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