Actual source code: mmgadapt.c

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

  4: PETSC_EXTERN PetscErrorCode DMAdaptMetric_Mmg_Plex(DM dm, Vec vertexMetric, DMLabel bdLabel, DMLabel rgLabel, DM *dmNew)
  5: {
  6:   MPI_Comm           comm;
  7:   const char        *bdName = "_boundary_";
  8:   const char        *rgName = "_regions_";
  9:   DM                 udm, cdm;
 10:   DMLabel            bdLabelNew, rgLabelNew;
 11:   const char        *bdLabelName, *rgLabelName;
 12:   PetscSection       coordSection;
 13:   Vec                coordinates;
 14:   const PetscScalar *coords, *met;
 15:   PetscReal         *vertices, *metric, *verticesNew, gradationFactor, hausdorffNumber;
 16:   PetscInt          *cells, *cellsNew, *cellTags, *cellTagsNew, *verTags, *verTagsNew;
 17:   PetscInt          *bdFaces, *faceTags, *facesNew, *faceTagsNew;
 18:   PetscInt          *corners, *requiredCells, *requiredVer, *ridges, *requiredFaces;
 19:   PetscInt           cStart, cEnd, c, numCells, fStart, fEnd, numFaceTags, f, vStart, vEnd, v, numVertices;
 20:   PetscInt           dim, off, coff, maxConeSize, bdSize, i, j, k, Neq, verbosity, pStart, pEnd;
 21:   PetscInt           numCellsNew, numVerticesNew, numCornersNew, numFacesNew;
 22:   PetscBool          flg = PETSC_FALSE, noInsert, noSwap, noMove, noSurf, isotropic, uniform;
 23:   MMG5_pMesh         mmg_mesh = NULL;
 24:   MMG5_pSol          mmg_metric = NULL;

 26:   PetscObjectGetComm((PetscObject) dm, &comm);
 27:   if (bdLabel) {
 28:     PetscObjectGetName((PetscObject) bdLabel, &bdLabelName);
 29:     PetscStrcmp(bdLabelName, bdName, &flg);
 31:   }
 32:   if (rgLabel) {
 33:     PetscObjectGetName((PetscObject) rgLabel, &rgLabelName);
 34:     PetscStrcmp(rgLabelName, rgName, &flg);
 36:   }

 38:   /* Get mesh information */
 39:   DMGetDimension(dm, &dim);
 40:   Neq  = (dim*(dim+1))/2;
 41:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
 42:   DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
 43:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
 44:   DMPlexUninterpolate(dm, &udm);
 45:   DMPlexGetMaxSizes(udm, &maxConeSize, NULL);
 46:   numCells    = cEnd - cStart;
 47:   numVertices = vEnd - vStart;

 49:   /* Get cell offsets */
 50:   PetscMalloc1(numCells*maxConeSize, &cells);
 51:   for (c = 0, coff = 0; c < numCells; ++c) {
 52:     const PetscInt *cone;
 53:     PetscInt        coneSize, cl;

 55:     DMPlexGetConeSize(udm, c, &coneSize);
 56:     DMPlexGetCone(udm, c, &cone);
 57:     for (cl = 0; cl < coneSize; ++cl) cells[coff++] = cone[cl] - vStart + 1;
 58:   }

 60:   /* Get vertex coordinate array */
 61:   DMGetCoordinateDM(dm, &cdm);
 62:   DMGetLocalSection(cdm, &coordSection);
 63:   DMGetCoordinatesLocal(dm, &coordinates);
 64:   VecGetArrayRead(coordinates, &coords);
 65:   PetscMalloc2(numVertices*Neq, &metric, dim*numVertices, &vertices);
 66:   for (v = 0; v < vEnd-vStart; ++v) {
 67:     PetscSectionGetOffset(coordSection, v+vStart, &off);
 68:     for (i = 0; i < dim; ++i) vertices[dim*v+i] = PetscRealPart(coords[off+i]);
 69:   }
 70:   VecRestoreArrayRead(coordinates, &coords);
 71:   DMDestroy(&udm);

 73:   /* Get face tags */
 74:   if (!bdLabel) {
 75:     flg = PETSC_TRUE;
 76:     DMLabelCreate(PETSC_COMM_SELF, bdName, &bdLabel);
 77:     DMPlexMarkBoundaryFaces(dm, 1, bdLabel);
 78:   }
 79:   DMLabelGetBounds(bdLabel, &pStart, &pEnd);
 80:   for (f = pStart, bdSize = 0, numFaceTags = 0; f < pEnd; ++f) {
 81:     PetscBool hasPoint;
 82:     PetscInt *closure = NULL, closureSize, cl;

 84:     DMLabelHasPoint(bdLabel, f, &hasPoint);
 85:     if ((!hasPoint) || (f < fStart) || (f >= fEnd)) continue;
 86:     numFaceTags++;

 88:     DMPlexGetTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure);
 89:     for (cl = 0; cl < closureSize*2; cl += 2) {
 90:       if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) ++bdSize;
 91:     }
 92:     DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure);
 93:   }
 94:   PetscMalloc2(bdSize, &bdFaces, numFaceTags, &faceTags);
 95:   for (f = pStart, bdSize = 0, numFaceTags = 0; f < pEnd; ++f) {
 96:     PetscBool hasPoint;
 97:     PetscInt *closure = NULL, closureSize, cl;

 99:     DMLabelHasPoint(bdLabel, f, &hasPoint);
100:     if ((!hasPoint) || (f < fStart) || (f >= fEnd)) continue;

102:     DMPlexGetTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure);
103:     for (cl = 0; cl < closureSize*2; cl += 2) {
104:       if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) bdFaces[bdSize++] = closure[cl] - vStart + 1;
105:     }
106:     DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure);
107:     DMLabelGetValue(bdLabel, f, &faceTags[numFaceTags++]);
108:   }
109:   if (flg) DMLabelDestroy(&bdLabel);

111:   /* Get cell tags */
112:   PetscCalloc2(numVertices, &verTags, numCells, &cellTags);
113:   if (rgLabel) {
114:     for (c = cStart; c < cEnd; ++c) DMLabelGetValue(rgLabel, c, &cellTags[c]);
115:   }

117:   /* Get metric */
118:   VecViewFromOptions(vertexMetric, NULL, "-adapt_metric_view");
119:   VecGetArrayRead(vertexMetric, &met);
120:   DMPlexMetricIsIsotropic(dm, &isotropic);
121:   DMPlexMetricIsUniform(dm, &uniform);
122:   for (v = 0; v < (vEnd-vStart); ++v) {
123:     for (i = 0, k = 0; i < dim; ++i) {
124:       for (j = i; j < dim; ++j) {
125:         if (isotropic) {
126:           if (i == j) {
127:             if (uniform) metric[Neq*v+k] = PetscRealPart(met[0]);
128:             else metric[Neq*v+k] = PetscRealPart(met[v]);
129:           } else metric[Neq*v+k] = 0.0;
130:         } else {
131:           metric[Neq*v+k] = PetscRealPart(met[dim*dim*v+dim*i+j]);
132:         }
133:         k++;
134:       }
135:     }
136:   }
137:   VecRestoreArrayRead(vertexMetric, &met);

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

189:   /* Retrieve mesh from Mmg */
190:   switch (dim) {
191:   case 2:
192:     numCornersNew = 3;
193:     MMG2D_Get_meshSize(mmg_mesh, &numVerticesNew, &numCellsNew, 0, &numFacesNew);
194:     PetscMalloc4(2*numVerticesNew, &verticesNew, numVerticesNew, &verTagsNew, numVerticesNew, &corners, numVerticesNew, &requiredVer);
195:     PetscMalloc3(3*numCellsNew, &cellsNew, numCellsNew, &cellTagsNew, numCellsNew, &requiredCells);
196:     PetscMalloc4(2*numFacesNew, &facesNew, numFacesNew, &faceTagsNew, numFacesNew, &ridges, numFacesNew, &requiredFaces);
197:     MMG2D_Get_vertices(mmg_mesh, verticesNew, verTagsNew, corners, requiredVer);
198:     MMG2D_Get_triangles(mmg_mesh, cellsNew, cellTagsNew, requiredCells);
199:     MMG2D_Get_edges(mmg_mesh, facesNew, faceTagsNew, ridges, requiredFaces);
200:     break;
201:   case 3:
202:     numCornersNew = 4;
203:     MMG3D_Get_meshSize(mmg_mesh, &numVerticesNew, &numCellsNew, 0, &numFacesNew, 0, 0);
204:     PetscMalloc4(3*numVerticesNew, &verticesNew, numVerticesNew, &verTagsNew, numVerticesNew, &corners, numVerticesNew, &requiredVer);
205:     PetscMalloc3(4*numCellsNew, &cellsNew, numCellsNew, &cellTagsNew, numCellsNew, &requiredCells);
206:     PetscMalloc4(3*numFacesNew, &facesNew, numFacesNew, &faceTagsNew, numFacesNew, &ridges, numFacesNew, &requiredFaces);
207:     MMG3D_Get_vertices(mmg_mesh, verticesNew, verTagsNew, corners, requiredVer);
208:     MMG3D_Get_tetrahedra(mmg_mesh, cellsNew, cellTagsNew, requiredCells);
209:     MMG3D_Get_triangles(mmg_mesh, facesNew, faceTagsNew, requiredFaces);

211:     /* Reorder for consistency with DMPlex */
212:     for (i = 0; i < numCellsNew; ++i) DMPlexInvertCell(DM_POLYTOPE_TETRAHEDRON, &cellsNew[4*i]);
213:     break;

215:   default: SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "No Mmg adaptation defined for dimension %" PetscInt_FMT, dim);
216:   }

218:   /* Create new Plex */
219:   for (i = 0; i < (dim+1)*numCellsNew; i++) cellsNew[i] -= 1;
220:   for (i = 0; i < dim*numFacesNew; i++) facesNew[i] -= 1;
221:   DMPlexCreateFromCellListParallelPetsc(comm, dim, numCellsNew, numVerticesNew, PETSC_DECIDE, numCornersNew, PETSC_TRUE, cellsNew, dim, verticesNew, NULL, NULL, dmNew);
222:   switch (dim) {
223:   case 2:
224:     MMG2D_Free_all(MMG5_ARG_start, MMG5_ARG_ppMesh, &mmg_mesh, MMG5_ARG_ppMet, &mmg_metric, MMG5_ARG_end);
225:     break;
226:   case 3:
227:     MMG3D_Free_all(MMG5_ARG_start, MMG5_ARG_ppMesh, &mmg_mesh, MMG5_ARG_ppMet, &mmg_metric, MMG5_ARG_end);
228:     break;
229:   default: SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "No Mmg adaptation defined for dimension %" PetscInt_FMT, dim);
230:   }
231:   PetscFree4(verticesNew, verTagsNew, corners, requiredVer);

233:   /* Get adapted mesh information */
234:   DMPlexGetHeightStratum(*dmNew, 0, &cStart, &cEnd);
235:   DMPlexGetHeightStratum(*dmNew, 1, &fStart, &fEnd);
236:   DMPlexGetDepthStratum(*dmNew, 0, &vStart, &vEnd);

238:   /* Rebuild boundary labels */
239:   DMCreateLabel(*dmNew, flg ? bdName : bdLabelName);
240:   DMGetLabel(*dmNew, flg ? bdName : bdLabelName, &bdLabelNew);
241:   for (i = 0; i < numFacesNew; i++) {
242:     PetscInt        numCoveredPoints, numFaces = 0, facePoints[3];
243:     const PetscInt *coveredPoints = NULL;

245:     for (j = 0; j < dim; ++j) facePoints[j] = facesNew[i*dim+j]+vStart;
246:     DMPlexGetFullJoin(*dmNew, dim, facePoints, &numCoveredPoints, &coveredPoints);
247:     for (j = 0; j < numCoveredPoints; ++j) {
248:       if (coveredPoints[j] >= fStart && coveredPoints[j] < fEnd) {
249:         numFaces++;
250:         f = j;
251:       }
252:     }
254:     DMLabelSetValue(bdLabelNew, coveredPoints[f], faceTagsNew[i]);
255:     DMPlexRestoreJoin(*dmNew, dim, facePoints, &numCoveredPoints, &coveredPoints);
256:   }
257:   PetscFree4(facesNew, faceTagsNew, ridges, requiredFaces);

259:   /* Rebuild cell labels */
260:   DMCreateLabel(*dmNew, rgLabel ? rgLabelName : rgName);
261:   DMGetLabel(*dmNew, rgLabel ? rgLabelName : rgName, &rgLabelNew);
262:   for (c = cStart; c < cEnd; ++c) DMLabelSetValue(rgLabelNew, c, cellTagsNew[c-cStart]);
263:   PetscFree3(cellsNew, cellTagsNew, requiredCells);

265:   return 0;
266: }