Actual source code: plexhdf5xdmf.c

  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;
 10:   size_t len;

 12:   PetscFunctionBegin;
 13:   PetscCall(PetscStrrchr(path, '/', &tmp));
 14:   PetscCall(PetscStrlen(tmp, &len));
 15:   PetscCall(PetscStrncpy(name, tmp, len + 1)); /* assuming adequate buffer */
 16:   if (tmp != path) {
 17:     /* '/' found, name is substring of path after last occurrence of '/'. */
 18:     /* Trim the '/name' part from path just by inserting null character. */
 19:     tmp--;
 20:     *tmp = '\0';
 21:   } else {
 22:     /* '/' not found, name = path, path = "/". */
 23:     PetscCall(PetscStrncpy(path, "/", 2)); /* assuming adequate buffer */
 24:   }
 25:   PetscFunctionReturn(PETSC_SUCCESS);
 26: }

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

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

 47:     PetscCall(PetscSectionGetDof(cs, p, &numCorners));
 48:     PetscCall(PetscSectionGetOffset(cs, p, &o));
 49:     switch (numCorners) {
 50:     case 4:
 51:       PetscCall(DMPlexInvertCell(DM_POLYTOPE_TETRAHEDRON, &cones[o]));
 52:       break;
 53:     case 6:
 54:       PetscCall(DMPlexInvertCell(DM_POLYTOPE_TRI_PRISM, &cones[o]));
 55:       break;
 56:     case 8:
 57:       PetscCall(DMPlexInvertCell(DM_POLYTOPE_HEXAHEDRON, &cones[o]));
 58:       break;
 59:     }
 60:   }
 61:   PetscFunctionReturn(PETSC_SUCCESS);
 62: }

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

 75:   PetscFunctionBegin;
 76:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
 77:   PetscCallMPI(MPI_Comm_rank(comm, &rank));

 79:   PetscOptionsBegin(PetscObjectComm((PetscObject)dm), ((PetscObject)dm)->prefix, "DMPlex HDF5/XDMF Loader Options", "PetscViewer");
 80:   PetscCall(PetscOptionsString("-dm_plex_hdf5_topology_path", "HDF5 path of topology dataset", NULL, topo_path, topo_path, sizeof(topo_path), NULL));
 81:   PetscCall(PetscOptionsString("-dm_plex_hdf5_geometry_path", "HDF5 path to geometry dataset", NULL, geom_path, geom_path, sizeof(geom_path), NULL));
 82:   PetscCall(PetscOptionsBool("-dm_plex_hdf5_force_sequential", "force sequential loading", NULL, seq, &seq, NULL));
 83:   PetscOptionsEnd();

 85:   PetscCall(SplitPath_Private(topo_path, topo_name));
 86:   PetscCall(SplitPath_Private(geom_path, geom_name));
 87:   PetscCall(PetscInfo(dm, "Topology group %s, name %s\n", topo_path, topo_name));
 88:   PetscCall(PetscInfo(dm, "Geometry group %s, name %s\n", geom_path, geom_name));

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

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

125:   PetscCall(PetscInfo(NULL, "Loaded mesh dimensions: numCells %" PetscInt_FMT " numCorners %" PetscInt_FMT " numVertices %" PetscInt_FMT " spatialDim %" PetscInt_FMT "\n", numCells, numCorners, numVertices, spatialDim));
126:   {
127:     const PetscScalar *coordinates_arr;
128:     PetscReal         *coordinates_arr_real;
129:     const PetscInt    *cells_arr;
130:     PetscSF            sfVert = NULL;
131:     PetscInt           i;

133:     PetscCall(VecGetArrayRead(coordinates, &coordinates_arr));
134:     PetscCall(ISGetIndices(cells, &cells_arr));

136:     if (PetscDefined(USE_COMPLEX)) {
137:       /* convert to real numbers if PetscScalar is complex */
138:       /*TODO More systematic would be to change all the function arguments to PetscScalar */
139:       PetscCall(PetscMalloc1(numVertices * spatialDim, &coordinates_arr_real));
140:       for (i = 0; i < numVertices * spatialDim; ++i) {
141:         coordinates_arr_real[i] = PetscRealPart(coordinates_arr[i]);
142:         PetscAssert(PetscImaginaryPart(coordinates_arr[i]) == 0.0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Vector of coordinates contains complex numbers but only real vectors are currently supported.");
143:       }
144:     } else coordinates_arr_real = (PetscReal *)coordinates_arr;

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

158:   /* scale coordinates - unlike in DMPlexLoad_HDF5_Internal, this can only be done after DM is populated */
159:   {
160:     PetscReal lengthScale;

162:     PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
163:     PetscCall(DMGetCoordinates(dm, &coordinates));
164:     PetscCall(VecScale(coordinates, 1.0 / lengthScale));
165:   }

167:   /* Read Labels */
168:   /* TODO: this probably does not work as elements get permuted */
169:   /* PetscCall(DMPlexLabelsLoad_HDF5_Internal(dm, viewer)); */
170:   PetscFunctionReturn(PETSC_SUCCESS);
171: }
172: #endif