Actual source code: pragmaticadapt.c

      1: #include <petsc/private/dmpleximpl.h>
      2: #include <pragmatic/cpragmatic.h>

      4: PETSC_EXTERN PetscErrorCode DMAdaptMetric_Pragmatic_Plex(DM dm, Vec vertexMetric, DMLabel bdLabel, DMLabel rgLabel, DM *dmNew)
      5: {
      6:   MPI_Comm    comm;
      7:   const char *bdName = "_boundary_";
      8: #if 0
      9:   DM                 odm = dm;
     10: #endif
     11:   DM                 udm, cdm;
     12:   DMLabel            bdLabelFull;
     13:   const char        *bdLabelName;
     14:   IS                 bdIS, globalVertexNum;
     15:   PetscSection       coordSection;
     16:   Vec                coordinates;
     17:   const PetscScalar *coords, *met;
     18:   const PetscInt    *bdFacesFull, *gV;
     19:   PetscInt          *bdFaces, *bdFaceIds, *l2gv;
     20:   PetscReal         *x, *y, *z, *metric;
     21:   PetscInt          *cells;
     22:   PetscInt           dim, cStart, cEnd, numCells, c, coff, vStart, vEnd, numVertices, numLocVertices, v;
     23:   PetscInt           off, maxConeSize, numBdFaces, f, bdSize, i, j, Nd;
     24:   PetscBool          flg, isotropic, uniform;
     25:   DMLabel            bdLabelNew;
     26:   PetscReal         *coordsNew;
     27:   PetscInt          *bdTags;
     28:   PetscReal         *xNew[3] = {NULL, NULL, NULL};
     29:   PetscInt          *cellsNew;
     30:   PetscInt           d, numCellsNew, numVerticesNew;
     31:   PetscInt           numCornersNew, fStart, fEnd;
     32:   PetscMPIInt        numProcs;

     34:   PetscFunctionBegin;
     35:   /* Check for FEM adjacency flags */
     36:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
     37:   PetscCallMPI(MPI_Comm_size(comm, &numProcs));
     38:   if (bdLabel) {
     39:     PetscCall(PetscObjectGetName((PetscObject)bdLabel, &bdLabelName));
     40:     PetscCall(PetscStrcmp(bdLabelName, bdName, &flg));
     41:     PetscCheck(!flg, comm, PETSC_ERR_ARG_WRONG, "\"%s\" cannot be used as label for boundary facets", bdLabelName);
     42:   }
     43:   PetscCheck(!rgLabel, comm, PETSC_ERR_ARG_WRONG, "Cannot currently preserve cell tags with Pragmatic");
     44: #if 0
     45:   /* Check for overlap by looking for cell in the SF */
     46:   if (!overlapped) {
     47:     PetscCall(DMPlexDistributeOverlap(odm, 1, NULL, &dm));
     48:     if (!dm) {dm = odm; PetscCall(PetscObjectReference((PetscObject) dm));}
     49:   }
     50: #endif

     52:   /* Get mesh information */
     53:   PetscCall(DMGetDimension(dm, &dim));
     54:   PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
     55:   PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
     56:   PetscCall(DMPlexUninterpolate(dm, &udm));
     57:   PetscCall(DMPlexGetMaxSizes(udm, &maxConeSize, NULL));
     58:   numCells = cEnd - cStart;
     59:   if (numCells == 0) {
     60:     PetscMPIInt rank;

     62:     PetscCallMPI(MPI_Comm_rank(comm, &rank));
     63:     SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot perform mesh adaptation because process %d does not own any cells.", rank);
     64:   }
     65:   numVertices = vEnd - vStart;
     66:   PetscCall(PetscCalloc5(numVertices, &x, numVertices, &y, numVertices, &z, numVertices * PetscSqr(dim), &metric, numCells * maxConeSize, &cells));

     68:   /* Get cell offsets */
     69:   for (c = 0, coff = 0; c < numCells; ++c) {
     70:     const PetscInt *cone;
     71:     PetscInt        coneSize, cl;

     73:     PetscCall(DMPlexGetConeSize(udm, c, &coneSize));
     74:     PetscCall(DMPlexGetCone(udm, c, &cone));
     75:     for (cl = 0; cl < coneSize; ++cl) cells[coff++] = cone[cl] - vStart;
     76:   }

     78:   /* Get local-to-global vertex map */
     79:   PetscCall(PetscCalloc1(numVertices, &l2gv));
     80:   PetscCall(DMPlexGetVertexNumbering(udm, &globalVertexNum));
     81:   PetscCall(ISGetIndices(globalVertexNum, &gV));
     82:   for (v = 0, numLocVertices = 0; v < numVertices; ++v) {
     83:     if (gV[v] >= 0) ++numLocVertices;
     84:     l2gv[v] = gV[v] < 0 ? -(gV[v] + 1) : gV[v];
     85:   }
     86:   PetscCall(ISRestoreIndices(globalVertexNum, &gV));
     87:   PetscCall(DMDestroy(&udm));

     89:   /* Get vertex coordinate arrays */
     90:   PetscCall(DMGetCoordinateDM(dm, &cdm));
     91:   PetscCall(DMGetLocalSection(cdm, &coordSection));
     92:   PetscCall(DMGetCoordinatesLocal(dm, &coordinates));
     93:   PetscCall(VecGetArrayRead(coordinates, &coords));
     94:   for (v = vStart; v < vEnd; ++v) {
     95:     PetscCall(PetscSectionGetOffset(coordSection, v, &off));
     96:     x[v - vStart] = PetscRealPart(coords[off + 0]);
     97:     if (dim > 1) y[v - vStart] = PetscRealPart(coords[off + 1]);
     98:     if (dim > 2) z[v - vStart] = PetscRealPart(coords[off + 2]);
     99:   }
    100:   PetscCall(VecRestoreArrayRead(coordinates, &coords));

    102:   /* Get boundary mesh */
    103:   PetscCall(DMLabelCreate(PETSC_COMM_SELF, bdName, &bdLabelFull));
    104:   PetscCall(DMPlexMarkBoundaryFaces(dm, 1, bdLabelFull));
    105:   PetscCall(DMLabelGetStratumIS(bdLabelFull, 1, &bdIS));
    106:   PetscCall(DMLabelGetStratumSize(bdLabelFull, 1, &numBdFaces));
    107:   PetscCall(ISGetIndices(bdIS, &bdFacesFull));
    108:   for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
    109:     PetscInt *closure = NULL;
    110:     PetscInt  closureSize, cl;

    112:     PetscCall(DMPlexGetTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure));
    113:     for (cl = 0; cl < closureSize * 2; cl += 2) {
    114:       if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) ++bdSize;
    115:     }
    116:     PetscCall(DMPlexRestoreTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure));
    117:   }
    118:   PetscCall(PetscMalloc2(bdSize, &bdFaces, numBdFaces, &bdFaceIds));
    119:   for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
    120:     PetscInt *closure = NULL;
    121:     PetscInt  closureSize, cl;

    123:     PetscCall(DMPlexGetTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure));
    124:     for (cl = 0; cl < closureSize * 2; cl += 2) {
    125:       if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) bdFaces[bdSize++] = closure[cl] - vStart;
    126:     }
    127:     PetscCall(DMPlexRestoreTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure));
    128:     if (bdLabel) PetscCall(DMLabelGetValue(bdLabel, bdFacesFull[f], &bdFaceIds[f]));
    129:     else bdFaceIds[f] = 1;
    130:   }
    131:   PetscCall(ISDestroy(&bdIS));
    132:   PetscCall(DMLabelDestroy(&bdLabelFull));

    134:   /* Get metric */
    135:   PetscCall(VecViewFromOptions(vertexMetric, NULL, "-adapt_metric_view"));
    136:   PetscCall(VecGetArrayRead(vertexMetric, &met));
    137:   PetscCall(DMPlexMetricIsIsotropic(dm, &isotropic));
    138:   PetscCall(DMPlexMetricIsUniform(dm, &uniform));
    139:   Nd = PetscSqr(dim);
    140:   for (v = 0; v < vEnd - vStart; ++v) {
    141:     for (i = 0; i < dim; ++i) {
    142:       for (j = 0; j < dim; ++j) {
    143:         if (isotropic) {
    144:           if (i == j) {
    145:             if (uniform) metric[Nd * v + dim * i + j] = PetscRealPart(met[0]);
    146:             else metric[Nd * v + dim * i + j] = PetscRealPart(met[v]);
    147:           } else metric[Nd * v + dim * i + j] = 0.0;
    148:         } else metric[Nd * v + dim * i + j] = PetscRealPart(met[Nd * v + dim * i + j]);
    149:       }
    150:     }
    151:   }
    152:   PetscCall(VecRestoreArrayRead(vertexMetric, &met));

    154: #if 0
    155:   /* Destroy overlap mesh */
    156:   PetscCall(DMDestroy(&dm));
    157: #endif
    158:   /* Send to Pragmatic and remesh */
    159:   PetscCall(PetscFPTrapPush(PETSC_FP_TRAP_OFF));
    160:   switch (dim) {
    161:   case 2:
    162:     PetscCallExternalVoid("pragmatic_2d_mpi_init", pragmatic_2d_mpi_init(&numVertices, &numCells, cells, x, y, l2gv, numLocVertices, comm));
    163:     break;
    164:   case 3:
    165:     PetscCallExternalVoid("pragmatic_3d_mpi_init", pragmatic_3d_mpi_init(&numVertices, &numCells, cells, x, y, z, l2gv, numLocVertices, comm));
    166:     break;
    167:   default:
    168:     SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic adaptation defined for dimension %" PetscInt_FMT, dim);
    169:   }
    170:   PetscCallExternalVoid("pragmatic_set_boundary", pragmatic_set_boundary(&numBdFaces, bdFaces, bdFaceIds));
    171:   PetscCallExternalVoid("pragmatic_set_metric", pragmatic_set_metric(metric));
    172:   PetscCallExternalVoid("pragmatic_adapt", pragmatic_adapt(((DM_Plex *)dm->data)->remeshBd ? 1 : 0));
    173:   PetscCall(PetscFree(l2gv));
    174:   PetscCall(PetscFPTrapPop());

    176:   /* Retrieve mesh from Pragmatic and create new plex */
    177:   PetscCallExternalVoid("pragmatic_get_info_mpi", pragmatic_get_info_mpi(&numVerticesNew, &numCellsNew));
    178:   PetscCall(PetscMalloc1(numVerticesNew * dim, &coordsNew));
    179:   switch (dim) {
    180:   case 2:
    181:     numCornersNew = 3;
    182:     PetscCall(PetscMalloc2(numVerticesNew, &xNew[0], numVerticesNew, &xNew[1]));
    183:     PetscCallExternalVoid("pragmatic_get_coords_2d_mpi", pragmatic_get_coords_2d_mpi(xNew[0], xNew[1]));
    184:     break;
    185:   case 3:
    186:     numCornersNew = 4;
    187:     PetscCall(PetscMalloc3(numVerticesNew, &xNew[0], numVerticesNew, &xNew[1], numVerticesNew, &xNew[2]));
    188:     PetscCallExternalVoid("pragmatic_get_coords_3d_mpi", pragmatic_get_coords_3d_mpi(xNew[0], xNew[1], xNew[2]));
    189:     break;
    190:   default:
    191:     SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic adaptation defined for dimension %" PetscInt_FMT, dim);
    192:   }
    193:   for (v = 0; v < numVerticesNew; ++v) {
    194:     for (d = 0; d < dim; ++d) coordsNew[v * dim + d] = xNew[d][v];
    195:   }
    196:   PetscCall(PetscMalloc1(numCellsNew * (dim + 1), &cellsNew));
    197:   PetscCallExternalVoid("pragmatic_get_elements", pragmatic_get_elements(cellsNew));
    198:   PetscCall(DMPlexCreateFromCellListParallelPetsc(comm, dim, numCellsNew, numVerticesNew, PETSC_DECIDE, numCornersNew, PETSC_TRUE, cellsNew, dim, coordsNew, NULL, NULL, dmNew));

    200:   /* Rebuild boundary label */
    201:   PetscCallExternalVoid("pragmatic_get_boundaryTags", pragmatic_get_boundaryTags(&bdTags));
    202:   PetscCall(DMCreateLabel(*dmNew, bdLabel ? bdLabelName : bdName));
    203:   PetscCall(DMGetLabel(*dmNew, bdLabel ? bdLabelName : bdName, &bdLabelNew));
    204:   PetscCall(DMPlexGetHeightStratum(*dmNew, 0, &cStart, &cEnd));
    205:   PetscCall(DMPlexGetHeightStratum(*dmNew, 1, &fStart, &fEnd));
    206:   PetscCall(DMPlexGetDepthStratum(*dmNew, 0, &vStart, &vEnd));
    207:   for (c = cStart; c < cEnd; ++c) {
    208:     /* Only for simplicial meshes */
    209:     coff = (c - cStart) * (dim + 1);

    211:     /* d is the local cell number of the vertex opposite to the face we are marking */
    212:     for (d = 0; d < dim + 1; ++d) {
    213:       if (bdTags[coff + d]) {
    214:         const PetscInt perm[4][4] = {
    215:           {-1, -1, -1, -1},
    216:           {-1, -1, -1, -1},
    217:           {1,  2,  0,  -1},
    218:           {3,  2,  1,  0 }
    219:         }; /* perm[d] = face opposite */
    220:         const PetscInt *cone;

    222:         /* Mark face opposite to this vertex: This pattern is specified in DMPlexGetRawFaces_Internal() */
    223:         PetscCall(DMPlexGetCone(*dmNew, c, &cone));
    224:         PetscCall(DMLabelSetValue(bdLabelNew, cone[perm[dim][d]], bdTags[coff + d]));
    225:       }
    226:     }
    227:   }

    229:   /* Clean up */
    230:   switch (dim) {
    231:   case 2:
    232:     PetscCall(PetscFree2(xNew[0], xNew[1]));
    233:     break;
    234:   case 3:
    235:     PetscCall(PetscFree3(xNew[0], xNew[1], xNew[2]));
    236:     break;
    237:   }
    238:   PetscCall(PetscFree(cellsNew));
    239:   PetscCall(PetscFree5(x, y, z, metric, cells));
    240:   PetscCall(PetscFree2(bdFaces, bdFaceIds));
    241:   PetscCall(PetscFree(coordsNew));
    242:   PetscCallExternalVoid("pragmatic_finalize", pragmatic_finalize());
    243:   PetscFunctionReturn(PETSC_SUCCESS);
    244: }