Actual source code: plexcreate.c

petsc-master 2020-02-20
Report Typos and Errors
  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_CreateFromCellList, DMPLEX_CreateFromCellList_Coordinates;

  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:   n    = 3;
1059:   PetscOptionsGetIntArray(NULL, NULL, "-dm_plex_box_faces", fac, &n, &flg);
1060:   for (i = 0; i < dim; ++i) fac[i] = faces ? faces[i] : (flg && i < n ? fac[i] : (dim == 1 ? 1 : 4-dim));
1061:   if (lower) for (i = 0; i < dim; ++i) low[i] = lower[i];
1062:   if (upper) for (i = 0; i < dim; ++i) upp[i] = upper[i];
1063:   if (periodicity) for (i = 0; i < dim; ++i) bdt[i] = periodicity[i];
1064:   /* Allow bounds to be specified from the command line */
1065:   n    = 3;
1066:   PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_lower", low, &n, &flg);
1067:   if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim);
1068:   n    = 3;
1069:   PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_upper", upp, &n, &flg);
1070:   if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim);

1072:   if (dim == 1)      {DMPlexCreateLineMesh_Internal(comm, fac[0], low[0], upp[0], bdt[0], dm);}
1073:   else if (simplex)  {DMPlexCreateBoxMesh_Simplex_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);}
1074:   else               {DMPlexCreateBoxMesh_Tensor_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);}
1075:   return(0);
1076: }

1078: /*@
1079:   DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells.

1081:   Collective

1083:   Input Parameters:
1084: + comm        - The communicator for the DM object
1085: . faces       - Number of faces per dimension, or NULL for (1, 1, 1)
1086: . lower       - The lower left corner, or NULL for (0, 0, 0)
1087: . upper       - The upper right corner, or NULL for (1, 1, 1)
1088: . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE
1089: . ordExt      - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first
1090: - interpolate - Flag to create intermediate mesh pieces (edges, faces)

1092:   Output Parameter:
1093: . dm  - The DM object

1095:   Level: beginner

1097: .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateWedgeCylinderMesh(), DMPlexExtrude(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1098: @*/
1099: PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool ordExt, PetscBool interpolate, DM *dm)
1100: {
1101:   DM             bdm, botdm;
1102:   PetscInt       i;
1103:   PetscInt       fac[3] = {0, 0, 0};
1104:   PetscReal      low[3] = {0, 0, 0};
1105:   PetscReal      upp[3] = {1, 1, 1};
1106:   DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};

1110:   for (i = 0; i < 3; ++i) fac[i] = faces ? (faces[i] > 0 ? faces[i] : 1) : 1;
1111:   if (lower) for (i = 0; i < 3; ++i) low[i] = lower[i];
1112:   if (upper) for (i = 0; i < 3; ++i) upp[i] = upper[i];
1113:   if (periodicity) for (i = 0; i < 3; ++i) bdt[i] = periodicity[i];
1114:   for (i = 0; i < 3; ++i) if (bdt[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity not yet supported");

1116:   DMCreate(comm, &bdm);
1117:   DMSetType(bdm, DMPLEX);
1118:   DMSetDimension(bdm, 1);
1119:   DMSetCoordinateDim(bdm, 2);
1120:   DMPlexCreateSquareBoundary(bdm, low, upp, fac);
1121:   DMPlexGenerate(bdm, NULL, PETSC_FALSE, &botdm);
1122:   DMDestroy(&bdm);
1123:   DMPlexExtrude(botdm, fac[2], upp[2] - low[2], ordExt, interpolate, dm);
1124:   if (low[2] != 0.0) {
1125:     Vec         v;
1126:     PetscScalar *x;
1127:     PetscInt    cDim, n;

1129:     DMGetCoordinatesLocal(*dm, &v);
1130:     VecGetBlockSize(v, &cDim);
1131:     VecGetLocalSize(v, &n);
1132:     VecGetArray(v, &x);
1133:     x   += cDim;
1134:     for (i=0; i<n; i+=cDim) x[i] += low[2];
1135:     VecRestoreArray(v,&x);
1136:     DMSetCoordinatesLocal(*dm, v);
1137:   }
1138:   DMDestroy(&botdm);
1139:   return(0);
1140: }

1142: /*@
1143:   DMPlexExtrude - Creates a (d+1)-D mesh by extruding a d-D mesh in the normal direction using prismatic cells.

1145:   Collective on idm

1147:   Input Parameters:
1148: + idm - The mesh to be extruted
1149: . layers - The number of layers
1150: . height - The height of the extruded layer
1151: . ordExt - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first
1152: - interpolate - Flag to create intermediate mesh pieces (edges, faces)

1154:   Output Parameter:
1155: . dm  - The DM object

1157:   Notes: The object created is an hybrid mesh, the vertex ordering in the cone of the cell is that of the prismatic cells

1159:   Level: advanced

1161: .seealso: DMPlexCreateWedgeCylinderMesh(), DMPlexCreateWedgeBoxMesh(), DMPlexSetHybridBounds(), DMSetType(), DMCreate()
1162: @*/
1163: PetscErrorCode DMPlexExtrude(DM idm, PetscInt layers, PetscReal height, PetscBool ordExt, PetscBool interpolate, DM* dm)
1164: {
1165:   PetscScalar       *coordsB;
1166:   const PetscScalar *coordsA;
1167:   PetscReal         *normals = NULL;
1168:   Vec               coordinatesA, coordinatesB;
1169:   PetscSection      coordSectionA, coordSectionB;
1170:   PetscInt          dim, cDim, cDimB, c, l, v, coordSize, *newCone;
1171:   PetscInt          cStart, cEnd, vStart, vEnd, cellV, numCells, numVertices;
1172:   PetscErrorCode    ierr;

1179:   DMGetDimension(idm, &dim);
1180:   if (dim < 1 || dim > 3) SETERRQ1(PetscObjectComm((PetscObject)idm), PETSC_ERR_SUP, "Support for dimension %D not coded", dim);

1182:   DMPlexGetHeightStratum(idm, 0, &cStart, &cEnd);
1183:   DMPlexGetDepthStratum(idm, 0, &vStart, &vEnd);
1184:   numCells = (cEnd - cStart)*layers;
1185:   numVertices = (vEnd - vStart)*(layers+1);
1186:   DMCreate(PetscObjectComm((PetscObject)idm), dm);
1187:   DMSetType(*dm, DMPLEX);
1188:   DMSetDimension(*dm, dim+1);
1189:   DMPlexSetChart(*dm, 0, numCells+numVertices);
1190:   for (c = cStart, cellV = 0; c < cEnd; ++c) {
1191:     PetscInt *closure = NULL;
1192:     PetscInt closureSize, numCorners = 0;

1194:     DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);
1195:     for (v = 0; v < closureSize*2; v += 2) if ((closure[v] >= vStart) && (closure[v] < vEnd)) numCorners++;
1196:     DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);
1197:     for (l = 0; l < layers; ++l) {
1198:       DMPlexSetConeSize(*dm, ordExt ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart, 2*numCorners);
1199:     }
1200:     cellV = PetscMax(numCorners,cellV);
1201:   }
1202:   DMPlexSetHybridBounds(*dm, 0, PETSC_DETERMINE, PETSC_DETERMINE, PETSC_DETERMINE);
1203:   DMSetUp(*dm);

1205:   DMGetCoordinateDim(idm, &cDim);
1206:   if (dim != cDim) {
1207:     PetscCalloc1(cDim*(vEnd - vStart), &normals);
1208:   }
1209:   PetscMalloc1(3*cellV,&newCone);
1210:   for (c = cStart; c < cEnd; ++c) {
1211:     PetscInt *closure = NULL;
1212:     PetscInt closureSize, numCorners = 0, l;
1213:     PetscReal normal[3] = {0, 0, 0};

1215:     if (normals) {
1216:       DMPlexComputeCellGeometryFVM(idm, c, NULL, NULL, normal);
1217:     }
1218:     DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);
1219:     for (v = 0; v < closureSize*2; v += 2) {
1220:       if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
1221:         PetscInt d;

1223:         newCone[numCorners++] = closure[v] - vStart;
1224:         if (normals) { for (d = 0; d < cDim; ++d) normals[cDim*(closure[v]-vStart)+d] += normal[d]; }
1225:       }
1226:     }
1227:     switch (numCorners) {
1228:     case 4: /* do nothing */
1229:     case 2: /* do nothing */
1230:       break;
1231:     case 3: /* from counter-clockwise to wedge ordering */
1232:       l = newCone[1];
1233:       newCone[1] = newCone[2];
1234:       newCone[2] = l;
1235:       break;
1236:     default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_SUP, "Unsupported number of corners: %D", numCorners);
1237:     }
1238:     DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);
1239:     for (l = 0; l < layers; ++l) {
1240:       PetscInt i;

1242:       for (i = 0; i < numCorners; ++i) {
1243:         newCone[  numCorners + i] = ordExt ? (layers+1)*newCone[i] + l     + numCells :     l*(vEnd - vStart) + newCone[i] + numCells;
1244:         newCone[2*numCorners + i] = ordExt ? (layers+1)*newCone[i] + l + 1 + numCells : (l+1)*(vEnd - vStart) + newCone[i] + numCells;
1245:       }
1246:       DMPlexSetCone(*dm, ordExt ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart, newCone + numCorners);
1247:     }
1248:   }
1249:   DMPlexSymmetrize(*dm);
1250:   DMPlexStratify(*dm);
1251:   PetscFree(newCone);

1253:   cDimB = cDim == dim ? cDim+1 : cDim;
1254:   DMGetCoordinateSection(*dm, &coordSectionB);
1255:   PetscSectionSetNumFields(coordSectionB, 1);
1256:   PetscSectionSetFieldComponents(coordSectionB, 0, cDimB);
1257:   PetscSectionSetChart(coordSectionB, numCells, numCells+numVertices);
1258:   for (v = numCells; v < numCells+numVertices; ++v) {
1259:     PetscSectionSetDof(coordSectionB, v, cDimB);
1260:     PetscSectionSetFieldDof(coordSectionB, v, 0, cDimB);
1261:   }
1262:   PetscSectionSetUp(coordSectionB);
1263:   PetscSectionGetStorageSize(coordSectionB, &coordSize);
1264:   VecCreate(PETSC_COMM_SELF, &coordinatesB);
1265:   PetscObjectSetName((PetscObject) coordinatesB, "coordinates");
1266:   VecSetSizes(coordinatesB, coordSize, PETSC_DETERMINE);
1267:   VecSetBlockSize(coordinatesB, cDimB);
1268:   VecSetType(coordinatesB,VECSTANDARD);

1270:   DMGetCoordinateSection(idm, &coordSectionA);
1271:   DMGetCoordinatesLocal(idm, &coordinatesA);
1272:   VecGetArray(coordinatesB, &coordsB);
1273:   VecGetArrayRead(coordinatesA, &coordsA);
1274:   for (v = vStart; v < vEnd; ++v) {
1275:     const PetscScalar *cptr;
1276:     PetscReal         ones2[2] = { 0., 1.}, ones3[3] = { 0., 0., 1.};
1277:     PetscReal         *normal, norm, h = height/layers;
1278:     PetscInt          offA, d, cDimA = cDim;

1280:     normal = normals ? normals + cDimB*(v - vStart) : (cDim > 1 ? ones3 : ones2);
1281:     if (normals) {
1282:       for (d = 0, norm = 0.0; d < cDimB; ++d) norm += normal[d]*normal[d];
1283:       for (d = 0; d < cDimB; ++d) normal[d] *= 1./PetscSqrtReal(norm);
1284:     }

1286:     PetscSectionGetOffset(coordSectionA, v, &offA);
1287:     cptr = coordsA + offA;
1288:     for (l = 0; l < layers+1; ++l) {
1289:       PetscInt offB, d, newV;

1291:       newV = ordExt ? (layers+1)*(v -vStart) + l + numCells : (vEnd -vStart)*l + (v -vStart) + numCells;
1292:       PetscSectionGetOffset(coordSectionB, newV, &offB);
1293:       for (d = 0; d < cDimA; ++d) { coordsB[offB+d]  = cptr[d]; }
1294:       for (d = 0; d < cDimB; ++d) { coordsB[offB+d] += l ? normal[d]*h : 0.0; }
1295:       cptr    = coordsB + offB;
1296:       cDimA   = cDimB;
1297:     }
1298:   }
1299:   VecRestoreArrayRead(coordinatesA, &coordsA);
1300:   VecRestoreArray(coordinatesB, &coordsB);
1301:   DMSetCoordinatesLocal(*dm, coordinatesB);
1302:   VecDestroy(&coordinatesB);
1303:   PetscFree(normals);
1304:   if (interpolate) {
1305:     DM idm;

1307:     DMPlexInterpolate(*dm, &idm);
1308:     DMPlexCopyCoordinates(*dm, idm);
1309:     DMDestroy(dm);
1310:     *dm  = idm;
1311:   }
1312:   return(0);
1313: }

1315: /*@C
1316:   DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database.

1318:   Logically Collective on dm

1320:   Input Parameters:
1321: + dm - the DM context
1322: - prefix - the prefix to prepend to all option names

1324:   Notes:
1325:   A hyphen (-) must NOT be given at the beginning of the prefix name.
1326:   The first character of all runtime options is AUTOMATICALLY the hyphen.

1328:   Level: advanced

1330: .seealso: SNESSetFromOptions()
1331: @*/
1332: PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[])
1333: {
1334:   DM_Plex       *mesh = (DM_Plex *) dm->data;

1339:   PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);
1340:   PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);
1341:   return(0);
1342: }

1344: /*@
1345:   DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra.

1347:   Collective

1349:   Input Parameters:
1350: + comm      - The communicator for the DM object
1351: . numRefine - The number of regular refinements to the basic 5 cell structure
1352: - periodicZ - The boundary type for the Z direction

1354:   Output Parameter:
1355: . dm  - The DM object

1357:   Note: Here is the output numbering looking from the bottom of the cylinder:
1358: $       17-----14
1359: $        |     |
1360: $        |  2  |
1361: $        |     |
1362: $ 17-----8-----7-----14
1363: $  |     |     |     |
1364: $  |  3  |  0  |  1  |
1365: $  |     |     |     |
1366: $ 19-----5-----6-----13
1367: $        |     |
1368: $        |  4  |
1369: $        |     |
1370: $       19-----13
1371: $
1372: $ and up through the top
1373: $
1374: $       18-----16
1375: $        |     |
1376: $        |  2  |
1377: $        |     |
1378: $ 18----10----11-----16
1379: $  |     |     |     |
1380: $  |  3  |  0  |  1  |
1381: $  |     |     |     |
1382: $ 20-----9----12-----15
1383: $        |     |
1384: $        |  4  |
1385: $        |     |
1386: $       20-----15

1388:   Level: beginner

1390: .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1391: @*/
1392: PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, PetscInt numRefine, DMBoundaryType periodicZ, DM *dm)
1393: {
1394:   const PetscInt dim = 3;
1395:   PetscInt       numCells, numVertices, r;
1396:   PetscMPIInt    rank;

1401:   MPI_Comm_rank(comm, &rank);
1402:   if (numRefine < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of refinements %D cannot be negative", numRefine);
1403:   DMCreate(comm, dm);
1404:   DMSetType(*dm, DMPLEX);
1405:   DMSetDimension(*dm, dim);
1406:   /* Create topology */
1407:   {
1408:     PetscInt cone[8], c;

1410:     numCells    = !rank ?  5 : 0;
1411:     numVertices = !rank ? 16 : 0;
1412:     if (periodicZ == DM_BOUNDARY_PERIODIC) {
1413:       numCells   *= 3;
1414:       numVertices = !rank ? 24 : 0;
1415:     }
1416:     DMPlexSetChart(*dm, 0, numCells+numVertices);
1417:     for (c = 0; c < numCells; c++) {DMPlexSetConeSize(*dm, c, 8);}
1418:     DMSetUp(*dm);
1419:     if (!rank) {
1420:       if (periodicZ == DM_BOUNDARY_PERIODIC) {
1421:         cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16;
1422:         cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34;
1423:         DMPlexSetCone(*dm, 0, cone);
1424:         cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23;
1425:         cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */
1426:         DMPlexSetCone(*dm, 1, cone);
1427:         cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17;
1428:         cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38;
1429:         DMPlexSetCone(*dm, 2, cone);
1430:         cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15;
1431:         cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38;
1432:         DMPlexSetCone(*dm, 3, cone);
1433:         cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23;
1434:         cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31;
1435:         DMPlexSetCone(*dm, 4, cone);

1437:         cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32;
1438:         cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20;
1439:         DMPlexSetCone(*dm, 5, cone);
1440:         cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36;
1441:         cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21;
1442:         DMPlexSetCone(*dm, 6, cone);
1443:         cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33;
1444:         cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28;
1445:         DMPlexSetCone(*dm, 7, cone);
1446:         cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31;
1447:         cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28;
1448:         DMPlexSetCone(*dm, 8, cone);
1449:         cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36;
1450:         cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19;
1451:         DMPlexSetCone(*dm, 9, cone);

1453:         cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22;
1454:         cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18;
1455:         DMPlexSetCone(*dm, 10, cone);
1456:         cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25;
1457:         cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17;
1458:         DMPlexSetCone(*dm, 11, cone);
1459:         cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21;
1460:         cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27;
1461:         DMPlexSetCone(*dm, 12, cone);
1462:         cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19;
1463:         cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27;
1464:         DMPlexSetCone(*dm, 13, cone);
1465:         cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25;
1466:         cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15;
1467:         DMPlexSetCone(*dm, 14, cone);
1468:       } else {
1469:         cone[0] =  5; cone[1] =  8; cone[2] =  7; cone[3] =  6;
1470:         cone[4] =  9; cone[5] = 12; cone[6] = 11; cone[7] = 10;
1471:         DMPlexSetCone(*dm, 0, cone);
1472:         cone[0] =  6; cone[1] =  7; cone[2] = 14; cone[3] = 13;
1473:         cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11;
1474:         DMPlexSetCone(*dm, 1, cone);
1475:         cone[0] =  8; cone[1] = 17; cone[2] = 14; cone[3] =  7;
1476:         cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18;
1477:         DMPlexSetCone(*dm, 2, cone);
1478:         cone[0] = 19; cone[1] = 17; cone[2] =  8; cone[3] =  5;
1479:         cone[4] = 20; cone[5] =  9; cone[6] = 10; cone[7] = 18;
1480:         DMPlexSetCone(*dm, 3, cone);
1481:         cone[0] = 19; cone[1] =  5; cone[2] =  6; cone[3] = 13;
1482:         cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] =  9;
1483:         DMPlexSetCone(*dm, 4, cone);
1484:       }
1485:     }
1486:     DMPlexSymmetrize(*dm);
1487:     DMPlexStratify(*dm);
1488:   }
1489:   /* Interpolate */
1490:   {
1491:     DM idm;

1493:     DMPlexInterpolate(*dm, &idm);
1494:     DMDestroy(dm);
1495:     *dm  = idm;
1496:   }
1497:   /* Create cube geometry */
1498:   {
1499:     Vec             coordinates;
1500:     PetscSection    coordSection;
1501:     PetscScalar    *coords;
1502:     PetscInt        coordSize, v;
1503:     const PetscReal dis = 1.0/PetscSqrtReal(2.0);
1504:     const PetscReal ds2 = dis/2.0;

1506:     /* Build coordinates */
1507:     DMGetCoordinateSection(*dm, &coordSection);
1508:     PetscSectionSetNumFields(coordSection, 1);
1509:     PetscSectionSetFieldComponents(coordSection, 0, dim);
1510:     PetscSectionSetChart(coordSection, numCells, numCells+numVertices);
1511:     for (v = numCells; v < numCells+numVertices; ++v) {
1512:       PetscSectionSetDof(coordSection, v, dim);
1513:       PetscSectionSetFieldDof(coordSection, v, 0, dim);
1514:     }
1515:     PetscSectionSetUp(coordSection);
1516:     PetscSectionGetStorageSize(coordSection, &coordSize);
1517:     VecCreate(PETSC_COMM_SELF, &coordinates);
1518:     PetscObjectSetName((PetscObject) coordinates, "coordinates");
1519:     VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1520:     VecSetBlockSize(coordinates, dim);
1521:     VecSetType(coordinates,VECSTANDARD);
1522:     VecGetArray(coordinates, &coords);
1523:     if (!rank) {
1524:       coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0;
1525:       coords[1*dim+0] =  ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0;
1526:       coords[2*dim+0] =  ds2; coords[2*dim+1] =  ds2; coords[2*dim+2] = 0.0;
1527:       coords[3*dim+0] = -ds2; coords[3*dim+1] =  ds2; coords[3*dim+2] = 0.0;
1528:       coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0;
1529:       coords[5*dim+0] = -ds2; coords[5*dim+1] =  ds2; coords[5*dim+2] = 1.0;
1530:       coords[6*dim+0] =  ds2; coords[6*dim+1] =  ds2; coords[6*dim+2] = 1.0;
1531:       coords[7*dim+0] =  ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0;
1532:       coords[ 8*dim+0] =  dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0;
1533:       coords[ 9*dim+0] =  dis; coords[ 9*dim+1] =  dis; coords[ 9*dim+2] = 0.0;
1534:       coords[10*dim+0] =  dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0;
1535:       coords[11*dim+0] =  dis; coords[11*dim+1] =  dis; coords[11*dim+2] = 1.0;
1536:       coords[12*dim+0] = -dis; coords[12*dim+1] =  dis; coords[12*dim+2] = 0.0;
1537:       coords[13*dim+0] = -dis; coords[13*dim+1] =  dis; coords[13*dim+2] = 1.0;
1538:       coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0;
1539:       coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0;
1540:       if (periodicZ == DM_BOUNDARY_PERIODIC) {
1541:         /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5;
1542:         /* 16 32 22 */ coords[17*dim+0] =  ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5;
1543:         /* 17 33 21 */ coords[18*dim+0] =  ds2; coords[18*dim+1] =  ds2; coords[18*dim+2] = 0.5;
1544:         /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] =  ds2; coords[19*dim+2] = 0.5;
1545:         /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5;
1546:         /* 23 36 25 */ coords[21*dim+0] =  dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5;
1547:         /* 24 37 26 */ coords[22*dim+0] =  dis; coords[22*dim+1] =  dis; coords[22*dim+2] = 0.5;
1548:         /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] =  dis; coords[23*dim+2] = 0.5;
1549:       }
1550:     }
1551:     VecRestoreArray(coordinates, &coords);
1552:     DMSetCoordinatesLocal(*dm, coordinates);
1553:     VecDestroy(&coordinates);
1554:   }
1555:   /* Create periodicity */
1556:   if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) {
1557:     PetscReal      L[3];
1558:     PetscReal      maxCell[3];
1559:     DMBoundaryType bdType[3];
1560:     PetscReal      lower[3] = {0.0, 0.0, 0.0};
1561:     PetscReal      upper[3] = {1.0, 1.0, 1.5};
1562:     PetscInt       i, numZCells = 3;

1564:     bdType[0] = DM_BOUNDARY_NONE;
1565:     bdType[1] = DM_BOUNDARY_NONE;
1566:     bdType[2] = periodicZ;
1567:     for (i = 0; i < dim; i++) {
1568:       L[i]       = upper[i] - lower[i];
1569:       maxCell[i] = 1.1 * (L[i] / numZCells);
1570:     }
1571:     DMSetPeriodicity(*dm, PETSC_TRUE, maxCell, L, bdType);
1572:   }
1573:   /* Refine topology */
1574:   for (r = 0; r < numRefine; ++r) {
1575:     DM rdm = NULL;

1577:     DMRefine(*dm, comm, &rdm);
1578:     DMDestroy(dm);
1579:     *dm  = rdm;
1580:   }
1581:   /* Remap geometry to cylinder
1582:        Interior square: Linear interpolation is correct
1583:        The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing
1584:        such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance

1586:          phi     = arctan(y/x)
1587:          d_close = sqrt(1/8 + 1/4 sin^2(phi))
1588:          d_far   = sqrt(1/2 + sin^2(phi))

1590:        so we remap them using

1592:          x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close)
1593:          y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close)

1595:        If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y.
1596:   */
1597:   {
1598:     Vec           coordinates;
1599:     PetscSection  coordSection;
1600:     PetscScalar  *coords;
1601:     PetscInt      vStart, vEnd, v;
1602:     const PetscReal dis = 1.0/PetscSqrtReal(2.0);
1603:     const PetscReal ds2 = 0.5*dis;

1605:     DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);
1606:     DMGetCoordinateSection(*dm, &coordSection);
1607:     DMGetCoordinatesLocal(*dm, &coordinates);
1608:     VecGetArray(coordinates, &coords);
1609:     for (v = vStart; v < vEnd; ++v) {
1610:       PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc;
1611:       PetscInt  off;

1613:       PetscSectionGetOffset(coordSection, v, &off);
1614:       if ((PetscAbsScalar(coords[off+0]) <= ds2) && (PetscAbsScalar(coords[off+1]) <= ds2)) continue;
1615:       x    = PetscRealPart(coords[off]);
1616:       y    = PetscRealPart(coords[off+1]);
1617:       phi  = PetscAtan2Real(y, x);
1618:       sinp = PetscSinReal(phi);
1619:       cosp = PetscCosReal(phi);
1620:       if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) {
1621:         dc = PetscAbsReal(ds2/sinp);
1622:         df = PetscAbsReal(dis/sinp);
1623:         xc = ds2*x/PetscAbsReal(y);
1624:         yc = ds2*PetscSignReal(y);
1625:       } else {
1626:         dc = PetscAbsReal(ds2/cosp);
1627:         df = PetscAbsReal(dis/cosp);
1628:         xc = ds2*PetscSignReal(x);
1629:         yc = ds2*y/PetscAbsReal(x);
1630:       }
1631:       coords[off+0] = xc + (coords[off+0] - xc)*(1.0 - dc)/(df - dc);
1632:       coords[off+1] = yc + (coords[off+1] - yc)*(1.0 - dc)/(df - dc);
1633:     }
1634:     VecRestoreArray(coordinates, &coords);
1635:     if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) {
1636:       DMLocalizeCoordinates(*dm);
1637:     }
1638:   }
1639:   return(0);
1640: }

1642: /*@
1643:   DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges.

1645:   Collective

1647:   Input Parameters:
1648: + comm - The communicator for the DM object
1649: . n    - The number of wedges around the origin
1650: - interpolate - Create edges and faces

1652:   Output Parameter:
1653: . dm  - The DM object

1655:   Level: beginner

1657: .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1658: @*/
1659: PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm)
1660: {
1661:   const PetscInt dim = 3;
1662:   PetscInt       numCells, numVertices;
1663:   PetscMPIInt    rank;

1668:   MPI_Comm_rank(comm, &rank);
1669:   if (n < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n);
1670:   DMCreate(comm, dm);
1671:   DMSetType(*dm, DMPLEX);
1672:   DMSetDimension(*dm, dim);
1673:   /* Create topology */
1674:   {
1675:     PetscInt cone[6], c;

1677:     numCells    = !rank ?        n : 0;
1678:     numVertices = !rank ?  2*(n+1) : 0;
1679:     DMPlexSetChart(*dm, 0, numCells+numVertices);
1680:     DMPlexSetHybridBounds(*dm, 0, PETSC_DETERMINE, PETSC_DETERMINE, PETSC_DETERMINE);
1681:     for (c = 0; c < numCells; c++) {DMPlexSetConeSize(*dm, c, 6);}
1682:     DMSetUp(*dm);
1683:     for (c = 0; c < numCells; c++) {
1684:       cone[0] =  c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n;
1685:       cone[3] =  c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n;
1686:       DMPlexSetCone(*dm, c, cone);
1687:     }
1688:     DMPlexSymmetrize(*dm);
1689:     DMPlexStratify(*dm);
1690:   }
1691:   /* Interpolate */
1692:   if (interpolate) {
1693:     DM idm;

1695:     DMPlexInterpolate(*dm, &idm);
1696:     DMDestroy(dm);
1697:     *dm  = idm;
1698:   }
1699:   /* Create cylinder geometry */
1700:   {
1701:     Vec          coordinates;
1702:     PetscSection coordSection;
1703:     PetscScalar *coords;
1704:     PetscInt     coordSize, v, c;

1706:     /* Build coordinates */
1707:     DMGetCoordinateSection(*dm, &coordSection);
1708:     PetscSectionSetNumFields(coordSection, 1);
1709:     PetscSectionSetFieldComponents(coordSection, 0, dim);
1710:     PetscSectionSetChart(coordSection, numCells, numCells+numVertices);
1711:     for (v = numCells; v < numCells+numVertices; ++v) {
1712:       PetscSectionSetDof(coordSection, v, dim);
1713:       PetscSectionSetFieldDof(coordSection, v, 0, dim);
1714:     }
1715:     PetscSectionSetUp(coordSection);
1716:     PetscSectionGetStorageSize(coordSection, &coordSize);
1717:     VecCreate(PETSC_COMM_SELF, &coordinates);
1718:     PetscObjectSetName((PetscObject) coordinates, "coordinates");
1719:     VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
1720:     VecSetBlockSize(coordinates, dim);
1721:     VecSetType(coordinates,VECSTANDARD);
1722:     VecGetArray(coordinates, &coords);
1723:     for (c = 0; c < numCells; c++) {
1724:       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;
1725:       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;
1726:     }
1727:     if (!rank) {
1728:       coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0;
1729:       coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0;
1730:     }
1731:     VecRestoreArray(coordinates, &coords);
1732:     DMSetCoordinatesLocal(*dm, coordinates);
1733:     VecDestroy(&coordinates);
1734:   }
1735:   return(0);
1736: }

1738: PETSC_STATIC_INLINE PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
1739: {
1740:   PetscReal prod = 0.0;
1741:   PetscInt  i;
1742:   for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]);
1743:   return PetscSqrtReal(prod);
1744: }
1745: PETSC_STATIC_INLINE PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[])
1746: {
1747:   PetscReal prod = 0.0;
1748:   PetscInt  i;
1749:   for (i = 0; i < dim; ++i) prod += x[i]*y[i];
1750:   return prod;
1751: }

1753: /*@
1754:   DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d.

1756:   Collective

1758:   Input Parameters:
1759: + comm  - The communicator for the DM object
1760: . dim   - The dimension
1761: - simplex - Use simplices, or tensor product cells

1763:   Output Parameter:
1764: . dm  - The DM object

1766:   Level: beginner

1768: .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate()
1769: @*/
1770: PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *dm)
1771: {
1772:   const PetscInt  embedDim = dim+1;
1773:   PetscSection    coordSection;
1774:   Vec             coordinates;
1775:   PetscScalar    *coords;
1776:   PetscReal      *coordsIn;
1777:   PetscInt        numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e;
1778:   PetscMPIInt     rank;
1779:   PetscErrorCode  ierr;

1783:   DMCreate(comm, dm);
1784:   DMSetType(*dm, DMPLEX);
1785:   DMSetDimension(*dm, dim);
1786:   DMSetCoordinateDim(*dm, dim+1);
1787:   MPI_Comm_rank(PetscObjectComm((PetscObject) *dm), &rank);
1788:   switch (dim) {
1789:   case 2:
1790:     if (simplex) {
1791:       DM              idm;
1792:       const PetscReal edgeLen     = 2.0/(1.0 + PETSC_PHI);
1793:       const PetscReal vertex[3]   = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)};
1794:       const PetscInt  degree      = 5;
1795:       PetscInt        s[3]        = {1, 1, 1};
1796:       PetscInt        cone[3];
1797:       PetscInt       *graph, p, i, j, k;

1799:       numCells    = !rank ? 20 : 0;
1800:       numVerts    = !rank ? 12 : 0;
1801:       firstVertex = numCells;
1802:       /* Use icosahedron, which for a unit sphere has coordinates which are all cyclic permutations of

1804:            (0, \pm 1/\phi+1, \pm \phi/\phi+1)

1806:          where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
1807:          length is then given by 2/\phi = 2 * 0.61803 = 1.23606.
1808:       */
1809:       /* Construct vertices */
1810:       PetscCalloc1(numVerts * embedDim, &coordsIn);
1811:       if (!rank) {
1812:         for (p = 0, i = 0; p < embedDim; ++p) {
1813:           for (s[1] = -1; s[1] < 2; s[1] += 2) {
1814:             for (s[2] = -1; s[2] < 2; s[2] += 2) {
1815:               for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim];
1816:               ++i;
1817:             }
1818:           }
1819:         }
1820:       }
1821:       /* Construct graph */
1822:       PetscCalloc1(numVerts * numVerts, &graph);
1823:       for (i = 0; i < numVerts; ++i) {
1824:         for (j = 0, k = 0; j < numVerts; ++j) {
1825:           if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;}
1826:         }
1827:         if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree);
1828:       }
1829:       /* Build Topology */
1830:       DMPlexSetChart(*dm, 0, numCells+numVerts);
1831:       for (c = 0; c < numCells; c++) {
1832:         DMPlexSetConeSize(*dm, c, embedDim);
1833:       }
1834:       DMSetUp(*dm); /* Allocate space for cones */
1835:       /* Cells */
1836:       for (i = 0, c = 0; i < numVerts; ++i) {
1837:         for (j = 0; j < i; ++j) {
1838:           for (k = 0; k < j; ++k) {
1839:             if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) {
1840:               cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k;
1841:               /* Check orientation */
1842:               {
1843:                 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}}};
1844:                 PetscReal normal[3];
1845:                 PetscInt  e, f;

1847:                 for (d = 0; d < embedDim; ++d) {
1848:                   normal[d] = 0.0;
1849:                   for (e = 0; e < embedDim; ++e) {
1850:                     for (f = 0; f < embedDim; ++f) {
1851:                       normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]);
1852:                     }
1853:                   }
1854:                 }
1855:                 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;}
1856:               }
1857:               DMPlexSetCone(*dm, c++, cone);
1858:             }
1859:           }
1860:         }
1861:       }
1862:       DMPlexSymmetrize(*dm);
1863:       DMPlexStratify(*dm);
1864:       PetscFree(graph);
1865:       /* Interpolate mesh */
1866:       DMPlexInterpolate(*dm, &idm);
1867:       DMDestroy(dm);
1868:       *dm  = idm;
1869:     } else {
1870:       /*
1871:         12-21--13
1872:          |     |
1873:         25  4  24
1874:          |     |
1875:   12-25--9-16--8-24--13
1876:    |     |     |     |
1877:   23  5 17  0 15  3  22
1878:    |     |     |     |
1879:   10-20--6-14--7-19--11
1880:          |     |
1881:         20  1  19
1882:          |     |
1883:         10-18--11
1884:          |     |
1885:         23  2  22
1886:          |     |
1887:         12-21--13
1888:        */
1889:       const PetscReal dist = 1.0/PetscSqrtReal(3.0);
1890:       PetscInt        cone[4], ornt[4];

1892:       numCells    = !rank ?  6 : 0;
1893:       numEdges    = !rank ? 12 : 0;
1894:       numVerts    = !rank ?  8 : 0;
1895:       firstVertex = numCells;
1896:       firstEdge   = numCells + numVerts;
1897:       /* Build Topology */
1898:       DMPlexSetChart(*dm, 0, numCells+numEdges+numVerts);
1899:       for (c = 0; c < numCells; c++) {
1900:         DMPlexSetConeSize(*dm, c, 4);
1901:       }
1902:       for (e = firstEdge; e < firstEdge+numEdges; ++e) {
1903:         DMPlexSetConeSize(*dm, e, 2);
1904:       }
1905:       DMSetUp(*dm); /* Allocate space for cones */
1906:       if (!rank) {
1907:         /* Cell 0 */
1908:         cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17;
1909:         DMPlexSetCone(*dm, 0, cone);
1910:         ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0;
1911:         DMPlexSetConeOrientation(*dm, 0, ornt);
1912:         /* Cell 1 */
1913:         cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20;
1914:         DMPlexSetCone(*dm, 1, cone);
1915:         ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0;
1916:         DMPlexSetConeOrientation(*dm, 1, ornt);
1917:         /* Cell 2 */
1918:         cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23;
1919:         DMPlexSetCone(*dm, 2, cone);
1920:         ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0;
1921:         DMPlexSetConeOrientation(*dm, 2, ornt);
1922:         /* Cell 3 */
1923:         cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15;
1924:         DMPlexSetCone(*dm, 3, cone);
1925:         ornt[0] = -2; ornt[1] = -2; ornt[2] = 0; ornt[3] = -2;
1926:         DMPlexSetConeOrientation(*dm, 3, ornt);
1927:         /* Cell 4 */
1928:         cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25;
1929:         DMPlexSetCone(*dm, 4, cone);
1930:         ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = 0;
1931:         DMPlexSetConeOrientation(*dm, 4, ornt);
1932:         /* Cell 5 */
1933:         cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23;
1934:         DMPlexSetCone(*dm, 5, cone);
1935:         ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = -2;
1936:         DMPlexSetConeOrientation(*dm, 5, ornt);
1937:         /* Edges */
1938:         cone[0] =  6; cone[1] =  7;
1939:         DMPlexSetCone(*dm, 14, cone);
1940:         cone[0] =  7; cone[1] =  8;
1941:         DMPlexSetCone(*dm, 15, cone);
1942:         cone[0] =  8; cone[1] =  9;
1943:         DMPlexSetCone(*dm, 16, cone);
1944:         cone[0] =  9; cone[1] =  6;
1945:         DMPlexSetCone(*dm, 17, cone);
1946:         cone[0] = 10; cone[1] = 11;
1947:         DMPlexSetCone(*dm, 18, cone);
1948:         cone[0] = 11; cone[1] =  7;
1949:         DMPlexSetCone(*dm, 19, cone);
1950:         cone[0] =  6; cone[1] = 10;
1951:         DMPlexSetCone(*dm, 20, cone);
1952:         cone[0] = 12; cone[1] = 13;
1953:         DMPlexSetCone(*dm, 21, cone);
1954:         cone[0] = 13; cone[1] = 11;
1955:         DMPlexSetCone(*dm, 22, cone);
1956:         cone[0] = 10; cone[1] = 12;
1957:         DMPlexSetCone(*dm, 23, cone);
1958:         cone[0] = 13; cone[1] =  8;
1959:         DMPlexSetCone(*dm, 24, cone);
1960:         cone[0] = 12; cone[1] =  9;
1961:         DMPlexSetCone(*dm, 25, cone);
1962:       }
1963:       DMPlexSymmetrize(*dm);
1964:       DMPlexStratify(*dm);
1965:       /* Build coordinates */
1966:       PetscCalloc1(numVerts * embedDim, &coordsIn);
1967:       if (!rank) {
1968:         coordsIn[0*embedDim+0] = -dist; coordsIn[0*embedDim+1] =  dist; coordsIn[0*embedDim+2] = -dist;
1969:         coordsIn[1*embedDim+0] =  dist; coordsIn[1*embedDim+1] =  dist; coordsIn[1*embedDim+2] = -dist;
1970:         coordsIn[2*embedDim+0] =  dist; coordsIn[2*embedDim+1] = -dist; coordsIn[2*embedDim+2] = -dist;
1971:         coordsIn[3*embedDim+0] = -dist; coordsIn[3*embedDim+1] = -dist; coordsIn[3*embedDim+2] = -dist;
1972:         coordsIn[4*embedDim+0] = -dist; coordsIn[4*embedDim+1] =  dist; coordsIn[4*embedDim+2] =  dist;
1973:         coordsIn[5*embedDim+0] =  dist; coordsIn[5*embedDim+1] =  dist; coordsIn[5*embedDim+2] =  dist;
1974:         coordsIn[6*embedDim+0] = -dist; coordsIn[6*embedDim+1] = -dist; coordsIn[6*embedDim+2] =  dist;
1975:         coordsIn[7*embedDim+0] =  dist; coordsIn[7*embedDim+1] = -dist; coordsIn[7*embedDim+2] =  dist;
1976:       }
1977:     }
1978:     break;
1979:   case 3:
1980:     if (simplex) {
1981:       DM              idm;
1982:       const PetscReal edgeLen         = 1.0/PETSC_PHI;
1983:       const PetscReal vertexA[4]      = {0.5, 0.5, 0.5, 0.5};
1984:       const PetscReal vertexB[4]      = {1.0, 0.0, 0.0, 0.0};
1985:       const PetscReal vertexC[4]      = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0};
1986:       const PetscInt  degree          = 12;
1987:       PetscInt        s[4]            = {1, 1, 1};
1988:       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},
1989:                                          {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}};
1990:       PetscInt        cone[4];
1991:       PetscInt       *graph, p, i, j, k, l;

1993:       numCells    = !rank ? 600 : 0;
1994:       numVerts    = !rank ? 120 : 0;
1995:       firstVertex = numCells;
1996:       /* Use the 600-cell, which for a unit sphere has coordinates which are

1998:            1/2 (\pm 1, \pm 1,    \pm 1, \pm 1)                          16
1999:                (\pm 1,    0,       0,      0)  all cyclic permutations   8
2000:            1/2 (\pm 1, \pm phi, \pm 1/phi, 0)  all even permutations    96

2002:          where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge
2003:          length is then given by 1/\phi = 0.61803.

2005:          http://buzzard.pugetsound.edu/sage-practice/ch03s03.html
2006:          http://mathworld.wolfram.com/600-Cell.html
2007:       */
2008:       /* Construct vertices */
2009:       PetscCalloc1(numVerts * embedDim, &coordsIn);
2010:       i    = 0;
2011:       if (!rank) {
2012:         for (s[0] = -1; s[0] < 2; s[0] += 2) {
2013:           for (s[1] = -1; s[1] < 2; s[1] += 2) {
2014:             for (s[2] = -1; s[2] < 2; s[2] += 2) {
2015:               for (s[3] = -1; s[3] < 2; s[3] += 2) {
2016:                 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d];
2017:                 ++i;
2018:               }
2019:             }
2020:           }
2021:         }
2022:         for (p = 0; p < embedDim; ++p) {
2023:           s[1] = s[2] = s[3] = 1;
2024:           for (s[0] = -1; s[0] < 2; s[0] += 2) {
2025:             for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim];
2026:             ++i;
2027:           }
2028:         }
2029:         for (p = 0; p < 12; ++p) {
2030:           s[3] = 1;
2031:           for (s[0] = -1; s[0] < 2; s[0] += 2) {
2032:             for (s[1] = -1; s[1] < 2; s[1] += 2) {
2033:               for (s[2] = -1; s[2] < 2; s[2] += 2) {
2034:                 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]];
2035:                 ++i;
2036:               }
2037:             }
2038:           }
2039:         }
2040:       }
2041:       if (i != numVerts) SETERRQ2(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts);
2042:       /* Construct graph */
2043:       PetscCalloc1(numVerts * numVerts, &graph);
2044:       for (i = 0; i < numVerts; ++i) {
2045:         for (j = 0, k = 0; j < numVerts; ++j) {
2046:           if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;}
2047:         }
2048:         if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree);
2049:       }
2050:       /* Build Topology */
2051:       DMPlexSetChart(*dm, 0, numCells+numVerts);
2052:       for (c = 0; c < numCells; c++) {
2053:         DMPlexSetConeSize(*dm, c, embedDim);
2054:       }
2055:       DMSetUp(*dm); /* Allocate space for cones */
2056:       /* Cells */
2057:       if (!rank) {
2058:         for (i = 0, c = 0; i < numVerts; ++i) {
2059:           for (j = 0; j < i; ++j) {
2060:             for (k = 0; k < j; ++k) {
2061:               for (l = 0; l < k; ++l) {
2062:                 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] &&
2063:                     graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) {
2064:                   cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l;
2065:                   /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */
2066:                   {
2067:                     const PetscInt epsilon[4][4][4][4] = {{{{0,  0,  0,  0}, { 0, 0,  0,  0}, { 0,  0, 0,  0}, { 0,  0,  0, 0}},
2068:                                                            {{0,  0,  0,  0}, { 0, 0,  0,  0}, { 0,  0, 0,  1}, { 0,  0, -1, 0}},
2069:                                                            {{0,  0,  0,  0}, { 0, 0,  0, -1}, { 0,  0, 0,  0}, { 0,  1,  0, 0}},
2070:                                                            {{0,  0,  0,  0}, { 0, 0,  1,  0}, { 0, -1, 0,  0}, { 0,  0,  0, 0}}},

2072:                                                           {{{0,  0,  0,  0}, { 0, 0,  0,  0}, { 0,  0, 0, -1}, { 0,  0,  1, 0}},
2073:                                                            {{0,  0,  0,  0}, { 0, 0,  0,  0}, { 0,  0, 0,  0}, { 0,  0,  0, 0}},
2074:                                                            {{0,  0,  0,  1}, { 0, 0,  0,  0}, { 0,  0, 0,  0}, {-1,  0,  0, 0}},
2075:                                                            {{0,  0, -1,  0}, { 0, 0,  0,  0}, { 1,  0, 0,  0}, { 0,  0,  0, 0}}},

2077:                                                           {{{0,  0,  0,  0}, { 0, 0,  0,  1}, { 0,  0, 0,  0}, { 0, -1,  0, 0}},
2078:                                                            {{0,  0,  0, -1}, { 0, 0,  0,  0}, { 0,  0, 0,  0}, { 1,  0,  0, 0}},
2079:                                                            {{0,  0,  0,  0}, { 0, 0,  0,  0}, { 0,  0, 0,  0}, { 0,  0,  0, 0}},
2080:                                                            {{0,  1,  0,  0}, {-1, 0,  0,  0}, { 0,  0, 0,  0}, { 0,  0,  0, 0}}},

2082:                                                           {{{0,  0,  0,  0}, { 0, 0, -1,  0}, { 0,  1, 0,  0}, { 0,  0,  0, 0}},
2083:                                                            {{0,  0,  1,  0}, { 0, 0,  0,  0}, {-1,  0, 0,  0}, { 0,  0,  0, 0}},
2084:                                                            {{0, -1,  0,  0}, { 1, 0,  0,  0}, { 0,  0, 0,  0}, { 0,  0,  0, 0}},
2085:                                                            {{0,  0,  0,  0}, { 0, 0,  0,  0}, { 0,  0, 0,  0}, { 0,  0,  0, 0}}}};
2086:                     PetscReal normal[4];
2087:                     PetscInt  e, f, g;

2089:                     for (d = 0; d < embedDim; ++d) {
2090:                       normal[d] = 0.0;
2091:                       for (e = 0; e < embedDim; ++e) {
2092:                         for (f = 0; f < embedDim; ++f) {
2093:                           for (g = 0; g < embedDim; ++g) {
2094:                             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]);
2095:                           }
2096:                         }
2097:                       }
2098:                     }
2099:                     if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;}
2100:                   }
2101:                   DMPlexSetCone(*dm, c++, cone);
2102:                 }
2103:               }
2104:             }
2105:           }
2106:         }
2107:       }
2108:       DMPlexSymmetrize(*dm);
2109:       DMPlexStratify(*dm);
2110:       PetscFree(graph);
2111:       /* Interpolate mesh */
2112:       DMPlexInterpolate(*dm, &idm);
2113:       DMDestroy(dm);
2114:       *dm  = idm;
2115:       break;
2116:     }
2117:   default: SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim);
2118:   }
2119:   /* Create coordinates */
2120:   DMGetCoordinateSection(*dm, &coordSection);
2121:   PetscSectionSetNumFields(coordSection, 1);
2122:   PetscSectionSetFieldComponents(coordSection, 0, embedDim);
2123:   PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);
2124:   for (v = firstVertex; v < firstVertex+numVerts; ++v) {
2125:     PetscSectionSetDof(coordSection, v, embedDim);
2126:     PetscSectionSetFieldDof(coordSection, v, 0, embedDim);
2127:   }
2128:   PetscSectionSetUp(coordSection);
2129:   PetscSectionGetStorageSize(coordSection, &coordSize);
2130:   VecCreate(PETSC_COMM_SELF, &coordinates);
2131:   VecSetBlockSize(coordinates, embedDim);
2132:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
2133:   VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
2134:   VecSetType(coordinates,VECSTANDARD);
2135:   VecGetArray(coordinates, &coords);
2136:   for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];}
2137:   VecRestoreArray(coordinates, &coords);
2138:   DMSetCoordinatesLocal(*dm, coordinates);
2139:   VecDestroy(&coordinates);
2140:   PetscFree(coordsIn);
2141:   return(0);
2142: }

2144: /* External function declarations here */
2145: extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling);
2146: extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat);
2147: extern PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mat);
2148: extern PetscErrorCode DMCreateLocalSection_Plex(DM dm);
2149: extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm);
2150: extern PetscErrorCode DMCreateMatrix_Plex(DM dm,  Mat *J);
2151: extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm);
2152: extern PetscErrorCode DMCreateCoordinateField_Plex(DM dm, DMField *field);
2153: PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm);
2154: extern PetscErrorCode DMSetUp_Plex(DM dm);
2155: extern PetscErrorCode DMDestroy_Plex(DM dm);
2156: extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer);
2157: extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer);
2158: extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm);
2159: extern PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm);
2160: static PetscErrorCode DMInitialize_Plex(DM dm);

2162: /* Replace dm with the contents of dmNew
2163:    - Share the DM_Plex structure
2164:    - Share the coordinates
2165:    - Share the SF
2166: */
2167: static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew)
2168: {
2169:   PetscSF               sf;
2170:   DM                    coordDM, coarseDM;
2171:   Vec                   coords;
2172:   PetscBool             isper;
2173:   const PetscReal      *maxCell, *L;
2174:   const DMBoundaryType *bd;
2175:   PetscErrorCode        ierr;

2178:   DMGetPointSF(dmNew, &sf);
2179:   DMSetPointSF(dm, sf);
2180:   DMGetCoordinateDM(dmNew, &coordDM);
2181:   DMGetCoordinatesLocal(dmNew, &coords);
2182:   DMSetCoordinateDM(dm, coordDM);
2183:   DMSetCoordinatesLocal(dm, coords);
2184:   DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);
2185:   DMSetPeriodicity(dmNew, isper, maxCell, L, bd);
2186:   DMDestroy_Plex(dm);
2187:   DMInitialize_Plex(dm);
2188:   dm->data = dmNew->data;
2189:   ((DM_Plex *) dmNew->data)->refct++;
2190:   DMDestroyLabelLinkList_Internal(dm);
2191:   DMCopyLabels(dmNew, dm, PETSC_OWN_POINTER, PETSC_TRUE);
2192:   DMGetCoarseDM(dmNew,&coarseDM);
2193:   DMSetCoarseDM(dm,coarseDM);
2194:   return(0);
2195: }

2197: /* Swap dm with the contents of dmNew
2198:    - Swap the DM_Plex structure
2199:    - Swap the coordinates
2200:    - Swap the point PetscSF
2201: */
2202: static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB)
2203: {
2204:   DM              coordDMA, coordDMB;
2205:   Vec             coordsA,  coordsB;
2206:   PetscSF         sfA,      sfB;
2207:   void            *tmp;
2208:   DMLabelLink     listTmp;
2209:   DMLabel         depthTmp;
2210:   PetscInt        tmpI;
2211:   PetscErrorCode  ierr;

2214:   DMGetPointSF(dmA, &sfA);
2215:   DMGetPointSF(dmB, &sfB);
2216:   PetscObjectReference((PetscObject) sfA);
2217:   DMSetPointSF(dmA, sfB);
2218:   DMSetPointSF(dmB, sfA);
2219:   PetscObjectDereference((PetscObject) sfA);

2221:   DMGetCoordinateDM(dmA, &coordDMA);
2222:   DMGetCoordinateDM(dmB, &coordDMB);
2223:   PetscObjectReference((PetscObject) coordDMA);
2224:   DMSetCoordinateDM(dmA, coordDMB);
2225:   DMSetCoordinateDM(dmB, coordDMA);
2226:   PetscObjectDereference((PetscObject) coordDMA);

2228:   DMGetCoordinatesLocal(dmA, &coordsA);
2229:   DMGetCoordinatesLocal(dmB, &coordsB);
2230:   PetscObjectReference((PetscObject) coordsA);
2231:   DMSetCoordinatesLocal(dmA, coordsB);
2232:   DMSetCoordinatesLocal(dmB, coordsA);
2233:   PetscObjectDereference((PetscObject) coordsA);

2235:   tmp       = dmA->data;
2236:   dmA->data = dmB->data;
2237:   dmB->data = tmp;
2238:   listTmp   = dmA->labels;
2239:   dmA->labels = dmB->labels;
2240:   dmB->labels = listTmp;
2241:   depthTmp  = dmA->depthLabel;
2242:   dmA->depthLabel = dmB->depthLabel;
2243:   dmB->depthLabel = depthTmp;
2244:   depthTmp  = dmA->celltypeLabel;
2245:   dmA->celltypeLabel = dmB->celltypeLabel;
2246:   dmB->celltypeLabel = depthTmp;
2247:   tmpI         = dmA->levelup;
2248:   dmA->levelup = dmB->levelup;
2249:   dmB->levelup = tmpI;
2250:   return(0);
2251: }

2253: PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm)
2254: {
2255:   DM_Plex       *mesh = (DM_Plex*) dm->data;
2256:   PetscBool      flg;

2260:   /* Handle viewing */
2261:   PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL);
2262:   PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL,0);
2263:   PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL);
2264:   PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL,0);
2265:   DMMonitorSetFromOptions(dm, "-dm_plex_monitor_throughput", "Monitor the simulation throughput", "DMPlexMonitorThroughput", DMPlexMonitorThroughput, NULL, &flg);
2266:   if (flg) {PetscLogDefaultBegin();}
2267:   /* Point Location */
2268:   PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL);
2269:   /* Partitioning and distribution */
2270:   PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL);
2271:   /* Generation and remeshing */
2272:   PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL);
2273:   /* Projection behavior */
2274:   PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL,0);
2275:   PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);
2276:   /* Checking structure */
2277:   {
2278:     PetscBool   flg = PETSC_FALSE, flg2 = PETSC_FALSE, all = PETSC_FALSE;

2280:     PetscOptionsBool("-dm_plex_check_all", "Perform all checks", NULL, PETSC_FALSE, &all, &flg2);
2281:     PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2);
2282:     if (all || (flg && flg2)) {DMPlexCheckSymmetry(dm);}
2283:     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);
2284:     if (all || (flg && flg2)) {DMPlexCheckSkeleton(dm, 0);}
2285:     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);
2286:     if (all || (flg && flg2)) {DMPlexCheckFaces(dm, 0);}
2287:     PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2);
2288:     if (all || (flg && flg2)) {DMPlexCheckGeometry(dm);}
2289:     PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2);
2290:     if (all || (flg && flg2)) {DMPlexCheckPointSF(dm);}
2291:     PetscOptionsBool("-dm_plex_check_interface_cones", "Check points on inter-partition interfaces have conforming order of cone points", "DMPlexCheckInterfaceCones", PETSC_FALSE, &flg, &flg2);
2292:     if (all || (flg && flg2)) {DMPlexCheckInterfaceCones(dm);}
2293:   }

2295:   PetscPartitionerSetFromOptions(mesh->partitioner);
2296:   return(0);
2297: }

2299: static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm)
2300: {
2301:   PetscInt       refine = 0, coarsen = 0, r;
2302:   PetscBool      isHierarchy;

2307:   PetscOptionsHead(PetscOptionsObject,"DMPlex Options");
2308:   /* Handle DMPlex refinement */
2309:   PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL,0);
2310:   PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy,0);
2311:   if (refine) {DMPlexSetRefinementUniform(dm, PETSC_TRUE);}
2312:   if (refine && isHierarchy) {
2313:     DM *dms, coarseDM;

2315:     DMGetCoarseDM(dm, &coarseDM);
2316:     PetscObjectReference((PetscObject)coarseDM);
2317:     PetscMalloc1(refine,&dms);
2318:     DMRefineHierarchy(dm, refine, dms);
2319:     /* Total hack since we do not pass in a pointer */
2320:     DMPlexSwap_Static(dm, dms[refine-1]);
2321:     if (refine == 1) {
2322:       DMSetCoarseDM(dm, dms[0]);
2323:       DMPlexSetRegularRefinement(dm, PETSC_TRUE);
2324:     } else {
2325:       DMSetCoarseDM(dm, dms[refine-2]);
2326:       DMPlexSetRegularRefinement(dm, PETSC_TRUE);
2327:       DMSetCoarseDM(dms[0], dms[refine-1]);
2328:       DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);
2329:     }
2330:     DMSetCoarseDM(dms[refine-1], coarseDM);
2331:     PetscObjectDereference((PetscObject)coarseDM);
2332:     /* Free DMs */
2333:     for (r = 0; r < refine; ++r) {
2334:       DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);
2335:       DMDestroy(&dms[r]);
2336:     }
2337:     PetscFree(dms);
2338:   } else {
2339:     for (r = 0; r < refine; ++r) {
2340:       DM refinedMesh;

2342:       DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2343:       DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);
2344:       /* Total hack since we do not pass in a pointer */
2345:       DMPlexReplace_Static(dm, refinedMesh);
2346:       DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2347:       DMDestroy(&refinedMesh);
2348:     }
2349:   }
2350:   /* Handle DMPlex coarsening */
2351:   PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL,0);
2352:   PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy,0);
2353:   if (coarsen && isHierarchy) {
2354:     DM *dms;

2356:     PetscMalloc1(coarsen, &dms);
2357:     DMCoarsenHierarchy(dm, coarsen, dms);
2358:     /* Free DMs */
2359:     for (r = 0; r < coarsen; ++r) {
2360:       DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);
2361:       DMDestroy(&dms[r]);
2362:     }
2363:     PetscFree(dms);
2364:   } else {
2365:     for (r = 0; r < coarsen; ++r) {
2366:       DM coarseMesh;

2368:       DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2369:       DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);
2370:       /* Total hack since we do not pass in a pointer */
2371:       DMPlexReplace_Static(dm, coarseMesh);
2372:       DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2373:       DMDestroy(&coarseMesh);
2374:     }
2375:   }
2376:   /* Handle */
2377:   DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);
2378:   PetscOptionsTail();
2379:   return(0);
2380: }

2382: static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec)
2383: {

2387:   DMCreateGlobalVector_Section_Private(dm,vec);
2388:   /* VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM); */
2389:   VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);
2390:   VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);
2391:   VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);
2392:   VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);
2393:   return(0);
2394: }

2396: static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec)
2397: {

2401:   DMCreateLocalVector_Section_Private(dm,vec);
2402:   VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);
2403:   VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);
2404:   return(0);
2405: }

2407: static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd)
2408: {
2409:   PetscInt       depth, d;

2413:   DMPlexGetDepth(dm, &depth);
2414:   if (depth == 1) {
2415:     DMGetDimension(dm, &d);
2416:     if (dim == 0)      {DMPlexGetDepthStratum(dm, dim, pStart, pEnd);}
2417:     else if (dim == d) {DMPlexGetDepthStratum(dm, 1, pStart, pEnd);}
2418:     else               {*pStart = 0; *pEnd = 0;}
2419:   } else {
2420:     DMPlexGetDepthStratum(dm, dim, pStart, pEnd);
2421:   }
2422:   return(0);
2423: }

2425: static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[])
2426: {
2427:   PetscSF        sf;

2431:   DMGetPointSF(dm, &sf);
2432:   PetscSFGetRootRanks(sf, nranks, ranks, NULL, NULL, NULL);
2433:   return(0);
2434: }

2436: static PetscErrorCode DMInitialize_Plex(DM dm)
2437: {

2441:   dm->ops->view                            = DMView_Plex;
2442:   dm->ops->load                            = DMLoad_Plex;
2443:   dm->ops->setfromoptions                  = DMSetFromOptions_Plex;
2444:   dm->ops->clone                           = DMClone_Plex;
2445:   dm->ops->setup                           = DMSetUp_Plex;
2446:   dm->ops->createlocalsection              = DMCreateLocalSection_Plex;
2447:   dm->ops->createdefaultconstraints        = DMCreateDefaultConstraints_Plex;
2448:   dm->ops->createglobalvector              = DMCreateGlobalVector_Plex;
2449:   dm->ops->createlocalvector               = DMCreateLocalVector_Plex;
2450:   dm->ops->getlocaltoglobalmapping         = NULL;
2451:   dm->ops->createfieldis                   = NULL;
2452:   dm->ops->createcoordinatedm              = DMCreateCoordinateDM_Plex;
2453:   dm->ops->createcoordinatefield           = DMCreateCoordinateField_Plex;
2454:   dm->ops->getcoloring                     = NULL;
2455:   dm->ops->creatematrix                    = DMCreateMatrix_Plex;
2456:   dm->ops->createinterpolation             = DMCreateInterpolation_Plex;
2457:   dm->ops->createmassmatrix                = DMCreateMassMatrix_Plex;
2458:   dm->ops->createinjection                 = DMCreateInjection_Plex;
2459:   dm->ops->refine                          = DMRefine_Plex;
2460:   dm->ops->coarsen                         = DMCoarsen_Plex;
2461:   dm->ops->refinehierarchy                 = DMRefineHierarchy_Plex;
2462:   dm->ops->coarsenhierarchy                = DMCoarsenHierarchy_Plex;
2463:   dm->ops->adaptlabel                      = DMAdaptLabel_Plex;
2464:   dm->ops->adaptmetric                     = DMAdaptMetric_Plex;
2465:   dm->ops->globaltolocalbegin              = NULL;
2466:   dm->ops->globaltolocalend                = NULL;
2467:   dm->ops->localtoglobalbegin              = NULL;
2468:   dm->ops->localtoglobalend                = NULL;
2469:   dm->ops->destroy                         = DMDestroy_Plex;
2470:   dm->ops->createsubdm                     = DMCreateSubDM_Plex;
2471:   dm->ops->createsuperdm                   = DMCreateSuperDM_Plex;
2472:   dm->ops->getdimpoints                    = DMGetDimPoints_Plex;
2473:   dm->ops->locatepoints                    = DMLocatePoints_Plex;
2474:   dm->ops->projectfunctionlocal            = DMProjectFunctionLocal_Plex;
2475:   dm->ops->projectfunctionlabellocal       = DMProjectFunctionLabelLocal_Plex;
2476:   dm->ops->projectfieldlocal               = DMProjectFieldLocal_Plex;
2477:   dm->ops->projectfieldlabellocal          = DMProjectFieldLabelLocal_Plex;
2478:   dm->ops->computel2diff                   = DMComputeL2Diff_Plex;
2479:   dm->ops->computel2gradientdiff           = DMComputeL2GradientDiff_Plex;
2480:   dm->ops->computel2fielddiff              = DMComputeL2FieldDiff_Plex;
2481:   dm->ops->getneighbors                    = DMGetNeighbors_Plex;
2482:   PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);
2483:   PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);
2484:   PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C",DMCreateNeumannOverlap_Plex);
2485:   PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex);
2486:   return(0);
2487: }

2489: PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm)
2490: {
2491:   DM_Plex        *mesh = (DM_Plex *) dm->data;

2495:   mesh->refct++;
2496:   (*newdm)->data = mesh;
2497:   PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);
2498:   DMInitialize_Plex(*newdm);
2499:   return(0);
2500: }

2502: /*MC
2503:   DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram.
2504:                     In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is
2505:                     specified by a PetscSection object. Ownership in the global representation is determined by
2506:                     ownership of the underlying DMPlex points. This is specified by another PetscSection object.

2508:   Options Database Keys:
2509: + -dm_plex_hash_location             - Use grid hashing for point location
2510: . -dm_plex_partition_balance         - Attempt to evenly divide points on partition boundary between processes
2511: . -dm_plex_remesh_bd                 - Allow changes to the boundary on remeshing
2512: . -dm_plex_max_projection_height     - Maxmimum mesh point height used to project locally
2513: . -dm_plex_regular_refinement        - Use special nested projection algorithm for regular refinement
2514: . -dm_plex_check_symmetry            - Check that the adjacency information in the mesh is symmetric
2515: . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices
2516: . -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
2517: . -dm_plex_check_geometry            - Check that cells have positive volume
2518: . -dm_view :mesh.tex:ascii_latex     - View the mesh in LaTeX/TikZ
2519: . -dm_plex_view_scale <num>          - Scale the TikZ
2520: - -dm_plex_print_fem <num>           - View FEM assembly information, such as element vectors and matrices


2523:   Level: intermediate

2525: .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType()
2526: M*/

2528: PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm)
2529: {
2530:   DM_Plex        *mesh;
2531:   PetscInt       unit, d;

2536:   PetscNewLog(dm,&mesh);
2537:   dm->dim  = 0;
2538:   dm->data = mesh;

2540:   mesh->refct             = 1;
2541:   PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);
2542:   mesh->maxConeSize       = 0;
2543:   mesh->cones             = NULL;
2544:   mesh->coneOrientations  = NULL;
2545:   PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);
2546:   mesh->maxSupportSize    = 0;
2547:   mesh->supports          = NULL;
2548:   mesh->refinementUniform = PETSC_TRUE;
2549:   mesh->refinementLimit   = -1.0;
2550:   mesh->ghostCellStart    = -1;
2551:   mesh->interpolated      = DMPLEX_INTERPOLATED_INVALID;
2552:   mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID;

2554:   mesh->facesTmp = NULL;

2556:   mesh->tetgenOpts   = NULL;
2557:   mesh->triangleOpts = NULL;
2558:   PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);
2559:   mesh->remeshBd     = PETSC_FALSE;

2561:   mesh->subpointMap = NULL;

2563:   for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0;

2565:   mesh->regularRefinement   = PETSC_FALSE;
2566:   mesh->depthState          = -1;
2567:   mesh->celltypeState       = -1;
2568:   mesh->globalVertexNumbers = NULL;
2569:   mesh->globalCellNumbers   = NULL;
2570:   mesh->anchorSection       = NULL;
2571:   mesh->anchorIS            = NULL;
2572:   mesh->createanchors       = NULL;
2573:   mesh->computeanchormatrix = NULL;
2574:   mesh->parentSection       = NULL;
2575:   mesh->parents             = NULL;
2576:   mesh->childIDs            = NULL;
2577:   mesh->childSection        = NULL;
2578:   mesh->children            = NULL;
2579:   mesh->referenceTree       = NULL;
2580:   mesh->getchildsymmetry    = NULL;
2581:   for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE;
2582:   mesh->vtkCellHeight       = 0;
2583:   mesh->useAnchors          = PETSC_FALSE;

2585:   mesh->maxProjectionHeight = 0;

2587:   mesh->printSetValues = PETSC_FALSE;
2588:   mesh->printFEM       = 0;
2589:   mesh->printTol       = 1.0e-10;

2591:   DMInitialize_Plex(dm);
2592:   return(0);
2593: }

2595: /*@
2596:   DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram.

2598:   Collective

2600:   Input Parameter:
2601: . comm - The communicator for the DMPlex object

2603:   Output Parameter:
2604: . mesh  - The DMPlex object

2606:   Level: beginner

2608: @*/
2609: PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh)
2610: {

2615:   DMCreate(comm, mesh);
2616:   DMSetType(*mesh, DMPLEX);
2617:   return(0);
2618: }

2620: /*
2621:   This takes as input the common mesh generator output, a list of the vertices for each cell, but vertex numbers are global and an SF is built for them
2622: */
2623: /* TODO: invertCells and spaceDim arguments could be added also to to DMPlexCreateFromCellListParallel(), DMPlexBuildFromCellList_Internal() and DMPlexCreateFromCellList() */
2624: PetscErrorCode DMPlexBuildFromCellList_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscBool invertCells, PetscSF *sfVert)
2625: {
2626:   PetscSF         sfPoint;
2627:   PetscLayout     vLayout;
2628:   PetscHSetI      vhash;
2629:   PetscSFNode    *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex;
2630:   const PetscInt *vrange;
2631:   PetscInt        numVerticesAdj, off = 0, *verticesAdj, numVerticesGhost = 0, *localVertex, *cone, c, p, v, g;
2632:   PetscMPIInt     rank, size;
2633:   PetscErrorCode  ierr;

2636:   PetscLogEventBegin(DMPLEX_CreateFromCellList,dm,0,0,0);
2637:   MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
2638:   MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);
2639:   /* Partition vertices */
2640:   PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);
2641:   PetscLayoutSetLocalSize(vLayout, numVertices);
2642:   PetscLayoutSetBlockSize(vLayout, 1);
2643:   PetscLayoutSetUp(vLayout);
2644:   PetscLayoutGetRanges(vLayout, &vrange);
2645:   /* Count vertices and map them to procs */
2646:   PetscHSetICreate(&vhash);
2647:   for (c = 0; c < numCells; ++c) {
2648:     for (p = 0; p < numCorners; ++p) {
2649:       PetscHSetIAdd(vhash, cells[c*numCorners+p]);
2650:     }
2651:   }
2652:   PetscHSetIGetSize(vhash, &numVerticesAdj);
2653:   PetscMalloc1(numVerticesAdj, &verticesAdj);
2654:   PetscHSetIGetElems(vhash, &off, verticesAdj);
2655:   PetscHSetIDestroy(&vhash);
2656:   if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj);
2657:   PetscSortInt(numVerticesAdj, verticesAdj);
2658:   PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);
2659:   for (v = 0; v < numVerticesAdj; ++v) {
2660:     const PetscInt gv = verticesAdj[v];
2661:     PetscInt       vrank;

2663:     PetscFindInt(gv, size+1, vrange, &vrank);
2664:     vrank = vrank < 0 ? -(vrank+2) : vrank;
2665:     remoteVerticesAdj[v].index = gv - vrange[vrank];
2666:     remoteVerticesAdj[v].rank  = vrank;
2667:   }
2668:   /* Create cones */
2669:   DMPlexSetChart(dm, 0, numCells+numVerticesAdj);
2670:   for (c = 0; c < numCells; ++c) {DMPlexSetConeSize(dm, c, numCorners);}
2671:   DMSetUp(dm);
2672:   DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);
2673:   for (c = 0; c < numCells; ++c) {
2674:     for (p = 0; p < numCorners; ++p) {
2675:       const PetscInt gv = cells[c*numCorners+p];
2676:       PetscInt       lv;

2678:       PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);
2679:       if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv);
2680:       cone[p] = lv+numCells;
2681:     }
2682:     if (invertCells) { DMPlexInvertCell_Internal(spaceDim, numCorners, cone); }
2683:     DMPlexSetCone(dm, c, cone);
2684:   }
2685:   DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);
2686:   /* Create SF for vertices */
2687:   PetscSFCreate(PetscObjectComm((PetscObject)dm), sfVert);
2688:   PetscObjectSetName((PetscObject) *sfVert, "Vertex Ownership SF");
2689:   PetscSFSetFromOptions(*sfVert);
2690:   PetscSFSetGraph(*sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);
2691:   PetscFree(verticesAdj);
2692:   /* Build pointSF */
2693:   PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);
2694:   for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;}
2695:   for (v = 0; v < numVertices;    ++v) {vertexOwner[v].index = -1;         vertexOwner[v].rank = -1;}
2696:   PetscSFReduceBegin(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);
2697:   PetscSFReduceEnd(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);
2698:   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);
2699:   PetscSFBcastBegin(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);
2700:   PetscSFBcastEnd(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);
2701:   for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost;
2702:   PetscMalloc1(numVerticesGhost, &localVertex);
2703:   PetscMalloc1(numVerticesGhost, &remoteVertex);
2704:   for (v = 0, g = 0; v < numVerticesAdj; ++v) {
2705:     if (vertexLocal[v].rank != rank) {
2706:       localVertex[g]        = v+numCells;
2707:       remoteVertex[g].index = vertexLocal[v].index;
2708:       remoteVertex[g].rank  = vertexLocal[v].rank;
2709:       ++g;
2710:     }
2711:   }
2712:   PetscFree2(vertexLocal, vertexOwner);
2713:   if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost);
2714:   DMGetPointSF(dm, &sfPoint);
2715:   PetscObjectSetName((PetscObject) sfPoint, "point SF");
2716:   PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);
2717:   PetscLayoutDestroy(&vLayout);
2718:   /* Fill in the rest of the topology structure */
2719:   DMPlexSymmetrize(dm);
2720:   DMPlexStratify(dm);
2721:   PetscLogEventEnd(DMPLEX_CreateFromCellList,dm,0,0,0);
2722:   return(0);
2723: }

2725: /*
2726:   This takes as input the coordinates for each owned vertex
2727: */
2728: PetscErrorCode DMPlexBuildCoordinates_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numV, PetscSF sfVert, const PetscReal vertexCoords[])
2729: {
2730:   PetscSection   coordSection;
2731:   Vec            coordinates;
2732:   PetscScalar   *coords;
2733:   PetscInt       numVertices, numVerticesAdj, coordSize, v;

2737:   PetscLogEventBegin(DMPLEX_CreateFromCellList_Coordinates,dm,0,0,0);
2738:   DMSetCoordinateDim(dm, spaceDim);
2739:   PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);
2740:   DMGetCoordinateSection(dm, &coordSection);
2741:   PetscSectionSetNumFields(coordSection, 1);
2742:   PetscSectionSetFieldComponents(coordSection, 0, spaceDim);
2743:   PetscSectionSetChart(coordSection, numCells, numCells + numVerticesAdj);
2744:   for (v = numCells; v < numCells+numVerticesAdj; ++v) {
2745:     PetscSectionSetDof(coordSection, v, spaceDim);
2746:     PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);
2747:   }
2748:   PetscSectionSetUp(coordSection);
2749:   PetscSectionGetStorageSize(coordSection, &coordSize);
2750:   VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);
2751:   VecSetBlockSize(coordinates, spaceDim);
2752:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
2753:   VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
2754:   VecSetType(coordinates,VECSTANDARD);
2755:   VecGetArray(coordinates, &coords);
2756:   {
2757:     MPI_Datatype coordtype;

2759:     /* Need a temp buffer for coords if we have complex/single */
2760:     MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);
2761:     MPI_Type_commit(&coordtype);
2762: #if defined(PETSC_USE_COMPLEX)
2763:     {
2764:     PetscScalar *svertexCoords;
2765:     PetscInt    i;
2766:     PetscMalloc1(numV*spaceDim,&svertexCoords);
2767:     for (i=0; i<numV*spaceDim; i++) svertexCoords[i] = vertexCoords[i];
2768:     PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords);
2769:     PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords);
2770:     PetscFree(svertexCoords);
2771:     }
2772: #else
2773:     PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords);
2774:     PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords);
2775: #endif
2776:     MPI_Type_free(&coordtype);
2777:   }
2778:   VecRestoreArray(coordinates, &coords);
2779:   DMSetCoordinatesLocal(dm, coordinates);
2780:   VecDestroy(&coordinates);
2781:   PetscLogEventEnd(DMPLEX_CreateFromCellList_Coordinates,dm,0,0,0);
2782:   return(0);
2783: }

2785: /*@
2786:   DMPlexCreateFromCellListParallel - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM

2788:   Input Parameters:
2789: + comm - The communicator
2790: . dim - The topological dimension of the mesh
2791: . numCells - The number of cells owned by this process
2792: . numVertices - The number of vertices owned by this process
2793: . numCorners - The number of vertices for each cell
2794: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
2795: . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell
2796: . spaceDim - The spatial dimension used for coordinates
2797: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex

2799:   Output Parameter:
2800: + dm - The DM
2801: - vertexSF - Optional, SF describing complete vertex ownership

2803:   Note: Two triangles sharing a face
2804: $
2805: $        2
2806: $      / | \
2807: $     /  |  \
2808: $    /   |   \
2809: $   0  0 | 1  3
2810: $    \   |   /
2811: $     \  |  /
2812: $      \ | /
2813: $        1
2814: would have input
2815: $  numCells = 2, numVertices = 4
2816: $  cells = [0 1 2  1 3 2]
2817: $
2818: which would result in the DMPlex
2819: $
2820: $        4
2821: $      / | \
2822: $     /  |  \
2823: $    /   |   \
2824: $   2  0 | 1  5
2825: $    \   |   /
2826: $     \  |  /
2827: $      \ | /
2828: $        3

2830:   Level: beginner

2832: .seealso: DMPlexCreateFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate()
2833: @*/
2834: 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)
2835: {
2836:   PetscSF        sfVert;

2840:   DMCreate(comm, dm);
2841:   DMSetType(*dm, DMPLEX);
2844:   DMSetDimension(*dm, dim);
2845:   DMPlexBuildFromCellList_Parallel_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE, &sfVert);
2846:   if (interpolate) {
2847:     DM idm;

2849:     DMPlexInterpolate(*dm, &idm);
2850:     DMDestroy(dm);
2851:     *dm  = idm;
2852:   }
2853:   DMPlexBuildCoordinates_Parallel_Internal(*dm, spaceDim, numCells, numVertices, sfVert, vertexCoords);
2854:   if (vertexSF) *vertexSF = sfVert;
2855:   else {PetscSFDestroy(&sfVert);}
2856:   return(0);
2857: }

2859: /*
2860:   This takes as input the common mesh generator output, a list of the vertices for each cell
2861: */
2862: PetscErrorCode DMPlexBuildFromCellList_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscBool invertCells)
2863: {
2864:   PetscInt      *cone, c, p;

2868:   PetscLogEventBegin(DMPLEX_CreateFromCellList,dm,0,0,0);
2869:   DMPlexSetChart(dm, 0, numCells+numVertices);
2870:   for (c = 0; c < numCells; ++c) {
2871:     DMPlexSetConeSize(dm, c, numCorners);
2872:   }
2873:   DMSetUp(dm);
2874:   DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);
2875:   for (c = 0; c < numCells; ++c) {
2876:     for (p = 0; p < numCorners; ++p) {
2877:       cone[p] = cells[c*numCorners+p]+numCells;
2878:     }
2879:     if (invertCells) { DMPlexInvertCell_Internal(spaceDim, numCorners, cone); }
2880:     DMPlexSetCone(dm, c, cone);
2881:   }
2882:   DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);
2883:   DMPlexSymmetrize(dm);
2884:   DMPlexStratify(dm);
2885:   PetscLogEventEnd(DMPLEX_CreateFromCellList,dm,0,0,0);
2886:   return(0);
2887: }

2889: /*
2890:   This takes as input the coordinates for each vertex
2891: */
2892: PetscErrorCode DMPlexBuildCoordinates_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[])
2893: {
2894:   PetscSection   coordSection;
2895:   Vec            coordinates;
2896:   DM             cdm;
2897:   PetscScalar   *coords;
2898:   PetscInt       v, d;

2902:   PetscLogEventBegin(DMPLEX_CreateFromCellList_Coordinates,dm,0,0,0);
2903:   DMSetCoordinateDim(dm, spaceDim);
2904:   DMGetCoordinateSection(dm, &coordSection);
2905:   PetscSectionSetNumFields(coordSection, 1);
2906:   PetscSectionSetFieldComponents(coordSection, 0, spaceDim);
2907:   PetscSectionSetChart(coordSection, numCells, numCells + numVertices);
2908:   for (v = numCells; v < numCells+numVertices; ++v) {
2909:     PetscSectionSetDof(coordSection, v, spaceDim);
2910:     PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);
2911:   }
2912:   PetscSectionSetUp(coordSection);

2914:   DMGetCoordinateDM(dm, &cdm);
2915:   DMCreateLocalVector(cdm, &coordinates);
2916:   VecSetBlockSize(coordinates, spaceDim);
2917:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
2918:   VecGetArray(coordinates, &coords);
2919:   for (v = 0; v < numVertices; ++v) {
2920:     for (d = 0; d < spaceDim; ++d) {
2921:       coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d];
2922:     }
2923:   }
2924:   VecRestoreArray(coordinates, &coords);
2925:   DMSetCoordinatesLocal(dm, coordinates);
2926:   VecDestroy(&coordinates);
2927:   PetscLogEventEnd(DMPLEX_CreateFromCellList_Coordinates,dm,0,0,0);
2928:   return(0);
2929: }

2931: /*@
2932:   DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM

2934:   Input Parameters:
2935: + comm - The communicator
2936: . dim - The topological dimension of the mesh
2937: . numCells - The number of cells
2938: . numVertices - The number of vertices
2939: . numCorners - The number of vertices for each cell
2940: . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically
2941: . cells - An array of numCells*numCorners numbers, the vertices for each cell
2942: . spaceDim - The spatial dimension used for coordinates
2943: - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex

2945:   Output Parameter:
2946: . dm - The DM

2948:   Note: Two triangles sharing a face
2949: $
2950: $        2
2951: $      / | \
2952: $     /  |  \
2953: $    /   |   \
2954: $   0  0 | 1  3
2955: $    \   |   /
2956: $     \  |  /
2957: $      \ | /
2958: $        1
2959: would have input
2960: $  numCells = 2, numVertices = 4
2961: $  cells = [0 1 2  1 3 2]
2962: $
2963: which would result in the DMPlex
2964: $
2965: $        4
2966: $      / | \
2967: $     /  |  \
2968: $    /   |   \
2969: $   2  0 | 1  5
2970: $    \   |   /
2971: $     \  |  /
2972: $      \ | /
2973: $        3

2975:   Level: beginner

2977: .seealso: DMPlexCreateFromDAG(), DMPlexCreate()
2978: @*/
2979: 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)
2980: {

2984:   DMCreate(comm, dm);
2985:   DMSetType(*dm, DMPLEX);
2986:   DMSetDimension(*dm, dim);
2987:   DMPlexBuildFromCellList_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE);
2988:   if (interpolate) {
2989:     DM idm;

2991:     DMPlexInterpolate(*dm, &idm);
2992:     DMDestroy(dm);
2993:     *dm  = idm;
2994:   }
2995:   DMPlexBuildCoordinates_Internal(*dm, spaceDim, numCells, numVertices, vertexCoords);
2996:   return(0);
2997: }

2999: /*@
3000:   DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM

3002:   Input Parameters:
3003: + dm - The empty DM object, usually from DMCreate() and DMSetDimension()
3004: . depth - The depth of the DAG
3005: . numPoints - Array of size depth + 1 containing the number of points at each depth
3006: . coneSize - The cone size of each point
3007: . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point
3008: . coneOrientations - The orientation of each cone point
3009: - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim()

3011:   Output Parameter:
3012: . dm - The DM

3014:   Note: Two triangles sharing a face would have input
3015: $  depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0]
3016: $  cones = [2 3 4  3 5 4], coneOrientations = [0 0 0  0 0 0]
3017: $ vertexCoords = [-1.0 0.0  0.0 -1.0  0.0 1.0  1.0 0.0]
3018: $
3019: which would result in the DMPlex
3020: $
3021: $        4
3022: $      / | \
3023: $     /  |  \
3024: $    /   |   \
3025: $   2  0 | 1  5
3026: $    \   |   /
3027: $     \  |  /
3028: $      \ | /
3029: $        3
3030: $
3031: $ Notice that all points are numbered consecutively, unlikely DMPlexCreateFromCellList()

3033:   Level: advanced

3035: .seealso: DMPlexCreateFromCellList(), DMPlexCreate()
3036: @*/
3037: PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[])
3038: {
3039:   Vec            coordinates;
3040:   PetscSection   coordSection;
3041:   PetscScalar    *coords;
3042:   PetscInt       coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off;

3046:   DMGetDimension(dm, &dim);
3047:   DMGetCoordinateDim(dm, &dimEmbed);
3048:   if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %d cannot be less than intrinsic dimension %d",dimEmbed,dim);
3049:   for (d = 0; d <= depth; ++d) pEnd += numPoints[d];
3050:   DMPlexSetChart(dm, pStart, pEnd);
3051:   for (p = pStart; p < pEnd; ++p) {
3052:     DMPlexSetConeSize(dm, p, coneSize[p-pStart]);
3053:     if (firstVertex < 0 && !coneSize[p - pStart]) {
3054:       firstVertex = p - pStart;
3055:     }
3056:   }
3057:   if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %d vertices but could not find any", numPoints[0]);
3058:   DMSetUp(dm); /* Allocate space for cones */
3059:   for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) {
3060:     DMPlexSetCone(dm, p, &cones[off]);
3061:     DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);
3062:   }
3063:   DMPlexSymmetrize(dm);
3064:   DMPlexStratify(dm);
3065:   /* Build coordinates */
3066:   DMGetCoordinateSection(dm, &coordSection);
3067:   PetscSectionSetNumFields(coordSection, 1);
3068:   PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);
3069:   PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);
3070:   for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) {
3071:     PetscSectionSetDof(coordSection, v, dimEmbed);
3072:     PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);
3073:   }
3074:   PetscSectionSetUp(coordSection);
3075:   PetscSectionGetStorageSize(coordSection, &coordSize);
3076:   VecCreate(PETSC_COMM_SELF, &coordinates);
3077:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
3078:   VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
3079:   VecSetBlockSize(coordinates, dimEmbed);
3080:   VecSetType(coordinates,VECSTANDARD);
3081:   VecGetArray(coordinates, &coords);
3082:   for (v = 0; v < numPoints[0]; ++v) {
3083:     PetscInt off;

3085:     PetscSectionGetOffset(coordSection, v+firstVertex, &off);
3086:     for (d = 0; d < dimEmbed; ++d) {
3087:       coords[off+d] = vertexCoords[v*dimEmbed+d];
3088:     }
3089:   }
3090:   VecRestoreArray(coordinates, &coords);
3091:   DMSetCoordinatesLocal(dm, coordinates);
3092:   VecDestroy(&coordinates);
3093:   return(0);
3094: }

3096: /*@C
3097:   DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file.

3099: + comm        - The MPI communicator
3100: . filename    - Name of the .dat file
3101: - interpolate - Create faces and edges in the mesh

3103:   Output Parameter:
3104: . dm  - The DM object representing the mesh

3106:   Note: The format is the simplest possible:
3107: $ Ne
3108: $ v0 v1 ... vk
3109: $ Nv
3110: $ x y z marker

3112:   Level: beginner

3114: .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate()
3115: @*/
3116: PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
3117: {
3118:   DMLabel         marker;
3119:   PetscViewer     viewer;
3120:   Vec             coordinates;
3121:   PetscSection    coordSection;
3122:   PetscScalar    *coords;
3123:   char            line[PETSC_MAX_PATH_LEN];
3124:   PetscInt        dim = 3, cdim = 3, coordSize, v, c, d;
3125:   PetscMPIInt     rank;
3126:   int             snum, Nv, Nc;
3127:   PetscErrorCode  ierr;

3130:   MPI_Comm_rank(comm, &rank);
3131:   PetscViewerCreate(comm, &viewer);
3132:   PetscViewerSetType(viewer, PETSCVIEWERASCII);
3133:   PetscViewerFileSetMode(viewer, FILE_MODE_READ);
3134:   PetscViewerFileSetName(viewer, filename);
3135:   if (!rank) {
3136:     PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);
3137:     snum = sscanf(line, "%d %d", &Nc, &Nv);
3138:     if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
3139:   } else {
3140:     Nc = Nv = 0;
3141:   }
3142:   DMCreate(comm, dm);
3143:   DMSetType(*dm, DMPLEX);
3144:   DMPlexSetChart(*dm, 0, Nc+Nv);
3145:   DMSetDimension(*dm, dim);
3146:   DMSetCoordinateDim(*dm, cdim);
3147:   /* Read topology */
3148:   if (!rank) {
3149:     PetscInt cone[8], corners = 8;
3150:     int      vbuf[8], v;

3152:     for (c = 0; c < Nc; ++c) {DMPlexSetConeSize(*dm, c, corners);}
3153:     DMSetUp(*dm);
3154:     for (c = 0; c < Nc; ++c) {
3155:       PetscViewerRead(viewer, line, corners, NULL, PETSC_STRING);
3156:       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]);
3157:       if (snum != corners) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
3158:       for (v = 0; v < corners; ++v) cone[v] = vbuf[v] + Nc;
3159:       /* Hexahedra are inverted */
3160:       {
3161:         PetscInt tmp = cone[1];
3162:         cone[1] = cone[3];
3163:         cone[3] = tmp;
3164:       }
3165:       DMPlexSetCone(*dm, c, cone);
3166:     }
3167:   }
3168:   DMPlexSymmetrize(*dm);
3169:   DMPlexStratify(*dm);
3170:   /* Read coordinates */
3171:   DMGetCoordinateSection(*dm, &coordSection);
3172:   PetscSectionSetNumFields(coordSection, 1);
3173:   PetscSectionSetFieldComponents(coordSection, 0, cdim);
3174:   PetscSectionSetChart(coordSection, Nc, Nc + Nv);
3175:   for (v = Nc; v < Nc+Nv; ++v) {
3176:     PetscSectionSetDof(coordSection, v, cdim);
3177:     PetscSectionSetFieldDof(coordSection, v, 0, cdim);
3178:   }
3179:   PetscSectionSetUp(coordSection);
3180:   PetscSectionGetStorageSize(coordSection, &coordSize);
3181:   VecCreate(PETSC_COMM_SELF, &coordinates);
3182:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
3183:   VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
3184:   VecSetBlockSize(coordinates, cdim);
3185:   VecSetType(coordinates, VECSTANDARD);
3186:   VecGetArray(coordinates, &coords);
3187:   if (!rank) {
3188:     double x[3];
3189:     int    val;

3191:     DMCreateLabel(*dm, "marker");
3192:     DMGetLabel(*dm, "marker", &marker);
3193:     for (v = 0; v < Nv; ++v) {
3194:       PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);
3195:       snum = sscanf(line, "%lg %lg %lg %d", &x[0], &x[1], &x[2], &val);
3196:       if (snum != 4) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line);
3197:       for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d];
3198:       if (val) {DMLabelSetValue(marker, v+Nc, val);}
3199:     }
3200:   }
3201:   VecRestoreArray(coordinates, &coords);
3202:   DMSetCoordinatesLocal(*dm, coordinates);
3203:   VecDestroy(&coordinates);
3204:   PetscViewerDestroy(&viewer);
3205:   if (interpolate) {
3206:     DM      idm;
3207:     DMLabel bdlabel;

3209:     DMPlexInterpolate(*dm, &idm);
3210:     DMDestroy(dm);
3211:     *dm  = idm;

3213:     DMGetLabel(*dm, "marker", &bdlabel);
3214:     DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);
3215:     DMPlexLabelComplete(*dm, bdlabel);
3216:   }
3217:   return(0);
3218: }

3220: /*@C
3221:   DMPlexCreateFromFile - This takes a filename and produces a DM

3223:   Input Parameters:
3224: + comm - The communicator
3225: . filename - A file name
3226: - interpolate - Flag to create intermediate mesh pieces (edges, faces)

3228:   Output Parameter:
3229: . dm - The DM

3231:   Options Database Keys:
3232: . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5

3234:   Use -dm_plex_create_ prefix to pass options to the internal PetscViewer, e.g.
3235: $ -dm_plex_create_viewer_hdf5_collective

3237:   Level: beginner

3239: .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellList(), DMPlexCreate()
3240: @*/
3241: PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
3242: {
3243:   const char    *extGmsh    = ".msh";
3244:   const char    *extGmsh2   = ".msh2";
3245:   const char    *extGmsh4   = ".msh4";
3246:   const char    *extCGNS    = ".cgns";
3247:   const char    *extExodus  = ".exo";
3248:   const char    *extGenesis = ".gen";
3249:   const char    *extFluent  = ".cas";
3250:   const char    *extHDF5    = ".h5";
3251:   const char    *extMed     = ".med";
3252:   const char    *extPLY     = ".ply";
3253:   const char    *extCV      = ".dat";
3254:   size_t         len;
3255:   PetscBool      isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isCV;
3256:   PetscMPIInt    rank;

3262:   DMInitializePackage();
3263:   PetscLogEventBegin(DMPLEX_CreateFromFile,0,0,0,0);
3264:   MPI_Comm_rank(comm, &rank);
3265:   PetscStrlen(filename, &len);
3266:   if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path");
3267:   PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh,    4, &isGmsh);
3268:   PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh2,   5, &isGmsh2);
3269:   PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh4,   5, &isGmsh4);
3270:   PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS,    5, &isCGNS);
3271:   PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus,  4, &isExodus);
3272:   PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);
3273:   PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent,  4, &isFluent);
3274:   PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5,    3, &isHDF5);
3275:   PetscStrncmp(&filename[PetscMax(0,len-4)], extMed,     4, &isMed);
3276:   PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY,     4, &isPLY);
3277:   PetscStrncmp(&filename[PetscMax(0,len-4)], extCV,      4, &isCV);
3278:   if (isGmsh || isGmsh2 || isGmsh4) {
3279:     DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);
3280:   } else if (isCGNS) {
3281:     DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);
3282:   } else if (isExodus || isGenesis) {
3283:     DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);
3284:   } else if (isFluent) {
3285:     DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);
3286:   } else if (isHDF5) {
3287:     PetscBool      load_hdf5_xdmf = PETSC_FALSE;
3288:     PetscViewer viewer;

3290:     /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */
3291:     PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf",  5, &load_hdf5_xdmf);
3292:     PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);
3293:     PetscViewerCreate(comm, &viewer);
3294:     PetscViewerSetType(viewer, PETSCVIEWERHDF5);
3295:     PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_");
3296:     PetscViewerSetFromOptions(viewer);
3297:     PetscViewerFileSetMode(viewer, FILE_MODE_READ);
3298:     PetscViewerFileSetName(viewer, filename);
3299:     DMCreate(comm, dm);
3300:     DMSetType(*dm, DMPLEX);
3301:     if (load_hdf5_xdmf) {PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);}
3302:     DMLoad(*dm, viewer);
3303:     if (load_hdf5_xdmf) {PetscViewerPopFormat(viewer);}
3304:     PetscViewerDestroy(&viewer);

3306:     if (interpolate) {
3307:       DM idm;

3309:       DMPlexInterpolate(*dm, &idm);
3310:       DMDestroy(dm);
3311:       *dm  = idm;
3312:     }
3313:   } else if (isMed) {
3314:     DMPlexCreateMedFromFile(comm, filename, interpolate, dm);
3315:   } else if (isPLY) {
3316:     DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);
3317:   } else if (isCV) {
3318:     DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);
3319:   } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename);
3320:   PetscLogEventEnd(DMPLEX_CreateFromFile,0,0,0,0);
3321:   return(0);
3322: }

3324: /*@
3325:   DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell

3327:   Collective

3329:   Input Parameters:
3330: + comm    - The communicator
3331: . dim     - The spatial dimension
3332: - simplex - Flag for simplex, otherwise use a tensor-product cell

3334:   Output Parameter:
3335: . refdm - The reference cell

3337:   Level: intermediate

3339: .seealso:
3340: @*/
3341: PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm)
3342: {
3343:   DM             rdm;
3344:   Vec            coords;

3348:   DMCreate(comm, &rdm);
3349:   DMSetType(rdm, DMPLEX);
3350:   DMSetDimension(rdm, dim);
3351:   switch (dim) {
3352:   case 0:
3353:   {
3354:     PetscInt    numPoints[1]        = {1};
3355:     PetscInt    coneSize[1]         = {0};
3356:     PetscInt    cones[1]            = {0};
3357:     PetscInt    coneOrientations[1] = {0};
3358:     PetscScalar vertexCoords[1]     = {0.0};

3360:     DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3361:   }
3362:   break;
3363:   case 1:
3364:   {
3365:     PetscInt    numPoints[2]        = {2, 1};
3366:     PetscInt    coneSize[3]         = {2, 0, 0};
3367:     PetscInt    cones[2]            = {1, 2};
3368:     PetscInt    coneOrientations[2] = {0, 0};
3369:     PetscScalar vertexCoords[2]     = {-1.0,  1.0};

3371:     DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3372:   }
3373:   break;
3374:   case 2:
3375:     if (simplex) {
3376:       PetscInt    numPoints[2]        = {3, 1};
3377:       PetscInt    coneSize[4]         = {3, 0, 0, 0};
3378:       PetscInt    cones[3]            = {1, 2, 3};
3379:       PetscInt    coneOrientations[3] = {0, 0, 0};
3380:       PetscScalar vertexCoords[6]     = {-1.0, -1.0,  1.0, -1.0,  -1.0, 1.0};

3382:       DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3383:     } else {
3384:       PetscInt    numPoints[2]        = {4, 1};
3385:       PetscInt    coneSize[5]         = {4, 0, 0, 0, 0};
3386:       PetscInt    cones[4]            = {1, 2, 3, 4};
3387:       PetscInt    coneOrientations[4] = {0, 0, 0, 0};
3388:       PetscScalar vertexCoords[8]     = {-1.0, -1.0,  1.0, -1.0,  1.0, 1.0,  -1.0, 1.0};

3390:       DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3391:     }
3392:   break;
3393:   case 3:
3394:     if (simplex) {
3395:       PetscInt    numPoints[2]        = {4, 1};
3396:       PetscInt    coneSize[5]         = {4, 0, 0, 0, 0};
3397:       PetscInt    cones[4]            = {1, 3, 2, 4};
3398:       PetscInt    coneOrientations[4] = {0, 0, 0, 0};
3399:       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};

3401:       DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3402:     } else {
3403:       PetscInt    numPoints[2]        = {8, 1};
3404:       PetscInt    coneSize[9]         = {8, 0, 0, 0, 0, 0, 0, 0, 0};
3405:       PetscInt    cones[8]            = {1, 4, 3, 2, 5, 6, 7, 8};
3406:       PetscInt    coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0};
3407:       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,
3408:                                          -1.0, -1.0,  1.0,  1.0, -1.0,  1.0,  1.0, 1.0,  1.0,  -1.0, 1.0,  1.0};

3410:       DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);
3411:     }
3412:   break;
3413:   default:
3414:     SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %d", dim);
3415:   }
3416:   DMPlexInterpolate(rdm, refdm);
3417:   if (rdm->coordinateDM) {
3418:     DM           ncdm;
3419:     PetscSection cs;
3420:     PetscInt     pEnd = -1;

3422:     DMGetLocalSection(rdm->coordinateDM, &cs);
3423:     if (cs) {PetscSectionGetChart(cs, NULL, &pEnd);}
3424:     if (pEnd >= 0) {
3425:       DMClone(*refdm, &ncdm);
3426:       DMCopyDisc(rdm->coordinateDM, ncdm);
3427:       DMSetLocalSection(ncdm, cs);
3428:       DMSetCoordinateDM(*refdm, ncdm);
3429:       DMDestroy(&ncdm);
3430:     }
3431:   }
3432:   DMGetCoordinatesLocal(rdm, &coords);
3433:   if (coords) {
3434:     DMSetCoordinatesLocal(*refdm, coords);
3435:   } else {
3436:     DMGetCoordinates(rdm, &coords);
3437:     if (coords) {DMSetCoordinates(*refdm, coords);}
3438:   }
3439:   DMDestroy(&rdm);
3440:   return(0);
3441: }