Actual source code: plexcreate.c
petsc-3.12.0 2019-09-29
1: #define PETSCDM_DLL
2: #include <petsc/private/dmpleximpl.h>
3: #include <petsc/private/hashseti.h>
4: #include <petscsf.h>
6: /*@
7: DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement.
9: Collective
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: .seealso: DMSetType(), DMCreate()
25: @*/
26: PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscBool refinementUniform, PetscReal refinementLimit, DM *newdm)
27: {
28: DM dm;
29: PetscInt p;
30: PetscMPIInt rank;
34: DMCreate(comm, &dm);
35: DMSetType(dm, DMPLEX);
36: DMSetDimension(dm, dim);
37: MPI_Comm_rank(comm, &rank);
38: switch (dim) {
39: case 2:
40: if (simplex) {PetscObjectSetName((PetscObject) dm, "triangular");}
41: else {PetscObjectSetName((PetscObject) dm, "quadrilateral");}
42: break;
43: case 3:
44: if (simplex) {PetscObjectSetName((PetscObject) dm, "tetrahedral");}
45: else {PetscObjectSetName((PetscObject) dm, "hexahedral");}
46: break;
47: default:
48: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim);
49: }
50: if (rank) {
51: PetscInt numPoints[2] = {0, 0};
52: DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);
53: } else {
54: switch (dim) {
55: case 2:
56: if (simplex) {
57: PetscInt numPoints[2] = {4, 2};
58: PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0};
59: PetscInt cones[6] = {2, 3, 4, 5, 4, 3};
60: PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0};
61: PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5};
62: PetscInt markerPoints[8] = {2, 1, 3, 1, 4, 1, 5, 1};
64: DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
65: for (p = 0; p < 4; ++p) {DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);}
66: } else {
67: PetscInt numPoints[2] = {6, 2};
68: PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0};
69: PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4};
70: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
71: 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};
73: DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
74: }
75: break;
76: case 3:
77: if (simplex) {
78: PetscInt numPoints[2] = {5, 2};
79: PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0};
80: PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6};
81: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
82: 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};
83: PetscInt markerPoints[10] = {2, 1, 3, 1, 4, 1, 5, 1, 6, 1};
85: DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
86: for (p = 0; p < 5; ++p) {DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);}
87: } else {
88: PetscInt numPoints[2] = {12, 2};
89: PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
90: PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8};
91: PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
92: 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,
93: -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5,
94: 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5};
96: DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
97: }
98: break;
99: default:
100: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim);
101: }
102: }
103: *newdm = dm;
104: if (refinementLimit > 0.0) {
105: DM rdm;
106: const char *name;
108: DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);
109: DMPlexSetRefinementLimit(*newdm, refinementLimit);
110: DMRefine(*newdm, comm, &rdm);
111: PetscObjectGetName((PetscObject) *newdm, &name);
112: PetscObjectSetName((PetscObject) rdm, name);
113: DMDestroy(newdm);
114: *newdm = rdm;
115: }
116: if (interpolate) {
117: DM idm;
119: DMPlexInterpolate(*newdm, &idm);
120: DMDestroy(newdm);
121: *newdm = idm;
122: }
123: {
124: DM refinedMesh = NULL;
125: DM distributedMesh = NULL;
127: /* Distribute mesh over processes */
128: DMPlexDistribute(*newdm, 0, NULL, &distributedMesh);
129: if (distributedMesh) {
130: DMDestroy(newdm);
131: *newdm = distributedMesh;
132: }
133: if (refinementUniform) {
134: DMPlexSetRefinementUniform(*newdm, refinementUniform);
135: DMRefine(*newdm, comm, &refinedMesh);
136: if (refinedMesh) {
137: DMDestroy(newdm);
138: *newdm = refinedMesh;
139: }
140: }
141: }
142: return(0);
143: }
145: /*@
146: DMPlexCreateSquareBoundary - Creates a 1D mesh the is the boundary of a square lattice.
148: Collective
150: Input Parameters:
151: + comm - The communicator for the DM object
152: . lower - The lower left corner coordinates
153: . upper - The upper right corner coordinates
154: - edges - The number of cells in each direction
156: Output Parameter:
157: . dm - The DM object
159: Note: Here is the numbering returned for 2 cells in each direction:
160: $ 18--5-17--4--16
161: $ | | |
162: $ 6 10 3
163: $ | | |
164: $ 19-11-20--9--15
165: $ | | |
166: $ 7 8 2
167: $ | | |
168: $ 12--0-13--1--14
170: Level: beginner
172: .seealso: DMPlexCreateBoxMesh(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate()
173: @*/
174: PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
175: {
176: const PetscInt numVertices = (edges[0]+1)*(edges[1]+1);
177: const PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1];
178: PetscInt markerTop = 1;
179: PetscInt markerBottom = 1;
180: PetscInt markerRight = 1;
181: PetscInt markerLeft = 1;
182: PetscBool markerSeparate = PETSC_FALSE;
183: Vec coordinates;
184: PetscSection coordSection;
185: PetscScalar *coords;
186: PetscInt coordSize;
187: PetscMPIInt rank;
188: PetscInt v, vx, vy;
192: PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);
193: if (markerSeparate) {
194: markerTop = 3;
195: markerBottom = 1;
196: markerRight = 2;
197: markerLeft = 4;
198: }
199: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
200: if (!rank) {
201: PetscInt e, ex, ey;
203: DMPlexSetChart(dm, 0, numEdges+numVertices);
204: for (e = 0; e < numEdges; ++e) {
205: DMPlexSetConeSize(dm, e, 2);
206: }
207: DMSetUp(dm); /* Allocate space for cones */
208: for (vx = 0; vx <= edges[0]; vx++) {
209: for (ey = 0; ey < edges[1]; ey++) {
210: PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1);
211: PetscInt vertex = ey*(edges[0]+1) + vx + numEdges;
212: PetscInt cone[2];
214: cone[0] = vertex; cone[1] = vertex+edges[0]+1;
215: DMPlexSetCone(dm, edge, cone);
216: if (vx == edges[0]) {
217: DMSetLabelValue(dm, "marker", edge, markerRight);
218: DMSetLabelValue(dm, "marker", cone[0], markerRight);
219: if (ey == edges[1]-1) {
220: DMSetLabelValue(dm, "marker", cone[1], markerRight);
221: DMSetLabelValue(dm, "Face Sets", cone[1], markerRight);
222: }
223: } else if (vx == 0) {
224: DMSetLabelValue(dm, "marker", edge, markerLeft);
225: DMSetLabelValue(dm, "marker", cone[0], markerLeft);
226: if (ey == edges[1]-1) {
227: DMSetLabelValue(dm, "marker", cone[1], markerLeft);
228: DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft);
229: }
230: }
231: }
232: }
233: for (vy = 0; vy <= edges[1]; vy++) {
234: for (ex = 0; ex < edges[0]; ex++) {
235: PetscInt edge = vy*edges[0] + ex;
236: PetscInt vertex = vy*(edges[0]+1) + ex + numEdges;
237: PetscInt cone[2];
239: cone[0] = vertex; cone[1] = vertex+1;
240: DMPlexSetCone(dm, edge, cone);
241: if (vy == edges[1]) {
242: DMSetLabelValue(dm, "marker", edge, markerTop);
243: DMSetLabelValue(dm, "marker", cone[0], markerTop);
244: if (ex == edges[0]-1) {
245: DMSetLabelValue(dm, "marker", cone[1], markerTop);
246: DMSetLabelValue(dm, "Face Sets", cone[1], markerTop);
247: }
248: } else if (vy == 0) {
249: DMSetLabelValue(dm, "marker", edge, markerBottom);
250: DMSetLabelValue(dm, "marker", cone[0], markerBottom);
251: if (ex == edges[0]-1) {
252: DMSetLabelValue(dm, "marker", cone[1], markerBottom);
253: DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom);
254: }
255: }
256: }
257: }
258: }
259: DMPlexSymmetrize(dm);
260: DMPlexStratify(dm);
261: /* Build coordinates */
262: DMSetCoordinateDim(dm, 2);
263: DMGetCoordinateSection(dm, &coordSection);
264: PetscSectionSetNumFields(coordSection, 1);
265: PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);
266: PetscSectionSetFieldComponents(coordSection, 0, 2);
267: for (v = numEdges; v < numEdges+numVertices; ++v) {
268: PetscSectionSetDof(coordSection, v, 2);
269: PetscSectionSetFieldDof(coordSection, v, 0, 2);
270: }
271: PetscSectionSetUp(coordSection);
272: PetscSectionGetStorageSize(coordSection, &coordSize);
273: VecCreate(PETSC_COMM_SELF, &coordinates);
274: PetscObjectSetName((PetscObject) coordinates, "coordinates");
275: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
276: VecSetBlockSize(coordinates, 2);
277: VecSetType(coordinates,VECSTANDARD);
278: VecGetArray(coordinates, &coords);
279: for (vy = 0; vy <= edges[1]; ++vy) {
280: for (vx = 0; vx <= edges[0]; ++vx) {
281: coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx;
282: coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy;
283: }
284: }
285: VecRestoreArray(coordinates, &coords);
286: DMSetCoordinatesLocal(dm, coordinates);
287: VecDestroy(&coordinates);
288: return(0);
289: }
291: /*@
292: DMPlexCreateCubeBoundary - Creates a 2D mesh that is the boundary of a cubic lattice.
294: Collective
296: Input Parameters:
297: + comm - The communicator for the DM object
298: . lower - The lower left front corner coordinates
299: . upper - The upper right back corner coordinates
300: - edges - The number of cells in each direction
302: Output Parameter:
303: . dm - The DM object
305: Level: beginner
307: .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMSetType(), DMCreate()
308: @*/
309: PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[])
310: {
311: PetscInt vertices[3], numVertices;
312: PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2];
313: Vec coordinates;
314: PetscSection coordSection;
315: PetscScalar *coords;
316: PetscInt coordSize;
317: PetscMPIInt rank;
318: PetscInt v, vx, vy, vz;
319: PetscInt voffset, iface=0, cone[4];
323: 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");
324: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
325: vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1;
326: numVertices = vertices[0]*vertices[1]*vertices[2];
327: if (!rank) {
328: PetscInt f;
330: DMPlexSetChart(dm, 0, numFaces+numVertices);
331: for (f = 0; f < numFaces; ++f) {
332: DMPlexSetConeSize(dm, f, 4);
333: }
334: DMSetUp(dm); /* Allocate space for cones */
336: /* Side 0 (Top) */
337: for (vy = 0; vy < faces[1]; vy++) {
338: for (vx = 0; vx < faces[0]; vx++) {
339: voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx;
340: cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0];
341: DMPlexSetCone(dm, iface, cone);
342: DMSetLabelValue(dm, "marker", iface, 1);
343: DMSetLabelValue(dm, "marker", voffset+0, 1);
344: DMSetLabelValue(dm, "marker", voffset+1, 1);
345: DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);
346: DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);
347: iface++;
348: }
349: }
351: /* Side 1 (Bottom) */
352: for (vy = 0; vy < faces[1]; vy++) {
353: for (vx = 0; vx < faces[0]; vx++) {
354: voffset = numFaces + vy*(faces[0]+1) + vx;
355: cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1;
356: DMPlexSetCone(dm, iface, cone);
357: DMSetLabelValue(dm, "marker", iface, 1);
358: DMSetLabelValue(dm, "marker", voffset+0, 1);
359: DMSetLabelValue(dm, "marker", voffset+1, 1);
360: DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);
361: DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);
362: iface++;
363: }
364: }
366: /* Side 2 (Front) */
367: for (vz = 0; vz < faces[2]; vz++) {
368: for (vx = 0; vx < faces[0]; vx++) {
369: voffset = numFaces + vz*vertices[0]*vertices[1] + vx;
370: cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1];
371: DMPlexSetCone(dm, iface, cone);
372: DMSetLabelValue(dm, "marker", iface, 1);
373: DMSetLabelValue(dm, "marker", voffset+0, 1);
374: DMSetLabelValue(dm, "marker", voffset+1, 1);
375: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);
376: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);
377: iface++;
378: }
379: }
381: /* Side 3 (Back) */
382: for (vz = 0; vz < faces[2]; vz++) {
383: for (vx = 0; vx < faces[0]; vx++) {
384: voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx;
385: cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1;
386: cone[2] = voffset+1; cone[3] = voffset;
387: DMPlexSetCone(dm, iface, cone);
388: DMSetLabelValue(dm, "marker", iface, 1);
389: DMSetLabelValue(dm, "marker", voffset+0, 1);
390: DMSetLabelValue(dm, "marker", voffset+1, 1);
391: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);
392: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);
393: iface++;
394: }
395: }
397: /* Side 4 (Left) */
398: for (vz = 0; vz < faces[2]; vz++) {
399: for (vy = 0; vy < faces[1]; vy++) {
400: voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0];
401: cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1];
402: cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0];
403: DMPlexSetCone(dm, iface, cone);
404: DMSetLabelValue(dm, "marker", iface, 1);
405: DMSetLabelValue(dm, "marker", voffset+0, 1);
406: DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);
407: DMSetLabelValue(dm, "marker", voffset+vertices[1]+0, 1);
408: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);
409: iface++;
410: }
411: }
413: /* Side 5 (Right) */
414: for (vz = 0; vz < faces[2]; vz++) {
415: for (vy = 0; vy < faces[1]; vy++) {
416: voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + faces[0];
417: cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset;
418: cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0];
419: DMPlexSetCone(dm, iface, cone);
420: DMSetLabelValue(dm, "marker", iface, 1);
421: DMSetLabelValue(dm, "marker", voffset+0, 1);
422: DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);
423: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);
424: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);
425: iface++;
426: }
427: }
428: }
429: DMPlexSymmetrize(dm);
430: DMPlexStratify(dm);
431: /* Build coordinates */
432: DMSetCoordinateDim(dm, 3);
433: DMGetCoordinateSection(dm, &coordSection);
434: PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);
435: for (v = numFaces; v < numFaces+numVertices; ++v) {
436: PetscSectionSetDof(coordSection, v, 3);
437: }
438: PetscSectionSetUp(coordSection);
439: PetscSectionGetStorageSize(coordSection, &coordSize);
440: VecCreate(PETSC_COMM_SELF, &coordinates);
441: PetscObjectSetName((PetscObject) coordinates, "coordinates");
442: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
443: VecSetBlockSize(coordinates, 3);
444: VecSetType(coordinates,VECSTANDARD);
445: VecGetArray(coordinates, &coords);
446: for (vz = 0; vz <= faces[2]; ++vz) {
447: for (vy = 0; vy <= faces[1]; ++vy) {
448: for (vx = 0; vx <= faces[0]; ++vx) {
449: coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx;
450: coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy;
451: coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz;
452: }
453: }
454: }
455: VecRestoreArray(coordinates, &coords);
456: DMSetCoordinatesLocal(dm, coordinates);
457: VecDestroy(&coordinates);
458: return(0);
459: }
461: static PetscErrorCode DMPlexCreateLineMesh_Internal(MPI_Comm comm,PetscInt segments,PetscReal lower,PetscReal upper,DMBoundaryType bd,DM *dm)
462: {
463: PetscInt i,fStart,fEnd,numCells = 0,numVerts = 0;
464: PetscInt numPoints[2],*coneSize,*cones,*coneOrientations;
465: PetscScalar *vertexCoords;
466: PetscReal L,maxCell;
467: PetscBool markerSeparate = PETSC_FALSE;
468: PetscInt markerLeft = 1, faceMarkerLeft = 1;
469: PetscInt markerRight = 1, faceMarkerRight = 2;
470: PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE;
471: PetscMPIInt rank;
477: DMCreate(comm,dm);
478: DMSetType(*dm,DMPLEX);
479: DMSetDimension(*dm,1);
480: DMCreateLabel(*dm,"marker");
481: DMCreateLabel(*dm,"Face Sets");
483: MPI_Comm_rank(comm,&rank);
484: if (!rank) numCells = segments;
485: if (!rank) numVerts = segments + (wrap ? 0 : 1);
487: numPoints[0] = numVerts ; numPoints[1] = numCells;
488: PetscMalloc4(numCells+numVerts,&coneSize,numCells*2,&cones,numCells+numVerts,&coneOrientations,numVerts,&vertexCoords);
489: PetscArrayzero(coneOrientations,numCells+numVerts);
490: for (i = 0; i < numCells; ++i) { coneSize[i] = 2; }
491: for (i = 0; i < numVerts; ++i) { coneSize[numCells+i] = 0; }
492: for (i = 0; i < numCells; ++i) { cones[2*i] = numCells + i%numVerts; cones[2*i+1] = numCells + (i+1)%numVerts; }
493: for (i = 0; i < numVerts; ++i) { vertexCoords[i] = lower + (upper-lower)*((PetscReal)i/(PetscReal)numCells); }
494: DMPlexCreateFromDAG(*dm,1,numPoints,coneSize,cones,coneOrientations,vertexCoords);
495: PetscFree4(coneSize,cones,coneOrientations,vertexCoords);
497: PetscOptionsGetBool(((PetscObject)*dm)->options,((PetscObject)*dm)->prefix,"-dm_plex_separate_marker",&markerSeparate,NULL);
498: if (markerSeparate) { markerLeft = faceMarkerLeft; markerRight = faceMarkerRight;}
499: if (!wrap && !rank) {
500: DMPlexGetHeightStratum(*dm,1,&fStart,&fEnd);
501: DMSetLabelValue(*dm,"marker",fStart,markerLeft);
502: DMSetLabelValue(*dm,"marker",fEnd-1,markerRight);
503: DMSetLabelValue(*dm,"Face Sets",fStart,faceMarkerLeft);
504: DMSetLabelValue(*dm,"Face Sets",fEnd-1,faceMarkerRight);
505: }
506: if (wrap) {
507: L = upper - lower;
508: maxCell = (PetscReal)1.1*(L/(PetscReal)PetscMax(1,segments));
509: DMSetPeriodicity(*dm,PETSC_TRUE,&maxCell,&L,&bd);
510: }
511: return(0);
512: }
514: 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)
515: {
516: DM boundary;
517: PetscInt i;
522: for (i = 0; i < dim; ++i) if (periodicity[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity is not supported for simplex meshes");
523: DMCreate(comm, &boundary);
525: DMSetType(boundary, DMPLEX);
526: DMSetDimension(boundary, dim-1);
527: DMSetCoordinateDim(boundary, dim);
528: switch (dim) {
529: case 2: DMPlexCreateSquareBoundary(boundary, lower, upper, faces);break;
530: case 3: DMPlexCreateCubeBoundary(boundary, lower, upper, faces);break;
531: default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim);
532: }
533: DMPlexGenerate(boundary, NULL, interpolate, dm);
534: DMDestroy(&boundary);
535: return(0);
536: }
538: static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ)
539: {
540: DMLabel cutLabel = NULL;
541: PetscInt markerTop = 1, faceMarkerTop = 1;
542: PetscInt markerBottom = 1, faceMarkerBottom = 1;
543: PetscInt markerFront = 1, faceMarkerFront = 1;
544: PetscInt markerBack = 1, faceMarkerBack = 1;
545: PetscInt markerRight = 1, faceMarkerRight = 1;
546: PetscInt markerLeft = 1, faceMarkerLeft = 1;
547: PetscInt dim;
548: PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE;
549: PetscMPIInt rank;
553: DMGetDimension(dm,&dim);
554: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
555: DMCreateLabel(dm,"marker");
556: DMCreateLabel(dm,"Face Sets");
557: PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL);
558: if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ||
559: bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ||
560: bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) {
562: if (cutMarker) {DMCreateLabel(dm, "periodic_cut"); DMGetLabel(dm, "periodic_cut", &cutLabel);}
563: }
564: switch (dim) {
565: case 2:
566: faceMarkerTop = 3;
567: faceMarkerBottom = 1;
568: faceMarkerRight = 2;
569: faceMarkerLeft = 4;
570: break;
571: case 3:
572: faceMarkerBottom = 1;
573: faceMarkerTop = 2;
574: faceMarkerFront = 3;
575: faceMarkerBack = 4;
576: faceMarkerRight = 5;
577: faceMarkerLeft = 6;
578: break;
579: default:
580: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %d not supported",dim);
581: break;
582: }
583: PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);
584: if (markerSeparate) {
585: markerBottom = faceMarkerBottom;
586: markerTop = faceMarkerTop;
587: markerFront = faceMarkerFront;
588: markerBack = faceMarkerBack;
589: markerRight = faceMarkerRight;
590: markerLeft = faceMarkerLeft;
591: }
592: {
593: const PetscInt numXEdges = !rank ? edges[0] : 0;
594: const PetscInt numYEdges = !rank ? edges[1] : 0;
595: const PetscInt numZEdges = !rank ? edges[2] : 0;
596: const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0;
597: const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0;
598: const PetscInt numZVertices = !rank ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0;
599: const PetscInt numCells = numXEdges*numYEdges*numZEdges;
600: const PetscInt numXFaces = numYEdges*numZEdges;
601: const PetscInt numYFaces = numXEdges*numZEdges;
602: const PetscInt numZFaces = numXEdges*numYEdges;
603: const PetscInt numTotXFaces = numXVertices*numXFaces;
604: const PetscInt numTotYFaces = numYVertices*numYFaces;
605: const PetscInt numTotZFaces = numZVertices*numZFaces;
606: const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces;
607: const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices;
608: const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices;
609: const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices;
610: const PetscInt numVertices = numXVertices*numYVertices*numZVertices;
611: const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges;
612: const PetscInt firstVertex = (dim == 2) ? numFaces : numCells;
613: const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices;
614: const PetscInt firstYFace = firstXFace + numTotXFaces;
615: const PetscInt firstZFace = firstYFace + numTotYFaces;
616: const PetscInt firstXEdge = numCells + numFaces + numVertices;
617: const PetscInt firstYEdge = firstXEdge + numTotXEdges;
618: const PetscInt firstZEdge = firstYEdge + numTotYEdges;
619: Vec coordinates;
620: PetscSection coordSection;
621: PetscScalar *coords;
622: PetscInt coordSize;
623: PetscInt v, vx, vy, vz;
624: PetscInt c, f, fx, fy, fz, e, ex, ey, ez;
626: DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);
627: for (c = 0; c < numCells; c++) {
628: DMPlexSetConeSize(dm, c, 6);
629: }
630: for (f = firstXFace; f < firstXFace+numFaces; ++f) {
631: DMPlexSetConeSize(dm, f, 4);
632: }
633: for (e = firstXEdge; e < firstXEdge+numEdges; ++e) {
634: DMPlexSetConeSize(dm, e, 2);
635: }
636: DMSetUp(dm); /* Allocate space for cones */
637: /* Build cells */
638: for (fz = 0; fz < numZEdges; ++fz) {
639: for (fy = 0; fy < numYEdges; ++fy) {
640: for (fx = 0; fx < numXEdges; ++fx) {
641: PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx;
642: PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz;
643: PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices);
644: PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy;
645: PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices);
646: PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx;
647: PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices);
648: /* B, T, F, K, R, L */
649: PetscInt ornt[6] = {-4, 0, 0, -1, 0, -4}; /* ??? */
650: PetscInt cone[6];
652: /* no boundary twisting in 3D */
653: cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL;
654: DMPlexSetCone(dm, cell, cone);
655: DMPlexSetConeOrientation(dm, cell, ornt);
656: if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, cell, 2);}
657: if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, cell, 2);}
658: if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, cell, 2);}
659: }
660: }
661: }
662: /* Build x faces */
663: for (fz = 0; fz < numZEdges; ++fz) {
664: for (fy = 0; fy < numYEdges; ++fy) {
665: for (fx = 0; fx < numXVertices; ++fx) {
666: PetscInt face = firstXFace + (fz*numYEdges+fy)*numXVertices + fx;
667: PetscInt edgeL = firstZEdge + ( fy* numXVertices+fx)*numZEdges + fz;
668: PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz;
669: PetscInt edgeB = firstYEdge + ( fz* numXVertices+fx)*numYEdges + fy;
670: PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy;
671: PetscInt ornt[4] = {0, 0, -2, -2};
672: PetscInt cone[4];
674: if (dim == 3) {
675: /* markers */
676: if (bdX != DM_BOUNDARY_PERIODIC) {
677: if (fx == numXVertices-1) {
678: DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);
679: DMSetLabelValue(dm, "marker", face, markerRight);
680: }
681: else if (fx == 0) {
682: DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);
683: DMSetLabelValue(dm, "marker", face, markerLeft);
684: }
685: }
686: }
687: cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
688: DMPlexSetCone(dm, face, cone);
689: DMPlexSetConeOrientation(dm, face, ornt);
690: }
691: }
692: }
693: /* Build y faces */
694: for (fz = 0; fz < numZEdges; ++fz) {
695: for (fx = 0; fx < numXEdges; ++fx) {
696: for (fy = 0; fy < numYVertices; ++fy) {
697: PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy;
698: PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx )*numZEdges + fz;
699: PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz;
700: PetscInt edgeB = firstXEdge + ( fz *numYVertices+fy)*numXEdges + fx;
701: PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx;
702: PetscInt ornt[4] = {0, 0, -2, -2};
703: PetscInt cone[4];
705: if (dim == 3) {
706: /* markers */
707: if (bdY != DM_BOUNDARY_PERIODIC) {
708: if (fy == numYVertices-1) {
709: DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);
710: DMSetLabelValue(dm, "marker", face, markerBack);
711: }
712: else if (fy == 0) {
713: DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);
714: DMSetLabelValue(dm, "marker", face, markerFront);
715: }
716: }
717: }
718: cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
719: DMPlexSetCone(dm, face, cone);
720: DMPlexSetConeOrientation(dm, face, ornt);
721: }
722: }
723: }
724: /* Build z faces */
725: for (fy = 0; fy < numYEdges; ++fy) {
726: for (fx = 0; fx < numXEdges; ++fx) {
727: for (fz = 0; fz < numZVertices; fz++) {
728: PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz;
729: PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx )*numYEdges + fy;
730: PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy;
731: PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy )*numXEdges + fx;
732: PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx;
733: PetscInt ornt[4] = {0, 0, -2, -2};
734: PetscInt cone[4];
736: if (dim == 2) {
737: if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -2;}
738: if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;}
739: if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, face, 2);}
740: if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, face, 2);}
741: } else {
742: /* markers */
743: if (bdZ != DM_BOUNDARY_PERIODIC) {
744: if (fz == numZVertices-1) {
745: DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);
746: DMSetLabelValue(dm, "marker", face, markerTop);
747: }
748: else if (fz == 0) {
749: DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);
750: DMSetLabelValue(dm, "marker", face, markerBottom);
751: }
752: }
753: }
754: cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
755: DMPlexSetCone(dm, face, cone);
756: DMPlexSetConeOrientation(dm, face, ornt);
757: }
758: }
759: }
760: /* Build Z edges*/
761: for (vy = 0; vy < numYVertices; vy++) {
762: for (vx = 0; vx < numXVertices; vx++) {
763: for (ez = 0; ez < numZEdges; ez++) {
764: const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez;
765: const PetscInt vertexB = firstVertex + ( ez *numYVertices+vy)*numXVertices + vx;
766: const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx;
767: PetscInt cone[2];
769: if (dim == 3) {
770: if (bdX != DM_BOUNDARY_PERIODIC) {
771: if (vx == numXVertices-1) {
772: DMSetLabelValue(dm, "marker", edge, markerRight);
773: }
774: else if (vx == 0) {
775: DMSetLabelValue(dm, "marker", edge, markerLeft);
776: }
777: }
778: if (bdY != DM_BOUNDARY_PERIODIC) {
779: if (vy == numYVertices-1) {
780: DMSetLabelValue(dm, "marker", edge, markerBack);
781: }
782: else if (vy == 0) {
783: DMSetLabelValue(dm, "marker", edge, markerFront);
784: }
785: }
786: }
787: cone[0] = vertexB; cone[1] = vertexT;
788: DMPlexSetCone(dm, edge, cone);
789: }
790: }
791: }
792: /* Build Y edges*/
793: for (vz = 0; vz < numZVertices; vz++) {
794: for (vx = 0; vx < numXVertices; vx++) {
795: for (ey = 0; ey < numYEdges; ey++) {
796: const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx;
797: const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey;
798: const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx;
799: const PetscInt vertexK = firstVertex + nextv;
800: PetscInt cone[2];
802: cone[0] = vertexF; cone[1] = vertexK;
803: DMPlexSetCone(dm, edge, cone);
804: if (dim == 2) {
805: if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) {
806: if (vx == numXVertices-1) {
807: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);
808: DMSetLabelValue(dm, "marker", edge, markerRight);
809: DMSetLabelValue(dm, "marker", cone[0], markerRight);
810: if (ey == numYEdges-1) {
811: DMSetLabelValue(dm, "marker", cone[1], markerRight);
812: }
813: } else if (vx == 0) {
814: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);
815: DMSetLabelValue(dm, "marker", edge, markerLeft);
816: DMSetLabelValue(dm, "marker", cone[0], markerLeft);
817: if (ey == numYEdges-1) {
818: DMSetLabelValue(dm, "marker", cone[1], markerLeft);
819: }
820: }
821: } else {
822: if (vx == 0 && cutLabel) {
823: DMLabelSetValue(cutLabel, edge, 1);
824: DMLabelSetValue(cutLabel, cone[0], 1);
825: if (ey == numYEdges-1) {
826: DMLabelSetValue(cutLabel, cone[1], 1);
827: }
828: }
829: }
830: } else {
831: if (bdX != DM_BOUNDARY_PERIODIC) {
832: if (vx == numXVertices-1) {
833: DMSetLabelValue(dm, "marker", edge, markerRight);
834: } else if (vx == 0) {
835: DMSetLabelValue(dm, "marker", edge, markerLeft);
836: }
837: }
838: if (bdZ != DM_BOUNDARY_PERIODIC) {
839: if (vz == numZVertices-1) {
840: DMSetLabelValue(dm, "marker", edge, markerTop);
841: } else if (vz == 0) {
842: DMSetLabelValue(dm, "marker", edge, markerBottom);
843: }
844: }
845: }
846: }
847: }
848: }
849: /* Build X edges*/
850: for (vz = 0; vz < numZVertices; vz++) {
851: for (vy = 0; vy < numYVertices; vy++) {
852: for (ex = 0; ex < numXEdges; ex++) {
853: const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices;
854: const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex;
855: const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex;
856: const PetscInt vertexR = firstVertex + nextv;
857: PetscInt cone[2];
859: cone[0] = vertexL; cone[1] = vertexR;
860: DMPlexSetCone(dm, edge, cone);
861: if (dim == 2) {
862: if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) {
863: if (vy == numYVertices-1) {
864: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);
865: DMSetLabelValue(dm, "marker", edge, markerTop);
866: DMSetLabelValue(dm, "marker", cone[0], markerTop);
867: if (ex == numXEdges-1) {
868: DMSetLabelValue(dm, "marker", cone[1], markerTop);
869: }
870: } else if (vy == 0) {
871: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);
872: DMSetLabelValue(dm, "marker", edge, markerBottom);
873: DMSetLabelValue(dm, "marker", cone[0], markerBottom);
874: if (ex == numXEdges-1) {
875: DMSetLabelValue(dm, "marker", cone[1], markerBottom);
876: }
877: }
878: } else {
879: if (vy == 0 && cutLabel) {
880: DMLabelSetValue(cutLabel, edge, 1);
881: DMLabelSetValue(cutLabel, cone[0], 1);
882: if (ex == numXEdges-1) {
883: DMLabelSetValue(cutLabel, cone[1], 1);
884: }
885: }
886: }
887: } else {
888: if (bdY != DM_BOUNDARY_PERIODIC) {
889: if (vy == numYVertices-1) {
890: DMSetLabelValue(dm, "marker", edge, markerBack);
891: }
892: else if (vy == 0) {
893: DMSetLabelValue(dm, "marker", edge, markerFront);
894: }
895: }
896: if (bdZ != DM_BOUNDARY_PERIODIC) {
897: if (vz == numZVertices-1) {
898: DMSetLabelValue(dm, "marker", edge, markerTop);
899: }
900: else if (vz == 0) {
901: DMSetLabelValue(dm, "marker", edge, markerBottom);
902: }
903: }
904: }
905: }
906: }
907: }
908: DMPlexSymmetrize(dm);
909: DMPlexStratify(dm);
910: /* Build coordinates */
911: DMGetCoordinateSection(dm, &coordSection);
912: PetscSectionSetNumFields(coordSection, 1);
913: PetscSectionSetFieldComponents(coordSection, 0, dim);
914: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);
915: for (v = firstVertex; v < firstVertex+numVertices; ++v) {
916: PetscSectionSetDof(coordSection, v, dim);
917: PetscSectionSetFieldDof(coordSection, v, 0, dim);
918: }
919: PetscSectionSetUp(coordSection);
920: PetscSectionGetStorageSize(coordSection, &coordSize);
921: VecCreate(PETSC_COMM_SELF, &coordinates);
922: PetscObjectSetName((PetscObject) coordinates, "coordinates");
923: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
924: VecSetBlockSize(coordinates, dim);
925: VecSetType(coordinates,VECSTANDARD);
926: VecGetArray(coordinates, &coords);
927: for (vz = 0; vz < numZVertices; ++vz) {
928: for (vy = 0; vy < numYVertices; ++vy) {
929: for (vx = 0; vx < numXVertices; ++vx) {
930: coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx;
931: coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy;
932: if (dim == 3) {
933: coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz;
934: }
935: }
936: }
937: }
938: VecRestoreArray(coordinates, &coords);
939: DMSetCoordinatesLocal(dm, coordinates);
940: VecDestroy(&coordinates);
941: }
942: return(0);
943: }
945: 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)
946: {
947: PetscInt i;
952: DMCreate(comm, dm);
954: DMSetType(*dm, DMPLEX);
955: DMSetDimension(*dm, dim);
956: switch (dim) {
957: case 2: {DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], DM_BOUNDARY_NONE);break;}
958: case 3: {DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], periodicity[2]);break;}
959: default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim);
960: }
961: if (periodicity[0] == DM_BOUNDARY_PERIODIC || periodicity[0] == DM_BOUNDARY_TWIST ||
962: periodicity[1] == DM_BOUNDARY_PERIODIC || periodicity[1] == DM_BOUNDARY_TWIST ||
963: (dim > 2 && (periodicity[2] == DM_BOUNDARY_PERIODIC || periodicity[2] == DM_BOUNDARY_TWIST))) {
964: PetscReal L[3];
965: PetscReal maxCell[3];
967: for (i = 0; i < dim; i++) {
968: L[i] = upper[i] - lower[i];
969: maxCell[i] = 1.1 * (L[i] / PetscMax(1,faces[i]));
970: }
971: DMSetPeriodicity(*dm,PETSC_TRUE,maxCell,L,periodicity);
972: }
973: if (!interpolate) {
974: DM udm;
976: DMPlexUninterpolate(*dm, &udm);
977: DMPlexCopyCoordinates(*dm, udm);
978: DMDestroy(dm);
979: *dm = udm;
980: }
981: return(0);
982: }
984: /*@C
985: DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra).
987: Collective
989: Input Parameters:
990: + comm - The communicator for the DM object
991: . dim - The spatial dimension
992: . simplex - PETSC_TRUE for simplices, PETSC_FALSE for tensor cells
993: . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D
994: . lower - The lower left corner, or NULL for (0, 0, 0)
995: . upper - The upper right corner, or NULL for (1, 1, 1)
996: . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE
997: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
999: Output Parameter:
1000: . dm - The DM object
1002: Options Database Keys:
1003: + -dm_plex_box_lower <x,y,z> - Specify lower-left-bottom coordinates for the box
1004: - -dm_plex_box_upper <x,y,z> - Specify upper-right-top coordinates for the box
1006: Note: Here is the numbering returned for 2 faces in each direction for tensor cells:
1007: $ 10---17---11---18----12
1008: $ | | |
1009: $ | | |
1010: $ 20 2 22 3 24
1011: $ | | |
1012: $ | | |
1013: $ 7---15----8---16----9
1014: $ | | |
1015: $ | | |
1016: $ 19 0 21 1 23
1017: $ | | |
1018: $ | | |
1019: $ 4---13----5---14----6
1021: and for simplicial cells
1023: $ 14----8---15----9----16
1024: $ |\ 5 |\ 7 |
1025: $ | \ | \ |
1026: $ 13 2 14 3 15
1027: $ | 4 \ | 6 \ |
1028: $ | \ | \ |
1029: $ 11----6---12----7----13
1030: $ |\ |\ |
1031: $ | \ 1 | \ 3 |
1032: $ 10 0 11 1 12
1033: $ | 0 \ | 2 \ |
1034: $ | \ | \ |
1035: $ 8----4----9----5----10
1037: Level: beginner
1039: .seealso: DMPlexCreateFromFile(), DMPlexCreateHexCylinderMesh(), DMSetType(), DMCreate()
1040: @*/
1041: 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)
1042: {
1043: PetscInt fac[3] = {0, 0, 0};
1044: PetscReal low[3] = {0, 0, 0};
1045: PetscReal upp[3] = {1, 1, 1};
1046: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
1047: PetscInt i, n;
1048: PetscBool flg;
1052: n = 3;
1053: PetscOptionsGetIntArray(NULL, NULL, "-dm_plex_box_faces", fac, &n, &flg);
1054: for (i = 0; i < dim; ++i) fac[i] = faces ? faces[i] : (flg && i < n ? fac[i] : (dim == 1 ? 1 : 4-dim));
1055: if (lower) for (i = 0; i < dim; ++i) low[i] = lower[i];
1056: if (upper) for (i = 0; i < dim; ++i) upp[i] = upper[i];
1057: if (periodicity) for (i = 0; i < dim; ++i) bdt[i] = periodicity[i];
1058: /* Allow bounds to be specified from the command line */
1059: n = 3;
1060: PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_lower", low, &n, &flg);
1061: if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim);
1062: n = 3;
1063: PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_upper", upp, &n, &flg);
1064: if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim);
1066: if (dim == 1) {DMPlexCreateLineMesh_Internal(comm, fac[0], low[0], upp[0], bdt[0], dm);}
1067: else if (simplex) {DMPlexCreateBoxMesh_Simplex_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);}
1068: else {DMPlexCreateBoxMesh_Tensor_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);}
1069: return(0);
1070: }
1072: /*@
1073: DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells.
1075: Collective
1077: Input Parameters:
1078: + comm - The communicator for the DM object
1079: . faces - Number of faces per dimension, or NULL for (1, 1, 1)
1080: . lower - The lower left corner, or NULL for (0, 0, 0)
1081: . upper - The upper right corner, or NULL for (1, 1, 1)
1082: . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE
1083: . ordExt - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first
1084: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
1086: Output Parameter:
1087: . dm - The DM object
1089: Level: beginner
1091: .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateWedgeCylinderMesh(), DMPlexExtrude(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1092: @*/
1093: PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool ordExt, PetscBool interpolate, DM *dm)
1094: {
1095: DM bdm, botdm;
1096: PetscInt i;
1097: PetscInt fac[3] = {0, 0, 0};
1098: PetscReal low[3] = {0, 0, 0};
1099: PetscReal upp[3] = {1, 1, 1};
1100: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
1104: for (i = 0; i < 3; ++i) fac[i] = faces ? (faces[i] > 0 ? faces[i] : 1) : 1;
1105: if (lower) for (i = 0; i < 3; ++i) low[i] = lower[i];
1106: if (upper) for (i = 0; i < 3; ++i) upp[i] = upper[i];
1107: if (periodicity) for (i = 0; i < 3; ++i) bdt[i] = periodicity[i];
1108: for (i = 0; i < 3; ++i) if (bdt[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity not yet supported");
1110: DMCreate(comm, &bdm);
1111: DMSetType(bdm, DMPLEX);
1112: DMSetDimension(bdm, 1);
1113: DMSetCoordinateDim(bdm, 2);
1114: DMPlexCreateSquareBoundary(bdm, low, upp, fac);
1115: DMPlexGenerate(bdm, NULL, PETSC_FALSE, &botdm);
1116: DMDestroy(&bdm);
1117: DMPlexExtrude(botdm, fac[2], upp[2] - low[2], ordExt, interpolate, dm);
1118: if (low[2] != 0.0) {
1119: Vec v;
1120: PetscScalar *x;
1121: PetscInt cDim, n;
1123: DMGetCoordinatesLocal(*dm, &v);
1124: VecGetBlockSize(v, &cDim);
1125: VecGetLocalSize(v, &n);
1126: VecGetArray(v, &x);
1127: x += cDim;
1128: for (i=0; i<n; i+=cDim) x[i] += low[2];
1129: VecRestoreArray(v,&x);
1130: DMSetCoordinatesLocal(*dm, v);
1131: }
1132: DMDestroy(&botdm);
1133: return(0);
1134: }
1136: /*@
1137: DMPlexExtrude - Creates a (d+1)-D mesh by extruding a d-D mesh in the normal direction using prismatic cells.
1139: Collective on idm
1141: Input Parameters:
1142: + idm - The mesh to be extruted
1143: . layers - The number of layers
1144: . height - The height of the extruded layer
1145: . ordExt - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first
1146: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
1148: Output Parameter:
1149: . dm - The DM object
1151: Notes: The object created is an hybrid mesh, the vertex ordering in the cone of the cell is that of the prismatic cells
1153: Level: advanced
1155: .seealso: DMPlexCreateWedgeCylinderMesh(), DMPlexCreateWedgeBoxMesh(), DMPlexSetHybridBounds(), DMSetType(), DMCreate()
1156: @*/
1157: PetscErrorCode DMPlexExtrude(DM idm, PetscInt layers, PetscReal height, PetscBool ordExt, PetscBool interpolate, DM* dm)
1158: {
1159: PetscScalar *coordsB;
1160: const PetscScalar *coordsA;
1161: PetscReal *normals = NULL;
1162: Vec coordinatesA, coordinatesB;
1163: PetscSection coordSectionA, coordSectionB;
1164: PetscInt dim, cDim, cDimB, c, l, v, coordSize, *newCone;
1165: PetscInt cStart, cEnd, vStart, vEnd, cellV, numCells, numVertices;
1166: PetscErrorCode ierr;
1173: DMGetDimension(idm, &dim);
1174: if (dim < 1 || dim > 3) SETERRQ1(PetscObjectComm((PetscObject)idm), PETSC_ERR_SUP, "Support for dimension %D not coded", dim);
1176: DMPlexGetHeightStratum(idm, 0, &cStart, &cEnd);
1177: DMPlexGetDepthStratum(idm, 0, &vStart, &vEnd);
1178: numCells = (cEnd - cStart)*layers;
1179: numVertices = (vEnd - vStart)*(layers+1);
1180: DMCreate(PetscObjectComm((PetscObject)idm), dm);
1181: DMSetType(*dm, DMPLEX);
1182: DMSetDimension(*dm, dim+1);
1183: DMPlexSetChart(*dm, 0, numCells+numVertices);
1184: for (c = cStart, cellV = 0; c < cEnd; ++c) {
1185: PetscInt *closure = NULL;
1186: PetscInt closureSize, numCorners = 0;
1188: DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);
1189: for (v = 0; v < closureSize*2; v += 2) if ((closure[v] >= vStart) && (closure[v] < vEnd)) numCorners++;
1190: DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);
1191: for (l = 0; l < layers; ++l) {
1192: DMPlexSetConeSize(*dm, ordExt ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart, 2*numCorners);
1193: }
1194: cellV = PetscMax(numCorners,cellV);
1195: }
1196: DMPlexSetHybridBounds(*dm, 0, PETSC_DETERMINE, PETSC_DETERMINE, PETSC_DETERMINE);
1197: DMSetUp(*dm);
1199: DMGetCoordinateDim(idm, &cDim);
1200: if (dim != cDim) {
1201: PetscCalloc1(cDim*(vEnd - vStart), &normals);
1202: }
1203: PetscMalloc1(3*cellV,&newCone);
1204: for (c = cStart; c < cEnd; ++c) {
1205: PetscInt *closure = NULL;
1206: PetscInt closureSize, numCorners = 0, l;
1207: PetscReal normal[3] = {0, 0, 0};
1209: if (normals) {
1210: DMPlexComputeCellGeometryFVM(idm, c, NULL, NULL, normal);
1211: }
1212: DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);
1213: for (v = 0; v < closureSize*2; v += 2) {
1214: if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
1215: PetscInt d;
1217: newCone[numCorners++] = closure[v] - vStart;
1218: if (normals) { for (d = 0; d < cDim; ++d) normals[cDim*(closure[v]-vStart)+d] += normal[d]; }
1219: }
1220: }
1221: switch (numCorners) {
1222: case 4: /* do nothing */
1223: case 2: /* do nothing */
1224: break;
1225: case 3: /* from counter-clockwise to wedge ordering */
1226: l = newCone[1];
1227: newCone[1] = newCone[2];
1228: newCone[2] = l;
1229: break;
1230: default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_SUP, "Unsupported number of corners: %D", numCorners);
1231: }
1232: DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);
1233: for (l = 0; l < layers; ++l) {
1234: PetscInt i;
1236: for (i = 0; i < numCorners; ++i) {
1237: newCone[ numCorners + i] = ordExt ? (layers+1)*newCone[i] + l + numCells : l*(vEnd - vStart) + newCone[i] + numCells;
1238: newCone[2*numCorners + i] = ordExt ? (layers+1)*newCone[i] + l + 1 + numCells : (l+1)*(vEnd - vStart) + newCone[i] + numCells;
1239: }
1240: DMPlexSetCone(*dm, ordExt ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart, newCone + numCorners);
1241: }
1242: }
1243: DMPlexSymmetrize(*dm);
1244: DMPlexStratify(*dm);
1245: PetscFree(newCone);
1247: cDimB = cDim == dim ? cDim+1 : cDim;
1248: DMGetCoordinateSection(*dm, &coordSectionB);
1249: PetscSectionSetNumFields(coordSectionB, 1);
1250: PetscSectionSetFieldComponents(coordSectionB, 0, cDimB);
1251: PetscSectionSetChart(coordSectionB, numCells, numCells+numVertices);
1252: for (v = numCells; v < numCells+numVertices; ++v) {
1253: PetscSectionSetDof(coordSectionB, v, cDimB);
1254: PetscSectionSetFieldDof(coordSectionB, v, 0, cDimB);
1255: }
1256: PetscSectionSetUp(coordSectionB);
1257: PetscSectionGetStorageSize(coordSectionB, &coordSize);
1258: VecCreate(PETSC_COMM_SELF, &coordinatesB);
1259: PetscObjectSetName((PetscObject) coordinatesB, "coordinates");
1260: VecSetSizes(coordinatesB, coordSize, PETSC_DETERMINE);
1261: VecSetBlockSize(coordinatesB, cDimB);
1262: VecSetType(coordinatesB,VECSTANDARD);
1264: DMGetCoordinateSection(idm, &coordSectionA);
1265: DMGetCoordinatesLocal(idm, &coordinatesA);
1266: VecGetArray(coordinatesB, &coordsB);
1267: VecGetArrayRead(coordinatesA, &coordsA);
1268: for (v = vStart; v < vEnd; ++v) {
1269: const PetscScalar *cptr;
1270: PetscReal ones2[2] = { 0., 1.}, ones3[3] = { 0., 0., 1.};
1271: PetscReal *normal, norm, h = height/layers;
1272: PetscInt offA, d, cDimA = cDim;
1274: normal = normals ? normals + cDimB*(v - vStart) : (cDim > 1 ? ones3 : ones2);
1275: if (normals) {
1276: for (d = 0, norm = 0.0; d < cDimB; ++d) norm += normal[d]*normal[d];
1277: for (d = 0; d < cDimB; ++d) normal[d] *= 1./PetscSqrtReal(norm);
1278: }
1280: PetscSectionGetOffset(coordSectionA, v, &offA);
1281: cptr = coordsA + offA;
1282: for (l = 0; l < layers+1; ++l) {
1283: PetscInt offB, d, newV;
1285: newV = ordExt ? (layers+1)*(v -vStart) + l + numCells : (vEnd -vStart)*l + (v -vStart) + numCells;
1286: PetscSectionGetOffset(coordSectionB, newV, &offB);
1287: for (d = 0; d < cDimA; ++d) { coordsB[offB+d] = cptr[d]; }
1288: for (d = 0; d < cDimB; ++d) { coordsB[offB+d] += l ? normal[d]*h : 0.0; }
1289: cptr = coordsB + offB;
1290: cDimA = cDimB;
1291: }
1292: }
1293: VecRestoreArrayRead(coordinatesA, &coordsA);
1294: VecRestoreArray(coordinatesB, &coordsB);
1295: DMSetCoordinatesLocal(*dm, coordinatesB);
1296: VecDestroy(&coordinatesB);
1297: PetscFree(normals);
1298: if (interpolate) {
1299: DM idm;
1301: DMPlexInterpolate(*dm, &idm);
1302: DMPlexCopyCoordinates(*dm, idm);
1303: DMDestroy(dm);
1304: *dm = idm;
1305: }
1306: return(0);
1307: }
1309: /*@C
1310: DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database.
1312: Logically Collective on dm
1314: Input Parameters:
1315: + dm - the DM context
1316: - prefix - the prefix to prepend to all option names
1318: Notes:
1319: A hyphen (-) must NOT be given at the beginning of the prefix name.
1320: The first character of all runtime options is AUTOMATICALLY the hyphen.
1322: Level: advanced
1324: .seealso: SNESSetFromOptions()
1325: @*/
1326: PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[])
1327: {
1328: DM_Plex *mesh = (DM_Plex *) dm->data;
1333: PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);
1334: PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);
1335: return(0);
1336: }
1338: /*@
1339: DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra.
1341: Collective
1343: Input Parameters:
1344: + comm - The communicator for the DM object
1345: . numRefine - The number of regular refinements to the basic 5 cell structure
1346: - periodicZ - The boundary type for the Z direction
1348: Output Parameter:
1349: . dm - The DM object
1351: Note: Here is the output numbering looking from the bottom of the cylinder:
1352: $ 17-----14
1353: $ | |
1354: $ | 2 |
1355: $ | |
1356: $ 17-----8-----7-----14
1357: $ | | | |
1358: $ | 3 | 0 | 1 |
1359: $ | | | |
1360: $ 19-----5-----6-----13
1361: $ | |
1362: $ | 4 |
1363: $ | |
1364: $ 19-----13
1365: $
1366: $ and up through the top
1367: $
1368: $ 18-----16
1369: $ | |
1370: $ | 2 |
1371: $ | |
1372: $ 18----10----11-----16
1373: $ | | | |
1374: $ | 3 | 0 | 1 |
1375: $ | | | |
1376: $ 20-----9----12-----15
1377: $ | |
1378: $ | 4 |
1379: $ | |
1380: $ 20-----15
1382: Level: beginner
1384: .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1385: @*/
1386: PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, PetscInt numRefine, DMBoundaryType periodicZ, DM *dm)
1387: {
1388: const PetscInt dim = 3;
1389: PetscInt numCells, numVertices, r;
1390: PetscMPIInt rank;
1395: MPI_Comm_rank(comm, &rank);
1396: if (numRefine < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of refinements %D cannot be negative", numRefine);
1397: DMCreate(comm, dm);
1398: DMSetType(*dm, DMPLEX);
1399: DMSetDimension(*dm, dim);
1400: /* Create topology */
1401: {
1402: PetscInt cone[8], c;
1404: numCells = !rank ? 5 : 0;
1405: numVertices = !rank ? 16 : 0;
1406: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1407: numCells *= 3;
1408: numVertices = !rank ? 24 : 0;
1409: }
1410: DMPlexSetChart(*dm, 0, numCells+numVertices);
1411: for (c = 0; c < numCells; c++) {DMPlexSetConeSize(*dm, c, 8);}
1412: DMSetUp(*dm);
1413: if (!rank) {
1414: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1415: cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16;
1416: cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34;
1417: DMPlexSetCone(*dm, 0, cone);
1418: cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23;
1419: cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */
1420: DMPlexSetCone(*dm, 1, cone);
1421: cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17;
1422: cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38;
1423: DMPlexSetCone(*dm, 2, cone);
1424: cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15;
1425: cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38;
1426: DMPlexSetCone(*dm, 3, cone);
1427: cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23;
1428: cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31;
1429: DMPlexSetCone(*dm, 4, cone);
1431: cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32;
1432: cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20;
1433: DMPlexSetCone(*dm, 5, cone);
1434: cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36;
1435: cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21;
1436: DMPlexSetCone(*dm, 6, cone);
1437: cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33;
1438: cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28;
1439: DMPlexSetCone(*dm, 7, cone);
1440: cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31;
1441: cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28;
1442: DMPlexSetCone(*dm, 8, cone);
1443: cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36;
1444: cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19;
1445: DMPlexSetCone(*dm, 9, cone);
1447: cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22;
1448: cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18;
1449: DMPlexSetCone(*dm, 10, cone);
1450: cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25;
1451: cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17;
1452: DMPlexSetCone(*dm, 11, cone);
1453: cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21;
1454: cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27;
1455: DMPlexSetCone(*dm, 12, cone);
1456: cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19;
1457: cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27;
1458: DMPlexSetCone(*dm, 13, cone);
1459: cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25;
1460: cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15;
1461: DMPlexSetCone(*dm, 14, cone);
1462: } else {
1463: cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6;
1464: cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10;
1465: DMPlexSetCone(*dm, 0, cone);
1466: cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13;
1467: cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11;
1468: DMPlexSetCone(*dm, 1, cone);
1469: cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7;
1470: cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18;
1471: DMPlexSetCone(*dm, 2, cone);
1472: cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5;
1473: cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18;
1474: DMPlexSetCone(*dm, 3, cone);
1475: cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13;
1476: cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9;
1477: DMPlexSetCone(*dm, 4, cone);
1478: }
1479: }
1480: DMPlexSymmetrize(*dm);
1481: DMPlexStratify(*dm);
1482: }
1483: /* Interpolate */
1484: {
1485: DM idm;
1487: DMPlexInterpolate(*dm, &idm);
1488: DMDestroy(dm);
1489: *dm = idm;
1490: }
1491: /* Create cube geometry */
1492: {
1493: Vec coordinates;
1494: PetscSection coordSection;
1495: PetscScalar *coords;
1496: PetscInt coordSize, v;
1497: const PetscReal dis = 1.0/PetscSqrtReal(2.0);
1498: const PetscReal ds2 = dis/2.0;
1500: /* Build coordinates */
1501: DMGetCoordinateSection(*dm, &coordSection);
1502: PetscSectionSetNumFields(coordSection, 1);
1503: PetscSectionSetFieldComponents(coordSection, 0, dim);
1504: PetscSectionSetChart(coordSection, numCells, numCells+numVertices);
1505: for (v = numCells; v < numCells+numVertices; ++v) {
1506: PetscSectionSetDof(coordSection, v, dim);
1507: PetscSectionSetFieldDof(coordSection, v, 0, dim);
1508: }
1509: PetscSectionSetUp(coordSection);
1510: PetscSectionGetStorageSize(coordSection, &coordSize);
1511: VecCreate(PETSC_COMM_SELF, &coordinates);
1512: PetscObjectSetName((PetscObject) coordinates, "coordinates");
1513: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1514: VecSetBlockSize(coordinates, dim);
1515: VecSetType(coordinates,VECSTANDARD);
1516: VecGetArray(coordinates, &coords);
1517: if (!rank) {
1518: coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0;
1519: coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0;
1520: coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0;
1521: coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0;
1522: coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0;
1523: coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0;
1524: coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0;
1525: coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0;
1526: coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0;
1527: coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0;
1528: coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0;
1529: coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0;
1530: coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0;
1531: coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0;
1532: coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0;
1533: coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0;
1534: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1535: /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5;
1536: /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5;
1537: /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5;
1538: /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5;
1539: /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5;
1540: /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5;
1541: /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5;
1542: /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5;
1543: }
1544: }
1545: VecRestoreArray(coordinates, &coords);
1546: DMSetCoordinatesLocal(*dm, coordinates);
1547: VecDestroy(&coordinates);
1548: }
1549: /* Create periodicity */
1550: if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) {
1551: PetscReal L[3];
1552: PetscReal maxCell[3];
1553: DMBoundaryType bdType[3];
1554: PetscReal lower[3] = {0.0, 0.0, 0.0};
1555: PetscReal upper[3] = {1.0, 1.0, 1.5};
1556: PetscInt i, numZCells = 3;
1558: bdType[0] = DM_BOUNDARY_NONE;
1559: bdType[1] = DM_BOUNDARY_NONE;
1560: bdType[2] = periodicZ;
1561: for (i = 0; i < dim; i++) {
1562: L[i] = upper[i] - lower[i];
1563: maxCell[i] = 1.1 * (L[i] / numZCells);
1564: }
1565: DMSetPeriodicity(*dm, PETSC_TRUE, maxCell, L, bdType);
1566: }
1567: /* Refine topology */
1568: for (r = 0; r < numRefine; ++r) {
1569: DM rdm = NULL;
1571: DMRefine(*dm, comm, &rdm);
1572: DMDestroy(dm);
1573: *dm = rdm;
1574: }
1575: /* Remap geometry to cylinder
1576: Interior square: Linear interpolation is correct
1577: The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing
1578: such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance
1580: phi = arctan(y/x)
1581: d_close = sqrt(1/8 + 1/4 sin^2(phi))
1582: d_far = sqrt(1/2 + sin^2(phi))
1584: so we remap them using
1586: x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close)
1587: y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close)
1589: If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y.
1590: */
1591: {
1592: Vec coordinates;
1593: PetscSection coordSection;
1594: PetscScalar *coords;
1595: PetscInt vStart, vEnd, v;
1596: const PetscReal dis = 1.0/PetscSqrtReal(2.0);
1597: const PetscReal ds2 = 0.5*dis;
1599: DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);
1600: DMGetCoordinateSection(*dm, &coordSection);
1601: DMGetCoordinatesLocal(*dm, &coordinates);
1602: VecGetArray(coordinates, &coords);
1603: for (v = vStart; v < vEnd; ++v) {
1604: PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc;
1605: PetscInt off;
1607: PetscSectionGetOffset(coordSection, v, &off);
1608: if ((PetscAbsScalar(coords[off+0]) <= ds2) && (PetscAbsScalar(coords[off+1]) <= ds2)) continue;
1609: x = PetscRealPart(coords[off]);
1610: y = PetscRealPart(coords[off+1]);
1611: phi = PetscAtan2Real(y, x);
1612: sinp = PetscSinReal(phi);
1613: cosp = PetscCosReal(phi);
1614: if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) {
1615: dc = PetscAbsReal(ds2/sinp);
1616: df = PetscAbsReal(dis/sinp);
1617: xc = ds2*x/PetscAbsReal(y);
1618: yc = ds2*PetscSignReal(y);
1619: } else {
1620: dc = PetscAbsReal(ds2/cosp);
1621: df = PetscAbsReal(dis/cosp);
1622: xc = ds2*PetscSignReal(x);
1623: yc = ds2*y/PetscAbsReal(x);
1624: }
1625: coords[off+0] = xc + (coords[off+0] - xc)*(1.0 - dc)/(df - dc);
1626: coords[off+1] = yc + (coords[off+1] - yc)*(1.0 - dc)/(df - dc);
1627: }
1628: VecRestoreArray(coordinates, &coords);
1629: if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) {
1630: DMLocalizeCoordinates(*dm);
1631: }
1632: }
1633: return(0);
1634: }
1636: /*@
1637: DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges.
1639: Collective
1641: Input Parameters:
1642: + comm - The communicator for the DM object
1643: . n - The number of wedges around the origin
1644: - interpolate - Create edges and faces
1646: Output Parameter:
1647: . dm - The DM object
1649: Level: beginner
1651: .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1652: @*/
1653: PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm)
1654: {
1655: const PetscInt dim = 3;
1656: PetscInt numCells, numVertices;
1657: PetscMPIInt rank;
1662: MPI_Comm_rank(comm, &rank);
1663: if (n < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n);
1664: DMCreate(comm, dm);
1665: DMSetType(*dm, DMPLEX);
1666: DMSetDimension(*dm, dim);
1667: /* Create topology */
1668: {
1669: PetscInt cone[6], c;
1671: numCells = !rank ? n : 0;
1672: numVertices = !rank ? 2*(n+1) : 0;
1673: DMPlexSetChart(*dm, 0, numCells+numVertices);
1674: DMPlexSetHybridBounds(*dm, 0, PETSC_DETERMINE, PETSC_DETERMINE, PETSC_DETERMINE);
1675: for (c = 0; c < numCells; c++) {DMPlexSetConeSize(*dm, c, 6);}
1676: DMSetUp(*dm);
1677: for (c = 0; c < numCells; c++) {
1678: cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n;
1679: cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n;
1680: DMPlexSetCone(*dm, c, cone);
1681: }
1682: DMPlexSymmetrize(*dm);
1683: DMPlexStratify(*dm);
1684: }
1685: /* Interpolate */
1686: if (interpolate) {
1687: DM idm;
1689: DMPlexInterpolate(*dm, &idm);
1690: DMDestroy(dm);
1691: *dm = idm;
1692: }
1693: /* Create cylinder geometry */
1694: {
1695: Vec coordinates;
1696: PetscSection coordSection;
1697: PetscScalar *coords;
1698: PetscInt coordSize, v, c;
1700: /* Build coordinates */
1701: DMGetCoordinateSection(*dm, &coordSection);
1702: PetscSectionSetNumFields(coordSection, 1);
1703: PetscSectionSetFieldComponents(coordSection, 0, dim);
1704: PetscSectionSetChart(coordSection, numCells, numCells+numVertices);
1705: for (v = numCells; v < numCells+numVertices; ++v) {
1706: PetscSectionSetDof(coordSection, v, dim);
1707: PetscSectionSetFieldDof(coordSection, v, 0, dim);
1708: }
1709: PetscSectionSetUp(coordSection);
1710: PetscSectionGetStorageSize(coordSection, &coordSize);
1711: VecCreate(PETSC_COMM_SELF, &coordinates);
1712: PetscObjectSetName((PetscObject) coordinates, "coordinates");
1713: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1714: VecSetBlockSize(coordinates, dim);
1715: VecSetType(coordinates,VECSTANDARD);
1716: VecGetArray(coordinates, &coords);
1717: for (c = 0; c < numCells; c++) {
1718: 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;
1719: 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;
1720: }
1721: if (!rank) {
1722: coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0;
1723: coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0;
1724: }
1725: VecRestoreArray(coordinates, &coords);
1726: DMSetCoordinatesLocal(*dm, coordinates);
1727: VecDestroy(&coordinates);
1728: }
1729: return(0);
1730: }
1732: PETSC_STATIC_INLINE PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
1733: {
1734: PetscReal prod = 0.0;
1735: PetscInt i;
1736: for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]);
1737: return PetscSqrtReal(prod);
1738: }
1739: PETSC_STATIC_INLINE PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
1740: {
1741: PetscReal prod = 0.0;
1742: PetscInt i;
1743: for (i = 0; i < dim; ++i) prod += x[i]*y[i];
1744: return prod;
1745: }
1747: /*@
1748: DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d.
1750: Collective
1752: Input Parameters:
1753: + comm - The communicator for the DM object
1754: . dim - The dimension
1755: - simplex - Use simplices, or tensor product cells
1757: Output Parameter:
1758: . dm - The DM object
1760: Level: beginner
1762: .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1763: @*/
1764: PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *dm)
1765: {
1766: const PetscInt embedDim = dim+1;
1767: PetscSection coordSection;
1768: Vec coordinates;
1769: PetscScalar *coords;
1770: PetscReal *coordsIn;
1771: PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e;
1772: PetscMPIInt rank;
1773: PetscErrorCode ierr;
1777: DMCreate(comm, dm);
1778: DMSetType(*dm, DMPLEX);
1779: DMSetDimension(*dm, dim);
1780: DMSetCoordinateDim(*dm, dim+1);
1781: MPI_Comm_rank(PetscObjectComm((PetscObject) *dm), &rank);
1782: switch (dim) {
1783: case 2:
1784: if (simplex) {
1785: DM idm;
1786: const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI);
1787: const PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)};
1788: const PetscInt degree = 5;
1789: PetscInt s[3] = {1, 1, 1};
1790: PetscInt cone[3];
1791: PetscInt *graph, p, i, j, k;
1793: numCells = !rank ? 20 : 0;
1794: numVerts = !rank ? 12 : 0;
1795: firstVertex = numCells;
1796: /* Use icosahedron, which for a unit sphere has coordinates which are all cyclic permutations of
1798: (0, \pm 1/\phi+1, \pm \phi/\phi+1)
1800: where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
1801: length is then given by 2/\phi = 2 * 0.61803 = 1.23606.
1802: */
1803: /* Construct vertices */
1804: PetscCalloc1(numVerts * embedDim, &coordsIn);
1805: for (p = 0, i = 0; p < embedDim; ++p) {
1806: for (s[1] = -1; s[1] < 2; s[1] += 2) {
1807: for (s[2] = -1; s[2] < 2; s[2] += 2) {
1808: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim];
1809: ++i;
1810: }
1811: }
1812: }
1813: /* Construct graph */
1814: PetscCalloc1(numVerts * numVerts, &graph);
1815: for (i = 0; i < numVerts; ++i) {
1816: for (j = 0, k = 0; j < numVerts; ++j) {
1817: if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;}
1818: }
1819: if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree);
1820: }
1821: /* Build Topology */
1822: DMPlexSetChart(*dm, 0, numCells+numVerts);
1823: for (c = 0; c < numCells; c++) {
1824: DMPlexSetConeSize(*dm, c, embedDim);
1825: }
1826: DMSetUp(*dm); /* Allocate space for cones */
1827: /* Cells */
1828: for (i = 0, c = 0; i < numVerts; ++i) {
1829: for (j = 0; j < i; ++j) {
1830: for (k = 0; k < j; ++k) {
1831: if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) {
1832: cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k;
1833: /* Check orientation */
1834: {
1835: 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}}};
1836: PetscReal normal[3];
1837: PetscInt e, f;
1839: for (d = 0; d < embedDim; ++d) {
1840: normal[d] = 0.0;
1841: for (e = 0; e < embedDim; ++e) {
1842: for (f = 0; f < embedDim; ++f) {
1843: normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]);
1844: }
1845: }
1846: }
1847: if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;}
1848: }
1849: DMPlexSetCone(*dm, c++, cone);
1850: }
1851: }
1852: }
1853: }
1854: DMPlexSymmetrize(*dm);
1855: DMPlexStratify(*dm);
1856: PetscFree(graph);
1857: /* Interpolate mesh */
1858: DMPlexInterpolate(*dm, &idm);
1859: DMDestroy(dm);
1860: *dm = idm;
1861: } else {
1862: /*
1863: 12-21--13
1864: | |
1865: 25 4 24
1866: | |
1867: 12-25--9-16--8-24--13
1868: | | | |
1869: 23 5 17 0 15 3 22
1870: | | | |
1871: 10-20--6-14--7-19--11
1872: | |
1873: 20 1 19
1874: | |
1875: 10-18--11
1876: | |
1877: 23 2 22
1878: | |
1879: 12-21--13
1880: */
1881: const PetscReal dist = 1.0/PetscSqrtReal(3.0);
1882: PetscInt cone[4], ornt[4];
1884: numCells = !rank ? 6 : 0;
1885: numEdges = !rank ? 12 : 0;
1886: numVerts = !rank ? 8 : 0;
1887: firstVertex = numCells;
1888: firstEdge = numCells + numVerts;
1889: /* Build Topology */
1890: DMPlexSetChart(*dm, 0, numCells+numEdges+numVerts);
1891: for (c = 0; c < numCells; c++) {
1892: DMPlexSetConeSize(*dm, c, 4);
1893: }
1894: for (e = firstEdge; e < firstEdge+numEdges; ++e) {
1895: DMPlexSetConeSize(*dm, e, 2);
1896: }
1897: DMSetUp(*dm); /* Allocate space for cones */
1898: /* Cell 0 */
1899: cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17;
1900: DMPlexSetCone(*dm, 0, cone);
1901: ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0;
1902: DMPlexSetConeOrientation(*dm, 0, ornt);
1903: /* Cell 1 */
1904: cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20;
1905: DMPlexSetCone(*dm, 1, cone);
1906: ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0;
1907: DMPlexSetConeOrientation(*dm, 1, ornt);
1908: /* Cell 2 */
1909: cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23;
1910: DMPlexSetCone(*dm, 2, cone);
1911: ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0;
1912: DMPlexSetConeOrientation(*dm, 2, ornt);
1913: /* Cell 3 */
1914: cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15;
1915: DMPlexSetCone(*dm, 3, cone);
1916: ornt[0] = -2; ornt[1] = -2; ornt[2] = 0; ornt[3] = -2;
1917: DMPlexSetConeOrientation(*dm, 3, ornt);
1918: /* Cell 4 */
1919: cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25;
1920: DMPlexSetCone(*dm, 4, cone);
1921: ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = 0;
1922: DMPlexSetConeOrientation(*dm, 4, ornt);
1923: /* Cell 5 */
1924: cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23;
1925: DMPlexSetCone(*dm, 5, cone);
1926: ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = -2;
1927: DMPlexSetConeOrientation(*dm, 5, ornt);
1928: /* Edges */
1929: cone[0] = 6; cone[1] = 7;
1930: DMPlexSetCone(*dm, 14, cone);
1931: cone[0] = 7; cone[1] = 8;
1932: DMPlexSetCone(*dm, 15, cone);
1933: cone[0] = 8; cone[1] = 9;
1934: DMPlexSetCone(*dm, 16, cone);
1935: cone[0] = 9; cone[1] = 6;
1936: DMPlexSetCone(*dm, 17, cone);
1937: cone[0] = 10; cone[1] = 11;
1938: DMPlexSetCone(*dm, 18, cone);
1939: cone[0] = 11; cone[1] = 7;
1940: DMPlexSetCone(*dm, 19, cone);
1941: cone[0] = 6; cone[1] = 10;
1942: DMPlexSetCone(*dm, 20, cone);
1943: cone[0] = 12; cone[1] = 13;
1944: DMPlexSetCone(*dm, 21, cone);
1945: cone[0] = 13; cone[1] = 11;
1946: DMPlexSetCone(*dm, 22, cone);
1947: cone[0] = 10; cone[1] = 12;
1948: DMPlexSetCone(*dm, 23, cone);
1949: cone[0] = 13; cone[1] = 8;
1950: DMPlexSetCone(*dm, 24, cone);
1951: cone[0] = 12; cone[1] = 9;
1952: DMPlexSetCone(*dm, 25, cone);
1953: DMPlexSymmetrize(*dm);
1954: DMPlexStratify(*dm);
1955: /* Build coordinates */
1956: PetscCalloc1(numVerts * embedDim, &coordsIn);
1957: coordsIn[0*embedDim+0] = -dist; coordsIn[0*embedDim+1] = dist; coordsIn[0*embedDim+2] = -dist;
1958: coordsIn[1*embedDim+0] = dist; coordsIn[1*embedDim+1] = dist; coordsIn[1*embedDim+2] = -dist;
1959: coordsIn[2*embedDim+0] = dist; coordsIn[2*embedDim+1] = -dist; coordsIn[2*embedDim+2] = -dist;
1960: coordsIn[3*embedDim+0] = -dist; coordsIn[3*embedDim+1] = -dist; coordsIn[3*embedDim+2] = -dist;
1961: coordsIn[4*embedDim+0] = -dist; coordsIn[4*embedDim+1] = dist; coordsIn[4*embedDim+2] = dist;
1962: coordsIn[5*embedDim+0] = dist; coordsIn[5*embedDim+1] = dist; coordsIn[5*embedDim+2] = dist;
1963: coordsIn[6*embedDim+0] = -dist; coordsIn[6*embedDim+1] = -dist; coordsIn[6*embedDim+2] = dist;
1964: coordsIn[7*embedDim+0] = dist; coordsIn[7*embedDim+1] = -dist; coordsIn[7*embedDim+2] = dist;
1965: }
1966: break;
1967: case 3:
1968: if (simplex) {
1969: DM idm;
1970: const PetscReal edgeLen = 1.0/PETSC_PHI;
1971: const PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5};
1972: const PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0};
1973: const PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0};
1974: const PetscInt degree = 12;
1975: PetscInt s[4] = {1, 1, 1};
1976: 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},
1977: {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}};
1978: PetscInt cone[4];
1979: PetscInt *graph, p, i, j, k, l;
1981: numCells = !rank ? 600 : 0;
1982: numVerts = !rank ? 120 : 0;
1983: firstVertex = numCells;
1984: /* Use the 600-cell, which for a unit sphere has coordinates which are
1986: 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16
1987: (\pm 1, 0, 0, 0) all cyclic permutations 8
1988: 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96
1990: where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
1991: length is then given by 1/\phi = 0.61803.
1993: http://buzzard.pugetsound.edu/sage-practice/ch03s03.html
1994: http://mathworld.wolfram.com/600-Cell.html
1995: */
1996: /* Construct vertices */
1997: PetscCalloc1(numVerts * embedDim, &coordsIn);
1998: i = 0;
1999: for (s[0] = -1; s[0] < 2; s[0] += 2) {
2000: for (s[1] = -1; s[1] < 2; s[1] += 2) {
2001: for (s[2] = -1; s[2] < 2; s[2] += 2) {
2002: for (s[3] = -1; s[3] < 2; s[3] += 2) {
2003: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d];
2004: ++i;
2005: }
2006: }
2007: }
2008: }
2009: for (p = 0; p < embedDim; ++p) {
2010: s[1] = s[2] = s[3] = 1;
2011: for (s[0] = -1; s[0] < 2; s[0] += 2) {
2012: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim];
2013: ++i;
2014: }
2015: }
2016: for (p = 0; p < 12; ++p) {
2017: s[3] = 1;
2018: for (s[0] = -1; s[0] < 2; s[0] += 2) {
2019: for (s[1] = -1; s[1] < 2; s[1] += 2) {
2020: for (s[2] = -1; s[2] < 2; s[2] += 2) {
2021: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]];
2022: ++i;
2023: }
2024: }
2025: }
2026: }
2027: if (i != numVerts) SETERRQ2(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts);
2028: /* Construct graph */
2029: PetscCalloc1(numVerts * numVerts, &graph);
2030: for (i = 0; i < numVerts; ++i) {
2031: for (j = 0, k = 0; j < numVerts; ++j) {
2032: if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;}
2033: }
2034: if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree);
2035: }
2036: /* Build Topology */
2037: DMPlexSetChart(*dm, 0, numCells+numVerts);
2038: for (c = 0; c < numCells; c++) {
2039: DMPlexSetConeSize(*dm, c, embedDim);
2040: }
2041: DMSetUp(*dm); /* Allocate space for cones */
2042: /* Cells */
2043: for (i = 0, c = 0; i < numVerts; ++i) {
2044: for (j = 0; j < i; ++j) {
2045: for (k = 0; k < j; ++k) {
2046: for (l = 0; l < k; ++l) {
2047: if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] &&
2048: graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) {
2049: cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l;
2050: /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */
2051: {
2052: const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
2053: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}},
2054: {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}},
2055: {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}},
2057: {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}},
2058: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
2059: {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}},
2060: {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}},
2062: {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}},
2063: {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}},
2064: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
2065: {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}},
2067: {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}},
2068: {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}},
2069: {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
2070: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}};
2071: PetscReal normal[4];
2072: PetscInt e, f, g;
2074: for (d = 0; d < embedDim; ++d) {
2075: normal[d] = 0.0;
2076: for (e = 0; e < embedDim; ++e) {
2077: for (f = 0; f < embedDim; ++f) {
2078: for (g = 0; g < embedDim; ++g) {
2079: 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]);
2080: }
2081: }
2082: }
2083: }
2084: if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;}
2085: }
2086: DMPlexSetCone(*dm, c++, cone);
2087: }
2088: }
2089: }
2090: }
2091: }
2092: DMPlexSymmetrize(*dm);
2093: DMPlexStratify(*dm);
2094: PetscFree(graph);
2095: /* Interpolate mesh */
2096: DMPlexInterpolate(*dm, &idm);
2097: DMDestroy(dm);
2098: *dm = idm;
2099: break;
2100: }
2101: default: SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim);
2102: }
2103: /* Create coordinates */
2104: DMGetCoordinateSection(*dm, &coordSection);
2105: PetscSectionSetNumFields(coordSection, 1);
2106: PetscSectionSetFieldComponents(coordSection, 0, embedDim);
2107: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);
2108: for (v = firstVertex; v < firstVertex+numVerts; ++v) {
2109: PetscSectionSetDof(coordSection, v, embedDim);
2110: PetscSectionSetFieldDof(coordSection, v, 0, embedDim);
2111: }
2112: PetscSectionSetUp(coordSection);
2113: PetscSectionGetStorageSize(coordSection, &coordSize);
2114: VecCreate(PETSC_COMM_SELF, &coordinates);
2115: VecSetBlockSize(coordinates, embedDim);
2116: PetscObjectSetName((PetscObject) coordinates, "coordinates");
2117: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
2118: VecSetType(coordinates,VECSTANDARD);
2119: VecGetArray(coordinates, &coords);
2120: for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];}
2121: VecRestoreArray(coordinates, &coords);
2122: DMSetCoordinatesLocal(*dm, coordinates);
2123: VecDestroy(&coordinates);
2124: PetscFree(coordsIn);
2125: return(0);
2126: }
2128: /* External function declarations here */
2129: extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling);
2130: extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat);
2131: extern PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mat);
2132: extern PetscErrorCode DMCreateLocalSection_Plex(DM dm);
2133: extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm);
2134: extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J);
2135: extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm);
2136: extern PetscErrorCode DMCreateCoordinateField_Plex(DM dm, DMField *field);
2137: PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm);
2138: extern PetscErrorCode DMSetUp_Plex(DM dm);
2139: extern PetscErrorCode DMDestroy_Plex(DM dm);
2140: extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer);
2141: extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer);
2142: extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm);
2143: extern PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm);
2144: static PetscErrorCode DMInitialize_Plex(DM dm);
2146: /* Replace dm with the contents of dmNew
2147: - Share the DM_Plex structure
2148: - Share the coordinates
2149: - Share the SF
2150: */
2151: static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew)
2152: {
2153: PetscSF sf;
2154: DM coordDM, coarseDM;
2155: Vec coords;
2156: PetscBool isper;
2157: const PetscReal *maxCell, *L;
2158: const DMBoundaryType *bd;
2159: PetscErrorCode ierr;
2162: DMGetPointSF(dmNew, &sf);
2163: DMSetPointSF(dm, sf);
2164: DMGetCoordinateDM(dmNew, &coordDM);
2165: DMGetCoordinatesLocal(dmNew, &coords);
2166: DMSetCoordinateDM(dm, coordDM);
2167: DMSetCoordinatesLocal(dm, coords);
2168: DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);
2169: DMSetPeriodicity(dmNew, isper, maxCell, L, bd);
2170: DMDestroy_Plex(dm);
2171: DMInitialize_Plex(dm);
2172: dm->data = dmNew->data;
2173: ((DM_Plex *) dmNew->data)->refct++;
2174: dmNew->labels->refct++;
2175: if (!--(dm->labels->refct)) {
2176: DMLabelLink next = dm->labels->next;
2178: /* destroy the labels */
2179: while (next) {
2180: DMLabelLink tmp = next->next;
2182: DMLabelDestroy(&next->label);
2183: PetscFree(next);
2184: next = tmp;
2185: }
2186: PetscFree(dm->labels);
2187: }
2188: dm->labels = dmNew->labels;
2189: dm->depthLabel = dmNew->depthLabel;
2190: DMGetCoarseDM(dmNew,&coarseDM);
2191: DMSetCoarseDM(dm,coarseDM);
2192: return(0);
2193: }
2195: /* Swap dm with the contents of dmNew
2196: - Swap the DM_Plex structure
2197: - Swap the coordinates
2198: - Swap the point PetscSF
2199: */
2200: static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB)
2201: {
2202: DM coordDMA, coordDMB;
2203: Vec coordsA, coordsB;
2204: PetscSF sfA, sfB;
2205: void *tmp;
2206: DMLabelLinkList listTmp;
2207: DMLabel depthTmp;
2208: PetscInt tmpI;
2209: PetscErrorCode ierr;
2212: DMGetPointSF(dmA, &sfA);
2213: DMGetPointSF(dmB, &sfB);
2214: PetscObjectReference((PetscObject) sfA);
2215: DMSetPointSF(dmA, sfB);
2216: DMSetPointSF(dmB, sfA);
2217: PetscObjectDereference((PetscObject) sfA);
2219: DMGetCoordinateDM(dmA, &coordDMA);
2220: DMGetCoordinateDM(dmB, &coordDMB);
2221: PetscObjectReference((PetscObject) coordDMA);
2222: DMSetCoordinateDM(dmA, coordDMB);
2223: DMSetCoordinateDM(dmB, coordDMA);
2224: PetscObjectDereference((PetscObject) coordDMA);
2226: DMGetCoordinatesLocal(dmA, &coordsA);
2227: DMGetCoordinatesLocal(dmB, &coordsB);
2228: PetscObjectReference((PetscObject) coordsA);
2229: DMSetCoordinatesLocal(dmA, coordsB);
2230: DMSetCoordinatesLocal(dmB, coordsA);
2231: PetscObjectDereference((PetscObject) coordsA);
2233: tmp = dmA->data;
2234: dmA->data = dmB->data;
2235: dmB->data = tmp;
2236: listTmp = dmA->labels;
2237: dmA->labels = dmB->labels;
2238: dmB->labels = listTmp;
2239: depthTmp = dmA->depthLabel;
2240: dmA->depthLabel = dmB->depthLabel;
2241: dmB->depthLabel = depthTmp;
2242: tmpI = dmA->levelup;
2243: dmA->levelup = dmB->levelup;
2244: dmB->levelup = tmpI;
2245: return(0);
2246: }
2248: PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm)
2249: {
2250: DM_Plex *mesh = (DM_Plex*) dm->data;
2254: /* Handle viewing */
2255: PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL);
2256: PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL,0);
2257: PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL);
2258: PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL,0);
2259: /* Point Location */
2260: PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL);
2261: /* Partitioning and distribution */
2262: PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL);
2263: /* Generation and remeshing */
2264: PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL);
2265: /* Projection behavior */
2266: PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL,0);
2267: PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);
2268: /* Checking structure */
2269: {
2270: PetscBool flg = PETSC_FALSE, flg2 = PETSC_FALSE;
2272: PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2);
2273: if (flg && flg2) {DMPlexCheckSymmetry(dm);}
2274: PetscOptionsBool("-dm_plex_check_skeleton", "Check that each cell has the correct number of vertices (only for homogeneous simplex or tensor meshes)", "DMPlexCheckSkeleton", PETSC_FALSE, &flg, &flg2);
2275: if (flg && flg2) {DMPlexCheckSkeleton(dm, 0);}
2276: PetscOptionsBool("-dm_plex_check_faces", "Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type", "DMPlexCheckFaces", PETSC_FALSE, &flg, &flg2);
2277: if (flg && flg2) {DMPlexCheckFaces(dm, 0);}
2278: PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2);
2279: if (flg && flg2) {DMPlexCheckGeometry(dm);}
2280: }
2282: PetscPartitionerSetFromOptions(mesh->partitioner);
2283: return(0);
2284: }
2286: static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm)
2287: {
2288: PetscInt refine = 0, coarsen = 0, r;
2289: PetscBool isHierarchy;
2294: PetscOptionsHead(PetscOptionsObject,"DMPlex Options");
2295: /* Handle DMPlex refinement */
2296: PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL,0);
2297: PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy,0);
2298: if (refine) {DMPlexSetRefinementUniform(dm, PETSC_TRUE);}
2299: if (refine && isHierarchy) {
2300: DM *dms, coarseDM;
2302: DMGetCoarseDM(dm, &coarseDM);
2303: PetscObjectReference((PetscObject)coarseDM);
2304: PetscMalloc1(refine,&dms);
2305: DMRefineHierarchy(dm, refine, dms);
2306: /* Total hack since we do not pass in a pointer */
2307: DMPlexSwap_Static(dm, dms[refine-1]);
2308: if (refine == 1) {
2309: DMSetCoarseDM(dm, dms[0]);
2310: DMPlexSetRegularRefinement(dm, PETSC_TRUE);
2311: } else {
2312: DMSetCoarseDM(dm, dms[refine-2]);
2313: DMPlexSetRegularRefinement(dm, PETSC_TRUE);
2314: DMSetCoarseDM(dms[0], dms[refine-1]);
2315: DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);
2316: }
2317: DMSetCoarseDM(dms[refine-1], coarseDM);
2318: PetscObjectDereference((PetscObject)coarseDM);
2319: /* Free DMs */
2320: for (r = 0; r < refine; ++r) {
2321: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);
2322: DMDestroy(&dms[r]);
2323: }
2324: PetscFree(dms);
2325: } else {
2326: for (r = 0; r < refine; ++r) {
2327: DM refinedMesh;
2329: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2330: DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);
2331: /* Total hack since we do not pass in a pointer */
2332: DMPlexReplace_Static(dm, refinedMesh);
2333: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2334: DMDestroy(&refinedMesh);
2335: }
2336: }
2337: /* Handle DMPlex coarsening */
2338: PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL,0);
2339: PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy,0);
2340: if (coarsen && isHierarchy) {
2341: DM *dms;
2343: PetscMalloc1(coarsen, &dms);
2344: DMCoarsenHierarchy(dm, coarsen, dms);
2345: /* Free DMs */
2346: for (r = 0; r < coarsen; ++r) {
2347: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);
2348: DMDestroy(&dms[r]);
2349: }
2350: PetscFree(dms);
2351: } else {
2352: for (r = 0; r < coarsen; ++r) {
2353: DM coarseMesh;
2355: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2356: DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);
2357: /* Total hack since we do not pass in a pointer */
2358: DMPlexReplace_Static(dm, coarseMesh);
2359: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2360: DMDestroy(&coarseMesh);
2361: }
2362: }
2363: /* Handle */
2364: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2365: PetscOptionsTail();
2366: return(0);
2367: }
2369: static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec)
2370: {
2374: DMCreateGlobalVector_Section_Private(dm,vec);
2375: /* VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM); */
2376: VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);
2377: VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);
2378: VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);
2379: VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);
2380: return(0);
2381: }
2383: static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec)
2384: {
2388: DMCreateLocalVector_Section_Private(dm,vec);
2389: VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);
2390: VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);
2391: return(0);
2392: }
2394: static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd)
2395: {
2396: PetscInt depth, d;
2400: DMPlexGetDepth(dm, &depth);
2401: if (depth == 1) {
2402: DMGetDimension(dm, &d);
2403: if (dim == 0) {DMPlexGetDepthStratum(dm, dim, pStart, pEnd);}
2404: else if (dim == d) {DMPlexGetDepthStratum(dm, 1, pStart, pEnd);}
2405: else {*pStart = 0; *pEnd = 0;}
2406: } else {
2407: DMPlexGetDepthStratum(dm, dim, pStart, pEnd);
2408: }
2409: return(0);
2410: }
2412: static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[])
2413: {
2414: PetscSF sf;
2418: DMGetPointSF(dm, &sf);
2419: PetscSFGetRootRanks(sf, nranks, ranks, NULL, NULL, NULL);
2420: return(0);
2421: }
2423: static PetscErrorCode DMInitialize_Plex(DM dm)
2424: {
2428: dm->ops->view = DMView_Plex;
2429: dm->ops->load = DMLoad_Plex;
2430: dm->ops->setfromoptions = DMSetFromOptions_Plex;
2431: dm->ops->clone = DMClone_Plex;
2432: dm->ops->setup = DMSetUp_Plex;
2433: dm->ops->createlocalsection = DMCreateLocalSection_Plex;
2434: dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex;
2435: dm->ops->createglobalvector = DMCreateGlobalVector_Plex;
2436: dm->ops->createlocalvector = DMCreateLocalVector_Plex;
2437: dm->ops->getlocaltoglobalmapping = NULL;
2438: dm->ops->createfieldis = NULL;
2439: dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex;
2440: dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex;
2441: dm->ops->getcoloring = NULL;
2442: dm->ops->creatematrix = DMCreateMatrix_Plex;
2443: dm->ops->createinterpolation = DMCreateInterpolation_Plex;
2444: dm->ops->createmassmatrix = DMCreateMassMatrix_Plex;
2445: dm->ops->createinjection = DMCreateInjection_Plex;
2446: dm->ops->refine = DMRefine_Plex;
2447: dm->ops->coarsen = DMCoarsen_Plex;
2448: dm->ops->refinehierarchy = DMRefineHierarchy_Plex;
2449: dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex;
2450: dm->ops->adaptlabel = DMAdaptLabel_Plex;
2451: dm->ops->adaptmetric = DMAdaptMetric_Plex;
2452: dm->ops->globaltolocalbegin = NULL;
2453: dm->ops->globaltolocalend = NULL;
2454: dm->ops->localtoglobalbegin = NULL;
2455: dm->ops->localtoglobalend = NULL;
2456: dm->ops->destroy = DMDestroy_Plex;
2457: dm->ops->createsubdm = DMCreateSubDM_Plex;
2458: dm->ops->createsuperdm = DMCreateSuperDM_Plex;
2459: dm->ops->getdimpoints = DMGetDimPoints_Plex;
2460: dm->ops->locatepoints = DMLocatePoints_Plex;
2461: dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex;
2462: dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex;
2463: dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex;
2464: dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex;
2465: dm->ops->computel2diff = DMComputeL2Diff_Plex;
2466: dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex;
2467: dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex;
2468: dm->ops->getneighbors = DMGetNeighbors_Plex;
2469: PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);
2470: PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);
2471: PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C",DMCreateNeumannOverlap_Plex);
2472: PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex);
2473: return(0);
2474: }
2476: PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm)
2477: {
2478: DM_Plex *mesh = (DM_Plex *) dm->data;
2482: mesh->refct++;
2483: (*newdm)->data = mesh;
2484: PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);
2485: DMInitialize_Plex(*newdm);
2486: return(0);
2487: }
2489: /*MC
2490: DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram.
2491: In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is
2492: specified by a PetscSection object. Ownership in the global representation is determined by
2493: ownership of the underlying DMPlex points. This is specified by another PetscSection object.
2495: Options Database Keys:
2496: + -dm_plex_hash_location - Use grid hashing for point location
2497: . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes
2498: . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing
2499: . -dm_plex_max_projection_height - Maxmimum mesh point height used to project locally
2500: . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement
2501: . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric
2502: . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices
2503: . -dm_plex_check_faces <celltype> - Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type
2504: . -dm_plex_check_geometry - Check that cells have positive volume
2505: . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ
2506: . -dm_plex_view_scale <num> - Scale the TikZ
2507: - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices
2510: Level: intermediate
2512: .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType()
2513: M*/
2515: PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm)
2516: {
2517: DM_Plex *mesh;
2518: PetscInt unit, d;
2523: PetscNewLog(dm,&mesh);
2524: dm->dim = 0;
2525: dm->data = mesh;
2527: mesh->refct = 1;
2528: PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);
2529: mesh->maxConeSize = 0;
2530: mesh->cones = NULL;
2531: mesh->coneOrientations = NULL;
2532: PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);
2533: mesh->maxSupportSize = 0;
2534: mesh->supports = NULL;
2535: mesh->refinementUniform = PETSC_TRUE;
2536: mesh->refinementLimit = -1.0;
2538: mesh->facesTmp = NULL;
2540: mesh->tetgenOpts = NULL;
2541: mesh->triangleOpts = NULL;
2542: PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);
2543: mesh->remeshBd = PETSC_FALSE;
2545: mesh->subpointMap = NULL;
2547: for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0;
2549: mesh->regularRefinement = PETSC_FALSE;
2550: mesh->depthState = -1;
2551: mesh->globalVertexNumbers = NULL;
2552: mesh->globalCellNumbers = NULL;
2553: mesh->anchorSection = NULL;
2554: mesh->anchorIS = NULL;
2555: mesh->createanchors = NULL;
2556: mesh->computeanchormatrix = NULL;
2557: mesh->parentSection = NULL;
2558: mesh->parents = NULL;
2559: mesh->childIDs = NULL;
2560: mesh->childSection = NULL;
2561: mesh->children = NULL;
2562: mesh->referenceTree = NULL;
2563: mesh->getchildsymmetry = NULL;
2564: for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE;
2565: mesh->vtkCellHeight = 0;
2566: mesh->useAnchors = PETSC_FALSE;
2568: mesh->maxProjectionHeight = 0;
2570: mesh->printSetValues = PETSC_FALSE;
2571: mesh->printFEM = 0;
2572: mesh->printTol = 1.0e-10;
2574: DMInitialize_Plex(dm);
2575: return(0);
2576: }
2578: /*@
2579: DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram.
2581: Collective
2583: Input Parameter:
2584: . comm - The communicator for the DMPlex object
2586: Output Parameter:
2587: . mesh - The DMPlex object
2589: Level: beginner
2591: @*/
2592: PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh)
2593: {
2598: DMCreate(comm, mesh);
2599: DMSetType(*mesh, DMPLEX);
2600: return(0);
2601: }
2603: /*
2604: 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
2605: */
2606: /* TODO: invertCells and spaceDim arguments could be added also to to DMPlexCreateFromCellListParallel(), DMPlexBuildFromCellList_Internal() and DMPlexCreateFromCellList() */
2607: PetscErrorCode DMPlexBuildFromCellList_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscBool invertCells, PetscSF *sfVert)
2608: {
2609: PetscSF sfPoint;
2610: PetscLayout vLayout;
2611: PetscHSetI vhash;
2612: PetscSFNode *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex;
2613: const PetscInt *vrange;
2614: PetscInt numVerticesAdj, off = 0, *verticesAdj, numVerticesGhost = 0, *localVertex, *cone, c, p, v, g;
2615: PetscMPIInt rank, size;
2616: PetscErrorCode ierr;
2619: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
2620: MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);
2621: /* Partition vertices */
2622: PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);
2623: PetscLayoutSetLocalSize(vLayout, numVertices);
2624: PetscLayoutSetBlockSize(vLayout, 1);
2625: PetscLayoutSetUp(vLayout);
2626: PetscLayoutGetRanges(vLayout, &vrange);
2627: /* Count vertices and map them to procs */
2628: PetscHSetICreate(&vhash);
2629: for (c = 0; c < numCells; ++c) {
2630: for (p = 0; p < numCorners; ++p) {
2631: PetscHSetIAdd(vhash, cells[c*numCorners+p]);
2632: }
2633: }
2634: PetscHSetIGetSize(vhash, &numVerticesAdj);
2635: PetscMalloc1(numVerticesAdj, &verticesAdj);
2636: PetscHSetIGetElems(vhash, &off, verticesAdj);
2637: PetscHSetIDestroy(&vhash);
2638: if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj);
2639: PetscSortInt(numVerticesAdj, verticesAdj);
2640: PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);
2641: for (v = 0; v < numVerticesAdj; ++v) {
2642: const PetscInt gv = verticesAdj[v];
2643: PetscInt vrank;
2645: PetscFindInt(gv, size+1, vrange, &vrank);
2646: vrank = vrank < 0 ? -(vrank+2) : vrank;
2647: remoteVerticesAdj[v].index = gv - vrange[vrank];
2648: remoteVerticesAdj[v].rank = vrank;
2649: }
2650: /* Create cones */
2651: DMPlexSetChart(dm, 0, numCells+numVerticesAdj);
2652: for (c = 0; c < numCells; ++c) {DMPlexSetConeSize(dm, c, numCorners);}
2653: DMSetUp(dm);
2654: DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);
2655: for (c = 0; c < numCells; ++c) {
2656: for (p = 0; p < numCorners; ++p) {
2657: const PetscInt gv = cells[c*numCorners+p];
2658: PetscInt lv;
2660: PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);
2661: if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv);
2662: cone[p] = lv+numCells;
2663: }
2664: if (invertCells) { DMPlexInvertCell_Internal(spaceDim, numCorners, cone); }
2665: DMPlexSetCone(dm, c, cone);
2666: }
2667: DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);
2668: /* Create SF for vertices */
2669: PetscSFCreate(PetscObjectComm((PetscObject)dm), sfVert);
2670: PetscObjectSetName((PetscObject) *sfVert, "Vertex Ownership SF");
2671: PetscSFSetFromOptions(*sfVert);
2672: PetscSFSetGraph(*sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);
2673: PetscFree(verticesAdj);
2674: /* Build pointSF */
2675: PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);
2676: for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;}
2677: for (v = 0; v < numVertices; ++v) {vertexOwner[v].index = -1; vertexOwner[v].rank = -1;}
2678: PetscSFReduceBegin(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);
2679: PetscSFReduceEnd(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);
2680: 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);
2681: PetscSFBcastBegin(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);
2682: PetscSFBcastEnd(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);
2683: for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost;
2684: PetscMalloc1(numVerticesGhost, &localVertex);
2685: PetscMalloc1(numVerticesGhost, &remoteVertex);
2686: for (v = 0, g = 0; v < numVerticesAdj; ++v) {
2687: if (vertexLocal[v].rank != rank) {
2688: localVertex[g] = v+numCells;
2689: remoteVertex[g].index = vertexLocal[v].index;
2690: remoteVertex[g].rank = vertexLocal[v].rank;
2691: ++g;
2692: }
2693: }
2694: PetscFree2(vertexLocal, vertexOwner);
2695: if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost);
2696: DMGetPointSF(dm, &sfPoint);
2697: PetscObjectSetName((PetscObject) sfPoint, "point SF");
2698: PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);
2699: PetscLayoutDestroy(&vLayout);
2700: /* Fill in the rest of the topology structure */
2701: DMPlexSymmetrize(dm);
2702: DMPlexStratify(dm);
2703: return(0);
2704: }
2706: /*
2707: This takes as input the coordinates for each owned vertex
2708: */
2709: PetscErrorCode DMPlexBuildCoordinates_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numV, PetscSF sfVert, const PetscReal vertexCoords[])
2710: {
2711: PetscSection coordSection;
2712: Vec coordinates;
2713: PetscScalar *coords;
2714: PetscInt numVertices, numVerticesAdj, coordSize, v;
2718: DMSetCoordinateDim(dm, spaceDim);
2719: PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);
2720: DMGetCoordinateSection(dm, &coordSection);
2721: PetscSectionSetNumFields(coordSection, 1);
2722: PetscSectionSetFieldComponents(coordSection, 0, spaceDim);
2723: PetscSectionSetChart(coordSection, numCells, numCells + numVerticesAdj);
2724: for (v = numCells; v < numCells+numVerticesAdj; ++v) {
2725: PetscSectionSetDof(coordSection, v, spaceDim);
2726: PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);
2727: }
2728: PetscSectionSetUp(coordSection);
2729: PetscSectionGetStorageSize(coordSection, &coordSize);
2730: VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);
2731: VecSetBlockSize(coordinates, spaceDim);
2732: PetscObjectSetName((PetscObject) coordinates, "coordinates");
2733: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
2734: VecSetType(coordinates,VECSTANDARD);
2735: VecGetArray(coordinates, &coords);
2736: {
2737: MPI_Datatype coordtype;
2739: /* Need a temp buffer for coords if we have complex/single */
2740: MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);
2741: MPI_Type_commit(&coordtype);
2742: #if defined(PETSC_USE_COMPLEX)
2743: {
2744: PetscScalar *svertexCoords;
2745: PetscInt i;
2746: PetscMalloc1(numV*spaceDim,&svertexCoords);
2747: for (i=0; i<numV*spaceDim; i++) svertexCoords[i] = vertexCoords[i];
2748: PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords);
2749: PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords);
2750: PetscFree(svertexCoords);
2751: }
2752: #else
2753: PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords);
2754: PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords);
2755: #endif
2756: MPI_Type_free(&coordtype);
2757: }
2758: VecRestoreArray(coordinates, &coords);
2759: DMSetCoordinatesLocal(dm, coordinates);
2760: VecDestroy(&coordinates);
2761: return(0);
2762: }
2764: /*@
2765: DMPlexCreateFromCellListParallel - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM
2767: Input Parameters:
2768: + comm - The communicator
2769: . dim - The topological dimension of the mesh
2770: . numCells - The number of cells owned by this process
2771: . numVertices - The number of vertices owned by this process
2772: . numCorners - The number of vertices for each cell
2773: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
2774: . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell
2775: . spaceDim - The spatial dimension used for coordinates
2776: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
2778: Output Parameter:
2779: + dm - The DM
2780: - vertexSF - Optional, SF describing complete vertex ownership
2782: Note: Two triangles sharing a face
2783: $
2784: $ 2
2785: $ / | \
2786: $ / | \
2787: $ / | \
2788: $ 0 0 | 1 3
2789: $ \ | /
2790: $ \ | /
2791: $ \ | /
2792: $ 1
2793: would have input
2794: $ numCells = 2, numVertices = 4
2795: $ cells = [0 1 2 1 3 2]
2796: $
2797: which would result in the DMPlex
2798: $
2799: $ 4
2800: $ / | \
2801: $ / | \
2802: $ / | \
2803: $ 2 0 | 1 5
2804: $ \ | /
2805: $ \ | /
2806: $ \ | /
2807: $ 3
2809: Level: beginner
2811: .seealso: DMPlexCreateFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate()
2812: @*/
2813: 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)
2814: {
2815: PetscSF sfVert;
2819: DMCreate(comm, dm);
2820: DMSetType(*dm, DMPLEX);
2823: DMSetDimension(*dm, dim);
2824: DMPlexBuildFromCellList_Parallel_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE, &sfVert);
2825: if (interpolate) {
2826: DM idm;
2828: DMPlexInterpolate(*dm, &idm);
2829: DMDestroy(dm);
2830: *dm = idm;
2831: }
2832: DMPlexBuildCoordinates_Parallel_Internal(*dm, spaceDim, numCells, numVertices, sfVert, vertexCoords);
2833: if (vertexSF) *vertexSF = sfVert;
2834: else {PetscSFDestroy(&sfVert);}
2835: return(0);
2836: }
2838: /*
2839: This takes as input the common mesh generator output, a list of the vertices for each cell
2840: */
2841: PetscErrorCode DMPlexBuildFromCellList_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscBool invertCells)
2842: {
2843: PetscInt *cone, c, p;
2847: DMPlexSetChart(dm, 0, numCells+numVertices);
2848: for (c = 0; c < numCells; ++c) {
2849: DMPlexSetConeSize(dm, c, numCorners);
2850: }
2851: DMSetUp(dm);
2852: DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);
2853: for (c = 0; c < numCells; ++c) {
2854: for (p = 0; p < numCorners; ++p) {
2855: cone[p] = cells[c*numCorners+p]+numCells;
2856: }
2857: if (invertCells) { DMPlexInvertCell_Internal(spaceDim, numCorners, cone); }
2858: DMPlexSetCone(dm, c, cone);
2859: }
2860: DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);
2861: DMPlexSymmetrize(dm);
2862: DMPlexStratify(dm);
2863: return(0);
2864: }
2866: /*
2867: This takes as input the coordinates for each vertex
2868: */
2869: PetscErrorCode DMPlexBuildCoordinates_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[])
2870: {
2871: PetscSection coordSection;
2872: Vec coordinates;
2873: DM cdm;
2874: PetscScalar *coords;
2875: PetscInt v, d;
2879: DMSetCoordinateDim(dm, spaceDim);
2880: DMGetCoordinateSection(dm, &coordSection);
2881: PetscSectionSetNumFields(coordSection, 1);
2882: PetscSectionSetFieldComponents(coordSection, 0, spaceDim);
2883: PetscSectionSetChart(coordSection, numCells, numCells + numVertices);
2884: for (v = numCells; v < numCells+numVertices; ++v) {
2885: PetscSectionSetDof(coordSection, v, spaceDim);
2886: PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);
2887: }
2888: PetscSectionSetUp(coordSection);
2890: DMGetCoordinateDM(dm, &cdm);
2891: DMCreateLocalVector(cdm, &coordinates);
2892: VecSetBlockSize(coordinates, spaceDim);
2893: PetscObjectSetName((PetscObject) coordinates, "coordinates");
2894: VecGetArray(coordinates, &coords);
2895: for (v = 0; v < numVertices; ++v) {
2896: for (d = 0; d < spaceDim; ++d) {
2897: coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d];
2898: }
2899: }
2900: VecRestoreArray(coordinates, &coords);
2901: DMSetCoordinatesLocal(dm, coordinates);
2902: VecDestroy(&coordinates);
2903: return(0);
2904: }
2906: /*@
2907: DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM
2909: Input Parameters:
2910: + comm - The communicator
2911: . dim - The topological dimension of the mesh
2912: . numCells - The number of cells
2913: . numVertices - The number of vertices
2914: . numCorners - The number of vertices for each cell
2915: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
2916: . cells - An array of numCells*numCorners numbers, the vertices for each cell
2917: . spaceDim - The spatial dimension used for coordinates
2918: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
2920: Output Parameter:
2921: . dm - The DM
2923: Note: Two triangles sharing a face
2924: $
2925: $ 2
2926: $ / | \
2927: $ / | \
2928: $ / | \
2929: $ 0 0 | 1 3
2930: $ \ | /
2931: $ \ | /
2932: $ \ | /
2933: $ 1
2934: would have input
2935: $ numCells = 2, numVertices = 4
2936: $ cells = [0 1 2 1 3 2]
2937: $
2938: which would result in the DMPlex
2939: $
2940: $ 4
2941: $ / | \
2942: $ / | \
2943: $ / | \
2944: $ 2 0 | 1 5
2945: $ \ | /
2946: $ \ | /
2947: $ \ | /
2948: $ 3
2950: Level: beginner
2952: .seealso: DMPlexCreateFromDAG(), DMPlexCreate()
2953: @*/
2954: 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)
2955: {
2959: DMCreate(comm, dm);
2960: DMSetType(*dm, DMPLEX);
2961: DMSetDimension(*dm, dim);
2962: DMPlexBuildFromCellList_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE);
2963: if (interpolate) {
2964: DM idm;
2966: DMPlexInterpolate(*dm, &idm);
2967: DMDestroy(dm);
2968: *dm = idm;
2969: }
2970: DMPlexBuildCoordinates_Internal(*dm, spaceDim, numCells, numVertices, vertexCoords);
2971: return(0);
2972: }
2974: /*@
2975: DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM
2977: Input Parameters:
2978: + dm - The empty DM object, usually from DMCreate() and DMSetDimension()
2979: . depth - The depth of the DAG
2980: . numPoints - Array of size depth + 1 containing the number of points at each depth
2981: . coneSize - The cone size of each point
2982: . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point
2983: . coneOrientations - The orientation of each cone point
2984: - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim()
2986: Output Parameter:
2987: . dm - The DM
2989: Note: Two triangles sharing a face would have input
2990: $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0]
2991: $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0]
2992: $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0]
2993: $
2994: which would result in the DMPlex
2995: $
2996: $ 4
2997: $ / | \
2998: $ / | \
2999: $ / | \
3000: $ 2 0 | 1 5
3001: $ \ | /
3002: $ \ | /
3003: $ \ | /
3004: $ 3
3005: $
3006: $ Notice that all points are numbered consecutively, unlikely DMPlexCreateFromCellList()
3008: Level: advanced
3010: .seealso: DMPlexCreateFromCellList(), DMPlexCreate()
3011: @*/
3012: PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[])
3013: {
3014: Vec coordinates;
3015: PetscSection coordSection;
3016: PetscScalar *coords;
3017: PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off;
3021: DMGetDimension(dm, &dim);
3022: DMGetCoordinateDim(dm, &dimEmbed);
3023: if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %d cannot be less than intrinsic dimension %d",dimEmbed,dim);
3024: for (d = 0; d <= depth; ++d) pEnd += numPoints[d];
3025: DMPlexSetChart(dm, pStart, pEnd);
3026: for (p = pStart; p < pEnd; ++p) {
3027: DMPlexSetConeSize(dm, p, coneSize[p-pStart]);
3028: if (firstVertex < 0 && !coneSize[p - pStart]) {
3029: firstVertex = p - pStart;
3030: }
3031: }
3032: if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %d vertices but could not find any", numPoints[0]);
3033: DMSetUp(dm); /* Allocate space for cones */
3034: for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) {
3035: DMPlexSetCone(dm, p, &cones[off]);
3036: DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);
3037: }
3038: DMPlexSymmetrize(dm);
3039: DMPlexStratify(dm);
3040: /* Build coordinates */
3041: DMGetCoordinateSection(dm, &coordSection);
3042: PetscSectionSetNumFields(coordSection, 1);
3043: PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);
3044: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);
3045: for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) {
3046: PetscSectionSetDof(coordSection, v, dimEmbed);
3047: PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);
3048: }
3049: PetscSectionSetUp(coordSection);
3050: PetscSectionGetStorageSize(coordSection, &coordSize);
3051: VecCreate(PETSC_COMM_SELF, &coordinates);
3052: PetscObjectSetName((PetscObject) coordinates, "coordinates");
3053: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
3054: VecSetBlockSize(coordinates, dimEmbed);
3055: VecSetType(coordinates,VECSTANDARD);
3056: VecGetArray(coordinates, &coords);
3057: for (v = 0; v < numPoints[0]; ++v) {
3058: PetscInt off;
3060: PetscSectionGetOffset(coordSection, v+firstVertex, &off);
3061: for (d = 0; d < dimEmbed; ++d) {
3062: coords[off+d] = vertexCoords[v*dimEmbed+d];
3063: }
3064: }
3065: VecRestoreArray(coordinates, &coords);
3066: DMSetCoordinatesLocal(dm, coordinates);
3067: VecDestroy(&coordinates);
3068: return(0);
3069: }
3071: /*@C
3072: DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file.
3074: + comm - The MPI communicator
3075: . filename - Name of the .dat file
3076: - interpolate - Create faces and edges in the mesh
3078: Output Parameter:
3079: . dm - The DM object representing the mesh
3081: Note: The format is the simplest possible:
3082: $ Ne
3083: $ v0 v1 ... vk
3084: $ Nv
3085: $ x y z marker
3087: Level: beginner
3089: .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate()
3090: @*/
3091: PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
3092: {
3093: DMLabel marker;
3094: PetscViewer viewer;
3095: Vec coordinates;
3096: PetscSection coordSection;
3097: PetscScalar *coords;
3098: char line[PETSC_MAX_PATH_LEN];
3099: PetscInt dim = 3, cdim = 3, coordSize, v, c, d;
3100: PetscMPIInt rank;
3101: int snum, Nv, Nc;
3102: PetscErrorCode ierr;
3105: MPI_Comm_rank(comm, &rank);
3106: PetscViewerCreate(comm, &viewer);
3107: PetscViewerSetType(viewer, PETSCVIEWERASCII);
3108: PetscViewerFileSetMode(viewer, FILE_MODE_READ);
3109: PetscViewerFileSetName(viewer, filename);
3110: if (!rank) {
3111: PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);
3112: snum = sscanf(line, "%d %d", &Nc, &Nv);
3113: if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
3114: } else {
3115: Nc = Nv = 0;
3116: }
3117: DMCreate(comm, dm);
3118: DMSetType(*dm, DMPLEX);
3119: DMPlexSetChart(*dm, 0, Nc+Nv);
3120: DMSetDimension(*dm, dim);
3121: DMSetCoordinateDim(*dm, cdim);
3122: /* Read topology */
3123: if (!rank) {
3124: PetscInt cone[8], corners = 8;
3125: int vbuf[8], v;
3127: for (c = 0; c < Nc; ++c) {DMPlexSetConeSize(*dm, c, corners);}
3128: DMSetUp(*dm);
3129: for (c = 0; c < Nc; ++c) {
3130: PetscViewerRead(viewer, line, corners, NULL, PETSC_STRING);
3131: 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]);
3132: if (snum != corners) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
3133: for (v = 0; v < corners; ++v) cone[v] = vbuf[v] + Nc;
3134: /* Hexahedra are inverted */
3135: {
3136: PetscInt tmp = cone[1];
3137: cone[1] = cone[3];
3138: cone[3] = tmp;
3139: }
3140: DMPlexSetCone(*dm, c, cone);
3141: }
3142: }
3143: DMPlexSymmetrize(*dm);
3144: DMPlexStratify(*dm);
3145: /* Read coordinates */
3146: DMGetCoordinateSection(*dm, &coordSection);
3147: PetscSectionSetNumFields(coordSection, 1);
3148: PetscSectionSetFieldComponents(coordSection, 0, cdim);
3149: PetscSectionSetChart(coordSection, Nc, Nc + Nv);
3150: for (v = Nc; v < Nc+Nv; ++v) {
3151: PetscSectionSetDof(coordSection, v, cdim);
3152: PetscSectionSetFieldDof(coordSection, v, 0, cdim);
3153: }
3154: PetscSectionSetUp(coordSection);
3155: PetscSectionGetStorageSize(coordSection, &coordSize);
3156: VecCreate(PETSC_COMM_SELF, &coordinates);
3157: PetscObjectSetName((PetscObject) coordinates, "coordinates");
3158: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
3159: VecSetBlockSize(coordinates, cdim);
3160: VecSetType(coordinates, VECSTANDARD);
3161: VecGetArray(coordinates, &coords);
3162: if (!rank) {
3163: double x[3];
3164: int val;
3166: DMCreateLabel(*dm, "marker");
3167: DMGetLabel(*dm, "marker", &marker);
3168: for (v = 0; v < Nv; ++v) {
3169: PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);
3170: snum = sscanf(line, "%lg %lg %lg %d", &x[0], &x[1], &x[2], &val);
3171: if (snum != 4) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
3172: for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d];
3173: if (val) {DMLabelSetValue(marker, v+Nc, val);}
3174: }
3175: }
3176: VecRestoreArray(coordinates, &coords);
3177: DMSetCoordinatesLocal(*dm, coordinates);
3178: VecDestroy(&coordinates);
3179: PetscViewerDestroy(&viewer);
3180: if (interpolate) {
3181: DM idm;
3182: DMLabel bdlabel;
3184: DMPlexInterpolate(*dm, &idm);
3185: DMDestroy(dm);
3186: *dm = idm;
3188: DMGetLabel(*dm, "marker", &bdlabel);
3189: DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);
3190: DMPlexLabelComplete(*dm, bdlabel);
3191: }
3192: return(0);
3193: }
3195: /*@C
3196: DMPlexCreateFromFile - This takes a filename and produces a DM
3198: Input Parameters:
3199: + comm - The communicator
3200: . filename - A file name
3201: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
3203: Output Parameter:
3204: . dm - The DM
3206: Options Database Keys:
3207: . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5
3209: Level: beginner
3211: .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellList(), DMPlexCreate()
3212: @*/
3213: PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
3214: {
3215: const char *extGmsh = ".msh";
3216: const char *extGmsh2 = ".msh2";
3217: const char *extGmsh4 = ".msh4";
3218: const char *extCGNS = ".cgns";
3219: const char *extExodus = ".exo";
3220: const char *extGenesis = ".gen";
3221: const char *extFluent = ".cas";
3222: const char *extHDF5 = ".h5";
3223: const char *extMed = ".med";
3224: const char *extPLY = ".ply";
3225: const char *extCV = ".dat";
3226: size_t len;
3227: PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isCV;
3228: PetscMPIInt rank;
3234: MPI_Comm_rank(comm, &rank);
3235: PetscStrlen(filename, &len);
3236: if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path");
3237: PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);
3238: PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh2, 5, &isGmsh2);
3239: PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh4, 5, &isGmsh4);
3240: PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);
3241: PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);
3242: PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);
3243: PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);
3244: PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);
3245: PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);
3246: PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);
3247: PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);
3248: if (isGmsh || isGmsh2 || isGmsh4) {
3249: DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);
3250: } else if (isCGNS) {
3251: DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);
3252: } else if (isExodus || isGenesis) {
3253: DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);
3254: } else if (isFluent) {
3255: DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);
3256: } else if (isHDF5) {
3257: PetscBool load_hdf5_xdmf = PETSC_FALSE;
3258: PetscViewer viewer;
3260: /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */
3261: PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf", 5, &load_hdf5_xdmf);
3262: PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);
3263: PetscViewerCreate(comm, &viewer);
3264: PetscViewerSetType(viewer, PETSCVIEWERHDF5);
3265: PetscViewerFileSetMode(viewer, FILE_MODE_READ);
3266: PetscViewerFileSetName(viewer, filename);
3267: DMCreate(comm, dm);
3268: DMSetType(*dm, DMPLEX);
3269: if (load_hdf5_xdmf) {PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);}
3270: DMLoad(*dm, viewer);
3271: if (load_hdf5_xdmf) {PetscViewerPopFormat(viewer);}
3272: PetscViewerDestroy(&viewer);
3274: if (interpolate) {
3275: DM idm;
3277: DMPlexInterpolate(*dm, &idm);
3278: DMDestroy(dm);
3279: *dm = idm;
3280: }
3281: } else if (isMed) {
3282: DMPlexCreateMedFromFile(comm, filename, interpolate, dm);
3283: } else if (isPLY) {
3284: DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);
3285: } else if (isCV) {
3286: DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);
3287: } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename);
3288: return(0);
3289: }
3291: /*@
3292: DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell
3294: Collective
3296: Input Parameters:
3297: + comm - The communicator
3298: . dim - The spatial dimension
3299: - simplex - Flag for simplex, otherwise use a tensor-product cell
3301: Output Parameter:
3302: . refdm - The reference cell
3304: Level: intermediate
3306: .seealso:
3307: @*/
3308: PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm)
3309: {
3310: DM rdm;
3311: Vec coords;
3315: DMCreate(comm, &rdm);
3316: DMSetType(rdm, DMPLEX);
3317: DMSetDimension(rdm, dim);
3318: switch (dim) {
3319: case 0:
3320: {
3321: PetscInt numPoints[1] = {1};
3322: PetscInt coneSize[1] = {0};
3323: PetscInt cones[1] = {0};
3324: PetscInt coneOrientations[1] = {0};
3325: PetscScalar vertexCoords[1] = {0.0};
3327: DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3328: }
3329: break;
3330: case 1:
3331: {
3332: PetscInt numPoints[2] = {2, 1};
3333: PetscInt coneSize[3] = {2, 0, 0};
3334: PetscInt cones[2] = {1, 2};
3335: PetscInt coneOrientations[2] = {0, 0};
3336: PetscScalar vertexCoords[2] = {-1.0, 1.0};
3338: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3339: }
3340: break;
3341: case 2:
3342: if (simplex) {
3343: PetscInt numPoints[2] = {3, 1};
3344: PetscInt coneSize[4] = {3, 0, 0, 0};
3345: PetscInt cones[3] = {1, 2, 3};
3346: PetscInt coneOrientations[3] = {0, 0, 0};
3347: PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0};
3349: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3350: } else {
3351: PetscInt numPoints[2] = {4, 1};
3352: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
3353: PetscInt cones[4] = {1, 2, 3, 4};
3354: PetscInt coneOrientations[4] = {0, 0, 0, 0};
3355: PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0};
3357: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3358: }
3359: break;
3360: case 3:
3361: if (simplex) {
3362: PetscInt numPoints[2] = {4, 1};
3363: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
3364: PetscInt cones[4] = {1, 3, 2, 4};
3365: PetscInt coneOrientations[4] = {0, 0, 0, 0};
3366: 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};
3368: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3369: } else {
3370: PetscInt numPoints[2] = {8, 1};
3371: PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0};
3372: PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8};
3373: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
3374: 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,
3375: -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0};
3377: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3378: }
3379: break;
3380: default:
3381: SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %d", dim);
3382: }
3383: DMPlexInterpolate(rdm, refdm);
3384: if (rdm->coordinateDM) {
3385: DM ncdm;
3386: PetscSection cs;
3387: PetscInt pEnd = -1;
3389: DMGetLocalSection(rdm->coordinateDM, &cs);
3390: if (cs) {PetscSectionGetChart(cs, NULL, &pEnd);}
3391: if (pEnd >= 0) {
3392: DMClone(*refdm, &ncdm);
3393: DMCopyDisc(rdm->coordinateDM, ncdm);
3394: DMSetLocalSection(ncdm, cs);
3395: DMSetCoordinateDM(*refdm, ncdm);
3396: DMDestroy(&ncdm);
3397: }
3398: }
3399: DMGetCoordinatesLocal(rdm, &coords);
3400: if (coords) {
3401: DMSetCoordinatesLocal(*refdm, coords);
3402: } else {
3403: DMGetCoordinates(rdm, &coords);
3404: if (coords) {DMSetCoordinates(*refdm, coords);}
3405: }
3406: DMDestroy(&rdm);
3407: return(0);
3408: }