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:     PetscStackCallExternalVoid("pragmatic_2d_mpi_init", pragmatic_2d_mpi_init(&numVertices, &numCells, cells, x, y, l2gv, numLocVertices, comm));
163:     break;
164:   case 3:
165:     PetscStackCallExternalVoid("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:   PetscStackCallExternalVoid("pragmatic_set_boundary", pragmatic_set_boundary(&numBdFaces, bdFaces, bdFaceIds));
171:   PetscStackCallExternalVoid("pragmatic_set_metric", pragmatic_set_metric(metric));
172:   PetscStackCallExternalVoid("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:   PetscStackCallExternalVoid("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:     PetscStackCallExternalVoid("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:     PetscStackCallExternalVoid("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:   PetscStackCallExternalVoid("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:   PetscStackCallExternalVoid("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:   PetscStackCallExternalVoid("pragmatic_finalize", pragmatic_finalize());
243:   PetscFunctionReturn(PETSC_SUCCESS);
244: }