#include /*I "petscdmplex.h" I*/ #include <../src/sys/utils/hash.h> /* Logging support */ PetscLogEvent DMPLEX_Distribute, DMPLEX_Stratify; extern PetscErrorCode VecView_Seq(Vec, PetscViewer); extern PetscErrorCode VecView_MPI(Vec, PetscViewer); #undef __FUNCT__ #define __FUNCT__ "VecView_Plex_Local" PetscErrorCode VecView_Plex_Local(Vec v, PetscViewer viewer) { DM dm; PetscBool isvtk; PetscErrorCode ierr; PetscFunctionBegin; ierr = VecGetDM(v, &dm);CHKERRQ(ierr); if (!dm) SETERRQ(((PetscObject) v)->comm, PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK, &isvtk);CHKERRQ(ierr); if (isvtk) { PetscViewerVTKFieldType ft = PETSC_VTK_POINT_FIELD; PetscSection section; PetscInt dim, pStart, pEnd, cStart, fStart, vStart, cdof = 0, fdof = 0, vdof = 0; ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, PETSC_NULL);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 1, &fStart, PETSC_NULL);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, PETSC_NULL);CHKERRQ(ierr); ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); /* Assumes that numer of dofs per point of each stratum is constant, natural for VTK */ if ((cStart >= pStart) && (cStart < pEnd)) {ierr = PetscSectionGetDof(section, cStart, &cdof);CHKERRQ(ierr);} if ((fStart >= pStart) && (fStart < pEnd)) {ierr = PetscSectionGetDof(section, fStart, &fdof);CHKERRQ(ierr);} if ((vStart >= pStart) && (vStart < pEnd)) {ierr = PetscSectionGetDof(section, vStart, &vdof);CHKERRQ(ierr);} if (cdof && fdof && vdof) { /* Actually Q2 or some such, but visualize as Q1 */ ft = (cdof == dim) ? PETSC_VTK_POINT_VECTOR_FIELD : PETSC_VTK_POINT_FIELD; } else if (cdof && vdof) { SETERRQ(((PetscObject)viewer)->comm,PETSC_ERR_SUP,"No support for viewing mixed space with dofs at both vertices and cells"); } else if (cdof) { /* TODO: This assumption should be removed when there is a way of identifying whether a space is conceptually a * vector or just happens to have the same number of dofs as the dimension. */ if (cdof == dim) { ft = PETSC_VTK_CELL_VECTOR_FIELD; } else { ft = PETSC_VTK_CELL_FIELD; } } else if (vdof) { if (vdof == dim) { ft = PETSC_VTK_POINT_VECTOR_FIELD; } else { ft = PETSC_VTK_POINT_FIELD; } } else SETERRQ(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONG, "Could not classify input Vec for VTK"); ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr); /* viewer drops reference */ ierr = PetscObjectReference((PetscObject) v);CHKERRQ(ierr); /* viewer drops reference */ ierr = PetscViewerVTKAddField(viewer, (PetscObject) dm, DMPlexVTKWriteAll, ft, (PetscObject) v);CHKERRQ(ierr); } else { PetscBool isseq; ierr = PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);CHKERRQ(ierr); if (isseq) { ierr = VecView_Seq(v, viewer);CHKERRQ(ierr); } else { ierr = VecView_MPI(v, viewer);CHKERRQ(ierr); } } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "VecView_Plex" PetscErrorCode VecView_Plex(Vec v, PetscViewer viewer) { DM dm; PetscBool isvtk; PetscErrorCode ierr; PetscFunctionBegin; ierr = VecGetDM(v, &dm);CHKERRQ(ierr); if (!dm) SETERRQ(((PetscObject) v)->comm, PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK, &isvtk);CHKERRQ(ierr); if (isvtk) { Vec locv; const char *name; ierr = DMGetLocalVector(dm, &locv);CHKERRQ(ierr); ierr = PetscObjectGetName((PetscObject) v, &name);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) locv, name);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm, v, INSERT_VALUES, locv);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, v, INSERT_VALUES, locv);CHKERRQ(ierr); ierr = VecView_Plex_Local(locv, viewer);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &locv);CHKERRQ(ierr); } else { PetscBool isseq; ierr = PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);CHKERRQ(ierr); if (isseq) { ierr = VecView_Seq(v, viewer);CHKERRQ(ierr); } else { ierr = VecView_MPI(v, viewer);CHKERRQ(ierr); } } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexView_Ascii" PetscErrorCode DMPlexView_Ascii(DM dm, PetscViewer viewer) { DM_Plex *mesh = (DM_Plex *) dm->data; DM cdm; DMLabel markers; PetscSection coordSection; Vec coordinates; PetscViewerFormat format; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); ierr = DMGetDefaultSection(cdm, &coordSection);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = PetscViewerGetFormat(viewer, &format);CHKERRQ(ierr); if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { const char *name; PetscInt maxConeSize, maxSupportSize; PetscInt pStart, pEnd, p; PetscMPIInt rank, size; ierr = MPI_Comm_rank(((PetscObject) dm)->comm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(((PetscObject) dm)->comm, &size);CHKERRQ(ierr); ierr = PetscObjectGetName((PetscObject) dm, &name);CHKERRQ(ierr); ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); ierr = PetscViewerASCIISynchronizedAllow(viewer, PETSC_TRUE);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, "Mesh '%s':\n", name);CHKERRQ(ierr); ierr = PetscViewerASCIISynchronizedPrintf(viewer, "Max sizes cone: %D support: %D\n", maxConeSize, maxSupportSize);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, "orientation is missing\n", name);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, "cap --> base:\n", name);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { PetscInt dof, off, s; ierr = PetscSectionGetDof(mesh->supportSection, p, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(mesh->supportSection, p, &off);CHKERRQ(ierr); for (s = off; s < off+dof; ++s) { ierr = PetscViewerASCIISynchronizedPrintf(viewer, "[%D]: %D ----> %D\n", rank, p, mesh->supports[s]);CHKERRQ(ierr); } } ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, "base <-- cap:\n", name);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { PetscInt dof, off, c; ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); for (c = off; c < off+dof; ++c) { ierr = PetscViewerASCIISynchronizedPrintf(viewer, "[%D]: %D <---- %D (%D)\n", rank, p, mesh->cones[c], mesh->coneOrientations[c]);CHKERRQ(ierr); } } ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); ierr = PetscSectionGetChart(coordSection, &pStart, PETSC_NULL);CHKERRQ(ierr); if (pStart >= 0) {ierr = PetscSectionVecView(coordSection, coordinates, viewer);CHKERRQ(ierr);} ierr = DMPlexGetLabel(dm, "marker", &markers);CHKERRQ(ierr); if (markers) { ierr = DMLabelView(markers,viewer);CHKERRQ(ierr); } if (size > 1) { PetscSF sf; ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); ierr = PetscSFView(sf, viewer);CHKERRQ(ierr); } ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); } else if (format == PETSC_VIEWER_ASCII_LATEX) { const char *name; const char *colors[3] = {"red", "blue", "green"}; const int numColors = 3; PetscReal scale = 2.0; PetscScalar *coords; PetscInt depth, cStart, cEnd, c, vStart, vEnd, v, eStart = 0, eEnd = 0, e, p; PetscMPIInt rank, size; ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = MPI_Comm_rank(((PetscObject) dm)->comm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(((PetscObject) dm)->comm, &size);CHKERRQ(ierr); ierr = PetscObjectGetName((PetscObject) dm, &name);CHKERRQ(ierr); ierr = PetscViewerASCIISynchronizedAllow(viewer, PETSC_TRUE);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, "\ \\documentclass[crop,multi=false]{standalone}\n\n\ \\usepackage{tikz}\n\ \\usepackage{pgflibraryshapes}\n\ \\usetikzlibrary{backgrounds}\n\ \\usetikzlibrary{arrows}\n\ \\begin{document}\n\ \\section{%s}\n\ \\begin{center}\n", name, 8.0/scale);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, "Mesh for process ");CHKERRQ(ierr); for(p = 0; p < size; ++p) { if (p > 0 && p == size-1) { ierr = PetscViewerASCIIPrintf(viewer, ", and ", colors[p%numColors], p);CHKERRQ(ierr); } else if (p > 0) { ierr = PetscViewerASCIIPrintf(viewer, ", ", colors[p%numColors], p);CHKERRQ(ierr); } ierr = PetscViewerASCIIPrintf(viewer, "{\\textcolor{%s}%D}", colors[p%numColors], p);CHKERRQ(ierr); } ierr = PetscViewerASCIIPrintf(viewer, ".\n\n\n\ \\begin{tikzpicture}[scale = %g,font=\\fontsize{8}{8}\\selectfont]\n");CHKERRQ(ierr); /* Plot vertices */ ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, "\\path\n");CHKERRQ(ierr); for(v = vStart; v < vEnd; ++v) { PetscInt off, dof, d; ierr = PetscSectionGetDof(coordSection, v, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); ierr = PetscViewerASCIISynchronizedPrintf(viewer, "(");CHKERRQ(ierr); for (d = 0; d < dof; ++d) { if (d > 0) {ierr = PetscViewerASCIISynchronizedPrintf(viewer, ",");CHKERRQ(ierr);} ierr = PetscViewerASCIISynchronizedPrintf(viewer, "%G", scale*PetscRealPart(coords[off+d]));CHKERRQ(ierr); } ierr = PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%D) [draw,shape=circle,color=%s] {%D} --\n", v, rank, colors[rank%numColors], v);CHKERRQ(ierr); } ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, "(0,0);\n");CHKERRQ(ierr); /* Plot edges */ ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, "\\path\n");CHKERRQ(ierr); if (depth > 1) {ierr = DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd);CHKERRQ(ierr);} for(e = eStart; e < eEnd; ++e) { const PetscInt *cone; PetscInt coneSize, offA, offB, dof, d; ierr = DMPlexGetConeSize(dm, e, &coneSize);CHKERRQ(ierr); if (coneSize != 2) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONG, "Edge %d cone should have two vertices, not %d", e, coneSize); ierr = DMPlexGetCone(dm, e, &cone);CHKERRQ(ierr); ierr = PetscSectionGetDof(coordSection, cone[0], &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(coordSection, cone[0], &offA);CHKERRQ(ierr); ierr = PetscSectionGetOffset(coordSection, cone[1], &offB);CHKERRQ(ierr); ierr = PetscViewerASCIISynchronizedPrintf(viewer, "(");CHKERRQ(ierr); for (d = 0; d < dof; ++d) { if (d > 0) {ierr = PetscViewerASCIISynchronizedPrintf(viewer, ",");CHKERRQ(ierr);} ierr = PetscViewerASCIISynchronizedPrintf(viewer, "%G", scale*0.5*PetscRealPart(coords[offA+d]+coords[offB+d]));CHKERRQ(ierr); } ierr = PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%D) [draw,shape=circle,color=%s] {%D} --\n", e, rank, colors[rank%numColors], e);CHKERRQ(ierr); } ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, "(0,0);\n");CHKERRQ(ierr); /* Plot cells */ ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); for(c = cStart; c < cEnd; ++c) { PetscInt *closure = PETSC_NULL; PetscInt closureSize, firstPoint = -1; ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); ierr = PetscViewerASCIISynchronizedPrintf(viewer, "\\draw[color=%s] ", colors[rank%numColors]);CHKERRQ(ierr); for (p = 0; p < closureSize*2; p += 2) { const PetscInt point = closure[p]; if ((point < vStart) || (point >= vEnd)) continue; if (firstPoint >= 0) {ierr = PetscViewerASCIISynchronizedPrintf(viewer, " -- ");CHKERRQ(ierr);} ierr = PetscViewerASCIISynchronizedPrintf(viewer, "(%D_%D)", point, rank);CHKERRQ(ierr); if (firstPoint < 0) firstPoint = point; } /* Why doesn't this work? ierr = PetscViewerASCIISynchronizedPrintf(viewer, " -- cycle;\n");CHKERRQ(ierr); */ ierr = PetscViewerASCIISynchronizedPrintf(viewer, " -- (%D_%D);\n", firstPoint, rank);CHKERRQ(ierr); ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); } ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, "\\end{tikzpicture}\n\\end{center}\n");CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, "\\end{document}\n", name);CHKERRQ(ierr); } else { MPI_Comm comm = ((PetscObject) dm)->comm; PetscInt *sizes; PetscInt locDepth, depth, dim, d; PetscInt pStart, pEnd, p; PetscMPIInt size; ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, "Mesh in %D dimensions:\n", dim);CHKERRQ(ierr); ierr = DMPlexGetDepth(dm, &locDepth);CHKERRQ(ierr); ierr = MPI_Allreduce(&locDepth, &depth, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr); ierr = PetscMalloc(size * sizeof(PetscInt), &sizes);CHKERRQ(ierr); if (depth == 1) { ierr = DMPlexGetDepthStratum(dm, 0, &pStart, &pEnd);CHKERRQ(ierr); pEnd = pEnd - pStart; ierr = MPI_Gather(&pEnd, 1, MPIU_INT, sizes, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, " %D-cells:", 0);CHKERRQ(ierr); for (p = 0; p < size; ++p) {ierr = PetscViewerASCIIPrintf(viewer, " %D", sizes[p]);CHKERRQ(ierr);} ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &pStart, &pEnd);CHKERRQ(ierr); pEnd = pEnd - pStart; ierr = MPI_Gather(&pEnd, 1, MPIU_INT, sizes, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, " %D-cells:", dim);CHKERRQ(ierr); for (p = 0; p < size; ++p) {ierr = PetscViewerASCIIPrintf(viewer, " %D", sizes[p]);CHKERRQ(ierr);} ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr); } else { for (d = 0; d <= dim; d++) { ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); pEnd = pEnd - pStart; ierr = MPI_Gather(&pEnd, 1, MPIU_INT, sizes, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, " %D-cells:", d);CHKERRQ(ierr); for (p = 0; p < size; ++p) {ierr = PetscViewerASCIIPrintf(viewer, " %D", sizes[p]);CHKERRQ(ierr);} ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr); } } ierr = PetscFree(sizes);CHKERRQ(ierr); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMView_Plex" PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer) { PetscBool iascii, isbinary; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERBINARY, &isbinary);CHKERRQ(ierr); if (iascii) { ierr = DMPlexView_Ascii(dm, viewer);CHKERRQ(ierr); #if 0 } else if (isbinary) { ierr = DMPlexView_Binary(dm, viewer);CHKERRQ(ierr); #endif } else SETERRQ1(((PetscObject)viewer)->comm,PETSC_ERR_SUP,"Viewer type %s not supported by this mesh object", ((PetscObject)viewer)->type_name); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMDestroy_Plex" PetscErrorCode DMDestroy_Plex(DM dm) { DM_Plex *mesh = (DM_Plex *) dm->data; DMLabel next = mesh->labels; PetscErrorCode ierr; PetscFunctionBegin; if (--mesh->refct > 0) {PetscFunctionReturn(0);} ierr = PetscSectionDestroy(&mesh->coneSection);CHKERRQ(ierr); ierr = PetscFree(mesh->cones);CHKERRQ(ierr); ierr = PetscFree(mesh->coneOrientations);CHKERRQ(ierr); ierr = PetscSectionDestroy(&mesh->supportSection);CHKERRQ(ierr); ierr = PetscFree(mesh->supports);CHKERRQ(ierr); ierr = PetscFree(mesh->facesTmp);CHKERRQ(ierr); while(next) { DMLabel tmp = next->next; ierr = DMLabelDestroy(&next);CHKERRQ(ierr); next = tmp; } ierr = ISDestroy(&mesh->subpointMap);CHKERRQ(ierr); ierr = ISDestroy(&mesh->globalVertexNumbers);CHKERRQ(ierr); ierr = ISDestroy(&mesh->globalCellNumbers);CHKERRQ(ierr); /* This was originally freed in DMDestroy(), but that prevents reference counting of backend objects */ ierr = PetscFree(mesh);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetAdjacencySingleLevel_Private" PetscErrorCode DMPlexGetAdjacencySingleLevel_Private(DM dm, PetscInt p, PetscBool useClosure, const PetscInt *tmpClosure, PetscInt *adjSize, PetscInt adj[]) { const PetscInt *support = PETSC_NULL; PetscInt numAdj = 0, maxAdjSize = *adjSize, supportSize, s; PetscErrorCode ierr; PetscFunctionBegin; if (useClosure) { ierr = DMPlexGetConeSize(dm, p, &supportSize);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, p, &support);CHKERRQ(ierr); for (s = 0; s < supportSize; ++s) { const PetscInt *cone = PETSC_NULL; PetscInt coneSize, c, q; ierr = DMPlexGetSupportSize(dm, support[s], &coneSize);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, support[s], &cone);CHKERRQ(ierr); for (c = 0; c < coneSize; ++c) { for (q = 0; q < numAdj || (adj[numAdj++] = cone[c],0); ++q) { if (cone[c] == adj[q]) break; } if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize); } } } else { ierr = DMPlexGetSupportSize(dm, p, &supportSize);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, p, &support);CHKERRQ(ierr); for (s = 0; s < supportSize; ++s) { const PetscInt *cone = PETSC_NULL; PetscInt coneSize, c, q; ierr = DMPlexGetConeSize(dm, support[s], &coneSize);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); for (c = 0; c < coneSize; ++c) { for (q = 0; q < numAdj || (adj[numAdj++] = cone[c],0); ++q) { if (cone[c] == adj[q]) break; } if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize); } } } *adjSize = numAdj; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetAdjacency_Private" PetscErrorCode DMPlexGetAdjacency_Private(DM dm, PetscInt p, PetscBool useClosure, const PetscInt *tmpClosure, PetscInt *adjSize, PetscInt adj[]) { const PetscInt *star = tmpClosure; PetscInt numAdj = 0, maxAdjSize = *adjSize, starSize, s; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetTransitiveClosure(dm, p, useClosure, &starSize, (PetscInt **) &star);CHKERRQ(ierr); for (s = 2; s < starSize*2; s += 2) { const PetscInt *closure = PETSC_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); } *adjSize = numAdj; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSetPreallocationCenterDimension" PetscErrorCode DMPlexSetPreallocationCenterDimension(DM dm, PetscInt preallocCenterDim) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); mesh->preallocCenterDim = preallocCenterDim; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexPreallocateOperator" PetscErrorCode DMPlexPreallocateOperator(DM dm, PetscInt bs, PetscSection section, PetscSection sectionGlobal, PetscInt dnz[], PetscInt onz[], PetscInt dnzu[], PetscInt onzu[], Mat A, PetscBool fillMatrix) { DM_Plex *mesh = (DM_Plex *) dm->data; MPI_Comm comm = ((PetscObject) dm)->comm; PetscSF sf, sfDof, sfAdj; PetscSection leafSectionAdj, rootSectionAdj, sectionAdj; PetscInt nleaves, l, p; const PetscInt *leaves; const PetscSFNode *remotes; PetscInt dim, pStart, pEnd, numDof, globalOffStart, globalOffEnd, numCols; PetscInt *tmpClosure, *tmpAdj, *adj, *rootAdj, *cols, *remoteOffsets; PetscInt depth, maxConeSize, maxSupportSize, maxClosureSize, maxAdjSize, adjSize; PetscLayout rLayout; PetscInt locRows, rStart, rEnd, r; PetscMPIInt size; PetscBool useClosure, debug = PETSC_FALSE; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscOptionsGetBool(PETSC_NULL, "-dm_view_preallocation", &debug, PETSC_NULL);CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); /* Create dof SF based on point SF */ if (debug) { ierr = PetscPrintf(comm, "Input Section for Preallocation:\n");CHKERRQ(ierr); ierr = PetscSectionView(section, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(comm, "Input Global Section for Preallocation:\n");CHKERRQ(ierr); ierr = PetscSectionView(sectionGlobal, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(comm, "Input SF for Preallocation:\n");CHKERRQ(ierr); ierr = PetscSFView(sf, PETSC_NULL);CHKERRQ(ierr); } ierr = PetscSFCreateRemoteOffsets(sf, section, section, &remoteOffsets);CHKERRQ(ierr); ierr = PetscSFCreateSectionSF(sf, section, remoteOffsets, section, &sfDof);CHKERRQ(ierr); if (debug) { ierr = PetscPrintf(comm, "Dof SF for Preallocation:\n");CHKERRQ(ierr); ierr = PetscSFView(sfDof, PETSC_NULL);CHKERRQ(ierr); } /* Create section for dof adjacency (dof ==> # adj dof) */ /* FEM: Two points p and q are adjacent if q \in closure(star(p)), preallocCenterDim = dim */ /* FVM: Two points p and q are adjacent if q \in star(cone(p)), preallocCenterDim = dim-1 */ /* FVM++: Two points p and q are adjacent if q \in star(closure(p)), preallocCenterDim = 0 */ if (mesh->preallocCenterDim == dim) { useClosure = PETSC_FALSE; } else if (mesh->preallocCenterDim == 0) { useClosure = PETSC_TRUE; } else SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Do not support preallocation with center points of dimension %d", mesh->preallocCenterDim); ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); ierr = PetscSectionGetStorageSize(section, &numDof);CHKERRQ(ierr); ierr = PetscSectionCreate(comm, &leafSectionAdj);CHKERRQ(ierr); ierr = PetscSectionSetChart(leafSectionAdj, 0, numDof);CHKERRQ(ierr); ierr = PetscSectionCreate(comm, &rootSectionAdj);CHKERRQ(ierr); ierr = PetscSectionSetChart(rootSectionAdj, 0, numDof);CHKERRQ(ierr); /* Fill in the ghost dofs on the interface */ ierr = PetscSFGetGraph(sf, PETSC_NULL, &nleaves, &leaves, &remotes);CHKERRQ(ierr); ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); maxClosureSize = (PetscInt) (2*PetscMax(pow((PetscReal) mesh->maxConeSize, depth)+1, pow((PetscReal) mesh->maxSupportSize, depth)+1)); maxAdjSize = (PetscInt) (pow((PetscReal) mesh->maxConeSize, depth)*pow((PetscReal) mesh->maxSupportSize, depth)+1); ierr = PetscMalloc2(maxClosureSize,PetscInt,&tmpClosure,maxAdjSize,PetscInt,&tmpAdj);CHKERRQ(ierr); /* ** The bootstrapping process involves six rounds with similar structure of visiting neighbors of each point. 1. Visit unowned points on interface, count adjacencies placing in leafSectionAdj Reduce those counts to rootSectionAdj (now redundantly counting some interface points) 2. Visit owned points on interface, count adjacencies placing in rootSectionAdj Create sfAdj connecting rootSectionAdj and leafSectionAdj 3. Visit unowned points on interface, write adjacencies to adj Gather adj to rootAdj (note that there is redundancy in rootAdj when multiple procs find the same adjacencies) 4. Visit owned points on interface, write adjacencies to rootAdj Remove redundancy in rootAdj ** The last two traversals use transitive closure 5. Visit all owned points in the subdomain, count dofs for each point (sectionAdj) Allocate memory addressed by sectionAdj (cols) 6. Visit all owned points in the subdomain, insert dof adjacencies into cols ** Knowing all the column adjacencies, check ownership and sum into dnz and onz */ for (l = 0; l < nleaves; ++l) { PetscInt dof, off, d, q; PetscInt p = leaves[l], numAdj = maxAdjSize; ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr); ierr = DMPlexGetAdjacency_Private(dm, p, useClosure, tmpClosure, &numAdj, tmpAdj);CHKERRQ(ierr); for (q = 0; q < numAdj; ++q) { PetscInt ndof, ncdof; ierr = PetscSectionGetDof(section, tmpAdj[q], &ndof);CHKERRQ(ierr); ierr = PetscSectionGetConstraintDof(section, tmpAdj[q], &ncdof);CHKERRQ(ierr); for (d = off; d < off+dof; ++d) { ierr = PetscSectionAddDof(leafSectionAdj, d, ndof-ncdof);CHKERRQ(ierr); } } } ierr = PetscSectionSetUp(leafSectionAdj);CHKERRQ(ierr); if (debug) { ierr = PetscPrintf(comm, "Adjacency Section for Preallocation on Leaves:\n");CHKERRQ(ierr); ierr = PetscSectionView(leafSectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } /* Get maximum remote adjacency sizes for owned dofs on interface (roots) */ if (size > 1) { ierr = PetscSFReduceBegin(sfDof, MPIU_INT, leafSectionAdj->atlasDof, rootSectionAdj->atlasDof, MPI_SUM);CHKERRQ(ierr); ierr = PetscSFReduceEnd(sfDof, MPIU_INT, leafSectionAdj->atlasDof, rootSectionAdj->atlasDof, MPI_SUM);CHKERRQ(ierr); } if (debug) { ierr = PetscPrintf(comm, "Adjancency Section for Preallocation on Roots:\n");CHKERRQ(ierr); ierr = PetscSectionView(rootSectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } /* Add in local adjacency sizes for owned dofs on interface (roots) */ for (p = pStart; p < pEnd; ++p) { PetscInt numAdj = maxAdjSize, adof, dof, off, d, q; ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr); if (!dof) continue; ierr = PetscSectionGetDof(rootSectionAdj, off, &adof);CHKERRQ(ierr); if (adof <= 0) continue; ierr = DMPlexGetAdjacency_Private(dm, p, useClosure, tmpClosure, &numAdj, tmpAdj);CHKERRQ(ierr); for (q = 0; q < numAdj; ++q) { PetscInt ndof, ncdof; ierr = PetscSectionGetDof(section, tmpAdj[q], &ndof);CHKERRQ(ierr); ierr = PetscSectionGetConstraintDof(section, tmpAdj[q], &ncdof);CHKERRQ(ierr); for (d = off; d < off+dof; ++d) { ierr = PetscSectionAddDof(rootSectionAdj, d, ndof-ncdof);CHKERRQ(ierr); } } } ierr = PetscSectionSetUp(rootSectionAdj);CHKERRQ(ierr); if (debug) { ierr = PetscPrintf(comm, "Adjancency Section for Preallocation on Roots after local additions:\n");CHKERRQ(ierr); ierr = PetscSectionView(rootSectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } /* Create adj SF based on dof SF */ ierr = PetscSFCreateRemoteOffsets(sfDof, rootSectionAdj, leafSectionAdj, &remoteOffsets);CHKERRQ(ierr); ierr = PetscSFCreateSectionSF(sfDof, rootSectionAdj, remoteOffsets, leafSectionAdj, &sfAdj);CHKERRQ(ierr); if (debug) { ierr = PetscPrintf(comm, "Adjacency SF for Preallocation:\n");CHKERRQ(ierr); ierr = PetscSFView(sfAdj, PETSC_NULL);CHKERRQ(ierr); } ierr = PetscSFDestroy(&sfDof);CHKERRQ(ierr); /* Create leaf adjacency */ ierr = PetscSectionSetUp(leafSectionAdj);CHKERRQ(ierr); ierr = PetscSectionGetStorageSize(leafSectionAdj, &adjSize);CHKERRQ(ierr); ierr = PetscMalloc(adjSize * sizeof(PetscInt), &adj);CHKERRQ(ierr); ierr = PetscMemzero(adj, adjSize * sizeof(PetscInt));CHKERRQ(ierr); for (l = 0; l < nleaves; ++l) { PetscInt dof, off, d, q; PetscInt p = leaves[l], numAdj = maxAdjSize; ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr); ierr = DMPlexGetAdjacency_Private(dm, p, useClosure, tmpClosure, &numAdj, tmpAdj);CHKERRQ(ierr); for (d = off; d < off+dof; ++d) { PetscInt aoff, i = 0; ierr = PetscSectionGetOffset(leafSectionAdj, d, &aoff);CHKERRQ(ierr); for (q = 0; q < numAdj; ++q) { PetscInt ndof, ncdof, ngoff, nd; ierr = PetscSectionGetDof(section, tmpAdj[q], &ndof);CHKERRQ(ierr); ierr = PetscSectionGetConstraintDof(section, tmpAdj[q], &ncdof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(sectionGlobal, tmpAdj[q], &ngoff);CHKERRQ(ierr); for (nd = 0; nd < ndof-ncdof; ++nd) { adj[aoff+i] = (ngoff < 0 ? -(ngoff+1) : ngoff) + nd; ++i; } } } } /* Debugging */ if (debug) { IS tmp; ierr = PetscPrintf(comm, "Leaf adjacency indices\n");CHKERRQ(ierr); ierr = ISCreateGeneral(comm, adjSize, adj, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr); ierr = ISView(tmp, PETSC_NULL);CHKERRQ(ierr); } /* Gather adjacenct indices to root */ ierr = PetscSectionGetStorageSize(rootSectionAdj, &adjSize);CHKERRQ(ierr); ierr = PetscMalloc(adjSize * sizeof(PetscInt), &rootAdj);CHKERRQ(ierr); for (r = 0; r < adjSize; ++r) { rootAdj[r] = -1; } if (size > 1) { ierr = PetscSFGatherBegin(sfAdj, MPIU_INT, adj, rootAdj);CHKERRQ(ierr); ierr = PetscSFGatherEnd(sfAdj, MPIU_INT, adj, rootAdj);CHKERRQ(ierr); } ierr = PetscSFDestroy(&sfAdj);CHKERRQ(ierr); ierr = PetscFree(adj);CHKERRQ(ierr); /* Debugging */ if (debug) { IS tmp; ierr = PetscPrintf(comm, "Root adjacency indices after gather\n");CHKERRQ(ierr); ierr = ISCreateGeneral(comm, adjSize, rootAdj, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr); ierr = ISView(tmp, PETSC_NULL);CHKERRQ(ierr); } /* Add in local adjacency indices for owned dofs on interface (roots) */ for (p = pStart; p < pEnd; ++p) { PetscInt numAdj = maxAdjSize, adof, dof, off, d, q; ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr); if (!dof) continue; ierr = PetscSectionGetDof(rootSectionAdj, off, &adof);CHKERRQ(ierr); if (adof <= 0) continue; ierr = DMPlexGetAdjacency_Private(dm, p, useClosure, tmpClosure, &numAdj, tmpAdj);CHKERRQ(ierr); for (d = off; d < off+dof; ++d) { PetscInt adof, aoff, i; ierr = PetscSectionGetDof(rootSectionAdj, d, &adof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(rootSectionAdj, d, &aoff);CHKERRQ(ierr); i = adof-1; for (q = 0; q < numAdj; ++q) { PetscInt ndof, ncdof, ngoff, nd; ierr = PetscSectionGetDof(section, tmpAdj[q], &ndof);CHKERRQ(ierr); ierr = PetscSectionGetConstraintDof(section, tmpAdj[q], &ncdof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(sectionGlobal, tmpAdj[q], &ngoff);CHKERRQ(ierr); for (nd = 0; nd < ndof-ncdof; ++nd) { rootAdj[aoff+i] = ngoff < 0 ? -(ngoff+1)+nd: ngoff+nd; --i; } } } } /* Debugging */ if (debug) { IS tmp; ierr = PetscPrintf(comm, "Root adjacency indices\n");CHKERRQ(ierr); ierr = ISCreateGeneral(comm, adjSize, rootAdj, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr); ierr = ISView(tmp, PETSC_NULL);CHKERRQ(ierr); } /* Compress indices */ ierr = PetscSectionSetUp(rootSectionAdj);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { PetscInt dof, cdof, off, d; PetscInt adof, aoff; ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr); ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr); if (!dof) continue; ierr = PetscSectionGetDof(rootSectionAdj, off, &adof);CHKERRQ(ierr); if (adof <= 0) continue; for (d = off; d < off+dof-cdof; ++d) { ierr = PetscSectionGetDof(rootSectionAdj, d, &adof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(rootSectionAdj, d, &aoff);CHKERRQ(ierr); ierr = PetscSortRemoveDupsInt(&adof, &rootAdj[aoff]);CHKERRQ(ierr); ierr = PetscSectionSetDof(rootSectionAdj, d, adof);CHKERRQ(ierr); } } /* Debugging */ if (debug) { IS tmp; ierr = PetscPrintf(comm, "Adjancency Section for Preallocation on Roots after compression:\n");CHKERRQ(ierr); ierr = PetscSectionView(rootSectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(comm, "Root adjacency indices after compression\n");CHKERRQ(ierr); ierr = ISCreateGeneral(comm, adjSize, rootAdj, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr); ierr = ISView(tmp, PETSC_NULL);CHKERRQ(ierr); } /* Build adjacency section: Maps global indices to sets of adjacent global indices */ ierr = PetscSectionGetOffsetRange(sectionGlobal, &globalOffStart, &globalOffEnd);CHKERRQ(ierr); ierr = PetscSectionCreate(comm, §ionAdj);CHKERRQ(ierr); ierr = PetscSectionSetChart(sectionAdj, globalOffStart, globalOffEnd);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { PetscInt numAdj = maxAdjSize, dof, cdof, off, goff, d, q; PetscBool found = PETSC_TRUE; ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr); ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr); ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr); for (d = 0; d < dof-cdof; ++d) { PetscInt ldof, rdof; ierr = PetscSectionGetDof(leafSectionAdj, off+d, &ldof);CHKERRQ(ierr); ierr = PetscSectionGetDof(rootSectionAdj, off+d, &rdof);CHKERRQ(ierr); if (ldof > 0) { /* We do not own this point */ } else if (rdof > 0) { ierr = PetscSectionSetDof(sectionAdj, goff+d, rdof);CHKERRQ(ierr); } else { found = PETSC_FALSE; } } if (found) continue; ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr); ierr = DMPlexGetAdjacency_Private(dm, p, useClosure, tmpClosure, &numAdj, tmpAdj);CHKERRQ(ierr); for (q = 0; q < numAdj; ++q) { PetscInt ndof, ncdof, noff; /* Adjacent points may not be in the section chart */ if ((tmpAdj[q] < pStart) || (tmpAdj[q] >= pEnd)) continue; ierr = PetscSectionGetDof(section, tmpAdj[q], &ndof);CHKERRQ(ierr); ierr = PetscSectionGetConstraintDof(section, tmpAdj[q], &ncdof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(section, tmpAdj[q], &noff);CHKERRQ(ierr); for (d = goff; d < goff+dof-cdof; ++d) { ierr = PetscSectionAddDof(sectionAdj, d, ndof-ncdof);CHKERRQ(ierr); } } } ierr = PetscSectionSetUp(sectionAdj);CHKERRQ(ierr); if (debug) { ierr = PetscPrintf(comm, "Adjacency Section for Preallocation:\n");CHKERRQ(ierr); ierr = PetscSectionView(sectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } /* Get adjacent indices */ ierr = PetscSectionGetStorageSize(sectionAdj, &numCols);CHKERRQ(ierr); ierr = PetscMalloc(numCols * sizeof(PetscInt), &cols);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { PetscInt numAdj = maxAdjSize, dof, cdof, off, goff, d, q; PetscBool found = PETSC_TRUE; ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr); ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr); ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr); for (d = 0; d < dof-cdof; ++d) { PetscInt ldof, rdof; ierr = PetscSectionGetDof(leafSectionAdj, off+d, &ldof);CHKERRQ(ierr); ierr = PetscSectionGetDof(rootSectionAdj, off+d, &rdof);CHKERRQ(ierr); if (ldof > 0) { /* We do not own this point */ } else if (rdof > 0) { PetscInt aoff, roff; ierr = PetscSectionGetOffset(sectionAdj, goff+d, &aoff);CHKERRQ(ierr); ierr = PetscSectionGetOffset(rootSectionAdj, off+d, &roff);CHKERRQ(ierr); ierr = PetscMemcpy(&cols[aoff], &rootAdj[roff], rdof * sizeof(PetscInt));CHKERRQ(ierr); } else { found = PETSC_FALSE; } } if (found) continue; ierr = DMPlexGetAdjacency_Private(dm, p, useClosure, tmpClosure, &numAdj, tmpAdj);CHKERRQ(ierr); for (d = goff; d < goff+dof-cdof; ++d) { PetscInt adof, aoff, i = 0; ierr = PetscSectionGetDof(sectionAdj, d, &adof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(sectionAdj, d, &aoff);CHKERRQ(ierr); for (q = 0; q < numAdj; ++q) { PetscInt ndof, ncdof, ngoff, nd; const PetscInt *ncind; /* Adjacent points may not be in the section chart */ if ((tmpAdj[q] < pStart) || (tmpAdj[q] >= pEnd)) continue; ierr = PetscSectionGetDof(section, tmpAdj[q], &ndof);CHKERRQ(ierr); ierr = PetscSectionGetConstraintDof(section, tmpAdj[q], &ncdof);CHKERRQ(ierr); ierr = PetscSectionGetConstraintIndices(section, tmpAdj[q], &ncind);CHKERRQ(ierr); ierr = PetscSectionGetOffset(sectionGlobal, tmpAdj[q], &ngoff);CHKERRQ(ierr); for (nd = 0; nd < ndof-ncdof; ++nd, ++i) { cols[aoff+i] = ngoff < 0 ? -(ngoff+1)+nd: ngoff+nd; } } if (i != adof) SETERRQ4(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of entries %D != %D for dof %D (point %D)", i, adof, d, p); } } ierr = PetscSectionDestroy(&leafSectionAdj);CHKERRQ(ierr); ierr = PetscSectionDestroy(&rootSectionAdj);CHKERRQ(ierr); ierr = PetscFree(rootAdj);CHKERRQ(ierr); ierr = PetscFree2(tmpClosure, tmpAdj);CHKERRQ(ierr); /* Debugging */ if (debug) { IS tmp; ierr = PetscPrintf(comm, "Column indices\n");CHKERRQ(ierr); ierr = ISCreateGeneral(comm, numCols, cols, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr); ierr = ISView(tmp, PETSC_NULL);CHKERRQ(ierr); } /* Create allocation vectors from adjacency graph */ ierr = MatGetLocalSize(A, &locRows, PETSC_NULL);CHKERRQ(ierr); ierr = PetscLayoutCreate(((PetscObject) A)->comm, &rLayout);CHKERRQ(ierr); ierr = PetscLayoutSetLocalSize(rLayout, locRows);CHKERRQ(ierr); ierr = PetscLayoutSetBlockSize(rLayout, 1);CHKERRQ(ierr); ierr = PetscLayoutSetUp(rLayout);CHKERRQ(ierr); ierr = PetscLayoutGetRange(rLayout, &rStart, &rEnd);CHKERRQ(ierr); ierr = PetscLayoutDestroy(&rLayout);CHKERRQ(ierr); /* Only loop over blocks of rows */ if (rStart%bs || rEnd%bs) SETERRQ3(((PetscObject) A)->comm, PETSC_ERR_ARG_WRONG, "Invalid layout [%d, %d) for matrix, must be divisible by block size %d", rStart, rEnd, bs); for (r = rStart/bs; r < rEnd/bs; ++r) { const PetscInt row = r*bs; PetscInt numCols, cStart, c; ierr = PetscSectionGetDof(sectionAdj, row, &numCols);CHKERRQ(ierr); ierr = PetscSectionGetOffset(sectionAdj, row, &cStart);CHKERRQ(ierr); for (c = cStart; c < cStart+numCols; ++c) { if ((cols[c] >= rStart*bs) && (cols[c] < rEnd*bs)) { ++dnz[r-rStart]; if (cols[c] >= row) {++dnzu[r-rStart];} } else { ++onz[r-rStart]; if (cols[c] >= row) {++onzu[r-rStart];} } } } if (bs > 1) { for (r = 0; r < locRows/bs; ++r) { dnz[r] /= bs; onz[r] /= bs; dnzu[r] /= bs; onzu[r] /= bs; } } /* Set matrix pattern */ ierr = MatXAIJSetPreallocation(A, bs, dnz, onz, dnzu, onzu);CHKERRQ(ierr); ierr = MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); /* Fill matrix with zeros */ if (fillMatrix) { PetscScalar *values; PetscInt maxRowLen = 0; for (r = rStart; r < rEnd; ++r) { PetscInt len; ierr = PetscSectionGetDof(sectionAdj, r, &len);CHKERRQ(ierr); maxRowLen = PetscMax(maxRowLen, len); } ierr = PetscMalloc(maxRowLen * sizeof(PetscScalar), &values);CHKERRQ(ierr); ierr = PetscMemzero(values, maxRowLen * sizeof(PetscScalar));CHKERRQ(ierr); for (r = rStart; r < rEnd; ++r) { PetscInt numCols, cStart; ierr = PetscSectionGetDof(sectionAdj, r, &numCols);CHKERRQ(ierr); ierr = PetscSectionGetOffset(sectionAdj, r, &cStart);CHKERRQ(ierr); ierr = MatSetValues(A, 1, &r, numCols, &cols[cStart], values, INSERT_VALUES);CHKERRQ(ierr); } ierr = PetscFree(values);CHKERRQ(ierr); ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); } ierr = PetscSectionDestroy(§ionAdj);CHKERRQ(ierr); ierr = PetscFree(cols);CHKERRQ(ierr); PetscFunctionReturn(0); } #if 0 #undef __FUNCT__ #define __FUNCT__ "DMPlexPreallocateOperator_2" PetscErrorCode DMPlexPreallocateOperator_2(DM dm, PetscInt bs, PetscSection section, PetscSection sectionGlobal, PetscInt dnz[], PetscInt onz[], PetscInt dnzu[], PetscInt onzu[], Mat A, PetscBool fillMatrix) { PetscErrorCode ierr; PetscInt c,cStart,cEnd,pStart,pEnd; PetscInt *tmpClosure,*tmpAdj,*visits; PetscFunctionBegin; ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); maxClosureSize = 2*PetscMax(pow(mesh->maxConeSize, depth)+1, pow(mesh->maxSupportSize, depth)+1); ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); npoints = pEnd - pStart; ierr = PetscMalloc3(maxClosureSize,PetscInt,&tmpClosure,npoints,PetscInt,&lvisits,npoints,PetscInt,&visits);CHKERRQ(ierr); ierr = PetscMemzero(lvisits,(pEnd-pStart)*sizeof(PetscInt));CHKERRQ(ierr); ierr = PetscMemzero(visits,(pEnd-pStart)*sizeof(PetscInt));CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); for (c=cStart; ccomm, J);CHKERRQ(ierr); ierr = MatSetSizes(*J, localSize, localSize, PETSC_DETERMINE, PETSC_DETERMINE);CHKERRQ(ierr); ierr = MatSetType(*J, mtype);CHKERRQ(ierr); ierr = MatSetFromOptions(*J);CHKERRQ(ierr); ierr = PetscStrcmp(mtype, MATSHELL, &isShell);CHKERRQ(ierr); ierr = PetscStrcmp(mtype, MATBAIJ, &isBlock);CHKERRQ(ierr); ierr = PetscStrcmp(mtype, MATSEQBAIJ, &isSeqBlock);CHKERRQ(ierr); ierr = PetscStrcmp(mtype, MATMPIBAIJ, &isMPIBlock);CHKERRQ(ierr); ierr = PetscStrcmp(mtype, MATSBAIJ, &isSymBlock);CHKERRQ(ierr); ierr = PetscStrcmp(mtype, MATSEQSBAIJ, &isSymSeqBlock);CHKERRQ(ierr); ierr = PetscStrcmp(mtype, MATMPISBAIJ, &isSymMPIBlock);CHKERRQ(ierr); /* Check for symmetric storage */ isSymmetric = (PetscBool) (isSymBlock || isSymSeqBlock || isSymMPIBlock); if (isSymmetric) { ierr = MatSetOption(*J, MAT_IGNORE_LOWER_TRIANGULAR, PETSC_TRUE);CHKERRQ(ierr); } if (!isShell) { PetscBool fillMatrix = (PetscBool) !dm->prealloc_only; PetscInt *dnz, *onz, *dnzu, *onzu, bsLocal; if (bs < 0) { if (isBlock || isSeqBlock || isMPIBlock || isSymBlock || isSymSeqBlock || isSymMPIBlock) { PetscInt pStart, pEnd, p, dof; ierr = PetscSectionGetChart(sectionGlobal, &pStart, &pEnd);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { ierr = PetscSectionGetDof(sectionGlobal, p, &dof);CHKERRQ(ierr); if (dof) { bs = dof; break; } } } else { bs = 1; } /* Must have same blocksize on all procs (some might have no points) */ bsLocal = bs; ierr = MPI_Allreduce(&bsLocal, &bs, 1, MPIU_INT, MPI_MAX, ((PetscObject) dm)->comm);CHKERRQ(ierr); } ierr = PetscMalloc4(localSize/bs, PetscInt, &dnz, localSize/bs, PetscInt, &onz, localSize/bs, PetscInt, &dnzu, localSize/bs, PetscInt, &onzu);CHKERRQ(ierr); ierr = PetscMemzero(dnz, localSize/bs * sizeof(PetscInt));CHKERRQ(ierr); ierr = PetscMemzero(onz, localSize/bs * sizeof(PetscInt));CHKERRQ(ierr); ierr = PetscMemzero(dnzu, localSize/bs * sizeof(PetscInt));CHKERRQ(ierr); ierr = PetscMemzero(onzu, localSize/bs * sizeof(PetscInt));CHKERRQ(ierr); ierr = DMPlexPreallocateOperator(dm, bs, section, sectionGlobal, dnz, onz, dnzu, onzu, *J, fillMatrix);CHKERRQ(ierr); ierr = PetscFree4(dnz, onz, dnzu, onzu);CHKERRQ(ierr); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetDimension" /*@ DMPlexGetDimension - Return the topological mesh dimension Not collective Input Parameter: . mesh - The DMPlex Output Parameter: . dim - The topological mesh dimension Level: beginner .seealso: DMPlexCreate() @*/ PetscErrorCode DMPlexGetDimension(DM dm, PetscInt *dim) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(dim, 2); *dim = mesh->dim; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSetDimension" /*@ DMPlexSetDimension - Set the topological mesh dimension Collective on mesh Input Parameters: + mesh - The DMPlex - dim - The topological mesh dimension Level: beginner .seealso: DMPlexCreate() @*/ PetscErrorCode DMPlexSetDimension(DM dm, PetscInt dim) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidLogicalCollectiveInt(dm, dim, 2); mesh->dim = dim; mesh->preallocCenterDim = dim; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetChart" /*@ DMPlexGetChart - Return the interval for all mesh points [pStart, pEnd) Not collective Input Parameter: . mesh - The DMPlex Output Parameters: + pStart - The first mesh point - pEnd - The upper bound for mesh points Level: beginner .seealso: DMPlexCreate(), DMPlexSetChart() @*/ PetscErrorCode DMPlexGetChart(DM dm, PetscInt *pStart, PetscInt *pEnd) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = PetscSectionGetChart(mesh->coneSection, pStart, pEnd);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSetChart" /*@ DMPlexSetChart - Set the interval for all mesh points [pStart, pEnd) Not collective Input Parameters: + mesh - The DMPlex . pStart - The first mesh point - pEnd - The upper bound for mesh points Output Parameters: Level: beginner .seealso: DMPlexCreate(), DMPlexGetChart() @*/ PetscErrorCode DMPlexSetChart(DM dm, PetscInt pStart, PetscInt pEnd) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = PetscSectionSetChart(mesh->coneSection, pStart, pEnd);CHKERRQ(ierr); ierr = PetscSectionSetChart(mesh->supportSection, pStart, pEnd);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetConeSize" /*@ DMPlexGetConeSize - Return the number of in-edges for this point in the Sieve DAG Not collective Input Parameters: + mesh - The DMPlex - p - The Sieve point, which must lie in the chart set with DMPlexSetChart() Output Parameter: . size - The cone size for point p Level: beginner .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexSetChart() @*/ PetscErrorCode DMPlexGetConeSize(DM dm, PetscInt p, PetscInt *size) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(size, 3); ierr = PetscSectionGetDof(mesh->coneSection, p, size);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSetConeSize" /*@ DMPlexSetConeSize - Set the number of in-edges for this point in the Sieve DAG Not collective Input Parameters: + mesh - The DMPlex . p - The Sieve point, which must lie in the chart set with DMPlexSetChart() - size - The cone size for point p Output Parameter: Note: This should be called after DMPlexSetChart(). Level: beginner .seealso: DMPlexCreate(), DMPlexGetConeSize(), DMPlexSetChart() @*/ PetscErrorCode DMPlexSetConeSize(DM dm, PetscInt p, PetscInt size) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = PetscSectionSetDof(mesh->coneSection, p, size);CHKERRQ(ierr); mesh->maxConeSize = PetscMax(mesh->maxConeSize, size); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetCone" /*@C DMPlexGetCone - Return the points on the in-edges for this point in the Sieve DAG Not collective Input Parameters: + mesh - The DMPlex - p - The Sieve point, which must lie in the chart set with DMPlexSetChart() Output Parameter: . cone - An array of points which are on the in-edges for point p Level: beginner Note: This routine is not available in Fortran. .seealso: DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart() @*/ PetscErrorCode DMPlexGetCone(DM dm, PetscInt p, const PetscInt *cone[]) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt off; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(cone, 3); ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); *cone = &mesh->cones[off]; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSetCone" /*@ DMPlexSetCone - Set the points on the in-edges for this point in the Sieve DAG Not collective Input Parameters: + mesh - The DMPlex . p - The Sieve point, which must lie in the chart set with DMPlexSetChart() - cone - An array of points which are on the in-edges for point p Output Parameter: Note: This should be called after all calls to DMPlexSetConeSize() and DMSetUp(). Level: beginner .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp() @*/ PetscErrorCode DMPlexSetCone(DM dm, PetscInt p, const PetscInt cone[]) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt pStart, pEnd; PetscInt dof, off, c; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); if (dof) PetscValidPointer(cone, 3); ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); if ((p < pStart) || (p >= pEnd)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd); for (c = 0; c < dof; ++c) { if ((cone[c] < pStart) || (cone[c] >= pEnd)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone point %D is not in the valid range [%D, %D)", cone[c], pStart, pEnd); mesh->cones[off+c] = cone[c]; } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetConeOrientation" /*@C DMPlexGetConeOrientation - Return the orientations on the in-edges for this point in the Sieve DAG Not collective Input Parameters: + mesh - The DMPlex - p - The Sieve point, which must lie in the chart set with DMPlexSetChart() Output Parameter: . coneOrientation - An array of orientations which are on the in-edges for point p. An orientation is an integer giving the prescription for cone traversal. If it is negative, the cone is traversed in the opposite direction. Its value 'o', or if negative '-(o+1)', gives the index of the cone point on which to start. Level: beginner Note: This routine is not available in Fortran. .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetCone(), DMPlexSetChart() @*/ PetscErrorCode DMPlexGetConeOrientation(DM dm, PetscInt p, const PetscInt *coneOrientation[]) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt off; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); #if defined(PETSC_USE_DEBUG) { PetscInt dof; ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); if (dof) PetscValidPointer(coneOrientation, 3); } #endif ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); *coneOrientation = &mesh->coneOrientations[off]; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSetConeOrientation" /*@ DMPlexSetConeOrientation - Set the orientations on the in-edges for this point in the Sieve DAG Not collective Input Parameters: + mesh - The DMPlex . p - The Sieve point, which must lie in the chart set with DMPlexSetChart() - coneOrientation - An array of orientations which are on the in-edges for point p. An orientation is an integer giving the prescription for cone traversal. If it is negative, the cone is traversed in the opposite direction. Its value 'o', or if negative '-(o+1)', gives the index of the cone point on which to start. Output Parameter: Note: This should be called after all calls to DMPlexSetConeSize() and DMSetUp(). Level: beginner .seealso: DMPlexCreate(), DMPlexGetConeOrientation(), DMPlexSetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp() @*/ PetscErrorCode DMPlexSetConeOrientation(DM dm, PetscInt p, const PetscInt coneOrientation[]) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt pStart, pEnd; PetscInt dof, off, c; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); if (dof) PetscValidPointer(coneOrientation, 3); ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); if ((p < pStart) || (p >= pEnd)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd); for (c = 0; c < dof; ++c) { PetscInt cdof, o = coneOrientation[c]; ierr = PetscSectionGetDof(mesh->coneSection, mesh->cones[off+c], &cdof);CHKERRQ(ierr); if (o && ((o < -(cdof+1)) || (o >= cdof))) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone orientation %D is not in the valid range [%D. %D)", o, -(cdof+1), cdof); mesh->coneOrientations[off+c] = o; } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexInsertCone" PetscErrorCode DMPlexInsertCone(DM dm, PetscInt p, PetscInt conePos, PetscInt conePoint) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt pStart, pEnd; PetscInt dof, off; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); if ((p < pStart) || (p >= pEnd)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd); if ((conePoint < pStart) || (conePoint >= pEnd)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone point %D is not in the valid range [%D, %D)", conePoint, pStart, pEnd); if (conePos >= dof) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone position %D of point %D is not in the valid range [0, %D)", conePos, p, dof); mesh->cones[off+conePos] = conePoint; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetSupportSize" /*@ DMPlexGetSupportSize - Return the number of out-edges for this point in the Sieve DAG Not collective Input Parameters: + mesh - The DMPlex - p - The Sieve point, which must lie in the chart set with DMPlexSetChart() Output Parameter: . size - The support size for point p Level: beginner .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexSetChart(), DMPlexGetConeSize() @*/ PetscErrorCode DMPlexGetSupportSize(DM dm, PetscInt p, PetscInt *size) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(size, 3); ierr = PetscSectionGetDof(mesh->supportSection, p, size);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSetSupportSize" /*@ DMPlexSetSupportSize - Set the number of out-edges for this point in the Sieve DAG Not collective Input Parameters: + mesh - The DMPlex . p - The Sieve point, which must lie in the chart set with DMPlexSetChart() - size - The support size for point p Output Parameter: Note: This should be called after DMPlexSetChart(). Level: beginner .seealso: DMPlexCreate(), DMPlexGetSupportSize(), DMPlexSetChart() @*/ PetscErrorCode DMPlexSetSupportSize(DM dm, PetscInt p, PetscInt size) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = PetscSectionSetDof(mesh->supportSection, p, size);CHKERRQ(ierr); mesh->maxSupportSize = PetscMax(mesh->maxSupportSize, size); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetSupport" /*@C DMPlexGetSupport - Return the points on the out-edges for this point in the Sieve DAG Not collective Input Parameters: + mesh - The DMPlex - p - The Sieve point, which must lie in the chart set with DMPlexSetChart() Output Parameter: . support - An array of points which are on the out-edges for point p Level: beginner .seealso: DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone() @*/ PetscErrorCode DMPlexGetSupport(DM dm, PetscInt p, const PetscInt *support[]) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt off; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(support, 3); ierr = PetscSectionGetOffset(mesh->supportSection, p, &off);CHKERRQ(ierr); *support = &mesh->supports[off]; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSetSupport" /*@ DMPlexSetSupport - Set the points on the out-edges for this point in the Sieve DAG Not collective Input Parameters: + mesh - The DMPlex . p - The Sieve point, which must lie in the chart set with DMPlexSetChart() - support - An array of points which are on the in-edges for point p Output Parameter: Note: This should be called after all calls to DMPlexSetSupportSize() and DMSetUp(). Level: beginner .seealso: DMPlexCreate(), DMPlexGetSupport(), DMPlexSetChart(), DMPlexSetSupportSize(), DMSetUp() @*/ PetscErrorCode DMPlexSetSupport(DM dm, PetscInt p, const PetscInt support[]) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt pStart, pEnd; PetscInt dof, off, c; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = PetscSectionGetChart(mesh->supportSection, &pStart, &pEnd);CHKERRQ(ierr); ierr = PetscSectionGetDof(mesh->supportSection, p, &dof);CHKERRQ(ierr); if (dof) PetscValidPointer(support, 3); ierr = PetscSectionGetOffset(mesh->supportSection, p, &off);CHKERRQ(ierr); if ((p < pStart) || (p >= pEnd)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd); for (c = 0; c < dof; ++c) { if ((support[c] < pStart) || (support[c] >= pEnd)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Support point %D is not in the valid range [%D, %D)", support[c], pStart, pEnd); mesh->supports[off+c] = support[c]; } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexInsertSupport" PetscErrorCode DMPlexInsertSupport(DM dm, PetscInt p, PetscInt supportPos, PetscInt supportPoint) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt pStart, pEnd; PetscInt dof, off; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = PetscSectionGetChart(mesh->supportSection, &pStart, &pEnd);CHKERRQ(ierr); ierr = PetscSectionGetDof(mesh->supportSection, p, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(mesh->supportSection, p, &off);CHKERRQ(ierr); if ((p < pStart) || (p >= pEnd)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd); if ((supportPoint < pStart) || (supportPoint >= pEnd)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Support point %D is not in the valid range [%D, %D)", supportPoint, pStart, pEnd); if (supportPos >= dof) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Support position %D of point %D is not in the valid range [0, %D)", supportPos, p, dof); mesh->supports[off+supportPos] = supportPoint; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetTransitiveClosure" /*@C DMPlexGetTransitiveClosure - Return the points on the transitive closure of the in-edges or out-edges for this point in the Sieve DAG Not collective Input Parameters: + mesh - The DMPlex . p - The Sieve point, which must lie in the chart set with DMPlexSetChart() . useCone - PETSC_TRUE for in-edges, otherwise use out-edges - points - If points is PETSC_NULL on input, internal storage will be returned, otherwise the provided array is used Output Parameters: + numPoints - The number of points in the closure, so points[] is of size 2*numPoints - points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...] Note: If using internal storage (points is PETSC_NULL on input), each call overwrites the last output. Level: beginner .seealso: DMPlexRestoreTransitiveClosure(), DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone() @*/ PetscErrorCode DMPlexGetTransitiveClosure(DM dm, PetscInt p, PetscBool useCone, PetscInt *numPoints, PetscInt *points[]) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt *closure, *fifo; const PetscInt *tmp = PETSC_NULL, *tmpO = PETSC_NULL; PetscInt tmpSize, t; PetscInt depth = 0, maxSize; PetscInt closureSize = 2, fifoSize = 0, fifoStart = 0; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); maxSize = (PetscInt) (2*PetscMax(PetscMax(pow((PetscReal) mesh->maxConeSize, depth)+1, pow((PetscReal) mesh->maxSupportSize, depth)+1), depth+1)); ierr = DMGetWorkArray(dm, maxSize, PETSC_INT, &fifo);CHKERRQ(ierr); if (*points) { closure = *points; } else { ierr = DMGetWorkArray(dm, maxSize, PETSC_INT, &closure);CHKERRQ(ierr); } closure[0] = p; closure[1] = 0; /* This is only 1-level */ if (useCone) { ierr = DMPlexGetConeSize(dm, p, &tmpSize);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, p, &tmp);CHKERRQ(ierr); ierr = DMPlexGetConeOrientation(dm, p, &tmpO);CHKERRQ(ierr); } else { ierr = DMPlexGetSupportSize(dm, p, &tmpSize);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, p, &tmp);CHKERRQ(ierr); } for (t = 0; t < tmpSize; ++t, closureSize += 2, fifoSize += 2) { const PetscInt cp = tmp[t]; const PetscInt co = tmpO ? tmpO[t] : 0; closure[closureSize] = cp; closure[closureSize+1] = co; fifo[fifoSize] = cp; fifo[fifoSize+1] = co; } while(fifoSize - fifoStart) { const PetscInt q = fifo[fifoStart]; const PetscInt o = fifo[fifoStart+1]; const PetscInt rev = o >= 0 ? 0 : 1; const PetscInt off = rev ? -(o+1) : o; if (useCone) { ierr = DMPlexGetConeSize(dm, q, &tmpSize);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, q, &tmp);CHKERRQ(ierr); ierr = DMPlexGetConeOrientation(dm, q, &tmpO);CHKERRQ(ierr); } else { ierr = DMPlexGetSupportSize(dm, q, &tmpSize);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, q, &tmp);CHKERRQ(ierr); tmpO = PETSC_NULL; } for (t = 0; t < tmpSize; ++t) { const PetscInt i = ((rev ? tmpSize-t : t) + off)%tmpSize; const PetscInt cp = tmp[i]; /* Must propogate orientation */ const PetscInt co = tmpO ? (rev ? -(tmpO[i]+1) : tmpO[i]) : 0; PetscInt c; /* Check for duplicate */ for (c = 0; c < closureSize; c += 2) { if (closure[c] == cp) break; } if (c == closureSize) { closure[closureSize] = cp; closure[closureSize+1] = co; fifo[fifoSize] = cp; fifo[fifoSize+1] = co; closureSize += 2; fifoSize += 2; } } fifoStart += 2; } if (numPoints) *numPoints = closureSize/2; if (points) *points = closure; ierr = DMRestoreWorkArray(dm, maxSize, PETSC_INT, &fifo);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexRestoreTransitiveClosure" /*@C DMPlexRestoreTransitiveClosure - Restore the array of points on the transitive closure of the in-edges or out-edges for this point in the Sieve DAG Not collective Input Parameters: + mesh - The DMPlex . p - The Sieve point, which must lie in the chart set with DMPlexSetChart() . useCone - PETSC_TRUE for in-edges, otherwise use out-edges - points - If points is PETSC_NULL on input, internal storage will be returned, otherwise the provided array is used Output Parameters: + numPoints - The number of points in the closure, so points[] is of size 2*numPoints - points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...] Note: If not using internal storage (points is not PETSC_NULL on input), this call is unnecessary Level: beginner .seealso: DMPlexGetTransitiveClosure(), DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone() @*/ PetscErrorCode DMPlexRestoreTransitiveClosure(DM dm, PetscInt p, PetscBool useCone, PetscInt *numPoints, PetscInt *points[]) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = DMRestoreWorkArray(dm, 0, PETSC_INT, points);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetFaces" /* DMPlexGetFaces - Note: This will only work for cell-vertex meshes. */ PetscErrorCode DMPlexGetFaces(DM dm, PetscInt p, PetscInt *numFaces, PetscInt *faceSize, const PetscInt *faces[]) { DM_Plex *mesh = (DM_Plex *) dm->data; const PetscInt *cone = PETSC_NULL; PetscInt depth = 0, dim, coneSize; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); if (depth > 1) SETERRQ(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Faces can only be returned for cell-vertex meshes."); if (!mesh->facesTmp) {ierr = PetscMalloc(PetscSqr(PetscMax(mesh->maxConeSize, mesh->maxSupportSize)) * sizeof(PetscInt), &mesh->facesTmp);CHKERRQ(ierr);} ierr = DMPlexGetConeSize(dm, p, &coneSize);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, p, &cone);CHKERRQ(ierr); switch(dim) { case 2: switch(coneSize) { case 3: mesh->facesTmp[0] = cone[0]; mesh->facesTmp[1] = cone[1]; mesh->facesTmp[2] = cone[1]; mesh->facesTmp[3] = cone[2]; mesh->facesTmp[4] = cone[2]; mesh->facesTmp[5] = cone[0]; *numFaces = 3; *faceSize = 2; *faces = mesh->facesTmp; break; case 4: mesh->facesTmp[0] = cone[0]; mesh->facesTmp[1] = cone[1]; mesh->facesTmp[2] = cone[1]; mesh->facesTmp[3] = cone[2]; mesh->facesTmp[4] = cone[2]; mesh->facesTmp[5] = cone[3]; mesh->facesTmp[6] = cone[3]; mesh->facesTmp[7] = cone[0]; *numFaces = 4; *faceSize = 2; *faces = mesh->facesTmp; break; default: SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone size %D not supported for dimension %D", coneSize, dim); } break; case 3: switch(coneSize) { case 3: mesh->facesTmp[0] = cone[0]; mesh->facesTmp[1] = cone[1]; mesh->facesTmp[2] = cone[1]; mesh->facesTmp[3] = cone[2]; mesh->facesTmp[4] = cone[2]; mesh->facesTmp[5] = cone[0]; *numFaces = 3; *faceSize = 2; *faces = mesh->facesTmp; break; case 4: mesh->facesTmp[0] = cone[0]; mesh->facesTmp[1] = cone[1]; mesh->facesTmp[2] = cone[2]; mesh->facesTmp[3] = cone[0]; mesh->facesTmp[4] = cone[2]; mesh->facesTmp[5] = cone[3]; mesh->facesTmp[6] = cone[0]; mesh->facesTmp[7] = cone[3]; mesh->facesTmp[8] = cone[1]; mesh->facesTmp[9] = cone[1]; mesh->facesTmp[10] = cone[3]; mesh->facesTmp[11] = cone[2]; *numFaces = 4; *faceSize = 3; *faces = mesh->facesTmp; break; default: SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone size %D not supported for dimension %D", coneSize, dim); } break; default: SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Dimension %D not supported", dim); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetMaxSizes" /*@ DMPlexGetMaxSizes - Return the maximum number of in-edges (cone) and out-edges (support) for any point in the Sieve DAG Not collective Input Parameter: . mesh - The DMPlex Output Parameters: + maxConeSize - The maximum number of in-edges - maxSupportSize - The maximum number of out-edges Level: beginner .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexSetChart() @*/ PetscErrorCode DMPlexGetMaxSizes(DM dm, PetscInt *maxConeSize, PetscInt *maxSupportSize) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); if (maxConeSize) *maxConeSize = mesh->maxConeSize; if (maxSupportSize) *maxSupportSize = mesh->maxSupportSize; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMSetUp_Plex" PetscErrorCode DMSetUp_Plex(DM dm) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt size; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = PetscSectionSetUp(mesh->coneSection);CHKERRQ(ierr); ierr = PetscSectionGetStorageSize(mesh->coneSection, &size);CHKERRQ(ierr); ierr = PetscMalloc(size * sizeof(PetscInt), &mesh->cones);CHKERRQ(ierr); ierr = PetscMalloc(size * sizeof(PetscInt), &mesh->coneOrientations);CHKERRQ(ierr); ierr = PetscMemzero(mesh->coneOrientations, size * sizeof(PetscInt));CHKERRQ(ierr); if (mesh->maxSupportSize) { ierr = PetscSectionSetUp(mesh->supportSection);CHKERRQ(ierr); ierr = PetscSectionGetStorageSize(mesh->supportSection, &size);CHKERRQ(ierr); ierr = PetscMalloc(size * sizeof(PetscInt), &mesh->supports);CHKERRQ(ierr); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMCreateSubDM_Plex" PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm) { PetscSection section, sectionGlobal; PetscInt *subIndices; PetscInt subSize = 0, subOff = 0, nF, f, pStart, pEnd, p; PetscErrorCode ierr; PetscFunctionBegin; if (!numFields) PetscFunctionReturn(0); ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); ierr = DMGetDefaultGlobalSection(dm, §ionGlobal);CHKERRQ(ierr); if (!section) SETERRQ(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONG, "Must set default section for DMPlex before splitting fields"); if (!sectionGlobal) SETERRQ(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONG, "Must set default global section for DMPlex before splitting fields"); ierr = PetscSectionGetNumFields(section, &nF);CHKERRQ(ierr); if (numFields > nF) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONG, "Number of requested fields %d greater than number of DM fields %d", numFields, nF); ierr = PetscSectionGetChart(sectionGlobal, &pStart, &pEnd);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { PetscInt gdof; ierr = PetscSectionGetDof(sectionGlobal, p, &gdof);CHKERRQ(ierr); if (gdof > 0) { for (f = 0; f < numFields; ++f) { PetscInt fdof, fcdof; ierr = PetscSectionGetFieldDof(section, p, fields[f], &fdof);CHKERRQ(ierr); ierr = PetscSectionGetFieldConstraintDof(section, p, fields[f], &fcdof);CHKERRQ(ierr); subSize += fdof-fcdof; } } } ierr = PetscMalloc(subSize * sizeof(PetscInt), &subIndices);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { PetscInt gdof, goff; ierr = PetscSectionGetDof(sectionGlobal, p, &gdof);CHKERRQ(ierr); if (gdof > 0) { ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr); for (f = 0; f < numFields; ++f) { PetscInt fdof, fcdof, fc, f2, poff = 0; /* Can get rid of this loop by storing field information in the global section */ for (f2 = 0; f2 < fields[f]; ++f2) { ierr = PetscSectionGetFieldDof(section, p, f2, &fdof);CHKERRQ(ierr); ierr = PetscSectionGetFieldConstraintDof(section, p, f2, &fcdof);CHKERRQ(ierr); poff += fdof-fcdof; } ierr = PetscSectionGetFieldDof(section, p, fields[f], &fdof);CHKERRQ(ierr); ierr = PetscSectionGetFieldConstraintDof(section, p, fields[f], &fcdof);CHKERRQ(ierr); for (fc = 0; fc < fdof-fcdof; ++fc, ++subOff) { subIndices[subOff] = goff+poff+fc; } } } } if (is) {ierr = ISCreateGeneral(((PetscObject) dm)->comm, subSize, subIndices, PETSC_OWN_POINTER, is);CHKERRQ(ierr);} if (subdm) { PetscSection subsection; PetscBool haveNull = PETSC_FALSE; PetscInt f, nf = 0; ierr = DMPlexClone(dm, subdm);CHKERRQ(ierr); ierr = PetscSectionCreateSubsection(section, numFields, fields, &subsection);CHKERRQ(ierr); ierr = DMSetDefaultSection(*subdm, subsection);CHKERRQ(ierr); for (f = 0; f < numFields; ++f) { (*subdm)->nullspaceConstructors[f] = dm->nullspaceConstructors[fields[f]]; if ((*subdm)->nullspaceConstructors[f]) { haveNull = PETSC_TRUE; nf = f; } } if (haveNull) { MatNullSpace nullSpace; ierr = (*(*subdm)->nullspaceConstructors[nf])(*subdm, nf, &nullSpace);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) *is, "nullspace", (PetscObject) nullSpace);CHKERRQ(ierr); ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr); } if (dm->fields) { if (nF != dm->numFields) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONG, "The number of DM fields %d does not match the number of Section fields %d", dm->numFields, nF); ierr = DMSetNumFields(*subdm, numFields);CHKERRQ(ierr); for (f = 0; f < numFields; ++f) { ierr = PetscObjectListDuplicate(dm->fields[fields[f]]->olist, &(*subdm)->fields[f]->olist);CHKERRQ(ierr); } if (numFields == 1) { MatNullSpace space; Mat pmat; ierr = PetscObjectQuery((*subdm)->fields[0], "nullspace", (PetscObject *) &space);CHKERRQ(ierr); if (space) {ierr = PetscObjectCompose((PetscObject) *is, "nullspace", (PetscObject) space);CHKERRQ(ierr);} ierr = PetscObjectQuery((*subdm)->fields[0], "nearnullspace", (PetscObject *) &space);CHKERRQ(ierr); if (space) {ierr = PetscObjectCompose((PetscObject) *is, "nearnullspace", (PetscObject) space);CHKERRQ(ierr);} ierr = PetscObjectQuery((*subdm)->fields[0], "pmat", (PetscObject *) &pmat);CHKERRQ(ierr); if (pmat) {ierr = PetscObjectCompose((PetscObject) *is, "pmat", (PetscObject) pmat);CHKERRQ(ierr);} } } } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSymmetrize" /*@ DMPlexSymmetrize - Creates support (out-edge) information from cone (in-edge) inoformation Not collective Input Parameter: . mesh - The DMPlex Output Parameter: Note: This should be called after all calls to DMPlexSetCone() Level: beginner .seealso: DMPlexCreate(), DMPlexSetChart(), DMPlexSetConeSize(), DMPlexSetCone() @*/ PetscErrorCode DMPlexSymmetrize(DM dm) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt *offsets; PetscInt supportSize; PetscInt pStart, pEnd, p; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); if (mesh->supports) SETERRQ(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONGSTATE, "Supports were already setup in this DMPlex"); /* Calculate support sizes */ ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { PetscInt dof, off, c; ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); for (c = off; c < off+dof; ++c) { ierr = PetscSectionAddDof(mesh->supportSection, mesh->cones[c], 1);CHKERRQ(ierr); } } for (p = pStart; p < pEnd; ++p) { PetscInt dof; ierr = PetscSectionGetDof(mesh->supportSection, p, &dof);CHKERRQ(ierr); mesh->maxSupportSize = PetscMax(mesh->maxSupportSize, dof); } ierr = PetscSectionSetUp(mesh->supportSection);CHKERRQ(ierr); /* Calculate supports */ ierr = PetscSectionGetStorageSize(mesh->supportSection, &supportSize);CHKERRQ(ierr); ierr = PetscMalloc(supportSize * sizeof(PetscInt), &mesh->supports);CHKERRQ(ierr); ierr = PetscMalloc((pEnd - pStart) * sizeof(PetscInt), &offsets);CHKERRQ(ierr); ierr = PetscMemzero(offsets, (pEnd - pStart) * sizeof(PetscInt));CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { PetscInt dof, off, c; ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); for (c = off; c < off+dof; ++c) { const PetscInt q = mesh->cones[c]; PetscInt offS; ierr = PetscSectionGetOffset(mesh->supportSection, q, &offS);CHKERRQ(ierr); mesh->supports[offS+offsets[q]] = p; ++offsets[q]; } } ierr = PetscFree(offsets);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSetDepth_Private" PetscErrorCode DMPlexSetDepth_Private(DM dm, PetscInt p, PetscInt *depth) { PetscInt d; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetLabelValue(dm, "depth", p, &d);CHKERRQ(ierr); if (d < 0) { /* We are guaranteed that the point has a cone since the depth was not yet set */ const PetscInt *cone = PETSC_NULL; PetscInt dCone; ierr = DMPlexGetCone(dm, p, &cone);CHKERRQ(ierr); ierr = DMPlexSetDepth_Private(dm, cone[0], &dCone);CHKERRQ(ierr); d = dCone+1; ierr = DMPlexSetLabelValue(dm, "depth", p, d);CHKERRQ(ierr); } *depth = d; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexStratify" /*@ DMPlexStratify - The Sieve DAG for most topologies is a graded poset (http://en.wikipedia.org/wiki/Graded_poset), and can be illustrated by Hasse Diagram (a http://en.wikipedia.org/wiki/Hasse_diagram). The strata group all points of the same grade, and this function calculates the strata. This grade can be seen as the height (or depth) of the point in the DAG. Not collective Input Parameter: . mesh - The DMPlex Output Parameter: Notes: The normal association for the point grade is element dimension (or co-dimension). For instance, all vertices would have depth 0, and all edges depth 1. Likewise, all cells heights would have height 0, and all faces height 1. This should be called after all calls to DMPlexSymmetrize() Level: beginner .seealso: DMPlexCreate(), DMPlexSymmetrize() @*/ PetscErrorCode DMPlexStratify(DM dm) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt pStart, pEnd, p; PetscInt numRoots = 0, numLeaves = 0; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = PetscLogEventBegin(DMPLEX_Stratify,dm,0,0,0);CHKERRQ(ierr); /* Calculate depth */ ierr = PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); /* Initialize roots and count leaves */ for (p = pStart; p < pEnd; ++p) { PetscInt coneSize, supportSize; ierr = DMPlexGetConeSize(dm, p, &coneSize);CHKERRQ(ierr); ierr = DMPlexGetSupportSize(dm, p, &supportSize);CHKERRQ(ierr); if (!coneSize && supportSize) { ++numRoots; ierr = DMPlexSetLabelValue(dm, "depth", p, 0);CHKERRQ(ierr); } else if (!supportSize && coneSize) { ++numLeaves; } else if (!supportSize && !coneSize) { /* Isolated points */ ierr = DMPlexSetLabelValue(dm, "depth", p, 0);CHKERRQ(ierr); } } if (numRoots + numLeaves == (pEnd - pStart)) { for (p = pStart; p < pEnd; ++p) { PetscInt coneSize, supportSize; ierr = DMPlexGetConeSize(dm, p, &coneSize);CHKERRQ(ierr); ierr = DMPlexGetSupportSize(dm, p, &supportSize);CHKERRQ(ierr); if (!supportSize && coneSize) { ierr = DMPlexSetLabelValue(dm, "depth", p, 1);CHKERRQ(ierr); } } } else { /* This might be slow since lookup is not fast */ for (p = pStart; p < pEnd; ++p) { PetscInt depth; ierr = DMPlexSetDepth_Private(dm, p, &depth);CHKERRQ(ierr); } } ierr = PetscLogEventEnd(DMPLEX_Stratify,dm,0,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetJoin" /*@C DMPlexGetJoin - Get an array for the join of the set of points Not Collective Input Parameters: + dm - The DMPlex object . numPoints - The number of input points for the join - points - The input points Output Parameters: + numCoveredPoints - The number of points in the join - coveredPoints - The points in the join Level: intermediate Note: Currently, this is restricted to a single level join .keywords: mesh .seealso: DMPlexRestoreJoin(), DMPlexGetMeet() @*/ PetscErrorCode DMPlexGetJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt *join[2]; PetscInt joinSize, i = 0; PetscInt dof, off, p, c, m; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(points, 2); PetscValidPointer(numCoveredPoints, 3); PetscValidPointer(coveredPoints, 4); ierr = DMGetWorkArray(dm, mesh->maxSupportSize, PETSC_INT, &join[0]);CHKERRQ(ierr); ierr = DMGetWorkArray(dm, mesh->maxSupportSize, PETSC_INT, &join[1]);CHKERRQ(ierr); /* Copy in support of first point */ ierr = PetscSectionGetDof(mesh->supportSection, points[0], &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(mesh->supportSection, points[0], &off);CHKERRQ(ierr); for (joinSize = 0; joinSize < dof; ++joinSize) { join[i][joinSize] = mesh->supports[off+joinSize]; } /* Check each successive support */ for (p = 1; p < numPoints; ++p) { PetscInt newJoinSize = 0; ierr = PetscSectionGetDof(mesh->supportSection, points[p], &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(mesh->supportSection, points[p], &off);CHKERRQ(ierr); for (c = 0; c < dof; ++c) { const PetscInt point = mesh->supports[off+c]; for (m = 0; m < joinSize; ++m) { if (point == join[i][m]) { join[1-i][newJoinSize++] = point; break; } } } joinSize = newJoinSize; i = 1-i; } *numCoveredPoints = joinSize; *coveredPoints = join[i]; ierr = DMRestoreWorkArray(dm, mesh->maxSupportSize, PETSC_INT, &join[1-i]);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexRestoreJoin" /*@C DMPlexRestoreJoin - Restore an array for the join of the set of points Not Collective Input Parameters: + dm - The DMPlex object . numPoints - The number of input points for the join - points - The input points Output Parameters: + numCoveredPoints - The number of points in the join - coveredPoints - The points in the join Level: intermediate .keywords: mesh .seealso: DMPlexGetJoin(), DMPlexGetFullJoin(), DMPlexGetMeet() @*/ PetscErrorCode DMPlexRestoreJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(coveredPoints, 4); ierr = DMRestoreWorkArray(dm, 0, PETSC_INT, (void *) coveredPoints);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetFullJoin" /*@C DMPlexGetFullJoin - Get an array for the join of the set of points Not Collective Input Parameters: + dm - The DMPlex object . numPoints - The number of input points for the join - points - The input points Output Parameters: + numCoveredPoints - The number of points in the join - coveredPoints - The points in the join Level: intermediate .keywords: mesh .seealso: DMPlexGetJoin(), DMPlexRestoreJoin(), DMPlexGetMeet() @*/ PetscErrorCode DMPlexGetFullJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt *offsets, **closures; PetscInt *join[2]; PetscInt depth = 0, maxSize, joinSize = 0, i = 0; PetscInt p, d, c, m; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(points, 2); PetscValidPointer(numCoveredPoints, 3); PetscValidPointer(coveredPoints, 4); ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = PetscMalloc(numPoints * sizeof(PetscInt *), &closures);CHKERRQ(ierr); ierr = PetscMemzero(closures,numPoints*sizeof(PetscInt*));CHKERRQ(ierr); ierr = DMGetWorkArray(dm, numPoints*(depth+2), PETSC_INT, &offsets);CHKERRQ(ierr); maxSize = (PetscInt) (pow((PetscReal) mesh->maxSupportSize, depth)+1); ierr = DMGetWorkArray(dm, maxSize, PETSC_INT, &join[0]);CHKERRQ(ierr); ierr = DMGetWorkArray(dm, maxSize, PETSC_INT, &join[1]);CHKERRQ(ierr); for (p = 0; p < numPoints; ++p) { PetscInt closureSize; ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &closureSize, &closures[p]);CHKERRQ(ierr); offsets[p*(depth+2)+0] = 0; for (d = 0; d < depth+1; ++d) { PetscInt pStart, pEnd, i; ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); for (i = offsets[p*(depth+2)+d]; i < closureSize; ++i) { if ((pStart > closures[p][i*2]) || (pEnd <= closures[p][i*2])) { offsets[p*(depth+2)+d+1] = i; break; } } if (i == closureSize) offsets[p*(depth+2)+d+1] = i; } if (offsets[p*(depth+2)+depth+1] != closureSize) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Total size of closure %D should be %D", offsets[p*(depth+2)+depth+1], closureSize); } for (d = 0; d < depth+1; ++d) { PetscInt dof; /* Copy in support of first point */ dof = offsets[d+1] - offsets[d]; for (joinSize = 0; joinSize < dof; ++joinSize) { join[i][joinSize] = closures[0][(offsets[d]+joinSize)*2]; } /* Check each successive cone */ for (p = 1; p < numPoints && joinSize; ++p) { PetscInt newJoinSize = 0; dof = offsets[p*(depth+2)+d+1] - offsets[p*(depth+2)+d]; for (c = 0; c < dof; ++c) { const PetscInt point = closures[p][(offsets[p*(depth+2)+d]+c)*2]; for (m = 0; m < joinSize; ++m) { if (point == join[i][m]) { join[1-i][newJoinSize++] = point; break; } } } joinSize = newJoinSize; i = 1-i; } if (joinSize) break; } *numCoveredPoints = joinSize; *coveredPoints = join[i]; for (p = 0; p < numPoints; ++p) { ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, PETSC_NULL, &closures[p]);CHKERRQ(ierr); } ierr = PetscFree(closures);CHKERRQ(ierr); ierr = DMRestoreWorkArray(dm, numPoints*(depth+2), PETSC_INT, &offsets);CHKERRQ(ierr); ierr = DMRestoreWorkArray(dm, mesh->maxSupportSize, PETSC_INT, &join[1-i]);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetMeet" /*@C DMPlexGetMeet - Get an array for the meet of the set of points Not Collective Input Parameters: + dm - The DMPlex object . numPoints - The number of input points for the meet - points - The input points Output Parameters: + numCoveredPoints - The number of points in the meet - coveredPoints - The points in the meet Level: intermediate Note: Currently, this is restricted to a single level meet .keywords: mesh .seealso: DMPlexRestoreMeet(), DMPlexGetJoin() @*/ PetscErrorCode DMPlexGetMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveringPoints, const PetscInt **coveringPoints) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt *meet[2]; PetscInt meetSize, i = 0; PetscInt dof, off, p, c, m; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(points, 2); PetscValidPointer(numCoveringPoints, 3); PetscValidPointer(coveringPoints, 4); ierr = DMGetWorkArray(dm, mesh->maxConeSize, PETSC_INT, &meet[0]);CHKERRQ(ierr); ierr = DMGetWorkArray(dm, mesh->maxConeSize, PETSC_INT, &meet[1]);CHKERRQ(ierr); /* Copy in cone of first point */ ierr = PetscSectionGetDof(mesh->coneSection, points[0], &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(mesh->coneSection, points[0], &off);CHKERRQ(ierr); for (meetSize = 0; meetSize < dof; ++meetSize) { meet[i][meetSize] = mesh->cones[off+meetSize]; } /* Check each successive cone */ for (p = 1; p < numPoints; ++p) { PetscInt newMeetSize = 0; ierr = PetscSectionGetDof(mesh->coneSection, points[p], &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(mesh->coneSection, points[p], &off);CHKERRQ(ierr); for (c = 0; c < dof; ++c) { const PetscInt point = mesh->cones[off+c]; for (m = 0; m < meetSize; ++m) { if (point == meet[i][m]) { meet[1-i][newMeetSize++] = point; break; } } } meetSize = newMeetSize; i = 1-i; } *numCoveringPoints = meetSize; *coveringPoints = meet[i]; ierr = DMRestoreWorkArray(dm, mesh->maxConeSize, PETSC_INT, &meet[1-i]);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexRestoreMeet" /*@C DMPlexRestoreMeet - Restore an array for the meet of the set of points Not Collective Input Parameters: + dm - The DMPlex object . numPoints - The number of input points for the meet - points - The input points Output Parameters: + numCoveredPoints - The number of points in the meet - coveredPoints - The points in the meet Level: intermediate .keywords: mesh .seealso: DMPlexGetMeet(), DMPlexGetFullMeet(), DMPlexGetJoin() @*/ PetscErrorCode DMPlexRestoreMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(coveredPoints, 4); ierr = DMRestoreWorkArray(dm, 0, PETSC_INT, (void *) coveredPoints);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetFullMeet" /*@C DMPlexGetFullMeet - Get an array for the meet of the set of points Not Collective Input Parameters: + dm - The DMPlex object . numPoints - The number of input points for the meet - points - The input points Output Parameters: + numCoveredPoints - The number of points in the meet - coveredPoints - The points in the meet Level: intermediate .keywords: mesh .seealso: DMPlexGetMeet(), DMPlexRestoreMeet(), DMPlexGetJoin() @*/ PetscErrorCode DMPlexGetFullMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt *offsets, **closures; PetscInt *meet[2]; PetscInt height = 0, maxSize, meetSize = 0, i = 0; PetscInt p, h, c, m; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(points, 2); PetscValidPointer(numCoveredPoints, 3); PetscValidPointer(coveredPoints, 4); ierr = DMPlexGetDepth(dm, &height);CHKERRQ(ierr); ierr = PetscMalloc(numPoints * sizeof(PetscInt *), &closures);CHKERRQ(ierr); ierr = DMGetWorkArray(dm, numPoints*(height+2), PETSC_INT, &offsets);CHKERRQ(ierr); maxSize = (PetscInt) (pow((PetscReal) mesh->maxConeSize, height)+1); ierr = DMGetWorkArray(dm, maxSize, PETSC_INT, &meet[0]);CHKERRQ(ierr); ierr = DMGetWorkArray(dm, maxSize, PETSC_INT, &meet[1]);CHKERRQ(ierr); for (p = 0; p < numPoints; ++p) { PetscInt closureSize; ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closures[p]);CHKERRQ(ierr); offsets[p*(height+2)+0] = 0; for (h = 0; h < height+1; ++h) { PetscInt pStart, pEnd, i; ierr = DMPlexGetHeightStratum(dm, h, &pStart, &pEnd);CHKERRQ(ierr); for (i = offsets[p*(height+2)+h]; i < closureSize; ++i) { if ((pStart > closures[p][i*2]) || (pEnd <= closures[p][i*2])) { offsets[p*(height+2)+h+1] = i; break; } } if (i == closureSize) offsets[p*(height+2)+h+1] = i; } if (offsets[p*(height+2)+height+1] != closureSize) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Total size of closure %D should be %D", offsets[p*(height+2)+height+1], closureSize); } for (h = 0; h < height+1; ++h) { PetscInt dof; /* Copy in cone of first point */ dof = offsets[h+1] - offsets[h]; for (meetSize = 0; meetSize < dof; ++meetSize) { meet[i][meetSize] = closures[0][(offsets[h]+meetSize)*2]; } /* Check each successive cone */ for (p = 1; p < numPoints && meetSize; ++p) { PetscInt newMeetSize = 0; dof = offsets[p*(height+2)+h+1] - offsets[p*(height+2)+h]; for (c = 0; c < dof; ++c) { const PetscInt point = closures[p][(offsets[p*(height+2)+h]+c)*2]; for (m = 0; m < meetSize; ++m) { if (point == meet[i][m]) { meet[1-i][newMeetSize++] = point; break; } } } meetSize = newMeetSize; i = 1-i; } if (meetSize) break; } *numCoveredPoints = meetSize; *coveredPoints = meet[i]; for (p = 0; p < numPoints; ++p) { ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_TRUE, PETSC_NULL, &closures[p]);CHKERRQ(ierr); } ierr = PetscFree(closures);CHKERRQ(ierr); ierr = DMRestoreWorkArray(dm, numPoints*(height+2), PETSC_INT, &offsets);CHKERRQ(ierr); ierr = DMRestoreWorkArray(dm, mesh->maxConeSize, PETSC_INT, &meet[1-i]);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetNumFaceVertices" static PetscErrorCode DMPlexGetNumFaceVertices(DM dm, PetscInt numCorners, PetscInt *numFaceVertices) { MPI_Comm comm = ((PetscObject) dm)->comm; PetscInt cellDim; PetscErrorCode ierr; PetscFunctionBegin; PetscValidPointer(numFaceVertices,3); ierr = DMPlexGetDimension(dm, &cellDim);CHKERRQ(ierr); switch(cellDim) { case 0: *numFaceVertices = 0; break; case 1: *numFaceVertices = 1; break; case 2: switch(numCorners) { case 3: /* triangle */ *numFaceVertices = 2; /* Edge has 2 vertices */ break; case 4: /* quadrilateral */ *numFaceVertices = 2; /* Edge has 2 vertices */ break; case 6: /* quadratic triangle, tri and quad cohesive Lagrange cells */ *numFaceVertices = 3; /* Edge has 3 vertices */ break; case 9: /* quadratic quadrilateral, quadratic quad cohesive Lagrange cells */ *numFaceVertices = 3; /* Edge has 3 vertices */ break; default: SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of face corners %d for dimension %d", numCorners, cellDim); } break; case 3: switch(numCorners) { case 4: /* tetradehdron */ *numFaceVertices = 3; /* Face has 3 vertices */ break; case 6: /* tet cohesive cells */ *numFaceVertices = 4; /* Face has 4 vertices */ break; case 8: /* hexahedron */ *numFaceVertices = 4; /* Face has 4 vertices */ break; case 9: /* tet cohesive Lagrange cells */ *numFaceVertices = 6; /* Face has 6 vertices */ break; case 10: /* quadratic tetrahedron */ *numFaceVertices = 6; /* Face has 6 vertices */ break; case 12: /* hex cohesive Lagrange cells */ *numFaceVertices = 6; /* Face has 6 vertices */ break; case 18: /* quadratic tet cohesive Lagrange cells */ *numFaceVertices = 6; /* Face has 6 vertices */ break; case 27: /* quadratic hexahedron, quadratic hex cohesive Lagrange cells */ *numFaceVertices = 9; /* Face has 9 vertices */ break; default: SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of face corners %d for dimension %d", numCorners, cellDim); } break; default: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid cell dimension %d", cellDim); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexCreateNeighborCSR" PetscErrorCode DMPlexCreateNeighborCSR(DM dm, PetscInt *numVertices, PetscInt **offsets, PetscInt **adjacency) { const PetscInt maxFaceCases = 30; PetscInt numFaceCases = 0; PetscInt numFaceVertices[30]; /* maxFaceCases, C89 sucks sucks sucks */ PetscInt *off, *adj; PetscInt *neighborCells, *tmpClosure; PetscInt maxConeSize, maxSupportSize, maxClosure, maxNeighbors; PetscInt dim, depth = 0, cStart, cEnd, c, numCells, cell; PetscErrorCode ierr; PetscFunctionBegin; /* For parallel partitioning, I think you have to communicate supports */ ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); if (cEnd - cStart == 0) { if (numVertices) *numVertices = 0; if (offsets) *offsets = PETSC_NULL; if (adjacency) *adjacency = PETSC_NULL; PetscFunctionReturn(0); } numCells = cEnd - cStart; /* Setup face recognition */ { PetscInt cornersSeen[30] = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}; /* Could use PetscBT */ for (c = cStart; c < cEnd; ++c) { PetscInt corners; ierr = DMPlexGetConeSize(dm, c, &corners);CHKERRQ(ierr); if (!cornersSeen[corners]) { PetscInt nFV; if (numFaceCases >= maxFaceCases) SETERRQ(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Exceeded maximum number of face recognition cases"); cornersSeen[corners] = 1; ierr = DMPlexGetNumFaceVertices(dm, corners, &nFV);CHKERRQ(ierr); numFaceVertices[numFaceCases++] = nFV; } } } maxClosure = (PetscInt) (2*PetscMax(pow((PetscReal) maxConeSize, depth)+1, pow((PetscReal) maxSupportSize, depth)+1)); maxNeighbors = (PetscInt) (pow((PetscReal) maxConeSize, depth)*pow((PetscReal) maxSupportSize, depth)+1); ierr = PetscMalloc2(maxNeighbors,PetscInt,&neighborCells,maxClosure,PetscInt,&tmpClosure);CHKERRQ(ierr); ierr = PetscMalloc((numCells+1) * sizeof(PetscInt), &off);CHKERRQ(ierr); ierr = PetscMemzero(off, (numCells+1) * sizeof(PetscInt));CHKERRQ(ierr); /* Count neighboring cells */ for (cell = cStart; cell < cEnd; ++cell) { PetscInt numNeighbors = maxNeighbors, n; ierr = DMPlexGetAdjacencySingleLevel_Private(dm, cell, PETSC_TRUE, tmpClosure, &numNeighbors, neighborCells);CHKERRQ(ierr); /* Get meet with each cell, and check with recognizer (could optimize to check each pair only once) */ for (n = 0; n < numNeighbors; ++n) { PetscInt cellPair[2] = {cell, neighborCells[n]}; PetscBool found = depth > 1 ? PETSC_TRUE : PETSC_FALSE; PetscInt meetSize = 0; const PetscInt *meet = PETSC_NULL; if (cellPair[0] == cellPair[1]) continue; if (!found) { ierr = DMPlexGetMeet(dm, 2, cellPair, &meetSize, &meet);CHKERRQ(ierr); if (meetSize) { PetscInt f; for (f = 0; f < numFaceCases; ++f) { if (numFaceVertices[f] == meetSize) { found = PETSC_TRUE; break; } } } ierr = DMPlexRestoreMeet(dm, 2, cellPair, &meetSize, &meet);CHKERRQ(ierr); } if (found) { ++off[cell-cStart+1]; } } } /* Prefix sum */ for (cell = 1; cell <= numCells; ++cell) { off[cell] += off[cell-1]; } if (adjacency) { ierr = PetscMalloc(off[numCells] * sizeof(PetscInt), &adj);CHKERRQ(ierr); /* Get neighboring cells */ for (cell = cStart; cell < cEnd; ++cell) { PetscInt numNeighbors = maxNeighbors, n; PetscInt cellOffset = 0; ierr = DMPlexGetAdjacencySingleLevel_Private(dm, cell, PETSC_TRUE, tmpClosure, &numNeighbors, neighborCells);CHKERRQ(ierr); /* Get meet with each cell, and check with recognizer (could optimize to check each pair only once) */ for (n = 0; n < numNeighbors; ++n) { PetscInt cellPair[2] = {cell, neighborCells[n]}; PetscBool found = depth > 1 ? PETSC_TRUE : PETSC_FALSE; PetscInt meetSize = 0; const PetscInt *meet = PETSC_NULL; if (cellPair[0] == cellPair[1]) continue; if (!found) { ierr = DMPlexGetMeet(dm, 2, cellPair, &meetSize, &meet);CHKERRQ(ierr); if (meetSize) { PetscInt f; for (f = 0; f < numFaceCases; ++f) { if (numFaceVertices[f] == meetSize) { found = PETSC_TRUE; break; } } } ierr = DMPlexRestoreMeet(dm, 2, cellPair, &meetSize, &meet);CHKERRQ(ierr); } if (found) { adj[off[cell-cStart]+cellOffset] = neighborCells[n]; ++cellOffset; } } } } ierr = PetscFree2(neighborCells,tmpClosure);CHKERRQ(ierr); if (numVertices) *numVertices = numCells; if (offsets) *offsets = off; if (adjacency) *adjacency = adj; PetscFunctionReturn(0); } #ifdef PETSC_HAVE_CHACO #ifdef PETSC_HAVE_UNISTD_H #include #endif /* Chaco does not have an include file */ PETSC_EXTERN_C int interface(int nvtxs, int *start, int *adjacency, int *vwgts, float *ewgts, float *x, float *y, float *z, char *outassignname, char *outfilename, short *assignment, int architecture, int ndims_tot, int mesh_dims[3], double *goal, int global_method, int local_method, int rqi_flag, int vmax, int ndims, double eigtol, long seed); extern int FREE_GRAPH; #undef __FUNCT__ #define __FUNCT__ "DMPlexPartition_Chaco" PetscErrorCode DMPlexPartition_Chaco(DM dm, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection *partSection, IS *partition) { enum {DEFAULT_METHOD = 1, INERTIAL_METHOD = 3}; MPI_Comm comm = ((PetscObject) dm)->comm; int nvtxs = numVertices; /* number of vertices in full graph */ int *vwgts = NULL; /* weights for all vertices */ float *ewgts = NULL; /* weights for all edges */ float *x = NULL, *y = NULL, *z = NULL; /* coordinates for inertial method */ char *outassignname = NULL; /* name of assignment output file */ char *outfilename = NULL; /* output file name */ int architecture = 1; /* 0 => hypercube, d => d-dimensional mesh */ int ndims_tot = 0; /* total number of cube dimensions to divide */ int mesh_dims[3]; /* dimensions of mesh of processors */ double *goal = NULL; /* desired set sizes for each set */ int global_method = 1; /* global partitioning algorithm */ int local_method = 1; /* local partitioning algorithm */ int rqi_flag = 0; /* should I use RQI/Symmlq eigensolver? */ int vmax = 200; /* how many vertices to coarsen down to? */ int ndims = 1; /* number of eigenvectors (2^d sets) */ double eigtol = 0.001; /* tolerance on eigenvectors */ long seed = 123636512; /* for random graph mutations */ short int *assignment; /* Output partition */ int fd_stdout, fd_pipe[2]; PetscInt *points; PetscMPIInt commSize; int i, v, p; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_size(comm, &commSize);CHKERRQ(ierr); if (!numVertices) { ierr = PetscSectionCreate(comm, partSection);CHKERRQ(ierr); ierr = PetscSectionSetChart(*partSection, 0, commSize);CHKERRQ(ierr); ierr = PetscSectionSetUp(*partSection);CHKERRQ(ierr); ierr = ISCreateGeneral(comm, 0, PETSC_NULL, PETSC_OWN_POINTER, partition);CHKERRQ(ierr); PetscFunctionReturn(0); } FREE_GRAPH = 0; /* Do not let Chaco free my memory */ for (i = 0; i < start[numVertices]; ++i) { ++adjacency[i]; } if (global_method == INERTIAL_METHOD) { /* manager.createCellCoordinates(nvtxs, &x, &y, &z); */ SETERRQ(comm, PETSC_ERR_SUP, "Inertial partitioning not yet supported"); } mesh_dims[0] = commSize; mesh_dims[1] = 1; mesh_dims[2] = 1; ierr = PetscMalloc(nvtxs * sizeof(short int), &assignment);CHKERRQ(ierr); /* Chaco outputs to stdout. We redirect this to a buffer. */ /* TODO: check error codes for UNIX calls */ #ifdef PETSC_HAVE_UNISTD_H { int piperet; piperet = pipe(fd_pipe); if (piperet) SETERRQ(comm,PETSC_ERR_SYS,"Could not create pipe"); fd_stdout = dup(1); close(1); dup2(fd_pipe[1], 1); } #endif ierr = interface(nvtxs, (int *) start, (int *) adjacency, vwgts, ewgts, x, y, z, outassignname, outfilename, assignment, architecture, ndims_tot, mesh_dims, goal, global_method, local_method, rqi_flag, vmax, ndims, eigtol, seed); #ifdef PETSC_HAVE_UNISTD_H { char msgLog[10000]; int count; fflush(stdout); count = read(fd_pipe[0], msgLog, (10000-1)*sizeof(char)); if (count < 0) count = 0; msgLog[count] = 0; close(1); dup2(fd_stdout, 1); close(fd_stdout); close(fd_pipe[0]); close(fd_pipe[1]); if (ierr) SETERRQ1(comm, PETSC_ERR_LIB, "Error in Chaco library: %s", msgLog); } #endif /* Convert to PetscSection+IS */ ierr = PetscSectionCreate(comm, partSection);CHKERRQ(ierr); ierr = PetscSectionSetChart(*partSection, 0, commSize);CHKERRQ(ierr); for (v = 0; v < nvtxs; ++v) { ierr = PetscSectionAddDof(*partSection, assignment[v], 1);CHKERRQ(ierr); } ierr = PetscSectionSetUp(*partSection);CHKERRQ(ierr); ierr = PetscMalloc(nvtxs * sizeof(PetscInt), &points);CHKERRQ(ierr); for (p = 0, i = 0; p < commSize; ++p) { for (v = 0; v < nvtxs; ++v) { if (assignment[v] == p) points[i++] = v; } } if (i != nvtxs) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of points %D should be %D", i, nvtxs); ierr = ISCreateGeneral(comm, nvtxs, points, PETSC_OWN_POINTER, partition);CHKERRQ(ierr); if (global_method == INERTIAL_METHOD) { /* manager.destroyCellCoordinates(nvtxs, &x, &y, &z); */ } ierr = PetscFree(assignment);CHKERRQ(ierr); for (i = 0; i < start[numVertices]; ++i) { --adjacency[i]; } PetscFunctionReturn(0); } #endif #ifdef PETSC_HAVE_PARMETIS #undef __FUNCT__ #define __FUNCT__ "DMPlexPartition_ParMetis" PetscErrorCode DMPlexPartition_ParMetis(DM dm, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection *partSection, IS *partition) { PetscFunctionBegin; SETERRQ(((PetscObject) dm)->comm, PETSC_ERR_SUP, "ParMetis not yet supported"); PetscFunctionReturn(0); } #endif #undef __FUNCT__ #define __FUNCT__ "DMPlexEnlargePartition" /* Expand the partition by BFS on the adjacency graph */ PetscErrorCode DMPlexEnlargePartition(DM dm, const PetscInt start[], const PetscInt adjacency[], PetscSection origPartSection, IS origPartition, PetscSection *partSection, IS *partition) { PetscHashI h; const PetscInt *points; PetscInt **tmpPoints, *newPoints, totPoints = 0; PetscInt pStart, pEnd, part, q; PetscErrorCode ierr; PetscFunctionBegin; PetscHashICreate(h); ierr = PetscSectionCreate(((PetscObject) dm)->comm, partSection);CHKERRQ(ierr); ierr = PetscSectionGetChart(origPartSection, &pStart, &pEnd);CHKERRQ(ierr); ierr = PetscSectionSetChart(*partSection, pStart, pEnd);CHKERRQ(ierr); ierr = ISGetIndices(origPartition, &points);CHKERRQ(ierr); ierr = PetscMalloc((pEnd - pStart) * sizeof(PetscInt *), &tmpPoints);CHKERRQ(ierr); for(part = pStart; part < pEnd; ++part) { PetscInt numPoints, nP, numNewPoints, off, p, n = 0; PetscHashIClear(h); ierr = PetscSectionGetDof(origPartSection, part, &numPoints);CHKERRQ(ierr); ierr = PetscSectionGetOffset(origPartSection, part, &off);CHKERRQ(ierr); /* Add all existing points to h */ for(p = 0; p < numPoints; ++p) { const PetscInt point = points[off+p]; PetscHashIAdd(h, point, 1); } PetscHashISize(h, nP); if (nP != numPoints) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONG, "Invalid partition has %d points, but only %d were unique", numPoints, nP); /* Add all points in next BFS level */ /* TODO We are brute forcing here, but could check the adjacency size to find the boundary */ for(p = 0; p < numPoints; ++p) { const PetscInt point = points[off+p]; PetscInt s = start[point], e = start[point+1], a; for(a = s; a < e; ++a) { PetscHashIAdd(h, adjacency[a], 1); } } PetscHashISize(h, numNewPoints); ierr = PetscSectionSetDof(*partSection, part, numNewPoints);CHKERRQ(ierr); ierr = PetscMalloc(numNewPoints * sizeof(PetscInt), &tmpPoints[part]);CHKERRQ(ierr); if (numNewPoints) {PetscHashIGetKeys(h, n, tmpPoints[part]);} /* Should not need this conditional */ totPoints += numNewPoints; } ierr = ISRestoreIndices(origPartition, &points);CHKERRQ(ierr); PetscHashIDestroy(h); ierr = PetscSectionSetUp(*partSection);CHKERRQ(ierr); ierr = PetscMalloc(totPoints * sizeof(PetscInt), &newPoints);CHKERRQ(ierr); for(part = pStart, q = 0; part < pEnd; ++part) { PetscInt numPoints, p; ierr = PetscSectionGetDof(*partSection, part, &numPoints);CHKERRQ(ierr); for(p = 0; p < numPoints; ++p, ++q) { newPoints[q] = tmpPoints[part][p]; } ierr = PetscFree(tmpPoints[part]);CHKERRQ(ierr); } ierr = PetscFree(tmpPoints);CHKERRQ(ierr); ierr = ISCreateGeneral(((PetscObject) dm)->comm, totPoints, newPoints, PETSC_OWN_POINTER, partition);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexCreatePartition" /* DMPlexCreatePartition - Create a non-overlapping partition of the points at the given height Collective on DM Input Parameters: + dm - The DM . height - The height for points in the partition - enlarge - Expand each partition with neighbors Output Parameters: + partSection - The PetscSection giving the division of points by partition . partition - The list of points by partition . origPartSection - If enlarge is true, the PetscSection giving the division of points before enlarging by partition, otherwise PETSC_NULL - origPartition - If enlarge is true, the list of points before enlarging by partition, otherwise PETSC_NULL Level: developer .seealso DMPlexDistribute() */ PetscErrorCode DMPlexCreatePartition(DM dm, PetscInt height, PetscBool enlarge, PetscSection *partSection, IS *partition, PetscSection *origPartSection, IS *origPartition) { PetscMPIInt size; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_size(((PetscObject) dm)->comm, &size);CHKERRQ(ierr); *origPartSection = PETSC_NULL; *origPartition = PETSC_NULL; if (size == 1) { PetscInt *points; PetscInt cStart, cEnd, c; ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = PetscSectionCreate(((PetscObject) dm)->comm, partSection);CHKERRQ(ierr); ierr = PetscSectionSetChart(*partSection, 0, size);CHKERRQ(ierr); ierr = PetscSectionSetDof(*partSection, 0, cEnd-cStart);CHKERRQ(ierr); ierr = PetscSectionSetUp(*partSection);CHKERRQ(ierr); ierr = PetscMalloc((cEnd - cStart) * sizeof(PetscInt), &points);CHKERRQ(ierr); for (c = cStart; c < cEnd; ++c) { points[c] = c; } ierr = ISCreateGeneral(((PetscObject) dm)->comm, cEnd-cStart, points, PETSC_OWN_POINTER, partition);CHKERRQ(ierr); PetscFunctionReturn(0); } if (height == 0) { PetscInt numVertices; PetscInt *start = PETSC_NULL; PetscInt *adjacency = PETSC_NULL; ierr = DMPlexCreateNeighborCSR(dm, &numVertices, &start, &adjacency);CHKERRQ(ierr); if (1) { #ifdef PETSC_HAVE_CHACO ierr = DMPlexPartition_Chaco(dm, numVertices, start, adjacency, partSection, partition);CHKERRQ(ierr); #endif } else { #ifdef PETSC_HAVE_PARMETIS ierr = DMPlexPartition_ParMetis(dm, numVertices, start, adjacency, partSection, partition);CHKERRQ(ierr); #endif } if (enlarge) { *origPartSection = *partSection; *origPartition = *partition; ierr = DMPlexEnlargePartition(dm, start, adjacency, *origPartSection, *origPartition, partSection, partition);CHKERRQ(ierr); } ierr = PetscFree(start);CHKERRQ(ierr); ierr = PetscFree(adjacency);CHKERRQ(ierr); # if 0 } else if (height == 1) { /* Build the dual graph for faces and partition the hypergraph */ PetscInt numEdges; buildFaceCSRV(mesh, mesh->getFactory()->getNumbering(mesh, mesh->depth()-1), &numEdges, &start, &adjacency, GraphPartitioner::zeroBase()); GraphPartitioner().partition(numEdges, start, adjacency, partition, manager); destroyCSR(numEdges, start, adjacency); #endif } else SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid partition height %D", height); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexCreatePartitionClosure" PetscErrorCode DMPlexCreatePartitionClosure(DM dm, PetscSection pointSection, IS pointPartition, PetscSection *section, IS *partition) { /* const PetscInt height = 0; */ const PetscInt *partArray; PetscInt *allPoints, *partPoints = PETSC_NULL; PetscInt rStart, rEnd, rank, maxPartSize = 0, newSize; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscSectionGetChart(pointSection, &rStart, &rEnd);CHKERRQ(ierr); ierr = ISGetIndices(pointPartition, &partArray);CHKERRQ(ierr); ierr = PetscSectionCreate(((PetscObject) dm)->comm, section);CHKERRQ(ierr); ierr = PetscSectionSetChart(*section, rStart, rEnd);CHKERRQ(ierr); for (rank = rStart; rank < rEnd; ++rank) { PetscInt partSize = 0; PetscInt numPoints, offset, p; ierr = PetscSectionGetDof(pointSection, rank, &numPoints);CHKERRQ(ierr); ierr = PetscSectionGetOffset(pointSection, rank, &offset);CHKERRQ(ierr); for (p = 0; p < numPoints; ++p) { PetscInt point = partArray[offset+p], closureSize, c; PetscInt *closure = PETSC_NULL; /* TODO Include support for height > 0 case */ ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); /* Merge into existing points */ if (partSize+closureSize > maxPartSize) { PetscInt *tmpPoints; maxPartSize = PetscMax(partSize+closureSize, 2*maxPartSize); ierr = PetscMalloc(maxPartSize * sizeof(PetscInt), &tmpPoints);CHKERRQ(ierr); ierr = PetscMemcpy(tmpPoints, partPoints, partSize * sizeof(PetscInt));CHKERRQ(ierr); ierr = PetscFree(partPoints);CHKERRQ(ierr); partPoints = tmpPoints; } for (c = 0; c < closureSize; ++c) { partPoints[partSize+c] = closure[c*2]; } partSize += closureSize; ierr = PetscSortRemoveDupsInt(&partSize, partPoints);CHKERRQ(ierr); ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); } ierr = PetscSectionSetDof(*section, rank, partSize);CHKERRQ(ierr); } ierr = PetscSectionSetUp(*section);CHKERRQ(ierr); ierr = PetscSectionGetStorageSize(*section, &newSize);CHKERRQ(ierr); ierr = PetscMalloc(newSize * sizeof(PetscInt), &allPoints);CHKERRQ(ierr); for (rank = rStart; rank < rEnd; ++rank) { PetscInt partSize = 0, newOffset; PetscInt numPoints, offset, p; ierr = PetscSectionGetDof(pointSection, rank, &numPoints);CHKERRQ(ierr); ierr = PetscSectionGetOffset(pointSection, rank, &offset);CHKERRQ(ierr); for (p = 0; p < numPoints; ++p) { PetscInt point = partArray[offset+p], closureSize, c; PetscInt *closure = PETSC_NULL; /* TODO Include support for height > 0 case */ ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); /* Merge into existing points */ for (c = 0; c < closureSize; ++c) { partPoints[partSize+c] = closure[c*2]; } partSize += closureSize; ierr = PetscSortRemoveDupsInt(&partSize, partPoints);CHKERRQ(ierr); ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); } ierr = PetscSectionGetOffset(*section, rank, &newOffset);CHKERRQ(ierr); ierr = PetscMemcpy(&allPoints[newOffset], partPoints, partSize * sizeof(PetscInt));CHKERRQ(ierr); } ierr = ISRestoreIndices(pointPartition, &partArray);CHKERRQ(ierr); ierr = PetscFree(partPoints);CHKERRQ(ierr); ierr = ISCreateGeneral(((PetscObject) dm)->comm, newSize, allPoints, PETSC_OWN_POINTER, partition);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexDistributeField" /* Input Parameters: . originalSection , originalVec Output Parameters: . newSection . newVec */ PetscErrorCode DMPlexDistributeField(DM dm, PetscSF pointSF, PetscSection originalSection, Vec originalVec, PetscSection newSection, Vec newVec) { PetscSF fieldSF; PetscInt *remoteOffsets, fieldSize; PetscScalar *originalValues, *newValues; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr); ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr); ierr = VecSetSizes(newVec, fieldSize, PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetFromOptions(newVec);CHKERRQ(ierr); ierr = VecGetArray(originalVec, &originalValues);CHKERRQ(ierr); ierr = VecGetArray(newVec, &newValues);CHKERRQ(ierr); ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr); ierr = PetscSFBcastBegin(fieldSF, MPIU_SCALAR, originalValues, newValues);CHKERRQ(ierr); ierr = PetscSFBcastEnd(fieldSF, MPIU_SCALAR, originalValues, newValues);CHKERRQ(ierr); ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr); ierr = VecRestoreArray(newVec, &newValues);CHKERRQ(ierr); ierr = VecRestoreArray(originalVec, &originalValues);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexDistribute" /*@C DMPlexDistribute - Distributes the mesh and any associated sections. Not Collective Input Parameter: + dm - The original DMPlex object . partitioner - The partitioning package, or NULL for the default - overlap - The overlap of partitions, 0 is the default Output Parameter: . parallelMesh - The distributed DMPlex object, or PETSC_NULL Note: If the mesh was not distributed, the return value is PETSC_NULL Level: intermediate .keywords: mesh, elements .seealso: DMPlexCreate(), DMPlexDistributeByFace() @*/ PetscErrorCode DMPlexDistribute(DM dm, const char partitioner[], PetscInt overlap, DM *dmParallel) { DM_Plex *mesh = (DM_Plex *) dm->data, *pmesh; MPI_Comm comm = ((PetscObject) dm)->comm; const PetscInt height = 0; PetscInt dim, numRemoteRanks; IS origCellPart, cellPart, part; PetscSection origCellPartSection, cellPartSection, partSection; PetscSFNode *remoteRanks; PetscSF partSF, pointSF, coneSF; ISLocalToGlobalMapping renumbering; PetscSection originalConeSection, newConeSection; PetscInt *remoteOffsets; PetscInt *cones, *newCones, newConesSize; PetscBool flg; PetscMPIInt rank, numProcs, p; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(dmParallel,4); ierr = PetscLogEventBegin(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr); *dmParallel = PETSC_NULL; if (numProcs == 1) PetscFunctionReturn(0); ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); /* Create cell partition - We need to rewrite to use IS, use the MatPartition stuff */ if (overlap > 1) SETERRQ(((PetscObject) dm)->comm, PETSC_ERR_SUP, "Overlap > 1 not yet implemented"); ierr = DMPlexCreatePartition(dm, height, overlap > 0 ? PETSC_TRUE : PETSC_FALSE, &cellPartSection, &cellPart, &origCellPartSection, &origCellPart);CHKERRQ(ierr); /* Create SF assuming a serial partition for all processes: Could check for IS length here */ if (!rank) { numRemoteRanks = numProcs; } else { numRemoteRanks = 0; } ierr = PetscMalloc(numRemoteRanks * sizeof(PetscSFNode), &remoteRanks);CHKERRQ(ierr); for (p = 0; p < numRemoteRanks; ++p) { remoteRanks[p].rank = p; remoteRanks[p].index = 0; } ierr = PetscSFCreate(comm, &partSF);CHKERRQ(ierr); ierr = PetscSFSetGraph(partSF, 1, numRemoteRanks, PETSC_NULL, PETSC_OWN_POINTER, remoteRanks, PETSC_OWN_POINTER);CHKERRQ(ierr); ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr); if (flg) { ierr = PetscPrintf(comm, "Cell Partition:\n");CHKERRQ(ierr); ierr = PetscSectionView(cellPartSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = ISView(cellPart, PETSC_NULL);CHKERRQ(ierr); if (origCellPart) { ierr = PetscPrintf(comm, "Original Cell Partition:\n");CHKERRQ(ierr); ierr = PetscSectionView(origCellPartSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = ISView(origCellPart, PETSC_NULL);CHKERRQ(ierr); } ierr = PetscSFView(partSF, PETSC_NULL);CHKERRQ(ierr); } /* Close the partition over the mesh */ ierr = DMPlexCreatePartitionClosure(dm, cellPartSection, cellPart, &partSection, &part);CHKERRQ(ierr); ierr = ISDestroy(&cellPart);CHKERRQ(ierr); ierr = PetscSectionDestroy(&cellPartSection);CHKERRQ(ierr); /* Create new mesh */ ierr = DMPlexCreate(comm, dmParallel);CHKERRQ(ierr); ierr = DMPlexSetDimension(*dmParallel, dim);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) *dmParallel, "Parallel Mesh");CHKERRQ(ierr); pmesh = (DM_Plex *) (*dmParallel)->data; /* Distribute sieve points and the global point numbering (replaces creating remote bases) */ ierr = PetscSFConvertPartition(partSF, partSection, part, &renumbering, &pointSF);CHKERRQ(ierr); if (flg) { ierr = PetscPrintf(comm, "Point Partition:\n");CHKERRQ(ierr); ierr = PetscSectionView(partSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = ISView(part, PETSC_NULL);CHKERRQ(ierr); ierr = PetscSFView(pointSF, PETSC_NULL);CHKERRQ(ierr); ierr = PetscPrintf(comm, "Point Renumbering after partition:\n");CHKERRQ(ierr); ierr = ISLocalToGlobalMappingView(renumbering, PETSC_NULL);CHKERRQ(ierr); } /* Distribute cone section */ ierr = DMPlexGetConeSection(dm, &originalConeSection);CHKERRQ(ierr); ierr = DMPlexGetConeSection(*dmParallel, &newConeSection);CHKERRQ(ierr); ierr = PetscSFDistributeSection(pointSF, originalConeSection, &remoteOffsets, newConeSection);CHKERRQ(ierr); ierr = DMSetUp(*dmParallel);CHKERRQ(ierr); { PetscInt pStart, pEnd, p; ierr = PetscSectionGetChart(newConeSection, &pStart, &pEnd);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { PetscInt coneSize; ierr = PetscSectionGetDof(newConeSection, p, &coneSize);CHKERRQ(ierr); pmesh->maxConeSize = PetscMax(pmesh->maxConeSize, coneSize); } } /* Communicate and renumber cones */ ierr = PetscSFCreateSectionSF(pointSF, originalConeSection, remoteOffsets, newConeSection, &coneSF);CHKERRQ(ierr); ierr = DMPlexGetCones(dm, &cones);CHKERRQ(ierr); ierr = DMPlexGetCones(*dmParallel, &newCones);CHKERRQ(ierr); ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr); ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr); ierr = PetscSectionGetStorageSize(newConeSection, &newConesSize);CHKERRQ(ierr); ierr = ISGlobalToLocalMappingApply(renumbering, IS_GTOLM_MASK, newConesSize, newCones, PETSC_NULL, newCones);CHKERRQ(ierr); ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-cones_view", &flg);CHKERRQ(ierr); if (flg) { ierr = PetscPrintf(comm, "Serial Cone Section:\n");CHKERRQ(ierr); ierr = PetscSectionView(originalConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(comm, "Parallel Cone Section:\n");CHKERRQ(ierr); ierr = PetscSectionView(newConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscSFView(coneSF, PETSC_NULL);CHKERRQ(ierr); } ierr = DMPlexGetConeOrientations(dm, &cones);CHKERRQ(ierr); ierr = DMPlexGetConeOrientations(*dmParallel, &newCones);CHKERRQ(ierr); ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr); ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr); ierr = PetscSFDestroy(&coneSF);CHKERRQ(ierr); /* Create supports and stratify sieve */ { PetscInt pStart, pEnd; ierr = PetscSectionGetChart(pmesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); ierr = PetscSectionSetChart(pmesh->supportSection, pStart, pEnd);CHKERRQ(ierr); } ierr = DMPlexSymmetrize(*dmParallel);CHKERRQ(ierr); ierr = DMPlexStratify(*dmParallel);CHKERRQ(ierr); /* Distribute Coordinates */ { PetscSection originalCoordSection, newCoordSection; Vec originalCoordinates, newCoordinates; const char *name; ierr = DMPlexGetCoordinateSection(dm, &originalCoordSection);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(*dmParallel, &newCoordSection);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &originalCoordinates);CHKERRQ(ierr); ierr = VecCreate(comm, &newCoordinates);CHKERRQ(ierr); ierr = PetscObjectGetName((PetscObject) originalCoordinates, &name);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) newCoordinates, name);CHKERRQ(ierr); ierr = DMPlexDistributeField(dm, pointSF, originalCoordSection, originalCoordinates, newCoordSection, newCoordinates);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(*dmParallel, newCoordinates);CHKERRQ(ierr); ierr = VecDestroy(&newCoordinates);CHKERRQ(ierr); } /* Distribute labels */ { DMLabel next = mesh->labels, newNext = pmesh->labels; PetscInt numLabels = 0, l; /* Bcast number of labels */ while(next) {++numLabels; next = next->next;} ierr = MPI_Bcast(&numLabels, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); next = mesh->labels; for (l = 0; l < numLabels; ++l) { DMLabel newLabel; const PetscInt *partArray; char *name; PetscInt *stratumSizes = PETSC_NULL, *points = PETSC_NULL; PetscMPIInt *sendcnts = PETSC_NULL, *offsets = PETSC_NULL, *displs = PETSC_NULL; PetscInt nameSize, s, p; PetscBool isdepth; size_t len = 0; /* Bcast name (could filter for no points) */ if (!rank) {ierr = PetscStrlen(next->name, &len);CHKERRQ(ierr);} nameSize = len; ierr = MPI_Bcast(&nameSize, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); ierr = PetscMalloc(nameSize+1, &name);CHKERRQ(ierr); if (!rank) {ierr = PetscMemcpy(name, next->name, nameSize+1);CHKERRQ(ierr);} ierr = MPI_Bcast(name, nameSize+1, MPI_CHAR, 0, comm);CHKERRQ(ierr); ierr = PetscStrcmp(name, "depth", &isdepth);CHKERRQ(ierr); if (isdepth) {ierr = PetscFree(name);CHKERRQ(ierr); continue;} ierr = PetscNew(struct _n_DMLabel, &newLabel);CHKERRQ(ierr); newLabel->name = name; /* Bcast numStrata (could filter for no points in stratum) */ if (!rank) {newLabel->numStrata = next->numStrata;} ierr = MPI_Bcast(&newLabel->numStrata, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); ierr = PetscMalloc3(newLabel->numStrata,PetscInt,&newLabel->stratumValues, newLabel->numStrata,PetscInt,&newLabel->stratumSizes, newLabel->numStrata+1,PetscInt,&newLabel->stratumOffsets);CHKERRQ(ierr); /* Bcast stratumValues (could filter for no points in stratum) */ if (!rank) {ierr = PetscMemcpy(newLabel->stratumValues, next->stratumValues, next->numStrata * sizeof(PetscInt));CHKERRQ(ierr);} ierr = MPI_Bcast(newLabel->stratumValues, newLabel->numStrata, MPIU_INT, 0, comm);CHKERRQ(ierr); /* Find size on each process and Scatter */ if (!rank) { ierr = ISGetIndices(part, &partArray);CHKERRQ(ierr); ierr = PetscMalloc(numProcs*next->numStrata * sizeof(PetscInt), &stratumSizes);CHKERRQ(ierr); ierr = PetscMemzero(stratumSizes, numProcs*next->numStrata * sizeof(PetscInt));CHKERRQ(ierr); for (s = 0; s < next->numStrata; ++s) { for (p = next->stratumOffsets[s]; p < next->stratumOffsets[s]+next->stratumSizes[s]; ++p) { const PetscInt point = next->points[p]; PetscInt proc; for (proc = 0; proc < numProcs; ++proc) { PetscInt dof, off, pPart; ierr = PetscSectionGetDof(partSection, proc, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(partSection, proc, &off);CHKERRQ(ierr); for (pPart = off; pPart < off+dof; ++pPart) { if (partArray[pPart] == point) { ++stratumSizes[proc*next->numStrata+s]; break; } } } } } ierr = ISRestoreIndices(part, &partArray);CHKERRQ(ierr); } ierr = MPI_Scatter(stratumSizes, newLabel->numStrata, MPIU_INT, newLabel->stratumSizes, newLabel->numStrata, MPIU_INT, 0, comm);CHKERRQ(ierr); /* Calculate stratumOffsets */ newLabel->stratumOffsets[0] = 0; for (s = 0; s < newLabel->numStrata; ++s) { newLabel->stratumOffsets[s+1] = newLabel->stratumSizes[s] + newLabel->stratumOffsets[s]; } /* Pack points and Scatter */ if (!rank) { ierr = PetscMalloc3(numProcs,PetscMPIInt,&sendcnts,numProcs,PetscMPIInt,&offsets,numProcs+1,PetscMPIInt,&displs);CHKERRQ(ierr); displs[0] = 0; for (p = 0; p < numProcs; ++p) { sendcnts[p] = 0; for (s = 0; s < next->numStrata; ++s) { sendcnts[p] += stratumSizes[p*next->numStrata+s]; } offsets[p] = displs[p]; displs[p+1] = displs[p] + sendcnts[p]; } ierr = PetscMalloc(displs[numProcs] * sizeof(PetscInt), &points);CHKERRQ(ierr); for (s = 0; s < next->numStrata; ++s) { for (p = next->stratumOffsets[s]; p < next->stratumOffsets[s]+next->stratumSizes[s]; ++p) { const PetscInt point = next->points[p]; PetscInt proc; for (proc = 0; proc < numProcs; ++proc) { PetscInt dof, off, pPart; ierr = PetscSectionGetDof(partSection, proc, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(partSection, proc, &off);CHKERRQ(ierr); for (pPart = off; pPart < off+dof; ++pPart) { if (partArray[pPart] == point) { points[offsets[proc]++] = point; break; } } } } } } ierr = PetscMalloc(newLabel->stratumOffsets[newLabel->numStrata] * sizeof(PetscInt), &newLabel->points);CHKERRQ(ierr); ierr = MPI_Scatterv(points, sendcnts, displs, MPIU_INT, newLabel->points, newLabel->stratumOffsets[newLabel->numStrata], MPIU_INT, 0, comm);CHKERRQ(ierr); ierr = PetscFree(points);CHKERRQ(ierr); ierr = PetscFree3(sendcnts,offsets,displs);CHKERRQ(ierr); ierr = PetscFree(stratumSizes);CHKERRQ(ierr); /* Renumber points */ ierr = ISGlobalToLocalMappingApply(renumbering, IS_GTOLM_MASK, newLabel->stratumOffsets[newLabel->numStrata], newLabel->points, PETSC_NULL, newLabel->points);CHKERRQ(ierr); /* Sort points */ for (s = 0; s < newLabel->numStrata; ++s) { ierr = PetscSortInt(newLabel->stratumSizes[s], &newLabel->points[newLabel->stratumOffsets[s]]);CHKERRQ(ierr); } /* Insert into list */ if (newNext) { newNext->next = newLabel; } else { pmesh->labels = newLabel; } newNext = newLabel; if (!rank) {next = next->next;} } } /* Cleanup Partition */ ierr = ISLocalToGlobalMappingDestroy(&renumbering);CHKERRQ(ierr); ierr = PetscSFDestroy(&partSF);CHKERRQ(ierr); ierr = PetscSectionDestroy(&partSection);CHKERRQ(ierr); ierr = ISDestroy(&part);CHKERRQ(ierr); /* Create point SF for parallel mesh */ { const PetscInt *leaves; PetscSFNode *remotePoints, *rowners, *lowners; PetscInt numRoots, numLeaves, numGhostPoints = 0, p, gp, *ghostPoints; PetscInt pStart, pEnd; ierr = DMPlexGetChart(*dmParallel, &pStart, &pEnd);CHKERRQ(ierr); ierr = PetscSFGetGraph(pointSF, &numRoots, &numLeaves, &leaves, PETSC_NULL);CHKERRQ(ierr); ierr = PetscMalloc2(numRoots,PetscSFNode,&rowners,numLeaves,PetscSFNode,&lowners);CHKERRQ(ierr); for (p=0; p= 0) { /* Point already claimed so flag so that MAXLOC does not listen to us */ lowners[p].rank = -2; lowners[p].index = -2; } } for (p=0; psf, pEnd - pStart, numGhostPoints, ghostPoints, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); ierr = PetscSFSetFromOptions((*dmParallel)->sf);CHKERRQ(ierr); } /* Cleanup */ ierr = PetscSFDestroy(&pointSF);CHKERRQ(ierr); ierr = DMSetFromOptions(*dmParallel);CHKERRQ(ierr); ierr = PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexRenumber_Private" /* Reasons to renumber: 1) Permute points, e.g. bandwidth reduction (Renumber) a) Must not mix strata 2) Shift numbers for point insertion (Shift) a) Want operation brken into parts so that insertion can be interleaved renumbering - An IS which provides the new numbering */ PetscErrorCode DMPlexRenumber_Private(DM dm, IS renumbering) { PetscFunctionBegin; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexShiftPoint_Private" PETSC_STATIC_INLINE PetscInt DMPlexShiftPoint_Private(PetscInt p, PetscInt depth, PetscInt depthEnd[], PetscInt depthShift[]) { if (depth < 0) return p; /* Cells */ if (p < depthEnd[depth]) return p; /* Vertices */ if (p < depthEnd[0]) return p + depthShift[depth]; /* Faces */ if (p < depthEnd[depth-1]) return p + depthShift[depth] + depthShift[0]; /* Edges */ return p + depthShift[depth] + depthShift[0] + depthShift[depth-1]; } #undef __FUNCT__ #define __FUNCT__ "DMPlexShiftSizes_Private" PetscErrorCode DMPlexShiftSizes_Private(DM dm, PetscInt depthShift[], DM dmNew) { PetscInt *depthEnd; PetscInt depth = 0, d, pStart, pEnd, p; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); if (depth < 0) PetscFunctionReturn(0); ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); /* Step 1: Expand chart */ ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); for(d = 0; d <= depth; ++d) { pEnd += depthShift[d]; ierr = DMPlexGetDepthStratum(dm, d, PETSC_NULL, &depthEnd[d]);CHKERRQ(ierr); } ierr = DMPlexSetChart(dmNew, pStart, pEnd);CHKERRQ(ierr); /* Step 2: Set cone and support sizes */ for(d = 0; d <= depth; ++d) { ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); for(p = pStart; p < pEnd; ++p) { PetscInt newp = DMPlexShiftPoint_Private(p, depth, depthEnd, depthShift); PetscInt size; ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr); ierr = DMPlexSetConeSize(dmNew, newp, size);CHKERRQ(ierr); ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr); ierr = DMPlexSetSupportSize(dmNew, newp, size);CHKERRQ(ierr); } } ierr = PetscFree(depthEnd);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexShiftPoints_Private" PetscErrorCode DMPlexShiftPoints_Private(DM dm, PetscInt depthShift[], DM dmNew) { PetscInt *depthEnd, *newpoints; PetscInt depth = 0, d, maxConeSize, maxSupportSize, pStart, pEnd, p; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); if (depth < 0) PetscFunctionReturn(0); ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); ierr = PetscMalloc2(depth+1,PetscInt,&depthEnd,PetscMax(maxConeSize, maxSupportSize),PetscInt,&newpoints);CHKERRQ(ierr); for(d = 0; d <= depth; ++d) { ierr = DMPlexGetDepthStratum(dm, d, PETSC_NULL, &depthEnd[d]);CHKERRQ(ierr); } /* Step 5: Set cones and supports */ ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); for(p = pStart; p < pEnd; ++p) { const PetscInt *points = PETSC_NULL, *orientations = PETSC_NULL; PetscInt size, i, newp = DMPlexShiftPoint_Private(p, depth, depthEnd, depthShift); ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, p, &points);CHKERRQ(ierr); ierr = DMPlexGetConeOrientation(dm, p, &orientations);CHKERRQ(ierr); for(i = 0; i < size; ++i) { newpoints[i] = DMPlexShiftPoint_Private(points[i], depth, depthEnd, depthShift); } ierr = DMPlexSetCone(dmNew, newp, newpoints);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(dmNew, newp, orientations);CHKERRQ(ierr); ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, p, &points);CHKERRQ(ierr); for(i = 0; i < size; ++i) { newpoints[i] = DMPlexShiftPoint_Private(points[i], depth, depthEnd, depthShift); } ierr = DMPlexSetSupport(dmNew, newp, newpoints);CHKERRQ(ierr); } ierr = PetscFree2(depthEnd,newpoints);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexShiftCoordinates_Private" PetscErrorCode DMPlexShiftCoordinates_Private(DM dm, PetscInt depthShift[], DM dmNew) { PetscSection coordSection, newCoordSection; Vec coordinates; PetscInt *depthEnd; PetscInt dim, depth = 0, d, vStart, vEnd, v; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); for(d = 0; d <= depth; ++d) { ierr = DMPlexGetDepthStratum(dm, d, PETSC_NULL, &depthEnd[d]);CHKERRQ(ierr); } /* Step 8: Convert coordinates */ ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = PetscSectionCreate(((PetscObject) dm)->comm, &newCoordSection);CHKERRQ(ierr); ierr = PetscSectionSetNumFields(newCoordSection, 1);CHKERRQ(ierr); ierr = PetscSectionSetFieldComponents(newCoordSection, 0, dim);CHKERRQ(ierr); ierr = PetscSectionSetChart(newCoordSection, DMPlexShiftPoint_Private(vStart, depth, depthEnd, depthShift), DMPlexShiftPoint_Private(vEnd, depth, depthEnd, depthShift));CHKERRQ(ierr); for(v = vStart; v < vEnd; ++v) { const PetscInt newv = DMPlexShiftPoint_Private(v, depth, depthEnd, depthShift); ierr = PetscSectionSetDof(newCoordSection, newv, dim);CHKERRQ(ierr); ierr = PetscSectionSetFieldDof(newCoordSection, newv, 0, dim);CHKERRQ(ierr); } ierr = PetscSectionSetUp(newCoordSection);CHKERRQ(ierr); ierr = DMPlexSetCoordinateSection(dmNew, newCoordSection);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(dmNew, coordinates);CHKERRQ(ierr); ierr = PetscFree(depthEnd);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexShiftSF_Private" PetscErrorCode DMPlexShiftSF_Private(DM dm, PetscInt depthShift[], DM dmNew) { PetscInt *depthEnd; PetscInt depth = 0, d; PetscSF sfPoint, sfPointNew; const PetscSFNode *remotePoints; PetscSFNode *gremotePoints; const PetscInt *localPoints; PetscInt *glocalPoints, *newLocation, *newRemoteLocation; PetscInt numRoots, numLeaves, l, pStart, pEnd, totShift = 0; PetscMPIInt numProcs; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); for(d = 0; d <= depth; ++d) { totShift += depthShift[d]; ierr = DMPlexGetDepthStratum(dm, d, PETSC_NULL, &depthEnd[d]);CHKERRQ(ierr); } /* Step 9: Convert pointSF */ ierr = MPI_Comm_size(((PetscObject) dm)->comm, &numProcs);CHKERRQ(ierr); ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); ierr = DMGetPointSF(dmNew, &sfPointNew);CHKERRQ(ierr); ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); if (numRoots >= 0) { ierr = PetscMalloc2(numRoots,PetscInt,&newLocation,pEnd-pStart,PetscInt,&newRemoteLocation);CHKERRQ(ierr); for(l=0; lcomm, &rank);CHKERRQ(ierr); ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = PetscSFGetGraph(sfPoint, PETSC_NULL, &numLeaves, &leafLocal, &leafRemote);CHKERRQ(ierr); ierr = DMPlexCreateLabel(dmNew, "vtk");CHKERRQ(ierr); ierr = DMPlexCreateLabel(dmNew, "ghost");CHKERRQ(ierr); ierr = DMPlexGetLabel(dmNew, "vtk", &vtkLabel);CHKERRQ(ierr); ierr = DMPlexGetLabel(dmNew, "ghost", &ghostLabel);CHKERRQ(ierr); for(l = 0, c = cStart; l < numLeaves && c < cEnd; ++l, ++c) { for(; c < leafLocal[l] && c < cEnd; ++c) { ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); } if (leafLocal[l] >= cEnd) break; if (leafRemote[l].rank == rank) { ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); } else { ierr = DMLabelSetValue(ghostLabel, c, 2);CHKERRQ(ierr); } } for(; c < cEnd; ++c) { ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); } if (0) { ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);CHKERRQ(ierr); ierr = DMLabelView(vtkLabel, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = DMPlexGetHeightStratum(dmNew, 1, &fStart, &fEnd);CHKERRQ(ierr); for(f = fStart; f < fEnd; ++f) { PetscInt numCells; ierr = DMPlexGetSupportSize(dmNew, f, &numCells);CHKERRQ(ierr); if (numCells < 2) { ierr = DMLabelSetValue(ghostLabel, f, 1);CHKERRQ(ierr); } else { const PetscInt *cells = PETSC_NULL; PetscInt vA, vB; ierr = DMPlexGetSupport(dmNew, f, &cells);CHKERRQ(ierr); ierr = DMLabelGetValue(vtkLabel, cells[0], &vA);CHKERRQ(ierr); ierr = DMLabelGetValue(vtkLabel, cells[1], &vB);CHKERRQ(ierr); if (!vA && !vB) {ierr = DMLabelSetValue(ghostLabel, f, 1);CHKERRQ(ierr);} } } if (0) { ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);CHKERRQ(ierr); ierr = DMLabelView(ghostLabel, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexConstructGhostCells_2D" /*@C DMPlexConstructGhostCells - Construct ghost cells which connect to every boundary face Collective on dm Input Parameters: + dm - The original DM - labelName - The label specifying the boundary faces (this could be auto-generated) Output Parameters: + numGhostCells - The number of ghost cells added to the DM - dmGhosted - The new DM Level: developer .seealso: DMCreate() */ PetscErrorCode DMPlexConstructGhostCells_2D(DM dm, const char labelName[], PetscInt *numGhostCells, DM gdm) { DMLabel label; IS valueIS; const PetscInt *values; PetscInt *depthShift; PetscInt depth = 0, numFS, fs, ghostCell, cEnd, c; PetscErrorCode ierr; PetscFunctionBegin; /* Count ghost cells */ ierr = DMPlexGetLabel(dm, labelName ? labelName : "Face Sets", &label);CHKERRQ(ierr); ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); ierr = ISGetLocalSize(valueIS, &numFS);CHKERRQ(ierr); ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); *numGhostCells = 0; for(fs = 0; fs < numFS; ++fs) { PetscInt numBdFaces; ierr = DMLabelGetStratumSize(label, values[fs], &numBdFaces);CHKERRQ(ierr); *numGhostCells += numBdFaces; } ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthShift);CHKERRQ(ierr); ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); if (depth >= 0) {depthShift[depth] = *numGhostCells;} ierr = DMPlexShiftSizes_Private(dm, depthShift, gdm);CHKERRQ(ierr); /* Step 3: Set cone/support sizes for new points */ ierr = DMPlexGetHeightStratum(dm, 0, PETSC_NULL, &cEnd);CHKERRQ(ierr); for(c = cEnd; c < cEnd + *numGhostCells; ++c) { ierr = DMPlexSetConeSize(gdm, c, 1);CHKERRQ(ierr); } for(fs = 0; fs < numFS; ++fs) { IS faceIS; const PetscInt *faces; PetscInt numFaces, f; ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); for(f = 0; f < numFaces; ++f) { PetscInt size; ierr = DMPlexGetSupportSize(dm, faces[f], &size);CHKERRQ(ierr); if (size != 1) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONG, "DM has boundary face %d with %d support cells", faces[f], size); ierr = DMPlexSetSupportSize(gdm, faces[f] + *numGhostCells, 2);CHKERRQ(ierr); } ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); ierr = ISDestroy(&faceIS);CHKERRQ(ierr); } /* Step 4: Setup ghosted DM */ ierr = DMSetUp(gdm);CHKERRQ(ierr); ierr = DMPlexShiftPoints_Private(dm, depthShift, gdm);CHKERRQ(ierr); /* Step 6: Set cones and supports for new points */ ghostCell = cEnd; for(fs = 0; fs < numFS; ++fs) { IS faceIS; const PetscInt *faces; PetscInt numFaces, f; ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); for(f = 0; f < numFaces; ++f, ++ghostCell) { PetscInt newFace = faces[f] + *numGhostCells; ierr = DMPlexSetCone(gdm, ghostCell, &newFace);CHKERRQ(ierr); ierr = DMPlexInsertSupport(gdm, newFace, 1, ghostCell);CHKERRQ(ierr); } ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); ierr = ISDestroy(&faceIS);CHKERRQ(ierr); } ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); ierr = ISDestroy(&valueIS);CHKERRQ(ierr); /* Step 7: Stratify */ ierr = DMPlexStratify(gdm);CHKERRQ(ierr); ierr = DMPlexShiftCoordinates_Private(dm, depthShift, gdm);CHKERRQ(ierr); ierr = DMPlexShiftSF_Private(dm, depthShift, gdm);CHKERRQ(ierr); ierr = DMPlexShiftLabels_Private(dm, depthShift, gdm);CHKERRQ(ierr); ierr = PetscFree(depthShift);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexConstructGhostCells" /*@C DMPlexConstructGhostCells - Construct ghost cells which connect to every boundary face Collective on dm Input Parameters: + dm - The original DM - labelName - The label specifying the boundary faces (this could be auto-generated) Output Parameters: + numGhostCells - The number of ghost cells added to the DM - dmGhosted - The new DM Level: developer .seealso: DMCreate() */ PetscErrorCode DMPlexConstructGhostCells(DM dm, const char labelName[], PetscInt *numGhostCells, DM *dmGhosted) { DM gdm; PetscInt dim; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(numGhostCells, 3); PetscValidPointer(dmGhosted, 4); ierr = DMCreate(((PetscObject) dm)->comm, &gdm);CHKERRQ(ierr); ierr = DMSetType(gdm, DMPLEX);CHKERRQ(ierr); ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexSetDimension(gdm, dim);CHKERRQ(ierr); switch(dim) { case 2: ierr = DMPlexConstructGhostCells_2D(dm, labelName, numGhostCells, gdm);CHKERRQ(ierr); break; default: SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot construct ghost cells for dimension %d", dim); } ierr = DMSetFromOptions(gdm);CHKERRQ(ierr); *dmGhosted = gdm; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexInterpolate_2D" PetscErrorCode DMPlexInterpolate_2D(DM dm, DM *dmInt) { DM idm; DM_Plex *mesh; PetscHashIJ edgeTable; PetscInt *off; PetscInt dim, numCells, cStart, cEnd, c, numVertices, vStart, vEnd; PetscInt numEdges, firstEdge, edge, e; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); numCells = cEnd - cStart; numVertices = vEnd - vStart; firstEdge = numCells + numVertices; numEdges = 0 ; /* Count edges using algorithm from CreateNeighborCSR */ ierr = DMPlexCreateNeighborCSR(dm, PETSC_NULL, &off, PETSC_NULL);CHKERRQ(ierr); if (off) { PetscInt numCorners = 0; numEdges = off[numCells]/2; #if 0 /* Account for boundary edges: \sum_c 3 - neighbors = 3*numCells - totalNeighbors */ numEdges += 3*numCells - off[numCells]; #else /* Account for boundary edges: \sum_c #faces - #neighbors = \sum_c #cellVertices - #neighbors = totalCorners - totalNeighbors */ for(c = cStart; c < cEnd; ++c) { PetscInt coneSize; ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); numCorners += coneSize; } numEdges += numCorners - off[numCells]; #endif } #if 0 /* Check Euler characteristic V - E + F = 1 */ if (numVertices && (numVertices-numEdges+numCells != 1)) SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Euler characteristic of mesh is %d != 1", numVertices-numEdges+numCells); #endif /* Create interpolated mesh */ ierr = DMCreate(((PetscObject) dm)->comm, &idm);CHKERRQ(ierr); ierr = DMSetType(idm, DMPLEX);CHKERRQ(ierr); ierr = DMPlexSetDimension(idm, dim);CHKERRQ(ierr); ierr = DMPlexSetChart(idm, 0, numCells+numVertices+numEdges);CHKERRQ(ierr); for (c = 0; c < numCells; ++c) { PetscInt numCorners; ierr = DMPlexGetConeSize(dm, c, &numCorners);CHKERRQ(ierr); ierr = DMPlexSetConeSize(idm, c, numCorners);CHKERRQ(ierr); } for (e = firstEdge; e < firstEdge+numEdges; ++e) { ierr = DMPlexSetConeSize(idm, e, 2);CHKERRQ(ierr); } ierr = DMSetUp(idm);CHKERRQ(ierr); /* Get edge cones from subsets of cell vertices */ ierr = PetscHashIJCreate(&edgeTable);CHKERRQ(ierr); ierr = PetscHashIJSetMultivalued(edgeTable, PETSC_FALSE);CHKERRQ(ierr); for (c = 0, edge = firstEdge; c < numCells; ++c) { const PetscInt *cellFaces; PetscInt numCellFaces, faceSize, cf; ierr = DMPlexGetFaces(dm, c, &numCellFaces, &faceSize, &cellFaces);CHKERRQ(ierr); if (faceSize != 2) SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Triangles cannot have face of size %D", faceSize); for (cf = 0; cf < numCellFaces; ++cf) { #if 1 PetscHashIJKey key = {PetscMin(cellFaces[cf*faceSize+0], cellFaces[cf*faceSize+1]), PetscMax(cellFaces[cf*faceSize+0], cellFaces[cf*faceSize+1])}; ierr = PetscHashIJGet(edgeTable, key, &e);CHKERRQ(ierr); if (e < 0) { ierr = DMPlexSetCone(idm, edge, &cellFaces[cf*faceSize]);CHKERRQ(ierr); ierr = PetscHashIJAdd(edgeTable, key, edge);CHKERRQ(ierr); e = edge++; } #else PetscBool found = PETSC_FALSE; /* TODO Need join of vertices to check for existence of edges, which needs support (could set edge support), so just brute force for now */ for (e = firstEdge; e < edge; ++e) { const PetscInt *cone; ierr = DMPlexGetCone(idm, e, &cone);CHKERRQ(ierr); if (((cellFaces[cf*faceSize+0] == cone[0]) && (cellFaces[cf*faceSize+1] == cone[1])) || ((cellFaces[cf*faceSize+0] == cone[1]) && (cellFaces[cf*faceSize+1] == cone[0]))) { found = PETSC_TRUE; break; } } if (!found) { ierr = DMPlexSetCone(idm, edge, &cellFaces[cf*faceSize]);CHKERRQ(ierr); ++edge; } #endif ierr = DMPlexInsertCone(idm, c, cf, e);CHKERRQ(ierr); } } if (edge != firstEdge+numEdges) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Invalid number of edges %D should be %D", edge-firstEdge, numEdges); ierr = PetscHashIJDestroy(&edgeTable);CHKERRQ(ierr); ierr = PetscFree(off);CHKERRQ(ierr); ierr = DMPlexSymmetrize(idm);CHKERRQ(ierr); ierr = DMPlexStratify(idm);CHKERRQ(ierr); mesh = (DM_Plex *) (idm)->data; /* Orient edges */ for (c = 0; c < numCells; ++c) { const PetscInt *cone = PETSC_NULL, *cellFaces; PetscInt coneSize, coff, numCellFaces, faceSize, cf; ierr = DMPlexGetConeSize(idm, c, &coneSize);CHKERRQ(ierr); ierr = DMPlexGetCone(idm, c, &cone);CHKERRQ(ierr); ierr = PetscSectionGetOffset(mesh->coneSection, c, &coff);CHKERRQ(ierr); ierr = DMPlexGetFaces(dm, c, &numCellFaces, &faceSize, &cellFaces);CHKERRQ(ierr); if (coneSize != numCellFaces) SETERRQ3(((PetscObject) idm)->comm, PETSC_ERR_PLIB, "Invalid number of edges %D for cell %D should be %D", coneSize, c, numCellFaces); for (cf = 0; cf < numCellFaces; ++cf) { const PetscInt *econe = PETSC_NULL; PetscInt esize; ierr = DMPlexGetConeSize(idm, cone[cf], &esize);CHKERRQ(ierr); ierr = DMPlexGetCone(idm, cone[cf], &econe);CHKERRQ(ierr); if (esize != 2) SETERRQ2(((PetscObject) idm)->comm, PETSC_ERR_PLIB, "Invalid number of edge endpoints %D for edge %D should be 2", esize, cone[cf]); if ((cellFaces[cf*faceSize+0] == econe[0]) && (cellFaces[cf*faceSize+1] == econe[1])) { /* Correctly oriented */ mesh->coneOrientations[coff+cf] = 0; } else if ((cellFaces[cf*faceSize+0] == econe[1]) && (cellFaces[cf*faceSize+1] == econe[0])) { /* Start at index 1, and reverse orientation */ mesh->coneOrientations[coff+cf] = -(1+1); } } } *dmInt = idm; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexInterpolate_3D" PetscErrorCode DMPlexInterpolate_3D(DM dm, DM *dmInt) { DM idm, fdm; DM_Plex *mesh; PetscInt *off; const PetscInt numCorners = 4; PetscInt dim, numCells, cStart, cEnd, c, numVertices, vStart, vEnd; PetscInt numFaces, firstFace, face, f, numEdges, firstEdge, edge, e; PetscErrorCode ierr; PetscFunctionBegin; { ierr = PetscViewerPushFormat(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_ASCII_INFO_DETAIL);CHKERRQ(ierr); ierr = DMView(dm, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscViewerPopFormat(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); numCells = cEnd - cStart; numVertices = vEnd - vStart; firstFace = numCells + numVertices; numFaces = 0 ; /* Count faces using algorithm from CreateNeighborCSR */ ierr = DMPlexCreateNeighborCSR(dm, PETSC_NULL, &off, PETSC_NULL);CHKERRQ(ierr); if (off) { numFaces = off[numCells]/2; /* Account for boundary faces: \sum_c 4 - neighbors = 4*numCells - totalNeighbors */ numFaces += 4*numCells - off[numCells]; } /* Use Euler characteristic to get edges V - E + F - C = 1 */ firstEdge = firstFace + numFaces; numEdges = numVertices + numFaces - numCells - 1; /* Create interpolated mesh */ ierr = DMCreate(((PetscObject) dm)->comm, &idm);CHKERRQ(ierr); ierr = DMSetType(idm, DMPLEX);CHKERRQ(ierr); ierr = DMPlexSetDimension(idm, dim);CHKERRQ(ierr); ierr = DMPlexSetChart(idm, 0, numCells+numVertices+numFaces+numEdges);CHKERRQ(ierr); for (c = 0; c < numCells; ++c) { ierr = DMPlexSetConeSize(idm, c, numCorners);CHKERRQ(ierr); } for (f = firstFace; f < firstFace+numFaces; ++f) { ierr = DMPlexSetConeSize(idm, f, 3);CHKERRQ(ierr); } for (e = firstEdge; e < firstEdge+numEdges; ++e) { ierr = DMPlexSetConeSize(idm, e, 2);CHKERRQ(ierr); } ierr = DMSetUp(idm);CHKERRQ(ierr); /* Get face cones from subsets of cell vertices */ ierr = DMCreate(((PetscObject) dm)->comm, &fdm);CHKERRQ(ierr); ierr = DMSetType(fdm, DMPLEX);CHKERRQ(ierr); ierr = DMPlexSetDimension(fdm, dim);CHKERRQ(ierr); ierr = DMPlexSetChart(fdm, numCells, firstFace+numFaces);CHKERRQ(ierr); for (f = firstFace; f < firstFace+numFaces; ++f) { ierr = DMPlexSetConeSize(fdm, f, 3);CHKERRQ(ierr); } ierr = DMSetUp(fdm);CHKERRQ(ierr); for (c = 0, face = firstFace; c < numCells; ++c) { const PetscInt *cellFaces; PetscInt numCellFaces, faceSize, cf; ierr = DMPlexGetFaces(dm, c, &numCellFaces, &faceSize, &cellFaces);CHKERRQ(ierr); if (faceSize != 3) SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Tetrahedra cannot have face of size %D", faceSize); for (cf = 0; cf < numCellFaces; ++cf) { PetscBool found = PETSC_FALSE; /* TODO Need join of vertices to check for existence of edges, which needs support (could set edge support), so just brute force for now */ for (f = firstFace; f < face; ++f) { const PetscInt *cone = PETSC_NULL; ierr = DMPlexGetCone(idm, f, &cone);CHKERRQ(ierr); if (((cellFaces[cf*faceSize+0] == cone[0]) && (cellFaces[cf*faceSize+1] == cone[1]) && (cellFaces[cf*faceSize+2] == cone[2])) || ((cellFaces[cf*faceSize+0] == cone[1]) && (cellFaces[cf*faceSize+1] == cone[2]) && (cellFaces[cf*faceSize+2] == cone[0])) || ((cellFaces[cf*faceSize+0] == cone[2]) && (cellFaces[cf*faceSize+1] == cone[0]) && (cellFaces[cf*faceSize+2] == cone[1])) || ((cellFaces[cf*faceSize+0] == cone[0]) && (cellFaces[cf*faceSize+1] == cone[2]) && (cellFaces[cf*faceSize+2] == cone[1])) || ((cellFaces[cf*faceSize+0] == cone[2]) && (cellFaces[cf*faceSize+1] == cone[1]) && (cellFaces[cf*faceSize+2] == cone[0])) || ((cellFaces[cf*faceSize+0] == cone[1]) && (cellFaces[cf*faceSize+1] == cone[0]) && (cellFaces[cf*faceSize+2] == cone[2]))) { found = PETSC_TRUE; break; } } if (!found) { ierr = DMPlexSetCone(idm, face, &cellFaces[cf*faceSize]);CHKERRQ(ierr); /* Save the vertices for orientation calculation */ ierr = DMPlexSetCone(fdm, face, &cellFaces[cf*faceSize]);CHKERRQ(ierr); ++face; } ierr = DMPlexInsertCone(idm, c, cf, f);CHKERRQ(ierr); } } if (face != firstFace+numFaces) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Invalid number of faces %D should be %D", face-firstFace, numFaces); /* Get edge cones from subsets of face vertices */ for (f = firstFace, edge = firstEdge; f < firstFace+numFaces; ++f) { const PetscInt *cellFaces; PetscInt numCellFaces, faceSize, cf; ierr = DMPlexGetFaces(idm, f, &numCellFaces, &faceSize, &cellFaces);CHKERRQ(ierr); if (faceSize != 2) SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Triangles cannot have face of size %D", faceSize); for (cf = 0; cf < numCellFaces; ++cf) { PetscBool found = PETSC_FALSE; /* TODO Need join of vertices to check for existence of edges, which needs support (could set edge support), so just brute force for now */ for (e = firstEdge; e < edge; ++e) { const PetscInt *cone = PETSC_NULL; ierr = DMPlexGetCone(idm, e, &cone);CHKERRQ(ierr); if (((cellFaces[cf*faceSize+0] == cone[0]) && (cellFaces[cf*faceSize+1] == cone[1])) || ((cellFaces[cf*faceSize+0] == cone[1]) && (cellFaces[cf*faceSize+1] == cone[0]))) { found = PETSC_TRUE; break; } } if (!found) { ierr = DMPlexSetCone(idm, edge, &cellFaces[cf*faceSize]);CHKERRQ(ierr); ++edge; } ierr = DMPlexInsertCone(idm, f, cf, e);CHKERRQ(ierr); } } if (edge != firstEdge+numEdges) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Invalid number of edges %D should be %D", edge-firstEdge, numEdges); ierr = PetscFree(off);CHKERRQ(ierr); ierr = DMPlexSymmetrize(idm);CHKERRQ(ierr); ierr = DMPlexStratify(idm);CHKERRQ(ierr); mesh = (DM_Plex *) (idm)->data; /* Orient edges */ for (f = firstFace; f < firstFace+numFaces; ++f) { const PetscInt *cone, *cellFaces; PetscInt coneSize, coff, numCellFaces, faceSize, cf; ierr = DMPlexGetConeSize(idm, f, &coneSize);CHKERRQ(ierr); ierr = DMPlexGetCone(idm, f, &cone);CHKERRQ(ierr); ierr = PetscSectionGetOffset(mesh->coneSection, f, &coff);CHKERRQ(ierr); ierr = DMPlexGetFaces(fdm, f, &numCellFaces, &faceSize, &cellFaces);CHKERRQ(ierr); if (coneSize != numCellFaces) SETERRQ3(((PetscObject) idm)->comm, PETSC_ERR_PLIB, "Invalid number of edges %D for face %D should be %D", coneSize, f, numCellFaces); for (cf = 0; cf < numCellFaces; ++cf) { const PetscInt *econe; PetscInt esize; ierr = DMPlexGetConeSize(idm, cone[cf], &esize);CHKERRQ(ierr); ierr = DMPlexGetCone(idm, cone[cf], &econe);CHKERRQ(ierr); if (esize != 2) SETERRQ2(((PetscObject) idm)->comm, PETSC_ERR_PLIB, "Invalid number of edge endpoints %D for edge %D should be 2", esize, cone[cf]); if ((cellFaces[cf*faceSize+0] == econe[0]) && (cellFaces[cf*faceSize+1] == econe[1])) { /* Correctly oriented */ mesh->coneOrientations[coff+cf] = 0; } else if ((cellFaces[cf*faceSize+0] == econe[1]) && (cellFaces[cf*faceSize+1] == econe[0])) { /* Start at index 1, and reverse orientation */ mesh->coneOrientations[coff+cf] = -(1+1); } } } ierr = DMDestroy(&fdm);CHKERRQ(ierr); /* Orient faces */ for (c = 0; c < numCells; ++c) { const PetscInt *cone, *cellFaces; PetscInt coneSize, coff, numCellFaces, faceSize, cf; ierr = DMPlexGetConeSize(idm, c, &coneSize);CHKERRQ(ierr); ierr = DMPlexGetCone(idm, c, &cone);CHKERRQ(ierr); ierr = PetscSectionGetOffset(mesh->coneSection, c, &coff);CHKERRQ(ierr); ierr = DMPlexGetFaces(dm, c, &numCellFaces, &faceSize, &cellFaces);CHKERRQ(ierr); if (coneSize != numCellFaces) SETERRQ3(((PetscObject) idm)->comm, PETSC_ERR_PLIB, "Invalid number of edges %D for cell %D should be %D", coneSize, c, numCellFaces); for (cf = 0; cf < numCellFaces; ++cf) { PetscInt *origClosure = PETSC_NULL, *closure; PetscInt closureSize, i; ierr = DMPlexGetTransitiveClosure(idm, cone[cf], PETSC_TRUE, &closureSize, &origClosure);CHKERRQ(ierr); if (closureSize != 7) SETERRQ2(((PetscObject) idm)->comm, PETSC_ERR_PLIB, "Invalid closure size %D for face %D should be 7", closureSize, cone[cf]); for (i = 4; i < 7; ++i) { if ((origClosure[i*2] < vStart) || (origClosure[i*2] >= vEnd)) SETERRQ3(((PetscObject) idm)->comm, PETSC_ERR_PLIB, "Invalid closure point %D should be a vertex in [%D, %D)", origClosure[i*2], vStart, vEnd); } closure = &origClosure[4*2]; /* Remember that this is the orientation for edges, not vertices */ if ((cellFaces[cf*faceSize+0] == closure[0*2]) && (cellFaces[cf*faceSize+1] == closure[1*2]) && (cellFaces[cf*faceSize+2] == closure[2*2])) { /* Correctly oriented */ mesh->coneOrientations[coff+cf] = 0; } else if ((cellFaces[cf*faceSize+0] == closure[1*2]) && (cellFaces[cf*faceSize+1] == closure[2*2]) && (cellFaces[cf*faceSize+2] == closure[0*2])) { /* Shifted by 1 */ mesh->coneOrientations[coff+cf] = 1; } else if ((cellFaces[cf*faceSize+0] == closure[2*2]) && (cellFaces[cf*faceSize+1] == closure[0*2]) && (cellFaces[cf*faceSize+2] == closure[1*2])) { /* Shifted by 2 */ mesh->coneOrientations[coff+cf] = 2; } else if ((cellFaces[cf*faceSize+0] == closure[2*2]) && (cellFaces[cf*faceSize+1] == closure[1*2]) && (cellFaces[cf*faceSize+2] == closure[0*2])) { /* Start at edge 1, and reverse orientation */ mesh->coneOrientations[coff+cf] = -(1+1); } else if ((cellFaces[cf*faceSize+0] == closure[1*2]) && (cellFaces[cf*faceSize+1] == closure[0*2]) && (cellFaces[cf*faceSize+2] == closure[2*2])) { /* Start at index 0, and reverse orientation */ mesh->coneOrientations[coff+cf] = -(0+1); } else if ((cellFaces[cf*faceSize+0] == closure[0*2]) && (cellFaces[cf*faceSize+1] == closure[2*2]) && (cellFaces[cf*faceSize+2] == closure[1*2])) { /* Start at index 2, and reverse orientation */ mesh->coneOrientations[coff+cf] = -(2+1); } else SETERRQ3(((PetscObject) idm)->comm, PETSC_ERR_PLIB, "Face %D did not match local face %D in cell %D for any orientation", cone[cf], cf, c); ierr = DMPlexRestoreTransitiveClosure(idm, cone[cf], PETSC_TRUE, &closureSize, &origClosure);CHKERRQ(ierr); } } { ierr = PetscViewerPushFormat(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_ASCII_INFO_DETAIL);CHKERRQ(ierr); ierr = DMView(idm, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscViewerPopFormat(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } *dmInt = idm; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexBuildFromCellList_Private" /* This takes as input the common mesh generator output, a list of the vertices for each cell */ PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]) { PetscInt *cone, c, p; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); for (c = 0; c < numCells; ++c) { ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); } ierr = DMSetUp(dm);CHKERRQ(ierr); ierr = DMGetWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); for (c = 0; c < numCells; ++c) { for (p = 0; p < numCorners; ++p) { cone[p] = cells[c*numCorners+p]+numCells; } ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); } ierr = DMRestoreWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); ierr = DMPlexStratify(dm);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexBuildCoordinates_Private" /* This takes as input the coordinates for each vertex */ PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]) { PetscSection coordSection; Vec coordinates; PetscScalar *coords; PetscInt coordSize, v, d; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); for (v = numCells; v < numCells+numVertices; ++v) { ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); } ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); ierr = VecCreate(((PetscObject) dm)->comm, &coordinates);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); for (v = 0; v < numVertices; ++v) { for (d = 0; d < spaceDim; ++d) { coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; } } ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); ierr = VecDestroy(&coordinates);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexCreateFromCellList" /* This takes as input the common mesh generator output, a list of the vertices for each cell */ PetscErrorCode DMPlexCreateFromCellList(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, PetscBool interpolate, const int cells[], const double vertexCoords[], DM *dm) { PetscErrorCode ierr; PetscFunctionBegin; ierr = DMCreate(comm, dm);CHKERRQ(ierr); ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr); ierr = DMPlexBuildFromCellList_Private(*dm, numCells, numVertices, numCorners, cells);CHKERRQ(ierr); if (interpolate) { DM idm; switch(dim) { case 2: ierr = DMPlexInterpolate_2D(*dm, &idm);CHKERRQ(ierr);break; case 3: ierr = DMPlexInterpolate_3D(*dm, &idm);CHKERRQ(ierr);break; default: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "No mesh interpolation support for dimension %D", dim); } ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = idm; } ierr = DMPlexBuildCoordinates_Private(*dm, dim, numCells, numVertices, vertexCoords);CHKERRQ(ierr); PetscFunctionReturn(0); } #ifdef PETSC_HAVE_TRIANGLE #include #undef __FUNCT__ #define __FUNCT__ "InitInput_Triangle" PetscErrorCode InitInput_Triangle(struct triangulateio *inputCtx) { PetscFunctionBegin; inputCtx->numberofpoints = 0; inputCtx->numberofpointattributes = 0; inputCtx->pointlist = PETSC_NULL; inputCtx->pointattributelist = PETSC_NULL; inputCtx->pointmarkerlist = PETSC_NULL; inputCtx->numberofsegments = 0; inputCtx->segmentlist = PETSC_NULL; inputCtx->segmentmarkerlist = PETSC_NULL; inputCtx->numberoftriangleattributes = 0; inputCtx->trianglelist = PETSC_NULL; inputCtx->numberofholes = 0; inputCtx->holelist = PETSC_NULL; inputCtx->numberofregions = 0; inputCtx->regionlist = PETSC_NULL; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "InitOutput_Triangle" PetscErrorCode InitOutput_Triangle(struct triangulateio *outputCtx) { PetscFunctionBegin; outputCtx->numberofpoints = 0; outputCtx->pointlist = PETSC_NULL; outputCtx->pointattributelist = PETSC_NULL; outputCtx->pointmarkerlist = PETSC_NULL; outputCtx->numberoftriangles = 0; outputCtx->trianglelist = PETSC_NULL; outputCtx->triangleattributelist = PETSC_NULL; outputCtx->neighborlist = PETSC_NULL; outputCtx->segmentlist = PETSC_NULL; outputCtx->segmentmarkerlist = PETSC_NULL; outputCtx->numberofedges = 0; outputCtx->edgelist = PETSC_NULL; outputCtx->edgemarkerlist = PETSC_NULL; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "FiniOutput_Triangle" PetscErrorCode FiniOutput_Triangle(struct triangulateio *outputCtx) { PetscFunctionBegin; free(outputCtx->pointmarkerlist); free(outputCtx->edgelist); free(outputCtx->edgemarkerlist); free(outputCtx->trianglelist); free(outputCtx->neighborlist); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGenerate_Triangle" PetscErrorCode DMPlexGenerate_Triangle(DM boundary, PetscBool interpolate, DM *dm) { MPI_Comm comm = ((PetscObject) boundary)->comm; PetscInt dim = 2; const PetscBool createConvexHull = PETSC_FALSE; const PetscBool constrained = PETSC_FALSE; struct triangulateio in; struct triangulateio out; PetscInt vStart, vEnd, v, eStart, eEnd, e; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = InitInput_Triangle(&in);CHKERRQ(ierr); ierr = InitOutput_Triangle(&out);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(boundary, 0, &vStart, &vEnd);CHKERRQ(ierr); in.numberofpoints = vEnd - vStart; if (in.numberofpoints > 0) { PetscSection coordSection; Vec coordinates; PetscScalar *array; ierr = PetscMalloc(in.numberofpoints*dim * sizeof(double), &in.pointlist);CHKERRQ(ierr); ierr = PetscMalloc(in.numberofpoints * sizeof(int), &in.pointmarkerlist);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(boundary, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(boundary, &coordSection);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &array);CHKERRQ(ierr); for (v = vStart; v < vEnd; ++v) { const PetscInt idx = v - vStart; PetscInt off, d; ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); for (d = 0; d < dim; ++d) { in.pointlist[idx*dim + d] = PetscRealPart(array[off+d]); } ierr = DMPlexGetLabelValue(boundary, "marker", v, &in.pointmarkerlist[idx]);CHKERRQ(ierr); } ierr = VecRestoreArray(coordinates, &array);CHKERRQ(ierr); } ierr = DMPlexGetHeightStratum(boundary, 0, &eStart, &eEnd);CHKERRQ(ierr); in.numberofsegments = eEnd - eStart; if (in.numberofsegments > 0) { ierr = PetscMalloc(in.numberofsegments*2 * sizeof(int), &in.segmentlist);CHKERRQ(ierr); ierr = PetscMalloc(in.numberofsegments * sizeof(int), &in.segmentmarkerlist);CHKERRQ(ierr); for (e = eStart; e < eEnd; ++e) { const PetscInt idx = e - eStart; const PetscInt *cone; ierr = DMPlexGetCone(boundary, e, &cone);CHKERRQ(ierr); in.segmentlist[idx*2+0] = cone[0] - vStart; in.segmentlist[idx*2+1] = cone[1] - vStart; ierr = DMPlexGetLabelValue(boundary, "marker", e, &in.segmentmarkerlist[idx]);CHKERRQ(ierr); } } #if 0 /* Do not currently support holes */ PetscReal *holeCoords; PetscInt h, d; ierr = DMPlexGetHoles(boundary, &in.numberofholes, &holeCords);CHKERRQ(ierr); if (in.numberofholes > 0) { ierr = PetscMalloc(in.numberofholes*dim * sizeof(double), &in.holelist);CHKERRQ(ierr); for (h = 0; h < in.numberofholes; ++h) { for (d = 0; d < dim; ++d) { in.holelist[h*dim+d] = holeCoords[h*dim+d]; } } } #endif if (!rank) { char args[32]; /* Take away 'Q' for verbose output */ ierr = PetscStrcpy(args, "pqezQ");CHKERRQ(ierr); if (createConvexHull) { ierr = PetscStrcat(args, "c");CHKERRQ(ierr); } if (constrained) { ierr = PetscStrcpy(args, "zepDQ");CHKERRQ(ierr); } triangulate(args, &in, &out, PETSC_NULL); } ierr = PetscFree(in.pointlist);CHKERRQ(ierr); ierr = PetscFree(in.pointmarkerlist);CHKERRQ(ierr); ierr = PetscFree(in.segmentlist);CHKERRQ(ierr); ierr = PetscFree(in.segmentmarkerlist);CHKERRQ(ierr); ierr = PetscFree(in.holelist);CHKERRQ(ierr); { const PetscInt numCorners = 3; const PetscInt numCells = out.numberoftriangles; const PetscInt numVertices = out.numberofpoints; const int *cells = out.trianglelist; const double *meshCoords = out.pointlist; ierr = DMPlexCreateFromCellList(comm, dim, numCells, numVertices, numCorners, interpolate, cells, meshCoords, dm);CHKERRQ(ierr); /* Set labels */ for (v = 0; v < numVertices; ++v) { if (out.pointmarkerlist[v]) { ierr = DMPlexSetLabelValue(*dm, "marker", v+numCells, out.pointmarkerlist[v]);CHKERRQ(ierr); } } if (interpolate) { 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); ierr = DMPlexSetLabelValue(*dm, "marker", edges[0], out.edgemarkerlist[e]);CHKERRQ(ierr); ierr = DMPlexRestoreJoin(*dm, 2, vertices, &numEdges, &edges);CHKERRQ(ierr); } } } ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr); } #if 0 /* Do not currently support holes */ ierr = DMPlexCopyHoles(*dm, boundary);CHKERRQ(ierr); #endif ierr = FiniOutput_Triangle(&out);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexRefine_Triangle" PetscErrorCode DMPlexRefine_Triangle(DM dm, double *maxVolumes, DM *dmRefined) { MPI_Comm comm = ((PetscObject) dm)->comm; PetscInt dim = 2; struct triangulateio in; struct triangulateio out; PetscInt vStart, vEnd, v, cStart, cEnd, c, depth, depthGlobal; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = InitInput_Triangle(&in);CHKERRQ(ierr); ierr = InitOutput_Triangle(&out);CHKERRQ(ierr); ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = MPI_Allreduce(&depth, &depthGlobal, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); in.numberofpoints = vEnd - vStart; if (in.numberofpoints > 0) { PetscSection coordSection; Vec coordinates; PetscScalar *array; ierr = PetscMalloc(in.numberofpoints*dim * sizeof(double), &in.pointlist);CHKERRQ(ierr); ierr = PetscMalloc(in.numberofpoints * sizeof(int), &in.pointmarkerlist);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &array);CHKERRQ(ierr); for (v = vStart; v < vEnd; ++v) { const PetscInt idx = v - vStart; PetscInt off, d; ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); for (d = 0; d < dim; ++d) { in.pointlist[idx*dim + d] = PetscRealPart(array[off+d]); } ierr = DMPlexGetLabelValue(dm, "marker", v, &in.pointmarkerlist[idx]);CHKERRQ(ierr); } ierr = VecRestoreArray(coordinates, &array);CHKERRQ(ierr); } ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); in.numberofcorners = 3; in.numberoftriangles = cEnd - cStart; in.trianglearealist = (double *) maxVolumes; if (in.numberoftriangles > 0) { ierr = PetscMalloc(in.numberoftriangles*in.numberofcorners * sizeof(int), &in.trianglelist);CHKERRQ(ierr); for (c = cStart; c < cEnd; ++c) { const PetscInt idx = c - cStart; PetscInt *closure = PETSC_NULL; PetscInt closureSize; ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); if ((closureSize != 4) && (closureSize != 7)) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Mesh has cell which is not a triangle, %D vertices in closure", closureSize); for (v = 0; v < 3; ++v) { in.trianglelist[idx*in.numberofcorners + v] = closure[(v+closureSize-3)*2] - vStart; } ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); } } /* TODO: Segment markers are missing on input */ #if 0 /* Do not currently support holes */ PetscReal *holeCoords; PetscInt h, d; ierr = DMPlexGetHoles(boundary, &in.numberofholes, &holeCords);CHKERRQ(ierr); if (in.numberofholes > 0) { ierr = PetscMalloc(in.numberofholes*dim * sizeof(double), &in.holelist);CHKERRQ(ierr); for (h = 0; h < in.numberofholes; ++h) { for (d = 0; d < dim; ++d) { in.holelist[h*dim+d] = holeCoords[h*dim+d]; } } } #endif if (!rank) { char args[32]; /* Take away 'Q' for verbose output */ ierr = PetscStrcpy(args, "pqezQra");CHKERRQ(ierr); triangulate(args, &in, &out, PETSC_NULL); } ierr = PetscFree(in.pointlist);CHKERRQ(ierr); ierr = PetscFree(in.pointmarkerlist);CHKERRQ(ierr); ierr = PetscFree(in.segmentlist);CHKERRQ(ierr); ierr = PetscFree(in.segmentmarkerlist);CHKERRQ(ierr); ierr = PetscFree(in.trianglelist);CHKERRQ(ierr); { const PetscInt numCorners = 3; const PetscInt numCells = out.numberoftriangles; const PetscInt numVertices = out.numberofpoints; const int *cells = out.trianglelist; const double *meshCoords = out.pointlist; PetscBool interpolate = depthGlobal > 1 ? PETSC_TRUE : PETSC_FALSE; ierr = DMPlexCreateFromCellList(comm, dim, numCells, numVertices, numCorners, interpolate, cells, meshCoords, dmRefined);CHKERRQ(ierr); /* Set labels */ for (v = 0; v < numVertices; ++v) { if (out.pointmarkerlist[v]) { ierr = DMPlexSetLabelValue(*dmRefined, "marker", 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(*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); ierr = DMPlexSetLabelValue(*dmRefined, "marker", edges[0], out.edgemarkerlist[e]);CHKERRQ(ierr); ierr = DMPlexRestoreJoin(*dmRefined, 2, vertices, &numEdges, &edges);CHKERRQ(ierr); } } } ierr = DMPlexSetRefinementUniform(*dmRefined, PETSC_FALSE);CHKERRQ(ierr); } #if 0 /* Do not currently support holes */ ierr = DMPlexCopyHoles(*dm, boundary);CHKERRQ(ierr); #endif ierr = FiniOutput_Triangle(&out);CHKERRQ(ierr); PetscFunctionReturn(0); } #endif #ifdef PETSC_HAVE_TETGEN #include #undef __FUNCT__ #define __FUNCT__ "DMPlexGenerate_Tetgen" PetscErrorCode DMPlexGenerate_Tetgen(DM boundary, PetscBool interpolate, DM *dm) { MPI_Comm comm = ((PetscObject) boundary)->comm; const PetscInt dim = 3; ::tetgenio in; ::tetgenio out; PetscInt vStart, vEnd, v, fStart, fEnd, f; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(boundary, 0, &vStart, &vEnd);CHKERRQ(ierr); in.numberofpoints = vEnd - vStart; if (in.numberofpoints > 0) { PetscSection coordSection; Vec coordinates; PetscScalar *array; in.pointlist = new double[in.numberofpoints*dim]; in.pointmarkerlist = new int[in.numberofpoints]; ierr = DMGetCoordinatesLocal(boundary, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(boundary, &coordSection);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &array);CHKERRQ(ierr); for (v = vStart; v < vEnd; ++v) { const PetscInt idx = v - vStart; PetscInt off, d; ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); for (d = 0; d < dim; ++d) { in.pointlist[idx*dim + d] = array[off+d]; } ierr = DMPlexGetLabelValue(boundary, "marker", v, &in.pointmarkerlist[idx]);CHKERRQ(ierr); } ierr = VecRestoreArray(coordinates, &array);CHKERRQ(ierr); } ierr = DMPlexGetHeightStratum(boundary, 0, &fStart, &fEnd);CHKERRQ(ierr); in.numberoffacets = fEnd - fStart; if (in.numberoffacets > 0) { in.facetlist = new tetgenio::facet[in.numberoffacets]; in.facetmarkerlist = new int[in.numberoffacets]; for (f = fStart; f < fEnd; ++f) { const PetscInt idx = f - fStart; PetscInt *points = PETSC_NULL, numPoints, p, numVertices = 0, v; in.facetlist[idx].numberofpolygons = 1; in.facetlist[idx].polygonlist = new tetgenio::polygon[in.facetlist[idx].numberofpolygons]; 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; } } tetgenio::polygon *poly = in.facetlist[idx].polygonlist; poly->numberofvertices = numVertices; poly->vertexlist = new int[poly->numberofvertices]; for (v = 0; v < numVertices; ++v) { const PetscInt vIdx = points[v] - vStart; poly->vertexlist[v] = vIdx; } ierr = DMPlexGetLabelValue(boundary, "marker", f, &in.facetmarkerlist[idx]);CHKERRQ(ierr); ierr = DMPlexRestoreTransitiveClosure(boundary, f, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr); } } if (!rank) { char args[32]; /* Take away 'Q' for verbose output */ ierr = PetscStrcpy(args, "pqezQ");CHKERRQ(ierr); ::tetrahedralize(args, &in, &out); } { const PetscInt numCorners = 4; const PetscInt numCells = out.numberoftetrahedra; const PetscInt numVertices = out.numberofpoints; const int *cells = out.tetrahedronlist; const double *meshCoords = out.pointlist; ierr = DMPlexCreateFromCellList(comm, dim, numCells, numVertices, numCorners, interpolate, cells, meshCoords, dm);CHKERRQ(ierr); /* Set labels */ for (v = 0; v < numVertices; ++v) { if (out.pointmarkerlist[v]) { ierr = DMPlexSetLabelValue(*dm, "marker", 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); ierr = DMPlexSetLabelValue(*dm, "marker", 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 = DMPlexGetJoin(*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); ierr = DMPlexSetLabelValue(*dm, "marker", faces[0], out.trifacemarkerlist[f]);CHKERRQ(ierr); ierr = DMPlexRestoreJoin(*dm, 3, vertices, &numFaces, &faces);CHKERRQ(ierr); } } } ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexRefine_Tetgen" PetscErrorCode DMPlexRefine_Tetgen(DM dm, double *maxVolumes, DM *dmRefined) { MPI_Comm comm = ((PetscObject) dm)->comm; const PetscInt dim = 3; ::tetgenio in; ::tetgenio out; PetscInt vStart, vEnd, v, cStart, cEnd, c, depth, depthGlobal; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = MPI_Allreduce(&depth, &depthGlobal, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); in.numberofpoints = vEnd - vStart; if (in.numberofpoints > 0) { PetscSection coordSection; Vec coordinates; PetscScalar *array; in.pointlist = new double[in.numberofpoints*dim]; in.pointmarkerlist = new int[in.numberofpoints]; ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &array);CHKERRQ(ierr); for (v = vStart; v < vEnd; ++v) { const PetscInt idx = v - vStart; PetscInt off, d; ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); for (d = 0; d < dim; ++d) { in.pointlist[idx*dim + d] = array[off+d]; } ierr = DMPlexGetLabelValue(dm, "marker", v, &in.pointmarkerlist[idx]);CHKERRQ(ierr); } ierr = VecRestoreArray(coordinates, &array);CHKERRQ(ierr); } ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); in.numberofcorners = 4; in.numberoftetrahedra = cEnd - cStart; in.tetrahedronvolumelist = (double *) maxVolumes; if (in.numberoftetrahedra > 0) { in.tetrahedronlist = new int[in.numberoftetrahedra*in.numberofcorners]; for (c = cStart; c < cEnd; ++c) { const PetscInt idx = c - cStart; PetscInt *closure = PETSC_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); } } /* TODO: Put in boundary faces with markers */ if (!rank) { char args[32]; /* Take away 'Q' for verbose output */ /*ierr = PetscStrcpy(args, "qezQra");CHKERRQ(ierr); */ ierr = PetscStrcpy(args, "qezraVVVV");CHKERRQ(ierr); ::tetrahedralize(args, &in, &out); } in.tetrahedronvolumelist = NULL; { const PetscInt numCorners = 4; const PetscInt numCells = out.numberoftetrahedra; const PetscInt numVertices = out.numberofpoints; const int *cells = out.tetrahedronlist; const double *meshCoords = out.pointlist; PetscBool interpolate = depthGlobal > 1 ? PETSC_TRUE : PETSC_FALSE; ierr = DMPlexCreateFromCellList(comm, dim, numCells, numVertices, numCorners, interpolate, cells, meshCoords, dmRefined);CHKERRQ(ierr); /* Set labels */ for (v = 0; v < numVertices; ++v) { if (out.pointmarkerlist[v]) { ierr = DMPlexSetLabelValue(*dmRefined, "marker", 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); ierr = DMPlexSetLabelValue(*dmRefined, "marker", 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 = DMPlexGetJoin(*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); ierr = DMPlexSetLabelValue(*dmRefined, "marker", faces[0], out.trifacemarkerlist[f]);CHKERRQ(ierr); ierr = DMPlexRestoreJoin(*dmRefined, 3, vertices, &numFaces, &faces);CHKERRQ(ierr); } } } ierr = DMPlexSetRefinementUniform(*dmRefined, PETSC_FALSE);CHKERRQ(ierr); } PetscFunctionReturn(0); } #endif #ifdef PETSC_HAVE_CTETGEN #include "ctetgen.h" #undef __FUNCT__ #define __FUNCT__ "DMPlexGenerate_CTetgen" PetscErrorCode DMPlexGenerate_CTetgen(DM boundary, PetscBool interpolate, DM *dm) { MPI_Comm comm = ((PetscObject) boundary)->comm; const PetscInt dim = 3; PLC *in, *out; PetscInt verbose = 0, vStart, vEnd, v, fStart, fEnd, f; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscOptionsGetInt(((PetscObject) boundary)->prefix, "-ctetgen_verbose", &verbose, PETSC_NULL);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(boundary, 0, &vStart, &vEnd);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 = PetscMalloc(in->numberofpoints*dim * sizeof(PetscReal), &in->pointlist);CHKERRQ(ierr); ierr = PetscMalloc(in->numberofpoints * sizeof(int), &in->pointmarkerlist);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(boundary, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(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; ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); for (d = 0; d < dim; ++d) { in->pointlist[idx*dim + d] = PetscRealPart(array[off+d]); } ierr = DMPlexGetLabelValue(boundary, "marker", 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 = PetscMalloc(in->numberoffacets * sizeof(facet), &in->facetlist);CHKERRQ(ierr); ierr = PetscMalloc(in->numberoffacets * sizeof(int), &in->facetmarkerlist);CHKERRQ(ierr); for (f = fStart; f < fEnd; ++f) { const PetscInt idx = f - fStart; PetscInt *points = PETSC_NULL, numPoints, p, numVertices = 0, v, m; polygon *poly; in->facetlist[idx].numberofpolygons = 1; ierr = PetscMalloc(in->facetlist[idx].numberofpolygons * sizeof(polygon), &in->facetlist[idx].polygonlist);CHKERRQ(ierr); in->facetlist[idx].numberofholes = 0; in->facetlist[idx].holelist = PETSC_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 = PetscMalloc(poly->numberofvertices * sizeof(int), &poly->vertexlist);CHKERRQ(ierr); for (v = 0; v < numVertices; ++v) { const PetscInt vIdx = points[v] - vStart; poly->vertexlist[v] = vIdx; } ierr = DMPlexGetLabelValue(boundary, "marker", 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); } { const PetscInt numCorners = 4; const PetscInt numCells = out->numberoftetrahedra; const PetscInt numVertices = out->numberofpoints; const int *cells = out->tetrahedronlist; const double *meshCoords = out->pointlist; ierr = DMPlexCreateFromCellList(comm, dim, numCells, numVertices, numCorners, interpolate, cells, meshCoords, dm);CHKERRQ(ierr); /* Set labels */ for (v = 0; v < numVertices; ++v) { if (out->pointmarkerlist[v]) { ierr = DMPlexSetLabelValue(*dm, "marker", 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); ierr = DMPlexSetLabelValue(*dm, "marker", 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); ierr = DMPlexSetLabelValue(*dm, "marker", 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); } #undef __FUNCT__ #define __FUNCT__ "DMPlexRefine_CTetgen" PetscErrorCode DMPlexRefine_CTetgen(DM dm, PetscReal *maxVolumes, DM *dmRefined) { MPI_Comm comm = ((PetscObject) dm)->comm; const PetscInt dim = 3; PLC *in, *out; PetscInt verbose = 0, vStart, vEnd, v, cStart, cEnd, c, depth, depthGlobal; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscOptionsGetInt(((PetscObject) dm)->prefix, "-ctetgen_verbose", &verbose, PETSC_NULL);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = MPI_Allreduce(&depth, &depthGlobal, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);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 = PetscMalloc(in->numberofpoints*dim * sizeof(PetscReal), &in->pointlist);CHKERRQ(ierr); ierr = PetscMalloc(in->numberofpoints * sizeof(int), &in->pointmarkerlist);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(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; ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); for (d = 0; d < dim; ++d) { in->pointlist[idx*dim + d] = PetscRealPart(array[off+d]); } ierr = DMPlexGetLabelValue(dm, "marker", 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 = PetscMalloc(in->numberoftetrahedra*in->numberofcorners * sizeof(int), &in->tetrahedronlist);CHKERRQ(ierr); for (c = cStart; c < cEnd; ++c) { const PetscInt idx = c - cStart; PetscInt *closure = PETSC_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); } { const PetscInt numCorners = 4; const PetscInt numCells = out->numberoftetrahedra; const PetscInt numVertices = out->numberofpoints; const int *cells = out->tetrahedronlist; const double *meshCoords = out->pointlist; PetscBool interpolate = depthGlobal > 1 ? PETSC_TRUE : PETSC_FALSE; ierr = DMPlexCreateFromCellList(comm, dim, numCells, numVertices, numCorners, interpolate, cells, meshCoords, dmRefined);CHKERRQ(ierr); /* Set labels */ for (v = 0; v < numVertices; ++v) { if (out->pointmarkerlist[v]) { ierr = DMPlexSetLabelValue(*dmRefined, "marker", 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); ierr = DMPlexSetLabelValue(*dmRefined, "marker", 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); ierr = DMPlexSetLabelValue(*dmRefined, "marker", 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); } #endif #undef __FUNCT__ #define __FUNCT__ "DMPlexGenerate" /*@C DMPlexGenerate - Generates a mesh. Not Collective Input Parameters: + boundary - The DMPlex boundary object . name - The mesh generation package name - interpolate - Flag to create intermediate mesh elements Output Parameter: . mesh - The DMPlex object Level: intermediate .keywords: mesh, elements .seealso: DMPlexCreate(), DMRefine() @*/ PetscErrorCode DMPlexGenerate(DM boundary, const char name[], PetscBool interpolate, DM *mesh) { PetscInt dim; char genname[1024]; PetscBool isTriangle = PETSC_FALSE, isTetgen = PETSC_FALSE, isCTetgen = PETSC_FALSE, flg; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(boundary, DM_CLASSID, 1); PetscValidLogicalCollectiveBool(boundary, interpolate, 2); ierr = DMPlexGetDimension(boundary, &dim);CHKERRQ(ierr); ierr = PetscOptionsGetString(((PetscObject) boundary)->prefix, "-dm_plex_generator", genname, 1024, &flg);CHKERRQ(ierr); if (flg) {name = genname;} if (name) { ierr = PetscStrcmp(name, "triangle", &isTriangle);CHKERRQ(ierr); ierr = PetscStrcmp(name, "tetgen", &isTetgen);CHKERRQ(ierr); ierr = PetscStrcmp(name, "ctetgen", &isCTetgen);CHKERRQ(ierr); } switch(dim) { case 1: if (!name || isTriangle) { #ifdef PETSC_HAVE_TRIANGLE ierr = DMPlexGenerate_Triangle(boundary, interpolate, mesh);CHKERRQ(ierr); #else SETERRQ(((PetscObject) boundary)->comm, PETSC_ERR_SUP, "Mesh generation needs external package support.\nPlease reconfigure with --download-triangle."); #endif } else SETERRQ1(((PetscObject) boundary)->comm, PETSC_ERR_SUP, "Unknown 2D mesh generation package %s", name); break; case 2: if (!name || isCTetgen) { #ifdef PETSC_HAVE_CTETGEN ierr = DMPlexGenerate_CTetgen(boundary, interpolate, mesh);CHKERRQ(ierr); #else SETERRQ(((PetscObject) boundary)->comm, PETSC_ERR_SUP, "CTetgen needs external package support.\nPlease reconfigure with --download-ctetgen."); #endif } else if (isTetgen) { #ifdef PETSC_HAVE_TETGEN ierr = DMPlexGenerate_Tetgen(boundary, interpolate, mesh);CHKERRQ(ierr); #else SETERRQ(((PetscObject) boundary)->comm, PETSC_ERR_SUP, "Tetgen needs external package support.\nPlease reconfigure with --with-c-language=cxx --download-tetgen."); #endif } else SETERRQ1(((PetscObject) boundary)->comm, PETSC_ERR_SUP, "Unknown 3D mesh generation package %s", name); break; default: SETERRQ1(((PetscObject) boundary)->comm, PETSC_ERR_SUP, "Mesh generation for a dimension %d boundary is not supported.", dim); } PetscFunctionReturn(0); } typedef PetscInt CellRefiner; #undef __FUNCT__ #define __FUNCT__ "GetDepthStart_Private" PETSC_STATIC_INLINE PetscErrorCode GetDepthStart_Private(PetscInt depth, PetscInt depthSize[], PetscInt *cStart, PetscInt *fStart, PetscInt *eStart, PetscInt *vStart) { PetscFunctionBegin; if (cStart) *cStart = 0; if (vStart) *vStart = depthSize[depth]; if (fStart) *fStart = depthSize[depth] + depthSize[0]; if (eStart) *eStart = depthSize[depth] + depthSize[0] + depthSize[depth-1]; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "GetDepthEnd_Private" PETSC_STATIC_INLINE PetscErrorCode GetDepthEnd_Private(PetscInt depth, PetscInt depthSize[], PetscInt *cEnd, PetscInt *fEnd, PetscInt *eEnd, PetscInt *vEnd) { PetscFunctionBegin; if (cEnd) *cEnd = depthSize[depth]; if (vEnd) *vEnd = depthSize[depth] + depthSize[0]; if (fEnd) *fEnd = depthSize[depth] + depthSize[0] + depthSize[depth-1]; if (eEnd) *eEnd = depthSize[depth] + depthSize[0] + depthSize[depth-1] + depthSize[1]; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "CellRefinerGetSizes" PetscErrorCode CellRefinerGetSizes(CellRefiner refiner, DM dm, PetscInt depthSize[]) { PetscInt cStart, cEnd, cMax, vStart, vEnd, vMax, fStart, fEnd, fMax, eStart, eEnd, eMax; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); ierr = DMPlexGetHybridBounds(dm, &cMax, &fMax, &eMax, &vMax);CHKERRQ(ierr); switch(refiner) { case 1: /* Simplicial 2D */ depthSize[0] = vEnd - vStart + fEnd - fStart; /* Add a vertex on every face */ depthSize[1] = 2*(fEnd - fStart) + 3*(cEnd - cStart); /* Every face is split into 2 faces and 3 faces are added for each cell */ depthSize[2] = 4*(cEnd - cStart); /* Every cell split into 4 cells */ break; case 3: /* Hybrid 2D */ if (cMax < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No cell maximum specified in hybrid mesh"); cMax = PetscMin(cEnd, cMax); if (fMax < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No face maximum specified in hybrid mesh"); fMax = PetscMin(fEnd, fMax); depthSize[0] = vEnd - vStart + fMax - fStart; /* Add a vertex on every face, but not hybrid faces */ depthSize[1] = 2*(fMax - fStart) + 3*(cMax - cStart) + (fEnd - fMax) + (cEnd - cMax); /* Every interior face is split into 2 faces, 3 faces are added for each interior cell, and one in each hybrid cell */ depthSize[2] = 4*(cMax - cStart) + 2*(cEnd - cMax); /* Interior cells split into 4 cells, Hybrid cells split into 2 cells */ break; case 2: /* Hex 2D */ depthSize[0] = vEnd - vStart + cEnd - cStart + fEnd - fStart; /* Add a vertex on every face and cell */ depthSize[1] = 2*(fEnd - fStart) + 4*(cEnd - cStart); /* Every face is split into 2 faces and 4 faces are added for each cell */ depthSize[2] = 4*(cEnd - cStart); /* Every cell split into 4 cells */ break; default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown cell refiner %d", refiner); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "CellRefinerSetConeSizes" PetscErrorCode CellRefinerSetConeSizes(CellRefiner refiner, DM dm, PetscInt depthSize[], DM rdm) { PetscInt depth, cStart, cStartNew, cEnd, cMax, c, vStart, vStartNew, vEnd, vMax, v, fStart, fStartNew, fEnd, fMax, f, eStart, eStartNew, eEnd, eMax, r; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); ierr = DMPlexGetHybridBounds(dm, &cMax, &fMax, &eMax, &vMax);CHKERRQ(ierr); ierr = GetDepthStart_Private(depth, depthSize, &cStartNew, &fStartNew, &eStartNew, &vStartNew);CHKERRQ(ierr); switch(refiner) { case 1: /* Simplicial 2D */ /* All cells have 3 faces */ for(c = cStart; c < cEnd; ++c) { for(r = 0; r < 4; ++r) { const PetscInt newp = (c - cStart)*4 + r; ierr = DMPlexSetConeSize(rdm, newp, 3);CHKERRQ(ierr); } } /* Split faces have 2 vertices and the same cells as the parent */ for(f = fStart; f < fEnd; ++f) { for(r = 0; r < 2; ++r) { const PetscInt newp = fStartNew + (f - fStart)*2 + r; PetscInt size; ierr = DMPlexSetConeSize(rdm, newp, 2);CHKERRQ(ierr); ierr = DMPlexGetSupportSize(dm, f, &size);CHKERRQ(ierr); ierr = DMPlexSetSupportSize(rdm, newp, size);CHKERRQ(ierr); } } /* Interior faces have 2 vertices and 2 cells */ for(c = cStart; c < cEnd; ++c) { for(r = 0; r < 3; ++r) { const PetscInt newp = fStartNew + (fEnd - fStart)*2 + (c - cStart)*3 + r; ierr = DMPlexSetConeSize(rdm, newp, 2);CHKERRQ(ierr); ierr = DMPlexSetSupportSize(rdm, newp, 2);CHKERRQ(ierr); } } /* Old vertices have identical supports */ for(v = vStart; v < vEnd; ++v) { const PetscInt newp = vStartNew + (v - vStart); PetscInt size; ierr = DMPlexGetSupportSize(dm, v, &size);CHKERRQ(ierr); ierr = DMPlexSetSupportSize(rdm, newp, size);CHKERRQ(ierr); } /* Face vertices have 2 + cells*2 supports */ for(f = fStart; f < fEnd; ++f) { const PetscInt newp = vStartNew + (vEnd - vStart) + (f - fStart); PetscInt size; ierr = DMPlexGetSupportSize(dm, f, &size);CHKERRQ(ierr); ierr = DMPlexSetSupportSize(rdm, newp, 2 + size*2);CHKERRQ(ierr); } break; case 2: /* Hex 2D */ /* All cells have 4 faces */ for(c = cStart; c < cEnd; ++c) { for(r = 0; r < 4; ++r) { const PetscInt newp = (c - cStart)*4 + r; ierr = DMPlexSetConeSize(rdm, newp, 4);CHKERRQ(ierr); } } /* Split faces have 2 vertices and the same cells as the parent */ for(f = fStart; f < fEnd; ++f) { for(r = 0; r < 2; ++r) { const PetscInt newp = fStartNew + (f - fStart)*2 + r; PetscInt size; ierr = DMPlexSetConeSize(rdm, newp, 2);CHKERRQ(ierr); ierr = DMPlexGetSupportSize(dm, f, &size);CHKERRQ(ierr); ierr = DMPlexSetSupportSize(rdm, newp, size);CHKERRQ(ierr); } } /* Interior faces have 2 vertices and 2 cells */ for(c = cStart; c < cEnd; ++c) { for(r = 0; r < 4; ++r) { const PetscInt newp = fStartNew + (fEnd - fStart)*2 + (c - cStart)*4 + r; ierr = DMPlexSetConeSize(rdm, newp, 2);CHKERRQ(ierr); ierr = DMPlexSetSupportSize(rdm, newp, 2);CHKERRQ(ierr); } } /* Old vertices have identical supports */ for(v = vStart; v < vEnd; ++v) { const PetscInt newp = vStartNew + (v - vStart); PetscInt size; ierr = DMPlexGetSupportSize(dm, v, &size);CHKERRQ(ierr); ierr = DMPlexSetSupportSize(rdm, newp, size);CHKERRQ(ierr); } /* Face vertices have 2 + cells supports */ for(f = fStart; f < fEnd; ++f) { const PetscInt newp = vStartNew + (vEnd - vStart) + (f - fStart); PetscInt size; ierr = DMPlexGetSupportSize(dm, f, &size);CHKERRQ(ierr); ierr = DMPlexSetSupportSize(rdm, newp, 2 + size);CHKERRQ(ierr); } /* Cell vertices have 4 supports */ for(c = cStart; c < cEnd; ++c) { const PetscInt newp = vStartNew + (vEnd - vStart) + (fEnd - fStart) + (c - cStart); ierr = DMPlexSetSupportSize(rdm, newp, 4);CHKERRQ(ierr); } break; case 3: /* Hybrid 2D */ if (cMax < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No cell maximum specified in hybrid mesh"); cMax = PetscMin(cEnd, cMax); if (fMax < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No face maximum specified in hybrid mesh"); fMax = PetscMin(fEnd, fMax); ierr = DMPlexSetHybridBounds(rdm, cStartNew + (cMax - cStart)*4, fStartNew + (fMax - fStart)*2 + (cMax - cStart)*3, PETSC_DETERMINE, PETSC_DETERMINE);CHKERRQ(ierr); /* Interior cells have 3 faces */ for(c = cStart; c < cMax; ++c) { for(r = 0; r < 4; ++r) { const PetscInt newp = cStartNew + (c - cStart)*4 + r; ierr = DMPlexSetConeSize(rdm, newp, 3);CHKERRQ(ierr); } } /* Hybrid cells have 4 faces */ for(c = cMax; c < cEnd; ++c) { for(r = 0; r < 2; ++r) { const PetscInt newp = cStartNew + (cMax - cStart)*4 + (c - cMax)*2 + r; ierr = DMPlexSetConeSize(rdm, newp, 4);CHKERRQ(ierr); } } /* Interior split faces have 2 vertices and the same cells as the parent */ for(f = fStart; f < fMax; ++f) { for(r = 0; r < 2; ++r) { const PetscInt newp = fStartNew + (f - fStart)*2 + r; PetscInt size; ierr = DMPlexSetConeSize(rdm, newp, 2);CHKERRQ(ierr); ierr = DMPlexGetSupportSize(dm, f, &size);CHKERRQ(ierr); ierr = DMPlexSetSupportSize(rdm, newp, size);CHKERRQ(ierr); } } /* Interior cell faces have 2 vertices and 2 cells */ for(c = cStart; c < cMax; ++c) { for(r = 0; r < 3; ++r) { const PetscInt newp = fStartNew + (fMax - fStart)*2 + (c - cStart)*3 + r; ierr = DMPlexSetConeSize(rdm, newp, 2);CHKERRQ(ierr); ierr = DMPlexSetSupportSize(rdm, newp, 2);CHKERRQ(ierr); } } /* Hybrid faces have 2 vertices and the same cells */ for(f = fMax; f < fEnd; ++f) { const PetscInt newp = fStartNew + (fMax - fStart)*2 + (cMax - cStart)*3 + (f - fMax); PetscInt size; ierr = DMPlexSetConeSize(rdm, newp, 2);CHKERRQ(ierr); ierr = DMPlexGetSupportSize(dm, f, &size);CHKERRQ(ierr); ierr = DMPlexSetSupportSize(rdm, newp, size);CHKERRQ(ierr); } /* Hybrid cell faces have 2 vertices and 2 cells */ for(c = cMax; c < cEnd; ++c) { const PetscInt newp = fStartNew + (fMax - fStart)*2 + (cMax - cStart)*3 + (fEnd - fMax) + (c - cMax); ierr = DMPlexSetConeSize(rdm, newp, 2);CHKERRQ(ierr); ierr = DMPlexSetSupportSize(rdm, newp, 2);CHKERRQ(ierr); } /* Old vertices have identical supports */ for(v = vStart; v < vEnd; ++v) { const PetscInt newp = vStartNew + (v - vStart); PetscInt size; ierr = DMPlexGetSupportSize(dm, v, &size);CHKERRQ(ierr); ierr = DMPlexSetSupportSize(rdm, newp, size);CHKERRQ(ierr); } /* Face vertices have 2 + (2 interior, 1 hybrid) supports */ for(f = fStart; f < fMax; ++f) { const PetscInt newp = vStartNew + (vEnd - vStart) + (f - fStart); const PetscInt *support; PetscInt size, newSize = 2, s; ierr = DMPlexGetSupportSize(dm, f, &size);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, f, &support);CHKERRQ(ierr); for(s = 0; s < size; ++s) { if (support[s] >= cMax) { newSize += 1; } else { newSize += 2; } } ierr = DMPlexSetSupportSize(rdm, newp, newSize);CHKERRQ(ierr); } break; default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown cell refiner %d", refiner); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "CellRefinerSetCones" PetscErrorCode CellRefinerSetCones(CellRefiner refiner, DM dm, PetscInt depthSize[], DM rdm) { PetscInt depth, cStart, cEnd, cMax, cStartNew, cEndNew, c, vStart, vEnd, vMax, vStartNew, vEndNew, v, fStart, fEnd, fMax, fStartNew, fEndNew, f, eStart, eEnd, eMax, eStartNew, eEndNew, r, p; PetscInt maxSupportSize, *supportRef; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); ierr = DMPlexGetHybridBounds(dm, &cMax, &fMax, &eMax, &vMax);CHKERRQ(ierr); ierr = GetDepthStart_Private(depth, depthSize, &cStartNew, &fStartNew, &eStartNew, &vStartNew);CHKERRQ(ierr); ierr = GetDepthEnd_Private(depth, depthSize, &cEndNew, &fEndNew, &eEndNew, &vEndNew);CHKERRQ(ierr); switch(refiner) { case 1: /* Simplicial 2D */ /* 2 |\ | \ | \ | \ | C \ | \ | \ 2---1---1 |\ D / \ | 2 0 \ |A \ / B \ 0---0-------1 */ /* All cells have 3 faces */ for(c = cStart; c < cEnd; ++c) { const PetscInt newp = cStartNew + (c - cStart)*4; const PetscInt *cone, *ornt; PetscInt coneNew[3], orntNew[3]; ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); ierr = DMPlexGetConeOrientation(dm, c, &ornt);CHKERRQ(ierr); /* A triangle */ coneNew[0] = fStartNew + (cone[0] - fStart)*2 + (ornt[0] < 0 ? 1 : 0); orntNew[0] = ornt[0]; coneNew[1] = fStartNew + (fEnd - fStart)*2 + (c - cStart)*3 + 2; orntNew[1] = -2; coneNew[2] = fStartNew + (cone[2] - fStart)*2 + (ornt[2] < 0 ? 0 : 1); orntNew[2] = ornt[2]; ierr = DMPlexSetCone(rdm, newp+0, coneNew);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(rdm, newp+0, orntNew);CHKERRQ(ierr); #if 1 if ((newp+0 < cStartNew) || (newp+0 >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", newp+0, cStartNew, cEndNew); for(p = 0; p < 3; ++p) { if ((coneNew[p] < fStartNew) || (coneNew[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", coneNew[p], fStartNew, fEndNew); } #endif /* B triangle */ coneNew[0] = fStartNew + (cone[0] - fStart)*2 + (ornt[0] < 0 ? 0 : 1); orntNew[0] = ornt[0]; coneNew[1] = fStartNew + (cone[1] - fStart)*2 + (ornt[1] < 0 ? 1 : 0); orntNew[1] = ornt[1]; coneNew[2] = fStartNew + (fEnd - fStart)*2 + (c - cStart)*3 + 0; orntNew[2] = -2; ierr = DMPlexSetCone(rdm, newp+1, coneNew);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(rdm, newp+1, orntNew);CHKERRQ(ierr); #if 1 if ((newp+1 < cStartNew) || (newp+1 >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", newp+1, cStartNew, cEndNew); for(p = 0; p < 3; ++p) { if ((coneNew[p] < fStartNew) || (coneNew[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", coneNew[p], fStartNew, fEndNew); } #endif /* C triangle */ coneNew[0] = fStartNew + (fEnd - fStart)*2 + (c - cStart)*3 + 1; orntNew[0] = -2; coneNew[1] = fStartNew + (cone[1] - fStart)*2 + (ornt[1] < 0 ? 0 : 1); orntNew[1] = ornt[1]; coneNew[2] = fStartNew + (cone[2] - fStart)*2 + (ornt[2] < 0 ? 1 : 0); orntNew[2] = ornt[2]; ierr = DMPlexSetCone(rdm, newp+2, coneNew);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(rdm, newp+2, orntNew);CHKERRQ(ierr); #if 1 if ((newp+2 < cStartNew) || (newp+2 >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", newp+2, cStartNew, cEndNew); for(p = 0; p < 3; ++p) { if ((coneNew[p] < fStartNew) || (coneNew[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", coneNew[p], fStartNew, fEndNew); } #endif /* D triangle */ coneNew[0] = fStartNew + (fEnd - fStart)*2 + (c - cStart)*3 + 0; orntNew[0] = 0; coneNew[1] = fStartNew + (fEnd - fStart)*2 + (c - cStart)*3 + 1; orntNew[1] = 0; coneNew[2] = fStartNew + (fEnd - fStart)*2 + (c - cStart)*3 + 2; orntNew[2] = 0; ierr = DMPlexSetCone(rdm, newp+3, coneNew);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(rdm, newp+3, orntNew);CHKERRQ(ierr); #if 1 if ((newp+3 < cStartNew) || (newp+3 >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", newp+3, cStartNew, cEndNew); for(p = 0; p < 3; ++p) { if ((coneNew[p] < fStartNew) || (coneNew[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", coneNew[p], fStartNew, fEndNew); } #endif } /* Split faces have 2 vertices and the same cells as the parent */ ierr = DMPlexGetMaxSizes(dm, PETSC_NULL, &maxSupportSize);CHKERRQ(ierr); ierr = PetscMalloc((2 + maxSupportSize*2) * sizeof(PetscInt), &supportRef);CHKERRQ(ierr); for(f = fStart; f < fEnd; ++f) { const PetscInt newv = vStartNew + (vEnd - vStart) + (f - fStart); for(r = 0; r < 2; ++r) { const PetscInt newp = fStartNew + (f - fStart)*2 + r; const PetscInt *cone, *support; PetscInt coneNew[2], coneSize, c, supportSize, s; ierr = DMPlexGetCone(dm, f, &cone);CHKERRQ(ierr); coneNew[0] = vStartNew + (cone[0] - vStart); coneNew[1] = vStartNew + (cone[1] - vStart); coneNew[(r+1)%2] = newv; ierr = DMPlexSetCone(rdm, newp, coneNew);CHKERRQ(ierr); #if 1 if ((newp < fStartNew) || (newp >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", newp, fStartNew, fEndNew); for(p = 0; p < 2; ++p) { if ((coneNew[p] < vStartNew) || (coneNew[p] >= vEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a vertex [%d, %d)", coneNew[p], vStartNew, vEndNew); } #endif ierr = DMPlexGetSupportSize(dm, f, &supportSize);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, f, &support);CHKERRQ(ierr); for(s = 0; s < supportSize; ++s) { ierr = DMPlexGetConeSize(dm, support[s], &coneSize);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); for(c = 0; c < coneSize; ++c) { if (cone[c] == f) { break; } } supportRef[s] = cStartNew + (support[s] - cStart)*4 + (c+r)%3; } ierr = DMPlexSetSupport(rdm, newp, supportRef);CHKERRQ(ierr); #if 1 if ((newp < fStartNew) || (newp >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", newp, fStartNew, fEndNew); for(p = 0; p < supportSize; ++p) { if ((supportRef[p] < cStartNew) || (supportRef[p] >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", supportRef[p], cStartNew, cEndNew); } #endif } } /* Interior faces have 2 vertices and 2 cells */ for(c = cStart; c < cEnd; ++c) { const PetscInt *cone; ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); for(r = 0; r < 3; ++r) { const PetscInt newp = fStartNew + (fEnd - fStart)*2 + (c - cStart)*3 + r; PetscInt coneNew[2]; PetscInt supportNew[2]; coneNew[0] = vStartNew + (vEnd - vStart) + (cone[r] - fStart); coneNew[1] = vStartNew + (vEnd - vStart) + (cone[(r+1)%3] - fStart); ierr = DMPlexSetCone(rdm, newp, coneNew);CHKERRQ(ierr); #if 1 if ((newp < fStartNew) || (newp >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", newp, fStartNew, fEndNew); for(p = 0; p < 2; ++p) { if ((coneNew[p] < vStartNew) || (coneNew[p] >= vEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a vertex [%d, %d)", coneNew[p], vStartNew, vEndNew); } #endif supportNew[0] = (c - cStart)*4 + (r+1)%3; supportNew[1] = (c - cStart)*4 + 3; ierr = DMPlexSetSupport(rdm, newp, supportNew);CHKERRQ(ierr); #if 1 if ((newp < fStartNew) || (newp >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", newp, fStartNew, fEndNew); for(p = 0; p < 2; ++p) { if ((supportNew[p] < cStartNew) || (supportNew[p] >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", supportNew[p], cStartNew, cEndNew); } #endif } } /* Old vertices have identical supports */ for(v = vStart; v < vEnd; ++v) { const PetscInt newp = vStartNew + (v - vStart); const PetscInt *support, *cone; PetscInt size, s; ierr = DMPlexGetSupportSize(dm, v, &size);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, v, &support);CHKERRQ(ierr); for(s = 0; s < size; ++s) { PetscInt r = 0; ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); if (cone[1] == v) r = 1; supportRef[s] = fStartNew + (support[s] - fStart)*2 + r; } ierr = DMPlexSetSupport(rdm, newp, supportRef);CHKERRQ(ierr); #if 1 if ((newp < vStartNew) || (newp >= vEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a vertex [%d, %d)", newp, vStartNew, vEndNew); for(p = 0; p < size; ++p) { if ((supportRef[p] < fStartNew) || (supportRef[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", supportRef[p], fStartNew, fEndNew); } #endif } /* Face vertices have 2 + cells*2 supports */ for(f = fStart; f < fEnd; ++f) { const PetscInt newp = vStartNew + (vEnd - vStart) + (f - fStart); const PetscInt *cone, *support; PetscInt size, s; ierr = DMPlexGetSupportSize(dm, f, &size);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, f, &support);CHKERRQ(ierr); supportRef[0] = fStartNew + (f - fStart)*2 + 0; supportRef[1] = fStartNew + (f - fStart)*2 + 1; for(s = 0; s < size; ++s) { PetscInt r = 0; ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); if (cone[1] == f) r = 1; else if (cone[2] == f) r = 2; supportRef[2+s*2+0] = fStartNew + (fEnd - fStart)*2 + (support[s] - cStart)*3 + (r+2)%3; supportRef[2+s*2+1] = fStartNew + (fEnd - fStart)*2 + (support[s] - cStart)*3 + r; } ierr = DMPlexSetSupport(rdm, newp, supportRef);CHKERRQ(ierr); #if 1 if ((newp < vStartNew) || (newp >= vEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a vertex [%d, %d)", newp, vStartNew, vEndNew); for(p = 0; p < 2+size*2; ++p) { if ((supportRef[p] < fStartNew) || (supportRef[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", supportRef[p], fStartNew, fEndNew); } #endif } ierr = PetscFree(supportRef);CHKERRQ(ierr); break; case 2: /* Hex 2D */ /* 3---------2---------2 | | | | D 2 C | | | | 3----3----0----1----1 | | | | A 0 B | | | | 0---------0---------1 */ /* All cells have 4 faces */ for(c = cStart; c < cEnd; ++c) { const PetscInt newp = (c - cStart)*4; const PetscInt *cone, *ornt; PetscInt coneNew[4], orntNew[4]; ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); ierr = DMPlexGetConeOrientation(dm, c, &ornt);CHKERRQ(ierr); /* A quad */ coneNew[0] = fStartNew + (cone[0] - fStart)*2 + (ornt[0] < 0 ? 1 : 0); orntNew[0] = ornt[0]; coneNew[1] = fStartNew + (fEnd - fStart)*2 + (c - cStart)*4 + 0; orntNew[1] = 0; coneNew[2] = fStartNew + (fEnd - fStart)*2 + (c - cStart)*4 + 3; orntNew[2] = -2; coneNew[3] = fStartNew + (cone[3] - fStart)*2 + (ornt[3] < 0 ? 0 : 1); orntNew[3] = ornt[3]; ierr = DMPlexSetCone(rdm, newp+0, coneNew);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(rdm, newp+0, orntNew);CHKERRQ(ierr); #if 1 if ((newp+0 < cStartNew) || (newp+0 >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", newp+0, cStartNew, cEndNew); for(p = 0; p < 4; ++p) { if ((coneNew[p] < fStartNew) || (coneNew[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", coneNew[p], fStartNew, fEndNew); } #endif /* B quad */ coneNew[0] = fStartNew + (cone[0] - fStart)*2 + (ornt[0] < 0 ? 0 : 1); orntNew[0] = ornt[0]; coneNew[1] = fStartNew + (cone[1] - fStart)*2 + (ornt[1] < 0 ? 1 : 0); orntNew[1] = ornt[1]; coneNew[2] = fStartNew + (fEnd - fStart)*2 + (c - cStart)*4 + 1; orntNew[2] = 0; coneNew[3] = fStartNew + (fEnd - fStart)*2 + (c - cStart)*4 + 0; orntNew[3] = -2; ierr = DMPlexSetCone(rdm, newp+1, coneNew);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(rdm, newp+1, orntNew);CHKERRQ(ierr); #if 1 if ((newp+1 < cStartNew) || (newp+1 >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", newp+1, cStartNew, cEndNew); for(p = 0; p < 4; ++p) { if ((coneNew[p] < fStartNew) || (coneNew[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", coneNew[p], fStartNew, fEndNew); } #endif /* C quad */ coneNew[0] = fStartNew + (fEnd - fStart)*2 + (c - cStart)*4 + 1; orntNew[0] = -2; coneNew[1] = fStartNew + (cone[1] - fStart)*2 + (ornt[1] < 0 ? 0 : 1); orntNew[1] = ornt[1]; coneNew[2] = fStartNew + (cone[2] - fStart)*2 + (ornt[2] < 0 ? 1 : 0); orntNew[2] = ornt[2]; coneNew[3] = fStartNew + (fEnd - fStart)*2 + (c - cStart)*4 + 2; orntNew[3] = 0; ierr = DMPlexSetCone(rdm, newp+2, coneNew);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(rdm, newp+2, orntNew);CHKERRQ(ierr); #if 1 if ((newp+2 < cStartNew) || (newp+2 >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", newp+2, cStartNew, cEndNew); for(p = 0; p < 4; ++p) { if ((coneNew[p] < fStartNew) || (coneNew[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", coneNew[p], fStartNew, fEndNew); } #endif /* D quad */ coneNew[0] = fStartNew + (fEnd - fStart)*2 + (c - cStart)*4 + 3; orntNew[0] = 0; coneNew[1] = fStartNew + (fEnd - fStart)*2 + (c - cStart)*4 + 2; orntNew[1] = -2; coneNew[2] = fStartNew + (cone[2] - fStart)*2 + (ornt[2] < 0 ? 0 : 1); orntNew[2] = ornt[2]; coneNew[3] = fStartNew + (cone[3] - fStart)*2 + (ornt[3] < 0 ? 1 : 0); orntNew[3] = ornt[3]; ierr = DMPlexSetCone(rdm, newp+3, coneNew);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(rdm, newp+3, orntNew);CHKERRQ(ierr); #if 1 if ((newp+3 < cStartNew) || (newp+3 >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", newp+3, cStartNew, cEndNew); for(p = 0; p < 4; ++p) { if ((coneNew[p] < fStartNew) || (coneNew[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", coneNew[p], fStartNew, fEndNew); } #endif } /* Split faces have 2 vertices and the same cells as the parent */ ierr = DMPlexGetMaxSizes(dm, PETSC_NULL, &maxSupportSize);CHKERRQ(ierr); ierr = PetscMalloc((2 + maxSupportSize*2) * sizeof(PetscInt), &supportRef);CHKERRQ(ierr); for(f = fStart; f < fEnd; ++f) { const PetscInt newv = vStartNew + (vEnd - vStart) + (f - fStart); for(r = 0; r < 2; ++r) { const PetscInt newp = fStartNew + (f - fStart)*2 + r; const PetscInt *cone, *support; PetscInt coneNew[2], coneSize, c, supportSize, s; ierr = DMPlexGetCone(dm, f, &cone);CHKERRQ(ierr); coneNew[0] = vStartNew + (cone[0] - vStart); coneNew[1] = vStartNew + (cone[1] - vStart); coneNew[(r+1)%2] = newv; ierr = DMPlexSetCone(rdm, newp, coneNew);CHKERRQ(ierr); #if 1 if ((newp < fStartNew) || (newp >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", newp, fStartNew, fEndNew); for(p = 0; p < 2; ++p) { if ((coneNew[p] < vStartNew) || (coneNew[p] >= vEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a vertex [%d, %d)", coneNew[p], vStartNew, vEndNew); } #endif ierr = DMPlexGetSupportSize(dm, f, &supportSize);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, f, &support);CHKERRQ(ierr); for(s = 0; s < supportSize; ++s) { ierr = DMPlexGetConeSize(dm, support[s], &coneSize);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); for(c = 0; c < coneSize; ++c) { if (cone[c] == f) { break; } } supportRef[s] = cStartNew + (support[s] - cStart)*4 + (c+r)%4; } ierr = DMPlexSetSupport(rdm, newp, supportRef);CHKERRQ(ierr); #if 1 if ((newp < fStartNew) || (newp >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", newp, fStartNew, fEndNew); for(p = 0; p < supportSize; ++p) { if ((supportRef[p] < cStartNew) || (supportRef[p] >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", supportRef[p], cStartNew, cEndNew); } #endif } } /* Interior faces have 2 vertices and 2 cells */ for(c = cStart; c < cEnd; ++c) { const PetscInt *cone; PetscInt coneNew[2], supportNew[2]; ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); for(r = 0; r < 4; ++r) { const PetscInt newp = fStartNew + (fEnd - fStart)*2 + (c - cStart)*4 + r; coneNew[0] = vStartNew + (vEnd - vStart) + (cone[r] - fStart); coneNew[1] = vStartNew + (vEnd - vStart) + (fEnd - fStart) + (c - cStart); ierr = DMPlexSetCone(rdm, newp, coneNew);CHKERRQ(ierr); #if 1 if ((newp < fStartNew) || (newp >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", newp, fStartNew, fEndNew); for(p = 0; p < 2; ++p) { if ((coneNew[p] < vStartNew) || (coneNew[p] >= vEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a vertex [%d, %d)", coneNew[p], vStartNew, vEndNew); } #endif supportNew[0] = (c - cStart)*4 + r; supportNew[1] = (c - cStart)*4 + (r+1)%4; ierr = DMPlexSetSupport(rdm, newp, supportNew);CHKERRQ(ierr); #if 1 if ((newp < fStartNew) || (newp >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", newp, fStartNew, fEndNew); for(p = 0; p < 2; ++p) { if ((supportNew[p] < cStartNew) || (supportNew[p] >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", supportNew[p], cStartNew, cEndNew); } #endif } } /* Old vertices have identical supports */ for(v = vStart; v < vEnd; ++v) { const PetscInt newp = vStartNew + (v - vStart); const PetscInt *support, *cone; PetscInt size, s; ierr = DMPlexGetSupportSize(dm, v, &size);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, v, &support);CHKERRQ(ierr); for(s = 0; s < size; ++s) { PetscInt r = 0; ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); if (cone[1] == v) r = 1; supportRef[s] = fStartNew + (support[s] - fStart)*2 + r; } ierr = DMPlexSetSupport(rdm, newp, supportRef);CHKERRQ(ierr); #if 1 if ((newp < vStartNew) || (newp >= vEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a vertex [%d, %d)", newp, vStartNew, vEndNew); for(p = 0; p < size; ++p) { if ((supportRef[p] < fStartNew) || (supportRef[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", supportRef[p], fStartNew, fEndNew); } #endif } /* Face vertices have 2 + cells supports */ for(f = fStart; f < fEnd; ++f) { const PetscInt newp = vStartNew + (vEnd - vStart) + (f - fStart); const PetscInt *cone, *support; PetscInt size, s; ierr = DMPlexGetSupportSize(dm, f, &size);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, f, &support);CHKERRQ(ierr); supportRef[0] = fStartNew + (f - fStart)*2 + 0; supportRef[1] = fStartNew + (f - fStart)*2 + 1; for(s = 0; s < size; ++s) { PetscInt r = 0; ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); if (cone[1] == f) r = 1; else if (cone[2] == f) r = 2; else if (cone[3] == f) r = 3; supportRef[2+s] = fStartNew + (fEnd - fStart)*2 + (support[s] - cStart)*4 + r; } ierr = DMPlexSetSupport(rdm, newp, supportRef);CHKERRQ(ierr); #if 1 if ((newp < vStartNew) || (newp >= vEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a vertex [%d, %d)", newp, vStartNew, vEndNew); for(p = 0; p < 2+size; ++p) { if ((supportRef[p] < fStartNew) || (supportRef[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", supportRef[p], fStartNew, fEndNew); } #endif } /* Cell vertices have 4 supports */ for(c = cStart; c < cEnd; ++c) { const PetscInt newp = vStartNew + (vEnd - vStart) + (fEnd - fStart) + (c - cStart); PetscInt supportNew[4]; for(r = 0; r < 4; ++r) { supportNew[r] = fStartNew + (fEnd - fStart)*2 + (c - cStart)*4 + r; } ierr = DMPlexSetSupport(rdm, newp, supportNew);CHKERRQ(ierr); } break; case 3: if (cMax < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No cell maximum specified in hybrid mesh"); cMax = PetscMin(cEnd, cMax); if (fMax < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No face maximum specified in hybrid mesh"); fMax = PetscMin(fEnd, fMax); /* Interior cells have 3 faces */ for(c = cStart; c < cMax; ++c) { const PetscInt newp = cStartNew + (c - cStart)*4; const PetscInt *cone, *ornt; PetscInt coneNew[3], orntNew[3]; ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); ierr = DMPlexGetConeOrientation(dm, c, &ornt);CHKERRQ(ierr); /* A triangle */ coneNew[0] = fStartNew + (cone[0] - fStart)*2 + (ornt[0] < 0 ? 1 : 0); orntNew[0] = ornt[0]; coneNew[1] = fStartNew + (fMax - fStart)*2 + (c - cStart)*3 + 2; orntNew[1] = -2; coneNew[2] = fStartNew + (cone[2] - fStart)*2 + (ornt[2] < 0 ? 0 : 1); orntNew[2] = ornt[2]; ierr = DMPlexSetCone(rdm, newp+0, coneNew);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(rdm, newp+0, orntNew);CHKERRQ(ierr); #if 1 if ((newp+0 < cStartNew) || (newp+0 >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", newp+0, cStartNew, cEndNew); for(p = 0; p < 3; ++p) { if ((coneNew[p] < fStartNew) || (coneNew[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", coneNew[p], fStartNew, fEndNew); } #endif /* B triangle */ coneNew[0] = fStartNew + (cone[0] - fStart)*2 + (ornt[0] < 0 ? 0 : 1); orntNew[0] = ornt[0]; coneNew[1] = fStartNew + (cone[1] - fStart)*2 + (ornt[1] < 0 ? 1 : 0); orntNew[1] = ornt[1]; coneNew[2] = fStartNew + (fMax - fStart)*2 + (c - cStart)*3 + 0; orntNew[2] = -2; ierr = DMPlexSetCone(rdm, newp+1, coneNew);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(rdm, newp+1, orntNew);CHKERRQ(ierr); #if 1 if ((newp+1 < cStartNew) || (newp+1 >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", newp+1, cStartNew, cEndNew); for(p = 0; p < 3; ++p) { if ((coneNew[p] < fStartNew) || (coneNew[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", coneNew[p], fStartNew, fEndNew); } #endif /* C triangle */ coneNew[0] = fStartNew + (fMax - fStart)*2 + (c - cStart)*3 + 1; orntNew[0] = -2; coneNew[1] = fStartNew + (cone[1] - fStart)*2 + (ornt[1] < 0 ? 0 : 1); orntNew[1] = ornt[1]; coneNew[2] = fStartNew + (cone[2] - fStart)*2 + (ornt[2] < 0 ? 1 : 0); orntNew[2] = ornt[2]; ierr = DMPlexSetCone(rdm, newp+2, coneNew);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(rdm, newp+2, orntNew);CHKERRQ(ierr); #if 1 if ((newp+2 < cStartNew) || (newp+2 >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", newp+2, cStartNew, cEndNew); for(p = 0; p < 3; ++p) { if ((coneNew[p] < fStartNew) || (coneNew[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", coneNew[p], fStartNew, fEndNew); } #endif /* D triangle */ coneNew[0] = fStartNew + (fMax - fStart)*2 + (c - cStart)*3 + 0; orntNew[0] = 0; coneNew[1] = fStartNew + (fMax - fStart)*2 + (c - cStart)*3 + 1; orntNew[1] = 0; coneNew[2] = fStartNew + (fMax - fStart)*2 + (c - cStart)*3 + 2; orntNew[2] = 0; ierr = DMPlexSetCone(rdm, newp+3, coneNew);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(rdm, newp+3, orntNew);CHKERRQ(ierr); #if 1 if ((newp+3 < cStartNew) || (newp+3 >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", newp+3, cStartNew, cEndNew); for(p = 0; p < 3; ++p) { if ((coneNew[p] < fStartNew) || (coneNew[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", coneNew[p], fStartNew, fEndNew); } #endif } /* 2----3----3 | | | B | | | 0----4--- 1 | | | A | | | 0----2----1 */ /* Hybrid cells have 4 faces */ for(c = cMax; c < cEnd; ++c) { const PetscInt newp = cStartNew + (cMax - cStart)*4 + (c - cMax)*2; const PetscInt *cone, *ornt; PetscInt coneNew[4], orntNew[4]; ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); ierr = DMPlexGetConeOrientation(dm, c, &ornt);CHKERRQ(ierr); /* A quad */ coneNew[0] = fStartNew + (cone[0] - fStart)*2 + (ornt[0] < 0 ? 1 : 0); orntNew[0] = ornt[0]; coneNew[1] = fStartNew + (cone[1] - fStart)*2 + (ornt[1] < 0 ? 1 : 0); orntNew[1] = ornt[1]; coneNew[2] = fStartNew + (fMax - fStart)*2 + (cMax - cStart)*3 + (cone[2] - fMax); orntNew[2] = 0; coneNew[3] = fStartNew + (fMax - fStart)*2 + (cMax - cStart)*3 + (fEnd - fMax) + (c - cMax); orntNew[3] = 0; ierr = DMPlexSetCone(rdm, newp+0, coneNew);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(rdm, newp+0, orntNew);CHKERRQ(ierr); #if 1 if ((newp+0 < cStartNew) || (newp+0 >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", newp+0, cStartNew, cEndNew); for(p = 0; p < 4; ++p) { if ((coneNew[p] < fStartNew) || (coneNew[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", coneNew[p], fStartNew, fEndNew); } #endif /* B quad */ coneNew[0] = fStartNew + (cone[0] - fStart)*2 + (ornt[0] < 0 ? 0 : 1); orntNew[0] = ornt[0]; coneNew[1] = fStartNew + (cone[1] - fStart)*2 + (ornt[1] < 0 ? 0 : 1); orntNew[1] = ornt[1]; coneNew[2] = fStartNew + (fMax - fStart)*2 + (cMax - cStart)*3 + (fEnd - fMax) + (c - cMax); orntNew[2] = 0; coneNew[3] = fStartNew + (fMax - fStart)*2 + (cMax - cStart)*3 + (cone[3] - fMax); orntNew[3] = 0; ierr = DMPlexSetCone(rdm, newp+1, coneNew);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(rdm, newp+1, orntNew);CHKERRQ(ierr); #if 1 if ((newp+1 < cStartNew) || (newp+1 >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", newp+1, cStartNew, cEndNew); for(p = 0; p < 4; ++p) { if ((coneNew[p] < fStartNew) || (coneNew[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", coneNew[p], fStartNew, fEndNew); } #endif } /* Interior split faces have 2 vertices and the same cells as the parent */ ierr = DMPlexGetMaxSizes(dm, PETSC_NULL, &maxSupportSize);CHKERRQ(ierr); ierr = PetscMalloc((2 + maxSupportSize*2) * sizeof(PetscInt), &supportRef);CHKERRQ(ierr); for(f = fStart; f < fMax; ++f) { const PetscInt newv = vStartNew + (vEnd - vStart) + (f - fStart); for(r = 0; r < 2; ++r) { const PetscInt newp = fStartNew + (f - fStart)*2 + r; const PetscInt *cone, *support; PetscInt coneNew[2], coneSize, c, supportSize, s; ierr = DMPlexGetCone(dm, f, &cone);CHKERRQ(ierr); coneNew[0] = vStartNew + (cone[0] - vStart); coneNew[1] = vStartNew + (cone[1] - vStart); coneNew[(r+1)%2] = newv; ierr = DMPlexSetCone(rdm, newp, coneNew);CHKERRQ(ierr); #if 1 if ((newp < fStartNew) || (newp >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", newp, fStartNew, fEndNew); for(p = 0; p < 2; ++p) { if ((coneNew[p] < vStartNew) || (coneNew[p] >= vEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a vertex [%d, %d)", coneNew[p], vStartNew, vEndNew); } #endif ierr = DMPlexGetSupportSize(dm, f, &supportSize);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, f, &support);CHKERRQ(ierr); for(s = 0; s < supportSize; ++s) { if (support[s] >= cMax) { supportRef[s] = cStartNew + (cMax - cStart)*4 + (support[s] - cMax)*2 + r; } else { ierr = DMPlexGetConeSize(dm, support[s], &coneSize);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); for(c = 0; c < coneSize; ++c) { if (cone[c] == f) { break; } } supportRef[s] = cStartNew + (support[s] - cStart)*4 + (c+r)%3; } } ierr = DMPlexSetSupport(rdm, newp, supportRef);CHKERRQ(ierr); #if 1 if ((newp < fStartNew) || (newp >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", newp, fStartNew, fEndNew); for(p = 0; p < supportSize; ++p) { if ((supportRef[p] < cStartNew) || (supportRef[p] >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", supportRef[p], cStartNew, cEndNew); } #endif } } /* Interior cell faces have 2 vertices and 2 cells */ for(c = cStart; c < cMax; ++c) { const PetscInt *cone; ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); for(r = 0; r < 3; ++r) { const PetscInt newp = fStartNew + (fMax - fStart)*2 + (c - cStart)*3 + r; PetscInt coneNew[2]; PetscInt supportNew[2]; coneNew[0] = vStartNew + (vEnd - vStart) + (cone[r] - fStart); coneNew[1] = vStartNew + (vEnd - vStart) + (cone[(r+1)%3] - fStart); ierr = DMPlexSetCone(rdm, newp, coneNew);CHKERRQ(ierr); #if 1 if ((newp < fStartNew) || (newp >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", newp, fStartNew, fEndNew); for(p = 0; p < 2; ++p) { if ((coneNew[p] < vStartNew) || (coneNew[p] >= vEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a vertex [%d, %d)", coneNew[p], vStartNew, vEndNew); } #endif supportNew[0] = (c - cStart)*4 + (r+1)%3; supportNew[1] = (c - cStart)*4 + 3; ierr = DMPlexSetSupport(rdm, newp, supportNew);CHKERRQ(ierr); #if 1 if ((newp < fStartNew) || (newp >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", newp, fStartNew, fEndNew); for(p = 0; p < 2; ++p) { if ((supportNew[p] < cStartNew) || (supportNew[p] >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", supportNew[p], cStartNew, cEndNew); } #endif } } /* Interior hybrid faces have 2 vertices and the same cells */ for(f = fMax; f < fEnd; ++f) { const PetscInt newp = fStartNew + (fMax - fStart)*2 + (cMax - cStart)*3 + (f - fMax); const PetscInt *cone; const PetscInt *support; PetscInt coneNew[2]; PetscInt supportNew[2]; PetscInt size, s, r; ierr = DMPlexGetCone(dm, f, &cone);CHKERRQ(ierr); coneNew[0] = vStartNew + (cone[0] - vStart); coneNew[1] = vStartNew + (cone[1] - vStart); ierr = DMPlexSetCone(rdm, newp, coneNew);CHKERRQ(ierr); #if 1 if ((newp < fStartNew) || (newp >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", newp, fStartNew, fEndNew); for(p = 0; p < 2; ++p) { if ((coneNew[p] < vStartNew) || (coneNew[p] >= vEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a vertex [%d, %d)", coneNew[p], vStartNew, vEndNew); } #endif ierr = DMPlexGetSupportSize(dm, f, &size);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, f, &support);CHKERRQ(ierr); for(s = 0; s < size; ++s) { ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); for(r = 0; r < 2; ++r) { if (cone[r+2] == f) break; } supportNew[s] = (cMax - cStart)*4 + (support[s] - cMax)*2 + r; } ierr = DMPlexSetSupport(rdm, newp, supportNew);CHKERRQ(ierr); #if 1 if ((newp < fStartNew) || (newp >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", newp, fStartNew, fEndNew); for(p = 0; p < size; ++p) { if ((supportNew[p] < cStartNew) || (supportNew[p] >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", supportNew[p], cStartNew, cEndNew); } #endif } /* Cell hybrid faces have 2 vertices and 2 cells */ for(c = cMax; c < cEnd; ++c) { const PetscInt newp = fStartNew + (fMax - fStart)*2 + (cMax - cStart)*3 + (fEnd - fMax) + (c - cMax); const PetscInt *cone; PetscInt coneNew[2]; PetscInt supportNew[2]; ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); coneNew[0] = vStartNew + (vEnd - vStart) + (cone[0] - fStart); coneNew[1] = vStartNew + (vEnd - vStart) + (cone[1] - fStart); ierr = DMPlexSetCone(rdm, newp, coneNew);CHKERRQ(ierr); #if 1 if ((newp < fStartNew) || (newp >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", newp, fStartNew, fEndNew); for(p = 0; p < 2; ++p) { if ((coneNew[p] < vStartNew) || (coneNew[p] >= vEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a vertex [%d, %d)", coneNew[p], vStartNew, vEndNew); } #endif supportNew[0] = (cMax - cStart)*4 + (c - cMax)*2 + 0; supportNew[1] = (cMax - cStart)*4 + (c - cMax)*2 + 1; ierr = DMPlexSetSupport(rdm, newp, supportNew);CHKERRQ(ierr); #if 1 if ((newp < fStartNew) || (newp >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", newp, fStartNew, fEndNew); for(p = 0; p < 2; ++p) { if ((supportNew[p] < cStartNew) || (supportNew[p] >= cEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a cell [%d, %d)", supportNew[p], cStartNew, cEndNew); } #endif } /* Old vertices have identical supports */ for(v = vStart; v < vEnd; ++v) { const PetscInt newp = vStartNew + (v - vStart); const PetscInt *support, *cone; PetscInt size, s; ierr = DMPlexGetSupportSize(dm, v, &size);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, v, &support);CHKERRQ(ierr); for(s = 0; s < size; ++s) { if (support[s] >= fMax) { supportRef[s] = fStartNew + (fMax - fStart)*2 + (cMax - cStart)*3 + (support[s] - fMax); } else { PetscInt r = 0; ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); if (cone[1] == v) r = 1; supportRef[s] = fStartNew + (support[s] - fStart)*2 + r; } } ierr = DMPlexSetSupport(rdm, newp, supportRef);CHKERRQ(ierr); #if 1 if ((newp < vStartNew) || (newp >= vEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a vertex [%d, %d)", newp, vStartNew, vEndNew); for(p = 0; p < size; ++p) { if ((supportRef[p] < fStartNew) || (supportRef[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", supportRef[p], fStartNew, fEndNew); } #endif } /* Face vertices have 2 + (2 interior, 1 hybrid) supports */ for(f = fStart; f < fMax; ++f) { const PetscInt newp = vStartNew + (vEnd - vStart) + (f - fStart); const PetscInt *cone, *support; PetscInt size, newSize = 2, s; ierr = DMPlexGetSupportSize(dm, f, &size);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, f, &support);CHKERRQ(ierr); supportRef[0] = fStartNew + (f - fStart)*2 + 0; supportRef[1] = fStartNew + (f - fStart)*2 + 1; for(s = 0; s < size; ++s) { PetscInt r = 0; ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); if (support[s] >= cMax) { supportRef[newSize+0] = fStartNew + (fMax - fStart)*2 + (cMax - cStart)*3 + (fEnd - fMax) + (support[s] - cMax); newSize += 1; } else { if (cone[1] == f) r = 1; else if (cone[2] == f) r = 2; supportRef[newSize+0] = fStartNew + (fMax - fStart)*2 + (support[s] - cStart)*3 + (r+2)%3; supportRef[newSize+1] = fStartNew + (fMax - fStart)*2 + (support[s] - cStart)*3 + r; newSize += 2; } } ierr = DMPlexSetSupport(rdm, newp, supportRef);CHKERRQ(ierr); #if 1 if ((newp < vStartNew) || (newp >= vEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a vertex [%d, %d)", newp, vStartNew, vEndNew); for(p = 0; p < newSize; ++p) { if ((supportRef[p] < fStartNew) || (supportRef[p] >= fEndNew)) SETERRQ3(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Point %d is not a face [%d, %d)", supportRef[p], fStartNew, fEndNew); } #endif } ierr = PetscFree(supportRef);CHKERRQ(ierr); break; default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown cell refiner %d", refiner); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "CellRefinerSetCoordinates" PetscErrorCode CellRefinerSetCoordinates(CellRefiner refiner, DM dm, PetscInt depthSize[], DM rdm) { PetscSection coordSection, coordSectionNew; Vec coordinates, coordinatesNew; PetscScalar *coords, *coordsNew; PetscInt dim, depth, coordSizeNew, cStart, cEnd, c, vStart, vStartNew, vEnd, v, fStart, fEnd, fMax, f; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); ierr = DMPlexGetHybridBounds(dm, PETSC_NULL, &fMax, PETSC_NULL, PETSC_NULL);CHKERRQ(ierr); ierr = GetDepthStart_Private(depth, depthSize, PETSC_NULL, PETSC_NULL, PETSC_NULL, &vStartNew);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = PetscSectionCreate(((PetscObject) dm)->comm, &coordSectionNew);CHKERRQ(ierr); ierr = PetscSectionSetNumFields(coordSectionNew, 1);CHKERRQ(ierr); ierr = PetscSectionSetFieldComponents(coordSectionNew, 0, dim);CHKERRQ(ierr); ierr = PetscSectionSetChart(coordSectionNew, vStartNew, vStartNew+depthSize[0]);CHKERRQ(ierr); if (fMax < 0) fMax = fEnd; switch(refiner) { case 1: case 2: case 3: /* Simplicial and Hex 2D */ /* All vertices have the dim coordinates */ for(v = vStartNew; v < vStartNew+depthSize[0]; ++v) { ierr = PetscSectionSetDof(coordSectionNew, v, dim);CHKERRQ(ierr); ierr = PetscSectionSetFieldDof(coordSectionNew, v, 0, dim);CHKERRQ(ierr); } ierr = PetscSectionSetUp(coordSectionNew);CHKERRQ(ierr); ierr = DMPlexSetCoordinateSection(rdm, coordSectionNew);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = PetscSectionGetStorageSize(coordSectionNew, &coordSizeNew);CHKERRQ(ierr); ierr = VecCreate(((PetscObject) dm)->comm, &coordinatesNew);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) coordinatesNew, "coordinates");CHKERRQ(ierr); ierr = VecSetSizes(coordinatesNew, coordSizeNew, PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetFromOptions(coordinatesNew);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); ierr = VecGetArray(coordinatesNew, &coordsNew);CHKERRQ(ierr); /* Old vertices have the same coordinates */ for(v = vStart; v < vEnd; ++v) { const PetscInt newv = vStartNew + (v - vStart); PetscInt off, offnew, d; ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); ierr = PetscSectionGetOffset(coordSectionNew, newv, &offnew);CHKERRQ(ierr); for(d = 0; d < dim; ++d) { coordsNew[offnew+d] = coords[off+d]; } } /* Face vertices have the average of endpoint coordinates */ for(f = fStart; f < fMax; ++f) { const PetscInt newv = vStartNew + (vEnd - vStart) + (f - fStart); const PetscInt *cone; PetscInt coneSize, offA, offB, offnew, d; ierr = DMPlexGetConeSize(dm, f, &coneSize);CHKERRQ(ierr); if (coneSize != 2) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONG, "Face %d cone should have two vertices, not %d", f, coneSize); ierr = DMPlexGetCone(dm, f, &cone);CHKERRQ(ierr); ierr = PetscSectionGetOffset(coordSection, cone[0], &offA);CHKERRQ(ierr); ierr = PetscSectionGetOffset(coordSection, cone[1], &offB);CHKERRQ(ierr); ierr = PetscSectionGetOffset(coordSectionNew, newv, &offnew);CHKERRQ(ierr); for(d = 0; d < dim; ++d) { coordsNew[offnew+d] = 0.5*(coords[offA+d] + coords[offB+d]); } } /* Just Hex 2D */ if (refiner == 2) { /* Cell vertices have the average of corner coordinates */ for(c = cStart; c < cEnd; ++c) { const PetscInt newv = vStartNew + (vEnd - vStart) + (fEnd - fStart) + (c - cStart); PetscInt *cone = PETSC_NULL; PetscInt closureSize, coneSize = 0, offA, offB, offC, offD, offnew, p, d; ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &cone);CHKERRQ(ierr); for(p = 0; p < closureSize*2; p += 2) { const PetscInt point = cone[p]; if ((point >= vStart) && (point < vEnd)) { cone[coneSize++] = point; } } if (coneSize != 4) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONG, "Quad %d cone should have four vertices, not %d", c, coneSize); ierr = PetscSectionGetOffset(coordSection, cone[0], &offA);CHKERRQ(ierr); ierr = PetscSectionGetOffset(coordSection, cone[1], &offB);CHKERRQ(ierr); ierr = PetscSectionGetOffset(coordSection, cone[2], &offC);CHKERRQ(ierr); ierr = PetscSectionGetOffset(coordSection, cone[3], &offD);CHKERRQ(ierr); ierr = PetscSectionGetOffset(coordSectionNew, newv, &offnew);CHKERRQ(ierr); for(d = 0; d < dim; ++d) { coordsNew[offnew+d] = 0.25*(coords[offA+d] + coords[offB+d] + coords[offC+d] + coords[offD+d]); } ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &cone);CHKERRQ(ierr); } } ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); ierr = VecRestoreArray(coordinatesNew, &coordsNew);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(rdm, coordinatesNew);CHKERRQ(ierr); ierr = VecDestroy(&coordinatesNew);CHKERRQ(ierr); break; default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown cell refiner %d", refiner); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexCreateProcessSF" PetscErrorCode DMPlexCreateProcessSF(DM dm, PetscSF sfPoint, IS *processRanks, PetscSF *sfProcess) { PetscInt numRoots, numLeaves, l; const PetscInt *localPoints; const PetscSFNode *remotePoints; PetscInt *localPointsNew; PetscSFNode *remotePointsNew; PetscInt *ranks, *ranksNew; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); ierr = PetscMalloc(numLeaves * sizeof(PetscInt), &ranks);CHKERRQ(ierr); for(l = 0; l < numLeaves; ++l) { ranks[l] = remotePoints[l].rank; } ierr = PetscSortRemoveDupsInt(&numLeaves, ranks);CHKERRQ(ierr); ierr = PetscMalloc(numLeaves * sizeof(PetscInt), &ranksNew);CHKERRQ(ierr); ierr = PetscMalloc(numLeaves * sizeof(PetscInt), &localPointsNew);CHKERRQ(ierr); ierr = PetscMalloc(numLeaves * sizeof(PetscSFNode), &remotePointsNew);CHKERRQ(ierr); for(l = 0; l < numLeaves; ++l) { ranksNew[l] = ranks[l]; localPointsNew[l] = l; remotePointsNew[l].index = 0; remotePointsNew[l].rank = ranksNew[l]; } ierr = PetscFree(ranks);CHKERRQ(ierr); ierr = ISCreateGeneral(((PetscObject) dm)->comm, numLeaves, ranksNew, PETSC_OWN_POINTER, processRanks);CHKERRQ(ierr); ierr = PetscSFCreate(((PetscObject) dm)->comm, sfProcess);CHKERRQ(ierr); ierr = PetscSFSetFromOptions(*sfProcess);CHKERRQ(ierr); ierr = PetscSFSetGraph(*sfProcess, 1, numLeaves, localPointsNew, PETSC_OWN_POINTER, remotePointsNew, PETSC_OWN_POINTER);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "CellRefinerCreateSF" PetscErrorCode CellRefinerCreateSF(CellRefiner refiner, DM dm, PetscInt depthSize[], DM rdm) { PetscSF sf, sfNew, sfProcess; IS processRanks; MPI_Datatype depthType; PetscInt numRoots, numLeaves, numLeavesNew = 0, l, m; const PetscInt *localPoints, *neighbors; const PetscSFNode *remotePoints; PetscInt *localPointsNew; PetscSFNode *remotePointsNew; PetscInt *depthSizeOld, *rdepthSize, *rdepthSizeOld, *rdepthMaxOld, *rvStart, *rvStartNew, *reStart, *reStartNew, *rfStart, *rfStartNew, *rcStart, *rcStartNew; PetscInt depth, numNeighbors, pStartNew, pEndNew, cStart, cStartNew, cEnd, cMax, vStart, vStartNew, vEnd, vMax, fStart, fStartNew, fEnd, fMax, eStart, eStartNew, eEnd, eMax, r, n; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetChart(rdm, &pStartNew, &pEndNew);CHKERRQ(ierr); ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); ierr = DMPlexGetHybridBounds(dm, &cMax, &fMax, &eMax, &vMax);CHKERRQ(ierr); ierr = GetDepthStart_Private(depth, depthSize, &cStartNew, &fStartNew, &eStartNew, &vStartNew);CHKERRQ(ierr); switch(refiner) { case 3: if (cMax < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No cell maximum specified in hybrid mesh"); cMax = PetscMin(cEnd, cMax); if (fMax < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No face maximum specified in hybrid mesh"); fMax = PetscMin(fEnd, fMax); } ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); ierr = DMGetPointSF(rdm, &sfNew);CHKERRQ(ierr); /* Caculate size of new SF */ ierr = PetscSFGetGraph(sf, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); if (numRoots < 0) PetscFunctionReturn(0); for(l = 0; l < numLeaves; ++l) { const PetscInt p = localPoints[l]; switch(refiner) { case 1: /* Simplicial 2D */ if ((p >= vStart) && (p < vEnd)) { /* Old vertices stay the same */ ++numLeavesNew; } else if ((p >= fStart) && (p < fEnd)) { /* Old faces add new faces and vertex */ numLeavesNew += 1 + 2; } else if ((p >= cStart) && (p < cEnd)) { /* Old cells add new cells and interior faces */ numLeavesNew += 4 + 3; } break; case 2: /* Hex 2D */ if ((p >= vStart) && (p < vEnd)) { /* Old vertices stay the same */ ++numLeavesNew; } else if ((p >= fStart) && (p < fEnd)) { /* Old faces add new faces and vertex */ numLeavesNew += 1 + 2; } else if ((p >= cStart) && (p < cEnd)) { /* Old cells add new cells and interior faces */ numLeavesNew += 4 + 4; } break; default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown cell refiner %d", refiner); } } /* Communicate depthSizes for each remote rank */ ierr = DMPlexCreateProcessSF(dm, sf, &processRanks, &sfProcess);CHKERRQ(ierr); ierr = ISGetLocalSize(processRanks, &numNeighbors);CHKERRQ(ierr); ierr = PetscMalloc5((depth+1)*numNeighbors,PetscInt,&rdepthSize,numNeighbors,PetscInt,&rvStartNew,numNeighbors,PetscInt,&reStartNew,numNeighbors,PetscInt,&rfStartNew,numNeighbors,PetscInt,&rcStartNew);CHKERRQ(ierr); ierr = PetscMalloc7(depth+1,PetscInt,&depthSizeOld,(depth+1)*numNeighbors,PetscInt,&rdepthSizeOld,(depth+1)*numNeighbors,PetscInt,&rdepthMaxOld,numNeighbors,PetscInt,&rvStart,numNeighbors,PetscInt,&reStart,numNeighbors,PetscInt,&rfStart,numNeighbors,PetscInt,&rcStart);CHKERRQ(ierr); ierr = MPI_Type_contiguous(depth+1, MPIU_INT, &depthType);CHKERRQ(ierr); ierr = MPI_Type_commit(&depthType);CHKERRQ(ierr); ierr = PetscSFBcastBegin(sfProcess, depthType, depthSize, rdepthSize);CHKERRQ(ierr); ierr = PetscSFBcastEnd(sfProcess, depthType, depthSize, rdepthSize);CHKERRQ(ierr); for(n = 0; n < numNeighbors; ++n) { ierr = GetDepthStart_Private(depth, &rdepthSize[n*(depth+1)], &rcStartNew[n], &rfStartNew[n], &reStartNew[n], &rvStartNew[n]);CHKERRQ(ierr); } depthSizeOld[depth] = cMax; depthSizeOld[0] = vMax; depthSizeOld[depth-1] = fMax; depthSizeOld[1] = eMax; ierr = PetscSFBcastBegin(sfProcess, depthType, depthSizeOld, rdepthMaxOld);CHKERRQ(ierr); ierr = PetscSFBcastEnd(sfProcess, depthType, depthSizeOld, rdepthMaxOld);CHKERRQ(ierr); depthSizeOld[depth] = cEnd - cStart; depthSizeOld[0] = vEnd - vStart; depthSizeOld[depth-1] = fEnd - fStart; depthSizeOld[1] = eEnd - eStart; ierr = PetscSFBcastBegin(sfProcess, depthType, depthSizeOld, rdepthSizeOld);CHKERRQ(ierr); ierr = PetscSFBcastEnd(sfProcess, depthType, depthSizeOld, rdepthSizeOld);CHKERRQ(ierr); for(n = 0; n < numNeighbors; ++n) { ierr = GetDepthStart_Private(depth, &rdepthSizeOld[n*(depth+1)], &rcStart[n], &rfStart[n], &reStart[n], &rvStart[n]);CHKERRQ(ierr); } ierr = MPI_Type_free(&depthType);CHKERRQ(ierr); ierr = PetscSFDestroy(&sfProcess);CHKERRQ(ierr); /* Calculate new point SF */ ierr = PetscMalloc(numLeavesNew * sizeof(PetscInt), &localPointsNew);CHKERRQ(ierr); ierr = PetscMalloc(numLeavesNew * sizeof(PetscSFNode), &remotePointsNew);CHKERRQ(ierr); ierr = ISGetIndices(processRanks, &neighbors);CHKERRQ(ierr); for(l = 0, m = 0; l < numLeaves; ++l) { PetscInt p = localPoints[l]; PetscInt rp = remotePoints[l].index, n; PetscMPIInt rrank = remotePoints[l].rank; ierr = PetscFindInt(rrank, numNeighbors, neighbors, &n);CHKERRQ(ierr); if (n < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not locate remote rank %d", rrank); switch(refiner) { case 1: /* Simplicial 2D */ if ((p >= vStart) && (p < vEnd)) { /* Old vertices stay the same */ localPointsNew[m] = vStartNew + (p - vStart); remotePointsNew[m].index = rvStartNew[n] + (rp - rvStart[n]); remotePointsNew[m].rank = rrank; ++m; } else if ((p >= fStart) && (p < fEnd)) { /* Old faces add new faces and vertex */ localPointsNew[m] = vStartNew + (vEnd - vStart) + (p - fStart); remotePointsNew[m].index = rvStartNew[n] + rdepthSizeOld[n*(depth+1)+0] + (rp - rfStart[n]); remotePointsNew[m].rank = rrank; ++m; for(r = 0; r < 2; ++r, ++m) { localPointsNew[m] = fStartNew + (p - fStart)*2 + r; remotePointsNew[m].index = rfStartNew[n] + (rp - rfStart[n])*2 + r; remotePointsNew[m].rank = rrank; } } else if ((p >= cStart) && (p < cEnd)) { /* Old cells add new cells and interior faces */ for(r = 0; r < 4; ++r, ++m) { localPointsNew[m] = cStartNew + (p - cStart)*4 + r; remotePointsNew[m].index = rcStartNew[n] + (rp - rcStart[n])*4 + r; remotePointsNew[m].rank = rrank; } for(r = 0; r < 3; ++r, ++m) { localPointsNew[m] = fStartNew + (fEnd - fStart)*2 + (p - cStart)*3 + r; remotePointsNew[m].index = rfStartNew[n] + rdepthSizeOld[n*(depth+1)+depth-1]*2 + (rp - rcStart[n])*3 + r; remotePointsNew[m].rank = rrank; } } break; case 2: /* Hex 2D */ if ((p >= vStart) && (p < vEnd)) { /* Old vertices stay the same */ localPointsNew[m] = vStartNew + (p - vStart); remotePointsNew[m].index = rvStartNew[n] + (rp - rvStart[n]); remotePointsNew[m].rank = rrank; ++m; } else if ((p >= fStart) && (p < fEnd)) { /* Old faces add new faces and vertex */ localPointsNew[m] = vStartNew + (vEnd - vStart) + (p - fStart); remotePointsNew[m].index = rvStartNew[n] + rdepthSizeOld[n*(depth+1)+0] + (rp - rfStart[n]); remotePointsNew[m].rank = rrank; ++m; for(r = 0; r < 2; ++r, ++m) { localPointsNew[m] = fStartNew + (p - fStart)*2 + r; remotePointsNew[m].index = rfStartNew[n] + (rp - rfStart[n])*2 + r; remotePointsNew[m].rank = rrank; } } else if ((p >= cStart) && (p < cEnd)) { /* Old cells add new cells and interior faces */ for(r = 0; r < 4; ++r, ++m) { localPointsNew[m] = cStartNew + (p - cStart)*4 + r; remotePointsNew[m].index = rcStartNew[n] + (rp - rcStart[n])*4 + r; remotePointsNew[m].rank = rrank; } for(r = 0; r < 4; ++r, ++m) { localPointsNew[m] = fStartNew + (fEnd - fStart)*2 + (p - cStart)*4 + r; remotePointsNew[m].index = rfStartNew[n] + rdepthSizeOld[n*(depth+1)+depth-1]*2 + (rp - rcStart[n])*4 + r; remotePointsNew[m].rank = rrank; } } break; case 3: /* Hybrid simplicial 2D */ if ((p >= vStart) && (p < vEnd)) { /* Old vertices stay the same */ localPointsNew[m] = vStartNew + (p - vStart); remotePointsNew[m].index = rvStartNew[n] + (rp - rvStart[n]); remotePointsNew[m].rank = rrank; ++m; } else if ((p >= fStart) && (p < fMax)) { /* Old interior faces add new faces and vertex */ localPointsNew[m] = vStartNew + (vEnd - vStart) + (p - fStart); remotePointsNew[m].index = rvStartNew[n] + rdepthSizeOld[n*(depth+1)+0] + (rp - rfStart[n]); remotePointsNew[m].rank = rrank; ++m; for(r = 0; r < 2; ++r, ++m) { localPointsNew[m] = fStartNew + (p - fStart)*2 + r; remotePointsNew[m].index = rfStartNew[n] + (rp - rfStart[n])*2 + r; remotePointsNew[m].rank = rrank; } } else if ((p >= fMax) && (p < fEnd)) { /* Old hybrid faces stay the same */ localPointsNew[m] = fStartNew + (fMax - fStart)*2 + (p - fMax); remotePointsNew[m].index = rfStartNew[n] + (rdepthMaxOld[n*(depth+1)+depth-1] - rfStart[n])*2 + (rp - rdepthMaxOld[n*(depth+1)+depth-1]); remotePointsNew[m].rank = rrank; ++m; } else if ((p >= cStart) && (p < cMax)) { /* Old interior cells add new cells and interior faces */ for(r = 0; r < 4; ++r, ++m) { localPointsNew[m] = cStartNew + (p - cStart)*4 + r; remotePointsNew[m].index = rcStartNew[n] + (rp - rcStart[n])*4 + r; remotePointsNew[m].rank = rrank; } for(r = 0; r < 3; ++r, ++m) { localPointsNew[m] = fStartNew + (fMax - fStart)*2 + (p - cStart)*3 + r; remotePointsNew[m].index = rfStartNew[n] + (rdepthMaxOld[n*(depth+1)+depth-1] - rfStart[n])*2 + (rp - rcStart[n])*3 + r; remotePointsNew[m].rank = rrank; } } else if ((p >= cStart) && (p < cMax)) { /* Old hybrid cells add new cells and hybrid face */ for(r = 0; r < 2; ++r, ++m) { localPointsNew[m] = cStartNew + (p - cStart)*4 + r; remotePointsNew[m].index = rcStartNew[n] + (rp - rcStart[n])*4 + r; remotePointsNew[m].rank = rrank; } localPointsNew[m] = fStartNew + (fMax - fStart)*2 + (cMax - cStart)*3 + (p - cMax); remotePointsNew[m].index = rfStartNew[n] + (rdepthMaxOld[n*(depth+1)+depth-1] - rfStart[n])*2 + (rdepthMaxOld[n*(depth+1)+depth] - rcStart[n])*3 + (rp - rdepthMaxOld[n*(depth+1)+depth]); remotePointsNew[m].rank = rrank; ++m; } break; default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown cell refiner %d", refiner); } } ierr = ISRestoreIndices(processRanks, &neighbors);CHKERRQ(ierr); ierr = ISDestroy(&processRanks);CHKERRQ(ierr); ierr = PetscSFSetGraph(sfNew, pEndNew-pStartNew, numLeavesNew, localPointsNew, PETSC_OWN_POINTER, remotePointsNew, PETSC_OWN_POINTER);CHKERRQ(ierr); ierr = PetscFree5(rdepthSize,rvStartNew,reStartNew,rfStartNew,rcStartNew);CHKERRQ(ierr); ierr = PetscFree6(depthSizeOld,rdepthSizeOld,rvStart,reStart,rfStart,rcStart);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "CellRefinerCreateLabels" PetscErrorCode CellRefinerCreateLabels(CellRefiner refiner, DM dm, PetscInt depthSize[], DM rdm) { PetscInt numLabels, l; PetscInt newp, cStart, cStartNew, cEnd, cMax, vStart, vStartNew, vEnd, vMax, fStart, fStartNew, fEnd, fMax, eStart, eEnd, eMax, r; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); cStartNew = 0; vStartNew = depthSize[2]; fStartNew = depthSize[2] + depthSize[0]; ierr = DMPlexGetNumLabels(dm, &numLabels);CHKERRQ(ierr); ierr = DMPlexGetHybridBounds(dm, &cMax, &fMax, &eMax, &vMax);CHKERRQ(ierr); switch(refiner) { case 3: if (cMax < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No cell maximum specified in hybrid mesh"); cMax = PetscMin(cEnd, cMax); if (fMax < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No face maximum specified in hybrid mesh"); fMax = PetscMin(fEnd, fMax); } for(l = 0; l < numLabels; ++l) { DMLabel label, labelNew; const char *lname; PetscBool isDepth; IS valueIS; const PetscInt *values; PetscInt numValues, val; ierr = DMPlexGetLabelName(dm, l, &lname);CHKERRQ(ierr); ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr); if (isDepth) continue; ierr = DMPlexCreateLabel(rdm, lname);CHKERRQ(ierr); ierr = DMPlexGetLabel(dm, lname, &label);CHKERRQ(ierr); ierr = DMPlexGetLabel(rdm, lname, &labelNew);CHKERRQ(ierr); ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); ierr = ISGetLocalSize(valueIS, &numValues);CHKERRQ(ierr); ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); for(val = 0; val < numValues; ++val) { IS pointIS; const PetscInt *points; PetscInt numPoints, n; ierr = DMLabelGetStratumIS(label, values[val], &pointIS);CHKERRQ(ierr); ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr); ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); for(n = 0; n < numPoints; ++n) { const PetscInt p = points[n]; switch(refiner) { case 1: /* Simplicial 2D */ if ((p >= vStart) && (p < vEnd)) { /* Old vertices stay the same */ newp = vStartNew + (p - vStart); ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); } else if ((p >= fStart) && (p < fEnd)) { /* Old faces add new faces and vertex */ newp = vStartNew + (vEnd - vStart) + (p - fStart); ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); for(r = 0; r < 2; ++r) { newp = fStartNew + (p - fStart)*2 + r; ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); } } else if ((p >= cStart) && (p < cEnd)) { /* Old cells add new cells and interior faces */ for(r = 0; r < 4; ++r) { newp = cStartNew + (p - cStart)*4 + r; ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); } for(r = 0; r < 3; ++r) { newp = fStartNew + (fEnd - fStart)*2 + (p - cStart)*3 + r; ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); } } break; case 2: /* Hex 2D */ if ((p >= vStart) && (p < vEnd)) { /* Old vertices stay the same */ newp = vStartNew + (p - vStart); ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); } else if ((p >= fStart) && (p < fEnd)) { /* Old faces add new faces and vertex */ newp = vStartNew + (vEnd - vStart) + (p - fStart); ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); for(r = 0; r < 2; ++r) { newp = fStartNew + (p - fStart)*2 + r; ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); } } else if ((p >= cStart) && (p < cEnd)) { /* Old cells add new cells and interior faces and vertex */ for(r = 0; r < 4; ++r) { newp = cStartNew + (p - cStart)*4 + r; ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); } for(r = 0; r < 4; ++r) { newp = fStartNew + (fEnd - fStart)*2 + (p - cStart)*4 + r; ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); } newp = vStartNew + (vEnd - vStart) + (fEnd - fStart) + (p - cStart); ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); } break; case 3: /* Hybrid simplicial 2D */ if ((p >= vStart) && (p < vEnd)) { /* Old vertices stay the same */ newp = vStartNew + (p - vStart); ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); } else if ((p >= fStart) && (p < fMax)) { /* Old interior faces add new faces and vertex */ newp = vStartNew + (vEnd - vStart) + (p - fStart); ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); for(r = 0; r < 2; ++r) { newp = fStartNew + (p - fStart)*2 + r; ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); } } else if ((p >= fMax) && (p < fEnd)) { /* Old hybrid faces stay the same */ newp = fStartNew + (fMax - fStart)*2 + (p - fMax); ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); } else if ((p >= cStart) && (p < cMax)) { /* Old interior cells add new cells and interior faces */ for(r = 0; r < 4; ++r) { newp = cStartNew + (p - cStart)*4 + r; ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); } for(r = 0; r < 3; ++r) { newp = fStartNew + (fEnd - fStart)*2 + (p - cStart)*3 + r; ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); } } else if ((p >= cMax) && (p < cEnd)) { /* Old hybrid cells add new cells and hybrid face */ for(r = 0; r < 2; ++r) { newp = cStartNew + (cMax - cStart)*4 + (p - cMax)*2 + r; ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); } newp = fStartNew + (fMax - fStart)*2 + (cMax - cStart)*3 + (p - cMax); ierr = DMLabelSetValue(labelNew, newp, values[val]);CHKERRQ(ierr); } break; default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown cell refiner %d", refiner); } } ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); ierr = ISDestroy(&pointIS);CHKERRQ(ierr); } ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); ierr = ISDestroy(&valueIS);CHKERRQ(ierr); if (0) { ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);CHKERRQ(ierr); ierr = DMLabelView(labelNew, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexRefine_Uniform" /* This will only work for interpolated meshes */ PetscErrorCode DMPlexRefine_Uniform(DM dm, CellRefiner cellRefiner, DM *dmRefined) { DM rdm; PetscInt *depthSize; PetscInt dim, depth = 0, d, pStart = 0, pEnd = 0; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMCreate(((PetscObject) dm)->comm, &rdm);CHKERRQ(ierr); ierr = DMSetType(rdm, DMPLEX);CHKERRQ(ierr); ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexSetDimension(rdm, dim);CHKERRQ(ierr); /* Calculate number of new points of each depth */ ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthSize);CHKERRQ(ierr); ierr = PetscMemzero(depthSize, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); ierr = CellRefinerGetSizes(cellRefiner, dm, depthSize);CHKERRQ(ierr); /* Step 1: Set chart */ for(d = 0; d <= depth; ++d) { pEnd += depthSize[d]; } ierr = DMPlexSetChart(rdm, pStart, pEnd);CHKERRQ(ierr); /* Step 2: Set cone/support sizes */ ierr = CellRefinerSetConeSizes(cellRefiner, dm, depthSize, rdm);CHKERRQ(ierr); /* Step 3: Setup refined DM */ ierr = DMSetUp(rdm);CHKERRQ(ierr); /* Step 4: Set cones and supports */ ierr = CellRefinerSetCones(cellRefiner, dm, depthSize, rdm);CHKERRQ(ierr); /* Step 5: Stratify */ ierr = DMPlexStratify(rdm);CHKERRQ(ierr); /* Step 6: Set coordinates for vertices */ ierr = CellRefinerSetCoordinates(cellRefiner, dm, depthSize, rdm);CHKERRQ(ierr); /* Step 7: Create pointSF */ ierr = CellRefinerCreateSF(cellRefiner, dm, depthSize, rdm);CHKERRQ(ierr); /* Step 8: Create labels */ ierr = CellRefinerCreateLabels(cellRefiner, dm, depthSize, rdm);CHKERRQ(ierr); ierr = PetscFree(depthSize);CHKERRQ(ierr); *dmRefined = rdm; #if 0 DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt dim, cStart, cEnd, cMax, c, vStart, vEnd, vMax; /* ALE::ISieveVisitor::PointRetriever cV(std::max(1, sieve->getMaxConeSize())); */ PetscFunctionBegin; ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); /* PyLith: _refineCensored(newMesh, mesh, refiner); */ ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMPlexGetHybridBounds(dm, &cMax, PETSC_NULL, PETSC_NULL, &vMax);CHKERRQ(ierr); /* Count number of new cells which are normal and extra */ PetscInt cEnd2 = cMax >= 0 ? cMax : cEnd; PetscInt newNumCellsNormal = 0, newNumCellsExtra = 0, newNumCells; for(c = cStart; c < cEnd2; ++c) { PetscInt n; ierr = CellRefinerGetNumSubcells(c, &n);CHKERRQ(ierr); /* refiner.numNewCells */ newNumCellsNormal += n; } for(c = cEnd2; c < cEnd; ++c) { PetscInt n; ierr = CellRefinerGetNumSubcells(c, &n);CHKERRQ(ierr); /* refiner.numNewCells */ newNumCellsExtra += n; } newNumCells = newNumCellsNormal + newNumCellsExtra; /* Count number of new vertices which are normal and extra */ PetscInt vEnd2 = vMax >= 0 ? vMax : vEnd; PetscInt newNumVertices, newNumVerticesNormal, newNumVerticesExtra, newFirstVertex = newNumCells + (vEnd2 - vStart), newVertex = newFirstVertex; for(c = cStart; c < cEnd; ++c) { PetscInt *closure = PETSC_NULL; PetscInt closureSize, numCorners = 0, p; ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); for(p = 0; p < closureSize*2; p += 2) { const PetscInt point = closure[p]; if ((point >= vStart) && (point < vEnd)) { closure[numCorners++] = point; } } ierr = CellRefinerSplitCell(c, closure, numCorners, &newVertex);CHKERRQ(ierr); /* refiner.splitCell */ ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); } newNumVerticesNormal = newVertex - newFirstVertex + (vEnd2 - vStart); for(c = cEnd2; c < cEnd; ++c) { PetscInt *closure = PETSC_NULL; PetscInt closureSize, numCorners = 0, p; ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); for(p = 0; p < closureSize*2; p += 2) { const PetscInt point = closure[p]; if ((point >= vStart) && (point < vEnd)) { closure[numCorners++] = point; } } ierr = CellRefinerSplitCellExtra(c, closure, numCorners, &newVertex);CHKERRQ(ierr); /* refiner.splitCellUncensored */ ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); } /* for */ newNumVerticesExtra = newVertex - newFirstVertex - newNumVerticesNormal; newNumVertices = newNumVerticesNormal + newNumVerticesExtra; #if 1 PetscInt oldNumCellsNormal = cEnd2 - cStart; PetscInt oldNumCellsExtra = cEnd - cEnd2; ierr = PetscSynchronizedPrintf(comm, "[%d]Old normal cells [%d, %d)\n", rank, 0, oldNumCellsNormal); ierr = PetscSynchronizedPrintf(comm, "[%d]Old fault cells [%d, %d)\n", rank, oldNumCellsNormal+oldNumVerticesNormal+oldNumVerticesExtra, oldNumCellsNormal+oldNumVerticesNormal+oldNumVerticesExtra+oldNumCellsExtra); ierr = PetscSynchronizedPrintf(comm, "[%d]Old normal vertices [%d, %d)\n", rank, oldNumCellsNormal, oldNumCellsNormal+oldNumVerticesNormal); ierr = PetscSynchronizedPrintf(comm, "[%d]Old fault vertices [%d, %d)\n", rank, oldNumCellsNormal+oldNumVerticesNormal, oldNumCellsNormal+oldNumVerticesNormal+oldNumVerticesExtra); ierr = PetscSynchronizedPrintf(comm, "[%d]New normal cells [%d, %d)\n", rank, 0, newNumCellsNormal); ierr = PetscSynchronizedPrintf(comm, "[%d]New fault cells [%d, %d)\n", rank, newNumCellsNormal+newNumVerticesNormal+newNumVerticesExtra, newNumCellsNormal+newNumVerticesNormal+newNumVerticesExtra+newNumCellsExtra); ierr = PetscSynchronizedPrintf(comm, "[%d]New normal vertices [%d, %d)\n", rank, newNumCellsNormal, newNumCellsNormal+newNumVerticesNormal); ierr = PetscSynchronizedPrintf(comm, "[%d]New fault vertices [%d, %d)\n", rank, newNumCellsNormal+newNumVerticesNormal, newNumCellsNormal+newNumVerticesNormal+newNumVerticesExtra); ierr = PetscSynchronizedFlush(comm); #endif ierr = DMCreate(comm, dmRefined);CHKERRQ(ierr); ierr = DMSetType(*dmRefined, DMPLEX);CHKERRQ(ierr); ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr); ierr = DMPlexSetChart(*dmRefined, 0, newNumCells+newNumVertices);CHKERRQ(ierr); ierr = DMPlexGetHybridBounds(*dmRefined, newNumCellsNormal, PETSC_NULL, PETSC_NULL, newFirstVertex+newNumVerticesNormal);CHKERRQ(ierr); /* Set cone and support sizes for new normal cells */ PetscInt newCell = 0; for(c = cStart; c < cEnd2; ++c) { PetscInt coneSize, n, i; ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); ierr = CellRefinerGetNumSubcells(refiner, c, &n); /* refiner.getNewCells(&newCells, &numNewCells, *c_iter, cone, coneSize, *_orderOldMesh, *_orderNewMesh); */ for(i = 0; i < n; ++i, ++newCell) { ierr = DMPlexSetConeSize(*dmRefined, newCell, coneSize);CHKERRQ(ierr); } PetscInt *closure = PETSC_NULL; PetscInt closureSize, numCorners = 0, p; ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); for(p = 0; p < closureSize*2; p += 2) { const PetscInt point = closure[p]; if ((point >= vStart) && (point < vEnd)) { closure[numCorners++] = point; } } /* ierr = CellRefinerGetSubcells(refiner, c, numCorners, closure, &numNewCells, &newCells);CHKERRQ(ierr); // refiner.getNewCells(&newCells, &numNewCells, *c_iter, cone, coneSize, *_orderOldMesh, *_orderNewMesh); */ ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); } /* Reset current new cell value and loop over censored cells. */ curNewCell = _orderNewMesh->cellsCensored().min(); oldCellsEnd = _orderOldMesh->cellsCensored().end(); for (interval_type::const_iterator c_iter=_orderOldMesh->cellsCensored().begin(); c_iter != oldCellsEnd; ++c_iter) { /* Set new cone and support sizes */ cV.clear(); sieve->cone(*c_iter, cV); const point_type* cone = cV.getPoints(); const int coneSize = cV.getSize(); const point_type* newCells; int numNewCells = 0; refiner.getNewCells(&newCells, &numNewCells, *c_iter, cone, coneSize, *_orderOldMesh, *_orderNewMesh); for(int iCell=0; iCell < numNewCells; ++iCell, ++curNewCell) { newSieve->setConeSize(curNewCell, coneSize); for(int iVertex=0; iVertex < coneSize; ++iVertex) { newSieve->addSupportSize(newCells[iCell*coneSize+iVertex], 1); } /* for */ } /* for */ } /* for */ newSieve->allocate(); ierr = DMPlexSymmetrizeSizes();CHKERRQ(ierr); /* Create refined cells in new sieve. */ curNewCell = _orderNewMesh->cellsNormal().min(); oldCellsEnd = _orderOldMesh->cellsNormal().end(); for (interval_type::const_iterator c_iter=_orderOldMesh->cellsNormal().begin(); c_iter != oldCellsEnd; ++c_iter) { cV.clear(); sieve->cone(*c_iter, cV); const point_type *cone = cV.getPoints(); const int coneSize = cV.getSize(); const point_type* newCells; int numNewCells = 0; refiner.getNewCells(&newCells, &numNewCells, *c_iter, cone, coneSize, *_orderOldMesh, *_orderNewMesh); for(int iCell=0; iCell < numNewCells; ++iCell, ++curNewCell) { newSieve->setCone(&newCells[iCell*coneSize], curNewCell); } /* for */ } /* for */ curNewCell = _orderNewMesh->cellsCensored().min(); oldCellsEnd = _orderOldMesh->cellsCensored().end(); for (interval_type::const_iterator c_iter=_orderOldMesh->cellsCensored().begin(); c_iter != oldCellsEnd; ++c_iter) { cV.clear(); sieve->cone(*c_iter, cV); const point_type *cone = cV.getPoints(); const int coneSize = cV.getSize(); const point_type* newCells; int numNewCells = 0; refiner.getNewCells(&newCells, &numNewCells, *c_iter, cone, coneSize, *_orderOldMesh, *_orderNewMesh); for(int iCell=0; iCell < numNewCells; ++iCell, ++curNewCell) { newSieve->setCone(&newCells[iCell*coneSize], curNewCell); } /* for */ } /* for */ newSieve->symmetrize(); /* Set coordinates in refined mesh. */ const Obj& coordinates = mesh->getRealSection("coordinates"); assert(!coordinates.isNull()); const Obj& newCoordinates = newMesh->getRealSection("coordinates"); assert(!newCoordinates.isNull()); const mesh_type::label_sequence::const_iterator verticesEnd = vertices->end(); assert(vertices->size() > 0); const int spaceDim = coordinates->getFiberDimension(*vertices->begin()); assert(spaceDim > 0); newCoordinates->setChart(mesh_type::sieve_type::chart_type(_orderNewMesh->verticesNormal().min(), _orderNewMesh->verticesCensored().max())); const interval_type::const_iterator newVerticesEnd = _orderNewMesh->verticesCensored().end(); for (interval_type::const_iterator v_iter=_orderNewMesh->verticesNormal().begin(); v_iter != newVerticesEnd; ++v_iter) { newCoordinates->setFiberDimension(*v_iter, spaceDim); } /* for */ newCoordinates->allocatePoint(); interval_type::const_iterator oldVerticesEnd = _orderOldMesh->verticesNormal().end(); for (interval_type::const_iterator vOld_iter=_orderOldMesh->verticesNormal().begin(), vNew_iter=_orderNewMesh->verticesNormal().begin(); vOld_iter != oldVerticesEnd; ++vOld_iter, ++vNew_iter) { /*std::cout << "Copy coordinates from old vertex " << *vOld_iter << " to new vertex " << *vNew_iter << std::endl; */ newCoordinates->updatePoint(*vNew_iter, coordinates->restrictPoint(*vOld_iter)); } /* for */ oldVerticesEnd = _orderOldMesh->verticesCensored().end(); for (interval_type::const_iterator vOld_iter=_orderOldMesh->verticesCensored().begin(), vNew_iter=_orderNewMesh->verticesCensored().begin(); vOld_iter != oldVerticesEnd; ++vOld_iter, ++vNew_iter) { /*std::cout << "Copy coordinates from old vertex " << *vOld_iter << " to new vertex " << *vNew_iter << std::endl; */ newCoordinates->updatePoint(*vNew_iter, coordinates->restrictPoint(*vOld_iter)); } /* for */ refiner.setCoordsNewVertices(newCoordinates, coordinates); /* Create sensored depth */ const ALE::Obj& censoredLabel = newMesh->createLabel("censored depth"); assert(!censoredLabel.isNull()); mesh_type::DepthVisitor depthVisitor(*newSieve, _orderNewMesh->verticesCensored().min(), *censoredLabel); newSieve->roots(depthVisitor); while(depthVisitor.isModified()) { /* FIX: Avoid the copy here somehow by fixing the traversal */ std::vector modifiedPoints(depthVisitor.getModifiedPoints().begin(), depthVisitor.getModifiedPoints().end()); depthVisitor.clear(); newSieve->support(modifiedPoints, depthVisitor); } /* while */ /* Stratify refined mesh */ /* Calculate new point SF */ _calcNewOverlap(newMesh, mesh, refiner); /* Calculate new labels */ _createLabels(newMesh, mesh, refiner); #endif PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSetRefinementUniform" PetscErrorCode DMPlexSetRefinementUniform(DM dm, PetscBool refinementUniform) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); mesh->refinementUniform = refinementUniform; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetRefinementUniform" PetscErrorCode DMPlexGetRefinementUniform(DM dm, PetscBool *refinementUniform) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(refinementUniform, 2); *refinementUniform = mesh->refinementUniform; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSetRefinementLimit" PetscErrorCode DMPlexSetRefinementLimit(DM dm, PetscReal refinementLimit) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); mesh->refinementLimit = refinementLimit; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetRefinementLimit" PetscErrorCode DMPlexGetRefinementLimit(DM dm, PetscReal *refinementLimit) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(refinementLimit, 2); /* if (mesh->refinementLimit < 0) = getMaxVolume()/2.0; */ *refinementLimit = mesh->refinementLimit; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetCellRefiner_Private" PetscErrorCode DMPlexGetCellRefiner_Private(DM dm, CellRefiner *cellRefiner) { PetscInt dim, cStart, coneSize, cMax; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, PETSC_NULL);CHKERRQ(ierr); ierr = DMPlexGetConeSize(dm, cStart, &coneSize);CHKERRQ(ierr); ierr = DMPlexGetHybridBounds(dm, &cMax, PETSC_NULL, PETSC_NULL, PETSC_NULL);CHKERRQ(ierr); switch(dim) { case 2: switch(coneSize) { case 3: if (cMax >= 0) { *cellRefiner = 3; /* Hybrid */ } else { *cellRefiner = 1; /* Triangular */ } break; case 4: if (cMax >= 0) { *cellRefiner = 4; /* Hybrid */ } else { *cellRefiner = 2; /* Quadrilateral */ } break; default: SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown coneSize %d in dimension %d for cell refiner", coneSize, dim); } break; default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown dimension %d for cell refiner", dim); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMRefine_Plex" PetscErrorCode DMRefine_Plex(DM dm, MPI_Comm comm, DM *dmRefined) { PetscReal refinementLimit; PetscInt dim, cStart, cEnd; char genname[1024], *name = PETSC_NULL; PetscBool isUniform, isTriangle = PETSC_FALSE, isTetgen = PETSC_FALSE, isCTetgen = PETSC_FALSE, flg; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetRefinementUniform(dm, &isUniform);CHKERRQ(ierr); if (isUniform) { CellRefiner cellRefiner; ierr = DMPlexGetCellRefiner_Private(dm, &cellRefiner);CHKERRQ(ierr); ierr = DMPlexRefine_Uniform(dm, cellRefiner, dmRefined);CHKERRQ(ierr); PetscFunctionReturn(0); } ierr = DMPlexGetRefinementLimit(dm, &refinementLimit);CHKERRQ(ierr); if (refinementLimit == 0.0) PetscFunctionReturn(0); ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = PetscOptionsGetString(((PetscObject) dm)->prefix, "-dm_plex_generator", genname, 1024, &flg);CHKERRQ(ierr); if (flg) {name = genname;} if (name) { ierr = PetscStrcmp(name, "triangle", &isTriangle);CHKERRQ(ierr); ierr = PetscStrcmp(name, "tetgen", &isTetgen);CHKERRQ(ierr); ierr = PetscStrcmp(name, "ctetgen", &isCTetgen);CHKERRQ(ierr); } switch(dim) { case 2: if (!name || isTriangle) { #ifdef PETSC_HAVE_TRIANGLE double *maxVolumes; PetscInt c; ierr = PetscMalloc((cEnd - cStart) * sizeof(double), &maxVolumes);CHKERRQ(ierr); for (c = 0; c < cEnd-cStart; ++c) { maxVolumes[c] = refinementLimit; } ierr = DMPlexRefine_Triangle(dm, maxVolumes, dmRefined);CHKERRQ(ierr); #else SETERRQ(((PetscObject) dm)->comm, PETSC_ERR_SUP, "Mesh refinement needs external package support.\nPlease reconfigure with --download-triangle."); #endif } else SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_SUP, "Unknown 2D mesh generation package %s", name); break; case 3: if (!name || isCTetgen) { #ifdef PETSC_HAVE_CTETGEN PetscReal *maxVolumes; PetscInt c; ierr = PetscMalloc((cEnd - cStart) * sizeof(PetscReal), &maxVolumes);CHKERRQ(ierr); for (c = 0; c < cEnd-cStart; ++c) { maxVolumes[c] = refinementLimit; } ierr = DMPlexRefine_CTetgen(dm, maxVolumes, dmRefined);CHKERRQ(ierr); #else SETERRQ(((PetscObject) dm)->comm, PETSC_ERR_SUP, "CTetgen needs external package support.\nPlease reconfigure with --download-ctetgen."); #endif } else if (isTetgen) { #ifdef PETSC_HAVE_TETGEN double *maxVolumes; PetscInt c; ierr = PetscMalloc((cEnd - cStart) * sizeof(double), &maxVolumes);CHKERRQ(ierr); for (c = 0; c < cEnd-cStart; ++c) { maxVolumes[c] = refinementLimit; } ierr = DMPlexRefine_Tetgen(dm, maxVolumes, dmRefined);CHKERRQ(ierr); #else SETERRQ(((PetscObject) dm)->comm, PETSC_ERR_SUP, "Tetgen needs external package support.\nPlease reconfigure with --with-c-language=cxx --download-tetgen."); #endif } else SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_SUP, "Unknown 3D mesh generation package %s", name); break; default: SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_SUP, "Mesh refinement in dimension %d is not supported.", dim); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetDepth" /*@ DMPlexGetDepth - get the number of strata Not Collective Input Parameters: . dm - The DMPlex object Output Parameters: . depth - number of strata Level: developer Notes: DMPlexGetHeightStratum(dm,0,..) should return the same points as DMPlexGetDepthStratum(dm,depth,..). .keywords: mesh, points .seealso: DMPlexGetHeightStratum(), DMPlexGetDepthStratum() @*/ PetscErrorCode DMPlexGetDepth(DM dm, PetscInt *depth) { PetscInt d; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(depth, 2); ierr = DMPlexGetLabelSize(dm, "depth", &d);CHKERRQ(ierr); *depth = d-1; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetDepthStratum" /*@ DMPlexGetDepthStratum - Get the bounds [start, end) for all points at a certain depth. Not Collective Input Parameters: + dm - The DMPlex object - stratumValue - The requested depth Output Parameters: + start - The first point at this depth - end - One beyond the last point at this depth Level: developer .keywords: mesh, points .seealso: DMPlexGetHeightStratum(), DMPlexGetDepth() @*/ PetscErrorCode DMPlexGetDepthStratum(DM dm, PetscInt stratumValue, PetscInt *start, PetscInt *end) { DM_Plex *mesh = (DM_Plex *) dm->data; DMLabel next = mesh->labels; PetscBool flg = PETSC_FALSE; PetscInt depth; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); if (stratumValue < 0) { ierr = DMPlexGetChart(dm, start, end);CHKERRQ(ierr); PetscFunctionReturn(0); } else { PetscInt pStart, pEnd; if (start) {*start = 0;} if (end) {*end = 0;} ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); if (pStart == pEnd) {PetscFunctionReturn(0);} } ierr = DMPlexHasLabel(dm, "depth", &flg);CHKERRQ(ierr); if (!flg) SETERRQ(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONG, "No label named depth was found");CHKERRQ(ierr); /* We should have a generic GetLabel() and a Label class */ while(next) { ierr = PetscStrcmp("depth", next->name, &flg);CHKERRQ(ierr); if (flg) break; next = next->next; } /* Strata are sorted and contiguous -- In addition, depth/height is either full or 1-level */ depth = stratumValue; if ((depth < 0) || (depth >= next->numStrata)) { if (start) {*start = 0;} if (end) {*end = 0;} } else { if (start) {*start = next->points[next->stratumOffsets[depth]];} if (end) {*end = next->points[next->stratumOffsets[depth]+next->stratumSizes[depth]-1]+1;} } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetHeightStratum" /*@ DMPlexGetHeightStratum - Get the bounds [start, end) for all points at a certain height. Not Collective Input Parameters: + dm - The DMPlex object - stratumValue - The requested height Output Parameters: + start - The first point at this height - end - One beyond the last point at this height Level: developer .keywords: mesh, points .seealso: DMPlexGetDepthStratum(), DMPlexGetDepth() @*/ PetscErrorCode DMPlexGetHeightStratum(DM dm, PetscInt stratumValue, PetscInt *start, PetscInt *end) { DM_Plex *mesh = (DM_Plex *) dm->data; DMLabel next = mesh->labels; PetscBool flg = PETSC_FALSE; PetscInt depth; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); if (stratumValue < 0) { ierr = DMPlexGetChart(dm, start, end);CHKERRQ(ierr); } else { PetscInt pStart, pEnd; if (start) {*start = 0;} if (end) {*end = 0;} ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); if (pStart == pEnd) {PetscFunctionReturn(0);} } ierr = DMPlexHasLabel(dm, "depth", &flg);CHKERRQ(ierr); if (!flg) SETERRQ(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONG, "No label named depth was found");CHKERRQ(ierr); /* We should have a generic GetLabel() and a Label class */ while(next) { ierr = PetscStrcmp("depth", next->name, &flg);CHKERRQ(ierr); if (flg) break; next = next->next; } /* Strata are sorted and contiguous -- In addition, depth/height is either full or 1-level */ depth = next->stratumValues[next->numStrata-1] - stratumValue; if ((depth < 0) || (depth >= next->numStrata)) { if (start) {*start = 0;} if (end) {*end = 0;} } else { if (start) {*start = next->points[next->stratumOffsets[depth]];} if (end) {*end = next->points[next->stratumOffsets[depth]+next->stratumSizes[depth]-1]+1;} } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexCreateSectionInitial" /* Set the number of dof on each point and separate by fields */ PetscErrorCode DMPlexCreateSectionInitial(DM dm, PetscInt dim, PetscInt numFields,const PetscInt numComp[],const PetscInt numDof[], PetscSection *section) { PetscInt *numDofTot; PetscInt pStart = 0, pEnd = 0; PetscInt p, d, f; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscMalloc((dim+1) * sizeof(PetscInt), &numDofTot);CHKERRQ(ierr); for(d = 0; d <= dim; ++d) { numDofTot[d] = 0; for(f = 0; f < numFields; ++f) { numDofTot[d] += numDof[f*(dim+1)+d]; } } ierr = PetscSectionCreate(((PetscObject) dm)->comm, section);CHKERRQ(ierr); if (numFields > 0) { ierr = PetscSectionSetNumFields(*section, numFields);CHKERRQ(ierr); if (numComp) { for(f = 0; f < numFields; ++f) { ierr = PetscSectionSetFieldComponents(*section, f, numComp[f]);CHKERRQ(ierr); } } } ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); ierr = PetscSectionSetChart(*section, pStart, pEnd);CHKERRQ(ierr); for(d = 0; d <= dim; ++d) { ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); for(p = pStart; p < pEnd; ++p) { for(f = 0; f < numFields; ++f) { ierr = PetscSectionSetFieldDof(*section, p, f, numDof[f*(dim+1)+d]);CHKERRQ(ierr); } ierr = PetscSectionSetDof(*section, p, numDofTot[d]);CHKERRQ(ierr); } } ierr = PetscFree(numDofTot);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexCreateSectionBCDof" /* Set the number of dof on each point and separate by fields If constDof is PETSC_DETERMINE, constrain every dof on the point */ PetscErrorCode DMPlexCreateSectionBCDof(DM dm, PetscInt numBC,const PetscInt bcField[],const IS bcPoints[], PetscInt constDof, PetscSection section) { PetscInt numFields; PetscInt bc; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); for (bc = 0; bc < numBC; ++bc) { PetscInt field = 0; const PetscInt *idx; PetscInt n, i; if (numFields) {field = bcField[bc];} ierr = ISGetLocalSize(bcPoints[bc], &n);CHKERRQ(ierr); ierr = ISGetIndices(bcPoints[bc], &idx);CHKERRQ(ierr); for (i = 0; i < n; ++i) { const PetscInt p = idx[i]; PetscInt numConst = constDof; /* Constrain every dof on the point */ if (numConst < 0) { if (numFields) { ierr = PetscSectionGetFieldDof(section, p, field, &numConst);CHKERRQ(ierr); } else { ierr = PetscSectionGetDof(section, p, &numConst);CHKERRQ(ierr); } } if (numFields) { ierr = PetscSectionAddFieldConstraintDof(section, p, field, numConst);CHKERRQ(ierr); } ierr = PetscSectionAddConstraintDof(section, p, numConst);CHKERRQ(ierr); } ierr = ISRestoreIndices(bcPoints[bc], &idx);CHKERRQ(ierr); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexCreateSectionBCIndicesAll" /* Set the constrained indices on each point and separate by fields */ PetscErrorCode DMPlexCreateSectionBCIndicesAll(DM dm, PetscSection section) { PetscInt *maxConstraints; PetscInt numFields, f, pStart = 0, pEnd = 0, p; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); ierr = PetscMalloc((numFields+1) * sizeof(PetscInt), &maxConstraints);CHKERRQ(ierr); for(f = 0; f <= numFields; ++f) {maxConstraints[f] = 0;} for(p = pStart; p < pEnd; ++p) { PetscInt cdof; if (numFields) { for(f = 0; f < numFields; ++f) { ierr = PetscSectionGetFieldConstraintDof(section, p, f, &cdof);CHKERRQ(ierr); maxConstraints[f] = PetscMax(maxConstraints[f], cdof); } } else { ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr); maxConstraints[0] = PetscMax(maxConstraints[0], cdof); } } for (f = 0; f < numFields; ++f) { maxConstraints[numFields] += maxConstraints[f]; } if (maxConstraints[numFields]) { PetscInt *indices; ierr = PetscMalloc(maxConstraints[numFields] * sizeof(PetscInt), &indices);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { PetscInt cdof, d; ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr); if (cdof) { if (cdof > maxConstraints[numFields]) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_LIB, "Likely memory corruption, point %D cDof %D > maxConstraints %D", p, cdof, maxConstraints[numFields]); if (numFields) { PetscInt numConst = 0, foff = 0; for (f = 0; f < numFields; ++f) { PetscInt cfdof, fdof; ierr = PetscSectionGetFieldDof(section, p, f, &fdof);CHKERRQ(ierr); ierr = PetscSectionGetFieldConstraintDof(section, p, f, &cfdof);CHKERRQ(ierr); /* Change constraint numbering from absolute local dof number to field relative local dof number */ for(d = 0; d < cfdof; ++d) { indices[numConst+d] = d; } ierr = PetscSectionSetFieldConstraintIndices(section, p, f, &indices[numConst]);CHKERRQ(ierr); for(d = 0; d < cfdof; ++d) { indices[numConst+d] += foff; } numConst += cfdof; foff += fdof; } if (cdof != numConst) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of field constraints %D should be %D", numConst, cdof); } else { for (d = 0; d < cdof; ++d) { indices[d] = d; } } ierr = PetscSectionSetConstraintIndices(section, p, indices);CHKERRQ(ierr); } } ierr = PetscFree(indices);CHKERRQ(ierr); } ierr = PetscFree(maxConstraints);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexCreateSectionBCIndicesField" /* Set the constrained field indices on each point */ PetscErrorCode DMPlexCreateSectionBCIndicesField(DM dm, PetscInt field, IS bcPoints, IS constraintIndices, PetscSection section) { const PetscInt *points, *indices; PetscInt numFields, maxDof, numPoints, p, numConstraints; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); if ((field < 0) || (field >= numFields)) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Section field %d should be in [%d, %d)", field, 0, numFields); ierr = ISGetLocalSize(bcPoints, &numPoints);CHKERRQ(ierr); ierr = ISGetIndices(bcPoints, &points);CHKERRQ(ierr); if (!constraintIndices) { PetscInt *idx, i; ierr = PetscSectionGetMaxDof(section, &maxDof);CHKERRQ(ierr); ierr = PetscMalloc(maxDof * sizeof(PetscInt), &idx);CHKERRQ(ierr); for(i = 0; i < maxDof; ++i) {idx[i] = i;} for(p = 0; p < numPoints; ++p) { ierr = PetscSectionSetFieldConstraintIndices(section, points[p], field, idx);CHKERRQ(ierr); } ierr = PetscFree(idx);CHKERRQ(ierr); } else { ierr = ISGetLocalSize(constraintIndices, &numConstraints);CHKERRQ(ierr); ierr = ISGetIndices(constraintIndices, &indices);CHKERRQ(ierr); for(p = 0; p < numPoints; ++p) { PetscInt fcdof; ierr = PetscSectionGetFieldConstraintDof(section, points[p], field, &fcdof);CHKERRQ(ierr); if (fcdof != numConstraints) SETERRQ4(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONG, "Section point %d field %d has %d constraints, but yo ugave %d indices", p, field, fcdof, numConstraints); ierr = PetscSectionSetFieldConstraintIndices(section, points[p], field, indices);CHKERRQ(ierr); } ierr = ISRestoreIndices(constraintIndices, &indices);CHKERRQ(ierr); } ierr = ISRestoreIndices(bcPoints, &points);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexCreateSectionBCIndices" /* Set the constrained indices on each point and separate by fields */ PetscErrorCode DMPlexCreateSectionBCIndices(DM dm, PetscSection section) { PetscInt *indices; PetscInt numFields, maxDof, f, pStart = 0, pEnd = 0, p; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscSectionGetMaxDof(section, &maxDof);CHKERRQ(ierr); ierr = PetscMalloc(maxDof * sizeof(PetscInt), &indices);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); if (!numFields) SETERRQ(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONG, "This function only works after users have set field constraint indices."); ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { PetscInt cdof, d; ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr); if (cdof) { PetscInt numConst = 0, foff = 0; for (f = 0; f < numFields; ++f) { const PetscInt *fcind; PetscInt fdof, fcdof; ierr = PetscSectionGetFieldDof(section, p, f, &fdof);CHKERRQ(ierr); ierr = PetscSectionGetFieldConstraintDof(section, p, f, &fcdof);CHKERRQ(ierr); if (fcdof) {ierr = PetscSectionGetFieldConstraintIndices(section, p, f, &fcind);CHKERRQ(ierr);} /* Change constraint numbering from field relative local dof number to absolute local dof number */ for(d = 0; d < fcdof; ++d) { indices[numConst+d] = fcind[d]+foff; } foff += fdof; numConst += fcdof; } if (cdof != numConst) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_LIB, "Total number of field constraints %D should be %D", numConst, cdof); ierr = PetscSectionSetConstraintIndices(section, p, indices);CHKERRQ(ierr); } } ierr = PetscFree(indices);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexCreateSection" /*@C DMPlexCreateSection - Create a PetscSection based upon the dof layout specification provided. Not Collective Input Parameters: + dm - The DMPlex object . dim - The spatial dimension of the problem . numFields - The number of fields in the problem . numComp - An array of size numFields that holds the number of components for each field . numDof - An array of size numFields*(dim+1) which holds the number of dof for each field on a mesh piece of dimension d . numBC - The number of boundary conditions . bcField - An array of size numBC giving the field number for each boundry condition - bcPoints - An array of size numBC giving an IS holding the sieve points to which each boundary condition applies Output Parameter: . section - The PetscSection object Notes: numDof[f*(dim+1)+d] gives the number of dof for field f on sieve points of dimension d. For instance, numDof[1] is the nubmer of dof for field 0 on each edge. Level: developer .keywords: mesh, elements .seealso: DMPlexCreate(), PetscSectionCreate() @*/ PetscErrorCode DMPlexCreateSection(DM dm, PetscInt dim, PetscInt numFields,const PetscInt numComp[],const PetscInt numDof[], PetscInt numBC,const PetscInt bcField[],const IS bcPoints[], PetscSection *section) { PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexCreateSectionInitial(dm, dim, numFields, numComp, numDof, section);CHKERRQ(ierr); ierr = DMPlexCreateSectionBCDof(dm, numBC, bcField, bcPoints, PETSC_DETERMINE, *section);CHKERRQ(ierr); ierr = PetscSectionSetUp(*section);CHKERRQ(ierr); if (numBC) {ierr = DMPlexCreateSectionBCIndicesAll(dm, *section);CHKERRQ(ierr);} { PetscBool view = PETSC_FALSE; ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-section_view", &view);CHKERRQ(ierr); if (view) {ierr = PetscSectionView(*section, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);} } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMCreateCoordinateDM_Plex" PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm) { PetscSection section; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexClone(dm, cdm);CHKERRQ(ierr); ierr = PetscSectionCreate(((PetscObject) dm)->comm, §ion);CHKERRQ(ierr); ierr = DMSetDefaultSection(*cdm, section);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetCoordinateSection" /*@ DMPlexGetCoordinateSection - Retrieve the layout of coordinate values over the mesh. Not Collective Input Parameter: . dm - The DMPlex object Output Parameter: . section - The PetscSection object Level: intermediate .keywords: mesh, coordinates .seealso: DMGetCoordinateDM(), DMPlexGetDefaultSection(), DMPlexSetDefaultSection() @*/ PetscErrorCode DMPlexGetCoordinateSection(DM dm, PetscSection *section) { DM cdm; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(section, 2); ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); ierr = DMGetDefaultSection(cdm, section);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSetCoordinateSection" /*@ DMPlexSetCoordinateSection - Set the layout of coordinate values over the mesh. Not Collective Input Parameters: + dm - The DMPlex object - section - The PetscSection object Level: intermediate .keywords: mesh, coordinates .seealso: DMPlexGetCoordinateSection(), DMPlexGetDefaultSection(), DMPlexSetDefaultSection() @*/ PetscErrorCode DMPlexSetCoordinateSection(DM dm, PetscSection section) { DM cdm; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); ierr = DMSetDefaultSection(cdm, section);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetConeSection" PetscErrorCode DMPlexGetConeSection(DM dm, PetscSection *section) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); if (section) *section = mesh->coneSection; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetCones" PetscErrorCode DMPlexGetCones(DM dm, PetscInt *cones[]) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); if (cones) *cones = mesh->cones; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetConeOrientations" PetscErrorCode DMPlexGetConeOrientations(DM dm, PetscInt *coneOrientations[]) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); if (coneOrientations) *coneOrientations = mesh->coneOrientations; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexLocatePoint_Simplex_2D" PetscErrorCode DMPlexLocatePoint_Simplex_2D(DM dm, const PetscScalar point[], PetscInt c, PetscInt *cell) { const PetscInt embedDim = 2; PetscReal x = PetscRealPart(point[0]); PetscReal y = PetscRealPart(point[1]); PetscReal v0[2], J[4], invJ[4], detJ; PetscReal xi, eta; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexComputeCellGeometry(dm, c, v0, J, invJ, &detJ);CHKERRQ(ierr); xi = invJ[0*embedDim+0]*(x - v0[0]) + invJ[0*embedDim+1]*(y - v0[1]); eta = invJ[1*embedDim+0]*(x - v0[0]) + invJ[1*embedDim+1]*(y - v0[1]); if ((xi >= 0.0) && (eta >= 0.0) && (xi + eta <= 2.0)) { *cell = c; } else { *cell = -1; } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexLocatePoint_General_2D" PetscErrorCode DMPlexLocatePoint_General_2D(DM dm, const PetscScalar point[], PetscInt c, PetscInt *cell) { PetscSection coordSection; Vec coordsLocal; const PetscScalar *coords; const PetscInt faces[8] = {0, 1, 1, 2, 2, 3, 3, 0}; PetscReal x = PetscRealPart(point[0]); PetscReal y = PetscRealPart(point[1]); PetscInt crossings = 0, f; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, coordSection, coordsLocal, c, PETSC_NULL, &coords);CHKERRQ(ierr); for(f = 0; f < 4; ++f) { PetscReal x_i = PetscRealPart(coords[faces[2*f+0]*2+0]); PetscReal y_i = PetscRealPart(coords[faces[2*f+0]*2+1]); PetscReal x_j = PetscRealPart(coords[faces[2*f+1]*2+0]); PetscReal y_j = PetscRealPart(coords[faces[2*f+1]*2+1]); PetscReal slope = (y_j - y_i) / (x_j - x_i); PetscBool cond1 = (x_i <= x) && (x < x_j) ? PETSC_TRUE : PETSC_FALSE; PetscBool cond2 = (x_j <= x) && (x < x_i) ? PETSC_TRUE : PETSC_FALSE; PetscBool above = (y < slope * (x - x_i) + y_i) ? PETSC_TRUE : PETSC_FALSE; if ((cond1 || cond2) && above) ++crossings; } if (crossings % 2) { *cell = c; } else { *cell = -1; } ierr = DMPlexVecRestoreClosure(dm, coordSection, coordsLocal, c, PETSC_NULL, &coords);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexLocatePoint_Simplex_3D" PetscErrorCode DMPlexLocatePoint_Simplex_3D(DM dm, const PetscScalar point[], PetscInt c, PetscInt *cell) { const PetscInt embedDim = 3; PetscReal v0[3], J[9], invJ[9], detJ; PetscReal x = PetscRealPart(point[0]); PetscReal y = PetscRealPart(point[1]); PetscReal z = PetscRealPart(point[2]); PetscReal xi, eta, zeta; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexComputeCellGeometry(dm, c, v0, J, invJ, &detJ);CHKERRQ(ierr); xi = invJ[0*embedDim+0]*(x - v0[0]) + invJ[0*embedDim+1]*(y - v0[1]) + invJ[0*embedDim+2]*(z - v0[2]); eta = invJ[1*embedDim+0]*(x - v0[0]) + invJ[1*embedDim+1]*(y - v0[1]) + invJ[1*embedDim+2]*(z - v0[2]); zeta = invJ[2*embedDim+0]*(x - v0[0]) + invJ[2*embedDim+1]*(y - v0[1]) + invJ[2*embedDim+2]*(z - v0[2]); if ((xi >= 0.0) && (eta >= 0.0) && (zeta >= 0.0) && (xi + eta + zeta <= 2.0)) { *cell = c; } else { *cell = -1; } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexLocatePoint_General_3D" PetscErrorCode DMPlexLocatePoint_General_3D(DM dm, const PetscScalar point[], PetscInt c, PetscInt *cell) { PetscSection coordSection; Vec coordsLocal; const PetscScalar *coords; const PetscInt faces[24] = {0, 1, 2, 3, 5, 4, 7, 6, 1, 0, 4, 5, 3, 2, 6, 7, 1, 5, 6, 2, 0, 3, 7, 4}; PetscBool found = PETSC_TRUE; PetscInt f; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, coordSection, coordsLocal, c, PETSC_NULL, &coords);CHKERRQ(ierr); for(f = 0; f < 6; ++f) { /* Check the point is under plane */ /* Get face normal */ PetscReal v_i[3] = {PetscRealPart(coords[faces[f*4+3]*3+0]-coords[faces[f*4+0]*3+0]), PetscRealPart(coords[faces[f*4+3]*3+1]-coords[faces[f*4+0]*3+1]), PetscRealPart(coords[faces[f*4+3]*3+2]-coords[faces[f*4+0]*3+2])}; PetscReal v_j[3] = {PetscRealPart(coords[faces[f*4+1]*3+0]-coords[faces[f*4+0]*3+0]), PetscRealPart(coords[faces[f*4+1]*3+1]-coords[faces[f*4+0]*3+1]), PetscRealPart(coords[faces[f*4+1]*3+2]-coords[faces[f*4+0]*3+2])}; PetscReal normal[3] = {v_i[1]*v_j[2] - v_i[2]*v_j[1], v_i[2]*v_j[0] - v_i[0]*v_j[2], v_i[0]*v_j[1] - v_i[1]*v_j[0]}; PetscReal pp[3] = {PetscRealPart(coords[faces[f*4+0]*3+0] - point[0]), PetscRealPart(coords[faces[f*4+0]*3+1] - point[1]), PetscRealPart(coords[faces[f*4+0]*3+2] - point[2])}; PetscReal dot = normal[0]*pp[0] + normal[1]*pp[1] + normal[2]*pp[2]; /* Check that projected point is in face (2D location problem) */ if (dot < 0.0) { found = PETSC_FALSE; break; } } if (found) { *cell = c; } else { *cell = -1; } ierr = DMPlexVecRestoreClosure(dm, coordSection, coordsLocal, c, PETSC_NULL, &coords);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMLocatePoints_Plex" /* Need to implement using the guess */ PetscErrorCode DMLocatePoints_Plex(DM dm, Vec v, IS *cellIS) { PetscInt cell = -1/*, guess = -1*/; PetscInt bs, numPoints, p; PetscInt dim, cStart, cEnd, cMax, c, coneSize; PetscInt *cells; PetscScalar *a; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetHybridBounds(dm, &cMax, PETSC_NULL, PETSC_NULL, PETSC_NULL);CHKERRQ(ierr); if (cMax >= 0) {cEnd = PetscMin(cEnd, cMax);} ierr = VecGetLocalSize(v, &numPoints);CHKERRQ(ierr); ierr = VecGetBlockSize(v, &bs);CHKERRQ(ierr); ierr = VecGetArray(v, &a);CHKERRQ(ierr); if (bs != dim) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONG, "Block size for point vector %d must be the mesh coordinate dimension %d", bs, dim); numPoints /= bs; ierr = PetscMalloc(numPoints * sizeof(PetscInt), &cells);CHKERRQ(ierr); for(p = 0; p < numPoints; ++p) { const PetscScalar *point = &a[p*bs]; switch(dim) { case 2: for(c = cStart; c < cEnd; ++c) { ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); switch(coneSize) { case 3: ierr = DMPlexLocatePoint_Simplex_2D(dm, point, c, &cell);CHKERRQ(ierr); break; case 4: ierr = DMPlexLocatePoint_General_2D(dm, point, c, &cell);CHKERRQ(ierr); break; default: SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "No point location for cell with cone size %d", coneSize); } if (cell >= 0) break; } break; case 3: for(c = cStart; c < cEnd; ++c) { ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); switch(coneSize) { case 4: ierr = DMPlexLocatePoint_Simplex_3D(dm, point, c, &cell);CHKERRQ(ierr); break; case 8: ierr = DMPlexLocatePoint_General_3D(dm, point, c, &cell);CHKERRQ(ierr); break; default: SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "No point location for cell with cone size %d", coneSize); } if (cell >= 0) break; } break; default: SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "No point location for mesh dimension %d", dim); } cells[p] = cell; } ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); ierr = ISCreateGeneral(PETSC_COMM_SELF, numPoints, cells, PETSC_OWN_POINTER, cellIS);CHKERRQ(ierr); PetscFunctionReturn(0); } /******************************** FEM Support **********************************/ #undef __FUNCT__ #define __FUNCT__ "DMPlexVecGetClosure" /*@C DMPlexVecGetClosure - Get an array of the values on the closure of 'point' Not collective Input Parameters: + dm - The DM . section - The section describing the layout in v, or PETSC_NULL to use the default section . v - The local vector - point - The sieve point in the DM Output Parameters: + csize - The number of values in the closure, or PETSC_NULL - values - The array of values, which is a borrowed array and should not be freed Level: intermediate .seealso DMPlexVecRestoreClosure(), DMPlexVecSetClosure(), DMPlexMatSetClosure() @*/ PetscErrorCode DMPlexVecGetClosure(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, const PetscScalar *values[]) { PetscScalar *array, *vArray; PetscInt *points = PETSC_NULL; PetscInt offsets[32]; PetscInt numFields, size, numPoints, pStart, pEnd, p, q, f; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidHeaderSpecific(v, VEC_CLASSID, 3); if (!section) { ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); } ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); if (numFields > 31) SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %D limited to 31", numFields); ierr = PetscMemzero(offsets, 32 * sizeof(PetscInt));CHKERRQ(ierr); 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; for (p = 0, size = 0; p < numPoints*2; p += 2) { PetscInt dof, 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; } size += dof; } for (f = 1; f < numFields; ++f) { offsets[f+1] += offsets[f]; } if (numFields && offsets[numFields] != size) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Invalid size for closure %d should be %d", offsets[numFields], size); ierr = DMGetWorkArray(dm, size, PETSC_SCALAR, &array);CHKERRQ(ierr); ierr = VecGetArray(v, &vArray);CHKERRQ(ierr); for (p = 0; p < numPoints*2; p += 2) { PetscInt o = points[p+1]; PetscInt dof, off, d; PetscScalar *varr; ierr = PetscSectionGetDof(section, points[p], &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(section, points[p], &off);CHKERRQ(ierr); varr = &vArray[off]; if (numFields) { PetscInt fdof, foff, fcomp, f, c; for (f = 0, foff = 0; f < numFields; ++f) { ierr = PetscSectionGetFieldDof(section, points[p], f, &fdof);CHKERRQ(ierr); if (o >= 0) { for (d = 0; d < fdof; ++d, ++offsets[f]) { array[offsets[f]] = varr[foff+d]; } } else { ierr = PetscSectionGetFieldComponents(section, f, &fcomp);CHKERRQ(ierr); for (d = fdof/fcomp-1; d >= 0; --d) { for (c = 0; c < fcomp; ++c, ++offsets[f]) { array[offsets[f]] = varr[foff+d*fcomp+c]; } } } foff += fdof; } } else { if (o >= 0) { for (d = 0; d < dof; ++d, ++offsets[0]) { array[offsets[0]] = varr[d]; } } else { for (d = dof-1; d >= 0; --d, ++offsets[0]) { array[offsets[0]] = varr[d]; } } } } ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr); ierr = VecRestoreArray(v, &vArray);CHKERRQ(ierr); if (csize) *csize = size; *values = array; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexVecRestoreClosure" /*@C DMPlexVecRestoreClosure - Restore the array of the values on the closure of 'point' Not collective Input Parameters: + dm - The DM . section - The section describing the layout in v, or PETSC_NULL to use the default section . v - The local vector . point - The sieve point in the DM . csize - The number of values in the closure, or PETSC_NULL - values - The array of values, which is a borrowed array and should not be freed Level: intermediate .seealso DMPlexVecGetClosure(), DMPlexVecSetClosure(), DMPlexMatSetClosure() @*/ PetscErrorCode DMPlexVecRestoreClosure(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, const PetscScalar *values[]) { PetscInt size = 0; PetscErrorCode ierr; PetscFunctionBegin; /* Should work without recalculating size */ ierr = DMRestoreWorkArray(dm, size, PETSC_SCALAR, (void *) values);CHKERRQ(ierr); PetscFunctionReturn(0); } PETSC_STATIC_INLINE void add (PetscScalar *x, PetscScalar y) {*x += y;} PETSC_STATIC_INLINE void insert(PetscScalar *x, PetscScalar y) {*x = y;} #undef __FUNCT__ #define __FUNCT__ "updatePoint_private" PetscErrorCode updatePoint_private(PetscSection section, PetscInt point, PetscInt dof, void (*fuse)(PetscScalar *, PetscScalar), PetscBool setBC, PetscInt orientation, const PetscScalar values[], PetscScalar array[]) { PetscInt cdof; /* The number of constraints on this point */ const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ PetscScalar *a; PetscInt off, cind = 0, k; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscSectionGetConstraintDof(section, point, &cdof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(section, point, &off);CHKERRQ(ierr); a = &array[off]; if (!cdof || setBC) { if (orientation >= 0) { for (k = 0; k < dof; ++k) { fuse(&a[k], values[k]); } } else { for (k = 0; k < dof; ++k) { fuse(&a[k], values[dof-k-1]); } } } else { ierr = PetscSectionGetConstraintIndices(section, point, &cdofs);CHKERRQ(ierr); if (orientation >= 0) { for (k = 0; k < dof; ++k) { if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;} fuse(&a[k], values[k]); } } else { for (k = 0; k < dof; ++k) { if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;} fuse(&a[k], values[dof-k-1]); } } } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "updatePointFields_private" PetscErrorCode updatePointFields_private(PetscSection section, PetscInt point, PetscInt foffs[], void (*fuse)(PetscScalar *, PetscScalar), PetscBool setBC, PetscInt orientation, const PetscScalar values[], PetscScalar array[]) { PetscScalar *a; PetscInt numFields, off, foff, f; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); ierr = PetscSectionGetOffset(section, point, &off);CHKERRQ(ierr); a = &array[off]; for (f = 0, foff = 0; f < numFields; ++f) { PetscInt fdof, fcomp, fcdof; const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ PetscInt cind = 0, k, c; ierr = PetscSectionGetFieldComponents(section, f, &fcomp);CHKERRQ(ierr); ierr = PetscSectionGetFieldDof(section, point, f, &fdof);CHKERRQ(ierr); ierr = PetscSectionGetFieldConstraintDof(section, point, f, &fcdof);CHKERRQ(ierr); if (!fcdof || setBC) { if (orientation >= 0) { for (k = 0; k < fdof; ++k) { fuse(&a[foff+k], values[foffs[f]+k]); } } else { for (k = fdof/fcomp-1; k >= 0; --k) { for (c = 0; c < fcomp; ++c) { fuse(&a[foff+(fdof/fcomp-1-k)*fcomp+c], values[foffs[f]+k*fcomp+c]); } } } } else { ierr = PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);CHKERRQ(ierr); if (orientation >= 0) { for (k = 0; k < fdof; ++k) { if ((cind < fcdof) && (k == fcdofs[cind])) {++cind; continue;} fuse(&a[foff+k], values[foffs[f]+k]); } } else { for (k = fdof/fcomp-1; k >= 0; --k) { for (c = 0; c < fcomp; ++c) { if ((cind < fcdof) && (k*fcomp+c == fcdofs[cind])) {++cind; continue;} fuse(&a[foff+(fdof/fcomp-1-k)*fcomp+c], values[foffs[f]+k*fcomp+c]); } } } } foff += fdof; foffs[f] += fdof; } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexVecSetClosure" /*@C DMPlexVecSetClosure - Set an array of the values on the closure of 'point' Not collective Input Parameters: + dm - The DM . section - The section describing the layout in v, or PETSC_NULL to use the default sectionw . v - The local vector . point - The sieve point in the DM . values - The array of values, which is a borrowed array and should not be freed - mode - The insert mode, where INSERT_ALL_VALUES and ADD_ALL_VALUES also overwrite boundary conditions Level: intermediate .seealso DMPlexVecGetClosure(), DMPlexMatSetClosure() @*/ PetscErrorCode DMPlexVecSetClosure(DM dm, PetscSection section, Vec v, PetscInt point, const PetscScalar values[], InsertMode mode) { PetscScalar *array; PetscInt *points = PETSC_NULL; PetscInt offsets[32]; PetscInt numFields, numPoints, off, dof, pStart, pEnd, p, q, f; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidHeaderSpecific(v, VEC_CLASSID, 3); if (!section) { ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); } ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); if (numFields > 31) SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %D limited to 31", numFields); ierr = PetscMemzero(offsets, 32 * sizeof(PetscInt));CHKERRQ(ierr); 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; for (p = 0; p < numPoints*2; p += 2) { PetscInt fdof; for (f = 0; f < numFields; ++f) { ierr = PetscSectionGetFieldDof(section, points[p], f, &fdof);CHKERRQ(ierr); offsets[f+1] += fdof; } } for (f = 1; f < numFields; ++f) { offsets[f+1] += offsets[f]; } ierr = VecGetArray(v, &array);CHKERRQ(ierr); if (numFields) { switch(mode) { case INSERT_VALUES: for (p = 0; p < numPoints*2; p += 2) { PetscInt o = points[p+1]; updatePointFields_private(section, points[p], offsets, insert, PETSC_FALSE, o, values, array); } break; case INSERT_ALL_VALUES: for (p = 0; p < numPoints*2; p += 2) { PetscInt o = points[p+1]; updatePointFields_private(section, points[p], offsets, insert, PETSC_TRUE, o, values, array); } break; case ADD_VALUES: for (p = 0; p < numPoints*2; p += 2) { PetscInt o = points[p+1]; updatePointFields_private(section, points[p], offsets, add, PETSC_FALSE, o, values, array); } break; case ADD_ALL_VALUES: for (p = 0; p < numPoints*2; p += 2) { PetscInt o = points[p+1]; updatePointFields_private(section, points[p], offsets, add, PETSC_TRUE, o, values, array); } break; default: SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %D", mode); } } else { switch(mode) { case INSERT_VALUES: for (p = 0, off = 0; p < numPoints*2; p += 2, off += dof) { PetscInt o = points[p+1]; ierr = PetscSectionGetDof(section, points[p], &dof);CHKERRQ(ierr); updatePoint_private(section, points[p], dof, insert, PETSC_FALSE, o, &values[off], array); } break; case INSERT_ALL_VALUES: for (p = 0, off = 0; p < numPoints*2; p += 2, off += dof) { PetscInt o = points[p+1]; ierr = PetscSectionGetDof(section, points[p], &dof);CHKERRQ(ierr); updatePoint_private(section, points[p], dof, insert, PETSC_TRUE, o, &values[off], array); } break; case ADD_VALUES: for (p = 0, off = 0; p < numPoints*2; p += 2, off += dof) { PetscInt o = points[p+1]; ierr = PetscSectionGetDof(section, points[p], &dof);CHKERRQ(ierr); updatePoint_private(section, points[p], dof, add, PETSC_FALSE, o, &values[off], array); } break; case ADD_ALL_VALUES: for (p = 0, off = 0; p < numPoints*2; p += 2, off += dof) { PetscInt o = points[p+1]; ierr = PetscSectionGetDof(section, points[p], &dof);CHKERRQ(ierr); updatePoint_private(section, points[p], dof, add, PETSC_TRUE, o, &values[off], array); } break; default: SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %D", mode); } } ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr); ierr = VecRestoreArray(v, &array);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexPrintMatSetValues" PetscErrorCode DMPlexPrintMatSetValues(PetscViewer viewer, Mat A, PetscInt point, PetscInt numIndices, const PetscInt indices[], PetscScalar values[]) { PetscMPIInt rank; PetscInt i, j; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(((PetscObject) A)->comm, &rank);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer, "[%D]mat for sieve point %D\n", rank, point);CHKERRQ(ierr); for (i = 0; i < numIndices; i++) { ierr = PetscViewerASCIIPrintf(viewer, "[%D]mat indices[%D] = %D\n", rank, i, indices[i]);CHKERRQ(ierr); } for (i = 0; i < numIndices; i++) { ierr = PetscViewerASCIIPrintf(viewer, "[%D]", rank);CHKERRQ(ierr); for (j = 0; j < numIndices; j++) { #ifdef PETSC_USE_COMPLEX ierr = PetscViewerASCIIPrintf(viewer, " (%G,%G)", PetscRealPart(values[i*numIndices+j]), PetscImaginaryPart(values[i*numIndices+j]));CHKERRQ(ierr); #else ierr = PetscViewerASCIIPrintf(viewer, " %G", values[i*numIndices+j]);CHKERRQ(ierr); #endif } ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "indicesPoint_private" /* . off - The global offset of this point */ PetscErrorCode indicesPoint_private(PetscSection section, PetscInt point, PetscInt dof, PetscInt off, PetscBool setBC, PetscInt orientation, PetscInt indices[]) { PetscInt cdof; /* The number of constraints on this point */ const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ PetscInt cind = 0, k; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); ierr = PetscSectionGetConstraintDof(section, point, &cdof);CHKERRQ(ierr); if (!cdof || setBC) { if (orientation >= 0) { for (k = 0; k < dof; ++k) { indices[k] = off+k; } } else { for (k = 0; k < dof; ++k) { indices[dof-k-1] = off+k; } } } else { ierr = PetscSectionGetConstraintIndices(section, point, &cdofs);CHKERRQ(ierr); if (orientation >= 0) { for (k = 0; k < dof; ++k) { if ((cind < cdof) && (k == cdofs[cind])) { /* Insert check for returning constrained indices */ indices[k] = -(off+k+1); ++cind; } else { indices[k] = off+k-cind; } } } else { for (k = 0; k < dof; ++k) { if ((cind < cdof) && (k == cdofs[cind])) { /* Insert check for returning constrained indices */ indices[dof-k-1] = -(off+k+1); ++cind; } else { indices[dof-k-1] = off+k-cind; } } } } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "indicesPointFields_private" /* . off - The global offset of this point */ PetscErrorCode indicesPointFields_private(PetscSection section, PetscInt point, PetscInt off, PetscInt foffs[], PetscBool setBC, PetscInt orientation, PetscInt indices[]) { PetscInt numFields, foff, f; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); for (f = 0, foff = 0; f < numFields; ++f) { PetscInt fdof, fcomp, cfdof; const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ PetscInt cind = 0, k, c; ierr = PetscSectionGetFieldComponents(section, f, &fcomp);CHKERRQ(ierr); ierr = PetscSectionGetFieldDof(section, point, f, &fdof);CHKERRQ(ierr); ierr = PetscSectionGetFieldConstraintDof(section, point, f, &cfdof);CHKERRQ(ierr); if (!cfdof || setBC) { if (orientation >= 0) { for (k = 0; k < fdof; ++k) { indices[foffs[f]+k] = off+foff+k; } } else { for (k = fdof/fcomp-1; k >= 0; --k) { for (c = 0; c < fcomp; ++c) { indices[foffs[f]+k*fcomp+c] = off+foff+(fdof/fcomp-1-k)*fcomp+c; } } } } else { ierr = PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);CHKERRQ(ierr); if (orientation >= 0) { for (k = 0; k < fdof; ++k) { if ((cind < cfdof) && (k == fcdofs[cind])) { indices[foffs[f]+k] = -(off+foff+k+1); ++cind; } else { indices[foffs[f]+k] = off+foff+k-cind; } } } else { for (k = fdof/fcomp-1; k >= 0; --k) { for (c = 0; c < fcomp; ++c) { if ((cind < cfdof) && ((fdof/fcomp-1-k)*fcomp+c == fcdofs[cind])) { indices[foffs[f]+k*fcomp+c] = -(off+foff+(fdof/fcomp-1-k)*fcomp+c+1); ++cind; } else { indices[foffs[f]+k*fcomp+c] = off+foff+(fdof/fcomp-1-k)*fcomp+c-cind; } } } } } foff += fdof - cfdof; foffs[f] += fdof; } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexMatSetClosure" PetscErrorCode DMPlexMatSetClosure(DM dm, PetscSection section, PetscSection globalSection, Mat A, PetscInt point, PetscScalar values[], InsertMode mode) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt *points = PETSC_NULL; PetscInt *indices; PetscInt offsets[32]; PetscInt numFields, numPoints, numIndices, dof, off, globalOff, pStart, pEnd, p, q, f; PetscBool useDefault = !section ? PETSC_TRUE : PETSC_FALSE; PetscBool useGlobalDefault = !globalSection ? PETSC_TRUE : PETSC_FALSE; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidHeaderSpecific(A, MAT_CLASSID, 3); if (useDefault) { ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); } if (useGlobalDefault) { if (useDefault) { ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); } else { ierr = PetscSectionCreateGlobalSection(section, dm->sf, PETSC_FALSE, &globalSection);CHKERRQ(ierr); } } ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); if (numFields > 31) SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %D limited to 31", numFields); ierr = PetscMemzero(offsets, 32 * sizeof(PetscInt));CHKERRQ(ierr); 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; 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(((PetscObject) dm)->comm, 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, off += dof) { PetscInt o = points[p+1]; ierr = PetscSectionGetOffset(globalSection, points[p], &globalOff);CHKERRQ(ierr); indicesPoint_private(section, points[p], dof, globalOff < 0 ? -(globalOff+1) : globalOff, PETSC_FALSE, o, &indices[off]); } } if (useGlobalDefault && !useDefault) { ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr); } if (mesh->printSetValues) {ierr = DMPlexPrintMatSetValues(PETSC_VIEWER_STDOUT_SELF, A, point, numIndices, indices, values);CHKERRQ(ierr);} ierr = MatSetValues(A, numIndices, indices, numIndices, indices, values, mode); if (ierr) { PetscMPIInt rank; PetscErrorCode ierr2; ierr2 = MPI_Comm_rank(((PetscObject) A)->comm, &rank);CHKERRQ(ierr2); ierr2 = (*PetscErrorPrintf)("[%D]ERROR in DMPlexMatSetClosure\n", rank);CHKERRQ(ierr2); ierr2 = DMPlexPrintMatSetValues(PETSC_VIEWER_STDERR_SELF, A, point, numIndices, indices, values);CHKERRQ(ierr2); ierr2 = DMRestoreWorkArray(dm, numIndices, PETSC_INT, &indices);CHKERRQ(ierr2); CHKERRQ(ierr); } ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr); ierr = DMRestoreWorkArray(dm, numIndices, PETSC_INT, &indices);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeTriangleGeometry_private" PetscErrorCode DMPlexComputeTriangleGeometry_private(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) { PetscSection coordSection; Vec coordinates; const PetscScalar *coords; const PetscInt dim = 2; PetscInt d, f; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, PETSC_NULL, &coords);CHKERRQ(ierr); if (v0) { for (d = 0; d < dim; d++) { v0[d] = PetscRealPart(coords[d]); } } if (J) { for (d = 0; d < dim; d++) { for (f = 0; f < dim; f++) { J[d*dim+f] = 0.5*(PetscRealPart(coords[(f+1)*dim+d]) - PetscRealPart(coords[0*dim+d])); } } *detJ = J[0]*J[3] - J[1]*J[2]; #if 0 if (detJ < 0.0) { const PetscReal xLength = mesh->periodicity[0]; if (xLength != 0.0) { PetscReal v0x = coords[0*dim+0]; if (v0x == 0.0) { v0x = v0[0] = xLength; } for (f = 0; f < dim; f++) { const PetscReal px = coords[(f+1)*dim+0] == 0.0 ? xLength : coords[(f+1)*dim+0]; J[0*dim+f] = 0.5*(px - v0x); } } detJ = J[0]*J[3] - J[1]*J[2]; } #endif PetscLogFlops(8.0 + 3.0); } if (invJ) { const PetscReal invDet = 1.0/(*detJ); invJ[0] = invDet*J[3]; invJ[1] = -invDet*J[1]; invJ[2] = -invDet*J[2]; invJ[3] = invDet*J[0]; PetscLogFlops(5.0); } ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, PETSC_NULL, &coords);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeRectangleGeometry_private" PetscErrorCode DMPlexComputeRectangleGeometry_private(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) { PetscSection coordSection; Vec coordinates; const PetscScalar *coords; const PetscInt dim = 2; PetscInt d, f; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, PETSC_NULL, &coords);CHKERRQ(ierr); if (v0) { for (d = 0; d < dim; d++) { v0[d] = PetscRealPart(coords[d]); } } if (J) { for (d = 0; d < dim; d++) { for (f = 0; f < dim; f++) { J[d*dim+f] = 0.5*(PetscRealPart(coords[(f*2+1)*dim+d]) - PetscRealPart(coords[0*dim+d])); } } *detJ = J[0]*J[3] - J[1]*J[2]; PetscLogFlops(8.0 + 3.0); } if (invJ) { const PetscReal invDet = 1.0/(*detJ); invJ[0] = invDet*J[3]; invJ[1] = -invDet*J[1]; invJ[2] = -invDet*J[2]; invJ[3] = invDet*J[0]; PetscLogFlops(5.0); } ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, PETSC_NULL, &coords);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeTetrahedronGeometry_private" PetscErrorCode DMPlexComputeTetrahedronGeometry_private(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) { PetscSection coordSection; Vec coordinates; const PetscScalar *coords; const PetscInt dim = 3; PetscInt d, f; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, PETSC_NULL, &coords);CHKERRQ(ierr); if (v0) { for (d = 0; d < dim; d++) { v0[d] = PetscRealPart(coords[d]); } } if (J) { for (d = 0; d < dim; d++) { for (f = 0; f < dim; f++) { J[d*dim+f] = 0.5*(PetscRealPart(coords[(f+1)*dim+d]) - PetscRealPart(coords[0*dim+d])); } } /* ??? This does not work with CTetGen: The minus sign is here since I orient the first face to get the outward normal */ *detJ = (J[0*3+0]*(J[1*3+1]*J[2*3+2] - J[1*3+2]*J[2*3+1]) + J[0*3+1]*(J[1*3+2]*J[2*3+0] - J[1*3+0]*J[2*3+2]) + J[0*3+2]*(J[1*3+0]*J[2*3+1] - J[1*3+1]*J[2*3+0])); PetscLogFlops(18.0 + 12.0); } if (invJ) { const PetscReal invDet = 1.0/(*detJ); invJ[0*3+0] = invDet*(J[1*3+1]*J[2*3+2] - J[1*3+2]*J[2*3+1]); invJ[0*3+1] = invDet*(J[0*3+2]*J[2*3+1] - J[0*3+1]*J[2*3+2]); invJ[0*3+2] = invDet*(J[0*3+1]*J[1*3+2] - J[0*3+2]*J[1*3+1]); invJ[1*3+0] = invDet*(J[1*3+2]*J[2*3+0] - J[1*3+0]*J[2*3+2]); invJ[1*3+1] = invDet*(J[0*3+0]*J[2*3+2] - J[0*3+2]*J[2*3+0]); invJ[1*3+2] = invDet*(J[0*3+2]*J[1*3+0] - J[0*3+0]*J[1*3+2]); invJ[2*3+0] = invDet*(J[1*3+0]*J[2*3+1] - J[1*3+1]*J[2*3+0]); invJ[2*3+1] = invDet*(J[0*3+1]*J[2*3+0] - J[0*3+0]*J[2*3+1]); invJ[2*3+2] = invDet*(J[0*3+0]*J[1*3+1] - J[0*3+1]*J[1*3+0]); PetscLogFlops(37.0); } ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, PETSC_NULL, &coords);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeHexahedronGeometry_private" PetscErrorCode DMPlexComputeHexahedronGeometry_private(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) { PetscSection coordSection; Vec coordinates; const PetscScalar *coords; const PetscInt dim = 3; PetscInt d; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, PETSC_NULL, &coords);CHKERRQ(ierr); if (v0) { for (d = 0; d < dim; d++) { v0[d] = PetscRealPart(coords[d]); } } if (J) { for (d = 0; d < dim; d++) { J[d*dim+0] = 0.5*(PetscRealPart(coords[(0+1)*dim+d]) - PetscRealPart(coords[0*dim+d])); J[d*dim+1] = 0.5*(PetscRealPart(coords[(1+1)*dim+d]) - PetscRealPart(coords[0*dim+d])); J[d*dim+2] = 0.5*(PetscRealPart(coords[(3+1)*dim+d]) - PetscRealPart(coords[0*dim+d])); } *detJ = (J[0*3+0]*(J[1*3+1]*J[2*3+2] - J[1*3+2]*J[2*3+1]) + J[0*3+1]*(J[1*3+2]*J[2*3+0] - J[1*3+0]*J[2*3+2]) + J[0*3+2]*(J[1*3+0]*J[2*3+1] - J[1*3+1]*J[2*3+0])); PetscLogFlops(18.0 + 12.0); } if (invJ) { const PetscReal invDet = -1.0/(*detJ); invJ[0*3+0] = invDet*(J[1*3+1]*J[2*3+2] - J[1*3+2]*J[2*3+1]); invJ[0*3+1] = invDet*(J[0*3+2]*J[2*3+1] - J[0*3+1]*J[2*3+2]); invJ[0*3+2] = invDet*(J[0*3+1]*J[1*3+2] - J[0*3+2]*J[1*3+1]); invJ[1*3+0] = invDet*(J[1*3+2]*J[2*3+0] - J[1*3+0]*J[2*3+2]); invJ[1*3+1] = invDet*(J[0*3+0]*J[2*3+2] - J[0*3+2]*J[2*3+0]); invJ[1*3+2] = invDet*(J[0*3+2]*J[1*3+0] - J[0*3+0]*J[1*3+2]); invJ[2*3+0] = invDet*(J[1*3+0]*J[2*3+1] - J[1*3+1]*J[2*3+0]); invJ[2*3+1] = invDet*(J[0*3+1]*J[2*3+0] - J[0*3+0]*J[2*3+1]); invJ[2*3+2] = invDet*(J[0*3+0]*J[1*3+1] - J[0*3+1]*J[1*3+0]); PetscLogFlops(37.0); } *detJ *= 8.0; ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, PETSC_NULL, &coords);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeCellGeometry" /*@C DMPlexComputeCellGeometry - Compute the Jacobian, inverse Jacobian, and Jacobian determinant for a given cell Collective on DM Input Arguments: + dm - the DM - cell - the cell Output Arguments: + v0 - the translation part of this affine transform . J - the Jacobian of the transform to the reference element . invJ - the inverse of the Jacobian - detJ - the Jacobian determinant Level: advanced .seealso: DMPlexGetCoordinateSection(), DMPlexGetCoordinateVec() @*/ PetscErrorCode DMPlexComputeCellGeometry(DM dm, PetscInt cell, PetscReal *v0, PetscReal *J, PetscReal *invJ, PetscReal *detJ) { PetscInt dim, coneSize; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); switch(dim) { case 2: switch(coneSize) { case 3: ierr = DMPlexComputeTriangleGeometry_private(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); break; case 4: ierr = DMPlexComputeRectangleGeometry_private(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); break; default: SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_SUP, "Unsupported number of vertices %D in cell %D for element geometry computation", coneSize, cell); } break; case 3: switch(coneSize) { case 4: ierr = DMPlexComputeTetrahedronGeometry_private(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); break; case 8: ierr = DMPlexComputeHexahedronGeometry_private(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); break; default: SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_SUP, "Unsupported number of vertices %D in cell %D for element geometry computation", coneSize, cell); } break; default: SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_SUP, "Unsupported dimension %D for element geometry computation", dim); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetFaceOrientation" PetscErrorCode DMPlexGetFaceOrientation(DM dm, PetscInt cell, PetscInt numCorners, PetscInt indices[], PetscInt oppositeVertex, PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) { MPI_Comm comm = ((PetscObject) dm)->comm; PetscBool posOrient = PETSC_FALSE; const PetscInt debug = 0; PetscInt cellDim, faceSize, f; PetscErrorCode ierr; ierr = DMPlexGetDimension(dm, &cellDim);CHKERRQ(ierr); if (debug) {PetscPrintf(comm, "cellDim: %d numCorners: %d\n", cellDim, numCorners);CHKERRQ(ierr);} if (cellDim == numCorners-1) { /* Simplices */ faceSize = numCorners-1; posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; } else if (cellDim == 1 && numCorners == 3) { /* Quadratic line */ faceSize = 1; posOrient = PETSC_TRUE; } else if (cellDim == 2 && numCorners == 4) { /* Quads */ faceSize = 2; if ((indices[1] > indices[0]) && (indices[1] - indices[0] == 1)) { posOrient = PETSC_TRUE; } else if ((indices[0] == 3) && (indices[1] == 0)) { posOrient = PETSC_TRUE; } else { if (((indices[0] > indices[1]) && (indices[0] - indices[1] == 1)) || ((indices[0] == 0) && (indices[1] == 3))) { posOrient = PETSC_FALSE; } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossedge"); } } else if (cellDim == 2 && numCorners == 6) { /* Quadratic triangle (I hate this) */ /* Edges are determined by the first 2 vertices (corners of edges) */ const PetscInt faceSizeTri = 3; PetscInt sortedIndices[3], i, iFace; PetscBool found = PETSC_FALSE; PetscInt faceVerticesTriSorted[9] = { 0, 3, 4, /* bottom */ 1, 4, 5, /* right */ 2, 3, 5, /* left */ }; PetscInt faceVerticesTri[9] = { 0, 3, 4, /* bottom */ 1, 4, 5, /* right */ 2, 5, 3, /* left */ }; faceSize = faceSizeTri; for (i = 0; i < faceSizeTri; ++i) sortedIndices[i] = indices[i]; ierr = PetscSortInt(faceSizeTri, sortedIndices);CHKERRQ(ierr); for (iFace = 0; iFace < 3; ++iFace) { const PetscInt ii = iFace*faceSizeTri; PetscInt fVertex, cVertex; if ((sortedIndices[0] == faceVerticesTriSorted[ii+0]) && (sortedIndices[1] == faceVerticesTriSorted[ii+1])) { for (fVertex = 0; fVertex < faceSizeTri; ++fVertex) { for (cVertex = 0; cVertex < faceSizeTri; ++cVertex) { if (indices[cVertex] == faceVerticesTri[ii+fVertex]) { faceVertices[fVertex] = origVertices[cVertex]; break; } } } found = PETSC_TRUE; break; } } if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tri crossface"); if (posOriented) {*posOriented = PETSC_TRUE;} PetscFunctionReturn(0); } else if (cellDim == 2 && numCorners == 9) { /* Quadratic quad (I hate this) */ /* Edges are determined by the first 2 vertices (corners of edges) */ const PetscInt faceSizeQuad = 3; PetscInt sortedIndices[3], i, iFace; PetscBool found = PETSC_FALSE; PetscInt faceVerticesQuadSorted[12] = { 0, 1, 4, /* bottom */ 1, 2, 5, /* right */ 2, 3, 6, /* top */ 0, 3, 7, /* left */ }; PetscInt faceVerticesQuad[12] = { 0, 1, 4, /* bottom */ 1, 2, 5, /* right */ 2, 3, 6, /* top */ 3, 0, 7, /* left */ }; faceSize = faceSizeQuad; for (i = 0; i < faceSizeQuad; ++i) sortedIndices[i] = indices[i]; ierr = PetscSortInt(faceSizeQuad, sortedIndices);CHKERRQ(ierr); for (iFace = 0; iFace < 4; ++iFace) { const PetscInt ii = iFace*faceSizeQuad; PetscInt fVertex, cVertex; if ((sortedIndices[0] == faceVerticesQuadSorted[ii+0]) && (sortedIndices[1] == faceVerticesQuadSorted[ii+1])) { for (fVertex = 0; fVertex < faceSizeQuad; ++fVertex) { for (cVertex = 0; cVertex < faceSizeQuad; ++cVertex) { if (indices[cVertex] == faceVerticesQuad[ii+fVertex]) { faceVertices[fVertex] = origVertices[cVertex]; break; } } } found = PETSC_TRUE; break; } } if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossface"); if (posOriented) {*posOriented = PETSC_TRUE;} PetscFunctionReturn(0); } else if (cellDim == 3 && numCorners == 8) { /* Hexes A hex is two oriented quads with the normal of the first pointing up at the second. 7---6 /| /| 4---5 | | 3-|-2 |/ |/ 0---1 Faces are determined by the first 4 vertices (corners of faces) */ const PetscInt faceSizeHex = 4; PetscInt sortedIndices[4], i, iFace; PetscBool found = PETSC_FALSE; PetscInt faceVerticesHexSorted[24] = { 0, 1, 2, 3, /* bottom */ 4, 5, 6, 7, /* top */ 0, 1, 4, 5, /* front */ 1, 2, 5, 6, /* right */ 2, 3, 6, 7, /* back */ 0, 3, 4, 7, /* left */ }; PetscInt faceVerticesHex[24] = { 3, 2, 1, 0, /* bottom */ 4, 5, 6, 7, /* top */ 0, 1, 5, 4, /* front */ 1, 2, 6, 5, /* right */ 2, 3, 7, 6, /* back */ 3, 0, 4, 7, /* left */ }; faceSize = faceSizeHex; for (i = 0; i < faceSizeHex; ++i) sortedIndices[i] = indices[i]; ierr = PetscSortInt(faceSizeHex, sortedIndices);CHKERRQ(ierr); for (iFace = 0; iFace < 6; ++iFace) { const PetscInt ii = iFace*faceSizeHex; PetscInt fVertex, cVertex; if ((sortedIndices[0] == faceVerticesHexSorted[ii+0]) && (sortedIndices[1] == faceVerticesHexSorted[ii+1]) && (sortedIndices[2] == faceVerticesHexSorted[ii+2]) && (sortedIndices[3] == faceVerticesHexSorted[ii+3])) { for (fVertex = 0; fVertex < faceSizeHex; ++fVertex) { for (cVertex = 0; cVertex < faceSizeHex; ++cVertex) { if (indices[cVertex] == faceVerticesHex[ii+fVertex]) { faceVertices[fVertex] = origVertices[cVertex]; break; } } } found = PETSC_TRUE; break; } } if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); if (posOriented) {*posOriented = PETSC_TRUE;} PetscFunctionReturn(0); } else if (cellDim == 3 && numCorners == 10) { /* Quadratic tet */ /* Faces are determined by the first 3 vertices (corners of faces) */ const PetscInt faceSizeTet = 6; PetscInt sortedIndices[6], i, iFace; PetscBool found = PETSC_FALSE; PetscInt faceVerticesTetSorted[24] = { 0, 1, 2, 6, 7, 8, /* bottom */ 0, 3, 4, 6, 7, 9, /* front */ 1, 4, 5, 7, 8, 9, /* right */ 2, 3, 5, 6, 8, 9, /* left */ }; PetscInt faceVerticesTet[24] = { 0, 1, 2, 6, 7, 8, /* bottom */ 0, 4, 3, 6, 7, 9, /* front */ 1, 5, 4, 7, 8, 9, /* right */ 2, 3, 5, 8, 6, 9, /* left */ }; faceSize = faceSizeTet; for (i = 0; i < faceSizeTet; ++i) sortedIndices[i] = indices[i]; ierr = PetscSortInt(faceSizeTet, sortedIndices);CHKERRQ(ierr); for (iFace=0; iFace < 4; ++iFace) { const PetscInt ii = iFace*faceSizeTet; PetscInt fVertex, cVertex; if ((sortedIndices[0] == faceVerticesTetSorted[ii+0]) && (sortedIndices[1] == faceVerticesTetSorted[ii+1]) && (sortedIndices[2] == faceVerticesTetSorted[ii+2]) && (sortedIndices[3] == faceVerticesTetSorted[ii+3])) { for (fVertex = 0; fVertex < faceSizeTet; ++fVertex) { for (cVertex = 0; cVertex < faceSizeTet; ++cVertex) { if (indices[cVertex] == faceVerticesTet[ii+fVertex]) { faceVertices[fVertex] = origVertices[cVertex]; break; } } } found = PETSC_TRUE; break; } } if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tet crossface"); if (posOriented) {*posOriented = PETSC_TRUE;} PetscFunctionReturn(0); } else if (cellDim == 3 && numCorners == 27) { /* Quadratic hexes (I hate this) A hex is two oriented quads with the normal of the first pointing up at the second. 7---6 /| /| 4---5 | | 3-|-2 |/ |/ 0---1 Faces are determined by the first 4 vertices (corners of faces) */ const PetscInt faceSizeQuadHex = 9; PetscInt sortedIndices[9], i, iFace; PetscBool found = PETSC_FALSE; PetscInt faceVerticesQuadHexSorted[54] = { 0, 1, 2, 3, 8, 9, 10, 11, 24, /* bottom */ 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 0, 1, 4, 5, 8, 12, 16, 17, 22, /* front */ 1, 2, 5, 6, 9, 13, 17, 18, 21, /* right */ 2, 3, 6, 7, 10, 14, 18, 19, 23, /* back */ 0, 3, 4, 7, 11, 15, 16, 19, 20, /* left */ }; PetscInt faceVerticesQuadHex[54] = { 3, 2, 1, 0, 10, 9, 8, 11, 24, /* bottom */ 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 0, 1, 5, 4, 8, 17, 12, 16, 22, /* front */ 1, 2, 6, 5, 9, 18, 13, 17, 21, /* right */ 2, 3, 7, 6, 10, 19, 14, 18, 23, /* back */ 3, 0, 4, 7, 11, 16, 15, 19, 20 /* left */ }; faceSize = faceSizeQuadHex; for (i = 0; i < faceSizeQuadHex; ++i) sortedIndices[i] = indices[i]; ierr = PetscSortInt(faceSizeQuadHex, sortedIndices);CHKERRQ(ierr); for (iFace = 0; iFace < 6; ++iFace) { const PetscInt ii = iFace*faceSizeQuadHex; PetscInt fVertex, cVertex; if ((sortedIndices[0] == faceVerticesQuadHexSorted[ii+0]) && (sortedIndices[1] == faceVerticesQuadHexSorted[ii+1]) && (sortedIndices[2] == faceVerticesQuadHexSorted[ii+2]) && (sortedIndices[3] == faceVerticesQuadHexSorted[ii+3])) { for (fVertex = 0; fVertex < faceSizeQuadHex; ++fVertex) { for (cVertex = 0; cVertex < faceSizeQuadHex; ++cVertex) { if (indices[cVertex] == faceVerticesQuadHex[ii+fVertex]) { faceVertices[fVertex] = origVertices[cVertex]; break; } } } found = PETSC_TRUE; break; } } if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); if (posOriented) {*posOriented = PETSC_TRUE;} PetscFunctionReturn(0); } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Unknown cell type for faceOrientation()."); if (!posOrient) { if (debug) {ierr = PetscPrintf(comm, " Reversing initial face orientation\n");CHKERRQ(ierr);} for (f = 0; f < faceSize; ++f) { faceVertices[f] = origVertices[faceSize-1 - f]; } } else { if (debug) {ierr = PetscPrintf(comm, " Keeping initial face orientation\n");CHKERRQ(ierr);} for (f = 0; f < faceSize; ++f) { faceVertices[f] = origVertices[f]; } } if (posOriented) {*posOriented = posOrient;} PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetOrientedFace" /* Given a cell and a face, as a set of vertices, return the oriented face, as a set of vertices, in faceVertices The orientation is such that the face normal points out of the cell */ PetscErrorCode DMPlexGetOrientedFace(DM dm, PetscInt cell, PetscInt faceSize, const PetscInt face[], PetscInt numCorners, PetscInt indices[], PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) { const PetscInt *cone = PETSC_NULL; PetscInt coneSize, v, f, v2; PetscInt oppositeVertex = -1; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); for (v = 0, v2 = 0; v < coneSize; ++v) { PetscBool found = PETSC_FALSE; for (f = 0; f < faceSize; ++f) { if (face[f] == cone[v]) {found = PETSC_TRUE; break;} } if (found) { indices[v2] = v; origVertices[v2] = cone[v]; ++v2; } else { oppositeVertex = v; } } ierr = DMPlexGetFaceOrientation(dm, cell, numCorners, indices, oppositeVertex, origVertices, faceVertices, posOriented);CHKERRQ(ierr); PetscFunctionReturn(0); } PETSC_STATIC_INLINE PetscInt epsilon(PetscInt i, PetscInt j, PetscInt k) { switch(i) { case 0: switch(j) { case 0: return 0; case 1: switch(k) { case 0: return 0; case 1: return 0; case 2: return 1; } case 2: switch(k) { case 0: return 0; case 1: return -1; case 2: return 0; } } case 1: switch(j) { case 0: switch(k) { case 0: return 0; case 1: return 0; case 2: return -1; } case 1: return 0; case 2: switch(k) { case 0: return 1; case 1: return 0; case 2: return 0; } } case 2: switch(j) { case 0: switch(k) { case 0: return 0; case 1: return 1; case 2: return 0; } case 1: switch(k) { case 0: return -1; case 1: return 0; case 2: return 0; } case 2: return 0; } } return 0; } #undef __FUNCT__ #define __FUNCT__ "DMPlexCreateRigidBody" /*@C DMPlexCreateRigidBody - create rigid body modes from coordinates Collective on DM Input Arguments: + dm - the DM . section - the local section associated with the rigid field, or PETSC_NULL for the default section - globalSection - the global section associated with the rigid field, or PETSC_NULL for the default section Output Argument: . sp - the null space Note: This is necessary to take account of Dirichlet conditions on the displacements Level: advanced .seealso: MatNullSpaceCreate() @*/ PetscErrorCode DMPlexCreateRigidBody(DM dm, PetscSection section, PetscSection globalSection, MatNullSpace *sp) { MPI_Comm comm = ((PetscObject) dm)->comm; Vec coordinates, localMode, mode[6]; PetscSection coordSection; PetscScalar *coords; PetscInt dim, vStart, vEnd, v, n, m, d, i, j; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); if (dim == 1) { ierr = MatNullSpaceCreate(comm, PETSC_TRUE, 0, PETSC_NULL, sp);CHKERRQ(ierr); PetscFunctionReturn(0); } if (!section) {ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);} if (!globalSection) {ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr);} ierr = PetscSectionGetConstrainedStorageSize(globalSection, &n);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); m = (dim*(dim+1))/2; ierr = VecCreate(comm, &mode[0]);CHKERRQ(ierr); ierr = VecSetSizes(mode[0], n, PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetUp(mode[0]);CHKERRQ(ierr); for (i = 1; i < m; ++i) {ierr = VecDuplicate(mode[0], &mode[i]);CHKERRQ(ierr);} /* Assume P1 */ ierr = DMGetLocalVector(dm, &localMode);CHKERRQ(ierr); for (d = 0; d < dim; ++d) { PetscScalar values[3] = {0.0, 0.0, 0.0}; values[d] = 1.0; ierr = VecSet(localMode, 0.0);CHKERRQ(ierr); for (v = vStart; v < vEnd; ++v) { ierr = DMPlexVecSetClosure(dm, section, localMode, v, values, INSERT_VALUES);CHKERRQ(ierr); } ierr = DMLocalToGlobalBegin(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr); ierr = DMLocalToGlobalEnd(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr); } ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); for (d = dim; d < dim*(dim+1)/2; ++d) { PetscInt i, j, k = dim > 2 ? d - dim : d; ierr = VecSet(localMode, 0.0);CHKERRQ(ierr); for (v = vStart; v < vEnd; ++v) { PetscScalar values[3] = {0.0, 0.0, 0.0}; PetscInt off; ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); for (i = 0; i < dim; ++i) { for (j = 0; j < dim; ++j) { values[j] += epsilon(i, j, k)*PetscRealPart(coords[off+i]); } } ierr = DMPlexVecSetClosure(dm, section, localMode, v, values, INSERT_VALUES);CHKERRQ(ierr); } ierr = DMLocalToGlobalBegin(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr); ierr = DMLocalToGlobalEnd(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr); } ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &localMode);CHKERRQ(ierr); for (i = 0; i < dim; ++i) {ierr = VecNormalize(mode[i], PETSC_NULL);CHKERRQ(ierr);} /* Orthonormalize system */ for (i = dim; i < m; ++i) { PetscScalar dots[6]; ierr = VecMDot(mode[i], i, mode, dots);CHKERRQ(ierr); for (j = 0; j < i; ++j) dots[j] *= -1.0; ierr = VecMAXPY(mode[i], i, dots, mode);CHKERRQ(ierr); ierr = VecNormalize(mode[i], PETSC_NULL);CHKERRQ(ierr); } ierr = MatNullSpaceCreate(comm, PETSC_FALSE, m, mode, sp);CHKERRQ(ierr); for (i = 0; i< m; ++i) {ierr = VecDestroy(&mode[i]);CHKERRQ(ierr);} PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetHybridBounds" PetscErrorCode DMPlexGetHybridBounds(DM dm, PetscInt *cMax, PetscInt *fMax, PetscInt *eMax, PetscInt *vMax) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt dim; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); if (cMax) *cMax = mesh->hybridPointMax[dim]; if (fMax) *fMax = mesh->hybridPointMax[dim-1]; if (eMax) *eMax = mesh->hybridPointMax[1]; if (vMax) *vMax = mesh->hybridPointMax[0]; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSetHybridBounds" PetscErrorCode DMPlexSetHybridBounds(DM dm, PetscInt cMax, PetscInt fMax, PetscInt eMax, PetscInt vMax) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt dim; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); if (cMax >= 0) mesh->hybridPointMax[dim] = cMax; if (fMax >= 0) mesh->hybridPointMax[dim-1] = fMax; if (eMax >= 0) mesh->hybridPointMax[1] = eMax; if (vMax >= 0) mesh->hybridPointMax[0] = vMax; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetVTKCellHeight" PetscErrorCode DMPlexGetVTKCellHeight(DM dm, PetscInt *cellHeight) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(cellHeight, 2); *cellHeight = mesh->vtkCellHeight; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSetVTKCellHeight" PetscErrorCode DMPlexSetVTKCellHeight(DM dm, PetscInt cellHeight) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); mesh->vtkCellHeight = cellHeight; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexInsertFace_Private" /* DMPlexInsertFace_Private - Puts a face into the mesh Not collective Input Parameters: + dm - The DMPlex . numFaceVertex - The number of vertices in the face . faceVertices - The vertices in the face for dm . subfaceVertices - The vertices in the face for subdm . numCorners - The number of vertices in the cell . cell - A cell in dm containing the face . subcell - A cell in subdm containing the face . firstFace - First face in the mesh - newFacePoint - Next face in the mesh Output Parameters: . newFacePoint - Contains next face point number on input, updated on output Level: developer */ PetscErrorCode DMPlexInsertFace_Private(DM dm, DM subdm, PetscInt numFaceVertices, const PetscInt faceVertices[], const PetscInt subfaceVertices[], PetscInt numCorners, PetscInt cell, PetscInt subcell, PetscInt firstFace, PetscInt *newFacePoint) { MPI_Comm comm = ((PetscObject) dm)->comm; DM_Plex *submesh = (DM_Plex *) subdm->data; const PetscInt *faces; PetscInt numFaces, coneSize; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetConeSize(subdm, subcell, &coneSize);CHKERRQ(ierr); if (coneSize != 1) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone size of cell %d is %d != 1", cell, coneSize); #if 0 /* Cannot use this because support() has not been constructed yet */ ierr = DMPlexGetJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); #else { PetscInt f; numFaces = 0; ierr = DMGetWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); for(f = firstFace; f < *newFacePoint; ++f) { PetscInt dof, off, d; ierr = PetscSectionGetDof(submesh->coneSection, f, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(submesh->coneSection, f, &off);CHKERRQ(ierr); /* Yes, I know this is quadratic, but I expect the sizes to be <5 */ for(d = 0; d < dof; ++d) { const PetscInt p = submesh->cones[off+d]; PetscInt v; for(v = 0; v < numFaceVertices; ++v) { if (subfaceVertices[v] == p) break; } if (v == numFaceVertices) break; } if (d == dof) { numFaces = 1; ((PetscInt *) faces)[0] = f; } } } #endif if (numFaces > 1) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex set had %d faces, not one", numFaces); else if (numFaces == 1) { /* Add the other cell neighbor for this face */ ierr = DMPlexSetCone(subdm, cell, faces);CHKERRQ(ierr); } else { PetscInt *indices, *origVertices, *orientedVertices, *orientedSubVertices, v, ov; PetscBool posOriented; ierr = DMGetWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); origVertices = &orientedVertices[numFaceVertices]; indices = &orientedVertices[numFaceVertices*2]; orientedSubVertices = &orientedVertices[numFaceVertices*3]; ierr = DMPlexGetOrientedFace(dm, cell, numFaceVertices, faceVertices, numCorners, indices, origVertices, orientedVertices, &posOriented);CHKERRQ(ierr); /* TODO: I know that routine should return a permutation, not the indices */ for(v = 0; v < numFaceVertices; ++v) { const PetscInt vertex = faceVertices[v], subvertex = subfaceVertices[v]; for(ov = 0; ov < numFaceVertices; ++ov) { if (orientedVertices[ov] == vertex) { orientedSubVertices[ov] = subvertex; break; } } if (ov == numFaceVertices) SETERRQ1(comm, PETSC_ERR_PLIB, "Could not find face vertex %d in orientated set", vertex); } ierr = DMPlexSetCone(subdm, *newFacePoint, orientedSubVertices);CHKERRQ(ierr); ierr = DMPlexSetCone(subdm, subcell, newFacePoint);CHKERRQ(ierr); ierr = DMRestoreWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); ++(*newFacePoint); } ierr = DMPlexRestoreJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexCreateSubmesh" PetscErrorCode DMPlexCreateSubmesh(DM dm, const char label[], DM *subdm) { MPI_Comm comm = ((PetscObject) dm)->comm; DM_Plex *submesh; PetscBool boundaryFaces = PETSC_FALSE; PetscSection coordSection, subCoordSection; Vec coordinates, subCoordinates; PetscScalar *coords, *subCoords; IS labelIS; const PetscInt *subVertices; PetscInt *subVerticesActive, *tmpPoints; PetscInt *subCells = PETSC_NULL; PetscInt numSubVertices, numSubVerticesActive, firstSubVertex, numSubCells = 0, maxSubCells = 0, numOldSubCells; PetscInt *face, *subface, maxConeSize, numSubFaces = 0, firstSubFace, newFacePoint, nFV = 0, coordSize; PetscInt dim; /* Right now, do not specify dimension */ PetscInt cStart, cEnd, cMax, c, vStart, vEnd, vMax, v, p, corner, i, d, f; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMPlexGetMaxSizes(dm, &maxConeSize, PETSC_NULL);CHKERRQ(ierr); ierr = DMPlexGetHybridBounds(dm, &cMax, PETSC_NULL, PETSC_NULL, &vMax);CHKERRQ(ierr); if (cMax >= 0) {cEnd = PetscMin(cEnd, cMax);} if (vMax >= 0) {vEnd = PetscMin(vEnd, vMax);} ierr = DMGetWorkArray(dm, 2*maxConeSize, PETSC_INT, &face);CHKERRQ(ierr); subface = &face[maxConeSize]; ierr = DMCreate(comm, subdm);CHKERRQ(ierr); ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); ierr = DMPlexGetStratumIS(dm, label, 1, &labelIS);CHKERRQ(ierr); ierr = ISGetSize(labelIS, &numSubVertices);CHKERRQ(ierr); ierr = ISGetIndices(labelIS, &subVertices);CHKERRQ(ierr); maxSubCells = numSubVertices; ierr = PetscMalloc(maxSubCells * sizeof(PetscInt), &subCells);CHKERRQ(ierr); ierr = PetscMalloc(numSubVertices * sizeof(PetscInt), &subVerticesActive);CHKERRQ(ierr); ierr = PetscMemzero(subVerticesActive, numSubVertices * sizeof(PetscInt));CHKERRQ(ierr); for(v = 0; v < numSubVertices; ++v) { const PetscInt vertex = subVertices[v]; PetscInt *star = PETSC_NULL; PetscInt starSize, numCells = 0; ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); for(p = 0; p < starSize*2; p += 2) { const PetscInt point = star[p]; if ((point >= cStart) && (point < cEnd)) { star[numCells++] = point; } } numOldSubCells = numSubCells; for(c = 0; c < numCells; ++c) { const PetscInt cell = star[c]; PetscInt *closure = PETSC_NULL; PetscInt closureSize, numCorners = 0, faceSize = 0; PetscInt cellLoc; ierr = PetscFindInt(cell, numOldSubCells, subCells, &cellLoc);CHKERRQ(ierr); if (cellLoc >= 0) continue; ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); for(p = 0; p < closureSize*2; p += 2) { const PetscInt point = closure[p]; if ((point >= vStart) && (point < vEnd)) { closure[numCorners++] = point; } } if (!nFV) {ierr = DMPlexGetNumFaceVertices(dm, numCorners, &nFV);CHKERRQ(ierr);} for(corner = 0; corner < numCorners; ++corner) { const PetscInt cellVertex = closure[corner]; PetscInt subVertex; ierr = PetscFindInt(cellVertex, numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); if (subVertex >= 0) { /* contains submesh vertex */ for(i = 0; i < faceSize; ++i) {if (cellVertex == face[i]) break;} if (i == faceSize) { if (faceSize >= maxConeSize) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of vertices in face %d should not exceed %d", faceSize+1, maxConeSize); face[faceSize] = cellVertex; subface[faceSize] = subVertex; ++faceSize; } } } ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); if (faceSize >= nFV) { if (faceSize > nFV && !boundaryFaces) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); if (numSubCells >= maxSubCells) { PetscInt *tmpCells; maxSubCells *= 2; ierr = PetscMalloc(maxSubCells * sizeof(PetscInt), &tmpCells);CHKERRQ(ierr); ierr = PetscMemcpy(tmpCells, subCells, numSubCells * sizeof(PetscInt));CHKERRQ(ierr); ierr = PetscFree(subCells);CHKERRQ(ierr); subCells = tmpCells; } /* TOOD: Maybe overestimate then squeeze out empty faces */ if (faceSize > nFV) { /* TODO: This is tricky. Maybe just add all faces */ numSubFaces++; } else { numSubFaces++; } for(f = 0; f < faceSize; ++f) { subVerticesActive[subface[f]] = 1; } subCells[numSubCells++] = cell; } } ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); ierr = PetscSortRemoveDupsInt(&numSubCells, subCells);CHKERRQ(ierr); } /* Pick out active subvertices */ for(v = 0, numSubVerticesActive = 0; v < numSubVertices; ++v) { if (subVerticesActive[v]) { subVerticesActive[numSubVerticesActive++] = subVertices[v]; } } ierr = DMPlexSetChart(*subdm, 0, numSubCells+numSubFaces+numSubVerticesActive);CHKERRQ(ierr); /* Set cone sizes */ firstSubVertex = numSubCells; firstSubFace = numSubCells+numSubVerticesActive; newFacePoint = firstSubFace; for(c = 0; c < numSubCells; ++c) { ierr = DMPlexSetConeSize(*subdm, c, 1);CHKERRQ(ierr); } for(f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { ierr = DMPlexSetConeSize(*subdm, f, nFV);CHKERRQ(ierr); } ierr = DMSetUp(*subdm);CHKERRQ(ierr); /* Create face cones */ for(c = 0; c < numSubCells; ++c) { const PetscInt cell = subCells[c]; PetscInt *closure = PETSC_NULL; PetscInt closureSize, numCorners = 0, faceSize = 0; ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); for(p = 0; p < closureSize*2; p += 2) { const PetscInt point = closure[p]; if ((point >= vStart) && (point < vEnd)) { closure[numCorners++] = point; } } for(corner = 0; corner < numCorners; ++corner) { const PetscInt cellVertex = closure[corner]; PetscInt subVertex; ierr = PetscFindInt(cellVertex, numSubVerticesActive, subVerticesActive, &subVertex);CHKERRQ(ierr); if (subVertex >= 0) { /* contains submesh vertex */ for(i = 0; i < faceSize; ++i) {if (cellVertex == face[i]) break;} if (i == faceSize) { face[faceSize] = cellVertex; subface[faceSize] = numSubCells+subVertex; ++faceSize; } } } ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); if (faceSize >= nFV) { if (faceSize > nFV && !boundaryFaces) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); /* Here we allow a set of vertices to lie completely on a boundary cell (like a corner tetrahedron) */ /* We have to take all the faces, and discard those in the interior */ /* We check the join of the face vertices, which produces 2 cells if in the interior */ #if 0 /* This object just calls insert on each face that comes from subsets() */ /* In fact, we can just always acll subsets(), since when we pass a single face it is a single call */ FaceInserterV inserter(mesh, sieve, subSieve, f, *c_iter, numCorners, indices, &origVertices, &faceVertices, &submeshCells); PointArray faceVec(face->begin(), face->end()); subsets(faceVec, nFV, inserter); #endif ierr = DMPlexInsertFace_Private(dm, *subdm, faceSize, face, subface, numCorners, cell, c, firstSubFace, &newFacePoint);CHKERRQ(ierr); } } ierr = DMPlexSymmetrize(*subdm);CHKERRQ(ierr); ierr = DMPlexStratify(*subdm);CHKERRQ(ierr); /* Build coordinates */ ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(*subdm, &subCoordSection);CHKERRQ(ierr); ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVerticesActive);CHKERRQ(ierr); for (v = firstSubVertex; v < firstSubVertex+numSubVerticesActive; ++v) { ierr = PetscSectionSetDof(subCoordSection, v, dim);CHKERRQ(ierr); } ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); ierr = VecCreate(((PetscObject) dm)->comm, &subCoordinates);CHKERRQ(ierr); ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); for(v = 0; v < numSubVerticesActive; ++v) { const PetscInt vertex = subVerticesActive[v]; const PetscInt subVertex = firstSubVertex+v; PetscInt dof, off, sdof, soff; ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); ierr = PetscSectionGetDof(subCoordSection, subVertex, &sdof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(subCoordSection, subVertex, &soff);CHKERRQ(ierr); if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subVertex, vertex, dof); for(d = 0; d < dof; ++d) { subCoords[soff+d] = coords[off+d]; } } ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(*subdm, subCoordinates);CHKERRQ(ierr); ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); ierr = DMPlexSetVTKCellHeight(*subdm, 1);CHKERRQ(ierr); /* Create map from submesh points to original mesh points */ submesh = (DM_Plex *) (*subdm)->data; ierr = PetscMalloc((numSubCells+numSubVerticesActive) * sizeof(PetscInt), &tmpPoints);CHKERRQ(ierr); for(c = 0; c < numSubCells; ++c) { tmpPoints[c] = subCells[c]; } for(v = numSubCells; v < numSubCells+numSubVerticesActive; ++v) { tmpPoints[v] = subVerticesActive[v-numSubCells]; } ierr = ISCreateGeneral(comm, numSubCells+numSubVerticesActive, tmpPoints, PETSC_OWN_POINTER, &submesh->subpointMap);CHKERRQ(ierr); ierr = PetscFree(subCells);CHKERRQ(ierr); ierr = PetscFree(subVerticesActive);CHKERRQ(ierr); ierr = ISRestoreIndices(labelIS, &subVertices);CHKERRQ(ierr); ierr = ISDestroy(&labelIS);CHKERRQ(ierr); ierr = DMRestoreWorkArray(dm, 2*maxConeSize, PETSC_INT, &face);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexCreateNumbering_Private" /* We can easily have a form that takes an IS instead */ PetscErrorCode DMPlexCreateNumbering_Private(DM dm, PetscInt pStart, PetscInt pEnd, PetscSF sf, IS *numbering) { PetscSection section, globalSection; PetscInt *numbers, p; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscSectionCreate(((PetscObject) dm)->comm, §ion);CHKERRQ(ierr); ierr = PetscSectionSetChart(section, pStart, pEnd);CHKERRQ(ierr); for(p = pStart; p < pEnd; ++p) { ierr = PetscSectionSetDof(section, p, 1);CHKERRQ(ierr); } ierr = PetscSectionSetUp(section);CHKERRQ(ierr); ierr = PetscSectionCreateGlobalSection(section, sf, PETSC_FALSE, &globalSection);CHKERRQ(ierr); ierr = PetscMalloc((pEnd - pStart) * sizeof(PetscInt), &numbers);CHKERRQ(ierr); for(p = pStart; p < pEnd; ++p) { ierr = PetscSectionGetOffset(globalSection, p, &numbers[p-pStart]);CHKERRQ(ierr); } ierr = ISCreateGeneral(((PetscObject) dm)->comm, pEnd - pStart, numbers, PETSC_OWN_POINTER, numbering);CHKERRQ(ierr); ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr); ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetCellNumbering" PetscErrorCode DMPlexGetCellNumbering(DM dm, IS *globalCellNumbers) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt cellHeight, cStart, cEnd, cMax; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); if (!mesh->globalCellNumbers) { ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetHybridBounds(dm, &cMax, PETSC_NULL, PETSC_NULL, PETSC_NULL);CHKERRQ(ierr); if (cMax >= 0) {cEnd = PetscMin(cEnd, cMax);} ierr = DMPlexCreateNumbering_Private(dm, cStart, cEnd, dm->sf, &mesh->globalCellNumbers);CHKERRQ(ierr); } *globalCellNumbers = mesh->globalCellNumbers; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetVertexNumbering" PetscErrorCode DMPlexGetVertexNumbering(DM dm, IS *globalVertexNumbers) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt vStart, vEnd, vMax; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); if (!mesh->globalVertexNumbers) { ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMPlexGetHybridBounds(dm, PETSC_NULL, PETSC_NULL, PETSC_NULL, &vMax);CHKERRQ(ierr); if (vMax >= 0) {vEnd = PetscMin(vEnd, vMax);} ierr = DMPlexCreateNumbering_Private(dm, vStart, vEnd, dm->sf, &mesh->globalVertexNumbers);CHKERRQ(ierr); } *globalVertexNumbers = mesh->globalVertexNumbers; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetSubpointMap" PetscErrorCode DMPlexGetSubpointMap(DM dm, IS *subpointMap) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(subpointMap, 2); *subpointMap = mesh->subpointMap; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSetSubpointMap" /* Note: Should normally not be called by the user, since it is set in DMPlexCreateSubmesh() */ PetscErrorCode DMPlexSetSubpointMap(DM dm, IS subpointMap) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidHeaderSpecific(subpointMap, IS_CLASSID, 2); mesh->subpointMap = subpointMap; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexGetScale" PetscErrorCode DMPlexGetScale(DM dm, PetscUnit unit, PetscReal *scale) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(scale, 3); *scale = mesh->scale[unit]; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexSetScale" PetscErrorCode DMPlexSetScale(DM dm, PetscUnit unit, PetscReal scale) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); mesh->scale[unit] = scale; PetscFunctionReturn(0); } /******************************************************************************* This should be in a separate Discretization object, but I am not sure how to lay it out yet, so I am stuffing things here while I experiment. *******************************************************************************/ #undef __FUNCT__ #define __FUNCT__ "DMPlexSetFEMIntegration" PetscErrorCode DMPlexSetFEMIntegration(DM dm, PetscErrorCode (*integrateResidualFEM)(PetscInt, PetscInt, PetscInt, PetscQuadrature[], const PetscScalar[], const PetscReal[], const PetscReal[], const PetscReal[], const PetscReal[], void (*)(const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]), void (*)(const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]), PetscScalar[]), PetscErrorCode (*integrateJacobianActionFEM)(PetscInt, PetscInt, PetscInt, PetscQuadrature[], const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscReal[], const PetscReal[], const PetscReal[], void (**)(const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]), void (**)(const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]), void (**)(const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]), void (**)(const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]), PetscScalar[]), PetscErrorCode (*integrateJacobianFEM)(PetscInt, PetscInt, PetscInt, PetscInt, PetscQuadrature[], const PetscScalar[], const PetscReal[], const PetscReal[], const PetscReal[], const PetscReal[], void (*)(const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]), void (*)(const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]), void (*)(const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]), void (*)(const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]), PetscScalar[])) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); mesh->integrateResidualFEM = integrateResidualFEM; mesh->integrateJacobianActionFEM = integrateJacobianActionFEM; mesh->integrateJacobianFEM = integrateJacobianFEM; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexProjectFunctionLocal" PetscErrorCode DMPlexProjectFunctionLocal(DM dm, PetscInt numComp, PetscScalar (**funcs)(const PetscReal []), InsertMode mode, Vec localX) { Vec coordinates; PetscSection section, cSection; PetscInt dim, vStart, vEnd, v, c, d; PetscScalar *values, *cArray; PetscReal *coords; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &cSection);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = PetscMalloc(numComp * sizeof(PetscScalar), &values);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &cArray);CHKERRQ(ierr); ierr = PetscSectionGetDof(cSection, vStart, &dim);CHKERRQ(ierr); ierr = PetscMalloc(dim * sizeof(PetscReal),&coords);CHKERRQ(ierr); for (v = vStart; v < vEnd; ++v) { PetscInt dof, off; ierr = PetscSectionGetDof(cSection, v, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(cSection, v, &off);CHKERRQ(ierr); if (dof > dim) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_ARG_WRONG, "Cannot have more coordinates %d then dimensions %d", dof, dim); for(d = 0; d < dof; ++d) { coords[d] = PetscRealPart(cArray[off+d]); } for(c = 0; c < numComp; ++c) { values[c] = (*funcs[c])(coords); } ierr = VecSetValuesSection(localX, section, v, values, mode);CHKERRQ(ierr); } ierr = VecRestoreArray(coordinates, &cArray);CHKERRQ(ierr); /* Temporary, must be replaced by a projection on the finite element basis */ { PetscInt eStart = 0, eEnd = 0, e, depth; ierr = DMPlexGetLabelSize(dm, "depth", &depth);CHKERRQ(ierr); --depth; if (depth > 1) {ierr = DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd);CHKERRQ(ierr);} for (e = eStart; e < eEnd; ++e) { const PetscInt *cone = PETSC_NULL; PetscInt coneSize, d; PetscScalar *coordsA, *coordsB; ierr = DMPlexGetConeSize(dm, e, &coneSize);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, e, &cone);CHKERRQ(ierr); if (coneSize != 2) SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_ARG_SIZ, "Cone size %d for point %d should be 2", coneSize, e); ierr = VecGetValuesSection(coordinates, cSection, cone[0], &coordsA);CHKERRQ(ierr); ierr = VecGetValuesSection(coordinates, cSection, cone[1], &coordsB);CHKERRQ(ierr); for (d = 0; d < dim; ++d) { coords[d] = 0.5*(PetscRealPart(coordsA[d]) + PetscRealPart(coordsB[d])); } for (c = 0; c < numComp; ++c) { values[c] = (*funcs[c])(coords); } ierr = VecSetValuesSection(localX, section, e, values, mode);CHKERRQ(ierr); } } ierr = PetscFree(coords);CHKERRQ(ierr); ierr = PetscFree(values);CHKERRQ(ierr); #if 0 const PetscInt localDof = this->_mesh->sizeWithBC(s, *cells->begin()); PetscReal detJ; ierr = PetscMalloc(localDof * sizeof(PetscScalar), &values);CHKERRQ(ierr); ierr = PetscMalloc2(dim,PetscReal,&v0,dim*dim,PetscReal,&J);CHKERRQ(ierr); ALE::ISieveVisitor::PointRetriever pV((int) pow(this->_mesh->getSieve()->getMaxConeSize(), dim+1)+1, true); for (PetscInt c = cStart; c < cEnd; ++c) { ALE::ISieveTraversal::orientedClosure(*this->_mesh->getSieve(), c, pV); const PETSC_MESH_TYPE::point_type *oPoints = pV.getPoints(); const int oSize = pV.getSize(); int v = 0; ierr = DMPlexComputeCellGeometry(dm, c, v0, J, PETSC_NULL, &detJ);CHKERRQ(ierr); for (PetscInt cl = 0; cl < oSize; ++cl) { const PetscInt fDim; ierr = PetscSectionGetDof(oPoints[cl], &fDim);CHKERRQ(ierr); if (pointDim) { for (PetscInt d = 0; d < fDim; ++d, ++v) { values[v] = (*this->_options.integrate)(v0, J, v, initFunc); } } } ierr = DMPlexVecSetClosure(dm, PETSC_NULL, localX, c, values);CHKERRQ(ierr); pV.clear(); } ierr = PetscFree2(v0,J);CHKERRQ(ierr); ierr = PetscFree(values);CHKERRQ(ierr); #endif PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexProjectFunction" /*@C DMPlexProjectFunction - This projects the given function into the function space provided. Input Parameters: + dm - The DM . numComp - The number of components (functions) . funcs - The coordinate functions to evaluate - mode - The insertion mode for values Output Parameter: . X - vector Level: developer Note: This currently just calls the function with the coordinates of each vertex and edge midpoint, and stores the result in a vector. We will eventually fix it. ,seealso: DMPlexComputeL2Diff() */ PetscErrorCode DMPlexProjectFunction(DM dm, PetscInt numComp, PetscScalar (**funcs)(const PetscReal []), InsertMode mode, Vec X) { Vec localX; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); ierr = DMPlexProjectFunctionLocal(dm, numComp, funcs, mode, localX);CHKERRQ(ierr); ierr = DMLocalToGlobalBegin(dm, localX, mode, X);CHKERRQ(ierr); ierr = DMLocalToGlobalEnd(dm, localX, mode, X);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeL2Diff" /*@C DMPlexComputeL2Diff - This function computes the L_2 difference between a function u and an FEM interpolant solution u_h. Input Parameters: + dm - The DM . quad - The PetscQuadrature object for each field . funcs - The functions to evaluate for each field component - X - The coefficient vector u_h Output Parameter: . diff - The diff ||u - u_h||_2 Level: developer .seealso: DMPlexProjectFunction() */ PetscErrorCode DMPlexComputeL2Diff(DM dm, PetscQuadrature quad[], PetscScalar (**funcs)(const PetscReal []), Vec X, PetscReal *diff) { const PetscInt debug = 0; PetscSection section; Vec localX; PetscReal *coords, *v0, *J, *invJ, detJ; PetscReal localDiff = 0.0; PetscInt dim, numFields, numComponents = 0, cStart, cEnd, c, field, fieldOffset, comp; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); for (field = 0; field < numFields; ++field) { numComponents += quad[field].numComponents; } ierr = DMPlexProjectFunctionLocal(dm, numComponents, funcs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); ierr = PetscMalloc4(dim,PetscReal,&coords,dim,PetscReal,&v0,dim*dim,PetscReal,&J,dim*dim,PetscReal,&invJ);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); for (c = cStart; c < cEnd; ++c) { const PetscScalar *x; PetscReal elemDiff = 0.0; ierr = DMPlexComputeCellGeometry(dm, c, v0, J, invJ, &detJ);CHKERRQ(ierr); if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c); ierr = DMPlexVecGetClosure(dm, PETSC_NULL, localX, c, PETSC_NULL, &x);CHKERRQ(ierr); for (field = 0, comp = 0, fieldOffset = 0; field < numFields; ++field) { const PetscInt numQuadPoints = quad[field].numQuadPoints; const PetscReal *quadPoints = quad[field].quadPoints; const PetscReal *quadWeights = quad[field].quadWeights; const PetscInt numBasisFuncs = quad[field].numBasisFuncs; const PetscInt numBasisComps = quad[field].numComponents; const PetscReal *basis = quad[field].basis; PetscInt q, d, e, fc, f; if (debug) { char title[1024]; ierr = PetscSNPrintf(title, 1023, "Solution for Field %d", field);CHKERRQ(ierr); ierr = DMPrintCellVector(c, title, numBasisFuncs*numBasisComps, &x[fieldOffset]);CHKERRQ(ierr); } for (q = 0; q < numQuadPoints; ++q) { for (d = 0; d < dim; d++) { coords[d] = v0[d]; for (e = 0; e < dim; e++) { coords[d] += J[d*dim+e]*(quadPoints[q*dim+e] + 1.0); } } for (fc = 0; fc < numBasisComps; ++fc) { const PetscReal funcVal = PetscRealPart((*funcs[comp+fc])(coords)); PetscReal interpolant = 0.0; for (f = 0; f < numBasisFuncs; ++f) { const PetscInt fidx = f*numBasisComps+fc; interpolant += PetscRealPart(x[fieldOffset+fidx])*basis[q*numBasisFuncs*numBasisComps+fidx]; } if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %d field %d diff %g\n", c, field, PetscSqr(interpolant - funcVal)*quadWeights[q]*detJ);CHKERRQ(ierr);} elemDiff += PetscSqr(interpolant - funcVal)*quadWeights[q]*detJ; } } comp += numBasisComps; fieldOffset += numBasisFuncs*numBasisComps; } ierr = DMPlexVecRestoreClosure(dm, PETSC_NULL, localX, c, PETSC_NULL, &x);CHKERRQ(ierr); if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %d diff %g\n", c, elemDiff);CHKERRQ(ierr);} localDiff += elemDiff; } ierr = PetscFree4(coords,v0,J,invJ);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); ierr = MPI_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPI_SUM, PETSC_COMM_WORLD);CHKERRQ(ierr); *diff = PetscSqrtReal(*diff); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeResidualFEM" /*@ DMPlexComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user Input Parameters: + dm - The mesh . X - Local input vector - user - The user context Output Parameter: . F - Local output vector Note: The second member of the user context must be an FEMContext. We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, like a GPU, or vectorize on a multicore machine. .seealso: DMPlexComputeJacobianActionFEM() */ PetscErrorCode DMPlexComputeResidualFEM(DM dm, Vec X, Vec F, void *user) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFEM *fem = (PetscFEM *) &((DM *) user)[1]; PetscQuadrature *quad = fem->quad; PetscSection section; PetscReal *v0, *J, *invJ, *detJ; PetscScalar *elemVec, *u; PetscInt dim, numFields, field, numBatchesTmp = 1, numCells, cStart, cEnd, c; PetscInt cellDof = 0, numComponents = 0; PetscErrorCode ierr; PetscFunctionBegin; /* ierr = PetscLogEventBegin(ResidualFEMEvent,0,0,0,0);CHKERRQ(ierr); */ ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); numCells = cEnd - cStart; for (field = 0; field < numFields; ++field) { cellDof += quad[field].numBasisFuncs*quad[field].numComponents; numComponents += quad[field].numComponents; } ierr = DMPlexProjectFunctionLocal(dm, numComponents, fem->bcFuncs, INSERT_BC_VALUES, X);CHKERRQ(ierr); ierr = VecSet(F, 0.0);CHKERRQ(ierr); ierr = PetscMalloc6(numCells*cellDof,PetscScalar,&u,numCells*dim,PetscReal,&v0,numCells*dim*dim,PetscReal,&J,numCells*dim*dim,PetscReal,&invJ,numCells,PetscReal,&detJ,numCells*cellDof,PetscScalar,&elemVec);CHKERRQ(ierr); for (c = cStart; c < cEnd; ++c) { const PetscScalar *x; PetscInt i; ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr); if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c); ierr = DMPlexVecGetClosure(dm, PETSC_NULL, X, c, PETSC_NULL, &x);CHKERRQ(ierr); for (i = 0; i < cellDof; ++i) { u[c*cellDof+i] = x[i]; } ierr = DMPlexVecRestoreClosure(dm, PETSC_NULL, X, c, PETSC_NULL, &x);CHKERRQ(ierr); } for (field = 0; field < numFields; ++field) { const PetscInt numQuadPoints = quad[field].numQuadPoints; const PetscInt numBasisFuncs = quad[field].numBasisFuncs; void (*f0)(const PetscScalar u[], const PetscScalar gradU[], const PetscReal x[], PetscScalar f0[]) = fem->f0Funcs[field]; void (*f1)(const PetscScalar u[], const PetscScalar gradU[], const PetscReal x[], PetscScalar f1[]) = fem->f1Funcs[field]; /* Conforming batches */ PetscInt blockSize = numBasisFuncs*numQuadPoints; PetscInt numBlocks = 1; PetscInt batchSize = numBlocks * blockSize; PetscInt numBatches = numBatchesTmp; PetscInt numChunks = numCells / (numBatches*batchSize); /* Remainder */ PetscInt numRemainder = numCells % (numBatches * batchSize); PetscInt offset = numCells - numRemainder; ierr = (*mesh->integrateResidualFEM)(numChunks*numBatches*batchSize, numFields, field, quad, u, v0, J, invJ, detJ, f0, f1, elemVec);CHKERRQ(ierr); ierr = (*mesh->integrateResidualFEM)(numRemainder, numFields, field, quad, &u[offset*cellDof], &v0[offset*dim], &J[offset*dim*dim], &invJ[offset*dim*dim], &detJ[offset], f0, f1, &elemVec[offset*cellDof]);CHKERRQ(ierr); } for (c = cStart; c < cEnd; ++c) { if (mesh->printFEM > 1) {ierr = DMPrintCellVector(c, "Residual", cellDof, &elemVec[c*cellDof]);CHKERRQ(ierr);} ierr = DMPlexVecSetClosure(dm, PETSC_NULL, F, c, &elemVec[c*cellDof], ADD_VALUES);CHKERRQ(ierr); } ierr = PetscFree6(u,v0,J,invJ,detJ,elemVec);CHKERRQ(ierr); if (mesh->printFEM) { PetscMPIInt rank, numProcs; PetscInt p; ierr = MPI_Comm_rank(((PetscObject) dm)->comm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(((PetscObject) dm)->comm, &numProcs);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Residual:\n");CHKERRQ(ierr); for (p = 0; p < numProcs; ++p) { if (p == rank) { Vec f; ierr = VecDuplicate(F, &f);CHKERRQ(ierr); ierr = VecCopy(F, f);CHKERRQ(ierr); ierr = VecChop(f, 1.0e-10);CHKERRQ(ierr); ierr = VecView(f, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); ierr = VecDestroy(&f);CHKERRQ(ierr); ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); } ierr = PetscBarrier((PetscObject) dm);CHKERRQ(ierr); } } /* ierr = PetscLogEventEnd(ResidualFEMEvent,0,0,0,0);CHKERRQ(ierr); */ PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeJacobianActionFEM" /*@C DMPlexComputeJacobianActionFEM - Form the local action of Jacobian J(u) on the local input X using pointwise functions specified by the user Input Parameters: + dm - The mesh . J - The Jacobian shell matrix . X - Local input vector - user - The user context Output Parameter: . F - Local output vector Note: The second member of the user context must be an FEMContext. We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, like a GPU, or vectorize on a multicore machine. .seealso: DMPlexComputeResidualFEM() */ PetscErrorCode DMPlexComputeJacobianActionFEM(DM dm, Mat Jac, Vec X, Vec F, void *user) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFEM *fem = (PetscFEM *) &((DM *) user)[1]; PetscQuadrature *quad = fem->quad; PetscSection section; JacActionCtx *jctx; PetscReal *v0, *J, *invJ, *detJ; PetscScalar *elemVec, *u, *a; PetscInt dim, numFields, field, numBatchesTmp = 1, numCells, cStart, cEnd, c; PetscInt cellDof = 0; PetscErrorCode ierr; PetscFunctionBegin; /* ierr = PetscLogEventBegin(JacobianActionFEMEvent,0,0,0,0);CHKERRQ(ierr); */ ierr = MatShellGetContext(Jac, &jctx);CHKERRQ(ierr); ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); numCells = cEnd - cStart; for (field = 0; field < numFields; ++field) { cellDof += quad[field].numBasisFuncs*quad[field].numComponents; } ierr = VecSet(F, 0.0);CHKERRQ(ierr); ierr = PetscMalloc7(numCells*cellDof,PetscScalar,&u,numCells*cellDof,PetscScalar,&a,numCells*dim,PetscReal,&v0,numCells*dim*dim,PetscReal,&J,numCells*dim*dim,PetscReal,&invJ,numCells,PetscReal,&detJ,numCells*cellDof,PetscScalar,&elemVec);CHKERRQ(ierr); for (c = cStart; c < cEnd; ++c) { const PetscScalar *x; PetscInt i; ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr); if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c); ierr = DMPlexVecGetClosure(dm, PETSC_NULL, jctx->u, c, PETSC_NULL, &x);CHKERRQ(ierr); for (i = 0; i < cellDof; ++i) { u[c*cellDof+i] = x[i]; } ierr = DMPlexVecRestoreClosure(dm, PETSC_NULL, jctx->u, c, PETSC_NULL, &x);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, PETSC_NULL, X, c, PETSC_NULL, &x);CHKERRQ(ierr); for (i = 0; i < cellDof; ++i) { a[c*cellDof+i] = x[i]; } ierr = DMPlexVecRestoreClosure(dm, PETSC_NULL, X, c, PETSC_NULL, &x);CHKERRQ(ierr); } for (field = 0; field < numFields; ++field) { const PetscInt numQuadPoints = quad[field].numQuadPoints; const PetscInt numBasisFuncs = quad[field].numBasisFuncs; /* Conforming batches */ PetscInt blockSize = numBasisFuncs*numQuadPoints; PetscInt numBlocks = 1; PetscInt batchSize = numBlocks * blockSize; PetscInt numBatches = numBatchesTmp; PetscInt numChunks = numCells / (numBatches*batchSize); /* Remainder */ PetscInt numRemainder = numCells % (numBatches * batchSize); PetscInt offset = numCells - numRemainder; ierr = (*mesh->integrateJacobianActionFEM)(numChunks*numBatches*batchSize, numFields, field, quad, u, a, v0, J, invJ, detJ, fem->g0Funcs, fem->g1Funcs, fem->g2Funcs, fem->g3Funcs, elemVec);CHKERRQ(ierr); ierr = (*mesh->integrateJacobianActionFEM)(numRemainder, numFields, field, quad, &u[offset*cellDof], &a[offset*cellDof], &v0[offset*dim], &J[offset*dim*dim], &invJ[offset*dim*dim], &detJ[offset], fem->g0Funcs, fem->g1Funcs, fem->g2Funcs, fem->g3Funcs, &elemVec[offset*cellDof]);CHKERRQ(ierr); } for (c = cStart; c < cEnd; ++c) { if (mesh->printFEM > 1) {ierr = DMPrintCellVector(c, "Jacobian Action", cellDof, &elemVec[c*cellDof]);CHKERRQ(ierr);} ierr = DMPlexVecSetClosure(dm, PETSC_NULL, F, c, &elemVec[c*cellDof], ADD_VALUES);CHKERRQ(ierr); } ierr = PetscFree7(u,a,v0,J,invJ,detJ,elemVec);CHKERRQ(ierr); if (mesh->printFEM) { PetscMPIInt rank, numProcs; PetscInt p; ierr = MPI_Comm_rank(((PetscObject) dm)->comm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(((PetscObject) dm)->comm, &numProcs);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Jacobian Action:\n");CHKERRQ(ierr); for (p = 0; p < numProcs; ++p) { if (p == rank) {ierr = VecView(F, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);} ierr = PetscBarrier((PetscObject) dm);CHKERRQ(ierr); } } /* ierr = PetscLogEventEnd(JacobianActionFEMEvent,0,0,0,0);CHKERRQ(ierr); */ PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeJacobianFEM" /*@ DMPlexComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user. Input Parameters: + dm - The mesh . X - Local input vector - user - The user context Output Parameter: . Jac - Jacobian matrix Note: The second member of the user context must be an FEMContext. We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, like a GPU, or vectorize on a multicore machine. .seealso: FormFunctionLocal() */ PetscErrorCode DMPlexComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP, MatStructure *str,void *user) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscFEM *fem = (PetscFEM *) &((DM *) user)[1]; PetscQuadrature *quad = fem->quad; PetscSection section; PetscReal *v0, *J, *invJ, *detJ; PetscScalar *elemMat, *u; PetscInt dim, numFields, field, fieldI, numBatchesTmp = 1, numCells, cStart, cEnd, c; PetscInt cellDof = 0, numComponents = 0; PetscBool isShell; PetscErrorCode ierr; PetscFunctionBegin; /* ierr = PetscLogEventBegin(JacobianFEMEvent,0,0,0,0);CHKERRQ(ierr); */ ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); numCells = cEnd - cStart; for (field = 0; field < numFields; ++field) { cellDof += quad[field].numBasisFuncs*quad[field].numComponents; numComponents += quad[field].numComponents; } ierr = DMPlexProjectFunctionLocal(dm, numComponents, fem->bcFuncs, INSERT_BC_VALUES, X);CHKERRQ(ierr); ierr = MatZeroEntries(JacP);CHKERRQ(ierr); ierr = PetscMalloc6(numCells*cellDof,PetscScalar,&u,numCells*dim,PetscReal,&v0,numCells*dim*dim,PetscReal,&J,numCells*dim*dim,PetscReal,&invJ,numCells,PetscReal,&detJ,numCells*cellDof*cellDof,PetscScalar,&elemMat);CHKERRQ(ierr); for (c = cStart; c < cEnd; ++c) { const PetscScalar *x; PetscInt i; ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr); if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c); ierr = DMPlexVecGetClosure(dm, PETSC_NULL, X, c, PETSC_NULL, &x);CHKERRQ(ierr); for (i = 0; i < cellDof; ++i) { u[c*cellDof+i] = x[i]; } ierr = DMPlexVecRestoreClosure(dm, PETSC_NULL, X, c, PETSC_NULL, &x);CHKERRQ(ierr); } ierr = PetscMemzero(elemMat, numCells*cellDof*cellDof * sizeof(PetscScalar));CHKERRQ(ierr); for (fieldI = 0; fieldI < numFields; ++fieldI) { const PetscInt numQuadPoints = quad[fieldI].numQuadPoints; const PetscInt numBasisFuncs = quad[fieldI].numBasisFuncs; PetscInt fieldJ; for (fieldJ = 0; fieldJ < numFields; ++fieldJ) { void (*g0)(const PetscScalar u[], const PetscScalar gradU[], const PetscReal x[], PetscScalar g0[]) = fem->g0Funcs[fieldI*numFields+fieldJ]; void (*g1)(const PetscScalar u[], const PetscScalar gradU[], const PetscReal x[], PetscScalar g1[]) = fem->g1Funcs[fieldI*numFields+fieldJ]; void (*g2)(const PetscScalar u[], const PetscScalar gradU[], const PetscReal x[], PetscScalar g2[]) = fem->g2Funcs[fieldI*numFields+fieldJ]; void (*g3)(const PetscScalar u[], const PetscScalar gradU[], const PetscReal x[], PetscScalar g3[]) = fem->g3Funcs[fieldI*numFields+fieldJ]; /* Conforming batches */ PetscInt blockSize = numBasisFuncs*numQuadPoints; PetscInt numBlocks = 1; PetscInt batchSize = numBlocks * blockSize; PetscInt numBatches = numBatchesTmp; PetscInt numChunks = numCells / (numBatches*batchSize); /* Remainder */ PetscInt numRemainder = numCells % (numBatches * batchSize); PetscInt offset = numCells - numRemainder; ierr = (*mesh->integrateJacobianFEM)(numChunks*numBatches*batchSize, numFields, fieldI, fieldJ, quad, u, v0, J, invJ, detJ, g0, g1, g2, g3, elemMat);CHKERRQ(ierr); ierr = (*mesh->integrateJacobianFEM)(numRemainder, numFields, fieldI, fieldJ, quad, &u[offset*cellDof], &v0[offset*dim], &J[offset*dim*dim], &invJ[offset*dim*dim], &detJ[offset], g0, g1, g2, g3, &elemMat[offset*cellDof*cellDof]);CHKERRQ(ierr); } } for (c = cStart; c < cEnd; ++c) { if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, "Jacobian", cellDof, cellDof, &elemMat[c*cellDof*cellDof]);CHKERRQ(ierr);} ierr = DMPlexMatSetClosure(dm, PETSC_NULL, PETSC_NULL, JacP, c, &elemMat[c*cellDof*cellDof], ADD_VALUES);CHKERRQ(ierr); } ierr = PetscFree6(u,v0,J,invJ,detJ,elemMat);CHKERRQ(ierr); /* Assemble matrix, using the 2-step process: MatAssemblyBegin(), MatAssemblyEnd(). */ ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); if (mesh->printFEM) { ierr = PetscPrintf(PETSC_COMM_WORLD, "Jacobian:\n");CHKERRQ(ierr); ierr = MatChop(JacP, 1.0e-10);CHKERRQ(ierr); ierr = MatView(JacP, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } /* ierr = PetscLogEventEnd(JacobianFEMEvent,0,0,0,0);CHKERRQ(ierr); */ ierr = PetscObjectTypeCompare((PetscObject)Jac, MATSHELL, &isShell);CHKERRQ(ierr); if (isShell) { JacActionCtx *jctx; ierr = MatShellGetContext(Jac, &jctx);CHKERRQ(ierr); ierr = VecCopy(X, jctx->u);CHKERRQ(ierr); } *str = SAME_NONZERO_PATTERN; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "PetscSectionCreateGlobalSectionLabel" /*@C PetscSectionCreateGlobalSectionLabel - Create a section describing the global field layout using the local section and an SF describing the section point overlap. Input Parameters: + s - The PetscSection for the local field layout . sf - The SF describing parallel layout of the section points . includeConstraints - By default this is PETSC_FALSE, meaning that the global field vector will not possess constrained dofs . label - The label specifying the points - labelValue - The label stratum specifying the points Output Parameter: . gsection - The PetscSection for the global field layout Note: This gives negative sizes and offsets to points not owned by this process Level: developer .seealso: PetscSectionCreate() @*/ PetscErrorCode PetscSectionCreateGlobalSectionLabel(PetscSection s, PetscSF sf, PetscBool includeConstraints, DMLabel label, PetscInt labelValue, PetscSection *gsection) { PetscInt *neg; PetscInt pStart, pEnd, p, dof, cdof, off, globalOff = 0, nroots; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscSectionCreate(s->atlasLayout.comm, gsection);CHKERRQ(ierr); ierr = PetscSectionGetChart(s, &pStart, &pEnd);CHKERRQ(ierr); ierr = PetscSectionSetChart(*gsection, pStart, pEnd);CHKERRQ(ierr); ierr = PetscMalloc((pEnd - pStart) * sizeof(PetscInt), &neg);CHKERRQ(ierr); /* Mark ghost points with negative dof */ for (p = pStart; p < pEnd; ++p) { PetscInt value; ierr = DMLabelGetValue(label, p, &value);CHKERRQ(ierr); if (value != labelValue) continue; ierr = PetscSectionGetDof(s, p, &dof);CHKERRQ(ierr); ierr = PetscSectionSetDof(*gsection, p, dof);CHKERRQ(ierr); ierr = PetscSectionGetConstraintDof(s, p, &cdof);CHKERRQ(ierr); if (!includeConstraints && cdof > 0) {ierr = PetscSectionSetConstraintDof(*gsection, p, cdof);CHKERRQ(ierr);} neg[p-pStart] = -(dof+1); } ierr = PetscSectionSetUpBC(*gsection);CHKERRQ(ierr); ierr = PetscSFGetGraph(sf, &nroots, PETSC_NULL, PETSC_NULL, PETSC_NULL);CHKERRQ(ierr); if (nroots >= 0) { if (nroots > pEnd - pStart) { PetscInt *tmpDof; /* Help Jed: HAVE TO MAKE A BUFFER HERE THE SIZE OF THE COMPLETE SPACE AND THEN COPY INTO THE atlasDof FOR THIS SECTION */ ierr = PetscMalloc(nroots * sizeof(PetscInt), &tmpDof);CHKERRQ(ierr); ierr = PetscSFBcastBegin(sf, MPIU_INT, &neg[-pStart], tmpDof);CHKERRQ(ierr); ierr = PetscSFBcastEnd(sf, MPIU_INT, &neg[-pStart], tmpDof);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { if (tmpDof[p] < 0) {(*gsection)->atlasDof[p-pStart] = tmpDof[p];} } ierr = PetscFree(tmpDof);CHKERRQ(ierr); } else { ierr = PetscSFBcastBegin(sf, MPIU_INT, &neg[-pStart], &(*gsection)->atlasDof[-pStart]);CHKERRQ(ierr); ierr = PetscSFBcastEnd(sf, MPIU_INT, &neg[-pStart], &(*gsection)->atlasDof[-pStart]);CHKERRQ(ierr); } } /* Calculate new sizes, get proccess offset, and calculate point offsets */ for (p = 0, off = 0; p < pEnd-pStart; ++p) { cdof = (!includeConstraints && s->bc) ? s->bc->atlasDof[p] : 0; (*gsection)->atlasOff[p] = off; off += (*gsection)->atlasDof[p] > 0 ? (*gsection)->atlasDof[p]-cdof : 0; } ierr = MPI_Scan(&off, &globalOff, 1, MPIU_INT, MPI_SUM, s->atlasLayout.comm);CHKERRQ(ierr); globalOff -= off; for (p = 0, off = 0; p < pEnd-pStart; ++p) { (*gsection)->atlasOff[p] += globalOff; neg[p] = -((*gsection)->atlasOff[p]+1); } /* Put in negative offsets for ghost points */ if (nroots >= 0) { if (nroots > pEnd - pStart) { PetscInt *tmpOff; /* Help Jed: HAVE TO MAKE A BUFFER HERE THE SIZE OF THE COMPLETE SPACE AND THEN COPY INTO THE atlasDof FOR THIS SECTION */ ierr = PetscMalloc(nroots * sizeof(PetscInt), &tmpOff);CHKERRQ(ierr); ierr = PetscSFBcastBegin(sf, MPIU_INT, &neg[-pStart], tmpOff);CHKERRQ(ierr); ierr = PetscSFBcastEnd(sf, MPIU_INT, &neg[-pStart], tmpOff);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { if (tmpOff[p] < 0) {(*gsection)->atlasOff[p-pStart] = tmpOff[p];} } ierr = PetscFree(tmpOff);CHKERRQ(ierr); } else { ierr = PetscSFBcastBegin(sf, MPIU_INT, &neg[-pStart], &(*gsection)->atlasOff[-pStart]);CHKERRQ(ierr); ierr = PetscSFBcastEnd(sf, MPIU_INT, &neg[-pStart], &(*gsection)->atlasOff[-pStart]);CHKERRQ(ierr); } } ierr = PetscFree(neg);CHKERRQ(ierr); PetscFunctionReturn(0); }