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;

     35:   /* Check for FEM adjacency flags */
     36:   PetscObjectGetComm((PetscObject) dm, &comm);
     37:   MPI_Comm_size(comm, &numProcs);
     38:   if (bdLabel) {
     39:     PetscObjectGetName((PetscObject) bdLabel, &bdLabelName);
     40:     PetscStrcmp(bdLabelName, bdName, &flg);
     42:   }
     44: #if 0
     45:   /* Check for overlap by looking for cell in the SF */
     46:   if (!overlapped) {
     47:     DMPlexDistributeOverlap(odm, 1, NULL, &dm);
     48:     if (!dm) {dm = odm; PetscObjectReference((PetscObject) dm);}
     49:   }
     50: #endif

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

     62:     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:   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:     DMPlexGetConeSize(udm, c, &coneSize);
     74:     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:   PetscCalloc1(numVertices, &l2gv);
     80:   DMPlexGetVertexNumbering(udm, &globalVertexNum);
     81:   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:   ISRestoreIndices(globalVertexNum, &gV);
     87:   DMDestroy(&udm);

     89:   /* Get vertex coordinate arrays */
     90:   DMGetCoordinateDM(dm, &cdm);
     91:   DMGetLocalSection(cdm, &coordSection);
     92:   DMGetCoordinatesLocal(dm, &coordinates);
     93:   VecGetArrayRead(coordinates, &coords);
     94:   for (v = vStart; v < vEnd; ++v) {
     95:     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:   VecRestoreArrayRead(coordinates, &coords);

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

    112:     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:     DMPlexRestoreTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure);
    117:   }
    118:   PetscMalloc2(bdSize, &bdFaces, numBdFaces, &bdFaceIds);
    119:   for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
    120:     PetscInt *closure = NULL;
    121:     PetscInt  closureSize, cl;

    123:     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:     DMPlexRestoreTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure);
    128:     if (bdLabel) DMLabelGetValue(bdLabel, bdFacesFull[f], &bdFaceIds[f]);
    129:     else         {bdFaceIds[f] = 1;}
    130:   }
    131:   ISDestroy(&bdIS);
    132:   DMLabelDestroy(&bdLabelFull);

    134:   /* Get metric */
    135:   VecViewFromOptions(vertexMetric, NULL, "-adapt_metric_view");
    136:   VecGetArrayRead(vertexMetric, &met);
    137:   DMPlexMetricIsIsotropic(dm, &isotropic);
    138:   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:   VecRestoreArrayRead(vertexMetric, &met);

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

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

    195:   /* Rebuild boundary label */
    196:   pragmatic_get_boundaryTags(&bdTags);
    197:   DMCreateLabel(*dmNew, bdLabel ? bdLabelName : bdName);
    198:   DMGetLabel(*dmNew, bdLabel ? bdLabelName : bdName, &bdLabelNew);
    199:   DMPlexGetHeightStratum(*dmNew, 0, &cStart, &cEnd);
    200:   DMPlexGetHeightStratum(*dmNew, 1, &fStart, &fEnd);
    201:   DMPlexGetDepthStratum(*dmNew, 0, &vStart, &vEnd);
    202:   for (c = cStart; c < cEnd; ++c) {

    204:     /* Only for simplicial meshes */
    205:     coff = (c-cStart)*(dim+1);

    207:     /* d is the local cell number of the vertex opposite to the face we are marking */
    208:     for (d = 0; d < dim+1; ++d) {
    209:       if (bdTags[coff+d]) {
    210:         const PetscInt  perm[4][4] = {{-1, -1, -1, -1}, {-1, -1, -1, -1}, {1, 2, 0, -1}, {3, 2, 1, 0}}; /* perm[d] = face opposite */
    211:         const PetscInt *cone;

    213:         /* Mark face opposite to this vertex: This pattern is specified in DMPlexGetRawFaces_Internal() */
    214:         DMPlexGetCone(*dmNew, c, &cone);
    215:         DMLabelSetValue(bdLabelNew, cone[perm[dim][d]], bdTags[coff+d]);
    216:       }
    217:     }
    218:   }

    220:   /* Clean up */
    221:   switch (dim) {
    222:   case 2: PetscFree2(xNew[0], xNew[1]);
    223:   break;
    224:   case 3: PetscFree3(xNew[0], xNew[1], xNew[2]);
    225:   break;
    226:   }
    227:   PetscFree(cellsNew);
    228:   PetscFree5(x, y, z, metric, cells);
    229:   PetscFree2(bdFaces, bdFaceIds);
    230:   PetscFree(coordsNew);
    231:   pragmatic_finalize();
    232:   return 0;
    233: }