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: static PetscErrorCode SplitPath_Private(char path[], char name[])
7: {
8: char *tmp;
9: size_t len;
11: PetscFunctionBegin;
12: PetscCall(PetscStrrchr(path, '/', &tmp));
13: PetscCall(PetscStrlen(tmp, &len));
14: PetscCall(PetscStrncpy(name, tmp, len + 1)); /* assuming adequate buffer */
15: if (tmp != path) {
16: /* '/' found, name is substring of path after last occurrence 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: PetscCall(PetscStrncpy(path, "/", 2)); /* assuming adequate buffer */
23: }
24: PetscFunctionReturn(PETSC_SUCCESS);
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;
36: PetscFunctionBegin;
37: PetscCall(DMGetDimension(dm, &dim));
38: if (dim != 3) PetscFunctionReturn(PETSC_SUCCESS);
39: PetscCall(DMPlexGetCones(dm, &cones));
40: PetscCall(DMPlexGetConeSection(dm, &cs));
41: PetscCall(DMPlexGetVTKCellHeight(dm, &cHeight));
42: PetscCall(DMPlexGetHeightStratum(dm, cHeight, &cStart, &cEnd));
43: for (p = cStart; p < cEnd; p++) {
44: PetscInt numCorners, o;
46: PetscCall(PetscSectionGetDof(cs, p, &numCorners));
47: PetscCall(PetscSectionGetOffset(cs, p, &o));
48: switch (numCorners) {
49: case 4:
50: PetscCall(DMPlexInvertCell(DM_POLYTOPE_TETRAHEDRON, &cones[o]));
51: break;
52: case 6:
53: PetscCall(DMPlexInvertCell(DM_POLYTOPE_TRI_PRISM, &cones[o]));
54: break;
55: case 8:
56: PetscCall(DMPlexInvertCell(DM_POLYTOPE_HEXAHEDRON, &cones[o]));
57: break;
58: }
59: }
60: PetscFunctionReturn(PETSC_SUCCESS);
61: }
63: PetscErrorCode DMPlexLoad_HDF5_Xdmf_Internal(DM dm, PetscViewer viewer)
64: {
65: Vec coordinates;
66: IS cells;
67: PetscInt spatialDim, topoDim = -1, numCells, numVertices, NVertices, numCorners;
68: PetscMPIInt rank;
69: MPI_Comm comm;
70: char topo_path[PETSC_MAX_PATH_LEN] = "/viz/topology/cells", topo_name[PETSC_MAX_PATH_LEN];
71: char geom_path[PETSC_MAX_PATH_LEN] = "/geometry/vertices", geom_name[PETSC_MAX_PATH_LEN];
72: PetscBool seq = PETSC_FALSE;
74: PetscFunctionBegin;
75: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
76: PetscCallMPI(MPI_Comm_rank(comm, &rank));
78: PetscOptionsBegin(PetscObjectComm((PetscObject)dm), ((PetscObject)dm)->prefix, "DMPlex HDF5/XDMF Loader Options", "PetscViewer");
79: PetscCall(PetscOptionsString("-dm_plex_hdf5_topology_path", "HDF5 path of topology dataset", NULL, topo_path, topo_path, sizeof(topo_path), NULL));
80: PetscCall(PetscOptionsString("-dm_plex_hdf5_geometry_path", "HDF5 path to geometry dataset", NULL, geom_path, geom_path, sizeof(geom_path), NULL));
81: PetscCall(PetscOptionsBool("-dm_plex_hdf5_force_sequential", "force sequential loading", NULL, seq, &seq, NULL));
82: PetscOptionsEnd();
84: PetscCall(SplitPath_Private(topo_path, topo_name));
85: PetscCall(SplitPath_Private(geom_path, geom_name));
86: PetscCall(PetscInfo(dm, "Topology group %s, name %s\n", topo_path, topo_name));
87: PetscCall(PetscInfo(dm, "Geometry group %s, name %s\n", geom_path, geom_name));
89: /* Read topology */
90: PetscCall(PetscViewerHDF5PushGroup(viewer, topo_path));
91: PetscCall(ISCreate(comm, &cells));
92: PetscCall(PetscObjectSetName((PetscObject)cells, topo_name));
93: if (seq) {
94: PetscCall(PetscViewerHDF5ReadSizes(viewer, topo_name, NULL, &numCells));
95: PetscCall(PetscLayoutSetSize(cells->map, numCells));
96: numCells = rank == 0 ? numCells : 0;
97: PetscCall(PetscLayoutSetLocalSize(cells->map, numCells));
98: }
99: PetscCall(ISLoad(cells, viewer));
100: PetscCall(ISGetLocalSize(cells, &numCells));
101: PetscCall(ISGetBlockSize(cells, &numCorners));
102: PetscCall(PetscViewerHDF5ReadAttribute(viewer, topo_name, "cell_dim", PETSC_INT, &topoDim, &topoDim));
103: PetscCall(PetscViewerHDF5PopGroup(viewer));
104: numCells /= numCorners;
106: /* Read geometry */
107: PetscCall(PetscViewerHDF5PushGroup(viewer, geom_path));
108: PetscCall(VecCreate(comm, &coordinates));
109: PetscCall(PetscObjectSetName((PetscObject)coordinates, geom_name));
110: if (seq) {
111: PetscCall(PetscViewerHDF5ReadSizes(viewer, geom_name, NULL, &numVertices));
112: PetscCall(PetscLayoutSetSize(coordinates->map, numVertices));
113: numVertices = rank == 0 ? numVertices : 0;
114: PetscCall(PetscLayoutSetLocalSize(coordinates->map, numVertices));
115: }
116: PetscCall(VecLoad(coordinates, viewer));
117: PetscCall(VecGetLocalSize(coordinates, &numVertices));
118: PetscCall(VecGetSize(coordinates, &NVertices));
119: PetscCall(VecGetBlockSize(coordinates, &spatialDim));
120: PetscCall(PetscViewerHDF5PopGroup(viewer));
121: numVertices /= spatialDim;
122: NVertices /= spatialDim;
124: PetscCall(PetscInfo(NULL, "Loaded mesh dimensions: numCells %" PetscInt_FMT " numCorners %" PetscInt_FMT " numVertices %" PetscInt_FMT " spatialDim %" PetscInt_FMT "\n", numCells, numCorners, numVertices, spatialDim));
125: {
126: const PetscScalar *coordinates_arr;
127: PetscReal *coordinates_arr_real;
128: const PetscInt *cells_arr;
129: PetscSF sfVert = NULL;
130: PetscInt i;
132: PetscCall(VecGetArrayRead(coordinates, &coordinates_arr));
133: PetscCall(ISGetIndices(cells, &cells_arr));
135: if (PetscDefined(USE_COMPLEX)) {
136: /* convert to real numbers if PetscScalar is complex */
137: /*TODO More systematic would be to change all the function arguments to PetscScalar */
138: PetscCall(PetscMalloc1(numVertices * spatialDim, &coordinates_arr_real));
139: for (i = 0; i < numVertices * spatialDim; ++i) {
140: coordinates_arr_real[i] = PetscRealPart(coordinates_arr[i]);
141: 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.");
142: }
143: } else coordinates_arr_real = (PetscReal *)coordinates_arr;
145: PetscCall(DMSetDimension(dm, topoDim < 0 ? spatialDim : topoDim));
146: PetscCall(DMPlexBuildFromCellListParallel(dm, numCells, numVertices, NVertices, numCorners, cells_arr, &sfVert, NULL));
147: PetscCall(DMPlexInvertCells_XDMF_Private(dm));
148: PetscCall(DMPlexBuildCoordinatesFromCellListParallel(dm, spatialDim, sfVert, coordinates_arr_real));
149: PetscCall(VecRestoreArrayRead(coordinates, &coordinates_arr));
150: PetscCall(ISRestoreIndices(cells, &cells_arr));
151: PetscCall(PetscSFDestroy(&sfVert));
152: if (PetscDefined(USE_COMPLEX)) PetscCall(PetscFree(coordinates_arr_real));
153: }
154: PetscCall(ISDestroy(&cells));
155: PetscCall(VecDestroy(&coordinates));
157: /* scale coordinates - unlike in DMPlexLoad_HDF5_Internal, this can only be done after DM is populated */
158: {
159: PetscReal lengthScale;
161: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
162: PetscCall(DMGetCoordinates(dm, &coordinates));
163: PetscCall(VecScale(coordinates, 1.0 / lengthScale));
164: }
166: /* Read Labels */
167: /* TODO: this probably does not work as elements get permuted */
168: /* PetscCall(DMPlexLabelsLoad_HDF5_Internal(dm, viewer)); */
169: PetscFunctionReturn(PETSC_SUCCESS);
170: }