Actual source code: plexcreate.c
1: #define PETSCDM_DLL
2: #include <petsc/private/dmpleximpl.h>
3: #include <petsc/private/hashseti.h>
4: #include <petscsf.h>
5: #include <petscdmplextransform.h>
6: #include <petscdmlabelephemeral.h>
7: #include <petsc/private/kernels/blockmatmult.h>
8: #include <petsc/private/kernels/blockinvert.h>
10: #ifdef PETSC_HAVE_UNISTD_H
11: #include <unistd.h>
12: #endif
13: #include <errno.h>
15: PetscLogEvent DMPLEX_CreateFromFile, DMPLEX_CreateFromOptions, DMPLEX_BuildFromCellList, DMPLEX_BuildCoordinatesFromCellList;
17: /* External function declarations here */
18: static PetscErrorCode DMInitialize_Plex(DM dm);
20: /* This copies internal things in the Plex structure that we generally want when making a new, related Plex */
21: PetscErrorCode DMPlexCopy_Internal(DM dmin, PetscBool copyPeriodicity, PetscBool copyOverlap, DM dmout)
22: {
23: const PetscReal *maxCell, *Lstart, *L;
24: VecType vecType;
25: MatType matType;
26: PetscBool dist, useCeed;
27: DMReorderDefaultFlag reorder;
29: PetscFunctionBegin;
30: PetscCall(DMGetVecType(dmin, &vecType));
31: PetscCall(DMSetVecType(dmout, vecType));
32: PetscCall(DMGetMatType(dmin, &matType));
33: PetscCall(DMSetMatType(dmout, matType));
34: if (copyPeriodicity) {
35: PetscCall(DMGetPeriodicity(dmin, &maxCell, &Lstart, &L));
36: PetscCall(DMSetPeriodicity(dmout, maxCell, Lstart, L));
37: PetscCall(DMLocalizeCoordinates(dmout));
38: }
39: PetscCall(DMPlexDistributeGetDefault(dmin, &dist));
40: PetscCall(DMPlexDistributeSetDefault(dmout, dist));
41: PetscCall(DMPlexReorderGetDefault(dmin, &reorder));
42: PetscCall(DMPlexReorderSetDefault(dmout, reorder));
43: PetscCall(DMPlexGetUseCeed(dmin, &useCeed));
44: PetscCall(DMPlexSetUseCeed(dmout, useCeed));
45: ((DM_Plex *)dmout->data)->useHashLocation = ((DM_Plex *)dmin->data)->useHashLocation;
46: ((DM_Plex *)dmout->data)->printSetValues = ((DM_Plex *)dmin->data)->printSetValues;
47: ((DM_Plex *)dmout->data)->printFEM = ((DM_Plex *)dmin->data)->printFEM;
48: ((DM_Plex *)dmout->data)->printFVM = ((DM_Plex *)dmin->data)->printFVM;
49: ((DM_Plex *)dmout->data)->printL2 = ((DM_Plex *)dmin->data)->printL2;
50: ((DM_Plex *)dmout->data)->printLocate = ((DM_Plex *)dmin->data)->printLocate;
51: ((DM_Plex *)dmout->data)->printTol = ((DM_Plex *)dmin->data)->printTol;
52: if (copyOverlap) PetscCall(DMPlexSetOverlap_Plex(dmout, dmin, 0));
53: PetscFunctionReturn(PETSC_SUCCESS);
54: }
56: /* Replace dm with the contents of ndm, and then destroy ndm
57: - Share the DM_Plex structure
58: - Share the coordinates
59: - Share the SF
60: */
61: PetscErrorCode DMPlexReplace_Internal(DM dm, DM *ndm)
62: {
63: PetscSF sf;
64: DM dmNew = *ndm, coordDM, coarseDM;
65: Vec coords;
66: const PetscReal *maxCell, *Lstart, *L;
67: PetscInt dim, cdim;
69: PetscFunctionBegin;
70: if (dm == dmNew) {
71: PetscCall(DMDestroy(ndm));
72: PetscFunctionReturn(PETSC_SUCCESS);
73: }
74: dm->setupcalled = dmNew->setupcalled;
75: if (!dm->hdr.name) {
76: const char *name;
78: PetscCall(PetscObjectGetName((PetscObject)*ndm, &name));
79: PetscCall(PetscObjectSetName((PetscObject)dm, name));
80: }
81: PetscCall(DMGetDimension(dmNew, &dim));
82: PetscCall(DMSetDimension(dm, dim));
83: PetscCall(DMGetCoordinateDim(dmNew, &cdim));
84: PetscCall(DMSetCoordinateDim(dm, cdim));
85: PetscCall(DMGetPointSF(dmNew, &sf));
86: PetscCall(DMSetPointSF(dm, sf));
87: PetscCall(DMGetCoordinateDM(dmNew, &coordDM));
88: PetscCall(DMGetCoordinatesLocal(dmNew, &coords));
89: PetscCall(DMSetCoordinateDM(dm, coordDM));
90: PetscCall(DMSetCoordinatesLocal(dm, coords));
91: PetscCall(DMGetCellCoordinateDM(dmNew, &coordDM));
92: PetscCall(DMGetCellCoordinatesLocal(dmNew, &coords));
93: PetscCall(DMSetCellCoordinateDM(dm, coordDM));
94: PetscCall(DMSetCellCoordinatesLocal(dm, coords));
95: /* Do not want to create the coordinate field if it does not already exist, so do not call DMGetCoordinateField() */
96: PetscCall(DMFieldDestroy(&dm->coordinates[0].field));
97: dm->coordinates[0].field = dmNew->coordinates[0].field;
98: ((DM_Plex *)dmNew->data)->coordFunc = ((DM_Plex *)dm->data)->coordFunc;
99: PetscCall(DMGetPeriodicity(dmNew, &maxCell, &Lstart, &L));
100: PetscCall(DMSetPeriodicity(dm, maxCell, Lstart, L));
101: PetscCall(DMPlexGetGlobalToNaturalSF(dmNew, &sf));
102: PetscCall(DMPlexSetGlobalToNaturalSF(dm, sf));
103: PetscCall(DMDestroy_Plex(dm));
104: PetscCall(DMInitialize_Plex(dm));
105: dm->data = dmNew->data;
106: ((DM_Plex *)dmNew->data)->refct++;
107: {
108: PetscInt num_face_sfs;
109: const PetscSF *sfs;
110: PetscCall(DMPlexGetIsoperiodicFaceSF(dm, &num_face_sfs, &sfs));
111: PetscCall(DMPlexSetIsoperiodicFaceSF(dm, num_face_sfs, (PetscSF *)sfs)); // for the compose function effect on dm
112: }
113: PetscCall(DMDestroyLabelLinkList_Internal(dm));
114: PetscCall(DMCopyLabels(dmNew, dm, PETSC_OWN_POINTER, PETSC_TRUE, DM_COPY_LABELS_FAIL));
115: PetscCall(DMGetCoarseDM(dmNew, &coarseDM));
116: PetscCall(DMSetCoarseDM(dm, coarseDM));
117: PetscCall(DMDestroy(ndm));
118: PetscFunctionReturn(PETSC_SUCCESS);
119: }
121: /* Swap dm with the contents of dmNew
122: - Swap the DM_Plex structure
123: - Swap the coordinates
124: - Swap the point PetscSF
125: */
126: static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB)
127: {
128: DM coordDMA, coordDMB;
129: Vec coordsA, coordsB;
130: PetscSF sfA, sfB;
131: DMField fieldTmp;
132: void *tmp;
133: DMLabelLink listTmp;
134: DMLabel depthTmp;
135: PetscInt tmpI;
137: PetscFunctionBegin;
138: if (dmA == dmB) PetscFunctionReturn(PETSC_SUCCESS);
139: PetscCall(DMGetPointSF(dmA, &sfA));
140: PetscCall(DMGetPointSF(dmB, &sfB));
141: PetscCall(PetscObjectReference((PetscObject)sfA));
142: PetscCall(DMSetPointSF(dmA, sfB));
143: PetscCall(DMSetPointSF(dmB, sfA));
144: PetscCall(PetscObjectDereference((PetscObject)sfA));
146: PetscCall(DMGetCoordinateDM(dmA, &coordDMA));
147: PetscCall(DMGetCoordinateDM(dmB, &coordDMB));
148: PetscCall(PetscObjectReference((PetscObject)coordDMA));
149: PetscCall(DMSetCoordinateDM(dmA, coordDMB));
150: PetscCall(DMSetCoordinateDM(dmB, coordDMA));
151: PetscCall(PetscObjectDereference((PetscObject)coordDMA));
153: PetscCall(DMGetCoordinatesLocal(dmA, &coordsA));
154: PetscCall(DMGetCoordinatesLocal(dmB, &coordsB));
155: PetscCall(PetscObjectReference((PetscObject)coordsA));
156: PetscCall(DMSetCoordinatesLocal(dmA, coordsB));
157: PetscCall(DMSetCoordinatesLocal(dmB, coordsA));
158: PetscCall(PetscObjectDereference((PetscObject)coordsA));
160: PetscCall(DMGetCellCoordinateDM(dmA, &coordDMA));
161: PetscCall(DMGetCellCoordinateDM(dmB, &coordDMB));
162: PetscCall(PetscObjectReference((PetscObject)coordDMA));
163: PetscCall(DMSetCellCoordinateDM(dmA, coordDMB));
164: PetscCall(DMSetCellCoordinateDM(dmB, coordDMA));
165: PetscCall(PetscObjectDereference((PetscObject)coordDMA));
167: PetscCall(DMGetCellCoordinatesLocal(dmA, &coordsA));
168: PetscCall(DMGetCellCoordinatesLocal(dmB, &coordsB));
169: PetscCall(PetscObjectReference((PetscObject)coordsA));
170: PetscCall(DMSetCellCoordinatesLocal(dmA, coordsB));
171: PetscCall(DMSetCellCoordinatesLocal(dmB, coordsA));
172: PetscCall(PetscObjectDereference((PetscObject)coordsA));
174: fieldTmp = dmA->coordinates[0].field;
175: dmA->coordinates[0].field = dmB->coordinates[0].field;
176: dmB->coordinates[0].field = fieldTmp;
177: fieldTmp = dmA->coordinates[1].field;
178: dmA->coordinates[1].field = dmB->coordinates[1].field;
179: dmB->coordinates[1].field = fieldTmp;
180: tmp = dmA->data;
181: dmA->data = dmB->data;
182: dmB->data = tmp;
183: listTmp = dmA->labels;
184: dmA->labels = dmB->labels;
185: dmB->labels = listTmp;
186: depthTmp = dmA->depthLabel;
187: dmA->depthLabel = dmB->depthLabel;
188: dmB->depthLabel = depthTmp;
189: depthTmp = dmA->celltypeLabel;
190: dmA->celltypeLabel = dmB->celltypeLabel;
191: dmB->celltypeLabel = depthTmp;
192: tmpI = dmA->levelup;
193: dmA->levelup = dmB->levelup;
194: dmB->levelup = tmpI;
195: PetscFunctionReturn(PETSC_SUCCESS);
196: }
198: PetscErrorCode DMPlexInterpolateInPlace_Internal(DM dm)
199: {
200: DM idm;
202: PetscFunctionBegin;
203: PetscCall(DMPlexInterpolate(dm, &idm));
204: PetscCall(DMPlexCopyCoordinates(dm, idm));
205: PetscCall(DMPlexReplace_Internal(dm, &idm));
206: PetscFunctionReturn(PETSC_SUCCESS);
207: }
209: /*@C
210: DMPlexCreateCoordinateSpace - Creates a finite element space for the coordinates
212: Collective
214: Input Parameters:
215: + dm - The `DMPLEX`
216: . degree - The degree of the finite element or `PETSC_DECIDE`
217: . project - Flag to project current coordinates into the space
218: - coordFunc - An optional function to map new points from refinement to the surface
220: Level: advanced
222: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `PetscPointFunc`, `PetscFECreateLagrange()`, `DMGetCoordinateDM()`
223: @*/
224: PetscErrorCode DMPlexCreateCoordinateSpace(DM dm, PetscInt degree, PetscBool project, PetscPointFunc coordFunc)
225: {
226: DM_Plex *mesh = (DM_Plex *)dm->data;
227: PetscFE fe = NULL;
228: DM cdm;
229: PetscInt dim, dE, qorder, height;
231: PetscFunctionBegin;
232: PetscCall(DMGetDimension(dm, &dim));
233: PetscCall(DMGetCoordinateDim(dm, &dE));
234: qorder = degree;
235: PetscCall(DMGetCoordinateDM(dm, &cdm));
236: PetscObjectOptionsBegin((PetscObject)cdm);
237: PetscCall(PetscOptionsBoundedInt("-default_quadrature_order", "Quadrature order is one less than quadrature points per edge", "DMPlexCreateCoordinateSpace", qorder, &qorder, NULL, 0));
238: PetscOptionsEnd();
239: PetscCall(DMPlexGetVTKCellHeight(dm, &height));
240: if (degree >= 0) {
241: DMPolytopeType ct = DM_POLYTOPE_UNKNOWN;
242: PetscInt cStart, cEnd, gct;
244: PetscCall(DMPlexGetHeightStratum(dm, height, &cStart, &cEnd));
245: if (cEnd > cStart) PetscCall(DMPlexGetCellType(dm, cStart, &ct));
246: gct = (PetscInt)ct;
247: PetscCall(MPIU_Allreduce(MPI_IN_PLACE, &gct, 1, MPIU_INT, MPI_MIN, PetscObjectComm((PetscObject)dm)));
248: ct = (DMPolytopeType)gct;
249: // Work around current bug in PetscDualSpaceSetUp_Lagrange()
250: // Can be seen in plex_tutorials-ex10_1
251: if (ct != DM_POLYTOPE_SEG_PRISM_TENSOR && ct != DM_POLYTOPE_TRI_PRISM_TENSOR && ct != DM_POLYTOPE_QUAD_PRISM_TENSOR) PetscCall(PetscFECreateLagrangeByCell(PETSC_COMM_SELF, dim, dE, ct, degree, qorder, &fe));
252: }
253: PetscCall(DMSetCoordinateDisc(dm, fe, project));
254: PetscCall(PetscFEDestroy(&fe));
255: mesh->coordFunc = coordFunc;
256: PetscFunctionReturn(PETSC_SUCCESS);
257: }
259: /*@
260: DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement.
262: Collective
264: Input Parameters:
265: + comm - The communicator for the `DM` object
266: . dim - The spatial dimension
267: . simplex - Flag for simplicial cells, otherwise they are tensor product cells
268: . interpolate - Flag to create intermediate mesh pieces (edges, faces)
269: - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell
271: Output Parameter:
272: . newdm - The `DM` object
274: Level: beginner
276: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMSetType()`, `DMCreate()`
277: @*/
278: PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscReal refinementLimit, DM *newdm)
279: {
280: DM dm;
281: PetscMPIInt rank;
283: PetscFunctionBegin;
284: PetscCall(DMCreate(comm, &dm));
285: PetscCall(DMSetType(dm, DMPLEX));
286: PetscCall(DMSetDimension(dm, dim));
287: PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0));
288: PetscCallMPI(MPI_Comm_rank(comm, &rank));
289: switch (dim) {
290: case 2:
291: if (simplex) PetscCall(PetscObjectSetName((PetscObject)dm, "triangular"));
292: else PetscCall(PetscObjectSetName((PetscObject)dm, "quadrilateral"));
293: break;
294: case 3:
295: if (simplex) PetscCall(PetscObjectSetName((PetscObject)dm, "tetrahedral"));
296: else PetscCall(PetscObjectSetName((PetscObject)dm, "hexahedral"));
297: break;
298: default:
299: SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %" PetscInt_FMT, dim);
300: }
301: if (rank) {
302: PetscInt numPoints[2] = {0, 0};
303: PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL));
304: } else {
305: switch (dim) {
306: case 2:
307: if (simplex) {
308: PetscInt numPoints[2] = {4, 2};
309: PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0};
310: PetscInt cones[6] = {2, 3, 4, 5, 4, 3};
311: PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0};
312: PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5};
314: PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
315: } else {
316: PetscInt numPoints[2] = {6, 2};
317: PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0};
318: PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4};
319: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
320: 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};
322: PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
323: }
324: break;
325: case 3:
326: if (simplex) {
327: PetscInt numPoints[2] = {5, 2};
328: PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0};
329: PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6};
330: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
331: 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};
333: PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
334: } else {
335: PetscInt numPoints[2] = {12, 2};
336: PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
337: PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8};
338: PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
339: 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};
341: PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
342: }
343: break;
344: default:
345: SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %" PetscInt_FMT, dim);
346: }
347: }
348: PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0));
349: *newdm = dm;
350: if (refinementLimit > 0.0) {
351: DM rdm;
352: const char *name;
354: PetscCall(DMPlexSetRefinementUniform(*newdm, PETSC_FALSE));
355: PetscCall(DMPlexSetRefinementLimit(*newdm, refinementLimit));
356: PetscCall(DMRefine(*newdm, comm, &rdm));
357: PetscCall(PetscObjectGetName((PetscObject)*newdm, &name));
358: PetscCall(PetscObjectSetName((PetscObject)rdm, name));
359: PetscCall(DMDestroy(newdm));
360: *newdm = rdm;
361: }
362: if (interpolate) {
363: DM idm;
365: PetscCall(DMPlexInterpolate(*newdm, &idm));
366: PetscCall(DMDestroy(newdm));
367: *newdm = idm;
368: }
369: PetscFunctionReturn(PETSC_SUCCESS);
370: }
372: static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
373: {
374: const PetscInt numVertices = 2;
375: PetscInt markerRight = 1;
376: PetscInt markerLeft = 1;
377: PetscBool markerSeparate = PETSC_FALSE;
378: Vec coordinates;
379: PetscSection coordSection;
380: PetscScalar *coords;
381: PetscInt coordSize;
382: PetscMPIInt rank;
383: PetscInt cdim = 1, v;
385: PetscFunctionBegin;
386: PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL));
387: if (markerSeparate) {
388: markerRight = 2;
389: markerLeft = 1;
390: }
391: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
392: if (rank == 0) {
393: PetscCall(DMPlexSetChart(dm, 0, numVertices));
394: PetscCall(DMSetUp(dm)); /* Allocate space for cones */
395: PetscCall(DMSetLabelValue(dm, "marker", 0, markerLeft));
396: PetscCall(DMSetLabelValue(dm, "marker", 1, markerRight));
397: }
398: PetscCall(DMPlexSymmetrize(dm));
399: PetscCall(DMPlexStratify(dm));
400: /* Build coordinates */
401: PetscCall(DMSetCoordinateDim(dm, cdim));
402: PetscCall(DMGetCoordinateSection(dm, &coordSection));
403: PetscCall(PetscSectionSetNumFields(coordSection, 1));
404: PetscCall(PetscSectionSetChart(coordSection, 0, numVertices));
405: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, cdim));
406: for (v = 0; v < numVertices; ++v) {
407: PetscCall(PetscSectionSetDof(coordSection, v, cdim));
408: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, cdim));
409: }
410: PetscCall(PetscSectionSetUp(coordSection));
411: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
412: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
413: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
414: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
415: PetscCall(VecSetBlockSize(coordinates, cdim));
416: PetscCall(VecSetType(coordinates, VECSTANDARD));
417: PetscCall(VecGetArray(coordinates, &coords));
418: coords[0] = lower[0];
419: coords[1] = upper[0];
420: PetscCall(VecRestoreArray(coordinates, &coords));
421: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
422: PetscCall(VecDestroy(&coordinates));
423: PetscFunctionReturn(PETSC_SUCCESS);
424: }
426: static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
427: {
428: const PetscInt numVertices = (edges[0] + 1) * (edges[1] + 1);
429: const PetscInt numEdges = edges[0] * (edges[1] + 1) + (edges[0] + 1) * edges[1];
430: PetscInt markerTop = 1;
431: PetscInt markerBottom = 1;
432: PetscInt markerRight = 1;
433: PetscInt markerLeft = 1;
434: PetscBool markerSeparate = PETSC_FALSE;
435: Vec coordinates;
436: PetscSection coordSection;
437: PetscScalar *coords;
438: PetscInt coordSize;
439: PetscMPIInt rank;
440: PetscInt v, vx, vy;
442: PetscFunctionBegin;
443: PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL));
444: if (markerSeparate) {
445: markerTop = 3;
446: markerBottom = 1;
447: markerRight = 2;
448: markerLeft = 4;
449: }
450: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
451: if (rank == 0) {
452: PetscInt e, ex, ey;
454: PetscCall(DMPlexSetChart(dm, 0, numEdges + numVertices));
455: for (e = 0; e < numEdges; ++e) PetscCall(DMPlexSetConeSize(dm, e, 2));
456: PetscCall(DMSetUp(dm)); /* Allocate space for cones */
457: for (vx = 0; vx <= edges[0]; vx++) {
458: for (ey = 0; ey < edges[1]; ey++) {
459: PetscInt edge = vx * edges[1] + ey + edges[0] * (edges[1] + 1);
460: PetscInt vertex = ey * (edges[0] + 1) + vx + numEdges;
461: PetscInt cone[2];
463: cone[0] = vertex;
464: cone[1] = vertex + edges[0] + 1;
465: PetscCall(DMPlexSetCone(dm, edge, cone));
466: if (vx == edges[0]) {
467: PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight));
468: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight));
469: if (ey == edges[1] - 1) {
470: PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight));
471: PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerRight));
472: }
473: } else if (vx == 0) {
474: PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft));
475: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft));
476: if (ey == edges[1] - 1) {
477: PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft));
478: PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft));
479: }
480: }
481: }
482: }
483: for (vy = 0; vy <= edges[1]; vy++) {
484: for (ex = 0; ex < edges[0]; ex++) {
485: PetscInt edge = vy * edges[0] + ex;
486: PetscInt vertex = vy * (edges[0] + 1) + ex + numEdges;
487: PetscInt cone[2];
489: cone[0] = vertex;
490: cone[1] = vertex + 1;
491: PetscCall(DMPlexSetCone(dm, edge, cone));
492: if (vy == edges[1]) {
493: PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop));
494: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop));
495: if (ex == edges[0] - 1) {
496: PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop));
497: PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerTop));
498: }
499: } else if (vy == 0) {
500: PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom));
501: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom));
502: if (ex == edges[0] - 1) {
503: PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom));
504: PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom));
505: }
506: }
507: }
508: }
509: }
510: PetscCall(DMPlexSymmetrize(dm));
511: PetscCall(DMPlexStratify(dm));
512: /* Build coordinates */
513: PetscCall(DMSetCoordinateDim(dm, 2));
514: PetscCall(DMGetCoordinateSection(dm, &coordSection));
515: PetscCall(PetscSectionSetNumFields(coordSection, 1));
516: PetscCall(PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices));
517: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, 2));
518: for (v = numEdges; v < numEdges + numVertices; ++v) {
519: PetscCall(PetscSectionSetDof(coordSection, v, 2));
520: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, 2));
521: }
522: PetscCall(PetscSectionSetUp(coordSection));
523: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
524: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
525: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
526: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
527: PetscCall(VecSetBlockSize(coordinates, 2));
528: PetscCall(VecSetType(coordinates, VECSTANDARD));
529: PetscCall(VecGetArray(coordinates, &coords));
530: for (vy = 0; vy <= edges[1]; ++vy) {
531: for (vx = 0; vx <= edges[0]; ++vx) {
532: coords[(vy * (edges[0] + 1) + vx) * 2 + 0] = lower[0] + ((upper[0] - lower[0]) / edges[0]) * vx;
533: coords[(vy * (edges[0] + 1) + vx) * 2 + 1] = lower[1] + ((upper[1] - lower[1]) / edges[1]) * vy;
534: }
535: }
536: PetscCall(VecRestoreArray(coordinates, &coords));
537: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
538: PetscCall(VecDestroy(&coordinates));
539: PetscFunctionReturn(PETSC_SUCCESS);
540: }
542: static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[])
543: {
544: PetscInt vertices[3], numVertices;
545: PetscInt numFaces = 2 * faces[0] * faces[1] + 2 * faces[1] * faces[2] + 2 * faces[0] * faces[2];
546: PetscInt markerTop = 1;
547: PetscInt markerBottom = 1;
548: PetscInt markerFront = 1;
549: PetscInt markerBack = 1;
550: PetscInt markerRight = 1;
551: PetscInt markerLeft = 1;
552: PetscBool markerSeparate = PETSC_FALSE;
553: Vec coordinates;
554: PetscSection coordSection;
555: PetscScalar *coords;
556: PetscInt coordSize;
557: PetscMPIInt rank;
558: PetscInt v, vx, vy, vz;
559: PetscInt voffset, iface = 0, cone[4];
561: PetscFunctionBegin;
562: PetscCheck(faces[0] >= 1 && faces[1] >= 1 && faces[2] >= 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Must have at least 1 face per side");
563: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
564: PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL));
565: if (markerSeparate) {
566: markerBottom = 1;
567: markerTop = 2;
568: markerFront = 3;
569: markerBack = 4;
570: markerRight = 5;
571: markerLeft = 6;
572: }
573: vertices[0] = faces[0] + 1;
574: vertices[1] = faces[1] + 1;
575: vertices[2] = faces[2] + 1;
576: numVertices = vertices[0] * vertices[1] * vertices[2];
577: if (rank == 0) {
578: PetscInt f;
580: PetscCall(DMPlexSetChart(dm, 0, numFaces + numVertices));
581: for (f = 0; f < numFaces; ++f) PetscCall(DMPlexSetConeSize(dm, f, 4));
582: PetscCall(DMSetUp(dm)); /* Allocate space for cones */
584: /* Side 0 (Top) */
585: for (vy = 0; vy < faces[1]; vy++) {
586: for (vx = 0; vx < faces[0]; vx++) {
587: voffset = numFaces + vertices[0] * vertices[1] * (vertices[2] - 1) + vy * vertices[0] + vx;
588: cone[0] = voffset;
589: cone[1] = voffset + 1;
590: cone[2] = voffset + vertices[0] + 1;
591: cone[3] = voffset + vertices[0];
592: PetscCall(DMPlexSetCone(dm, iface, cone));
593: PetscCall(DMSetLabelValue(dm, "marker", iface, markerTop));
594: PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerTop));
595: PetscCall(DMSetLabelValue(dm, "marker", voffset + 1, markerTop));
596: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 0, markerTop));
597: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 1, markerTop));
598: iface++;
599: }
600: }
602: /* Side 1 (Bottom) */
603: for (vy = 0; vy < faces[1]; vy++) {
604: for (vx = 0; vx < faces[0]; vx++) {
605: voffset = numFaces + vy * (faces[0] + 1) + vx;
606: cone[0] = voffset + 1;
607: cone[1] = voffset;
608: cone[2] = voffset + vertices[0];
609: cone[3] = voffset + vertices[0] + 1;
610: PetscCall(DMPlexSetCone(dm, iface, cone));
611: PetscCall(DMSetLabelValue(dm, "marker", iface, markerBottom));
612: PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerBottom));
613: PetscCall(DMSetLabelValue(dm, "marker", voffset + 1, markerBottom));
614: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 0, markerBottom));
615: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 1, markerBottom));
616: iface++;
617: }
618: }
620: /* Side 2 (Front) */
621: for (vz = 0; vz < faces[2]; vz++) {
622: for (vx = 0; vx < faces[0]; vx++) {
623: voffset = numFaces + vz * vertices[0] * vertices[1] + vx;
624: cone[0] = voffset;
625: cone[1] = voffset + 1;
626: cone[2] = voffset + vertices[0] * vertices[1] + 1;
627: cone[3] = voffset + vertices[0] * vertices[1];
628: PetscCall(DMPlexSetCone(dm, iface, cone));
629: PetscCall(DMSetLabelValue(dm, "marker", iface, markerFront));
630: PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerFront));
631: PetscCall(DMSetLabelValue(dm, "marker", voffset + 1, markerFront));
632: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 0, markerFront));
633: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 1, markerFront));
634: iface++;
635: }
636: }
638: /* Side 3 (Back) */
639: for (vz = 0; vz < faces[2]; vz++) {
640: for (vx = 0; vx < faces[0]; vx++) {
641: voffset = numFaces + vz * vertices[0] * vertices[1] + vertices[0] * (vertices[1] - 1) + vx;
642: cone[0] = voffset + vertices[0] * vertices[1];
643: cone[1] = voffset + vertices[0] * vertices[1] + 1;
644: cone[2] = voffset + 1;
645: cone[3] = voffset;
646: PetscCall(DMPlexSetCone(dm, iface, cone));
647: PetscCall(DMSetLabelValue(dm, "marker", iface, markerBack));
648: PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerBack));
649: PetscCall(DMSetLabelValue(dm, "marker", voffset + 1, markerBack));
650: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 0, markerBack));
651: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 1, markerBack));
652: iface++;
653: }
654: }
656: /* Side 4 (Left) */
657: for (vz = 0; vz < faces[2]; vz++) {
658: for (vy = 0; vy < faces[1]; vy++) {
659: voffset = numFaces + vz * vertices[0] * vertices[1] + vy * vertices[0];
660: cone[0] = voffset;
661: cone[1] = voffset + vertices[0] * vertices[1];
662: cone[2] = voffset + vertices[0] * vertices[1] + vertices[0];
663: cone[3] = voffset + vertices[0];
664: PetscCall(DMPlexSetCone(dm, iface, cone));
665: PetscCall(DMSetLabelValue(dm, "marker", iface, markerLeft));
666: PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerLeft));
667: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 0, markerLeft));
668: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[1] + 0, markerLeft));
669: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + vertices[0], markerLeft));
670: iface++;
671: }
672: }
674: /* Side 5 (Right) */
675: for (vz = 0; vz < faces[2]; vz++) {
676: for (vy = 0; vy < faces[1]; vy++) {
677: voffset = numFaces + vz * vertices[0] * vertices[1] + vy * vertices[0] + faces[0];
678: cone[0] = voffset + vertices[0] * vertices[1];
679: cone[1] = voffset;
680: cone[2] = voffset + vertices[0];
681: cone[3] = voffset + vertices[0] * vertices[1] + vertices[0];
682: PetscCall(DMPlexSetCone(dm, iface, cone));
683: PetscCall(DMSetLabelValue(dm, "marker", iface, markerRight));
684: PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerRight));
685: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 0, markerRight));
686: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 0, markerRight));
687: PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + vertices[0], markerRight));
688: iface++;
689: }
690: }
691: }
692: PetscCall(DMPlexSymmetrize(dm));
693: PetscCall(DMPlexStratify(dm));
694: /* Build coordinates */
695: PetscCall(DMSetCoordinateDim(dm, 3));
696: PetscCall(DMGetCoordinateSection(dm, &coordSection));
697: PetscCall(PetscSectionSetNumFields(coordSection, 1));
698: PetscCall(PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices));
699: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, 3));
700: for (v = numFaces; v < numFaces + numVertices; ++v) {
701: PetscCall(PetscSectionSetDof(coordSection, v, 3));
702: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, 3));
703: }
704: PetscCall(PetscSectionSetUp(coordSection));
705: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
706: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
707: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
708: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
709: PetscCall(VecSetBlockSize(coordinates, 3));
710: PetscCall(VecSetType(coordinates, VECSTANDARD));
711: PetscCall(VecGetArray(coordinates, &coords));
712: for (vz = 0; vz <= faces[2]; ++vz) {
713: for (vy = 0; vy <= faces[1]; ++vy) {
714: for (vx = 0; vx <= faces[0]; ++vx) {
715: coords[((vz * (faces[1] + 1) + vy) * (faces[0] + 1) + vx) * 3 + 0] = lower[0] + ((upper[0] - lower[0]) / faces[0]) * vx;
716: coords[((vz * (faces[1] + 1) + vy) * (faces[0] + 1) + vx) * 3 + 1] = lower[1] + ((upper[1] - lower[1]) / faces[1]) * vy;
717: coords[((vz * (faces[1] + 1) + vy) * (faces[0] + 1) + vx) * 3 + 2] = lower[2] + ((upper[2] - lower[2]) / faces[2]) * vz;
718: }
719: }
720: }
721: PetscCall(VecRestoreArray(coordinates, &coords));
722: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
723: PetscCall(VecDestroy(&coordinates));
724: PetscFunctionReturn(PETSC_SUCCESS);
725: }
727: static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate)
728: {
729: PetscFunctionBegin;
731: PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0));
732: PetscCall(DMSetDimension(dm, dim - 1));
733: PetscCall(DMSetCoordinateDim(dm, dim));
734: switch (dim) {
735: case 1:
736: PetscCall(DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(dm, lower, upper, faces));
737: break;
738: case 2:
739: PetscCall(DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(dm, lower, upper, faces));
740: break;
741: case 3:
742: PetscCall(DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(dm, lower, upper, faces));
743: break;
744: default:
745: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Dimension not supported: %" PetscInt_FMT, dim);
746: }
747: PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0));
748: if (interpolate) PetscCall(DMPlexInterpolateInPlace_Internal(dm));
749: PetscFunctionReturn(PETSC_SUCCESS);
750: }
752: /*@C
753: DMPlexCreateBoxSurfaceMesh - Creates a mesh on the surface of the tensor product of unit intervals (box) using tensor cells (hexahedra).
755: Collective
757: Input Parameters:
758: + comm - The communicator for the `DM` object
759: . dim - The spatial dimension of the box, so the resulting mesh is has dimension `dim`-1
760: . faces - Number of faces per dimension, or `NULL` for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D
761: . lower - The lower left corner, or `NULL` for (0, 0, 0)
762: . upper - The upper right corner, or `NULL` for (1, 1, 1)
763: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
765: Output Parameter:
766: . dm - The `DM` object
768: Level: beginner
770: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMSetFromOptions()`, `DMPlexCreateBoxMesh()`, `DMPlexCreateFromFile()`, `DMSetType()`, `DMCreate()`
771: @*/
772: PetscErrorCode DMPlexCreateBoxSurfaceMesh(MPI_Comm comm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate, DM *dm)
773: {
774: PetscInt fac[3] = {1, 1, 1};
775: PetscReal low[3] = {0, 0, 0};
776: PetscReal upp[3] = {1, 1, 1};
778: PetscFunctionBegin;
779: PetscCall(DMCreate(comm, dm));
780: PetscCall(DMSetType(*dm, DMPLEX));
781: PetscCall(DMPlexCreateBoxSurfaceMesh_Internal(*dm, dim, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, interpolate));
782: PetscFunctionReturn(PETSC_SUCCESS);
783: }
785: static PetscErrorCode DMPlexCreateLineMesh_Internal(DM dm, PetscInt segments, PetscReal lower, PetscReal upper, DMBoundaryType bd)
786: {
787: PetscInt i, fStart, fEnd, numCells = 0, numVerts = 0;
788: PetscInt numPoints[2], *coneSize, *cones, *coneOrientations;
789: PetscScalar *vertexCoords;
790: PetscReal L, maxCell;
791: PetscBool markerSeparate = PETSC_FALSE;
792: PetscInt markerLeft = 1, faceMarkerLeft = 1;
793: PetscInt markerRight = 1, faceMarkerRight = 2;
794: PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE;
795: PetscMPIInt rank;
797: PetscFunctionBegin;
798: PetscAssertPointer(dm, 1);
800: PetscCall(DMSetDimension(dm, 1));
801: PetscCall(DMCreateLabel(dm, "marker"));
802: PetscCall(DMCreateLabel(dm, "Face Sets"));
804: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
805: if (rank == 0) numCells = segments;
806: if (rank == 0) numVerts = segments + (wrap ? 0 : 1);
808: numPoints[0] = numVerts;
809: numPoints[1] = numCells;
810: PetscCall(PetscMalloc4(numCells + numVerts, &coneSize, numCells * 2, &cones, numCells + numVerts, &coneOrientations, numVerts, &vertexCoords));
811: PetscCall(PetscArrayzero(coneOrientations, numCells + numVerts));
812: for (i = 0; i < numCells; ++i) coneSize[i] = 2;
813: for (i = 0; i < numVerts; ++i) coneSize[numCells + i] = 0;
814: for (i = 0; i < numCells; ++i) {
815: cones[2 * i] = numCells + i % numVerts;
816: cones[2 * i + 1] = numCells + (i + 1) % numVerts;
817: }
818: for (i = 0; i < numVerts; ++i) vertexCoords[i] = lower + (upper - lower) * ((PetscReal)i / (PetscReal)numCells);
819: PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
820: PetscCall(PetscFree4(coneSize, cones, coneOrientations, vertexCoords));
822: PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL));
823: if (markerSeparate) {
824: markerLeft = faceMarkerLeft;
825: markerRight = faceMarkerRight;
826: }
827: if (!wrap && rank == 0) {
828: PetscCall(DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd));
829: PetscCall(DMSetLabelValue(dm, "marker", fStart, markerLeft));
830: PetscCall(DMSetLabelValue(dm, "marker", fEnd - 1, markerRight));
831: PetscCall(DMSetLabelValue(dm, "Face Sets", fStart, faceMarkerLeft));
832: PetscCall(DMSetLabelValue(dm, "Face Sets", fEnd - 1, faceMarkerRight));
833: }
834: if (wrap) {
835: L = upper - lower;
836: maxCell = (PetscReal)1.1 * (L / (PetscReal)PetscMax(1, segments));
837: PetscCall(DMSetPeriodicity(dm, &maxCell, &lower, &L));
838: }
839: PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE));
840: PetscFunctionReturn(PETSC_SUCCESS);
841: }
843: static PetscErrorCode DMPlexCreateBoxMesh_Simplex_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate)
844: {
845: DM boundary, vol;
846: DMLabel bdlabel;
848: PetscFunctionBegin;
849: PetscAssertPointer(dm, 1);
850: 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");
851: PetscCall(DMCreate(PetscObjectComm((PetscObject)dm), &boundary));
852: PetscCall(DMSetType(boundary, DMPLEX));
853: PetscCall(DMPlexCreateBoxSurfaceMesh_Internal(boundary, dim, faces, lower, upper, PETSC_FALSE));
854: PetscCall(DMPlexGenerate(boundary, NULL, interpolate, &vol));
855: PetscCall(DMGetLabel(vol, "marker", &bdlabel));
856: if (bdlabel) PetscCall(DMPlexLabelComplete(vol, bdlabel));
857: PetscCall(DMPlexCopy_Internal(dm, PETSC_TRUE, PETSC_FALSE, vol));
858: PetscCall(DMPlexReplace_Internal(dm, &vol));
859: PetscCall(DMDestroy(&boundary));
860: PetscFunctionReturn(PETSC_SUCCESS);
861: }
863: static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ)
864: {
865: DMLabel cutLabel = NULL;
866: PetscInt markerTop = 1, faceMarkerTop = 1;
867: PetscInt markerBottom = 1, faceMarkerBottom = 1;
868: PetscInt markerFront = 1, faceMarkerFront = 1;
869: PetscInt markerBack = 1, faceMarkerBack = 1;
870: PetscInt markerRight = 1, faceMarkerRight = 1;
871: PetscInt markerLeft = 1, faceMarkerLeft = 1;
872: PetscInt dim;
873: PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE;
874: PetscMPIInt rank;
876: PetscFunctionBegin;
877: PetscCall(DMGetDimension(dm, &dim));
878: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
879: PetscCall(DMCreateLabel(dm, "marker"));
880: PetscCall(DMCreateLabel(dm, "Face Sets"));
881: PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL));
882: 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) {
883: if (cutMarker) {
884: PetscCall(DMCreateLabel(dm, "periodic_cut"));
885: PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
886: }
887: }
888: switch (dim) {
889: case 2:
890: faceMarkerTop = 3;
891: faceMarkerBottom = 1;
892: faceMarkerRight = 2;
893: faceMarkerLeft = 4;
894: break;
895: case 3:
896: faceMarkerBottom = 1;
897: faceMarkerTop = 2;
898: faceMarkerFront = 3;
899: faceMarkerBack = 4;
900: faceMarkerRight = 5;
901: faceMarkerLeft = 6;
902: break;
903: default:
904: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Dimension %" PetscInt_FMT " not supported", dim);
905: }
906: PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL));
907: if (markerSeparate) {
908: markerBottom = faceMarkerBottom;
909: markerTop = faceMarkerTop;
910: markerFront = faceMarkerFront;
911: markerBack = faceMarkerBack;
912: markerRight = faceMarkerRight;
913: markerLeft = faceMarkerLeft;
914: }
915: {
916: const PetscInt numXEdges = rank == 0 ? edges[0] : 0;
917: const PetscInt numYEdges = rank == 0 ? edges[1] : 0;
918: const PetscInt numZEdges = rank == 0 ? edges[2] : 0;
919: const PetscInt numXVertices = rank == 0 ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0] + 1) : 0;
920: const PetscInt numYVertices = rank == 0 ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1] + 1) : 0;
921: const PetscInt numZVertices = rank == 0 ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2] + 1) : 0;
922: const PetscInt numCells = numXEdges * numYEdges * numZEdges;
923: const PetscInt numXFaces = numYEdges * numZEdges;
924: const PetscInt numYFaces = numXEdges * numZEdges;
925: const PetscInt numZFaces = numXEdges * numYEdges;
926: const PetscInt numTotXFaces = numXVertices * numXFaces;
927: const PetscInt numTotYFaces = numYVertices * numYFaces;
928: const PetscInt numTotZFaces = numZVertices * numZFaces;
929: const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces;
930: const PetscInt numTotXEdges = numXEdges * numYVertices * numZVertices;
931: const PetscInt numTotYEdges = numYEdges * numXVertices * numZVertices;
932: const PetscInt numTotZEdges = numZEdges * numXVertices * numYVertices;
933: const PetscInt numVertices = numXVertices * numYVertices * numZVertices;
934: const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges;
935: const PetscInt firstVertex = (dim == 2) ? numFaces : numCells;
936: const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices;
937: const PetscInt firstYFace = firstXFace + numTotXFaces;
938: const PetscInt firstZFace = firstYFace + numTotYFaces;
939: const PetscInt firstXEdge = numCells + numFaces + numVertices;
940: const PetscInt firstYEdge = firstXEdge + numTotXEdges;
941: const PetscInt firstZEdge = firstYEdge + numTotYEdges;
942: Vec coordinates;
943: PetscSection coordSection;
944: PetscScalar *coords;
945: PetscInt coordSize;
946: PetscInt v, vx, vy, vz;
947: PetscInt c, f, fx, fy, fz, e, ex, ey, ez;
949: PetscCall(DMPlexSetChart(dm, 0, numCells + numFaces + numEdges + numVertices));
950: for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 6));
951: for (f = firstXFace; f < firstXFace + numFaces; ++f) PetscCall(DMPlexSetConeSize(dm, f, 4));
952: for (e = firstXEdge; e < firstXEdge + numEdges; ++e) PetscCall(DMPlexSetConeSize(dm, e, 2));
953: PetscCall(DMSetUp(dm)); /* Allocate space for cones */
954: /* Build cells */
955: for (fz = 0; fz < numZEdges; ++fz) {
956: for (fy = 0; fy < numYEdges; ++fy) {
957: for (fx = 0; fx < numXEdges; ++fx) {
958: PetscInt cell = (fz * numYEdges + fy) * numXEdges + fx;
959: PetscInt faceB = firstZFace + (fy * numXEdges + fx) * numZVertices + fz;
960: PetscInt faceT = firstZFace + (fy * numXEdges + fx) * numZVertices + ((fz + 1) % numZVertices);
961: PetscInt faceF = firstYFace + (fz * numXEdges + fx) * numYVertices + fy;
962: PetscInt faceK = firstYFace + (fz * numXEdges + fx) * numYVertices + ((fy + 1) % numYVertices);
963: PetscInt faceL = firstXFace + (fz * numYEdges + fy) * numXVertices + fx;
964: PetscInt faceR = firstXFace + (fz * numYEdges + fy) * numXVertices + ((fx + 1) % numXVertices);
965: /* B, T, F, K, R, L */
966: PetscInt ornt[6] = {-2, 0, 0, -3, 0, -2}; /* ??? */
967: PetscInt cone[6];
969: /* no boundary twisting in 3D */
970: cone[0] = faceB;
971: cone[1] = faceT;
972: cone[2] = faceF;
973: cone[3] = faceK;
974: cone[4] = faceR;
975: cone[5] = faceL;
976: PetscCall(DMPlexSetCone(dm, cell, cone));
977: PetscCall(DMPlexSetConeOrientation(dm, cell, ornt));
978: if (bdX != DM_BOUNDARY_NONE && fx == numXEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, cell, 2));
979: if (bdY != DM_BOUNDARY_NONE && fy == numYEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, cell, 2));
980: if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, cell, 2));
981: }
982: }
983: }
984: /* Build x faces */
985: for (fz = 0; fz < numZEdges; ++fz) {
986: for (fy = 0; fy < numYEdges; ++fy) {
987: for (fx = 0; fx < numXVertices; ++fx) {
988: PetscInt face = firstXFace + (fz * numYEdges + fy) * numXVertices + fx;
989: PetscInt edgeL = firstZEdge + (fy * numXVertices + fx) * numZEdges + fz;
990: PetscInt edgeR = firstZEdge + (((fy + 1) % numYVertices) * numXVertices + fx) * numZEdges + fz;
991: PetscInt edgeB = firstYEdge + (fz * numXVertices + fx) * numYEdges + fy;
992: PetscInt edgeT = firstYEdge + (((fz + 1) % numZVertices) * numXVertices + fx) * numYEdges + fy;
993: PetscInt ornt[4] = {0, 0, -1, -1};
994: PetscInt cone[4];
996: if (dim == 3) {
997: /* markers */
998: if (bdX != DM_BOUNDARY_PERIODIC) {
999: if (fx == numXVertices - 1) {
1000: PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight));
1001: PetscCall(DMSetLabelValue(dm, "marker", face, markerRight));
1002: } else if (fx == 0) {
1003: PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft));
1004: PetscCall(DMSetLabelValue(dm, "marker", face, markerLeft));
1005: }
1006: }
1007: }
1008: cone[0] = edgeB;
1009: cone[1] = edgeR;
1010: cone[2] = edgeT;
1011: cone[3] = edgeL;
1012: PetscCall(DMPlexSetCone(dm, face, cone));
1013: PetscCall(DMPlexSetConeOrientation(dm, face, ornt));
1014: }
1015: }
1016: }
1017: /* Build y faces */
1018: for (fz = 0; fz < numZEdges; ++fz) {
1019: for (fx = 0; fx < numXEdges; ++fx) {
1020: for (fy = 0; fy < numYVertices; ++fy) {
1021: PetscInt face = firstYFace + (fz * numXEdges + fx) * numYVertices + fy;
1022: PetscInt edgeL = firstZEdge + (fy * numXVertices + fx) * numZEdges + fz;
1023: PetscInt edgeR = firstZEdge + (fy * numXVertices + ((fx + 1) % numXVertices)) * numZEdges + fz;
1024: PetscInt edgeB = firstXEdge + (fz * numYVertices + fy) * numXEdges + fx;
1025: PetscInt edgeT = firstXEdge + (((fz + 1) % numZVertices) * numYVertices + fy) * numXEdges + fx;
1026: PetscInt ornt[4] = {0, 0, -1, -1};
1027: PetscInt cone[4];
1029: if (dim == 3) {
1030: /* markers */
1031: if (bdY != DM_BOUNDARY_PERIODIC) {
1032: if (fy == numYVertices - 1) {
1033: PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack));
1034: PetscCall(DMSetLabelValue(dm, "marker", face, markerBack));
1035: } else if (fy == 0) {
1036: PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront));
1037: PetscCall(DMSetLabelValue(dm, "marker", face, markerFront));
1038: }
1039: }
1040: }
1041: cone[0] = edgeB;
1042: cone[1] = edgeR;
1043: cone[2] = edgeT;
1044: cone[3] = edgeL;
1045: PetscCall(DMPlexSetCone(dm, face, cone));
1046: PetscCall(DMPlexSetConeOrientation(dm, face, ornt));
1047: }
1048: }
1049: }
1050: /* Build z faces */
1051: for (fy = 0; fy < numYEdges; ++fy) {
1052: for (fx = 0; fx < numXEdges; ++fx) {
1053: for (fz = 0; fz < numZVertices; fz++) {
1054: PetscInt face = firstZFace + (fy * numXEdges + fx) * numZVertices + fz;
1055: PetscInt edgeL = firstYEdge + (fz * numXVertices + fx) * numYEdges + fy;
1056: PetscInt edgeR = firstYEdge + (fz * numXVertices + ((fx + 1) % numXVertices)) * numYEdges + fy;
1057: PetscInt edgeB = firstXEdge + (fz * numYVertices + fy) * numXEdges + fx;
1058: PetscInt edgeT = firstXEdge + (fz * numYVertices + ((fy + 1) % numYVertices)) * numXEdges + fx;
1059: PetscInt ornt[4] = {0, 0, -1, -1};
1060: PetscInt cone[4];
1062: if (dim == 2) {
1063: if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges - 1) {
1064: edgeR += numYEdges - 1 - 2 * fy;
1065: ornt[1] = -1;
1066: }
1067: if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges - 1) {
1068: edgeT += numXEdges - 1 - 2 * fx;
1069: ornt[2] = 0;
1070: }
1071: if (bdX != DM_BOUNDARY_NONE && fx == numXEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, face, 2));
1072: if (bdY != DM_BOUNDARY_NONE && fy == numYEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, face, 2));
1073: } else {
1074: /* markers */
1075: if (bdZ != DM_BOUNDARY_PERIODIC) {
1076: if (fz == numZVertices - 1) {
1077: PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop));
1078: PetscCall(DMSetLabelValue(dm, "marker", face, markerTop));
1079: } else if (fz == 0) {
1080: PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom));
1081: PetscCall(DMSetLabelValue(dm, "marker", face, markerBottom));
1082: }
1083: }
1084: }
1085: cone[0] = edgeB;
1086: cone[1] = edgeR;
1087: cone[2] = edgeT;
1088: cone[3] = edgeL;
1089: PetscCall(DMPlexSetCone(dm, face, cone));
1090: PetscCall(DMPlexSetConeOrientation(dm, face, ornt));
1091: }
1092: }
1093: }
1094: /* Build Z edges*/
1095: for (vy = 0; vy < numYVertices; vy++) {
1096: for (vx = 0; vx < numXVertices; vx++) {
1097: for (ez = 0; ez < numZEdges; ez++) {
1098: const PetscInt edge = firstZEdge + (vy * numXVertices + vx) * numZEdges + ez;
1099: const PetscInt vertexB = firstVertex + (ez * numYVertices + vy) * numXVertices + vx;
1100: const PetscInt vertexT = firstVertex + (((ez + 1) % numZVertices) * numYVertices + vy) * numXVertices + vx;
1101: PetscInt cone[2];
1103: cone[0] = vertexB;
1104: cone[1] = vertexT;
1105: PetscCall(DMPlexSetCone(dm, edge, cone));
1106: if (dim == 3) {
1107: if (bdX != DM_BOUNDARY_PERIODIC) {
1108: if (vx == numXVertices - 1) {
1109: PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight));
1110: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight));
1111: if (ez == numZEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight));
1112: } else if (vx == 0) {
1113: PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft));
1114: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft));
1115: if (ez == numZEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft));
1116: }
1117: }
1118: if (bdY != DM_BOUNDARY_PERIODIC) {
1119: if (vy == numYVertices - 1) {
1120: PetscCall(DMSetLabelValue(dm, "marker", edge, markerBack));
1121: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBack));
1122: if (ez == numZEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBack));
1123: } else if (vy == 0) {
1124: PetscCall(DMSetLabelValue(dm, "marker", edge, markerFront));
1125: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerFront));
1126: if (ez == numZEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerFront));
1127: }
1128: }
1129: }
1130: }
1131: }
1132: }
1133: /* Build Y edges*/
1134: for (vz = 0; vz < numZVertices; vz++) {
1135: for (vx = 0; vx < numXVertices; vx++) {
1136: for (ey = 0; ey < numYEdges; ey++) {
1137: const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges - 1) ? (numXVertices - vx - 1) : (vz * numYVertices + ((ey + 1) % numYVertices)) * numXVertices + vx;
1138: const PetscInt edge = firstYEdge + (vz * numXVertices + vx) * numYEdges + ey;
1139: const PetscInt vertexF = firstVertex + (vz * numYVertices + ey) * numXVertices + vx;
1140: const PetscInt vertexK = firstVertex + nextv;
1141: PetscInt cone[2];
1143: cone[0] = vertexF;
1144: cone[1] = vertexK;
1145: PetscCall(DMPlexSetCone(dm, edge, cone));
1146: if (dim == 2) {
1147: if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) {
1148: if (vx == numXVertices - 1) {
1149: PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight));
1150: PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight));
1151: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight));
1152: if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight));
1153: } else if (vx == 0) {
1154: PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft));
1155: PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft));
1156: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft));
1157: if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft));
1158: }
1159: } else {
1160: if (vx == 0 && cutLabel) {
1161: PetscCall(DMLabelSetValue(cutLabel, edge, 1));
1162: PetscCall(DMLabelSetValue(cutLabel, cone[0], 1));
1163: if (ey == numYEdges - 1) PetscCall(DMLabelSetValue(cutLabel, cone[1], 1));
1164: }
1165: }
1166: } else {
1167: if (bdX != DM_BOUNDARY_PERIODIC) {
1168: if (vx == numXVertices - 1) {
1169: PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight));
1170: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight));
1171: if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight));
1172: } else if (vx == 0) {
1173: PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft));
1174: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft));
1175: if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft));
1176: }
1177: }
1178: if (bdZ != DM_BOUNDARY_PERIODIC) {
1179: if (vz == numZVertices - 1) {
1180: PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop));
1181: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop));
1182: if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop));
1183: } else if (vz == 0) {
1184: PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom));
1185: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom));
1186: if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom));
1187: }
1188: }
1189: }
1190: }
1191: }
1192: }
1193: /* Build X edges*/
1194: for (vz = 0; vz < numZVertices; vz++) {
1195: for (vy = 0; vy < numYVertices; vy++) {
1196: for (ex = 0; ex < numXEdges; ex++) {
1197: const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges - 1) ? (numYVertices - vy - 1) * numXVertices : (vz * numYVertices + vy) * numXVertices + (ex + 1) % numXVertices;
1198: const PetscInt edge = firstXEdge + (vz * numYVertices + vy) * numXEdges + ex;
1199: const PetscInt vertexL = firstVertex + (vz * numYVertices + vy) * numXVertices + ex;
1200: const PetscInt vertexR = firstVertex + nextv;
1201: PetscInt cone[2];
1203: cone[0] = vertexL;
1204: cone[1] = vertexR;
1205: PetscCall(DMPlexSetCone(dm, edge, cone));
1206: if (dim == 2) {
1207: if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) {
1208: if (vy == numYVertices - 1) {
1209: PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop));
1210: PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop));
1211: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop));
1212: if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop));
1213: } else if (vy == 0) {
1214: PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom));
1215: PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom));
1216: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom));
1217: if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom));
1218: }
1219: } else {
1220: if (vy == 0 && cutLabel) {
1221: PetscCall(DMLabelSetValue(cutLabel, edge, 1));
1222: PetscCall(DMLabelSetValue(cutLabel, cone[0], 1));
1223: if (ex == numXEdges - 1) PetscCall(DMLabelSetValue(cutLabel, cone[1], 1));
1224: }
1225: }
1226: } else {
1227: if (bdY != DM_BOUNDARY_PERIODIC) {
1228: if (vy == numYVertices - 1) {
1229: PetscCall(DMSetLabelValue(dm, "marker", edge, markerBack));
1230: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBack));
1231: if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBack));
1232: } else if (vy == 0) {
1233: PetscCall(DMSetLabelValue(dm, "marker", edge, markerFront));
1234: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerFront));
1235: if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerFront));
1236: }
1237: }
1238: if (bdZ != DM_BOUNDARY_PERIODIC) {
1239: if (vz == numZVertices - 1) {
1240: PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop));
1241: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop));
1242: if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop));
1243: } else if (vz == 0) {
1244: PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom));
1245: PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom));
1246: if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom));
1247: }
1248: }
1249: }
1250: }
1251: }
1252: }
1253: PetscCall(DMPlexSymmetrize(dm));
1254: PetscCall(DMPlexStratify(dm));
1255: /* Build coordinates */
1256: PetscCall(DMGetCoordinateSection(dm, &coordSection));
1257: PetscCall(PetscSectionSetNumFields(coordSection, 1));
1258: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim));
1259: PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex + numVertices));
1260: for (v = firstVertex; v < firstVertex + numVertices; ++v) {
1261: PetscCall(PetscSectionSetDof(coordSection, v, dim));
1262: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim));
1263: }
1264: PetscCall(PetscSectionSetUp(coordSection));
1265: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
1266: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
1267: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
1268: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
1269: PetscCall(VecSetBlockSize(coordinates, dim));
1270: PetscCall(VecSetType(coordinates, VECSTANDARD));
1271: PetscCall(VecGetArray(coordinates, &coords));
1272: for (vz = 0; vz < numZVertices; ++vz) {
1273: for (vy = 0; vy < numYVertices; ++vy) {
1274: for (vx = 0; vx < numXVertices; ++vx) {
1275: coords[((vz * numYVertices + vy) * numXVertices + vx) * dim + 0] = lower[0] + ((upper[0] - lower[0]) / numXEdges) * vx;
1276: coords[((vz * numYVertices + vy) * numXVertices + vx) * dim + 1] = lower[1] + ((upper[1] - lower[1]) / numYEdges) * vy;
1277: if (dim == 3) coords[((vz * numYVertices + vy) * numXVertices + vx) * dim + 2] = lower[2] + ((upper[2] - lower[2]) / numZEdges) * vz;
1278: }
1279: }
1280: }
1281: PetscCall(VecRestoreArray(coordinates, &coords));
1282: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
1283: PetscCall(VecDestroy(&coordinates));
1284: }
1285: PetscFunctionReturn(PETSC_SUCCESS);
1286: }
1288: static PetscErrorCode DMPlexCreateBoxMesh_Tensor_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[])
1289: {
1290: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
1291: PetscInt fac[3] = {0, 0, 0}, d;
1293: PetscFunctionBegin;
1294: PetscAssertPointer(dm, 1);
1296: PetscCall(DMSetDimension(dm, dim));
1297: for (d = 0; d < dim; ++d) {
1298: fac[d] = faces[d];
1299: bdt[d] = periodicity[d];
1300: }
1301: PetscCall(DMPlexCreateCubeMesh_Internal(dm, lower, upper, fac, bdt[0], bdt[1], bdt[2]));
1302: 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))) {
1303: PetscReal L[3] = {-1., -1., 0.};
1304: PetscReal maxCell[3] = {-1., -1., 0.};
1306: for (d = 0; d < dim; ++d) {
1307: if (periodicity[d] != DM_BOUNDARY_NONE) {
1308: L[d] = upper[d] - lower[d];
1309: maxCell[d] = 1.1 * (L[d] / PetscMax(1, faces[d]));
1310: }
1311: }
1312: PetscCall(DMSetPeriodicity(dm, maxCell, lower, L));
1313: }
1314: PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE));
1315: PetscFunctionReturn(PETSC_SUCCESS);
1316: }
1318: 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)
1319: {
1320: PetscFunctionBegin;
1321: PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0));
1322: if (shape == DM_SHAPE_ZBOX) PetscCall(DMPlexCreateBoxMesh_Tensor_SFC_Internal(dm, dim, faces, lower, upper, periodicity, interpolate));
1323: else if (dim == 1) PetscCall(DMPlexCreateLineMesh_Internal(dm, faces[0], lower[0], upper[0], periodicity[0]));
1324: else if (simplex) PetscCall(DMPlexCreateBoxMesh_Simplex_Internal(dm, dim, faces, lower, upper, periodicity, interpolate));
1325: else PetscCall(DMPlexCreateBoxMesh_Tensor_Internal(dm, dim, faces, lower, upper, periodicity));
1326: if (!interpolate && dim > 1 && !simplex) {
1327: DM udm;
1329: PetscCall(DMPlexUninterpolate(dm, &udm));
1330: PetscCall(DMPlexCopyCoordinates(dm, udm));
1331: PetscCall(DMPlexReplace_Internal(dm, &udm));
1332: }
1333: PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0));
1334: PetscFunctionReturn(PETSC_SUCCESS);
1335: }
1337: /*@
1338: DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra).
1340: Collective
1342: Input Parameters:
1343: + comm - The communicator for the `DM` object
1344: . dim - The spatial dimension
1345: . simplex - `PETSC_TRUE` for simplices, `PETSC_FALSE` for tensor cells
1346: . faces - Number of faces per dimension, or `NULL` for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D
1347: . lower - The lower left corner, or `NULL` for (0, 0, 0)
1348: . upper - The upper right corner, or `NULL` for (1, 1, 1)
1349: . periodicity - The boundary type for the X,Y,Z direction, or `NULL` for `DM_BOUNDARY_NONE`
1350: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
1352: Output Parameter:
1353: . dm - The `DM` object
1355: Level: beginner
1357: Note:
1358: To customize this mesh using options, use
1359: .vb
1360: DMCreate(comm, &dm);
1361: DMSetType(dm, DMPLEX);
1362: DMSetFromOptions(dm);
1363: .ve
1364: and use the options in `DMSetFromOptions()`.
1366: Here is the numbering returned for 2 faces in each direction for tensor cells\:
1367: .vb
1368: 10---17---11---18----12
1369: | | |
1370: | | |
1371: 20 2 22 3 24
1372: | | |
1373: | | |
1374: 7---15----8---16----9
1375: | | |
1376: | | |
1377: 19 0 21 1 23
1378: | | |
1379: | | |
1380: 4---13----5---14----6
1381: .ve
1382: and for simplicial cells
1383: .vb
1384: 14----8---15----9----16
1385: |\ 5 |\ 7 |
1386: | \ | \ |
1387: 13 2 14 3 15
1388: | 4 \ | 6 \ |
1389: | \ | \ |
1390: 11----6---12----7----13
1391: |\ |\ |
1392: | \ 1 | \ 3 |
1393: 10 0 11 1 12
1394: | 0 \ | 2 \ |
1395: | \ | \ |
1396: 8----4----9----5----10
1397: .ve
1399: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMSetFromOptions()`, `DMPlexCreateFromFile()`, `DMPlexCreateHexCylinderMesh()`, `DMSetType()`, `DMCreate()`
1400: @*/
1401: PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate, DM *dm)
1402: {
1403: PetscInt fac[3] = {1, 1, 1};
1404: PetscReal low[3] = {0, 0, 0};
1405: PetscReal upp[3] = {1, 1, 1};
1406: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
1408: PetscFunctionBegin;
1409: PetscCall(DMCreate(comm, dm));
1410: PetscCall(DMSetType(*dm, DMPLEX));
1411: PetscCall(DMPlexCreateBoxMesh_Internal(*dm, DM_SHAPE_BOX, dim, simplex, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt, interpolate));
1412: if (periodicity) PetscCall(DMLocalizeCoordinates(*dm));
1413: PetscFunctionReturn(PETSC_SUCCESS);
1414: }
1416: static PetscErrorCode DMPlexCreateWedgeBoxMesh_Internal(DM dm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[])
1417: {
1418: DM bdm, vol;
1419: PetscInt i;
1421: PetscFunctionBegin;
1422: // TODO Now we can support periodicity
1423: for (i = 0; i < 3; ++i) PetscCheck(periodicity[i] == DM_BOUNDARY_NONE, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Periodicity not yet supported");
1424: PetscCall(DMCreate(PetscObjectComm((PetscObject)dm), &bdm));
1425: PetscCall(DMSetType(bdm, DMPLEX));
1426: PetscCall(DMSetDimension(bdm, 2));
1427: PetscCall(PetscLogEventBegin(DMPLEX_Generate, bdm, 0, 0, 0));
1428: PetscCall(DMPlexCreateBoxMesh_Simplex_Internal(bdm, 2, faces, lower, upper, periodicity, PETSC_TRUE));
1429: PetscCall(DMPlexExtrude(bdm, faces[2], upper[2] - lower[2], PETSC_TRUE, PETSC_FALSE, PETSC_FALSE, NULL, NULL, &vol));
1430: PetscCall(PetscLogEventEnd(DMPLEX_Generate, bdm, 0, 0, 0));
1431: PetscCall(DMDestroy(&bdm));
1432: PetscCall(DMPlexReplace_Internal(dm, &vol));
1433: if (lower[2] != 0.0) {
1434: Vec v;
1435: PetscScalar *x;
1436: PetscInt cDim, n;
1438: PetscCall(DMGetCoordinatesLocal(dm, &v));
1439: PetscCall(VecGetBlockSize(v, &cDim));
1440: PetscCall(VecGetLocalSize(v, &n));
1441: PetscCall(VecGetArray(v, &x));
1442: x += cDim;
1443: for (i = 0; i < n; i += cDim) x[i] += lower[2];
1444: PetscCall(VecRestoreArray(v, &x));
1445: PetscCall(DMSetCoordinatesLocal(dm, v));
1446: }
1447: PetscFunctionReturn(PETSC_SUCCESS);
1448: }
1450: /*@
1451: DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tessellating the (x,y) plane and extruding in the third direction using wedge cells.
1453: Collective
1455: Input Parameters:
1456: + comm - The communicator for the `DM` object
1457: . faces - Number of faces per dimension, or `NULL` for (1, 1, 1)
1458: . lower - The lower left corner, or `NULL` for (0, 0, 0)
1459: . upper - The upper right corner, or `NULL` for (1, 1, 1)
1460: . periodicity - The boundary type for the X,Y,Z direction, or `NULL` for `DM_BOUNDARY_NONE`
1461: . orderHeight - If `PETSC_TRUE`, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first
1462: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
1464: Output Parameter:
1465: . dm - The `DM` object
1467: Level: beginner
1469: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateHexCylinderMesh()`, `DMPlexCreateWedgeCylinderMesh()`, `DMExtrude()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()`
1470: @*/
1471: PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool orderHeight, PetscBool interpolate, DM *dm)
1472: {
1473: PetscInt fac[3] = {1, 1, 1};
1474: PetscReal low[3] = {0, 0, 0};
1475: PetscReal upp[3] = {1, 1, 1};
1476: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
1478: PetscFunctionBegin;
1479: PetscCall(DMCreate(comm, dm));
1480: PetscCall(DMSetType(*dm, DMPLEX));
1481: PetscCall(DMPlexCreateWedgeBoxMesh_Internal(*dm, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt));
1482: if (!interpolate) {
1483: DM udm;
1485: PetscCall(DMPlexUninterpolate(*dm, &udm));
1486: PetscCall(DMPlexReplace_Internal(*dm, &udm));
1487: }
1488: if (periodicity) PetscCall(DMLocalizeCoordinates(*dm));
1489: PetscFunctionReturn(PETSC_SUCCESS);
1490: }
1492: /*
1493: DMPlexTensorPointLexicographic_Private - Returns all tuples of size 'len' with nonnegative integers that are all less than or equal to 'max' for that dimension.
1495: Input Parameters:
1496: + len - The length of the tuple
1497: . max - The maximum for each dimension, so values are in [0, max)
1498: - tup - A tuple of length len+1: tup[len] > 0 indicates a stopping condition
1500: Output Parameter:
1501: . tup - A tuple of `len` integers whose entries are at most `max`
1503: Level: developer
1505: Note:
1506: Ordering is lexicographic with lowest index as least significant in ordering.
1507: 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}.
1509: .seealso: PetscDualSpaceTensorPointLexicographic_Internal(), PetscDualSpaceLatticePointLexicographic_Internal()
1510: */
1511: static PetscErrorCode DMPlexTensorPointLexicographic_Private(PetscInt len, const PetscInt max[], PetscInt tup[])
1512: {
1513: PetscInt i;
1515: PetscFunctionBegin;
1516: for (i = 0; i < len; ++i) {
1517: if (tup[i] < max[i] - 1) {
1518: break;
1519: } else {
1520: tup[i] = 0;
1521: }
1522: }
1523: if (i == len) tup[i - 1] = max[i - 1];
1524: else ++tup[i];
1525: PetscFunctionReturn(PETSC_SUCCESS);
1526: }
1528: static PetscInt TupleToIndex_Private(PetscInt len, const PetscInt max[], const PetscInt tup[])
1529: {
1530: PetscInt i, idx = tup[len - 1];
1532: for (i = len - 2; i >= 0; --i) {
1533: idx *= max[i];
1534: idx += tup[i];
1535: }
1536: return idx;
1537: }
1539: static PetscErrorCode DestroyExtent_Private(void *extent)
1540: {
1541: return PetscFree(extent);
1542: }
1544: static PetscErrorCode DMPlexCreateHypercubicMesh_Internal(DM dm, PetscInt dim, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], const DMBoundaryType bd[])
1545: {
1546: Vec coordinates;
1547: PetscSection coordSection;
1548: DMLabel cutLabel = NULL;
1549: PetscBool cutMarker = PETSC_FALSE;
1550: PetscBool periodic = PETSC_FALSE;
1551: PetscInt numCells = 1, c;
1552: PetscInt numVertices = 1, v;
1553: PetscScalar *coords;
1554: PetscInt *vertices, *vert, *vtmp, *supp, cone[2];
1555: PetscInt d, e, cell = 0, coordSize;
1556: PetscMPIInt rank;
1558: PetscFunctionBegin;
1559: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
1560: PetscCall(DMSetDimension(dm, dim));
1561: PetscCall(PetscCalloc4(dim, &vertices, dim, &vert, dim, &vtmp, 2 * dim, &supp));
1562: PetscCall(DMCreateLabel(dm, "marker"));
1563: PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL));
1564: for (d = 0; d < dim; ++d) periodic = (periodic || bd[d] == DM_BOUNDARY_PERIODIC) ? PETSC_TRUE : PETSC_FALSE;
1565: if (periodic && cutMarker) {
1566: PetscCall(DMCreateLabel(dm, "periodic_cut"));
1567: PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
1568: }
1569: for (d = 0; d < dim; ++d) PetscCheck(bd[d] == DM_BOUNDARY_PERIODIC, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Hypercubic mesh must be periodic now");
1570: for (d = 0; d < dim; ++d) {
1571: vertices[d] = edges[d];
1572: numVertices *= vertices[d];
1573: }
1574: numCells = numVertices * dim;
1575: PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices));
1576: for (c = 0; c < numCells; ++c) PetscCall(DMPlexSetConeSize(dm, c, 2));
1577: for (v = numCells; v < numCells + numVertices; ++v) PetscCall(DMPlexSetSupportSize(dm, v, 2 * dim));
1578: /* TODO Loop over boundary and reset support sizes */
1579: PetscCall(DMSetUp(dm)); /* Allocate space for cones and supports */
1580: /* Build cell cones and vertex supports */
1581: PetscCall(DMCreateLabel(dm, "celltype"));
1582: while (vert[dim - 1] < vertices[dim - 1]) {
1583: const PetscInt vertex = TupleToIndex_Private(dim, vertices, vert) + numCells;
1584: PetscInt s = 0;
1586: PetscCall(PetscPrintf(PETSC_COMM_SELF, "Vertex %" PetscInt_FMT ":", vertex));
1587: for (d = 0; d < dim; ++d) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, vert[d]));
1588: PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n"));
1589: PetscCall(DMPlexSetCellType(dm, vertex, DM_POLYTOPE_POINT));
1590: for (d = 0; d < dim; ++d) {
1591: for (e = 0; e < dim; ++e) vtmp[e] = vert[e];
1592: vtmp[d] = (vert[d] + 1) % vertices[d];
1593: cone[0] = vertex;
1594: cone[1] = TupleToIndex_Private(dim, vertices, vtmp) + numCells;
1595: PetscCall(PetscPrintf(PETSC_COMM_SELF, " Vertex %" PetscInt_FMT ":", cone[1]));
1596: for (e = 0; e < dim; ++e) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, vtmp[e]));
1597: PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n"));
1598: PetscCall(DMPlexSetCone(dm, cell, cone));
1599: PetscCall(DMPlexSetCellType(dm, cell, DM_POLYTOPE_SEGMENT));
1600: PetscCall(PetscPrintf(PETSC_COMM_SELF, " Edge %" PetscInt_FMT " (%" PetscInt_FMT " %" PetscInt_FMT ")\n", cell, cone[0], cone[1]));
1601: ++cell;
1602: }
1603: for (d = 0; d < dim; ++d) {
1604: for (e = 0; e < dim; ++e) vtmp[e] = vert[e];
1605: vtmp[d] = (vert[d] + vertices[d] - 1) % vertices[d];
1606: supp[s++] = TupleToIndex_Private(dim, vertices, vtmp) * dim + d;
1607: supp[s++] = (vertex - numCells) * dim + d;
1608: PetscCall(DMPlexSetSupport(dm, vertex, supp));
1609: }
1610: PetscCall(DMPlexTensorPointLexicographic_Private(dim, vertices, vert));
1611: }
1612: PetscCall(DMPlexStratify(dm));
1613: /* Build coordinates */
1614: PetscCall(DMGetCoordinateSection(dm, &coordSection));
1615: PetscCall(PetscSectionSetNumFields(coordSection, 1));
1616: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim));
1617: PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices));
1618: for (v = numCells; v < numCells + numVertices; ++v) {
1619: PetscCall(PetscSectionSetDof(coordSection, v, dim));
1620: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim));
1621: }
1622: PetscCall(PetscSectionSetUp(coordSection));
1623: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
1624: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
1625: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
1626: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
1627: PetscCall(VecSetBlockSize(coordinates, dim));
1628: PetscCall(VecSetType(coordinates, VECSTANDARD));
1629: PetscCall(VecGetArray(coordinates, &coords));
1630: for (d = 0; d < dim; ++d) vert[d] = 0;
1631: while (vert[dim - 1] < vertices[dim - 1]) {
1632: const PetscInt vertex = TupleToIndex_Private(dim, vertices, vert);
1634: for (d = 0; d < dim; ++d) coords[vertex * dim + d] = lower[d] + ((upper[d] - lower[d]) / vertices[d]) * vert[d];
1635: PetscCall(PetscPrintf(PETSC_COMM_SELF, "Vertex %" PetscInt_FMT ":", vertex));
1636: for (d = 0; d < dim; ++d) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, vert[d]));
1637: for (d = 0; d < dim; ++d) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %g", (double)PetscRealPart(coords[vertex * dim + d])));
1638: PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n"));
1639: PetscCall(DMPlexTensorPointLexicographic_Private(dim, vertices, vert));
1640: }
1641: PetscCall(VecRestoreArray(coordinates, &coords));
1642: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
1643: PetscCall(VecDestroy(&coordinates));
1644: PetscCall(PetscFree4(vertices, vert, vtmp, supp));
1645: //PetscCall(DMSetPeriodicity(dm, NULL, lower, upper));
1646: // Attach the extent
1647: {
1648: PetscContainer c;
1649: PetscInt *extent;
1651: PetscCall(PetscMalloc1(dim, &extent));
1652: for (PetscInt d = 0; d < dim; ++d) extent[d] = edges[d];
1653: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &c));
1654: PetscCall(PetscContainerSetUserDestroy(c, DestroyExtent_Private));
1655: PetscCall(PetscContainerSetPointer(c, extent));
1656: PetscCall(PetscObjectCompose((PetscObject)dm, "_extent", (PetscObject)c));
1657: PetscCall(PetscContainerDestroy(&c));
1658: }
1659: PetscFunctionReturn(PETSC_SUCCESS);
1660: }
1662: /*@C
1663: DMPlexCreateHypercubicMesh - Creates a periodic mesh on the tensor product of unit intervals using only vertices and edges.
1665: Collective
1667: Input Parameters:
1668: + comm - The communicator for the DM object
1669: . dim - The spatial dimension
1670: . edges - Number of edges per dimension, or `NULL` for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D
1671: . lower - The lower left corner, or `NULL` for (0, 0, 0)
1672: - upper - The upper right corner, or `NULL` for (1, 1, 1)
1674: Output Parameter:
1675: . dm - The DM object
1677: Level: beginner
1679: Note:
1680: If you want to customize this mesh using options, you just need to
1681: .vb
1682: DMCreate(comm, &dm);
1683: DMSetType(dm, DMPLEX);
1684: DMSetFromOptions(dm);
1685: .ve
1686: and use the options on the `DMSetFromOptions()` page.
1688: The vertices are numbered is lexicographic order, and the dim edges exiting a vertex in the positive orthant are number consecutively,
1689: .vb
1690: 18--0-19--2-20--4-18
1691: | | | |
1692: 13 15 17 13
1693: | | | |
1694: 24-12-25-14-26-16-24
1695: | | | |
1696: 7 9 11 7
1697: | | | |
1698: 21--6-22--8-23-10-21
1699: | | | |
1700: 1 3 5 1
1701: | | | |
1702: 18--0-19--2-20--4-18
1703: .ve
1705: .seealso: `DMSetFromOptions()`, `DMPlexCreateFromFile()`, `DMPlexCreateHexCylinderMesh()`, `DMSetType()`, `DMCreate()`
1706: @*/
1707: PetscErrorCode DMPlexCreateHypercubicMesh(MPI_Comm comm, PetscInt dim, const PetscInt edges[], const PetscReal lower[], const PetscReal upper[], DM *dm)
1708: {
1709: PetscInt *edg;
1710: PetscReal *low, *upp;
1711: DMBoundaryType *bdt;
1712: PetscInt d;
1714: PetscFunctionBegin;
1715: PetscCall(DMCreate(comm, dm));
1716: PetscCall(DMSetType(*dm, DMPLEX));
1717: PetscCall(PetscMalloc4(dim, &edg, dim, &low, dim, &upp, dim, &bdt));
1718: for (d = 0; d < dim; ++d) {
1719: edg[d] = edges ? edges[d] : 1;
1720: low[d] = lower ? lower[d] : 0.;
1721: upp[d] = upper ? upper[d] : 1.;
1722: bdt[d] = DM_BOUNDARY_PERIODIC;
1723: }
1724: PetscCall(DMPlexCreateHypercubicMesh_Internal(*dm, dim, low, upp, edg, bdt));
1725: PetscCall(PetscFree4(edg, low, upp, bdt));
1726: PetscFunctionReturn(PETSC_SUCCESS);
1727: }
1729: /*@
1730: DMPlexSetOptionsPrefix - Sets the prefix used for searching for all `DM` options in the database.
1732: Logically Collective
1734: Input Parameters:
1735: + dm - the `DM` context
1736: - prefix - the prefix to prepend to all option names
1738: Level: advanced
1740: Note:
1741: A hyphen (-) must NOT be given at the beginning of the prefix name.
1742: The first character of all runtime options is AUTOMATICALLY the hyphen.
1744: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `SNESSetFromOptions()`
1745: @*/
1746: PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[])
1747: {
1748: DM_Plex *mesh = (DM_Plex *)dm->data;
1750: PetscFunctionBegin;
1752: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dm, prefix));
1753: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)mesh->partitioner, prefix));
1754: PetscFunctionReturn(PETSC_SUCCESS);
1755: }
1757: /* Remap geometry to cylinder
1758: TODO: This only works for a single refinement, then it is broken
1760: Interior square: Linear interpolation is correct
1761: The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing
1762: such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance
1764: phi = arctan(y/x)
1765: d_close = sqrt(1/8 + 1/4 sin^2(phi))
1766: d_far = sqrt(1/2 + sin^2(phi))
1768: so we remap them using
1770: x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close)
1771: y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close)
1773: If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y.
1774: */
1775: 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[])
1776: {
1777: const PetscReal dis = 1.0 / PetscSqrtReal(2.0);
1778: const PetscReal ds2 = 0.5 * dis;
1780: if ((PetscAbsScalar(u[0]) <= ds2) && (PetscAbsScalar(u[1]) <= ds2)) {
1781: f0[0] = u[0];
1782: f0[1] = u[1];
1783: } else {
1784: PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc;
1786: x = PetscRealPart(u[0]);
1787: y = PetscRealPart(u[1]);
1788: phi = PetscAtan2Real(y, x);
1789: sinp = PetscSinReal(phi);
1790: cosp = PetscCosReal(phi);
1791: if ((PetscAbsReal(phi) > PETSC_PI / 4.0) && (PetscAbsReal(phi) < 3.0 * PETSC_PI / 4.0)) {
1792: dc = PetscAbsReal(ds2 / sinp);
1793: df = PetscAbsReal(dis / sinp);
1794: xc = ds2 * x / PetscAbsReal(y);
1795: yc = ds2 * PetscSignReal(y);
1796: } else {
1797: dc = PetscAbsReal(ds2 / cosp);
1798: df = PetscAbsReal(dis / cosp);
1799: xc = ds2 * PetscSignReal(x);
1800: yc = ds2 * y / PetscAbsReal(x);
1801: }
1802: f0[0] = xc + (u[0] - xc) * (1.0 - dc) / (df - dc);
1803: f0[1] = yc + (u[1] - yc) * (1.0 - dc) / (df - dc);
1804: }
1805: f0[2] = u[2];
1806: }
1808: static PetscErrorCode DMPlexCreateHexCylinderMesh_Internal(DM dm, DMBoundaryType periodicZ, PetscInt Nr)
1809: {
1810: const PetscInt dim = 3;
1811: PetscInt numCells, numVertices;
1812: PetscMPIInt rank;
1814: PetscFunctionBegin;
1815: PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0));
1816: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
1817: PetscCall(DMSetDimension(dm, dim));
1818: /* Create topology */
1819: {
1820: PetscInt cone[8], c;
1822: numCells = rank == 0 ? 5 : 0;
1823: numVertices = rank == 0 ? 16 : 0;
1824: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1825: numCells *= 3;
1826: numVertices = rank == 0 ? 24 : 0;
1827: }
1828: PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices));
1829: for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 8));
1830: PetscCall(DMSetUp(dm));
1831: if (rank == 0) {
1832: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1833: cone[0] = 15;
1834: cone[1] = 18;
1835: cone[2] = 17;
1836: cone[3] = 16;
1837: cone[4] = 31;
1838: cone[5] = 32;
1839: cone[6] = 33;
1840: cone[7] = 34;
1841: PetscCall(DMPlexSetCone(dm, 0, cone));
1842: cone[0] = 16;
1843: cone[1] = 17;
1844: cone[2] = 24;
1845: cone[3] = 23;
1846: cone[4] = 32;
1847: cone[5] = 36;
1848: cone[6] = 37;
1849: cone[7] = 33; /* 22 25 26 21 */
1850: PetscCall(DMPlexSetCone(dm, 1, cone));
1851: cone[0] = 18;
1852: cone[1] = 27;
1853: cone[2] = 24;
1854: cone[3] = 17;
1855: cone[4] = 34;
1856: cone[5] = 33;
1857: cone[6] = 37;
1858: cone[7] = 38;
1859: PetscCall(DMPlexSetCone(dm, 2, cone));
1860: cone[0] = 29;
1861: cone[1] = 27;
1862: cone[2] = 18;
1863: cone[3] = 15;
1864: cone[4] = 35;
1865: cone[5] = 31;
1866: cone[6] = 34;
1867: cone[7] = 38;
1868: PetscCall(DMPlexSetCone(dm, 3, cone));
1869: cone[0] = 29;
1870: cone[1] = 15;
1871: cone[2] = 16;
1872: cone[3] = 23;
1873: cone[4] = 35;
1874: cone[5] = 36;
1875: cone[6] = 32;
1876: cone[7] = 31;
1877: PetscCall(DMPlexSetCone(dm, 4, cone));
1879: cone[0] = 31;
1880: cone[1] = 34;
1881: cone[2] = 33;
1882: cone[3] = 32;
1883: cone[4] = 19;
1884: cone[5] = 22;
1885: cone[6] = 21;
1886: cone[7] = 20;
1887: PetscCall(DMPlexSetCone(dm, 5, cone));
1888: cone[0] = 32;
1889: cone[1] = 33;
1890: cone[2] = 37;
1891: cone[3] = 36;
1892: cone[4] = 22;
1893: cone[5] = 25;
1894: cone[6] = 26;
1895: cone[7] = 21;
1896: PetscCall(DMPlexSetCone(dm, 6, cone));
1897: cone[0] = 34;
1898: cone[1] = 38;
1899: cone[2] = 37;
1900: cone[3] = 33;
1901: cone[4] = 20;
1902: cone[5] = 21;
1903: cone[6] = 26;
1904: cone[7] = 28;
1905: PetscCall(DMPlexSetCone(dm, 7, cone));
1906: cone[0] = 35;
1907: cone[1] = 38;
1908: cone[2] = 34;
1909: cone[3] = 31;
1910: cone[4] = 30;
1911: cone[5] = 19;
1912: cone[6] = 20;
1913: cone[7] = 28;
1914: PetscCall(DMPlexSetCone(dm, 8, cone));
1915: cone[0] = 35;
1916: cone[1] = 31;
1917: cone[2] = 32;
1918: cone[3] = 36;
1919: cone[4] = 30;
1920: cone[5] = 25;
1921: cone[6] = 22;
1922: cone[7] = 19;
1923: PetscCall(DMPlexSetCone(dm, 9, cone));
1925: cone[0] = 19;
1926: cone[1] = 20;
1927: cone[2] = 21;
1928: cone[3] = 22;
1929: cone[4] = 15;
1930: cone[5] = 16;
1931: cone[6] = 17;
1932: cone[7] = 18;
1933: PetscCall(DMPlexSetCone(dm, 10, cone));
1934: cone[0] = 22;
1935: cone[1] = 21;
1936: cone[2] = 26;
1937: cone[3] = 25;
1938: cone[4] = 16;
1939: cone[5] = 23;
1940: cone[6] = 24;
1941: cone[7] = 17;
1942: PetscCall(DMPlexSetCone(dm, 11, cone));
1943: cone[0] = 20;
1944: cone[1] = 28;
1945: cone[2] = 26;
1946: cone[3] = 21;
1947: cone[4] = 18;
1948: cone[5] = 17;
1949: cone[6] = 24;
1950: cone[7] = 27;
1951: PetscCall(DMPlexSetCone(dm, 12, cone));
1952: cone[0] = 30;
1953: cone[1] = 28;
1954: cone[2] = 20;
1955: cone[3] = 19;
1956: cone[4] = 29;
1957: cone[5] = 15;
1958: cone[6] = 18;
1959: cone[7] = 27;
1960: PetscCall(DMPlexSetCone(dm, 13, cone));
1961: cone[0] = 30;
1962: cone[1] = 19;
1963: cone[2] = 22;
1964: cone[3] = 25;
1965: cone[4] = 29;
1966: cone[5] = 23;
1967: cone[6] = 16;
1968: cone[7] = 15;
1969: PetscCall(DMPlexSetCone(dm, 14, cone));
1970: } else {
1971: cone[0] = 5;
1972: cone[1] = 8;
1973: cone[2] = 7;
1974: cone[3] = 6;
1975: cone[4] = 9;
1976: cone[5] = 12;
1977: cone[6] = 11;
1978: cone[7] = 10;
1979: PetscCall(DMPlexSetCone(dm, 0, cone));
1980: cone[0] = 6;
1981: cone[1] = 7;
1982: cone[2] = 14;
1983: cone[3] = 13;
1984: cone[4] = 12;
1985: cone[5] = 15;
1986: cone[6] = 16;
1987: cone[7] = 11;
1988: PetscCall(DMPlexSetCone(dm, 1, cone));
1989: cone[0] = 8;
1990: cone[1] = 17;
1991: cone[2] = 14;
1992: cone[3] = 7;
1993: cone[4] = 10;
1994: cone[5] = 11;
1995: cone[6] = 16;
1996: cone[7] = 18;
1997: PetscCall(DMPlexSetCone(dm, 2, cone));
1998: cone[0] = 19;
1999: cone[1] = 17;
2000: cone[2] = 8;
2001: cone[3] = 5;
2002: cone[4] = 20;
2003: cone[5] = 9;
2004: cone[6] = 10;
2005: cone[7] = 18;
2006: PetscCall(DMPlexSetCone(dm, 3, cone));
2007: cone[0] = 19;
2008: cone[1] = 5;
2009: cone[2] = 6;
2010: cone[3] = 13;
2011: cone[4] = 20;
2012: cone[5] = 15;
2013: cone[6] = 12;
2014: cone[7] = 9;
2015: PetscCall(DMPlexSetCone(dm, 4, cone));
2016: }
2017: }
2018: PetscCall(DMPlexSymmetrize(dm));
2019: PetscCall(DMPlexStratify(dm));
2020: }
2021: /* Create cube geometry */
2022: {
2023: Vec coordinates;
2024: PetscSection coordSection;
2025: PetscScalar *coords;
2026: PetscInt coordSize, v;
2027: const PetscReal dis = 1.0 / PetscSqrtReal(2.0);
2028: const PetscReal ds2 = dis / 2.0;
2030: /* Build coordinates */
2031: PetscCall(DMGetCoordinateSection(dm, &coordSection));
2032: PetscCall(PetscSectionSetNumFields(coordSection, 1));
2033: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim));
2034: PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices));
2035: for (v = numCells; v < numCells + numVertices; ++v) {
2036: PetscCall(PetscSectionSetDof(coordSection, v, dim));
2037: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim));
2038: }
2039: PetscCall(PetscSectionSetUp(coordSection));
2040: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
2041: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
2042: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
2043: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
2044: PetscCall(VecSetBlockSize(coordinates, dim));
2045: PetscCall(VecSetType(coordinates, VECSTANDARD));
2046: PetscCall(VecGetArray(coordinates, &coords));
2047: if (rank == 0) {
2048: coords[0 * dim + 0] = -ds2;
2049: coords[0 * dim + 1] = -ds2;
2050: coords[0 * dim + 2] = 0.0;
2051: coords[1 * dim + 0] = ds2;
2052: coords[1 * dim + 1] = -ds2;
2053: coords[1 * dim + 2] = 0.0;
2054: coords[2 * dim + 0] = ds2;
2055: coords[2 * dim + 1] = ds2;
2056: coords[2 * dim + 2] = 0.0;
2057: coords[3 * dim + 0] = -ds2;
2058: coords[3 * dim + 1] = ds2;
2059: coords[3 * dim + 2] = 0.0;
2060: coords[4 * dim + 0] = -ds2;
2061: coords[4 * dim + 1] = -ds2;
2062: coords[4 * dim + 2] = 1.0;
2063: coords[5 * dim + 0] = -ds2;
2064: coords[5 * dim + 1] = ds2;
2065: coords[5 * dim + 2] = 1.0;
2066: coords[6 * dim + 0] = ds2;
2067: coords[6 * dim + 1] = ds2;
2068: coords[6 * dim + 2] = 1.0;
2069: coords[7 * dim + 0] = ds2;
2070: coords[7 * dim + 1] = -ds2;
2071: coords[7 * dim + 2] = 1.0;
2072: coords[8 * dim + 0] = dis;
2073: coords[8 * dim + 1] = -dis;
2074: coords[8 * dim + 2] = 0.0;
2075: coords[9 * dim + 0] = dis;
2076: coords[9 * dim + 1] = dis;
2077: coords[9 * dim + 2] = 0.0;
2078: coords[10 * dim + 0] = dis;
2079: coords[10 * dim + 1] = -dis;
2080: coords[10 * dim + 2] = 1.0;
2081: coords[11 * dim + 0] = dis;
2082: coords[11 * dim + 1] = dis;
2083: coords[11 * dim + 2] = 1.0;
2084: coords[12 * dim + 0] = -dis;
2085: coords[12 * dim + 1] = dis;
2086: coords[12 * dim + 2] = 0.0;
2087: coords[13 * dim + 0] = -dis;
2088: coords[13 * dim + 1] = dis;
2089: coords[13 * dim + 2] = 1.0;
2090: coords[14 * dim + 0] = -dis;
2091: coords[14 * dim + 1] = -dis;
2092: coords[14 * dim + 2] = 0.0;
2093: coords[15 * dim + 0] = -dis;
2094: coords[15 * dim + 1] = -dis;
2095: coords[15 * dim + 2] = 1.0;
2096: if (periodicZ == DM_BOUNDARY_PERIODIC) {
2097: /* 15 31 19 */ coords[16 * dim + 0] = -ds2;
2098: coords[16 * dim + 1] = -ds2;
2099: coords[16 * dim + 2] = 0.5;
2100: /* 16 32 22 */ coords[17 * dim + 0] = ds2;
2101: coords[17 * dim + 1] = -ds2;
2102: coords[17 * dim + 2] = 0.5;
2103: /* 17 33 21 */ coords[18 * dim + 0] = ds2;
2104: coords[18 * dim + 1] = ds2;
2105: coords[18 * dim + 2] = 0.5;
2106: /* 18 34 20 */ coords[19 * dim + 0] = -ds2;
2107: coords[19 * dim + 1] = ds2;
2108: coords[19 * dim + 2] = 0.5;
2109: /* 29 35 30 */ coords[20 * dim + 0] = -dis;
2110: coords[20 * dim + 1] = -dis;
2111: coords[20 * dim + 2] = 0.5;
2112: /* 23 36 25 */ coords[21 * dim + 0] = dis;
2113: coords[21 * dim + 1] = -dis;
2114: coords[21 * dim + 2] = 0.5;
2115: /* 24 37 26 */ coords[22 * dim + 0] = dis;
2116: coords[22 * dim + 1] = dis;
2117: coords[22 * dim + 2] = 0.5;
2118: /* 27 38 28 */ coords[23 * dim + 0] = -dis;
2119: coords[23 * dim + 1] = dis;
2120: coords[23 * dim + 2] = 0.5;
2121: }
2122: }
2123: PetscCall(VecRestoreArray(coordinates, &coords));
2124: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
2125: PetscCall(VecDestroy(&coordinates));
2126: }
2127: /* Create periodicity */
2128: if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) {
2129: PetscReal L[3] = {-1., -1., 0.};
2130: PetscReal maxCell[3] = {-1., -1., 0.};
2131: PetscReal lower[3] = {0.0, 0.0, 0.0};
2132: PetscReal upper[3] = {1.0, 1.0, 1.5};
2133: PetscInt numZCells = 3;
2135: L[2] = upper[2] - lower[2];
2136: maxCell[2] = 1.1 * (L[2] / numZCells);
2137: PetscCall(DMSetPeriodicity(dm, maxCell, lower, L));
2138: }
2139: {
2140: DM cdm;
2141: PetscDS cds;
2142: PetscScalar c[2] = {1.0, 1.0};
2144: PetscCall(DMPlexCreateCoordinateSpace(dm, 1, PETSC_TRUE, NULL));
2145: PetscCall(DMGetCoordinateDM(dm, &cdm));
2146: PetscCall(DMGetDS(cdm, &cds));
2147: PetscCall(PetscDSSetConstants(cds, 2, c));
2148: }
2149: PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0));
2151: /* Wait for coordinate creation before doing in-place modification */
2152: PetscCall(DMPlexInterpolateInPlace_Internal(dm));
2154: char oldprefix[PETSC_MAX_PATH_LEN];
2155: const char *prefix;
2157: PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm, &prefix));
2158: PetscCall(PetscStrncpy(oldprefix, prefix, PETSC_MAX_PATH_LEN));
2159: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dm, "petsc_cyl_ref_"));
2160: for (PetscInt r = 0; r < PetscMax(0, Nr); ++r) {
2161: DM rdm;
2163: PetscCall(DMRefine(dm, PetscObjectComm((PetscObject)dm), &rdm));
2164: PetscCall(DMPlexReplace_Internal(dm, &rdm));
2165: }
2166: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dm, oldprefix));
2167: PetscCall(DMPlexRemapGeometry(dm, 0.0, snapToCylinder));
2169: DMLabel bdlabel, edgelabel;
2170: IS faceIS;
2171: const PetscInt *faces;
2172: PetscInt Nf;
2174: PetscCall(DMCreateLabel(dm, "marker"));
2175: PetscCall(DMGetLabel(dm, "marker", &bdlabel));
2176: PetscCall(DMCreateLabel(dm, "generatrix"));
2177: PetscCall(DMGetLabel(dm, "generatrix", &edgelabel));
2178: PetscCall(DMPlexMarkBoundaryFaces(dm, PETSC_DETERMINE, bdlabel));
2179: // Remove faces on top and bottom
2180: PetscCall(DMLabelGetStratumIS(bdlabel, 1, &faceIS));
2181: if (faceIS) {
2182: PetscCall(ISGetLocalSize(faceIS, &Nf));
2183: PetscCall(ISGetIndices(faceIS, &faces));
2184: for (PetscInt f = 0; f < Nf; ++f) {
2185: PetscReal vol, normal[3];
2187: PetscCall(DMPlexComputeCellGeometryFVM(dm, faces[f], &vol, NULL, normal));
2188: if (PetscAbsReal(normal[2]) < PETSC_SMALL) PetscCall(DMLabelSetValue(edgelabel, faces[f], 1));
2189: }
2190: PetscCall(ISRestoreIndices(faceIS, &faces));
2191: PetscCall(ISDestroy(&faceIS));
2192: }
2193: PetscCall(DMPlexLabelComplete(dm, bdlabel));
2194: PetscCall(DMPlexLabelComplete(dm, edgelabel));
2195: PetscFunctionReturn(PETSC_SUCCESS);
2196: }
2198: /*@
2199: DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra.
2201: Collective
2203: Input Parameters:
2204: + comm - The communicator for the `DM` object
2205: . periodicZ - The boundary type for the Z direction
2206: - Nr - The number of refinements to carry out
2208: Output Parameter:
2209: . dm - The `DM` object
2211: Level: beginner
2213: Note:
2214: Here is the output numbering looking from the bottom of the cylinder\:
2215: .vb
2216: 17-----14
2217: | |
2218: | 2 |
2219: | |
2220: 17-----8-----7-----14
2221: | | | |
2222: | 3 | 0 | 1 |
2223: | | | |
2224: 19-----5-----6-----13
2225: | |
2226: | 4 |
2227: | |
2228: 19-----13
2230: and up through the top
2232: 18-----16
2233: | |
2234: | 2 |
2235: | |
2236: 18----10----11-----16
2237: | | | |
2238: | 3 | 0 | 1 |
2239: | | | |
2240: 20-----9----12-----15
2241: | |
2242: | 4 |
2243: | |
2244: 20-----15
2245: .ve
2247: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()`
2248: @*/
2249: PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, DMBoundaryType periodicZ, PetscInt Nr, DM *dm)
2250: {
2251: PetscFunctionBegin;
2252: PetscAssertPointer(dm, 4);
2253: PetscCall(DMCreate(comm, dm));
2254: PetscCall(DMSetType(*dm, DMPLEX));
2255: PetscCall(DMPlexCreateHexCylinderMesh_Internal(*dm, periodicZ, Nr));
2256: PetscFunctionReturn(PETSC_SUCCESS);
2257: }
2259: static PetscErrorCode DMPlexCreateWedgeCylinderMesh_Internal(DM dm, PetscInt n, PetscBool interpolate)
2260: {
2261: const PetscInt dim = 3;
2262: PetscInt numCells, numVertices, v;
2263: PetscMPIInt rank;
2265: PetscFunctionBegin;
2266: PetscCheck(n >= 0, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %" PetscInt_FMT " cannot be negative", n);
2267: PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0));
2268: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
2269: PetscCall(DMSetDimension(dm, dim));
2270: /* Must create the celltype label here so that we do not automatically try to compute the types */
2271: PetscCall(DMCreateLabel(dm, "celltype"));
2272: /* Create topology */
2273: {
2274: PetscInt cone[6], c;
2276: numCells = rank == 0 ? n : 0;
2277: numVertices = rank == 0 ? 2 * (n + 1) : 0;
2278: PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices));
2279: for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 6));
2280: PetscCall(DMSetUp(dm));
2281: for (c = 0; c < numCells; c++) {
2282: cone[0] = c + n * 1;
2283: cone[1] = (c + 1) % n + n * 1;
2284: cone[2] = 0 + 3 * n;
2285: cone[3] = c + n * 2;
2286: cone[4] = (c + 1) % n + n * 2;
2287: cone[5] = 1 + 3 * n;
2288: PetscCall(DMPlexSetCone(dm, c, cone));
2289: PetscCall(DMPlexSetCellType(dm, c, DM_POLYTOPE_TRI_PRISM_TENSOR));
2290: }
2291: PetscCall(DMPlexSymmetrize(dm));
2292: PetscCall(DMPlexStratify(dm));
2293: }
2294: for (v = numCells; v < numCells + numVertices; ++v) PetscCall(DMPlexSetCellType(dm, v, DM_POLYTOPE_POINT));
2295: /* Create cylinder geometry */
2296: {
2297: Vec coordinates;
2298: PetscSection coordSection;
2299: PetscScalar *coords;
2300: PetscInt coordSize, c;
2302: /* Build coordinates */
2303: PetscCall(DMGetCoordinateSection(dm, &coordSection));
2304: PetscCall(PetscSectionSetNumFields(coordSection, 1));
2305: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim));
2306: PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices));
2307: for (v = numCells; v < numCells + numVertices; ++v) {
2308: PetscCall(PetscSectionSetDof(coordSection, v, dim));
2309: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim));
2310: }
2311: PetscCall(PetscSectionSetUp(coordSection));
2312: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
2313: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
2314: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
2315: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
2316: PetscCall(VecSetBlockSize(coordinates, dim));
2317: PetscCall(VecSetType(coordinates, VECSTANDARD));
2318: PetscCall(VecGetArray(coordinates, &coords));
2319: for (c = 0; c < numCells; c++) {
2320: coords[(c + 0 * n) * dim + 0] = PetscCosReal(2.0 * c * PETSC_PI / n);
2321: coords[(c + 0 * n) * dim + 1] = PetscSinReal(2.0 * c * PETSC_PI / n);
2322: coords[(c + 0 * n) * dim + 2] = 1.0;
2323: coords[(c + 1 * n) * dim + 0] = PetscCosReal(2.0 * c * PETSC_PI / n);
2324: coords[(c + 1 * n) * dim + 1] = PetscSinReal(2.0 * c * PETSC_PI / n);
2325: coords[(c + 1 * n) * dim + 2] = 0.0;
2326: }
2327: if (rank == 0) {
2328: coords[(2 * n + 0) * dim + 0] = 0.0;
2329: coords[(2 * n + 0) * dim + 1] = 0.0;
2330: coords[(2 * n + 0) * dim + 2] = 1.0;
2331: coords[(2 * n + 1) * dim + 0] = 0.0;
2332: coords[(2 * n + 1) * dim + 1] = 0.0;
2333: coords[(2 * n + 1) * dim + 2] = 0.0;
2334: }
2335: PetscCall(VecRestoreArray(coordinates, &coords));
2336: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
2337: PetscCall(VecDestroy(&coordinates));
2338: }
2339: PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0));
2340: /* Interpolate */
2341: if (interpolate) PetscCall(DMPlexInterpolateInPlace_Internal(dm));
2342: PetscFunctionReturn(PETSC_SUCCESS);
2343: }
2345: /*@
2346: DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges.
2348: Collective
2350: Input Parameters:
2351: + comm - The communicator for the `DM` object
2352: . n - The number of wedges around the origin
2353: - interpolate - Create edges and faces
2355: Output Parameter:
2356: . dm - The `DM` object
2358: Level: beginner
2360: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateHexCylinderMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()`
2361: @*/
2362: PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm)
2363: {
2364: PetscFunctionBegin;
2365: PetscAssertPointer(dm, 4);
2366: PetscCall(DMCreate(comm, dm));
2367: PetscCall(DMSetType(*dm, DMPLEX));
2368: PetscCall(DMPlexCreateWedgeCylinderMesh_Internal(*dm, n, interpolate));
2369: PetscFunctionReturn(PETSC_SUCCESS);
2370: }
2372: static inline PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
2373: {
2374: PetscReal prod = 0.0;
2375: PetscInt i;
2376: for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]);
2377: return PetscSqrtReal(prod);
2378: }
2380: static inline PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
2381: {
2382: PetscReal prod = 0.0;
2383: PetscInt i;
2384: for (i = 0; i < dim; ++i) prod += x[i] * y[i];
2385: return prod;
2386: }
2388: /* The first constant is the sphere radius */
2389: 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[])
2390: {
2391: PetscReal r = PetscRealPart(constants[0]);
2392: PetscReal norm2 = 0.0, fac;
2393: PetscInt n = uOff[1] - uOff[0], d;
2395: for (d = 0; d < n; ++d) norm2 += PetscSqr(PetscRealPart(u[d]));
2396: fac = r / PetscSqrtReal(norm2);
2397: for (d = 0; d < n; ++d) f0[d] = u[d] * fac;
2398: }
2400: static PetscErrorCode DMPlexCreateSphereMesh_Internal(DM dm, PetscInt dim, PetscBool simplex, PetscReal R)
2401: {
2402: const PetscInt embedDim = dim + 1;
2403: PetscSection coordSection;
2404: Vec coordinates;
2405: PetscScalar *coords;
2406: PetscReal *coordsIn;
2407: PetscInt numCells, numEdges, numVerts = 0, firstVertex = 0, v, firstEdge, coordSize, d, e;
2408: PetscMPIInt rank;
2410: PetscFunctionBegin;
2412: PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0));
2413: PetscCall(DMSetDimension(dm, dim));
2414: PetscCall(DMSetCoordinateDim(dm, dim + 1));
2415: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
2416: switch (dim) {
2417: case 1:
2418: numCells = 16;
2419: numVerts = numCells;
2421: // Build Topology
2422: PetscCall(DMPlexSetChart(dm, 0, numCells + numVerts));
2423: for (PetscInt c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, embedDim));
2424: PetscCall(DMSetUp(dm));
2425: for (PetscInt c = 0; c < numCells; ++c) {
2426: PetscInt cone[2];
2428: cone[0] = c + numCells;
2429: cone[1] = (c + 1) % numVerts + numCells;
2430: PetscCall(DMPlexSetCone(dm, c, cone));
2431: }
2432: PetscCall(DMPlexSymmetrize(dm));
2433: PetscCall(DMPlexStratify(dm));
2434: PetscCall(PetscMalloc1(numVerts * embedDim, &coordsIn));
2435: for (PetscInt v = 0; v < numVerts; ++v) {
2436: const PetscReal rad = 2. * PETSC_PI * v / numVerts;
2438: coordsIn[v * embedDim + 0] = PetscCosReal(rad);
2439: coordsIn[v * embedDim + 1] = PetscSinReal(rad);
2440: }
2441: break;
2442: case 2:
2443: if (simplex) {
2444: const PetscReal radius = PetscSqrtReal(1 + PETSC_PHI * PETSC_PHI) / (1.0 + PETSC_PHI);
2445: const PetscReal edgeLen = 2.0 / (1.0 + PETSC_PHI) * (R / radius);
2446: const PetscInt degree = 5;
2447: PetscReal vertex[3] = {0.0, 1.0 / (1.0 + PETSC_PHI), PETSC_PHI / (1.0 + PETSC_PHI)};
2448: PetscInt s[3] = {1, 1, 1};
2449: PetscInt cone[3];
2450: PetscInt *graph;
2452: vertex[0] *= R / radius;
2453: vertex[1] *= R / radius;
2454: vertex[2] *= R / radius;
2455: numCells = rank == 0 ? 20 : 0;
2456: numVerts = rank == 0 ? 12 : 0;
2457: firstVertex = numCells;
2458: /* Use icosahedron, which for a R-sphere has coordinates which are all cyclic permutations of
2460: (0, \pm 1/\phi+1, \pm \phi/\phi+1)
2462: where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
2463: length is then given by 2/(1+\phi) = 2 * 0.38197 = 0.76393.
2464: */
2465: /* Construct vertices */
2466: PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn));
2467: if (rank == 0) {
2468: for (PetscInt p = 0, i = 0; p < embedDim; ++p) {
2469: for (s[1] = -1; s[1] < 2; s[1] += 2) {
2470: for (s[2] = -1; s[2] < 2; s[2] += 2) {
2471: for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[(d + p) % embedDim] * vertex[(d + p) % embedDim];
2472: ++i;
2473: }
2474: }
2475: }
2476: }
2477: /* Construct graph */
2478: PetscCall(PetscCalloc1(numVerts * numVerts, &graph));
2479: for (PetscInt i = 0; i < numVerts; ++i) {
2480: PetscInt k = 0;
2481: for (PetscInt j = 0; j < numVerts; ++j) {
2482: if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i * embedDim], &coordsIn[j * embedDim]) - edgeLen) < PETSC_SMALL) {
2483: graph[i * numVerts + j] = 1;
2484: ++k;
2485: }
2486: }
2487: PetscCheck(k == degree, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid icosahedron, vertex %" PetscInt_FMT " degree %" PetscInt_FMT " != %" PetscInt_FMT, i, k, degree);
2488: }
2489: /* Build Topology */
2490: PetscCall(DMPlexSetChart(dm, 0, numCells + numVerts));
2491: for (PetscInt c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, embedDim));
2492: PetscCall(DMSetUp(dm)); /* Allocate space for cones */
2493: /* Cells */
2494: for (PetscInt i = 0, c = 0; i < numVerts; ++i) {
2495: for (PetscInt j = 0; j < i; ++j) {
2496: for (PetscInt k = 0; k < j; ++k) {
2497: if (graph[i * numVerts + j] && graph[j * numVerts + k] && graph[k * numVerts + i]) {
2498: cone[0] = firstVertex + i;
2499: cone[1] = firstVertex + j;
2500: cone[2] = firstVertex + k;
2501: /* Check orientation */
2502: {
2503: const PetscInt epsilon[3][3][3] = {
2504: {{0, 0, 0}, {0, 0, 1}, {0, -1, 0}},
2505: {{0, 0, -1}, {0, 0, 0}, {1, 0, 0} },
2506: {{0, 1, 0}, {-1, 0, 0}, {0, 0, 0} }
2507: };
2508: PetscReal normal[3];
2509: PetscInt e, f;
2511: for (d = 0; d < embedDim; ++d) {
2512: normal[d] = 0.0;
2513: for (e = 0; e < embedDim; ++e) {
2514: 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]);
2515: }
2516: }
2517: if (DotReal(embedDim, normal, &coordsIn[i * embedDim]) < 0) {
2518: PetscInt tmp = cone[1];
2519: cone[1] = cone[2];
2520: cone[2] = tmp;
2521: }
2522: }
2523: PetscCall(DMPlexSetCone(dm, c++, cone));
2524: }
2525: }
2526: }
2527: }
2528: PetscCall(DMPlexSymmetrize(dm));
2529: PetscCall(DMPlexStratify(dm));
2530: PetscCall(PetscFree(graph));
2531: } else {
2532: /*
2533: 12-21--13
2534: | |
2535: 25 4 24
2536: | |
2537: 12-25--9-16--8-24--13
2538: | | | |
2539: 23 5 17 0 15 3 22
2540: | | | |
2541: 10-20--6-14--7-19--11
2542: | |
2543: 20 1 19
2544: | |
2545: 10-18--11
2546: | |
2547: 23 2 22
2548: | |
2549: 12-21--13
2550: */
2551: PetscInt cone[4], ornt[4];
2553: numCells = rank == 0 ? 6 : 0;
2554: numEdges = rank == 0 ? 12 : 0;
2555: numVerts = rank == 0 ? 8 : 0;
2556: firstVertex = numCells;
2557: firstEdge = numCells + numVerts;
2558: /* Build Topology */
2559: PetscCall(DMPlexSetChart(dm, 0, numCells + numEdges + numVerts));
2560: for (PetscInt c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 4));
2561: for (e = firstEdge; e < firstEdge + numEdges; ++e) PetscCall(DMPlexSetConeSize(dm, e, 2));
2562: PetscCall(DMSetUp(dm)); /* Allocate space for cones */
2563: if (rank == 0) {
2564: /* Cell 0 */
2565: cone[0] = 14;
2566: cone[1] = 15;
2567: cone[2] = 16;
2568: cone[3] = 17;
2569: PetscCall(DMPlexSetCone(dm, 0, cone));
2570: ornt[0] = 0;
2571: ornt[1] = 0;
2572: ornt[2] = 0;
2573: ornt[3] = 0;
2574: PetscCall(DMPlexSetConeOrientation(dm, 0, ornt));
2575: /* Cell 1 */
2576: cone[0] = 18;
2577: cone[1] = 19;
2578: cone[2] = 14;
2579: cone[3] = 20;
2580: PetscCall(DMPlexSetCone(dm, 1, cone));
2581: ornt[0] = 0;
2582: ornt[1] = 0;
2583: ornt[2] = -1;
2584: ornt[3] = 0;
2585: PetscCall(DMPlexSetConeOrientation(dm, 1, ornt));
2586: /* Cell 2 */
2587: cone[0] = 21;
2588: cone[1] = 22;
2589: cone[2] = 18;
2590: cone[3] = 23;
2591: PetscCall(DMPlexSetCone(dm, 2, cone));
2592: ornt[0] = 0;
2593: ornt[1] = 0;
2594: ornt[2] = -1;
2595: ornt[3] = 0;
2596: PetscCall(DMPlexSetConeOrientation(dm, 2, ornt));
2597: /* Cell 3 */
2598: cone[0] = 19;
2599: cone[1] = 22;
2600: cone[2] = 24;
2601: cone[3] = 15;
2602: PetscCall(DMPlexSetCone(dm, 3, cone));
2603: ornt[0] = -1;
2604: ornt[1] = -1;
2605: ornt[2] = 0;
2606: ornt[3] = -1;
2607: PetscCall(DMPlexSetConeOrientation(dm, 3, ornt));
2608: /* Cell 4 */
2609: cone[0] = 16;
2610: cone[1] = 24;
2611: cone[2] = 21;
2612: cone[3] = 25;
2613: PetscCall(DMPlexSetCone(dm, 4, cone));
2614: ornt[0] = -1;
2615: ornt[1] = -1;
2616: ornt[2] = -1;
2617: ornt[3] = 0;
2618: PetscCall(DMPlexSetConeOrientation(dm, 4, ornt));
2619: /* Cell 5 */
2620: cone[0] = 20;
2621: cone[1] = 17;
2622: cone[2] = 25;
2623: cone[3] = 23;
2624: PetscCall(DMPlexSetCone(dm, 5, cone));
2625: ornt[0] = -1;
2626: ornt[1] = -1;
2627: ornt[2] = -1;
2628: ornt[3] = -1;
2629: PetscCall(DMPlexSetConeOrientation(dm, 5, ornt));
2630: /* Edges */
2631: cone[0] = 6;
2632: cone[1] = 7;
2633: PetscCall(DMPlexSetCone(dm, 14, cone));
2634: cone[0] = 7;
2635: cone[1] = 8;
2636: PetscCall(DMPlexSetCone(dm, 15, cone));
2637: cone[0] = 8;
2638: cone[1] = 9;
2639: PetscCall(DMPlexSetCone(dm, 16, cone));
2640: cone[0] = 9;
2641: cone[1] = 6;
2642: PetscCall(DMPlexSetCone(dm, 17, cone));
2643: cone[0] = 10;
2644: cone[1] = 11;
2645: PetscCall(DMPlexSetCone(dm, 18, cone));
2646: cone[0] = 11;
2647: cone[1] = 7;
2648: PetscCall(DMPlexSetCone(dm, 19, cone));
2649: cone[0] = 6;
2650: cone[1] = 10;
2651: PetscCall(DMPlexSetCone(dm, 20, cone));
2652: cone[0] = 12;
2653: cone[1] = 13;
2654: PetscCall(DMPlexSetCone(dm, 21, cone));
2655: cone[0] = 13;
2656: cone[1] = 11;
2657: PetscCall(DMPlexSetCone(dm, 22, cone));
2658: cone[0] = 10;
2659: cone[1] = 12;
2660: PetscCall(DMPlexSetCone(dm, 23, cone));
2661: cone[0] = 13;
2662: cone[1] = 8;
2663: PetscCall(DMPlexSetCone(dm, 24, cone));
2664: cone[0] = 12;
2665: cone[1] = 9;
2666: PetscCall(DMPlexSetCone(dm, 25, cone));
2667: }
2668: PetscCall(DMPlexSymmetrize(dm));
2669: PetscCall(DMPlexStratify(dm));
2670: /* Build coordinates */
2671: PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn));
2672: if (rank == 0) {
2673: coordsIn[0 * embedDim + 0] = -R;
2674: coordsIn[0 * embedDim + 1] = R;
2675: coordsIn[0 * embedDim + 2] = -R;
2676: coordsIn[1 * embedDim + 0] = R;
2677: coordsIn[1 * embedDim + 1] = R;
2678: coordsIn[1 * embedDim + 2] = -R;
2679: coordsIn[2 * embedDim + 0] = R;
2680: coordsIn[2 * embedDim + 1] = -R;
2681: coordsIn[2 * embedDim + 2] = -R;
2682: coordsIn[3 * embedDim + 0] = -R;
2683: coordsIn[3 * embedDim + 1] = -R;
2684: coordsIn[3 * embedDim + 2] = -R;
2685: coordsIn[4 * embedDim + 0] = -R;
2686: coordsIn[4 * embedDim + 1] = R;
2687: coordsIn[4 * embedDim + 2] = R;
2688: coordsIn[5 * embedDim + 0] = R;
2689: coordsIn[5 * embedDim + 1] = R;
2690: coordsIn[5 * embedDim + 2] = R;
2691: coordsIn[6 * embedDim + 0] = -R;
2692: coordsIn[6 * embedDim + 1] = -R;
2693: coordsIn[6 * embedDim + 2] = R;
2694: coordsIn[7 * embedDim + 0] = R;
2695: coordsIn[7 * embedDim + 1] = -R;
2696: coordsIn[7 * embedDim + 2] = R;
2697: }
2698: }
2699: break;
2700: case 3:
2701: if (simplex) {
2702: const PetscReal edgeLen = 1.0 / PETSC_PHI;
2703: PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5};
2704: PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0};
2705: PetscReal vertexC[4] = {0.5, 0.5 * PETSC_PHI, 0.5 / PETSC_PHI, 0.0};
2706: const PetscInt degree = 12;
2707: PetscInt s[4] = {1, 1, 1};
2708: PetscInt evenPerm[12][4] = {
2709: {0, 1, 2, 3},
2710: {0, 2, 3, 1},
2711: {0, 3, 1, 2},
2712: {1, 0, 3, 2},
2713: {1, 2, 0, 3},
2714: {1, 3, 2, 0},
2715: {2, 0, 1, 3},
2716: {2, 1, 3, 0},
2717: {2, 3, 0, 1},
2718: {3, 0, 2, 1},
2719: {3, 1, 0, 2},
2720: {3, 2, 1, 0}
2721: };
2722: PetscInt cone[4];
2723: PetscInt *graph, p, i, j, k, l;
2725: vertexA[0] *= R;
2726: vertexA[1] *= R;
2727: vertexA[2] *= R;
2728: vertexA[3] *= R;
2729: vertexB[0] *= R;
2730: vertexB[1] *= R;
2731: vertexB[2] *= R;
2732: vertexB[3] *= R;
2733: vertexC[0] *= R;
2734: vertexC[1] *= R;
2735: vertexC[2] *= R;
2736: vertexC[3] *= R;
2737: numCells = rank == 0 ? 600 : 0;
2738: numVerts = rank == 0 ? 120 : 0;
2739: firstVertex = numCells;
2740: /* Use the 600-cell, which for a unit sphere has coordinates which are
2742: 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16
2743: (\pm 1, 0, 0, 0) all cyclic permutations 8
2744: 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96
2746: where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
2747: length is then given by 1/\phi = 0.61803.
2749: http://buzzard.pugetsound.edu/sage-practice/ch03s03.html
2750: http://mathworld.wolfram.com/600-Cell.html
2751: */
2752: /* Construct vertices */
2753: PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn));
2754: i = 0;
2755: if (rank == 0) {
2756: for (s[0] = -1; s[0] < 2; s[0] += 2) {
2757: for (s[1] = -1; s[1] < 2; s[1] += 2) {
2758: for (s[2] = -1; s[2] < 2; s[2] += 2) {
2759: for (s[3] = -1; s[3] < 2; s[3] += 2) {
2760: for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[d] * vertexA[d];
2761: ++i;
2762: }
2763: }
2764: }
2765: }
2766: for (p = 0; p < embedDim; ++p) {
2767: s[1] = s[2] = s[3] = 1;
2768: for (s[0] = -1; s[0] < 2; s[0] += 2) {
2769: for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[(d + p) % embedDim] * vertexB[(d + p) % embedDim];
2770: ++i;
2771: }
2772: }
2773: for (p = 0; p < 12; ++p) {
2774: s[3] = 1;
2775: for (s[0] = -1; s[0] < 2; s[0] += 2) {
2776: for (s[1] = -1; s[1] < 2; s[1] += 2) {
2777: for (s[2] = -1; s[2] < 2; s[2] += 2) {
2778: for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[evenPerm[p][d]] * vertexC[evenPerm[p][d]];
2779: ++i;
2780: }
2781: }
2782: }
2783: }
2784: }
2785: PetscCheck(i == numVerts, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertices %" PetscInt_FMT " != %" PetscInt_FMT, i, numVerts);
2786: /* Construct graph */
2787: PetscCall(PetscCalloc1(numVerts * numVerts, &graph));
2788: for (i = 0; i < numVerts; ++i) {
2789: for (j = 0, k = 0; j < numVerts; ++j) {
2790: if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i * embedDim], &coordsIn[j * embedDim]) - edgeLen) < PETSC_SMALL) {
2791: graph[i * numVerts + j] = 1;
2792: ++k;
2793: }
2794: }
2795: PetscCheck(k == degree, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertex %" PetscInt_FMT " degree %" PetscInt_FMT " != %" PetscInt_FMT, i, k, degree);
2796: }
2797: /* Build Topology */
2798: PetscCall(DMPlexSetChart(dm, 0, numCells + numVerts));
2799: for (PetscInt c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, embedDim));
2800: PetscCall(DMSetUp(dm)); /* Allocate space for cones */
2801: /* Cells */
2802: if (rank == 0) {
2803: for (PetscInt i = 0, c = 0; i < numVerts; ++i) {
2804: for (j = 0; j < i; ++j) {
2805: for (k = 0; k < j; ++k) {
2806: for (l = 0; l < k; ++l) {
2807: 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]) {
2808: cone[0] = firstVertex + i;
2809: cone[1] = firstVertex + j;
2810: cone[2] = firstVertex + k;
2811: cone[3] = firstVertex + l;
2812: /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */
2813: {
2814: const PetscInt epsilon[4][4][4][4] = {
2815: {{{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}}},
2817: {{{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}}},
2819: {{{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}}},
2821: {{{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}} }
2822: };
2823: PetscReal normal[4];
2824: PetscInt e, f, g;
2826: for (d = 0; d < embedDim; ++d) {
2827: normal[d] = 0.0;
2828: for (e = 0; e < embedDim; ++e) {
2829: for (f = 0; f < embedDim; ++f) {
2830: for (g = 0; g < embedDim; ++g) {
2831: 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]);
2832: }
2833: }
2834: }
2835: }
2836: if (DotReal(embedDim, normal, &coordsIn[i * embedDim]) < 0) {
2837: PetscInt tmp = cone[1];
2838: cone[1] = cone[2];
2839: cone[2] = tmp;
2840: }
2841: }
2842: PetscCall(DMPlexSetCone(dm, c++, cone));
2843: }
2844: }
2845: }
2846: }
2847: }
2848: }
2849: PetscCall(DMPlexSymmetrize(dm));
2850: PetscCall(DMPlexStratify(dm));
2851: PetscCall(PetscFree(graph));
2852: }
2853: break;
2854: default:
2855: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported dimension for sphere: %" PetscInt_FMT, dim);
2856: }
2857: /* Create coordinates */
2858: PetscCall(DMGetCoordinateSection(dm, &coordSection));
2859: PetscCall(PetscSectionSetNumFields(coordSection, 1));
2860: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, embedDim));
2861: PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex + numVerts));
2862: for (v = firstVertex; v < firstVertex + numVerts; ++v) {
2863: PetscCall(PetscSectionSetDof(coordSection, v, embedDim));
2864: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, embedDim));
2865: }
2866: PetscCall(PetscSectionSetUp(coordSection));
2867: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
2868: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
2869: PetscCall(VecSetBlockSize(coordinates, embedDim));
2870: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
2871: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
2872: PetscCall(VecSetType(coordinates, VECSTANDARD));
2873: PetscCall(VecGetArray(coordinates, &coords));
2874: for (v = 0; v < numVerts; ++v)
2875: for (d = 0; d < embedDim; ++d) coords[v * embedDim + d] = coordsIn[v * embedDim + d];
2876: PetscCall(VecRestoreArray(coordinates, &coords));
2877: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
2878: PetscCall(VecDestroy(&coordinates));
2879: PetscCall(PetscFree(coordsIn));
2880: {
2881: DM cdm;
2882: PetscDS cds;
2883: PetscScalar c = R;
2885: PetscCall(DMPlexCreateCoordinateSpace(dm, 1, PETSC_TRUE, snapToSphere));
2886: PetscCall(DMGetCoordinateDM(dm, &cdm));
2887: PetscCall(DMGetDS(cdm, &cds));
2888: PetscCall(PetscDSSetConstants(cds, 1, &c));
2889: }
2890: PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0));
2891: /* Wait for coordinate creation before doing in-place modification */
2892: if (simplex) PetscCall(DMPlexInterpolateInPlace_Internal(dm));
2893: PetscFunctionReturn(PETSC_SUCCESS);
2894: }
2896: typedef void (*TPSEvaluateFunc)(const PetscReal[], PetscReal *, PetscReal[], PetscReal (*)[3]);
2898: /*
2899: The Schwarz P implicit surface is
2901: f(x) = cos(x0) + cos(x1) + cos(x2) = 0
2902: */
2903: static void TPSEvaluate_SchwarzP(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3])
2904: {
2905: PetscReal c[3] = {PetscCosReal(y[0] * PETSC_PI), PetscCosReal(y[1] * PETSC_PI), PetscCosReal(y[2] * PETSC_PI)};
2906: PetscReal g[3] = {-PetscSinReal(y[0] * PETSC_PI), -PetscSinReal(y[1] * PETSC_PI), -PetscSinReal(y[2] * PETSC_PI)};
2907: f[0] = c[0] + c[1] + c[2];
2908: for (PetscInt i = 0; i < 3; i++) {
2909: grad[i] = PETSC_PI * g[i];
2910: for (PetscInt j = 0; j < 3; j++) hess[i][j] = (i == j) ? -PetscSqr(PETSC_PI) * c[i] : 0.;
2911: }
2912: }
2914: // u[] is a tentative normal on input. Replace with the implicit function gradient in the same direction
2915: static PetscErrorCode TPSExtrudeNormalFunc_SchwarzP(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt r, PetscScalar u[], void *ctx)
2916: {
2917: for (PetscInt i = 0; i < 3; i++) u[i] = -PETSC_PI * PetscSinReal(x[i] * PETSC_PI);
2918: return PETSC_SUCCESS;
2919: }
2921: /*
2922: The Gyroid implicit surface is
2924: 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)
2926: */
2927: static void TPSEvaluate_Gyroid(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3])
2928: {
2929: PetscReal s[3] = {PetscSinReal(PETSC_PI * y[0]), PetscSinReal(PETSC_PI * (y[1] + .5)), PetscSinReal(PETSC_PI * (y[2] + .25))};
2930: PetscReal c[3] = {PetscCosReal(PETSC_PI * y[0]), PetscCosReal(PETSC_PI * (y[1] + .5)), PetscCosReal(PETSC_PI * (y[2] + .25))};
2931: f[0] = s[0] * c[1] + s[1] * c[2] + s[2] * c[0];
2932: grad[0] = PETSC_PI * (c[0] * c[1] - s[2] * s[0]);
2933: grad[1] = PETSC_PI * (c[1] * c[2] - s[0] * s[1]);
2934: grad[2] = PETSC_PI * (c[2] * c[0] - s[1] * s[2]);
2935: hess[0][0] = -PetscSqr(PETSC_PI) * (s[0] * c[1] + s[2] * c[0]);
2936: hess[0][1] = -PetscSqr(PETSC_PI) * (c[0] * s[1]);
2937: hess[0][2] = -PetscSqr(PETSC_PI) * (c[2] * s[0]);
2938: hess[1][0] = -PetscSqr(PETSC_PI) * (s[1] * c[2] + s[0] * c[1]);
2939: hess[1][1] = -PetscSqr(PETSC_PI) * (c[1] * s[2]);
2940: hess[2][2] = -PetscSqr(PETSC_PI) * (c[0] * s[1]);
2941: hess[2][0] = -PetscSqr(PETSC_PI) * (s[2] * c[0] + s[1] * c[2]);
2942: hess[2][1] = -PetscSqr(PETSC_PI) * (c[2] * s[0]);
2943: hess[2][2] = -PetscSqr(PETSC_PI) * (c[1] * s[2]);
2944: }
2946: // u[] is a tentative normal on input. Replace with the implicit function gradient in the same direction
2947: static PetscErrorCode TPSExtrudeNormalFunc_Gyroid(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt r, PetscScalar u[], void *ctx)
2948: {
2949: PetscReal s[3] = {PetscSinReal(PETSC_PI * x[0]), PetscSinReal(PETSC_PI * (x[1] + .5)), PetscSinReal(PETSC_PI * (x[2] + .25))};
2950: PetscReal c[3] = {PetscCosReal(PETSC_PI * x[0]), PetscCosReal(PETSC_PI * (x[1] + .5)), PetscCosReal(PETSC_PI * (x[2] + .25))};
2951: u[0] = PETSC_PI * (c[0] * c[1] - s[2] * s[0]);
2952: u[1] = PETSC_PI * (c[1] * c[2] - s[0] * s[1]);
2953: u[2] = PETSC_PI * (c[2] * c[0] - s[1] * s[2]);
2954: return PETSC_SUCCESS;
2955: }
2957: /*
2958: We wish to solve
2960: min_y || y - x ||^2 subject to f(y) = 0
2962: Let g(y) = grad(f). The minimization problem is equivalent to asking to satisfy
2963: f(y) = 0 and (y-x) is parallel to g(y). We do this by using Householder QR to obtain a basis for the
2964: tangent space and ask for both components in the tangent space to be zero.
2966: Take g to be a column vector and compute the "full QR" factorization Q R = g,
2967: where Q = I - 2 n n^T is a symmetric orthogonal matrix.
2968: The first column of Q is parallel to g so the remaining two columns span the null space.
2969: Let Qn = Q[:,1:] be those remaining columns. Then Qn Qn^T is an orthogonal projector into the tangent space.
2970: Since Q is symmetric, this is equivalent to multiplying by Q and taking the last two entries.
2971: In total, we have a system of 3 equations in 3 unknowns:
2973: f(y) = 0 1 equation
2974: Qn^T (y - x) = 0 2 equations
2976: Here, we compute the residual and Jacobian of this system.
2977: */
2978: static void TPSNearestPointResJac(TPSEvaluateFunc feval, const PetscScalar x[], const PetscScalar y[], PetscScalar res[], PetscScalar J[])
2979: {
2980: PetscReal yreal[3] = {PetscRealPart(y[0]), PetscRealPart(y[1]), PetscRealPart(y[2])};
2981: PetscReal d[3] = {PetscRealPart(y[0] - x[0]), PetscRealPart(y[1] - x[1]), PetscRealPart(y[2] - x[2])};
2982: PetscReal f, grad[3], n[3], norm, norm_y[3], nd, nd_y[3], sign;
2983: PetscReal n_y[3][3] = {
2984: {0, 0, 0},
2985: {0, 0, 0},
2986: {0, 0, 0}
2987: };
2989: feval(yreal, &f, grad, n_y);
2991: for (PetscInt i = 0; i < 3; i++) n[i] = grad[i];
2992: norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2]));
2993: for (PetscInt i = 0; i < 3; i++) norm_y[i] = 1. / norm * n[i] * n_y[i][i];
2995: // Define the Householder reflector
2996: sign = n[0] >= 0 ? 1. : -1.;
2997: n[0] += norm * sign;
2998: for (PetscInt i = 0; i < 3; i++) n_y[0][i] += norm_y[i] * sign;
3000: norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2]));
3001: norm_y[0] = 1. / norm * (n[0] * n_y[0][0]);
3002: norm_y[1] = 1. / norm * (n[0] * n_y[0][1] + n[1] * n_y[1][1]);
3003: norm_y[2] = 1. / norm * (n[0] * n_y[0][2] + n[2] * n_y[2][2]);
3005: for (PetscInt i = 0; i < 3; i++) {
3006: n[i] /= norm;
3007: for (PetscInt j = 0; j < 3; j++) {
3008: // note that n[i] is n_old[i]/norm when executing the code below
3009: n_y[i][j] = n_y[i][j] / norm - n[i] / norm * norm_y[j];
3010: }
3011: }
3013: nd = n[0] * d[0] + n[1] * d[1] + n[2] * d[2];
3014: 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];
3016: res[0] = f;
3017: res[1] = d[1] - 2 * n[1] * nd;
3018: res[2] = d[2] - 2 * n[2] * nd;
3019: // J[j][i] is J_{ij} (column major)
3020: for (PetscInt j = 0; j < 3; j++) {
3021: J[0 + j * 3] = grad[j];
3022: J[1 + j * 3] = (j == 1) * 1. - 2 * (n_y[1][j] * nd + n[1] * nd_y[j]);
3023: J[2 + j * 3] = (j == 2) * 1. - 2 * (n_y[2][j] * nd + n[2] * nd_y[j]);
3024: }
3025: }
3027: /*
3028: Project x to the nearest point on the implicit surface using Newton's method.
3029: */
3030: static PetscErrorCode TPSNearestPoint(TPSEvaluateFunc feval, PetscScalar x[])
3031: {
3032: PetscScalar y[3] = {x[0], x[1], x[2]}; // Initial guess
3034: PetscFunctionBegin;
3035: for (PetscInt iter = 0; iter < 10; iter++) {
3036: PetscScalar res[3], J[9];
3037: PetscReal resnorm;
3038: TPSNearestPointResJac(feval, x, y, res, J);
3039: resnorm = PetscSqrtReal(PetscSqr(PetscRealPart(res[0])) + PetscSqr(PetscRealPart(res[1])) + PetscSqr(PetscRealPart(res[2])));
3040: if (0) { // Turn on this monitor if you need to confirm quadratic convergence
3041: 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])));
3042: }
3043: if (resnorm < PETSC_SMALL) break;
3045: // Take the Newton step
3046: PetscCall(PetscKernel_A_gets_inverse_A_3(J, 0., PETSC_FALSE, NULL));
3047: PetscKernel_v_gets_v_minus_A_times_w_3(y, J, res);
3048: }
3049: for (PetscInt i = 0; i < 3; i++) x[i] = y[i];
3050: PetscFunctionReturn(PETSC_SUCCESS);
3051: }
3053: const char *const DMPlexTPSTypes[] = {"SCHWARZ_P", "GYROID", "DMPlexTPSType", "DMPLEX_TPS_", NULL};
3055: static PetscErrorCode DMPlexCreateTPSMesh_Internal(DM dm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscBool tps_distribute, PetscInt refinements, PetscInt layers, PetscReal thickness)
3056: {
3057: PetscMPIInt rank;
3058: PetscInt topoDim = 2, spaceDim = 3, numFaces = 0, numVertices = 0, numEdges = 0;
3059: PetscInt(*edges)[2] = NULL, *edgeSets = NULL;
3060: PetscInt *cells_flat = NULL;
3061: PetscReal *vtxCoords = NULL;
3062: TPSEvaluateFunc evalFunc = NULL;
3063: PetscSimplePointFn *normalFunc = NULL;
3064: DMLabel label;
3066: PetscFunctionBegin;
3067: PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0));
3068: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
3069: 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);
3070: switch (tpstype) {
3071: case DMPLEX_TPS_SCHWARZ_P:
3072: 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");
3073: if (rank == 0) {
3074: PetscInt(*cells)[6][4][4] = NULL; // [junction, junction-face, cell, conn]
3075: PetscInt Njunctions = 0, Ncuts = 0, Npipes[3], vcount;
3076: PetscReal L = 1;
3078: Npipes[0] = (extent[0] + 1) * extent[1] * extent[2];
3079: Npipes[1] = extent[0] * (extent[1] + 1) * extent[2];
3080: Npipes[2] = extent[0] * extent[1] * (extent[2] + 1);
3081: Njunctions = extent[0] * extent[1] * extent[2];
3082: Ncuts = 2 * (extent[0] * extent[1] + extent[1] * extent[2] + extent[2] * extent[0]);
3083: numVertices = 4 * (Npipes[0] + Npipes[1] + Npipes[2]) + 8 * Njunctions;
3084: PetscCall(PetscMalloc1(3 * numVertices, &vtxCoords));
3085: PetscCall(PetscMalloc1(Njunctions, &cells));
3086: PetscCall(PetscMalloc1(Ncuts * 4, &edges));
3087: PetscCall(PetscMalloc1(Ncuts * 4, &edgeSets));
3088: // x-normal pipes
3089: vcount = 0;
3090: for (PetscInt i = 0; i < extent[0] + 1; i++) {
3091: for (PetscInt j = 0; j < extent[1]; j++) {
3092: for (PetscInt k = 0; k < extent[2]; k++) {
3093: for (PetscInt l = 0; l < 4; l++) {
3094: vtxCoords[vcount++] = (2 * i - 1) * L;
3095: vtxCoords[vcount++] = 2 * j * L + PetscCosReal((2 * l + 1) * PETSC_PI / 4) * L / 2;
3096: vtxCoords[vcount++] = 2 * k * L + PetscSinReal((2 * l + 1) * PETSC_PI / 4) * L / 2;
3097: }
3098: }
3099: }
3100: }
3101: // y-normal pipes
3102: for (PetscInt i = 0; i < extent[0]; i++) {
3103: for (PetscInt j = 0; j < extent[1] + 1; j++) {
3104: for (PetscInt k = 0; k < extent[2]; k++) {
3105: for (PetscInt l = 0; l < 4; l++) {
3106: vtxCoords[vcount++] = 2 * i * L + PetscSinReal((2 * l + 1) * PETSC_PI / 4) * L / 2;
3107: vtxCoords[vcount++] = (2 * j - 1) * L;
3108: vtxCoords[vcount++] = 2 * k * L + PetscCosReal((2 * l + 1) * PETSC_PI / 4) * L / 2;
3109: }
3110: }
3111: }
3112: }
3113: // z-normal pipes
3114: for (PetscInt i = 0; i < extent[0]; i++) {
3115: for (PetscInt j = 0; j < extent[1]; j++) {
3116: for (PetscInt k = 0; k < extent[2] + 1; k++) {
3117: for (PetscInt l = 0; l < 4; l++) {
3118: vtxCoords[vcount++] = 2 * i * L + PetscCosReal((2 * l + 1) * PETSC_PI / 4) * L / 2;
3119: vtxCoords[vcount++] = 2 * j * L + PetscSinReal((2 * l + 1) * PETSC_PI / 4) * L / 2;
3120: vtxCoords[vcount++] = (2 * k - 1) * L;
3121: }
3122: }
3123: }
3124: }
3125: // junctions
3126: for (PetscInt i = 0; i < extent[0]; i++) {
3127: for (PetscInt j = 0; j < extent[1]; j++) {
3128: for (PetscInt k = 0; k < extent[2]; k++) {
3129: const PetscInt J = (i * extent[1] + j) * extent[2] + k, Jvoff = (Npipes[0] + Npipes[1] + Npipes[2]) * 4 + J * 8;
3130: PetscCheck(vcount / 3 == Jvoff, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unexpected vertex count");
3131: for (PetscInt ii = 0; ii < 2; ii++) {
3132: for (PetscInt jj = 0; jj < 2; jj++) {
3133: for (PetscInt kk = 0; kk < 2; kk++) {
3134: double Ls = (1 - sqrt(2) / 4) * L;
3135: vtxCoords[vcount++] = 2 * i * L + (2 * ii - 1) * Ls;
3136: vtxCoords[vcount++] = 2 * j * L + (2 * jj - 1) * Ls;
3137: vtxCoords[vcount++] = 2 * k * L + (2 * kk - 1) * Ls;
3138: }
3139: }
3140: }
3141: const PetscInt jfaces[3][2][4] = {
3142: {{3, 1, 0, 2}, {7, 5, 4, 6}}, // x-aligned
3143: {{5, 4, 0, 1}, {7, 6, 2, 3}}, // y-aligned
3144: {{6, 2, 0, 4}, {7, 3, 1, 5}} // z-aligned
3145: };
3146: const PetscInt pipe_lo[3] = {// vertex numbers of pipes
3147: ((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};
3148: const PetscInt pipe_hi[3] = {// vertex numbers of pipes
3149: (((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};
3150: for (PetscInt dir = 0; dir < 3; dir++) { // x,y,z
3151: const PetscInt ijk[3] = {i, j, k};
3152: for (PetscInt l = 0; l < 4; l++) { // rotations
3153: cells[J][dir * 2 + 0][l][0] = pipe_lo[dir] + l;
3154: cells[J][dir * 2 + 0][l][1] = Jvoff + jfaces[dir][0][l];
3155: cells[J][dir * 2 + 0][l][2] = Jvoff + jfaces[dir][0][(l - 1 + 4) % 4];
3156: cells[J][dir * 2 + 0][l][3] = pipe_lo[dir] + (l - 1 + 4) % 4;
3157: cells[J][dir * 2 + 1][l][0] = Jvoff + jfaces[dir][1][l];
3158: cells[J][dir * 2 + 1][l][1] = pipe_hi[dir] + l;
3159: cells[J][dir * 2 + 1][l][2] = pipe_hi[dir] + (l - 1 + 4) % 4;
3160: cells[J][dir * 2 + 1][l][3] = Jvoff + jfaces[dir][1][(l - 1 + 4) % 4];
3161: if (ijk[dir] == 0) {
3162: edges[numEdges][0] = pipe_lo[dir] + l;
3163: edges[numEdges][1] = pipe_lo[dir] + (l + 1) % 4;
3164: edgeSets[numEdges] = dir * 2 + 1;
3165: numEdges++;
3166: }
3167: if (ijk[dir] + 1 == extent[dir]) {
3168: edges[numEdges][0] = pipe_hi[dir] + l;
3169: edges[numEdges][1] = pipe_hi[dir] + (l + 1) % 4;
3170: edgeSets[numEdges] = dir * 2 + 2;
3171: numEdges++;
3172: }
3173: }
3174: }
3175: }
3176: }
3177: }
3178: PetscCheck(numEdges == Ncuts * 4, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Edge count %" PetscInt_FMT " incompatible with number of cuts %" PetscInt_FMT, numEdges, Ncuts);
3179: numFaces = 24 * Njunctions;
3180: cells_flat = cells[0][0][0];
3181: }
3182: evalFunc = TPSEvaluate_SchwarzP;
3183: normalFunc = TPSExtrudeNormalFunc_SchwarzP;
3184: break;
3185: case DMPLEX_TPS_GYROID:
3186: if (rank == 0) {
3187: // This is a coarse mesh approximation of the gyroid shifted to being the zero of the level set
3188: //
3189: // 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)
3190: //
3191: // on the cell [0,2]^3.
3192: //
3193: // Think about dividing that cell into four columns, and focus on the column [0,1]x[0,1]x[0,2].
3194: // If you looked at the gyroid in that column at different slices of z you would see that it kind of spins
3195: // like a boomerang:
3196: //
3197: // z = 0 z = 1/4 z = 1/2 z = 3/4 //
3198: // ----- ------- ------- ------- //
3199: // //
3200: // + + + + + + + \ + //
3201: // \ / \ //
3202: // \ `-_ _-' / } //
3203: // *-_ `-' _-' / //
3204: // + `-+ + + +-' + + / + //
3205: // //
3206: // //
3207: // z = 1 z = 5/4 z = 3/2 z = 7/4 //
3208: // ----- ------- ------- ------- //
3209: // //
3210: // +-_ + + + + _-+ + / + //
3211: // `-_ _-_ _-` / //
3212: // \ _-' `-_ / { //
3213: // \ / \ //
3214: // + + + + + + + \ + //
3215: //
3216: //
3217: // This course mesh approximates each of these slices by two line segments,
3218: // and then connects the segments in consecutive layers with quadrilateral faces.
3219: // All of the end points of the segments are multiples of 1/4 except for the
3220: // point * in the picture for z = 0 above and the similar points in other layers.
3221: // That point is at (gamma, gamma, 0), where gamma is calculated below.
3222: //
3223: // The column [1,2]x[1,2]x[0,2] looks the same as this column;
3224: // The columns [1,2]x[0,1]x[0,2] and [0,1]x[1,2]x[0,2] are mirror images.
3225: //
3226: // As for how this method turned into the names given to the vertices:
3227: // that was not systematic, it was just the way it worked out in my handwritten notes.
3229: PetscInt facesPerBlock = 64;
3230: PetscInt vertsPerBlock = 56;
3231: PetscInt extentPlus[3];
3232: PetscInt numBlocks, numBlocksPlus;
3233: 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;
3234: const PetscInt pattern[64][4] = {
3235: /* face to vertex within the coarse discretization of a single gyroid block */
3236: /* layer 0 */
3237: {A, C, K, G },
3238: {C, B, II, K },
3239: {D, A, H, L },
3240: {B + 56 * 1, D, L, J },
3241: {E, B + 56 * 1, J, N },
3242: {A + 56 * 2, E, N, H + 56 * 2 },
3243: {F, A + 56 * 2, G + 56 * 2, M },
3244: {B, F, M, II },
3245: /* layer 1 */
3246: {G, K, Q, O },
3247: {K, II, P, Q },
3248: {L, H, O + 56 * 1, R },
3249: {J, L, R, P },
3250: {N, J, P, S },
3251: {H + 56 * 2, N, S, O + 56 * 3 },
3252: {M, G + 56 * 2, O + 56 * 2, T },
3253: {II, M, T, P },
3254: /* layer 2 */
3255: {O, Q, Y, U },
3256: {Q, P, W, Y },
3257: {R, O + 56 * 1, U + 56 * 1, Ap },
3258: {P, R, Ap, W },
3259: {S, P, X, Bp },
3260: {O + 56 * 3, S, Bp, V + 56 * 1 },
3261: {T, O + 56 * 2, V, Z },
3262: {P, T, Z, X },
3263: /* layer 3 */
3264: {U, Y, Ep, Dp },
3265: {Y, W, Cp, Ep },
3266: {Ap, U + 56 * 1, Dp + 56 * 1, Gp },
3267: {W, Ap, Gp, Cp },
3268: {Bp, X, Cp + 56 * 2, Fp },
3269: {V + 56 * 1, Bp, Fp, Dp + 56 * 1},
3270: {Z, V, Dp, Hp },
3271: {X, Z, Hp, Cp + 56 * 2},
3272: /* layer 4 */
3273: {Dp, Ep, Mp, Kp },
3274: {Ep, Cp, Ip, Mp },
3275: {Gp, Dp + 56 * 1, Lp, Np },
3276: {Cp, Gp, Np, Jp },
3277: {Fp, Cp + 56 * 2, Jp + 56 * 2, Pp },
3278: {Dp + 56 * 1, Fp, Pp, Lp },
3279: {Hp, Dp, Kp, Op },
3280: {Cp + 56 * 2, Hp, Op, Ip + 56 * 2},
3281: /* layer 5 */
3282: {Kp, Mp, Sp, Rp },
3283: {Mp, Ip, Qp, Sp },
3284: {Np, Lp, Rp, Tp },
3285: {Jp, Np, Tp, Qp + 56 * 1},
3286: {Pp, Jp + 56 * 2, Qp + 56 * 3, Up },
3287: {Lp, Pp, Up, Rp },
3288: {Op, Kp, Rp, Vp },
3289: {Ip + 56 * 2, Op, Vp, Qp + 56 * 2},
3290: /* layer 6 */
3291: {Rp, Sp, Aq, Yp },
3292: {Sp, Qp, Wp, Aq },
3293: {Tp, Rp, Yp, Cq },
3294: {Qp + 56 * 1, Tp, Cq, Wp + 56 * 1},
3295: {Up, Qp + 56 * 3, Xp + 56 * 1, Dq },
3296: {Rp, Up, Dq, Zp },
3297: {Vp, Rp, Zp, Bq },
3298: {Qp + 56 * 2, Vp, Bq, Xp },
3299: /* layer 7 (the top is the periodic image of the bottom of layer 0) */
3300: {Yp, Aq, C + 56 * 4, A + 56 * 4 },
3301: {Aq, Wp, B + 56 * 4, C + 56 * 4 },
3302: {Cq, Yp, A + 56 * 4, D + 56 * 4 },
3303: {Wp + 56 * 1, Cq, D + 56 * 4, B + 56 * 5 },
3304: {Dq, Xp + 56 * 1, B + 56 * 5, E + 56 * 4 },
3305: {Zp, Dq, E + 56 * 4, A + 56 * 6 },
3306: {Bq, Zp, A + 56 * 6, F + 56 * 4 },
3307: {Xp, Bq, F + 56 * 4, B + 56 * 4 }
3308: };
3309: const PetscReal gamma = PetscAcosReal((PetscSqrtReal(3.) - 1.) / PetscSqrtReal(2.)) / PETSC_PI;
3310: const PetscReal patternCoords[56][3] = {
3311: {1., 0., 0. }, /* A */
3312: {0., 1., 0. }, /* B */
3313: {gamma, gamma, 0. }, /* C */
3314: {1 + gamma, 1 - gamma, 0. }, /* D */
3315: {2 - gamma, 2 - gamma, 0. }, /* E */
3316: {1 - gamma, 1 + gamma, 0. }, /* F */
3318: {.5, 0, .25 }, /* G */
3319: {1.5, 0., .25 }, /* H */
3320: {.5, 1., .25 }, /* II */
3321: {1.5, 1., .25 }, /* J */
3322: {.25, .5, .25 }, /* K */
3323: {1.25, .5, .25 }, /* L */
3324: {.75, 1.5, .25 }, /* M */
3325: {1.75, 1.5, .25 }, /* N */
3327: {0., 0., .5 }, /* O */
3328: {1., 1., .5 }, /* P */
3329: {gamma, 1 - gamma, .5 }, /* Q */
3330: {1 + gamma, gamma, .5 }, /* R */
3331: {2 - gamma, 1 + gamma, .5 }, /* S */
3332: {1 - gamma, 2 - gamma, .5 }, /* T */
3334: {0., .5, .75 }, /* U */
3335: {0., 1.5, .75 }, /* V */
3336: {1., .5, .75 }, /* W */
3337: {1., 1.5, .75 }, /* X */
3338: {.5, .75, .75 }, /* Y */
3339: {.5, 1.75, .75 }, /* Z */
3340: {1.5, .25, .75 }, /* Ap */
3341: {1.5, 1.25, .75 }, /* Bp */
3343: {1., 0., 1. }, /* Cp */
3344: {0., 1., 1. }, /* Dp */
3345: {1 - gamma, 1 - gamma, 1. }, /* Ep */
3346: {1 + gamma, 1 + gamma, 1. }, /* Fp */
3347: {2 - gamma, gamma, 1. }, /* Gp */
3348: {gamma, 2 - gamma, 1. }, /* Hp */
3350: {.5, 0., 1.25}, /* Ip */
3351: {1.5, 0., 1.25}, /* Jp */
3352: {.5, 1., 1.25}, /* Kp */
3353: {1.5, 1., 1.25}, /* Lp */
3354: {.75, .5, 1.25}, /* Mp */
3355: {1.75, .5, 1.25}, /* Np */
3356: {.25, 1.5, 1.25}, /* Op */
3357: {1.25, 1.5, 1.25}, /* Pp */
3359: {0., 0., 1.5 }, /* Qp */
3360: {1., 1., 1.5 }, /* Rp */
3361: {1 - gamma, gamma, 1.5 }, /* Sp */
3362: {2 - gamma, 1 - gamma, 1.5 }, /* Tp */
3363: {1 + gamma, 2 - gamma, 1.5 }, /* Up */
3364: {gamma, 1 + gamma, 1.5 }, /* Vp */
3366: {0., .5, 1.75}, /* Wp */
3367: {0., 1.5, 1.75}, /* Xp */
3368: {1., .5, 1.75}, /* Yp */
3369: {1., 1.5, 1.75}, /* Zp */
3370: {.5, .25, 1.75}, /* Aq */
3371: {.5, 1.25, 1.75}, /* Bq */
3372: {1.5, .75, 1.75}, /* Cq */
3373: {1.5, 1.75, 1.75}, /* Dq */
3374: };
3375: PetscInt(*cells)[64][4] = NULL;
3376: PetscBool *seen;
3377: PetscInt *vertToTrueVert;
3378: PetscInt count;
3380: for (PetscInt i = 0; i < 3; i++) extentPlus[i] = extent[i] + 1;
3381: numBlocks = 1;
3382: for (PetscInt i = 0; i < 3; i++) numBlocks *= extent[i];
3383: numBlocksPlus = 1;
3384: for (PetscInt i = 0; i < 3; i++) numBlocksPlus *= extentPlus[i];
3385: numFaces = numBlocks * facesPerBlock;
3386: PetscCall(PetscMalloc1(numBlocks, &cells));
3387: PetscCall(PetscCalloc1(numBlocksPlus * vertsPerBlock, &seen));
3388: for (PetscInt k = 0; k < extent[2]; k++) {
3389: for (PetscInt j = 0; j < extent[1]; j++) {
3390: for (PetscInt i = 0; i < extent[0]; i++) {
3391: for (PetscInt f = 0; f < facesPerBlock; f++) {
3392: for (PetscInt v = 0; v < 4; v++) {
3393: PetscInt vertRaw = pattern[f][v];
3394: PetscInt blockidx = vertRaw / 56;
3395: PetscInt patternvert = vertRaw % 56;
3396: PetscInt xplus = (blockidx & 1);
3397: PetscInt yplus = (blockidx & 2) >> 1;
3398: PetscInt zplus = (blockidx & 4) >> 2;
3399: PetscInt zcoord = (periodic && periodic[2] == DM_BOUNDARY_PERIODIC) ? ((k + zplus) % extent[2]) : (k + zplus);
3400: PetscInt ycoord = (periodic && periodic[1] == DM_BOUNDARY_PERIODIC) ? ((j + yplus) % extent[1]) : (j + yplus);
3401: PetscInt xcoord = (periodic && periodic[0] == DM_BOUNDARY_PERIODIC) ? ((i + xplus) % extent[0]) : (i + xplus);
3402: PetscInt vert = ((zcoord * extentPlus[1] + ycoord) * extentPlus[0] + xcoord) * 56 + patternvert;
3404: cells[(k * extent[1] + j) * extent[0] + i][f][v] = vert;
3405: seen[vert] = PETSC_TRUE;
3406: }
3407: }
3408: }
3409: }
3410: }
3411: for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++)
3412: if (seen[i]) numVertices++;
3413: count = 0;
3414: PetscCall(PetscMalloc1(numBlocksPlus * vertsPerBlock, &vertToTrueVert));
3415: PetscCall(PetscMalloc1(numVertices * 3, &vtxCoords));
3416: for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++) vertToTrueVert[i] = -1;
3417: for (PetscInt k = 0; k < extentPlus[2]; k++) {
3418: for (PetscInt j = 0; j < extentPlus[1]; j++) {
3419: for (PetscInt i = 0; i < extentPlus[0]; i++) {
3420: for (PetscInt v = 0; v < vertsPerBlock; v++) {
3421: PetscInt vIdx = ((k * extentPlus[1] + j) * extentPlus[0] + i) * vertsPerBlock + v;
3423: if (seen[vIdx]) {
3424: PetscInt thisVert;
3426: vertToTrueVert[vIdx] = thisVert = count++;
3428: for (PetscInt d = 0; d < 3; d++) vtxCoords[3 * thisVert + d] = patternCoords[v][d];
3429: vtxCoords[3 * thisVert + 0] += i * 2;
3430: vtxCoords[3 * thisVert + 1] += j * 2;
3431: vtxCoords[3 * thisVert + 2] += k * 2;
3432: }
3433: }
3434: }
3435: }
3436: }
3437: for (PetscInt i = 0; i < numBlocks; i++) {
3438: for (PetscInt f = 0; f < facesPerBlock; f++) {
3439: for (PetscInt v = 0; v < 4; v++) cells[i][f][v] = vertToTrueVert[cells[i][f][v]];
3440: }
3441: }
3442: PetscCall(PetscFree(vertToTrueVert));
3443: PetscCall(PetscFree(seen));
3444: cells_flat = cells[0][0];
3445: numEdges = 0;
3446: for (PetscInt i = 0; i < numFaces; i++) {
3447: for (PetscInt e = 0; e < 4; e++) {
3448: PetscInt ev[] = {cells_flat[i * 4 + e], cells_flat[i * 4 + ((e + 1) % 4)]};
3449: const PetscReal *evCoords[] = {&vtxCoords[3 * ev[0]], &vtxCoords[3 * ev[1]]};
3451: for (PetscInt d = 0; d < 3; d++) {
3452: if (!periodic || periodic[0] != DM_BOUNDARY_PERIODIC) {
3453: if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) numEdges++;
3454: if (evCoords[0][d] == 2. * extent[d] && evCoords[1][d] == 2. * extent[d]) numEdges++;
3455: }
3456: }
3457: }
3458: }
3459: PetscCall(PetscMalloc1(numEdges, &edges));
3460: PetscCall(PetscMalloc1(numEdges, &edgeSets));
3461: for (PetscInt edge = 0, i = 0; i < numFaces; i++) {
3462: for (PetscInt e = 0; e < 4; e++) {
3463: PetscInt ev[] = {cells_flat[i * 4 + e], cells_flat[i * 4 + ((e + 1) % 4)]};
3464: const PetscReal *evCoords[] = {&vtxCoords[3 * ev[0]], &vtxCoords[3 * ev[1]]};
3466: for (PetscInt d = 0; d < 3; d++) {
3467: if (!periodic || periodic[d] != DM_BOUNDARY_PERIODIC) {
3468: if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) {
3469: edges[edge][0] = ev[0];
3470: edges[edge][1] = ev[1];
3471: edgeSets[edge++] = 2 * d;
3472: }
3473: if (evCoords[0][d] == 2. * extent[d] && evCoords[1][d] == 2. * extent[d]) {
3474: edges[edge][0] = ev[0];
3475: edges[edge][1] = ev[1];
3476: edgeSets[edge++] = 2 * d + 1;
3477: }
3478: }
3479: }
3480: }
3481: }
3482: }
3483: evalFunc = TPSEvaluate_Gyroid;
3484: normalFunc = TPSExtrudeNormalFunc_Gyroid;
3485: break;
3486: }
3488: PetscCall(DMSetDimension(dm, topoDim));
3489: if (rank == 0) PetscCall(DMPlexBuildFromCellList(dm, numFaces, numVertices, 4, cells_flat));
3490: else PetscCall(DMPlexBuildFromCellList(dm, 0, 0, 0, NULL));
3491: PetscCall(PetscFree(cells_flat));
3492: {
3493: DM idm;
3494: PetscCall(DMPlexInterpolate(dm, &idm));
3495: PetscCall(DMPlexReplace_Internal(dm, &idm));
3496: }
3497: if (rank == 0) PetscCall(DMPlexBuildCoordinatesFromCellList(dm, spaceDim, vtxCoords));
3498: else PetscCall(DMPlexBuildCoordinatesFromCellList(dm, spaceDim, NULL));
3499: PetscCall(PetscFree(vtxCoords));
3501: PetscCall(DMCreateLabel(dm, "Face Sets"));
3502: PetscCall(DMGetLabel(dm, "Face Sets", &label));
3503: for (PetscInt e = 0; e < numEdges; e++) {
3504: PetscInt njoin;
3505: const PetscInt *join, verts[] = {numFaces + edges[e][0], numFaces + edges[e][1]};
3506: PetscCall(DMPlexGetJoin(dm, 2, verts, &njoin, &join));
3507: 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]);
3508: PetscCall(DMLabelSetValue(label, join[0], edgeSets[e]));
3509: PetscCall(DMPlexRestoreJoin(dm, 2, verts, &njoin, &join));
3510: }
3511: PetscCall(PetscFree(edges));
3512: PetscCall(PetscFree(edgeSets));
3513: if (tps_distribute) {
3514: DM pdm = NULL;
3515: PetscPartitioner part;
3517: PetscCall(DMPlexGetPartitioner(dm, &part));
3518: PetscCall(PetscPartitionerSetFromOptions(part));
3519: PetscCall(DMPlexDistribute(dm, 0, NULL, &pdm));
3520: if (pdm) PetscCall(DMPlexReplace_Internal(dm, &pdm));
3521: // Do not auto-distribute again
3522: PetscCall(DMPlexDistributeSetDefault(dm, PETSC_FALSE));
3523: }
3525: PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE));
3526: for (PetscInt refine = 0; refine < refinements; refine++) {
3527: PetscInt m;
3528: DM dmf;
3529: Vec X;
3530: PetscScalar *x;
3531: PetscCall(DMRefine(dm, MPI_COMM_NULL, &dmf));
3532: PetscCall(DMPlexReplace_Internal(dm, &dmf));
3534: PetscCall(DMGetCoordinatesLocal(dm, &X));
3535: PetscCall(VecGetLocalSize(X, &m));
3536: PetscCall(VecGetArray(X, &x));
3537: for (PetscInt i = 0; i < m; i += 3) PetscCall(TPSNearestPoint(evalFunc, &x[i]));
3538: PetscCall(VecRestoreArray(X, &x));
3539: }
3541: // Face Sets has already been propagated to new vertices during refinement; this propagates to the initial vertices.
3542: PetscCall(DMGetLabel(dm, "Face Sets", &label));
3543: PetscCall(DMPlexLabelComplete(dm, label));
3545: PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0));
3547: if (thickness > 0) {
3548: DM edm, cdm, ecdm;
3549: DMPlexTransform tr;
3550: const char *prefix;
3551: PetscOptions options;
3552: // Code from DMPlexExtrude
3553: PetscCall(DMPlexTransformCreate(PetscObjectComm((PetscObject)dm), &tr));
3554: PetscCall(DMPlexTransformSetDM(tr, dm));
3555: PetscCall(DMPlexTransformSetType(tr, DMPLEXEXTRUDE));
3556: PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm, &prefix));
3557: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)tr, prefix));
3558: PetscCall(PetscObjectGetOptions((PetscObject)dm, &options));
3559: PetscCall(PetscObjectSetOptions((PetscObject)tr, options));
3560: PetscCall(DMPlexTransformExtrudeSetLayers(tr, layers));
3561: PetscCall(DMPlexTransformExtrudeSetThickness(tr, thickness));
3562: PetscCall(DMPlexTransformExtrudeSetTensor(tr, PETSC_FALSE));
3563: PetscCall(DMPlexTransformExtrudeSetSymmetric(tr, PETSC_TRUE));
3564: PetscCall(DMPlexTransformExtrudeSetNormalFunction(tr, normalFunc));
3565: PetscCall(DMPlexTransformSetFromOptions(tr));
3566: PetscCall(PetscObjectSetOptions((PetscObject)tr, NULL));
3567: PetscCall(DMPlexTransformSetUp(tr));
3568: PetscCall(PetscObjectViewFromOptions((PetscObject)tr, NULL, "-dm_plex_tps_transform_view"));
3569: PetscCall(DMPlexTransformApply(tr, dm, &edm));
3570: PetscCall(DMCopyDisc(dm, edm));
3571: PetscCall(DMGetCoordinateDM(dm, &cdm));
3572: PetscCall(DMGetCoordinateDM(edm, &ecdm));
3573: PetscCall(DMCopyDisc(cdm, ecdm));
3574: PetscCall(DMPlexTransformCreateDiscLabels(tr, edm));
3575: PetscCall(DMPlexTransformDestroy(&tr));
3576: if (edm) {
3577: ((DM_Plex *)edm->data)->printFEM = ((DM_Plex *)dm->data)->printFEM;
3578: ((DM_Plex *)edm->data)->printL2 = ((DM_Plex *)dm->data)->printL2;
3579: ((DM_Plex *)edm->data)->printLocate = ((DM_Plex *)dm->data)->printLocate;
3580: }
3581: PetscCall(DMPlexReplace_Internal(dm, &edm));
3582: }
3583: PetscFunctionReturn(PETSC_SUCCESS);
3584: }
3586: /*@
3587: DMPlexCreateTPSMesh - Create a distributed, interpolated mesh of a triply-periodic surface
3589: Collective
3591: Input Parameters:
3592: + comm - The communicator for the `DM` object
3593: . tpstype - Type of triply-periodic surface
3594: . extent - Array of length 3 containing number of periods in each direction
3595: . periodic - array of length 3 with periodicity, or `NULL` for non-periodic
3596: . tps_distribute - Distribute 2D manifold mesh prior to refinement and extrusion (more scalable)
3597: . refinements - Number of factor-of-2 refinements of 2D manifold mesh
3598: . layers - Number of cell layers extruded in normal direction
3599: - thickness - Thickness in normal direction
3601: Output Parameter:
3602: . dm - The `DM` object
3604: Level: beginner
3606: Notes:
3607: This meshes the surface of the Schwarz P or Gyroid surfaces. Schwarz P is the simplest member of the triply-periodic minimal surfaces.
3608: <https://en.wikipedia.org/wiki/Schwarz_minimal_surface#Schwarz_P_(%22Primitive%22)> and can be cut with "clean" boundaries.
3609: 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.
3610: Our implementation creates a very coarse mesh of the surface and refines (by 4-way splitting) as many times as requested.
3611: On each refinement, all vertices are projected to their nearest point on the surface.
3612: This projection could readily be extended to related surfaces.
3614: See {cite}`maskery2018insights`
3616: The face (edge) sets for the Schwarz P surface are numbered $1(-x), 2(+x), 3(-y), 4(+y), 5(-z), 6(+z)$.
3617: When the mesh is refined, "Face Sets" contain the new vertices (created during refinement).
3618: Use `DMPlexLabelComplete()` to propagate to coarse-level vertices.
3620: Developer Notes:
3621: The Gyroid mesh does not currently mark boundary sets.
3623: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateSphereMesh()`, `DMSetType()`, `DMCreate()`
3624: @*/
3625: PetscErrorCode DMPlexCreateTPSMesh(MPI_Comm comm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscBool tps_distribute, PetscInt refinements, PetscInt layers, PetscReal thickness, DM *dm)
3626: {
3627: PetscFunctionBegin;
3628: PetscCall(DMCreate(comm, dm));
3629: PetscCall(DMSetType(*dm, DMPLEX));
3630: PetscCall(DMPlexCreateTPSMesh_Internal(*dm, tpstype, extent, periodic, tps_distribute, refinements, layers, thickness));
3631: PetscFunctionReturn(PETSC_SUCCESS);
3632: }
3634: /*@
3635: DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d.
3637: Collective
3639: Input Parameters:
3640: + comm - The communicator for the `DM` object
3641: . dim - The dimension
3642: . simplex - Use simplices, or tensor product cells
3643: - R - The radius
3645: Output Parameter:
3646: . dm - The `DM` object
3648: Level: beginner
3650: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateBallMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()`
3651: @*/
3652: PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscReal R, DM *dm)
3653: {
3654: PetscFunctionBegin;
3655: PetscAssertPointer(dm, 5);
3656: PetscCall(DMCreate(comm, dm));
3657: PetscCall(DMSetType(*dm, DMPLEX));
3658: PetscCall(DMPlexCreateSphereMesh_Internal(*dm, dim, simplex, R));
3659: PetscFunctionReturn(PETSC_SUCCESS);
3660: }
3662: static PetscErrorCode DMPlexCreateBallMesh_Internal(DM dm, PetscInt dim, PetscReal R)
3663: {
3664: DM sdm, vol;
3665: DMLabel bdlabel;
3666: const char *prefix;
3668: PetscFunctionBegin;
3669: PetscCall(DMCreate(PetscObjectComm((PetscObject)dm), &sdm));
3670: PetscCall(DMSetType(sdm, DMPLEX));
3671: PetscCall(DMGetOptionsPrefix(dm, &prefix));
3672: PetscCall(DMSetOptionsPrefix(sdm, prefix));
3673: PetscCall(DMAppendOptionsPrefix(sdm, "bd_"));
3674: PetscCall(DMPlexDistributeSetDefault(sdm, PETSC_FALSE));
3675: PetscCall(DMPlexCreateSphereMesh_Internal(sdm, dim - 1, PETSC_TRUE, R));
3676: PetscCall(DMSetFromOptions(sdm));
3677: PetscCall(DMViewFromOptions(sdm, NULL, "-dm_view"));
3678: PetscCall(DMPlexGenerate(sdm, NULL, PETSC_TRUE, &vol));
3679: PetscCall(DMDestroy(&sdm));
3680: PetscCall(DMPlexReplace_Internal(dm, &vol));
3681: PetscCall(DMCreateLabel(dm, "marker"));
3682: PetscCall(DMGetLabel(dm, "marker", &bdlabel));
3683: PetscCall(DMPlexMarkBoundaryFaces(dm, PETSC_DETERMINE, bdlabel));
3684: PetscCall(DMPlexLabelComplete(dm, bdlabel));
3685: PetscFunctionReturn(PETSC_SUCCESS);
3686: }
3688: /*@
3689: DMPlexCreateBallMesh - Creates a simplex mesh on the d-dimensional ball, B^d.
3691: Collective
3693: Input Parameters:
3694: + comm - The communicator for the `DM` object
3695: . dim - The dimension
3696: - R - The radius
3698: Output Parameter:
3699: . dm - The `DM` object
3701: Options Database Key:
3702: . bd_dm_refine - This will refine the surface mesh preserving the sphere geometry
3704: Level: beginner
3706: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateSphereMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()`
3707: @*/
3708: PetscErrorCode DMPlexCreateBallMesh(MPI_Comm comm, PetscInt dim, PetscReal R, DM *dm)
3709: {
3710: PetscFunctionBegin;
3711: PetscCall(DMCreate(comm, dm));
3712: PetscCall(DMSetType(*dm, DMPLEX));
3713: PetscCall(DMPlexCreateBallMesh_Internal(*dm, dim, R));
3714: PetscFunctionReturn(PETSC_SUCCESS);
3715: }
3717: static PetscErrorCode DMPlexCreateReferenceCell_Internal(DM rdm, DMPolytopeType ct)
3718: {
3719: PetscFunctionBegin;
3720: switch (ct) {
3721: case DM_POLYTOPE_POINT: {
3722: PetscInt numPoints[1] = {1};
3723: PetscInt coneSize[1] = {0};
3724: PetscInt cones[1] = {0};
3725: PetscInt coneOrientations[1] = {0};
3726: PetscScalar vertexCoords[1] = {0.0};
3728: PetscCall(DMSetDimension(rdm, 0));
3729: PetscCall(DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords));
3730: } break;
3731: case DM_POLYTOPE_SEGMENT: {
3732: PetscInt numPoints[2] = {2, 1};
3733: PetscInt coneSize[3] = {2, 0, 0};
3734: PetscInt cones[2] = {1, 2};
3735: PetscInt coneOrientations[2] = {0, 0};
3736: PetscScalar vertexCoords[2] = {-1.0, 1.0};
3738: PetscCall(DMSetDimension(rdm, 1));
3739: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
3740: } break;
3741: case DM_POLYTOPE_POINT_PRISM_TENSOR: {
3742: PetscInt numPoints[2] = {2, 1};
3743: PetscInt coneSize[3] = {2, 0, 0};
3744: PetscInt cones[2] = {1, 2};
3745: PetscInt coneOrientations[2] = {0, 0};
3746: PetscScalar vertexCoords[2] = {-1.0, 1.0};
3748: PetscCall(DMSetDimension(rdm, 1));
3749: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
3750: } break;
3751: case DM_POLYTOPE_TRIANGLE: {
3752: PetscInt numPoints[2] = {3, 1};
3753: PetscInt coneSize[4] = {3, 0, 0, 0};
3754: PetscInt cones[3] = {1, 2, 3};
3755: PetscInt coneOrientations[3] = {0, 0, 0};
3756: PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0};
3758: PetscCall(DMSetDimension(rdm, 2));
3759: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
3760: } break;
3761: case DM_POLYTOPE_QUADRILATERAL: {
3762: PetscInt numPoints[2] = {4, 1};
3763: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
3764: PetscInt cones[4] = {1, 2, 3, 4};
3765: PetscInt coneOrientations[4] = {0, 0, 0, 0};
3766: PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0};
3768: PetscCall(DMSetDimension(rdm, 2));
3769: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
3770: } break;
3771: case DM_POLYTOPE_SEG_PRISM_TENSOR: {
3772: PetscInt numPoints[2] = {4, 1};
3773: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
3774: PetscInt cones[4] = {1, 2, 3, 4};
3775: PetscInt coneOrientations[4] = {0, 0, 0, 0};
3776: PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, 1.0};
3778: PetscCall(DMSetDimension(rdm, 2));
3779: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
3780: } break;
3781: case DM_POLYTOPE_TETRAHEDRON: {
3782: PetscInt numPoints[2] = {4, 1};
3783: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
3784: PetscInt cones[4] = {1, 2, 3, 4};
3785: PetscInt coneOrientations[4] = {0, 0, 0, 0};
3786: 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};
3788: PetscCall(DMSetDimension(rdm, 3));
3789: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
3790: } break;
3791: case DM_POLYTOPE_HEXAHEDRON: {
3792: PetscInt numPoints[2] = {8, 1};
3793: PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0};
3794: PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8};
3795: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
3796: 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};
3798: PetscCall(DMSetDimension(rdm, 3));
3799: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
3800: } break;
3801: case DM_POLYTOPE_TRI_PRISM: {
3802: PetscInt numPoints[2] = {6, 1};
3803: PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0};
3804: PetscInt cones[6] = {1, 2, 3, 4, 5, 6};
3805: PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0};
3806: 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};
3808: PetscCall(DMSetDimension(rdm, 3));
3809: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
3810: } break;
3811: case DM_POLYTOPE_TRI_PRISM_TENSOR: {
3812: PetscInt numPoints[2] = {6, 1};
3813: PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0};
3814: PetscInt cones[6] = {1, 2, 3, 4, 5, 6};
3815: PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0};
3816: 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};
3818: PetscCall(DMSetDimension(rdm, 3));
3819: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
3820: } break;
3821: case DM_POLYTOPE_QUAD_PRISM_TENSOR: {
3822: PetscInt numPoints[2] = {8, 1};
3823: PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0};
3824: PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8};
3825: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
3826: 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};
3828: PetscCall(DMSetDimension(rdm, 3));
3829: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
3830: } break;
3831: case DM_POLYTOPE_PYRAMID: {
3832: PetscInt numPoints[2] = {5, 1};
3833: PetscInt coneSize[6] = {5, 0, 0, 0, 0, 0};
3834: PetscInt cones[5] = {1, 2, 3, 4, 5};
3835: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
3836: 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};
3838: PetscCall(DMSetDimension(rdm, 3));
3839: PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords));
3840: } break;
3841: default:
3842: SETERRQ(PetscObjectComm((PetscObject)rdm), PETSC_ERR_ARG_WRONG, "Cannot create reference cell for cell type %s", DMPolytopeTypes[ct]);
3843: }
3844: {
3845: PetscInt Nv, v;
3847: /* Must create the celltype label here so that we do not automatically try to compute the types */
3848: PetscCall(DMCreateLabel(rdm, "celltype"));
3849: PetscCall(DMPlexSetCellType(rdm, 0, ct));
3850: PetscCall(DMPlexGetChart(rdm, NULL, &Nv));
3851: for (v = 1; v < Nv; ++v) PetscCall(DMPlexSetCellType(rdm, v, DM_POLYTOPE_POINT));
3852: }
3853: PetscCall(DMPlexInterpolateInPlace_Internal(rdm));
3854: PetscCall(PetscObjectSetName((PetscObject)rdm, DMPolytopeTypes[ct]));
3855: PetscFunctionReturn(PETSC_SUCCESS);
3856: }
3858: /*@
3859: DMPlexCreateReferenceCell - Create a `DMPLEX` with the appropriate FEM reference cell
3861: Collective
3863: Input Parameters:
3864: + comm - The communicator
3865: - ct - The cell type of the reference cell
3867: Output Parameter:
3868: . refdm - The reference cell
3870: Level: intermediate
3872: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateBoxMesh()`
3873: @*/
3874: PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, DMPolytopeType ct, DM *refdm)
3875: {
3876: PetscFunctionBegin;
3877: PetscCall(DMCreate(comm, refdm));
3878: PetscCall(DMSetType(*refdm, DMPLEX));
3879: PetscCall(DMPlexCreateReferenceCell_Internal(*refdm, ct));
3880: PetscFunctionReturn(PETSC_SUCCESS);
3881: }
3883: static PetscErrorCode DMPlexCreateBoundaryLabel_Private(DM dm, const char name[])
3884: {
3885: DM plex;
3886: DMLabel label;
3887: PetscBool hasLabel;
3889: PetscFunctionBegin;
3890: PetscCall(DMHasLabel(dm, name, &hasLabel));
3891: if (hasLabel) PetscFunctionReturn(PETSC_SUCCESS);
3892: PetscCall(DMCreateLabel(dm, name));
3893: PetscCall(DMGetLabel(dm, name, &label));
3894: PetscCall(DMConvert(dm, DMPLEX, &plex));
3895: PetscCall(DMPlexMarkBoundaryFaces(plex, 1, label));
3896: PetscCall(DMPlexLabelComplete(plex, label));
3897: PetscCall(DMDestroy(&plex));
3898: PetscFunctionReturn(PETSC_SUCCESS);
3899: }
3901: /*
3902: 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.
3904: (x, y) -> (r, theta) = (x[1], (x[0] - lower[0]) * 2\pi/(upper[0] - lower[0]))
3905: */
3906: 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[])
3907: {
3908: const PetscReal low = PetscRealPart(constants[0]);
3909: const PetscReal upp = PetscRealPart(constants[1]);
3910: const PetscReal r = PetscRealPart(u[1]);
3911: const PetscReal th = 2. * PETSC_PI * (PetscRealPart(u[0]) - low) / (upp - low);
3913: f0[0] = r * PetscCosReal(th);
3914: f0[1] = r * PetscSinReal(th);
3915: }
3917: // Insert vertices and their joins, marked by depth
3918: static PetscErrorCode ProcessCohesiveLabel_Vertices(DM dm, DMLabel label, DMLabel vlabel, PetscInt val, PetscInt n, const PetscInt vertices[])
3919: {
3920: PetscFunctionBegin;
3921: PetscCall(DMPlexMarkSubmesh_Interpolated(dm, vlabel, val, PETSC_FALSE, PETSC_FALSE, label, NULL));
3922: PetscFunctionReturn(PETSC_SUCCESS);
3923: }
3925: // Insert faces and their closures, marked by depth
3926: static PetscErrorCode ProcessCohesiveLabel_Faces(DM dm, DMLabel label, PetscInt n, const PetscInt faces[])
3927: {
3928: PetscFunctionBegin;
3929: for (PetscInt p = 0; p < n; ++p) {
3930: const PetscInt point = faces[p];
3931: PetscInt *closure = NULL;
3932: PetscInt clSize, pdepth;
3934: PetscCall(DMPlexGetPointDepth(dm, point, &pdepth));
3935: PetscCall(DMLabelSetValue(label, point, pdepth));
3936: PetscCall(DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &clSize, &closure));
3937: for (PetscInt cl = 0; cl < clSize * 2; cl += 2) {
3938: PetscCall(DMPlexGetPointDepth(dm, closure[cl], &pdepth));
3939: PetscCall(DMLabelSetValue(label, closure[cl], pdepth));
3940: }
3941: PetscCall(DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &clSize, &closure));
3942: }
3943: PetscFunctionReturn(PETSC_SUCCESS);
3944: }
3946: PETSC_EXTERN PetscErrorCode PetscOptionsFindPairPrefix_Private(PetscOptions, const char pre[], const char name[], const char *option[], const char *value[], PetscBool *flg);
3948: const char *const DMPlexShapes[] = {"box", "box_surface", "ball", "sphere", "cylinder", "schwarz_p", "gyroid", "doublet", "annulus", "hypercubic", "zbox", "unknown", "DMPlexShape", "DM_SHAPE_", NULL};
3950: static PetscErrorCode DMPlexCreateFromOptions_Internal(PetscOptionItems *PetscOptionsObject, PetscBool *useCoordSpace, DM dm)
3951: {
3952: DMPlexShape shape = DM_SHAPE_BOX;
3953: DMPolytopeType cell = DM_POLYTOPE_TRIANGLE;
3954: PetscInt dim = 2;
3955: PetscBool simplex = PETSC_TRUE, interpolate = PETSC_TRUE, adjCone = PETSC_FALSE, adjClosure = PETSC_TRUE, refDomain = PETSC_FALSE;
3956: PetscBool flg, flg2, fflg, strflg, bdfflg, nameflg;
3957: MPI_Comm comm;
3958: char filename[PETSC_MAX_PATH_LEN] = "<unspecified>";
3959: char bdFilename[PETSC_MAX_PATH_LEN] = "<unspecified>";
3960: char plexname[PETSC_MAX_PATH_LEN] = "";
3961: const char *option;
3963: PetscFunctionBegin;
3964: PetscCall(PetscLogEventBegin(DMPLEX_CreateFromOptions, dm, 0, 0, 0));
3965: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
3966: /* TODO Turn this into a registration interface */
3967: PetscCall(PetscOptionsString("-dm_plex_filename", "File containing a mesh", "DMPlexCreateFromFile", filename, filename, sizeof(filename), &fflg));
3968: PetscCall(PetscOptionsString("-dm_plex_file_contents", "Contents of a file format in a string", "DMPlexCreateFromFile", filename, filename, sizeof(filename), &strflg));
3969: PetscCall(PetscOptionsString("-dm_plex_boundary_filename", "File containing a mesh boundary", "DMPlexCreateFromFile", bdFilename, bdFilename, sizeof(bdFilename), &bdfflg));
3970: PetscCall(PetscOptionsString("-dm_plex_name", "Name of the mesh in the file", "DMPlexCreateFromFile", plexname, plexname, sizeof(plexname), &nameflg));
3971: PetscCall(PetscOptionsEnum("-dm_plex_cell", "Cell shape", "", DMPolytopeTypes, (PetscEnum)cell, (PetscEnum *)&cell, NULL));
3972: PetscCall(PetscOptionsBool("-dm_plex_reference_cell_domain", "Use a reference cell domain", "", refDomain, &refDomain, NULL));
3973: PetscCall(PetscOptionsEnum("-dm_plex_shape", "Shape for built-in mesh", "", DMPlexShapes, (PetscEnum)shape, (PetscEnum *)&shape, &flg));
3974: PetscCall(PetscOptionsBoundedInt("-dm_plex_dim", "Topological dimension of the mesh", "DMGetDimension", dim, &dim, &flg, 0));
3975: PetscCall(PetscOptionsBool("-dm_plex_simplex", "Mesh cell shape", "", simplex, &simplex, &flg));
3976: PetscCall(PetscOptionsBool("-dm_plex_interpolate", "Flag to create edges and faces automatically", "", interpolate, &interpolate, &flg));
3977: PetscCall(PetscOptionsBool("-dm_plex_adj_cone", "Set adjacency direction", "DMSetBasicAdjacency", adjCone, &adjCone, &flg));
3978: PetscCall(PetscOptionsBool("-dm_plex_adj_closure", "Set adjacency size", "DMSetBasicAdjacency", adjClosure, &adjClosure, &flg2));
3979: if (flg || flg2) PetscCall(DMSetBasicAdjacency(dm, adjCone, adjClosure));
3981: switch (cell) {
3982: case DM_POLYTOPE_POINT:
3983: case DM_POLYTOPE_SEGMENT:
3984: case DM_POLYTOPE_POINT_PRISM_TENSOR:
3985: case DM_POLYTOPE_TRIANGLE:
3986: case DM_POLYTOPE_QUADRILATERAL:
3987: case DM_POLYTOPE_TETRAHEDRON:
3988: case DM_POLYTOPE_HEXAHEDRON:
3989: *useCoordSpace = PETSC_TRUE;
3990: break;
3991: default:
3992: *useCoordSpace = PETSC_FALSE;
3993: break;
3994: }
3996: if (fflg) {
3997: DM dmnew;
3998: const char *name;
4000: PetscCall(PetscObjectGetName((PetscObject)dm, &name));
4001: PetscCall(DMPlexCreateFromFile(PetscObjectComm((PetscObject)dm), filename, nameflg ? plexname : name, interpolate, &dmnew));
4002: PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew));
4003: PetscCall(DMPlexReplace_Internal(dm, &dmnew));
4004: } else if (refDomain) {
4005: PetscCall(DMPlexCreateReferenceCell_Internal(dm, cell));
4006: } else if (bdfflg) {
4007: DM bdm, dmnew;
4008: const char *name;
4010: PetscCall(PetscObjectGetName((PetscObject)dm, &name));
4011: PetscCall(DMPlexCreateFromFile(PetscObjectComm((PetscObject)dm), bdFilename, nameflg ? plexname : name, interpolate, &bdm));
4012: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)bdm, "bd_"));
4013: PetscCall(DMSetFromOptions(bdm));
4014: PetscCall(DMPlexGenerate(bdm, NULL, interpolate, &dmnew));
4015: PetscCall(DMDestroy(&bdm));
4016: PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew));
4017: PetscCall(DMPlexReplace_Internal(dm, &dmnew));
4018: } else if (strflg) {
4019: DM dmnew;
4020: PetscViewer viewer;
4021: const char *contents;
4022: char *strname;
4023: char tmpdir[PETSC_MAX_PATH_LEN];
4024: char tmpfilename[PETSC_MAX_PATH_LEN];
4025: char name[PETSC_MAX_PATH_LEN];
4026: MPI_Comm comm;
4027: PetscMPIInt rank;
4029: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
4030: PetscCallMPI(MPI_Comm_rank(comm, &rank));
4031: PetscCall(PetscStrchr(filename, ':', &strname));
4032: PetscCheck(strname, comm, PETSC_ERR_ARG_WRONG, "File contents must have the form \"ext:string_name\", not %s", filename);
4033: strname[0] = '\0';
4034: ++strname;
4035: PetscCall(PetscDLSym(NULL, strname, (void **)&contents));
4036: PetscCheck(contents, comm, PETSC_ERR_ARG_WRONG, "Could not locate mesh string %s", strname);
4037: PetscCall(PetscGetTmp(comm, tmpdir, PETSC_MAX_PATH_LEN));
4038: PetscCall(PetscStrlcat(tmpdir, "/meshXXXXXX", PETSC_MAX_PATH_LEN));
4039: PetscCall(PetscMkdtemp(tmpdir));
4040: PetscCall(PetscSNPrintf(tmpfilename, PETSC_MAX_PATH_LEN, "%s/mesh.%s", tmpdir, filename));
4041: PetscCall(PetscViewerASCIIOpen(comm, tmpfilename, &viewer));
4042: PetscCall(PetscViewerASCIIPrintf(viewer, "%s\n", contents));
4043: PetscCall(PetscViewerDestroy(&viewer));
4044: PetscCall(DMPlexCreateFromFile(PetscObjectComm((PetscObject)dm), tmpfilename, plexname, interpolate, &dmnew));
4045: PetscCall(PetscRMTree(tmpdir));
4046: PetscCall(PetscSNPrintf(name, PETSC_MAX_PATH_LEN, "%s Mesh", strname));
4047: PetscCall(PetscObjectSetName((PetscObject)dm, name));
4048: PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew));
4049: PetscCall(DMPlexReplace_Internal(dm, &dmnew));
4050: } else {
4051: PetscCall(PetscObjectSetName((PetscObject)dm, DMPlexShapes[shape]));
4052: switch (shape) {
4053: case DM_SHAPE_BOX:
4054: case DM_SHAPE_ZBOX:
4055: case DM_SHAPE_ANNULUS: {
4056: PetscInt faces[3] = {0, 0, 0};
4057: PetscReal lower[3] = {0, 0, 0};
4058: PetscReal upper[3] = {1, 1, 1};
4059: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
4060: PetscBool isAnnular = shape == DM_SHAPE_ANNULUS ? PETSC_TRUE : PETSC_FALSE;
4061: PetscInt i, n;
4063: n = dim;
4064: for (i = 0; i < dim; ++i) faces[i] = (dim == 1 ? 1 : 4 - dim);
4065: PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg));
4066: n = 3;
4067: PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg));
4068: PetscCheck(!flg || !(n != dim), comm, PETSC_ERR_ARG_SIZ, "Lower box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim);
4069: n = 3;
4070: PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg));
4071: PetscCheck(!flg || !(n != dim), comm, PETSC_ERR_ARG_SIZ, "Upper box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim);
4072: n = 3;
4073: PetscCall(PetscOptionsEnumArray("-dm_plex_box_bd", "Boundary type for each dimension", "", DMBoundaryTypes, (PetscEnum *)bdt, &n, &flg));
4074: PetscCheck(!flg || !(n != dim), comm, PETSC_ERR_ARG_SIZ, "Box boundary types had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim);
4076: PetscCheck(!isAnnular || dim == 2, comm, PETSC_ERR_ARG_OUTOFRANGE, "Only two dimensional annuli have been implemented");
4077: if (isAnnular)
4078: for (i = 0; i < dim - 1; ++i) bdt[i] = DM_BOUNDARY_PERIODIC;
4080: switch (cell) {
4081: case DM_POLYTOPE_TRI_PRISM_TENSOR:
4082: PetscCall(DMPlexCreateWedgeBoxMesh_Internal(dm, faces, lower, upper, bdt));
4083: if (!interpolate) {
4084: DM udm;
4086: PetscCall(DMPlexUninterpolate(dm, &udm));
4087: PetscCall(DMPlexReplace_Internal(dm, &udm));
4088: }
4089: break;
4090: default:
4091: PetscCall(DMPlexCreateBoxMesh_Internal(dm, shape, dim, simplex, faces, lower, upper, bdt, interpolate));
4092: break;
4093: }
4094: if (isAnnular) {
4095: DM cdm;
4096: PetscDS cds;
4097: PetscScalar bounds[2] = {lower[0], upper[0]};
4099: // Fix coordinates for annular region
4100: PetscCall(DMSetPeriodicity(dm, NULL, NULL, NULL));
4101: PetscCall(DMSetCellCoordinatesLocal(dm, NULL));
4102: PetscCall(DMSetCellCoordinates(dm, NULL));
4103: PetscCall(DMPlexCreateCoordinateSpace(dm, 1, PETSC_TRUE, NULL));
4104: PetscCall(DMGetCoordinateDM(dm, &cdm));
4105: PetscCall(DMGetDS(cdm, &cds));
4106: PetscCall(PetscDSSetConstants(cds, 2, bounds));
4107: PetscCall(DMPlexRemapGeometry(dm, 0.0, boxToAnnulus));
4108: }
4109: } break;
4110: case DM_SHAPE_BOX_SURFACE: {
4111: PetscInt faces[3] = {0, 0, 0};
4112: PetscReal lower[3] = {0, 0, 0};
4113: PetscReal upper[3] = {1, 1, 1};
4114: PetscInt i, n;
4116: n = dim + 1;
4117: for (i = 0; i < dim + 1; ++i) faces[i] = (dim + 1 == 1 ? 1 : 4 - (dim + 1));
4118: PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg));
4119: n = 3;
4120: PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg));
4121: 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);
4122: n = 3;
4123: PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg));
4124: 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);
4125: PetscCall(DMPlexCreateBoxSurfaceMesh_Internal(dm, dim + 1, faces, lower, upper, interpolate));
4126: } break;
4127: case DM_SHAPE_SPHERE: {
4128: PetscReal R = 1.0;
4130: PetscCall(PetscOptionsReal("-dm_plex_sphere_radius", "Radius of the sphere", "", R, &R, &flg));
4131: PetscCall(DMPlexCreateSphereMesh_Internal(dm, dim, simplex, R));
4132: } break;
4133: case DM_SHAPE_BALL: {
4134: PetscReal R = 1.0;
4136: PetscCall(PetscOptionsReal("-dm_plex_ball_radius", "Radius of the ball", "", R, &R, &flg));
4137: PetscCall(DMPlexCreateBallMesh_Internal(dm, dim, R));
4138: } break;
4139: case DM_SHAPE_CYLINDER: {
4140: DMBoundaryType bdt = DM_BOUNDARY_NONE;
4141: PetscInt Nw = 6;
4142: PetscInt Nr = 0;
4144: PetscCall(PetscOptionsEnum("-dm_plex_cylinder_bd", "Boundary type in the z direction", "", DMBoundaryTypes, (PetscEnum)bdt, (PetscEnum *)&bdt, NULL));
4145: PetscCall(PetscOptionsInt("-dm_plex_cylinder_num_wedges", "Number of wedges around the cylinder", "", Nw, &Nw, NULL));
4146: PetscCall(PetscOptionsInt("-dm_plex_cylinder_num_refine", "Number of refinements before projection", "", Nr, &Nr, NULL));
4147: switch (cell) {
4148: case DM_POLYTOPE_TRI_PRISM_TENSOR:
4149: PetscCall(DMPlexCreateWedgeCylinderMesh_Internal(dm, Nw, interpolate));
4150: break;
4151: default:
4152: PetscCall(DMPlexCreateHexCylinderMesh_Internal(dm, bdt, Nr));
4153: break;
4154: }
4155: } break;
4156: case DM_SHAPE_SCHWARZ_P: // fallthrough
4157: case DM_SHAPE_GYROID: {
4158: PetscInt extent[3] = {1, 1, 1}, refine = 0, layers = 0, three;
4159: PetscReal thickness = 0.;
4160: DMBoundaryType periodic[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
4161: DMPlexTPSType tps_type = shape == DM_SHAPE_SCHWARZ_P ? DMPLEX_TPS_SCHWARZ_P : DMPLEX_TPS_GYROID;
4162: PetscBool tps_distribute;
4163: PetscCall(PetscOptionsIntArray("-dm_plex_tps_extent", "Number of replicas for each of three dimensions", NULL, extent, (three = 3, &three), NULL));
4164: PetscCall(PetscOptionsInt("-dm_plex_tps_refine", "Number of refinements", NULL, refine, &refine, NULL));
4165: PetscCall(PetscOptionsEnumArray("-dm_plex_tps_periodic", "Periodicity in each of three dimensions", NULL, DMBoundaryTypes, (PetscEnum *)periodic, (three = 3, &three), NULL));
4166: PetscCall(PetscOptionsInt("-dm_plex_tps_layers", "Number of layers in volumetric extrusion (or zero to not extrude)", NULL, layers, &layers, NULL));
4167: PetscCall(PetscOptionsReal("-dm_plex_tps_thickness", "Thickness of volumetric extrusion", NULL, thickness, &thickness, NULL));
4168: PetscCall(DMPlexDistributeGetDefault(dm, &tps_distribute));
4169: PetscCall(PetscOptionsBool("-dm_plex_tps_distribute", "Distribute the 2D mesh prior to refinement and extrusion", NULL, tps_distribute, &tps_distribute, NULL));
4170: PetscCall(DMPlexCreateTPSMesh_Internal(dm, tps_type, extent, periodic, tps_distribute, refine, layers, thickness));
4171: } break;
4172: case DM_SHAPE_DOUBLET: {
4173: DM dmnew;
4174: PetscReal rl = 0.0;
4176: PetscCall(PetscOptionsReal("-dm_plex_doublet_refinementlimit", "Refinement limit", NULL, rl, &rl, NULL));
4177: PetscCall(DMPlexCreateDoublet(PetscObjectComm((PetscObject)dm), dim, simplex, interpolate, rl, &dmnew));
4178: PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew));
4179: PetscCall(DMPlexReplace_Internal(dm, &dmnew));
4180: } break;
4181: case DM_SHAPE_HYPERCUBIC: {
4182: PetscInt *edges;
4183: PetscReal *lower, *upper;
4184: DMBoundaryType *bdt;
4185: PetscInt n, d;
4187: *useCoordSpace = PETSC_FALSE;
4188: PetscCall(PetscMalloc4(dim, &edges, dim, &lower, dim, &upper, dim, &bdt));
4189: for (d = 0; d < dim; ++d) {
4190: edges[d] = 1;
4191: lower[d] = 0.;
4192: upper[d] = 1.;
4193: bdt[d] = DM_BOUNDARY_PERIODIC;
4194: }
4195: n = dim;
4196: PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", edges, &n, &flg));
4197: n = dim;
4198: PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg));
4199: PetscCheck(!flg || n == dim, comm, PETSC_ERR_ARG_SIZ, "Lower box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim);
4200: n = dim;
4201: PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg));
4202: PetscCheck(!flg || n == dim, comm, PETSC_ERR_ARG_SIZ, "Upper box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim);
4203: n = dim;
4204: PetscCall(PetscOptionsEnumArray("-dm_plex_box_bd", "Boundary type for each dimension", "", DMBoundaryTypes, (PetscEnum *)bdt, &n, &flg));
4205: PetscCheck(!flg || n == dim, comm, PETSC_ERR_ARG_SIZ, "Box boundary types had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim);
4206: PetscCall(DMPlexCreateHypercubicMesh_Internal(dm, dim, lower, upper, edges, bdt));
4207: PetscCall(PetscFree4(edges, lower, upper, bdt));
4208: } break;
4209: default:
4210: SETERRQ(comm, PETSC_ERR_SUP, "Domain shape %s is unsupported", DMPlexShapes[shape]);
4211: }
4212: }
4213: PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE));
4214: if (!((PetscObject)dm)->name && nameflg) PetscCall(PetscObjectSetName((PetscObject)dm, plexname));
4215: // Allow label creation
4216: PetscCall(PetscOptionsFindPairPrefix_Private(NULL, ((PetscObject)dm)->prefix, "-dm_plex_label_", &option, NULL, &flg));
4217: if (flg) {
4218: DMLabel label;
4219: PetscInt points[1024], n = 1024;
4220: char fulloption[PETSC_MAX_PATH_LEN];
4221: const char *name = &option[14];
4223: PetscCall(DMCreateLabel(dm, name));
4224: PetscCall(DMGetLabel(dm, name, &label));
4225: fulloption[0] = '-';
4226: fulloption[1] = 0;
4227: PetscCall(PetscStrlcat(fulloption, option, PETSC_MAX_PATH_LEN));
4228: PetscCall(PetscOptionsGetIntArray(NULL, ((PetscObject)dm)->prefix, fulloption, points, &n, NULL));
4229: for (PetscInt p = 0; p < n; ++p) PetscCall(DMLabelSetValue(label, points[p], 1));
4230: }
4231: // Allow cohesive label creation
4232: // Faces are input, completed, and all points are marked with their depth
4233: PetscCall(PetscOptionsFindPairPrefix_Private(NULL, ((PetscObject)dm)->prefix, "-dm_plex_cohesive_label_", &option, NULL, &flg));
4234: if (flg) {
4235: DMLabel label;
4236: PetscInt points[1024], n, pStart, pEnd, Nl = 1;
4237: PetscBool noCreate = PETSC_FALSE;
4238: char fulloption[PETSC_MAX_PATH_LEN];
4239: char name[PETSC_MAX_PATH_LEN];
4240: size_t len;
4242: PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
4243: PetscCall(PetscStrncpy(name, &option[23], PETSC_MAX_PATH_LEN));
4244: PetscCall(PetscStrlen(name, &len));
4245: if (name[len - 1] == '0') Nl = 10;
4246: for (PetscInt l = 0; l < Nl; ++l) {
4247: if (l > 0) name[len - 1] = '0' + l;
4248: fulloption[0] = 0;
4249: PetscCall(PetscStrlcat(fulloption, "-dm_plex_cohesive_label_", 32));
4250: PetscCall(PetscStrlcat(fulloption, name, PETSC_MAX_PATH_LEN - 32));
4251: n = 1024;
4252: PetscCall(PetscOptionsGetIntArray(NULL, ((PetscObject)dm)->prefix, fulloption, points, &n, &flg));
4253: if (!flg) break;
4254: PetscCall(DMHasLabel(dm, name, &noCreate));
4255: if (noCreate) {
4256: DMLabel inlabel;
4257: IS pointIS;
4258: const PetscInt *lpoints;
4259: PetscInt pdep, ln, inval = points[0];
4260: char newname[PETSC_MAX_PATH_LEN];
4262: PetscCheck(n == 1, comm, PETSC_ERR_ARG_WRONG, "Must specify a label value with this option");
4263: PetscCall(DMGetLabel(dm, name, &inlabel));
4264: PetscCall(DMLabelGetStratumIS(inlabel, inval, &pointIS));
4265: PetscCall(ISGetLocalSize(pointIS, &ln));
4266: PetscCall(ISGetIndices(pointIS, &lpoints));
4267: PetscCall(DMPlexGetPointDepth(dm, lpoints[0], &pdep));
4268: PetscCall(PetscSNPrintf(newname, PETSC_MAX_PATH_LEN, "%s%" PetscInt_FMT, name, points[0]));
4269: PetscCall(DMCreateLabel(dm, newname));
4270: PetscCall(DMGetLabel(dm, newname, &label));
4271: if (!pdep) PetscCall(ProcessCohesiveLabel_Vertices(dm, label, inlabel, inval, ln, lpoints));
4272: else PetscCall(ProcessCohesiveLabel_Faces(dm, label, ln, lpoints));
4273: PetscCall(ISRestoreIndices(pointIS, &lpoints));
4274: PetscCall(ISDestroy(&pointIS));
4275: } else {
4276: PetscCall(DMCreateLabel(dm, name));
4277: PetscCall(DMGetLabel(dm, name, &label));
4278: if (pStart >= pEnd) n = 0;
4279: PetscCall(ProcessCohesiveLabel_Faces(dm, label, n, points));
4280: }
4281: PetscCall(DMPlexOrientLabel(dm, label));
4282: PetscCall(DMPlexLabelCohesiveComplete(dm, label, NULL, 1, PETSC_FALSE, PETSC_FALSE, NULL));
4283: }
4284: }
4285: PetscCall(DMViewFromOptions(dm, NULL, "-created_dm_view"));
4286: PetscCall(PetscLogEventEnd(DMPLEX_CreateFromOptions, dm, 0, 0, 0));
4287: PetscFunctionReturn(PETSC_SUCCESS);
4288: }
4290: PetscErrorCode DMSetFromOptions_NonRefinement_Plex(DM dm, PetscOptionItems *PetscOptionsObject)
4291: {
4292: DM_Plex *mesh = (DM_Plex *)dm->data;
4293: PetscBool flg, flg2;
4294: char bdLabel[PETSC_MAX_PATH_LEN];
4295: char method[PETSC_MAX_PATH_LEN];
4297: PetscFunctionBegin;
4298: /* Handle viewing */
4299: PetscCall(PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL));
4300: PetscCall(PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level for all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL, 0));
4301: PetscCall(PetscOptionsBoundedInt("-dm_plex_print_fvm", "Debug output level for all fvm computations", "DMPlexSNESComputeResidualFVM", 0, &mesh->printFVM, NULL, 0));
4302: PetscCall(PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL));
4303: PetscCall(PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL, 0));
4304: PetscCall(PetscOptionsBoundedInt("-dm_plex_print_locate", "Debug output level all point location computations", "DMLocatePoints", 0, &mesh->printLocate, NULL, 0));
4305: PetscCall(DMMonitorSetFromOptions(dm, "-dm_plex_monitor_throughput", "Monitor the simulation throughput", "DMPlexMonitorThroughput", DMPlexMonitorThroughput, NULL, &flg));
4306: if (flg) PetscCall(PetscLogDefaultBegin());
4307: /* Labeling */
4308: PetscCall(PetscOptionsString("-dm_plex_boundary_label", "Label to mark the mesh boundary", "", bdLabel, bdLabel, sizeof(bdLabel), &flg));
4309: if (flg) PetscCall(DMPlexCreateBoundaryLabel_Private(dm, bdLabel));
4310: /* Point Location */
4311: PetscCall(PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL));
4312: /* Partitioning and distribution */
4313: PetscCall(PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL));
4314: /* Reordering */
4315: PetscCall(PetscOptionsBool("-dm_reorder_section", "Compute point permutation for local section", "DMReorderSectionSetDefault", PETSC_FALSE, &flg2, &flg));
4316: if (flg) PetscCall(DMReorderSectionSetDefault(dm, flg2 ? DM_REORDER_DEFAULT_TRUE : DM_REORDER_DEFAULT_FALSE));
4317: PetscCall(PetscOptionsString("-dm_reorder_section_type", "Reordering method for local section", "DMReorderSectionSetType", method, method, PETSC_MAX_PATH_LEN, &flg));
4318: if (flg) PetscCall(DMReorderSectionSetType(dm, method));
4319: /* Generation and remeshing */
4320: PetscCall(PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL));
4321: /* Projection behavior */
4322: PetscCall(PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maximum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL, 0));
4323: PetscCall(PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL));
4324: /* Checking structure */
4325: {
4326: PetscBool all = PETSC_FALSE;
4328: PetscCall(PetscOptionsBool("-dm_plex_check_all", "Perform all basic checks", "DMPlexCheck", PETSC_FALSE, &all, NULL));
4329: if (all) {
4330: PetscCall(DMPlexCheck(dm));
4331: } else {
4332: PetscCall(PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2));
4333: if (flg && flg2) PetscCall(DMPlexCheckSymmetry(dm));
4334: 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));
4335: if (flg && flg2) PetscCall(DMPlexCheckSkeleton(dm, 0));
4336: 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));
4337: if (flg && flg2) PetscCall(DMPlexCheckFaces(dm, 0));
4338: PetscCall(PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2));
4339: if (flg && flg2) PetscCall(DMPlexCheckGeometry(dm));
4340: PetscCall(PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2));
4341: if (flg && flg2) PetscCall(DMPlexCheckPointSF(dm, NULL, PETSC_FALSE));
4342: PetscCall(PetscOptionsBool("-dm_plex_check_interface_cones", "Check points on inter-partition interfaces have conforming order of cone points", "DMPlexCheckInterfaceCones", PETSC_FALSE, &flg, &flg2));
4343: if (flg && flg2) PetscCall(DMPlexCheckInterfaceCones(dm));
4344: }
4345: PetscCall(PetscOptionsBool("-dm_plex_check_cell_shape", "Check cell shape", "DMPlexCheckCellShape", PETSC_FALSE, &flg, &flg2));
4346: if (flg && flg2) PetscCall(DMPlexCheckCellShape(dm, PETSC_TRUE, PETSC_DETERMINE));
4347: }
4348: {
4349: PetscReal scale = 1.0;
4351: PetscCall(PetscOptionsReal("-dm_plex_scale", "Scale factor for mesh coordinates", "DMPlexScale", scale, &scale, &flg));
4352: if (flg) {
4353: Vec coordinates, coordinatesLocal;
4355: PetscCall(DMGetCoordinates(dm, &coordinates));
4356: PetscCall(DMGetCoordinatesLocal(dm, &coordinatesLocal));
4357: PetscCall(VecScale(coordinates, scale));
4358: PetscCall(VecScale(coordinatesLocal, scale));
4359: }
4360: }
4361: PetscCall(PetscPartitionerSetFromOptions(mesh->partitioner));
4362: PetscFunctionReturn(PETSC_SUCCESS);
4363: }
4365: PetscErrorCode DMSetFromOptions_Overlap_Plex(DM dm, PetscOptionItems *PetscOptionsObject, PetscInt *overlap)
4366: {
4367: PetscInt numOvLabels = 16, numOvExLabels = 16;
4368: char *ovLabelNames[16], *ovExLabelNames[16];
4369: PetscInt numOvValues = 16, numOvExValues = 16, l;
4370: PetscBool flg;
4372: PetscFunctionBegin;
4373: PetscCall(PetscOptionsBoundedInt("-dm_distribute_overlap", "The size of the overlap halo", "DMPlexDistribute", *overlap, overlap, NULL, 0));
4374: PetscCall(PetscOptionsStringArray("-dm_distribute_overlap_labels", "List of overlap label names", "DMPlexDistribute", ovLabelNames, &numOvLabels, &flg));
4375: if (!flg) numOvLabels = 0;
4376: if (numOvLabels) {
4377: ((DM_Plex *)dm->data)->numOvLabels = numOvLabels;
4378: for (l = 0; l < numOvLabels; ++l) {
4379: PetscCall(DMGetLabel(dm, ovLabelNames[l], &((DM_Plex *)dm->data)->ovLabels[l]));
4380: PetscCheck(((DM_Plex *)dm->data)->ovLabels[l], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid label name %s", ovLabelNames[l]);
4381: PetscCall(PetscFree(ovLabelNames[l]));
4382: }
4383: PetscCall(PetscOptionsIntArray("-dm_distribute_overlap_values", "List of overlap label values", "DMPlexDistribute", ((DM_Plex *)dm->data)->ovValues, &numOvValues, &flg));
4384: if (!flg) numOvValues = 0;
4385: 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);
4387: PetscCall(PetscOptionsStringArray("-dm_distribute_overlap_exclude_labels", "List of overlap exclude label names", "DMPlexDistribute", ovExLabelNames, &numOvExLabels, &flg));
4388: if (!flg) numOvExLabels = 0;
4389: ((DM_Plex *)dm->data)->numOvExLabels = numOvExLabels;
4390: for (l = 0; l < numOvExLabels; ++l) {
4391: PetscCall(DMGetLabel(dm, ovExLabelNames[l], &((DM_Plex *)dm->data)->ovExLabels[l]));
4392: PetscCheck(((DM_Plex *)dm->data)->ovExLabels[l], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid label name %s", ovExLabelNames[l]);
4393: PetscCall(PetscFree(ovExLabelNames[l]));
4394: }
4395: PetscCall(PetscOptionsIntArray("-dm_distribute_overlap_exclude_values", "List of overlap exclude label values", "DMPlexDistribute", ((DM_Plex *)dm->data)->ovExValues, &numOvExValues, &flg));
4396: if (!flg) numOvExValues = 0;
4397: 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);
4398: }
4399: PetscFunctionReturn(PETSC_SUCCESS);
4400: }
4402: static PetscErrorCode DMSetFromOptions_Plex(DM dm, PetscOptionItems *PetscOptionsObject)
4403: {
4404: PetscFunctionList ordlist;
4405: char oname[256];
4406: char sublabelname[PETSC_MAX_PATH_LEN] = "";
4407: DMReorderDefaultFlag reorder;
4408: PetscReal volume = -1.0;
4409: PetscInt prerefine = 0, refine = 0, r, coarsen = 0, overlap = 0, extLayers = 0, dim;
4410: PetscBool uniformOrig = PETSC_FALSE, created = PETSC_FALSE, uniform = PETSC_TRUE, distribute, saveSF = PETSC_FALSE, interpolate = PETSC_TRUE, coordSpace = PETSC_TRUE, remap = PETSC_TRUE, ghostCells = PETSC_FALSE, isHierarchy, flg;
4412: PetscFunctionBegin;
4413: PetscOptionsHeadBegin(PetscOptionsObject, "DMPlex Options");
4414: if (dm->cloneOpts) goto non_refine;
4415: /* Handle automatic creation */
4416: PetscCall(DMGetDimension(dm, &dim));
4417: if (dim < 0) {
4418: PetscCall(DMPlexCreateFromOptions_Internal(PetscOptionsObject, &coordSpace, dm));
4419: created = PETSC_TRUE;
4420: }
4421: PetscCall(DMGetDimension(dm, &dim));
4422: /* Handle interpolation before distribution */
4423: PetscCall(PetscOptionsBool("-dm_plex_interpolate_pre", "Flag to interpolate mesh before distribution", "", interpolate, &interpolate, &flg));
4424: if (flg) {
4425: DMPlexInterpolatedFlag interpolated;
4427: PetscCall(DMPlexIsInterpolated(dm, &interpolated));
4428: if (interpolated == DMPLEX_INTERPOLATED_FULL && !interpolate) {
4429: DM udm;
4431: PetscCall(DMPlexUninterpolate(dm, &udm));
4432: PetscCall(DMPlexReplace_Internal(dm, &udm));
4433: } else if (interpolated != DMPLEX_INTERPOLATED_FULL && interpolate) {
4434: DM idm;
4436: PetscCall(DMPlexInterpolate(dm, &idm));
4437: PetscCall(DMPlexReplace_Internal(dm, &idm));
4438: }
4439: }
4440: // Handle submesh selection before distribution
4441: PetscCall(PetscOptionsString("-dm_plex_submesh", "Label to use for submesh selection", "", sublabelname, sublabelname, PETSC_MAX_PATH_LEN, &flg));
4442: if (flg) {
4443: DM subdm;
4444: DMLabel label;
4445: IS valueIS, pointIS;
4446: const PetscInt *values, *points;
4447: PetscBool markedFaces = PETSC_FALSE;
4448: PetscInt Nv, value, Np;
4450: PetscCall(DMGetLabel(dm, sublabelname, &label));
4451: PetscCall(DMLabelGetNumValues(label, &Nv));
4452: PetscCheck(Nv == 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only a single label value is currently supported for submesh selection, not %" PetscInt_FMT, Nv);
4453: PetscCall(DMLabelGetValueIS(label, &valueIS));
4454: PetscCall(ISGetIndices(valueIS, &values));
4455: value = values[0];
4456: PetscCall(ISRestoreIndices(valueIS, &values));
4457: PetscCall(ISDestroy(&valueIS));
4458: PetscCall(DMLabelGetStratumSize(label, value, &Np));
4459: PetscCall(DMLabelGetStratumIS(label, value, &pointIS));
4460: PetscCall(ISGetIndices(pointIS, &points));
4461: for (PetscInt p = 0; p < Np; ++p) {
4462: PetscInt pdepth;
4464: PetscCall(DMPlexGetPointDepth(dm, points[p], &pdepth));
4465: if (pdepth) {
4466: markedFaces = PETSC_TRUE;
4467: break;
4468: }
4469: }
4470: PetscCall(ISRestoreIndices(pointIS, &points));
4471: PetscCall(ISDestroy(&pointIS));
4472: PetscCall(DMPlexCreateSubmesh(dm, label, value, markedFaces, &subdm));
4473: PetscCall(DMPlexReplace_Internal(dm, &subdm));
4474: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
4475: }
4476: /* Handle DMPlex refinement before distribution */
4477: PetscCall(DMPlexGetRefinementUniform(dm, &uniformOrig));
4478: PetscCall(PetscOptionsBoundedInt("-dm_refine_pre", "The number of refinements before distribution", "DMCreate", prerefine, &prerefine, NULL, 0));
4479: PetscCall(PetscOptionsBool("-dm_refine_remap_pre", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL));
4480: PetscCall(PetscOptionsBool("-dm_refine_uniform_pre", "Flag for uniform refinement before distribution", "DMCreate", uniform, &uniform, &flg));
4481: if (flg) PetscCall(DMPlexSetRefinementUniform(dm, uniform));
4482: PetscCall(PetscOptionsReal("-dm_refine_volume_limit_pre", "The maximum cell volume after refinement before distribution", "DMCreate", volume, &volume, &flg));
4483: if (flg) {
4484: PetscCall(DMPlexSetRefinementUniform(dm, PETSC_FALSE));
4485: PetscCall(DMPlexSetRefinementLimit(dm, volume));
4486: prerefine = PetscMax(prerefine, 1);
4487: }
4488: if (prerefine) PetscCall(DMLocalizeCoordinates(dm));
4489: for (r = 0; r < prerefine; ++r) {
4490: DM rdm;
4491: PetscPointFunc coordFunc = ((DM_Plex *)dm->data)->coordFunc;
4493: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
4494: PetscCall(DMRefine(dm, PetscObjectComm((PetscObject)dm), &rdm));
4495: PetscCall(DMPlexReplace_Internal(dm, &rdm));
4496: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
4497: if (coordFunc && remap) {
4498: PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc));
4499: ((DM_Plex *)dm->data)->coordFunc = coordFunc;
4500: }
4501: }
4502: PetscCall(DMPlexSetRefinementUniform(dm, uniformOrig));
4503: /* Handle DMPlex extrusion before distribution */
4504: PetscCall(PetscOptionsBoundedInt("-dm_extrude", "The number of layers to extrude", "", extLayers, &extLayers, NULL, 0));
4505: if (extLayers) {
4506: DM edm;
4508: PetscCall(DMExtrude(dm, extLayers, &edm));
4509: PetscCall(DMPlexReplace_Internal(dm, &edm));
4510: ((DM_Plex *)dm->data)->coordFunc = NULL;
4511: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
4512: extLayers = 0;
4513: PetscCall(DMGetDimension(dm, &dim));
4514: }
4515: /* Handle DMPlex reordering before distribution */
4516: PetscCall(DMPlexReorderGetDefault(dm, &reorder));
4517: PetscCall(MatGetOrderingList(&ordlist));
4518: PetscCall(PetscStrncpy(oname, MATORDERINGNATURAL, sizeof(oname)));
4519: PetscCall(PetscOptionsFList("-dm_plex_reorder", "Set mesh reordering type", "DMPlexGetOrdering", ordlist, MATORDERINGNATURAL, oname, sizeof(oname), &flg));
4520: if (reorder == DM_REORDER_DEFAULT_TRUE || flg) {
4521: DM pdm;
4522: IS perm;
4524: PetscCall(DMPlexGetOrdering(dm, oname, NULL, &perm));
4525: PetscCall(DMPlexPermute(dm, perm, &pdm));
4526: PetscCall(ISDestroy(&perm));
4527: PetscCall(DMPlexReplace_Internal(dm, &pdm));
4528: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
4529: }
4530: /* Handle DMPlex distribution */
4531: PetscCall(DMPlexDistributeGetDefault(dm, &distribute));
4532: PetscCall(PetscOptionsBool("-dm_distribute", "Flag to redistribute a mesh among processes", "DMPlexDistribute", distribute, &distribute, NULL));
4533: PetscCall(PetscOptionsBool("-dm_distribute_save_sf", "Flag to save the migration SF", "DMPlexSetMigrationSF", saveSF, &saveSF, NULL));
4534: PetscCall(DMSetFromOptions_Overlap_Plex(dm, PetscOptionsObject, &overlap));
4535: if (distribute) {
4536: DM pdm = NULL;
4537: PetscPartitioner part;
4538: PetscSF sfMigration;
4540: PetscCall(DMPlexGetPartitioner(dm, &part));
4541: PetscCall(PetscPartitionerSetFromOptions(part));
4542: PetscCall(DMPlexDistribute(dm, overlap, &sfMigration, &pdm));
4543: if (pdm) PetscCall(DMPlexReplace_Internal(dm, &pdm));
4544: if (saveSF) PetscCall(DMPlexSetMigrationSF(dm, sfMigration));
4545: PetscCall(PetscSFDestroy(&sfMigration));
4546: }
4547: /* Must check CEED options before creating function space for coordinates */
4548: {
4549: PetscBool useCeed = PETSC_FALSE, flg;
4551: PetscCall(PetscOptionsBool("-dm_plex_use_ceed", "Use LibCEED as the FEM backend", "DMPlexSetUseCeed", useCeed, &useCeed, &flg));
4552: if (flg) PetscCall(DMPlexSetUseCeed(dm, useCeed));
4553: }
4554: /* Create coordinate space */
4555: if (created) {
4556: DM_Plex *mesh = (DM_Plex *)dm->data;
4557: PetscInt degree = 1, deg;
4558: PetscInt height = 0;
4559: DM cdm;
4560: PetscBool flg, localize = PETSC_TRUE, sparseLocalize = PETSC_TRUE;
4562: PetscCall(PetscOptionsBool("-dm_coord_space", "Use an FEM space for coordinates", "", coordSpace, &coordSpace, &flg));
4563: PetscCall(PetscOptionsInt("-dm_coord_petscspace_degree", "FEM degree for coordinate space", "", degree, °ree, NULL));
4564: PetscCall(DMGetCoordinateDegree_Internal(dm, °));
4565: if (coordSpace && deg <= 1) PetscCall(DMPlexCreateCoordinateSpace(dm, degree, PETSC_TRUE, mesh->coordFunc));
4566: PetscCall(DMGetCoordinateDM(dm, &cdm));
4567: if (flg && !coordSpace) {
4568: PetscDS cds;
4569: PetscObject obj;
4570: PetscClassId id;
4572: PetscCall(DMGetDS(cdm, &cds));
4573: PetscCall(PetscDSGetDiscretization(cds, 0, &obj));
4574: PetscCall(PetscObjectGetClassId(obj, &id));
4575: if (id == PETSCFE_CLASSID) {
4576: PetscContainer dummy;
4578: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &dummy));
4579: PetscCall(PetscObjectSetName((PetscObject)dummy, "coordinates"));
4580: PetscCall(DMSetField(cdm, 0, NULL, (PetscObject)dummy));
4581: PetscCall(PetscContainerDestroy(&dummy));
4582: PetscCall(DMClearDS(cdm));
4583: }
4584: mesh->coordFunc = NULL;
4585: }
4586: PetscCall(PetscOptionsBool("-dm_localize", "Localize mesh coordinates", "", localize, &localize, NULL));
4587: PetscCall(PetscOptionsBool("-dm_sparse_localize", "Localize only necessary cells", "DMSetSparseLocalize", sparseLocalize, &sparseLocalize, &flg));
4588: if (flg) PetscCall(DMSetSparseLocalize(dm, sparseLocalize));
4589: PetscCall(PetscOptionsInt("-dm_localize_height", "Localize edges and faces in addition to cells", "", height, &height, &flg));
4590: if (flg) PetscCall(DMPlexSetMaxProjectionHeight(cdm, height));
4591: if (localize) PetscCall(DMLocalizeCoordinates(dm));
4592: }
4593: /* Handle DMPlex refinement */
4594: remap = PETSC_TRUE;
4595: PetscCall(PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL, 0));
4596: PetscCall(PetscOptionsBool("-dm_refine_remap", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL));
4597: PetscCall(PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy, 0));
4598: if (refine) PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE));
4599: if (refine && isHierarchy) {
4600: DM *dms, coarseDM;
4602: PetscCall(DMGetCoarseDM(dm, &coarseDM));
4603: PetscCall(PetscObjectReference((PetscObject)coarseDM));
4604: PetscCall(PetscMalloc1(refine, &dms));
4605: PetscCall(DMRefineHierarchy(dm, refine, dms));
4606: /* Total hack since we do not pass in a pointer */
4607: PetscCall(DMPlexSwap_Static(dm, dms[refine - 1]));
4608: if (refine == 1) {
4609: PetscCall(DMSetCoarseDM(dm, dms[0]));
4610: PetscCall(DMPlexSetRegularRefinement(dm, PETSC_TRUE));
4611: } else {
4612: PetscCall(DMSetCoarseDM(dm, dms[refine - 2]));
4613: PetscCall(DMPlexSetRegularRefinement(dm, PETSC_TRUE));
4614: PetscCall(DMSetCoarseDM(dms[0], dms[refine - 1]));
4615: PetscCall(DMPlexSetRegularRefinement(dms[0], PETSC_TRUE));
4616: }
4617: PetscCall(DMSetCoarseDM(dms[refine - 1], coarseDM));
4618: PetscCall(PetscObjectDereference((PetscObject)coarseDM));
4619: /* Free DMs */
4620: for (r = 0; r < refine; ++r) {
4621: PetscCall(DMSetFromOptions_NonRefinement_Plex(dms[r], PetscOptionsObject));
4622: PetscCall(DMDestroy(&dms[r]));
4623: }
4624: PetscCall(PetscFree(dms));
4625: } else {
4626: for (r = 0; r < refine; ++r) {
4627: DM rdm;
4628: PetscPointFunc coordFunc = ((DM_Plex *)dm->data)->coordFunc;
4630: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
4631: PetscCall(DMRefine(dm, PetscObjectComm((PetscObject)dm), &rdm));
4632: /* Total hack since we do not pass in a pointer */
4633: PetscCall(DMPlexReplace_Internal(dm, &rdm));
4634: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
4635: if (coordFunc && remap) {
4636: PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc));
4637: ((DM_Plex *)dm->data)->coordFunc = coordFunc;
4638: }
4639: }
4640: }
4641: /* Handle DMPlex coarsening */
4642: PetscCall(PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL, 0));
4643: PetscCall(PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy, 0));
4644: if (coarsen && isHierarchy) {
4645: DM *dms;
4647: PetscCall(PetscMalloc1(coarsen, &dms));
4648: PetscCall(DMCoarsenHierarchy(dm, coarsen, dms));
4649: /* Free DMs */
4650: for (r = 0; r < coarsen; ++r) {
4651: PetscCall(DMSetFromOptions_NonRefinement_Plex(dms[r], PetscOptionsObject));
4652: PetscCall(DMDestroy(&dms[r]));
4653: }
4654: PetscCall(PetscFree(dms));
4655: } else {
4656: for (r = 0; r < coarsen; ++r) {
4657: DM cdm;
4658: PetscPointFunc coordFunc = ((DM_Plex *)dm->data)->coordFunc;
4660: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
4661: PetscCall(DMCoarsen(dm, PetscObjectComm((PetscObject)dm), &cdm));
4662: /* Total hack since we do not pass in a pointer */
4663: PetscCall(DMPlexReplace_Internal(dm, &cdm));
4664: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
4665: if (coordFunc) {
4666: PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc));
4667: ((DM_Plex *)dm->data)->coordFunc = coordFunc;
4668: }
4669: }
4670: }
4671: // Handle coordinate remapping
4672: remap = PETSC_FALSE;
4673: PetscCall(PetscOptionsBool("-dm_coord_remap", "Flag to control coordinate remapping", "", remap, &remap, NULL));
4674: if (remap) {
4675: DMPlexCoordMap map = DM_COORD_MAP_NONE;
4676: PetscPointFunc mapFunc = NULL;
4677: PetscScalar params[16];
4678: PetscInt Np = PETSC_STATIC_ARRAY_LENGTH(params), cdim;
4679: MPI_Comm comm;
4681: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
4682: PetscCall(DMGetCoordinateDim(dm, &cdim));
4683: PetscCall(PetscOptionsScalarArray("-dm_coord_map_params", "Parameters for the coordinate remapping", "", params, &Np, &flg));
4684: if (!flg) Np = 0;
4685: // TODO Allow user to pass a map function by name
4686: PetscCall(PetscOptionsEnum("-dm_coord_map", "Coordinate mapping for built-in mesh", "", DMPlexCoordMaps, (PetscEnum)map, (PetscEnum *)&map, &flg));
4687: if (flg) {
4688: switch (map) {
4689: case DM_COORD_MAP_NONE:
4690: mapFunc = coordMap_identity;
4691: break;
4692: case DM_COORD_MAP_SHEAR:
4693: mapFunc = coordMap_shear;
4694: if (!Np) {
4695: Np = cdim + 1;
4696: params[0] = 0;
4697: for (PetscInt d = 1; d <= cdim; ++d) params[d] = 1.0;
4698: }
4699: 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);
4700: break;
4701: case DM_COORD_MAP_FLARE:
4702: mapFunc = coordMap_flare;
4703: if (!Np) {
4704: Np = cdim + 1;
4705: params[0] = 0;
4706: for (PetscInt d = 1; d <= cdim; ++d) params[d] = 1.0;
4707: }
4708: 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);
4709: break;
4710: case DM_COORD_MAP_ANNULUS:
4711: mapFunc = coordMap_annulus;
4712: if (!Np) {
4713: Np = 2;
4714: params[0] = 1.;
4715: params[1] = 2.;
4716: }
4717: PetscCheck(Np == 2, comm, PETSC_ERR_ARG_WRONG, "The annulus coordinate map must have 2 parameters, not %" PetscInt_FMT, Np);
4718: break;
4719: case DM_COORD_MAP_SHELL:
4720: mapFunc = coordMap_shell;
4721: if (!Np) {
4722: Np = 2;
4723: params[0] = 1.;
4724: params[1] = 2.;
4725: }
4726: PetscCheck(Np == 2, comm, PETSC_ERR_ARG_WRONG, "The spherical shell coordinate map must have 2 parameters, not %" PetscInt_FMT, Np);
4727: break;
4728: default:
4729: mapFunc = coordMap_identity;
4730: }
4731: }
4732: if (Np) {
4733: DM cdm;
4734: PetscDS cds;
4736: PetscCall(DMGetCoordinateDM(dm, &cdm));
4737: PetscCall(DMGetDS(cdm, &cds));
4738: PetscCall(PetscDSSetConstants(cds, Np, params));
4739: }
4740: PetscCall(DMPlexRemapGeometry(dm, 0.0, mapFunc));
4741: }
4742: /* Handle ghost cells */
4743: PetscCall(PetscOptionsBool("-dm_plex_create_fv_ghost_cells", "Flag to create finite volume ghost cells on the boundary", "DMCreate", ghostCells, &ghostCells, NULL));
4744: if (ghostCells) {
4745: DM gdm;
4746: char lname[PETSC_MAX_PATH_LEN];
4748: lname[0] = '\0';
4749: PetscCall(PetscOptionsString("-dm_plex_fv_ghost_cells_label", "Label name for ghost cells boundary", "DMCreate", lname, lname, sizeof(lname), &flg));
4750: PetscCall(DMPlexConstructGhostCells(dm, flg ? lname : NULL, NULL, &gdm));
4751: PetscCall(DMPlexReplace_Internal(dm, &gdm));
4752: }
4753: /* Handle 1D order */
4754: if (reorder != DM_REORDER_DEFAULT_FALSE && dim == 1) {
4755: DM cdm, rdm;
4756: PetscDS cds;
4757: PetscObject obj;
4758: PetscClassId id = PETSC_OBJECT_CLASSID;
4759: IS perm;
4760: PetscInt Nf;
4761: PetscBool distributed;
4763: PetscCall(DMPlexIsDistributed(dm, &distributed));
4764: PetscCall(DMGetCoordinateDM(dm, &cdm));
4765: PetscCall(DMGetDS(cdm, &cds));
4766: PetscCall(PetscDSGetNumFields(cds, &Nf));
4767: if (Nf) {
4768: PetscCall(PetscDSGetDiscretization(cds, 0, &obj));
4769: PetscCall(PetscObjectGetClassId(obj, &id));
4770: }
4771: if (!distributed && id != PETSCFE_CLASSID) {
4772: PetscCall(DMPlexGetOrdering1D(dm, &perm));
4773: PetscCall(DMPlexPermute(dm, perm, &rdm));
4774: PetscCall(DMPlexReplace_Internal(dm, &rdm));
4775: PetscCall(ISDestroy(&perm));
4776: }
4777: }
4778: /* Handle */
4779: non_refine:
4780: PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject));
4781: PetscOptionsHeadEnd();
4782: PetscFunctionReturn(PETSC_SUCCESS);
4783: }
4785: static PetscErrorCode DMCreateGlobalVector_Plex(DM dm, Vec *vec)
4786: {
4787: PetscFunctionBegin;
4788: PetscCall(DMCreateGlobalVector_Section_Private(dm, vec));
4789: /* PetscCall(VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM)); */
4790: PetscCall(VecSetOperation(*vec, VECOP_VIEW, (void (*)(void))VecView_Plex));
4791: PetscCall(VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void))VecView_Plex_Native));
4792: PetscCall(VecSetOperation(*vec, VECOP_LOAD, (void (*)(void))VecLoad_Plex));
4793: PetscCall(VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void))VecLoad_Plex_Native));
4794: PetscFunctionReturn(PETSC_SUCCESS);
4795: }
4797: static PetscErrorCode DMCreateLocalVector_Plex(DM dm, Vec *vec)
4798: {
4799: PetscFunctionBegin;
4800: PetscCall(DMCreateLocalVector_Section_Private(dm, vec));
4801: PetscCall(VecSetOperation(*vec, VECOP_VIEW, (void (*)(void))VecView_Plex_Local));
4802: PetscCall(VecSetOperation(*vec, VECOP_LOAD, (void (*)(void))VecLoad_Plex_Local));
4803: PetscFunctionReturn(PETSC_SUCCESS);
4804: }
4806: static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd)
4807: {
4808: PetscInt depth, d;
4810: PetscFunctionBegin;
4811: PetscCall(DMPlexGetDepth(dm, &depth));
4812: if (depth == 1) {
4813: PetscCall(DMGetDimension(dm, &d));
4814: if (dim == 0) PetscCall(DMPlexGetDepthStratum(dm, dim, pStart, pEnd));
4815: else if (dim == d) PetscCall(DMPlexGetDepthStratum(dm, 1, pStart, pEnd));
4816: else {
4817: *pStart = 0;
4818: *pEnd = 0;
4819: }
4820: } else {
4821: PetscCall(DMPlexGetDepthStratum(dm, dim, pStart, pEnd));
4822: }
4823: PetscFunctionReturn(PETSC_SUCCESS);
4824: }
4826: static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[])
4827: {
4828: PetscSF sf;
4829: PetscInt niranks, njranks, n;
4830: const PetscMPIInt *iranks, *jranks;
4831: DM_Plex *data = (DM_Plex *)dm->data;
4833: PetscFunctionBegin;
4834: PetscCall(DMGetPointSF(dm, &sf));
4835: if (!data->neighbors) {
4836: PetscCall(PetscSFSetUp(sf));
4837: PetscCall(PetscSFGetRootRanks(sf, &njranks, &jranks, NULL, NULL, NULL));
4838: PetscCall(PetscSFGetLeafRanks(sf, &niranks, &iranks, NULL, NULL));
4839: PetscCall(PetscMalloc1(njranks + niranks + 1, &data->neighbors));
4840: PetscCall(PetscArraycpy(data->neighbors + 1, jranks, njranks));
4841: PetscCall(PetscArraycpy(data->neighbors + njranks + 1, iranks, niranks));
4842: n = njranks + niranks;
4843: PetscCall(PetscSortRemoveDupsMPIInt(&n, data->neighbors + 1));
4844: /* The following cast should never fail: can't have more neighbors than PETSC_MPI_INT_MAX */
4845: PetscCall(PetscMPIIntCast(n, data->neighbors));
4846: }
4847: if (nranks) *nranks = data->neighbors[0];
4848: if (ranks) {
4849: if (data->neighbors[0]) *ranks = data->neighbors + 1;
4850: else *ranks = NULL;
4851: }
4852: PetscFunctionReturn(PETSC_SUCCESS);
4853: }
4855: PETSC_INTERN PetscErrorCode DMInterpolateSolution_Plex(DM, DM, Mat, Vec, Vec);
4857: static PetscErrorCode DMInitialize_Plex(DM dm)
4858: {
4859: PetscFunctionBegin;
4860: dm->ops->view = DMView_Plex;
4861: dm->ops->load = DMLoad_Plex;
4862: dm->ops->setfromoptions = DMSetFromOptions_Plex;
4863: dm->ops->clone = DMClone_Plex;
4864: dm->ops->setup = DMSetUp_Plex;
4865: dm->ops->createlocalsection = DMCreateLocalSection_Plex;
4866: dm->ops->createsectionpermutation = DMCreateSectionPermutation_Plex;
4867: dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex;
4868: dm->ops->createglobalvector = DMCreateGlobalVector_Plex;
4869: dm->ops->createlocalvector = DMCreateLocalVector_Plex;
4870: dm->ops->getlocaltoglobalmapping = NULL;
4871: dm->ops->createfieldis = NULL;
4872: dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex;
4873: dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex;
4874: dm->ops->getcoloring = NULL;
4875: dm->ops->creatematrix = DMCreateMatrix_Plex;
4876: dm->ops->createinterpolation = DMCreateInterpolation_Plex;
4877: dm->ops->createmassmatrix = DMCreateMassMatrix_Plex;
4878: dm->ops->createmassmatrixlumped = DMCreateMassMatrixLumped_Plex;
4879: dm->ops->createinjection = DMCreateInjection_Plex;
4880: dm->ops->refine = DMRefine_Plex;
4881: dm->ops->coarsen = DMCoarsen_Plex;
4882: dm->ops->refinehierarchy = DMRefineHierarchy_Plex;
4883: dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex;
4884: dm->ops->extrude = DMExtrude_Plex;
4885: dm->ops->globaltolocalbegin = NULL;
4886: dm->ops->globaltolocalend = NULL;
4887: dm->ops->localtoglobalbegin = NULL;
4888: dm->ops->localtoglobalend = NULL;
4889: dm->ops->destroy = DMDestroy_Plex;
4890: dm->ops->createsubdm = DMCreateSubDM_Plex;
4891: dm->ops->createsuperdm = DMCreateSuperDM_Plex;
4892: dm->ops->getdimpoints = DMGetDimPoints_Plex;
4893: dm->ops->locatepoints = DMLocatePoints_Plex;
4894: dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex;
4895: dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex;
4896: dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex;
4897: dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex;
4898: dm->ops->projectbdfieldlabellocal = DMProjectBdFieldLabelLocal_Plex;
4899: dm->ops->computel2diff = DMComputeL2Diff_Plex;
4900: dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex;
4901: dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex;
4902: dm->ops->getneighbors = DMGetNeighbors_Plex;
4903: dm->ops->getlocalboundingbox = DMGetLocalBoundingBox_Coordinates;
4904: dm->ops->createdomaindecomposition = DMCreateDomainDecomposition_Plex;
4905: dm->ops->createddscatters = DMCreateDomainDecompositionScatters_Plex;
4906: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexInsertBoundaryValues_C", DMPlexInsertBoundaryValues_Plex));
4907: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexInsertTimeDerivativeBoundaryValues_C", DMPlexInsertTimeDerivativeBoundaryValues_Plex));
4908: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMSetUpGLVisViewer_C", DMSetUpGLVisViewer_Plex));
4909: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMCreateNeumannOverlap_C", DMCreateNeumannOverlap_Plex));
4910: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexDistributeGetDefault_C", DMPlexDistributeGetDefault_Plex));
4911: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexDistributeSetDefault_C", DMPlexDistributeSetDefault_Plex));
4912: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexReorderGetDefault_C", DMPlexReorderGetDefault_Plex));
4913: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexReorderSetDefault_C", DMPlexReorderSetDefault_Plex));
4914: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMReorderSectionGetDefault_C", DMReorderSectionGetDefault_Plex));
4915: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMReorderSectionSetDefault_C", DMReorderSectionSetDefault_Plex));
4916: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMReorderSectionGetType_C", DMReorderSectionGetType_Plex));
4917: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMReorderSectionSetType_C", DMReorderSectionSetType_Plex));
4918: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMInterpolateSolution_C", DMInterpolateSolution_Plex));
4919: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexGetOverlap_C", DMPlexGetOverlap_Plex));
4920: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexSetOverlap_C", DMPlexSetOverlap_Plex));
4921: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexGetUseCeed_C", DMPlexGetUseCeed_Plex));
4922: PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexSetUseCeed_C", DMPlexSetUseCeed_Plex));
4923: PetscFunctionReturn(PETSC_SUCCESS);
4924: }
4926: PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm)
4927: {
4928: DM_Plex *mesh = (DM_Plex *)dm->data;
4929: const PetscSF *face_sfs;
4930: PetscInt num_face_sfs;
4932: PetscFunctionBegin;
4933: mesh->refct++;
4934: (*newdm)->data = mesh;
4935: PetscCall(DMPlexGetIsoperiodicFaceSF(dm, &num_face_sfs, &face_sfs));
4936: PetscCall(DMPlexSetIsoperiodicFaceSF(*newdm, num_face_sfs, (PetscSF *)face_sfs));
4937: PetscCall(PetscObjectChangeTypeName((PetscObject)*newdm, DMPLEX));
4938: PetscCall(DMInitialize_Plex(*newdm));
4939: PetscFunctionReturn(PETSC_SUCCESS);
4940: }
4942: /*MC
4943: DMPLEX = "plex" - A `DM` object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram.
4944: In the local representation, `Vec`s contain all unknowns in the interior and shared boundary. This is
4945: specified by a PetscSection object. Ownership in the global representation is determined by
4946: ownership of the underlying `DMPLEX` points. This is specified by another `PetscSection` object.
4948: Options Database Keys:
4949: + -dm_refine_pre - Refine mesh before distribution
4950: + -dm_refine_uniform_pre - Choose uniform or generator-based refinement
4951: + -dm_refine_volume_limit_pre - Cell volume limit after pre-refinement using generator
4952: . -dm_distribute - Distribute mesh across processes
4953: . -dm_distribute_overlap - Number of cells to overlap for distribution
4954: . -dm_refine - Refine mesh after distribution
4955: . -dm_localize <bool> - Whether to localize coordinates for periodic meshes
4956: . -dm_sparse_localize <bool> - Whether to only localize cells on the periodic boundary
4957: . -dm_plex_hash_location - Use grid hashing for point location
4958: . -dm_plex_hash_box_faces <n,m,p> - The number of divisions in each direction of the grid hash
4959: . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes
4960: . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing
4961: . -dm_plex_max_projection_height - Maximum mesh point height used to project locally
4962: . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement
4963: . -dm_plex_reorder_section - Use specialized blocking if available
4964: . -dm_plex_check_all - Perform all checks below
4965: . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric
4966: . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices
4967: . -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
4968: . -dm_plex_check_geometry - Check that cells have positive volume
4969: . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ
4970: . -dm_plex_view_scale <num> - Scale the TikZ
4971: . -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices
4972: - -dm_plex_print_fvm <num> - View FVM assembly information, such as flux updates
4974: Level: intermediate
4976: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMType`, `DMPlexCreate()`, `DMCreate()`, `DMSetType()`, `PetscSection`
4977: M*/
4979: PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm)
4980: {
4981: DM_Plex *mesh;
4982: PetscInt unit;
4984: PetscFunctionBegin;
4985: PetscCall(PetscCitationsRegister(PlexCitation, &Plexcite));
4987: PetscCall(PetscNew(&mesh));
4988: dm->reorderSection = DM_REORDER_DEFAULT_NOTSET;
4989: dm->data = mesh;
4991: mesh->refct = 1;
4992: PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection));
4993: PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection));
4994: mesh->refinementUniform = PETSC_TRUE;
4995: mesh->refinementLimit = -1.0;
4996: mesh->distDefault = PETSC_TRUE;
4997: mesh->reorderDefault = DM_REORDER_DEFAULT_NOTSET;
4998: mesh->distributionName = NULL;
4999: mesh->interpolated = DMPLEX_INTERPOLATED_INVALID;
5000: mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID;
5002: PetscCall(PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner));
5003: mesh->remeshBd = PETSC_FALSE;
5005: for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0;
5007: mesh->depthState = -1;
5008: mesh->celltypeState = -1;
5009: mesh->printTol = 1.0e-10;
5011: PetscCall(DMInitialize_Plex(dm));
5012: PetscFunctionReturn(PETSC_SUCCESS);
5013: }
5015: /*@
5016: DMPlexCreate - Creates a `DMPLEX` object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram.
5018: Collective
5020: Input Parameter:
5021: . comm - The communicator for the `DMPLEX` object
5023: Output Parameter:
5024: . mesh - The `DMPLEX` object
5026: Level: beginner
5028: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMType`, `DMCreate()`, `DMSetType()`
5029: @*/
5030: PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh)
5031: {
5032: PetscFunctionBegin;
5033: PetscAssertPointer(mesh, 2);
5034: PetscCall(DMCreate(comm, mesh));
5035: PetscCall(DMSetType(*mesh, DMPLEX));
5036: PetscFunctionReturn(PETSC_SUCCESS);
5037: }
5039: /*@C
5040: DMPlexBuildFromCellListParallel - Build distributed `DMPLEX` topology from a list of vertices for each cell (common mesh generator output)
5042: Collective; No Fortran Support
5044: Input Parameters:
5045: + dm - The `DM`
5046: . numCells - The number of cells owned by this process
5047: . numVertices - The number of vertices to be owned by this process, or `PETSC_DECIDE`
5048: . NVertices - The global number of vertices, or `PETSC_DETERMINE`
5049: . numCorners - The number of vertices for each cell
5050: - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell
5052: Output Parameters:
5053: + vertexSF - (Optional) `PetscSF` describing complete vertex ownership
5054: - verticesAdjSaved - (Optional) vertex adjacency array
5056: Level: advanced
5058: Notes:
5059: Two triangles sharing a face
5060: .vb
5062: 2
5063: / | \
5064: / | \
5065: / | \
5066: 0 0 | 1 3
5067: \ | /
5068: \ | /
5069: \ | /
5070: 1
5071: .ve
5072: would have input
5073: .vb
5074: numCells = 2, numVertices = 4
5075: cells = [0 1 2 1 3 2]
5076: .ve
5077: which would result in the `DMPLEX`
5078: .vb
5080: 4
5081: / | \
5082: / | \
5083: / | \
5084: 2 0 | 1 5
5085: \ | /
5086: \ | /
5087: \ | /
5088: 3
5089: .ve
5091: Vertices are implicitly numbered consecutively 0,...,NVertices.
5092: Each rank owns a chunk of numVertices consecutive vertices.
5093: If numVertices is `PETSC_DECIDE`, PETSc will distribute them as evenly as possible using PetscLayout.
5094: If NVertices is `PETSC_DETERMINE` and numVertices is PETSC_DECIDE, NVertices is computed by PETSc as the maximum vertex index in cells + 1.
5095: If only NVertices is `PETSC_DETERMINE`, it is computed as the sum of numVertices over all ranks.
5097: The cell distribution is arbitrary non-overlapping, independent of the vertex distribution.
5099: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildFromCellList()`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildCoordinatesFromCellListParallel()`,
5100: `PetscSF`
5101: @*/
5102: PetscErrorCode DMPlexBuildFromCellListParallel(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, const PetscInt cells[], PetscSF *vertexSF, PetscInt **verticesAdjSaved)
5103: {
5104: PetscSF sfPoint;
5105: PetscLayout layout;
5106: PetscInt numVerticesAdj, *verticesAdj, *cones, c, p;
5108: PetscFunctionBegin;
5110: PetscCall(PetscLogEventBegin(DMPLEX_BuildFromCellList, dm, 0, 0, 0));
5111: /* Get/check global number of vertices */
5112: {
5113: PetscInt NVerticesInCells, i;
5114: const PetscInt len = numCells * numCorners;
5116: /* NVerticesInCells = max(cells) + 1 */
5117: NVerticesInCells = PETSC_MIN_INT;
5118: for (i = 0; i < len; i++)
5119: if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i];
5120: ++NVerticesInCells;
5121: PetscCall(MPIU_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm)));
5123: if (numVertices == PETSC_DECIDE && NVertices == PETSC_DECIDE) NVertices = NVerticesInCells;
5124: else
5125: 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);
5126: }
5127: /* Count locally unique vertices */
5128: {
5129: PetscHSetI vhash;
5130: PetscInt off = 0;
5132: PetscCall(PetscHSetICreate(&vhash));
5133: for (c = 0; c < numCells; ++c) {
5134: for (p = 0; p < numCorners; ++p) PetscCall(PetscHSetIAdd(vhash, cells[c * numCorners + p]));
5135: }
5136: PetscCall(PetscHSetIGetSize(vhash, &numVerticesAdj));
5137: if (!verticesAdjSaved) PetscCall(PetscMalloc1(numVerticesAdj, &verticesAdj));
5138: else verticesAdj = *verticesAdjSaved;
5139: PetscCall(PetscHSetIGetElems(vhash, &off, verticesAdj));
5140: PetscCall(PetscHSetIDestroy(&vhash));
5141: PetscCheck(off == numVerticesAdj, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %" PetscInt_FMT " should be %" PetscInt_FMT, off, numVerticesAdj);
5142: }
5143: PetscCall(PetscSortInt(numVerticesAdj, verticesAdj));
5144: /* Create cones */
5145: PetscCall(DMPlexSetChart(dm, 0, numCells + numVerticesAdj));
5146: for (c = 0; c < numCells; ++c) PetscCall(DMPlexSetConeSize(dm, c, numCorners));
5147: PetscCall(DMSetUp(dm));
5148: PetscCall(DMPlexGetCones(dm, &cones));
5149: for (c = 0; c < numCells; ++c) {
5150: for (p = 0; p < numCorners; ++p) {
5151: const PetscInt gv = cells[c * numCorners + p];
5152: PetscInt lv;
5154: /* Positions within verticesAdj form 0-based local vertex numbering;
5155: we need to shift it by numCells to get correct DAG points (cells go first) */
5156: PetscCall(PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv));
5157: PetscCheck(lv >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %" PetscInt_FMT " in local connectivity", gv);
5158: cones[c * numCorners + p] = lv + numCells;
5159: }
5160: }
5161: /* Build point sf */
5162: PetscCall(PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &layout));
5163: PetscCall(PetscLayoutSetSize(layout, NVertices));
5164: PetscCall(PetscLayoutSetLocalSize(layout, numVertices));
5165: PetscCall(PetscLayoutSetBlockSize(layout, 1));
5166: PetscCall(PetscSFCreateByMatchingIndices(layout, numVerticesAdj, verticesAdj, NULL, numCells, numVerticesAdj, verticesAdj, NULL, numCells, vertexSF, &sfPoint));
5167: PetscCall(PetscLayoutDestroy(&layout));
5168: if (!verticesAdjSaved) PetscCall(PetscFree(verticesAdj));
5169: PetscCall(PetscObjectSetName((PetscObject)sfPoint, "point SF"));
5170: if (dm->sf) {
5171: const char *prefix;
5173: PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm->sf, &prefix));
5174: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)sfPoint, prefix));
5175: }
5176: PetscCall(DMSetPointSF(dm, sfPoint));
5177: PetscCall(PetscSFDestroy(&sfPoint));
5178: if (vertexSF) PetscCall(PetscObjectSetName((PetscObject)*vertexSF, "Vertex Ownership SF"));
5179: /* Fill in the rest of the topology structure */
5180: PetscCall(DMPlexSymmetrize(dm));
5181: PetscCall(DMPlexStratify(dm));
5182: PetscCall(PetscLogEventEnd(DMPLEX_BuildFromCellList, dm, 0, 0, 0));
5183: PetscFunctionReturn(PETSC_SUCCESS);
5184: }
5186: /*@
5187: DMPlexBuildCoordinatesFromCellListParallel - Build `DM` coordinates from a list of coordinates for each owned vertex (common mesh generator output)
5189: Collective; No Fortran Support
5191: Input Parameters:
5192: + dm - The `DM`
5193: . spaceDim - The spatial dimension used for coordinates
5194: . sfVert - `PetscSF` describing complete vertex ownership
5195: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
5197: Level: advanced
5199: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildFromCellListParallel()`
5200: @*/
5201: PetscErrorCode DMPlexBuildCoordinatesFromCellListParallel(DM dm, PetscInt spaceDim, PetscSF sfVert, const PetscReal vertexCoords[])
5202: {
5203: PetscSection coordSection;
5204: Vec coordinates;
5205: PetscScalar *coords;
5206: PetscInt numVertices, numVerticesAdj, coordSize, v, vStart, vEnd;
5208: PetscFunctionBegin;
5209: PetscCall(PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0));
5210: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
5211: PetscCheck(vStart >= 0 && vEnd >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first.");
5212: PetscCall(DMSetCoordinateDim(dm, spaceDim));
5213: PetscCall(PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL));
5214: 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);
5215: PetscCall(DMGetCoordinateSection(dm, &coordSection));
5216: PetscCall(PetscSectionSetNumFields(coordSection, 1));
5217: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spaceDim));
5218: PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd));
5219: for (v = vStart; v < vEnd; ++v) {
5220: PetscCall(PetscSectionSetDof(coordSection, v, spaceDim));
5221: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spaceDim));
5222: }
5223: PetscCall(PetscSectionSetUp(coordSection));
5224: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
5225: PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &coordinates));
5226: PetscCall(VecSetBlockSize(coordinates, spaceDim));
5227: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
5228: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
5229: PetscCall(VecSetType(coordinates, VECSTANDARD));
5230: PetscCall(VecGetArray(coordinates, &coords));
5231: {
5232: MPI_Datatype coordtype;
5234: /* Need a temp buffer for coords if we have complex/single */
5235: PetscCallMPI(MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype));
5236: PetscCallMPI(MPI_Type_commit(&coordtype));
5237: #if defined(PETSC_USE_COMPLEX)
5238: {
5239: PetscScalar *svertexCoords;
5240: PetscInt i;
5241: PetscCall(PetscMalloc1(numVertices * spaceDim, &svertexCoords));
5242: for (i = 0; i < numVertices * spaceDim; i++) svertexCoords[i] = vertexCoords[i];
5243: PetscCall(PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords, MPI_REPLACE));
5244: PetscCall(PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords, MPI_REPLACE));
5245: PetscCall(PetscFree(svertexCoords));
5246: }
5247: #else
5248: PetscCall(PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords, MPI_REPLACE));
5249: PetscCall(PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords, MPI_REPLACE));
5250: #endif
5251: PetscCallMPI(MPI_Type_free(&coordtype));
5252: }
5253: PetscCall(VecRestoreArray(coordinates, &coords));
5254: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
5255: PetscCall(VecDestroy(&coordinates));
5256: PetscCall(PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0));
5257: PetscFunctionReturn(PETSC_SUCCESS);
5258: }
5260: /*@
5261: DMPlexCreateFromCellListParallelPetsc - Create distributed `DMPLEX` from a list of vertices for each cell (common mesh generator output)
5263: Collective
5265: Input Parameters:
5266: + comm - The communicator
5267: . dim - The topological dimension of the mesh
5268: . numCells - The number of cells owned by this process
5269: . numVertices - The number of vertices owned by this process, or `PETSC_DECIDE`
5270: . NVertices - The global number of vertices, or `PETSC_DECIDE`
5271: . numCorners - The number of vertices for each cell
5272: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
5273: . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell
5274: . spaceDim - The spatial dimension used for coordinates
5275: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
5277: Output Parameters:
5278: + dm - The `DM`
5279: . vertexSF - (Optional) `PetscSF` describing complete vertex ownership
5280: - verticesAdj - (Optional) vertex adjacency array
5282: Level: intermediate
5284: Notes:
5285: This function is just a convenient sequence of `DMCreate()`, `DMSetType()`, `DMSetDimension()`,
5286: `DMPlexBuildFromCellListParallel()`, `DMPlexInterpolate()`, `DMPlexBuildCoordinatesFromCellListParallel()`
5288: See `DMPlexBuildFromCellListParallel()` for an example and details about the topology-related parameters.
5290: See `DMPlexBuildCoordinatesFromCellListParallel()` for details about the geometry-related parameters.
5292: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromCellListPetsc()`, `DMPlexBuildFromCellListParallel()`, `DMPlexBuildCoordinatesFromCellListParallel()`, `DMPlexCreateFromDAG()`, `DMPlexCreate()`
5293: @*/
5294: 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[], PetscSF *vertexSF, PetscInt **verticesAdj, DM *dm)
5295: {
5296: PetscSF sfVert;
5298: PetscFunctionBegin;
5299: PetscCall(DMCreate(comm, dm));
5300: PetscCall(DMSetType(*dm, DMPLEX));
5303: PetscCall(DMSetDimension(*dm, dim));
5304: PetscCall(DMPlexBuildFromCellListParallel(*dm, numCells, numVertices, NVertices, numCorners, cells, &sfVert, verticesAdj));
5305: if (interpolate) {
5306: DM idm;
5308: PetscCall(DMPlexInterpolate(*dm, &idm));
5309: PetscCall(DMDestroy(dm));
5310: *dm = idm;
5311: }
5312: PetscCall(DMPlexBuildCoordinatesFromCellListParallel(*dm, spaceDim, sfVert, vertexCoords));
5313: if (vertexSF) *vertexSF = sfVert;
5314: else PetscCall(PetscSFDestroy(&sfVert));
5315: PetscFunctionReturn(PETSC_SUCCESS);
5316: }
5318: /*@
5319: DMPlexBuildFromCellList - Build `DMPLEX` topology from a list of vertices for each cell (common mesh generator output)
5321: Collective; No Fortran Support
5323: Input Parameters:
5324: + dm - The `DM`
5325: . numCells - The number of cells owned by this process
5326: . numVertices - The number of vertices owned by this process, or `PETSC_DETERMINE`
5327: . numCorners - The number of vertices for each cell
5328: - cells - An array of `numCells` x `numCorners` numbers, the global vertex numbers for each cell
5330: Level: advanced
5332: Notes:
5333: Two triangles sharing a face
5334: .vb
5336: 2
5337: / | \
5338: / | \
5339: / | \
5340: 0 0 | 1 3
5341: \ | /
5342: \ | /
5343: \ | /
5344: 1
5345: .ve
5346: would have input
5347: .vb
5348: numCells = 2, numVertices = 4
5349: cells = [0 1 2 1 3 2]
5350: .ve
5351: which would result in the `DMPLEX`
5352: .vb
5354: 4
5355: / | \
5356: / | \
5357: / | \
5358: 2 0 | 1 5
5359: \ | /
5360: \ | /
5361: \ | /
5362: 3
5363: .ve
5365: If numVertices is `PETSC_DETERMINE`, it is computed by PETSc as the maximum vertex index in cells + 1.
5367: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildFromCellListParallel()`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromCellListPetsc()`
5368: @*/
5369: PetscErrorCode DMPlexBuildFromCellList(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[])
5370: {
5371: PetscInt *cones, c, p, dim;
5373: PetscFunctionBegin;
5374: PetscCall(PetscLogEventBegin(DMPLEX_BuildFromCellList, dm, 0, 0, 0));
5375: PetscCall(DMGetDimension(dm, &dim));
5376: /* Get/check global number of vertices */
5377: {
5378: PetscInt NVerticesInCells, i;
5379: const PetscInt len = numCells * numCorners;
5381: /* NVerticesInCells = max(cells) + 1 */
5382: NVerticesInCells = PETSC_MIN_INT;
5383: for (i = 0; i < len; i++)
5384: if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i];
5385: ++NVerticesInCells;
5387: if (numVertices == PETSC_DECIDE) numVertices = NVerticesInCells;
5388: else
5389: 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);
5390: }
5391: PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices));
5392: for (c = 0; c < numCells; ++c) PetscCall(DMPlexSetConeSize(dm, c, numCorners));
5393: PetscCall(DMSetUp(dm));
5394: PetscCall(DMPlexGetCones(dm, &cones));
5395: for (c = 0; c < numCells; ++c) {
5396: for (p = 0; p < numCorners; ++p) cones[c * numCorners + p] = cells[c * numCorners + p] + numCells;
5397: }
5398: PetscCall(DMPlexSymmetrize(dm));
5399: PetscCall(DMPlexStratify(dm));
5400: PetscCall(PetscLogEventEnd(DMPLEX_BuildFromCellList, dm, 0, 0, 0));
5401: PetscFunctionReturn(PETSC_SUCCESS);
5402: }
5404: /*@
5405: DMPlexBuildCoordinatesFromCellList - Build `DM` coordinates from a list of coordinates for each owned vertex (common mesh generator output)
5407: Collective
5409: Input Parameters:
5410: + dm - The `DM`
5411: . spaceDim - The spatial dimension used for coordinates
5412: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
5414: Level: advanced
5416: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildCoordinatesFromCellListParallel()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexBuildFromCellList()`
5417: @*/
5418: PetscErrorCode DMPlexBuildCoordinatesFromCellList(DM dm, PetscInt spaceDim, const PetscReal vertexCoords[])
5419: {
5420: PetscSection coordSection;
5421: Vec coordinates;
5422: DM cdm;
5423: PetscScalar *coords;
5424: PetscInt v, vStart, vEnd, d;
5426: PetscFunctionBegin;
5427: PetscCall(PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0));
5428: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
5429: PetscCheck(vStart >= 0 && vEnd >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first.");
5430: PetscCall(DMSetCoordinateDim(dm, spaceDim));
5431: PetscCall(DMGetCoordinateSection(dm, &coordSection));
5432: PetscCall(PetscSectionSetNumFields(coordSection, 1));
5433: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spaceDim));
5434: PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd));
5435: for (v = vStart; v < vEnd; ++v) {
5436: PetscCall(PetscSectionSetDof(coordSection, v, spaceDim));
5437: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spaceDim));
5438: }
5439: PetscCall(PetscSectionSetUp(coordSection));
5441: PetscCall(DMGetCoordinateDM(dm, &cdm));
5442: PetscCall(DMCreateLocalVector(cdm, &coordinates));
5443: PetscCall(VecSetBlockSize(coordinates, spaceDim));
5444: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
5445: PetscCall(VecGetArrayWrite(coordinates, &coords));
5446: for (v = 0; v < vEnd - vStart; ++v) {
5447: for (d = 0; d < spaceDim; ++d) coords[v * spaceDim + d] = vertexCoords[v * spaceDim + d];
5448: }
5449: PetscCall(VecRestoreArrayWrite(coordinates, &coords));
5450: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
5451: PetscCall(VecDestroy(&coordinates));
5452: PetscCall(PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0));
5453: PetscFunctionReturn(PETSC_SUCCESS);
5454: }
5456: /*@
5457: DMPlexCreateFromCellListPetsc - Create `DMPLEX` from a list of vertices for each cell (common mesh generator output), but only process 0 takes in the input
5459: Collective
5461: Input Parameters:
5462: + comm - The communicator
5463: . dim - The topological dimension of the mesh
5464: . numCells - The number of cells, only on process 0
5465: . numVertices - The number of vertices owned by this process, or `PETSC_DECIDE`, only on process 0
5466: . numCorners - The number of vertices for each cell, only on process 0
5467: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
5468: . cells - An array of numCells*numCorners numbers, the vertices for each cell, only on process 0
5469: . spaceDim - The spatial dimension used for coordinates
5470: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex, only on process 0
5472: Output Parameter:
5473: . dm - The `DM`, which only has points on process 0
5475: Level: intermediate
5477: Notes:
5478: This function is just a convenient sequence of `DMCreate()`, `DMSetType()`, `DMSetDimension()`, `DMPlexBuildFromCellList()`,
5479: `DMPlexInterpolate()`, `DMPlexBuildCoordinatesFromCellList()`
5481: See `DMPlexBuildFromCellList()` for an example and details about the topology-related parameters.
5482: See `DMPlexBuildCoordinatesFromCellList()` for details about the geometry-related parameters.
5483: See `DMPlexCreateFromCellListParallelPetsc()` for parallel input
5485: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildFromCellList()`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromDAG()`, `DMPlexCreate()`
5486: @*/
5487: 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)
5488: {
5489: PetscMPIInt rank;
5491: PetscFunctionBegin;
5492: 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.");
5493: PetscCallMPI(MPI_Comm_rank(comm, &rank));
5494: PetscCall(DMCreate(comm, dm));
5495: PetscCall(DMSetType(*dm, DMPLEX));
5496: PetscCall(DMSetDimension(*dm, dim));
5497: if (rank == 0) PetscCall(DMPlexBuildFromCellList(*dm, numCells, numVertices, numCorners, cells));
5498: else PetscCall(DMPlexBuildFromCellList(*dm, 0, 0, 0, NULL));
5499: if (interpolate) {
5500: DM idm;
5502: PetscCall(DMPlexInterpolate(*dm, &idm));
5503: PetscCall(DMDestroy(dm));
5504: *dm = idm;
5505: }
5506: if (rank == 0) PetscCall(DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, vertexCoords));
5507: else PetscCall(DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, NULL));
5508: PetscFunctionReturn(PETSC_SUCCESS);
5509: }
5511: /*@
5512: DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a `DM`
5514: Input Parameters:
5515: + dm - The empty `DM` object, usually from `DMCreate()` and `DMSetDimension()`
5516: . depth - The depth of the DAG
5517: . numPoints - Array of size depth + 1 containing the number of points at each `depth`
5518: . coneSize - The cone size of each point
5519: . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point
5520: . coneOrientations - The orientation of each cone point
5521: - vertexCoords - An array of `numPoints`[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via `DMSetCoordinateDim()`
5523: Output Parameter:
5524: . dm - The `DM`
5526: Level: advanced
5528: Note:
5529: Two triangles sharing a face would have input
5530: .vb
5531: depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0]
5532: cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0]
5533: vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0]
5534: .ve
5535: which would result in the DMPlex
5536: .vb
5537: 4
5538: / | \
5539: / | \
5540: / | \
5541: 2 0 | 1 5
5542: \ | /
5543: \ | /
5544: \ | /
5545: 3
5546: .ve
5547: Notice that all points are numbered consecutively, unlike `DMPlexCreateFromCellListPetsc()`
5549: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()`
5550: @*/
5551: PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[])
5552: {
5553: Vec coordinates;
5554: PetscSection coordSection;
5555: PetscScalar *coords;
5556: PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off;
5558: PetscFunctionBegin;
5559: PetscCall(DMGetDimension(dm, &dim));
5560: PetscCall(DMGetCoordinateDim(dm, &dimEmbed));
5561: PetscCheck(dimEmbed >= dim, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Embedding dimension %" PetscInt_FMT " cannot be less than intrinsic dimension %" PetscInt_FMT, dimEmbed, dim);
5562: for (d = 0; d <= depth; ++d) pEnd += numPoints[d];
5563: PetscCall(DMPlexSetChart(dm, pStart, pEnd));
5564: for (p = pStart; p < pEnd; ++p) {
5565: PetscCall(DMPlexSetConeSize(dm, p, coneSize[p - pStart]));
5566: if (firstVertex < 0 && !coneSize[p - pStart]) firstVertex = p - pStart;
5567: }
5568: PetscCheck(firstVertex >= 0 || !numPoints[0], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Expected %" PetscInt_FMT " vertices but could not find any", numPoints[0]);
5569: PetscCall(DMSetUp(dm)); /* Allocate space for cones */
5570: for (p = pStart, off = 0; p < pEnd; off += coneSize[p - pStart], ++p) {
5571: PetscCall(DMPlexSetCone(dm, p, &cones[off]));
5572: PetscCall(DMPlexSetConeOrientation(dm, p, &coneOrientations[off]));
5573: }
5574: PetscCall(DMPlexSymmetrize(dm));
5575: PetscCall(DMPlexStratify(dm));
5576: /* Build coordinates */
5577: PetscCall(DMGetCoordinateSection(dm, &coordSection));
5578: PetscCall(PetscSectionSetNumFields(coordSection, 1));
5579: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dimEmbed));
5580: PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex + numPoints[0]));
5581: for (v = firstVertex; v < firstVertex + numPoints[0]; ++v) {
5582: PetscCall(PetscSectionSetDof(coordSection, v, dimEmbed));
5583: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed));
5584: }
5585: PetscCall(PetscSectionSetUp(coordSection));
5586: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
5587: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
5588: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
5589: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
5590: PetscCall(VecSetBlockSize(coordinates, dimEmbed));
5591: PetscCall(VecSetType(coordinates, VECSTANDARD));
5592: if (vertexCoords) {
5593: PetscCall(VecGetArray(coordinates, &coords));
5594: for (v = 0; v < numPoints[0]; ++v) {
5595: PetscInt off;
5597: PetscCall(PetscSectionGetOffset(coordSection, v + firstVertex, &off));
5598: for (d = 0; d < dimEmbed; ++d) coords[off + d] = vertexCoords[v * dimEmbed + d];
5599: }
5600: }
5601: PetscCall(VecRestoreArray(coordinates, &coords));
5602: PetscCall(DMSetCoordinatesLocal(dm, coordinates));
5603: PetscCall(VecDestroy(&coordinates));
5604: PetscFunctionReturn(PETSC_SUCCESS);
5605: }
5607: /*
5608: DMPlexCreateCellVertexFromFile - Create a `DMPLEX` mesh from a simple cell-vertex file.
5610: Collective
5612: + comm - The MPI communicator
5613: . filename - Name of the .dat file
5614: - interpolate - Create faces and edges in the mesh
5616: Output Parameter:
5617: . dm - The `DM` object representing the mesh
5619: Level: beginner
5621: Note:
5622: The format is the simplest possible:
5623: .vb
5624: dim Ne Nv Nc Nl
5625: v_1 v_2 ... v_Nc
5626: ...
5627: x y z marker_1 ... marker_Nl
5628: .ve
5630: Developer Note:
5631: Should use a `PetscViewer` not a filename
5633: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromFile()`, `DMPlexCreateGmsh()`, `DMPlexCreate()`
5634: */
5635: static PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
5636: {
5637: DMLabel marker;
5638: PetscViewer viewer;
5639: Vec coordinates;
5640: PetscSection coordSection;
5641: PetscScalar *coords;
5642: char line[PETSC_MAX_PATH_LEN];
5643: PetscInt cdim, coordSize, v, c, d;
5644: PetscMPIInt rank;
5645: int snum, dim, Nv, Nc, Ncn, Nl;
5647: PetscFunctionBegin;
5648: PetscCallMPI(MPI_Comm_rank(comm, &rank));
5649: PetscCall(PetscViewerCreate(comm, &viewer));
5650: PetscCall(PetscViewerSetType(viewer, PETSCVIEWERASCII));
5651: PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ));
5652: PetscCall(PetscViewerFileSetName(viewer, filename));
5653: if (rank == 0) {
5654: PetscCall(PetscViewerRead(viewer, line, 5, NULL, PETSC_STRING));
5655: snum = sscanf(line, "%d %d %d %d %d", &dim, &Nc, &Nv, &Ncn, &Nl);
5656: PetscCheck(snum == 5, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
5657: } else {
5658: Nc = Nv = Ncn = Nl = 0;
5659: }
5660: PetscCallMPI(MPI_Bcast(&dim, 1, MPI_INT, 0, comm));
5661: cdim = (PetscInt)dim;
5662: PetscCall(DMCreate(comm, dm));
5663: PetscCall(DMSetType(*dm, DMPLEX));
5664: PetscCall(DMPlexSetChart(*dm, 0, Nc + Nv));
5665: PetscCall(DMSetDimension(*dm, (PetscInt)dim));
5666: PetscCall(DMSetCoordinateDim(*dm, cdim));
5667: /* Read topology */
5668: if (rank == 0) {
5669: char format[PETSC_MAX_PATH_LEN];
5670: PetscInt cone[8];
5671: int vbuf[8], v;
5673: for (c = 0; c < Ncn; ++c) {
5674: format[c * 3 + 0] = '%';
5675: format[c * 3 + 1] = 'd';
5676: format[c * 3 + 2] = ' ';
5677: }
5678: format[Ncn * 3 - 1] = '\0';
5679: for (c = 0; c < Nc; ++c) PetscCall(DMPlexSetConeSize(*dm, c, Ncn));
5680: PetscCall(DMSetUp(*dm));
5681: for (c = 0; c < Nc; ++c) {
5682: PetscCall(PetscViewerRead(viewer, line, Ncn, NULL, PETSC_STRING));
5683: switch (Ncn) {
5684: case 2:
5685: snum = sscanf(line, format, &vbuf[0], &vbuf[1]);
5686: break;
5687: case 3:
5688: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2]);
5689: break;
5690: case 4:
5691: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3]);
5692: break;
5693: case 6:
5694: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5]);
5695: break;
5696: case 8:
5697: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5], &vbuf[6], &vbuf[7]);
5698: break;
5699: default:
5700: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "No cell shape with %d vertices", Ncn);
5701: }
5702: PetscCheck(snum == Ncn, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
5703: for (v = 0; v < Ncn; ++v) cone[v] = vbuf[v] + Nc;
5704: /* Hexahedra are inverted */
5705: if (Ncn == 8) {
5706: PetscInt tmp = cone[1];
5707: cone[1] = cone[3];
5708: cone[3] = tmp;
5709: }
5710: PetscCall(DMPlexSetCone(*dm, c, cone));
5711: }
5712: }
5713: PetscCall(DMPlexSymmetrize(*dm));
5714: PetscCall(DMPlexStratify(*dm));
5715: /* Read coordinates */
5716: PetscCall(DMGetCoordinateSection(*dm, &coordSection));
5717: PetscCall(PetscSectionSetNumFields(coordSection, 1));
5718: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, cdim));
5719: PetscCall(PetscSectionSetChart(coordSection, Nc, Nc + Nv));
5720: for (v = Nc; v < Nc + Nv; ++v) {
5721: PetscCall(PetscSectionSetDof(coordSection, v, cdim));
5722: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, cdim));
5723: }
5724: PetscCall(PetscSectionSetUp(coordSection));
5725: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
5726: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
5727: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
5728: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
5729: PetscCall(VecSetBlockSize(coordinates, cdim));
5730: PetscCall(VecSetType(coordinates, VECSTANDARD));
5731: PetscCall(VecGetArray(coordinates, &coords));
5732: if (rank == 0) {
5733: char format[PETSC_MAX_PATH_LEN];
5734: double x[3];
5735: int l, val[3];
5737: if (Nl) {
5738: for (l = 0; l < Nl; ++l) {
5739: format[l * 3 + 0] = '%';
5740: format[l * 3 + 1] = 'd';
5741: format[l * 3 + 2] = ' ';
5742: }
5743: format[Nl * 3 - 1] = '\0';
5744: PetscCall(DMCreateLabel(*dm, "marker"));
5745: PetscCall(DMGetLabel(*dm, "marker", &marker));
5746: }
5747: for (v = 0; v < Nv; ++v) {
5748: PetscCall(PetscViewerRead(viewer, line, 3 + Nl, NULL, PETSC_STRING));
5749: snum = sscanf(line, "%lg %lg %lg", &x[0], &x[1], &x[2]);
5750: PetscCheck(snum == 3, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
5751: switch (Nl) {
5752: case 0:
5753: snum = 0;
5754: break;
5755: case 1:
5756: snum = sscanf(line, format, &val[0]);
5757: break;
5758: case 2:
5759: snum = sscanf(line, format, &val[0], &val[1]);
5760: break;
5761: case 3:
5762: snum = sscanf(line, format, &val[0], &val[1], &val[2]);
5763: break;
5764: default:
5765: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Request support for %d labels", Nl);
5766: }
5767: PetscCheck(snum == Nl, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
5768: for (d = 0; d < cdim; ++d) coords[v * cdim + d] = x[d];
5769: for (l = 0; l < Nl; ++l) PetscCall(DMLabelSetValue(marker, v + Nc, val[l]));
5770: }
5771: }
5772: PetscCall(VecRestoreArray(coordinates, &coords));
5773: PetscCall(DMSetCoordinatesLocal(*dm, coordinates));
5774: PetscCall(VecDestroy(&coordinates));
5775: PetscCall(PetscViewerDestroy(&viewer));
5776: if (interpolate) {
5777: DM idm;
5778: DMLabel bdlabel;
5780: PetscCall(DMPlexInterpolate(*dm, &idm));
5781: PetscCall(DMDestroy(dm));
5782: *dm = idm;
5784: if (!Nl) {
5785: PetscCall(DMCreateLabel(*dm, "marker"));
5786: PetscCall(DMGetLabel(*dm, "marker", &bdlabel));
5787: PetscCall(DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel));
5788: PetscCall(DMPlexLabelComplete(*dm, bdlabel));
5789: }
5790: }
5791: PetscFunctionReturn(PETSC_SUCCESS);
5792: }
5794: /*@
5795: DMPlexCreateFromFile - This takes a filename and produces a `DM`
5797: Collective
5799: Input Parameters:
5800: + comm - The communicator
5801: . filename - A file name
5802: . plexname - The object name of the resulting `DM`, also used for intra-datafile lookup by some formats
5803: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
5805: Output Parameter:
5806: . dm - The `DM`
5808: Options Database Key:
5809: . -dm_plex_create_from_hdf5_xdmf - use the `PETSC_VIEWER_HDF5_XDMF` format for reading HDF5
5811: Use `-dm_plex_create_ prefix` to pass options to the internal `PetscViewer`, e.g.
5812: $ -dm_plex_create_viewer_hdf5_collective
5814: Level: beginner
5816: Notes:
5817: Using `PETSCVIEWERHDF5` type with `PETSC_VIEWER_HDF5_PETSC` format, one can save multiple `DMPLEX`
5818: meshes in a single HDF5 file. This in turn requires one to name the `DMPLEX` object with `PetscObjectSetName()`
5819: before saving it with `DMView()` and before loading it with `DMLoad()` for identification of the mesh object.
5820: The input parameter name is thus used to name the `DMPLEX` object when `DMPlexCreateFromFile()` internally
5821: calls `DMLoad()`. Currently, name is ignored for other viewer types and/or formats.
5823: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromDAG()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()`, `PetscObjectSetName()`, `DMView()`, `DMLoad()`
5824: @*/
5825: PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], const char plexname[], PetscBool interpolate, DM *dm)
5826: {
5827: const char extGmsh[] = ".msh";
5828: const char extGmsh2[] = ".msh2";
5829: const char extGmsh4[] = ".msh4";
5830: const char extCGNS[] = ".cgns";
5831: const char extExodus[] = ".exo";
5832: const char extExodus_e[] = ".e";
5833: const char extGenesis[] = ".gen";
5834: const char extFluent[] = ".cas";
5835: const char extHDF5[] = ".h5";
5836: const char extXDMFHDF5[] = ".xdmf.h5";
5837: const char extPLY[] = ".ply";
5838: const char extEGADSLite[] = ".egadslite";
5839: const char extEGADS[] = ".egads";
5840: const char extIGES[] = ".igs";
5841: const char extSTEP[] = ".stp";
5842: const char extCV[] = ".dat";
5843: size_t len;
5844: PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isPLY, isEGADSLite, isEGADS, isIGES, isSTEP, isCV, isXDMFHDF5;
5845: PetscMPIInt rank;
5847: PetscFunctionBegin;
5848: PetscAssertPointer(filename, 2);
5849: if (plexname) PetscAssertPointer(plexname, 3);
5850: PetscAssertPointer(dm, 5);
5851: PetscCall(DMInitializePackage());
5852: PetscCall(PetscLogEventBegin(DMPLEX_CreateFromFile, 0, 0, 0, 0));
5853: PetscCallMPI(MPI_Comm_rank(comm, &rank));
5854: PetscCall(PetscStrlen(filename, &len));
5855: PetscCheck(len, comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path");
5857: #define CheckExtension(extension__, is_extension__) \
5858: do { \
5859: PetscAssert(sizeof(extension__), comm, PETSC_ERR_PLIB, "Zero-size extension: %s", extension__); \
5860: /* don't count the null-terminator at the end */ \
5861: const size_t ext_len = sizeof(extension__) - 1; \
5862: if (len < ext_len) { \
5863: is_extension__ = PETSC_FALSE; \
5864: } else { \
5865: PetscCall(PetscStrncmp(filename + len - ext_len, extension__, ext_len, &is_extension__)); \
5866: } \
5867: } while (0)
5869: CheckExtension(extGmsh, isGmsh);
5870: CheckExtension(extGmsh2, isGmsh2);
5871: CheckExtension(extGmsh4, isGmsh4);
5872: CheckExtension(extCGNS, isCGNS);
5873: CheckExtension(extExodus, isExodus);
5874: if (!isExodus) CheckExtension(extExodus_e, isExodus);
5875: CheckExtension(extGenesis, isGenesis);
5876: CheckExtension(extFluent, isFluent);
5877: CheckExtension(extHDF5, isHDF5);
5878: CheckExtension(extPLY, isPLY);
5879: CheckExtension(extEGADSLite, isEGADSLite);
5880: CheckExtension(extEGADS, isEGADS);
5881: CheckExtension(extIGES, isIGES);
5882: CheckExtension(extSTEP, isSTEP);
5883: CheckExtension(extCV, isCV);
5884: CheckExtension(extXDMFHDF5, isXDMFHDF5);
5886: #undef CheckExtension
5888: if (isGmsh || isGmsh2 || isGmsh4) {
5889: PetscCall(DMPlexCreateGmshFromFile(comm, filename, interpolate, dm));
5890: } else if (isCGNS) {
5891: PetscCall(DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm));
5892: } else if (isExodus || isGenesis) {
5893: PetscCall(DMPlexCreateExodusFromFile(comm, filename, interpolate, dm));
5894: } else if (isFluent) {
5895: PetscCall(DMPlexCreateFluentFromFile(comm, filename, interpolate, dm));
5896: } else if (isHDF5) {
5897: PetscViewer viewer;
5899: /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */
5900: PetscCall(PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &isXDMFHDF5, NULL));
5901: PetscCall(PetscViewerCreate(comm, &viewer));
5902: PetscCall(PetscViewerSetType(viewer, PETSCVIEWERHDF5));
5903: PetscCall(PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_"));
5904: PetscCall(PetscViewerSetFromOptions(viewer));
5905: PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ));
5906: PetscCall(PetscViewerFileSetName(viewer, filename));
5908: PetscCall(DMCreate(comm, dm));
5909: PetscCall(PetscObjectSetName((PetscObject)*dm, plexname));
5910: PetscCall(DMSetType(*dm, DMPLEX));
5911: if (isXDMFHDF5) PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF));
5912: PetscCall(DMLoad(*dm, viewer));
5913: if (isXDMFHDF5) PetscCall(PetscViewerPopFormat(viewer));
5914: PetscCall(PetscViewerDestroy(&viewer));
5916: if (interpolate) {
5917: DM idm;
5919: PetscCall(DMPlexInterpolate(*dm, &idm));
5920: PetscCall(DMDestroy(dm));
5921: *dm = idm;
5922: }
5923: } else if (isPLY) {
5924: PetscCall(DMPlexCreatePLYFromFile(comm, filename, interpolate, dm));
5925: } else if (isEGADSLite || isEGADS || isIGES || isSTEP) {
5926: if (isEGADSLite) PetscCall(DMPlexCreateEGADSLiteFromFile(comm, filename, dm));
5927: else PetscCall(DMPlexCreateEGADSFromFile(comm, filename, dm));
5928: if (!interpolate) {
5929: DM udm;
5931: PetscCall(DMPlexUninterpolate(*dm, &udm));
5932: PetscCall(DMDestroy(dm));
5933: *dm = udm;
5934: }
5935: } else if (isCV) {
5936: PetscCall(DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm));
5937: } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename);
5938: PetscCall(PetscStrlen(plexname, &len));
5939: if (len) PetscCall(PetscObjectSetName((PetscObject)*dm, plexname));
5940: PetscCall(PetscLogEventEnd(DMPLEX_CreateFromFile, 0, 0, 0, 0));
5941: PetscFunctionReturn(PETSC_SUCCESS);
5942: }
5944: /*@
5945: 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.
5947: Input Parameters:
5948: + tr - The `DMPlexTransform`
5949: - prefix - An options prefix, or NULL
5951: Output Parameter:
5952: . dm - The `DM`
5954: Level: beginner
5956: Notes:
5957: 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.
5959: .seealso: `DMPlexCreateFromFile`, `DMPlexCreateFromDAG()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()`
5960: @*/
5961: PetscErrorCode DMPlexCreateEphemeral(DMPlexTransform tr, const char prefix[], DM *dm)
5962: {
5963: DM bdm, bcdm, cdm;
5964: Vec coordinates, coordinatesNew;
5965: PetscSection cs;
5966: PetscInt cdim, Nl;
5968: PetscFunctionBegin;
5969: PetscCall(DMCreate(PetscObjectComm((PetscObject)tr), dm));
5970: PetscCall(DMSetType(*dm, DMPLEX));
5971: ((DM_Plex *)(*dm)->data)->interpolated = DMPLEX_INTERPOLATED_FULL;
5972: // Handle coordinates
5973: PetscCall(DMPlexTransformGetDM(tr, &bdm));
5974: PetscCall(DMPlexTransformSetDimensions(tr, bdm, *dm));
5975: PetscCall(DMGetCoordinateDim(*dm, &cdim));
5976: PetscCall(DMGetCoordinateDM(bdm, &bcdm));
5977: PetscCall(DMGetCoordinateDM(*dm, &cdm));
5978: PetscCall(DMCopyDisc(bcdm, cdm));
5979: PetscCall(DMGetLocalSection(cdm, &cs));
5980: PetscCall(PetscSectionSetNumFields(cs, 1));
5981: PetscCall(PetscSectionSetFieldComponents(cs, 0, cdim));
5982: PetscCall(DMGetCoordinatesLocal(bdm, &coordinates));
5983: PetscCall(VecDuplicate(coordinates, &coordinatesNew));
5984: PetscCall(VecCopy(coordinates, coordinatesNew));
5985: PetscCall(DMSetCoordinatesLocal(*dm, coordinatesNew));
5986: PetscCall(VecDestroy(&coordinatesNew));
5988: PetscCall(PetscObjectReference((PetscObject)tr));
5989: PetscCall(DMPlexTransformDestroy(&((DM_Plex *)(*dm)->data)->tr));
5990: ((DM_Plex *)(*dm)->data)->tr = tr;
5991: PetscCall(DMPlexDistributeSetDefault(*dm, PETSC_FALSE));
5992: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)*dm, prefix));
5993: PetscCall(DMSetFromOptions(*dm));
5995: PetscCall(DMGetNumLabels(bdm, &Nl));
5996: for (PetscInt l = 0; l < Nl; ++l) {
5997: DMLabel label, labelNew;
5998: const char *lname;
5999: PetscBool isDepth, isCellType;
6001: PetscCall(DMGetLabelName(bdm, l, &lname));
6002: PetscCall(PetscStrcmp(lname, "depth", &isDepth));
6003: if (isDepth) continue;
6004: PetscCall(PetscStrcmp(lname, "celltype", &isCellType));
6005: if (isCellType) continue;
6006: PetscCall(DMCreateLabel(*dm, lname));
6007: PetscCall(DMGetLabel(bdm, lname, &label));
6008: PetscCall(DMGetLabel(*dm, lname, &labelNew));
6009: PetscCall(DMLabelSetType(labelNew, DMLABELEPHEMERAL));
6010: PetscCall(DMLabelEphemeralSetLabel(labelNew, label));
6011: PetscCall(DMLabelEphemeralSetTransform(labelNew, tr));
6012: PetscCall(DMLabelSetUp(labelNew));
6013: }
6014: PetscFunctionReturn(PETSC_SUCCESS);
6015: }