diff --git a/AMDiS/CMakeLists.txt b/AMDiS/CMakeLists.txt
index e895215e7e3817c411efb96180e58b9d8601656e..ee38f54ebfc6a3945ed60472000d6156b7c04377 100644
--- a/AMDiS/CMakeLists.txt
+++ b/AMDiS/CMakeLists.txt
@@ -197,6 +197,7 @@ if(ENABLE_PARALLEL_DOMAIN)
find_package(PETSc REQUIRED)
include_directories(${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
SET(PARALLEL_DOMAIN_AMDIS_SRC
+ ${SOURCE_DIR}/parallel/CheckerPartitioner.cc
${SOURCE_DIR}/parallel/ElementObjectData.cc
${SOURCE_DIR}/parallel/MeshDistributor.cc
${SOURCE_DIR}/parallel/MeshManipulation.cc
diff --git a/AMDiS/other/include/Makefile_AMDiS.mk b/AMDiS/other/include/Makefile_AMDiS.mk
index b001345d5fa8047fa9825633be72c8ebda197cda..0488e77964842b0fdf524a0afc0579eaf00fd56d 100644
--- a/AMDiS/other/include/Makefile_AMDiS.mk
+++ b/AMDiS/other/include/Makefile_AMDiS.mk
@@ -77,7 +77,7 @@ ifeq ($(strip $(USE_PARALLEL_AMDIS)), 1)
endif
CPPFLAGS += -DHAVE_PARALLEL_DOMAIN_AMDIS
- INCLUDES += $(PETSC_INCLUDE)
+ INCLUDES += $(PETSC_CC_INCLUDES)
LIBS += $(PARMETIS_LIB) -lmpi $(PETSC_LIB)
LIBS += $(ZOLTAN_LIB)
else
diff --git a/AMDiS/src/Element.cc b/AMDiS/src/Element.cc
index 7a5e20579965e2bee92026bf344ead165f639527..5631f9c1714f9925964421010f5e3e0c7449efbb 100644
--- a/AMDiS/src/Element.cc
+++ b/AMDiS/src/Element.cc
@@ -18,6 +18,7 @@
#include "ElementRegion_ED.h"
#include "Serializer.h"
#include "MeshStructure.h"
+#include "BasisFunction.h"
namespace AMDiS {
@@ -622,4 +623,15 @@ namespace AMDiS {
file.close();
}
+
+ void Element::getAllDofs(FiniteElemSpace* feSpace,
+ BoundaryObject bound,
+ DofContainer& dofs)
+ {
+ getNodeDofs(feSpace, bound, dofs);
+
+ if (feSpace->getBasisFcts()->getDegree() > 1)
+ getHigherOrderDofs(feSpace, bound, dofs);
+ }
+
}
diff --git a/AMDiS/src/Element.h b/AMDiS/src/Element.h
index 68a437019e58573a67fd47b090065f0307458f68..edc2656473a606817ac53eb4560be32f6a95341e 100644
--- a/AMDiS/src/Element.h
+++ b/AMDiS/src/Element.h
@@ -411,32 +411,38 @@ namespace AMDiS {
virtual int getChildType(int elType) const = 0;
/** \brief
- * Traverses an edge/face of a given element (this includes also all children of
- * the element having the same edge/face). All vertex dofs alonge this edge/face
- * are assembled and put together to a list.
+ * Traverses a vertex/edge/face of a given element (this includes also all
+ * children of the element having the same edge/face). All DOFs on mesh
+ * nodes alonge this vertex/edge/face are assembled and put together to
+ * a list.
*
* \param[in] feSpace FE space which is used to get the dofs.
- * \param[in] bound Defines the edge/face of the element on which
- * all vertex dofs are assembled.
+ * \param[in] bound Defines the vertex/edge/face of the element on
+ * which all vertex dofs are assembled.
* \param[out] dofs List of dofs, where the result is stored.
*/
- virtual void getVertexDofs(FiniteElemSpace* feSpace,
- BoundaryObject bound,
- DofContainer& dofs) const = 0;
+ virtual void getNodeDofs(FiniteElemSpace* feSpace,
+ BoundaryObject bound,
+ DofContainer& dofs) const = 0;
/** \brief
- * Traverses an edge/face of a given element (this includes also all children of
- * the element having the same edge/face). All non vertex dofs alonge this edge/face
- * are assembled and put together to a list.
+ * Traverses a vertex/edge/face of a given element (this includes also all
+ * children of the element having the same edge/face). All DOFs belonging
+ * to higher order basis functions alonge this vertex/edge/face are
+ * assembled and put together to a list.
*
* \param[in] feSpace FE space which is used to get the dofs.
* \param[in] bound Defines the edge/face of the element on which
* all non vertex dofs are assembled.
* \param[out] dofs All dofs are put to this dof list.
*/
- virtual void getNonVertexDofs(FiniteElemSpace* feSpace,
- BoundaryObject bound,
- DofContainer& dofs) const = 0;
+ virtual void getHigherOrderDofs(FiniteElemSpace* feSpace,
+ BoundaryObject bound,
+ DofContainer& dofs) const = 0;
+
+ void getAllDofs(FiniteElemSpace* feSpace,
+ BoundaryObject bound,
+ DofContainer& dofs);
/** \} */
diff --git a/AMDiS/src/Line.h b/AMDiS/src/Line.h
index f41e9bec05e8651b7c70385cbd0ebd57b92f5fb5..3b7c58a45b036e6a18bc7d040cd7bfeb6a454385 100644
--- a/AMDiS/src/Line.h
+++ b/AMDiS/src/Line.h
@@ -173,15 +173,15 @@ namespace AMDiS {
return "Line";
}
- void getVertexDofs(FiniteElemSpace*, BoundaryObject, DofContainer&) const
+ void getNodeDofs(FiniteElemSpace*, BoundaryObject, DofContainer&) const
{
- FUNCNAME("Line::getVertexDofs()");
+ FUNCNAME("Line::getNodeDofs()");
ERROR_EXIT("Not yet implemented!\n");
}
- void getNonVertexDofs(FiniteElemSpace*, BoundaryObject, DofContainer&) const
+ void getHigherOrderDofs(FiniteElemSpace*, BoundaryObject, DofContainer&) const
{
- FUNCNAME("Line::getNonVertexDofs()");
+ FUNCNAME("Line::getHigherOrderDofs()");
ERROR_EXIT("Not yet implemented!\n");
}
diff --git a/AMDiS/src/Makefile.am b/AMDiS/src/Makefile.am
index c85b4be8584bd07c8152e01f11e3ee1e4c2b44fa..fc437c35a3cbfd62828f531da89fa72afb0d7d43 100644
--- a/AMDiS/src/Makefile.am
+++ b/AMDiS/src/Makefile.am
@@ -12,6 +12,7 @@ PARALLEL_INCLUDES =
if USE_PARALLEL_DOMAIN_AMDIS
PARALLEL_AMDIS_SOURCES += \
+ parallel/CheckerPartitioner.cc \
parallel/ElementObjectData.cc \
parallel/MeshDistributor.cc \
parallel/MeshManipulation.cc \
@@ -247,6 +248,7 @@ io/ValueWriter.h \
io/VtkWriter.h \
io/VtkWriter.hh \
itl/minres.hpp \
+parallel/CheckerPartitioner.h \
parallel/ElementObjectData.h \
parallel/InteriorBoundary.h \
parallel/MeshDistributor.h \
diff --git a/AMDiS/src/Makefile.in b/AMDiS/src/Makefile.in
index 5cea50252713046e1b49eded18401973625a68da..3f5a03d0d712122addd4bb48f0e41ad1be9f9e0e 100644
--- a/AMDiS/src/Makefile.in
+++ b/AMDiS/src/Makefile.in
@@ -38,6 +38,7 @@ POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_1 = \
+@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ parallel/CheckerPartitioner.cc \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ parallel/ElementObjectData.cc \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ parallel/MeshDistributor.cc \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ parallel/MeshManipulation.cc \
@@ -88,10 +89,11 @@ am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(includedir)"
libLTLIBRARIES_INSTALL = $(INSTALL)
LTLIBRARIES = $(lib_LTLIBRARIES)
libamdis_la_LIBADD =
-am__libamdis_la_SOURCES_DIST = parallel/ElementObjectData.cc \
- parallel/MeshDistributor.cc parallel/MeshManipulation.cc \
- parallel/MeshPartitioner.cc parallel/MpiHelper.cc \
- parallel/ParallelDebug.cc parallel/ParallelProblemStatBase.cc \
+am__libamdis_la_SOURCES_DIST = parallel/CheckerPartitioner.cc \
+ parallel/ElementObjectData.cc parallel/MeshDistributor.cc \
+ parallel/MeshManipulation.cc parallel/MeshPartitioner.cc \
+ parallel/MpiHelper.cc parallel/ParallelDebug.cc \
+ parallel/ParallelProblemStatBase.cc \
parallel/ParMetisPartitioner.cc parallel/PetscProblemStat.cc \
parallel/PetscSolver.cc parallel/StdMpi.cc \
parallel/ZoltanPartitioner.cc AdaptBase.cc AdaptInfo.cc \
@@ -130,7 +132,8 @@ am__libamdis_la_SOURCES_DIST = parallel/ElementObjectData.cc \
io/ValueWriter.cc io/VtkWriter.cc parallel/InteriorBoundary.cc \
time/RosenbrockAdaptInstationary.cc time/RosenbrockMethod.cc \
time/RosenbrockStationary.cc
-@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__objects_1 = libamdis_la-ElementObjectData.lo \
+@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__objects_1 = libamdis_la-CheckerPartitioner.lo \
+@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-ElementObjectData.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-MeshDistributor.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-MeshManipulation.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-MeshPartitioner.lo \
@@ -568,6 +571,7 @@ io/ValueWriter.h \
io/VtkWriter.h \
io/VtkWriter.hh \
itl/minres.hpp \
+parallel/CheckerPartitioner.h \
parallel/ElementObjectData.h \
parallel/InteriorBoundary.h \
parallel/MeshDistributor.h \
@@ -822,6 +826,7 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-BasisFunction.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Boundary.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-BoundaryManager.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-CheckerPartitioner.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Cholesky.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-CoarseningManager.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-CoarseningManager1d.Plo@am__quote@
@@ -976,6 +981,13 @@ distclean-compile:
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(LTCXXCOMPILE) -c -o $@ $<
+libamdis_la-CheckerPartitioner.lo: parallel/CheckerPartitioner.cc
+@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-CheckerPartitioner.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-CheckerPartitioner.Tpo" -c -o libamdis_la-CheckerPartitioner.lo `test -f 'parallel/CheckerPartitioner.cc' || echo '$(srcdir)/'`parallel/CheckerPartitioner.cc; \
+@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-CheckerPartitioner.Tpo" "$(DEPDIR)/libamdis_la-CheckerPartitioner.Plo"; else rm -f "$(DEPDIR)/libamdis_la-CheckerPartitioner.Tpo"; exit 1; fi
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='parallel/CheckerPartitioner.cc' object='libamdis_la-CheckerPartitioner.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) $(CXXFLAGS) -c -o libamdis_la-CheckerPartitioner.lo `test -f 'parallel/CheckerPartitioner.cc' || echo '$(srcdir)/'`parallel/CheckerPartitioner.cc
+
libamdis_la-ElementObjectData.lo: parallel/ElementObjectData.cc
@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ElementObjectData.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ElementObjectData.Tpo" -c -o libamdis_la-ElementObjectData.lo `test -f 'parallel/ElementObjectData.cc' || echo '$(srcdir)/'`parallel/ElementObjectData.cc; \
@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-ElementObjectData.Tpo" "$(DEPDIR)/libamdis_la-ElementObjectData.Plo"; else rm -f "$(DEPDIR)/libamdis_la-ElementObjectData.Tpo"; exit 1; fi
diff --git a/AMDiS/src/Mesh.cc b/AMDiS/src/Mesh.cc
index 0cb7333953cc3a0683f4d7f232a4b0ddfb259280..13acef6b185c3adf76e6e32b3d5e408a23e493ea 100644
--- a/AMDiS/src/Mesh.cc
+++ b/AMDiS/src/Mesh.cc
@@ -77,11 +77,11 @@ namespace AMDiS {
const Flag Mesh::CALL_REVERSE_MODE = 0X8000L;
- std::vector<DegreeOfFreedom> Mesh::dof_used;
+ vector<DegreeOfFreedom> Mesh::dof_used;
const int Mesh::MAX_DOF = 100;
- std::map<std::pair<DegreeOfFreedom, int>, DegreeOfFreedom*> Mesh::serializedDOFs;
+ map<pair<DegreeOfFreedom, int>, DegreeOfFreedom*> Mesh::serializedDOFs;
- Mesh::Mesh(std::string aName, int dimension)
+ Mesh::Mesh(string aName, int dimension)
: name(aName),
dim(dimension),
nVertices(0),
@@ -186,7 +186,7 @@ namespace AMDiS {
// mapIndex[i] is the index of the MacroElement element in the vector
// macroElements, for which holds: element->getIndex() = i
- std::map<int, int> mapIndex;
+ map<int, int> mapIndex;
// We use this map for coping the DOFs of the Elements within the
// MacroElements objects.
@@ -198,7 +198,7 @@ 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();
+ for (deque<MacroElement*>::const_iterator it = m.macroElements.begin();
it != m.macroElements.end(); ++it, insertCounter++) {
// Create new MacroElement.
@@ -214,13 +214,13 @@ namespace AMDiS {
macroElements.push_back(el);
// Update the index map.
- mapIndex.insert(std::pair<int, int>(el->getIndex(), insertCounter));
+ mapIndex.insert(pair<int, int>(el->getIndex(), insertCounter));
}
// Now we have to go through all the new MacroElements, and update the neighbour
// connections.
insertCounter = 0;
- for (std::deque<MacroElement*>::const_iterator it = m.macroElements.begin();
+ for (deque<MacroElement*>::const_iterator it = m.macroElements.begin();
it != m.macroElements.end();
++it, insertCounter++) {
// Go through all neighbours.
@@ -275,8 +275,8 @@ namespace AMDiS {
{
FUNCNAME("Mesh::removeMacroElement()");
- typedef std::map<const DegreeOfFreedom*, std::set<MacroElement*> > DofElMap;
- typedef std::map<const DegreeOfFreedom*, GeoIndex> DofPosMap;
+ typedef map<const DegreeOfFreedom*, std::set<MacroElement*> > DofElMap;
+ typedef map<const DegreeOfFreedom*, GeoIndex> DofPosMap;
TEST_EXIT(admin.size() == 1)("Not yet implemented for multiple admins!\n");
TEST_EXIT(admin[0])("There is something wrong!\n");
@@ -305,12 +305,12 @@ namespace AMDiS {
// === Remove macro elements from mesh macro element list. ===
- // Removing arbitrary elements from an std::deque is very slow. Therefore, we
+ // Removing arbitrary elements from an deque is very slow. Therefore, we
// create a new deque with all macro elements that should not be deleted. The
// macro element deque is than replaced by the new created one.
- std::deque<MacroElement*> newMacroElements;
- for (std::deque<MacroElement*>::iterator elIter = macroElements.begin();
+ deque<MacroElement*> newMacroElements;
+ for (deque<MacroElement*>::iterator elIter = macroElements.begin();
elIter != macroElements.end(); ++elIter) {
// If the current mesh macro element should not be deleted, i.e., it is not a
// member of the list of macro elements to be deleted, is is inserted to the new
@@ -416,7 +416,7 @@ namespace AMDiS {
localAdmin->setMesh(this);
- TEST_EXIT(std::find(admin.begin(), admin.end(), localAdmin) == admin.end())
+ TEST_EXIT(find(admin.begin(), admin.end(), localAdmin) == admin.end())
("admin %s is already associated to mesh %s\n",
localAdmin->getName().c_str(), this->getName().c_str());
@@ -479,7 +479,7 @@ namespace AMDiS {
compressAdmin->getHoleCount() < 1)
continue;
- std::vector<int> newDofIndex(size);
+ vector<int> newDofIndex(size);
compressAdmin->compress(newDofIndex);
Flag fill_flag = (preserveCoarseDOFs ?
@@ -559,7 +559,7 @@ namespace AMDiS {
}
- const DOFAdmin *Mesh::createDOFAdmin(std::string lname, DimVec<int> lnDof)
+ const DOFAdmin *Mesh::createDOFAdmin(string lname, DimVec<int> lnDof)
{
FUNCNAME("Mesh::createDOFAdmin()");
@@ -905,10 +905,12 @@ namespace AMDiS {
const FiniteElemSpace* feSpace,
WorldVector<double>& coords)
{
+ FUNCNAME("Mesh::getDofIndexCoords()");
+
DimVec<double>* baryCoords;
bool found = false;
TraverseStack stack;
- std::vector<DegreeOfFreedom> dofVec(feSpace->getBasisFcts()->getNumber());
+ vector<DegreeOfFreedom> dofVec(feSpace->getBasisFcts()->getNumber());
ElInfo *elInfo = stack.traverseFirst(this, -1,
Mesh::CALL_LEAF_EL | Mesh::FILL_COORDS);
@@ -938,9 +940,11 @@ namespace AMDiS {
void Mesh::getDofIndexCoords(const FiniteElemSpace* feSpace,
DOFVector<WorldVector<double> >& coords)
{
+ FUNCNAME("Mesh::getDofIndexCoords()");
+
const BasisFunction* basFcts = feSpace->getBasisFcts();
int nBasFcts = basFcts->getNumber();
- std::vector<DegreeOfFreedom> dofVec(nBasFcts);
+ vector<DegreeOfFreedom> dofVec(nBasFcts);
TraverseStack stack;
ElInfo *elInfo =
@@ -958,6 +962,27 @@ namespace AMDiS {
}
+ void Mesh::getAllDofs(FiniteElemSpace *feSpace,
+ std::set<const DegreeOfFreedom*>& allDofs)
+ {
+ FUNCNAME("Mesh::getAllDofs()");
+
+ ElementDofIterator elDofIt(feSpace);
+ allDofs.clear();
+
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(this, -1, Mesh::CALL_LEAF_EL);
+ while (elInfo) {
+ elDofIt.reset(elInfo->getElement());
+ do {
+ allDofs.insert(elDofIt.getDofPtr());
+ } while(elDofIt.next());
+
+ elInfo = stack.traverseNext(elInfo);
+ }
+ }
+
+
void Mesh::setDiameter(const WorldVector<double>& w)
{
diam = w;
@@ -970,7 +995,7 @@ namespace AMDiS {
}
- void Mesh::serialize(std::ostream &out)
+ void Mesh::serialize(ostream &out)
{
serializedDOFs.clear();
@@ -1022,7 +1047,7 @@ namespace AMDiS {
// === Write periodic associations. ===
int mapSize = periodicAssociations.size();
SerUtil::serialize(out, mapSize);
- for (std::map<BoundaryType, VertexVector*>::iterator it = periodicAssociations.begin();
+ for (map<BoundaryType, VertexVector*>::iterator it = periodicAssociations.begin();
it != periodicAssociations.end(); ++it) {
BoundaryType b = it->first;
@@ -1046,7 +1071,7 @@ namespace AMDiS {
}
- void Mesh::deserialize(std::istream &in)
+ void Mesh::deserialize(istream &in)
{
FUNCNAME("Mesh::deserialize()");
@@ -1100,7 +1125,7 @@ namespace AMDiS {
}
SerUtil::deserialize(in, size);
- std::vector< std::vector<int> > neighbourIndices(size);
+ vector< vector<int> > neighbourIndices(size);
deleteMeshStructure();
@@ -1110,7 +1135,7 @@ namespace AMDiS {
// decomposition based parallelization. Therefore we create a temporary map
// from macro element indices to the continous index of \ref macroElements. This
// will be used later to find the correct neighbours of the macro elements.
- std::map<int, int> elIndexVecIndex;
+ map<int, int> elIndexVecIndex;
macroElements.resize(size);
for (int i = 0; i < size; i++) {
@@ -1177,9 +1202,9 @@ namespace AMDiS {
TEST_EXIT(admin.size() > 0)("No DOF admin defined!\n");
- std::string macroFilename("");
- std::string valueFilename("");
- std::string periodicFilename("");
+ string macroFilename("");
+ string valueFilename("");
+ string periodicFilename("");
int check = 1;
GET_PARAMETER(0, name + "->macro file name", ¯oFilename);
@@ -1206,8 +1231,8 @@ namespace AMDiS {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
- void Mesh::checkParallelMacroFile(std::string ¯oFilename,
- std::string &periodicFilename,
+ void Mesh::checkParallelMacroFile(string ¯oFilename,
+ string &periodicFilename,
int check)
{
FUNCNAME("Mesh::checkParallelMacroFile()");
@@ -1260,7 +1285,8 @@ namespace AMDiS {
// => gr = log_2(nProcs * 10 / nMacroElements)
double scale = 10.0 * MPI::COMM_WORLD.Get_size() / nMacroElements;
- nParallelPreRefinements = static_cast<int>(std::max(0.0, ceil(log(scale) / log(2))));
+ nParallelPreRefinements =
+ static_cast<int>(std::max(0.0, ceil(log(scale) / log(2))));
if (dim == 3) {
int newElType = (elType + nParallelPreRefinements) % 3;
@@ -1299,7 +1325,7 @@ namespace AMDiS {
// === If macro weights are explicitly given, we cannot change the mesh. ===
- std::string macroWeightsFilename = "";
+ string macroWeightsFilename = "";
GET_PARAMETER(0, name + "->macro weights", ¯oWeightsFilename);
if (macroWeightsFilename != "") {
ERROR_EXIT("Should not happen!\n");
@@ -1315,12 +1341,14 @@ namespace AMDiS {
srand(time(NULL));
filenameRandomNumber = rand() % 1000000;
}
+ MPI::COMM_WORLD.Barrier();
MPI::COMM_WORLD.Bcast(&filenameRandomNumber, 1, MPI_INT, 0);
+ MPI::COMM_WORLD.Barrier();
- std::stringstream newMacroFilename;
+ stringstream newMacroFilename;
newMacroFilename << macroFilename << "." << filenameRandomNumber << ".tmp";
- std::stringstream newPeriodicFilename;
+ stringstream newPeriodicFilename;
newPeriodicFilename << periodicFilename << "." << filenameRandomNumber << ".tmp";
@@ -1363,7 +1391,7 @@ namespace AMDiS {
else
globalRefinements -= nParallelPreRefinements;
- std::stringstream oss;
+ stringstream oss;
oss << globalRefinements;
ADD_PARAMETER(0, name + "->global refinements", oss.str().c_str());
@@ -1382,8 +1410,8 @@ namespace AMDiS {
bool Mesh::associated(DegreeOfFreedom dof1, DegreeOfFreedom dof2)
{
- std::map<BoundaryType, VertexVector*>::iterator it;
- std::map<BoundaryType, VertexVector*>::iterator end = periodicAssociations.end();
+ map<BoundaryType, VertexVector*>::iterator it;
+ map<BoundaryType, VertexVector*>::iterator end = periodicAssociations.end();
for (it = periodicAssociations.begin(); it != end; ++it)
if ((*(it->second))[dof1] == dof2)
return true;
@@ -1394,9 +1422,9 @@ namespace AMDiS {
bool Mesh::indirectlyAssociated(DegreeOfFreedom dof1, DegreeOfFreedom dof2)
{
- std::vector<DegreeOfFreedom> associatedToDOF1;
- std::map<BoundaryType, VertexVector*>::iterator it;
- std::map<BoundaryType, VertexVector*>::iterator end = periodicAssociations.end();
+ vector<DegreeOfFreedom> associatedToDOF1;
+ map<BoundaryType, VertexVector*>::iterator it;
+ map<BoundaryType, VertexVector*>::iterator end = periodicAssociations.end();
DegreeOfFreedom dof, assDOF;
associatedToDOF1.push_back(dof1);
@@ -1444,7 +1472,7 @@ namespace AMDiS {
{
Element::deletedDOFs.clear();
- for (std::deque<MacroElement*>::const_iterator it = macroElements.begin();
+ for (deque<MacroElement*>::const_iterator it = macroElements.begin();
it != macroElements.end(); ++it) {
(*it)->getElement()->deleteElementDOFs();
delete *it;
diff --git a/AMDiS/src/Mesh.h b/AMDiS/src/Mesh.h
index 0a86767c50fe162b6d40c4ef2aebec324a15ab5c..c7f1d729bf6683725b877797eb9410ed6da0ddac 100644
--- a/AMDiS/src/Mesh.h
+++ b/AMDiS/src/Mesh.h
@@ -50,6 +50,9 @@
namespace AMDiS {
+ using namespace std;
+
+
/** \ingroup Triangulation
* \brief
* A Mesh holds all information about a triangulation.
@@ -58,7 +61,7 @@ namespace AMDiS {
{
public:
/// Creates a mesh with the given name of dimension dim
- Mesh(std::string name, int dim);
+ Mesh(string name, int dim);
/// Destructor
virtual ~Mesh();
@@ -83,7 +86,7 @@ namespace AMDiS {
}
/// Returns \ref name of the mesh
- inline std::string getName() const
+ inline string getName() const
{
return name;
}
@@ -197,7 +200,7 @@ namespace AMDiS {
* are needed at the different positions (see \ref DOFAdmin::nrDOF).
* A pointer to the created DOFAdmin is returned.
*/
- const DOFAdmin* createDOFAdmin(std::string lname, DimVec<int> nDof);
+ const DOFAdmin* createDOFAdmin(string lname, DimVec<int> nDof);
/** \brief
* Returns the size of \ref admin which is the number of the DOFAdmins
@@ -230,7 +233,7 @@ namespace AMDiS {
}
/// Returns an iterator to the begin of \ref macroElements
- inline std::deque<MacroElement*>::iterator firstMacroElement()
+ inline deque<MacroElement*>::iterator firstMacroElement()
{
return macroElements.begin();
}
@@ -242,13 +245,13 @@ namespace AMDiS {
}
/// Returns an iterator to the end of \ref macroElements
- inline std::deque<MacroElement*>::iterator endOfMacroElements()
+ inline deque<MacroElement*>::iterator endOfMacroElements()
{
return macroElements.end();
}
/// Returns \ref macroElements, the list of all macro elements in the mesh.
- std::deque<MacroElement*>& getMacroElements()
+ deque<MacroElement*>& getMacroElements()
{
return macroElements;
}
@@ -260,7 +263,7 @@ namespace AMDiS {
*/
/// Sets \ref name of the mesh
- inline void setName(std::string aName)
+ inline void setName(string aName)
{
name = aName;
}
@@ -496,16 +499,25 @@ namespace AMDiS {
WorldVector<double>& coords);
/** \brief
- * Traverse the whole mesh and stores to each DOF of the given finite element space
- * the coordinates in a given DOFVector. Works in the same way as the function
- * \ref getDofIndexCoords defined above.
+ * Traverse the whole mesh and stores to each DOF of the given finite
+ * element space the coordinates in a given DOFVector. Works in the same
+ * way as the function \ref getDofIndexCoords defined above.
*
- * @param[in] feSpace The fe soace to be used for the search.
- * @param[out] coords DOF vector that stores the coordinates to each dof.
+ * @param[in] feSpace The FE space to be used for the search.
+ * @param[out] coords DOF vector that stores the coordinates to each DOF.
*/
void getDofIndexCoords(const FiniteElemSpace* feSpace,
DOFVector<WorldVector<double> >& coords);
+ /** \brief
+ * Traverse the mesh and get all DOFs in this mesh for a given FE space.
+ *
+ * @param[in] feSpace The FE space to be used for collecting DOFs.
+ * @param[out] allDofs The set which is filled with all DOFs.
+ */
+ void getAllDofs(FiniteElemSpace *feSpace,
+ std::set<const DegreeOfFreedom*>& allDofs);
+
/// Returns FILL_ANY_?D
inline static const Flag& getFillAnyFlag(int dim)
{
@@ -526,10 +538,10 @@ namespace AMDiS {
}
/// Serialize the mesh to a file.
- void serialize(std::ostream &out);
+ void serialize(ostream &out);
/// Deserialize a mesh from a file.
- void deserialize(std::istream &in);
+ void deserialize(istream &in);
/// Returns \ref elementIndex and increments it by 1.
inline int getNextElementIndex()
@@ -544,7 +556,7 @@ namespace AMDiS {
}
///
- inline std::map<BoundaryType, VertexVector*>& getPeriodicAssociations()
+ inline map<BoundaryType, VertexVector*>& getPeriodicAssociations()
{
return periodicAssociations;
}
@@ -707,8 +719,8 @@ namespace AMDiS {
* AMDiS macro mesh, the value must be 1 and 0
* otherwise.
*/
- void checkParallelMacroFile(std::string ¯oFilename,
- std::string &periodicFilename,
+ void checkParallelMacroFile(string ¯oFilename,
+ string &periodicFilename,
int check);
#endif
@@ -717,7 +729,7 @@ namespace AMDiS {
static const int MAX_DOF;
/// Name of this Mesh
- std::string name;
+ string name;
/// Dimension of this Mesh. Doesn't have to be equal to dimension of world.
int dim;
@@ -810,13 +822,13 @@ namespace AMDiS {
DimVec<int> node;
/// List of all DOFAdmins
- std::vector<DOFAdmin*> admin;
+ vector<DOFAdmin*> admin;
/// List of all MacroElements of this Mesh
- std::deque<MacroElement*> macroElements;
+ deque<MacroElement*> macroElements;
/// Used by check functions
- static std::vector<DegreeOfFreedom> dof_used;
+ static vector<DegreeOfFreedom> dof_used;
/** \brief
* This map is used for serialization and deserialization of mesh elements.
@@ -828,7 +840,7 @@ namespace AMDiS {
* When a state should be deserialized, the information can be used to construct
* exactly the same dof structure.
*/
- static std::map<std::pair<DegreeOfFreedom, int>, DegreeOfFreedom*> serializedDOFs;
+ static map<pair<DegreeOfFreedom, int>, DegreeOfFreedom*> serializedDOFs;
/** \brief
* Used while mesh refinement. To create new elements
@@ -848,7 +860,7 @@ namespace AMDiS {
bool initialized;
/// Map of managed periodic vertex associations.
- std::map<BoundaryType, VertexVector*> periodicAssociations;
+ map<BoundaryType, VertexVector*> periodicAssociations;
/** \brief
* If the mesh has been created by reading a macro file, here the information are
diff --git a/AMDiS/src/Tetrahedron.cc b/AMDiS/src/Tetrahedron.cc
index f2b40d1a3b70c42ade49f334a7e007fb8a8221f2..605c8fa769ecd296588ed1c00cc6a87e20a0770f 100644
--- a/AMDiS/src/Tetrahedron.cc
+++ b/AMDiS/src/Tetrahedron.cc
@@ -200,21 +200,21 @@ namespace AMDiS {
}
- void Tetrahedron::getVertexDofs(FiniteElemSpace* feSpace,
- BoundaryObject bound,
- DofContainer& dofs) const
+ void Tetrahedron::getNodeDofs(FiniteElemSpace* feSpace,
+ BoundaryObject bound,
+ DofContainer& dofs) const
{
- FUNCNAME("Tetrahedron::getVertexDofs()");
+ FUNCNAME("Tetrahedron::getNodeDofs()");
switch (bound.subObj) {
case VERTEX:
dofs.push_back(dof[bound.ithObj]);
break;
case EDGE:
- getVertexDofsAtEdge(feSpace, bound, dofs);
+ getNodeDofsAtEdge(feSpace, bound, dofs);
break;
case FACE:
- getVertexDofsAtFace(feSpace, bound, dofs);
+ getNodeDofsAtFace(feSpace, bound, dofs);
break;
default:
ERROR_EXIT("Should not happen!\n");
@@ -222,13 +222,11 @@ namespace AMDiS {
}
- void Tetrahedron::getVertexDofsAtFace(FiniteElemSpace* feSpace,
- BoundaryObject bound,
- DofContainer& dofs) const
+ void Tetrahedron::getNodeDofsAtFace(FiniteElemSpace* feSpace,
+ BoundaryObject bound,
+ DofContainer& dofs) const
{
- FUNCNAME("Tetrahedron::getVertexDofsAtFace()");
-
- // MSG("go at el %d with face %d\n", this->getIndex(), bound.ithObj);
+ FUNCNAME("Tetrahedron::getNodeDofsAtFace()");
if (!child[0])
return;
@@ -238,14 +236,14 @@ namespace AMDiS {
{
BoundaryObject nextBound = bound;
prepareNextBound(nextBound, 1);
- child[1]->getVertexDofs(feSpace, nextBound, dofs);
+ child[1]->getNodeDofs(feSpace, nextBound, dofs);
}
break;
case 1:
{
BoundaryObject nextBound = bound;
prepareNextBound(nextBound, 0);
- child[0]->getVertexDofs(feSpace, nextBound, dofs);
+ child[0]->getNodeDofs(feSpace, nextBound, dofs);
}
break;
@@ -265,19 +263,19 @@ namespace AMDiS {
addDof = false;
if (bound.reverseMode) {
- child[1]->getVertexDofs(feSpace, nextBound1, dofs);
+ child[1]->getNodeDofs(feSpace, nextBound1, dofs);
if (addDof)
dofs.push_back(child[0]->getDof(3));
- child[0]->getVertexDofs(feSpace, nextBound0, dofs);
+ child[0]->getNodeDofs(feSpace, nextBound0, dofs);
} else {
- child[0]->getVertexDofs(feSpace, nextBound0, dofs);
+ child[0]->getNodeDofs(feSpace, nextBound0, dofs);
if (addDof)
dofs.push_back(child[0]->getDof(3));
- child[1]->getVertexDofs(feSpace, nextBound1, dofs);
+ child[1]->getNodeDofs(feSpace, nextBound1, dofs);
}
}
break;
@@ -287,11 +285,11 @@ namespace AMDiS {
}
- void Tetrahedron::getVertexDofsAtEdge(FiniteElemSpace* feSpace,
- BoundaryObject bound,
- DofContainer& dofs) const
+ void Tetrahedron::getNodeDofsAtEdge(FiniteElemSpace* feSpace,
+ BoundaryObject bound,
+ DofContainer& dofs) const
{
- FUNCNAME("Tetrahedron::getVertexDofsAtEdge()");
+ FUNCNAME("Tetrahedron::getNodeDofsAtEdge()");
if (!child[0])
return;
@@ -306,13 +304,13 @@ namespace AMDiS {
nextBound1.reverseMode = false;
if (bound.reverseMode) {
- child[1]->getVertexDofs(feSpace, nextBound0, dofs);
+ child[1]->getNodeDofs(feSpace, nextBound0, dofs);
dofs.push_back(child[0]->getDof(3));
- child[0]->getVertexDofs(feSpace, nextBound1, dofs);
+ child[0]->getNodeDofs(feSpace, nextBound1, dofs);
} else {
- child[0]->getVertexDofs(feSpace, nextBound0, dofs);
+ child[0]->getNodeDofs(feSpace, nextBound0, dofs);
dofs.push_back(child[0]->getDof(3));
- child[1]->getVertexDofs(feSpace, nextBound1, dofs);
+ child[1]->getNodeDofs(feSpace, nextBound1, dofs);
}
break;
@@ -320,17 +318,17 @@ namespace AMDiS {
TEST_EXIT_DBG(nextBound0.ithObj == nextBound1.ithObj)("Should not happen!\n");
if (nextBound0.ithObj != -1)
- child[0]->getVertexDofs(feSpace, nextBound0, dofs);
+ child[0]->getNodeDofs(feSpace, nextBound0, dofs);
break;
default:
TEST_EXIT_DBG(nextBound0.ithObj == -1 || nextBound1.ithObj == -1)
("This should not happen!\n");
if (nextBound0.ithObj != -1)
- child[0]->getVertexDofs(feSpace, nextBound0, dofs);
+ child[0]->getNodeDofs(feSpace, nextBound0, dofs);
if (nextBound1.ithObj != -1)
- child[1]->getVertexDofs(feSpace, nextBound1, dofs);
+ child[1]->getNodeDofs(feSpace, nextBound1, dofs);
}
}
@@ -361,11 +359,11 @@ namespace AMDiS {
}
- void Tetrahedron::getNonVertexDofs(FiniteElemSpace* feSpace,
- BoundaryObject bound,
- DofContainer& dofs) const
+ void Tetrahedron::getHigherOrderDofs(FiniteElemSpace* feSpace,
+ BoundaryObject bound,
+ DofContainer& dofs) const
{
- FUNCNAME("Tetrahedron::getNonVertexDofs()");
+ FUNCNAME("Tetrahedron::getHigherOrderDofs()");
switch (bound.subObj) {
case VERTEX:
@@ -387,12 +385,12 @@ namespace AMDiS {
if (childFace0 != -1) {
nextBound.ithObj = childFace0;
- child[0]->getNonVertexDofs(feSpace, nextBound, dofs);
+ child[0]->getHigherOrderDofs(feSpace, nextBound, dofs);
}
if (childFace1 != -1) {
nextBound.ithObj = childFace1;
- child[1]->getNonVertexDofs(feSpace, nextBound, dofs);
+ child[1]->getHigherOrderDofs(feSpace, nextBound, dofs);
}
} else {
ElementDofIterator elDofIter(feSpace, true);
diff --git a/AMDiS/src/Tetrahedron.h b/AMDiS/src/Tetrahedron.h
index 9adb1c6594e8cea4c11d617063369de269dec82b..07984d3c8091da53721522633db203710b72ed57 100644
--- a/AMDiS/src/Tetrahedron.h
+++ b/AMDiS/src/Tetrahedron.h
@@ -136,21 +136,21 @@ namespace AMDiS {
return "Tetrahedron";
}
- void getVertexDofs(FiniteElemSpace* feSpace,
- BoundaryObject bound,
- DofContainer& dofs) const;
+ void getNodeDofs(FiniteElemSpace* feSpace,
+ BoundaryObject bound,
+ DofContainer& dofs) const;
- void getVertexDofsAtFace(FiniteElemSpace* feSpace,
- BoundaryObject bound,
- DofContainer& dofs) const;
+ void getNodeDofsAtFace(FiniteElemSpace* feSpace,
+ BoundaryObject bound,
+ DofContainer& dofs) const;
- void getVertexDofsAtEdge(FiniteElemSpace* feSpace,
- BoundaryObject bound,
- DofContainer& dofs) const;
+ void getNodeDofsAtEdge(FiniteElemSpace* feSpace,
+ BoundaryObject bound,
+ DofContainer& dofs) const;
- void getNonVertexDofs(FiniteElemSpace* feSpace,
- BoundaryObject bound,
- DofContainer& dofs) const;
+ void getHigherOrderDofs(FiniteElemSpace* feSpace,
+ BoundaryObject bound,
+ DofContainer& dofs) const;
void prepareNextBound(BoundaryObject &bound, int ithChild) const;
diff --git a/AMDiS/src/Triangle.cc b/AMDiS/src/Triangle.cc
index a60cc4368630ed93e3c939aa38c62ca1eab04a71..fec3579d7ba9b12dc5b9311301e82fc0fbfbe06e 100644
--- a/AMDiS/src/Triangle.cc
+++ b/AMDiS/src/Triangle.cc
@@ -87,11 +87,11 @@ namespace AMDiS {
}
- void Triangle::getVertexDofs(FiniteElemSpace* feSpace,
- BoundaryObject bound,
- DofContainer& dofs) const
+ void Triangle::getNodeDofs(FiniteElemSpace* feSpace,
+ BoundaryObject bound,
+ DofContainer& dofs) const
{
- FUNCNAME("Triangle::getVertexDofs()");
+ FUNCNAME("Triangle::getNodeDofs()");
if (bound.subObj == VERTEX) {
dofs.push_back(dof[bound.ithObj]);
@@ -108,16 +108,16 @@ namespace AMDiS {
if (child[1] && child[1]->getFirstChild()) {
if (bound.reverseMode) {
nextBound.ithObj = 1;
- child[1]->getSecondChild()->getVertexDofs(feSpace, nextBound, dofs);
+ child[1]->getSecondChild()->getNodeDofs(feSpace, nextBound, dofs);
dofs.push_back(child[1]->getFirstChild()->getDof(2));
nextBound.ithObj = 0;
- child[1]->getFirstChild()->getVertexDofs(feSpace, nextBound, dofs);
+ child[1]->getFirstChild()->getNodeDofs(feSpace, nextBound, dofs);
} else {
nextBound.ithObj = 0;
- child[1]->getFirstChild()->getVertexDofs(feSpace, nextBound, dofs);
+ child[1]->getFirstChild()->getNodeDofs(feSpace, nextBound, dofs);
dofs.push_back(child[1]->getFirstChild()->getDof(2));
nextBound.ithObj = 1;
- child[1]->getSecondChild()->getVertexDofs(feSpace, nextBound, dofs);
+ child[1]->getSecondChild()->getNodeDofs(feSpace, nextBound, dofs);
}
}
}
@@ -127,16 +127,16 @@ namespace AMDiS {
if (child[0] && child[0]->getFirstChild()) {
if (bound.reverseMode) {
nextBound.ithObj = 1;
- child[0]->getSecondChild()->getVertexDofs(feSpace, nextBound, dofs);
+ child[0]->getSecondChild()->getNodeDofs(feSpace, nextBound, dofs);
dofs.push_back(child[0]->getFirstChild()->getDof(2));
nextBound.ithObj = 0;
- child[0]->getFirstChild()->getVertexDofs(feSpace, nextBound, dofs);
+ child[0]->getFirstChild()->getNodeDofs(feSpace, nextBound, dofs);
} else {
nextBound.ithObj = 0;
- child[0]->getFirstChild()->getVertexDofs(feSpace, nextBound, dofs);
+ child[0]->getFirstChild()->getNodeDofs(feSpace, nextBound, dofs);
dofs.push_back(child[0]->getFirstChild()->getDof(2));
nextBound.ithObj = 1;
- child[0]->getSecondChild()->getVertexDofs(feSpace, nextBound, dofs);
+ child[0]->getSecondChild()->getNodeDofs(feSpace, nextBound, dofs);
}
}
}
@@ -145,16 +145,16 @@ namespace AMDiS {
if (child[0]) {
if (bound.reverseMode) {
nextBound.ithObj = 1;
- child[1]->getVertexDofs(feSpace, nextBound, dofs);
+ child[1]->getNodeDofs(feSpace, nextBound, dofs);
dofs.push_back(child[0]->getDof(2));
nextBound.ithObj = 0;
- child[0]->getVertexDofs(feSpace, nextBound, dofs);
+ child[0]->getNodeDofs(feSpace, nextBound, dofs);
} else {
nextBound.ithObj = 0;
- child[0]->getVertexDofs(feSpace, nextBound, dofs);
+ child[0]->getNodeDofs(feSpace, nextBound, dofs);
dofs.push_back(child[0]->getDof(2));
nextBound.ithObj = 1;
- child[1]->getVertexDofs(feSpace, nextBound, dofs);
+ child[1]->getNodeDofs(feSpace, nextBound, dofs);
}
}
break;
@@ -164,11 +164,11 @@ namespace AMDiS {
}
- void Triangle::getNonVertexDofs(FiniteElemSpace* feSpace,
- BoundaryObject bound,
- DofContainer& dofs) const
+ void Triangle::getHigherOrderDofs(FiniteElemSpace* feSpace,
+ BoundaryObject bound,
+ DofContainer& dofs) const
{
- FUNCNAME("Triange::getNonVertexDofs()");
+ FUNCNAME("Triange::getHigherOrderDofs()");
if (bound.subObj == VERTEX)
return;
@@ -182,7 +182,7 @@ namespace AMDiS {
case 0:
if (child[1]) {
nextBound.ithObj = 2;
- child[1]->getNonVertexDofs(feSpace, nextBound, dofs);
+ child[1]->getHigherOrderDofs(feSpace, nextBound, dofs);
} else {
addThisEdge = true;
}
@@ -191,7 +191,7 @@ namespace AMDiS {
case 1:
if (child[0]) {
nextBound.ithObj = 2;
- child[0]->getNonVertexDofs(feSpace, nextBound, dofs);
+ child[0]->getHigherOrderDofs(feSpace, nextBound, dofs);
} else {
addThisEdge = true;
}
@@ -201,14 +201,14 @@ namespace AMDiS {
if (child[0]) {
if (bound.reverseMode) {
nextBound.ithObj = 1;
- child[1]->getNonVertexDofs(feSpace, nextBound, dofs);
+ child[1]->getHigherOrderDofs(feSpace, nextBound, dofs);
nextBound.ithObj = 0;
- child[0]->getNonVertexDofs(feSpace, nextBound, dofs);
+ child[0]->getHigherOrderDofs(feSpace, nextBound, dofs);
} else {
nextBound.ithObj = 0;
- child[0]->getNonVertexDofs(feSpace, nextBound, dofs);
+ child[0]->getHigherOrderDofs(feSpace, nextBound, dofs);
nextBound.ithObj = 1;
- child[1]->getNonVertexDofs(feSpace, nextBound, dofs);
+ child[1]->getHigherOrderDofs(feSpace, nextBound, dofs);
}
} else {
addThisEdge = true;
diff --git a/AMDiS/src/Triangle.h b/AMDiS/src/Triangle.h
index f6a7f0450e80013269fc82e845aeb3f1f791e58f..4af74f260a22e46b550c76bbffc5bd786410f36e 100644
--- a/AMDiS/src/Triangle.h
+++ b/AMDiS/src/Triangle.h
@@ -194,13 +194,13 @@ namespace AMDiS {
return "Triangle";
}
- void getVertexDofs(FiniteElemSpace* feSpace,
- BoundaryObject bound,
- DofContainer& dofs) const;
-
- void getNonVertexDofs(FiniteElemSpace* feSpace,
- BoundaryObject bound,
- DofContainer& dofs) const;
+ void getNodeDofs(FiniteElemSpace* feSpace,
+ BoundaryObject bound,
+ DofContainer& dofs) const;
+
+ void getHigherOrderDofs(FiniteElemSpace* feSpace,
+ BoundaryObject bound,
+ DofContainer& dofs) const;
protected:
/** \brief
diff --git a/AMDiS/src/parallel/CheckerPartitioner.cc b/AMDiS/src/parallel/CheckerPartitioner.cc
new file mode 100644
index 0000000000000000000000000000000000000000..f4db85177909e7d57a773f913c2b95d34e7d6db6
--- /dev/null
+++ b/AMDiS/src/parallel/CheckerPartitioner.cc
@@ -0,0 +1,41 @@
+//
+// Software License for AMDiS
+//
+// Copyright (c) 2010 Dresden University of Technology
+// All rights reserved.
+// Authors: Simon Vey, Thomas Witkowski et al.
+//
+// This file is part of AMDiS
+//
+// See also license.opensource.txt in the distribution.
+
+
+#include "parallel/CheckerPartitioner.h"
+#include "Traverse.h"
+
+
+namespace AMDiS {
+
+ void CheckerPartitioner::createInitialPartitioning()
+ {
+ FUNCNAME("CheckerPartitioner::createInitialPartitioning()");
+
+ int mpiRank = mpiComm->Get_rank();
+ int mpiSize = mpiComm->Get_size();
+
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL);
+ while (elInfo) {
+ Element *el = elInfo->getElement();
+ int elIndex = el->getIndex();
+ int elInRank = elIndex / 2;
+ TEST_EXIT_DBG(elInRank < mpiSize)("Should not happen!\n");
+
+ elementInRank[elIndex] = (elInRank == mpiRank);
+ partitionMap[elIndex] = elInRank;
+
+ elInfo = stack.traverseNext(elInfo);
+ }
+ }
+
+}
diff --git a/AMDiS/src/parallel/CheckerPartitioner.h b/AMDiS/src/parallel/CheckerPartitioner.h
new file mode 100644
index 0000000000000000000000000000000000000000..26fc87e19283e985f01ae4c28bf47f5a0b297916
--- /dev/null
+++ b/AMDiS/src/parallel/CheckerPartitioner.h
@@ -0,0 +1,56 @@
+// ============================================================================
+// == ==
+// == AMDiS - Adaptive multidimensional simulations ==
+// == ==
+// == http://www.amdis-fem.org ==
+// == ==
+// ============================================================================
+//
+// Software License for AMDiS
+//
+// Copyright (c) 2010 Dresden University of Technology
+// All rights reserved.
+// Authors: Simon Vey, Thomas Witkowski et al.
+//
+// This file is part of AMDiS
+//
+// See also license.opensource.txt in the distribution.
+
+
+
+/** \file CheckerPartitioner.h */
+
+#ifndef AMDIS_CHECKER_PARTITIONER_H
+#define AMDIS_CHECKER_PARTITIONER_H
+
+#include "AMDiS_fwd.h"
+#include "Global.h"
+#include "parallel/MeshPartitioner.h"
+
+namespace AMDiS {
+
+ class CheckerPartitioner : public MeshPartitioner
+ {
+ public:
+ CheckerPartitioner(MPI::Intracomm *comm)
+ : MeshPartitioner(comm)
+ {}
+
+ ~CheckerPartitioner() {}
+
+ void createInitialPartitioning();
+
+ /// \ref MeshPartitioner::partition
+ bool partition(map<int, double> &elemWeights, PartitionMode mode = INITIAL)
+ {
+ return true;
+ }
+
+ void createPartitionMap(map<int, int>& pMap)
+ {
+ pMap = partitionMap;
+ }
+ };
+}
+
+#endif
diff --git a/AMDiS/src/parallel/InteriorBoundary.cc b/AMDiS/src/parallel/InteriorBoundary.cc
index 0e70b9e555b68474087ef3c2936aa3fafa5fbf72..2413e3f9f267cb2ee869691dfa2063e6a850c584 100644
--- a/AMDiS/src/parallel/InteriorBoundary.cc
+++ b/AMDiS/src/parallel/InteriorBoundary.cc
@@ -18,6 +18,27 @@
namespace AMDiS {
+ BoundaryObject::BoundaryObject()
+ : elType(0),
+ reverseMode(false),
+ excludedSubstructures(0)
+ {}
+
+
+ BoundaryObject::BoundaryObject(Element *e,
+ int eType,
+ GeoIndex sObj,
+ int iObj,
+ bool rMode)
+ : el(e),
+ elIndex(e->getIndex()),
+ elType(eType),
+ subObj(sObj),
+ ithObj(iObj),
+ reverseMode(rMode),
+ excludedSubstructures(0)
+ {}
+
bool BoundaryObject::computeReverseMode(BoundaryObject &obj0,
BoundaryObject &obj1,
diff --git a/AMDiS/src/parallel/InteriorBoundary.h b/AMDiS/src/parallel/InteriorBoundary.h
index a8b805b5aeada30a8e3ae56181786c5d5cab3b24..0b5a7fc3a9ec765fbdb10bab4735509db9555603 100644
--- a/AMDiS/src/parallel/InteriorBoundary.h
+++ b/AMDiS/src/parallel/InteriorBoundary.h
@@ -38,21 +38,13 @@ namespace AMDiS {
/// Defines the geometrical objects that forms the boundary;
struct BoundaryObject {
- BoundaryObject()
- : elType(0),
- reverseMode(false),
- excludedSubstructures(0)
- {}
+ BoundaryObject();
- BoundaryObject(Element *e, int eType, GeoIndex sObj, int iObj, bool rMode = false)
- : el(e),
- elIndex(e->getIndex()),
- elType(eType),
- subObj(sObj),
- ithObj(iObj),
- reverseMode(rMode),
- excludedSubstructures(0)
- {}
+ BoundaryObject(Element *e,
+ int eType,
+ GeoIndex sObj,
+ int iObj,
+ bool rMode = false);
static bool computeReverseMode(BoundaryObject &obj0,
BoundaryObject &obj1,
diff --git a/AMDiS/src/parallel/MeshDistributor.cc b/AMDiS/src/parallel/MeshDistributor.cc
index d85c82c6a49ce9bdb80fae252f5579b4cdcba420..07866cfdf642031a07732e1a4b97623a252a86a7 100644
--- a/AMDiS/src/parallel/MeshDistributor.cc
+++ b/AMDiS/src/parallel/MeshDistributor.cc
@@ -26,6 +26,7 @@
#include "parallel/ParMetisPartitioner.h"
#include "parallel/ZoltanPartitioner.h"
#include "parallel/SimplePartitioner.h"
+#include "parallel/CheckerPartitioner.h"
#include "parallel/MpiHelper.h"
#include "io/ElementFileWriter.h"
#include "io/MacroInfo.h"
@@ -112,6 +113,9 @@ namespace AMDiS {
#endif
}
+ if (partStr == "checker")
+ partitioner = new CheckerPartitioner(&mpiComm);
+
if (partStr == "simple")
partitioner = new SimplePartitioner(&mpiComm);
@@ -1658,43 +1662,25 @@ namespace AMDiS {
debug::createSortedDofs(mesh, elMap);
#endif
- typedef std::set<const DegreeOfFreedom*> DofSet;
-
- // === Get all DOFs in ranks partition. ===
+ sendDofs.clear();
+ recvDofs.clear();
- ElementDofIterator elDofIt(feSpace);
- DofSet rankDofSet;
-
- TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
- while (elInfo) {
- elDofIt.reset(elInfo->getElement());
- do {
- rankDofSet.insert(elDofIt.getDofPtr());
- } while(elDofIt.next());
- elInfo = stack.traverseNext(elInfo);
- }
+ // === Get all DOFs in ranks partition. ===
+ std::set<const DegreeOfFreedom*> rankDofSet;
+ mesh->getAllDofs(feSpace, rankDofSet);
- DofContainer rankDofs;
- for (DofSet::iterator it = rankDofSet.begin(); it != rankDofSet.end(); ++it)
- rankDofs.push_back(*it);
+ DofContainer rankDofs(rankDofSet.begin(), rankDofSet.end());
sort(rankDofs.begin(), rankDofs.end(), cmpDofsByValue);
int nRankAllDofs = rankDofs.size();
- // === Traverse on interior boundaries and move all not ranked owned DOFs from ===
- // === rankDofs to boundaryDofs. ===
-
- sendDofs.clear();
- recvDofs.clear();
-
+ // === Traverse interior boundaries and get all DOFs on them. ===
for (InteriorBoundary::iterator it(myIntBoundary); !it.end(); ++it) {
DofContainer dofs;
- it->rankObj.el->getVertexDofs(feSpace, it->rankObj, dofs);
- it->rankObj.el->getNonVertexDofs(feSpace, it->rankObj, dofs);
+ it->rankObj.el->getAllDofs(feSpace, it->rankObj, dofs);
for (unsigned int i = 0; i < dofs.size(); i++)
sendDofs[it.getRank()].push_back(dofs[i]);
@@ -1703,8 +1689,7 @@ namespace AMDiS {
for (InteriorBoundary::iterator it(otherIntBoundary); !it.end(); ++it) {
DofContainer dofs;
- it->rankObj.el->getVertexDofs(feSpace, it->rankObj, dofs);
- it->rankObj.el->getNonVertexDofs(feSpace, it->rankObj, dofs);
+ it->rankObj.el->getAllDofs(feSpace, it->rankObj, dofs);
for (unsigned int i = 0; i < dofs.size(); i++) {
DofContainer::iterator eraseIt =
@@ -1717,32 +1702,26 @@ namespace AMDiS {
}
- nRankDofs = rankDofs.size();
-
- // === Get starting position for global rank dof ordering. ====
+ // === Get starting position for global rank DOF ordering. ====
+ nRankDofs = rankDofs.size();
mpiComm.Scan(&nRankDofs, &rstart, 1, MPI_INT, MPI_SUM);
rstart -= nRankDofs;
+ // === Stores for all rank owned DOFs a new global index. ===
+ DofIndexMap rankDofsNewGlobalIndex;
+ for (int i = 0; i < nRankDofs; i++)
+ rankDofsNewGlobalIndex[rankDofs[i]] = i + rstart;
+
+
// === Calculate number of overall DOFs of all partitions. ===
nOverallDofs = 0;
mpiComm.Allreduce(&nRankDofs, &nOverallDofs, 1, MPI_INT, MPI_SUM);
- // First, we set all dofs in ranks partition to be owend by the rank. Later,
- // the dofs in ranks partition that are owned by other rank are set to false.
- isRankDof.clear();
- for (int i = 0; i < nRankAllDofs; i++)
- isRankDof[i] = true;
- // Stores for all rank owned dofs a new global index.
- DofIndexMap rankDofsNewGlobalIndex;
- for (int i = 0; i < nRankDofs; i++)
- rankDofsNewGlobalIndex[rankDofs[i]] = i + rstart;
-
-
- // === Send new DOF indices. ===
+ // === Send and receive new DOF indices. ===
#if (DEBUG != 0)
ParallelDebug::testDofContainerCommunication(*this, sendDofs, recvDofs);
@@ -1763,6 +1742,13 @@ namespace AMDiS {
stdMpi.startCommunication();
+ // First, we set all DOFs in ranks partition to be owend by the rank. Than,
+ // the DOFs in ranks partition that are owned by other rank are set to false.
+ isRankDof.clear();
+ for (int i = 0; i < nRankAllDofs; i++)
+ isRankDof[i] = true;
+
+
for (RankToDofContainer::iterator recvIt = recvDofs.begin();
recvIt != recvDofs.end(); ++recvIt) {
int j = 0;
@@ -1774,7 +1760,7 @@ namespace AMDiS {
}
- // === Create now the local to global index and local to dof index mappings. ===
+ // === Create now the local to global index and local to DOF index mappings. ===
mapLocalGlobalDofs.clear();
mapLocalDofIndex.clear();
@@ -1784,10 +1770,10 @@ namespace AMDiS {
mapLocalGlobalDofs[*(dofIt->first)] = dofIt->second;
for (int i = 0; i < nRankDofs; i++)
- mapLocalDofIndex[i] = *(rankDofs[i]);
+ mapLocalDofIndex[i] = *(rankDofs[i]);
- // === Update dof admins due to new number of dofs. ===
+ // === Update dof admins due to new number of DOFs. ===
lastMeshChangeIndex = mesh->getChangeIndex();
@@ -1849,10 +1835,8 @@ namespace AMDiS {
TEST_EXIT_DBG(bound.neighObj.el)("No neigh object!\n");
DofContainer dofs0, dofs1;
- bound.rankObj.el->getVertexDofs(feSpace, bound.rankObj, dofs0);
- bound.rankObj.el->getNonVertexDofs(feSpace, bound.rankObj, dofs0);
- bound.neighObj.el->getVertexDofs(feSpace, bound.neighObj, dofs1);
- bound.neighObj.el->getNonVertexDofs(feSpace, bound.neighObj, dofs1);
+ bound.rankObj.el->getAllDofs(feSpace, bound.rankObj, dofs0);
+ bound.neighObj.el->getAllDofs(feSpace, bound.neighObj, dofs1);
TEST_EXIT_DBG(dofs0.size() == dofs1.size())
("Number of DOFs does not fit together: %d %d\n",
@@ -1878,8 +1862,7 @@ namespace AMDiS {
boundIt != it->second.end(); ++boundIt) {
int nDofs = dofs.size();
- boundIt->rankObj.el->getVertexDofs(feSpace, boundIt->rankObj, dofs);
- boundIt->rankObj.el->getNonVertexDofs(feSpace, boundIt->rankObj, dofs);
+ boundIt->rankObj.el->getAllDofs(feSpace, boundIt->rankObj, dofs);
for (unsigned int i = 0; i < (dofs.size() - nDofs); i++)
rankToDofType[it->first].push_back(boundIt->type);
@@ -1931,7 +1914,6 @@ namespace AMDiS {
StdMpi<PeriodicDofMap> stdMpi2(mpiComm);
-
for (RankToBoundMap::iterator it = periodicBoundary.boundary.begin();
it != periodicBoundary.boundary.end(); ++it) {
if (it->first == mpiRank)
@@ -1945,8 +1927,7 @@ namespace AMDiS {
continue;
DofContainer dofs;
- boundIt->rankObj.el->getVertexDofs(feSpace, boundIt->rankObj, dofs);
- boundIt->rankObj.el->getNonVertexDofs(feSpace, boundIt->rankObj, dofs);
+ boundIt->rankObj.el->getAllDofs(feSpace, boundIt->rankObj, dofs);
for (unsigned int i = 0; i < dofs.size(); i++) {
DegreeOfFreedom globalDof = mapLocalGlobalDofs[*dofs[i]];
diff --git a/AMDiS/src/parallel/MeshManipulation.cc b/AMDiS/src/parallel/MeshManipulation.cc
index e17f001194de3a3b01f6d01e5ea24d34f66b4934..b0439acfaa7877af20cca2b4bcb3f462784d1e1c 100644
--- a/AMDiS/src/parallel/MeshManipulation.cc
+++ b/AMDiS/src/parallel/MeshManipulation.cc
@@ -135,10 +135,8 @@ namespace AMDiS {
DofContainer dofs0, dofs1;
- el0->getVertexDofs(feSpace, b0, dofs0);
- el0->getNonVertexDofs(feSpace, b0, dofs0);
- el1->getVertexDofs(feSpace, b1, dofs1);
- el1->getNonVertexDofs(feSpace, b1, dofs1);
+ el0->getAllDofs(feSpace, b0, dofs0);
+ el1->getAllDofs(feSpace, b1, dofs1);
#if (DEBUG != 0)
debug::testDofsByCoords(feSpace, dofs0, dofs1);
@@ -177,10 +175,8 @@ namespace AMDiS {
DofContainer dofs0, dofs1;
- el0->getVertexDofs(feSpace, b0, dofs0);
- el0->getNonVertexDofs(feSpace, b0, dofs0);
- el1->getVertexDofs(feSpace, b1, dofs1);
- el1->getNonVertexDofs(feSpace, b1, dofs1);
+ el0->getAllDofs(feSpace, b0, dofs0);
+ el1->getAllDofs(feSpace, b1, dofs1);
#if (DEBUG != 0)
debug::testDofsByCoords(feSpace, dofs0, dofs1);
diff --git a/AMDiS/src/parallel/MeshPartitioner.cc b/AMDiS/src/parallel/MeshPartitioner.cc
index fb832a2810764108a9b1d6538447e3c123237a7e..5d29a67be68e0d54f592f31d00dd3dbdf874fb57 100644
--- a/AMDiS/src/parallel/MeshPartitioner.cc
+++ b/AMDiS/src/parallel/MeshPartitioner.cc
@@ -34,7 +34,7 @@ namespace AMDiS {
TraverseStack stack;
ElInfo *elInfo =
stack.traverseFirst(mesh, 0,
- Mesh::CALL_EL_LEVEL | Mesh::FILL_NEIGH | Mesh::FILL_COORDS | Mesh::FILL_BOUND);
+ Mesh::CALL_EL_LEVEL | Mesh::FILL_NEIGH | Mesh::FILL_BOUND);
while (elInfo) {
Element *el = elInfo->getElement();
int elIndex = el->getIndex();
@@ -51,7 +51,6 @@ namespace AMDiS {
elementInRank[elIndex] = (elInRank == mpiRank);
partitionMap[elIndex] = elInRank;
}
-
elInfo = stack.traverseNext(elInfo);
}
diff --git a/AMDiS/src/parallel/MeshPartitioner.h b/AMDiS/src/parallel/MeshPartitioner.h
index c8db60cec4cb4f23c9d565285bcecdd171af894f..e5e2f4fcbb706e776c6c4b6920d359a9286cf74f 100644
--- a/AMDiS/src/parallel/MeshPartitioner.h
+++ b/AMDiS/src/parallel/MeshPartitioner.h
@@ -60,7 +60,7 @@ namespace AMDiS {
virtual ~MeshPartitioner() {}
/// Creates an initial paritioning of the AMDiS mesh.
- void createInitialPartitioning();
+ virtual void createInitialPartitioning();
virtual bool partition(map<int, double> &elemWeights,
PartitionMode mode = INITIAL) = 0;
diff --git a/AMDiS/src/parallel/ParallelDebug.cc b/AMDiS/src/parallel/ParallelDebug.cc
index 904b70872cb5d1a6306ff806957a97d7de298532..d7b5e06aa173ea50733e011e28902589c9c066db 100644
--- a/AMDiS/src/parallel/ParallelDebug.cc
+++ b/AMDiS/src/parallel/ParallelDebug.cc
@@ -260,8 +260,7 @@ namespace AMDiS {
continue;
DofContainer dofs;
- boundIt->rankObj.el->getVertexDofs(pdb.feSpace, boundIt->rankObj, dofs);
- boundIt->rankObj.el->getNonVertexDofs(pdb.feSpace, boundIt->rankObj, dofs);
+ boundIt->rankObj.el->getAllDofs(pdb.feSpace, boundIt->rankObj, dofs);
for (unsigned int i = 0; i < dofs.size(); i++) {
WorldVector<double> c;
diff --git a/AMDiS/src/parallel/PetscProblemStat.cc b/AMDiS/src/parallel/PetscProblemStat.cc
index ea6b54372d7b90922f65bb753199e2d375da18e4..a5566466ef0ef75462d1eaa047f6973ddee9de3d 100644
--- a/AMDiS/src/parallel/PetscProblemStat.cc
+++ b/AMDiS/src/parallel/PetscProblemStat.cc
@@ -587,7 +587,6 @@ namespace AMDiS {
FUNCNAME("PetscProblemStat::solvePetscMatrix()");
// === Set old solution to be initiual guess for PETSc solver. ===
-
if (!zeroStartVector) {
VecSet(petscSolVec, 0.0);
@@ -598,7 +597,6 @@ namespace AMDiS {
VecAssemblyEnd(petscSolVec);
}
-
// === Init PETSc solver. ===
KSP solver;
@@ -611,6 +609,7 @@ namespace AMDiS {
// Do not delete the solution vector, use it for the initial guess.
if (!zeroStartVector)
KSPSetInitialGuessNonzero(solver, PETSC_TRUE);
+
// === Run PETSc. ===
diff --git a/AMDiS/src/parallel/PetscSolver.cc b/AMDiS/src/parallel/PetscSolver.cc
index 0522681d5b8ea8e3b676181911bf475141889687..680cab4f92ed4d69c3b0fc350fd795226370d78c 100644
--- a/AMDiS/src/parallel/PetscSolver.cc
+++ b/AMDiS/src/parallel/PetscSolver.cc
@@ -67,7 +67,7 @@ namespace AMDiS {
void PetscSolverSchur::providePetscSolver(KSP &solver, PC &pc)
{
FUNCNAME("PetscSolverSchur::providePetscProblemStat()");
-
+
typedef map<int, DofContainer> RankToDofContainer;
typedef map<DegreeOfFreedom, bool> DofIndexToBool;