1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petsc/private/viewercgnsimpl.h> 3 4 #include <pcgnslib.h> 5 #include <cgns_io.h> 6 7 #if !defined(CGNS_ENUMT) 8 #define CGNS_ENUMT(a) a 9 #endif 10 #if !defined(CGNS_ENUMV) 11 #define CGNS_ENUMV(a) a 12 #endif 13 // Permute plex closure ordering to CGNS 14 static PetscErrorCode DMPlexCGNSGetPermutation_Internal(DMPolytopeType cell_type, PetscInt closure_size, CGNS_ENUMT(ElementType_t) * element_type, const int **perm) 15 { 16 CGNS_ENUMT(ElementType_t) element_type_tmp; 17 18 // https://cgns.github.io/CGNS_docs_current/sids/conv.html#unstructgrid 19 static const int bar_2[2] = {0, 1}; 20 static const int bar_3[3] = {1, 2, 0}; 21 static const int bar_4[4] = {2, 3, 0, 1}; 22 static const int bar_5[5] = {3, 4, 0, 1, 2}; 23 static const int tri_3[3] = {0, 1, 2}; 24 static const int tri_6[6] = {3, 4, 5, 0, 1, 2}; 25 static const int tri_10[10] = {7, 8, 9, 1, 2, 3, 4, 5, 6, 0}; 26 static const int quad_4[4] = {0, 1, 2, 3}; 27 static const int quad_9[9] = { 28 5, 6, 7, 8, // vertices 29 1, 2, 3, 4, // edges 30 0, // center 31 }; 32 static const int quad_16[] = { 33 12, 13, 14, 15, // vertices 34 4, 5, 6, 7, 8, 9, 10, 11, // edges 35 0, 1, 3, 2, // centers 36 }; 37 static const int quad_25[] = { 38 21, 22, 23, 24, // vertices 39 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, // edges 40 0, 1, 2, 5, 8, 7, 6, 3, 4, // centers 41 }; 42 static const int tetra_4[4] = {0, 2, 1, 3}; 43 static const int tetra_10[10] = {6, 8, 7, 9, 2, 1, 0, 3, 5, 4}; 44 static const int tetra_20[20] = { 45 16, 18, 17, 19, // vertices 46 9, 8, 7, 6, 5, 4, // bottom edges 47 10, 11, 14, 15, 13, 12, // side edges 48 0, 2, 3, 1, // faces 49 }; 50 static const int hexa_8[8] = {0, 3, 2, 1, 4, 5, 6, 7}; 51 static const int hexa_27[27] = { 52 19, 22, 21, 20, 23, 24, 25, 26, // vertices 53 10, 9, 8, 7, // bottom edges 54 16, 15, 18, 17, // mid edges 55 11, 12, 13, 14, // top edges 56 1, 3, 5, 4, 6, 2, // faces 57 0, // center 58 }; 59 static const int hexa_64[64] = { 60 // debug with $PETSC_ARCH/tests/dm/impls/plex/tests/ex49 -dm_plex_simplex 0 -dm_plex_dim 3 -dm_plex_box_faces 1,1,1 -dm_coord_petscspace_degree 3 61 56, 59, 58, 57, 60, 61, 62, 63, // vertices 62 39, 38, 37, 36, 35, 34, 33, 32, // bottom edges 63 51, 50, 48, 49, 52, 53, 55, 54, // mid edges; Paraview needs edge 21-22 swapped with 23-24 64 40, 41, 42, 43, 44, 45, 46, 47, // top edges 65 8, 10, 11, 9, // z-minus face 66 16, 17, 19, 18, // y-minus face 67 24, 25, 27, 26, // x-plus face 68 20, 21, 23, 22, // y-plus face 69 30, 28, 29, 31, // x-minus face 70 12, 13, 15, 14, // z-plus face 71 0, 1, 3, 2, 4, 5, 7, 6, // center 72 }; 73 74 PetscFunctionBegin; 75 element_type_tmp = CGNS_ENUMV(ElementTypeNull); 76 *perm = NULL; 77 switch (cell_type) { 78 case DM_POLYTOPE_SEGMENT: 79 switch (closure_size) { 80 case 2: 81 element_type_tmp = CGNS_ENUMV(BAR_2); 82 *perm = bar_2; 83 case 3: 84 element_type_tmp = CGNS_ENUMV(BAR_3); 85 *perm = bar_3; 86 case 4: 87 element_type_tmp = CGNS_ENUMV(BAR_4); 88 *perm = bar_4; 89 break; 90 case 5: 91 element_type_tmp = CGNS_ENUMV(BAR_5); 92 *perm = bar_5; 93 break; 94 default: 95 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cell type %s with closure size %" PetscInt_FMT, DMPolytopeTypes[cell_type], closure_size); 96 } 97 break; 98 case DM_POLYTOPE_TRIANGLE: 99 switch (closure_size) { 100 case 3: 101 element_type_tmp = CGNS_ENUMV(TRI_3); 102 *perm = tri_3; 103 break; 104 case 6: 105 element_type_tmp = CGNS_ENUMV(TRI_6); 106 *perm = tri_6; 107 break; 108 case 10: 109 element_type_tmp = CGNS_ENUMV(TRI_10); 110 *perm = tri_10; 111 break; 112 default: 113 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cell type %s with closure size %" PetscInt_FMT, DMPolytopeTypes[cell_type], closure_size); 114 } 115 break; 116 case DM_POLYTOPE_QUADRILATERAL: 117 switch (closure_size) { 118 case 4: 119 element_type_tmp = CGNS_ENUMV(QUAD_4); 120 *perm = quad_4; 121 break; 122 case 9: 123 element_type_tmp = CGNS_ENUMV(QUAD_9); 124 *perm = quad_9; 125 break; 126 case 16: 127 element_type_tmp = CGNS_ENUMV(QUAD_16); 128 *perm = quad_16; 129 break; 130 case 25: 131 element_type_tmp = CGNS_ENUMV(QUAD_25); 132 *perm = quad_25; 133 break; 134 default: 135 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cell type %s with closure size %" PetscInt_FMT, DMPolytopeTypes[cell_type], closure_size); 136 } 137 break; 138 case DM_POLYTOPE_TETRAHEDRON: 139 switch (closure_size) { 140 case 4: 141 element_type_tmp = CGNS_ENUMV(TETRA_4); 142 *perm = tetra_4; 143 break; 144 case 10: 145 element_type_tmp = CGNS_ENUMV(TETRA_10); 146 *perm = tetra_10; 147 break; 148 case 20: 149 element_type_tmp = CGNS_ENUMV(TETRA_20); 150 *perm = tetra_20; 151 break; 152 default: 153 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cell type %s with closure size %" PetscInt_FMT, DMPolytopeTypes[cell_type], closure_size); 154 } 155 break; 156 case DM_POLYTOPE_HEXAHEDRON: 157 switch (closure_size) { 158 case 8: 159 element_type_tmp = CGNS_ENUMV(HEXA_8); 160 *perm = hexa_8; 161 break; 162 case 27: 163 element_type_tmp = CGNS_ENUMV(HEXA_27); 164 *perm = hexa_27; 165 break; 166 case 64: 167 element_type_tmp = CGNS_ENUMV(HEXA_64); 168 *perm = hexa_64; 169 break; 170 default: 171 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cell type %s with closure size %" PetscInt_FMT, DMPolytopeTypes[cell_type], closure_size); 172 } 173 break; 174 default: 175 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cell type %s with closure size %" PetscInt_FMT, DMPolytopeTypes[cell_type], closure_size); 176 } 177 if (element_type) *element_type = element_type_tmp; 178 PetscFunctionReturn(PETSC_SUCCESS); 179 } 180 181 /* 182 Input Parameters: 183 + cellType - The CGNS-defined element type 184 185 Output Parameters: 186 + dmcelltype - The equivalent DMPolytopeType for the cellType 187 . numCorners - Number of corners of the polytope 188 - dim - The topological dimension of the polytope 189 190 CGNS elements defined in: https://cgns.github.io/CGNS_docs_current/sids/conv.html#unstructgrid 191 */ 192 static inline PetscErrorCode CGNSElementTypeGetTopologyInfo(CGNS_ENUMT(ElementType_t) cellType, DMPolytopeType *dmcelltype, PetscInt *numCorners, PetscInt *dim) 193 { 194 DMPolytopeType _dmcelltype; 195 196 PetscFunctionBeginUser; 197 switch (cellType) { 198 case CGNS_ENUMV(BAR_2): 199 case CGNS_ENUMV(BAR_3): 200 case CGNS_ENUMV(BAR_4): 201 case CGNS_ENUMV(BAR_5): 202 _dmcelltype = DM_POLYTOPE_SEGMENT; 203 break; 204 case CGNS_ENUMV(TRI_3): 205 case CGNS_ENUMV(TRI_6): 206 case CGNS_ENUMV(TRI_9): 207 case CGNS_ENUMV(TRI_10): 208 case CGNS_ENUMV(TRI_12): 209 case CGNS_ENUMV(TRI_15): 210 _dmcelltype = DM_POLYTOPE_TRIANGLE; 211 break; 212 case CGNS_ENUMV(QUAD_4): 213 case CGNS_ENUMV(QUAD_8): 214 case CGNS_ENUMV(QUAD_9): 215 case CGNS_ENUMV(QUAD_12): 216 case CGNS_ENUMV(QUAD_16): 217 case CGNS_ENUMV(QUAD_P4_16): 218 case CGNS_ENUMV(QUAD_25): 219 _dmcelltype = DM_POLYTOPE_QUADRILATERAL; 220 break; 221 case CGNS_ENUMV(TETRA_4): 222 case CGNS_ENUMV(TETRA_10): 223 case CGNS_ENUMV(TETRA_16): 224 case CGNS_ENUMV(TETRA_20): 225 case CGNS_ENUMV(TETRA_22): 226 case CGNS_ENUMV(TETRA_34): 227 case CGNS_ENUMV(TETRA_35): 228 _dmcelltype = DM_POLYTOPE_TETRAHEDRON; 229 break; 230 case CGNS_ENUMV(PYRA_5): 231 case CGNS_ENUMV(PYRA_13): 232 case CGNS_ENUMV(PYRA_14): 233 case CGNS_ENUMV(PYRA_21): 234 case CGNS_ENUMV(PYRA_29): 235 case CGNS_ENUMV(PYRA_P4_29): 236 case CGNS_ENUMV(PYRA_30): 237 case CGNS_ENUMV(PYRA_50): 238 case CGNS_ENUMV(PYRA_55): 239 _dmcelltype = DM_POLYTOPE_PYRAMID; 240 break; 241 case CGNS_ENUMV(PENTA_6): 242 case CGNS_ENUMV(PENTA_15): 243 case CGNS_ENUMV(PENTA_18): 244 case CGNS_ENUMV(PENTA_24): 245 case CGNS_ENUMV(PENTA_33): 246 case CGNS_ENUMV(PENTA_38): 247 case CGNS_ENUMV(PENTA_40): 248 case CGNS_ENUMV(PENTA_66): 249 case CGNS_ENUMV(PENTA_75): 250 _dmcelltype = DM_POLYTOPE_TRI_PRISM; 251 break; 252 case CGNS_ENUMV(HEXA_8): 253 case CGNS_ENUMV(HEXA_20): 254 case CGNS_ENUMV(HEXA_27): 255 case CGNS_ENUMV(HEXA_32): 256 case CGNS_ENUMV(HEXA_44): 257 case CGNS_ENUMV(HEXA_56): 258 case CGNS_ENUMV(HEXA_64): 259 case CGNS_ENUMV(HEXA_98): 260 case CGNS_ENUMV(HEXA_125): 261 _dmcelltype = DM_POLYTOPE_HEXAHEDRON; 262 break; 263 case CGNS_ENUMV(MIXED): 264 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid CGNS ElementType_t: MIXED"); 265 default: 266 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid CGNS ElementType_t: %d", (int)cellType); 267 } 268 269 if (dmcelltype) *dmcelltype = _dmcelltype; 270 if (numCorners) *numCorners = DMPolytopeTypeGetNumVertices(_dmcelltype); 271 if (dim) *dim = DMPolytopeTypeGetDim(_dmcelltype); 272 PetscFunctionReturn(PETSC_SUCCESS); 273 } 274 275 /* 276 Input Parameters: 277 + cellType - The CGNS-defined cell type 278 279 Output Parameters: 280 + numClosure - Number of nodes that define the function space on the cell 281 - pOrder - The polynomial order of the cell 282 283 CGNS elements defined in: https://cgns.github.io/CGNS_docs_current/sids/conv.html#unstructgrid 284 285 Note: we only support "full" elements, ie. not seredipity elements 286 */ 287 static inline PetscErrorCode CGNSElementTypeGetDiscretizationInfo(CGNS_ENUMT(ElementType_t) cellType, PetscInt *numClosure, PetscInt *pOrder) 288 { 289 PetscInt _numClosure, _pOrder; 290 291 PetscFunctionBeginUser; 292 switch (cellType) { 293 case CGNS_ENUMV(BAR_2): 294 _numClosure = 2; 295 _pOrder = 1; 296 break; 297 case CGNS_ENUMV(BAR_3): 298 _numClosure = 3; 299 _pOrder = 2; 300 break; 301 case CGNS_ENUMV(BAR_4): 302 _numClosure = 4; 303 _pOrder = 3; 304 break; 305 case CGNS_ENUMV(BAR_5): 306 _numClosure = 5; 307 _pOrder = 4; 308 break; 309 case CGNS_ENUMV(TRI_3): 310 _numClosure = 3; 311 _pOrder = 1; 312 break; 313 case CGNS_ENUMV(TRI_6): 314 _numClosure = 6; 315 _pOrder = 2; 316 break; 317 case CGNS_ENUMV(TRI_10): 318 _numClosure = 10; 319 _pOrder = 3; 320 break; 321 case CGNS_ENUMV(TRI_15): 322 _numClosure = 15; 323 _pOrder = 4; 324 break; 325 case CGNS_ENUMV(QUAD_4): 326 _numClosure = 4; 327 _pOrder = 1; 328 break; 329 case CGNS_ENUMV(QUAD_9): 330 _numClosure = 9; 331 _pOrder = 2; 332 break; 333 case CGNS_ENUMV(QUAD_16): 334 _numClosure = 16; 335 _pOrder = 3; 336 break; 337 case CGNS_ENUMV(QUAD_25): 338 _numClosure = 25; 339 _pOrder = 4; 340 break; 341 case CGNS_ENUMV(TETRA_4): 342 _numClosure = 4; 343 _pOrder = 1; 344 break; 345 case CGNS_ENUMV(TETRA_10): 346 _numClosure = 10; 347 _pOrder = 2; 348 break; 349 case CGNS_ENUMV(TETRA_20): 350 _numClosure = 20; 351 _pOrder = 3; 352 break; 353 case CGNS_ENUMV(TETRA_35): 354 _numClosure = 35; 355 _pOrder = 4; 356 break; 357 case CGNS_ENUMV(PYRA_5): 358 _numClosure = 5; 359 _pOrder = 1; 360 break; 361 case CGNS_ENUMV(PYRA_14): 362 _numClosure = 14; 363 _pOrder = 2; 364 break; 365 case CGNS_ENUMV(PYRA_30): 366 _numClosure = 30; 367 _pOrder = 3; 368 break; 369 case CGNS_ENUMV(PYRA_55): 370 _numClosure = 55; 371 _pOrder = 4; 372 break; 373 case CGNS_ENUMV(PENTA_6): 374 _numClosure = 6; 375 _pOrder = 1; 376 break; 377 case CGNS_ENUMV(PENTA_18): 378 _numClosure = 18; 379 _pOrder = 2; 380 break; 381 case CGNS_ENUMV(PENTA_40): 382 _numClosure = 40; 383 _pOrder = 3; 384 break; 385 case CGNS_ENUMV(PENTA_75): 386 _numClosure = 75; 387 _pOrder = 4; 388 break; 389 case CGNS_ENUMV(HEXA_8): 390 _numClosure = 8; 391 _pOrder = 1; 392 break; 393 case CGNS_ENUMV(HEXA_27): 394 _numClosure = 27; 395 _pOrder = 2; 396 break; 397 case CGNS_ENUMV(HEXA_64): 398 _numClosure = 64; 399 _pOrder = 3; 400 break; 401 case CGNS_ENUMV(HEXA_125): 402 _numClosure = 125; 403 _pOrder = 4; 404 break; 405 case CGNS_ENUMV(MIXED): 406 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid CGNS ElementType_t: MIXED"); 407 default: 408 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unsupported or Invalid cell type %d", (int)cellType); 409 } 410 if (numClosure) *numClosure = _numClosure; 411 if (pOrder) *pOrder = _pOrder; 412 PetscFunctionReturn(PETSC_SUCCESS); 413 } 414 415 static PetscErrorCode PetscCGNSDataType(PetscDataType pd, CGNS_ENUMT(DataType_t) * cd) 416 { 417 PetscFunctionBegin; 418 switch (pd) { 419 case PETSC_FLOAT: 420 *cd = CGNS_ENUMV(RealSingle); 421 break; 422 case PETSC_DOUBLE: 423 *cd = CGNS_ENUMV(RealDouble); 424 break; 425 case PETSC_COMPLEX: 426 *cd = CGNS_ENUMV(ComplexDouble); 427 break; 428 default: 429 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Data type %s", PetscDataTypes[pd]); 430 } 431 PetscFunctionReturn(PETSC_SUCCESS); 432 } 433 434 PetscErrorCode DMPlexCreateCGNSFromFile_Internal(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 435 { 436 int cgid = -1; 437 PetscBool use_parallel_viewer = PETSC_FALSE; 438 439 PetscFunctionBegin; 440 PetscAssertPointer(filename, 2); 441 PetscCall(PetscViewerCGNSRegisterLogEvents_Internal()); 442 PetscCall(PetscOptionsGetBool(NULL, NULL, "-dm_plex_cgns_parallel", &use_parallel_viewer, NULL)); 443 444 if (use_parallel_viewer) { 445 PetscCallCGNS(cgp_mpi_comm(comm)); 446 PetscCallCGNSOpen(cgp_open(filename, CG_MODE_READ, &cgid), 0, 0); 447 PetscCheck(cgid > 0, PETSC_COMM_SELF, PETSC_ERR_LIB, "cgp_open(\"%s\",...) did not return a valid file ID", filename); 448 PetscCall(DMPlexCreateCGNS(comm, cgid, interpolate, dm)); 449 PetscCallCGNSClose(cgp_close(cgid), 0, 0); 450 } else { 451 PetscCallCGNSOpen(cg_open(filename, CG_MODE_READ, &cgid), 0, 0); 452 PetscCheck(cgid > 0, PETSC_COMM_SELF, PETSC_ERR_LIB, "cg_open(\"%s\",...) did not return a valid file ID", filename); 453 PetscCall(DMPlexCreateCGNS(comm, cgid, interpolate, dm)); 454 PetscCallCGNSClose(cg_close(cgid), 0, 0); 455 } 456 PetscFunctionReturn(PETSC_SUCCESS); 457 } 458 459 PetscErrorCode DMPlexCreateCGNS_Internal_Serial(MPI_Comm comm, PetscInt cgid, PetscBool interpolate, DM *dm) 460 { 461 PetscMPIInt num_proc, rank; 462 DM cdm; 463 DMLabel label; 464 PetscSection coordSection; 465 Vec coordinates; 466 PetscScalar *coords; 467 PetscInt *cellStart, *vertStart, v; 468 PetscInt labelIdRange[2], labelId; 469 /* Read from file */ 470 char basename[CGIO_MAX_NAME_LENGTH + 1]; 471 char buffer[CGIO_MAX_NAME_LENGTH + 1]; 472 int dim = 0, physDim = 0, coordDim = 0, numVertices = 0, numCells = 0; 473 int nzones = 0; 474 const int B = 1; // Only support single base 475 476 PetscFunctionBegin; 477 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 478 PetscCallMPI(MPI_Comm_size(comm, &num_proc)); 479 PetscCall(DMCreate(comm, dm)); 480 PetscCall(DMSetType(*dm, DMPLEX)); 481 482 /* Open CGNS II file and read basic information on rank 0, then broadcast to all processors */ 483 if (rank == 0) { 484 int nbases, z; 485 486 PetscCallCGNSRead(cg_nbases(cgid, &nbases), *dm, 0); 487 PetscCheck(nbases <= 1, PETSC_COMM_SELF, PETSC_ERR_LIB, "CGNS file must have a single base, not %d", nbases); 488 PetscCallCGNSRead(cg_base_read(cgid, B, basename, &dim, &physDim), *dm, 0); 489 PetscCallCGNSRead(cg_nzones(cgid, B, &nzones), *dm, 0); 490 PetscCall(PetscCalloc2(nzones + 1, &cellStart, nzones + 1, &vertStart)); 491 for (z = 1; z <= nzones; ++z) { 492 cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */ 493 494 PetscCallCGNSRead(cg_zone_read(cgid, B, z, buffer, sizes), *dm, 0); 495 numVertices += sizes[0]; 496 numCells += sizes[1]; 497 cellStart[z] += sizes[1] + cellStart[z - 1]; 498 vertStart[z] += sizes[0] + vertStart[z - 1]; 499 } 500 for (z = 1; z <= nzones; ++z) vertStart[z] += numCells; 501 coordDim = dim; 502 } 503 PetscCallMPI(MPI_Bcast(basename, CGIO_MAX_NAME_LENGTH + 1, MPI_CHAR, 0, comm)); 504 PetscCallMPI(MPI_Bcast(&dim, 1, MPI_INT, 0, comm)); 505 PetscCallMPI(MPI_Bcast(&coordDim, 1, MPI_INT, 0, comm)); 506 PetscCallMPI(MPI_Bcast(&nzones, 1, MPI_INT, 0, comm)); 507 508 PetscCall(PetscObjectSetName((PetscObject)*dm, basename)); 509 PetscCall(DMSetDimension(*dm, dim)); 510 PetscCall(DMCreateLabel(*dm, "celltype")); 511 PetscCall(DMPlexSetChart(*dm, 0, numCells + numVertices)); 512 513 /* Read zone information */ 514 if (rank == 0) { 515 int z, c, c_loc; 516 517 /* Read the cell set connectivity table and build mesh topology 518 CGNS standard requires that cells in a zone be numbered sequentially and be pairwise disjoint. */ 519 /* First set sizes */ 520 for (z = 1, c = 0; z <= nzones; ++z) { 521 CGNS_ENUMT(ZoneType_t) zonetype; 522 int nsections; 523 CGNS_ENUMT(ElementType_t) cellType; 524 cgsize_t start, end; 525 int nbndry, parentFlag; 526 PetscInt numCorners, pOrder; 527 DMPolytopeType ctype; 528 const int S = 1; // Only support single section 529 530 PetscCallCGNSRead(cg_zone_type(cgid, B, z, &zonetype), *dm, 0); 531 PetscCheck(zonetype != CGNS_ENUMV(Structured), PETSC_COMM_SELF, PETSC_ERR_LIB, "Can only handle Unstructured zones for CGNS"); 532 PetscCallCGNSRead(cg_nsections(cgid, B, z, &nsections), *dm, 0); 533 PetscCheck(nsections <= 1, PETSC_COMM_SELF, PETSC_ERR_LIB, "CGNS file must have a single section, not %d", nsections); 534 PetscCallCGNSRead(cg_section_read(cgid, B, z, S, buffer, &cellType, &start, &end, &nbndry, &parentFlag), *dm, 0); 535 if (cellType == CGNS_ENUMV(MIXED)) { 536 cgsize_t elementDataSize, *elements; 537 PetscInt off; 538 539 PetscCallCGNSRead(cg_ElementDataSize(cgid, B, z, S, &elementDataSize), *dm, 0); 540 PetscCall(PetscMalloc1(elementDataSize, &elements)); 541 PetscCallCGNSReadData(cg_poly_elements_read(cgid, B, z, S, elements, NULL, NULL), *dm, 0); 542 for (c_loc = start, off = 0; c_loc <= end; ++c_loc, ++c) { 543 PetscCall(CGNSElementTypeGetTopologyInfo((CGNS_ENUMT(ElementType_t))elements[off], &ctype, &numCorners, NULL)); 544 PetscCall(CGNSElementTypeGetDiscretizationInfo((CGNS_ENUMT(ElementType_t))elements[off], NULL, &pOrder)); 545 PetscCheck(pOrder == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Serial CGNS reader only supports first order elements, not %" PetscInt_FMT " order", pOrder); 546 PetscCall(DMPlexSetConeSize(*dm, c, numCorners)); 547 PetscCall(DMPlexSetCellType(*dm, c, ctype)); 548 off += numCorners + 1; 549 } 550 PetscCall(PetscFree(elements)); 551 } else { 552 PetscCall(CGNSElementTypeGetTopologyInfo(cellType, &ctype, &numCorners, NULL)); 553 PetscCall(CGNSElementTypeGetDiscretizationInfo(cellType, NULL, &pOrder)); 554 PetscCheck(pOrder == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Serial CGNS reader only supports first order elements, not %" PetscInt_FMT " order", pOrder); 555 for (c_loc = start; c_loc <= end; ++c_loc, ++c) { 556 PetscCall(DMPlexSetConeSize(*dm, c, numCorners)); 557 PetscCall(DMPlexSetCellType(*dm, c, ctype)); 558 } 559 } 560 } 561 for (v = numCells; v < numCells + numVertices; ++v) PetscCall(DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT)); 562 } 563 564 PetscCall(DMSetUp(*dm)); 565 566 PetscCall(DMCreateLabel(*dm, "zone")); 567 if (rank == 0) { 568 int z, c, c_loc, v_loc; 569 570 PetscCall(DMGetLabel(*dm, "zone", &label)); 571 for (z = 1, c = 0; z <= nzones; ++z) { 572 CGNS_ENUMT(ElementType_t) cellType; 573 cgsize_t elementDataSize, *elements, start, end; 574 int nbndry, parentFlag; 575 PetscInt *cone, numc, numCorners, maxCorners = 27, pOrder; 576 const int S = 1; // Only support single section 577 578 PetscCallCGNSRead(cg_section_read(cgid, B, z, S, buffer, &cellType, &start, &end, &nbndry, &parentFlag), *dm, 0); 579 numc = end - start; 580 PetscCallCGNSRead(cg_ElementDataSize(cgid, B, z, S, &elementDataSize), *dm, 0); 581 PetscCall(PetscMalloc2(elementDataSize, &elements, maxCorners, &cone)); 582 PetscCallCGNSReadData(cg_poly_elements_read(cgid, B, z, S, elements, NULL, NULL), *dm, 0); 583 if (cellType == CGNS_ENUMV(MIXED)) { 584 /* CGNS uses Fortran-based indexing, DMPlex uses C-style and numbers cell first then vertices. */ 585 for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) { 586 PetscCall(CGNSElementTypeGetTopologyInfo((CGNS_ENUMT(ElementType_t))elements[v], NULL, &numCorners, NULL)); 587 PetscCall(CGNSElementTypeGetDiscretizationInfo((CGNS_ENUMT(ElementType_t))elements[v], NULL, &pOrder)); 588 PetscCheck(pOrder == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Serial CGNS reader only supports first order elements, not %" PetscInt_FMT " order", pOrder); 589 ++v; 590 for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) cone[v_loc] = elements[v] + numCells - 1; 591 PetscCall(DMPlexReorderCell(*dm, c, cone)); 592 PetscCall(DMPlexSetCone(*dm, c, cone)); 593 PetscCall(DMLabelSetValue(label, c, z)); 594 } 595 } else { 596 PetscCall(CGNSElementTypeGetTopologyInfo(cellType, NULL, &numCorners, NULL)); 597 PetscCall(CGNSElementTypeGetDiscretizationInfo(cellType, NULL, &pOrder)); 598 PetscCheck(pOrder == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Serial CGNS reader only supports first order elements, not %" PetscInt_FMT " order", pOrder); 599 /* CGNS uses Fortran-based indexing, DMPlex uses C-style and numbers cell first then vertices. */ 600 for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) { 601 for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) cone[v_loc] = elements[v] + numCells - 1; 602 PetscCall(DMPlexReorderCell(*dm, c, cone)); 603 PetscCall(DMPlexSetCone(*dm, c, cone)); 604 PetscCall(DMLabelSetValue(label, c, z)); 605 } 606 } 607 PetscCall(PetscFree2(elements, cone)); 608 } 609 } 610 611 PetscCall(DMPlexSymmetrize(*dm)); 612 PetscCall(DMPlexStratify(*dm)); 613 if (interpolate) PetscCall(DMPlexInterpolateInPlace_Internal(*dm)); 614 615 /* Read coordinates */ 616 PetscCall(DMSetCoordinateDim(*dm, coordDim)); 617 PetscCall(DMGetCoordinateDM(*dm, &cdm)); 618 PetscCall(DMGetLocalSection(cdm, &coordSection)); 619 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 620 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, coordDim)); 621 PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices)); 622 for (v = numCells; v < numCells + numVertices; ++v) { 623 PetscCall(PetscSectionSetDof(coordSection, v, dim)); 624 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, coordDim)); 625 } 626 PetscCall(PetscSectionSetUp(coordSection)); 627 628 PetscCall(DMCreateLocalVector(cdm, &coordinates)); 629 PetscCall(VecGetArray(coordinates, &coords)); 630 if (rank == 0) { 631 PetscInt off = 0; 632 float *x[3]; 633 int z, d; 634 635 PetscCall(PetscMalloc3(numVertices, &x[0], numVertices, &x[1], numVertices, &x[2])); 636 for (z = 1; z <= nzones; ++z) { 637 CGNS_ENUMT(DataType_t) datatype; 638 cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */ 639 cgsize_t range_min[3] = {1, 1, 1}; 640 cgsize_t range_max[3] = {1, 1, 1}; 641 int ngrids, ncoords; 642 643 PetscCallCGNSRead(cg_zone_read(cgid, B, z, buffer, sizes), *dm, 0); 644 range_max[0] = sizes[0]; 645 PetscCallCGNSRead(cg_ngrids(cgid, B, z, &ngrids), *dm, 0); 646 PetscCheck(ngrids <= 1, PETSC_COMM_SELF, PETSC_ERR_LIB, "CGNS file must have a single grid, not %d", ngrids); 647 PetscCallCGNSRead(cg_ncoords(cgid, B, z, &ncoords), *dm, 0); 648 PetscCheck(ncoords == coordDim, PETSC_COMM_SELF, PETSC_ERR_LIB, "CGNS file must have a coordinate array for each dimension, not %d", ncoords); 649 for (d = 0; d < coordDim; ++d) { 650 PetscCallCGNSRead(cg_coord_info(cgid, B, z, 1 + d, &datatype, buffer), *dm, 0); 651 PetscCallCGNSReadData(cg_coord_read(cgid, B, z, buffer, CGNS_ENUMV(RealSingle), range_min, range_max, x[d]), *dm, 0); 652 } 653 if (coordDim >= 1) { 654 for (v = 0; v < sizes[0]; ++v) coords[(v + off) * coordDim + 0] = x[0][v]; 655 } 656 if (coordDim >= 2) { 657 for (v = 0; v < sizes[0]; ++v) coords[(v + off) * coordDim + 1] = x[1][v]; 658 } 659 if (coordDim >= 3) { 660 for (v = 0; v < sizes[0]; ++v) coords[(v + off) * coordDim + 2] = x[2][v]; 661 } 662 off += sizes[0]; 663 } 664 PetscCall(PetscFree3(x[0], x[1], x[2])); 665 } 666 PetscCall(VecRestoreArray(coordinates, &coords)); 667 668 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 669 PetscCall(VecSetBlockSize(coordinates, coordDim)); 670 PetscCall(DMSetCoordinatesLocal(*dm, coordinates)); 671 PetscCall(VecDestroy(&coordinates)); 672 673 /* Read boundary conditions */ 674 PetscCall(DMGetNumLabels(*dm, &labelIdRange[0])); 675 if (rank == 0) { 676 CGNS_ENUMT(BCType_t) bctype; 677 CGNS_ENUMT(DataType_t) datatype; 678 CGNS_ENUMT(PointSetType_t) pointtype; 679 cgsize_t *points; 680 PetscReal *normals; 681 int normal[3]; 682 char *bcname = buffer; 683 cgsize_t npoints, nnormals; 684 int z, nbc, bc, c, ndatasets; 685 686 for (z = 1; z <= nzones; ++z) { 687 PetscCallCGNSRead(cg_nbocos(cgid, B, z, &nbc), *dm, 0); 688 for (bc = 1; bc <= nbc; ++bc) { 689 PetscCallCGNSRead(cg_boco_info(cgid, B, z, bc, bcname, &bctype, &pointtype, &npoints, normal, &nnormals, &datatype, &ndatasets), *dm, 0); 690 PetscCall(DMCreateLabel(*dm, bcname)); 691 PetscCall(DMGetLabel(*dm, bcname, &label)); 692 PetscCall(PetscMalloc2(npoints, &points, nnormals, &normals)); 693 PetscCallCGNSReadData(cg_boco_read(cgid, B, z, bc, points, (void *)normals), *dm, 0); 694 if (pointtype == CGNS_ENUMV(ElementRange)) { 695 // Range of cells: assuming half-open interval 696 for (c = points[0]; c < points[1]; ++c) PetscCall(DMLabelSetValue(label, c - cellStart[z - 1], 1)); 697 } else if (pointtype == CGNS_ENUMV(ElementList)) { 698 // List of cells 699 for (c = 0; c < npoints; ++c) PetscCall(DMLabelSetValue(label, points[c] - cellStart[z - 1], 1)); 700 } else if (pointtype == CGNS_ENUMV(PointRange)) { 701 CGNS_ENUMT(GridLocation_t) gridloc; 702 703 // List of points: 704 PetscCallCGNS(cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end")); 705 PetscCallCGNSRead(cg_gridlocation_read(&gridloc), *dm, 0); 706 // Range of points: assuming half-open interval 707 for (c = points[0]; c < points[1]; ++c) { 708 if (gridloc == CGNS_ENUMV(Vertex)) PetscCall(DMLabelSetValue(label, c - vertStart[z - 1], 1)); 709 else PetscCall(DMLabelSetValue(label, c - cellStart[z - 1], 1)); 710 } 711 } else if (pointtype == CGNS_ENUMV(PointList)) { 712 CGNS_ENUMT(GridLocation_t) gridloc; 713 714 // List of points: 715 PetscCallCGNS(cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end")); 716 PetscCallCGNSRead(cg_gridlocation_read(&gridloc), *dm, 0); 717 for (c = 0; c < npoints; ++c) { 718 if (gridloc == CGNS_ENUMV(Vertex)) PetscCall(DMLabelSetValue(label, points[c] - vertStart[z - 1], 1)); 719 else PetscCall(DMLabelSetValue(label, points[c] - cellStart[z - 1], 1)); 720 } 721 } else SETERRQ(comm, PETSC_ERR_SUP, "Unsupported point set type %d", (int)pointtype); 722 PetscCall(PetscFree2(points, normals)); 723 } 724 } 725 PetscCall(PetscFree2(cellStart, vertStart)); 726 } 727 PetscCall(DMGetNumLabels(*dm, &labelIdRange[1])); 728 PetscCallMPI(MPI_Bcast(labelIdRange, 2, MPIU_INT, 0, comm)); 729 730 /* Create BC labels at all processes */ 731 for (labelId = labelIdRange[0]; labelId < labelIdRange[1]; ++labelId) { 732 char *labelName = buffer; 733 size_t len = sizeof(buffer); 734 const char *locName; 735 736 if (rank == 0) { 737 PetscCall(DMGetLabelByNum(*dm, labelId, &label)); 738 PetscCall(PetscObjectGetName((PetscObject)label, &locName)); 739 PetscCall(PetscStrncpy(labelName, locName, len)); 740 } 741 PetscCallMPI(MPI_Bcast(labelName, (PetscMPIInt)len, MPIU_INT, 0, comm)); 742 PetscCallMPI(DMCreateLabel(*dm, labelName)); 743 } 744 PetscFunctionReturn(PETSC_SUCCESS); 745 } 746 747 PetscErrorCode DMPlexCreateCGNS_Internal_Parallel(MPI_Comm comm, PetscInt cgid, PetscBool interpolate, DM *dm) 748 { 749 PetscMPIInt num_proc, rank; 750 /* Read from file */ 751 char basename[CGIO_MAX_NAME_LENGTH + 1]; 752 char buffer[CGIO_MAX_NAME_LENGTH + 1]; 753 int dim = 0, physDim = 0, coordDim = 0; 754 PetscInt NVertices = 0, NCells = 0; 755 int nzones = 0, nbases; 756 int z = 1; // Only supports single zone files 757 int B = 1; // Only supports single base 758 759 PetscFunctionBegin; 760 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 761 PetscCallMPI(MPI_Comm_size(comm, &num_proc)); 762 PetscCall(DMCreate(comm, dm)); 763 PetscCall(DMSetType(*dm, DMPLEX)); 764 765 PetscCallCGNSRead(cg_nbases(cgid, &nbases), *dm, 0); 766 PetscCheck(nbases <= 1, PETSC_COMM_SELF, PETSC_ERR_LIB, "CGNS file must have a single base, not %d", nbases); 767 // From the CGNS web page cell_dim phys_dim (embedding space in PETSc) CGNS defines as length of spatial vectors/components) 768 PetscCallCGNSRead(cg_base_read(cgid, B, basename, &dim, &physDim), *dm, 0); 769 PetscCallCGNSRead(cg_nzones(cgid, B, &nzones), *dm, 0); 770 PetscCheck(nzones == 1, PETSC_COMM_SELF, PETSC_ERR_LIB, "Parallel reader limited to one zone, not %d", nzones); 771 { 772 cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */ 773 774 PetscCallCGNSRead(cg_zone_read(cgid, B, z, buffer, sizes), *dm, 0); 775 NVertices = sizes[0]; 776 NCells = sizes[1]; 777 } 778 779 PetscCall(PetscObjectSetName((PetscObject)*dm, basename)); 780 PetscCall(DMSetDimension(*dm, dim)); 781 coordDim = dim; 782 783 // This is going to be a headache for mixed-topology and multiple sections. We may have to restore reading the data twice (once before the SetChart 784 // call to get this right but continuing for now with single section, single topology, one zone. 785 // establish element ranges for my rank 786 PetscInt mystarte, myende, mystartv, myendv, myownede, myownedv; 787 PetscLayout elem_map, vtx_map; 788 PetscCall(PetscLayoutCreateFromSizes(comm, PETSC_DECIDE, NCells, 1, &elem_map)); 789 PetscCall(PetscLayoutCreateFromSizes(comm, PETSC_DECIDE, NVertices, 1, &vtx_map)); 790 PetscCall(PetscLayoutGetRange(elem_map, &mystarte, &myende)); 791 PetscCall(PetscLayoutGetLocalSize(elem_map, &myownede)); 792 PetscCall(PetscLayoutGetRange(vtx_map, &mystartv, &myendv)); 793 PetscCall(PetscLayoutGetLocalSize(vtx_map, &myownedv)); 794 795 // -- Build Plex in parallel 796 DMPolytopeType dm_cell_type = DM_POLYTOPE_UNKNOWN; 797 PetscInt pOrder = 1, numClosure = -1; 798 cgsize_t *elements; 799 { 800 int nsections; 801 PetscInt *elementsQ1, numCorners = -1; 802 const int *perm; 803 cgsize_t start, end; // Throwaway 804 805 cg_nsections(cgid, B, z, &nsections); 806 // Read element connectivity 807 for (int index_sect = 1; index_sect <= nsections; index_sect++) { 808 int nbndry, parentFlag; 809 PetscInt cell_dim; 810 CGNS_ENUMT(ElementType_t) cellType; 811 812 PetscCallCGNSRead(cg_section_read(cgid, B, z, index_sect, buffer, &cellType, &start, &end, &nbndry, &parentFlag), *dm, 0); 813 814 PetscCall(CGNSElementTypeGetTopologyInfo(cellType, &dm_cell_type, &numCorners, &cell_dim)); 815 // Skip over element that are not max dimension (ie. boundary elements) 816 if (cell_dim != dim) continue; 817 PetscCall(CGNSElementTypeGetDiscretizationInfo(cellType, &numClosure, &pOrder)); 818 PetscCall(PetscMalloc1(myownede * numClosure, &elements)); 819 PetscCallCGNSReadData(cgp_elements_read_data(cgid, B, z, index_sect, mystarte + 1, myende, elements), *dm, 0); 820 for (PetscInt v = 0; v < myownede * numClosure; ++v) elements[v] -= 1; // 0 based 821 break; 822 } 823 824 // Create corners-only connectivity 825 PetscCall(PetscMalloc1(myownede * numCorners, &elementsQ1)); 826 PetscCall(DMPlexCGNSGetPermutation_Internal(dm_cell_type, numCorners, NULL, &perm)); 827 for (PetscInt e = 0; e < myownede; ++e) { 828 for (PetscInt v = 0; v < numCorners; ++v) elementsQ1[e * numCorners + perm[v]] = elements[e * numClosure + v]; 829 } 830 831 // Build cell-vertex Plex 832 PetscCall(DMPlexBuildFromCellListParallel(*dm, myownede, myownedv, NVertices, numCorners, elementsQ1, NULL, NULL)); 833 PetscCall(DMViewFromOptions(*dm, NULL, "-corner_dm_view")); 834 PetscCall(PetscFree(elementsQ1)); 835 } 836 837 if (interpolate) PetscCall(DMPlexInterpolateInPlace_Internal(*dm)); 838 839 // -- Create SF for naive nodal-data read to elements 840 PetscSF plex_to_cgns_sf; 841 { 842 PetscInt nleaves, num_comp; 843 PetscInt *leaf, num_leaves = 0; 844 PetscInt cStart, cEnd; 845 const int *perm; 846 PetscSF cgns_to_local_sf; 847 PetscSection local_section; 848 PetscFE fe; 849 850 // sfNatural requires PetscSection to handle DMDistribute, so we use PetscFE to define the section 851 // Use number of components = 1 to work with just the nodes themselves 852 PetscCall(PetscFECreateLagrangeByCell(PETSC_COMM_SELF, dim, 1, dm_cell_type, pOrder, PETSC_DETERMINE, &fe)); 853 PetscCall(PetscObjectSetName((PetscObject)fe, "FE for sfNatural")); 854 PetscCall(DMAddField(*dm, NULL, (PetscObject)fe)); 855 PetscCall(DMCreateDS(*dm)); 856 PetscCall(PetscFEDestroy(&fe)); 857 858 PetscCall(DMGetLocalSection(*dm, &local_section)); 859 PetscCall(PetscSectionViewFromOptions(local_section, NULL, "-fe_natural_section_view")); 860 PetscCall(PetscSectionGetFieldComponents(local_section, 0, &num_comp)); 861 PetscCall(PetscSectionGetStorageSize(local_section, &nleaves)); 862 nleaves /= num_comp; 863 PetscCall(PetscMalloc1(nleaves, &leaf)); 864 for (PetscInt i = 0; i < nleaves; i++) leaf[i] = -1; 865 866 // Get the permutation from CGNS closure numbering to PLEX closure numbering 867 PetscCall(DMPlexCGNSGetPermutation_Internal(dm_cell_type, numClosure, NULL, &perm)); 868 PetscCall(DMPlexGetHeightStratum(*dm, 0, &cStart, &cEnd)); 869 for (PetscInt cell = cStart; cell < cEnd; ++cell) { 870 PetscInt num_closure_dof, *closure_idx = NULL; 871 872 PetscCall(DMPlexGetClosureIndices(*dm, local_section, local_section, cell, PETSC_FALSE, &num_closure_dof, &closure_idx, NULL, NULL)); 873 PetscAssert(numClosure * num_comp == num_closure_dof, comm, PETSC_ERR_PLIB, "Closure dof size does not match polytope"); 874 for (PetscInt i = 0; i < numClosure; i++) { 875 PetscInt li = closure_idx[perm[i] * num_comp] / num_comp; 876 if (li < 0) continue; 877 878 PetscInt cgns_idx = elements[cell * numClosure + i]; 879 if (leaf[li] == -1) { 880 leaf[li] = cgns_idx; 881 num_leaves++; 882 } else PetscAssert(leaf[li] == cgns_idx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "leaf does not match previously set"); 883 } 884 PetscCall(DMPlexRestoreClosureIndices(*dm, local_section, local_section, cell, PETSC_FALSE, &num_closure_dof, &closure_idx, NULL, NULL)); 885 } 886 PetscAssert(num_leaves == nleaves, PETSC_COMM_SELF, PETSC_ERR_PLIB, "leaf count in closure does not match nleaves"); 887 PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)*dm), &cgns_to_local_sf)); 888 PetscCall(PetscSFSetGraphLayout(cgns_to_local_sf, vtx_map, nleaves, NULL, PETSC_USE_POINTER, leaf)); 889 PetscCall(PetscObjectSetName((PetscObject)cgns_to_local_sf, "CGNS to Plex SF")); 890 PetscCall(PetscSFViewFromOptions(cgns_to_local_sf, NULL, "-CGNStoPlex_sf_view")); 891 PetscCall(PetscFree(leaf)); 892 PetscCall(PetscFree(elements)); 893 894 { // Convert cgns_to_local to global_to_cgns 895 PetscSF sectionsf, cgns_to_global_sf; 896 897 PetscCall(DMGetSectionSF(*dm, §ionsf)); 898 PetscCall(PetscSFComposeInverse(cgns_to_local_sf, sectionsf, &cgns_to_global_sf)); 899 PetscCall(PetscSFDestroy(&cgns_to_local_sf)); 900 PetscCall(PetscSFCreateInverseSF(cgns_to_global_sf, &plex_to_cgns_sf)); 901 PetscCall(PetscObjectSetName((PetscObject)plex_to_cgns_sf, "Global Plex to CGNS")); 902 PetscCall(PetscSFDestroy(&cgns_to_global_sf)); 903 } 904 } 905 906 { // -- Set coordinates for DM 907 PetscScalar *coords; 908 float *x[3]; 909 double *xd[3]; 910 PetscBool read_with_double; 911 PetscFE cfe; 912 913 // Setup coordinate space first. Use pOrder here for isoparametric; revisit with CPEX-0045 High Order. 914 PetscCall(PetscFECreateLagrangeByCell(PETSC_COMM_SELF, dim, coordDim, dm_cell_type, pOrder, PETSC_DETERMINE, &cfe)); 915 PetscCall(DMSetCoordinateDisc(*dm, cfe, PETSC_FALSE, PETSC_FALSE)); 916 PetscCall(PetscFEDestroy(&cfe)); 917 918 { // Determine if coords are written in single or double precision 919 CGNS_ENUMT(DataType_t) datatype; 920 921 PetscCallCGNSRead(cg_coord_info(cgid, B, z, 1, &datatype, buffer), *dm, 0); 922 read_with_double = datatype == CGNS_ENUMV(RealDouble) ? PETSC_TRUE : PETSC_FALSE; 923 } 924 925 // Read coords from file and set into component-major ordering 926 if (read_with_double) PetscCall(PetscMalloc3(myownedv, &xd[0], myownedv, &xd[1], myownedv, &xd[2])); 927 else PetscCall(PetscMalloc3(myownedv, &x[0], myownedv, &x[1], myownedv, &x[2])); 928 PetscCall(PetscMalloc1(myownedv * coordDim, &coords)); 929 { 930 cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */ 931 cgsize_t range_min[3] = {mystartv + 1, 1, 1}; 932 cgsize_t range_max[3] = {myendv, 1, 1}; 933 int ngrids, ncoords; 934 935 PetscCallCGNSRead(cg_zone_read(cgid, B, z, buffer, sizes), *dm, 0); 936 PetscCallCGNSRead(cg_ngrids(cgid, B, z, &ngrids), *dm, 0); 937 PetscCheck(ngrids <= 1, PETSC_COMM_SELF, PETSC_ERR_LIB, "CGNS file must have a single grid, not %d", ngrids); 938 PetscCallCGNSRead(cg_ncoords(cgid, B, z, &ncoords), *dm, 0); 939 PetscCheck(ncoords == coordDim, PETSC_COMM_SELF, PETSC_ERR_LIB, "CGNS file must have a coordinate array for each dimension, not %d", ncoords); 940 if (read_with_double) { 941 for (int d = 0; d < coordDim; ++d) PetscCallCGNSReadData(cgp_coord_read_data(cgid, B, z, (d + 1), range_min, range_max, xd[d]), *dm, 0); 942 if (coordDim >= 1) { 943 for (PetscInt v = 0; v < myownedv; ++v) coords[v * coordDim + 0] = xd[0][v]; 944 } 945 if (coordDim >= 2) { 946 for (PetscInt v = 0; v < myownedv; ++v) coords[v * coordDim + 1] = xd[1][v]; 947 } 948 if (coordDim >= 3) { 949 for (PetscInt v = 0; v < myownedv; ++v) coords[v * coordDim + 2] = xd[2][v]; 950 } 951 } else { 952 for (int d = 0; d < coordDim; ++d) PetscCallCGNSReadData(cgp_coord_read_data(cgid, 1, z, (d + 1), range_min, range_max, x[d]), *dm, 0); 953 if (coordDim >= 1) { 954 for (PetscInt v = 0; v < myownedv; ++v) coords[v * coordDim + 0] = x[0][v]; 955 } 956 if (coordDim >= 2) { 957 for (PetscInt v = 0; v < myownedv; ++v) coords[v * coordDim + 1] = x[1][v]; 958 } 959 if (coordDim >= 3) { 960 for (PetscInt v = 0; v < myownedv; ++v) coords[v * coordDim + 2] = x[2][v]; 961 } 962 } 963 } 964 if (read_with_double) PetscCall(PetscFree3(xd[0], xd[1], xd[2])); 965 else PetscCall(PetscFree3(x[0], x[1], x[2])); 966 967 { // Reduce CGNS-ordered coordinate nodes to Plex ordering, and set DM's coordinates 968 Vec coord_global; 969 MPI_Datatype unit; 970 PetscScalar *coord_global_array; 971 DM cdm; 972 973 PetscCall(DMGetCoordinateDM(*dm, &cdm)); 974 PetscCall(DMCreateGlobalVector(cdm, &coord_global)); 975 PetscCall(VecGetArrayWrite(coord_global, &coord_global_array)); 976 PetscCallMPI(MPI_Type_contiguous(coordDim, MPIU_SCALAR, &unit)); 977 PetscCallMPI(MPI_Type_commit(&unit)); 978 PetscCall(PetscSFReduceBegin(plex_to_cgns_sf, unit, coords, coord_global_array, MPI_REPLACE)); 979 PetscCall(PetscSFReduceEnd(plex_to_cgns_sf, unit, coords, coord_global_array, MPI_REPLACE)); 980 PetscCall(VecRestoreArrayWrite(coord_global, &coord_global_array)); 981 PetscCallMPI(MPI_Type_free(&unit)); 982 PetscCall(DMSetCoordinates(*dm, coord_global)); 983 PetscCall(VecDestroy(&coord_global)); 984 } 985 PetscCall(PetscFree(coords)); 986 } 987 988 // -- Set sfNatural for solution vectors in CGNS file 989 // NOTE: We set sfNatural to be the map between the original CGNS ordering of nodes and the Plex ordering of nodes. 990 PetscCall(PetscSFViewFromOptions(plex_to_cgns_sf, NULL, "-sfNatural_init_view")); 991 PetscCall(DMSetNaturalSF(*dm, plex_to_cgns_sf)); 992 PetscCall(DMSetUseNatural(*dm, PETSC_TRUE)); 993 PetscCall(PetscSFDestroy(&plex_to_cgns_sf)); 994 995 PetscCall(PetscLayoutDestroy(&elem_map)); 996 PetscCall(PetscLayoutDestroy(&vtx_map)); 997 PetscFunctionReturn(PETSC_SUCCESS); 998 } 999 1000 // node_l2g must be freed 1001 static PetscErrorCode DMPlexCreateNodeNumbering(DM dm, PetscInt *num_local_nodes, PetscInt *num_global_nodes, PetscInt *nStart, PetscInt *nEnd, const PetscInt **node_l2g) 1002 { 1003 PetscSection local_section; 1004 PetscSF point_sf; 1005 PetscInt pStart, pEnd, spStart, spEnd, *points, nleaves, ncomp, *nodes; 1006 PetscMPIInt comm_size; 1007 const PetscInt *ilocal, field = 0; 1008 1009 PetscFunctionBegin; 1010 *num_local_nodes = -1; 1011 *num_global_nodes = -1; 1012 *nStart = -1; 1013 *nEnd = -1; 1014 *node_l2g = NULL; 1015 1016 PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)dm), &comm_size)); 1017 PetscCall(DMGetLocalSection(dm, &local_section)); 1018 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 1019 PetscCall(PetscSectionGetChart(local_section, &spStart, &spEnd)); 1020 PetscCall(DMGetPointSF(dm, &point_sf)); 1021 if (comm_size == 1) nleaves = 0; 1022 else PetscCall(PetscSFGetGraph(point_sf, NULL, &nleaves, &ilocal, NULL)); 1023 PetscCall(PetscSectionGetFieldComponents(local_section, field, &ncomp)); 1024 1025 PetscInt local_node = 0, owned_node = 0, owned_start = 0; 1026 for (PetscInt p = spStart, leaf = 0; p < spEnd; p++) { 1027 PetscInt dof; 1028 PetscCall(PetscSectionGetFieldDof(local_section, p, field, &dof)); 1029 PetscAssert(dof % ncomp == 0, PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Field dof %" PetscInt_FMT " must be divisible by components %" PetscInt_FMT, dof, ncomp); 1030 local_node += dof / ncomp; 1031 if (leaf < nleaves && p == ilocal[leaf]) { // skip points owned by a different process 1032 leaf++; 1033 } else { 1034 owned_node += dof / ncomp; 1035 } 1036 } 1037 PetscCallMPI(MPI_Exscan(&owned_node, &owned_start, 1, MPIU_INT, MPI_SUM, PetscObjectComm((PetscObject)dm))); 1038 PetscCall(PetscMalloc1(pEnd - pStart, &points)); 1039 owned_node = 0; 1040 for (PetscInt p = spStart, leaf = 0; p < spEnd; p++) { 1041 if (leaf < nleaves && p == ilocal[leaf]) { // skip points owned by a different process 1042 points[p - pStart] = -1; 1043 leaf++; 1044 continue; 1045 } 1046 PetscInt dof, offset; 1047 PetscCall(PetscSectionGetFieldDof(local_section, p, field, &dof)); 1048 PetscCall(PetscSectionGetFieldOffset(local_section, p, field, &offset)); 1049 PetscAssert(offset % ncomp == 0, PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Field offset %" PetscInt_FMT " must be divisible by components %" PetscInt_FMT, offset, ncomp); 1050 points[p - pStart] = owned_start + owned_node; 1051 owned_node += dof / ncomp; 1052 } 1053 if (comm_size > 1) { 1054 PetscCall(PetscSFBcastBegin(point_sf, MPIU_INT, points, points, MPI_REPLACE)); 1055 PetscCall(PetscSFBcastEnd(point_sf, MPIU_INT, points, points, MPI_REPLACE)); 1056 } 1057 1058 // Set up global indices for each local node 1059 PetscCall(PetscMalloc1(local_node, &nodes)); 1060 for (PetscInt p = spStart; p < spEnd; p++) { 1061 PetscInt dof, offset; 1062 PetscCall(PetscSectionGetFieldDof(local_section, p, field, &dof)); 1063 PetscCall(PetscSectionGetFieldOffset(local_section, p, field, &offset)); 1064 for (PetscInt n = 0; n < dof / ncomp; n++) nodes[offset / ncomp + n] = points[p - pStart] + n; 1065 } 1066 PetscCall(PetscFree(points)); 1067 *num_local_nodes = local_node; 1068 *nStart = owned_start; 1069 *nEnd = owned_start + owned_node; 1070 PetscCallMPI(MPIU_Allreduce(&owned_node, num_global_nodes, 1, MPIU_INT, MPI_SUM, PetscObjectComm((PetscObject)dm))); 1071 *node_l2g = nodes; 1072 PetscFunctionReturn(PETSC_SUCCESS); 1073 } 1074 1075 PetscErrorCode DMView_PlexCGNS(DM dm, PetscViewer viewer) 1076 { 1077 PetscViewer_CGNS *cgv = (PetscViewer_CGNS *)viewer->data; 1078 PetscInt fvGhostStart; 1079 PetscInt topo_dim, coord_dim, num_global_elems; 1080 PetscInt cStart, cEnd, num_local_nodes, num_global_nodes, nStart, nEnd; 1081 const PetscInt *node_l2g; 1082 Vec coord; 1083 DM colloc_dm, cdm; 1084 PetscMPIInt size; 1085 const char *dm_name; 1086 int base, zone; 1087 cgsize_t isize[3]; 1088 1089 PetscFunctionBegin; 1090 if (!cgv->file_num) { 1091 PetscInt time_step; 1092 PetscCall(DMGetOutputSequenceNumber(dm, &time_step, NULL)); 1093 PetscCall(PetscViewerCGNSFileOpen_Internal(viewer, time_step)); 1094 } 1095 PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size)); 1096 PetscCall(DMGetDimension(dm, &topo_dim)); 1097 PetscCall(DMGetCoordinateDim(dm, &coord_dim)); 1098 PetscCall(PetscObjectGetName((PetscObject)dm, &dm_name)); 1099 PetscCallCGNSWrite(cg_base_write(cgv->file_num, dm_name, topo_dim, coord_dim, &base), dm, viewer); 1100 PetscCallCGNS(cg_goto(cgv->file_num, base, NULL)); 1101 PetscCallCGNSWrite(cg_dataclass_write(CGNS_ENUMV(NormalizedByDimensional)), dm, viewer); 1102 1103 { 1104 PetscFE fe, fe_coord; 1105 PetscClassId ds_id; 1106 PetscDualSpace dual_space, dual_space_coord; 1107 PetscInt num_fields, field_order = -1, field_order_coord; 1108 PetscBool is_simplex; 1109 PetscCall(DMGetNumFields(dm, &num_fields)); 1110 if (num_fields > 0) { 1111 PetscCall(DMGetField(dm, 0, NULL, (PetscObject *)&fe)); 1112 PetscCall(PetscObjectGetClassId((PetscObject)fe, &ds_id)); 1113 if (ds_id != PETSCFE_CLASSID) { 1114 fe = NULL; 1115 if (ds_id == PETSCFV_CLASSID) field_order = -1; // use whatever is present for coords; field will be CellCenter 1116 else field_order = 1; // assume vertex-based linear elements 1117 } 1118 } else fe = NULL; 1119 if (fe) { 1120 PetscCall(PetscFEGetDualSpace(fe, &dual_space)); 1121 PetscCall(PetscDualSpaceGetOrder(dual_space, &field_order)); 1122 } 1123 PetscCall(DMGetCoordinateDM(dm, &cdm)); 1124 PetscCall(DMGetField(cdm, 0, NULL, (PetscObject *)&fe_coord)); 1125 { 1126 PetscClassId id; 1127 PetscCall(PetscObjectGetClassId((PetscObject)fe_coord, &id)); 1128 if (id != PETSCFE_CLASSID) fe_coord = NULL; 1129 } 1130 if (fe_coord) { 1131 PetscCall(PetscFEGetDualSpace(fe_coord, &dual_space_coord)); 1132 PetscCall(PetscDualSpaceGetOrder(dual_space_coord, &field_order_coord)); 1133 } else field_order_coord = 1; 1134 if (field_order > 0 && field_order != field_order_coord) { 1135 PetscInt quadrature_order = field_order; 1136 PetscCall(DMClone(dm, &colloc_dm)); 1137 { // Inform the new colloc_dm that it is a coordinate DM so isoperiodic affine corrections can be applied 1138 const PetscSF *face_sfs; 1139 PetscInt num_face_sfs; 1140 PetscCall(DMPlexGetIsoperiodicFaceSF(dm, &num_face_sfs, &face_sfs)); 1141 PetscCall(DMPlexSetIsoperiodicFaceSF(colloc_dm, num_face_sfs, (PetscSF *)face_sfs)); 1142 if (face_sfs) colloc_dm->periodic.setup = DMPeriodicCoordinateSetUp_Internal; 1143 } 1144 PetscCall(DMPlexIsSimplex(dm, &is_simplex)); 1145 PetscCall(PetscFECreateLagrange(PetscObjectComm((PetscObject)dm), topo_dim, coord_dim, is_simplex, field_order, quadrature_order, &fe)); 1146 PetscCall(DMSetCoordinateDisc(colloc_dm, fe, PETSC_FALSE, PETSC_TRUE)); 1147 PetscCall(PetscFEDestroy(&fe)); 1148 } else { 1149 PetscCall(PetscObjectReference((PetscObject)dm)); 1150 colloc_dm = dm; 1151 } 1152 } 1153 PetscCall(DMGetCoordinateDM(colloc_dm, &cdm)); 1154 PetscCall(DMPlexCreateNodeNumbering(cdm, &num_local_nodes, &num_global_nodes, &nStart, &nEnd, &node_l2g)); 1155 PetscCall(DMGetCoordinatesLocal(colloc_dm, &coord)); 1156 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 1157 PetscCall(DMPlexGetCellTypeStratum(dm, DM_POLYTOPE_FV_GHOST, &fvGhostStart, NULL)); 1158 if (fvGhostStart >= 0) cEnd = fvGhostStart; 1159 num_global_elems = cEnd - cStart; 1160 PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &num_global_elems, 1, MPIU_INT, MPI_SUM, PetscObjectComm((PetscObject)dm))); 1161 isize[0] = num_global_nodes; 1162 isize[1] = num_global_elems; 1163 isize[2] = 0; 1164 PetscCallCGNSWrite(cg_zone_write(cgv->file_num, base, "Zone", isize, CGNS_ENUMV(Unstructured), &zone), dm, viewer); 1165 1166 { 1167 const PetscScalar *X; 1168 PetscScalar *x; 1169 int coord_ids[3]; 1170 1171 PetscCall(VecGetArrayRead(coord, &X)); 1172 for (PetscInt d = 0; d < coord_dim; d++) { 1173 const double exponents[] = {0, 1, 0, 0, 0}; 1174 char coord_name[64]; 1175 PetscCall(PetscSNPrintf(coord_name, sizeof coord_name, "Coordinate%c", 'X' + (int)d)); 1176 PetscCallCGNSWrite(cgp_coord_write(cgv->file_num, base, zone, CGNS_ENUMV(RealDouble), coord_name, &coord_ids[d]), dm, viewer); 1177 PetscCallCGNS(cg_goto(cgv->file_num, base, "Zone_t", zone, "GridCoordinates", 0, coord_name, 0, NULL)); 1178 PetscCallCGNSWrite(cg_exponents_write(CGNS_ENUMV(RealDouble), exponents), dm, viewer); 1179 } 1180 1181 int section; 1182 cgsize_t e_owned, e_global, e_start, *conn = NULL; 1183 const int *perm; 1184 CGNS_ENUMT(ElementType_t) element_type = CGNS_ENUMV(ElementTypeNull); 1185 { 1186 PetscCall(PetscMalloc1(nEnd - nStart, &x)); 1187 for (PetscInt d = 0; d < coord_dim; d++) { 1188 for (PetscInt n = 0; n < num_local_nodes; n++) { 1189 PetscInt gn = node_l2g[n]; 1190 if (gn < nStart || nEnd <= gn) continue; 1191 x[gn - nStart] = X[n * coord_dim + d]; 1192 } 1193 // CGNS nodes use 1-based indexing 1194 cgsize_t start = nStart + 1, end = nEnd; 1195 PetscCallCGNSWriteData(cgp_coord_write_data(cgv->file_num, base, zone, coord_ids[d], &start, &end, x), dm, viewer); 1196 } 1197 PetscCall(PetscFree(x)); 1198 PetscCall(VecRestoreArrayRead(coord, &X)); 1199 } 1200 1201 e_owned = cEnd - cStart; 1202 if (e_owned > 0) { 1203 DMPolytopeType cell_type; 1204 1205 PetscCall(DMPlexGetCellType(dm, cStart, &cell_type)); 1206 for (PetscInt i = cStart, c = 0; i < cEnd; i++) { 1207 PetscInt closure_dof, *closure_indices, elem_size; 1208 1209 PetscCall(DMPlexGetClosureIndices(cdm, cdm->localSection, cdm->localSection, i, PETSC_FALSE, &closure_dof, &closure_indices, NULL, NULL)); 1210 elem_size = closure_dof / coord_dim; 1211 if (!conn) PetscCall(PetscMalloc1(e_owned * elem_size, &conn)); 1212 PetscCall(DMPlexCGNSGetPermutation_Internal(cell_type, closure_dof / coord_dim, &element_type, &perm)); 1213 for (PetscInt j = 0; j < elem_size; j++) conn[c++] = node_l2g[closure_indices[perm[j] * coord_dim] / coord_dim] + 1; 1214 PetscCall(DMPlexRestoreClosureIndices(cdm, cdm->localSection, cdm->localSection, i, PETSC_FALSE, &closure_dof, &closure_indices, NULL, NULL)); 1215 } 1216 } 1217 1218 { // Get global element_type (for ranks that do not have owned elements) 1219 PetscInt local_element_type, global_element_type; 1220 1221 local_element_type = e_owned > 0 ? element_type : -1; 1222 PetscCallMPI(MPIU_Allreduce(&local_element_type, &global_element_type, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)viewer))); 1223 if (local_element_type != -1) PetscCheck(local_element_type == global_element_type, PETSC_COMM_SELF, PETSC_ERR_SUP, "Ranks with different element types not supported"); 1224 element_type = (CGNS_ENUMT(ElementType_t))global_element_type; 1225 } 1226 PetscCallMPI(MPIU_Allreduce(&e_owned, &e_global, 1, MPIU_CGSIZE, MPI_SUM, PetscObjectComm((PetscObject)dm))); 1227 PetscCheck(e_global == num_global_elems, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unexpected number of elements %" PRIdCGSIZE " vs %" PetscInt_FMT, e_global, num_global_elems); 1228 e_start = 0; 1229 PetscCallMPI(MPI_Exscan(&e_owned, &e_start, 1, MPIU_CGSIZE, MPI_SUM, PetscObjectComm((PetscObject)dm))); 1230 PetscCallCGNSWrite(cgp_section_write(cgv->file_num, base, zone, "Elem", element_type, 1, e_global, 0, §ion), dm, viewer); 1231 PetscCallCGNSWriteData(cgp_elements_write_data(cgv->file_num, base, zone, section, e_start + 1, e_start + e_owned, conn), dm, viewer); 1232 PetscCall(PetscFree(conn)); 1233 1234 cgv->base = base; 1235 cgv->zone = zone; 1236 cgv->node_l2g = node_l2g; 1237 cgv->num_local_nodes = num_local_nodes; 1238 cgv->nStart = nStart; 1239 cgv->nEnd = nEnd; 1240 cgv->eStart = e_start; 1241 cgv->eEnd = e_start + e_owned; 1242 if (1) { 1243 PetscMPIInt rank; 1244 int *efield; 1245 int sol, field; 1246 DMLabel label; 1247 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 1248 PetscCall(PetscMalloc1(e_owned, &efield)); 1249 for (PetscInt i = 0; i < e_owned; i++) efield[i] = rank; 1250 PetscCallCGNSWrite(cg_sol_write(cgv->file_num, base, zone, "CellInfo", CGNS_ENUMV(CellCenter), &sol), dm, viewer); 1251 PetscCallCGNSWrite(cgp_field_write(cgv->file_num, base, zone, sol, CGNS_ENUMV(Integer), "Rank", &field), dm, viewer); 1252 cgsize_t start = e_start + 1, end = e_start + e_owned; 1253 PetscCallCGNSWriteData(cgp_field_write_data(cgv->file_num, base, zone, sol, field, &start, &end, efield), dm, viewer); 1254 PetscCall(DMGetLabel(dm, "Cell Sets", &label)); 1255 if (label) { 1256 for (PetscInt c = cStart; c < cEnd; c++) { 1257 PetscInt value; 1258 PetscCall(DMLabelGetValue(label, c, &value)); 1259 efield[c - cStart] = value; 1260 } 1261 PetscCallCGNSWrite(cgp_field_write(cgv->file_num, base, zone, sol, CGNS_ENUMV(Integer), "CellSet", &field), dm, viewer); 1262 PetscCallCGNSWriteData(cgp_field_write_data(cgv->file_num, base, zone, sol, field, &start, &end, efield), dm, viewer); 1263 } 1264 PetscCall(PetscFree(efield)); 1265 } 1266 } 1267 PetscCall(DMDestroy(&colloc_dm)); 1268 PetscFunctionReturn(PETSC_SUCCESS); 1269 } 1270 1271 PetscErrorCode VecView_Plex_Local_CGNS(Vec V, PetscViewer viewer) 1272 { 1273 PetscViewer_CGNS *cgv = (PetscViewer_CGNS *)viewer->data; 1274 DM dm; 1275 PetscSection section; 1276 PetscInt time_step, num_fields, pStart, pEnd, fvGhostStart; 1277 PetscReal time, *time_slot; 1278 size_t *step_slot; 1279 const PetscScalar *v; 1280 char solution_name[PETSC_MAX_PATH_LEN]; 1281 int sol; 1282 1283 PetscFunctionBegin; 1284 PetscCall(VecGetDM(V, &dm)); 1285 PetscCall(DMGetLocalSection(dm, §ion)); 1286 PetscCall(PetscSectionGetChart(section, &pStart, &pEnd)); 1287 PetscCall(DMPlexGetCellTypeStratum(dm, DM_POLYTOPE_FV_GHOST, &fvGhostStart, NULL)); 1288 if (fvGhostStart >= 0) pEnd = fvGhostStart; 1289 1290 if (!cgv->node_l2g) PetscCall(DMView(dm, viewer)); 1291 if (!cgv->grid_loc) { // Determine if writing to cell-centers or to nodes 1292 PetscInt cStart, cEnd; 1293 PetscInt local_grid_loc, global_grid_loc; 1294 1295 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 1296 if (fvGhostStart >= 0) cEnd = fvGhostStart; 1297 if (cgv->num_local_nodes == 0) local_grid_loc = -1; 1298 else if (cStart == pStart && cEnd == pEnd) local_grid_loc = CGNS_ENUMV(CellCenter); 1299 else local_grid_loc = CGNS_ENUMV(Vertex); 1300 1301 PetscCallMPI(MPIU_Allreduce(&local_grid_loc, &global_grid_loc, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)viewer))); 1302 if (local_grid_loc != -1) 1303 PetscCheck(local_grid_loc == global_grid_loc, PETSC_COMM_SELF, PETSC_ERR_SUP, "Ranks with different grid locations not supported. Local has %" PetscInt_FMT ", allreduce returned %" PetscInt_FMT, local_grid_loc, global_grid_loc); 1304 PetscCheck((global_grid_loc == CGNS_ENUMV(CellCenter)) || (global_grid_loc == CGNS_ENUMV(Vertex)), PetscObjectComm((PetscObject)viewer), PETSC_ERR_SUP, "Grid location should only be CellCenter (%d) or Vertex(%d), but have %" PetscInt_FMT, CGNS_ENUMV(CellCenter), CGNS_ENUMV(Vertex), global_grid_loc); 1305 cgv->grid_loc = (CGNS_ENUMT(GridLocation_t))global_grid_loc; 1306 } 1307 if (!cgv->nodal_field) { 1308 switch (cgv->grid_loc) { 1309 case CGNS_ENUMV(Vertex): { 1310 PetscCall(PetscMalloc1(cgv->nEnd - cgv->nStart, &cgv->nodal_field)); 1311 } break; 1312 case CGNS_ENUMV(CellCenter): { 1313 PetscCall(PetscMalloc1(cgv->eEnd - cgv->eStart, &cgv->nodal_field)); 1314 } break; 1315 default: 1316 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Can only write for Vertex and CellCenter grid locations"); 1317 } 1318 } 1319 if (!cgv->output_times) PetscCall(PetscSegBufferCreate(sizeof(PetscReal), 20, &cgv->output_times)); 1320 if (!cgv->output_steps) PetscCall(PetscSegBufferCreate(sizeof(size_t), 20, &cgv->output_steps)); 1321 1322 PetscCall(DMGetOutputSequenceNumber(dm, &time_step, &time)); 1323 if (time_step < 0) { 1324 time_step = 0; 1325 time = 0.; 1326 } 1327 // Avoid "Duplicate child name found" error by not writing an already-written solution. 1328 // This usually occurs when a solution is written and then diverges on the very next timestep. 1329 if (time_step == cgv->previous_output_step) PetscFunctionReturn(PETSC_SUCCESS); 1330 1331 PetscCall(PetscSegBufferGet(cgv->output_times, 1, &time_slot)); 1332 *time_slot = time; 1333 PetscCall(PetscSegBufferGet(cgv->output_steps, 1, &step_slot)); 1334 *step_slot = cgv->previous_output_step = time_step; 1335 PetscCall(PetscSNPrintf(solution_name, sizeof solution_name, "FlowSolution%" PetscInt_FMT, time_step)); 1336 PetscCallCGNSWrite(cg_sol_write(cgv->file_num, cgv->base, cgv->zone, solution_name, cgv->grid_loc, &sol), V, viewer); 1337 PetscCall(VecGetArrayRead(V, &v)); 1338 PetscCall(PetscSectionGetNumFields(section, &num_fields)); 1339 for (PetscInt field = 0; field < num_fields; field++) { 1340 PetscInt ncomp; 1341 const char *field_name; 1342 PetscCall(PetscSectionGetFieldName(section, field, &field_name)); 1343 PetscCall(PetscSectionGetFieldComponents(section, field, &ncomp)); 1344 for (PetscInt comp = 0; comp < ncomp; comp++) { 1345 int cgfield; 1346 const char *comp_name; 1347 char cgns_field_name[32]; // CGNS max field name is 32 1348 CGNS_ENUMT(DataType_t) datatype; 1349 PetscCall(PetscSectionGetComponentName(section, field, comp, &comp_name)); 1350 if (ncomp == 1 && comp_name[0] == '0' && comp_name[1] == '\0' && field_name[0] != '\0') PetscCall(PetscStrncpy(cgns_field_name, field_name, sizeof cgns_field_name)); 1351 else if (field_name[0] == '\0') PetscCall(PetscStrncpy(cgns_field_name, comp_name, sizeof cgns_field_name)); 1352 else PetscCall(PetscSNPrintf(cgns_field_name, sizeof cgns_field_name, "%s.%s", field_name, comp_name)); 1353 PetscCall(PetscCGNSDataType(PETSC_SCALAR, &datatype)); 1354 PetscCallCGNSWrite(cgp_field_write(cgv->file_num, cgv->base, cgv->zone, sol, datatype, cgns_field_name, &cgfield), V, viewer); 1355 for (PetscInt p = pStart, n = 0; p < pEnd; p++) { 1356 PetscInt off, dof; 1357 PetscCall(PetscSectionGetFieldDof(section, p, field, &dof)); 1358 if (dof == 0) continue; 1359 PetscCall(PetscSectionGetFieldOffset(section, p, field, &off)); 1360 for (PetscInt c = comp; c < dof; c += ncomp, n++) { 1361 switch (cgv->grid_loc) { 1362 case CGNS_ENUMV(Vertex): { 1363 PetscInt gn = cgv->node_l2g[n]; 1364 if (gn < cgv->nStart || cgv->nEnd <= gn) continue; 1365 cgv->nodal_field[gn - cgv->nStart] = v[off + c]; 1366 } break; 1367 case CGNS_ENUMV(CellCenter): { 1368 cgv->nodal_field[n] = v[off + c]; 1369 } break; 1370 default: 1371 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Can only pack for Vertex and CellCenter grid locations"); 1372 } 1373 } 1374 } 1375 // CGNS nodes use 1-based indexing 1376 cgsize_t start, end; 1377 switch (cgv->grid_loc) { 1378 case CGNS_ENUMV(Vertex): { 1379 start = cgv->nStart + 1; 1380 end = cgv->nEnd; 1381 } break; 1382 case CGNS_ENUMV(CellCenter): { 1383 start = cgv->eStart + 1; 1384 end = cgv->eEnd; 1385 } break; 1386 default: 1387 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Can only write for Vertex and CellCenter grid locations"); 1388 } 1389 PetscCallCGNSWriteData(cgp_field_write_data(cgv->file_num, cgv->base, cgv->zone, sol, cgfield, &start, &end, cgv->nodal_field), V, viewer); 1390 } 1391 } 1392 PetscCall(VecRestoreArrayRead(V, &v)); 1393 PetscCall(PetscViewerCGNSCheckBatch_Internal(viewer)); 1394 PetscFunctionReturn(PETSC_SUCCESS); 1395 } 1396 1397 PetscErrorCode VecLoad_Plex_CGNS_Internal(Vec V, PetscViewer viewer) 1398 { 1399 MPI_Comm comm; 1400 char buffer[CGIO_MAX_NAME_LENGTH + 1]; 1401 PetscViewer_CGNS *cgv = (PetscViewer_CGNS *)viewer->data; 1402 int cgid = cgv->file_num; 1403 PetscBool use_parallel_viewer = PETSC_FALSE; 1404 int z = 1; // Only support one zone 1405 int B = 1; // Only support one base 1406 int numComp; 1407 PetscInt V_numComps, mystartv, myendv, myownedv; 1408 1409 PetscFunctionBeginUser; 1410 PetscCall(PetscObjectGetComm((PetscObject)V, &comm)); 1411 1412 PetscCall(PetscOptionsGetBool(NULL, NULL, "-dm_plex_cgns_parallel", &use_parallel_viewer, NULL)); 1413 PetscCheck(use_parallel_viewer, comm, PETSC_ERR_USER_INPUT, "Cannot use VecLoad with CGNS file in serial reader; use -dm_plex_cgns_parallel to enable parallel reader"); 1414 1415 { // Get CGNS node ownership information 1416 int nbases, nzones; 1417 PetscInt NVertices; 1418 PetscLayout vtx_map; 1419 cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */ 1420 1421 PetscCallCGNSRead(cg_nbases(cgid, &nbases), V, viewer); 1422 PetscCheck(nbases <= 1, PETSC_COMM_SELF, PETSC_ERR_LIB, "CGNS file must have a single base, not %d", nbases); 1423 PetscCallCGNSRead(cg_nzones(cgid, B, &nzones), V, viewer); 1424 PetscCheck(nzones == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "limited to one zone %d", (int)nzones); 1425 1426 PetscCallCGNSRead(cg_zone_read(cgid, B, z, buffer, sizes), V, viewer); 1427 NVertices = sizes[0]; 1428 1429 PetscCall(PetscLayoutCreateFromSizes(comm, PETSC_DECIDE, NVertices, 1, &vtx_map)); 1430 PetscCall(PetscLayoutGetRange(vtx_map, &mystartv, &myendv)); 1431 PetscCall(PetscLayoutGetLocalSize(vtx_map, &myownedv)); 1432 PetscCall(PetscLayoutDestroy(&vtx_map)); 1433 } 1434 1435 { // -- Read data from file into Vec 1436 PetscScalar *fields = NULL; 1437 PetscSF sfNatural; 1438 1439 { // Check compatibility between sfNatural and the data source and sink 1440 DM dm; 1441 PetscInt nleaves, nroots, V_local_size; 1442 1443 PetscCall(VecGetDM(V, &dm)); 1444 PetscCall(DMGetNaturalSF(dm, &sfNatural)); 1445 PetscCheck(sfNatural, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "DM of Vec must have sfNatural"); 1446 PetscCall(PetscSFGetGraph(sfNatural, &nroots, &nleaves, NULL, NULL)); 1447 PetscCall(VecGetLocalSize(V, &V_local_size)); 1448 PetscCheck(nleaves == myownedv, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Number of locally owned vertices (% " PetscInt_FMT ") must match number of leaves in sfNatural (% " PetscInt_FMT ")", myownedv, nleaves); 1449 PetscCheck(V_local_size % nroots == 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Local Vec size (% " PetscInt_FMT ") not evenly divisible by number of roots in sfNatural (% " PetscInt_FMT ")", V_local_size, nroots); 1450 V_numComps = V_local_size / nroots; 1451 } 1452 1453 { // Read data into component-major ordering 1454 int isol, numSols; 1455 CGNS_ENUMT(DataType_t) datatype; 1456 double *fields_CGNS; 1457 1458 PetscCallCGNSRead(cg_nsols(cgid, B, z, &numSols), V, viewer); 1459 PetscCall(PetscViewerCGNSGetSolutionFileIndex_Internal(viewer, &isol)); 1460 PetscCallCGNSRead(cg_nfields(cgid, B, z, isol, &numComp), V, viewer); 1461 PetscCheck(V_numComps == numComp, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Vec sized for % " PetscInt_FMT " components per node, but file has %d components per node", V_numComps, numComp); 1462 1463 cgsize_t range_min[3] = {mystartv + 1, 1, 1}; 1464 cgsize_t range_max[3] = {myendv, 1, 1}; 1465 PetscCall(PetscMalloc1(myownedv * numComp, &fields_CGNS)); 1466 PetscCall(PetscMalloc1(myownedv * numComp, &fields)); 1467 for (int d = 0; d < numComp; ++d) { 1468 PetscCallCGNSRead(cg_field_info(cgid, B, z, isol, (d + 1), &datatype, buffer), V, viewer); 1469 PetscCheck(datatype == CGNS_ENUMV(RealDouble), PETSC_COMM_SELF, PETSC_ERR_ARG_NOTSAMETYPE, "Field %s in file is not of type double", buffer); 1470 PetscCallCGNSReadData(cgp_field_read_data(cgid, B, z, isol, (d + 1), range_min, range_max, &fields_CGNS[d * myownedv]), V, viewer); 1471 } 1472 for (int d = 0; d < numComp; ++d) { 1473 for (PetscInt v = 0; v < myownedv; ++v) fields[v * numComp + d] = fields_CGNS[d * myownedv + v]; 1474 } 1475 PetscCall(PetscFree(fields_CGNS)); 1476 } 1477 1478 { // Reduce fields into Vec array 1479 PetscScalar *V_array; 1480 MPI_Datatype fieldtype; 1481 1482 PetscCall(VecGetArrayWrite(V, &V_array)); 1483 PetscCallMPI(MPI_Type_contiguous(numComp, MPIU_SCALAR, &fieldtype)); 1484 PetscCallMPI(MPI_Type_commit(&fieldtype)); 1485 PetscCall(PetscSFReduceBegin(sfNatural, fieldtype, fields, V_array, MPI_REPLACE)); 1486 PetscCall(PetscSFReduceEnd(sfNatural, fieldtype, fields, V_array, MPI_REPLACE)); 1487 PetscCallMPI(MPI_Type_free(&fieldtype)); 1488 PetscCall(VecRestoreArrayWrite(V, &V_array)); 1489 } 1490 PetscCall(PetscFree(fields)); 1491 } 1492 PetscFunctionReturn(PETSC_SUCCESS); 1493 } 1494