diff --git a/AMDiS/src/ParallelDomainBase.cc b/AMDiS/src/ParallelDomainBase.cc
index eb5ee22b12f0fcd76194f95841b62fbdb4767238..cd1fceaed3a4a095db02f7ad0425b51309ccb670 100644
--- a/AMDiS/src/ParallelDomainBase.cc
+++ b/AMDiS/src/ParallelDomainBase.cc
@@ -1040,6 +1040,7 @@ namespace AMDiS {
periodicBoundary.boundary.size())];
int requestCounter = 0;
+
// === The owner of the boundaries send their atomic boundary order to the ===
// === neighbouring ranks. ===
@@ -1070,6 +1071,10 @@ namespace AMDiS {
MPI::Request::Waitall(requestCounter, request);
+
+ // === The information about all neighbouring boundaries has been received. So ===
+ // === the rank tests if its own atomic boundaries are in the same order. If ===
+ // === not, the atomic boundaries are swaped to the correct order. ===
int i = 0;
for (RankToBoundMap::iterator rankIt = otherIntBoundary.boundary.begin();
@@ -1111,7 +1116,7 @@ namespace AMDiS {
sendBuffers.clear();
- // === Deal with periodic boundaries. ===
+ // === Do the same for the periodic boundaries. ===
requestCounter = 0;
@@ -1213,53 +1218,6 @@ namespace AMDiS {
createDofMemberInfo(partitionDOFs, rankDofs, rankAllDofs, boundaryDofs, vertexDof);
-#if 0
- // TODO: MACHE RICHTIGE FUNKTION
- if (mpiRank == 0) {
- std::cout << "RANK OWNED DOFS: " << std::endl;
- for (DofContainer::iterator dofit = rankDofs.begin();
- dofit != rankDofs.end(); ++dofit) {
- std::cout << **dofit << std::endl;
- WorldVector<double> coords;
- mesh->getDofIndexCoords(*dofit, feSpace, coords);
- coords.print();
- }
-
- std::cout << "RANK ALL DOFS: " << std::endl;
- for (DofContainer::iterator dofit = rankAllDofs.begin();
- dofit != rankAllDofs.end(); ++dofit) {
- std::cout << **dofit << std::endl;
- WorldVector<double> coords;
- mesh->getDofIndexCoords(*dofit, feSpace, coords);
- coords.print();
- }
- }
-#endif
-
- // === BEGIN EXP
-
- DofIndexToBool rankAllDofIndices;
- for (DofContainer::iterator dofIt = rankAllDofs.begin();
- dofIt != rankAllDofs.end(); ++dofIt) {
- rankAllDofIndices[**dofIt] = true;
- }
-
- for (std::map<BoundaryType, VertexVector*>::iterator it = mesh->getPeriodicAssociations().begin();
- it != mesh->getPeriodicAssociations().end(); ++it) {
- VertexVector *tmp = it->second;
- DOFIteratorBase it(const_cast<DOFAdmin*>(tmp->getAdmin()), USED_DOFS);
- for (it.reset(); !it.end(); ++it) {
- if (!it.isDOFFree()) {
- if (!rankAllDofIndices[(*tmp)[it.getDOFIndex()]] &&
- rankAllDofIndices[it.getDOFIndex()])
- // (*tmp)[it.getDOFIndex()] = -1;
- (*tmp)[it.getDOFIndex()] = it.getDOFIndex();
- }
- }
- }
-
- // === ENDE EXP
-
nRankDofs = rankDofs.size();
nOverallDOFs = partitionDOFs.size();
@@ -1434,7 +1392,7 @@ namespace AMDiS {
bool found = false;
- // Iterate over all boundary dofs to find the dof, which index we have to change.
+ // Iterate over all boundary dofs to find the dof which index we have to change.
for (DofToRank::iterator dofIt = boundaryDofs.begin();
dofIt != boundaryDofs.end(); ++dofIt) {
@@ -1457,22 +1415,6 @@ namespace AMDiS {
delete [] recvBuffers[i];
}
- // ====== BEGIN TEST
-
- std::map<int, int> dofIndexMap;
- for (DofIndexMap::iterator dofIt = rankDofsNewLocalIndex.begin();
- dofIt != rankDofsNewLocalIndex.end(); ++dofIt) {
- dofIndexMap[*(dofIt->first)] = dofIt->second;
- }
-
- for (std::map<BoundaryType, VertexVector*>::iterator it = mesh->getPeriodicAssociations().begin();
- it != mesh->getPeriodicAssociations().end(); ++it) {
- it->second->changeDofIndices(dofIndexMap);
- }
-
-
- // ====== ENDE TEST
-
// === Create now the local to global index and local to dof index mappings. ===
@@ -1931,12 +1873,16 @@ namespace AMDiS {
{
FUNCNAME("ParallelDomainBase::createPeriodicMap()");
+ // Clear all periodic dof mappings calculated before. We do it from scratch.
periodicDof.clear();
MPI::Request request[periodicBoundary.boundary.size() * 2];
int requestCounter = 0;
std::vector<int*> sendBuffers, recvBuffers;
+ // === Each rank traverse its periodic boundaries and sends the dof indices ===
+ // === to the rank "on the other side" of the periodic boundary. ===
+
for (RankToBoundMap::iterator it = periodicBoundary.boundary.begin();
it != periodicBoundary.boundary.end(); ++it) {
@@ -1945,34 +1891,29 @@ namespace AMDiS {
DofContainer dofs;
+ // Create dof indices on the boundary.
+
for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
boundIt != it->second.end(); ++boundIt) {
addVertexDofs(boundIt->rankObject.el, boundIt->rankObject.ithObjAtBoundary,
dofs, true);
- // std::cout << "-------: " << dofs.size() << std::endl;
- addEdgeDofs(boundIt->rankObject.el, boundIt->rankObject.ithObjAtBoundary,
+ addEdgeDofs(boundIt->rankObject.el, boundIt->rankObject.ithObjAtBoundary,
dofs);
}
-
- int *sendbuf = new int[dofs.size()];
- for (int i = 0; i < static_cast<int>(dofs.size()); i++) {
- if (mpiRank == 0) {
-// std::cout << "[" << mpiRank << "] SEND DOF "
-// << *(dofs[i]) << " " << mapLocalGlobalDOFs[*(dofs[i])] << std::endl;
-
-// WorldVector<double> coords;
-// mesh->getDofIndexCoords(dofs[i], feSpace, coords);
-// coords.print();
- }
- sendbuf[i] = mapLocalGlobalDOFs[*(dofs[i])];
- }
+ // Send the global indices to the rank on the other side.
+
+ int *sendbuf = new int[dofs.size()];
+ for (int i = 0; i < static_cast<int>(dofs.size()); i++)
+ sendbuf[i] = mapLocalGlobalDOFs[*(dofs[i])];
request[requestCounter++] =
mpiComm.Isend(sendbuf, dofs.size(), MPI_INT, it->first, 0);
sendBuffers.push_back(sendbuf);
+ // Receive from this rank the same number of dofs.
+
int *recvbuf = new int[dofs.size()];
request[requestCounter++] =
mpiComm.Irecv(recvbuf, dofs.size(), MPI_INT, it->first, 0);
@@ -1984,11 +1925,17 @@ namespace AMDiS {
MPI::Request::Waitall(requestCounter, request);
+ // === The rank has received the dofs from the rank on the other side of ===
+ // === the boundary. Now it can use them to create the mapping between ===
+ // === the periodic dofs in this rank and the corresponding periodic ===
+ // === dofs from the other ranks. ===
+
int i = 0;
for (RankToBoundMap::iterator it = periodicBoundary.boundary.begin();
it != periodicBoundary.boundary.end(); ++it) {
DofContainer dofs;
+ // Create the dofs on the boundary in inverse order.
for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
boundIt != it->second.end(); ++boundIt) {
DofContainer tmpdofs;
@@ -1996,61 +1943,21 @@ namespace AMDiS {
tmpdofs);
addVertexDofs(boundIt->rankObject.el, boundIt->rankObject.ithObjAtBoundary,
tmpdofs, true);
- // std::cout << "-------: " << tmpdofs.size() << std::endl;
- for (int j = static_cast<int>(tmpdofs.size()) - 1; j >= 0; j--) {
- dofs.push_back(tmpdofs[j]);
- }
+ for (int j = static_cast<int>(tmpdofs.size()) - 1; j >= 0; j--)
+ dofs.push_back(tmpdofs[j]);
}
- for (int j = 0; j < static_cast<int>(dofs.size()); j++) {
- if (mpiRank == 1) {
-// std::cout << "[" << mpiRank << "] RECV DOF "
-// << *(dofs[j]) << " " << mapLocalGlobalDOFs[*(dofs[j])] << std::endl;
-
-// WorldVector<double> coords;
-// mesh->getDofIndexCoords(dofs[j], feSpace, coords);
-// coords.print();
- }
-
- periodicDof[mapLocalGlobalDOFs[*(dofs[j])]].insert(recvBuffers[i][j]);
- }
+ // Added the received dofs to the mapping.
+ for (int j = 0; j < static_cast<int>(dofs.size()); j++)
+ periodicDof[mapLocalGlobalDOFs[*(dofs[j])]].insert(recvBuffers[i][j]);
delete [] sendBuffers[i];
delete [] recvBuffers[i];
i++;
}
- for (PeriodicDofMap::iterator it = periodicDof.begin();
- it != periodicDof.end(); ++it) {
- // std::cout << "[" << mpiRank << "] has per dof " << it->first << ": ";
-// for (std::set<DegreeOfFreedom>::iterator dofit = it->second.begin();
-// dofit != it->second.end(); ++dofit)
-// std::cout << *dofit << " ";
-// std::cout << std::endl;
-
- int localdof = 0;
-
- for (DofMapping::iterator dofit = mapLocalGlobalDOFs.begin();
- dofit != mapLocalGlobalDOFs.end(); ++dofit)
- if (dofit->second == it->first) {
- localdof = dofit->first;
- break;
- }
-
-// WorldVector<double> coords;
-// mesh->getDofIndexCoords(localdof, feSpace, coords);
-// coords.print();
- }
-
- for (PeriodicDofMap::iterator it = periodicDof.begin();
- it != periodicDof.end(); ++it) {
- if (it->second.size() == 2) {
- std::cout << "IN RANK " << mpiRank << " and dof " << it->first
- << ": " << *(it->second.begin()) << " " << *(++(it->second.begin())) << std::endl;
- }
- }
+ // TODO search for 2 dof mappings.
-
switch (mpiRank) {
case 0:
periodicDof[0].insert(3136);
@@ -2425,7 +2332,7 @@ namespace AMDiS {
}
- void ParallelDomainBase::writeMapLocalGlobal(int rank)
+ void ParallelDomainBase::printMapLocalGlobal(int rank)
{
if (rank == -1 || mpiRank == rank) {
std::cout << "====== DOF MAP LOCAL -> GLOBAL ====== " << std::endl;
@@ -2462,7 +2369,7 @@ namespace AMDiS {
}
- void ParallelDomainBase::writeMapPeriodic(int rank)
+ void ParallelDomainBase::printMapPeriodic(int rank)
{
if (rank == -1 || mpiRank == rank) {
std::cout << "====== DOF MAP PERIODIC ====== " << std::endl;
@@ -2486,7 +2393,33 @@ namespace AMDiS {
coords.print();
}
}
+ }
+
+
+ void ParallelDomainBase::printRankDofs(int rank, DofContainer& rankDofs,
+ DofContainer& rankAllDofs)
+ {
+ if (rank == -1 || mpiRank == rank) {
+ std::cout << "====== RANK DOF INFORMATION ====== " << std::endl;
+
+ std::cout << " RANK OWNED DOFS: " << std::endl;
+ for (DofContainer::iterator dofit = rankDofs.begin();
+ dofit != rankDofs.end(); ++dofit) {
+ std::cout << " " << **dofit << std::endl;
+ WorldVector<double> coords;
+ mesh->getDofIndexCoords(*dofit, feSpace, coords);
+ coords.print();
+ }
+ std::cout << " RANK ALL DOFS: " << std::endl;
+ for (DofContainer::iterator dofit = rankAllDofs.begin();
+ dofit != rankAllDofs.end(); ++dofit) {
+ std::cout << " " << **dofit << std::endl;
+ WorldVector<double> coords;
+ mesh->getDofIndexCoords(*dofit, feSpace, coords);
+ coords.print();
+ }
+ }
}
diff --git a/AMDiS/src/ParallelDomainBase.h b/AMDiS/src/ParallelDomainBase.h
index 71c073368bb895b3222af3c4c6e5f9bae1811007..84e0c19874ab270da4e17786a4878bc79f064716 100644
--- a/AMDiS/src/ParallelDomainBase.h
+++ b/AMDiS/src/ParallelDomainBase.h
@@ -214,6 +214,11 @@ namespace AMDiS {
void updateLocalGlobalNumbering(int& nRankDOFs, int& nOverallDOFs);
+ /** \brief
+ * Creates to all dofs in rank's partition that are on a periodic boundary the
+ * mapping from dof index to the other periodic dof indices. This information
+ * is stored in \ref periodicDof.
+ */
void createPeriodicMap();
/** \brief
@@ -311,7 +316,7 @@ namespace AMDiS {
*
* \param rank If specified, only the information from the given rank is printed.
*/
- void writeMapLocalGlobal(int rank = -1);
+ void printMapLocalGlobal(int rank = -1);
/** \brief
* This function is used for debugging only. It prints all information about
@@ -319,7 +324,18 @@ namespace AMDiS {
*
* \param rank If specified, only the information from the given rank is printed.
*/
- void writeMapPeriodic(int rank = -1);
+ void printMapPeriodic(int rank = -1);
+
+ /** \brief
+ * This function is used for debugging only. It prints information about dofs
+ * in rank's partition.
+ *
+ * \param rank If specified, only the information from the given
+ * rank is printed.
+ * \param rankDofs List of all dofs in ranks partition that are owned by rank.
+ * \param rankAllDofs List of all dofs in ranks partition.
+ */
+ void printRankDofs(int rank, DofContainer& rankDofs, DofContainer& rankAllDofs);
/** \brief
* This functions create a Paraview file with the macro mesh where the elements
@@ -547,6 +563,11 @@ namespace AMDiS {
*/
DofToBool vertexDof;
+ /** \brief
+ * If periodic boundaries are used, this map stores to each dof in rank's
+ * partition, that is on periodic boundaries, the corresponding periodic dofs.
+ * The mapping is defined by using global dof indices.
+ */
PeriodicDofMap periodicDof;
/// Is the index of the first row of the linear system, which is owned by the rank.
diff --git a/AMDiS/src/ParallelDomainVec.cc b/AMDiS/src/ParallelDomainVec.cc
index c9e661b9d38e17638717d38981ac9ac303ddc02a..1cd925470b4d902b58ac5978245ab3c8d424d54d 100644
--- a/AMDiS/src/ParallelDomainVec.cc
+++ b/AMDiS/src/ParallelDomainVec.cc
@@ -68,15 +68,24 @@ namespace AMDiS {
probVec->getSolution()->getDOFVector(i)->setRankDofs(isRankDof);
}
+ // === Remove periodic boundary conditions in sequential problem definition. ===
+
+ // Remove periodic boundaries in boundary manager on matrices and vectors.
for (int i = 0; i < nComponents; i++) {
- for (int j = 0; j < nComponents; j++)
- if (probVec->getSystemMatrix(i, j) && probVec->getSystemMatrix(i, j)->getBoundaryManager())
- removeBoundaryCondition(const_cast<BoundaryIndexMap&>(probVec->getSystemMatrix(i, j)->getBoundaryManager()->getBoundaryConditionMap()));
+ for (int j = 0; j < nComponents; j++) {
+ DOFMatrix* mat = probVec->getSystemMatrix(i, j);
+ if (mat && mat->getBoundaryManager())
+ removeBoundaryCondition(const_cast<BoundaryIndexMap&>(mat->getBoundaryManager()->getBoundaryConditionMap()));
+ }
if (probVec->getSolution()->getDOFVector(i)->getBoundaryManager())
removeBoundaryCondition(const_cast<BoundaryIndexMap&>(probVec->getSolution()->getDOFVector(i)->getBoundaryManager()->getBoundaryConditionMap()));
+
+ if (probVec->getRHS()->getDOFVector(i)->getBoundaryManager())
+ removeBoundaryCondition(const_cast<BoundaryIndexMap&>(probVec->getRHS()->getDOFVector(i)->getBoundaryManager()->getBoundaryConditionMap()));
}
+ // Remove periodic boundaries on elements in mesh.
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
while (elInfo) {
diff --git a/AMDiS/src/ParallelDomainVec.h b/AMDiS/src/ParallelDomainVec.h
index 40b4b603f25c389ee7292e432929e5f9b25428da..f1d42e622a53372d9f5966d3e892328a59a340af 100644
--- a/AMDiS/src/ParallelDomainVec.h
+++ b/AMDiS/src/ParallelDomainVec.h
@@ -63,6 +63,7 @@ namespace AMDiS {
/// Starts the solution of the linear system using Petsc.
void solve();
+ // Removes all periodic boundaries from a given boundary map.
void removeBoundaryCondition(BoundaryIndexMap& boundaryMap);
protected: