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