Actual source code: plexcreate.c
petsc-3.12.5 2020-03-29
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
1005: - -dm_plex_box_faces <m,n,p> - Number of faces in each linear direction
1007: Notes:
1008: The options database keys above take lists of length d in d dimensions.
1010: Here is the numbering returned for 2 faces in each direction for tensor cells:
1011: $ 10---17---11---18----12
1012: $ | | |
1013: $ | | |
1014: $ 20 2 22 3 24
1015: $ | | |
1016: $ | | |
1017: $ 7---15----8---16----9
1018: $ | | |
1019: $ | | |
1020: $ 19 0 21 1 23
1021: $ | | |
1022: $ | | |
1023: $ 4---13----5---14----6
1025: and for simplicial cells
1027: $ 14----8---15----9----16
1028: $ |\ 5 |\ 7 |
1029: $ | \ | \ |
1030: $ 13 2 14 3 15
1031: $ | 4 \ | 6 \ |
1032: $ | \ | \ |
1033: $ 11----6---12----7----13
1034: $ |\ |\ |
1035: $ | \ 1 | \ 3 |
1036: $ 10 0 11 1 12
1037: $ | 0 \ | 2 \ |
1038: $ | \ | \ |
1039: $ 8----4----9----5----10
1041: Level: beginner
1043: .seealso: DMPlexCreateFromFile(), DMPlexCreateHexCylinderMesh(), DMSetType(), DMCreate()
1044: @*/
1045: 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)
1046: {
1047: PetscInt fac[3] = {0, 0, 0};
1048: PetscReal low[3] = {0, 0, 0};
1049: PetscReal upp[3] = {1, 1, 1};
1050: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
1051: PetscInt i, n;
1052: PetscBool flg;
1056: n = 3;
1057: PetscOptionsGetIntArray(NULL, NULL, "-dm_plex_box_faces", fac, &n, &flg);
1058: for (i = 0; i < dim; ++i) fac[i] = faces ? faces[i] : (flg && i < n ? fac[i] : (dim == 1 ? 1 : 4-dim));
1059: if (lower) for (i = 0; i < dim; ++i) low[i] = lower[i];
1060: if (upper) for (i = 0; i < dim; ++i) upp[i] = upper[i];
1061: if (periodicity) for (i = 0; i < dim; ++i) bdt[i] = periodicity[i];
1062: /* Allow bounds to be specified from the command line */
1063: n = 3;
1064: PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_lower", low, &n, &flg);
1065: if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim);
1066: n = 3;
1067: PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_upper", upp, &n, &flg);
1068: if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim);
1070: if (dim == 1) {DMPlexCreateLineMesh_Internal(comm, fac[0], low[0], upp[0], bdt[0], dm);}
1071: else if (simplex) {DMPlexCreateBoxMesh_Simplex_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);}
1072: else {DMPlexCreateBoxMesh_Tensor_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);}
1073: return(0);
1074: }
1076: /*@
1077: DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells.
1079: Collective
1081: Input Parameters:
1082: + comm - The communicator for the DM object
1083: . faces - Number of faces per dimension, or NULL for (1, 1, 1)
1084: . lower - The lower left corner, or NULL for (0, 0, 0)
1085: . upper - The upper right corner, or NULL for (1, 1, 1)
1086: . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE
1087: . ordExt - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first
1088: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
1090: Output Parameter:
1091: . dm - The DM object
1093: Level: beginner
1095: .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateWedgeCylinderMesh(), DMPlexExtrude(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1096: @*/
1097: PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool ordExt, PetscBool interpolate, DM *dm)
1098: {
1099: DM bdm, botdm;
1100: PetscInt i;
1101: PetscInt fac[3] = {0, 0, 0};
1102: PetscReal low[3] = {0, 0, 0};
1103: PetscReal upp[3] = {1, 1, 1};
1104: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
1108: for (i = 0; i < 3; ++i) fac[i] = faces ? (faces[i] > 0 ? faces[i] : 1) : 1;
1109: if (lower) for (i = 0; i < 3; ++i) low[i] = lower[i];
1110: if (upper) for (i = 0; i < 3; ++i) upp[i] = upper[i];
1111: if (periodicity) for (i = 0; i < 3; ++i) bdt[i] = periodicity[i];
1112: for (i = 0; i < 3; ++i) if (bdt[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity not yet supported");
1114: DMCreate(comm, &bdm);
1115: DMSetType(bdm, DMPLEX);
1116: DMSetDimension(bdm, 1);
1117: DMSetCoordinateDim(bdm, 2);
1118: DMPlexCreateSquareBoundary(bdm, low, upp, fac);
1119: DMPlexGenerate(bdm, NULL, PETSC_FALSE, &botdm);
1120: DMDestroy(&bdm);
1121: DMPlexExtrude(botdm, fac[2], upp[2] - low[2], ordExt, interpolate, dm);
1122: if (low[2] != 0.0) {
1123: Vec v;
1124: PetscScalar *x;
1125: PetscInt cDim, n;
1127: DMGetCoordinatesLocal(*dm, &v);
1128: VecGetBlockSize(v, &cDim);
1129: VecGetLocalSize(v, &n);
1130: VecGetArray(v, &x);
1131: x += cDim;
1132: for (i=0; i<n; i+=cDim) x[i] += low[2];
1133: VecRestoreArray(v,&x);
1134: DMSetCoordinatesLocal(*dm, v);
1135: }
1136: DMDestroy(&botdm);
1137: return(0);
1138: }
1140: /*@
1141: DMPlexExtrude - Creates a (d+1)-D mesh by extruding a d-D mesh in the normal direction using prismatic cells.
1143: Collective on idm
1145: Input Parameters:
1146: + idm - The mesh to be extruted
1147: . layers - The number of layers
1148: . height - The height of the extruded layer
1149: . ordExt - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first
1150: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
1152: Output Parameter:
1153: . dm - The DM object
1155: Notes: The object created is an hybrid mesh, the vertex ordering in the cone of the cell is that of the prismatic cells
1157: Level: advanced
1159: .seealso: DMPlexCreateWedgeCylinderMesh(), DMPlexCreateWedgeBoxMesh(), DMPlexSetHybridBounds(), DMSetType(), DMCreate()
1160: @*/
1161: PetscErrorCode DMPlexExtrude(DM idm, PetscInt layers, PetscReal height, PetscBool ordExt, PetscBool interpolate, DM* dm)
1162: {
1163: PetscScalar *coordsB;
1164: const PetscScalar *coordsA;
1165: PetscReal *normals = NULL;
1166: Vec coordinatesA, coordinatesB;
1167: PetscSection coordSectionA, coordSectionB;
1168: PetscInt dim, cDim, cDimB, c, l, v, coordSize, *newCone;
1169: PetscInt cStart, cEnd, vStart, vEnd, cellV, numCells, numVertices;
1170: PetscErrorCode ierr;
1177: DMGetDimension(idm, &dim);
1178: if (dim < 1 || dim > 3) SETERRQ1(PetscObjectComm((PetscObject)idm), PETSC_ERR_SUP, "Support for dimension %D not coded", dim);
1180: DMPlexGetHeightStratum(idm, 0, &cStart, &cEnd);
1181: DMPlexGetDepthStratum(idm, 0, &vStart, &vEnd);
1182: numCells = (cEnd - cStart)*layers;
1183: numVertices = (vEnd - vStart)*(layers+1);
1184: DMCreate(PetscObjectComm((PetscObject)idm), dm);
1185: DMSetType(*dm, DMPLEX);
1186: DMSetDimension(*dm, dim+1);
1187: DMPlexSetChart(*dm, 0, numCells+numVertices);
1188: for (c = cStart, cellV = 0; c < cEnd; ++c) {
1189: PetscInt *closure = NULL;
1190: PetscInt closureSize, numCorners = 0;
1192: DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);
1193: for (v = 0; v < closureSize*2; v += 2) if ((closure[v] >= vStart) && (closure[v] < vEnd)) numCorners++;
1194: DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);
1195: for (l = 0; l < layers; ++l) {
1196: DMPlexSetConeSize(*dm, ordExt ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart, 2*numCorners);
1197: }
1198: cellV = PetscMax(numCorners,cellV);
1199: }
1200: DMPlexSetHybridBounds(*dm, 0, PETSC_DETERMINE, PETSC_DETERMINE, PETSC_DETERMINE);
1201: DMSetUp(*dm);
1203: DMGetCoordinateDim(idm, &cDim);
1204: if (dim != cDim) {
1205: PetscCalloc1(cDim*(vEnd - vStart), &normals);
1206: }
1207: PetscMalloc1(3*cellV,&newCone);
1208: for (c = cStart; c < cEnd; ++c) {
1209: PetscInt *closure = NULL;
1210: PetscInt closureSize, numCorners = 0, l;
1211: PetscReal normal[3] = {0, 0, 0};
1213: if (normals) {
1214: DMPlexComputeCellGeometryFVM(idm, c, NULL, NULL, normal);
1215: }
1216: DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);
1217: for (v = 0; v < closureSize*2; v += 2) {
1218: if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
1219: PetscInt d;
1221: newCone[numCorners++] = closure[v] - vStart;
1222: if (normals) { for (d = 0; d < cDim; ++d) normals[cDim*(closure[v]-vStart)+d] += normal[d]; }
1223: }
1224: }
1225: switch (numCorners) {
1226: case 4: /* do nothing */
1227: case 2: /* do nothing */
1228: break;
1229: case 3: /* from counter-clockwise to wedge ordering */
1230: l = newCone[1];
1231: newCone[1] = newCone[2];
1232: newCone[2] = l;
1233: break;
1234: default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_SUP, "Unsupported number of corners: %D", numCorners);
1235: }
1236: DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);
1237: for (l = 0; l < layers; ++l) {
1238: PetscInt i;
1240: for (i = 0; i < numCorners; ++i) {
1241: newCone[ numCorners + i] = ordExt ? (layers+1)*newCone[i] + l + numCells : l*(vEnd - vStart) + newCone[i] + numCells;
1242: newCone[2*numCorners + i] = ordExt ? (layers+1)*newCone[i] + l + 1 + numCells : (l+1)*(vEnd - vStart) + newCone[i] + numCells;
1243: }
1244: DMPlexSetCone(*dm, ordExt ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart, newCone + numCorners);
1245: }
1246: }
1247: DMPlexSymmetrize(*dm);
1248: DMPlexStratify(*dm);
1249: PetscFree(newCone);
1251: cDimB = cDim == dim ? cDim+1 : cDim;
1252: DMGetCoordinateSection(*dm, &coordSectionB);
1253: PetscSectionSetNumFields(coordSectionB, 1);
1254: PetscSectionSetFieldComponents(coordSectionB, 0, cDimB);
1255: PetscSectionSetChart(coordSectionB, numCells, numCells+numVertices);
1256: for (v = numCells; v < numCells+numVertices; ++v) {
1257: PetscSectionSetDof(coordSectionB, v, cDimB);
1258: PetscSectionSetFieldDof(coordSectionB, v, 0, cDimB);
1259: }
1260: PetscSectionSetUp(coordSectionB);
1261: PetscSectionGetStorageSize(coordSectionB, &coordSize);
1262: VecCreate(PETSC_COMM_SELF, &coordinatesB);
1263: PetscObjectSetName((PetscObject) coordinatesB, "coordinates");
1264: VecSetSizes(coordinatesB, coordSize, PETSC_DETERMINE);
1265: VecSetBlockSize(coordinatesB, cDimB);
1266: VecSetType(coordinatesB,VECSTANDARD);
1268: DMGetCoordinateSection(idm, &coordSectionA);
1269: DMGetCoordinatesLocal(idm, &coordinatesA);
1270: VecGetArray(coordinatesB, &coordsB);
1271: VecGetArrayRead(coordinatesA, &coordsA);
1272: for (v = vStart; v < vEnd; ++v) {
1273: const PetscScalar *cptr;
1274: PetscReal ones2[2] = { 0., 1.}, ones3[3] = { 0., 0., 1.};
1275: PetscReal *normal, norm, h = height/layers;
1276: PetscInt offA, d, cDimA = cDim;
1278: normal = normals ? normals + cDimB*(v - vStart) : (cDim > 1 ? ones3 : ones2);
1279: if (normals) {
1280: for (d = 0, norm = 0.0; d < cDimB; ++d) norm += normal[d]*normal[d];
1281: for (d = 0; d < cDimB; ++d) normal[d] *= 1./PetscSqrtReal(norm);
1282: }
1284: PetscSectionGetOffset(coordSectionA, v, &offA);
1285: cptr = coordsA + offA;
1286: for (l = 0; l < layers+1; ++l) {
1287: PetscInt offB, d, newV;
1289: newV = ordExt ? (layers+1)*(v -vStart) + l + numCells : (vEnd -vStart)*l + (v -vStart) + numCells;
1290: PetscSectionGetOffset(coordSectionB, newV, &offB);
1291: for (d = 0; d < cDimA; ++d) { coordsB[offB+d] = cptr[d]; }
1292: for (d = 0; d < cDimB; ++d) { coordsB[offB+d] += l ? normal[d]*h : 0.0; }
1293: cptr = coordsB + offB;
1294: cDimA = cDimB;
1295: }
1296: }
1297: VecRestoreArrayRead(coordinatesA, &coordsA);
1298: VecRestoreArray(coordinatesB, &coordsB);
1299: DMSetCoordinatesLocal(*dm, coordinatesB);
1300: VecDestroy(&coordinatesB);
1301: PetscFree(normals);
1302: if (interpolate) {
1303: DM idm;
1305: DMPlexInterpolate(*dm, &idm);
1306: DMPlexCopyCoordinates(*dm, idm);
1307: DMDestroy(dm);
1308: *dm = idm;
1309: }
1310: return(0);
1311: }
1313: /*@C
1314: DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database.
1316: Logically Collective on dm
1318: Input Parameters:
1319: + dm - the DM context
1320: - prefix - the prefix to prepend to all option names
1322: Notes:
1323: A hyphen (-) must NOT be given at the beginning of the prefix name.
1324: The first character of all runtime options is AUTOMATICALLY the hyphen.
1326: Level: advanced
1328: .seealso: SNESSetFromOptions()
1329: @*/
1330: PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[])
1331: {
1332: DM_Plex *mesh = (DM_Plex *) dm->data;
1337: PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);
1338: PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);
1339: return(0);
1340: }
1342: /*@
1343: DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra.
1345: Collective
1347: Input Parameters:
1348: + comm - The communicator for the DM object
1349: . numRefine - The number of regular refinements to the basic 5 cell structure
1350: - periodicZ - The boundary type for the Z direction
1352: Output Parameter:
1353: . dm - The DM object
1355: Note: Here is the output numbering looking from the bottom of the cylinder:
1356: $ 17-----14
1357: $ | |
1358: $ | 2 |
1359: $ | |
1360: $ 17-----8-----7-----14
1361: $ | | | |
1362: $ | 3 | 0 | 1 |
1363: $ | | | |
1364: $ 19-----5-----6-----13
1365: $ | |
1366: $ | 4 |
1367: $ | |
1368: $ 19-----13
1369: $
1370: $ and up through the top
1371: $
1372: $ 18-----16
1373: $ | |
1374: $ | 2 |
1375: $ | |
1376: $ 18----10----11-----16
1377: $ | | | |
1378: $ | 3 | 0 | 1 |
1379: $ | | | |
1380: $ 20-----9----12-----15
1381: $ | |
1382: $ | 4 |
1383: $ | |
1384: $ 20-----15
1386: Level: beginner
1388: .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1389: @*/
1390: PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, PetscInt numRefine, DMBoundaryType periodicZ, DM *dm)
1391: {
1392: const PetscInt dim = 3;
1393: PetscInt numCells, numVertices, r;
1394: PetscMPIInt rank;
1399: MPI_Comm_rank(comm, &rank);
1400: if (numRefine < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of refinements %D cannot be negative", numRefine);
1401: DMCreate(comm, dm);
1402: DMSetType(*dm, DMPLEX);
1403: DMSetDimension(*dm, dim);
1404: /* Create topology */
1405: {
1406: PetscInt cone[8], c;
1408: numCells = !rank ? 5 : 0;
1409: numVertices = !rank ? 16 : 0;
1410: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1411: numCells *= 3;
1412: numVertices = !rank ? 24 : 0;
1413: }
1414: DMPlexSetChart(*dm, 0, numCells+numVertices);
1415: for (c = 0; c < numCells; c++) {DMPlexSetConeSize(*dm, c, 8);}
1416: DMSetUp(*dm);
1417: if (!rank) {
1418: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1419: cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16;
1420: cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34;
1421: DMPlexSetCone(*dm, 0, cone);
1422: cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23;
1423: cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */
1424: DMPlexSetCone(*dm, 1, cone);
1425: cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17;
1426: cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38;
1427: DMPlexSetCone(*dm, 2, cone);
1428: cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15;
1429: cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38;
1430: DMPlexSetCone(*dm, 3, cone);
1431: cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23;
1432: cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31;
1433: DMPlexSetCone(*dm, 4, cone);
1435: cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32;
1436: cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20;
1437: DMPlexSetCone(*dm, 5, cone);
1438: cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36;
1439: cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21;
1440: DMPlexSetCone(*dm, 6, cone);
1441: cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33;
1442: cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28;
1443: DMPlexSetCone(*dm, 7, cone);
1444: cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31;
1445: cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28;
1446: DMPlexSetCone(*dm, 8, cone);
1447: cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36;
1448: cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19;
1449: DMPlexSetCone(*dm, 9, cone);
1451: cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22;
1452: cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18;
1453: DMPlexSetCone(*dm, 10, cone);
1454: cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25;
1455: cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17;
1456: DMPlexSetCone(*dm, 11, cone);
1457: cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21;
1458: cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27;
1459: DMPlexSetCone(*dm, 12, cone);
1460: cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19;
1461: cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27;
1462: DMPlexSetCone(*dm, 13, cone);
1463: cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25;
1464: cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15;
1465: DMPlexSetCone(*dm, 14, cone);
1466: } else {
1467: cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6;
1468: cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10;
1469: DMPlexSetCone(*dm, 0, cone);
1470: cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13;
1471: cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11;
1472: DMPlexSetCone(*dm, 1, cone);
1473: cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7;
1474: cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18;
1475: DMPlexSetCone(*dm, 2, cone);
1476: cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5;
1477: cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18;
1478: DMPlexSetCone(*dm, 3, cone);
1479: cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13;
1480: cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9;
1481: DMPlexSetCone(*dm, 4, cone);
1482: }
1483: }
1484: DMPlexSymmetrize(*dm);
1485: DMPlexStratify(*dm);
1486: }
1487: /* Interpolate */
1488: {
1489: DM idm;
1491: DMPlexInterpolate(*dm, &idm);
1492: DMDestroy(dm);
1493: *dm = idm;
1494: }
1495: /* Create cube geometry */
1496: {
1497: Vec coordinates;
1498: PetscSection coordSection;
1499: PetscScalar *coords;
1500: PetscInt coordSize, v;
1501: const PetscReal dis = 1.0/PetscSqrtReal(2.0);
1502: const PetscReal ds2 = dis/2.0;
1504: /* Build coordinates */
1505: DMGetCoordinateSection(*dm, &coordSection);
1506: PetscSectionSetNumFields(coordSection, 1);
1507: PetscSectionSetFieldComponents(coordSection, 0, dim);
1508: PetscSectionSetChart(coordSection, numCells, numCells+numVertices);
1509: for (v = numCells; v < numCells+numVertices; ++v) {
1510: PetscSectionSetDof(coordSection, v, dim);
1511: PetscSectionSetFieldDof(coordSection, v, 0, dim);
1512: }
1513: PetscSectionSetUp(coordSection);
1514: PetscSectionGetStorageSize(coordSection, &coordSize);
1515: VecCreate(PETSC_COMM_SELF, &coordinates);
1516: PetscObjectSetName((PetscObject) coordinates, "coordinates");
1517: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1518: VecSetBlockSize(coordinates, dim);
1519: VecSetType(coordinates,VECSTANDARD);
1520: VecGetArray(coordinates, &coords);
1521: if (!rank) {
1522: coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0;
1523: coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0;
1524: coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0;
1525: coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0;
1526: coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0;
1527: coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0;
1528: coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0;
1529: coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0;
1530: coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0;
1531: coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0;
1532: coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0;
1533: coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0;
1534: coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0;
1535: coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0;
1536: coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0;
1537: coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0;
1538: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1539: /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5;
1540: /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5;
1541: /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5;
1542: /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5;
1543: /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5;
1544: /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5;
1545: /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5;
1546: /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5;
1547: }
1548: }
1549: VecRestoreArray(coordinates, &coords);
1550: DMSetCoordinatesLocal(*dm, coordinates);
1551: VecDestroy(&coordinates);
1552: }
1553: /* Create periodicity */
1554: if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) {
1555: PetscReal L[3];
1556: PetscReal maxCell[3];
1557: DMBoundaryType bdType[3];
1558: PetscReal lower[3] = {0.0, 0.0, 0.0};
1559: PetscReal upper[3] = {1.0, 1.0, 1.5};
1560: PetscInt i, numZCells = 3;
1562: bdType[0] = DM_BOUNDARY_NONE;
1563: bdType[1] = DM_BOUNDARY_NONE;
1564: bdType[2] = periodicZ;
1565: for (i = 0; i < dim; i++) {
1566: L[i] = upper[i] - lower[i];
1567: maxCell[i] = 1.1 * (L[i] / numZCells);
1568: }
1569: DMSetPeriodicity(*dm, PETSC_TRUE, maxCell, L, bdType);
1570: }
1571: /* Refine topology */
1572: for (r = 0; r < numRefine; ++r) {
1573: DM rdm = NULL;
1575: DMRefine(*dm, comm, &rdm);
1576: DMDestroy(dm);
1577: *dm = rdm;
1578: }
1579: /* Remap geometry to cylinder
1580: Interior square: Linear interpolation is correct
1581: The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing
1582: such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance
1584: phi = arctan(y/x)
1585: d_close = sqrt(1/8 + 1/4 sin^2(phi))
1586: d_far = sqrt(1/2 + sin^2(phi))
1588: so we remap them using
1590: x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close)
1591: y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close)
1593: If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y.
1594: */
1595: {
1596: Vec coordinates;
1597: PetscSection coordSection;
1598: PetscScalar *coords;
1599: PetscInt vStart, vEnd, v;
1600: const PetscReal dis = 1.0/PetscSqrtReal(2.0);
1601: const PetscReal ds2 = 0.5*dis;
1603: DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);
1604: DMGetCoordinateSection(*dm, &coordSection);
1605: DMGetCoordinatesLocal(*dm, &coordinates);
1606: VecGetArray(coordinates, &coords);
1607: for (v = vStart; v < vEnd; ++v) {
1608: PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc;
1609: PetscInt off;
1611: PetscSectionGetOffset(coordSection, v, &off);
1612: if ((PetscAbsScalar(coords[off+0]) <= ds2) && (PetscAbsScalar(coords[off+1]) <= ds2)) continue;
1613: x = PetscRealPart(coords[off]);
1614: y = PetscRealPart(coords[off+1]);
1615: phi = PetscAtan2Real(y, x);
1616: sinp = PetscSinReal(phi);
1617: cosp = PetscCosReal(phi);
1618: if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) {
1619: dc = PetscAbsReal(ds2/sinp);
1620: df = PetscAbsReal(dis/sinp);
1621: xc = ds2*x/PetscAbsReal(y);
1622: yc = ds2*PetscSignReal(y);
1623: } else {
1624: dc = PetscAbsReal(ds2/cosp);
1625: df = PetscAbsReal(dis/cosp);
1626: xc = ds2*PetscSignReal(x);
1627: yc = ds2*y/PetscAbsReal(x);
1628: }
1629: coords[off+0] = xc + (coords[off+0] - xc)*(1.0 - dc)/(df - dc);
1630: coords[off+1] = yc + (coords[off+1] - yc)*(1.0 - dc)/(df - dc);
1631: }
1632: VecRestoreArray(coordinates, &coords);
1633: if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) {
1634: DMLocalizeCoordinates(*dm);
1635: }
1636: }
1637: return(0);
1638: }
1640: /*@
1641: DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges.
1643: Collective
1645: Input Parameters:
1646: + comm - The communicator for the DM object
1647: . n - The number of wedges around the origin
1648: - interpolate - Create edges and faces
1650: Output Parameter:
1651: . dm - The DM object
1653: Level: beginner
1655: .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1656: @*/
1657: PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm)
1658: {
1659: const PetscInt dim = 3;
1660: PetscInt numCells, numVertices;
1661: PetscMPIInt rank;
1666: MPI_Comm_rank(comm, &rank);
1667: if (n < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n);
1668: DMCreate(comm, dm);
1669: DMSetType(*dm, DMPLEX);
1670: DMSetDimension(*dm, dim);
1671: /* Create topology */
1672: {
1673: PetscInt cone[6], c;
1675: numCells = !rank ? n : 0;
1676: numVertices = !rank ? 2*(n+1) : 0;
1677: DMPlexSetChart(*dm, 0, numCells+numVertices);
1678: DMPlexSetHybridBounds(*dm, 0, PETSC_DETERMINE, PETSC_DETERMINE, PETSC_DETERMINE);
1679: for (c = 0; c < numCells; c++) {DMPlexSetConeSize(*dm, c, 6);}
1680: DMSetUp(*dm);
1681: for (c = 0; c < numCells; c++) {
1682: cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n;
1683: cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n;
1684: DMPlexSetCone(*dm, c, cone);
1685: }
1686: DMPlexSymmetrize(*dm);
1687: DMPlexStratify(*dm);
1688: }
1689: /* Interpolate */
1690: if (interpolate) {
1691: DM idm;
1693: DMPlexInterpolate(*dm, &idm);
1694: DMDestroy(dm);
1695: *dm = idm;
1696: }
1697: /* Create cylinder geometry */
1698: {
1699: Vec coordinates;
1700: PetscSection coordSection;
1701: PetscScalar *coords;
1702: PetscInt coordSize, v, c;
1704: /* Build coordinates */
1705: DMGetCoordinateSection(*dm, &coordSection);
1706: PetscSectionSetNumFields(coordSection, 1);
1707: PetscSectionSetFieldComponents(coordSection, 0, dim);
1708: PetscSectionSetChart(coordSection, numCells, numCells+numVertices);
1709: for (v = numCells; v < numCells+numVertices; ++v) {
1710: PetscSectionSetDof(coordSection, v, dim);
1711: PetscSectionSetFieldDof(coordSection, v, 0, dim);
1712: }
1713: PetscSectionSetUp(coordSection);
1714: PetscSectionGetStorageSize(coordSection, &coordSize);
1715: VecCreate(PETSC_COMM_SELF, &coordinates);
1716: PetscObjectSetName((PetscObject) coordinates, "coordinates");
1717: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1718: VecSetBlockSize(coordinates, dim);
1719: VecSetType(coordinates,VECSTANDARD);
1720: VecGetArray(coordinates, &coords);
1721: for (c = 0; c < numCells; c++) {
1722: 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;
1723: 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;
1724: }
1725: if (!rank) {
1726: coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0;
1727: coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0;
1728: }
1729: VecRestoreArray(coordinates, &coords);
1730: DMSetCoordinatesLocal(*dm, coordinates);
1731: VecDestroy(&coordinates);
1732: }
1733: return(0);
1734: }
1736: PETSC_STATIC_INLINE PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
1737: {
1738: PetscReal prod = 0.0;
1739: PetscInt i;
1740: for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]);
1741: return PetscSqrtReal(prod);
1742: }
1743: PETSC_STATIC_INLINE PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
1744: {
1745: PetscReal prod = 0.0;
1746: PetscInt i;
1747: for (i = 0; i < dim; ++i) prod += x[i]*y[i];
1748: return prod;
1749: }
1751: /*@
1752: DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d.
1754: Collective
1756: Input Parameters:
1757: + comm - The communicator for the DM object
1758: . dim - The dimension
1759: - simplex - Use simplices, or tensor product cells
1761: Output Parameter:
1762: . dm - The DM object
1764: Level: beginner
1766: .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1767: @*/
1768: PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *dm)
1769: {
1770: const PetscInt embedDim = dim+1;
1771: PetscSection coordSection;
1772: Vec coordinates;
1773: PetscScalar *coords;
1774: PetscReal *coordsIn;
1775: PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e;
1776: PetscMPIInt rank;
1777: PetscErrorCode ierr;
1781: DMCreate(comm, dm);
1782: DMSetType(*dm, DMPLEX);
1783: DMSetDimension(*dm, dim);
1784: DMSetCoordinateDim(*dm, dim+1);
1785: MPI_Comm_rank(PetscObjectComm((PetscObject) *dm), &rank);
1786: switch (dim) {
1787: case 2:
1788: if (simplex) {
1789: DM idm;
1790: const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI);
1791: const PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)};
1792: const PetscInt degree = 5;
1793: PetscInt s[3] = {1, 1, 1};
1794: PetscInt cone[3];
1795: PetscInt *graph, p, i, j, k;
1797: numCells = !rank ? 20 : 0;
1798: numVerts = !rank ? 12 : 0;
1799: firstVertex = numCells;
1800: /* Use icosahedron, which for a unit sphere has coordinates which are all cyclic permutations of
1802: (0, \pm 1/\phi+1, \pm \phi/\phi+1)
1804: where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
1805: length is then given by 2/\phi = 2 * 0.61803 = 1.23606.
1806: */
1807: /* Construct vertices */
1808: PetscCalloc1(numVerts * embedDim, &coordsIn);
1809: if (!rank) {
1810: for (p = 0, i = 0; p < embedDim; ++p) {
1811: for (s[1] = -1; s[1] < 2; s[1] += 2) {
1812: for (s[2] = -1; s[2] < 2; s[2] += 2) {
1813: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim];
1814: ++i;
1815: }
1816: }
1817: }
1818: }
1819: /* Construct graph */
1820: PetscCalloc1(numVerts * numVerts, &graph);
1821: for (i = 0; i < numVerts; ++i) {
1822: for (j = 0, k = 0; j < numVerts; ++j) {
1823: if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;}
1824: }
1825: if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree);
1826: }
1827: /* Build Topology */
1828: DMPlexSetChart(*dm, 0, numCells+numVerts);
1829: for (c = 0; c < numCells; c++) {
1830: DMPlexSetConeSize(*dm, c, embedDim);
1831: }
1832: DMSetUp(*dm); /* Allocate space for cones */
1833: /* Cells */
1834: for (i = 0, c = 0; i < numVerts; ++i) {
1835: for (j = 0; j < i; ++j) {
1836: for (k = 0; k < j; ++k) {
1837: if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) {
1838: cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k;
1839: /* Check orientation */
1840: {
1841: 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}}};
1842: PetscReal normal[3];
1843: PetscInt e, f;
1845: for (d = 0; d < embedDim; ++d) {
1846: normal[d] = 0.0;
1847: for (e = 0; e < embedDim; ++e) {
1848: for (f = 0; f < embedDim; ++f) {
1849: normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]);
1850: }
1851: }
1852: }
1853: if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;}
1854: }
1855: DMPlexSetCone(*dm, c++, cone);
1856: }
1857: }
1858: }
1859: }
1860: DMPlexSymmetrize(*dm);
1861: DMPlexStratify(*dm);
1862: PetscFree(graph);
1863: /* Interpolate mesh */
1864: DMPlexInterpolate(*dm, &idm);
1865: DMDestroy(dm);
1866: *dm = idm;
1867: } else {
1868: /*
1869: 12-21--13
1870: | |
1871: 25 4 24
1872: | |
1873: 12-25--9-16--8-24--13
1874: | | | |
1875: 23 5 17 0 15 3 22
1876: | | | |
1877: 10-20--6-14--7-19--11
1878: | |
1879: 20 1 19
1880: | |
1881: 10-18--11
1882: | |
1883: 23 2 22
1884: | |
1885: 12-21--13
1886: */
1887: const PetscReal dist = 1.0/PetscSqrtReal(3.0);
1888: PetscInt cone[4], ornt[4];
1890: numCells = !rank ? 6 : 0;
1891: numEdges = !rank ? 12 : 0;
1892: numVerts = !rank ? 8 : 0;
1893: firstVertex = numCells;
1894: firstEdge = numCells + numVerts;
1895: /* Build Topology */
1896: DMPlexSetChart(*dm, 0, numCells+numEdges+numVerts);
1897: for (c = 0; c < numCells; c++) {
1898: DMPlexSetConeSize(*dm, c, 4);
1899: }
1900: for (e = firstEdge; e < firstEdge+numEdges; ++e) {
1901: DMPlexSetConeSize(*dm, e, 2);
1902: }
1903: DMSetUp(*dm); /* Allocate space for cones */
1904: if (!rank) {
1905: /* Cell 0 */
1906: cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17;
1907: DMPlexSetCone(*dm, 0, cone);
1908: ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0;
1909: DMPlexSetConeOrientation(*dm, 0, ornt);
1910: /* Cell 1 */
1911: cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20;
1912: DMPlexSetCone(*dm, 1, cone);
1913: ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0;
1914: DMPlexSetConeOrientation(*dm, 1, ornt);
1915: /* Cell 2 */
1916: cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23;
1917: DMPlexSetCone(*dm, 2, cone);
1918: ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0;
1919: DMPlexSetConeOrientation(*dm, 2, ornt);
1920: /* Cell 3 */
1921: cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15;
1922: DMPlexSetCone(*dm, 3, cone);
1923: ornt[0] = -2; ornt[1] = -2; ornt[2] = 0; ornt[3] = -2;
1924: DMPlexSetConeOrientation(*dm, 3, ornt);
1925: /* Cell 4 */
1926: cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25;
1927: DMPlexSetCone(*dm, 4, cone);
1928: ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = 0;
1929: DMPlexSetConeOrientation(*dm, 4, ornt);
1930: /* Cell 5 */
1931: cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23;
1932: DMPlexSetCone(*dm, 5, cone);
1933: ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = -2;
1934: DMPlexSetConeOrientation(*dm, 5, ornt);
1935: /* Edges */
1936: cone[0] = 6; cone[1] = 7;
1937: DMPlexSetCone(*dm, 14, cone);
1938: cone[0] = 7; cone[1] = 8;
1939: DMPlexSetCone(*dm, 15, cone);
1940: cone[0] = 8; cone[1] = 9;
1941: DMPlexSetCone(*dm, 16, cone);
1942: cone[0] = 9; cone[1] = 6;
1943: DMPlexSetCone(*dm, 17, cone);
1944: cone[0] = 10; cone[1] = 11;
1945: DMPlexSetCone(*dm, 18, cone);
1946: cone[0] = 11; cone[1] = 7;
1947: DMPlexSetCone(*dm, 19, cone);
1948: cone[0] = 6; cone[1] = 10;
1949: DMPlexSetCone(*dm, 20, cone);
1950: cone[0] = 12; cone[1] = 13;
1951: DMPlexSetCone(*dm, 21, cone);
1952: cone[0] = 13; cone[1] = 11;
1953: DMPlexSetCone(*dm, 22, cone);
1954: cone[0] = 10; cone[1] = 12;
1955: DMPlexSetCone(*dm, 23, cone);
1956: cone[0] = 13; cone[1] = 8;
1957: DMPlexSetCone(*dm, 24, cone);
1958: cone[0] = 12; cone[1] = 9;
1959: DMPlexSetCone(*dm, 25, cone);
1960: }
1961: DMPlexSymmetrize(*dm);
1962: DMPlexStratify(*dm);
1963: /* Build coordinates */
1964: PetscCalloc1(numVerts * embedDim, &coordsIn);
1965: if (!rank) {
1966: coordsIn[0*embedDim+0] = -dist; coordsIn[0*embedDim+1] = dist; coordsIn[0*embedDim+2] = -dist;
1967: coordsIn[1*embedDim+0] = dist; coordsIn[1*embedDim+1] = dist; coordsIn[1*embedDim+2] = -dist;
1968: coordsIn[2*embedDim+0] = dist; coordsIn[2*embedDim+1] = -dist; coordsIn[2*embedDim+2] = -dist;
1969: coordsIn[3*embedDim+0] = -dist; coordsIn[3*embedDim+1] = -dist; coordsIn[3*embedDim+2] = -dist;
1970: coordsIn[4*embedDim+0] = -dist; coordsIn[4*embedDim+1] = dist; coordsIn[4*embedDim+2] = dist;
1971: coordsIn[5*embedDim+0] = dist; coordsIn[5*embedDim+1] = dist; coordsIn[5*embedDim+2] = dist;
1972: coordsIn[6*embedDim+0] = -dist; coordsIn[6*embedDim+1] = -dist; coordsIn[6*embedDim+2] = dist;
1973: coordsIn[7*embedDim+0] = dist; coordsIn[7*embedDim+1] = -dist; coordsIn[7*embedDim+2] = dist;
1974: }
1975: }
1976: break;
1977: case 3:
1978: if (simplex) {
1979: DM idm;
1980: const PetscReal edgeLen = 1.0/PETSC_PHI;
1981: const PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5};
1982: const PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0};
1983: const PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0};
1984: const PetscInt degree = 12;
1985: PetscInt s[4] = {1, 1, 1};
1986: 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},
1987: {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}};
1988: PetscInt cone[4];
1989: PetscInt *graph, p, i, j, k, l;
1991: numCells = !rank ? 600 : 0;
1992: numVerts = !rank ? 120 : 0;
1993: firstVertex = numCells;
1994: /* Use the 600-cell, which for a unit sphere has coordinates which are
1996: 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16
1997: (\pm 1, 0, 0, 0) all cyclic permutations 8
1998: 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96
2000: where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
2001: length is then given by 1/\phi = 0.61803.
2003: http://buzzard.pugetsound.edu/sage-practice/ch03s03.html
2004: http://mathworld.wolfram.com/600-Cell.html
2005: */
2006: /* Construct vertices */
2007: PetscCalloc1(numVerts * embedDim, &coordsIn);
2008: i = 0;
2009: if (!rank) {
2010: for (s[0] = -1; s[0] < 2; s[0] += 2) {
2011: for (s[1] = -1; s[1] < 2; s[1] += 2) {
2012: for (s[2] = -1; s[2] < 2; s[2] += 2) {
2013: for (s[3] = -1; s[3] < 2; s[3] += 2) {
2014: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d];
2015: ++i;
2016: }
2017: }
2018: }
2019: }
2020: for (p = 0; p < embedDim; ++p) {
2021: s[1] = s[2] = s[3] = 1;
2022: for (s[0] = -1; s[0] < 2; s[0] += 2) {
2023: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim];
2024: ++i;
2025: }
2026: }
2027: for (p = 0; p < 12; ++p) {
2028: s[3] = 1;
2029: for (s[0] = -1; s[0] < 2; s[0] += 2) {
2030: for (s[1] = -1; s[1] < 2; s[1] += 2) {
2031: for (s[2] = -1; s[2] < 2; s[2] += 2) {
2032: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]];
2033: ++i;
2034: }
2035: }
2036: }
2037: }
2038: }
2039: if (i != numVerts) SETERRQ2(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts);
2040: /* Construct graph */
2041: PetscCalloc1(numVerts * numVerts, &graph);
2042: for (i = 0; i < numVerts; ++i) {
2043: for (j = 0, k = 0; j < numVerts; ++j) {
2044: if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;}
2045: }
2046: if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree);
2047: }
2048: /* Build Topology */
2049: DMPlexSetChart(*dm, 0, numCells+numVerts);
2050: for (c = 0; c < numCells; c++) {
2051: DMPlexSetConeSize(*dm, c, embedDim);
2052: }
2053: DMSetUp(*dm); /* Allocate space for cones */
2054: /* Cells */
2055: if (!rank) {
2056: for (i = 0, c = 0; i < numVerts; ++i) {
2057: for (j = 0; j < i; ++j) {
2058: for (k = 0; k < j; ++k) {
2059: for (l = 0; l < k; ++l) {
2060: if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] &&
2061: graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) {
2062: cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l;
2063: /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */
2064: {
2065: const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
2066: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}},
2067: {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}},
2068: {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}},
2070: {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}},
2071: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
2072: {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}},
2073: {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}},
2075: {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}},
2076: {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}},
2077: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
2078: {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}},
2080: {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}},
2081: {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}},
2082: {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
2083: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}};
2084: PetscReal normal[4];
2085: PetscInt e, f, g;
2087: for (d = 0; d < embedDim; ++d) {
2088: normal[d] = 0.0;
2089: for (e = 0; e < embedDim; ++e) {
2090: for (f = 0; f < embedDim; ++f) {
2091: for (g = 0; g < embedDim; ++g) {
2092: 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]);
2093: }
2094: }
2095: }
2096: }
2097: if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;}
2098: }
2099: DMPlexSetCone(*dm, c++, cone);
2100: }
2101: }
2102: }
2103: }
2104: }
2105: }
2106: DMPlexSymmetrize(*dm);
2107: DMPlexStratify(*dm);
2108: PetscFree(graph);
2109: /* Interpolate mesh */
2110: DMPlexInterpolate(*dm, &idm);
2111: DMDestroy(dm);
2112: *dm = idm;
2113: break;
2114: }
2115: default: SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim);
2116: }
2117: /* Create coordinates */
2118: DMGetCoordinateSection(*dm, &coordSection);
2119: PetscSectionSetNumFields(coordSection, 1);
2120: PetscSectionSetFieldComponents(coordSection, 0, embedDim);
2121: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);
2122: for (v = firstVertex; v < firstVertex+numVerts; ++v) {
2123: PetscSectionSetDof(coordSection, v, embedDim);
2124: PetscSectionSetFieldDof(coordSection, v, 0, embedDim);
2125: }
2126: PetscSectionSetUp(coordSection);
2127: PetscSectionGetStorageSize(coordSection, &coordSize);
2128: VecCreate(PETSC_COMM_SELF, &coordinates);
2129: VecSetBlockSize(coordinates, embedDim);
2130: PetscObjectSetName((PetscObject) coordinates, "coordinates");
2131: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
2132: VecSetType(coordinates,VECSTANDARD);
2133: VecGetArray(coordinates, &coords);
2134: for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];}
2135: VecRestoreArray(coordinates, &coords);
2136: DMSetCoordinatesLocal(*dm, coordinates);
2137: VecDestroy(&coordinates);
2138: PetscFree(coordsIn);
2139: return(0);
2140: }
2142: /* External function declarations here */
2143: extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling);
2144: extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat);
2145: extern PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mat);
2146: extern PetscErrorCode DMCreateLocalSection_Plex(DM dm);
2147: extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm);
2148: extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J);
2149: extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm);
2150: extern PetscErrorCode DMCreateCoordinateField_Plex(DM dm, DMField *field);
2151: PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm);
2152: extern PetscErrorCode DMSetUp_Plex(DM dm);
2153: extern PetscErrorCode DMDestroy_Plex(DM dm);
2154: extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer);
2155: extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer);
2156: extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm);
2157: extern PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm);
2158: static PetscErrorCode DMInitialize_Plex(DM dm);
2160: /* Replace dm with the contents of dmNew
2161: - Share the DM_Plex structure
2162: - Share the coordinates
2163: - Share the SF
2164: */
2165: static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew)
2166: {
2167: PetscSF sf;
2168: DM coordDM, coarseDM;
2169: Vec coords;
2170: PetscBool isper;
2171: const PetscReal *maxCell, *L;
2172: const DMBoundaryType *bd;
2173: PetscErrorCode ierr;
2176: DMGetPointSF(dmNew, &sf);
2177: DMSetPointSF(dm, sf);
2178: DMGetCoordinateDM(dmNew, &coordDM);
2179: DMGetCoordinatesLocal(dmNew, &coords);
2180: DMSetCoordinateDM(dm, coordDM);
2181: DMSetCoordinatesLocal(dm, coords);
2182: DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);
2183: DMSetPeriodicity(dmNew, isper, maxCell, L, bd);
2184: DMDestroy_Plex(dm);
2185: DMInitialize_Plex(dm);
2186: dm->data = dmNew->data;
2187: ((DM_Plex *) dmNew->data)->refct++;
2188: dmNew->labels->refct++;
2189: if (!--(dm->labels->refct)) {
2190: DMLabelLink next = dm->labels->next;
2192: /* destroy the labels */
2193: while (next) {
2194: DMLabelLink tmp = next->next;
2196: DMLabelDestroy(&next->label);
2197: PetscFree(next);
2198: next = tmp;
2199: }
2200: PetscFree(dm->labels);
2201: }
2202: dm->labels = dmNew->labels;
2203: dm->depthLabel = dmNew->depthLabel;
2204: DMGetCoarseDM(dmNew,&coarseDM);
2205: DMSetCoarseDM(dm,coarseDM);
2206: return(0);
2207: }
2209: /* Swap dm with the contents of dmNew
2210: - Swap the DM_Plex structure
2211: - Swap the coordinates
2212: - Swap the point PetscSF
2213: */
2214: static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB)
2215: {
2216: DM coordDMA, coordDMB;
2217: Vec coordsA, coordsB;
2218: PetscSF sfA, sfB;
2219: void *tmp;
2220: DMLabelLinkList listTmp;
2221: DMLabel depthTmp;
2222: PetscInt tmpI;
2223: PetscErrorCode ierr;
2226: DMGetPointSF(dmA, &sfA);
2227: DMGetPointSF(dmB, &sfB);
2228: PetscObjectReference((PetscObject) sfA);
2229: DMSetPointSF(dmA, sfB);
2230: DMSetPointSF(dmB, sfA);
2231: PetscObjectDereference((PetscObject) sfA);
2233: DMGetCoordinateDM(dmA, &coordDMA);
2234: DMGetCoordinateDM(dmB, &coordDMB);
2235: PetscObjectReference((PetscObject) coordDMA);
2236: DMSetCoordinateDM(dmA, coordDMB);
2237: DMSetCoordinateDM(dmB, coordDMA);
2238: PetscObjectDereference((PetscObject) coordDMA);
2240: DMGetCoordinatesLocal(dmA, &coordsA);
2241: DMGetCoordinatesLocal(dmB, &coordsB);
2242: PetscObjectReference((PetscObject) coordsA);
2243: DMSetCoordinatesLocal(dmA, coordsB);
2244: DMSetCoordinatesLocal(dmB, coordsA);
2245: PetscObjectDereference((PetscObject) coordsA);
2247: tmp = dmA->data;
2248: dmA->data = dmB->data;
2249: dmB->data = tmp;
2250: listTmp = dmA->labels;
2251: dmA->labels = dmB->labels;
2252: dmB->labels = listTmp;
2253: depthTmp = dmA->depthLabel;
2254: dmA->depthLabel = dmB->depthLabel;
2255: dmB->depthLabel = depthTmp;
2256: tmpI = dmA->levelup;
2257: dmA->levelup = dmB->levelup;
2258: dmB->levelup = tmpI;
2259: return(0);
2260: }
2262: PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm)
2263: {
2264: DM_Plex *mesh = (DM_Plex*) dm->data;
2268: /* Handle viewing */
2269: PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL);
2270: PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL,0);
2271: PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL);
2272: PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL,0);
2273: /* Point Location */
2274: PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL);
2275: /* Partitioning and distribution */
2276: PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL);
2277: /* Generation and remeshing */
2278: PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL);
2279: /* Projection behavior */
2280: PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL,0);
2281: PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);
2282: /* Checking structure */
2283: {
2284: PetscBool flg = PETSC_FALSE, flg2 = PETSC_FALSE;
2286: PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2);
2287: if (flg && flg2) {DMPlexCheckSymmetry(dm);}
2288: 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);
2289: if (flg && flg2) {DMPlexCheckSkeleton(dm, 0);}
2290: 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);
2291: if (flg && flg2) {DMPlexCheckFaces(dm, 0);}
2292: PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2);
2293: if (flg && flg2) {DMPlexCheckGeometry(dm);}
2294: }
2296: PetscPartitionerSetFromOptions(mesh->partitioner);
2297: return(0);
2298: }
2300: static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm)
2301: {
2302: PetscInt refine = 0, coarsen = 0, r;
2303: PetscBool isHierarchy;
2308: PetscOptionsHead(PetscOptionsObject,"DMPlex Options");
2309: /* Handle DMPlex refinement */
2310: PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL,0);
2311: PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy,0);
2312: if (refine) {DMPlexSetRefinementUniform(dm, PETSC_TRUE);}
2313: if (refine && isHierarchy) {
2314: DM *dms, coarseDM;
2316: DMGetCoarseDM(dm, &coarseDM);
2317: PetscObjectReference((PetscObject)coarseDM);
2318: PetscMalloc1(refine,&dms);
2319: DMRefineHierarchy(dm, refine, dms);
2320: /* Total hack since we do not pass in a pointer */
2321: DMPlexSwap_Static(dm, dms[refine-1]);
2322: if (refine == 1) {
2323: DMSetCoarseDM(dm, dms[0]);
2324: DMPlexSetRegularRefinement(dm, PETSC_TRUE);
2325: } else {
2326: DMSetCoarseDM(dm, dms[refine-2]);
2327: DMPlexSetRegularRefinement(dm, PETSC_TRUE);
2328: DMSetCoarseDM(dms[0], dms[refine-1]);
2329: DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);
2330: }
2331: DMSetCoarseDM(dms[refine-1], coarseDM);
2332: PetscObjectDereference((PetscObject)coarseDM);
2333: /* Free DMs */
2334: for (r = 0; r < refine; ++r) {
2335: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);
2336: DMDestroy(&dms[r]);
2337: }
2338: PetscFree(dms);
2339: } else {
2340: for (r = 0; r < refine; ++r) {
2341: DM refinedMesh;
2343: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2344: DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);
2345: /* Total hack since we do not pass in a pointer */
2346: DMPlexReplace_Static(dm, refinedMesh);
2347: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2348: DMDestroy(&refinedMesh);
2349: }
2350: }
2351: /* Handle DMPlex coarsening */
2352: PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL,0);
2353: PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy,0);
2354: if (coarsen && isHierarchy) {
2355: DM *dms;
2357: PetscMalloc1(coarsen, &dms);
2358: DMCoarsenHierarchy(dm, coarsen, dms);
2359: /* Free DMs */
2360: for (r = 0; r < coarsen; ++r) {
2361: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);
2362: DMDestroy(&dms[r]);
2363: }
2364: PetscFree(dms);
2365: } else {
2366: for (r = 0; r < coarsen; ++r) {
2367: DM coarseMesh;
2369: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2370: DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);
2371: /* Total hack since we do not pass in a pointer */
2372: DMPlexReplace_Static(dm, coarseMesh);
2373: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2374: DMDestroy(&coarseMesh);
2375: }
2376: }
2377: /* Handle */
2378: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2379: PetscOptionsTail();
2380: return(0);
2381: }
2383: static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec)
2384: {
2388: DMCreateGlobalVector_Section_Private(dm,vec);
2389: /* VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM); */
2390: VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);
2391: VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);
2392: VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);
2393: VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);
2394: return(0);
2395: }
2397: static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec)
2398: {
2402: DMCreateLocalVector_Section_Private(dm,vec);
2403: VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);
2404: VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);
2405: return(0);
2406: }
2408: static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd)
2409: {
2410: PetscInt depth, d;
2414: DMPlexGetDepth(dm, &depth);
2415: if (depth == 1) {
2416: DMGetDimension(dm, &d);
2417: if (dim == 0) {DMPlexGetDepthStratum(dm, dim, pStart, pEnd);}
2418: else if (dim == d) {DMPlexGetDepthStratum(dm, 1, pStart, pEnd);}
2419: else {*pStart = 0; *pEnd = 0;}
2420: } else {
2421: DMPlexGetDepthStratum(dm, dim, pStart, pEnd);
2422: }
2423: return(0);
2424: }
2426: static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[])
2427: {
2428: PetscSF sf;
2432: DMGetPointSF(dm, &sf);
2433: PetscSFGetRootRanks(sf, nranks, ranks, NULL, NULL, NULL);
2434: return(0);
2435: }
2437: static PetscErrorCode DMInitialize_Plex(DM dm)
2438: {
2442: dm->ops->view = DMView_Plex;
2443: dm->ops->load = DMLoad_Plex;
2444: dm->ops->setfromoptions = DMSetFromOptions_Plex;
2445: dm->ops->clone = DMClone_Plex;
2446: dm->ops->setup = DMSetUp_Plex;
2447: dm->ops->createlocalsection = DMCreateLocalSection_Plex;
2448: dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex;
2449: dm->ops->createglobalvector = DMCreateGlobalVector_Plex;
2450: dm->ops->createlocalvector = DMCreateLocalVector_Plex;
2451: dm->ops->getlocaltoglobalmapping = NULL;
2452: dm->ops->createfieldis = NULL;
2453: dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex;
2454: dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex;
2455: dm->ops->getcoloring = NULL;
2456: dm->ops->creatematrix = DMCreateMatrix_Plex;
2457: dm->ops->createinterpolation = DMCreateInterpolation_Plex;
2458: dm->ops->createmassmatrix = DMCreateMassMatrix_Plex;
2459: dm->ops->createinjection = DMCreateInjection_Plex;
2460: dm->ops->refine = DMRefine_Plex;
2461: dm->ops->coarsen = DMCoarsen_Plex;
2462: dm->ops->refinehierarchy = DMRefineHierarchy_Plex;
2463: dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex;
2464: dm->ops->adaptlabel = DMAdaptLabel_Plex;
2465: dm->ops->adaptmetric = DMAdaptMetric_Plex;
2466: dm->ops->globaltolocalbegin = NULL;
2467: dm->ops->globaltolocalend = NULL;
2468: dm->ops->localtoglobalbegin = NULL;
2469: dm->ops->localtoglobalend = NULL;
2470: dm->ops->destroy = DMDestroy_Plex;
2471: dm->ops->createsubdm = DMCreateSubDM_Plex;
2472: dm->ops->createsuperdm = DMCreateSuperDM_Plex;
2473: dm->ops->getdimpoints = DMGetDimPoints_Plex;
2474: dm->ops->locatepoints = DMLocatePoints_Plex;
2475: dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex;
2476: dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex;
2477: dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex;
2478: dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex;
2479: dm->ops->computel2diff = DMComputeL2Diff_Plex;
2480: dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex;
2481: dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex;
2482: dm->ops->getneighbors = DMGetNeighbors_Plex;
2483: PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);
2484: PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);
2485: PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C",DMCreateNeumannOverlap_Plex);
2486: PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex);
2487: return(0);
2488: }
2490: PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm)
2491: {
2492: DM_Plex *mesh = (DM_Plex *) dm->data;
2496: mesh->refct++;
2497: (*newdm)->data = mesh;
2498: PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);
2499: DMInitialize_Plex(*newdm);
2500: return(0);
2501: }
2503: /*MC
2504: DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram.
2505: In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is
2506: specified by a PetscSection object. Ownership in the global representation is determined by
2507: ownership of the underlying DMPlex points. This is specified by another PetscSection object.
2509: Options Database Keys:
2510: + -dm_plex_hash_location - Use grid hashing for point location
2511: . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes
2512: . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing
2513: . -dm_plex_max_projection_height - Maxmimum mesh point height used to project locally
2514: . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement
2515: . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric
2516: . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices
2517: . -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
2518: . -dm_plex_check_geometry - Check that cells have positive volume
2519: . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ
2520: . -dm_plex_view_scale <num> - Scale the TikZ
2521: - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices
2524: Level: intermediate
2526: .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType()
2527: M*/
2529: PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm)
2530: {
2531: DM_Plex *mesh;
2532: PetscInt unit, d;
2537: PetscNewLog(dm,&mesh);
2538: dm->dim = 0;
2539: dm->data = mesh;
2541: mesh->refct = 1;
2542: PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);
2543: mesh->maxConeSize = 0;
2544: mesh->cones = NULL;
2545: mesh->coneOrientations = NULL;
2546: PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);
2547: mesh->maxSupportSize = 0;
2548: mesh->supports = NULL;
2549: mesh->refinementUniform = PETSC_TRUE;
2550: mesh->refinementLimit = -1.0;
2552: mesh->facesTmp = NULL;
2554: mesh->tetgenOpts = NULL;
2555: mesh->triangleOpts = NULL;
2556: PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);
2557: mesh->remeshBd = PETSC_FALSE;
2559: mesh->subpointMap = NULL;
2561: for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0;
2563: mesh->regularRefinement = PETSC_FALSE;
2564: mesh->depthState = -1;
2565: mesh->globalVertexNumbers = NULL;
2566: mesh->globalCellNumbers = NULL;
2567: mesh->anchorSection = NULL;
2568: mesh->anchorIS = NULL;
2569: mesh->createanchors = NULL;
2570: mesh->computeanchormatrix = NULL;
2571: mesh->parentSection = NULL;
2572: mesh->parents = NULL;
2573: mesh->childIDs = NULL;
2574: mesh->childSection = NULL;
2575: mesh->children = NULL;
2576: mesh->referenceTree = NULL;
2577: mesh->getchildsymmetry = NULL;
2578: for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE;
2579: mesh->vtkCellHeight = 0;
2580: mesh->useAnchors = PETSC_FALSE;
2582: mesh->maxProjectionHeight = 0;
2584: mesh->printSetValues = PETSC_FALSE;
2585: mesh->printFEM = 0;
2586: mesh->printTol = 1.0e-10;
2588: DMInitialize_Plex(dm);
2589: return(0);
2590: }
2592: /*@
2593: DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram.
2595: Collective
2597: Input Parameter:
2598: . comm - The communicator for the DMPlex object
2600: Output Parameter:
2601: . mesh - The DMPlex object
2603: Level: beginner
2605: @*/
2606: PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh)
2607: {
2612: DMCreate(comm, mesh);
2613: DMSetType(*mesh, DMPLEX);
2614: return(0);
2615: }
2617: /*
2618: 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
2619: */
2620: /* TODO: invertCells and spaceDim arguments could be added also to to DMPlexCreateFromCellListParallel(), DMPlexBuildFromCellList_Internal() and DMPlexCreateFromCellList() */
2621: PetscErrorCode DMPlexBuildFromCellList_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscBool invertCells, PetscSF *sfVert)
2622: {
2623: PetscSF sfPoint;
2624: PetscLayout vLayout;
2625: PetscHSetI vhash;
2626: PetscSFNode *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex;
2627: const PetscInt *vrange;
2628: PetscInt numVerticesAdj, off = 0, *verticesAdj, numVerticesGhost = 0, *localVertex, *cone, c, p, v, g;
2629: PetscMPIInt rank, size;
2630: PetscErrorCode ierr;
2633: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
2634: MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);
2635: /* Partition vertices */
2636: PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);
2637: PetscLayoutSetLocalSize(vLayout, numVertices);
2638: PetscLayoutSetBlockSize(vLayout, 1);
2639: PetscLayoutSetUp(vLayout);
2640: PetscLayoutGetRanges(vLayout, &vrange);
2641: /* Count vertices and map them to procs */
2642: PetscHSetICreate(&vhash);
2643: for (c = 0; c < numCells; ++c) {
2644: for (p = 0; p < numCorners; ++p) {
2645: PetscHSetIAdd(vhash, cells[c*numCorners+p]);
2646: }
2647: }
2648: PetscHSetIGetSize(vhash, &numVerticesAdj);
2649: PetscMalloc1(numVerticesAdj, &verticesAdj);
2650: PetscHSetIGetElems(vhash, &off, verticesAdj);
2651: PetscHSetIDestroy(&vhash);
2652: if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj);
2653: PetscSortInt(numVerticesAdj, verticesAdj);
2654: PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);
2655: for (v = 0; v < numVerticesAdj; ++v) {
2656: const PetscInt gv = verticesAdj[v];
2657: PetscInt vrank;
2659: PetscFindInt(gv, size+1, vrange, &vrank);
2660: vrank = vrank < 0 ? -(vrank+2) : vrank;
2661: remoteVerticesAdj[v].index = gv - vrange[vrank];
2662: remoteVerticesAdj[v].rank = vrank;
2663: }
2664: /* Create cones */
2665: DMPlexSetChart(dm, 0, numCells+numVerticesAdj);
2666: for (c = 0; c < numCells; ++c) {DMPlexSetConeSize(dm, c, numCorners);}
2667: DMSetUp(dm);
2668: DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);
2669: for (c = 0; c < numCells; ++c) {
2670: for (p = 0; p < numCorners; ++p) {
2671: const PetscInt gv = cells[c*numCorners+p];
2672: PetscInt lv;
2674: PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);
2675: if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv);
2676: cone[p] = lv+numCells;
2677: }
2678: if (invertCells) { DMPlexInvertCell_Internal(spaceDim, numCorners, cone); }
2679: DMPlexSetCone(dm, c, cone);
2680: }
2681: DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);
2682: /* Create SF for vertices */
2683: PetscSFCreate(PetscObjectComm((PetscObject)dm), sfVert);
2684: PetscObjectSetName((PetscObject) *sfVert, "Vertex Ownership SF");
2685: PetscSFSetFromOptions(*sfVert);
2686: PetscSFSetGraph(*sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);
2687: PetscFree(verticesAdj);
2688: /* Build pointSF */
2689: PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);
2690: for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;}
2691: for (v = 0; v < numVertices; ++v) {vertexOwner[v].index = -1; vertexOwner[v].rank = -1;}
2692: PetscSFReduceBegin(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);
2693: PetscSFReduceEnd(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);
2694: 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);
2695: PetscSFBcastBegin(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);
2696: PetscSFBcastEnd(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);
2697: for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost;
2698: PetscMalloc1(numVerticesGhost, &localVertex);
2699: PetscMalloc1(numVerticesGhost, &remoteVertex);
2700: for (v = 0, g = 0; v < numVerticesAdj; ++v) {
2701: if (vertexLocal[v].rank != rank) {
2702: localVertex[g] = v+numCells;
2703: remoteVertex[g].index = vertexLocal[v].index;
2704: remoteVertex[g].rank = vertexLocal[v].rank;
2705: ++g;
2706: }
2707: }
2708: PetscFree2(vertexLocal, vertexOwner);
2709: if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost);
2710: DMGetPointSF(dm, &sfPoint);
2711: PetscObjectSetName((PetscObject) sfPoint, "point SF");
2712: PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);
2713: PetscLayoutDestroy(&vLayout);
2714: /* Fill in the rest of the topology structure */
2715: DMPlexSymmetrize(dm);
2716: DMPlexStratify(dm);
2717: return(0);
2718: }
2720: /*
2721: This takes as input the coordinates for each owned vertex
2722: */
2723: PetscErrorCode DMPlexBuildCoordinates_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numV, PetscSF sfVert, const PetscReal vertexCoords[])
2724: {
2725: PetscSection coordSection;
2726: Vec coordinates;
2727: PetscScalar *coords;
2728: PetscInt numVertices, numVerticesAdj, coordSize, v;
2732: DMSetCoordinateDim(dm, spaceDim);
2733: PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);
2734: DMGetCoordinateSection(dm, &coordSection);
2735: PetscSectionSetNumFields(coordSection, 1);
2736: PetscSectionSetFieldComponents(coordSection, 0, spaceDim);
2737: PetscSectionSetChart(coordSection, numCells, numCells + numVerticesAdj);
2738: for (v = numCells; v < numCells+numVerticesAdj; ++v) {
2739: PetscSectionSetDof(coordSection, v, spaceDim);
2740: PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);
2741: }
2742: PetscSectionSetUp(coordSection);
2743: PetscSectionGetStorageSize(coordSection, &coordSize);
2744: VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);
2745: VecSetBlockSize(coordinates, spaceDim);
2746: PetscObjectSetName((PetscObject) coordinates, "coordinates");
2747: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
2748: VecSetType(coordinates,VECSTANDARD);
2749: VecGetArray(coordinates, &coords);
2750: {
2751: MPI_Datatype coordtype;
2753: /* Need a temp buffer for coords if we have complex/single */
2754: MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);
2755: MPI_Type_commit(&coordtype);
2756: #if defined(PETSC_USE_COMPLEX)
2757: {
2758: PetscScalar *svertexCoords;
2759: PetscInt i;
2760: PetscMalloc1(numV*spaceDim,&svertexCoords);
2761: for (i=0; i<numV*spaceDim; i++) svertexCoords[i] = vertexCoords[i];
2762: PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords);
2763: PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords);
2764: PetscFree(svertexCoords);
2765: }
2766: #else
2767: PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords);
2768: PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords);
2769: #endif
2770: MPI_Type_free(&coordtype);
2771: }
2772: VecRestoreArray(coordinates, &coords);
2773: DMSetCoordinatesLocal(dm, coordinates);
2774: VecDestroy(&coordinates);
2775: return(0);
2776: }
2778: /*@
2779: DMPlexCreateFromCellListParallel - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM
2781: Input Parameters:
2782: + comm - The communicator
2783: . dim - The topological dimension of the mesh
2784: . numCells - The number of cells owned by this process
2785: . numVertices - The number of vertices owned by this process
2786: . numCorners - The number of vertices for each cell
2787: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
2788: . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell
2789: . spaceDim - The spatial dimension used for coordinates
2790: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
2792: Output Parameter:
2793: + dm - The DM
2794: - vertexSF - Optional, SF describing complete vertex ownership
2796: Note: Two triangles sharing a face
2797: $
2798: $ 2
2799: $ / | \
2800: $ / | \
2801: $ / | \
2802: $ 0 0 | 1 3
2803: $ \ | /
2804: $ \ | /
2805: $ \ | /
2806: $ 1
2807: would have input
2808: $ numCells = 2, numVertices = 4
2809: $ cells = [0 1 2 1 3 2]
2810: $
2811: which would result in the DMPlex
2812: $
2813: $ 4
2814: $ / | \
2815: $ / | \
2816: $ / | \
2817: $ 2 0 | 1 5
2818: $ \ | /
2819: $ \ | /
2820: $ \ | /
2821: $ 3
2823: Level: beginner
2825: .seealso: DMPlexCreateFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate()
2826: @*/
2827: 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)
2828: {
2829: PetscSF sfVert;
2833: DMCreate(comm, dm);
2834: DMSetType(*dm, DMPLEX);
2837: DMSetDimension(*dm, dim);
2838: DMPlexBuildFromCellList_Parallel_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE, &sfVert);
2839: if (interpolate) {
2840: DM idm;
2842: DMPlexInterpolate(*dm, &idm);
2843: DMDestroy(dm);
2844: *dm = idm;
2845: }
2846: DMPlexBuildCoordinates_Parallel_Internal(*dm, spaceDim, numCells, numVertices, sfVert, vertexCoords);
2847: if (vertexSF) *vertexSF = sfVert;
2848: else {PetscSFDestroy(&sfVert);}
2849: return(0);
2850: }
2852: /*
2853: This takes as input the common mesh generator output, a list of the vertices for each cell
2854: */
2855: PetscErrorCode DMPlexBuildFromCellList_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscBool invertCells)
2856: {
2857: PetscInt *cone, c, p;
2861: DMPlexSetChart(dm, 0, numCells+numVertices);
2862: for (c = 0; c < numCells; ++c) {
2863: DMPlexSetConeSize(dm, c, numCorners);
2864: }
2865: DMSetUp(dm);
2866: DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);
2867: for (c = 0; c < numCells; ++c) {
2868: for (p = 0; p < numCorners; ++p) {
2869: cone[p] = cells[c*numCorners+p]+numCells;
2870: }
2871: if (invertCells) { DMPlexInvertCell_Internal(spaceDim, numCorners, cone); }
2872: DMPlexSetCone(dm, c, cone);
2873: }
2874: DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);
2875: DMPlexSymmetrize(dm);
2876: DMPlexStratify(dm);
2877: return(0);
2878: }
2880: /*
2881: This takes as input the coordinates for each vertex
2882: */
2883: PetscErrorCode DMPlexBuildCoordinates_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[])
2884: {
2885: PetscSection coordSection;
2886: Vec coordinates;
2887: DM cdm;
2888: PetscScalar *coords;
2889: PetscInt v, d;
2893: DMSetCoordinateDim(dm, spaceDim);
2894: DMGetCoordinateSection(dm, &coordSection);
2895: PetscSectionSetNumFields(coordSection, 1);
2896: PetscSectionSetFieldComponents(coordSection, 0, spaceDim);
2897: PetscSectionSetChart(coordSection, numCells, numCells + numVertices);
2898: for (v = numCells; v < numCells+numVertices; ++v) {
2899: PetscSectionSetDof(coordSection, v, spaceDim);
2900: PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);
2901: }
2902: PetscSectionSetUp(coordSection);
2904: DMGetCoordinateDM(dm, &cdm);
2905: DMCreateLocalVector(cdm, &coordinates);
2906: VecSetBlockSize(coordinates, spaceDim);
2907: PetscObjectSetName((PetscObject) coordinates, "coordinates");
2908: VecGetArray(coordinates, &coords);
2909: for (v = 0; v < numVertices; ++v) {
2910: for (d = 0; d < spaceDim; ++d) {
2911: coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d];
2912: }
2913: }
2914: VecRestoreArray(coordinates, &coords);
2915: DMSetCoordinatesLocal(dm, coordinates);
2916: VecDestroy(&coordinates);
2917: return(0);
2918: }
2920: /*@
2921: DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM
2923: Input Parameters:
2924: + comm - The communicator
2925: . dim - The topological dimension of the mesh
2926: . numCells - The number of cells
2927: . numVertices - The number of vertices
2928: . numCorners - The number of vertices for each cell
2929: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
2930: . cells - An array of numCells*numCorners numbers, the vertices for each cell
2931: . spaceDim - The spatial dimension used for coordinates
2932: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
2934: Output Parameter:
2935: . dm - The DM
2937: Note: Two triangles sharing a face
2938: $
2939: $ 2
2940: $ / | \
2941: $ / | \
2942: $ / | \
2943: $ 0 0 | 1 3
2944: $ \ | /
2945: $ \ | /
2946: $ \ | /
2947: $ 1
2948: would have input
2949: $ numCells = 2, numVertices = 4
2950: $ cells = [0 1 2 1 3 2]
2951: $
2952: which would result in the DMPlex
2953: $
2954: $ 4
2955: $ / | \
2956: $ / | \
2957: $ / | \
2958: $ 2 0 | 1 5
2959: $ \ | /
2960: $ \ | /
2961: $ \ | /
2962: $ 3
2964: Level: beginner
2966: .seealso: DMPlexCreateFromDAG(), DMPlexCreate()
2967: @*/
2968: 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)
2969: {
2973: DMCreate(comm, dm);
2974: DMSetType(*dm, DMPLEX);
2975: DMSetDimension(*dm, dim);
2976: DMPlexBuildFromCellList_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE);
2977: if (interpolate) {
2978: DM idm;
2980: DMPlexInterpolate(*dm, &idm);
2981: DMDestroy(dm);
2982: *dm = idm;
2983: }
2984: DMPlexBuildCoordinates_Internal(*dm, spaceDim, numCells, numVertices, vertexCoords);
2985: return(0);
2986: }
2988: /*@
2989: DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM
2991: Input Parameters:
2992: + dm - The empty DM object, usually from DMCreate() and DMSetDimension()
2993: . depth - The depth of the DAG
2994: . numPoints - Array of size depth + 1 containing the number of points at each depth
2995: . coneSize - The cone size of each point
2996: . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point
2997: . coneOrientations - The orientation of each cone point
2998: - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim()
3000: Output Parameter:
3001: . dm - The DM
3003: Note: Two triangles sharing a face would have input
3004: $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0]
3005: $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0]
3006: $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0]
3007: $
3008: which would result in the DMPlex
3009: $
3010: $ 4
3011: $ / | \
3012: $ / | \
3013: $ / | \
3014: $ 2 0 | 1 5
3015: $ \ | /
3016: $ \ | /
3017: $ \ | /
3018: $ 3
3019: $
3020: $ Notice that all points are numbered consecutively, unlikely DMPlexCreateFromCellList()
3022: Level: advanced
3024: .seealso: DMPlexCreateFromCellList(), DMPlexCreate()
3025: @*/
3026: PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[])
3027: {
3028: Vec coordinates;
3029: PetscSection coordSection;
3030: PetscScalar *coords;
3031: PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off;
3035: DMGetDimension(dm, &dim);
3036: DMGetCoordinateDim(dm, &dimEmbed);
3037: if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %d cannot be less than intrinsic dimension %d",dimEmbed,dim);
3038: for (d = 0; d <= depth; ++d) pEnd += numPoints[d];
3039: DMPlexSetChart(dm, pStart, pEnd);
3040: for (p = pStart; p < pEnd; ++p) {
3041: DMPlexSetConeSize(dm, p, coneSize[p-pStart]);
3042: if (firstVertex < 0 && !coneSize[p - pStart]) {
3043: firstVertex = p - pStart;
3044: }
3045: }
3046: if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %d vertices but could not find any", numPoints[0]);
3047: DMSetUp(dm); /* Allocate space for cones */
3048: for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) {
3049: DMPlexSetCone(dm, p, &cones[off]);
3050: DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);
3051: }
3052: DMPlexSymmetrize(dm);
3053: DMPlexStratify(dm);
3054: /* Build coordinates */
3055: DMGetCoordinateSection(dm, &coordSection);
3056: PetscSectionSetNumFields(coordSection, 1);
3057: PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);
3058: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);
3059: for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) {
3060: PetscSectionSetDof(coordSection, v, dimEmbed);
3061: PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);
3062: }
3063: PetscSectionSetUp(coordSection);
3064: PetscSectionGetStorageSize(coordSection, &coordSize);
3065: VecCreate(PETSC_COMM_SELF, &coordinates);
3066: PetscObjectSetName((PetscObject) coordinates, "coordinates");
3067: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
3068: VecSetBlockSize(coordinates, dimEmbed);
3069: VecSetType(coordinates,VECSTANDARD);
3070: VecGetArray(coordinates, &coords);
3071: for (v = 0; v < numPoints[0]; ++v) {
3072: PetscInt off;
3074: PetscSectionGetOffset(coordSection, v+firstVertex, &off);
3075: for (d = 0; d < dimEmbed; ++d) {
3076: coords[off+d] = vertexCoords[v*dimEmbed+d];
3077: }
3078: }
3079: VecRestoreArray(coordinates, &coords);
3080: DMSetCoordinatesLocal(dm, coordinates);
3081: VecDestroy(&coordinates);
3082: return(0);
3083: }
3085: /*@C
3086: DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file.
3088: + comm - The MPI communicator
3089: . filename - Name of the .dat file
3090: - interpolate - Create faces and edges in the mesh
3092: Output Parameter:
3093: . dm - The DM object representing the mesh
3095: Note: The format is the simplest possible:
3096: $ Ne
3097: $ v0 v1 ... vk
3098: $ Nv
3099: $ x y z marker
3101: Level: beginner
3103: .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate()
3104: @*/
3105: PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
3106: {
3107: DMLabel marker;
3108: PetscViewer viewer;
3109: Vec coordinates;
3110: PetscSection coordSection;
3111: PetscScalar *coords;
3112: char line[PETSC_MAX_PATH_LEN];
3113: PetscInt dim = 3, cdim = 3, coordSize, v, c, d;
3114: PetscMPIInt rank;
3115: int snum, Nv, Nc;
3116: PetscErrorCode ierr;
3119: MPI_Comm_rank(comm, &rank);
3120: PetscViewerCreate(comm, &viewer);
3121: PetscViewerSetType(viewer, PETSCVIEWERASCII);
3122: PetscViewerFileSetMode(viewer, FILE_MODE_READ);
3123: PetscViewerFileSetName(viewer, filename);
3124: if (!rank) {
3125: PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);
3126: snum = sscanf(line, "%d %d", &Nc, &Nv);
3127: if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
3128: } else {
3129: Nc = Nv = 0;
3130: }
3131: DMCreate(comm, dm);
3132: DMSetType(*dm, DMPLEX);
3133: DMPlexSetChart(*dm, 0, Nc+Nv);
3134: DMSetDimension(*dm, dim);
3135: DMSetCoordinateDim(*dm, cdim);
3136: /* Read topology */
3137: if (!rank) {
3138: PetscInt cone[8], corners = 8;
3139: int vbuf[8], v;
3141: for (c = 0; c < Nc; ++c) {DMPlexSetConeSize(*dm, c, corners);}
3142: DMSetUp(*dm);
3143: for (c = 0; c < Nc; ++c) {
3144: PetscViewerRead(viewer, line, corners, NULL, PETSC_STRING);
3145: 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]);
3146: if (snum != corners) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
3147: for (v = 0; v < corners; ++v) cone[v] = vbuf[v] + Nc;
3148: /* Hexahedra are inverted */
3149: {
3150: PetscInt tmp = cone[1];
3151: cone[1] = cone[3];
3152: cone[3] = tmp;
3153: }
3154: DMPlexSetCone(*dm, c, cone);
3155: }
3156: }
3157: DMPlexSymmetrize(*dm);
3158: DMPlexStratify(*dm);
3159: /* Read coordinates */
3160: DMGetCoordinateSection(*dm, &coordSection);
3161: PetscSectionSetNumFields(coordSection, 1);
3162: PetscSectionSetFieldComponents(coordSection, 0, cdim);
3163: PetscSectionSetChart(coordSection, Nc, Nc + Nv);
3164: for (v = Nc; v < Nc+Nv; ++v) {
3165: PetscSectionSetDof(coordSection, v, cdim);
3166: PetscSectionSetFieldDof(coordSection, v, 0, cdim);
3167: }
3168: PetscSectionSetUp(coordSection);
3169: PetscSectionGetStorageSize(coordSection, &coordSize);
3170: VecCreate(PETSC_COMM_SELF, &coordinates);
3171: PetscObjectSetName((PetscObject) coordinates, "coordinates");
3172: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
3173: VecSetBlockSize(coordinates, cdim);
3174: VecSetType(coordinates, VECSTANDARD);
3175: VecGetArray(coordinates, &coords);
3176: if (!rank) {
3177: double x[3];
3178: int val;
3180: DMCreateLabel(*dm, "marker");
3181: DMGetLabel(*dm, "marker", &marker);
3182: for (v = 0; v < Nv; ++v) {
3183: PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);
3184: snum = sscanf(line, "%lg %lg %lg %d", &x[0], &x[1], &x[2], &val);
3185: if (snum != 4) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
3186: for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d];
3187: if (val) {DMLabelSetValue(marker, v+Nc, val);}
3188: }
3189: }
3190: VecRestoreArray(coordinates, &coords);
3191: DMSetCoordinatesLocal(*dm, coordinates);
3192: VecDestroy(&coordinates);
3193: PetscViewerDestroy(&viewer);
3194: if (interpolate) {
3195: DM idm;
3196: DMLabel bdlabel;
3198: DMPlexInterpolate(*dm, &idm);
3199: DMDestroy(dm);
3200: *dm = idm;
3202: DMGetLabel(*dm, "marker", &bdlabel);
3203: DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);
3204: DMPlexLabelComplete(*dm, bdlabel);
3205: }
3206: return(0);
3207: }
3209: /*@C
3210: DMPlexCreateFromFile - This takes a filename and produces a DM
3212: Input Parameters:
3213: + comm - The communicator
3214: . filename - A file name
3215: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
3217: Output Parameter:
3218: . dm - The DM
3220: Options Database Keys:
3221: . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5
3223: Level: beginner
3225: .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellList(), DMPlexCreate()
3226: @*/
3227: PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
3228: {
3229: const char *extGmsh = ".msh";
3230: const char *extGmsh2 = ".msh2";
3231: const char *extGmsh4 = ".msh4";
3232: const char *extCGNS = ".cgns";
3233: const char *extExodus = ".exo";
3234: const char *extGenesis = ".gen";
3235: const char *extFluent = ".cas";
3236: const char *extHDF5 = ".h5";
3237: const char *extMed = ".med";
3238: const char *extPLY = ".ply";
3239: const char *extCV = ".dat";
3240: size_t len;
3241: PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isCV;
3242: PetscMPIInt rank;
3248: MPI_Comm_rank(comm, &rank);
3249: PetscStrlen(filename, &len);
3250: if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path");
3251: PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);
3252: PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh2, 5, &isGmsh2);
3253: PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh4, 5, &isGmsh4);
3254: PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);
3255: PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);
3256: PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);
3257: PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);
3258: PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);
3259: PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);
3260: PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);
3261: PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);
3262: if (isGmsh || isGmsh2 || isGmsh4) {
3263: DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);
3264: } else if (isCGNS) {
3265: DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);
3266: } else if (isExodus || isGenesis) {
3267: DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);
3268: } else if (isFluent) {
3269: DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);
3270: } else if (isHDF5) {
3271: PetscBool load_hdf5_xdmf = PETSC_FALSE;
3272: PetscViewer viewer;
3274: /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */
3275: PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf", 5, &load_hdf5_xdmf);
3276: PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);
3277: PetscViewerCreate(comm, &viewer);
3278: PetscViewerSetType(viewer, PETSCVIEWERHDF5);
3279: PetscViewerFileSetMode(viewer, FILE_MODE_READ);
3280: PetscViewerFileSetName(viewer, filename);
3281: DMCreate(comm, dm);
3282: DMSetType(*dm, DMPLEX);
3283: if (load_hdf5_xdmf) {PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);}
3284: DMLoad(*dm, viewer);
3285: if (load_hdf5_xdmf) {PetscViewerPopFormat(viewer);}
3286: PetscViewerDestroy(&viewer);
3288: if (interpolate) {
3289: DM idm;
3291: DMPlexInterpolate(*dm, &idm);
3292: DMDestroy(dm);
3293: *dm = idm;
3294: }
3295: } else if (isMed) {
3296: DMPlexCreateMedFromFile(comm, filename, interpolate, dm);
3297: } else if (isPLY) {
3298: DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);
3299: } else if (isCV) {
3300: DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);
3301: } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename);
3302: return(0);
3303: }
3305: /*@
3306: DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell
3308: Collective
3310: Input Parameters:
3311: + comm - The communicator
3312: . dim - The spatial dimension
3313: - simplex - Flag for simplex, otherwise use a tensor-product cell
3315: Output Parameter:
3316: . refdm - The reference cell
3318: Level: intermediate
3320: .seealso:
3321: @*/
3322: PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm)
3323: {
3324: DM rdm;
3325: Vec coords;
3329: DMCreate(comm, &rdm);
3330: DMSetType(rdm, DMPLEX);
3331: DMSetDimension(rdm, dim);
3332: switch (dim) {
3333: case 0:
3334: {
3335: PetscInt numPoints[1] = {1};
3336: PetscInt coneSize[1] = {0};
3337: PetscInt cones[1] = {0};
3338: PetscInt coneOrientations[1] = {0};
3339: PetscScalar vertexCoords[1] = {0.0};
3341: DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3342: }
3343: break;
3344: case 1:
3345: {
3346: PetscInt numPoints[2] = {2, 1};
3347: PetscInt coneSize[3] = {2, 0, 0};
3348: PetscInt cones[2] = {1, 2};
3349: PetscInt coneOrientations[2] = {0, 0};
3350: PetscScalar vertexCoords[2] = {-1.0, 1.0};
3352: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3353: }
3354: break;
3355: case 2:
3356: if (simplex) {
3357: PetscInt numPoints[2] = {3, 1};
3358: PetscInt coneSize[4] = {3, 0, 0, 0};
3359: PetscInt cones[3] = {1, 2, 3};
3360: PetscInt coneOrientations[3] = {0, 0, 0};
3361: PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0};
3363: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3364: } else {
3365: PetscInt numPoints[2] = {4, 1};
3366: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
3367: PetscInt cones[4] = {1, 2, 3, 4};
3368: PetscInt coneOrientations[4] = {0, 0, 0, 0};
3369: PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0};
3371: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3372: }
3373: break;
3374: case 3:
3375: if (simplex) {
3376: PetscInt numPoints[2] = {4, 1};
3377: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
3378: PetscInt cones[4] = {1, 3, 2, 4};
3379: PetscInt coneOrientations[4] = {0, 0, 0, 0};
3380: 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};
3382: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3383: } else {
3384: PetscInt numPoints[2] = {8, 1};
3385: PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0};
3386: PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8};
3387: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
3388: 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,
3389: -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0};
3391: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3392: }
3393: break;
3394: default:
3395: SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %d", dim);
3396: }
3397: DMPlexInterpolate(rdm, refdm);
3398: if (rdm->coordinateDM) {
3399: DM ncdm;
3400: PetscSection cs;
3401: PetscInt pEnd = -1;
3403: DMGetLocalSection(rdm->coordinateDM, &cs);
3404: if (cs) {PetscSectionGetChart(cs, NULL, &pEnd);}
3405: if (pEnd >= 0) {
3406: DMClone(*refdm, &ncdm);
3407: DMCopyDisc(rdm->coordinateDM, ncdm);
3408: DMSetLocalSection(ncdm, cs);
3409: DMSetCoordinateDM(*refdm, ncdm);
3410: DMDestroy(&ncdm);
3411: }
3412: }
3413: DMGetCoordinatesLocal(rdm, &coords);
3414: if (coords) {
3415: DMSetCoordinatesLocal(*refdm, coords);
3416: } else {
3417: DMGetCoordinates(rdm, &coords);
3418: if (coords) {DMSetCoordinates(*refdm, coords);}
3419: }
3420: DMDestroy(&rdm);
3421: return(0);
3422: }