Actual source code: mmgadapt.c

      1: #include "../mmgcommon.h" /*I      "petscdmplex.h"   I*/
      2: #include <mmg/libmmg.h>

      4: PetscBool  MmgCite       = PETSC_FALSE;
      5: const char MmgCitation[] = "@article{DAPOGNY2014358,\n"
      6:                            "  title   = {Three-dimensional adaptive domain remeshing, implicit domain meshing, and applications to free and moving boundary problems},\n"
      7:                            "  journal = {Journal of Computational Physics},\n"
      8:                            "  author  = {C. Dapogny and C. Dobrzynski and P. Frey},\n"
      9:                            "  volume  = {262},\n"
     10:                            "  pages   = {358--378},\n"
     11:                            "  doi     = {10.1016/j.jcp.2014.01.005},\n"
     12:                            "  year    = {2014}\n}\n";

     14: PETSC_EXTERN PetscErrorCode DMAdaptMetric_Mmg_Plex(DM dm, Vec vertexMetric, DMLabel bdLabel, DMLabel rgLabel, DM *dmNew)
     15: {
     16:   MPI_Comm           comm;
     17:   const char        *bdName = "_boundary_";
     18:   const char        *rgName = "_regions_";
     19:   DM                 udm, cdm;
     20:   DMLabel            bdLabelNew, rgLabelNew;
     21:   const char        *bdLabelName, *rgLabelName;
     22:   PetscSection       coordSection;
     23:   Vec                coordinates;
     24:   const PetscScalar *coords, *met;
     25:   PetscReal         *vertices, *metric, *verticesNew, gradationFactor, hausdorffNumber;
     26:   PetscInt          *cells, *cellsNew, *cellTags, *cellTagsNew, *verTags, *verTagsNew;
     27:   PetscInt          *bdFaces, *faceTags, *facesNew, *faceTagsNew;
     28:   int               *corners, *requiredCells, *requiredVer, *ridges, *requiredFaces;
     29:   PetscInt           cStart, cEnd, c, numCells, fStart, fEnd, numFaceTags, f, vStart, vEnd, v, numVertices;
     30:   PetscInt           dim, off, coff, maxConeSize, bdSize, i, j, k, Neq, verbosity, pStart, pEnd;
     31:   PetscInt           numCellsNew, numVerticesNew, numCornersNew, numFacesNew;
     32:   PetscBool          flg        = PETSC_FALSE, noInsert, noSwap, noMove, noSurf, isotropic, uniform;
     33:   MMG5_pMesh         mmg_mesh   = NULL;
     34:   MMG5_pSol          mmg_metric = NULL;

     36:   PetscFunctionBegin;
     37:   PetscCall(PetscCitationsRegister(MmgCitation, &MmgCite));
     38:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
     39:   if (bdLabel) {
     40:     PetscCall(PetscObjectGetName((PetscObject)bdLabel, &bdLabelName));
     41:     PetscCall(PetscStrcmp(bdLabelName, bdName, &flg));
     42:     PetscCheck(!flg, comm, PETSC_ERR_ARG_WRONG, "\"%s\" cannot be used as label for boundary facets", bdLabelName);
     43:   }
     44:   if (rgLabel) {
     45:     PetscCall(PetscObjectGetName((PetscObject)rgLabel, &rgLabelName));
     46:     PetscCall(PetscStrcmp(rgLabelName, rgName, &flg));
     47:     PetscCheck(!flg, comm, PETSC_ERR_ARG_WRONG, "\"%s\" cannot be used as label for element tags", rgLabelName);
     48:   }

     50:   /* Get mesh information */
     51:   PetscCall(DMGetDimension(dm, &dim));
     52:   Neq = (dim * (dim + 1)) / 2;
     53:   PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
     54:   PetscCall(DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd));
     55:   PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
     56:   PetscCall(DMPlexUninterpolate(dm, &udm));
     57:   PetscCall(DMPlexGetMaxSizes(udm, &maxConeSize, NULL));
     58:   numCells    = cEnd - cStart;
     59:   numVertices = vEnd - vStart;

     61:   /* Get cell offsets */
     62:   PetscCall(PetscMalloc1(numCells * maxConeSize, &cells));
     63:   for (c = 0, coff = 0; c < numCells; ++c) {
     64:     const PetscInt *cone;
     65:     PetscInt        coneSize, cl;

     67:     PetscCall(DMPlexGetConeSize(udm, c, &coneSize));
     68:     PetscCall(DMPlexGetCone(udm, c, &cone));
     69:     for (cl = 0; cl < coneSize; ++cl) cells[coff++] = cone[cl] - vStart + 1;
     70:   }

     72:   /* Get vertex coordinate array */
     73:   PetscCall(DMGetCoordinateDM(dm, &cdm));
     74:   PetscCall(DMGetLocalSection(cdm, &coordSection));
     75:   PetscCall(DMGetCoordinatesLocal(dm, &coordinates));
     76:   PetscCall(VecGetArrayRead(coordinates, &coords));
     77:   PetscCall(PetscMalloc2(numVertices * Neq, &metric, dim * numVertices, &vertices));
     78:   for (v = 0; v < vEnd - vStart; ++v) {
     79:     PetscCall(PetscSectionGetOffset(coordSection, v + vStart, &off));
     80:     for (i = 0; i < dim; ++i) vertices[dim * v + i] = PetscRealPart(coords[off + i]);
     81:   }
     82:   PetscCall(VecRestoreArrayRead(coordinates, &coords));
     83:   PetscCall(DMDestroy(&udm));

     85:   /* Get face tags */
     86:   if (!bdLabel) {
     87:     flg = PETSC_TRUE;
     88:     PetscCall(DMLabelCreate(PETSC_COMM_SELF, bdName, &bdLabel));
     89:     PetscCall(DMPlexMarkBoundaryFaces(dm, 1, bdLabel));
     90:   }
     91:   PetscCall(DMLabelGetBounds(bdLabel, &pStart, &pEnd));
     92:   for (f = pStart, bdSize = 0, numFaceTags = 0; f < pEnd; ++f) {
     93:     PetscBool hasPoint;
     94:     PetscInt *closure = NULL, closureSize, cl;

     96:     PetscCall(DMLabelHasPoint(bdLabel, f, &hasPoint));
     97:     if ((!hasPoint) || (f < fStart) || (f >= fEnd)) continue;
     98:     numFaceTags++;

    100:     PetscCall(DMPlexGetTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure));
    101:     for (cl = 0; cl < closureSize * 2; cl += 2) {
    102:       if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) ++bdSize;
    103:     }
    104:     PetscCall(DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure));
    105:   }
    106:   PetscCall(PetscMalloc2(bdSize, &bdFaces, numFaceTags, &faceTags));
    107:   for (f = pStart, bdSize = 0, numFaceTags = 0; f < pEnd; ++f) {
    108:     PetscBool hasPoint;
    109:     PetscInt *closure = NULL, closureSize, cl;

    111:     PetscCall(DMLabelHasPoint(bdLabel, f, &hasPoint));
    112:     if ((!hasPoint) || (f < fStart) || (f >= fEnd)) continue;

    114:     PetscCall(DMPlexGetTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure));
    115:     for (cl = 0; cl < closureSize * 2; cl += 2) {
    116:       if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) bdFaces[bdSize++] = closure[cl] - vStart + 1;
    117:     }
    118:     PetscCall(DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure));
    119:     PetscCall(DMLabelGetValue(bdLabel, f, &faceTags[numFaceTags++]));
    120:   }
    121:   if (flg) PetscCall(DMLabelDestroy(&bdLabel));

    123:   /* Get cell tags */
    124:   PetscCall(PetscCalloc2(numVertices, &verTags, numCells, &cellTags));
    125:   if (rgLabel) {
    126:     for (c = cStart; c < cEnd; ++c) PetscCall(DMLabelGetValue(rgLabel, c, &cellTags[c]));
    127:   }

    129:   /* Get metric */
    130:   PetscCall(VecViewFromOptions(vertexMetric, NULL, "-adapt_metric_view"));
    131:   PetscCall(VecGetArrayRead(vertexMetric, &met));
    132:   PetscCall(DMPlexMetricIsIsotropic(dm, &isotropic));
    133:   PetscCall(DMPlexMetricIsUniform(dm, &uniform));
    134:   for (v = 0; v < (vEnd - vStart); ++v) {
    135:     for (i = 0, k = 0; i < dim; ++i) {
    136:       for (j = i; j < dim; ++j) {
    137:         if (isotropic) {
    138:           if (i == j) {
    139:             if (uniform) metric[Neq * v + k] = PetscRealPart(met[0]);
    140:             else metric[Neq * v + k] = PetscRealPart(met[v]);
    141:           } else metric[Neq * v + k] = 0.0;
    142:         } else {
    143:           metric[Neq * v + k] = PetscRealPart(met[dim * dim * v + dim * i + j]);
    144:         }
    145:         k++;
    146:       }
    147:     }
    148:   }
    149:   PetscCall(VecRestoreArrayRead(vertexMetric, &met));

    151:   /* Send mesh to Mmg and remesh */
    152:   PetscCall(DMPlexMetricGetVerbosity(dm, &verbosity));
    153:   PetscCall(DMPlexMetricGetGradationFactor(dm, &gradationFactor));
    154:   PetscCall(DMPlexMetricGetHausdorffNumber(dm, &hausdorffNumber));
    155:   PetscCall(DMPlexMetricNoInsertion(dm, &noInsert));
    156:   PetscCall(DMPlexMetricNoSwapping(dm, &noSwap));
    157:   PetscCall(DMPlexMetricNoMovement(dm, &noMove));
    158:   PetscCall(DMPlexMetricNoSurf(dm, &noSurf));
    159:   switch (dim) {
    160:   case 2:
    161:     PetscCallMMG_NONSTANDARD(MMG2D_Init_mesh, MMG5_ARG_start, MMG5_ARG_ppMesh, &mmg_mesh, MMG5_ARG_ppMet, &mmg_metric, MMG5_ARG_end);
    162:     PetscCallMMG_NONSTANDARD(MMG2D_Set_iparameter, mmg_mesh, mmg_metric, MMG2D_IPARAM_noinsert, noInsert);
    163:     PetscCallMMG_NONSTANDARD(MMG2D_Set_iparameter, mmg_mesh, mmg_metric, MMG2D_IPARAM_noswap, noSwap);
    164:     PetscCallMMG_NONSTANDARD(MMG2D_Set_iparameter, mmg_mesh, mmg_metric, MMG2D_IPARAM_nomove, noMove);
    165:     PetscCallMMG_NONSTANDARD(MMG2D_Set_iparameter, mmg_mesh, mmg_metric, MMG2D_IPARAM_nosurf, noSurf);
    166:     PetscCallMMG_NONSTANDARD(MMG2D_Set_iparameter, mmg_mesh, mmg_metric, MMG2D_IPARAM_verbose, verbosity);
    167:     PetscCallMMG_NONSTANDARD(MMG2D_Set_dparameter, mmg_mesh, mmg_metric, MMG2D_DPARAM_hgrad, gradationFactor);
    168:     PetscCallMMG_NONSTANDARD(MMG2D_Set_dparameter, mmg_mesh, mmg_metric, MMG2D_DPARAM_hausd, hausdorffNumber);
    169:     PetscCallMMG_NONSTANDARD(MMG2D_Set_meshSize, mmg_mesh, numVertices, numCells, 0, numFaceTags);
    170:     PetscCallMMG_NONSTANDARD(MMG2D_Set_vertices, mmg_mesh, vertices, verTags);
    171:     PetscCallMMG_NONSTANDARD(MMG2D_Set_triangles, mmg_mesh, cells, cellTags);
    172:     PetscCallMMG_NONSTANDARD(MMG2D_Set_edges, mmg_mesh, bdFaces, faceTags);
    173:     PetscCallMMG_NONSTANDARD(MMG2D_Set_solSize, mmg_mesh, mmg_metric, MMG5_Vertex, numVertices, MMG5_Tensor);
    174:     PetscCallMMG_NONSTANDARD(MMG2D_Set_tensorSols, mmg_metric, metric);
    175:     PetscCallMMG(MMG2D_mmg2dlib, mmg_mesh, mmg_metric);
    176:     break;
    177:   case 3:
    178:     PetscCallMMG_NONSTANDARD(MMG3D_Init_mesh, MMG5_ARG_start, MMG5_ARG_ppMesh, &mmg_mesh, MMG5_ARG_ppMet, &mmg_metric, MMG5_ARG_end);
    179:     PetscCallMMG_NONSTANDARD(MMG3D_Set_iparameter, mmg_mesh, mmg_metric, MMG3D_IPARAM_noinsert, noInsert);
    180:     PetscCallMMG_NONSTANDARD(MMG3D_Set_iparameter, mmg_mesh, mmg_metric, MMG3D_IPARAM_noswap, noSwap);
    181:     PetscCallMMG_NONSTANDARD(MMG3D_Set_iparameter, mmg_mesh, mmg_metric, MMG3D_IPARAM_nomove, noMove);
    182:     PetscCallMMG_NONSTANDARD(MMG3D_Set_iparameter, mmg_mesh, mmg_metric, MMG3D_IPARAM_nosurf, noSurf);
    183:     PetscCallMMG_NONSTANDARD(MMG3D_Set_iparameter, mmg_mesh, mmg_metric, MMG3D_IPARAM_verbose, verbosity);
    184:     PetscCallMMG_NONSTANDARD(MMG3D_Set_dparameter, mmg_mesh, mmg_metric, MMG3D_DPARAM_hgrad, gradationFactor);
    185:     PetscCallMMG_NONSTANDARD(MMG3D_Set_dparameter, mmg_mesh, mmg_metric, MMG3D_DPARAM_hausd, hausdorffNumber);
    186:     PetscCallMMG_NONSTANDARD(MMG3D_Set_meshSize, mmg_mesh, numVertices, numCells, 0, numFaceTags, 0, 0);
    187:     PetscCallMMG_NONSTANDARD(MMG3D_Set_vertices, mmg_mesh, vertices, verTags);
    188:     PetscCallMMG_NONSTANDARD(MMG3D_Set_tetrahedra, mmg_mesh, cells, cellTags);
    189:     PetscCallMMG_NONSTANDARD(MMG3D_Set_triangles, mmg_mesh, bdFaces, faceTags);
    190:     PetscCallMMG_NONSTANDARD(MMG3D_Set_solSize, mmg_mesh, mmg_metric, MMG5_Vertex, numVertices, MMG5_Tensor);
    191:     PetscCallMMG_NONSTANDARD(MMG3D_Set_tensorSols, mmg_metric, metric);
    192:     PetscCallMMG(MMG3D_mmg3dlib, mmg_mesh, mmg_metric);
    193:     break;
    194:   default:
    195:     SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "No Mmg adaptation defined for dimension %" PetscInt_FMT, dim);
    196:   }
    197:   PetscCall(PetscFree(cells));
    198:   PetscCall(PetscFree2(metric, vertices));
    199:   PetscCall(PetscFree2(bdFaces, faceTags));
    200:   PetscCall(PetscFree2(verTags, cellTags));

    202:   /* Retrieve mesh from Mmg */
    203:   switch (dim) {
    204:   case 2:
    205:     numCornersNew = 3;
    206:     PetscCallMMG_NONSTANDARD(MMG2D_Get_meshSize, mmg_mesh, &numVerticesNew, &numCellsNew, 0, &numFacesNew);
    207:     PetscCall(PetscMalloc4(2 * numVerticesNew, &verticesNew, numVerticesNew, &verTagsNew, numVerticesNew, &corners, numVerticesNew, &requiredVer));
    208:     PetscCall(PetscMalloc3(3 * numCellsNew, &cellsNew, numCellsNew, &cellTagsNew, numCellsNew, &requiredCells));
    209:     PetscCall(PetscMalloc4(2 * numFacesNew, &facesNew, numFacesNew, &faceTagsNew, numFacesNew, &ridges, numFacesNew, &requiredFaces));
    210:     PetscCallMMG_NONSTANDARD(MMG2D_Get_vertices, mmg_mesh, verticesNew, verTagsNew, corners, requiredVer);
    211:     PetscCallMMG_NONSTANDARD(MMG2D_Get_triangles, mmg_mesh, cellsNew, cellTagsNew, requiredCells);
    212:     PetscCallMMG_NONSTANDARD(MMG2D_Get_edges, mmg_mesh, facesNew, faceTagsNew, ridges, requiredFaces);
    213:     break;
    214:   case 3:
    215:     numCornersNew = 4;
    216:     PetscCallMMG_NONSTANDARD(MMG3D_Get_meshSize, mmg_mesh, &numVerticesNew, &numCellsNew, 0, &numFacesNew, 0, 0);
    217:     PetscCall(PetscMalloc4(3 * numVerticesNew, &verticesNew, numVerticesNew, &verTagsNew, numVerticesNew, &corners, numVerticesNew, &requiredVer));
    218:     PetscCall(PetscMalloc3(4 * numCellsNew, &cellsNew, numCellsNew, &cellTagsNew, numCellsNew, &requiredCells));
    219:     PetscCall(PetscMalloc4(3 * numFacesNew, &facesNew, numFacesNew, &faceTagsNew, numFacesNew, &ridges, numFacesNew, &requiredFaces));
    220:     PetscCallMMG_NONSTANDARD(MMG3D_Get_vertices, mmg_mesh, verticesNew, verTagsNew, corners, requiredVer);
    221:     PetscCallMMG_NONSTANDARD(MMG3D_Get_tetrahedra, mmg_mesh, cellsNew, cellTagsNew, requiredCells);
    222:     PetscCallMMG_NONSTANDARD(MMG3D_Get_triangles, mmg_mesh, facesNew, faceTagsNew, requiredFaces);

    224:     /* Reorder for consistency with DMPlex */
    225:     for (i = 0; i < numCellsNew; ++i) PetscCall(DMPlexInvertCell(DM_POLYTOPE_TETRAHEDRON, &cellsNew[4 * i]));
    226:     break;

    228:   default:
    229:     SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "No Mmg adaptation defined for dimension %" PetscInt_FMT, dim);
    230:   }

    232:   /* Create new Plex */
    233:   for (i = 0; i < (dim + 1) * numCellsNew; i++) cellsNew[i] -= 1;
    234:   for (i = 0; i < dim * numFacesNew; i++) facesNew[i] -= 1;
    235:   PetscCall(DMPlexCreateFromCellListParallelPetsc(comm, dim, numCellsNew, numVerticesNew, PETSC_DECIDE, numCornersNew, PETSC_TRUE, cellsNew, dim, verticesNew, NULL, NULL, dmNew));
    236:   switch (dim) {
    237:   case 2:
    238:     PetscCallMMG_NONSTANDARD(MMG2D_Free_all, MMG5_ARG_start, MMG5_ARG_ppMesh, &mmg_mesh, MMG5_ARG_ppMet, &mmg_metric, MMG5_ARG_end);
    239:     break;
    240:   case 3:
    241:     PetscCallMMG_NONSTANDARD(MMG3D_Free_all, MMG5_ARG_start, MMG5_ARG_ppMesh, &mmg_mesh, MMG5_ARG_ppMet, &mmg_metric, MMG5_ARG_end);
    242:     break;
    243:   default:
    244:     SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "No Mmg adaptation defined for dimension %" PetscInt_FMT, dim);
    245:   }
    246:   PetscCall(PetscFree4(verticesNew, verTagsNew, corners, requiredVer));

    248:   /* Get adapted mesh information */
    249:   PetscCall(DMPlexGetHeightStratum(*dmNew, 0, &cStart, &cEnd));
    250:   PetscCall(DMPlexGetHeightStratum(*dmNew, 1, &fStart, &fEnd));
    251:   PetscCall(DMPlexGetDepthStratum(*dmNew, 0, &vStart, &vEnd));

    253:   /* Rebuild boundary labels */
    254:   PetscCall(DMCreateLabel(*dmNew, flg ? bdName : bdLabelName));
    255:   PetscCall(DMGetLabel(*dmNew, flg ? bdName : bdLabelName, &bdLabelNew));
    256:   for (i = 0; i < numFacesNew; i++) {
    257:     PetscInt        numCoveredPoints, numFaces = 0, facePoints[3];
    258:     const PetscInt *coveredPoints = NULL;

    260:     for (j = 0; j < dim; ++j) facePoints[j] = facesNew[i * dim + j] + vStart;
    261:     PetscCall(DMPlexGetFullJoin(*dmNew, dim, facePoints, &numCoveredPoints, &coveredPoints));
    262:     for (j = 0; j < numCoveredPoints; ++j) {
    263:       if (coveredPoints[j] >= fStart && coveredPoints[j] < fEnd) {
    264:         numFaces++;
    265:         f = j;
    266:       }
    267:     }
    268:     PetscCheck(numFaces == 1, comm, PETSC_ERR_ARG_OUTOFRANGE, "%" PetscInt_FMT " vertices cannot define more than 1 facet (%" PetscInt_FMT ")", dim, numFaces);
    269:     PetscCall(DMLabelSetValue(bdLabelNew, coveredPoints[f], faceTagsNew[i]));
    270:     PetscCall(DMPlexRestoreJoin(*dmNew, dim, facePoints, &numCoveredPoints, &coveredPoints));
    271:   }
    272:   PetscCall(PetscFree4(facesNew, faceTagsNew, ridges, requiredFaces));

    274:   /* Rebuild cell labels */
    275:   PetscCall(DMCreateLabel(*dmNew, rgLabel ? rgLabelName : rgName));
    276:   PetscCall(DMGetLabel(*dmNew, rgLabel ? rgLabelName : rgName, &rgLabelNew));
    277:   for (c = cStart; c < cEnd; ++c) PetscCall(DMLabelSetValue(rgLabelNew, c, cellTagsNew[c - cStart]));
    278:   PetscCall(PetscFree3(cellsNew, cellTagsNew, requiredCells));
    279:   PetscFunctionReturn(PETSC_SUCCESS);
    280: }