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: PetscStrrchr(path,'/',&tmp);
12: PetscStrcpy(name,tmp);
13: if (tmp != path) {
14: /* '/' found, name is substring of path after last occurence of '/'. */
15: /* Trim the '/name' part from path just by inserting null character. */
16: tmp--;
17: *tmp = '\0';
18: } else {
19: /* '/' not found, name = path, path = "/". */
20: PetscStrcpy(path,"/");
21: }
22: return 0;
23: }
25: /*
26: - invert (involute) cells of some types according to XDMF/VTK numbering of vertices in a cells
27: - cell type is identified using the number of vertices
28: */
29: static PetscErrorCode DMPlexInvertCells_XDMF_Private(DM dm)
30: {
31: PetscInt dim, *cones, cHeight, cStart, cEnd, p;
32: PetscSection cs;
34: DMGetDimension(dm, &dim);
35: if (dim != 3) return 0;
36: DMPlexGetCones(dm, &cones);
37: DMPlexGetConeSection(dm, &cs);
38: DMPlexGetVTKCellHeight(dm, &cHeight);
39: DMPlexGetHeightStratum(dm, cHeight, &cStart, &cEnd);
40: for (p=cStart; p<cEnd; p++) {
41: PetscInt numCorners, o;
43: PetscSectionGetDof(cs, p, &numCorners);
44: PetscSectionGetOffset(cs, p, &o);
45: switch (numCorners) {
46: case 4: DMPlexInvertCell(DM_POLYTOPE_TETRAHEDRON,&cones[o]); break;
47: case 6: DMPlexInvertCell(DM_POLYTOPE_TRI_PRISM,&cones[o]); break;
48: case 8: DMPlexInvertCell(DM_POLYTOPE_HEXAHEDRON,&cones[o]); break;
49: }
50: }
51: return 0;
52: }
54: PetscErrorCode DMPlexLoad_HDF5_Xdmf_Internal(DM dm, PetscViewer viewer)
55: {
56: Vec coordinates;
57: IS cells;
58: PetscInt spatialDim, topoDim = -1, numCells, numVertices, NVertices, numCorners;
59: PetscMPIInt rank;
60: MPI_Comm comm;
61: PetscErrorCode ierr;
62: char topo_path[PETSC_MAX_PATH_LEN]="/viz/topology/cells", topo_name[PETSC_MAX_PATH_LEN];
63: char geom_path[PETSC_MAX_PATH_LEN]="/geometry/vertices", geom_name[PETSC_MAX_PATH_LEN];
64: PetscBool seq = PETSC_FALSE;
66: PetscObjectGetComm((PetscObject)dm, &comm);
67: MPI_Comm_rank(comm, &rank);
69: PetscOptionsBegin(PetscObjectComm((PetscObject)dm),((PetscObject)dm)->prefix,"DMPlex HDF5/XDMF Loader Options","PetscViewer");
70: PetscOptionsString("-dm_plex_hdf5_topology_path","HDF5 path of topology dataset",NULL,topo_path,topo_path,sizeof(topo_path),NULL);
71: PetscOptionsString("-dm_plex_hdf5_geometry_path","HDF5 path to geometry dataset",NULL,geom_path,geom_path,sizeof(geom_path),NULL);
72: PetscOptionsBool("-dm_plex_hdf5_force_sequential","force sequential loading",NULL,seq,&seq,NULL);
73: PetscOptionsEnd();
75: SplitPath_Private(topo_path, topo_name);
76: SplitPath_Private(geom_path, geom_name);
77: PetscInfo(dm, "Topology group %s, name %s\n", topo_path, topo_name);
78: PetscInfo(dm, "Geometry group %s, name %s\n", geom_path, geom_name);
80: /* Read topology */
81: PetscViewerHDF5PushGroup(viewer, topo_path);
82: ISCreate(comm, &cells);
83: PetscObjectSetName((PetscObject) cells, topo_name);
84: if (seq) {
85: PetscViewerHDF5ReadSizes(viewer, topo_name, NULL, &numCells);
86: PetscLayoutSetSize(cells->map, numCells);
87: numCells = rank == 0 ? numCells : 0;
88: PetscLayoutSetLocalSize(cells->map, numCells);
89: }
90: ISLoad(cells, viewer);
91: ISGetLocalSize(cells, &numCells);
92: ISGetBlockSize(cells, &numCorners);
93: PetscViewerHDF5ReadAttribute(viewer, topo_name, "cell_dim", PETSC_INT, &topoDim, &topoDim);
94: PetscViewerHDF5PopGroup(viewer);
95: numCells /= numCorners;
97: /* Read geometry */
98: PetscViewerHDF5PushGroup(viewer, geom_path);
99: VecCreate(comm, &coordinates);
100: PetscObjectSetName((PetscObject) coordinates, geom_name);
101: if (seq) {
102: PetscViewerHDF5ReadSizes(viewer, geom_name, NULL, &numVertices);
103: PetscLayoutSetSize(coordinates->map, numVertices);
104: numVertices = rank == 0 ? numVertices : 0;
105: PetscLayoutSetLocalSize(coordinates->map, numVertices);
106: }
107: VecLoad(coordinates, viewer);
108: VecGetLocalSize(coordinates, &numVertices);
109: VecGetSize(coordinates, &NVertices);
110: VecGetBlockSize(coordinates, &spatialDim);
111: PetscViewerHDF5PopGroup(viewer);
112: numVertices /= spatialDim;
113: NVertices /= spatialDim;
115: PetscInfo(NULL, "Loaded mesh dimensions: numCells %D numCorners %D numVertices %D spatialDim %D\n", numCells, numCorners, numVertices, spatialDim);
116: {
117: const PetscScalar *coordinates_arr;
118: PetscReal *coordinates_arr_real;
119: const PetscInt *cells_arr;
120: PetscSF sfVert = NULL;
121: PetscInt i;
123: VecGetArrayRead(coordinates, &coordinates_arr);
124: ISGetIndices(cells, &cells_arr);
126: if (PetscDefined(USE_COMPLEX)) {
127: /* convert to real numbers if PetscScalar is complex */
128: /*TODO More systematic would be to change all the function arguments to PetscScalar */
129: PetscMalloc1(numVertices*spatialDim, &coordinates_arr_real);
130: for (i = 0; i < numVertices*spatialDim; ++i) {
131: coordinates_arr_real[i] = PetscRealPart(coordinates_arr[i]);
132: if (PetscUnlikelyDebug(PetscImaginaryPart(coordinates_arr[i]))) {
133: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Vector of coordinates contains complex numbers but only real vectors are currently supported.");
134: }
135: }
136: } else coordinates_arr_real = (PetscReal*)coordinates_arr;
138: DMSetDimension(dm, topoDim < 0 ? spatialDim : topoDim);
139: DMPlexBuildFromCellListParallel(dm, numCells, numVertices, NVertices, numCorners, cells_arr, &sfVert, NULL);
140: DMPlexInvertCells_XDMF_Private(dm);
141: DMPlexBuildCoordinatesFromCellListParallel(dm, spatialDim, sfVert, coordinates_arr_real);
142: VecRestoreArrayRead(coordinates, &coordinates_arr);
143: ISRestoreIndices(cells, &cells_arr);
144: PetscSFDestroy(&sfVert);
145: if (PetscDefined(USE_COMPLEX)) PetscFree(coordinates_arr_real);
146: }
147: ISDestroy(&cells);
148: VecDestroy(&coordinates);
150: /* scale coordinates - unlike in DMPlexLoad_HDF5_Internal, this can only be done after DM is populated */
151: {
152: PetscReal lengthScale;
154: DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale);
155: DMGetCoordinates(dm, &coordinates);
156: VecScale(coordinates, 1.0/lengthScale);
157: }
159: /* Read Labels */
160: /* TODO: this probably does not work as elements get permuted */
161: /* DMPlexLabelsLoad_HDF5_Internal(dm, viewer); */
162: return 0;
163: }
164: #endif