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); }
/* This is to fix the tetrahedron orientation from TetGen */ static PetscErrorCode DMPlexInvertCells_Internal(PetscInt dim, PetscInt numCells, PetscInt numCorners, int cells[]) { PetscInt bound = numCells*numCorners, coff; PetscErrorCode ierr; PetscFunctionBegin; for (coff = 0; coff < bound; coff += numCorners) { ierr = DMPlexInvertCell(dim, numCorners, &cells[coff]);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); }
/*@ DMPlexCreateGmsh - Create a DMPlex mesh from a Gmsh file. Collective on comm Input Parameters: + comm - The MPI communicator . viewer - The Viewer associated with a Gmsh file - interpolate - Create faces and edges in the mesh Output Parameter: . dm - The DM object representing the mesh Note: http://www.geuz.org/gmsh/doc/texinfo/#MSH-ASCII-file-format Level: beginner .keywords: mesh,Gmsh .seealso: DMPLEX, DMCreate() @*/ PetscErrorCode DMPlexCreateGmsh(MPI_Comm comm, PetscViewer viewer, PetscBool interpolate, DM *dm) { FILE *fd; PetscSection coordSection; Vec coordinates; PetscScalar *coords, *coordsIn = NULL; PetscInt dim = 0, coordSize, c, v, d; int numVertices = 0, numCells = 0, snum; long fpos = 0; PetscMPIInt num_proc, rank; char line[PETSC_MAX_PATH_LEN]; PetscBool match; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &num_proc);CHKERRQ(ierr); ierr = DMCreate(comm, dm);CHKERRQ(ierr); ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); if (!rank) { PetscBool match; int fileType, dataSize; ierr = PetscViewerASCIIGetPointer(viewer, &fd);CHKERRQ(ierr); /* Read header */ fgets(line, PETSC_MAX_PATH_LEN, fd); ierr = PetscStrncmp(line, "$MeshFormat\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr); if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file"); snum = fscanf(fd, "2.2 %d %d\n", &fileType, &dataSize);CHKERRQ(snum != 2); if (fileType) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File type %d is not a valid Gmsh ASCII file", fileType); if (dataSize != sizeof(double)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Data size %d is not valid for a Gmsh file", dataSize); fgets(line, PETSC_MAX_PATH_LEN, fd); ierr = PetscStrncmp(line, "$EndMeshFormat\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr); if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file"); /* Read vertices */ fgets(line, PETSC_MAX_PATH_LEN, fd); ierr = PetscStrncmp(line, "$Nodes\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr); if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file"); snum = fscanf(fd, "%d\n", &numVertices);CHKERRQ(snum != 1); ierr = PetscMalloc(numVertices*3 * sizeof(PetscScalar), &coordsIn);CHKERRQ(ierr); for (v = 0; v < numVertices; ++v) { double x, y, z; int i; snum = fscanf(fd, "%d %lg %lg %lg\n", &i, &x, &y, &z);CHKERRQ(snum != 4); coordsIn[v*3+0] = x; coordsIn[v*3+1] = y; coordsIn[v*3+2] = z; if (i != v+1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid node number %d should be %d", i, v+1); } fgets(line, PETSC_MAX_PATH_LEN, fd); ierr = PetscStrncmp(line, "$EndNodes\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr); if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file"); /* Read cells */ fgets(line, PETSC_MAX_PATH_LEN, fd); ierr = PetscStrncmp(line, "$Elements\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr); if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file"); snum = fscanf(fd, "%d\n", &numCells);CHKERRQ(snum != 1); } ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); if (!rank) { fpos = ftell(fd); for (c = 0; c < numCells; ++c) { PetscInt numCorners, t; int cone[8], i, cellType, numTags, tag; snum = fscanf(fd, "%d %d %d", &i, &cellType, &numTags);CHKERRQ(snum != 3); if (numTags) for (t = 0; t < numTags; ++t) {snum = fscanf(fd, "%d", &tag);CHKERRQ(snum != 1);} switch (cellType) { case 1: /* 2-node line */ dim = 1; numCorners = 2; snum = fscanf(fd, "%d %d\n", &cone[0], &cone[1]);CHKERRQ(snum != numCorners); break; case 2: /* 3-node triangle */ dim = 2; numCorners = 3; snum = fscanf(fd, "%d %d %d\n", &cone[0], &cone[1], &cone[2]);CHKERRQ(snum != numCorners); break; case 3: /* 4-node quadrangle */ dim = 2; numCorners = 4; snum = fscanf(fd, "%d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3]);CHKERRQ(snum != numCorners); break; case 4: /* 4-node tetrahedron */ dim = 3; numCorners = 4; snum = fscanf(fd, "%d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3]);CHKERRQ(snum != numCorners); break; case 5: /* 8-node hexahedron */ dim = 3; numCorners = 8; snum = fscanf(fd, "%d %d %d %d %d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3], &cone[4], &cone[5], &cone[6], &cone[7]);CHKERRQ(snum != numCorners); break; default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unsupported Gmsh element type %d", cellType); } ierr = DMPlexSetConeSize(*dm, c, numCorners);CHKERRQ(ierr); if (i != c+1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell number %d should be %d", i, c+1); } } ierr = DMSetUp(*dm);CHKERRQ(ierr); if (!rank) { ierr = fseek(fd, fpos, SEEK_SET);CHKERRQ(ierr); for (c = 0; c < numCells; ++c) { PetscInt pcone[8], numCorners, corner, t; int cone[8], i, cellType, numTags, tag; snum = fscanf(fd, "%d %d %d", &i, &cellType, &numTags);CHKERRQ(snum != 3); if (numTags) for (t = 0; t < numTags; ++t) {snum = fscanf(fd, "%d", &tag);CHKERRQ(snum != 1);} switch (cellType) { case 1: /* 2-node line */ dim = 1; numCorners = 2; snum = fscanf(fd, "%d %d\n", &cone[0], &cone[1]);CHKERRQ(snum != numCorners); break; case 2: /* 3-node triangle */ dim = 2; numCorners = 3; snum = fscanf(fd, "%d %d %d\n", &cone[0], &cone[1], &cone[2]);CHKERRQ(snum != numCorners); break; case 3: /* 4-node quadrangle */ dim = 2; numCorners = 4; snum = fscanf(fd, "%d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3]);CHKERRQ(snum != numCorners); break; case 4: /* 4-node tetrahedron */ dim = 3; numCorners = 4; snum = fscanf(fd, "%d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3]);CHKERRQ(snum != numCorners); ierr = DMPlexInvertCell(dim, numCorners, cone);CHKERRQ(ierr); break; case 5: /* 8-node hexahedron */ dim = 3; numCorners = 8; snum = fscanf(fd, "%d %d %d %d %d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3], &cone[4], &cone[5], &cone[6], &cone[7]);CHKERRQ(snum != numCorners); ierr = DMPlexInvertCell(dim, numCorners, cone);CHKERRQ(ierr); break; default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unsupported Gmsh element type %d", cellType); } for (corner = 0; corner < numCorners; ++corner) pcone[corner] = cone[corner] + numCells-1; ierr = DMPlexSetCone(*dm, c, pcone);CHKERRQ(ierr); if (i != c+1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell number %d should be %d", i, c+1); } fgets(line, PETSC_MAX_PATH_LEN, fd); ierr = PetscStrncmp(line, "$EndElements\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr); if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file"); } ierr = MPI_Bcast(&dim, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr); ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); ierr = DMPlexStratify(*dm);CHKERRQ(ierr); if (interpolate) { DM idm; ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = idm; } /* Read coordinates */ ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); for (v = numCells; v < numCells+numVertices; ++v) { ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); } ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); ierr = VecCreate(comm, &coordinates);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); if (!rank) { for (v = 0; v < numVertices; ++v) { for (d = 0; d < dim; ++d) { coords[v*dim+d] = coordsIn[v*3+d]; } } } ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); ierr = PetscFree(coordsIn);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); ierr = VecDestroy(&coordinates);CHKERRQ(ierr); PetscFunctionReturn(0); }