diff --git a/AMDiS/src/Traverse.cc b/AMDiS/src/Traverse.cc
index b8149f8db4afab787f00abff687b1aae94800900..ca1f20b1dae1642128d7daabad5811d4ed6dafc3 100644
--- a/AMDiS/src/Traverse.cc
+++ b/AMDiS/src/Traverse.cc
@@ -28,7 +28,7 @@ namespace AMDiS {
ElInfo* TraverseStack::traverseFirst(Mesh *mesh, int level, Flag fill_flag)
{
FUNCNAME("TraverseStack::traverseFirst()");
-
+
TEST_EXIT_DBG(fill_flag.isSet(Mesh::CALL_REVERSE_MODE) == false ||
fill_flag.isSet(Mesh::CALL_EVERY_EL_PREORDER))
("Not yet implemented!\n");
diff --git a/AMDiS/src/io/FileWriter.cc b/AMDiS/src/io/FileWriter.cc
index ba198dc8e10a109579f8bb520b16f38630424c8c..b67440da15b1c1dba33f4579e37f43a834ced612 100644
--- a/AMDiS/src/io/FileWriter.cc
+++ b/AMDiS/src/io/FileWriter.cc
@@ -159,14 +159,6 @@ namespace AMDiS {
// vtkVectorWriter.setWriteAs3dVector(writeAs3dVector);
// vtkVectorWriter.writeFile(fn + paraviewFileExt);
-#if HAVE_PARALLEL_DOMAIN_AMDIS
- ERROR_EXIT("Simon must make some work in this, does not compile in parallel!\n");
-// if (MPI::COMM_WORLD.Get_rank() == 0)
-// vtkVectorWriter.writeParallelFile(paraFilename + paraviewParallelFileExt,
-// MPI::COMM_WORLD.Get_size(),
-// filename, postfix);
-#endif
-
MSG("ParaView file written to %s\n", (fn + paraviewFileExt).c_str());
}
diff --git a/AMDiS/src/parallel/ElementObjectDatabase.cc b/AMDiS/src/parallel/ElementObjectDatabase.cc
index a484363fa2d8a20f90baaba204ad3ec1f8a56fee..93308fb6937cc6621173c1f5f5507418076748d4 100644
--- a/AMDiS/src/parallel/ElementObjectDatabase.cc
+++ b/AMDiS/src/parallel/ElementObjectDatabase.cc
@@ -140,6 +140,12 @@ namespace AMDiS {
if (periodicVertices.size() == 0)
return;
+ // === Calculate smallest periodic boundary ID in mesh. ===
+
+ smallestPeriodicBcType = 0;
+ for (map<BoundaryType, VertexVector*>::iterator it = mesh->getPeriodicAssociations().begin();
+ it != mesh->getPeriodicAssociations().end(); ++it)
+ smallestPeriodicBcType = std::min(smallestPeriodicBcType, it->first);
// === Get all vertex DOFs that have multiple periodic associations. ===
diff --git a/AMDiS/src/parallel/ElementObjectDatabase.h b/AMDiS/src/parallel/ElementObjectDatabase.h
index bb8d857ad7dfc067d9b71aa825b5df8765de3b7a..b68005ad799eac238b51ac7c7150dd239e7297d1 100644
--- a/AMDiS/src/parallel/ElementObjectDatabase.h
+++ b/AMDiS/src/parallel/ElementObjectDatabase.h
@@ -450,6 +450,14 @@ namespace AMDiS {
return (periodicVertices.size() != 0);
}
+ /// Returns true if the given boundary type is larger or equal to the smallest
+ /// periodic boundary ID in mesh. See \ref smallestPeriodicBcType for more
+ /// information.
+ bool isValidPeriodicType(BoundaryType t) const
+ {
+ return (t >= smallestPeriodicBcType);
+ }
+
/// Write the element database to disk.
void serialize(ostream &out);
@@ -574,15 +582,21 @@ namespace AMDiS {
map<pair<BoundaryType, BoundaryType>, BoundaryType> bConnMap;
- // The following three data structures store periodic DOFs, edges and faces.
+ /// The following three data structures store periodic DOFs, edges and faces.
PerBoundMap<DegreeOfFreedom>::type periodicVertices;
PerBoundMap<DofEdge>::type periodicEdges;
PerBoundMap<DofFace>::type periodicFaces;
- // Stores to each vertex all its periodic associations.
+ /// Defines the smallest boudary ID for periodic boundary conditions. This is
+ /// required to distinguish between "real" periodic boundaries and periodic
+ /// boundary IDs that are set by the parallel algorithm for indirectly
+ /// connected boundaries.
+ BoundaryType smallestPeriodicBcType;
+
+ /// Stores to each vertex all its periodic associations.
map<DegreeOfFreedom, std::set<BoundaryType> > periodicDofAssoc;
- // Stores to each edge all its periodic associations.
+ /// Stores to each edge all its periodic associations.
map<DofEdge, std::set<DofEdge> > periodicEdgeAssoc;
map<pair<ElementObjectData, ElementObjectData>, bool> edgeReverseMode;
diff --git a/AMDiS/src/parallel/MeshDistributor.cc b/AMDiS/src/parallel/MeshDistributor.cc
index 452543424c4bb669a5c46c47734a7ea15513f035..c02706bef0a7881eabfd155750d0af5076f8c9fd 100644
--- a/AMDiS/src/parallel/MeshDistributor.cc
+++ b/AMDiS/src/parallel/MeshDistributor.cc
@@ -132,6 +132,8 @@ namespace AMDiS {
{
FUNCNAME("MeshDistributor::initParallelization()");
+ MSG("RUN INIT\n");
+
if (initialized)
return;
@@ -2067,13 +2069,6 @@ namespace AMDiS {
{
FUNCNAME("MeshDistributor::createPeriodicMap()");
-
-// vector<ElementObjectData> objs = elObjDb.getElements(0);
-// MSG("SIZE OF 0-DOF is: %d\n", objs.size());
-
-// for (int i = 0; i < objs.size(); i++)
-// MSG("0-DOF IN EL %d - %d\n", objs[i].elIndex, objs[i].ithObject);
-
StdMpi<vector<int> > stdMpi(mpiComm, false);
// === Each rank traverse its periodic boundaries and sends the DOF ===
@@ -2112,15 +2107,8 @@ namespace AMDiS {
DegreeOfFreedom globalDof1 =
dofFeData[feSpace].mapDofToGlobal[*(dofs1[j])];
- if (!periodicMap.isPeriodicOnBound(feSpace, type, globalDof0)) {
-// if (globalDof0 == 0) {
-// MSG("A-ADD DOF 0 at BOUND: %d %d %d <-> %d %d %d \n",
-// bound.rankObj.elIndex, bound.rankObj.subObj, bound.rankObj.ithObj,
-// bound.neighObj.elIndex, bound.neighObj.subObj, bound.neighObj.ithObj);
-// }
-
+ if (!periodicMap.isPeriodicOnBound(feSpace, type, globalDof0))
periodicMap.add(feSpace, type, globalDof0, globalDof1);
- }
}
}
@@ -2132,9 +2120,6 @@ namespace AMDiS {
for (vector<AtomicBoundary>::iterator boundIt = it->second.begin();
boundIt != it->second.end(); ++boundIt) {
-// MSG(" NOW ADD DOFS ON PER BOUND EL %d %d with rank %d\n",
-// boundIt->rankObj.elIndex, boundIt->rankObj.subObj, it->first);
-
int nDofs = dofs.size();
boundIt->rankObj.el->getAllDofs(feSpace, boundIt->rankObj, dofs);
@@ -2177,14 +2162,8 @@ namespace AMDiS {
// Check if this global DOF with the corresponding boundary type was
// not added before by another periodic boundary from other rank.
- if (!periodicMap.isPeriodicOnBound(feSpace, type, globalDofIndex)) {
-// MSG("B-ADD DOF %d -> %d at BOUND from rank %d\n",
-// globalDofIndex,
-// mapGlobalDofIndex,
-// it->first);
-
+ if (!periodicMap.isPeriodicOnBound(feSpace, type, globalDofIndex))
periodicMap.add(feSpace, type, globalDofIndex, mapGlobalDofIndex);
- }
}
}
@@ -2201,7 +2180,9 @@ namespace AMDiS {
for (vector<AtomicBoundary>::iterator boundIt = it->second.begin();
boundIt != it->second.end(); ++boundIt) {
- if (boundIt->type >= -3)
+ // If the boundary type is a normal periodic BC, continue. We just
+ // operate on indirectly connected periodic boundaries.
+ if (elObjDb.isValidPeriodicType(boundIt->type))
continue;
DofContainer dofs;
@@ -2217,15 +2198,9 @@ namespace AMDiS {
for (std::set<BoundaryType>::iterator perAscIt = assoc.begin();
perAscIt != assoc.end(); ++perAscIt)
- if (*perAscIt >= -3) {
-// MSG(" add map DOF %d -> %d (%d)\n",
-// globalDof,
-// periodicMap.map(feSpace, *perAscIt, globalDof),
-// *perAscIt);
-
+ if (elObjDb.isValidPeriodicType(*perAscIt))
perObjMap[*perAscIt][globalDof] =
- periodicMap.map(feSpace, *perAscIt, globalDof);
- }
+ periodicMap.map(feSpace, *perAscIt, globalDof);
}
}
@@ -2240,7 +2215,7 @@ namespace AMDiS {
// DOFs. I'm note sure what is correct here.
for (map<int, PeriodicDofMap>::iterator it = stdMpi2.getRecvData().begin();
it != stdMpi2.getRecvData().end(); ++it)
- periodicMap.add(feSpace, it->second);
+ periodicMap.add(feSpace, it->second, false);
}
diff --git a/AMDiS/src/parallel/MeshDistributor.h b/AMDiS/src/parallel/MeshDistributor.h
index 49c79d5da4a16453e3fe455a42a2fdbe0151a93d..95cea99cd2afcdaaff734e3dfb1f858f0c84aa6f 100644
--- a/AMDiS/src/parallel/MeshDistributor.h
+++ b/AMDiS/src/parallel/MeshDistributor.h
@@ -443,11 +443,13 @@ namespace AMDiS {
void getAllBoundaryDofs(const FiniteElemSpace *feSpace,
DofContainer& dofs);
+ const ElementObjectDatabase& getElementObjectDb()
+ {
+ return elObjDb;
+ }
- public:
/// Adds a stationary problem to the global mesh distributor objects.
static void addProblemStatGlobal(ProblemStatSeq *probStat);
-
protected:
void addProblemStat(ProblemStatSeq *probStat);
diff --git a/AMDiS/src/parallel/PeriodicMap.cc b/AMDiS/src/parallel/PeriodicMap.cc
index 31636ce06cf155fb0c919b65e482884e94c3d741..5dfd1b50873f032ee22384f422f4dad0e3bf1902 100644
--- a/AMDiS/src/parallel/PeriodicMap.cc
+++ b/AMDiS/src/parallel/PeriodicMap.cc
@@ -16,14 +16,15 @@
namespace AMDiS {
void PeriodicMap::add(const FiniteElemSpace *feSpace,
- PeriodicDofMap &newMap)
+ PeriodicDofMap &newMap,
+ bool a)
{
FUNCNAME("PeriodicMap::add()");
for (PeriodicDofMap::iterator it = newMap.begin(); it != newMap.end(); ++it)
for (DofMap::iterator dofIt =it->second.begin();
dofIt != it->second.end(); ++dofIt)
- add(feSpace, it->first, dofIt->second, dofIt->first);
+ add(feSpace, it->first, dofIt->second, dofIt->first, a);
}
diff --git a/AMDiS/src/parallel/PeriodicMap.h b/AMDiS/src/parallel/PeriodicMap.h
index 11da11dab7c2ac0c5c93790870fc5761c88bc7a3..8a0814880f5a0bf59c7b449d202b90bd7375e325 100644
--- a/AMDiS/src/parallel/PeriodicMap.h
+++ b/AMDiS/src/parallel/PeriodicMap.h
@@ -101,7 +101,8 @@ namespace AMDiS {
/// this DOFs that maps to a different DOF index than the given one.
inline void add(const FiniteElemSpace *feSpace,
BoundaryType type,
- DegreeOfFreedom dof0, DegreeOfFreedom dof1)
+ DegreeOfFreedom dof0, DegreeOfFreedom dof1,
+ bool a = true)
{
FUNCNAME("PeriodicMap::map()");
@@ -110,12 +111,13 @@ namespace AMDiS {
("Should not happen!\n");
periodicDofMap[feSpace][type][dof0] = dof1;
- periodicDofAssociations[feSpace][dof0].insert(type);
+ if (a)
+ periodicDofAssociations[feSpace][dof0].insert(type);
}
/// Adds a whole periodic mapping to the current one.
- void add(const FiniteElemSpace *feSpace, PeriodicDofMap &newMap);
+ void add(const FiniteElemSpace *feSpace, PeriodicDofMap &newMap, bool a = true);
/// For a given global DOF index, this function returns the set of periodic
diff --git a/AMDiS/src/parallel/PetscSolverGlobalMatrix.cc b/AMDiS/src/parallel/PetscSolverGlobalMatrix.cc
index a621412e6a452635b1e86d9c0313ac510e546421..3e30747d17c7579d447c6e56175278d1a02a9ad8 100644
--- a/AMDiS/src/parallel/PetscSolverGlobalMatrix.cc
+++ b/AMDiS/src/parallel/PetscSolverGlobalMatrix.cc
@@ -307,7 +307,7 @@ namespace AMDiS {
std::set<int>& perColAsc = perMap.getAssociations(colFe, globalColDof);
for (std::set<int>::iterator it = perColAsc.begin();
it != perColAsc.end(); ++it)
- if (*it >= -3)
+ if (meshDistributor->getElementObjectDb().isValidPeriodicType(*it))
perAsc.insert(*it);
// Scale value to the number of periodic associations of the column index.
@@ -322,7 +322,7 @@ namespace AMDiS {
// First, add the original matrix index.
newCols.push_back(globalColDof);
-
+
// And add all periodic matrix indices.
for (std::set<int>::iterator it = perAsc.begin();
it != perAsc.end(); ++it) {
@@ -377,14 +377,14 @@ namespace AMDiS {
std::set<int>& perColAsc = perMap.getAssociations(colFe, globalColDof);
for (std::set<int>::iterator it = perColAsc.begin();
it != perColAsc.end(); ++it)
- if (*it >= -3)
+ if (meshDistributor->getElementObjectDb().isValidPeriodicType(*it))
perAsc.insert(*it);
}
std::set<int>& perRowAsc = perMap.getAssociations(rowFe, globalRowDof);
for (std::set<int>::iterator it = perRowAsc.begin();
it != perRowAsc.end(); ++it)
- if (*it >= -3)
+ if (meshDistributor->getElementObjectDb().isValidPeriodicType(*it))
perAsc.insert(*it);
// Scale the value with respect to the number of periodic associations.