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Commit e8cfacab authored by Thomas Witkowski's avatar Thomas Witkowski
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First work in repartitioning in parallel computations. A lot of clean up in code structure.

parent f6559482
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AMDiS/CMakeLists.txt
View file @ e8cfacab
......@@ -75,6 +75,7 @@ SET(AMDIS_SRC ${SOURCE_DIR}/DOFIndexed.cc
${SOURCE_DIR}/CreatorMap.cc
${SOURCE_DIR}/ProblemInterpolScal.cc
${SOURCE_DIR}/ProblemInterpolVec.cc
${SOURCE_DIR}/MacroInfo.cc
${SOURCE_DIR}/MacroReader.cc
${SOURCE_DIR}/ValueReader.cc
${SOURCE_DIR}/Projection.cc
......@@ -165,10 +166,6 @@ if(ENABLE_PARMETIS)
CMAKE_FORCE_CXX_COMPILER(mpiCC "MPI C++ compiler")
include_directories( ${LIB_DIR}/ParMetis-3.1)
SET(PARALLEL_AMDIS_SRC ${SOURCE_DIR}/ConditionalEstimator.cc ${SOURCE_DIR}/ConditionalMarker.cc
${SOURCE_DIR}/ParallelProblem.cc ${SOURCE_DIR}/ParMetisPartitioner.cc
${SOURCE_DIR}/PollutionError.cc)
SET(COMPILEFLAGS "${COMPILEFLAGS} -DHAVE_PARALLEL_AMDIS=1")
INSTALL(FILES ${LIB_DIR}/ParMetis-3.1/parmetis.h
${LIB_DIR}/ParMetis-3.1/libparmetis.a
${LIB_DIR}/ParMetis-3.1/libmetis.a
......@@ -179,6 +176,7 @@ endif(ENABLE_PARMETIS)
if(ENABLE_PARALLEL_DOMAIN)
include_directories(${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
SET(PARALLEL_DOMAIN_AMDIS_SRC
${SOURCE_DIR}/parallel/ParMetisPartitioner.cc
${SOURCE_DIR}/parallel/MeshDistributor.cc
${SOURCE_DIR}/parallel/StdMpi.cc
${SOURCE_DIR}/parallel/ParallelDebug.cc
......@@ -247,7 +245,7 @@ SET(COMPOSITE_FEM_SRC ${COMPOSITE_SOURCE_DIR}/CFE_Integration.cc ${COMPOSITE_SOU
include_directories(${MTL_DIR})
include_directories(${SOURCE_DIR})
add_library(amdis SHARED ${AMDIS_SRC} ${PARALLEL_AMDIS_SRC} ${PARALLEL_DOMAIN_AMDIS_SRC})
add_library(amdis SHARED ${AMDIS_SRC} ${PARALLEL_DOMAIN_AMDIS_SRC})
add_library(compositeFEM SHARED ${COMPOSITE_FEM_SRC})
target_link_libraries(compositeFEM amdis)
......
AMDiS/bin/Makefile.am
View file @ e8cfacab
......@@ -10,25 +10,13 @@ AMDIS_INCLUDES = -I$(SOURCE_DIR)
libamdis_la_CXXFLAGS =
if USE_PARALLEL_AMDIS
PARALLEL_AMDIS_SOURCES = \
$(PARALLEL_DIR)/ConditionalEstimator.h $(PARALLEL_DIR)/ConditionalEstimator.cc \
$(PARALLEL_DIR)/ConditionalMarker.h \ $(PARALLEL_DIR)/ConditionalMarker.cc \
$(PARALLEL_DIR)/ParallelError.h $(PARALLEL_DIR)/ParallelError.hh \
$(PARALLEL_DIR)/ParallelProblem.h $(PARALLEL_DIR)/ParallelProblem.cc \
$(PARALLEL_DIR)/ParMetisPartitioner.h $(PARALLEL_DIR)/ParMetisPartitioner.cc \
$(PARALLEL_DIR)/PartitionElementData.h \
$(PARALLEL_DIR)/PollutionError.h $(PARALLEL_DIR)/PollutionError.cc
PARALLEL_INCLUDES = -I$(MPI_DIR)/include -I$(PARMETIS_DIR)
libamdis_la_CXXFLAGS += -DHAVE_PARALLEL_AMDIS=1
else
PARALLEL_AMDIS_SOURCES =
PARALLEL_INCLUDES =
endif
PARALLEL_AMDIS_SOURCES =
PARALLEL_INCLUDES =
if USE_PARALLEL_DOMAIN_AMDIS
PARALLEL_AMDIS_SOURCES += \
$(SOURCE_DIR)/parallel/StdMpi.h $(SOURCE_DIR)/parallel/StdMpi.cc \
$(SOURCE_DIR)/parallel/ParMetisPartitioner.h $(SOURCE_DIR)/parallel/ParMetisPartitioner.cc \
$(SOURCE_DIR)/parallel/MeshDistributor.h $(SOURCE_DIR)/parallel/MeshDistributor.cc \
$(SOURCE_DIR)/parallel/ParallelDebug.h $(SOURCE_DIR)/parallel/ParallelDebug.cc \
$(SOURCE_DIR)/parallel/ParallelProblemStatBase.h \
......@@ -98,6 +86,7 @@ $(SOURCE_DIR)/ProblemInterpolVec.h $(SOURCE_DIR)/ProblemInterpolVec.cc \
$(SOURCE_DIR)/Serializable.h \
$(SOURCE_DIR)/BallProject.h \
$(SOURCE_DIR)/CylinderProject.h \
$(SOURCE_DIR)/MacroInfo.h $(SOURCE_DIR)/MacroInfo.cc \
$(SOURCE_DIR)/MacroReader.h $(SOURCE_DIR)/MacroReader.cc \
$(SOURCE_DIR)/ValueReader.h $(SOURCE_DIR)/ValueReader.cc \
$(SOURCE_DIR)/Projection.h $(SOURCE_DIR)/Projection.cc \
......
AMDiS/bin/Makefile.in
View file @ e8cfacab
......@@ -34,9 +34,9 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
@USE_PARALLEL_AMDIS_TRUE@am__append_1 = -DHAVE_PARALLEL_AMDIS=1
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_2 = \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_1 = \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/StdMpi.h $(SOURCE_DIR)/parallel/StdMpi.cc \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/ParMetisPartitioner.h $(SOURCE_DIR)/parallel/ParMetisPartitioner.cc \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/MeshDistributor.h $(SOURCE_DIR)/parallel/MeshDistributor.cc \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/ParallelDebug.h $(SOURCE_DIR)/parallel/ParallelDebug.cc \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/ParallelProblemStatBase.h \
......@@ -44,19 +44,19 @@ host_triplet = @host@
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/MpiHelper.h $(SOURCE_DIR)/parallel/MpiHelper.cc \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/ElementObjectData.h $(SOURCE_DIR)/parallel/ElementObjectData.cc
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_3 = -DHAVE_PARALLEL_DOMAIN_AMDIS=1
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_4 = -I$(PETSC_DIR)/include -I$(PETSC_DIR)/$(PETSC_ARCH)/include
@ENABLE_UMFPACK_TRUE@am__append_5 = -DHAVE_UMFPACK=1 -DMTL_HAS_UMFPACK
@ENABLE_UMFPACK_TRUE@am__append_6 = -I$(LIB_DIR)/UFconfig \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_2 = -DHAVE_PARALLEL_DOMAIN_AMDIS=1
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_3 = -I$(PETSC_DIR)/include -I$(PETSC_DIR)/$(PETSC_ARCH)/include
@ENABLE_UMFPACK_TRUE@am__append_4 = -DHAVE_UMFPACK=1 -DMTL_HAS_UMFPACK
@ENABLE_UMFPACK_TRUE@am__append_5 = -I$(LIB_DIR)/UFconfig \
@ENABLE_UMFPACK_TRUE@ -I$(LIB_DIR)/AMD/Include \
@ENABLE_UMFPACK_TRUE@ -I$(LIB_DIR)/UMFPACK/Include
@ENABLE_MKL_TRUE@am__append_7 = -DHAVE_MKL=1 -I${MKL_INC}
@ENABLE_DUNE_TRUE@am__append_8 = -DHAVE_DUNE=1
@ENABLE_DUNE_TRUE@am__append_9 = -I$(DUNE_DIR)
@ENABLE_BOOST_TRUE@am__append_10 = -DHAVE_BOOST=1
@AMDIS_DEBUG_TRUE@am__append_11 = -g -O0 -Wall -DDEBUG=1 $(OPENMP_FLAG) $(INCLUDES) #-pedantic
@AMDIS_DEBUG_FALSE@am__append_12 = -O2 -Wall -DDEBUG=0 -DNDEBUG $(OPENMP_FLAG) -ftemplate-depth-100 $(INCLUDES) #-pedantic
@ENABLE_MKL_TRUE@am__append_6 = -DHAVE_MKL=1 -I${MKL_INC}
@ENABLE_DUNE_TRUE@am__append_7 = -DHAVE_DUNE=1
@ENABLE_DUNE_TRUE@am__append_8 = -I$(DUNE_DIR)
@ENABLE_BOOST_TRUE@am__append_9 = -DHAVE_BOOST=1
@AMDIS_DEBUG_TRUE@am__append_10 = -g -O0 -Wall -DDEBUG=1 $(OPENMP_FLAG) $(INCLUDES) #-pedantic
@AMDIS_DEBUG_FALSE@am__append_11 = -O2 -Wall -DDEBUG=0 -DNDEBUG $(OPENMP_FLAG) -ftemplate-depth-100 $(INCLUDES) #-pedantic
subdir = bin
DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
......@@ -92,6 +92,8 @@ LTLIBRARIES = $(lib_LTLIBRARIES)
libamdis_la_LIBADD =
am__libamdis_la_SOURCES_DIST = $(SOURCE_DIR)/parallel/StdMpi.h \
$(SOURCE_DIR)/parallel/StdMpi.cc \
$(SOURCE_DIR)/parallel/ParMetisPartitioner.h \
$(SOURCE_DIR)/parallel/ParMetisPartitioner.cc \
$(SOURCE_DIR)/parallel/MeshDistributor.h \
$(SOURCE_DIR)/parallel/MeshDistributor.cc \
$(SOURCE_DIR)/parallel/ParallelDebug.h \
......@@ -103,24 +105,12 @@ am__libamdis_la_SOURCES_DIST = $(SOURCE_DIR)/parallel/StdMpi.h \
$(SOURCE_DIR)/parallel/MpiHelper.cc \
$(SOURCE_DIR)/parallel/ElementObjectData.h \
$(SOURCE_DIR)/parallel/ElementObjectData.cc \
$(PARALLEL_DIR)/ConditionalEstimator.h \
$(PARALLEL_DIR)/ConditionalEstimator.cc \
$(PARALLEL_DIR)/ConditionalMarker.h \ \
$(PARALLEL_DIR)/ConditionalMarker.cc \
$(PARALLEL_DIR)/ParallelError.h \
$(PARALLEL_DIR)/ParallelError.hh \
$(PARALLEL_DIR)/ParallelProblem.h \
$(PARALLEL_DIR)/ParallelProblem.cc \
$(PARALLEL_DIR)/ParMetisPartitioner.h \
$(PARALLEL_DIR)/ParMetisPartitioner.cc \
$(PARALLEL_DIR)/PartitionElementData.h \
$(PARALLEL_DIR)/PollutionError.h \
$(PARALLEL_DIR)/PollutionError.cc $(SOURCE_DIR)/DOFIndexed.h \
$(SOURCE_DIR)/DOFIndexed.cc $(SOURCE_DIR)/GNUPlotWriter.h \
$(SOURCE_DIR)/GNUPlotWriter.cc $(SOURCE_DIR)/VertexVector.h \
$(SOURCE_DIR)/VertexVector.cc $(SOURCE_DIR)/PeriodicBC.h \
$(SOURCE_DIR)/PeriodicBC.cc $(SOURCE_DIR)/Recovery.h \
$(SOURCE_DIR)/Recovery.cc $(SOURCE_DIR)/RecoveryEstimator.h \
$(SOURCE_DIR)/DOFIndexed.h $(SOURCE_DIR)/DOFIndexed.cc \
$(SOURCE_DIR)/GNUPlotWriter.h $(SOURCE_DIR)/GNUPlotWriter.cc \
$(SOURCE_DIR)/VertexVector.h $(SOURCE_DIR)/VertexVector.cc \
$(SOURCE_DIR)/PeriodicBC.h $(SOURCE_DIR)/PeriodicBC.cc \
$(SOURCE_DIR)/Recovery.h $(SOURCE_DIR)/Recovery.cc \
$(SOURCE_DIR)/RecoveryEstimator.h \
$(SOURCE_DIR)/RecoveryEstimator.cc \
$(SOURCE_DIR)/ResidualEstimator.h \
$(SOURCE_DIR)/ResidualEstimator.cc $(SOURCE_DIR)/Cholesky.h \
......@@ -146,7 +136,8 @@ am__libamdis_la_SOURCES_DIST = $(SOURCE_DIR)/parallel/StdMpi.h \
$(SOURCE_DIR)/ProblemInterpolVec.h \
$(SOURCE_DIR)/ProblemInterpolVec.cc \
$(SOURCE_DIR)/Serializable.h $(SOURCE_DIR)/BallProject.h \
$(SOURCE_DIR)/CylinderProject.h $(SOURCE_DIR)/MacroReader.h \
$(SOURCE_DIR)/CylinderProject.h $(SOURCE_DIR)/MacroInfo.h \
$(SOURCE_DIR)/MacroInfo.cc $(SOURCE_DIR)/MacroReader.h \
$(SOURCE_DIR)/MacroReader.cc $(SOURCE_DIR)/ValueReader.h \
$(SOURCE_DIR)/ValueReader.cc $(SOURCE_DIR)/Projection.h \
$(SOURCE_DIR)/Projection.cc $(SOURCE_DIR)/SubAssembler.h \
......@@ -199,7 +190,7 @@ am__libamdis_la_SOURCES_DIST = $(SOURCE_DIR)/parallel/StdMpi.h \
$(SOURCE_DIR)/Estimator.cc $(SOURCE_DIR)/FiniteElemSpace.h \
$(SOURCE_DIR)/FixVec.h $(SOURCE_DIR)/FixVec.hh \
$(SOURCE_DIR)/FixVecConvert.h $(SOURCE_DIR)/Flag.h \
$(SOURCE_DIR)/Global.h $(SOURCE_DIR)/UmfPackSolver.h \
$(SOURCE_DIR)/Global.h $(SOURCE_DIR)/UmfPackSolver.h \ \
$(SOURCE_DIR)/UmfPackSolver.hh $(SOURCE_DIR)/Lagrange.h \
$(SOURCE_DIR)/Line.h $(SOURCE_DIR)/MacroElement.h \
$(SOURCE_DIR)/MacroWriter.h $(SOURCE_DIR)/Markings.h \
......@@ -267,19 +258,13 @@ am__libamdis_la_SOURCES_DIST = $(SOURCE_DIR)/parallel/StdMpi.h \
$(SOURCE_DIR)/time/RosenbrockMethod.h \
$(SOURCE_DIR)/time/RosenbrockMethod.cc
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__objects_1 = libamdis_la-StdMpi.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-ParMetisPartitioner.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-MeshDistributor.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-ParallelDebug.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-PetscSolver.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-MpiHelper.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-ElementObjectData.lo
@USE_PARALLEL_AMDIS_FALSE@am__objects_2 = $(am__objects_1)
@USE_PARALLEL_AMDIS_TRUE@am__objects_2 = \
@USE_PARALLEL_AMDIS_TRUE@ libamdis_la-ConditionalEstimator.lo \
@USE_PARALLEL_AMDIS_TRUE@ libamdis_la-ConditionalMarker.lo \
@USE_PARALLEL_AMDIS_TRUE@ libamdis_la-ParallelProblem.lo \
@USE_PARALLEL_AMDIS_TRUE@ libamdis_la-ParMetisPartitioner.lo \
@USE_PARALLEL_AMDIS_TRUE@ libamdis_la-PollutionError.lo \
@USE_PARALLEL_AMDIS_TRUE@ $(am__objects_1)
am__objects_2 = $(am__objects_1)
am_libamdis_la_OBJECTS = $(am__objects_2) libamdis_la-DOFIndexed.lo \
libamdis_la-GNUPlotWriter.lo libamdis_la-VertexVector.lo \
libamdis_la-PeriodicBC.lo libamdis_la-Recovery.lo \
......@@ -292,9 +277,10 @@ am_libamdis_la_OBJECTS = $(am__objects_2) libamdis_la-DOFIndexed.lo \
libamdis_la-ElementData.lo \
libamdis_la-ComponentTraverseInfo.lo libamdis_la-CreatorMap.lo \
libamdis_la-ProblemInterpolScal.lo \
libamdis_la-ProblemInterpolVec.lo libamdis_la-MacroReader.lo \
libamdis_la-ValueReader.lo libamdis_la-Projection.lo \
libamdis_la-SubAssembler.lo libamdis_la-ZeroOrderAssembler.lo \
libamdis_la-ProblemInterpolVec.lo libamdis_la-MacroInfo.lo \
libamdis_la-MacroReader.lo libamdis_la-ValueReader.lo \
libamdis_la-Projection.lo libamdis_la-SubAssembler.lo \
libamdis_la-ZeroOrderAssembler.lo \
libamdis_la-FirstOrderAssembler.lo \
libamdis_la-SecondOrderAssembler.lo libamdis_la-Assembler.lo \
libamdis_la-AdaptInfo.lo libamdis_la-Marker.lo \
......@@ -511,28 +497,13 @@ SOURCE_DIR = ../src
LIB_DIR = ../lib
PARALLEL_DIR = $(SOURCE_DIR)
PARMETIS_DIR = ../lib/ParMetis-3.1
AMDIS_INCLUDES = -I$(SOURCE_DIR) $(am__append_4) $(am__append_6) \
$(am__append_9)
libamdis_la_CXXFLAGS = $(am__append_1) $(am__append_3) $(am__append_5) \
$(am__append_7) $(am__append_8) $(am__append_10) \
$(am__append_11) $(am__append_12)
@USE_PARALLEL_AMDIS_FALSE@PARALLEL_AMDIS_SOURCES = $(am__append_2)
@USE_PARALLEL_AMDIS_TRUE@PARALLEL_AMDIS_SOURCES = $(PARALLEL_DIR)/ConditionalEstimator.h \
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/ConditionalEstimator.cc \
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/ConditionalMarker.h \ \
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/ConditionalMarker.cc \
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/ParallelError.h \
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/ParallelError.hh \
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/ParallelProblem.h \
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/ParallelProblem.cc \
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/ParMetisPartitioner.h \
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/ParMetisPartitioner.cc \
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/PartitionElementData.h \
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/PollutionError.h \
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/PollutionError.cc \
@USE_PARALLEL_AMDIS_TRUE@ $(am__append_2)
@USE_PARALLEL_AMDIS_FALSE@PARALLEL_INCLUDES =
@USE_PARALLEL_AMDIS_TRUE@PARALLEL_INCLUDES = -I$(MPI_DIR)/include -I$(PARMETIS_DIR)
AMDIS_INCLUDES = -I$(SOURCE_DIR) $(am__append_3) $(am__append_5) \
$(am__append_8)
libamdis_la_CXXFLAGS = $(am__append_2) $(am__append_4) $(am__append_6) \
$(am__append_7) $(am__append_9) $(am__append_10) \
$(am__append_11)
PARALLEL_AMDIS_SOURCES = $(am__append_1)
PARALLEL_INCLUDES =
TEMPLATE_INCLUDES = -I../lib/mtl4
INCLUDES = $(AMDIS_INCLUDES) $(PARALLEL_INCLUDES) $(TEMPLATE_INCLUDES)
libamdis_la_SOURCES = \
......@@ -563,6 +534,7 @@ $(SOURCE_DIR)/ProblemInterpolVec.h $(SOURCE_DIR)/ProblemInterpolVec.cc \
$(SOURCE_DIR)/Serializable.h \
$(SOURCE_DIR)/BallProject.h \
$(SOURCE_DIR)/CylinderProject.h \
$(SOURCE_DIR)/MacroInfo.h $(SOURCE_DIR)/MacroInfo.cc \
$(SOURCE_DIR)/MacroReader.h $(SOURCE_DIR)/MacroReader.cc \
$(SOURCE_DIR)/ValueReader.h $(SOURCE_DIR)/ValueReader.cc \
$(SOURCE_DIR)/Projection.h $(SOURCE_DIR)/Projection.cc \
......@@ -810,8 +782,6 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-CoarseningManager2d.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-CoarseningManager3d.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ComponentTraverseInfo.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ConditionalEstimator.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ConditionalMarker.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-CreatorMap.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-DOFAdmin.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-DOFIndexed.Plo@am__quote@
......@@ -844,6 +814,7 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-LeafData.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Line.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-MacroElement.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-MacroInfo.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-MacroReader.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-MacroWriter.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Marker.Plo@am__quote@
......@@ -856,13 +827,11 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-OperatorTerm.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ParMetisPartitioner.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ParallelDebug.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ParallelProblem.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Parameters.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Parametric.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-PeriodicBC.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-PetscSolver.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-PngWriter.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-PollutionError.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-PovrayWriter.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ProblemInstat.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ProblemInterpolScal.Plo@am__quote@
......@@ -943,6 +912,13 @@ libamdis_la-StdMpi.lo: $(SOURCE_DIR)/parallel/StdMpi.cc
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-StdMpi.lo `test -f '$(SOURCE_DIR)/parallel/StdMpi.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/StdMpi.cc
libamdis_la-ParMetisPartitioner.lo: $(SOURCE_DIR)/parallel/ParMetisPartitioner.cc
@am__fastdepCXX_TRUE@ $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ParMetisPartitioner.lo -MD -MP -MF $(DEPDIR)/libamdis_la-ParMetisPartitioner.Tpo -c -o libamdis_la-ParMetisPartitioner.lo `test -f '$(SOURCE_DIR)/parallel/ParMetisPartitioner.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/ParMetisPartitioner.cc
@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libamdis_la-ParMetisPartitioner.Tpo $(DEPDIR)/libamdis_la-ParMetisPartitioner.Plo
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/parallel/ParMetisPartitioner.cc' object='libamdis_la-ParMetisPartitioner.lo' libtool=yes @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ParMetisPartitioner.lo `test -f '$(SOURCE_DIR)/parallel/ParMetisPartitioner.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/ParMetisPartitioner.cc
libamdis_la-MeshDistributor.lo: $(SOURCE_DIR)/parallel/MeshDistributor.cc
@am__fastdepCXX_TRUE@ $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-MeshDistributor.lo -MD -MP -MF $(DEPDIR)/libamdis_la-MeshDistributor.Tpo -c -o libamdis_la-MeshDistributor.lo `test -f '$(SOURCE_DIR)/parallel/MeshDistributor.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/MeshDistributor.cc
@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libamdis_la-MeshDistributor.Tpo $(DEPDIR)/libamdis_la-MeshDistributor.Plo
......@@ -978,41 +954,6 @@ libamdis_la-ElementObjectData.lo: $(SOURCE_DIR)/parallel/ElementObjectData.cc
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ElementObjectData.lo `test -f '$(SOURCE_DIR)/parallel/ElementObjectData.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/ElementObjectData.cc
libamdis_la-ConditionalEstimator.lo: $(PARALLEL_DIR)/ConditionalEstimator.cc
@am__fastdepCXX_TRUE@ $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ConditionalEstimator.lo -MD -MP -MF $(DEPDIR)/libamdis_la-ConditionalEstimator.Tpo -c -o libamdis_la-ConditionalEstimator.lo `test -f '$(PARALLEL_DIR)/ConditionalEstimator.cc' || echo '$(srcdir)/'`$(PARALLEL_DIR)/ConditionalEstimator.cc
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libamdis_la-ConditionalMarker.lo: $(PARALLEL_DIR)/ConditionalMarker.cc
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libamdis_la-ParallelProblem.lo: $(PARALLEL_DIR)/ParallelProblem.cc
@am__fastdepCXX_TRUE@ $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ParallelProblem.lo -MD -MP -MF $(DEPDIR)/libamdis_la-ParallelProblem.Tpo -c -o libamdis_la-ParallelProblem.lo `test -f '$(PARALLEL_DIR)/ParallelProblem.cc' || echo '$(srcdir)/'`$(PARALLEL_DIR)/ParallelProblem.cc
@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libamdis_la-ParallelProblem.Tpo $(DEPDIR)/libamdis_la-ParallelProblem.Plo
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libamdis_la-ParMetisPartitioner.lo: $(PARALLEL_DIR)/ParMetisPartitioner.cc
@am__fastdepCXX_TRUE@ $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ParMetisPartitioner.lo -MD -MP -MF $(DEPDIR)/libamdis_la-ParMetisPartitioner.Tpo -c -o libamdis_la-ParMetisPartitioner.lo `test -f '$(PARALLEL_DIR)/ParMetisPartitioner.cc' || echo '$(srcdir)/'`$(PARALLEL_DIR)/ParMetisPartitioner.cc
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libamdis_la-PollutionError.lo: $(PARALLEL_DIR)/PollutionError.cc
@am__fastdepCXX_TRUE@ $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-PollutionError.lo -MD -MP -MF $(DEPDIR)/libamdis_la-PollutionError.Tpo -c -o libamdis_la-PollutionError.lo `test -f '$(PARALLEL_DIR)/PollutionError.cc' || echo '$(srcdir)/'`$(PARALLEL_DIR)/PollutionError.cc
@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libamdis_la-PollutionError.Tpo $(DEPDIR)/libamdis_la-PollutionError.Plo
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libamdis_la-DOFIndexed.lo: $(SOURCE_DIR)/DOFIndexed.cc
@am__fastdepCXX_TRUE@ $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-DOFIndexed.lo -MD -MP -MF $(DEPDIR)/libamdis_la-DOFIndexed.Tpo -c -o libamdis_la-DOFIndexed.lo `test -f '$(SOURCE_DIR)/DOFIndexed.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/DOFIndexed.cc
@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libamdis_la-DOFIndexed.Tpo $(DEPDIR)/libamdis_la-DOFIndexed.Plo
......@@ -1146,6 +1087,13 @@ libamdis_la-ProblemInterpolVec.lo: $(SOURCE_DIR)/ProblemInterpolVec.cc
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ProblemInterpolVec.lo `test -f '$(SOURCE_DIR)/ProblemInterpolVec.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/ProblemInterpolVec.cc
libamdis_la-MacroInfo.lo: $(SOURCE_DIR)/MacroInfo.cc
@am__fastdepCXX_TRUE@ $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-MacroInfo.lo -MD -MP -MF $(DEPDIR)/libamdis_la-MacroInfo.Tpo -c -o libamdis_la-MacroInfo.lo `test -f '$(SOURCE_DIR)/MacroInfo.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/MacroInfo.cc
@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libamdis_la-MacroInfo.Tpo $(DEPDIR)/libamdis_la-MacroInfo.Plo
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libamdis_la-MacroReader.lo: $(SOURCE_DIR)/MacroReader.cc
@am__fastdepCXX_TRUE@ $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-MacroReader.lo -MD -MP -MF $(DEPDIR)/libamdis_la-MacroReader.Tpo -c -o libamdis_la-MacroReader.lo `test -f '$(SOURCE_DIR)/MacroReader.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/MacroReader.cc
@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libamdis_la-MacroReader.Tpo $(DEPDIR)/libamdis_la-MacroReader.Plo
......
AMDiS/src/CoarseningManager1d.cc
View file @ e8cfacab
......@@ -75,7 +75,7 @@ namespace AMDiS {
}
if (mesh->getNumberOfDOFs(CENTER) && !mesh->queryCoarseDOFs()) {
parent->setDOF(mesh->getNode(CENTER), mesh->getDOF(CENTER));
parent->setDOF(mesh->getNode(CENTER), mesh->getDof(CENTER));
}
/*--------------------------------------------------------------------------*/
......
AMDiS/src/CoarseningManager2d.cc
View file @ e8cfacab
......@@ -84,7 +84,7 @@ namespace AMDiS {
// get new dof on el at the midpoint of the coarsening edge
if (!el->getDOF(node + 2)) {
el->setDOF(node + 2, mesh->getDOF(EDGE));
el->setDOF(node + 2, mesh->getDof(EDGE));
if (neigh)
neigh->setDOF(node + 2, const_cast<int*>(el->getDOF(node + 2)));
}
......
AMDiS/src/CoarseningManager3d.cc
View file @ e8cfacab
......@@ -324,7 +324,7 @@ namespace AMDiS {
/****************************************************************************/
node = mesh->getNode(EDGE);
if (!(dof = const_cast<int*>( el->getDOF(node))))
dof = mesh->getDOF(EDGE);
dof = mesh->getDof(EDGE);
} else {
dof = NULL;
}
......
AMDiS/src/ConditionalEstimator.cc deleted 100644 → 0
View file @ f6559482
#include "ConditionalEstimator.h"
#include "ElInfo.h"
#include "PartitionElementData.h"
#include "Element.h"
#include "Traverse.h"
#include "mpi.h"
namespace AMDiS {
ConditionalEstimator::ConditionalEstimator(Estimator* decorated)
: decoratedEstimator_(decorated),
elementCount_(0),
row_(decorated ? decorated->getRow() : 0)
{
FUNCNAME("ConditionalEstimator::ConditionalEstimator(Estimator* decorated)");
if (decorated!=NULL) {
name = decorated->getName();
int swap;
int retVal =
Parameters::getGlobalParameter(0, name + "->estimate outer", "%d", &swap);
if (retVal > 0)
estimateOut = (bool)swap;
else
estimateOut = false;
}
}
double ConditionalEstimator::estimate(double ts)
{
if (decoratedEstimator_) {
double partition_sum = 0.0;
elementCount_ = 0;
decoratedEstimator_->init(ts);
mesh = decoratedEstimator_->getMesh();
traverseFlag = decoratedEstimator_->getTraverseFlag();
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1, traverseFlag);
while (elInfo) {
PartitionElementData *elData = dynamic_cast<PartitionElementData*>
(elInfo->getElement()->getElementData(PARTITION_ED));
TEST_EXIT_DBG(elInfo->getElement()->isLeaf())("element not leaf\n");
TEST_EXIT_DBG(elData)("no partition data on leaf element %d (rank %d)\n",
elInfo->getElement()->getIndex(),
MPI::COMM_WORLD.Get_rank());
PartitionStatus status = elData->getPartitionStatus();
if (status == IN || status == OVERLAP || (estimateOut && status==OUT))
decoratedEstimator_->estimateElement(elInfo);
else
elInfo->getElement()->setMark(0);
elInfo = stack.traverseNext(elInfo);
}
elInfo = stack.traverseFirst(mesh, -1, traverseFlag);
while (elInfo) {
PartitionElementData *elData = dynamic_cast<PartitionElementData*>
(elInfo->getElement()->getElementData(PARTITION_ED));
PartitionStatus status = elData->getPartitionStatus();
if (status == IN || status==OVERLAP || (estimateOut && status==OUT)) {
elementCount_++;
partition_sum += elInfo->getElement()->getEstimation(row_);
}
elInfo = stack.traverseNext(elInfo);
}
// !!! test !!!
double total_sum = 0.0;
MPI::COMM_WORLD.Allreduce(&partition_sum,
&total_sum,
1,
MPI_DOUBLE,
MPI_SUM);
decoratedEstimator_->setErrorSum(total_sum);
double total_max = 0.0;
est_max = decoratedEstimator_->getErrorMax();
MPI::COMM_WORLD.Allreduce(&est_max,
&total_max,
1,
MPI_DOUBLE,
MPI_MAX);
decoratedEstimator_->setErrorMax(total_max);
decoratedEstimator_->exit();
est_sum = decoratedEstimator_->getErrorSum();
est_max = decoratedEstimator_->getErrorMax();
// !!! test !!!
#if 0
decoratedEstimator_->exit();
est_sum = sqrt(partition_sum); //decoratedEstimator_->getErrorSum();
est_t_sum = decoratedEstimator_->getTimeEst();
est_max = decoratedEstimator_->getErrorMax();
#endif
// MSG("rank %d , estimate %e (total %e) elements %d (total %d)\n",
// MPI::COMM_WORLD.Get_rank(), est_sum, total_sum,
// elementCount_,
// mesh->getNumberOfLeaves());
return est_sum;
} else {
return 0.0;
}
}
}
AMDiS/src/ConditionalMarker.cc deleted 100644 → 0
View file @ f6559482
#include "ConditionalMarker.h"
namespace AMDiS
{
ConditionalMarker::ConditionalMarker(const std::string name_,
int row,
Marker *decoratedMarker,
int globalCoarseGridLevel,
int localCoarseGridLevel)
: Marker(name_, row),
decoratedMarker_(decoratedMarker),
globalCoarseGridLevel_(globalCoarseGridLevel),
localCoarseGridLevel_(localCoarseGridLevel)
{
if (decoratedMarker != NULL)
name = decoratedMarker->getName();
else
std::cout << "no decorated Marker, mark outer path is" << name << "->mark outer" << std::endl;
int swap;
int retVal = Parameters::getGlobalParameter(0, name + "->mark outer", "%d", &swap);
if (retVal>0)
markOuter = (bool)swap;
else
markOuter = false;
MSG("markOuter:" + markOuter);
}
void ConditionalMarker::initMarking(AdaptInfo *adaptInfo, Mesh *mesh)
{
if (decoratedMarker_)
decoratedMarker_->initMarking(adaptInfo, mesh);
}
void ConditionalMarker::finishMarking(AdaptInfo *adaptInfo)
{
if (decoratedMarker_) {
int tmp = decoratedMarker_->getElMarkRefine();
MPI::COMM_WORLD.Allreduce(&tmp,
&elMarkRefine,
1,
MPI_INT,
MPI_SUM);
tmp = decoratedMarker_->getElMarkCoarsen();
MPI::COMM_WORLD.Allreduce(&tmp,
&elMarkCoarsen,
1,
MPI_INT,
MPI_SUM);
decoratedMarker_->finishMarking(adaptInfo);
}
}
void ConditionalMarker::markElement(AdaptInfo *adaptInfo, ElInfo *elInfo)
{
FUNCNAME("ConditionalMarker::markElement()");
if (decoratedMarker_) {
PartitionElementData *elData =
dynamic_cast<PartitionElementData*>(elInfo->getElement()->
getElementData(PARTITION_ED));
TEST_EXIT_DBG(elData)("no partition data\n");
decoratedMarker_->markElement(adaptInfo, elInfo);
if (!markOuter && elData->getPartitionStatus() == OUT) {
Element *element = elInfo->getElement();
if (element->getMark() > 0)
element->setMark(0);
}
int minLevel =
elData->getPartitionStatus() != OUT ?
localCoarseGridLevel_ :
globalCoarseGridLevel_;
if (elData->getLevel() + elInfo->getElement()->getMark() < minLevel)
elInfo->getElement()->setMark(-(elData->getLevel() - minLevel));
}
}
}
AMDiS/src/ConditionalMarker.h deleted 100644 → 0
View file @ f6559482
// ============================================================================
// == ==
// == AMDiS - Adaptive multidimensional simulations ==
// == ==
// ============================================================================
// == ==
// == crystal growth group ==
// == ==
// == Stiftung caesar ==
// == Ludwig-Erhard-Allee 2 ==
// == 53175 Bonn ==
// == germany ==
// == ==
// ============================================================================
// == ==
// == http://www.caesar.de/cg/AMDiS ==
// == ==