1 #define PETSCDM_DLL 2 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 4 #undef I /* Very old CGNS stupidly uses I as a variable, which fails when using complex. Curse you idiot package managers */ 5 #if defined(PETSC_HAVE_CGNS) 6 #include <cgnslib.h> 7 #include <cgns_io.h> 8 #endif 9 #if !defined(CGNS_ENUMT) 10 #define CGNS_ENUMT(a) a 11 #endif 12 #if !defined(CGNS_ENUMV) 13 #define CGNS_ENUMV(a) a 14 #endif 15 16 /*@C 17 DMPlexCreateCGNS - Create a DMPlex mesh from a CGNS file. 18 19 Collective on comm 20 21 Input Parameters: 22 + comm - The MPI communicator 23 . filename - The name of the CGNS file 24 - interpolate - Create faces and edges in the mesh 25 26 Output Parameter: 27 . dm - The DM object representing the mesh 28 29 Note: http://www.grc.nasa.gov/WWW/cgns/CGNS_docs_current/index.html 30 31 Level: beginner 32 33 .keywords: mesh,CGNS 34 .seealso: DMPlexCreate(), DMPlexCreateCGNS(), DMPlexCreateExodus() 35 @*/ 36 PetscErrorCode DMPlexCreateCGNSFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 37 { 38 PetscMPIInt rank; 39 PetscErrorCode ierr; 40 #if defined(PETSC_HAVE_CGNS) 41 int cgid = -1; 42 #endif 43 44 PetscFunctionBegin; 45 PetscValidCharPointer(filename, 2); 46 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 47 #if defined(PETSC_HAVE_CGNS) 48 if (!rank) { 49 ierr = cg_open(filename, CG_MODE_READ, &cgid);CHKERRQ(ierr); 50 if (cgid <= 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "cg_open(\"%s\",...) did not return a valid file ID", filename); 51 } 52 ierr = DMPlexCreateCGNS(comm, cgid, interpolate, dm);CHKERRQ(ierr); 53 if (!rank) {ierr = cg_close(cgid);CHKERRQ(ierr);} 54 #else 55 SETERRQ(comm, PETSC_ERR_SUP, "Loading meshes requires CGNS support. Reconfigure using --with-cgns-dir"); 56 #endif 57 PetscFunctionReturn(0); 58 } 59 60 /*@ 61 DMPlexCreateCGNS - Create a DMPlex mesh from a CGNS file ID. 62 63 Collective on comm 64 65 Input Parameters: 66 + comm - The MPI communicator 67 . cgid - The CG id associated with a file and obtained using cg_open 68 - interpolate - Create faces and edges in the mesh 69 70 Output Parameter: 71 . dm - The DM object representing the mesh 72 73 Note: http://www.grc.nasa.gov/WWW/cgns/CGNS_docs_current/index.html 74 75 Level: beginner 76 77 .keywords: mesh,CGNS 78 .seealso: DMPlexCreate(), DMPlexCreateExodus() 79 @*/ 80 PetscErrorCode DMPlexCreateCGNS(MPI_Comm comm, PetscInt cgid, PetscBool interpolate, DM *dm) 81 { 82 #if defined(PETSC_HAVE_CGNS) 83 PetscMPIInt num_proc, rank; 84 PetscSection coordSection; 85 Vec coordinates; 86 PetscScalar *coords; 87 PetscInt *cellStart, *vertStart; 88 PetscInt coordSize, v; 89 PetscErrorCode ierr; 90 /* Read from file */ 91 char basename[CGIO_MAX_NAME_LENGTH+1]; 92 char buffer[CGIO_MAX_NAME_LENGTH+1]; 93 int dim = 0, physDim = 0, numVertices = 0, numCells = 0; 94 int nzones = 0; 95 #endif 96 97 PetscFunctionBegin; 98 #if defined(PETSC_HAVE_CGNS) 99 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 100 ierr = MPI_Comm_size(comm, &num_proc);CHKERRQ(ierr); 101 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 102 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 103 /* Open CGNS II file and read basic informations on rank 0, then broadcast to all processors */ 104 if (!rank) { 105 int nbases, z; 106 107 ierr = cg_nbases(cgid, &nbases);CHKERRQ(ierr); 108 if (nbases > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single base, not %d\n",nbases); 109 ierr = cg_base_read(cgid, 1, basename, &dim, &physDim);CHKERRQ(ierr); 110 ierr = cg_nzones(cgid, 1, &nzones);CHKERRQ(ierr); 111 ierr = PetscCalloc2(nzones+1, &cellStart, nzones+1, &vertStart);CHKERRQ(ierr); 112 for (z = 1; z <= nzones; ++z) { 113 cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */ 114 115 ierr = cg_zone_read(cgid, 1, z, buffer, sizes);CHKERRQ(ierr); 116 numVertices += sizes[0]; 117 numCells += sizes[1]; 118 cellStart[z] += sizes[1] + cellStart[z-1]; 119 vertStart[z] += sizes[0] + vertStart[z-1]; 120 } 121 for (z = 1; z <= nzones; ++z) { 122 vertStart[z] += numCells; 123 } 124 } 125 ierr = MPI_Bcast(basename, CGIO_MAX_NAME_LENGTH+1, MPI_CHAR, 0, comm);CHKERRQ(ierr); 126 ierr = MPI_Bcast(&dim, 1, MPI_INT, 0, comm);CHKERRQ(ierr); 127 ierr = MPI_Bcast(&nzones, 1, MPI_INT, 0, comm);CHKERRQ(ierr); 128 ierr = PetscObjectSetName((PetscObject) *dm, basename);CHKERRQ(ierr); 129 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 130 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 131 132 /* Read zone information */ 133 if (!rank) { 134 int z, c, c_loc, v, v_loc; 135 136 /* Read the cell set connectivity table and build mesh topology 137 CGNS standard requires that cells in a zone be numbered sequentially and be pairwise disjoint. */ 138 /* First set sizes */ 139 for (z = 1, c = 0; z <= nzones; ++z) { 140 CGNS_ENUMT( ZoneType_t ) zonetype; 141 int nsections; 142 CGNS_ENUMT( ElementType_t ) cellType; 143 cgsize_t start, end; 144 int nbndry, parentFlag; 145 PetscInt numCorners; 146 147 ierr = cg_zone_type(cgid, 1, z, &zonetype);CHKERRQ(ierr); 148 if (zonetype == CGNS_ENUMV( Structured )) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Can only handle Unstructured zones for CGNS"); 149 ierr = cg_nsections(cgid, 1, z, &nsections);CHKERRQ(ierr); 150 if (nsections > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single section, not %d\n",nsections); 151 ierr = cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);CHKERRQ(ierr); 152 /* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */ 153 if (cellType == CGNS_ENUMV( MIXED )) { 154 cgsize_t elementDataSize, *elements; 155 PetscInt off; 156 157 ierr = cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);CHKERRQ(ierr); 158 ierr = PetscMalloc1(elementDataSize, &elements);CHKERRQ(ierr); 159 ierr = cg_elements_read(cgid, 1, z, 1, elements, NULL);CHKERRQ(ierr); 160 for (c_loc = start, off = 0; c_loc <= end; ++c_loc, ++c) { 161 switch (elements[off]) { 162 case CGNS_ENUMV( TRI_3 ): numCorners = 3;break; 163 case CGNS_ENUMV( QUAD_4 ): numCorners = 4;break; 164 case CGNS_ENUMV( TETRA_4 ): numCorners = 4;break; 165 case CGNS_ENUMV( HEXA_8 ): numCorners = 8;break; 166 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) elements[off]); 167 } 168 ierr = DMPlexSetConeSize(*dm, c, numCorners);CHKERRQ(ierr); 169 off += numCorners+1; 170 } 171 ierr = PetscFree(elements);CHKERRQ(ierr); 172 } else { 173 switch (cellType) { 174 case CGNS_ENUMV( TRI_3 ): numCorners = 3;break; 175 case CGNS_ENUMV( QUAD_4 ): numCorners = 4;break; 176 case CGNS_ENUMV( TETRA_4 ): numCorners = 4;break; 177 case CGNS_ENUMV( HEXA_8 ): numCorners = 8;break; 178 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType); 179 } 180 for (c_loc = start; c_loc <= end; ++c_loc, ++c) { 181 ierr = DMPlexSetConeSize(*dm, c, numCorners);CHKERRQ(ierr); 182 } 183 } 184 } 185 ierr = DMSetUp(*dm);CHKERRQ(ierr); 186 for (z = 1, c = 0; z <= nzones; ++z) { 187 CGNS_ENUMT( ElementType_t ) cellType; 188 cgsize_t *elements, elementDataSize, start, end; 189 int nbndry, parentFlag; 190 PetscInt *cone, numc, numCorners, maxCorners = 27; 191 192 ierr = cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);CHKERRQ(ierr); 193 numc = end - start; 194 /* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */ 195 ierr = cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);CHKERRQ(ierr); 196 ierr = PetscMalloc2(elementDataSize,&elements,maxCorners,&cone);CHKERRQ(ierr); 197 ierr = cg_elements_read(cgid, 1, z, 1, elements, NULL);CHKERRQ(ierr); 198 if (cellType == CGNS_ENUMV( MIXED )) { 199 /* CGNS uses Fortran-based indexing, DMPlex uses C-style and numbers cell first then vertices. */ 200 for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) { 201 switch (elements[v]) { 202 case CGNS_ENUMV( TRI_3 ): numCorners = 3;break; 203 case CGNS_ENUMV( QUAD_4 ): numCorners = 4;break; 204 case CGNS_ENUMV( TETRA_4 ): numCorners = 4;break; 205 case CGNS_ENUMV( HEXA_8 ): numCorners = 8;break; 206 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) elements[v]); 207 } 208 ++v; 209 for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) { 210 cone[v_loc] = elements[v]+numCells-1; 211 } 212 /* Tetrahedra are inverted */ 213 if (elements[v] == CGNS_ENUMV( TETRA_4 )) { 214 PetscInt tmp = cone[0]; 215 cone[0] = cone[1]; 216 cone[1] = tmp; 217 } 218 /* Hexahedra are inverted */ 219 if (elements[v] == CGNS_ENUMV( HEXA_8 )) { 220 PetscInt tmp = cone[5]; 221 cone[5] = cone[7]; 222 cone[7] = tmp; 223 } 224 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 225 ierr = DMSetLabelValue(*dm, "zone", c, z);CHKERRQ(ierr); 226 } 227 } else { 228 switch (cellType) { 229 case CGNS_ENUMV( TRI_3 ): numCorners = 3;break; 230 case CGNS_ENUMV( QUAD_4 ): numCorners = 4;break; 231 case CGNS_ENUMV( TETRA_4 ): numCorners = 4;break; 232 case CGNS_ENUMV( HEXA_8 ): numCorners = 8;break; 233 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType); 234 } 235 236 /* CGNS uses Fortran-based indexing, DMPlex uses C-style and numbers cell first then vertices. */ 237 for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) { 238 for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) { 239 cone[v_loc] = elements[v]+numCells-1; 240 } 241 /* Tetrahedra are inverted */ 242 if (cellType == CGNS_ENUMV( TETRA_4 )) { 243 PetscInt tmp = cone[0]; 244 cone[0] = cone[1]; 245 cone[1] = tmp; 246 } 247 /* Hexahedra are inverted, and they give the top first */ 248 if (cellType == CGNS_ENUMV( HEXA_8 )) { 249 PetscInt tmp = cone[5]; 250 cone[5] = cone[7]; 251 cone[7] = tmp; 252 } 253 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 254 ierr = DMSetLabelValue(*dm, "zone", c, z);CHKERRQ(ierr); 255 } 256 } 257 ierr = PetscFree2(elements,cone);CHKERRQ(ierr); 258 } 259 } 260 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 261 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 262 if (interpolate) { 263 DM idm = NULL; 264 265 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 266 /* Maintain zone label */ 267 { 268 DMLabel label; 269 270 ierr = DMRemoveLabel(*dm, "zone", &label);CHKERRQ(ierr); 271 if (label) {ierr = DMAddLabel(idm, label);CHKERRQ(ierr);} 272 } 273 ierr = DMDestroy(dm);CHKERRQ(ierr); 274 *dm = idm; 275 } 276 277 /* Read coordinates */ 278 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 279 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 280 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 281 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); 282 for (v = numCells; v < numCells+numVertices; ++v) { 283 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 284 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 285 } 286 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 287 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 288 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 289 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 290 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 291 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 292 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 293 if (!rank) { 294 PetscInt off = 0; 295 float *x[3]; 296 int z, d; 297 298 ierr = PetscMalloc3(numVertices,&x[0],numVertices,&x[1],numVertices,&x[2]);CHKERRQ(ierr); 299 for (z = 1; z <= nzones; ++z) { 300 CGNS_ENUMT( DataType_t ) datatype; 301 cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */ 302 cgsize_t range_min[3] = {1, 1, 1}; 303 cgsize_t range_max[3] = {1, 1, 1}; 304 int ngrids, ncoords; 305 306 307 ierr = cg_zone_read(cgid, 1, z, buffer, sizes);CHKERRQ(ierr); 308 range_max[0] = sizes[0]; 309 ierr = cg_ngrids(cgid, 1, z, &ngrids);CHKERRQ(ierr); 310 if (ngrids > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single grid, not %d\n",ngrids); 311 ierr = cg_ncoords(cgid, 1, z, &ncoords);CHKERRQ(ierr); 312 if (ncoords != dim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a coordinate array for each dimension, not %d\n",ncoords); 313 for (d = 0; d < dim; ++d) { 314 ierr = cg_coord_info(cgid, 1, z, 1+d, &datatype, buffer);CHKERRQ(ierr); 315 ierr = cg_coord_read(cgid, 1, z, buffer, CGNS_ENUMV( RealSingle ), range_min, range_max, x[d]);CHKERRQ(ierr); 316 } 317 if (dim > 0) { 318 for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+0] = x[0][v]; 319 } 320 if (dim > 1) { 321 for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+1] = x[1][v]; 322 } 323 if (dim > 2) { 324 for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+2] = x[2][v]; 325 } 326 off += sizes[0]; 327 } 328 ierr = PetscFree3(x[0],x[1],x[2]);CHKERRQ(ierr); 329 } 330 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 331 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 332 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 333 /* Read boundary conditions */ 334 if (!rank) { 335 DMLabel label; 336 CGNS_ENUMT( BCType_t ) bctype; 337 CGNS_ENUMT( DataType_t ) datatype; 338 CGNS_ENUMT( PointSetType_t ) pointtype; 339 cgsize_t *points; 340 PetscReal *normals; 341 int normal[3]; 342 char *bcname = buffer; 343 cgsize_t npoints, nnormals; 344 int z, nbc, bc, c, ndatasets; 345 346 for (z = 1; z <= nzones; ++z) { 347 ierr = cg_nbocos(cgid, 1, z, &nbc);CHKERRQ(ierr); 348 for (bc = 1; bc <= nbc; ++bc) { 349 ierr = cg_boco_info(cgid, 1, z, bc, bcname, &bctype, &pointtype, &npoints, normal, &nnormals, &datatype, &ndatasets);CHKERRQ(ierr); 350 ierr = DMCreateLabel(*dm, bcname);CHKERRQ(ierr); 351 ierr = DMGetLabel(*dm, bcname, &label);CHKERRQ(ierr); 352 ierr = PetscMalloc2(npoints, &points, nnormals, &normals);CHKERRQ(ierr); 353 ierr = cg_boco_read(cgid, 1, z, bc, points, (void *) normals);CHKERRQ(ierr); 354 if (pointtype == CGNS_ENUMV( ElementRange )) { 355 /* Range of cells: assuming half-open interval since the documentation sucks */ 356 for (c = points[0]; c < points[1]; ++c) { 357 ierr = DMLabelSetValue(label, c - cellStart[z-1], 1);CHKERRQ(ierr); 358 } 359 } else if (pointtype == CGNS_ENUMV( ElementList )) { 360 /* List of cells */ 361 for (c = 0; c < npoints; ++c) { 362 ierr = DMLabelSetValue(label, points[c] - cellStart[z-1], 1);CHKERRQ(ierr); 363 } 364 } else if (pointtype == CGNS_ENUMV( PointRange )) { 365 CGNS_ENUMT( GridLocation_t ) gridloc; 366 367 /* List of points: Oh please, someone get the CGNS developers away from a computer. This is unconscionable. */ 368 ierr = cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end");CHKERRQ(ierr); 369 ierr = cg_gridlocation_read(&gridloc);CHKERRQ(ierr); 370 /* Range of points: assuming half-open interval since the documentation sucks */ 371 for (c = points[0]; c < points[1]; ++c) { 372 if (gridloc == CGNS_ENUMV( Vertex )) {ierr = DMLabelSetValue(label, c - vertStart[z-1], 1);CHKERRQ(ierr);} 373 else {ierr = DMLabelSetValue(label, c - cellStart[z-1], 1);CHKERRQ(ierr);} 374 } 375 } else if (pointtype == CGNS_ENUMV( PointList )) { 376 CGNS_ENUMT( GridLocation_t ) gridloc; 377 378 /* List of points: Oh please, someone get the CGNS developers away from a computer. This is unconscionable. */ 379 ierr = cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end"); 380 ierr = cg_gridlocation_read(&gridloc); 381 for (c = 0; c < npoints; ++c) { 382 if (gridloc == CGNS_ENUMV( Vertex )) {ierr = DMLabelSetValue(label, points[c] - vertStart[z-1], 1);CHKERRQ(ierr);} 383 else {ierr = DMLabelSetValue(label, points[c] - cellStart[z-1], 1);CHKERRQ(ierr);} 384 } 385 } else SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported point set type %d", (int) pointtype); 386 ierr = PetscFree2(points, normals);CHKERRQ(ierr); 387 } 388 } 389 ierr = PetscFree2(cellStart, vertStart);CHKERRQ(ierr); 390 } 391 #else 392 SETERRQ(comm, PETSC_ERR_SUP, "This method requires CGNS support. Reconfigure using --with-cgns-dir"); 393 #endif 394 PetscFunctionReturn(0); 395 } 396