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); }
static PetscErrorCode ScrambleOrientation(DM dm, AppCtx *user) { PetscInt h, cStart, cEnd, c; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = DMPlexGetVTKCellHeight(dm, &h);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, h, &cStart, &cEnd);CHKERRQ(ierr); for (c = cStart; c < cEnd; ++c) { /* Could use PetscRand instead */ if (c%2) {ierr = DMPlexReverseCell(dm, c);CHKERRQ(ierr);} } PetscFunctionReturn(0); }
PetscErrorCode DMPlexVTKWritePartition_ASCII(DM dm, FILE *fp) { MPI_Comm comm; PetscInt numCells = 0, cellHeight; PetscInt numLabelCells, cMax, cStart, cEnd, c; PetscMPIInt numProcs, rank, proc, tag; PetscBool hasLabel; 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 = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);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; for (c = cStart; c < cEnd; ++c) { if (hasLabel) { PetscInt value; ierr = DMPlexGetLabelValue(dm, "vtk", c, &value);CHKERRQ(ierr); if (value != 1) continue; } ++numCells; } if (!rank) { for (c = 0; c < numCells; ++c) {ierr = PetscFPrintf(comm, fp, "%d\n", rank);CHKERRQ(ierr);} for (proc = 1; proc < numProcs; ++proc) { MPI_Status status; ierr = MPI_Recv(&numCells, 1, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr); for (c = 0; c < numCells; ++c) {ierr = PetscFPrintf(comm, fp, "%d\n", proc);CHKERRQ(ierr);} } } else { ierr = MPI_Send(&numCells, 1, MPIU_INT, 0, tag, comm);CHKERRQ(ierr); } 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); }
PetscErrorCode DMPlexVTKWriteSection_ASCII(DM dm, PetscSection section, PetscSection globalSection, Vec v, FILE *fp, PetscInt enforceDof, PetscInt precision, PetscReal scale) { MPI_Comm comm; const MPI_Datatype mpiType = MPIU_SCALAR; PetscScalar *array; PetscInt numDof = 0, maxDof; PetscInt numLabelCells, cellHeight, cMax, cStart, cEnd, numLabelVertices, vMax, vStart, vEnd, pStart, pEnd, p; PetscMPIInt numProcs, rank, proc, tag; PetscBool hasLabel; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); PetscValidHeaderSpecific(dm,DM_CLASSID,1); PetscValidHeaderSpecific(v,VEC_CLASSID,4); if (precision < 0) precision = 6; ierr = PetscCommGetNewTag(comm, &tag);CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); /* VTK only wants the values at cells or vertices */ 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, &vMax);CHKERRQ(ierr); if (cMax >= 0) cEnd = PetscMin(cEnd, cMax); if (vMax >= 0) vEnd = PetscMin(vEnd, vMax); pStart = PetscMax(PetscMin(cStart, vStart), pStart); pEnd = PetscMin(PetscMax(cEnd, vEnd), pEnd); ierr = DMPlexGetStratumSize(dm, "vtk", 1, &numLabelCells);CHKERRQ(ierr); ierr = DMPlexGetStratumSize(dm, "vtk", 2, &numLabelVertices);CHKERRQ(ierr); hasLabel = numLabelCells > 0 || numLabelVertices > 0 ? PETSC_TRUE : PETSC_FALSE; for (p = pStart; p < pEnd; ++p) { /* Reject points not either cells or vertices */ if (((p < cStart) || (p >= cEnd)) && ((p < vStart) || (p >= vEnd))) continue; if (hasLabel) { PetscInt value; if (((p >= cStart) && (p < cEnd) && numLabelCells) || ((p >= vStart) && (p < vEnd) && numLabelVertices)) { ierr = DMPlexGetLabelValue(dm, "vtk", p, &value);CHKERRQ(ierr); if (value != 1) continue; } } ierr = PetscSectionGetDof(section, p, &numDof);CHKERRQ(ierr); if (numDof) break; } ierr = MPI_Allreduce(&numDof, &maxDof, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr); enforceDof = PetscMax(enforceDof, maxDof); ierr = VecGetArray(v, &array);CHKERRQ(ierr); if (!rank) { char formatString[8]; ierr = PetscSNPrintf(formatString, 8, "%%.%de", precision);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { /* Here we lose a way to filter points by keeping them out of the Numbering */ PetscInt dof, off, goff, d; /* Reject points not either cells or vertices */ if (((p < cStart) || (p >= cEnd)) && ((p < vStart) || (p >= vEnd))) continue; if (hasLabel) { PetscInt value; if (((p >= cStart) && (p < cEnd) && numLabelCells) || ((p >= vStart) && (p < vEnd) && numLabelVertices)) { ierr = DMPlexGetLabelValue(dm, "vtk", p, &value);CHKERRQ(ierr); if (value != 1) continue; } } ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr); ierr = PetscSectionGetOffset(globalSection, p, &goff);CHKERRQ(ierr); if (dof && goff >= 0) { for (d = 0; d < dof; d++) { if (d > 0) { ierr = PetscFPrintf(comm, fp, " ");CHKERRQ(ierr); } ierr = PetscFPrintf(comm, fp, formatString, PetscRealPart(array[off+d])*scale);CHKERRQ(ierr); } for (d = dof; d < enforceDof; d++) { ierr = PetscFPrintf(comm, fp, " 0.0");CHKERRQ(ierr); } ierr = PetscFPrintf(comm, fp, "\n");CHKERRQ(ierr); } } for (proc = 1; proc < numProcs; ++proc) { PetscScalar *remoteValues; PetscInt size = 0, d; MPI_Status status; ierr = MPI_Recv(&size, 1, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr); ierr = PetscMalloc1(size, &remoteValues);CHKERRQ(ierr); ierr = MPI_Recv(remoteValues, size, mpiType, proc, tag, comm, &status);CHKERRQ(ierr); for (p = 0; p < size/maxDof; ++p) { for (d = 0; d < maxDof; ++d) { if (d > 0) { ierr = PetscFPrintf(comm, fp, " ");CHKERRQ(ierr); } ierr = PetscFPrintf(comm, fp, formatString, PetscRealPart(remoteValues[p*maxDof+d])*scale);CHKERRQ(ierr); } for (d = maxDof; d < enforceDof; ++d) { ierr = PetscFPrintf(comm, fp, " 0.0");CHKERRQ(ierr); } ierr = PetscFPrintf(comm, fp, "\n");CHKERRQ(ierr); } ierr = PetscFree(remoteValues);CHKERRQ(ierr); } } else { PetscScalar *localValues; PetscInt size, k = 0; ierr = PetscSectionGetStorageSize(section, &size);CHKERRQ(ierr); ierr = PetscMalloc1(size, &localValues);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { PetscInt dof, off, goff, d; /* Reject points not either cells or vertices */ if (((p < cStart) || (p >= cEnd)) && ((p < vStart) || (p >= vEnd))) continue; if (hasLabel) { PetscInt value; if (((p >= cStart) && (p < cEnd) && numLabelCells) || ((p >= vStart) && (p < vEnd) && numLabelVertices)) { ierr = DMPlexGetLabelValue(dm, "vtk", p, &value);CHKERRQ(ierr); if (value != 1) continue; } } ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr); ierr = PetscSectionGetOffset(globalSection, p, &goff);CHKERRQ(ierr); if (goff >= 0) { for (d = 0; d < dof; ++d) { localValues[k++] = array[off+d]; } } } ierr = MPI_Send(&k, 1, MPIU_INT, 0, tag, comm);CHKERRQ(ierr); ierr = MPI_Send(localValues, k, mpiType, 0, tag, comm);CHKERRQ(ierr); ierr = PetscFree(localValues);CHKERRQ(ierr); } ierr = VecRestoreArray(v, &array);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); }
/*@ DMPlexOrient - Give a consistent orientation to the input mesh Input Parameters: . dm - The DM Note: The orientation data for the DM are change in-place. $ This routine will fail for non-orientable surfaces, such as the Moebius strip. Level: advanced .seealso: DMCreate(), DMPLEX @*/ PetscErrorCode DMPlexOrient(DM dm) { MPI_Comm comm; PetscSF sf; const PetscInt *lpoints; const PetscSFNode *rpoints; PetscSFNode *rorntComp = NULL, *lorntComp = NULL; PetscInt *numNeighbors, **neighbors; PetscSFNode *nrankComp; PetscBool *match, *flipped; PetscBT seenCells, flippedCells, seenFaces; PetscInt *faceFIFO, fTop, fBottom, *cellComp, *faceComp; PetscInt numLeaves, numRoots, dim, h, cStart, cEnd, c, cell, fStart, fEnd, face, off, totNeighbors = 0; PetscMPIInt rank, size, numComponents, comp = 0; PetscBool flg, flg2; PetscViewer viewer = NULL, selfviewer = NULL; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-orientation_view", &flg);CHKERRQ(ierr); ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-orientation_view_synchronized", &flg2);CHKERRQ(ierr); ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); ierr = PetscSFGetGraph(sf, &numRoots, &numLeaves, &lpoints, &rpoints);CHKERRQ(ierr); /* Truth Table mismatch flips do action mismatch flipA ^ flipB action F 0 flips no F F F F 1 flip yes F T T F 2 flips no T F T T 0 flips yes T T F T 1 flip no T 2 flips yes */ ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexGetVTKCellHeight(dm, &h);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, h, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, h+1, &fStart, &fEnd);CHKERRQ(ierr); ierr = PetscBTCreate(cEnd - cStart, &seenCells);CHKERRQ(ierr); ierr = PetscBTMemzero(cEnd - cStart, seenCells);CHKERRQ(ierr); ierr = PetscBTCreate(cEnd - cStart, &flippedCells);CHKERRQ(ierr); ierr = PetscBTMemzero(cEnd - cStart, flippedCells);CHKERRQ(ierr); ierr = PetscBTCreate(fEnd - fStart, &seenFaces);CHKERRQ(ierr); ierr = PetscBTMemzero(fEnd - fStart, seenFaces);CHKERRQ(ierr); ierr = PetscCalloc3(fEnd - fStart, &faceFIFO, cEnd-cStart, &cellComp, fEnd-fStart, &faceComp);CHKERRQ(ierr); /* OLD STYLE - Add an integer array over cells and faces (component) for connected component number Foreach component - Mark the initial cell as seen - Process component as usual - Set component for all seenCells - Wipe seenCells and seenFaces (flippedCells can stay) - Generate parallel adjacency for component using SF and seenFaces - Collect numComponents adj data from each proc to 0 - Build same serial graph - Use same solver - Use Scatterv to to send back flipped flags for each component - Negate flippedCells by component NEW STYLE - Create the adj on each process - Bootstrap to complete graph on proc 0 */ /* Loop over components */ for (cell = cStart; cell < cEnd; ++cell) cellComp[cell-cStart] = -1; do { /* Look for first unmarked cell */ for (cell = cStart; cell < cEnd; ++cell) if (cellComp[cell-cStart] < 0) break; if (cell >= cEnd) break; /* Initialize FIFO with first cell in component */ { const PetscInt *cone; PetscInt coneSize; fTop = fBottom = 0; ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); for (c = 0; c < coneSize; ++c) { faceFIFO[fBottom++] = cone[c]; ierr = PetscBTSet(seenFaces, cone[c]-fStart);CHKERRQ(ierr); } ierr = PetscBTSet(seenCells, cell-cStart);CHKERRQ(ierr); } /* Consider each face in FIFO */ while (fTop < fBottom) { ierr = DMPlexCheckFace_Internal(dm, faceFIFO, &fTop, &fBottom, cStart, fStart, fEnd, seenCells, flippedCells, seenFaces);CHKERRQ(ierr); } /* Set component for cells and faces */ for (cell = 0; cell < cEnd-cStart; ++cell) { if (PetscBTLookup(seenCells, cell)) cellComp[cell] = comp; } for (face = 0; face < fEnd-fStart; ++face) { if (PetscBTLookup(seenFaces, face)) faceComp[face] = comp; } /* Wipe seenCells and seenFaces for next component */ ierr = PetscBTMemzero(fEnd - fStart, seenFaces);CHKERRQ(ierr); ierr = PetscBTMemzero(cEnd - cStart, seenCells);CHKERRQ(ierr); ++comp; } while (1); numComponents = comp; if (flg) { PetscViewer v; ierr = PetscViewerASCIIGetStdout(comm, &v);CHKERRQ(ierr); ierr = PetscViewerASCIIPushSynchronized(v);CHKERRQ(ierr); ierr = PetscViewerASCIISynchronizedPrintf(v, "[%d]BT for serial flipped cells:\n", rank);CHKERRQ(ierr); ierr = PetscBTView(cEnd-cStart, flippedCells, v);CHKERRQ(ierr); ierr = PetscViewerFlush(v);CHKERRQ(ierr); ierr = PetscViewerASCIIPopSynchronized(v);CHKERRQ(ierr); } /* Now all subdomains are oriented, but we need a consistent parallel orientation */ if (numLeaves >= 0) { /* Store orientations of boundary faces*/ ierr = PetscCalloc2(numRoots,&rorntComp,numRoots,&lorntComp);CHKERRQ(ierr); for (face = fStart; face < fEnd; ++face) { const PetscInt *cone, *support, *ornt; PetscInt coneSize, supportSize; ierr = DMPlexGetSupportSize(dm, face, &supportSize);CHKERRQ(ierr); if (supportSize != 1) continue; ierr = DMPlexGetSupport(dm, face, &support);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, support[0], &cone);CHKERRQ(ierr); ierr = DMPlexGetConeSize(dm, support[0], &coneSize);CHKERRQ(ierr); ierr = DMPlexGetConeOrientation(dm, support[0], &ornt);CHKERRQ(ierr); for (c = 0; c < coneSize; ++c) if (cone[c] == face) break; if (dim == 1) { /* Use cone position instead, shifted to -1 or 1 */ if (PetscBTLookup(flippedCells, support[0]-cStart)) rorntComp[face].rank = 1-c*2; else rorntComp[face].rank = c*2-1; } else { if (PetscBTLookup(flippedCells, support[0]-cStart)) rorntComp[face].rank = ornt[c] < 0 ? -1 : 1; else rorntComp[face].rank = ornt[c] < 0 ? 1 : -1; } rorntComp[face].index = faceComp[face-fStart]; } /* Communicate boundary edge orientations */ ierr = PetscSFBcastBegin(sf, MPIU_2INT, rorntComp, lorntComp);CHKERRQ(ierr); ierr = PetscSFBcastEnd(sf, MPIU_2INT, rorntComp, lorntComp);CHKERRQ(ierr); } /* Get process adjacency */ ierr = PetscMalloc2(numComponents, &numNeighbors, numComponents, &neighbors);CHKERRQ(ierr); viewer = PETSC_VIEWER_STDOUT_(PetscObjectComm((PetscObject)dm)); if (flg2) {ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr);} ierr = PetscViewerGetSubViewer(viewer,PETSC_COMM_SELF,&selfviewer);CHKERRQ(ierr); for (comp = 0; comp < numComponents; ++comp) { PetscInt l, n; numNeighbors[comp] = 0; ierr = PetscMalloc1(PetscMax(numLeaves, 0), &neighbors[comp]);CHKERRQ(ierr); /* I know this is p^2 time in general, but for bounded degree its alright */ for (l = 0; l < numLeaves; ++l) { const PetscInt face = lpoints[l]; /* Find a representative face (edge) separating pairs of procs */ if ((face >= fStart) && (face < fEnd) && (faceComp[face-fStart] == comp)) { const PetscInt rrank = rpoints[l].rank; const PetscInt rcomp = lorntComp[face].index; for (n = 0; n < numNeighbors[comp]; ++n) if ((rrank == rpoints[neighbors[comp][n]].rank) && (rcomp == lorntComp[lpoints[neighbors[comp][n]]].index)) break; if (n >= numNeighbors[comp]) { PetscInt supportSize; ierr = DMPlexGetSupportSize(dm, face, &supportSize);CHKERRQ(ierr); if (supportSize != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Boundary faces should see one cell, not %d", supportSize); if (flg) {ierr = PetscViewerASCIIPrintf(selfviewer, "[%d]: component %d, Found representative leaf %d (face %d) connecting to face %d on (%d, %d) with orientation %d\n", rank, comp, l, face, rpoints[l].index, rrank, rcomp, lorntComp[face].rank);CHKERRQ(ierr);} neighbors[comp][numNeighbors[comp]++] = l; } } } totNeighbors += numNeighbors[comp]; } ierr = PetscViewerRestoreSubViewer(viewer,PETSC_COMM_SELF,&selfviewer);CHKERRQ(ierr); ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); if (flg2) {ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr);} ierr = PetscMalloc2(totNeighbors, &nrankComp, totNeighbors, &match);CHKERRQ(ierr); for (comp = 0, off = 0; comp < numComponents; ++comp) { PetscInt n; for (n = 0; n < numNeighbors[comp]; ++n, ++off) { const PetscInt face = lpoints[neighbors[comp][n]]; const PetscInt o = rorntComp[face].rank*lorntComp[face].rank; if (o < 0) match[off] = PETSC_TRUE; else if (o > 0) match[off] = PETSC_FALSE; else SETERRQ5(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid face %d (%d, %d) neighbor: %d comp: %d", face, rorntComp[face], lorntComp[face], neighbors[comp][n], comp); nrankComp[off].rank = rpoints[neighbors[comp][n]].rank; nrankComp[off].index = lorntComp[lpoints[neighbors[comp][n]]].index; } ierr = PetscFree(neighbors[comp]);CHKERRQ(ierr); } /* Collect the graph on 0 */ if (numLeaves >= 0) { Mat G; PetscBT seenProcs, flippedProcs; PetscInt *procFIFO, pTop, pBottom; PetscInt *N = NULL, *Noff; PetscSFNode *adj = NULL; PetscBool *val = NULL; PetscMPIInt *recvcounts = NULL, *displs = NULL, *Nc, p, o; PetscMPIInt size = 0; ierr = PetscCalloc1(numComponents, &flipped);CHKERRQ(ierr); if (!rank) {ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);} ierr = PetscCalloc4(size, &recvcounts, size+1, &displs, size, &Nc, size+1, &Noff);CHKERRQ(ierr); ierr = MPI_Gather(&numComponents, 1, MPI_INT, Nc, 1, MPI_INT, 0, comm);CHKERRQ(ierr); for (p = 0; p < size; ++p) { displs[p+1] = displs[p] + Nc[p]; } if (!rank) {ierr = PetscMalloc1(displs[size],&N);CHKERRQ(ierr);} ierr = MPI_Gatherv(numNeighbors, numComponents, MPIU_INT, N, Nc, displs, MPIU_INT, 0, comm);CHKERRQ(ierr); for (p = 0, o = 0; p < size; ++p) { recvcounts[p] = 0; for (c = 0; c < Nc[p]; ++c, ++o) recvcounts[p] += N[o]; displs[p+1] = displs[p] + recvcounts[p]; } if (!rank) {ierr = PetscMalloc2(displs[size], &adj, displs[size], &val);CHKERRQ(ierr);} ierr = MPI_Gatherv(nrankComp, totNeighbors, MPIU_2INT, adj, recvcounts, displs, MPIU_2INT, 0, comm);CHKERRQ(ierr); ierr = MPI_Gatherv(match, totNeighbors, MPIU_BOOL, val, recvcounts, displs, MPIU_BOOL, 0, comm);CHKERRQ(ierr); ierr = PetscFree2(numNeighbors, neighbors);CHKERRQ(ierr); if (!rank) { for (p = 1; p <= size; ++p) {Noff[p] = Noff[p-1] + Nc[p-1];} if (flg) { PetscInt n; for (p = 0, off = 0; p < size; ++p) { for (c = 0; c < Nc[p]; ++c) { ierr = PetscPrintf(PETSC_COMM_SELF, "Proc %d Comp %d:\n", p, c);CHKERRQ(ierr); for (n = 0; n < N[Noff[p]+c]; ++n, ++off) { ierr = PetscPrintf(PETSC_COMM_SELF, " edge (%d, %d) (%d):\n", adj[off].rank, adj[off].index, val[off]);CHKERRQ(ierr); } } } } /* Symmetrize the graph */ ierr = MatCreate(PETSC_COMM_SELF, &G);CHKERRQ(ierr); ierr = MatSetSizes(G, Noff[size], Noff[size], Noff[size], Noff[size]);CHKERRQ(ierr); ierr = MatSetUp(G);CHKERRQ(ierr); for (p = 0, off = 0; p < size; ++p) { for (c = 0; c < Nc[p]; ++c) { const PetscInt r = Noff[p]+c; PetscInt n; for (n = 0; n < N[r]; ++n, ++off) { const PetscInt q = Noff[adj[off].rank] + adj[off].index; const PetscScalar o = val[off] ? 1.0 : 0.0; ierr = MatSetValues(G, 1, &r, 1, &q, &o, INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(G, 1, &q, 1, &r, &o, INSERT_VALUES);CHKERRQ(ierr); } } } ierr = MatAssemblyBegin(G, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(G, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = PetscBTCreate(Noff[size], &seenProcs);CHKERRQ(ierr); ierr = PetscBTMemzero(Noff[size], seenProcs);CHKERRQ(ierr); ierr = PetscBTCreate(Noff[size], &flippedProcs);CHKERRQ(ierr); ierr = PetscBTMemzero(Noff[size], flippedProcs);CHKERRQ(ierr); ierr = PetscMalloc1(Noff[size], &procFIFO);CHKERRQ(ierr); pTop = pBottom = 0; for (p = 0; p < Noff[size]; ++p) { if (PetscBTLookup(seenProcs, p)) continue; /* Initialize FIFO with next proc */ procFIFO[pBottom++] = p; ierr = PetscBTSet(seenProcs, p);CHKERRQ(ierr); /* Consider each proc in FIFO */ while (pTop < pBottom) { const PetscScalar *ornt; const PetscInt *neighbors; PetscInt proc, nproc, seen, flippedA, flippedB, mismatch, numNeighbors, n; proc = procFIFO[pTop++]; flippedA = PetscBTLookup(flippedProcs, proc) ? 1 : 0; ierr = MatGetRow(G, proc, &numNeighbors, &neighbors, &ornt);CHKERRQ(ierr); /* Loop over neighboring procs */ for (n = 0; n < numNeighbors; ++n) { nproc = neighbors[n]; mismatch = PetscRealPart(ornt[n]) > 0.5 ? 0 : 1; seen = PetscBTLookup(seenProcs, nproc); flippedB = PetscBTLookup(flippedProcs, nproc) ? 1 : 0; if (mismatch ^ (flippedA ^ flippedB)) { if (seen) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Previously seen procs %d and %d do not match: Fault mesh is non-orientable", proc, nproc); if (!flippedB) { ierr = PetscBTSet(flippedProcs, nproc);CHKERRQ(ierr); } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Inconsistent mesh orientation: Fault mesh is non-orientable"); } else if (mismatch && flippedA && flippedB) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Attempt to flip already flipped cell: Fault mesh is non-orientable"); if (!seen) { procFIFO[pBottom++] = nproc; ierr = PetscBTSet(seenProcs, nproc);CHKERRQ(ierr); } } } } ierr = PetscFree(procFIFO);CHKERRQ(ierr); ierr = MatDestroy(&G);CHKERRQ(ierr); ierr = PetscFree2(adj, val);CHKERRQ(ierr); ierr = PetscBTDestroy(&seenProcs);CHKERRQ(ierr); } /* Scatter flip flags */ { PetscBool *flips = NULL; if (!rank) { ierr = PetscMalloc1(Noff[size], &flips);CHKERRQ(ierr); for (p = 0; p < Noff[size]; ++p) { flips[p] = PetscBTLookup(flippedProcs, p) ? PETSC_TRUE : PETSC_FALSE; if (flg && flips[p]) {ierr = PetscPrintf(comm, "Flipping Proc+Comp %d:\n", p);CHKERRQ(ierr);} } for (p = 0; p < size; ++p) { displs[p+1] = displs[p] + Nc[p]; } } ierr = MPI_Scatterv(flips, Nc, displs, MPIU_BOOL, flipped, numComponents, MPIU_BOOL, 0, comm);CHKERRQ(ierr); ierr = PetscFree(flips);CHKERRQ(ierr); } if (!rank) {ierr = PetscBTDestroy(&flippedProcs);CHKERRQ(ierr);} ierr = PetscFree(N);CHKERRQ(ierr); ierr = PetscFree4(recvcounts, displs, Nc, Noff);CHKERRQ(ierr); ierr = PetscFree2(nrankComp, match);CHKERRQ(ierr); /* Decide whether to flip cells in each component */ for (c = 0; c < cEnd-cStart; ++c) {if (flipped[cellComp[c]]) {ierr = PetscBTNegate(flippedCells, c);CHKERRQ(ierr);}} ierr = PetscFree(flipped);CHKERRQ(ierr); } if (flg) { PetscViewer v; ierr = PetscViewerASCIIGetStdout(comm, &v);CHKERRQ(ierr); ierr = PetscViewerASCIIPushSynchronized(v);CHKERRQ(ierr); ierr = PetscViewerASCIISynchronizedPrintf(v, "[%d]BT for parallel flipped cells:\n", rank);CHKERRQ(ierr); ierr = PetscBTView(cEnd-cStart, flippedCells, v);CHKERRQ(ierr); ierr = PetscViewerFlush(v);CHKERRQ(ierr); ierr = PetscViewerASCIIPopSynchronized(v);CHKERRQ(ierr); } /* Reverse flipped cells in the mesh */ for (c = cStart; c < cEnd; ++c) { if (PetscBTLookup(flippedCells, c-cStart)) { ierr = DMPlexReverseCell(dm, c);CHKERRQ(ierr); } } ierr = PetscBTDestroy(&seenCells);CHKERRQ(ierr); ierr = PetscBTDestroy(&flippedCells);CHKERRQ(ierr); ierr = PetscBTDestroy(&seenFaces);CHKERRQ(ierr); ierr = PetscFree2(numNeighbors, neighbors);CHKERRQ(ierr); ierr = PetscFree2(rorntComp, lorntComp);CHKERRQ(ierr); ierr = PetscFree3(faceFIFO, cellComp, faceComp);CHKERRQ(ierr); PetscFunctionReturn(0); }