCE_DIR}/muParserCallback.cpp
+ ${MUPARSER_SOURCE_DIR}/muParserComplex.cpp
+ ${MUPARSER_SOURCE_DIR}/muParserDLL.cpp
+ ${MUPARSER_SOURCE_DIR}/muParserError.cpp
+ ${MUPARSER_SOURCE_DIR}/muParserInt.cpp
+ ${MUPARSER_SOURCE_DIR}/muParserTest.cpp
+ ${MUPARSER_SOURCE_DIR}/muParserTokenReader.cpp)
+
+target_include_directories(muparser PUBLIC ${MUPARSER_INCLUDE_DIR})
+
+if (ENABLE_CXX11)
+ set_property(TARGET muparser PROPERTY CXX_STANDARD 11)
+ set_property(TARGET muparser PROPERTY CXX_STANDARD_REQUIRED ON)
+ target_compile_definitions(muparser PRIVATE HAS_CXX11=1)
+endif (ENABLE_CXX11)
+
+# specify how to install this target:
+# -----------------------------------
+
+file(GLOB MUPARSER_HEADERS "${MUPARSER_SOURCE_DIR}/include/*.h")
+install(FILES ${MUPARSER_HEADERS}
+ DESTINATION include/amdis/muparser)
+install(TARGETS muparser
+ DESTINATION lib/amdis/ )
\ No newline at end of file
diff --git a/AMDiS/src/Config.h b/AMDiS/src/Config.h
index 5e52b3bc5417810db44c8435cb11edf0335dbe4b..1e52cdd5d72debb03202494ab7b86e3b846bc451 100644
--- a/AMDiS/src/Config.h
+++ b/AMDiS/src/Config.h
@@ -29,6 +29,15 @@
#define AMDIS_VERSION "AMDiS: Version 0.9.1"
#endif
+#ifdef DEBUG
+#undef DEBUG
+#endif
+#ifdef NDEBUG
+#define DEBUG 0
+#else
+#define DEBUG 1
+#endif
+
#include <boost/config.hpp>
#define CACHE_LINE 16
diff --git a/AMDiS/src/Initfile.cc b/AMDiS/src/Initfile.cc
index 3ae5752b3f39cf4391a2c977985394c74cd8fe97..e91fe37a3ffa2441aaaf31ca96d0ec27ce17b572 100644
--- a/AMDiS/src/Initfile.cc
+++ b/AMDiS/src/Initfile.cc
@@ -25,6 +25,9 @@
#include <sstream>
#include<boost/tokenizer.hpp>
+// a parser for arithmetic expressions
+#include "muParser.h"
+
using namespace std;
namespace AMDiS {
@@ -50,7 +53,19 @@ namespace AMDiS {
string name;
string value;
};
+
+ namespace detail
+ {
+ double mu_parser_eval(std::string const& valStr)
+ {
+ mu::Parser parser;
+ parser.DefineConst(_T("M_PI"), m_pi);
+ parser.DefineConst(_T("M_E"), m_e);
+ parser.SetExpr(valStr);
+ return parser.Eval();
+ }
+ }
Initfile* Initfile::singlett = NULL;
std::set<std::string> Initfile::fn_include_list;
diff --git a/AMDiS/src/Initfile.h b/AMDiS/src/Initfile.h
index 57e406f672e03ce8db957d33955e7d4f723bc90d..723b5777a9a0fd8acedf1c22c73d77193b3278a7 100644
--- a/AMDiS/src/Initfile.h
+++ b/AMDiS/src/Initfile.h
@@ -40,9 +40,6 @@
#include <boost/type_traits.hpp>
-// a parser for arithmetic expressions
-#include "muParser.h"
-
namespace AMDiS {
namespace detail {
@@ -127,6 +124,9 @@ namespace AMDiS {
// throw NoDelim("cannot detect the delimiter in " + value);
return 0;
}
+
+
+ double mu_parser_eval(std::string const& valStr);
/// convert string to string
@@ -149,13 +149,7 @@ namespace AMDiS {
using boost::lexical_cast;
using boost::numeric_cast;
- mu::Parser parser;
- parser.DefineConst(_T("M_PI"), m_pi);
- parser.DefineConst(_T("M_E"), m_e);
-
- // try {
- parser.SetExpr(valStr);
- value = numeric_cast< T >(parser.Eval());
+ value = numeric_cast< T >(mu_parser_eval(valStr));
/* } catch (boost::bad_lexical_cast e) { */
/* throw WrongValueFormat< T >(valStr); */
/* } catch (boost::bad_numeric_cast e) { */
@@ -452,7 +446,7 @@ namespace AMDiS {
} else
throw std::runtime_error("unknown error_code (" + boost::lexical_cast<std::string>(error_code) + ") returned for tag '" + tag + "'");
- } catch(mu::ParserError& e) {
+ } catch(...) {
std::string parser_error = "Could not parse: " + tag;
throw std::runtime_error(parser_error);
}
diff --git a/AMDiS/src/parallel/MeshDistributor.h b/AMDiS/src/parallel/MeshDistributor.h
index 14deb45f5a0b41b00601d9c10cdd07e1feca303d..26ae91942ade665dd9cd27ee81328cbe599c98d1 100644
--- a/AMDiS/src/parallel/MeshDistributor.h
+++ b/AMDiS/src/parallel/MeshDistributor.h
@@ -491,6 +491,65 @@ void synchMultiVector(DOFVector<T> &vec, std::vector<DOFVector<T>*> additionalVe
synchVector(allDOFVectors);
}
+
+ /** \brief
+ * Synchronize \p vec using indicator vector \p additionalVecs, e.g. let
+ * additionalVecs[0] be 1 on all dofs the value should be taken from my rank
+ * and 0 elsewhere.
+ */
+ // op(std::vector<T>& out, std::vector<T> const& in)
+ template<typename T, typename Operator>
+ void synchMultiVector(DOFVector<T> &vec, std::vector<DOFVector<T>*> additionalVecs, Operator op)
+ {
+ // get FE space and check equal FE space
+ const FiniteElemSpace *fe = vec.getFeSpace();
+ MultiLevelDofComm& dofComm = dofComms[fe->getMesh()];
+
+ typedef typename std::vector<DOFVector<T>*>::iterator Iterator;
+
+ int nLevels = levelData.getNumberOfLevels();
+ for (int level = nLevels - 1; level >= 0; level--)
+ {
+ StdMpi < std::vector<std::vector<T> > > stdMpi(levelData.getMpiComm(level));
+
+ for (DofComm::Iterator it(dofComm[level].getRecvDofs(), fe); !it.end(); it.nextRank())
+ {
+ std::vector<std::vector<T> > dofs;
+ dofs.reserve(it.getDofs().size());
+ for (; !it.endDofIter(); it.nextDof())
+ {
+ std::vector<T> values;
+ values.reserve(additionalVecs.size() + 1);
+ values.push_back( vec[it.getDofIndex()] );
+ for (Iterator vecIt = additionalVecs.begin(); vecIt != additionalVecs.end(); ++vecIt )
+ values.push_back( (**vecIt)[it.getDofIndex()] );
+ dofs.push_back( values );
+ }
+ stdMpi.send(it.getRank(), dofs);
+ }
+
+ for (DofComm::Iterator it(dofComm[level].getSendDofs(), fe); !it.end(); it.nextRank())
+ stdMpi.recv(it.getRank());
+
+ stdMpi.startCommunication();
+
+ for (DofComm::Iterator it(dofComm[level].getSendDofs(), fe);
+ !it.end(); it.nextRank()) {
+ for (; !it.endDofIter(); it.nextDof()) {
+ std::vector<T> values;
+ values.reserve(additionalVecs.size() + 1);
+ values.push_back( vec[it.getDofIndex()] );
+ for (Iterator vecIt = additionalVecs.begin(); vecIt != additionalVecs.end(); ++vecIt )
+ values.push_back( (**vecIt)[it.getDofIndex()] );
+
+ op(values, stdMpi.getRecvData(it.getRank())[it.getDofCounter()]);
+ }
+ }
+ }
+
+ synchVector(vec);
+ }
+
/** \brief
* This function must be used if the values of a DOFVector must be
* synchronised over all ranks. That means, that each rank sends the
diff --git a/demo/CMakeLists.txt b/demo/CMakeLists.txt
index 98c2184ec468baf1a1b8532e17b2bc16ee1b540d..3c5aee9811fe8401bad4b94bfd015824cecc9884 100644
--- a/demo/CMakeLists.txt
+++ b/demo/CMakeLists.txt
@@ -4,11 +4,13 @@ cmake_minimum_required(VERSION 2.8)
#find_package(AMDIS REQUIRED COMPONENTS umfpack )
find_package(AMDIS REQUIRED)
-if(AMDIS_FOUND)
- message(STATUS "AMDiS was found.")
- include(${AMDIS_USE_FILE})
- SET(BASIS_LIBS ${AMDIS_LIBRARIES})
-endif(AMDIS_FOUND)
+if (AMDIS_FOUND)
+ message(STATUS "AMDiS was found.")
+# include(${AMDIS_USE_FILE})
+ set(BASIS_LIBS AMDiS)
+ get_target_property(AMDIS_INCLUDE_DIRS AMDiS INTERFACE_INCLUDE_DIRECTORIES)
+ message("AMDiS-Include-Dirs: ${AMDIS_INCLUDE_DIRS}")
+endif (AMDIS_FOUND)
set(ball src/ball.cc)
set(bunny src/bunny.cc)