static PetscErrorCode DMPlexGetAdjacency_Transitive_Internal(DM dm, PetscInt p, PetscBool useClosure, PetscInt *adjSize, PetscInt adj[])
{
PetscInt *star = NULL;
PetscInt numAdj = 0, maxAdjSize = *adjSize, starSize, s;
PetscErrorCode ierr;
PetscFunctionBeginHot;
ierr = DMPlexGetTransitiveClosure(dm, p, useClosure, &starSize, &star);CHKERRQ(ierr);
for (s = 0; s < starSize*2; s += 2) {
const PetscInt *closure = NULL;
PetscInt closureSize, c, q;
ierr = DMPlexGetTransitiveClosure(dm, star[s], (PetscBool)!useClosure, &closureSize, (PetscInt**) &closure);CHKERRQ(ierr);
for (c = 0; c < closureSize*2; c += 2) {
for (q = 0; q < numAdj || (adj[numAdj++] = closure[c],0); ++q) {
if (closure[c] == adj[q]) break;
}
if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
}
ierr = DMPlexRestoreTransitiveClosure(dm, star[s], (PetscBool)!useClosure, &closureSize, (PetscInt**) &closure);CHKERRQ(ierr);
}
ierr = DMPlexRestoreTransitiveClosure(dm, p, useClosure, &starSize, &star);CHKERRQ(ierr);
*adjSize = numAdj;
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 = 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);
}
PetscErrorCode CompareCones(DM dm, DM idm)
{
PetscInt cStart, cEnd, c, vStart, vEnd, v;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {
const PetscInt *cone;
PetscInt *points = NULL, numPoints, p, numVertices = 0, coneSize;
ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr);
ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr);
ierr = DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr);
for (p = 0; p < numPoints*2; p += 2) {
const PetscInt point = points[p];
if ((point >= vStart) && (point < vEnd)) points[numVertices++] = point;
}
if (numVertices != coneSize) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "In cell %d, cone size %d != %d vertices in closure", c, coneSize, numVertices);
for (v = 0; v < numVertices; ++v) {
if (cone[v] != points[v]) SETERRQ4(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "In cell %d, cone point %d is %d != %d vertex in closure", c, v, cone[v], points[v]);
}
ierr = DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
static PetscErrorCode DMPlexGetVTKConnectivity(DM dm,PieceInfo *piece,PetscVTKInt **oconn,PetscVTKInt **ooffsets,PetscVTKType **otypes)
{
PetscErrorCode ierr;
PetscVTKInt *conn,*offsets;
PetscVTKType *types;
PetscInt dim,vStart,vEnd,cStart,cEnd,pStart,pEnd,cellHeight,cMax,numLabelCells,hasLabel,c,v,countcell,countconn;
PetscFunctionBegin;
ierr = PetscMalloc3(piece->nconn,PetscVTKInt,&conn,piece->ncells,PetscVTKInt,&offsets,piece->ncells,PetscVTKType,&types);CHKERRQ(ierr);
ierr = DMPlexGetDimension(dm,&dim);CHKERRQ(ierr);
ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr);
ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr);
if (cMax >= 0) cEnd = PetscMin(cEnd, cMax);
ierr = DMPlexGetStratumSize(dm, "vtk", 1, &numLabelCells);CHKERRQ(ierr);
hasLabel = numLabelCells > 0 ? PETSC_TRUE : PETSC_FALSE;
countcell = 0;
countconn = 0;
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL;
PetscInt closureSize,nverts,celltype,startoffset,nC=0;
if (hasLabel) {
PetscInt value;
ierr = DMPlexGetLabelValue(dm, "vtk", c, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
startoffset = countconn;
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (v = 0; v < closureSize*2; v += 2) {
if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
conn[countconn++] = closure[v] - vStart;
++nC;
}
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
ierr = DMPlexInvertCell(dim, nC, &conn[countconn-nC]);CHKERRQ(ierr);
offsets[countcell] = countconn;
nverts = countconn - startoffset;
ierr = DMPlexVTKGetCellType(dm,dim,nverts,&celltype);CHKERRQ(ierr);
types[countcell] = celltype;
countcell++;
}
if (countcell != piece->ncells) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Inconsistent cell count");
if (countconn != piece->nconn) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Inconsistent connectivity count");
*oconn = conn;
*ooffsets = offsets;
*otypes = types;
PetscFunctionReturn(0);
}
PetscErrorCode TestTransitiveClosure(DM dm, AppCtx *user)
{
PetscInt numRuns, cStart, cEnd, c, i;
PetscReal maxTimePerRun = user->maxClosureTime;
PetscStageLog stageLog;
PetscEventPerfLog eventLog;
PetscInt stage;
PetscLogEvent event;
PetscEventPerfInfo eventInfo;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLogStageRegister("DMPlex Transitive Closure Test", &stage);CHKERRQ(ierr);
ierr = PetscLogEventRegister("TransitiveClosure", PETSC_OBJECT_CLASSID, &event);CHKERRQ(ierr);
ierr = PetscLogStagePush(stage);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = PetscLogEventBegin(event,0,0,0,0);CHKERRQ(ierr);
for (i = 0; i < user->iterations; ++i) {
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL;
PetscInt closureSize;
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
}
}
ierr = PetscLogEventEnd(event,0,0,0,0);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = PetscLogGetStageLog(&stageLog);
ierr = PetscStageLogGetEventPerfLog(stageLog, stage, &eventLog);
numRuns = (cEnd-cStart) * user->iterations;
eventInfo = eventLog->eventInfo[event];
if (eventInfo.count != 1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of event calls %d should be %d", eventInfo.count, 1);
if ((PetscInt) eventInfo.flops != 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of event flops %d should be %d", (PetscInt) eventInfo.flops, 0);
if (eventInfo.time > maxTimePerRun * numRuns) {
ierr = PetscPrintf(PETSC_COMM_SELF, "Closures: %d Average time per cone: %gs standard: %gs\n", numRuns, eventInfo.time/numRuns, maxTimePerRun);
if (user->errors) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Average time for closure %g > standard %g", eventInfo.time/numRuns, maxTimePerRun);
}
PetscFunctionReturn(0);
}
PetscErrorCode DMPlexVTKWriteCells_ASCII(DM dm, FILE *fp, PetscInt *totalCells)
{
MPI_Comm comm;
DMLabel label;
IS globalVertexNumbers = NULL;
const PetscInt *gvertex;
PetscInt dim;
PetscInt numCorners = 0, totCorners = 0, maxCorners, *corners;
PetscInt numCells = 0, totCells = 0, maxCells, cellHeight;
PetscInt numLabelCells, maxLabelCells, cMax, cStart, cEnd, c, vStart, vEnd, v;
PetscMPIInt numProcs, rank, proc, tag;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
ierr = PetscCommGetNewTag(comm, &tag);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr);
if (cMax >= 0) cEnd = PetscMin(cEnd, cMax);
ierr = DMPlexGetLabel(dm, "vtk", &label);CHKERRQ(ierr);
ierr = DMPlexGetStratumSize(dm, "vtk", 1, &numLabelCells);CHKERRQ(ierr);
ierr = MPI_Allreduce(&numLabelCells, &maxLabelCells, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr);
if (!maxLabelCells) label = NULL;
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL;
PetscInt closureSize, value;
if (label) {
ierr = DMLabelGetValue(label, c, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (v = 0; v < closureSize*2; v += 2) {
if ((closure[v] >= vStart) && (closure[v] < vEnd)) ++numCorners;
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
++numCells;
}
maxCells = numCells;
ierr = MPI_Reduce(&numCells, &totCells, 1, MPIU_INT, MPI_SUM, 0, comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&numCells, &maxCells, 1, MPIU_INT, MPI_MAX, 0, comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&numCorners, &totCorners, 1, MPIU_INT, MPI_SUM, 0, comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&numCorners, &maxCorners, 1, MPIU_INT, MPI_MAX, 0, comm);CHKERRQ(ierr);
ierr = DMPlexGetVertexNumbering(dm, &globalVertexNumbers);CHKERRQ(ierr);
ierr = ISGetIndices(globalVertexNumbers, &gvertex);CHKERRQ(ierr);
ierr = PetscMalloc1(maxCells, &corners);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "CELLS %d %d\n", totCells, totCorners+totCells);CHKERRQ(ierr);
if (!rank) {
PetscInt *remoteVertices;
int *vertices;
ierr = PetscMalloc1(maxCorners, &vertices);CHKERRQ(ierr);
for (c = cStart, numCells = 0; c < cEnd; ++c) {
PetscInt *closure = NULL;
PetscInt closureSize, value, nC = 0;
if (label) {
ierr = DMLabelGetValue(label, c, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (v = 0; v < closureSize*2; v += 2) {
if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
const PetscInt gv = gvertex[closure[v] - vStart];
vertices[nC++] = gv < 0 ? -(gv+1) : gv;
}
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
corners[numCells++] = nC;
ierr = PetscFPrintf(comm, fp, "%d ", nC);CHKERRQ(ierr);
ierr = DMPlexInvertCell(dim, nC, vertices);CHKERRQ(ierr);
for (v = 0; v < nC; ++v) {
ierr = PetscFPrintf(comm, fp, " %d", vertices[v]);CHKERRQ(ierr);
}
ierr = PetscFPrintf(comm, fp, "\n");CHKERRQ(ierr);
}
if (numProcs > 1) {ierr = PetscMalloc1(maxCorners+maxCells, &remoteVertices);CHKERRQ(ierr);}
for (proc = 1; proc < numProcs; ++proc) {
MPI_Status status;
ierr = MPI_Recv(&numCorners, 1, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr);
ierr = MPI_Recv(remoteVertices, numCorners, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr);
for (c = 0; c < numCorners;) {
PetscInt nC = remoteVertices[c++];
for (v = 0; v < nC; ++v, ++c) {
vertices[v] = remoteVertices[c];
}
ierr = DMPlexInvertCell(dim, nC, vertices);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "%d ", nC);CHKERRQ(ierr);
for (v = 0; v < nC; ++v) {
ierr = PetscFPrintf(comm, fp, " %d", vertices[v]);CHKERRQ(ierr);
}
ierr = PetscFPrintf(comm, fp, "\n");CHKERRQ(ierr);
}
}
if (numProcs > 1) {ierr = PetscFree(remoteVertices);CHKERRQ(ierr);}
ierr = PetscFree(vertices);CHKERRQ(ierr);
} else {
PetscInt *localVertices, numSend = numCells+numCorners, k = 0;
ierr = PetscMalloc1(numSend, &localVertices);CHKERRQ(ierr);
for (c = cStart, numCells = 0; c < cEnd; ++c) {
PetscInt *closure = NULL;
PetscInt closureSize, value, nC = 0;
if (label) {
ierr = DMLabelGetValue(label, c, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (v = 0; v < closureSize*2; v += 2) {
if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
const PetscInt gv = gvertex[closure[v] - vStart];
closure[nC++] = gv < 0 ? -(gv+1) : gv;
}
}
corners[numCells++] = nC;
localVertices[k++] = nC;
for (v = 0; v < nC; ++v, ++k) {
localVertices[k] = closure[v];
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
}
if (k != numSend) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Invalid number of vertices to send %d should be %d", k, numSend);
ierr = MPI_Send(&numSend, 1, MPIU_INT, 0, tag, comm);CHKERRQ(ierr);
ierr = MPI_Send(localVertices, numSend, MPIU_INT, 0, tag, comm);CHKERRQ(ierr);
ierr = PetscFree(localVertices);CHKERRQ(ierr);
}
ierr = ISRestoreIndices(globalVertexNumbers, &gvertex);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "CELL_TYPES %d\n", totCells);CHKERRQ(ierr);
if (!rank) {
PetscInt cellType;
for (c = 0; c < numCells; ++c) {
ierr = DMPlexVTKGetCellType(dm, dim, corners[c], &cellType);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "%d\n", cellType);CHKERRQ(ierr);
}
for (proc = 1; proc < numProcs; ++proc) {
MPI_Status status;
ierr = MPI_Recv(&numCells, 1, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr);
ierr = MPI_Recv(corners, numCells, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr);
for (c = 0; c < numCells; ++c) {
ierr = DMPlexVTKGetCellType(dm, dim, corners[c], &cellType);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "%d\n", cellType);CHKERRQ(ierr);
}
}
} else {
ierr = MPI_Send(&numCells, 1, MPIU_INT, 0, tag, comm);CHKERRQ(ierr);
ierr = MPI_Send(corners, numCells, MPIU_INT, 0, tag, comm);CHKERRQ(ierr);
}
ierr = PetscFree(corners);CHKERRQ(ierr);
*totalCells = totCells;
PetscFunctionReturn(0);
}
/*@C
DMPlexGetIndex - Get the index of 'point'. It returns the global indices.
Not collective
Input Parameters:
+ dm - The DM
. section - The section describing the layout in v, or NULL to use the default section
. globalSection - The section describing the layout in v, or NULL to use the default global section
. point - The sieve point in the DM
. NumOfIndices - The number of the indices for this point
. indices - The indices of this point
Level: intermediate
.seealso DMPlexVecSetClosure()
@*/
PetscErrorCode DMPlexGetIndex(DM dm, PetscSection section, PetscSection globalSection, PetscInt point, PetscInt *NumOfIndices, PetscInt index[])
{
PetscSection clSection;
IS clPoints;
PetscInt *points = NULL;
const PetscInt *clp;
PetscInt *indices;
PetscInt offsets[32];
PetscInt numFields, numIndices, numPoints, dof, off, globalOff, pStart, pEnd, p, q, f;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
if (!section) {ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);}
PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2);
if (!globalSection) {ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr);}
PetscValidHeaderSpecific(globalSection, PETSC_SECTION_CLASSID, 3);
ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr);
if (numFields > 31) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %D limited to 31", numFields);
ierr = PetscMemzero(offsets, 32 * sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscSectionGetClosureIndex(section, (PetscObject) dm, &clSection, &clPoints);CHKERRQ(ierr);
if (!clPoints) {
ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr);
/* Compress out points not in the section */
ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr);
for (p = 0, q = 0; p < numPoints*2; p += 2) {
if ((points[p] >= pStart) && (points[p] < pEnd)) {
points[q*2] = points[p];
points[q*2+1] = points[p+1];
++q;
}
}
numPoints = q;
} else {
PetscInt dof, off;
ierr = PetscSectionGetDof(clSection, point, &dof);CHKERRQ(ierr);
numPoints = dof/2;
ierr = PetscSectionGetOffset(clSection, point, &off);CHKERRQ(ierr);
ierr = ISGetIndices(clPoints, &clp);CHKERRQ(ierr);
points = (PetscInt *) &clp[off];
}
for (p = 0, numIndices = 0; p < numPoints*2; p += 2) {
PetscInt fdof;
ierr = PetscSectionGetDof(section, points[p], &dof);CHKERRQ(ierr);
for (f = 0; f < numFields; ++f) {
ierr = PetscSectionGetFieldDof(section, points[p], f, &fdof);CHKERRQ(ierr);
offsets[f+1] += fdof;
}
numIndices += dof;
}
for (f = 1; f < numFields; ++f) offsets[f+1] += offsets[f];
if (numFields && offsets[numFields] != numIndices) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid size for closure %d should be %d", offsets[numFields], numIndices);
ierr = DMGetWorkArray(dm, numIndices, PETSC_INT, &indices);CHKERRQ(ierr);
if (numFields) {
for (p = 0; p < numPoints*2; p += 2) {
PetscInt o = points[p+1];
ierr = PetscSectionGetOffset(globalSection, points[p], &globalOff);CHKERRQ(ierr);
indicesPointFields_private(section, points[p], globalOff < 0 ? -(globalOff+1) : globalOff, offsets, PETSC_FALSE, o, indices);
}
} else {
for (p = 0, off = 0; p < numPoints*2; p += 2) {
PetscInt o = points[p+1];
ierr = PetscSectionGetOffset(globalSection, points[p], &globalOff);CHKERRQ(ierr);
indicesPoint_private(section, points[p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, o, indices);
}
}
if (!clPoints) {
ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr);
} else {
ierr = ISRestoreIndices(clPoints, &clp);CHKERRQ(ierr);
}
{
/*Out put the number of indices and the value of indices on this point*/
PetscInt j;
*NumOfIndices = numIndices;
for(j = 0; j < numIndices; j++){
index[j] = indices[j];
}
}
ierr = DMRestoreWorkArray(dm, numIndices, PETSC_INT, &indices);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PETSC_EXTERN PetscErrorCode DMPlexRefine_CTetgen(DM dm, PetscReal *maxVolumes, DM *dmRefined)
{
MPI_Comm comm;
const PetscInt dim = 3;
const char *labelName = "marker";
PLC *in, *out;
DMLabel label;
PetscInt verbose = 0, vStart, vEnd, v, cStart, cEnd, c, depth, depthGlobal;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,((PetscObject) dm)->prefix, "-ctetgen_verbose", &verbose, NULL);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr);
ierr = MPIU_Allreduce(&depth, &depthGlobal, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMGetLabel(dm, labelName, &label);CHKERRQ(ierr);
ierr = PLCCreate(&in);CHKERRQ(ierr);
ierr = PLCCreate(&out);CHKERRQ(ierr);
in->numberofpoints = vEnd - vStart;
if (in->numberofpoints > 0) {
PetscSection coordSection;
Vec coordinates;
PetscScalar *array;
ierr = PetscMalloc1(in->numberofpoints*dim, &in->pointlist);CHKERRQ(ierr);
ierr = PetscMalloc1(in->numberofpoints, &in->pointmarkerlist);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &array);CHKERRQ(ierr);
for (v = vStart; v < vEnd; ++v) {
const PetscInt idx = v - vStart;
PetscInt off, d, m = -1;
ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
for (d = 0; d < dim; ++d) {
in->pointlist[idx*dim + d] = PetscRealPart(array[off+d]);
}
if (label) {ierr = DMLabelGetValue(label, v, &m);CHKERRQ(ierr);}
in->pointmarkerlist[idx] = (int) m;
}
ierr = VecRestoreArray(coordinates, &array);CHKERRQ(ierr);
}
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
in->numberofcorners = 4;
in->numberoftetrahedra = cEnd - cStart;
in->tetrahedronvolumelist = maxVolumes;
if (in->numberoftetrahedra > 0) {
ierr = PetscMalloc1(in->numberoftetrahedra*in->numberofcorners, &in->tetrahedronlist);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {
const PetscInt idx = c - cStart;
PetscInt *closure = NULL;
PetscInt closureSize;
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
if ((closureSize != 5) && (closureSize != 15)) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Mesh has cell which is not a tetrahedron, %D vertices in closure", closureSize);
for (v = 0; v < 4; ++v) {
in->tetrahedronlist[idx*in->numberofcorners + v] = closure[(v+closureSize-4)*2] - vStart;
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
}
}
if (!rank) {
TetGenOpts t;
ierr = TetGenOptsInitialize(&t);CHKERRQ(ierr);
t.in = dm; /* Should go away */
t.refine = 1;
t.varvolume = 1;
t.quality = 1;
t.edgesout = 1;
t.zeroindex = 1;
t.quiet = 1;
t.verbose = verbose; /* Change this */
ierr = TetGenCheckOpts(&t);CHKERRQ(ierr);
ierr = TetGenTetrahedralize(&t, in, out);CHKERRQ(ierr);
}
in->tetrahedronvolumelist = NULL;
{
DMLabel rlabel = NULL;
const PetscInt numCorners = 4;
const PetscInt numCells = out->numberoftetrahedra;
const PetscInt numVertices = out->numberofpoints;
double *meshCoords;
int *cells = out->tetrahedronlist;
PetscBool interpolate = depthGlobal > 1 ? PETSC_TRUE : PETSC_FALSE;
if (sizeof (PetscReal) == sizeof (double)) {
meshCoords = (double *) out->pointlist;
}
else {
PetscInt i;
ierr = PetscMalloc1(3 * numVertices,&meshCoords);CHKERRQ(ierr);
for (i = 0; i < 3 * numVertices; i++) {
meshCoords[i] = (PetscReal) out->pointlist[i];
}
}
ierr = DMPlexInvertCells_Internal(dim, numCells, numCorners, cells);CHKERRQ(ierr);
ierr = DMPlexCreateFromCellList(comm, dim, numCells, numVertices, numCorners, interpolate, cells, dim, meshCoords, dmRefined);CHKERRQ(ierr);
if (sizeof (PetscReal) != sizeof (double)) {
ierr = PetscFree(meshCoords);CHKERRQ(ierr);
}
if (label) {ierr = DMCreateLabel(*dmRefined, labelName); ierr = DMGetLabel(*dmRefined, labelName, &rlabel);}
/* Set labels */
for (v = 0; v < numVertices; ++v) {
if (out->pointmarkerlist[v]) {
if (rlabel) {ierr = DMLabelSetValue(rlabel, v+numCells, out->pointmarkerlist[v]);CHKERRQ(ierr);}
}
}
if (interpolate) {
PetscInt e, f;
for (e = 0; e < out->numberofedges; e++) {
if (out->edgemarkerlist[e]) {
const PetscInt vertices[2] = {out->edgelist[e*2+0]+numCells, out->edgelist[e*2+1]+numCells};
const PetscInt *edges;
PetscInt numEdges;
ierr = DMPlexGetJoin(*dmRefined, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
if (numEdges != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Two vertices must cover only one edge, not %D", numEdges);
if (rlabel) {ierr = DMLabelSetValue(rlabel, edges[0], out->edgemarkerlist[e]);CHKERRQ(ierr);}
ierr = DMPlexRestoreJoin(*dmRefined, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
}
}
for (f = 0; f < out->numberoftrifaces; f++) {
if (out->trifacemarkerlist[f]) {
const PetscInt vertices[3] = {out->trifacelist[f*3+0]+numCells, out->trifacelist[f*3+1]+numCells, out->trifacelist[f*3+2]+numCells};
const PetscInt *faces;
PetscInt numFaces;
ierr = DMPlexGetFullJoin(*dmRefined, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
if (numFaces != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Three vertices must cover only one face, not %D", numFaces);
if (rlabel) {ierr = DMLabelSetValue(rlabel, faces[0], out->trifacemarkerlist[f]);CHKERRQ(ierr);}
ierr = DMPlexRestoreJoin(*dmRefined, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
}
}
}
ierr = DMPlexSetRefinementUniform(*dmRefined, PETSC_FALSE);CHKERRQ(ierr);
}
ierr = PLCDestroy(&in);CHKERRQ(ierr);
ierr = PLCDestroy(&out);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PETSC_EXTERN PetscErrorCode DMPlexGenerate_CTetgen(DM boundary, PetscBool interpolate, DM *dm)
{
MPI_Comm comm;
const PetscInt dim = 3;
const char *labelName = "marker";
PLC *in, *out;
DMLabel label;
PetscInt verbose = 0, vStart, vEnd, v, fStart, fEnd, f;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)boundary,&comm);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,((PetscObject) boundary)->prefix, "-ctetgen_verbose", &verbose, NULL);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(boundary, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMGetLabel(boundary, labelName, &label);CHKERRQ(ierr);
ierr = PLCCreate(&in);CHKERRQ(ierr);
ierr = PLCCreate(&out);CHKERRQ(ierr);
in->numberofpoints = vEnd - vStart;
if (in->numberofpoints > 0) {
PetscSection coordSection;
Vec coordinates;
PetscScalar *array;
ierr = PetscMalloc1(in->numberofpoints*dim, &in->pointlist);CHKERRQ(ierr);
ierr = PetscMalloc1(in->numberofpoints, &in->pointmarkerlist);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(boundary, &coordinates);CHKERRQ(ierr);
ierr = DMGetCoordinateSection(boundary, &coordSection);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &array);CHKERRQ(ierr);
for (v = vStart; v < vEnd; ++v) {
const PetscInt idx = v - vStart;
PetscInt off, d, m = -1;
ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
for (d = 0; d < dim; ++d) {
in->pointlist[idx*dim + d] = PetscRealPart(array[off+d]);
}
if (label) {ierr = DMLabelGetValue(label, v, &m);CHKERRQ(ierr);}
in->pointmarkerlist[idx] = (int) m;
}
ierr = VecRestoreArray(coordinates, &array);CHKERRQ(ierr);
}
ierr = DMPlexGetHeightStratum(boundary, 0, &fStart, &fEnd);CHKERRQ(ierr);
in->numberoffacets = fEnd - fStart;
if (in->numberoffacets > 0) {
ierr = PetscMalloc1(in->numberoffacets, &in->facetlist);CHKERRQ(ierr);
ierr = PetscMalloc1(in->numberoffacets, &in->facetmarkerlist);CHKERRQ(ierr);
for (f = fStart; f < fEnd; ++f) {
const PetscInt idx = f - fStart;
PetscInt *points = NULL, numPoints, p, numVertices = 0, v, m = -1;
polygon *poly;
in->facetlist[idx].numberofpolygons = 1;
ierr = PetscMalloc1(in->facetlist[idx].numberofpolygons, &in->facetlist[idx].polygonlist);CHKERRQ(ierr);
in->facetlist[idx].numberofholes = 0;
in->facetlist[idx].holelist = NULL;
ierr = DMPlexGetTransitiveClosure(boundary, f, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr);
for (p = 0; p < numPoints*2; p += 2) {
const PetscInt point = points[p];
if ((point >= vStart) && (point < vEnd)) points[numVertices++] = point;
}
poly = in->facetlist[idx].polygonlist;
poly->numberofvertices = numVertices;
ierr = PetscMalloc1(poly->numberofvertices, &poly->vertexlist);CHKERRQ(ierr);
for (v = 0; v < numVertices; ++v) {
const PetscInt vIdx = points[v] - vStart;
poly->vertexlist[v] = vIdx;
}
if (label) {ierr = DMLabelGetValue(label, f, &m);CHKERRQ(ierr);}
in->facetmarkerlist[idx] = (int) m;
ierr = DMPlexRestoreTransitiveClosure(boundary, f, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr);
}
}
if (!rank) {
TetGenOpts t;
ierr = TetGenOptsInitialize(&t);CHKERRQ(ierr);
t.in = boundary; /* Should go away */
t.plc = 1;
t.quality = 1;
t.edgesout = 1;
t.zeroindex = 1;
t.quiet = 1;
t.verbose = verbose;
ierr = TetGenCheckOpts(&t);CHKERRQ(ierr);
ierr = TetGenTetrahedralize(&t, in, out);CHKERRQ(ierr);
}
{
DMLabel glabel = NULL;
const PetscInt numCorners = 4;
const PetscInt numCells = out->numberoftetrahedra;
const PetscInt numVertices = out->numberofpoints;
double *meshCoords;
int *cells = out->tetrahedronlist;
if (sizeof (PetscReal) == sizeof (double)) {
meshCoords = (double *) out->pointlist;
}
else {
PetscInt i;
ierr = PetscMalloc1(3 * numVertices,&meshCoords);CHKERRQ(ierr);
for (i = 0; i < 3 * numVertices; i++) {
meshCoords[i] = (PetscReal) out->pointlist[i];
}
}
ierr = DMPlexInvertCells_Internal(dim, numCells, numCorners, cells);CHKERRQ(ierr);
ierr = DMPlexCreateFromCellList(comm, dim, numCells, numVertices, numCorners, interpolate, cells, dim, meshCoords, dm);CHKERRQ(ierr);
if (sizeof (PetscReal) != sizeof (double)) {
ierr = PetscFree(meshCoords);CHKERRQ(ierr);
}
if (label) {ierr = DMCreateLabel(*dm, labelName); ierr = DMGetLabel(*dm, labelName, &glabel);}
/* Set labels */
for (v = 0; v < numVertices; ++v) {
if (out->pointmarkerlist[v]) {
if (glabel) {ierr = DMLabelSetValue(glabel, v+numCells, out->pointmarkerlist[v]);CHKERRQ(ierr);}
}
}
if (interpolate) {
PetscInt e;
for (e = 0; e < out->numberofedges; e++) {
if (out->edgemarkerlist[e]) {
const PetscInt vertices[2] = {out->edgelist[e*2+0]+numCells, out->edgelist[e*2+1]+numCells};
const PetscInt *edges;
PetscInt numEdges;
ierr = DMPlexGetJoin(*dm, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
if (numEdges != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Two vertices must cover only one edge, not %D", numEdges);
if (glabel) {ierr = DMLabelSetValue(glabel, edges[0], out->edgemarkerlist[e]);CHKERRQ(ierr);}
ierr = DMPlexRestoreJoin(*dm, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
}
}
for (f = 0; f < out->numberoftrifaces; f++) {
if (out->trifacemarkerlist[f]) {
const PetscInt vertices[3] = {out->trifacelist[f*3+0]+numCells, out->trifacelist[f*3+1]+numCells, out->trifacelist[f*3+2]+numCells};
const PetscInt *faces;
PetscInt numFaces;
ierr = DMPlexGetFullJoin(*dm, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
if (numFaces != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Three vertices must cover only one face, not %D", numFaces);
if (glabel) {ierr = DMLabelSetValue(glabel, faces[0], out->trifacemarkerlist[f]);CHKERRQ(ierr);}
ierr = DMPlexRestoreJoin(*dm, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
}
}
}
ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr);
}
ierr = PLCDestroy(&in);CHKERRQ(ierr);
ierr = PLCDestroy(&out);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Write all fields that have been provided to the viewer
Multi-block XML format with binary appended data.
*/
PetscErrorCode DMPlexVTKWriteAll_VTU(DM dm,PetscViewer viewer)
{
MPI_Comm comm;
PetscViewer_VTK *vtk = (PetscViewer_VTK*)viewer->data;
PetscViewerVTKObjectLink link;
FILE *fp;
PetscMPIInt rank,size,tag;
PetscErrorCode ierr;
PetscInt dim,cellHeight,cStart,cEnd,vStart,vEnd,cMax,numLabelCells,hasLabel,c,v,r,i;
PieceInfo piece,*gpiece = NULL;
void *buffer = NULL;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
#if defined(PETSC_USE_COMPLEX)
SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Complex values not supported");
#endif
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
tag = ((PetscObject)viewer)->tag;
ierr = PetscFOpen(comm,vtk->filename,"wb",&fp);CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp,"<?xml version=\"1.0\"?>\n");CHKERRQ(ierr);
#if defined(PETSC_WORDS_BIGENDIAN)
ierr = PetscFPrintf(comm,fp,"<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"BigEndian\">\n");CHKERRQ(ierr);
#else
ierr = PetscFPrintf(comm,fp,"<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\">\n");CHKERRQ(ierr);
#endif
ierr = PetscFPrintf(comm,fp," <UnstructuredGrid>\n");CHKERRQ(ierr);
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr);
if (cMax >= 0) cEnd = PetscMin(cEnd, cMax);
ierr = DMPlexGetStratumSize(dm, "vtk", 1, &numLabelCells);CHKERRQ(ierr);
hasLabel = numLabelCells > 0 ? PETSC_TRUE : PETSC_FALSE;
piece.nvertices = vEnd - vStart;
piece.ncells = 0;
piece.nconn = 0;
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL;
PetscInt closureSize;
if (hasLabel) {
PetscInt value;
ierr = DMPlexGetLabelValue(dm, "vtk", c, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (v = 0; v < closureSize*2; v += 2) {
if ((closure[v] >= vStart) && (closure[v] < vEnd)) piece.nconn++;
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
piece.ncells++;
}
if (!rank) {ierr = PetscMalloc(size*sizeof(piece),&gpiece);CHKERRQ(ierr);}
ierr = MPI_Gather((PetscInt*)&piece,sizeof(piece)/sizeof(PetscInt),MPIU_INT,(PetscInt*)gpiece,sizeof(piece)/sizeof(PetscInt),MPIU_INT,0,comm);CHKERRQ(ierr);
/*
* Write file header
*/
if (!rank) {
PetscInt boffset = 0;
for (r=0; r<size; r++) {
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <Piece NumberOfPoints=\"%D\" NumberOfCells=\"%D\">\n",gpiece[r].nvertices,gpiece[r].ncells);CHKERRQ(ierr);
/* Coordinate positions */
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <Points>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <DataArray type=\"%s\" Name=\"Position\" NumberOfComponents=\"3\" format=\"appended\" offset=\"%D\" />\n",precision,boffset);CHKERRQ(ierr);
boffset += gpiece[r].nvertices*3*sizeof(PetscScalar) + sizeof(int);
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," </Points>\n");CHKERRQ(ierr);
/* Cell connectivity */
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <Cells>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <DataArray type=\"Int32\" Name=\"connectivity\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%D\" />\n",boffset);CHKERRQ(ierr);
boffset += gpiece[r].nconn*sizeof(PetscInt) + sizeof(int);
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <DataArray type=\"Int32\" Name=\"offsets\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%D\" />\n",boffset);CHKERRQ(ierr);
boffset += gpiece[r].ncells*sizeof(PetscInt) + sizeof(int);
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <DataArray type=\"UInt8\" Name=\"types\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%D\" />\n",boffset);CHKERRQ(ierr);
boffset += gpiece[r].ncells*sizeof(unsigned char) + sizeof(int);
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," </Cells>\n");CHKERRQ(ierr);
/*
* Cell Data headers
*/
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <CellData>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <DataArray type=\"Int32\" Name=\"Rank\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%D\" />\n",boffset);CHKERRQ(ierr);
boffset += gpiece[r].ncells*sizeof(int) + sizeof(int);
/* all the vectors */
for (link=vtk->link; link; link=link->next) {
Vec X = (Vec)link->vec;
PetscInt bs,nfields,field;
const char *vecname = "";
if ((link->ft != PETSC_VTK_CELL_FIELD) && (link->ft != PETSC_VTK_CELL_VECTOR_FIELD)) continue;
if (((PetscObject)X)->name || link != vtk->link) { /* If the object is already named, use it. If it is past the first link, name it to disambiguate. */
ierr = PetscObjectGetName((PetscObject)X,&vecname);CHKERRQ(ierr);
}
ierr = PetscSectionGetDof(dm->defaultSection,cStart,&bs);CHKERRQ(ierr);
ierr = PetscSectionGetNumFields(dm->defaultSection,&nfields);CHKERRQ(ierr);
for (field=0,i=0; field<(nfields?nfields:1); field++) {
PetscInt fbs,j;
const char *fieldname = NULL;
char buf[256];
if (nfields) { /* We have user-defined fields/components */
ierr = PetscSectionGetFieldDof(dm->defaultSection,cStart,field,&fbs);CHKERRQ(ierr);
ierr = PetscSectionGetFieldName(dm->defaultSection,field,&fieldname);CHKERRQ(ierr);
} else fbs = bs; /* Say we have one field with 'bs' components */
if (!fieldname) {
ierr = PetscSNPrintf(buf,sizeof(buf),"CellField%D",field);CHKERRQ(ierr);
fieldname = buf;
}
for (j=0; j<fbs; j++) {
ierr = PetscFPrintf(comm,fp," <DataArray type=\"%s\" Name=\"%s%s.%D\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%D\" />\n",precision,vecname,fieldname,j,boffset);CHKERRQ(ierr);
boffset += gpiece[r].ncells*sizeof(PetscScalar) + sizeof(int);
i++;
}
}
if (i != bs) SETERRQ2(comm,PETSC_ERR_PLIB,"Total number of field components %D != block size %D",i,bs);
}
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," </CellData>\n");CHKERRQ(ierr);
/*
* Point Data headers
*/
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <PointData>\n");CHKERRQ(ierr);
for (link=vtk->link; link; link=link->next) {
Vec X = (Vec)link->vec;
PetscInt bs,nfields,field;
const char *vecname = "";
if ((link->ft != PETSC_VTK_POINT_FIELD) && (link->ft != PETSC_VTK_POINT_VECTOR_FIELD)) continue;
if (((PetscObject)X)->name || link != vtk->link) { /* If the object is already named, use it. If it is past the first link, name it to disambiguate. */
ierr = PetscObjectGetName((PetscObject)X,&vecname);CHKERRQ(ierr);
}
ierr = PetscSectionGetDof(dm->defaultSection,vStart,&bs);CHKERRQ(ierr);
ierr = PetscSectionGetNumFields(dm->defaultSection,&nfields);CHKERRQ(ierr);
for (field=0,i=0; field<(nfields?nfields:1); field++) {
PetscInt fbs,j;
const char *fieldname = NULL;
char buf[256];
if (nfields) { /* We have user-defined fields/components */
ierr = PetscSectionGetFieldDof(dm->defaultSection,vStart,field,&fbs);CHKERRQ(ierr);
ierr = PetscSectionGetFieldName(dm->defaultSection,field,&fieldname);CHKERRQ(ierr);
} else fbs = bs; /* Say we have one field with 'bs' components */
if (!fieldname) {
ierr = PetscSNPrintf(buf,sizeof(buf),"PointField%D",field);CHKERRQ(ierr);
fieldname = buf;
}
for (j=0; j<fbs; j++) {
ierr = PetscFPrintf(comm,fp," <DataArray type=\"%s\" Name=\"%s%s.%D\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%D\" />\n",precision,vecname,fieldname,j,boffset);CHKERRQ(ierr);
boffset += gpiece[r].nvertices*sizeof(PetscScalar) + sizeof(int);
}
}
}
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," </PointData>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," </Piece>\n");CHKERRQ(ierr);
}
}
ierr = PetscFPrintf(comm,fp," </UnstructuredGrid>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp," <AppendedData encoding=\"raw\">\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp,"_");CHKERRQ(ierr);
if (!rank) {
PetscInt maxsize = 0;
for (r=0; r<size; r++) {
maxsize = PetscMax(maxsize, (PetscInt) (gpiece[r].nvertices*3*sizeof(PetscScalar)));
maxsize = PetscMax(maxsize, (PetscInt) (gpiece[r].ncells*sizeof(PetscScalar)));
maxsize = PetscMax(maxsize, (PetscInt) (gpiece[r].nconn*sizeof(PetscVTKInt)));
}
ierr = PetscMalloc(maxsize,&buffer);CHKERRQ(ierr);
}
for (r=0; r<size; r++) {
if (r == rank) {
PetscInt nsend;
{ /* Position */
const PetscScalar *x;
PetscScalar *y = NULL;
Vec coords;
nsend = piece.nvertices*3;
ierr = DMGetCoordinatesLocal(dm,&coords);CHKERRQ(ierr);
ierr = VecGetArrayRead(coords,&x);CHKERRQ(ierr);
if (dim != 3) {
ierr = PetscMalloc(piece.nvertices*3*sizeof(PetscScalar),&y);CHKERRQ(ierr);
for (i=0; i<piece.nvertices; i++) {
y[i*3+0] = x[i*dim+0];
y[i*3+1] = (dim > 1) ? x[i*dim+1] : 0;
y[i*3+2] = 0;
}
}
ierr = TransferWrite(viewer,fp,r,0,y ? y : x,buffer,nsend,PETSC_SCALAR,tag);CHKERRQ(ierr);
ierr = PetscFree(y);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(coords,&x);CHKERRQ(ierr);
}
{ /* Connectivity, offsets, types */
PetscVTKInt *connectivity = NULL,*offsets;
PetscVTKType *types;
ierr = DMPlexGetVTKConnectivity(dm,&piece,&connectivity,&offsets,&types);CHKERRQ(ierr);
ierr = TransferWrite(viewer,fp,r,0,connectivity,buffer,piece.nconn,PETSC_INT32,tag);CHKERRQ(ierr);
ierr = TransferWrite(viewer,fp,r,0,offsets,buffer,piece.ncells,PETSC_INT32,tag);CHKERRQ(ierr);
ierr = TransferWrite(viewer,fp,r,0,types,buffer,piece.ncells,PETSC_UINT8,tag);CHKERRQ(ierr);
ierr = PetscFree3(connectivity,offsets,types);CHKERRQ(ierr);
}
{ /* Owners (cell data) */
PetscVTKInt *owners;
ierr = PetscMalloc(piece.ncells*sizeof(PetscVTKInt),&owners);CHKERRQ(ierr);
for (i=0; i<piece.ncells; i++) owners[i] = rank;
ierr = TransferWrite(viewer,fp,r,0,owners,buffer,piece.ncells,PETSC_INT32,tag);CHKERRQ(ierr);
ierr = PetscFree(owners);CHKERRQ(ierr);
}
/* Cell data */
for (link=vtk->link; link; link=link->next) {
Vec X = (Vec)link->vec;
const PetscScalar *x;
PetscScalar *y;
PetscInt bs;
if ((link->ft != PETSC_VTK_CELL_FIELD) && (link->ft != PETSC_VTK_CELL_VECTOR_FIELD)) continue;
ierr = PetscSectionGetDof(dm->defaultSection,cStart,&bs);CHKERRQ(ierr);
ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr);
ierr = PetscMalloc(piece.ncells*sizeof(PetscScalar),&y);CHKERRQ(ierr);
for (i=0; i<bs; i++) {
PetscInt cnt;
for (c=cStart,cnt=0; c<cEnd; c++) {
const PetscScalar *xpoint;
if (hasLabel) { /* Ignore some cells */
PetscInt value;
ierr = DMPlexGetLabelValue(dm, "vtk", c, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
ierr = DMPlexPointLocalRead(dm,c,x,&xpoint);CHKERRQ(ierr);
y[cnt++] = xpoint[i];
}
if (cnt != piece.ncells) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Count does not match");
ierr = TransferWrite(viewer,fp,r,0,y,buffer,piece.ncells,PETSC_SCALAR,tag);CHKERRQ(ierr);
}
ierr = PetscFree(y);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr);
}
for (link=vtk->link; link; link=link->next) {
Vec X = (Vec)link->vec;
const PetscScalar *x;
PetscScalar *y;
PetscInt bs;
if ((link->ft != PETSC_VTK_POINT_FIELD) && (link->ft != PETSC_VTK_POINT_VECTOR_FIELD)) continue;
ierr = PetscSectionGetDof(dm->defaultSection,vStart,&bs);CHKERRQ(ierr);
ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr);
ierr = PetscMalloc(piece.nvertices*sizeof(PetscScalar),&y);CHKERRQ(ierr);
for (i=0; i<bs; i++) {
PetscInt cnt;
for (v=vStart,cnt=0; v<vEnd; v++) {
const PetscScalar *xpoint;
ierr = DMPlexPointLocalRead(dm,v,x,&xpoint);CHKERRQ(ierr);
y[cnt++] = xpoint[i];
}
if (cnt != piece.nvertices) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Count does not match");
ierr = TransferWrite(viewer,fp,r,0,y,buffer,piece.nvertices,PETSC_SCALAR,tag);CHKERRQ(ierr);
}
ierr = PetscFree(y);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr);
}
} else if (!rank) {
ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].nvertices*3,PETSC_SCALAR,tag);CHKERRQ(ierr); /* positions */
ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].nconn,PETSC_INT32,tag);CHKERRQ(ierr); /* connectivity */
ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].ncells,PETSC_INT32,tag);CHKERRQ(ierr); /* offsets */
ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].ncells,PETSC_UINT8,tag);CHKERRQ(ierr); /* types */
ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].ncells,PETSC_INT32,tag);CHKERRQ(ierr); /* owner rank (cells) */
/* all cell data */
for (link=vtk->link; link; link=link->next) {
PetscInt bs;
if ((link->ft != PETSC_VTK_CELL_FIELD) && (link->ft != PETSC_VTK_CELL_VECTOR_FIELD)) continue;
ierr = PetscSectionGetDof(dm->defaultSection,cStart,&bs);CHKERRQ(ierr);
for (i=0; i<bs; i++) {
ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].ncells,PETSC_SCALAR,tag);CHKERRQ(ierr);
}
}
/* all point data */
for (link=vtk->link; link; link=link->next) {
PetscInt bs;
if ((link->ft != PETSC_VTK_POINT_FIELD) && (link->ft != PETSC_VTK_POINT_VECTOR_FIELD)) continue;
ierr = PetscSectionGetDof(dm->defaultSection,vStart,&bs);CHKERRQ(ierr);
for (i=0; i<bs; i++) {
ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].nvertices,PETSC_SCALAR,tag);CHKERRQ(ierr);
}
}
}
}
ierr = PetscFree(gpiece);CHKERRQ(ierr);
ierr = PetscFree(buffer);CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp,"\n </AppendedData>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp,"</VTKFile>\n");CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMCoarsen_Plex(DM dm, MPI_Comm comm, DM *dmCoarsened)
{
DM_Plex *mesh = (DM_Plex*) dm->data;
#ifdef PETSC_HAVE_PRAGMATIC
DM udm, coordDM;
DMLabel bd;
Mat A;
Vec coordinates, mb, mx;
PetscSection coordSection;
const PetscScalar *coords;
double *coarseCoords;
IS bdIS;
PetscReal *x, *y, *z, *eqns, *metric;
PetscReal coarseRatio = PetscSqr(0.5);
const PetscInt *faces;
PetscInt *cells, *bdFaces, *bdFaceIds;
PetscInt dim, numCorners, cStart, cEnd, numCells, numCoarseCells, c, vStart, vEnd, numVertices, numCoarseVertices, v, numBdFaces, f, maxConeSize, size, bdSize, coff;
#endif
PetscErrorCode ierr;
PetscFunctionBegin;
#ifdef PETSC_HAVE_PRAGMATIC
if (!mesh->coarseMesh) {
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(dm, &coordDM);CHKERRQ(ierr);
ierr = DMGetDefaultSection(coordDM, &coordSection);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr);
ierr = DMPlexGetMaxSizes(udm, &maxConeSize, NULL);CHKERRQ(ierr);
numCells = cEnd - cStart;
numVertices = vEnd - vStart;
ierr = PetscCalloc5(numVertices, &x, numVertices, &y, numVertices, &z, numVertices*PetscSqr(dim), &metric, numCells*maxConeSize, &cells);CHKERRQ(ierr);
ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr);
for (v = vStart; v < vEnd; ++v) {
PetscInt off;
ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
x[v-vStart] = coords[off+0];
y[v-vStart] = coords[off+1];
if (dim > 2) z[v-vStart] = coords[off+2];
}
ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr);
for (c = 0, coff = 0; c < numCells; ++c) {
const PetscInt *cone;
PetscInt coneSize, cl;
ierr = DMPlexGetConeSize(udm, c, &coneSize);CHKERRQ(ierr);
ierr = DMPlexGetCone(udm, c, &cone);CHKERRQ(ierr);
for (cl = 0; cl < coneSize; ++cl) cells[coff++] = cone[cl] - vStart;
}
switch (dim) {
case 2:
pragmatic_2d_init(&numVertices, &numCells, cells, x, y);
break;
case 3:
pragmatic_3d_init(&numVertices, &numCells, cells, x, y, z);
break;
default:
SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic coarsening defined for dimension %d", dim);
}
/* Create boundary mesh */
ierr = DMLabelCreate("boundary", &bd);CHKERRQ(ierr);
ierr = DMPlexMarkBoundaryFaces(dm, bd);CHKERRQ(ierr);
ierr = DMLabelGetStratumIS(bd, 1, &bdIS);CHKERRQ(ierr);
ierr = DMLabelGetStratumSize(bd, 1, &numBdFaces);CHKERRQ(ierr);
ierr = ISGetIndices(bdIS, &faces);CHKERRQ(ierr);
for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
PetscInt *closure = NULL;
PetscInt closureSize, cl;
ierr = DMPlexGetTransitiveClosure(dm, faces[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (cl = 0; cl < closureSize*2; cl += 2) {
if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) ++bdSize;
}
ierr = DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
}
ierr = PetscMalloc2(bdSize, &bdFaces, numBdFaces, &bdFaceIds);CHKERRQ(ierr);
for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
PetscInt *closure = NULL;
PetscInt closureSize, cl;
ierr = DMPlexGetTransitiveClosure(dm, faces[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (cl = 0; cl < closureSize*2; cl += 2) {
if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) bdFaces[bdSize++] = closure[cl] - vStart;
}
/* TODO Fix */
bdFaceIds[f] = 1;
ierr = DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
}
ierr = ISDestroy(&bdIS);CHKERRQ(ierr);
ierr = DMLabelDestroy(&bd);CHKERRQ(ierr);
pragmatic_set_boundary(&numBdFaces, bdFaces, bdFaceIds);
/* Create metric */
size = (dim*(dim+1))/2;
ierr = PetscMalloc1(PetscSqr(size), &eqns);CHKERRQ(ierr);
ierr = MatCreateSeqDense(PETSC_COMM_SELF, size, size, eqns, &A);CHKERRQ(ierr);
ierr = MatCreateVecs(A, &mx, &mb);CHKERRQ(ierr);
ierr = VecSet(mb, 1.0);CHKERRQ(ierr);
for (c = 0; c < numCells; ++c) {
const PetscScalar *sol;
PetscScalar *cellCoords = NULL;
PetscReal e[3], vol;
const PetscInt *cone;
PetscInt coneSize, cl, i, j, d, r;
ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, c, NULL, &cellCoords);CHKERRQ(ierr);
/* Only works for simplices */
for (i = 0, r = 0; i < dim+1; ++i) {
for (j = 0; j < i; ++j, ++r) {
for (d = 0; d < dim; ++d) e[d] = cellCoords[i*dim+d] - cellCoords[j*dim+d];
/* FORTRAN ORDERING */
if (dim == 2) {
eqns[0*size+r] = PetscSqr(e[0]);
eqns[1*size+r] = 2.0*e[0]*e[1];
eqns[2*size+r] = PetscSqr(e[1]);
} else {
eqns[0*size+r] = PetscSqr(e[0]);
eqns[1*size+r] = 2.0*e[0]*e[1];
eqns[2*size+r] = 2.0*e[0]*e[2];
eqns[3*size+r] = PetscSqr(e[1]);
eqns[4*size+r] = 2.0*e[1]*e[2];
eqns[5*size+r] = PetscSqr(e[2]);
}
}
}
ierr = MatSetUnfactored(A);CHKERRQ(ierr);
ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, c, NULL, &cellCoords);CHKERRQ(ierr);
ierr = MatLUFactor(A, NULL, NULL, NULL);CHKERRQ(ierr);
ierr = MatSolve(A, mb, mx);CHKERRQ(ierr);
ierr = VecGetArrayRead(mx, &sol);CHKERRQ(ierr);
ierr = DMPlexComputeCellGeometryFVM(dm, c, &vol, NULL, NULL);CHKERRQ(ierr);
ierr = DMPlexGetCone(udm, c, &cone);CHKERRQ(ierr);
ierr = DMPlexGetConeSize(udm, c, &coneSize);CHKERRQ(ierr);
for (cl = 0; cl < coneSize; ++cl) {
const PetscInt v = cone[cl] - vStart;
if (dim == 2) {
metric[v*4+0] += vol*coarseRatio*sol[0];
metric[v*4+1] += vol*coarseRatio*sol[1];
metric[v*4+2] += vol*coarseRatio*sol[1];
metric[v*4+3] += vol*coarseRatio*sol[2];
} else {
metric[v*9+0] += vol*coarseRatio*sol[0];
metric[v*9+1] += vol*coarseRatio*sol[1];
metric[v*9+3] += vol*coarseRatio*sol[1];
metric[v*9+2] += vol*coarseRatio*sol[2];
metric[v*9+6] += vol*coarseRatio*sol[2];
metric[v*9+4] += vol*coarseRatio*sol[3];
metric[v*9+5] += vol*coarseRatio*sol[4];
metric[v*9+7] += vol*coarseRatio*sol[4];
metric[v*9+8] += vol*coarseRatio*sol[5];
}
}
ierr = VecRestoreArrayRead(mx, &sol);CHKERRQ(ierr);
}
for (v = 0; v < numVertices; ++v) {
const PetscInt *support;
PetscInt supportSize, s;
PetscReal vol, totVol = 0.0;
ierr = DMPlexGetSupport(udm, v+vStart, &support);CHKERRQ(ierr);
ierr = DMPlexGetSupportSize(udm, v+vStart, &supportSize);CHKERRQ(ierr);
for (s = 0; s < supportSize; ++s) {ierr = DMPlexComputeCellGeometryFVM(dm, support[s], &vol, NULL, NULL);CHKERRQ(ierr); totVol += vol;}
for (s = 0; s < PetscSqr(dim); ++s) metric[v*PetscSqr(dim)+s] /= totVol;
}
ierr = VecDestroy(&mx);CHKERRQ(ierr);
ierr = VecDestroy(&mb);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = DMDestroy(&udm);CHKERRQ(ierr);
ierr = PetscFree(eqns);CHKERRQ(ierr);
pragmatic_set_metric(metric);
pragmatic_adapt();
/* Read out mesh */
pragmatic_get_info(&numCoarseVertices, &numCoarseCells);
ierr = PetscMalloc1(numCoarseVertices*dim, &coarseCoords);CHKERRQ(ierr);
switch (dim) {
case 2:
pragmatic_get_coords_2d(x, y);
numCorners = 3;
for (v = 0; v < numCoarseVertices; ++v) {coarseCoords[v*2+0] = x[v]; coarseCoords[v*2+1] = y[v];}
break;
case 3:
pragmatic_get_coords_3d(x, y, z);
numCorners = 4;
for (v = 0; v < numCoarseVertices; ++v) {coarseCoords[v*3+0] = x[v]; coarseCoords[v*3+1] = y[v]; coarseCoords[v*3+2] = z[v];}
break;
default:
SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic coarsening defined for dimension %d", dim);
}
pragmatic_get_elements(cells);
/* TODO Read out markers for boundary */
ierr = DMPlexCreateFromCellList(PetscObjectComm((PetscObject) dm), dim, numCoarseCells, numCoarseVertices, numCorners, PETSC_TRUE, cells, dim, coarseCoords, &mesh->coarseMesh);CHKERRQ(ierr);
pragmatic_finalize();
ierr = PetscFree5(x, y, z, metric, cells);CHKERRQ(ierr);
ierr = PetscFree2(bdFaces, bdFaceIds);CHKERRQ(ierr);
ierr = PetscFree(coarseCoords);CHKERRQ(ierr);
}
#endif
ierr = PetscObjectReference((PetscObject) mesh->coarseMesh);CHKERRQ(ierr);
*dmCoarsened = mesh->coarseMesh;
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);
}
