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 <petsc/private/kernels/blockmatmult.h>
7: #include <petsc/private/kernels/blockinvert.h>
9: PetscLogEvent DMPLEX_CreateFromFile, DMPLEX_BuildFromCellList, DMPLEX_BuildCoordinatesFromCellList;
11: /* External function declarations here */
12: static PetscErrorCode DMInitialize_Plex(DM dm);
14: /* This copies internal things in the Plex structure that we generally want when making a new, related Plex */
15: PetscErrorCode DMPlexCopy_Internal(DM dmin, PetscBool copyPeriodicity, DM dmout)
16: {
17: const DMBoundaryType *bd;
18: const PetscReal *maxCell, *L;
19: PetscBool isper, dist;
21: if (copyPeriodicity) {
22: DMGetPeriodicity(dmin, &isper, &maxCell, &L, &bd);
23: DMSetPeriodicity(dmout, isper, maxCell, L, bd);
24: }
25: DMPlexDistributeGetDefault(dmin, &dist);
26: DMPlexDistributeSetDefault(dmout, dist);
27: ((DM_Plex *) dmout->data)->useHashLocation = ((DM_Plex *) dmin->data)->useHashLocation;
28: return 0;
29: }
31: /* Replace dm with the contents of ndm, and then destroy ndm
32: - Share the DM_Plex structure
33: - Share the coordinates
34: - Share the SF
35: */
36: static PetscErrorCode DMPlexReplace_Static(DM dm, DM *ndm)
37: {
38: PetscSF sf;
39: DM dmNew = *ndm, coordDM, coarseDM;
40: Vec coords;
41: PetscBool isper;
42: const PetscReal *maxCell, *L;
43: const DMBoundaryType *bd;
44: PetscInt dim, cdim;
46: if (dm == dmNew) {
47: DMDestroy(ndm);
48: return 0;
49: }
50: dm->setupcalled = dmNew->setupcalled;
51: DMGetDimension(dmNew, &dim);
52: DMSetDimension(dm, dim);
53: DMGetCoordinateDim(dmNew, &cdim);
54: DMSetCoordinateDim(dm, cdim);
55: DMGetPointSF(dmNew, &sf);
56: DMSetPointSF(dm, sf);
57: DMGetCoordinateDM(dmNew, &coordDM);
58: DMGetCoordinatesLocal(dmNew, &coords);
59: DMSetCoordinateDM(dm, coordDM);
60: DMSetCoordinatesLocal(dm, coords);
61: /* Do not want to create the coordinate field if it does not already exist, so do not call DMGetCoordinateField() */
62: DMFieldDestroy(&dm->coordinateField);
63: dm->coordinateField = dmNew->coordinateField;
64: ((DM_Plex *) dmNew->data)->coordFunc = ((DM_Plex *) dm->data)->coordFunc;
65: DMGetPeriodicity(dmNew, &isper, &maxCell, &L, &bd);
66: DMSetPeriodicity(dm, isper, maxCell, L, bd);
67: DMDestroy_Plex(dm);
68: DMInitialize_Plex(dm);
69: dm->data = dmNew->data;
70: ((DM_Plex *) dmNew->data)->refct++;
71: DMDestroyLabelLinkList_Internal(dm);
72: DMCopyLabels(dmNew, dm, PETSC_OWN_POINTER, PETSC_TRUE, DM_COPY_LABELS_FAIL);
73: DMGetCoarseDM(dmNew,&coarseDM);
74: DMSetCoarseDM(dm,coarseDM);
75: DMDestroy(ndm);
76: return 0;
77: }
79: /* Swap dm with the contents of dmNew
80: - Swap the DM_Plex structure
81: - Swap the coordinates
82: - Swap the point PetscSF
83: */
84: static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB)
85: {
86: DM coordDMA, coordDMB;
87: Vec coordsA, coordsB;
88: PetscSF sfA, sfB;
89: DMField fieldTmp;
90: void *tmp;
91: DMLabelLink listTmp;
92: DMLabel depthTmp;
93: PetscInt tmpI;
95: if (dmA == dmB) return 0;
96: DMGetPointSF(dmA, &sfA);
97: DMGetPointSF(dmB, &sfB);
98: PetscObjectReference((PetscObject) sfA);
99: DMSetPointSF(dmA, sfB);
100: DMSetPointSF(dmB, sfA);
101: PetscObjectDereference((PetscObject) sfA);
103: DMGetCoordinateDM(dmA, &coordDMA);
104: DMGetCoordinateDM(dmB, &coordDMB);
105: PetscObjectReference((PetscObject) coordDMA);
106: DMSetCoordinateDM(dmA, coordDMB);
107: DMSetCoordinateDM(dmB, coordDMA);
108: PetscObjectDereference((PetscObject) coordDMA);
110: DMGetCoordinatesLocal(dmA, &coordsA);
111: DMGetCoordinatesLocal(dmB, &coordsB);
112: PetscObjectReference((PetscObject) coordsA);
113: DMSetCoordinatesLocal(dmA, coordsB);
114: DMSetCoordinatesLocal(dmB, coordsA);
115: PetscObjectDereference((PetscObject) coordsA);
117: fieldTmp = dmA->coordinateField;
118: dmA->coordinateField = dmB->coordinateField;
119: dmB->coordinateField = fieldTmp;
120: tmp = dmA->data;
121: dmA->data = dmB->data;
122: dmB->data = tmp;
123: listTmp = dmA->labels;
124: dmA->labels = dmB->labels;
125: dmB->labels = listTmp;
126: depthTmp = dmA->depthLabel;
127: dmA->depthLabel = dmB->depthLabel;
128: dmB->depthLabel = depthTmp;
129: depthTmp = dmA->celltypeLabel;
130: dmA->celltypeLabel = dmB->celltypeLabel;
131: dmB->celltypeLabel = depthTmp;
132: tmpI = dmA->levelup;
133: dmA->levelup = dmB->levelup;
134: dmB->levelup = tmpI;
135: return 0;
136: }
138: static PetscErrorCode DMPlexInterpolateInPlace_Internal(DM dm)
139: {
140: DM idm;
142: DMPlexInterpolate(dm, &idm);
143: DMPlexCopyCoordinates(dm, idm);
144: DMPlexReplace_Static(dm, &idm);
145: return 0;
146: }
148: /*@C
149: DMPlexCreateCoordinateSpace - Creates a finite element space for the coordinates
151: Collective
153: Input Parameters:
154: + DM - The DM
155: . degree - The degree of the finite element or PETSC_DECIDE
156: - coordFunc - An optional function to map new points from refinement to the surface
158: Level: advanced
160: .seealso: PetscFECreateLagrange(), DMGetCoordinateDM()
161: @*/
162: PetscErrorCode DMPlexCreateCoordinateSpace(DM dm, PetscInt degree, PetscPointFunc coordFunc)
163: {
164: DM_Plex *mesh = (DM_Plex *) dm->data;
165: DM cdm;
166: PetscDS cds;
167: PetscFE fe;
168: PetscClassId id;
170: DMGetCoordinateDM(dm, &cdm);
171: DMGetDS(cdm, &cds);
172: PetscDSGetDiscretization(cds, 0, (PetscObject *) &fe);
173: PetscObjectGetClassId((PetscObject) fe, &id);
174: if (id != PETSCFE_CLASSID) {
175: PetscBool simplex;
176: PetscInt dim, dE, qorder;
179: DMGetDimension(dm, &dim);
180: DMGetCoordinateDim(dm, &dE);
181: qorder = degree;
182: PetscObjectOptionsBegin((PetscObject) cdm);
183: PetscOptionsBoundedInt("-coord_dm_default_quadrature_order", "Quadrature order is one less than quadrature points per edge", "DMPlexCreateCoordinateSpace", qorder, &qorder, NULL, 0);
184: PetscOptionsEnd();
185: if (degree == PETSC_DECIDE) fe = NULL;
186: else {
187: DMPlexIsSimplex(dm, &simplex);
188: PetscFECreateLagrange(PETSC_COMM_SELF, dim, dE, simplex, degree, qorder, &fe);
189: }
190: DMProjectCoordinates(dm, fe);
191: PetscFEDestroy(&fe);
192: }
193: mesh->coordFunc = coordFunc;
194: return 0;
195: }
197: /*@
198: DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement.
200: Collective
202: Input Parameters:
203: + comm - The communicator for the DM object
204: . dim - The spatial dimension
205: . simplex - Flag for simplicial cells, otherwise they are tensor product cells
206: . interpolate - Flag to create intermediate mesh pieces (edges, faces)
207: - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell
209: Output Parameter:
210: . dm - The DM object
212: Level: beginner
214: .seealso: DMSetType(), DMCreate()
215: @*/
216: PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscReal refinementLimit, DM *newdm)
217: {
218: DM dm;
219: PetscMPIInt rank;
221: DMCreate(comm, &dm);
222: DMSetType(dm, DMPLEX);
223: DMSetDimension(dm, dim);
224: MPI_Comm_rank(comm, &rank);
225: switch (dim) {
226: case 2:
227: if (simplex) PetscObjectSetName((PetscObject) dm, "triangular");
228: else PetscObjectSetName((PetscObject) dm, "quadrilateral");
229: break;
230: case 3:
231: if (simplex) PetscObjectSetName((PetscObject) dm, "tetrahedral");
232: else PetscObjectSetName((PetscObject) dm, "hexahedral");
233: break;
234: default:
235: SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %D", dim);
236: }
237: if (rank) {
238: PetscInt numPoints[2] = {0, 0};
239: DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);
240: } else {
241: switch (dim) {
242: case 2:
243: if (simplex) {
244: PetscInt numPoints[2] = {4, 2};
245: PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0};
246: PetscInt cones[6] = {2, 3, 4, 5, 4, 3};
247: PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0};
248: PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5};
250: DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
251: } else {
252: PetscInt numPoints[2] = {6, 2};
253: PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0};
254: PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4};
255: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
256: 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};
258: DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
259: }
260: break;
261: case 3:
262: if (simplex) {
263: PetscInt numPoints[2] = {5, 2};
264: PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0};
265: PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6};
266: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
267: 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};
269: DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
270: } else {
271: PetscInt numPoints[2] = {12, 2};
272: PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
273: PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8};
274: PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
275: 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,
276: -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5,
277: 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5};
279: DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
280: }
281: break;
282: default:
283: SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %D", dim);
284: }
285: }
286: *newdm = dm;
287: if (refinementLimit > 0.0) {
288: DM rdm;
289: const char *name;
291: DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);
292: DMPlexSetRefinementLimit(*newdm, refinementLimit);
293: DMRefine(*newdm, comm, &rdm);
294: PetscObjectGetName((PetscObject) *newdm, &name);
295: PetscObjectSetName((PetscObject) rdm, name);
296: DMDestroy(newdm);
297: *newdm = rdm;
298: }
299: if (interpolate) {
300: DM idm;
302: DMPlexInterpolate(*newdm, &idm);
303: DMDestroy(newdm);
304: *newdm = idm;
305: }
306: return 0;
307: }
309: static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
310: {
311: const PetscInt numVertices = 2;
312: PetscInt markerRight = 1;
313: PetscInt markerLeft = 1;
314: PetscBool markerSeparate = PETSC_FALSE;
315: Vec coordinates;
316: PetscSection coordSection;
317: PetscScalar *coords;
318: PetscInt coordSize;
319: PetscMPIInt rank;
320: PetscInt cdim = 1, v;
322: PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);
323: if (markerSeparate) {
324: markerRight = 2;
325: markerLeft = 1;
326: }
327: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
328: if (!rank) {
329: DMPlexSetChart(dm, 0, numVertices);
330: DMSetUp(dm); /* Allocate space for cones */
331: DMSetLabelValue(dm, "marker", 0, markerLeft);
332: DMSetLabelValue(dm, "marker", 1, markerRight);
333: }
334: DMPlexSymmetrize(dm);
335: DMPlexStratify(dm);
336: /* Build coordinates */
337: DMSetCoordinateDim(dm, cdim);
338: DMGetCoordinateSection(dm, &coordSection);
339: PetscSectionSetNumFields(coordSection, 1);
340: PetscSectionSetChart(coordSection, 0, numVertices);
341: PetscSectionSetFieldComponents(coordSection, 0, cdim);
342: for (v = 0; v < numVertices; ++v) {
343: PetscSectionSetDof(coordSection, v, cdim);
344: PetscSectionSetFieldDof(coordSection, v, 0, cdim);
345: }
346: PetscSectionSetUp(coordSection);
347: PetscSectionGetStorageSize(coordSection, &coordSize);
348: VecCreate(PETSC_COMM_SELF, &coordinates);
349: PetscObjectSetName((PetscObject) coordinates, "coordinates");
350: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
351: VecSetBlockSize(coordinates, cdim);
352: VecSetType(coordinates,VECSTANDARD);
353: VecGetArray(coordinates, &coords);
354: coords[0] = lower[0];
355: coords[1] = upper[0];
356: VecRestoreArray(coordinates, &coords);
357: DMSetCoordinatesLocal(dm, coordinates);
358: VecDestroy(&coordinates);
359: return 0;
360: }
362: static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
363: {
364: const PetscInt numVertices = (edges[0]+1)*(edges[1]+1);
365: const PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1];
366: PetscInt markerTop = 1;
367: PetscInt markerBottom = 1;
368: PetscInt markerRight = 1;
369: PetscInt markerLeft = 1;
370: PetscBool markerSeparate = PETSC_FALSE;
371: Vec coordinates;
372: PetscSection coordSection;
373: PetscScalar *coords;
374: PetscInt coordSize;
375: PetscMPIInt rank;
376: PetscInt v, vx, vy;
378: PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);
379: if (markerSeparate) {
380: markerTop = 3;
381: markerBottom = 1;
382: markerRight = 2;
383: markerLeft = 4;
384: }
385: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
386: if (rank == 0) {
387: PetscInt e, ex, ey;
389: DMPlexSetChart(dm, 0, numEdges+numVertices);
390: for (e = 0; e < numEdges; ++e) {
391: DMPlexSetConeSize(dm, e, 2);
392: }
393: DMSetUp(dm); /* Allocate space for cones */
394: for (vx = 0; vx <= edges[0]; vx++) {
395: for (ey = 0; ey < edges[1]; ey++) {
396: PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1);
397: PetscInt vertex = ey*(edges[0]+1) + vx + numEdges;
398: PetscInt cone[2];
400: cone[0] = vertex; cone[1] = vertex+edges[0]+1;
401: DMPlexSetCone(dm, edge, cone);
402: if (vx == edges[0]) {
403: DMSetLabelValue(dm, "marker", edge, markerRight);
404: DMSetLabelValue(dm, "marker", cone[0], markerRight);
405: if (ey == edges[1]-1) {
406: DMSetLabelValue(dm, "marker", cone[1], markerRight);
407: DMSetLabelValue(dm, "Face Sets", cone[1], markerRight);
408: }
409: } else if (vx == 0) {
410: DMSetLabelValue(dm, "marker", edge, markerLeft);
411: DMSetLabelValue(dm, "marker", cone[0], markerLeft);
412: if (ey == edges[1]-1) {
413: DMSetLabelValue(dm, "marker", cone[1], markerLeft);
414: DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft);
415: }
416: }
417: }
418: }
419: for (vy = 0; vy <= edges[1]; vy++) {
420: for (ex = 0; ex < edges[0]; ex++) {
421: PetscInt edge = vy*edges[0] + ex;
422: PetscInt vertex = vy*(edges[0]+1) + ex + numEdges;
423: PetscInt cone[2];
425: cone[0] = vertex; cone[1] = vertex+1;
426: DMPlexSetCone(dm, edge, cone);
427: if (vy == edges[1]) {
428: DMSetLabelValue(dm, "marker", edge, markerTop);
429: DMSetLabelValue(dm, "marker", cone[0], markerTop);
430: if (ex == edges[0]-1) {
431: DMSetLabelValue(dm, "marker", cone[1], markerTop);
432: DMSetLabelValue(dm, "Face Sets", cone[1], markerTop);
433: }
434: } else if (vy == 0) {
435: DMSetLabelValue(dm, "marker", edge, markerBottom);
436: DMSetLabelValue(dm, "marker", cone[0], markerBottom);
437: if (ex == edges[0]-1) {
438: DMSetLabelValue(dm, "marker", cone[1], markerBottom);
439: DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom);
440: }
441: }
442: }
443: }
444: }
445: DMPlexSymmetrize(dm);
446: DMPlexStratify(dm);
447: /* Build coordinates */
448: DMSetCoordinateDim(dm, 2);
449: DMGetCoordinateSection(dm, &coordSection);
450: PetscSectionSetNumFields(coordSection, 1);
451: PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);
452: PetscSectionSetFieldComponents(coordSection, 0, 2);
453: for (v = numEdges; v < numEdges+numVertices; ++v) {
454: PetscSectionSetDof(coordSection, v, 2);
455: PetscSectionSetFieldDof(coordSection, v, 0, 2);
456: }
457: PetscSectionSetUp(coordSection);
458: PetscSectionGetStorageSize(coordSection, &coordSize);
459: VecCreate(PETSC_COMM_SELF, &coordinates);
460: PetscObjectSetName((PetscObject) coordinates, "coordinates");
461: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
462: VecSetBlockSize(coordinates, 2);
463: VecSetType(coordinates,VECSTANDARD);
464: VecGetArray(coordinates, &coords);
465: for (vy = 0; vy <= edges[1]; ++vy) {
466: for (vx = 0; vx <= edges[0]; ++vx) {
467: coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx;
468: coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy;
469: }
470: }
471: VecRestoreArray(coordinates, &coords);
472: DMSetCoordinatesLocal(dm, coordinates);
473: VecDestroy(&coordinates);
474: return 0;
475: }
477: static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[])
478: {
479: PetscInt vertices[3], numVertices;
480: PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2];
481: Vec coordinates;
482: PetscSection coordSection;
483: PetscScalar *coords;
484: PetscInt coordSize;
485: PetscMPIInt rank;
486: PetscInt v, vx, vy, vz;
487: PetscInt voffset, iface=0, cone[4];
490: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
491: vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1;
492: numVertices = vertices[0]*vertices[1]*vertices[2];
493: if (rank == 0) {
494: PetscInt f;
496: DMPlexSetChart(dm, 0, numFaces+numVertices);
497: for (f = 0; f < numFaces; ++f) {
498: DMPlexSetConeSize(dm, f, 4);
499: }
500: DMSetUp(dm); /* Allocate space for cones */
502: /* Side 0 (Top) */
503: for (vy = 0; vy < faces[1]; vy++) {
504: for (vx = 0; vx < faces[0]; vx++) {
505: voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx;
506: cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0];
507: DMPlexSetCone(dm, iface, cone);
508: DMSetLabelValue(dm, "marker", iface, 1);
509: DMSetLabelValue(dm, "marker", voffset+0, 1);
510: DMSetLabelValue(dm, "marker", voffset+1, 1);
511: DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);
512: DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);
513: iface++;
514: }
515: }
517: /* Side 1 (Bottom) */
518: for (vy = 0; vy < faces[1]; vy++) {
519: for (vx = 0; vx < faces[0]; vx++) {
520: voffset = numFaces + vy*(faces[0]+1) + vx;
521: cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1;
522: DMPlexSetCone(dm, iface, cone);
523: DMSetLabelValue(dm, "marker", iface, 1);
524: DMSetLabelValue(dm, "marker", voffset+0, 1);
525: DMSetLabelValue(dm, "marker", voffset+1, 1);
526: DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);
527: DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);
528: iface++;
529: }
530: }
532: /* Side 2 (Front) */
533: for (vz = 0; vz < faces[2]; vz++) {
534: for (vx = 0; vx < faces[0]; vx++) {
535: voffset = numFaces + vz*vertices[0]*vertices[1] + vx;
536: cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1];
537: DMPlexSetCone(dm, iface, cone);
538: DMSetLabelValue(dm, "marker", iface, 1);
539: DMSetLabelValue(dm, "marker", voffset+0, 1);
540: DMSetLabelValue(dm, "marker", voffset+1, 1);
541: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);
542: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);
543: iface++;
544: }
545: }
547: /* Side 3 (Back) */
548: for (vz = 0; vz < faces[2]; vz++) {
549: for (vx = 0; vx < faces[0]; vx++) {
550: voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx;
551: cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1;
552: cone[2] = voffset+1; cone[3] = voffset;
553: DMPlexSetCone(dm, iface, cone);
554: DMSetLabelValue(dm, "marker", iface, 1);
555: DMSetLabelValue(dm, "marker", voffset+0, 1);
556: DMSetLabelValue(dm, "marker", voffset+1, 1);
557: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);
558: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);
559: iface++;
560: }
561: }
563: /* Side 4 (Left) */
564: for (vz = 0; vz < faces[2]; vz++) {
565: for (vy = 0; vy < faces[1]; vy++) {
566: voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0];
567: cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1];
568: cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0];
569: DMPlexSetCone(dm, iface, cone);
570: DMSetLabelValue(dm, "marker", iface, 1);
571: DMSetLabelValue(dm, "marker", voffset+0, 1);
572: DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);
573: DMSetLabelValue(dm, "marker", voffset+vertices[1]+0, 1);
574: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);
575: iface++;
576: }
577: }
579: /* Side 5 (Right) */
580: for (vz = 0; vz < faces[2]; vz++) {
581: for (vy = 0; vy < faces[1]; vy++) {
582: voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + faces[0];
583: cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset;
584: cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0];
585: DMPlexSetCone(dm, iface, cone);
586: DMSetLabelValue(dm, "marker", iface, 1);
587: DMSetLabelValue(dm, "marker", voffset+0, 1);
588: DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);
589: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);
590: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);
591: iface++;
592: }
593: }
594: }
595: DMPlexSymmetrize(dm);
596: DMPlexStratify(dm);
597: /* Build coordinates */
598: DMSetCoordinateDim(dm, 3);
599: DMGetCoordinateSection(dm, &coordSection);
600: PetscSectionSetNumFields(coordSection, 1);
601: PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);
602: PetscSectionSetFieldComponents(coordSection, 0, 3);
603: for (v = numFaces; v < numFaces+numVertices; ++v) {
604: PetscSectionSetDof(coordSection, v, 3);
605: PetscSectionSetFieldDof(coordSection, v, 0, 3);
606: }
607: PetscSectionSetUp(coordSection);
608: PetscSectionGetStorageSize(coordSection, &coordSize);
609: VecCreate(PETSC_COMM_SELF, &coordinates);
610: PetscObjectSetName((PetscObject) coordinates, "coordinates");
611: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
612: VecSetBlockSize(coordinates, 3);
613: VecSetType(coordinates,VECSTANDARD);
614: VecGetArray(coordinates, &coords);
615: for (vz = 0; vz <= faces[2]; ++vz) {
616: for (vy = 0; vy <= faces[1]; ++vy) {
617: for (vx = 0; vx <= faces[0]; ++vx) {
618: coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx;
619: coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy;
620: coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz;
621: }
622: }
623: }
624: VecRestoreArray(coordinates, &coords);
625: DMSetCoordinatesLocal(dm, coordinates);
626: VecDestroy(&coordinates);
627: return 0;
628: }
630: static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate)
631: {
633: DMSetDimension(dm, dim-1);
634: DMSetCoordinateDim(dm, dim);
635: switch (dim) {
636: case 1: DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(dm, lower, upper, faces);break;
637: case 2: DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(dm, lower, upper, faces);break;
638: case 3: DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(dm, lower, upper, faces);break;
639: default: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Dimension not supported: %D", dim);
640: }
641: if (interpolate) DMPlexInterpolateInPlace_Internal(dm);
642: return 0;
643: }
645: /*@C
646: DMPlexCreateBoxSurfaceMesh - Creates a mesh on the surface of the tensor product of unit intervals (box) using tensor cells (hexahedra).
648: Collective
650: Input Parameters:
651: + comm - The communicator for the DM object
652: . dim - The spatial dimension of the box, so the resulting mesh is has dimension dim-1
653: . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D
654: . lower - The lower left corner, or NULL for (0, 0, 0)
655: . upper - The upper right corner, or NULL for (1, 1, 1)
656: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
658: Output Parameter:
659: . dm - The DM object
661: Level: beginner
663: .seealso: DMSetFromOptions(), DMPlexCreateBoxMesh(), DMPlexCreateFromFile(), DMSetType(), DMCreate()
664: @*/
665: PetscErrorCode DMPlexCreateBoxSurfaceMesh(MPI_Comm comm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate, DM *dm)
666: {
667: PetscInt fac[3] = {1, 1, 1};
668: PetscReal low[3] = {0, 0, 0};
669: PetscReal upp[3] = {1, 1, 1};
671: DMCreate(comm,dm);
672: DMSetType(*dm,DMPLEX);
673: DMPlexCreateBoxSurfaceMesh_Internal(*dm, dim, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, interpolate);
674: return 0;
675: }
677: static PetscErrorCode DMPlexCreateLineMesh_Internal(DM dm,PetscInt segments,PetscReal lower,PetscReal upper,DMBoundaryType bd)
678: {
679: PetscInt i,fStart,fEnd,numCells = 0,numVerts = 0;
680: PetscInt numPoints[2],*coneSize,*cones,*coneOrientations;
681: PetscScalar *vertexCoords;
682: PetscReal L,maxCell;
683: PetscBool markerSeparate = PETSC_FALSE;
684: PetscInt markerLeft = 1, faceMarkerLeft = 1;
685: PetscInt markerRight = 1, faceMarkerRight = 2;
686: PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE;
687: PetscMPIInt rank;
691: DMSetDimension(dm,1);
692: DMCreateLabel(dm,"marker");
693: DMCreateLabel(dm,"Face Sets");
695: MPI_Comm_rank(PetscObjectComm((PetscObject) dm),&rank);
696: if (rank == 0) numCells = segments;
697: if (rank == 0) numVerts = segments + (wrap ? 0 : 1);
699: numPoints[0] = numVerts ; numPoints[1] = numCells;
700: PetscMalloc4(numCells+numVerts,&coneSize,numCells*2,&cones,numCells+numVerts,&coneOrientations,numVerts,&vertexCoords);
701: PetscArrayzero(coneOrientations,numCells+numVerts);
702: for (i = 0; i < numCells; ++i) { coneSize[i] = 2; }
703: for (i = 0; i < numVerts; ++i) { coneSize[numCells+i] = 0; }
704: for (i = 0; i < numCells; ++i) { cones[2*i] = numCells + i%numVerts; cones[2*i+1] = numCells + (i+1)%numVerts; }
705: for (i = 0; i < numVerts; ++i) { vertexCoords[i] = lower + (upper-lower)*((PetscReal)i/(PetscReal)numCells); }
706: DMPlexCreateFromDAG(dm,1,numPoints,coneSize,cones,coneOrientations,vertexCoords);
707: PetscFree4(coneSize,cones,coneOrientations,vertexCoords);
709: PetscOptionsGetBool(((PetscObject)dm)->options,((PetscObject)dm)->prefix,"-dm_plex_separate_marker",&markerSeparate,NULL);
710: if (markerSeparate) { markerLeft = faceMarkerLeft; markerRight = faceMarkerRight;}
711: if (!wrap && rank == 0) {
712: DMPlexGetHeightStratum(dm,1,&fStart,&fEnd);
713: DMSetLabelValue(dm,"marker",fStart,markerLeft);
714: DMSetLabelValue(dm,"marker",fEnd-1,markerRight);
715: DMSetLabelValue(dm,"Face Sets",fStart,faceMarkerLeft);
716: DMSetLabelValue(dm,"Face Sets",fEnd-1,faceMarkerRight);
717: }
718: if (wrap) {
719: L = upper - lower;
720: maxCell = (PetscReal)1.1*(L/(PetscReal)PetscMax(1,segments));
721: DMSetPeriodicity(dm,PETSC_TRUE,&maxCell,&L,&bd);
722: }
723: DMPlexSetRefinementUniform(dm, PETSC_TRUE);
724: return 0;
725: }
727: static PetscErrorCode DMPlexCreateBoxMesh_Simplex_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate)
728: {
729: DM boundary, vol;
730: PetscInt i;
734: DMCreate(PetscObjectComm((PetscObject) dm), &boundary);
735: DMSetType(boundary, DMPLEX);
736: DMPlexCreateBoxSurfaceMesh_Internal(boundary, dim, faces, lower, upper, PETSC_FALSE);
737: DMPlexGenerate(boundary, NULL, interpolate, &vol);
738: DMPlexCopy_Internal(dm, PETSC_TRUE, vol);
739: DMPlexReplace_Static(dm, &vol);
740: DMDestroy(&boundary);
741: return 0;
742: }
744: static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ)
745: {
746: DMLabel cutLabel = NULL;
747: PetscInt markerTop = 1, faceMarkerTop = 1;
748: PetscInt markerBottom = 1, faceMarkerBottom = 1;
749: PetscInt markerFront = 1, faceMarkerFront = 1;
750: PetscInt markerBack = 1, faceMarkerBack = 1;
751: PetscInt markerRight = 1, faceMarkerRight = 1;
752: PetscInt markerLeft = 1, faceMarkerLeft = 1;
753: PetscInt dim;
754: PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE;
755: PetscMPIInt rank;
757: DMGetDimension(dm,&dim);
758: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
759: DMCreateLabel(dm,"marker");
760: DMCreateLabel(dm,"Face Sets");
761: PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL);
762: if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ||
763: bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ||
764: bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) {
766: if (cutMarker) {DMCreateLabel(dm, "periodic_cut")); PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel);}
767: }
768: switch (dim) {
769: case 2:
770: faceMarkerTop = 3;
771: faceMarkerBottom = 1;
772: faceMarkerRight = 2;
773: faceMarkerLeft = 4;
774: break;
775: case 3:
776: faceMarkerBottom = 1;
777: faceMarkerTop = 2;
778: faceMarkerFront = 3;
779: faceMarkerBack = 4;
780: faceMarkerRight = 5;
781: faceMarkerLeft = 6;
782: break;
783: default:
784: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %D not supported",dim);
785: }
786: PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);
787: if (markerSeparate) {
788: markerBottom = faceMarkerBottom;
789: markerTop = faceMarkerTop;
790: markerFront = faceMarkerFront;
791: markerBack = faceMarkerBack;
792: markerRight = faceMarkerRight;
793: markerLeft = faceMarkerLeft;
794: }
795: {
796: const PetscInt numXEdges = rank == 0 ? edges[0] : 0;
797: const PetscInt numYEdges = rank == 0 ? edges[1] : 0;
798: const PetscInt numZEdges = rank == 0 ? edges[2] : 0;
799: const PetscInt numXVertices = rank == 0 ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0;
800: const PetscInt numYVertices = rank == 0 ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0;
801: const PetscInt numZVertices = rank == 0 ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0;
802: const PetscInt numCells = numXEdges*numYEdges*numZEdges;
803: const PetscInt numXFaces = numYEdges*numZEdges;
804: const PetscInt numYFaces = numXEdges*numZEdges;
805: const PetscInt numZFaces = numXEdges*numYEdges;
806: const PetscInt numTotXFaces = numXVertices*numXFaces;
807: const PetscInt numTotYFaces = numYVertices*numYFaces;
808: const PetscInt numTotZFaces = numZVertices*numZFaces;
809: const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces;
810: const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices;
811: const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices;
812: const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices;
813: const PetscInt numVertices = numXVertices*numYVertices*numZVertices;
814: const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges;
815: const PetscInt firstVertex = (dim == 2) ? numFaces : numCells;
816: const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices;
817: const PetscInt firstYFace = firstXFace + numTotXFaces;
818: const PetscInt firstZFace = firstYFace + numTotYFaces;
819: const PetscInt firstXEdge = numCells + numFaces + numVertices;
820: const PetscInt firstYEdge = firstXEdge + numTotXEdges;
821: const PetscInt firstZEdge = firstYEdge + numTotYEdges;
822: Vec coordinates;
823: PetscSection coordSection;
824: PetscScalar *coords;
825: PetscInt coordSize;
826: PetscInt v, vx, vy, vz;
827: PetscInt c, f, fx, fy, fz, e, ex, ey, ez;
829: DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);
830: for (c = 0; c < numCells; c++) {
831: DMPlexSetConeSize(dm, c, 6);
832: }
833: for (f = firstXFace; f < firstXFace+numFaces; ++f) {
834: DMPlexSetConeSize(dm, f, 4);
835: }
836: for (e = firstXEdge; e < firstXEdge+numEdges; ++e) {
837: DMPlexSetConeSize(dm, e, 2);
838: }
839: DMSetUp(dm); /* Allocate space for cones */
840: /* Build cells */
841: for (fz = 0; fz < numZEdges; ++fz) {
842: for (fy = 0; fy < numYEdges; ++fy) {
843: for (fx = 0; fx < numXEdges; ++fx) {
844: PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx;
845: PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz;
846: PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices);
847: PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy;
848: PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices);
849: PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx;
850: PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices);
851: /* B, T, F, K, R, L */
852: PetscInt ornt[6] = {-2, 0, 0, -3, 0, -2}; /* ??? */
853: PetscInt cone[6];
855: /* no boundary twisting in 3D */
856: cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL;
857: DMPlexSetCone(dm, cell, cone);
858: DMPlexSetConeOrientation(dm, cell, ornt);
859: if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) DMLabelSetValue(cutLabel, cell, 2);
860: if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) DMLabelSetValue(cutLabel, cell, 2);
861: if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) DMLabelSetValue(cutLabel, cell, 2);
862: }
863: }
864: }
865: /* Build x faces */
866: for (fz = 0; fz < numZEdges; ++fz) {
867: for (fy = 0; fy < numYEdges; ++fy) {
868: for (fx = 0; fx < numXVertices; ++fx) {
869: PetscInt face = firstXFace + (fz*numYEdges+fy) *numXVertices+fx;
870: PetscInt edgeL = firstZEdge + (fy *numXVertices+fx)*numZEdges + fz;
871: PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz;
872: PetscInt edgeB = firstYEdge + (fz *numXVertices+fx)*numYEdges + fy;
873: PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy;
874: PetscInt ornt[4] = {0, 0, -1, -1};
875: PetscInt cone[4];
877: if (dim == 3) {
878: /* markers */
879: if (bdX != DM_BOUNDARY_PERIODIC) {
880: if (fx == numXVertices-1) {
881: DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);
882: DMSetLabelValue(dm, "marker", face, markerRight);
883: }
884: else if (fx == 0) {
885: DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);
886: DMSetLabelValue(dm, "marker", face, markerLeft);
887: }
888: }
889: }
890: cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
891: DMPlexSetCone(dm, face, cone);
892: DMPlexSetConeOrientation(dm, face, ornt);
893: }
894: }
895: }
896: /* Build y faces */
897: for (fz = 0; fz < numZEdges; ++fz) {
898: for (fx = 0; fx < numXEdges; ++fx) {
899: for (fy = 0; fy < numYVertices; ++fy) {
900: PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy;
901: PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx)*numZEdges + fz;
902: PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz;
903: PetscInt edgeB = firstXEdge + (fz *numYVertices+fy)*numXEdges + fx;
904: PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx;
905: PetscInt ornt[4] = {0, 0, -1, -1};
906: PetscInt cone[4];
908: if (dim == 3) {
909: /* markers */
910: if (bdY != DM_BOUNDARY_PERIODIC) {
911: if (fy == numYVertices-1) {
912: DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);
913: DMSetLabelValue(dm, "marker", face, markerBack);
914: }
915: else if (fy == 0) {
916: DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);
917: DMSetLabelValue(dm, "marker", face, markerFront);
918: }
919: }
920: }
921: cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
922: DMPlexSetCone(dm, face, cone);
923: DMPlexSetConeOrientation(dm, face, ornt);
924: }
925: }
926: }
927: /* Build z faces */
928: for (fy = 0; fy < numYEdges; ++fy) {
929: for (fx = 0; fx < numXEdges; ++fx) {
930: for (fz = 0; fz < numZVertices; fz++) {
931: PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz;
932: PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx)*numYEdges + fy;
933: PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy;
934: PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy)*numXEdges + fx;
935: PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx;
936: PetscInt ornt[4] = {0, 0, -1, -1};
937: PetscInt cone[4];
939: if (dim == 2) {
940: if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -1;}
941: if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;}
942: if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) DMLabelSetValue(cutLabel, face, 2);
943: if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) DMLabelSetValue(cutLabel, face, 2);
944: } else {
945: /* markers */
946: if (bdZ != DM_BOUNDARY_PERIODIC) {
947: if (fz == numZVertices-1) {
948: DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);
949: DMSetLabelValue(dm, "marker", face, markerTop);
950: }
951: else if (fz == 0) {
952: DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);
953: DMSetLabelValue(dm, "marker", face, markerBottom);
954: }
955: }
956: }
957: cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
958: DMPlexSetCone(dm, face, cone);
959: DMPlexSetConeOrientation(dm, face, ornt);
960: }
961: }
962: }
963: /* Build Z edges*/
964: for (vy = 0; vy < numYVertices; vy++) {
965: for (vx = 0; vx < numXVertices; vx++) {
966: for (ez = 0; ez < numZEdges; ez++) {
967: const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez;
968: const PetscInt vertexB = firstVertex + (ez *numYVertices+vy)*numXVertices + vx;
969: const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx;
970: PetscInt cone[2];
972: if (dim == 3) {
973: if (bdX != DM_BOUNDARY_PERIODIC) {
974: if (vx == numXVertices-1) {
975: DMSetLabelValue(dm, "marker", edge, markerRight);
976: }
977: else if (vx == 0) {
978: DMSetLabelValue(dm, "marker", edge, markerLeft);
979: }
980: }
981: if (bdY != DM_BOUNDARY_PERIODIC) {
982: if (vy == numYVertices-1) {
983: DMSetLabelValue(dm, "marker", edge, markerBack);
984: }
985: else if (vy == 0) {
986: DMSetLabelValue(dm, "marker", edge, markerFront);
987: }
988: }
989: }
990: cone[0] = vertexB; cone[1] = vertexT;
991: DMPlexSetCone(dm, edge, cone);
992: }
993: }
994: }
995: /* Build Y edges*/
996: for (vz = 0; vz < numZVertices; vz++) {
997: for (vx = 0; vx < numXVertices; vx++) {
998: for (ey = 0; ey < numYEdges; ey++) {
999: const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx;
1000: const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey;
1001: const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx;
1002: const PetscInt vertexK = firstVertex + nextv;
1003: PetscInt cone[2];
1005: cone[0] = vertexF; cone[1] = vertexK;
1006: DMPlexSetCone(dm, edge, cone);
1007: if (dim == 2) {
1008: if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) {
1009: if (vx == numXVertices-1) {
1010: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);
1011: DMSetLabelValue(dm, "marker", edge, markerRight);
1012: DMSetLabelValue(dm, "marker", cone[0], markerRight);
1013: if (ey == numYEdges-1) {
1014: DMSetLabelValue(dm, "marker", cone[1], markerRight);
1015: }
1016: } else if (vx == 0) {
1017: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);
1018: DMSetLabelValue(dm, "marker", edge, markerLeft);
1019: DMSetLabelValue(dm, "marker", cone[0], markerLeft);
1020: if (ey == numYEdges-1) {
1021: DMSetLabelValue(dm, "marker", cone[1], markerLeft);
1022: }
1023: }
1024: } else {
1025: if (vx == 0 && cutLabel) {
1026: DMLabelSetValue(cutLabel, edge, 1);
1027: DMLabelSetValue(cutLabel, cone[0], 1);
1028: if (ey == numYEdges-1) {
1029: DMLabelSetValue(cutLabel, cone[1], 1);
1030: }
1031: }
1032: }
1033: } else {
1034: if (bdX != DM_BOUNDARY_PERIODIC) {
1035: if (vx == numXVertices-1) {
1036: DMSetLabelValue(dm, "marker", edge, markerRight);
1037: } else if (vx == 0) {
1038: DMSetLabelValue(dm, "marker", edge, markerLeft);
1039: }
1040: }
1041: if (bdZ != DM_BOUNDARY_PERIODIC) {
1042: if (vz == numZVertices-1) {
1043: DMSetLabelValue(dm, "marker", edge, markerTop);
1044: } else if (vz == 0) {
1045: DMSetLabelValue(dm, "marker", edge, markerBottom);
1046: }
1047: }
1048: }
1049: }
1050: }
1051: }
1052: /* Build X edges*/
1053: for (vz = 0; vz < numZVertices; vz++) {
1054: for (vy = 0; vy < numYVertices; vy++) {
1055: for (ex = 0; ex < numXEdges; ex++) {
1056: const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices;
1057: const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex;
1058: const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex;
1059: const PetscInt vertexR = firstVertex + nextv;
1060: PetscInt cone[2];
1062: cone[0] = vertexL; cone[1] = vertexR;
1063: DMPlexSetCone(dm, edge, cone);
1064: if (dim == 2) {
1065: if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) {
1066: if (vy == numYVertices-1) {
1067: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);
1068: DMSetLabelValue(dm, "marker", edge, markerTop);
1069: DMSetLabelValue(dm, "marker", cone[0], markerTop);
1070: if (ex == numXEdges-1) {
1071: DMSetLabelValue(dm, "marker", cone[1], markerTop);
1072: }
1073: } else if (vy == 0) {
1074: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);
1075: DMSetLabelValue(dm, "marker", edge, markerBottom);
1076: DMSetLabelValue(dm, "marker", cone[0], markerBottom);
1077: if (ex == numXEdges-1) {
1078: DMSetLabelValue(dm, "marker", cone[1], markerBottom);
1079: }
1080: }
1081: } else {
1082: if (vy == 0 && cutLabel) {
1083: DMLabelSetValue(cutLabel, edge, 1);
1084: DMLabelSetValue(cutLabel, cone[0], 1);
1085: if (ex == numXEdges-1) {
1086: DMLabelSetValue(cutLabel, cone[1], 1);
1087: }
1088: }
1089: }
1090: } else {
1091: if (bdY != DM_BOUNDARY_PERIODIC) {
1092: if (vy == numYVertices-1) {
1093: DMSetLabelValue(dm, "marker", edge, markerBack);
1094: }
1095: else if (vy == 0) {
1096: DMSetLabelValue(dm, "marker", edge, markerFront);
1097: }
1098: }
1099: if (bdZ != DM_BOUNDARY_PERIODIC) {
1100: if (vz == numZVertices-1) {
1101: DMSetLabelValue(dm, "marker", edge, markerTop);
1102: }
1103: else if (vz == 0) {
1104: DMSetLabelValue(dm, "marker", edge, markerBottom);
1105: }
1106: }
1107: }
1108: }
1109: }
1110: }
1111: DMPlexSymmetrize(dm);
1112: DMPlexStratify(dm);
1113: /* Build coordinates */
1114: DMGetCoordinateSection(dm, &coordSection);
1115: PetscSectionSetNumFields(coordSection, 1);
1116: PetscSectionSetFieldComponents(coordSection, 0, dim);
1117: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);
1118: for (v = firstVertex; v < firstVertex+numVertices; ++v) {
1119: PetscSectionSetDof(coordSection, v, dim);
1120: PetscSectionSetFieldDof(coordSection, v, 0, dim);
1121: }
1122: PetscSectionSetUp(coordSection);
1123: PetscSectionGetStorageSize(coordSection, &coordSize);
1124: VecCreate(PETSC_COMM_SELF, &coordinates);
1125: PetscObjectSetName((PetscObject) coordinates, "coordinates");
1126: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1127: VecSetBlockSize(coordinates, dim);
1128: VecSetType(coordinates,VECSTANDARD);
1129: VecGetArray(coordinates, &coords);
1130: for (vz = 0; vz < numZVertices; ++vz) {
1131: for (vy = 0; vy < numYVertices; ++vy) {
1132: for (vx = 0; vx < numXVertices; ++vx) {
1133: coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx;
1134: coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy;
1135: if (dim == 3) {
1136: coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz;
1137: }
1138: }
1139: }
1140: }
1141: VecRestoreArray(coordinates, &coords);
1142: DMSetCoordinatesLocal(dm, coordinates);
1143: VecDestroy(&coordinates);
1144: }
1145: return 0;
1146: }
1148: static PetscErrorCode DMPlexCreateBoxMesh_Tensor_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[])
1149: {
1150: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
1151: PetscInt fac[3] = {0, 0, 0}, d;
1155: DMSetDimension(dm, dim);
1156: for (d = 0; d < dim; ++d) {fac[d] = faces[d]; bdt[d] = periodicity[d];}
1157: DMPlexCreateCubeMesh_Internal(dm, lower, upper, fac, bdt[0], bdt[1], bdt[2]);
1158: if (periodicity[0] == DM_BOUNDARY_PERIODIC || periodicity[0] == DM_BOUNDARY_TWIST ||
1159: periodicity[1] == DM_BOUNDARY_PERIODIC || periodicity[1] == DM_BOUNDARY_TWIST ||
1160: (dim > 2 && (periodicity[2] == DM_BOUNDARY_PERIODIC || periodicity[2] == DM_BOUNDARY_TWIST))) {
1161: PetscReal L[3];
1162: PetscReal maxCell[3];
1164: for (d = 0; d < dim; ++d) {
1165: L[d] = upper[d] - lower[d];
1166: maxCell[d] = 1.1 * (L[d] / PetscMax(1, faces[d]));
1167: }
1168: DMSetPeriodicity(dm, PETSC_TRUE, maxCell, L, periodicity);
1169: }
1170: DMPlexSetRefinementUniform(dm, PETSC_TRUE);
1171: return 0;
1172: }
1174: static PetscErrorCode DMPlexCreateBoxMesh_Internal(DM dm, PetscInt dim, PetscBool simplex, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate)
1175: {
1176: if (dim == 1) DMPlexCreateLineMesh_Internal(dm, faces[0], lower[0], upper[0], periodicity[0]);
1177: else if (simplex) DMPlexCreateBoxMesh_Simplex_Internal(dm, dim, faces, lower, upper, periodicity, interpolate);
1178: else DMPlexCreateBoxMesh_Tensor_Internal(dm, dim, faces, lower, upper, periodicity);
1179: if (!interpolate && dim > 1 && !simplex) {
1180: DM udm;
1182: DMPlexUninterpolate(dm, &udm);
1183: DMPlexCopyCoordinates(dm, udm);
1184: DMPlexReplace_Static(dm, &udm);
1185: }
1186: return 0;
1187: }
1189: /*@C
1190: DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra).
1192: Collective
1194: Input Parameters:
1195: + comm - The communicator for the DM object
1196: . dim - The spatial dimension
1197: . simplex - PETSC_TRUE for simplices, PETSC_FALSE for tensor cells
1198: . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D
1199: . lower - The lower left corner, or NULL for (0, 0, 0)
1200: . upper - The upper right corner, or NULL for (1, 1, 1)
1201: . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE
1202: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
1204: Output Parameter:
1205: . dm - The DM object
1207: Note: If you want to customize this mesh using options, you just need to
1208: $ DMCreate(comm, &dm);
1209: $ DMSetType(dm, DMPLEX);
1210: $ DMSetFromOptions(dm);
1211: and use the options on the DMSetFromOptions() page.
1213: Here is the numbering returned for 2 faces in each direction for tensor cells:
1214: $ 10---17---11---18----12
1215: $ | | |
1216: $ | | |
1217: $ 20 2 22 3 24
1218: $ | | |
1219: $ | | |
1220: $ 7---15----8---16----9
1221: $ | | |
1222: $ | | |
1223: $ 19 0 21 1 23
1224: $ | | |
1225: $ | | |
1226: $ 4---13----5---14----6
1228: and for simplicial cells
1230: $ 14----8---15----9----16
1231: $ |\ 5 |\ 7 |
1232: $ | \ | \ |
1233: $ 13 2 14 3 15
1234: $ | 4 \ | 6 \ |
1235: $ | \ | \ |
1236: $ 11----6---12----7----13
1237: $ |\ |\ |
1238: $ | \ 1 | \ 3 |
1239: $ 10 0 11 1 12
1240: $ | 0 \ | 2 \ |
1241: $ | \ | \ |
1242: $ 8----4----9----5----10
1244: Level: beginner
1246: .seealso: DMSetFromOptions(), DMPlexCreateFromFile(), DMPlexCreateHexCylinderMesh(), DMSetType(), DMCreate()
1247: @*/
1248: 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)
1249: {
1250: PetscInt fac[3] = {1, 1, 1};
1251: PetscReal low[3] = {0, 0, 0};
1252: PetscReal upp[3] = {1, 1, 1};
1253: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
1255: DMCreate(comm,dm);
1256: DMSetType(*dm,DMPLEX);
1257: DMPlexCreateBoxMesh_Internal(*dm, dim, simplex, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt, interpolate);
1258: return 0;
1259: }
1261: static PetscErrorCode DMPlexCreateWedgeBoxMesh_Internal(DM dm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[])
1262: {
1263: DM bdm, vol;
1264: PetscInt i;
1267: DMCreate(PetscObjectComm((PetscObject) dm), &bdm);
1268: DMSetType(bdm, DMPLEX);
1269: DMSetDimension(bdm, 2);
1270: DMPlexCreateBoxMesh_Simplex_Internal(bdm, 2, faces, lower, upper, periodicity, PETSC_TRUE);
1271: DMPlexExtrude(bdm, faces[2], upper[2] - lower[2], PETSC_TRUE, PETSC_FALSE, NULL, NULL, &vol);
1272: DMDestroy(&bdm);
1273: DMPlexReplace_Static(dm, &vol);
1274: if (lower[2] != 0.0) {
1275: Vec v;
1276: PetscScalar *x;
1277: PetscInt cDim, n;
1279: DMGetCoordinatesLocal(dm, &v);
1280: VecGetBlockSize(v, &cDim);
1281: VecGetLocalSize(v, &n);
1282: VecGetArray(v, &x);
1283: x += cDim;
1284: for (i = 0; i < n; i += cDim) x[i] += lower[2];
1285: VecRestoreArray(v,&x);
1286: DMSetCoordinatesLocal(dm, v);
1287: }
1288: return 0;
1289: }
1291: /*@
1292: DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells.
1294: Collective
1296: Input Parameters:
1297: + comm - The communicator for the DM object
1298: . faces - Number of faces per dimension, or NULL for (1, 1, 1)
1299: . lower - The lower left corner, or NULL for (0, 0, 0)
1300: . upper - The upper right corner, or NULL for (1, 1, 1)
1301: . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE
1302: . orderHeight - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first
1303: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
1305: Output Parameter:
1306: . dm - The DM object
1308: Level: beginner
1310: .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateWedgeCylinderMesh(), DMExtrude(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1311: @*/
1312: PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool orderHeight, PetscBool interpolate, DM *dm)
1313: {
1314: PetscInt fac[3] = {1, 1, 1};
1315: PetscReal low[3] = {0, 0, 0};
1316: PetscReal upp[3] = {1, 1, 1};
1317: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
1319: DMCreate(comm,dm);
1320: DMSetType(*dm,DMPLEX);
1321: DMPlexCreateWedgeBoxMesh_Internal(*dm, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt);
1322: if (!interpolate) {
1323: DM udm;
1325: DMPlexUninterpolate(*dm, &udm);
1326: DMPlexReplace_Static(*dm, &udm);
1327: }
1328: return 0;
1329: }
1331: /*@C
1332: DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database.
1334: Logically Collective on dm
1336: Input Parameters:
1337: + dm - the DM context
1338: - prefix - the prefix to prepend to all option names
1340: Notes:
1341: A hyphen (-) must NOT be given at the beginning of the prefix name.
1342: The first character of all runtime options is AUTOMATICALLY the hyphen.
1344: Level: advanced
1346: .seealso: SNESSetFromOptions()
1347: @*/
1348: PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[])
1349: {
1350: DM_Plex *mesh = (DM_Plex *) dm->data;
1353: PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);
1354: PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);
1355: return 0;
1356: }
1358: /* Remap geometry to cylinder
1359: TODO: This only works for a single refinement, then it is broken
1361: Interior square: Linear interpolation is correct
1362: The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing
1363: such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance
1365: phi = arctan(y/x)
1366: d_close = sqrt(1/8 + 1/4 sin^2(phi))
1367: d_far = sqrt(1/2 + sin^2(phi))
1369: so we remap them using
1371: x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close)
1372: y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close)
1374: If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y.
1375: */
1376: static void snapToCylinder(PetscInt dim, PetscInt Nf, PetscInt NfAux,
1377: const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
1378: const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
1379: PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[])
1380: {
1381: const PetscReal dis = 1.0/PetscSqrtReal(2.0);
1382: const PetscReal ds2 = 0.5*dis;
1384: if ((PetscAbsScalar(u[0]) <= ds2) && (PetscAbsScalar(u[1]) <= ds2)) {
1385: f0[0] = u[0];
1386: f0[1] = u[1];
1387: } else {
1388: PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc;
1390: x = PetscRealPart(u[0]);
1391: y = PetscRealPart(u[1]);
1392: phi = PetscAtan2Real(y, x);
1393: sinp = PetscSinReal(phi);
1394: cosp = PetscCosReal(phi);
1395: if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) {
1396: dc = PetscAbsReal(ds2/sinp);
1397: df = PetscAbsReal(dis/sinp);
1398: xc = ds2*x/PetscAbsReal(y);
1399: yc = ds2*PetscSignReal(y);
1400: } else {
1401: dc = PetscAbsReal(ds2/cosp);
1402: df = PetscAbsReal(dis/cosp);
1403: xc = ds2*PetscSignReal(x);
1404: yc = ds2*y/PetscAbsReal(x);
1405: }
1406: f0[0] = xc + (u[0] - xc)*(1.0 - dc)/(df - dc);
1407: f0[1] = yc + (u[1] - yc)*(1.0 - dc)/(df - dc);
1408: }
1409: f0[2] = u[2];
1410: }
1412: static PetscErrorCode DMPlexCreateHexCylinderMesh_Internal(DM dm, DMBoundaryType periodicZ)
1413: {
1414: const PetscInt dim = 3;
1415: PetscInt numCells, numVertices;
1416: PetscMPIInt rank;
1418: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
1419: DMSetDimension(dm, dim);
1420: /* Create topology */
1421: {
1422: PetscInt cone[8], c;
1424: numCells = rank == 0 ? 5 : 0;
1425: numVertices = rank == 0 ? 16 : 0;
1426: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1427: numCells *= 3;
1428: numVertices = rank == 0 ? 24 : 0;
1429: }
1430: DMPlexSetChart(dm, 0, numCells+numVertices);
1431: for (c = 0; c < numCells; c++) DMPlexSetConeSize(dm, c, 8);
1432: DMSetUp(dm);
1433: if (rank == 0) {
1434: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1435: cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16;
1436: cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34;
1437: DMPlexSetCone(dm, 0, cone);
1438: cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23;
1439: cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */
1440: DMPlexSetCone(dm, 1, cone);
1441: cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17;
1442: cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38;
1443: DMPlexSetCone(dm, 2, cone);
1444: cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15;
1445: cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38;
1446: DMPlexSetCone(dm, 3, cone);
1447: cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23;
1448: cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31;
1449: DMPlexSetCone(dm, 4, cone);
1451: cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32;
1452: cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20;
1453: DMPlexSetCone(dm, 5, cone);
1454: cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36;
1455: cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21;
1456: DMPlexSetCone(dm, 6, cone);
1457: cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33;
1458: cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28;
1459: DMPlexSetCone(dm, 7, cone);
1460: cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31;
1461: cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28;
1462: DMPlexSetCone(dm, 8, cone);
1463: cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36;
1464: cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19;
1465: DMPlexSetCone(dm, 9, cone);
1467: cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22;
1468: cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18;
1469: DMPlexSetCone(dm, 10, cone);
1470: cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25;
1471: cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17;
1472: DMPlexSetCone(dm, 11, cone);
1473: cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21;
1474: cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27;
1475: DMPlexSetCone(dm, 12, cone);
1476: cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19;
1477: cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27;
1478: DMPlexSetCone(dm, 13, cone);
1479: cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25;
1480: cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15;
1481: DMPlexSetCone(dm, 14, cone);
1482: } else {
1483: cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6;
1484: cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10;
1485: DMPlexSetCone(dm, 0, cone);
1486: cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13;
1487: cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11;
1488: DMPlexSetCone(dm, 1, cone);
1489: cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7;
1490: cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18;
1491: DMPlexSetCone(dm, 2, cone);
1492: cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5;
1493: cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18;
1494: DMPlexSetCone(dm, 3, cone);
1495: cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13;
1496: cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9;
1497: DMPlexSetCone(dm, 4, cone);
1498: }
1499: }
1500: DMPlexSymmetrize(dm);
1501: DMPlexStratify(dm);
1502: }
1503: /* Create cube geometry */
1504: {
1505: Vec coordinates;
1506: PetscSection coordSection;
1507: PetscScalar *coords;
1508: PetscInt coordSize, v;
1509: const PetscReal dis = 1.0/PetscSqrtReal(2.0);
1510: const PetscReal ds2 = dis/2.0;
1512: /* Build coordinates */
1513: DMGetCoordinateSection(dm, &coordSection);
1514: PetscSectionSetNumFields(coordSection, 1);
1515: PetscSectionSetFieldComponents(coordSection, 0, dim);
1516: PetscSectionSetChart(coordSection, numCells, numCells+numVertices);
1517: for (v = numCells; v < numCells+numVertices; ++v) {
1518: PetscSectionSetDof(coordSection, v, dim);
1519: PetscSectionSetFieldDof(coordSection, v, 0, dim);
1520: }
1521: PetscSectionSetUp(coordSection);
1522: PetscSectionGetStorageSize(coordSection, &coordSize);
1523: VecCreate(PETSC_COMM_SELF, &coordinates);
1524: PetscObjectSetName((PetscObject) coordinates, "coordinates");
1525: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1526: VecSetBlockSize(coordinates, dim);
1527: VecSetType(coordinates,VECSTANDARD);
1528: VecGetArray(coordinates, &coords);
1529: if (rank == 0) {
1530: coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0;
1531: coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0;
1532: coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0;
1533: coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0;
1534: coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0;
1535: coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0;
1536: coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0;
1537: coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0;
1538: coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0;
1539: coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0;
1540: coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0;
1541: coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0;
1542: coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0;
1543: coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0;
1544: coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0;
1545: coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0;
1546: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1547: /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5;
1548: /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5;
1549: /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5;
1550: /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5;
1551: /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5;
1552: /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5;
1553: /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5;
1554: /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5;
1555: }
1556: }
1557: VecRestoreArray(coordinates, &coords);
1558: DMSetCoordinatesLocal(dm, coordinates);
1559: VecDestroy(&coordinates);
1560: }
1561: /* Create periodicity */
1562: if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) {
1563: PetscReal L[3];
1564: PetscReal maxCell[3];
1565: DMBoundaryType bdType[3];
1566: PetscReal lower[3] = {0.0, 0.0, 0.0};
1567: PetscReal upper[3] = {1.0, 1.0, 1.5};
1568: PetscInt i, numZCells = 3;
1570: bdType[0] = DM_BOUNDARY_NONE;
1571: bdType[1] = DM_BOUNDARY_NONE;
1572: bdType[2] = periodicZ;
1573: for (i = 0; i < dim; i++) {
1574: L[i] = upper[i] - lower[i];
1575: maxCell[i] = 1.1 * (L[i] / numZCells);
1576: }
1577: DMSetPeriodicity(dm, PETSC_TRUE, maxCell, L, bdType);
1578: }
1579: {
1580: DM cdm;
1581: PetscDS cds;
1582: PetscScalar c[2] = {1.0, 1.0};
1584: DMPlexCreateCoordinateSpace(dm, 1, snapToCylinder);
1585: DMGetCoordinateDM(dm, &cdm);
1586: DMGetDS(cdm, &cds);
1587: PetscDSSetConstants(cds, 2, c);
1588: }
1589: /* Wait for coordinate creation before doing in-place modification */
1590: DMPlexInterpolateInPlace_Internal(dm);
1591: return 0;
1592: }
1594: /*@
1595: DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra.
1597: Collective
1599: Input Parameters:
1600: + comm - The communicator for the DM object
1601: - periodicZ - The boundary type for the Z direction
1603: Output Parameter:
1604: . dm - The DM object
1606: Note:
1607: Here is the output numbering looking from the bottom of the cylinder:
1608: $ 17-----14
1609: $ | |
1610: $ | 2 |
1611: $ | |
1612: $ 17-----8-----7-----14
1613: $ | | | |
1614: $ | 3 | 0 | 1 |
1615: $ | | | |
1616: $ 19-----5-----6-----13
1617: $ | |
1618: $ | 4 |
1619: $ | |
1620: $ 19-----13
1621: $
1622: $ and up through the top
1623: $
1624: $ 18-----16
1625: $ | |
1626: $ | 2 |
1627: $ | |
1628: $ 18----10----11-----16
1629: $ | | | |
1630: $ | 3 | 0 | 1 |
1631: $ | | | |
1632: $ 20-----9----12-----15
1633: $ | |
1634: $ | 4 |
1635: $ | |
1636: $ 20-----15
1638: Level: beginner
1640: .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1641: @*/
1642: PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, DMBoundaryType periodicZ, DM *dm)
1643: {
1645: DMCreate(comm, dm);
1646: DMSetType(*dm, DMPLEX);
1647: DMPlexCreateHexCylinderMesh_Internal(*dm, periodicZ);
1648: return 0;
1649: }
1651: static PetscErrorCode DMPlexCreateWedgeCylinderMesh_Internal(DM dm, PetscInt n, PetscBool interpolate)
1652: {
1653: const PetscInt dim = 3;
1654: PetscInt numCells, numVertices, v;
1655: PetscMPIInt rank;
1658: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
1659: DMSetDimension(dm, dim);
1660: /* Must create the celltype label here so that we do not automatically try to compute the types */
1661: DMCreateLabel(dm, "celltype");
1662: /* Create topology */
1663: {
1664: PetscInt cone[6], c;
1666: numCells = rank == 0 ? n : 0;
1667: numVertices = rank == 0 ? 2*(n+1) : 0;
1668: DMPlexSetChart(dm, 0, numCells+numVertices);
1669: for (c = 0; c < numCells; c++) DMPlexSetConeSize(dm, c, 6);
1670: DMSetUp(dm);
1671: for (c = 0; c < numCells; c++) {
1672: cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n;
1673: cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n;
1674: DMPlexSetCone(dm, c, cone);
1675: DMPlexSetCellType(dm, c, DM_POLYTOPE_TRI_PRISM_TENSOR);
1676: }
1677: DMPlexSymmetrize(dm);
1678: DMPlexStratify(dm);
1679: }
1680: for (v = numCells; v < numCells+numVertices; ++v) {
1681: DMPlexSetCellType(dm, v, DM_POLYTOPE_POINT);
1682: }
1683: /* Create cylinder geometry */
1684: {
1685: Vec coordinates;
1686: PetscSection coordSection;
1687: PetscScalar *coords;
1688: PetscInt coordSize, c;
1690: /* Build coordinates */
1691: DMGetCoordinateSection(dm, &coordSection);
1692: PetscSectionSetNumFields(coordSection, 1);
1693: PetscSectionSetFieldComponents(coordSection, 0, dim);
1694: PetscSectionSetChart(coordSection, numCells, numCells+numVertices);
1695: for (v = numCells; v < numCells+numVertices; ++v) {
1696: PetscSectionSetDof(coordSection, v, dim);
1697: PetscSectionSetFieldDof(coordSection, v, 0, dim);
1698: }
1699: PetscSectionSetUp(coordSection);
1700: PetscSectionGetStorageSize(coordSection, &coordSize);
1701: VecCreate(PETSC_COMM_SELF, &coordinates);
1702: PetscObjectSetName((PetscObject) coordinates, "coordinates");
1703: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1704: VecSetBlockSize(coordinates, dim);
1705: VecSetType(coordinates,VECSTANDARD);
1706: VecGetArray(coordinates, &coords);
1707: for (c = 0; c < numCells; c++) {
1708: coords[(c+0*n)*dim+0] = PetscCosReal(2.0*c*PETSC_PI/n); coords[(c+0*n)*dim+1] = PetscSinReal(2.0*c*PETSC_PI/n); coords[(c+0*n)*dim+2] = 1.0;
1709: coords[(c+1*n)*dim+0] = PetscCosReal(2.0*c*PETSC_PI/n); coords[(c+1*n)*dim+1] = PetscSinReal(2.0*c*PETSC_PI/n); coords[(c+1*n)*dim+2] = 0.0;
1710: }
1711: if (rank == 0) {
1712: coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0;
1713: coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0;
1714: }
1715: VecRestoreArray(coordinates, &coords);
1716: DMSetCoordinatesLocal(dm, coordinates);
1717: VecDestroy(&coordinates);
1718: }
1719: /* Interpolate */
1720: if (interpolate) DMPlexInterpolateInPlace_Internal(dm);
1721: return 0;
1722: }
1724: /*@
1725: DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges.
1727: Collective
1729: Input Parameters:
1730: + comm - The communicator for the DM object
1731: . n - The number of wedges around the origin
1732: - interpolate - Create edges and faces
1734: Output Parameter:
1735: . dm - The DM object
1737: Level: beginner
1739: .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1740: @*/
1741: PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm)
1742: {
1744: DMCreate(comm, dm);
1745: DMSetType(*dm, DMPLEX);
1746: DMPlexCreateWedgeCylinderMesh_Internal(*dm, n, interpolate);
1747: return 0;
1748: }
1750: static inline PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
1751: {
1752: PetscReal prod = 0.0;
1753: PetscInt i;
1754: for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]);
1755: return PetscSqrtReal(prod);
1756: }
1757: static inline PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
1758: {
1759: PetscReal prod = 0.0;
1760: PetscInt i;
1761: for (i = 0; i < dim; ++i) prod += x[i]*y[i];
1762: return prod;
1763: }
1765: /* The first constant is the sphere radius */
1766: static void snapToSphere(PetscInt dim, PetscInt Nf, PetscInt NfAux,
1767: const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
1768: const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
1769: PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[])
1770: {
1771: PetscReal r = PetscRealPart(constants[0]);
1772: PetscReal norm2 = 0.0, fac;
1773: PetscInt n = uOff[1] - uOff[0], d;
1775: for (d = 0; d < n; ++d) norm2 += PetscSqr(PetscRealPart(u[d]));
1776: fac = r/PetscSqrtReal(norm2);
1777: for (d = 0; d < n; ++d) f0[d] = u[d]*fac;
1778: }
1780: static PetscErrorCode DMPlexCreateSphereMesh_Internal(DM dm, PetscInt dim, PetscBool simplex, PetscReal R)
1781: {
1782: const PetscInt embedDim = dim+1;
1783: PetscSection coordSection;
1784: Vec coordinates;
1785: PetscScalar *coords;
1786: PetscReal *coordsIn;
1787: PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e;
1788: PetscMPIInt rank;
1791: DMSetDimension(dm, dim);
1792: DMSetCoordinateDim(dm, dim+1);
1793: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
1794: switch (dim) {
1795: case 2:
1796: if (simplex) {
1797: const PetscReal radius = PetscSqrtReal(1 + PETSC_PHI*PETSC_PHI)/(1.0 + PETSC_PHI);
1798: const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI) * (R/radius);
1799: const PetscInt degree = 5;
1800: PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)};
1801: PetscInt s[3] = {1, 1, 1};
1802: PetscInt cone[3];
1803: PetscInt *graph, p, i, j, k;
1805: vertex[0] *= R/radius; vertex[1] *= R/radius; vertex[2] *= R/radius;
1806: numCells = rank == 0 ? 20 : 0;
1807: numVerts = rank == 0 ? 12 : 0;
1808: firstVertex = numCells;
1809: /* Use icosahedron, which for a R-sphere has coordinates which are all cyclic permutations of
1811: (0, \pm 1/\phi+1, \pm \phi/\phi+1)
1813: where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
1814: length is then given by 2/(1+\phi) = 2 * 0.38197 = 0.76393.
1815: */
1816: /* Construct vertices */
1817: PetscCalloc1(numVerts * embedDim, &coordsIn);
1818: if (rank == 0) {
1819: for (p = 0, i = 0; p < embedDim; ++p) {
1820: for (s[1] = -1; s[1] < 2; s[1] += 2) {
1821: for (s[2] = -1; s[2] < 2; s[2] += 2) {
1822: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim];
1823: ++i;
1824: }
1825: }
1826: }
1827: }
1828: /* Construct graph */
1829: PetscCalloc1(numVerts * numVerts, &graph);
1830: for (i = 0; i < numVerts; ++i) {
1831: for (j = 0, k = 0; j < numVerts; ++j) {
1832: if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;}
1833: }
1835: }
1836: /* Build Topology */
1837: DMPlexSetChart(dm, 0, numCells+numVerts);
1838: for (c = 0; c < numCells; c++) {
1839: DMPlexSetConeSize(dm, c, embedDim);
1840: }
1841: DMSetUp(dm); /* Allocate space for cones */
1842: /* Cells */
1843: for (i = 0, c = 0; i < numVerts; ++i) {
1844: for (j = 0; j < i; ++j) {
1845: for (k = 0; k < j; ++k) {
1846: if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) {
1847: cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k;
1848: /* Check orientation */
1849: {
1850: const PetscInt epsilon[3][3][3] = {{{0, 0, 0}, {0, 0, 1}, {0, -1, 0}}, {{0, 0, -1}, {0, 0, 0}, {1, 0, 0}}, {{0, 1, 0}, {-1, 0, 0}, {0, 0, 0}}};
1851: PetscReal normal[3];
1852: PetscInt e, f;
1854: for (d = 0; d < embedDim; ++d) {
1855: normal[d] = 0.0;
1856: for (e = 0; e < embedDim; ++e) {
1857: for (f = 0; f < embedDim; ++f) {
1858: normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]);
1859: }
1860: }
1861: }
1862: if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;}
1863: }
1864: DMPlexSetCone(dm, c++, cone);
1865: }
1866: }
1867: }
1868: }
1869: DMPlexSymmetrize(dm);
1870: DMPlexStratify(dm);
1871: PetscFree(graph);
1872: } else {
1873: /*
1874: 12-21--13
1875: | |
1876: 25 4 24
1877: | |
1878: 12-25--9-16--8-24--13
1879: | | | |
1880: 23 5 17 0 15 3 22
1881: | | | |
1882: 10-20--6-14--7-19--11
1883: | |
1884: 20 1 19
1885: | |
1886: 10-18--11
1887: | |
1888: 23 2 22
1889: | |
1890: 12-21--13
1891: */
1892: PetscInt cone[4], ornt[4];
1894: numCells = rank == 0 ? 6 : 0;
1895: numEdges = rank == 0 ? 12 : 0;
1896: numVerts = rank == 0 ? 8 : 0;
1897: firstVertex = numCells;
1898: firstEdge = numCells + numVerts;
1899: /* Build Topology */
1900: DMPlexSetChart(dm, 0, numCells+numEdges+numVerts);
1901: for (c = 0; c < numCells; c++) {
1902: DMPlexSetConeSize(dm, c, 4);
1903: }
1904: for (e = firstEdge; e < firstEdge+numEdges; ++e) {
1905: DMPlexSetConeSize(dm, e, 2);
1906: }
1907: DMSetUp(dm); /* Allocate space for cones */
1908: if (rank == 0) {
1909: /* Cell 0 */
1910: cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17;
1911: DMPlexSetCone(dm, 0, cone);
1912: ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0;
1913: DMPlexSetConeOrientation(dm, 0, ornt);
1914: /* Cell 1 */
1915: cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20;
1916: DMPlexSetCone(dm, 1, cone);
1917: ornt[0] = 0; ornt[1] = 0; ornt[2] = -1; ornt[3] = 0;
1918: DMPlexSetConeOrientation(dm, 1, ornt);
1919: /* Cell 2 */
1920: cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23;
1921: DMPlexSetCone(dm, 2, cone);
1922: ornt[0] = 0; ornt[1] = 0; ornt[2] = -1; ornt[3] = 0;
1923: DMPlexSetConeOrientation(dm, 2, ornt);
1924: /* Cell 3 */
1925: cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15;
1926: DMPlexSetCone(dm, 3, cone);
1927: ornt[0] = -1; ornt[1] = -1; ornt[2] = 0; ornt[3] = -1;
1928: DMPlexSetConeOrientation(dm, 3, ornt);
1929: /* Cell 4 */
1930: cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25;
1931: DMPlexSetCone(dm, 4, cone);
1932: ornt[0] = -1; ornt[1] = -1; ornt[2] = -1; ornt[3] = 0;
1933: DMPlexSetConeOrientation(dm, 4, ornt);
1934: /* Cell 5 */
1935: cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23;
1936: DMPlexSetCone(dm, 5, cone);
1937: ornt[0] = -1; ornt[1] = -1; ornt[2] = -1; ornt[3] = -1;
1938: DMPlexSetConeOrientation(dm, 5, ornt);
1939: /* Edges */
1940: cone[0] = 6; cone[1] = 7;
1941: DMPlexSetCone(dm, 14, cone);
1942: cone[0] = 7; cone[1] = 8;
1943: DMPlexSetCone(dm, 15, cone);
1944: cone[0] = 8; cone[1] = 9;
1945: DMPlexSetCone(dm, 16, cone);
1946: cone[0] = 9; cone[1] = 6;
1947: DMPlexSetCone(dm, 17, cone);
1948: cone[0] = 10; cone[1] = 11;
1949: DMPlexSetCone(dm, 18, cone);
1950: cone[0] = 11; cone[1] = 7;
1951: DMPlexSetCone(dm, 19, cone);
1952: cone[0] = 6; cone[1] = 10;
1953: DMPlexSetCone(dm, 20, cone);
1954: cone[0] = 12; cone[1] = 13;
1955: DMPlexSetCone(dm, 21, cone);
1956: cone[0] = 13; cone[1] = 11;
1957: DMPlexSetCone(dm, 22, cone);
1958: cone[0] = 10; cone[1] = 12;
1959: DMPlexSetCone(dm, 23, cone);
1960: cone[0] = 13; cone[1] = 8;
1961: DMPlexSetCone(dm, 24, cone);
1962: cone[0] = 12; cone[1] = 9;
1963: DMPlexSetCone(dm, 25, cone);
1964: }
1965: DMPlexSymmetrize(dm);
1966: DMPlexStratify(dm);
1967: /* Build coordinates */
1968: PetscCalloc1(numVerts * embedDim, &coordsIn);
1969: if (rank == 0) {
1970: coordsIn[0*embedDim+0] = -R; coordsIn[0*embedDim+1] = R; coordsIn[0*embedDim+2] = -R;
1971: coordsIn[1*embedDim+0] = R; coordsIn[1*embedDim+1] = R; coordsIn[1*embedDim+2] = -R;
1972: coordsIn[2*embedDim+0] = R; coordsIn[2*embedDim+1] = -R; coordsIn[2*embedDim+2] = -R;
1973: coordsIn[3*embedDim+0] = -R; coordsIn[3*embedDim+1] = -R; coordsIn[3*embedDim+2] = -R;
1974: coordsIn[4*embedDim+0] = -R; coordsIn[4*embedDim+1] = R; coordsIn[4*embedDim+2] = R;
1975: coordsIn[5*embedDim+0] = R; coordsIn[5*embedDim+1] = R; coordsIn[5*embedDim+2] = R;
1976: coordsIn[6*embedDim+0] = -R; coordsIn[6*embedDim+1] = -R; coordsIn[6*embedDim+2] = R;
1977: coordsIn[7*embedDim+0] = R; coordsIn[7*embedDim+1] = -R; coordsIn[7*embedDim+2] = R;
1978: }
1979: }
1980: break;
1981: case 3:
1982: if (simplex) {
1983: const PetscReal edgeLen = 1.0/PETSC_PHI;
1984: PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5};
1985: PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0};
1986: PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0};
1987: const PetscInt degree = 12;
1988: PetscInt s[4] = {1, 1, 1};
1989: PetscInt evenPerm[12][4] = {{0, 1, 2, 3}, {0, 2, 3, 1}, {0, 3, 1, 2}, {1, 0, 3, 2}, {1, 2, 0, 3}, {1, 3, 2, 0},
1990: {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}};
1991: PetscInt cone[4];
1992: PetscInt *graph, p, i, j, k, l;
1994: vertexA[0] *= R; vertexA[1] *= R; vertexA[2] *= R; vertexA[3] *= R;
1995: vertexB[0] *= R; vertexB[1] *= R; vertexB[2] *= R; vertexB[3] *= R;
1996: vertexC[0] *= R; vertexC[1] *= R; vertexC[2] *= R; vertexC[3] *= R;
1997: numCells = rank == 0 ? 600 : 0;
1998: numVerts = rank == 0 ? 120 : 0;
1999: firstVertex = numCells;
2000: /* Use the 600-cell, which for a unit sphere has coordinates which are
2002: 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16
2003: (\pm 1, 0, 0, 0) all cyclic permutations 8
2004: 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96
2006: where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
2007: length is then given by 1/\phi = 0.61803.
2009: http://buzzard.pugetsound.edu/sage-practice/ch03s03.html
2010: http://mathworld.wolfram.com/600-Cell.html
2011: */
2012: /* Construct vertices */
2013: PetscCalloc1(numVerts * embedDim, &coordsIn);
2014: i = 0;
2015: if (rank == 0) {
2016: for (s[0] = -1; s[0] < 2; s[0] += 2) {
2017: for (s[1] = -1; s[1] < 2; s[1] += 2) {
2018: for (s[2] = -1; s[2] < 2; s[2] += 2) {
2019: for (s[3] = -1; s[3] < 2; s[3] += 2) {
2020: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d];
2021: ++i;
2022: }
2023: }
2024: }
2025: }
2026: for (p = 0; p < embedDim; ++p) {
2027: s[1] = s[2] = s[3] = 1;
2028: for (s[0] = -1; s[0] < 2; s[0] += 2) {
2029: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim];
2030: ++i;
2031: }
2032: }
2033: for (p = 0; p < 12; ++p) {
2034: s[3] = 1;
2035: for (s[0] = -1; s[0] < 2; s[0] += 2) {
2036: for (s[1] = -1; s[1] < 2; s[1] += 2) {
2037: for (s[2] = -1; s[2] < 2; s[2] += 2) {
2038: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]];
2039: ++i;
2040: }
2041: }
2042: }
2043: }
2044: }
2046: /* Construct graph */
2047: PetscCalloc1(numVerts * numVerts, &graph);
2048: for (i = 0; i < numVerts; ++i) {
2049: for (j = 0, k = 0; j < numVerts; ++j) {
2050: if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;}
2051: }
2053: }
2054: /* Build Topology */
2055: DMPlexSetChart(dm, 0, numCells+numVerts);
2056: for (c = 0; c < numCells; c++) {
2057: DMPlexSetConeSize(dm, c, embedDim);
2058: }
2059: DMSetUp(dm); /* Allocate space for cones */
2060: /* Cells */
2061: if (rank == 0) {
2062: for (i = 0, c = 0; i < numVerts; ++i) {
2063: for (j = 0; j < i; ++j) {
2064: for (k = 0; k < j; ++k) {
2065: for (l = 0; l < k; ++l) {
2066: if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] &&
2067: graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) {
2068: cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l;
2069: /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */
2070: {
2071: const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
2072: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}},
2073: {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}},
2074: {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}},
2076: {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}},
2077: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
2078: {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}},
2079: {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}},
2081: {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}},
2082: {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}},
2083: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
2084: {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}},
2086: {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}},
2087: {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}},
2088: {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
2089: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}};
2090: PetscReal normal[4];
2091: PetscInt e, f, g;
2093: for (d = 0; d < embedDim; ++d) {
2094: normal[d] = 0.0;
2095: for (e = 0; e < embedDim; ++e) {
2096: for (f = 0; f < embedDim; ++f) {
2097: for (g = 0; g < embedDim; ++g) {
2098: 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]);
2099: }
2100: }
2101: }
2102: }
2103: if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;}
2104: }
2105: DMPlexSetCone(dm, c++, cone);
2106: }
2107: }
2108: }
2109: }
2110: }
2111: }
2112: DMPlexSymmetrize(dm);
2113: DMPlexStratify(dm);
2114: PetscFree(graph);
2115: break;
2116: }
2117: default: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim);
2118: }
2119: /* Create coordinates */
2120: DMGetCoordinateSection(dm, &coordSection);
2121: PetscSectionSetNumFields(coordSection, 1);
2122: PetscSectionSetFieldComponents(coordSection, 0, embedDim);
2123: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);
2124: for (v = firstVertex; v < firstVertex+numVerts; ++v) {
2125: PetscSectionSetDof(coordSection, v, embedDim);
2126: PetscSectionSetFieldDof(coordSection, v, 0, embedDim);
2127: }
2128: PetscSectionSetUp(coordSection);
2129: PetscSectionGetStorageSize(coordSection, &coordSize);
2130: VecCreate(PETSC_COMM_SELF, &coordinates);
2131: VecSetBlockSize(coordinates, embedDim);
2132: PetscObjectSetName((PetscObject) coordinates, "coordinates");
2133: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
2134: VecSetType(coordinates,VECSTANDARD);
2135: VecGetArray(coordinates, &coords);
2136: for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];}
2137: VecRestoreArray(coordinates, &coords);
2138: DMSetCoordinatesLocal(dm, coordinates);
2139: VecDestroy(&coordinates);
2140: PetscFree(coordsIn);
2141: {
2142: DM cdm;
2143: PetscDS cds;
2144: PetscScalar c = R;
2146: DMPlexCreateCoordinateSpace(dm, 1, snapToSphere);
2147: DMGetCoordinateDM(dm, &cdm);
2148: DMGetDS(cdm, &cds);
2149: PetscDSSetConstants(cds, 1, &c);
2150: }
2151: /* Wait for coordinate creation before doing in-place modification */
2152: if (simplex) DMPlexInterpolateInPlace_Internal(dm);
2153: return 0;
2154: }
2156: typedef void (*TPSEvaluateFunc)(const PetscReal[], PetscReal*, PetscReal[], PetscReal(*)[3]);
2158: /*
2159: The Schwarz P implicit surface is
2161: f(x) = cos(x0) + cos(x1) + cos(x2) = 0
2162: */
2163: static void TPSEvaluate_SchwarzP(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3])
2164: {
2165: PetscReal c[3] = {PetscCosReal(y[0] * PETSC_PI), PetscCosReal(y[1] * PETSC_PI), PetscCosReal(y[2] * PETSC_PI)};
2166: PetscReal g[3] = {-PetscSinReal(y[0] * PETSC_PI), -PetscSinReal(y[1] * PETSC_PI), -PetscSinReal(y[2] * PETSC_PI)};
2167: f[0] = c[0] + c[1] + c[2];
2168: for (PetscInt i=0; i<3; i++) {
2169: grad[i] = PETSC_PI * g[i];
2170: for (PetscInt j=0; j<3; j++) {
2171: hess[i][j] = (i == j) ? -PetscSqr(PETSC_PI) * c[i] : 0.;
2172: }
2173: }
2174: }
2176: // u[] is a tentative normal on input. Replace with the implicit function gradient in the same direction
2177: static PetscErrorCode TPSExtrudeNormalFunc_SchwarzP(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt r, PetscScalar u[], void *ctx) {
2178: for (PetscInt i=0; i<3; i++) {
2179: u[i] = -PETSC_PI * PetscSinReal(x[i] * PETSC_PI);
2180: }
2181: return 0;
2182: }
2184: /*
2185: The Gyroid implicit surface is
2187: 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)
2189: */
2190: static void TPSEvaluate_Gyroid(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3])
2191: {
2192: PetscReal s[3] = {PetscSinReal(PETSC_PI * y[0]), PetscSinReal(PETSC_PI * (y[1] + .5)), PetscSinReal(PETSC_PI * (y[2] + .25))};
2193: PetscReal c[3] = {PetscCosReal(PETSC_PI * y[0]), PetscCosReal(PETSC_PI * (y[1] + .5)), PetscCosReal(PETSC_PI * (y[2] + .25))};
2194: f[0] = s[0] * c[1] + s[1] * c[2] + s[2] * c[0];
2195: grad[0] = PETSC_PI * (c[0] * c[1] - s[2] * s[0]);
2196: grad[1] = PETSC_PI * (c[1] * c[2] - s[0] * s[1]);
2197: grad[2] = PETSC_PI * (c[2] * c[0] - s[1] * s[2]);
2198: hess[0][0] = -PetscSqr(PETSC_PI) * (s[0] * c[1] + s[2] * c[0]);
2199: hess[0][1] = -PetscSqr(PETSC_PI) * (c[0] * s[1]);
2200: hess[0][2] = -PetscSqr(PETSC_PI) * (c[2] * s[0]);
2201: hess[1][0] = -PetscSqr(PETSC_PI) * (s[1] * c[2] + s[0] * c[1]);
2202: hess[1][1] = -PetscSqr(PETSC_PI) * (c[1] * s[2]);
2203: hess[2][2] = -PetscSqr(PETSC_PI) * (c[0] * s[1]);
2204: hess[2][0] = -PetscSqr(PETSC_PI) * (s[2] * c[0] + s[1] * c[2]);
2205: hess[2][1] = -PetscSqr(PETSC_PI) * (c[2] * s[0]);
2206: hess[2][2] = -PetscSqr(PETSC_PI) * (c[1] * s[2]);
2207: }
2209: // u[] is a tentative normal on input. Replace with the implicit function gradient in the same direction
2210: static PetscErrorCode TPSExtrudeNormalFunc_Gyroid(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt r, PetscScalar u[], void *ctx) {
2211: PetscReal s[3] = {PetscSinReal(PETSC_PI * x[0]), PetscSinReal(PETSC_PI * (x[1] + .5)), PetscSinReal(PETSC_PI * (x[2] + .25))};
2212: PetscReal c[3] = {PetscCosReal(PETSC_PI * x[0]), PetscCosReal(PETSC_PI * (x[1] + .5)), PetscCosReal(PETSC_PI * (x[2] + .25))};
2213: u[0] = PETSC_PI * (c[0] * c[1] - s[2] * s[0]);
2214: u[1] = PETSC_PI * (c[1] * c[2] - s[0] * s[1]);
2215: u[2] = PETSC_PI * (c[2] * c[0] - s[1] * s[2]);
2216: return 0;
2217: }
2219: /*
2220: We wish to solve
2222: min_y || y - x ||^2 subject to f(y) = 0
2224: Let g(y) = grad(f). The minimization problem is equivalent to asking to satisfy
2225: f(y) = 0 and (y-x) is parallel to g(y). We do this by using Householder QR to obtain a basis for the
2226: tangent space and ask for both components in the tangent space to be zero.
2228: Take g to be a column vector and compute the "full QR" factorization Q R = g,
2229: where Q = I - 2 n n^T is a symmetric orthogonal matrix.
2230: The first column of Q is parallel to g so the remaining two columns span the null space.
2231: Let Qn = Q[:,1:] be those remaining columns. Then Qn Qn^T is an orthogonal projector into the tangent space.
2232: Since Q is symmetric, this is equivalent to multipyling by Q and taking the last two entries.
2233: In total, we have a system of 3 equations in 3 unknowns:
2235: f(y) = 0 1 equation
2236: Qn^T (y - x) = 0 2 equations
2238: Here, we compute the residual and Jacobian of this system.
2239: */
2240: static void TPSNearestPointResJac(TPSEvaluateFunc feval, const PetscScalar x[], const PetscScalar y[], PetscScalar res[], PetscScalar J[])
2241: {
2242: PetscReal yreal[3] = {PetscRealPart(y[0]), PetscRealPart(y[1]), PetscRealPart(y[2])};
2243: PetscReal d[3] = {PetscRealPart(y[0] - x[0]), PetscRealPart(y[1] - x[1]), PetscRealPart(y[2] - x[2])};
2244: PetscReal f, grad[3], n[3], norm, norm_y[3], nd, nd_y[3], sign;
2245: PetscReal n_y[3][3] = {{0,0,0},{0,0,0},{0,0,0}};
2247: feval(yreal, &f, grad, n_y);
2249: for (PetscInt i=0; i<3; i++) n[i] = grad[i];
2250: norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2]));
2251: for (PetscInt i=0; i<3; i++) {
2252: norm_y[i] = 1. / norm * n[i] * n_y[i][i];
2253: }
2255: // Define the Householder reflector
2256: sign = n[0] >= 0 ? 1. : -1.;
2257: n[0] += norm * sign;
2258: for (PetscInt i=0; i<3; i++) n_y[0][i] += norm_y[i] * sign;
2260: norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2]));
2261: norm_y[0] = 1. / norm * (n[0] * n_y[0][0]);
2262: norm_y[1] = 1. / norm * (n[0] * n_y[0][1] + n[1] * n_y[1][1]);
2263: norm_y[2] = 1. / norm * (n[0] * n_y[0][2] + n[2] * n_y[2][2]);
2265: for (PetscInt i=0; i<3; i++) {
2266: n[i] /= norm;
2267: for (PetscInt j=0; j<3; j++) {
2268: // note that n[i] is n_old[i]/norm when executing the code below
2269: n_y[i][j] = n_y[i][j] / norm - n[i] / norm * norm_y[j];
2270: }
2271: }
2273: nd = n[0] * d[0] + n[1] * d[1] + n[2] * d[2];
2274: 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];
2276: res[0] = f;
2277: res[1] = d[1] - 2 * n[1] * nd;
2278: res[2] = d[2] - 2 * n[2] * nd;
2279: // J[j][i] is J_{ij} (column major)
2280: for (PetscInt j=0; j<3; j++) {
2281: J[0 + j*3] = grad[j];
2282: J[1 + j*3] = (j == 1)*1. - 2 * (n_y[1][j] * nd + n[1] * nd_y[j]);
2283: J[2 + j*3] = (j == 2)*1. - 2 * (n_y[2][j] * nd + n[2] * nd_y[j]);
2284: }
2285: }
2287: /*
2288: Project x to the nearest point on the implicit surface using Newton's method.
2289: */
2290: static PetscErrorCode TPSNearestPoint(TPSEvaluateFunc feval, PetscScalar x[])
2291: {
2292: PetscScalar y[3] = {x[0], x[1], x[2]}; // Initial guess
2294: for (PetscInt iter=0; iter<10; iter++) {
2295: PetscScalar res[3], J[9];
2296: PetscReal resnorm;
2297: TPSNearestPointResJac(feval, x, y, res, J);
2298: resnorm = PetscSqrtReal(PetscSqr(PetscRealPart(res[0])) + PetscSqr(PetscRealPart(res[1])) + PetscSqr(PetscRealPart(res[2])));
2299: if (0) { // Turn on this monitor if you need to confirm quadratic convergence
2300: PetscPrintf(PETSC_COMM_SELF, "[%D] res [%g %g %g]\n", iter, PetscRealPart(res[0]), PetscRealPart(res[1]), PetscRealPart(res[2]));
2301: }
2302: if (resnorm < PETSC_SMALL) break;
2304: // Take the Newton step
2305: PetscKernel_A_gets_inverse_A_3(J, 0., PETSC_FALSE, NULL);
2306: PetscKernel_v_gets_v_minus_A_times_w_3(y, J, res);
2307: }
2308: for (PetscInt i=0; i<3; i++) x[i] = y[i];
2309: return 0;
2310: }
2312: const char *const DMPlexTPSTypes[] = {"SCHWARZ_P", "GYROID", "DMPlexTPSType", "DMPLEX_TPS_", NULL};
2314: static PetscErrorCode DMPlexCreateTPSMesh_Internal(DM dm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscBool tps_distribute, PetscInt refinements, PetscInt layers, PetscReal thickness)
2315: {
2316: PetscMPIInt rank;
2317: PetscInt topoDim = 2, spaceDim = 3, numFaces = 0, numVertices = 0, numEdges = 0;
2318: PetscInt (*edges)[2] = NULL, *edgeSets = NULL;
2319: PetscInt *cells_flat = NULL;
2320: PetscReal *vtxCoords = NULL;
2321: TPSEvaluateFunc evalFunc = NULL;
2322: PetscSimplePointFunc normalFunc = NULL;
2323: DMLabel label;
2325: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
2327: switch (tpstype) {
2328: case DMPLEX_TPS_SCHWARZ_P:
2330: if (!rank) {
2331: PetscInt (*cells)[6][4][4] = NULL; // [junction, junction-face, cell, conn]
2332: PetscInt Njunctions = 0, Ncuts = 0, Npipes[3], vcount;
2333: PetscReal L = 1;
2335: Npipes[0] = (extent[0] + 1) * extent[1] * extent[2];
2336: Npipes[1] = extent[0] * (extent[1] + 1) * extent[2];
2337: Npipes[2] = extent[0] * extent[1] * (extent[2] + 1);
2338: Njunctions = extent[0] * extent[1] * extent[2];
2339: Ncuts = 2 * (extent[0] * extent[1] + extent[1] * extent[2] + extent[2] * extent[0]);
2340: numVertices = 4 * (Npipes[0] + Npipes[1] + Npipes[2]) + 8 * Njunctions;
2341: PetscMalloc1(3*numVertices, &vtxCoords);
2342: PetscMalloc1(Njunctions, &cells);
2343: PetscMalloc1(Ncuts*4, &edges);
2344: PetscMalloc1(Ncuts*4, &edgeSets);
2345: // x-normal pipes
2346: vcount = 0;
2347: for (PetscInt i=0; i<extent[0]+1; i++) {
2348: for (PetscInt j=0; j<extent[1]; j++) {
2349: for (PetscInt k=0; k<extent[2]; k++) {
2350: for (PetscInt l=0; l<4; l++) {
2351: vtxCoords[vcount++] = (2*i - 1) * L;
2352: vtxCoords[vcount++] = 2 * j * L + PetscCosReal((2*l + 1) * PETSC_PI / 4) * L / 2;
2353: vtxCoords[vcount++] = 2 * k * L + PetscSinReal((2*l + 1) * PETSC_PI / 4) * L / 2;
2354: }
2355: }
2356: }
2357: }
2358: // y-normal pipes
2359: for (PetscInt i=0; i<extent[0]; i++) {
2360: for (PetscInt j=0; j<extent[1]+1; j++) {
2361: for (PetscInt k=0; k<extent[2]; k++) {
2362: for (PetscInt l=0; l<4; l++) {
2363: vtxCoords[vcount++] = 2 * i * L + PetscSinReal((2*l + 1) * PETSC_PI / 4) * L / 2;
2364: vtxCoords[vcount++] = (2*j - 1) * L;
2365: vtxCoords[vcount++] = 2 * k * L + PetscCosReal((2*l + 1) * PETSC_PI / 4) * L / 2;
2366: }
2367: }
2368: }
2369: }
2370: // z-normal pipes
2371: for (PetscInt i=0; i<extent[0]; i++) {
2372: for (PetscInt j=0; j<extent[1]; j++) {
2373: for (PetscInt k=0; k<extent[2]+1; k++) {
2374: for (PetscInt l=0; l<4; l++) {
2375: vtxCoords[vcount++] = 2 * i * L + PetscCosReal((2*l + 1) * PETSC_PI / 4) * L / 2;
2376: vtxCoords[vcount++] = 2 * j * L + PetscSinReal((2*l + 1) * PETSC_PI / 4) * L / 2;
2377: vtxCoords[vcount++] = (2*k - 1) * L;
2378: }
2379: }
2380: }
2381: }
2382: // junctions
2383: for (PetscInt i=0; i<extent[0]; i++) {
2384: for (PetscInt j=0; j<extent[1]; j++) {
2385: for (PetscInt k=0; k<extent[2]; k++) {
2386: const PetscInt J = (i*extent[1] + j)*extent[2] + k, Jvoff = (Npipes[0] + Npipes[1] + Npipes[2])*4 + J*8;
2388: for (PetscInt ii=0; ii<2; ii++) {
2389: for (PetscInt jj=0; jj<2; jj++) {
2390: for (PetscInt kk=0; kk<2; kk++) {
2391: double Ls = (1 - sqrt(2) / 4) * L;
2392: vtxCoords[vcount++] = 2*i*L + (2*ii-1) * Ls;
2393: vtxCoords[vcount++] = 2*j*L + (2*jj-1) * Ls;
2394: vtxCoords[vcount++] = 2*k*L + (2*kk-1) * Ls;
2395: }
2396: }
2397: }
2398: const PetscInt jfaces[3][2][4] = {
2399: {{3,1,0,2}, {7,5,4,6}}, // x-aligned
2400: {{5,4,0,1}, {7,6,2,3}}, // y-aligned
2401: {{6,2,0,4}, {7,3,1,5}} // z-aligned
2402: };
2403: const PetscInt pipe_lo[3] = { // vertex numbers of pipes
2404: ((i * extent[1] + j) * extent[2] + k)*4,
2405: ((i * (extent[1] + 1) + j) * extent[2] + k + Npipes[0])*4,
2406: ((i * extent[1] + j) * (extent[2]+1) + k + Npipes[0] + Npipes[1])*4
2407: };
2408: const PetscInt pipe_hi[3] = { // vertex numbers of pipes
2409: (((i + 1) * extent[1] + j) * extent[2] + k)*4,
2410: ((i * (extent[1] + 1) + j + 1) * extent[2] + k + Npipes[0])*4,
2411: ((i * extent[1] + j) * (extent[2]+1) + k + 1 + Npipes[0] + Npipes[1])*4
2412: };
2413: for (PetscInt dir=0; dir<3; dir++) { // x,y,z
2414: const PetscInt ijk[3] = {i, j, k};
2415: for (PetscInt l=0; l<4; l++) { // rotations
2416: cells[J][dir*2+0][l][0] = pipe_lo[dir] + l;
2417: cells[J][dir*2+0][l][1] = Jvoff + jfaces[dir][0][l];
2418: cells[J][dir*2+0][l][2] = Jvoff + jfaces[dir][0][(l-1+4)%4];
2419: cells[J][dir*2+0][l][3] = pipe_lo[dir] + (l-1+4)%4;
2420: cells[J][dir*2+1][l][0] = Jvoff + jfaces[dir][1][l];
2421: cells[J][dir*2+1][l][1] = pipe_hi[dir] + l;
2422: cells[J][dir*2+1][l][2] = pipe_hi[dir] + (l-1+4)%4;
2423: cells[J][dir*2+1][l][3] = Jvoff + jfaces[dir][1][(l-1+4)%4];
2424: if (ijk[dir] == 0) {
2425: edges[numEdges][0] = pipe_lo[dir] + l;
2426: edges[numEdges][1] = pipe_lo[dir] + (l+1) % 4;
2427: edgeSets[numEdges] = dir*2 + 1;
2428: numEdges++;
2429: }
2430: if (ijk[dir] + 1 == extent[dir]) {
2431: edges[numEdges][0] = pipe_hi[dir] + l;
2432: edges[numEdges][1] = pipe_hi[dir] + (l+1) % 4;
2433: edgeSets[numEdges] = dir*2 + 2;
2434: numEdges++;
2435: }
2436: }
2437: }
2438: }
2439: }
2440: }
2442: numFaces = 24 * Njunctions;
2443: cells_flat = cells[0][0][0];
2444: }
2445: evalFunc = TPSEvaluate_SchwarzP;
2446: normalFunc = TPSExtrudeNormalFunc_SchwarzP;
2447: break;
2448: case DMPLEX_TPS_GYROID:
2449: if (!rank) {
2450: // This is a coarse mesh approximation of the gyroid shifted to being the zero of the level set
2451: //
2452: // 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)
2453: //
2454: // on the cell [0,2]^3.
2455: //
2456: // Think about dividing that cell into four columns, and focus on the column [0,1]x[0,1]x[0,2].
2457: // If you looked at the gyroid in that column at different slices of z you would see that it kind of spins
2458: // like a boomerang:
2459: //
2460: // z = 0 z = 1/4 z = 1/2 z = 3/4 //
2461: // ----- ------- ------- ------- //
2462: // //
2463: // + + + + + + + \ + //
2464: // \ / \ //
2465: // \ `-_ _-' / } //
2466: // *-_ `-' _-' / //
2467: // + `-+ + + +-' + + / + //
2468: // //
2469: // //
2470: // z = 1 z = 5/4 z = 3/2 z = 7/4 //
2471: // ----- ------- ------- ------- //
2472: // //
2473: // +-_ + + + + _-+ + / + //
2474: // `-_ _-_ _-` / //
2475: // \ _-' `-_ / { //
2476: // \ / \ //
2477: // + + + + + + + \ + //
2478: //
2479: //
2480: // This course mesh approximates each of these slices by two line segments,
2481: // and then connects the segments in consecutive layers with quadrilateral faces.
2482: // All of the end points of the segments are multiples of 1/4 except for the
2483: // point * in the picture for z = 0 above and the similar points in other layers.
2484: // That point is at (gamma, gamma, 0), where gamma is calculated below.
2485: //
2486: // The column [1,2]x[1,2]x[0,2] looks the same as this column;
2487: // The columns [1,2]x[0,1]x[0,2] and [0,1]x[1,2]x[0,2] are mirror images.
2488: //
2489: // As for how this method turned into the names given to the vertices:
2490: // that was not systematic, it was just the way it worked out in my handwritten notes.
2492: PetscInt facesPerBlock = 64;
2493: PetscInt vertsPerBlock = 56;
2494: PetscInt extentPlus[3];
2495: PetscInt numBlocks, numBlocksPlus;
2496: const PetscInt A = 0, B = 1, C = 2, D = 3, E = 4, F = 5, G = 6, H = 7,
2497: II = 8, J = 9, K = 10, L = 11, M = 12, N = 13, O = 14, P = 15,
2498: Q = 16, R = 17, S = 18, T = 19, U = 20, V = 21, W = 22, X = 23,
2499: Y = 24, Z = 25, Ap = 26, Bp = 27, Cp = 28, Dp = 29, Ep = 30, Fp = 31,
2500: Gp = 32, Hp = 33, Ip = 34, Jp = 35, Kp = 36, Lp = 37, Mp = 38, Np = 39,
2501: Op = 40, Pp = 41, Qp = 42, Rp = 43, Sp = 44, Tp = 45, Up = 46, Vp = 47,
2502: Wp = 48, Xp = 49, Yp = 50, Zp = 51, Aq = 52, Bq = 53, Cq = 54, Dq = 55;
2503: const PetscInt pattern[64][4] =
2504: { /* face to vertex within the coarse discretization of a single gyroid block */
2505: /* layer 0 */
2506: {A,C,K,G},{C,B,II,K},{D,A,H,L},{B+56*1,D,L,J},{E,B+56*1,J,N},{A+56*2,E,N,H+56*2},{F,A+56*2,G+56*2,M},{B,F,M,II},
2507: /* layer 1 */
2508: {G,K,Q,O},{K,II,P,Q},{L,H,O+56*1,R},{J,L,R,P},{N,J,P,S},{H+56*2,N,S,O+56*3},{M,G+56*2,O+56*2,T},{II,M,T,P},
2509: /* layer 2 */
2510: {O,Q,Y,U},{Q,P,W,Y},{R,O+56*1,U+56*1,Ap},{P,R,Ap,W},{S,P,X,Bp},{O+56*3,S,Bp,V+56*1},{T,O+56*2,V,Z},{P,T,Z,X},
2511: /* layer 3 */
2512: {U,Y,Ep,Dp},{Y,W,Cp,Ep},{Ap,U+56*1,Dp+56*1,Gp},{W,Ap,Gp,Cp},{Bp,X,Cp+56*2,Fp},{V+56*1,Bp,Fp,Dp+56*1},{Z,V,Dp,Hp},{X,Z,Hp,Cp+56*2},
2513: /* layer 4 */
2514: {Dp,Ep,Mp,Kp},{Ep,Cp,Ip,Mp},{Gp,Dp+56*1,Lp,Np},{Cp,Gp,Np,Jp},{Fp,Cp+56*2,Jp+56*2,Pp},{Dp+56*1,Fp,Pp,Lp},{Hp,Dp,Kp,Op},{Cp+56*2,Hp,Op,Ip+56*2},
2515: /* layer 5 */
2516: {Kp,Mp,Sp,Rp},{Mp,Ip,Qp,Sp},{Np,Lp,Rp,Tp},{Jp,Np,Tp,Qp+56*1},{Pp,Jp+56*2,Qp+56*3,Up},{Lp,Pp,Up,Rp},{Op,Kp,Rp,Vp},{Ip+56*2,Op,Vp,Qp+56*2},
2517: /* layer 6 */
2518: {Rp,Sp,Aq,Yp},{Sp,Qp,Wp,Aq},{Tp,Rp,Yp,Cq},{Qp+56*1,Tp,Cq,Wp+56*1},{Up,Qp+56*3,Xp+56*1,Dq},{Rp,Up,Dq,Zp},{Vp,Rp,Zp,Bq},{Qp+56*2,Vp,Bq,Xp},
2519: /* layer 7 (the top is the periodic image of the bottom of layer 0) */
2520: {Yp,Aq,C+56*4,A+56*4},{Aq,Wp,B+56*4,C+56*4},{Cq,Yp,A+56*4,D+56*4},{Wp+56*1,Cq,D+56*4,B+56*5},{Dq,Xp+56*1,B+56*5,E+56*4},{Zp,Dq,E+56*4,A+56*6},{Bq,Zp,A+56*6,F+56*4},{Xp,Bq,F+56*4,B+56*4}
2521: };
2522: const PetscReal gamma = PetscAcosReal((PetscSqrtReal(3.)-1.) / PetscSqrtReal(2.)) / PETSC_PI;
2523: const PetscReal patternCoords[56][3] =
2524: {
2525: /* A */ {1.,0.,0.},
2526: /* B */ {0.,1.,0.},
2527: /* C */ {gamma,gamma,0.},
2528: /* D */ {1+gamma,1-gamma,0.},
2529: /* E */ {2-gamma,2-gamma,0.},
2530: /* F */ {1-gamma,1+gamma,0.},
2532: /* G */ {.5,0,.25},
2533: /* H */ {1.5,0.,.25},
2534: /* II */ {.5,1.,.25},
2535: /* J */ {1.5,1.,.25},
2536: /* K */ {.25,.5,.25},
2537: /* L */ {1.25,.5,.25},
2538: /* M */ {.75,1.5,.25},
2539: /* N */ {1.75,1.5,.25},
2541: /* O */ {0.,0.,.5},
2542: /* P */ {1.,1.,.5},
2543: /* Q */ {gamma,1-gamma,.5},
2544: /* R */ {1+gamma,gamma,.5},
2545: /* S */ {2-gamma,1+gamma,.5},
2546: /* T */ {1-gamma,2-gamma,.5},
2548: /* U */ {0.,.5,.75},
2549: /* V */ {0.,1.5,.75},
2550: /* W */ {1.,.5,.75},
2551: /* X */ {1.,1.5,.75},
2552: /* Y */ {.5,.75,.75},
2553: /* Z */ {.5,1.75,.75},
2554: /* Ap */ {1.5,.25,.75},
2555: /* Bp */ {1.5,1.25,.75},
2557: /* Cp */ {1.,0.,1.},
2558: /* Dp */ {0.,1.,1.},
2559: /* Ep */ {1-gamma,1-gamma,1.},
2560: /* Fp */ {1+gamma,1+gamma,1.},
2561: /* Gp */ {2-gamma,gamma,1.},
2562: /* Hp */ {gamma,2-gamma,1.},
2564: /* Ip */ {.5,0.,1.25},
2565: /* Jp */ {1.5,0.,1.25},
2566: /* Kp */ {.5,1.,1.25},
2567: /* Lp */ {1.5,1.,1.25},
2568: /* Mp */ {.75,.5,1.25},
2569: /* Np */ {1.75,.5,1.25},
2570: /* Op */ {.25,1.5,1.25},
2571: /* Pp */ {1.25,1.5,1.25},
2573: /* Qp */ {0.,0.,1.5},
2574: /* Rp */ {1.,1.,1.5},
2575: /* Sp */ {1-gamma,gamma,1.5},
2576: /* Tp */ {2-gamma,1-gamma,1.5},
2577: /* Up */ {1+gamma,2-gamma,1.5},
2578: /* Vp */ {gamma,1+gamma,1.5},
2580: /* Wp */ {0.,.5,1.75},
2581: /* Xp */ {0.,1.5,1.75},
2582: /* Yp */ {1.,.5,1.75},
2583: /* Zp */ {1.,1.5,1.75},
2584: /* Aq */ {.5,.25,1.75},
2585: /* Bq */ {.5,1.25,1.75},
2586: /* Cq */ {1.5,.75,1.75},
2587: /* Dq */ {1.5,1.75,1.75},
2588: };
2589: PetscInt (*cells)[64][4] = NULL;
2590: PetscBool *seen;
2591: PetscInt *vertToTrueVert;
2592: PetscInt count;
2594: for (PetscInt i = 0; i < 3; i++) extentPlus[i] = extent[i] + 1;
2595: numBlocks = 1;
2596: for (PetscInt i = 0; i < 3; i++) numBlocks *= extent[i];
2597: numBlocksPlus = 1;
2598: for (PetscInt i = 0; i < 3; i++) numBlocksPlus *= extentPlus[i];
2599: numFaces = numBlocks * facesPerBlock;
2600: PetscMalloc1(numBlocks, &cells);
2601: PetscCalloc1(numBlocksPlus * vertsPerBlock,&seen);
2602: for (PetscInt k = 0; k < extent[2]; k++) {
2603: for (PetscInt j = 0; j < extent[1]; j++) {
2604: for (PetscInt i = 0; i < extent[0]; i++) {
2605: for (PetscInt f = 0; f < facesPerBlock; f++) {
2606: for (PetscInt v = 0; v < 4; v++) {
2607: PetscInt vertRaw = pattern[f][v];
2608: PetscInt blockidx = vertRaw / 56;
2609: PetscInt patternvert = vertRaw % 56;
2610: PetscInt xplus = (blockidx & 1);
2611: PetscInt yplus = (blockidx & 2) >> 1;
2612: PetscInt zplus = (blockidx & 4) >> 2;
2613: PetscInt zcoord = (periodic && periodic[2] == DM_BOUNDARY_PERIODIC) ? ((k + zplus) % extent[2]) : (k + zplus);
2614: PetscInt ycoord = (periodic && periodic[1] == DM_BOUNDARY_PERIODIC) ? ((j + yplus) % extent[1]) : (j + yplus);
2615: PetscInt xcoord = (periodic && periodic[0] == DM_BOUNDARY_PERIODIC) ? ((i + xplus) % extent[0]) : (i + xplus);
2616: PetscInt vert = ((zcoord * extentPlus[1] + ycoord) * extentPlus[0] + xcoord) * 56 + patternvert;
2618: cells[(k * extent[1] + j) * extent[0] + i][f][v] = vert;
2619: seen[vert] = PETSC_TRUE;
2620: }
2621: }
2622: }
2623: }
2624: }
2625: for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++) if (seen[i]) numVertices++;
2626: count = 0;
2627: PetscMalloc1(numBlocksPlus * vertsPerBlock, &vertToTrueVert);
2628: PetscMalloc1(numVertices * 3, &vtxCoords);
2629: for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++) vertToTrueVert[i] = -1;
2630: for (PetscInt k = 0; k < extentPlus[2]; k++) {
2631: for (PetscInt j = 0; j < extentPlus[1]; j++) {
2632: for (PetscInt i = 0; i < extentPlus[0]; i++) {
2633: for (PetscInt v = 0; v < vertsPerBlock; v++) {
2634: PetscInt vIdx = ((k * extentPlus[1] + j) * extentPlus[0] + i) * vertsPerBlock + v;
2636: if (seen[vIdx]) {
2637: PetscInt thisVert;
2639: vertToTrueVert[vIdx] = thisVert = count++;
2641: for (PetscInt d = 0; d < 3; d++) vtxCoords[3 * thisVert + d] = patternCoords[v][d];
2642: vtxCoords[3 * thisVert + 0] += i * 2;
2643: vtxCoords[3 * thisVert + 1] += j * 2;
2644: vtxCoords[3 * thisVert + 2] += k * 2;
2645: }
2646: }
2647: }
2648: }
2649: }
2650: for (PetscInt i = 0; i < numBlocks; i++) {
2651: for (PetscInt f = 0; f < facesPerBlock; f++) {
2652: for (PetscInt v = 0; v < 4; v++) {
2653: cells[i][f][v] = vertToTrueVert[cells[i][f][v]];
2654: }
2655: }
2656: }
2657: PetscFree(vertToTrueVert);
2658: PetscFree(seen);
2659: cells_flat = cells[0][0];
2660: numEdges = 0;
2661: for (PetscInt i = 0; i < numFaces; i++) {
2662: for (PetscInt e = 0; e < 4; e++) {
2663: PetscInt ev[] = {cells_flat[i*4 + e], cells_flat[i*4 + ((e+1)%4)]};
2664: const PetscReal *evCoords[] = {&vtxCoords[3*ev[0]], &vtxCoords[3*ev[1]]};
2666: for (PetscInt d = 0; d < 3; d++) {
2667: if (!periodic || periodic[0] != DM_BOUNDARY_PERIODIC) {
2668: if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) numEdges++;
2669: if (evCoords[0][d] == 2.*extent[d] && evCoords[1][d] == 2.*extent[d]) numEdges++;
2670: }
2671: }
2672: }
2673: }
2674: PetscMalloc1(numEdges, &edges);
2675: PetscMalloc1(numEdges, &edgeSets);
2676: for (PetscInt edge = 0, i = 0; i < numFaces; i++) {
2677: for (PetscInt e = 0; e < 4; e++) {
2678: PetscInt ev[] = {cells_flat[i*4 + e], cells_flat[i*4 + ((e+1)%4)]};
2679: const PetscReal *evCoords[] = {&vtxCoords[3*ev[0]], &vtxCoords[3*ev[1]]};
2681: for (PetscInt d = 0; d < 3; d++) {
2682: if (!periodic || periodic[d] != DM_BOUNDARY_PERIODIC) {
2683: if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) {
2684: edges[edge][0] = ev[0];
2685: edges[edge][1] = ev[1];
2686: edgeSets[edge++] = 2 * d;
2687: }
2688: if (evCoords[0][d] == 2.*extent[d] && evCoords[1][d] == 2.*extent[d]) {
2689: edges[edge][0] = ev[0];
2690: edges[edge][1] = ev[1];
2691: edgeSets[edge++] = 2 * d + 1;
2692: }
2693: }
2694: }
2695: }
2696: }
2697: }
2698: evalFunc = TPSEvaluate_Gyroid;
2699: normalFunc = TPSExtrudeNormalFunc_Gyroid;
2700: break;
2701: }
2703: DMSetDimension(dm, topoDim);
2704: if (!rank) DMPlexBuildFromCellList(dm, numFaces, numVertices, 4, cells_flat);
2705: else DMPlexBuildFromCellList(dm, 0, 0, 0, NULL);
2706: PetscFree(cells_flat);
2707: {
2708: DM idm;
2709: DMPlexInterpolate(dm, &idm);
2710: DMPlexReplace_Static(dm, &idm);
2711: }
2712: if (!rank) DMPlexBuildCoordinatesFromCellList(dm, spaceDim, vtxCoords);
2713: else DMPlexBuildCoordinatesFromCellList(dm, spaceDim, NULL);
2714: PetscFree(vtxCoords);
2716: DMCreateLabel(dm, "Face Sets");
2717: DMGetLabel(dm, "Face Sets", &label);
2718: for (PetscInt e=0; e<numEdges; e++) {
2719: PetscInt njoin;
2720: const PetscInt *join, verts[] = {numFaces + edges[e][0], numFaces + edges[e][1]};
2721: DMPlexGetJoin(dm, 2, verts, &njoin, &join);
2723: DMLabelSetValue(label, join[0], edgeSets[e]);
2724: DMPlexRestoreJoin(dm, 2, verts, &njoin, &join);
2725: }
2726: PetscFree(edges);
2727: PetscFree(edgeSets);
2728: if (tps_distribute) {
2729: DM pdm = NULL;
2730: PetscPartitioner part;
2732: DMPlexGetPartitioner(dm, &part);
2733: PetscPartitionerSetFromOptions(part);
2734: DMPlexDistribute(dm, 0, NULL, &pdm);
2735: if (pdm) {
2736: DMPlexReplace_Static(dm, &pdm);
2737: }
2738: // Do not auto-distribute again
2739: DMPlexDistributeSetDefault(dm, PETSC_FALSE);
2740: }
2742: DMPlexSetRefinementUniform(dm, PETSC_TRUE);
2743: for (PetscInt refine=0; refine<refinements; refine++) {
2744: PetscInt m;
2745: DM dmf;
2746: Vec X;
2747: PetscScalar *x;
2748: DMRefine(dm, MPI_COMM_NULL, &dmf);
2749: DMPlexReplace_Static(dm, &dmf);
2751: DMGetCoordinatesLocal(dm, &X);
2752: VecGetLocalSize(X, &m);
2753: VecGetArray(X, &x);
2754: for (PetscInt i=0; i<m; i+=3) {
2755: TPSNearestPoint(evalFunc, &x[i]);
2756: }
2757: VecRestoreArray(X, &x);
2758: }
2760: // Face Sets has already been propagated to new vertices during refinement; this propagates to the initial vertices.
2761: DMGetLabel(dm, "Face Sets", &label);
2762: DMPlexLabelComplete(dm, label);
2764: if (thickness > 0) {
2765: DM edm,cdm,ecdm;
2766: DMPlexTransform tr;
2767: const char *prefix;
2768: PetscOptions options;
2769: // Code from DMPlexExtrude
2770: DMPlexTransformCreate(PetscObjectComm((PetscObject)dm), &tr);
2771: DMPlexTransformSetDM(tr, dm);
2772: DMPlexTransformSetType(tr, DMPLEXEXTRUDE);
2773: PetscObjectGetOptionsPrefix((PetscObject) dm, &prefix);
2774: PetscObjectSetOptionsPrefix((PetscObject) tr, prefix);
2775: PetscObjectGetOptions((PetscObject) dm, &options);
2776: PetscObjectSetOptions((PetscObject) tr, options);
2777: DMPlexTransformExtrudeSetLayers(tr, layers);
2778: DMPlexTransformExtrudeSetThickness(tr, thickness);
2779: DMPlexTransformExtrudeSetTensor(tr, PETSC_FALSE);
2780: DMPlexTransformExtrudeSetSymmetric(tr, PETSC_TRUE);
2781: DMPlexTransformExtrudeSetNormalFunction(tr, normalFunc);
2782: DMPlexTransformSetFromOptions(tr);
2783: PetscObjectSetOptions((PetscObject) tr, NULL);
2784: DMPlexTransformSetUp(tr);
2785: PetscObjectViewFromOptions((PetscObject) tr, NULL, "-dm_plex_tps_transform_view");
2786: DMPlexTransformApply(tr, dm, &edm);
2787: DMCopyDisc(dm, edm);
2788: DMGetCoordinateDM(dm, &cdm);
2789: DMGetCoordinateDM(edm, &ecdm);
2790: DMCopyDisc(cdm, ecdm);
2791: DMPlexTransformCreateDiscLabels(tr, edm);
2792: DMPlexTransformDestroy(&tr);
2793: if (edm) {
2794: ((DM_Plex *)edm->data)->printFEM = ((DM_Plex *)dm->data)->printFEM;
2795: ((DM_Plex *)edm->data)->printL2 = ((DM_Plex *)dm->data)->printL2;
2796: }
2797: DMPlexReplace_Static(dm, &edm);
2798: }
2799: return 0;
2800: }
2802: /*@
2803: DMPlexCreateTPSMesh - Create a distributed, interpolated mesh of a triply-periodic surface
2805: Collective
2807: Input Parameters:
2808: + comm - The communicator for the DM object
2809: . tpstype - Type of triply-periodic surface
2810: . extent - Array of length 3 containing number of periods in each direction
2811: . periodic - array of length 3 with periodicity, or NULL for non-periodic
2812: . tps_distribute - Distribute 2D manifold mesh prior to refinement and extrusion (more scalable)
2813: . refinements - Number of factor-of-2 refinements of 2D manifold mesh
2814: . layers - Number of cell layers extruded in normal direction
2815: - thickness - Thickness in normal direction
2817: Output Parameter:
2818: . dm - The DM object
2820: Notes:
2821: This meshes the surface of the Schwarz P or Gyroid surfaces. Schwarz P is is the simplest member of the triply-periodic minimal surfaces.
2822: https://en.wikipedia.org/wiki/Schwarz_minimal_surface#Schwarz_P_(%22Primitive%22) and can be cut with "clean" boundaries.
2823: 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.
2824: Our implementation creates a very coarse mesh of the surface and refines (by 4-way splitting) as many times as requested.
2825: On each refinement, all vertices are projected to their nearest point on the surface.
2826: This projection could readily be extended to related surfaces.
2828: The face (edge) sets for the Schwarz P surface are numbered 1(-x), 2(+x), 3(-y), 4(+y), 5(-z), 6(+z).
2829: When the mesh is refined, "Face Sets" contain the new vertices (created during refinement). Use DMPlexLabelComplete() to propagate to coarse-level vertices.
2831: References:
2832: . * - Maskery et al, Insights into the mechanical properties of several triply periodic minimal surface lattice structures made by polymer additive manufacturing, 2017. https://doi.org/10.1016/j.polymer.2017.11.049
2834: Developer Notes:
2835: The Gyroid mesh does not currently mark boundary sets.
2837: Level: beginner
2839: .seealso: DMPlexCreateSphereMesh(), DMSetType(), DMCreate()
2840: @*/
2841: PetscErrorCode DMPlexCreateTPSMesh(MPI_Comm comm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscBool tps_distribute, PetscInt refinements, PetscInt layers, PetscReal thickness, DM *dm)
2842: {
2843: DMCreate(comm, dm);
2844: DMSetType(*dm, DMPLEX);
2845: DMPlexCreateTPSMesh_Internal(*dm, tpstype, extent, periodic, tps_distribute, refinements, layers, thickness);
2846: return 0;
2847: }
2849: /*@
2850: DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d.
2852: Collective
2854: Input Parameters:
2855: + comm - The communicator for the DM object
2856: . dim - The dimension
2857: . simplex - Use simplices, or tensor product cells
2858: - R - The radius
2860: Output Parameter:
2861: . dm - The DM object
2863: Level: beginner
2865: .seealso: DMPlexCreateBallMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
2866: @*/
2867: PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscReal R, DM *dm)
2868: {
2870: DMCreate(comm, dm);
2871: DMSetType(*dm, DMPLEX);
2872: DMPlexCreateSphereMesh_Internal(*dm, dim, simplex, R);
2873: return 0;
2874: }
2876: static PetscErrorCode DMPlexCreateBallMesh_Internal(DM dm, PetscInt dim, PetscReal R)
2877: {
2878: DM sdm, vol;
2879: DMLabel bdlabel;
2881: DMCreate(PetscObjectComm((PetscObject) dm), &sdm);
2882: DMSetType(sdm, DMPLEX);
2883: PetscObjectSetOptionsPrefix((PetscObject) sdm, "bd_");
2884: DMPlexCreateSphereMesh_Internal(sdm, dim-1, PETSC_TRUE, R);
2885: DMSetFromOptions(sdm);
2886: DMViewFromOptions(sdm, NULL, "-dm_view");
2887: DMPlexGenerate(sdm, NULL, PETSC_TRUE, &vol);
2888: DMDestroy(&sdm);
2889: DMPlexReplace_Static(dm, &vol);
2890: DMCreateLabel(dm, "marker");
2891: DMGetLabel(dm, "marker", &bdlabel);
2892: DMPlexMarkBoundaryFaces(dm, PETSC_DETERMINE, bdlabel);
2893: DMPlexLabelComplete(dm, bdlabel);
2894: return 0;
2895: }
2897: /*@
2898: DMPlexCreateBallMesh - Creates a simplex mesh on the d-dimensional ball, B^d.
2900: Collective
2902: Input Parameters:
2903: + comm - The communicator for the DM object
2904: . dim - The dimension
2905: - R - The radius
2907: Output Parameter:
2908: . dm - The DM object
2910: Options Database Keys:
2911: - bd_dm_refine - This will refine the surface mesh preserving the sphere geometry
2913: Level: beginner
2915: .seealso: DMPlexCreateSphereMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
2916: @*/
2917: PetscErrorCode DMPlexCreateBallMesh(MPI_Comm comm, PetscInt dim, PetscReal R, DM *dm)
2918: {
2919: DMCreate(comm, dm);
2920: DMSetType(*dm, DMPLEX);
2921: DMPlexCreateBallMesh_Internal(*dm, dim, R);
2922: return 0;
2923: }
2925: static PetscErrorCode DMPlexCreateReferenceCell_Internal(DM rdm, DMPolytopeType ct)
2926: {
2927: switch (ct) {
2928: case DM_POLYTOPE_POINT:
2929: {
2930: PetscInt numPoints[1] = {1};
2931: PetscInt coneSize[1] = {0};
2932: PetscInt cones[1] = {0};
2933: PetscInt coneOrientations[1] = {0};
2934: PetscScalar vertexCoords[1] = {0.0};
2936: DMSetDimension(rdm, 0);
2937: DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);
2938: }
2939: break;
2940: case DM_POLYTOPE_SEGMENT:
2941: {
2942: PetscInt numPoints[2] = {2, 1};
2943: PetscInt coneSize[3] = {2, 0, 0};
2944: PetscInt cones[2] = {1, 2};
2945: PetscInt coneOrientations[2] = {0, 0};
2946: PetscScalar vertexCoords[2] = {-1.0, 1.0};
2948: DMSetDimension(rdm, 1);
2949: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
2950: }
2951: break;
2952: case DM_POLYTOPE_POINT_PRISM_TENSOR:
2953: {
2954: PetscInt numPoints[2] = {2, 1};
2955: PetscInt coneSize[3] = {2, 0, 0};
2956: PetscInt cones[2] = {1, 2};
2957: PetscInt coneOrientations[2] = {0, 0};
2958: PetscScalar vertexCoords[2] = {-1.0, 1.0};
2960: DMSetDimension(rdm, 1);
2961: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
2962: }
2963: break;
2964: case DM_POLYTOPE_TRIANGLE:
2965: {
2966: PetscInt numPoints[2] = {3, 1};
2967: PetscInt coneSize[4] = {3, 0, 0, 0};
2968: PetscInt cones[3] = {1, 2, 3};
2969: PetscInt coneOrientations[3] = {0, 0, 0};
2970: PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0};
2972: DMSetDimension(rdm, 2);
2973: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
2974: }
2975: break;
2976: case DM_POLYTOPE_QUADRILATERAL:
2977: {
2978: PetscInt numPoints[2] = {4, 1};
2979: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
2980: PetscInt cones[4] = {1, 2, 3, 4};
2981: PetscInt coneOrientations[4] = {0, 0, 0, 0};
2982: PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0};
2984: DMSetDimension(rdm, 2);
2985: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
2986: }
2987: break;
2988: case DM_POLYTOPE_SEG_PRISM_TENSOR:
2989: {
2990: PetscInt numPoints[2] = {4, 1};
2991: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
2992: PetscInt cones[4] = {1, 2, 3, 4};
2993: PetscInt coneOrientations[4] = {0, 0, 0, 0};
2994: PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, 1.0};
2996: DMSetDimension(rdm, 2);
2997: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
2998: }
2999: break;
3000: case DM_POLYTOPE_TETRAHEDRON:
3001: {
3002: PetscInt numPoints[2] = {4, 1};
3003: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
3004: PetscInt cones[4] = {1, 2, 3, 4};
3005: PetscInt coneOrientations[4] = {0, 0, 0, 0};
3006: 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};
3008: DMSetDimension(rdm, 3);
3009: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3010: }
3011: break;
3012: case DM_POLYTOPE_HEXAHEDRON:
3013: {
3014: PetscInt numPoints[2] = {8, 1};
3015: PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0};
3016: PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8};
3017: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
3018: 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,
3019: -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0};
3021: DMSetDimension(rdm, 3);
3022: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3023: }
3024: break;
3025: case DM_POLYTOPE_TRI_PRISM:
3026: {
3027: PetscInt numPoints[2] = {6, 1};
3028: PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0};
3029: PetscInt cones[6] = {1, 2, 3, 4, 5, 6};
3030: PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0};
3031: PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, -1.0, -1.0,
3032: -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0};
3034: DMSetDimension(rdm, 3);
3035: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3036: }
3037: break;
3038: case DM_POLYTOPE_TRI_PRISM_TENSOR:
3039: {
3040: PetscInt numPoints[2] = {6, 1};
3041: PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0};
3042: PetscInt cones[6] = {1, 2, 3, 4, 5, 6};
3043: PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0};
3044: PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0,
3045: -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0};
3047: DMSetDimension(rdm, 3);
3048: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3049: }
3050: break;
3051: case DM_POLYTOPE_QUAD_PRISM_TENSOR:
3052: {
3053: PetscInt numPoints[2] = {8, 1};
3054: PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0};
3055: PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8};
3056: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
3057: 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,
3058: -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0};
3060: DMSetDimension(rdm, 3);
3061: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3062: }
3063: break;
3064: case DM_POLYTOPE_PYRAMID:
3065: {
3066: PetscInt numPoints[2] = {5, 1};
3067: PetscInt coneSize[6] = {5, 0, 0, 0, 0, 0};
3068: PetscInt cones[5] = {1, 2, 3, 4, 5};
3069: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
3070: 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,
3071: 0.0, 0.0, 1.0};
3073: DMSetDimension(rdm, 3);
3074: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3075: }
3076: break;
3077: default: SETERRQ(PetscObjectComm((PetscObject) rdm), PETSC_ERR_ARG_WRONG, "Cannot create reference cell for cell type %s", DMPolytopeTypes[ct]);
3078: }
3079: {
3080: PetscInt Nv, v;
3082: /* Must create the celltype label here so that we do not automatically try to compute the types */
3083: DMCreateLabel(rdm, "celltype");
3084: DMPlexSetCellType(rdm, 0, ct);
3085: DMPlexGetChart(rdm, NULL, &Nv);
3086: for (v = 1; v < Nv; ++v) DMPlexSetCellType(rdm, v, DM_POLYTOPE_POINT);
3087: }
3088: DMPlexInterpolateInPlace_Internal(rdm);
3089: PetscObjectSetName((PetscObject) rdm, DMPolytopeTypes[ct]);
3090: return 0;
3091: }
3093: /*@
3094: DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell
3096: Collective
3098: Input Parameters:
3099: + comm - The communicator
3100: - ct - The cell type of the reference cell
3102: Output Parameter:
3103: . refdm - The reference cell
3105: Level: intermediate
3107: .seealso: DMPlexCreateReferenceCell(), DMPlexCreateBoxMesh()
3108: @*/
3109: PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, DMPolytopeType ct, DM *refdm)
3110: {
3111: DMCreate(comm, refdm);
3112: DMSetType(*refdm, DMPLEX);
3113: DMPlexCreateReferenceCell_Internal(*refdm, ct);
3114: return 0;
3115: }
3117: static PetscErrorCode DMPlexCreateBoundaryLabel_Private(DM dm, const char name[])
3118: {
3119: DM plex;
3120: DMLabel label;
3121: PetscBool hasLabel;
3124: DMHasLabel(dm, name, &hasLabel);
3125: if (hasLabel) return 0;
3126: DMCreateLabel(dm, name);
3127: DMGetLabel(dm, name, &label);
3128: DMConvert(dm, DMPLEX, &plex);
3129: DMPlexMarkBoundaryFaces(plex, 1, label);
3130: DMDestroy(&plex);
3131: return 0;
3132: }
3134: const char * const DMPlexShapes[] = {"box", "box_surface", "ball", "sphere", "cylinder", "schwarz_p", "gyroid", "doublet", "unknown", "DMPlexShape", "DM_SHAPE_", NULL};
3136: static PetscErrorCode DMPlexCreateFromOptions_Internal(PetscOptionItems *PetscOptionsObject, PetscBool *useCoordSpace, DM dm)
3137: {
3138: DMPlexShape shape = DM_SHAPE_BOX;
3139: DMPolytopeType cell = DM_POLYTOPE_TRIANGLE;
3140: PetscInt dim = 2;
3141: PetscBool simplex = PETSC_TRUE, interpolate = PETSC_TRUE, adjCone = PETSC_FALSE, adjClosure = PETSC_TRUE, refDomain = PETSC_FALSE;
3142: PetscBool flg, flg2, fflg, bdfflg, nameflg;
3143: MPI_Comm comm;
3144: char filename[PETSC_MAX_PATH_LEN] = "<unspecified>";
3145: char bdFilename[PETSC_MAX_PATH_LEN] = "<unspecified>";
3146: char plexname[PETSC_MAX_PATH_LEN] = "";
3148: PetscObjectGetComm((PetscObject) dm, &comm);
3149: /* TODO Turn this into a registration interface */
3150: PetscOptionsString("-dm_plex_filename", "File containing a mesh", "DMPlexCreateFromFile", filename, filename, sizeof(filename), &fflg);
3151: PetscOptionsString("-dm_plex_boundary_filename", "File containing a mesh boundary", "DMPlexCreateFromFile", bdFilename, bdFilename, sizeof(bdFilename), &bdfflg);
3152: PetscOptionsString("-dm_plex_name", "Name of the mesh in the file", "DMPlexCreateFromFile", plexname, plexname, sizeof(plexname), &nameflg);
3153: PetscOptionsEnum("-dm_plex_cell", "Cell shape", "", DMPolytopeTypes, (PetscEnum) cell, (PetscEnum *) &cell, NULL);
3154: PetscOptionsBool("-dm_plex_reference_cell_domain", "Use a reference cell domain", "", refDomain, &refDomain, NULL);
3155: PetscOptionsEnum("-dm_plex_shape", "Shape for built-in mesh", "", DMPlexShapes, (PetscEnum) shape, (PetscEnum *) &shape, &flg);
3156: PetscOptionsBoundedInt("-dm_plex_dim", "Topological dimension of the mesh", "DMGetDimension", dim, &dim, &flg, 0);
3158: PetscOptionsBool("-dm_plex_simplex", "Mesh cell shape", "", simplex, &simplex, &flg);
3159: PetscOptionsBool("-dm_plex_interpolate", "Flag to create edges and faces automatically", "", interpolate, &interpolate, &flg);
3160: PetscOptionsBool("-dm_plex_adj_cone", "Set adjacency direction", "DMSetBasicAdjacency", adjCone, &adjCone, &flg);
3161: PetscOptionsBool("-dm_plex_adj_closure", "Set adjacency size", "DMSetBasicAdjacency", adjClosure, &adjClosure, &flg2);
3162: if (flg || flg2) DMSetBasicAdjacency(dm, adjCone, adjClosure);
3164: switch (cell) {
3165: case DM_POLYTOPE_POINT:
3166: case DM_POLYTOPE_SEGMENT:
3167: case DM_POLYTOPE_POINT_PRISM_TENSOR:
3168: case DM_POLYTOPE_TRIANGLE:
3169: case DM_POLYTOPE_QUADRILATERAL:
3170: case DM_POLYTOPE_TETRAHEDRON:
3171: case DM_POLYTOPE_HEXAHEDRON:
3172: *useCoordSpace = PETSC_TRUE;break;
3173: default: *useCoordSpace = PETSC_FALSE;break;
3174: }
3176: if (fflg) {
3177: DM dmnew;
3179: DMPlexCreateFromFile(PetscObjectComm((PetscObject) dm), filename, plexname, interpolate, &dmnew);
3180: DMPlexCopy_Internal(dm, PETSC_FALSE, dmnew);
3181: DMPlexReplace_Static(dm, &dmnew);
3182: } else if (refDomain) {
3183: DMPlexCreateReferenceCell_Internal(dm, cell);
3184: } else if (bdfflg) {
3185: DM bdm, dmnew;
3187: DMPlexCreateFromFile(PetscObjectComm((PetscObject) dm), bdFilename, plexname, interpolate, &bdm);
3188: PetscObjectSetOptionsPrefix((PetscObject) bdm, "bd_");
3189: DMSetFromOptions(bdm);
3190: DMPlexGenerate(bdm, NULL, interpolate, &dmnew);
3191: DMDestroy(&bdm);
3192: DMPlexCopy_Internal(dm, PETSC_FALSE, dmnew);
3193: DMPlexReplace_Static(dm, &dmnew);
3194: } else {
3195: PetscObjectSetName((PetscObject) dm, DMPlexShapes[shape]);
3196: switch (shape) {
3197: case DM_SHAPE_BOX:
3198: {
3199: PetscInt faces[3] = {0, 0, 0};
3200: PetscReal lower[3] = {0, 0, 0};
3201: PetscReal upper[3] = {1, 1, 1};
3202: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
3203: PetscInt i, n;
3205: n = dim;
3206: for (i = 0; i < dim; ++i) faces[i] = (dim == 1 ? 1 : 4-dim);
3207: PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg);
3208: n = 3;
3209: PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg);
3211: n = 3;
3212: PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg);
3214: n = 3;
3215: PetscOptionsEnumArray("-dm_plex_box_bd", "Boundary type for each dimension", "", DMBoundaryTypes, (PetscEnum *) bdt, &n, &flg);
3217: switch (cell) {
3218: case DM_POLYTOPE_TRI_PRISM_TENSOR:
3219: DMPlexCreateWedgeBoxMesh_Internal(dm, faces, lower, upper, bdt);
3220: if (!interpolate) {
3221: DM udm;
3223: DMPlexUninterpolate(dm, &udm);
3224: DMPlexReplace_Static(dm, &udm);
3225: }
3226: break;
3227: default:
3228: DMPlexCreateBoxMesh_Internal(dm, dim, simplex, faces, lower, upper, bdt, interpolate);
3229: break;
3230: }
3231: }
3232: break;
3233: case DM_SHAPE_BOX_SURFACE:
3234: {
3235: PetscInt faces[3] = {0, 0, 0};
3236: PetscReal lower[3] = {0, 0, 0};
3237: PetscReal upper[3] = {1, 1, 1};
3238: PetscInt i, n;
3240: n = dim+1;
3241: for (i = 0; i < dim+1; ++i) faces[i] = (dim+1 == 1 ? 1 : 4-(dim+1));
3242: PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg);
3243: n = 3;
3244: PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg);
3246: n = 3;
3247: PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg);
3249: DMPlexCreateBoxSurfaceMesh_Internal(dm, dim+1, faces, lower, upper, interpolate);
3250: }
3251: break;
3252: case DM_SHAPE_SPHERE:
3253: {
3254: PetscReal R = 1.0;
3256: PetscOptionsReal("-dm_plex_sphere_radius", "Radius of the sphere", "", R, &R, &flg);
3257: DMPlexCreateSphereMesh_Internal(dm, dim, simplex, R);
3258: }
3259: break;
3260: case DM_SHAPE_BALL:
3261: {
3262: PetscReal R = 1.0;
3264: PetscOptionsReal("-dm_plex_ball_radius", "Radius of the ball", "", R, &R, &flg);
3265: DMPlexCreateBallMesh_Internal(dm, dim, R);
3266: }
3267: break;
3268: case DM_SHAPE_CYLINDER:
3269: {
3270: DMBoundaryType bdt = DM_BOUNDARY_NONE;
3271: PetscInt Nw = 6;
3273: PetscOptionsEnum("-dm_plex_cylinder_bd", "Boundary type in the z direction", "", DMBoundaryTypes, (PetscEnum) bdt, (PetscEnum *) &bdt, NULL);
3274: PetscOptionsInt("-dm_plex_cylinder_num_wedges", "Number of wedges around the cylinder", "", Nw, &Nw, NULL);
3275: switch (cell) {
3276: case DM_POLYTOPE_TRI_PRISM_TENSOR:
3277: DMPlexCreateWedgeCylinderMesh_Internal(dm, Nw, interpolate);
3278: break;
3279: default:
3280: DMPlexCreateHexCylinderMesh_Internal(dm, bdt);
3281: break;
3282: }
3283: }
3284: break;
3285: case DM_SHAPE_SCHWARZ_P: // fallthrough
3286: case DM_SHAPE_GYROID:
3287: {
3288: PetscInt extent[3] = {1,1,1}, refine = 0, layers = 0, three;
3289: PetscReal thickness = 0.;
3290: DMBoundaryType periodic[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
3291: DMPlexTPSType tps_type = shape == DM_SHAPE_SCHWARZ_P ? DMPLEX_TPS_SCHWARZ_P : DMPLEX_TPS_GYROID;
3292: PetscBool tps_distribute;
3293: PetscOptionsIntArray("-dm_plex_tps_extent", "Number of replicas for each of three dimensions", NULL, extent, (three=3, &three), NULL);
3294: PetscOptionsInt("-dm_plex_tps_refine", "Number of refinements", NULL, refine, &refine, NULL);
3295: PetscOptionsEnumArray("-dm_plex_tps_periodic", "Periodicity in each of three dimensions", NULL, DMBoundaryTypes, (PetscEnum*)periodic, (three=3, &three), NULL);
3296: PetscOptionsInt("-dm_plex_tps_layers", "Number of layers in volumetric extrusion (or zero to not extrude)", NULL, layers, &layers, NULL);
3297: PetscOptionsReal("-dm_plex_tps_thickness", "Thickness of volumetric extrusion", NULL, thickness, &thickness, NULL);
3298: DMPlexDistributeGetDefault(dm, &tps_distribute);
3299: PetscOptionsBool("-dm_plex_tps_distribute", "Distribute the 2D mesh prior to refinement and extrusion", NULL, tps_distribute, &tps_distribute, NULL);
3300: DMPlexCreateTPSMesh_Internal(dm, tps_type, extent, periodic, tps_distribute, refine, layers, thickness);
3301: }
3302: break;
3303: case DM_SHAPE_DOUBLET:
3304: {
3305: DM dmnew;
3306: PetscReal rl = 0.0;
3308: PetscOptionsReal("-dm_plex_doublet_refinementlimit", "Refinement limit", NULL, rl, &rl, NULL);
3309: DMPlexCreateDoublet(PetscObjectComm((PetscObject)dm), dim, simplex, interpolate, rl, &dmnew);
3310: DMPlexCopy_Internal(dm, PETSC_FALSE, dmnew);
3311: DMPlexReplace_Static(dm, &dmnew);
3312: }
3313: break;
3314: default: SETERRQ(comm, PETSC_ERR_SUP, "Domain shape %s is unsupported", DMPlexShapes[shape]);
3315: }
3316: }
3317: DMPlexSetRefinementUniform(dm, PETSC_TRUE);
3318: if (!((PetscObject)dm)->name && nameflg) {
3319: PetscObjectSetName((PetscObject)dm, plexname);
3320: }
3321: return 0;
3322: }
3324: PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject, DM dm)
3325: {
3326: DM_Plex *mesh = (DM_Plex*) dm->data;
3327: PetscBool flg;
3328: char bdLabel[PETSC_MAX_PATH_LEN];
3330: /* Handle viewing */
3331: PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL);
3332: PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL,0);
3333: PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL);
3334: PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL,0);
3335: DMMonitorSetFromOptions(dm, "-dm_plex_monitor_throughput", "Monitor the simulation throughput", "DMPlexMonitorThroughput", DMPlexMonitorThroughput, NULL, &flg);
3336: if (flg) PetscLogDefaultBegin();
3337: /* Labeling */
3338: PetscOptionsString("-dm_plex_boundary_label", "Label to mark the mesh boundary", "", bdLabel, bdLabel, sizeof(bdLabel), &flg);
3339: if (flg) DMPlexCreateBoundaryLabel_Private(dm, bdLabel);
3340: /* Point Location */
3341: PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL);
3342: /* Partitioning and distribution */
3343: PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL);
3344: /* Generation and remeshing */
3345: PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL);
3346: /* Projection behavior */
3347: PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL,0);
3348: PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);
3349: /* Checking structure */
3350: {
3351: PetscBool flg = PETSC_FALSE, flg2 = PETSC_FALSE, all = PETSC_FALSE;
3353: PetscOptionsBool("-dm_plex_check_all", "Perform all checks", NULL, PETSC_FALSE, &all, &flg2);
3354: PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2);
3355: if (all || (flg && flg2)) DMPlexCheckSymmetry(dm);
3356: 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);
3357: if (all || (flg && flg2)) DMPlexCheckSkeleton(dm, 0);
3358: 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);
3359: if (all || (flg && flg2)) DMPlexCheckFaces(dm, 0);
3360: PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2);
3361: if (all || (flg && flg2)) DMPlexCheckGeometry(dm);
3362: PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2);
3363: if (all || (flg && flg2)) DMPlexCheckPointSF(dm);
3364: PetscOptionsBool("-dm_plex_check_interface_cones", "Check points on inter-partition interfaces have conforming order of cone points", "DMPlexCheckInterfaceCones", PETSC_FALSE, &flg, &flg2);
3365: if (all || (flg && flg2)) DMPlexCheckInterfaceCones(dm);
3366: PetscOptionsBool("-dm_plex_check_cell_shape", "Check cell shape", "DMPlexCheckCellShape", PETSC_FALSE, &flg, &flg2);
3367: if (flg && flg2) DMPlexCheckCellShape(dm, PETSC_TRUE, PETSC_DETERMINE);
3368: }
3369: {
3370: PetscReal scale = 1.0;
3372: PetscOptionsReal("-dm_plex_scale", "Scale factor for mesh coordinates", "DMPlexScale", scale, &scale, &flg);
3373: if (flg) {
3374: Vec coordinates, coordinatesLocal;
3376: DMGetCoordinates(dm, &coordinates);
3377: DMGetCoordinatesLocal(dm, &coordinatesLocal);
3378: VecScale(coordinates, scale);
3379: VecScale(coordinatesLocal, scale);
3380: }
3381: }
3382: PetscPartitionerSetFromOptions(mesh->partitioner);
3383: return 0;
3384: }
3386: static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm)
3387: {
3388: PetscFunctionList ordlist;
3389: char oname[256];
3390: PetscReal volume = -1.0;
3391: PetscInt prerefine = 0, refine = 0, r, coarsen = 0, overlap = 0, extLayers = 0, dim;
3392: PetscBool uniformOrig, created = PETSC_FALSE, uniform = PETSC_TRUE, distribute, interpolate = PETSC_TRUE, coordSpace = PETSC_TRUE, remap = PETSC_TRUE, ghostCells = PETSC_FALSE, isHierarchy, ignoreModel = PETSC_FALSE, flg;
3395: PetscOptionsHead(PetscOptionsObject,"DMPlex Options");
3396: /* Handle automatic creation */
3397: DMGetDimension(dm, &dim);
3398: if (dim < 0) {DMPlexCreateFromOptions_Internal(PetscOptionsObject, &coordSpace, dm);created = PETSC_TRUE;}
3399: /* Handle interpolation before distribution */
3400: PetscOptionsBool("-dm_plex_interpolate_pre", "Flag to interpolate mesh before distribution", "", interpolate, &interpolate, &flg);
3401: if (flg) {
3402: DMPlexInterpolatedFlag interpolated;
3404: DMPlexIsInterpolated(dm, &interpolated);
3405: if (interpolated == DMPLEX_INTERPOLATED_FULL && !interpolate) {
3406: DM udm;
3408: DMPlexUninterpolate(dm, &udm);
3409: DMPlexReplace_Static(dm, &udm);
3410: } else if (interpolated != DMPLEX_INTERPOLATED_FULL && interpolate) {
3411: DM idm;
3413: DMPlexInterpolate(dm, &idm);
3414: DMPlexReplace_Static(dm, &idm);
3415: }
3416: }
3417: /* Handle DMPlex refinement before distribution */
3418: PetscOptionsBool("-dm_refine_ignore_model", "Flag to ignore the geometry model when refining", "DMCreate", ignoreModel, &ignoreModel, &flg);
3419: if (flg) {((DM_Plex *) dm->data)->ignoreModel = ignoreModel;}
3420: DMPlexGetRefinementUniform(dm, &uniformOrig);
3421: PetscOptionsBoundedInt("-dm_refine_pre", "The number of refinements before distribution", "DMCreate", prerefine, &prerefine, NULL,0);
3422: PetscOptionsBool("-dm_refine_remap_pre", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL);
3423: PetscOptionsBool("-dm_refine_uniform_pre", "Flag for uniform refinement before distribution", "DMCreate", uniform, &uniform, &flg);
3424: if (flg) DMPlexSetRefinementUniform(dm, uniform);
3425: PetscOptionsReal("-dm_refine_volume_limit_pre", "The maximum cell volume after refinement before distribution", "DMCreate", volume, &volume, &flg);
3426: if (flg) {
3427: DMPlexSetRefinementUniform(dm, PETSC_FALSE);
3428: DMPlexSetRefinementLimit(dm, volume);
3429: prerefine = PetscMax(prerefine, 1);
3430: }
3431: for (r = 0; r < prerefine; ++r) {
3432: DM rdm;
3433: PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc;
3435: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
3436: DMRefine(dm, PetscObjectComm((PetscObject) dm), &rdm);
3437: DMPlexReplace_Static(dm, &rdm);
3438: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
3439: if (coordFunc && remap) {
3440: DMPlexRemapGeometry(dm, 0.0, coordFunc);
3441: ((DM_Plex*) dm->data)->coordFunc = coordFunc;
3442: }
3443: }
3444: DMPlexSetRefinementUniform(dm, uniformOrig);
3445: /* Handle DMPlex extrusion before distribution */
3446: PetscOptionsBoundedInt("-dm_extrude", "The number of layers to extrude", "", extLayers, &extLayers, NULL, 0);
3447: if (extLayers) {
3448: DM edm;
3450: DMExtrude(dm, extLayers, &edm);
3451: DMPlexReplace_Static(dm, &edm);
3452: ((DM_Plex *) dm->data)->coordFunc = NULL;
3453: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
3454: extLayers = 0;
3455: }
3456: /* Handle DMPlex reordering before distribution */
3457: MatGetOrderingList(&ordlist);
3458: PetscOptionsFList("-dm_plex_reorder", "Set mesh reordering type", "DMPlexGetOrdering", ordlist, MATORDERINGNATURAL, oname, sizeof(oname), &flg);
3459: if (flg) {
3460: DM pdm;
3461: IS perm;
3463: DMPlexGetOrdering(dm, oname, NULL, &perm);
3464: DMPlexPermute(dm, perm, &pdm);
3465: ISDestroy(&perm);
3466: DMPlexReplace_Static(dm, &pdm);
3467: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
3468: }
3469: /* Handle DMPlex distribution */
3470: DMPlexDistributeGetDefault(dm, &distribute);
3471: PetscOptionsBool("-dm_distribute", "Flag to redistribute a mesh among processes", "DMCreate", distribute, &distribute, NULL);
3472: PetscOptionsBoundedInt("-dm_distribute_overlap", "The size of the overlap halo", "DMCreate", overlap, &overlap, NULL, 0);
3473: if (distribute) {
3474: DM pdm = NULL;
3475: PetscPartitioner part;
3477: DMPlexGetPartitioner(dm, &part);
3478: PetscPartitionerSetFromOptions(part);
3479: DMPlexDistribute(dm, overlap, NULL, &pdm);
3480: if (pdm) {
3481: DMPlexReplace_Static(dm, &pdm);
3482: }
3483: }
3484: /* Create coordinate space */
3485: if (created) {
3486: DM_Plex *mesh = (DM_Plex *) dm->data;
3487: PetscInt degree = 1;
3488: PetscBool periodic, flg;
3490: PetscOptionsBool("-dm_coord_space", "Use an FEM space for coordinates", "", coordSpace, &coordSpace, &flg);
3491: PetscOptionsInt("-dm_coord_petscspace_degree", "FEM degree for coordinate space", "", degree, °ree, NULL);
3492: if (coordSpace) DMPlexCreateCoordinateSpace(dm, degree, mesh->coordFunc);
3493: if (flg && !coordSpace) {
3494: DM cdm;
3495: PetscDS cds;
3496: PetscObject obj;
3497: PetscClassId id;
3499: DMGetCoordinateDM(dm, &cdm);
3500: DMGetDS(cdm, &cds);
3501: PetscDSGetDiscretization(cds, 0, &obj);
3502: PetscObjectGetClassId(obj, &id);
3503: if (id == PETSCFE_CLASSID) {
3504: PetscContainer dummy;
3506: PetscContainerCreate(PETSC_COMM_SELF, &dummy);
3507: PetscObjectSetName((PetscObject) dummy, "coordinates");
3508: DMSetField(cdm, 0, NULL, (PetscObject) dummy);
3509: PetscContainerDestroy(&dummy);
3510: DMClearDS(cdm);
3511: }
3512: mesh->coordFunc = NULL;
3513: }
3514: DMLocalizeCoordinates(dm);
3515: DMGetPeriodicity(dm, &periodic, NULL, NULL, NULL);
3516: if (periodic) DMSetPeriodicity(dm, PETSC_TRUE, NULL, NULL, NULL);
3517: }
3518: /* Handle DMPlex refinement */
3519: remap = PETSC_TRUE;
3520: PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL,0);
3521: PetscOptionsBool("-dm_refine_remap", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL);
3522: PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy,0);
3523: if (refine) DMPlexSetRefinementUniform(dm, PETSC_TRUE);
3524: if (refine && isHierarchy) {
3525: DM *dms, coarseDM;
3527: DMGetCoarseDM(dm, &coarseDM);
3528: PetscObjectReference((PetscObject)coarseDM);
3529: PetscMalloc1(refine,&dms);
3530: DMRefineHierarchy(dm, refine, dms);
3531: /* Total hack since we do not pass in a pointer */
3532: DMPlexSwap_Static(dm, dms[refine-1]);
3533: if (refine == 1) {
3534: DMSetCoarseDM(dm, dms[0]);
3535: DMPlexSetRegularRefinement(dm, PETSC_TRUE);
3536: } else {
3537: DMSetCoarseDM(dm, dms[refine-2]);
3538: DMPlexSetRegularRefinement(dm, PETSC_TRUE);
3539: DMSetCoarseDM(dms[0], dms[refine-1]);
3540: DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);
3541: }
3542: DMSetCoarseDM(dms[refine-1], coarseDM);
3543: PetscObjectDereference((PetscObject)coarseDM);
3544: /* Free DMs */
3545: for (r = 0; r < refine; ++r) {
3546: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);
3547: DMDestroy(&dms[r]);
3548: }
3549: PetscFree(dms);
3550: } else {
3551: for (r = 0; r < refine; ++r) {
3552: DM rdm;
3553: PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc;
3555: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
3556: DMRefine(dm, PetscObjectComm((PetscObject) dm), &rdm);
3557: /* Total hack since we do not pass in a pointer */
3558: DMPlexReplace_Static(dm, &rdm);
3559: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
3560: if (coordFunc && remap) {
3561: DMPlexRemapGeometry(dm, 0.0, coordFunc);
3562: ((DM_Plex*) dm->data)->coordFunc = coordFunc;
3563: }
3564: }
3565: }
3566: /* Handle DMPlex coarsening */
3567: PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL,0);
3568: PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy,0);
3569: if (coarsen && isHierarchy) {
3570: DM *dms;
3572: PetscMalloc1(coarsen, &dms);
3573: DMCoarsenHierarchy(dm, coarsen, dms);
3574: /* Free DMs */
3575: for (r = 0; r < coarsen; ++r) {
3576: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);
3577: DMDestroy(&dms[r]);
3578: }
3579: PetscFree(dms);
3580: } else {
3581: for (r = 0; r < coarsen; ++r) {
3582: DM cdm;
3583: PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc;
3585: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
3586: DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &cdm);
3587: /* Total hack since we do not pass in a pointer */
3588: DMPlexReplace_Static(dm, &cdm);
3589: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
3590: if (coordFunc) {
3591: DMPlexRemapGeometry(dm, 0.0, coordFunc);
3592: ((DM_Plex*) dm->data)->coordFunc = coordFunc;
3593: }
3594: }
3595: }
3596: /* Handle ghost cells */
3597: PetscOptionsBool("-dm_plex_create_fv_ghost_cells", "Flag to create finite volume ghost cells on the boundary", "DMCreate", ghostCells, &ghostCells, NULL);
3598: if (ghostCells) {
3599: DM gdm;
3600: char lname[PETSC_MAX_PATH_LEN];
3602: lname[0] = '\0';
3603: PetscOptionsString("-dm_plex_fv_ghost_cells_label", "Label name for ghost cells boundary", "DMCreate", lname, lname, sizeof(lname), &flg);
3604: DMPlexConstructGhostCells(dm, flg ? lname : NULL, NULL, &gdm);
3605: DMPlexReplace_Static(dm, &gdm);
3606: }
3607: /* Handle 1D order */
3608: {
3609: DM cdm, rdm;
3610: PetscDS cds;
3611: PetscObject obj;
3612: PetscClassId id = PETSC_OBJECT_CLASSID;
3613: IS perm;
3614: PetscInt dim, Nf;
3615: PetscBool distributed;
3617: DMGetDimension(dm, &dim);
3618: DMPlexIsDistributed(dm, &distributed);
3619: DMGetCoordinateDM(dm, &cdm);
3620: DMGetDS(cdm, &cds);
3621: PetscDSGetNumFields(cds, &Nf);
3622: if (Nf) {
3623: PetscDSGetDiscretization(cds, 0, &obj);
3624: PetscObjectGetClassId(obj, &id);
3625: }
3626: if (dim == 1 && !distributed && id != PETSCFE_CLASSID) {
3627: DMPlexGetOrdering1D(dm, &perm);
3628: DMPlexPermute(dm, perm, &rdm);
3629: DMPlexReplace_Static(dm, &rdm);
3630: ISDestroy(&perm);
3631: }
3632: }
3633: /* Handle */
3634: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
3635: PetscOptionsTail();
3636: return 0;
3637: }
3639: static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec)
3640: {
3641: DMCreateGlobalVector_Section_Private(dm,vec);
3642: /* VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM); */
3643: VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);
3644: VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);
3645: VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);
3646: VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);
3647: return 0;
3648: }
3650: static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec)
3651: {
3652: DMCreateLocalVector_Section_Private(dm,vec);
3653: VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);
3654: VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);
3655: return 0;
3656: }
3658: static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd)
3659: {
3660: PetscInt depth, d;
3662: DMPlexGetDepth(dm, &depth);
3663: if (depth == 1) {
3664: DMGetDimension(dm, &d);
3665: if (dim == 0) DMPlexGetDepthStratum(dm, dim, pStart, pEnd);
3666: else if (dim == d) DMPlexGetDepthStratum(dm, 1, pStart, pEnd);
3667: else {*pStart = 0; *pEnd = 0;}
3668: } else {
3669: DMPlexGetDepthStratum(dm, dim, pStart, pEnd);
3670: }
3671: return 0;
3672: }
3674: static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[])
3675: {
3676: PetscSF sf;
3677: PetscInt niranks, njranks, n;
3678: const PetscMPIInt *iranks, *jranks;
3679: DM_Plex *data = (DM_Plex*) dm->data;
3681: DMGetPointSF(dm, &sf);
3682: if (!data->neighbors) {
3683: PetscSFSetUp(sf);
3684: PetscSFGetRootRanks(sf, &njranks, &jranks, NULL, NULL, NULL);
3685: PetscSFGetLeafRanks(sf, &niranks, &iranks, NULL, NULL);
3686: PetscMalloc1(njranks + niranks + 1, &data->neighbors);
3687: PetscArraycpy(data->neighbors + 1, jranks, njranks);
3688: PetscArraycpy(data->neighbors + njranks + 1, iranks, niranks);
3689: n = njranks + niranks;
3690: PetscSortRemoveDupsMPIInt(&n, data->neighbors + 1);
3691: /* The following cast should never fail: can't have more neighbors than PETSC_MPI_INT_MAX */
3692: PetscMPIIntCast(n, data->neighbors);
3693: }
3694: if (nranks) *nranks = data->neighbors[0];
3695: if (ranks) {
3696: if (data->neighbors[0]) *ranks = data->neighbors + 1;
3697: else *ranks = NULL;
3698: }
3699: return 0;
3700: }
3702: PETSC_INTERN PetscErrorCode DMInterpolateSolution_Plex(DM, DM, Mat, Vec, Vec);
3704: static PetscErrorCode DMInitialize_Plex(DM dm)
3705: {
3706: dm->ops->view = DMView_Plex;
3707: dm->ops->load = DMLoad_Plex;
3708: dm->ops->setfromoptions = DMSetFromOptions_Plex;
3709: dm->ops->clone = DMClone_Plex;
3710: dm->ops->setup = DMSetUp_Plex;
3711: dm->ops->createlocalsection = DMCreateLocalSection_Plex;
3712: dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex;
3713: dm->ops->createglobalvector = DMCreateGlobalVector_Plex;
3714: dm->ops->createlocalvector = DMCreateLocalVector_Plex;
3715: dm->ops->getlocaltoglobalmapping = NULL;
3716: dm->ops->createfieldis = NULL;
3717: dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex;
3718: dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex;
3719: dm->ops->getcoloring = NULL;
3720: dm->ops->creatematrix = DMCreateMatrix_Plex;
3721: dm->ops->createinterpolation = DMCreateInterpolation_Plex;
3722: dm->ops->createmassmatrix = DMCreateMassMatrix_Plex;
3723: dm->ops->createmassmatrixlumped = DMCreateMassMatrixLumped_Plex;
3724: dm->ops->createinjection = DMCreateInjection_Plex;
3725: dm->ops->refine = DMRefine_Plex;
3726: dm->ops->coarsen = DMCoarsen_Plex;
3727: dm->ops->refinehierarchy = DMRefineHierarchy_Plex;
3728: dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex;
3729: dm->ops->extrude = DMExtrude_Plex;
3730: dm->ops->globaltolocalbegin = NULL;
3731: dm->ops->globaltolocalend = NULL;
3732: dm->ops->localtoglobalbegin = NULL;
3733: dm->ops->localtoglobalend = NULL;
3734: dm->ops->destroy = DMDestroy_Plex;
3735: dm->ops->createsubdm = DMCreateSubDM_Plex;
3736: dm->ops->createsuperdm = DMCreateSuperDM_Plex;
3737: dm->ops->getdimpoints = DMGetDimPoints_Plex;
3738: dm->ops->locatepoints = DMLocatePoints_Plex;
3739: dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex;
3740: dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex;
3741: dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex;
3742: dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex;
3743: dm->ops->projectbdfieldlabellocal = DMProjectBdFieldLabelLocal_Plex;
3744: dm->ops->computel2diff = DMComputeL2Diff_Plex;
3745: dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex;
3746: dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex;
3747: dm->ops->getneighbors = DMGetNeighbors_Plex;
3748: PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);
3749: PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertTimeDerviativeBoundaryValues_C",DMPlexInsertTimeDerivativeBoundaryValues_Plex);
3750: PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);
3751: PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C",DMCreateNeumannOverlap_Plex);
3752: PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex);
3753: PetscObjectComposeFunction((PetscObject)dm,"DMPlexDistributeGetDefault_C",DMPlexDistributeGetDefault_Plex);
3754: PetscObjectComposeFunction((PetscObject)dm,"DMPlexDistributeSetDefault_C",DMPlexDistributeSetDefault_Plex);
3755: PetscObjectComposeFunction((PetscObject)dm,"DMInterpolateSolution_C",DMInterpolateSolution_Plex);
3756: return 0;
3757: }
3759: PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm)
3760: {
3761: DM_Plex *mesh = (DM_Plex *) dm->data;
3763: mesh->refct++;
3764: (*newdm)->data = mesh;
3765: PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);
3766: DMInitialize_Plex(*newdm);
3767: return 0;
3768: }
3770: /*MC
3771: DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram.
3772: In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is
3773: specified by a PetscSection object. Ownership in the global representation is determined by
3774: ownership of the underlying DMPlex points. This is specified by another PetscSection object.
3776: Options Database Keys:
3777: + -dm_refine_pre - Refine mesh before distribution
3778: + -dm_refine_uniform_pre - Choose uniform or generator-based refinement
3779: + -dm_refine_volume_limit_pre - Cell volume limit after pre-refinement using generator
3780: . -dm_distribute - Distribute mesh across processes
3781: . -dm_distribute_overlap - Number of cells to overlap for distribution
3782: . -dm_refine - Refine mesh after distribution
3783: . -dm_plex_hash_location - Use grid hashing for point location
3784: . -dm_plex_hash_box_faces <n,m,p> - The number of divisions in each direction of the grid hash
3785: . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes
3786: . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing
3787: . -dm_plex_max_projection_height - Maxmimum mesh point height used to project locally
3788: . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement
3789: . -dm_plex_check_all - Perform all shecks below
3790: . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric
3791: . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices
3792: . -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
3793: . -dm_plex_check_geometry - Check that cells have positive volume
3794: . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ
3795: . -dm_plex_view_scale <num> - Scale the TikZ
3796: - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices
3798: Level: intermediate
3800: .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType()
3801: M*/
3803: PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm)
3804: {
3805: DM_Plex *mesh;
3806: PetscInt unit;
3809: PetscNewLog(dm,&mesh);
3810: dm->data = mesh;
3812: mesh->refct = 1;
3813: PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);
3814: mesh->cones = NULL;
3815: mesh->coneOrientations = NULL;
3816: PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);
3817: mesh->supports = NULL;
3818: mesh->refinementUniform = PETSC_TRUE;
3819: mesh->refinementLimit = -1.0;
3820: mesh->distDefault = PETSC_TRUE;
3821: mesh->interpolated = DMPLEX_INTERPOLATED_INVALID;
3822: mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID;
3824: mesh->facesTmp = NULL;
3826: mesh->tetgenOpts = NULL;
3827: mesh->triangleOpts = NULL;
3828: PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);
3829: mesh->remeshBd = PETSC_FALSE;
3831: mesh->subpointMap = NULL;
3833: for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0;
3835: mesh->regularRefinement = PETSC_FALSE;
3836: mesh->depthState = -1;
3837: mesh->celltypeState = -1;
3838: mesh->globalVertexNumbers = NULL;
3839: mesh->globalCellNumbers = NULL;
3840: mesh->anchorSection = NULL;
3841: mesh->anchorIS = NULL;
3842: mesh->createanchors = NULL;
3843: mesh->computeanchormatrix = NULL;
3844: mesh->parentSection = NULL;
3845: mesh->parents = NULL;
3846: mesh->childIDs = NULL;
3847: mesh->childSection = NULL;
3848: mesh->children = NULL;
3849: mesh->referenceTree = NULL;
3850: mesh->getchildsymmetry = NULL;
3851: mesh->vtkCellHeight = 0;
3852: mesh->useAnchors = PETSC_FALSE;
3854: mesh->maxProjectionHeight = 0;
3856: mesh->neighbors = NULL;
3858: mesh->printSetValues = PETSC_FALSE;
3859: mesh->printFEM = 0;
3860: mesh->printTol = 1.0e-10;
3862: DMInitialize_Plex(dm);
3863: return 0;
3864: }
3866: /*@
3867: DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram.
3869: Collective
3871: Input Parameter:
3872: . comm - The communicator for the DMPlex object
3874: Output Parameter:
3875: . mesh - The DMPlex object
3877: Level: beginner
3879: @*/
3880: PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh)
3881: {
3883: DMCreate(comm, mesh);
3884: DMSetType(*mesh, DMPLEX);
3885: return 0;
3886: }
3888: /*@C
3889: DMPlexBuildFromCellListParallel - Build distributed DMPLEX topology from a list of vertices for each cell (common mesh generator output)
3891: Input Parameters:
3892: + dm - The DM
3893: . numCells - The number of cells owned by this process
3894: . numVertices - The number of vertices to be owned by this process, or PETSC_DECIDE
3895: . NVertices - The global number of vertices, or PETSC_DETERMINE
3896: . numCorners - The number of vertices for each cell
3897: - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell
3899: Output Parameters:
3900: + vertexSF - (Optional) SF describing complete vertex ownership
3901: - verticesAdjSaved - (Optional) vertex adjacency array
3903: Notes:
3904: Two triangles sharing a face
3905: $
3906: $ 2
3907: $ / | \
3908: $ / | \
3909: $ / | \
3910: $ 0 0 | 1 3
3911: $ \ | /
3912: $ \ | /
3913: $ \ | /
3914: $ 1
3915: would have input
3916: $ numCells = 2, numVertices = 4
3917: $ cells = [0 1 2 1 3 2]
3918: $
3919: which would result in the DMPlex
3920: $
3921: $ 4
3922: $ / | \
3923: $ / | \
3924: $ / | \
3925: $ 2 0 | 1 5
3926: $ \ | /
3927: $ \ | /
3928: $ \ | /
3929: $ 3
3931: Vertices are implicitly numbered consecutively 0,...,NVertices.
3932: Each rank owns a chunk of numVertices consecutive vertices.
3933: If numVertices is PETSC_DECIDE, PETSc will distribute them as evenly as possible using PetscLayout.
3934: If NVertices is PETSC_DETERMINE and numVertices is PETSC_DECIDE, NVertices is computed by PETSc as the maximum vertex index in cells + 1.
3935: If only NVertices is PETSC_DETERMINE, it is computed as the sum of numVertices over all ranks.
3937: The cell distribution is arbitrary non-overlapping, independent of the vertex distribution.
3939: Not currently supported in Fortran.
3941: Level: advanced
3943: .seealso: DMPlexBuildFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildCoordinatesFromCellListParallel()
3944: @*/
3945: PetscErrorCode DMPlexBuildFromCellListParallel(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, const PetscInt cells[], PetscSF *vertexSF, PetscInt **verticesAdjSaved)
3946: {
3947: PetscSF sfPoint;
3948: PetscLayout layout;
3949: PetscInt numVerticesAdj, *verticesAdj, *cones, c, p;
3952: PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);
3953: /* Get/check global number of vertices */
3954: {
3955: PetscInt NVerticesInCells, i;
3956: const PetscInt len = numCells * numCorners;
3958: /* NVerticesInCells = max(cells) + 1 */
3959: NVerticesInCells = PETSC_MIN_INT;
3960: for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i];
3961: ++NVerticesInCells;
3962: MPI_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject) dm));
3964: if (numVertices == PETSC_DECIDE && NVertices == PETSC_DECIDE) NVertices = NVerticesInCells;
3966: }
3967: /* Count locally unique vertices */
3968: {
3969: PetscHSetI vhash;
3970: PetscInt off = 0;
3972: PetscHSetICreate(&vhash);
3973: for (c = 0; c < numCells; ++c) {
3974: for (p = 0; p < numCorners; ++p) {
3975: PetscHSetIAdd(vhash, cells[c*numCorners+p]);
3976: }
3977: }
3978: PetscHSetIGetSize(vhash, &numVerticesAdj);
3979: if (!verticesAdjSaved) PetscMalloc1(numVerticesAdj, &verticesAdj);
3980: else { verticesAdj = *verticesAdjSaved; }
3981: PetscHSetIGetElems(vhash, &off, verticesAdj);
3982: PetscHSetIDestroy(&vhash);
3984: }
3985: PetscSortInt(numVerticesAdj, verticesAdj);
3986: /* Create cones */
3987: DMPlexSetChart(dm, 0, numCells+numVerticesAdj);
3988: for (c = 0; c < numCells; ++c) DMPlexSetConeSize(dm, c, numCorners);
3989: DMSetUp(dm);
3990: DMPlexGetCones(dm,&cones);
3991: for (c = 0; c < numCells; ++c) {
3992: for (p = 0; p < numCorners; ++p) {
3993: const PetscInt gv = cells[c*numCorners+p];
3994: PetscInt lv;
3996: /* Positions within verticesAdj form 0-based local vertex numbering;
3997: we need to shift it by numCells to get correct DAG points (cells go first) */
3998: PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);
4000: cones[c*numCorners+p] = lv+numCells;
4001: }
4002: }
4003: /* Build point sf */
4004: PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &layout);
4005: PetscLayoutSetSize(layout, NVertices);
4006: PetscLayoutSetLocalSize(layout, numVertices);
4007: PetscLayoutSetBlockSize(layout, 1);
4008: PetscSFCreateByMatchingIndices(layout, numVerticesAdj, verticesAdj, NULL, numCells, numVerticesAdj, verticesAdj, NULL, numCells, vertexSF, &sfPoint);
4009: PetscLayoutDestroy(&layout);
4010: if (!verticesAdjSaved) PetscFree(verticesAdj);
4011: PetscObjectSetName((PetscObject) sfPoint, "point SF");
4012: if (dm->sf) {
4013: const char *prefix;
4015: PetscObjectGetOptionsPrefix((PetscObject)dm->sf, &prefix);
4016: PetscObjectSetOptionsPrefix((PetscObject)sfPoint, prefix);
4017: }
4018: DMSetPointSF(dm, sfPoint);
4019: PetscSFDestroy(&sfPoint);
4020: if (vertexSF) PetscObjectSetName((PetscObject)(*vertexSF), "Vertex Ownership SF");
4021: /* Fill in the rest of the topology structure */
4022: DMPlexSymmetrize(dm);
4023: DMPlexStratify(dm);
4024: PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);
4025: return 0;
4026: }
4028: /*@C
4029: DMPlexBuildCoordinatesFromCellListParallel - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output)
4031: Input Parameters:
4032: + dm - The DM
4033: . spaceDim - The spatial dimension used for coordinates
4034: . sfVert - SF describing complete vertex ownership
4035: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
4037: Level: advanced
4039: Notes:
4040: Not currently supported in Fortran.
4042: .seealso: DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellListParallel()
4043: @*/
4044: PetscErrorCode DMPlexBuildCoordinatesFromCellListParallel(DM dm, PetscInt spaceDim, PetscSF sfVert, const PetscReal vertexCoords[])
4045: {
4046: PetscSection coordSection;
4047: Vec coordinates;
4048: PetscScalar *coords;
4049: PetscInt numVertices, numVerticesAdj, coordSize, v, vStart, vEnd;
4051: PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);
4052: DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
4054: DMSetCoordinateDim(dm, spaceDim);
4055: PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);
4057: DMGetCoordinateSection(dm, &coordSection);
4058: PetscSectionSetNumFields(coordSection, 1);
4059: PetscSectionSetFieldComponents(coordSection, 0, spaceDim);
4060: PetscSectionSetChart(coordSection, vStart, vEnd);
4061: for (v = vStart; v < vEnd; ++v) {
4062: PetscSectionSetDof(coordSection, v, spaceDim);
4063: PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);
4064: }
4065: PetscSectionSetUp(coordSection);
4066: PetscSectionGetStorageSize(coordSection, &coordSize);
4067: VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);
4068: VecSetBlockSize(coordinates, spaceDim);
4069: PetscObjectSetName((PetscObject) coordinates, "coordinates");
4070: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
4071: VecSetType(coordinates,VECSTANDARD);
4072: VecGetArray(coordinates, &coords);
4073: {
4074: MPI_Datatype coordtype;
4076: /* Need a temp buffer for coords if we have complex/single */
4077: MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);
4078: MPI_Type_commit(&coordtype);
4079: #if defined(PETSC_USE_COMPLEX)
4080: {
4081: PetscScalar *svertexCoords;
4082: PetscInt i;
4083: PetscMalloc1(numVertices*spaceDim,&svertexCoords);
4084: for (i=0; i<numVertices*spaceDim; i++) svertexCoords[i] = vertexCoords[i];
4085: PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords,MPI_REPLACE);
4086: PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords,MPI_REPLACE);
4087: PetscFree(svertexCoords);
4088: }
4089: #else
4090: PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords,MPI_REPLACE);
4091: PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords,MPI_REPLACE);
4092: #endif
4093: MPI_Type_free(&coordtype);
4094: }
4095: VecRestoreArray(coordinates, &coords);
4096: DMSetCoordinatesLocal(dm, coordinates);
4097: VecDestroy(&coordinates);
4098: PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);
4099: return 0;
4100: }
4102: /*@
4103: DMPlexCreateFromCellListParallelPetsc - Create distributed DMPLEX from a list of vertices for each cell (common mesh generator output)
4105: Input Parameters:
4106: + comm - The communicator
4107: . dim - The topological dimension of the mesh
4108: . numCells - The number of cells owned by this process
4109: . numVertices - The number of vertices owned by this process, or PETSC_DECIDE
4110: . NVertices - The global number of vertices, or PETSC_DECIDE
4111: . numCorners - The number of vertices for each cell
4112: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
4113: . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell
4114: . spaceDim - The spatial dimension used for coordinates
4115: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
4117: Output Parameters:
4118: + dm - The DM
4119: . vertexSF - (Optional) SF describing complete vertex ownership
4120: - verticesAdjSaved - (Optional) vertex adjacency array
4122: Notes:
4123: This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(),
4124: DMPlexBuildFromCellListParallel(), DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellListParallel()
4126: See DMPlexBuildFromCellListParallel() for an example and details about the topology-related parameters.
4127: See DMPlexBuildCoordinatesFromCellListParallel() for details about the geometry-related parameters.
4129: Level: intermediate
4131: .seealso: DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromDAG(), DMPlexCreate()
4132: @*/
4133: 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)
4134: {
4135: PetscSF sfVert;
4137: DMCreate(comm, dm);
4138: DMSetType(*dm, DMPLEX);
4141: DMSetDimension(*dm, dim);
4142: DMPlexBuildFromCellListParallel(*dm, numCells, numVertices, NVertices, numCorners, cells, &sfVert, verticesAdj);
4143: if (interpolate) {
4144: DM idm;
4146: DMPlexInterpolate(*dm, &idm);
4147: DMDestroy(dm);
4148: *dm = idm;
4149: }
4150: DMPlexBuildCoordinatesFromCellListParallel(*dm, spaceDim, sfVert, vertexCoords);
4151: if (vertexSF) *vertexSF = sfVert;
4152: else PetscSFDestroy(&sfVert);
4153: return 0;
4154: }
4156: /*@C
4157: DMPlexBuildFromCellList - Build DMPLEX topology from a list of vertices for each cell (common mesh generator output)
4159: Input Parameters:
4160: + dm - The DM
4161: . numCells - The number of cells owned by this process
4162: . numVertices - The number of vertices owned by this process, or PETSC_DETERMINE
4163: . numCorners - The number of vertices for each cell
4164: - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell
4166: Level: advanced
4168: Notes:
4169: Two triangles sharing a face
4170: $
4171: $ 2
4172: $ / | \
4173: $ / | \
4174: $ / | \
4175: $ 0 0 | 1 3
4176: $ \ | /
4177: $ \ | /
4178: $ \ | /
4179: $ 1
4180: would have input
4181: $ numCells = 2, numVertices = 4
4182: $ cells = [0 1 2 1 3 2]
4183: $
4184: which would result in the DMPlex
4185: $
4186: $ 4
4187: $ / | \
4188: $ / | \
4189: $ / | \
4190: $ 2 0 | 1 5
4191: $ \ | /
4192: $ \ | /
4193: $ \ | /
4194: $ 3
4196: If numVertices is PETSC_DETERMINE, it is computed by PETSc as the maximum vertex index in cells + 1.
4198: Not currently supported in Fortran.
4200: .seealso: DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListPetsc()
4201: @*/
4202: PetscErrorCode DMPlexBuildFromCellList(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[])
4203: {
4204: PetscInt *cones, c, p, dim;
4206: PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);
4207: DMGetDimension(dm, &dim);
4208: /* Get/check global number of vertices */
4209: {
4210: PetscInt NVerticesInCells, i;
4211: const PetscInt len = numCells * numCorners;
4213: /* NVerticesInCells = max(cells) + 1 */
4214: NVerticesInCells = PETSC_MIN_INT;
4215: for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i];
4216: ++NVerticesInCells;
4218: if (numVertices == PETSC_DECIDE) numVertices = NVerticesInCells;
4220: }
4221: DMPlexSetChart(dm, 0, numCells+numVertices);
4222: for (c = 0; c < numCells; ++c) {
4223: DMPlexSetConeSize(dm, c, numCorners);
4224: }
4225: DMSetUp(dm);
4226: DMPlexGetCones(dm,&cones);
4227: for (c = 0; c < numCells; ++c) {
4228: for (p = 0; p < numCorners; ++p) {
4229: cones[c*numCorners+p] = cells[c*numCorners+p]+numCells;
4230: }
4231: }
4232: DMPlexSymmetrize(dm);
4233: DMPlexStratify(dm);
4234: PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);
4235: return 0;
4236: }
4238: /*@C
4239: DMPlexBuildCoordinatesFromCellList - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output)
4241: Input Parameters:
4242: + dm - The DM
4243: . spaceDim - The spatial dimension used for coordinates
4244: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
4246: Level: advanced
4248: Notes:
4249: Not currently supported in Fortran.
4251: .seealso: DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellList()
4252: @*/
4253: PetscErrorCode DMPlexBuildCoordinatesFromCellList(DM dm, PetscInt spaceDim, const PetscReal vertexCoords[])
4254: {
4255: PetscSection coordSection;
4256: Vec coordinates;
4257: DM cdm;
4258: PetscScalar *coords;
4259: PetscInt v, vStart, vEnd, d;
4261: PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);
4262: DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
4264: DMSetCoordinateDim(dm, spaceDim);
4265: DMGetCoordinateSection(dm, &coordSection);
4266: PetscSectionSetNumFields(coordSection, 1);
4267: PetscSectionSetFieldComponents(coordSection, 0, spaceDim);
4268: PetscSectionSetChart(coordSection, vStart, vEnd);
4269: for (v = vStart; v < vEnd; ++v) {
4270: PetscSectionSetDof(coordSection, v, spaceDim);
4271: PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);
4272: }
4273: PetscSectionSetUp(coordSection);
4275: DMGetCoordinateDM(dm, &cdm);
4276: DMCreateLocalVector(cdm, &coordinates);
4277: VecSetBlockSize(coordinates, spaceDim);
4278: PetscObjectSetName((PetscObject) coordinates, "coordinates");
4279: VecGetArrayWrite(coordinates, &coords);
4280: for (v = 0; v < vEnd-vStart; ++v) {
4281: for (d = 0; d < spaceDim; ++d) {
4282: coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d];
4283: }
4284: }
4285: VecRestoreArrayWrite(coordinates, &coords);
4286: DMSetCoordinatesLocal(dm, coordinates);
4287: VecDestroy(&coordinates);
4288: PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);
4289: return 0;
4290: }
4292: /*@
4293: DMPlexCreateFromCellListPetsc - Create DMPLEX from a list of vertices for each cell (common mesh generator output), but only process 0 takes in the input
4295: Collective on comm
4297: Input Parameters:
4298: + comm - The communicator
4299: . dim - The topological dimension of the mesh
4300: . numCells - The number of cells, only on process 0
4301: . numVertices - The number of vertices owned by this process, or PETSC_DECIDE, only on process 0
4302: . numCorners - The number of vertices for each cell, only on process 0
4303: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
4304: . cells - An array of numCells*numCorners numbers, the vertices for each cell, only on process 0
4305: . spaceDim - The spatial dimension used for coordinates
4306: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex, only on process 0
4308: Output Parameter:
4309: . dm - The DM, which only has points on process 0
4311: Notes:
4312: This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), DMPlexBuildFromCellList(),
4313: DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellList()
4315: See DMPlexBuildFromCellList() for an example and details about the topology-related parameters.
4316: See DMPlexBuildCoordinatesFromCellList() for details about the geometry-related parameters.
4317: See DMPlexCreateFromCellListParallelPetsc() for parallel input
4319: Level: intermediate
4321: .seealso: DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellList(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate()
4322: @*/
4323: 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)
4324: {
4325: PetscMPIInt rank;
4328: MPI_Comm_rank(comm, &rank);
4329: DMCreate(comm, dm);
4330: DMSetType(*dm, DMPLEX);
4331: DMSetDimension(*dm, dim);
4332: if (!rank) DMPlexBuildFromCellList(*dm, numCells, numVertices, numCorners, cells);
4333: else DMPlexBuildFromCellList(*dm, 0, 0, 0, NULL);
4334: if (interpolate) {
4335: DM idm;
4337: DMPlexInterpolate(*dm, &idm);
4338: DMDestroy(dm);
4339: *dm = idm;
4340: }
4341: if (!rank) DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, vertexCoords);
4342: else DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, NULL);
4343: return 0;
4344: }
4346: /*@
4347: DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM
4349: Input Parameters:
4350: + dm - The empty DM object, usually from DMCreate() and DMSetDimension()
4351: . depth - The depth of the DAG
4352: . numPoints - Array of size depth + 1 containing the number of points at each depth
4353: . coneSize - The cone size of each point
4354: . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point
4355: . coneOrientations - The orientation of each cone point
4356: - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim()
4358: Output Parameter:
4359: . dm - The DM
4361: Note: Two triangles sharing a face would have input
4362: $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0]
4363: $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0]
4364: $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0]
4365: $
4366: which would result in the DMPlex
4367: $
4368: $ 4
4369: $ / | \
4370: $ / | \
4371: $ / | \
4372: $ 2 0 | 1 5
4373: $ \ | /
4374: $ \ | /
4375: $ \ | /
4376: $ 3
4377: $
4378: $ Notice that all points are numbered consecutively, unlike DMPlexCreateFromCellListPetsc()
4380: Level: advanced
4382: .seealso: DMPlexCreateFromCellListPetsc(), DMPlexCreate()
4383: @*/
4384: PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[])
4385: {
4386: Vec coordinates;
4387: PetscSection coordSection;
4388: PetscScalar *coords;
4389: PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off;
4391: DMGetDimension(dm, &dim);
4392: DMGetCoordinateDim(dm, &dimEmbed);
4394: for (d = 0; d <= depth; ++d) pEnd += numPoints[d];
4395: DMPlexSetChart(dm, pStart, pEnd);
4396: for (p = pStart; p < pEnd; ++p) {
4397: DMPlexSetConeSize(dm, p, coneSize[p-pStart]);
4398: if (firstVertex < 0 && !coneSize[p - pStart]) {
4399: firstVertex = p - pStart;
4400: }
4401: }
4403: DMSetUp(dm); /* Allocate space for cones */
4404: for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) {
4405: DMPlexSetCone(dm, p, &cones[off]);
4406: DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);
4407: }
4408: DMPlexSymmetrize(dm);
4409: DMPlexStratify(dm);
4410: /* Build coordinates */
4411: DMGetCoordinateSection(dm, &coordSection);
4412: PetscSectionSetNumFields(coordSection, 1);
4413: PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);
4414: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);
4415: for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) {
4416: PetscSectionSetDof(coordSection, v, dimEmbed);
4417: PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);
4418: }
4419: PetscSectionSetUp(coordSection);
4420: PetscSectionGetStorageSize(coordSection, &coordSize);
4421: VecCreate(PETSC_COMM_SELF, &coordinates);
4422: PetscObjectSetName((PetscObject) coordinates, "coordinates");
4423: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
4424: VecSetBlockSize(coordinates, dimEmbed);
4425: VecSetType(coordinates,VECSTANDARD);
4426: if (vertexCoords) {
4427: VecGetArray(coordinates, &coords);
4428: for (v = 0; v < numPoints[0]; ++v) {
4429: PetscInt off;
4431: PetscSectionGetOffset(coordSection, v+firstVertex, &off);
4432: for (d = 0; d < dimEmbed; ++d) {
4433: coords[off+d] = vertexCoords[v*dimEmbed+d];
4434: }
4435: }
4436: }
4437: VecRestoreArray(coordinates, &coords);
4438: DMSetCoordinatesLocal(dm, coordinates);
4439: VecDestroy(&coordinates);
4440: return 0;
4441: }
4443: /*@C
4444: DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file.
4446: + comm - The MPI communicator
4447: . filename - Name of the .dat file
4448: - interpolate - Create faces and edges in the mesh
4450: Output Parameter:
4451: . dm - The DM object representing the mesh
4453: Note: The format is the simplest possible:
4454: $ Ne
4455: $ v0 v1 ... vk
4456: $ Nv
4457: $ x y z marker
4459: Level: beginner
4461: .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate()
4462: @*/
4463: PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
4464: {
4465: DMLabel marker;
4466: PetscViewer viewer;
4467: Vec coordinates;
4468: PetscSection coordSection;
4469: PetscScalar *coords;
4470: char line[PETSC_MAX_PATH_LEN];
4471: PetscInt dim = 3, cdim = 3, coordSize, v, c, d;
4472: PetscMPIInt rank;
4473: int snum, Nv, Nc, Ncn, Nl;
4475: MPI_Comm_rank(comm, &rank);
4476: PetscViewerCreate(comm, &viewer);
4477: PetscViewerSetType(viewer, PETSCVIEWERASCII);
4478: PetscViewerFileSetMode(viewer, FILE_MODE_READ);
4479: PetscViewerFileSetName(viewer, filename);
4480: if (rank == 0) {
4481: PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);
4482: snum = sscanf(line, "%d %d %d %d", &Nc, &Nv, &Ncn, &Nl);
4484: } else {
4485: Nc = Nv = Ncn = Nl = 0;
4486: }
4487: DMCreate(comm, dm);
4488: DMSetType(*dm, DMPLEX);
4489: DMPlexSetChart(*dm, 0, Nc+Nv);
4490: DMSetDimension(*dm, dim);
4491: DMSetCoordinateDim(*dm, cdim);
4492: /* Read topology */
4493: if (rank == 0) {
4494: char format[PETSC_MAX_PATH_LEN];
4495: PetscInt cone[8];
4496: int vbuf[8], v;
4498: for (c = 0; c < Ncn; ++c) {format[c*3+0] = '%'; format[c*3+1] = 'd'; format[c*3+2] = ' ';}
4499: format[Ncn*3-1] = '\0';
4500: for (c = 0; c < Nc; ++c) DMPlexSetConeSize(*dm, c, Ncn);
4501: DMSetUp(*dm);
4502: for (c = 0; c < Nc; ++c) {
4503: PetscViewerRead(viewer, line, Ncn, NULL, PETSC_STRING);
4504: switch (Ncn) {
4505: case 2: snum = sscanf(line, format, &vbuf[0], &vbuf[1]);break;
4506: case 3: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2]);break;
4507: case 4: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3]);break;
4508: case 6: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5]);break;
4509: case 8: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5], &vbuf[6], &vbuf[7]);break;
4510: default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "No cell shape with %D vertices", Ncn);
4511: }
4513: for (v = 0; v < Ncn; ++v) cone[v] = vbuf[v] + Nc;
4514: /* Hexahedra are inverted */
4515: if (Ncn == 8) {
4516: PetscInt tmp = cone[1];
4517: cone[1] = cone[3];
4518: cone[3] = tmp;
4519: }
4520: DMPlexSetCone(*dm, c, cone);
4521: }
4522: }
4523: DMPlexSymmetrize(*dm);
4524: DMPlexStratify(*dm);
4525: /* Read coordinates */
4526: DMGetCoordinateSection(*dm, &coordSection);
4527: PetscSectionSetNumFields(coordSection, 1);
4528: PetscSectionSetFieldComponents(coordSection, 0, cdim);
4529: PetscSectionSetChart(coordSection, Nc, Nc + Nv);
4530: for (v = Nc; v < Nc+Nv; ++v) {
4531: PetscSectionSetDof(coordSection, v, cdim);
4532: PetscSectionSetFieldDof(coordSection, v, 0, cdim);
4533: }
4534: PetscSectionSetUp(coordSection);
4535: PetscSectionGetStorageSize(coordSection, &coordSize);
4536: VecCreate(PETSC_COMM_SELF, &coordinates);
4537: PetscObjectSetName((PetscObject) coordinates, "coordinates");
4538: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
4539: VecSetBlockSize(coordinates, cdim);
4540: VecSetType(coordinates, VECSTANDARD);
4541: VecGetArray(coordinates, &coords);
4542: if (rank == 0) {
4543: char format[PETSC_MAX_PATH_LEN];
4544: double x[3];
4545: int l, val[3];
4547: if (Nl) {
4548: for (l = 0; l < Nl; ++l) {format[l*3+0] = '%'; format[l*3+1] = 'd'; format[l*3+2] = ' ';}
4549: format[Nl*3-1] = '\0';
4550: DMCreateLabel(*dm, "marker");
4551: DMGetLabel(*dm, "marker", &marker);
4552: }
4553: for (v = 0; v < Nv; ++v) {
4554: PetscViewerRead(viewer, line, 3+Nl, NULL, PETSC_STRING);
4555: snum = sscanf(line, "%lg %lg %lg", &x[0], &x[1], &x[2]);
4557: switch (Nl) {
4558: case 0: snum = 0;break;
4559: case 1: snum = sscanf(line, format, &val[0]);break;
4560: case 2: snum = sscanf(line, format, &val[0], &val[1]);break;
4561: case 3: snum = sscanf(line, format, &val[0], &val[1], &val[2]);break;
4562: default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Request support for %D labels", Nl);
4563: }
4565: for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d];
4566: for (l = 0; l < Nl; ++l) DMLabelSetValue(marker, v+Nc, val[l]);
4567: }
4568: }
4569: VecRestoreArray(coordinates, &coords);
4570: DMSetCoordinatesLocal(*dm, coordinates);
4571: VecDestroy(&coordinates);
4572: PetscViewerDestroy(&viewer);
4573: if (interpolate) {
4574: DM idm;
4575: DMLabel bdlabel;
4577: DMPlexInterpolate(*dm, &idm);
4578: DMDestroy(dm);
4579: *dm = idm;
4581: if (!Nl) {
4582: DMCreateLabel(*dm, "marker");
4583: DMGetLabel(*dm, "marker", &bdlabel);
4584: DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);
4585: DMPlexLabelComplete(*dm, bdlabel);
4586: }
4587: }
4588: return 0;
4589: }
4591: /*@C
4592: DMPlexCreateFromFile - This takes a filename and produces a DM
4594: Input Parameters:
4595: + comm - The communicator
4596: . filename - A file name
4597: . plexname - The object name of the resulting DM, also used for intra-datafile lookup by some formats
4598: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
4600: Output Parameter:
4601: . dm - The DM
4603: Options Database Keys:
4604: . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5
4606: Use -dm_plex_create_ prefix to pass options to the internal PetscViewer, e.g.
4607: $ -dm_plex_create_viewer_hdf5_collective
4609: Notes:
4610: Using PETSCVIEWERHDF5 type with PETSC_VIEWER_HDF5_PETSC format, one can save multiple DMPlex
4611: meshes in a single HDF5 file. This in turn requires one to name the DMPlex object with PetscObjectSetName()
4612: before saving it with DMView() and before loading it with DMLoad() for identification of the mesh object.
4613: The input parameter name is thus used to name the DMPlex object when DMPlexCreateFromFile() internally
4614: calls DMLoad(). Currently, name is ignored for other viewer types and/or formats.
4616: Level: beginner
4618: .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellListPetsc(), DMPlexCreate(), PetscObjectSetName(), DMView(), DMLoad()
4619: @*/
4620: PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], const char plexname[], PetscBool interpolate, DM *dm)
4621: {
4622: const char extGmsh[] = ".msh";
4623: const char extGmsh2[] = ".msh2";
4624: const char extGmsh4[] = ".msh4";
4625: const char extCGNS[] = ".cgns";
4626: const char extExodus[] = ".exo";
4627: const char extExodus_e[] = ".e";
4628: const char extGenesis[] = ".gen";
4629: const char extFluent[] = ".cas";
4630: const char extHDF5[] = ".h5";
4631: const char extMed[] = ".med";
4632: const char extPLY[] = ".ply";
4633: const char extEGADSLite[] = ".egadslite";
4634: const char extEGADS[] = ".egads";
4635: const char extIGES[] = ".igs";
4636: const char extSTEP[] = ".stp";
4637: const char extCV[] = ".dat";
4638: size_t len;
4639: PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isEGADSLite, isEGADS, isIGES, isSTEP, isCV;
4640: PetscMPIInt rank;
4645: DMInitializePackage();
4646: PetscLogEventBegin(DMPLEX_CreateFromFile,0,0,0,0);
4647: MPI_Comm_rank(comm, &rank);
4648: PetscStrlen(filename, &len);
4651: #define CheckExtension(extension__,is_extension__) do { \
4652: PetscAssert(sizeof(extension__), comm, PETSC_ERR_PLIB, "Zero-size extension: %s", extension__); \
4653: /* don't count the null-terminator at the end */ \
4654: const size_t ext_len = sizeof(extension__)-1; \
4655: if (len < ext_len) { \
4656: is_extension__ = PETSC_FALSE; \
4657: } else { \
4658: PetscStrncmp(filename+len-ext_len, extension__, ext_len, &is_extension__); \
4659: } \
4660: } while (0)
4662: CheckExtension(extGmsh, isGmsh);
4663: CheckExtension(extGmsh2, isGmsh2);
4664: CheckExtension(extGmsh4, isGmsh4);
4665: CheckExtension(extCGNS, isCGNS);
4666: CheckExtension(extExodus, isExodus);
4667: if (!isExodus) CheckExtension(extExodus_e, isExodus);
4668: CheckExtension(extGenesis, isGenesis);
4669: CheckExtension(extFluent, isFluent);
4670: CheckExtension(extHDF5, isHDF5);
4671: CheckExtension(extMed, isMed);
4672: CheckExtension(extPLY, isPLY);
4673: CheckExtension(extEGADSLite, isEGADSLite);
4674: CheckExtension(extEGADS, isEGADS);
4675: CheckExtension(extIGES, isIGES);
4676: CheckExtension(extSTEP, isSTEP);
4677: CheckExtension(extCV, isCV);
4679: #undef CheckExtension
4681: if (isGmsh || isGmsh2 || isGmsh4) {
4682: DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);
4683: } else if (isCGNS) {
4684: DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);
4685: } else if (isExodus || isGenesis) {
4686: DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);
4687: } else if (isFluent) {
4688: DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);
4689: } else if (isHDF5) {
4690: PetscBool load_hdf5_xdmf = PETSC_FALSE;
4691: PetscViewer viewer;
4693: /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */
4694: PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf", 5, &load_hdf5_xdmf);
4695: PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);
4696: PetscViewerCreate(comm, &viewer);
4697: PetscViewerSetType(viewer, PETSCVIEWERHDF5);
4698: PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_");
4699: PetscViewerSetFromOptions(viewer);
4700: PetscViewerFileSetMode(viewer, FILE_MODE_READ);
4701: PetscViewerFileSetName(viewer, filename);
4703: DMCreate(comm, dm);
4704: PetscObjectSetName((PetscObject)(*dm), plexname);
4705: DMSetType(*dm, DMPLEX);
4706: if (load_hdf5_xdmf) PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);
4707: DMLoad(*dm, viewer);
4708: if (load_hdf5_xdmf) PetscViewerPopFormat(viewer);
4709: PetscViewerDestroy(&viewer);
4711: if (interpolate) {
4712: DM idm;
4714: DMPlexInterpolate(*dm, &idm);
4715: DMDestroy(dm);
4716: *dm = idm;
4717: }
4718: } else if (isMed) {
4719: DMPlexCreateMedFromFile(comm, filename, interpolate, dm);
4720: } else if (isPLY) {
4721: DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);
4722: } else if (isEGADSLite || isEGADS || isIGES || isSTEP) {
4723: if (isEGADSLite) DMPlexCreateEGADSLiteFromFile(comm, filename, dm);
4724: else DMPlexCreateEGADSFromFile(comm, filename, dm);
4725: if (!interpolate) {
4726: DM udm;
4728: DMPlexUninterpolate(*dm, &udm);
4729: DMDestroy(dm);
4730: *dm = udm;
4731: }
4732: } else if (isCV) {
4733: DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);
4734: } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename);
4735: PetscStrlen(plexname, &len);
4736: if (len) PetscObjectSetName((PetscObject)(*dm), plexname);
4737: PetscLogEventEnd(DMPLEX_CreateFromFile,0,0,0,0);
4738: return 0;
4739: }