/*@
DMPlexUninterpolate - Take in a mesh with all intermediate faces, edges, etc. and return a cell-vertex mesh
Collective on DM
Input Parameter:
. dm - The complete DMPlex object
Output Parameter:
. dmUnint - The DMPlex object with only cells and vertices
Level: intermediate
.keywords: mesh
.seealso: DMPlexInterpolate(), DMPlexCreateFromCellList()
@*/
PetscErrorCode DMPlexUninterpolate(DM dm, DM *dmUnint)
{
DM udm;
PetscInt dim, vStart, vEnd, cStart, cEnd, c, maxConeSize = 0, *cone;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
if (dim <= 1) {
ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr);
*dmUnint = dm;
PetscFunctionReturn(0);
}
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMCreate(PetscObjectComm((PetscObject) dm), &udm);CHKERRQ(ierr);
ierr = DMSetType(udm, DMPLEX);CHKERRQ(ierr);
ierr = DMPlexSetDimension(udm, dim);CHKERRQ(ierr);
ierr = DMPlexSetChart(udm, cStart, vEnd);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL, closureSize, cl, coneSize = 0;
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (cl = 0; cl < closureSize*2; cl += 2) {
const PetscInt p = closure[cl];
if ((p >= vStart) && (p < vEnd)) ++coneSize;
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
ierr = DMPlexSetConeSize(udm, c, coneSize);CHKERRQ(ierr);
maxConeSize = PetscMax(maxConeSize, coneSize);
}
ierr = DMSetUp(udm);CHKERRQ(ierr);
ierr = PetscMalloc1(maxConeSize, &cone);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL, closureSize, cl, coneSize = 0;
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (cl = 0; cl < closureSize*2; cl += 2) {
const PetscInt p = closure[cl];
if ((p >= vStart) && (p < vEnd)) cone[coneSize++] = p;
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
ierr = DMPlexSetCone(udm, c, cone);CHKERRQ(ierr);
}
ierr = PetscFree(cone);CHKERRQ(ierr);
ierr = DMPlexSymmetrize(udm);CHKERRQ(ierr);
ierr = DMPlexStratify(udm);CHKERRQ(ierr);
*dmUnint = udm;
PetscFunctionReturn(0);
}
/*
This takes as input the raw Hasse Diagram data
*/
PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[])
{
Vec coordinates;
PetscSection coordSection;
PetscScalar *coords;
PetscInt coordSize, firstVertex = numPoints[depth], pStart = 0, pEnd = 0, p, v, dim, d, off;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
for (d = 0; d <= depth; ++d) pEnd += numPoints[d];
ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr);
}
ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */
for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) {
ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr);
ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr);
}
ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
ierr = DMPlexStratify(dm);CHKERRQ(ierr);
/* Build coordinates */
ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr);
for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) {
ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
for (v = 0; v < numPoints[0]; ++v) {
PetscInt off;
ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr);
for (d = 0; d < dim; ++d) {
coords[off+d] = vertexCoords[v*dim+d];
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
This takes as input the common mesh generator output, a list of the vertices for each cell
*/
PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[])
{
PetscInt *cone, c, p;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr);
for (c = 0; c < numCells; ++c) {
ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);
}
ierr = DMSetUp(dm);CHKERRQ(ierr);
ierr = DMGetWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr);
for (c = 0; c < numCells; ++c) {
for (p = 0; p < numCorners; ++p) {
cone[p] = cells[c*numCorners+p]+numCells;
}
ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr);
}
ierr = DMRestoreWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr);
ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
ierr = DMPlexStratify(dm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
DMPlexDistribute - Distributes the mesh and any associated sections.
Not Collective
Input Parameter:
+ dm - The original DMPlex object
. partitioner - The partitioning package, or NULL for the default
- overlap - The overlap of partitions, 0 is the default
Output Parameter:
+ sf - The PetscSF used for point distribution
- parallelMesh - The distributed DMPlex object, or NULL
Note: If the mesh was not distributed, the return value is NULL.
The user can control the definition of adjacency for the mesh using DMPlexGetAdjacencyUseCone() and
DMPlexSetAdjacencyUseClosure(). They should choose the combination appropriate for the function
representation on the mesh.
Level: intermediate
.keywords: mesh, elements
.seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure()
@*/
PetscErrorCode DMPlexDistribute(DM dm, const char partitioner[], PetscInt overlap, PetscSF *sf, DM *dmParallel)
{
DM_Plex *mesh = (DM_Plex*) dm->data, *pmesh;
MPI_Comm comm;
const PetscInt height = 0;
PetscInt dim, numRemoteRanks;
IS origCellPart, origPart, cellPart, part;
PetscSection origCellPartSection, origPartSection, cellPartSection, partSection;
PetscSFNode *remoteRanks;
PetscSF partSF, pointSF, coneSF;
ISLocalToGlobalMapping renumbering;
PetscSection originalConeSection, newConeSection;
PetscInt *remoteOffsets;
PetscInt *cones, *newCones, newConesSize;
PetscBool flg;
PetscMPIInt rank, numProcs, p;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
if (sf) PetscValidPointer(sf,4);
PetscValidPointer(dmParallel,5);
ierr = PetscLogEventBegin(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr);
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
*dmParallel = NULL;
if (numProcs == 1) PetscFunctionReturn(0);
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
/* Create cell partition - We need to rewrite to use IS, use the MatPartition stuff */
ierr = PetscLogEventBegin(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr);
if (overlap > 1) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Overlap > 1 not yet implemented");
ierr = DMPlexCreatePartition(dm, partitioner, height, overlap > 0 ? PETSC_TRUE : PETSC_FALSE, &cellPartSection, &cellPart, &origCellPartSection, &origCellPart);CHKERRQ(ierr);
/* Create SF assuming a serial partition for all processes: Could check for IS length here */
if (!rank) numRemoteRanks = numProcs;
else numRemoteRanks = 0;
ierr = PetscMalloc1(numRemoteRanks, &remoteRanks);CHKERRQ(ierr);
for (p = 0; p < numRemoteRanks; ++p) {
remoteRanks[p].rank = p;
remoteRanks[p].index = 0;
}
ierr = PetscSFCreate(comm, &partSF);CHKERRQ(ierr);
ierr = PetscSFSetGraph(partSF, 1, numRemoteRanks, NULL, PETSC_OWN_POINTER, remoteRanks, PETSC_OWN_POINTER);CHKERRQ(ierr);
ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(comm, "Cell Partition:\n");CHKERRQ(ierr);
ierr = PetscSectionView(cellPartSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISView(cellPart, NULL);CHKERRQ(ierr);
if (origCellPart) {
ierr = PetscPrintf(comm, "Original Cell Partition:\n");CHKERRQ(ierr);
ierr = PetscSectionView(origCellPartSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISView(origCellPart, NULL);CHKERRQ(ierr);
}
ierr = PetscSFView(partSF, NULL);CHKERRQ(ierr);
}
/* Close the partition over the mesh */
ierr = DMPlexCreatePartitionClosure(dm, cellPartSection, cellPart, &partSection, &part);CHKERRQ(ierr);
ierr = ISDestroy(&cellPart);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&cellPartSection);CHKERRQ(ierr);
/* Create new mesh */
ierr = DMPlexCreate(comm, dmParallel);CHKERRQ(ierr);
ierr = DMPlexSetDimension(*dmParallel, dim);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) *dmParallel, "Parallel Mesh");CHKERRQ(ierr);
pmesh = (DM_Plex*) (*dmParallel)->data;
/* Distribute sieve points and the global point numbering (replaces creating remote bases) */
ierr = PetscSFConvertPartition(partSF, partSection, part, &renumbering, &pointSF);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(comm, "Point Partition:\n");CHKERRQ(ierr);
ierr = PetscSectionView(partSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISView(part, NULL);CHKERRQ(ierr);
ierr = PetscSFView(pointSF, NULL);CHKERRQ(ierr);
ierr = PetscPrintf(comm, "Point Renumbering after partition:\n");CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingView(renumbering, NULL);CHKERRQ(ierr);
}
ierr = PetscLogEventEnd(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr);
ierr = PetscLogEventBegin(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr);
/* Distribute cone section */
ierr = DMPlexGetConeSection(dm, &originalConeSection);CHKERRQ(ierr);
ierr = DMPlexGetConeSection(*dmParallel, &newConeSection);CHKERRQ(ierr);
ierr = PetscSFDistributeSection(pointSF, originalConeSection, &remoteOffsets, newConeSection);CHKERRQ(ierr);
ierr = DMSetUp(*dmParallel);CHKERRQ(ierr);
{
PetscInt pStart, pEnd, p;
ierr = PetscSectionGetChart(newConeSection, &pStart, &pEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt coneSize;
ierr = PetscSectionGetDof(newConeSection, p, &coneSize);CHKERRQ(ierr);
pmesh->maxConeSize = PetscMax(pmesh->maxConeSize, coneSize);
}
}
/* Communicate and renumber cones */
ierr = PetscSFCreateSectionSF(pointSF, originalConeSection, remoteOffsets, newConeSection, &coneSF);CHKERRQ(ierr);
ierr = DMPlexGetCones(dm, &cones);CHKERRQ(ierr);
ierr = DMPlexGetCones(*dmParallel, &newCones);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(newConeSection, &newConesSize);CHKERRQ(ierr);
ierr = ISGlobalToLocalMappingApplyBlock(renumbering, IS_GTOLM_MASK, newConesSize, newCones, NULL, newCones);CHKERRQ(ierr);
ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-cones_view", &flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(comm, "Serial Cone Section:\n");CHKERRQ(ierr);
ierr = PetscSectionView(originalConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(comm, "Parallel Cone Section:\n");CHKERRQ(ierr);
ierr = PetscSectionView(newConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscSFView(coneSF, NULL);CHKERRQ(ierr);
}
ierr = DMPlexGetConeOrientations(dm, &cones);CHKERRQ(ierr);
ierr = DMPlexGetConeOrientations(*dmParallel, &newCones);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
ierr = PetscSFDestroy(&coneSF);CHKERRQ(ierr);
ierr = PetscLogEventEnd(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr);
/* Create supports and stratify sieve */
{
PetscInt pStart, pEnd;
ierr = PetscSectionGetChart(pmesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr);
ierr = PetscSectionSetChart(pmesh->supportSection, pStart, pEnd);CHKERRQ(ierr);
}
ierr = DMPlexSymmetrize(*dmParallel);CHKERRQ(ierr);
ierr = DMPlexStratify(*dmParallel);CHKERRQ(ierr);
/* Distribute Coordinates */
{
PetscSection originalCoordSection, newCoordSection;
Vec originalCoordinates, newCoordinates;
PetscInt bs;
const char *name;
ierr = DMGetCoordinateSection(dm, &originalCoordSection);CHKERRQ(ierr);
ierr = DMGetCoordinateSection(*dmParallel, &newCoordSection);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &originalCoordinates);CHKERRQ(ierr);
ierr = VecCreate(comm, &newCoordinates);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject) originalCoordinates, &name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) newCoordinates, name);CHKERRQ(ierr);
ierr = DMPlexDistributeField(dm, pointSF, originalCoordSection, originalCoordinates, newCoordSection, newCoordinates);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(*dmParallel, newCoordinates);CHKERRQ(ierr);
ierr = VecGetBlockSize(originalCoordinates, &bs);CHKERRQ(ierr);
ierr = VecSetBlockSize(newCoordinates, bs);CHKERRQ(ierr);
ierr = VecDestroy(&newCoordinates);CHKERRQ(ierr);
}
/* Distribute labels */
ierr = PetscLogEventBegin(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr);
{
DMLabel next = mesh->labels, newNext = pmesh->labels;
PetscInt numLabels = 0, l;
/* Bcast number of labels */
while (next) {++numLabels; next = next->next;}
ierr = MPI_Bcast(&numLabels, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
next = mesh->labels;
for (l = 0; l < numLabels; ++l) {
DMLabel labelNew;
PetscBool isdepth;
/* Skip "depth" because it is recreated */
if (!rank) {ierr = PetscStrcmp(next->name, "depth", &isdepth);CHKERRQ(ierr);}
ierr = MPI_Bcast(&isdepth, 1, MPIU_BOOL, 0, comm);CHKERRQ(ierr);
if (isdepth) {if (!rank) next = next->next; continue;}
ierr = DMLabelDistribute(next, partSection, part, renumbering, &labelNew);CHKERRQ(ierr);
/* Insert into list */
if (newNext) newNext->next = labelNew;
else pmesh->labels = labelNew;
newNext = labelNew;
if (!rank) next = next->next;
}
}
ierr = PetscLogEventEnd(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr);
/* Setup hybrid structure */
{
const PetscInt *gpoints;
PetscInt depth, n, d;
for (d = 0; d <= dim; ++d) {pmesh->hybridPointMax[d] = mesh->hybridPointMax[d];}
ierr = MPI_Bcast(pmesh->hybridPointMax, dim+1, MPIU_INT, 0, comm);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetSize(renumbering, &n);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetIndices(renumbering, &gpoints);CHKERRQ(ierr);
ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr);
for (d = 0; d <= dim; ++d) {
PetscInt pmax = pmesh->hybridPointMax[d], newmax = 0, pEnd, stratum[2], p;
if (pmax < 0) continue;
ierr = DMPlexGetDepthStratum(dm, d > depth ? depth : d, &stratum[0], &stratum[1]);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(*dmParallel, d, NULL, &pEnd);CHKERRQ(ierr);
ierr = MPI_Bcast(stratum, 2, MPIU_INT, 0, comm);CHKERRQ(ierr);
for (p = 0; p < n; ++p) {
const PetscInt point = gpoints[p];
if ((point >= stratum[0]) && (point < stratum[1]) && (point >= pmax)) ++newmax;
}
if (newmax > 0) pmesh->hybridPointMax[d] = pEnd - newmax;
else pmesh->hybridPointMax[d] = -1;
}
ierr = ISLocalToGlobalMappingRestoreIndices(renumbering, &gpoints);CHKERRQ(ierr);
}
/* Cleanup Partition */
ierr = ISLocalToGlobalMappingDestroy(&renumbering);CHKERRQ(ierr);
ierr = PetscSFDestroy(&partSF);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&partSection);CHKERRQ(ierr);
ierr = ISDestroy(&part);CHKERRQ(ierr);
/* Create point SF for parallel mesh */
ierr = PetscLogEventBegin(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr);
{
const PetscInt *leaves;
PetscSFNode *remotePoints, *rowners, *lowners;
PetscInt numRoots, numLeaves, numGhostPoints = 0, p, gp, *ghostPoints;
PetscInt pStart, pEnd;
ierr = DMPlexGetChart(*dmParallel, &pStart, &pEnd);CHKERRQ(ierr);
ierr = PetscSFGetGraph(pointSF, &numRoots, &numLeaves, &leaves, NULL);CHKERRQ(ierr);
ierr = PetscMalloc2(numRoots,&rowners,numLeaves,&lowners);CHKERRQ(ierr);
for (p=0; p<numRoots; p++) {
rowners[p].rank = -1;
rowners[p].index = -1;
}
if (origCellPart) {
/* Make sure points in the original partition are not assigned to other procs */
const PetscInt *origPoints;
ierr = DMPlexCreatePartitionClosure(dm, origCellPartSection, origCellPart, &origPartSection, &origPart);CHKERRQ(ierr);
ierr = ISGetIndices(origPart, &origPoints);CHKERRQ(ierr);
for (p = 0; p < numProcs; ++p) {
PetscInt dof, off, d;
ierr = PetscSectionGetDof(origPartSection, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(origPartSection, p, &off);CHKERRQ(ierr);
for (d = off; d < off+dof; ++d) {
rowners[origPoints[d]].rank = p;
}
}
ierr = ISRestoreIndices(origPart, &origPoints);CHKERRQ(ierr);
ierr = ISDestroy(&origPart);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&origPartSection);CHKERRQ(ierr);
}
ierr = ISDestroy(&origCellPart);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&origCellPartSection);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr);
for (p = 0; p < numLeaves; ++p) {
if (lowners[p].rank < 0 || lowners[p].rank == rank) { /* Either put in a bid or we know we own it */
lowners[p].rank = rank;
lowners[p].index = leaves ? leaves[p] : p;
} else if (lowners[p].rank >= 0) { /* Point already claimed so flag so that MAXLOC does not listen to us */
lowners[p].rank = -2;
lowners[p].index = -2;
}
}
for (p=0; p<numRoots; p++) { /* Root must not participate in the rediction, flag so that MAXLOC does not use */
rowners[p].rank = -3;
rowners[p].index = -3;
}
ierr = PetscSFReduceBegin(pointSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr);
ierr = PetscSFReduceEnd(pointSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr);
for (p = 0; p < numLeaves; ++p) {
if (lowners[p].rank < 0 || lowners[p].index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cell partition corrupt: point not claimed");
if (lowners[p].rank != rank) ++numGhostPoints;
}
ierr = PetscMalloc1(numGhostPoints, &ghostPoints);CHKERRQ(ierr);
ierr = PetscMalloc1(numGhostPoints, &remotePoints);CHKERRQ(ierr);
for (p = 0, gp = 0; p < numLeaves; ++p) {
if (lowners[p].rank != rank) {
ghostPoints[gp] = leaves ? leaves[p] : p;
remotePoints[gp].rank = lowners[p].rank;
remotePoints[gp].index = lowners[p].index;
++gp;
}
}
ierr = PetscFree2(rowners,lowners);CHKERRQ(ierr);
ierr = PetscSFSetGraph((*dmParallel)->sf, pEnd - pStart, numGhostPoints, ghostPoints, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr);
ierr = PetscSFSetFromOptions((*dmParallel)->sf);CHKERRQ(ierr);
}
pmesh->useCone = mesh->useCone;
pmesh->useClosure = mesh->useClosure;
ierr = PetscLogEventEnd(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr);
/* Copy BC */
ierr = DMPlexCopyBoundary(dm, *dmParallel);CHKERRQ(ierr);
/* Cleanup */
if (sf) {*sf = pointSF;}
else {ierr = PetscSFDestroy(&pointSF);CHKERRQ(ierr);}
ierr = DMSetFromOptions(*dmParallel);CHKERRQ(ierr);
ierr = PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void PETSC_STDCALL dmplexsymmetrize_(DM dm, int *__ierr ){
*__ierr = DMPlexSymmetrize(
(DM)PetscToPointer((dm) ));
}
/*@
DMPlexCreateExodus - Create a DMPlex mesh from an ExodusII file ID.
Collective on comm
Input Parameters:
+ comm - The MPI communicator
. exoid - The ExodusII id associated with a exodus file and obtained using ex_open
- interpolate - Create faces and edges in the mesh
Output Parameter:
. dm - The DM object representing the mesh
Level: beginner
.keywords: mesh,ExodusII
.seealso: DMPLEX, DMCreate()
@*/
PetscErrorCode DMPlexCreateExodus(MPI_Comm comm, PetscInt exoid, PetscBool interpolate, DM *dm)
{
#if defined(PETSC_HAVE_EXODUSII)
PetscMPIInt num_proc, rank;
PetscSection coordSection;
Vec coordinates;
PetscScalar *coords;
PetscInt coordSize, v;
PetscErrorCode ierr;
/* Read from ex_get_init() */
char title[PETSC_MAX_PATH_LEN+1];
int dim = 0, numVertices = 0, numCells = 0;
int num_cs = 0, num_vs = 0, num_fs = 0;
#endif
PetscFunctionBegin;
#if defined(PETSC_HAVE_EXODUSII)
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &num_proc);CHKERRQ(ierr);
ierr = DMCreate(comm, dm);CHKERRQ(ierr);
ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
/* Open EXODUS II file and read basic informations on rank 0, then broadcast to all processors */
if (!rank) {
ierr = PetscMemzero(title,(PETSC_MAX_PATH_LEN+1)*sizeof(char));CHKERRQ(ierr);
ierr = ex_get_init(exoid, title, &dim, &numVertices, &numCells, &num_cs, &num_vs, &num_fs);
if (ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"ExodusII ex_get_init() failed with error code %D\n",ierr);
if (!num_cs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Exodus file does not contain any cell set\n");
}
ierr = MPI_Bcast(title, PETSC_MAX_PATH_LEN+1, MPI_CHAR, 0, comm);CHKERRQ(ierr);
ierr = MPI_Bcast(&dim, 1, MPI_INT, 0, comm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) *dm, title);CHKERRQ(ierr);
ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr);
ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr);
/* Read cell sets information */
if (!rank) {
PetscInt *cone;
int c, cs, c_loc, v, v_loc;
/* Read from ex_get_elem_blk_ids() */
int *cs_id;
/* Read from ex_get_elem_block() */
char buffer[PETSC_MAX_PATH_LEN+1];
int num_cell_in_set, num_vertex_per_cell, num_attr;
/* Read from ex_get_elem_conn() */
int *cs_connect;
/* Get cell sets IDs */
ierr = PetscMalloc1(num_cs, &cs_id);CHKERRQ(ierr);
ierr = ex_get_elem_blk_ids(exoid, cs_id);CHKERRQ(ierr);
/* Read the cell set connectivity table and build mesh topology
EXO standard requires that cells in cell sets be numbered sequentially and be pairwise disjoint. */
/* First set sizes */
for (cs = 0, c = 0; cs < num_cs; cs++) {
ierr = ex_get_elem_block(exoid, cs_id[cs], buffer, &num_cell_in_set, &num_vertex_per_cell, &num_attr);CHKERRQ(ierr);
for (c_loc = 0; c_loc < num_cell_in_set; ++c_loc, ++c) {
ierr = DMPlexSetConeSize(*dm, c, num_vertex_per_cell);CHKERRQ(ierr);
}
}
ierr = DMSetUp(*dm);CHKERRQ(ierr);
for (cs = 0, c = 0; cs < num_cs; cs++) {
ierr = ex_get_elem_block(exoid, cs_id[cs], buffer, &num_cell_in_set, &num_vertex_per_cell, &num_attr);CHKERRQ(ierr);
ierr = PetscMalloc2(num_vertex_per_cell*num_cell_in_set,&cs_connect,num_vertex_per_cell,&cone);CHKERRQ(ierr);
ierr = ex_get_elem_conn(exoid, cs_id[cs], cs_connect);CHKERRQ(ierr);
/* EXO uses Fortran-based indexing, sieve uses C-style and numbers cell first then vertices. */
for (c_loc = 0, v = 0; c_loc < num_cell_in_set; ++c_loc, ++c) {
for (v_loc = 0; v_loc < num_vertex_per_cell; ++v_loc, ++v) {
cone[v_loc] = cs_connect[v]+numCells-1;
}
if (dim == 3) {
/* Tetrahedra are inverted */
if (num_vertex_per_cell == 4) {
PetscInt tmp = cone[0];
cone[0] = cone[1];
cone[1] = tmp;
}
/* Hexahedra are inverted */
if (num_vertex_per_cell == 8) {
PetscInt tmp = cone[1];
cone[1] = cone[3];
cone[3] = tmp;
}
}
ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr);
ierr = DMSetLabelValue(*dm, "Cell Sets", c, cs_id[cs]);CHKERRQ(ierr);
}
ierr = PetscFree2(cs_connect,cone);CHKERRQ(ierr);
}
ierr = PetscFree(cs_id);CHKERRQ(ierr);
}
ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr);
ierr = DMPlexStratify(*dm);CHKERRQ(ierr);
if (interpolate) {
DM idm = NULL;
ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr);
/* Maintain Cell Sets label */
{
DMLabel label;
ierr = DMRemoveLabel(*dm, "Cell Sets", &label);CHKERRQ(ierr);
if (label) {ierr = DMAddLabel(idm, label);CHKERRQ(ierr);}
}
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = idm;
}
/* Create vertex set label */
if (!rank && (num_vs > 0)) {
int vs, v;
/* Read from ex_get_node_set_ids() */
int *vs_id;
/* Read from ex_get_node_set_param() */
int num_vertex_in_set, num_attr;
/* Read from ex_get_node_set() */
int *vs_vertex_list;
/* Get vertex set ids */
ierr = PetscMalloc1(num_vs, &vs_id);CHKERRQ(ierr);
ierr = ex_get_node_set_ids(exoid, vs_id);CHKERRQ(ierr);
for (vs = 0; vs < num_vs; ++vs) {
ierr = ex_get_node_set_param(exoid, vs_id[vs], &num_vertex_in_set, &num_attr);CHKERRQ(ierr);
ierr = PetscMalloc1(num_vertex_in_set, &vs_vertex_list);CHKERRQ(ierr);
ierr = ex_get_node_set(exoid, vs_id[vs], vs_vertex_list);CHKERRQ(ierr);
for (v = 0; v < num_vertex_in_set; ++v) {
ierr = DMSetLabelValue(*dm, "Vertex Sets", vs_vertex_list[v]+numCells-1, vs_id[vs]);CHKERRQ(ierr);
}
ierr = PetscFree(vs_vertex_list);CHKERRQ(ierr);
}
ierr = PetscFree(vs_id);CHKERRQ(ierr);
}
/* Read coordinates */
ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr);
for (v = numCells; v < numCells+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr);
ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
if (!rank) {
float *x, *y, *z;
ierr = PetscMalloc3(numVertices,&x,numVertices,&y,numVertices,&z);CHKERRQ(ierr);
ierr = ex_get_coord(exoid, x, y, z);CHKERRQ(ierr);
if (dim > 0) {
for (v = 0; v < numVertices; ++v) coords[v*dim+0] = x[v];
}
if (dim > 1) {
for (v = 0; v < numVertices; ++v) coords[v*dim+1] = y[v];
}
if (dim > 2) {
for (v = 0; v < numVertices; ++v) coords[v*dim+2] = z[v];
}
ierr = PetscFree3(x,y,z);CHKERRQ(ierr);
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
/* Create side set label */
if (!rank && interpolate && (num_fs > 0)) {
int fs, f, voff;
/* Read from ex_get_side_set_ids() */
int *fs_id;
/* Read from ex_get_side_set_param() */
int num_side_in_set, num_dist_fact_in_set;
/* Read from ex_get_side_set_node_list() */
int *fs_vertex_count_list, *fs_vertex_list;
/* Get side set ids */
ierr = PetscMalloc1(num_fs, &fs_id);CHKERRQ(ierr);
ierr = ex_get_side_set_ids(exoid, fs_id);CHKERRQ(ierr);
for (fs = 0; fs < num_fs; ++fs) {
ierr = ex_get_side_set_param(exoid, fs_id[fs], &num_side_in_set, &num_dist_fact_in_set);CHKERRQ(ierr);
ierr = PetscMalloc2(num_side_in_set,&fs_vertex_count_list,num_side_in_set*4,&fs_vertex_list);CHKERRQ(ierr);
ierr = ex_get_side_set_node_list(exoid, fs_id[fs], fs_vertex_count_list, fs_vertex_list);CHKERRQ(ierr);
for (f = 0, voff = 0; f < num_side_in_set; ++f) {
const PetscInt *faces = NULL;
PetscInt faceSize = fs_vertex_count_list[f], numFaces;
PetscInt faceVertices[4], v;
if (faceSize > 4) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "ExodusII side cannot have %d > 4 vertices", faceSize);
for (v = 0; v < faceSize; ++v, ++voff) {
faceVertices[v] = fs_vertex_list[voff]+numCells-1;
}
ierr = DMPlexGetFullJoin(*dm, faceSize, faceVertices, &numFaces, &faces);CHKERRQ(ierr);
if (numFaces != 1) SETERRQ3(comm, PETSC_ERR_ARG_WRONG, "Invalid ExodusII side %d in set %d maps to %d faces", f, fs, numFaces);
ierr = DMSetLabelValue(*dm, "Face Sets", faces[0], fs_id[fs]);CHKERRQ(ierr);
ierr = DMPlexRestoreJoin(*dm, faceSize, faceVertices, &numFaces, &faces);CHKERRQ(ierr);
}
ierr = PetscFree2(fs_vertex_count_list,fs_vertex_list);CHKERRQ(ierr);
}
ierr = PetscFree(fs_id);CHKERRQ(ierr);
}
#else
SETERRQ(comm, PETSC_ERR_SUP, "This method requires ExodusII support. Reconfigure using --download-exodusii");
#endif
PetscFunctionReturn(0);
}
/*@
DMPlexCreateCGNS - Create a DMPlex mesh from a CGNS file ID.
Collective on comm
Input Parameters:
+ comm - The MPI communicator
. cgid - The CG id associated with a file and obtained using cg_open
- interpolate - Create faces and edges in the mesh
Output Parameter:
. dm - The DM object representing the mesh
Note: http://www.grc.nasa.gov/WWW/cgns/CGNS_docs_current/index.html
Level: beginner
.keywords: mesh,CGNS
.seealso: DMPlexCreate(), DMPlexCreateExodus()
@*/
PetscErrorCode DMPlexCreateCGNS(MPI_Comm comm, PetscInt cgid, PetscBool interpolate, DM *dm)
{
#if defined(PETSC_HAVE_CGNS)
PetscMPIInt num_proc, rank;
PetscSection coordSection;
Vec coordinates;
PetscScalar *coords;
PetscInt *cellStart, *vertStart;
PetscInt coordSize, v;
PetscErrorCode ierr;
/* Read from file */
char basename[CGIO_MAX_NAME_LENGTH+1];
char buffer[CGIO_MAX_NAME_LENGTH+1];
int dim = 0, physDim = 0, numVertices = 0, numCells = 0;
int nzones = 0;
#endif
PetscFunctionBegin;
#if defined(PETSC_HAVE_CGNS)
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &num_proc);CHKERRQ(ierr);
ierr = DMCreate(comm, dm);CHKERRQ(ierr);
ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
/* Open CGNS II file and read basic informations on rank 0, then broadcast to all processors */
if (!rank) {
int nbases, z;
ierr = cg_nbases(cgid, &nbases);CHKERRQ(ierr);
if (nbases > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single base, not %d\n",nbases);
ierr = cg_base_read(cgid, 1, basename, &dim, &physDim);CHKERRQ(ierr);
ierr = cg_nzones(cgid, 1, &nzones);CHKERRQ(ierr);
ierr = PetscCalloc2(nzones+1, &cellStart, nzones+1, &vertStart);CHKERRQ(ierr);
for (z = 1; z <= nzones; ++z) {
cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */
ierr = cg_zone_read(cgid, 1, z, buffer, sizes);CHKERRQ(ierr);
numVertices += sizes[0];
numCells += sizes[1];
cellStart[z] += sizes[1] + cellStart[z-1];
vertStart[z] += sizes[0] + vertStart[z-1];
}
for (z = 1; z <= nzones; ++z) {
vertStart[z] += numCells;
}
}
ierr = MPI_Bcast(basename, CGIO_MAX_NAME_LENGTH+1, MPI_CHAR, 0, comm);CHKERRQ(ierr);
ierr = MPI_Bcast(&dim, 1, MPI_INT, 0, comm);CHKERRQ(ierr);
ierr = MPI_Bcast(&nzones, 1, MPI_INT, 0, comm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) *dm, basename);CHKERRQ(ierr);
ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr);
ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr);
/* Read zone information */
if (!rank) {
int z, c, c_loc, v, v_loc;
/* Read the cell set connectivity table and build mesh topology
CGNS standard requires that cells in a zone be numbered sequentially and be pairwise disjoint. */
/* First set sizes */
for (z = 1, c = 0; z <= nzones; ++z) {
ZoneType_t zonetype;
int nsections;
ElementType_t cellType;
cgsize_t start, end;
int nbndry, parentFlag;
PetscInt numCorners;
ierr = cg_zone_type(cgid, 1, z, &zonetype);CHKERRQ(ierr);
if (zonetype == Structured) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Can only handle Unstructured zones for CGNS");
ierr = cg_nsections(cgid, 1, z, &nsections);CHKERRQ(ierr);
if (nsections > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single section, not %d\n",nsections);
ierr = cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);CHKERRQ(ierr);
/* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */
if (cellType == MIXED) {
cgsize_t elementDataSize, *elements;
PetscInt off;
ierr = cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);CHKERRQ(ierr);
ierr = PetscMalloc1(elementDataSize, &elements);CHKERRQ(ierr);
ierr = cg_elements_read(cgid, 1, z, 1, elements, NULL);CHKERRQ(ierr);
for (c_loc = start, off = 0; c_loc <= end; ++c_loc, ++c) {
switch (elements[off]) {
case TRI_3: numCorners = 3;break;
case QUAD_4: numCorners = 4;break;
case TETRA_4: numCorners = 4;break;
case HEXA_8: numCorners = 8;break;
default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) elements[off]);
}
ierr = DMPlexSetConeSize(*dm, c, numCorners);CHKERRQ(ierr);
off += numCorners+1;
}
ierr = PetscFree(elements);CHKERRQ(ierr);
} else {
switch (cellType) {
case TRI_3: numCorners = 3;break;
case QUAD_4: numCorners = 4;break;
case TETRA_4: numCorners = 4;break;
case HEXA_8: numCorners = 8;break;
default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType);
}
for (c_loc = start; c_loc <= end; ++c_loc, ++c) {
ierr = DMPlexSetConeSize(*dm, c, numCorners);CHKERRQ(ierr);
}
}
}
ierr = DMSetUp(*dm);CHKERRQ(ierr);
for (z = 1, c = 0; z <= nzones; ++z) {
ElementType_t cellType;
cgsize_t *elements, elementDataSize, start, end;
int nbndry, parentFlag;
PetscInt *cone, numc, numCorners, maxCorners = 27;
ierr = cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);CHKERRQ(ierr);
numc = end - start;
/* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */
ierr = cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);CHKERRQ(ierr);
ierr = PetscMalloc2(elementDataSize,&elements,maxCorners,&cone);CHKERRQ(ierr);
ierr = cg_elements_read(cgid, 1, z, 1, elements, NULL);CHKERRQ(ierr);
if (cellType == MIXED) {
/* CGNS uses Fortran-based indexing, sieve uses C-style and numbers cell first then vertices. */
for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) {
switch (elements[v]) {
case TRI_3: numCorners = 3;break;
case QUAD_4: numCorners = 4;break;
case TETRA_4: numCorners = 4;break;
case HEXA_8: numCorners = 8;break;
default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) elements[v]);
}
++v;
for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) {
cone[v_loc] = elements[v]+numCells-1;
}
/* Tetrahedra are inverted */
if (elements[v] == TETRA_4) {
PetscInt tmp = cone[0];
cone[0] = cone[1];
cone[1] = tmp;
}
/* Hexahedra are inverted */
if (elements[v] == HEXA_8) {
PetscInt tmp = cone[5];
cone[5] = cone[7];
cone[7] = tmp;
}
ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(*dm, "zone", c, z);CHKERRQ(ierr);
}
} else {
switch (cellType) {
case TRI_3: numCorners = 3;break;
case QUAD_4: numCorners = 4;break;
case TETRA_4: numCorners = 4;break;
case HEXA_8: numCorners = 8;break;
default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType);
}
/* CGNS uses Fortran-based indexing, sieve uses C-style and numbers cell first then vertices. */
for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) {
for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) {
cone[v_loc] = elements[v]+numCells-1;
}
/* Tetrahedra are inverted */
if (cellType == TETRA_4) {
PetscInt tmp = cone[0];
cone[0] = cone[1];
cone[1] = tmp;
}
/* Hexahedra are inverted, and they give the top first */
if (cellType == HEXA_8) {
PetscInt tmp = cone[5];
cone[5] = cone[7];
cone[7] = tmp;
}
ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(*dm, "zone", c, z);CHKERRQ(ierr);
}
}
ierr = PetscFree2(elements,cone);CHKERRQ(ierr);
}
}
ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr);
ierr = DMPlexStratify(*dm);CHKERRQ(ierr);
if (interpolate) {
DM idm = NULL;
ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr);
/* Maintain zone label */
{
DMLabel label;
ierr = DMPlexRemoveLabel(*dm, "zone", &label);CHKERRQ(ierr);
if (label) {ierr = DMPlexAddLabel(idm, label);CHKERRQ(ierr);}
}
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = idm;
}
/* Read coordinates */
ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr);
for (v = numCells; v < numCells+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(comm, &coordinates);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
if (!rank) {
PetscInt off = 0;
float *x[3];
int z, d;
ierr = PetscMalloc3(numVertices,&x[0],numVertices,&x[1],numVertices,&x[2]);CHKERRQ(ierr);
for (z = 1; z <= nzones; ++z) {
DataType_t datatype;
cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */
cgsize_t range_min[3] = {1, 1, 1};
cgsize_t range_max[3] = {1, 1, 1};
int ngrids, ncoords;
ierr = cg_zone_read(cgid, 1, z, buffer, sizes);CHKERRQ(ierr);
range_max[0] = sizes[0];
ierr = cg_ngrids(cgid, 1, z, &ngrids);CHKERRQ(ierr);
if (ngrids > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single grid, not %d\n",ngrids);
ierr = cg_ncoords(cgid, 1, z, &ncoords);CHKERRQ(ierr);
if (ncoords != dim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a coordinate array for each dimension, not %d\n",ncoords);
for (d = 0; d < dim; ++d) {
ierr = cg_coord_info(cgid, 1, z, 1+d, &datatype, buffer);CHKERRQ(ierr);
ierr = cg_coord_read(cgid, 1, z, buffer, RealSingle, range_min, range_max, x[d]);CHKERRQ(ierr);
}
if (dim > 0) {
for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+0] = x[0][v];
}
if (dim > 1) {
for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+1] = x[1][v];
}
if (dim > 2) {
for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+2] = x[2][v];
}
off += sizes[0];
}
ierr = PetscFree3(x[0],x[1],x[2]);CHKERRQ(ierr);
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
/* Read boundary conditions */
if (!rank) {
DMLabel label;
BCType_t bctype;
DataType_t datatype;
PointSetType_t pointtype;
cgsize_t *points;
PetscReal *normals;
int normal[3];
char *bcname = buffer;
cgsize_t npoints, nnormals;
int z, nbc, bc, c, ndatasets;
for (z = 1; z <= nzones; ++z) {
ierr = cg_nbocos(cgid, 1, z, &nbc);CHKERRQ(ierr);
for (bc = 1; bc <= nbc; ++bc) {
ierr = cg_boco_info(cgid, 1, z, bc, bcname, &bctype, &pointtype, &npoints, normal, &nnormals, &datatype, &ndatasets);CHKERRQ(ierr);
ierr = DMPlexCreateLabel(*dm, bcname);CHKERRQ(ierr);
ierr = DMPlexGetLabel(*dm, bcname, &label);CHKERRQ(ierr);
ierr = PetscMalloc2(npoints, &points, nnormals, &normals);CHKERRQ(ierr);
ierr = cg_boco_read(cgid, 1, z, bc, points, (void *) normals);CHKERRQ(ierr);
if (pointtype == ElementRange) {
/* Range of cells: assuming half-open interval since the documentation sucks */
for (c = points[0]; c < points[1]; ++c) {
ierr = DMLabelSetValue(label, c - cellStart[z-1], 1);CHKERRQ(ierr);
}
} else if (pointtype == ElementList) {
/* List of cells */
for (c = 0; c < npoints; ++c) {
ierr = DMLabelSetValue(label, points[c] - cellStart[z-1], 1);CHKERRQ(ierr);
}
} else if (pointtype == PointRange) {
GridLocation_t gridloc;
/* List of points: Oh please, someone get the CGNS developers away from a computer. This is unconscionable. */
ierr = cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end");CHKERRQ(ierr);
ierr = cg_gridlocation_read(&gridloc);CHKERRQ(ierr);
/* Range of points: assuming half-open interval since the documentation sucks */
for (c = points[0]; c < points[1]; ++c) {
if (gridloc == Vertex) {ierr = DMLabelSetValue(label, c - vertStart[z-1], 1);CHKERRQ(ierr);}
else {ierr = DMLabelSetValue(label, c - cellStart[z-1], 1);CHKERRQ(ierr);}
}
} else if (pointtype == PointList) {
GridLocation_t gridloc;
/* List of points: Oh please, someone get the CGNS developers away from a computer. This is unconscionable. */
ierr = cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end");
ierr = cg_gridlocation_read(&gridloc);
for (c = 0; c < npoints; ++c) {
if (gridloc == Vertex) {ierr = DMLabelSetValue(label, points[c] - vertStart[z-1], 1);CHKERRQ(ierr);}
else {ierr = DMLabelSetValue(label, points[c] - cellStart[z-1], 1);CHKERRQ(ierr);}
}
} else SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported point set type %d", (int) pointtype);
ierr = PetscFree2(points, normals);CHKERRQ(ierr);
}
}
ierr = PetscFree2(cellStart, vertStart);CHKERRQ(ierr);
}
#else
SETERRQ(comm, PETSC_ERR_SUP, "This method requires CGNS support. Reconfigure using --with-cgns-dir");
#endif
PetscFunctionReturn(0);
}
/*@C
DMPlexCreateFluent - Create a DMPlex mesh from a Fluent mesh file.
Collective on comm
Input Parameters:
+ comm - The MPI communicator
. viewer - The Viewer associated with a Fluent mesh file
- interpolate - Create faces and edges in the mesh
Output Parameter:
. dm - The DM object representing the mesh
Note: http://aerojet.engr.ucdavis.edu/fluenthelp/html/ug/node1490.htm
Level: beginner
.keywords: mesh, fluent, case
.seealso: DMPLEX, DMCreate()
@*/
PetscErrorCode DMPlexCreateFluent(MPI_Comm comm, PetscViewer viewer, PetscBool interpolate, DM *dm)
{
PetscMPIInt rank;
PetscInt c, f, v, dim = PETSC_DETERMINE, numCells = 0, numVertices = 0, numCellVertices = PETSC_DETERMINE;
PetscInt numFaces = PETSC_DETERMINE, numFaceEntries = PETSC_DETERMINE, numFaceVertices = PETSC_DETERMINE;
PetscInt *faces = NULL, *cellVertices, *faceZoneIDs = NULL;
PetscInt d, coordSize;
PetscScalar *coords, *coordsIn = NULL;
PetscSection coordSection;
Vec coordinates;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
if (!rank) {
FluentSection s;
do {
ierr = DMPlexCreateFluent_ReadSection(viewer, &s);CHKERRQ(ierr);
if (s.index == 2) { /* Dimension */
dim = s.nd;
} else if (s.index == 10 || s.index == 2010) { /* Vertices */
if (s.zoneID == 0) numVertices = s.last;
else {
if (coordsIn) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Currently no support for multiple coordinate sets in Fluent files");
coordsIn = (PetscScalar *) s.data;
}
} else if (s.index == 12 || s.index == 2012) { /* Cells */
if (s.zoneID == 0) numCells = s.last;
else {
switch (s.nd) {
case 0: numCellVertices = PETSC_DETERMINE; break;
case 1: numCellVertices = 3; break; /* triangular */
case 2: numCellVertices = 4; break; /* tetrahedral */
case 3: numCellVertices = 4; break; /* quadrilateral */
case 4: numCellVertices = 8; break; /* hexahedral */
case 5: numCellVertices = 5; break; /* pyramid */
case 6: numCellVertices = 6; break; /* wedge */
default: numCellVertices = PETSC_DETERMINE;
}
}
} else if (s.index == 13 || s.index == 2013) { /* Facets */
if (s.zoneID == 0) { /* Header section */
numFaces = s.last - s.first + 1;
if (s.nd == 0 || s.nd == 5) numFaceVertices = PETSC_DETERMINE;
else numFaceVertices = s.nd;
} else { /* Data section */
if (numFaceVertices != PETSC_DETERMINE && s.nd != numFaceVertices) {
SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mixed facets in Fluent files are not supported");
}
if (numFaces < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No header section for facets in Fluent file");
if (numFaceVertices == PETSC_DETERMINE) numFaceVertices = s.nd;
numFaceEntries = numFaceVertices + 2;
if (!faces) {ierr = PetscMalloc1(numFaces*numFaceEntries, &faces);CHKERRQ(ierr);}
if (!faceZoneIDs) {ierr = PetscMalloc1(numFaces, &faceZoneIDs);CHKERRQ(ierr);}
ierr = PetscMemcpy(&(faces[(s.first-1)*numFaceEntries]), s.data, (s.last-s.first+1)*numFaceEntries*sizeof(PetscInt));CHKERRQ(ierr);
/* Record the zoneID for each face set */
for (f = s.first -1; f < s.last; f++) faceZoneIDs[f] = s.zoneID;
ierr = PetscFree(s.data);CHKERRQ(ierr);
}
}
} while (s.index >= 0);
}
ierr = MPI_Bcast(&dim, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
if (dim < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Fluent file does not include dimension");
/* Allocate cell-vertex mesh */
ierr = DMCreate(comm, dm);CHKERRQ(ierr);
ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr);
ierr = DMPlexSetChart(*dm, 0, numCells + numVertices);CHKERRQ(ierr);
if (!rank) {
if (numCells < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown number of cells in Fluent file");
/* If no cell type was given we assume simplices */
if (numCellVertices == PETSC_DETERMINE) numCellVertices = numFaceVertices + 1;
for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(*dm, c, numCellVertices);CHKERRQ(ierr);}
}
ierr = DMSetUp(*dm);CHKERRQ(ierr);
if (!rank) {
/* Derive cell-vertex list from face-vertex and face-cell maps */
ierr = PetscMalloc1(numCells*numCellVertices, &cellVertices);CHKERRQ(ierr);
for (c = 0; c < numCells*numCellVertices; c++) cellVertices[c] = -1;
for (f = 0; f < numFaces; f++) {
PetscInt *cell;
const PetscInt cl = faces[f*numFaceEntries + numFaceVertices];
const PetscInt cr = faces[f*numFaceEntries + numFaceVertices + 1];
const PetscInt *face = &(faces[f*numFaceEntries]);
if (cl > 0) {
cell = &(cellVertices[(cl-1) * numCellVertices]);
for (v = 0; v < numFaceVertices; v++) {
PetscBool found = PETSC_FALSE;
for (c = 0; c < numCellVertices; c++) {
if (cell[c] < 0) break;
if (cell[c] == face[v]-1 + numCells) {found = PETSC_TRUE; break;}
}
if (!found) cell[c] = face[v]-1 + numCells;
}
}
if (cr > 0) {
cell = &(cellVertices[(cr-1) * numCellVertices]);
for (v = 0; v < numFaceVertices; v++) {
PetscBool found = PETSC_FALSE;
for (c = 0; c < numCellVertices; c++) {
if (cell[c] < 0) break;
if (cell[c] == face[v]-1 + numCells) {found = PETSC_TRUE; break;}
}
if (!found) cell[c] = face[v]-1 + numCells;
}
}
}
for (c = 0; c < numCells; c++) {
ierr = DMPlexSetCone(*dm, c, &(cellVertices[c*numCellVertices]));CHKERRQ(ierr);
}
}
ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr);
ierr = DMPlexStratify(*dm);CHKERRQ(ierr);
if (interpolate) {
DM idm = NULL;
ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = idm;
}
if (!rank) {
PetscInt fi, joinSize, meetSize, *fverts, cells[2];
const PetscInt *join, *meet;
ierr = PetscMalloc1(numFaceVertices, &fverts);CHKERRQ(ierr);
/* Mark facets by finding the full join of all adjacent vertices */
for (f = 0; f < numFaces; f++) {
const PetscInt cl = faces[f*numFaceEntries + numFaceVertices] - 1;
const PetscInt cr = faces[f*numFaceEntries + numFaceVertices + 1] - 1;
if (cl > 0 && cr > 0) {
/* If we know both adjoining cells we can use a single-level meet */
cells[0] = cl; cells[1] = cr;
ierr = DMPlexGetMeet(*dm, 2, cells, &meetSize, &meet);CHKERRQ(ierr);
if (meetSize != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not determine Plex facet for Fluent face %d", f);
ierr = DMPlexSetLabelValue(*dm, "Face Sets", meet[0], faceZoneIDs[f]);CHKERRQ(ierr);
ierr = DMPlexRestoreMeet(*dm, numFaceVertices, fverts, &meetSize, &meet);CHKERRQ(ierr);
} else {
for (fi = 0; fi < numFaceVertices; fi++) fverts[fi] = faces[f*numFaceEntries + fi] + numCells - 1;
ierr = DMPlexGetFullJoin(*dm, numFaceVertices, fverts, &joinSize, &join);CHKERRQ(ierr);
if (joinSize != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not determine Plex facet for Fluent face %d", f);
ierr = DMPlexSetLabelValue(*dm, "Face Sets", join[0], faceZoneIDs[f]);CHKERRQ(ierr);
ierr = DMPlexRestoreJoin(*dm, numFaceVertices, fverts, &joinSize, &join);CHKERRQ(ierr);
}
}
ierr = PetscFree(fverts);CHKERRQ(ierr);
}
/* Read coordinates */
ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr);
for (v = numCells; v < numCells+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(comm, &coordinates);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
if (!rank) {
for (v = 0; v < numVertices; ++v) {
for (d = 0; d < dim; ++d) {
coords[v*dim+d] = coordsIn[v*dim+d];
}
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
if (!rank) {
ierr = PetscFree(cellVertices);CHKERRQ(ierr);
ierr = PetscFree(faces);CHKERRQ(ierr);
ierr = PetscFree(faceZoneIDs);CHKERRQ(ierr);
ierr = PetscFree(coordsIn);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/* Two triangles separated by a zero-volume cell with 6 vertices
5--16--8
/ | | \
11 | | 12
/ | | \
3 0 10 2 14 1 6
\ | | /
9 | | 13
\ | | /
4--15--7
*/
PetscErrorCode CreateSimplexHybrid_2D(MPI_Comm comm, DM dm)
{
Vec coordinates;
PetscSection coordSection;
PetscScalar *coords;
PetscInt numVertices = 0, numEdges = 0, numCells = 0, cMax = PETSC_DETERMINE, fMax = PETSC_DETERMINE;
PetscInt firstVertex, firstEdge, coordSize;
PetscInt v, e;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
if (!rank) {
numVertices = 3 + 3;
numEdges = 6 + 2;
numCells = 3;
cMax = 2;
fMax = 15;
}
firstVertex = numCells;
firstEdge = numCells + numVertices;
ierr = DMPlexSetChart(dm, 0, numCells+numEdges+numVertices);CHKERRQ(ierr);
if (numCells) {
ierr = DMPlexSetConeSize(dm, 0, 3);CHKERRQ(ierr);
ierr = DMPlexSetConeSize(dm, 1, 3);CHKERRQ(ierr);
ierr = DMPlexSetConeSize(dm, 2, 4);CHKERRQ(ierr);
}
for(e = firstEdge; e < firstEdge+numEdges; ++e) {
ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr);
}
ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */
ierr = DMPlexSetHybridBounds(dm, cMax, PETSC_DETERMINE, fMax, PETSC_DETERMINE);CHKERRQ(ierr); /* Indicate a hybrid mesh */
/* Build cells */
if (numCells > 0) {
const PetscInt cone[3] = {9, 10, 11};
const PetscInt ornt[3] = {0, 0, 0};
const PetscInt cell = 0;
ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr);
ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr);
}
if (numCells > 1) {
const PetscInt cone[3] = {12, 14, 13};
const PetscInt ornt[3] = { 0, -2, 0};
const PetscInt cell = 1;
ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr);
ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr);
}
if (numCells > 2) {
const PetscInt cone[4] = {10, 14, 15, 16};
const PetscInt ornt[4] = { 0, 0, 0, 0};
const PetscInt cell = 2;
ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr);
ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr);
}
/* Build edges*/
if (numEdges > 0) {
const PetscInt cone[2] = {3, 4};
const PetscInt edge = 9;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", edge, 1);CHKERRQ(ierr);
}
if (numEdges > 1) {
const PetscInt cone[2] = {4, 5};
const PetscInt edge = 10;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
}
if (numEdges > 2) {
const PetscInt cone[2] = {5, 3};
const PetscInt edge = 11;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", edge, 1);CHKERRQ(ierr);
}
if (numEdges > 3) {
const PetscInt cone[2] = {6, 8};
const PetscInt edge = 12;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", edge, 1);CHKERRQ(ierr);
}
if (numEdges > 4) {
const PetscInt cone[2] = {7, 6};
const PetscInt edge = 13;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", edge, 1);CHKERRQ(ierr);
}
if (numEdges > 5) {
const PetscInt cone[2] = {7, 8};
const PetscInt edge = 14;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
}
if (numEdges > 6) {
const PetscInt cone[2] = {4, 7};
const PetscInt edge = 15;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
}
if (numEdges > 7) {
const PetscInt cone[2] = {5, 8};
const PetscInt edge = 16;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
}
ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
ierr = DMPlexStratify(dm);CHKERRQ(ierr);
/* Build coordinates */
ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr);
for(v = firstVertex; v < firstVertex+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(((PetscObject) dm)->comm, &coordinates);CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
if (numVertices) {
coords[0] = -0.5; coords[1] = 0.5;
coords[2] = -0.2; coords[3] = 0.0;
coords[4] = -0.2; coords[5] = 1.0;
coords[6] = 0.5; coords[7] = 0.5;
coords[8] = 0.2; coords[9] = 0.0;
coords[10] = 0.2; coords[11] = 1.0;
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Simple square boundary:
18--5-17--4--16
| | |
6 10 3
| | |
19-11-20--9--15
| | |
7 8 2
| | |
12--0-13--1--14
*/
PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
{
PetscInt numVertices = (edges[0]+1)*(edges[1]+1);
PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1];
PetscInt markerTop = 1;
PetscInt markerBottom = 1;
PetscInt markerRight = 1;
PetscInt markerLeft = 1;
PetscBool markerSeparate = PETSC_FALSE;
Vec coordinates;
PetscSection coordSection;
PetscScalar *coords;
PetscInt coordSize;
PetscMPIInt rank;
PetscInt v, vx, vy;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr);
if (markerSeparate) {
markerTop = 1;
markerBottom = 0;
markerRight = 0;
markerLeft = 0;
}
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr);
if (!rank) {
PetscInt e, ex, ey;
ierr = DMPlexSetChart(dm, 0, numEdges+numVertices);CHKERRQ(ierr);
for (e = 0; e < numEdges; ++e) {
ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr);
}
ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */
for (vx = 0; vx <= edges[0]; vx++) {
for (ey = 0; ey < edges[1]; ey++) {
PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1);
PetscInt vertex = ey*(edges[0]+1) + vx + numEdges;
PetscInt cone[2];
cone[0] = vertex; cone[1] = vertex+edges[0]+1;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
if (vx == edges[0]) {
ierr = DMPlexSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr);
if (ey == edges[1]-1) {
ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr);
}
} else if (vx == 0) {
ierr = DMPlexSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr);
if (ey == edges[1]-1) {
ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr);
}
}
}
}
for (vy = 0; vy <= edges[1]; vy++) {
for (ex = 0; ex < edges[0]; ex++) {
PetscInt edge = vy*edges[0] + ex;
PetscInt vertex = vy*(edges[0]+1) + ex + numEdges;
PetscInt cone[2];
cone[0] = vertex; cone[1] = vertex+1;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
if (vy == edges[1]) {
ierr = DMPlexSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr);
if (ex == edges[0]-1) {
ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr);
}
} else if (vy == 0) {
ierr = DMPlexSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr);
if (ex == edges[0]-1) {
ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr);
}
}
}
}
}
ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
ierr = DMPlexStratify(dm);CHKERRQ(ierr);
/* Build coordinates */
ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);CHKERRQ(ierr);
for (v = numEdges; v < numEdges+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
for (vy = 0; vy <= edges[1]; ++vy) {
for (vx = 0; vx <= edges[0]; ++vx) {
coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx;
coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy;
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Simple square mesh:
22--8-23--9--24
| | |
13 2 14 3 15
| | |
19--6-20--7--21
| | |
10 0 11 1 12
| | |
16--4-17--5--18
*/
PetscErrorCode DMPlexCreateSquareMesh(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
{
PetscInt markerTop = 1;
PetscInt markerBottom = 1;
PetscInt markerRight = 1;
PetscInt markerLeft = 1;
PetscBool markerSeparate = PETSC_FALSE;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr);
if (markerSeparate) {
markerTop = 3;
markerBottom = 1;
markerRight = 2;
markerLeft = 4;
}
{
const PetscInt numXEdges = !rank ? edges[0] : 0;
const PetscInt numYEdges = !rank ? edges[1] : 0;
const PetscInt numXVertices = !rank ? edges[0]+1 : 0;
const PetscInt numYVertices = !rank ? edges[1]+1 : 0;
const PetscInt numTotXEdges = numXEdges*numYVertices;
const PetscInt numTotYEdges = numYEdges*numXVertices;
const PetscInt numVertices = numXVertices*numYVertices;
const PetscInt numEdges = numTotXEdges + numTotYEdges;
const PetscInt numFaces = numXEdges*numYEdges;
const PetscInt firstVertex = numFaces;
const PetscInt firstXEdge = numFaces + numVertices;
const PetscInt firstYEdge = numFaces + numVertices + numTotXEdges;
Vec coordinates;
PetscSection coordSection;
PetscScalar *coords;
PetscInt coordSize;
PetscInt v, vx, vy;
PetscInt f, fx, fy, e, ex, ey;
ierr = DMPlexSetChart(dm, 0, numFaces+numEdges+numVertices);CHKERRQ(ierr);
for (f = 0; f < numFaces; ++f) {
ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr);
}
for (e = firstXEdge; e < firstXEdge+numEdges; ++e) {
ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr);
}
ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */
/* Build faces */
for (fy = 0; fy < numYEdges; fy++) {
for (fx = 0; fx < numXEdges; fx++) {
const PetscInt face = fy*numXEdges + fx;
const PetscInt edgeL = firstYEdge + fx*numYEdges + fy;
const PetscInt edgeB = firstXEdge + fy*numXEdges + fx;
const PetscInt ornt[4] = {0, 0, -2, -2};
PetscInt cone[4];
cone[0] = edgeB; cone[1] = edgeL+numYEdges; cone[2] = edgeB+numXEdges; cone[3] = edgeL;
ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr);
ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr);
}
}
/* Build Y edges*/
for (vx = 0; vx < numXVertices; vx++) {
for (ey = 0; ey < numYEdges; ey++) {
const PetscInt edge = firstYEdge + vx*numYEdges + ey;
const PetscInt vertex = firstVertex + ey*numXVertices + vx;
PetscInt cone[2];
cone[0] = vertex; cone[1] = vertex+numXVertices;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
if (vx == numXVertices-1) {
ierr = DMPlexSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr);
if (ey == numYEdges-1) {
ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr);
}
} else if (vx == 0) {
ierr = DMPlexSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr);
if (ey == numYEdges-1) {
ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr);
}
}
}
}
/* Build X edges*/
for (vy = 0; vy < numYVertices; vy++) {
for (ex = 0; ex < numXEdges; ex++) {
const PetscInt edge = firstXEdge + vy*numXEdges + ex;
const PetscInt vertex = firstVertex + vy*numXVertices + ex;
PetscInt cone[2];
cone[0] = vertex; cone[1] = vertex+1;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
if (vy == numYVertices-1) {
ierr = DMPlexSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr);
if (ex == numXEdges-1) {
ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr);
}
} else if (vy == 0) {
ierr = DMPlexSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr);
if (ex == numXEdges-1) {
ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr);
}
}
}
}
ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
ierr = DMPlexStratify(dm);CHKERRQ(ierr);
/* Build coordinates */
ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr);
for (v = firstVertex; v < firstVertex+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
for (vy = 0; vy < numYVertices; ++vy) {
for (vx = 0; vx < numXVertices; ++vx) {
coords[(vy*numXVertices+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx;
coords[(vy*numXVertices+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy;
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*
Simple cubic boundary:
2-------3
/| /|
6-------7 |
| | | |
| 0-----|-1
|/ |/
4-------5
*/
PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[])
{
PetscInt numVertices = (faces[0]+1)*(faces[1]+1)*(faces[2]+1);
PetscInt numFaces = 6;
Vec coordinates;
PetscSection coordSection;
PetscScalar *coords;
PetscInt coordSize;
PetscMPIInt rank;
PetscInt v, vx, vy, vz;
PetscErrorCode ierr;
PetscFunctionBegin;
if ((faces[0] < 1) || (faces[1] < 1) || (faces[2] < 1)) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Must have at least 1 face per side");
if ((faces[0] > 1) || (faces[1] > 1) || (faces[2] > 1)) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Currently can't handle more than 1 face per side");
ierr = PetscMalloc(numVertices*2 * sizeof(PetscReal), &coords);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr);
if (!rank) {
PetscInt f;
ierr = DMPlexSetChart(dm, 0, numFaces+numVertices);CHKERRQ(ierr);
for (f = 0; f < numFaces; ++f) {
ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr);
}
ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */
for (v = 0; v < numFaces+numVertices; ++v) {
ierr = DMPlexSetLabelValue(dm, "marker", v, 1);CHKERRQ(ierr);
}
{ /* Side 0 (Front) */
PetscInt cone[4];
cone[0] = numFaces+4; cone[1] = numFaces+5; cone[2] = numFaces+7; cone[3] = numFaces+6;
ierr = DMPlexSetCone(dm, 0, cone);CHKERRQ(ierr);
}
{ /* Side 1 (Back) */
PetscInt cone[4];
cone[0] = numFaces+1; cone[1] = numFaces+0; cone[2] = numFaces+2; cone[3] = numFaces+3;
ierr = DMPlexSetCone(dm, 1, cone);CHKERRQ(ierr);
}
{ /* Side 2 (Bottom) */
PetscInt cone[4];
cone[0] = numFaces+0; cone[1] = numFaces+1; cone[2] = numFaces+5; cone[3] = numFaces+4;
ierr = DMPlexSetCone(dm, 2, cone);CHKERRQ(ierr);
}
{ /* Side 3 (Top) */
PetscInt cone[4];
cone[0] = numFaces+6; cone[1] = numFaces+7; cone[2] = numFaces+3; cone[3] = numFaces+2;
ierr = DMPlexSetCone(dm, 3, cone);CHKERRQ(ierr);
}
{ /* Side 4 (Left) */
PetscInt cone[4];
cone[0] = numFaces+0; cone[1] = numFaces+4; cone[2] = numFaces+6; cone[3] = numFaces+2;
ierr = DMPlexSetCone(dm, 4, cone);CHKERRQ(ierr);
}
{ /* Side 5 (Right) */
PetscInt cone[4];
cone[0] = numFaces+5; cone[1] = numFaces+1; cone[2] = numFaces+3; cone[3] = numFaces+7;
ierr = DMPlexSetCone(dm, 5, cone);CHKERRQ(ierr);
}
}
ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
ierr = DMPlexStratify(dm);CHKERRQ(ierr);
/* Build coordinates */
ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr);
for (v = numFaces; v < numFaces+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
for (vz = 0; vz <= faces[2]; ++vz) {
for (vy = 0; vy <= faces[1]; ++vy) {
for (vx = 0; vx <= faces[0]; ++vx) {
coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx;
coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy;
coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz;
}
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
}
/* Hexahedra are inverted */
if (num_vertex_per_cell == 8) {
PetscInt tmp = cone[1];
cone[1] = cone[3];
cone[3] = tmp;
}
}
ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(*dm, "Cell Sets", c, cs_id[cs]);CHKERRQ(ierr);
}
ierr = PetscFree2(cs_connect,cone);CHKERRQ(ierr);
}
ierr = PetscFree(cs_id);CHKERRQ(ierr);
}
ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr);
ierr = DMPlexStratify(*dm);CHKERRQ(ierr);
if (interpolate) {
DM idm;
ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr);
/* Maintain Cell Sets label */
{
DMLabel label;
ierr = DMPlexRemoveLabel(*dm, "Cell Sets", &label);CHKERRQ(ierr);
if (label) {ierr = DMPlexAddLabel(idm, label);CHKERRQ(ierr);}
}
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = idm;
}
/*@
DMPlexCreateGmsh - Create a DMPlex mesh from a Gmsh file viewer
Collective on comm
Input Parameters:
+ comm - The MPI communicator
. viewer - The Viewer associated with a Gmsh file
- interpolate - Create faces and edges in the mesh
Output Parameter:
. dm - The DM object representing the mesh
Note: http://www.geuz.org/gmsh/doc/texinfo/#MSH-ASCII-file-format
and http://www.geuz.org/gmsh/doc/texinfo/#MSH-binary-file-format
Level: beginner
.keywords: mesh,Gmsh
.seealso: DMPLEX, DMCreate()
@*/
PetscErrorCode DMPlexCreateGmsh(MPI_Comm comm, PetscViewer viewer, PetscBool interpolate, DM *dm)
{
PetscViewerType vtype;
GmshElement *gmsh_elem;
PetscSection coordSection;
Vec coordinates;
PetscScalar *coords, *coordsIn = NULL;
PetscInt dim = 0, coordSize, c, v, d, r, cell;
int i, numVertices = 0, numCells = 0, trueNumCells = 0, numRegions = 0, snum;
PetscMPIInt num_proc, rank;
char line[PETSC_MAX_PATH_LEN];
PetscBool match, binary, bswap = PETSC_FALSE;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &num_proc);CHKERRQ(ierr);
ierr = DMCreate(comm, dm);CHKERRQ(ierr);
ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
ierr = PetscLogEventBegin(DMPLEX_CreateGmsh,*dm,0,0,0);CHKERRQ(ierr);
ierr = PetscViewerGetType(viewer, &vtype);CHKERRQ(ierr);
ierr = PetscStrcmp(vtype, PETSCVIEWERBINARY, &binary);CHKERRQ(ierr);
if (!rank || binary) {
PetscBool match;
int fileType, dataSize;
float version;
/* Read header */
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
ierr = PetscStrncmp(line, "$MeshFormat", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
ierr = PetscViewerRead(viewer, line, 3, NULL, PETSC_STRING);CHKERRQ(ierr);
snum = sscanf(line, "%f %d %d", &version, &fileType, &dataSize);
if (snum != 3) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Gmsh file header: %s", line);
if (version < 2.0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Gmsh file must be at least version 2.0");
if (dataSize != sizeof(double)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Data size %d is not valid for a Gmsh file", dataSize);
if (binary) {
int checkInt;
ierr = PetscViewerRead(viewer, &checkInt, 1, NULL, PETSC_ENUM);CHKERRQ(ierr);
if (checkInt != 1) {
ierr = PetscByteSwap(&checkInt, PETSC_ENUM, 1);CHKERRQ(ierr);
if (checkInt == 1) bswap = PETSC_TRUE;
else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File type %d is not a valid Gmsh binary file", fileType);
}
} else if (fileType) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File type %d is not a valid Gmsh ASCII file", fileType);
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
ierr = PetscStrncmp(line, "$EndMeshFormat", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
/* OPTIONAL Read physical names */
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
ierr = PetscStrncmp(line, "$PhysicalNames", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (match) {
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
snum = sscanf(line, "%d", &numRegions);
if (snum != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
for (r = 0; r < numRegions; ++r) {
PetscInt rdim, tag;
ierr = PetscViewerRead(viewer, &rdim, 1, NULL, PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerRead(viewer, &tag, 1, NULL, PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
}
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
ierr = PetscStrncmp(line, "$EndPhysicalNames", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
/* Initial read for vertex section */
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
}
/* Read vertices */
ierr = PetscStrncmp(line, "$Nodes", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
snum = sscanf(line, "%d", &numVertices);
if (snum != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
ierr = PetscMalloc1(numVertices*3, &coordsIn);CHKERRQ(ierr);
if (binary) {
size_t doubleSize, intSize;
PetscInt elementSize;
char *buffer;
PetscScalar *baseptr;
ierr = PetscDataTypeGetSize(PETSC_ENUM, &intSize);CHKERRQ(ierr);
ierr = PetscDataTypeGetSize(PETSC_DOUBLE, &doubleSize);CHKERRQ(ierr);
elementSize = (intSize + 3*doubleSize);
ierr = PetscMalloc1(elementSize*numVertices, &buffer);CHKERRQ(ierr);
ierr = PetscViewerRead(viewer, buffer, elementSize*numVertices, NULL, PETSC_CHAR);CHKERRQ(ierr);
if (bswap) ierr = PetscByteSwap(buffer, PETSC_CHAR, elementSize*numVertices);CHKERRQ(ierr);
for (v = 0; v < numVertices; ++v) {
baseptr = ((PetscScalar*)(buffer+v*elementSize+intSize));
coordsIn[v*3+0] = baseptr[0];
coordsIn[v*3+1] = baseptr[1];
coordsIn[v*3+2] = baseptr[2];
}
ierr = PetscFree(buffer);CHKERRQ(ierr);
} else {
for (v = 0; v < numVertices; ++v) {
ierr = PetscViewerRead(viewer, &i, 1, NULL, PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerRead(viewer, &(coordsIn[v*3]), 3, NULL, PETSC_DOUBLE);CHKERRQ(ierr);
if (i != (int)v+1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid node number %d should be %d", i, v+1);
}
}
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);;
ierr = PetscStrncmp(line, "$EndNodes", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
/* Read cells */
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);;
ierr = PetscStrncmp(line, "$Elements", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);;
snum = sscanf(line, "%d", &numCells);
if (snum != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
}
if (!rank || binary) {
/* Gmsh elements can be of any dimension/co-dimension, so we need to traverse the
file contents multiple times to figure out the true number of cells and facets
in the given mesh. To make this more efficient we read the file contents only
once and store them in memory, while determining the true number of cells. */
ierr = DMPlexCreateGmsh_ReadElement(viewer, numCells, binary, bswap, &gmsh_elem);CHKERRQ(ierr);
for (trueNumCells=0, c = 0; c < numCells; ++c) {
if (gmsh_elem[c].dim > dim) {dim = gmsh_elem[c].dim; trueNumCells = 0;}
if (gmsh_elem[c].dim == dim) trueNumCells++;
}
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);;
ierr = PetscStrncmp(line, "$EndElements", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
}
/* For binary we read on all ranks, but only build the plex on rank 0 */
if (binary && rank) {trueNumCells = 0; numVertices = 0;};
/* Allocate the cell-vertex mesh */
ierr = DMPlexSetChart(*dm, 0, trueNumCells+numVertices);CHKERRQ(ierr);
if (!rank) {
for (cell = 0, c = 0; c < numCells; ++c) {
if (gmsh_elem[c].dim == dim) {
ierr = DMPlexSetConeSize(*dm, cell, gmsh_elem[c].numNodes);CHKERRQ(ierr);
cell++;
}
}
}
ierr = DMSetUp(*dm);CHKERRQ(ierr);
/* Add cell-vertex connections */
if (!rank) {
PetscInt pcone[8], corner;
for (cell = 0, c = 0; c < numCells; ++c) {
if (gmsh_elem[c].dim == dim) {
for (corner = 0; corner < gmsh_elem[c].numNodes; ++corner) {
pcone[corner] = gmsh_elem[c].nodes[corner] + trueNumCells-1;
}
if (dim == 3) {
/* Tetrahedra are inverted */
if (gmsh_elem[c].numNodes == 4) {
PetscInt tmp = pcone[0];
pcone[0] = pcone[1];
pcone[1] = tmp;
}
/* Hexahedra are inverted */
if (gmsh_elem[c].numNodes == 8) {
PetscInt tmp = pcone[1];
pcone[1] = pcone[3];
pcone[3] = tmp;
}
}
ierr = DMPlexSetCone(*dm, cell, pcone);CHKERRQ(ierr);
cell++;
}
}
}
ierr = MPI_Bcast(&dim, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr);
ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr);
ierr = DMPlexStratify(*dm);CHKERRQ(ierr);
if (interpolate) {
DM idm = NULL;
ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = idm;
}
if (!rank) {
/* Apply boundary IDs by finding the relevant facets with vertex joins */
PetscInt pcone[8], corner, vStart, vEnd;
ierr = DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
for (c = 0; c < numCells; ++c) {
if (gmsh_elem[c].dim == dim-1) {
PetscInt joinSize;
const PetscInt *join;
for (corner = 0; corner < gmsh_elem[c].numNodes; ++corner) {
pcone[corner] = gmsh_elem[c].nodes[corner] + vStart - 1;
}
ierr = DMPlexGetFullJoin(*dm, gmsh_elem[c].numNodes, (const PetscInt *) pcone, &joinSize, &join);CHKERRQ(ierr);
if (joinSize != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not determine Plex facet for element %d", gmsh_elem[c].id);
ierr = DMSetLabelValue(*dm, "Face Sets", join[0], gmsh_elem[c].tags[0]);CHKERRQ(ierr);
ierr = DMPlexRestoreJoin(*dm, gmsh_elem[c].numNodes, (const PetscInt *) pcone, &joinSize, &join);CHKERRQ(ierr);
}
}
/* Create cell sets */
for (cell = 0, c = 0; c < numCells; ++c) {
if (gmsh_elem[c].dim == dim) {
if (gmsh_elem[c].numTags > 0) {
ierr = DMSetLabelValue(*dm, "Cell Sets", cell, gmsh_elem[c].tags[0]);CHKERRQ(ierr);
cell++;
}
}
}
}
/* Read coordinates */
ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, trueNumCells, trueNumCells + numVertices);CHKERRQ(ierr);
for (v = trueNumCells; v < trueNumCells+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr);
ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
if (!rank) {
for (v = 0; v < numVertices; ++v) {
for (d = 0; d < dim; ++d) {
coords[v*dim+d] = coordsIn[v*3+d];
}
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = PetscFree(coordsIn);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
/* Clean up intermediate storage */
if (!rank || binary) ierr = PetscFree(gmsh_elem);CHKERRQ(ierr);
ierr = PetscLogEventEnd(DMPLEX_CreateGmsh,*dm,0,0,0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMPlexCreateGmsh - Create a DMPlex mesh from a Gmsh file.
Collective on comm
Input Parameters:
+ comm - The MPI communicator
. viewer - The Viewer associated with a Gmsh file
- interpolate - Create faces and edges in the mesh
Output Parameter:
. dm - The DM object representing the mesh
Note: http://www.geuz.org/gmsh/doc/texinfo/#MSH-ASCII-file-format
Level: beginner
.keywords: mesh,Gmsh
.seealso: DMPLEX, DMCreate()
@*/
PetscErrorCode DMPlexCreateGmsh(MPI_Comm comm, PetscViewer viewer, PetscBool interpolate, DM *dm)
{
FILE *fd;
PetscSection coordSection;
Vec coordinates;
PetscScalar *coords, *coordsIn = NULL;
PetscInt dim = 0, coordSize, c, v, d;
int numVertices = 0, numCells = 0, snum;
long fpos = 0;
PetscMPIInt num_proc, rank;
char line[PETSC_MAX_PATH_LEN];
PetscBool match;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &num_proc);CHKERRQ(ierr);
ierr = DMCreate(comm, dm);CHKERRQ(ierr);
ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
if (!rank) {
PetscBool match;
int fileType, dataSize;
ierr = PetscViewerASCIIGetPointer(viewer, &fd);CHKERRQ(ierr);
/* Read header */
fgets(line, PETSC_MAX_PATH_LEN, fd);
ierr = PetscStrncmp(line, "$MeshFormat\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
snum = fscanf(fd, "2.2 %d %d\n", &fileType, &dataSize);CHKERRQ(snum != 2);
if (fileType) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File type %d is not a valid Gmsh ASCII file", fileType);
if (dataSize != sizeof(double)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Data size %d is not valid for a Gmsh file", dataSize);
fgets(line, PETSC_MAX_PATH_LEN, fd);
ierr = PetscStrncmp(line, "$EndMeshFormat\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
/* Read vertices */
fgets(line, PETSC_MAX_PATH_LEN, fd);
ierr = PetscStrncmp(line, "$Nodes\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
snum = fscanf(fd, "%d\n", &numVertices);CHKERRQ(snum != 1);
ierr = PetscMalloc(numVertices*3 * sizeof(PetscScalar), &coordsIn);CHKERRQ(ierr);
for (v = 0; v < numVertices; ++v) {
double x, y, z;
int i;
snum = fscanf(fd, "%d %lg %lg %lg\n", &i, &x, &y, &z);CHKERRQ(snum != 4);
coordsIn[v*3+0] = x; coordsIn[v*3+1] = y; coordsIn[v*3+2] = z;
if (i != v+1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid node number %d should be %d", i, v+1);
}
fgets(line, PETSC_MAX_PATH_LEN, fd);
ierr = PetscStrncmp(line, "$EndNodes\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
/* Read cells */
fgets(line, PETSC_MAX_PATH_LEN, fd);
ierr = PetscStrncmp(line, "$Elements\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
snum = fscanf(fd, "%d\n", &numCells);CHKERRQ(snum != 1);
}
ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr);
if (!rank) {
fpos = ftell(fd);
for (c = 0; c < numCells; ++c) {
PetscInt numCorners, t;
int cone[8], i, cellType, numTags, tag;
snum = fscanf(fd, "%d %d %d", &i, &cellType, &numTags);CHKERRQ(snum != 3);
if (numTags) for (t = 0; t < numTags; ++t) {snum = fscanf(fd, "%d", &tag);CHKERRQ(snum != 1);}
switch (cellType) {
case 1: /* 2-node line */
dim = 1;
numCorners = 2;
snum = fscanf(fd, "%d %d\n", &cone[0], &cone[1]);CHKERRQ(snum != numCorners);
break;
case 2: /* 3-node triangle */
dim = 2;
numCorners = 3;
snum = fscanf(fd, "%d %d %d\n", &cone[0], &cone[1], &cone[2]);CHKERRQ(snum != numCorners);
break;
case 3: /* 4-node quadrangle */
dim = 2;
numCorners = 4;
snum = fscanf(fd, "%d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3]);CHKERRQ(snum != numCorners);
break;
case 4: /* 4-node tetrahedron */
dim = 3;
numCorners = 4;
snum = fscanf(fd, "%d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3]);CHKERRQ(snum != numCorners);
break;
case 5: /* 8-node hexahedron */
dim = 3;
numCorners = 8;
snum = fscanf(fd, "%d %d %d %d %d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3], &cone[4], &cone[5], &cone[6], &cone[7]);CHKERRQ(snum != numCorners);
break;
default:
SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unsupported Gmsh element type %d", cellType);
}
ierr = DMPlexSetConeSize(*dm, c, numCorners);CHKERRQ(ierr);
if (i != c+1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell number %d should be %d", i, c+1);
}
}
ierr = DMSetUp(*dm);CHKERRQ(ierr);
if (!rank) {
ierr = fseek(fd, fpos, SEEK_SET);CHKERRQ(ierr);
for (c = 0; c < numCells; ++c) {
PetscInt pcone[8], numCorners, corner, t;
int cone[8], i, cellType, numTags, tag;
snum = fscanf(fd, "%d %d %d", &i, &cellType, &numTags);CHKERRQ(snum != 3);
if (numTags) for (t = 0; t < numTags; ++t) {snum = fscanf(fd, "%d", &tag);CHKERRQ(snum != 1);}
switch (cellType) {
case 1: /* 2-node line */
dim = 1;
numCorners = 2;
snum = fscanf(fd, "%d %d\n", &cone[0], &cone[1]);CHKERRQ(snum != numCorners);
break;
case 2: /* 3-node triangle */
dim = 2;
numCorners = 3;
snum = fscanf(fd, "%d %d %d\n", &cone[0], &cone[1], &cone[2]);CHKERRQ(snum != numCorners);
break;
case 3: /* 4-node quadrangle */
dim = 2;
numCorners = 4;
snum = fscanf(fd, "%d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3]);CHKERRQ(snum != numCorners);
break;
case 4: /* 4-node tetrahedron */
dim = 3;
numCorners = 4;
snum = fscanf(fd, "%d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3]);CHKERRQ(snum != numCorners);
ierr = DMPlexInvertCell(dim, numCorners, cone);CHKERRQ(ierr);
break;
case 5: /* 8-node hexahedron */
dim = 3;
numCorners = 8;
snum = fscanf(fd, "%d %d %d %d %d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3], &cone[4], &cone[5], &cone[6], &cone[7]);CHKERRQ(snum != numCorners);
ierr = DMPlexInvertCell(dim, numCorners, cone);CHKERRQ(ierr);
break;
default:
SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unsupported Gmsh element type %d", cellType);
}
for (corner = 0; corner < numCorners; ++corner) pcone[corner] = cone[corner] + numCells-1;
ierr = DMPlexSetCone(*dm, c, pcone);CHKERRQ(ierr);
if (i != c+1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell number %d should be %d", i, c+1);
}
fgets(line, PETSC_MAX_PATH_LEN, fd);
ierr = PetscStrncmp(line, "$EndElements\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
}
ierr = MPI_Bcast(&dim, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr);
ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr);
ierr = DMPlexStratify(*dm);CHKERRQ(ierr);
if (interpolate) {
DM idm;
ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = idm;
}
/* Read coordinates */
ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr);
for (v = numCells; v < numCells+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(comm, &coordinates);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
if (!rank) {
for (v = 0; v < numVertices; ++v) {
for (d = 0; d < dim; ++d) {
coords[v*dim+d] = coordsIn[v*3+d];
}
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = PetscFree(coordsIn);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/* This interpolates faces for cells at some stratum */
static PetscErrorCode DMPlexInterpolateFaces_Internal(DM dm, PetscInt cellDepth, DM idm)
{
PetscHashIJKL faceTable;
PetscInt *pStart, *pEnd;
PetscInt cellDim, depth, faceDepth = cellDepth, numPoints = 0, faceSizeAll = 0, face, c, d;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetDimension(dm, &cellDim);CHKERRQ(ierr);
ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr);
++depth;
++cellDepth;
cellDim -= depth - cellDepth;
ierr = PetscMalloc2(depth+1,PetscInt,&pStart,depth+1,PetscInt,&pEnd);CHKERRQ(ierr);
for (d = depth-1; d >= faceDepth; --d) {
ierr = DMPlexGetDepthStratum(dm, d, &pStart[d+1], &pEnd[d+1]);CHKERRQ(ierr);
}
ierr = DMPlexGetDepthStratum(dm, -1, NULL, &pStart[faceDepth]);CHKERRQ(ierr);
pEnd[faceDepth] = pStart[faceDepth];
for (d = faceDepth-1; d >= 0; --d) {
ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr);
}
if (pEnd[cellDepth] > pStart[cellDepth]) {ierr = DMPlexGetFaces_Internal(dm, cellDim, pStart[cellDepth], NULL, &faceSizeAll, NULL);CHKERRQ(ierr);}
if (faceSizeAll > 4) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Do not support interpolation of meshes with faces of %D vertices", faceSizeAll);
ierr = PetscHashIJKLCreate(&faceTable);CHKERRQ(ierr);
ierr = PetscHashIJKLSetMultivalued(faceTable, PETSC_FALSE);CHKERRQ(ierr);
for (c = pStart[cellDepth], face = pStart[faceDepth]; c < pEnd[cellDepth]; ++c) {
const PetscInt *cellFaces;
PetscInt numCellFaces, faceSize, cf, f;
ierr = DMPlexGetFaces_Internal(dm, cellDim, c, &numCellFaces, &faceSize, &cellFaces);CHKERRQ(ierr);
if (faceSize != faceSizeAll) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Inconsistent face for cell %D of size %D != %D", c, faceSize, faceSizeAll);
for (cf = 0; cf < numCellFaces; ++cf) {
const PetscInt *cellFace = &cellFaces[cf*faceSize];
PetscHashIJKLKey key;
if (faceSize == 2) {
key.i = PetscMin(cellFace[0], cellFace[1]);
key.j = PetscMax(cellFace[0], cellFace[1]);
} else {
key.i = cellFace[0]; key.j = cellFace[1]; key.k = cellFace[2]; key.l = faceSize > 3 ? cellFace[3] : 0;
ierr = PetscSortInt(faceSize, (PetscInt *) &key);
}
ierr = PetscHashIJKLGet(faceTable, key, &f);CHKERRQ(ierr);
if (f < 0) {
ierr = PetscHashIJKLAdd(faceTable, key, face);CHKERRQ(ierr);
f = face++;
}
}
}
pEnd[faceDepth] = face;
ierr = PetscHashIJKLDestroy(&faceTable);CHKERRQ(ierr);
/* Count new points */
for (d = 0; d <= depth; ++d) {
numPoints += pEnd[d]-pStart[d];
}
ierr = DMPlexSetChart(idm, 0, numPoints);CHKERRQ(ierr);
/* Set cone sizes */
for (d = 0; d <= depth; ++d) {
PetscInt coneSize, p;
if (d == faceDepth) {
for (p = pStart[d]; p < pEnd[d]; ++p) {
/* I see no way to do this if we admit faces of different shapes */
ierr = DMPlexSetConeSize(idm, p, faceSizeAll);CHKERRQ(ierr);
}
} else if (d == cellDepth) {
for (p = pStart[d]; p < pEnd[d]; ++p) {
/* Number of cell faces may be different from number of cell vertices*/
ierr = DMPlexGetFaces_Internal(dm, cellDim, p, &coneSize, NULL, NULL);CHKERRQ(ierr);
ierr = DMPlexSetConeSize(idm, p, coneSize);CHKERRQ(ierr);
}
} else {
for (p = pStart[d]; p < pEnd[d]; ++p) {
ierr = DMPlexGetConeSize(dm, p, &coneSize);CHKERRQ(ierr);
ierr = DMPlexSetConeSize(idm, p, coneSize);CHKERRQ(ierr);
}
}
}
ierr = DMSetUp(idm);CHKERRQ(ierr);
/* Get face cones from subsets of cell vertices */
if (faceSizeAll > 4) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Do not support interpolation of meshes with faces of %D vertices", faceSizeAll);
ierr = PetscHashIJKLCreate(&faceTable);CHKERRQ(ierr);
ierr = PetscHashIJKLSetMultivalued(faceTable, PETSC_FALSE);CHKERRQ(ierr);
for (d = depth; d > cellDepth; --d) {
const PetscInt *cone;
PetscInt p;
for (p = pStart[d]; p < pEnd[d]; ++p) {
ierr = DMPlexGetCone(dm, p, &cone);CHKERRQ(ierr);
ierr = DMPlexSetCone(idm, p, cone);CHKERRQ(ierr);
ierr = DMPlexGetConeOrientation(dm, p, &cone);CHKERRQ(ierr);
ierr = DMPlexSetConeOrientation(idm, p, cone);CHKERRQ(ierr);
}
}
for (c = pStart[cellDepth], face = pStart[faceDepth]; c < pEnd[cellDepth]; ++c) {
const PetscInt *cellFaces;
PetscInt numCellFaces, faceSize, cf, f;
ierr = DMPlexGetFaces_Internal(dm, cellDim, c, &numCellFaces, &faceSize, &cellFaces);CHKERRQ(ierr);
if (faceSize != faceSizeAll) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Inconsistent face for cell %D of size %D != %D", c, faceSize, faceSizeAll);
for (cf = 0; cf < numCellFaces; ++cf) {
const PetscInt *cellFace = &cellFaces[cf*faceSize];
PetscHashIJKLKey key;
if (faceSize == 2) {
key.i = PetscMin(cellFace[0], cellFace[1]);
key.j = PetscMax(cellFace[0], cellFace[1]);
} else {
key.i = cellFace[0]; key.j = cellFace[1]; key.k = cellFace[2]; key.l = faceSize > 3 ? cellFace[3] : 0;
ierr = PetscSortInt(faceSize, (PetscInt *) &key);
}
ierr = PetscHashIJKLGet(faceTable, key, &f);CHKERRQ(ierr);
if (f < 0) {
ierr = DMPlexSetCone(idm, face, cellFace);CHKERRQ(ierr);
ierr = PetscHashIJKLAdd(faceTable, key, face);CHKERRQ(ierr);
f = face++;
ierr = DMPlexInsertCone(idm, c, cf, f);CHKERRQ(ierr);
} else {
const PetscInt *cone;
PetscInt coneSize, ornt, i, j;
ierr = DMPlexInsertCone(idm, c, cf, f);CHKERRQ(ierr);
/* Orient face */
ierr = DMPlexGetConeSize(idm, f, &coneSize);CHKERRQ(ierr);
ierr = DMPlexGetCone(idm, f, &cone);CHKERRQ(ierr);
if (coneSize != faceSize) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of face vertices %D for face %D should be %D", coneSize, f, faceSize);
/* - First find the initial vertex */
for (i = 0; i < faceSize; ++i) if (cellFace[0] == cone[i]) break;
/* - Try forward comparison */
for (j = 0; j < faceSize; ++j) if (cellFace[j] != cone[(i+j)%faceSize]) break;
if (j == faceSize) {
if ((faceSize == 2) && (i == 1)) ornt = -2;
else ornt = i;
} else {
/* - Try backward comparison */
for (j = 0; j < faceSize; ++j) if (cellFace[j] != cone[(i+faceSize-j)%faceSize]) break;
if (j == faceSize) ornt = -(i+1);
else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not determine face orientation");
}
ierr = DMPlexInsertConeOrientation(idm, c, cf, ornt);CHKERRQ(ierr);
}
}
}
if (face != pEnd[faceDepth]) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid number of faces %D should be %D", face-pStart[faceDepth], pEnd[faceDepth]-pStart[faceDepth]);
ierr = PetscFree2(pStart,pEnd);CHKERRQ(ierr);
ierr = PetscHashIJKLDestroy(&faceTable);CHKERRQ(ierr);
ierr = DMPlexSymmetrize(idm);CHKERRQ(ierr);
ierr = DMPlexStratify(idm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMPlexUninterpolate - Take in a mesh with all intermediate faces, edges, etc. and return a cell-vertex mesh
Collective on DM
Input Parameter:
. dm - The complete DMPlex object
Output Parameter:
. dmUnint - The DMPlex object with only cells and vertices
Level: intermediate
.keywords: mesh
.seealso: DMPlexInterpolate(), DMPlexCreateFromCellList()
@*/
PetscErrorCode DMPlexUninterpolate(DM dm, DM *dmUnint)
{
DM udm;
PetscInt dim, vStart, vEnd, cStart, cEnd, c, maxConeSize = 0, *cone;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
if (dim <= 1) {
ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr);
*dmUnint = dm;
PetscFunctionReturn(0);
}
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMCreate(PetscObjectComm((PetscObject) dm), &udm);CHKERRQ(ierr);
ierr = DMSetType(udm, DMPLEX);CHKERRQ(ierr);
ierr = DMSetDimension(udm, dim);CHKERRQ(ierr);
ierr = DMPlexSetChart(udm, cStart, vEnd);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL, closureSize, cl, coneSize = 0;
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (cl = 0; cl < closureSize*2; cl += 2) {
const PetscInt p = closure[cl];
if ((p >= vStart) && (p < vEnd)) ++coneSize;
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
ierr = DMPlexSetConeSize(udm, c, coneSize);CHKERRQ(ierr);
maxConeSize = PetscMax(maxConeSize, coneSize);
}
ierr = DMSetUp(udm);CHKERRQ(ierr);
ierr = PetscMalloc1(maxConeSize, &cone);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL, closureSize, cl, coneSize = 0;
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (cl = 0; cl < closureSize*2; cl += 2) {
const PetscInt p = closure[cl];
if ((p >= vStart) && (p < vEnd)) cone[coneSize++] = p;
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
ierr = DMPlexSetCone(udm, c, cone);CHKERRQ(ierr);
}
ierr = PetscFree(cone);CHKERRQ(ierr);
ierr = DMPlexSymmetrize(udm);CHKERRQ(ierr);
ierr = DMPlexStratify(udm);CHKERRQ(ierr);
/* Reduce SF */
{
PetscSF sfPoint, sfPointUn;
const PetscSFNode *remotePoints;
const PetscInt *localPoints;
PetscSFNode *remotePointsUn;
PetscInt *localPointsUn;
PetscInt vEnd, numRoots, numLeaves, l;
PetscInt numLeavesUn = 0, n = 0;
PetscErrorCode ierr;
/* Get original SF information */
ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr);
ierr = DMGetPointSF(udm, &sfPointUn);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, NULL, &vEnd);CHKERRQ(ierr);
ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr);
/* Allocate space for cells and vertices */
for (l = 0; l < numLeaves; ++l) if (localPoints[l] < vEnd) numLeavesUn++;
/* Fill in leaves */
if (vEnd >= 0) {
ierr = PetscMalloc1(numLeavesUn, &remotePointsUn);CHKERRQ(ierr);
ierr = PetscMalloc1(numLeavesUn, &localPointsUn);CHKERRQ(ierr);
for (l = 0; l < numLeaves; l++) {
if (localPoints[l] < vEnd) {
localPointsUn[n] = localPoints[l];
remotePointsUn[n].rank = remotePoints[l].rank;
remotePointsUn[n].index = remotePoints[l].index;
++n;
}
}
if (n != numLeavesUn) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Inconsistent number of leaves %d != %d", n, numLeavesUn);
ierr = PetscSFSetGraph(sfPointUn, vEnd, numLeavesUn, localPointsUn, PETSC_OWN_POINTER, remotePointsUn, PETSC_OWN_POINTER);CHKERRQ(ierr);
}
}
*dmUnint = udm;
PetscFunctionReturn(0);
}