diff --git a/AMDiS/libtool b/AMDiS/libtool
index e96f67065e881c5fbc2155783211a810082e9175..5a2f54ef84b5a52ab88b3d32d582ea20b7737675 100755
--- a/AMDiS/libtool
+++ b/AMDiS/libtool
@@ -82,13 +82,13 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="gcc"
+LTCC="/usr/lib/openmpi/1.3.2-gcc//bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="gcc"
+CC="/usr/lib/openmpi/1.3.2-gcc//bin/mpicc"
# Is the compiler the GNU C compiler?
with_gcc=yes
@@ -174,7 +174,7 @@ dlopen_self=unknown
dlopen_self_static=unknown
# Compiler flag to prevent dynamic linking.
-link_static_flag="-static"
+link_static_flag=""
# Compiler flag to turn off builtin functions.
no_builtin_flag=" -fno-builtin"
@@ -6801,13 +6801,13 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="gcc"
+LTCC="/usr/lib/openmpi/1.3.2-gcc//bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="g++"
+CC="/usr/lib/openmpi/1.3.2-gcc//bin/mpiCC"
# Is the compiler the GNU C compiler?
with_gcc=yes
@@ -6893,7 +6893,7 @@ dlopen_self=unknown
dlopen_self_static=unknown
# Compiler flag to prevent dynamic linking.
-link_static_flag="-static"
+link_static_flag=""
# Compiler flag to turn off builtin functions.
no_builtin_flag=" -fno-builtin"
@@ -6960,11 +6960,11 @@ predeps=""
# Dependencies to place after the objects being linked to create a
# shared library.
-postdeps="-lstdc++ -lm -lgcc_s -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/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"`
+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"
@@ -7109,7 +7109,7 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="gcc"
+LTCC="/usr/lib/openmpi/1.3.2-gcc//bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
diff --git a/AMDiS/src/AMDiS_fwd.h b/AMDiS/src/AMDiS_fwd.h
index 8834a3f6c4262c57718886419149567bb13caa73..eb64993d8b1df767bf943c88416cb84183416f53 100644
--- a/AMDiS/src/AMDiS_fwd.h
+++ b/AMDiS/src/AMDiS_fwd.h
@@ -58,6 +58,7 @@ namespace AMDiS {
class MacroInfo;
class Marker;
class Mesh;
+ class MeshStructure;
class OEMSolver;
class Operator;
class OperatorTerm;
diff --git a/AMDiS/src/DOFMatrix.cc b/AMDiS/src/DOFMatrix.cc
index a4a71ed5d2be4a95cc4280ba6ba2c0a93e382c11..fcc84633746208c484027612b498c13ad333fe34 100644
--- a/AMDiS/src/DOFMatrix.cc
+++ b/AMDiS/src/DOFMatrix.cc
@@ -195,7 +195,7 @@ namespace AMDiS {
if (condition && condition->isDirichlet()) {
if (condition->applyBoundaryCondition()) {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
- if (rankDofs[rowIndices[i]])
+ if ((*rankDofs)[rowIndices[i]])
applyDBCs.insert(static_cast<int>(row));
#else
applyDBCs.insert(static_cast<int>(row));
diff --git a/AMDiS/src/DOFMatrix.h b/AMDiS/src/DOFMatrix.h
index ff03a6a0a92958e23412394880f6d815bee61c3c..11fd8c8ca070fdd94f75178f17d5171cc265335b 100644
--- a/AMDiS/src/DOFMatrix.h
+++ b/AMDiS/src/DOFMatrix.h
@@ -406,7 +406,7 @@ namespace AMDiS {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
void setRankDofs(std::map<DegreeOfFreedom, bool>& dofmap)
{
- rankDofs = dofmap;
+ rankDofs = &dofmap;
}
#endif
@@ -488,7 +488,7 @@ namespace AMDiS {
int nnzPerRow;
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
- std::map<DegreeOfFreedom, bool> rankDofs;
+ std::map<DegreeOfFreedom, bool> *rankDofs;
#endif
/// Inserter object: implemented as pointer, allocated and deallocated as needed
diff --git a/AMDiS/src/DOFVector.h b/AMDiS/src/DOFVector.h
index 89c7df7e41a24dd8714382f335167961d91a8235..5993d2a5065a766a45237e87b54fc2b297f35903 100644
--- a/AMDiS/src/DOFVector.h
+++ b/AMDiS/src/DOFVector.h
@@ -211,16 +211,15 @@ namespace AMDiS {
}
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
- inline void setRankDofs(std::map<DegreeOfFreedom, bool> dofmap)
+ inline void setRankDofs(std::map<DegreeOfFreedom, bool> &dofmap)
{
- rankDofs.clear();
-
- // rankDofs = dofmap;
+ // rankDofs = &dofmap;
}
inline bool isRankDof(DegreeOfFreedom dof)
{
- return rankDofs[dof];
+ TEST_EXIT_DBG(rankDofs)("No rank dofs set!\n");
+ return (*rankDofs)[dof];
}
#endif
@@ -269,7 +268,7 @@ namespace AMDiS {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
public:
- std::map<DegreeOfFreedom, bool> rankDofs;
+ std::map<DegreeOfFreedom, bool> *rankDofs;
#endif
};
diff --git a/AMDiS/src/DirichletBC.cc b/AMDiS/src/DirichletBC.cc
index be0b9deb48cafe1f2e57f1554d30b65e2183b077..0ba49876a34f289dfad4fa7f9ad34a90e1c3cfa0 100644
--- a/AMDiS/src/DirichletBC.cc
+++ b/AMDiS/src/DirichletBC.cc
@@ -54,7 +54,7 @@ namespace AMDiS {
for (int i = 0; i < nBasFcts; i++) {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
- if (vector->isRankDof(dofIndices[i]))
+ // if (vector->isRankDof(dofIndices[i]))
#endif
if (localBound[i] == boundaryType) {
if (f) {
diff --git a/AMDiS/src/ElInfo.h b/AMDiS/src/ElInfo.h
index d00b3ca17a89daa4454ee8c85f2e7dda98e88769..b61dc357befd0d580a996c230169090cef728cc4 100644
--- a/AMDiS/src/ElInfo.h
+++ b/AMDiS/src/ElInfo.h
@@ -344,10 +344,7 @@ namespace AMDiS {
*/
double calcDet(const FixVec<WorldVector<double>, VERTEX> &coords) const;
- /** \brief
- * Checks whether flag is set in ElInfo's \ref fillFlag. If not, the program
- * exits.
- */
+ /// Checks whether flag is set in ElInfo's \ref fillFlag. If not, the program exits.
void testFlag(const Flag& flag) const;
/** \brief
@@ -411,7 +408,7 @@ namespace AMDiS {
ERROR("virtual function not implemented in this sub-class ");
- return(0.0);
+ return 0.0;
}
/// Get ElInfo's \ref elType.
diff --git a/AMDiS/src/Element.cc b/AMDiS/src/Element.cc
index 94b987ffdf8ddd5ace7178b7e3daebcd3337866b..e4022eab75f1b13a41c0935aeb5b2ff3eeca8225 100644
--- a/AMDiS/src/Element.cc
+++ b/AMDiS/src/Element.cc
@@ -5,6 +5,7 @@
#include "FixVec.h"
#include "ElementRegion_ED.h"
#include "Serializer.h"
+#include "MeshStructure.h"
namespace AMDiS {
@@ -565,4 +566,31 @@ namespace AMDiS {
return result;
}
+ void fitElementToMeshCode(RefinementManager *refineManager, MeshStructure &code,
+ Element *el, int ithSide, int elType)
+ {
+ if (code.isLeafElement())
+ return;
+
+ if (el->isLeaf()) {
+ el->setMark(1);
+ refineManager->refineMesh(el->getMesh());
+ }
+
+ int s1 = el->getSideOfChild(0, ithSide, elType);
+ int s2 = el->getSideOfChild(1, ithSide, elType);
+
+ code.nextElement();
+
+ if (s1 != -1)
+ fitElementToMeshCode(refineManager, code,
+ el->getFirstChild(), s1, el->getChildType(elType));
+
+ code.nextElement();
+
+ if (s2 != -1)
+ fitElementToMeshCode(refineManager, code,
+ el->getSecondChild(), s2, el->getChildType(elType));
+ }
+
}
diff --git a/AMDiS/src/Element.h b/AMDiS/src/Element.h
index 9a304a1ef70425ba59e6a5fae8e7235435137711..9f9d60d4de5b0af0f7192be3e9e960e9a0eb249c 100644
--- a/AMDiS/src/Element.h
+++ b/AMDiS/src/Element.h
@@ -574,6 +574,11 @@ namespace AMDiS {
friend class Mesh;
};
+ void fitElementToMeshCode(RefinementManager *refineManager,
+ MeshStructure &code,
+ Element *el,
+ int ithSide,
+ int elType);
}
#endif // AMDIS_ELEMENT_H
diff --git a/AMDiS/src/FiniteElemSpace.h b/AMDiS/src/FiniteElemSpace.h
index 81a95708d34a954396eab70b52b3c1d4fb8f8898..359f8f7049f03abea73902dcdeb4383c76ef95f6 100644
--- a/AMDiS/src/FiniteElemSpace.h
+++ b/AMDiS/src/FiniteElemSpace.h
@@ -46,7 +46,7 @@ namespace AMDiS {
static FiniteElemSpace *provideFESpace(DOFAdmin *admin,
const BasisFunction *basFcts,
Mesh *mesh,
- std::string name_ = "");
+ std::string name = "");
/// Destructor.
~FiniteElemSpace();
@@ -92,7 +92,7 @@ namespace AMDiS {
* Constructs a FiniteElemSpace with name name_ and the given DOFAdmin,
* BasisFunction and Mesh.
*/
- FiniteElemSpace(DOFAdmin* admin_,
+ FiniteElemSpace(DOFAdmin* admin,
const BasisFunction* basisFcts,
Mesh* mesh,
std::string name = "");
diff --git a/AMDiS/src/Mesh.h b/AMDiS/src/Mesh.h
index 2779915d46fd2aee7b1543ab029d16007390b597..80e050f48e81f6330c05177bad4a455ee5c940fb 100644
--- a/AMDiS/src/Mesh.h
+++ b/AMDiS/src/Mesh.h
@@ -99,7 +99,7 @@ namespace AMDiS {
}
/// Returns \ref dim of the mesh
- inline int getDim() const \
+ inline int getDim() const
{
return dim;
}
diff --git a/AMDiS/src/MeshStructure.h b/AMDiS/src/MeshStructure.h
index 9e5c64879017c96ca07c91ef5c40f510dbcf264f..7617f52d6ec8ff1da9e908bc4245195f3ecda222 100644
--- a/AMDiS/src/MeshStructure.h
+++ b/AMDiS/src/MeshStructure.h
@@ -53,6 +53,10 @@ namespace AMDiS {
reset();
}
+ /** \brief
+ * Sets all position counters, that are used to traverse the code, to the starting
+ * position. The code itself is not changed.
+ */
void reset();
inline void commit()
diff --git a/AMDiS/src/ParallelDomainBase.cc b/AMDiS/src/ParallelDomainBase.cc
index 6393fe4ebddd91d86a6fb75ad678adeb97c652c5..2f243b29eaaf38d46caa6ca365e888a03be46794 100644
--- a/AMDiS/src/ParallelDomainBase.cc
+++ b/AMDiS/src/ParallelDomainBase.cc
@@ -40,13 +40,13 @@ namespace AMDiS {
ParallelDomainBase::ParallelDomainBase(ProblemIterationInterface *iIF,
ProblemTimeInterface *tIF,
FiniteElemSpace *fe,
- RefinementManager *refineManager)
+ RefinementManager *refinementManager)
: iterationIF(iIF),
timeIF(tIF),
name(iIF->getName()),
feSpace(fe),
mesh(fe->getMesh()),
- refinementManager(refineManager),
+ refineManager(refinementManager),
initialPartitionMesh(true),
nRankDofs(0),
rstart(0),
@@ -100,14 +100,7 @@ namespace AMDiS {
// === Create new global and local DOF numbering. ===
- // Set of all DOFs of the rank.
- std::vector<const DegreeOfFreedom*> rankDofs;
- // Number of DOFs in ranks partition that are owned by the rank.
- nRankDofs = 0;
- // Number of all DOFs in the macro mesh.
- int nOverallDOFs = 0;
-
- createLocalGlobalNumbering(rankDofs, nRankDofs, nOverallDOFs);
+ createLocalGlobalNumbering();
// === Create interior boundary information ===
@@ -120,6 +113,7 @@ namespace AMDiS {
#if (DEBUG != 0)
dbgTestElementMap(elMap);
dbgTestInteriorBoundary();
+ dbgTestCommonDofs(true);
#endif
// === Reset all DOFAdmins of the mesh. ===
@@ -136,33 +130,14 @@ namespace AMDiS {
GET_PARAMETER(0, mesh->getName() + "->global refinements", "%d", &globalRefinement);
if (globalRefinement > 0) {
- refinementManager->globalRefine(mesh, globalRefinement);
-
-#if (DEBUG != 0)
- elMap.clear();
- dbgCreateElementMap(elMap);
-#endif
-
- updateLocalGlobalNumbering(nRankDofs, nOverallDOFs);
+ refineManager->globalRefine(mesh, globalRefinement);
- updateDofAdmins();
-
-#if (DEBUG != 0)
- dbgTestElementMap(elMap);
-#endif
+ updateLocalGlobalNumbering();
// === Update periodic mapping, if there are periodic boundaries. ===
+
createPeriodicMap();
}
-
- lastMeshChangeIndex = mesh->getChangeIndex();
-
-#if (DEBUG != 0)
- dbgTestCommonDofs(true);
-#endif
-
- nRankRows = nRankDofs * nComponents;
- nOverallRows = nOverallDOFs * nComponents;
}
@@ -759,6 +734,8 @@ namespace AMDiS {
void ParallelDomainBase::checkMeshChange()
{
+ FUNCNAME("ParallelDomainBase::checkMeshChange()");
+
// === If mesh has not been changed, return. ===
if (mesh->getChangeIndex() == lastMeshChangeIndex)
@@ -811,8 +788,14 @@ namespace AMDiS {
elCode.init(boundIt->rankObj.el, boundIt->rankObj.ithObj,
boundIt->rankObj.elType);
- if (elCode.getCode() != recvCodes[i].getCode())
+ if (elCode.getCode() != recvCodes[i].getCode()) {
+ TEST_EXIT_DBG(refineManager)("Refinement manager is not set correctly!\n");
+ // recvCodes[i].reset();
+// fitElementToMeshCode(refineManager, recvCodes[i], boundIt->rankObj.el,
+// boundIt->rankObj.ithObj, boundIt->rankObj.elType);
+
meshFitTogether = false;
+ }
i++;
}
@@ -823,7 +806,7 @@ namespace AMDiS {
exit(0);
}
- lastMeshChangeIndex = mesh->getChangeIndex();
+ updateLocalGlobalNumbering();
}
@@ -1207,23 +1190,21 @@ namespace AMDiS {
}
- void ParallelDomainBase::createLocalGlobalNumbering(DofContainer& rankDofs,
- int& nRankDofs,
- int& nOverallDOFs)
+ void ParallelDomainBase::createLocalGlobalNumbering()
{
FUNCNAME("ParallelDomainBase::createLocalGlobalNumbering()");
// === Get rank information about DOFs. ===
// Stores to each DOF pointer the set of ranks the DOF is part of.
- std::map<const DegreeOfFreedom*, std::set<int> > partitionDOFs;
- DofContainer rankAllDofs;
+ DofToPartitions partitionDofs;
+ DofContainer rankDofs, rankAllDofs;
DofToRank boundaryDofs;
- createDofMemberInfo(partitionDOFs, rankDofs, rankAllDofs, boundaryDofs, vertexDof);
+ createDofMemberInfo(partitionDofs, rankDofs, rankAllDofs, boundaryDofs, vertexDof);
nRankDofs = rankDofs.size();
- nOverallDOFs = partitionDOFs.size();
+ int nOverallDofs = partitionDofs.size();
// === Get starting position for global rank dof ordering. ====
@@ -1284,8 +1265,8 @@ namespace AMDiS {
// If the boundary dof is a rank dof, it must be send to other ranks.
// Search for all ranks that have this dof too.
- for (std::set<int>::iterator itRanks = partitionDOFs[it->first].begin();
- itRanks != partitionDOFs[it->first].end();
+ for (std::set<int>::iterator itRanks = partitionDofs[it->first].begin();
+ itRanks != partitionDofs[it->first].end();
++itRanks) {
if (*itRanks != mpiRank) {
TEST_EXIT_DBG(rankDofsNewGlobalIndex.count(it->first) == 1)
@@ -1376,12 +1357,22 @@ namespace AMDiS {
createLocalMappings(rankDofsNewLocalIndex, rankOwnedDofsNewLocalIndex,
rankDofsNewGlobalIndex);
+
+ nRankRows = nRankDofs * nComponents;
+ nOverallRows = nOverallDofs * nComponents;
+
+ lastMeshChangeIndex = mesh->getChangeIndex();
}
- void ParallelDomainBase::updateLocalGlobalNumbering(int& nRankDofs, int& nOverallDOFs)
+ void ParallelDomainBase::updateLocalGlobalNumbering()
{
FUNCNAME("ParallelDomainBase::updateLocalGlobalNumbering()");
+#if (DEBUG != 0)
+ ElementIdxToDofs elMap;
+ dbgCreateElementMap(elMap);
+#endif
+
typedef std::set<const DegreeOfFreedom*> DofSet;
// === Get all DOFs in ranks partition. ===
@@ -1525,10 +1516,11 @@ namespace AMDiS {
// === Calculate number of overall DOFs of all partitions. ===
- mpiComm.Allreduce(&nRankDofs, &nOverallDOFs, 1, MPI_INT, MPI_SUM);
+ int nOverallDofs = 0;
+ mpiComm.Allreduce(&nRankDofs, &nOverallDofs, 1, MPI_INT, MPI_SUM);
- // Do not change the indices now, but create a new indexing a store it here.
+ // Do not change the indices now, but create a new indexing and store it here.
DofIndexMap rankDofsNewLocalIndex;
isRankDof.clear();
int i = 0;
@@ -1611,6 +1603,20 @@ namespace AMDiS {
createLocalMappings(rankDofsNewLocalIndex, rankOwnedDofsNewLocalIndex,
rankDofsNewGlobalIndex);
+
+ nRankRows = nRankDofs * nComponents;
+ nOverallRows = nOverallDofs * nComponents;
+
+ // === Update dof admins due to new number of dofs. ===
+
+ updateDofAdmins();
+
+ lastMeshChangeIndex = mesh->getChangeIndex();
+
+#if (DEBUG != 0)
+ dbgTestElementMap(elMap);
+ dbgTestCommonDofs(true);
+#endif
}
void ParallelDomainBase::createLocalMappings(DofIndexMap &rankDofsNewLocalIndex,
@@ -1722,7 +1728,6 @@ namespace AMDiS {
sort(rankOwnedDofs.begin(), rankOwnedDofs.end(), cmpDofsByValue);
}
-
void ParallelDomainBase::createPeriodicMap()
{
FUNCNAME("ParallelDomainBase::createPeriodicMap()");
diff --git a/AMDiS/src/ParallelDomainBase.h b/AMDiS/src/ParallelDomainBase.h
index ffbb576a783d4afae729b498ba21f1d56dca4d72..28533eca4b776609240c991dd4de54765df5c3c5 100644
--- a/AMDiS/src/ParallelDomainBase.h
+++ b/AMDiS/src/ParallelDomainBase.h
@@ -201,20 +201,11 @@ namespace AMDiS {
/// Removes all macro elements from the mesh that are not part of ranks partition.
void removeMacroElements();
+ /// Creates from a macro mesh a correct local and global DOF index numbering.
+ void createLocalGlobalNumbering();
- /** \brief
- * Creates from a macro mesh a correct local and global DOF index numbering.
- *
- * \param[out] rankDOFs Returns all DOFs from the macro mesh, which are owned
- * by the rank after partitioning the macro mesh.
- * \param[out] nRankDOFs Number of DOFs owned by rank.
- * \param[out] nOverallDOFs Number of all DOFs in macro mesh.
- */
- void createLocalGlobalNumbering(DofContainer& rankDOFs,
- int& nRankDOFs,
- int& nOverallDOFs);
-
- void updateLocalGlobalNumbering(int& nRankDOFs, int& nOverallDOFs);
+ /// Updates the local and global DOF numbering after the mesh has been changed.
+ void updateLocalGlobalNumbering();
/** \brief
* Creates to all dofs in rank's partition that are on a periodic boundary the
@@ -452,12 +443,16 @@ namespace AMDiS {
/// Mesh of the problem.
Mesh *mesh;
+ /** \brief
+ * A refinement manager that should be used on the mesh. It is used to refine
+ * elements at interior boundaries in order to fit together with elements on the
+ * other side of the interior boundary.
+ */
+ RefinementManager *refineManager;
+
/// Info level.
int info;
- /// Refinement manager for the mesh.
- RefinementManager *refinementManager;
-
/// Pointer to the paritioner which is used to devide a mesh into partitions.
ParMetisPartitioner *partitioner;
diff --git a/AMDiS/src/ProblemVec.cc b/AMDiS/src/ProblemVec.cc
index 7c1ed6cc8729fd9db73863315f124e290dadcb8e..8f3d1cf967a1c003dad941c646c25e64cdb1fb87 100644
--- a/AMDiS/src/ProblemVec.cc
+++ b/AMDiS/src/ProblemVec.cc
@@ -621,7 +621,6 @@ namespace AMDiS {
FUNCNAME("ProblemVec::buildAfterCoarsen()");
// printOpenmpTraverseInfo(this, true);
- // buildAfterCoarsen_sebastianMode(adaptInfo, flag);
clock_t first = clock();
#ifdef _OPENMP
@@ -791,200 +790,6 @@ namespace AMDiS {
#endif
}
- void ProblemVec::buildAfterCoarsen_sebastianMode(AdaptInfo *adaptInfo, Flag flag)
- {
- FUNCNAME("ProblemVec::buildAfterCoarsen()");
-
- clock_t first = clock();
-#ifdef _OPENMP
- double wtime = omp_get_wtime();
-#endif
-
- for (int i = 0; i < static_cast<int>(meshes.size()); i++)
- meshes[i]->dofCompress();
-
- Flag assembleFlag =
- flag |
- (*systemMatrix)[0][0]->getAssembleFlag() |
- rhs->getDOFVector(0)->getAssembleFlag() |
- Mesh::CALL_LEAF_EL |
- Mesh::FILL_COORDS |
- Mesh::FILL_DET |
- Mesh::FILL_GRD_LAMBDA |
- Mesh::FILL_NEIGH;
-
- if (useGetBound)
- assembleFlag |= Mesh::FILL_BOUND;
-
- traverseInfo.updateStatus();
-
- // Used to calculate the overall number of non zero entries.
- int nnz = 0;
-
-
- /// === INITIALIZE ===
-
- for (int i = 0; i < nComponents; i++) {
- MSG("%d DOFs for %s\n",
- componentSpaces[i]->getAdmin()->getUsedSize(),
- componentSpaces[i]->getName().c_str());
-
- rhs->getDOFVector(i)->set(0.0);
-
- for (int j = 0; j < nComponents; j++) {
- // Only if this variable is true, the current matrix will be assembled.
- bool assembleMatrix = true;
- // The DOFMatrix which should be assembled (or not, if assembleMatrix
- // will be set to false).
- DOFMatrix *matrix = (*systemMatrix)[i][j];
-
- if (matrix)
- matrix->calculateNnz();
-
- // If the matrix was assembled before and it is marked to be assembled
- // only once, it will not be assembled.
- if (assembleMatrixOnlyOnce[i][j] && assembledMatrix[i][j]) {
- assembleMatrix = false;
- } else if (matrix) {
- matrix->getBaseMatrix().
- change_dim(componentSpaces[i]->getAdmin()->getUsedSize(),
- componentSpaces[j]->getAdmin()->getUsedSize());
-
- set_to_zero(matrix->getBaseMatrix());
- }
-
- // If there is no DOFMatrix, e.g., if it is completly 0, do not assemble.
- if (!matrix || !assembleMatrix)
- assembleMatrix = false;
-
- // If the matrix should not be assembled, the rhs vector has to be considered.
- // This will be only done, if i == j. So, if both is not true, we can jump
- // to the next matrix.
- if (!assembleMatrix && i != j) {
- if (matrix)
- nnz += matrix->getBaseMatrix().nnz();
-
- continue;
- }
-
- if (assembleMatrix && matrix->getBoundaryManager())
- matrix->getBoundaryManager()->initMatrix(matrix);
-
- if (matrix && assembleMatrix)
- matrix->startInsertion(matrix->getNnz());
- }
- }
-
-
- // === TRAVERSE ===
-
- Mesh *mesh = componentMeshes[0];
- const FiniteElemSpace *feSpace = componentSpaces[0];
- const BasisFunction *basisFcts = feSpace->getBasisFcts();
- ElementMatrix elMat(basisFcts->getNumber(), basisFcts->getNumber());
- ElementMatrix tmpElMat(elMat);
- ElementVector elVec(basisFcts->getNumber());
- ElementVector tmpElVec(elVec);
- TraverseStack stack;
- BoundaryType *bound =
- useGetBound ? new BoundaryType[basisFcts->getNumber()] : NULL;
- ElInfo *elInfo = stack.traverseFirst(mesh, -1, assembleFlag);
- while (elInfo) {
- if (useGetBound)
- basisFcts->getBound(elInfo, bound);
-
- for (std::map<Operator*, std::vector<OperatorPos> >::iterator opIt = operators.begin();
- opIt != operators.end(); ++opIt) {
- if (opIt->first->getNeedDualTraverse() == true)
- continue;
-
- if (opFlags[opIt->first].isSet(Operator::MATRIX_OPERATOR)) {
- set_to_zero(elMat);
- opIt->first->getElementMatrix(elInfo, elMat, 1.0);
- }
- if (opFlags[opIt->first].isSet(Operator::VECTOR_OPERATOR)) {
- set_to_zero(elVec);
- opIt->first->getElementVector(elInfo, elVec, 1.0);
- }
-
- for (std::vector<OperatorPos>::iterator posIt = opIt->second.begin();
- posIt != opIt->second.end(); ++posIt) {
-
- if (posIt->operatorType.isSet(Operator::MATRIX_OPERATOR)) {
- if (*(posIt->factor) == 1.0) {
- (*systemMatrix)[posIt->row][posIt->col]->addElementMatrix(elMat, bound, elInfo, NULL);
- } else {
- tmpElMat = *(posIt->factor) * elMat;
- (*systemMatrix)[posIt->row][posIt->col]->addElementMatrix(tmpElMat, bound, elInfo, NULL);
- }
- }
-
- if (posIt->operatorType.isSet(Operator::VECTOR_OPERATOR)) {
- if (*(posIt->factor) == 1.0) {
- rhs->getDOFVector(posIt->row)->addElementVector(1.0, elVec, bound, elInfo);
- } else {
- tmpElVec = *(posIt->factor) * elVec;
- rhs->getDOFVector(posIt->row)->addElementVector(1.0, tmpElVec, bound, elInfo);
- }
- }
- }
- }
-
- elInfo = stack.traverseNext(elInfo);
- }
-
- if (useGetBound)
- delete [] bound;
-
- // === FINELIZE ===
-
- for (int i = 0; i < nComponents; i++) {
- for (int j = 0; j < nComponents; j++) {
- bool assembleMatrix = true;
- DOFMatrix *matrix = (*systemMatrix)[i][j];
-
- if (assembleMatrixOnlyOnce[i][j] && assembledMatrix[i][j])
- assembleMatrix = false;
- if (!matrix || !assembleMatrix)
- assembleMatrix = false;
- if (!assembleMatrix && i != j)
- continue;
-
- assembledMatrix[i][j] = true;
-
- if (assembleMatrix) {
- matrix->removeRowsWithDBC(matrix->getApplyDBCs());
- matrix->finishInsertion();
- }
- if (assembleMatrix && matrix->getBoundaryManager())
- matrix->getBoundaryManager()->exitMatrix(matrix);
- if (matrix)
- nnz += matrix->getBaseMatrix().nnz();
- }
-
- assembleBoundaryConditions(rhs->getDOFVector(i),
- solution->getDOFVector(i),
- componentMeshes[i],
- assembleFlag);
- }
-
- solverMatrix.setMatrix(*systemMatrix);
-
- createPrecon();
-
- INFO(info, 8)("fillin of assembled matrix: %d\n", nnz);
-
-#ifdef _OPENMP
- INFO(info, 8)("buildAfterCoarsen needed %.5f seconds system time / %.5f seconds wallclock time\n",
- TIME_USED(first, clock()), omp_get_wtime() - wtime);
-#else
- INFO(info, 8)("buildAfterCoarsen needed %.5f seconds\n",
- TIME_USED(first, clock()));
-#endif
-
- exit(0);
-
- }
void ProblemVec::createPrecon()
{
@@ -1564,11 +1369,10 @@ namespace AMDiS {
DOFVector<double>::Iterator it1(sol, USED_DOFS);
DOFVector<double>::Iterator it2(tmp, USED_DOFS);
for (it1.reset(), it2.reset(); !it1.end(); ++it1, ++it2) {
- if ((abs(*it1) <= DBL_TOL) || (abs(*it2) <= DBL_TOL)) {
+ if (abs(*it1) <= DBL_TOL || abs(*it2) <= DBL_TOL)
*it2 = 0.0;
- } else {
+ else
*it2 = abs(*it2 / *it1);
- }
}
// Compute estimate for every mesh element
diff --git a/AMDiS/src/ProblemVec.h b/AMDiS/src/ProblemVec.h
index 9dab27d02eaea17e62a24aaf2dff9645045e20e3..b65c4e6974c5ef21ca9f9d980affcf6de2d934cb 100644
--- a/AMDiS/src/ProblemVec.h
+++ b/AMDiS/src/ProblemVec.h
@@ -178,8 +178,6 @@ namespace AMDiS {
bool assembleMatrix = true,
bool assembleVector = true);
- void buildAfterCoarsen_sebastianMode(AdaptInfo *adaptInfo, Flag flag);
-
void createPrecon();
diff --git a/AMDiS/src/StdMpi.h b/AMDiS/src/StdMpi.h
index 1307ae46e7afb663d98d3592094c4f854823ba5b..a0909ab6a7af4921b3baa49488923cfe10227b14 100644
--- a/AMDiS/src/StdMpi.h
+++ b/AMDiS/src/StdMpi.h
@@ -36,7 +36,7 @@ namespace AMDiS {
int intSizeOf(std::vector<MeshStructure> &data)
{
int s = 0;
- for (int i = 0; i < data.size(); i++)
+ for (unsigned int i = 0; i < data.size(); i++)
s += data[i].getCode().size() + 2;
return s;
@@ -71,10 +71,10 @@ namespace AMDiS {
void makeBuf(std::vector<MeshStructure> &data, unsigned long int *buf)
{
int pos = 0;
- for (int i = 0; i < data.size(); i++) {
+ for (unsigned int i = 0; i < data.size(); i++) {
buf[pos++] = data[i].getCode().size();
buf[pos++] = data[i].getNumElements();
- for (int j = 0; j < data[i].getCode().size(); j++)
+ for (unsigned int j = 0; j < data[i].getCode().size(); j++)
buf[pos++] = data[i].getCode()[j];
}
}
diff --git a/AMDiS/src/SurfaceQuadrature.cc b/AMDiS/src/SurfaceQuadrature.cc
index a52ca1ddd617d0f699ab413ef35733ac71c7f60a..4b78d2cab0b68dd06ee7e6f6c97e81d1e73410c6 100644
--- a/AMDiS/src/SurfaceQuadrature.cc
+++ b/AMDiS/src/SurfaceQuadrature.cc
@@ -5,16 +5,16 @@
namespace AMDiS {
- SurfaceQuadrature::SurfaceQuadrature(Quadrature *quad,
- VectorOfFixVecs<DimVec<double> > &coords)
+ SurfaceQuadrature::SurfaceQuadrature(Quadrature *q,
+ VectorOfFixVecs<DimVec<double> > &c)
: Quadrature((quad->getName() + " surface").c_str(),
quad->getDegree(),
quad->getDim() + 1,
quad->getNumPoints(),
NULL,
quad->getWeight()),
- quad_(quad),
- coords_(coords)
+ quad(q),
+ coords(c)
{
lambda = new VectorOfFixVecs<DimVec<double> >(dim, n_points, NO_INIT);
@@ -28,27 +28,27 @@ namespace AMDiS {
for (int j = 0; j < dim; j++)
for (int k = 0; k < dim + 1; k++)
- (*lambda)[i][k] += origin[j] * coords_[j][k];
+ (*lambda)[i][k] += origin[j] * coords[j][k];
}
}
- void SurfaceQuadrature::scaleSurfaceQuadrature(VectorOfFixVecs<DimVec<double> >&coords)
+ void SurfaceQuadrature::scaleSurfaceQuadrature(VectorOfFixVecs<DimVec<double> >&c)
{
// copy coords
for (int i = 0; i < dim; i++)
- coords_[i] = coords[i];
+ coords[i] = c[i];
// for each integration point
for (int i = 0; i < n_points; i++) {
// get coords of quadrature point in dim-1
- DimVec<double> origin = quad_->getLambda(i);
+ DimVec<double> origin = quad->getLambda(i);
for (int j = 0; j < dim + 1; j++)
(*lambda)[i][j] = 0.0;
for (int j = 0; j < dim; j++)
for (int k = 0; k < dim+1; k++)
- (*lambda)[i][k] += origin[j] * coords_[j][k];
+ (*lambda)[i][k] += origin[j] * coords[j][k];
}
}
diff --git a/AMDiS/src/SurfaceQuadrature.h b/AMDiS/src/SurfaceQuadrature.h
index 2a3e156afe2e61b29b7d7c1a692999d57af28efa..9a977e6e6ae57f9974909cc02c9d0cf438644860 100644
--- a/AMDiS/src/SurfaceQuadrature.h
+++ b/AMDiS/src/SurfaceQuadrature.h
@@ -51,9 +51,9 @@ namespace AMDiS {
protected:
/// Pointer to the original quadrature
- Quadrature *quad_;
+ Quadrature *quad;
- VectorOfFixVecs<DimVec<double> > coords_;
+ VectorOfFixVecs<DimVec<double> > coords;
};
}
diff --git a/AMDiS/src/TimedObject.h b/AMDiS/src/TimedObject.h
index d29aa32860344d665df6b76fa7e3dd262e2b7226..a4879d170363205da9187adb4fc937a4c96ca1ff 100644
--- a/AMDiS/src/TimedObject.h
+++ b/AMDiS/src/TimedObject.h
@@ -39,9 +39,9 @@ namespace AMDiS {
{}
/// Sets the time pointer.
- inline void setTimePtr(double *timePtr_)
+ inline void setTimePtr(double *ptr)
{
- timePtr = timePtr_;
+ timePtr = ptr;
}
/// Returns the time pointer.
diff --git a/AMDiS/src/TraverseParallel.h b/AMDiS/src/TraverseParallel.h
index c155dfc1d7aa4714cddb594872de607f811b3361..c61e299b61c95183484044d17fd7ae6a03b795b6 100644
--- a/AMDiS/src/TraverseParallel.h
+++ b/AMDiS/src/TraverseParallel.h
@@ -40,7 +40,7 @@ namespace AMDiS {
~TraverseParallelStack();
- ElInfo* traverseFirst(Mesh *mesh, int level, Flag fill_flag);
+ ElInfo* traverseFirst(Mesh *mesh, int level, Flag fillFlag);
inline ElInfo* traverseNext(ElInfo* elInfoOld)
{