Skip to content

GitLab

Commit 7856d906 authored by Thomas Witkowski's avatar Thomas Witkowski
Browse files
Options

Periodic boundary conditions with mixed finite elements in parallel should work now.

parent 6bfde321
Hide whitespace changes
Inline Side-by-side
Showing with 436 additions and 265 deletions
AMDiS/src/DOFMatrix.cc
View file @ 7856d906
......@@ -57,7 +57,7 @@ namespace AMDiS {
FUNCNAME("DOFMatrix::DOFMatrix()");
TEST_EXIT(rowFeSpace)("No fe space for row!\n");
if (!colFeSpace)
colFeSpace = rowFeSpace;
......@@ -211,16 +211,18 @@ namespace AMDiS {
using namespace mtl;
#if 0
std::cout << "----- PRINT MAT " << rowElInfo->getElement()->getIndex() << "--------" << std::endl;
std::cout << elMat << std::endl;
std::cout << "rows: ";
for (int i = 0; i < rowIndices.size(); i++)
std::cout << rowIndices[i] << " ";
std::cout << std::endl;
std::cout << "cols: ";
for (int i = 0; i < colIndices.size(); i++)
std::cout << colIndices[i] << " ";
std::cout << std::endl;
if (MPI::COMM_WORLD.Get_rank() == 0) {
std::cout << "----- PRINT MAT " << rowElInfo->getElement()->getIndex() << "--------" << std::endl;
std::cout << elMat << std::endl;
std::cout << "rows: ";
for (int i = 0; i < rowIndices.size(); i++)
std::cout << rowIndices[i] << " ";
std::cout << std::endl;
std::cout << "cols: ";
for (int i = 0; i < colIndices.size(); i++)
std::cout << colIndices[i] << " ";
std::cout << std::endl;
}
#endif
for (int i = 0; i < nRow; i++) {
......@@ -229,7 +231,7 @@ namespace AMDiS {
BoundaryCondition *condition =
bound ? boundaryManager->getBoundaryCondition(bound[i]) : NULL;
if (condition && condition->isDirichlet()) {
if (condition && condition->isDirichlet()) {
if (condition->applyBoundaryCondition()) {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
if ((*rankDofs)[rowIndices[i]])
......@@ -241,8 +243,9 @@ namespace AMDiS {
} else {
for (int j = 0; j < nCol; j++) {
DegreeOfFreedom col = colIndices[j];
if (fabs(elMat[i][j]) > 1e-10)
if (fabs(elMat[i][j]) > 1e-10) {
ins[row][col] += elMat[i][j];
}
}
}
}
......@@ -259,7 +262,9 @@ namespace AMDiS {
{}
void DOFMatrix::assemble(double factor, ElInfo *elInfo, const BoundaryType *bound)
void DOFMatrix::assemble(double factor,
ElInfo *elInfo,
const BoundaryType *bound)
{
FUNCNAME("DOFMatrix::assemble()");
......@@ -278,7 +283,9 @@ namespace AMDiS {
}
void DOFMatrix::assemble(double factor, ElInfo *elInfo, const BoundaryType *bound,
void DOFMatrix::assemble(double factor,
ElInfo *elInfo,
const BoundaryType *bound,
Operator *op)
{
FUNCNAME("DOFMatrix::assemble()");
......
AMDiS/src/ProblemStat.cc
View file @ 7856d906
......@@ -1356,6 +1356,10 @@ namespace AMDiS {
{
FUNCNAME("ProblemStat::addMatrixOperator()");
TEST_EXIT(i < nComponents && j < nComponents)
("Cannot add matrix operator at position %d/%d. The stationary problem has only %d components!\n",
i, j, nComponents);
TEST_EXIT(!boundaryConditionSet)
("Do not add operators after boundary conditions were set!\n");
......@@ -1402,6 +1406,10 @@ namespace AMDiS {
{
FUNCNAME("ProblemStat::addVectorOperator()");
TEST_EXIT(i < nComponents)
("Cannot add vector operator at position %d. The stationary problem has only %d components!\n",
i, nComponents);
TEST_EXIT(!boundaryConditionSet)
("Do not add operators after boundary conditions were set!\n");
......
AMDiS/src/SubAssembler.h
View file @ 7856d906
......@@ -64,17 +64,13 @@ namespace AMDiS {
/// Destructor
virtual ~SubAssembler() {}
/** \brief
* Calculates the element matrix for elInfo and adds it to mat. Memory
* for mat must be provided by the caller.
*/
/// Calculates the element matrix for elInfo and adds it to mat. Memory for
/// mat must be provided by the caller.
virtual void calculateElementMatrix(const ElInfo *elInfo,
ElementMatrix& mat) = 0;
/** \brief
* Calculates the element vector for elInfo and adds it to vec. Memory
* for vec must be provided by the caller.
*/
/// Calculates the element vector for elInfo and adds it to vec. Memory for
/// vec must be provided by the caller.
virtual void calculateElementVector(const ElInfo *elInfo,
ElementVector& vec) = 0;
......@@ -104,10 +100,8 @@ namespace AMDiS {
WorldVector<double>* getCoordsAtQPs(const ElInfo* elInfo,
Quadrature *quad = NULL);
/** \brief
* DOFVector dv evaluated at quadrature points.
* Used by \ref OperatorTerm::initElement().
*/
/// DOFVector dv evaluated at quadrature points.
/// Used by \ref OperatorTerm::initElement().
template<typename T>
void getVectorAtQPs(DOFVectorBase<T>* dv,
const ElInfo* elInfo,
......@@ -122,10 +116,8 @@ namespace AMDiS {
Quadrature *quad,
mtl::dense_vector<T>& vecAtQPs);
/** \brief
* Gradients of DOFVector dv evaluated at quadrature points.
* Used by \ref OperatorTerm::initElement().
*/
/// Gradients of DOFVector dv evaluated at quadrature points.
/// Used by \ref OperatorTerm::initElement().
template<typename T>
void getGradientsAtQPs( DOFVectorBase<T>* dv,
const ElInfo* elInfo,
......@@ -139,11 +131,10 @@ namespace AMDiS {
Quadrature *quad,
mtl::dense_vector<typename GradientType<T>::type>& grdAtQPs);
/** \brief
* The comp'th component of the derivative of DOFVector dv evaluated at quadrature points.
* Used by \ref OperatorTerm::initElement().
* Attention: not caching at the moment! Using cache if gradients for read but not for write
*/
/// The comp'th component of the derivative of DOFVector dv evaluated at
/// quadrature points. Used by \ref OperatorTerm::initElement().
/// Attention: not caching at the moment! Using cache if gradients for read
/// but not for write.
template<typename T>
void getDerivativeAtQPs(DOFVectorBase<T>* dv,
const ElInfo* elInfo,
......@@ -159,11 +150,9 @@ namespace AMDiS {
int comp,
mtl::dense_vector<T>& grdAtQPs);
/** \brief
* Called once for each ElInfo when \ref calculateElementMatrix() or
* \ref calculateElementVector() is called for the first time for this
* Element.
*/
/// Called once for each ElInfo when \ref calculateElementMatrix() or
/// \ref calculateElementVector() is called for the first time for this
/// Element.
virtual void initElement(const ElInfo *smallElInfo,
const ElInfo *largeElInfo = NULL,
Quadrature *quad = NULL);
......@@ -202,16 +191,12 @@ namespace AMDiS {
/// Column FiniteElemSpace.
const FiniteElemSpace *colFeSpace;
/** \brief
* Number of rows of the element matrix and length of the element
* vector. Is equal to the number of row basis functions
*/
/// Number of rows of the element matrix and length of the element
/// vector. Is equal to the number of row basis functions
int nRow;
/** \brief
* Number of columns of the element matrix. Is equal to the number
* of column basis functions
*/
/// Number of columns of the element matrix. Is equal to the number
/// of column basis functions
int nCol;
/// Used for \ref getVectorAtQPs() and \ref getGradientsAtQPs().
......@@ -230,16 +215,15 @@ namespace AMDiS {
std::map<const void*, ValuesAtQPs* > cachedValuesAtQPs;
std::map<const void*, ValuesAtQPs* > cachedGradientsAtQPs;
/** \brief
* Set and updated by \ref initElement() for each ElInfo.
* coordsAtQPs[i] points to the coordinates of the i-th quadrature point.
*/
/// Set and updated by \ref initElement() for each ElInfo.
/// coordsAtQPs[i] points to the coordinates of the i-th quadrature point.
WorldVector<double> *coordsAtQPs;
/// Used for \ref getCoordsAtQPs().
bool coordsValid;
/// Used for \ref getCoordsAtQP(). Stores the number of allocated WorldVectors.
/// Used for \ref getCoordsAtQP(). Stores the number of allocated
/// WorldVectors.
int coordsNumAllocated;
/// Quadrature object to be used for assembling.
......
AMDiS/src/Tetrahedron.cc
View file @ 7856d906
......@@ -376,6 +376,48 @@ namespace AMDiS {
return;
break;
case EDGE:
{
// === Create boundary information objects for children elements. ===
BoundaryObject nextBound0 = bound;
prepareNextBound(nextBound0, 0);
BoundaryObject nextBound1 = bound;
prepareNextBound(nextBound1, 1);
// === Check for boundary on children elements. ===
if ((nextBound0.ithObj >= 0 || nextBound1.ithObj >= 0) && child[0]) {
// So, the edge is contained in at least on of the children and the
// element is also refined. Then we have go down further in refinement
// hierarchie.
if (bound.reverseMode) {
if (nextBound1.ithObj >= 0)
child[1]->getHigherOrderDofs(feSpace, nextBound1, dofs);
if (nextBound0.ithObj >= 0)
child[0]->getHigherOrderDofs(feSpace, nextBound0, dofs);
} else {
if (nextBound0.ithObj >= 0)
child[0]->getHigherOrderDofs(feSpace, nextBound0, dofs);
if (nextBound1.ithObj >= 0)
child[1]->getHigherOrderDofs(feSpace, nextBound1, dofs);
}
} else {
// Either the edge is not contained in further refined children, or
// the element is not refined further on this edge. Then we can get
// all the DOFs on this edge.
ElementDofIterator elDofIter(feSpace, true);
elDofIter.reset(this);
do {
if (elDofIter.getCurrentPos() == 1 &&
elDofIter.getCurrentElementPos() == bound.ithObj)
dofs.push_back(elDofIter.getDofPtr());
} while(elDofIter.next());
}
}
break;
case FACE:
{
......@@ -403,10 +445,8 @@ namespace AMDiS {
elDofIter.reset(this);
do {
if (elDofIter.getCurrentPos() == 2 &&
elDofIter.getCurrentElementPos() == bound.ithObj) {
ERROR_EXIT("Check this, if it will really work!\n");
elDofIter.getCurrentElementPos() == bound.ithObj)
dofs.push_back(elDofIter.getDofPtr());
}
} while(elDofIter.next());
}
}
......
AMDiS/src/Tetrahedron.h
View file @ 7856d906
......@@ -324,10 +324,10 @@ namespace AMDiS {
static const int sideOfChild[3][2][4];
/** \brief
* edgeOfChild[elType][i][j] is the local edge number of the j-th edge within the
* i-th children of an element of elType. If the value is -1, the edge is not
* included in the element's child. Note that the 0 edge is included in both
* children only by its half.
* edgeOfChild[elType][i][j] is the local edge number of the j-th edge within
* the i-th children of an element of elType. If the value is -1, the edge is
* not included in the element's child. Note that the 0 edge is included in
* both children only by its half.
*/
static const int edgeOfChild[3][2][6];
......
AMDiS/src/Triangle.cc
View file @ 7856d906
......@@ -169,7 +169,7 @@ namespace AMDiS {
break;
default:
ERROR_EXIT("Should never happen!\n");
}
}
}
......
AMDiS/src/ZeroOrderAssembler.cc
View file @ 7856d906
......@@ -77,9 +77,9 @@ namespace AMDiS {
newAssembler = new StandardZOA(op, assembler, quad);
} else {
if (pwConst)
newAssembler = new PrecalcZOA(op, assembler, quad);
newAssembler = new PrecalcZOA(op, assembler, quad);
else
newAssembler = new FastQuadZOA(op, assembler, quad);
newAssembler = new FastQuadZOA(op, assembler, quad);
}
subAssemblers->push_back(newAssembler);
......
AMDiS/src/parallel/ElementObjectData.cc
View file @ 7856d906
......@@ -85,9 +85,12 @@ namespace AMDiS {
periodicFaces[make_pair(face0, face1)] = elInfo->getBoundary(i);
/// Add all three vertices of the face to be periodic.
periodicVertices[make_pair(face0.get<0>(), face1.get<0>())] = boundaryType;
periodicVertices[make_pair(face0.get<1>(), face1.get<1>())] = boundaryType;
periodicVertices[make_pair(face0.get<2>(), face1.get<2>())] = boundaryType;
periodicVertices[make_pair(face0.get<0>(), face1.get<0>())] =
boundaryType;
periodicVertices[make_pair(face0.get<1>(), face1.get<1>())] =
boundaryType;
periodicVertices[make_pair(face0.get<2>(), face1.get<2>())] =
boundaryType;
periodicDofAssoc[face0.get<0>()].insert(boundaryType);
periodicDofAssoc[face0.get<1>()].insert(boundaryType);
......@@ -131,8 +134,8 @@ namespace AMDiS {
TEST_EXIT_DBG(mesh)("Mesh not set!\n");
// === Return, if there are no periodic vertices, i.e., there are no no ===
// === periodic boundaries in the mesh. ===
// === Return, if there are no periodic vertices, i.e., there are no ===
// === periodic boundaries in the mesh. ===
if (periodicVertices.size() == 0)
return;
......@@ -141,9 +144,9 @@ namespace AMDiS {
// === Get all vertex DOFs that have multiple periodic associations. ===
// We group all vertices together, that have either two or three periodic
// associations. For rectangular domains in 2D, the four corner vertices have all
// two periodic associations. For box domains in 3D, the eight corner vertices
// have all three periodic associations.
// associations. For rectangular domains in 2D, the four corner vertices have
// all two periodic associations. For box domains in 3D, the eight corner
// vertices have all three periodic associations.
vector<DegreeOfFreedom> multPeriodicDof2, multPeriodicDof3;
for (map<DegreeOfFreedom, std::set<BoundaryType> >::iterator it = periodicDofAssoc.begin();
......
AMDiS/src/parallel/ElementObjectData.h
View file @ 7856d906
......@@ -126,11 +126,11 @@ namespace AMDiS {
/** \brief
* Creates final data of the periodic boundaries. Must be called after all
* elements of the mesh are added to the object database. Then this functions
* search for interectly connected vertices in periodic boundaries. This is only
* the case, if there are more than one boundary conditions. Then, e.g., in 2D,
* all edges of a square are iterectly connected. In 3D, if the macro mesh is a
* box, all eight vertex nodes and always four of the 12 edges are iterectly
* connected.
* search for indirectly connected vertices in periodic boundaries. This is
* only the case, if there are more than one boundary conditions. Then, e.g.,
* in 2D, all edges of a square are iterectly connected. In 3D, if the macro
* mesh is a box, all eight vertex nodes and always four of the 12 edges are
* indirectly connected.
*/
void createPeriodicData(const FiniteElemSpace *feSpace);
......
AMDiS/src/parallel/MeshDistributor.cc
View file @ 7856d906
......@@ -289,17 +289,17 @@ namespace AMDiS {
// We have to remove the VertexVectors, which contain periodic assoiciations,
// because they are not valid anymore after some macro elements have been removed
// and the corresponding DOFs were deleted.
// because they are not valid anymore after some macro elements have been
// removed and the corresponding DOFs were deleted.
for (map<BoundaryType, VertexVector*>::iterator it = mesh->getPeriodicAssociations().begin();
it != mesh->getPeriodicAssociations().end(); ++it)
const_cast<DOFAdmin&>(mesh->getDofAdmin(0)).removeDOFContainer(dynamic_cast<DOFContainer*>(it->second));
updateLocalGlobalNumbering();
// === In 3D we have to make some test, if the resulting mesh is valid. If ===
// === it is not valid, there is no possiblity yet to fix this problem, just ===
// === exit with an error message. ===
// === In 3D we have to make some test, if the resulting mesh is valid. ===
// === If it is not valid, there is no possiblity yet to fix this ===
// === problem, just exit with an error message. ===
check3dValidMesh();
......@@ -320,7 +320,7 @@ namespace AMDiS {
// === Create periodic DOF mapping, if there are periodic boundaries. ===
createPeriodicMap(feSpaces[0]);
createPeriodicMap();
#if (DEBUG != 0)
ParallelDebug::testPeriodicBoundary(*this);
......@@ -335,25 +335,20 @@ namespace AMDiS {
refineManager->globalRefine(mesh, globalRefinement);
updateLocalGlobalNumbering();
// === Update periodic mapping, if there are periodic boundaries. ===
createPeriodicMap(feSpaces[0]);
createPeriodicMap();
#if (DEBUG != 0)
ParallelDebug::testPeriodicBoundary(*this);
#endif
}
/// === Set DOF rank information to all matrices and vectors. ===
// Set DOF rank information to all matrices and vectors.
setRankDofs();
// === Remove periodic boundary conditions in sequential problem definition. ===
// Remove periodic boundary conditions in sequential problem definition.
removePeriodicBoundaryConditions();
initialized = true;
......@@ -364,6 +359,9 @@ namespace AMDiS {
{
FUNCNAME("MeshDistributor::addProblemStat()");
TEST_EXIT_DBG(probStat->getFeSpaces().size())
("No FE spaces in stationary problem!\n");
// === Add FE spaces from stationary problem to mesh distributor. ===
for (unsigned int i = 0; i < probStat->getFeSpaces().size(); i++) {
......@@ -845,21 +843,20 @@ namespace AMDiS {
#endif
// === Because the mesh has been changed, update the DOF numbering and mappings. ===
// Because the mesh has been changed, update the DOF numbering and mappings.
updateLocalGlobalNumbering();
// Update periodic mapping, if there are periodic boundaries.
createPeriodicMap();
// === Update periodic mapping, if there are periodic boundaries. ===
createPeriodicMap(feSpaces[0]);
#if (DEBUG != 0)
ParallelDebug::testPeriodicBoundary(*this);
#endif
// === The mesh has changed, so check if it is required to repartition the mesh. ===
// === The mesh has changed, so check if it is required to repartition ===
// === the mesh. ===
nMeshChangesAfterLastRepartitioning++;
......@@ -900,7 +897,8 @@ namespace AMDiS {
maxDofs = std::max(maxDofs, nDofsInRank[i]);
}
int avrgDofs = nOverallDofs / mpiSize;
double imbalance = (static_cast<double>(maxDofs - avrgDofs) / avrgDofs) * 100.0;
double imbalance =
(static_cast<double>(maxDofs - avrgDofs) / avrgDofs) * 100.0;
MSG("Imbalancing factor: %.1f\%\n", imbalance);
}
......@@ -1202,7 +1200,8 @@ namespace AMDiS {
it != newMacroEl.end(); ++it) {
MacroElement *mel = *it;
// First, reset all neighbour relations. The correct neighbours will be set later.
// First, reset all neighbour relations. The correct neighbours will be
// set later.
for (int i = 0; i < mesh->getGeo(NEIGH); i++)
mel->setNeighbour(i, NULL);
......@@ -1259,7 +1258,8 @@ namespace AMDiS {
stdMpi2.startCommunication();
// === Adapte the new macro elements due to the received mesh structure codes. ===
// === Adapte the new macro elements due to the received mesh ===
// === structure codes. ===
for (map<int, vector<int> >::iterator it = partitioner->getRecvElements().begin();
it != partitioner->getRecvElements().end(); ++it) {
......@@ -1348,7 +1348,7 @@ namespace AMDiS {
// === Update periodic mapping, if there are periodic boundaries. ===
createPeriodicMap(feSpaces[0]);
createPeriodicMap();
#if (DEBUG != 0)
......@@ -1435,25 +1435,21 @@ namespace AMDiS {
macroElIndexMap[el->getIndex()] = el;
macroElIndexTypeMap[el->getIndex()] = elInfo->getType();
// === Add all sub object of the element to the variable elObjects. ===
// Add all sub object of the element to the variable elObjects.
elObjects.addElement(elInfo);
elInfo = stack.traverseNext(elInfo);
}
// === Create periodic data, if there are periodic boundary conditions. ===
if (elObjects.hasPeriodicData()) {
TEST_EXIT(feSpaces.size() == 1)
("Sebastian: Na, dass funktioniert auch noch nicht mit mehreren FE spaces. Du weisst schon, wen du jetzt mobben kannst :)!\n");
}
// Create periodic data, if there are periodic boundary conditions.
elObjects.createPeriodicData(feSpaces[0]);
// === Create data about the reverse modes of neighbouring elements. ===
// Create data about the reverse modes of neighbouring elements.
elObjects.createReverseModeData(feSpaces[0], macroElIndexMap,
macroElIndexTypeMap);
// === Create mesh element data for this rank. ===
// Create mesh element data for this rank.
elObjects.createRankData(partitionMap);
}
......@@ -1482,7 +1478,8 @@ namespace AMDiS {
int owner = elObjects.getIterateOwner();
ElementObjectData& rankBoundEl = objData[mpiRank];
TEST_EXIT_DBG(macroElIndexMap[rankBoundEl.elIndex])("Should not happen!\n");
TEST_EXIT_DBG(macroElIndexMap[rankBoundEl.elIndex])
("Should not happen!\n");
AtomicBoundary bound;
bound.rankObj.el = macroElIndexMap[rankBoundEl.elIndex];
......@@ -1555,12 +1552,8 @@ namespace AMDiS {
if (elObjects.isInRank(it->first.first, mpiRank) == false)
continue;
TEST_EXIT(feSpaces.size() == 1)("Does not work for multiple fe spaces!\n");
WorldVector<double> c0, c1;
mesh->getDofIndexCoords(it->first.first, feSpaces[0], c0);
mesh->getDofIndexCoords(it->first.second, feSpaces[0], c1);
ElementObjectData& perDofEl0 = elObjects.getElementsInRank(it->first.first)[mpiRank];
ElementObjectData& perDofEl0 =
elObjects.getElementsInRank(it->first.first)[mpiRank];
for (map<int, ElementObjectData>::iterator elIt = elObjects.getElementsInRank(it->first.second).begin();
elIt != elObjects.getElementsInRank(it->first.second).end(); ++elIt) {
......@@ -1665,16 +1658,19 @@ namespace AMDiS {
b = bound;
if (mpiRank > otherElementRank)
b.neighObj.reverseMode = elObjects.getFaceReverseMode(perFaceEl0, perFaceEl1);
b.neighObj.reverseMode =
elObjects.getFaceReverseMode(perFaceEl0, perFaceEl1);
else
b.rankObj.reverseMode = elObjects.getFaceReverseMode(perFaceEl0, perFaceEl1);
b.rankObj.reverseMode =
elObjects.getFaceReverseMode(perFaceEl0, perFaceEl1);
}
}
// === Once we have this information, we must care about the order of the atomic ===
// === bounds in the three boundary handling object. Eventually all the bound- ===
// === aries have to be in the same order on both ranks that share the bounday. ===
// === Once we have this information, we must care about the order of the ===
// === atomic bounds in the three boundary handling object. Eventually ===
// === all the boundaries have to be in the same order on both ranks that ===
// === share the bounday. ===
StdMpi<vector<AtomicBoundary> > stdMpi(mpiComm);
stdMpi.send(myIntBoundary.boundary);
......@@ -1682,16 +1678,17 @@ namespace AMDiS {
stdMpi.startCommunication();
// === 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. ===
// === 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. ===
for (RankToBoundMap::iterator rankIt = otherIntBoundary.boundary.begin();
rankIt != otherIntBoundary.boundary.end(); ++rankIt) {
// === We have received from rank "rankIt->first" the ordered list of element ===
// === indices. Now, we have to sort the corresponding list in this rank to ===
// === get the same order. ===
// === We have received from rank "rankIt->first" the ordered list of ===
// === element indices. Now, we have to sort the corresponding list in ===
// === this rank to get the same order. ===
for (unsigned int j = 0; j < rankIt->second.size(); j++) {
......@@ -1706,7 +1703,8 @@ namespace AMDiS {
if ((rankIt->second)[k].neighObj == recvedBound)
break;
// The element must always be found, because the list is just in another order.
// The element must always be found, because the list is just in
// another order.
TEST_EXIT_DBG(k < rankIt->second.size())("Should never happen!\n");