Actual source code: plexcreate.c
petsc-3.8.4 2018-03-24
1: #define PETSCDM_DLL
2: #include <petsc/private/dmpleximpl.h>
3: #include <petscdmda.h>
4: #include <petscsf.h>
6: /*@
7: DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement.
9: Collective on MPI_Comm
11: Input Parameters:
12: + comm - The communicator for the DM object
13: . dim - The spatial dimension
14: . simplex - Flag for simplicial cells, otherwise they are tensor product cells
15: . interpolate - Flag to create intermediate mesh pieces (edges, faces)
16: . refinementUniform - Flag for uniform parallel refinement
17: - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell
19: Output Parameter:
20: . dm - The DM object
22: Level: beginner
24: .keywords: DM, create
25: .seealso: DMSetType(), DMCreate()
26: @*/
27: PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscBool refinementUniform, PetscReal refinementLimit, DM *newdm)
28: {
29: DM dm;
30: PetscInt p;
31: PetscMPIInt rank;
35: DMCreate(comm, &dm);
36: DMSetType(dm, DMPLEX);
37: DMSetDimension(dm, dim);
38: MPI_Comm_rank(comm, &rank);
39: switch (dim) {
40: case 2:
41: if (simplex) {PetscObjectSetName((PetscObject) dm, "triangular");}
42: else {PetscObjectSetName((PetscObject) dm, "quadrilateral");}
43: break;
44: case 3:
45: if (simplex) {PetscObjectSetName((PetscObject) dm, "tetrahedral");}
46: else {PetscObjectSetName((PetscObject) dm, "hexahedral");}
47: break;
48: default:
49: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim);
50: }
51: if (rank) {
52: PetscInt numPoints[2] = {0, 0};
53: DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);
54: } else {
55: switch (dim) {
56: case 2:
57: if (simplex) {
58: PetscInt numPoints[2] = {4, 2};
59: PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0};
60: PetscInt cones[6] = {2, 3, 4, 5, 4, 3};
61: PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0};
62: PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5};
63: PetscInt markerPoints[8] = {2, 1, 3, 1, 4, 1, 5, 1};
65: DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
66: for (p = 0; p < 4; ++p) {DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);}
67: } else {
68: PetscInt numPoints[2] = {6, 2};
69: PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0};
70: PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4};
71: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
72: 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};
74: DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
75: }
76: break;
77: case 3:
78: if (simplex) {
79: PetscInt numPoints[2] = {5, 2};
80: PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0};
81: PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6};
82: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
83: 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};
84: PetscInt markerPoints[10] = {2, 1, 3, 1, 4, 1, 5, 1, 6, 1};
86: DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
87: for (p = 0; p < 5; ++p) {DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);}
88: } else {
89: PetscInt numPoints[2] = {12, 2};
90: PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
91: PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8};
92: PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
93: 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,
94: -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5,
95: 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5};
97: DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
98: }
99: break;
100: default:
101: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim);
102: }
103: }
104: *newdm = dm;
105: if (refinementLimit > 0.0) {
106: DM rdm;
107: const char *name;
109: DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);
110: DMPlexSetRefinementLimit(*newdm, refinementLimit);
111: DMRefine(*newdm, comm, &rdm);
112: PetscObjectGetName((PetscObject) *newdm, &name);
113: PetscObjectSetName((PetscObject) rdm, name);
114: DMDestroy(newdm);
115: *newdm = rdm;
116: }
117: if (interpolate) {
118: DM idm = NULL;
119: const char *name;
121: DMPlexInterpolate(*newdm, &idm);
122: PetscObjectGetName((PetscObject) *newdm, &name);
123: PetscObjectSetName((PetscObject) idm, name);
124: DMPlexCopyCoordinates(*newdm, idm);
125: DMCopyLabels(*newdm, idm);
126: DMDestroy(newdm);
127: *newdm = idm;
128: }
129: {
130: DM refinedMesh = NULL;
131: DM distributedMesh = NULL;
133: /* Distribute mesh over processes */
134: DMPlexDistribute(*newdm, 0, NULL, &distributedMesh);
135: if (distributedMesh) {
136: DMDestroy(newdm);
137: *newdm = distributedMesh;
138: }
139: if (refinementUniform) {
140: DMPlexSetRefinementUniform(*newdm, refinementUniform);
141: DMRefine(*newdm, comm, &refinedMesh);
142: if (refinedMesh) {
143: DMDestroy(newdm);
144: *newdm = refinedMesh;
145: }
146: }
147: }
148: return(0);
149: }
151: /*@
152: DMPlexCreateSquareBoundary - Creates a 1D mesh the is the boundary of a square lattice.
154: Collective on MPI_Comm
156: Input Parameters:
157: + comm - The communicator for the DM object
158: . lower - The lower left corner coordinates
159: . upper - The upper right corner coordinates
160: - edges - The number of cells in each direction
162: Output Parameter:
163: . dm - The DM object
165: Note: Here is the numbering returned for 2 cells in each direction:
166: $ 18--5-17--4--16
167: $ | | |
168: $ 6 10 3
169: $ | | |
170: $ 19-11-20--9--15
171: $ | | |
172: $ 7 8 2
173: $ | | |
174: $ 12--0-13--1--14
176: Level: beginner
178: .keywords: DM, create
179: .seealso: DMPlexCreateBoxMesh(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate()
180: @*/
181: PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
182: {
183: const PetscInt numVertices = (edges[0]+1)*(edges[1]+1);
184: const PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1];
185: PetscInt markerTop = 1;
186: PetscInt markerBottom = 1;
187: PetscInt markerRight = 1;
188: PetscInt markerLeft = 1;
189: PetscBool markerSeparate = PETSC_FALSE;
190: Vec coordinates;
191: PetscSection coordSection;
192: PetscScalar *coords;
193: PetscInt coordSize;
194: PetscMPIInt rank;
195: PetscInt v, vx, vy;
199: PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);
200: if (markerSeparate) {
201: markerTop = 3;
202: markerBottom = 1;
203: markerRight = 2;
204: markerLeft = 4;
205: }
206: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
207: if (!rank) {
208: PetscInt e, ex, ey;
210: DMPlexSetChart(dm, 0, numEdges+numVertices);
211: for (e = 0; e < numEdges; ++e) {
212: DMPlexSetConeSize(dm, e, 2);
213: }
214: DMSetUp(dm); /* Allocate space for cones */
215: for (vx = 0; vx <= edges[0]; vx++) {
216: for (ey = 0; ey < edges[1]; ey++) {
217: PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1);
218: PetscInt vertex = ey*(edges[0]+1) + vx + numEdges;
219: PetscInt cone[2];
221: cone[0] = vertex; cone[1] = vertex+edges[0]+1;
222: DMPlexSetCone(dm, edge, cone);
223: if (vx == edges[0]) {
224: DMSetLabelValue(dm, "marker", edge, markerRight);
225: DMSetLabelValue(dm, "marker", cone[0], markerRight);
226: if (ey == edges[1]-1) {
227: DMSetLabelValue(dm, "marker", cone[1], markerRight);
228: DMSetLabelValue(dm, "Face Sets", cone[1], markerRight);
229: }
230: } else if (vx == 0) {
231: DMSetLabelValue(dm, "marker", edge, markerLeft);
232: DMSetLabelValue(dm, "marker", cone[0], markerLeft);
233: if (ey == edges[1]-1) {
234: DMSetLabelValue(dm, "marker", cone[1], markerLeft);
235: DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft);
236: }
237: }
238: }
239: }
240: for (vy = 0; vy <= edges[1]; vy++) {
241: for (ex = 0; ex < edges[0]; ex++) {
242: PetscInt edge = vy*edges[0] + ex;
243: PetscInt vertex = vy*(edges[0]+1) + ex + numEdges;
244: PetscInt cone[2];
246: cone[0] = vertex; cone[1] = vertex+1;
247: DMPlexSetCone(dm, edge, cone);
248: if (vy == edges[1]) {
249: DMSetLabelValue(dm, "marker", edge, markerTop);
250: DMSetLabelValue(dm, "marker", cone[0], markerTop);
251: if (ex == edges[0]-1) {
252: DMSetLabelValue(dm, "marker", cone[1], markerTop);
253: DMSetLabelValue(dm, "Face Sets", cone[1], markerTop);
254: }
255: } else if (vy == 0) {
256: DMSetLabelValue(dm, "marker", edge, markerBottom);
257: DMSetLabelValue(dm, "marker", cone[0], markerBottom);
258: if (ex == edges[0]-1) {
259: DMSetLabelValue(dm, "marker", cone[1], markerBottom);
260: DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom);
261: }
262: }
263: }
264: }
265: }
266: DMPlexSymmetrize(dm);
267: DMPlexStratify(dm);
268: /* Build coordinates */
269: DMSetCoordinateDim(dm, 2);
270: DMGetCoordinateSection(dm, &coordSection);
271: PetscSectionSetNumFields(coordSection, 1);
272: PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);
273: PetscSectionSetFieldComponents(coordSection, 0, 2);
274: for (v = numEdges; v < numEdges+numVertices; ++v) {
275: PetscSectionSetDof(coordSection, v, 2);
276: PetscSectionSetFieldDof(coordSection, v, 0, 2);
277: }
278: PetscSectionSetUp(coordSection);
279: PetscSectionGetStorageSize(coordSection, &coordSize);
280: VecCreate(PETSC_COMM_SELF, &coordinates);
281: PetscObjectSetName((PetscObject) coordinates, "coordinates");
282: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
283: VecSetBlockSize(coordinates, 2);
284: VecSetType(coordinates,VECSTANDARD);
285: VecGetArray(coordinates, &coords);
286: for (vy = 0; vy <= edges[1]; ++vy) {
287: for (vx = 0; vx <= edges[0]; ++vx) {
288: coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx;
289: coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy;
290: }
291: }
292: VecRestoreArray(coordinates, &coords);
293: DMSetCoordinatesLocal(dm, coordinates);
294: VecDestroy(&coordinates);
295: return(0);
296: }
298: /*@
299: DMPlexCreateCubeBoundary - Creates a 2D mesh that is the boundary of a cubic lattice.
301: Collective on MPI_Comm
303: Input Parameters:
304: + comm - The communicator for the DM object
305: . lower - The lower left front corner coordinates
306: . upper - The upper right back corner coordinates
307: - edges - The number of cells in each direction
309: Output Parameter:
310: . dm - The DM object
312: Level: beginner
314: .keywords: DM, create
315: .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMSetType(), DMCreate()
316: @*/
317: PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[])
318: {
319: PetscInt vertices[3], numVertices;
320: PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2];
321: Vec coordinates;
322: PetscSection coordSection;
323: PetscScalar *coords;
324: PetscInt coordSize;
325: PetscMPIInt rank;
326: PetscInt v, vx, vy, vz;
327: PetscInt voffset, iface=0, cone[4];
331: if ((faces[0] < 1) || (faces[1] < 1) || (faces[2] < 1)) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Must have at least 1 face per side");
332: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
333: vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1;
334: numVertices = vertices[0]*vertices[1]*vertices[2];
335: if (!rank) {
336: PetscInt f;
338: DMPlexSetChart(dm, 0, numFaces+numVertices);
339: for (f = 0; f < numFaces; ++f) {
340: DMPlexSetConeSize(dm, f, 4);
341: }
342: DMSetUp(dm); /* Allocate space for cones */
343: for (v = 0; v < numFaces+numVertices; ++v) {
344: DMSetLabelValue(dm, "marker", v, 1);
345: }
347: /* Side 0 (Top) */
348: for (vy = 0; vy < faces[1]; vy++) {
349: for (vx = 0; vx < faces[0]; vx++) {
350: voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx;
351: cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0];
352: DMPlexSetCone(dm, iface, cone);
353: iface++;
354: }
355: }
357: /* Side 1 (Bottom) */
358: for (vy = 0; vy < faces[1]; vy++) {
359: for (vx = 0; vx < faces[0]; vx++) {
360: voffset = numFaces + vy*(faces[0]+1) + vx;
361: cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1;
362: DMPlexSetCone(dm, iface, cone);
363: iface++;
364: }
365: }
367: /* Side 2 (Front) */
368: for (vz = 0; vz < faces[2]; vz++) {
369: for (vx = 0; vx < faces[0]; vx++) {
370: voffset = numFaces + vz*vertices[0]*vertices[1] + vx;
371: cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1];
372: DMPlexSetCone(dm, iface, cone);
373: iface++;
374: }
375: }
377: /* Side 3 (Back) */
378: for (vz = 0; vz < faces[2]; vz++) {
379: for (vx = 0; vx < faces[0]; vx++) {
380: voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx;
381: cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1;
382: cone[2] = voffset+1; cone[3] = voffset;
383: DMPlexSetCone(dm, iface, cone);
384: iface++;
385: }
386: }
388: /* Side 4 (Left) */
389: for (vz = 0; vz < faces[2]; vz++) {
390: for (vy = 0; vy < faces[1]; vy++) {
391: voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0];
392: cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1];
393: cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0];
394: DMPlexSetCone(dm, iface, cone);
395: iface++;
396: }
397: }
399: /* Side 5 (Right) */
400: for (vz = 0; vz < faces[2]; vz++) {
401: for (vy = 0; vy < faces[1]; vy++) {
402: voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + faces[0];
403: cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset;
404: cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0];
405: DMPlexSetCone(dm, iface, cone);
406: iface++;
407: }
408: }
409: }
410: DMPlexSymmetrize(dm);
411: DMPlexStratify(dm);
412: /* Build coordinates */
413: DMSetCoordinateDim(dm, 3);
414: DMGetCoordinateSection(dm, &coordSection);
415: PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);
416: for (v = numFaces; v < numFaces+numVertices; ++v) {
417: PetscSectionSetDof(coordSection, v, 3);
418: }
419: PetscSectionSetUp(coordSection);
420: PetscSectionGetStorageSize(coordSection, &coordSize);
421: VecCreate(PETSC_COMM_SELF, &coordinates);
422: PetscObjectSetName((PetscObject) coordinates, "coordinates");
423: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
424: VecSetBlockSize(coordinates, 3);
425: VecSetType(coordinates,VECSTANDARD);
426: VecGetArray(coordinates, &coords);
427: for (vz = 0; vz <= faces[2]; ++vz) {
428: for (vy = 0; vy <= faces[1]; ++vy) {
429: for (vx = 0; vx <= faces[0]; ++vx) {
430: coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx;
431: coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy;
432: coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz;
433: }
434: }
435: }
436: VecRestoreArray(coordinates, &coords);
437: DMSetCoordinatesLocal(dm, coordinates);
438: VecDestroy(&coordinates);
439: return(0);
440: }
442: /*@
443: DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices.
445: Collective on MPI_Comm
447: Input Parameters:
448: + comm - The communicator for the DM object
449: . dim - The spatial dimension
450: . numFaces - Number of faces per dimension
451: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
453: Output Parameter:
454: . dm - The DM object
456: Level: beginner
458: .keywords: DM, create
459: .seealso: DMPlexCreateHexBoxMesh(), DMSetType(), DMCreate()
460: @*/
461: PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscInt numFaces, PetscBool interpolate, DM *dm)
462: {
463: DM boundary;
468: DMCreate(comm, &boundary);
470: DMSetType(boundary, DMPLEX);
471: DMSetDimension(boundary, dim-1);
472: DMSetCoordinateDim(boundary, dim);
473: switch (dim) {
474: case 2:
475: {
476: PetscReal lower[2] = {0.0, 0.0};
477: PetscReal upper[2] = {1.0, 1.0};
478: PetscInt edges[2];
480: edges[0] = numFaces; edges[1] = numFaces;
481: DMPlexCreateSquareBoundary(boundary, lower, upper, edges);
482: break;
483: }
484: case 3:
485: {
486: PetscReal lower[3] = {0.0, 0.0, 0.0};
487: PetscReal upper[3] = {1.0, 1.0, 1.0};
488: PetscInt faces[3];
490: faces[0] = numFaces; faces[1] = numFaces; faces[2] = numFaces;
491: DMPlexCreateCubeBoundary(boundary, lower, upper, faces);
492: break;
493: }
494: default:
495: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim);
496: }
497: DMPlexGenerate(boundary, NULL, interpolate, dm);
498: DMDestroy(&boundary);
499: return(0);
500: }
502: static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ)
503: {
504: DMLabel cutLabel = NULL;
505: PetscInt markerTop = 1, faceMarkerTop = 1;
506: PetscInt markerBottom = 1, faceMarkerBottom = 1;
507: PetscInt markerFront = 1, faceMarkerFront = 1;
508: PetscInt markerBack = 1, faceMarkerBack = 1;
509: PetscInt markerRight = 1, faceMarkerRight = 1;
510: PetscInt markerLeft = 1, faceMarkerLeft = 1;
511: PetscInt dim;
512: PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE;
513: PetscMPIInt rank;
517: DMGetDimension(dm,&dim);
518: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
519: DMCreateLabel(dm,"marker");
520: DMCreateLabel(dm,"Face Sets");
521: PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL);
522: if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ||
523: bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ||
524: bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) {
526: if (cutMarker) {DMCreateLabel(dm, "periodic_cut"); DMGetLabel(dm, "periodic_cut", &cutLabel);}
527: }
528: switch (dim) {
529: case 2:
530: faceMarkerTop = 3;
531: faceMarkerBottom = 1;
532: faceMarkerRight = 2;
533: faceMarkerLeft = 4;
534: break;
535: case 3:
536: faceMarkerBottom = 1;
537: faceMarkerTop = 2;
538: faceMarkerFront = 3;
539: faceMarkerBack = 4;
540: faceMarkerRight = 5;
541: faceMarkerLeft = 6;
542: break;
543: default:
544: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %d not supported",dim);
545: break;
546: }
547: PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);
548: if (markerSeparate) {
549: markerBottom = faceMarkerBottom;
550: markerTop = faceMarkerTop;
551: markerFront = faceMarkerFront;
552: markerBack = faceMarkerBack;
553: markerRight = faceMarkerRight;
554: markerLeft = faceMarkerLeft;
555: }
556: {
557: const PetscInt numXEdges = !rank ? edges[0] : 0;
558: const PetscInt numYEdges = !rank ? edges[1] : 0;
559: const PetscInt numZEdges = !rank ? edges[2] : 0;
560: const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0;
561: const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0;
562: const PetscInt numZVertices = !rank ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0;
563: const PetscInt numCells = numXEdges*numYEdges*numZEdges;
564: const PetscInt numXFaces = numYEdges*numZEdges;
565: const PetscInt numYFaces = numXEdges*numZEdges;
566: const PetscInt numZFaces = numXEdges*numYEdges;
567: const PetscInt numTotXFaces = numXVertices*numXFaces;
568: const PetscInt numTotYFaces = numYVertices*numYFaces;
569: const PetscInt numTotZFaces = numZVertices*numZFaces;
570: const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces;
571: const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices;
572: const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices;
573: const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices;
574: const PetscInt numVertices = numXVertices*numYVertices*numZVertices;
575: const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges;
576: const PetscInt firstVertex = (dim == 2) ? numFaces : numCells;
577: const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices;
578: const PetscInt firstYFace = firstXFace + numTotXFaces;
579: const PetscInt firstZFace = firstYFace + numTotYFaces;
580: const PetscInt firstXEdge = numCells + numFaces + numVertices;
581: const PetscInt firstYEdge = firstXEdge + numTotXEdges;
582: const PetscInt firstZEdge = firstYEdge + numTotYEdges;
583: Vec coordinates;
584: PetscSection coordSection;
585: PetscScalar *coords;
586: PetscInt coordSize;
587: PetscInt v, vx, vy, vz;
588: PetscInt c, f, fx, fy, fz, e, ex, ey, ez;
590: DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);
591: for (c = 0; c < numCells; c++) {
592: DMPlexSetConeSize(dm, c, 6);
593: }
594: for (f = firstXFace; f < firstXFace+numFaces; ++f) {
595: DMPlexSetConeSize(dm, f, 4);
596: }
597: for (e = firstXEdge; e < firstXEdge+numEdges; ++e) {
598: DMPlexSetConeSize(dm, e, 2);
599: }
600: DMSetUp(dm); /* Allocate space for cones */
601: /* Build cells */
602: for (fz = 0; fz < numZEdges; ++fz) {
603: for (fy = 0; fy < numYEdges; ++fy) {
604: for (fx = 0; fx < numXEdges; ++fx) {
605: PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx;
606: PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz;
607: PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices);
608: PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy;
609: PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices);
610: PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx;
611: PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices);
612: /* B, T, F, K, R, L */
613: PetscInt ornt[6] = {-4, 0, 0, -1, 0, -4}; /* ??? */
614: PetscInt cone[6];
616: /* no boundary twisting in 3D */
617: cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL;
618: DMPlexSetCone(dm, cell, cone);
619: DMPlexSetConeOrientation(dm, cell, ornt);
620: if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, cell, 2);}
621: if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, cell, 2);}
622: if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, cell, 2);}
623: }
624: }
625: }
626: /* Build x faces */
627: for (fz = 0; fz < numZEdges; ++fz) {
628: for (fy = 0; fy < numYEdges; ++fy) {
629: for (fx = 0; fx < numXVertices; ++fx) {
630: PetscInt face = firstXFace + (fz*numYEdges+fy)*numXVertices + fx;
631: PetscInt edgeL = firstZEdge + ( fy* numXVertices+fx)*numZEdges + fz;
632: PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz;
633: PetscInt edgeB = firstYEdge + ( fz* numXVertices+fx)*numYEdges + fy;
634: PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy;
635: PetscInt ornt[4] = {0, 0, -2, -2};
636: PetscInt cone[4];
638: if (dim == 3) {
639: /* markers */
640: if (bdX != DM_BOUNDARY_PERIODIC) {
641: if (fx == numXVertices-1) {
642: DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);
643: DMSetLabelValue(dm, "marker", face, markerRight);
644: }
645: else if (fx == 0) {
646: DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);
647: DMSetLabelValue(dm, "marker", face, markerLeft);
648: }
649: }
650: }
651: cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
652: DMPlexSetCone(dm, face, cone);
653: DMPlexSetConeOrientation(dm, face, ornt);
654: }
655: }
656: }
657: /* Build y faces */
658: for (fz = 0; fz < numZEdges; ++fz) {
659: for (fx = 0; fx < numXEdges; ++fx) {
660: for (fy = 0; fy < numYVertices; ++fy) {
661: PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy;
662: PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx )*numZEdges + fz;
663: PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz;
664: PetscInt edgeB = firstXEdge + ( fz *numYVertices+fy)*numXEdges + fx;
665: PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx;
666: PetscInt ornt[4] = {0, 0, -2, -2};
667: PetscInt cone[4];
669: if (dim == 3) {
670: /* markers */
671: if (bdY != DM_BOUNDARY_PERIODIC) {
672: if (fy == numYVertices-1) {
673: DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);
674: DMSetLabelValue(dm, "marker", face, markerBack);
675: }
676: else if (fy == 0) {
677: DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);
678: DMSetLabelValue(dm, "marker", face, markerFront);
679: }
680: }
681: }
682: cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
683: DMPlexSetCone(dm, face, cone);
684: DMPlexSetConeOrientation(dm, face, ornt);
685: }
686: }
687: }
688: /* Build z faces */
689: for (fy = 0; fy < numYEdges; ++fy) {
690: for (fx = 0; fx < numXEdges; ++fx) {
691: for (fz = 0; fz < numZVertices; fz++) {
692: PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz;
693: PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx )*numYEdges + fy;
694: PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy;
695: PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy )*numXEdges + fx;
696: PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx;
697: PetscInt ornt[4] = {0, 0, -2, -2};
698: PetscInt cone[4];
700: if (dim == 2) {
701: if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -2;}
702: if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;}
703: if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, face, 2);}
704: if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, face, 2);}
705: } else {
706: /* markers */
707: if (bdZ != DM_BOUNDARY_PERIODIC) {
708: if (fz == numZVertices-1) {
709: DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);
710: DMSetLabelValue(dm, "marker", face, markerTop);
711: }
712: else if (fz == 0) {
713: DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);
714: DMSetLabelValue(dm, "marker", face, markerBottom);
715: }
716: }
717: }
718: cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
719: DMPlexSetCone(dm, face, cone);
720: DMPlexSetConeOrientation(dm, face, ornt);
721: }
722: }
723: }
724: /* Build Z edges*/
725: for (vy = 0; vy < numYVertices; vy++) {
726: for (vx = 0; vx < numXVertices; vx++) {
727: for (ez = 0; ez < numZEdges; ez++) {
728: const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez;
729: const PetscInt vertexB = firstVertex + ( ez *numYVertices+vy)*numXVertices + vx;
730: const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx;
731: PetscInt cone[2];
733: if (dim == 3) {
734: if (bdX != DM_BOUNDARY_PERIODIC) {
735: if (vx == numXVertices-1) {
736: DMSetLabelValue(dm, "marker", edge, markerRight);
737: }
738: else if (vx == 0) {
739: DMSetLabelValue(dm, "marker", edge, markerLeft);
740: }
741: }
742: if (bdY != DM_BOUNDARY_PERIODIC) {
743: if (vy == numYVertices-1) {
744: DMSetLabelValue(dm, "marker", edge, markerBack);
745: }
746: else if (vy == 0) {
747: DMSetLabelValue(dm, "marker", edge, markerFront);
748: }
749: }
750: }
751: cone[0] = vertexB; cone[1] = vertexT;
752: DMPlexSetCone(dm, edge, cone);
753: }
754: }
755: }
756: /* Build Y edges*/
757: for (vz = 0; vz < numZVertices; vz++) {
758: for (vx = 0; vx < numXVertices; vx++) {
759: for (ey = 0; ey < numYEdges; ey++) {
760: const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx;
761: const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey;
762: const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx;
763: const PetscInt vertexK = firstVertex + nextv;
764: PetscInt cone[2];
766: cone[0] = vertexF; cone[1] = vertexK;
767: DMPlexSetCone(dm, edge, cone);
768: if (dim == 2) {
769: if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) {
770: if (vx == numXVertices-1) {
771: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);
772: DMSetLabelValue(dm, "marker", edge, markerRight);
773: DMSetLabelValue(dm, "marker", cone[0], markerRight);
774: if (ey == numYEdges-1) {
775: DMSetLabelValue(dm, "marker", cone[1], markerRight);
776: }
777: } else if (vx == 0) {
778: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);
779: DMSetLabelValue(dm, "marker", edge, markerLeft);
780: DMSetLabelValue(dm, "marker", cone[0], markerLeft);
781: if (ey == numYEdges-1) {
782: DMSetLabelValue(dm, "marker", cone[1], markerLeft);
783: }
784: }
785: } else {
786: if (vx == 0 && cutLabel) {
787: DMLabelSetValue(cutLabel, edge, 1);
788: DMLabelSetValue(cutLabel, cone[0], 1);
789: if (ey == numYEdges-1) {
790: DMLabelSetValue(cutLabel, cone[1], 1);
791: }
792: }
793: }
794: } else {
795: if (bdX != DM_BOUNDARY_PERIODIC) {
796: if (vx == numXVertices-1) {
797: DMSetLabelValue(dm, "marker", edge, markerRight);
798: } else if (vx == 0) {
799: DMSetLabelValue(dm, "marker", edge, markerLeft);
800: }
801: }
802: if (bdZ != DM_BOUNDARY_PERIODIC) {
803: if (vz == numZVertices-1) {
804: DMSetLabelValue(dm, "marker", edge, markerTop);
805: } else if (vz == 0) {
806: DMSetLabelValue(dm, "marker", edge, markerBottom);
807: }
808: }
809: }
810: }
811: }
812: }
813: /* Build X edges*/
814: for (vz = 0; vz < numZVertices; vz++) {
815: for (vy = 0; vy < numYVertices; vy++) {
816: for (ex = 0; ex < numXEdges; ex++) {
817: const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices;
818: const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex;
819: const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex;
820: const PetscInt vertexR = firstVertex + nextv;
821: PetscInt cone[2];
823: cone[0] = vertexL; cone[1] = vertexR;
824: DMPlexSetCone(dm, edge, cone);
825: if (dim == 2) {
826: if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) {
827: if (vy == numYVertices-1) {
828: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);
829: DMSetLabelValue(dm, "marker", edge, markerTop);
830: DMSetLabelValue(dm, "marker", cone[0], markerTop);
831: if (ex == numXEdges-1) {
832: DMSetLabelValue(dm, "marker", cone[1], markerTop);
833: }
834: } else if (vy == 0) {
835: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);
836: DMSetLabelValue(dm, "marker", edge, markerBottom);
837: DMSetLabelValue(dm, "marker", cone[0], markerBottom);
838: if (ex == numXEdges-1) {
839: DMSetLabelValue(dm, "marker", cone[1], markerBottom);
840: }
841: }
842: } else {
843: if (vy == 0 && cutLabel) {
844: DMLabelSetValue(cutLabel, edge, 1);
845: DMLabelSetValue(cutLabel, cone[0], 1);
846: if (ex == numXEdges-1) {
847: DMLabelSetValue(cutLabel, cone[1], 1);
848: }
849: }
850: }
851: } else {
852: if (bdY != DM_BOUNDARY_PERIODIC) {
853: if (vy == numYVertices-1) {
854: DMSetLabelValue(dm, "marker", edge, markerBack);
855: }
856: else if (vy == 0) {
857: DMSetLabelValue(dm, "marker", edge, markerFront);
858: }
859: }
860: if (bdZ != DM_BOUNDARY_PERIODIC) {
861: if (vz == numZVertices-1) {
862: DMSetLabelValue(dm, "marker", edge, markerTop);
863: }
864: else if (vz == 0) {
865: DMSetLabelValue(dm, "marker", edge, markerBottom);
866: }
867: }
868: }
869: }
870: }
871: }
872: DMPlexSymmetrize(dm);
873: DMPlexStratify(dm);
874: /* Build coordinates */
875: DMGetCoordinateSection(dm, &coordSection);
876: PetscSectionSetNumFields(coordSection, 1);
877: PetscSectionSetFieldComponents(coordSection, 0, dim);
878: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);
879: for (v = firstVertex; v < firstVertex+numVertices; ++v) {
880: PetscSectionSetDof(coordSection, v, dim);
881: PetscSectionSetFieldDof(coordSection, v, 0, dim);
882: }
883: PetscSectionSetUp(coordSection);
884: PetscSectionGetStorageSize(coordSection, &coordSize);
885: VecCreate(PETSC_COMM_SELF, &coordinates);
886: PetscObjectSetName((PetscObject) coordinates, "coordinates");
887: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
888: VecSetBlockSize(coordinates, dim);
889: VecSetType(coordinates,VECSTANDARD);
890: VecGetArray(coordinates, &coords);
891: for (vz = 0; vz < numZVertices; ++vz) {
892: for (vy = 0; vy < numYVertices; ++vy) {
893: for (vx = 0; vx < numXVertices; ++vx) {
894: coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx;
895: coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy;
896: if (dim == 3) {
897: coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz;
898: }
899: }
900: }
901: }
902: VecRestoreArray(coordinates, &coords);
903: DMSetCoordinatesLocal(dm, coordinates);
904: VecDestroy(&coordinates);
905: }
906: return(0);
907: }
909: /*@
910: DMPlexCreateHexBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using hexahedra.
912: Collective on MPI_Comm
914: Input Parameters:
915: + comm - The communicator for the DM object
916: . dim - The spatial dimension
917: . periodicX - The boundary type for the X direction
918: . periodicY - The boundary type for the Y direction
919: . periodicZ - The boundary type for the Z direction
920: - cells - The number of cells in each direction
922: Output Parameter:
923: . dm - The DM object
925: Note: Here is the numbering returned for 2 cells in each direction:
926: $ 22--8-23--9--24
927: $ | | |
928: $ 13 2 14 3 15
929: $ | | |
930: $ 19--6-20--7--21
931: $ | | |
932: $ 10 0 11 1 12
933: $ | | |
934: $ 16--4-17--5--18
936: Level: beginner
938: .keywords: DM, create
939: .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
940: @*/
941: PetscErrorCode DMPlexCreateHexBoxMesh(MPI_Comm comm, PetscInt dim, const PetscInt cells[], DMBoundaryType periodicX, DMBoundaryType periodicY, DMBoundaryType periodicZ, DM *dm)
942: {
943: PetscInt i;
948: DMCreate(comm, dm);
950: DMSetType(*dm, DMPLEX);
951: DMSetDimension(*dm, dim);
952: switch (dim) {
953: case 2:
954: {
955: PetscReal lower[3] = {0.0, 0.0, 0.0};
956: PetscReal upper[3] = {1.0, 1.0, 0.0};
957: PetscInt edges[3];
959: edges[0] = cells[0];
960: edges[1] = cells[1];
961: edges[2] = 0;
963: DMPlexCreateCubeMesh_Internal(*dm, lower, upper, edges, periodicX, periodicY, DM_BOUNDARY_NONE);
964: if (periodicX == DM_BOUNDARY_PERIODIC || periodicX == DM_BOUNDARY_TWIST ||
965: periodicY == DM_BOUNDARY_PERIODIC || periodicY == DM_BOUNDARY_TWIST) {
966: PetscReal L[2];
967: PetscReal maxCell[2];
968: DMBoundaryType bdType[2];
970: bdType[0] = periodicX;
971: bdType[1] = periodicY;
972: for (i = 0; i < dim; i++) {
973: L[i] = upper[i] - lower[i];
974: maxCell[i] = 1.1 * (L[i] / PetscMax(1,cells[i]));
975: }
977: DMSetPeriodicity(*dm,PETSC_TRUE,maxCell,L,bdType);
978: }
979: break;
980: }
981: case 3:
982: {
983: PetscReal lower[3] = {0.0, 0.0, 0.0};
984: PetscReal upper[3] = {1.0, 1.0, 1.0};
986: DMPlexCreateCubeMesh_Internal(*dm, lower, upper, cells, periodicX, periodicY, periodicZ);
987: if (periodicX == DM_BOUNDARY_PERIODIC || periodicX == DM_BOUNDARY_TWIST ||
988: periodicY == DM_BOUNDARY_PERIODIC || periodicY == DM_BOUNDARY_TWIST ||
989: periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) {
990: PetscReal L[3];
991: PetscReal maxCell[3];
992: DMBoundaryType bdType[3];
994: bdType[0] = periodicX;
995: bdType[1] = periodicY;
996: bdType[2] = periodicZ;
997: for (i = 0; i < dim; i++) {
998: L[i] = upper[i] - lower[i];
999: maxCell[i] = 1.1 * (L[i] / cells[i]);
1000: }
1002: DMSetPeriodicity(*dm,PETSC_TRUE,maxCell,L,bdType);
1003: }
1004: break;
1005: }
1006: default:
1007: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim);
1008: }
1009: return(0);
1010: }
1012: /*@C
1013: DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database.
1015: Logically Collective on DM
1017: Input Parameters:
1018: + dm - the DM context
1019: - prefix - the prefix to prepend to all option names
1021: Notes:
1022: A hyphen (-) must NOT be given at the beginning of the prefix name.
1023: The first character of all runtime options is AUTOMATICALLY the hyphen.
1025: Level: advanced
1027: .seealso: SNESSetFromOptions()
1028: @*/
1029: PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[])
1030: {
1031: DM_Plex *mesh = (DM_Plex *) dm->data;
1036: PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);
1037: PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);
1038: return(0);
1039: }
1041: /*@
1042: DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra.
1044: Collective on MPI_Comm
1046: Input Parameters:
1047: + comm - The communicator for the DM object
1048: . numRefine - The number of regular refinements to the basic 5 cell structure
1049: - periodicZ - The boundary type for the Z direction
1051: Output Parameter:
1052: . dm - The DM object
1054: Note: Here is the output numbering looking from the bottom of the cylinder:
1055: $ 17-----14
1056: $ | |
1057: $ | 2 |
1058: $ | |
1059: $ 17-----8-----7-----14
1060: $ | | | |
1061: $ | 3 | 0 | 1 |
1062: $ | | | |
1063: $ 19-----5-----6-----13
1064: $ | |
1065: $ | 4 |
1066: $ | |
1067: $ 19-----13
1068: $
1069: $ and up through the top
1070: $
1071: $ 18-----16
1072: $ | |
1073: $ | 2 |
1074: $ | |
1075: $ 18----10----11-----16
1076: $ | | | |
1077: $ | 3 | 0 | 1 |
1078: $ | | | |
1079: $ 20-----9----12-----15
1080: $ | |
1081: $ | 4 |
1082: $ | |
1083: $ 20-----15
1085: Level: beginner
1087: .keywords: DM, create
1088: .seealso: DMPlexCreateHexBoxMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1089: @*/
1090: PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, PetscInt numRefine, DMBoundaryType periodicZ, DM *dm)
1091: {
1092: const PetscInt dim = 3;
1093: PetscInt numCells, numVertices, r;
1098: if (numRefine < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of refinements %D cannot be negative", numRefine);
1099: DMCreate(comm, dm);
1100: DMSetType(*dm, DMPLEX);
1101: DMSetDimension(*dm, dim);
1102: /* Create topology */
1103: {
1104: PetscInt cone[8], c;
1106: numCells = 5;
1107: numVertices = 16;
1108: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1109: numCells *= 3;
1110: numVertices = 24;
1111: }
1112: DMPlexSetChart(*dm, 0, numCells+numVertices);
1113: for (c = 0; c < numCells; c++) {DMPlexSetConeSize(*dm, c, 8);}
1114: DMSetUp(*dm);
1115: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1116: cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16;
1117: cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34;
1118: DMPlexSetCone(*dm, 0, cone);
1119: cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23;
1120: cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */
1121: DMPlexSetCone(*dm, 1, cone);
1122: cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17;
1123: cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38;
1124: DMPlexSetCone(*dm, 2, cone);
1125: cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15;
1126: cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38;
1127: DMPlexSetCone(*dm, 3, cone);
1128: cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23;
1129: cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31;
1130: DMPlexSetCone(*dm, 4, cone);
1132: cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32;
1133: cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20;
1134: DMPlexSetCone(*dm, 5, cone);
1135: cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36;
1136: cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21;
1137: DMPlexSetCone(*dm, 6, cone);
1138: cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33;
1139: cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28;
1140: DMPlexSetCone(*dm, 7, cone);
1141: cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31;
1142: cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28;
1143: DMPlexSetCone(*dm, 8, cone);
1144: cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36;
1145: cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19;
1146: DMPlexSetCone(*dm, 9, cone);
1148: cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22;
1149: cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18;
1150: DMPlexSetCone(*dm, 10, cone);
1151: cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25;
1152: cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17;
1153: DMPlexSetCone(*dm, 11, cone);
1154: cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21;
1155: cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27;
1156: DMPlexSetCone(*dm, 12, cone);
1157: cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19;
1158: cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27;
1159: DMPlexSetCone(*dm, 13, cone);
1160: cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25;
1161: cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15;
1162: DMPlexSetCone(*dm, 14, cone);
1163: } else {
1164: cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6;
1165: cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10;
1166: DMPlexSetCone(*dm, 0, cone);
1167: cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13;
1168: cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11;
1169: DMPlexSetCone(*dm, 1, cone);
1170: cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7;
1171: cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18;
1172: DMPlexSetCone(*dm, 2, cone);
1173: cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5;
1174: cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18;
1175: DMPlexSetCone(*dm, 3, cone);
1176: cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13;
1177: cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9;
1178: DMPlexSetCone(*dm, 4, cone);
1179: }
1180: DMPlexSymmetrize(*dm);
1181: DMPlexStratify(*dm);
1182: }
1183: /* Interpolate */
1184: {
1185: DM idm = NULL;
1187: DMPlexInterpolate(*dm, &idm);
1188: DMDestroy(dm);
1189: *dm = idm;
1190: }
1191: /* Create cube geometry */
1192: {
1193: Vec coordinates;
1194: PetscSection coordSection;
1195: PetscScalar *coords;
1196: PetscInt coordSize, v;
1197: const PetscReal dis = 1.0/PetscSqrtReal(2.0);
1198: const PetscReal ds2 = dis/2.0;
1200: /* Build coordinates */
1201: DMGetCoordinateSection(*dm, &coordSection);
1202: PetscSectionSetNumFields(coordSection, 1);
1203: PetscSectionSetFieldComponents(coordSection, 0, dim);
1204: PetscSectionSetChart(coordSection, numCells, numCells+numVertices);
1205: for (v = numCells; v < numCells+numVertices; ++v) {
1206: PetscSectionSetDof(coordSection, v, dim);
1207: PetscSectionSetFieldDof(coordSection, v, 0, dim);
1208: }
1209: PetscSectionSetUp(coordSection);
1210: PetscSectionGetStorageSize(coordSection, &coordSize);
1211: VecCreate(PETSC_COMM_SELF, &coordinates);
1212: PetscObjectSetName((PetscObject) coordinates, "coordinates");
1213: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1214: VecSetBlockSize(coordinates, dim);
1215: VecSetType(coordinates,VECSTANDARD);
1216: VecGetArray(coordinates, &coords);
1217: coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0;
1218: coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0;
1219: coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0;
1220: coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0;
1221: coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0;
1222: coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0;
1223: coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0;
1224: coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0;
1225: coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0;
1226: coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0;
1227: coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0;
1228: coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0;
1229: coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0;
1230: coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0;
1231: coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0;
1232: coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0;
1233: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1234: /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5;
1235: /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5;
1236: /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5;
1237: /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5;
1238: /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5;
1239: /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5;
1240: /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5;
1241: /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5;
1242: }
1243: VecRestoreArray(coordinates, &coords);
1244: DMSetCoordinatesLocal(*dm, coordinates);
1245: VecDestroy(&coordinates);
1246: }
1247: /* Create periodicity */
1248: if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) {
1249: PetscReal L[3];
1250: PetscReal maxCell[3];
1251: DMBoundaryType bdType[3];
1252: PetscReal lower[3] = {0.0, 0.0, 0.0};
1253: PetscReal upper[3] = {1.0, 1.0, 1.5};
1254: PetscInt i, numZCells = 3;
1256: bdType[0] = DM_BOUNDARY_NONE;
1257: bdType[1] = DM_BOUNDARY_NONE;
1258: bdType[2] = periodicZ;
1259: for (i = 0; i < dim; i++) {
1260: L[i] = upper[i] - lower[i];
1261: maxCell[i] = 1.1 * (L[i] / numZCells);
1262: }
1263: DMSetPeriodicity(*dm, PETSC_TRUE, maxCell, L, bdType);
1264: }
1265: /* Refine topology */
1266: for (r = 0; r < numRefine; ++r) {
1267: DM rdm = NULL;
1269: DMRefine(*dm, comm, &rdm);
1270: DMDestroy(dm);
1271: *dm = rdm;
1272: }
1273: /* Remap geometry to cylinder
1274: Interior square: Linear interpolation is correct
1275: The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing
1276: such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance
1278: phi = arctan(y/x)
1279: d_close = sqrt(1/8 + 1/4 sin^2(phi))
1280: d_far = sqrt(1/2 + sin^2(phi))
1282: so we remap them using
1284: x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close)
1285: y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close)
1287: If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y.
1288: */
1289: {
1290: Vec coordinates;
1291: PetscSection coordSection;
1292: PetscScalar *coords;
1293: PetscInt vStart, vEnd, v;
1294: const PetscReal dis = 1.0/PetscSqrtReal(2.0);
1295: const PetscReal ds2 = 0.5*dis;
1297: DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);
1298: DMGetCoordinateSection(*dm, &coordSection);
1299: DMGetCoordinatesLocal(*dm, &coordinates);
1300: VecGetArray(coordinates, &coords);
1301: for (v = vStart; v < vEnd; ++v) {
1302: PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc;
1303: PetscInt off;
1305: PetscSectionGetOffset(coordSection, v, &off);
1306: if ((PetscAbsScalar(coords[off+0]) <= ds2) && (PetscAbsScalar(coords[off+1]) <= ds2)) continue;
1307: x = PetscRealPart(coords[off]);
1308: y = PetscRealPart(coords[off+1]);
1309: phi = PetscAtan2Real(y, x);
1310: sinp = PetscSinReal(phi);
1311: cosp = PetscCosReal(phi);
1312: if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) {
1313: dc = PetscAbsReal(ds2/sinp);
1314: df = PetscAbsReal(dis/sinp);
1315: xc = ds2*x/PetscAbsReal(y);
1316: yc = ds2*PetscSignReal(y);
1317: } else {
1318: dc = PetscAbsReal(ds2/cosp);
1319: df = PetscAbsReal(dis/cosp);
1320: xc = ds2*PetscSignReal(x);
1321: yc = ds2*y/PetscAbsReal(x);
1322: }
1323: coords[off+0] = xc + (coords[off+0] - xc)*(1.0 - dc)/(df - dc);
1324: coords[off+1] = yc + (coords[off+1] - yc)*(1.0 - dc)/(df - dc);
1325: }
1326: VecRestoreArray(coordinates, &coords);
1327: if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) {
1328: DMLocalizeCoordinates(*dm);
1329: }
1330: }
1331: return(0);
1332: }
1334: /*@
1335: DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges.
1337: Collective on MPI_Comm
1339: Input Parameters:
1340: + comm - The communicator for the DM object
1341: . n - The number of wedges around the origin
1342: - interpolate - Create edges and faces
1344: Output Parameter:
1345: . dm - The DM object
1347: Level: beginner
1349: .keywords: DM, create
1350: .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateHexBoxMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1351: @*/
1352: PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm)
1353: {
1354: const PetscInt dim = 3;
1355: PetscInt numCells, numVertices;
1360: if (n < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n);
1361: DMCreate(comm, dm);
1362: DMSetType(*dm, DMPLEX);
1363: DMSetDimension(*dm, dim);
1364: /* Create topology */
1365: {
1366: PetscInt cone[6], c;
1368: numCells = n;
1369: numVertices = 2*(n+1);
1370: DMPlexSetChart(*dm, 0, numCells+numVertices);
1371: for (c = 0; c < numCells; c++) {DMPlexSetConeSize(*dm, c, 6);}
1372: DMSetUp(*dm);
1373: for (c = 0; c < numCells; c++) {
1374: cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n;
1375: cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n;
1376: DMPlexSetCone(*dm, c, cone);
1377: }
1378: DMPlexSymmetrize(*dm);
1379: DMPlexStratify(*dm);
1380: }
1381: /* Interpolate */
1382: if (interpolate) {
1383: DM idm = NULL;
1385: DMPlexInterpolate(*dm, &idm);
1386: DMDestroy(dm);
1387: *dm = idm;
1388: }
1389: /* Create cylinder geometry */
1390: {
1391: Vec coordinates;
1392: PetscSection coordSection;
1393: PetscScalar *coords;
1394: PetscInt coordSize, v, c;
1396: /* Build coordinates */
1397: DMGetCoordinateSection(*dm, &coordSection);
1398: PetscSectionSetNumFields(coordSection, 1);
1399: PetscSectionSetFieldComponents(coordSection, 0, dim);
1400: PetscSectionSetChart(coordSection, numCells, numCells+numVertices);
1401: for (v = numCells; v < numCells+numVertices; ++v) {
1402: PetscSectionSetDof(coordSection, v, dim);
1403: PetscSectionSetFieldDof(coordSection, v, 0, dim);
1404: }
1405: PetscSectionSetUp(coordSection);
1406: PetscSectionGetStorageSize(coordSection, &coordSize);
1407: VecCreate(PETSC_COMM_SELF, &coordinates);
1408: PetscObjectSetName((PetscObject) coordinates, "coordinates");
1409: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1410: VecSetBlockSize(coordinates, dim);
1411: VecSetType(coordinates,VECSTANDARD);
1412: VecGetArray(coordinates, &coords);
1413: for (c = 0; c < numCells; c++) {
1414: 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;
1415: 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;
1416: }
1417: coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0;
1418: coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0;
1419: VecRestoreArray(coordinates, &coords);
1420: DMSetCoordinatesLocal(*dm, coordinates);
1421: VecDestroy(&coordinates);
1422: }
1423: return(0);
1424: }
1426: PETSC_STATIC_INLINE PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
1427: {
1428: PetscReal prod = 0.0;
1429: PetscInt i;
1430: for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]);
1431: return PetscSqrtReal(prod);
1432: }
1433: PETSC_STATIC_INLINE PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
1434: {
1435: PetscReal prod = 0.0;
1436: PetscInt i;
1437: for (i = 0; i < dim; ++i) prod += x[i]*y[i];
1438: return prod;
1439: }
1441: /*@
1442: DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d.
1444: Collective on MPI_Comm
1446: Input Parameters:
1447: . comm - The communicator for the DM object
1448: . dim - The dimension
1449: - simplex - Use simplices, or tensor product cells
1451: Output Parameter:
1452: . dm - The DM object
1454: Level: beginner
1456: .keywords: DM, create
1457: .seealso: DMPlexCreateBoxMesh(), DMPlexCreateHexBoxMesh(), DMSetType(), DMCreate()
1458: @*/
1459: PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *dm)
1460: {
1461: const PetscInt embedDim = dim+1;
1462: PetscSection coordSection;
1463: Vec coordinates;
1464: PetscScalar *coords;
1465: PetscReal *coordsIn;
1466: PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e;
1467: PetscMPIInt rank;
1468: PetscErrorCode ierr;
1472: DMCreate(comm, dm);
1473: DMSetType(*dm, DMPLEX);
1474: DMSetDimension(*dm, dim);
1475: DMSetCoordinateDim(*dm, dim+1);
1476: MPI_Comm_rank(PetscObjectComm((PetscObject) *dm), &rank);
1477: switch (dim) {
1478: case 2:
1479: if (simplex) {
1480: DM idm = NULL;
1481: const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI);
1482: const PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)};
1483: const PetscInt degree = 5;
1484: PetscInt s[3] = {1, 1, 1};
1485: PetscInt cone[3];
1486: PetscInt *graph, p, i, j, k;
1488: numCells = !rank ? 20 : 0;
1489: numVerts = !rank ? 12 : 0;
1490: firstVertex = numCells;
1491: /* Use icosahedron, which for a unit sphere has coordinates which are all cyclic permutations of
1493: (0, \pm 1/\phi+1, \pm \phi/\phi+1)
1495: where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
1496: length is then given by 2/\phi = 2 * 2.73606 = 5.47214.
1497: */
1498: /* Construct vertices */
1499: PetscCalloc1(numVerts * embedDim, &coordsIn);
1500: for (p = 0, i = 0; p < embedDim; ++p) {
1501: for (s[1] = -1; s[1] < 2; s[1] += 2) {
1502: for (s[2] = -1; s[2] < 2; s[2] += 2) {
1503: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim];
1504: ++i;
1505: }
1506: }
1507: }
1508: /* Construct graph */
1509: PetscCalloc1(numVerts * numVerts, &graph);
1510: for (i = 0; i < numVerts; ++i) {
1511: for (j = 0, k = 0; j < numVerts; ++j) {
1512: if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;}
1513: }
1514: if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree);
1515: }
1516: /* Build Topology */
1517: DMPlexSetChart(*dm, 0, numCells+numVerts);
1518: for (c = 0; c < numCells; c++) {
1519: DMPlexSetConeSize(*dm, c, embedDim);
1520: }
1521: DMSetUp(*dm); /* Allocate space for cones */
1522: /* Cells */
1523: for (i = 0, c = 0; i < numVerts; ++i) {
1524: for (j = 0; j < i; ++j) {
1525: for (k = 0; k < j; ++k) {
1526: if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) {
1527: cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k;
1528: /* Check orientation */
1529: {
1530: 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}}};
1531: PetscReal normal[3];
1532: PetscInt e, f;
1534: for (d = 0; d < embedDim; ++d) {
1535: normal[d] = 0.0;
1536: for (e = 0; e < embedDim; ++e) {
1537: for (f = 0; f < embedDim; ++f) {
1538: normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]);
1539: }
1540: }
1541: }
1542: if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;}
1543: }
1544: DMPlexSetCone(*dm, c++, cone);
1545: }
1546: }
1547: }
1548: }
1549: DMPlexSymmetrize(*dm);
1550: DMPlexStratify(*dm);
1551: PetscFree(graph);
1552: /* Interpolate mesh */
1553: DMPlexInterpolate(*dm, &idm);
1554: DMDestroy(dm);
1555: *dm = idm;
1556: } else {
1557: /*
1558: 12-21--13
1559: | |
1560: 25 4 24
1561: | |
1562: 12-25--9-16--8-24--13
1563: | | | |
1564: 23 5 17 0 15 3 22
1565: | | | |
1566: 10-20--6-14--7-19--11
1567: | |
1568: 20 1 19
1569: | |
1570: 10-18--11
1571: | |
1572: 23 2 22
1573: | |
1574: 12-21--13
1575: */
1576: const PetscReal dist = 1.0/PetscSqrtReal(3.0);
1577: PetscInt cone[4], ornt[4];
1579: numCells = !rank ? 6 : 0;
1580: numEdges = !rank ? 12 : 0;
1581: numVerts = !rank ? 8 : 0;
1582: firstVertex = numCells;
1583: firstEdge = numCells + numVerts;
1584: /* Build Topology */
1585: DMPlexSetChart(*dm, 0, numCells+numEdges+numVerts);
1586: for (c = 0; c < numCells; c++) {
1587: DMPlexSetConeSize(*dm, c, 4);
1588: }
1589: for (e = firstEdge; e < firstEdge+numEdges; ++e) {
1590: DMPlexSetConeSize(*dm, e, 2);
1591: }
1592: DMSetUp(*dm); /* Allocate space for cones */
1593: /* Cell 0 */
1594: cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17;
1595: DMPlexSetCone(*dm, 0, cone);
1596: ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0;
1597: DMPlexSetConeOrientation(*dm, 0, ornt);
1598: /* Cell 1 */
1599: cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20;
1600: DMPlexSetCone(*dm, 1, cone);
1601: ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0;
1602: DMPlexSetConeOrientation(*dm, 1, ornt);
1603: /* Cell 2 */
1604: cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23;
1605: DMPlexSetCone(*dm, 2, cone);
1606: ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0;
1607: DMPlexSetConeOrientation(*dm, 2, ornt);
1608: /* Cell 3 */
1609: cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15;
1610: DMPlexSetCone(*dm, 3, cone);
1611: ornt[0] = -2; ornt[1] = -2; ornt[2] = 0; ornt[3] = -2;
1612: DMPlexSetConeOrientation(*dm, 3, ornt);
1613: /* Cell 4 */
1614: cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25;
1615: DMPlexSetCone(*dm, 4, cone);
1616: ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = 0;
1617: DMPlexSetConeOrientation(*dm, 4, ornt);
1618: /* Cell 5 */
1619: cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23;
1620: DMPlexSetCone(*dm, 5, cone);
1621: ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = -2;
1622: DMPlexSetConeOrientation(*dm, 5, ornt);
1623: /* Edges */
1624: cone[0] = 6; cone[1] = 7;
1625: DMPlexSetCone(*dm, 14, cone);
1626: cone[0] = 7; cone[1] = 8;
1627: DMPlexSetCone(*dm, 15, cone);
1628: cone[0] = 8; cone[1] = 9;
1629: DMPlexSetCone(*dm, 16, cone);
1630: cone[0] = 9; cone[1] = 6;
1631: DMPlexSetCone(*dm, 17, cone);
1632: cone[0] = 10; cone[1] = 11;
1633: DMPlexSetCone(*dm, 18, cone);
1634: cone[0] = 11; cone[1] = 7;
1635: DMPlexSetCone(*dm, 19, cone);
1636: cone[0] = 6; cone[1] = 10;
1637: DMPlexSetCone(*dm, 20, cone);
1638: cone[0] = 12; cone[1] = 13;
1639: DMPlexSetCone(*dm, 21, cone);
1640: cone[0] = 13; cone[1] = 11;
1641: DMPlexSetCone(*dm, 22, cone);
1642: cone[0] = 10; cone[1] = 12;
1643: DMPlexSetCone(*dm, 23, cone);
1644: cone[0] = 13; cone[1] = 8;
1645: DMPlexSetCone(*dm, 24, cone);
1646: cone[0] = 12; cone[1] = 9;
1647: DMPlexSetCone(*dm, 25, cone);
1648: DMPlexSymmetrize(*dm);
1649: DMPlexStratify(*dm);
1650: /* Build coordinates */
1651: PetscCalloc1(numVerts * embedDim, &coordsIn);
1652: coordsIn[0*embedDim+0] = -dist; coordsIn[0*embedDim+1] = dist; coordsIn[0*embedDim+2] = -dist;
1653: coordsIn[1*embedDim+0] = dist; coordsIn[1*embedDim+1] = dist; coordsIn[1*embedDim+2] = -dist;
1654: coordsIn[2*embedDim+0] = dist; coordsIn[2*embedDim+1] = -dist; coordsIn[2*embedDim+2] = -dist;
1655: coordsIn[3*embedDim+0] = -dist; coordsIn[3*embedDim+1] = -dist; coordsIn[3*embedDim+2] = -dist;
1656: coordsIn[4*embedDim+0] = -dist; coordsIn[4*embedDim+1] = dist; coordsIn[4*embedDim+2] = dist;
1657: coordsIn[5*embedDim+0] = dist; coordsIn[5*embedDim+1] = dist; coordsIn[5*embedDim+2] = dist;
1658: coordsIn[6*embedDim+0] = -dist; coordsIn[6*embedDim+1] = -dist; coordsIn[6*embedDim+2] = dist;
1659: coordsIn[7*embedDim+0] = dist; coordsIn[7*embedDim+1] = -dist; coordsIn[7*embedDim+2] = dist;
1660: }
1661: break;
1662: case 3:
1663: if (simplex) {
1664: DM idm = NULL;
1665: const PetscReal edgeLen = 1.0/PETSC_PHI;
1666: const PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5};
1667: const PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0};
1668: const PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0};
1669: const PetscInt degree = 12;
1670: PetscInt s[4] = {1, 1, 1};
1671: 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},
1672: {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}};
1673: PetscInt cone[4];
1674: PetscInt *graph, p, i, j, k, l;
1676: numCells = !rank ? 600 : 0;
1677: numVerts = !rank ? 120 : 0;
1678: firstVertex = numCells;
1679: /* Use the 600-cell, which for a unit sphere has coordinates which are
1681: 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16
1682: (\pm 1, 0, 0, 0) all cyclic permutations 8
1683: 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96
1685: where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
1686: length is then given by 1/\phi = 2.73606.
1688: http://buzzard.pugetsound.edu/sage-practice/ch03s03.html
1689: http://mathworld.wolfram.com/600-Cell.html
1690: */
1691: /* Construct vertices */
1692: PetscCalloc1(numVerts * embedDim, &coordsIn);
1693: i = 0;
1694: for (s[0] = -1; s[0] < 2; s[0] += 2) {
1695: for (s[1] = -1; s[1] < 2; s[1] += 2) {
1696: for (s[2] = -1; s[2] < 2; s[2] += 2) {
1697: for (s[3] = -1; s[3] < 2; s[3] += 2) {
1698: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d];
1699: ++i;
1700: }
1701: }
1702: }
1703: }
1704: for (p = 0; p < embedDim; ++p) {
1705: s[1] = s[2] = s[3] = 1;
1706: for (s[0] = -1; s[0] < 2; s[0] += 2) {
1707: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim];
1708: ++i;
1709: }
1710: }
1711: for (p = 0; p < 12; ++p) {
1712: s[3] = 1;
1713: for (s[0] = -1; s[0] < 2; s[0] += 2) {
1714: for (s[1] = -1; s[1] < 2; s[1] += 2) {
1715: for (s[2] = -1; s[2] < 2; s[2] += 2) {
1716: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]];
1717: ++i;
1718: }
1719: }
1720: }
1721: }
1722: if (i != numVerts) SETERRQ2(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts);
1723: /* Construct graph */
1724: PetscCalloc1(numVerts * numVerts, &graph);
1725: for (i = 0; i < numVerts; ++i) {
1726: for (j = 0, k = 0; j < numVerts; ++j) {
1727: if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;}
1728: }
1729: if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree);
1730: }
1731: /* Build Topology */
1732: DMPlexSetChart(*dm, 0, numCells+numVerts);
1733: for (c = 0; c < numCells; c++) {
1734: DMPlexSetConeSize(*dm, c, embedDim);
1735: }
1736: DMSetUp(*dm); /* Allocate space for cones */
1737: /* Cells */
1738: for (i = 0, c = 0; i < numVerts; ++i) {
1739: for (j = 0; j < i; ++j) {
1740: for (k = 0; k < j; ++k) {
1741: for (l = 0; l < k; ++l) {
1742: if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] &&
1743: graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) {
1744: cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l;
1745: /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */
1746: {
1747: const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
1748: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}},
1749: {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}},
1750: {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}},
1752: {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}},
1753: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
1754: {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}},
1755: {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}},
1757: {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}},
1758: {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}},
1759: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
1760: {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}},
1762: {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}},
1763: {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}},
1764: {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
1765: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}};
1766: PetscReal normal[4];
1767: PetscInt e, f, g;
1769: for (d = 0; d < embedDim; ++d) {
1770: normal[d] = 0.0;
1771: for (e = 0; e < embedDim; ++e) {
1772: for (f = 0; f < embedDim; ++f) {
1773: for (g = 0; g < embedDim; ++g) {
1774: 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]);
1775: }
1776: }
1777: }
1778: }
1779: if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;}
1780: }
1781: DMPlexSetCone(*dm, c++, cone);
1782: }
1783: }
1784: }
1785: }
1786: }
1787: DMPlexSymmetrize(*dm);
1788: DMPlexStratify(*dm);
1789: PetscFree(graph);
1790: /* Interpolate mesh */
1791: DMPlexInterpolate(*dm, &idm);
1792: DMDestroy(dm);
1793: *dm = idm;
1794: break;
1795: }
1796: default: SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim);
1797: }
1798: /* Create coordinates */
1799: DMGetCoordinateSection(*dm, &coordSection);
1800: PetscSectionSetNumFields(coordSection, 1);
1801: PetscSectionSetFieldComponents(coordSection, 0, embedDim);
1802: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);
1803: for (v = firstVertex; v < firstVertex+numVerts; ++v) {
1804: PetscSectionSetDof(coordSection, v, embedDim);
1805: PetscSectionSetFieldDof(coordSection, v, 0, embedDim);
1806: }
1807: PetscSectionSetUp(coordSection);
1808: PetscSectionGetStorageSize(coordSection, &coordSize);
1809: VecCreate(PETSC_COMM_SELF, &coordinates);
1810: VecSetBlockSize(coordinates, embedDim);
1811: PetscObjectSetName((PetscObject) coordinates, "coordinates");
1812: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1813: VecSetType(coordinates,VECSTANDARD);
1814: VecGetArray(coordinates, &coords);
1815: for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];}
1816: VecRestoreArray(coordinates, &coords);
1817: DMSetCoordinatesLocal(*dm, coordinates);
1818: VecDestroy(&coordinates);
1819: PetscFree(coordsIn);
1820: return(0);
1821: }
1823: /* External function declarations here */
1824: extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling);
1825: extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat);
1826: extern PetscErrorCode DMCreateDefaultSection_Plex(DM dm);
1827: extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm);
1828: extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J);
1829: extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm);
1830: PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm);
1831: extern PetscErrorCode DMSetUp_Plex(DM dm);
1832: extern PetscErrorCode DMDestroy_Plex(DM dm);
1833: extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer);
1834: extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer);
1835: extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm);
1836: static PetscErrorCode DMInitialize_Plex(DM dm);
1838: /* Replace dm with the contents of dmNew
1839: - Share the DM_Plex structure
1840: - Share the coordinates
1841: - Share the SF
1842: */
1843: static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew)
1844: {
1845: PetscSF sf;
1846: DM coordDM, coarseDM;
1847: Vec coords;
1848: PetscBool isper;
1849: const PetscReal *maxCell, *L;
1850: const DMBoundaryType *bd;
1851: PetscErrorCode ierr;
1854: DMGetPointSF(dmNew, &sf);
1855: DMSetPointSF(dm, sf);
1856: DMGetCoordinateDM(dmNew, &coordDM);
1857: DMGetCoordinatesLocal(dmNew, &coords);
1858: DMSetCoordinateDM(dm, coordDM);
1859: DMSetCoordinatesLocal(dm, coords);
1860: DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);
1861: DMSetPeriodicity(dmNew, isper, maxCell, L, bd);
1862: DMDestroy_Plex(dm);
1863: DMInitialize_Plex(dm);
1864: dm->data = dmNew->data;
1865: ((DM_Plex *) dmNew->data)->refct++;
1866: dmNew->labels->refct++;
1867: if (!--(dm->labels->refct)) {
1868: DMLabelLink next = dm->labels->next;
1870: /* destroy the labels */
1871: while (next) {
1872: DMLabelLink tmp = next->next;
1874: DMLabelDestroy(&next->label);
1875: PetscFree(next);
1876: next = tmp;
1877: }
1878: PetscFree(dm->labels);
1879: }
1880: dm->labels = dmNew->labels;
1881: dm->depthLabel = dmNew->depthLabel;
1882: DMGetCoarseDM(dmNew,&coarseDM);
1883: DMSetCoarseDM(dm,coarseDM);
1884: return(0);
1885: }
1887: /* Swap dm with the contents of dmNew
1888: - Swap the DM_Plex structure
1889: - Swap the coordinates
1890: - Swap the point PetscSF
1891: */
1892: static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB)
1893: {
1894: DM coordDMA, coordDMB;
1895: Vec coordsA, coordsB;
1896: PetscSF sfA, sfB;
1897: void *tmp;
1898: DMLabelLinkList listTmp;
1899: DMLabel depthTmp;
1900: PetscErrorCode ierr;
1903: DMGetPointSF(dmA, &sfA);
1904: DMGetPointSF(dmB, &sfB);
1905: PetscObjectReference((PetscObject) sfA);
1906: DMSetPointSF(dmA, sfB);
1907: DMSetPointSF(dmB, sfA);
1908: PetscObjectDereference((PetscObject) sfA);
1910: DMGetCoordinateDM(dmA, &coordDMA);
1911: DMGetCoordinateDM(dmB, &coordDMB);
1912: PetscObjectReference((PetscObject) coordDMA);
1913: DMSetCoordinateDM(dmA, coordDMB);
1914: DMSetCoordinateDM(dmB, coordDMA);
1915: PetscObjectDereference((PetscObject) coordDMA);
1917: DMGetCoordinatesLocal(dmA, &coordsA);
1918: DMGetCoordinatesLocal(dmB, &coordsB);
1919: PetscObjectReference((PetscObject) coordsA);
1920: DMSetCoordinatesLocal(dmA, coordsB);
1921: DMSetCoordinatesLocal(dmB, coordsA);
1922: PetscObjectDereference((PetscObject) coordsA);
1924: tmp = dmA->data;
1925: dmA->data = dmB->data;
1926: dmB->data = tmp;
1927: listTmp = dmA->labels;
1928: dmA->labels = dmB->labels;
1929: dmB->labels = listTmp;
1930: depthTmp = dmA->depthLabel;
1931: dmA->depthLabel = dmB->depthLabel;
1932: dmB->depthLabel = depthTmp;
1933: return(0);
1934: }
1936: PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm)
1937: {
1938: DM_Plex *mesh = (DM_Plex*) dm->data;
1942: /* Handle viewing */
1943: PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMView", PETSC_FALSE, &mesh->printSetValues, NULL);
1944: PetscOptionsInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMView", 0, &mesh->printFEM, NULL);
1945: PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMView", mesh->printTol, &mesh->printTol, NULL);
1946: /* Point Location */
1947: PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMView", PETSC_FALSE, &mesh->useHashLocation, NULL);
1948: /* Generation and remeshing */
1949: PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMView", PETSC_FALSE, &mesh->remeshBd, NULL);
1950: /* Projection behavior */
1951: PetscOptionsInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL);
1952: PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);
1954: PetscPartitionerSetFromOptions(mesh->partitioner);
1955: return(0);
1956: }
1958: static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm)
1959: {
1960: PetscInt refine = 0, coarsen = 0, r;
1961: PetscBool isHierarchy;
1966: PetscOptionsHead(PetscOptionsObject,"DMPlex Options");
1967: /* Handle DMPlex refinement */
1968: PetscOptionsInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL);
1969: PetscOptionsInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy);
1970: if (refine) {DMPlexSetRefinementUniform(dm, PETSC_TRUE);}
1971: if (refine && isHierarchy) {
1972: DM *dms, coarseDM;
1974: DMGetCoarseDM(dm, &coarseDM);
1975: PetscObjectReference((PetscObject)coarseDM);
1976: PetscMalloc1(refine,&dms);
1977: DMRefineHierarchy(dm, refine, dms);
1978: /* Total hack since we do not pass in a pointer */
1979: DMPlexSwap_Static(dm, dms[refine-1]);
1980: if (refine == 1) {
1981: DMSetCoarseDM(dm, dms[0]);
1982: DMPlexSetRegularRefinement(dm, PETSC_TRUE);
1983: } else {
1984: DMSetCoarseDM(dm, dms[refine-2]);
1985: DMPlexSetRegularRefinement(dm, PETSC_TRUE);
1986: DMSetCoarseDM(dms[0], dms[refine-1]);
1987: DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);
1988: }
1989: DMSetCoarseDM(dms[refine-1], coarseDM);
1990: PetscObjectDereference((PetscObject)coarseDM);
1991: /* Free DMs */
1992: for (r = 0; r < refine; ++r) {
1993: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);
1994: DMDestroy(&dms[r]);
1995: }
1996: PetscFree(dms);
1997: } else {
1998: for (r = 0; r < refine; ++r) {
1999: DM refinedMesh;
2001: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2002: DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);
2003: /* Total hack since we do not pass in a pointer */
2004: DMPlexReplace_Static(dm, refinedMesh);
2005: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2006: DMDestroy(&refinedMesh);
2007: }
2008: }
2009: /* Handle DMPlex coarsening */
2010: PetscOptionsInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL);
2011: PetscOptionsInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy);
2012: if (coarsen && isHierarchy) {
2013: DM *dms;
2015: PetscMalloc1(coarsen, &dms);
2016: DMCoarsenHierarchy(dm, coarsen, dms);
2017: /* Free DMs */
2018: for (r = 0; r < coarsen; ++r) {
2019: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);
2020: DMDestroy(&dms[r]);
2021: }
2022: PetscFree(dms);
2023: } else {
2024: for (r = 0; r < coarsen; ++r) {
2025: DM coarseMesh;
2027: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2028: DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);
2029: /* Total hack since we do not pass in a pointer */
2030: DMPlexReplace_Static(dm, coarseMesh);
2031: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2032: DMDestroy(&coarseMesh);
2033: }
2034: }
2035: /* Handle */
2036: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2037: PetscOptionsTail();
2038: return(0);
2039: }
2041: static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec)
2042: {
2046: DMCreateGlobalVector_Section_Private(dm,vec);
2047: /* VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM); */
2048: VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);
2049: VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);
2050: VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);
2051: VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);
2052: return(0);
2053: }
2055: static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec)
2056: {
2060: DMCreateLocalVector_Section_Private(dm,vec);
2061: VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);
2062: VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);
2063: return(0);
2064: }
2066: static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd)
2067: {
2068: PetscInt depth, d;
2072: DMPlexGetDepth(dm, &depth);
2073: if (depth == 1) {
2074: DMGetDimension(dm, &d);
2075: if (dim == 0) {DMPlexGetDepthStratum(dm, dim, pStart, pEnd);}
2076: else if (dim == d) {DMPlexGetDepthStratum(dm, 1, pStart, pEnd);}
2077: else {*pStart = 0; *pEnd = 0;}
2078: } else {
2079: DMPlexGetDepthStratum(dm, dim, pStart, pEnd);
2080: }
2081: return(0);
2082: }
2084: static PetscErrorCode DMGetNeighors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[])
2085: {
2086: PetscSF sf;
2090: DMGetPointSF(dm, &sf);
2091: PetscSFGetRanks(sf, nranks, ranks, NULL, NULL, NULL);
2092: return(0);
2093: }
2095: static PetscErrorCode DMInitialize_Plex(DM dm)
2096: {
2100: dm->ops->view = DMView_Plex;
2101: dm->ops->load = DMLoad_Plex;
2102: dm->ops->setfromoptions = DMSetFromOptions_Plex;
2103: dm->ops->clone = DMClone_Plex;
2104: dm->ops->setup = DMSetUp_Plex;
2105: dm->ops->createdefaultsection = DMCreateDefaultSection_Plex;
2106: dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex;
2107: dm->ops->createglobalvector = DMCreateGlobalVector_Plex;
2108: dm->ops->createlocalvector = DMCreateLocalVector_Plex;
2109: dm->ops->getlocaltoglobalmapping = NULL;
2110: dm->ops->createfieldis = NULL;
2111: dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex;
2112: dm->ops->getcoloring = NULL;
2113: dm->ops->creatematrix = DMCreateMatrix_Plex;
2114: dm->ops->createinterpolation = DMCreateInterpolation_Plex;
2115: dm->ops->getaggregates = NULL;
2116: dm->ops->getinjection = DMCreateInjection_Plex;
2117: dm->ops->refine = DMRefine_Plex;
2118: dm->ops->coarsen = DMCoarsen_Plex;
2119: dm->ops->refinehierarchy = DMRefineHierarchy_Plex;
2120: dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex;
2121: dm->ops->adaptlabel = DMAdaptLabel_Plex;
2122: dm->ops->adaptmetric = DMAdaptMetric_Plex;
2123: dm->ops->globaltolocalbegin = NULL;
2124: dm->ops->globaltolocalend = NULL;
2125: dm->ops->localtoglobalbegin = NULL;
2126: dm->ops->localtoglobalend = NULL;
2127: dm->ops->destroy = DMDestroy_Plex;
2128: dm->ops->createsubdm = DMCreateSubDM_Plex;
2129: dm->ops->getdimpoints = DMGetDimPoints_Plex;
2130: dm->ops->locatepoints = DMLocatePoints_Plex;
2131: dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex;
2132: dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex;
2133: dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex;
2134: dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex;
2135: dm->ops->computel2diff = DMComputeL2Diff_Plex;
2136: dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex;
2137: dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex;
2138: dm->ops->getneighbors = DMGetNeighors_Plex;
2139: PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);
2140: PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);
2141: return(0);
2142: }
2144: PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm)
2145: {
2146: DM_Plex *mesh = (DM_Plex *) dm->data;
2150: mesh->refct++;
2151: (*newdm)->data = mesh;
2152: PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);
2153: DMInitialize_Plex(*newdm);
2154: return(0);
2155: }
2157: /*MC
2158: DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram.
2159: In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is
2160: specified by a PetscSection object. Ownership in the global representation is determined by
2161: ownership of the underlying DMPlex points. This is specified by another PetscSection object.
2163: Level: intermediate
2165: .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType()
2166: M*/
2168: PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm)
2169: {
2170: DM_Plex *mesh;
2171: PetscInt unit, d;
2176: PetscNewLog(dm,&mesh);
2177: dm->dim = 0;
2178: dm->data = mesh;
2180: mesh->refct = 1;
2181: PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);
2182: mesh->maxConeSize = 0;
2183: mesh->cones = NULL;
2184: mesh->coneOrientations = NULL;
2185: PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);
2186: mesh->maxSupportSize = 0;
2187: mesh->supports = NULL;
2188: mesh->refinementUniform = PETSC_TRUE;
2189: mesh->refinementLimit = -1.0;
2191: mesh->facesTmp = NULL;
2193: mesh->tetgenOpts = NULL;
2194: mesh->triangleOpts = NULL;
2195: PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);
2196: mesh->remeshBd = PETSC_FALSE;
2198: mesh->subpointMap = NULL;
2200: for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0;
2202: mesh->regularRefinement = PETSC_FALSE;
2203: mesh->depthState = -1;
2204: mesh->globalVertexNumbers = NULL;
2205: mesh->globalCellNumbers = NULL;
2206: mesh->anchorSection = NULL;
2207: mesh->anchorIS = NULL;
2208: mesh->createanchors = NULL;
2209: mesh->computeanchormatrix = NULL;
2210: mesh->parentSection = NULL;
2211: mesh->parents = NULL;
2212: mesh->childIDs = NULL;
2213: mesh->childSection = NULL;
2214: mesh->children = NULL;
2215: mesh->referenceTree = NULL;
2216: mesh->getchildsymmetry = NULL;
2217: for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE;
2218: mesh->vtkCellHeight = 0;
2219: mesh->useCone = PETSC_FALSE;
2220: mesh->useClosure = PETSC_TRUE;
2221: mesh->useAnchors = PETSC_FALSE;
2223: mesh->maxProjectionHeight = 0;
2225: mesh->printSetValues = PETSC_FALSE;
2226: mesh->printFEM = 0;
2227: mesh->printTol = 1.0e-10;
2229: DMInitialize_Plex(dm);
2230: return(0);
2231: }
2233: /*@
2234: DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram.
2236: Collective on MPI_Comm
2238: Input Parameter:
2239: . comm - The communicator for the DMPlex object
2241: Output Parameter:
2242: . mesh - The DMPlex object
2244: Level: beginner
2246: .keywords: DMPlex, create
2247: @*/
2248: PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh)
2249: {
2254: DMCreate(comm, mesh);
2255: DMSetType(*mesh, DMPLEX);
2256: return(0);
2257: }
2259: /*
2260: This takes as input the common mesh generator output, a list of the vertices for each cell, but vertex numbers are global and an SF is built for them
2261: */
2262: static PetscErrorCode DMPlexBuildFromCellList_Parallel_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscSF *sfVert)
2263: {
2264: PetscSF sfPoint;
2265: PetscLayout vLayout;
2266: PetscHashI vhash;
2267: PetscSFNode *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex;
2268: const PetscInt *vrange;
2269: PetscInt numVerticesAdj, off, *verticesAdj, numVerticesGhost = 0, *localVertex, *cone, c, p, v, g;
2270: PETSC_UNUSED PetscHashIIter ret, iter;
2271: PetscMPIInt rank, size;
2272: PetscErrorCode ierr;
2275: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
2276: MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);
2277: /* Partition vertices */
2278: PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);
2279: PetscLayoutSetLocalSize(vLayout, numVertices);
2280: PetscLayoutSetBlockSize(vLayout, 1);
2281: PetscLayoutSetUp(vLayout);
2282: PetscLayoutGetRanges(vLayout, &vrange);
2283: /* Count vertices and map them to procs */
2284: PetscHashICreate(vhash);
2285: for (c = 0; c < numCells; ++c) {
2286: for (p = 0; p < numCorners; ++p) {
2287: PetscHashIPut(vhash, cells[c*numCorners+p], ret, iter);
2288: }
2289: }
2290: PetscHashISize(vhash, numVerticesAdj);
2291: PetscMalloc1(numVerticesAdj, &verticesAdj);
2292: off = 0; PetscHashIGetKeys(vhash, &off, verticesAdj);
2293: if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj);
2294: PetscSortInt(numVerticesAdj, verticesAdj);
2295: PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);
2296: for (v = 0; v < numVerticesAdj; ++v) {
2297: const PetscInt gv = verticesAdj[v];
2298: PetscInt vrank;
2300: PetscFindInt(gv, size+1, vrange, &vrank);
2301: vrank = vrank < 0 ? -(vrank+2) : vrank;
2302: remoteVerticesAdj[v].index = gv - vrange[vrank];
2303: remoteVerticesAdj[v].rank = vrank;
2304: }
2305: /* Create cones */
2306: DMPlexSetChart(dm, 0, numCells+numVerticesAdj);
2307: for (c = 0; c < numCells; ++c) {DMPlexSetConeSize(dm, c, numCorners);}
2308: DMSetUp(dm);
2309: DMGetWorkArray(dm, numCorners, PETSC_INT, &cone);
2310: for (c = 0; c < numCells; ++c) {
2311: for (p = 0; p < numCorners; ++p) {
2312: const PetscInt gv = cells[c*numCorners+p];
2313: PetscInt lv;
2315: PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);
2316: if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv);
2317: cone[p] = lv+numCells;
2318: }
2319: DMPlexSetCone(dm, c, cone);
2320: }
2321: DMRestoreWorkArray(dm, numCorners, PETSC_INT, &cone);
2322: /* Create SF for vertices */
2323: PetscSFCreate(PetscObjectComm((PetscObject)dm), sfVert);
2324: PetscObjectSetName((PetscObject) *sfVert, "Vertex Ownership SF");
2325: PetscSFSetFromOptions(*sfVert);
2326: PetscSFSetGraph(*sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);
2327: PetscFree(verticesAdj);
2328: /* Build pointSF */
2329: PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);
2330: for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;}
2331: for (v = 0; v < numVertices; ++v) {vertexOwner[v].index = -1; vertexOwner[v].rank = -1;}
2332: PetscSFReduceBegin(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);
2333: PetscSFReduceEnd(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);
2334: for (v = 0; v < numVertices; ++v) if (vertexOwner[v].rank < 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Global vertex %d on rank %d was unclaimed", v + vrange[rank], rank);
2335: PetscSFBcastBegin(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);
2336: PetscSFBcastEnd(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);
2337: for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost;
2338: PetscMalloc1(numVerticesGhost, &localVertex);
2339: PetscMalloc1(numVerticesGhost, &remoteVertex);
2340: for (v = 0, g = 0; v < numVerticesAdj; ++v) {
2341: if (vertexLocal[v].rank != rank) {
2342: localVertex[g] = v+numCells;
2343: remoteVertex[g].index = vertexLocal[v].index;
2344: remoteVertex[g].rank = vertexLocal[v].rank;
2345: ++g;
2346: }
2347: }
2348: PetscFree2(vertexLocal, vertexOwner);
2349: if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost);
2350: DMGetPointSF(dm, &sfPoint);
2351: PetscObjectSetName((PetscObject) sfPoint, "point SF");
2352: PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);
2353: PetscLayoutDestroy(&vLayout);
2354: PetscHashIDestroy(vhash);
2355: /* Fill in the rest of the topology structure */
2356: DMPlexSymmetrize(dm);
2357: DMPlexStratify(dm);
2358: return(0);
2359: }
2361: /*
2362: This takes as input the coordinates for each owned vertex
2363: */
2364: static PetscErrorCode DMPlexBuildCoordinates_Parallel_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numV, PetscSF sfVert, const PetscReal vertexCoords[])
2365: {
2366: PetscSection coordSection;
2367: Vec coordinates;
2368: PetscScalar *coords;
2369: PetscInt numVertices, numVerticesAdj, coordSize, v;
2373: DMSetCoordinateDim(dm, spaceDim);
2374: PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);
2375: DMGetCoordinateSection(dm, &coordSection);
2376: PetscSectionSetNumFields(coordSection, 1);
2377: PetscSectionSetFieldComponents(coordSection, 0, spaceDim);
2378: PetscSectionSetChart(coordSection, numCells, numCells + numVerticesAdj);
2379: for (v = numCells; v < numCells+numVerticesAdj; ++v) {
2380: PetscSectionSetDof(coordSection, v, spaceDim);
2381: PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);
2382: }
2383: PetscSectionSetUp(coordSection);
2384: PetscSectionGetStorageSize(coordSection, &coordSize);
2385: VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);
2386: VecSetBlockSize(coordinates, spaceDim);
2387: PetscObjectSetName((PetscObject) coordinates, "coordinates");
2388: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
2389: VecSetType(coordinates,VECSTANDARD);
2390: VecGetArray(coordinates, &coords);
2391: {
2392: MPI_Datatype coordtype;
2394: /* Need a temp buffer for coords if we have complex/single */
2395: MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);
2396: MPI_Type_commit(&coordtype);
2397: #if defined(PETSC_USE_COMPLEX)
2398: {
2399: PetscScalar *svertexCoords;
2400: PetscInt i;
2401: PetscMalloc1(numV*spaceDim,&svertexCoords);
2402: for (i=0; i<numV*spaceDim; i++) svertexCoords[i] = vertexCoords[i];
2403: PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords);
2404: PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords);
2405: PetscFree(svertexCoords);
2406: }
2407: #else
2408: PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords);
2409: PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords);
2410: #endif
2411: MPI_Type_free(&coordtype);
2412: }
2413: VecRestoreArray(coordinates, &coords);
2414: DMSetCoordinatesLocal(dm, coordinates);
2415: VecDestroy(&coordinates);
2416: return(0);
2417: }
2419: /*@C
2420: DMPlexCreateFromCellListParallel - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM
2422: Input Parameters:
2423: + comm - The communicator
2424: . dim - The topological dimension of the mesh
2425: . numCells - The number of cells owned by this process
2426: . numVertices - The number of vertices owned by this process
2427: . numCorners - The number of vertices for each cell
2428: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
2429: . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell
2430: . spaceDim - The spatial dimension used for coordinates
2431: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
2433: Output Parameter:
2434: + dm - The DM
2435: - vertexSF - Optional, SF describing complete vertex ownership
2437: Note: Two triangles sharing a face
2438: $
2439: $ 2
2440: $ / | \
2441: $ / | \
2442: $ / | \
2443: $ 0 0 | 1 3
2444: $ \ | /
2445: $ \ | /
2446: $ \ | /
2447: $ 1
2448: would have input
2449: $ numCells = 2, numVertices = 4
2450: $ cells = [0 1 2 1 3 2]
2451: $
2452: which would result in the DMPlex
2453: $
2454: $ 4
2455: $ / | \
2456: $ / | \
2457: $ / | \
2458: $ 2 0 | 1 5
2459: $ \ | /
2460: $ \ | /
2461: $ \ | /
2462: $ 3
2464: Level: beginner
2466: .seealso: DMPlexCreateFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate()
2467: @*/
2468: PetscErrorCode DMPlexCreateFromCellListParallel(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, PetscBool interpolate, const int cells[], PetscInt spaceDim, const PetscReal vertexCoords[], PetscSF *vertexSF, DM *dm)
2469: {
2470: PetscSF sfVert;
2474: DMCreate(comm, dm);
2475: DMSetType(*dm, DMPLEX);
2478: DMSetDimension(*dm, dim);
2479: DMPlexBuildFromCellList_Parallel_Private(*dm, numCells, numVertices, numCorners, cells, &sfVert);
2480: if (interpolate) {
2481: DM idm = NULL;
2483: DMPlexInterpolate(*dm, &idm);
2484: DMDestroy(dm);
2485: *dm = idm;
2486: }
2487: DMPlexBuildCoordinates_Parallel_Private(*dm, spaceDim, numCells, numVertices,sfVert, vertexCoords);
2488: if (vertexSF) *vertexSF = sfVert;
2489: else {PetscSFDestroy(&sfVert);}
2490: return(0);
2491: }
2493: /*
2494: This takes as input the common mesh generator output, a list of the vertices for each cell
2495: */
2496: static PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[])
2497: {
2498: PetscInt *cone, c, p;
2502: DMPlexSetChart(dm, 0, numCells+numVertices);
2503: for (c = 0; c < numCells; ++c) {
2504: DMPlexSetConeSize(dm, c, numCorners);
2505: }
2506: DMSetUp(dm);
2507: DMGetWorkArray(dm, numCorners, PETSC_INT, &cone);
2508: for (c = 0; c < numCells; ++c) {
2509: for (p = 0; p < numCorners; ++p) {
2510: cone[p] = cells[c*numCorners+p]+numCells;
2511: }
2512: DMPlexSetCone(dm, c, cone);
2513: }
2514: DMRestoreWorkArray(dm, numCorners, PETSC_INT, &cone);
2515: DMPlexSymmetrize(dm);
2516: DMPlexStratify(dm);
2517: return(0);
2518: }
2520: /*
2521: This takes as input the coordinates for each vertex
2522: */
2523: static PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[])
2524: {
2525: PetscSection coordSection;
2526: Vec coordinates;
2527: DM cdm;
2528: PetscScalar *coords;
2529: PetscInt v, d;
2533: DMSetCoordinateDim(dm, spaceDim);
2534: DMGetCoordinateSection(dm, &coordSection);
2535: PetscSectionSetNumFields(coordSection, 1);
2536: PetscSectionSetFieldComponents(coordSection, 0, spaceDim);
2537: PetscSectionSetChart(coordSection, numCells, numCells + numVertices);
2538: for (v = numCells; v < numCells+numVertices; ++v) {
2539: PetscSectionSetDof(coordSection, v, spaceDim);
2540: PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);
2541: }
2542: PetscSectionSetUp(coordSection);
2544: DMGetCoordinateDM(dm, &cdm);
2545: DMCreateLocalVector(cdm, &coordinates);
2546: VecSetBlockSize(coordinates, spaceDim);
2547: PetscObjectSetName((PetscObject) coordinates, "coordinates");
2548: VecGetArray(coordinates, &coords);
2549: for (v = 0; v < numVertices; ++v) {
2550: for (d = 0; d < spaceDim; ++d) {
2551: coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d];
2552: }
2553: }
2554: VecRestoreArray(coordinates, &coords);
2555: DMSetCoordinatesLocal(dm, coordinates);
2556: VecDestroy(&coordinates);
2557: return(0);
2558: }
2560: /*@C
2561: DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM
2563: Input Parameters:
2564: + comm - The communicator
2565: . dim - The topological dimension of the mesh
2566: . numCells - The number of cells
2567: . numVertices - The number of vertices
2568: . numCorners - The number of vertices for each cell
2569: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
2570: . cells - An array of numCells*numCorners numbers, the vertices for each cell
2571: . spaceDim - The spatial dimension used for coordinates
2572: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
2574: Output Parameter:
2575: . dm - The DM
2577: Note: Two triangles sharing a face
2578: $
2579: $ 2
2580: $ / | \
2581: $ / | \
2582: $ / | \
2583: $ 0 0 | 1 3
2584: $ \ | /
2585: $ \ | /
2586: $ \ | /
2587: $ 1
2588: would have input
2589: $ numCells = 2, numVertices = 4
2590: $ cells = [0 1 2 1 3 2]
2591: $
2592: which would result in the DMPlex
2593: $
2594: $ 4
2595: $ / | \
2596: $ / | \
2597: $ / | \
2598: $ 2 0 | 1 5
2599: $ \ | /
2600: $ \ | /
2601: $ \ | /
2602: $ 3
2604: Level: beginner
2606: .seealso: DMPlexCreateFromDAG(), DMPlexCreate()
2607: @*/
2608: PetscErrorCode DMPlexCreateFromCellList(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, PetscBool interpolate, const int cells[], PetscInt spaceDim, const double vertexCoords[], DM *dm)
2609: {
2613: DMCreate(comm, dm);
2614: DMSetType(*dm, DMPLEX);
2615: DMSetDimension(*dm, dim);
2616: DMPlexBuildFromCellList_Private(*dm, numCells, numVertices, numCorners, cells);
2617: if (interpolate) {
2618: DM idm = NULL;
2620: DMPlexInterpolate(*dm, &idm);
2621: DMDestroy(dm);
2622: *dm = idm;
2623: }
2624: DMPlexBuildCoordinates_Private(*dm, spaceDim, numCells, numVertices, vertexCoords);
2625: return(0);
2626: }
2628: /*@
2629: DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM
2631: Input Parameters:
2632: + dm - The empty DM object, usually from DMCreate() and DMSetDimension()
2633: . depth - The depth of the DAG
2634: . numPoints - The number of points at each depth
2635: . coneSize - The cone size of each point
2636: . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point
2637: . coneOrientations - The orientation of each cone point
2638: - vertexCoords - An array of numVertices*dim numbers, the coordinates of each vertex
2640: Output Parameter:
2641: . dm - The DM
2643: Note: Two triangles sharing a face would have input
2644: $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0]
2645: $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0]
2646: $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0]
2647: $
2648: which would result in the DMPlex
2649: $
2650: $ 4
2651: $ / | \
2652: $ / | \
2653: $ / | \
2654: $ 2 0 | 1 5
2655: $ \ | /
2656: $ \ | /
2657: $ \ | /
2658: $ 3
2659: $
2660: $ Notice that all points are numbered consecutively, unlikely DMPlexCreateFromCellList()
2662: Level: advanced
2664: .seealso: DMPlexCreateFromCellList(), DMPlexCreate()
2665: @*/
2666: PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[])
2667: {
2668: Vec coordinates;
2669: PetscSection coordSection;
2670: PetscScalar *coords;
2671: PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off;
2675: DMGetDimension(dm, &dim);
2676: DMGetCoordinateDim(dm, &dimEmbed);
2677: if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %d cannot be less than intrinsic dimension %d",dimEmbed,dim);
2678: for (d = 0; d <= depth; ++d) pEnd += numPoints[d];
2679: DMPlexSetChart(dm, pStart, pEnd);
2680: for (p = pStart; p < pEnd; ++p) {
2681: DMPlexSetConeSize(dm, p, coneSize[p-pStart]);
2682: if (firstVertex < 0 && !coneSize[p - pStart]) {
2683: firstVertex = p - pStart;
2684: }
2685: }
2686: if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %d vertices but could not find any", numPoints[0]);
2687: DMSetUp(dm); /* Allocate space for cones */
2688: for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) {
2689: DMPlexSetCone(dm, p, &cones[off]);
2690: DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);
2691: }
2692: DMPlexSymmetrize(dm);
2693: DMPlexStratify(dm);
2694: /* Build coordinates */
2695: DMGetCoordinateSection(dm, &coordSection);
2696: PetscSectionSetNumFields(coordSection, 1);
2697: PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);
2698: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);
2699: for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) {
2700: PetscSectionSetDof(coordSection, v, dimEmbed);
2701: PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);
2702: }
2703: PetscSectionSetUp(coordSection);
2704: PetscSectionGetStorageSize(coordSection, &coordSize);
2705: VecCreate(PETSC_COMM_SELF, &coordinates);
2706: PetscObjectSetName((PetscObject) coordinates, "coordinates");
2707: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
2708: VecSetBlockSize(coordinates, dimEmbed);
2709: VecSetType(coordinates,VECSTANDARD);
2710: VecGetArray(coordinates, &coords);
2711: for (v = 0; v < numPoints[0]; ++v) {
2712: PetscInt off;
2714: PetscSectionGetOffset(coordSection, v+firstVertex, &off);
2715: for (d = 0; d < dimEmbed; ++d) {
2716: coords[off+d] = vertexCoords[v*dimEmbed+d];
2717: }
2718: }
2719: VecRestoreArray(coordinates, &coords);
2720: DMSetCoordinatesLocal(dm, coordinates);
2721: VecDestroy(&coordinates);
2722: return(0);
2723: }
2725: /*@C
2726: DMPlexCreateFromFile - This takes a filename and produces a DM
2728: Input Parameters:
2729: + comm - The communicator
2730: . filename - A file name
2731: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
2733: Output Parameter:
2734: . dm - The DM
2736: Level: beginner
2738: .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellList(), DMPlexCreate()
2739: @*/
2740: PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
2741: {
2742: const char *extGmsh = ".msh";
2743: const char *extCGNS = ".cgns";
2744: const char *extExodus = ".exo";
2745: const char *extGenesis = ".gen";
2746: const char *extFluent = ".cas";
2747: const char *extHDF5 = ".h5";
2748: const char *extMed = ".med";
2749: const char *extPLY = ".ply";
2750: size_t len;
2751: PetscBool isGmsh, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY;
2752: PetscMPIInt rank;
2758: MPI_Comm_rank(comm, &rank);
2759: PetscStrlen(filename, &len);
2760: if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path");
2761: PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);
2762: PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);
2763: PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);
2764: PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);
2765: PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);
2766: PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);
2767: PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);
2768: PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);
2769: if (isGmsh) {
2770: DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);
2771: } else if (isCGNS) {
2772: DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);
2773: } else if (isExodus || isGenesis) {
2774: DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);
2775: } else if (isFluent) {
2776: DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);
2777: } else if (isHDF5) {
2778: PetscViewer viewer;
2780: PetscViewerCreate(comm, &viewer);
2781: PetscViewerSetType(viewer, PETSCVIEWERHDF5);
2782: PetscViewerFileSetMode(viewer, FILE_MODE_READ);
2783: PetscViewerFileSetName(viewer, filename);
2784: DMCreate(comm, dm);
2785: DMSetType(*dm, DMPLEX);
2786: DMLoad(*dm, viewer);
2787: PetscViewerDestroy(&viewer);
2788: } else if (isMed) {
2789: DMPlexCreateMedFromFile(comm, filename, interpolate, dm);
2790: } else if (isPLY) {
2791: DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);
2792: } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename);
2793: return(0);
2794: }
2796: /*@
2797: DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell
2799: Collective on comm
2801: Input Parameters:
2802: + comm - The communicator
2803: . dim - The spatial dimension
2804: - simplex - Flag for simplex, otherwise use a tensor-product cell
2806: Output Parameter:
2807: . refdm - The reference cell
2809: Level: intermediate
2811: .keywords: reference cell
2812: .seealso:
2813: @*/
2814: PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm)
2815: {
2816: DM rdm;
2817: Vec coords;
2821: DMCreate(comm, &rdm);
2822: DMSetType(rdm, DMPLEX);
2823: DMSetDimension(rdm, dim);
2824: switch (dim) {
2825: case 0:
2826: {
2827: PetscInt numPoints[1] = {1};
2828: PetscInt coneSize[1] = {0};
2829: PetscInt cones[1] = {0};
2830: PetscInt coneOrientations[1] = {0};
2831: PetscScalar vertexCoords[1] = {0.0};
2833: DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);
2834: }
2835: break;
2836: case 1:
2837: {
2838: PetscInt numPoints[2] = {2, 1};
2839: PetscInt coneSize[3] = {2, 0, 0};
2840: PetscInt cones[2] = {1, 2};
2841: PetscInt coneOrientations[2] = {0, 0};
2842: PetscScalar vertexCoords[2] = {-1.0, 1.0};
2844: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
2845: }
2846: break;
2847: case 2:
2848: if (simplex) {
2849: PetscInt numPoints[2] = {3, 1};
2850: PetscInt coneSize[4] = {3, 0, 0, 0};
2851: PetscInt cones[3] = {1, 2, 3};
2852: PetscInt coneOrientations[3] = {0, 0, 0};
2853: PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0};
2855: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
2856: } else {
2857: PetscInt numPoints[2] = {4, 1};
2858: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
2859: PetscInt cones[4] = {1, 2, 3, 4};
2860: PetscInt coneOrientations[4] = {0, 0, 0, 0};
2861: PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0};
2863: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
2864: }
2865: break;
2866: case 3:
2867: if (simplex) {
2868: PetscInt numPoints[2] = {4, 1};
2869: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
2870: PetscInt cones[4] = {1, 3, 2, 4};
2871: PetscInt coneOrientations[4] = {0, 0, 0, 0};
2872: 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};
2874: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
2875: } else {
2876: PetscInt numPoints[2] = {8, 1};
2877: PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0};
2878: PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8};
2879: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
2880: 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,
2881: -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0};
2883: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
2884: }
2885: break;
2886: default:
2887: SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %d", dim);
2888: }
2889: *refdm = NULL;
2890: DMPlexInterpolate(rdm, refdm);
2891: if (rdm->coordinateDM) {
2892: DM ncdm;
2893: PetscSection cs;
2894: PetscInt pEnd = -1;
2896: DMGetDefaultSection(rdm->coordinateDM, &cs);
2897: if (cs) {PetscSectionGetChart(cs, NULL, &pEnd);}
2898: if (pEnd >= 0) {
2899: DMClone(rdm->coordinateDM, &ncdm);
2900: DMSetDefaultSection(ncdm, cs);
2901: DMSetCoordinateDM(*refdm, ncdm);
2902: DMDestroy(&ncdm);
2903: }
2904: }
2905: DMGetCoordinatesLocal(rdm, &coords);
2906: if (coords) {
2907: DMSetCoordinatesLocal(*refdm, coords);
2908: } else {
2909: DMGetCoordinates(rdm, &coords);
2910: if (coords) {DMSetCoordinates(*refdm, coords);}
2911: }
2912: DMDestroy(&rdm);
2913: return(0);
2914: }