From 7083229fc8a31f2714c16059cd9c6f28cc54f7ab Mon Sep 17 00:00:00 2001
From: Thomas Witkowski <thomas.witkowski@gmx.de>
Date: Tue, 8 Dec 2009 16:21:48 +0000
Subject: [PATCH] Work on adaptivity in parallelization code.
---
AMDiS/bin/Makefile.am | 21 ++--
AMDiS/bin/Makefile.in | 58 +++++------
AMDiS/libtool | 66 ++++++-------
AMDiS/src/AMDiS.h | 2 +-
AMDiS/src/CoarseningManager.cc | 27 ++---
AMDiS/src/Mesh.cc | 57 ++++++-----
AMDiS/src/Mesh.h | 23 ++++-
AMDiS/src/MeshStructure.cc | 93 ++++++++---------
AMDiS/src/MeshStructure.h | 63 ++++++------
AMDiS/src/MeshStructure_ED.h | 43 ++++----
AMDiS/src/ParallelDomainBase.cc | 165 +++++++++++--------------------
AMDiS/src/ParallelDomainBase.h | 22 +++--
AMDiS/src/ParallelDomainScal.cc | 62 ------------
AMDiS/src/ParallelDomainScal.h | 63 ------------
AMDiS/src/RefinementManager.cc | 13 ++-
AMDiS/src/RefinementManager2d.cc | 3 +-
16 files changed, 312 insertions(+), 469 deletions(-)
delete mode 100644 AMDiS/src/ParallelDomainScal.cc
delete mode 100644 AMDiS/src/ParallelDomainScal.h
diff --git a/AMDiS/bin/Makefile.am b/AMDiS/bin/Makefile.am
index 62593ec7..2dd03c77 100644
--- a/AMDiS/bin/Makefile.am
+++ b/AMDiS/bin/Makefile.am
@@ -14,8 +14,6 @@ if USE_PARALLEL_AMDIS
PARALLEL_AMDIS_SOURCES = \
$(PARALLEL_DIR)/ConditionalEstimator.h $(PARALLEL_DIR)/ConditionalEstimator.cc \
$(PARALLEL_DIR)/ConditionalMarker.h \
- $(PARALLEL_DIR)/MeshStructure.h $(PARALLEL_DIR)/MeshStructure.cc \
- $(PARALLEL_DIR)/MeshStructure_ED.h \
$(PARALLEL_DIR)/ParallelError.h $(PARALLEL_DIR)/ParallelError.hh \
$(PARALLEL_DIR)/ParallelProblem.h $(PARALLEL_DIR)/ParallelProblem.cc \
$(PARALLEL_DIR)/ParMetisPartitioner.h $(PARALLEL_DIR)/ParMetisPartitioner.cc \
@@ -30,7 +28,6 @@ endif
if USE_PARALLEL_DOMAIN_AMDIS
PARALLEL_AMDIS_SOURCES += \
$(PARALLEL_DIR)/ParallelDomainBase.h $(PARALLEL_DIR)/ParallelDomainBase.cc \
- $(PARALLEL_DIR)/ParallelDomainScal.h $(PARALLEL_DIR)/ParallelDomainScal.cc \
$(PARALLEL_DIR)/ParallelDomainVec.h $(PARALLEL_DIR)/ParallelDomainVec.cc
libamdis_la_CXXFLAGS += -DHAVE_PARALLEL_DOMAIN_AMDIS=1
AMDIS_INCLUDES += -I$(PETSC_DIR)/include -I$(PETSC_DIR)/$(PETSC_ARCH)/include
@@ -121,6 +118,8 @@ $(SOURCE_DIR)/ElInfo.cc \
$(SOURCE_DIR)/ElInfoStack.h $(SOURCE_DIR)/ElInfoStack.cc \
$(SOURCE_DIR)/Operator.h $(SOURCE_DIR)/Operator.cc \
$(SOURCE_DIR)/Mesh.cc \
+$(SOURCE_DIR)/MeshStructure.h $(SOURCE_DIR)/MeshStructure.cc \
+$(SOURCE_DIR)/MeshStructure_ED.h \
$(SOURCE_DIR)/AMDiS.h \
$(SOURCE_DIR)/AdaptStationary.h $(SOURCE_DIR)/AdaptStationary.cc \
$(SOURCE_DIR)/AdaptInstationary.h $(SOURCE_DIR)/AdaptInstationary.cc \
@@ -130,9 +129,19 @@ $(SOURCE_DIR)/Boundary.h \
$(SOURCE_DIR)/ITL_Solver.h \
$(SOURCE_DIR)/CoarseningManager.h \
$(SOURCE_DIR)/CoarseningManager1d.h $(SOURCE_DIR)/CoarseningManager2d.h $(SOURCE_DIR)/CoarseningManager3d.h \
-$(SOURCE_DIR)/DOFAdmin.h $(SOURCE_DIR)/DOFIterator.h $(SOURCE_DIR)/DOFMatrix.h $(SOURCE_DIR)/DOFVector.h $(SOURCE_DIR)/DOFVector.hh $(SOURCE_DIR)/DOFVector.cc $(SOURCE_DIR)/Element.h $(SOURCE_DIR)/ElementConnection.h \
-$(SOURCE_DIR)/ElInfo.h $(SOURCE_DIR)/ElInfo1d.h $(SOURCE_DIR)/ElInfo2d.h $(SOURCE_DIR)/ElInfo3d.h $(SOURCE_DIR)/Error.h \
-$(SOURCE_DIR)/Error.hh $(SOURCE_DIR)/Estimator.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)/DOFAdmin.h \
+$(SOURCE_DIR)/DOFIterator.h \
+$(SOURCE_DIR)/DOFMatrix.h \
+$(SOURCE_DIR)/DOFVector.h $(SOURCE_DIR)/DOFVector.hh $(SOURCE_DIR)/DOFVector.cc \
+$(SOURCE_DIR)/Element.h $(SOURCE_DIR)/ElementConnection.h \
+$(SOURCE_DIR)/ElInfo.h $(SOURCE_DIR)/ElInfo1d.h $(SOURCE_DIR)/ElInfo2d.h $(SOURCE_DIR)/ElInfo3d.h \
+$(SOURCE_DIR)/Error.h $(SOURCE_DIR)/Error.hh \
+$(SOURCE_DIR)/Estimator.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)/UmfPackSolver.hh \
$(SOURCE_DIR)/Lagrange.h $(SOURCE_DIR)/Line.h \
$(SOURCE_DIR)/MacroElement.h $(SOURCE_DIR)/MacroWriter.h \
diff --git a/AMDiS/bin/Makefile.in b/AMDiS/bin/Makefile.in
index aeed7614..1ef135b2 100644
--- a/AMDiS/bin/Makefile.in
+++ b/AMDiS/bin/Makefile.in
@@ -39,7 +39,6 @@ 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@ $(PARALLEL_DIR)/ParallelDomainBase.h $(PARALLEL_DIR)/ParallelDomainBase.cc \
-@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(PARALLEL_DIR)/ParallelDomainScal.h $(PARALLEL_DIR)/ParallelDomainScal.cc \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(PARALLEL_DIR)/ParallelDomainVec.h $(PARALLEL_DIR)/ParallelDomainVec.cc
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_3 = -DHAVE_PARALLEL_DOMAIN_AMDIS=1
@@ -75,16 +74,11 @@ LTLIBRARIES = $(lib_LTLIBRARIES)
libamdis_la_LIBADD =
am__libamdis_la_SOURCES_DIST = $(PARALLEL_DIR)/ParallelDomainBase.h \
$(PARALLEL_DIR)/ParallelDomainBase.cc \
- $(PARALLEL_DIR)/ParallelDomainScal.h \
- $(PARALLEL_DIR)/ParallelDomainScal.cc \
$(PARALLEL_DIR)/ParallelDomainVec.h \
$(PARALLEL_DIR)/ParallelDomainVec.cc \
$(PARALLEL_DIR)/ConditionalEstimator.h \
$(PARALLEL_DIR)/ConditionalEstimator.cc \
$(PARALLEL_DIR)/ConditionalMarker.h \
- $(PARALLEL_DIR)/MeshStructure.h \
- $(PARALLEL_DIR)/MeshStructure.cc \
- $(PARALLEL_DIR)/MeshStructure_ED.h \
$(PARALLEL_DIR)/ParallelError.h \
$(PARALLEL_DIR)/ParallelError.hh \
$(PARALLEL_DIR)/ParallelProblem.h \
@@ -151,7 +145,9 @@ am__libamdis_la_SOURCES_DIST = $(PARALLEL_DIR)/ParallelDomainBase.h \
$(SOURCE_DIR)/ElementFileWriter.cc $(SOURCE_DIR)/ElInfo.cc \
$(SOURCE_DIR)/ElInfoStack.h $(SOURCE_DIR)/ElInfoStack.cc \
$(SOURCE_DIR)/Operator.h $(SOURCE_DIR)/Operator.cc \
- $(SOURCE_DIR)/Mesh.cc $(SOURCE_DIR)/AMDiS.h \
+ $(SOURCE_DIR)/Mesh.cc $(SOURCE_DIR)/MeshStructure.h \
+ $(SOURCE_DIR)/MeshStructure.cc \
+ $(SOURCE_DIR)/MeshStructure_ED.h $(SOURCE_DIR)/AMDiS.h \
$(SOURCE_DIR)/AdaptStationary.h \
$(SOURCE_DIR)/AdaptStationary.cc \
$(SOURCE_DIR)/AdaptInstationary.h \
@@ -232,12 +228,10 @@ am__libamdis_la_SOURCES_DIST = $(PARALLEL_DIR)/ParallelDomainBase.h \
$(SOURCE_DIR)/parareal/AdaptParaReal.h \
$(SOURCE_DIR)/parareal/AdaptParaReal.cc
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__objects_1 = libamdis_la-ParallelDomainBase.lo \
-@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-ParallelDomainScal.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-ParallelDomainVec.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-MeshStructure.lo \
@USE_PARALLEL_AMDIS_TRUE@ libamdis_la-ParallelProblem.lo \
@USE_PARALLEL_AMDIS_TRUE@ libamdis_la-ParMetisPartitioner.lo \
@USE_PARALLEL_AMDIS_TRUE@ $(am__objects_1)
@@ -264,7 +258,8 @@ am_libamdis_la_OBJECTS = $(am__objects_2) libamdis_la-DOFIndexed.lo \
libamdis_la-RobinBC.lo libamdis_la-FileWriter.lo \
libamdis_la-ElementFileWriter.lo libamdis_la-ElInfo.lo \
libamdis_la-ElInfoStack.lo libamdis_la-Operator.lo \
- libamdis_la-Mesh.lo libamdis_la-AdaptStationary.lo \
+ libamdis_la-Mesh.lo libamdis_la-MeshStructure.lo \
+ libamdis_la-AdaptStationary.lo \
libamdis_la-AdaptInstationary.lo libamdis_la-DOFVector.lo \
libamdis_la-Estimator.lo libamdis_la-ProblemInstat.lo \
libamdis_la-ProblemNonLin.lo libamdis_la-NonLinUpdater.lo \
@@ -465,9 +460,6 @@ libamdis_la_CXXFLAGS = $(am__append_1) $(am__append_3) $(am__append_5) \
@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)/MeshStructure.h \
-@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/MeshStructure.cc \
-@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/MeshStructure_ED.h \
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/ParallelError.h \
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/ParallelError.hh \
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/ParallelProblem.h \
@@ -535,6 +527,8 @@ $(SOURCE_DIR)/ElInfo.cc \
$(SOURCE_DIR)/ElInfoStack.h $(SOURCE_DIR)/ElInfoStack.cc \
$(SOURCE_DIR)/Operator.h $(SOURCE_DIR)/Operator.cc \
$(SOURCE_DIR)/Mesh.cc \
+$(SOURCE_DIR)/MeshStructure.h $(SOURCE_DIR)/MeshStructure.cc \
+$(SOURCE_DIR)/MeshStructure_ED.h \
$(SOURCE_DIR)/AMDiS.h \
$(SOURCE_DIR)/AdaptStationary.h $(SOURCE_DIR)/AdaptStationary.cc \
$(SOURCE_DIR)/AdaptInstationary.h $(SOURCE_DIR)/AdaptInstationary.cc \
@@ -544,9 +538,19 @@ $(SOURCE_DIR)/Boundary.h \
$(SOURCE_DIR)/ITL_Solver.h \
$(SOURCE_DIR)/CoarseningManager.h \
$(SOURCE_DIR)/CoarseningManager1d.h $(SOURCE_DIR)/CoarseningManager2d.h $(SOURCE_DIR)/CoarseningManager3d.h \
-$(SOURCE_DIR)/DOFAdmin.h $(SOURCE_DIR)/DOFIterator.h $(SOURCE_DIR)/DOFMatrix.h $(SOURCE_DIR)/DOFVector.h $(SOURCE_DIR)/DOFVector.hh $(SOURCE_DIR)/DOFVector.cc $(SOURCE_DIR)/Element.h $(SOURCE_DIR)/ElementConnection.h \
-$(SOURCE_DIR)/ElInfo.h $(SOURCE_DIR)/ElInfo1d.h $(SOURCE_DIR)/ElInfo2d.h $(SOURCE_DIR)/ElInfo3d.h $(SOURCE_DIR)/Error.h \
-$(SOURCE_DIR)/Error.hh $(SOURCE_DIR)/Estimator.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)/DOFAdmin.h \
+$(SOURCE_DIR)/DOFIterator.h \
+$(SOURCE_DIR)/DOFMatrix.h \
+$(SOURCE_DIR)/DOFVector.h $(SOURCE_DIR)/DOFVector.hh $(SOURCE_DIR)/DOFVector.cc \
+$(SOURCE_DIR)/Element.h $(SOURCE_DIR)/ElementConnection.h \
+$(SOURCE_DIR)/ElInfo.h $(SOURCE_DIR)/ElInfo1d.h $(SOURCE_DIR)/ElInfo2d.h $(SOURCE_DIR)/ElInfo3d.h \
+$(SOURCE_DIR)/Error.h $(SOURCE_DIR)/Error.hh \
+$(SOURCE_DIR)/Estimator.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)/UmfPackSolver.hh \
$(SOURCE_DIR)/Lagrange.h $(SOURCE_DIR)/Line.h \
$(SOURCE_DIR)/MacroElement.h $(SOURCE_DIR)/MacroWriter.h \
@@ -768,7 +772,6 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Operator.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-ParallelDomainBase.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ParallelDomainScal.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ParallelDomainVec.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@
@@ -848,13 +851,6 @@ libamdis_la-ParallelDomainBase.lo: $(PARALLEL_DIR)/ParallelDomainBase.cc
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ParallelDomainBase.lo `test -f '$(PARALLEL_DIR)/ParallelDomainBase.cc' || echo '$(srcdir)/'`$(PARALLEL_DIR)/ParallelDomainBase.cc
-libamdis_la-ParallelDomainScal.lo: $(PARALLEL_DIR)/ParallelDomainScal.cc
-@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ParallelDomainScal.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ParallelDomainScal.Tpo" -c -o libamdis_la-ParallelDomainScal.lo `test -f '$(PARALLEL_DIR)/ParallelDomainScal.cc' || echo '$(srcdir)/'`$(PARALLEL_DIR)/ParallelDomainScal.cc; \
-@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-ParallelDomainScal.Tpo" "$(DEPDIR)/libamdis_la-ParallelDomainScal.Plo"; else rm -f "$(DEPDIR)/libamdis_la-ParallelDomainScal.Tpo"; exit 1; fi
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(PARALLEL_DIR)/ParallelDomainScal.cc' object='libamdis_la-ParallelDomainScal.lo' libtool=yes @AMDEPBACKSLASH@
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ParallelDomainScal.lo `test -f '$(PARALLEL_DIR)/ParallelDomainScal.cc' || echo '$(srcdir)/'`$(PARALLEL_DIR)/ParallelDomainScal.cc
-
libamdis_la-ParallelDomainVec.lo: $(PARALLEL_DIR)/ParallelDomainVec.cc
@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ParallelDomainVec.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ParallelDomainVec.Tpo" -c -o libamdis_la-ParallelDomainVec.lo `test -f '$(PARALLEL_DIR)/ParallelDomainVec.cc' || echo '$(srcdir)/'`$(PARALLEL_DIR)/ParallelDomainVec.cc; \
@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-ParallelDomainVec.Tpo" "$(DEPDIR)/libamdis_la-ParallelDomainVec.Plo"; else rm -f "$(DEPDIR)/libamdis_la-ParallelDomainVec.Tpo"; exit 1; fi
@@ -869,13 +865,6 @@ libamdis_la-ConditionalEstimator.lo: $(PARALLEL_DIR)/ConditionalEstimator.cc
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ConditionalEstimator.lo `test -f '$(PARALLEL_DIR)/ConditionalEstimator.cc' || echo '$(srcdir)/'`$(PARALLEL_DIR)/ConditionalEstimator.cc
-libamdis_la-MeshStructure.lo: $(PARALLEL_DIR)/MeshStructure.cc
-@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-MeshStructure.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-MeshStructure.Tpo" -c -o libamdis_la-MeshStructure.lo `test -f '$(PARALLEL_DIR)/MeshStructure.cc' || echo '$(srcdir)/'`$(PARALLEL_DIR)/MeshStructure.cc; \
-@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-MeshStructure.Tpo" "$(DEPDIR)/libamdis_la-MeshStructure.Plo"; else rm -f "$(DEPDIR)/libamdis_la-MeshStructure.Tpo"; exit 1; fi
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(PARALLEL_DIR)/MeshStructure.cc' object='libamdis_la-MeshStructure.lo' libtool=yes @AMDEPBACKSLASH@
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-MeshStructure.lo `test -f '$(PARALLEL_DIR)/MeshStructure.cc' || echo '$(srcdir)/'`$(PARALLEL_DIR)/MeshStructure.cc
-
libamdis_la-ParallelProblem.lo: $(PARALLEL_DIR)/ParallelProblem.cc
@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --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)/'`$(PARALLEL_DIR)/ParallelProblem.cc; \
@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-ParallelProblem.Tpo" "$(DEPDIR)/libamdis_la-ParallelProblem.Plo"; else rm -f "$(DEPDIR)/libamdis_la-ParallelProblem.Tpo"; exit 1; fi
@@ -1170,6 +1159,13 @@ libamdis_la-Mesh.lo: $(SOURCE_DIR)/Mesh.cc
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-Mesh.lo `test -f '$(SOURCE_DIR)/Mesh.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/Mesh.cc
+libamdis_la-MeshStructure.lo: $(SOURCE_DIR)/MeshStructure.cc
+@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-MeshStructure.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-MeshStructure.Tpo" -c -o libamdis_la-MeshStructure.lo `test -f '$(SOURCE_DIR)/MeshStructure.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/MeshStructure.cc; \
+@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-MeshStructure.Tpo" "$(DEPDIR)/libamdis_la-MeshStructure.Plo"; else rm -f "$(DEPDIR)/libamdis_la-MeshStructure.Tpo"; exit 1; fi
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/MeshStructure.cc' object='libamdis_la-MeshStructure.lo' libtool=yes @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-MeshStructure.lo `test -f '$(SOURCE_DIR)/MeshStructure.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/MeshStructure.cc
+
libamdis_la-AdaptStationary.lo: $(SOURCE_DIR)/AdaptStationary.cc
@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-AdaptStationary.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-AdaptStationary.Tpo" -c -o libamdis_la-AdaptStationary.lo `test -f '$(SOURCE_DIR)/AdaptStationary.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/AdaptStationary.cc; \
@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-AdaptStationary.Tpo" "$(DEPDIR)/libamdis_la-AdaptStationary.Plo"; else rm -f "$(DEPDIR)/libamdis_la-AdaptStationary.Tpo"; exit 1; fi
diff --git a/AMDiS/libtool b/AMDiS/libtool
index 702bb183..5a2f54ef 100755
--- a/AMDiS/libtool
+++ b/AMDiS/libtool
@@ -30,10 +30,10 @@
# the same distribution terms that you use for the rest of that program.
# A sed program that does not truncate output.
-SED="/usr/bin/sed"
+SED="/bin/sed"
# Sed that helps us avoid accidentally triggering echo(1) options like -n.
-Xsed="/usr/bin/sed -e 1s/^X//"
+Xsed="/bin/sed -e 1s/^X//"
# The HP-UX ksh and POSIX shell print the target directory to stdout
# if CDPATH is set.
@@ -44,7 +44,7 @@ available_tags=" CXX F77"
# ### BEGIN LIBTOOL CONFIG
-# Libtool was configured on host deimos102:
+# Libtool was configured on host NWRW15:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -66,12 +66,12 @@ fast_install=yes
# The host system.
host_alias=
-host=x86_64-unknown-linux-gnu
+host=i686-pc-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=x86_64-unknown-linux-gnu
+build=i686-pc-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
@@ -82,25 +82,25 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="/usr/lib/openmpi/1.3.2-gcc//bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+CC="/usr/lib/openmpi/1.3.2-gcc//bin/mpicc"
# Is the compiler the GNU C compiler?
with_gcc=yes
-gcc_dir=`gcc -print-file-name=. | /usr/bin/sed 's,/\.$,,'`
+gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
gcc_ver=`gcc -dumpversion`
# An ERE matcher.
EGREP="grep -E"
# The linker used to build libraries.
-LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
+LD="/usr/bin/ld"
# Whether we need hard or soft links.
LN_S="ln -s"
@@ -328,10 +328,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
link_all_deplibs=unknown
# Compile-time system search path for libraries
-sys_lib_search_path_spec=`echo "/lib64 /usr/lib64 /usr/local/lib64" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+sys_lib_search_path_spec=`echo " /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../ /lib/i386-redhat-linux/4.1.2/ /lib/ /usr/lib/i386-redhat-linux/4.1.2/ /usr/lib/" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/x86_64-suse-linux/lib /usr/local/lib64 /usr/local/lib /opt/kde3/lib64 /opt/kde3/lib /opt/gnome/lib64 /opt/gnome/lib /lib64 /lib /usr/lib64 /usr/lib /opt/cluster/intel/cce/9.1.042/lib /opt/cluster/intel/fce/9.1.036/lib /opt/cluster/Pathscale3.0/lib/2.9.99 /opt/cluster/Pathscale3.0/lib/2.9.99/32 /work/licsoft/compilers/pgi/linux86-64/6.2/lib /work/licsoft/compilers/pgi/linux86-64/6.2/libso "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib /usr/lib/qt4/lib "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
@@ -6763,7 +6763,7 @@ build_old_libs=`case $build_libtool_libs in yes) $echo no;; *) $echo yes;; esac`
# End:
# ### BEGIN LIBTOOL TAG CONFIG: CXX
-# Libtool was configured on host deimos102:
+# Libtool was configured on host NWRW15:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -6785,12 +6785,12 @@ fast_install=yes
# The host system.
host_alias=
-host=x86_64-unknown-linux-gnu
+host=i686-pc-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=x86_64-unknown-linux-gnu
+build=i686-pc-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
@@ -6801,25 +6801,25 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="/usr/lib/openmpi/1.3.2-gcc//bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpiCC"
+CC="/usr/lib/openmpi/1.3.2-gcc//bin/mpiCC"
# Is the compiler the GNU C compiler?
with_gcc=yes
-gcc_dir=`gcc -print-file-name=. | /usr/bin/sed 's,/\.$,,'`
+gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
gcc_ver=`gcc -dumpversion`
# An ERE matcher.
EGREP="grep -E"
# The linker used to build libraries.
-LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
+LD="/usr/bin/ld"
# Whether we need hard or soft links.
LN_S="ln -s"
@@ -6948,11 +6948,11 @@ striplib="strip --strip-unneeded"
# Dependencies to place before the objects being linked to create a
# shared library.
-predep_objects=`echo "/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/crti.o /usr/lib64/gcc/x86_64-suse-linux/4.1.2/crtbeginS.o" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+predep_objects=`echo "/usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crti.o /usr/lib/gcc/i386-redhat-linux/4.1.2/crtbeginS.o" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Dependencies to place after the objects being linked to create a
# shared library.
-postdep_objects=`echo "/usr/lib64/gcc/x86_64-suse-linux/4.1.2/crtendS.o /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/crtn.o" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+postdep_objects=`echo "/usr/lib/gcc/i386-redhat-linux/4.1.2/crtendS.o /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crtn.o" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Dependencies to place before the objects being linked to create a
# shared library.
@@ -6960,11 +6960,11 @@ predeps=""
# Dependencies to place after the objects being linked to create a
# shared library.
-postdeps="-lmpi_cxx -lmpi -lopen-rte -lopen-pal -libverbs -lrt -lnuma -ldl -lnsl -lutil -ldl -lstdc++ -lm -lgcc_s -lpthread -lc -lgcc_s"
+postdeps="-lmpi_cxx -lmpi -lopen-rte -lopen-pal -ldl -lnsl -lutil -ldl -lstdc++ -lm -lgcc_s -lpthread -lc -lgcc_s"
# The library search path used internally by the compiler when linking
# a shared library.
-compiler_lib_search_path=`echo "-L/usr/lib64 -L/licsoft/libraries/openmpi/1.2.6/64bit/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2 -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../.." | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+compiler_lib_search_path=`echo "-L/usr/lib/openmpi/1.3.2-gcc/lib -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2/../../.." | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Method to check whether dependent libraries are shared objects.
deplibs_check_method="pass_all"
@@ -7044,10 +7044,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
link_all_deplibs=unknown
# Compile-time system search path for libraries
-sys_lib_search_path_spec=`echo "/lib64 /usr/lib64 /usr/local/lib64" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+sys_lib_search_path_spec=`echo " /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../ /lib/i386-redhat-linux/4.1.2/ /lib/ /usr/lib/i386-redhat-linux/4.1.2/ /usr/lib/" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/x86_64-suse-linux/lib /usr/local/lib64 /usr/local/lib /opt/kde3/lib64 /opt/kde3/lib /opt/gnome/lib64 /opt/gnome/lib /lib64 /lib /usr/lib64 /usr/lib /opt/cluster/intel/cce/9.1.042/lib /opt/cluster/intel/fce/9.1.036/lib /opt/cluster/Pathscale3.0/lib/2.9.99 /opt/cluster/Pathscale3.0/lib/2.9.99/32 /work/licsoft/compilers/pgi/linux86-64/6.2/lib /work/licsoft/compilers/pgi/linux86-64/6.2/libso "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib /usr/lib/qt4/lib "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
@@ -7071,7 +7071,7 @@ include_expsyms=""
# ### BEGIN LIBTOOL TAG CONFIG: F77
-# Libtool was configured on host deimos102:
+# Libtool was configured on host NWRW15:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -7093,12 +7093,12 @@ fast_install=yes
# The host system.
host_alias=
-host=x86_64-unknown-linux-gnu
+host=i686-pc-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=x86_64-unknown-linux-gnu
+build=i686-pc-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
@@ -7109,7 +7109,7 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="/usr/lib/openmpi/1.3.2-gcc//bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
@@ -7118,16 +7118,16 @@ LTCFLAGS="-g -O2"
CC="g77"
# Is the compiler the GNU C compiler?
-with_gcc=
+with_gcc=yes
-gcc_dir=`gcc -print-file-name=. | /usr/bin/sed 's,/\.$,,'`
+gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
gcc_ver=`gcc -dumpversion`
# An ERE matcher.
EGREP="grep -E"
# The linker used to build libraries.
-LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
+LD="/usr/bin/ld"
# Whether we need hard or soft links.
LN_S="ln -s"
@@ -7355,10 +7355,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
link_all_deplibs=unknown
# Compile-time system search path for libraries
-sys_lib_search_path_spec=`echo "/lib64 /usr/lib64 /usr/local/lib64" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+sys_lib_search_path_spec=`echo " /usr/lib/gcc/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../i386-redhat-linux/lib/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../ /lib/i386-redhat-linux/3.4.6/ /lib/ /usr/lib/i386-redhat-linux/3.4.6/ /usr/lib/" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/x86_64-suse-linux/lib /usr/local/lib64 /usr/local/lib /opt/kde3/lib64 /opt/kde3/lib /opt/gnome/lib64 /opt/gnome/lib /lib64 /lib /usr/lib64 /usr/lib /opt/cluster/intel/cce/9.1.042/lib /opt/cluster/intel/fce/9.1.036/lib /opt/cluster/Pathscale3.0/lib/2.9.99 /opt/cluster/Pathscale3.0/lib/2.9.99/32 /work/licsoft/compilers/pgi/linux86-64/6.2/lib /work/licsoft/compilers/pgi/linux86-64/6.2/libso "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib /usr/lib/qt4/lib "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
diff --git a/AMDiS/src/AMDiS.h b/AMDiS/src/AMDiS.h
index f0d73e1a..f102b77c 100644
--- a/AMDiS/src/AMDiS.h
+++ b/AMDiS/src/AMDiS.h
@@ -49,6 +49,7 @@
#include "Marker.h"
#include "MatrixVector.h"
#include "Mesh.h"
+#include "MeshStructure.h"
#include "ComponentTraverseInfo.h"
#include "Newton.h"
#include "NewtonS.h"
@@ -94,7 +95,6 @@
#include "parareal/AdaptParaReal.h"
#if HAVE_PARALLEL_DOMAIN_AMDIS
-#include "ParallelDomainScal.h"
#include "ParallelDomainVec.h"
#endif
diff --git a/AMDiS/src/CoarseningManager.cc b/AMDiS/src/CoarseningManager.cc
index 51f34507..1b31a92a 100644
--- a/AMDiS/src/CoarseningManager.cc
+++ b/AMDiS/src/CoarseningManager.cc
@@ -6,14 +6,9 @@
#include "MacroElement.h"
#include "RCNeighbourList.h"
#include "FixVec.h"
-//#include "PeriodicBC.h"
namespace AMDiS {
- /****************************************************************************/
- /* tries to coarsen every element of mesh at least mark times */
- /****************************************************************************/
-
Flag CoarseningManager::globalCoarsen(Mesh *aMesh, int mark)
{
if (mark >= 0)
@@ -50,12 +45,6 @@ namespace AMDiS {
}
}
-
- /****************************************************************************/
- /* cleanup_after_coarsen: */
- /* resets the element marks */
- /****************************************************************************/
-
void CoarseningManager::cleanUpAfterCoarsen()
{
TraverseStack stack;
@@ -67,15 +56,10 @@ namespace AMDiS {
}
}
- /****************************************************************************/
- /* coarsenMesh: */
- /* traversal routine for recursiv coarsening of a triangulation */
- /****************************************************************************/
-
Flag CoarseningManager::coarsenMesh(Mesh *aMesh)
{
mesh = aMesh;
- int n_elements = mesh->getNumberOfLeaves();
+ int nElements = mesh->getNumberOfLeaves();
spreadCoarsenMark();
@@ -95,9 +79,14 @@ namespace AMDiS {
cleanUpAfterCoarsen();
- n_elements -= mesh->getNumberOfLeaves();
+ nElements -= mesh->getNumberOfLeaves();
- return(n_elements ? MESH_COARSENED : Flag(0));
+ if (nElements != 0) {
+ aMesh->incChangeIndex();
+ return MESH_COARSENED;
+ } else {
+ return Flag(0);
+ }
}
}
diff --git a/AMDiS/src/Mesh.cc b/AMDiS/src/Mesh.cc
index 9d7fee4b..cb317eb5 100644
--- a/AMDiS/src/Mesh.cc
+++ b/AMDiS/src/Mesh.cc
@@ -92,6 +92,7 @@ namespace AMDiS {
elementIndex(-1),
initialized(false),
macroFileInfo(NULL),
+ changeIndex(0),
final_lambda(dimension, DEFAULT_VALUE, 0.0)
{
@@ -122,27 +123,22 @@ namespace AMDiS {
Element::deletedDOFs.clear();
for (std::deque<MacroElement*>::const_iterator it = macroElements.begin();
- it != macroElements.end();
- ++it) {
+ it != macroElements.end(); ++it) {
(*it)->getElement()->deleteElementDOFs();
delete *it;
}
Element::deletedDOFs.clear();
- if (macroFileInfo != NULL) {
- delete macroFileInfo;
- }
- if (elementPrototype) {
- delete elementPrototype;
- }
- if (elementDataPrototype) {
- delete elementDataPrototype;
- }
+ if (macroFileInfo != NULL)
+ delete macroFileInfo;
+ if (elementPrototype)
+ delete elementPrototype;
+ if (elementDataPrototype)
+ delete elementDataPrototype;
- for (int i = 0; i < static_cast<int>(admin.size()); i++) {
- delete admin[i];
- }
+ for (int i = 0; i < static_cast<int>(admin.size()); i++)
+ delete admin[i];
}
Mesh& Mesh::operator=(const Mesh& m)
@@ -200,8 +196,7 @@ namespace AMDiS {
// Go through all MacroElements of mesh m, and create for every a new
// MacroElement in this mesh.
for (std::deque<MacroElement*>::const_iterator it = m.macroElements.begin();
- it != m.macroElements.end();
- ++it, insertCounter++) {
+ it != m.macroElements.end(); ++it, insertCounter++) {
// Create new MacroElement.
MacroElement *el = new MacroElement(dim);
@@ -287,8 +282,7 @@ namespace AMDiS {
// Determine all dof owner macro elements.
for (std::deque<MacroElement*>::iterator macroIt = macroElements.begin();
- macroIt != macroElements.end();
- ++macroIt) {
+ macroIt != macroElements.end(); ++macroIt) {
elDofIter.reset((*macroIt)->getElement());
do {
dofsOwner[elDofIter.getDofPtr()].insert(*macroIt);
@@ -817,18 +811,22 @@ namespace AMDiS {
if (lambda[0] >= lambda[1]) {
c_el_info->fillElInfo(0, el_info);
c_lambda[0] = lambda[0] - lambda[1];
- c_lambda[1] = lambda[Tetrahedron::childVertex[(dynamic_cast<ElInfo3d*>(el_info))->
- getType()][0][1]];
- c_lambda[2] = lambda[Tetrahedron::childVertex[(dynamic_cast<ElInfo3d*>(el_info))->
- getType()][0][2]];
+ c_lambda[1] =
+ lambda[Tetrahedron::childVertex[(dynamic_cast<ElInfo3d*>(el_info))->
+ getType()][0][1]];
+ c_lambda[2] =
+ lambda[Tetrahedron::childVertex[(dynamic_cast<ElInfo3d*>(el_info))->
+ getType()][0][2]];
c_lambda[3] = 2.0 * lambda[1];
} else {
c_el_info->fillElInfo(1, el_info);
c_lambda[0] = lambda[1] - lambda[0];
- c_lambda[1] = lambda[Tetrahedron::childVertex[(dynamic_cast<ElInfo3d*>(el_info))->
- getType()][1][1]];
- c_lambda[2] = lambda[Tetrahedron::childVertex[(dynamic_cast<ElInfo3d*>(el_info))->
- getType()][1][2]];
+ c_lambda[1] =
+ lambda[Tetrahedron::childVertex[(dynamic_cast<ElInfo3d*>(el_info))->
+ getType()][1][1]];
+ c_lambda[2] =
+ lambda[Tetrahedron::childVertex[(dynamic_cast<ElInfo3d*>(el_info))->
+ getType()][1][2]];
c_lambda[3] = 2.0 * lambda[0];
}
}
@@ -917,13 +915,14 @@ namespace AMDiS {
diam[i] = w;
}
-
- int Mesh::newDOFFct1(ElInfo* ei) {
+ int Mesh::newDOFFct1(ElInfo* ei)
+ {
ei->getElement()->newDOFFct1(compressAdmin);
return 0;
}
- int Mesh::newDOFFct2(ElInfo* ei) {
+ int Mesh::newDOFFct2(ElInfo* ei)
+ {
ei->getElement()->newDOFFct2(compressAdmin);
return 0;
}
diff --git a/AMDiS/src/Mesh.h b/AMDiS/src/Mesh.h
index 3b7ad11d..2779915d 100644
--- a/AMDiS/src/Mesh.h
+++ b/AMDiS/src/Mesh.h
@@ -546,6 +546,18 @@ namespace AMDiS {
return macroFileInfo;
}
+ /// Increment the value of mesh change index, see \ref changeIndex.
+ inline void incChangeIndex()
+ {
+ changeIndex++;
+ }
+
+ /// Returns the mesh change index, see \ref changeIndex.
+ inline long getChangeIndex()
+ {
+ return changeIndex;
+ }
+
///
void clearMacroFileInfo();
@@ -773,11 +785,18 @@ namespace AMDiS {
std::map<BoundaryType, VertexVector*> periodicAssociations;
/** \brief
- * If the mesh has been created by reading a macro file, here
- * the information are stored about the content of the file.
+ * If the mesh has been created by reading a macro file, here the information are
+ * are stored about the content of the file.
*/
MacroInfo *macroFileInfo;
+ /** \brief
+ * This index is incremented every time the mesh is changed, e.g. by the refinement
+ * or the coarsening manager. It can be used by other object if the mesh has been
+ * changed by first copying this variable elsewhere and comparing its values.
+ */
+ long changeIndex;
+
protected:
/// for findElement-Fcts
DimVec<double> final_lambda;
diff --git a/AMDiS/src/MeshStructure.cc b/AMDiS/src/MeshStructure.cc
index 74d046b8..b79b10d1 100644
--- a/AMDiS/src/MeshStructure.cc
+++ b/AMDiS/src/MeshStructure.cc
@@ -10,38 +10,40 @@
namespace AMDiS {
- const int MeshStructure::unsignedLongSize_ = sizeof(unsigned long int) * 8;
+ const int MeshStructure::unsignedLongSize = sizeof(unsigned long int) * 8;
- void MeshStructure::insertElement(bool isLeaf) {
+ void MeshStructure::insertElement(bool isLeaf)
+ {
// overflow? -> next index
- if (pos_ >= unsignedLongSize_) {
- code_.push_back(currentCode_);
- pos_ = 0;
- currentCode_ = 0;
+ if (pos >= unsignedLongSize) {
+ code.push_back(currentCode);
+ pos = 0;
+ currentCode = 0;
}
// insert element in binary code
if (!isLeaf) {
unsigned long int one = 1;
- currentCode_ += (one << pos_);
+ currentCode += (one << pos);
}
- pos_++;
- numElements_++;
+ pos++;
+ nElements++;
}
void MeshStructure::clear()
{
- currentCode_ = 0;
- code_.resize(0);
- pos_ = 0;
- numElements_ = 0;
- currentElement_ = 0;
+ currentCode = 0;
+ code.resize(0);
+ pos = 0;
+ nElements = 0;
+ currentElement = 0;
}
void MeshStructure::init(Mesh *mesh)
{
clear();
+
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
while (elInfo) {
@@ -52,44 +54,50 @@ namespace AMDiS {
commit();
}
- void MeshStructure::reset() {
- currentIndex_ = 0;
- currentCode_ = code_[0];
- pos_ = 0;
- currentElement_ = 0;
+ void MeshStructure::reset()
+ {
+ currentIndex = 0;
+ currentCode = code[0];
+ pos = 0;
+ currentElement = 0;
}
bool MeshStructure::nextElement(MeshStructure *insert)
{
- if(insert) {
+ FUNCNAME("MeshStructure::nextElement()");
+
+ if (insert)
insert->insertElement(isLeafElement());
- }
- pos_++;
- currentElement_++;
+ pos++;
+ currentElement++;
- if(currentElement_ >= numElements_) return false;
+ if (currentElement >= nElements)
+ return false;
- if(pos_ >= unsignedLongSize_) {
- currentIndex_++;
- TEST_EXIT_DBG(currentIndex_ < static_cast<int>(code_.size()))
- ("end of structure reached\n");
- pos_ = 0;
- currentCode_ = code_[currentIndex_];
+ if (pos >= unsignedLongSize) {
+ currentIndex++;
+ TEST_EXIT_DBG(currentIndex < static_cast<int>(code.size()))
+ ("End of structure reached!\n");
+ pos = 0;
+ currentCode = code[currentIndex];
} else {
- currentCode_ >>= 1;
+ currentCode >>= 1;
}
+
return true;
}
bool MeshStructure::skipBranch(MeshStructure *insert)
{
+ FUNCNAME("MeshStructure::skipBranch()");
+
if (isLeafElement()) {
return nextElement(insert);
} else {
bool cont = nextElement(insert);
cont = skipBranch(insert); // left branch
- TEST_EXIT_DBG(cont)("invalid structure\n");
+ TEST_EXIT_DBG(cont)("Invalid structure!\n");
cont = skipBranch(insert); // righ branch
return cont;
}
@@ -99,6 +107,8 @@ namespace AMDiS {
MeshStructure *structure2,
MeshStructure *result)
{
+ FUNCNAME("MeshStructure::merge()");
+
result->clear();
structure1->reset();
structure2->reset();
@@ -118,7 +128,7 @@ namespace AMDiS {
cont2 = structure2->nextElement();
}
}
- TEST_EXIT_DBG(cont1 == cont2)("structures don't match\n");
+ TEST_EXIT_DBG(cont1 == cont2)("Structures don't match!\n");
cont = cont1;
}
@@ -132,23 +142,19 @@ namespace AMDiS {
{
FUNCNAME("MeshStructure::fitMeshToStructure()");
- TraverseStack stack;
- ElInfo *elInfo;
-
-
bool cont = true;
// decorate leaf data
reset();
- elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
while (elInfo) {
TEST_EXIT(cont)("unexpected structure code end!\n");
Element *element = elInfo->getElement();
- if (isLeafElement()) {
- TEST_EXIT(element->isLeaf())("mesh finer than code\n");
- };
+ if (isLeafElement())
+ TEST_EXIT_DBG(element->isLeaf())("mesh finer than code\n");
if (element->isLeaf() && !isLeafElement()) {
MeshStructure *structure = new MeshStructure();
@@ -159,11 +165,10 @@ namespace AMDiS {
if (checkPartition) {
PartitionElementData *partitionData = dynamic_cast<PartitionElementData*>
(element->getElementData(PARTITION_ED));
- TEST_EXIT(partitionData)("no partition element data\n");
+ TEST_EXIT_DBG(partitionData)("no partition element data\n");
PartitionStatus status = partitionData->getPartitionStatus();
- if ((debugMode == false) && (status == OUT || status == UNDEFINED)) {
+ if (debugMode == false && (status == OUT || status == UNDEFINED))
decorate = false;
- }
}
if (decorate) {
diff --git a/AMDiS/src/MeshStructure.h b/AMDiS/src/MeshStructure.h
index 92ef5a5c..d5f312f8 100644
--- a/AMDiS/src/MeshStructure.h
+++ b/AMDiS/src/MeshStructure.h
@@ -1,6 +1,6 @@
// ============================================================================
// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
+// == Amdis - Adaptive multidimensional simulations ==
// == ==
// ============================================================================
// == ==
@@ -32,11 +32,11 @@ namespace AMDiS {
{
public:
MeshStructure()
- : currentIndex_(0),
- currentCode_(0),
- pos_(0),
- currentElement_(0),
- numElements_(0)
+ : currentIndex(0),
+ currentCode(0),
+ pos(0),
+ currentElement(0),
+ nElements(0)
{}
void clear();
@@ -44,10 +44,10 @@ namespace AMDiS {
/// Creates a mesh structure code from a Mesh object by traversing it in preorder.
void init(Mesh *mesh);
- void init(const std::vector<unsigned long int>& code, int numElements)
+ void init(const std::vector<unsigned long int>& initCode, int n)
{
- code_ = code;
- numElements_ = numElements;
+ code = initCode;
+ nElements = n;
reset();
}
@@ -55,8 +55,8 @@ namespace AMDiS {
inline void commit()
{
- if (pos_ > 0)
- code_.push_back(currentCode_);
+ if (pos > 0)
+ code.push_back(currentCode);
reset();
}
@@ -68,25 +68,25 @@ namespace AMDiS {
inline bool isLeafElement()
{
- return (currentCode_ & 1) == 0;
+ return (currentCode & 1) == 0;
}
/** \brief
- * Merges a mesh structure code with its own mesh structure code. The
- * result overwrites the own mesh structure code.
+ * Merges a mesh structure code with its own mesh structure code. The result
+ * overwrites the own mesh structure code.
*/
- void merge(MeshStructure *structure)
+ void merge(MeshStructure *struc)
{
MeshStructure temp(*this);
- merge(&temp, structure, this);
+ merge(&temp, struc, this);
}
/** \brief
* Fits a given mesh to the mesh structure code.
*
- * \param debugMode In debugMode, the whole mesh is fitted to the mesh
- * structure code. Otherwise, the mesh is fitted only on the partition
- * of the current process.
+ * \param debugMode In debugMode, the whole mesh is fitted to the mesh structure
+ * code. Otherwise, the mesh is fitted only on the partition
+ * of the current process.
*/
void fitMeshToStructure(Mesh *mesh,
RefinementManager *manager,
@@ -114,24 +114,21 @@ namespace AMDiS {
/// Returns the mesh structure code.
inline const std::vector<unsigned long int>& getCode()
{
- return code_;
+ return code;
}
inline int getNumElements()
{
- return numElements_;
+ return nElements;
}
inline int getCurrentElement()
{
- return currentElement_;
+ return currentElement;
}
protected:
- /** \brief
- * Insert a new element to the structure code. Is used by the init
- * function.
- */
+ /// Insert a new element to the structure code. Is used by the init function.
void insertElement(bool isLeaf);
/// Merges two mesh structure codes to one structure code.
@@ -140,19 +137,19 @@ namespace AMDiS {
MeshStructure *result);
protected:
- std::vector<unsigned long int> code_;
+ std::vector<unsigned long int> code;
- int currentIndex_;
+ int currentIndex;
- unsigned long int currentCode_;
+ unsigned long int currentCode;
- int pos_;
+ int pos;
- int currentElement_;
+ int currentElement;
- int numElements_;
+ int nElements;
- static const int unsignedLongSize_;
+ static const int unsignedLongSize;
};
}
diff --git a/AMDiS/src/MeshStructure_ED.h b/AMDiS/src/MeshStructure_ED.h
index 5a74ee05..f086228a 100644
--- a/AMDiS/src/MeshStructure_ED.h
+++ b/AMDiS/src/MeshStructure_ED.h
@@ -19,8 +19,8 @@
/** \file MeshStructure.h */
-#ifndef AMDIS_MESHSTRUCTURE_ED_H
-#define AMDIS_MESHSTRUCTURE_ED_H
+#ifndef AMDIS_MESHSTRUCTUREED_H
+#define AMDIS_MESHSTRUCTUREED_H
#include <vector>
#include "MeshStructure.h"
@@ -36,12 +36,12 @@ namespace AMDiS {
public:
MeshStructure_ED(ElementData *decorated = NULL)
: ElementData(decorated),
- structure_(NULL)
+ structure(NULL)
{}
virtual ~MeshStructure_ED()
- {
- delete structure_;
+ {
+ delete structure;
}
virtual bool refineElementData(Element* parent,
@@ -49,31 +49,31 @@ namespace AMDiS {
Element* child2,
int elType)
{
- ElementData::refineElementData(parent, child1, child2, elType);
+ FUNCNAME("MeshStructureED::refineElementData()");
- structure_->reset();
+ ElementData::refineElementData(parent, child1, child2, elType);
- TEST_EXIT(structure_)("no structure\n");
+ structure->reset();
- TEST_EXIT(!structure_->isLeafElement())
- ("don't store leaf structures\n");
+ TEST_EXIT_DBG(structure)("No structure!\n");
+ TEST_EXIT_DBG(!structure->isLeafElement())("Don't store leaf structures!\n");
- structure_->nextElement();
+ structure->nextElement();
- if (!structure_->isLeafElement()) {
+ if (!structure->isLeafElement()) {
MeshStructure *structure1 = new MeshStructure();
- structure_->skipBranch(structure1);
+ structure->skipBranch(structure1);
structure1->commit();
MeshStructure_ED *elData1 = new MeshStructure_ED(child1->getElementData());
elData1->setStructure(structure1);
child1->setElementData(elData1);
} else {
- structure_->nextElement();
+ structure->nextElement();
}
- if (!structure_->isLeafElement()) {
+ if (!structure->isLeafElement()) {
MeshStructure *structure2 = new MeshStructure();
- structure_->skipBranch(structure2);
+ structure->skipBranch(structure2);
structure2->commit();
MeshStructure_ED *elData2 = new MeshStructure_ED(child2->getElementData());
elData2->setStructure(structure2);
@@ -81,7 +81,7 @@ namespace AMDiS {
}
return true;
- };
+ }
virtual const int getTypeID() const
{
@@ -92,21 +92,22 @@ namespace AMDiS {
{
if (typeID == MESH_STRUCTURE)
return true;
+
return false;
}
- inline void setStructure(MeshStructure *structure)
+ inline void setStructure(MeshStructure *s)
{
- structure_ = structure;
+ structure = s;
}
inline MeshStructure *getStructure()
{
- return structure_;
+ return structure;
}
protected:
- MeshStructure *structure_;
+ MeshStructure *structure;
};
}
diff --git a/AMDiS/src/ParallelDomainBase.cc b/AMDiS/src/ParallelDomainBase.cc
index e91e663d..2fdde4b5 100644
--- a/AMDiS/src/ParallelDomainBase.cc
+++ b/AMDiS/src/ParallelDomainBase.cc
@@ -50,7 +50,8 @@ namespace AMDiS {
nRankDofs(0),
rstart(0),
nComponents(1),
- deserialized(false)
+ deserialized(false),
+ lastMeshChangeIndex(0)
{
FUNCNAME("ParallelDomainBase::ParalleDomainBase()");
@@ -153,6 +154,8 @@ namespace AMDiS {
createPeriodicMap();
}
+ lastMeshChangeIndex = mesh->getChangeIndex();
+
#if (DEBUG != 0)
dbgTestCommonDofs(true);
#endif
@@ -364,40 +367,6 @@ namespace AMDiS {
}
- void ParallelDomainBase::fillPetscMatrix(DOFMatrix *mat, DOFVector<double> *vec)
- {
- FUNCNAME("ParallelDomainBase::fillPetscMatrix()");
-
- ERROR_EXIT("Not yet tested for scalar problem definition!\n");
-
- MatCreate(PETSC_COMM_WORLD, &petscMatrix);
- MatSetSizes(petscMatrix, nRankRows, nRankRows, nOverallRows, nOverallRows);
- MatSetType(petscMatrix, MATAIJ);
-
- VecCreate(PETSC_COMM_WORLD, &petscRhsVec);
- VecSetSizes(petscRhsVec, nRankRows, nOverallRows);
- VecSetType(petscRhsVec, VECMPI);
-
- VecCreate(PETSC_COMM_WORLD, &petscSolVec);
- VecSetSizes(petscSolVec, nRankRows, nOverallRows);
- VecSetType(petscSolVec, VECMPI);
-
- VecCreate(PETSC_COMM_WORLD, &petscTmpVec);
- VecSetSizes(petscTmpVec, nRankRows, nOverallRows);
- VecSetType(petscTmpVec, VECMPI);
-
- setDofMatrix(mat);
-
- MatAssemblyBegin(petscMatrix, MAT_FINAL_ASSEMBLY);
- MatAssemblyEnd(petscMatrix, MAT_FINAL_ASSEMBLY);
-
- setDofVector(petscRhsVec, vec);
-
- VecAssemblyBegin(petscRhsVec);
- VecAssemblyEnd(petscRhsVec);
- }
-
-
void ParallelDomainBase::fillPetscMatrix(Matrix<DOFMatrix*> *mat, SystemVector *vec)
{
FUNCNAME("ParallelDomainBase::fillPetscMatrix()");
@@ -634,79 +603,6 @@ namespace AMDiS {
}
- void ParallelDomainBase::solvePetscMatrix(DOFVector<double> *vec)
- {
- FUNCNAME("ParallelDomainBase::solvePetscMatrix()");
-
- ERROR_EXIT("Not yet tested for scalar problem definition!\n");
-
- KSP ksp;
- KSPCreate(PETSC_COMM_WORLD, &ksp);
- KSPSetOperators(ksp, petscMatrix, petscMatrix, SAME_NONZERO_PATTERN);
- KSPSetTolerances(ksp, 1.e-7, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT);
- KSPSetType(ksp, KSPBCGS);
- KSPMonitorSet(ksp, myKSPMonitor, PETSC_NULL, 0);
- KSPSolve(ksp, petscRhsVec, petscSolVec);
-
- PetscScalar *vecPointer;
- VecGetArray(petscSolVec, &vecPointer);
-
- for (int i = 0; i < nRankDofs; i++)
- (*vec)[mapLocalToDofIndex[i]] = vecPointer[i];
-
- VecRestoreArray(petscSolVec, &vecPointer);
-
- std::vector<double*> sendBuffers(sendDofs.size());
- std::vector<double*> recvBuffers(recvDofs.size());
-
- MPI::Request request[sendDofs.size() + recvDofs.size()];
- int requestCounter = 0;
-
- int i = 0;
- for (RankToDofContainer::iterator sendIt = sendDofs.begin();
- sendIt != sendDofs.end(); ++sendIt, i++) {
- int nSendDOFs = sendIt->second.size();
- sendBuffers[i] = new double[nSendDOFs];
-
- for (int j = 0; j < nSendDOFs; j++)
- sendBuffers[i][j] = (*vec)[*((sendIt->second)[j])];
-
- request[requestCounter++] =
- mpiComm.Isend(sendBuffers[i], nSendDOFs, MPI_DOUBLE, sendIt->first, 0);
- }
-
- i = 0;
- for (RankToDofContainer::iterator recvIt = recvDofs.begin();
- recvIt != recvDofs.end(); ++recvIt, i++) {
- int nRecvDOFs = recvIt->second.size();
- recvBuffers[i] = new double[nRecvDOFs];
-
- request[requestCounter++] =
- mpiComm.Irecv(recvBuffers[i], nRecvDOFs, MPI_DOUBLE, recvIt->first, 0);
- }
-
-
- MPI::Request::Waitall(requestCounter, request);
-
- i = 0;
- for (RankToDofContainer::iterator recvIt = recvDofs.begin();
- recvIt != recvDofs.end(); ++recvIt, i++) {
- for (int j = 0; j < static_cast<int>(recvIt->second.size()); j++)
- (*vec)[*(recvIt->second)[j]] = recvBuffers[i][j];
-
- delete [] recvBuffers[i];
- }
-
- for (int i = 0; i < static_cast<int>(sendBuffers.size()); i++)
- delete [] sendBuffers[i];
-
- MatDestroy(petscMatrix);
- VecDestroy(petscRhsVec);
- VecDestroy(petscSolVec);
- VecDestroy(petscTmpVec);
- }
-
-
void ParallelDomainBase::solvePetscMatrix(SystemVector &vec)
{
FUNCNAME("ParallelDomainBase::solvePetscMatrix()");
@@ -859,6 +755,18 @@ namespace AMDiS {
#endif
}
+
+ void ParallelDomainBase::checkMeshChange()
+ {
+ if (mesh->getChangeIndex() == lastMeshChangeIndex)
+ return;
+
+ std::cout << "MESH HAS BEEN CHANGED!" << std::endl;
+ exit(0);
+
+ lastMeshChangeIndex = mesh->getChangeIndex();
+ }
+
void ParallelDomainBase::serialize(std::ostream &out, DofContainer &data)
{
@@ -1914,8 +1822,7 @@ namespace AMDiS {
{
FUNCNAME("ParallelDomainBase::oneIteration()");
- Flag flag = dynamic_cast<StandardProblemIteration*>(iterationIF)->
- buildAndAdapt(adaptInfo, toDo);
+ Flag flag = buildAndAdapt(adaptInfo, toDo);
if (toDo.isSet(SOLVE))
solve();
@@ -1930,6 +1837,44 @@ namespace AMDiS {
}
+ Flag ParallelDomainBase::buildAndAdapt(AdaptInfo *adaptInfo, Flag toDo)
+ {
+ FUNCNAME("StandardProblemIteration::buildAndAdapt()");
+
+ Flag flag = 0, markFlag = 0;
+ ProblemStatBase *problem = iterationIF->getProblem();
+
+ if (toDo.isSet(MARK))
+ markFlag = problem->markElements(adaptInfo);
+ else
+ markFlag = 3;
+
+ if (toDo.isSet(BUILD))
+ problem->buildBeforeRefine(adaptInfo, markFlag);
+
+ // refine
+ if (toDo.isSet(ADAPT) && markFlag.isSet(MESH_REFINED))
+ flag = problem->refineMesh(adaptInfo);
+
+ if (toDo.isSet(BUILD))
+ problem->buildBeforeCoarsen(adaptInfo, markFlag);
+
+ // coarsen
+ if (toDo.isSet(ADAPT) && markFlag.isSet(MESH_COARSENED))
+ flag |= problem->coarsenMesh(adaptInfo);
+
+ checkMeshChange();
+
+ if (toDo.isSet(BUILD))
+ problem->buildAfterCoarsen(adaptInfo, markFlag, true, true);
+
+ if (toDo.isSet(BUILD_RHS))
+ problem->buildAfterCoarsen(adaptInfo, markFlag, false, true);
+
+ return flag;
+ }
+
+
void ParallelDomainBase::serialize(std::ostream &out)
{
SerUtil::serialize(out, elemWeights);
diff --git a/AMDiS/src/ParallelDomainBase.h b/AMDiS/src/ParallelDomainBase.h
index 22255b38..ffbb576a 100644
--- a/AMDiS/src/ParallelDomainBase.h
+++ b/AMDiS/src/ParallelDomainBase.h
@@ -151,6 +151,8 @@ namespace AMDiS {
virtual Flag oneIteration(AdaptInfo *adaptInfo, Flag toDo = FULL_ITERATION);
+ virtual Flag buildAndAdapt(AdaptInfo *adaptInfo, Flag toDo);
+
virtual void endIteration(AdaptInfo *adaptInfo)
{
iterationIF->endIteration(adaptInfo);
@@ -174,12 +176,8 @@ namespace AMDiS {
return nRankDofs;
}
- void fillPetscMatrix(DOFMatrix *mat, DOFVector<double> *vec);
-
void fillPetscMatrix(Matrix<DOFMatrix*> *mat, SystemVector *vec);
- void solvePetscMatrix(DOFVector<double> *vec);
-
void solvePetscMatrix(SystemVector &vec);
virtual ProblemStatBase *getProblem(int number = 0)
@@ -260,18 +258,16 @@ namespace AMDiS {
DofToRank& boundaryDofs,
DofToBool& vertexDof);
- /** \brief
- * Takes a dof matrix and sends the values to the global petsc matrix.
- */
+ /// Takes a dof matrix and sends the values to the global petsc matrix.
void setDofMatrix(DOFMatrix* mat, int dispMult = 1,
int dispAddRow = 0, int dispAddCol = 0);
- /** \brief
- * Takes a dof vector and sends its values to a given petsc vector.
- */
+ /// Takes a dof vector and sends its values to a given petsc vector.
void setDofVector(Vec& petscVec, DOFVector<double>* vec,
int disMult = 1, int dispAdd = 0);
+ void checkMeshChange();
+
void dbgCreateElementMap(ElementIdxToDofs &elMap);
void dbgTestElementMap(ElementIdxToDofs &elMap);
@@ -576,6 +572,12 @@ namespace AMDiS {
* a serialization file.
*/
bool deserialized;
+
+ /** \brief
+ * Stores the mesh change index. This is used to recognize changes in the mesh
+ * structure (e.g. through refinement or coarsening managers).
+ */
+ long lastMeshChangeIndex;
};
}
diff --git a/AMDiS/src/ParallelDomainScal.cc b/AMDiS/src/ParallelDomainScal.cc
deleted file mode 100644
index c837efed..00000000
--- a/AMDiS/src/ParallelDomainScal.cc
+++ /dev/null
@@ -1,62 +0,0 @@
-#include "ParallelDomainScal.h"
-#include "ProblemScal.h"
-#include "ProblemInstat.h"
-#include "DOFVector.h"
-
-namespace AMDiS {
-
- ParallelDomainScal::ParallelDomainScal(ProblemScal *problem,
- ProblemInstatScal *problemInstat)
- : ParallelDomainBase(problem,
- problemInstat,
- problem->getFESpace(),
- problem->getRefinementManager()),
- probScal(problem)
- {
- info = problem->getInfo();
-
- // Create parallel serialization file writer, if needed.
- int writeSerialization = 0;
- GET_PARAMETER(0, name + "->output->write serialization", "%d", &writeSerialization);
- if (writeSerialization)
- problem->getFileWriterList().push_back(new Serializer<ParallelDomainScal>(this));
- }
-
- void ParallelDomainScal::initParallelization(AdaptInfo *adaptInfo)
- {
- FUNCNAME("ParallelDomainScal::initParallelization()");
-
- ParallelDomainBase::initParallelization(adaptInfo);
-
- DOFMatrix* m = probScal->getSystemMatrix();
-
- TEST_EXIT(m)("No DOF Matrix!\n");
- m->setRankDofs(isRankDof);
-
- probScal->getRHS()->setRankDofs(isRankDof);
- probScal->getSolution()->setRankDofs(isRankDof);
- }
-
- void ParallelDomainScal::solve()
- {
- FUNCNAME("ParallelDomainScal::solve()");
-
-#ifdef _OPENMP
- double wtime = omp_get_wtime();
-#endif
- clock_t first = clock();
-
- fillPetscMatrix(probScal->getSystemMatrix(), probScal->getRHS());
- solvePetscMatrix(probScal->getSolution());
-
-#ifdef _OPENMP
- INFO(info, 8)("solution of discrete system needed %.5f seconds system time / %.5f seconds wallclock time\n",
- TIME_USED(first, clock()),
- omp_get_wtime() - wtime);
-#else
- INFO(info, 8)("solution of discrete system needed %.5f seconds\n",
- TIME_USED(first, clock()));
-#endif
- }
-
-}
diff --git a/AMDiS/src/ParallelDomainScal.h b/AMDiS/src/ParallelDomainScal.h
deleted file mode 100644
index bb534f48..00000000
--- a/AMDiS/src/ParallelDomainScal.h
+++ /dev/null
@@ -1,63 +0,0 @@
-// ============================================================================
-// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == TU Dresden ==
-// == ==
-// == Institut für Wissenschaftliches Rechnen ==
-// == Zellescher Weg 12-14 ==
-// == 01069 Dresden ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == https://gforge.zih.tu-dresden.de/projects/amdis/ ==
-// == ==
-// ============================================================================
-
-/** \file ParallelDomainScal.h */
-
-#ifndef AMDIS_PARALLELDOMAINSCAL_H
-#define AMDIS_PARALLELDOMAINSCAL_H
-
-#include "ParallelDomainBase.h"
-#include "ProblemScal.h"
-
-namespace AMDiS {
-
- class ParallelDomainScal : public ParallelDomainBase
- {
- public:
- ParallelDomainScal(ProblemScal *problem,
- ProblemInstatScal *problemInstat);
-
- void initParallelization(AdaptInfo *adaptInfo);
-
- // Writes all data of this object to an output stream.
- virtual void serialize(std::ostream &out)
- {
- probScal->serialize(out);
- ParallelDomainBase::serialize(out);
- }
-
- // Reads the object data from an input stream.
- virtual void deserialize(std::istream &in)
- {
- probScal->deserialize(in);
- ParallelDomainBase::deserialize(in);
- }
-
- protected:
- /// Starts the solution of the linear system using Petsc.
- void solve();
-
- protected:
- /// Pointer to the stationary problem.
- ProblemScal *probScal;
- };
-
-}
-
-#endif // AMDIS_PARALLELDOMAINSCAL_H
diff --git a/AMDiS/src/RefinementManager.cc b/AMDiS/src/RefinementManager.cc
index fa82560e..757c0dd3 100644
--- a/AMDiS/src/RefinementManager.cc
+++ b/AMDiS/src/RefinementManager.cc
@@ -41,7 +41,7 @@ namespace AMDiS {
FUNCNAME("RefinementManager::refineMesh()");
mesh = aMesh;
- int n_elements = mesh->getNumberOfLeaves();
+ int nElements = mesh->getNumberOfLeaves();
ElInfo *elInfo;
newCoords = false;
stack = new TraverseStack;
@@ -67,9 +67,14 @@ namespace AMDiS {
delete stack;
- n_elements = mesh->getNumberOfLeaves() - n_elements;
-
- return(n_elements ? MESH_REFINED : Flag(0));
+ nElements -= mesh->getNumberOfLeaves();
+
+ if (nElements != 0) {
+ aMesh->incChangeIndex();
+ return MESH_REFINED;
+ } else {
+ return Flag(0);
+ }
}
}
diff --git a/AMDiS/src/RefinementManager2d.cc b/AMDiS/src/RefinementManager2d.cc
index 47502a11..4db3aaa9 100644
--- a/AMDiS/src/RefinementManager2d.cc
+++ b/AMDiS/src/RefinementManager2d.cc
@@ -150,7 +150,8 @@ namespace AMDiS {
{
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1,
- Mesh::CALL_EVERY_EL_PREORDER | Mesh::FILL_BOUND | Mesh::FILL_COORDS);
+ Mesh::CALL_EVERY_EL_PREORDER |
+ Mesh::FILL_BOUND | Mesh::FILL_COORDS);
while (elInfo) {
newCoordsFct(elInfo);
elInfo = stack.traverseNext(elInfo);
--
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