Actual source code: plexmed.c

petsc-3.11.3 2019-06-26
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  1: #define PETSCDM_DLL
  2:  #include <petsc/private/dmpleximpl.h>

  4: #if defined(PETSC_HAVE_MED)
  5: #include <med.h>
  6: #endif

  8: /*@C
  9:   DMPlexCreateMedFromFile - Create a DMPlex mesh from a (Salome-)Med file.

 11: + comm        - The MPI communicator
 12: . filename    - Name of the .med file
 13: - interpolate - Create faces and edges in the mesh

 15:   Output Parameter:
 16: . dm  - The DM object representing the mesh

 18:   Note: http://www.salome-platform.org/user-section/about/med, http://docs.salome-platform.org/latest/MED_index.html

 20:   Level: beginner

 22: .seealso: DMPlexCreateFromFile(), DMPlexCreateGmsh(), DMPlexCreate()
 23: @*/
 24: PetscErrorCode DMPlexCreateMedFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
 25: {
 26:   PetscMPIInt     rank, size;
 27: #if defined(PETSC_HAVE_MED)
 28:   PetscInt        i, ngeo, fileID, cellID, facetID, spaceDim, meshDim;
 29:   PetscInt        numVertices = 0, numCells = 0, c, numCorners, numCellsLocal, numVerticesLocal;
 30:   med_int        *medCellList;
 31:   int            *cellList;
 32:   med_float      *coordinates = NULL;
 33:   PetscReal      *vertcoords = NULL;
 34:   PetscLayout     vLayout, cLayout;
 35:   const PetscInt *vrange, *crange;
 36:   PetscSF         sfVertices;
 37:   char           *axisname, *unitname, meshname[MED_NAME_SIZE+1], geotypename[MED_NAME_SIZE+1];
 38:   char            meshdescription[MED_COMMENT_SIZE+1], dtunit[MED_SNAME_SIZE+1];
 39:   med_sorting_type sortingtype;
 40:   med_mesh_type   meshtype;
 41:   med_axis_type   axistype;
 42:   med_bool        coordinatechangement, geotransformation;
 43:   med_geometry_type geotype[2];
 44:   med_filter      vfilter = MED_FILTER_INIT;
 45:   med_filter      cfilter = MED_FILTER_INIT;
 46: #endif
 47:   PetscErrorCode  ierr;

 50:   MPI_Comm_rank(comm, &rank);
 51:   MPI_Comm_size(comm, &size);
 52: #if defined(PETSC_HAVE_MED)
 53:   fileID = MEDfileOpen(filename, MED_ACC_RDONLY);
 54:   if (fileID < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Unable to open .med mesh file: %s", filename);
 55:   if (MEDnMesh(fileID) < 1) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "No meshes found in .med mesh file: %s", filename);
 56:   spaceDim = MEDmeshnAxis(fileID, 1);
 57:   if (spaceDim < 1) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Mesh of unknown space dimension found in .med mesh file: %s", filename);
 58:   /* Read general mesh information */
 59:   PetscMalloc1(MED_SNAME_SIZE*spaceDim+1, &axisname);
 60:   PetscMalloc1(MED_SNAME_SIZE*spaceDim+1, &unitname);
 61:   {
 62:     med_int medMeshDim, medNstep;
 63:     med_int medSpaceDim = spaceDim;

 65:     MEDmeshInfo(fileID, 1, meshname, &medSpaceDim, &medMeshDim, &meshtype, meshdescription,
 66:                        dtunit, &sortingtype, &medNstep, &axistype, axisname, unitname);
 67:     spaceDim = medSpaceDim;
 68:     meshDim  = medMeshDim;
 69:   }
 70:   PetscFree(axisname);
 71:   PetscFree(unitname);
 72:   /* Partition mesh coordinates */
 73:   numVertices = MEDmeshnEntity(fileID, meshname, MED_NO_DT, MED_NO_IT, MED_NODE, MED_NO_GEOTYPE,
 74:                                MED_COORDINATE, MED_NO_CMODE,&coordinatechangement, &geotransformation);
 75:   PetscLayoutCreate(comm, &vLayout);
 76:   PetscLayoutSetSize(vLayout, numVertices);
 77:   PetscLayoutSetBlockSize(vLayout, 1);
 78:   PetscLayoutSetUp(vLayout);
 79:   PetscLayoutGetRanges(vLayout, &vrange);
 80:   numVerticesLocal = vrange[rank+1]-vrange[rank];
 81:   MEDfilterBlockOfEntityCr(fileID, numVertices, 1, spaceDim, MED_ALL_CONSTITUENT, MED_FULL_INTERLACE, MED_COMPACT_STMODE,
 82:                                   MED_NO_PROFILE, vrange[rank]+1, 1, numVerticesLocal, 1, 1, &vfilter);
 83:   /* Read mesh coordinates */
 84:   if (numVertices < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "No nodes found in .med mesh file: %s", filename);
 85:   PetscMalloc1(numVerticesLocal*spaceDim, &coordinates);
 86:   MEDmeshNodeCoordinateAdvancedRd(fileID, meshname, MED_NO_DT, MED_NO_IT, &vfilter, coordinates);
 87:   /* Read the types of entity sets in the mesh */
 88:   ngeo = MEDmeshnEntity(fileID, meshname, MED_NO_DT, MED_NO_IT, MED_CELL,MED_GEO_ALL, MED_CONNECTIVITY,
 89:                         MED_NODAL, &coordinatechangement, &geotransformation);
 90:   if (ngeo < 1) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "No cells found in .med mesh file: %s", filename);
 91:   if (ngeo > 2) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Currently no support for hybrid meshes in .med mesh file: %s", filename);
 92:   MEDmeshEntityInfo(fileID, meshname, MED_NO_DT, MED_NO_IT, MED_CELL, 1, geotypename, &(geotype[0]));
 93:   if (ngeo > 1) {MEDmeshEntityInfo(fileID, meshname, MED_NO_DT, MED_NO_IT, MED_CELL, 2, geotypename, &(geotype[1]));}
 94:   else geotype[1] = 0;
 95:   /* Determine topological dim and set ID for cells */
 96:   cellID = geotype[0]/100 > geotype[1]/100 ? 0 : 1;
 97:   facetID = geotype[0]/100 > geotype[1]/100 ? 1 : 0;
 98:   meshDim = geotype[cellID] / 100;
 99:   numCorners = geotype[cellID] % 100;
100:   /* Partition cells */
101:   numCells = MEDmeshnEntity(fileID, meshname, MED_NO_DT, MED_NO_IT, MED_CELL, geotype[cellID],
102:                             MED_CONNECTIVITY, MED_NODAL,&coordinatechangement, &geotransformation);
103:   PetscLayoutCreate(comm, &cLayout);
104:   PetscLayoutSetSize(cLayout, numCells);
105:   PetscLayoutSetBlockSize(cLayout, 1);
106:   PetscLayoutSetUp(cLayout);
107:   PetscLayoutGetRanges(cLayout, &crange);
108:   numCellsLocal = crange[rank+1]-crange[rank];
109:   MEDfilterBlockOfEntityCr(fileID, numCells, 1, numCorners, MED_ALL_CONSTITUENT, MED_FULL_INTERLACE, MED_COMPACT_STMODE,
110:                                   MED_NO_PROFILE, crange[rank]+1, 1, numCellsLocal, 1, 1, &cfilter);
111:   /* Read cell connectivity */
112:   if (numCells < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "No cells found in .med mesh file: %s", filename);
113:   PetscMalloc1(numCellsLocal*numCorners, &medCellList);
114:   MEDmeshElementConnectivityAdvancedRd(fileID, meshname, MED_NO_DT, MED_NO_IT, MED_CELL, geotype[cellID],
115:                                               MED_NODAL, &cfilter, medCellList);
116:   if (sizeof(med_int) == sizeof(int)) {
117:     cellList = (int *) medCellList;
118:     medCellList = NULL;
119:   } else {
120:     PetscMalloc1(numCellsLocal*numCorners, &cellList);
121:     for (i = 0; i < numCellsLocal*numCorners; i++) cellList[i] = medCellList[i];
122:     PetscFree(medCellList);
123:   }
124:   for (i = 0; i < numCellsLocal*numCorners; i++) cellList[i]--; /* Correct entity counting */
125:   /* Generate the DM */
126:   if (sizeof(med_float) == sizeof(PetscReal)) {
127:     vertcoords = (PetscReal *) coordinates;
128:   } else {
129:     PetscMalloc1(numVerticesLocal*spaceDim, &vertcoords);
130:     for (i = 0; i < numVerticesLocal*spaceDim; i++) vertcoords[i] = coordinates[i];
131:   }
132:   /* Account for cell inversion */
133:   for (c = 0; c < numCellsLocal; ++c) {
134:     PetscInt *pcone = &cellList[c*numCorners];

136:     if (meshDim == 3) {
137:       /* Tetrahedra are inverted */
138:       if (numCorners == 4) {
139:         PetscInt tmp = pcone[0];
140:         pcone[0] = pcone[1];
141:         pcone[1] = tmp;
142:       }
143:       /* Hexahedra are inverted */
144:       if (numCorners == 8) {
145:         PetscInt tmp = pcone[4+1];
146:         pcone[4+1] = pcone[4+3];
147:         pcone[4+3] = tmp;
148:       }
149:     }
150:   }
151:   DMPlexCreateFromCellListParallel(comm, meshDim, numCellsLocal, numVerticesLocal, numCorners, interpolate, cellList, spaceDim, coordinates, &sfVertices, dm);
152:   if (sizeof(med_float) == sizeof(PetscReal)) {
153:     vertcoords = NULL;
154:   } else {
155:     PetscFree(vertcoords);
156:   }

158:   if (ngeo > 1) {
159:     PetscInt        numFacets = 0, numFacetsLocal, numFacetCorners, numFacetsRendezvous;
160:     PetscInt        c, f, v, vStart, joinSize, vertices[8];
161:     med_int        *medFacetList;
162:     PetscInt       *facetList, *facetListRendezvous, *facetIDs, *facetIDsRendezvous, *facetListRemote, *facetIDsRemote;
163:     const PetscInt *frange, *join;
164:     PetscLayout     fLayout;
165:     med_filter      ffilter = MED_FILTER_INIT, fidfilter = MED_FILTER_INIT;
166:     PetscSection facetSectionRemote, facetSectionIDsRemote;
167:     /* Partition facets */
168:     numFacets = MEDmeshnEntity(fileID, meshname, MED_NO_DT, MED_NO_IT, MED_CELL, geotype[facetID],
169:                                MED_CONNECTIVITY, MED_NODAL,&coordinatechangement, &geotransformation);
170:     numFacetCorners = geotype[facetID] % 100;
171:     PetscLayoutCreate(comm, &fLayout);
172:     PetscLayoutSetSize(fLayout, numFacets);
173:     PetscLayoutSetBlockSize(fLayout, 1);
174:     PetscLayoutSetUp(fLayout);
175:     PetscLayoutGetRanges(fLayout, &frange);
176:     numFacetsLocal = frange[rank+1]-frange[rank];
177:     MEDfilterBlockOfEntityCr(fileID, numFacets, 1, numFacetCorners, MED_ALL_CONSTITUENT, MED_FULL_INTERLACE, MED_COMPACT_STMODE,
178:                                     MED_NO_PROFILE, frange[rank]+1, 1, numFacetsLocal, 1, 1, &ffilter);
179:     MEDfilterBlockOfEntityCr(fileID, numFacets, 1, 1, MED_ALL_CONSTITUENT, MED_FULL_INTERLACE, MED_COMPACT_STMODE,
180:                                     MED_NO_PROFILE, frange[rank]+1, 1, numFacetsLocal, 1, 1, &fidfilter);
181:     /* Read facet connectivity */
182:     DMPlexGetDepthStratum(*dm, 0, &vStart, NULL);
183:     PetscMalloc1(numFacetsLocal*numFacetCorners, &medFacetList);
184:     PetscCalloc1(numFacetsLocal, &facetIDs);
185:     MEDmeshElementConnectivityAdvancedRd(fileID, meshname, MED_NO_DT, MED_NO_IT, MED_CELL, geotype[facetID],
186:                                                 MED_NODAL, &ffilter, medFacetList);
187:     if (sizeof(med_int) == sizeof(PetscInt)) {
188:       facetList = (PetscInt *) medFacetList;
189:       medFacetList = NULL;
190:     } else {
191:       PetscMalloc1(numFacetsLocal*numFacetCorners, &facetList);
192:       for (i = 0; i < numFacetsLocal*numFacetCorners; i++) facetList[i] = medFacetList[i];
193:       PetscFree(medFacetList);
194:     }
195:     for (i = 0; i < numFacetsLocal*numFacetCorners; i++) facetList[i]--; /* Correct entity counting */
196:     /* Read facet IDs */
197:     MEDmeshEntityAttributeAdvancedRd(fileID, meshname, MED_FAMILY_NUMBER, MED_NO_DT, MED_NO_IT, MED_CELL,
198:                                             geotype[facetID], &fidfilter, facetIDs);
199:     {
200:       /* Send facets and IDs to a rendezvous partition that is based on the initial vertex partitioning. */
201:       PetscInt           p, r;
202:       PetscSFNode       *remoteProc;
203:       DMLabel            lblFacetRendezvous, lblFacetMigration;
204:       PetscSection       facetSection, facetSectionRendezvous;
205:       PetscSF            sfProcess, sfFacetMigration;
206:       const PetscSFNode *remoteVertices;
207:       DMLabelCreate(PETSC_COMM_SELF, "Facet Rendezvous", &lblFacetRendezvous);
208:       DMLabelCreate(PETSC_COMM_SELF, "Facet Migration", &lblFacetMigration);
209:       PetscSFGetGraph(sfVertices, NULL, NULL, NULL, &remoteVertices);
210:       for (f = 0; f < numFacetsLocal; f++) {
211:         for (v = 0; v < numFacetCorners; v++) {
212:           /* Find vertex owner on rendezvous partition and mark in label */
213:           const PetscInt vertex = facetList[f*numFacetCorners+v];
214:           r = rank; while (vrange[r] > vertex) r--; while (vrange[r + 1] < vertex) r++;
215:           DMLabelSetValue(lblFacetRendezvous, f, r);
216:         }
217:       }
218:       /* Build a global process SF */
219:       PetscMalloc1(size, &remoteProc);
220:       for (p = 0; p < size; ++p) {
221:         remoteProc[p].rank  = p;
222:         remoteProc[p].index = rank;
223:       }
224:       PetscSFCreate(comm, &sfProcess);
225:       PetscObjectSetName((PetscObject) sfProcess, "Process SF");
226:       PetscSFSetGraph(sfProcess, size, size, NULL, PETSC_OWN_POINTER, remoteProc, PETSC_OWN_POINTER);
227:       /* Convert facet rendezvous label into SF for migration */
228:       DMPlexPartitionLabelInvert(*dm, lblFacetRendezvous, sfProcess, lblFacetMigration);
229:       DMPlexPartitionLabelCreateSF(*dm, lblFacetMigration, &sfFacetMigration);
230:       /* Migrate facet connectivity data */
231:       PetscSectionCreate(comm, &facetSection);
232:       PetscSectionSetChart(facetSection, 0, numFacetsLocal);
233:       for (f = 0; f < numFacetsLocal; f++) {PetscSectionSetDof(facetSection, f, numFacetCorners);}
234:       PetscSectionSetUp(facetSection);
235:       PetscSectionCreate(comm, &facetSectionRendezvous);
236:       DMPlexDistributeData(*dm, sfFacetMigration, facetSection, MPIU_INT, facetList, facetSectionRendezvous, (void**) &facetListRendezvous);
237:       /* Migrate facet IDs */
238:       PetscSFGetGraph(sfFacetMigration, NULL, &numFacetsRendezvous, NULL, NULL);
239:       PetscMalloc1(numFacetsRendezvous, &facetIDsRendezvous);
240:       PetscSFBcastBegin(sfFacetMigration, MPIU_INT, facetIDs, facetIDsRendezvous);
241:       PetscSFBcastEnd(sfFacetMigration, MPIU_INT, facetIDs, facetIDsRendezvous);
242:       /* Clean up */
243:       DMLabelDestroy(&lblFacetRendezvous);
244:       DMLabelDestroy(&lblFacetMigration);
245:       PetscSFDestroy(&sfProcess);
246:       PetscSFDestroy(&sfFacetMigration);
247:       PetscSectionDestroy(&facetSection);
248:       PetscSectionDestroy(&facetSectionRendezvous);
249:     }
250:     {
251:       /* On the rendevouz partition we build a vertex-wise section/array of facets and IDs. */
252:       PetscInt               sizeVertexFacets, offset, sizeFacetIDsRemote;
253:       PetscInt              *vertexFacets, *vertexIdx, *vertexFacetIDs;
254:       PetscSection           facetSectionVertices, facetSectionIDs;
255:       ISLocalToGlobalMapping ltogVertexNumbering;
256:       PetscSectionCreate(comm, &facetSectionVertices);
257:       PetscSectionSetChart(facetSectionVertices, 0, numVerticesLocal);
258:       PetscSectionCreate(comm, &facetSectionIDs);
259:       PetscSectionSetChart(facetSectionIDs, 0, numVerticesLocal);
260:       for (f = 0; f < numFacetsRendezvous*numFacetCorners; f++) {
261:         const PetscInt vertex = facetListRendezvous[f];
262:         if (vrange[rank] <= vertex && vertex < vrange[rank+1]) {
263:           PetscSectionAddDof(facetSectionIDs, vertex-vrange[rank], 1);
264:           PetscSectionAddDof(facetSectionVertices, vertex-vrange[rank], numFacetCorners);
265:         }
266:       }
267:       PetscSectionSetUp(facetSectionVertices);
268:       PetscSectionSetUp(facetSectionIDs);
269:       PetscSectionGetStorageSize(facetSectionVertices, &sizeVertexFacets);
270:       PetscSectionGetStorageSize(facetSectionVertices, &sizeFacetIDsRemote);
271:       PetscMalloc1(sizeVertexFacets, &vertexFacets);
272:       PetscMalloc1(sizeFacetIDsRemote, &vertexFacetIDs);
273:       PetscCalloc1(numVerticesLocal, &vertexIdx);
274:       for (f = 0; f < numFacetsRendezvous; f++) {
275:         for (c = 0; c < numFacetCorners; c++) {
276:           const PetscInt vertex = facetListRendezvous[f*numFacetCorners+c];
277:           if (vrange[rank] <= vertex && vertex < vrange[rank+1]) {
278:             /* Flip facet connectivities and IDs to a vertex-wise layout */
279:             PetscSectionGetOffset(facetSectionVertices, vertex-vrange[rank], &offset);
280:             offset += vertexIdx[vertex-vrange[rank]] * numFacetCorners;
281:             PetscMemcpy(&(vertexFacets[offset]), &(facetListRendezvous[f*numFacetCorners]), numFacetCorners*sizeof(PetscInt));
282:             PetscSectionGetOffset(facetSectionIDs, vertex-vrange[rank], &offset);
283:             offset += vertexIdx[vertex-vrange[rank]];
284:             vertexFacetIDs[offset] = facetIDsRendezvous[f];
285:             vertexIdx[vertex-vrange[rank]]++;
286:           }
287:         }
288:       }
289:       /* Distribute the vertex-wise facet connectivities over the vertexSF */
290:       PetscSectionCreate(comm, &facetSectionRemote);
291:       DMPlexDistributeData(*dm, sfVertices, facetSectionVertices, MPIU_INT, vertexFacets, facetSectionRemote, (void**) &facetListRemote);
292:       PetscSectionCreate(comm, &facetSectionIDsRemote);
293:       DMPlexDistributeData(*dm, sfVertices, facetSectionIDs, MPIU_INT, vertexFacetIDs, facetSectionIDsRemote, (void**) &facetIDsRemote);
294:       /* Convert facet connectivities to local vertex numbering */
295:       PetscSectionGetStorageSize(facetSectionRemote, &sizeVertexFacets);
296:       ISLocalToGlobalMappingCreateSF(sfVertices, vrange[rank], &ltogVertexNumbering);
297:       ISGlobalToLocalMappingApplyBlock(ltogVertexNumbering, IS_GTOLM_MASK, sizeVertexFacets, facetListRemote, NULL, facetListRemote);
298:       /* Clean up */
299:       PetscFree(vertexFacets);
300:       PetscFree(vertexIdx);
301:       PetscFree(vertexFacetIDs);
302:       PetscSectionDestroy(&facetSectionVertices);
303:       PetscSectionDestroy(&facetSectionIDs);
304:       ISLocalToGlobalMappingDestroy(&ltogVertexNumbering);
305:     }
306:     {
307:       PetscInt offset, dof;
308:       DMLabel lblFaceSets;
309:       PetscBool verticesLocal;
310:       /* Identify and mark facets locally with facet joins */
311:       DMCreateLabel(*dm, "Face Sets");
312:       DMGetLabel(*dm, "Face Sets", &lblFaceSets);
313:       /* We need to set a new default value here, since -1 is a legitimate facet ID */
314:       DMLabelSetDefaultValue(lblFaceSets, -666666666);
315:       for (v = 0; v < numVerticesLocal; v++) {
316:         PetscSectionGetOffset(facetSectionRemote, v, &offset);
317:         PetscSectionGetDof(facetSectionRemote, v, &dof);
318:         for (f = 0; f < dof; f += numFacetCorners) {
319:           for (verticesLocal = PETSC_TRUE, c = 0; c < numFacetCorners; ++c) {
320:             if (facetListRemote[offset+f+c] < 0) {verticesLocal = PETSC_FALSE; break;}
321:             vertices[c] = vStart + facetListRemote[offset+f+c];
322:           }
323:           if (verticesLocal) {
324:             DMPlexGetFullJoin(*dm, numFacetCorners, (const PetscInt*)vertices, &joinSize, &join);
325:             if (joinSize == 1) {
326:               DMLabelSetValue(lblFaceSets, join[0], facetIDsRemote[(offset+f) / numFacetCorners]);
327:             }
328:             DMPlexRestoreJoin(*dm, numFacetCorners, (const PetscInt*)vertices, &joinSize, &join);
329:           }
330:         }
331:       }
332:     }
333:     PetscFree(facetList);
334:     PetscFree(facetListRendezvous);
335:     PetscFree(facetListRemote);
336:     PetscFree(facetIDs);
337:     PetscFree(facetIDsRendezvous);
338:     PetscFree(facetIDsRemote);
339:     PetscLayoutDestroy(&fLayout);
340:     PetscSectionDestroy(&facetSectionRemote);
341:     PetscSectionDestroy(&facetSectionIDsRemote);
342:   }
343:   MEDfileClose(fileID);
344:   PetscFree(coordinates);
345:   PetscFree(cellList);
346:   PetscLayoutDestroy(&vLayout);
347:   PetscLayoutDestroy(&cLayout);
348:   PetscSFDestroy(&sfVertices);
349: #else
350:   SETERRQ(comm, PETSC_ERR_SUP, "This method requires Med mesh reader support. Reconfigure using --download-med");
351: #endif
352:   return(0);
353: }