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;

 13:   PetscStrrchr(path,'/',&tmp);
 14:   PetscStrcpy(name,tmp);
 15:   if (tmp != path) {
 16:     /* '/' found, name is substring of path after last occurence 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:     PetscStrcpy(path,"/");
 23:   }
 24:   return(0);
 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;

 38:   DMGetDimension(dm, &dim);
 39:   if (dim != 3) return(0);
 40:   DMPlexGetCones(dm, &cones);
 41:   DMPlexGetConeSection(dm, &cs);
 42:   DMPlexGetVTKCellHeight(dm, &cHeight);
 43:   DMPlexGetHeightStratum(dm, cHeight, &cStart, &cEnd);
 44:   for (p=cStart; p<cEnd; p++) {
 45:     PetscInt numCorners, o;

 47:     PetscSectionGetDof(cs, p, &numCorners);
 48:     PetscSectionGetOffset(cs, p, &o);
 49:     switch (numCorners) {
 50:       case 4: DMPlexInvertCell(DM_POLYTOPE_TETRAHEDRON,&cones[o]); break;
 51:       case 6: DMPlexInvertCell(DM_POLYTOPE_TRI_PRISM,&cones[o]); break;
 52:       case 8: DMPlexInvertCell(DM_POLYTOPE_HEXAHEDRON,&cones[o]); break;
 53:     }
 54:   }
 55:   return(0);
 56: }

 58: PetscErrorCode DMPlexLoad_HDF5_Xdmf_Internal(DM dm, PetscViewer viewer)
 59: {
 60:   Vec             coordinates;
 61:   IS              cells;
 62:   PetscInt        spatialDim, topoDim = -1, numCells, numVertices, NVertices, numCorners;
 63:   PetscMPIInt     rank;
 64:   MPI_Comm        comm;
 65:   PetscErrorCode  ierr;
 66:   char            topo_path[PETSC_MAX_PATH_LEN]="/viz/topology/cells", topo_name[PETSC_MAX_PATH_LEN];
 67:   char            geom_path[PETSC_MAX_PATH_LEN]="/geometry/vertices",  geom_name[PETSC_MAX_PATH_LEN];
 68:   PetscBool       seq = PETSC_FALSE, hasCellDim = PETSC_FALSE;

 71:   PetscObjectGetComm((PetscObject)dm, &comm);
 72:   MPI_Comm_rank(comm, &rank);

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

 80:   SplitPath_Private(topo_path, topo_name);
 81:   SplitPath_Private(geom_path, geom_name);
 82:   PetscInfo2(dm, "Topology group %s, name %s\n", topo_path, topo_name);
 83:   PetscInfo2(dm, "Geometry group %s, name %s\n", geom_path, geom_name);

 85:   /* Read topology */
 86:   PetscViewerHDF5PushGroup(viewer, topo_path);
 87:   ISCreate(comm, &cells);
 88:   PetscObjectSetName((PetscObject) cells, topo_name);
 89:   if (seq) {
 90:     PetscViewerHDF5ReadSizes(viewer, topo_name, NULL, &numCells);
 91:     PetscLayoutSetSize(cells->map, numCells);
 92:     numCells = !rank ? numCells : 0;
 93:     PetscLayoutSetLocalSize(cells->map, numCells);
 94:   }
 95:   ISLoad(cells, viewer);
 96:   ISGetLocalSize(cells, &numCells);
 97:   ISGetBlockSize(cells, &numCorners);
 98:   PetscViewerHDF5HasAttribute(viewer, topo_name, "cell_dim", &hasCellDim);
 99:   if (hasCellDim) {PetscViewerHDF5ReadAttribute(viewer, topo_name, "cell_dim", PETSC_INT, &topoDim);}
100:   PetscViewerHDF5PopGroup(viewer);
101:   numCells /= numCorners;

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

121:   PetscInfo4(NULL, "Loaded mesh dimensions: numCells %D numCorners %D numVertices %D spatialDim %D\n", numCells, numCorners, numVertices, spatialDim);
122:   {
123:     const PetscScalar *coordinates_arr;
124:     PetscReal         *coordinates_arr_real;
125:     const PetscInt    *cells_arr;
126:     PetscSF           sfVert = NULL;
127:     PetscInt          i;

129:     VecGetArrayRead(coordinates, &coordinates_arr);
130:     ISGetIndices(cells, &cells_arr);

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

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

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

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

165:   /* Read Labels */
166:   /* TODO: this probably does not work as elements get permuted */
167:   /* DMPlexLoadLabels_HDF5_Internal(dm, viewer); */
168:   return(0);
169: }
170: #endif