Actual source code: plexcreate.c
petsc-master 2020-08-25
1: #define PETSCDM_DLL
2: #include <petsc/private/dmpleximpl.h>
3: #include <petsc/private/hashseti.h>
4: #include <petscsf.h>
6: PetscLogEvent DMPLEX_CreateFromFile, DMPLEX_BuildFromCellList, DMPLEX_BuildCoordinatesFromCellList;
8: /*@
9: DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement.
11: Collective
13: Input Parameters:
14: + comm - The communicator for the DM object
15: . dim - The spatial dimension
16: . simplex - Flag for simplicial cells, otherwise they are tensor product cells
17: . interpolate - Flag to create intermediate mesh pieces (edges, faces)
18: . refinementUniform - Flag for uniform parallel refinement
19: - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell
21: Output Parameter:
22: . dm - The DM object
24: Level: beginner
26: .seealso: DMSetType(), DMCreate()
27: @*/
28: PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscBool refinementUniform, PetscReal refinementLimit, DM *newdm)
29: {
30: DM dm;
31: PetscInt p;
32: PetscMPIInt rank;
36: DMCreate(comm, &dm);
37: DMSetType(dm, DMPLEX);
38: DMSetDimension(dm, dim);
39: MPI_Comm_rank(comm, &rank);
40: switch (dim) {
41: case 2:
42: if (simplex) {PetscObjectSetName((PetscObject) dm, "triangular");}
43: else {PetscObjectSetName((PetscObject) dm, "quadrilateral");}
44: break;
45: case 3:
46: if (simplex) {PetscObjectSetName((PetscObject) dm, "tetrahedral");}
47: else {PetscObjectSetName((PetscObject) dm, "hexahedral");}
48: break;
49: default:
50: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %D", dim);
51: }
52: if (rank) {
53: PetscInt numPoints[2] = {0, 0};
54: DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);
55: } else {
56: switch (dim) {
57: case 2:
58: if (simplex) {
59: PetscInt numPoints[2] = {4, 2};
60: PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0};
61: PetscInt cones[6] = {2, 3, 4, 5, 4, 3};
62: PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0};
63: PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5};
64: PetscInt markerPoints[8] = {2, 1, 3, 1, 4, 1, 5, 1};
66: DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
67: for (p = 0; p < 4; ++p) {DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);}
68: } else {
69: PetscInt numPoints[2] = {6, 2};
70: PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0};
71: PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4};
72: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
73: 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};
75: DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
76: }
77: break;
78: case 3:
79: if (simplex) {
80: PetscInt numPoints[2] = {5, 2};
81: PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0};
82: PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6};
83: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
84: 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};
85: PetscInt markerPoints[10] = {2, 1, 3, 1, 4, 1, 5, 1, 6, 1};
87: DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
88: for (p = 0; p < 5; ++p) {DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);}
89: } else {
90: PetscInt numPoints[2] = {12, 2};
91: PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
92: PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8};
93: PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
94: 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,
95: -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5,
96: 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5};
98: DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
99: }
100: break;
101: default:
102: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %D", dim);
103: }
104: }
105: *newdm = dm;
106: if (refinementLimit > 0.0) {
107: DM rdm;
108: const char *name;
110: DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);
111: DMPlexSetRefinementLimit(*newdm, refinementLimit);
112: DMRefine(*newdm, comm, &rdm);
113: PetscObjectGetName((PetscObject) *newdm, &name);
114: PetscObjectSetName((PetscObject) rdm, name);
115: DMDestroy(newdm);
116: *newdm = rdm;
117: }
118: if (interpolate) {
119: DM idm;
121: DMPlexInterpolate(*newdm, &idm);
122: DMDestroy(newdm);
123: *newdm = idm;
124: }
125: {
126: DM refinedMesh = NULL;
127: DM distributedMesh = NULL;
129: /* Distribute mesh over processes */
130: DMPlexDistribute(*newdm, 0, NULL, &distributedMesh);
131: if (distributedMesh) {
132: DMDestroy(newdm);
133: *newdm = distributedMesh;
134: }
135: if (refinementUniform) {
136: DMPlexSetRefinementUniform(*newdm, refinementUniform);
137: DMRefine(*newdm, comm, &refinedMesh);
138: if (refinedMesh) {
139: DMDestroy(newdm);
140: *newdm = refinedMesh;
141: }
142: }
143: }
144: return(0);
145: }
147: /*@
148: DMPlexCreateSquareBoundary - Creates a 1D mesh the is the boundary of a square lattice.
150: Collective
152: Input Parameters:
153: + comm - The communicator for the DM object
154: . lower - The lower left corner coordinates
155: . upper - The upper right corner coordinates
156: - edges - The number of cells in each direction
158: Output Parameter:
159: . dm - The DM object
161: Note: Here is the numbering returned for 2 cells in each direction:
162: $ 18--5-17--4--16
163: $ | | |
164: $ 6 10 3
165: $ | | |
166: $ 19-11-20--9--15
167: $ | | |
168: $ 7 8 2
169: $ | | |
170: $ 12--0-13--1--14
172: Level: beginner
174: .seealso: DMPlexCreateBoxMesh(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate()
175: @*/
176: PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
177: {
178: const PetscInt numVertices = (edges[0]+1)*(edges[1]+1);
179: const PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1];
180: PetscInt markerTop = 1;
181: PetscInt markerBottom = 1;
182: PetscInt markerRight = 1;
183: PetscInt markerLeft = 1;
184: PetscBool markerSeparate = PETSC_FALSE;
185: Vec coordinates;
186: PetscSection coordSection;
187: PetscScalar *coords;
188: PetscInt coordSize;
189: PetscMPIInt rank;
190: PetscInt v, vx, vy;
194: PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);
195: if (markerSeparate) {
196: markerTop = 3;
197: markerBottom = 1;
198: markerRight = 2;
199: markerLeft = 4;
200: }
201: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
202: if (!rank) {
203: PetscInt e, ex, ey;
205: DMPlexSetChart(dm, 0, numEdges+numVertices);
206: for (e = 0; e < numEdges; ++e) {
207: DMPlexSetConeSize(dm, e, 2);
208: }
209: DMSetUp(dm); /* Allocate space for cones */
210: for (vx = 0; vx <= edges[0]; vx++) {
211: for (ey = 0; ey < edges[1]; ey++) {
212: PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1);
213: PetscInt vertex = ey*(edges[0]+1) + vx + numEdges;
214: PetscInt cone[2];
216: cone[0] = vertex; cone[1] = vertex+edges[0]+1;
217: DMPlexSetCone(dm, edge, cone);
218: if (vx == edges[0]) {
219: DMSetLabelValue(dm, "marker", edge, markerRight);
220: DMSetLabelValue(dm, "marker", cone[0], markerRight);
221: if (ey == edges[1]-1) {
222: DMSetLabelValue(dm, "marker", cone[1], markerRight);
223: DMSetLabelValue(dm, "Face Sets", cone[1], markerRight);
224: }
225: } else if (vx == 0) {
226: DMSetLabelValue(dm, "marker", edge, markerLeft);
227: DMSetLabelValue(dm, "marker", cone[0], markerLeft);
228: if (ey == edges[1]-1) {
229: DMSetLabelValue(dm, "marker", cone[1], markerLeft);
230: DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft);
231: }
232: }
233: }
234: }
235: for (vy = 0; vy <= edges[1]; vy++) {
236: for (ex = 0; ex < edges[0]; ex++) {
237: PetscInt edge = vy*edges[0] + ex;
238: PetscInt vertex = vy*(edges[0]+1) + ex + numEdges;
239: PetscInt cone[2];
241: cone[0] = vertex; cone[1] = vertex+1;
242: DMPlexSetCone(dm, edge, cone);
243: if (vy == edges[1]) {
244: DMSetLabelValue(dm, "marker", edge, markerTop);
245: DMSetLabelValue(dm, "marker", cone[0], markerTop);
246: if (ex == edges[0]-1) {
247: DMSetLabelValue(dm, "marker", cone[1], markerTop);
248: DMSetLabelValue(dm, "Face Sets", cone[1], markerTop);
249: }
250: } else if (vy == 0) {
251: DMSetLabelValue(dm, "marker", edge, markerBottom);
252: DMSetLabelValue(dm, "marker", cone[0], markerBottom);
253: if (ex == edges[0]-1) {
254: DMSetLabelValue(dm, "marker", cone[1], markerBottom);
255: DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom);
256: }
257: }
258: }
259: }
260: }
261: DMPlexSymmetrize(dm);
262: DMPlexStratify(dm);
263: /* Build coordinates */
264: DMSetCoordinateDim(dm, 2);
265: DMGetCoordinateSection(dm, &coordSection);
266: PetscSectionSetNumFields(coordSection, 1);
267: PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);
268: PetscSectionSetFieldComponents(coordSection, 0, 2);
269: for (v = numEdges; v < numEdges+numVertices; ++v) {
270: PetscSectionSetDof(coordSection, v, 2);
271: PetscSectionSetFieldDof(coordSection, v, 0, 2);
272: }
273: PetscSectionSetUp(coordSection);
274: PetscSectionGetStorageSize(coordSection, &coordSize);
275: VecCreate(PETSC_COMM_SELF, &coordinates);
276: PetscObjectSetName((PetscObject) coordinates, "coordinates");
277: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
278: VecSetBlockSize(coordinates, 2);
279: VecSetType(coordinates,VECSTANDARD);
280: VecGetArray(coordinates, &coords);
281: for (vy = 0; vy <= edges[1]; ++vy) {
282: for (vx = 0; vx <= edges[0]; ++vx) {
283: coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx;
284: coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy;
285: }
286: }
287: VecRestoreArray(coordinates, &coords);
288: DMSetCoordinatesLocal(dm, coordinates);
289: VecDestroy(&coordinates);
290: return(0);
291: }
293: /*@
294: DMPlexCreateCubeBoundary - Creates a 2D mesh that is the boundary of a cubic lattice.
296: Collective
298: Input Parameters:
299: + comm - The communicator for the DM object
300: . lower - The lower left front corner coordinates
301: . upper - The upper right back corner coordinates
302: - faces - The number of faces in each direction (the same as the number of cells)
304: Output Parameter:
305: . dm - The DM object
307: Level: beginner
309: .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMSetType(), DMCreate()
310: @*/
311: PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[])
312: {
313: PetscInt vertices[3], numVertices;
314: PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2];
315: Vec coordinates;
316: PetscSection coordSection;
317: PetscScalar *coords;
318: PetscInt coordSize;
319: PetscMPIInt rank;
320: PetscInt v, vx, vy, vz;
321: PetscInt voffset, iface=0, cone[4];
325: 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");
326: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
327: vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1;
328: numVertices = vertices[0]*vertices[1]*vertices[2];
329: if (!rank) {
330: PetscInt f;
332: DMPlexSetChart(dm, 0, numFaces+numVertices);
333: for (f = 0; f < numFaces; ++f) {
334: DMPlexSetConeSize(dm, f, 4);
335: }
336: DMSetUp(dm); /* Allocate space for cones */
338: /* Side 0 (Top) */
339: for (vy = 0; vy < faces[1]; vy++) {
340: for (vx = 0; vx < faces[0]; vx++) {
341: voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx;
342: cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0];
343: DMPlexSetCone(dm, iface, cone);
344: DMSetLabelValue(dm, "marker", iface, 1);
345: DMSetLabelValue(dm, "marker", voffset+0, 1);
346: DMSetLabelValue(dm, "marker", voffset+1, 1);
347: DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);
348: DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);
349: iface++;
350: }
351: }
353: /* Side 1 (Bottom) */
354: for (vy = 0; vy < faces[1]; vy++) {
355: for (vx = 0; vx < faces[0]; vx++) {
356: voffset = numFaces + vy*(faces[0]+1) + vx;
357: cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1;
358: DMPlexSetCone(dm, iface, cone);
359: DMSetLabelValue(dm, "marker", iface, 1);
360: DMSetLabelValue(dm, "marker", voffset+0, 1);
361: DMSetLabelValue(dm, "marker", voffset+1, 1);
362: DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);
363: DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);
364: iface++;
365: }
366: }
368: /* Side 2 (Front) */
369: for (vz = 0; vz < faces[2]; vz++) {
370: for (vx = 0; vx < faces[0]; vx++) {
371: voffset = numFaces + vz*vertices[0]*vertices[1] + vx;
372: cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1];
373: DMPlexSetCone(dm, iface, cone);
374: DMSetLabelValue(dm, "marker", iface, 1);
375: DMSetLabelValue(dm, "marker", voffset+0, 1);
376: DMSetLabelValue(dm, "marker", voffset+1, 1);
377: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);
378: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);
379: iface++;
380: }
381: }
383: /* Side 3 (Back) */
384: for (vz = 0; vz < faces[2]; vz++) {
385: for (vx = 0; vx < faces[0]; vx++) {
386: voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx;
387: cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1;
388: cone[2] = voffset+1; cone[3] = voffset;
389: DMPlexSetCone(dm, iface, cone);
390: DMSetLabelValue(dm, "marker", iface, 1);
391: DMSetLabelValue(dm, "marker", voffset+0, 1);
392: DMSetLabelValue(dm, "marker", voffset+1, 1);
393: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);
394: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);
395: iface++;
396: }
397: }
399: /* Side 4 (Left) */
400: for (vz = 0; vz < faces[2]; vz++) {
401: for (vy = 0; vy < faces[1]; vy++) {
402: voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0];
403: cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1];
404: cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0];
405: DMPlexSetCone(dm, iface, cone);
406: DMSetLabelValue(dm, "marker", iface, 1);
407: DMSetLabelValue(dm, "marker", voffset+0, 1);
408: DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);
409: DMSetLabelValue(dm, "marker", voffset+vertices[1]+0, 1);
410: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);
411: iface++;
412: }
413: }
415: /* Side 5 (Right) */
416: for (vz = 0; vz < faces[2]; vz++) {
417: for (vy = 0; vy < faces[1]; vy++) {
418: voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + faces[0];
419: cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset;
420: cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0];
421: DMPlexSetCone(dm, iface, cone);
422: DMSetLabelValue(dm, "marker", iface, 1);
423: DMSetLabelValue(dm, "marker", voffset+0, 1);
424: DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);
425: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);
426: DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);
427: iface++;
428: }
429: }
430: }
431: DMPlexSymmetrize(dm);
432: DMPlexStratify(dm);
433: /* Build coordinates */
434: DMSetCoordinateDim(dm, 3);
435: DMGetCoordinateSection(dm, &coordSection);
436: PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);
437: for (v = numFaces; v < numFaces+numVertices; ++v) {
438: PetscSectionSetDof(coordSection, v, 3);
439: }
440: PetscSectionSetUp(coordSection);
441: PetscSectionGetStorageSize(coordSection, &coordSize);
442: VecCreate(PETSC_COMM_SELF, &coordinates);
443: PetscObjectSetName((PetscObject) coordinates, "coordinates");
444: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
445: VecSetBlockSize(coordinates, 3);
446: VecSetType(coordinates,VECSTANDARD);
447: VecGetArray(coordinates, &coords);
448: for (vz = 0; vz <= faces[2]; ++vz) {
449: for (vy = 0; vy <= faces[1]; ++vy) {
450: for (vx = 0; vx <= faces[0]; ++vx) {
451: coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx;
452: coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy;
453: coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz;
454: }
455: }
456: }
457: VecRestoreArray(coordinates, &coords);
458: DMSetCoordinatesLocal(dm, coordinates);
459: VecDestroy(&coordinates);
460: return(0);
461: }
463: static PetscErrorCode DMPlexCreateLineMesh_Internal(MPI_Comm comm,PetscInt segments,PetscReal lower,PetscReal upper,DMBoundaryType bd,DM *dm)
464: {
465: PetscInt i,fStart,fEnd,numCells = 0,numVerts = 0;
466: PetscInt numPoints[2],*coneSize,*cones,*coneOrientations;
467: PetscScalar *vertexCoords;
468: PetscReal L,maxCell;
469: PetscBool markerSeparate = PETSC_FALSE;
470: PetscInt markerLeft = 1, faceMarkerLeft = 1;
471: PetscInt markerRight = 1, faceMarkerRight = 2;
472: PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE;
473: PetscMPIInt rank;
479: DMCreate(comm,dm);
480: DMSetType(*dm,DMPLEX);
481: DMSetDimension(*dm,1);
482: DMCreateLabel(*dm,"marker");
483: DMCreateLabel(*dm,"Face Sets");
485: MPI_Comm_rank(comm,&rank);
486: if (!rank) numCells = segments;
487: if (!rank) numVerts = segments + (wrap ? 0 : 1);
489: numPoints[0] = numVerts ; numPoints[1] = numCells;
490: PetscMalloc4(numCells+numVerts,&coneSize,numCells*2,&cones,numCells+numVerts,&coneOrientations,numVerts,&vertexCoords);
491: PetscArrayzero(coneOrientations,numCells+numVerts);
492: for (i = 0; i < numCells; ++i) { coneSize[i] = 2; }
493: for (i = 0; i < numVerts; ++i) { coneSize[numCells+i] = 0; }
494: for (i = 0; i < numCells; ++i) { cones[2*i] = numCells + i%numVerts; cones[2*i+1] = numCells + (i+1)%numVerts; }
495: for (i = 0; i < numVerts; ++i) { vertexCoords[i] = lower + (upper-lower)*((PetscReal)i/(PetscReal)numCells); }
496: DMPlexCreateFromDAG(*dm,1,numPoints,coneSize,cones,coneOrientations,vertexCoords);
497: PetscFree4(coneSize,cones,coneOrientations,vertexCoords);
499: PetscOptionsGetBool(((PetscObject)*dm)->options,((PetscObject)*dm)->prefix,"-dm_plex_separate_marker",&markerSeparate,NULL);
500: if (markerSeparate) { markerLeft = faceMarkerLeft; markerRight = faceMarkerRight;}
501: if (!wrap && !rank) {
502: DMPlexGetHeightStratum(*dm,1,&fStart,&fEnd);
503: DMSetLabelValue(*dm,"marker",fStart,markerLeft);
504: DMSetLabelValue(*dm,"marker",fEnd-1,markerRight);
505: DMSetLabelValue(*dm,"Face Sets",fStart,faceMarkerLeft);
506: DMSetLabelValue(*dm,"Face Sets",fEnd-1,faceMarkerRight);
507: }
508: if (wrap) {
509: L = upper - lower;
510: maxCell = (PetscReal)1.1*(L/(PetscReal)PetscMax(1,segments));
511: DMSetPeriodicity(*dm,PETSC_TRUE,&maxCell,&L,&bd);
512: }
513: return(0);
514: }
516: 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)
517: {
518: DM boundary;
519: PetscInt i;
524: for (i = 0; i < dim; ++i) if (periodicity[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity is not supported for simplex meshes");
525: DMCreate(comm, &boundary);
527: DMSetType(boundary, DMPLEX);
528: DMSetDimension(boundary, dim-1);
529: DMSetCoordinateDim(boundary, dim);
530: switch (dim) {
531: case 2: DMPlexCreateSquareBoundary(boundary, lower, upper, faces);break;
532: case 3: DMPlexCreateCubeBoundary(boundary, lower, upper, faces);break;
533: default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %D", dim);
534: }
535: DMPlexGenerate(boundary, NULL, interpolate, dm);
536: DMDestroy(&boundary);
537: return(0);
538: }
540: static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ)
541: {
542: DMLabel cutLabel = NULL;
543: PetscInt markerTop = 1, faceMarkerTop = 1;
544: PetscInt markerBottom = 1, faceMarkerBottom = 1;
545: PetscInt markerFront = 1, faceMarkerFront = 1;
546: PetscInt markerBack = 1, faceMarkerBack = 1;
547: PetscInt markerRight = 1, faceMarkerRight = 1;
548: PetscInt markerLeft = 1, faceMarkerLeft = 1;
549: PetscInt dim;
550: PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE;
551: PetscMPIInt rank;
555: DMGetDimension(dm,&dim);
556: MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
557: DMCreateLabel(dm,"marker");
558: DMCreateLabel(dm,"Face Sets");
559: PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL);
560: if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ||
561: bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ||
562: bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) {
564: if (cutMarker) {DMCreateLabel(dm, "periodic_cut"); DMGetLabel(dm, "periodic_cut", &cutLabel);}
565: }
566: switch (dim) {
567: case 2:
568: faceMarkerTop = 3;
569: faceMarkerBottom = 1;
570: faceMarkerRight = 2;
571: faceMarkerLeft = 4;
572: break;
573: case 3:
574: faceMarkerBottom = 1;
575: faceMarkerTop = 2;
576: faceMarkerFront = 3;
577: faceMarkerBack = 4;
578: faceMarkerRight = 5;
579: faceMarkerLeft = 6;
580: break;
581: default:
582: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %D not supported",dim);
583: break;
584: }
585: PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);
586: if (markerSeparate) {
587: markerBottom = faceMarkerBottom;
588: markerTop = faceMarkerTop;
589: markerFront = faceMarkerFront;
590: markerBack = faceMarkerBack;
591: markerRight = faceMarkerRight;
592: markerLeft = faceMarkerLeft;
593: }
594: {
595: const PetscInt numXEdges = !rank ? edges[0] : 0;
596: const PetscInt numYEdges = !rank ? edges[1] : 0;
597: const PetscInt numZEdges = !rank ? edges[2] : 0;
598: const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0;
599: const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0;
600: const PetscInt numZVertices = !rank ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0;
601: const PetscInt numCells = numXEdges*numYEdges*numZEdges;
602: const PetscInt numXFaces = numYEdges*numZEdges;
603: const PetscInt numYFaces = numXEdges*numZEdges;
604: const PetscInt numZFaces = numXEdges*numYEdges;
605: const PetscInt numTotXFaces = numXVertices*numXFaces;
606: const PetscInt numTotYFaces = numYVertices*numYFaces;
607: const PetscInt numTotZFaces = numZVertices*numZFaces;
608: const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces;
609: const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices;
610: const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices;
611: const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices;
612: const PetscInt numVertices = numXVertices*numYVertices*numZVertices;
613: const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges;
614: const PetscInt firstVertex = (dim == 2) ? numFaces : numCells;
615: const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices;
616: const PetscInt firstYFace = firstXFace + numTotXFaces;
617: const PetscInt firstZFace = firstYFace + numTotYFaces;
618: const PetscInt firstXEdge = numCells + numFaces + numVertices;
619: const PetscInt firstYEdge = firstXEdge + numTotXEdges;
620: const PetscInt firstZEdge = firstYEdge + numTotYEdges;
621: Vec coordinates;
622: PetscSection coordSection;
623: PetscScalar *coords;
624: PetscInt coordSize;
625: PetscInt v, vx, vy, vz;
626: PetscInt c, f, fx, fy, fz, e, ex, ey, ez;
628: DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);
629: for (c = 0; c < numCells; c++) {
630: DMPlexSetConeSize(dm, c, 6);
631: }
632: for (f = firstXFace; f < firstXFace+numFaces; ++f) {
633: DMPlexSetConeSize(dm, f, 4);
634: }
635: for (e = firstXEdge; e < firstXEdge+numEdges; ++e) {
636: DMPlexSetConeSize(dm, e, 2);
637: }
638: DMSetUp(dm); /* Allocate space for cones */
639: /* Build cells */
640: for (fz = 0; fz < numZEdges; ++fz) {
641: for (fy = 0; fy < numYEdges; ++fy) {
642: for (fx = 0; fx < numXEdges; ++fx) {
643: PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx;
644: PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz;
645: PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices);
646: PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy;
647: PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices);
648: PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx;
649: PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices);
650: /* B, T, F, K, R, L */
651: PetscInt ornt[6] = {-4, 0, 0, -1, 0, -4}; /* ??? */
652: PetscInt cone[6];
654: /* no boundary twisting in 3D */
655: cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL;
656: DMPlexSetCone(dm, cell, cone);
657: DMPlexSetConeOrientation(dm, cell, ornt);
658: if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, cell, 2);}
659: if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, cell, 2);}
660: if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, cell, 2);}
661: }
662: }
663: }
664: /* Build x faces */
665: for (fz = 0; fz < numZEdges; ++fz) {
666: for (fy = 0; fy < numYEdges; ++fy) {
667: for (fx = 0; fx < numXVertices; ++fx) {
668: PetscInt face = firstXFace + (fz*numYEdges+fy) *numXVertices+fx;
669: PetscInt edgeL = firstZEdge + (fy *numXVertices+fx)*numZEdges + fz;
670: PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz;
671: PetscInt edgeB = firstYEdge + (fz *numXVertices+fx)*numYEdges + fy;
672: PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy;
673: PetscInt ornt[4] = {0, 0, -2, -2};
674: PetscInt cone[4];
676: if (dim == 3) {
677: /* markers */
678: if (bdX != DM_BOUNDARY_PERIODIC) {
679: if (fx == numXVertices-1) {
680: DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);
681: DMSetLabelValue(dm, "marker", face, markerRight);
682: }
683: else if (fx == 0) {
684: DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);
685: DMSetLabelValue(dm, "marker", face, markerLeft);
686: }
687: }
688: }
689: cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
690: DMPlexSetCone(dm, face, cone);
691: DMPlexSetConeOrientation(dm, face, ornt);
692: }
693: }
694: }
695: /* Build y faces */
696: for (fz = 0; fz < numZEdges; ++fz) {
697: for (fx = 0; fx < numXEdges; ++fx) {
698: for (fy = 0; fy < numYVertices; ++fy) {
699: PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy;
700: PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx)*numZEdges + fz;
701: PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz;
702: PetscInt edgeB = firstXEdge + (fz *numYVertices+fy)*numXEdges + fx;
703: PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx;
704: PetscInt ornt[4] = {0, 0, -2, -2};
705: PetscInt cone[4];
707: if (dim == 3) {
708: /* markers */
709: if (bdY != DM_BOUNDARY_PERIODIC) {
710: if (fy == numYVertices-1) {
711: DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);
712: DMSetLabelValue(dm, "marker", face, markerBack);
713: }
714: else if (fy == 0) {
715: DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);
716: DMSetLabelValue(dm, "marker", face, markerFront);
717: }
718: }
719: }
720: cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
721: DMPlexSetCone(dm, face, cone);
722: DMPlexSetConeOrientation(dm, face, ornt);
723: }
724: }
725: }
726: /* Build z faces */
727: for (fy = 0; fy < numYEdges; ++fy) {
728: for (fx = 0; fx < numXEdges; ++fx) {
729: for (fz = 0; fz < numZVertices; fz++) {
730: PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz;
731: PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx)*numYEdges + fy;
732: PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy;
733: PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy)*numXEdges + fx;
734: PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx;
735: PetscInt ornt[4] = {0, 0, -2, -2};
736: PetscInt cone[4];
738: if (dim == 2) {
739: if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -2;}
740: if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;}
741: if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, face, 2);}
742: if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {DMLabelSetValue(cutLabel, face, 2);}
743: } else {
744: /* markers */
745: if (bdZ != DM_BOUNDARY_PERIODIC) {
746: if (fz == numZVertices-1) {
747: DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);
748: DMSetLabelValue(dm, "marker", face, markerTop);
749: }
750: else if (fz == 0) {
751: DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);
752: DMSetLabelValue(dm, "marker", face, markerBottom);
753: }
754: }
755: }
756: cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL;
757: DMPlexSetCone(dm, face, cone);
758: DMPlexSetConeOrientation(dm, face, ornt);
759: }
760: }
761: }
762: /* Build Z edges*/
763: for (vy = 0; vy < numYVertices; vy++) {
764: for (vx = 0; vx < numXVertices; vx++) {
765: for (ez = 0; ez < numZEdges; ez++) {
766: const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez;
767: const PetscInt vertexB = firstVertex + (ez *numYVertices+vy)*numXVertices + vx;
768: const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx;
769: PetscInt cone[2];
771: if (dim == 3) {
772: if (bdX != DM_BOUNDARY_PERIODIC) {
773: if (vx == numXVertices-1) {
774: DMSetLabelValue(dm, "marker", edge, markerRight);
775: }
776: else if (vx == 0) {
777: DMSetLabelValue(dm, "marker", edge, markerLeft);
778: }
779: }
780: if (bdY != DM_BOUNDARY_PERIODIC) {
781: if (vy == numYVertices-1) {
782: DMSetLabelValue(dm, "marker", edge, markerBack);
783: }
784: else if (vy == 0) {
785: DMSetLabelValue(dm, "marker", edge, markerFront);
786: }
787: }
788: }
789: cone[0] = vertexB; cone[1] = vertexT;
790: DMPlexSetCone(dm, edge, cone);
791: }
792: }
793: }
794: /* Build Y edges*/
795: for (vz = 0; vz < numZVertices; vz++) {
796: for (vx = 0; vx < numXVertices; vx++) {
797: for (ey = 0; ey < numYEdges; ey++) {
798: const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx;
799: const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey;
800: const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx;
801: const PetscInt vertexK = firstVertex + nextv;
802: PetscInt cone[2];
804: cone[0] = vertexF; cone[1] = vertexK;
805: DMPlexSetCone(dm, edge, cone);
806: if (dim == 2) {
807: if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) {
808: if (vx == numXVertices-1) {
809: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);
810: DMSetLabelValue(dm, "marker", edge, markerRight);
811: DMSetLabelValue(dm, "marker", cone[0], markerRight);
812: if (ey == numYEdges-1) {
813: DMSetLabelValue(dm, "marker", cone[1], markerRight);
814: }
815: } else if (vx == 0) {
816: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);
817: DMSetLabelValue(dm, "marker", edge, markerLeft);
818: DMSetLabelValue(dm, "marker", cone[0], markerLeft);
819: if (ey == numYEdges-1) {
820: DMSetLabelValue(dm, "marker", cone[1], markerLeft);
821: }
822: }
823: } else {
824: if (vx == 0 && cutLabel) {
825: DMLabelSetValue(cutLabel, edge, 1);
826: DMLabelSetValue(cutLabel, cone[0], 1);
827: if (ey == numYEdges-1) {
828: DMLabelSetValue(cutLabel, cone[1], 1);
829: }
830: }
831: }
832: } else {
833: if (bdX != DM_BOUNDARY_PERIODIC) {
834: if (vx == numXVertices-1) {
835: DMSetLabelValue(dm, "marker", edge, markerRight);
836: } else if (vx == 0) {
837: DMSetLabelValue(dm, "marker", edge, markerLeft);
838: }
839: }
840: if (bdZ != DM_BOUNDARY_PERIODIC) {
841: if (vz == numZVertices-1) {
842: DMSetLabelValue(dm, "marker", edge, markerTop);
843: } else if (vz == 0) {
844: DMSetLabelValue(dm, "marker", edge, markerBottom);
845: }
846: }
847: }
848: }
849: }
850: }
851: /* Build X edges*/
852: for (vz = 0; vz < numZVertices; vz++) {
853: for (vy = 0; vy < numYVertices; vy++) {
854: for (ex = 0; ex < numXEdges; ex++) {
855: const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices;
856: const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex;
857: const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex;
858: const PetscInt vertexR = firstVertex + nextv;
859: PetscInt cone[2];
861: cone[0] = vertexL; cone[1] = vertexR;
862: DMPlexSetCone(dm, edge, cone);
863: if (dim == 2) {
864: if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) {
865: if (vy == numYVertices-1) {
866: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);
867: DMSetLabelValue(dm, "marker", edge, markerTop);
868: DMSetLabelValue(dm, "marker", cone[0], markerTop);
869: if (ex == numXEdges-1) {
870: DMSetLabelValue(dm, "marker", cone[1], markerTop);
871: }
872: } else if (vy == 0) {
873: DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);
874: DMSetLabelValue(dm, "marker", edge, markerBottom);
875: DMSetLabelValue(dm, "marker", cone[0], markerBottom);
876: if (ex == numXEdges-1) {
877: DMSetLabelValue(dm, "marker", cone[1], markerBottom);
878: }
879: }
880: } else {
881: if (vy == 0 && cutLabel) {
882: DMLabelSetValue(cutLabel, edge, 1);
883: DMLabelSetValue(cutLabel, cone[0], 1);
884: if (ex == numXEdges-1) {
885: DMLabelSetValue(cutLabel, cone[1], 1);
886: }
887: }
888: }
889: } else {
890: if (bdY != DM_BOUNDARY_PERIODIC) {
891: if (vy == numYVertices-1) {
892: DMSetLabelValue(dm, "marker", edge, markerBack);
893: }
894: else if (vy == 0) {
895: DMSetLabelValue(dm, "marker", edge, markerFront);
896: }
897: }
898: if (bdZ != DM_BOUNDARY_PERIODIC) {
899: if (vz == numZVertices-1) {
900: DMSetLabelValue(dm, "marker", edge, markerTop);
901: }
902: else if (vz == 0) {
903: DMSetLabelValue(dm, "marker", edge, markerBottom);
904: }
905: }
906: }
907: }
908: }
909: }
910: DMPlexSymmetrize(dm);
911: DMPlexStratify(dm);
912: /* Build coordinates */
913: DMGetCoordinateSection(dm, &coordSection);
914: PetscSectionSetNumFields(coordSection, 1);
915: PetscSectionSetFieldComponents(coordSection, 0, dim);
916: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);
917: for (v = firstVertex; v < firstVertex+numVertices; ++v) {
918: PetscSectionSetDof(coordSection, v, dim);
919: PetscSectionSetFieldDof(coordSection, v, 0, dim);
920: }
921: PetscSectionSetUp(coordSection);
922: PetscSectionGetStorageSize(coordSection, &coordSize);
923: VecCreate(PETSC_COMM_SELF, &coordinates);
924: PetscObjectSetName((PetscObject) coordinates, "coordinates");
925: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
926: VecSetBlockSize(coordinates, dim);
927: VecSetType(coordinates,VECSTANDARD);
928: VecGetArray(coordinates, &coords);
929: for (vz = 0; vz < numZVertices; ++vz) {
930: for (vy = 0; vy < numYVertices; ++vy) {
931: for (vx = 0; vx < numXVertices; ++vx) {
932: coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx;
933: coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy;
934: if (dim == 3) {
935: coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz;
936: }
937: }
938: }
939: }
940: VecRestoreArray(coordinates, &coords);
941: DMSetCoordinatesLocal(dm, coordinates);
942: VecDestroy(&coordinates);
943: }
944: return(0);
945: }
947: 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)
948: {
949: PetscInt i;
954: DMCreate(comm, dm);
956: DMSetType(*dm, DMPLEX);
957: DMSetDimension(*dm, dim);
958: switch (dim) {
959: case 2: {DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], DM_BOUNDARY_NONE);break;}
960: case 3: {DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], periodicity[2]);break;}
961: default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %D", dim);
962: }
963: if (periodicity[0] == DM_BOUNDARY_PERIODIC || periodicity[0] == DM_BOUNDARY_TWIST ||
964: periodicity[1] == DM_BOUNDARY_PERIODIC || periodicity[1] == DM_BOUNDARY_TWIST ||
965: (dim > 2 && (periodicity[2] == DM_BOUNDARY_PERIODIC || periodicity[2] == DM_BOUNDARY_TWIST))) {
966: PetscReal L[3];
967: PetscReal maxCell[3];
969: for (i = 0; i < dim; i++) {
970: L[i] = upper[i] - lower[i];
971: maxCell[i] = 1.1 * (L[i] / PetscMax(1,faces[i]));
972: }
973: DMSetPeriodicity(*dm,PETSC_TRUE,maxCell,L,periodicity);
974: }
975: if (!interpolate) {
976: DM udm;
978: DMPlexUninterpolate(*dm, &udm);
979: DMPlexCopyCoordinates(*dm, udm);
980: DMDestroy(dm);
981: *dm = udm;
982: }
983: return(0);
984: }
986: /*@C
987: DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra).
989: Collective
991: Input Parameters:
992: + comm - The communicator for the DM object
993: . dim - The spatial dimension
994: . simplex - PETSC_TRUE for simplices, PETSC_FALSE for tensor cells
995: . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D
996: . lower - The lower left corner, or NULL for (0, 0, 0)
997: . upper - The upper right corner, or NULL for (1, 1, 1)
998: . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE
999: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
1001: Output Parameter:
1002: . dm - The DM object
1004: Options Database Keys:
1005: + -dm_plex_box_lower <x,y,z> - Specify lower-left-bottom coordinates for the box
1006: . -dm_plex_box_upper <x,y,z> - Specify upper-right-top coordinates for the box
1007: - -dm_plex_box_faces <m,n,p> - Number of faces in each linear direction
1009: Notes:
1010: The options database keys above take lists of length d in d dimensions.
1012: Here is the numbering returned for 2 faces in each direction for tensor cells:
1013: $ 10---17---11---18----12
1014: $ | | |
1015: $ | | |
1016: $ 20 2 22 3 24
1017: $ | | |
1018: $ | | |
1019: $ 7---15----8---16----9
1020: $ | | |
1021: $ | | |
1022: $ 19 0 21 1 23
1023: $ | | |
1024: $ | | |
1025: $ 4---13----5---14----6
1027: and for simplicial cells
1029: $ 14----8---15----9----16
1030: $ |\ 5 |\ 7 |
1031: $ | \ | \ |
1032: $ 13 2 14 3 15
1033: $ | 4 \ | 6 \ |
1034: $ | \ | \ |
1035: $ 11----6---12----7----13
1036: $ |\ |\ |
1037: $ | \ 1 | \ 3 |
1038: $ 10 0 11 1 12
1039: $ | 0 \ | 2 \ |
1040: $ | \ | \ |
1041: $ 8----4----9----5----10
1043: Level: beginner
1045: .seealso: DMPlexCreateFromFile(), DMPlexCreateHexCylinderMesh(), DMSetType(), DMCreate()
1046: @*/
1047: 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)
1048: {
1049: PetscInt fac[3] = {0, 0, 0};
1050: PetscReal low[3] = {0, 0, 0};
1051: PetscReal upp[3] = {1, 1, 1};
1052: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
1053: PetscInt i, n;
1054: PetscBool flg;
1058: PetscOptionsGetInt(NULL, NULL, "-dm_plex_box_dim", &dim, &flg);
1059: if ((dim < 0) || (dim > 3)) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Dimension %D should be in [1, 3]", dim);
1060: PetscOptionsGetBool(NULL, NULL, "-dm_plex_box_simplex", &simplex, &flg);
1061: n = 3;
1062: PetscOptionsGetIntArray(NULL, NULL, "-dm_plex_box_faces", fac, &n, &flg);
1063: for (i = 0; i < dim; ++i) fac[i] = faces ? faces[i] : (flg && i < n ? fac[i] : (dim == 1 ? 1 : 4-dim));
1064: if (lower) for (i = 0; i < dim; ++i) low[i] = lower[i];
1065: if (upper) for (i = 0; i < dim; ++i) upp[i] = upper[i];
1066: if (periodicity) for (i = 0; i < dim; ++i) bdt[i] = periodicity[i];
1067: /* Allow bounds to be specified from the command line */
1068: n = 3;
1069: PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_lower", low, &n, &flg);
1070: if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim);
1071: n = 3;
1072: PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_upper", upp, &n, &flg);
1073: if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim);
1075: if (dim == 1) {DMPlexCreateLineMesh_Internal(comm, fac[0], low[0], upp[0], bdt[0], dm);}
1076: else if (simplex) {DMPlexCreateBoxMesh_Simplex_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);}
1077: else {DMPlexCreateBoxMesh_Tensor_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);}
1078: return(0);
1079: }
1081: /*@
1082: DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells.
1084: Collective
1086: Input Parameters:
1087: + comm - The communicator for the DM object
1088: . faces - Number of faces per dimension, or NULL for (1, 1, 1)
1089: . lower - The lower left corner, or NULL for (0, 0, 0)
1090: . upper - The upper right corner, or NULL for (1, 1, 1)
1091: . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE
1092: . orderHeight - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first
1093: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
1095: Output Parameter:
1096: . dm - The DM object
1098: Level: beginner
1100: .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateWedgeCylinderMesh(), DMPlexExtrude(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1101: @*/
1102: PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool orderHeight, PetscBool interpolate, DM *dm)
1103: {
1104: DM bdm, botdm;
1105: PetscInt i;
1106: PetscInt fac[3] = {0, 0, 0};
1107: PetscReal low[3] = {0, 0, 0};
1108: PetscReal upp[3] = {1, 1, 1};
1109: DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
1113: for (i = 0; i < 3; ++i) fac[i] = faces ? (faces[i] > 0 ? faces[i] : 1) : 1;
1114: if (lower) for (i = 0; i < 3; ++i) low[i] = lower[i];
1115: if (upper) for (i = 0; i < 3; ++i) upp[i] = upper[i];
1116: if (periodicity) for (i = 0; i < 3; ++i) bdt[i] = periodicity[i];
1117: for (i = 0; i < 3; ++i) if (bdt[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity not yet supported");
1119: DMCreate(comm, &bdm);
1120: DMSetType(bdm, DMPLEX);
1121: DMSetDimension(bdm, 1);
1122: DMSetCoordinateDim(bdm, 2);
1123: DMPlexCreateSquareBoundary(bdm, low, upp, fac);
1124: DMPlexGenerate(bdm, NULL, PETSC_FALSE, &botdm);
1125: DMDestroy(&bdm);
1126: DMPlexExtrude(botdm, fac[2], upp[2] - low[2], orderHeight, NULL, interpolate, dm);
1127: if (low[2] != 0.0) {
1128: Vec v;
1129: PetscScalar *x;
1130: PetscInt cDim, n;
1132: DMGetCoordinatesLocal(*dm, &v);
1133: VecGetBlockSize(v, &cDim);
1134: VecGetLocalSize(v, &n);
1135: VecGetArray(v, &x);
1136: x += cDim;
1137: for (i=0; i<n; i+=cDim) x[i] += low[2];
1138: VecRestoreArray(v,&x);
1139: DMSetCoordinatesLocal(*dm, v);
1140: }
1141: DMDestroy(&botdm);
1142: return(0);
1143: }
1145: /*@C
1146: DMPlexExtrude - Creates a (d+1)-D mesh by extruding a d-D mesh in the normal direction using prismatic cells.
1148: Collective on idm
1150: Input Parameters:
1151: + idm - The mesh to be extruded
1152: . layers - The number of layers, or PETSC_DETERMINE to use the default
1153: . height - The height of the extruded layer, or PETSC_DETERMINE to use the default
1154: . orderHeight - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first
1155: . extNormal - The normal direction in which the mesh should be extruded, or NULL to extrude using the surface normal
1156: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
1158: Output Parameter:
1159: . dm - The DM object
1161: Notes:
1162: The mesh created has prismatic cells, and the vertex ordering in the cone of the cell is that of the tensor prismatic cells. Not currently supported in Fortran.
1164: Options Database Keys:
1165: + -dm_plex_extrude_layers <k> - Sets the nubmer of layers k
1166: . -dm_plex_extrude_height <h> - Sets the height h of each layer
1167: . -dm_plex_extrude_order_height - If true, order cells by height first
1168: - -dm_plex_extrude_normal <n0,...,nd> - Sets the normal vector along which to extrude
1170: Level: advanced
1172: .seealso: DMPlexCreateWedgeCylinderMesh(), DMPlexCreateWedgeBoxMesh(), DMSetType(), DMCreate()
1173: @*/
1174: PetscErrorCode DMPlexExtrude(DM idm, PetscInt layers, PetscReal height, PetscBool orderHeight, const PetscReal extNormal[], PetscBool interpolate, DM* dm)
1175: {
1176: PetscScalar *coordsB;
1177: const PetscScalar *coordsA;
1178: PetscReal *normals = NULL;
1179: PetscReal clNormal[3];
1180: Vec coordinatesA, coordinatesB;
1181: PetscSection coordSectionA, coordSectionB;
1182: PetscInt dim, cDim, cDimB, c, l, v, coordSize, *newCone;
1183: PetscInt cStart, cEnd, vStart, vEnd, cellV, numCells, numVertices;
1184: const char *prefix;
1185: PetscBool haveCLNormal;
1186: PetscErrorCode ierr;
1193: DMGetDimension(idm, &dim);
1194: DMGetCoordinateDim(idm, &cDim);
1195: cDimB = cDim == dim ? cDim+1 : cDim;
1196: if (dim < 1 || dim > 3) SETERRQ1(PetscObjectComm((PetscObject)idm), PETSC_ERR_SUP, "Support for dimension %D not coded", dim);
1198: PetscObjectGetOptionsPrefix((PetscObject) idm, &prefix);
1199: if (layers < 0) layers = 1;
1200: PetscOptionsGetInt(NULL, prefix, "-dm_plex_extrude_layers", &layers, NULL);
1201: if (layers <= 0) SETERRQ1(PetscObjectComm((PetscObject) idm), PETSC_ERR_ARG_OUTOFRANGE, "Number of layers %D must be positive", layers);
1202: if (height < 0.) height = 1.;
1203: PetscOptionsGetReal(NULL, prefix, "-dm_plex_extrude_height", &height, NULL);
1204: if (height <= 0.) SETERRQ1(PetscObjectComm((PetscObject) idm), PETSC_ERR_ARG_OUTOFRANGE, "Height of layers %g must be positive", (double) height);
1205: PetscOptionsGetBool(NULL, prefix, "-dm_plex_extrude_order_height", &orderHeight, NULL);
1206: c = 3;
1207: PetscOptionsGetRealArray(NULL, prefix, "-dm_plex_extrude_normal", clNormal, &c, &haveCLNormal);
1208: if (haveCLNormal && c != cDimB) SETERRQ2(PetscObjectComm((PetscObject)idm), PETSC_ERR_ARG_SIZ, "Input normal has size %D != %D extruded coordinate dimension", c, cDimB);
1210: DMPlexGetHeightStratum(idm, 0, &cStart, &cEnd);
1211: DMPlexGetDepthStratum(idm, 0, &vStart, &vEnd);
1212: numCells = (cEnd - cStart)*layers;
1213: numVertices = (vEnd - vStart)*(layers+1);
1214: DMCreate(PetscObjectComm((PetscObject)idm), dm);
1215: DMSetType(*dm, DMPLEX);
1216: DMSetDimension(*dm, dim+1);
1217: DMPlexSetChart(*dm, 0, numCells+numVertices);
1218: /* Must create the celltype label here so that we do not automatically try to compute the types */
1219: DMCreateLabel(*dm, "celltype");
1220: for (c = cStart, cellV = 0; c < cEnd; ++c) {
1221: DMPolytopeType ct, nct;
1222: PetscInt *closure = NULL;
1223: PetscInt closureSize, numCorners = 0;
1225: DMPlexGetCellType(idm, c, &ct);
1226: switch (ct) {
1227: case DM_POLYTOPE_SEGMENT: nct = DM_POLYTOPE_SEG_PRISM_TENSOR;break;
1228: case DM_POLYTOPE_TRIANGLE: nct = DM_POLYTOPE_TRI_PRISM_TENSOR;break;
1229: case DM_POLYTOPE_QUADRILATERAL: nct = DM_POLYTOPE_QUAD_PRISM_TENSOR;break;
1230: default: nct = DM_POLYTOPE_UNKNOWN;
1231: }
1232: DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);
1233: for (v = 0; v < closureSize*2; v += 2) if ((closure[v] >= vStart) && (closure[v] < vEnd)) numCorners++;
1234: DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);
1235: for (l = 0; l < layers; ++l) {
1236: const PetscInt cell = orderHeight ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart;
1238: DMPlexSetConeSize(*dm, cell, 2*numCorners);
1239: DMPlexSetCellType(*dm, cell, nct);
1240: }
1241: cellV = PetscMax(numCorners,cellV);
1242: }
1243: DMSetUp(*dm);
1245: if (dim != cDim && !(extNormal || haveCLNormal)) {PetscCalloc1(cDim*(vEnd - vStart), &normals);}
1246: PetscMalloc1(3*cellV,&newCone);
1247: for (c = cStart; c < cEnd; ++c) {
1248: PetscInt *closure = NULL;
1249: PetscInt closureSize, numCorners = 0, l;
1250: PetscReal normal[3] = {0, 0, 0};
1252: if (normals) {DMPlexComputeCellGeometryFVM(idm, c, NULL, NULL, normal);}
1253: DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);
1254: for (v = 0; v < closureSize*2; v += 2) {
1255: if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
1256: PetscInt d;
1258: newCone[numCorners++] = closure[v] - vStart;
1259: if (normals) {for (d = 0; d < cDim; ++d) normals[cDim*(closure[v]-vStart)+d] += normal[d];}
1260: }
1261: }
1262: DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);
1263: for (l = 0; l < layers; ++l) {
1264: PetscInt i;
1266: for (i = 0; i < numCorners; ++i) {
1267: newCone[ numCorners + i] = orderHeight ? (layers+1)*newCone[i] + l + numCells : l*(vEnd - vStart) + newCone[i] + numCells;
1268: newCone[2*numCorners + i] = orderHeight ? (layers+1)*newCone[i] + l + 1 + numCells : (l+1)*(vEnd - vStart) + newCone[i] + numCells;
1269: }
1270: DMPlexSetCone(*dm, orderHeight ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart, newCone + numCorners);
1271: }
1272: }
1273: DMPlexSymmetrize(*dm);
1274: DMPlexStratify(*dm);
1275: PetscFree(newCone);
1277: DMGetCoordinateSection(*dm, &coordSectionB);
1278: PetscSectionSetNumFields(coordSectionB, 1);
1279: PetscSectionSetFieldComponents(coordSectionB, 0, cDimB);
1280: PetscSectionSetChart(coordSectionB, numCells, numCells+numVertices);
1281: for (v = numCells; v < numCells+numVertices; ++v) {
1282: PetscSectionSetDof(coordSectionB, v, cDimB);
1283: PetscSectionSetFieldDof(coordSectionB, v, 0, cDimB);
1284: DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT);
1285: }
1286: PetscSectionSetUp(coordSectionB);
1287: PetscSectionGetStorageSize(coordSectionB, &coordSize);
1288: VecCreate(PETSC_COMM_SELF, &coordinatesB);
1289: PetscObjectSetName((PetscObject) coordinatesB, "coordinates");
1290: VecSetSizes(coordinatesB, coordSize, PETSC_DETERMINE);
1291: VecSetBlockSize(coordinatesB, cDimB);
1292: VecSetType(coordinatesB,VECSTANDARD);
1294: DMGetCoordinateSection(idm, &coordSectionA);
1295: DMGetCoordinatesLocal(idm, &coordinatesA);
1296: VecGetArray(coordinatesB, &coordsB);
1297: VecGetArrayRead(coordinatesA, &coordsA);
1298: for (v = vStart; v < vEnd; ++v) {
1299: const PetscScalar *cptr;
1300: PetscReal ones2[2] = { 0., 1.}, ones3[3] = { 0., 0., 1.};
1301: PetscReal normal[3];
1302: PetscReal norm, h = height/layers;
1303: PetscInt offA, d, cDimA = cDim;
1305: if (normals) {for (d = 0; d < cDimB; ++d) normal[d] = normals[cDimB*(v - vStart)+d];}
1306: else if (haveCLNormal) {for (d = 0; d < cDimB; ++d) normal[d] = clNormal[d];}
1307: else if (extNormal) {for (d = 0; d < cDimB; ++d) normal[d] = extNormal[d];}
1308: else if (cDimB == 2) {for (d = 0; d < cDimB; ++d) normal[d] = ones2[d];}
1309: else if (cDimB == 3) {for (d = 0; d < cDimB; ++d) normal[d] = ones3[d];}
1310: else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unable to determine normal for extrusion");
1311: for (d = 0, norm = 0.0; d < cDimB; ++d) norm += normal[d]*normal[d];
1312: for (d = 0; d < cDimB; ++d) normal[d] *= 1./PetscSqrtReal(norm);
1314: PetscSectionGetOffset(coordSectionA, v, &offA);
1315: cptr = coordsA + offA;
1316: for (l = 0; l < layers+1; ++l) {
1317: PetscInt offB, d, newV;
1319: newV = orderHeight ? (layers+1)*(v -vStart) + l + numCells : (vEnd -vStart)*l + (v -vStart) + numCells;
1320: PetscSectionGetOffset(coordSectionB, newV, &offB);
1321: for (d = 0; d < cDimA; ++d) { coordsB[offB+d] = cptr[d]; }
1322: for (d = 0; d < cDimB; ++d) { coordsB[offB+d] += l ? normal[d]*h : 0.0; }
1323: cptr = coordsB + offB;
1324: cDimA = cDimB;
1325: }
1326: }
1327: VecRestoreArrayRead(coordinatesA, &coordsA);
1328: VecRestoreArray(coordinatesB, &coordsB);
1329: DMSetCoordinatesLocal(*dm, coordinatesB);
1330: VecDestroy(&coordinatesB);
1331: PetscFree(normals);
1332: if (interpolate) {
1333: DM idm;
1335: DMPlexInterpolate(*dm, &idm);
1336: DMPlexCopyCoordinates(*dm, idm);
1337: DMDestroy(dm);
1338: *dm = idm;
1339: }
1340: return(0);
1341: }
1343: /*@C
1344: DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database.
1346: Logically Collective on dm
1348: Input Parameters:
1349: + dm - the DM context
1350: - prefix - the prefix to prepend to all option names
1352: Notes:
1353: A hyphen (-) must NOT be given at the beginning of the prefix name.
1354: The first character of all runtime options is AUTOMATICALLY the hyphen.
1356: Level: advanced
1358: .seealso: SNESSetFromOptions()
1359: @*/
1360: PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[])
1361: {
1362: DM_Plex *mesh = (DM_Plex *) dm->data;
1367: PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);
1368: PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);
1369: return(0);
1370: }
1372: /*@
1373: DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra.
1375: Collective
1377: Input Parameters:
1378: + comm - The communicator for the DM object
1379: . numRefine - The number of regular refinements to the basic 5 cell structure
1380: - periodicZ - The boundary type for the Z direction
1382: Output Parameter:
1383: . dm - The DM object
1385: Note: Here is the output numbering looking from the bottom of the cylinder:
1386: $ 17-----14
1387: $ | |
1388: $ | 2 |
1389: $ | |
1390: $ 17-----8-----7-----14
1391: $ | | | |
1392: $ | 3 | 0 | 1 |
1393: $ | | | |
1394: $ 19-----5-----6-----13
1395: $ | |
1396: $ | 4 |
1397: $ | |
1398: $ 19-----13
1399: $
1400: $ and up through the top
1401: $
1402: $ 18-----16
1403: $ | |
1404: $ | 2 |
1405: $ | |
1406: $ 18----10----11-----16
1407: $ | | | |
1408: $ | 3 | 0 | 1 |
1409: $ | | | |
1410: $ 20-----9----12-----15
1411: $ | |
1412: $ | 4 |
1413: $ | |
1414: $ 20-----15
1416: Level: beginner
1418: .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1419: @*/
1420: PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, PetscInt numRefine, DMBoundaryType periodicZ, DM *dm)
1421: {
1422: const PetscInt dim = 3;
1423: PetscInt numCells, numVertices, r;
1424: PetscMPIInt rank;
1429: MPI_Comm_rank(comm, &rank);
1430: if (numRefine < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of refinements %D cannot be negative", numRefine);
1431: DMCreate(comm, dm);
1432: DMSetType(*dm, DMPLEX);
1433: DMSetDimension(*dm, dim);
1434: /* Create topology */
1435: {
1436: PetscInt cone[8], c;
1438: numCells = !rank ? 5 : 0;
1439: numVertices = !rank ? 16 : 0;
1440: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1441: numCells *= 3;
1442: numVertices = !rank ? 24 : 0;
1443: }
1444: DMPlexSetChart(*dm, 0, numCells+numVertices);
1445: for (c = 0; c < numCells; c++) {DMPlexSetConeSize(*dm, c, 8);}
1446: DMSetUp(*dm);
1447: if (!rank) {
1448: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1449: cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16;
1450: cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34;
1451: DMPlexSetCone(*dm, 0, cone);
1452: cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23;
1453: cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */
1454: DMPlexSetCone(*dm, 1, cone);
1455: cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17;
1456: cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38;
1457: DMPlexSetCone(*dm, 2, cone);
1458: cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15;
1459: cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38;
1460: DMPlexSetCone(*dm, 3, cone);
1461: cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23;
1462: cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31;
1463: DMPlexSetCone(*dm, 4, cone);
1465: cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32;
1466: cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20;
1467: DMPlexSetCone(*dm, 5, cone);
1468: cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36;
1469: cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21;
1470: DMPlexSetCone(*dm, 6, cone);
1471: cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33;
1472: cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28;
1473: DMPlexSetCone(*dm, 7, cone);
1474: cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31;
1475: cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28;
1476: DMPlexSetCone(*dm, 8, cone);
1477: cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36;
1478: cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19;
1479: DMPlexSetCone(*dm, 9, cone);
1481: cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22;
1482: cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18;
1483: DMPlexSetCone(*dm, 10, cone);
1484: cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25;
1485: cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17;
1486: DMPlexSetCone(*dm, 11, cone);
1487: cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21;
1488: cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27;
1489: DMPlexSetCone(*dm, 12, cone);
1490: cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19;
1491: cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27;
1492: DMPlexSetCone(*dm, 13, cone);
1493: cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25;
1494: cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15;
1495: DMPlexSetCone(*dm, 14, cone);
1496: } else {
1497: cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6;
1498: cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10;
1499: DMPlexSetCone(*dm, 0, cone);
1500: cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13;
1501: cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11;
1502: DMPlexSetCone(*dm, 1, cone);
1503: cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7;
1504: cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18;
1505: DMPlexSetCone(*dm, 2, cone);
1506: cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5;
1507: cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18;
1508: DMPlexSetCone(*dm, 3, cone);
1509: cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13;
1510: cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9;
1511: DMPlexSetCone(*dm, 4, cone);
1512: }
1513: }
1514: DMPlexSymmetrize(*dm);
1515: DMPlexStratify(*dm);
1516: }
1517: /* Interpolate */
1518: {
1519: DM idm;
1521: DMPlexInterpolate(*dm, &idm);
1522: DMDestroy(dm);
1523: *dm = idm;
1524: }
1525: /* Create cube geometry */
1526: {
1527: Vec coordinates;
1528: PetscSection coordSection;
1529: PetscScalar *coords;
1530: PetscInt coordSize, v;
1531: const PetscReal dis = 1.0/PetscSqrtReal(2.0);
1532: const PetscReal ds2 = dis/2.0;
1534: /* Build coordinates */
1535: DMGetCoordinateSection(*dm, &coordSection);
1536: PetscSectionSetNumFields(coordSection, 1);
1537: PetscSectionSetFieldComponents(coordSection, 0, dim);
1538: PetscSectionSetChart(coordSection, numCells, numCells+numVertices);
1539: for (v = numCells; v < numCells+numVertices; ++v) {
1540: PetscSectionSetDof(coordSection, v, dim);
1541: PetscSectionSetFieldDof(coordSection, v, 0, dim);
1542: }
1543: PetscSectionSetUp(coordSection);
1544: PetscSectionGetStorageSize(coordSection, &coordSize);
1545: VecCreate(PETSC_COMM_SELF, &coordinates);
1546: PetscObjectSetName((PetscObject) coordinates, "coordinates");
1547: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1548: VecSetBlockSize(coordinates, dim);
1549: VecSetType(coordinates,VECSTANDARD);
1550: VecGetArray(coordinates, &coords);
1551: if (!rank) {
1552: coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0;
1553: coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0;
1554: coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0;
1555: coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0;
1556: coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0;
1557: coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0;
1558: coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0;
1559: coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0;
1560: coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0;
1561: coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0;
1562: coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0;
1563: coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0;
1564: coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0;
1565: coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0;
1566: coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0;
1567: coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0;
1568: if (periodicZ == DM_BOUNDARY_PERIODIC) {
1569: /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5;
1570: /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5;
1571: /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5;
1572: /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5;
1573: /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5;
1574: /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5;
1575: /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5;
1576: /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5;
1577: }
1578: }
1579: VecRestoreArray(coordinates, &coords);
1580: DMSetCoordinatesLocal(*dm, coordinates);
1581: VecDestroy(&coordinates);
1582: }
1583: /* Create periodicity */
1584: if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) {
1585: PetscReal L[3];
1586: PetscReal maxCell[3];
1587: DMBoundaryType bdType[3];
1588: PetscReal lower[3] = {0.0, 0.0, 0.0};
1589: PetscReal upper[3] = {1.0, 1.0, 1.5};
1590: PetscInt i, numZCells = 3;
1592: bdType[0] = DM_BOUNDARY_NONE;
1593: bdType[1] = DM_BOUNDARY_NONE;
1594: bdType[2] = periodicZ;
1595: for (i = 0; i < dim; i++) {
1596: L[i] = upper[i] - lower[i];
1597: maxCell[i] = 1.1 * (L[i] / numZCells);
1598: }
1599: DMSetPeriodicity(*dm, PETSC_TRUE, maxCell, L, bdType);
1600: }
1601: /* Refine topology */
1602: for (r = 0; r < numRefine; ++r) {
1603: DM rdm = NULL;
1605: DMRefine(*dm, comm, &rdm);
1606: DMDestroy(dm);
1607: *dm = rdm;
1608: }
1609: /* Remap geometry to cylinder
1610: Interior square: Linear interpolation is correct
1611: The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing
1612: such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance
1614: phi = arctan(y/x)
1615: d_close = sqrt(1/8 + 1/4 sin^2(phi))
1616: d_far = sqrt(1/2 + sin^2(phi))
1618: so we remap them using
1620: x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close)
1621: y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close)
1623: If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y.
1624: */
1625: {
1626: Vec coordinates;
1627: PetscSection coordSection;
1628: PetscScalar *coords;
1629: PetscInt vStart, vEnd, v;
1630: const PetscReal dis = 1.0/PetscSqrtReal(2.0);
1631: const PetscReal ds2 = 0.5*dis;
1633: DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);
1634: DMGetCoordinateSection(*dm, &coordSection);
1635: DMGetCoordinatesLocal(*dm, &coordinates);
1636: VecGetArray(coordinates, &coords);
1637: for (v = vStart; v < vEnd; ++v) {
1638: PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc;
1639: PetscInt off;
1641: PetscSectionGetOffset(coordSection, v, &off);
1642: if ((PetscAbsScalar(coords[off+0]) <= ds2) && (PetscAbsScalar(coords[off+1]) <= ds2)) continue;
1643: x = PetscRealPart(coords[off]);
1644: y = PetscRealPart(coords[off+1]);
1645: phi = PetscAtan2Real(y, x);
1646: sinp = PetscSinReal(phi);
1647: cosp = PetscCosReal(phi);
1648: if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) {
1649: dc = PetscAbsReal(ds2/sinp);
1650: df = PetscAbsReal(dis/sinp);
1651: xc = ds2*x/PetscAbsReal(y);
1652: yc = ds2*PetscSignReal(y);
1653: } else {
1654: dc = PetscAbsReal(ds2/cosp);
1655: df = PetscAbsReal(dis/cosp);
1656: xc = ds2*PetscSignReal(x);
1657: yc = ds2*y/PetscAbsReal(x);
1658: }
1659: coords[off+0] = xc + (coords[off+0] - xc)*(1.0 - dc)/(df - dc);
1660: coords[off+1] = yc + (coords[off+1] - yc)*(1.0 - dc)/(df - dc);
1661: }
1662: VecRestoreArray(coordinates, &coords);
1663: if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) {
1664: DMLocalizeCoordinates(*dm);
1665: }
1666: }
1667: return(0);
1668: }
1670: /*@
1671: DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges.
1673: Collective
1675: Input Parameters:
1676: + comm - The communicator for the DM object
1677: . n - The number of wedges around the origin
1678: - interpolate - Create edges and faces
1680: Output Parameter:
1681: . dm - The DM object
1683: Level: beginner
1685: .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1686: @*/
1687: PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm)
1688: {
1689: const PetscInt dim = 3;
1690: PetscInt numCells, numVertices, v;
1691: PetscMPIInt rank;
1696: MPI_Comm_rank(comm, &rank);
1697: if (n < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n);
1698: DMCreate(comm, dm);
1699: DMSetType(*dm, DMPLEX);
1700: DMSetDimension(*dm, dim);
1701: /* Must create the celltype label here so that we do not automatically try to compute the types */
1702: DMCreateLabel(*dm, "celltype");
1703: /* Create topology */
1704: {
1705: PetscInt cone[6], c;
1707: numCells = !rank ? n : 0;
1708: numVertices = !rank ? 2*(n+1) : 0;
1709: DMPlexSetChart(*dm, 0, numCells+numVertices);
1710: for (c = 0; c < numCells; c++) {DMPlexSetConeSize(*dm, c, 6);}
1711: DMSetUp(*dm);
1712: for (c = 0; c < numCells; c++) {
1713: cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n;
1714: cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n;
1715: DMPlexSetCone(*dm, c, cone);
1716: DMPlexSetCellType(*dm, c, DM_POLYTOPE_TRI_PRISM_TENSOR);
1717: }
1718: DMPlexSymmetrize(*dm);
1719: DMPlexStratify(*dm);
1720: }
1721: for (v = numCells; v < numCells+numVertices; ++v) {
1722: DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT);
1723: }
1724: /* Interpolate */
1725: if (interpolate) {
1726: DM idm;
1728: DMPlexInterpolate(*dm, &idm);
1729: DMDestroy(dm);
1730: *dm = idm;
1731: }
1732: /* Create cylinder geometry */
1733: {
1734: Vec coordinates;
1735: PetscSection coordSection;
1736: PetscScalar *coords;
1737: PetscInt coordSize, c;
1739: /* Build coordinates */
1740: DMGetCoordinateSection(*dm, &coordSection);
1741: PetscSectionSetNumFields(coordSection, 1);
1742: PetscSectionSetFieldComponents(coordSection, 0, dim);
1743: PetscSectionSetChart(coordSection, numCells, numCells+numVertices);
1744: for (v = numCells; v < numCells+numVertices; ++v) {
1745: PetscSectionSetDof(coordSection, v, dim);
1746: PetscSectionSetFieldDof(coordSection, v, 0, dim);
1747: }
1748: PetscSectionSetUp(coordSection);
1749: PetscSectionGetStorageSize(coordSection, &coordSize);
1750: VecCreate(PETSC_COMM_SELF, &coordinates);
1751: PetscObjectSetName((PetscObject) coordinates, "coordinates");
1752: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1753: VecSetBlockSize(coordinates, dim);
1754: VecSetType(coordinates,VECSTANDARD);
1755: VecGetArray(coordinates, &coords);
1756: for (c = 0; c < numCells; c++) {
1757: 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;
1758: 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;
1759: }
1760: if (!rank) {
1761: coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0;
1762: coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0;
1763: }
1764: VecRestoreArray(coordinates, &coords);
1765: DMSetCoordinatesLocal(*dm, coordinates);
1766: VecDestroy(&coordinates);
1767: }
1768: return(0);
1769: }
1771: PETSC_STATIC_INLINE PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
1772: {
1773: PetscReal prod = 0.0;
1774: PetscInt i;
1775: for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]);
1776: return PetscSqrtReal(prod);
1777: }
1778: PETSC_STATIC_INLINE PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
1779: {
1780: PetscReal prod = 0.0;
1781: PetscInt i;
1782: for (i = 0; i < dim; ++i) prod += x[i]*y[i];
1783: return prod;
1784: }
1786: /* The first constant is the sphere radius */
1787: static void snapToSphere(PetscInt dim, PetscInt Nf, PetscInt NfAux,
1788: const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
1789: const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
1790: PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[])
1791: {
1792: PetscReal r = PetscRealPart(constants[0]);
1793: PetscReal norm2 = 0.0, fac;
1794: PetscInt n = uOff[1] - uOff[0], d;
1796: for (d = 0; d < n; ++d) norm2 += PetscSqr(PetscRealPart(u[d]));
1797: fac = r/PetscSqrtReal(norm2);
1798: for (d = 0; d < n; ++d) f0[d] = u[d]*fac;
1799: }
1801: /*@
1802: DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d.
1804: Collective
1806: Input Parameters:
1807: + comm - The communicator for the DM object
1808: . dim - The dimension
1809: . simplex - Use simplices, or tensor product cells
1810: - R - The radius
1812: Output Parameter:
1813: . dm - The DM object
1815: Level: beginner
1817: .seealso: DMPlexCreateBallMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1818: @*/
1819: PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscReal R, DM *dm)
1820: {
1821: const PetscInt embedDim = dim+1;
1822: PetscSection coordSection;
1823: Vec coordinates;
1824: PetscScalar *coords;
1825: PetscReal *coordsIn;
1826: PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e;
1827: PetscMPIInt rank;
1828: PetscErrorCode ierr;
1832: DMCreate(comm, dm);
1833: DMSetType(*dm, DMPLEX);
1834: DMSetDimension(*dm, dim);
1835: DMSetCoordinateDim(*dm, dim+1);
1836: MPI_Comm_rank(PetscObjectComm((PetscObject) *dm), &rank);
1837: switch (dim) {
1838: case 2:
1839: if (simplex) {
1840: DM idm;
1841: const PetscReal radius = PetscSqrtReal(1 + PETSC_PHI*PETSC_PHI)/(1.0 + PETSC_PHI);
1842: const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI) * (R/radius);
1843: const PetscInt degree = 5;
1844: PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)};
1845: PetscInt s[3] = {1, 1, 1};
1846: PetscInt cone[3];
1847: PetscInt *graph, p, i, j, k;
1849: vertex[0] *= R/radius; vertex[1] *= R/radius; vertex[2] *= R/radius;
1850: numCells = !rank ? 20 : 0;
1851: numVerts = !rank ? 12 : 0;
1852: firstVertex = numCells;
1853: /* Use icosahedron, which for a R-sphere has coordinates which are all cyclic permutations of
1855: (0, \pm 1/\phi+1, \pm \phi/\phi+1)
1857: where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
1858: length is then given by 2/(1+\phi) = 2 * 0.38197 = 0.76393.
1859: */
1860: /* Construct vertices */
1861: PetscCalloc1(numVerts * embedDim, &coordsIn);
1862: if (!rank) {
1863: for (p = 0, i = 0; p < embedDim; ++p) {
1864: for (s[1] = -1; s[1] < 2; s[1] += 2) {
1865: for (s[2] = -1; s[2] < 2; s[2] += 2) {
1866: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim];
1867: ++i;
1868: }
1869: }
1870: }
1871: }
1872: /* Construct graph */
1873: PetscCalloc1(numVerts * numVerts, &graph);
1874: for (i = 0; i < numVerts; ++i) {
1875: for (j = 0, k = 0; j < numVerts; ++j) {
1876: if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;}
1877: }
1878: if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree);
1879: }
1880: /* Build Topology */
1881: DMPlexSetChart(*dm, 0, numCells+numVerts);
1882: for (c = 0; c < numCells; c++) {
1883: DMPlexSetConeSize(*dm, c, embedDim);
1884: }
1885: DMSetUp(*dm); /* Allocate space for cones */
1886: /* Cells */
1887: for (i = 0, c = 0; i < numVerts; ++i) {
1888: for (j = 0; j < i; ++j) {
1889: for (k = 0; k < j; ++k) {
1890: if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) {
1891: cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k;
1892: /* Check orientation */
1893: {
1894: 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}}};
1895: PetscReal normal[3];
1896: PetscInt e, f;
1898: for (d = 0; d < embedDim; ++d) {
1899: normal[d] = 0.0;
1900: for (e = 0; e < embedDim; ++e) {
1901: for (f = 0; f < embedDim; ++f) {
1902: normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]);
1903: }
1904: }
1905: }
1906: if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;}
1907: }
1908: DMPlexSetCone(*dm, c++, cone);
1909: }
1910: }
1911: }
1912: }
1913: DMPlexSymmetrize(*dm);
1914: DMPlexStratify(*dm);
1915: PetscFree(graph);
1916: /* Interpolate mesh */
1917: DMPlexInterpolate(*dm, &idm);
1918: DMDestroy(dm);
1919: *dm = idm;
1920: } else {
1921: /*
1922: 12-21--13
1923: | |
1924: 25 4 24
1925: | |
1926: 12-25--9-16--8-24--13
1927: | | | |
1928: 23 5 17 0 15 3 22
1929: | | | |
1930: 10-20--6-14--7-19--11
1931: | |
1932: 20 1 19
1933: | |
1934: 10-18--11
1935: | |
1936: 23 2 22
1937: | |
1938: 12-21--13
1939: */
1940: PetscInt cone[4], ornt[4];
1942: numCells = !rank ? 6 : 0;
1943: numEdges = !rank ? 12 : 0;
1944: numVerts = !rank ? 8 : 0;
1945: firstVertex = numCells;
1946: firstEdge = numCells + numVerts;
1947: /* Build Topology */
1948: DMPlexSetChart(*dm, 0, numCells+numEdges+numVerts);
1949: for (c = 0; c < numCells; c++) {
1950: DMPlexSetConeSize(*dm, c, 4);
1951: }
1952: for (e = firstEdge; e < firstEdge+numEdges; ++e) {
1953: DMPlexSetConeSize(*dm, e, 2);
1954: }
1955: DMSetUp(*dm); /* Allocate space for cones */
1956: if (!rank) {
1957: /* Cell 0 */
1958: cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17;
1959: DMPlexSetCone(*dm, 0, cone);
1960: ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0;
1961: DMPlexSetConeOrientation(*dm, 0, ornt);
1962: /* Cell 1 */
1963: cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20;
1964: DMPlexSetCone(*dm, 1, cone);
1965: ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0;
1966: DMPlexSetConeOrientation(*dm, 1, ornt);
1967: /* Cell 2 */
1968: cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23;
1969: DMPlexSetCone(*dm, 2, cone);
1970: ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0;
1971: DMPlexSetConeOrientation(*dm, 2, ornt);
1972: /* Cell 3 */
1973: cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15;
1974: DMPlexSetCone(*dm, 3, cone);
1975: ornt[0] = -2; ornt[1] = -2; ornt[2] = 0; ornt[3] = -2;
1976: DMPlexSetConeOrientation(*dm, 3, ornt);
1977: /* Cell 4 */
1978: cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25;
1979: DMPlexSetCone(*dm, 4, cone);
1980: ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = 0;
1981: DMPlexSetConeOrientation(*dm, 4, ornt);
1982: /* Cell 5 */
1983: cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23;
1984: DMPlexSetCone(*dm, 5, cone);
1985: ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = -2;
1986: DMPlexSetConeOrientation(*dm, 5, ornt);
1987: /* Edges */
1988: cone[0] = 6; cone[1] = 7;
1989: DMPlexSetCone(*dm, 14, cone);
1990: cone[0] = 7; cone[1] = 8;
1991: DMPlexSetCone(*dm, 15, cone);
1992: cone[0] = 8; cone[1] = 9;
1993: DMPlexSetCone(*dm, 16, cone);
1994: cone[0] = 9; cone[1] = 6;
1995: DMPlexSetCone(*dm, 17, cone);
1996: cone[0] = 10; cone[1] = 11;
1997: DMPlexSetCone(*dm, 18, cone);
1998: cone[0] = 11; cone[1] = 7;
1999: DMPlexSetCone(*dm, 19, cone);
2000: cone[0] = 6; cone[1] = 10;
2001: DMPlexSetCone(*dm, 20, cone);
2002: cone[0] = 12; cone[1] = 13;
2003: DMPlexSetCone(*dm, 21, cone);
2004: cone[0] = 13; cone[1] = 11;
2005: DMPlexSetCone(*dm, 22, cone);
2006: cone[0] = 10; cone[1] = 12;
2007: DMPlexSetCone(*dm, 23, cone);
2008: cone[0] = 13; cone[1] = 8;
2009: DMPlexSetCone(*dm, 24, cone);
2010: cone[0] = 12; cone[1] = 9;
2011: DMPlexSetCone(*dm, 25, cone);
2012: }
2013: DMPlexSymmetrize(*dm);
2014: DMPlexStratify(*dm);
2015: /* Build coordinates */
2016: PetscCalloc1(numVerts * embedDim, &coordsIn);
2017: if (!rank) {
2018: coordsIn[0*embedDim+0] = -R; coordsIn[0*embedDim+1] = R; coordsIn[0*embedDim+2] = -R;
2019: coordsIn[1*embedDim+0] = R; coordsIn[1*embedDim+1] = R; coordsIn[1*embedDim+2] = -R;
2020: coordsIn[2*embedDim+0] = R; coordsIn[2*embedDim+1] = -R; coordsIn[2*embedDim+2] = -R;
2021: coordsIn[3*embedDim+0] = -R; coordsIn[3*embedDim+1] = -R; coordsIn[3*embedDim+2] = -R;
2022: coordsIn[4*embedDim+0] = -R; coordsIn[4*embedDim+1] = R; coordsIn[4*embedDim+2] = R;
2023: coordsIn[5*embedDim+0] = R; coordsIn[5*embedDim+1] = R; coordsIn[5*embedDim+2] = R;
2024: coordsIn[6*embedDim+0] = -R; coordsIn[6*embedDim+1] = -R; coordsIn[6*embedDim+2] = R;
2025: coordsIn[7*embedDim+0] = R; coordsIn[7*embedDim+1] = -R; coordsIn[7*embedDim+2] = R;
2026: }
2027: }
2028: break;
2029: case 3:
2030: if (simplex) {
2031: DM idm;
2032: const PetscReal edgeLen = 1.0/PETSC_PHI;
2033: PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5};
2034: PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0};
2035: PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0};
2036: const PetscInt degree = 12;
2037: PetscInt s[4] = {1, 1, 1};
2038: 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},
2039: {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}};
2040: PetscInt cone[4];
2041: PetscInt *graph, p, i, j, k, l;
2043: vertexA[0] *= R; vertexA[1] *= R; vertexA[2] *= R; vertexA[3] *= R;
2044: vertexB[0] *= R; vertexB[1] *= R; vertexB[2] *= R; vertexB[3] *= R;
2045: vertexC[0] *= R; vertexC[1] *= R; vertexC[2] *= R; vertexC[3] *= R;
2046: numCells = !rank ? 600 : 0;
2047: numVerts = !rank ? 120 : 0;
2048: firstVertex = numCells;
2049: /* Use the 600-cell, which for a unit sphere has coordinates which are
2051: 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16
2052: (\pm 1, 0, 0, 0) all cyclic permutations 8
2053: 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96
2055: where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
2056: length is then given by 1/\phi = 0.61803.
2058: http://buzzard.pugetsound.edu/sage-practice/ch03s03.html
2059: http://mathworld.wolfram.com/600-Cell.html
2060: */
2061: /* Construct vertices */
2062: PetscCalloc1(numVerts * embedDim, &coordsIn);
2063: i = 0;
2064: if (!rank) {
2065: for (s[0] = -1; s[0] < 2; s[0] += 2) {
2066: for (s[1] = -1; s[1] < 2; s[1] += 2) {
2067: for (s[2] = -1; s[2] < 2; s[2] += 2) {
2068: for (s[3] = -1; s[3] < 2; s[3] += 2) {
2069: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d];
2070: ++i;
2071: }
2072: }
2073: }
2074: }
2075: for (p = 0; p < embedDim; ++p) {
2076: s[1] = s[2] = s[3] = 1;
2077: for (s[0] = -1; s[0] < 2; s[0] += 2) {
2078: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim];
2079: ++i;
2080: }
2081: }
2082: for (p = 0; p < 12; ++p) {
2083: s[3] = 1;
2084: for (s[0] = -1; s[0] < 2; s[0] += 2) {
2085: for (s[1] = -1; s[1] < 2; s[1] += 2) {
2086: for (s[2] = -1; s[2] < 2; s[2] += 2) {
2087: for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]];
2088: ++i;
2089: }
2090: }
2091: }
2092: }
2093: }
2094: if (i != numVerts) SETERRQ2(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts);
2095: /* Construct graph */
2096: PetscCalloc1(numVerts * numVerts, &graph);
2097: for (i = 0; i < numVerts; ++i) {
2098: for (j = 0, k = 0; j < numVerts; ++j) {
2099: if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;}
2100: }
2101: if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree);
2102: }
2103: /* Build Topology */
2104: DMPlexSetChart(*dm, 0, numCells+numVerts);
2105: for (c = 0; c < numCells; c++) {
2106: DMPlexSetConeSize(*dm, c, embedDim);
2107: }
2108: DMSetUp(*dm); /* Allocate space for cones */
2109: /* Cells */
2110: if (!rank) {
2111: for (i = 0, c = 0; i < numVerts; ++i) {
2112: for (j = 0; j < i; ++j) {
2113: for (k = 0; k < j; ++k) {
2114: for (l = 0; l < k; ++l) {
2115: if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] &&
2116: graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) {
2117: cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l;
2118: /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */
2119: {
2120: const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
2121: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}},
2122: {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}},
2123: {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}},
2125: {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}},
2126: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
2127: {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}},
2128: {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}},
2130: {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}},
2131: {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}},
2132: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
2133: {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}},
2135: {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}},
2136: {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}},
2137: {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}},
2138: {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}};
2139: PetscReal normal[4];
2140: PetscInt e, f, g;
2142: for (d = 0; d < embedDim; ++d) {
2143: normal[d] = 0.0;
2144: for (e = 0; e < embedDim; ++e) {
2145: for (f = 0; f < embedDim; ++f) {
2146: for (g = 0; g < embedDim; ++g) {
2147: 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]);
2148: }
2149: }
2150: }
2151: }
2152: if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;}
2153: }
2154: DMPlexSetCone(*dm, c++, cone);
2155: }
2156: }
2157: }
2158: }
2159: }
2160: }
2161: DMPlexSymmetrize(*dm);
2162: DMPlexStratify(*dm);
2163: PetscFree(graph);
2164: /* Interpolate mesh */
2165: DMPlexInterpolate(*dm, &idm);
2166: DMDestroy(dm);
2167: *dm = idm;
2168: break;
2169: }
2170: default: SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim);
2171: }
2172: /* Create coordinates */
2173: DMGetCoordinateSection(*dm, &coordSection);
2174: PetscSectionSetNumFields(coordSection, 1);
2175: PetscSectionSetFieldComponents(coordSection, 0, embedDim);
2176: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);
2177: for (v = firstVertex; v < firstVertex+numVerts; ++v) {
2178: PetscSectionSetDof(coordSection, v, embedDim);
2179: PetscSectionSetFieldDof(coordSection, v, 0, embedDim);
2180: }
2181: PetscSectionSetUp(coordSection);
2182: PetscSectionGetStorageSize(coordSection, &coordSize);
2183: VecCreate(PETSC_COMM_SELF, &coordinates);
2184: VecSetBlockSize(coordinates, embedDim);
2185: PetscObjectSetName((PetscObject) coordinates, "coordinates");
2186: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
2187: VecSetType(coordinates,VECSTANDARD);
2188: VecGetArray(coordinates, &coords);
2189: for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];}
2190: VecRestoreArray(coordinates, &coords);
2191: DMSetCoordinatesLocal(*dm, coordinates);
2192: VecDestroy(&coordinates);
2193: PetscFree(coordsIn);
2194: /* Create coordinate function space */
2195: {
2196: DM cdm;
2197: PetscDS cds;
2198: PetscFE fe;
2199: PetscScalar radius = R;
2200: PetscInt dT, dE;
2202: DMGetCoordinateDM(*dm, &cdm);
2203: DMGetDimension(*dm, &dT);
2204: DMGetCoordinateDim(*dm, &dE);
2205: PetscFECreateLagrange(PETSC_COMM_SELF, dT, dE, simplex, 1, -1, &fe);
2206: DMSetField(cdm, 0, NULL, (PetscObject) fe);
2207: PetscFEDestroy(&fe);
2208: DMCreateDS(cdm);
2210: DMGetDS(cdm, &cds);
2211: PetscDSSetConstants(cds, 1, &radius);
2212: }
2213: ((DM_Plex *) (*dm)->data)->coordFunc = snapToSphere;
2214: return(0);
2215: }
2217: /*@
2218: DMPlexCreateBallMesh - Creates a simplex mesh on the d-dimensional ball, B^d.
2220: Collective
2222: Input Parameters:
2223: + comm - The communicator for the DM object
2224: . dim - The dimension
2225: - R - The radius
2227: Output Parameter:
2228: . dm - The DM object
2230: Options Database Keys:
2231: - bd_dm_refine - This will refine the surface mesh preserving the sphere geometry
2233: Level: beginner
2235: .seealso: DMPlexCreateSphereMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
2236: @*/
2237: PetscErrorCode DMPlexCreateBallMesh(MPI_Comm comm, PetscInt dim, PetscReal R, DM *dm)
2238: {
2239: DM sdm;
2240: DMLabel bdlabel;
2244: DMPlexCreateSphereMesh(comm, dim-1, PETSC_TRUE, R, &sdm);
2245: PetscObjectSetOptionsPrefix((PetscObject) sdm, "bd_");
2246: DMSetFromOptions(sdm);
2247: DMPlexGenerate(sdm, NULL, PETSC_TRUE, dm);
2248: DMDestroy(&sdm);
2249: DMCreateLabel(*dm, "marker");
2250: DMGetLabel(*dm, "marker", &bdlabel);
2251: DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);
2252: DMPlexLabelComplete(*dm, bdlabel);
2253: return(0);
2254: }
2256: /* External function declarations here */
2257: extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling);
2258: extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat);
2259: extern PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mat);
2260: extern PetscErrorCode DMCreateLocalSection_Plex(DM dm);
2261: extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm);
2262: extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J);
2263: extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm);
2264: extern PetscErrorCode DMCreateCoordinateField_Plex(DM dm, DMField *field);
2265: PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm);
2266: extern PetscErrorCode DMSetUp_Plex(DM dm);
2267: extern PetscErrorCode DMDestroy_Plex(DM dm);
2268: extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer);
2269: extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer);
2270: extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm);
2271: extern PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm);
2272: static PetscErrorCode DMInitialize_Plex(DM dm);
2274: /* Replace dm with the contents of dmNew
2275: - Share the DM_Plex structure
2276: - Share the coordinates
2277: - Share the SF
2278: */
2279: static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew)
2280: {
2281: PetscSF sf;
2282: DM coordDM, coarseDM;
2283: DMField coordField;
2284: Vec coords;
2285: PetscBool isper;
2286: const PetscReal *maxCell, *L;
2287: const DMBoundaryType *bd;
2288: PetscErrorCode ierr;
2291: DMGetPointSF(dmNew, &sf);
2292: DMSetPointSF(dm, sf);
2293: DMGetCoordinateDM(dmNew, &coordDM);
2294: DMGetCoordinatesLocal(dmNew, &coords);
2295: DMGetCoordinateField(dmNew, &coordField);
2296: DMSetCoordinateDM(dm, coordDM);
2297: DMSetCoordinatesLocal(dm, coords);
2298: DMSetCoordinateField(dm, coordField);
2299: DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);
2300: DMSetPeriodicity(dmNew, isper, maxCell, L, bd);
2301: DMDestroy_Plex(dm);
2302: DMInitialize_Plex(dm);
2303: dm->data = dmNew->data;
2304: ((DM_Plex *) dmNew->data)->refct++;
2305: DMDestroyLabelLinkList_Internal(dm);
2306: DMCopyLabels(dmNew, dm, PETSC_OWN_POINTER, PETSC_TRUE);
2307: DMGetCoarseDM(dmNew,&coarseDM);
2308: DMSetCoarseDM(dm,coarseDM);
2309: return(0);
2310: }
2312: /* Swap dm with the contents of dmNew
2313: - Swap the DM_Plex structure
2314: - Swap the coordinates
2315: - Swap the point PetscSF
2316: */
2317: static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB)
2318: {
2319: DM coordDMA, coordDMB;
2320: Vec coordsA, coordsB;
2321: PetscSF sfA, sfB;
2322: void *tmp;
2323: DMLabelLink listTmp;
2324: DMLabel depthTmp;
2325: PetscInt tmpI;
2326: PetscErrorCode ierr;
2329: DMGetPointSF(dmA, &sfA);
2330: DMGetPointSF(dmB, &sfB);
2331: PetscObjectReference((PetscObject) sfA);
2332: DMSetPointSF(dmA, sfB);
2333: DMSetPointSF(dmB, sfA);
2334: PetscObjectDereference((PetscObject) sfA);
2336: DMGetCoordinateDM(dmA, &coordDMA);
2337: DMGetCoordinateDM(dmB, &coordDMB);
2338: PetscObjectReference((PetscObject) coordDMA);
2339: DMSetCoordinateDM(dmA, coordDMB);
2340: DMSetCoordinateDM(dmB, coordDMA);
2341: PetscObjectDereference((PetscObject) coordDMA);
2343: DMGetCoordinatesLocal(dmA, &coordsA);
2344: DMGetCoordinatesLocal(dmB, &coordsB);
2345: PetscObjectReference((PetscObject) coordsA);
2346: DMSetCoordinatesLocal(dmA, coordsB);
2347: DMSetCoordinatesLocal(dmB, coordsA);
2348: PetscObjectDereference((PetscObject) coordsA);
2350: tmp = dmA->data;
2351: dmA->data = dmB->data;
2352: dmB->data = tmp;
2353: listTmp = dmA->labels;
2354: dmA->labels = dmB->labels;
2355: dmB->labels = listTmp;
2356: depthTmp = dmA->depthLabel;
2357: dmA->depthLabel = dmB->depthLabel;
2358: dmB->depthLabel = depthTmp;
2359: depthTmp = dmA->celltypeLabel;
2360: dmA->celltypeLabel = dmB->celltypeLabel;
2361: dmB->celltypeLabel = depthTmp;
2362: tmpI = dmA->levelup;
2363: dmA->levelup = dmB->levelup;
2364: dmB->levelup = tmpI;
2365: return(0);
2366: }
2368: PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm)
2369: {
2370: DM_Plex *mesh = (DM_Plex*) dm->data;
2371: PetscBool flg;
2375: /* Handle viewing */
2376: PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL);
2377: PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL,0);
2378: PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL);
2379: PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL,0);
2380: DMMonitorSetFromOptions(dm, "-dm_plex_monitor_throughput", "Monitor the simulation throughput", "DMPlexMonitorThroughput", DMPlexMonitorThroughput, NULL, &flg);
2381: if (flg) {PetscLogDefaultBegin();}
2382: /* Point Location */
2383: PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL);
2384: /* Partitioning and distribution */
2385: PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL);
2386: /* Generation and remeshing */
2387: PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL);
2388: /* Projection behavior */
2389: PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL,0);
2390: PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);
2391: PetscOptionsEnum("-dm_plex_cell_refiner", "Strategy for cell refinment", "ex40.c", DMPlexCellRefinerTypes, (PetscEnum) mesh->cellRefiner, (PetscEnum *) &mesh->cellRefiner, NULL);
2392: /* Checking structure */
2393: {
2394: PetscBool flg = PETSC_FALSE, flg2 = PETSC_FALSE, all = PETSC_FALSE;
2396: PetscOptionsBool("-dm_plex_check_all", "Perform all checks", NULL, PETSC_FALSE, &all, &flg2);
2397: PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2);
2398: if (all || (flg && flg2)) {DMPlexCheckSymmetry(dm);}
2399: 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);
2400: if (all || (flg && flg2)) {DMPlexCheckSkeleton(dm, 0);}
2401: 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);
2402: if (all || (flg && flg2)) {DMPlexCheckFaces(dm, 0);}
2403: PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2);
2404: if (all || (flg && flg2)) {DMPlexCheckGeometry(dm);}
2405: PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2);
2406: if (all || (flg && flg2)) {DMPlexCheckPointSF(dm);}
2407: PetscOptionsBool("-dm_plex_check_interface_cones", "Check points on inter-partition interfaces have conforming order of cone points", "DMPlexCheckInterfaceCones", PETSC_FALSE, &flg, &flg2);
2408: if (all || (flg && flg2)) {DMPlexCheckInterfaceCones(dm);}
2409: PetscOptionsBool("-dm_plex_check_cell_shape", "Check cell shape", "DMPlexCheckCellShape", PETSC_FALSE, &flg, &flg2);
2410: if (flg && flg2) {DMPlexCheckCellShape(dm, PETSC_TRUE, PETSC_DETERMINE);}
2411: }
2413: PetscPartitionerSetFromOptions(mesh->partitioner);
2414: return(0);
2415: }
2417: static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm)
2418: {
2419: PetscInt prerefine = 0, refine = 0, r, coarsen = 0, overlap = 0;
2420: PetscBool distribute = PETSC_FALSE, isHierarchy;
2425: PetscOptionsHead(PetscOptionsObject,"DMPlex Options");
2426: /* Handle DMPlex refinement before distribution */
2427: PetscOptionsBoundedInt("-dm_refine_pre", "The number of uniform refinements before distribution", "DMCreate", prerefine, &prerefine, NULL,0);
2428: if (prerefine) {DMPlexSetRefinementUniform(dm, PETSC_TRUE);}
2429: for (r = 0; r < prerefine; ++r) {
2430: DM rdm;
2431: PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc;
2433: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2434: DMRefine(dm, PetscObjectComm((PetscObject) dm), &rdm);
2435: /* Total hack since we do not pass in a pointer */
2436: DMPlexReplace_Static(dm, rdm);
2437: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2438: if (coordFunc) {
2439: DMPlexRemapGeometry(dm, 0.0, coordFunc);
2440: ((DM_Plex*) dm->data)->coordFunc = coordFunc;
2441: }
2442: DMDestroy(&rdm);
2443: }
2444: /* Handle DMPlex distribution */
2445: PetscOptionsBool("-dm_distribute", "Flag to redistribute a mesh among processes", "DMCreate", distribute, &distribute, NULL);
2446: PetscOptionsBoundedInt("-dm_distribute_overlap", "The size of the overlap halo", "DMCreate", overlap, &overlap, NULL, 0);
2447: if (distribute) {
2448: DM pdm = NULL;
2449: PetscPartitioner part;
2451: DMPlexGetPartitioner(dm, &part);
2452: PetscPartitionerSetFromOptions(part);
2453: DMPlexDistribute(dm, overlap, NULL, &pdm);
2454: if (pdm) {
2455: DMPlexReplace_Static(dm, pdm);
2456: DMDestroy(&pdm);
2457: }
2458: }
2459: /* Handle DMPlex refinement */
2460: PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL,0);
2461: PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy,0);
2462: if (refine) {DMPlexSetRefinementUniform(dm, PETSC_TRUE);}
2463: if (refine && isHierarchy) {
2464: DM *dms, coarseDM;
2466: DMGetCoarseDM(dm, &coarseDM);
2467: PetscObjectReference((PetscObject)coarseDM);
2468: PetscMalloc1(refine,&dms);
2469: DMRefineHierarchy(dm, refine, dms);
2470: /* Total hack since we do not pass in a pointer */
2471: DMPlexSwap_Static(dm, dms[refine-1]);
2472: if (refine == 1) {
2473: DMSetCoarseDM(dm, dms[0]);
2474: DMPlexSetRegularRefinement(dm, PETSC_TRUE);
2475: } else {
2476: DMSetCoarseDM(dm, dms[refine-2]);
2477: DMPlexSetRegularRefinement(dm, PETSC_TRUE);
2478: DMSetCoarseDM(dms[0], dms[refine-1]);
2479: DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);
2480: }
2481: DMSetCoarseDM(dms[refine-1], coarseDM);
2482: PetscObjectDereference((PetscObject)coarseDM);
2483: /* Free DMs */
2484: for (r = 0; r < refine; ++r) {
2485: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);
2486: DMDestroy(&dms[r]);
2487: }
2488: PetscFree(dms);
2489: } else {
2490: for (r = 0; r < refine; ++r) {
2491: DM refinedMesh;
2492: PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc;
2494: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2495: DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);
2496: /* Total hack since we do not pass in a pointer */
2497: DMPlexReplace_Static(dm, refinedMesh);
2498: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2499: if (coordFunc) {
2500: DMPlexRemapGeometry(dm, 0.0, coordFunc);
2501: ((DM_Plex*) dm->data)->coordFunc = coordFunc;
2502: }
2503: DMDestroy(&refinedMesh);
2504: }
2505: }
2506: /* Handle DMPlex coarsening */
2507: PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL,0);
2508: PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy,0);
2509: if (coarsen && isHierarchy) {
2510: DM *dms;
2512: PetscMalloc1(coarsen, &dms);
2513: DMCoarsenHierarchy(dm, coarsen, dms);
2514: /* Free DMs */
2515: for (r = 0; r < coarsen; ++r) {
2516: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);
2517: DMDestroy(&dms[r]);
2518: }
2519: PetscFree(dms);
2520: } else {
2521: for (r = 0; r < coarsen; ++r) {
2522: DM coarseMesh;
2524: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2525: DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);
2526: /* Total hack since we do not pass in a pointer */
2527: DMPlexReplace_Static(dm, coarseMesh);
2528: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2529: DMDestroy(&coarseMesh);
2530: }
2531: }
2532: /* Handle */
2533: DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2534: PetscOptionsTail();
2535: return(0);
2536: }
2538: static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec)
2539: {
2543: DMCreateGlobalVector_Section_Private(dm,vec);
2544: /* VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM); */
2545: VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);
2546: VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);
2547: VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);
2548: VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);
2549: return(0);
2550: }
2552: static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec)
2553: {
2557: DMCreateLocalVector_Section_Private(dm,vec);
2558: VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);
2559: VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);
2560: return(0);
2561: }
2563: static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd)
2564: {
2565: PetscInt depth, d;
2569: DMPlexGetDepth(dm, &depth);
2570: if (depth == 1) {
2571: DMGetDimension(dm, &d);
2572: if (dim == 0) {DMPlexGetDepthStratum(dm, dim, pStart, pEnd);}
2573: else if (dim == d) {DMPlexGetDepthStratum(dm, 1, pStart, pEnd);}
2574: else {*pStart = 0; *pEnd = 0;}
2575: } else {
2576: DMPlexGetDepthStratum(dm, dim, pStart, pEnd);
2577: }
2578: return(0);
2579: }
2581: static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[])
2582: {
2583: PetscSF sf;
2584: PetscInt niranks, njranks, n;
2585: const PetscMPIInt *iranks, *jranks;
2586: DM_Plex *data = (DM_Plex*) dm->data;
2587: PetscErrorCode ierr;
2590: DMGetPointSF(dm, &sf);
2591: if (!data->neighbors) {
2592: PetscSFGetRootRanks(sf, &njranks, &jranks, NULL, NULL, NULL);
2593: PetscSFGetLeafRanks(sf, &niranks, &iranks, NULL, NULL);
2594: PetscMalloc1(njranks + niranks + 1, &data->neighbors);
2595: PetscArraycpy(data->neighbors + 1, jranks, njranks);
2596: PetscArraycpy(data->neighbors + njranks + 1, iranks, niranks);
2597: n = njranks + niranks;
2598: PetscSortRemoveDupsMPIInt(&n, data->neighbors + 1);
2599: /* The following cast should never fail: can't have more neighbors than PETSC_MPI_INT_MAX */
2600: PetscMPIIntCast(n, data->neighbors);
2601: }
2602: if (nranks) *nranks = data->neighbors[0];
2603: if (ranks) {
2604: if (data->neighbors[0]) *ranks = data->neighbors + 1;
2605: else *ranks = NULL;
2606: }
2607: return(0);
2608: }
2610: static PetscErrorCode DMInitialize_Plex(DM dm)
2611: {
2615: dm->ops->view = DMView_Plex;
2616: dm->ops->load = DMLoad_Plex;
2617: dm->ops->setfromoptions = DMSetFromOptions_Plex;
2618: dm->ops->clone = DMClone_Plex;
2619: dm->ops->setup = DMSetUp_Plex;
2620: dm->ops->createlocalsection = DMCreateLocalSection_Plex;
2621: dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex;
2622: dm->ops->createglobalvector = DMCreateGlobalVector_Plex;
2623: dm->ops->createlocalvector = DMCreateLocalVector_Plex;
2624: dm->ops->getlocaltoglobalmapping = NULL;
2625: dm->ops->createfieldis = NULL;
2626: dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex;
2627: dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex;
2628: dm->ops->getcoloring = NULL;
2629: dm->ops->creatematrix = DMCreateMatrix_Plex;
2630: dm->ops->createinterpolation = DMCreateInterpolation_Plex;
2631: dm->ops->createmassmatrix = DMCreateMassMatrix_Plex;
2632: dm->ops->createinjection = DMCreateInjection_Plex;
2633: dm->ops->refine = DMRefine_Plex;
2634: dm->ops->coarsen = DMCoarsen_Plex;
2635: dm->ops->refinehierarchy = DMRefineHierarchy_Plex;
2636: dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex;
2637: dm->ops->adaptlabel = DMAdaptLabel_Plex;
2638: dm->ops->adaptmetric = DMAdaptMetric_Plex;
2639: dm->ops->globaltolocalbegin = NULL;
2640: dm->ops->globaltolocalend = NULL;
2641: dm->ops->localtoglobalbegin = NULL;
2642: dm->ops->localtoglobalend = NULL;
2643: dm->ops->destroy = DMDestroy_Plex;
2644: dm->ops->createsubdm = DMCreateSubDM_Plex;
2645: dm->ops->createsuperdm = DMCreateSuperDM_Plex;
2646: dm->ops->getdimpoints = DMGetDimPoints_Plex;
2647: dm->ops->locatepoints = DMLocatePoints_Plex;
2648: dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex;
2649: dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex;
2650: dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex;
2651: dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex;
2652: dm->ops->projectbdfieldlabellocal = DMProjectBdFieldLabelLocal_Plex;
2653: dm->ops->computel2diff = DMComputeL2Diff_Plex;
2654: dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex;
2655: dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex;
2656: dm->ops->getneighbors = DMGetNeighbors_Plex;
2657: PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);
2658: PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertTimeDerviativeBoundaryValues_C",DMPlexInsertTimeDerivativeBoundaryValues_Plex);
2659: PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);
2660: PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C",DMCreateNeumannOverlap_Plex);
2661: PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex);
2662: return(0);
2663: }
2665: PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm)
2666: {
2667: DM_Plex *mesh = (DM_Plex *) dm->data;
2671: mesh->refct++;
2672: (*newdm)->data = mesh;
2673: PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);
2674: DMInitialize_Plex(*newdm);
2675: return(0);
2676: }
2678: /*MC
2679: DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram.
2680: In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is
2681: specified by a PetscSection object. Ownership in the global representation is determined by
2682: ownership of the underlying DMPlex points. This is specified by another PetscSection object.
2684: Options Database Keys:
2685: + -dm_plex_hash_location - Use grid hashing for point location
2686: . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes
2687: . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing
2688: . -dm_plex_max_projection_height - Maxmimum mesh point height used to project locally
2689: . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement
2690: . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric
2691: . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices
2692: . -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
2693: . -dm_plex_check_geometry - Check that cells have positive volume
2694: . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ
2695: . -dm_plex_view_scale <num> - Scale the TikZ
2696: - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices
2699: Level: intermediate
2701: .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType()
2702: M*/
2704: PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm)
2705: {
2706: DM_Plex *mesh;
2707: PetscInt unit;
2712: PetscNewLog(dm,&mesh);
2713: dm->dim = 0;
2714: dm->data = mesh;
2716: mesh->refct = 1;
2717: PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);
2718: mesh->maxConeSize = 0;
2719: mesh->cones = NULL;
2720: mesh->coneOrientations = NULL;
2721: PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);
2722: mesh->maxSupportSize = 0;
2723: mesh->supports = NULL;
2724: mesh->refinementUniform = PETSC_TRUE;
2725: mesh->refinementLimit = -1.0;
2726: mesh->interpolated = DMPLEX_INTERPOLATED_INVALID;
2727: mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID;
2729: mesh->facesTmp = NULL;
2731: mesh->tetgenOpts = NULL;
2732: mesh->triangleOpts = NULL;
2733: PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);
2734: mesh->remeshBd = PETSC_FALSE;
2736: mesh->subpointMap = NULL;
2738: for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0;
2740: mesh->regularRefinement = PETSC_FALSE;
2741: mesh->depthState = -1;
2742: mesh->celltypeState = -1;
2743: mesh->globalVertexNumbers = NULL;
2744: mesh->globalCellNumbers = NULL;
2745: mesh->anchorSection = NULL;
2746: mesh->anchorIS = NULL;
2747: mesh->createanchors = NULL;
2748: mesh->computeanchormatrix = NULL;
2749: mesh->parentSection = NULL;
2750: mesh->parents = NULL;
2751: mesh->childIDs = NULL;
2752: mesh->childSection = NULL;
2753: mesh->children = NULL;
2754: mesh->referenceTree = NULL;
2755: mesh->getchildsymmetry = NULL;
2756: mesh->vtkCellHeight = 0;
2757: mesh->useAnchors = PETSC_FALSE;
2759: mesh->maxProjectionHeight = 0;
2761: mesh->neighbors = NULL;
2763: mesh->printSetValues = PETSC_FALSE;
2764: mesh->printFEM = 0;
2765: mesh->printTol = 1.0e-10;
2767: DMInitialize_Plex(dm);
2768: return(0);
2769: }
2771: /*@
2772: DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram.
2774: Collective
2776: Input Parameter:
2777: . comm - The communicator for the DMPlex object
2779: Output Parameter:
2780: . mesh - The DMPlex object
2782: Level: beginner
2784: @*/
2785: PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh)
2786: {
2791: DMCreate(comm, mesh);
2792: DMSetType(*mesh, DMPLEX);
2793: return(0);
2794: }
2796: /*@C
2797: DMPlexBuildFromCellListParallel - Build distributed DMPLEX topology from a list of vertices for each cell (common mesh generator output)
2799: Input Parameters:
2800: + dm - The DM
2801: . numCells - The number of cells owned by this process
2802: . numVertices - The number of vertices owned by this process, or PETSC_DECIDE
2803: . NVertices - The global number of vertices, or PETSC_DECIDE
2804: . numCorners - The number of vertices for each cell
2805: - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell
2807: Output Parameter:
2808: . vertexSF - (Optional) SF describing complete vertex ownership
2810: Notes:
2811: Two triangles sharing a face
2812: $
2813: $ 2
2814: $ / | \
2815: $ / | \
2816: $ / | \
2817: $ 0 0 | 1 3
2818: $ \ | /
2819: $ \ | /
2820: $ \ | /
2821: $ 1
2822: would have input
2823: $ numCells = 2, numVertices = 4
2824: $ cells = [0 1 2 1 3 2]
2825: $
2826: which would result in the DMPlex
2827: $
2828: $ 4
2829: $ / | \
2830: $ / | \
2831: $ / | \
2832: $ 2 0 | 1 5
2833: $ \ | /
2834: $ \ | /
2835: $ \ | /
2836: $ 3
2838: Vertices are implicitly numbered consecutively 0,...,NVertices.
2839: Each rank owns a chunk of numVertices consecutive vertices.
2840: If numVertices is PETSC_DECIDE, PETSc will distribute them as evenly as possible using PetscLayout.
2841: If both NVertices and numVertices are PETSC_DECIDE, NVertices is computed by PETSc as the maximum vertex index in cells + 1.
2842: If only NVertices is PETSC_DECIDE, it is computed as the sum of numVertices over all ranks.
2844: The cell distribution is arbitrary non-overlapping, independent of the vertex distribution.
2846: Not currently supported in Fortran.
2848: Level: advanced
2850: .seealso: DMPlexBuildFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildCoordinatesFromCellListParallel()
2851: @*/
2852: PetscErrorCode DMPlexBuildFromCellListParallel(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, const PetscInt cells[], PetscSF *vertexSF)
2853: {
2854: PetscSF sfPoint, sfVert;
2855: PetscLayout vLayout;
2856: PetscHSetI vhash;
2857: PetscSFNode *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex;
2858: const PetscInt *vrange;
2859: PetscInt numVerticesAdj, off = 0, *verticesAdj, numVerticesGhost = 0, *localVertex, *cones, c, p, v, g, dim;
2860: PetscMPIInt rank, size;
2861: PetscErrorCode ierr;
2865: PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);
2866: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
2867: MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);
2868: DMGetDimension(dm, &dim);
2869: /* Get/check global number of vertices */
2870: {
2871: PetscInt NVerticesInCells, i;
2872: const PetscInt len = numCells * numCorners;
2874: /* NVerticesInCells = max(cells) + 1 */
2875: NVerticesInCells = PETSC_MIN_INT;
2876: for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i];
2877: ++NVerticesInCells;
2878: MPI_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject) dm));
2880: if (numVertices == PETSC_DECIDE && NVertices == PETSC_DECIDE) NVertices = NVerticesInCells;
2881: else if (NVertices != PETSC_DECIDE && NVertices < NVerticesInCells) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Specified global number of vertices %D must be greater than or equal to the number of vertices in cells %D",NVertices,NVerticesInCells);
2882: }
2883: /* Partition vertices */
2884: PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);
2885: PetscLayoutSetLocalSize(vLayout, numVertices);
2886: PetscLayoutSetSize(vLayout, NVertices);
2887: PetscLayoutSetBlockSize(vLayout, 1);
2888: PetscLayoutSetUp(vLayout);
2889: PetscLayoutGetRanges(vLayout, &vrange);
2890: /* Count vertices and map them to procs */
2891: PetscHSetICreate(&vhash);
2892: for (c = 0; c < numCells; ++c) {
2893: for (p = 0; p < numCorners; ++p) {
2894: PetscHSetIAdd(vhash, cells[c*numCorners+p]);
2895: }
2896: }
2897: PetscHSetIGetSize(vhash, &numVerticesAdj);
2898: PetscMalloc1(numVerticesAdj, &verticesAdj);
2899: PetscHSetIGetElems(vhash, &off, verticesAdj);
2900: PetscHSetIDestroy(&vhash);
2901: if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj);
2902: PetscSortInt(numVerticesAdj, verticesAdj);
2903: PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);
2904: for (v = 0; v < numVerticesAdj; ++v) {
2905: const PetscInt gv = verticesAdj[v];
2906: PetscInt vrank;
2908: PetscFindInt(gv, size+1, vrange, &vrank);
2909: vrank = vrank < 0 ? -(vrank+2) : vrank;
2910: remoteVerticesAdj[v].index = gv - vrange[vrank];
2911: remoteVerticesAdj[v].rank = vrank;
2912: }
2913: /* Create cones */
2914: DMPlexSetChart(dm, 0, numCells+numVerticesAdj);
2915: for (c = 0; c < numCells; ++c) {DMPlexSetConeSize(dm, c, numCorners);}
2916: DMSetUp(dm);
2917: DMPlexGetCones(dm,&cones);
2918: for (c = 0; c < numCells; ++c) {
2919: for (p = 0; p < numCorners; ++p) {
2920: const PetscInt gv = cells[c*numCorners+p];
2921: PetscInt lv;
2923: PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);
2924: if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv);
2925: cones[c*numCorners+p] = lv+numCells;
2926: }
2927: }
2928: /* Create SF for vertices */
2929: PetscSFCreate(PetscObjectComm((PetscObject)dm), &sfVert);
2930: PetscObjectSetName((PetscObject) sfVert, "Vertex Ownership SF");
2931: PetscSFSetFromOptions(sfVert);
2932: PetscSFSetGraph(sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);
2933: PetscFree(verticesAdj);
2934: /* Build pointSF */
2935: PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);
2936: for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;}
2937: for (v = 0; v < numVertices; ++v) {vertexOwner[v].index = -1; vertexOwner[v].rank = -1;}
2938: PetscSFReduceBegin(sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);
2939: PetscSFReduceEnd(sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);
2940: 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);
2941: PetscSFBcastBegin(sfVert, MPIU_2INT, vertexOwner, vertexLocal);
2942: PetscSFBcastEnd(sfVert, MPIU_2INT, vertexOwner, vertexLocal);
2943: for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost;
2944: PetscMalloc1(numVerticesGhost, &localVertex);
2945: PetscMalloc1(numVerticesGhost, &remoteVertex);
2946: for (v = 0, g = 0; v < numVerticesAdj; ++v) {
2947: if (vertexLocal[v].rank != rank) {
2948: localVertex[g] = v+numCells;
2949: remoteVertex[g].index = vertexLocal[v].index;
2950: remoteVertex[g].rank = vertexLocal[v].rank;
2951: ++g;
2952: }
2953: }
2954: PetscFree2(vertexLocal, vertexOwner);
2955: if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost);
2956: DMGetPointSF(dm, &sfPoint);
2957: PetscObjectSetName((PetscObject) sfPoint, "point SF");
2958: PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);
2959: PetscLayoutDestroy(&vLayout);
2960: /* Fill in the rest of the topology structure */
2961: DMPlexSymmetrize(dm);
2962: DMPlexStratify(dm);
2963: PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);
2964: if (vertexSF) *vertexSF = sfVert;
2965: else {PetscSFDestroy(&sfVert);}
2966: return(0);
2967: }
2969: /*@C
2970: DMPlexBuildCoordinatesFromCellListParallel - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output)
2972: Input Parameters:
2973: + dm - The DM
2974: . spaceDim - The spatial dimension used for coordinates
2975: . sfVert - SF describing complete vertex ownership
2976: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
2978: Level: advanced
2980: Notes:
2981: Not currently supported in Fortran.
2983: .seealso: DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellListParallel()
2984: @*/
2985: PetscErrorCode DMPlexBuildCoordinatesFromCellListParallel(DM dm, PetscInt spaceDim, PetscSF sfVert, const PetscReal vertexCoords[])
2986: {
2987: PetscSection coordSection;
2988: Vec coordinates;
2989: PetscScalar *coords;
2990: PetscInt numVertices, numVerticesAdj, coordSize, v, vStart, vEnd;
2994: PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);
2995: DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
2996: if (vStart < 0 || vEnd < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first.");
2997: DMSetCoordinateDim(dm, spaceDim);
2998: PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);
2999: if (vEnd - vStart != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Supplied sfVert has wrong number of leaves = %D != %D = vEnd - vStart",numVerticesAdj,vEnd - vStart);
3000: DMGetCoordinateSection(dm, &coordSection);
3001: PetscSectionSetNumFields(coordSection, 1);
3002: PetscSectionSetFieldComponents(coordSection, 0, spaceDim);
3003: PetscSectionSetChart(coordSection, vStart, vEnd);
3004: for (v = vStart; v < vEnd; ++v) {
3005: PetscSectionSetDof(coordSection, v, spaceDim);
3006: PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);
3007: }
3008: PetscSectionSetUp(coordSection);
3009: PetscSectionGetStorageSize(coordSection, &coordSize);
3010: VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);
3011: VecSetBlockSize(coordinates, spaceDim);
3012: PetscObjectSetName((PetscObject) coordinates, "coordinates");
3013: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
3014: VecSetType(coordinates,VECSTANDARD);
3015: VecGetArray(coordinates, &coords);
3016: {
3017: MPI_Datatype coordtype;
3019: /* Need a temp buffer for coords if we have complex/single */
3020: MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);
3021: MPI_Type_commit(&coordtype);
3022: #if defined(PETSC_USE_COMPLEX)
3023: {
3024: PetscScalar *svertexCoords;
3025: PetscInt i;
3026: PetscMalloc1(numVertices*spaceDim,&svertexCoords);
3027: for (i=0; i<numVertices*spaceDim; i++) svertexCoords[i] = vertexCoords[i];
3028: PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords);
3029: PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords);
3030: PetscFree(svertexCoords);
3031: }
3032: #else
3033: PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords);
3034: PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords);
3035: #endif
3036: MPI_Type_free(&coordtype);
3037: }
3038: VecRestoreArray(coordinates, &coords);
3039: DMSetCoordinatesLocal(dm, coordinates);
3040: VecDestroy(&coordinates);
3041: PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);
3042: return(0);
3043: }
3045: /*@
3046: DMPlexCreateFromCellListParallelPetsc - Create distributed DMPLEX from a list of vertices for each cell (common mesh generator output)
3048: Input Parameters:
3049: + comm - The communicator
3050: . dim - The topological dimension of the mesh
3051: . numCells - The number of cells owned by this process
3052: . numVertices - The number of vertices owned by this process, or PETSC_DECIDE
3053: . NVertices - The global number of vertices, or PETSC_DECIDE
3054: . numCorners - The number of vertices for each cell
3055: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
3056: . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell
3057: . spaceDim - The spatial dimension used for coordinates
3058: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
3060: Output Parameter:
3061: + dm - The DM
3062: - vertexSF - (Optional) SF describing complete vertex ownership
3064: Notes:
3065: This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(),
3066: DMPlexBuildFromCellListParallel(), DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellListParallel()
3068: See DMPlexBuildFromCellListParallel() for an example and details about the topology-related parameters.
3069: See DMPlexBuildCoordinatesFromCellListParallel() for details about the geometry-related parameters.
3071: Level: intermediate
3073: .seealso: DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromDAG(), DMPlexCreate()
3074: @*/
3075: PetscErrorCode DMPlexCreateFromCellListParallelPetsc(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, PetscBool interpolate, const PetscInt cells[], PetscInt spaceDim, const PetscReal vertexCoords[], PetscSF *vertexSF, DM *dm)
3076: {
3077: PetscSF sfVert;
3081: DMCreate(comm, dm);
3082: DMSetType(*dm, DMPLEX);
3085: DMSetDimension(*dm, dim);
3086: DMPlexBuildFromCellListParallel(*dm, numCells, numVertices, NVertices, numCorners, cells, &sfVert);
3087: if (interpolate) {
3088: DM idm;
3090: DMPlexInterpolate(*dm, &idm);
3091: DMDestroy(dm);
3092: *dm = idm;
3093: }
3094: DMPlexBuildCoordinatesFromCellListParallel(*dm, spaceDim, sfVert, vertexCoords);
3095: if (vertexSF) *vertexSF = sfVert;
3096: else {PetscSFDestroy(&sfVert);}
3097: return(0);
3098: }
3101: /*@
3102: DMPlexCreateFromCellListParallel - Deprecated, use DMPlexCreateFromCellListParallelPetsc()
3104: Level: deprecated
3106: .seealso: DMPlexCreateFromCellListParallelPetsc()
3107: @*/
3108: 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)
3109: {
3111: PetscInt i;
3112: PetscInt *pintCells;
3115: if (sizeof(int) > sizeof(PetscInt)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Size of int %zd greater than size of PetscInt %zd. Reconfigure PETSc --with-64-bit-indices=1", sizeof(int), sizeof(PetscInt));
3116: if (sizeof(int) == sizeof(PetscInt)) {
3117: pintCells = (PetscInt *) cells;
3118: } else {
3119: PetscMalloc1(numCells*numCorners, &pintCells);
3120: for (i = 0; i < numCells*numCorners; i++) {
3121: pintCells[i] = (PetscInt) cells[i];
3122: }
3123: }
3124: DMPlexCreateFromCellListParallelPetsc(comm, dim, numCells, numVertices, PETSC_DECIDE, numCorners, interpolate, pintCells, spaceDim, vertexCoords, vertexSF, dm);
3125: if (sizeof(int) != sizeof(PetscInt)) {
3126: PetscFree(pintCells);
3127: }
3128: return(0);
3129: }
3131: /*@C
3132: DMPlexBuildFromCellList - Build DMPLEX topology from a list of vertices for each cell (common mesh generator output)
3134: Input Parameters:
3135: + dm - The DM
3136: . numCells - The number of cells owned by this process
3137: . numVertices - The number of vertices owned by this process, or PETSC_DECIDE
3138: . numCorners - The number of vertices for each cell
3139: - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell
3141: Level: advanced
3143: Notes:
3144: Two triangles sharing a face
3145: $
3146: $ 2
3147: $ / | \
3148: $ / | \
3149: $ / | \
3150: $ 0 0 | 1 3
3151: $ \ | /
3152: $ \ | /
3153: $ \ | /
3154: $ 1
3155: would have input
3156: $ numCells = 2, numVertices = 4
3157: $ cells = [0 1 2 1 3 2]
3158: $
3159: which would result in the DMPlex
3160: $
3161: $ 4
3162: $ / | \
3163: $ / | \
3164: $ / | \
3165: $ 2 0 | 1 5
3166: $ \ | /
3167: $ \ | /
3168: $ \ | /
3169: $ 3
3171: If numVertices is PETSC_DECIDE, it is computed by PETSc as the maximum vertex index in cells + 1.
3173: Not currently supported in Fortran.
3175: .seealso: DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListPetsc()
3176: @*/
3177: PetscErrorCode DMPlexBuildFromCellList(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[])
3178: {
3179: PetscInt *cones, c, p, dim;
3183: PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);
3184: DMGetDimension(dm, &dim);
3185: /* Get/check global number of vertices */
3186: {
3187: PetscInt NVerticesInCells, i;
3188: const PetscInt len = numCells * numCorners;
3190: /* NVerticesInCells = max(cells) + 1 */
3191: NVerticesInCells = PETSC_MIN_INT;
3192: for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i];
3193: ++NVerticesInCells;
3195: if (numVertices == PETSC_DECIDE) numVertices = NVerticesInCells;
3196: else if (numVertices < NVerticesInCells) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Specified number of vertices %D must be greater than or equal to the number of vertices in cells %D",numVertices,NVerticesInCells);
3197: }
3198: DMPlexSetChart(dm, 0, numCells+numVertices);
3199: for (c = 0; c < numCells; ++c) {
3200: DMPlexSetConeSize(dm, c, numCorners);
3201: }
3202: DMSetUp(dm);
3203: DMPlexGetCones(dm,&cones);
3204: for (c = 0; c < numCells; ++c) {
3205: for (p = 0; p < numCorners; ++p) {
3206: cones[c*numCorners+p] = cells[c*numCorners+p]+numCells;
3207: }
3208: }
3209: DMPlexSymmetrize(dm);
3210: DMPlexStratify(dm);
3211: PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);
3212: return(0);
3213: }
3215: /*@C
3216: DMPlexBuildCoordinatesFromCellList - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output)
3218: Input Parameters:
3219: + dm - The DM
3220: . spaceDim - The spatial dimension used for coordinates
3221: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
3223: Level: advanced
3225: Notes:
3226: Not currently supported in Fortran.
3228: .seealso: DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellList()
3229: @*/
3230: PetscErrorCode DMPlexBuildCoordinatesFromCellList(DM dm, PetscInt spaceDim, const PetscReal vertexCoords[])
3231: {
3232: PetscSection coordSection;
3233: Vec coordinates;
3234: DM cdm;
3235: PetscScalar *coords;
3236: PetscInt v, vStart, vEnd, d;
3240: PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);
3241: DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
3242: if (vStart < 0 || vEnd < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first.");
3243: DMSetCoordinateDim(dm, spaceDim);
3244: DMGetCoordinateSection(dm, &coordSection);
3245: PetscSectionSetNumFields(coordSection, 1);
3246: PetscSectionSetFieldComponents(coordSection, 0, spaceDim);
3247: PetscSectionSetChart(coordSection, vStart, vEnd);
3248: for (v = vStart; v < vEnd; ++v) {
3249: PetscSectionSetDof(coordSection, v, spaceDim);
3250: PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);
3251: }
3252: PetscSectionSetUp(coordSection);
3254: DMGetCoordinateDM(dm, &cdm);
3255: DMCreateLocalVector(cdm, &coordinates);
3256: VecSetBlockSize(coordinates, spaceDim);
3257: PetscObjectSetName((PetscObject) coordinates, "coordinates");
3258: VecGetArrayWrite(coordinates, &coords);
3259: for (v = 0; v < vEnd-vStart; ++v) {
3260: for (d = 0; d < spaceDim; ++d) {
3261: coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d];
3262: }
3263: }
3264: VecRestoreArrayWrite(coordinates, &coords);
3265: DMSetCoordinatesLocal(dm, coordinates);
3266: VecDestroy(&coordinates);
3267: PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);
3268: return(0);
3269: }
3271: /*@
3272: DMPlexCreateFromCellListPetsc - Create DMPLEX from a list of vertices for each cell (common mesh generator output)
3274: Input Parameters:
3275: + comm - The communicator
3276: . dim - The topological dimension of the mesh
3277: . numCells - The number of cells
3278: . numVertices - The number of vertices owned by this process, or PETSC_DECIDE
3279: . numCorners - The number of vertices for each cell
3280: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
3281: . cells - An array of numCells*numCorners numbers, the vertices for each cell
3282: . spaceDim - The spatial dimension used for coordinates
3283: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex
3285: Output Parameter:
3286: . dm - The DM
3288: Notes:
3289: This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), DMPlexBuildFromCellList(),
3290: DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellList()
3292: See DMPlexBuildFromCellList() for an example and details about the topology-related parameters.
3293: See DMPlexBuildCoordinatesFromCellList() for details about the geometry-related parameters.
3295: Level: intermediate
3297: .seealso: DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellList(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate()
3298: @*/
3299: PetscErrorCode DMPlexCreateFromCellListPetsc(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, PetscBool interpolate, const PetscInt cells[], PetscInt spaceDim, const PetscReal vertexCoords[], DM *dm)
3300: {
3304: if (!dim) SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "This is not appropriate for 0-dimensional meshes. Consider either creating the DM using DMPlexCreateFromDAG(), by hand, or using DMSwarm.");
3305: DMCreate(comm, dm);
3306: DMSetType(*dm, DMPLEX);
3307: DMSetDimension(*dm, dim);
3308: DMPlexBuildFromCellList(*dm, numCells, numVertices, numCorners, cells);
3309: if (interpolate) {
3310: DM idm;
3312: DMPlexInterpolate(*dm, &idm);
3313: DMDestroy(dm);
3314: *dm = idm;
3315: }
3316: DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, vertexCoords);
3317: return(0);
3318: }
3320: /*@
3321: DMPlexCreateFromCellList - Deprecated, use DMPlexCreateFromCellListPetsc()
3323: Level: deprecated
3325: .seealso: DMPlexCreateFromCellListPetsc()
3326: @*/
3327: 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)
3328: {
3330: PetscInt i;
3331: PetscInt *pintCells;
3332: PetscReal *prealVC;
3335: if (sizeof(int) > sizeof(PetscInt)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Size of int %zd greater than size of PetscInt %zd. Reconfigure PETSc --with-64-bit-indices=1", sizeof(int), sizeof(PetscInt));
3336: if (sizeof(int) == sizeof(PetscInt)) {
3337: pintCells = (PetscInt *) cells;
3338: } else {
3339: PetscMalloc1(numCells*numCorners, &pintCells);
3340: for (i = 0; i < numCells*numCorners; i++) {
3341: pintCells[i] = (PetscInt) cells[i];
3342: }
3343: }
3344: if (sizeof(double) > sizeof(PetscReal)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Size of double %zd greater than size of PetscReal %zd. Reconfigure PETSc --with-precision=<higher precision>.", sizeof(double), sizeof(PetscReal));
3345: if (sizeof(double) == sizeof(PetscReal)) {
3346: prealVC = (PetscReal *) vertexCoords;
3347: } else {
3348: PetscMalloc1(numVertices*spaceDim, &prealVC);
3349: for (i = 0; i < numVertices*spaceDim; i++) {
3350: prealVC[i] = (PetscReal) vertexCoords[i];
3351: }
3352: }
3353: DMPlexCreateFromCellListPetsc(comm, dim, numCells, numVertices, numCorners, interpolate, pintCells, spaceDim, prealVC, dm);
3354: if (sizeof(int) != sizeof(PetscInt)) {
3355: PetscFree(pintCells);
3356: }
3357: if (sizeof(double) != sizeof(PetscReal)) {
3358: PetscFree(prealVC);
3359: }
3360: return(0);
3361: }
3363: /*@
3364: DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM
3366: Input Parameters:
3367: + dm - The empty DM object, usually from DMCreate() and DMSetDimension()
3368: . depth - The depth of the DAG
3369: . numPoints - Array of size depth + 1 containing the number of points at each depth
3370: . coneSize - The cone size of each point
3371: . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point
3372: . coneOrientations - The orientation of each cone point
3373: - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim()
3375: Output Parameter:
3376: . dm - The DM
3378: Note: Two triangles sharing a face would have input
3379: $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0]
3380: $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0]
3381: $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0]
3382: $
3383: which would result in the DMPlex
3384: $
3385: $ 4
3386: $ / | \
3387: $ / | \
3388: $ / | \
3389: $ 2 0 | 1 5
3390: $ \ | /
3391: $ \ | /
3392: $ \ | /
3393: $ 3
3394: $
3395: $ Notice that all points are numbered consecutively, unlike DMPlexCreateFromCellListPetsc()
3397: Level: advanced
3399: .seealso: DMPlexCreateFromCellListPetsc(), DMPlexCreate()
3400: @*/
3401: PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[])
3402: {
3403: Vec coordinates;
3404: PetscSection coordSection;
3405: PetscScalar *coords;
3406: PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off;
3410: DMGetDimension(dm, &dim);
3411: DMGetCoordinateDim(dm, &dimEmbed);
3412: if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %D cannot be less than intrinsic dimension %d",dimEmbed,dim);
3413: for (d = 0; d <= depth; ++d) pEnd += numPoints[d];
3414: DMPlexSetChart(dm, pStart, pEnd);
3415: for (p = pStart; p < pEnd; ++p) {
3416: DMPlexSetConeSize(dm, p, coneSize[p-pStart]);
3417: if (firstVertex < 0 && !coneSize[p - pStart]) {
3418: firstVertex = p - pStart;
3419: }
3420: }
3421: if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %D vertices but could not find any", numPoints[0]);
3422: DMSetUp(dm); /* Allocate space for cones */
3423: for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) {
3424: DMPlexSetCone(dm, p, &cones[off]);
3425: DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);
3426: }
3427: DMPlexSymmetrize(dm);
3428: DMPlexStratify(dm);
3429: /* Build coordinates */
3430: DMGetCoordinateSection(dm, &coordSection);
3431: PetscSectionSetNumFields(coordSection, 1);
3432: PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);
3433: PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);
3434: for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) {
3435: PetscSectionSetDof(coordSection, v, dimEmbed);
3436: PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);
3437: }
3438: PetscSectionSetUp(coordSection);
3439: PetscSectionGetStorageSize(coordSection, &coordSize);
3440: VecCreate(PETSC_COMM_SELF, &coordinates);
3441: PetscObjectSetName((PetscObject) coordinates, "coordinates");
3442: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
3443: VecSetBlockSize(coordinates, dimEmbed);
3444: VecSetType(coordinates,VECSTANDARD);
3445: VecGetArray(coordinates, &coords);
3446: for (v = 0; v < numPoints[0]; ++v) {
3447: PetscInt off;
3449: PetscSectionGetOffset(coordSection, v+firstVertex, &off);
3450: for (d = 0; d < dimEmbed; ++d) {
3451: coords[off+d] = vertexCoords[v*dimEmbed+d];
3452: }
3453: }
3454: VecRestoreArray(coordinates, &coords);
3455: DMSetCoordinatesLocal(dm, coordinates);
3456: VecDestroy(&coordinates);
3457: return(0);
3458: }
3460: /*@C
3461: DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file.
3463: + comm - The MPI communicator
3464: . filename - Name of the .dat file
3465: - interpolate - Create faces and edges in the mesh
3467: Output Parameter:
3468: . dm - The DM object representing the mesh
3470: Note: The format is the simplest possible:
3471: $ Ne
3472: $ v0 v1 ... vk
3473: $ Nv
3474: $ x y z marker
3476: Level: beginner
3478: .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate()
3479: @*/
3480: PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
3481: {
3482: DMLabel marker;
3483: PetscViewer viewer;
3484: Vec coordinates;
3485: PetscSection coordSection;
3486: PetscScalar *coords;
3487: char line[PETSC_MAX_PATH_LEN];
3488: PetscInt dim = 3, cdim = 3, coordSize, v, c, d;
3489: PetscMPIInt rank;
3490: int snum, Nv, Nc;
3491: PetscErrorCode ierr;
3494: MPI_Comm_rank(comm, &rank);
3495: PetscViewerCreate(comm, &viewer);
3496: PetscViewerSetType(viewer, PETSCVIEWERASCII);
3497: PetscViewerFileSetMode(viewer, FILE_MODE_READ);
3498: PetscViewerFileSetName(viewer, filename);
3499: if (!rank) {
3500: PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);
3501: snum = sscanf(line, "%d %d", &Nc, &Nv);
3502: if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
3503: } else {
3504: Nc = Nv = 0;
3505: }
3506: DMCreate(comm, dm);
3507: DMSetType(*dm, DMPLEX);
3508: DMPlexSetChart(*dm, 0, Nc+Nv);
3509: DMSetDimension(*dm, dim);
3510: DMSetCoordinateDim(*dm, cdim);
3511: /* Read topology */
3512: if (!rank) {
3513: PetscInt cone[8], corners = 8;
3514: int vbuf[8], v;
3516: for (c = 0; c < Nc; ++c) {DMPlexSetConeSize(*dm, c, corners);}
3517: DMSetUp(*dm);
3518: for (c = 0; c < Nc; ++c) {
3519: PetscViewerRead(viewer, line, corners, NULL, PETSC_STRING);
3520: 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]);
3521: if (snum != corners) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
3522: for (v = 0; v < corners; ++v) cone[v] = vbuf[v] + Nc;
3523: /* Hexahedra are inverted */
3524: {
3525: PetscInt tmp = cone[1];
3526: cone[1] = cone[3];
3527: cone[3] = tmp;
3528: }
3529: DMPlexSetCone(*dm, c, cone);
3530: }
3531: }
3532: DMPlexSymmetrize(*dm);
3533: DMPlexStratify(*dm);
3534: /* Read coordinates */
3535: DMGetCoordinateSection(*dm, &coordSection);
3536: PetscSectionSetNumFields(coordSection, 1);
3537: PetscSectionSetFieldComponents(coordSection, 0, cdim);
3538: PetscSectionSetChart(coordSection, Nc, Nc + Nv);
3539: for (v = Nc; v < Nc+Nv; ++v) {
3540: PetscSectionSetDof(coordSection, v, cdim);
3541: PetscSectionSetFieldDof(coordSection, v, 0, cdim);
3542: }
3543: PetscSectionSetUp(coordSection);
3544: PetscSectionGetStorageSize(coordSection, &coordSize);
3545: VecCreate(PETSC_COMM_SELF, &coordinates);
3546: PetscObjectSetName((PetscObject) coordinates, "coordinates");
3547: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
3548: VecSetBlockSize(coordinates, cdim);
3549: VecSetType(coordinates, VECSTANDARD);
3550: VecGetArray(coordinates, &coords);
3551: if (!rank) {
3552: double x[3];
3553: int val;
3555: DMCreateLabel(*dm, "marker");
3556: DMGetLabel(*dm, "marker", &marker);
3557: for (v = 0; v < Nv; ++v) {
3558: PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);
3559: snum = sscanf(line, "%lg %lg %lg %d", &x[0], &x[1], &x[2], &val);
3560: if (snum != 4) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
3561: for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d];
3562: if (val) {DMLabelSetValue(marker, v+Nc, val);}
3563: }
3564: }
3565: VecRestoreArray(coordinates, &coords);
3566: DMSetCoordinatesLocal(*dm, coordinates);
3567: VecDestroy(&coordinates);
3568: PetscViewerDestroy(&viewer);
3569: if (interpolate) {
3570: DM idm;
3571: DMLabel bdlabel;
3573: DMPlexInterpolate(*dm, &idm);
3574: DMDestroy(dm);
3575: *dm = idm;
3577: DMGetLabel(*dm, "marker", &bdlabel);
3578: DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);
3579: DMPlexLabelComplete(*dm, bdlabel);
3580: }
3581: return(0);
3582: }
3584: /*@C
3585: DMPlexCreateFromFile - This takes a filename and produces a DM
3587: Input Parameters:
3588: + comm - The communicator
3589: . filename - A file name
3590: - interpolate - Flag to create intermediate mesh pieces (edges, faces)
3592: Output Parameter:
3593: . dm - The DM
3595: Options Database Keys:
3596: . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5
3598: Use -dm_plex_create_ prefix to pass options to the internal PetscViewer, e.g.
3599: $ -dm_plex_create_viewer_hdf5_collective
3601: Level: beginner
3603: .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellListPetsc(), DMPlexCreate()
3604: @*/
3605: PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
3606: {
3607: const char *extGmsh = ".msh";
3608: const char *extGmsh2 = ".msh2";
3609: const char *extGmsh4 = ".msh4";
3610: const char *extCGNS = ".cgns";
3611: const char *extExodus = ".exo";
3612: const char *extGenesis = ".gen";
3613: const char *extFluent = ".cas";
3614: const char *extHDF5 = ".h5";
3615: const char *extMed = ".med";
3616: const char *extPLY = ".ply";
3617: const char *extCV = ".dat";
3618: size_t len;
3619: PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isCV;
3620: PetscMPIInt rank;
3626: DMInitializePackage();
3627: PetscLogEventBegin(DMPLEX_CreateFromFile,0,0,0,0);
3628: MPI_Comm_rank(comm, &rank);
3629: PetscStrlen(filename, &len);
3630: if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path");
3631: PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);
3632: PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh2, 5, &isGmsh2);
3633: PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh4, 5, &isGmsh4);
3634: PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);
3635: PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);
3636: PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);
3637: PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);
3638: PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);
3639: PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);
3640: PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);
3641: PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);
3642: if (isGmsh || isGmsh2 || isGmsh4) {
3643: DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);
3644: } else if (isCGNS) {
3645: DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);
3646: } else if (isExodus || isGenesis) {
3647: DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);
3648: } else if (isFluent) {
3649: DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);
3650: } else if (isHDF5) {
3651: PetscBool load_hdf5_xdmf = PETSC_FALSE;
3652: PetscViewer viewer;
3654: /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */
3655: PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf", 5, &load_hdf5_xdmf);
3656: PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);
3657: PetscViewerCreate(comm, &viewer);
3658: PetscViewerSetType(viewer, PETSCVIEWERHDF5);
3659: PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_");
3660: PetscViewerSetFromOptions(viewer);
3661: PetscViewerFileSetMode(viewer, FILE_MODE_READ);
3662: PetscViewerFileSetName(viewer, filename);
3663: DMCreate(comm, dm);
3664: DMSetType(*dm, DMPLEX);
3665: if (load_hdf5_xdmf) {PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);}
3666: DMLoad(*dm, viewer);
3667: if (load_hdf5_xdmf) {PetscViewerPopFormat(viewer);}
3668: PetscViewerDestroy(&viewer);
3670: if (interpolate) {
3671: DM idm;
3673: DMPlexInterpolate(*dm, &idm);
3674: DMDestroy(dm);
3675: *dm = idm;
3676: }
3677: } else if (isMed) {
3678: DMPlexCreateMedFromFile(comm, filename, interpolate, dm);
3679: } else if (isPLY) {
3680: DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);
3681: } else if (isCV) {
3682: DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);
3683: } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename);
3684: PetscLogEventEnd(DMPLEX_CreateFromFile,0,0,0,0);
3685: return(0);
3686: }
3688: /*@
3689: DMPlexCreateReferenceCellByType - Create a DMPLEX with the appropriate FEM reference cell
3691: Collective
3693: Input Parameters:
3694: + comm - The communicator
3695: - ct - The cell type of the reference cell
3697: Output Parameter:
3698: . refdm - The reference cell
3700: Level: intermediate
3702: .seealso: DMPlexCreateReferenceCell(), DMPlexCreateBoxMesh()
3703: @*/
3704: PetscErrorCode DMPlexCreateReferenceCellByType(MPI_Comm comm, DMPolytopeType ct, DM *refdm)
3705: {
3706: DM rdm;
3707: Vec coords;
3711: DMCreate(comm, &rdm);
3712: DMSetType(rdm, DMPLEX);
3713: switch (ct) {
3714: case DM_POLYTOPE_POINT:
3715: {
3716: PetscInt numPoints[1] = {1};
3717: PetscInt coneSize[1] = {0};
3718: PetscInt cones[1] = {0};
3719: PetscInt coneOrientations[1] = {0};
3720: PetscScalar vertexCoords[1] = {0.0};
3722: DMSetDimension(rdm, 0);
3723: DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3724: }
3725: break;
3726: case DM_POLYTOPE_SEGMENT:
3727: {
3728: PetscInt numPoints[2] = {2, 1};
3729: PetscInt coneSize[3] = {2, 0, 0};
3730: PetscInt cones[2] = {1, 2};
3731: PetscInt coneOrientations[2] = {0, 0};
3732: PetscScalar vertexCoords[2] = {-1.0, 1.0};
3734: DMSetDimension(rdm, 1);
3735: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3736: }
3737: break;
3738: case DM_POLYTOPE_TRIANGLE:
3739: {
3740: PetscInt numPoints[2] = {3, 1};
3741: PetscInt coneSize[4] = {3, 0, 0, 0};
3742: PetscInt cones[3] = {1, 2, 3};
3743: PetscInt coneOrientations[3] = {0, 0, 0};
3744: PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0};
3746: DMSetDimension(rdm, 2);
3747: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3748: }
3749: break;
3750: case DM_POLYTOPE_QUADRILATERAL:
3751: {
3752: PetscInt numPoints[2] = {4, 1};
3753: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
3754: PetscInt cones[4] = {1, 2, 3, 4};
3755: PetscInt coneOrientations[4] = {0, 0, 0, 0};
3756: PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0};
3758: DMSetDimension(rdm, 2);
3759: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3760: }
3761: break;
3762: case DM_POLYTOPE_SEG_PRISM_TENSOR:
3763: {
3764: PetscInt numPoints[2] = {4, 1};
3765: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
3766: PetscInt cones[4] = {1, 2, 3, 4};
3767: PetscInt coneOrientations[4] = {0, 0, 0, 0};
3768: PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, 1.0};
3770: DMSetDimension(rdm, 2);
3771: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3772: }
3773: break;
3774: case DM_POLYTOPE_TETRAHEDRON:
3775: {
3776: PetscInt numPoints[2] = {4, 1};
3777: PetscInt coneSize[5] = {4, 0, 0, 0, 0};
3778: PetscInt cones[4] = {1, 3, 2, 4};
3779: PetscInt coneOrientations[4] = {0, 0, 0, 0};
3780: 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};
3782: DMSetDimension(rdm, 3);
3783: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3784: }
3785: break;
3786: case DM_POLYTOPE_HEXAHEDRON:
3787: {
3788: PetscInt numPoints[2] = {8, 1};
3789: PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0};
3790: PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8};
3791: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
3792: 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,
3793: -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0};
3795: DMSetDimension(rdm, 3);
3796: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3797: }
3798: break;
3799: case DM_POLYTOPE_TRI_PRISM:
3800: {
3801: PetscInt numPoints[2] = {6, 1};
3802: PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0};
3803: PetscInt cones[6] = {1, 3, 2, 4, 5, 6};
3804: PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0};
3805: PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0,
3806: -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0};
3808: DMSetDimension(rdm, 3);
3809: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3810: }
3811: break;
3812: case DM_POLYTOPE_TRI_PRISM_TENSOR:
3813: {
3814: PetscInt numPoints[2] = {6, 1};
3815: PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0};
3816: PetscInt cones[6] = {1, 2, 3, 4, 5, 6};
3817: PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0};
3818: PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0,
3819: -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0};
3821: DMSetDimension(rdm, 3);
3822: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3823: }
3824: break;
3825: case DM_POLYTOPE_QUAD_PRISM_TENSOR:
3826: {
3827: PetscInt numPoints[2] = {8, 1};
3828: PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0};
3829: PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8};
3830: PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
3831: 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,
3832: -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0};
3834: DMSetDimension(rdm, 3);
3835: DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3836: }
3837: break;
3838: default: SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for cell type %s", DMPolytopeTypes[ct]);
3839: }
3840: {
3841: PetscInt Nv, v;
3843: /* Must create the celltype label here so that we do not automatically try to compute the types */
3844: DMCreateLabel(rdm, "celltype");
3845: DMPlexSetCellType(rdm, 0, ct);
3846: DMPlexGetChart(rdm, NULL, &Nv);
3847: for (v = 1; v < Nv; ++v) {DMPlexSetCellType(rdm, v, DM_POLYTOPE_POINT);}
3848: }
3849: DMPlexInterpolate(rdm, refdm);
3850: if (rdm->coordinateDM) {
3851: DM ncdm;
3852: PetscSection cs;
3853: PetscInt pEnd = -1;
3855: DMGetLocalSection(rdm->coordinateDM, &cs);
3856: if (cs) {PetscSectionGetChart(cs, NULL, &pEnd);}
3857: if (pEnd >= 0) {
3858: DMClone(*refdm, &ncdm);
3859: DMCopyDisc(rdm->coordinateDM, ncdm);
3860: DMSetLocalSection(ncdm, cs);
3861: DMSetCoordinateDM(*refdm, ncdm);
3862: DMDestroy(&ncdm);
3863: }
3864: }
3865: DMGetCoordinatesLocal(rdm, &coords);
3866: if (coords) {
3867: DMSetCoordinatesLocal(*refdm, coords);
3868: } else {
3869: DMGetCoordinates(rdm, &coords);
3870: if (coords) {DMSetCoordinates(*refdm, coords);}
3871: }
3872: DMDestroy(&rdm);
3873: return(0);
3874: }
3876: /*@
3877: DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell
3879: Collective
3881: Input Parameters:
3882: + comm - The communicator
3883: . dim - The spatial dimension
3884: - simplex - Flag for simplex, otherwise use a tensor-product cell
3886: Output Parameter:
3887: . refdm - The reference cell
3889: Level: intermediate
3891: .seealso: DMPlexCreateReferenceCellByType(), DMPlexCreateBoxMesh()
3892: @*/
3893: PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm)
3894: {
3898: switch (dim) {
3899: case 0: DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_POINT, refdm);break;
3900: case 1: DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_SEGMENT, refdm);break;
3901: case 2:
3902: if (simplex) {DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_TRIANGLE, refdm);}
3903: else {DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_QUADRILATERAL, refdm);}
3904: break;
3905: case 3:
3906: if (simplex) {DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_TETRAHEDRON, refdm);}
3907: else {DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_HEXAHEDRON, refdm);}
3908: break;
3909: default:
3910: SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %D", dim);
3911: }
3912: return(0);
3913: }