Actual source code: plexcreate.c
petsc-3.9.4 2018-09-11
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;
120: DMPlexInterpolate(*newdm, &idm);
121: DMDestroy(newdm);
122: *newdm = idm;
123: }
124: {
125: DM refinedMesh = NULL;
126: DM distributedMesh = NULL;
128: /* Distribute mesh over processes */
129: DMPlexDistribute(*newdm, 0, NULL, &distributedMesh);
130: if (distributedMesh) {
131: DMDestroy(newdm);
132: *newdm = distributedMesh;
133: }
134: if (refinementUniform) {
135: DMPlexSetRefinementUniform(*newdm, refinementUniform);
136: DMRefine(*newdm, comm, &refinedMesh);
137: if (refinedMesh) {
138: DMDestroy(newdm);
139: *newdm = refinedMesh;
140: }
141: }
142: }
143: return(0);
144: }
146: /*@
147: DMPlexCreateSquareBoundary - Creates a 1D mesh the is the boundary of a square lattice.
149: Collective on MPI_Comm
151: Input Parameters:
152: + comm - The communicator for the DM object
153: . lower - The lower left corner coordinates
154: . upper - The upper right corner coordinates
155: - edges - The number of cells in each direction
157: Output Parameter:
158: . dm - The DM object
160: Note: Here is the numbering returned for 2 cells in each direction:
161: $ 18--5-17--4--16
162: $ | | |
163: $ 6 10 3
164: $ | | |
165: $ 19-11-20--9--15
166: $ | | |
167: $ 7 8 2
168: $ | | |
169: $ 12--0-13--1--14
171: Level: beginner
173: .keywords: DM, create
174: .seealso: DMPlexCreateBoxMesh(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate()
175: @*/
176: PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
177: {
178: const PetscInt numVertices = (edges[0]+1)*(edges[1]+1);
179: const PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1];
180: PetscInt markerTop = 1;
181: PetscInt markerBottom = 1;
182: PetscInt markerRight = 1;
183: PetscInt markerLeft = 1;
184: PetscBool markerSeparate = PETSC_FALSE;
185: Vec coordinates;
186: PetscSection coordSection;
187: PetscScalar *coords;
188: PetscInt coordSize;
189: PetscMPIInt rank;
190: PetscInt v, vx, vy;
194: PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);
195: if (markerSeparate) {
196: markerTop = 3;
197: markerBottom = 1;
198: markerRight = 2;
199: markerLeft = 4;
200: }
201: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
202: if (!rank) {
203: PetscInt e, ex, ey;
205: DMPlexSetChart(dm, 0, numEdges+numVertices);
206: for (e = 0; e < numEdges; ++e) {
207: DMPlexSetConeSize(dm, e, 2);
208: }
209: DMSetUp(dm); /* Allocate space for cones */
210: for (vx = 0; vx <= edges[0]; vx++) {
211: for (ey = 0; ey < edges[1]; ey++) {
212: PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1);
213: PetscInt vertex = ey*(edges[0]+1) + vx + numEdges;
214: PetscInt cone[2];
216: cone[0] = vertex; cone[1] = vertex+edges[0]+1;
217: DMPlexSetCone(dm, edge, cone);
218: if (vx == edges[0]) {
219: DMSetLabelValue(dm, "marker", edge, markerRight);
220: DMSetLabelValue(dm, "marker", cone[0], markerRight);
221: if (ey == edges[1]-1) {
222: DMSetLabelValue(dm, "marker", cone[1], markerRight);
223: DMSetLabelValue(dm, "Face Sets", cone[1], markerRight);
224: }
225: } else if (vx == 0) {
226: DMSetLabelValue(dm, "marker", edge, markerLeft);
227: DMSetLabelValue(dm, "marker", cone[0], markerLeft);
228: if (ey == edges[1]-1) {
229: DMSetLabelValue(dm, "marker", cone[1], markerLeft);
230: DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft);
231: }
232: }
233: }
234: }
235: for (vy = 0; vy <= edges[1]; vy++) {
236: for (ex = 0; ex < edges[0]; ex++) {
237: PetscInt edge = vy*edges[0] + ex;
238: PetscInt vertex = vy*(edges[0]+1) + ex + numEdges;
239: PetscInt cone[2];
241: cone[0] = vertex; cone[1] = vertex+1;
242: DMPlexSetCone(dm, edge, cone);
243: if (vy == edges[1]) {
244: DMSetLabelValue(dm, "marker", edge, markerTop);
245: DMSetLabelValue(dm, "marker", cone[0], markerTop);
246: if (ex == edges[0]-1) {
247: DMSetLabelValue(dm, "marker", cone[1], markerTop);
248: DMSetLabelValue(dm, "Face Sets", cone[1], markerTop);
249: }
250: } else if (vy == 0) {
251: DMSetLabelValue(dm, "marker", edge, markerBottom);
252: DMSetLabelValue(dm, "marker", cone[0], markerBottom);
253: if (ex == edges[0]-1) {
254: DMSetLabelValue(dm, "marker", cone[1], markerBottom);
255: DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom);
256: }
257: }
258: }
259: }
260: }
261: DMPlexSymmetrize(dm);
262: DMPlexStratify(dm);
263: /* Build coordinates */
264: DMSetCoordinateDim(dm, 2);
265: DMGetCoordinateSection(dm, &coordSection);
266: PetscSectionSetNumFields(coordSection, 1);
267: PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);
268: PetscSectionSetFieldComponents(coordSection, 0, 2);
269: for (v = numEdges; v < numEdges+numVertices; ++v) {
270: PetscSectionSetDof(coordSection, v, 2);
271: PetscSectionSetFieldDof(coordSection, v, 0, 2);
272: }
273: PetscSectionSetUp(coordSection);
274: PetscSectionGetStorageSize(coordSection, &coordSize);
275: VecCreate(PETSC_COMM_SELF, &coordinates);
276: PetscObjectSetName((PetscObject) coordinates, "coordinates");
277: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
278: VecSetBlockSize(coordinates, 2);
279: VecSetType(coordinates,VECSTANDARD);
280: VecGetArray(coordinates, &coords);
281: for (vy = 0; vy <= edges[1]; ++vy) {
282: for (vx = 0; vx <= edges[0]; ++vx) {
283: coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx;
284: coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy;
285: }
286: }
287: VecRestoreArray(coordinates, &coords);
288: DMSetCoordinatesLocal(dm, coordinates);
289: VecDestroy(&coordinates);
290: return(0);
291: }
293: /*@
294: DMPlexCreateCubeBoundary - Creates a 2D mesh that is the boundary of a cubic lattice.
296: Collective on MPI_Comm
298: Input Parameters:
299: + comm - The communicator for the DM object
300: . lower - The lower left front corner coordinates
301: . upper - The upper right back corner coordinates
302: - edges - The number of cells in each direction
304: Output Parameter:
305: . dm - The DM object
307: Level: beginner
309: .keywords: DM, create
310: .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMSetType(), DMCreate()
311: @*/
312: PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[])
313: {
314: PetscInt vertices[3], numVertices;
315: PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2];
316: Vec coordinates;
317: PetscSection coordSection;
318: PetscScalar *coords;
319: PetscInt coordSize;
320: PetscMPIInt rank;
321: PetscInt v, vx, vy, vz;
322: PetscInt voffset, iface=0, cone[4];
326: 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");
327: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
328: vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1;
329: numVertices = vertices[0]*vertices[1]*vertices[2];
330: if (!rank) {
331: PetscInt f;
333: DMPlexSetChart(dm, 0, numFaces+numVertices);
334: for (f = 0; f < numFaces; ++f) {
335: DMPlexSetConeSize(dm, f, 4);
336: }
337: DMSetUp(dm); /* Allocate space for cones */
338: for (v = 0; v < numFaces+numVertices; ++v) {
339: DMSetLabelValue(dm, "marker", v, 1);
340: }
342: /* Side 0 (Top) */
343: for (vy = 0; vy < faces[1]; vy++) {
344: for (vx = 0; vx < faces[0]; vx++) {
345: voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx;
346: cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0];
347: DMPlexSetCone(dm, iface, cone);
348: iface++;
349: }
350: }
352: /* Side 1 (Bottom) */
353: for (vy = 0; vy < faces[1]; vy++) {
354: for (vx = 0; vx < faces[0]; vx++) {
355: voffset = numFaces + vy*(faces[0]+1) + vx;
356: cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1;
357: DMPlexSetCone(dm, iface, cone);
358: iface++;
359: }
360: }
362: /* Side 2 (Front) */
363: for (vz = 0; vz < faces[2]; vz++) {
364: for (vx = 0; vx < faces[0]; vx++) {
365: voffset = numFaces + vz*vertices[0]*vertices[1] + vx;
366: cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1];
367: DMPlexSetCone(dm, iface, cone);
368: iface++;
369: }
370: }
372: /* Side 3 (Back) */
373: for (vz = 0; vz < faces[2]; vz++) {
374: for (vx = 0; vx < faces[0]; vx++) {
375: voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx;
376: cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1;
377: cone[2] = voffset+1; cone[3] = voffset;
378: DMPlexSetCone(dm, iface, cone);
379: iface++;
380: }
381: }
383: /* Side 4 (Left) */
384: for (vz = 0; vz < faces[2]; vz++) {
385: for (vy = 0; vy < faces[1]; vy++) {
386: voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0];
387: cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1];
388: cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0];
389: DMPlexSetCone(dm, iface, cone);
390: iface++;
391: }
392: }
394: /* Side 5 (Right) */
395: for (vz = 0; vz < faces[2]; vz++) {
396: for (vy = 0; vy < faces[1]; vy++) {
397: voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + faces[0];
398: cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset;
399: cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0];
400: DMPlexSetCone(dm, iface, cone);
401: iface++;
402: }
403: }
404: }
405: DMPlexSymmetrize(dm);
406: DMPlexStratify(dm);
407: /* Build coordinates */
408: DMSetCoordinateDim(dm, 3);
409: DMGetCoordinateSection(dm, &coordSection);
410: PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);
411: for (v = numFaces; v < numFaces+numVertices; ++v) {
412: PetscSectionSetDof(coordSection, v, 3);
413: }
414: PetscSectionSetUp(coordSection);
415: PetscSectionGetStorageSize(coordSection, &coordSize);
416: VecCreate(PETSC_COMM_SELF, &coordinates);
417: PetscObjectSetName((PetscObject) coordinates, "coordinates");
418: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
419: VecSetBlockSize(coordinates, 3);
420: VecSetType(coordinates,VECSTANDARD);
421: VecGetArray(coordinates, &coords);
422: for (vz = 0; vz <= faces[2]; ++vz) {
423: for (vy = 0; vy <= faces[1]; ++vy) {
424: for (vx = 0; vx <= faces[0]; ++vx) {
425: coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx;
426: coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy;
427: coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz;
428: }
429: }
430: }
431: VecRestoreArray(coordinates, &coords);
432: DMSetCoordinatesLocal(dm, coordinates);
433: VecDestroy(&coordinates);
434: return(0);
435: }
437: static PetscErrorCode DMPlexCreateLineMesh_Internal(MPI_Comm comm,PetscInt segments,PetscReal lower,PetscReal upper,DMBoundaryType bd,DM *dm)
438: {
439: PetscInt i,fStart,fEnd,numCells = 0,numVerts = 0;
440: PetscInt numPoints[2],*coneSize,*cones,*coneOrientations;
441: PetscScalar *vertexCoords;
442: PetscReal L,maxCell;
443: PetscBool markerSeparate = PETSC_FALSE;
444: PetscInt markerLeft = 1, faceMarkerLeft = 1;
445: PetscInt markerRight = 1, faceMarkerRight = 2;
446: PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE;
447: PetscMPIInt rank;
453: DMCreate(comm,dm);
454: DMSetType(*dm,DMPLEX);
455: DMSetDimension(*dm,1);
456: DMCreateLabel(*dm,"marker");
457: DMCreateLabel(*dm,"Face Sets");
459: MPI_Comm_rank(comm,&rank);
460: if (!rank) numCells = segments;
461: if (!rank) numVerts = segments + (wrap ? 0 : 1);
463: numPoints[0] = numVerts ; numPoints[1] = numCells;
464: PetscMalloc4(numCells+numVerts,&coneSize,numCells*2,&cones,numCells+numVerts,&coneOrientations,numVerts,&vertexCoords);
465: PetscMemzero(coneOrientations,(numCells+numVerts)*sizeof(PetscInt));
466: for (i = 0; i < numCells; ++i) { coneSize[i] = 2; }
467: for (i = 0; i < numVerts; ++i) { coneSize[numCells+i] = 0; }
468: for (i = 0; i < numCells; ++i) { cones[2*i] = numCells + i%numVerts; cones[2*i+1] = numCells + (i+1)%numVerts; }
469: for (i = 0; i < numVerts; ++i) { vertexCoords[i] = lower + (upper-lower)*((PetscReal)i/(PetscReal)numCells); }
470: DMPlexCreateFromDAG(*dm,1,numPoints,coneSize,cones,coneOrientations,vertexCoords);
471: PetscFree4(coneSize,cones,coneOrientations,vertexCoords);
473: PetscOptionsGetBool(((PetscObject)*dm)->options,((PetscObject)*dm)->prefix,"-dm_plex_separate_marker",&markerSeparate,NULL);
474: if (markerSeparate) { markerLeft = faceMarkerLeft; markerRight = faceMarkerRight;}
475: if (!wrap && !rank) {
476: DMPlexGetHeightStratum(*dm,1,&fStart,&fEnd);
477: DMSetLabelValue(*dm,"marker",fStart,markerLeft);
478: DMSetLabelValue(*dm,"marker",fEnd-1,markerRight);
479: DMSetLabelValue(*dm,"Face Sets",fStart,faceMarkerLeft);
480: DMSetLabelValue(*dm,"Face Sets",fEnd-1,faceMarkerRight);
481: }
482: if (wrap) {
483: L = upper - lower;
484: maxCell = (PetscReal)1.1*(L/(PetscReal)PetscMax(1,segments));
485: DMSetPeriodicity(*dm,PETSC_TRUE,&maxCell,&L,&bd);
486: }
487: return(0);
488: }
490: static PetscErrorCode DMPlexCreateBoxMesh_Simplex_Internal(MPI_Comm comm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate, DM *dm)
491: {
492: DM boundary;
493: PetscInt i;
498: for (i = 0; i < dim; ++i) if (periodicity[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity is not supported for simplex meshes");
499: DMCreate(comm, &boundary);
501: DMSetType(boundary, DMPLEX);
502: DMSetDimension(boundary, dim-1);
503: DMSetCoordinateDim(boundary, dim);
504: switch (dim) {
505: case 2: DMPlexCreateSquareBoundary(boundary, lower, upper, faces);break;
506: case 3: DMPlexCreateCubeBoundary(boundary, lower, upper, faces);break;
507: default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim);
508: }
509: DMPlexGenerate(boundary, NULL, interpolate, dm);
510: DMDestroy(&boundary);
511: return(0);
512: }
514: static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ)
515: {
516: DMLabel cutLabel = NULL;
517: PetscInt markerTop = 1, faceMarkerTop = 1;
518: PetscInt markerBottom = 1, faceMarkerBottom = 1;
519: PetscInt markerFront = 1, faceMarkerFront = 1;
520: PetscInt markerBack = 1, faceMarkerBack = 1;
521: PetscInt markerRight = 1, faceMarkerRight = 1;
522: PetscInt markerLeft = 1, faceMarkerLeft = 1;
523: PetscInt dim;
524: PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE;
525: PetscMPIInt rank;
529: DMGetDimension(dm,&dim);
530: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
531: DMCreateLabel(dm,"marker");
532: DMCreateLabel(dm,"Face Sets");
533: PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL);
534: if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ||
535: bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ||
536: bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) {
538: if (cutMarker) {DMCreateLabel(dm, "periodic_cut"); DMGetLabel(dm, "periodic_cut", &cutLabel);}
539: }
540: switch (dim) {
541: case 2:
542: faceMarkerTop = 3;
543: faceMarkerBottom = 1;
544: faceMarkerRight = 2;
545: faceMarkerLeft = 4;
546: break;
547: case 3:
548: faceMarkerBottom = 1;
549: faceMarkerTop = 2;
550: faceMarkerFront = 3;
551: faceMarkerBack = 4;
552: faceMarkerRight = 5;
553: faceMarkerLeft = 6;
554: break;
555: default:
556: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %d not supported",dim);
557: break;
558: }
559: PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);
560: if (markerSeparate) {
561: markerBottom = faceMarkerBottom;
562: markerTop = faceMarkerTop;
563: markerFront = faceMarkerFront;
564: markerBack = faceMarkerBack;
565: markerRight = faceMarkerRight;
566: markerLeft = faceMarkerLeft;
567: }
568: {
569: const PetscInt numXEdges = !rank ? edges[0] : 0;
570: const PetscInt numYEdges = !rank ? edges[1] : 0;
571: const PetscInt numZEdges = !rank ? edges[2] : 0;
572: const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0;
573: const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0;
574: const PetscInt numZVertices = !rank ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0;
575: const PetscInt numCells = numXEdges*numYEdges*numZEdges;
576: const PetscInt numXFaces = numYEdges*numZEdges;
577: const PetscInt numYFaces = numXEdges*numZEdges;
578: const PetscInt numZFaces = numXEdges*numYEdges;
579: const PetscInt numTotXFaces = numXVertices*numXFaces;
580: const PetscInt numTotYFaces = numYVertices*numYFaces;
581: const PetscInt numTotZFaces = numZVertices*numZFaces;
582: const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces;
583: const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices;
584: const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices;
585: const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices;
586: const PetscInt numVertices = numXVertices*numYVertices*numZVertices;
587: const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges;
588: const PetscInt firstVertex = (dim == 2) ? numFaces : numCells;
589: const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices;
590: const PetscInt firstYFace = firstXFace + numTotXFaces;
591: const PetscInt firstZFace = firstYFace + numTotYFaces;
592: const PetscInt firstXEdge = numCells + numFaces + numVertices;
593: const PetscInt firstYEdge = firstXEdge + numTotXEdges;
594: const PetscInt firstZEdge = firstYEdge + numTotYEdges;
595: Vec coordinates;
596: PetscSection coordSection;
597: PetscScalar *coords;
598: PetscInt coordSize;
599: PetscInt v, vx, vy, vz;
600: PetscInt c, f, fx, fy, fz, e, ex, ey, ez;
602: DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);
603: for (c = 0; c < numCells; c++) {
604: DMPlexSetConeSize(dm, c, 6);
605: }
606: for (f = firstXFace; f < firstXFace+numFaces; ++f) {
607: DMPlexSetConeSize(dm, f, 4);
608: }
609: for (e = firstXEdge; e < firstXEdge+numEdges; ++e) {
610: DMPlexSetConeSize(dm, e, 2);
611: }
612: DMSetUp(dm); /* Allocate space for cones */
613: /* Build cells */
614: for (fz = 0; fz < numZEdges; ++fz) {
615: for (fy = 0; fy < numYEdges; ++fy) {
616: for (fx = 0; fx < numXEdges; ++fx) {
617: PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx;
618: PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz;
619: PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices);
620: PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy;
621: PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices);
622: PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx;
623: PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices);
624: /* B, T, F, K, R, L */
625: PetscInt ornt[6] = {-4, 0, 0, -1, 0, -4}; /* ??? */
626: PetscInt cone[6];
628: /* no boundary twisting in 3D */
629: cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL;
630: DMPlexSetCone(dm, cell, cone);
631: DMPlexSetConeOrientation(dm, cell, ornt);
632: if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, cell, 2);}
633: if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, cell, 2);}
634: if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, cell, 2);}
635: }
636: }
637: }
638: /* Build x faces */
639: for (fz = 0; fz < numZEdges; ++fz) {
640: for (fy = 0; fy < numYEdges; ++fy) {
641: for (fx = 0; fx < numXVertices; ++fx) {
642: PetscInt face = firstXFace + (fz*numYEdges+fy)*numXVertices + fx;
643: PetscInt edgeL = firstZEdge + ( fy* numXVertices+fx)*numZEdges + fz;
644: PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz;
645: PetscInt edgeB = firstYEdge + ( fz* numXVertices+fx)*numYEdges + fy;
646: PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy;
647: PetscInt ornt[4] = {0, 0, -2, -2};
648: PetscInt cone[4];
650: if (dim == 3) {
651: /* markers */
652: if (bdX != DM_BOUNDARY_PERIODIC) {
653: if (fx == numXVertices-1) {
654: DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);
655: DMSetLabelValue(dm, "marker", face, markerRight);
656: }
657: else if (fx == 0) {
658: DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);
659: DMSetLabelValue(dm, "marker", face, markerLeft);
660: }
661: }
662: }
663: cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
664: DMPlexSetCone(dm, face, cone);
665: DMPlexSetConeOrientation(dm, face, ornt);
666: }
667: }
668: }
669: /* Build y faces */
670: for (fz = 0; fz < numZEdges; ++fz) {
671: for (fx = 0; fx < numXEdges; ++fx) {
672: for (fy = 0; fy < numYVertices; ++fy) {
673: PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy;
674: PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx )*numZEdges + fz;
675: PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz;
676: PetscInt edgeB = firstXEdge + ( fz *numYVertices+fy)*numXEdges + fx;
677: PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx;
678: PetscInt ornt[4] = {0, 0, -2, -2};
679: PetscInt cone[4];
681: if (dim == 3) {
682: /* markers */
683: if (bdY != DM_BOUNDARY_PERIODIC) {
684: if (fy == numYVertices-1) {
685: DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);
686: DMSetLabelValue(dm, "marker", face, markerBack);
687: }
688: else if (fy == 0) {
689: DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);
690: DMSetLabelValue(dm, "marker", face, markerFront);
691: }
692: }
693: }
694: cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
695: DMPlexSetCone(dm, face, cone);
696: DMPlexSetConeOrientation(dm, face, ornt);
697: }
698: }
699: }
700: /* Build z faces */
701: for (fy = 0; fy < numYEdges; ++fy) {
702: for (fx = 0; fx < numXEdges; ++fx) {
703: for (fz = 0; fz < numZVertices; fz++) {
704: PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz;
705: PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx )*numYEdges + fy;
706: PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy;
707: PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy )*numXEdges + fx;
708: PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx;
709: PetscInt ornt[4] = {0, 0, -2, -2};
710: PetscInt cone[4];
712: if (dim == 2) {
713: if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -2;}
714: if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;}
715: if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, face, 2);}
716: if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, face, 2);}
717: } else {
718: /* markers */
719: if (bdZ != DM_BOUNDARY_PERIODIC) {
720: if (fz == numZVertices-1) {
721: DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);
722: DMSetLabelValue(dm, "marker", face, markerTop);
723: }
724: else if (fz == 0) {
725: DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);
726: DMSetLabelValue(dm, "marker", face, markerBottom);
727: }
728: }
729: }
730: cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
731: DMPlexSetCone(dm, face, cone);
732: DMPlexSetConeOrientation(dm, face, ornt);
733: }
734: }
735: }
736: /* Build Z edges*/
737: for (vy = 0; vy < numYVertices; vy++) {
738: for (vx = 0; vx < numXVertices; vx++) {
739: for (ez = 0; ez < numZEdges; ez++) {
740: const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez;
741: const PetscInt vertexB = firstVertex + ( ez *numYVertices+vy)*numXVertices + vx;
742: const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx;
743: PetscInt cone[2];
745: if (dim == 3) {
746: if (bdX != DM_BOUNDARY_PERIODIC) {
747: if (vx == numXVertices-1) {
748: DMSetLabelValue(dm, "marker", edge, markerRight);
749: }
750: else if (vx == 0) {
751: DMSetLabelValue(dm, "marker", edge, markerLeft);
752: }
753: }
754: if (bdY != DM_BOUNDARY_PERIODIC) {
755: if (vy == numYVertices-1) {
756: DMSetLabelValue(dm, "marker", edge, markerBack);
757: }
758: else if (vy == 0) {
759: DMSetLabelValue(dm, "marker", edge, markerFront);
760: }
761: }
762: }
763: cone[0] = vertexB; cone[1] = vertexT;
764: DMPlexSetCone(dm, edge, cone);
765: }
766: }
767: }
768: /* Build Y edges*/
769: for (vz = 0; vz < numZVertices; vz++) {
770: for (vx = 0; vx < numXVertices; vx++) {
771: for (ey = 0; ey < numYEdges; ey++) {
772: const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx;
773: const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey;
774: const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx;
775: const PetscInt vertexK = firstVertex + nextv;
776: PetscInt cone[2];
778: cone[0] = vertexF; cone[1] = vertexK;
779: DMPlexSetCone(dm, edge, cone);
780: if (dim == 2) {
781: if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) {
782: if (vx == numXVertices-1) {
783: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);
784: DMSetLabelValue(dm, "marker", edge, markerRight);
785: DMSetLabelValue(dm, "marker", cone[0], markerRight);
786: if (ey == numYEdges-1) {
787: DMSetLabelValue(dm, "marker", cone[1], markerRight);
788: }
789: } else if (vx == 0) {
790: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);
791: DMSetLabelValue(dm, "marker", edge, markerLeft);
792: DMSetLabelValue(dm, "marker", cone[0], markerLeft);
793: if (ey == numYEdges-1) {
794: DMSetLabelValue(dm, "marker", cone[1], markerLeft);
795: }
796: }
797: } else {
798: if (vx == 0 && cutLabel) {
799: DMLabelSetValue(cutLabel, edge, 1);
800: DMLabelSetValue(cutLabel, cone[0], 1);
801: if (ey == numYEdges-1) {
802: DMLabelSetValue(cutLabel, cone[1], 1);
803: }
804: }
805: }
806: } else {
807: if (bdX != DM_BOUNDARY_PERIODIC) {
808: if (vx == numXVertices-1) {
809: DMSetLabelValue(dm, "marker", edge, markerRight);
810: } else if (vx == 0) {
811: DMSetLabelValue(dm, "marker", edge, markerLeft);
812: }
813: }
814: if (bdZ != DM_BOUNDARY_PERIODIC) {
815: if (vz == numZVertices-1) {
816: DMSetLabelValue(dm, "marker", edge, markerTop);
817: } else if (vz == 0) {
818: DMSetLabelValue(dm, "marker", edge, markerBottom);
819: }
820: }
821: }
822: }
823: }
824: }
825: /* Build X edges*/
826: for (vz = 0; vz < numZVertices; vz++) {
827: for (vy = 0; vy < numYVertices; vy++) {
828: for (ex = 0; ex < numXEdges; ex++) {
829: const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices;
830: const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex;
831: const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex;
832: const PetscInt vertexR = firstVertex + nextv;
833: PetscInt cone[2];
835: cone[0] = vertexL; cone[1] = vertexR;
836: DMPlexSetCone(dm, edge, cone);
837: if (dim == 2) {
838: if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) {
839: if (vy == numYVertices-1) {
840: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);
841: DMSetLabelValue(dm, "marker", edge, markerTop);
842: DMSetLabelValue(dm, "marker", cone[0], markerTop);
843: if (ex == numXEdges-1) {
844: DMSetLabelValue(dm, "marker", cone[1], markerTop);
845: }
846: } else if (vy == 0) {
847: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);
848: DMSetLabelValue(dm, "marker", edge, markerBottom);
849: DMSetLabelValue(dm, "marker", cone[0], markerBottom);
850: if (ex == numXEdges-1) {
851: DMSetLabelValue(dm, "marker", cone[1], markerBottom);
852: }
853: }
854: } else {
855: if (vy == 0 && cutLabel) {
856: DMLabelSetValue(cutLabel, edge, 1);
857: DMLabelSetValue(cutLabel, cone[0], 1);
858: if (ex == numXEdges-1) {
859: DMLabelSetValue(cutLabel, cone[1], 1);
860: }
861: }
862: }
863: } else {
864: if (bdY != DM_BOUNDARY_PERIODIC) {
865: if (vy == numYVertices-1) {
866: DMSetLabelValue(dm, "marker", edge, markerBack);
867: }
868: else if (vy == 0) {
869: DMSetLabelValue(dm, "marker", edge, markerFront);
870: }
871: }
872: if (bdZ != DM_BOUNDARY_PERIODIC) {
873: if (vz == numZVertices-1) {
874: DMSetLabelValue(dm, "marker", edge, markerTop);
875: }
876: else if (vz == 0) {
877: DMSetLabelValue(dm, "marker", edge, markerBottom);
878: }
879: }
880: }
881: }
882: }
883: }
884: DMPlexSymmetrize(dm);
885: DMPlexStratify(dm);
886: /* Build coordinates */
887: DMGetCoordinateSection(dm, &coordSection);
888: PetscSectionSetNumFields(coordSection, 1);
889: PetscSectionSetFieldComponents(coordSection, 0, dim);
890: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);
891: for (v = firstVertex; v < firstVertex+numVertices; ++v) {
892: PetscSectionSetDof(coordSection, v, dim);
893: PetscSectionSetFieldDof(coordSection, v, 0, dim);
894: }
895: PetscSectionSetUp(coordSection);
896: PetscSectionGetStorageSize(coordSection, &coordSize);
897: VecCreate(PETSC_COMM_SELF, &coordinates);
898: PetscObjectSetName((PetscObject) coordinates, "coordinates");
899: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
900: VecSetBlockSize(coordinates, dim);
901: VecSetType(coordinates,VECSTANDARD);
902: VecGetArray(coordinates, &coords);
903: for (vz = 0; vz < numZVertices; ++vz) {
904: for (vy = 0; vy < numYVertices; ++vy) {
905: for (vx = 0; vx < numXVertices; ++vx) {
906: coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx;
907: coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy;
908: if (dim == 3) {
909: coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz;
910: }
911: }
912: }
913: }
914: VecRestoreArray(coordinates, &coords);
915: DMSetCoordinatesLocal(dm, coordinates);
916: VecDestroy(&coordinates);
917: }
918: return(0);
919: }
921: static PetscErrorCode DMPlexCreateBoxMesh_Tensor_Internal(MPI_Comm comm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate, DM *dm)
922: {
923: PetscInt i;
928: DMCreate(comm, dm);
930: DMSetType(*dm, DMPLEX);
931: DMSetDimension(*dm, dim);
932: switch (dim) {
933: case 2: {DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], DM_BOUNDARY_NONE);break;}
934: case 3: {DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], periodicity[2]);break;}
935: default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim);
936: }
937: if (periodicity[0] == DM_BOUNDARY_PERIODIC || periodicity[0] == DM_BOUNDARY_TWIST ||
938: periodicity[1] == DM_BOUNDARY_PERIODIC || periodicity[1] == DM_BOUNDARY_TWIST ||
939: (dim > 2 && (periodicity[2] == DM_BOUNDARY_PERIODIC || periodicity[2] == DM_BOUNDARY_TWIST))) {
940: PetscReal L[3];
941: PetscReal maxCell[3];
943: for (i = 0; i < dim; i++) {
944: L[i] = upper[i] - lower[i];
945: maxCell[i] = 1.1 * (L[i] / PetscMax(1,faces[i]));
946: }
947: DMSetPeriodicity(*dm,PETSC_TRUE,maxCell,L,periodicity);
948: }
949: if (!interpolate) {
950: DM udm;
952: DMPlexUninterpolate(*dm, &udm);
953: DMPlexCopyCoordinates(*dm, udm);
954: DMDestroy(dm);
955: *dm = udm;
956: }
957: return(0);
958: }
960: /*@C
961: DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra).
963: Collective on MPI_Comm
965: Input Parameters:
966: + comm - The communicator for the DM object
967: . dim - The spatial dimension
968: . simplex - PETSC_TRUE for simplices, PETSC_FALSE for tensor cells
969: . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D
970: . lower - The lower left corner, or NULL for (0, 0, 0)
971: . upper - The upper right corner, or NULL for (1, 1, 1)
972: . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE
973: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
975: Output Parameter:
976: . dm - The DM object
978: Note: Here is the numbering returned for 2 faces in each direction for tensor cells:
979: $ 10---17---11---18----12
980: $ | | |
981: $ | | |
982: $ 20 2 22 3 24
983: $ | | |
984: $ | | |
985: $ 7---15----8---16----9
986: $ | | |
987: $ | | |
988: $ 19 0 21 1 23
989: $ | | |
990: $ | | |
991: $ 4---13----5---14----6
993: and for simplicial cells
995: $ 14----8---15----9----16
996: $ |\ 5 |\ 7 |
997: $ | \ | \ |
998: $ 13 2 14 3 15
999: $ | 4 \ | 6 \ |
1000: $ | \ | \ |
1001: $ 11----6---12----7----13
1002: $ |\ |\ |
1003: $ | \ 1 | \ 3 |
1004: $ 10 0 11 1 12
1005: $ | 0 \ | 2 \ |
1006: $ | \ | \ |
1007: $ 8----4----9----5----10
1009: Level: beginner
1011: .keywords: DM, create
1012: .seealso: DMPlexCreateFromFile(), DMPlexCreateHexCylinderMesh(), DMSetType(), DMCreate()
1013: @*/
1014: PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate, DM *dm)
1015: {
1016: PetscInt i;
1017: PetscInt fac[3] = {0, 0, 0};
1018: PetscReal low[3] = {0, 0, 0};
1019: PetscReal upp[3] = {1, 1, 1};
1020: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
1024: for (i = 0; i < dim; ++i) fac[i] = faces ? faces[i] : (dim == 1 ? 1 : 4-dim);
1025: if (lower) for (i = 0; i < dim; ++i) low[i] = lower[i];
1026: if (upper) for (i = 0; i < dim; ++i) upp[i] = upper[i];
1027: if (periodicity) for (i = 0; i < dim; ++i) bdt[i] = periodicity[i];
1029: if (dim == 1) {DMPlexCreateLineMesh_Internal(comm, fac[0], low[0], upp[0], bdt[0], dm);}
1030: else if (simplex) {DMPlexCreateBoxMesh_Simplex_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);}
1031: else {DMPlexCreateBoxMesh_Tensor_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);}
1032: return(0);
1033: }
1035: /*@C
1036: DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database.
1038: Logically Collective on DM
1040: Input Parameters:
1041: + dm - the DM context
1042: - prefix - the prefix to prepend to all option names
1044: Notes:
1045: A hyphen (-) must NOT be given at the beginning of the prefix name.
1046: The first character of all runtime options is AUTOMATICALLY the hyphen.
1048: Level: advanced
1050: .seealso: SNESSetFromOptions()
1051: @*/
1052: PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[])
1053: {
1054: DM_Plex *mesh = (DM_Plex *) dm->data;
1059: PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);
1060: PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);
1061: return(0);
1062: }
1064: /*@
1065: DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra.
1067: Collective on MPI_Comm
1069: Input Parameters:
1070: + comm - The communicator for the DM object
1071: . numRefine - The number of regular refinements to the basic 5 cell structure
1072: - periodicZ - The boundary type for the Z direction
1074: Output Parameter:
1075: . dm - The DM object
1077: Note: Here is the output numbering looking from the bottom of the cylinder:
1078: $ 17-----14
1079: $ | |
1080: $ | 2 |
1081: $ | |
1082: $ 17-----8-----7-----14
1083: $ | | | |
1084: $ | 3 | 0 | 1 |
1085: $ | | | |
1086: $ 19-----5-----6-----13
1087: $ | |
1088: $ | 4 |
1089: $ | |
1090: $ 19-----13
1091: $
1092: $ and up through the top
1093: $
1094: $ 18-----16
1095: $ | |
1096: $ | 2 |
1097: $ | |
1098: $ 18----10----11-----16
1099: $ | | | |
1100: $ | 3 | 0 | 1 |
1101: $ | | | |
1102: $ 20-----9----12-----15
1103: $ | |
1104: $ | 4 |
1105: $ | |
1106: $ 20-----15
1108: Level: beginner
1110: .keywords: DM, create
1111: .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1112: @*/
1113: PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, PetscInt numRefine, DMBoundaryType periodicZ, DM *dm)
1114: {
1115: const PetscInt dim = 3;
1116: PetscInt numCells, numVertices, r;
1117: PetscMPIInt rank;
1122: MPI_Comm_rank(comm, &rank);
1123: if (numRefine < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of refinements %D cannot be negative", numRefine);
1124: DMCreate(comm, dm);
1125: DMSetType(*dm, DMPLEX);
1126: DMSetDimension(*dm, dim);
1127: /* Create topology */
1128: {
1129: PetscInt cone[8], c;
1131: numCells = !rank ? 5 : 0;
1132: numVertices = !rank ? 16 : 0;
1133: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1134: numCells *= 3;
1135: numVertices = !rank ? 24 : 0;
1136: }
1137: DMPlexSetChart(*dm, 0, numCells+numVertices);
1138: for (c = 0; c < numCells; c++) {DMPlexSetConeSize(*dm, c, 8);}
1139: DMSetUp(*dm);
1140: if (!rank) {
1141: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1142: cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16;
1143: cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34;
1144: DMPlexSetCone(*dm, 0, cone);
1145: cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23;
1146: cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */
1147: DMPlexSetCone(*dm, 1, cone);
1148: cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17;
1149: cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38;
1150: DMPlexSetCone(*dm, 2, cone);
1151: cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15;
1152: cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38;
1153: DMPlexSetCone(*dm, 3, cone);
1154: cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23;
1155: cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31;
1156: DMPlexSetCone(*dm, 4, cone);
1158: cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32;
1159: cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20;
1160: DMPlexSetCone(*dm, 5, cone);
1161: cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36;
1162: cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21;
1163: DMPlexSetCone(*dm, 6, cone);
1164: cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33;
1165: cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28;
1166: DMPlexSetCone(*dm, 7, cone);
1167: cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31;
1168: cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28;
1169: DMPlexSetCone(*dm, 8, cone);
1170: cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36;
1171: cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19;
1172: DMPlexSetCone(*dm, 9, cone);
1174: cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22;
1175: cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18;
1176: DMPlexSetCone(*dm, 10, cone);
1177: cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25;
1178: cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17;
1179: DMPlexSetCone(*dm, 11, cone);
1180: cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21;
1181: cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27;
1182: DMPlexSetCone(*dm, 12, cone);
1183: cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19;
1184: cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27;
1185: DMPlexSetCone(*dm, 13, cone);
1186: cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25;
1187: cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15;
1188: DMPlexSetCone(*dm, 14, cone);
1189: } else {
1190: cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6;
1191: cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10;
1192: DMPlexSetCone(*dm, 0, cone);
1193: cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13;
1194: cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11;
1195: DMPlexSetCone(*dm, 1, cone);
1196: cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7;
1197: cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18;
1198: DMPlexSetCone(*dm, 2, cone);
1199: cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5;
1200: cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18;
1201: DMPlexSetCone(*dm, 3, cone);
1202: cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13;
1203: cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9;
1204: DMPlexSetCone(*dm, 4, cone);
1205: }
1206: }
1207: DMPlexSymmetrize(*dm);
1208: DMPlexStratify(*dm);
1209: }
1210: /* Interpolate */
1211: {
1212: DM idm;
1214: DMPlexInterpolate(*dm, &idm);
1215: DMDestroy(dm);
1216: *dm = idm;
1217: }
1218: /* Create cube geometry */
1219: {
1220: Vec coordinates;
1221: PetscSection coordSection;
1222: PetscScalar *coords;
1223: PetscInt coordSize, v;
1224: const PetscReal dis = 1.0/PetscSqrtReal(2.0);
1225: const PetscReal ds2 = dis/2.0;
1227: /* Build coordinates */
1228: DMGetCoordinateSection(*dm, &coordSection);
1229: PetscSectionSetNumFields(coordSection, 1);
1230: PetscSectionSetFieldComponents(coordSection, 0, dim);
1231: PetscSectionSetChart(coordSection, numCells, numCells+numVertices);
1232: for (v = numCells; v < numCells+numVertices; ++v) {
1233: PetscSectionSetDof(coordSection, v, dim);
1234: PetscSectionSetFieldDof(coordSection, v, 0, dim);
1235: }
1236: PetscSectionSetUp(coordSection);
1237: PetscSectionGetStorageSize(coordSection, &coordSize);
1238: VecCreate(PETSC_COMM_SELF, &coordinates);
1239: PetscObjectSetName((PetscObject) coordinates, "coordinates");
1240: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1241: VecSetBlockSize(coordinates, dim);
1242: VecSetType(coordinates,VECSTANDARD);
1243: VecGetArray(coordinates, &coords);
1244: if (!rank) {
1245: coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0;
1246: coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0;
1247: coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0;
1248: coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0;
1249: coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0;
1250: coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0;
1251: coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0;
1252: coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0;
1253: coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0;
1254: coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0;
1255: coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0;
1256: coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0;
1257: coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0;
1258: coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0;
1259: coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0;
1260: coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0;
1261: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1262: /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5;
1263: /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5;
1264: /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5;
1265: /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5;
1266: /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5;
1267: /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5;
1268: /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5;
1269: /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5;
1270: }
1271: }
1272: VecRestoreArray(coordinates, &coords);
1273: DMSetCoordinatesLocal(*dm, coordinates);
1274: VecDestroy(&coordinates);
1275: }
1276: /* Create periodicity */
1277: if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) {
1278: PetscReal L[3];
1279: PetscReal maxCell[3];
1280: DMBoundaryType bdType[3];
1281: PetscReal lower[3] = {0.0, 0.0, 0.0};
1282: PetscReal upper[3] = {1.0, 1.0, 1.5};
1283: PetscInt i, numZCells = 3;
1285: bdType[0] = DM_BOUNDARY_NONE;
1286: bdType[1] = DM_BOUNDARY_NONE;
1287: bdType[2] = periodicZ;
1288: for (i = 0; i < dim; i++) {
1289: L[i] = upper[i] - lower[i];
1290: maxCell[i] = 1.1 * (L[i] / numZCells);
1291: }
1292: DMSetPeriodicity(*dm, PETSC_TRUE, maxCell, L, bdType);
1293: }
1294: /* Refine topology */
1295: for (r = 0; r < numRefine; ++r) {
1296: DM rdm = NULL;
1298: DMRefine(*dm, comm, &rdm);
1299: DMDestroy(dm);
1300: *dm = rdm;
1301: }
1302: /* Remap geometry to cylinder
1303: Interior square: Linear interpolation is correct
1304: The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing
1305: such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance
1307: phi = arctan(y/x)
1308: d_close = sqrt(1/8 + 1/4 sin^2(phi))
1309: d_far = sqrt(1/2 + sin^2(phi))
1311: so we remap them using
1313: x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close)
1314: y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close)
1316: If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y.
1317: */
1318: {
1319: Vec coordinates;
1320: PetscSection coordSection;
1321: PetscScalar *coords;
1322: PetscInt vStart, vEnd, v;
1323: const PetscReal dis = 1.0/PetscSqrtReal(2.0);
1324: const PetscReal ds2 = 0.5*dis;
1326: DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);
1327: DMGetCoordinateSection(*dm, &coordSection);
1328: DMGetCoordinatesLocal(*dm, &coordinates);
1329: VecGetArray(coordinates, &coords);
1330: for (v = vStart; v < vEnd; ++v) {
1331: PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc;
1332: PetscInt off;
1334: PetscSectionGetOffset(coordSection, v, &off);
1335: if ((PetscAbsScalar(coords[off+0]) <= ds2) && (PetscAbsScalar(coords[off+1]) <= ds2)) continue;
1336: x = PetscRealPart(coords[off]);
1337: y = PetscRealPart(coords[off+1]);
1338: phi = PetscAtan2Real(y, x);
1339: sinp = PetscSinReal(phi);
1340: cosp = PetscCosReal(phi);
1341: if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) {
1342: dc = PetscAbsReal(ds2/sinp);
1343: df = PetscAbsReal(dis/sinp);
1344: xc = ds2*x/PetscAbsReal(y);
1345: yc = ds2*PetscSignReal(y);
1346: } else {
1347: dc = PetscAbsReal(ds2/cosp);
1348: df = PetscAbsReal(dis/cosp);
1349: xc = ds2*PetscSignReal(x);
1350: yc = ds2*y/PetscAbsReal(x);
1351: }
1352: coords[off+0] = xc + (coords[off+0] - xc)*(1.0 - dc)/(df - dc);
1353: coords[off+1] = yc + (coords[off+1] - yc)*(1.0 - dc)/(df - dc);
1354: }
1355: VecRestoreArray(coordinates, &coords);
1356: if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) {
1357: DMLocalizeCoordinates(*dm);
1358: }
1359: }
1360: return(0);
1361: }
1363: /*@
1364: DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges.
1366: Collective on MPI_Comm
1368: Input Parameters:
1369: + comm - The communicator for the DM object
1370: . n - The number of wedges around the origin
1371: - interpolate - Create edges and faces
1373: Output Parameter:
1374: . dm - The DM object
1376: Level: beginner
1378: .keywords: DM, create
1379: .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1380: @*/
1381: PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm)
1382: {
1383: const PetscInt dim = 3;
1384: PetscInt numCells, numVertices;
1385: PetscMPIInt rank;
1390: MPI_Comm_rank(comm, &rank);
1391: if (n < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n);
1392: DMCreate(comm, dm);
1393: DMSetType(*dm, DMPLEX);
1394: DMSetDimension(*dm, dim);
1395: /* Create topology */
1396: {
1397: PetscInt cone[6], c;
1399: numCells = !rank ? n : 0;
1400: numVertices = !rank ? 2*(n+1) : 0;
1401: DMPlexSetChart(*dm, 0, numCells+numVertices);
1402: for (c = 0; c < numCells; c++) {DMPlexSetConeSize(*dm, c, 6);}
1403: DMSetUp(*dm);
1404: for (c = 0; c < numCells; c++) {
1405: cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n;
1406: cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n;
1407: DMPlexSetCone(*dm, c, cone);
1408: }
1409: DMPlexSymmetrize(*dm);
1410: DMPlexStratify(*dm);
1411: }
1412: /* Interpolate */
1413: if (interpolate) {
1414: DM idm;
1416: DMPlexInterpolate(*dm, &idm);
1417: DMDestroy(dm);
1418: *dm = idm;
1419: }
1420: /* Create cylinder geometry */
1421: {
1422: Vec coordinates;
1423: PetscSection coordSection;
1424: PetscScalar *coords;
1425: PetscInt coordSize, v, c;
1427: /* Build coordinates */
1428: DMGetCoordinateSection(*dm, &coordSection);
1429: PetscSectionSetNumFields(coordSection, 1);
1430: PetscSectionSetFieldComponents(coordSection, 0, dim);
1431: PetscSectionSetChart(coordSection, numCells, numCells+numVertices);
1432: for (v = numCells; v < numCells+numVertices; ++v) {
1433: PetscSectionSetDof(coordSection, v, dim);
1434: PetscSectionSetFieldDof(coordSection, v, 0, dim);
1435: }
1436: PetscSectionSetUp(coordSection);
1437: PetscSectionGetStorageSize(coordSection, &coordSize);
1438: VecCreate(PETSC_COMM_SELF, &coordinates);
1439: PetscObjectSetName((PetscObject) coordinates, "coordinates");
1440: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1441: VecSetBlockSize(coordinates, dim);
1442: VecSetType(coordinates,VECSTANDARD);
1443: VecGetArray(coordinates, &coords);
1444: for (c = 0; c < numCells; c++) {
1445: 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;
1446: 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;
1447: }
1448: if (!rank) {
1449: coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0;
1450: coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0;
1451: }
1452: VecRestoreArray(coordinates, &coords);
1453: DMSetCoordinatesLocal(*dm, coordinates);
1454: VecDestroy(&coordinates);
1455: }
1456: return(0);
1457: }
1459: PETSC_STATIC_INLINE PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
1460: {
1461: PetscReal prod = 0.0;
1462: PetscInt i;
1463: for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]);
1464: return PetscSqrtReal(prod);
1465: }
1466: PETSC_STATIC_INLINE PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
1467: {
1468: PetscReal prod = 0.0;
1469: PetscInt i;
1470: for (i = 0; i < dim; ++i) prod += x[i]*y[i];
1471: return prod;
1472: }
1474: /*@
1475: DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d.
1477: Collective on MPI_Comm
1479: Input Parameters:
1480: . comm - The communicator for the DM object
1481: . dim - The dimension
1482: - simplex - Use simplices, or tensor product cells
1484: Output Parameter:
1485: . dm - The DM object
1487: Level: beginner
1489: .keywords: DM, create
1490: .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1491: @*/
1492: PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *dm)
1493: {
1494: const PetscInt embedDim = dim+1;
1495: PetscSection coordSection;
1496: Vec coordinates;
1497: PetscScalar *coords;
1498: PetscReal *coordsIn;
1499: PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e;
1500: PetscMPIInt rank;
1501: PetscErrorCode ierr;
1505: DMCreate(comm, dm);
1506: DMSetType(*dm, DMPLEX);
1507: DMSetDimension(*dm, dim);
1508: DMSetCoordinateDim(*dm, dim+1);
1509: MPI_Comm_rank(PetscObjectComm((PetscObject) *dm), &rank);
1510: switch (dim) {
1511: case 2:
1512: if (simplex) {
1513: DM idm;
1514: const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI);
1515: const PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)};
1516: const PetscInt degree = 5;
1517: PetscInt s[3] = {1, 1, 1};
1518: PetscInt cone[3];
1519: PetscInt *graph, p, i, j, k;
1521: numCells = !rank ? 20 : 0;
1522: numVerts = !rank ? 12 : 0;
1523: firstVertex = numCells;
1524: /* Use icosahedron, which for a unit sphere has coordinates which are all cyclic permutations of
1526: (0, \pm 1/\phi+1, \pm \phi/\phi+1)
1528: where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
1529: length is then given by 2/\phi = 2 * 2.73606 = 5.47214.
1530: */
1531: /* Construct vertices */
1532: PetscCalloc1(numVerts * embedDim, &coordsIn);
1533: for (p = 0, i = 0; p < embedDim; ++p) {
1534: for (s[1] = -1; s[1] < 2; s[1] += 2) {
1535: for (s[2] = -1; s[2] < 2; s[2] += 2) {
1536: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim];
1537: ++i;
1538: }
1539: }
1540: }
1541: /* Construct graph */
1542: PetscCalloc1(numVerts * numVerts, &graph);
1543: for (i = 0; i < numVerts; ++i) {
1544: for (j = 0, k = 0; j < numVerts; ++j) {
1545: if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;}
1546: }
1547: if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree);
1548: }
1549: /* Build Topology */
1550: DMPlexSetChart(*dm, 0, numCells+numVerts);
1551: for (c = 0; c < numCells; c++) {
1552: DMPlexSetConeSize(*dm, c, embedDim);
1553: }
1554: DMSetUp(*dm); /* Allocate space for cones */
1555: /* Cells */
1556: for (i = 0, c = 0; i < numVerts; ++i) {
1557: for (j = 0; j < i; ++j) {
1558: for (k = 0; k < j; ++k) {
1559: if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) {
1560: cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k;
1561: /* Check orientation */
1562: {
1563: 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}}};
1564: PetscReal normal[3];
1565: PetscInt e, f;
1567: for (d = 0; d < embedDim; ++d) {
1568: normal[d] = 0.0;
1569: for (e = 0; e < embedDim; ++e) {
1570: for (f = 0; f < embedDim; ++f) {
1571: normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]);
1572: }
1573: }
1574: }
1575: if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;}
1576: }
1577: DMPlexSetCone(*dm, c++, cone);
1578: }
1579: }
1580: }
1581: }
1582: DMPlexSymmetrize(*dm);
1583: DMPlexStratify(*dm);
1584: PetscFree(graph);
1585: /* Interpolate mesh */
1586: DMPlexInterpolate(*dm, &idm);
1587: DMDestroy(dm);
1588: *dm = idm;
1589: } else {
1590: /*
1591: 12-21--13
1592: | |
1593: 25 4 24
1594: | |
1595: 12-25--9-16--8-24--13
1596: | | | |
1597: 23 5 17 0 15 3 22
1598: | | | |
1599: 10-20--6-14--7-19--11
1600: | |
1601: 20 1 19
1602: | |
1603: 10-18--11
1604: | |
1605: 23 2 22
1606: | |
1607: 12-21--13
1608: */
1609: const PetscReal dist = 1.0/PetscSqrtReal(3.0);
1610: PetscInt cone[4], ornt[4];
1612: numCells = !rank ? 6 : 0;
1613: numEdges = !rank ? 12 : 0;
1614: numVerts = !rank ? 8 : 0;
1615: firstVertex = numCells;
1616: firstEdge = numCells + numVerts;
1617: /* Build Topology */
1618: DMPlexSetChart(*dm, 0, numCells+numEdges+numVerts);
1619: for (c = 0; c < numCells; c++) {
1620: DMPlexSetConeSize(*dm, c, 4);
1621: }
1622: for (e = firstEdge; e < firstEdge+numEdges; ++e) {
1623: DMPlexSetConeSize(*dm, e, 2);
1624: }
1625: DMSetUp(*dm); /* Allocate space for cones */
1626: /* Cell 0 */
1627: cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17;
1628: DMPlexSetCone(*dm, 0, cone);
1629: ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0;
1630: DMPlexSetConeOrientation(*dm, 0, ornt);
1631: /* Cell 1 */
1632: cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20;
1633: DMPlexSetCone(*dm, 1, cone);
1634: ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0;
1635: DMPlexSetConeOrientation(*dm, 1, ornt);
1636: /* Cell 2 */
1637: cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23;
1638: DMPlexSetCone(*dm, 2, cone);
1639: ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0;
1640: DMPlexSetConeOrientation(*dm, 2, ornt);
1641: /* Cell 3 */
1642: cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15;
1643: DMPlexSetCone(*dm, 3, cone);
1644: ornt[0] = -2; ornt[1] = -2; ornt[2] = 0; ornt[3] = -2;
1645: DMPlexSetConeOrientation(*dm, 3, ornt);
1646: /* Cell 4 */
1647: cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25;
1648: DMPlexSetCone(*dm, 4, cone);
1649: ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = 0;
1650: DMPlexSetConeOrientation(*dm, 4, ornt);
1651: /* Cell 5 */
1652: cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23;
1653: DMPlexSetCone(*dm, 5, cone);
1654: ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = -2;
1655: DMPlexSetConeOrientation(*dm, 5, ornt);
1656: /* Edges */
1657: cone[0] = 6; cone[1] = 7;
1658: DMPlexSetCone(*dm, 14, cone);
1659: cone[0] = 7; cone[1] = 8;
1660: DMPlexSetCone(*dm, 15, cone);
1661: cone[0] = 8; cone[1] = 9;
1662: DMPlexSetCone(*dm, 16, cone);
1663: cone[0] = 9; cone[1] = 6;
1664: DMPlexSetCone(*dm, 17, cone);
1665: cone[0] = 10; cone[1] = 11;
1666: DMPlexSetCone(*dm, 18, cone);
1667: cone[0] = 11; cone[1] = 7;
1668: DMPlexSetCone(*dm, 19, cone);
1669: cone[0] = 6; cone[1] = 10;
1670: DMPlexSetCone(*dm, 20, cone);
1671: cone[0] = 12; cone[1] = 13;
1672: DMPlexSetCone(*dm, 21, cone);
1673: cone[0] = 13; cone[1] = 11;
1674: DMPlexSetCone(*dm, 22, cone);
1675: cone[0] = 10; cone[1] = 12;
1676: DMPlexSetCone(*dm, 23, cone);
1677: cone[0] = 13; cone[1] = 8;
1678: DMPlexSetCone(*dm, 24, cone);
1679: cone[0] = 12; cone[1] = 9;
1680: DMPlexSetCone(*dm, 25, cone);
1681: DMPlexSymmetrize(*dm);
1682: DMPlexStratify(*dm);
1683: /* Build coordinates */
1684: PetscCalloc1(numVerts * embedDim, &coordsIn);
1685: coordsIn[0*embedDim+0] = -dist; coordsIn[0*embedDim+1] = dist; coordsIn[0*embedDim+2] = -dist;
1686: coordsIn[1*embedDim+0] = dist; coordsIn[1*embedDim+1] = dist; coordsIn[1*embedDim+2] = -dist;
1687: coordsIn[2*embedDim+0] = dist; coordsIn[2*embedDim+1] = -dist; coordsIn[2*embedDim+2] = -dist;
1688: coordsIn[3*embedDim+0] = -dist; coordsIn[3*embedDim+1] = -dist; coordsIn[3*embedDim+2] = -dist;
1689: coordsIn[4*embedDim+0] = -dist; coordsIn[4*embedDim+1] = dist; coordsIn[4*embedDim+2] = dist;
1690: coordsIn[5*embedDim+0] = dist; coordsIn[5*embedDim+1] = dist; coordsIn[5*embedDim+2] = dist;
1691: coordsIn[6*embedDim+0] = -dist; coordsIn[6*embedDim+1] = -dist; coordsIn[6*embedDim+2] = dist;
1692: coordsIn[7*embedDim+0] = dist; coordsIn[7*embedDim+1] = -dist; coordsIn[7*embedDim+2] = dist;
1693: }
1694: break;
1695: case 3:
1696: if (simplex) {
1697: DM idm;
1698: const PetscReal edgeLen = 1.0/PETSC_PHI;
1699: const PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5};
1700: const PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0};
1701: const PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0};
1702: const PetscInt degree = 12;
1703: PetscInt s[4] = {1, 1, 1};
1704: 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},
1705: {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}};
1706: PetscInt cone[4];
1707: PetscInt *graph, p, i, j, k, l;
1709: numCells = !rank ? 600 : 0;
1710: numVerts = !rank ? 120 : 0;
1711: firstVertex = numCells;
1712: /* Use the 600-cell, which for a unit sphere has coordinates which are
1714: 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16
1715: (\pm 1, 0, 0, 0) all cyclic permutations 8
1716: 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96
1718: where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
1719: length is then given by 1/\phi = 2.73606.
1721: http://buzzard.pugetsound.edu/sage-practice/ch03s03.html
1722: http://mathworld.wolfram.com/600-Cell.html
1723: */
1724: /* Construct vertices */
1725: PetscCalloc1(numVerts * embedDim, &coordsIn);
1726: i = 0;
1727: for (s[0] = -1; s[0] < 2; s[0] += 2) {
1728: for (s[1] = -1; s[1] < 2; s[1] += 2) {
1729: for (s[2] = -1; s[2] < 2; s[2] += 2) {
1730: for (s[3] = -1; s[3] < 2; s[3] += 2) {
1731: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d];
1732: ++i;
1733: }
1734: }
1735: }
1736: }
1737: for (p = 0; p < embedDim; ++p) {
1738: s[1] = s[2] = s[3] = 1;
1739: for (s[0] = -1; s[0] < 2; s[0] += 2) {
1740: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim];
1741: ++i;
1742: }
1743: }
1744: for (p = 0; p < 12; ++p) {
1745: s[3] = 1;
1746: for (s[0] = -1; s[0] < 2; s[0] += 2) {
1747: for (s[1] = -1; s[1] < 2; s[1] += 2) {
1748: for (s[2] = -1; s[2] < 2; s[2] += 2) {
1749: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]];
1750: ++i;
1751: }
1752: }
1753: }
1754: }
1755: if (i != numVerts) SETERRQ2(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts);
1756: /* Construct graph */
1757: PetscCalloc1(numVerts * numVerts, &graph);
1758: for (i = 0; i < numVerts; ++i) {
1759: for (j = 0, k = 0; j < numVerts; ++j) {
1760: if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;}
1761: }
1762: if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree);
1763: }
1764: /* Build Topology */
1765: DMPlexSetChart(*dm, 0, numCells+numVerts);
1766: for (c = 0; c < numCells; c++) {
1767: DMPlexSetConeSize(*dm, c, embedDim);
1768: }
1769: DMSetUp(*dm); /* Allocate space for cones */
1770: /* Cells */
1771: for (i = 0, c = 0; i < numVerts; ++i) {
1772: for (j = 0; j < i; ++j) {
1773: for (k = 0; k < j; ++k) {
1774: for (l = 0; l < k; ++l) {
1775: if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] &&
1776: graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) {
1777: cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l;
1778: /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */
1779: {
1780: const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
1781: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}},
1782: {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}},
1783: {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}},
1785: {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}},
1786: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
1787: {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}},
1788: {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}},
1790: {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}},
1791: {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}},
1792: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
1793: {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}},
1795: {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}},
1796: {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}},
1797: {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
1798: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}};
1799: PetscReal normal[4];
1800: PetscInt e, f, g;
1802: for (d = 0; d < embedDim; ++d) {
1803: normal[d] = 0.0;
1804: for (e = 0; e < embedDim; ++e) {
1805: for (f = 0; f < embedDim; ++f) {
1806: for (g = 0; g < embedDim; ++g) {
1807: 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]);
1808: }
1809: }
1810: }
1811: }
1812: if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;}
1813: }
1814: DMPlexSetCone(*dm, c++, cone);
1815: }
1816: }
1817: }
1818: }
1819: }
1820: DMPlexSymmetrize(*dm);
1821: DMPlexStratify(*dm);
1822: PetscFree(graph);
1823: /* Interpolate mesh */
1824: DMPlexInterpolate(*dm, &idm);
1825: DMDestroy(dm);
1826: *dm = idm;
1827: break;
1828: }
1829: default: SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim);
1830: }
1831: /* Create coordinates */
1832: DMGetCoordinateSection(*dm, &coordSection);
1833: PetscSectionSetNumFields(coordSection, 1);
1834: PetscSectionSetFieldComponents(coordSection, 0, embedDim);
1835: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);
1836: for (v = firstVertex; v < firstVertex+numVerts; ++v) {
1837: PetscSectionSetDof(coordSection, v, embedDim);
1838: PetscSectionSetFieldDof(coordSection, v, 0, embedDim);
1839: }
1840: PetscSectionSetUp(coordSection);
1841: PetscSectionGetStorageSize(coordSection, &coordSize);
1842: VecCreate(PETSC_COMM_SELF, &coordinates);
1843: VecSetBlockSize(coordinates, embedDim);
1844: PetscObjectSetName((PetscObject) coordinates, "coordinates");
1845: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1846: VecSetType(coordinates,VECSTANDARD);
1847: VecGetArray(coordinates, &coords);
1848: for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];}
1849: VecRestoreArray(coordinates, &coords);
1850: DMSetCoordinatesLocal(*dm, coordinates);
1851: VecDestroy(&coordinates);
1852: PetscFree(coordsIn);
1853: return(0);
1854: }
1856: /* External function declarations here */
1857: extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling);
1858: extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat);
1859: extern PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mat);
1860: extern PetscErrorCode DMCreateDefaultSection_Plex(DM dm);
1861: extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm);
1862: extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J);
1863: extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm);
1864: PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm);
1865: extern PetscErrorCode DMSetUp_Plex(DM dm);
1866: extern PetscErrorCode DMDestroy_Plex(DM dm);
1867: extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer);
1868: extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer);
1869: extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm);
1870: extern PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm);
1871: static PetscErrorCode DMInitialize_Plex(DM dm);
1873: /* Replace dm with the contents of dmNew
1874: - Share the DM_Plex structure
1875: - Share the coordinates
1876: - Share the SF
1877: */
1878: static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew)
1879: {
1880: PetscSF sf;
1881: DM coordDM, coarseDM;
1882: Vec coords;
1883: PetscBool isper;
1884: const PetscReal *maxCell, *L;
1885: const DMBoundaryType *bd;
1886: PetscErrorCode ierr;
1889: DMGetPointSF(dmNew, &sf);
1890: DMSetPointSF(dm, sf);
1891: DMGetCoordinateDM(dmNew, &coordDM);
1892: DMGetCoordinatesLocal(dmNew, &coords);
1893: DMSetCoordinateDM(dm, coordDM);
1894: DMSetCoordinatesLocal(dm, coords);
1895: DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);
1896: DMSetPeriodicity(dmNew, isper, maxCell, L, bd);
1897: DMDestroy_Plex(dm);
1898: DMInitialize_Plex(dm);
1899: dm->data = dmNew->data;
1900: ((DM_Plex *) dmNew->data)->refct++;
1901: dmNew->labels->refct++;
1902: if (!--(dm->labels->refct)) {
1903: DMLabelLink next = dm->labels->next;
1905: /* destroy the labels */
1906: while (next) {
1907: DMLabelLink tmp = next->next;
1909: DMLabelDestroy(&next->label);
1910: PetscFree(next);
1911: next = tmp;
1912: }
1913: PetscFree(dm->labels);
1914: }
1915: dm->labels = dmNew->labels;
1916: dm->depthLabel = dmNew->depthLabel;
1917: DMGetCoarseDM(dmNew,&coarseDM);
1918: DMSetCoarseDM(dm,coarseDM);
1919: return(0);
1920: }
1922: /* Swap dm with the contents of dmNew
1923: - Swap the DM_Plex structure
1924: - Swap the coordinates
1925: - Swap the point PetscSF
1926: */
1927: static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB)
1928: {
1929: DM coordDMA, coordDMB;
1930: Vec coordsA, coordsB;
1931: PetscSF sfA, sfB;
1932: void *tmp;
1933: DMLabelLinkList listTmp;
1934: DMLabel depthTmp;
1935: PetscErrorCode ierr;
1938: DMGetPointSF(dmA, &sfA);
1939: DMGetPointSF(dmB, &sfB);
1940: PetscObjectReference((PetscObject) sfA);
1941: DMSetPointSF(dmA, sfB);
1942: DMSetPointSF(dmB, sfA);
1943: PetscObjectDereference((PetscObject) sfA);
1945: DMGetCoordinateDM(dmA, &coordDMA);
1946: DMGetCoordinateDM(dmB, &coordDMB);
1947: PetscObjectReference((PetscObject) coordDMA);
1948: DMSetCoordinateDM(dmA, coordDMB);
1949: DMSetCoordinateDM(dmB, coordDMA);
1950: PetscObjectDereference((PetscObject) coordDMA);
1952: DMGetCoordinatesLocal(dmA, &coordsA);
1953: DMGetCoordinatesLocal(dmB, &coordsB);
1954: PetscObjectReference((PetscObject) coordsA);
1955: DMSetCoordinatesLocal(dmA, coordsB);
1956: DMSetCoordinatesLocal(dmB, coordsA);
1957: PetscObjectDereference((PetscObject) coordsA);
1959: tmp = dmA->data;
1960: dmA->data = dmB->data;
1961: dmB->data = tmp;
1962: listTmp = dmA->labels;
1963: dmA->labels = dmB->labels;
1964: dmB->labels = listTmp;
1965: depthTmp = dmA->depthLabel;
1966: dmA->depthLabel = dmB->depthLabel;
1967: dmB->depthLabel = depthTmp;
1968: return(0);
1969: }
1971: PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm)
1972: {
1973: DM_Plex *mesh = (DM_Plex*) dm->data;
1977: /* Handle viewing */
1978: PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMView", PETSC_FALSE, &mesh->printSetValues, NULL);
1979: PetscOptionsInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMView", 0, &mesh->printFEM, NULL);
1980: PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMView", mesh->printTol, &mesh->printTol, NULL);
1981: /* Point Location */
1982: PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMView", PETSC_FALSE, &mesh->useHashLocation, NULL);
1983: /* Generation and remeshing */
1984: PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMView", PETSC_FALSE, &mesh->remeshBd, NULL);
1985: /* Projection behavior */
1986: PetscOptionsInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL);
1987: PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);
1989: PetscPartitionerSetFromOptions(mesh->partitioner);
1990: return(0);
1991: }
1993: static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm)
1994: {
1995: PetscInt refine = 0, coarsen = 0, r;
1996: PetscBool isHierarchy;
2001: PetscOptionsHead(PetscOptionsObject,"DMPlex Options");
2002: /* Handle DMPlex refinement */
2003: PetscOptionsInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL);
2004: PetscOptionsInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy);
2005: if (refine) {DMPlexSetRefinementUniform(dm, PETSC_TRUE);}
2006: if (refine && isHierarchy) {
2007: DM *dms, coarseDM;
2009: DMGetCoarseDM(dm, &coarseDM);
2010: PetscObjectReference((PetscObject)coarseDM);
2011: PetscMalloc1(refine,&dms);
2012: DMRefineHierarchy(dm, refine, dms);
2013: /* Total hack since we do not pass in a pointer */
2014: DMPlexSwap_Static(dm, dms[refine-1]);
2015: if (refine == 1) {
2016: DMSetCoarseDM(dm, dms[0]);
2017: DMPlexSetRegularRefinement(dm, PETSC_TRUE);
2018: } else {
2019: DMSetCoarseDM(dm, dms[refine-2]);
2020: DMPlexSetRegularRefinement(dm, PETSC_TRUE);
2021: DMSetCoarseDM(dms[0], dms[refine-1]);
2022: DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);
2023: }
2024: DMSetCoarseDM(dms[refine-1], coarseDM);
2025: PetscObjectDereference((PetscObject)coarseDM);
2026: /* Free DMs */
2027: for (r = 0; r < refine; ++r) {
2028: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);
2029: DMDestroy(&dms[r]);
2030: }
2031: PetscFree(dms);
2032: } else {
2033: for (r = 0; r < refine; ++r) {
2034: DM refinedMesh;
2036: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2037: DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);
2038: /* Total hack since we do not pass in a pointer */
2039: DMPlexReplace_Static(dm, refinedMesh);
2040: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2041: DMDestroy(&refinedMesh);
2042: }
2043: }
2044: /* Handle DMPlex coarsening */
2045: PetscOptionsInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL);
2046: PetscOptionsInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy);
2047: if (coarsen && isHierarchy) {
2048: DM *dms;
2050: PetscMalloc1(coarsen, &dms);
2051: DMCoarsenHierarchy(dm, coarsen, dms);
2052: /* Free DMs */
2053: for (r = 0; r < coarsen; ++r) {
2054: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);
2055: DMDestroy(&dms[r]);
2056: }
2057: PetscFree(dms);
2058: } else {
2059: for (r = 0; r < coarsen; ++r) {
2060: DM coarseMesh;
2062: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2063: DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);
2064: /* Total hack since we do not pass in a pointer */
2065: DMPlexReplace_Static(dm, coarseMesh);
2066: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2067: DMDestroy(&coarseMesh);
2068: }
2069: }
2070: /* Handle */
2071: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2072: PetscOptionsTail();
2073: return(0);
2074: }
2076: static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec)
2077: {
2081: DMCreateGlobalVector_Section_Private(dm,vec);
2082: /* VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM); */
2083: VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);
2084: VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);
2085: VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);
2086: VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);
2087: return(0);
2088: }
2090: static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec)
2091: {
2095: DMCreateLocalVector_Section_Private(dm,vec);
2096: VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);
2097: VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);
2098: return(0);
2099: }
2101: static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd)
2102: {
2103: PetscInt depth, d;
2107: DMPlexGetDepth(dm, &depth);
2108: if (depth == 1) {
2109: DMGetDimension(dm, &d);
2110: if (dim == 0) {DMPlexGetDepthStratum(dm, dim, pStart, pEnd);}
2111: else if (dim == d) {DMPlexGetDepthStratum(dm, 1, pStart, pEnd);}
2112: else {*pStart = 0; *pEnd = 0;}
2113: } else {
2114: DMPlexGetDepthStratum(dm, dim, pStart, pEnd);
2115: }
2116: return(0);
2117: }
2119: static PetscErrorCode DMGetNeighors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[])
2120: {
2121: PetscSF sf;
2125: DMGetPointSF(dm, &sf);
2126: PetscSFGetRanks(sf, nranks, ranks, NULL, NULL, NULL);
2127: return(0);
2128: }
2130: static PetscErrorCode DMHasCreateInjection_Plex(DM dm, PetscBool *flg)
2131: {
2135: *flg = PETSC_TRUE;
2136: return(0);
2137: }
2139: static PetscErrorCode DMInitialize_Plex(DM dm)
2140: {
2144: dm->ops->view = DMView_Plex;
2145: dm->ops->load = DMLoad_Plex;
2146: dm->ops->setfromoptions = DMSetFromOptions_Plex;
2147: dm->ops->clone = DMClone_Plex;
2148: dm->ops->setup = DMSetUp_Plex;
2149: dm->ops->createdefaultsection = DMCreateDefaultSection_Plex;
2150: dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex;
2151: dm->ops->createglobalvector = DMCreateGlobalVector_Plex;
2152: dm->ops->createlocalvector = DMCreateLocalVector_Plex;
2153: dm->ops->getlocaltoglobalmapping = NULL;
2154: dm->ops->createfieldis = NULL;
2155: dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex;
2156: dm->ops->getcoloring = NULL;
2157: dm->ops->creatematrix = DMCreateMatrix_Plex;
2158: dm->ops->createinterpolation = DMCreateInterpolation_Plex;
2159: dm->ops->createmassmatrix = DMCreateMassMatrix_Plex;
2160: dm->ops->getaggregates = NULL;
2161: dm->ops->getinjection = DMCreateInjection_Plex;
2162: dm->ops->hascreateinjection = DMHasCreateInjection_Plex;
2163: dm->ops->refine = DMRefine_Plex;
2164: dm->ops->coarsen = DMCoarsen_Plex;
2165: dm->ops->refinehierarchy = DMRefineHierarchy_Plex;
2166: dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex;
2167: dm->ops->adaptlabel = DMAdaptLabel_Plex;
2168: dm->ops->adaptmetric = DMAdaptMetric_Plex;
2169: dm->ops->globaltolocalbegin = NULL;
2170: dm->ops->globaltolocalend = NULL;
2171: dm->ops->localtoglobalbegin = NULL;
2172: dm->ops->localtoglobalend = NULL;
2173: dm->ops->destroy = DMDestroy_Plex;
2174: dm->ops->createsubdm = DMCreateSubDM_Plex;
2175: dm->ops->createsuperdm = DMCreateSuperDM_Plex;
2176: dm->ops->getdimpoints = DMGetDimPoints_Plex;
2177: dm->ops->locatepoints = DMLocatePoints_Plex;
2178: dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex;
2179: dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex;
2180: dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex;
2181: dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex;
2182: dm->ops->computel2diff = DMComputeL2Diff_Plex;
2183: dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex;
2184: dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex;
2185: dm->ops->getneighbors = DMGetNeighors_Plex;
2186: PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);
2187: PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);
2188: return(0);
2189: }
2191: PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm)
2192: {
2193: DM_Plex *mesh = (DM_Plex *) dm->data;
2197: mesh->refct++;
2198: (*newdm)->data = mesh;
2199: PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);
2200: DMInitialize_Plex(*newdm);
2201: return(0);
2202: }
2204: /*MC
2205: DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram.
2206: In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is
2207: specified by a PetscSection object. Ownership in the global representation is determined by
2208: ownership of the underlying DMPlex points. This is specified by another PetscSection object.
2210: Level: intermediate
2212: .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType()
2213: M*/
2215: PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm)
2216: {
2217: DM_Plex *mesh;
2218: PetscInt unit, d;
2223: PetscNewLog(dm,&mesh);
2224: dm->dim = 0;
2225: dm->data = mesh;
2227: mesh->refct = 1;
2228: PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);
2229: mesh->maxConeSize = 0;
2230: mesh->cones = NULL;
2231: mesh->coneOrientations = NULL;
2232: PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);
2233: mesh->maxSupportSize = 0;
2234: mesh->supports = NULL;
2235: mesh->refinementUniform = PETSC_TRUE;
2236: mesh->refinementLimit = -1.0;
2238: mesh->facesTmp = NULL;
2240: mesh->tetgenOpts = NULL;
2241: mesh->triangleOpts = NULL;
2242: PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);
2243: mesh->remeshBd = PETSC_FALSE;
2245: mesh->subpointMap = NULL;
2247: for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0;
2249: mesh->regularRefinement = PETSC_FALSE;
2250: mesh->depthState = -1;
2251: mesh->globalVertexNumbers = NULL;
2252: mesh->globalCellNumbers = NULL;
2253: mesh->anchorSection = NULL;
2254: mesh->anchorIS = NULL;
2255: mesh->createanchors = NULL;
2256: mesh->computeanchormatrix = NULL;
2257: mesh->parentSection = NULL;
2258: mesh->parents = NULL;
2259: mesh->childIDs = NULL;
2260: mesh->childSection = NULL;
2261: mesh->children = NULL;
2262: mesh->referenceTree = NULL;
2263: mesh->getchildsymmetry = NULL;
2264: for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE;
2265: mesh->vtkCellHeight = 0;
2266: mesh->useAnchors = PETSC_FALSE;
2268: mesh->maxProjectionHeight = 0;
2270: mesh->printSetValues = PETSC_FALSE;
2271: mesh->printFEM = 0;
2272: mesh->printTol = 1.0e-10;
2274: DMInitialize_Plex(dm);
2275: return(0);
2276: }
2278: /*@
2279: DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram.
2281: Collective on MPI_Comm
2283: Input Parameter:
2284: . comm - The communicator for the DMPlex object
2286: Output Parameter:
2287: . mesh - The DMPlex object
2289: Level: beginner
2291: .keywords: DMPlex, create
2292: @*/
2293: PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh)
2294: {
2299: DMCreate(comm, mesh);
2300: DMSetType(*mesh, DMPLEX);
2301: return(0);
2302: }
2304: /*
2305: 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
2306: */
2307: static PetscErrorCode DMPlexBuildFromCellList_Parallel_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscSF *sfVert)
2308: {
2309: PetscSF sfPoint;
2310: PetscLayout vLayout;
2311: PetscHashI vhash;
2312: PetscSFNode *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex;
2313: const PetscInt *vrange;
2314: PetscInt numVerticesAdj, off, *verticesAdj, numVerticesGhost = 0, *localVertex, *cone, c, p, v, g;
2315: PETSC_UNUSED PetscHashIIter ret, iter;
2316: PetscMPIInt rank, size;
2317: PetscErrorCode ierr;
2320: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
2321: MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);
2322: /* Partition vertices */
2323: PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);
2324: PetscLayoutSetLocalSize(vLayout, numVertices);
2325: PetscLayoutSetBlockSize(vLayout, 1);
2326: PetscLayoutSetUp(vLayout);
2327: PetscLayoutGetRanges(vLayout, &vrange);
2328: /* Count vertices and map them to procs */
2329: PetscHashICreate(vhash);
2330: for (c = 0; c < numCells; ++c) {
2331: for (p = 0; p < numCorners; ++p) {
2332: PetscHashIPut(vhash, cells[c*numCorners+p], ret, iter);
2333: }
2334: }
2335: PetscHashISize(vhash, numVerticesAdj);
2336: PetscMalloc1(numVerticesAdj, &verticesAdj);
2337: off = 0; PetscHashIGetKeys(vhash, &off, verticesAdj);
2338: if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj);
2339: PetscSortInt(numVerticesAdj, verticesAdj);
2340: PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);
2341: for (v = 0; v < numVerticesAdj; ++v) {
2342: const PetscInt gv = verticesAdj[v];
2343: PetscInt vrank;
2345: PetscFindInt(gv, size+1, vrange, &vrank);
2346: vrank = vrank < 0 ? -(vrank+2) : vrank;
2347: remoteVerticesAdj[v].index = gv - vrange[vrank];
2348: remoteVerticesAdj[v].rank = vrank;
2349: }
2350: /* Create cones */
2351: DMPlexSetChart(dm, 0, numCells+numVerticesAdj);
2352: for (c = 0; c < numCells; ++c) {DMPlexSetConeSize(dm, c, numCorners);}
2353: DMSetUp(dm);
2354: DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);
2355: for (c = 0; c < numCells; ++c) {
2356: for (p = 0; p < numCorners; ++p) {
2357: const PetscInt gv = cells[c*numCorners+p];
2358: PetscInt lv;
2360: PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);
2361: if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv);
2362: cone[p] = lv+numCells;
2363: }
2364: DMPlexSetCone(dm, c, cone);
2365: }
2366: DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);
2367: /* Create SF for vertices */
2368: PetscSFCreate(PetscObjectComm((PetscObject)dm), sfVert);
2369: PetscObjectSetName((PetscObject) *sfVert, "Vertex Ownership SF");
2370: PetscSFSetFromOptions(*sfVert);
2371: PetscSFSetGraph(*sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);
2372: PetscFree(verticesAdj);
2373: /* Build pointSF */
2374: PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);
2375: for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;}
2376: for (v = 0; v < numVertices; ++v) {vertexOwner[v].index = -1; vertexOwner[v].rank = -1;}
2377: PetscSFReduceBegin(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);
2378: PetscSFReduceEnd(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);
2379: 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);
2380: PetscSFBcastBegin(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);
2381: PetscSFBcastEnd(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);
2382: for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost;
2383: PetscMalloc1(numVerticesGhost, &localVertex);
2384: PetscMalloc1(numVerticesGhost, &remoteVertex);
2385: for (v = 0, g = 0; v < numVerticesAdj; ++v) {
2386: if (vertexLocal[v].rank != rank) {
2387: localVertex[g] = v+numCells;
2388: remoteVertex[g].index = vertexLocal[v].index;
2389: remoteVertex[g].rank = vertexLocal[v].rank;
2390: ++g;
2391: }
2392: }
2393: PetscFree2(vertexLocal, vertexOwner);
2394: if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost);
2395: DMGetPointSF(dm, &sfPoint);
2396: PetscObjectSetName((PetscObject) sfPoint, "point SF");
2397: PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);
2398: PetscLayoutDestroy(&vLayout);
2399: PetscHashIDestroy(vhash);
2400: /* Fill in the rest of the topology structure */
2401: DMPlexSymmetrize(dm);
2402: DMPlexStratify(dm);
2403: return(0);
2404: }
2406: /*
2407: This takes as input the coordinates for each owned vertex
2408: */
2409: static PetscErrorCode DMPlexBuildCoordinates_Parallel_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numV, PetscSF sfVert, const PetscReal vertexCoords[])
2410: {
2411: PetscSection coordSection;
2412: Vec coordinates;
2413: PetscScalar *coords;
2414: PetscInt numVertices, numVerticesAdj, coordSize, v;
2418: DMSetCoordinateDim(dm, spaceDim);
2419: PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);
2420: DMGetCoordinateSection(dm, &coordSection);
2421: PetscSectionSetNumFields(coordSection, 1);
2422: PetscSectionSetFieldComponents(coordSection, 0, spaceDim);
2423: PetscSectionSetChart(coordSection, numCells, numCells + numVerticesAdj);
2424: for (v = numCells; v < numCells+numVerticesAdj; ++v) {
2425: PetscSectionSetDof(coordSection, v, spaceDim);
2426: PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);
2427: }
2428: PetscSectionSetUp(coordSection);
2429: PetscSectionGetStorageSize(coordSection, &coordSize);
2430: VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);
2431: VecSetBlockSize(coordinates, spaceDim);
2432: PetscObjectSetName((PetscObject) coordinates, "coordinates");
2433: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
2434: VecSetType(coordinates,VECSTANDARD);
2435: VecGetArray(coordinates, &coords);
2436: {
2437: MPI_Datatype coordtype;
2439: /* Need a temp buffer for coords if we have complex/single */
2440: MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);
2441: MPI_Type_commit(&coordtype);
2442: #if defined(PETSC_USE_COMPLEX)
2443: {
2444: PetscScalar *svertexCoords;
2445: PetscInt i;
2446: PetscMalloc1(numV*spaceDim,&svertexCoords);
2447: for (i=0; i<numV*spaceDim; i++) svertexCoords[i] = vertexCoords[i];
2448: PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords);
2449: PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords);
2450: PetscFree(svertexCoords);
2451: }
2452: #else
2453: PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords);
2454: PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords);
2455: #endif
2456: MPI_Type_free(&coordtype);
2457: }
2458: VecRestoreArray(coordinates, &coords);
2459: DMSetCoordinatesLocal(dm, coordinates);
2460: VecDestroy(&coordinates);
2461: return(0);
2462: }
2464: /*@C
2465: DMPlexCreateFromCellListParallel - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM
2467: Input Parameters:
2468: + comm - The communicator
2469: . dim - The topological dimension of the mesh
2470: . numCells - The number of cells owned by this process
2471: . numVertices - The number of vertices owned by this process
2472: . numCorners - The number of vertices for each cell
2473: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
2474: . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell
2475: . spaceDim - The spatial dimension used for coordinates
2476: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
2478: Output Parameter:
2479: + dm - The DM
2480: - vertexSF - Optional, SF describing complete vertex ownership
2482: Note: Two triangles sharing a face
2483: $
2484: $ 2
2485: $ / | \
2486: $ / | \
2487: $ / | \
2488: $ 0 0 | 1 3
2489: $ \ | /
2490: $ \ | /
2491: $ \ | /
2492: $ 1
2493: would have input
2494: $ numCells = 2, numVertices = 4
2495: $ cells = [0 1 2 1 3 2]
2496: $
2497: which would result in the DMPlex
2498: $
2499: $ 4
2500: $ / | \
2501: $ / | \
2502: $ / | \
2503: $ 2 0 | 1 5
2504: $ \ | /
2505: $ \ | /
2506: $ \ | /
2507: $ 3
2509: Level: beginner
2511: .seealso: DMPlexCreateFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate()
2512: @*/
2513: 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)
2514: {
2515: PetscSF sfVert;
2519: DMCreate(comm, dm);
2520: DMSetType(*dm, DMPLEX);
2523: DMSetDimension(*dm, dim);
2524: DMPlexBuildFromCellList_Parallel_Private(*dm, numCells, numVertices, numCorners, cells, &sfVert);
2525: if (interpolate) {
2526: DM idm;
2528: DMPlexInterpolate(*dm, &idm);
2529: DMDestroy(dm);
2530: *dm = idm;
2531: }
2532: DMPlexBuildCoordinates_Parallel_Private(*dm, spaceDim, numCells, numVertices,sfVert, vertexCoords);
2533: if (vertexSF) *vertexSF = sfVert;
2534: else {PetscSFDestroy(&sfVert);}
2535: return(0);
2536: }
2538: /*
2539: This takes as input the common mesh generator output, a list of the vertices for each cell
2540: */
2541: static PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[])
2542: {
2543: PetscInt *cone, c, p;
2547: DMPlexSetChart(dm, 0, numCells+numVertices);
2548: for (c = 0; c < numCells; ++c) {
2549: DMPlexSetConeSize(dm, c, numCorners);
2550: }
2551: DMSetUp(dm);
2552: DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);
2553: for (c = 0; c < numCells; ++c) {
2554: for (p = 0; p < numCorners; ++p) {
2555: cone[p] = cells[c*numCorners+p]+numCells;
2556: }
2557: DMPlexSetCone(dm, c, cone);
2558: }
2559: DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);
2560: DMPlexSymmetrize(dm);
2561: DMPlexStratify(dm);
2562: return(0);
2563: }
2565: /*
2566: This takes as input the coordinates for each vertex
2567: */
2568: static PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[])
2569: {
2570: PetscSection coordSection;
2571: Vec coordinates;
2572: DM cdm;
2573: PetscScalar *coords;
2574: PetscInt v, d;
2578: DMSetCoordinateDim(dm, spaceDim);
2579: DMGetCoordinateSection(dm, &coordSection);
2580: PetscSectionSetNumFields(coordSection, 1);
2581: PetscSectionSetFieldComponents(coordSection, 0, spaceDim);
2582: PetscSectionSetChart(coordSection, numCells, numCells + numVertices);
2583: for (v = numCells; v < numCells+numVertices; ++v) {
2584: PetscSectionSetDof(coordSection, v, spaceDim);
2585: PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);
2586: }
2587: PetscSectionSetUp(coordSection);
2589: DMGetCoordinateDM(dm, &cdm);
2590: DMCreateLocalVector(cdm, &coordinates);
2591: VecSetBlockSize(coordinates, spaceDim);
2592: PetscObjectSetName((PetscObject) coordinates, "coordinates");
2593: VecGetArray(coordinates, &coords);
2594: for (v = 0; v < numVertices; ++v) {
2595: for (d = 0; d < spaceDim; ++d) {
2596: coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d];
2597: }
2598: }
2599: VecRestoreArray(coordinates, &coords);
2600: DMSetCoordinatesLocal(dm, coordinates);
2601: VecDestroy(&coordinates);
2602: return(0);
2603: }
2605: /*@C
2606: DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM
2608: Input Parameters:
2609: + comm - The communicator
2610: . dim - The topological dimension of the mesh
2611: . numCells - The number of cells
2612: . numVertices - The number of vertices
2613: . numCorners - The number of vertices for each cell
2614: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
2615: . cells - An array of numCells*numCorners numbers, the vertices for each cell
2616: . spaceDim - The spatial dimension used for coordinates
2617: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
2619: Output Parameter:
2620: . dm - The DM
2622: Note: Two triangles sharing a face
2623: $
2624: $ 2
2625: $ / | \
2626: $ / | \
2627: $ / | \
2628: $ 0 0 | 1 3
2629: $ \ | /
2630: $ \ | /
2631: $ \ | /
2632: $ 1
2633: would have input
2634: $ numCells = 2, numVertices = 4
2635: $ cells = [0 1 2 1 3 2]
2636: $
2637: which would result in the DMPlex
2638: $
2639: $ 4
2640: $ / | \
2641: $ / | \
2642: $ / | \
2643: $ 2 0 | 1 5
2644: $ \ | /
2645: $ \ | /
2646: $ \ | /
2647: $ 3
2649: Level: beginner
2651: .seealso: DMPlexCreateFromDAG(), DMPlexCreate()
2652: @*/
2653: 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)
2654: {
2658: DMCreate(comm, dm);
2659: DMSetType(*dm, DMPLEX);
2660: DMSetDimension(*dm, dim);
2661: DMPlexBuildFromCellList_Private(*dm, numCells, numVertices, numCorners, cells);
2662: if (interpolate) {
2663: DM idm;
2665: DMPlexInterpolate(*dm, &idm);
2666: DMDestroy(dm);
2667: *dm = idm;
2668: }
2669: DMPlexBuildCoordinates_Private(*dm, spaceDim, numCells, numVertices, vertexCoords);
2670: return(0);
2671: }
2673: /*@
2674: DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM
2676: Input Parameters:
2677: + dm - The empty DM object, usually from DMCreate() and DMSetDimension()
2678: . depth - The depth of the DAG
2679: . numPoints - The number of points at each depth
2680: . coneSize - The cone size of each point
2681: . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point
2682: . coneOrientations - The orientation of each cone point
2683: - vertexCoords - An array of numVertices*dim numbers, the coordinates of each vertex
2685: Output Parameter:
2686: . dm - The DM
2688: Note: Two triangles sharing a face would have input
2689: $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0]
2690: $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0]
2691: $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0]
2692: $
2693: which would result in the DMPlex
2694: $
2695: $ 4
2696: $ / | \
2697: $ / | \
2698: $ / | \
2699: $ 2 0 | 1 5
2700: $ \ | /
2701: $ \ | /
2702: $ \ | /
2703: $ 3
2704: $
2705: $ Notice that all points are numbered consecutively, unlikely DMPlexCreateFromCellList()
2707: Level: advanced
2709: .seealso: DMPlexCreateFromCellList(), DMPlexCreate()
2710: @*/
2711: PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[])
2712: {
2713: Vec coordinates;
2714: PetscSection coordSection;
2715: PetscScalar *coords;
2716: PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off;
2720: DMGetDimension(dm, &dim);
2721: DMGetCoordinateDim(dm, &dimEmbed);
2722: if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %d cannot be less than intrinsic dimension %d",dimEmbed,dim);
2723: for (d = 0; d <= depth; ++d) pEnd += numPoints[d];
2724: DMPlexSetChart(dm, pStart, pEnd);
2725: for (p = pStart; p < pEnd; ++p) {
2726: DMPlexSetConeSize(dm, p, coneSize[p-pStart]);
2727: if (firstVertex < 0 && !coneSize[p - pStart]) {
2728: firstVertex = p - pStart;
2729: }
2730: }
2731: if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %d vertices but could not find any", numPoints[0]);
2732: DMSetUp(dm); /* Allocate space for cones */
2733: for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) {
2734: DMPlexSetCone(dm, p, &cones[off]);
2735: DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);
2736: }
2737: DMPlexSymmetrize(dm);
2738: DMPlexStratify(dm);
2739: /* Build coordinates */
2740: DMGetCoordinateSection(dm, &coordSection);
2741: PetscSectionSetNumFields(coordSection, 1);
2742: PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);
2743: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);
2744: for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) {
2745: PetscSectionSetDof(coordSection, v, dimEmbed);
2746: PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);
2747: }
2748: PetscSectionSetUp(coordSection);
2749: PetscSectionGetStorageSize(coordSection, &coordSize);
2750: VecCreate(PETSC_COMM_SELF, &coordinates);
2751: PetscObjectSetName((PetscObject) coordinates, "coordinates");
2752: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
2753: VecSetBlockSize(coordinates, dimEmbed);
2754: VecSetType(coordinates,VECSTANDARD);
2755: VecGetArray(coordinates, &coords);
2756: for (v = 0; v < numPoints[0]; ++v) {
2757: PetscInt off;
2759: PetscSectionGetOffset(coordSection, v+firstVertex, &off);
2760: for (d = 0; d < dimEmbed; ++d) {
2761: coords[off+d] = vertexCoords[v*dimEmbed+d];
2762: }
2763: }
2764: VecRestoreArray(coordinates, &coords);
2765: DMSetCoordinatesLocal(dm, coordinates);
2766: VecDestroy(&coordinates);
2767: return(0);
2768: }
2770: /*@C
2771: DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file.
2773: + comm - The MPI communicator
2774: . filename - Name of the .dat file
2775: - interpolate - Create faces and edges in the mesh
2777: Output Parameter:
2778: . dm - The DM object representing the mesh
2780: Note: The format is the simplest possible:
2781: $ Ne
2782: $ v0 v1 ... vk
2783: $ Nv
2784: $ x y z marker
2786: Level: beginner
2788: .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate()
2789: @*/
2790: PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
2791: {
2792: DMLabel marker;
2793: PetscViewer viewer;
2794: Vec coordinates;
2795: PetscSection coordSection;
2796: PetscScalar *coords;
2797: char line[PETSC_MAX_PATH_LEN];
2798: PetscInt dim = 3, cdim = 3, coordSize, v, c, d;
2799: PetscMPIInt rank;
2800: int snum, Nv, Nc;
2801: PetscErrorCode ierr;
2804: MPI_Comm_rank(comm, &rank);
2805: PetscViewerCreate(comm, &viewer);
2806: PetscViewerSetType(viewer, PETSCVIEWERASCII);
2807: PetscViewerFileSetMode(viewer, FILE_MODE_READ);
2808: PetscViewerFileSetName(viewer, filename);
2809: if (!rank) {
2810: PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);
2811: snum = sscanf(line, "%d %d", &Nc, &Nv);
2812: if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
2813: } else {
2814: Nc = Nv = 0;
2815: }
2816: DMCreate(comm, dm);
2817: DMSetType(*dm, DMPLEX);
2818: DMPlexSetChart(*dm, 0, Nc+Nv);
2819: DMSetDimension(*dm, dim);
2820: DMSetCoordinateDim(*dm, cdim);
2821: /* Read topology */
2822: if (!rank) {
2823: PetscInt cone[8], corners = 8;
2824: int vbuf[8], v;
2826: for (c = 0; c < Nc; ++c) {DMPlexSetConeSize(*dm, c, corners);}
2827: DMSetUp(*dm);
2828: for (c = 0; c < Nc; ++c) {
2829: PetscViewerRead(viewer, line, corners, NULL, PETSC_STRING);
2830: snum = sscanf(line, "%d %d %d %d %d %d %d %d", &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5], &vbuf[6], &vbuf[7]);
2831: if (snum != corners) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
2832: for (v = 0; v < corners; ++v) cone[v] = vbuf[v] + Nc;
2833: /* Hexahedra are inverted */
2834: {
2835: PetscInt tmp = cone[1];
2836: cone[1] = cone[3];
2837: cone[3] = tmp;
2838: }
2839: DMPlexSetCone(*dm, c, cone);
2840: }
2841: }
2842: DMPlexSymmetrize(*dm);
2843: DMPlexStratify(*dm);
2844: /* Read coordinates */
2845: DMGetCoordinateSection(*dm, &coordSection);
2846: PetscSectionSetNumFields(coordSection, 1);
2847: PetscSectionSetFieldComponents(coordSection, 0, cdim);
2848: PetscSectionSetChart(coordSection, Nc, Nc + Nv);
2849: for (v = Nc; v < Nc+Nv; ++v) {
2850: PetscSectionSetDof(coordSection, v, cdim);
2851: PetscSectionSetFieldDof(coordSection, v, 0, cdim);
2852: }
2853: PetscSectionSetUp(coordSection);
2854: PetscSectionGetStorageSize(coordSection, &coordSize);
2855: VecCreate(PETSC_COMM_SELF, &coordinates);
2856: PetscObjectSetName((PetscObject) coordinates, "coordinates");
2857: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
2858: VecSetBlockSize(coordinates, cdim);
2859: VecSetType(coordinates, VECSTANDARD);
2860: VecGetArray(coordinates, &coords);
2861: if (!rank) {
2862: double x[3];
2863: int val;
2865: DMCreateLabel(*dm, "marker");
2866: DMGetLabel(*dm, "marker", &marker);
2867: for (v = 0; v < Nv; ++v) {
2868: PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);
2869: snum = sscanf(line, "%lg %lg %lg %d", &x[0], &x[1], &x[2], &val);
2870: if (snum != 4) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
2871: for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d];
2872: if (val) {DMLabelSetValue(marker, v+Nc, val);}
2873: }
2874: }
2875: VecRestoreArray(coordinates, &coords);
2876: DMSetCoordinatesLocal(*dm, coordinates);
2877: VecDestroy(&coordinates);
2878: PetscViewerDestroy(&viewer);
2879: if (interpolate) {
2880: DM idm;
2881: DMLabel bdlabel;
2883: DMPlexInterpolate(*dm, &idm);
2884: DMDestroy(dm);
2885: *dm = idm;
2887: DMGetLabel(*dm, "marker", &bdlabel);
2888: DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);
2889: DMPlexLabelComplete(*dm, bdlabel);
2890: }
2891: return(0);
2892: }
2894: /*@C
2895: DMPlexCreateFromFile - This takes a filename and produces a DM
2897: Input Parameters:
2898: + comm - The communicator
2899: . filename - A file name
2900: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
2902: Output Parameter:
2903: . dm - The DM
2905: Level: beginner
2907: .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellList(), DMPlexCreate()
2908: @*/
2909: PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
2910: {
2911: const char *extGmsh = ".msh";
2912: const char *extCGNS = ".cgns";
2913: const char *extExodus = ".exo";
2914: const char *extGenesis = ".gen";
2915: const char *extFluent = ".cas";
2916: const char *extHDF5 = ".h5";
2917: const char *extMed = ".med";
2918: const char *extPLY = ".ply";
2919: const char *extCV = ".dat";
2920: size_t len;
2921: PetscBool isGmsh, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isCV;
2922: PetscMPIInt rank;
2928: MPI_Comm_rank(comm, &rank);
2929: PetscStrlen(filename, &len);
2930: if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path");
2931: PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);
2932: PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);
2933: PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);
2934: PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);
2935: PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);
2936: PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);
2937: PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);
2938: PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);
2939: PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);
2940: if (isGmsh) {
2941: DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);
2942: } else if (isCGNS) {
2943: DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);
2944: } else if (isExodus || isGenesis) {
2945: DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);
2946: } else if (isFluent) {
2947: DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);
2948: } else if (isHDF5) {
2949: PetscViewer viewer;
2951: PetscViewerCreate(comm, &viewer);
2952: PetscViewerSetType(viewer, PETSCVIEWERHDF5);
2953: PetscViewerFileSetMode(viewer, FILE_MODE_READ);
2954: PetscViewerFileSetName(viewer, filename);
2955: DMCreate(comm, dm);
2956: DMSetType(*dm, DMPLEX);
2957: DMLoad(*dm, viewer);
2958: PetscViewerDestroy(&viewer);
2960: if (interpolate) {
2961: DM idm;
2963: DMPlexInterpolate(*dm, &idm);
2964: DMDestroy(dm);
2965: *dm = idm;
2966: }
2967: } else if (isMed) {
2968: DMPlexCreateMedFromFile(comm, filename, interpolate, dm);
2969: } else if (isPLY) {
2970: DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);
2971: } else if (isCV) {
2972: DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);
2973: } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename);
2974: return(0);
2975: }
2977: /*@
2978: DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell
2980: Collective on comm
2982: Input Parameters:
2983: + comm - The communicator
2984: . dim - The spatial dimension
2985: - simplex - Flag for simplex, otherwise use a tensor-product cell
2987: Output Parameter:
2988: . refdm - The reference cell
2990: Level: intermediate
2992: .keywords: reference cell
2993: .seealso:
2994: @*/
2995: PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm)
2996: {
2997: DM rdm;
2998: Vec coords;
3002: DMCreate(comm, &rdm);
3003: DMSetType(rdm, DMPLEX);
3004: DMSetDimension(rdm, dim);
3005: switch (dim) {
3006: case 0:
3007: {
3008: PetscInt numPoints[1] = {1};
3009: PetscInt coneSize[1] = {0};
3010: PetscInt cones[1] = {0};
3011: PetscInt coneOrientations[1] = {0};
3012: PetscScalar vertexCoords[1] = {0.0};
3014: DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3015: }
3016: break;
3017: case 1:
3018: {
3019: PetscInt numPoints[2] = {2, 1};
3020: PetscInt coneSize[3] = {2, 0, 0};
3021: PetscInt cones[2] = {1, 2};
3022: PetscInt coneOrientations[2] = {0, 0};
3023: PetscScalar vertexCoords[2] = {-1.0, 1.0};
3025: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3026: }
3027: break;
3028: case 2:
3029: if (simplex) {
3030: PetscInt numPoints[2] = {3, 1};
3031: PetscInt coneSize[4] = {3, 0, 0, 0};
3032: PetscInt cones[3] = {1, 2, 3};
3033: PetscInt coneOrientations[3] = {0, 0, 0};
3034: PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0};
3036: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3037: } else {
3038: PetscInt numPoints[2] = {4, 1};
3039: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
3040: PetscInt cones[4] = {1, 2, 3, 4};
3041: PetscInt coneOrientations[4] = {0, 0, 0, 0};
3042: PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0};
3044: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3045: }
3046: break;
3047: case 3:
3048: if (simplex) {
3049: PetscInt numPoints[2] = {4, 1};
3050: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
3051: PetscInt cones[4] = {1, 3, 2, 4};
3052: PetscInt coneOrientations[4] = {0, 0, 0, 0};
3053: 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};
3055: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3056: } else {
3057: PetscInt numPoints[2] = {8, 1};
3058: PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0};
3059: PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8};
3060: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
3061: 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,
3062: -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0};
3064: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3065: }
3066: break;
3067: default:
3068: SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %d", dim);
3069: }
3070: DMPlexInterpolate(rdm, refdm);
3071: if (rdm->coordinateDM) {
3072: DM ncdm;
3073: PetscSection cs;
3074: PetscInt pEnd = -1;
3076: DMGetDefaultSection(rdm->coordinateDM, &cs);
3077: if (cs) {PetscSectionGetChart(cs, NULL, &pEnd);}
3078: if (pEnd >= 0) {
3079: DMClone(rdm->coordinateDM, &ncdm);
3080: DMSetDefaultSection(ncdm, cs);
3081: DMSetCoordinateDM(*refdm, ncdm);
3082: DMDestroy(&ncdm);
3083: }
3084: }
3085: DMGetCoordinatesLocal(rdm, &coords);
3086: if (coords) {
3087: DMSetCoordinatesLocal(*refdm, coords);
3088: } else {
3089: DMGetCoordinates(rdm, &coords);
3090: if (coords) {DMSetCoordinates(*refdm, coords);}
3091: }
3092: DMDestroy(&rdm);
3093: return(0);
3094: }