Actual source code: plexcreate.c
1: #include <petsc/private/dmpleximpl.h>
2: #include <petsc/private/hashseti.h>
3: #include <petscsf.h>
4: #include <petscdmplextransform.h>
5: #include <petscdmlabelephemeral.h>
6: #include <petsc/private/kernels/blockmatmult.h>
7: #include <petsc/private/kernels/blockinvert.h>
9: #ifdef PETSC_HAVE_UNISTD_H
10: #include <unistd.h>
11: #endif
12: #include <errno.h>
14: PetscLogEvent DMPLEX_CreateFromFile, DMPLEX_CreateFromOptions, DMPLEX_BuildFromCellList, DMPLEX_BuildCoordinatesFromCellList;
16: /* External function declarations here */
17: static PetscErrorCode DMInitialize_Plex(DM dm);
19: PETSC_EXTERN PetscErrorCode DMPlexCheckEGADS_Private(DM dm)
20: {
21: PetscObject modelObj;
23: PetscFunctionBegin;
24: PetscCall(PetscObjectQuery((PetscObject)dm, "EGADS Model", &modelObj));
25: PetscCheck(modelObj, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Input DM must have attached EGADS Geometry Model");
26: PetscFunctionReturn(PETSC_SUCCESS);
27: }
29: static PetscErrorCode DMPlexCopyContext_Private(DM dmin, const char name[], DM dmout)
30: {
31: PetscObject obj;
33: PetscFunctionBegin;
34: PetscCall(PetscObjectQuery((PetscObject)dmin, name, &obj));
35: if (obj) PetscCall(PetscObjectCompose((PetscObject)dmout, name, obj));
36: PetscFunctionReturn(PETSC_SUCCESS);
37: }
39: static PetscErrorCode DMPlexSwapContext_Private(DM dmA, const char name[], DM dmB)
40: {
41: PetscObject objA, objB;
43: PetscFunctionBegin;
44: PetscCall(PetscObjectQuery((PetscObject)dmA, name, &objA));
45: PetscCall(PetscObjectQuery((PetscObject)dmB, name, &objB));
46: PetscCall(PetscObjectReference(objA));
47: PetscCall(PetscObjectReference(objB));
48: PetscCall(PetscObjectCompose((PetscObject)dmA, name, objB));
49: PetscCall(PetscObjectCompose((PetscObject)dmB, name, objA));
50: PetscCall(PetscObjectDereference(objA));
51: PetscCall(PetscObjectDereference(objB));
52: PetscFunctionReturn(PETSC_SUCCESS);
53: }
55: PetscErrorCode DMPlexCopyEGADSInfo_Internal(DM dmin, DM dmout)
56: {
57: PetscFunctionBegin;
58: PetscCall(DMPlexCopyContext_Private(dmin, "EGADS Model", dmout));
59: PetscCall(DMPlexCopyContext_Private(dmin, "EGADS Context", dmout));
60: PetscCall(DMPlexCopyContext_Private(dmin, "EGADSlite Model", dmout));
61: PetscCall(DMPlexCopyContext_Private(dmin, "EGADSlite Context", dmout));
62: PetscFunctionReturn(PETSC_SUCCESS);
63: }
65: static PetscErrorCode DMPlexSwapEGADSInfo_Private(DM dmA, DM dmB)
66: {
67: PetscFunctionBegin;
68: PetscCall(DMPlexSwapContext_Private(dmA, "EGADS Model", dmB));
69: PetscCall(DMPlexSwapContext_Private(dmA, "EGADS Context", dmB));
70: PetscCall(DMPlexSwapContext_Private(dmA, "EGADSlite Model", dmB));
71: PetscCall(DMPlexSwapContext_Private(dmA, "EGADSlite Context", dmB));
72: PetscFunctionReturn(PETSC_SUCCESS);
73: }
75: /* This copies internal things in the Plex structure that we generally want when making a new, related Plex */
76: PetscErrorCode DMPlexCopy_Internal(DM dmin, PetscBool copyPeriodicity, PetscBool copyOverlap, DM dmout)
77: {
78: const PetscReal *maxCell, *Lstart, *L;
79: VecType vecType;
80: MatType matType;
81: PetscBool dist, useCeed, balance_partition;
82: DMReorderDefaultFlag reorder;
84: PetscFunctionBegin;
85: if (dmin == dmout) PetscFunctionReturn(PETSC_SUCCESS);
86: PetscCall(DMGetVecType(dmin, &vecType));
87: PetscCall(DMSetVecType(dmout, vecType));
88: PetscCall(DMGetMatType(dmin, &matType));
89: PetscCall(DMSetMatType(dmout, matType));
90: if (copyPeriodicity) {
91: PetscCall(DMGetPeriodicity(dmin, &maxCell, &Lstart, &L));
92: PetscCall(DMSetPeriodicity(dmout, maxCell, Lstart, L));
93: PetscCall(DMLocalizeCoordinates(dmout));
94: }
95: PetscCall(DMPlexDistributeGetDefault(dmin, &dist));
96: PetscCall(DMPlexDistributeSetDefault(dmout, dist));
97: PetscCall(DMPlexReorderGetDefault(dmin, &reorder));
98: PetscCall(DMPlexReorderSetDefault(dmout, reorder));
99: PetscCall(DMPlexGetUseCeed(dmin, &useCeed));
100: PetscCall(DMPlexSetUseCeed(dmout, useCeed));
101: PetscCall(DMPlexGetPartitionBalance(dmin, &balance_partition));
102: PetscCall(DMPlexSetPartitionBalance(dmout, balance_partition));
103: ((DM_Plex *)dmout->data)->useHashLocation = ((DM_Plex *)dmin->data)->useHashLocation;
104: ((DM_Plex *)dmout->data)->printSetValues = ((DM_Plex *)dmin->data)->printSetValues;
105: ((DM_Plex *)dmout->data)->printFEM = ((DM_Plex *)dmin->data)->printFEM;
106: ((DM_Plex *)dmout->data)->printFVM = ((DM_Plex *)dmin->data)->printFVM;
107: ((DM_Plex *)dmout->data)->printL2 = ((DM_Plex *)dmin->data)->printL2;
108: ((DM_Plex *)dmout->data)->printLocate = ((DM_Plex *)dmin->data)->printLocate;
109: ((DM_Plex *)dmout->data)->printProject = ((DM_Plex *)dmin->data)->printProject;
110: ((DM_Plex *)dmout->data)->printTol = ((DM_Plex *)dmin->data)->printTol;
111: if (copyOverlap) PetscCall(DMPlexSetOverlap_Plex(dmout, dmin, 0));
112: PetscCall(DMPlexCopyEGADSInfo_Internal(dmin, dmout));
113: PetscFunctionReturn(PETSC_SUCCESS);
114: }
116: /* Replace dm with the contents of ndm, and then destroy ndm
117: - Share the DM_Plex structure
118: - Share the coordinates
119: - Share the SF
120: */
121: PetscErrorCode DMPlexReplace_Internal(DM dm, DM *ndm)
122: {
123: PetscSF sf;
124: DM dmNew = *ndm, coordDM, coarseDM;
125: Vec coords;
126: PetscPointFn *coordFunc;
127: const PetscReal *maxCell, *Lstart, *L;
128: PetscInt dim, cdim;
129: PetscBool use_natural;
131: PetscFunctionBegin;
132: if (dm == dmNew) {
133: PetscCall(DMDestroy(ndm));
134: PetscFunctionReturn(PETSC_SUCCESS);
135: }
136: dm->setupcalled = dmNew->setupcalled;
137: if (!dm->hdr.name) {
138: const char *name;
140: PetscCall(PetscObjectGetName((PetscObject)*ndm, &name));
141: PetscCall(PetscObjectSetName((PetscObject)dm, name));
142: }
143: {
144: PetscInt ndim;
146: // If topological dimensions are the same, we retain the old coordinate map,
147: // otherwise we overwrite with the new one
148: PetscCall(DMGetDimension(dm, &dim));
149: PetscCall(DMGetDimension(dmNew, &ndim));
150: PetscCall(DMPlexGetCoordinateMap(dm, &coordFunc));
151: if (dim == ndim) PetscCall(DMPlexSetCoordinateMap(dmNew, coordFunc));
152: }
153: PetscCall(DMGetDimension(dmNew, &dim));
154: PetscCall(DMSetDimension(dm, dim));
155: PetscCall(DMGetCoordinateDim(dmNew, &cdim));
156: PetscCall(DMSetCoordinateDim(dm, cdim));
157: PetscCall(DMGetPointSF(dmNew, &sf));
158: PetscCall(DMSetPointSF(dm, sf));
159: PetscCall(DMGetCoordinateDM(dmNew, &coordDM));
160: PetscCall(DMGetCoordinatesLocal(dmNew, &coords));
161: PetscCall(DMSetCoordinateDM(dm, coordDM));
162: PetscCall(DMSetCoordinatesLocal(dm, coords));
163: PetscCall(DMGetCellCoordinateDM(dmNew, &coordDM));
164: PetscCall(DMGetCellCoordinatesLocal(dmNew, &coords));
165: PetscCall(DMSetCellCoordinateDM(dm, coordDM));
166: PetscCall(DMSetCellCoordinatesLocal(dm, coords));
167: /* Do not want to create the coordinate field if it does not already exist, so do not call DMGetCoordinateField() */
168: PetscCall(DMFieldDestroy(&dm->coordinates[0].field));
169: dm->coordinates[0].field = dmNew->coordinates[0].field;
170: PetscCall(DMGetPeriodicity(dmNew, &maxCell, &Lstart, &L));
171: PetscCall(DMSetPeriodicity(dm, maxCell, Lstart, L));
172: PetscCall(DMGetNaturalSF(dmNew, &sf));
173: PetscCall(DMSetNaturalSF(dm, sf));
174: PetscCall(DMGetUseNatural(dmNew, &use_natural));
175: PetscCall(DMSetUseNatural(dm, use_natural));
176: PetscCall(DMDestroy_Plex(dm));
177: PetscCall(DMInitialize_Plex(dm));
178: dm->data = dmNew->data;
179: ((DM_Plex *)dmNew->data)->refct++;
180: {
181: PetscInt num_face_sfs;
182: const PetscSF *sfs;
183: PetscCall(DMPlexGetIsoperiodicFaceSF(dm, &num_face_sfs, &sfs));
184: PetscCall(DMPlexSetIsoperiodicFaceSF(dm, num_face_sfs, (PetscSF *)sfs)); // for the compose function effect on dm
185: }
186: PetscCall(DMDestroyLabelLinkList_Internal(dm));
187: PetscCall(DMCopyLabels(dmNew, dm, PETSC_OWN_POINTER, PETSC_TRUE, DM_COPY_LABELS_FAIL));
188: PetscCall(DMGetCoarseDM(dmNew, &coarseDM));
189: PetscCall(DMSetCoarseDM(dm, coarseDM));
190: PetscCall(DMPlexCopyEGADSInfo_Internal(dmNew, dm));
191: PetscCall(DMDestroy(ndm));
192: PetscFunctionReturn(PETSC_SUCCESS);
193: }
195: /* Swap dm with the contents of dmNew
196: - Swap the DM_Plex structure
197: - Swap the coordinates
198: - Swap the point PetscSF
199: */
200: static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB)
201: {
202: DM coordDMA, coordDMB;
203: Vec coordsA, coordsB;
204: PetscSF sfA, sfB;
205: DMField fieldTmp;
206: void *tmp;
207: DMLabelLink listTmp;
208: DMLabel depthTmp;
209: PetscInt tmpI;
211: PetscFunctionBegin;
212: if (dmA == dmB) PetscFunctionReturn(PETSC_SUCCESS);
213: PetscCall(DMGetPointSF(dmA, &sfA));
214: PetscCall(DMGetPointSF(dmB, &sfB));
215: PetscCall(PetscObjectReference((PetscObject)sfA));
216: PetscCall(DMSetPointSF(dmA, sfB));
217: PetscCall(DMSetPointSF(dmB, sfA));
218: PetscCall(PetscObjectDereference((PetscObject)sfA));
220: PetscCall(DMGetCoordinateDM(dmA, &coordDMA));
221: PetscCall(DMGetCoordinateDM(dmB, &coordDMB));
222: PetscCall(PetscObjectReference((PetscObject)coordDMA));
223: PetscCall(DMSetCoordinateDM(dmA, coordDMB));
224: PetscCall(DMSetCoordinateDM(dmB, coordDMA));
225: PetscCall(PetscObjectDereference((PetscObject)coordDMA));
227: PetscCall(DMGetCoordinatesLocal(dmA, &coordsA));
228: PetscCall(DMGetCoordinatesLocal(dmB, &coordsB));
229: PetscCall(PetscObjectReference((PetscObject)coordsA));
230: PetscCall(DMSetCoordinatesLocal(dmA, coordsB));
231: PetscCall(DMSetCoordinatesLocal(dmB, coordsA));
232: PetscCall(PetscObjectDereference((PetscObject)coordsA));
234: PetscCall(DMGetCellCoordinateDM(dmA, &coordDMA));
235: PetscCall(DMGetCellCoordinateDM(dmB, &coordDMB));
236: PetscCall(PetscObjectReference((PetscObject)coordDMA));
237: PetscCall(DMSetCellCoordinateDM(dmA, coordDMB));
238: PetscCall(DMSetCellCoordinateDM(dmB, coordDMA));
239: PetscCall(PetscObjectDereference((PetscObject)coordDMA));
241: PetscCall(DMGetCellCoordinatesLocal(dmA, &coordsA));
242: PetscCall(DMGetCellCoordinatesLocal(dmB, &coordsB));
243: PetscCall(PetscObjectReference((PetscObject)coordsA));
244: PetscCall(DMSetCellCoordinatesLocal(dmA, coordsB));
245: PetscCall(DMSetCellCoordinatesLocal(dmB, coordsA));
246: PetscCall(PetscObjectDereference((PetscObject)coordsA));
248: PetscCall(DMPlexSwapEGADSInfo_Private(dmA, dmB));
250: fieldTmp = dmA->coordinates[0].field;
251: dmA->coordinates[0].field = dmB->coordinates[0].field;
252: dmB->coordinates[0].field = fieldTmp;
253: fieldTmp = dmA->coordinates[1].field;
254: dmA->coordinates[1].field = dmB->coordinates[1].field;
255: dmB->coordinates[1].field = fieldTmp;
256: tmp = dmA->data;
257: dmA->data = dmB->data;
258: dmB->data = tmp;
259: listTmp = dmA->labels;
260: dmA->labels = dmB->labels;
261: dmB->labels = listTmp;
262: depthTmp = dmA->depthLabel;
263: dmA->depthLabel = dmB->depthLabel;
264: dmB->depthLabel = depthTmp;
265: depthTmp = dmA->celltypeLabel;
266: dmA->celltypeLabel = dmB->celltypeLabel;
267: dmB->celltypeLabel = depthTmp;
268: tmpI = dmA->levelup;
269: dmA->levelup = dmB->levelup;
270: dmB->levelup = tmpI;
271: PetscFunctionReturn(PETSC_SUCCESS);
272: }
274: PetscErrorCode DMPlexInterpolateInPlace_Internal(DM dm)
275: {
276: DM idm;
278: PetscFunctionBegin;
279: PetscCall(DMPlexInterpolate(dm, &idm));
280: PetscCall(DMPlexCopyCoordinates(dm, idm));
281: PetscCall(DMPlexReplace_Internal(dm, &idm));
282: PetscFunctionReturn(PETSC_SUCCESS);
283: }
285: /*@C
286: DMPlexCreateCoordinateSpace - Creates a finite element space for the coordinates
288: Collective
290: Input Parameters:
291: + dm - The `DMPLEX`
292: . degree - The degree of the finite element or `PETSC_DECIDE`
293: . localized - Flag to create a localized (DG) coordinate space
294: - project - Flag to project current coordinates into the space
296: Level: advanced
298: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `PetscPointFn`, `PetscFECreateLagrange()`, `DMGetCoordinateDM()`, `DMPlexSetCoordinateMap()`
299: @*/
300: PetscErrorCode DMPlexCreateCoordinateSpace(DM dm, PetscInt degree, PetscBool localized, PetscBool project)
301: {
302: PetscFE fe = NULL;
303: DM cdm;
304: PetscInt dim, cdim, dE, qorder, height;
306: PetscFunctionBegin;
307: PetscCall(DMGetDimension(dm, &dim));
308: cdim = dim;
309: PetscCall(DMGetCoordinateDim(dm, &dE));
310: qorder = degree;
311: PetscCall(DMGetCoordinateDM(dm, &cdm));
312: PetscObjectOptionsBegin((PetscObject)cdm);
313: PetscCall(PetscOptionsBoundedInt("-default_quadrature_order", "Quadrature order is one less than quadrature points per edge", "DMPlexCreateCoordinateSpace", qorder, &qorder, NULL, 0));
314: PetscCall(PetscOptionsBoundedInt("-dm_plex_coordinate_dim", "Set the coordinate dimension", "DMPlexCreateCoordinateSpace", cdim, &cdim, NULL, dim));
315: PetscOptionsEnd();
316: PetscCall(DMPlexGetVTKCellHeight(dm, &height));
317: if (cdim > dim) {
318: DM cdm;
319: PetscSection cs, csNew;
320: Vec coordinates, coordinatesNew;
321: VecType vectype;
322: IS idx;
323: PetscInt *indices;
324: PetscInt bs, n;
326: // Recreate coordinate section
327: {
328: const char *fieldName = NULL, *compName = NULL;
329: PetscInt Nc, pStart, pEnd;
331: PetscCall(DMGetCoordinateDM(dm, &cdm));
332: PetscCall(DMGetLocalSection(cdm, &cs));
333: PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)cs), &csNew));
334: PetscCall(PetscSectionSetNumFields(csNew, 1));
335: PetscCall(PetscSectionGetFieldName(cs, 0, &fieldName));
336: PetscCall(PetscSectionSetFieldName(csNew, 0, fieldName));
337: PetscCall(PetscSectionGetFieldComponents(cs, 0, &Nc));
338: PetscCall(PetscSectionSetFieldComponents(csNew, 0, cdim));
339: for (PetscInt c = 0; c < Nc; ++c) {
340: PetscCall(PetscSectionGetComponentName(cs, 0, c, &compName));
341: PetscCall(PetscSectionSetComponentName(csNew, 0, c, compName));
342: }
343: PetscCall(PetscSectionGetChart(cs, &pStart, &pEnd));
344: PetscCall(PetscSectionSetChart(csNew, pStart, pEnd));
345: for (PetscInt p = pStart; p < pEnd; ++p) {
346: PetscInt dof;
348: PetscCall(PetscSectionGetDof(cs, p, &dof));
349: if (dof) {
350: PetscCall(PetscSectionSetDof(csNew, p, cdim));
351: PetscCall(PetscSectionSetFieldDof(csNew, p, 0, cdim));
352: }
353: }
354: PetscCall(PetscSectionSetUp(csNew));
355: }
356: PetscCall(DMSetLocalSection(cdm, csNew));
357: PetscCall(PetscSectionDestroy(&csNew));
358: // Reset coordinate dimension for coordinate DM
359: PetscCall(DMSetCoordinateDim(cdm, cdim));
360: PetscCall(DMSetCoordinateField(cdm, NULL));
361: // Inject coordinates into higher dimension
362: PetscCall(DMGetCoordinatesLocal(dm, &coordinates));
363: PetscCall(VecGetBlockSize(coordinates, &bs));
364: PetscCheck(bs == dim, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "We can only inject simple coordinates into a higher dimension");
365: PetscCall(VecCreate(PetscObjectComm((PetscObject)coordinates), &coordinatesNew));
366: PetscCall(VecGetType(coordinates, &vectype));
367: PetscCall(VecSetType(coordinatesNew, vectype));
368: PetscCall(VecGetLocalSize(coordinates, &n));
369: PetscCheck(!(n % bs), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "We can only inject simple coordinates into a higher dimension");
370: n /= bs;
371: PetscCall(VecSetSizes(coordinatesNew, n * cdim, PETSC_DETERMINE));
372: PetscCall(VecSetUp(coordinatesNew));
373: PetscCall(PetscMalloc1(n * bs, &indices));
374: for (PetscInt i = 0; i < n; ++i)
375: for (PetscInt b = 0; b < bs; ++b) indices[i * bs + b] = i * cdim + b;
376: PetscCall(ISCreateGeneral(PETSC_COMM_SELF, n * bs, indices, PETSC_OWN_POINTER, &idx));
377: PetscCall(VecISCopy(coordinatesNew, idx, SCATTER_FORWARD, coordinates));
378: PetscCall(ISDestroy(&idx));
379: PetscCall(DMSetCoordinatesLocal(dm, coordinatesNew));
380: PetscCall(VecDestroy(&coordinatesNew));
381: PetscCall(DMSetCoordinateDim(dm, cdim));
382: {
383: PetscInt gn;
385: PetscCall(DMGetCoordinates(dm, &coordinatesNew));
386: PetscCall(VecGetLocalSize(coordinatesNew, &gn));
387: PetscCheck(gn == n * cdim, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Global coordinate size %" PetscInt_FMT " != %" PetscInt_FMT "local coordinate size", gn, n * cdim);
388: }
389: dE = cdim;
390: project = PETSC_FALSE;
391: }
392: if (degree >= 0) {
393: DMPolytopeType ct = DM_POLYTOPE_UNKNOWN;
394: PetscInt cStart, cEnd, gct;
396: PetscCall(DMPlexGetHeightStratum(dm, height, &cStart, &cEnd));
397: if (cEnd > cStart) PetscCall(DMPlexGetCellType(dm, cStart, &ct));
398: gct = (PetscInt)ct;
399: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &gct, 1, MPIU_INT, MPI_MIN, PetscObjectComm((PetscObject)dm)));
400: ct = (DMPolytopeType)gct;
401: // Work around current bug in PetscDualSpaceSetUp_Lagrange()
402: // Can be seen in plex_tutorials-ex10_1
403: if (ct != DM_POLYTOPE_SEG_PRISM_TENSOR && ct != DM_POLYTOPE_TRI_PRISM_TENSOR && ct != DM_POLYTOPE_QUAD_PRISM_TENSOR) {
404: PetscCall(PetscFECreateLagrangeByCell(PETSC_COMM_SELF, dim, dE, ct, degree, qorder, &fe));
405: if (localized) {
406: PetscFE dgfe = NULL;
408: PetscCall(PetscFECreateBrokenElement(fe, &dgfe));
409: PetscCall(PetscFEDestroy(&fe));
410: fe = dgfe;
411: }
412: }
413: }
414: PetscCall(DMSetCoordinateDisc(dm, fe, localized, project));
415: PetscCall(PetscFEDestroy(&fe));
416: PetscFunctionReturn(PETSC_SUCCESS);
417: }
419: /*@
420: DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement.
422: Collective
424: Input Parameters:
425: + comm - The communicator for the `DM` object
426: . dim - The spatial dimension
427: . simplex - Flag for simplicial cells, otherwise they are tensor product cells
428: . interpolate - Flag to create intermediate mesh pieces (edges, faces)
429: - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell
431: Output Parameter:
432: . newdm - The `DM` object
434: Level: beginner
436: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMSetType()`, `DMCreate()`
437: @*/
438: PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscReal refinementLimit, DM *newdm)
439: {
440: DM dm;
441: PetscMPIInt rank;
443: PetscFunctionBegin;
444: PetscCall(DMCreate(comm, &dm));
445: PetscCall(DMSetType(dm, DMPLEX));
446: PetscCall(DMSetDimension(dm, dim));
447: PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0));
448: PetscCallMPI(MPI_Comm_rank(comm, &rank));
449: switch (dim) {
450: case 2:
451: if (simplex) PetscCall(PetscObjectSetName((PetscObject)dm, "triangular"));
452: else PetscCall(PetscObjectSetName((PetscObject)dm, "quadrilateral"));
453: break;
454: case 3:
455: if (simplex) PetscCall(PetscObjectSetName((PetscObject)dm, "tetrahedral"));
456: else PetscCall(PetscObjectSetName((PetscObject)dm, "hexahedral"));
457: break;
458: default:
459: SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %" PetscInt_FMT, dim);
460: }
461: if (rank) {
462: PetscInt numPoints[2] = {0, 0};
463: PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL));
464: } else {
465: switch (dim) {
466: case 2:
467: if (simplex) {
468: PetscInt numPoints[2] = {4, 2};
469: PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0};
470: PetscInt cones[6] = {2, 3, 4, 5, 4, 3};
471: PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0};
472: PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5};
474: PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
475: } else {
476: PetscInt numPoints[2] = {6, 2};
477: PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0};
478: PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4};
479: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
480: PetscScalar vertexCoords[12] = {-1.0, -0.5, 0.0, -0.5, 0.0, 0.5, -1.0, 0.5, 1.0, -0.5, 1.0, 0.5};
482: PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
483: }
484: break;
485: case 3:
486: if (simplex) {
487: PetscInt numPoints[2] = {5, 2};
488: PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0};
489: PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6};
490: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
491: PetscScalar vertexCoords[15] = {-1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0};
493: PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
494: } else {
495: PetscInt numPoints[2] = {12, 2};
496: PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
497: PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8};
498: PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
499: PetscScalar vertexCoords[36] = {-1.0, -0.5, -0.5, -1.0, 0.5, -0.5, 0.0, 0.5, -0.5, 0.0, -0.5, -0.5, -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5, 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5};
501: PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
502: }
503: break;
504: default:
505: SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %" PetscInt_FMT, dim);
506: }
507: }
508: PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0));
509: *newdm = dm;
510: if (refinementLimit > 0.0) {
511: DM rdm;
512: const char *name;
514: PetscCall(DMPlexSetRefinementUniform(*newdm, PETSC_FALSE));
515: PetscCall(DMPlexSetRefinementLimit(*newdm, refinementLimit));
516: PetscCall(DMRefine(*newdm, comm, &rdm));
517: PetscCall(PetscObjectGetName((PetscObject)*newdm, &name));
518: PetscCall(PetscObjectSetName((PetscObject)rdm, name));
519: PetscCall(DMDestroy(newdm));
520: *newdm = rdm;
521: }
522: if (interpolate) {
523: DM idm;
525: PetscCall(DMPlexInterpolate(*newdm, &idm));
526: PetscCall(DMDestroy(newdm));
527: *newdm = idm;
528: }
529: PetscFunctionReturn(PETSC_SUCCESS);
530: }
532: static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
533: {
534: const PetscInt numVertices = 2;
535: PetscInt markerRight = 1;
536: PetscInt markerLeft = 1;
537: PetscBool markerSeparate = PETSC_FALSE;
538: Vec coordinates;
539: PetscSection coordSection;
540: PetscScalar *coords;
541: PetscInt coordSize;
542: PetscMPIInt rank;
543: PetscInt cdim = 1, v;
545: PetscFunctionBegin;
546: PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL));
547: if (markerSeparate) {
548: markerRight = 2;
549: markerLeft = 1;
550: }
551: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
552: if (rank == 0) {
553: PetscCall(DMPlexSetChart(dm, 0, numVertices));
554: PetscCall(DMSetUp(dm)); /* Allocate space for cones */
555: PetscCall(DMSetLabelValue(dm, "marker", 0, markerLeft));
556: PetscCall(DMSetLabelValue(dm, "marker", 1, markerRight));
557: }
558: PetscCall(DMPlexSymmetrize(dm));
559: PetscCall(DMPlexStratify(dm));
560: /* Build coordinates */
561: PetscCall(DMSetCoordinateDim(dm, cdim));
562: PetscCall(DMGetCoordinateSection(dm, &coordSection));
563: PetscCall(PetscSectionSetNumFields(coordSection, 1));
564: PetscCall(PetscSectionSetChart(coordSection, 0, numVertices));
565: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, cdim));
566: for (v = 0; v < numVertices; ++v) {
567: PetscCall(PetscSectionSetDof(coordSection, v, cdim));
568: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, cdim));
569: }
570: PetscCall(PetscSectionSetUp(coordSection));
571: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
572: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
573: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
574: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
575: PetscCall(VecSetBlockSize(coordinates, cdim));
576: PetscCall(VecSetType(coordinates, VECSTANDARD));
577: PetscCall(VecGetArray(coordinates, &coords));
578: coords[0] = lower[0];
579: coords[1] = upper[0];
580: PetscCall(VecRestoreArray(coordinates, &coords));
581: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
582: PetscCall(VecDestroy(&coordinates));
583: PetscFunctionReturn(PETSC_SUCCESS);
584: }
586: static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
587: {
588: const PetscInt numVertices = (edges[0] + 1) * (edges[1] + 1);
589: const PetscInt numEdges = edges[0] * (edges[1] + 1) + (edges[0] + 1) * edges[1];
590: PetscInt markerTop = 1;
591: PetscInt markerBottom = 1;
592: PetscInt markerRight = 1;
593: PetscInt markerLeft = 1;
594: PetscBool markerSeparate = PETSC_FALSE;
595: Vec coordinates;
596: PetscSection coordSection;
597: PetscScalar *coords;
598: PetscInt coordSize;
599: PetscMPIInt rank;
600: PetscInt v, vx, vy;
602: PetscFunctionBegin;
603: PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL));
604: if (markerSeparate) {
605: markerTop = 3;
606: markerBottom = 1;
607: markerRight = 2;
608: markerLeft = 4;
609: }
610: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
611: if (rank == 0) {
612: PetscInt e, ex, ey;
614: PetscCall(DMPlexSetChart(dm, 0, numEdges + numVertices));
615: for (e = 0; e < numEdges; ++e) PetscCall(DMPlexSetConeSize(dm, e, 2));
616: PetscCall(DMSetUp(dm)); /* Allocate space for cones */
617: for (vx = 0; vx <= edges[0]; vx++) {
618: for (ey = 0; ey < edges[1]; ey++) {
619: PetscInt edge = vx * edges[1] + ey + edges[0] * (edges[1] + 1);
620: PetscInt vertex = ey * (edges[0] + 1) + vx + numEdges;
621: PetscInt cone[2];
623: cone[0] = vertex;
624: cone[1] = vertex + edges[0] + 1;
625: PetscCall(DMPlexSetCone(dm, edge, cone));
626: if (vx == edges[0]) {
627: PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight));
628: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight));
629: if (ey == edges[1] - 1) {
630: PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight));
631: PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerRight));
632: }
633: } else if (vx == 0) {
634: PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft));
635: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft));
636: if (ey == edges[1] - 1) {
637: PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft));
638: PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft));
639: }
640: }
641: }
642: }
643: for (vy = 0; vy <= edges[1]; vy++) {
644: for (ex = 0; ex < edges[0]; ex++) {
645: PetscInt edge = vy * edges[0] + ex;
646: PetscInt vertex = vy * (edges[0] + 1) + ex + numEdges;
647: PetscInt cone[2];
649: cone[0] = vertex;
650: cone[1] = vertex + 1;
651: PetscCall(DMPlexSetCone(dm, edge, cone));
652: if (vy == edges[1]) {
653: PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop));
654: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop));
655: if (ex == edges[0] - 1) {
656: PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop));
657: PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerTop));
658: }
659: } else if (vy == 0) {
660: PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom));
661: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom));
662: if (ex == edges[0] - 1) {
663: PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom));
664: PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom));
665: }
666: }
667: }
668: }
669: }
670: PetscCall(DMPlexSymmetrize(dm));
671: PetscCall(DMPlexStratify(dm));
672: /* Build coordinates */
673: PetscCall(DMSetCoordinateDim(dm, 2));
674: PetscCall(DMGetCoordinateSection(dm, &coordSection));
675: PetscCall(PetscSectionSetNumFields(coordSection, 1));
676: PetscCall(PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices));
677: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, 2));
678: for (v = numEdges; v < numEdges + numVertices; ++v) {
679: PetscCall(PetscSectionSetDof(coordSection, v, 2));
680: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, 2));
681: }
682: PetscCall(PetscSectionSetUp(coordSection));
683: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
684: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
685: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
686: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
687: PetscCall(VecSetBlockSize(coordinates, 2));
688: PetscCall(VecSetType(coordinates, VECSTANDARD));
689: PetscCall(VecGetArray(coordinates, &coords));
690: for (vy = 0; vy <= edges[1]; ++vy) {
691: for (vx = 0; vx <= edges[0]; ++vx) {
692: coords[(vy * (edges[0] + 1) + vx) * 2 + 0] = lower[0] + ((upper[0] - lower[0]) / edges[0]) * vx;
693: coords[(vy * (edges[0] + 1) + vx) * 2 + 1] = lower[1] + ((upper[1] - lower[1]) / edges[1]) * vy;
694: }
695: }
696: PetscCall(VecRestoreArray(coordinates, &coords));
697: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
698: PetscCall(VecDestroy(&coordinates));
699: PetscFunctionReturn(PETSC_SUCCESS);
700: }
702: static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[])
703: {
704: PetscInt vertices[3], numVertices;
705: PetscInt numFaces = 2 * faces[0] * faces[1] + 2 * faces[1] * faces[2] + 2 * faces[0] * faces[2];
706: PetscInt markerTop = 1;
707: PetscInt markerBottom = 1;
708: PetscInt markerFront = 1;
709: PetscInt markerBack = 1;
710: PetscInt markerRight = 1;
711: PetscInt markerLeft = 1;
712: PetscBool markerSeparate = PETSC_FALSE;
713: Vec coordinates;
714: PetscSection coordSection;
715: PetscScalar *coords;
716: PetscInt coordSize;
717: PetscMPIInt rank;
718: PetscInt v, vx, vy, vz;
719: PetscInt voffset, iface = 0, cone[4];
721: PetscFunctionBegin;
722: PetscCheck(faces[0] >= 1 && faces[1] >= 1 && faces[2] >= 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Must have at least 1 face per side");
723: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
724: PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL));
725: if (markerSeparate) {
726: markerBottom = 1;
727: markerTop = 2;
728: markerFront = 3;
729: markerBack = 4;
730: markerRight = 5;
731: markerLeft = 6;
732: }
733: vertices[0] = faces[0] + 1;
734: vertices[1] = faces[1] + 1;
735: vertices[2] = faces[2] + 1;
736: numVertices = vertices[0] * vertices[1] * vertices[2];
737: if (rank == 0) {
738: PetscInt f;
740: PetscCall(DMPlexSetChart(dm, 0, numFaces + numVertices));
741: for (f = 0; f < numFaces; ++f) PetscCall(DMPlexSetConeSize(dm, f, 4));
742: PetscCall(DMSetUp(dm)); /* Allocate space for cones */
744: /* Side 0 (Top) */
745: for (vy = 0; vy < faces[1]; vy++) {
746: for (vx = 0; vx < faces[0]; vx++) {
747: voffset = numFaces + vertices[0] * vertices[1] * (vertices[2] - 1) + vy * vertices[0] + vx;
748: cone[0] = voffset;
749: cone[1] = voffset + 1;
750: cone[2] = voffset + vertices[0] + 1;
751: cone[3] = voffset + vertices[0];
752: PetscCall(DMPlexSetCone(dm, iface, cone));
753: PetscCall(DMSetLabelValue(dm, "marker", iface, markerTop));
754: PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerTop));
755: PetscCall(DMSetLabelValue(dm, "marker", voffset + 1, markerTop));
756: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 0, markerTop));
757: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 1, markerTop));
758: iface++;
759: }
760: }
762: /* Side 1 (Bottom) */
763: for (vy = 0; vy < faces[1]; vy++) {
764: for (vx = 0; vx < faces[0]; vx++) {
765: voffset = numFaces + vy * (faces[0] + 1) + vx;
766: cone[0] = voffset + 1;
767: cone[1] = voffset;
768: cone[2] = voffset + vertices[0];
769: cone[3] = voffset + vertices[0] + 1;
770: PetscCall(DMPlexSetCone(dm, iface, cone));
771: PetscCall(DMSetLabelValue(dm, "marker", iface, markerBottom));
772: PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerBottom));
773: PetscCall(DMSetLabelValue(dm, "marker", voffset + 1, markerBottom));
774: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 0, markerBottom));
775: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 1, markerBottom));
776: iface++;
777: }
778: }
780: /* Side 2 (Front) */
781: for (vz = 0; vz < faces[2]; vz++) {
782: for (vx = 0; vx < faces[0]; vx++) {
783: voffset = numFaces + vz * vertices[0] * vertices[1] + vx;
784: cone[0] = voffset;
785: cone[1] = voffset + 1;
786: cone[2] = voffset + vertices[0] * vertices[1] + 1;
787: cone[3] = voffset + vertices[0] * vertices[1];
788: PetscCall(DMPlexSetCone(dm, iface, cone));
789: PetscCall(DMSetLabelValue(dm, "marker", iface, markerFront));
790: PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerFront));
791: PetscCall(DMSetLabelValue(dm, "marker", voffset + 1, markerFront));
792: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 0, markerFront));
793: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 1, markerFront));
794: iface++;
795: }
796: }
798: /* Side 3 (Back) */
799: for (vz = 0; vz < faces[2]; vz++) {
800: for (vx = 0; vx < faces[0]; vx++) {
801: voffset = numFaces + vz * vertices[0] * vertices[1] + vertices[0] * (vertices[1] - 1) + vx;
802: cone[0] = voffset + vertices[0] * vertices[1];
803: cone[1] = voffset + vertices[0] * vertices[1] + 1;
804: cone[2] = voffset + 1;
805: cone[3] = voffset;
806: PetscCall(DMPlexSetCone(dm, iface, cone));
807: PetscCall(DMSetLabelValue(dm, "marker", iface, markerBack));
808: PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerBack));
809: PetscCall(DMSetLabelValue(dm, "marker", voffset + 1, markerBack));
810: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 0, markerBack));
811: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 1, markerBack));
812: iface++;
813: }
814: }
816: /* Side 4 (Left) */
817: for (vz = 0; vz < faces[2]; vz++) {
818: for (vy = 0; vy < faces[1]; vy++) {
819: voffset = numFaces + vz * vertices[0] * vertices[1] + vy * vertices[0];
820: cone[0] = voffset;
821: cone[1] = voffset + vertices[0] * vertices[1];
822: cone[2] = voffset + vertices[0] * vertices[1] + vertices[0];
823: cone[3] = voffset + vertices[0];
824: PetscCall(DMPlexSetCone(dm, iface, cone));
825: PetscCall(DMSetLabelValue(dm, "marker", iface, markerLeft));
826: PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerLeft));
827: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 0, markerLeft));
828: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[1] + 0, markerLeft));
829: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + vertices[0], markerLeft));
830: iface++;
831: }
832: }
834: /* Side 5 (Right) */
835: for (vz = 0; vz < faces[2]; vz++) {
836: for (vy = 0; vy < faces[1]; vy++) {
837: voffset = numFaces + vz * vertices[0] * vertices[1] + vy * vertices[0] + faces[0];
838: cone[0] = voffset + vertices[0] * vertices[1];
839: cone[1] = voffset;
840: cone[2] = voffset + vertices[0];
841: cone[3] = voffset + vertices[0] * vertices[1] + vertices[0];
842: PetscCall(DMPlexSetCone(dm, iface, cone));
843: PetscCall(DMSetLabelValue(dm, "marker", iface, markerRight));
844: PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerRight));
845: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 0, markerRight));
846: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 0, markerRight));
847: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + vertices[0], markerRight));
848: iface++;
849: }
850: }
851: }
852: PetscCall(DMPlexSymmetrize(dm));
853: PetscCall(DMPlexStratify(dm));
854: /* Build coordinates */
855: PetscCall(DMSetCoordinateDim(dm, 3));
856: PetscCall(DMGetCoordinateSection(dm, &coordSection));
857: PetscCall(PetscSectionSetNumFields(coordSection, 1));
858: PetscCall(PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices));
859: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, 3));
860: for (v = numFaces; v < numFaces + numVertices; ++v) {
861: PetscCall(PetscSectionSetDof(coordSection, v, 3));
862: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, 3));
863: }
864: PetscCall(PetscSectionSetUp(coordSection));
865: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
866: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
867: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
868: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
869: PetscCall(VecSetBlockSize(coordinates, 3));
870: PetscCall(VecSetType(coordinates, VECSTANDARD));
871: PetscCall(VecGetArray(coordinates, &coords));
872: for (vz = 0; vz <= faces[2]; ++vz) {
873: for (vy = 0; vy <= faces[1]; ++vy) {
874: for (vx = 0; vx <= faces[0]; ++vx) {
875: coords[((vz * (faces[1] + 1) + vy) * (faces[0] + 1) + vx) * 3 + 0] = lower[0] + ((upper[0] - lower[0]) / faces[0]) * vx;
876: coords[((vz * (faces[1] + 1) + vy) * (faces[0] + 1) + vx) * 3 + 1] = lower[1] + ((upper[1] - lower[1]) / faces[1]) * vy;
877: coords[((vz * (faces[1] + 1) + vy) * (faces[0] + 1) + vx) * 3 + 2] = lower[2] + ((upper[2] - lower[2]) / faces[2]) * vz;
878: }
879: }
880: }
881: PetscCall(VecRestoreArray(coordinates, &coords));
882: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
883: PetscCall(VecDestroy(&coordinates));
884: PetscFunctionReturn(PETSC_SUCCESS);
885: }
887: static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate)
888: {
889: PetscFunctionBegin;
891: PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0));
892: PetscCall(DMSetDimension(dm, dim - 1));
893: PetscCall(DMSetCoordinateDim(dm, dim));
894: switch (dim) {
895: case 1:
896: PetscCall(DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(dm, lower, upper, faces));
897: break;
898: case 2:
899: PetscCall(DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(dm, lower, upper, faces));
900: break;
901: case 3:
902: PetscCall(DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(dm, lower, upper, faces));
903: break;
904: default:
905: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Dimension not supported: %" PetscInt_FMT, dim);
906: }
907: PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0));
908: if (interpolate) PetscCall(DMPlexInterpolateInPlace_Internal(dm));
909: PetscFunctionReturn(PETSC_SUCCESS);
910: }
912: /*@C
913: DMPlexCreateBoxSurfaceMesh - Creates a mesh on the surface of the tensor product of unit intervals (box) using tensor cells (hexahedra).
915: Collective
917: Input Parameters:
918: + comm - The communicator for the `DM` object
919: . dim - The spatial dimension of the box, so the resulting mesh is has dimension `dim`-1
920: . faces - Number of faces per dimension, or `NULL` for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D
921: . lower - The lower left corner, or `NULL` for (0, 0, 0)
922: . upper - The upper right corner, or `NULL` for (1, 1, 1)
923: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
925: Output Parameter:
926: . dm - The `DM` object
928: Level: beginner
930: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMSetFromOptions()`, `DMPlexCreateBoxMesh()`, `DMPlexCreateFromFile()`, `DMSetType()`, `DMCreate()`
931: @*/
932: PetscErrorCode DMPlexCreateBoxSurfaceMesh(MPI_Comm comm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate, DM *dm)
933: {
934: PetscInt fac[3] = {1, 1, 1};
935: PetscReal low[3] = {0, 0, 0};
936: PetscReal upp[3] = {1, 1, 1};
938: PetscFunctionBegin;
939: PetscCall(DMCreate(comm, dm));
940: PetscCall(DMSetType(*dm, DMPLEX));
941: PetscCall(DMPlexCreateBoxSurfaceMesh_Internal(*dm, dim, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, interpolate));
942: PetscFunctionReturn(PETSC_SUCCESS);
943: }
945: static PetscErrorCode DMPlexCreateLineMesh_Internal(DM dm, PetscInt segments, PetscReal lower, PetscReal upper, DMBoundaryType bd)
946: {
947: PetscInt i, fStart, fEnd, numCells = 0, numVerts = 0;
948: PetscInt numPoints[2], *coneSize, *cones, *coneOrientations;
949: PetscScalar *vertexCoords;
950: PetscReal L, maxCell;
951: PetscBool markerSeparate = PETSC_FALSE;
952: PetscInt markerLeft = 1, faceMarkerLeft = 1;
953: PetscInt markerRight = 1, faceMarkerRight = 2;
954: PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE;
955: PetscMPIInt rank;
957: PetscFunctionBegin;
958: PetscAssertPointer(dm, 1);
960: PetscCall(DMSetDimension(dm, 1));
961: PetscCall(DMCreateLabel(dm, "marker"));
962: PetscCall(DMCreateLabel(dm, "Face Sets"));
964: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
965: if (rank == 0) numCells = segments;
966: if (rank == 0) numVerts = segments + (wrap ? 0 : 1);
968: numPoints[0] = numVerts;
969: numPoints[1] = numCells;
970: PetscCall(PetscMalloc4(numCells + numVerts, &coneSize, numCells * 2, &cones, numCells + numVerts, &coneOrientations, numVerts, &vertexCoords));
971: PetscCall(PetscArrayzero(coneOrientations, numCells + numVerts));
972: for (i = 0; i < numCells; ++i) coneSize[i] = 2;
973: for (i = 0; i < numVerts; ++i) coneSize[numCells + i] = 0;
974: for (i = 0; i < numCells; ++i) {
975: cones[2 * i] = numCells + i % numVerts;
976: cones[2 * i + 1] = numCells + (i + 1) % numVerts;
977: }
978: for (i = 0; i < numVerts; ++i) vertexCoords[i] = lower + (upper - lower) * ((PetscReal)i / (PetscReal)numCells);
979: PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
980: PetscCall(PetscFree4(coneSize, cones, coneOrientations, vertexCoords));
982: PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL));
983: if (markerSeparate) {
984: markerLeft = faceMarkerLeft;
985: markerRight = faceMarkerRight;
986: }
987: if (!wrap && rank == 0) {
988: PetscCall(DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd));
989: PetscCall(DMSetLabelValue(dm, "marker", fStart, markerLeft));
990: PetscCall(DMSetLabelValue(dm, "marker", fEnd - 1, markerRight));
991: PetscCall(DMSetLabelValue(dm, "Face Sets", fStart, faceMarkerLeft));
992: PetscCall(DMSetLabelValue(dm, "Face Sets", fEnd - 1, faceMarkerRight));
993: }
994: if (wrap) {
995: L = upper - lower;
996: maxCell = (PetscReal)1.1 * (L / (PetscReal)PetscMax(1, segments));
997: PetscCall(DMSetPeriodicity(dm, &maxCell, &lower, &L));
998: }
999: PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE));
1000: PetscFunctionReturn(PETSC_SUCCESS);
1001: }
1003: // Creates "Face Sets" label based on the standard box labeling conventions
1004: static PetscErrorCode DMPlexSetBoxLabel_Internal(DM dm, const DMBoundaryType periodicity[])
1005: {
1006: DM cdm;
1007: PetscSection csection;
1008: Vec coordinates;
1009: DMLabel label;
1010: IS faces_is;
1011: PetscInt dim, num_face = 0;
1012: const PetscInt *faces;
1013: PetscInt faceMarkerBottom, faceMarkerTop, faceMarkerFront, faceMarkerBack, faceMarkerRight, faceMarkerLeft;
1015: PetscFunctionBeginUser;
1016: PetscCall(DMGetDimension(dm, &dim));
1017: PetscCheck((dim == 2) || (dim == 3), PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "DMPlex box labeling only supports 2D and 3D meshes, received DM of dimension %" PetscInt_FMT, dim);
1018: // Get Face Sets label
1019: PetscCall(DMGetLabel(dm, "Face Sets", &label));
1020: if (label) {
1021: PetscCall(DMLabelReset(label));
1022: } else {
1023: PetscCall(DMCreateLabel(dm, "Face Sets"));
1024: PetscCall(DMGetLabel(dm, "Face Sets", &label));
1025: }
1026: PetscCall(DMPlexMarkBoundaryFaces(dm, 1, label));
1027: PetscCall(DMGetStratumIS(dm, "Face Sets", 1, &faces_is));
1029: switch (dim) {
1030: case 2:
1031: faceMarkerTop = 3;
1032: faceMarkerBottom = 1;
1033: faceMarkerRight = 2;
1034: faceMarkerLeft = 4;
1035: break;
1036: case 3:
1037: faceMarkerBottom = 1;
1038: faceMarkerTop = 2;
1039: faceMarkerFront = 3;
1040: faceMarkerBack = 4;
1041: faceMarkerRight = 5;
1042: faceMarkerLeft = 6;
1043: break;
1044: default:
1045: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Dimension %" PetscInt_FMT " not supported", dim);
1046: }
1048: if (faces_is) PetscCall(ISGetLocalSize(faces_is, &num_face));
1049: if (faces_is) PetscCall(ISGetIndices(faces_is, &faces));
1050: PetscCall(DMGetCoordinatesLocal(dm, &coordinates));
1051: PetscCall(DMGetCoordinateDM(dm, &cdm));
1052: PetscCall(DMGetLocalSection(cdm, &csection));
1053: for (PetscInt f = 0; f < num_face; ++f) {
1054: PetscScalar *coords = NULL;
1055: PetscInt face = faces[f], flip = 1, label_value = -1, coords_size;
1057: { // Determine if orientation of face is flipped
1058: PetscInt num_cells_support, num_faces, start = -1;
1059: const PetscInt *orients, *cell_faces, *cells;
1061: PetscCall(DMPlexGetSupport(dm, face, &cells));
1062: PetscCall(DMPlexGetSupportSize(dm, face, &num_cells_support));
1063: PetscCheck(num_cells_support == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Expected one cell in support of exterior face, but got %" PetscInt_FMT " cells", num_cells_support);
1064: PetscCall(DMPlexGetCone(dm, cells[0], &cell_faces));
1065: PetscCall(DMPlexGetConeSize(dm, cells[0], &num_faces));
1066: for (PetscInt i = 0; i < num_faces; i++) {
1067: if (cell_faces[i] == face) start = i;
1068: }
1069: PetscCheck(start >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_CORRUPT, "Could not find face %" PetscInt_FMT " in cone of its support", face);
1070: PetscCall(DMPlexGetConeOrientation(dm, cells[0], &orients));
1071: if (orients[start] < 0) flip = -1;
1072: }
1074: // Cannot use DMPlexComputeCellGeometryFVM() for high-order geometry, so must calculate normal vectors manually
1075: // Use the vertices (depth 0) of coordinate DM to calculate normal vector
1076: PetscCall(DMPlexVecGetClosureAtDepth_Internal(cdm, csection, coordinates, face, 0, &coords_size, &coords));
1077: switch (dim) {
1078: case 2: {
1079: PetscScalar vec[2];
1081: for (PetscInt d = 0; d < dim; ++d) vec[d] = flip * (PetscRealPart(coords[1 * dim + d]) - PetscRealPart(coords[0 * dim + d]));
1082: PetscScalar normal[] = {vec[1], -vec[0]};
1083: if (PetscAbsScalar(normal[0]) > PetscAbsScalar(normal[1])) {
1084: label_value = PetscRealPart(normal[0]) > 0 ? faceMarkerRight : faceMarkerLeft;
1085: } else {
1086: label_value = PetscRealPart(normal[1]) > 0 ? faceMarkerTop : faceMarkerBottom;
1087: }
1088: } break;
1089: case 3: {
1090: PetscScalar vec1[3], vec2[3], normal[3];
1092: for (PetscInt d = 0; d < dim; ++d) {
1093: vec1[d] = PetscRealPart(coords[1 * dim + d]) - PetscRealPart(coords[0 * dim + d]);
1094: vec2[d] = PetscRealPart(coords[2 * dim + d]) - PetscRealPart(coords[1 * dim + d]);
1095: }
1097: // Calculate normal vector via cross-product
1098: normal[0] = flip * ((vec1[1] * vec2[2]) - (vec1[2] * vec2[1]));
1099: normal[1] = flip * ((vec1[2] * vec2[0]) - (vec1[0] * vec2[2]));
1100: normal[2] = flip * ((vec1[0] * vec2[1]) - (vec1[1] * vec2[0]));
1102: if (PetscAbsScalar(normal[0]) > PetscAbsScalar(normal[1])) {
1103: if (PetscAbsScalar(normal[0]) > PetscAbsScalar(normal[2])) {
1104: label_value = PetscRealPart(normal[0]) > 0 ? faceMarkerRight : faceMarkerLeft;
1105: } else {
1106: label_value = PetscRealPart(normal[2]) > 0 ? faceMarkerTop : faceMarkerBottom;
1107: }
1108: } else {
1109: if (PetscAbsScalar(normal[1]) > PetscAbsScalar(normal[2])) {
1110: label_value = PetscRealPart(normal[1]) > 0 ? faceMarkerBack : faceMarkerFront;
1111: } else {
1112: label_value = PetscRealPart(normal[2]) > 0 ? faceMarkerTop : faceMarkerBottom;
1113: }
1114: }
1115: } break;
1116: }
1118: PetscInt previous_label_value; // always 1 due to DMPlexMarkBoundaryFaces call above
1119: PetscCall(DMGetLabelValue(dm, "Face Sets", face, &previous_label_value));
1120: PetscCall(DMClearLabelValue(dm, "Face Sets", face, previous_label_value));
1121: PetscCall(DMSetLabelValue(dm, "Face Sets", face, label_value));
1122: PetscCall(DMPlexVecRestoreClosure(cdm, csection, coordinates, face, &coords_size, &coords));
1123: }
1124: if (faces_is) PetscCall(ISRestoreIndices(faces_is, &faces));
1125: PetscCall(ISDestroy(&faces_is));
1127: // Create Isoperiodic SF from newly-created face labels
1128: PetscSF periodicsfs[3];
1129: PetscInt periodic_sf_index = 0;
1130: PetscScalar transform[3][4][4] = {{{0.}}};
1131: for (PetscInt d = 0; d < dim; d++) {
1132: IS donor_is, periodic_is;
1133: const PetscInt *donor_faces = NULL, *periodic_faces = NULL;
1134: PetscInt num_donor = 0, num_periodic = 0;
1135: PetscSF centroidsf;
1136: PetscReal donor_to_periodic_distance;
1137: const PetscInt face_pairings[2][3][2] = {
1138: // 2D face pairings, {donor, periodic}
1139: {{4, 2}, {1, 3}},
1140: // 3D face pairings
1141: {{5, 6}, {3, 4}, {1, 2}}
1142: };
1144: if (periodicity[d] != DM_BOUNDARY_PERIODIC) continue;
1145: {
1146: // Compute centroidsf, which is the mapping from donor faces to periodic faces
1147: // Matches the centroid of the faces together, ignoring the periodic direction component (which should not match between donor and periodic face)
1148: PetscInt coords_size, centroid_comps = dim - 1;
1149: PetscScalar *coords = NULL;
1150: PetscReal *donor_centroids, *periodic_centroids;
1151: PetscReal loc_periodic[2] = {PETSC_MIN_REAL, PETSC_MIN_REAL}, loc_periodic_global[2]; // Location of donor (0) and periodic (1) faces in periodic direction
1153: PetscCall(DMGetStratumIS(dm, "Face Sets", face_pairings[dim - 2][d][0], &donor_is));
1154: PetscCall(DMGetStratumIS(dm, "Face Sets", face_pairings[dim - 2][d][1], &periodic_is));
1155: if (donor_is) {
1156: PetscCall(ISGetLocalSize(donor_is, &num_donor));
1157: PetscCall(ISGetIndices(donor_is, &donor_faces));
1158: }
1159: if (periodic_is) {
1160: PetscCall(ISGetLocalSize(periodic_is, &num_periodic));
1161: PetscCall(ISGetIndices(periodic_is, &periodic_faces));
1162: }
1163: PetscCall(PetscCalloc2(num_donor * centroid_comps, &donor_centroids, num_periodic * centroid_comps, &periodic_centroids));
1164: for (PetscInt f = 0; f < num_donor; f++) {
1165: PetscInt face = donor_faces[f], num_coords;
1166: PetscCall(DMPlexVecGetClosureAtDepth_Internal(cdm, csection, coordinates, face, 0, &coords_size, &coords));
1167: num_coords = coords_size / dim;
1168: for (PetscInt c = 0; c < num_coords; c++) {
1169: PetscInt comp_index = 0;
1170: loc_periodic[0] = PetscRealPart(coords[c * dim + d]);
1171: for (PetscInt i = 0; i < dim; i++) {
1172: if (i == d) continue; // Periodic direction not used for centroid calculation
1173: donor_centroids[f * centroid_comps + comp_index] += PetscRealPart(coords[c * dim + i]) / num_coords;
1174: comp_index++;
1175: }
1176: }
1177: PetscCall(DMPlexVecRestoreClosure(cdm, csection, coordinates, face, &coords_size, &coords));
1178: }
1180: for (PetscInt f = 0; f < num_periodic; f++) {
1181: PetscInt face = periodic_faces[f], num_coords;
1182: PetscCall(DMPlexVecGetClosureAtDepth_Internal(cdm, csection, coordinates, face, 0, &coords_size, &coords));
1183: num_coords = coords_size / dim;
1184: for (PetscInt c = 0; c < num_coords; c++) {
1185: PetscInt comp_index = 0;
1186: loc_periodic[1] = PetscRealPart(coords[c * dim + d]);
1187: for (PetscInt i = 0; i < dim; i++) {
1188: if (i == d) continue; // Periodic direction not used for centroid calculation
1189: periodic_centroids[f * centroid_comps + comp_index] += PetscRealPart(coords[c * dim + i]) / num_coords;
1190: comp_index++;
1191: }
1192: }
1193: PetscCall(DMPlexVecRestoreClosure(cdm, csection, coordinates, face, &coords_size, &coords));
1194: }
1195: PetscCallMPI(MPIU_Allreduce(loc_periodic, loc_periodic_global, 2, MPIU_REAL, MPIU_MAX, PetscObjectComm((PetscObject)dm)));
1196: donor_to_periodic_distance = loc_periodic_global[1] - loc_periodic_global[0];
1198: PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)dm), ¢roidsf));
1199: PetscCall(PetscSFSetGraphFromCoordinates(centroidsf, num_donor, num_periodic, centroid_comps, 1e-10, donor_centroids, periodic_centroids));
1200: PetscCall(PetscSFViewFromOptions(centroidsf, NULL, "-dm_plex_box_label_centroid_sf_view"));
1201: PetscCall(PetscFree2(donor_centroids, periodic_centroids));
1202: }
1204: { // Create Isoperiodic SF using centroidsSF
1205: PetscInt pStart, pEnd;
1206: PetscInt *leaf_faces;
1207: const PetscSFNode *firemote;
1208: PetscSFNode *isoperiodic_leaves;
1210: PetscCall(PetscMalloc1(num_periodic, &leaf_faces));
1211: PetscCall(PetscSFBcastBegin(centroidsf, MPIU_INT, donor_faces, leaf_faces, MPI_REPLACE));
1212: PetscCall(PetscSFBcastEnd(centroidsf, MPIU_INT, donor_faces, leaf_faces, MPI_REPLACE));
1214: PetscCall(PetscMalloc1(num_periodic, &isoperiodic_leaves));
1215: PetscCall(PetscSFGetGraph(centroidsf, NULL, NULL, NULL, &firemote));
1216: for (PetscInt l = 0; l < num_periodic; ++l) {
1217: isoperiodic_leaves[l].index = leaf_faces[l];
1218: isoperiodic_leaves[l].rank = firemote[l].rank;
1219: }
1221: PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
1222: PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)dm), &periodicsfs[periodic_sf_index]));
1223: PetscCall(PetscSFSetGraph(periodicsfs[periodic_sf_index], pEnd - pStart, num_periodic, (PetscInt *)periodic_faces, PETSC_COPY_VALUES, isoperiodic_leaves, PETSC_OWN_POINTER));
1224: PetscCall(PetscSFViewFromOptions(periodicsfs[periodic_sf_index], NULL, "-dm_plex_box_label_periodic_sf_view"));
1225: PetscCall(PetscFree(leaf_faces));
1226: }
1228: transform[periodic_sf_index][0][0] = 1;
1229: transform[periodic_sf_index][1][1] = 1;
1230: transform[periodic_sf_index][2][2] = 1;
1231: transform[periodic_sf_index][3][3] = 1;
1232: transform[periodic_sf_index][d][3] = donor_to_periodic_distance;
1234: periodic_sf_index++;
1235: PetscCall(PetscSFDestroy(¢roidsf));
1236: if (donor_is) {
1237: PetscCall(ISRestoreIndices(donor_is, &donor_faces));
1238: PetscCall(ISDestroy(&donor_is));
1239: }
1240: if (periodic_is) {
1241: PetscCall(ISRestoreIndices(periodic_is, &periodic_faces));
1242: PetscCall(ISDestroy(&periodic_is));
1243: }
1244: PetscCall(DMClearLabelStratum(dm, "Face Sets", face_pairings[dim - 2][d][0]));
1245: PetscCall(DMClearLabelStratum(dm, "Face Sets", face_pairings[dim - 2][d][1]));
1246: }
1247: PetscCall(DMPlexSetIsoperiodicFaceSF(dm, periodic_sf_index, periodicsfs));
1248: PetscCall(DMPlexSetIsoperiodicFaceTransform(dm, periodic_sf_index, (const PetscScalar *)transform));
1249: for (PetscInt p = 0; p < periodic_sf_index; p++) PetscCall(PetscSFDestroy(&periodicsfs[p]));
1251: { // Update coordinate DM with new Face Sets label
1252: DM cdm;
1253: DMLabel oldFaceSets, newFaceSets;
1254: PetscCall(DMGetCoordinateDM(dm, &cdm));
1255: PetscCall(DMGetLabel(cdm, "Face Sets", &oldFaceSets));
1256: if (oldFaceSets) PetscCall(DMRemoveLabelBySelf(cdm, &oldFaceSets, PETSC_FALSE));
1257: PetscCall(DMLabelDuplicate(label, &newFaceSets));
1258: PetscCall(DMAddLabel(cdm, newFaceSets));
1259: PetscCall(DMLabelDestroy(&newFaceSets));
1260: }
1261: PetscFunctionReturn(PETSC_SUCCESS);
1262: }
1264: static PetscErrorCode DMPlexCreateSquareMesh_Simplex_CrissCross(DM dm, const PetscInt edges[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType bd[])
1265: {
1266: PetscInt markerTop = 1, faceMarkerTop = 3;
1267: PetscInt markerBottom = 1, faceMarkerBottom = 1;
1268: PetscInt markerRight = 1, faceMarkerRight = 2;
1269: PetscInt markerLeft = 1, faceMarkerLeft = 4;
1270: PetscBool markerSeparate = PETSC_FALSE;
1271: DMBoundaryType bdX = bd[0], bdY = bd[1];
1272: PetscMPIInt rank;
1274: PetscFunctionBegin;
1275: PetscCheck(bdX == DM_BOUNDARY_NONE || bdX == DM_BOUNDARY_PERIODIC, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Not implemented for boundary type %s", DMBoundaryTypes[bdX]);
1276: PetscCheck(bdY == DM_BOUNDARY_NONE || bdY == DM_BOUNDARY_PERIODIC, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Not implemented for boundary type %s", DMBoundaryTypes[bdY]);
1277: PetscCall(DMSetDimension(dm, 2));
1278: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
1279: PetscCall(DMCreateLabel(dm, "marker"));
1280: PetscCall(DMCreateLabel(dm, "Face Sets"));
1281: PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL));
1282: if (markerSeparate) {
1283: markerBottom = faceMarkerBottom;
1284: markerTop = faceMarkerTop;
1285: markerRight = faceMarkerRight;
1286: markerLeft = faceMarkerLeft;
1287: }
1288: {
1289: const PetscInt numXEdges = rank == 0 ? edges[0] : 0;
1290: const PetscInt numYEdges = rank == 0 ? edges[1] : 0;
1291: const PetscInt numZEdges = rank == 0 ? 4 * edges[0] * edges[1] : 0; /* Z-edges are the 4 internal edges per cell */
1292: const PetscInt numXVertices = rank == 0 ? (bdX == DM_BOUNDARY_PERIODIC ? edges[0] : edges[0] + 1) : 0;
1293: const PetscInt numYVertices = rank == 0 ? (bdY == DM_BOUNDARY_PERIODIC ? edges[1] : edges[1] + 1) : 0;
1294: const PetscInt numZVertices = rank == 0 ? edges[0] * edges[1] : 0;
1295: const PetscInt numCells = 4 * numXEdges * numYEdges;
1296: const PetscInt numTotXEdges = numXEdges * numYVertices;
1297: const PetscInt numTotYEdges = numYEdges * numXVertices;
1298: const PetscInt numVertices = numXVertices * numYVertices + numZVertices;
1299: const PetscInt numEdges = numTotXEdges + numTotYEdges + numZEdges;
1300: const PetscInt firstVertex = numCells;
1301: const PetscInt firstXEdge = numCells + numVertices;
1302: const PetscInt firstYEdge = firstXEdge + numTotXEdges;
1303: const PetscInt firstZEdge = firstYEdge + numTotYEdges;
1304: Vec coordinates;
1305: PetscSection coordSection;
1306: PetscScalar *coords;
1307: PetscInt coordSize;
1308: PetscInt v, vx, vy;
1309: PetscInt c, e, ex, ey;
1311: PetscCall(DMPlexSetChart(dm, 0, numCells + numEdges + numVertices));
1312: for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 3));
1313: for (e = firstXEdge; e < firstXEdge + numEdges; ++e) PetscCall(DMPlexSetConeSize(dm, e, 2));
1314: PetscCall(DMSetUp(dm));
1316: /* Build cells and Z-edges */
1317: for (ey = 0; ey < numYEdges; ++ey) {
1318: for (ex = 0; ex < numXEdges; ++ex) {
1319: const PetscInt exp1 = (ex + 1) % numXVertices;
1320: const PetscInt eyp1 = (ey + 1) % numYVertices;
1321: const PetscInt ez = firstZEdge + 4 * (ey * numXEdges + ex);
1322: const PetscInt vc = firstVertex + numXVertices * numYVertices + ey * numXEdges + ex;
1323: const PetscInt v0 = firstVertex + ey * numXVertices + ex;
1324: const PetscInt v1 = firstVertex + ey * numXVertices + exp1;
1325: const PetscInt v2 = firstVertex + eyp1 * numXVertices + exp1;
1326: const PetscInt v3 = firstVertex + eyp1 * numXVertices + ex;
1327: const PetscInt e0 = firstXEdge + ey * numXEdges + ex;
1328: const PetscInt e1 = firstYEdge + exp1 * numYEdges + ey;
1329: const PetscInt e2 = firstXEdge + eyp1 * numXEdges + ex;
1330: const PetscInt e3 = firstYEdge + ex * numYEdges + ey;
1332: const PetscInt cones[] = {ez, e0, ez + 1, ez + 1, e1, ez + 2, ez + 2, e2, ez + 3, ez + 3, e3, ez};
1333: const PetscInt ornts[] = {-1, 0, 0, -1, 0, 0, -1, -1, 0, -1, -1, 0};
1334: const PetscInt verts[] = {v0, vc, v1, vc, v2, vc, v3, vc};
1336: for (c = 0; c < 4; c++) {
1337: PetscInt cell = 4 * (ey * numXEdges + ex) + c;
1338: PetscInt edge = ez + c;
1340: PetscCall(DMPlexSetCone(dm, cell, cones + 3 * c));
1341: PetscCall(DMPlexSetConeOrientation(dm, cell, ornts + 3 * c));
1342: PetscCall(DMPlexSetCone(dm, edge, verts + 2 * c));
1343: }
1344: }
1345: }
1347: /* Build Y edges*/
1348: for (vx = 0; vx < numXVertices; vx++) {
1349: for (ey = 0; ey < numYEdges; ey++) {
1350: const PetscInt edge = firstYEdge + vx * numYEdges + ey;
1351: const PetscInt v0 = firstVertex + ey * numXVertices + vx;
1352: const PetscInt v1 = firstVertex + ((ey + 1) % numYVertices) * numXVertices + vx;
1353: const PetscInt cone[] = {v0, v1};
1355: PetscCall(DMPlexSetCone(dm, edge, cone));
1356: if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) {
1357: if (vx == numXVertices - 1) {
1358: PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight));
1359: PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight));
1360: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight));
1361: if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight));
1362: } else if (vx == 0) {
1363: PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft));
1364: PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft));
1365: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft));
1366: if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft));
1367: }
1368: }
1369: }
1370: }
1372: /* Build X edges*/
1373: for (vy = 0; vy < numYVertices; vy++) {
1374: for (ex = 0; ex < numXEdges; ex++) {
1375: const PetscInt edge = firstXEdge + vy * numXEdges + ex;
1376: const PetscInt v0 = firstVertex + vy * numXVertices + ex;
1377: const PetscInt v1 = firstVertex + vy * numXVertices + (ex + 1) % numXVertices;
1378: const PetscInt cone[] = {v0, v1};
1380: PetscCall(DMPlexSetCone(dm, edge, cone));
1381: if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) {
1382: if (vy == numYVertices - 1) {
1383: PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop));
1384: PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop));
1385: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop));
1386: if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop));
1387: } else if (vy == 0) {
1388: PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom));
1389: PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom));
1390: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom));
1391: if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom));
1392: }
1393: }
1394: }
1395: }
1397: /* Compute support, stratify, and celltype label */
1398: PetscCall(DMPlexSymmetrize(dm));
1399: PetscCall(DMPlexStratify(dm));
1400: PetscCall(DMPlexComputeCellTypes(dm));
1402: /* Build coordinates */
1403: PetscCall(DMGetCoordinateSection(dm, &coordSection));
1404: PetscCall(PetscSectionSetNumFields(coordSection, 1));
1405: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, 2));
1406: PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex + numVertices));
1407: for (v = firstVertex; v < firstVertex + numVertices; ++v) {
1408: PetscCall(PetscSectionSetDof(coordSection, v, 2));
1409: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, 2));
1410: }
1411: PetscCall(PetscSectionSetUp(coordSection));
1412: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
1413: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
1414: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
1415: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
1416: PetscCall(VecSetBlockSize(coordinates, 2));
1417: PetscCall(VecSetType(coordinates, VECSTANDARD));
1418: PetscCall(VecGetArray(coordinates, &coords));
1419: for (vy = 0; vy < numYVertices; ++vy) {
1420: for (vx = 0; vx < numXVertices; ++vx) {
1421: coords[2 * (vy * numXVertices + vx) + 0] = lower[0] + ((upper[0] - lower[0]) / numXEdges) * vx;
1422: coords[2 * (vy * numXVertices + vx) + 1] = lower[1] + ((upper[1] - lower[1]) / numYEdges) * vy;
1423: }
1424: }
1425: for (ey = 0; ey < numYEdges; ++ey) {
1426: for (ex = 0; ex < numXEdges; ++ex) {
1427: const PetscInt c = ey * numXEdges + ex + numYVertices * numXVertices;
1429: coords[2 * c + 0] = lower[0] + ((upper[0] - lower[0]) / numXEdges) * (ex + 0.5);
1430: coords[2 * c + 1] = lower[1] + ((upper[1] - lower[1]) / numYEdges) * (ey + 0.5);
1431: }
1432: }
1433: PetscCall(VecRestoreArray(coordinates, &coords));
1434: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
1435: PetscCall(VecDestroy(&coordinates));
1437: /* handle periodic BC */
1438: if (bdX == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_PERIODIC) {
1439: PetscReal L[2] = {-1., -1.};
1440: PetscReal maxCell[2] = {-1., -1.};
1442: for (PetscInt d = 0; d < 2; ++d) {
1443: if (bd[d] != DM_BOUNDARY_NONE) {
1444: L[d] = upper[d] - lower[d];
1445: maxCell[d] = 1.1 * (L[d] / PetscMax(1, edges[d]));
1446: }
1447: }
1448: PetscCall(DMSetPeriodicity(dm, maxCell, lower, L));
1449: }
1450: }
1451: PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE));
1452: PetscFunctionReturn(PETSC_SUCCESS);
1453: }
1455: static PetscErrorCode DMPlexCreateBoxMesh_Simplex_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate)
1456: {
1457: DM boundary, vol;
1458: DMLabel bdlabel;
1459: PetscBool crisscross = PETSC_FALSE;
1461: PetscFunctionBegin;
1462: PetscAssertPointer(dm, 1);
1463: if (dim == 2) PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_box_crisscross", &crisscross, NULL));
1464: if (crisscross) {
1465: PetscCall(DMPlexCreateSquareMesh_Simplex_CrissCross(dm, faces, lower, upper, periodicity));
1466: } else {
1467: for (PetscInt i = 0; i < dim; ++i) PetscCheck(periodicity[i] == DM_BOUNDARY_NONE, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Periodicity is not supported for simplex meshes");
1468: PetscCall(DMCreate(PetscObjectComm((PetscObject)dm), &boundary));
1469: PetscCall(DMSetType(boundary, DMPLEX));
1470: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)boundary, ((PetscObject)dm)->prefix));
1471: PetscCall(DMPlexCreateBoxSurfaceMesh_Internal(boundary, dim, faces, lower, upper, PETSC_FALSE));
1472: PetscCall(DMPlexGenerate(boundary, NULL, interpolate, &vol));
1473: PetscCall(DMGetLabel(vol, "marker", &bdlabel));
1474: if (bdlabel) PetscCall(DMPlexLabelComplete(vol, bdlabel));
1475: PetscCall(DMPlexCopy_Internal(dm, PETSC_TRUE, PETSC_FALSE, vol));
1476: PetscCall(DMPlexReplace_Internal(dm, &vol));
1477: PetscCall(DMDestroy(&boundary));
1478: }
1479: if (interpolate) {
1480: PetscCall(DMPlexInterpolateInPlace_Internal(dm));
1481: PetscCall(DMPlexSetBoxLabel_Internal(dm, periodicity));
1482: }
1483: PetscFunctionReturn(PETSC_SUCCESS);
1484: }
1486: static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ)
1487: {
1488: DMLabel cutLabel = NULL;
1489: PetscInt markerTop = 1, faceMarkerTop = 1;
1490: PetscInt markerBottom = 1, faceMarkerBottom = 1;
1491: PetscInt markerFront = 1, faceMarkerFront = 1;
1492: PetscInt markerBack = 1, faceMarkerBack = 1;
1493: PetscInt markerRight = 1, faceMarkerRight = 1;
1494: PetscInt markerLeft = 1, faceMarkerLeft = 1;
1495: PetscInt dim;
1496: PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE;
1497: PetscMPIInt rank;
1499: PetscFunctionBegin;
1500: PetscCall(DMGetDimension(dm, &dim));
1501: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
1502: PetscCall(DMCreateLabel(dm, "marker"));
1503: PetscCall(DMCreateLabel(dm, "Face Sets"));
1504: PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL));
1505: if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST || bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST || bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) {
1506: if (cutMarker) {
1507: PetscCall(DMCreateLabel(dm, "periodic_cut"));
1508: PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
1509: }
1510: }
1511: switch (dim) {
1512: case 2:
1513: faceMarkerTop = 3;
1514: faceMarkerBottom = 1;
1515: faceMarkerRight = 2;
1516: faceMarkerLeft = 4;
1517: break;
1518: case 3:
1519: faceMarkerBottom = 1;
1520: faceMarkerTop = 2;
1521: faceMarkerFront = 3;
1522: faceMarkerBack = 4;
1523: faceMarkerRight = 5;
1524: faceMarkerLeft = 6;
1525: break;
1526: default:
1527: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Dimension %" PetscInt_FMT " not supported", dim);
1528: }
1529: PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL));
1530: if (markerSeparate) {
1531: markerBottom = faceMarkerBottom;
1532: markerTop = faceMarkerTop;
1533: markerFront = faceMarkerFront;
1534: markerBack = faceMarkerBack;
1535: markerRight = faceMarkerRight;
1536: markerLeft = faceMarkerLeft;
1537: }
1538: {
1539: const PetscInt numXEdges = rank == 0 ? edges[0] : 0;
1540: const PetscInt numYEdges = rank == 0 ? edges[1] : 0;
1541: const PetscInt numZEdges = rank == 0 ? edges[2] : 0;
1542: const PetscInt numXVertices = rank == 0 ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0] + 1) : 0;
1543: const PetscInt numYVertices = rank == 0 ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1] + 1) : 0;
1544: const PetscInt numZVertices = rank == 0 ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2] + 1) : 0;
1545: const PetscInt numCells = numXEdges * numYEdges * numZEdges;
1546: const PetscInt numXFaces = numYEdges * numZEdges;
1547: const PetscInt numYFaces = numXEdges * numZEdges;
1548: const PetscInt numZFaces = numXEdges * numYEdges;
1549: const PetscInt numTotXFaces = numXVertices * numXFaces;
1550: const PetscInt numTotYFaces = numYVertices * numYFaces;
1551: const PetscInt numTotZFaces = numZVertices * numZFaces;
1552: const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces;
1553: const PetscInt numTotXEdges = numXEdges * numYVertices * numZVertices;
1554: const PetscInt numTotYEdges = numYEdges * numXVertices * numZVertices;
1555: const PetscInt numTotZEdges = numZEdges * numXVertices * numYVertices;
1556: const PetscInt numVertices = numXVertices * numYVertices * numZVertices;
1557: const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges;
1558: const PetscInt firstVertex = (dim == 2) ? numFaces : numCells;
1559: const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices;
1560: const PetscInt firstYFace = firstXFace + numTotXFaces;
1561: const PetscInt firstZFace = firstYFace + numTotYFaces;
1562: const PetscInt firstXEdge = numCells + numFaces + numVertices;
1563: const PetscInt firstYEdge = firstXEdge + numTotXEdges;
1564: const PetscInt firstZEdge = firstYEdge + numTotYEdges;
1565: Vec coordinates;
1566: PetscSection coordSection;
1567: PetscScalar *coords;
1568: PetscInt coordSize;
1569: PetscInt v, vx, vy, vz;
1570: PetscInt c, f, fx, fy, fz, e, ex, ey, ez;
1572: PetscCall(DMPlexSetChart(dm, 0, numCells + numFaces + numEdges + numVertices));
1573: for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 6));
1574: for (f = firstXFace; f < firstXFace + numFaces; ++f) PetscCall(DMPlexSetConeSize(dm, f, 4));
1575: for (e = firstXEdge; e < firstXEdge + numEdges; ++e) PetscCall(DMPlexSetConeSize(dm, e, 2));
1576: PetscCall(DMSetUp(dm)); /* Allocate space for cones */
1577: /* Build cells */
1578: for (fz = 0; fz < numZEdges; ++fz) {
1579: for (fy = 0; fy < numYEdges; ++fy) {
1580: for (fx = 0; fx < numXEdges; ++fx) {
1581: PetscInt cell = (fz * numYEdges + fy) * numXEdges + fx;
1582: PetscInt faceB = firstZFace + (fy * numXEdges + fx) * numZVertices + fz;
1583: PetscInt faceT = firstZFace + (fy * numXEdges + fx) * numZVertices + ((fz + 1) % numZVertices);
1584: PetscInt faceF = firstYFace + (fz * numXEdges + fx) * numYVertices + fy;
1585: PetscInt faceK = firstYFace + (fz * numXEdges + fx) * numYVertices + ((fy + 1) % numYVertices);
1586: PetscInt faceL = firstXFace + (fz * numYEdges + fy) * numXVertices + fx;
1587: PetscInt faceR = firstXFace + (fz * numYEdges + fy) * numXVertices + ((fx + 1) % numXVertices);
1588: /* B, T, F, K, R, L */
1589: PetscInt ornt[6] = {-2, 0, 0, -3, 0, -2}; /* ??? */
1590: PetscInt cone[6];
1592: /* no boundary twisting in 3D */
1593: cone[0] = faceB;
1594: cone[1] = faceT;
1595: cone[2] = faceF;
1596: cone[3] = faceK;
1597: cone[4] = faceR;
1598: cone[5] = faceL;
1599: PetscCall(DMPlexSetCone(dm, cell, cone));
1600: PetscCall(DMPlexSetConeOrientation(dm, cell, ornt));
1601: if (bdX != DM_BOUNDARY_NONE && fx == numXEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, cell, 2));
1602: if (bdY != DM_BOUNDARY_NONE && fy == numYEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, cell, 2));
1603: if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, cell, 2));
1604: }
1605: }
1606: }
1607: /* Build x faces */
1608: for (fz = 0; fz < numZEdges; ++fz) {
1609: for (fy = 0; fy < numYEdges; ++fy) {
1610: for (fx = 0; fx < numXVertices; ++fx) {
1611: PetscInt face = firstXFace + (fz * numYEdges + fy) * numXVertices + fx;
1612: PetscInt edgeL = firstZEdge + (fy * numXVertices + fx) * numZEdges + fz;
1613: PetscInt edgeR = firstZEdge + (((fy + 1) % numYVertices) * numXVertices + fx) * numZEdges + fz;
1614: PetscInt edgeB = firstYEdge + (fz * numXVertices + fx) * numYEdges + fy;
1615: PetscInt edgeT = firstYEdge + (((fz + 1) % numZVertices) * numXVertices + fx) * numYEdges + fy;
1616: PetscInt ornt[4] = {0, 0, -1, -1};
1617: PetscInt cone[4];
1619: if (dim == 3) {
1620: /* markers */
1621: if (bdX != DM_BOUNDARY_PERIODIC) {
1622: if (fx == numXVertices - 1) {
1623: PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight));
1624: PetscCall(DMSetLabelValue(dm, "marker", face, markerRight));
1625: } else if (fx == 0) {
1626: PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft));
1627: PetscCall(DMSetLabelValue(dm, "marker", face, markerLeft));
1628: }
1629: }
1630: }
1631: cone[0] = edgeB;
1632: cone[1] = edgeR;
1633: cone[2] = edgeT;
1634: cone[3] = edgeL;
1635: PetscCall(DMPlexSetCone(dm, face, cone));
1636: PetscCall(DMPlexSetConeOrientation(dm, face, ornt));
1637: }
1638: }
1639: }
1640: /* Build y faces */
1641: for (fz = 0; fz < numZEdges; ++fz) {
1642: for (fx = 0; fx < numXEdges; ++fx) {
1643: for (fy = 0; fy < numYVertices; ++fy) {
1644: PetscInt face = firstYFace + (fz * numXEdges + fx) * numYVertices + fy;
1645: PetscInt edgeL = firstZEdge + (fy * numXVertices + fx) * numZEdges + fz;
1646: PetscInt edgeR = firstZEdge + (fy * numXVertices + ((fx + 1) % numXVertices)) * numZEdges + fz;
1647: PetscInt edgeB = firstXEdge + (fz * numYVertices + fy) * numXEdges + fx;
1648: PetscInt edgeT = firstXEdge + (((fz + 1) % numZVertices) * numYVertices + fy) * numXEdges + fx;
1649: PetscInt ornt[4] = {0, 0, -1, -1};
1650: PetscInt cone[4];
1652: if (dim == 3) {
1653: /* markers */
1654: if (bdY != DM_BOUNDARY_PERIODIC) {
1655: if (fy == numYVertices - 1) {
1656: PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack));
1657: PetscCall(DMSetLabelValue(dm, "marker", face, markerBack));
1658: } else if (fy == 0) {
1659: PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront));
1660: PetscCall(DMSetLabelValue(dm, "marker", face, markerFront));
1661: }
1662: }
1663: }
1664: cone[0] = edgeB;
1665: cone[1] = edgeR;
1666: cone[2] = edgeT;
1667: cone[3] = edgeL;
1668: PetscCall(DMPlexSetCone(dm, face, cone));
1669: PetscCall(DMPlexSetConeOrientation(dm, face, ornt));
1670: }
1671: }
1672: }
1673: /* Build z faces */
1674: for (fy = 0; fy < numYEdges; ++fy) {
1675: for (fx = 0; fx < numXEdges; ++fx) {
1676: for (fz = 0; fz < numZVertices; fz++) {
1677: PetscInt face = firstZFace + (fy * numXEdges + fx) * numZVertices + fz;
1678: PetscInt edgeL = firstYEdge + (fz * numXVertices + fx) * numYEdges + fy;
1679: PetscInt edgeR = firstYEdge + (fz * numXVertices + ((fx + 1) % numXVertices)) * numYEdges + fy;
1680: PetscInt edgeB = firstXEdge + (fz * numYVertices + fy) * numXEdges + fx;
1681: PetscInt edgeT = firstXEdge + (fz * numYVertices + ((fy + 1) % numYVertices)) * numXEdges + fx;
1682: PetscInt ornt[4] = {0, 0, -1, -1};
1683: PetscInt cone[4];
1685: if (dim == 2) {
1686: if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges - 1) {
1687: edgeR += numYEdges - 1 - 2 * fy;
1688: ornt[1] = -1;
1689: }
1690: if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges - 1) {
1691: edgeT += numXEdges - 1 - 2 * fx;
1692: ornt[2] = 0;
1693: }
1694: if (bdX != DM_BOUNDARY_NONE && fx == numXEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, face, 2));
1695: if (bdY != DM_BOUNDARY_NONE && fy == numYEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, face, 2));
1696: } else {
1697: /* markers */
1698: if (bdZ != DM_BOUNDARY_PERIODIC) {
1699: if (fz == numZVertices - 1) {
1700: PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop));
1701: PetscCall(DMSetLabelValue(dm, "marker", face, markerTop));
1702: } else if (fz == 0) {
1703: PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom));
1704: PetscCall(DMSetLabelValue(dm, "marker", face, markerBottom));
1705: }
1706: }
1707: }
1708: cone[0] = edgeB;
1709: cone[1] = edgeR;
1710: cone[2] = edgeT;
1711: cone[3] = edgeL;
1712: PetscCall(DMPlexSetCone(dm, face, cone));
1713: PetscCall(DMPlexSetConeOrientation(dm, face, ornt));
1714: }
1715: }
1716: }
1717: /* Build Z edges*/
1718: for (vy = 0; vy < numYVertices; vy++) {
1719: for (vx = 0; vx < numXVertices; vx++) {
1720: for (ez = 0; ez < numZEdges; ez++) {
1721: const PetscInt edge = firstZEdge + (vy * numXVertices + vx) * numZEdges + ez;
1722: const PetscInt vertexB = firstVertex + (ez * numYVertices + vy) * numXVertices + vx;
1723: const PetscInt vertexT = firstVertex + (((ez + 1) % numZVertices) * numYVertices + vy) * numXVertices + vx;
1724: PetscInt cone[2];
1726: cone[0] = vertexB;
1727: cone[1] = vertexT;
1728: PetscCall(DMPlexSetCone(dm, edge, cone));
1729: if (dim == 3) {
1730: if (bdX != DM_BOUNDARY_PERIODIC) {
1731: if (vx == numXVertices - 1) {
1732: PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight));
1733: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight));
1734: if (ez == numZEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight));
1735: } else if (vx == 0) {
1736: PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft));
1737: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft));
1738: if (ez == numZEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft));
1739: }
1740: }
1741: if (bdY != DM_BOUNDARY_PERIODIC) {
1742: if (vy == numYVertices - 1) {
1743: PetscCall(DMSetLabelValue(dm, "marker", edge, markerBack));
1744: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBack));
1745: if (ez == numZEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBack));
1746: } else if (vy == 0) {
1747: PetscCall(DMSetLabelValue(dm, "marker", edge, markerFront));
1748: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerFront));
1749: if (ez == numZEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerFront));
1750: }
1751: }
1752: }
1753: }
1754: }
1755: }
1756: /* Build Y edges*/
1757: for (vz = 0; vz < numZVertices; vz++) {
1758: for (vx = 0; vx < numXVertices; vx++) {
1759: for (ey = 0; ey < numYEdges; ey++) {
1760: const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges - 1) ? (numXVertices - vx - 1) : (vz * numYVertices + ((ey + 1) % numYVertices)) * numXVertices + vx;
1761: const PetscInt edge = firstYEdge + (vz * numXVertices + vx) * numYEdges + ey;
1762: const PetscInt vertexF = firstVertex + (vz * numYVertices + ey) * numXVertices + vx;
1763: const PetscInt vertexK = firstVertex + nextv;
1764: PetscInt cone[2];
1766: cone[0] = vertexF;
1767: cone[1] = vertexK;
1768: PetscCall(DMPlexSetCone(dm, edge, cone));
1769: if (dim == 2) {
1770: if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) {
1771: if (vx == numXVertices - 1) {
1772: PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight));
1773: PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight));
1774: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight));
1775: if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight));
1776: } else if (vx == 0) {
1777: PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft));
1778: PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft));
1779: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft));
1780: if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft));
1781: }
1782: } else {
1783: if (vx == 0 && cutLabel) {
1784: PetscCall(DMLabelSetValue(cutLabel, edge, 1));
1785: PetscCall(DMLabelSetValue(cutLabel, cone[0], 1));
1786: if (ey == numYEdges - 1) PetscCall(DMLabelSetValue(cutLabel, cone[1], 1));
1787: }
1788: }
1789: } else {
1790: if (bdX != DM_BOUNDARY_PERIODIC) {
1791: if (vx == numXVertices - 1) {
1792: PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight));
1793: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight));
1794: if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight));
1795: } else if (vx == 0) {
1796: PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft));
1797: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft));
1798: if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft));
1799: }
1800: }
1801: if (bdZ != DM_BOUNDARY_PERIODIC) {
1802: if (vz == numZVertices - 1) {
1803: PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop));
1804: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop));
1805: if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop));
1806: } else if (vz == 0) {
1807: PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom));
1808: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom));
1809: if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom));
1810: }
1811: }
1812: }
1813: }
1814: }
1815: }
1816: /* Build X edges*/
1817: for (vz = 0; vz < numZVertices; vz++) {
1818: for (vy = 0; vy < numYVertices; vy++) {
1819: for (ex = 0; ex < numXEdges; ex++) {
1820: const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges - 1) ? (numYVertices - vy - 1) * numXVertices : (vz * numYVertices + vy) * numXVertices + (ex + 1) % numXVertices;
1821: const PetscInt edge = firstXEdge + (vz * numYVertices + vy) * numXEdges + ex;
1822: const PetscInt vertexL = firstVertex + (vz * numYVertices + vy) * numXVertices + ex;
1823: const PetscInt vertexR = firstVertex + nextv;
1824: PetscInt cone[2];
1826: cone[0] = vertexL;
1827: cone[1] = vertexR;
1828: PetscCall(DMPlexSetCone(dm, edge, cone));
1829: if (dim == 2) {
1830: if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) {
1831: if (vy == numYVertices - 1) {
1832: PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop));
1833: PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop));
1834: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop));
1835: if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop));
1836: } else if (vy == 0) {
1837: PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom));
1838: PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom));
1839: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom));
1840: if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom));
1841: }
1842: } else {
1843: if (vy == 0 && cutLabel) {
1844: PetscCall(DMLabelSetValue(cutLabel, edge, 1));
1845: PetscCall(DMLabelSetValue(cutLabel, cone[0], 1));
1846: if (ex == numXEdges - 1) PetscCall(DMLabelSetValue(cutLabel, cone[1], 1));
1847: }
1848: }
1849: } else {
1850: if (bdY != DM_BOUNDARY_PERIODIC) {
1851: if (vy == numYVertices - 1) {
1852: PetscCall(DMSetLabelValue(dm, "marker", edge, markerBack));
1853: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBack));
1854: if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBack));
1855: } else if (vy == 0) {
1856: PetscCall(DMSetLabelValue(dm, "marker", edge, markerFront));
1857: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerFront));
1858: if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerFront));
1859: }
1860: }
1861: if (bdZ != DM_BOUNDARY_PERIODIC) {
1862: if (vz == numZVertices - 1) {
1863: PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop));
1864: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop));
1865: if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop));
1866: } else if (vz == 0) {
1867: PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom));
1868: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom));
1869: if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom));
1870: }
1871: }
1872: }
1873: }
1874: }
1875: }
1876: PetscCall(DMPlexSymmetrize(dm));
1877: PetscCall(DMPlexStratify(dm));
1878: /* Build coordinates */
1879: PetscCall(DMGetCoordinateSection(dm, &coordSection));
1880: PetscCall(PetscSectionSetNumFields(coordSection, 1));
1881: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim));
1882: PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex + numVertices));
1883: for (v = firstVertex; v < firstVertex + numVertices; ++v) {
1884: PetscCall(PetscSectionSetDof(coordSection, v, dim));
1885: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim));
1886: }
1887: PetscCall(PetscSectionSetUp(coordSection));
1888: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
1889: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
1890: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
1891: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
1892: PetscCall(VecSetBlockSize(coordinates, dim));
1893: PetscCall(VecSetType(coordinates, VECSTANDARD));
1894: PetscCall(VecGetArray(coordinates, &coords));
1895: for (vz = 0; vz < numZVertices; ++vz) {
1896: for (vy = 0; vy < numYVertices; ++vy) {
1897: for (vx = 0; vx < numXVertices; ++vx) {
1898: coords[((vz * numYVertices + vy) * numXVertices + vx) * dim + 0] = lower[0] + ((upper[0] - lower[0]) / numXEdges) * vx;
1899: coords[((vz * numYVertices + vy) * numXVertices + vx) * dim + 1] = lower[1] + ((upper[1] - lower[1]) / numYEdges) * vy;
1900: if (dim == 3) coords[((vz * numYVertices + vy) * numXVertices + vx) * dim + 2] = lower[2] + ((upper[2] - lower[2]) / numZEdges) * vz;
1901: }
1902: }
1903: }
1904: PetscCall(VecRestoreArray(coordinates, &coords));
1905: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
1906: PetscCall(VecDestroy(&coordinates));
1907: }
1908: PetscFunctionReturn(PETSC_SUCCESS);
1909: }
1911: static PetscErrorCode DMPlexCreateBoxMesh_Tensor_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[])
1912: {
1913: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
1914: PetscInt fac[3] = {0, 0, 0}, d;
1916: PetscFunctionBegin;
1917: PetscAssertPointer(dm, 1);
1919: PetscCall(DMSetDimension(dm, dim));
1920: for (d = 0; d < dim; ++d) {
1921: fac[d] = faces[d];
1922: bdt[d] = periodicity[d];
1923: }
1924: PetscCall(DMPlexCreateCubeMesh_Internal(dm, lower, upper, fac, bdt[0], bdt[1], bdt[2]));
1925: if (periodicity[0] == DM_BOUNDARY_PERIODIC || periodicity[0] == DM_BOUNDARY_TWIST || periodicity[1] == DM_BOUNDARY_PERIODIC || periodicity[1] == DM_BOUNDARY_TWIST || (dim > 2 && (periodicity[2] == DM_BOUNDARY_PERIODIC || periodicity[2] == DM_BOUNDARY_TWIST))) {
1926: PetscReal L[3] = {-1., -1., 0.};
1927: PetscReal maxCell[3] = {-1., -1., 0.};
1929: for (d = 0; d < dim; ++d) {
1930: if (periodicity[d] != DM_BOUNDARY_NONE) {
1931: L[d] = upper[d] - lower[d];
1932: maxCell[d] = 1.1 * (L[d] / PetscMax(1, faces[d]));
1933: }
1934: }
1935: PetscCall(DMSetPeriodicity(dm, maxCell, lower, L));
1936: }
1937: PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE));
1938: PetscFunctionReturn(PETSC_SUCCESS);
1939: }
1941: static PetscErrorCode DMPlexCreateBoxMesh_Internal(DM dm, DMPlexShape shape, PetscInt dim, PetscBool simplex, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate)
1942: {
1943: PetscFunctionBegin;
1944: PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0));
1945: if (shape == DM_SHAPE_ZBOX) PetscCall(DMPlexCreateBoxMesh_Tensor_SFC_Internal(dm, dim, faces, lower, upper, periodicity, interpolate));
1946: else if (dim == 1) PetscCall(DMPlexCreateLineMesh_Internal(dm, faces[0], lower[0], upper[0], periodicity[0]));
1947: else if (simplex) PetscCall(DMPlexCreateBoxMesh_Simplex_Internal(dm, dim, faces, lower, upper, periodicity, interpolate));
1948: else PetscCall(DMPlexCreateBoxMesh_Tensor_Internal(dm, dim, faces, lower, upper, periodicity));
1949: if (!interpolate && dim > 1 && !simplex) {
1950: DM udm;
1952: PetscCall(DMPlexUninterpolate(dm, &udm));
1953: PetscCall(DMPlexCopyCoordinates(dm, udm));
1954: PetscCall(DMPlexReplace_Internal(dm, &udm));
1955: }
1956: PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0));
1957: PetscFunctionReturn(PETSC_SUCCESS);
1958: }
1960: /*@
1961: DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra).
1963: Collective
1965: Input Parameters:
1966: + comm - The communicator for the `DM` object
1967: . dim - The spatial dimension
1968: . simplex - `PETSC_TRUE` for simplices, `PETSC_FALSE` for tensor cells
1969: . faces - Number of faces per dimension, or `NULL` for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D
1970: . lower - The lower left corner, or `NULL` for (0, 0, 0)
1971: . upper - The upper right corner, or `NULL` for (1, 1, 1)
1972: . periodicity - The boundary type for the X,Y,Z direction, or `NULL` for `DM_BOUNDARY_NONE`
1973: . interpolate - Flag to create intermediate mesh pieces (edges, faces)
1974: . localizationHeight - Flag to localize edges and faces in addition to cells; only significant for periodic meshes
1975: - sparseLocalize - Flag to localize coordinates only for cells near the periodic boundary; only significant for periodic meshes
1977: Output Parameter:
1978: . dm - The `DM` object
1980: Level: beginner
1982: Note:
1983: To customize this mesh using options, use
1984: .vb
1985: DMCreate(comm, &dm);
1986: DMSetType(dm, DMPLEX);
1987: DMSetFromOptions(dm);
1988: .ve
1989: and use the options in `DMSetFromOptions()`.
1991: Here is the numbering returned for 2 faces in each direction for tensor cells\:
1992: .vb
1993: 10---17---11---18----12
1994: | | |
1995: | | |
1996: 20 2 22 3 24
1997: | | |
1998: | | |
1999: 7---15----8---16----9
2000: | | |
2001: | | |
2002: 19 0 21 1 23
2003: | | |
2004: | | |
2005: 4---13----5---14----6
2006: .ve
2007: and for simplicial cells
2008: .vb
2009: 14----8---15----9----16
2010: |\ 5 |\ 7 |
2011: | \ | \ |
2012: 13 2 14 3 15
2013: | 4 \ | 6 \ |
2014: | \ | \ |
2015: 11----6---12----7----13
2016: |\ |\ |
2017: | \ 1 | \ 3 |
2018: 10 0 11 1 12
2019: | 0 \ | 2 \ |
2020: | \ | \ |
2021: 8----4----9----5----10
2022: .ve
2024: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMSetFromOptions()`, `DMPlexCreateFromFile()`, `DMPlexCreateHexCylinderMesh()`, `DMSetType()`, `DMCreate()`
2025: @*/
2026: PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate, PetscInt localizationHeight, PetscBool sparseLocalize, DM *dm)
2027: {
2028: PetscInt fac[3] = {1, 1, 1};
2029: PetscReal low[3] = {0, 0, 0};
2030: PetscReal upp[3] = {1, 1, 1};
2031: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
2033: PetscFunctionBegin;
2034: PetscCall(DMCreate(comm, dm));
2035: PetscCall(DMSetType(*dm, DMPLEX));
2036: PetscCall(DMPlexCreateBoxMesh_Internal(*dm, DM_SHAPE_BOX, dim, simplex, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt, interpolate));
2037: if (periodicity) {
2038: DM cdm;
2040: PetscCall(DMGetCoordinateDM(*dm, &cdm));
2041: PetscCall(DMPlexSetMaxProjectionHeight(cdm, localizationHeight));
2042: PetscCall(DMSetSparseLocalize(*dm, sparseLocalize));
2043: PetscCall(DMLocalizeCoordinates(*dm));
2044: }
2045: PetscFunctionReturn(PETSC_SUCCESS);
2046: }
2048: static PetscErrorCode DMPlexCreateWedgeBoxMesh_Internal(DM dm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[])
2049: {
2050: DM bdm, vol;
2051: PetscInt i;
2053: PetscFunctionBegin;
2054: // TODO Now we can support periodicity
2055: for (i = 0; i < 3; ++i) PetscCheck(periodicity[i] == DM_BOUNDARY_NONE, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Periodicity not yet supported");
2056: PetscCall(DMCreate(PetscObjectComm((PetscObject)dm), &bdm));
2057: PetscCall(DMSetType(bdm, DMPLEX));
2058: PetscCall(DMSetDimension(bdm, 2));
2059: PetscCall(PetscLogEventBegin(DMPLEX_Generate, bdm, 0, 0, 0));
2060: PetscCall(DMPlexCreateBoxMesh_Simplex_Internal(bdm, 2, faces, lower, upper, periodicity, PETSC_TRUE));
2061: PetscCall(DMPlexExtrude(bdm, faces[2], upper[2] - lower[2], PETSC_TRUE, PETSC_FALSE, PETSC_FALSE, NULL, NULL, NULL, &vol));
2062: PetscCall(PetscLogEventEnd(DMPLEX_Generate, bdm, 0, 0, 0));
2063: PetscCall(DMDestroy(&bdm));
2064: PetscCall(DMPlexReplace_Internal(dm, &vol));
2065: if (lower[2] != 0.0) {
2066: Vec v;
2067: PetscScalar *x;
2068: PetscInt cDim, n;
2070: PetscCall(DMGetCoordinatesLocal(dm, &v));
2071: PetscCall(VecGetBlockSize(v, &cDim));
2072: PetscCall(VecGetLocalSize(v, &n));
2073: PetscCall(VecGetArray(v, &x));
2074: x += cDim;
2075: for (i = 0; i < n; i += cDim) x[i] += lower[2];
2076: PetscCall(VecRestoreArray(v, &x));
2077: PetscCall(DMSetCoordinatesLocal(dm, v));
2078: }
2079: PetscFunctionReturn(PETSC_SUCCESS);
2080: }
2082: /*@
2083: DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tessellating the (x,y) plane and extruding in the third direction using wedge cells.
2085: Collective
2087: Input Parameters:
2088: + comm - The communicator for the `DM` object
2089: . faces - Number of faces per dimension, or `NULL` for (1, 1, 1)
2090: . lower - The lower left corner, or `NULL` for (0, 0, 0)
2091: . upper - The upper right corner, or `NULL` for (1, 1, 1)
2092: . periodicity - The boundary type for the X,Y,Z direction, or `NULL` for `DM_BOUNDARY_NONE`
2093: . orderHeight - If `PETSC_TRUE`, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first
2094: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
2096: Output Parameter:
2097: . dm - The `DM` object
2099: Level: beginner
2101: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateHexCylinderMesh()`, `DMPlexCreateWedgeCylinderMesh()`, `DMExtrude()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()`
2102: @*/
2103: PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool orderHeight, PetscBool interpolate, DM *dm)
2104: {
2105: PetscInt fac[3] = {1, 1, 1};
2106: PetscReal low[3] = {0, 0, 0};
2107: PetscReal upp[3] = {1, 1, 1};
2108: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
2110: PetscFunctionBegin;
2111: PetscCall(DMCreate(comm, dm));
2112: PetscCall(DMSetType(*dm, DMPLEX));
2113: PetscCall(DMPlexCreateWedgeBoxMesh_Internal(*dm, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt));
2114: if (!interpolate) {
2115: DM udm;
2117: PetscCall(DMPlexUninterpolate(*dm, &udm));
2118: PetscCall(DMPlexReplace_Internal(*dm, &udm));
2119: }
2120: if (periodicity) PetscCall(DMLocalizeCoordinates(*dm));
2121: PetscFunctionReturn(PETSC_SUCCESS);
2122: }
2124: /*
2125: DMPlexTensorPointLexicographic_Private - Returns all tuples of size 'len' with nonnegative integers that are all less than or equal to 'max' for that dimension.
2127: Input Parameters:
2128: + len - The length of the tuple
2129: . max - The maximum for each dimension, so values are in [0, max)
2130: - tup - A tuple of length len+1: tup[len] > 0 indicates a stopping condition
2132: Output Parameter:
2133: . tup - A tuple of `len` integers whose entries are at most `max`
2135: Level: developer
2137: Note:
2138: Ordering is lexicographic with lowest index as least significant in ordering.
2139: e.g. for len == 2 and max == 2, this will return, in order, {0,0}, {1,0}, {2,0}, {0,1}, {1,1}, {2,1}, {0,2}, {1,2}, {2,2}.
2141: .seealso: PetscDualSpaceTensorPointLexicographic_Internal(), PetscDualSpaceLatticePointLexicographic_Internal()
2142: */
2143: static PetscErrorCode DMPlexTensorPointLexicographic_Private(PetscInt len, const PetscInt max[], PetscInt tup[])
2144: {
2145: PetscInt i;
2147: PetscFunctionBegin;
2148: for (i = 0; i < len; ++i) {
2149: if (tup[i] < max[i] - 1) {
2150: break;
2151: } else {
2152: tup[i] = 0;
2153: }
2154: }
2155: if (i == len) tup[i - 1] = max[i - 1];
2156: else ++tup[i];
2157: PetscFunctionReturn(PETSC_SUCCESS);
2158: }
2160: static PetscInt TupleToIndex_Private(PetscInt len, const PetscInt max[], const PetscInt tup[])
2161: {
2162: PetscInt idx = tup[len - 1];
2164: for (PetscInt i = len - 2; i >= 0; --i) {
2165: idx *= max[i];
2166: idx += tup[i];
2167: }
2168: return idx;
2169: }
2171: static void IndexToTuple_Private(PetscInt len, const PetscInt max[], PetscInt idx, PetscInt tup[])
2172: {
2173: for (PetscInt i = 0; i < len; ++i) {
2174: tup[i] = idx % max[i];
2175: idx = (idx - tup[i]) / max[i];
2176: }
2177: }
2179: static void TupleToRanks_Private(PetscInt len, const PetscInt max[], const PetscInt procs[], const PetscInt tup[], PetscInt ranks[])
2180: {
2181: for (PetscInt i = 0; i < len; ++i) {
2182: const PetscInt div = max[i] / procs[i];
2183: const PetscInt rem = max[i] % procs[i];
2184: const PetscInt idx = (tup[i] < 0 ? max[i] + tup[i] : tup[i]) % max[i];
2186: if (idx < rem * (div + 1)) ranks[i] = idx / (div + 1);
2187: else ranks[i] = rem + (idx - rem * (div + 1)) / div;
2188: }
2189: }
2191: static void RanksToSizes_Private(PetscInt len, const PetscInt max[], const PetscInt procs[], const PetscInt ranks[], PetscInt sizes[])
2192: {
2193: for (PetscInt i = 0; i < len; ++i) {
2194: const PetscInt div = max[i] / procs[i];
2195: const PetscInt rem = max[i] % procs[i];
2197: sizes[i] = ranks[i] < rem ? div + 1 : div;
2198: }
2199: }
2201: /*
2202: In serial, the mesh is completely periodic. In parallel, we will include a layer of ghost vertices around the patch, so our edges will not wrap around in parallel. This will instead be handled by the SF.
2204: The cone for all edges will always be complete. Even in the presence of boundaries, we will keep all support sizes constant. When an edge would not exist in the support, we will create one to wrap back periodically. This allows for uniform stencils, and that edge will not be used for computation.
2206: All point which do not attain the vertex lower or upper bound in any dimension are owned, the rest are leaves owned by another process and present in the SF.
2208: Parallel Layout:
2210: We create a cubic process grid of dimension P^{1/d} on each side. The IndexToTuple_Private() function maps the global rank to the local rank in each dimension. We divide edges using the PETSc distribution rule in each dimension, and then add overlap. TupleToRanks_Private() returns the local rank in ech dimension for a tuple. RanksToSizes_Private() gives the size in each dimension for the domain with those local ranks.
2211: */
2212: static PetscErrorCode DMPlexCreateHypercubicMesh_Internal(DM dm, PetscInt dim, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], PetscInt overlap, const DMBoundaryType bd[])
2213: {
2214: const PetscInt debug = ((DM_Plex *)dm->data)->printAdj;
2215: PetscSF sf;
2216: Vec coordinates;
2217: PetscSection coordSection;
2218: DMLabel cutLabel = NULL;
2219: PetscBool cutMarker = PETSC_FALSE;
2220: PetscBool periodic = PETSC_FALSE;
2221: PetscInt numCells = 1;
2222: PetscInt numVertices = 1;
2223: PetscSFNode *remotes;
2224: PetscScalar *coords;
2225: PetscInt *procs; // The number of processes along each dimension
2226: PetscInt *lrank; // Rank in each dimension, lrank[d] \in [0, procs[d])
2227: PetscInt *ledges; // The number of edges along each dimension for this process
2228: PetscInt *vstart; // The first vertex along each dimension on this processes
2229: PetscInt *vertices; // The number of vertices along each dimension on this process
2230: PetscInt *rvert; // The global (not local) vertex number along each dimension
2231: PetscInt *rrank; // The rank along each dimension for the process owning rvert[]
2232: PetscInt *rvertices; // The number of vertices along each dimension for the process rrank[]
2233: PetscInt *vert, *vtmp, *supp, cone[2], *leaves;
2234: PetscInt cell = 0, coordSize, Nl = 0, Nl2 = 0;
2235: PetscMPIInt rank, size;
2236: MPI_Comm comm;
2238: PetscFunctionBegin;
2239: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2240: PetscCallMPI(MPI_Comm_rank(comm, &rank));
2241: PetscCallMPI(MPI_Comm_size(comm, &size));
2242: PetscCall(DMSetDimension(dm, dim));
2243: PetscCall(DMPlexDistributeSetDefault(dm, PETSC_FALSE));
2244: PetscCall(PetscCalloc4(dim, &procs, dim, &lrank, dim, &rrank, 2 * dim, &supp));
2245: PetscCall(PetscCalloc7(dim, &ledges, dim, &vertices, dim, &rvertices, dim, &vert, dim, &rvert, dim, &vstart, dim, &vtmp));
2246: PetscCall(DMCreateLabel(dm, "marker"));
2247: PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL));
2248: for (PetscInt d = 0; d < dim; ++d) periodic = (periodic || bd[d] == DM_BOUNDARY_PERIODIC) ? PETSC_TRUE : PETSC_FALSE;
2249: if (periodic && cutMarker) {
2250: PetscCall(DMCreateLabel(dm, "periodic_cut"));
2251: PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
2252: }
2253: for (PetscInt d = 0; d < dim; ++d) PetscCheck(bd[d] == DM_BOUNDARY_PERIODIC, comm, PETSC_ERR_SUP, "Hypercubic mesh must be periodic now");
2254: overlap = overlap == PETSC_DETERMINE ? 1 : overlap;
2255: PetscCheck(overlap >= 1, comm, PETSC_ERR_SUP, "Overlap %" PetscInt_FMT " must be greater than 0", overlap);
2256: if (size > 1) {
2257: PetscInt Npr = 1;
2259: // Make process grid
2260: if (debug) PetscCall(PetscPrintf(comm, "Process grid:"));
2261: for (PetscInt d = 0; d < dim; ++d) {
2262: procs[d] = PetscRintReal(PetscPowReal(size, 1. / dim));
2263: Npr *= procs[d];
2264: if (debug) PetscCall(PetscPrintf(comm, " %" PetscInt_FMT, procs[d]));
2265: }
2266: if (debug) PetscCall(PetscPrintf(comm, "\n"));
2267: PetscCheck(Npr == size, comm, PETSC_ERR_PLIB, "Process grid size %" PetscInt_FMT " != %d comm size", Npr, size);
2268: IndexToTuple_Private(dim, procs, rank, lrank);
2269: for (PetscInt d = 0; d < dim; ++d) {
2270: ledges[d] = edges[d] / procs[d] + (edges[d] % procs[d] > lrank[d] ? 1 : 0);
2271: vstart[d] = 0;
2272: for (PetscInt r = 0; r < lrank[d]; ++r) vstart[d] += edges[d] / procs[d] + (edges[d] % procs[d] > r ? 1 : 0);
2273: vstart[d] -= overlap; // For halo
2274: }
2275: } else {
2276: for (PetscInt d = 0; d < dim; ++d) {
2277: procs[d] = 1;
2278: ledges[d] = edges[d];
2279: }
2280: }
2281: // Calculate local patch size
2282: for (PetscInt d = 0; d < dim; ++d) {
2283: vertices[d] = ledges[d] + (procs[d] > 1 ? 2 * overlap : 0);
2284: numVertices *= vertices[d];
2285: }
2286: numCells = numVertices * dim;
2287: PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices));
2288: for (PetscInt c = 0; c < numCells; ++c) PetscCall(DMPlexSetConeSize(dm, c, 2));
2289: for (PetscInt v = numCells; v < numCells + numVertices; ++v) PetscCall(DMPlexSetSupportSize(dm, v, 2 * dim));
2290: PetscCall(DMSetUp(dm)); /* Allocate space for cones and supports */
2291: /* Build cell cones and vertex supports */
2292: PetscCall(DMCreateLabel(dm, "celltype"));
2293: if (debug) PetscCall(PetscSynchronizedPrintf(comm, "Topology for rank %d:\n", rank));
2294: while (vert[dim - 1] < vertices[dim - 1]) {
2295: const PetscInt vertex = TupleToIndex_Private(dim, vertices, vert) + numCells;
2296: PetscInt s = 0;
2297: PetscBool leaf = PETSC_FALSE;
2299: if (debug) {
2300: PetscCall(PetscSynchronizedPrintf(comm, "Vertex %" PetscInt_FMT ":", vertex));
2301: for (PetscInt d = 0; d < dim; ++d) PetscCall(PetscSynchronizedPrintf(comm, " %" PetscInt_FMT, vert[d]));
2302: PetscCall(PetscSynchronizedPrintf(comm, "\n"));
2303: }
2304: PetscCall(DMPlexSetCellType(dm, vertex, DM_POLYTOPE_POINT));
2305: // Define edge cones
2306: for (PetscInt d = 0; d < dim; ++d) {
2307: for (PetscInt e = 0; e < dim; ++e) vtmp[e] = vert[e];
2308: vtmp[d] = (vert[d] + 1) % vertices[d];
2309: cone[0] = vertex;
2310: cone[1] = TupleToIndex_Private(dim, vertices, vtmp) + numCells;
2311: if (debug) {
2312: PetscCall(PetscSynchronizedPrintf(comm, " Vertex %" PetscInt_FMT ":", cone[1]));
2313: for (PetscInt e = 0; e < dim; ++e) PetscCall(PetscSynchronizedPrintf(comm, " %" PetscInt_FMT, vtmp[e]));
2314: PetscCall(PetscSynchronizedPrintf(comm, "\n"));
2315: }
2316: PetscCall(DMPlexSetCone(dm, cell, cone));
2317: PetscCall(DMPlexSetCellType(dm, cell, DM_POLYTOPE_SEGMENT));
2318: if (debug) PetscCall(PetscSynchronizedPrintf(comm, " Edge %" PetscInt_FMT " (%" PetscInt_FMT " %" PetscInt_FMT ")\n", cell, cone[0], cone[1]));
2319: ++cell;
2320: // Shared vertices are any in the first or last overlap layers
2321: if (vert[d] < overlap || vert[d] >= vertices[d] - overlap) leaf = PETSC_TRUE;
2322: }
2323: if (size > 1 && leaf) ++Nl;
2324: // Define vertex supports
2325: for (PetscInt d = 0; d < dim; ++d) {
2326: for (PetscInt e = 0; e < dim; ++e) vtmp[e] = vert[e];
2327: vtmp[d] = (vert[d] + vertices[d] - 1) % vertices[d];
2328: supp[s++] = TupleToIndex_Private(dim, vertices, vtmp) * dim + d;
2329: supp[s++] = (vertex - numCells) * dim + d;
2330: PetscCall(DMPlexSetSupport(dm, vertex, supp));
2331: }
2332: PetscCall(DMPlexTensorPointLexicographic_Private(dim, vertices, vert));
2333: }
2334: if (debug) PetscCall(PetscSynchronizedFlush(comm, NULL));
2335: PetscCall(DMPlexStratify(dm));
2336: // Allocate for SF
2337: PetscCall(PetscMalloc1(Nl, &leaves));
2338: PetscCall(PetscMalloc1(Nl, &remotes));
2339: // Build coordinates
2340: PetscCall(DMGetCoordinateSection(dm, &coordSection));
2341: PetscCall(PetscSectionSetNumFields(coordSection, 1));
2342: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim));
2343: PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices));
2344: for (PetscInt v = numCells; v < numCells + numVertices; ++v) {
2345: PetscCall(PetscSectionSetDof(coordSection, v, dim));
2346: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim));
2347: }
2348: PetscCall(PetscSectionSetUp(coordSection));
2349: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
2350: PetscCall(VecCreate(comm, &coordinates));
2351: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
2352: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
2353: PetscCall(VecSetBlockSize(coordinates, dim));
2354: PetscCall(VecSetType(coordinates, VECSTANDARD));
2355: PetscCall(VecGetArray(coordinates, &coords));
2356: if (debug) PetscCall(PetscSynchronizedPrintf(comm, "Geometry for rank %d:\n", rank));
2357: for (PetscInt d = 0; d < dim; ++d) vert[d] = 0;
2358: while (vert[dim - 1] < vertices[dim - 1]) {
2359: const PetscInt vertex = TupleToIndex_Private(dim, vertices, vert);
2360: PetscBool leaf = PETSC_FALSE;
2362: for (PetscInt d = 0; d < dim; ++d) {
2363: coords[vertex * dim + d] = lower[d] + ((upper[d] - lower[d]) / edges[d]) * (vert[d] + vstart[d]);
2364: if (vert[d] < overlap || vert[d] >= vertices[d] - overlap) leaf = PETSC_TRUE;
2365: }
2366: if (size > 1 && leaf) {
2367: PetscInt rnumCells = 1;
2369: for (PetscInt d = 0; d < dim; ++d) rvert[d] = vert[d] + vstart[d];
2370: TupleToRanks_Private(dim, edges, procs, rvert, rrank);
2371: leaves[Nl2] = vertex + numCells;
2372: remotes[Nl2].rank = TupleToIndex_Private(dim, procs, rrank);
2373: RanksToSizes_Private(dim, edges, procs, rrank, rvertices);
2374: for (PetscInt d = 0; d < dim; ++d) {
2375: rvertices[d] += 2 * overlap; // Add halo
2376: rnumCells *= rvertices[d];
2377: }
2378: rnumCells *= dim;
2379: for (PetscInt d = 0; d < dim; ++d) {
2380: const PetscInt diff = rrank[d] - lrank[d];
2382: if (!diff) rvert[d] = vert[d]; // Vertex is local
2383: else if (rvert[d] < 0) rvert[d] = rvertices[d] - 1 + rvert[d]; // Wrap around at the bottom
2384: else if (rvert[d] >= edges[d]) rvert[d] = rvert[d] - edges[d] + 1; // Wrap around at the top
2385: else if (diff == -1) rvert[d] = rvertices[d] - 1 + (vert[d] - overlap);
2386: else if (diff == 1) rvert[d] = (vertices[d] - vert[d] - 1) + overlap;
2387: else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Process distance %" PetscInt_FMT " in direction %" PetscInt_FMT " should not be possible", diff, d);
2388: }
2389: remotes[Nl2].index = TupleToIndex_Private(dim, rvertices, rvert) + rnumCells;
2390: if (debug) PetscCall(PetscSynchronizedPrintf(comm, "Shared Vertex %" PetscInt_FMT " (%" PetscInt_FMT ", %" PetscInt_FMT ")\n", leaves[Nl2], remotes[Nl2].rank, remotes[Nl2].index));
2391: ++Nl2;
2392: }
2393: if (debug) {
2394: PetscCall(PetscSynchronizedPrintf(comm, "Vertex %" PetscInt_FMT ":", vertex));
2395: for (PetscInt d = 0; d < dim; ++d) PetscCall(PetscSynchronizedPrintf(comm, " %" PetscInt_FMT, vert[d] + vstart[d]));
2396: for (PetscInt d = 0; d < dim; ++d) PetscCall(PetscSynchronizedPrintf(comm, " %g", (double)PetscRealPart(coords[vertex * dim + d])));
2397: PetscCall(PetscSynchronizedPrintf(comm, "\n"));
2398: }
2399: PetscCall(DMPlexTensorPointLexicographic_Private(dim, vertices, vert));
2400: }
2401: if (debug) PetscCall(PetscSynchronizedFlush(comm, NULL));
2402: PetscCall(VecRestoreArray(coordinates, &coords));
2403: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
2404: PetscCall(VecDestroy(&coordinates));
2405: // Build SF
2406: PetscCheck(Nl == Nl2, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Initial number of leaves %" PetscInt_FMT " != %" PetscInt_FMT " final number", Nl, Nl2);
2407: PetscCall(DMGetPointSF(dm, &sf));
2408: PetscCall(PetscSFSetGraph(sf, numCells + numVertices, Nl, leaves, PETSC_OWN_POINTER, remotes, PETSC_OWN_POINTER));
2409: if (debug) PetscCall(PetscSFView(sf, PETSC_VIEWER_STDOUT_WORLD));
2410: //PetscCall(DMSetPeriodicity(dm, NULL, lower, upper));
2411: // Attach the extent
2412: {
2413: PetscContainer c;
2414: PetscInt *extent, *lextent;
2416: PetscCall(PetscMalloc1(dim, &extent));
2417: PetscCall(PetscMalloc1(dim, &lextent));
2418: for (PetscInt d = 0; d < dim; ++d) {
2419: extent[d] = edges[d];
2420: lextent[d] = ledges[d];
2421: }
2422: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &c));
2423: PetscCall(PetscContainerSetCtxDestroy(c, PetscCtxDestroyDefault));
2424: PetscCall(PetscContainerSetPointer(c, extent));
2425: PetscCall(PetscObjectCompose((PetscObject)dm, "_extent", (PetscObject)c));
2426: PetscCall(PetscContainerDestroy(&c));
2427: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &c));
2428: PetscCall(PetscContainerSetCtxDestroy(c, PetscCtxDestroyDefault));
2429: PetscCall(PetscContainerSetPointer(c, lextent));
2430: PetscCall(PetscObjectCompose((PetscObject)dm, "_lextent", (PetscObject)c));
2431: PetscCall(PetscContainerDestroy(&c));
2432: }
2433: PetscCall(PetscFree4(procs, lrank, rrank, supp));
2434: PetscCall(PetscFree7(ledges, vertices, rvertices, vert, rvert, vstart, vtmp));
2435: PetscFunctionReturn(PETSC_SUCCESS);
2436: }
2438: /*@C
2439: DMPlexCreateHypercubicMesh - Creates a periodic mesh on the tensor product of unit intervals using only vertices and edges.
2441: Collective
2443: Input Parameters:
2444: + comm - The communicator for the `DM` object
2445: . dim - The spatial dimension
2446: . edges - Number of edges per dimension, or `NULL` for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D
2447: . lower - The lower left corner, or `NULL` for (0, 0, 0)
2448: . upper - The upper right corner, or `NULL` for (1, 1, 1)
2449: - overlap - The number of vertices in each direction to include in the overlap (default is 1)
2451: Output Parameter:
2452: . dm - The DM object
2454: Level: beginner
2456: Note:
2457: If you want to customize this mesh using options, you just need to
2458: .vb
2459: DMCreate(comm, &dm);
2460: DMSetType(dm, DMPLEX);
2461: DMSetFromOptions(dm);
2462: .ve
2463: and use the options on the `DMSetFromOptions()` page.
2465: The vertices are numbered is lexicographic order, and the dim edges exiting a vertex in the positive orthant are number consecutively,
2466: .vb
2467: 18--0-19--2-20--4-18
2468: | | | |
2469: 13 15 17 13
2470: | | | |
2471: 24-12-25-14-26-16-24
2472: | | | |
2473: 7 9 11 7
2474: | | | |
2475: 21--6-22--8-23-10-21
2476: | | | |
2477: 1 3 5 1
2478: | | | |
2479: 18--0-19--2-20--4-18
2480: .ve
2482: .seealso: `DMSetFromOptions()`, `DMPlexCreateFromFile()`, `DMPlexCreateHexCylinderMesh()`, `DMSetType()`, `DMCreate()`
2483: @*/
2484: PetscErrorCode DMPlexCreateHypercubicMesh(MPI_Comm comm, PetscInt dim, const PetscInt edges[], const PetscReal lower[], const PetscReal upper[], PetscInt overlap, DM *dm)
2485: {
2486: PetscInt *edg;
2487: PetscReal *low, *upp;
2488: DMBoundaryType *bdt;
2489: PetscInt d;
2491: PetscFunctionBegin;
2492: PetscCall(DMCreate(comm, dm));
2493: PetscCall(DMSetType(*dm, DMPLEX));
2494: PetscCall(PetscMalloc4(dim, &edg, dim, &low, dim, &upp, dim, &bdt));
2495: for (d = 0; d < dim; ++d) {
2496: edg[d] = edges ? edges[d] : 1;
2497: low[d] = lower ? lower[d] : 0.;
2498: upp[d] = upper ? upper[d] : 1.;
2499: bdt[d] = DM_BOUNDARY_PERIODIC;
2500: }
2501: PetscCall(DMPlexCreateHypercubicMesh_Internal(*dm, dim, low, upp, edg, overlap, bdt));
2502: PetscCall(PetscFree4(edg, low, upp, bdt));
2503: PetscFunctionReturn(PETSC_SUCCESS);
2504: }
2506: /*@
2507: DMPlexSetOptionsPrefix - Sets the prefix used for searching for all `DM` options in the database.
2509: Logically Collective
2511: Input Parameters:
2512: + dm - the `DM` context
2513: - prefix - the prefix to prepend to all option names
2515: Level: advanced
2517: Note:
2518: A hyphen (-) must NOT be given at the beginning of the prefix name.
2519: The first character of all runtime options is AUTOMATICALLY the hyphen.
2521: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `SNESSetFromOptions()`
2522: @*/
2523: PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[])
2524: {
2525: DM_Plex *mesh = (DM_Plex *)dm->data;
2527: PetscFunctionBegin;
2529: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dm, prefix));
2530: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)mesh->partitioner, prefix));
2531: PetscFunctionReturn(PETSC_SUCCESS);
2532: }
2534: /* Remap geometry to cylinder
2535: TODO: This only works for a single refinement, then it is broken
2537: Interior square: Linear interpolation is correct
2538: The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing
2539: such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance
2541: phi = arctan(y/x)
2542: d_close = sqrt(1/8 + 1/4 sin^2(phi))
2543: d_far = sqrt(1/2 + sin^2(phi))
2545: so we remap them using
2547: x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close)
2548: y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close)
2550: If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y.
2551: */
2552: static void snapToCylinder(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[])
2553: {
2554: const PetscReal dis = 1.0 / PetscSqrtReal(2.0);
2555: const PetscReal ds2 = 0.5 * dis;
2557: if ((PetscAbsScalar(u[0]) <= ds2) && (PetscAbsScalar(u[1]) <= ds2)) {
2558: f0[0] = u[0];
2559: f0[1] = u[1];
2560: } else {
2561: PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc;
2563: x = PetscRealPart(u[0]);
2564: y = PetscRealPart(u[1]);
2565: phi = PetscAtan2Real(y, x);
2566: sinp = PetscSinReal(phi);
2567: cosp = PetscCosReal(phi);
2568: if ((PetscAbsReal(phi) > PETSC_PI / 4.0) && (PetscAbsReal(phi) < 3.0 * PETSC_PI / 4.0)) {
2569: dc = PetscAbsReal(ds2 / sinp);
2570: df = PetscAbsReal(dis / sinp);
2571: xc = ds2 * x / PetscAbsReal(y);
2572: yc = ds2 * PetscSignReal(y);
2573: } else {
2574: dc = PetscAbsReal(ds2 / cosp);
2575: df = PetscAbsReal(dis / cosp);
2576: xc = ds2 * PetscSignReal(x);
2577: yc = ds2 * y / PetscAbsReal(x);
2578: }
2579: f0[0] = xc + (u[0] - xc) * (1.0 - dc) / (df - dc);
2580: f0[1] = yc + (u[1] - yc) * (1.0 - dc) / (df - dc);
2581: }
2582: f0[2] = u[2];
2583: }
2585: static PetscErrorCode DMPlexCreateHexCylinderMesh_Internal(DM dm, DMBoundaryType periodicZ, PetscInt Nr)
2586: {
2587: const PetscInt dim = 3;
2588: PetscInt numCells, numVertices;
2589: PetscMPIInt rank;
2591: PetscFunctionBegin;
2592: PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0));
2593: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
2594: PetscCall(DMSetDimension(dm, dim));
2595: /* Create topology */
2596: {
2597: PetscInt cone[8], c;
2599: numCells = rank == 0 ? 5 : 0;
2600: numVertices = rank == 0 ? 16 : 0;
2601: if (periodicZ == DM_BOUNDARY_PERIODIC) {
2602: numCells *= 3;
2603: numVertices = rank == 0 ? 24 : 0;
2604: }
2605: PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices));
2606: for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 8));
2607: PetscCall(DMSetUp(dm));
2608: if (rank == 0) {
2609: if (periodicZ == DM_BOUNDARY_PERIODIC) {
2610: cone[0] = 15;
2611: cone[1] = 18;
2612: cone[2] = 17;
2613: cone[3] = 16;
2614: cone[4] = 31;
2615: cone[5] = 32;
2616: cone[6] = 33;
2617: cone[7] = 34;
2618: PetscCall(DMPlexSetCone(dm, 0, cone));
2619: cone[0] = 16;
2620: cone[1] = 17;
2621: cone[2] = 24;
2622: cone[3] = 23;
2623: cone[4] = 32;
2624: cone[5] = 36;
2625: cone[6] = 37;
2626: cone[7] = 33; /* 22 25 26 21 */
2627: PetscCall(DMPlexSetCone(dm, 1, cone));
2628: cone[0] = 18;
2629: cone[1] = 27;
2630: cone[2] = 24;
2631: cone[3] = 17;
2632: cone[4] = 34;
2633: cone[5] = 33;
2634: cone[6] = 37;
2635: cone[7] = 38;
2636: PetscCall(DMPlexSetCone(dm, 2, cone));
2637: cone[0] = 29;
2638: cone[1] = 27;
2639: cone[2] = 18;
2640: cone[3] = 15;
2641: cone[4] = 35;
2642: cone[5] = 31;
2643: cone[6] = 34;
2644: cone[7] = 38;
2645: PetscCall(DMPlexSetCone(dm, 3, cone));
2646: cone[0] = 29;
2647: cone[1] = 15;
2648: cone[2] = 16;
2649: cone[3] = 23;
2650: cone[4] = 35;
2651: cone[5] = 36;
2652: cone[6] = 32;
2653: cone[7] = 31;
2654: PetscCall(DMPlexSetCone(dm, 4, cone));
2656: cone[0] = 31;
2657: cone[1] = 34;
2658: cone[2] = 33;
2659: cone[3] = 32;
2660: cone[4] = 19;
2661: cone[5] = 22;
2662: cone[6] = 21;
2663: cone[7] = 20;
2664: PetscCall(DMPlexSetCone(dm, 5, cone));
2665: cone[0] = 32;
2666: cone[1] = 33;
2667: cone[2] = 37;
2668: cone[3] = 36;
2669: cone[4] = 22;
2670: cone[5] = 25;
2671: cone[6] = 26;
2672: cone[7] = 21;
2673: PetscCall(DMPlexSetCone(dm, 6, cone));
2674: cone[0] = 34;
2675: cone[1] = 38;
2676: cone[2] = 37;
2677: cone[3] = 33;
2678: cone[4] = 20;
2679: cone[5] = 21;
2680: cone[6] = 26;
2681: cone[7] = 28;
2682: PetscCall(DMPlexSetCone(dm, 7, cone));
2683: cone[0] = 35;
2684: cone[1] = 38;
2685: cone[2] = 34;
2686: cone[3] = 31;
2687: cone[4] = 30;
2688: cone[5] = 19;
2689: cone[6] = 20;
2690: cone[7] = 28;
2691: PetscCall(DMPlexSetCone(dm, 8, cone));
2692: cone[0] = 35;
2693: cone[1] = 31;
2694: cone[2] = 32;
2695: cone[3] = 36;
2696: cone[4] = 30;
2697: cone[5] = 25;
2698: cone[6] = 22;
2699: cone[7] = 19;
2700: PetscCall(DMPlexSetCone(dm, 9, cone));
2702: cone[0] = 19;
2703: cone[1] = 20;
2704: cone[2] = 21;
2705: cone[3] = 22;
2706: cone[4] = 15;
2707: cone[5] = 16;
2708: cone[6] = 17;
2709: cone[7] = 18;
2710: PetscCall(DMPlexSetCone(dm, 10, cone));
2711: cone[0] = 22;
2712: cone[1] = 21;
2713: cone[2] = 26;
2714: cone[3] = 25;
2715: cone[4] = 16;
2716: cone[5] = 23;
2717: cone[6] = 24;
2718: cone[7] = 17;
2719: PetscCall(DMPlexSetCone(dm, 11, cone));
2720: cone[0] = 20;
2721: cone[1] = 28;
2722: cone[2] = 26;
2723: cone[3] = 21;
2724: cone[4] = 18;
2725: cone[5] = 17;
2726: cone[6] = 24;
2727: cone[7] = 27;
2728: PetscCall(DMPlexSetCone(dm, 12, cone));
2729: cone[0] = 30;
2730: cone[1] = 28;
2731: cone[2] = 20;
2732: cone[3] = 19;
2733: cone[4] = 29;
2734: cone[5] = 15;
2735: cone[6] = 18;
2736: cone[7] = 27;
2737: PetscCall(DMPlexSetCone(dm, 13, cone));
2738: cone[0] = 30;
2739: cone[1] = 19;
2740: cone[2] = 22;
2741: cone[3] = 25;
2742: cone[4] = 29;
2743: cone[5] = 23;
2744: cone[6] = 16;
2745: cone[7] = 15;
2746: PetscCall(DMPlexSetCone(dm, 14, cone));
2747: } else {
2748: cone[0] = 5;
2749: cone[1] = 8;
2750: cone[2] = 7;
2751: cone[3] = 6;
2752: cone[4] = 9;
2753: cone[5] = 12;
2754: cone[6] = 11;
2755: cone[7] = 10;
2756: PetscCall(DMPlexSetCone(dm, 0, cone));
2757: cone[0] = 6;
2758: cone[1] = 7;
2759: cone[2] = 14;
2760: cone[3] = 13;
2761: cone[4] = 12;
2762: cone[5] = 15;
2763: cone[6] = 16;
2764: cone[7] = 11;
2765: PetscCall(DMPlexSetCone(dm, 1, cone));
2766: cone[0] = 8;
2767: cone[1] = 17;
2768: cone[2] = 14;
2769: cone[3] = 7;
2770: cone[4] = 10;
2771: cone[5] = 11;
2772: cone[6] = 16;
2773: cone[7] = 18;
2774: PetscCall(DMPlexSetCone(dm, 2, cone));
2775: cone[0] = 19;
2776: cone[1] = 17;
2777: cone[2] = 8;
2778: cone[3] = 5;
2779: cone[4] = 20;
2780: cone[5] = 9;
2781: cone[6] = 10;
2782: cone[7] = 18;
2783: PetscCall(DMPlexSetCone(dm, 3, cone));
2784: cone[0] = 19;
2785: cone[1] = 5;
2786: cone[2] = 6;
2787: cone[3] = 13;
2788: cone[4] = 20;
2789: cone[5] = 15;
2790: cone[6] = 12;
2791: cone[7] = 9;
2792: PetscCall(DMPlexSetCone(dm, 4, cone));
2793: }
2794: }
2795: PetscCall(DMPlexSymmetrize(dm));
2796: PetscCall(DMPlexStratify(dm));
2797: }
2798: /* Create cube geometry */
2799: {
2800: Vec coordinates;
2801: PetscSection coordSection;
2802: PetscScalar *coords;
2803: PetscInt coordSize, v;
2804: const PetscReal dis = 1.0 / PetscSqrtReal(2.0);
2805: const PetscReal ds2 = dis / 2.0;
2807: /* Build coordinates */
2808: PetscCall(DMGetCoordinateSection(dm, &coordSection));
2809: PetscCall(PetscSectionSetNumFields(coordSection, 1));
2810: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim));
2811: PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices));
2812: for (v = numCells; v < numCells + numVertices; ++v) {
2813: PetscCall(PetscSectionSetDof(coordSection, v, dim));
2814: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim));
2815: }
2816: PetscCall(PetscSectionSetUp(coordSection));
2817: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
2818: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
2819: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
2820: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
2821: PetscCall(VecSetBlockSize(coordinates, dim));
2822: PetscCall(VecSetType(coordinates, VECSTANDARD));
2823: PetscCall(VecGetArray(coordinates, &coords));
2824: if (rank == 0) {
2825: coords[0 * dim + 0] = -ds2;
2826: coords[0 * dim + 1] = -ds2;
2827: coords[0 * dim + 2] = 0.0;
2828: coords[1 * dim + 0] = ds2;
2829: coords[1 * dim + 1] = -ds2;
2830: coords[1 * dim + 2] = 0.0;
2831: coords[2 * dim + 0] = ds2;
2832: coords[2 * dim + 1] = ds2;
2833: coords[2 * dim + 2] = 0.0;
2834: coords[3 * dim + 0] = -ds2;
2835: coords[3 * dim + 1] = ds2;
2836: coords[3 * dim + 2] = 0.0;
2837: coords[4 * dim + 0] = -ds2;
2838: coords[4 * dim + 1] = -ds2;
2839: coords[4 * dim + 2] = 1.0;
2840: coords[5 * dim + 0] = -ds2;
2841: coords[5 * dim + 1] = ds2;
2842: coords[5 * dim + 2] = 1.0;
2843: coords[6 * dim + 0] = ds2;
2844: coords[6 * dim + 1] = ds2;
2845: coords[6 * dim + 2] = 1.0;
2846: coords[7 * dim + 0] = ds2;
2847: coords[7 * dim + 1] = -ds2;
2848: coords[7 * dim + 2] = 1.0;
2849: coords[8 * dim + 0] = dis;
2850: coords[8 * dim + 1] = -dis;
2851: coords[8 * dim + 2] = 0.0;
2852: coords[9 * dim + 0] = dis;
2853: coords[9 * dim + 1] = dis;
2854: coords[9 * dim + 2] = 0.0;
2855: coords[10 * dim + 0] = dis;
2856: coords[10 * dim + 1] = -dis;
2857: coords[10 * dim + 2] = 1.0;
2858: coords[11 * dim + 0] = dis;
2859: coords[11 * dim + 1] = dis;
2860: coords[11 * dim + 2] = 1.0;
2861: coords[12 * dim + 0] = -dis;
2862: coords[12 * dim + 1] = dis;
2863: coords[12 * dim + 2] = 0.0;
2864: coords[13 * dim + 0] = -dis;
2865: coords[13 * dim + 1] = dis;
2866: coords[13 * dim + 2] = 1.0;
2867: coords[14 * dim + 0] = -dis;
2868: coords[14 * dim + 1] = -dis;
2869: coords[14 * dim + 2] = 0.0;
2870: coords[15 * dim + 0] = -dis;
2871: coords[15 * dim + 1] = -dis;
2872: coords[15 * dim + 2] = 1.0;
2873: if (periodicZ == DM_BOUNDARY_PERIODIC) {
2874: /* 15 31 19 */ coords[16 * dim + 0] = -ds2;
2875: coords[16 * dim + 1] = -ds2;
2876: coords[16 * dim + 2] = 0.5;
2877: /* 16 32 22 */ coords[17 * dim + 0] = ds2;
2878: coords[17 * dim + 1] = -ds2;
2879: coords[17 * dim + 2] = 0.5;
2880: /* 17 33 21 */ coords[18 * dim + 0] = ds2;
2881: coords[18 * dim + 1] = ds2;
2882: coords[18 * dim + 2] = 0.5;
2883: /* 18 34 20 */ coords[19 * dim + 0] = -ds2;
2884: coords[19 * dim + 1] = ds2;
2885: coords[19 * dim + 2] = 0.5;
2886: /* 29 35 30 */ coords[20 * dim + 0] = -dis;
2887: coords[20 * dim + 1] = -dis;
2888: coords[20 * dim + 2] = 0.5;
2889: /* 23 36 25 */ coords[21 * dim + 0] = dis;
2890: coords[21 * dim + 1] = -dis;
2891: coords[21 * dim + 2] = 0.5;
2892: /* 24 37 26 */ coords[22 * dim + 0] = dis;
2893: coords[22 * dim + 1] = dis;
2894: coords[22 * dim + 2] = 0.5;
2895: /* 27 38 28 */ coords[23 * dim + 0] = -dis;
2896: coords[23 * dim + 1] = dis;
2897: coords[23 * dim + 2] = 0.5;
2898: }
2899: }
2900: PetscCall(VecRestoreArray(coordinates, &coords));
2901: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
2902: PetscCall(VecDestroy(&coordinates));
2903: }
2904: /* Create periodicity */
2905: if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) {
2906: PetscReal L[3] = {-1., -1., 0.};
2907: PetscReal maxCell[3] = {-1., -1., 0.};
2908: PetscReal lower[3] = {0.0, 0.0, 0.0};
2909: PetscReal upper[3] = {1.0, 1.0, 1.5};
2910: PetscInt numZCells = 3;
2912: L[2] = upper[2] - lower[2];
2913: maxCell[2] = 1.1 * (L[2] / numZCells);
2914: PetscCall(DMSetPeriodicity(dm, maxCell, lower, L));
2915: }
2916: {
2917: DM cdm;
2918: PetscDS cds;
2919: PetscScalar c[2] = {1.0, 1.0};
2921: PetscCall(DMPlexCreateCoordinateSpace(dm, 1, PETSC_FALSE, PETSC_TRUE));
2922: PetscCall(DMGetCoordinateDM(dm, &cdm));
2923: PetscCall(DMGetDS(cdm, &cds));
2924: PetscCall(PetscDSSetConstants(cds, 2, c));
2925: }
2926: PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0));
2928: /* Wait for coordinate creation before doing in-place modification */
2929: PetscCall(DMPlexInterpolateInPlace_Internal(dm));
2931: char oldprefix[PETSC_MAX_PATH_LEN];
2932: const char *prefix;
2934: PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm, &prefix));
2935: PetscCall(PetscStrncpy(oldprefix, prefix, PETSC_MAX_PATH_LEN));
2936: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dm, "petsc_cyl_ref_"));
2937: for (PetscInt r = 0; r < PetscMax(0, Nr); ++r) {
2938: DM rdm;
2940: PetscCall(DMRefine(dm, PetscObjectComm((PetscObject)dm), &rdm));
2941: PetscCall(DMPlexReplace_Internal(dm, &rdm));
2942: }
2943: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dm, oldprefix));
2944: PetscCall(DMPlexRemapGeometry(dm, 0.0, snapToCylinder));
2946: DMLabel bdlabel, edgelabel;
2947: IS faceIS;
2948: const PetscInt *faces;
2949: PetscInt Nf;
2951: PetscCall(DMCreateLabel(dm, "marker"));
2952: PetscCall(DMGetLabel(dm, "marker", &bdlabel));
2953: PetscCall(DMCreateLabel(dm, "generatrix"));
2954: PetscCall(DMGetLabel(dm, "generatrix", &edgelabel));
2955: PetscCall(DMPlexMarkBoundaryFaces(dm, PETSC_DETERMINE, bdlabel));
2956: // Remove faces on top and bottom
2957: PetscCall(DMLabelGetStratumIS(bdlabel, 1, &faceIS));
2958: if (faceIS) {
2959: PetscCall(ISGetLocalSize(faceIS, &Nf));
2960: PetscCall(ISGetIndices(faceIS, &faces));
2961: for (PetscInt f = 0; f < Nf; ++f) {
2962: PetscReal vol, normal[3];
2964: PetscCall(DMPlexComputeCellGeometryFVM(dm, faces[f], &vol, NULL, normal));
2965: if (PetscAbsReal(normal[2]) < PETSC_SMALL) PetscCall(DMLabelSetValue(edgelabel, faces[f], 1));
2966: }
2967: PetscCall(ISRestoreIndices(faceIS, &faces));
2968: PetscCall(ISDestroy(&faceIS));
2969: }
2970: PetscCall(DMPlexLabelComplete(dm, bdlabel));
2971: PetscCall(DMPlexLabelComplete(dm, edgelabel));
2972: PetscFunctionReturn(PETSC_SUCCESS);
2973: }
2975: /*@
2976: DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra.
2978: Collective
2980: Input Parameters:
2981: + comm - The communicator for the `DM` object
2982: . periodicZ - The boundary type for the Z direction
2983: - Nr - The number of refinements to carry out
2985: Output Parameter:
2986: . dm - The `DM` object
2988: Level: beginner
2990: Note:
2991: Here is the output numbering looking from the bottom of the cylinder\:
2992: .vb
2993: 17-----14
2994: | |
2995: | 2 |
2996: | |
2997: 17-----8-----7-----14
2998: | | | |
2999: | 3 | 0 | 1 |
3000: | | | |
3001: 19-----5-----6-----13
3002: | |
3003: | 4 |
3004: | |
3005: 19-----13
3007: and up through the top
3009: 18-----16
3010: | |
3011: | 2 |
3012: | |
3013: 18----10----11-----16
3014: | | | |
3015: | 3 | 0 | 1 |
3016: | | | |
3017: 20-----9----12-----15
3018: | |
3019: | 4 |
3020: | |
3021: 20-----15
3022: .ve
3024: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()`
3025: @*/
3026: PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, DMBoundaryType periodicZ, PetscInt Nr, DM *dm)
3027: {
3028: PetscFunctionBegin;
3029: PetscAssertPointer(dm, 4);
3030: PetscCall(DMCreate(comm, dm));
3031: PetscCall(DMSetType(*dm, DMPLEX));
3032: PetscCall(DMPlexCreateHexCylinderMesh_Internal(*dm, periodicZ, Nr));
3033: PetscFunctionReturn(PETSC_SUCCESS);
3034: }
3036: static PetscErrorCode DMPlexCreateWedgeCylinderMesh_Internal(DM dm, PetscInt n, PetscBool interpolate)
3037: {
3038: const PetscInt dim = 3;
3039: PetscInt numCells, numVertices, v;
3040: PetscMPIInt rank;
3042: PetscFunctionBegin;
3043: PetscCheck(n >= 0, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %" PetscInt_FMT " cannot be negative", n);
3044: PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0));
3045: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
3046: PetscCall(DMSetDimension(dm, dim));
3047: /* Must create the celltype label here so that we do not automatically try to compute the types */
3048: PetscCall(DMCreateLabel(dm, "celltype"));
3049: /* Create topology */
3050: {
3051: PetscInt cone[6], c;
3053: numCells = rank == 0 ? n : 0;
3054: numVertices = rank == 0 ? 2 * (n + 1) : 0;
3055: PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices));
3056: for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 6));
3057: PetscCall(DMSetUp(dm));
3058: for (c = 0; c < numCells; c++) {
3059: cone[0] = c + n * 1;
3060: cone[1] = (c + 1) % n + n * 1;
3061: cone[2] = 0 + 3 * n;
3062: cone[3] = c + n * 2;
3063: cone[4] = (c + 1) % n + n * 2;
3064: cone[5] = 1 + 3 * n;
3065: PetscCall(DMPlexSetCone(dm, c, cone));
3066: PetscCall(DMPlexSetCellType(dm, c, DM_POLYTOPE_TRI_PRISM_TENSOR));
3067: }
3068: PetscCall(DMPlexSymmetrize(dm));
3069: PetscCall(DMPlexStratify(dm));
3070: }
3071: for (v = numCells; v < numCells + numVertices; ++v) PetscCall(DMPlexSetCellType(dm, v, DM_POLYTOPE_POINT));
3072: /* Create cylinder geometry */
3073: {
3074: Vec coordinates;
3075: PetscSection coordSection;
3076: PetscScalar *coords;
3077: PetscInt coordSize, c;
3079: /* Build coordinates */
3080: PetscCall(DMGetCoordinateSection(dm, &coordSection));
3081: PetscCall(PetscSectionSetNumFields(coordSection, 1));
3082: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim));
3083: PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices));
3084: for (v = numCells; v < numCells + numVertices; ++v) {
3085: PetscCall(PetscSectionSetDof(coordSection, v, dim));
3086: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim));
3087: }
3088: PetscCall(PetscSectionSetUp(coordSection));
3089: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
3090: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
3091: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
3092: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
3093: PetscCall(VecSetBlockSize(coordinates, dim));
3094: PetscCall(VecSetType(coordinates, VECSTANDARD));
3095: PetscCall(VecGetArray(coordinates, &coords));
3096: for (c = 0; c < numCells; c++) {
3097: coords[(c + 0 * n) * dim + 0] = PetscCosReal(2.0 * c * PETSC_PI / n);
3098: coords[(c + 0 * n) * dim + 1] = PetscSinReal(2.0 * c * PETSC_PI / n);
3099: coords[(c + 0 * n) * dim + 2] = 1.0;
3100: coords[(c + 1 * n) * dim + 0] = PetscCosReal(2.0 * c * PETSC_PI / n);
3101: coords[(c + 1 * n) * dim + 1] = PetscSinReal(2.0 * c * PETSC_PI / n);
3102: coords[(c + 1 * n) * dim + 2] = 0.0;
3103: }
3104: if (rank == 0) {
3105: coords[(2 * n + 0) * dim + 0] = 0.0;
3106: coords[(2 * n + 0) * dim + 1] = 0.0;
3107: coords[(2 * n + 0) * dim + 2] = 1.0;
3108: coords[(2 * n + 1) * dim + 0] = 0.0;
3109: coords[(2 * n + 1) * dim + 1] = 0.0;
3110: coords[(2 * n + 1) * dim + 2] = 0.0;
3111: }
3112: PetscCall(VecRestoreArray(coordinates, &coords));
3113: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
3114: PetscCall(VecDestroy(&coordinates));
3115: }
3116: PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0));
3117: /* Interpolate */
3118: if (interpolate) PetscCall(DMPlexInterpolateInPlace_Internal(dm));
3119: PetscFunctionReturn(PETSC_SUCCESS);
3120: }
3122: /*@
3123: DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges.
3125: Collective
3127: Input Parameters:
3128: + comm - The communicator for the `DM` object
3129: . n - The number of wedges around the origin
3130: - interpolate - Create edges and faces
3132: Output Parameter:
3133: . dm - The `DM` object
3135: Level: beginner
3137: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateHexCylinderMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()`
3138: @*/
3139: PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm)
3140: {
3141: PetscFunctionBegin;
3142: PetscAssertPointer(dm, 4);
3143: PetscCall(DMCreate(comm, dm));
3144: PetscCall(DMSetType(*dm, DMPLEX));
3145: PetscCall(DMPlexCreateWedgeCylinderMesh_Internal(*dm, n, interpolate));
3146: PetscFunctionReturn(PETSC_SUCCESS);
3147: }
3149: static inline PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
3150: {
3151: PetscReal prod = 0.0;
3152: PetscInt i;
3153: for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]);
3154: return PetscSqrtReal(prod);
3155: }
3157: static inline PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
3158: {
3159: PetscReal prod = 0.0;
3160: PetscInt i;
3161: for (i = 0; i < dim; ++i) prod += x[i] * y[i];
3162: return prod;
3163: }
3165: /* The first constant is the sphere radius */
3166: static void snapToSphere(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[])
3167: {
3168: PetscReal r = PetscRealPart(constants[0]);
3169: PetscReal norm2 = 0.0, fac;
3170: PetscInt n = uOff[1] - uOff[0], d;
3172: for (d = 0; d < n; ++d) norm2 += PetscSqr(PetscRealPart(u[d]));
3173: fac = r / PetscSqrtReal(norm2);
3174: for (d = 0; d < n; ++d) f0[d] = u[d] * fac;
3175: }
3177: static PetscErrorCode DMPlexCreateSphereMesh_Internal(DM dm, PetscInt dim, PetscBool simplex, PetscReal R)
3178: {
3179: const PetscInt embedDim = dim + 1;
3180: PetscSection coordSection;
3181: Vec coordinates;
3182: PetscScalar *coords;
3183: PetscReal *coordsIn;
3184: PetscInt numCells, numEdges, numVerts = 0, firstVertex = 0, v, firstEdge, coordSize, d, e;
3185: PetscMPIInt rank;
3187: PetscFunctionBegin;
3189: PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0));
3190: PetscCall(DMSetDimension(dm, dim));
3191: PetscCall(DMSetCoordinateDim(dm, dim + 1));
3192: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
3193: switch (dim) {
3194: case 1:
3195: numCells = 16;
3196: numVerts = numCells;
3198: // Build Topology
3199: PetscCall(DMPlexSetChart(dm, 0, numCells + numVerts));
3200: for (PetscInt c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, embedDim));
3201: PetscCall(DMSetUp(dm));
3202: for (PetscInt c = 0; c < numCells; ++c) {
3203: PetscInt cone[2];
3205: cone[0] = c + numCells;
3206: cone[1] = (c + 1) % numVerts + numCells;
3207: PetscCall(DMPlexSetCone(dm, c, cone));
3208: }
3209: PetscCall(DMPlexSymmetrize(dm));
3210: PetscCall(DMPlexStratify(dm));
3211: PetscCall(PetscMalloc1(numVerts * embedDim, &coordsIn));
3212: for (PetscInt v = 0; v < numVerts; ++v) {
3213: const PetscReal rad = 2. * PETSC_PI * v / numVerts;
3215: coordsIn[v * embedDim + 0] = PetscCosReal(rad);
3216: coordsIn[v * embedDim + 1] = PetscSinReal(rad);
3217: }
3218: break;
3219: case 2:
3220: if (simplex) {
3221: const PetscReal radius = PetscSqrtReal(1 + PETSC_PHI * PETSC_PHI) / (1.0 + PETSC_PHI);
3222: const PetscReal edgeLen = 2.0 / (1.0 + PETSC_PHI) * (R / radius);
3223: const PetscInt degree = 5;
3224: PetscReal vertex[3] = {0.0, 1.0 / (1.0 + PETSC_PHI), PETSC_PHI / (1.0 + PETSC_PHI)};
3225: PetscInt s[3] = {1, 1, 1};
3226: PetscInt cone[3];
3227: PetscInt *graph;
3229: vertex[0] *= R / radius;
3230: vertex[1] *= R / radius;
3231: vertex[2] *= R / radius;
3232: numCells = rank == 0 ? 20 : 0;
3233: numVerts = rank == 0 ? 12 : 0;
3234: firstVertex = numCells;
3235: /* Use icosahedron, which for a R-sphere has coordinates which are all cyclic permutations of
3237: (0, \pm 1/\phi+1, \pm \phi/\phi+1)
3239: where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
3240: length is then given by 2/(1+\phi) = 2 * 0.38197 = 0.76393.
3241: */
3242: /* Construct vertices */
3243: PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn));
3244: if (rank == 0) {
3245: for (PetscInt p = 0, i = 0; p < embedDim; ++p) {
3246: for (s[1] = -1; s[1] < 2; s[1] += 2) {
3247: for (s[2] = -1; s[2] < 2; s[2] += 2) {
3248: for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[(d + p) % embedDim] * vertex[(d + p) % embedDim];
3249: ++i;
3250: }
3251: }
3252: }
3253: }
3254: /* Construct graph */
3255: PetscCall(PetscCalloc1(numVerts * numVerts, &graph));
3256: for (PetscInt i = 0; i < numVerts; ++i) {
3257: PetscInt k = 0;
3258: for (PetscInt j = 0; j < numVerts; ++j) {
3259: if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i * embedDim], &coordsIn[j * embedDim]) - edgeLen) < PETSC_SMALL) {
3260: graph[i * numVerts + j] = 1;
3261: ++k;
3262: }
3263: }
3264: PetscCheck(k == degree, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid icosahedron, vertex %" PetscInt_FMT " degree %" PetscInt_FMT " != %" PetscInt_FMT, i, k, degree);
3265: }
3266: /* Build Topology */
3267: PetscCall(DMPlexSetChart(dm, 0, numCells + numVerts));
3268: for (PetscInt c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, embedDim));
3269: PetscCall(DMSetUp(dm)); /* Allocate space for cones */
3270: /* Cells */
3271: for (PetscInt i = 0, c = 0; i < numVerts; ++i) {
3272: for (PetscInt j = 0; j < i; ++j) {
3273: for (PetscInt k = 0; k < j; ++k) {
3274: if (graph[i * numVerts + j] && graph[j * numVerts + k] && graph[k * numVerts + i]) {
3275: cone[0] = firstVertex + i;
3276: cone[1] = firstVertex + j;
3277: cone[2] = firstVertex + k;
3278: /* Check orientation */
3279: {
3280: const PetscInt epsilon[3][3][3] = {
3281: {{0, 0, 0}, {0, 0, 1}, {0, -1, 0}},
3282: {{0, 0, -1}, {0, 0, 0}, {1, 0, 0} },
3283: {{0, 1, 0}, {-1, 0, 0}, {0, 0, 0} }
3284: };
3285: PetscReal normal[3];
3286: PetscInt e, f;
3288: for (d = 0; d < embedDim; ++d) {
3289: normal[d] = 0.0;
3290: for (e = 0; e < embedDim; ++e) {
3291: for (f = 0; f < embedDim; ++f) normal[d] += epsilon[d][e][f] * (coordsIn[j * embedDim + e] - coordsIn[i * embedDim + e]) * (coordsIn[k * embedDim + f] - coordsIn[i * embedDim + f]);
3292: }
3293: }
3294: if (DotReal(embedDim, normal, &coordsIn[i * embedDim]) < 0) {
3295: PetscInt tmp = cone[1];
3296: cone[1] = cone[2];
3297: cone[2] = tmp;
3298: }
3299: }
3300: PetscCall(DMPlexSetCone(dm, c++, cone));
3301: }
3302: }
3303: }
3304: }
3305: PetscCall(DMPlexSymmetrize(dm));
3306: PetscCall(DMPlexStratify(dm));
3307: PetscCall(PetscFree(graph));
3308: } else {
3309: /*
3310: 12-21--13
3311: | |
3312: 25 4 24
3313: | |
3314: 12-25--9-16--8-24--13
3315: | | | |
3316: 23 5 17 0 15 3 22
3317: | | | |
3318: 10-20--6-14--7-19--11
3319: | |
3320: 20 1 19
3321: | |
3322: 10-18--11
3323: | |
3324: 23 2 22
3325: | |
3326: 12-21--13
3327: */
3328: PetscInt cone[4], ornt[4];
3330: numCells = rank == 0 ? 6 : 0;
3331: numEdges = rank == 0 ? 12 : 0;
3332: numVerts = rank == 0 ? 8 : 0;
3333: firstVertex = numCells;
3334: firstEdge = numCells + numVerts;
3335: /* Build Topology */
3336: PetscCall(DMPlexSetChart(dm, 0, numCells + numEdges + numVerts));
3337: for (PetscInt c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 4));
3338: for (e = firstEdge; e < firstEdge + numEdges; ++e) PetscCall(DMPlexSetConeSize(dm, e, 2));
3339: PetscCall(DMSetUp(dm)); /* Allocate space for cones */
3340: if (rank == 0) {
3341: /* Cell 0 */
3342: cone[0] = 14;
3343: cone[1] = 15;
3344: cone[2] = 16;
3345: cone[3] = 17;
3346: PetscCall(DMPlexSetCone(dm, 0, cone));
3347: ornt[0] = 0;
3348: ornt[1] = 0;
3349: ornt[2] = 0;
3350: ornt[3] = 0;
3351: PetscCall(DMPlexSetConeOrientation(dm, 0, ornt));
3352: /* Cell 1 */
3353: cone[0] = 18;
3354: cone[1] = 19;
3355: cone[2] = 14;
3356: cone[3] = 20;
3357: PetscCall(DMPlexSetCone(dm, 1, cone));
3358: ornt[0] = 0;
3359: ornt[1] = 0;
3360: ornt[2] = -1;
3361: ornt[3] = 0;
3362: PetscCall(DMPlexSetConeOrientation(dm, 1, ornt));
3363: /* Cell 2 */
3364: cone[0] = 21;
3365: cone[1] = 22;
3366: cone[2] = 18;
3367: cone[3] = 23;
3368: PetscCall(DMPlexSetCone(dm, 2, cone));
3369: ornt[0] = 0;
3370: ornt[1] = 0;
3371: ornt[2] = -1;
3372: ornt[3] = 0;
3373: PetscCall(DMPlexSetConeOrientation(dm, 2, ornt));
3374: /* Cell 3 */
3375: cone[0] = 19;
3376: cone[1] = 22;
3377: cone[2] = 24;
3378: cone[3] = 15;
3379: PetscCall(DMPlexSetCone(dm, 3, cone));
3380: ornt[0] = -1;
3381: ornt[1] = -1;
3382: ornt[2] = 0;
3383: ornt[3] = -1;
3384: PetscCall(DMPlexSetConeOrientation(dm, 3, ornt));
3385: /* Cell 4 */
3386: cone[0] = 16;
3387: cone[1] = 24;
3388: cone[2] = 21;
3389: cone[3] = 25;
3390: PetscCall(DMPlexSetCone(dm, 4, cone));
3391: ornt[0] = -1;
3392: ornt[1] = -1;
3393: ornt[2] = -1;
3394: ornt[3] = 0;
3395: PetscCall(DMPlexSetConeOrientation(dm, 4, ornt));
3396: /* Cell 5 */
3397: cone[0] = 20;
3398: cone[1] = 17;
3399: cone[2] = 25;
3400: cone[3] = 23;
3401: PetscCall(DMPlexSetCone(dm, 5, cone));
3402: ornt[0] = -1;
3403: ornt[1] = -1;
3404: ornt[2] = -1;
3405: ornt[3] = -1;
3406: PetscCall(DMPlexSetConeOrientation(dm, 5, ornt));
3407: /* Edges */
3408: cone[0] = 6;
3409: cone[1] = 7;
3410: PetscCall(DMPlexSetCone(dm, 14, cone));
3411: cone[0] = 7;
3412: cone[1] = 8;
3413: PetscCall(DMPlexSetCone(dm, 15, cone));
3414: cone[0] = 8;
3415: cone[1] = 9;
3416: PetscCall(DMPlexSetCone(dm, 16, cone));
3417: cone[0] = 9;
3418: cone[1] = 6;
3419: PetscCall(DMPlexSetCone(dm, 17, cone));
3420: cone[0] = 10;
3421: cone[1] = 11;
3422: PetscCall(DMPlexSetCone(dm, 18, cone));
3423: cone[0] = 11;
3424: cone[1] = 7;
3425: PetscCall(DMPlexSetCone(dm, 19, cone));
3426: cone[0] = 6;
3427: cone[1] = 10;
3428: PetscCall(DMPlexSetCone(dm, 20, cone));
3429: cone[0] = 12;
3430: cone[1] = 13;
3431: PetscCall(DMPlexSetCone(dm, 21, cone));
3432: cone[0] = 13;
3433: cone[1] = 11;
3434: PetscCall(DMPlexSetCone(dm, 22, cone));
3435: cone[0] = 10;
3436: cone[1] = 12;
3437: PetscCall(DMPlexSetCone(dm, 23, cone));
3438: cone[0] = 13;
3439: cone[1] = 8;
3440: PetscCall(DMPlexSetCone(dm, 24, cone));
3441: cone[0] = 12;
3442: cone[1] = 9;
3443: PetscCall(DMPlexSetCone(dm, 25, cone));
3444: }
3445: PetscCall(DMPlexSymmetrize(dm));
3446: PetscCall(DMPlexStratify(dm));
3447: /* Build coordinates */
3448: PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn));
3449: if (rank == 0) {
3450: coordsIn[0 * embedDim + 0] = -R;
3451: coordsIn[0 * embedDim + 1] = R;
3452: coordsIn[0 * embedDim + 2] = -R;
3453: coordsIn[1 * embedDim + 0] = R;
3454: coordsIn[1 * embedDim + 1] = R;
3455: coordsIn[1 * embedDim + 2] = -R;
3456: coordsIn[2 * embedDim + 0] = R;
3457: coordsIn[2 * embedDim + 1] = -R;
3458: coordsIn[2 * embedDim + 2] = -R;
3459: coordsIn[3 * embedDim + 0] = -R;
3460: coordsIn[3 * embedDim + 1] = -R;
3461: coordsIn[3 * embedDim + 2] = -R;
3462: coordsIn[4 * embedDim + 0] = -R;
3463: coordsIn[4 * embedDim + 1] = R;
3464: coordsIn[4 * embedDim + 2] = R;
3465: coordsIn[5 * embedDim + 0] = R;
3466: coordsIn[5 * embedDim + 1] = R;
3467: coordsIn[5 * embedDim + 2] = R;
3468: coordsIn[6 * embedDim + 0] = -R;
3469: coordsIn[6 * embedDim + 1] = -R;
3470: coordsIn[6 * embedDim + 2] = R;
3471: coordsIn[7 * embedDim + 0] = R;
3472: coordsIn[7 * embedDim + 1] = -R;
3473: coordsIn[7 * embedDim + 2] = R;
3474: }
3475: }
3476: break;
3477: case 3:
3478: if (simplex) {
3479: const PetscReal edgeLen = 1.0 / PETSC_PHI;
3480: PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5};
3481: PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0};
3482: PetscReal vertexC[4] = {0.5, 0.5 * PETSC_PHI, 0.5 / PETSC_PHI, 0.0};
3483: const PetscInt degree = 12;
3484: PetscInt s[4] = {1, 1, 1};
3485: PetscInt evenPerm[12][4] = {
3486: {0, 1, 2, 3},
3487: {0, 2, 3, 1},
3488: {0, 3, 1, 2},
3489: {1, 0, 3, 2},
3490: {1, 2, 0, 3},
3491: {1, 3, 2, 0},
3492: {2, 0, 1, 3},
3493: {2, 1, 3, 0},
3494: {2, 3, 0, 1},
3495: {3, 0, 2, 1},
3496: {3, 1, 0, 2},
3497: {3, 2, 1, 0}
3498: };
3499: PetscInt cone[4];
3500: PetscInt *graph, p, i, j, k, l;
3502: vertexA[0] *= R;
3503: vertexA[1] *= R;
3504: vertexA[2] *= R;
3505: vertexA[3] *= R;
3506: vertexB[0] *= R;
3507: vertexB[1] *= R;
3508: vertexB[2] *= R;
3509: vertexB[3] *= R;
3510: vertexC[0] *= R;
3511: vertexC[1] *= R;
3512: vertexC[2] *= R;
3513: vertexC[3] *= R;
3514: numCells = rank == 0 ? 600 : 0;
3515: numVerts = rank == 0 ? 120 : 0;
3516: firstVertex = numCells;
3517: /* Use the 600-cell, which for a unit sphere has coordinates which are
3519: 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16
3520: (\pm 1, 0, 0, 0) all cyclic permutations 8
3521: 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96
3523: where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
3524: length is then given by 1/\phi = 0.61803.
3526: http://buzzard.pugetsound.edu/sage-practice/ch03s03.html
3527: http://mathworld.wolfram.com/600-Cell.html
3528: */
3529: /* Construct vertices */
3530: PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn));
3531: i = 0;
3532: if (rank == 0) {
3533: for (s[0] = -1; s[0] < 2; s[0] += 2) {
3534: for (s[1] = -1; s[1] < 2; s[1] += 2) {
3535: for (s[2] = -1; s[2] < 2; s[2] += 2) {
3536: for (s[3] = -1; s[3] < 2; s[3] += 2) {
3537: for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[d] * vertexA[d];
3538: ++i;
3539: }
3540: }
3541: }
3542: }
3543: for (p = 0; p < embedDim; ++p) {
3544: s[1] = s[2] = s[3] = 1;
3545: for (s[0] = -1; s[0] < 2; s[0] += 2) {
3546: for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[(d + p) % embedDim] * vertexB[(d + p) % embedDim];
3547: ++i;
3548: }
3549: }
3550: for (p = 0; p < 12; ++p) {
3551: s[3] = 1;
3552: for (s[0] = -1; s[0] < 2; s[0] += 2) {
3553: for (s[1] = -1; s[1] < 2; s[1] += 2) {
3554: for (s[2] = -1; s[2] < 2; s[2] += 2) {
3555: for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[evenPerm[p][d]] * vertexC[evenPerm[p][d]];
3556: ++i;
3557: }
3558: }
3559: }
3560: }
3561: }
3562: PetscCheck(i == numVerts, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertices %" PetscInt_FMT " != %" PetscInt_FMT, i, numVerts);
3563: /* Construct graph */
3564: PetscCall(PetscCalloc1(numVerts * numVerts, &graph));
3565: for (i = 0; i < numVerts; ++i) {
3566: for (j = 0, k = 0; j < numVerts; ++j) {
3567: if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i * embedDim], &coordsIn[j * embedDim]) - edgeLen) < PETSC_SMALL) {
3568: graph[i * numVerts + j] = 1;
3569: ++k;
3570: }
3571: }
3572: PetscCheck(k == degree, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertex %" PetscInt_FMT " degree %" PetscInt_FMT " != %" PetscInt_FMT, i, k, degree);
3573: }
3574: /* Build Topology */
3575: PetscCall(DMPlexSetChart(dm, 0, numCells + numVerts));
3576: for (PetscInt c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, embedDim));
3577: PetscCall(DMSetUp(dm)); /* Allocate space for cones */
3578: /* Cells */
3579: if (rank == 0) {
3580: for (PetscInt i = 0, c = 0; i < numVerts; ++i) {
3581: for (j = 0; j < i; ++j) {
3582: for (k = 0; k < j; ++k) {
3583: for (l = 0; l < k; ++l) {
3584: if (graph[i * numVerts + j] && graph[j * numVerts + k] && graph[k * numVerts + i] && graph[l * numVerts + i] && graph[l * numVerts + j] && graph[l * numVerts + k]) {
3585: cone[0] = firstVertex + i;
3586: cone[1] = firstVertex + j;
3587: cone[2] = firstVertex + k;
3588: cone[3] = firstVertex + l;
3589: /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */
3590: {
3591: const PetscInt epsilon[4][4][4][4] = {
3592: {{{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, 1}, {0, 0, -1, 0}}, {{0, 0, 0, 0}, {0, 0, 0, -1}, {0, 0, 0, 0}, {0, 1, 0, 0}}, {{0, 0, 0, 0}, {0, 0, 1, 0}, {0, -1, 0, 0}, {0, 0, 0, 0}}},
3594: {{{0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, -1}, {0, 0, 1, 0}}, {{0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0}}, {{0, 0, 0, 1}, {0, 0, 0, 0}, {0, 0, 0, 0}, {-1, 0, 0, 0}}, {{0, 0, -1, 0}, {0, 0, 0, 0}, {1, 0, 0, 0}, {0, 0, 0, 0}}},
3596: {{{0, 0, 0, 0}, {0, 0, 0, 1}, {0, 0, 0, 0}, {0, -1, 0, 0}}, {{0, 0, 0, -1}, {0, 0, 0, 0}, {0, 0, 0, 0}, {1, 0, 0, 0}}, {{0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0}}, {{0, 1, 0, 0}, {-1, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0}}},
3598: {{{0, 0, 0, 0}, {0, 0, -1, 0}, {0, 1, 0, 0}, {0, 0, 0, 0}}, {{0, 0, 1, 0}, {0, 0, 0, 0}, {-1, 0, 0, 0}, {0, 0, 0, 0}}, {{0, -1, 0, 0}, {1, 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}} }
3599: };
3600: PetscReal normal[4];
3601: PetscInt e, f, g;
3603: for (d = 0; d < embedDim; ++d) {
3604: normal[d] = 0.0;
3605: for (e = 0; e < embedDim; ++e) {
3606: for (f = 0; f < embedDim; ++f) {
3607: for (g = 0; g < embedDim; ++g) {
3608: normal[d] += epsilon[d][e][f][g] * (coordsIn[j * embedDim + e] - coordsIn[i * embedDim + e]) * (coordsIn[k * embedDim + f] - coordsIn[i * embedDim + f]) * (coordsIn[l * embedDim + f] - coordsIn[i * embedDim + f]);
3609: }
3610: }
3611: }
3612: }
3613: if (DotReal(embedDim, normal, &coordsIn[i * embedDim]) < 0) {
3614: PetscInt tmp = cone[1];
3615: cone[1] = cone[2];
3616: cone[2] = tmp;
3617: }
3618: }
3619: PetscCall(DMPlexSetCone(dm, c++, cone));
3620: }
3621: }
3622: }
3623: }
3624: }
3625: }
3626: PetscCall(DMPlexSymmetrize(dm));
3627: PetscCall(DMPlexStratify(dm));
3628: PetscCall(PetscFree(graph));
3629: }
3630: break;
3631: default:
3632: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported dimension for sphere: %" PetscInt_FMT, dim);
3633: }
3634: /* Create coordinates */
3635: PetscCall(DMGetCoordinateSection(dm, &coordSection));
3636: PetscCall(PetscSectionSetNumFields(coordSection, 1));
3637: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, embedDim));
3638: PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex + numVerts));
3639: for (v = firstVertex; v < firstVertex + numVerts; ++v) {
3640: PetscCall(PetscSectionSetDof(coordSection, v, embedDim));
3641: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, embedDim));
3642: }
3643: PetscCall(PetscSectionSetUp(coordSection));
3644: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
3645: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
3646: PetscCall(VecSetBlockSize(coordinates, embedDim));
3647: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
3648: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
3649: PetscCall(VecSetType(coordinates, VECSTANDARD));
3650: PetscCall(VecGetArray(coordinates, &coords));
3651: for (v = 0; v < numVerts; ++v)
3652: for (d = 0; d < embedDim; ++d) coords[v * embedDim + d] = coordsIn[v * embedDim + d];
3653: PetscCall(VecRestoreArray(coordinates, &coords));
3654: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
3655: PetscCall(VecDestroy(&coordinates));
3656: PetscCall(PetscFree(coordsIn));
3657: {
3658: DM cdm;
3659: PetscDS cds;
3660: PetscScalar c = R;
3662: PetscCall(DMPlexSetCoordinateMap(dm, snapToSphere));
3663: PetscCall(DMPlexCreateCoordinateSpace(dm, 1, PETSC_FALSE, PETSC_TRUE));
3664: PetscCall(DMGetCoordinateDM(dm, &cdm));
3665: PetscCall(DMGetDS(cdm, &cds));
3666: PetscCall(PetscDSSetConstants(cds, 1, &c));
3667: }
3668: PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0));
3669: /* Wait for coordinate creation before doing in-place modification */
3670: if (simplex) PetscCall(DMPlexInterpolateInPlace_Internal(dm));
3671: PetscFunctionReturn(PETSC_SUCCESS);
3672: }
3674: typedef void (*TPSEvaluateFunc)(const PetscReal[], PetscReal *, PetscReal[], PetscReal (*)[3]);
3676: /*
3677: The Schwarz P implicit surface is
3679: f(x) = cos(x0) + cos(x1) + cos(x2) = 0
3680: */
3681: static void TPSEvaluate_SchwarzP(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3])
3682: {
3683: PetscReal c[3] = {PetscCosReal(y[0] * PETSC_PI), PetscCosReal(y[1] * PETSC_PI), PetscCosReal(y[2] * PETSC_PI)};
3684: PetscReal g[3] = {-PetscSinReal(y[0] * PETSC_PI), -PetscSinReal(y[1] * PETSC_PI), -PetscSinReal(y[2] * PETSC_PI)};
3685: f[0] = c[0] + c[1] + c[2];
3686: for (PetscInt i = 0; i < 3; i++) {
3687: grad[i] = PETSC_PI * g[i];
3688: for (PetscInt j = 0; j < 3; j++) hess[i][j] = (i == j) ? -PetscSqr(PETSC_PI) * c[i] : 0.;
3689: }
3690: }
3692: // u[] is a tentative normal on input. Replace with the implicit function gradient in the same direction
3693: static PetscErrorCode TPSExtrudeNormalFunc_SchwarzP(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt r, PetscScalar u[], void *ctx)
3694: {
3695: for (PetscInt i = 0; i < 3; i++) u[i] = -PETSC_PI * PetscSinReal(x[i] * PETSC_PI);
3696: return PETSC_SUCCESS;
3697: }
3699: /*
3700: The Gyroid implicit surface is
3702: f(x,y,z) = sin(pi * x) * cos (pi * (y + 1/2)) + sin(pi * (y + 1/2)) * cos(pi * (z + 1/4)) + sin(pi * (z + 1/4)) * cos(pi * x)
3704: */
3705: static void TPSEvaluate_Gyroid(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3])
3706: {
3707: PetscReal s[3] = {PetscSinReal(PETSC_PI * y[0]), PetscSinReal(PETSC_PI * (y[1] + .5)), PetscSinReal(PETSC_PI * (y[2] + .25))};
3708: PetscReal c[3] = {PetscCosReal(PETSC_PI * y[0]), PetscCosReal(PETSC_PI * (y[1] + .5)), PetscCosReal(PETSC_PI * (y[2] + .25))};
3709: f[0] = s[0] * c[1] + s[1] * c[2] + s[2] * c[0];
3710: grad[0] = PETSC_PI * (c[0] * c[1] - s[2] * s[0]);
3711: grad[1] = PETSC_PI * (c[1] * c[2] - s[0] * s[1]);
3712: grad[2] = PETSC_PI * (c[2] * c[0] - s[1] * s[2]);
3713: hess[0][0] = -PetscSqr(PETSC_PI) * (s[0] * c[1] + s[2] * c[0]);
3714: hess[0][1] = -PetscSqr(PETSC_PI) * (c[0] * s[1]);
3715: hess[0][2] = -PetscSqr(PETSC_PI) * (c[2] * s[0]);
3716: hess[1][0] = -PetscSqr(PETSC_PI) * (s[1] * c[2] + s[0] * c[1]);
3717: hess[1][1] = -PetscSqr(PETSC_PI) * (c[1] * s[2]);
3718: hess[2][2] = -PetscSqr(PETSC_PI) * (c[0] * s[1]);
3719: hess[2][0] = -PetscSqr(PETSC_PI) * (s[2] * c[0] + s[1] * c[2]);
3720: hess[2][1] = -PetscSqr(PETSC_PI) * (c[2] * s[0]);
3721: hess[2][2] = -PetscSqr(PETSC_PI) * (c[1] * s[2]);
3722: }
3724: // u[] is a tentative normal on input. Replace with the implicit function gradient in the same direction
3725: static PetscErrorCode TPSExtrudeNormalFunc_Gyroid(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt r, PetscScalar u[], void *ctx)
3726: {
3727: PetscReal s[3] = {PetscSinReal(PETSC_PI * x[0]), PetscSinReal(PETSC_PI * (x[1] + .5)), PetscSinReal(PETSC_PI * (x[2] + .25))};
3728: PetscReal c[3] = {PetscCosReal(PETSC_PI * x[0]), PetscCosReal(PETSC_PI * (x[1] + .5)), PetscCosReal(PETSC_PI * (x[2] + .25))};
3729: u[0] = PETSC_PI * (c[0] * c[1] - s[2] * s[0]);
3730: u[1] = PETSC_PI * (c[1] * c[2] - s[0] * s[1]);
3731: u[2] = PETSC_PI * (c[2] * c[0] - s[1] * s[2]);
3732: return PETSC_SUCCESS;
3733: }
3735: /*
3736: We wish to solve
3738: min_y || y - x ||^2 subject to f(y) = 0
3740: Let g(y) = grad(f). The minimization problem is equivalent to asking to satisfy
3741: f(y) = 0 and (y-x) is parallel to g(y). We do this by using Householder QR to obtain a basis for the
3742: tangent space and ask for both components in the tangent space to be zero.
3744: Take g to be a column vector and compute the "full QR" factorization Q R = g,
3745: where Q = I - 2 n n^T is a symmetric orthogonal matrix.
3746: The first column of Q is parallel to g so the remaining two columns span the null space.
3747: Let Qn = Q[:,1:] be those remaining columns. Then Qn Qn^T is an orthogonal projector into the tangent space.
3748: Since Q is symmetric, this is equivalent to multiplying by Q and taking the last two entries.
3749: In total, we have a system of 3 equations in 3 unknowns:
3751: f(y) = 0 1 equation
3752: Qn^T (y - x) = 0 2 equations
3754: Here, we compute the residual and Jacobian of this system.
3755: */
3756: static void TPSNearestPointResJac(TPSEvaluateFunc feval, const PetscScalar x[], const PetscScalar y[], PetscScalar res[], PetscScalar J[])
3757: {
3758: PetscReal yreal[3] = {PetscRealPart(y[0]), PetscRealPart(y[1]), PetscRealPart(y[2])};
3759: PetscReal d[3] = {PetscRealPart(y[0] - x[0]), PetscRealPart(y[1] - x[1]), PetscRealPart(y[2] - x[2])};
3760: PetscReal f, grad[3], n[3], norm, norm_y[3], nd, nd_y[3], sign;
3761: PetscReal n_y[3][3] = {
3762: {0, 0, 0},
3763: {0, 0, 0},
3764: {0, 0, 0}
3765: };
3767: feval(yreal, &f, grad, n_y);
3769: for (PetscInt i = 0; i < 3; i++) n[i] = grad[i];
3770: norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2]));
3771: for (PetscInt i = 0; i < 3; i++) norm_y[i] = 1. / norm * n[i] * n_y[i][i];
3773: // Define the Householder reflector
3774: sign = n[0] >= 0 ? 1. : -1.;
3775: n[0] += norm * sign;
3776: for (PetscInt i = 0; i < 3; i++) n_y[0][i] += norm_y[i] * sign;
3778: norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2]));
3779: norm_y[0] = 1. / norm * (n[0] * n_y[0][0]);
3780: norm_y[1] = 1. / norm * (n[0] * n_y[0][1] + n[1] * n_y[1][1]);
3781: norm_y[2] = 1. / norm * (n[0] * n_y[0][2] + n[2] * n_y[2][2]);
3783: for (PetscInt i = 0; i < 3; i++) {
3784: n[i] /= norm;
3785: for (PetscInt j = 0; j < 3; j++) {
3786: // note that n[i] is n_old[i]/norm when executing the code below
3787: n_y[i][j] = n_y[i][j] / norm - n[i] / norm * norm_y[j];
3788: }
3789: }
3791: nd = n[0] * d[0] + n[1] * d[1] + n[2] * d[2];
3792: for (PetscInt i = 0; i < 3; i++) nd_y[i] = n[i] + n_y[0][i] * d[0] + n_y[1][i] * d[1] + n_y[2][i] * d[2];
3794: res[0] = f;
3795: res[1] = d[1] - 2 * n[1] * nd;
3796: res[2] = d[2] - 2 * n[2] * nd;
3797: // J[j][i] is J_{ij} (column major)
3798: for (PetscInt j = 0; j < 3; j++) {
3799: J[0 + j * 3] = grad[j];
3800: J[1 + j * 3] = (j == 1) * 1. - 2 * (n_y[1][j] * nd + n[1] * nd_y[j]);
3801: J[2 + j * 3] = (j == 2) * 1. - 2 * (n_y[2][j] * nd + n[2] * nd_y[j]);
3802: }
3803: }
3805: /*
3806: Project x to the nearest point on the implicit surface using Newton's method.
3807: */
3808: static PetscErrorCode TPSNearestPoint(TPSEvaluateFunc feval, PetscScalar x[])
3809: {
3810: PetscScalar y[3] = {x[0], x[1], x[2]}; // Initial guess
3812: PetscFunctionBegin;
3813: for (PetscInt iter = 0; iter < 10; iter++) {
3814: PetscScalar res[3], J[9];
3815: PetscReal resnorm;
3816: TPSNearestPointResJac(feval, x, y, res, J);
3817: resnorm = PetscSqrtReal(PetscSqr(PetscRealPart(res[0])) + PetscSqr(PetscRealPart(res[1])) + PetscSqr(PetscRealPart(res[2])));
3818: if (0) { // Turn on this monitor if you need to confirm quadratic convergence
3819: PetscCall(PetscPrintf(PETSC_COMM_SELF, "[%" PetscInt_FMT "] res [%g %g %g]\n", iter, (double)PetscRealPart(res[0]), (double)PetscRealPart(res[1]), (double)PetscRealPart(res[2])));
3820: }
3821: if (resnorm < PETSC_SMALL) break;
3823: // Take the Newton step
3824: PetscCall(PetscKernel_A_gets_inverse_A_3(J, 0., PETSC_FALSE, NULL));
3825: PetscKernel_v_gets_v_minus_A_times_w_3(y, J, res);
3826: }
3827: for (PetscInt i = 0; i < 3; i++) x[i] = y[i];
3828: PetscFunctionReturn(PETSC_SUCCESS);
3829: }
3831: const char *const DMPlexTPSTypes[] = {"SCHWARZ_P", "GYROID", "DMPlexTPSType", "DMPLEX_TPS_", NULL};
3833: static PetscErrorCode DMPlexCreateTPSMesh_Internal(DM dm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscBool tps_distribute, PetscInt refinements, PetscInt layers, PetscReal thickness)
3834: {
3835: PetscMPIInt rank;
3836: PetscInt topoDim = 2, spaceDim = 3, numFaces = 0, numVertices = 0, numEdges = 0;
3837: PetscInt (*edges)[2] = NULL, *edgeSets = NULL;
3838: PetscInt *cells_flat = NULL;
3839: PetscReal *vtxCoords = NULL;
3840: TPSEvaluateFunc evalFunc = NULL;
3841: PetscSimplePointFn *normalFunc = NULL;
3842: DMLabel label;
3844: PetscFunctionBegin;
3845: PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0));
3846: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
3847: PetscCheck((layers != 0) ^ (thickness == 0.), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_INCOMP, "Layers %" PetscInt_FMT " must be nonzero iff thickness %g is nonzero", layers, (double)thickness);
3848: switch (tpstype) {
3849: case DMPLEX_TPS_SCHWARZ_P:
3850: PetscCheck(!periodic || (periodic[0] == DM_BOUNDARY_NONE && periodic[1] == DM_BOUNDARY_NONE && periodic[2] == DM_BOUNDARY_NONE), PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Schwarz P does not support periodic meshes");
3851: if (rank == 0) {
3852: PetscInt (*cells)[6][4][4] = NULL; // [junction, junction-face, cell, conn]
3853: PetscInt Njunctions = 0, Ncuts = 0, Npipes[3], vcount;
3854: PetscReal L = 1;
3856: Npipes[0] = (extent[0] + 1) * extent[1] * extent[2];
3857: Npipes[1] = extent[0] * (extent[1] + 1) * extent[2];
3858: Npipes[2] = extent[0] * extent[1] * (extent[2] + 1);
3859: Njunctions = extent[0] * extent[1] * extent[2];
3860: Ncuts = 2 * (extent[0] * extent[1] + extent[1] * extent[2] + extent[2] * extent[0]);
3861: numVertices = 4 * (Npipes[0] + Npipes[1] + Npipes[2]) + 8 * Njunctions;
3862: PetscCall(PetscMalloc1(3 * numVertices, &vtxCoords));
3863: PetscCall(PetscMalloc1(Njunctions, &cells));
3864: PetscCall(PetscMalloc1(Ncuts * 4, &edges));
3865: PetscCall(PetscMalloc1(Ncuts * 4, &edgeSets));
3866: // x-normal pipes
3867: vcount = 0;
3868: for (PetscInt i = 0; i < extent[0] + 1; i++) {
3869: for (PetscInt j = 0; j < extent[1]; j++) {
3870: for (PetscInt k = 0; k < extent[2]; k++) {
3871: for (PetscInt l = 0; l < 4; l++) {
3872: vtxCoords[vcount++] = (2 * i - 1) * L;
3873: vtxCoords[vcount++] = 2 * j * L + PetscCosReal((2 * l + 1) * PETSC_PI / 4) * L / 2;
3874: vtxCoords[vcount++] = 2 * k * L + PetscSinReal((2 * l + 1) * PETSC_PI / 4) * L / 2;
3875: }
3876: }
3877: }
3878: }
3879: // y-normal pipes
3880: for (PetscInt i = 0; i < extent[0]; i++) {
3881: for (PetscInt j = 0; j < extent[1] + 1; j++) {
3882: for (PetscInt k = 0; k < extent[2]; k++) {
3883: for (PetscInt l = 0; l < 4; l++) {
3884: vtxCoords[vcount++] = 2 * i * L + PetscSinReal((2 * l + 1) * PETSC_PI / 4) * L / 2;
3885: vtxCoords[vcount++] = (2 * j - 1) * L;
3886: vtxCoords[vcount++] = 2 * k * L + PetscCosReal((2 * l + 1) * PETSC_PI / 4) * L / 2;
3887: }
3888: }
3889: }
3890: }
3891: // z-normal pipes
3892: for (PetscInt i = 0; i < extent[0]; i++) {
3893: for (PetscInt j = 0; j < extent[1]; j++) {
3894: for (PetscInt k = 0; k < extent[2] + 1; k++) {
3895: for (PetscInt l = 0; l < 4; l++) {
3896: vtxCoords[vcount++] = 2 * i * L + PetscCosReal((2 * l + 1) * PETSC_PI / 4) * L / 2;
3897: vtxCoords[vcount++] = 2 * j * L + PetscSinReal((2 * l + 1) * PETSC_PI / 4) * L / 2;
3898: vtxCoords[vcount++] = (2 * k - 1) * L;
3899: }
3900: }
3901: }
3902: }
3903: // junctions
3904: for (PetscInt i = 0; i < extent[0]; i++) {
3905: for (PetscInt j = 0; j < extent[1]; j++) {
3906: for (PetscInt k = 0; k < extent[2]; k++) {
3907: const PetscInt J = (i * extent[1] + j) * extent[2] + k, Jvoff = (Npipes[0] + Npipes[1] + Npipes[2]) * 4 + J * 8;
3908: PetscCheck(vcount / 3 == Jvoff, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unexpected vertex count");
3909: for (PetscInt ii = 0; ii < 2; ii++) {
3910: for (PetscInt jj = 0; jj < 2; jj++) {
3911: for (PetscInt kk = 0; kk < 2; kk++) {
3912: double Ls = (1 - sqrt(2) / 4) * L;
3913: vtxCoords[vcount++] = 2 * i * L + (2 * ii - 1) * Ls;
3914: vtxCoords[vcount++] = 2 * j * L + (2 * jj - 1) * Ls;
3915: vtxCoords[vcount++] = 2 * k * L + (2 * kk - 1) * Ls;
3916: }
3917: }
3918: }
3919: const PetscInt jfaces[3][2][4] = {
3920: {{3, 1, 0, 2}, {7, 5, 4, 6}}, // x-aligned
3921: {{5, 4, 0, 1}, {7, 6, 2, 3}}, // y-aligned
3922: {{6, 2, 0, 4}, {7, 3, 1, 5}} // z-aligned
3923: };
3924: const PetscInt pipe_lo[3] = {// vertex numbers of pipes
3925: ((i * extent[1] + j) * extent[2] + k) * 4, ((i * (extent[1] + 1) + j) * extent[2] + k + Npipes[0]) * 4, ((i * extent[1] + j) * (extent[2] + 1) + k + Npipes[0] + Npipes[1]) * 4};
3926: const PetscInt pipe_hi[3] = {// vertex numbers of pipes
3927: (((i + 1) * extent[1] + j) * extent[2] + k) * 4, ((i * (extent[1] + 1) + j + 1) * extent[2] + k + Npipes[0]) * 4, ((i * extent[1] + j) * (extent[2] + 1) + k + 1 + Npipes[0] + Npipes[1]) * 4};
3928: for (PetscInt dir = 0; dir < 3; dir++) { // x,y,z
3929: const PetscInt ijk[3] = {i, j, k};
3930: for (PetscInt l = 0; l < 4; l++) { // rotations
3931: cells[J][dir * 2 + 0][l][0] = pipe_lo[dir] + l;
3932: cells[J][dir * 2 + 0][l][1] = Jvoff + jfaces[dir][0][l];
3933: cells[J][dir * 2 + 0][l][2] = Jvoff + jfaces[dir][0][(l - 1 + 4) % 4];
3934: cells[J][dir * 2 + 0][l][3] = pipe_lo[dir] + (l - 1 + 4) % 4;
3935: cells[J][dir * 2 + 1][l][0] = Jvoff + jfaces[dir][1][l];
3936: cells[J][dir * 2 + 1][l][1] = pipe_hi[dir] + l;
3937: cells[J][dir * 2 + 1][l][2] = pipe_hi[dir] + (l - 1 + 4) % 4;
3938: cells[J][dir * 2 + 1][l][3] = Jvoff + jfaces[dir][1][(l - 1 + 4) % 4];
3939: if (ijk[dir] == 0) {
3940: edges[numEdges][0] = pipe_lo[dir] + l;
3941: edges[numEdges][1] = pipe_lo[dir] + (l + 1) % 4;
3942: edgeSets[numEdges] = dir * 2 + 1;
3943: numEdges++;
3944: }
3945: if (ijk[dir] + 1 == extent[dir]) {
3946: edges[numEdges][0] = pipe_hi[dir] + l;
3947: edges[numEdges][1] = pipe_hi[dir] + (l + 1) % 4;
3948: edgeSets[numEdges] = dir * 2 + 2;
3949: numEdges++;
3950: }
3951: }
3952: }
3953: }
3954: }
3955: }
3956: PetscCheck(numEdges == Ncuts * 4, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Edge count %" PetscInt_FMT " incompatible with number of cuts %" PetscInt_FMT, numEdges, Ncuts);
3957: numFaces = 24 * Njunctions;
3958: cells_flat = cells[0][0][0];
3959: }
3960: evalFunc = TPSEvaluate_SchwarzP;
3961: normalFunc = TPSExtrudeNormalFunc_SchwarzP;
3962: break;
3963: case DMPLEX_TPS_GYROID:
3964: if (rank == 0) {
3965: // This is a coarse mesh approximation of the gyroid shifted to being the zero of the level set
3966: //
3967: // sin(pi*x)*cos(pi*(y+1/2)) + sin(pi*(y+1/2))*cos(pi*(z+1/4)) + sin(pi*(z+1/4))*cos(x)
3968: //
3969: // on the cell [0,2]^3.
3970: //
3971: // Think about dividing that cell into four columns, and focus on the column [0,1]x[0,1]x[0,2].
3972: // If you looked at the gyroid in that column at different slices of z you would see that it kind of spins
3973: // like a boomerang:
3974: //
3975: // z = 0 z = 1/4 z = 1/2 z = 3/4 //
3976: // ----- ------- ------- ------- //
3977: // //
3978: // + + + + + + + \ + //
3979: // \ / \ //
3980: // \ `-_ _-' / } //
3981: // *-_ `-' _-' / //
3982: // + `-+ + + +-' + + / + //
3983: // //
3984: // //
3985: // z = 1 z = 5/4 z = 3/2 z = 7/4 //
3986: // ----- ------- ------- ------- //
3987: // //
3988: // +-_ + + + + _-+ + / + //
3989: // `-_ _-_ _-` / //
3990: // \ _-' `-_ / { //
3991: // \ / \ //
3992: // + + + + + + + \ + //
3993: //
3994: //
3995: // This course mesh approximates each of these slices by two line segments,
3996: // and then connects the segments in consecutive layers with quadrilateral faces.
3997: // All of the end points of the segments are multiples of 1/4 except for the
3998: // point * in the picture for z = 0 above and the similar points in other layers.
3999: // That point is at (gamma, gamma, 0), where gamma is calculated below.
4000: //
4001: // The column [1,2]x[1,2]x[0,2] looks the same as this column;
4002: // The columns [1,2]x[0,1]x[0,2] and [0,1]x[1,2]x[0,2] are mirror images.
4003: //
4004: // As for how this method turned into the names given to the vertices:
4005: // that was not systematic, it was just the way it worked out in my handwritten notes.
4007: PetscInt facesPerBlock = 64;
4008: PetscInt vertsPerBlock = 56;
4009: PetscInt extentPlus[3];
4010: PetscInt numBlocks, numBlocksPlus;
4011: const PetscInt A = 0, B = 1, C = 2, D = 3, E = 4, F = 5, G = 6, H = 7, II = 8, J = 9, K = 10, L = 11, M = 12, N = 13, O = 14, P = 15, Q = 16, R = 17, S = 18, T = 19, U = 20, V = 21, W = 22, X = 23, Y = 24, Z = 25, Ap = 26, Bp = 27, Cp = 28, Dp = 29, Ep = 30, Fp = 31, Gp = 32, Hp = 33, Ip = 34, Jp = 35, Kp = 36, Lp = 37, Mp = 38, Np = 39, Op = 40, Pp = 41, Qp = 42, Rp = 43, Sp = 44, Tp = 45, Up = 46, Vp = 47, Wp = 48, Xp = 49, Yp = 50, Zp = 51, Aq = 52, Bq = 53, Cq = 54, Dq = 55;
4012: const PetscInt pattern[64][4] = {
4013: /* face to vertex within the coarse discretization of a single gyroid block */
4014: /* layer 0 */
4015: {A, C, K, G },
4016: {C, B, II, K },
4017: {D, A, H, L },
4018: {B + 56 * 1, D, L, J },
4019: {E, B + 56 * 1, J, N },
4020: {A + 56 * 2, E, N, H + 56 * 2 },
4021: {F, A + 56 * 2, G + 56 * 2, M },
4022: {B, F, M, II },
4023: /* layer 1 */
4024: {G, K, Q, O },
4025: {K, II, P, Q },
4026: {L, H, O + 56 * 1, R },
4027: {J, L, R, P },
4028: {N, J, P, S },
4029: {H + 56 * 2, N, S, O + 56 * 3 },
4030: {M, G + 56 * 2, O + 56 * 2, T },
4031: {II, M, T, P },
4032: /* layer 2 */
4033: {O, Q, Y, U },
4034: {Q, P, W, Y },
4035: {R, O + 56 * 1, U + 56 * 1, Ap },
4036: {P, R, Ap, W },
4037: {S, P, X, Bp },
4038: {O + 56 * 3, S, Bp, V + 56 * 1 },
4039: {T, O + 56 * 2, V, Z },
4040: {P, T, Z, X },
4041: /* layer 3 */
4042: {U, Y, Ep, Dp },
4043: {Y, W, Cp, Ep },
4044: {Ap, U + 56 * 1, Dp + 56 * 1, Gp },
4045: {W, Ap, Gp, Cp },
4046: {Bp, X, Cp + 56 * 2, Fp },
4047: {V + 56 * 1, Bp, Fp, Dp + 56 * 1},
4048: {Z, V, Dp, Hp },
4049: {X, Z, Hp, Cp + 56 * 2},
4050: /* layer 4 */
4051: {Dp, Ep, Mp, Kp },
4052: {Ep, Cp, Ip, Mp },
4053: {Gp, Dp + 56 * 1, Lp, Np },
4054: {Cp, Gp, Np, Jp },
4055: {Fp, Cp + 56 * 2, Jp + 56 * 2, Pp },
4056: {Dp + 56 * 1, Fp, Pp, Lp },
4057: {Hp, Dp, Kp, Op },
4058: {Cp + 56 * 2, Hp, Op, Ip + 56 * 2},
4059: /* layer 5 */
4060: {Kp, Mp, Sp, Rp },
4061: {Mp, Ip, Qp, Sp },
4062: {Np, Lp, Rp, Tp },
4063: {Jp, Np, Tp, Qp + 56 * 1},
4064: {Pp, Jp + 56 * 2, Qp + 56 * 3, Up },
4065: {Lp, Pp, Up, Rp },
4066: {Op, Kp, Rp, Vp },
4067: {Ip + 56 * 2, Op, Vp, Qp + 56 * 2},
4068: /* layer 6 */
4069: {Rp, Sp, Aq, Yp },
4070: {Sp, Qp, Wp, Aq },
4071: {Tp, Rp, Yp, Cq },
4072: {Qp + 56 * 1, Tp, Cq, Wp + 56 * 1},
4073: {Up, Qp + 56 * 3, Xp + 56 * 1, Dq },
4074: {Rp, Up, Dq, Zp },
4075: {Vp, Rp, Zp, Bq },
4076: {Qp + 56 * 2, Vp, Bq, Xp },
4077: /* layer 7 (the top is the periodic image of the bottom of layer 0) */
4078: {Yp, Aq, C + 56 * 4, A + 56 * 4 },
4079: {Aq, Wp, B + 56 * 4, C + 56 * 4 },
4080: {Cq, Yp, A + 56 * 4, D + 56 * 4 },
4081: {Wp + 56 * 1, Cq, D + 56 * 4, B + 56 * 5 },
4082: {Dq, Xp + 56 * 1, B + 56 * 5, E + 56 * 4 },
4083: {Zp, Dq, E + 56 * 4, A + 56 * 6 },
4084: {Bq, Zp, A + 56 * 6, F + 56 * 4 },
4085: {Xp, Bq, F + 56 * 4, B + 56 * 4 }
4086: };
4087: const PetscReal gamma = PetscAcosReal((PetscSqrtReal(3.) - 1.) / PetscSqrtReal(2.)) / PETSC_PI;
4088: const PetscReal patternCoords[56][3] = {
4089: {1., 0., 0. }, /* A */
4090: {0., 1., 0. }, /* B */
4091: {gamma, gamma, 0. }, /* C */
4092: {1 + gamma, 1 - gamma, 0. }, /* D */
4093: {2 - gamma, 2 - gamma, 0. }, /* E */
4094: {1 - gamma, 1 + gamma, 0. }, /* F */
4096: {.5, 0, .25 }, /* G */
4097: {1.5, 0., .25 }, /* H */
4098: {.5, 1., .25 }, /* II */
4099: {1.5, 1., .25 }, /* J */
4100: {.25, .5, .25 }, /* K */
4101: {1.25, .5, .25 }, /* L */
4102: {.75, 1.5, .25 }, /* M */
4103: {1.75, 1.5, .25 }, /* N */
4105: {0., 0., .5 }, /* O */
4106: {1., 1., .5 }, /* P */
4107: {gamma, 1 - gamma, .5 }, /* Q */
4108: {1 + gamma, gamma, .5 }, /* R */
4109: {2 - gamma, 1 + gamma, .5 }, /* S */
4110: {1 - gamma, 2 - gamma, .5 }, /* T */
4112: {0., .5, .75 }, /* U */
4113: {0., 1.5, .75 }, /* V */
4114: {1., .5, .75 }, /* W */
4115: {1., 1.5, .75 }, /* X */
4116: {.5, .75, .75 }, /* Y */
4117: {.5, 1.75, .75 }, /* Z */
4118: {1.5, .25, .75 }, /* Ap */
4119: {1.5, 1.25, .75 }, /* Bp */
4121: {1., 0., 1. }, /* Cp */
4122: {0., 1., 1. }, /* Dp */
4123: {1 - gamma, 1 - gamma, 1. }, /* Ep */
4124: {1 + gamma, 1 + gamma, 1. }, /* Fp */
4125: {2 - gamma, gamma, 1. }, /* Gp */
4126: {gamma, 2 - gamma, 1. }, /* Hp */
4128: {.5, 0., 1.25}, /* Ip */
4129: {1.5, 0., 1.25}, /* Jp */
4130: {.5, 1., 1.25}, /* Kp */
4131: {1.5, 1., 1.25}, /* Lp */
4132: {.75, .5, 1.25}, /* Mp */
4133: {1.75, .5, 1.25}, /* Np */
4134: {.25, 1.5, 1.25}, /* Op */
4135: {1.25, 1.5, 1.25}, /* Pp */
4137: {0., 0., 1.5 }, /* Qp */
4138: {1., 1., 1.5 }, /* Rp */
4139: {1 - gamma, gamma, 1.5 }, /* Sp */
4140: {2 - gamma, 1 - gamma, 1.5 }, /* Tp */
4141: {1 + gamma, 2 - gamma, 1.5 }, /* Up */
4142: {gamma, 1 + gamma, 1.5 }, /* Vp */
4144: {0., .5, 1.75}, /* Wp */
4145: {0., 1.5, 1.75}, /* Xp */
4146: {1., .5, 1.75}, /* Yp */
4147: {1., 1.5, 1.75}, /* Zp */
4148: {.5, .25, 1.75}, /* Aq */
4149: {.5, 1.25, 1.75}, /* Bq */
4150: {1.5, .75, 1.75}, /* Cq */
4151: {1.5, 1.75, 1.75}, /* Dq */
4152: };
4153: PetscInt (*cells)[64][4] = NULL;
4154: PetscBool *seen;
4155: PetscInt *vertToTrueVert;
4156: PetscInt count;
4158: for (PetscInt i = 0; i < 3; i++) extentPlus[i] = extent[i] + 1;
4159: numBlocks = 1;
4160: for (PetscInt i = 0; i < 3; i++) numBlocks *= extent[i];
4161: numBlocksPlus = 1;
4162: for (PetscInt i = 0; i < 3; i++) numBlocksPlus *= extentPlus[i];
4163: numFaces = numBlocks * facesPerBlock;
4164: PetscCall(PetscMalloc1(numBlocks, &cells));
4165: PetscCall(PetscCalloc1(numBlocksPlus * vertsPerBlock, &seen));
4166: for (PetscInt k = 0; k < extent[2]; k++) {
4167: for (PetscInt j = 0; j < extent[1]; j++) {
4168: for (PetscInt i = 0; i < extent[0]; i++) {
4169: for (PetscInt f = 0; f < facesPerBlock; f++) {
4170: for (PetscInt v = 0; v < 4; v++) {
4171: PetscInt vertRaw = pattern[f][v];
4172: PetscInt blockidx = vertRaw / 56;
4173: PetscInt patternvert = vertRaw % 56;
4174: PetscInt xplus = (blockidx & 1);
4175: PetscInt yplus = (blockidx & 2) >> 1;
4176: PetscInt zplus = (blockidx & 4) >> 2;
4177: PetscInt zcoord = (periodic && periodic[2] == DM_BOUNDARY_PERIODIC) ? ((k + zplus) % extent[2]) : (k + zplus);
4178: PetscInt ycoord = (periodic && periodic[1] == DM_BOUNDARY_PERIODIC) ? ((j + yplus) % extent[1]) : (j + yplus);
4179: PetscInt xcoord = (periodic && periodic[0] == DM_BOUNDARY_PERIODIC) ? ((i + xplus) % extent[0]) : (i + xplus);
4180: PetscInt vert = ((zcoord * extentPlus[1] + ycoord) * extentPlus[0] + xcoord) * 56 + patternvert;
4182: cells[(k * extent[1] + j) * extent[0] + i][f][v] = vert;
4183: seen[vert] = PETSC_TRUE;
4184: }
4185: }
4186: }
4187: }
4188: }
4189: for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++)
4190: if (seen[i]) numVertices++;
4191: count = 0;
4192: PetscCall(PetscMalloc1(numBlocksPlus * vertsPerBlock, &vertToTrueVert));
4193: PetscCall(PetscMalloc1(numVertices * 3, &vtxCoords));
4194: for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++) vertToTrueVert[i] = -1;
4195: for (PetscInt k = 0; k < extentPlus[2]; k++) {
4196: for (PetscInt j = 0; j < extentPlus[1]; j++) {
4197: for (PetscInt i = 0; i < extentPlus[0]; i++) {
4198: for (PetscInt v = 0; v < vertsPerBlock; v++) {
4199: PetscInt vIdx = ((k * extentPlus[1] + j) * extentPlus[0] + i) * vertsPerBlock + v;
4201: if (seen[vIdx]) {
4202: PetscInt thisVert;
4204: vertToTrueVert[vIdx] = thisVert = count++;
4206: for (PetscInt d = 0; d < 3; d++) vtxCoords[3 * thisVert + d] = patternCoords[v][d];
4207: vtxCoords[3 * thisVert + 0] += i * 2;
4208: vtxCoords[3 * thisVert + 1] += j * 2;
4209: vtxCoords[3 * thisVert + 2] += k * 2;
4210: }
4211: }
4212: }
4213: }
4214: }
4215: for (PetscInt i = 0; i < numBlocks; i++) {
4216: for (PetscInt f = 0; f < facesPerBlock; f++) {
4217: for (PetscInt v = 0; v < 4; v++) cells[i][f][v] = vertToTrueVert[cells[i][f][v]];
4218: }
4219: }
4220: PetscCall(PetscFree(vertToTrueVert));
4221: PetscCall(PetscFree(seen));
4222: cells_flat = cells[0][0];
4223: numEdges = 0;
4224: for (PetscInt i = 0; i < numFaces; i++) {
4225: for (PetscInt e = 0; e < 4; e++) {
4226: PetscInt ev[] = {cells_flat[i * 4 + e], cells_flat[i * 4 + ((e + 1) % 4)]};
4227: const PetscReal *evCoords[] = {&vtxCoords[3 * ev[0]], &vtxCoords[3 * ev[1]]};
4229: for (PetscInt d = 0; d < 3; d++) {
4230: if (!periodic || periodic[0] != DM_BOUNDARY_PERIODIC) {
4231: if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) numEdges++;
4232: if (evCoords[0][d] == 2. * extent[d] && evCoords[1][d] == 2. * extent[d]) numEdges++;
4233: }
4234: }
4235: }
4236: }
4237: PetscCall(PetscMalloc1(numEdges, &edges));
4238: PetscCall(PetscMalloc1(numEdges, &edgeSets));
4239: for (PetscInt edge = 0, i = 0; i < numFaces; i++) {
4240: for (PetscInt e = 0; e < 4; e++) {
4241: PetscInt ev[] = {cells_flat[i * 4 + e], cells_flat[i * 4 + ((e + 1) % 4)]};
4242: const PetscReal *evCoords[] = {&vtxCoords[3 * ev[0]], &vtxCoords[3 * ev[1]]};
4244: for (PetscInt d = 0; d < 3; d++) {
4245: if (!periodic || periodic[d] != DM_BOUNDARY_PERIODIC) {
4246: if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) {
4247: edges[edge][0] = ev[0];
4248: edges[edge][1] = ev[1];
4249: edgeSets[edge++] = 2 * d;
4250: }
4251: if (evCoords[0][d] == 2. * extent[d] && evCoords[1][d] == 2. * extent[d]) {
4252: edges[edge][0] = ev[0];
4253: edges[edge][1] = ev[1];
4254: edgeSets[edge++] = 2 * d + 1;
4255: }
4256: }
4257: }
4258: }
4259: }
4260: }
4261: evalFunc = TPSEvaluate_Gyroid;
4262: normalFunc = TPSExtrudeNormalFunc_Gyroid;
4263: break;
4264: }
4266: PetscCall(DMSetDimension(dm, topoDim));
4267: if (rank == 0) PetscCall(DMPlexBuildFromCellList(dm, numFaces, numVertices, 4, cells_flat));
4268: else PetscCall(DMPlexBuildFromCellList(dm, 0, 0, 0, NULL));
4269: PetscCall(PetscFree(cells_flat));
4270: {
4271: DM idm;
4272: PetscCall(DMPlexInterpolate(dm, &idm));
4273: PetscCall(DMPlexReplace_Internal(dm, &idm));
4274: }
4275: if (rank == 0) PetscCall(DMPlexBuildCoordinatesFromCellList(dm, spaceDim, vtxCoords));
4276: else PetscCall(DMPlexBuildCoordinatesFromCellList(dm, spaceDim, NULL));
4277: PetscCall(PetscFree(vtxCoords));
4279: PetscCall(DMCreateLabel(dm, "Face Sets"));
4280: PetscCall(DMGetLabel(dm, "Face Sets", &label));
4281: for (PetscInt e = 0; e < numEdges; e++) {
4282: PetscInt njoin;
4283: const PetscInt *join, verts[] = {numFaces + edges[e][0], numFaces + edges[e][1]};
4284: PetscCall(DMPlexGetJoin(dm, 2, verts, &njoin, &join));
4285: PetscCheck(njoin == 1, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Expected unique join of vertices %" PetscInt_FMT " and %" PetscInt_FMT, edges[e][0], edges[e][1]);
4286: PetscCall(DMLabelSetValue(label, join[0], edgeSets[e]));
4287: PetscCall(DMPlexRestoreJoin(dm, 2, verts, &njoin, &join));
4288: }
4289: PetscCall(PetscFree(edges));
4290: PetscCall(PetscFree(edgeSets));
4291: if (tps_distribute) {
4292: DM pdm = NULL;
4293: PetscPartitioner part;
4295: PetscCall(DMPlexGetPartitioner(dm, &part));
4296: PetscCall(PetscPartitionerSetFromOptions(part));
4297: PetscCall(DMPlexDistribute(dm, 0, NULL, &pdm));
4298: if (pdm) PetscCall(DMPlexReplace_Internal(dm, &pdm));
4299: // Do not auto-distribute again
4300: PetscCall(DMPlexDistributeSetDefault(dm, PETSC_FALSE));
4301: }
4303: PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE));
4304: for (PetscInt refine = 0; refine < refinements; refine++) {
4305: PetscInt m;
4306: DM dmf, cdm, cdmf;
4307: Vec X;
4308: PetscScalar *x;
4310: PetscCall(DMRefine(dm, MPI_COMM_NULL, &dmf));
4311: PetscCall(DMGetCoordinateDM(dm, &cdm));
4312: PetscCall(DMGetCoordinateDM(dmf, &cdmf));
4313: PetscCall(DMCopyDisc(cdm, cdmf));
4314: PetscCall(DMPlexReplace_Internal(dm, &dmf));
4316: PetscCall(DMGetCoordinatesLocal(dm, &X));
4317: PetscCall(VecGetLocalSize(X, &m));
4318: PetscCall(VecGetArray(X, &x));
4319: for (PetscInt i = 0; i < m; i += 3) PetscCall(TPSNearestPoint(evalFunc, &x[i]));
4320: PetscCall(VecRestoreArray(X, &x));
4321: }
4323: // Face Sets has already been propagated to new vertices during refinement; this propagates to the initial vertices.
4324: PetscCall(DMGetLabel(dm, "Face Sets", &label));
4325: PetscCall(DMPlexLabelComplete(dm, label));
4327: PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0));
4329: if (thickness > 0) {
4330: DM edm, cdm, ecdm;
4331: DMPlexTransform tr;
4332: const char *prefix;
4333: PetscOptions options;
4334: // Code from DMPlexExtrude
4335: PetscCall(DMPlexTransformCreate(PetscObjectComm((PetscObject)dm), &tr));
4336: PetscCall(DMPlexTransformSetDM(tr, dm));
4337: PetscCall(DMPlexTransformSetType(tr, DMPLEXEXTRUDETYPE));
4338: PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm, &prefix));
4339: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)tr, prefix));
4340: PetscCall(PetscObjectGetOptions((PetscObject)dm, &options));
4341: PetscCall(PetscObjectSetOptions((PetscObject)tr, options));
4342: PetscCall(DMPlexTransformExtrudeSetLayers(tr, layers));
4343: PetscCall(DMPlexTransformExtrudeSetThickness(tr, thickness));
4344: PetscCall(DMPlexTransformExtrudeSetTensor(tr, PETSC_FALSE));
4345: PetscCall(DMPlexTransformExtrudeSetSymmetric(tr, PETSC_TRUE));
4346: PetscCall(DMPlexTransformExtrudeSetNormalFunction(tr, normalFunc));
4347: PetscCall(DMPlexTransformSetFromOptions(tr));
4348: PetscCall(PetscObjectSetOptions((PetscObject)tr, NULL));
4349: PetscCall(DMPlexTransformSetUp(tr));
4350: PetscCall(PetscObjectViewFromOptions((PetscObject)tr, NULL, "-dm_plex_tps_transform_view"));
4351: PetscCall(DMPlexTransformApply(tr, dm, &edm));
4352: PetscCall(DMCopyDisc(dm, edm));
4353: PetscCall(DMGetCoordinateDM(dm, &cdm));
4354: PetscCall(DMGetCoordinateDM(edm, &ecdm));
4355: PetscCall(DMCopyDisc(cdm, ecdm));
4356: PetscCall(DMPlexTransformCreateDiscLabels(tr, edm));
4357: PetscCall(DMPlexTransformDestroy(&tr));
4358: PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, edm));
4359: PetscCall(DMPlexReplace_Internal(dm, &edm));
4360: }
4361: PetscFunctionReturn(PETSC_SUCCESS);
4362: }
4364: /*@
4365: DMPlexCreateTPSMesh - Create a distributed, interpolated mesh of a triply-periodic surface
4367: Collective
4369: Input Parameters:
4370: + comm - The communicator for the `DM` object
4371: . tpstype - Type of triply-periodic surface
4372: . extent - Array of length 3 containing number of periods in each direction
4373: . periodic - array of length 3 with periodicity, or `NULL` for non-periodic
4374: . tps_distribute - Distribute 2D manifold mesh prior to refinement and extrusion (more scalable)
4375: . refinements - Number of factor-of-2 refinements of 2D manifold mesh
4376: . layers - Number of cell layers extruded in normal direction
4377: - thickness - Thickness in normal direction
4379: Output Parameter:
4380: . dm - The `DM` object
4382: Level: beginner
4384: Notes:
4385: This meshes the surface of the Schwarz P or Gyroid surfaces. Schwarz P is the simplest member of the triply-periodic minimal surfaces.
4386: <https://en.wikipedia.org/wiki/Schwarz_minimal_surface#Schwarz_P_(%22Primitive%22)> and can be cut with "clean" boundaries.
4387: The Gyroid <https://en.wikipedia.org/wiki/Gyroid> is another triply-periodic minimal surface with applications in additive manufacturing; it is much more difficult to "cut" since there are no planes of symmetry.
4388: Our implementation creates a very coarse mesh of the surface and refines (by 4-way splitting) as many times as requested.
4389: On each refinement, all vertices are projected to their nearest point on the surface.
4390: This projection could readily be extended to related surfaces.
4392: See {cite}`maskery2018insights`
4394: The face (edge) sets for the Schwarz P surface are numbered $1(-x), 2(+x), 3(-y), 4(+y), 5(-z), 6(+z)$.
4395: When the mesh is refined, "Face Sets" contain the new vertices (created during refinement).
4396: Use `DMPlexLabelComplete()` to propagate to coarse-level vertices.
4398: Developer Notes:
4399: The Gyroid mesh does not currently mark boundary sets.
4401: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateSphereMesh()`, `DMSetType()`, `DMCreate()`
4402: @*/
4403: PetscErrorCode DMPlexCreateTPSMesh(MPI_Comm comm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscBool tps_distribute, PetscInt refinements, PetscInt layers, PetscReal thickness, DM *dm)
4404: {
4405: PetscFunctionBegin;
4406: PetscCall(DMCreate(comm, dm));
4407: PetscCall(DMSetType(*dm, DMPLEX));
4408: PetscCall(DMPlexCreateTPSMesh_Internal(*dm, tpstype, extent, periodic, tps_distribute, refinements, layers, thickness));
4409: PetscFunctionReturn(PETSC_SUCCESS);
4410: }
4412: /*@
4413: DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d.
4415: Collective
4417: Input Parameters:
4418: + comm - The communicator for the `DM` object
4419: . dim - The dimension
4420: . simplex - Use simplices, or tensor product cells
4421: - R - The radius
4423: Output Parameter:
4424: . dm - The `DM` object
4426: Level: beginner
4428: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateBallMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()`
4429: @*/
4430: PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscReal R, DM *dm)
4431: {
4432: PetscFunctionBegin;
4433: PetscAssertPointer(dm, 5);
4434: PetscCall(DMCreate(comm, dm));
4435: PetscCall(DMSetType(*dm, DMPLEX));
4436: PetscCall(DMPlexCreateSphereMesh_Internal(*dm, dim, simplex, R));
4437: PetscFunctionReturn(PETSC_SUCCESS);
4438: }
4440: static PetscErrorCode DMPlexCreateBallMesh_Internal(DM dm, PetscInt dim, PetscReal R)
4441: {
4442: DM sdm, vol;
4443: DMLabel bdlabel;
4444: const char *prefix;
4446: PetscFunctionBegin;
4447: PetscCall(DMCreate(PetscObjectComm((PetscObject)dm), &sdm));
4448: PetscCall(DMSetType(sdm, DMPLEX));
4449: PetscCall(DMGetOptionsPrefix(dm, &prefix));
4450: PetscCall(DMSetOptionsPrefix(sdm, prefix));
4451: PetscCall(DMAppendOptionsPrefix(sdm, "bd_"));
4452: PetscCall(DMPlexDistributeSetDefault(sdm, PETSC_FALSE));
4453: PetscCall(DMPlexCreateSphereMesh_Internal(sdm, dim - 1, PETSC_TRUE, R));
4454: PetscCall(DMSetFromOptions(sdm));
4455: PetscCall(DMViewFromOptions(sdm, NULL, "-dm_view"));
4456: PetscCall(DMPlexGenerate(sdm, NULL, PETSC_TRUE, &vol));
4457: PetscCall(DMDestroy(&sdm));
4458: PetscCall(DMPlexReplace_Internal(dm, &vol));
4459: PetscCall(DMCreateLabel(dm, "marker"));
4460: PetscCall(DMGetLabel(dm, "marker", &bdlabel));
4461: PetscCall(DMPlexMarkBoundaryFaces(dm, PETSC_DETERMINE, bdlabel));
4462: PetscCall(DMPlexLabelComplete(dm, bdlabel));
4463: PetscFunctionReturn(PETSC_SUCCESS);
4464: }
4466: /*@
4467: DMPlexCreateBallMesh - Creates a simplex mesh on the d-dimensional ball, B^d.
4469: Collective
4471: Input Parameters:
4472: + comm - The communicator for the `DM` object
4473: . dim - The dimension
4474: - R - The radius
4476: Output Parameter:
4477: . dm - The `DM` object
4479: Options Database Key:
4480: . bd_dm_refine - This will refine the surface mesh preserving the sphere geometry
4482: Level: beginner
4484: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateSphereMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()`
4485: @*/
4486: PetscErrorCode DMPlexCreateBallMesh(MPI_Comm comm, PetscInt dim, PetscReal R, DM *dm)
4487: {
4488: PetscFunctionBegin;
4489: PetscCall(DMCreate(comm, dm));
4490: PetscCall(DMSetType(*dm, DMPLEX));
4491: PetscCall(DMPlexCreateBallMesh_Internal(*dm, dim, R));
4492: PetscFunctionReturn(PETSC_SUCCESS);
4493: }
4495: static PetscErrorCode DMPlexCreateReferenceCell_Internal(DM rdm, DMPolytopeType ct)
4496: {
4497: PetscFunctionBegin;
4498: switch (ct) {
4499: case DM_POLYTOPE_POINT: {
4500: PetscInt numPoints[1] = {1};
4501: PetscInt coneSize[1] = {0};
4502: PetscInt cones[1] = {0};
4503: PetscInt coneOrientations[1] = {0};
4504: PetscScalar vertexCoords[1] = {0.0};
4506: PetscCall(DMSetDimension(rdm, 0));
4507: PetscCall(DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords));
4508: } break;
4509: case DM_POLYTOPE_SEGMENT: {
4510: PetscInt numPoints[2] = {2, 1};
4511: PetscInt coneSize[3] = {2, 0, 0};
4512: PetscInt cones[2] = {1, 2};
4513: PetscInt coneOrientations[2] = {0, 0};
4514: PetscScalar vertexCoords[2] = {-1.0, 1.0};
4516: PetscCall(DMSetDimension(rdm, 1));
4517: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
4518: } break;
4519: case DM_POLYTOPE_POINT_PRISM_TENSOR: {
4520: PetscInt numPoints[2] = {2, 1};
4521: PetscInt coneSize[3] = {2, 0, 0};
4522: PetscInt cones[2] = {1, 2};
4523: PetscInt coneOrientations[2] = {0, 0};
4524: PetscScalar vertexCoords[2] = {-1.0, 1.0};
4526: PetscCall(DMSetDimension(rdm, 1));
4527: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
4528: } break;
4529: case DM_POLYTOPE_TRIANGLE: {
4530: PetscInt numPoints[2] = {3, 1};
4531: PetscInt coneSize[4] = {3, 0, 0, 0};
4532: PetscInt cones[3] = {1, 2, 3};
4533: PetscInt coneOrientations[3] = {0, 0, 0};
4534: PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0};
4536: PetscCall(DMSetDimension(rdm, 2));
4537: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
4538: } break;
4539: case DM_POLYTOPE_QUADRILATERAL: {
4540: PetscInt numPoints[2] = {4, 1};
4541: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
4542: PetscInt cones[4] = {1, 2, 3, 4};
4543: PetscInt coneOrientations[4] = {0, 0, 0, 0};
4544: PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0};
4546: PetscCall(DMSetDimension(rdm, 2));
4547: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
4548: } break;
4549: case DM_POLYTOPE_SEG_PRISM_TENSOR: {
4550: PetscInt numPoints[2] = {4, 1};
4551: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
4552: PetscInt cones[4] = {1, 2, 3, 4};
4553: PetscInt coneOrientations[4] = {0, 0, 0, 0};
4554: PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, 1.0};
4556: PetscCall(DMSetDimension(rdm, 2));
4557: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
4558: } break;
4559: case DM_POLYTOPE_TETRAHEDRON: {
4560: PetscInt numPoints[2] = {4, 1};
4561: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
4562: PetscInt cones[4] = {1, 2, 3, 4};
4563: PetscInt coneOrientations[4] = {0, 0, 0, 0};
4564: PetscScalar vertexCoords[12] = {-1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, -1.0, -1.0, -1.0, -1.0, 1.0};
4566: PetscCall(DMSetDimension(rdm, 3));
4567: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
4568: } break;
4569: case DM_POLYTOPE_HEXAHEDRON: {
4570: PetscInt numPoints[2] = {8, 1};
4571: PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0};
4572: PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8};
4573: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
4574: PetscScalar vertexCoords[24] = {-1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, -1.0, -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0};
4576: PetscCall(DMSetDimension(rdm, 3));
4577: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
4578: } break;
4579: case DM_POLYTOPE_TRI_PRISM: {
4580: PetscInt numPoints[2] = {6, 1};
4581: PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0};
4582: PetscInt cones[6] = {1, 2, 3, 4, 5, 6};
4583: PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0};
4584: PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, -1.0, -1.0, -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0};
4586: PetscCall(DMSetDimension(rdm, 3));
4587: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
4588: } break;
4589: case DM_POLYTOPE_TRI_PRISM_TENSOR: {
4590: PetscInt numPoints[2] = {6, 1};
4591: PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0};
4592: PetscInt cones[6] = {1, 2, 3, 4, 5, 6};
4593: PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0};
4594: PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0};
4596: PetscCall(DMSetDimension(rdm, 3));
4597: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
4598: } break;
4599: case DM_POLYTOPE_QUAD_PRISM_TENSOR: {
4600: PetscInt numPoints[2] = {8, 1};
4601: PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0};
4602: PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8};
4603: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
4604: PetscScalar vertexCoords[24] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0};
4606: PetscCall(DMSetDimension(rdm, 3));
4607: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
4608: } break;
4609: case DM_POLYTOPE_PYRAMID: {
4610: PetscInt numPoints[2] = {5, 1};
4611: PetscInt coneSize[6] = {5, 0, 0, 0, 0, 0};
4612: PetscInt cones[5] = {1, 2, 3, 4, 5};
4613: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
4614: PetscScalar vertexCoords[24] = {-1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, -1.0, 0.0, 0.0, 1.0};
4616: PetscCall(DMSetDimension(rdm, 3));
4617: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
4618: } break;
4619: default:
4620: SETERRQ(PetscObjectComm((PetscObject)rdm), PETSC_ERR_ARG_WRONG, "Cannot create reference cell for cell type %s", DMPolytopeTypes[ct]);
4621: }
4622: {
4623: PetscInt Nv, v;
4625: /* Must create the celltype label here so that we do not automatically try to compute the types */
4626: PetscCall(DMCreateLabel(rdm, "celltype"));
4627: PetscCall(DMPlexSetCellType(rdm, 0, ct));
4628: PetscCall(DMPlexGetChart(rdm, NULL, &Nv));
4629: for (v = 1; v < Nv; ++v) PetscCall(DMPlexSetCellType(rdm, v, DM_POLYTOPE_POINT));
4630: }
4631: PetscCall(DMPlexInterpolateInPlace_Internal(rdm));
4632: PetscCall(PetscObjectSetName((PetscObject)rdm, DMPolytopeTypes[ct]));
4633: PetscFunctionReturn(PETSC_SUCCESS);
4634: }
4636: /*@
4637: DMPlexCreateReferenceCell - Create a `DMPLEX` with the appropriate FEM reference cell
4639: Collective
4641: Input Parameters:
4642: + comm - The communicator
4643: - ct - The cell type of the reference cell
4645: Output Parameter:
4646: . refdm - The reference cell
4648: Level: intermediate
4650: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateBoxMesh()`
4651: @*/
4652: PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, DMPolytopeType ct, DM *refdm)
4653: {
4654: PetscFunctionBegin;
4655: PetscCall(DMCreate(comm, refdm));
4656: PetscCall(DMSetType(*refdm, DMPLEX));
4657: PetscCall(DMPlexCreateReferenceCell_Internal(*refdm, ct));
4658: PetscFunctionReturn(PETSC_SUCCESS);
4659: }
4661: static PetscErrorCode DMPlexCreateBoundaryLabel_Private(DM dm, const char name[])
4662: {
4663: DM plex;
4664: DMLabel label;
4665: PetscBool hasLabel;
4667: PetscFunctionBegin;
4668: PetscCall(DMHasLabel(dm, name, &hasLabel));
4669: if (hasLabel) PetscFunctionReturn(PETSC_SUCCESS);
4670: PetscCall(DMCreateLabel(dm, name));
4671: PetscCall(DMGetLabel(dm, name, &label));
4672: PetscCall(DMConvert(dm, DMPLEX, &plex));
4673: PetscCall(DMPlexMarkBoundaryFaces(plex, 1, label));
4674: PetscCall(DMPlexLabelComplete(plex, label));
4675: PetscCall(DMDestroy(&plex));
4676: PetscFunctionReturn(PETSC_SUCCESS);
4677: }
4679: /*
4680: We use the last coordinate as the radius, the inner radius is lower[dim-1] and the outer radius is upper[dim-1]. Then we map the first coordinate around the circle.
4682: (x, y) -> (r, theta) = (x[1], (x[0] - lower[0]) * 2\pi/(upper[0] - lower[0]))
4683: */
4684: static void boxToAnnulus(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[])
4685: {
4686: const PetscReal low = PetscRealPart(constants[0]);
4687: const PetscReal upp = PetscRealPart(constants[1]);
4688: const PetscReal r = PetscRealPart(u[1]);
4689: const PetscReal th = 2. * PETSC_PI * (PetscRealPart(u[0]) - low) / (upp - low);
4691: f0[0] = r * PetscCosReal(th);
4692: f0[1] = r * PetscSinReal(th);
4693: }
4695: // Insert vertices and their joins, marked by depth
4696: static PetscErrorCode ProcessCohesiveLabel_Vertices(DM dm, DMLabel label, DMLabel vlabel, PetscInt val, PetscInt n, const PetscInt vertices[])
4697: {
4698: PetscFunctionBegin;
4699: PetscCall(DMPlexMarkSubmesh_Interpolated(dm, vlabel, val, PETSC_FALSE, PETSC_FALSE, label, NULL));
4700: PetscFunctionReturn(PETSC_SUCCESS);
4701: }
4703: // Insert faces and their closures, marked by depth
4704: static PetscErrorCode ProcessCohesiveLabel_Faces(DM dm, DMLabel label, PetscInt n, const PetscInt faces[])
4705: {
4706: PetscFunctionBegin;
4707: for (PetscInt p = 0; p < n; ++p) {
4708: const PetscInt point = faces[p];
4709: PetscInt *closure = NULL;
4710: PetscInt clSize, pdepth;
4712: PetscCall(DMPlexGetPointDepth(dm, point, &pdepth));
4713: PetscCall(DMLabelSetValue(label, point, pdepth));
4714: PetscCall(DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &clSize, &closure));
4715: for (PetscInt cl = 0; cl < clSize * 2; cl += 2) {
4716: PetscCall(DMPlexGetPointDepth(dm, closure[cl], &pdepth));
4717: PetscCall(DMLabelSetValue(label, closure[cl], pdepth));
4718: }
4719: PetscCall(DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &clSize, &closure));
4720: }
4721: PetscFunctionReturn(PETSC_SUCCESS);
4722: }
4724: PETSC_EXTERN PetscErrorCode PetscOptionsFindPairPrefix_Private(PetscOptions, const char pre[], const char name[], const char *option[], const char *value[], PetscBool *flg);
4726: const char *const DMPlexShapes[] = {"box", "box_surface", "ball", "sphere", "cylinder", "schwarz_p", "gyroid", "doublet", "annulus", "hypercubic", "zbox", "unknown", "DMPlexShape", "DM_SHAPE_", NULL};
4728: static PetscErrorCode DMPlexCreateFromOptions_Internal(PetscOptionItems PetscOptionsObject, PetscBool *useCoordSpace, DM dm)
4729: {
4730: DMPlexShape shape = DM_SHAPE_BOX;
4731: DMPolytopeType cell = DM_POLYTOPE_TRIANGLE;
4732: PetscInt dim = 2;
4733: PetscBool simplex = PETSC_TRUE, interpolate = PETSC_TRUE, orient = PETSC_FALSE, adjCone = PETSC_FALSE, adjClosure = PETSC_TRUE, refDomain = PETSC_FALSE;
4734: PetscBool flg, flg2, fflg, strflg, bdfflg, nameflg;
4735: MPI_Comm comm;
4736: char filename[PETSC_MAX_PATH_LEN] = "<unspecified>";
4737: char bdFilename[PETSC_MAX_PATH_LEN] = "<unspecified>";
4738: char plexname[PETSC_MAX_PATH_LEN] = "";
4739: const char *option;
4741: PetscFunctionBegin;
4742: PetscCall(PetscLogEventBegin(DMPLEX_CreateFromOptions, dm, 0, 0, 0));
4743: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
4744: /* TODO Turn this into a registration interface */
4745: PetscCall(PetscOptionsString("-dm_plex_filename", "File containing a mesh", "DMPlexCreateFromFile", filename, filename, sizeof(filename), &fflg));
4746: PetscCall(PetscOptionsString("-dm_plex_file_contents", "Contents of a file format in a string", "DMPlexCreateFromFile", filename, filename, sizeof(filename), &strflg));
4747: PetscCall(PetscOptionsString("-dm_plex_boundary_filename", "File containing a mesh boundary", "DMPlexCreateFromFile", bdFilename, bdFilename, sizeof(bdFilename), &bdfflg));
4748: PetscCall(PetscOptionsString("-dm_plex_name", "Name of the mesh in the file", "DMPlexCreateFromFile", plexname, plexname, sizeof(plexname), &nameflg));
4749: PetscCall(PetscOptionsEnum("-dm_plex_cell", "Cell shape", "", DMPolytopeTypes, (PetscEnum)cell, (PetscEnum *)&cell, NULL));
4750: PetscCall(PetscOptionsBool("-dm_plex_reference_cell_domain", "Use a reference cell domain", "", refDomain, &refDomain, NULL));
4751: PetscCall(PetscOptionsEnum("-dm_plex_shape", "Shape for built-in mesh", "", DMPlexShapes, (PetscEnum)shape, (PetscEnum *)&shape, &flg));
4752: PetscCall(PetscOptionsBoundedInt("-dm_plex_dim", "Topological dimension of the mesh", "DMGetDimension", dim, &dim, &flg, 0));
4753: PetscCall(PetscOptionsBool("-dm_plex_simplex", "Mesh cell shape", "", simplex, &simplex, &flg));
4754: PetscCall(PetscOptionsBool("-dm_plex_interpolate", "Flag to create edges and faces automatically", "", interpolate, &interpolate, &flg));
4755: PetscCall(PetscOptionsBool("-dm_plex_orient", "Orient the constructed mesh", "DMPlexOrient", orient, &orient, &flg));
4756: PetscCall(PetscOptionsBool("-dm_plex_adj_cone", "Set adjacency direction", "DMSetBasicAdjacency", adjCone, &adjCone, &flg));
4757: PetscCall(PetscOptionsBool("-dm_plex_adj_closure", "Set adjacency size", "DMSetBasicAdjacency", adjClosure, &adjClosure, &flg2));
4758: if (flg || flg2) PetscCall(DMSetBasicAdjacency(dm, adjCone, adjClosure));
4759: PetscCall(PetscOptionsBoundedInt("-dm_plex_print_adj", "Debug output level all adjacency computations", "", 0, &((DM_Plex *)dm->data)->printAdj, NULL, 0));
4761: switch (cell) {
4762: case DM_POLYTOPE_POINT:
4763: case DM_POLYTOPE_SEGMENT:
4764: case DM_POLYTOPE_POINT_PRISM_TENSOR:
4765: case DM_POLYTOPE_TRIANGLE:
4766: case DM_POLYTOPE_QUADRILATERAL:
4767: case DM_POLYTOPE_TETRAHEDRON:
4768: case DM_POLYTOPE_HEXAHEDRON:
4769: *useCoordSpace = PETSC_TRUE;
4770: break;
4771: default:
4772: *useCoordSpace = PETSC_FALSE;
4773: break;
4774: }
4776: if (fflg) {
4777: DM dmnew;
4778: const char *name;
4780: PetscCall(PetscObjectGetName((PetscObject)dm, &name));
4781: PetscCall(DMPlexCreateFromFile(PetscObjectComm((PetscObject)dm), filename, nameflg ? plexname : name, interpolate, &dmnew));
4782: PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew));
4783: PetscCall(DMPlexReplace_Internal(dm, &dmnew));
4784: } else if (refDomain) {
4785: PetscCall(DMPlexCreateReferenceCell_Internal(dm, cell));
4786: } else if (bdfflg) {
4787: DM bdm, dmnew;
4788: const char *name;
4790: PetscCall(PetscObjectGetName((PetscObject)dm, &name));
4791: PetscCall(DMPlexCreateFromFile(PetscObjectComm((PetscObject)dm), bdFilename, nameflg ? plexname : name, interpolate, &bdm));
4792: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)bdm, "bd_"));
4793: PetscCall(DMSetFromOptions(bdm));
4794: PetscCall(DMPlexGenerate(bdm, NULL, interpolate, &dmnew));
4795: PetscCall(DMDestroy(&bdm));
4796: PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew));
4797: PetscCall(DMPlexReplace_Internal(dm, &dmnew));
4798: } else if (strflg) {
4799: DM dmnew;
4800: PetscViewer viewer;
4801: const char *contents;
4802: char *strname;
4803: char tmpdir[PETSC_MAX_PATH_LEN];
4804: char tmpfilename[PETSC_MAX_PATH_LEN];
4805: char name[PETSC_MAX_PATH_LEN];
4806: MPI_Comm comm;
4807: PetscMPIInt rank;
4809: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
4810: PetscCallMPI(MPI_Comm_rank(comm, &rank));
4811: PetscCall(PetscStrchr(filename, ':', &strname));
4812: PetscCheck(strname, comm, PETSC_ERR_ARG_WRONG, "File contents must have the form \"ext:string_name\", not %s", filename);
4813: strname[0] = '\0';
4814: ++strname;
4815: PetscCall(PetscDLSym(NULL, strname, (void **)&contents));
4816: PetscCheck(contents, comm, PETSC_ERR_ARG_WRONG, "Could not locate mesh string %s", strname);
4817: PetscCall(PetscGetTmp(comm, tmpdir, PETSC_MAX_PATH_LEN));
4818: PetscCall(PetscStrlcat(tmpdir, "/meshXXXXXX", PETSC_MAX_PATH_LEN));
4819: PetscCall(PetscMkdtemp(tmpdir));
4820: PetscCall(PetscSNPrintf(tmpfilename, PETSC_MAX_PATH_LEN, "%s/mesh.%s", tmpdir, filename));
4821: PetscCall(PetscViewerASCIIOpen(comm, tmpfilename, &viewer));
4822: PetscCall(PetscViewerASCIIPrintf(viewer, "%s\n", contents));
4823: PetscCall(PetscViewerDestroy(&viewer));
4824: PetscCall(DMPlexCreateFromFile(PetscObjectComm((PetscObject)dm), tmpfilename, plexname, interpolate, &dmnew));
4825: PetscCall(PetscRMTree(tmpdir));
4826: PetscCall(PetscSNPrintf(name, PETSC_MAX_PATH_LEN, "%s Mesh", strname));
4827: PetscCall(PetscObjectSetName((PetscObject)dm, name));
4828: PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew));
4829: PetscCall(DMPlexReplace_Internal(dm, &dmnew));
4830: } else {
4831: PetscCall(PetscObjectSetName((PetscObject)dm, DMPlexShapes[shape]));
4832: switch (shape) {
4833: case DM_SHAPE_BOX:
4834: case DM_SHAPE_ZBOX:
4835: case DM_SHAPE_ANNULUS: {
4836: PetscInt faces[3] = {0, 0, 0};
4837: PetscReal lower[3] = {0, 0, 0};
4838: PetscReal upper[3] = {1, 1, 1};
4839: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
4840: PetscBool isAnnular = shape == DM_SHAPE_ANNULUS ? PETSC_TRUE : PETSC_FALSE;
4841: PetscInt i, n;
4843: n = dim;
4844: for (i = 0; i < dim; ++i) faces[i] = (dim == 1 ? 1 : 4 - dim);
4845: PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg));
4846: n = 3;
4847: PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg));
4848: PetscCheck(!flg || !(n != dim), comm, PETSC_ERR_ARG_SIZ, "Lower box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim);
4849: n = 3;
4850: PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg));
4851: PetscCheck(!flg || !(n != dim), comm, PETSC_ERR_ARG_SIZ, "Upper box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim);
4852: n = 3;
4853: PetscCall(PetscOptionsEnumArray("-dm_plex_box_bd", "Boundary type for each dimension", "", DMBoundaryTypes, (PetscEnum *)bdt, &n, &flg));
4854: PetscCheck(!flg || !(n != dim), comm, PETSC_ERR_ARG_SIZ, "Box boundary types had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim);
4856: PetscCheck(!isAnnular || dim == 2, comm, PETSC_ERR_ARG_OUTOFRANGE, "Only two dimensional annuli have been implemented");
4857: if (isAnnular)
4858: for (i = 0; i < dim - 1; ++i) bdt[i] = DM_BOUNDARY_PERIODIC;
4860: switch (cell) {
4861: case DM_POLYTOPE_TRI_PRISM_TENSOR:
4862: PetscCall(DMPlexCreateWedgeBoxMesh_Internal(dm, faces, lower, upper, bdt));
4863: if (!interpolate) {
4864: DM udm;
4866: PetscCall(DMPlexUninterpolate(dm, &udm));
4867: PetscCall(DMPlexReplace_Internal(dm, &udm));
4868: }
4869: break;
4870: default:
4871: PetscCall(DMPlexCreateBoxMesh_Internal(dm, shape, dim, simplex, faces, lower, upper, bdt, interpolate));
4872: break;
4873: }
4874: if (isAnnular) {
4875: DM cdm;
4876: PetscDS cds;
4877: PetscScalar bounds[2] = {lower[0], upper[0]};
4879: // Fix coordinates for annular region
4880: PetscCall(DMSetPeriodicity(dm, NULL, NULL, NULL));
4881: PetscCall(DMSetCellCoordinatesLocal(dm, NULL));
4882: PetscCall(DMSetCellCoordinates(dm, NULL));
4883: PetscCall(DMPlexCreateCoordinateSpace(dm, 1, PETSC_FALSE, PETSC_TRUE));
4884: PetscCall(DMGetCoordinateDM(dm, &cdm));
4885: PetscCall(DMGetDS(cdm, &cds));
4886: PetscCall(PetscDSSetConstants(cds, 2, bounds));
4887: PetscCall(DMPlexRemapGeometry(dm, 0.0, boxToAnnulus));
4888: }
4889: } break;
4890: case DM_SHAPE_BOX_SURFACE: {
4891: PetscInt faces[3] = {0, 0, 0};
4892: PetscReal lower[3] = {0, 0, 0};
4893: PetscReal upper[3] = {1, 1, 1};
4894: PetscInt i, n;
4896: n = dim + 1;
4897: for (i = 0; i < dim + 1; ++i) faces[i] = (dim + 1 == 1 ? 1 : 4 - (dim + 1));
4898: PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg));
4899: n = 3;
4900: PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg));
4901: PetscCheck(!flg || !(n != dim + 1), comm, PETSC_ERR_ARG_SIZ, "Lower box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim + 1);
4902: n = 3;
4903: PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg));
4904: PetscCheck(!flg || !(n != dim + 1), comm, PETSC_ERR_ARG_SIZ, "Upper box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim + 1);
4905: PetscCall(DMPlexCreateBoxSurfaceMesh_Internal(dm, dim + 1, faces, lower, upper, interpolate));
4906: } break;
4907: case DM_SHAPE_SPHERE: {
4908: PetscReal R = 1.0;
4910: PetscCall(PetscOptionsReal("-dm_plex_sphere_radius", "Radius of the sphere", "", R, &R, &flg));
4911: PetscCall(DMPlexCreateSphereMesh_Internal(dm, dim, simplex, R));
4912: } break;
4913: case DM_SHAPE_BALL: {
4914: PetscReal R = 1.0;
4916: PetscCall(PetscOptionsReal("-dm_plex_ball_radius", "Radius of the ball", "", R, &R, &flg));
4917: PetscCall(DMPlexCreateBallMesh_Internal(dm, dim, R));
4918: } break;
4919: case DM_SHAPE_CYLINDER: {
4920: DMBoundaryType bdt = DM_BOUNDARY_NONE;
4921: PetscInt Nw = 6;
4922: PetscInt Nr = 0;
4924: PetscCall(PetscOptionsEnum("-dm_plex_cylinder_bd", "Boundary type in the z direction", "", DMBoundaryTypes, (PetscEnum)bdt, (PetscEnum *)&bdt, NULL));
4925: PetscCall(PetscOptionsInt("-dm_plex_cylinder_num_wedges", "Number of wedges around the cylinder", "", Nw, &Nw, NULL));
4926: PetscCall(PetscOptionsInt("-dm_plex_cylinder_num_refine", "Number of refinements before projection", "", Nr, &Nr, NULL));
4927: switch (cell) {
4928: case DM_POLYTOPE_TRI_PRISM_TENSOR:
4929: PetscCall(DMPlexCreateWedgeCylinderMesh_Internal(dm, Nw, interpolate));
4930: break;
4931: default:
4932: PetscCall(DMPlexCreateHexCylinderMesh_Internal(dm, bdt, Nr));
4933: break;
4934: }
4935: } break;
4936: case DM_SHAPE_SCHWARZ_P: // fallthrough
4937: case DM_SHAPE_GYROID: {
4938: PetscInt extent[3] = {1, 1, 1}, refine = 0, layers = 0, three;
4939: PetscReal thickness = 0.;
4940: DMBoundaryType periodic[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
4941: DMPlexTPSType tps_type = shape == DM_SHAPE_SCHWARZ_P ? DMPLEX_TPS_SCHWARZ_P : DMPLEX_TPS_GYROID;
4942: PetscBool tps_distribute;
4943: PetscCall(PetscOptionsIntArray("-dm_plex_tps_extent", "Number of replicas for each of three dimensions", NULL, extent, (three = 3, &three), NULL));
4944: PetscCall(PetscOptionsInt("-dm_plex_tps_refine", "Number of refinements", NULL, refine, &refine, NULL));
4945: PetscCall(PetscOptionsEnumArray("-dm_plex_tps_periodic", "Periodicity in each of three dimensions", NULL, DMBoundaryTypes, (PetscEnum *)periodic, (three = 3, &three), NULL));
4946: PetscCall(PetscOptionsInt("-dm_plex_tps_layers", "Number of layers in volumetric extrusion (or zero to not extrude)", NULL, layers, &layers, NULL));
4947: PetscCall(PetscOptionsReal("-dm_plex_tps_thickness", "Thickness of volumetric extrusion", NULL, thickness, &thickness, NULL));
4948: PetscCall(DMPlexDistributeGetDefault(dm, &tps_distribute));
4949: PetscCall(PetscOptionsBool("-dm_plex_tps_distribute", "Distribute the 2D mesh prior to refinement and extrusion", NULL, tps_distribute, &tps_distribute, NULL));
4950: PetscCall(DMPlexCreateTPSMesh_Internal(dm, tps_type, extent, periodic, tps_distribute, refine, layers, thickness));
4951: } break;
4952: case DM_SHAPE_DOUBLET: {
4953: DM dmnew;
4954: PetscReal rl = 0.0;
4956: PetscCall(PetscOptionsReal("-dm_plex_doublet_refinementlimit", "Refinement limit", NULL, rl, &rl, NULL));
4957: PetscCall(DMPlexCreateDoublet(PetscObjectComm((PetscObject)dm), dim, simplex, interpolate, rl, &dmnew));
4958: PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew));
4959: PetscCall(DMPlexReplace_Internal(dm, &dmnew));
4960: } break;
4961: case DM_SHAPE_HYPERCUBIC: {
4962: PetscInt *edges, overlap = 1;
4963: PetscReal *lower, *upper;
4964: DMBoundaryType *bdt;
4965: PetscInt n, d;
4967: *useCoordSpace = PETSC_FALSE;
4968: PetscCall(PetscMalloc4(dim, &edges, dim, &lower, dim, &upper, dim, &bdt));
4969: for (d = 0; d < dim; ++d) {
4970: edges[d] = 1;
4971: lower[d] = 0.;
4972: upper[d] = 1.;
4973: bdt[d] = DM_BOUNDARY_PERIODIC;
4974: }
4975: n = dim;
4976: PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", edges, &n, &flg));
4977: n = dim;
4978: PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg));
4979: PetscCheck(!flg || n == dim, comm, PETSC_ERR_ARG_SIZ, "Lower box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim);
4980: n = dim;
4981: PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg));
4982: PetscCheck(!flg || n == dim, comm, PETSC_ERR_ARG_SIZ, "Upper box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim);
4983: n = dim;
4984: PetscCall(PetscOptionsEnumArray("-dm_plex_box_bd", "Boundary type for each dimension", "", DMBoundaryTypes, (PetscEnum *)bdt, &n, &flg));
4985: PetscCheck(!flg || n == dim, comm, PETSC_ERR_ARG_SIZ, "Box boundary types had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim);
4986: PetscCall(PetscOptionsBoundedInt("-dm_distribute_overlap", "The size of the overlap halo", "DMPlexDistribute", overlap, &overlap, NULL, 0));
4987: PetscCall(DMPlexCreateHypercubicMesh_Internal(dm, dim, lower, upper, edges, overlap, bdt));
4988: PetscCall(PetscFree4(edges, lower, upper, bdt));
4989: } break;
4990: default:
4991: SETERRQ(comm, PETSC_ERR_SUP, "Domain shape %s is unsupported", DMPlexShapes[shape]);
4992: }
4993: }
4994: PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE));
4995: if (!((PetscObject)dm)->name && nameflg) PetscCall(PetscObjectSetName((PetscObject)dm, plexname));
4996: if (orient) PetscCall(DMPlexOrient(dm));
4997: // Allow label creation
4998: PetscCall(PetscOptionsFindPairPrefix_Private(NULL, ((PetscObject)dm)->prefix, "-dm_plex_label_", &option, NULL, &flg));
4999: if (flg) {
5000: DMLabel label;
5001: PetscInt *points, cStart, cEnd, n;
5002: char fulloption[PETSC_MAX_PATH_LEN];
5003: const char *name = &option[14];
5005: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
5006: n = PetscMax(cEnd - cStart, 1024);
5007: PetscCall(PetscMalloc1(n, &points));
5008: PetscCall(DMCreateLabel(dm, name));
5009: PetscCall(DMGetLabel(dm, name, &label));
5010: fulloption[0] = '-';
5011: fulloption[1] = 0;
5012: PetscCall(PetscStrlcat(fulloption, option, PETSC_MAX_PATH_LEN));
5013: PetscCall(PetscOptionsGetIntArray(NULL, ((PetscObject)dm)->prefix, fulloption, points, &n, NULL));
5014: for (PetscInt p = 0; p < n; ++p) PetscCall(DMLabelSetValue(label, points[p], 1));
5015: PetscCall(PetscFree(points));
5016: }
5017: // Allow cohesive label creation
5018: // Faces are input, completed, and all points are marked with their depth
5019: PetscCall(PetscOptionsFindPairPrefix_Private(NULL, ((PetscObject)dm)->prefix, "-dm_plex_cohesive_label_", &option, NULL, &flg));
5020: if (flg) {
5021: DMLabel label;
5022: PetscInt points[1024], n, pStart, pEnd, Nl = 1;
5023: PetscBool noCreate = PETSC_FALSE;
5024: char fulloption[PETSC_MAX_PATH_LEN];
5025: char name[PETSC_MAX_PATH_LEN];
5026: size_t len;
5028: PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
5029: PetscCall(PetscStrncpy(name, &option[23], PETSC_MAX_PATH_LEN));
5030: PetscCall(PetscStrlen(name, &len));
5031: if (name[len - 1] == '0') Nl = 10;
5032: for (PetscInt l = 0; l < Nl; ++l) {
5033: if (l > 0) name[len - 1] = (char)('0' + l);
5034: fulloption[0] = 0;
5035: PetscCall(PetscStrlcat(fulloption, "-dm_plex_cohesive_label_", 32));
5036: PetscCall(PetscStrlcat(fulloption, name, PETSC_MAX_PATH_LEN - 32));
5037: n = 1024;
5038: PetscCall(PetscOptionsGetIntArray(NULL, ((PetscObject)dm)->prefix, fulloption, points, &n, &flg));
5039: if (!flg) break;
5040: PetscCall(DMHasLabel(dm, name, &noCreate));
5041: if (noCreate) {
5042: DMLabel inlabel;
5043: IS pointIS;
5044: const PetscInt *lpoints;
5045: PetscInt pdep, ln, inval = points[0];
5046: char newname[PETSC_MAX_PATH_LEN];
5048: PetscCheck(n == 1, comm, PETSC_ERR_ARG_WRONG, "Must specify a label value with this option");
5049: PetscCall(DMGetLabel(dm, name, &inlabel));
5050: PetscCall(DMLabelGetStratumIS(inlabel, inval, &pointIS));
5051: PetscCall(ISGetLocalSize(pointIS, &ln));
5052: PetscCall(ISGetIndices(pointIS, &lpoints));
5053: PetscCall(DMPlexGetPointDepth(dm, lpoints[0], &pdep));
5054: PetscCall(PetscSNPrintf(newname, PETSC_MAX_PATH_LEN, "%s%" PetscInt_FMT, name, points[0]));
5055: PetscCall(DMCreateLabel(dm, newname));
5056: PetscCall(DMGetLabel(dm, newname, &label));
5057: if (!pdep) PetscCall(ProcessCohesiveLabel_Vertices(dm, label, inlabel, inval, ln, lpoints));
5058: else PetscCall(ProcessCohesiveLabel_Faces(dm, label, ln, lpoints));
5059: PetscCall(ISRestoreIndices(pointIS, &lpoints));
5060: PetscCall(ISDestroy(&pointIS));
5061: } else {
5062: PetscCall(DMCreateLabel(dm, name));
5063: PetscCall(DMGetLabel(dm, name, &label));
5064: if (pStart >= pEnd) n = 0;
5065: PetscCall(ProcessCohesiveLabel_Faces(dm, label, n, points));
5066: }
5067: PetscCall(DMPlexOrientLabel(dm, label));
5068: PetscCall(DMPlexLabelCohesiveComplete(dm, label, NULL, 1, PETSC_FALSE, PETSC_FALSE, NULL));
5069: }
5070: }
5071: PetscCall(DMViewFromOptions(dm, NULL, "-created_dm_view"));
5072: PetscCall(PetscLogEventEnd(DMPLEX_CreateFromOptions, dm, 0, 0, 0));
5073: PetscFunctionReturn(PETSC_SUCCESS);
5074: }
5076: PetscErrorCode DMSetFromOptions_NonRefinement_Plex(DM dm, PetscOptionItems PetscOptionsObject)
5077: {
5078: DM_Plex *mesh = (DM_Plex *)dm->data;
5079: PetscBool flg, flg2;
5080: char bdLabel[PETSC_MAX_PATH_LEN];
5081: char method[PETSC_MAX_PATH_LEN];
5083: PetscFunctionBegin;
5084: /* Handle viewing */
5085: PetscCall(PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL));
5086: PetscCall(PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level for all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL, 0));
5087: PetscCall(PetscOptionsBoundedInt("-dm_plex_print_fvm", "Debug output level for all fvm computations", "DMPlexSNESComputeResidualFVM", 0, &mesh->printFVM, NULL, 0));
5088: PetscCall(PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL));
5089: PetscCall(PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL, 0));
5090: PetscCall(PetscOptionsBoundedInt("-dm_plex_print_locate", "Debug output level all point location computations", "DMLocatePoints", 0, &mesh->printLocate, NULL, 0));
5091: PetscCall(PetscOptionsBoundedInt("-dm_plex_print_project", "Debug output level all projection computations", "DMPlexProject", 0, &mesh->printProject, NULL, 0));
5092: PetscCall(DMMonitorSetFromOptions(dm, "-dm_plex_monitor_throughput", "Monitor the simulation throughput", "DMPlexMonitorThroughput", DMPlexMonitorThroughput, NULL, &flg));
5093: if (flg) PetscCall(PetscLogDefaultBegin());
5094: // Interpolation
5095: PetscCall(PetscOptionsBool("-dm_plex_interpolate_prefer_tensor", "When different orderings exist, prefer the tensor order", "DMPlexSetInterpolationPreferTensor", mesh->interpolatePreferTensor, &mesh->interpolatePreferTensor, NULL));
5096: /* Labeling */
5097: PetscCall(PetscOptionsString("-dm_plex_boundary_label", "Label to mark the mesh boundary", "", NULL, bdLabel, sizeof(bdLabel), &flg));
5098: if (flg) PetscCall(DMPlexCreateBoundaryLabel_Private(dm, bdLabel));
5099: /* Point Location */
5100: PetscCall(PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL));
5101: /* Partitioning and distribution */
5102: PetscCall(PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL));
5103: /* Reordering */
5104: PetscCall(PetscOptionsBool("-dm_reorder_section", "Compute point permutation for local section", "DMReorderSectionSetDefault", PETSC_FALSE, &flg2, &flg));
5105: if (flg) PetscCall(DMReorderSectionSetDefault(dm, flg2 ? DM_REORDER_DEFAULT_TRUE : DM_REORDER_DEFAULT_FALSE));
5106: PetscCall(PetscOptionsString("-dm_reorder_section_type", "Reordering method for local section", "DMReorderSectionSetType", NULL, method, PETSC_MAX_PATH_LEN, &flg));
5107: if (flg) PetscCall(DMReorderSectionSetType(dm, method));
5108: /* Generation and remeshing */
5109: PetscCall(PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL));
5110: PetscCall(PetscOptionsBool("-dm_plex_save_transform", "Save the transform producing this mesh", "DMAdapt", PETSC_FALSE, &mesh->saveTransform, NULL));
5111: /* Projection behavior */
5112: PetscCall(PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maximum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL, 0));
5113: PetscCall(PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL));
5114: /* Checking structure */
5115: {
5116: PetscBool all = PETSC_FALSE;
5118: PetscCall(PetscOptionsBool("-dm_plex_check_all", "Perform all basic checks", "DMPlexCheck", PETSC_FALSE, &all, NULL));
5119: if (all) {
5120: PetscCall(DMPlexCheck(dm));
5121: } else {
5122: PetscCall(PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2));
5123: if (flg && flg2) PetscCall(DMPlexCheckSymmetry(dm));
5124: PetscCall(PetscOptionsBool("-dm_plex_check_skeleton", "Check that each cell has the correct number of vertices (only for homogeneous simplex or tensor meshes)", "DMPlexCheckSkeleton", PETSC_FALSE, &flg, &flg2));
5125: if (flg && flg2) PetscCall(DMPlexCheckSkeleton(dm, 0));
5126: PetscCall(PetscOptionsBool("-dm_plex_check_faces", "Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type", "DMPlexCheckFaces", PETSC_FALSE, &flg, &flg2));
5127: if (flg && flg2) PetscCall(DMPlexCheckFaces(dm, 0));
5128: PetscCall(PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2));
5129: if (flg && flg2) PetscCall(DMPlexCheckGeometry(dm));
5130: PetscCall(PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2));
5131: if (flg && flg2) PetscCall(DMPlexCheckPointSF(dm, NULL, PETSC_FALSE));
5132: PetscCall(PetscOptionsBool("-dm_plex_check_interface_cones", "Check points on inter-partition interfaces have conforming order of cone points", "DMPlexCheckInterfaceCones", PETSC_FALSE, &flg, &flg2));
5133: if (flg && flg2) PetscCall(DMPlexCheckInterfaceCones(dm));
5134: }
5135: PetscCall(PetscOptionsBool("-dm_plex_check_cell_shape", "Check cell shape", "DMPlexCheckCellShape", PETSC_FALSE, &flg, &flg2));
5136: if (flg && flg2) PetscCall(DMPlexCheckCellShape(dm, PETSC_TRUE, PETSC_DETERMINE));
5137: }
5138: {
5139: PetscReal scale = 1.0;
5141: PetscCall(PetscOptionsReal("-dm_plex_scale", "Scale factor for mesh coordinates", "DMPlexScale", scale, &scale, &flg));
5142: if (flg) {
5143: Vec coordinates, coordinatesLocal;
5145: PetscCall(DMGetCoordinates(dm, &coordinates));
5146: PetscCall(DMGetCoordinatesLocal(dm, &coordinatesLocal));
5147: PetscCall(VecScale(coordinates, scale));
5148: PetscCall(VecScale(coordinatesLocal, scale));
5149: }
5150: }
5151: PetscCall(PetscPartitionerSetFromOptions(mesh->partitioner));
5152: PetscFunctionReturn(PETSC_SUCCESS);
5153: }
5155: PetscErrorCode DMSetFromOptions_Overlap_Plex(DM dm, PetscOptionItems PetscOptionsObject, PetscInt *overlap)
5156: {
5157: PetscInt numOvLabels = 16, numOvExLabels = 16;
5158: char *ovLabelNames[16], *ovExLabelNames[16];
5159: PetscInt numOvValues = 16, numOvExValues = 16, l;
5160: PetscBool flg;
5162: PetscFunctionBegin;
5163: PetscCall(PetscOptionsBoundedInt("-dm_distribute_overlap", "The size of the overlap halo", "DMPlexDistribute", *overlap, overlap, NULL, 0));
5164: PetscCall(PetscOptionsStringArray("-dm_distribute_overlap_labels", "List of overlap label names", "DMPlexDistribute", ovLabelNames, &numOvLabels, &flg));
5165: if (!flg) numOvLabels = 0;
5166: if (numOvLabels) {
5167: ((DM_Plex *)dm->data)->numOvLabels = numOvLabels;
5168: for (l = 0; l < numOvLabels; ++l) {
5169: PetscCall(DMGetLabel(dm, ovLabelNames[l], &((DM_Plex *)dm->data)->ovLabels[l]));
5170: PetscCheck(((DM_Plex *)dm->data)->ovLabels[l], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid label name %s", ovLabelNames[l]);
5171: PetscCall(PetscFree(ovLabelNames[l]));
5172: }
5173: PetscCall(PetscOptionsIntArray("-dm_distribute_overlap_values", "List of overlap label values", "DMPlexDistribute", ((DM_Plex *)dm->data)->ovValues, &numOvValues, &flg));
5174: if (!flg) numOvValues = 0;
5175: PetscCheck(numOvLabels == numOvValues, PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "The number of labels %" PetscInt_FMT " must match the number of values %" PetscInt_FMT, numOvLabels, numOvValues);
5177: PetscCall(PetscOptionsStringArray("-dm_distribute_overlap_exclude_labels", "List of overlap exclude label names", "DMPlexDistribute", ovExLabelNames, &numOvExLabels, &flg));
5178: if (!flg) numOvExLabels = 0;
5179: ((DM_Plex *)dm->data)->numOvExLabels = numOvExLabels;
5180: for (l = 0; l < numOvExLabels; ++l) {
5181: PetscCall(DMGetLabel(dm, ovExLabelNames[l], &((DM_Plex *)dm->data)->ovExLabels[l]));
5182: PetscCheck(((DM_Plex *)dm->data)->ovExLabels[l], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid label name %s", ovExLabelNames[l]);
5183: PetscCall(PetscFree(ovExLabelNames[l]));
5184: }
5185: PetscCall(PetscOptionsIntArray("-dm_distribute_overlap_exclude_values", "List of overlap exclude label values", "DMPlexDistribute", ((DM_Plex *)dm->data)->ovExValues, &numOvExValues, &flg));
5186: if (!flg) numOvExValues = 0;
5187: PetscCheck(numOvExLabels == numOvExValues, PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "The number of exclude labels %" PetscInt_FMT " must match the number of values %" PetscInt_FMT, numOvExLabels, numOvExValues);
5188: }
5189: PetscFunctionReturn(PETSC_SUCCESS);
5190: }
5192: static PetscErrorCode DMSetFromOptions_Plex(DM dm, PetscOptionItems PetscOptionsObject)
5193: {
5194: PetscFunctionList ordlist;
5195: char oname[256];
5196: char sublabelname[PETSC_MAX_PATH_LEN] = "";
5197: DMReorderDefaultFlag reorder;
5198: PetscReal volume = -1.0;
5199: PetscInt prerefine = 0, refine = 0, r, coarsen = 0, overlap = 0, extLayers = 0, dim;
5200: PetscBool uniformOrig = PETSC_FALSE, uniform = PETSC_TRUE, distribute, saveSF = PETSC_FALSE, interpolate = PETSC_TRUE, coordSpace = PETSC_FALSE, remap = PETSC_TRUE, ghostCells = PETSC_FALSE, isHierarchy, flg;
5202: PetscFunctionBegin;
5203: PetscOptionsHeadBegin(PetscOptionsObject, "DMPlex Options");
5204: if (dm->cloneOpts) goto non_refine;
5205: /* Handle automatic creation */
5206: PetscCall(DMGetDimension(dm, &dim));
5207: if (dim < 0) PetscCall(DMPlexCreateFromOptions_Internal(PetscOptionsObject, &coordSpace, dm));
5208: PetscCall(DMGetDimension(dm, &dim));
5209: /* Handle interpolation before distribution */
5210: PetscCall(PetscOptionsBool("-dm_plex_interpolate_pre", "Flag to interpolate mesh before distribution", "", interpolate, &interpolate, &flg));
5211: if (flg) {
5212: DMPlexInterpolatedFlag interpolated;
5214: PetscCall(DMPlexIsInterpolated(dm, &interpolated));
5215: if (interpolated == DMPLEX_INTERPOLATED_FULL && !interpolate) {
5216: DM udm;
5218: PetscCall(DMPlexUninterpolate(dm, &udm));
5219: PetscCall(DMPlexReplace_Internal(dm, &udm));
5220: } else if (interpolated != DMPLEX_INTERPOLATED_FULL && interpolate) {
5221: DM idm;
5223: PetscCall(DMPlexInterpolate(dm, &idm));
5224: PetscCall(DMPlexReplace_Internal(dm, &idm));
5225: }
5226: }
5227: // Handle submesh selection before distribution
5228: PetscCall(PetscOptionsString("-dm_plex_submesh", "Label to use for submesh selection", "", sublabelname, sublabelname, PETSC_MAX_PATH_LEN, &flg));
5229: if (flg) {
5230: DM subdm;
5231: DMLabel label;
5232: IS valueIS, pointIS;
5233: const PetscInt *values, *points;
5234: PetscBool markedFaces = PETSC_FALSE;
5235: PetscInt Nv, value, Np;
5237: PetscCall(DMGetLabel(dm, sublabelname, &label));
5238: PetscCall(DMLabelGetNumValues(label, &Nv));
5239: PetscCheck(Nv == 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only a single label value is currently supported for submesh selection, not %" PetscInt_FMT, Nv);
5240: PetscCall(DMLabelGetValueIS(label, &valueIS));
5241: PetscCall(ISGetIndices(valueIS, &values));
5242: value = values[0];
5243: PetscCall(ISRestoreIndices(valueIS, &values));
5244: PetscCall(ISDestroy(&valueIS));
5245: PetscCall(DMLabelGetStratumSize(label, value, &Np));
5246: PetscCall(DMLabelGetStratumIS(label, value, &pointIS));
5247: PetscCall(ISGetIndices(pointIS, &points));
5248: for (PetscInt p = 0; p < Np; ++p) {
5249: PetscInt pdepth;
5251: PetscCall(DMPlexGetPointDepth(dm, points[p], &pdepth));
5252: if (pdepth) {
5253: markedFaces = PETSC_TRUE;
5254: break;
5255: }
5256: }
5257: PetscCall(ISRestoreIndices(pointIS, &points));
5258: PetscCall(ISDestroy(&pointIS));
5259: PetscCall(DMPlexCreateSubmesh(dm, label, value, markedFaces, &subdm));
5260: PetscCall(DMPlexReplace_Internal(dm, &subdm));
5261: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
5262: }
5263: /* Handle DMPlex refinement before distribution */
5264: PetscCall(DMPlexGetRefinementUniform(dm, &uniformOrig));
5265: PetscCall(PetscOptionsBoundedInt("-dm_refine_pre", "The number of refinements before distribution", "DMCreate", prerefine, &prerefine, NULL, 0));
5266: PetscCall(PetscOptionsBool("-dm_refine_remap_pre", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL));
5267: PetscCall(PetscOptionsBool("-dm_refine_uniform_pre", "Flag for uniform refinement before distribution", "DMCreate", uniform, &uniform, &flg));
5268: if (flg) PetscCall(DMPlexSetRefinementUniform(dm, uniform));
5269: PetscCall(PetscOptionsReal("-dm_refine_volume_limit_pre", "The maximum cell volume after refinement before distribution", "DMCreate", volume, &volume, &flg));
5270: if (flg) {
5271: PetscCall(DMPlexSetRefinementUniform(dm, PETSC_FALSE));
5272: PetscCall(DMPlexSetRefinementLimit(dm, volume));
5273: prerefine = PetscMax(prerefine, 1);
5274: }
5275: if (prerefine) PetscCall(DMLocalizeCoordinates(dm));
5276: for (r = 0; r < prerefine; ++r) {
5277: DM rdm;
5278: PetscPointFn *coordFunc;
5280: PetscCall(DMPlexGetCoordinateMap(dm, &coordFunc));
5281: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
5282: PetscCall(DMRefine(dm, PetscObjectComm((PetscObject)dm), &rdm));
5283: PetscCall(DMPlexReplace_Internal(dm, &rdm));
5284: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
5285: if (coordFunc && remap) {
5286: PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc));
5287: PetscCall(DMPlexSetCoordinateMap(dm, coordFunc));
5288: }
5289: }
5290: PetscCall(DMPlexSetRefinementUniform(dm, uniformOrig));
5291: /* Handle DMPlex extrusion before distribution */
5292: PetscCall(PetscOptionsBoundedInt("-dm_extrude", "The number of layers to extrude", "", extLayers, &extLayers, NULL, 0));
5293: if (extLayers) {
5294: DM edm;
5296: PetscCall(DMExtrude(dm, extLayers, &edm));
5297: PetscCall(DMPlexReplace_Internal(dm, &edm));
5298: PetscCall(DMPlexSetCoordinateMap(dm, NULL));
5299: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
5300: extLayers = 0;
5301: PetscCall(DMGetDimension(dm, &dim));
5302: }
5303: /* Handle DMPlex reordering before distribution */
5304: PetscCall(DMPlexReorderGetDefault(dm, &reorder));
5305: PetscCall(MatGetOrderingList(&ordlist));
5306: PetscCall(PetscStrncpy(oname, MATORDERINGNATURAL, sizeof(oname)));
5307: PetscCall(PetscOptionsFList("-dm_plex_reorder", "Set mesh reordering type", "DMPlexGetOrdering", ordlist, MATORDERINGNATURAL, oname, sizeof(oname), &flg));
5308: if (reorder == DM_REORDER_DEFAULT_TRUE || flg) {
5309: DM pdm;
5310: IS perm;
5312: PetscCall(DMPlexGetOrdering(dm, oname, NULL, &perm));
5313: PetscCall(DMPlexPermute(dm, perm, &pdm));
5314: PetscCall(ISDestroy(&perm));
5315: PetscCall(DMPlexReplace_Internal(dm, &pdm));
5316: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
5317: }
5318: /* Handle DMPlex distribution */
5319: PetscCall(DMPlexDistributeGetDefault(dm, &distribute));
5320: PetscCall(PetscOptionsBool("-dm_distribute", "Flag to redistribute a mesh among processes", "DMPlexDistribute", distribute, &distribute, NULL));
5321: PetscCall(PetscOptionsBool("-dm_distribute_save_sf", "Flag to save the migration SF", "DMPlexSetMigrationSF", saveSF, &saveSF, NULL));
5322: PetscCall(DMSetFromOptions_Overlap_Plex(dm, PetscOptionsObject, &overlap));
5323: if (distribute) {
5324: DM pdm = NULL;
5325: PetscPartitioner part;
5326: PetscSF sfMigration;
5327: PetscBool use_partition_balance;
5329: PetscCall(DMPlexGetPartitioner(dm, &part));
5330: PetscCall(PetscPartitionerSetFromOptions(part));
5331: PetscCall(DMPlexGetPartitionBalance(dm, &use_partition_balance));
5332: PetscCall(PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", use_partition_balance, &use_partition_balance, &flg));
5333: if (flg) PetscCall(DMPlexSetPartitionBalance(dm, use_partition_balance));
5334: PetscCall(DMPlexDistribute(dm, overlap, &sfMigration, &pdm));
5335: if (pdm) {
5336: // Delete the local section to force the existing one to be rebuilt with the distributed DM
5337: PetscCall(DMSetLocalSection(dm, pdm->localSection));
5338: PetscCall(DMPlexReplace_Internal(dm, &pdm));
5339: }
5340: if (saveSF) PetscCall(DMPlexSetMigrationSF(dm, sfMigration));
5341: PetscCall(PetscSFDestroy(&sfMigration));
5342: }
5344: {
5345: PetscBool useBoxLabel = PETSC_FALSE;
5346: PetscCall(PetscOptionsBool("-dm_plex_box_label", "Create 'Face Sets' assuming boundary faces align with cartesian directions", "DMCreate", useBoxLabel, &useBoxLabel, NULL));
5347: if (useBoxLabel) {
5348: PetscInt n = 3;
5349: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
5351: PetscCall(PetscOptionsEnumArray("-dm_plex_box_label_bd", "Boundary type for each dimension when using -dm_plex_box_label", "", DMBoundaryTypes, (PetscEnum *)bdt, &n, &flg));
5352: PetscCheck(!flg || !(n != dim), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_SIZ, "Box boundary types had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim);
5353: PetscCall(DMPlexSetBoxLabel_Internal(dm, bdt));
5354: }
5355: }
5356: /* Must check CEED options before creating function space for coordinates */
5357: {
5358: PetscBool useCeed = PETSC_FALSE, flg;
5360: PetscCall(PetscOptionsBool("-dm_plex_use_ceed", "Use LibCEED as the FEM backend", "DMPlexSetUseCeed", useCeed, &useCeed, &flg));
5361: if (flg) PetscCall(DMPlexSetUseCeed(dm, useCeed));
5362: }
5363: /* Create coordinate space */
5364: PetscCall(PetscOptionsBool("-dm_coord_space", "Use an FEM space for coordinates", "", coordSpace, &coordSpace, NULL));
5365: if (coordSpace) {
5366: PetscInt degree = 1, deg;
5367: PetscInt height = 0;
5368: DM cdm;
5369: PetscBool localize = PETSC_TRUE, sparseLocalize = PETSC_TRUE;
5371: PetscCall(PetscOptionsInt("-dm_coord_petscspace_degree", "FEM degree for coordinate space", "", degree, °ree, NULL));
5372: PetscCall(DMGetCoordinateDegree_Internal(dm, °));
5373: if (coordSpace && deg <= 1) PetscCall(DMPlexCreateCoordinateSpace(dm, degree, PETSC_FALSE, PETSC_TRUE));
5374: PetscCall(DMGetCoordinateDM(dm, &cdm));
5375: if (!coordSpace) {
5376: PetscDS cds;
5377: PetscObject obj;
5378: PetscClassId id;
5380: PetscCall(DMGetDS(cdm, &cds));
5381: PetscCall(PetscDSGetDiscretization(cds, 0, &obj));
5382: PetscCall(PetscObjectGetClassId(obj, &id));
5383: if (id == PETSCFE_CLASSID) {
5384: PetscContainer dummy;
5386: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &dummy));
5387: PetscCall(PetscObjectSetName((PetscObject)dummy, "coordinates"));
5388: PetscCall(DMSetField(cdm, 0, NULL, (PetscObject)dummy));
5389: PetscCall(PetscContainerDestroy(&dummy));
5390: PetscCall(DMClearDS(cdm));
5391: }
5392: PetscCall(DMPlexSetCoordinateMap(dm, NULL));
5393: }
5394: PetscCall(PetscOptionsBool("-dm_localize", "Localize mesh coordinates", "", localize, &localize, NULL));
5395: PetscCall(PetscOptionsBool("-dm_sparse_localize", "Localize only necessary cells", "DMSetSparseLocalize", sparseLocalize, &sparseLocalize, &flg));
5396: if (flg) PetscCall(DMSetSparseLocalize(dm, sparseLocalize));
5397: PetscCall(PetscOptionsInt("-dm_localize_height", "Localize edges and faces in addition to cells", "", height, &height, &flg));
5398: if (flg) PetscCall(DMPlexSetMaxProjectionHeight(cdm, height));
5399: if (localize) PetscCall(DMLocalizeCoordinates(dm));
5400: }
5401: /* Handle DMPlex refinement */
5402: remap = PETSC_TRUE;
5403: PetscCall(PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL, 0));
5404: PetscCall(PetscOptionsBool("-dm_refine_remap", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL));
5405: PetscCall(PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy, 0));
5406: if (refine) PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE));
5407: if (refine && isHierarchy) {
5408: DM *dms, coarseDM;
5410: PetscCall(DMGetCoarseDM(dm, &coarseDM));
5411: PetscCall(PetscObjectReference((PetscObject)coarseDM));
5412: PetscCall(PetscMalloc1(refine, &dms));
5413: PetscCall(DMRefineHierarchy(dm, refine, dms));
5414: /* Total hack since we do not pass in a pointer */
5415: PetscCall(DMPlexSwap_Static(dm, dms[refine - 1]));
5416: if (refine == 1) {
5417: PetscCall(DMSetCoarseDM(dm, dms[0]));
5418: PetscCall(DMPlexSetRegularRefinement(dm, PETSC_TRUE));
5419: } else {
5420: PetscCall(DMSetCoarseDM(dm, dms[refine - 2]));
5421: PetscCall(DMPlexSetRegularRefinement(dm, PETSC_TRUE));
5422: PetscCall(DMSetCoarseDM(dms[0], dms[refine - 1]));
5423: PetscCall(DMPlexSetRegularRefinement(dms[0], PETSC_TRUE));
5424: }
5425: PetscCall(DMSetCoarseDM(dms[refine - 1], coarseDM));
5426: PetscCall(PetscObjectDereference((PetscObject)coarseDM));
5427: /* Free DMs */
5428: for (r = 0; r < refine; ++r) {
5429: PetscCall(DMSetFromOptions_NonRefinement_Plex(dms[r], PetscOptionsObject));
5430: PetscCall(DMDestroy(&dms[r]));
5431: }
5432: PetscCall(PetscFree(dms));
5433: } else {
5434: for (r = 0; r < refine; ++r) {
5435: DM rdm;
5436: PetscPointFn *coordFunc;
5438: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
5439: PetscCall(DMRefine(dm, PetscObjectComm((PetscObject)dm), &rdm));
5440: /* Total hack since we do not pass in a pointer */
5441: PetscCall(DMPlexReplace_Internal(dm, &rdm));
5442: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
5443: PetscCall(DMPlexGetCoordinateMap(dm, &coordFunc));
5444: if (coordFunc && remap) {
5445: PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc));
5446: PetscCall(DMPlexSetCoordinateMap(dm, coordFunc));
5447: }
5448: }
5449: }
5450: /* Handle DMPlex coarsening */
5451: PetscCall(PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL, 0));
5452: PetscCall(PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy, 0));
5453: if (coarsen && isHierarchy) {
5454: DM *dms;
5456: PetscCall(PetscMalloc1(coarsen, &dms));
5457: PetscCall(DMCoarsenHierarchy(dm, coarsen, dms));
5458: /* Free DMs */
5459: for (r = 0; r < coarsen; ++r) {
5460: PetscCall(DMSetFromOptions_NonRefinement_Plex(dms[r], PetscOptionsObject));
5461: PetscCall(DMDestroy(&dms[r]));
5462: }
5463: PetscCall(PetscFree(dms));
5464: } else {
5465: for (r = 0; r < coarsen; ++r) {
5466: DM cdm;
5467: PetscPointFn *coordFunc;
5469: PetscCall(DMPlexGetCoordinateMap(dm, &coordFunc));
5470: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
5471: PetscCall(DMCoarsen(dm, PetscObjectComm((PetscObject)dm), &cdm));
5472: /* Total hack since we do not pass in a pointer */
5473: PetscCall(DMPlexReplace_Internal(dm, &cdm));
5474: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
5475: if (coordFunc) {
5476: PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc));
5477: PetscCall(DMPlexSetCoordinateMap(dm, coordFunc));
5478: }
5479: }
5480: }
5481: // Handle coordinate remapping
5482: remap = PETSC_FALSE;
5483: PetscCall(PetscOptionsBool("-dm_coord_remap", "Flag to control coordinate remapping", "", remap, &remap, NULL));
5484: if (remap) {
5485: DMPlexCoordMap map = DM_COORD_MAP_NONE;
5486: PetscPointFn *mapFunc = NULL;
5487: PetscScalar params[16];
5488: PetscInt Np = PETSC_STATIC_ARRAY_LENGTH(params), cdim;
5489: MPI_Comm comm;
5491: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
5492: PetscCall(DMGetCoordinateDim(dm, &cdim));
5493: PetscCall(PetscOptionsScalarArray("-dm_coord_map_params", "Parameters for the coordinate remapping", "", params, &Np, &flg));
5494: if (!flg) Np = 0;
5495: // TODO Allow user to pass a map function by name
5496: PetscCall(PetscOptionsEnum("-dm_coord_map", "Coordinate mapping for built-in mesh", "", DMPlexCoordMaps, (PetscEnum)map, (PetscEnum *)&map, &flg));
5497: if (flg) {
5498: switch (map) {
5499: case DM_COORD_MAP_NONE:
5500: mapFunc = coordMap_identity;
5501: break;
5502: case DM_COORD_MAP_SHEAR:
5503: mapFunc = coordMap_shear;
5504: if (!Np) {
5505: Np = cdim + 1;
5506: params[0] = 0;
5507: for (PetscInt d = 1; d <= cdim; ++d) params[d] = 1.0;
5508: }
5509: PetscCheck(Np == cdim + 1, comm, PETSC_ERR_ARG_WRONG, "The shear coordinate map must have cdim + 1 = %" PetscInt_FMT " parameters, not %" PetscInt_FMT, cdim + 1, Np);
5510: break;
5511: case DM_COORD_MAP_FLARE:
5512: mapFunc = coordMap_flare;
5513: if (!Np) {
5514: Np = cdim + 1;
5515: params[0] = 0;
5516: for (PetscInt d = 1; d <= cdim; ++d) params[d] = 1.0;
5517: }
5518: PetscCheck(Np == cdim + 1, comm, PETSC_ERR_ARG_WRONG, "The flare coordinate map must have cdim + 1 = %" PetscInt_FMT " parameters, not %" PetscInt_FMT, cdim + 1, Np);
5519: break;
5520: case DM_COORD_MAP_ANNULUS:
5521: mapFunc = coordMap_annulus;
5522: if (!Np) {
5523: Np = 2;
5524: params[0] = 1.;
5525: params[1] = 2.;
5526: }
5527: PetscCheck(Np == 2, comm, PETSC_ERR_ARG_WRONG, "The annulus coordinate map must have 2 parameters, not %" PetscInt_FMT, Np);
5528: break;
5529: case DM_COORD_MAP_SHELL:
5530: mapFunc = coordMap_shell;
5531: if (!Np) {
5532: Np = 2;
5533: params[0] = 1.;
5534: params[1] = 2.;
5535: }
5536: PetscCheck(Np == 2, comm, PETSC_ERR_ARG_WRONG, "The spherical shell coordinate map must have 2 parameters, not %" PetscInt_FMT, Np);
5537: break;
5538: case DM_COORD_MAP_SINUSOID:
5539: mapFunc = coordMap_sinusoid;
5540: if (!Np) {
5541: Np = 3;
5542: params[0] = 1.;
5543: params[1] = 1.;
5544: params[2] = 1.;
5545: }
5546: PetscCheck(Np == 3, comm, PETSC_ERR_ARG_WRONG, "The sinusoidal coordinate map must have 3 parameters, not %" PetscInt_FMT, Np);
5547: break;
5548: default:
5549: mapFunc = coordMap_identity;
5550: }
5551: }
5552: if (Np) {
5553: DM cdm;
5554: PetscDS cds;
5556: PetscCall(DMGetCoordinateDM(dm, &cdm));
5557: PetscCall(DMGetDS(cdm, &cds));
5558: PetscCall(PetscDSSetConstants(cds, Np, params));
5559: }
5560: PetscCall(DMPlexRemapGeometry(dm, 0.0, mapFunc));
5561: }
5562: /* Handle ghost cells */
5563: PetscCall(PetscOptionsBool("-dm_plex_create_fv_ghost_cells", "Flag to create finite volume ghost cells on the boundary", "DMCreate", ghostCells, &ghostCells, NULL));
5564: if (ghostCells) {
5565: DM gdm;
5566: char lname[PETSC_MAX_PATH_LEN];
5568: lname[0] = '\0';
5569: PetscCall(PetscOptionsString("-dm_plex_fv_ghost_cells_label", "Label name for ghost cells boundary", "DMCreate", lname, lname, sizeof(lname), &flg));
5570: PetscCall(DMPlexConstructGhostCells(dm, flg ? lname : NULL, NULL, &gdm));
5571: PetscCall(DMPlexReplace_Internal(dm, &gdm));
5572: }
5573: /* Handle 1D order */
5574: if (reorder != DM_REORDER_DEFAULT_FALSE && dim == 1) {
5575: DM cdm, rdm;
5576: PetscDS cds;
5577: PetscObject obj;
5578: PetscClassId id = PETSC_OBJECT_CLASSID;
5579: IS perm;
5580: PetscInt Nf;
5581: PetscBool distributed;
5583: PetscCall(DMPlexIsDistributed(dm, &distributed));
5584: PetscCall(DMGetCoordinateDM(dm, &cdm));
5585: PetscCall(DMGetDS(cdm, &cds));
5586: PetscCall(PetscDSGetNumFields(cds, &Nf));
5587: if (Nf) {
5588: PetscCall(PetscDSGetDiscretization(cds, 0, &obj));
5589: PetscCall(PetscObjectGetClassId(obj, &id));
5590: }
5591: if (!distributed && id != PETSCFE_CLASSID) {
5592: PetscCall(DMPlexGetOrdering1D(dm, &perm));
5593: PetscCall(DMPlexPermute(dm, perm, &rdm));
5594: PetscCall(DMPlexReplace_Internal(dm, &rdm));
5595: PetscCall(ISDestroy(&perm));
5596: }
5597: }
5598: /* Handle */
5599: non_refine:
5600: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
5601: char *phases[16];
5602: PetscInt Nphases = 16;
5603: PetscCall(PetscOptionsStringArray("-dm_plex_option_phases", "Option phase prefixes", "DMSetFromOptions", phases, &Nphases, &flg));
5604: PetscOptionsHeadEnd();
5606: // Phases
5607: if (flg) {
5608: DM cdm;
5609: char *oldPrefix, *oldCoordPrefix;
5610: const char *tmp;
5612: PetscCall(DMGetCoordinateDM(dm, &cdm));
5613: PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm, &tmp));
5614: PetscCall(PetscStrallocpy(tmp, &oldPrefix));
5615: PetscCall(PetscObjectGetOptionsPrefix((PetscObject)cdm, &tmp));
5616: PetscCall(PetscStrallocpy(tmp, &oldCoordPrefix));
5617: for (PetscInt ph = 0; ph < Nphases; ++ph) {
5618: PetscCall(PetscObjectAppendOptionsPrefix((PetscObject)dm, phases[ph]));
5619: PetscCall(PetscObjectAppendOptionsPrefix((PetscObject)cdm, phases[ph]));
5620: PetscCall(PetscInfo(dm, "Options phase %s for DM %s\n", phases[ph], dm->hdr.name));
5621: PetscCall(DMSetFromOptions(dm));
5622: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dm, oldPrefix));
5623: PetscCall(DMGetCoordinateDM(dm, &cdm));
5624: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)cdm, oldCoordPrefix));
5625: PetscCall(PetscFree(phases[ph]));
5626: }
5627: PetscCall(PetscFree(oldPrefix));
5628: PetscCall(PetscFree(oldCoordPrefix));
5629: }
5630: PetscFunctionReturn(PETSC_SUCCESS);
5631: }
5633: static PetscErrorCode DMCreateGlobalVector_Plex(DM dm, Vec *vec)
5634: {
5635: PetscFunctionBegin;
5636: PetscCall(DMCreateGlobalVector_Section_Private(dm, vec));
5637: /* PetscCall(VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM)); */
5638: PetscCall(VecSetOperation(*vec, VECOP_VIEW, (PetscErrorCodeFn *)VecView_Plex));
5639: PetscCall(VecSetOperation(*vec, VECOP_VIEWNATIVE, (PetscErrorCodeFn *)VecView_Plex_Native));
5640: PetscCall(VecSetOperation(*vec, VECOP_LOAD, (PetscErrorCodeFn *)VecLoad_Plex));
5641: PetscCall(VecSetOperation(*vec, VECOP_LOADNATIVE, (PetscErrorCodeFn *)VecLoad_Plex_Native));
5642: PetscFunctionReturn(PETSC_SUCCESS);
5643: }
5645: static PetscErrorCode DMCreateLocalVector_Plex(DM dm, Vec *vec)
5646: {
5647: PetscFunctionBegin;
5648: PetscCall(DMCreateLocalVector_Section_Private(dm, vec));
5649: PetscCall(VecSetOperation(*vec, VECOP_VIEW, (PetscErrorCodeFn *)VecView_Plex_Local));
5650: PetscCall(VecSetOperation(*vec, VECOP_LOAD, (PetscErrorCodeFn *)VecLoad_Plex_Local));
5651: PetscFunctionReturn(PETSC_SUCCESS);
5652: }
5654: static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd)
5655: {
5656: PetscInt depth, d;
5658: PetscFunctionBegin;
5659: PetscCall(DMPlexGetDepth(dm, &depth));
5660: if (depth == 1) {
5661: PetscCall(DMGetDimension(dm, &d));
5662: if (dim == 0) PetscCall(DMPlexGetDepthStratum(dm, dim, pStart, pEnd));
5663: else if (dim == d) PetscCall(DMPlexGetDepthStratum(dm, 1, pStart, pEnd));
5664: else {
5665: *pStart = 0;
5666: *pEnd = 0;
5667: }
5668: } else {
5669: PetscCall(DMPlexGetDepthStratum(dm, dim, pStart, pEnd));
5670: }
5671: PetscFunctionReturn(PETSC_SUCCESS);
5672: }
5674: static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[])
5675: {
5676: PetscSF sf;
5677: PetscMPIInt niranks, njranks;
5678: PetscInt n;
5679: const PetscMPIInt *iranks, *jranks;
5680: DM_Plex *data = (DM_Plex *)dm->data;
5682: PetscFunctionBegin;
5683: PetscCall(DMGetPointSF(dm, &sf));
5684: if (!data->neighbors) {
5685: PetscCall(PetscSFSetUp(sf));
5686: PetscCall(PetscSFGetRootRanks(sf, &njranks, &jranks, NULL, NULL, NULL));
5687: PetscCall(PetscSFGetLeafRanks(sf, &niranks, &iranks, NULL, NULL));
5688: PetscCall(PetscMalloc1(njranks + niranks + 1, &data->neighbors));
5689: PetscCall(PetscArraycpy(data->neighbors + 1, jranks, njranks));
5690: PetscCall(PetscArraycpy(data->neighbors + njranks + 1, iranks, niranks));
5691: n = njranks + niranks;
5692: PetscCall(PetscSortRemoveDupsMPIInt(&n, data->neighbors + 1));
5693: /* The following cast should never fail: can't have more neighbors than PETSC_MPI_INT_MAX */
5694: PetscCall(PetscMPIIntCast(n, data->neighbors));
5695: }
5696: if (nranks) *nranks = data->neighbors[0];
5697: if (ranks) {
5698: if (data->neighbors[0]) *ranks = data->neighbors + 1;
5699: else *ranks = NULL;
5700: }
5701: PetscFunctionReturn(PETSC_SUCCESS);
5702: }
5704: PETSC_INTERN PetscErrorCode DMInterpolateSolution_Plex(DM, DM, Mat, Vec, Vec);
5706: static PetscErrorCode DMInitialize_Plex(DM dm)
5707: {
5708: PetscFunctionBegin;
5709: dm->ops->view = DMView_Plex;
5710: dm->ops->load = DMLoad_Plex;
5711: dm->ops->setfromoptions = DMSetFromOptions_Plex;
5712: dm->ops->clone = DMClone_Plex;
5713: dm->ops->setup = DMSetUp_Plex;
5714: dm->ops->createlocalsection = DMCreateLocalSection_Plex;
5715: dm->ops->createsectionpermutation = DMCreateSectionPermutation_Plex;
5716: dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex;
5717: dm->ops->createglobalvector = DMCreateGlobalVector_Plex;
5718: dm->ops->createlocalvector = DMCreateLocalVector_Plex;
5719: dm->ops->getlocaltoglobalmapping = NULL;
5720: dm->ops->createfieldis = NULL;
5721: dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex;
5722: dm->ops->createcellcoordinatedm = DMCreateCellCoordinateDM_Plex;
5723: dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex;
5724: dm->ops->getcoloring = NULL;
5725: dm->ops->creatematrix = DMCreateMatrix_Plex;
5726: dm->ops->createinterpolation = DMCreateInterpolation_Plex;
5727: dm->ops->createmassmatrix = DMCreateMassMatrix_Plex;
5728: dm->ops->createmassmatrixlumped = DMCreateMassMatrixLumped_Plex;
5729: dm->ops->creategradientmatrix = DMCreateGradientMatrix_Plex;
5730: dm->ops->createinjection = DMCreateInjection_Plex;
5731: dm->ops->refine = DMRefine_Plex;
5732: dm->ops->coarsen = DMCoarsen_Plex;
5733: dm->ops->refinehierarchy = DMRefineHierarchy_Plex;
5734: dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex;
5735: dm->ops->extrude = DMExtrude_Plex;
5736: dm->ops->globaltolocalbegin = NULL;
5737: dm->ops->globaltolocalend = NULL;
5738: dm->ops->localtoglobalbegin = NULL;
5739: dm->ops->localtoglobalend = NULL;
5740: dm->ops->destroy = DMDestroy_Plex;
5741: dm->ops->createsubdm = DMCreateSubDM_Plex;
5742: dm->ops->createsuperdm = DMCreateSuperDM_Plex;
5743: dm->ops->getdimpoints = DMGetDimPoints_Plex;
5744: dm->ops->locatepoints = DMLocatePoints_Plex;
5745: dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex;
5746: dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex;
5747: dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex;
5748: dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex;
5749: dm->ops->projectbdfieldlabellocal = DMProjectBdFieldLabelLocal_Plex;
5750: dm->ops->computel2diff = DMComputeL2Diff_Plex;
5751: dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex;
5752: dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex;
5753: dm->ops->getneighbors = DMGetNeighbors_Plex;
5754: dm->ops->getlocalboundingbox = DMGetLocalBoundingBox_Coordinates;
5755: dm->ops->createdomaindecomposition = DMCreateDomainDecomposition_Plex;
5756: dm->ops->createddscatters = DMCreateDomainDecompositionScatters_Plex;
5757: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexInsertBoundaryValues_C", DMPlexInsertBoundaryValues_Plex));
5758: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexInsertTimeDerivativeBoundaryValues_C", DMPlexInsertTimeDerivativeBoundaryValues_Plex));
5759: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexInsertBounds_C", DMPlexInsertBounds_Plex));
5760: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMSetUpGLVisViewer_C", DMSetUpGLVisViewer_Plex));
5761: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMCreateNeumannOverlap_C", DMCreateNeumannOverlap_Plex));
5762: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexDistributeGetDefault_C", DMPlexDistributeGetDefault_Plex));
5763: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexDistributeSetDefault_C", DMPlexDistributeSetDefault_Plex));
5764: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexReorderGetDefault_C", DMPlexReorderGetDefault_Plex));
5765: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexReorderSetDefault_C", DMPlexReorderSetDefault_Plex));
5766: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMReorderSectionGetDefault_C", DMReorderSectionGetDefault_Plex));
5767: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMReorderSectionSetDefault_C", DMReorderSectionSetDefault_Plex));
5768: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMReorderSectionGetType_C", DMReorderSectionGetType_Plex));
5769: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMReorderSectionSetType_C", DMReorderSectionSetType_Plex));
5770: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMInterpolateSolution_C", DMInterpolateSolution_Plex));
5771: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexGetOverlap_C", DMPlexGetOverlap_Plex));
5772: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexSetOverlap_C", DMPlexSetOverlap_Plex));
5773: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexGetUseCeed_C", DMPlexGetUseCeed_Plex));
5774: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexSetUseCeed_C", DMPlexSetUseCeed_Plex));
5775: PetscFunctionReturn(PETSC_SUCCESS);
5776: }
5778: PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm)
5779: {
5780: DM_Plex *mesh = (DM_Plex *)dm->data;
5781: const PetscSF *face_sfs;
5782: PetscInt num_face_sfs;
5784: PetscFunctionBegin;
5785: mesh->refct++;
5786: (*newdm)->data = mesh;
5787: PetscCall(DMPlexGetIsoperiodicFaceSF(dm, &num_face_sfs, &face_sfs));
5788: PetscCall(DMPlexSetIsoperiodicFaceSF(*newdm, num_face_sfs, (PetscSF *)face_sfs));
5789: PetscCall(PetscObjectChangeTypeName((PetscObject)*newdm, DMPLEX));
5790: PetscCall(DMInitialize_Plex(*newdm));
5791: PetscFunctionReturn(PETSC_SUCCESS);
5792: }
5794: /*MC
5795: DMPLEX = "plex" - A `DM` object that encapsulates an unstructured mesh (or grid), or CW Complex {cite}`cwcomplex`,
5796: which can be expressed using a Hasse Diagram {cite}`hassediagram`.
5797: In the local representation, `Vec`s contain all unknowns in the interior and shared boundary. This is
5798: specified by a `PetscSection` object. Ownership in the global representation is determined by
5799: ownership of the underlying `DMPLEX` points. This is specified by another `PetscSection` object.
5801: Options Database Keys:
5802: + -dm_refine_pre - Refine mesh before distribution
5803: + -dm_refine_uniform_pre - Choose uniform or generator-based refinement
5804: + -dm_refine_volume_limit_pre - Cell volume limit after pre-refinement using generator
5805: . -dm_distribute - Distribute mesh across processes
5806: . -dm_distribute_overlap - Number of cells to overlap for distribution
5807: . -dm_refine - Refine mesh after distribution
5808: . -dm_localize <bool> - Whether to localize coordinates for periodic meshes
5809: . -dm_sparse_localize <bool> - Whether to only localize cells on the periodic boundary
5810: . -dm_plex_hash_location - Use grid hashing for point location
5811: . -dm_plex_hash_box_faces <n,m,p> - The number of divisions in each direction of the grid hash
5812: . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes
5813: . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing
5814: . -dm_plex_max_projection_height - Maximum mesh point height used to project locally
5815: . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement
5816: . -dm_plex_reorder_section - Use specialized blocking if available
5817: . -dm_plex_check_all - Perform all checks below
5818: . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric
5819: . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices
5820: . -dm_plex_check_faces <celltype> - Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type
5821: . -dm_plex_check_geometry - Check that cells have positive volume
5822: . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ
5823: . -dm_plex_view_scale <num> - Scale the TikZ
5824: . -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices
5825: - -dm_plex_print_fvm <num> - View FVM assembly information, such as flux updates
5827: Level: intermediate
5829: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMType`, `DMPlexCreate()`, `DMCreate()`, `DMSetType()`, `PetscSection`
5830: M*/
5832: PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm)
5833: {
5834: DM_Plex *mesh;
5835: PetscInt unit;
5837: PetscFunctionBegin;
5838: PetscCall(PetscCitationsRegister(PlexCitation, &Plexcite));
5840: PetscCall(PetscNew(&mesh));
5841: dm->reorderSection = DM_REORDER_DEFAULT_NOTSET;
5842: dm->data = mesh;
5844: mesh->refct = 1;
5845: PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection));
5846: PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection));
5847: mesh->refinementUniform = PETSC_TRUE;
5848: mesh->refinementLimit = -1.0;
5849: mesh->distDefault = PETSC_TRUE;
5850: mesh->reorderDefault = DM_REORDER_DEFAULT_NOTSET;
5851: mesh->distributionName = NULL;
5852: mesh->interpolated = DMPLEX_INTERPOLATED_INVALID;
5853: mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID;
5854: mesh->interpolatePreferTensor = PETSC_TRUE;
5856: PetscCall(PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner));
5857: mesh->remeshBd = PETSC_FALSE;
5859: for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0;
5861: mesh->depthState = -1;
5862: mesh->celltypeState = -1;
5863: mesh->printTol = 1.0e-10;
5864: mesh->nonempty_comm = MPI_COMM_SELF;
5866: PetscCall(DMInitialize_Plex(dm));
5867: PetscFunctionReturn(PETSC_SUCCESS);
5868: }
5870: /*@
5871: DMPlexCreate - Creates a `DMPLEX` object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram.
5873: Collective
5875: Input Parameter:
5876: . comm - The communicator for the `DMPLEX` object
5878: Output Parameter:
5879: . mesh - The `DMPLEX` object
5881: Level: beginner
5883: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMType`, `DMCreate()`, `DMSetType()`
5884: @*/
5885: PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh)
5886: {
5887: PetscFunctionBegin;
5888: PetscAssertPointer(mesh, 2);
5889: PetscCall(DMCreate(comm, mesh));
5890: PetscCall(DMSetType(*mesh, DMPLEX));
5891: PetscFunctionReturn(PETSC_SUCCESS);
5892: }
5894: /*@C
5895: DMPlexBuildFromCellListParallel - Build a distributed `DMPLEX` topology from a list of vertices for each cell (common mesh generator output) where all cells have the same celltype
5897: Collective; No Fortran Support
5899: Input Parameters:
5900: + dm - The `DM`
5901: . numCells - The number of cells owned by this process
5902: . numVertices - The number of vertices to be owned by this process, or `PETSC_DECIDE`
5903: . NVertices - The global number of vertices, or `PETSC_DETERMINE`
5904: . numCorners - The number of vertices for each cell
5905: - cells - An array of $ numCells \times numCorners$ numbers, the global vertex numbers for each cell
5907: Output Parameters:
5908: + vertexSF - (Optional) `PetscSF` describing complete vertex ownership
5909: - verticesAdjSaved - (Optional) vertex adjacency array
5911: Level: advanced
5913: Notes:
5914: Two triangles sharing a face
5915: .vb
5917: 2
5918: / | \
5919: / | \
5920: / | \
5921: 0 0 | 1 3
5922: \ | /
5923: \ | /
5924: \ | /
5925: 1
5926: .ve
5927: would have input
5928: .vb
5929: numCells = 2, numVertices = 4
5930: cells = [0 1 2 1 3 2]
5931: .ve
5932: which would result in the `DMPLEX`
5933: .vb
5935: 4
5936: / | \
5937: / | \
5938: / | \
5939: 2 0 | 1 5
5940: \ | /
5941: \ | /
5942: \ | /
5943: 3
5944: .ve
5946: Vertices are implicitly numbered consecutively $0, \ldots, \mathrm{NVertices}$.
5948: Each process owns a chunk of `numVertices` consecutive vertices.
5950: If `numVertices` is `PETSC_DECIDE`, PETSc will distribute them as evenly as possible using `PetscLayout`.
5952: If `NVertices` is `PETSC_DETERMINE` and `numVertices` is `PETSC_DECIDE`, `NVertices` is computed by PETSc as the maximum vertex index in $ cells + 1 $.
5954: If only `NVertices` is `PETSC_DETERMINE`, it is computed as the sum of `numVertices` over all processes.
5956: The cell distribution is arbitrary non-overlapping, independent of the vertex distribution.
5958: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildFromCellList()`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildCoordinatesFromCellListParallel()`,
5959: `PetscSF`
5960: @*/
5961: PetscErrorCode DMPlexBuildFromCellListParallel(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, const PetscInt cells[], PeOp PetscSF *vertexSF, PeOp PetscInt *verticesAdjSaved[])
5962: {
5963: PetscSF sfPoint;
5964: PetscLayout layout;
5965: PetscInt numVerticesAdj, *verticesAdj, *cones, c, p;
5967: PetscFunctionBegin;
5969: PetscCall(PetscLogEventBegin(DMPLEX_BuildFromCellList, dm, 0, 0, 0));
5970: /* Get/check global number of vertices */
5971: {
5972: PetscInt NVerticesInCells, i;
5973: const PetscInt len = numCells * numCorners;
5975: /* NVerticesInCells = max(cells) + 1 */
5976: NVerticesInCells = PETSC_INT_MIN;
5977: for (i = 0; i < len; i++)
5978: if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i];
5979: ++NVerticesInCells;
5980: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm)));
5982: if (numVertices == PETSC_DECIDE && NVertices == PETSC_DECIDE) NVertices = NVerticesInCells;
5983: else
5984: PetscCheck(NVertices == PETSC_DECIDE || NVertices >= NVerticesInCells, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Specified global number of vertices %" PetscInt_FMT " must be greater than or equal to the number of vertices in cells %" PetscInt_FMT, NVertices, NVerticesInCells);
5985: }
5986: /* Count locally unique vertices */
5987: {
5988: PetscHSetI vhash;
5989: PetscInt off = 0;
5991: PetscCall(PetscHSetICreate(&vhash));
5992: for (c = 0; c < numCells; ++c) {
5993: for (p = 0; p < numCorners; ++p) PetscCall(PetscHSetIAdd(vhash, cells[c * numCorners + p]));
5994: }
5995: PetscCall(PetscHSetIGetSize(vhash, &numVerticesAdj));
5996: if (!verticesAdjSaved) PetscCall(PetscMalloc1(numVerticesAdj, &verticesAdj));
5997: else verticesAdj = *verticesAdjSaved;
5998: PetscCall(PetscHSetIGetElems(vhash, &off, verticesAdj));
5999: PetscCall(PetscHSetIDestroy(&vhash));
6000: PetscCheck(off == numVerticesAdj, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %" PetscInt_FMT " should be %" PetscInt_FMT, off, numVerticesAdj);
6001: }
6002: PetscCall(PetscSortInt(numVerticesAdj, verticesAdj));
6003: /* Create cones */
6004: PetscCall(DMPlexSetChart(dm, 0, numCells + numVerticesAdj));
6005: for (c = 0; c < numCells; ++c) PetscCall(DMPlexSetConeSize(dm, c, numCorners));
6006: PetscCall(DMSetUp(dm));
6007: PetscCall(DMPlexGetCones(dm, &cones));
6008: for (c = 0; c < numCells; ++c) {
6009: for (p = 0; p < numCorners; ++p) {
6010: const PetscInt gv = cells[c * numCorners + p];
6011: PetscInt lv;
6013: /* Positions within verticesAdj form 0-based local vertex numbering;
6014: we need to shift it by numCells to get correct DAG points (cells go first) */
6015: PetscCall(PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv));
6016: PetscCheck(lv >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %" PetscInt_FMT " in local connectivity", gv);
6017: cones[c * numCorners + p] = lv + numCells;
6018: }
6019: }
6020: /* Build point sf */
6021: PetscCall(PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &layout));
6022: PetscCall(PetscLayoutSetSize(layout, NVertices));
6023: PetscCall(PetscLayoutSetLocalSize(layout, numVertices));
6024: PetscCall(PetscLayoutSetBlockSize(layout, 1));
6025: PetscCall(PetscSFCreateByMatchingIndices(layout, numVerticesAdj, verticesAdj, NULL, numCells, numVerticesAdj, verticesAdj, NULL, numCells, vertexSF, &sfPoint));
6026: PetscCall(PetscLayoutDestroy(&layout));
6027: if (!verticesAdjSaved) PetscCall(PetscFree(verticesAdj));
6028: PetscCall(PetscObjectSetName((PetscObject)sfPoint, "point SF"));
6029: if (dm->sf) {
6030: const char *prefix;
6032: PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm->sf, &prefix));
6033: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)sfPoint, prefix));
6034: }
6035: PetscCall(DMSetPointSF(dm, sfPoint));
6036: PetscCall(PetscSFDestroy(&sfPoint));
6037: if (vertexSF) PetscCall(PetscObjectSetName((PetscObject)*vertexSF, "Vertex Ownership SF"));
6038: /* Fill in the rest of the topology structure */
6039: PetscCall(DMPlexSymmetrize(dm));
6040: PetscCall(DMPlexStratify(dm));
6041: PetscCall(PetscLogEventEnd(DMPLEX_BuildFromCellList, dm, 0, 0, 0));
6042: PetscFunctionReturn(PETSC_SUCCESS);
6043: }
6045: /*@C
6046: DMPlexBuildFromCellSectionParallel - Build distributed `DMPLEX` topology from a list of vertices for each cell (common mesh generator output) allowing multiple celltypes
6048: Collective; No Fortran Support
6050: Input Parameters:
6051: + dm - The `DM`
6052: . numCells - The number of cells owned by this process
6053: . numVertices - The number of vertices to be owned by this process, or `PETSC_DECIDE`
6054: . NVertices - The global number of vertices, or `PETSC_DETERMINE`
6055: . cellSection - The `PetscSection` giving the number of vertices for each cell (layout of cells)
6056: - cells - An array of the global vertex numbers for each cell
6058: Output Parameters:
6059: + vertexSF - (Optional) `PetscSF` describing complete vertex ownership
6060: - verticesAdjSaved - (Optional) vertex adjacency array
6062: Level: advanced
6064: Notes:
6065: A triangle and quadrilateral sharing a face
6066: .vb
6067: 2----------3
6068: / | |
6069: / | |
6070: / | |
6071: 0 0 | 1 |
6072: \ | |
6073: \ | |
6074: \ | |
6075: 1----------4
6076: .ve
6077: would have input
6078: .vb
6079: numCells = 2, numVertices = 5
6080: cells = [0 1 2 1 4 3 2]
6081: .ve
6082: which would result in the `DMPLEX`
6083: .vb
6084: 4----------5
6085: / | |
6086: / | |
6087: / | |
6088: 2 0 | 1 |
6089: \ | |
6090: \ | |
6091: \ | |
6092: 3----------6
6093: .ve
6095: Vertices are implicitly numbered consecutively 0,...,NVertices.
6096: Each rank owns a chunk of numVertices consecutive vertices.
6097: If numVertices is `PETSC_DECIDE`, PETSc will distribute them as evenly as possible using PetscLayout.
6098: If NVertices is `PETSC_DETERMINE` and numVertices is PETSC_DECIDE, NVertices is computed by PETSc as the maximum vertex index in cells + 1.
6099: If only NVertices is `PETSC_DETERMINE`, it is computed as the sum of numVertices over all ranks.
6101: The cell distribution is arbitrary non-overlapping, independent of the vertex distribution.
6103: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildFromCellListParallel()`, `DMPlexCreateFromCellSectionParallel()`, `DMPlexBuildCoordinatesFromCellListParallel()`,
6104: `PetscSF`
6105: @*/
6106: PetscErrorCode DMPlexBuildFromCellSectionParallel(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscSection cellSection, const PetscInt cells[], PeOp PetscSF *vertexSF, PeOp PetscInt *verticesAdjSaved[])
6107: {
6108: PetscSF sfPoint;
6109: PetscLayout layout;
6110: PetscInt numVerticesAdj, *verticesAdj, *cones, cStart, cEnd, len;
6112: PetscFunctionBegin;
6114: PetscCall(PetscLogEventBegin(DMPLEX_BuildFromCellList, dm, 0, 0, 0));
6115: PetscCall(PetscSectionGetChart(cellSection, &cStart, &cEnd));
6116: PetscCall(PetscSectionGetStorageSize(cellSection, &len));
6117: PetscCheck(cStart == 0 && cEnd == numCells, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Section chart [%" PetscInt_FMT ", %" PetscInt_FMT ") should be [0, %" PetscInt_FMT ")", cStart, cEnd, numCells);
6118: /* Get/check global number of vertices */
6119: {
6120: PetscInt NVerticesInCells;
6122: /* NVerticesInCells = max(cells) + 1 */
6123: NVerticesInCells = PETSC_MIN_INT;
6124: for (PetscInt i = 0; i < len; i++)
6125: if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i];
6126: ++NVerticesInCells;
6127: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm)));
6129: if (numVertices == PETSC_DECIDE && NVertices == PETSC_DECIDE) NVertices = NVerticesInCells;
6130: else
6131: PetscCheck(NVertices == PETSC_DECIDE || NVertices >= NVerticesInCells, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Specified global number of vertices %" PetscInt_FMT " must be greater than or equal to the number of vertices in cells %" PetscInt_FMT, NVertices, NVerticesInCells);
6132: }
6133: /* Count locally unique vertices */
6134: {
6135: PetscHSetI vhash;
6136: PetscInt off = 0;
6138: PetscCall(PetscHSetICreate(&vhash));
6139: for (PetscInt i = 0; i < len; i++) PetscCall(PetscHSetIAdd(vhash, cells[i]));
6140: PetscCall(PetscHSetIGetSize(vhash, &numVerticesAdj));
6141: if (!verticesAdjSaved) PetscCall(PetscMalloc1(numVerticesAdj, &verticesAdj));
6142: else verticesAdj = *verticesAdjSaved;
6143: PetscCall(PetscHSetIGetElems(vhash, &off, verticesAdj));
6144: PetscCall(PetscHSetIDestroy(&vhash));
6145: PetscCheck(off == numVerticesAdj, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %" PetscInt_FMT " should be %" PetscInt_FMT, off, numVerticesAdj);
6146: }
6147: PetscCall(PetscSortInt(numVerticesAdj, verticesAdj));
6148: /* Create cones */
6149: PetscCall(DMPlexSetChart(dm, 0, numCells + numVerticesAdj));
6150: for (PetscInt c = 0; c < numCells; ++c) {
6151: PetscInt dof;
6153: PetscCall(PetscSectionGetDof(cellSection, c, &dof));
6154: PetscCall(DMPlexSetConeSize(dm, c, dof));
6155: }
6156: PetscCall(DMSetUp(dm));
6157: PetscCall(DMPlexGetCones(dm, &cones));
6158: for (PetscInt c = 0; c < numCells; ++c) {
6159: PetscInt dof, off;
6161: PetscCall(PetscSectionGetDof(cellSection, c, &dof));
6162: PetscCall(PetscSectionGetOffset(cellSection, c, &off));
6163: for (PetscInt p = off; p < off + dof; ++p) {
6164: const PetscInt gv = cells[p];
6165: PetscInt lv;
6167: /* Positions within verticesAdj form 0-based local vertex numbering;
6168: we need to shift it by numCells to get correct DAG points (cells go first) */
6169: PetscCall(PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv));
6170: PetscCheck(lv >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %" PetscInt_FMT " in local connectivity", gv);
6171: cones[p] = lv + numCells;
6172: }
6173: }
6174: /* Build point sf */
6175: PetscCall(PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &layout));
6176: PetscCall(PetscLayoutSetSize(layout, NVertices));
6177: PetscCall(PetscLayoutSetLocalSize(layout, numVertices));
6178: PetscCall(PetscLayoutSetBlockSize(layout, 1));
6179: PetscCall(PetscSFCreateByMatchingIndices(layout, numVerticesAdj, verticesAdj, NULL, numCells, numVerticesAdj, verticesAdj, NULL, numCells, vertexSF, &sfPoint));
6180: PetscCall(PetscLayoutDestroy(&layout));
6181: if (!verticesAdjSaved) PetscCall(PetscFree(verticesAdj));
6182: PetscCall(PetscObjectSetName((PetscObject)sfPoint, "point SF"));
6183: if (dm->sf) {
6184: const char *prefix;
6186: PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm->sf, &prefix));
6187: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)sfPoint, prefix));
6188: }
6189: PetscCall(DMSetPointSF(dm, sfPoint));
6190: PetscCall(PetscSFDestroy(&sfPoint));
6191: if (vertexSF) PetscCall(PetscObjectSetName((PetscObject)*vertexSF, "Vertex Ownership SF"));
6192: /* Fill in the rest of the topology structure */
6193: PetscCall(DMPlexSymmetrize(dm));
6194: PetscCall(DMPlexStratify(dm));
6195: PetscCall(PetscLogEventEnd(DMPLEX_BuildFromCellList, dm, 0, 0, 0));
6196: PetscFunctionReturn(PETSC_SUCCESS);
6197: }
6199: /*@
6200: DMPlexBuildCoordinatesFromCellListParallel - Build `DM` coordinates from a list of coordinates for each owned vertex (common mesh generator output)
6202: Collective; No Fortran Support
6204: Input Parameters:
6205: + dm - The `DM`
6206: . spaceDim - The spatial dimension used for coordinates
6207: . sfVert - `PetscSF` describing complete vertex ownership
6208: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
6210: Level: advanced
6212: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildFromCellListParallel()`
6213: @*/
6214: PetscErrorCode DMPlexBuildCoordinatesFromCellListParallel(DM dm, PetscInt spaceDim, PetscSF sfVert, const PetscReal vertexCoords[])
6215: {
6216: PetscSection coordSection;
6217: Vec coordinates;
6218: PetscScalar *coords;
6219: PetscInt numVertices, numVerticesAdj, coordSize, v, vStart, vEnd;
6220: PetscMPIInt spaceDimi;
6222: PetscFunctionBegin;
6223: PetscCall(PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0));
6224: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
6225: PetscCheck(vStart >= 0 && vEnd >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first.");
6226: PetscCall(DMSetCoordinateDim(dm, spaceDim));
6227: PetscCall(PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL));
6228: PetscCheck(vEnd - vStart == numVerticesAdj, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Supplied sfVert has wrong number of leaves = %" PetscInt_FMT " != %" PetscInt_FMT " = vEnd - vStart", numVerticesAdj, vEnd - vStart);
6229: PetscCall(DMGetCoordinateSection(dm, &coordSection));
6230: PetscCall(PetscSectionSetNumFields(coordSection, 1));
6231: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spaceDim));
6232: PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd));
6233: for (v = vStart; v < vEnd; ++v) {
6234: PetscCall(PetscSectionSetDof(coordSection, v, spaceDim));
6235: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spaceDim));
6236: }
6237: PetscCall(PetscSectionSetUp(coordSection));
6238: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
6239: PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &coordinates));
6240: PetscCall(VecSetBlockSize(coordinates, spaceDim));
6241: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
6242: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
6243: PetscCall(VecSetType(coordinates, VECSTANDARD));
6244: PetscCall(VecGetArray(coordinates, &coords));
6245: {
6246: MPI_Datatype coordtype;
6248: /* Need a temp buffer for coords if we have complex/single */
6249: PetscCall(PetscMPIIntCast(spaceDim, &spaceDimi));
6250: PetscCallMPI(MPI_Type_contiguous(spaceDimi, MPIU_SCALAR, &coordtype));
6251: PetscCallMPI(MPI_Type_commit(&coordtype));
6252: #if defined(PETSC_USE_COMPLEX)
6253: {
6254: PetscScalar *svertexCoords;
6255: PetscInt i;
6256: PetscCall(PetscMalloc1(numVertices * spaceDim, &svertexCoords));
6257: for (i = 0; i < numVertices * spaceDim; i++) svertexCoords[i] = vertexCoords[i];
6258: PetscCall(PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords, MPI_REPLACE));
6259: PetscCall(PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords, MPI_REPLACE));
6260: PetscCall(PetscFree(svertexCoords));
6261: }
6262: #else
6263: PetscCall(PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords, MPI_REPLACE));
6264: PetscCall(PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords, MPI_REPLACE));
6265: #endif
6266: PetscCallMPI(MPI_Type_free(&coordtype));
6267: }
6268: PetscCall(VecRestoreArray(coordinates, &coords));
6269: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
6270: PetscCall(VecDestroy(&coordinates));
6271: PetscCall(PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0));
6272: PetscFunctionReturn(PETSC_SUCCESS);
6273: }
6275: /*@
6276: DMPlexCreateFromCellListParallelPetsc - Create distributed `DMPLEX` from a list of vertices for each cell (common mesh generator output) where all cells have the same celltype
6278: Collective
6280: Input Parameters:
6281: + comm - The communicator
6282: . dim - The topological dimension of the mesh
6283: . numCells - The number of cells owned by this process
6284: . numVertices - The number of vertices owned by this process, or `PETSC_DECIDE`
6285: . NVertices - The global number of vertices, or `PETSC_DECIDE`
6286: . numCorners - The number of vertices for each cell
6287: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
6288: . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell
6289: . spaceDim - The spatial dimension used for coordinates
6290: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
6292: Output Parameters:
6293: + dm - The `DM`
6294: . vertexSF - (Optional) `PetscSF` describing complete vertex ownership
6295: - verticesAdj - (Optional) vertex adjacency array
6297: Level: intermediate
6299: Notes:
6300: This function is just a convenient sequence of `DMCreate()`, `DMSetType()`, `DMSetDimension()`,
6301: `DMPlexBuildFromCellListParallel()`, `DMPlexInterpolate()`, `DMPlexBuildCoordinatesFromCellListParallel()`
6303: See `DMPlexBuildFromCellListParallel()` for an example and details about the topology-related parameters.
6305: See `DMPlexBuildCoordinatesFromCellListParallel()` for details about the geometry-related parameters.
6307: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromCellListPetsc()`, `DMPlexBuildFromCellListParallel()`, `DMPlexBuildCoordinatesFromCellListParallel()`, `DMPlexCreateFromDAG()`, `DMPlexCreate()`
6308: @*/
6309: PetscErrorCode DMPlexCreateFromCellListParallelPetsc(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, PetscBool interpolate, const PetscInt cells[], PetscInt spaceDim, const PetscReal vertexCoords[], PeOp PetscSF *vertexSF, PeOp PetscInt *verticesAdj[], DM *dm)
6310: {
6311: PetscSF sfVert;
6313: PetscFunctionBegin;
6314: PetscCall(DMCreate(comm, dm));
6315: PetscCall(DMSetType(*dm, DMPLEX));
6318: PetscCall(DMSetDimension(*dm, dim));
6319: PetscCall(DMPlexBuildFromCellListParallel(*dm, numCells, numVertices, NVertices, numCorners, cells, &sfVert, verticesAdj));
6320: if (interpolate) {
6321: DM idm;
6323: PetscCall(DMPlexInterpolate(*dm, &idm));
6324: PetscCall(DMDestroy(dm));
6325: *dm = idm;
6326: }
6327: PetscCall(DMPlexBuildCoordinatesFromCellListParallel(*dm, spaceDim, sfVert, vertexCoords));
6328: if (vertexSF) *vertexSF = sfVert;
6329: else PetscCall(PetscSFDestroy(&sfVert));
6330: PetscFunctionReturn(PETSC_SUCCESS);
6331: }
6333: /*@
6334: DMPlexCreateFromCellSectionParallel - Create distributed `DMPLEX` from a list of vertices for each cell (common mesh generator output) and supports multiple celltypes
6336: Collective
6338: Input Parameters:
6339: + comm - The communicator
6340: . dim - The topological dimension of the mesh
6341: . numCells - The number of cells owned by this process
6342: . numVertices - The number of vertices owned by this process, or `PETSC_DECIDE`
6343: . NVertices - The global number of vertices, or `PETSC_DECIDE`
6344: . cellSection - The `PetscSection` giving the number of vertices for each cell (layout of cells)
6345: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
6346: . cells - An array of the global vertex numbers for each cell
6347: . spaceDim - The spatial dimension used for coordinates
6348: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
6350: Output Parameters:
6351: + dm - The `DM`
6352: . vertexSF - (Optional) `PetscSF` describing complete vertex ownership
6353: - verticesAdj - (Optional) vertex adjacency array
6355: Level: intermediate
6357: Notes:
6358: This function is just a convenient sequence of `DMCreate()`, `DMSetType()`, `DMSetDimension()`,
6359: `DMPlexBuildFromCellSectionParallel()`, `DMPlexInterpolate()`, `DMPlexBuildCoordinatesFromCellListParallel()`
6361: See `DMPlexBuildFromCellSectionParallel()` for an example and details about the topology-related parameters.
6363: See `DMPlexBuildCoordinatesFromCellListParallel()` for details about the geometry-related parameters.
6365: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromCellListPetsc()`, `DMPlexBuildFromCellListParallel()`, `DMPlexBuildCoordinatesFromCellListParallel()`, `DMPlexCreateFromDAG()`, `DMPlexCreate()`
6366: @*/
6367: PetscErrorCode DMPlexCreateFromCellSectionParallel(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscSection cellSection, PetscBool interpolate, const PetscInt cells[], PetscInt spaceDim, const PetscReal vertexCoords[], PeOp PetscSF *vertexSF, PeOp PetscInt *verticesAdj[], DM *dm)
6368: {
6369: PetscSF sfVert;
6371: PetscFunctionBegin;
6372: PetscCall(DMCreate(comm, dm));
6373: PetscCall(DMSetType(*dm, DMPLEX));
6376: PetscCall(DMSetDimension(*dm, dim));
6377: PetscCall(DMPlexBuildFromCellSectionParallel(*dm, numCells, numVertices, NVertices, cellSection, cells, &sfVert, verticesAdj));
6378: if (interpolate) {
6379: DM idm;
6381: PetscCall(DMPlexInterpolate(*dm, &idm));
6382: PetscCall(DMDestroy(dm));
6383: *dm = idm;
6384: }
6385: PetscCall(DMPlexBuildCoordinatesFromCellListParallel(*dm, spaceDim, sfVert, vertexCoords));
6386: if (vertexSF) *vertexSF = sfVert;
6387: else PetscCall(PetscSFDestroy(&sfVert));
6388: PetscFunctionReturn(PETSC_SUCCESS);
6389: }
6391: /*@
6392: DMPlexBuildFromCellList - Build `DMPLEX` topology from a list of vertices for each cell (common mesh generator output)
6394: Collective; No Fortran Support
6396: Input Parameters:
6397: + dm - The `DM`
6398: . numCells - The number of cells owned by this process
6399: . numVertices - The number of vertices owned by this process, or `PETSC_DETERMINE`
6400: . numCorners - The number of vertices for each cell
6401: - cells - An array of `numCells` x `numCorners` numbers, the global vertex numbers for each cell
6403: Level: advanced
6405: Notes:
6406: Two triangles sharing a face
6407: .vb
6409: 2
6410: / | \
6411: / | \
6412: / | \
6413: 0 0 | 1 3
6414: \ | /
6415: \ | /
6416: \ | /
6417: 1
6418: .ve
6419: would have input
6420: .vb
6421: numCells = 2, numVertices = 4
6422: cells = [0 1 2 1 3 2]
6423: .ve
6424: which would result in the `DMPLEX`
6425: .vb
6427: 4
6428: / | \
6429: / | \
6430: / | \
6431: 2 0 | 1 5
6432: \ | /
6433: \ | /
6434: \ | /
6435: 3
6436: .ve
6438: If numVertices is `PETSC_DETERMINE`, it is computed by PETSc as the maximum vertex index in cells + 1.
6440: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildFromCellListParallel()`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromCellListPetsc()`
6441: @*/
6442: PetscErrorCode DMPlexBuildFromCellList(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[])
6443: {
6444: PetscInt *cones, c, p, dim;
6446: PetscFunctionBegin;
6447: PetscCall(PetscLogEventBegin(DMPLEX_BuildFromCellList, dm, 0, 0, 0));
6448: PetscCall(DMGetDimension(dm, &dim));
6449: /* Get/check global number of vertices */
6450: {
6451: PetscInt NVerticesInCells, i;
6452: const PetscInt len = numCells * numCorners;
6454: /* NVerticesInCells = max(cells) + 1 */
6455: NVerticesInCells = PETSC_INT_MIN;
6456: for (i = 0; i < len; i++)
6457: if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i];
6458: ++NVerticesInCells;
6460: if (numVertices == PETSC_DECIDE) numVertices = NVerticesInCells;
6461: else
6462: PetscCheck(numVertices >= NVerticesInCells, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Specified number of vertices %" PetscInt_FMT " must be greater than or equal to the number of vertices in cells %" PetscInt_FMT, numVertices, NVerticesInCells);
6463: }
6464: PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices));
6465: for (c = 0; c < numCells; ++c) PetscCall(DMPlexSetConeSize(dm, c, numCorners));
6466: PetscCall(DMSetUp(dm));
6467: PetscCall(DMPlexGetCones(dm, &cones));
6468: for (c = 0; c < numCells; ++c) {
6469: for (p = 0; p < numCorners; ++p) cones[c * numCorners + p] = cells[c * numCorners + p] + numCells;
6470: }
6471: PetscCall(DMPlexSymmetrize(dm));
6472: PetscCall(DMPlexStratify(dm));
6473: PetscCall(PetscLogEventEnd(DMPLEX_BuildFromCellList, dm, 0, 0, 0));
6474: PetscFunctionReturn(PETSC_SUCCESS);
6475: }
6477: /*@
6478: DMPlexBuildCoordinatesFromCellList - Build `DM` coordinates from a list of coordinates for each owned vertex (common mesh generator output)
6480: Collective
6482: Input Parameters:
6483: + dm - The `DM`
6484: . spaceDim - The spatial dimension used for coordinates
6485: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
6487: Level: advanced
6489: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildCoordinatesFromCellListParallel()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexBuildFromCellList()`
6490: @*/
6491: PetscErrorCode DMPlexBuildCoordinatesFromCellList(DM dm, PetscInt spaceDim, const PetscReal vertexCoords[])
6492: {
6493: PetscSection coordSection;
6494: Vec coordinates;
6495: DM cdm;
6496: PetscScalar *coords;
6497: PetscInt v, vStart, vEnd, d;
6499: PetscFunctionBegin;
6500: PetscCall(PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0));
6501: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
6502: PetscCheck(vStart >= 0 && vEnd >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first.");
6503: PetscCall(DMSetCoordinateDim(dm, spaceDim));
6504: PetscCall(DMGetCoordinateSection(dm, &coordSection));
6505: PetscCall(PetscSectionSetNumFields(coordSection, 1));
6506: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spaceDim));
6507: PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd));
6508: for (v = vStart; v < vEnd; ++v) {
6509: PetscCall(PetscSectionSetDof(coordSection, v, spaceDim));
6510: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spaceDim));
6511: }
6512: PetscCall(PetscSectionSetUp(coordSection));
6514: PetscCall(DMGetCoordinateDM(dm, &cdm));
6515: PetscCall(DMCreateLocalVector(cdm, &coordinates));
6516: PetscCall(VecSetBlockSize(coordinates, spaceDim));
6517: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
6518: PetscCall(VecGetArrayWrite(coordinates, &coords));
6519: for (v = 0; v < vEnd - vStart; ++v) {
6520: for (d = 0; d < spaceDim; ++d) coords[v * spaceDim + d] = vertexCoords[v * spaceDim + d];
6521: }
6522: PetscCall(VecRestoreArrayWrite(coordinates, &coords));
6523: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
6524: PetscCall(VecDestroy(&coordinates));
6525: PetscCall(PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0));
6526: PetscFunctionReturn(PETSC_SUCCESS);
6527: }
6529: /*@
6530: DMPlexCreateFromCellListPetsc - Create `DMPLEX` from a list of vertices for each cell (common mesh generator output), but only process 0 takes in the input
6532: Collective
6534: Input Parameters:
6535: + comm - The communicator
6536: . dim - The topological dimension of the mesh
6537: . numCells - The number of cells, only on process 0
6538: . numVertices - The number of vertices owned by this process, or `PETSC_DECIDE`, only on process 0
6539: . numCorners - The number of vertices for each cell, only on process 0
6540: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
6541: . cells - An array of $ numCells \times numCorners$ numbers, the vertices for each cell, only on process 0
6542: . spaceDim - The spatial dimension used for coordinates
6543: - vertexCoords - An array of $ numVertices \times spaceDim$ numbers, the coordinates of each vertex, only on process 0
6545: Output Parameter:
6546: . dm - The `DM`, which only has points on process 0
6548: Level: intermediate
6550: Notes:
6551: This function is just a convenient sequence of `DMCreate()`, `DMSetType()`, `DMSetDimension()`, `DMPlexBuildFromCellList()`,
6552: `DMPlexInterpolate()`, `DMPlexBuildCoordinatesFromCellList()`
6554: See `DMPlexBuildFromCellList()` for an example and details about the topology-related parameters.
6555: See `DMPlexBuildCoordinatesFromCellList()` for details about the geometry-related parameters.
6556: See `DMPlexCreateFromCellListParallelPetsc()` for parallel input
6558: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildFromCellList()`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromDAG()`, `DMPlexCreate()`
6559: @*/
6560: PetscErrorCode DMPlexCreateFromCellListPetsc(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, PetscBool interpolate, const PetscInt cells[], PetscInt spaceDim, const PetscReal vertexCoords[], DM *dm)
6561: {
6562: PetscMPIInt rank;
6564: PetscFunctionBegin;
6565: PetscCheck(dim, comm, PETSC_ERR_ARG_OUTOFRANGE, "This is not appropriate for 0-dimensional meshes. Consider either creating the DM using DMPlexCreateFromDAG(), by hand, or using DMSwarm.");
6566: PetscCallMPI(MPI_Comm_rank(comm, &rank));
6567: PetscCall(DMCreate(comm, dm));
6568: PetscCall(DMSetType(*dm, DMPLEX));
6569: PetscCall(DMSetDimension(*dm, dim));
6570: if (rank == 0) PetscCall(DMPlexBuildFromCellList(*dm, numCells, numVertices, numCorners, cells));
6571: else PetscCall(DMPlexBuildFromCellList(*dm, 0, 0, 0, NULL));
6572: if (interpolate) {
6573: DM idm;
6575: PetscCall(DMPlexInterpolate(*dm, &idm));
6576: PetscCall(DMDestroy(dm));
6577: *dm = idm;
6578: }
6579: if (rank == 0) PetscCall(DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, vertexCoords));
6580: else PetscCall(DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, NULL));
6581: PetscFunctionReturn(PETSC_SUCCESS);
6582: }
6584: /*@
6585: DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a `DM`
6587: Input Parameters:
6588: + dm - The empty `DM` object, usually from `DMCreate()` and `DMSetDimension()`
6589: . depth - The depth of the DAG
6590: . numPoints - Array of size $ depth + 1 $ containing the number of points at each `depth`
6591: . coneSize - The cone size of each point
6592: . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point
6593: . coneOrientations - The orientation of each cone point
6594: - vertexCoords - An array of $ numPoints[0] \times spacedim $ numbers representing the coordinates of each vertex, with `spacedim` the value set via `DMSetCoordinateDim()`
6596: Output Parameter:
6597: . dm - The `DM`
6599: Level: advanced
6601: Note:
6602: Two triangles sharing a face would have input
6603: .vb
6604: depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0]
6605: cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0]
6606: vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0]
6607: .ve
6608: which would result in the DMPlex
6609: .vb
6610: 4
6611: / | \
6612: / | \
6613: / | \
6614: 2 0 | 1 5
6615: \ | /
6616: \ | /
6617: \ | /
6618: 3
6619: .ve
6620: Notice that all points are numbered consecutively, unlike `DMPlexCreateFromCellListPetsc()`
6622: Developer Note:
6623: This does not create anything so should not have create in the name.
6625: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()`
6626: @*/
6627: PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[])
6628: {
6629: Vec coordinates;
6630: PetscSection coordSection;
6631: PetscScalar *coords;
6632: PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off;
6634: PetscFunctionBegin;
6635: PetscCall(DMGetDimension(dm, &dim));
6636: PetscCall(DMGetCoordinateDim(dm, &dimEmbed));
6637: PetscCheck(dimEmbed >= dim, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Embedding dimension %" PetscInt_FMT " cannot be less than intrinsic dimension %" PetscInt_FMT, dimEmbed, dim);
6638: for (d = 0; d <= depth; ++d) pEnd += numPoints[d];
6639: PetscCall(DMPlexSetChart(dm, pStart, pEnd));
6640: for (p = pStart; p < pEnd; ++p) {
6641: PetscCall(DMPlexSetConeSize(dm, p, coneSize[p - pStart]));
6642: if (firstVertex < 0 && !coneSize[p - pStart]) firstVertex = p - pStart;
6643: }
6644: PetscCheck(firstVertex >= 0 || !numPoints[0], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Expected %" PetscInt_FMT " vertices but could not find any", numPoints[0]);
6645: PetscCall(DMSetUp(dm)); /* Allocate space for cones */
6646: for (p = pStart, off = 0; p < pEnd; off += coneSize[p - pStart], ++p) {
6647: PetscCall(DMPlexSetCone(dm, p, &cones[off]));
6648: PetscCall(DMPlexSetConeOrientation(dm, p, &coneOrientations[off]));
6649: }
6650: PetscCall(DMPlexSymmetrize(dm));
6651: PetscCall(DMPlexStratify(dm));
6652: /* Build coordinates */
6653: PetscCall(DMGetCoordinateSection(dm, &coordSection));
6654: PetscCall(PetscSectionSetNumFields(coordSection, 1));
6655: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dimEmbed));
6656: PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex + numPoints[0]));
6657: for (v = firstVertex; v < firstVertex + numPoints[0]; ++v) {
6658: PetscCall(PetscSectionSetDof(coordSection, v, dimEmbed));
6659: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed));
6660: }
6661: PetscCall(PetscSectionSetUp(coordSection));
6662: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
6663: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
6664: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
6665: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
6666: PetscCall(VecSetBlockSize(coordinates, PetscMax(dimEmbed, 1)));
6667: PetscCall(VecSetType(coordinates, VECSTANDARD));
6668: if (vertexCoords) {
6669: PetscCall(VecGetArray(coordinates, &coords));
6670: for (v = 0; v < numPoints[0]; ++v) {
6671: PetscInt off;
6673: PetscCall(PetscSectionGetOffset(coordSection, v + firstVertex, &off));
6674: for (d = 0; d < dimEmbed; ++d) coords[off + d] = vertexCoords[v * dimEmbed + d];
6675: }
6676: }
6677: PetscCall(VecRestoreArray(coordinates, &coords));
6678: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
6679: PetscCall(VecDestroy(&coordinates));
6680: PetscFunctionReturn(PETSC_SUCCESS);
6681: }
6683: /*
6684: DMPlexCreateCellVertexFromFile - Create a `DMPLEX` mesh from a simple cell-vertex file.
6686: Collective
6688: + comm - The MPI communicator
6689: . filename - Name of the .dat file
6690: - interpolate - Create faces and edges in the mesh
6692: Output Parameter:
6693: . dm - The `DM` object representing the mesh
6695: Level: beginner
6697: Note:
6698: The format is the simplest possible:
6699: .vb
6700: dim Ne Nv Nc Nl
6701: v_1 v_2 ... v_Nc
6702: ...
6703: x y z marker_1 ... marker_Nl
6704: .ve
6706: Developer Note:
6707: Should use a `PetscViewer` not a filename
6709: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromFile()`, `DMPlexCreateGmsh()`, `DMPlexCreate()`
6710: */
6711: static PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
6712: {
6713: DMLabel marker;
6714: PetscViewer viewer;
6715: Vec coordinates;
6716: PetscSection coordSection;
6717: PetscScalar *coords;
6718: char line[PETSC_MAX_PATH_LEN];
6719: PetscInt cdim, coordSize, v, c, d;
6720: PetscMPIInt rank;
6721: int snum, dim, Nv, Nc, Ncn, Nl;
6723: PetscFunctionBegin;
6724: PetscCallMPI(MPI_Comm_rank(comm, &rank));
6725: PetscCall(PetscViewerCreate(comm, &viewer));
6726: PetscCall(PetscViewerSetType(viewer, PETSCVIEWERASCII));
6727: PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ));
6728: PetscCall(PetscViewerFileSetName(viewer, filename));
6729: if (rank == 0) {
6730: PetscCall(PetscViewerRead(viewer, line, 5, NULL, PETSC_STRING));
6731: snum = sscanf(line, "%d %d %d %d %d", &dim, &Nc, &Nv, &Ncn, &Nl);
6732: PetscCheck(snum == 5, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
6733: } else {
6734: Nc = Nv = Ncn = Nl = 0;
6735: }
6736: PetscCallMPI(MPI_Bcast(&dim, 1, MPI_INT, 0, comm));
6737: cdim = dim;
6738: PetscCall(DMCreate(comm, dm));
6739: PetscCall(DMSetType(*dm, DMPLEX));
6740: PetscCall(DMPlexSetChart(*dm, 0, Nc + Nv));
6741: PetscCall(DMSetDimension(*dm, dim));
6742: PetscCall(DMSetCoordinateDim(*dm, cdim));
6743: /* Read topology */
6744: if (rank == 0) {
6745: char format[PETSC_MAX_PATH_LEN];
6746: PetscInt cone[8];
6747: int vbuf[8], v;
6749: for (c = 0; c < Ncn; ++c) {
6750: format[c * 3 + 0] = '%';
6751: format[c * 3 + 1] = 'd';
6752: format[c * 3 + 2] = ' ';
6753: }
6754: format[Ncn * 3 - 1] = '\0';
6755: for (c = 0; c < Nc; ++c) PetscCall(DMPlexSetConeSize(*dm, c, Ncn));
6756: PetscCall(DMSetUp(*dm));
6757: for (c = 0; c < Nc; ++c) {
6758: PetscCall(PetscViewerRead(viewer, line, Ncn, NULL, PETSC_STRING));
6759: switch (Ncn) {
6760: case 2:
6761: snum = sscanf(line, format, &vbuf[0], &vbuf[1]);
6762: break;
6763: case 3:
6764: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2]);
6765: break;
6766: case 4:
6767: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3]);
6768: break;
6769: case 6:
6770: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5]);
6771: break;
6772: case 8:
6773: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5], &vbuf[6], &vbuf[7]);
6774: break;
6775: default:
6776: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "No cell shape with %d vertices", Ncn);
6777: }
6778: PetscCheck(snum == Ncn, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
6779: for (v = 0; v < Ncn; ++v) cone[v] = vbuf[v] + Nc;
6780: /* Hexahedra are inverted */
6781: if (Ncn == 8) {
6782: PetscInt tmp = cone[1];
6783: cone[1] = cone[3];
6784: cone[3] = tmp;
6785: }
6786: PetscCall(DMPlexSetCone(*dm, c, cone));
6787: }
6788: }
6789: PetscCall(DMPlexSymmetrize(*dm));
6790: PetscCall(DMPlexStratify(*dm));
6791: /* Read coordinates */
6792: PetscCall(DMGetCoordinateSection(*dm, &coordSection));
6793: PetscCall(PetscSectionSetNumFields(coordSection, 1));
6794: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, cdim));
6795: PetscCall(PetscSectionSetChart(coordSection, Nc, Nc + Nv));
6796: for (v = Nc; v < Nc + Nv; ++v) {
6797: PetscCall(PetscSectionSetDof(coordSection, v, cdim));
6798: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, cdim));
6799: }
6800: PetscCall(PetscSectionSetUp(coordSection));
6801: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
6802: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
6803: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
6804: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
6805: PetscCall(VecSetBlockSize(coordinates, cdim));
6806: PetscCall(VecSetType(coordinates, VECSTANDARD));
6807: PetscCall(VecGetArray(coordinates, &coords));
6808: if (rank == 0) {
6809: char format[PETSC_MAX_PATH_LEN];
6810: double x[3];
6811: int l, val[3];
6813: if (Nl) {
6814: for (l = 0; l < Nl; ++l) {
6815: format[l * 3 + 0] = '%';
6816: format[l * 3 + 1] = 'd';
6817: format[l * 3 + 2] = ' ';
6818: }
6819: format[Nl * 3 - 1] = '\0';
6820: PetscCall(DMCreateLabel(*dm, "marker"));
6821: PetscCall(DMGetLabel(*dm, "marker", &marker));
6822: }
6823: for (v = 0; v < Nv; ++v) {
6824: PetscCall(PetscViewerRead(viewer, line, 3 + Nl, NULL, PETSC_STRING));
6825: snum = sscanf(line, "%lg %lg %lg", &x[0], &x[1], &x[2]);
6826: PetscCheck(snum == 3, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
6827: switch (Nl) {
6828: case 0:
6829: snum = 0;
6830: break;
6831: case 1:
6832: snum = sscanf(line, format, &val[0]);
6833: break;
6834: case 2:
6835: snum = sscanf(line, format, &val[0], &val[1]);
6836: break;
6837: case 3:
6838: snum = sscanf(line, format, &val[0], &val[1], &val[2]);
6839: break;
6840: default:
6841: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Request support for %d labels", Nl);
6842: }
6843: PetscCheck(snum == Nl, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
6844: for (d = 0; d < cdim; ++d) coords[v * cdim + d] = x[d];
6845: for (l = 0; l < Nl; ++l) PetscCall(DMLabelSetValue(marker, v + Nc, val[l]));
6846: }
6847: }
6848: PetscCall(VecRestoreArray(coordinates, &coords));
6849: PetscCall(DMSetCoordinatesLocal(*dm, coordinates));
6850: PetscCall(VecDestroy(&coordinates));
6851: PetscCall(PetscViewerDestroy(&viewer));
6852: if (interpolate) {
6853: DM idm;
6854: DMLabel bdlabel;
6856: PetscCall(DMPlexInterpolate(*dm, &idm));
6857: PetscCall(DMDestroy(dm));
6858: *dm = idm;
6860: if (!Nl) {
6861: PetscCall(DMCreateLabel(*dm, "marker"));
6862: PetscCall(DMGetLabel(*dm, "marker", &bdlabel));
6863: PetscCall(DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel));
6864: PetscCall(DMPlexLabelComplete(*dm, bdlabel));
6865: }
6866: }
6867: PetscFunctionReturn(PETSC_SUCCESS);
6868: }
6870: /*
6871: DMPlexCreateSTLFromFile - Create a `DMPLEX` mesh from an STL file.
6873: Collective
6875: + comm - The MPI communicator
6876: . filename - Name of the .dat file
6877: - interpolate - Create faces and edges in the mesh
6879: Output Parameter:
6880: . dm - The `DM` object representing the mesh
6882: Level: beginner
6884: Notes:
6885: The binary format is:
6886: .vb
6887: UINT8[80] - Header - 80 bytes
6888: UINT32 - Number of triangles - 04 bytes
6889: foreach triangle - 50 bytes
6890: REAL32[3] - Normal vector - 12 bytes
6891: REAL32[3] - Vertex 1 - 12 bytes
6892: REAL32[3] - Vertex 2 - 12 bytes
6893: REAL32[3] - Vertex 3 - 12 bytes
6894: UINT16 - Attribute byte count - 02 bytes
6895: end
6896: .ve
6898: The format is here <https://en.wikipedia.org/wiki/STL_(file_format)>
6900: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromFile()`, `DMPlexCreateGmsh()`, `DMPlexCreate()`
6901: */
6902: static PetscErrorCode DMPlexCreateSTLFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
6903: {
6904: PetscViewer viewer;
6905: Vec coordinates;
6906: PetscSection coordSection;
6907: PetscScalar *coords;
6908: PetscInt coordSize;
6909: char line[PETSC_MAX_PATH_LEN];
6910: PetscBT bt;
6911: float *trialCoords = NULL;
6912: PetscInt *cells = NULL;
6913: PetscBool isascii;
6914: PetscMPIInt rank;
6915: PetscInt Nc, Nv, nv = 0;
6917: PetscFunctionBegin;
6918: PetscCallMPI(MPI_Comm_rank(comm, &rank));
6919: PetscCall(PetscViewerCreate(comm, &viewer));
6920: PetscCall(PetscViewerSetType(viewer, PETSCVIEWERBINARY));
6921: PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ));
6922: PetscCall(PetscViewerFileSetName(viewer, filename));
6923: if (rank == 0) {
6924: int num;
6926: PetscCall(PetscViewerRead(viewer, line, 5, NULL, PETSC_CHAR));
6927: line[5] = 0;
6928: PetscCall(PetscStrncmp(line, "solid", 5, &isascii));
6929: PetscCheck(!isascii, comm, PETSC_ERR_SUP, "No support for ASCII yet");
6930: PetscCall(PetscViewerRead(viewer, line, 75, NULL, PETSC_CHAR));
6931: line[75] = 0;
6932: PetscCall(PetscViewerRead(viewer, &num, 1, NULL, PETSC_INT32));
6933: PetscCall(PetscByteSwap(&num, PETSC_INT32, 1));
6934: Nc = num;
6935: // Read facet coordinates
6936: PetscCall(PetscMalloc1(Nc * 9, &trialCoords));
6937: for (PetscInt c = 0; c < Nc; ++c) {
6938: double normal[3];
6939: short int dummy;
6941: PetscCall(PetscViewerRead(viewer, normal, 3, NULL, PETSC_FLOAT));
6942: PetscCall(PetscViewerRead(viewer, &trialCoords[c * 9 + 0], 9, NULL, PETSC_FLOAT));
6943: PetscCall(PetscByteSwap(&trialCoords[c * 9 + 0], PETSC_FLOAT, 9));
6944: PetscCall(PetscViewerRead(viewer, &dummy, 1, NULL, PETSC_SHORT));
6945: }
6946: PetscCall(PetscMalloc1(Nc * 3, &cells));
6947: // Find unique vertices
6948: PetscCall(PetscBTCreate(Nc * 3, &bt));
6949: PetscCall(PetscBTMemzero(Nc * 3, bt));
6950: PetscCall(PetscBTSet(bt, 0));
6951: PetscCall(PetscBTSet(bt, 1));
6952: PetscCall(PetscBTSet(bt, 2));
6953: Nv = 0;
6954: cells[0] = Nc + Nv++;
6955: cells[1] = Nc + Nv++;
6956: cells[2] = Nc + Nv++;
6957: for (PetscInt v = 3; v < Nc * 3; ++v) {
6958: PetscBool match = PETSC_FALSE;
6960: for (PetscInt w = 0, x = 0; w < v; ++w) {
6961: if (PetscBTLookup(bt, w)) {
6962: if (trialCoords[v * 3 + 0] == trialCoords[w * 3 + 0] && trialCoords[v * 3 + 1] == trialCoords[w * 3 + 1] && trialCoords[v * 3 + 2] == trialCoords[w * 3 + 2]) {
6963: match = PETSC_TRUE;
6964: cells[v] = Nc + x;
6965: break;
6966: }
6967: ++x;
6968: }
6969: }
6970: if (!match) {
6971: PetscCall(PetscBTSet(bt, v));
6972: cells[v] = Nc + Nv++;
6973: }
6974: }
6975: } else {
6976: Nc = Nv = 0;
6977: }
6978: for (PetscInt v = 3; v < Nc * 3; ++v) PetscCheck(cells[v] < Nc + Nv, comm, PETSC_ERR_PLIB, "Invalid cells[%" PetscInt_FMT "]: %" PetscInt_FMT, v, cells[v]);
6979: PetscCall(DMCreate(comm, dm));
6980: PetscCall(DMSetType(*dm, DMPLEX));
6981: PetscCall(DMPlexSetChart(*dm, 0, Nc + Nv));
6982: PetscCall(DMSetDimension(*dm, 2));
6983: PetscCall(DMSetCoordinateDim(*dm, 3));
6984: for (PetscInt c = 0; c < Nc; ++c) PetscCall(DMPlexSetConeSize(*dm, c, 3));
6985: PetscCall(DMSetUp(*dm));
6986: for (PetscInt c = 0; c < Nc; ++c) PetscCall(DMPlexSetCone(*dm, c, &cells[c * 3]));
6987: PetscCall(PetscFree(cells));
6988: PetscCall(DMPlexSymmetrize(*dm));
6989: PetscCall(DMPlexStratify(*dm));
6991: PetscCall(DMGetCoordinateSection(*dm, &coordSection));
6992: PetscCall(PetscSectionSetNumFields(coordSection, 1));
6993: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, 3));
6994: PetscCall(PetscSectionSetChart(coordSection, Nc, Nc + Nv));
6995: for (PetscInt v = Nc; v < Nc + Nv; ++v) {
6996: PetscCall(PetscSectionSetDof(coordSection, v, 3));
6997: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, 3));
6998: }
6999: PetscCall(PetscSectionSetUp(coordSection));
7000: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
7001: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
7002: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
7003: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
7004: PetscCall(VecSetBlockSize(coordinates, 3));
7005: PetscCall(VecSetType(coordinates, VECSTANDARD));
7006: PetscCall(VecGetArray(coordinates, &coords));
7007: for (PetscInt tv = 0; tv < Nc * 3; ++tv) {
7008: if (PetscBTLookup(bt, tv)) {
7009: for (PetscInt d = 0; d < 3; ++d) coords[nv * 3 + d] = trialCoords[tv * 3 + d];
7010: ++nv;
7011: }
7012: }
7013: PetscCheck(nv == Nv, comm, PETSC_ERR_PLIB, "Number of vertices copied %" PetscInt_FMT " != %" PetscInt_FMT " number of mesh vertices", nv, Nv);
7014: PetscCall(PetscFree(trialCoords));
7015: PetscCall(PetscBTDestroy(&bt));
7016: PetscCall(VecRestoreArray(coordinates, &coords));
7017: PetscCall(DMSetCoordinatesLocal(*dm, coordinates));
7018: PetscCall(VecDestroy(&coordinates));
7019: PetscCall(PetscViewerDestroy(&viewer));
7020: if (interpolate) {
7021: DM idm;
7023: PetscCall(DMPlexInterpolate(*dm, &idm));
7024: PetscCall(DMDestroy(dm));
7025: *dm = idm;
7026: }
7027: PetscFunctionReturn(PETSC_SUCCESS);
7028: }
7030: /*
7031: DMPlexCreateShapefile - Create a `DMPLEX` mesh from the ESRI Shapefile format.
7033: Collective
7035: + comm - The MPI communicator
7036: - viewer - `PetscViewer` for the .shp file
7038: Output Parameter:
7039: . dm - The `DM` object representing the mesh
7041: Level: beginner
7043: Note:
7044: The format is specified at [Wikipedia](https://en.wikipedia.org/wiki/Shapefile) and [ESRI](https://www.esri.com/content/dam/esrisites/sitecore-archive/Files/Pdfs/library/whitepapers/pdfs/shapefile.pdf).
7046: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromFile()`, `DMPlexCreateGmsh()`, `DMPlexCreate()`
7047: */
7048: static PetscErrorCode DMPlexCreateShapefile(MPI_Comm comm, PetscViewer viewer, DM *dm)
7049: {
7050: Vec coordinates;
7051: PetscSection coordSection;
7052: PetscScalar *coords;
7053: PetscInt cdim = 2, coordSize;
7054: int dim = 1, Nv, Nc, vOff;
7055: double *points = NULL;
7056: double mbr[4], zb[2], mb[2];
7057: PetscMPIInt rank;
7059: PetscFunctionBegin;
7060: PetscCallMPI(MPI_Comm_rank(comm, &rank));
7061: if (rank == 0) {
7062: PetscInt cnt;
7063: int magic, dummy[5], len, version, shtype, totlen = 0;
7065: // Read header
7066: PetscCall(PetscViewerBinaryRead(viewer, &magic, 1, &cnt, PETSC_INT32));
7067: PetscCheck(cnt == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: could not read bytes 0-3");
7068: PetscCheck(magic == 0x0000270a, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: invalid magic number %X", magic);
7069: PetscCall(PetscViewerBinaryRead(viewer, dummy, 5, &cnt, PETSC_INT32));
7070: PetscCheck(cnt == 5, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: could not read bytes 4-23");
7071: PetscCall(PetscViewerBinaryRead(viewer, &len, 1, &cnt, PETSC_INT32));
7072: PetscCheck(cnt == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: could not read bytes 24-27");
7073: PetscCall(PetscViewerBinaryRead(viewer, &version, 1, &cnt, PETSC_INT32));
7074: PetscCall(PetscByteSwap(&version, PETSC_INT32, 1));
7075: PetscCheck(cnt == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: could not read bytes 28-31");
7076: PetscCall(PetscInfo(viewer, "Shapefile: version %d file length %d\n", version, len));
7077: PetscCall(PetscViewerBinaryRead(viewer, &shtype, 1, &cnt, PETSC_INT32));
7078: PetscCall(PetscByteSwap(&shtype, PETSC_INT32, 1));
7079: PetscCheck(cnt == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: could not read bytes 32-35");
7080: PetscCall(PetscInfo(viewer, "Shapefile: shape type %d\n", shtype));
7081: PetscCall(PetscViewerBinaryRead(viewer, mbr, 4, &cnt, PETSC_DOUBLE));
7082: PetscCall(PetscByteSwap(mbr, PETSC_DOUBLE, 4));
7083: PetscCheck(cnt == 4, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: could not read bytes 36-67");
7084: PetscCall(PetscInfo(viewer, "Shapefile: minimum bounding rectangle (%g, %g) -- (%g, %g)\n", mbr[0], mbr[1], mbr[2], mbr[3]));
7085: PetscCall(PetscViewerBinaryRead(viewer, zb, 2, &cnt, PETSC_DOUBLE));
7086: PetscCall(PetscByteSwap(zb, PETSC_DOUBLE, 2));
7087: PetscCheck(cnt == 2, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: could not read bytes 68-83");
7088: PetscCall(PetscInfo(viewer, "Shapefile: Z bounds (%g) -- (%g)\n", zb[0], zb[1]));
7089: PetscCall(PetscViewerBinaryRead(viewer, mb, 2, &cnt, PETSC_DOUBLE));
7090: PetscCall(PetscByteSwap(mb, PETSC_DOUBLE, 2));
7091: PetscCheck(cnt == 2, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: could not read bytes 84-99");
7092: PetscCall(PetscInfo(viewer, "Shapefile: M bounds (%g) -- (%g)\n", mb[0], mb[1]));
7093: totlen += 100;
7094: {
7095: int rnum, rlen, rshtype, rnpart, rnp;
7096: double rmbr[4];
7097: int *partOffsets;
7099: // Read record header
7100: PetscCall(PetscViewerBinaryRead(viewer, &rnum, 1, &cnt, PETSC_INT32));
7101: PetscCheck(cnt == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: could not read record header bytes 0-3");
7102: PetscCall(PetscViewerBinaryRead(viewer, &rlen, 1, &cnt, PETSC_INT32));
7103: PetscCheck(cnt == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: could not read record header bytes 4-7");
7104: PetscCall(PetscInfo(viewer, "Shapefile: record %d length %d\n", rnum, rlen));
7105: totlen += 8;
7106: // Read record
7107: PetscCall(PetscViewerBinaryRead(viewer, &rshtype, 1, &cnt, PETSC_INT32));
7108: PetscCall(PetscByteSwap(&rshtype, PETSC_INT32, 1));
7109: PetscCheck(cnt == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: could not read record bytes 0-3");
7110: PetscCall(PetscInfo(viewer, "Shapefile: record shape type %d\n", rshtype));
7111: totlen += 4;
7112: switch (rshtype) {
7113: case 5: // Polygon
7114: PetscCall(PetscViewerBinaryRead(viewer, rmbr, 4, &cnt, PETSC_DOUBLE));
7115: PetscCall(PetscByteSwap(rmbr, PETSC_DOUBLE, 4));
7116: PetscCheck(cnt == 4, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: could not read record bytes 4-35");
7117: PetscCall(PetscInfo(viewer, "Shapefile: record minimum bounding rectangle (%g, %g) -- (%g, %g)\n", rmbr[0], rmbr[1], rmbr[2], rmbr[3]));
7118: PetscCall(PetscViewerBinaryRead(viewer, &rnpart, 1, &cnt, PETSC_INT32));
7119: PetscCall(PetscByteSwap(&rnpart, PETSC_INT32, 1));
7120: PetscCheck(cnt == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: could not read record bytes 36-39");
7121: PetscCall(PetscInfo(viewer, "Shapefile: record shape number of parts %d\n", rnpart));
7122: PetscCall(PetscViewerBinaryRead(viewer, &rnp, 1, &cnt, PETSC_INT32));
7123: PetscCall(PetscByteSwap(&rnp, PETSC_INT32, 1));
7124: PetscCheck(cnt == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: could not read record bytes 36-39");
7125: PetscCall(PetscInfo(viewer, "Shapefile: record shape number of points %d\n", rnp));
7126: totlen += 40;
7127: PetscCall(PetscMalloc1(rnpart, &partOffsets));
7128: PetscCall(PetscViewerBinaryRead(viewer, partOffsets, rnpart, &cnt, PETSC_INT32));
7129: PetscCall(PetscByteSwap(partOffsets, PETSC_INT32, rnpart));
7130: PetscCheck(cnt == rnpart, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: could not read record part offsets");
7131: totlen += 4 * rnpart;
7132: PetscCall(PetscMalloc1(rnp * 2, &points));
7133: PetscCall(PetscViewerBinaryRead(viewer, points, rnp * 2, &cnt, PETSC_DOUBLE));
7134: PetscCall(PetscByteSwap(points, PETSC_DOUBLE, rnp * 2));
7135: PetscCheck(cnt == rnp * 2, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Shapefile file: could not read record points");
7136: totlen += 8 * rnp * 2;
7137: PetscCheck(totlen == 2 * len, PETSC_COMM_SELF, PETSC_ERR_SUP, "Unable to parse Shapefile file: only support a single object: %d != %d", totlen, 2 * len);
7138: // Only get the last polygon now
7139: vOff = partOffsets[rnpart - 1];
7140: Nv = rnp - vOff;
7141: Nc = Nv - 1;
7142: PetscCall(PetscInfo(viewer, "Shapefile: record first polygon size %d totlen %d\n", Nv, totlen));
7143: PetscCall(PetscFree(partOffsets));
7144: break;
7145: default:
7146: PetscCheck(0, PETSC_COMM_SELF, PETSC_ERR_SUP, "Only support polygons right now");
7147: }
7148: }
7149: } else {
7150: Nc = Nv = vOff = 0;
7151: }
7152: PetscCallMPI(MPI_Bcast(&dim, 1, MPI_INT, 0, comm));
7153: PetscCall(DMCreate(comm, dm));
7154: PetscCall(DMSetType(*dm, DMPLEX));
7155: PetscCall(DMPlexSetChart(*dm, 0, Nc + Nv));
7156: PetscCall(DMSetDimension(*dm, dim));
7157: PetscCall(DMSetCoordinateDim(*dm, cdim));
7158: // Topology of a circle
7159: if (rank == 0) {
7160: for (PetscInt c = 0; c < Nc; ++c) PetscCall(DMPlexSetConeSize(*dm, c, 2));
7161: PetscCall(DMSetUp(*dm));
7162: for (PetscInt c = 0; c < Nc; ++c) {
7163: PetscInt cone[2] = {Nc + c, Nc + c + 1};
7165: PetscCall(DMPlexSetCone(*dm, c, cone));
7166: }
7167: }
7168: PetscCall(DMPlexSymmetrize(*dm));
7169: PetscCall(DMPlexStratify(*dm));
7170: // Set coordinates
7171: PetscCall(DMGetCoordinateSection(*dm, &coordSection));
7172: PetscCall(PetscSectionSetNumFields(coordSection, 1));
7173: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, cdim));
7174: PetscCall(PetscSectionSetChart(coordSection, Nc, Nc + Nv));
7175: for (PetscInt v = Nc; v < Nc + Nv; ++v) {
7176: PetscCall(PetscSectionSetDof(coordSection, v, cdim));
7177: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, cdim));
7178: }
7179: PetscCall(PetscSectionSetUp(coordSection));
7180: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
7181: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
7182: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
7183: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
7184: PetscCall(VecSetBlockSize(coordinates, cdim));
7185: PetscCall(VecSetType(coordinates, VECSTANDARD));
7186: PetscCall(VecGetArray(coordinates, &coords));
7187: for (PetscInt v = 0; v < Nv; ++v) {
7188: coords[v * cdim + 0] = points[(v + vOff) * cdim + 0] - mbr[0];
7189: coords[v * cdim + 1] = points[(v + vOff) * cdim + 1] - mbr[1];
7190: }
7191: PetscCall(PetscFree(points));
7192: PetscCall(VecRestoreArray(coordinates, &coords));
7193: PetscCall(DMSetCoordinatesLocal(*dm, coordinates));
7194: PetscCall(VecDestroy(&coordinates));
7195: PetscFunctionReturn(PETSC_SUCCESS);
7196: }
7198: /*
7199: DMPlexCreateShapefileFromFile - Create a `DMPLEX` mesh from the ESRI Shapefile format.
7201: Collective
7203: + comm - The MPI communicator
7204: . filename - Name of the .shp file
7206: Output Parameter:
7207: . dm - The `DM` object representing the mesh
7209: Level: beginner
7211: Note:
7212: The format is specified at [Wikipedia](https://en.wikipedia.org/wiki/Shapefile) and [ESRI](https://www.esri.com/content/dam/esrisites/sitecore-archive/Files/Pdfs/library/whitepapers/pdfs/shapefile.pdf).
7214: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromFile()`, `DMPlexCreateGmsh()`, `DMPlexCreate()`
7215: */
7216: static PetscErrorCode DMPlexCreateShapefileFromFile(MPI_Comm comm, const char filename[], DM *dm)
7217: {
7218: PetscViewer viewer;
7220: PetscFunctionBegin;
7221: PetscCall(PetscViewerCreate(comm, &viewer));
7222: PetscCall(PetscViewerSetType(viewer, PETSCVIEWERBINARY));
7223: PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ));
7224: PetscCall(PetscViewerFileSetName(viewer, filename));
7225: PetscCall(DMPlexCreateShapefile(comm, viewer, dm));
7226: PetscCall(PetscViewerDestroy(&viewer));
7227: PetscFunctionReturn(PETSC_SUCCESS);
7228: }
7230: /*@
7231: DMPlexCreateFromFile - This takes a filename and produces a `DM`
7233: Collective
7235: Input Parameters:
7236: + comm - The communicator
7237: . filename - A file name
7238: . plexname - The object name of the resulting `DM`, also used for intra-datafile lookup by some formats
7239: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
7241: Output Parameter:
7242: . dm - The `DM`
7244: Options Database Key:
7245: . -dm_plex_create_from_hdf5_xdmf - use the `PETSC_VIEWER_HDF5_XDMF` format for reading HDF5
7247: Use `-dm_plex_create_ prefix` to pass options to the internal `PetscViewer`, e.g. `-dm_plex_create_viewer_hdf5_collective`
7249: Level: beginner
7251: Notes:
7252: Using `PETSCVIEWERHDF5` type with `PETSC_VIEWER_HDF5_PETSC` format, one can save multiple `DMPLEX`
7253: meshes in a single HDF5 file. This in turn requires one to name the `DMPLEX` object with `PetscObjectSetName()`
7254: before saving it with `DMView()` and before loading it with `DMLoad()` for identification of the mesh object.
7255: The input parameter name is thus used to name the `DMPLEX` object when `DMPlexCreateFromFile()` internally
7256: calls `DMLoad()`. Currently, name is ignored for other viewer types and/or formats.
7258: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromDAG()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()`, `PetscObjectSetName()`, `DMView()`, `DMLoad()`
7259: @*/
7260: PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], const char plexname[], PetscBool interpolate, DM *dm)
7261: {
7262: const char extGmsh[] = ".msh";
7263: const char extGmsh2[] = ".msh2";
7264: const char extGmsh4[] = ".msh4";
7265: const char extCGNS[] = ".cgns";
7266: const char extExodus[] = ".exo";
7267: const char extExodus_e[] = ".e";
7268: const char extGenesis[] = ".gen";
7269: const char extFluent[] = ".cas";
7270: const char extHDF5[] = ".h5";
7271: const char extXDMFHDF5[] = ".xdmf.h5";
7272: const char extPLY[] = ".ply";
7273: const char extEGADSlite[] = ".egadslite";
7274: const char extEGADS[] = ".egads";
7275: const char extIGES[] = ".igs";
7276: const char extIGES2[] = ".iges";
7277: const char extSTEP[] = ".stp";
7278: const char extSTEP2[] = ".step";
7279: const char extBREP[] = ".brep";
7280: const char extCV[] = ".dat";
7281: const char extSTL[] = ".stl";
7282: const char extSHP[] = ".shp";
7283: size_t len;
7284: PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isPLY, isEGADSlite, isEGADS, isIGES, isIGES2, isSTEP, isSTEP2, isBREP, isCV, isSTL, isSHP, isXDMFHDF5;
7285: PetscMPIInt rank;
7287: PetscFunctionBegin;
7288: PetscAssertPointer(filename, 2);
7289: if (plexname) PetscAssertPointer(plexname, 3);
7290: PetscAssertPointer(dm, 5);
7291: PetscCall(DMInitializePackage());
7292: PetscCall(PetscLogEventBegin(DMPLEX_CreateFromFile, 0, 0, 0, 0));
7293: PetscCallMPI(MPI_Comm_rank(comm, &rank));
7294: PetscCall(PetscStrlen(filename, &len));
7295: PetscCheck(len, comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path");
7297: #define CheckExtension(extension__, is_extension__) \
7298: do { \
7299: PetscAssert(sizeof(extension__), comm, PETSC_ERR_PLIB, "Zero-size extension: %s", extension__); \
7300: /* don't count the null-terminator at the end */ \
7301: const size_t ext_len = sizeof(extension__) - 1; \
7302: if (len < ext_len) { \
7303: is_extension__ = PETSC_FALSE; \
7304: } else { \
7305: PetscCall(PetscStrncmp(filename + len - ext_len, extension__, ext_len, &is_extension__)); \
7306: } \
7307: } while (0)
7309: CheckExtension(extGmsh, isGmsh);
7310: CheckExtension(extGmsh2, isGmsh2);
7311: CheckExtension(extGmsh4, isGmsh4);
7312: CheckExtension(extCGNS, isCGNS);
7313: CheckExtension(extExodus, isExodus);
7314: if (!isExodus) CheckExtension(extExodus_e, isExodus);
7315: CheckExtension(extGenesis, isGenesis);
7316: CheckExtension(extFluent, isFluent);
7317: CheckExtension(extHDF5, isHDF5);
7318: CheckExtension(extPLY, isPLY);
7319: CheckExtension(extEGADSlite, isEGADSlite);
7320: CheckExtension(extEGADS, isEGADS);
7321: CheckExtension(extIGES, isIGES);
7322: CheckExtension(extIGES2, isIGES2);
7323: CheckExtension(extSTEP, isSTEP);
7324: CheckExtension(extSTEP2, isSTEP2);
7325: CheckExtension(extBREP, isBREP);
7326: CheckExtension(extCV, isCV);
7327: CheckExtension(extSTL, isSTL);
7328: CheckExtension(extSHP, isSHP);
7329: CheckExtension(extXDMFHDF5, isXDMFHDF5);
7331: #undef CheckExtension
7333: if (isGmsh || isGmsh2 || isGmsh4) {
7334: PetscCall(DMPlexCreateGmshFromFile(comm, filename, interpolate, dm));
7335: } else if (isCGNS) {
7336: PetscCall(DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm));
7337: } else if (isExodus || isGenesis) {
7338: PetscCall(DMPlexCreateExodusFromFile(comm, filename, interpolate, dm));
7339: } else if (isFluent) {
7340: PetscCall(DMPlexCreateFluentFromFile(comm, filename, interpolate, dm));
7341: } else if (isHDF5) {
7342: PetscViewer viewer;
7344: /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */
7345: PetscCall(PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &isXDMFHDF5, NULL));
7346: PetscCall(PetscViewerCreate(comm, &viewer));
7347: PetscCall(PetscViewerSetType(viewer, PETSCVIEWERHDF5));
7348: PetscCall(PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_"));
7349: PetscCall(PetscViewerSetFromOptions(viewer));
7350: PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ));
7351: PetscCall(PetscViewerFileSetName(viewer, filename));
7353: PetscCall(DMCreate(comm, dm));
7354: PetscCall(PetscObjectSetName((PetscObject)*dm, plexname));
7355: PetscCall(DMSetType(*dm, DMPLEX));
7356: if (isXDMFHDF5) PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF));
7357: PetscCall(DMLoad(*dm, viewer));
7358: if (isXDMFHDF5) PetscCall(PetscViewerPopFormat(viewer));
7359: PetscCall(PetscViewerDestroy(&viewer));
7361: if (interpolate) {
7362: DM idm;
7364: PetscCall(DMPlexInterpolate(*dm, &idm));
7365: PetscCall(DMDestroy(dm));
7366: *dm = idm;
7367: }
7368: } else if (isPLY) {
7369: PetscCall(DMPlexCreatePLYFromFile(comm, filename, interpolate, dm));
7370: } else if (isEGADSlite || isEGADS || isIGES || isIGES2 || isSTEP || isSTEP2 || isBREP) {
7371: PetscCall(DMPlexCreateGeomFromFile(comm, filename, dm, isEGADSlite));
7373: if (!interpolate) {
7374: DM udm;
7376: PetscCall(DMPlexUninterpolate(*dm, &udm));
7377: PetscCall(DMDestroy(dm));
7378: *dm = udm;
7379: }
7380: } else if (isCV) {
7381: PetscCall(DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm));
7382: } else if (isSTL) {
7383: PetscCall(DMPlexCreateSTLFromFile(comm, filename, interpolate, dm));
7384: } else if (isSHP) {
7385: PetscCall(DMPlexCreateShapefileFromFile(comm, filename, dm));
7386: } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename);
7387: PetscCall(PetscStrlen(plexname, &len));
7388: if (len) PetscCall(PetscObjectSetName((PetscObject)*dm, plexname));
7389: PetscCall(PetscLogEventEnd(DMPLEX_CreateFromFile, 0, 0, 0, 0));
7390: PetscFunctionReturn(PETSC_SUCCESS);
7391: }
7393: /*@
7394: DMPlexCreateEphemeral - This takes a `DMPlexTransform` and a base `DMPlex` and produces an ephemeral `DM`, meaning one that is created on the fly in response to queries.
7396: Input Parameters:
7397: + tr - The `DMPlexTransform`
7398: - prefix - An options prefix, or NULL
7400: Output Parameter:
7401: . dm - The `DM`
7403: Level: beginner
7405: Notes:
7406: An emphemeral mesh is one that is not stored concretely, as in the default `DMPLEX` implementation, but rather is produced on the fly in response to queries, using information from the transform and the base mesh.
7408: .seealso: `DMPlexCreateFromFile`, `DMPlexCreateFromDAG()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()`
7409: @*/
7410: PetscErrorCode DMPlexCreateEphemeral(DMPlexTransform tr, const char prefix[], DM *dm)
7411: {
7412: DM bdm, bcdm, cdm;
7413: Vec coordinates, coordinatesNew;
7414: PetscSection cs;
7415: PetscInt cdim, Nl;
7417: PetscFunctionBegin;
7418: PetscCall(DMCreate(PetscObjectComm((PetscObject)tr), dm));
7419: PetscCall(DMSetType(*dm, DMPLEX));
7420: ((DM_Plex *)(*dm)->data)->interpolated = DMPLEX_INTERPOLATED_FULL;
7421: // Handle coordinates
7422: PetscCall(DMPlexTransformGetDM(tr, &bdm));
7423: PetscCall(DMPlexTransformSetDimensions(tr, bdm, *dm));
7424: PetscCall(DMGetCoordinateDim(*dm, &cdim));
7425: PetscCall(DMGetCoordinateDM(bdm, &bcdm));
7426: PetscCall(DMGetCoordinateDM(*dm, &cdm));
7427: PetscCall(DMCopyDisc(bcdm, cdm));
7428: PetscCall(DMGetLocalSection(cdm, &cs));
7429: PetscCall(PetscSectionSetNumFields(cs, 1));
7430: PetscCall(PetscSectionSetFieldComponents(cs, 0, cdim));
7431: PetscCall(DMGetCoordinatesLocal(bdm, &coordinates));
7432: PetscCall(VecDuplicate(coordinates, &coordinatesNew));
7433: PetscCall(VecCopy(coordinates, coordinatesNew));
7434: PetscCall(DMSetCoordinatesLocal(*dm, coordinatesNew));
7435: PetscCall(VecDestroy(&coordinatesNew));
7437: PetscCall(PetscObjectReference((PetscObject)tr));
7438: PetscCall(DMPlexTransformDestroy(&((DM_Plex *)(*dm)->data)->tr));
7439: ((DM_Plex *)(*dm)->data)->tr = tr;
7440: PetscCall(DMPlexDistributeSetDefault(*dm, PETSC_FALSE));
7441: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)*dm, prefix));
7442: PetscCall(DMSetFromOptions(*dm));
7444: PetscCall(DMGetNumLabels(bdm, &Nl));
7445: for (PetscInt l = 0; l < Nl; ++l) {
7446: DMLabel label, labelNew;
7447: const char *lname;
7448: PetscBool isDepth, isCellType;
7450: PetscCall(DMGetLabelName(bdm, l, &lname));
7451: PetscCall(PetscStrcmp(lname, "depth", &isDepth));
7452: if (isDepth) continue;
7453: PetscCall(PetscStrcmp(lname, "celltype", &isCellType));
7454: if (isCellType) continue;
7455: PetscCall(DMCreateLabel(*dm, lname));
7456: PetscCall(DMGetLabel(bdm, lname, &label));
7457: PetscCall(DMGetLabel(*dm, lname, &labelNew));
7458: PetscCall(DMLabelSetType(labelNew, DMLABELEPHEMERAL));
7459: PetscCall(DMLabelEphemeralSetLabel(labelNew, label));
7460: PetscCall(DMLabelEphemeralSetTransform(labelNew, tr));
7461: PetscCall(DMLabelSetUp(labelNew));
7462: }
7463: PetscFunctionReturn(PETSC_SUCCESS);
7464: }