1 #define PETSCDM_DLL 2 #include <petsc-private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 4 #define PETSC_HAVE_CGNS 1 5 #if defined(PETSC_HAVE_CGNS) 6 #include <cgnslib.h> 7 #include <cgns_io.h> 8 #endif 9 10 #undef __FUNCT__ 11 #define __FUNCT__ "DMPlexCreateCGNS" 12 /*@ 13 DMPlexCreateCGNS - Create a DMPlex mesh from a CGNS file. 14 15 Collective on comm 16 17 Input Parameters: 18 + comm - The MPI communicator 19 . cgid - The CG id associated with a file and obtained using cg_open 20 - interpolate - Create faces and edges in the mesh 21 22 Output Parameter: 23 . dm - The DM object representing the mesh 24 25 Note: http://www.grc.nasa.gov/WWW/cgns/CGNS_docs_current/index.html 26 27 Level: beginner 28 29 .keywords: mesh,CGNS 30 .seealso: DMPlexCreate(), DMPlexCreateExodus() 31 @*/ 32 PetscErrorCode DMPlexCreateCGNS(MPI_Comm comm, PetscInt cgid, PetscBool interpolate, DM *dm) 33 { 34 #if defined(PETSC_HAVE_CGNS) 35 PetscMPIInt num_proc, rank; 36 PetscSection coordSection; 37 Vec coordinates; 38 PetscScalar *coords; 39 PetscInt coordSize, v; 40 PetscErrorCode ierr; 41 /* Read from file */ 42 char basename[CGIO_MAX_NAME_LENGTH+1]; 43 char buffer[CGIO_MAX_NAME_LENGTH+1]; 44 int dim = 0, physDim = 0, numVertices = 0, numCells = 0; 45 int nzones = 0; 46 #endif 47 48 PetscFunctionBegin; 49 #if defined(PETSC_HAVE_CGNS) 50 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 51 ierr = MPI_Comm_size(comm, &num_proc);CHKERRQ(ierr); 52 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 53 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 54 /* Open CGNS II file and read basic informations on rank 0, then broadcast to all processors */ 55 if (!rank) { 56 int nbases, z; 57 58 ierr = cg_nbases(cgid, &nbases);CHKERRQ(ierr); 59 if (nbases > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single base, not %d\n",nbases); 60 ierr = cg_base_read(cgid, 1, basename, &dim, &physDim);CHKERRQ(ierr); 61 ierr = cg_nzones(cgid, 1, &nzones);CHKERRQ(ierr); 62 for (z = 1; z <= nzones; ++z) { 63 cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */ 64 65 ierr = cg_zone_read(cgid, 1, z, buffer, sizes);CHKERRQ(ierr); 66 numVertices += sizes[0]; 67 numCells += sizes[1]; 68 } 69 } 70 ierr = MPI_Bcast(basename, CGIO_MAX_NAME_LENGTH+1, MPI_CHAR, 0, comm);CHKERRQ(ierr); 71 ierr = MPI_Bcast(&dim, 1, MPI_INT, 0, comm);CHKERRQ(ierr); 72 ierr = MPI_Bcast(&nzones, 1, MPI_INT, 0, comm);CHKERRQ(ierr); 73 ierr = PetscObjectSetName((PetscObject) *dm, basename);CHKERRQ(ierr); 74 ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr); 75 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 76 77 /* Read zone information */ 78 if (!rank) { 79 int z, c, c_loc, v, v_loc; 80 81 /* Read the cell set connectivity table and build mesh topology 82 CGNS standard requires that cells in a zone be numbered sequentially and be pairwise disjoint. */ 83 /* First set sizes */ 84 for (z = 1, c = 0; z <= nzones; ++z) { 85 ZoneType_t zonetype; 86 int nsections; 87 ElementType_t cellType; 88 cgsize_t start, end; 89 int nbndry, parentFlag; 90 PetscInt numCorners; 91 92 ierr = cg_zone_type(cgid, 1, z, &zonetype);CHKERRQ(ierr); 93 if (zonetype == Structured) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Can only handle Unstructured zones for CGNS"); 94 ierr = cg_nsections(cgid, 1, z, &nsections);CHKERRQ(ierr); 95 if (nsections > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single section, not %d\n",nsections); 96 ierr = cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);CHKERRQ(ierr); 97 /* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */ 98 if (cellType == MIXED) { 99 cgsize_t elementDataSize, *elements; 100 PetscInt off; 101 102 ierr = cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);CHKERRQ(ierr); 103 ierr = PetscMalloc(elementDataSize * sizeof(cgsize_t), &elements);CHKERRQ(ierr); 104 ierr = cg_elements_read(cgid, 1, z, 1, elements, NULL);CHKERRQ(ierr); 105 for (c_loc = start, off = 0; c_loc < end; ++c_loc, ++c) { 106 cellType = elements[off]; 107 switch (cellType) { 108 case TRI_3: numCorners = 3;break; 109 case QUAD_4: numCorners = 4;break; 110 case TETRA_4: numCorners = 4;break; 111 case HEXA_8: numCorners = 8;break; 112 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType); 113 } 114 ierr = DMPlexSetConeSize(*dm, c, numCorners);CHKERRQ(ierr); 115 off += numCorners+1; 116 } 117 ierr = PetscFree(elements);CHKERRQ(ierr); 118 } else { 119 switch (cellType) { 120 case TRI_3: numCorners = 3;break; 121 case QUAD_4: numCorners = 4;break; 122 case TETRA_4: numCorners = 4;break; 123 case HEXA_8: numCorners = 8;break; 124 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType); 125 } 126 for (c_loc = start; c_loc < end; ++c_loc, ++c) { 127 ierr = DMPlexSetConeSize(*dm, c, numCorners);CHKERRQ(ierr); 128 } 129 } 130 } 131 ierr = DMSetUp(*dm);CHKERRQ(ierr); 132 for (z = 1, c = 0; z <= nzones; ++z) { 133 ElementType_t cellType; 134 cgsize_t *elements, elementDataSize, start, end; 135 int nbndry, parentFlag; 136 PetscInt *cone, numc, numCorners, maxCorners = 27; 137 138 ierr = cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);CHKERRQ(ierr); 139 numc = end - start; 140 /* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */ 141 ierr = cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);CHKERRQ(ierr); 142 ierr = PetscMalloc2(elementDataSize,cgsize_t,&elements,maxCorners,PetscInt,&cone);CHKERRQ(ierr); 143 ierr = cg_elements_read(cgid, 1, z, 1, elements, NULL);CHKERRQ(ierr); 144 if (cellType == MIXED) { 145 /* CGNS uses Fortran-based indexing, sieve uses C-style and numbers cell first then vertices. */ 146 for (c_loc = 0, v = 0; c_loc < numc; ++c_loc, ++c) { 147 cellType = elements[v]; ++v; 148 switch (cellType) { 149 case TRI_3: numCorners = 3;break; 150 case QUAD_4: numCorners = 4;break; 151 case TETRA_4: numCorners = 4;break; 152 case HEXA_8: numCorners = 8;break; 153 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType); 154 } 155 for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) { 156 cone[v_loc] = elements[v]+numCells-1; 157 } 158 /* Tetrahedra are inverted */ 159 if (cellType == TETRA_4) { 160 PetscInt tmp = cone[0]; 161 cone[0] = cone[1]; 162 cone[1] = tmp; 163 } 164 /* Hexahedra are inverted */ 165 if (cellType == HEXA_8) { 166 PetscInt tmp = cone[1]; 167 cone[1] = cone[3]; 168 cone[3] = tmp; 169 } 170 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 171 ierr = DMPlexSetLabelValue(*dm, "zone", c, z);CHKERRQ(ierr); 172 } 173 } else { 174 switch (cellType) { 175 case TRI_3: numCorners = 3;break; 176 case QUAD_4: numCorners = 4;break; 177 case TETRA_4: numCorners = 4;break; 178 case HEXA_8: numCorners = 8;break; 179 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType); 180 } 181 182 /* CGNS uses Fortran-based indexing, sieve uses C-style and numbers cell first then vertices. */ 183 for (c_loc = 0, v = 0; c_loc < numc; ++c_loc, ++c) { 184 for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) { 185 cone[v_loc] = elements[v]+numCells-1; 186 } 187 /* Tetrahedra are inverted */ 188 if (cellType == TETRA_4) { 189 PetscInt tmp = cone[0]; 190 cone[0] = cone[1]; 191 cone[1] = tmp; 192 } 193 /* Hexahedra are inverted */ 194 if (cellType == HEXA_8) { 195 PetscInt tmp = cone[1]; 196 cone[1] = cone[3]; 197 cone[3] = tmp; 198 } 199 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 200 ierr = DMPlexSetLabelValue(*dm, "zone", c, z);CHKERRQ(ierr); 201 } 202 } 203 ierr = PetscFree2(elements,cone);CHKERRQ(ierr); 204 } 205 } 206 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 207 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 208 if (interpolate) { 209 DM idm; 210 211 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 212 /* Maintain zone label */ 213 { 214 DMLabel label; 215 216 ierr = DMPlexRemoveLabel(*dm, "zone", &label);CHKERRQ(ierr); 217 if (label) {ierr = DMPlexAddLabel(idm, label);CHKERRQ(ierr);} 218 } 219 ierr = DMDestroy(dm);CHKERRQ(ierr); 220 *dm = idm; 221 } 222 223 /* Read coordinates */ 224 ierr = DMPlexGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 225 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 226 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 227 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); 228 for (v = numCells; v < numCells+numVertices; ++v) { 229 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 230 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 231 } 232 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 233 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 234 ierr = VecCreate(comm, &coordinates);CHKERRQ(ierr); 235 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 236 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 237 ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr); 238 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 239 if (!rank) { 240 PetscInt off = 0; 241 float *x[3]; 242 int z, c, d; 243 244 ierr = PetscMalloc3(numVertices,float,&x[0],numVertices,float,&x[1],numVertices,float,&x[2]);CHKERRQ(ierr); 245 for (z = 1, c = 0; z <= nzones; ++z) { 246 DataType_t datatype; 247 cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */ 248 cgsize_t range_min[3] = {1, 1, 1}; 249 cgsize_t range_max[3] = {1, 1, 1}; 250 int ngrids, ncoords; 251 252 253 ierr = cg_zone_read(cgid, 1, z, buffer, sizes);CHKERRQ(ierr); 254 range_max[0] = sizes[0]; 255 ierr = cg_ngrids(cgid, 1, z, &ngrids);CHKERRQ(ierr); 256 if (ngrids > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single grid, not %d\n",ngrids); 257 ierr = cg_ncoords(cgid, 1, z, &ncoords);CHKERRQ(ierr); 258 if (ncoords != dim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a coordinate array for each dimension, not %d\n",ncoords); 259 for (d = 0; d < dim; ++d) { 260 ierr = cg_coord_info(cgid, 1, z, 1, &datatype, buffer);CHKERRQ(ierr); 261 ierr = cg_coord_read(cgid, 1, z, buffer, RealSingle, range_min, range_max, x[d]);CHKERRQ(ierr); 262 } 263 if (dim > 0) { 264 for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+0] = x[0][v]; 265 } 266 if (dim > 1) { 267 for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+1] = x[1][v]; 268 } 269 if (dim > 2) { 270 for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+2] = x[2][v]; 271 } 272 off += sizes[0]; 273 } 274 ierr = PetscFree3(x[0],x[1],x[2]);CHKERRQ(ierr); 275 } 276 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 277 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 278 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 279 #else 280 SETERRQ(comm, PETSC_ERR_SUP, "This method requires CGNS support. Reconfigure using --with-cgns-dir"); 281 #endif 282 PetscFunctionReturn(0); 283 } 284