Actual source code: plexcgns2.c
1: #define PETSCDM_DLL
2: #include <petsc/private/dmpleximpl.h>
3: #include <petsc/private/viewercgnsimpl.h>
5: #include <pcgnslib.h>
6: #include <cgns_io.h>
8: #if !defined(CGNS_ENUMT)
9: #define CGNS_ENUMT(a) a
10: #endif
11: #if !defined(CGNS_ENUMV)
12: #define CGNS_ENUMV(a) a
13: #endif
14: // Permute plex closure ordering to CGNS
15: static PetscErrorCode DMPlexCGNSGetPermutation_Internal(DMPolytopeType cell_type, PetscInt closure_size, CGNS_ENUMT(ElementType_t) * element_type, const int **perm)
16: {
17: CGNS_ENUMT(ElementType_t) element_type_tmp;
19: // https://cgns.github.io/CGNS_docs_current/sids/conv.html#unstructgrid
20: static const int bar_2[2] = {0, 1};
21: static const int bar_3[3] = {1, 2, 0};
22: static const int bar_4[4] = {2, 3, 0, 1};
23: static const int bar_5[5] = {3, 4, 0, 1, 2};
24: static const int tri_3[3] = {0, 1, 2};
25: static const int tri_6[6] = {3, 4, 5, 0, 1, 2};
26: static const int tri_10[10] = {7, 8, 9, 1, 2, 3, 4, 5, 6, 0};
27: static const int quad_4[4] = {0, 1, 2, 3};
28: static const int quad_9[9] = {
29: 5, 6, 7, 8, // vertices
30: 1, 2, 3, 4, // edges
31: 0, // center
32: };
33: static const int quad_16[] = {
34: 12, 13, 14, 15, // vertices
35: 4, 5, 6, 7, 8, 9, 10, 11, // edges
36: 0, 1, 3, 2, // centers
37: };
38: static const int quad_25[] = {
39: 21, 22, 23, 24, // vertices
40: 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, // edges
41: 0, 1, 2, 5, 8, 7, 6, 3, 4, // centers
42: };
43: static const int tetra_4[4] = {0, 2, 1, 3};
44: static const int tetra_10[10] = {6, 8, 7, 9, 2, 1, 0, 3, 5, 4};
45: static const int tetra_20[20] = {
46: 16, 18, 17, 19, // vertices
47: 9, 8, 7, 6, 5, 4, // bottom edges
48: 10, 11, 14, 15, 13, 12, // side edges
49: 0, 2, 3, 1, // faces
50: };
51: static const int hexa_8[8] = {0, 3, 2, 1, 4, 5, 6, 7};
52: static const int hexa_27[27] = {
53: 19, 22, 21, 20, 23, 24, 25, 26, // vertices
54: 10, 9, 8, 7, // bottom edges
55: 16, 15, 18, 17, // mid edges
56: 11, 12, 13, 14, // top edges
57: 1, 3, 5, 4, 6, 2, // faces
58: 0, // center
59: };
60: static const int hexa_64[64] = {
61: // 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
62: 56, 59, 58, 57, 60, 61, 62, 63, // vertices
63: 39, 38, 37, 36, 35, 34, 33, 32, // bottom edges
64: 51, 50, 48, 49, 52, 53, 55, 54, // mid edges; Paraview needs edge 21-22 swapped with 23-24
65: 40, 41, 42, 43, 44, 45, 46, 47, // top edges
66: 8, 10, 11, 9, // z-minus face
67: 16, 17, 19, 18, // y-minus face
68: 24, 25, 27, 26, // x-plus face
69: 20, 21, 23, 22, // y-plus face
70: 30, 28, 29, 31, // x-minus face
71: 12, 13, 15, 14, // z-plus face
72: 0, 1, 3, 2, 4, 5, 7, 6, // center
73: };
75: PetscFunctionBegin;
76: element_type_tmp = CGNS_ENUMV(ElementTypeNull);
77: *perm = NULL;
78: switch (cell_type) {
79: case DM_POLYTOPE_SEGMENT:
80: switch (closure_size) {
81: case 2:
82: element_type_tmp = CGNS_ENUMV(BAR_2);
83: *perm = bar_2;
84: case 3:
85: element_type_tmp = CGNS_ENUMV(BAR_3);
86: *perm = bar_3;
87: case 4:
88: element_type_tmp = CGNS_ENUMV(BAR_4);
89: *perm = bar_4;
90: break;
91: case 5:
92: element_type_tmp = CGNS_ENUMV(BAR_5);
93: *perm = bar_5;
94: break;
95: default:
96: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cell type %s with closure size %" PetscInt_FMT, DMPolytopeTypes[cell_type], closure_size);
97: }
98: break;
99: case DM_POLYTOPE_TRIANGLE:
100: switch (closure_size) {
101: case 3:
102: element_type_tmp = CGNS_ENUMV(TRI_3);
103: *perm = tri_3;
104: break;
105: case 6:
106: element_type_tmp = CGNS_ENUMV(TRI_6);
107: *perm = tri_6;
108: break;
109: case 10:
110: element_type_tmp = CGNS_ENUMV(TRI_10);
111: *perm = tri_10;
112: break;
113: default:
114: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cell type %s with closure size %" PetscInt_FMT, DMPolytopeTypes[cell_type], closure_size);
115: }
116: break;
117: case DM_POLYTOPE_QUADRILATERAL:
118: switch (closure_size) {
119: case 4:
120: element_type_tmp = CGNS_ENUMV(QUAD_4);
121: *perm = quad_4;
122: break;
123: case 9:
124: element_type_tmp = CGNS_ENUMV(QUAD_9);
125: *perm = quad_9;
126: break;
127: case 16:
128: element_type_tmp = CGNS_ENUMV(QUAD_16);
129: *perm = quad_16;
130: break;
131: case 25:
132: element_type_tmp = CGNS_ENUMV(QUAD_25);
133: *perm = quad_25;
134: break;
135: default:
136: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cell type %s with closure size %" PetscInt_FMT, DMPolytopeTypes[cell_type], closure_size);
137: }
138: break;
139: case DM_POLYTOPE_TETRAHEDRON:
140: switch (closure_size) {
141: case 4:
142: element_type_tmp = CGNS_ENUMV(TETRA_4);
143: *perm = tetra_4;
144: break;
145: case 10:
146: element_type_tmp = CGNS_ENUMV(TETRA_10);
147: *perm = tetra_10;
148: break;
149: case 20:
150: element_type_tmp = CGNS_ENUMV(TETRA_20);
151: *perm = tetra_20;
152: break;
153: default:
154: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cell type %s with closure size %" PetscInt_FMT, DMPolytopeTypes[cell_type], closure_size);
155: }
156: break;
157: case DM_POLYTOPE_HEXAHEDRON:
158: switch (closure_size) {
159: case 8:
160: element_type_tmp = CGNS_ENUMV(HEXA_8);
161: *perm = hexa_8;
162: break;
163: case 27:
164: element_type_tmp = CGNS_ENUMV(HEXA_27);
165: *perm = hexa_27;
166: break;
167: case 64:
168: element_type_tmp = CGNS_ENUMV(HEXA_64);
169: *perm = hexa_64;
170: break;
171: default:
172: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cell type %s with closure size %" PetscInt_FMT, DMPolytopeTypes[cell_type], closure_size);
173: }
174: break;
175: default:
176: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cell type %s with closure size %" PetscInt_FMT, DMPolytopeTypes[cell_type], closure_size);
177: }
178: if (element_type) *element_type = element_type_tmp;
179: PetscFunctionReturn(PETSC_SUCCESS);
180: }
182: /*
183: Input Parameters:
184: + cellType - The CGNS-defined element type
186: Output Parameters:
187: + dmcelltype - The equivalent DMPolytopeType for the cellType
188: . numCorners - Number of corners of the polytope
189: - dim - The topological dimension of the polytope
191: CGNS elements defined in: https://cgns.github.io/CGNS_docs_current/sids/conv.html#unstructgrid
192: */
193: static inline PetscErrorCode CGNSElementTypeGetTopologyInfo(CGNS_ENUMT(ElementType_t) cellType, DMPolytopeType *dmcelltype, PetscInt *numCorners, PetscInt *dim)
194: {
195: DMPolytopeType _dmcelltype;
197: PetscFunctionBeginUser;
198: switch (cellType) {
199: case CGNS_ENUMV(BAR_2):
200: case CGNS_ENUMV(BAR_3):
201: case CGNS_ENUMV(BAR_4):
202: case CGNS_ENUMV(BAR_5):
203: _dmcelltype = DM_POLYTOPE_SEGMENT;
204: break;
205: case CGNS_ENUMV(TRI_3):
206: case CGNS_ENUMV(TRI_6):
207: case CGNS_ENUMV(TRI_9):
208: case CGNS_ENUMV(TRI_10):
209: case CGNS_ENUMV(TRI_12):
210: case CGNS_ENUMV(TRI_15):
211: _dmcelltype = DM_POLYTOPE_TRIANGLE;
212: break;
213: case CGNS_ENUMV(QUAD_4):
214: case CGNS_ENUMV(QUAD_8):
215: case CGNS_ENUMV(QUAD_9):
216: case CGNS_ENUMV(QUAD_12):
217: case CGNS_ENUMV(QUAD_16):
218: case CGNS_ENUMV(QUAD_P4_16):
219: case CGNS_ENUMV(QUAD_25):
220: _dmcelltype = DM_POLYTOPE_QUADRILATERAL;
221: break;
222: case CGNS_ENUMV(TETRA_4):
223: case CGNS_ENUMV(TETRA_10):
224: case CGNS_ENUMV(TETRA_16):
225: case CGNS_ENUMV(TETRA_20):
226: case CGNS_ENUMV(TETRA_22):
227: case CGNS_ENUMV(TETRA_34):
228: case CGNS_ENUMV(TETRA_35):
229: _dmcelltype = DM_POLYTOPE_TETRAHEDRON;
230: break;
231: case CGNS_ENUMV(PYRA_5):
232: case CGNS_ENUMV(PYRA_13):
233: case CGNS_ENUMV(PYRA_14):
234: case CGNS_ENUMV(PYRA_21):
235: case CGNS_ENUMV(PYRA_29):
236: case CGNS_ENUMV(PYRA_P4_29):
237: case CGNS_ENUMV(PYRA_30):
238: case CGNS_ENUMV(PYRA_50):
239: case CGNS_ENUMV(PYRA_55):
240: _dmcelltype = DM_POLYTOPE_PYRAMID;
241: break;
242: case CGNS_ENUMV(PENTA_6):
243: case CGNS_ENUMV(PENTA_15):
244: case CGNS_ENUMV(PENTA_18):
245: case CGNS_ENUMV(PENTA_24):
246: case CGNS_ENUMV(PENTA_33):
247: case CGNS_ENUMV(PENTA_38):
248: case CGNS_ENUMV(PENTA_40):
249: case CGNS_ENUMV(PENTA_66):
250: case CGNS_ENUMV(PENTA_75):
251: _dmcelltype = DM_POLYTOPE_TRI_PRISM;
252: break;
253: case CGNS_ENUMV(HEXA_8):
254: case CGNS_ENUMV(HEXA_20):
255: case CGNS_ENUMV(HEXA_27):
256: case CGNS_ENUMV(HEXA_32):
257: case CGNS_ENUMV(HEXA_44):
258: case CGNS_ENUMV(HEXA_56):
259: case CGNS_ENUMV(HEXA_64):
260: case CGNS_ENUMV(HEXA_98):
261: case CGNS_ENUMV(HEXA_125):
262: _dmcelltype = DM_POLYTOPE_HEXAHEDRON;
263: break;
264: case CGNS_ENUMV(MIXED):
265: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid CGNS ElementType_t: MIXED");
266: default:
267: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid CGNS ElementType_t: %d", (int)cellType);
268: }
270: if (dmcelltype) *dmcelltype = _dmcelltype;
271: if (numCorners) *numCorners = DMPolytopeTypeGetNumVertices(_dmcelltype);
272: if (dim) *dim = DMPolytopeTypeGetDim(_dmcelltype);
273: PetscFunctionReturn(PETSC_SUCCESS);
274: }
276: /*
277: Input Parameters:
278: + cellType - The CGNS-defined cell type
280: Output Parameters:
281: + numClosure - Number of nodes that define the function space on the cell
282: - pOrder - The polynomial order of the cell
284: CGNS elements defined in: https://cgns.github.io/CGNS_docs_current/sids/conv.html#unstructgrid
286: Note: we only support "full" elements, ie. not seredipity elements
287: */
288: static inline PetscErrorCode CGNSElementTypeGetDiscretizationInfo(CGNS_ENUMT(ElementType_t) cellType, PetscInt *numClosure, PetscInt *pOrder)
289: {
290: PetscInt _numClosure, _pOrder;
292: PetscFunctionBeginUser;
293: switch (cellType) {
294: case CGNS_ENUMV(BAR_2):
295: _numClosure = 2;
296: _pOrder = 1;
297: break;
298: case CGNS_ENUMV(BAR_3):
299: _numClosure = 3;
300: _pOrder = 2;
301: break;
302: case CGNS_ENUMV(BAR_4):
303: _numClosure = 4;
304: _pOrder = 3;
305: break;
306: case CGNS_ENUMV(BAR_5):
307: _numClosure = 5;
308: _pOrder = 4;
309: break;
310: case CGNS_ENUMV(TRI_3):
311: _numClosure = 3;
312: _pOrder = 1;
313: break;
314: case CGNS_ENUMV(TRI_6):
315: _numClosure = 6;
316: _pOrder = 2;
317: break;
318: case CGNS_ENUMV(TRI_10):
319: _numClosure = 10;
320: _pOrder = 3;
321: break;
322: case CGNS_ENUMV(TRI_15):
323: _numClosure = 15;
324: _pOrder = 4;
325: break;
326: case CGNS_ENUMV(QUAD_4):
327: _numClosure = 4;
328: _pOrder = 1;
329: break;
330: case CGNS_ENUMV(QUAD_9):
331: _numClosure = 9;
332: _pOrder = 2;
333: break;
334: case CGNS_ENUMV(QUAD_16):
335: _numClosure = 16;
336: _pOrder = 3;
337: break;
338: case CGNS_ENUMV(QUAD_25):
339: _numClosure = 25;
340: _pOrder = 4;
341: break;
342: case CGNS_ENUMV(TETRA_4):
343: _numClosure = 4;
344: _pOrder = 1;
345: break;
346: case CGNS_ENUMV(TETRA_10):
347: _numClosure = 10;
348: _pOrder = 2;
349: break;
350: case CGNS_ENUMV(TETRA_20):
351: _numClosure = 20;
352: _pOrder = 3;
353: break;
354: case CGNS_ENUMV(TETRA_35):
355: _numClosure = 35;
356: _pOrder = 4;
357: break;
358: case CGNS_ENUMV(PYRA_5):
359: _numClosure = 5;
360: _pOrder = 1;
361: break;
362: case CGNS_ENUMV(PYRA_14):
363: _numClosure = 14;
364: _pOrder = 2;
365: break;
366: case CGNS_ENUMV(PYRA_30):
367: _numClosure = 30;
368: _pOrder = 3;
369: break;
370: case CGNS_ENUMV(PYRA_55):
371: _numClosure = 55;
372: _pOrder = 4;
373: break;
374: case CGNS_ENUMV(PENTA_6):
375: _numClosure = 6;
376: _pOrder = 1;
377: break;
378: case CGNS_ENUMV(PENTA_18):
379: _numClosure = 18;
380: _pOrder = 2;
381: break;
382: case CGNS_ENUMV(PENTA_40):
383: _numClosure = 40;
384: _pOrder = 3;
385: break;
386: case CGNS_ENUMV(PENTA_75):
387: _numClosure = 75;
388: _pOrder = 4;
389: break;
390: case CGNS_ENUMV(HEXA_8):
391: _numClosure = 8;
392: _pOrder = 1;
393: break;
394: case CGNS_ENUMV(HEXA_27):
395: _numClosure = 27;
396: _pOrder = 2;
397: break;
398: case CGNS_ENUMV(HEXA_64):
399: _numClosure = 64;
400: _pOrder = 3;
401: break;
402: case CGNS_ENUMV(HEXA_125):
403: _numClosure = 125;
404: _pOrder = 4;
405: break;
406: case CGNS_ENUMV(MIXED):
407: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid CGNS ElementType_t: MIXED");
408: default:
409: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unsupported or Invalid cell type %d", (int)cellType);
410: }
411: if (numClosure) *numClosure = _numClosure;
412: if (pOrder) *pOrder = _pOrder;
413: PetscFunctionReturn(PETSC_SUCCESS);
414: }
416: static PetscErrorCode PetscCGNSDataType(PetscDataType pd, CGNS_ENUMT(DataType_t) * cd)
417: {
418: PetscFunctionBegin;
419: switch (pd) {
420: case PETSC_FLOAT:
421: *cd = CGNS_ENUMV(RealSingle);
422: break;
423: case PETSC_DOUBLE:
424: *cd = CGNS_ENUMV(RealDouble);
425: break;
426: case PETSC_COMPLEX:
427: *cd = CGNS_ENUMV(ComplexDouble);
428: break;
429: default:
430: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Data type %s", PetscDataTypes[pd]);
431: }
432: PetscFunctionReturn(PETSC_SUCCESS);
433: }
435: PetscErrorCode DMPlexCreateCGNSFromFile_Internal(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
436: {
437: int cgid = -1;
438: PetscBool use_parallel_viewer = PETSC_FALSE;
440: PetscFunctionBegin;
441: PetscAssertPointer(filename, 2);
442: PetscCall(PetscViewerCGNSRegisterLogEvents_Internal());
443: PetscCall(PetscOptionsGetBool(NULL, NULL, "-dm_plex_cgns_parallel", &use_parallel_viewer, NULL));
445: if (use_parallel_viewer) {
446: PetscCallCGNS(cgp_mpi_comm(comm));
447: PetscCallCGNSOpen(cgp_open(filename, CG_MODE_READ, &cgid), 0, 0);
448: PetscCheck(cgid > 0, PETSC_COMM_SELF, PETSC_ERR_LIB, "cgp_open(\"%s\",...) did not return a valid file ID", filename);
449: PetscCall(DMPlexCreateCGNS(comm, cgid, interpolate, dm));
450: PetscCallCGNSClose(cgp_close(cgid), 0, 0);
451: } else {
452: PetscCallCGNSOpen(cg_open(filename, CG_MODE_READ, &cgid), 0, 0);
453: PetscCheck(cgid > 0, PETSC_COMM_SELF, PETSC_ERR_LIB, "cg_open(\"%s\",...) did not return a valid file ID", filename);
454: PetscCall(DMPlexCreateCGNS(comm, cgid, interpolate, dm));
455: PetscCallCGNSClose(cg_close(cgid), 0, 0);
456: }
457: PetscFunctionReturn(PETSC_SUCCESS);
458: }
460: PetscErrorCode DMPlexCreateCGNS_Internal_Serial(MPI_Comm comm, PetscInt cgid, PetscBool interpolate, DM *dm)
461: {
462: PetscMPIInt num_proc, rank;
463: DM cdm;
464: DMLabel label;
465: PetscSection coordSection;
466: Vec coordinates;
467: PetscScalar *coords;
468: PetscInt *cellStart, *vertStart, v;
469: PetscInt labelIdRange[2], labelId;
470: /* Read from file */
471: char basename[CGIO_MAX_NAME_LENGTH + 1];
472: char buffer[CGIO_MAX_NAME_LENGTH + 1];
473: int dim = 0, physDim = 0, coordDim = 0, numVertices = 0, numCells = 0;
474: int nzones = 0;
475: const int B = 1; // Only support single base
477: PetscFunctionBegin;
478: PetscCallMPI(MPI_Comm_rank(comm, &rank));
479: PetscCallMPI(MPI_Comm_size(comm, &num_proc));
480: PetscCall(DMCreate(comm, dm));
481: PetscCall(DMSetType(*dm, DMPLEX));
483: /* Open CGNS II file and read basic information on rank 0, then broadcast to all processors */
484: if (rank == 0) {
485: int nbases, z;
487: PetscCallCGNSRead(cg_nbases(cgid, &nbases), *dm, 0);
488: PetscCheck(nbases <= 1, PETSC_COMM_SELF, PETSC_ERR_LIB, "CGNS file must have a single base, not %d", nbases);
489: PetscCallCGNSRead(cg_base_read(cgid, B, basename, &dim, &physDim), *dm, 0);
490: PetscCallCGNSRead(cg_nzones(cgid, B, &nzones), *dm, 0);
491: PetscCall(PetscCalloc2(nzones + 1, &cellStart, nzones + 1, &vertStart));
492: for (z = 1; z <= nzones; ++z) {
493: cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */
495: PetscCallCGNSRead(cg_zone_read(cgid, B, z, buffer, sizes), *dm, 0);
496: numVertices += sizes[0];
497: numCells += sizes[1];
498: cellStart[z] += sizes[1] + cellStart[z - 1];
499: vertStart[z] += sizes[0] + vertStart[z - 1];
500: }
501: for (z = 1; z <= nzones; ++z) vertStart[z] += numCells;
502: coordDim = dim;
503: }
504: PetscCallMPI(MPI_Bcast(basename, CGIO_MAX_NAME_LENGTH + 1, MPI_CHAR, 0, comm));
505: PetscCallMPI(MPI_Bcast(&dim, 1, MPI_INT, 0, comm));
506: PetscCallMPI(MPI_Bcast(&coordDim, 1, MPI_INT, 0, comm));
507: PetscCallMPI(MPI_Bcast(&nzones, 1, MPI_INT, 0, comm));
509: PetscCall(PetscObjectSetName((PetscObject)*dm, basename));
510: PetscCall(DMSetDimension(*dm, dim));
511: PetscCall(DMCreateLabel(*dm, "celltype"));
512: PetscCall(DMPlexSetChart(*dm, 0, numCells + numVertices));
514: /* Read zone information */
515: if (rank == 0) {
516: int z, c, c_loc;
518: /* Read the cell set connectivity table and build mesh topology
519: CGNS standard requires that cells in a zone be numbered sequentially and be pairwise disjoint. */
520: /* First set sizes */
521: for (z = 1, c = 0; z <= nzones; ++z) {
522: CGNS_ENUMT(ZoneType_t) zonetype;
523: int nsections;
524: CGNS_ENUMT(ElementType_t) cellType;
525: cgsize_t start, end;
526: int nbndry, parentFlag;
527: PetscInt numCorners, pOrder;
528: DMPolytopeType ctype;
529: const int S = 1; // Only support single section
531: PetscCallCGNSRead(cg_zone_type(cgid, B, z, &zonetype), *dm, 0);
532: PetscCheck(zonetype != CGNS_ENUMV(Structured), PETSC_COMM_SELF, PETSC_ERR_LIB, "Can only handle Unstructured zones for CGNS");
533: PetscCallCGNSRead(cg_nsections(cgid, B, z, &nsections), *dm, 0);
534: PetscCheck(nsections <= 1, PETSC_COMM_SELF, PETSC_ERR_LIB, "CGNS file must have a single section, not %d", nsections);
535: PetscCallCGNSRead(cg_section_read(cgid, B, z, S, buffer, &cellType, &start, &end, &nbndry, &parentFlag), *dm, 0);
536: if (cellType == CGNS_ENUMV(MIXED)) {
537: cgsize_t elementDataSize, *elements;
538: PetscInt off;
540: PetscCallCGNSRead(cg_ElementDataSize(cgid, B, z, S, &elementDataSize), *dm, 0);
541: PetscCall(PetscMalloc1(elementDataSize, &elements));
542: PetscCallCGNSReadData(cg_poly_elements_read(cgid, B, z, S, elements, NULL, NULL), *dm, 0);
543: for (c_loc = start, off = 0; c_loc <= end; ++c_loc, ++c) {
544: PetscCall(CGNSElementTypeGetTopologyInfo((CGNS_ENUMT(ElementType_t))elements[off], &ctype, &numCorners, NULL));
545: PetscCall(CGNSElementTypeGetDiscretizationInfo((CGNS_ENUMT(ElementType_t))elements[off], NULL, &pOrder));
546: PetscCheck(pOrder == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Serial CGNS reader only supports first order elements, not %" PetscInt_FMT " order", pOrder);
547: PetscCall(DMPlexSetConeSize(*dm, c, numCorners));
548: PetscCall(DMPlexSetCellType(*dm, c, ctype));
549: off += numCorners + 1;
550: }
551: PetscCall(PetscFree(elements));
552: } else {
553: PetscCall(CGNSElementTypeGetTopologyInfo(cellType, &ctype, &numCorners, NULL));
554: PetscCall(CGNSElementTypeGetDiscretizationInfo(cellType, NULL, &pOrder));
555: PetscCheck(pOrder == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Serial CGNS reader only supports first order elements, not %" PetscInt_FMT " order", pOrder);
556: for (c_loc = start; c_loc <= end; ++c_loc, ++c) {
557: PetscCall(DMPlexSetConeSize(*dm, c, numCorners));
558: PetscCall(DMPlexSetCellType(*dm, c, ctype));
559: }
560: }
561: }
562: for (v = numCells; v < numCells + numVertices; ++v) PetscCall(DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT));
563: }
565: PetscCall(DMSetUp(*dm));
567: PetscCall(DMCreateLabel(*dm, "zone"));
568: if (rank == 0) {
569: int z, c, c_loc, v_loc;
571: PetscCall(DMGetLabel(*dm, "zone", &label));
572: for (z = 1, c = 0; z <= nzones; ++z) {
573: CGNS_ENUMT(ElementType_t) cellType;
574: cgsize_t elementDataSize, *elements, start, end;
575: int nbndry, parentFlag;
576: PetscInt *cone, numc, numCorners, maxCorners = 27, pOrder;
577: const int S = 1; // Only support single section
579: PetscCallCGNSRead(cg_section_read(cgid, B, z, S, buffer, &cellType, &start, &end, &nbndry, &parentFlag), *dm, 0);
580: numc = end - start;
581: PetscCallCGNSRead(cg_ElementDataSize(cgid, B, z, S, &elementDataSize), *dm, 0);
582: PetscCall(PetscMalloc2(elementDataSize, &elements, maxCorners, &cone));
583: PetscCallCGNSReadData(cg_poly_elements_read(cgid, B, z, S, elements, NULL, NULL), *dm, 0);
584: if (cellType == CGNS_ENUMV(MIXED)) {
585: /* CGNS uses Fortran-based indexing, DMPlex uses C-style and numbers cell first then vertices. */
586: for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) {
587: PetscCall(CGNSElementTypeGetTopologyInfo((CGNS_ENUMT(ElementType_t))elements[v], NULL, &numCorners, NULL));
588: PetscCall(CGNSElementTypeGetDiscretizationInfo((CGNS_ENUMT(ElementType_t))elements[v], NULL, &pOrder));
589: PetscCheck(pOrder == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Serial CGNS reader only supports first order elements, not %" PetscInt_FMT " order", pOrder);
590: ++v;
591: for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) cone[v_loc] = elements[v] + numCells - 1;
592: PetscCall(DMPlexReorderCell(*dm, c, cone));
593: PetscCall(DMPlexSetCone(*dm, c, cone));
594: PetscCall(DMLabelSetValue(label, c, z));
595: }
596: } else {
597: PetscCall(CGNSElementTypeGetTopologyInfo(cellType, NULL, &numCorners, NULL));
598: PetscCall(CGNSElementTypeGetDiscretizationInfo(cellType, NULL, &pOrder));
599: PetscCheck(pOrder == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Serial CGNS reader only supports first order elements, not %" PetscInt_FMT " order", pOrder);
600: /* CGNS uses Fortran-based indexing, DMPlex uses C-style and numbers cell first then vertices. */
601: for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) {
602: for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) cone[v_loc] = elements[v] + numCells - 1;
603: PetscCall(DMPlexReorderCell(*dm, c, cone));
604: PetscCall(DMPlexSetCone(*dm, c, cone));
605: PetscCall(DMLabelSetValue(label, c, z));
606: }
607: }
608: PetscCall(PetscFree2(elements, cone));
609: }
610: }
612: PetscCall(DMPlexSymmetrize(*dm));
613: PetscCall(DMPlexStratify(*dm));
614: if (interpolate) PetscCall(DMPlexInterpolateInPlace_Internal(*dm));
616: /* Read coordinates */
617: PetscCall(DMSetCoordinateDim(*dm, coordDim));
618: PetscCall(DMGetCoordinateDM(*dm, &cdm));
619: PetscCall(DMGetLocalSection(cdm, &coordSection));
620: PetscCall(PetscSectionSetNumFields(coordSection, 1));
621: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, coordDim));
622: PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices));
623: for (v = numCells; v < numCells + numVertices; ++v) {
624: PetscCall(PetscSectionSetDof(coordSection, v, dim));
625: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, coordDim));
626: }
627: PetscCall(PetscSectionSetUp(coordSection));
629: PetscCall(DMCreateLocalVector(cdm, &coordinates));
630: PetscCall(VecGetArray(coordinates, &coords));
631: if (rank == 0) {
632: PetscInt off = 0;
633: float *x[3];
634: int z, d;
636: PetscCall(PetscMalloc3(numVertices, &x[0], numVertices, &x[1], numVertices, &x[2]));
637: for (z = 1; z <= nzones; ++z) {
638: CGNS_ENUMT(DataType_t) datatype;
639: cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */
640: cgsize_t range_min[3] = {1, 1, 1};
641: cgsize_t range_max[3] = {1, 1, 1};
642: int ngrids, ncoords;
644: PetscCallCGNSRead(cg_zone_read(cgid, B, z, buffer, sizes), *dm, 0);
645: range_max[0] = sizes[0];
646: PetscCallCGNSRead(cg_ngrids(cgid, B, z, &ngrids), *dm, 0);
647: PetscCheck(ngrids <= 1, PETSC_COMM_SELF, PETSC_ERR_LIB, "CGNS file must have a single grid, not %d", ngrids);
648: PetscCallCGNSRead(cg_ncoords(cgid, B, z, &ncoords), *dm, 0);
649: PetscCheck(ncoords == coordDim, PETSC_COMM_SELF, PETSC_ERR_LIB, "CGNS file must have a coordinate array for each dimension, not %d", ncoords);
650: for (d = 0; d < coordDim; ++d) {
651: PetscCallCGNSRead(cg_coord_info(cgid, B, z, 1 + d, &datatype, buffer), *dm, 0);
652: PetscCallCGNSReadData(cg_coord_read(cgid, B, z, buffer, CGNS_ENUMV(RealSingle), range_min, range_max, x[d]), *dm, 0);
653: }
654: if (coordDim >= 1) {
655: for (v = 0; v < sizes[0]; ++v) coords[(v + off) * coordDim + 0] = x[0][v];
656: }
657: if (coordDim >= 2) {
658: for (v = 0; v < sizes[0]; ++v) coords[(v + off) * coordDim + 1] = x[1][v];
659: }
660: if (coordDim >= 3) {
661: for (v = 0; v < sizes[0]; ++v) coords[(v + off) * coordDim + 2] = x[2][v];
662: }
663: off += sizes[0];
664: }
665: PetscCall(PetscFree3(x[0], x[1], x[2]));
666: }
667: PetscCall(VecRestoreArray(coordinates, &coords));
669: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
670: PetscCall(VecSetBlockSize(coordinates, coordDim));
671: PetscCall(DMSetCoordinatesLocal(*dm, coordinates));
672: PetscCall(VecDestroy(&coordinates));
674: /* Read boundary conditions */
675: PetscCall(DMGetNumLabels(*dm, &labelIdRange[0]));
676: if (rank == 0) {
677: CGNS_ENUMT(BCType_t) bctype;
678: CGNS_ENUMT(DataType_t) datatype;
679: CGNS_ENUMT(PointSetType_t) pointtype;
680: cgsize_t *points;
681: PetscReal *normals;
682: int normal[3];
683: char *bcname = buffer;
684: cgsize_t npoints, nnormals;
685: int z, nbc, bc, c, ndatasets;
687: for (z = 1; z <= nzones; ++z) {
688: PetscCallCGNSRead(cg_nbocos(cgid, B, z, &nbc), *dm, 0);
689: for (bc = 1; bc <= nbc; ++bc) {
690: PetscCallCGNSRead(cg_boco_info(cgid, B, z, bc, bcname, &bctype, &pointtype, &npoints, normal, &nnormals, &datatype, &ndatasets), *dm, 0);
691: PetscCall(DMCreateLabel(*dm, bcname));
692: PetscCall(DMGetLabel(*dm, bcname, &label));
693: PetscCall(PetscMalloc2(npoints, &points, nnormals, &normals));
694: PetscCallCGNSReadData(cg_boco_read(cgid, B, z, bc, points, (void *)normals), *dm, 0);
695: if (pointtype == CGNS_ENUMV(ElementRange)) {
696: // Range of cells: assuming half-open interval
697: for (c = points[0]; c < points[1]; ++c) PetscCall(DMLabelSetValue(label, c - cellStart[z - 1], 1));
698: } else if (pointtype == CGNS_ENUMV(ElementList)) {
699: // List of cells
700: for (c = 0; c < npoints; ++c) PetscCall(DMLabelSetValue(label, points[c] - cellStart[z - 1], 1));
701: } else if (pointtype == CGNS_ENUMV(PointRange)) {
702: CGNS_ENUMT(GridLocation_t) gridloc;
704: // List of points:
705: PetscCallCGNS(cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end"));
706: PetscCallCGNSRead(cg_gridlocation_read(&gridloc), *dm, 0);
707: // Range of points: assuming half-open interval
708: for (c = points[0]; c < points[1]; ++c) {
709: if (gridloc == CGNS_ENUMV(Vertex)) PetscCall(DMLabelSetValue(label, c - vertStart[z - 1], 1));
710: else PetscCall(DMLabelSetValue(label, c - cellStart[z - 1], 1));
711: }
712: } else if (pointtype == CGNS_ENUMV(PointList)) {
713: CGNS_ENUMT(GridLocation_t) gridloc;
715: // List of points:
716: PetscCallCGNS(cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end"));
717: PetscCallCGNSRead(cg_gridlocation_read(&gridloc), *dm, 0);
718: for (c = 0; c < npoints; ++c) {
719: if (gridloc == CGNS_ENUMV(Vertex)) PetscCall(DMLabelSetValue(label, points[c] - vertStart[z - 1], 1));
720: else PetscCall(DMLabelSetValue(label, points[c] - cellStart[z - 1], 1));
721: }
722: } else SETERRQ(comm, PETSC_ERR_SUP, "Unsupported point set type %d", (int)pointtype);
723: PetscCall(PetscFree2(points, normals));
724: }
725: }
726: PetscCall(PetscFree2(cellStart, vertStart));
727: }
728: PetscCall(DMGetNumLabels(*dm, &labelIdRange[1]));
729: PetscCallMPI(MPI_Bcast(labelIdRange, 2, MPIU_INT, 0, comm));
731: /* Create BC labels at all processes */
732: for (labelId = labelIdRange[0]; labelId < labelIdRange[1]; ++labelId) {
733: char *labelName = buffer;
734: size_t len = sizeof(buffer);
735: const char *locName;
737: if (rank == 0) {
738: PetscCall(DMGetLabelByNum(*dm, labelId, &label));
739: PetscCall(PetscObjectGetName((PetscObject)label, &locName));
740: PetscCall(PetscStrncpy(labelName, locName, len));
741: }
742: PetscCallMPI(MPI_Bcast(labelName, (PetscMPIInt)len, MPIU_INT, 0, comm));
743: PetscCallMPI(DMCreateLabel(*dm, labelName));
744: }
745: PetscFunctionReturn(PETSC_SUCCESS);
746: }
748: PetscErrorCode DMPlexCreateCGNS_Internal_Parallel(MPI_Comm comm, PetscInt cgid, PetscBool interpolate, DM *dm)
749: {
750: PetscMPIInt num_proc, rank;
751: /* Read from file */
752: char basename[CGIO_MAX_NAME_LENGTH + 1];
753: char buffer[CGIO_MAX_NAME_LENGTH + 1];
754: int dim = 0, physDim = 0, coordDim = 0;
755: PetscInt NVertices = 0, NCells = 0;
756: int nzones = 0, nbases;
757: int z = 1; // Only supports single zone files
758: int B = 1; // Only supports single base
760: PetscFunctionBegin;
761: PetscCallMPI(MPI_Comm_rank(comm, &rank));
762: PetscCallMPI(MPI_Comm_size(comm, &num_proc));
763: PetscCall(DMCreate(comm, dm));
764: PetscCall(DMSetType(*dm, DMPLEX));
766: PetscCallCGNSRead(cg_nbases(cgid, &nbases), *dm, 0);
767: PetscCheck(nbases <= 1, PETSC_COMM_SELF, PETSC_ERR_LIB, "CGNS file must have a single base, not %d", nbases);
768: // From the CGNS web page cell_dim phys_dim (embedding space in PETSC) CGNS defines as length of spatial vectors/components)
769: PetscCallCGNSRead(cg_base_read(cgid, B, basename, &dim, &physDim), *dm, 0);
770: PetscCallCGNSRead(cg_nzones(cgid, B, &nzones), *dm, 0);
771: PetscCheck(nzones == 1, PETSC_COMM_SELF, PETSC_ERR_LIB, "Parallel reader limited to one zone, not %d", nzones);
772: {
773: cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */
775: PetscCallCGNSRead(cg_zone_read(cgid, B, z, buffer, sizes), *dm, 0);
776: NVertices = sizes[0];
777: NCells = sizes[1];
778: }
780: PetscCall(PetscObjectSetName((PetscObject)*dm, basename));
781: PetscCall(DMSetDimension(*dm, dim));
782: coordDim = dim;
784: // 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
785: // call to get this right but continuing for now with single section, single topology, one zone.
786: // establish element ranges for my rank
787: PetscInt mystarte, myende, mystartv, myendv, myownede, myownedv;
788: PetscLayout elem_map, vtx_map;
789: PetscCall(PetscLayoutCreateFromSizes(comm, PETSC_DECIDE, NCells, 1, &elem_map));
790: PetscCall(PetscLayoutCreateFromSizes(comm, PETSC_DECIDE, NVertices, 1, &vtx_map));
791: PetscCall(PetscLayoutGetRange(elem_map, &mystarte, &myende));
792: PetscCall(PetscLayoutGetLocalSize(elem_map, &myownede));
793: PetscCall(PetscLayoutGetRange(vtx_map, &mystartv, &myendv));
794: PetscCall(PetscLayoutGetLocalSize(vtx_map, &myownedv));
796: // -- Build Plex in parallel
797: DMPolytopeType dm_cell_type = DM_POLYTOPE_UNKNOWN;
798: PetscInt pOrder = 1, numClosure = -1;
799: cgsize_t *elements;
800: {
801: int nsections;
802: PetscInt *elementsQ1, numCorners = -1;
803: const int *perm;
804: cgsize_t start, end; // Throwaway
806: cg_nsections(cgid, B, z, &nsections);
807: // Read element connectivity
808: for (int index_sect = 1; index_sect <= nsections; index_sect++) {
809: int nbndry, parentFlag;
810: PetscInt cell_dim;
811: CGNS_ENUMT(ElementType_t) cellType;
813: PetscCallCGNSRead(cg_section_read(cgid, B, z, index_sect, buffer, &cellType, &start, &end, &nbndry, &parentFlag), *dm, 0);
815: PetscCall(CGNSElementTypeGetTopologyInfo(cellType, &dm_cell_type, &numCorners, &cell_dim));
816: // Skip over element that are not max dimension (ie. boundary elements)
817: if (cell_dim != dim) continue;
818: PetscCall(CGNSElementTypeGetDiscretizationInfo(cellType, &numClosure, &pOrder));
819: PetscCall(PetscMalloc1(myownede * numClosure, &elements));
820: PetscCallCGNSReadData(cgp_elements_read_data(cgid, B, z, index_sect, mystarte + 1, myende, elements), *dm, 0);
821: for (PetscInt v = 0; v < myownede * numClosure; ++v) elements[v] -= 1; // 0 based
822: break;
823: }
825: // Create corners-only connectivity
826: PetscCall(PetscMalloc1(myownede * numCorners, &elementsQ1));
827: PetscCall(DMPlexCGNSGetPermutation_Internal(dm_cell_type, numCorners, NULL, &perm));
828: for (PetscInt e = 0; e < myownede; ++e) {
829: for (PetscInt v = 0; v < numCorners; ++v) elementsQ1[e * numCorners + perm[v]] = elements[e * numClosure + v];
830: }
832: // Build cell-vertex Plex
833: PetscCall(DMPlexBuildFromCellListParallel(*dm, myownede, myownedv, NVertices, numCorners, elementsQ1, NULL, NULL));
834: PetscCall(DMViewFromOptions(*dm, NULL, "-corner_dm_view"));
835: PetscCall(PetscFree(elementsQ1));
836: }
838: if (interpolate) PetscCall(DMPlexInterpolateInPlace_Internal(*dm));
840: // -- Create SF for naive nodal-data read to elements
841: PetscSF plex_to_cgns_sf;
842: {
843: PetscInt nleaves, num_comp;
844: PetscInt *leaf, num_leaves = 0;
845: PetscInt cStart, cEnd;
846: const int *perm;
847: PetscSF cgns_to_local_sf;
848: PetscSection local_section;
849: PetscFE fe;
851: // sfNatural requires PetscSection to handle DMDistribute, so we use PetscFE to define the section
852: // Use number of components = 1 to work with just the nodes themselves
853: PetscCall(PetscFECreateLagrangeByCell(PETSC_COMM_SELF, dim, 1, dm_cell_type, pOrder, PETSC_DETERMINE, &fe));
854: PetscCall(PetscObjectSetName((PetscObject)fe, "FE for sfNatural"));
855: PetscCall(DMAddField(*dm, NULL, (PetscObject)fe));
856: PetscCall(DMCreateDS(*dm));
857: PetscCall(PetscFEDestroy(&fe));
859: PetscCall(DMGetLocalSection(*dm, &local_section));
860: PetscCall(PetscSectionViewFromOptions(local_section, NULL, "-fe_natural_section_view"));
861: PetscCall(PetscSectionGetFieldComponents(local_section, 0, &num_comp));
862: PetscCall(PetscSectionGetStorageSize(local_section, &nleaves));
863: nleaves /= num_comp;
864: PetscCall(PetscMalloc1(nleaves, &leaf));
865: for (PetscInt i = 0; i < nleaves; i++) leaf[i] = -1;
867: // Get the permutation from CGNS closure numbering to PLEX closure numbering
868: PetscCall(DMPlexCGNSGetPermutation_Internal(dm_cell_type, numClosure, NULL, &perm));
869: PetscCall(DMPlexGetHeightStratum(*dm, 0, &cStart, &cEnd));
870: for (PetscInt cell = cStart; cell < cEnd; ++cell) {
871: PetscInt num_closure_dof, *closure_idx = NULL;
873: PetscCall(DMPlexGetClosureIndices(*dm, local_section, local_section, cell, PETSC_FALSE, &num_closure_dof, &closure_idx, NULL, NULL));
874: PetscAssert(numClosure * num_comp == num_closure_dof, comm, PETSC_ERR_PLIB, "Closure dof size does not match polytope");
875: for (PetscInt i = 0; i < numClosure; i++) {
876: PetscInt li = closure_idx[perm[i] * num_comp] / num_comp;
877: if (li < 0) continue;
879: PetscInt cgns_idx = elements[cell * numClosure + i];
880: if (leaf[li] == -1) {
881: leaf[li] = cgns_idx;
882: num_leaves++;
883: } else PetscAssert(leaf[li] == cgns_idx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "leaf does not match previously set");
884: }
885: PetscCall(DMPlexRestoreClosureIndices(*dm, local_section, local_section, cell, PETSC_FALSE, &num_closure_dof, &closure_idx, NULL, NULL));
886: }
887: PetscAssert(num_leaves == nleaves, PETSC_COMM_SELF, PETSC_ERR_PLIB, "leaf count in closure does not match nleaves");
888: PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)*dm), &cgns_to_local_sf));
889: PetscCall(PetscSFSetGraphLayout(cgns_to_local_sf, vtx_map, nleaves, NULL, PETSC_USE_POINTER, leaf));
890: PetscCall(PetscObjectSetName((PetscObject)cgns_to_local_sf, "CGNS to Plex SF"));
891: PetscCall(PetscSFViewFromOptions(cgns_to_local_sf, NULL, "-CGNStoPlex_sf_view"));
892: PetscCall(PetscFree(leaf));
893: PetscCall(PetscFree(elements));
895: { // Convert cgns_to_local to global_to_cgns
896: PetscSF sectionsf, cgns_to_global_sf;
898: PetscCall(DMGetSectionSF(*dm, §ionsf));
899: PetscCall(PetscSFComposeInverse(cgns_to_local_sf, sectionsf, &cgns_to_global_sf));
900: PetscCall(PetscSFDestroy(&cgns_to_local_sf));
901: PetscCall(PetscSFCreateInverseSF(cgns_to_global_sf, &plex_to_cgns_sf));
902: PetscCall(PetscObjectSetName((PetscObject)plex_to_cgns_sf, "Global Plex to CGNS"));
903: PetscCall(PetscSFDestroy(&cgns_to_global_sf));
904: }
905: }
907: { // -- Set coordinates for DM
908: PetscScalar *coords;
909: float *x[3];
910: double *xd[3];
911: PetscBool read_with_double;
912: PetscFE cfe;
914: // Setup coordinate space first. Use pOrder here for isoparametric; revisit with CPEX-0045 High Order.
915: PetscCall(PetscFECreateLagrangeByCell(PETSC_COMM_SELF, dim, coordDim, dm_cell_type, pOrder, PETSC_DETERMINE, &cfe));
916: PetscCall(DMSetCoordinateDisc(*dm, cfe, PETSC_FALSE));
917: PetscCall(PetscFEDestroy(&cfe));
919: { // Determine if coords are written in single or double precision
920: CGNS_ENUMT(DataType_t) datatype;
922: PetscCallCGNSRead(cg_coord_info(cgid, B, z, 1, &datatype, buffer), *dm, 0);
923: read_with_double = datatype == CGNS_ENUMV(RealDouble) ? PETSC_TRUE : PETSC_FALSE;
924: }
926: // Read coords from file and set into component-major ordering
927: if (read_with_double) PetscCall(PetscMalloc3(myownedv, &xd[0], myownedv, &xd[1], myownedv, &xd[2]));
928: else PetscCall(PetscMalloc3(myownedv, &x[0], myownedv, &x[1], myownedv, &x[2]));
929: PetscCall(PetscMalloc1(myownedv * coordDim, &coords));
930: {
931: cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */
932: cgsize_t range_min[3] = {mystartv + 1, 1, 1};
933: cgsize_t range_max[3] = {myendv, 1, 1};
934: int ngrids, ncoords;
936: PetscCallCGNSRead(cg_zone_read(cgid, B, z, buffer, sizes), *dm, 0);
937: PetscCallCGNSRead(cg_ngrids(cgid, B, z, &ngrids), *dm, 0);
938: PetscCheck(ngrids <= 1, PETSC_COMM_SELF, PETSC_ERR_LIB, "CGNS file must have a single grid, not %d", ngrids);
939: PetscCallCGNSRead(cg_ncoords(cgid, B, z, &ncoords), *dm, 0);
940: PetscCheck(ncoords == coordDim, PETSC_COMM_SELF, PETSC_ERR_LIB, "CGNS file must have a coordinate array for each dimension, not %d", ncoords);
941: if (read_with_double) {
942: 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);
943: if (coordDim >= 1) {
944: for (PetscInt v = 0; v < myownedv; ++v) coords[v * coordDim + 0] = xd[0][v];
945: }
946: if (coordDim >= 2) {
947: for (PetscInt v = 0; v < myownedv; ++v) coords[v * coordDim + 1] = xd[1][v];
948: }
949: if (coordDim >= 3) {
950: for (PetscInt v = 0; v < myownedv; ++v) coords[v * coordDim + 2] = xd[2][v];
951: }
952: } else {
953: 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);
954: if (coordDim >= 1) {
955: for (PetscInt v = 0; v < myownedv; ++v) coords[v * coordDim + 0] = x[0][v];
956: }
957: if (coordDim >= 2) {
958: for (PetscInt v = 0; v < myownedv; ++v) coords[v * coordDim + 1] = x[1][v];
959: }
960: if (coordDim >= 3) {
961: for (PetscInt v = 0; v < myownedv; ++v) coords[v * coordDim + 2] = x[2][v];
962: }
963: }
964: }
965: if (read_with_double) PetscCall(PetscFree3(xd[0], xd[1], xd[2]));
966: else PetscCall(PetscFree3(x[0], x[1], x[2]));
968: { // Reduce CGNS-ordered coordinate nodes to Plex ordering, and set DM's coordinates
969: Vec coord_global;
970: MPI_Datatype unit;
971: PetscScalar *coord_global_array;
972: DM cdm;
974: PetscCall(DMGetCoordinateDM(*dm, &cdm));
975: PetscCall(DMCreateGlobalVector(cdm, &coord_global));
976: PetscCall(VecGetArrayWrite(coord_global, &coord_global_array));
977: PetscCallMPI(MPI_Type_contiguous(coordDim, MPIU_SCALAR, &unit));
978: PetscCallMPI(MPI_Type_commit(&unit));
979: PetscCall(PetscSFReduceBegin(plex_to_cgns_sf, unit, coords, coord_global_array, MPI_REPLACE));
980: PetscCall(PetscSFReduceEnd(plex_to_cgns_sf, unit, coords, coord_global_array, MPI_REPLACE));
981: PetscCall(VecRestoreArrayWrite(coord_global, &coord_global_array));
982: PetscCallMPI(MPI_Type_free(&unit));
983: PetscCall(DMSetCoordinates(*dm, coord_global));
984: PetscCall(VecDestroy(&coord_global));
985: }
986: PetscCall(PetscFree(coords));
987: }
989: // -- Set sfNatural for solution vectors in CGNS file
990: // NOTE: We set sfNatural to be the map between the original CGNS ordering of nodes and the Plex ordering of nodes.
991: PetscCall(PetscSFViewFromOptions(plex_to_cgns_sf, NULL, "-sfNatural_init_view"));
992: PetscCall(DMSetNaturalSF(*dm, plex_to_cgns_sf));
993: PetscCall(DMSetUseNatural(*dm, PETSC_TRUE));
994: PetscCall(PetscSFDestroy(&plex_to_cgns_sf));
996: PetscCall(PetscLayoutDestroy(&elem_map));
997: PetscCall(PetscLayoutDestroy(&vtx_map));
998: PetscFunctionReturn(PETSC_SUCCESS);
999: }
1001: // node_l2g must be freed
1002: static PetscErrorCode DMPlexCreateNodeNumbering(DM dm, PetscInt *num_local_nodes, PetscInt *num_global_nodes, PetscInt *nStart, PetscInt *nEnd, const PetscInt **node_l2g)
1003: {
1004: PetscSection local_section;
1005: PetscSF point_sf;
1006: PetscInt pStart, pEnd, spStart, spEnd, *points, nleaves, ncomp, *nodes;
1007: PetscMPIInt comm_size;
1008: const PetscInt *ilocal, field = 0;
1010: PetscFunctionBegin;
1011: *num_local_nodes = -1;
1012: *num_global_nodes = -1;
1013: *nStart = -1;
1014: *nEnd = -1;
1015: *node_l2g = NULL;
1017: PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)dm), &comm_size));
1018: PetscCall(DMGetLocalSection(dm, &local_section));
1019: PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
1020: PetscCall(PetscSectionGetChart(local_section, &spStart, &spEnd));
1021: PetscCall(DMGetPointSF(dm, &point_sf));
1022: if (comm_size == 1) nleaves = 0;
1023: else PetscCall(PetscSFGetGraph(point_sf, NULL, &nleaves, &ilocal, NULL));
1024: PetscCall(PetscSectionGetFieldComponents(local_section, field, &ncomp));
1026: PetscInt local_node = 0, owned_node = 0, owned_start = 0;
1027: for (PetscInt p = spStart, leaf = 0; p < spEnd; p++) {
1028: PetscInt dof;
1029: PetscCall(PetscSectionGetFieldDof(local_section, p, field, &dof));
1030: PetscAssert(dof % ncomp == 0, PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Field dof %" PetscInt_FMT " must be divisible by components %" PetscInt_FMT, dof, ncomp);
1031: local_node += dof / ncomp;
1032: if (leaf < nleaves && p == ilocal[leaf]) { // skip points owned by a different process
1033: leaf++;
1034: } else {
1035: owned_node += dof / ncomp;
1036: }
1037: }
1038: PetscCallMPI(MPI_Exscan(&owned_node, &owned_start, 1, MPIU_INT, MPI_SUM, PetscObjectComm((PetscObject)dm)));
1039: PetscCall(PetscMalloc1(pEnd - pStart, &points));
1040: owned_node = 0;
1041: for (PetscInt p = spStart, leaf = 0; p < spEnd; p++) {
1042: if (leaf < nleaves && p == ilocal[leaf]) { // skip points owned by a different process
1043: points[p - pStart] = -1;
1044: leaf++;
1045: continue;
1046: }
1047: PetscInt dof, offset;
1048: PetscCall(PetscSectionGetFieldDof(local_section, p, field, &dof));
1049: PetscCall(PetscSectionGetFieldOffset(local_section, p, field, &offset));
1050: PetscAssert(offset % ncomp == 0, PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Field offset %" PetscInt_FMT " must be divisible by components %" PetscInt_FMT, offset, ncomp);
1051: points[p - pStart] = owned_start + owned_node;
1052: owned_node += dof / ncomp;
1053: }
1054: if (comm_size > 1) {
1055: PetscCall(PetscSFBcastBegin(point_sf, MPIU_INT, points, points, MPI_REPLACE));
1056: PetscCall(PetscSFBcastEnd(point_sf, MPIU_INT, points, points, MPI_REPLACE));
1057: }
1059: // Set up global indices for each local node
1060: PetscCall(PetscMalloc1(local_node, &nodes));
1061: for (PetscInt p = spStart; p < spEnd; p++) {
1062: PetscInt dof, offset;
1063: PetscCall(PetscSectionGetFieldDof(local_section, p, field, &dof));
1064: PetscCall(PetscSectionGetFieldOffset(local_section, p, field, &offset));
1065: for (PetscInt n = 0; n < dof / ncomp; n++) nodes[offset / ncomp + n] = points[p - pStart] + n;
1066: }
1067: PetscCall(PetscFree(points));
1068: *num_local_nodes = local_node;
1069: *nStart = owned_start;
1070: *nEnd = owned_start + owned_node;
1071: PetscCallMPI(MPIU_Allreduce(&owned_node, num_global_nodes, 1, MPIU_INT, MPI_SUM, PetscObjectComm((PetscObject)dm)));
1072: *node_l2g = nodes;
1073: PetscFunctionReturn(PETSC_SUCCESS);
1074: }
1076: PetscErrorCode DMView_PlexCGNS(DM dm, PetscViewer viewer)
1077: {
1078: PetscViewer_CGNS *cgv = (PetscViewer_CGNS *)viewer->data;
1079: PetscInt fvGhostStart;
1080: PetscInt topo_dim, coord_dim, num_global_elems;
1081: PetscInt cStart, cEnd, num_local_nodes, num_global_nodes, nStart, nEnd;
1082: const PetscInt *node_l2g;
1083: Vec coord;
1084: DM colloc_dm, cdm;
1085: PetscMPIInt size;
1086: const char *dm_name;
1087: int base, zone;
1088: cgsize_t isize[3];
1090: PetscFunctionBegin;
1091: if (!cgv->file_num) {
1092: PetscInt time_step;
1093: PetscCall(DMGetOutputSequenceNumber(dm, &time_step, NULL));
1094: PetscCall(PetscViewerCGNSFileOpen_Internal(viewer, time_step));
1095: }
1096: PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size));
1097: PetscCall(DMGetDimension(dm, &topo_dim));
1098: PetscCall(DMGetCoordinateDim(dm, &coord_dim));
1099: PetscCall(PetscObjectGetName((PetscObject)dm, &dm_name));
1100: PetscCallCGNSWrite(cg_base_write(cgv->file_num, dm_name, topo_dim, coord_dim, &base), dm, viewer);
1101: PetscCallCGNS(cg_goto(cgv->file_num, base, NULL));
1102: PetscCallCGNSWrite(cg_dataclass_write(CGNS_ENUMV(NormalizedByDimensional)), dm, viewer);
1104: {
1105: PetscFE fe, fe_coord;
1106: PetscClassId ds_id;
1107: PetscDualSpace dual_space, dual_space_coord;
1108: PetscInt num_fields, field_order = -1, field_order_coord;
1109: PetscBool is_simplex;
1110: PetscCall(DMGetNumFields(dm, &num_fields));
1111: if (num_fields > 0) {
1112: PetscCall(DMGetField(dm, 0, NULL, (PetscObject *)&fe));
1113: PetscCall(PetscObjectGetClassId((PetscObject)fe, &ds_id));
1114: if (ds_id != PETSCFE_CLASSID) {
1115: fe = NULL;
1116: if (ds_id == PETSCFV_CLASSID) field_order = -1; // use whatever is present for coords; field will be CellCenter
1117: else field_order = 1; // assume vertex-based linear elements
1118: }
1119: } else fe = NULL;
1120: if (fe) {
1121: PetscCall(PetscFEGetDualSpace(fe, &dual_space));
1122: PetscCall(PetscDualSpaceGetOrder(dual_space, &field_order));
1123: }
1124: PetscCall(DMGetCoordinateDM(dm, &cdm));
1125: PetscCall(DMGetField(cdm, 0, NULL, (PetscObject *)&fe_coord));
1126: {
1127: PetscClassId id;
1128: PetscCall(PetscObjectGetClassId((PetscObject)fe_coord, &id));
1129: if (id != PETSCFE_CLASSID) fe_coord = NULL;
1130: }
1131: if (fe_coord) {
1132: PetscCall(PetscFEGetDualSpace(fe_coord, &dual_space_coord));
1133: PetscCall(PetscDualSpaceGetOrder(dual_space_coord, &field_order_coord));
1134: } else field_order_coord = 1;
1135: if (field_order > 0 && field_order != field_order_coord) {
1136: PetscInt quadrature_order = field_order;
1137: PetscCall(DMClone(dm, &colloc_dm));
1138: { // Inform the new colloc_dm that it is a coordinate DM so isoperiodic affine corrections can be applied
1139: const PetscSF *face_sfs;
1140: PetscInt num_face_sfs;
1141: PetscCall(DMPlexGetIsoperiodicFaceSF(dm, &num_face_sfs, &face_sfs));
1142: PetscCall(DMPlexSetIsoperiodicFaceSF(colloc_dm, num_face_sfs, (PetscSF *)face_sfs));
1143: if (face_sfs) colloc_dm->periodic.setup = DMPeriodicCoordinateSetUp_Internal;
1144: }
1145: PetscCall(DMPlexIsSimplex(dm, &is_simplex));
1146: PetscCall(PetscFECreateLagrange(PetscObjectComm((PetscObject)dm), topo_dim, coord_dim, is_simplex, field_order, quadrature_order, &fe));
1147: PetscCall(DMSetCoordinateDisc(colloc_dm, fe, PETSC_TRUE));
1148: PetscCall(PetscFEDestroy(&fe));
1149: } else {
1150: PetscCall(PetscObjectReference((PetscObject)dm));
1151: colloc_dm = dm;
1152: }
1153: }
1154: PetscCall(DMGetCoordinateDM(colloc_dm, &cdm));
1155: PetscCall(DMPlexCreateNodeNumbering(cdm, &num_local_nodes, &num_global_nodes, &nStart, &nEnd, &node_l2g));
1156: PetscCall(DMGetCoordinatesLocal(colloc_dm, &coord));
1157: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
1158: PetscCall(DMPlexGetCellTypeStratum(dm, DM_POLYTOPE_FV_GHOST, &fvGhostStart, NULL));
1159: if (fvGhostStart >= 0) cEnd = fvGhostStart;
1160: num_global_elems = cEnd - cStart;
1161: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &num_global_elems, 1, MPIU_INT, MPI_SUM, PetscObjectComm((PetscObject)dm)));
1162: isize[0] = num_global_nodes;
1163: isize[1] = num_global_elems;
1164: isize[2] = 0;
1165: PetscCallCGNSWrite(cg_zone_write(cgv->file_num, base, "Zone", isize, CGNS_ENUMV(Unstructured), &zone), dm, viewer);
1167: {
1168: const PetscScalar *X;
1169: PetscScalar *x;
1170: int coord_ids[3];
1172: PetscCall(VecGetArrayRead(coord, &X));
1173: for (PetscInt d = 0; d < coord_dim; d++) {
1174: const double exponents[] = {0, 1, 0, 0, 0};
1175: char coord_name[64];
1176: PetscCall(PetscSNPrintf(coord_name, sizeof coord_name, "Coordinate%c", 'X' + (int)d));
1177: PetscCallCGNSWrite(cgp_coord_write(cgv->file_num, base, zone, CGNS_ENUMV(RealDouble), coord_name, &coord_ids[d]), dm, viewer);
1178: PetscCallCGNS(cg_goto(cgv->file_num, base, "Zone_t", zone, "GridCoordinates", 0, coord_name, 0, NULL));
1179: PetscCallCGNSWrite(cg_exponents_write(CGNS_ENUMV(RealDouble), exponents), dm, viewer);
1180: }
1182: int section;
1183: cgsize_t e_owned, e_global, e_start, *conn = NULL;
1184: const int *perm;
1185: CGNS_ENUMT(ElementType_t) element_type = CGNS_ENUMV(ElementTypeNull);
1186: {
1187: PetscCall(PetscMalloc1(nEnd - nStart, &x));
1188: for (PetscInt d = 0; d < coord_dim; d++) {
1189: for (PetscInt n = 0; n < num_local_nodes; n++) {
1190: PetscInt gn = node_l2g[n];
1191: if (gn < nStart || nEnd <= gn) continue;
1192: x[gn - nStart] = X[n * coord_dim + d];
1193: }
1194: // CGNS nodes use 1-based indexing
1195: cgsize_t start = nStart + 1, end = nEnd;
1196: PetscCallCGNSWriteData(cgp_coord_write_data(cgv->file_num, base, zone, coord_ids[d], &start, &end, x), dm, viewer);
1197: }
1198: PetscCall(PetscFree(x));
1199: PetscCall(VecRestoreArrayRead(coord, &X));
1200: }
1202: e_owned = cEnd - cStart;
1203: if (e_owned > 0) {
1204: DMPolytopeType cell_type;
1206: PetscCall(DMPlexGetCellType(dm, cStart, &cell_type));
1207: for (PetscInt i = cStart, c = 0; i < cEnd; i++) {
1208: PetscInt closure_dof, *closure_indices, elem_size;
1210: PetscCall(DMPlexGetClosureIndices(cdm, cdm->localSection, cdm->localSection, i, PETSC_FALSE, &closure_dof, &closure_indices, NULL, NULL));
1211: elem_size = closure_dof / coord_dim;
1212: if (!conn) PetscCall(PetscMalloc1(e_owned * elem_size, &conn));
1213: PetscCall(DMPlexCGNSGetPermutation_Internal(cell_type, closure_dof / coord_dim, &element_type, &perm));
1214: for (PetscInt j = 0; j < elem_size; j++) conn[c++] = node_l2g[closure_indices[perm[j] * coord_dim] / coord_dim] + 1;
1215: PetscCall(DMPlexRestoreClosureIndices(cdm, cdm->localSection, cdm->localSection, i, PETSC_FALSE, &closure_dof, &closure_indices, NULL, NULL));
1216: }
1217: }
1219: { // Get global element_type (for ranks that do not have owned elements)
1220: PetscInt local_element_type, global_element_type;
1222: local_element_type = e_owned > 0 ? element_type : -1;
1223: PetscCallMPI(MPIU_Allreduce(&local_element_type, &global_element_type, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)viewer)));
1224: 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");
1225: element_type = (CGNS_ENUMT(ElementType_t))global_element_type;
1226: }
1227: PetscCallMPI(MPIU_Allreduce(&e_owned, &e_global, 1, MPIU_CGSIZE, MPI_SUM, PetscObjectComm((PetscObject)dm)));
1228: 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);
1229: e_start = 0;
1230: PetscCallMPI(MPI_Exscan(&e_owned, &e_start, 1, MPIU_CGSIZE, MPI_SUM, PetscObjectComm((PetscObject)dm)));
1231: PetscCallCGNSWrite(cgp_section_write(cgv->file_num, base, zone, "Elem", element_type, 1, e_global, 0, §ion), dm, viewer);
1232: PetscCallCGNSWriteData(cgp_elements_write_data(cgv->file_num, base, zone, section, e_start + 1, e_start + e_owned, conn), dm, viewer);
1233: PetscCall(PetscFree(conn));
1235: cgv->base = base;
1236: cgv->zone = zone;
1237: cgv->node_l2g = node_l2g;
1238: cgv->num_local_nodes = num_local_nodes;
1239: cgv->nStart = nStart;
1240: cgv->nEnd = nEnd;
1241: cgv->eStart = e_start;
1242: cgv->eEnd = e_start + e_owned;
1243: if (1) {
1244: PetscMPIInt rank;
1245: int *efield;
1246: int sol, field;
1247: DMLabel label;
1248: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
1249: PetscCall(PetscMalloc1(e_owned, &efield));
1250: for (PetscInt i = 0; i < e_owned; i++) efield[i] = rank;
1251: PetscCallCGNSWrite(cg_sol_write(cgv->file_num, base, zone, "CellInfo", CGNS_ENUMV(CellCenter), &sol), dm, viewer);
1252: PetscCallCGNSWrite(cgp_field_write(cgv->file_num, base, zone, sol, CGNS_ENUMV(Integer), "Rank", &field), dm, viewer);
1253: cgsize_t start = e_start + 1, end = e_start + e_owned;
1254: PetscCallCGNSWriteData(cgp_field_write_data(cgv->file_num, base, zone, sol, field, &start, &end, efield), dm, viewer);
1255: PetscCall(DMGetLabel(dm, "Cell Sets", &label));
1256: if (label) {
1257: for (PetscInt c = cStart; c < cEnd; c++) {
1258: PetscInt value;
1259: PetscCall(DMLabelGetValue(label, c, &value));
1260: efield[c - cStart] = value;
1261: }
1262: PetscCallCGNSWrite(cgp_field_write(cgv->file_num, base, zone, sol, CGNS_ENUMV(Integer), "CellSet", &field), dm, viewer);
1263: PetscCallCGNSWriteData(cgp_field_write_data(cgv->file_num, base, zone, sol, field, &start, &end, efield), dm, viewer);
1264: }
1265: PetscCall(PetscFree(efield));
1266: }
1267: }
1268: PetscCall(DMDestroy(&colloc_dm));
1269: PetscFunctionReturn(PETSC_SUCCESS);
1270: }
1272: PetscErrorCode VecView_Plex_Local_CGNS(Vec V, PetscViewer viewer)
1273: {
1274: PetscViewer_CGNS *cgv = (PetscViewer_CGNS *)viewer->data;
1275: DM dm;
1276: PetscSection section;
1277: PetscInt time_step, num_fields, pStart, pEnd, fvGhostStart;
1278: PetscReal time, *time_slot;
1279: size_t *step_slot;
1280: const PetscScalar *v;
1281: char solution_name[PETSC_MAX_PATH_LEN];
1282: int sol;
1284: PetscFunctionBegin;
1285: PetscCall(VecGetDM(V, &dm));
1286: PetscCall(DMGetLocalSection(dm, §ion));
1287: PetscCall(PetscSectionGetChart(section, &pStart, &pEnd));
1288: PetscCall(DMPlexGetCellTypeStratum(dm, DM_POLYTOPE_FV_GHOST, &fvGhostStart, NULL));
1289: if (fvGhostStart >= 0) pEnd = fvGhostStart;
1291: if (!cgv->node_l2g) PetscCall(DMView(dm, viewer));
1292: if (!cgv->grid_loc) { // Determine if writing to cell-centers or to nodes
1293: PetscInt cStart, cEnd;
1294: PetscInt local_grid_loc, global_grid_loc;
1296: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
1297: if (fvGhostStart >= 0) cEnd = fvGhostStart;
1298: if (cgv->num_local_nodes == 0) local_grid_loc = -1;
1299: else if (cStart == pStart && cEnd == pEnd) local_grid_loc = CGNS_ENUMV(CellCenter);
1300: else local_grid_loc = CGNS_ENUMV(Vertex);
1302: PetscCallMPI(MPIU_Allreduce(&local_grid_loc, &global_grid_loc, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)viewer)));
1303: if (local_grid_loc != -1)
1304: 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);
1305: 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);
1306: cgv->grid_loc = (CGNS_ENUMT(GridLocation_t))global_grid_loc;
1307: }
1308: if (!cgv->nodal_field) {
1309: switch (cgv->grid_loc) {
1310: case CGNS_ENUMV(Vertex): {
1311: PetscCall(PetscMalloc1(cgv->nEnd - cgv->nStart, &cgv->nodal_field));
1312: } break;
1313: case CGNS_ENUMV(CellCenter): {
1314: PetscCall(PetscMalloc1(cgv->eEnd - cgv->eStart, &cgv->nodal_field));
1315: } break;
1316: default:
1317: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Can only write for Vertex and CellCenter grid locations");
1318: }
1319: }
1320: if (!cgv->output_times) PetscCall(PetscSegBufferCreate(sizeof(PetscReal), 20, &cgv->output_times));
1321: if (!cgv->output_steps) PetscCall(PetscSegBufferCreate(sizeof(size_t), 20, &cgv->output_steps));
1323: PetscCall(DMGetOutputSequenceNumber(dm, &time_step, &time));
1324: if (time_step < 0) {
1325: time_step = 0;
1326: time = 0.;
1327: }
1328: PetscCall(PetscSegBufferGet(cgv->output_times, 1, &time_slot));
1329: *time_slot = time;
1330: PetscCall(PetscSegBufferGet(cgv->output_steps, 1, &step_slot));
1331: *step_slot = time_step;
1332: PetscCall(PetscSNPrintf(solution_name, sizeof solution_name, "FlowSolution%" PetscInt_FMT, time_step));
1333: PetscCallCGNSWrite(cg_sol_write(cgv->file_num, cgv->base, cgv->zone, solution_name, cgv->grid_loc, &sol), V, viewer);
1334: PetscCall(VecGetArrayRead(V, &v));
1335: PetscCall(PetscSectionGetNumFields(section, &num_fields));
1336: for (PetscInt field = 0; field < num_fields; field++) {
1337: PetscInt ncomp;
1338: const char *field_name;
1339: PetscCall(PetscSectionGetFieldName(section, field, &field_name));
1340: PetscCall(PetscSectionGetFieldComponents(section, field, &ncomp));
1341: for (PetscInt comp = 0; comp < ncomp; comp++) {
1342: int cgfield;
1343: const char *comp_name;
1344: char cgns_field_name[32]; // CGNS max field name is 32
1345: CGNS_ENUMT(DataType_t) datatype;
1346: PetscCall(PetscSectionGetComponentName(section, field, comp, &comp_name));
1347: 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));
1348: else if (field_name[0] == '\0') PetscCall(PetscStrncpy(cgns_field_name, comp_name, sizeof cgns_field_name));
1349: else PetscCall(PetscSNPrintf(cgns_field_name, sizeof cgns_field_name, "%s.%s", field_name, comp_name));
1350: PetscCall(PetscCGNSDataType(PETSC_SCALAR, &datatype));
1351: PetscCallCGNSWrite(cgp_field_write(cgv->file_num, cgv->base, cgv->zone, sol, datatype, cgns_field_name, &cgfield), V, viewer);
1352: for (PetscInt p = pStart, n = 0; p < pEnd; p++) {
1353: PetscInt off, dof;
1354: PetscCall(PetscSectionGetFieldDof(section, p, field, &dof));
1355: if (dof == 0) continue;
1356: PetscCall(PetscSectionGetFieldOffset(section, p, field, &off));
1357: for (PetscInt c = comp; c < dof; c += ncomp, n++) {
1358: switch (cgv->grid_loc) {
1359: case CGNS_ENUMV(Vertex): {
1360: PetscInt gn = cgv->node_l2g[n];
1361: if (gn < cgv->nStart || cgv->nEnd <= gn) continue;
1362: cgv->nodal_field[gn - cgv->nStart] = v[off + c];
1363: } break;
1364: case CGNS_ENUMV(CellCenter): {
1365: cgv->nodal_field[n] = v[off + c];
1366: } break;
1367: default:
1368: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Can only pack for Vertex and CellCenter grid locations");
1369: }
1370: }
1371: }
1372: // CGNS nodes use 1-based indexing
1373: cgsize_t start, end;
1374: switch (cgv->grid_loc) {
1375: case CGNS_ENUMV(Vertex): {
1376: start = cgv->nStart + 1;
1377: end = cgv->nEnd;
1378: } break;
1379: case CGNS_ENUMV(CellCenter): {
1380: start = cgv->eStart + 1;
1381: end = cgv->eEnd;
1382: } break;
1383: default:
1384: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Can only write for Vertex and CellCenter grid locations");
1385: }
1386: PetscCallCGNSWriteData(cgp_field_write_data(cgv->file_num, cgv->base, cgv->zone, sol, cgfield, &start, &end, cgv->nodal_field), V, viewer);
1387: }
1388: }
1389: PetscCall(VecRestoreArrayRead(V, &v));
1390: PetscCall(PetscViewerCGNSCheckBatch_Internal(viewer));
1391: PetscFunctionReturn(PETSC_SUCCESS);
1392: }
1394: PetscErrorCode VecLoad_Plex_CGNS_Internal(Vec V, PetscViewer viewer)
1395: {
1396: MPI_Comm comm;
1397: char buffer[CGIO_MAX_NAME_LENGTH + 1];
1398: PetscViewer_CGNS *cgv = (PetscViewer_CGNS *)viewer->data;
1399: int cgid = cgv->file_num;
1400: PetscBool use_parallel_viewer = PETSC_FALSE;
1401: int z = 1; // Only support one zone
1402: int B = 1; // Only support one base
1403: int numComp;
1404: PetscInt V_numComps, mystartv, myendv, myownedv;
1406: PetscFunctionBeginUser;
1407: PetscCall(PetscObjectGetComm((PetscObject)V, &comm));
1409: PetscCall(PetscOptionsGetBool(NULL, NULL, "-dm_plex_cgns_parallel", &use_parallel_viewer, NULL));
1410: 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");
1412: { // Get CGNS node ownership information
1413: int nbases, nzones;
1414: PetscInt NVertices;
1415: PetscLayout vtx_map;
1416: cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */
1418: PetscCallCGNSRead(cg_nbases(cgid, &nbases), V, viewer);
1419: PetscCheck(nbases <= 1, PETSC_COMM_SELF, PETSC_ERR_LIB, "CGNS file must have a single base, not %d", nbases);
1420: PetscCallCGNSRead(cg_nzones(cgid, B, &nzones), V, viewer);
1421: PetscCheck(nzones == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "limited to one zone %d", (int)nzones);
1423: PetscCallCGNSRead(cg_zone_read(cgid, B, z, buffer, sizes), V, viewer);
1424: NVertices = sizes[0];
1426: PetscCall(PetscLayoutCreateFromSizes(comm, PETSC_DECIDE, NVertices, 1, &vtx_map));
1427: PetscCall(PetscLayoutGetRange(vtx_map, &mystartv, &myendv));
1428: PetscCall(PetscLayoutGetLocalSize(vtx_map, &myownedv));
1429: PetscCall(PetscLayoutDestroy(&vtx_map));
1430: }
1432: { // -- Read data from file into Vec
1433: PetscScalar *fields = NULL;
1434: PetscSF sfNatural;
1436: { // Check compatibility between sfNatural and the data source and sink
1437: DM dm;
1438: PetscInt nleaves, nroots, V_local_size;
1440: PetscCall(VecGetDM(V, &dm));
1441: PetscCall(DMGetNaturalSF(dm, &sfNatural));
1442: PetscCheck(sfNatural, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "DM of Vec must have sfNatural");
1443: PetscCall(PetscSFGetGraph(sfNatural, &nroots, &nleaves, NULL, NULL));
1444: PetscCall(VecGetLocalSize(V, &V_local_size));
1445: 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);
1446: 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);
1447: V_numComps = V_local_size / nroots;
1448: }
1450: { // Read data into component-major ordering
1451: int isol, numSols;
1452: CGNS_ENUMT(DataType_t) datatype;
1453: double *fields_CGNS;
1455: PetscCallCGNSRead(cg_nsols(cgid, B, z, &numSols), V, viewer);
1456: PetscCall(PetscViewerCGNSGetSolutionFileIndex_Internal(viewer, &isol));
1457: PetscCallCGNSRead(cg_nfields(cgid, B, z, isol, &numComp), V, viewer);
1458: 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);
1460: cgsize_t range_min[3] = {mystartv + 1, 1, 1};
1461: cgsize_t range_max[3] = {myendv, 1, 1};
1462: PetscCall(PetscMalloc1(myownedv * numComp, &fields_CGNS));
1463: PetscCall(PetscMalloc1(myownedv * numComp, &fields));
1464: for (int d = 0; d < numComp; ++d) {
1465: PetscCallCGNSRead(cg_field_info(cgid, B, z, isol, (d + 1), &datatype, buffer), V, viewer);
1466: PetscCheck(datatype == CGNS_ENUMV(RealDouble), PETSC_COMM_SELF, PETSC_ERR_ARG_NOTSAMETYPE, "Field %s in file is not of type double", buffer);
1467: PetscCallCGNSReadData(cgp_field_read_data(cgid, B, z, isol, (d + 1), range_min, range_max, &fields_CGNS[d * myownedv]), V, viewer);
1468: }
1469: for (int d = 0; d < numComp; ++d) {
1470: for (PetscInt v = 0; v < myownedv; ++v) fields[v * numComp + d] = fields_CGNS[d * myownedv + v];
1471: }
1472: PetscCall(PetscFree(fields_CGNS));
1473: }
1475: { // Reduce fields into Vec array
1476: PetscScalar *V_array;
1477: MPI_Datatype fieldtype;
1479: PetscCall(VecGetArrayWrite(V, &V_array));
1480: PetscCallMPI(MPI_Type_contiguous(numComp, MPIU_SCALAR, &fieldtype));
1481: PetscCallMPI(MPI_Type_commit(&fieldtype));
1482: PetscCall(PetscSFReduceBegin(sfNatural, fieldtype, fields, V_array, MPI_REPLACE));
1483: PetscCall(PetscSFReduceEnd(sfNatural, fieldtype, fields, V_array, MPI_REPLACE));
1484: PetscCallMPI(MPI_Type_free(&fieldtype));
1485: PetscCall(VecRestoreArrayWrite(V, &V_array));
1486: }
1487: PetscCall(PetscFree(fields));
1488: }
1489: PetscFunctionReturn(PETSC_SUCCESS);
1490: }