Actual source code: plexmed.c
petsc-3.10.5 2019-03-28
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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("Facet Rendezvous", &lblFacetRendezvous);
    208:       DMLabelCreate("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: }