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;

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

 26: /*
 27:   - invert (involute) cells of some types according to XDMF/VTK numbering of vertices in a cells
 28:   - cell type is identified using the number of vertices
 29: */
 30: static PetscErrorCode DMPlexInvertCells_XDMF_Private(DM dm)
 31: {
 32:   PetscInt     dim, *cones, cHeight, cStart, cEnd, p;
 33:   PetscSection cs;

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

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

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

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

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

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

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

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

123:   PetscCall(PetscInfo(NULL, "Loaded mesh dimensions: numCells %" PetscInt_FMT " numCorners %" PetscInt_FMT " numVertices %" PetscInt_FMT " spatialDim %" PetscInt_FMT "\n", numCells, numCorners, numVertices, spatialDim));
124:   {
125:     const PetscScalar *coordinates_arr;
126:     PetscReal         *coordinates_arr_real;
127:     const PetscInt    *cells_arr;
128:     PetscSF            sfVert = NULL;
129:     PetscInt           i;

131:     PetscCall(VecGetArrayRead(coordinates, &coordinates_arr));
132:     PetscCall(ISGetIndices(cells, &cells_arr));

134:     if (PetscDefined(USE_COMPLEX)) {
135:       /* convert to real numbers if PetscScalar is complex */
136:       /*TODO More systematic would be to change all the function arguments to PetscScalar */
137:       PetscCall(PetscMalloc1(numVertices * spatialDim, &coordinates_arr_real));
138:       for (i = 0; i < numVertices * spatialDim; ++i) {
139:         coordinates_arr_real[i] = PetscRealPart(coordinates_arr[i]);
140:         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.");
141:       }
142:     } else coordinates_arr_real = (PetscReal *)coordinates_arr;

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

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

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

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