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: }