Actual source code: plexgmsh.c
1: #include <petsc/private/dmpleximpl.h>
2: #include <petsc/private/hashmapi.h>
4: #include <../src/dm/impls/plex/gmshlex.h>
6: #define GMSH_LEXORDER_ITEM(T, p) \
7: static int *GmshLexOrder_##T##_##p(void) \
8: { \
9: static int Gmsh_LexOrder_##T##_##p[GmshNumNodes_##T(p)] = {-1}; \
10: int *lex = Gmsh_LexOrder_##T##_##p; \
11: if (lex[0] == -1) (void)GmshLexOrder_##T(p, lex, 0); \
12: return lex; \
13: }
15: static int *GmshLexOrder_QUA_2_Serendipity(void)
16: {
17: static int Gmsh_LexOrder_QUA_2_Serendipity[9] = {-1};
18: int *lex = Gmsh_LexOrder_QUA_2_Serendipity;
19: if (lex[0] == -1) {
20: /* Vertices */
21: lex[0] = 0;
22: lex[2] = 1;
23: lex[8] = 2;
24: lex[6] = 3;
25: /* Edges */
26: lex[1] = 4;
27: lex[5] = 5;
28: lex[7] = 6;
29: lex[3] = 7;
30: /* Cell */
31: lex[4] = -8;
32: }
33: return lex;
34: }
36: static int *GmshLexOrder_HEX_2_Serendipity(void)
37: {
38: static int Gmsh_LexOrder_HEX_2_Serendipity[27] = {-1};
39: int *lex = Gmsh_LexOrder_HEX_2_Serendipity;
40: if (lex[0] == -1) {
41: /* Vertices */
42: lex[0] = 0;
43: lex[2] = 1;
44: lex[8] = 2;
45: lex[6] = 3;
46: lex[18] = 4;
47: lex[20] = 5;
48: lex[26] = 6;
49: lex[24] = 7;
50: /* Edges */
51: lex[1] = 8;
52: lex[3] = 9;
53: lex[9] = 10;
54: lex[5] = 11;
55: lex[11] = 12;
56: lex[7] = 13;
57: lex[17] = 14;
58: lex[15] = 15;
59: lex[19] = 16;
60: lex[21] = 17;
61: lex[23] = 18;
62: lex[25] = 19;
63: /* Faces */
64: lex[4] = -20;
65: lex[10] = -21;
66: lex[12] = -22;
67: lex[14] = -23;
68: lex[16] = -24;
69: lex[22] = -25;
70: /* Cell */
71: lex[13] = -26;
72: }
73: return lex;
74: }
76: #define GMSH_LEXORDER_LIST(T) \
77: GMSH_LEXORDER_ITEM(T, 1) \
78: GMSH_LEXORDER_ITEM(T, 2) \
79: GMSH_LEXORDER_ITEM(T, 3) \
80: GMSH_LEXORDER_ITEM(T, 4) \
81: GMSH_LEXORDER_ITEM(T, 5) \
82: GMSH_LEXORDER_ITEM(T, 6) \
83: GMSH_LEXORDER_ITEM(T, 7) \
84: GMSH_LEXORDER_ITEM(T, 8) \
85: GMSH_LEXORDER_ITEM(T, 9) \
86: GMSH_LEXORDER_ITEM(T, 10)
88: GMSH_LEXORDER_ITEM(VTX, 0)
89: GMSH_LEXORDER_LIST(SEG)
90: GMSH_LEXORDER_LIST(TRI)
91: GMSH_LEXORDER_LIST(QUA)
92: GMSH_LEXORDER_LIST(TET)
93: GMSH_LEXORDER_LIST(HEX)
94: GMSH_LEXORDER_LIST(PRI)
95: GMSH_LEXORDER_LIST(PYR)
97: typedef enum {
98: GMSH_VTX = 0,
99: GMSH_SEG = 1,
100: GMSH_TRI = 2,
101: GMSH_QUA = 3,
102: GMSH_TET = 4,
103: GMSH_HEX = 5,
104: GMSH_PRI = 6,
105: GMSH_PYR = 7,
106: GMSH_NUM_POLYTOPES = 8
107: } GmshPolytopeType;
109: typedef struct {
110: int cellType;
111: int polytope;
112: int dim;
113: int order;
114: int numVerts;
115: int numNodes;
116: int *(*lexorder)(void);
117: } GmshCellInfo;
119: #define GmshCellEntry(cellType, polytope, dim, order) {cellType, GMSH_##polytope, dim, order, GmshNumNodes_##polytope(1), GmshNumNodes_##polytope(order), GmshLexOrder_##polytope##_##order}
121: static const GmshCellInfo GmshCellTable[] = {
122: GmshCellEntry(15, VTX, 0, 0),
124: GmshCellEntry(1, SEG, 1, 1), GmshCellEntry(8, SEG, 1, 2), GmshCellEntry(26, SEG, 1, 3),
125: GmshCellEntry(27, SEG, 1, 4), GmshCellEntry(28, SEG, 1, 5), GmshCellEntry(62, SEG, 1, 6),
126: GmshCellEntry(63, SEG, 1, 7), GmshCellEntry(64, SEG, 1, 8), GmshCellEntry(65, SEG, 1, 9),
127: GmshCellEntry(66, SEG, 1, 10),
129: GmshCellEntry(2, TRI, 2, 1), GmshCellEntry(9, TRI, 2, 2), GmshCellEntry(21, TRI, 2, 3),
130: GmshCellEntry(23, TRI, 2, 4), GmshCellEntry(25, TRI, 2, 5), GmshCellEntry(42, TRI, 2, 6),
131: GmshCellEntry(43, TRI, 2, 7), GmshCellEntry(44, TRI, 2, 8), GmshCellEntry(45, TRI, 2, 9),
132: GmshCellEntry(46, TRI, 2, 10),
134: GmshCellEntry(3, QUA, 2, 1), GmshCellEntry(10, QUA, 2, 2), {16, GMSH_QUA, 2, 2, 4, 8, GmshLexOrder_QUA_2_Serendipity},
135: GmshCellEntry(36, QUA, 2, 3), GmshCellEntry(37, QUA, 2, 4), GmshCellEntry(38, QUA, 2, 5),
136: GmshCellEntry(47, QUA, 2, 6), GmshCellEntry(48, QUA, 2, 7), GmshCellEntry(49, QUA, 2, 8),
137: GmshCellEntry(50, QUA, 2, 9), GmshCellEntry(51, QUA, 2, 10),
139: GmshCellEntry(4, TET, 3, 1), GmshCellEntry(11, TET, 3, 2), GmshCellEntry(29, TET, 3, 3),
140: GmshCellEntry(30, TET, 3, 4), GmshCellEntry(31, TET, 3, 5), GmshCellEntry(71, TET, 3, 6),
141: GmshCellEntry(72, TET, 3, 7), GmshCellEntry(73, TET, 3, 8), GmshCellEntry(74, TET, 3, 9),
142: GmshCellEntry(75, TET, 3, 10),
144: GmshCellEntry(5, HEX, 3, 1), GmshCellEntry(12, HEX, 3, 2), {17, GMSH_HEX, 3, 2, 8, 20, GmshLexOrder_HEX_2_Serendipity},
145: GmshCellEntry(92, HEX, 3, 3), GmshCellEntry(93, HEX, 3, 4), GmshCellEntry(94, HEX, 3, 5),
146: GmshCellEntry(95, HEX, 3, 6), GmshCellEntry(96, HEX, 3, 7), GmshCellEntry(97, HEX, 3, 8),
147: GmshCellEntry(98, HEX, 3, 9), GmshCellEntry(-1, HEX, 3, 10),
149: GmshCellEntry(6, PRI, 3, 1), GmshCellEntry(13, PRI, 3, 2), GmshCellEntry(90, PRI, 3, 3),
150: GmshCellEntry(91, PRI, 3, 4), GmshCellEntry(106, PRI, 3, 5), GmshCellEntry(107, PRI, 3, 6),
151: GmshCellEntry(108, PRI, 3, 7), GmshCellEntry(109, PRI, 3, 8), GmshCellEntry(110, PRI, 3, 9),
152: GmshCellEntry(-1, PRI, 3, 10),
154: GmshCellEntry(7, PYR, 3, 1), GmshCellEntry(14, PYR, 3, 2), GmshCellEntry(118, PYR, 3, 3),
155: GmshCellEntry(119, PYR, 3, 4), GmshCellEntry(120, PYR, 3, 5), GmshCellEntry(121, PYR, 3, 6),
156: GmshCellEntry(122, PYR, 3, 7), GmshCellEntry(123, PYR, 3, 8), GmshCellEntry(124, PYR, 3, 9),
157: GmshCellEntry(-1, PYR, 3, 10)
159: #if 0
160: {20, GMSH_TRI, 2, 3, 3, 9, NULL},
161: {18, GMSH_PRI, 3, 2, 6, 15, NULL},
162: {19, GMSH_PYR, 3, 2, 5, 13, NULL},
163: #endif
164: };
166: static GmshCellInfo GmshCellMap[150];
168: static PetscErrorCode GmshCellInfoSetUp(void)
169: {
170: size_t i, n;
171: static PetscBool called = PETSC_FALSE;
173: PetscFunctionBegin;
174: if (called) PetscFunctionReturn(PETSC_SUCCESS);
175: called = PETSC_TRUE;
176: n = PETSC_STATIC_ARRAY_LENGTH(GmshCellMap);
177: for (i = 0; i < n; ++i) {
178: GmshCellMap[i].cellType = -1;
179: GmshCellMap[i].polytope = -1;
180: }
181: n = PETSC_STATIC_ARRAY_LENGTH(GmshCellTable);
182: for (i = 0; i < n; ++i) {
183: if (GmshCellTable[i].cellType <= 0) continue;
184: GmshCellMap[GmshCellTable[i].cellType] = GmshCellTable[i];
185: }
186: PetscFunctionReturn(PETSC_SUCCESS);
187: }
189: #define GmshCellTypeCheck(ct) \
190: PetscMacroReturnStandard(const int _ct_ = (int)ct; PetscCheck(_ct_ >= 0 && _ct_ < (int)PETSC_STATIC_ARRAY_LENGTH(GmshCellMap), PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid Gmsh element type %d", _ct_); PetscCheck(GmshCellMap[_ct_].cellType == _ct_, PETSC_COMM_SELF, PETSC_ERR_SUP, "Unsupported Gmsh element type %d", _ct_); \
191: PetscCheck(GmshCellMap[_ct_].polytope != -1, PETSC_COMM_SELF, PETSC_ERR_SUP, "Unsupported Gmsh element type %d", _ct_);)
193: typedef struct {
194: PetscViewer viewer;
195: int fileFormat;
196: int dataSize;
197: PetscBool binary;
198: PetscBool byteSwap;
199: size_t wlen;
200: void *wbuf;
201: size_t slen;
202: void *sbuf;
203: PetscInt *nbuf;
204: PetscInt nodeStart;
205: PetscInt nodeEnd;
206: PetscInt *nodeMap;
207: } GmshFile;
209: /*
210: Returns an array of count items each with a sizeof(eltsize)
211: */
212: static PetscErrorCode GmshBufferGet(GmshFile *gmsh, PetscCount count, size_t eltsize, void *buf)
213: {
214: size_t size = count * eltsize;
216: PetscFunctionBegin;
217: if (gmsh->wlen < size) {
218: PetscCall(PetscFree(gmsh->wbuf));
219: PetscCall(PetscMalloc(size, &gmsh->wbuf));
220: gmsh->wlen = size;
221: }
222: *(void **)buf = size ? gmsh->wbuf : NULL;
223: PetscFunctionReturn(PETSC_SUCCESS);
224: }
226: /*
227: Returns an array of count items each with the size determined by the GmshFile
228: */
229: static PetscErrorCode GmshBufferSizeGet(GmshFile *gmsh, PetscCount count, void *buf)
230: {
231: size_t dataSize = (size_t)gmsh->dataSize;
232: size_t size = count * dataSize;
234: PetscFunctionBegin;
235: if (gmsh->slen < size) {
236: PetscCall(PetscFree(gmsh->sbuf));
237: PetscCall(PetscMalloc(size, &gmsh->sbuf));
238: gmsh->slen = size;
239: }
240: *(void **)buf = size ? gmsh->sbuf : NULL;
241: PetscFunctionReturn(PETSC_SUCCESS);
242: }
244: /*
245: Reads an array of count items each with the size determined by the PetscDataType
246: */
247: static PetscErrorCode GmshRead(GmshFile *gmsh, void *buf, PetscCount count, PetscDataType dtype)
248: {
249: PetscInt icount;
251: PetscFunctionBegin;
252: PetscCall(PetscIntCast(count, &icount));
253: PetscCall(PetscViewerRead(gmsh->viewer, buf, icount, NULL, dtype));
254: if (gmsh->byteSwap) PetscCall(PetscByteSwap(buf, dtype, icount));
255: PetscFunctionReturn(PETSC_SUCCESS);
256: }
258: static PetscErrorCode GmshReadString(GmshFile *gmsh, char *buf, PetscCount count)
259: {
260: PetscInt icount;
262: PetscFunctionBegin;
263: PetscCall(PetscIntCast(count, &icount));
264: PetscCall(PetscViewerRead(gmsh->viewer, buf, icount, NULL, PETSC_STRING));
265: PetscFunctionReturn(PETSC_SUCCESS);
266: }
268: static PetscErrorCode GmshMatch(PETSC_UNUSED GmshFile *gmsh, const char Section[], char line[PETSC_MAX_PATH_LEN], PetscBool *match)
269: {
270: PetscFunctionBegin;
271: PetscCall(PetscStrcmp(line, Section, match));
272: PetscFunctionReturn(PETSC_SUCCESS);
273: }
275: static PetscErrorCode GmshExpect(GmshFile *gmsh, const char Section[], char line[PETSC_MAX_PATH_LEN])
276: {
277: PetscBool match;
279: PetscFunctionBegin;
280: PetscCall(GmshMatch(gmsh, Section, line, &match));
281: PetscCheck(match, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "File is not a valid Gmsh file, expecting %s, not %s", Section, line);
282: PetscFunctionReturn(PETSC_SUCCESS);
283: }
285: static PetscErrorCode GmshReadSection(GmshFile *gmsh, char line[PETSC_MAX_PATH_LEN])
286: {
287: PetscBool match;
289: PetscFunctionBegin;
290: while (PETSC_TRUE) {
291: PetscCall(GmshReadString(gmsh, line, 1));
292: PetscCall(GmshMatch(gmsh, "$Comments", line, &match));
293: if (!match) break;
294: while (PETSC_TRUE) {
295: PetscCall(GmshReadString(gmsh, line, 1));
296: PetscCall(GmshMatch(gmsh, "$EndComments", line, &match));
297: if (match) break;
298: }
299: }
300: PetscFunctionReturn(PETSC_SUCCESS);
301: }
303: static PetscErrorCode GmshReadEndSection(GmshFile *gmsh, const char EndSection[], char line[PETSC_MAX_PATH_LEN])
304: {
305: PetscFunctionBegin;
306: PetscCall(GmshReadString(gmsh, line, 1));
307: PetscCall(GmshExpect(gmsh, EndSection, line));
308: PetscFunctionReturn(PETSC_SUCCESS);
309: }
311: /*
312: Read into buf[] count number of PetscInt integers (the file storage size may be different than PetscInt)
313: */
314: static PetscErrorCode GmshReadPetscInt(GmshFile *gmsh, PetscInt *buf, PetscCount count)
315: {
316: PetscCount i;
317: size_t dataSize = (size_t)gmsh->dataSize;
319: PetscFunctionBegin;
320: if (dataSize == sizeof(PetscInt)) {
321: PetscCall(GmshRead(gmsh, buf, count, PETSC_INT));
322: } else if (dataSize == sizeof(int)) {
323: int *ibuf = NULL;
324: PetscCall(GmshBufferSizeGet(gmsh, count, &ibuf));
325: PetscCall(GmshRead(gmsh, ibuf, count, PETSC_ENUM));
326: for (i = 0; i < count; ++i) buf[i] = (PetscInt)ibuf[i];
327: } else if (dataSize == sizeof(long)) {
328: long *ibuf = NULL;
329: PetscCall(GmshBufferSizeGet(gmsh, count, &ibuf));
330: PetscCall(GmshRead(gmsh, ibuf, count, PETSC_LONG));
331: for (i = 0; i < count; ++i) buf[i] = (PetscInt)ibuf[i];
332: } else if (dataSize == sizeof(PetscInt64)) {
333: PetscInt64 *ibuf = NULL;
334: PetscCall(GmshBufferSizeGet(gmsh, count, &ibuf));
335: PetscCall(GmshRead(gmsh, ibuf, count, PETSC_INT64));
336: for (i = 0; i < count; ++i) buf[i] = (PetscInt)ibuf[i];
337: }
338: PetscFunctionReturn(PETSC_SUCCESS);
339: }
341: /*
342: Read into buf[] count number of PetscCount integers (the file storage size may be different than PetscCount)
343: */
344: static PetscErrorCode GmshReadPetscCount(GmshFile *gmsh, PetscCount *buf, PetscCount count)
345: {
346: PetscCount i;
347: size_t dataSize = (size_t)gmsh->dataSize;
349: PetscFunctionBegin;
350: if (dataSize == sizeof(PetscCount)) {
351: PetscCall(GmshRead(gmsh, buf, count, PETSC_COUNT));
352: } else if (dataSize == sizeof(int)) {
353: int *ibuf = NULL;
354: PetscCall(GmshBufferSizeGet(gmsh, count, &ibuf));
355: PetscCall(GmshRead(gmsh, ibuf, count, PETSC_ENUM));
356: for (i = 0; i < count; ++i) buf[i] = (PetscCount)ibuf[i];
357: } else if (dataSize == sizeof(long)) {
358: long *ibuf = NULL;
359: PetscCall(GmshBufferSizeGet(gmsh, count, &ibuf));
360: PetscCall(GmshRead(gmsh, ibuf, count, PETSC_LONG));
361: for (i = 0; i < count; ++i) buf[i] = (PetscCount)ibuf[i];
362: } else if (dataSize == sizeof(PetscInt64)) {
363: PetscInt64 *ibuf = NULL;
364: PetscCall(GmshBufferSizeGet(gmsh, count, &ibuf));
365: PetscCall(GmshRead(gmsh, ibuf, count, PETSC_INT64));
366: for (i = 0; i < count; ++i) buf[i] = (PetscCount)ibuf[i];
367: }
368: PetscFunctionReturn(PETSC_SUCCESS);
369: }
371: /*
372: Read into buf[] count number of PetscEnum integers
373: */
374: static PetscErrorCode GmshReadInt(GmshFile *gmsh, int *buf, PetscCount count)
375: {
376: PetscFunctionBegin;
377: PetscCall(GmshRead(gmsh, buf, count, PETSC_ENUM));
378: PetscFunctionReturn(PETSC_SUCCESS);
379: }
381: /*
382: Read into buf[] count number of double
383: */
384: static PetscErrorCode GmshReadDouble(GmshFile *gmsh, double *buf, PetscCount count)
385: {
386: PetscFunctionBegin;
387: PetscCall(GmshRead(gmsh, buf, count, PETSC_DOUBLE));
388: PetscFunctionReturn(PETSC_SUCCESS);
389: }
391: #define GMSH_MAX_TAGS 16
393: typedef struct {
394: PetscInt id; /* Entity ID */
395: PetscInt dim; /* Dimension */
396: double bbox[6]; /* Bounding box */
397: PetscInt numTags; /* Size of tag array */
398: int tags[GMSH_MAX_TAGS]; /* Tag array */
399: } GmshEntity;
401: typedef struct {
402: GmshEntity *entity[4];
403: PetscHMapI entityMap[4];
404: } GmshEntities;
406: static PetscErrorCode GmshEntitiesCreate(PetscCount count[4], GmshEntities **entities)
407: {
408: PetscFunctionBegin;
409: PetscCall(PetscNew(entities));
410: for (PetscInt dim = 0; dim < 4; ++dim) {
411: PetscCall(PetscCalloc1(count[dim], &(*entities)->entity[dim]));
412: PetscCall(PetscHMapICreate(&(*entities)->entityMap[dim]));
413: }
414: PetscFunctionReturn(PETSC_SUCCESS);
415: }
417: static PetscErrorCode GmshEntitiesDestroy(GmshEntities **entities)
418: {
419: PetscInt dim;
421: PetscFunctionBegin;
422: if (!*entities) PetscFunctionReturn(PETSC_SUCCESS);
423: for (dim = 0; dim < 4; ++dim) {
424: PetscCall(PetscFree((*entities)->entity[dim]));
425: PetscCall(PetscHMapIDestroy(&(*entities)->entityMap[dim]));
426: }
427: PetscCall(PetscFree(*entities));
428: PetscFunctionReturn(PETSC_SUCCESS);
429: }
431: static PetscErrorCode GmshEntitiesAdd(GmshEntities *entities, PetscInt index, PetscInt dim, PetscInt eid, GmshEntity **entity)
432: {
433: PetscFunctionBegin;
434: PetscCall(PetscHMapISet(entities->entityMap[dim], eid, index));
435: entities->entity[dim][index].dim = dim;
436: entities->entity[dim][index].id = eid;
437: if (entity) *entity = &entities->entity[dim][index];
438: PetscFunctionReturn(PETSC_SUCCESS);
439: }
441: static PetscErrorCode GmshEntitiesGet(GmshEntities *entities, PetscInt dim, PetscInt eid, GmshEntity **entity)
442: {
443: PetscInt index;
445: PetscFunctionBegin;
446: PetscCall(PetscHMapIGet(entities->entityMap[dim], eid, &index));
447: *entity = &entities->entity[dim][index];
448: PetscFunctionReturn(PETSC_SUCCESS);
449: }
451: typedef struct {
452: PetscInt *id; /* Node IDs */
453: double *xyz; /* Coordinates */
454: PetscInt *tag; /* Physical tag */
455: } GmshNodes;
457: static PetscErrorCode GmshNodesCreate(PetscCount count, GmshNodes **nodes)
458: {
459: PetscFunctionBegin;
460: PetscCall(PetscNew(nodes));
461: PetscCall(PetscMalloc1(count * 1, &(*nodes)->id));
462: PetscCall(PetscMalloc1(count * 3, &(*nodes)->xyz));
463: PetscCall(PetscMalloc1(count * GMSH_MAX_TAGS, &(*nodes)->tag));
464: PetscFunctionReturn(PETSC_SUCCESS);
465: }
467: static PetscErrorCode GmshNodesDestroy(GmshNodes **nodes)
468: {
469: PetscFunctionBegin;
470: if (!*nodes) PetscFunctionReturn(PETSC_SUCCESS);
471: PetscCall(PetscFree((*nodes)->id));
472: PetscCall(PetscFree((*nodes)->xyz));
473: PetscCall(PetscFree((*nodes)->tag));
474: PetscCall(PetscFree(*nodes));
475: PetscFunctionReturn(PETSC_SUCCESS);
476: }
478: typedef struct {
479: PetscInt id; /* Element ID */
480: PetscInt dim; /* Dimension */
481: PetscInt cellType; /* Cell type */
482: PetscInt numVerts; /* Size of vertex array */
483: PetscInt numNodes; /* Size of node array */
484: PetscInt *nodes; /* Vertex/Node array */
485: PetscInt numTags; /* Size of physical tag array */
486: int tags[GMSH_MAX_TAGS]; /* Physical tag array */
487: } GmshElement;
489: static PetscErrorCode GmshElementsCreate(PetscCount count, GmshElement **elements)
490: {
491: PetscFunctionBegin;
492: PetscCall(PetscCalloc1(count, elements));
493: PetscFunctionReturn(PETSC_SUCCESS);
494: }
496: static PetscErrorCode GmshElementsDestroy(GmshElement **elements)
497: {
498: PetscFunctionBegin;
499: if (!*elements) PetscFunctionReturn(PETSC_SUCCESS);
500: PetscCall(PetscFree(*elements));
501: PetscFunctionReturn(PETSC_SUCCESS);
502: }
504: typedef struct {
505: PetscInt dim;
506: PetscInt order;
507: GmshEntities *entities;
508: PetscInt numNodes;
509: GmshNodes *nodelist;
510: PetscInt numElems;
511: GmshElement *elements;
512: PetscInt numVerts;
513: PetscInt numCells;
514: PetscInt *periodMap;
515: PetscInt *vertexMap;
516: PetscSegBuffer segbuf;
517: PetscInt numRegions;
518: PetscInt *regionDims;
519: PetscInt *regionTags;
520: char **regionNames;
521: } GmshMesh;
523: static PetscErrorCode GmshMeshCreate(GmshMesh **mesh)
524: {
525: PetscFunctionBegin;
526: PetscCall(PetscNew(mesh));
527: PetscCall(PetscSegBufferCreate(sizeof(PetscInt), 0, &(*mesh)->segbuf));
528: PetscFunctionReturn(PETSC_SUCCESS);
529: }
531: static PetscErrorCode GmshMeshDestroy(GmshMesh **mesh)
532: {
533: PetscInt r;
535: PetscFunctionBegin;
536: if (!*mesh) PetscFunctionReturn(PETSC_SUCCESS);
537: PetscCall(GmshEntitiesDestroy(&(*mesh)->entities));
538: PetscCall(GmshNodesDestroy(&(*mesh)->nodelist));
539: PetscCall(GmshElementsDestroy(&(*mesh)->elements));
540: PetscCall(PetscFree((*mesh)->periodMap));
541: PetscCall(PetscFree((*mesh)->vertexMap));
542: PetscCall(PetscSegBufferDestroy(&(*mesh)->segbuf));
543: for (r = 0; r < (*mesh)->numRegions; ++r) PetscCall(PetscFree((*mesh)->regionNames[r]));
544: PetscCall(PetscFree3((*mesh)->regionDims, (*mesh)->regionTags, (*mesh)->regionNames));
545: PetscCall(PetscFree(*mesh));
546: PetscFunctionReturn(PETSC_SUCCESS);
547: }
549: static PetscErrorCode GmshReadNodes_v22(GmshFile *gmsh, GmshMesh *mesh)
550: {
551: PetscViewer viewer = gmsh->viewer;
552: PetscBool byteSwap = gmsh->byteSwap;
553: char line[PETSC_MAX_PATH_LEN];
554: int n, t, num, nid, snum;
555: GmshNodes *nodes;
557: PetscFunctionBegin;
558: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
559: snum = sscanf(line, "%d", &num);
560: PetscCheck(snum == 1, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "File is not a valid Gmsh file");
561: PetscCall(GmshNodesCreate(num, &nodes));
562: mesh->numNodes = num;
563: mesh->nodelist = nodes;
564: for (n = 0; n < num; ++n) {
565: double *xyz = nodes->xyz + n * 3;
566: PetscCall(PetscViewerRead(viewer, &nid, 1, NULL, PETSC_ENUM));
567: PetscCall(PetscViewerRead(viewer, xyz, 3, NULL, PETSC_DOUBLE));
568: if (byteSwap) PetscCall(PetscByteSwap(&nid, PETSC_ENUM, 1));
569: if (byteSwap) PetscCall(PetscByteSwap(xyz, PETSC_DOUBLE, 3));
570: nodes->id[n] = nid;
571: for (t = 0; t < GMSH_MAX_TAGS; ++t) nodes->tag[n * GMSH_MAX_TAGS + t] = -1;
572: }
573: PetscFunctionReturn(PETSC_SUCCESS);
574: }
576: /* Gmsh elements can be of any dimension/co-dimension, so we need to traverse the
577: file contents multiple times to figure out the true number of cells and facets
578: in the given mesh. To make this more efficient we read the file contents only
579: once and store them in memory, while determining the true number of cells. */
580: static PetscErrorCode GmshReadElements_v22(GmshFile *gmsh, GmshMesh *mesh)
581: {
582: PetscViewer viewer = gmsh->viewer;
583: PetscBool binary = gmsh->binary;
584: PetscBool byteSwap = gmsh->byteSwap;
585: char line[PETSC_MAX_PATH_LEN];
586: int i, c, p, num, ibuf[1 + 4 + 1000], snum;
587: int cellType, numElem, numVerts, numNodes, numTags;
588: GmshElement *elements;
589: PetscInt *nodeMap = gmsh->nodeMap;
591: PetscFunctionBegin;
592: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
593: snum = sscanf(line, "%d", &num);
594: PetscCheck(snum == 1, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "File is not a valid Gmsh file");
595: PetscCall(GmshElementsCreate(num, &elements));
596: mesh->numElems = num;
597: mesh->elements = elements;
598: for (c = 0; c < num;) {
599: PetscCall(PetscViewerRead(viewer, ibuf, 3, NULL, PETSC_ENUM));
600: if (byteSwap) PetscCall(PetscByteSwap(ibuf, PETSC_ENUM, 3));
602: cellType = binary ? ibuf[0] : ibuf[1];
603: numElem = binary ? ibuf[1] : 1;
604: numTags = ibuf[2];
606: PetscCall(GmshCellTypeCheck(cellType));
607: numVerts = GmshCellMap[cellType].numVerts;
608: numNodes = GmshCellMap[cellType].numNodes;
610: for (i = 0; i < numElem; ++i, ++c) {
611: GmshElement *element = elements + c;
612: const int off = binary ? 0 : 1, nint = 1 + numTags + numNodes - off;
613: const int *id = ibuf, *nodes = ibuf + 1 + numTags, *tags = ibuf + 1;
614: PetscCall(PetscViewerRead(viewer, ibuf + off, nint, NULL, PETSC_ENUM));
615: if (byteSwap) PetscCall(PetscByteSwap(ibuf + off, PETSC_ENUM, nint));
616: element->id = id[0];
617: element->dim = GmshCellMap[cellType].dim;
618: element->cellType = cellType;
619: element->numVerts = numVerts;
620: element->numNodes = numNodes;
621: element->numTags = PetscMin(numTags, GMSH_MAX_TAGS);
622: PetscCall(PetscSegBufferGet(mesh->segbuf, (size_t)element->numNodes, &element->nodes));
623: for (p = 0; p < element->numNodes; p++) element->nodes[p] = nodeMap[nodes[p]];
624: for (p = 0; p < element->numTags; p++) element->tags[p] = tags[p];
625: }
626: }
627: PetscFunctionReturn(PETSC_SUCCESS);
628: }
630: /*
631: $Entities
632: numPoints(unsigned long) numCurves(unsigned long)
633: numSurfaces(unsigned long) numVolumes(unsigned long)
634: // points
635: tag(int) boxMinX(double) boxMinY(double) boxMinZ(double)
636: boxMaxX(double) boxMaxY(double) boxMaxZ(double)
637: numPhysicals(unsigned long) phyisicalTag[...](int)
638: ...
639: // curves
640: tag(int) boxMinX(double) boxMinY(double) boxMinZ(double)
641: boxMaxX(double) boxMaxY(double) boxMaxZ(double)
642: numPhysicals(unsigned long) physicalTag[...](int)
643: numBREPVert(unsigned long) tagBREPVert[...](int)
644: ...
645: // surfaces
646: tag(int) boxMinX(double) boxMinY(double) boxMinZ(double)
647: boxMaxX(double) boxMaxY(double) boxMaxZ(double)
648: numPhysicals(unsigned long) physicalTag[...](int)
649: numBREPCurve(unsigned long) tagBREPCurve[...](int)
650: ...
651: // volumes
652: tag(int) boxMinX(double) boxMinY(double) boxMinZ(double)
653: boxMaxX(double) boxMaxY(double) boxMaxZ(double)
654: numPhysicals(unsigned long) physicalTag[...](int)
655: numBREPSurfaces(unsigned long) tagBREPSurfaces[...](int)
656: ...
657: $EndEntities
658: */
659: static PetscErrorCode GmshReadEntities_v40(GmshFile *gmsh, GmshMesh *mesh)
660: {
661: PetscViewer viewer = gmsh->viewer;
662: PetscBool byteSwap = gmsh->byteSwap;
663: long lnum, lbuf[4];
664: int dim, eid, numTags, *ibuf, t;
665: PetscCount index, count[4];
666: PetscInt i, num;
667: GmshEntity *entity = NULL;
669: PetscFunctionBegin;
670: PetscCall(PetscViewerRead(viewer, lbuf, 4, NULL, PETSC_LONG));
671: if (byteSwap) PetscCall(PetscByteSwap(lbuf, PETSC_LONG, 4));
672: for (i = 0; i < 4; ++i) count[i] = (PetscCount)lbuf[i];
673: PetscCall(GmshEntitiesCreate(count, &mesh->entities));
674: for (dim = 0; dim < 4; ++dim) {
675: for (index = 0; index < count[dim]; ++index) {
676: PetscCall(PetscViewerRead(viewer, &eid, 1, NULL, PETSC_ENUM));
677: if (byteSwap) PetscCall(PetscByteSwap(&eid, PETSC_ENUM, 1));
678: PetscCall(GmshEntitiesAdd(mesh->entities, (PetscInt)index, dim, eid, &entity));
679: PetscCall(PetscViewerRead(viewer, entity->bbox, 6, NULL, PETSC_DOUBLE));
680: if (byteSwap) PetscCall(PetscByteSwap(entity->bbox, PETSC_DOUBLE, 6));
681: PetscCall(PetscViewerRead(viewer, &lnum, 1, NULL, PETSC_LONG));
682: if (byteSwap) PetscCall(PetscByteSwap(&lnum, PETSC_LONG, 1));
683: PetscCall(PetscIntCast(lnum, &num));
684: PetscCall(GmshBufferGet(gmsh, num, sizeof(int), &ibuf));
685: PetscCall(PetscViewerRead(viewer, ibuf, num, NULL, PETSC_ENUM));
686: if (byteSwap) PetscCall(PetscByteSwap(ibuf, PETSC_ENUM, num));
687: entity->numTags = numTags = (int)PetscMin(num, GMSH_MAX_TAGS);
688: for (t = 0; t < numTags; ++t) entity->tags[t] = ibuf[t];
689: if (dim == 0) continue;
690: PetscCall(PetscViewerRead(viewer, &lnum, 1, NULL, PETSC_LONG));
691: if (byteSwap) PetscCall(PetscByteSwap(&lnum, PETSC_LONG, 1));
692: PetscCall(GmshBufferGet(gmsh, lnum, sizeof(int), &ibuf));
693: PetscCall(PetscIntCast(lnum, &num));
694: PetscCall(PetscViewerRead(viewer, ibuf, num, NULL, PETSC_ENUM));
695: if (byteSwap) PetscCall(PetscByteSwap(ibuf, PETSC_ENUM, num));
696: }
697: }
698: PetscFunctionReturn(PETSC_SUCCESS);
699: }
701: /*
702: $Nodes
703: numEntityBlocks(unsigned long) numNodes(unsigned long)
704: tagEntity(int) dimEntity(int) typeNode(int) numNodes(unsigned long)
705: tag(int) x(double) y(double) z(double)
706: ...
707: ...
708: $EndNodes
709: */
710: static PetscErrorCode GmshReadNodes_v40(GmshFile *gmsh, GmshMesh *mesh)
711: {
712: PetscViewer viewer = gmsh->viewer;
713: PetscBool byteSwap = gmsh->byteSwap;
714: long block, node, n, t, numEntityBlocks, numTotalNodes, numNodes;
715: int info[3], nid;
716: GmshNodes *nodes;
718: PetscFunctionBegin;
719: PetscCall(PetscViewerRead(viewer, &numEntityBlocks, 1, NULL, PETSC_LONG));
720: if (byteSwap) PetscCall(PetscByteSwap(&numEntityBlocks, PETSC_LONG, 1));
721: PetscCall(PetscViewerRead(viewer, &numTotalNodes, 1, NULL, PETSC_LONG));
722: if (byteSwap) PetscCall(PetscByteSwap(&numTotalNodes, PETSC_LONG, 1));
723: PetscCall(GmshNodesCreate(numTotalNodes, &nodes));
724: PetscCall(PetscIntCast(numTotalNodes, &mesh->numNodes));
725: mesh->nodelist = nodes;
726: for (n = 0, block = 0; block < numEntityBlocks; ++block) {
727: PetscCall(PetscViewerRead(viewer, info, 3, NULL, PETSC_ENUM));
728: PetscCall(PetscViewerRead(viewer, &numNodes, 1, NULL, PETSC_LONG));
729: if (byteSwap) PetscCall(PetscByteSwap(&numNodes, PETSC_LONG, 1));
730: if (gmsh->binary) {
731: size_t nbytes = sizeof(int) + 3 * sizeof(double);
732: char *cbuf = NULL; /* dummy value to prevent warning from compiler about possible uninitialized value */
733: PetscInt icnt;
735: PetscCall(GmshBufferGet(gmsh, numNodes, nbytes, &cbuf));
736: PetscCall(PetscIntCast(numNodes * nbytes, &icnt));
737: PetscCall(PetscViewerRead(viewer, cbuf, icnt, NULL, PETSC_CHAR));
738: for (node = 0; node < numNodes; ++node, ++n) {
739: char *cnid = cbuf + node * nbytes, *cxyz = cnid + sizeof(int);
740: double *xyz = nodes->xyz + n * 3;
742: if (!PetscBinaryBigEndian()) PetscCall(PetscByteSwap(cnid, PETSC_ENUM, 1));
743: if (!PetscBinaryBigEndian()) PetscCall(PetscByteSwap(cxyz, PETSC_DOUBLE, 3));
744: PetscCall(PetscMemcpy(&nid, cnid, sizeof(int)));
745: PetscCall(PetscMemcpy(xyz, cxyz, 3 * sizeof(double)));
746: if (byteSwap) PetscCall(PetscByteSwap(&nid, PETSC_ENUM, 1));
747: if (byteSwap) PetscCall(PetscByteSwap(xyz, PETSC_DOUBLE, 3));
748: nodes->id[n] = nid;
749: for (t = 0; t < GMSH_MAX_TAGS; ++t) nodes->tag[n * GMSH_MAX_TAGS + t] = -1;
750: }
751: } else {
752: for (node = 0; node < numNodes; ++node, ++n) {
753: double *xyz = nodes->xyz + n * 3;
755: PetscCall(PetscViewerRead(viewer, &nid, 1, NULL, PETSC_ENUM));
756: PetscCall(PetscViewerRead(viewer, xyz, 3, NULL, PETSC_DOUBLE));
757: if (byteSwap) PetscCall(PetscByteSwap(&nid, PETSC_ENUM, 1));
758: if (byteSwap) PetscCall(PetscByteSwap(xyz, PETSC_DOUBLE, 3));
759: nodes->id[n] = nid;
760: for (t = 0; t < GMSH_MAX_TAGS; ++t) nodes->tag[n * GMSH_MAX_TAGS + t] = -1;
761: }
762: }
763: }
764: PetscFunctionReturn(PETSC_SUCCESS);
765: }
767: /*
768: $Elements
769: numEntityBlocks(unsigned long) numElements(unsigned long)
770: tagEntity(int) dimEntity(int) typeEle(int) numElements(unsigned long)
771: tag(int) numVert[...](int)
772: ...
773: ...
774: $EndElements
775: */
776: static PetscErrorCode GmshReadElements_v40(GmshFile *gmsh, GmshMesh *mesh)
777: {
778: PetscViewer viewer = gmsh->viewer;
779: PetscBool byteSwap = gmsh->byteSwap;
780: long c, block, numEntityBlocks, numTotalElements, elem, numElements;
781: int p, info[3], *ibuf = NULL;
782: int eid, dim, cellType, numVerts, numNodes, numTags;
783: GmshEntity *entity = NULL;
784: GmshElement *elements;
785: PetscInt *nodeMap = gmsh->nodeMap, icnt;
787: PetscFunctionBegin;
788: PetscCall(PetscViewerRead(viewer, &numEntityBlocks, 1, NULL, PETSC_LONG));
789: if (byteSwap) PetscCall(PetscByteSwap(&numEntityBlocks, PETSC_LONG, 1));
790: PetscCall(PetscViewerRead(viewer, &numTotalElements, 1, NULL, PETSC_LONG));
791: if (byteSwap) PetscCall(PetscByteSwap(&numTotalElements, PETSC_LONG, 1));
792: PetscCall(GmshElementsCreate(numTotalElements, &elements));
793: PetscCall(PetscIntCast(numTotalElements, &mesh->numElems));
794: mesh->elements = elements;
795: for (c = 0, block = 0; block < numEntityBlocks; ++block) {
796: PetscCall(PetscViewerRead(viewer, info, 3, NULL, PETSC_ENUM));
797: if (byteSwap) PetscCall(PetscByteSwap(info, PETSC_ENUM, 3));
798: eid = info[0];
799: dim = info[1];
800: cellType = info[2];
801: PetscCall(GmshEntitiesGet(mesh->entities, dim, eid, &entity));
802: PetscCall(GmshCellTypeCheck(cellType));
803: numVerts = GmshCellMap[cellType].numVerts;
804: numNodes = GmshCellMap[cellType].numNodes;
805: numTags = (int)entity->numTags;
806: PetscCall(PetscViewerRead(viewer, &numElements, 1, NULL, PETSC_LONG));
807: if (byteSwap) PetscCall(PetscByteSwap(&numElements, PETSC_LONG, 1));
808: PetscCall(GmshBufferGet(gmsh, (1 + numNodes) * numElements, sizeof(int), &ibuf));
809: PetscCall(PetscIntCast((1 + numNodes) * numElements, &icnt));
810: PetscCall(PetscViewerRead(viewer, ibuf, icnt, NULL, PETSC_ENUM));
811: if (byteSwap) PetscCall(PetscByteSwap(ibuf, PETSC_ENUM, (1 + numNodes) * numElements));
812: for (elem = 0; elem < numElements; ++elem, ++c) {
813: GmshElement *element = elements + c;
814: const int *id = ibuf + elem * (1 + numNodes), *nodes = id + 1;
815: element->id = id[0];
816: element->dim = dim;
817: element->cellType = cellType;
818: element->numVerts = numVerts;
819: element->numNodes = numNodes;
820: element->numTags = numTags;
821: PetscCall(PetscSegBufferGet(mesh->segbuf, (size_t)element->numNodes, &element->nodes));
822: for (p = 0; p < element->numNodes; p++) element->nodes[p] = nodeMap[nodes[p]];
823: for (p = 0; p < element->numTags; p++) element->tags[p] = entity->tags[p];
824: }
825: }
826: PetscFunctionReturn(PETSC_SUCCESS);
827: }
829: static PetscErrorCode GmshReadPeriodic_v40(GmshFile *gmsh, PetscInt periodicMap[])
830: {
831: PetscViewer viewer = gmsh->viewer;
832: int fileFormat = gmsh->fileFormat;
833: PetscBool binary = gmsh->binary;
834: PetscBool byteSwap = gmsh->byteSwap;
835: int numPeriodic, snum, i;
836: char line[PETSC_MAX_PATH_LEN];
837: PetscInt *nodeMap = gmsh->nodeMap;
839: PetscFunctionBegin;
840: if (fileFormat == 22 || !binary) {
841: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
842: snum = sscanf(line, "%d", &numPeriodic);
843: PetscCheck(snum == 1, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "File is not a valid Gmsh file");
844: } else {
845: PetscCall(PetscViewerRead(viewer, &numPeriodic, 1, NULL, PETSC_ENUM));
846: if (byteSwap) PetscCall(PetscByteSwap(&numPeriodic, PETSC_ENUM, 1));
847: }
848: for (i = 0; i < numPeriodic; i++) {
849: int ibuf[3], correspondingDim = -1, correspondingTag = -1, primaryTag = -1, correspondingNode, primaryNode;
850: long j, nNodes;
851: double affine[16];
853: if (fileFormat == 22 || !binary) {
854: PetscCall(PetscViewerRead(viewer, line, 3, NULL, PETSC_STRING));
855: snum = sscanf(line, "%d %d %d", &correspondingDim, &correspondingTag, &primaryTag);
856: PetscCheck(snum == 3, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "File is not a valid Gmsh file");
857: } else {
858: PetscCall(PetscViewerRead(viewer, ibuf, 3, NULL, PETSC_ENUM));
859: if (byteSwap) PetscCall(PetscByteSwap(ibuf, PETSC_ENUM, 3));
860: correspondingDim = ibuf[0];
861: correspondingTag = ibuf[1];
862: primaryTag = ibuf[2];
863: }
864: (void)correspondingDim;
865: (void)correspondingTag;
866: (void)primaryTag; /* unused */
868: if (fileFormat == 22 || !binary) {
869: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
870: snum = sscanf(line, "%ld", &nNodes);
871: if (snum != 1) { /* discard transformation and try again */
872: PetscCall(PetscViewerRead(viewer, line, -PETSC_MAX_PATH_LEN, NULL, PETSC_STRING));
873: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
874: snum = sscanf(line, "%ld", &nNodes);
875: PetscCheck(snum == 1, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "File is not a valid Gmsh file");
876: }
877: } else {
878: PetscCall(PetscViewerRead(viewer, &nNodes, 1, NULL, PETSC_LONG));
879: if (byteSwap) PetscCall(PetscByteSwap(&nNodes, PETSC_LONG, 1));
880: if (nNodes == -1) { /* discard transformation and try again */
881: PetscCall(PetscViewerRead(viewer, affine, 16, NULL, PETSC_DOUBLE));
882: PetscCall(PetscViewerRead(viewer, &nNodes, 1, NULL, PETSC_LONG));
883: if (byteSwap) PetscCall(PetscByteSwap(&nNodes, PETSC_LONG, 1));
884: }
885: }
887: for (j = 0; j < nNodes; j++) {
888: if (fileFormat == 22 || !binary) {
889: PetscCall(PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING));
890: snum = sscanf(line, "%d %d", &correspondingNode, &primaryNode);
891: PetscCheck(snum == 2, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "File is not a valid Gmsh file");
892: } else {
893: PetscCall(PetscViewerRead(viewer, ibuf, 2, NULL, PETSC_ENUM));
894: if (byteSwap) PetscCall(PetscByteSwap(ibuf, PETSC_ENUM, 2));
895: correspondingNode = ibuf[0];
896: primaryNode = ibuf[1];
897: }
898: correspondingNode = (int)nodeMap[correspondingNode];
899: primaryNode = (int)nodeMap[primaryNode];
900: periodicMap[correspondingNode] = primaryNode;
901: }
902: }
903: PetscFunctionReturn(PETSC_SUCCESS);
904: }
906: /* http://gmsh.info/dev/doc/texinfo/gmsh.html#MSH-file-format
907: $Entities
908: numPoints(size_t) numCurves(size_t)
909: numSurfaces(size_t) numVolumes(size_t)
910: pointTag(int) X(double) Y(double) Z(double)
911: numPhysicalTags(size_t) physicalTag(int) ...
912: ...
913: curveTag(int) minX(double) minY(double) minZ(double)
914: maxX(double) maxY(double) maxZ(double)
915: numPhysicalTags(size_t) physicalTag(int) ...
916: numBoundingPoints(size_t) pointTag(int) ...
917: ...
918: surfaceTag(int) minX(double) minY(double) minZ(double)
919: maxX(double) maxY(double) maxZ(double)
920: numPhysicalTags(size_t) physicalTag(int) ...
921: numBoundingCurves(size_t) curveTag(int) ...
922: ...
923: volumeTag(int) minX(double) minY(double) minZ(double)
924: maxX(double) maxY(double) maxZ(double)
925: numPhysicalTags(size_t) physicalTag(int) ...
926: numBoundngSurfaces(size_t) surfaceTag(int) ...
927: ...
928: $EndEntities
929: */
930: static PetscErrorCode GmshReadEntities_v41(GmshFile *gmsh, GmshMesh *mesh)
931: {
932: PetscCount count[4], index, numTags;
933: int dim, eid, *tags = NULL;
934: GmshEntity *entity = NULL;
936: PetscFunctionBegin;
937: PetscCall(GmshReadPetscCount(gmsh, count, 4));
938: PetscCall(GmshEntitiesCreate(count, &mesh->entities));
939: for (dim = 0; dim < 4; ++dim) {
940: for (index = 0; index < count[dim]; ++index) {
941: PetscCall(GmshReadInt(gmsh, &eid, 1));
942: PetscCall(GmshEntitiesAdd(mesh->entities, (PetscInt)index, dim, eid, &entity));
943: PetscCall(GmshReadDouble(gmsh, entity->bbox, (dim == 0) ? 3 : 6));
944: PetscCall(GmshReadPetscCount(gmsh, &numTags, 1));
945: PetscCall(GmshBufferGet(gmsh, numTags, sizeof(int), &tags));
946: PetscCall(GmshReadInt(gmsh, tags, numTags));
947: PetscCheck(numTags <= GMSH_MAX_TAGS, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "PETSc currently supports up to %" PetscInt_FMT " tags per entity, not %" PetscCount_FMT, (PetscInt)GMSH_MAX_TAGS, numTags);
948: PetscCall(PetscIntCast(numTags, &entity->numTags));
949: for (PetscInt i = 0; i < entity->numTags; ++i) entity->tags[i] = tags[i];
950: if (dim == 0) continue;
951: PetscCall(GmshReadPetscCount(gmsh, &numTags, 1));
952: PetscCall(GmshBufferGet(gmsh, numTags, sizeof(int), &tags));
953: PetscCall(GmshReadInt(gmsh, tags, numTags));
954: /* Currently, we do not save the ids for the bounding entities */
955: }
956: }
957: PetscFunctionReturn(PETSC_SUCCESS);
958: }
960: /* http://gmsh.info/dev/doc/texinfo/gmsh.html#MSH-file-format
961: $Nodes
962: numEntityBlocks(size_t) numNodes(size_t)
963: minNodeTag(size_t) maxNodeTag(size_t)
964: entityDim(int) entityTag(int) parametric(int; 0 or 1) numNodesBlock(size_t)
965: nodeTag(size_t)
966: ...
967: x(double) y(double) z(double)
968: < u(double; if parametric and entityDim = 1 or entityDim = 2) >
969: < v(double; if parametric and entityDim = 2) >
970: ...
971: ...
972: $EndNodes
973: */
974: static PetscErrorCode GmshReadNodes_v41(GmshFile *gmsh, GmshMesh *mesh)
975: {
976: int info[3], dim, eid, parametric;
977: PetscCount sizes[4], numEntityBlocks, numNodes, numNodesBlock = 0;
978: PetscInt numTags;
979: GmshEntity *entity = NULL;
980: GmshNodes *nodes;
982: PetscFunctionBegin;
983: PetscCall(GmshReadPetscCount(gmsh, sizes, 4));
984: numEntityBlocks = sizes[0];
985: numNodes = sizes[1];
986: PetscCall(GmshNodesCreate(numNodes, &nodes));
987: PetscCall(PetscIntCast(numNodes, &mesh->numNodes));
988: mesh->nodelist = nodes;
989: if (numEntityBlocks && !mesh->entities) PetscCall(PetscInfo(NULL, "File specifies %" PetscCount_FMT " entity blocks, but was missing the $Entities section\n", numEntityBlocks));
990: for (PetscCount block = 0, node = 0; block < numEntityBlocks; ++block, node += numNodesBlock) {
991: PetscCall(GmshReadInt(gmsh, info, 3));
992: dim = info[0];
993: eid = info[1];
994: parametric = info[2];
995: if (mesh->entities) PetscCall(GmshEntitiesGet(mesh->entities, dim, eid, &entity));
996: numTags = entity ? entity->numTags : 0;
997: PetscCheck(!parametric, PETSC_COMM_SELF, PETSC_ERR_SUP, "Parametric coordinates not supported");
998: PetscCall(GmshReadPetscCount(gmsh, &numNodesBlock, 1));
999: PetscCall(GmshReadPetscInt(gmsh, nodes->id + node, numNodesBlock));
1000: PetscCall(GmshReadDouble(gmsh, nodes->xyz + node * 3, numNodesBlock * 3));
1001: for (PetscCount n = 0; n < numNodesBlock; ++n) {
1002: PetscInt *tags = &nodes->tag[node * GMSH_MAX_TAGS];
1004: for (PetscInt t = 0; t < numTags; ++t) tags[n * GMSH_MAX_TAGS + t] = entity->tags[t];
1005: for (PetscInt t = numTags; t < GMSH_MAX_TAGS; ++t) tags[n * GMSH_MAX_TAGS + t] = -1;
1006: }
1007: }
1008: PetscCall(PetscIntCast(sizes[2], &gmsh->nodeStart));
1009: PetscCall(PetscIntCast(sizes[3] + 1, &gmsh->nodeEnd));
1010: PetscFunctionReturn(PETSC_SUCCESS);
1011: }
1013: /* http://gmsh.info/dev/doc/texinfo/gmsh.html#MSH-file-format
1014: $Elements
1015: numEntityBlocks(size_t) numElements(size_t)
1016: minElementTag(size_t) maxElementTag(size_t)
1017: entityDim(int) entityTag(int) elementType(int; see below) numElementsBlock(size_t)
1018: elementTag(size_t) nodeTag(size_t) ...
1019: ...
1020: ...
1021: $EndElements
1022: */
1023: static PetscErrorCode GmshReadElements_v41(GmshFile *gmsh, GmshMesh *mesh)
1024: {
1025: int info[3], eid, dim, cellType;
1026: PetscCount sizes[4], numEntityBlocks, numElements, numBlockElements, numVerts, numNodes, numTags, block, elem, c, p;
1027: GmshEntity *entity = NULL;
1028: GmshElement *elements;
1029: PetscInt *nodeMap = gmsh->nodeMap, *ibuf = NULL;
1031: PetscFunctionBegin;
1032: PetscCall(GmshReadPetscCount(gmsh, sizes, 4));
1033: numEntityBlocks = sizes[0];
1034: numElements = sizes[1];
1035: PetscCall(GmshElementsCreate(numElements, &elements));
1036: PetscCall(PetscIntCast(numElements, &mesh->numElems));
1037: mesh->elements = elements;
1038: if (numEntityBlocks && !mesh->entities) PetscCall(PetscInfo(NULL, "File specifies %" PetscCount_FMT " entity blocks, but was missing the $Entities section\n", numEntityBlocks));
1039: for (c = 0, block = 0; block < numEntityBlocks; ++block) {
1040: PetscCall(GmshReadInt(gmsh, info, 3));
1041: dim = info[0];
1042: eid = info[1];
1043: cellType = info[2];
1044: if (mesh->entities) PetscCall(GmshEntitiesGet(mesh->entities, dim, eid, &entity));
1045: PetscCall(GmshCellTypeCheck(cellType));
1046: numVerts = GmshCellMap[cellType].numVerts;
1047: numNodes = GmshCellMap[cellType].numNodes;
1048: numTags = entity ? entity->numTags : 0;
1049: PetscCall(GmshReadPetscCount(gmsh, &numBlockElements, 1));
1050: PetscCall(GmshBufferGet(gmsh, (1 + numNodes) * numBlockElements, sizeof(PetscInt), &ibuf));
1051: PetscCall(GmshReadPetscInt(gmsh, ibuf, (1 + numNodes) * numBlockElements));
1052: for (elem = 0; elem < numBlockElements; ++elem, ++c) {
1053: GmshElement *element = elements + c;
1054: const PetscInt *id = ibuf + elem * (1 + numNodes), *nodes = id + 1;
1056: element->id = id[0];
1057: element->dim = dim;
1058: element->cellType = cellType;
1059: PetscCall(PetscIntCast(numVerts, &element->numVerts));
1060: PetscCall(PetscIntCast(numNodes, &element->numNodes));
1061: PetscCall(PetscIntCast(numTags, &element->numTags));
1062: PetscCall(PetscSegBufferGet(mesh->segbuf, element->numNodes, &element->nodes));
1063: for (p = 0; p < element->numNodes; p++) element->nodes[p] = nodeMap[nodes[p]];
1064: for (p = 0; p < element->numTags; p++) element->tags[p] = entity->tags[p];
1065: }
1066: }
1067: PetscFunctionReturn(PETSC_SUCCESS);
1068: }
1070: /* http://gmsh.info/dev/doc/texinfo/gmsh.html#MSH-file-format
1071: $Periodic
1072: numPeriodicLinks(size_t)
1073: entityDim(int) entityTag(int) entityTagPrimary(int)
1074: numAffine(size_t) value(double) ...
1075: numCorrespondingNodes(size_t)
1076: nodeTag(size_t) nodeTagPrimary(size_t)
1077: ...
1078: ...
1079: $EndPeriodic
1080: */
1081: static PetscErrorCode GmshReadPeriodic_v41(GmshFile *gmsh, PetscInt periodicMap[])
1082: {
1083: int info[3];
1084: double dbuf[16];
1085: PetscCount numPeriodicLinks, numAffine, numCorrespondingNodes;
1086: PetscInt *nodeMap = gmsh->nodeMap, *nodeTags = NULL;
1088: PetscFunctionBegin;
1089: PetscCall(GmshReadPetscCount(gmsh, &numPeriodicLinks, 1));
1090: for (PetscCount link = 0; link < numPeriodicLinks; ++link) {
1091: PetscCall(GmshReadInt(gmsh, info, 3));
1092: PetscCall(GmshReadPetscCount(gmsh, &numAffine, 1));
1093: PetscCall(GmshReadDouble(gmsh, dbuf, numAffine));
1094: PetscCall(GmshReadPetscCount(gmsh, &numCorrespondingNodes, 1));
1095: PetscCall(GmshBufferGet(gmsh, numCorrespondingNodes, sizeof(PetscInt), &nodeTags));
1096: PetscCall(GmshReadPetscInt(gmsh, nodeTags, numCorrespondingNodes * 2));
1097: for (PetscCount node = 0; node < numCorrespondingNodes; ++node) {
1098: PetscInt correspondingNode = nodeMap[nodeTags[node * 2 + 0]];
1099: PetscInt primaryNode = nodeMap[nodeTags[node * 2 + 1]];
1101: periodicMap[correspondingNode] = primaryNode;
1102: }
1103: }
1104: PetscFunctionReturn(PETSC_SUCCESS);
1105: }
1107: /* http://gmsh.info/dev/doc/texinfo/gmsh.html#MSH-file-format
1108: $MeshFormat // same as MSH version 2
1109: version(ASCII double; currently 4.1)
1110: file-type(ASCII int; 0 for ASCII mode, 1 for binary mode)
1111: data-size(ASCII int; sizeof(size_t))
1112: < int with value one; only in binary mode, to detect endianness >
1113: $EndMeshFormat
1114: */
1115: static PetscErrorCode GmshReadMeshFormat(GmshFile *gmsh)
1116: {
1117: char line[PETSC_MAX_PATH_LEN];
1118: int snum, fileType, fileFormat, dataSize, checkEndian;
1119: float version;
1121: PetscFunctionBegin;
1122: PetscCall(GmshReadString(gmsh, line, 3));
1123: snum = sscanf(line, "%f %d %d", &version, &fileType, &dataSize);
1124: fileFormat = (int)roundf(version * 10);
1125: PetscCheck(snum == 3, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Unable to parse Gmsh file header: %s", line);
1126: PetscCheck(fileFormat >= 22, PETSC_COMM_SELF, PETSC_ERR_SUP, "Gmsh file version %3.1f must be at least 2.2", (double)version);
1127: PetscCheck((int)version != 3, PETSC_COMM_SELF, PETSC_ERR_SUP, "Gmsh file version %3.1f not supported", (double)version);
1128: PetscCheck(fileFormat <= 41, PETSC_COMM_SELF, PETSC_ERR_SUP, "Gmsh file version %3.1f must be at most 4.1", (double)version);
1129: PetscCheck(!gmsh->binary || fileType, PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Viewer is binary but Gmsh file is ASCII");
1130: PetscCheck(gmsh->binary || !fileType, PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Viewer is ASCII but Gmsh file is binary");
1131: PetscCheck(fileFormat > 40 || dataSize == sizeof(double), PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Data size %d is not valid for a Gmsh file", dataSize);
1132: PetscCheck(fileFormat < 41 || dataSize == sizeof(int) || dataSize == sizeof(PetscInt64), PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Data size %d is not valid for a Gmsh file", dataSize);
1133: gmsh->fileFormat = fileFormat;
1134: gmsh->dataSize = dataSize;
1135: gmsh->byteSwap = PETSC_FALSE;
1136: if (gmsh->binary) {
1137: PetscCall(GmshReadInt(gmsh, &checkEndian, 1));
1138: if (checkEndian != 1) {
1139: PetscCall(PetscByteSwap(&checkEndian, PETSC_ENUM, 1));
1140: PetscCheck(checkEndian == 1, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Unable to detect endianness in Gmsh file header: %s", line);
1141: gmsh->byteSwap = PETSC_TRUE;
1142: }
1143: }
1144: PetscFunctionReturn(PETSC_SUCCESS);
1145: }
1147: /* http://gmsh.info/dev/doc/texinfo/gmsh.html#MSH-file-format
1148: Neper: https://neper.info/ adds this section
1150: $MeshVersion
1151: <major>.<minor>,<patch>
1152: $EndMeshVersion
1153: */
1154: static PetscErrorCode GmshReadMeshVersion(GmshFile *gmsh)
1155: {
1156: char line[PETSC_MAX_PATH_LEN];
1157: int snum, major, minor, patch;
1159: PetscFunctionBegin;
1160: PetscCall(GmshReadString(gmsh, line, 1));
1161: snum = sscanf(line, "%d.%d.%d", &major, &minor, &patch);
1162: PetscCheck(snum == 3, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Unable to parse Gmsh file header: %s", line);
1163: PetscFunctionReturn(PETSC_SUCCESS);
1164: }
1166: /* http://gmsh.info/dev/doc/texinfo/gmsh.html#MSH-file-format
1167: Neper: https://neper.info/ adds this section
1169: $Domain
1170: <shape>
1171: $EndDomain
1172: */
1173: static PetscErrorCode GmshReadMeshDomain(GmshFile *gmsh)
1174: {
1175: char line[PETSC_MAX_PATH_LEN];
1177: PetscFunctionBegin;
1178: PetscCall(GmshReadString(gmsh, line, 1));
1179: PetscFunctionReturn(PETSC_SUCCESS);
1180: }
1182: /*
1183: PhysicalNames
1184: numPhysicalNames(ASCII int)
1185: dimension(ASCII int) physicalTag(ASCII int) "name"(127 characters max)
1186: ...
1187: $EndPhysicalNames
1188: */
1189: static PetscErrorCode GmshReadPhysicalNames(GmshFile *gmsh, GmshMesh *mesh)
1190: {
1191: char line[PETSC_MAX_PATH_LEN], name[128 + 2], *p = NULL, *q = NULL, *r = NULL;
1192: int snum, region, dim, tag;
1194: PetscFunctionBegin;
1195: PetscCall(GmshReadString(gmsh, line, 1));
1196: snum = sscanf(line, "%d", ®ion);
1197: mesh->numRegions = region;
1198: PetscCheck(snum == 1, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "File is not a valid Gmsh file");
1199: PetscCall(PetscMalloc3(mesh->numRegions, &mesh->regionDims, mesh->numRegions, &mesh->regionTags, mesh->numRegions, &mesh->regionNames));
1200: for (region = 0; region < mesh->numRegions; ++region) {
1201: PetscCall(GmshReadString(gmsh, line, 2));
1202: snum = sscanf(line, "%d %d", &dim, &tag);
1203: PetscCheck(snum == 2, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "File is not a valid Gmsh file");
1204: PetscCall(GmshReadString(gmsh, line, -(PetscInt)sizeof(line)));
1205: PetscCall(PetscStrchr(line, '"', &p));
1206: PetscCheck(p, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "File is not a valid Gmsh file");
1207: PetscCall(PetscStrrchr(line, '"', &q));
1208: PetscCheck(q != p, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "File is not a valid Gmsh file");
1209: PetscCall(PetscStrrchr(line, ':', &r));
1210: if (p != r) q = r;
1211: PetscCall(PetscStrncpy(name, p + 1, (size_t)(q - p - 1)));
1212: mesh->regionDims[region] = dim;
1213: mesh->regionTags[region] = tag;
1214: PetscCall(PetscStrallocpy(name, &mesh->regionNames[region]));
1215: }
1216: PetscFunctionReturn(PETSC_SUCCESS);
1217: }
1219: static PetscErrorCode GmshReadEntities(GmshFile *gmsh, GmshMesh *mesh)
1220: {
1221: PetscFunctionBegin;
1222: switch (gmsh->fileFormat) {
1223: case 41:
1224: PetscCall(GmshReadEntities_v41(gmsh, mesh));
1225: break;
1226: default:
1227: PetscCall(GmshReadEntities_v40(gmsh, mesh));
1228: break;
1229: }
1230: PetscFunctionReturn(PETSC_SUCCESS);
1231: }
1233: static PetscErrorCode GmshReadNodes(GmshFile *gmsh, GmshMesh *mesh)
1234: {
1235: PetscFunctionBegin;
1236: switch (gmsh->fileFormat) {
1237: case 41:
1238: PetscCall(GmshReadNodes_v41(gmsh, mesh));
1239: break;
1240: case 40:
1241: PetscCall(GmshReadNodes_v40(gmsh, mesh));
1242: break;
1243: default:
1244: PetscCall(GmshReadNodes_v22(gmsh, mesh));
1245: break;
1246: }
1248: { /* Gmsh v2.2/v4.0 does not provide min/max node tags */
1249: if (mesh->numNodes > 0 && gmsh->nodeEnd >= gmsh->nodeStart) {
1250: PetscInt tagMin = PETSC_INT_MAX, tagMax = PETSC_INT_MIN, n;
1251: GmshNodes *nodes = mesh->nodelist;
1252: for (n = 0; n < mesh->numNodes; ++n) {
1253: const PetscInt tag = nodes->id[n];
1254: tagMin = PetscMin(tag, tagMin);
1255: tagMax = PetscMax(tag, tagMax);
1256: }
1257: gmsh->nodeStart = tagMin;
1258: gmsh->nodeEnd = tagMax + 1;
1259: }
1260: }
1262: { /* Support for sparse node tags */
1263: PetscInt n, t;
1264: GmshNodes *nodes = mesh->nodelist;
1265: PetscCall(PetscMalloc1(gmsh->nodeEnd - gmsh->nodeStart, &gmsh->nbuf));
1266: for (t = 0; t < gmsh->nodeEnd - gmsh->nodeStart; ++t) gmsh->nbuf[t] = PETSC_INT_MIN;
1267: gmsh->nodeMap = gmsh->nbuf - gmsh->nodeStart;
1268: for (n = 0; n < mesh->numNodes; ++n) {
1269: const PetscInt tag = nodes->id[n];
1270: PetscCheck(gmsh->nodeMap[tag] < 0, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Repeated node tag %" PetscInt_FMT, tag);
1271: gmsh->nodeMap[tag] = n;
1272: }
1273: }
1274: PetscFunctionReturn(PETSC_SUCCESS);
1275: }
1277: static PetscErrorCode GmshReadElements(GmshFile *gmsh, GmshMesh *mesh)
1278: {
1279: PetscFunctionBegin;
1280: switch (gmsh->fileFormat) {
1281: case 41:
1282: PetscCall(GmshReadElements_v41(gmsh, mesh));
1283: break;
1284: case 40:
1285: PetscCall(GmshReadElements_v40(gmsh, mesh));
1286: break;
1287: default:
1288: PetscCall(GmshReadElements_v22(gmsh, mesh));
1289: break;
1290: }
1292: { /* Reorder elements by codimension and polytope type */
1293: PetscInt ne = mesh->numElems;
1294: GmshElement *elements = mesh->elements;
1295: PetscInt keymap[GMSH_NUM_POLYTOPES], nk = 0;
1296: PetscInt offset[GMSH_NUM_POLYTOPES + 1], e, k;
1298: for (k = 0; k < GMSH_NUM_POLYTOPES; ++k) keymap[k] = PETSC_INT_MIN;
1299: PetscCall(PetscMemzero(offset, sizeof(offset)));
1301: keymap[GMSH_TET] = nk++;
1302: keymap[GMSH_HEX] = nk++;
1303: keymap[GMSH_PRI] = nk++;
1304: keymap[GMSH_PYR] = nk++;
1305: keymap[GMSH_TRI] = nk++;
1306: keymap[GMSH_QUA] = nk++;
1307: keymap[GMSH_SEG] = nk++;
1308: keymap[GMSH_VTX] = nk++;
1310: PetscCall(GmshElementsCreate(mesh->numElems, &mesh->elements));
1311: #define key(eid) keymap[GmshCellMap[elements[eid].cellType].polytope]
1312: for (e = 0; e < ne; ++e) offset[1 + key(e)]++;
1313: for (k = 1; k < nk; ++k) offset[k] += offset[k - 1];
1314: for (e = 0; e < ne; ++e) mesh->elements[offset[key(e)]++] = elements[e];
1315: #undef key
1316: PetscCall(GmshElementsDestroy(&elements));
1317: }
1319: { /* Mesh dimension and order */
1320: GmshElement *elem = mesh->numElems ? mesh->elements : NULL;
1321: mesh->dim = elem ? GmshCellMap[elem->cellType].dim : 0;
1322: mesh->order = elem ? GmshCellMap[elem->cellType].order : 0;
1323: }
1325: {
1326: PetscBT vtx;
1327: PetscInt dim = mesh->dim, e, n, v;
1329: PetscCall(PetscBTCreate(mesh->numNodes, &vtx));
1331: /* Compute number of cells and set of vertices */
1332: mesh->numCells = 0;
1333: for (e = 0; e < mesh->numElems; ++e) {
1334: GmshElement *elem = mesh->elements + e;
1335: if (elem->dim == dim && dim > 0) mesh->numCells++;
1336: for (v = 0; v < elem->numVerts; v++) PetscCall(PetscBTSet(vtx, elem->nodes[v]));
1337: }
1339: /* Compute numbering for vertices */
1340: mesh->numVerts = 0;
1341: PetscCall(PetscMalloc1(mesh->numNodes, &mesh->vertexMap));
1342: for (n = 0; n < mesh->numNodes; ++n) mesh->vertexMap[n] = PetscBTLookup(vtx, n) ? mesh->numVerts++ : PETSC_INT_MIN;
1344: PetscCall(PetscBTDestroy(&vtx));
1345: }
1346: PetscFunctionReturn(PETSC_SUCCESS);
1347: }
1349: static PetscErrorCode GmshReadPeriodic(GmshFile *gmsh, GmshMesh *mesh)
1350: {
1351: PetscInt n;
1353: PetscFunctionBegin;
1354: PetscCall(PetscMalloc1(mesh->numNodes, &mesh->periodMap));
1355: for (n = 0; n < mesh->numNodes; ++n) mesh->periodMap[n] = n;
1356: switch (gmsh->fileFormat) {
1357: case 41:
1358: PetscCall(GmshReadPeriodic_v41(gmsh, mesh->periodMap));
1359: break;
1360: default:
1361: PetscCall(GmshReadPeriodic_v40(gmsh, mesh->periodMap));
1362: break;
1363: }
1365: /* Find canonical primary nodes */
1366: for (n = 0; n < mesh->numNodes; ++n)
1367: while (mesh->periodMap[n] != mesh->periodMap[mesh->periodMap[n]]) mesh->periodMap[n] = mesh->periodMap[mesh->periodMap[n]];
1369: /* Renumber vertices (filter out correspondings) */
1370: mesh->numVerts = 0;
1371: for (n = 0; n < mesh->numNodes; ++n)
1372: if (mesh->vertexMap[n] >= 0) /* is vertex */
1373: if (mesh->periodMap[n] == n) /* is primary */
1374: mesh->vertexMap[n] = mesh->numVerts++;
1375: for (n = 0; n < mesh->numNodes; ++n)
1376: if (mesh->vertexMap[n] >= 0) /* is vertex */
1377: if (mesh->periodMap[n] != n) /* is corresponding */
1378: mesh->vertexMap[n] = mesh->vertexMap[mesh->periodMap[n]];
1379: PetscFunctionReturn(PETSC_SUCCESS);
1380: }
1382: #define DM_POLYTOPE_VERTEX DM_POLYTOPE_POINT
1383: static const DMPolytopeType DMPolytopeMap[] = {
1384: /* GMSH_VTX */ DM_POLYTOPE_VERTEX,
1385: /* GMSH_SEG */ DM_POLYTOPE_SEGMENT,
1386: /* GMSH_TRI */ DM_POLYTOPE_TRIANGLE,
1387: /* GMSH_QUA */ DM_POLYTOPE_QUADRILATERAL,
1388: /* GMSH_TET */ DM_POLYTOPE_TETRAHEDRON,
1389: /* GMSH_HEX */ DM_POLYTOPE_HEXAHEDRON,
1390: /* GMSH_PRI */ DM_POLYTOPE_TRI_PRISM,
1391: /* GMSH_PYR */ DM_POLYTOPE_PYRAMID, DM_POLYTOPE_UNKNOWN};
1393: static inline DMPolytopeType DMPolytopeTypeFromGmsh(PetscInt cellType)
1394: {
1395: return DMPolytopeMap[GmshCellMap[cellType].polytope];
1396: }
1398: static PetscErrorCode GmshCreateFE(MPI_Comm comm, const char prefix[], PetscBool isSimplex, PetscBool continuity, PetscDTNodeType nodeType, PetscInt dim, PetscInt Nc, PetscInt k, PetscFE *fem)
1399: {
1400: DM K;
1401: PetscSpace P;
1402: PetscDualSpace Q;
1403: PetscQuadrature q, fq;
1404: PetscBool isTensor = isSimplex ? PETSC_FALSE : PETSC_TRUE;
1405: PetscBool endpoint = PETSC_TRUE;
1406: char name[32];
1408: PetscFunctionBegin;
1409: /* Create space */
1410: PetscCall(PetscSpaceCreate(comm, &P));
1411: PetscCall(PetscSpaceSetType(P, PETSCSPACEPOLYNOMIAL));
1412: PetscCall(PetscSpacePolynomialSetTensor(P, isTensor));
1413: PetscCall(PetscSpaceSetNumComponents(P, Nc));
1414: PetscCall(PetscSpaceSetNumVariables(P, dim));
1415: PetscCall(PetscSpaceSetDegree(P, k, PETSC_DETERMINE));
1416: if (prefix) {
1417: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)P, prefix));
1418: PetscCall(PetscSpaceSetFromOptions(P));
1419: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)P, NULL));
1420: PetscCall(PetscSpaceGetDegree(P, &k, NULL));
1421: }
1422: PetscCall(PetscSpaceSetUp(P));
1423: /* Create dual space */
1424: PetscCall(PetscDualSpaceCreate(comm, &Q));
1425: PetscCall(PetscDualSpaceSetType(Q, PETSCDUALSPACELAGRANGE));
1426: PetscCall(PetscDualSpaceLagrangeSetTensor(Q, isTensor));
1427: PetscCall(PetscDualSpaceLagrangeSetContinuity(Q, continuity));
1428: PetscCall(PetscDualSpaceLagrangeSetNodeType(Q, nodeType, endpoint, 0));
1429: PetscCall(PetscDualSpaceSetNumComponents(Q, Nc));
1430: PetscCall(PetscDualSpaceSetOrder(Q, k));
1431: PetscCall(DMPlexCreateReferenceCell(PETSC_COMM_SELF, DMPolytopeTypeSimpleShape(dim, isSimplex), &K));
1432: PetscCall(PetscDualSpaceSetDM(Q, K));
1433: PetscCall(DMDestroy(&K));
1434: if (prefix) {
1435: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)Q, prefix));
1436: PetscCall(PetscDualSpaceSetFromOptions(Q));
1437: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)Q, NULL));
1438: }
1439: PetscCall(PetscDualSpaceSetUp(Q));
1440: /* Create quadrature */
1441: if (isSimplex) {
1442: PetscCall(PetscDTStroudConicalQuadrature(dim, 1, k + 1, -1, +1, &q));
1443: PetscCall(PetscDTStroudConicalQuadrature(dim - 1, 1, k + 1, -1, +1, &fq));
1444: } else {
1445: PetscCall(PetscDTGaussTensorQuadrature(dim, 1, k + 1, -1, +1, &q));
1446: PetscCall(PetscDTGaussTensorQuadrature(dim - 1, 1, k + 1, -1, +1, &fq));
1447: }
1448: /* Create finite element */
1449: PetscCall(PetscFECreate(comm, fem));
1450: PetscCall(PetscFESetType(*fem, PETSCFEBASIC));
1451: PetscCall(PetscFESetNumComponents(*fem, Nc));
1452: PetscCall(PetscFESetBasisSpace(*fem, P));
1453: PetscCall(PetscFESetDualSpace(*fem, Q));
1454: PetscCall(PetscFESetQuadrature(*fem, q));
1455: PetscCall(PetscFESetFaceQuadrature(*fem, fq));
1456: if (prefix) {
1457: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)*fem, prefix));
1458: PetscCall(PetscFESetFromOptions(*fem));
1459: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)*fem, NULL));
1460: }
1461: PetscCall(PetscFESetUp(*fem));
1462: /* Cleanup */
1463: PetscCall(PetscSpaceDestroy(&P));
1464: PetscCall(PetscDualSpaceDestroy(&Q));
1465: PetscCall(PetscQuadratureDestroy(&q));
1466: PetscCall(PetscQuadratureDestroy(&fq));
1467: /* Set finite element name */
1468: PetscCall(PetscSNPrintf(name, sizeof(name), "%s%" PetscInt_FMT, isSimplex ? "P" : "Q", k));
1469: PetscCall(PetscFESetName(*fem, name));
1470: PetscFunctionReturn(PETSC_SUCCESS);
1471: }
1473: /*@
1474: DMPlexCreateGmshFromFile - Create a `DMPLEX` mesh from a Gmsh file
1476: Input Parameters:
1477: + comm - The MPI communicator
1478: . filename - Name of the Gmsh file
1479: - interpolate - Create faces and edges in the mesh
1481: Output Parameter:
1482: . dm - The `DM` object representing the mesh
1484: Level: beginner
1486: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromFile()`, `DMPlexCreateGmsh()`, `DMPlexCreate()`
1487: @*/
1488: PetscErrorCode DMPlexCreateGmshFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
1489: {
1490: PetscViewer viewer;
1491: PetscMPIInt rank;
1492: int fileType;
1493: PetscViewerType vtype;
1495: PetscFunctionBegin;
1496: PetscCallMPI(MPI_Comm_rank(comm, &rank));
1498: /* Determine Gmsh file type (ASCII or binary) from file header */
1499: if (rank == 0) {
1500: GmshFile gmsh[1];
1501: char line[PETSC_MAX_PATH_LEN];
1502: int snum;
1503: float version;
1504: int fileFormat;
1506: PetscCall(PetscArrayzero(gmsh, 1));
1507: PetscCall(PetscViewerCreate(PETSC_COMM_SELF, &gmsh->viewer));
1508: PetscCall(PetscViewerSetType(gmsh->viewer, PETSCVIEWERASCII));
1509: PetscCall(PetscViewerFileSetMode(gmsh->viewer, FILE_MODE_READ));
1510: PetscCall(PetscViewerFileSetName(gmsh->viewer, filename));
1511: /* Read only the first two lines of the Gmsh file */
1512: PetscCall(GmshReadSection(gmsh, line));
1513: PetscCall(GmshExpect(gmsh, "$MeshFormat", line));
1514: PetscCall(GmshReadString(gmsh, line, 2));
1515: snum = sscanf(line, "%f %d", &version, &fileType);
1516: fileFormat = (int)roundf(version * 10);
1517: PetscCheck(snum == 2, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Unable to parse Gmsh file header: %s", line);
1518: PetscCheck(fileFormat >= 22, PETSC_COMM_SELF, PETSC_ERR_SUP, "Gmsh file version %3.1f must be at least 2.2", (double)version);
1519: PetscCheck((int)version != 3, PETSC_COMM_SELF, PETSC_ERR_SUP, "Gmsh file version %3.1f not supported", (double)version);
1520: PetscCheck(fileFormat <= 41, PETSC_COMM_SELF, PETSC_ERR_SUP, "Gmsh file version %3.1f must be at most 4.1", (double)version);
1521: PetscCall(PetscViewerDestroy(&gmsh->viewer));
1522: }
1523: PetscCallMPI(MPI_Bcast(&fileType, 1, MPI_INT, 0, comm));
1524: vtype = (fileType == 0) ? PETSCVIEWERASCII : PETSCVIEWERBINARY;
1526: /* Create appropriate viewer and build plex */
1527: PetscCall(PetscViewerCreate(comm, &viewer));
1528: PetscCall(PetscViewerSetType(viewer, vtype));
1529: PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ));
1530: PetscCall(PetscViewerFileSetName(viewer, filename));
1531: PetscCall(DMPlexCreateGmsh(comm, viewer, interpolate, dm));
1532: PetscCall(PetscViewerDestroy(&viewer));
1533: PetscFunctionReturn(PETSC_SUCCESS);
1534: }
1536: /*@
1537: DMPlexCreateGmsh - Create a `DMPLEX` mesh from a Gmsh file viewer
1539: Collective
1541: Input Parameters:
1542: + comm - The MPI communicator
1543: . viewer - The `PetscViewer` associated with a Gmsh file
1544: - interpolate - Create faces and edges in the mesh
1546: Output Parameter:
1547: . dm - The `DM` object representing the mesh
1549: Options Database Keys:
1550: + -dm_plex_gmsh_hybrid - Force triangular prisms to use tensor order
1551: . -dm_plex_gmsh_periodic - Read Gmsh periodic section and construct a periodic Plex
1552: . -dm_plex_gmsh_highorder - Generate high-order coordinates
1553: . -dm_plex_gmsh_project - Project high-order coordinates to a different space, use the prefix dm_plex_gmsh_project_ to define the space
1554: . -dm_plex_gmsh_use_generic - Generate generic labels, i.e. Cell Sets, Face Sets, etc.
1555: . -dm_plex_gmsh_use_regions - Generate labels with region names
1556: . -dm_plex_gmsh_mark_vertices - Add vertices to generated labels
1557: . -dm_plex_gmsh_mark_vertices_strict - Add vertices included in a region to generated labels
1558: . -dm_plex_gmsh_multiple_tags - Allow multiple tags for default labels
1559: - -dm_plex_gmsh_spacedim <d> - Embedding space dimension, if different from topological dimension
1561: Level: beginner
1563: Notes:
1564: The Gmsh file format is described in <http://gmsh.info/doc/texinfo/gmsh.html#MSH-file-format>
1566: By default, the "Cell Sets", "Face Sets", and "Vertex Sets" labels are created, and only insert the first tag on a point. By using `-dm_plex_gmsh_multiple_tags`, all tags can be inserted. Alternatively, `-dm_plex_gmsh_use_regions` creates labels based on the region names from the `PhysicalNames` section, and all tags are used, but you can retain the generic labels using `-dm_plex_gmsh_use_generic`.
1568: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMCreate()`
1569: @*/
1570: PetscErrorCode DMPlexCreateGmsh(MPI_Comm comm, PetscViewer viewer, PetscBool interpolate, DM *dm)
1571: {
1572: GmshMesh *mesh = NULL;
1573: PetscViewer parentviewer = NULL;
1574: PetscBT periodicVerts = NULL;
1575: PetscBT *periodicCells = NULL;
1576: DM cdm, cdmCell = NULL;
1577: PetscSection cs, csCell = NULL;
1578: Vec coordinates, coordinatesCell;
1579: DMLabel cellSets = NULL, faceSets = NULL, edgeSets = NULL, vertSets = NULL, marker = NULL, *regionSets;
1580: PetscInt dim = 0, coordDim = -1, order = 0, maxHeight = 0;
1581: PetscInt numNodes = 0, numElems = 0, numVerts = 0, numCells = 0, vStart, vEnd;
1582: PetscInt cell, cone[8], e, n, v, d;
1583: PetscBool usegeneric = PETSC_TRUE, useregions = PETSC_FALSE, markvertices = PETSC_FALSE, markverticesstrict = PETSC_FALSE, multipleTags = PETSC_FALSE;
1584: PetscBool flg, binary, hybrid = interpolate, periodic = PETSC_TRUE;
1585: PetscBool highOrder = PETSC_TRUE, highOrderSet, project = PETSC_FALSE;
1586: PetscBool isSimplex = PETSC_FALSE, isHybrid = PETSC_FALSE, hasTetra = PETSC_FALSE;
1587: PetscMPIInt rank;
1589: PetscFunctionBegin;
1590: PetscCallMPI(MPI_Comm_rank(comm, &rank));
1591: PetscObjectOptionsBegin((PetscObject)viewer);
1592: PetscOptionsHeadBegin(PetscOptionsObject, "DMPlex Gmsh options");
1593: PetscCall(PetscOptionsBool("-dm_plex_gmsh_hybrid", "Force triangular prisms to use tensor order", "DMPlexCreateGmsh", hybrid, &hybrid, NULL));
1594: PetscCall(PetscOptionsBool("-dm_plex_gmsh_periodic", "Read Gmsh periodic section", "DMPlexCreateGmsh", periodic, &periodic, NULL));
1595: PetscCall(PetscOptionsBool("-dm_plex_gmsh_highorder", "Generate high-order coordinates", "DMPlexCreateGmsh", highOrder, &highOrder, &highOrderSet));
1596: PetscCall(PetscOptionsBool("-dm_plex_gmsh_project", "Project high-order coordinates to a different space", "DMPlexCreateGmsh", project, &project, NULL));
1597: PetscCall(PetscOptionsBool("-dm_plex_gmsh_use_regions", "Generate labels with region names", "DMPlexCreateGmsh", useregions, &useregions, NULL));
1598: PetscCall(PetscOptionsBool("-dm_plex_gmsh_use_generic", "Generate generic labels, i.e. Cell Sets, Face Sets, etc", "DMPlexCreateGmsh", usegeneric, &usegeneric, &flg));
1599: if (!flg && useregions) usegeneric = PETSC_FALSE;
1600: PetscCall(PetscOptionsBool("-dm_plex_gmsh_mark_vertices", "Add vertices to generated labels", "DMPlexCreateGmsh", markvertices, &markvertices, NULL));
1601: PetscCall(PetscOptionsBool("-dm_plex_gmsh_mark_vertices_strict", "Add only directly tagged vertices to generated labels", "DMPlexCreateGmsh", markverticesstrict, &markverticesstrict, NULL));
1602: PetscCall(PetscOptionsBool("-dm_plex_gmsh_multiple_tags", "Allow multiple tags for default labels", "DMPlexCreateGmsh", multipleTags, &multipleTags, NULL));
1603: PetscCall(PetscOptionsBoundedInt("-dm_plex_gmsh_spacedim", "Embedding space dimension", "DMPlexCreateGmsh", coordDim, &coordDim, NULL, PETSC_DECIDE));
1604: PetscCall(PetscOptionsBoundedInt("-dm_localize_height", "Localize edges and faces in addition to cells", "", maxHeight, &maxHeight, NULL, 0));
1605: PetscOptionsHeadEnd();
1606: PetscOptionsEnd();
1608: PetscCall(GmshCellInfoSetUp());
1610: PetscCall(DMCreate(comm, dm));
1611: PetscCall(DMSetType(*dm, DMPLEX));
1612: PetscCall(PetscLogEventBegin(DMPLEX_CreateGmsh, *dm, NULL, NULL, NULL));
1614: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERBINARY, &binary));
1616: /* Binary viewers read on all ranks, get subviewer to read only in rank 0 */
1617: if (binary) {
1618: parentviewer = viewer;
1619: PetscCall(PetscViewerGetSubViewer(parentviewer, PETSC_COMM_SELF, &viewer));
1620: }
1622: if (rank == 0) {
1623: GmshFile gmsh[1];
1624: char line[PETSC_MAX_PATH_LEN];
1625: PetscBool match;
1627: PetscCall(PetscArrayzero(gmsh, 1));
1628: gmsh->viewer = viewer;
1629: gmsh->binary = binary;
1631: PetscCall(GmshMeshCreate(&mesh));
1633: /* Read mesh format */
1634: PetscCall(GmshReadSection(gmsh, line));
1635: PetscCall(GmshExpect(gmsh, "$MeshFormat", line));
1636: PetscCall(GmshReadMeshFormat(gmsh));
1637: PetscCall(GmshReadEndSection(gmsh, "$EndMeshFormat", line));
1639: /* OPTIONAL Read mesh version (Neper only) */
1640: PetscCall(GmshReadSection(gmsh, line));
1641: PetscCall(GmshMatch(gmsh, "$MeshVersion", line, &match));
1642: if (match) {
1643: PetscCall(GmshExpect(gmsh, "$MeshVersion", line));
1644: PetscCall(GmshReadMeshVersion(gmsh));
1645: PetscCall(GmshReadEndSection(gmsh, "$EndMeshVersion", line));
1646: /* Initial read for entity section */
1647: PetscCall(GmshReadSection(gmsh, line));
1648: }
1650: /* OPTIONAL Read mesh domain (Neper only) */
1651: PetscCall(GmshMatch(gmsh, "$Domain", line, &match));
1652: if (match) {
1653: PetscCall(GmshExpect(gmsh, "$Domain", line));
1654: PetscCall(GmshReadMeshDomain(gmsh));
1655: PetscCall(GmshReadEndSection(gmsh, "$EndDomain", line));
1656: /* Initial read for entity section */
1657: PetscCall(GmshReadSection(gmsh, line));
1658: }
1660: /* OPTIONAL Read physical names */
1661: PetscCall(GmshMatch(gmsh, "$PhysicalNames", line, &match));
1662: if (match) {
1663: PetscCall(GmshExpect(gmsh, "$PhysicalNames", line));
1664: PetscCall(GmshReadPhysicalNames(gmsh, mesh));
1665: PetscCall(GmshReadEndSection(gmsh, "$EndPhysicalNames", line));
1666: /* Initial read for entity section */
1667: PetscCall(GmshReadSection(gmsh, line));
1668: }
1670: /* OPTIONAL Read entities */
1671: if (gmsh->fileFormat >= 40) {
1672: PetscCall(GmshMatch(gmsh, "$Entities", line, &match));
1673: if (match) {
1674: PetscCall(GmshExpect(gmsh, "$Entities", line));
1675: PetscCall(GmshReadEntities(gmsh, mesh));
1676: PetscCall(GmshReadEndSection(gmsh, "$EndEntities", line));
1677: /* Initial read for nodes section */
1678: PetscCall(GmshReadSection(gmsh, line));
1679: }
1680: }
1682: /* Read nodes */
1683: PetscCall(GmshExpect(gmsh, "$Nodes", line));
1684: PetscCall(GmshReadNodes(gmsh, mesh));
1685: PetscCall(GmshReadEndSection(gmsh, "$EndNodes", line));
1687: /* Read elements */
1688: PetscCall(GmshReadSection(gmsh, line));
1689: PetscCall(GmshExpect(gmsh, "$Elements", line));
1690: PetscCall(GmshReadElements(gmsh, mesh));
1691: PetscCall(GmshReadEndSection(gmsh, "$EndElements", line));
1693: /* Read periodic section (OPTIONAL) */
1694: if (periodic) {
1695: PetscCall(GmshReadSection(gmsh, line));
1696: PetscCall(GmshMatch(gmsh, "$Periodic", line, &periodic));
1697: }
1698: if (periodic) {
1699: PetscCall(GmshExpect(gmsh, "$Periodic", line));
1700: PetscCall(GmshReadPeriodic(gmsh, mesh));
1701: PetscCall(GmshReadEndSection(gmsh, "$EndPeriodic", line));
1702: }
1704: PetscCall(PetscFree(gmsh->wbuf));
1705: PetscCall(PetscFree(gmsh->sbuf));
1706: PetscCall(PetscFree(gmsh->nbuf));
1708: dim = mesh->dim;
1709: order = mesh->order;
1710: numNodes = mesh->numNodes;
1711: numElems = mesh->numElems;
1712: numVerts = mesh->numVerts;
1713: numCells = mesh->numCells;
1715: {
1716: GmshElement *elemA = mesh->numCells > 0 ? mesh->elements : NULL;
1717: GmshElement *elemB = PetscSafePointerPlusOffset(elemA, mesh->numCells - 1);
1718: int ptA = elemA ? GmshCellMap[elemA->cellType].polytope : -1;
1719: int ptB = elemB ? GmshCellMap[elemB->cellType].polytope : -1;
1720: isSimplex = (ptA == GMSH_QUA || ptA == GMSH_HEX) ? PETSC_FALSE : PETSC_TRUE;
1721: isHybrid = (ptA == ptB) ? PETSC_FALSE : PETSC_TRUE;
1722: hasTetra = (ptA == GMSH_TET) ? PETSC_TRUE : PETSC_FALSE;
1723: }
1724: }
1726: if (parentviewer) PetscCall(PetscViewerRestoreSubViewer(parentviewer, PETSC_COMM_SELF, &viewer));
1728: {
1729: int buf[6];
1731: buf[0] = (int)dim;
1732: buf[1] = (int)order;
1733: buf[2] = periodic;
1734: buf[3] = isSimplex;
1735: buf[4] = isHybrid;
1736: buf[5] = hasTetra;
1738: PetscCallMPI(MPI_Bcast(buf, 6, MPI_INT, 0, comm));
1740: dim = buf[0];
1741: order = buf[1];
1742: periodic = buf[2] ? PETSC_TRUE : PETSC_FALSE;
1743: isSimplex = buf[3] ? PETSC_TRUE : PETSC_FALSE;
1744: isHybrid = buf[4] ? PETSC_TRUE : PETSC_FALSE;
1745: hasTetra = buf[5] ? PETSC_TRUE : PETSC_FALSE;
1746: }
1748: if (!highOrderSet) highOrder = (order > 1) ? PETSC_TRUE : PETSC_FALSE;
1749: PetscCheck(!highOrder || !isHybrid, comm, PETSC_ERR_SUP, "No support for discretization on hybrid meshes yet");
1751: /* We do not want this label automatically computed, instead we fill it here */
1752: PetscCall(DMCreateLabel(*dm, "celltype"));
1754: /* Allocate the cell-vertex mesh */
1755: PetscCall(DMPlexSetChart(*dm, 0, numCells + numVerts));
1756: for (cell = 0; cell < numCells; ++cell) {
1757: GmshElement *elem = mesh->elements + cell;
1758: DMPolytopeType ctype = DMPolytopeTypeFromGmsh(elem->cellType);
1759: if (hybrid && hasTetra && ctype == DM_POLYTOPE_TRI_PRISM) ctype = DM_POLYTOPE_TRI_PRISM_TENSOR;
1760: PetscCall(DMPlexSetConeSize(*dm, cell, elem->numVerts));
1761: PetscCall(DMPlexSetCellType(*dm, cell, ctype));
1762: }
1763: for (v = numCells; v < numCells + numVerts; ++v) PetscCall(DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT));
1764: PetscCall(DMSetUp(*dm));
1766: /* Add cell-vertex connections */
1767: for (cell = 0; cell < numCells; ++cell) {
1768: GmshElement *elem = mesh->elements + cell;
1769: for (v = 0; v < elem->numVerts; ++v) {
1770: const PetscInt nn = elem->nodes[v];
1771: const PetscInt vv = mesh->vertexMap[nn];
1772: cone[v] = numCells + vv;
1773: }
1774: PetscCall(DMPlexReorderCell(*dm, cell, cone));
1775: PetscCall(DMPlexSetCone(*dm, cell, cone));
1776: }
1778: PetscCall(DMSetDimension(*dm, dim));
1779: PetscCall(DMPlexSymmetrize(*dm));
1780: PetscCall(DMPlexStratify(*dm));
1781: if (interpolate) {
1782: DM idm;
1784: PetscCall(DMPlexInterpolate(*dm, &idm));
1785: PetscCall(DMDestroy(dm));
1786: *dm = idm;
1787: }
1788: PetscCall(DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd));
1790: if (rank == 0) {
1791: const PetscInt Nr = useregions ? mesh->numRegions : 0;
1793: PetscCall(PetscCalloc1(Nr, ®ionSets));
1794: for (cell = 0, e = 0; e < numElems; ++e) {
1795: GmshElement *elem = mesh->elements + e;
1797: /* Create cell sets */
1798: if (elem->dim == dim && dim > 0) {
1799: if (elem->numTags > 0) {
1800: PetscInt Nt = elem->numTags, t, r;
1802: for (t = 0; t < Nt; ++t) {
1803: const PetscInt tag = elem->tags[t];
1804: const PetscBool generic = usegeneric && (!t || multipleTags) ? PETSC_TRUE : PETSC_FALSE;
1806: if (generic) PetscCall(DMSetLabelValue_Fast(*dm, &cellSets, "Cell Sets", cell, tag));
1807: for (r = 0; r < Nr; ++r) {
1808: if (mesh->regionDims[r] != dim) continue;
1809: if (mesh->regionTags[r] == tag) PetscCall(DMSetLabelValue_Fast(*dm, ®ionSets[r], mesh->regionNames[r], cell, tag));
1810: }
1811: }
1812: }
1813: cell++;
1814: }
1816: /* Create face sets */
1817: if (elem->numTags && interpolate && elem->dim == dim - 1) {
1818: PetscInt joinSize;
1819: const PetscInt *join = NULL;
1820: PetscInt Nt = elem->numTags, pdepth;
1822: /* Find the relevant facet with vertex joins */
1823: for (v = 0; v < elem->numVerts; ++v) {
1824: const PetscInt nn = elem->nodes[v];
1825: const PetscInt vv = mesh->vertexMap[nn];
1826: cone[v] = vStart + vv;
1827: }
1828: PetscCall(DMPlexGetFullJoin(*dm, elem->numVerts, cone, &joinSize, &join));
1829: PetscCheck(joinSize == 1, PETSC_COMM_SELF, PETSC_ERR_SUP, "Could not determine Plex facet for Gmsh element %" PetscInt_FMT " (Plex cell %" PetscInt_FMT ")", elem->id, e);
1830: PetscCall(DMPlexGetPointDepth(*dm, join[0], &pdepth));
1831: PetscCheck(pdepth == dim - 1, PETSC_COMM_SELF, PETSC_ERR_SUP, "Plex facet %" PetscInt_FMT " for Gmsh element %" PetscInt_FMT " had depth %" PetscInt_FMT " != %" PetscInt_FMT, join[0], elem->id, pdepth, dim - 1);
1832: for (PetscInt t = 0; t < Nt; ++t) {
1833: const PetscInt tag = elem->tags[t];
1834: const PetscBool generic = usegeneric && (!t || multipleTags) ? PETSC_TRUE : PETSC_FALSE;
1836: if (generic) PetscCall(DMSetLabelValue_Fast(*dm, &faceSets, "Face Sets", join[0], tag));
1837: for (PetscInt r = 0; r < Nr; ++r) {
1838: if (mesh->regionDims[r] != dim - 1) continue;
1839: if (mesh->regionTags[r] == tag) PetscCall(DMSetLabelValue_Fast(*dm, ®ionSets[r], mesh->regionNames[r], join[0], tag));
1840: }
1841: }
1842: PetscCall(DMPlexRestoreJoin(*dm, elem->numVerts, cone, &joinSize, &join));
1843: }
1845: /* Create edge sets */
1846: if (elem->numTags && interpolate && dim > 2 && elem->dim == 1) {
1847: PetscInt joinSize;
1848: const PetscInt *join = NULL;
1849: PetscInt Nt = elem->numTags, t, r;
1851: /* Find the relevant edge with vertex joins */
1852: for (v = 0; v < elem->numVerts; ++v) {
1853: const PetscInt nn = elem->nodes[v];
1854: const PetscInt vv = mesh->vertexMap[nn];
1855: cone[v] = vStart + vv;
1856: }
1857: PetscCall(DMPlexGetJoin(*dm, elem->numVerts, cone, &joinSize, &join));
1858: PetscCheck(joinSize == 1, PETSC_COMM_SELF, PETSC_ERR_SUP, "Could not determine Plex edge for Gmsh element %" PetscInt_FMT " (Plex cell %" PetscInt_FMT ")", elem->id, e);
1859: for (t = 0; t < Nt; ++t) {
1860: const PetscInt tag = elem->tags[t];
1861: const PetscBool generic = usegeneric && (!t || multipleTags) ? PETSC_TRUE : PETSC_FALSE;
1863: if (generic) PetscCall(DMSetLabelValue_Fast(*dm, &edgeSets, "Edge Sets", join[0], tag));
1864: for (r = 0; r < Nr; ++r) {
1865: if (mesh->regionDims[r] != 1) continue;
1866: if (mesh->regionTags[r] == tag) PetscCall(DMSetLabelValue_Fast(*dm, ®ionSets[r], mesh->regionNames[r], join[0], tag));
1867: }
1868: }
1869: PetscCall(DMPlexRestoreJoin(*dm, elem->numVerts, cone, &joinSize, &join));
1870: }
1872: /* Create vertex sets */
1873: if (elem->numTags && elem->dim == 0 && (markverticesstrict || markvertices)) {
1874: const PetscInt nn = elem->nodes[0];
1875: const PetscInt vv = mesh->vertexMap[nn];
1876: PetscInt Nt = elem->numTags;
1878: for (PetscInt t = 0; t < Nt; ++t) {
1879: const PetscInt tag = elem->tags[t];
1881: if (vv < 0) continue;
1882: if (usegeneric) PetscCall(DMSetLabelValue_Fast(*dm, &vertSets, "Vertex Sets", vStart + vv, tag));
1883: for (PetscInt r = 0; r < Nr; ++r) {
1884: if (mesh->regionDims[r] != 0) continue;
1885: if (mesh->regionTags[r] == tag) PetscCall(DMSetLabelValue_Fast(*dm, ®ionSets[r], mesh->regionNames[r], vStart + vv, tag));
1886: }
1887: }
1888: }
1889: }
1890: if (markvertices) {
1891: for (v = 0; v < numNodes; ++v) {
1892: const PetscInt vv = mesh->vertexMap[v];
1893: const PetscInt *tags = &mesh->nodelist->tag[v * GMSH_MAX_TAGS];
1894: PetscInt r, t;
1896: if (vv < 0) continue;
1897: for (t = 0; t < GMSH_MAX_TAGS; ++t) {
1898: const PetscInt tag = tags[t];
1899: const PetscBool generic = usegeneric && (!t || multipleTags) ? PETSC_TRUE : PETSC_FALSE;
1901: if (tag == -1) continue;
1902: if (generic) PetscCall(DMSetLabelValue_Fast(*dm, &vertSets, "Vertex Sets", vStart + vv, tag));
1903: for (r = 0; r < Nr; ++r) {
1904: if (mesh->regionTags[r] == tag) PetscCall(DMSetLabelValue_Fast(*dm, ®ionSets[r], mesh->regionNames[r], vStart + vv, tag));
1905: }
1906: }
1907: }
1908: }
1909: PetscCall(PetscFree(regionSets));
1910: }
1912: { /* Create Cell/Face/Edge/Vertex Sets labels at all processes */
1913: enum {
1914: n = 5
1915: };
1916: PetscBool flag[n];
1918: flag[0] = cellSets ? PETSC_TRUE : PETSC_FALSE;
1919: flag[1] = faceSets ? PETSC_TRUE : PETSC_FALSE;
1920: flag[2] = edgeSets ? PETSC_TRUE : PETSC_FALSE;
1921: flag[3] = vertSets ? PETSC_TRUE : PETSC_FALSE;
1922: flag[4] = marker ? PETSC_TRUE : PETSC_FALSE;
1923: PetscCallMPI(MPI_Bcast(flag, n, MPI_C_BOOL, 0, comm));
1924: if (flag[0]) PetscCall(DMCreateLabel(*dm, "Cell Sets"));
1925: if (flag[1]) PetscCall(DMCreateLabel(*dm, "Face Sets"));
1926: if (flag[2]) PetscCall(DMCreateLabel(*dm, "Edge Sets"));
1927: if (flag[3]) PetscCall(DMCreateLabel(*dm, "Vertex Sets"));
1928: if (flag[4]) PetscCall(DMCreateLabel(*dm, "marker"));
1929: }
1931: if (periodic) {
1932: PetscCall(PetscBTCreate(numVerts, &periodicVerts));
1933: for (n = 0; n < numNodes; ++n) {
1934: if (mesh->vertexMap[n] >= 0) {
1935: if (PetscUnlikely(mesh->periodMap[n] != n)) {
1936: PetscInt m = mesh->periodMap[n];
1937: PetscCall(PetscBTSet(periodicVerts, mesh->vertexMap[n]));
1938: PetscCall(PetscBTSet(periodicVerts, mesh->vertexMap[m]));
1939: }
1940: }
1941: }
1942: PetscCall(DMGetCoordinateDM(*dm, &cdm));
1943: PetscCall(PetscMalloc1(maxHeight + 1, &periodicCells));
1944: for (PetscInt h = 0; h <= maxHeight; ++h) {
1945: PetscInt pStart, pEnd;
1947: PetscCall(DMPlexGetHeightStratum(*dm, h, &pStart, &pEnd));
1948: PetscCall(PetscBTCreate(pEnd - pStart, &periodicCells[h]));
1949: for (PetscInt p = pStart; p < pEnd; ++p) {
1950: PetscInt *closure = NULL;
1951: PetscInt Ncl;
1953: PetscCall(DMPlexGetTransitiveClosure(*dm, p, PETSC_TRUE, &Ncl, &closure));
1954: for (PetscInt cl = 0; cl < Ncl * 2; cl += 2) {
1955: if (closure[cl] >= vStart && closure[cl] < vEnd) {
1956: if (PetscUnlikely(PetscBTLookup(periodicVerts, closure[cl] - vStart))) {
1957: PetscCall(PetscBTSet(periodicCells[h], p - pStart));
1958: break;
1959: }
1960: }
1961: }
1962: PetscCall(DMPlexRestoreTransitiveClosure(*dm, p, PETSC_TRUE, &Ncl, &closure));
1963: }
1964: }
1965: }
1967: /* Setup coordinate DM */
1968: if (coordDim < 0) coordDim = dim;
1969: PetscCall(DMSetCoordinateDim(*dm, coordDim));
1970: PetscCall(DMGetCoordinateDM(*dm, &cdm));
1971: if (highOrder) {
1972: PetscFE fe;
1973: PetscBool continuity = periodic ? PETSC_FALSE : PETSC_TRUE;
1974: PetscDTNodeType nodeType = PETSCDTNODES_EQUISPACED;
1976: if (isSimplex) continuity = PETSC_FALSE; /* XXX FIXME Requires DMPlexSetClosurePermutationLexicographic() */
1978: PetscCall(GmshCreateFE(comm, NULL, isSimplex, continuity, nodeType, dim, coordDim, order, &fe));
1979: PetscCall(PetscFEViewFromOptions(fe, NULL, "-dm_plex_gmsh_fe_view"));
1980: PetscCall(DMSetField(cdm, 0, NULL, (PetscObject)fe));
1981: PetscCall(PetscFEDestroy(&fe));
1982: PetscCall(DMCreateDS(cdm));
1983: }
1984: if (periodic) {
1985: PetscCall(DMClone(cdm, &cdmCell));
1986: PetscCall(DMSetCellCoordinateDM(*dm, cdmCell));
1987: }
1989: /* Create coordinates */
1990: if (highOrder) {
1991: PetscInt maxDof = GmshNumNodes_HEX(order) * coordDim;
1992: double *coords = mesh ? mesh->nodelist->xyz : NULL;
1993: PetscSection section;
1994: PetscScalar *cellCoords;
1996: PetscCall(DMSetLocalSection(cdm, NULL));
1997: PetscCall(DMGetLocalSection(cdm, &cs));
1998: PetscCall(PetscSectionClone(cs, §ion));
1999: PetscCall(DMPlexSetClosurePermutationTensor(cdm, 0, section)); /* XXX Implement DMPlexSetClosurePermutationLexicographic() */
2001: PetscCall(DMCreateLocalVector(cdm, &coordinates));
2002: PetscCall(PetscMalloc1(maxDof, &cellCoords));
2003: for (cell = 0; cell < numCells; ++cell) {
2004: GmshElement *elem = mesh->elements + cell;
2005: const int *lexorder = GmshCellMap[elem->cellType].lexorder();
2006: int s = 0;
2007: for (n = 0; n < elem->numNodes; ++n) {
2008: while (lexorder[n + s] < 0) ++s;
2009: const PetscInt node = elem->nodes[lexorder[n + s]];
2010: for (d = 0; d < coordDim; ++d) cellCoords[(n + s) * coordDim + d] = (PetscReal)coords[node * 3 + d];
2011: }
2012: if (s) {
2013: /* For the coordinate mapping we weight vertices by -1/4 and edges by 1/2, which we get from Q_2 interpolation */
2014: PetscReal quaCenterWeights[9] = {-0.25, 0.5, -0.25, 0.5, 0.0, 0.5, -0.25, 0.5, -0.25};
2015: /* For the coordinate mapping we weight vertices by -1/4 and edges by 1/2, which we get from Q_2 interpolation */
2016: PetscReal hexBottomWeights[27] = {-0.25, 0.5, -0.25, 0.5, 0.0, 0.5, -0.25, 0.5, -0.25, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
2017: PetscReal hexFrontWeights[27] = {-0.25, 0.5, -0.25, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -0.25, 0.5, -0.25, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
2018: PetscReal hexLeftWeights[27] = {-0.25, 0.0, 0.0, 0.5, 0.0, 0.0, -0.25, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, -0.25, 0.0, 0.0, 0.5, 0.0, 0.0, -0.25, 0.0, 0.0};
2019: PetscReal hexRightWeights[27] = {0.0, 0.0, -0.25, 0.0, 0.0, 0.5, 0.0, 0.0, -0.25, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, -0.25, 0.0, 0.0, 0.5, 0.0, 0.0, -0.25};
2020: PetscReal hexBackWeights[27] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -0.25, 0.5, -0.25, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -0.25, 0.5, -0.25};
2021: PetscReal hexTopWeights[27] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -0.25, 0.5, -0.25, 0.5, 0.0, 0.5, -0.25, 0.5, -0.25};
2022: PetscReal hexCenterWeights[27] = {-0.25, 0.25, -0.25, 0.25, 0.0, 0.25, -0.25, 0.25, -0.25, 0.25, 0.0, 0.25, 0.0, 0.0, 0.0, 0.25, 0.0, 0.25, -0.25, 0.25, -0.25, 0.25, 0.0, 0.25, -0.25, 0.25, -0.25};
2023: PetscReal *sdWeights2[9] = {NULL, NULL, NULL, NULL, quaCenterWeights, NULL, NULL, NULL, NULL};
2024: PetscReal *sdWeights3[27] = {NULL, NULL, NULL, NULL, hexBottomWeights, NULL, NULL, NULL, NULL, NULL, hexFrontWeights, NULL, hexLeftWeights, hexCenterWeights, hexRightWeights, NULL, hexBackWeights, NULL,
2025: NULL, NULL, NULL, NULL, hexTopWeights, NULL, NULL, NULL, NULL};
2026: PetscReal **sdWeights[4] = {NULL, NULL, sdWeights2, sdWeights3};
2028: /* Missing entries in serendipity cell, only works for 8-node quad and 20-node hex */
2029: for (n = 0; n < elem->numNodes + s; ++n) {
2030: if (lexorder[n] >= 0) continue;
2031: for (d = 0; d < coordDim; ++d) cellCoords[n * coordDim + d] = 0.0;
2032: for (int bn = 0; bn < elem->numNodes + s; ++bn) {
2033: if (lexorder[bn] < 0) continue;
2034: const PetscReal *weights = sdWeights[coordDim][n];
2035: const PetscInt bnode = elem->nodes[lexorder[bn]];
2036: for (d = 0; d < coordDim; ++d) cellCoords[n * coordDim + d] += weights[bn] * (PetscReal)coords[bnode * 3 + d];
2037: }
2038: }
2039: }
2040: PetscCall(DMPlexVecSetClosure(cdm, section, coordinates, cell, cellCoords, INSERT_VALUES));
2041: }
2042: PetscCall(PetscSectionDestroy(§ion));
2043: PetscCall(PetscFree(cellCoords));
2044: } else {
2045: PetscInt *nodeMap;
2046: double *coords = mesh ? mesh->nodelist->xyz : NULL;
2047: PetscScalar *pointCoords;
2049: PetscCall(DMGetCoordinateSection(*dm, &cs));
2050: PetscCall(PetscSectionSetNumFields(cs, 1));
2051: PetscCall(PetscSectionSetFieldComponents(cs, 0, coordDim));
2052: PetscCall(PetscSectionSetChart(cs, numCells, numCells + numVerts));
2053: for (v = numCells; v < numCells + numVerts; ++v) {
2054: PetscCall(PetscSectionSetDof(cs, v, coordDim));
2055: PetscCall(PetscSectionSetFieldDof(cs, v, 0, coordDim));
2056: }
2057: PetscCall(PetscSectionSetUp(cs));
2059: /* We need to localize coordinates on cells */
2060: if (periodic) {
2061: PetscInt newStart = PETSC_INT_MAX, newEnd = -1, pStart, pEnd;
2063: PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)cdmCell), &csCell));
2064: PetscCall(PetscSectionSetNumFields(csCell, 1));
2065: PetscCall(PetscSectionSetFieldComponents(csCell, 0, coordDim));
2066: for (PetscInt h = 0; h <= maxHeight; h++) {
2067: PetscCall(DMPlexGetHeightStratum(cdmCell, h, &pStart, &pEnd));
2068: newStart = PetscMin(newStart, pStart);
2069: newEnd = PetscMax(newEnd, pEnd);
2070: }
2071: PetscCall(PetscSectionSetChart(csCell, newStart, newEnd));
2072: for (PetscInt h = 0; h <= maxHeight; h++) {
2073: PetscCall(DMPlexGetHeightStratum(cdmCell, h, &pStart, &pEnd));
2074: for (PetscInt p = pStart; p < pEnd; ++p) {
2075: PetscInt *closure = NULL;
2076: PetscInt Ncl, Nv = 0;
2078: if (PetscUnlikely(PetscBTLookup(periodicCells[h], p - pStart))) {
2079: PetscCall(DMPlexGetTransitiveClosure(*dm, p, PETSC_TRUE, &Ncl, &closure));
2080: for (PetscInt cl = 0; cl < Ncl * 2; cl += 2) {
2081: if (closure[cl] >= vStart && closure[cl] < vEnd) ++Nv;
2082: }
2083: PetscCall(DMPlexRestoreTransitiveClosure(*dm, p, PETSC_TRUE, &Ncl, &closure));
2084: PetscCall(PetscSectionSetDof(csCell, p, Nv * coordDim));
2085: PetscCall(PetscSectionSetFieldDof(csCell, p, 0, Nv * coordDim));
2086: }
2087: }
2088: }
2089: PetscCall(PetscSectionSetUp(csCell));
2090: PetscCall(DMSetCellCoordinateSection(*dm, PETSC_DETERMINE, csCell));
2091: }
2093: PetscCall(DMCreateLocalVector(cdm, &coordinates));
2094: PetscCall(VecGetArray(coordinates, &pointCoords));
2095: PetscCall(PetscMalloc1(numVerts, &nodeMap));
2096: for (n = 0; n < numNodes; n++)
2097: if (mesh->vertexMap[n] >= 0) nodeMap[mesh->vertexMap[n]] = n;
2098: for (v = 0; v < numVerts; ++v) {
2099: PetscInt off, node = nodeMap[v];
2101: PetscCall(PetscSectionGetOffset(cs, numCells + v, &off));
2102: for (d = 0; d < coordDim; ++d) pointCoords[off + d] = (PetscReal)coords[node * 3 + d];
2103: }
2104: PetscCall(VecRestoreArray(coordinates, &pointCoords));
2106: if (periodic) {
2107: PetscInt cStart, cEnd;
2109: PetscCall(DMPlexGetHeightStratum(cdmCell, 0, &cStart, &cEnd));
2110: PetscCall(DMCreateLocalVector(cdmCell, &coordinatesCell));
2111: PetscCall(VecGetArray(coordinatesCell, &pointCoords));
2112: for (PetscInt c = cStart; c < cEnd; ++c) {
2113: GmshElement *elem = mesh->elements + c - cStart;
2114: PetscInt *closure = NULL;
2115: PetscInt verts[8];
2116: PetscInt Ncl, Nv = 0;
2118: for (PetscInt v = 0; v < elem->numVerts; ++v) cone[v] = elem->nodes[v];
2119: PetscCall(DMPlexReorderCell(cdmCell, c, cone));
2120: PetscCall(DMPlexGetTransitiveClosure(cdmCell, c, PETSC_TRUE, &Ncl, &closure));
2121: for (PetscInt cl = 0; cl < Ncl * 2; cl += 2) {
2122: if (closure[cl] >= vStart && closure[cl] < vEnd) verts[Nv++] = closure[cl];
2123: }
2124: PetscCheck(Nv == elem->numVerts, PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Number of vertices %" PetscInt_FMT " in closure does not match number of vertices %" PetscInt_FMT " in Gmsh cell", Nv, elem->numVerts);
2125: for (PetscInt cl = 0; cl < Ncl * 2; cl += 2) {
2126: const PetscInt point = closure[cl];
2127: PetscInt hStart, h;
2129: PetscCall(DMPlexGetPointHeight(cdmCell, point, &h));
2130: if (h > maxHeight) continue;
2131: PetscCall(DMPlexGetHeightStratum(cdmCell, h, &hStart, NULL));
2132: if (PetscUnlikely(PetscBTLookup(periodicCells[h], point - hStart))) {
2133: PetscInt *pclosure = NULL;
2134: PetscInt Npcl, off, v;
2136: PetscCall(PetscSectionGetOffset(csCell, point, &off));
2137: PetscCall(DMPlexGetTransitiveClosure(cdmCell, point, PETSC_TRUE, &Npcl, &pclosure));
2138: for (PetscInt pcl = 0; pcl < Npcl * 2; pcl += 2) {
2139: if (pclosure[pcl] >= vStart && pclosure[pcl] < vEnd) {
2140: for (v = 0; v < Nv; ++v)
2141: if (verts[v] == pclosure[pcl]) break;
2142: PetscCheck(v < Nv, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find vertex %" PetscInt_FMT " in closure of cell %" PetscInt_FMT, pclosure[pcl], c);
2143: for (PetscInt d = 0; d < coordDim; ++d) pointCoords[off++] = (PetscReal)coords[cone[v] * 3 + d];
2144: ++v;
2145: }
2146: }
2147: PetscCall(DMPlexRestoreTransitiveClosure(cdmCell, point, PETSC_TRUE, &Npcl, &pclosure));
2148: }
2149: }
2150: PetscCall(DMPlexRestoreTransitiveClosure(cdmCell, c, PETSC_TRUE, &Ncl, &closure));
2151: }
2152: PetscCall(VecSetBlockSize(coordinatesCell, coordDim));
2153: PetscCall(VecRestoreArray(coordinatesCell, &pointCoords));
2154: PetscCall(DMSetCellCoordinatesLocal(*dm, coordinatesCell));
2155: PetscCall(VecDestroy(&coordinatesCell));
2156: }
2157: PetscCall(PetscFree(nodeMap));
2158: PetscCall(PetscSectionDestroy(&csCell));
2159: PetscCall(DMDestroy(&cdmCell));
2160: }
2162: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
2163: PetscCall(VecSetBlockSize(coordinates, coordDim));
2164: PetscCall(DMSetCoordinatesLocal(*dm, coordinates));
2165: PetscCall(VecDestroy(&coordinates));
2167: PetscCall(GmshMeshDestroy(&mesh));
2168: PetscCall(PetscBTDestroy(&periodicVerts));
2169: if (periodic) {
2170: for (PetscInt h = 0; h <= maxHeight; ++h) PetscCall(PetscBTDestroy(periodicCells + h));
2171: PetscCall(PetscFree(periodicCells));
2172: }
2174: if (highOrder && project) {
2175: PetscFE fe;
2176: const char prefix[] = "dm_plex_gmsh_project_";
2177: PetscBool continuity = periodic ? PETSC_FALSE : PETSC_TRUE;
2178: PetscDTNodeType nodeType = PETSCDTNODES_GAUSSJACOBI;
2180: if (isSimplex) continuity = PETSC_FALSE; /* XXX FIXME Requires DMPlexSetClosurePermutationLexicographic() */
2181: PetscCall(GmshCreateFE(comm, prefix, isSimplex, continuity, nodeType, dim, coordDim, order, &fe));
2182: PetscCall(PetscFEViewFromOptions(fe, NULL, "-dm_plex_gmsh_project_fe_view"));
2183: PetscCall(DMSetCoordinateDisc(*dm, fe, PETSC_FALSE, PETSC_TRUE));
2184: PetscCall(PetscFEDestroy(&fe));
2185: }
2187: PetscCall(PetscLogEventEnd(DMPLEX_CreateGmsh, *dm, NULL, NULL, NULL));
2188: PetscFunctionReturn(PETSC_SUCCESS);
2189: }