Actual source code: plexhdf5xdmf.c
petsc-3.15.0 2021-03-30
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      1: #include <petsc/private/dmpleximpl.h>
      2: #include <petsc/private/isimpl.h>
      3: #include <petsc/private/vecimpl.h>
      4: #include <petsclayouthdf5.h>

      6: #if defined(PETSC_HAVE_HDF5)
      7: static PetscErrorCode SplitPath_Private(char path[], char name[])
      8: {
      9:   char *tmp;

     13:   PetscStrrchr(path,'/',&tmp);
     14:   PetscStrcpy(name,tmp);
     15:   if (tmp != path) {
     16:     /* '/' found, name is substring of path after last occurence of '/'. */
     17:     /* Trim the '/name' part from path just by inserting null character. */
     18:     tmp--;
     19:     *tmp = '\0';
     20:   } else {
     21:     /* '/' not found, name = path, path = "/". */
     22:     PetscStrcpy(path,"/");
     23:   }
     24:   return(0);
     25: }

     27: /*
     28:   - invert (involute) cells of some types according to XDMF/VTK numbering of vertices in a cells
     29:   - cell type is identified using the number of vertices
     30: */
     31: static PetscErrorCode DMPlexInvertCells_XDMF_Private(DM dm)
     32: {
     33:   PetscInt       dim, *cones, cHeight, cStart, cEnd, p;
     34:   PetscSection   cs;

     38:   DMGetDimension(dm, &dim);
     39:   if (dim != 3) return(0);
     40:   DMPlexGetCones(dm, &cones);
     41:   DMPlexGetConeSection(dm, &cs);
     42:   DMPlexGetVTKCellHeight(dm, &cHeight);
     43:   DMPlexGetHeightStratum(dm, cHeight, &cStart, &cEnd);
     44:   for (p=cStart; p<cEnd; p++) {
     45:     PetscInt numCorners, o;

     47:     PetscSectionGetDof(cs, p, &numCorners);
     48:     PetscSectionGetOffset(cs, p, &o);
     49:     switch (numCorners) {
     50:       case 4: DMPlexInvertCell(DM_POLYTOPE_TETRAHEDRON,&cones[o]); break;
     51:       case 6: DMPlexInvertCell(DM_POLYTOPE_TRI_PRISM,&cones[o]); break;
     52:       case 8: DMPlexInvertCell(DM_POLYTOPE_HEXAHEDRON,&cones[o]); break;
     53:     }
     54:   }
     55:   return(0);
     56: }

     58: PetscErrorCode DMPlexLoad_HDF5_Xdmf_Internal(DM dm, PetscViewer viewer)
     59: {
     60:   Vec             coordinates;
     61:   IS              cells;
     62:   PetscInt        spatialDim, topoDim = -1, numCells, numVertices, NVertices, numCorners;
     63:   PetscMPIInt     rank;
     64:   MPI_Comm        comm;
     65:   PetscErrorCode  ierr;
     66:   char            topo_path[PETSC_MAX_PATH_LEN]="/viz/topology/cells", topo_name[PETSC_MAX_PATH_LEN];
     67:   char            geom_path[PETSC_MAX_PATH_LEN]="/geometry/vertices",  geom_name[PETSC_MAX_PATH_LEN];
     68:   PetscBool       seq = PETSC_FALSE, hasCellDim = PETSC_FALSE;

     71:   PetscObjectGetComm((PetscObject)dm, &comm);
     72:   MPI_Comm_rank(comm, &rank);

     74:   PetscOptionsBegin(PetscObjectComm((PetscObject)dm),((PetscObject)dm)->prefix,"DMPlex HDF5/XDMF Loader Options","PetscViewer");
     75:   PetscOptionsString("-dm_plex_hdf5_topology_path","HDF5 path of topology dataset",NULL,topo_path,topo_path,sizeof(topo_path),NULL);
     76:   PetscOptionsString("-dm_plex_hdf5_geometry_path","HDF5 path to geometry dataset",NULL,geom_path,geom_path,sizeof(geom_path),NULL);
     77:   PetscOptionsBool("-dm_plex_hdf5_force_sequential","force sequential loading",NULL,seq,&seq,NULL);
     78:   PetscOptionsEnd();

     80:   SplitPath_Private(topo_path, topo_name);
     81:   SplitPath_Private(geom_path, geom_name);
     82:   PetscInfo2(dm, "Topology group %s, name %s\n", topo_path, topo_name);
     83:   PetscInfo2(dm, "Geometry group %s, name %s\n", geom_path, geom_name);

     85:   /* Read topology */
     86:   PetscViewerHDF5PushGroup(viewer, topo_path);
     87:   ISCreate(comm, &cells);
     88:   PetscObjectSetName((PetscObject) cells, topo_name);
     89:   if (seq) {
     90:     PetscViewerHDF5ReadSizes(viewer, topo_name, NULL, &numCells);
     91:     PetscLayoutSetSize(cells->map, numCells);
     92:     numCells = !rank ? numCells : 0;
     93:     PetscLayoutSetLocalSize(cells->map, numCells);
     94:   }
     95:   ISLoad(cells, viewer);
     96:   ISGetLocalSize(cells, &numCells);
     97:   ISGetBlockSize(cells, &numCorners);
     98:   PetscViewerHDF5HasAttribute(viewer, topo_name, "cell_dim", &hasCellDim);
     99:   if (hasCellDim) {PetscViewerHDF5ReadAttribute(viewer, topo_name, "cell_dim", PETSC_INT, &topoDim);}
    100:   PetscViewerHDF5PopGroup(viewer);
    101:   numCells /= numCorners;

    103:   /* Read geometry */
    104:   PetscViewerHDF5PushGroup(viewer, geom_path);
    105:   VecCreate(comm, &coordinates);
    106:   PetscObjectSetName((PetscObject) coordinates, geom_name);
    107:   if (seq) {
    108:     PetscViewerHDF5ReadSizes(viewer, geom_name, NULL, &numVertices);
    109:     PetscLayoutSetSize(coordinates->map, numVertices);
    110:     numVertices = !rank ? numVertices : 0;
    111:     PetscLayoutSetLocalSize(coordinates->map, numVertices);
    112:   }
    113:   VecLoad(coordinates, viewer);
    114:   VecGetLocalSize(coordinates, &numVertices);
    115:   VecGetSize(coordinates, &NVertices);
    116:   VecGetBlockSize(coordinates, &spatialDim);
    117:   PetscViewerHDF5PopGroup(viewer);
    118:   numVertices /= spatialDim;
    119:   NVertices /= spatialDim;

    121:   PetscInfo4(NULL, "Loaded mesh dimensions: numCells %D numCorners %D numVertices %D spatialDim %D\n", numCells, numCorners, numVertices, spatialDim);
    122:   {
    123:     const PetscScalar *coordinates_arr;
    124:     PetscReal         *coordinates_arr_real;
    125:     const PetscInt    *cells_arr;
    126:     PetscSF           sfVert = NULL;
    127:     PetscInt          i;

    129:     VecGetArrayRead(coordinates, &coordinates_arr);
    130:     ISGetIndices(cells, &cells_arr);

    132:     if (PetscDefined(USE_COMPLEX)) {
    133:       /* convert to real numbers if PetscScalar is complex */
    134:       /*TODO More systematic would be to change all the function arguments to PetscScalar */
    135:       PetscMalloc1(numVertices*spatialDim, &coordinates_arr_real);
    136:       for (i = 0; i < numVertices*spatialDim; ++i) {
    137:         coordinates_arr_real[i] = PetscRealPart(coordinates_arr[i]);
    138:         if (PetscUnlikelyDebug(PetscImaginaryPart(coordinates_arr[i]))) {
    139:           SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Vector of coordinates contains complex numbers but only real vectors are currently supported.");
    140:         }
    141:       }
    142:     } else coordinates_arr_real = (PetscReal*)coordinates_arr;

    144:     DMSetDimension(dm, topoDim < 0 ? spatialDim : topoDim);
    145:     DMPlexBuildFromCellListParallel(dm, numCells, numVertices, NVertices, numCorners, cells_arr, &sfVert);
    146:     DMPlexInvertCells_XDMF_Private(dm);
    147:     DMPlexBuildCoordinatesFromCellListParallel(dm, spatialDim, sfVert, coordinates_arr_real);
    148:     VecRestoreArrayRead(coordinates, &coordinates_arr);
    149:     ISRestoreIndices(cells, &cells_arr);
    150:     PetscSFDestroy(&sfVert);
    151:     if (PetscDefined(USE_COMPLEX)) {PetscFree(coordinates_arr_real);}
    152:   }
    153:   ISDestroy(&cells);
    154:   VecDestroy(&coordinates);

    156:   /* scale coordinates - unlike in DMPlexLoad_HDF5_Internal, this can only be done after DM is populated */
    157:   {
    158:     PetscReal lengthScale;

    160:     DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale);
    161:     DMGetCoordinates(dm, &coordinates);
    162:     VecScale(coordinates, 1.0/lengthScale);
    163:   }

    165:   /* Read Labels */
    166:   /* TODO: this probably does not work as elements get permuted */
    167:   /* DMPlexLoadLabels_HDF5_Internal(dm, viewer); */
    168:   return(0);
    169: }
    170: #endif