Actual source code: plexmed.c

      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: https://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:   med_idt         fileID;
     29:   PetscInt        i, ngeo, spaceDim, meshDim;
     30:   PetscInt        numVertices = 0, numCells = 0, c, numCorners, numCellsLocal, numVerticesLocal;
     31:   med_int        *medCellList;
     32:   PetscInt       *cellList;
     33:   med_float      *coordinates = NULL;
     34:   PetscReal      *vertcoords = NULL;
     35:   PetscLayout     vLayout, cLayout;
     36:   const PetscInt *vrange, *crange;
     37:   PetscSF         sfVertices;
     38:   char           *axisname, *unitname, meshname[MED_NAME_SIZE+1], geotypename[MED_NAME_SIZE+1];
     39:   char            meshdescription[MED_COMMENT_SIZE+1], dtunit[MED_SNAME_SIZE+1];
     40:   med_sorting_type sortingtype;
     41:   med_mesh_type   meshtype;
     42:   med_axis_type   axistype;
     43:   med_bool        coordinatechangement, geotransformation, hdfok, medok;
     44:   med_geometry_type geotype[2], cellID, facetID;
     45:   med_filter      vfilter = MED_FILTER_INIT;
     46:   med_filter      cfilter = MED_FILTER_INIT;
     47:   med_err         mederr;
     48:   med_int         major, minor, release;
     49: #endif

     51:   MPI_Comm_rank(comm, &rank);
     52:   MPI_Comm_size(comm, &size);
     53: #if defined(PETSC_HAVE_MED)
     54:   mederr = MEDfileCompatibility(filename, &hdfok, &medok);

     59:   fileID = MEDfileOpen(filename, MED_ACC_RDONLY);
     61:   mederr = MEDfileNumVersionRd(fileID, &major, &minor, &release);
     63:   spaceDim = MEDmeshnAxis(fileID, 1);
     65:   /* Read general mesh information */
     66:   PetscMalloc1(MED_SNAME_SIZE*spaceDim+1, &axisname);
     67:   PetscMalloc1(MED_SNAME_SIZE*spaceDim+1, &unitname);
     68:   {
     69:     med_int medMeshDim, medNstep;
     70:     med_int medSpaceDim = spaceDim;

     72:     PetscStackCallStandard(MEDmeshInfo,fileID, 1, meshname, &medSpaceDim, &medMeshDim, &meshtype, meshdescription,dtunit, &sortingtype, &medNstep, &axistype, axisname, unitname);
     73:     spaceDim = medSpaceDim;
     74:     meshDim  = medMeshDim;
     75:   }
     76:   PetscFree(axisname);
     77:   PetscFree(unitname);
     78:   /* Partition mesh coordinates */
     79:   numVertices = MEDmeshnEntity(fileID, meshname, MED_NO_DT, MED_NO_IT, MED_NODE, MED_NO_GEOTYPE,
     80:                                MED_COORDINATE, MED_NO_CMODE,&coordinatechangement, &geotransformation);
     81:   PetscLayoutCreate(comm, &vLayout);
     82:   PetscLayoutSetSize(vLayout, numVertices);
     83:   PetscLayoutSetBlockSize(vLayout, 1);
     84:   PetscLayoutSetUp(vLayout);
     85:   PetscLayoutGetRanges(vLayout, &vrange);
     86:   numVerticesLocal = vrange[rank+1]-vrange[rank];
     87:   PetscStackCallStandard(MEDfilterBlockOfEntityCr,fileID, numVertices, 1, spaceDim, MED_ALL_CONSTITUENT, MED_FULL_INTERLACE, MED_COMPACT_STMODE,MED_NO_PROFILE, vrange[rank]+1, 1, numVerticesLocal, 1, 1, &vfilter);
     88:   /* Read mesh coordinates */
     90:   PetscMalloc1(numVerticesLocal*spaceDim, &coordinates);
     91:   PetscStackCallStandard(MEDmeshNodeCoordinateAdvancedRd,fileID, meshname, MED_NO_DT, MED_NO_IT, &vfilter, coordinates);
     92:   /* Read the types of entity sets in the mesh */
     93:   ngeo = MEDmeshnEntity(fileID, meshname, MED_NO_DT, MED_NO_IT, MED_CELL,MED_GEO_ALL, MED_CONNECTIVITY,
     94:                         MED_NODAL, &coordinatechangement, &geotransformation);
     97:   PetscStackCallStandard(MEDmeshEntityInfo,fileID, meshname, MED_NO_DT, MED_NO_IT, MED_CELL, 1, geotypename, &(geotype[0]));
     98:   if (ngeo > 1) PetscStackCallStandard(MEDmeshEntityInfo,fileID, meshname, MED_NO_DT, MED_NO_IT, MED_CELL, 2, geotypename, &(geotype[1]));
     99:   else geotype[1] = 0;
    100:   /* Determine topological dim and set ID for cells */
    101:   cellID = geotype[0]/100 > geotype[1]/100 ? 0 : 1;
    102:   facetID = geotype[0]/100 > geotype[1]/100 ? 1 : 0;
    103:   meshDim = geotype[cellID] / 100;
    104:   numCorners = geotype[cellID] % 100;
    105:   /* Partition cells */
    106:   numCells = MEDmeshnEntity(fileID, meshname, MED_NO_DT, MED_NO_IT, MED_CELL, geotype[cellID],
    107:                             MED_CONNECTIVITY, MED_NODAL,&coordinatechangement, &geotransformation);
    108:   PetscLayoutCreate(comm, &cLayout);
    109:   PetscLayoutSetSize(cLayout, numCells);
    110:   PetscLayoutSetBlockSize(cLayout, 1);
    111:   PetscLayoutSetUp(cLayout);
    112:   PetscLayoutGetRanges(cLayout, &crange);
    113:   numCellsLocal = crange[rank+1]-crange[rank];
    114:   PetscStackCallStandard(MEDfilterBlockOfEntityCr,fileID, numCells, 1, numCorners, MED_ALL_CONSTITUENT, MED_FULL_INTERLACE, MED_COMPACT_STMODE,MED_NO_PROFILE, crange[rank]+1, 1, numCellsLocal, 1, 1, &cfilter);
    115:   /* Read cell connectivity */
    117:   PetscMalloc1(numCellsLocal*numCorners, &medCellList);
    118:   PetscStackCallStandard(MEDmeshElementConnectivityAdvancedRd,fileID, meshname, MED_NO_DT, MED_NO_IT, MED_CELL, geotype[cellID],MED_NODAL, &cfilter, medCellList);
    120:   PetscMalloc1(numCellsLocal*numCorners, &cellList);
    121:   for (i = 0; i < numCellsLocal*numCorners; i++) {
    122:     cellList[i] = ((PetscInt) medCellList[i]) - 1; /* Correct entity counting */
    123:   }
    124:   PetscFree(medCellList);
    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] = (PetscReal) 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:       /* Hexahedra are inverted */
    138:       if (numCorners == 8) {
    139:         PetscInt tmp = pcone[4+1];
    140:         pcone[4+1] = pcone[4+3];
    141:         pcone[4+3] = tmp;
    142:       }
    143:     }
    144:   }
    145:   DMPlexCreateFromCellListParallelPetsc(comm, meshDim, numCellsLocal, numVerticesLocal, numVertices, numCorners, interpolate, cellList, spaceDim, vertcoords, &sfVertices, NULL, dm);
    146:   if (sizeof(med_float) == sizeof(PetscReal)) {
    147:     vertcoords = NULL;
    148:   } else {
    149:     PetscFree(vertcoords);
    150:   }
    151:   if (ngeo > 1) {
    152:     PetscInt        numFacets = 0, numFacetsLocal, numFacetCorners, numFacetsRendezvous;
    153:     PetscInt        c, f, v, vStart, joinSize, vertices[8];
    154:     PetscInt       *facetList, *facetListRendezvous, *facetIDs, *facetIDsRendezvous, *facetListRemote, *facetIDsRemote;
    155:     const PetscInt *frange, *join;
    156:     PetscLayout     fLayout;
    157:     med_filter      ffilter = MED_FILTER_INIT, fidfilter = MED_FILTER_INIT;
    158:     PetscSection    facetSectionRemote, facetSectionIDsRemote;
    159:     /* Partition facets */
    160:     numFacets = MEDmeshnEntity(fileID, meshname, MED_NO_DT, MED_NO_IT, MED_CELL, geotype[facetID],
    161:                                MED_CONNECTIVITY, MED_NODAL,&coordinatechangement, &geotransformation);
    162:     numFacetCorners = geotype[facetID] % 100;
    163:     PetscLayoutCreate(comm, &fLayout);
    164:     PetscLayoutSetSize(fLayout, numFacets);
    165:     PetscLayoutSetBlockSize(fLayout, 1);
    166:     PetscLayoutSetUp(fLayout);
    167:     PetscLayoutGetRanges(fLayout, &frange);
    168:     numFacetsLocal = frange[rank+1]-frange[rank];
    169:     PetscStackCallStandard(MEDfilterBlockOfEntityCr,fileID, numFacets, 1, numFacetCorners, MED_ALL_CONSTITUENT, MED_FULL_INTERLACE, MED_COMPACT_STMODE,MED_NO_PROFILE, frange[rank]+1, 1, numFacetsLocal, 1, 1, &ffilter);
    170:     PetscStackCallStandard(MEDfilterBlockOfEntityCr,fileID, numFacets, 1, 1, MED_ALL_CONSTITUENT, MED_FULL_INTERLACE, MED_COMPACT_STMODE,MED_NO_PROFILE, frange[rank]+1, 1, numFacetsLocal, 1, 1, &fidfilter);
    171:     DMPlexGetDepthStratum(*dm, 0, &vStart, NULL);
    172:     PetscMalloc1(numFacetsLocal, &facetIDs);
    173:     PetscMalloc1(numFacetsLocal*numFacetCorners, &facetList);

    175:     /* Read facet connectivity */
    176:     {
    177:       med_int *medFacetList;

    179:       PetscMalloc1(numFacetsLocal*numFacetCorners, &medFacetList);
    180:       PetscStackCallStandard(MEDmeshElementConnectivityAdvancedRd,fileID, meshname, MED_NO_DT, MED_NO_IT, MED_CELL, geotype[facetID], MED_NODAL, &ffilter, medFacetList);
    181:       for (i = 0; i < numFacetsLocal*numFacetCorners; i++) {
    182:         facetList[i] = ((PetscInt) medFacetList[i]) - 1 ; /* Correct entity counting */
    183:       }
    184:       PetscFree(medFacetList);
    185:     }

    187:     /* Read facet IDs */
    188:     {
    189:       med_int *medFacetIDs;

    191:       PetscMalloc1(numFacetsLocal, &medFacetIDs);
    192:       PetscStackCallStandard(MEDmeshEntityAttributeAdvancedRd,fileID, meshname, MED_FAMILY_NUMBER, MED_NO_DT, MED_NO_IT, MED_CELL, geotype[facetID], &fidfilter, medFacetIDs);
    193:       for (i = 0; i < numFacetsLocal; i++) {
    194:         facetIDs[i] = (PetscInt) medFacetIDs[i];
    195:       }
    196:       PetscFree(medFacetIDs);
    197:     }

    199:     /* Send facets and IDs to a rendezvous partition that is based on the initial vertex partitioning. */
    200:     {
    201:       PetscInt           r;
    202:       DMLabel            lblFacetRendezvous, lblFacetMigration;
    203:       PetscSection       facetSection, facetSectionRendezvous;
    204:       PetscSF            sfProcess, sfFacetMigration;
    205:       const PetscSFNode *remoteVertices;
    206:       DMLabelCreate(PETSC_COMM_SELF, "Facet Rendezvous", &lblFacetRendezvous);
    207:       DMLabelCreate(PETSC_COMM_SELF, "Facet Migration", &lblFacetMigration);
    208:       PetscSFGetGraph(sfVertices, NULL, NULL, NULL, &remoteVertices);
    209:       for (f = 0; f < numFacetsLocal; f++) {
    210:         for (v = 0; v < numFacetCorners; v++) {
    211:           /* Find vertex owner on rendezvous partition and mark in label */
    212:           const PetscInt vertex = facetList[f*numFacetCorners+v];
    213:           r = rank; while (vrange[r] > vertex) r--; while (vrange[r + 1] < vertex) r++;
    214:           DMLabelSetValue(lblFacetRendezvous, f, r);
    215:         }
    216:       }
    217:       /* Build a global process SF */
    218:       PetscSFCreate(comm,&sfProcess);
    219:       PetscSFSetGraphWithPattern(sfProcess,NULL,PETSCSF_PATTERN_ALLTOALL);
    220:       PetscObjectSetName((PetscObject) sfProcess, "Process SF");
    221:       /* Convert facet rendezvous label into SF for migration */
    222:       DMPlexPartitionLabelInvert(*dm, lblFacetRendezvous, sfProcess, lblFacetMigration);
    223:       DMPlexPartitionLabelCreateSF(*dm, lblFacetMigration, &sfFacetMigration);
    224:       /* Migrate facet connectivity data */
    225:       PetscSectionCreate(comm, &facetSection);
    226:       PetscSectionSetChart(facetSection, 0, numFacetsLocal);
    227:       for (f = 0; f < numFacetsLocal; f++) PetscSectionSetDof(facetSection, f, numFacetCorners);
    228:       PetscSectionSetUp(facetSection);
    229:       PetscSectionCreate(comm, &facetSectionRendezvous);
    230:       DMPlexDistributeData(*dm, sfFacetMigration, facetSection, MPIU_INT, facetList, facetSectionRendezvous, (void**) &facetListRendezvous);
    231:       /* Migrate facet IDs */
    232:       PetscSFGetGraph(sfFacetMigration, NULL, &numFacetsRendezvous, NULL, NULL);
    233:       PetscMalloc1(numFacetsRendezvous, &facetIDsRendezvous);
    234:       PetscSFBcastBegin(sfFacetMigration, MPIU_INT, facetIDs, facetIDsRendezvous,MPI_REPLACE);
    235:       PetscSFBcastEnd(sfFacetMigration, MPIU_INT, facetIDs, facetIDsRendezvous,MPI_REPLACE);
    236:       /* Clean up */
    237:       DMLabelDestroy(&lblFacetRendezvous);
    238:       DMLabelDestroy(&lblFacetMigration);
    239:       PetscSFDestroy(&sfProcess);
    240:       PetscSFDestroy(&sfFacetMigration);
    241:       PetscSectionDestroy(&facetSection);
    242:       PetscSectionDestroy(&facetSectionRendezvous);
    243:     }

    245:     /* On the rendevouz partition we build a vertex-wise section/array of facets and IDs. */
    246:     {
    247:       PetscInt               sizeVertexFacets, offset, sizeFacetIDsRemote;
    248:       PetscInt              *vertexFacets, *vertexIdx, *vertexFacetIDs;
    249:       PetscSection           facetSectionVertices, facetSectionIDs;
    250:       ISLocalToGlobalMapping ltogVertexNumbering;
    251:       PetscSectionCreate(comm, &facetSectionVertices);
    252:       PetscSectionSetChart(facetSectionVertices, 0, numVerticesLocal);
    253:       PetscSectionCreate(comm, &facetSectionIDs);
    254:       PetscSectionSetChart(facetSectionIDs, 0, numVerticesLocal);
    255:       for (f = 0; f < numFacetsRendezvous*numFacetCorners; f++) {
    256:         const PetscInt vertex = facetListRendezvous[f];
    257:         if (vrange[rank] <= vertex && vertex < vrange[rank+1]) {
    258:           PetscSectionAddDof(facetSectionIDs, vertex-vrange[rank], 1);
    259:           PetscSectionAddDof(facetSectionVertices, vertex-vrange[rank], numFacetCorners);
    260:         }
    261:       }
    262:       PetscSectionSetUp(facetSectionVertices);
    263:       PetscSectionSetUp(facetSectionIDs);
    264:       PetscSectionGetStorageSize(facetSectionVertices, &sizeVertexFacets);
    265:       PetscSectionGetStorageSize(facetSectionVertices, &sizeFacetIDsRemote);
    266:       PetscMalloc1(sizeVertexFacets, &vertexFacets);
    267:       PetscMalloc1(sizeFacetIDsRemote, &vertexFacetIDs);
    268:       PetscCalloc1(numVerticesLocal, &vertexIdx);
    269:       for (f = 0; f < numFacetsRendezvous; f++) {
    270:         for (c = 0; c < numFacetCorners; c++) {
    271:           const PetscInt vertex = facetListRendezvous[f*numFacetCorners+c];
    272:           if (vrange[rank] <= vertex && vertex < vrange[rank+1]) {
    273:             /* Flip facet connectivities and IDs to a vertex-wise layout */
    274:             PetscSectionGetOffset(facetSectionVertices, vertex-vrange[rank], &offset);
    275:             offset += vertexIdx[vertex-vrange[rank]] * numFacetCorners;
    276:             PetscArraycpy(&(vertexFacets[offset]), &(facetListRendezvous[f*numFacetCorners]), numFacetCorners);
    277:             PetscSectionGetOffset(facetSectionIDs, vertex-vrange[rank], &offset);
    278:             offset += vertexIdx[vertex-vrange[rank]];
    279:             vertexFacetIDs[offset] = facetIDsRendezvous[f];
    280:             vertexIdx[vertex-vrange[rank]]++;
    281:           }
    282:         }
    283:       }
    284:       /* Distribute the vertex-wise facet connectivities over the vertexSF */
    285:       PetscSectionCreate(comm, &facetSectionRemote);
    286:       DMPlexDistributeData(*dm, sfVertices, facetSectionVertices, MPIU_INT, vertexFacets, facetSectionRemote, (void**) &facetListRemote);
    287:       PetscSectionCreate(comm, &facetSectionIDsRemote);
    288:       DMPlexDistributeData(*dm, sfVertices, facetSectionIDs, MPIU_INT, vertexFacetIDs, facetSectionIDsRemote, (void**) &facetIDsRemote);
    289:       /* Convert facet connectivities to local vertex numbering */
    290:       PetscSectionGetStorageSize(facetSectionRemote, &sizeVertexFacets);
    291:       ISLocalToGlobalMappingCreateSF(sfVertices, vrange[rank], &ltogVertexNumbering);
    292:       ISGlobalToLocalMappingApplyBlock(ltogVertexNumbering, IS_GTOLM_MASK, sizeVertexFacets, facetListRemote, NULL, facetListRemote);
    293:       /* Clean up */
    294:       PetscFree(vertexFacets);
    295:       PetscFree(vertexIdx);
    296:       PetscFree(vertexFacetIDs);
    297:       PetscSectionDestroy(&facetSectionVertices);
    298:       PetscSectionDestroy(&facetSectionIDs);
    299:       ISLocalToGlobalMappingDestroy(&ltogVertexNumbering);
    300:     }
    301:     {
    302:       PetscInt offset, dof;
    303:       DMLabel lblFaceSets;
    304:       PetscBool verticesLocal;
    305:       /* Identify and mark facets locally with facet joins */
    306:       DMCreateLabel(*dm, "Face Sets");
    307:       DMGetLabel(*dm, "Face Sets", &lblFaceSets);
    308:       /* We need to set a new default value here, since -1 is a legitimate facet ID */
    309:       DMLabelSetDefaultValue(lblFaceSets, -666666666);
    310:       for (v = 0; v < numVerticesLocal; v++) {
    311:         PetscSectionGetOffset(facetSectionRemote, v, &offset);
    312:         PetscSectionGetDof(facetSectionRemote, v, &dof);
    313:         for (f = 0; f < dof; f += numFacetCorners) {
    314:           for (verticesLocal = PETSC_TRUE, c = 0; c < numFacetCorners; ++c) {
    315:             if (facetListRemote[offset+f+c] < 0) {verticesLocal = PETSC_FALSE; break;}
    316:             vertices[c] = vStart + facetListRemote[offset+f+c];
    317:           }
    318:           if (verticesLocal) {
    319:             DMPlexGetFullJoin(*dm, numFacetCorners, (const PetscInt*)vertices, &joinSize, &join);
    320:             if (joinSize == 1) {
    321:               DMLabelSetValue(lblFaceSets, join[0], facetIDsRemote[(offset+f) / numFacetCorners]);
    322:             }
    323:             DMPlexRestoreJoin(*dm, numFacetCorners, (const PetscInt*)vertices, &joinSize, &join);
    324:           }
    325:         }
    326:       }
    327:     }
    328:     PetscFree(facetList);
    329:     PetscFree(facetListRendezvous);
    330:     PetscFree(facetListRemote);
    331:     PetscFree(facetIDs);
    332:     PetscFree(facetIDsRendezvous);
    333:     PetscFree(facetIDsRemote);
    334:     PetscLayoutDestroy(&fLayout);
    335:     PetscSectionDestroy(&facetSectionRemote);
    336:     PetscSectionDestroy(&facetSectionIDsRemote);
    337:   }
    338:   MEDfileClose(fileID);
    339:   PetscFree(coordinates);
    340:   PetscFree(cellList);
    341:   PetscLayoutDestroy(&vLayout);
    342:   PetscLayoutDestroy(&cLayout);
    343:   PetscSFDestroy(&sfVertices);
    344:   return 0;
    345: #else
    346:   SETERRQ(comm, PETSC_ERR_SUP, "This method requires Med mesh reader support. Reconfigure using --download-med");
    347: #endif
    348: }