Actual source code: plexsubmesh.c

petsc-master 2015-06-01
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  1: #include <petsc/private/dmpleximpl.h>   /*I      "petscdmplex.h"   I*/
  2: #include <petscsf.h>

  6: PetscErrorCode DMPlexMarkBoundaryFaces_Internal(DM dm, PetscInt cellHeight, DMLabel label)
  7: {
  8:   PetscInt       fStart, fEnd, f;

 13:   DMPlexGetHeightStratum(dm, cellHeight+1, &fStart, &fEnd);
 14:   for (f = fStart; f < fEnd; ++f) {
 15:     PetscInt supportSize;

 17:     DMPlexGetSupportSize(dm, f, &supportSize);
 18:     if (supportSize == 1) {DMLabelSetValue(label, f, 1);}
 19:   }
 20:   return(0);
 21: }

 25: /*@
 26:   DMPlexMarkBoundaryFaces - Mark all faces on the boundary

 28:   Not Collective

 30:   Input Parameter:
 31: . dm - The original DM

 33:   Output Parameter:
 34: . label - The DMLabel marking boundary faces with value 1

 36:   Level: developer

 38: .seealso: DMLabelCreate(), DMPlexCreateLabel()
 39: @*/
 40: PetscErrorCode DMPlexMarkBoundaryFaces(DM dm, DMLabel label)
 41: {

 45:   DMPlexMarkBoundaryFaces_Internal(dm, 0, label);
 46:   return(0);
 47: }

 51: /*@
 52:   DMPlexLabelComplete - Starting with a label marking points on a surface, we add the transitive closure to the surface

 54:   Input Parameters:
 55: + dm - The DM
 56: - label - A DMLabel marking the surface points

 58:   Output Parameter:
 59: . label - A DMLabel marking all surface points in the transitive closure

 61:   Level: developer

 63: .seealso: DMPlexLabelCohesiveComplete()
 64: @*/
 65: PetscErrorCode DMPlexLabelComplete(DM dm, DMLabel label)
 66: {
 67:   IS              valueIS;
 68:   const PetscInt *values;
 69:   PetscInt        numValues, v;
 70:   PetscErrorCode  ierr;

 73:   DMLabelGetNumValues(label, &numValues);
 74:   DMLabelGetValueIS(label, &valueIS);
 75:   ISGetIndices(valueIS, &values);
 76:   for (v = 0; v < numValues; ++v) {
 77:     IS              pointIS;
 78:     const PetscInt *points;
 79:     PetscInt        numPoints, p;

 81:     DMLabelGetStratumSize(label, values[v], &numPoints);
 82:     DMLabelGetStratumIS(label, values[v], &pointIS);
 83:     ISGetIndices(pointIS, &points);
 84:     for (p = 0; p < numPoints; ++p) {
 85:       PetscInt *closure = NULL;
 86:       PetscInt  closureSize, c;

 88:       DMPlexGetTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closure);
 89:       for (c = 0; c < closureSize*2; c += 2) {
 90:         DMLabelSetValue(label, closure[c], values[v]);
 91:       }
 92:       DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closure);
 93:     }
 94:     ISRestoreIndices(pointIS, &points);
 95:     ISDestroy(&pointIS);
 96:   }
 97:   ISRestoreIndices(valueIS, &values);
 98:   ISDestroy(&valueIS);
 99:   return(0);
100: }

104: /*@
105:   DMPlexLabelAddCells - Starting with a label marking faces on a surface, we add a cell for each face

107:   Input Parameters:
108: + dm - The DM
109: - label - A DMLabel marking the surface points

111:   Output Parameter:
112: . label - A DMLabel incorporating cells

114:   Level: developer

116:   Note: The cells allow FEM boundary conditions to be applied using the cell geometry

118: .seealso: DMPlexLabelComplete(), DMPlexLabelCohesiveComplete()
119: @*/
120: PetscErrorCode DMPlexLabelAddCells(DM dm, DMLabel label)
121: {
122:   IS              valueIS;
123:   const PetscInt *values;
124:   PetscInt        numValues, v, cStart, cEnd, cEndInterior;
125:   PetscErrorCode  ierr;

128:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
129:   DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);
130:   cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
131:   DMLabelGetNumValues(label, &numValues);
132:   DMLabelGetValueIS(label, &valueIS);
133:   ISGetIndices(valueIS, &values);
134:   for (v = 0; v < numValues; ++v) {
135:     IS              pointIS;
136:     const PetscInt *points;
137:     PetscInt        numPoints, p;

139:     DMLabelGetStratumSize(label, values[v], &numPoints);
140:     DMLabelGetStratumIS(label, values[v], &pointIS);
141:     ISGetIndices(pointIS, &points);
142:     for (p = 0; p < numPoints; ++p) {
143:       PetscInt *closure = NULL;
144:       PetscInt  closureSize, point, cl;

146:       DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &closureSize, &closure);
147:       for (cl = closureSize-1; cl > 0; --cl) {
148:         point = closure[cl*2];
149:         if ((point >= cStart) && (point < cEnd)) {DMLabelSetValue(label, point, values[v]); break;}
150:       }
151:       DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, &closureSize, &closure);
152:     }
153:     ISRestoreIndices(pointIS, &points);
154:     ISDestroy(&pointIS);
155:   }
156:   ISRestoreIndices(valueIS, &values);
157:   ISDestroy(&valueIS);
158:   return(0);
159: }

163: PETSC_STATIC_INLINE PetscInt DMPlexShiftPoint_Internal(PetscInt p, PetscInt depth, PetscInt depthMax[], PetscInt depthEnd[], PetscInt depthShift[])
164: {
165:   if (depth < 0) return p;
166:   /* Normal Cells                 */ if (p < depthMax[depth])                return p;
167:   /* Hybrid Cells+Normal Vertices */ if (p < depthMax[0])                    return p + depthShift[depth];
168:   /* Hybrid Vertices+Normal Faces */ if (depth < 2 || p < depthMax[depth-1]) return p + depthShift[depth] + depthShift[0];
169:   /* Hybrid Faces+Normal Edges    */ if (depth < 3 || p < depthMax[depth-2]) return p + depthShift[depth] + depthShift[0] + depthShift[depth-1];
170:   /* Hybrid Edges                 */                                         return p + depthShift[depth] + depthShift[0] + depthShift[depth-1] + depthShift[depth-2];
171: }

175: static PetscErrorCode DMPlexShiftSizes_Internal(DM dm, PetscInt depthShift[], DM dmNew)
176: {
177:   PetscInt      *depthMax, *depthEnd;
178:   PetscInt       depth = 0, d, pStart, pEnd, p;

182:   DMPlexGetDepth(dm, &depth);
183:   if (depth < 0) return(0);
184:   PetscMalloc2(depth+1,&depthMax,depth+1,&depthEnd);
185:   /* Step 1: Expand chart */
186:   DMPlexGetChart(dm, &pStart, &pEnd);
187:   DMPlexGetHybridBounds(dm, &depthMax[depth], depth > 0 ? &depthMax[depth-1] : NULL, &depthMax[1], &depthMax[0]);
188:   for (d = 0; d <= depth; ++d) {
189:     pEnd += depthShift[d];
190:     DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);
191:     depthMax[d] = depthMax[d] < 0 ? depthEnd[d] : depthMax[d];
192:   }
193:   DMPlexSetChart(dmNew, pStart, pEnd);
194:   /* Step 2: Set cone and support sizes */
195:   for (d = 0; d <= depth; ++d) {
196:     DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
197:     for (p = pStart; p < pEnd; ++p) {
198:       PetscInt newp = DMPlexShiftPoint_Internal(p, depth, depthMax, depthEnd, depthShift);
199:       PetscInt size;

201:       DMPlexGetConeSize(dm, p, &size);
202:       DMPlexSetConeSize(dmNew, newp, size);
203:       DMPlexGetSupportSize(dm, p, &size);
204:       DMPlexSetSupportSize(dmNew, newp, size);
205:     }
206:   }
207:   PetscFree2(depthMax,depthEnd);
208:   return(0);
209: }

213: static PetscErrorCode DMPlexShiftPoints_Internal(DM dm, PetscInt depthShift[], DM dmNew)
214: {
215:   PetscInt      *depthEnd, *depthMax, *newpoints;
216:   PetscInt       depth = 0, d, maxConeSize, maxSupportSize, maxConeSizeNew, maxSupportSizeNew, pStart, pEnd, p;

220:   DMPlexGetDepth(dm, &depth);
221:   if (depth < 0) return(0);
222:   DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);
223:   DMPlexGetMaxSizes(dmNew, &maxConeSizeNew, &maxSupportSizeNew);
224:   PetscMalloc3(depth+1,&depthEnd,depth+1,&depthMax,PetscMax(PetscMax(maxConeSize, maxSupportSize), PetscMax(maxConeSizeNew, maxSupportSizeNew)),&newpoints);
225:   DMPlexGetHybridBounds(dm, &depthMax[depth], depth > 0 ? &depthMax[depth-1] : NULL, &depthMax[1], &depthMax[0]);
226:   for (d = 0; d <= depth; ++d) {
227:     DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);
228:     depthMax[d] = depthMax[d] < 0 ? depthEnd[d] : depthMax[d];
229:   }
230:   /* Step 5: Set cones and supports */
231:   DMPlexGetChart(dm, &pStart, &pEnd);
232:   for (p = pStart; p < pEnd; ++p) {
233:     const PetscInt *points = NULL, *orientations = NULL;
234:     PetscInt        size,sizeNew, i, newp = DMPlexShiftPoint_Internal(p, depth, depthMax, depthEnd, depthShift);

236:     DMPlexGetConeSize(dm, p, &size);
237:     DMPlexGetCone(dm, p, &points);
238:     DMPlexGetConeOrientation(dm, p, &orientations);
239:     for (i = 0; i < size; ++i) {
240:       newpoints[i] = DMPlexShiftPoint_Internal(points[i], depth, depthMax, depthEnd, depthShift);
241:     }
242:     DMPlexSetCone(dmNew, newp, newpoints);
243:     DMPlexSetConeOrientation(dmNew, newp, orientations);
244:     DMPlexGetSupportSize(dm, p, &size);
245:     DMPlexGetSupportSize(dmNew, newp, &sizeNew);
246:     DMPlexGetSupport(dm, p, &points);
247:     for (i = 0; i < size; ++i) {
248:       newpoints[i] = DMPlexShiftPoint_Internal(points[i], depth, depthMax, depthEnd, depthShift);
249:     }
250:     for (i = size; i < sizeNew; ++i) newpoints[i] = 0;
251:     DMPlexSetSupport(dmNew, newp, newpoints);
252:   }
253:   PetscFree3(depthEnd,depthMax,newpoints);
254:   return(0);
255: }

259: static PetscErrorCode DMPlexShiftCoordinates_Internal(DM dm, PetscInt depthShift[], DM dmNew)
260: {
261:   PetscSection   coordSection, newCoordSection;
262:   Vec            coordinates, newCoordinates;
263:   PetscScalar   *coords, *newCoords;
264:   PetscInt      *depthEnd, coordSize;
265:   PetscInt       dim, depth = 0, d, vStart, vEnd, vStartNew, vEndNew, v;

269:   DMGetDimension(dm, &dim);
270:   DMPlexGetDepth(dm, &depth);
271:   PetscMalloc1(depth+1, &depthEnd);
272:   for (d = 0; d <= depth; ++d) {
273:     DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);
274:   }
275:   /* Step 8: Convert coordinates */
276:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
277:   DMPlexGetDepthStratum(dmNew, 0, &vStartNew, &vEndNew);
278:   DMGetCoordinateSection(dm, &coordSection);
279:   PetscSectionCreate(PetscObjectComm((PetscObject)dm), &newCoordSection);
280:   PetscSectionSetNumFields(newCoordSection, 1);
281:   PetscSectionSetFieldComponents(newCoordSection, 0, dim);
282:   PetscSectionSetChart(newCoordSection, vStartNew, vEndNew);
283:   for (v = vStartNew; v < vEndNew; ++v) {
284:     PetscSectionSetDof(newCoordSection, v, dim);
285:     PetscSectionSetFieldDof(newCoordSection, v, 0, dim);
286:   }
287:   PetscSectionSetUp(newCoordSection);
288:   DMSetCoordinateSection(dmNew, PETSC_DETERMINE, newCoordSection);
289:   PetscSectionGetStorageSize(newCoordSection, &coordSize);
290:   VecCreate(PetscObjectComm((PetscObject)dm), &newCoordinates);
291:   PetscObjectSetName((PetscObject) newCoordinates, "coordinates");
292:   VecSetSizes(newCoordinates, coordSize, PETSC_DETERMINE);
293:   VecSetBlockSize(newCoordinates, dim);
294:   VecSetType(newCoordinates,VECSTANDARD);
295:   DMSetCoordinatesLocal(dmNew, newCoordinates);
296:   DMGetCoordinatesLocal(dm, &coordinates);
297:   VecGetArray(coordinates, &coords);
298:   VecGetArray(newCoordinates, &newCoords);
299:   for (v = vStart; v < vEnd; ++v) {
300:     PetscInt dof, off, noff, d;

302:     PetscSectionGetDof(coordSection, v, &dof);
303:     PetscSectionGetOffset(coordSection, v, &off);
304:     PetscSectionGetOffset(newCoordSection, DMPlexShiftPoint_Internal(v, depth, depthEnd, depthEnd, depthShift), &noff);
305:     for (d = 0; d < dof; ++d) {
306:       newCoords[noff+d] = coords[off+d];
307:     }
308:   }
309:   VecRestoreArray(coordinates, &coords);
310:   VecRestoreArray(newCoordinates, &newCoords);
311:   VecDestroy(&newCoordinates);
312:   PetscSectionDestroy(&newCoordSection);
313:   PetscFree(depthEnd);
314:   return(0);
315: }

319: static PetscErrorCode DMPlexShiftSF_Internal(DM dm, PetscInt depthShift[], DM dmNew)
320: {
321:   PetscInt          *depthMax, *depthEnd;
322:   PetscInt           depth = 0, d;
323:   PetscSF            sfPoint, sfPointNew;
324:   const PetscSFNode *remotePoints;
325:   PetscSFNode       *gremotePoints;
326:   const PetscInt    *localPoints;
327:   PetscInt          *glocalPoints, *newLocation, *newRemoteLocation;
328:   PetscInt           numRoots, numLeaves, l, pStart, pEnd, totShift = 0;
329:   PetscErrorCode     ierr;

332:   DMPlexGetDepth(dm, &depth);
333:   PetscMalloc2(depth+1,&depthMax,depth+1,&depthEnd);
334:   DMPlexGetHybridBounds(dm, depth >= 0 ? &depthMax[depth] : NULL, depth>1 ? &depthMax[depth-1] : NULL, depth>2 ? &depthMax[1] : NULL, depth >= 0 ? &depthMax[0] : NULL);
335:   for (d = 0; d <= depth; ++d) {
336:     totShift += depthShift[d];
337:     DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);
338:     depthMax[d] = depthMax[d] < 0 ? depthEnd[d] : depthMax[d];
339:   }
340:   /* Step 9: Convert pointSF */
341:   DMGetPointSF(dm, &sfPoint);
342:   DMGetPointSF(dmNew, &sfPointNew);
343:   DMPlexGetChart(dm, &pStart, &pEnd);
344:   PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);
345:   if (numRoots >= 0) {
346:     PetscMalloc2(numRoots,&newLocation,pEnd-pStart,&newRemoteLocation);
347:     for (l=0; l<numRoots; l++) newLocation[l] = DMPlexShiftPoint_Internal(l, depth, depthMax, depthEnd, depthShift);
348:     PetscSFBcastBegin(sfPoint, MPIU_INT, newLocation, newRemoteLocation);
349:     PetscSFBcastEnd(sfPoint, MPIU_INT, newLocation, newRemoteLocation);
350:     PetscMalloc1(numLeaves,    &glocalPoints);
351:     PetscMalloc1(numLeaves, &gremotePoints);
352:     for (l = 0; l < numLeaves; ++l) {
353:       glocalPoints[l]        = DMPlexShiftPoint_Internal(localPoints[l], depth, depthMax, depthEnd, depthShift);
354:       gremotePoints[l].rank  = remotePoints[l].rank;
355:       gremotePoints[l].index = newRemoteLocation[localPoints[l]];
356:     }
357:     PetscFree2(newLocation,newRemoteLocation);
358:     PetscSFSetGraph(sfPointNew, numRoots + totShift, numLeaves, glocalPoints, PETSC_OWN_POINTER, gremotePoints, PETSC_OWN_POINTER);
359:   }
360:   PetscFree2(depthMax,depthEnd);
361:   return(0);
362: }

366: static PetscErrorCode DMPlexShiftLabels_Internal(DM dm, PetscInt depthShift[], DM dmNew)
367: {
368:   PetscSF            sfPoint;
369:   DMLabel            vtkLabel, ghostLabel;
370:   PetscInt          *depthMax, *depthEnd;
371:   const PetscSFNode *leafRemote;
372:   const PetscInt    *leafLocal;
373:   PetscInt           depth = 0, d, numLeaves, numLabels, l, cStart, cEnd, c, fStart, fEnd, f;
374:   PetscMPIInt        rank;
375:   PetscErrorCode     ierr;

378:   DMPlexGetDepth(dm, &depth);
379:   PetscMalloc2(depth+1,&depthMax,depth+1,&depthEnd);
380:   DMPlexGetHybridBounds(dm, depth >= 0 ? &depthMax[depth] : NULL, depth>1 ? &depthMax[depth-1] : NULL, depth>2 ? &depthMax[1] : NULL, depth >= 0 ? &depthMax[0] : NULL);
381:   for (d = 0; d <= depth; ++d) {
382:     DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);
383:     depthMax[d] = depthMax[d] < 0 ? depthEnd[d] : depthMax[d];
384:   }
385:   /* Step 10: Convert labels */
386:   DMPlexGetNumLabels(dm, &numLabels);
387:   for (l = 0; l < numLabels; ++l) {
388:     DMLabel         label, newlabel;
389:     const char     *lname;
390:     PetscBool       isDepth;
391:     IS              valueIS;
392:     const PetscInt *values;
393:     PetscInt        numValues, val;

395:     DMPlexGetLabelName(dm, l, &lname);
396:     PetscStrcmp(lname, "depth", &isDepth);
397:     if (isDepth) continue;
398:     DMPlexCreateLabel(dmNew, lname);
399:     DMPlexGetLabel(dm, lname, &label);
400:     DMPlexGetLabel(dmNew, lname, &newlabel);
401:     DMLabelGetValueIS(label, &valueIS);
402:     ISGetLocalSize(valueIS, &numValues);
403:     ISGetIndices(valueIS, &values);
404:     for (val = 0; val < numValues; ++val) {
405:       IS              pointIS;
406:       const PetscInt *points;
407:       PetscInt        numPoints, p;

409:       DMLabelGetStratumIS(label, values[val], &pointIS);
410:       ISGetLocalSize(pointIS, &numPoints);
411:       ISGetIndices(pointIS, &points);
412:       for (p = 0; p < numPoints; ++p) {
413:         const PetscInt newpoint = DMPlexShiftPoint_Internal(points[p], depth, depthMax, depthEnd, depthShift);

415:         DMLabelSetValue(newlabel, newpoint, values[val]);
416:       }
417:       ISRestoreIndices(pointIS, &points);
418:       ISDestroy(&pointIS);
419:     }
420:     ISRestoreIndices(valueIS, &values);
421:     ISDestroy(&valueIS);
422:   }
423:   PetscFree2(depthMax,depthEnd);
424:   /* Step 11: Make label for output (vtk) and to mark ghost points (ghost) */
425:   MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
426:   DMGetPointSF(dm, &sfPoint);
427:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
428:   PetscSFGetGraph(sfPoint, NULL, &numLeaves, &leafLocal, &leafRemote);
429:   DMPlexCreateLabel(dmNew, "vtk");
430:   DMPlexCreateLabel(dmNew, "ghost");
431:   DMPlexGetLabel(dmNew, "vtk", &vtkLabel);
432:   DMPlexGetLabel(dmNew, "ghost", &ghostLabel);
433:   for (l = 0, c = cStart; l < numLeaves && c < cEnd; ++l, ++c) {
434:     for (; c < leafLocal[l] && c < cEnd; ++c) {
435:       DMLabelSetValue(vtkLabel, c, 1);
436:     }
437:     if (leafLocal[l] >= cEnd) break;
438:     if (leafRemote[l].rank == rank) {
439:       DMLabelSetValue(vtkLabel, c, 1);
440:     } else {
441:       DMLabelSetValue(ghostLabel, c, 2);
442:     }
443:   }
444:   for (; c < cEnd; ++c) {
445:     DMLabelSetValue(vtkLabel, c, 1);
446:   }
447:   if (0) {
448:     PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);
449:     DMLabelView(vtkLabel, PETSC_VIEWER_STDOUT_WORLD);
450:     PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);
451:   }
452:   DMPlexGetHeightStratum(dmNew, 1, &fStart, &fEnd);
453:   for (f = fStart; f < fEnd; ++f) {
454:     PetscInt numCells;

456:     DMPlexGetSupportSize(dmNew, f, &numCells);
457:     if (numCells < 2) {
458:       DMLabelSetValue(ghostLabel, f, 1);
459:     } else {
460:       const PetscInt *cells = NULL;
461:       PetscInt        vA, vB;

463:       DMPlexGetSupport(dmNew, f, &cells);
464:       DMLabelGetValue(vtkLabel, cells[0], &vA);
465:       DMLabelGetValue(vtkLabel, cells[1], &vB);
466:       if (!vA && !vB) {DMLabelSetValue(ghostLabel, f, 1);}
467:     }
468:   }
469:   if (0) {
470:     PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);
471:     DMLabelView(ghostLabel, PETSC_VIEWER_STDOUT_WORLD);
472:     PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);
473:   }
474:   return(0);
475: }

479: static PetscErrorCode DMPlexConstructGhostCells_Internal(DM dm, DMLabel label, PetscInt *numGhostCells, DM gdm)
480: {
481:   PetscSF         sf;
482:   IS              valueIS;
483:   const PetscInt *values, *leaves;
484:   PetscInt       *depthShift;
485:   PetscInt        depth = 0, nleaves, loc, Ng, numFS, fs, fStart, fEnd, ghostCell, cEnd, c;
486:   PetscErrorCode  ierr;

489:   DMGetPointSF(dm, &sf);
490:   PetscSFGetGraph(sf, NULL, &nleaves, &leaves, NULL);
491:   nleaves = PetscMax(0, nleaves);
492:   DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
493:   /* Count ghost cells */
494:   DMLabelGetValueIS(label, &valueIS);
495:   ISGetLocalSize(valueIS, &numFS);
496:   ISGetIndices(valueIS, &values);
497:   Ng   = 0;
498:   for (fs = 0; fs < numFS; ++fs) {
499:     IS              faceIS;
500:     const PetscInt *faces;
501:     PetscInt        numFaces, f, numBdFaces = 0;

503:     DMLabelGetStratumIS(label, values[fs], &faceIS);
504:     ISGetLocalSize(faceIS, &numFaces);
505:     ISGetIndices(faceIS, &faces);
506:     for (f = 0; f < numFaces; ++f) {
507:       PetscFindInt(faces[f], nleaves, leaves, &loc);
508:       if (loc >= 0) continue;
509:       if ((faces[f] >= fStart) && (faces[f] < fEnd)) ++numBdFaces;
510:     }
511:     Ng += numBdFaces;
512:     ISDestroy(&faceIS);
513:   }
514:   DMPlexGetDepth(dm, &depth);
515:   PetscMalloc1(depth+1, &depthShift);
516:   PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));
517:   if (depth >= 0) depthShift[depth] = Ng;
518:   DMPlexShiftSizes_Internal(dm, depthShift, gdm);
519:   /* Step 3: Set cone/support sizes for new points */
520:   DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);
521:   DMPlexSetHybridBounds(gdm, cEnd, PETSC_DETERMINE, PETSC_DETERMINE, PETSC_DETERMINE);
522:   for (c = cEnd; c < cEnd + Ng; ++c) {
523:     DMPlexSetConeSize(gdm, c, 1);
524:   }
525:   for (fs = 0; fs < numFS; ++fs) {
526:     IS              faceIS;
527:     const PetscInt *faces;
528:     PetscInt        numFaces, f;

530:     DMLabelGetStratumIS(label, values[fs], &faceIS);
531:     ISGetLocalSize(faceIS, &numFaces);
532:     ISGetIndices(faceIS, &faces);
533:     for (f = 0; f < numFaces; ++f) {
534:       PetscInt size;

536:       PetscFindInt(faces[f], nleaves, leaves, &loc);
537:       if (loc >= 0) continue;
538:       if ((faces[f] < fStart) || (faces[f] >= fEnd)) continue;
539:       DMPlexGetSupportSize(dm, faces[f], &size);
540:       if (size != 1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "DM has boundary face %d with %d support cells", faces[f], size);
541:       DMPlexSetSupportSize(gdm, faces[f] + Ng, 2);
542:     }
543:     ISRestoreIndices(faceIS, &faces);
544:     ISDestroy(&faceIS);
545:   }
546:   /* Step 4: Setup ghosted DM */
547:   DMSetUp(gdm);
548:   DMPlexShiftPoints_Internal(dm, depthShift, gdm);
549:   /* Step 6: Set cones and supports for new points */
550:   ghostCell = cEnd;
551:   for (fs = 0; fs < numFS; ++fs) {
552:     IS              faceIS;
553:     const PetscInt *faces;
554:     PetscInt        numFaces, f;

556:     DMLabelGetStratumIS(label, values[fs], &faceIS);
557:     ISGetLocalSize(faceIS, &numFaces);
558:     ISGetIndices(faceIS, &faces);
559:     for (f = 0; f < numFaces; ++f) {
560:       PetscInt newFace = faces[f] + Ng;

562:       PetscFindInt(faces[f], nleaves, leaves, &loc);
563:       if (loc >= 0) continue;
564:       if ((faces[f] < fStart) || (faces[f] >= fEnd)) continue;
565:       DMPlexSetCone(gdm, ghostCell, &newFace);
566:       DMPlexInsertSupport(gdm, newFace, 1, ghostCell);
567:       ++ghostCell;
568:     }
569:     ISRestoreIndices(faceIS, &faces);
570:     ISDestroy(&faceIS);
571:   }
572:   ISRestoreIndices(valueIS, &values);
573:   ISDestroy(&valueIS);
574:   /* Step 7: Stratify */
575:   DMPlexStratify(gdm);
576:   DMPlexShiftCoordinates_Internal(dm, depthShift, gdm);
577:   DMPlexShiftSF_Internal(dm, depthShift, gdm);
578:   DMPlexShiftLabels_Internal(dm, depthShift, gdm);
579:   PetscFree(depthShift);
580:   /* Step 7: Periodicity */
581:   if (dm->maxCell) {
582:     const PetscReal *maxCell, *L;
583:     const DMBoundaryType *bd;
584:     DMGetPeriodicity(dm,  &maxCell, &L, &bd);
585:     DMSetPeriodicity(gdm,  maxCell,  L,  bd);
586:   }
587:   if (numGhostCells) *numGhostCells = Ng;
588:   return(0);
589: }

593: /*@C
594:   DMPlexConstructGhostCells - Construct ghost cells which connect to every boundary face

596:   Collective on dm

598:   Input Parameters:
599: + dm - The original DM
600: - labelName - The label specifying the boundary faces, or "Face Sets" if this is NULL

602:   Output Parameters:
603: + numGhostCells - The number of ghost cells added to the DM
604: - dmGhosted - The new DM

606:   Note: If no label exists of that name, one will be created marking all boundary faces

608:   Level: developer

610: .seealso: DMCreate()
611: @*/
612: PetscErrorCode DMPlexConstructGhostCells(DM dm, const char labelName[], PetscInt *numGhostCells, DM *dmGhosted)
613: {
614:   DM             gdm;
615:   DMLabel        label;
616:   const char    *name = labelName ? labelName : "Face Sets";
617:   PetscInt       dim;
618:   PetscBool      flag;

625:   DMCreate(PetscObjectComm((PetscObject)dm), &gdm);
626:   DMSetType(gdm, DMPLEX);
627:   DMGetDimension(dm, &dim);
628:   DMSetDimension(gdm, dim);
629:   DMPlexGetAdjacencyUseCone(dm, &flag);
630:   DMPlexSetAdjacencyUseCone(gdm, flag);
631:   DMPlexGetAdjacencyUseClosure(dm, &flag);
632:   DMPlexSetAdjacencyUseClosure(gdm, flag);
633:   DMPlexGetLabel(dm, name, &label);
634:   if (!label) {
635:     /* Get label for boundary faces */
636:     DMPlexCreateLabel(dm, name);
637:     DMPlexGetLabel(dm, name, &label);
638:     DMPlexMarkBoundaryFaces(dm, label);
639:   }
640:   DMPlexConstructGhostCells_Internal(dm, label, numGhostCells, gdm);
641:   DMPlexCopyBoundary(dm, gdm);
642:   *dmGhosted = gdm;
643:   return(0);
644: }

648: /*
649:   We are adding three kinds of points here:
650:     Replicated:     Copies of points which exist in the mesh, such as vertices identified across a fault
651:     Non-replicated: Points which exist on the fault, but are not replicated
652:     Hybrid:         Entirely new points, such as cohesive cells

654:   When creating subsequent cohesive cells, we shift the old hybrid cells to the end of the numbering at
655:   each depth so that the new split/hybrid points can be inserted as a block.
656: */
657: static PetscErrorCode DMPlexConstructCohesiveCells_Internal(DM dm, DMLabel label, DM sdm)
658: {
659:   MPI_Comm         comm;
660:   IS               valueIS;
661:   PetscInt         numSP = 0;       /* The number of depths for which we have replicated points */
662:   const PetscInt  *values;          /* List of depths for which we have replicated points */
663:   IS              *splitIS;
664:   IS              *unsplitIS;
665:   PetscInt        *numSplitPoints;     /* The number of replicated points at each depth */
666:   PetscInt        *numUnsplitPoints;   /* The number of non-replicated points at each depth which still give rise to hybrid points */
667:   PetscInt        *numHybridPoints;    /* The number of new hybrid points at each depth */
668:   PetscInt        *numHybridPointsOld; /* The number of existing hybrid points at each depth */
669:   const PetscInt **splitPoints;        /* Replicated points for each depth */
670:   const PetscInt **unsplitPoints;      /* Non-replicated points for each depth */
671:   PetscSection     coordSection;
672:   Vec              coordinates;
673:   PetscScalar     *coords;
674:   PetscInt         depths[4];          /* Depths in the order that plex points are numbered */
675:   PetscInt        *depthMax;           /* The first hybrid point at each depth in the original mesh */
676:   PetscInt        *depthEnd;           /* The point limit at each depth in the original mesh */
677:   PetscInt        *depthShift;         /* Number of replicated+hybrid points at each depth */
678:   PetscInt        *depthOffset;        /* Prefix sums of depthShift */
679:   PetscInt        *pMaxNew;            /* The first replicated point at each depth in the new mesh, hybrids come after this */
680:   PetscInt        *coneNew, *coneONew, *supportNew;
681:   PetscInt         shift = 100, shift2 = 200, depth = 0, dep, dim, d, sp, maxConeSize, maxSupportSize, maxConeSizeNew, maxSupportSizeNew, numLabels, vStart, vEnd, pEnd, p, v;
682:   PetscErrorCode   ierr;

685:   PetscObjectGetComm((PetscObject)dm,&comm);
686:   DMGetDimension(dm, &dim);
687:   DMPlexGetDepth(dm, &depth);
688:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
689:   depths[0] = depth;
690:   depths[1] = 0;
691:   depths[2] = depth-1;
692:   depths[3] = 1;
693:   /* Count split points and add cohesive cells */
694:   DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);
695:   PetscMalloc6(depth+1,&depthMax,depth+1,&depthEnd,depth+1,&depthShift,depth+1,&depthOffset,depth+1,&pMaxNew,depth+1,&numHybridPointsOld);
696:   PetscMalloc7(depth+1,&splitIS,depth+1,&unsplitIS,depth+1,&numSplitPoints,depth+1,&numUnsplitPoints,depth+1,&numHybridPoints,depth+1,&splitPoints,depth+1,&unsplitPoints);
697:   PetscMemzero(depthShift,  (depth+1) * sizeof(PetscInt));
698:   PetscMemzero(depthOffset, (depth+1) * sizeof(PetscInt));
699:   DMPlexGetHybridBounds(dm, depth >= 0 ? &depthMax[depth] : NULL, depth>1 ? &depthMax[depth-1] : NULL, depth>2 ? &depthMax[1] : NULL, depth >= 0 ? &depthMax[0] : NULL);
700:   for (d = 0; d <= depth; ++d) {
701:     DMPlexGetDepthStratum(dm, d, NULL, &pMaxNew[d]);
702:     depthEnd[d]           = pMaxNew[d];
703:     depthMax[d]           = depthMax[d] < 0 ? depthEnd[d] : depthMax[d];
704:     numSplitPoints[d]     = 0;
705:     numUnsplitPoints[d]   = 0;
706:     numHybridPoints[d]    = 0;
707:     numHybridPointsOld[d] = depthMax[d] < 0 ? 0 : depthEnd[d] - depthMax[d];
708:     splitPoints[d]        = NULL;
709:     unsplitPoints[d]      = NULL;
710:     splitIS[d]            = NULL;
711:     unsplitIS[d]          = NULL;
712:   }
713:   if (label) {
714:     DMLabelGetValueIS(label, &valueIS);
715:     ISGetLocalSize(valueIS, &numSP);
716:     ISGetIndices(valueIS, &values);
717:   }
718:   for (sp = 0; sp < numSP; ++sp) {
719:     const PetscInt dep = values[sp];

721:     if ((dep < 0) || (dep > depth)) continue;
722:     DMLabelGetStratumIS(label, dep, &splitIS[dep]);
723:     if (splitIS[dep]) {
724:       ISGetLocalSize(splitIS[dep], &numSplitPoints[dep]);
725:       ISGetIndices(splitIS[dep], &splitPoints[dep]);
726:     }
727:     DMLabelGetStratumIS(label, shift2+dep, &unsplitIS[dep]);
728:     if (unsplitIS[dep]) {
729:       ISGetLocalSize(unsplitIS[dep], &numUnsplitPoints[dep]);
730:       ISGetIndices(unsplitIS[dep], &unsplitPoints[dep]);
731:     }
732:   }
733:   /* Calculate number of hybrid points */
734:   for (d = 1; d <= depth; ++d) numHybridPoints[d]     = numSplitPoints[d-1] + numUnsplitPoints[d-1]; /* There is a hybrid cell/face/edge for every split face/edge/vertex   */
735:   for (d = 0; d <= depth; ++d) depthShift[d]          = numSplitPoints[d] + numHybridPoints[d];
736:   for (d = 1; d <= depth; ++d) depthOffset[depths[d]] = depthOffset[depths[d-1]] + depthShift[depths[d-1]];
737:   for (d = 0; d <= depth; ++d) pMaxNew[d]            += depthOffset[d] - numHybridPointsOld[d];
738:   DMPlexShiftSizes_Internal(dm, depthShift, sdm);
739:   /* Step 3: Set cone/support sizes for new points */
740:   for (dep = 0; dep <= depth; ++dep) {
741:     for (p = 0; p < numSplitPoints[dep]; ++p) {
742:       const PetscInt  oldp   = splitPoints[dep][p];
743:       const PetscInt  newp   = DMPlexShiftPoint_Internal(oldp, depth, depthMax, depthEnd, depthShift) /*oldp + depthOffset[dep]*/;
744:       const PetscInt  splitp = p    + pMaxNew[dep];
745:       const PetscInt *support;
746:       PetscInt        coneSize, supportSize, qf, qn, qp, e;

748:       DMPlexGetConeSize(dm, oldp, &coneSize);
749:       DMPlexSetConeSize(sdm, splitp, coneSize);
750:       DMPlexGetSupportSize(dm, oldp, &supportSize);
751:       DMPlexSetSupportSize(sdm, splitp, supportSize);
752:       if (dep == depth-1) {
753:         const PetscInt hybcell = p + pMaxNew[dep+1] + numSplitPoints[dep+1];

755:         /* Add cohesive cells, they are prisms */
756:         DMPlexSetConeSize(sdm, hybcell, 2 + coneSize);
757:       } else if (dep == 0) {
758:         const PetscInt hybedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1];

760:         DMPlexGetSupport(dm, oldp, &support);
761:         for (e = 0, qn = 0, qp = 0, qf = 0; e < supportSize; ++e) {
762:           PetscInt val;

764:           DMLabelGetValue(label, support[e], &val);
765:           if (val == 1) ++qf;
766:           if ((val == 1) || (val ==  (shift + 1))) ++qn;
767:           if ((val == 1) || (val == -(shift + 1))) ++qp;
768:         }
769:         /* Split old vertex: Edges into original vertex and new cohesive edge */
770:         DMPlexSetSupportSize(sdm, newp, qn+1);
771:         /* Split new vertex: Edges into split vertex and new cohesive edge */
772:         DMPlexSetSupportSize(sdm, splitp, qp+1);
773:         /* Add hybrid edge */
774:         DMPlexSetConeSize(sdm, hybedge, 2);
775:         DMPlexSetSupportSize(sdm, hybedge, qf);
776:       } else if (dep == dim-2) {
777:         const PetscInt hybface = p + pMaxNew[dep+1] + numSplitPoints[dep+1];

779:         DMPlexGetSupport(dm, oldp, &support);
780:         for (e = 0, qn = 0, qp = 0, qf = 0; e < supportSize; ++e) {
781:           PetscInt val;

783:           DMLabelGetValue(label, support[e], &val);
784:           if (val == dim-1) ++qf;
785:           if ((val == dim-1) || (val ==  (shift + dim-1))) ++qn;
786:           if ((val == dim-1) || (val == -(shift + dim-1))) ++qp;
787:         }
788:         /* Split old edge: Faces into original edge and cohesive face (positive side?) */
789:         DMPlexSetSupportSize(sdm, newp, qn+1);
790:         /* Split new edge: Faces into split edge and cohesive face (negative side?) */
791:         DMPlexSetSupportSize(sdm, splitp, qp+1);
792:         /* Add hybrid face */
793:         DMPlexSetConeSize(sdm, hybface, 4);
794:         DMPlexSetSupportSize(sdm, hybface, qf);
795:       }
796:     }
797:   }
798:   for (dep = 0; dep <= depth; ++dep) {
799:     for (p = 0; p < numUnsplitPoints[dep]; ++p) {
800:       const PetscInt  oldp   = unsplitPoints[dep][p];
801:       const PetscInt  newp   = DMPlexShiftPoint_Internal(oldp, depth, depthMax, depthEnd, depthShift) /*oldp + depthOffset[dep]*/;
802:       const PetscInt *support;
803:       PetscInt        coneSize, supportSize, qf, e, s;

805:       DMPlexGetConeSize(dm, oldp, &coneSize);
806:       DMPlexGetSupportSize(dm, oldp, &supportSize);
807:       DMPlexGetSupport(dm, oldp, &support);
808:       if (dep == 0) {
809:         const PetscInt hybedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1] + numSplitPoints[dep];

811:         /* Unsplit vertex: Edges into original vertex, split edges, and new cohesive edge twice */
812:         for (s = 0, qf = 0; s < supportSize; ++s, ++qf) {
813:           PetscFindInt(support[s], numSplitPoints[dep+1], splitPoints[dep+1], &e);
814:           if (e >= 0) ++qf;
815:         }
816:         DMPlexSetSupportSize(sdm, newp, qf+2);
817:         /* Add hybrid edge */
818:         DMPlexSetConeSize(sdm, hybedge, 2);
819:         for (e = 0, qf = 0; e < supportSize; ++e) {
820:           PetscInt val;

822:           DMLabelGetValue(label, support[e], &val);
823:           /* Split and unsplit edges produce hybrid faces */
824:           if (val == 1) ++qf;
825:           if (val == (shift2 + 1)) ++qf;
826:         }
827:         DMPlexSetSupportSize(sdm, hybedge, qf);
828:       } else if (dep == dim-2) {
829:         const PetscInt hybface = p + pMaxNew[dep+1] + numSplitPoints[dep+1] + numSplitPoints[dep];
830:         PetscInt       val;

832:         for (e = 0, qf = 0; e < supportSize; ++e) {
833:           DMLabelGetValue(label, support[e], &val);
834:           if (val == dim-1) qf += 2;
835:           else              ++qf;
836:         }
837:         /* Unsplit edge: Faces into original edge, split face, and cohesive face twice */
838:         DMPlexSetSupportSize(sdm, newp, qf+2);
839:         /* Add hybrid face */
840:         for (e = 0, qf = 0; e < supportSize; ++e) {
841:           DMLabelGetValue(label, support[e], &val);
842:           if (val == dim-1) ++qf;
843:         }
844:         DMPlexSetConeSize(sdm, hybface, 4);
845:         DMPlexSetSupportSize(sdm, hybface, qf);
846:       }
847:     }
848:   }
849:   /* Step 4: Setup split DM */
850:   DMSetUp(sdm);
851:   DMPlexShiftPoints_Internal(dm, depthShift, sdm);
852:   DMPlexGetMaxSizes(sdm, &maxConeSizeNew, &maxSupportSizeNew);
853:   PetscMalloc3(PetscMax(maxConeSize, maxConeSizeNew)*3,&coneNew,PetscMax(maxConeSize, maxConeSizeNew)*3,&coneONew,PetscMax(maxSupportSize, maxSupportSizeNew),&supportNew);
854:   /* Step 6: Set cones and supports for new points */
855:   for (dep = 0; dep <= depth; ++dep) {
856:     for (p = 0; p < numSplitPoints[dep]; ++p) {
857:       const PetscInt  oldp   = splitPoints[dep][p];
858:       const PetscInt  newp   = DMPlexShiftPoint_Internal(oldp, depth, depthMax, depthEnd, depthShift) /*oldp + depthOffset[dep]*/;
859:       const PetscInt  splitp = p    + pMaxNew[dep];
860:       const PetscInt *cone, *support, *ornt;
861:       PetscInt        coneSize, supportSize, q, qf, qn, qp, v, e, s;

863:       DMPlexGetConeSize(dm, oldp, &coneSize);
864:       DMPlexGetCone(dm, oldp, &cone);
865:       DMPlexGetConeOrientation(dm, oldp, &ornt);
866:       DMPlexGetSupportSize(dm, oldp, &supportSize);
867:       DMPlexGetSupport(dm, oldp, &support);
868:       if (dep == depth-1) {
869:         PetscBool       hasUnsplit = PETSC_FALSE;
870:         const PetscInt  hybcell    = p + pMaxNew[dep+1] + numSplitPoints[dep+1];
871:         const PetscInt *supportF;

873:         /* Split face:       copy in old face to new face to start */
874:         DMPlexGetSupport(sdm, newp,  &supportF);
875:         DMPlexSetSupport(sdm, splitp, supportF);
876:         /* Split old face:   old vertices/edges in cone so no change */
877:         /* Split new face:   new vertices/edges in cone */
878:         for (q = 0; q < coneSize; ++q) {
879:           PetscFindInt(cone[q], numSplitPoints[dep-1], splitPoints[dep-1], &v);
880:           if (v < 0) {
881:             PetscFindInt(cone[q], numUnsplitPoints[dep-1], unsplitPoints[dep-1], &v);
882:             if (v < 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate point %d in split or unsplit points of depth %d", cone[q], dep-1);
883:             coneNew[2+q] = DMPlexShiftPoint_Internal(cone[q], depth, depthMax, depthEnd, depthShift) /*cone[q] + depthOffset[dep-1]*/;
884:             hasUnsplit   = PETSC_TRUE;
885:           } else {
886:             coneNew[2+q] = v + pMaxNew[dep-1];
887:             if (dep > 1) {
888:               const PetscInt *econe;
889:               PetscInt        econeSize, r, vs, vu;

891:               DMPlexGetConeSize(dm, cone[q], &econeSize);
892:               DMPlexGetCone(dm, cone[q], &econe);
893:               for (r = 0; r < econeSize; ++r) {
894:                 PetscFindInt(econe[r], numSplitPoints[dep-2],   splitPoints[dep-2],   &vs);
895:                 PetscFindInt(econe[r], numUnsplitPoints[dep-2], unsplitPoints[dep-2], &vu);
896:                 if (vs >= 0) continue;
897:                 if (vu < 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate point %d in split or unsplit points of depth %d", econe[r], dep-2);
898:                 hasUnsplit   = PETSC_TRUE;
899:               }
900:             }
901:           }
902:         }
903:         DMPlexSetCone(sdm, splitp, &coneNew[2]);
904:         DMPlexSetConeOrientation(sdm, splitp, ornt);
905:         /* Face support */
906:         for (s = 0; s < supportSize; ++s) {
907:           PetscInt val;

909:           DMLabelGetValue(label, support[s], &val);
910:           if (val < 0) {
911:             /* Split old face:   Replace negative side cell with cohesive cell */
912:              DMPlexInsertSupport(sdm, newp, s, hybcell);
913:           } else {
914:             /* Split new face:   Replace positive side cell with cohesive cell */
915:             DMPlexInsertSupport(sdm, splitp, s, hybcell);
916:             /* Get orientation for cohesive face */
917:             {
918:               const PetscInt *ncone, *nconeO;
919:               PetscInt        nconeSize, nc;

921:               DMPlexGetConeSize(dm, support[s], &nconeSize);
922:               DMPlexGetCone(dm, support[s], &ncone);
923:               DMPlexGetConeOrientation(dm, support[s], &nconeO);
924:               for (nc = 0; nc < nconeSize; ++nc) {
925:                 if (ncone[nc] == oldp) {
926:                   coneONew[0] = nconeO[nc];
927:                   break;
928:                 }
929:               }
930:               if (nc >= nconeSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate face %d in neighboring cell %d", oldp, support[s]);
931:             }
932:           }
933:         }
934:         /* Cohesive cell:    Old and new split face, then new cohesive faces */
935:         coneNew[0]  = newp;   /* Extracted negative side orientation above */
936:         coneNew[1]  = splitp;
937:         coneONew[1] = coneONew[0];
938:         for (q = 0; q < coneSize; ++q) {
939:           PetscFindInt(cone[q], numSplitPoints[dep-1], splitPoints[dep-1], &v);
940:           if (v < 0) {
941:             PetscFindInt(cone[q], numUnsplitPoints[dep-1], unsplitPoints[dep-1], &v);
942:             coneNew[2+q]  = v + pMaxNew[dep] + numSplitPoints[dep] + numSplitPoints[dep-1];
943:             coneONew[2+q] = 0;
944:           } else {
945:             coneNew[2+q]  = v + pMaxNew[dep] + numSplitPoints[dep];
946:           }
947:           coneONew[2+q] = 0;
948:         }
949:         DMPlexSetCone(sdm, hybcell, coneNew);
950:         DMPlexSetConeOrientation(sdm, hybcell, coneONew);
951:         /* Label the hybrid cells on the boundary of the split */
952:         if (hasUnsplit) {DMLabelSetValue(label, -hybcell, dim);}
953:       } else if (dep == 0) {
954:         const PetscInt hybedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1];

956:         /* Split old vertex: Edges in old split faces and new cohesive edge */
957:         for (e = 0, qn = 0; e < supportSize; ++e) {
958:           PetscInt val;

960:           DMLabelGetValue(label, support[e], &val);
961:           if ((val == 1) || (val == (shift + 1))) {
962:             supportNew[qn++] = DMPlexShiftPoint_Internal(support[e], depth, depthMax, depthEnd, depthShift) /*support[e] + depthOffset[dep+1]*/;
963:           }
964:         }
965:         supportNew[qn] = hybedge;
966:         DMPlexSetSupport(sdm, newp, supportNew);
967:         /* Split new vertex: Edges in new split faces and new cohesive edge */
968:         for (e = 0, qp = 0; e < supportSize; ++e) {
969:           PetscInt val, edge;

971:           DMLabelGetValue(label, support[e], &val);
972:           if (val == 1) {
973:             PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &edge);
974:             if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]);
975:             supportNew[qp++] = edge + pMaxNew[dep+1];
976:           } else if (val == -(shift + 1)) {
977:             supportNew[qp++] = DMPlexShiftPoint_Internal(support[e], depth, depthMax, depthEnd, depthShift) /*support[e] + depthOffset[dep+1]*/;
978:           }
979:         }
980:         supportNew[qp] = hybedge;
981:         DMPlexSetSupport(sdm, splitp, supportNew);
982:         /* Hybrid edge:    Old and new split vertex */
983:         coneNew[0] = newp;
984:         coneNew[1] = splitp;
985:         DMPlexSetCone(sdm, hybedge, coneNew);
986:         for (e = 0, qf = 0; e < supportSize; ++e) {
987:           PetscInt val, edge;

989:           DMLabelGetValue(label, support[e], &val);
990:           if (val == 1) {
991:             PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &edge);
992:             if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]);
993:             supportNew[qf++] = edge + pMaxNew[dep+2] + numSplitPoints[dep+2];
994:           }
995:         }
996:         DMPlexSetSupport(sdm, hybedge, supportNew);
997:       } else if (dep == dim-2) {
998:         const PetscInt hybface = p + pMaxNew[dep+1] + numSplitPoints[dep+1];

1000:         /* Split old edge:   old vertices in cone so no change */
1001:         /* Split new edge:   new vertices in cone */
1002:         for (q = 0; q < coneSize; ++q) {
1003:           PetscFindInt(cone[q], numSplitPoints[dep-1], splitPoints[dep-1], &v);
1004:           if (v < 0) {
1005:             PetscFindInt(cone[q], numUnsplitPoints[dep-1], unsplitPoints[dep-1], &v);
1006:             if (v < 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate point %d in split or unsplit points of depth %d", cone[q], dep-1);
1007:             coneNew[q] = DMPlexShiftPoint_Internal(cone[q], depth, depthMax, depthEnd, depthShift) /*cone[q] + depthOffset[dep-1]*/;
1008:           } else {
1009:             coneNew[q] = v + pMaxNew[dep-1];
1010:           }
1011:         }
1012:         DMPlexSetCone(sdm, splitp, coneNew);
1013:         /* Split old edge: Faces in positive side cells and old split faces */
1014:         for (e = 0, q = 0; e < supportSize; ++e) {
1015:           PetscInt val;

1017:           DMLabelGetValue(label, support[e], &val);
1018:           if (val == dim-1) {
1019:             supportNew[q++] = DMPlexShiftPoint_Internal(support[e], depth, depthMax, depthEnd, depthShift) /*support[e] + depthOffset[dep+1]*/;
1020:           } else if (val == (shift + dim-1)) {
1021:             supportNew[q++] = DMPlexShiftPoint_Internal(support[e], depth, depthMax, depthEnd, depthShift) /*support[e] + depthOffset[dep+1]*/;
1022:           }
1023:         }
1024:         supportNew[q++] = p + pMaxNew[dep+1] + numSplitPoints[dep+1];
1025:         DMPlexSetSupport(sdm, newp, supportNew);
1026:         /* Split new edge: Faces in negative side cells and new split faces */
1027:         for (e = 0, q = 0; e < supportSize; ++e) {
1028:           PetscInt val, face;

1030:           DMLabelGetValue(label, support[e], &val);
1031:           if (val == dim-1) {
1032:             PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &face);
1033:             if (face < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Face %d is not a split face", support[e]);
1034:             supportNew[q++] = face + pMaxNew[dep+1];
1035:           } else if (val == -(shift + dim-1)) {
1036:             supportNew[q++] = DMPlexShiftPoint_Internal(support[e], depth, depthMax, depthEnd, depthShift) /*support[e] + depthOffset[dep+1]*/;
1037:           }
1038:         }
1039:         supportNew[q++] = p + pMaxNew[dep+1] + numSplitPoints[dep+1];
1040:         DMPlexSetSupport(sdm, splitp, supportNew);
1041:         /* Hybrid face */
1042:         coneNew[0] = newp;
1043:         coneNew[1] = splitp;
1044:         for (v = 0; v < coneSize; ++v) {
1045:           PetscInt vertex;
1046:           PetscFindInt(cone[v], numSplitPoints[dep-1], splitPoints[dep-1], &vertex);
1047:           if (vertex < 0) {
1048:             PetscFindInt(cone[v], numUnsplitPoints[dep-1], unsplitPoints[dep-1], &vertex);
1049:             if (vertex < 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate point %d in split or unsplit points of depth %d", cone[v], dep-1);
1050:             coneNew[2+v] = vertex + pMaxNew[dep] + numSplitPoints[dep] + numSplitPoints[dep-1];
1051:           } else {
1052:             coneNew[2+v] = vertex + pMaxNew[dep] + numSplitPoints[dep];
1053:           }
1054:         }
1055:         DMPlexSetCone(sdm, hybface, coneNew);
1056:         for (e = 0, qf = 0; e < supportSize; ++e) {
1057:           PetscInt val, face;

1059:           DMLabelGetValue(label, support[e], &val);
1060:           if (val == dim-1) {
1061:             PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &face);
1062:             if (face < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Face %d is not a split face", support[e]);
1063:             supportNew[qf++] = face + pMaxNew[dep+2] + numSplitPoints[dep+2];
1064:           }
1065:         }
1066:         DMPlexSetSupport(sdm, hybface, supportNew);
1067:       }
1068:     }
1069:   }
1070:   for (dep = 0; dep <= depth; ++dep) {
1071:     for (p = 0; p < numUnsplitPoints[dep]; ++p) {
1072:       const PetscInt  oldp   = unsplitPoints[dep][p];
1073:       const PetscInt  newp   = DMPlexShiftPoint_Internal(oldp, depth, depthMax, depthEnd, depthShift) /*oldp + depthOffset[dep]*/;
1074:       const PetscInt *cone, *support, *ornt;
1075:       PetscInt        coneSize, supportSize, supportSizeNew, q, qf, e, f, s;

1077:       DMPlexGetConeSize(dm, oldp, &coneSize);
1078:       DMPlexGetCone(dm, oldp, &cone);
1079:       DMPlexGetConeOrientation(dm, oldp, &ornt);
1080:       DMPlexGetSupportSize(dm, oldp, &supportSize);
1081:       DMPlexGetSupport(dm, oldp, &support);
1082:       if (dep == 0) {
1083:         const PetscInt hybedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1] + numSplitPoints[dep];

1085:         /* Unsplit vertex */
1086:         DMPlexGetSupportSize(sdm, newp, &supportSizeNew);
1087:         for (s = 0, q = 0; s < supportSize; ++s) {
1088:           supportNew[q++] = DMPlexShiftPoint_Internal(support[s], depth, depthMax, depthEnd, depthShift) /*support[s] + depthOffset[dep+1]*/;
1089:           PetscFindInt(support[s], numSplitPoints[dep+1], splitPoints[dep+1], &e);
1090:           if (e >= 0) {
1091:             supportNew[q++] = e + pMaxNew[dep+1];
1092:           }
1093:         }
1094:         supportNew[q++] = hybedge;
1095:         supportNew[q++] = hybedge;
1096:         if (q != supportSizeNew) SETERRQ3(comm, PETSC_ERR_ARG_WRONG, "Support size %d != %d for vertex %d", q, supportSizeNew, newp);
1097:         DMPlexSetSupport(sdm, newp, supportNew);
1098:         /* Hybrid edge */
1099:         coneNew[0] = newp;
1100:         coneNew[1] = newp;
1101:         DMPlexSetCone(sdm, hybedge, coneNew);
1102:         for (e = 0, qf = 0; e < supportSize; ++e) {
1103:           PetscInt val, edge;

1105:           DMLabelGetValue(label, support[e], &val);
1106:           if (val == 1) {
1107:             PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &edge);
1108:             if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]);
1109:             supportNew[qf++] = edge + pMaxNew[dep+2] + numSplitPoints[dep+2];
1110:           } else if  (val ==  (shift2 + 1)) {
1111:             PetscFindInt(support[e], numUnsplitPoints[dep+1], unsplitPoints[dep+1], &edge);
1112:             if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a unsplit edge", support[e]);
1113:             supportNew[qf++] = edge + pMaxNew[dep+2] + numSplitPoints[dep+2] + numSplitPoints[dep+1];
1114:           }
1115:         }
1116:         DMPlexSetSupport(sdm, hybedge, supportNew);
1117:       } else if (dep == dim-2) {
1118:         const PetscInt hybface = p + pMaxNew[dep+1] + numSplitPoints[dep+1] + numSplitPoints[dep];

1120:         /* Unsplit edge: Faces into original edge, split face, and hybrid face twice */
1121:         for (f = 0, qf = 0; f < supportSize; ++f) {
1122:           PetscInt val, face;

1124:           DMLabelGetValue(label, support[f], &val);
1125:           if (val == dim-1) {
1126:             PetscFindInt(support[f], numSplitPoints[dep+1], splitPoints[dep+1], &face);
1127:             if (face < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Face %d is not a split face", support[f]);
1128:             supportNew[qf++] = DMPlexShiftPoint_Internal(support[f], depth, depthMax, depthEnd, depthShift) /*support[f] + depthOffset[dep+1]*/;
1129:             supportNew[qf++] = face + pMaxNew[dep+1];
1130:           } else {
1131:             supportNew[qf++] = DMPlexShiftPoint_Internal(support[f], depth, depthMax, depthEnd, depthShift) /*support[f] + depthOffset[dep+1]*/;
1132:           }
1133:         }
1134:         supportNew[qf++] = hybface;
1135:         supportNew[qf++] = hybface;
1136:         DMPlexGetSupportSize(sdm, newp, &supportSizeNew);
1137:         if (qf != supportSizeNew) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Support size for unsplit edge %d is %d != %d\n", newp, qf, supportSizeNew);
1138:         DMPlexSetSupport(sdm, newp, supportNew);
1139:         /* Add hybrid face */
1140:         coneNew[0] = newp;
1141:         coneNew[1] = newp;
1142:         PetscFindInt(cone[0], numUnsplitPoints[dep-1], unsplitPoints[dep-1], &v);
1143:         if (v < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex %d is not an unsplit vertex", cone[0]);
1144:         coneNew[2] = v + pMaxNew[dep] + numSplitPoints[dep] + numSplitPoints[dep-1];
1145:         PetscFindInt(cone[1], numUnsplitPoints[dep-1], unsplitPoints[dep-1], &v);
1146:         if (v < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex %d is not an unsplit vertex", cone[1]);
1147:         coneNew[3] = v + pMaxNew[dep] + numSplitPoints[dep] + numSplitPoints[dep-1];
1148:         DMPlexSetCone(sdm, hybface, coneNew);
1149:         for (f = 0, qf = 0; f < supportSize; ++f) {
1150:           PetscInt val, face;

1152:           DMLabelGetValue(label, support[f], &val);
1153:           if (val == dim-1) {
1154:             PetscFindInt(support[f], numSplitPoints[dep+1], splitPoints[dep+1], &face);
1155:             supportNew[qf++] = face + pMaxNew[dep+2] + numSplitPoints[dep+2];
1156:           }
1157:         }
1158:         DMPlexGetSupportSize(sdm, hybface, &supportSizeNew);
1159:         if (qf != supportSizeNew) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Support size for hybrid face %d is %d != %d\n", hybface, qf, supportSizeNew);
1160:         DMPlexSetSupport(sdm, hybface, supportNew);
1161:       }
1162:     }
1163:   }
1164:   /* Step 6b: Replace split points in negative side cones */
1165:   for (sp = 0; sp < numSP; ++sp) {
1166:     PetscInt        dep = values[sp];
1167:     IS              pIS;
1168:     PetscInt        numPoints;
1169:     const PetscInt *points;

1171:     if (dep >= 0) continue;
1172:     DMLabelGetStratumIS(label, dep, &pIS);
1173:     if (!pIS) continue;
1174:     dep  = -dep - shift;
1175:     ISGetLocalSize(pIS, &numPoints);
1176:     ISGetIndices(pIS, &points);
1177:     for (p = 0; p < numPoints; ++p) {
1178:       const PetscInt  oldp = points[p];
1179:       const PetscInt  newp = DMPlexShiftPoint_Internal(oldp, depth, depthMax, depthEnd, depthShift) /*depthOffset[dep] + oldp*/;
1180:       const PetscInt *cone;
1181:       PetscInt        coneSize, c;
1182:       /* PetscBool       replaced = PETSC_FALSE; */

1184:       /* Negative edge: replace split vertex */
1185:       /* Negative cell: replace split face */
1186:       DMPlexGetConeSize(sdm, newp, &coneSize);
1187:       DMPlexGetCone(sdm, newp, &cone);
1188:       for (c = 0; c < coneSize; ++c) {
1189:         const PetscInt coldp = cone[c] - depthOffset[dep-1];
1190:         PetscInt       csplitp, cp, val;

1192:         DMLabelGetValue(label, coldp, &val);
1193:         if (val == dep-1) {
1194:           PetscFindInt(coldp, numSplitPoints[dep-1], splitPoints[dep-1], &cp);
1195:           if (cp < 0) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "Point %d is not a split point of dimension %d", oldp, dep-1);
1196:           csplitp  = pMaxNew[dep-1] + cp;
1197:           DMPlexInsertCone(sdm, newp, c, csplitp);
1198:           /* replaced = PETSC_TRUE; */
1199:         }
1200:       }
1201:       /* Cells with only a vertex or edge on the submesh have no replacement */
1202:       /* if (!replaced) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "The cone of point %d does not contain split points", oldp); */
1203:     }
1204:     ISRestoreIndices(pIS, &points);
1205:     ISDestroy(&pIS);
1206:   }
1207:   /* Step 7: Stratify */
1208:   DMPlexStratify(sdm);
1209:   /* Step 8: Coordinates */
1210:   DMPlexShiftCoordinates_Internal(dm, depthShift, sdm);
1211:   DMGetCoordinateSection(sdm, &coordSection);
1212:   DMGetCoordinatesLocal(sdm, &coordinates);
1213:   VecGetArray(coordinates, &coords);
1214:   for (v = 0; v < (numSplitPoints ? numSplitPoints[0] : 0); ++v) {
1215:     const PetscInt newp   = DMPlexShiftPoint_Internal(splitPoints[0][v], depth, depthMax, depthEnd, depthShift) /*depthOffset[0] + splitPoints[0][v]*/;
1216:     const PetscInt splitp = pMaxNew[0] + v;
1217:     PetscInt       dof, off, soff, d;

1219:     PetscSectionGetDof(coordSection, newp, &dof);
1220:     PetscSectionGetOffset(coordSection, newp, &off);
1221:     PetscSectionGetOffset(coordSection, splitp, &soff);
1222:     for (d = 0; d < dof; ++d) coords[soff+d] = coords[off+d];
1223:   }
1224:   VecRestoreArray(coordinates, &coords);
1225:   /* Step 9: SF, if I can figure this out we can split the mesh in parallel */
1226:   DMPlexShiftSF_Internal(dm, depthShift, sdm);
1227:   /* Step 10: Labels */
1228:   DMPlexShiftLabels_Internal(dm, depthShift, sdm);
1229:   DMPlexGetNumLabels(sdm, &numLabels);
1230:   for (dep = 0; dep <= depth; ++dep) {
1231:     for (p = 0; p < numSplitPoints[dep]; ++p) {
1232:       const PetscInt newp   = DMPlexShiftPoint_Internal(splitPoints[dep][p], depth, depthMax, depthEnd, depthShift) /*depthOffset[dep] + splitPoints[dep][p]*/;
1233:       const PetscInt splitp = pMaxNew[dep] + p;
1234:       PetscInt       l;

1236:       for (l = 0; l < numLabels; ++l) {
1237:         DMLabel     mlabel;
1238:         const char *lname;
1239:         PetscInt    val;
1240:         PetscBool   isDepth;

1242:         DMPlexGetLabelName(sdm, l, &lname);
1243:         PetscStrcmp(lname, "depth", &isDepth);
1244:         if (isDepth) continue;
1245:         DMPlexGetLabel(sdm, lname, &mlabel);
1246:         DMLabelGetValue(mlabel, newp, &val);
1247:         if (val >= 0) {
1248:           DMLabelSetValue(mlabel, splitp, val);
1249: #if 0
1250:           /* Do not put cohesive edges into the label */
1251:           if (dep == 0) {
1252:             const PetscInt cedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1];
1253:             DMLabelSetValue(mlabel, cedge, val);
1254:           } else if (dep == dim-2) {
1255:             const PetscInt cface = p + pMaxNew[dep+1] + numSplitPoints[dep+1];
1256:             DMLabelSetValue(mlabel, cface, val);
1257:           }
1258:           /* Do not put cohesive faces into the label */
1259: #endif
1260:         }
1261:       }
1262:     }
1263:   }
1264:   for (sp = 0; sp < numSP; ++sp) {
1265:     const PetscInt dep = values[sp];

1267:     if ((dep < 0) || (dep > depth)) continue;
1268:     if (splitIS[dep]) {ISRestoreIndices(splitIS[dep], &splitPoints[dep]);}
1269:     ISDestroy(&splitIS[dep]);
1270:     if (unsplitIS[dep]) {ISRestoreIndices(unsplitIS[dep], &unsplitPoints[dep]);}
1271:     ISDestroy(&unsplitIS[dep]);
1272:   }
1273:   if (label) {
1274:     ISRestoreIndices(valueIS, &values);
1275:     ISDestroy(&valueIS);
1276:   }
1277:   for (d = 0; d <= depth; ++d) {
1278:     DMPlexGetDepthStratum(sdm, d, NULL, &pEnd);
1279:     pMaxNew[d] = pEnd - numHybridPoints[d] - numHybridPointsOld[d];
1280:   }
1281:   DMPlexSetHybridBounds(sdm, depth >= 0 ? pMaxNew[depth] : PETSC_DETERMINE, depth>1 ? pMaxNew[depth-1] : PETSC_DETERMINE, depth>2 ? pMaxNew[1] : PETSC_DETERMINE, depth >= 0 ? pMaxNew[0] : PETSC_DETERMINE);
1282:   PetscFree3(coneNew, coneONew, supportNew);
1283:   PetscFree6(depthMax, depthEnd, depthShift, depthOffset, pMaxNew, numHybridPointsOld);
1284:   PetscFree7(splitIS, unsplitIS, numSplitPoints, numUnsplitPoints, numHybridPoints, splitPoints, unsplitPoints);
1285:   return(0);
1286: }

1290: /*@C
1291:   DMPlexConstructCohesiveCells - Construct cohesive cells which split the face along an internal interface

1293:   Collective on dm

1295:   Input Parameters:
1296: + dm - The original DM
1297: - label - The label specifying the boundary faces (this could be auto-generated)

1299:   Output Parameters:
1300: - dmSplit - The new DM

1302:   Level: developer

1304: .seealso: DMCreate(), DMPlexLabelCohesiveComplete()
1305: @*/
1306: PetscErrorCode DMPlexConstructCohesiveCells(DM dm, DMLabel label, DM *dmSplit)
1307: {
1308:   DM             sdm;
1309:   PetscInt       dim;

1315:   DMCreate(PetscObjectComm((PetscObject)dm), &sdm);
1316:   DMSetType(sdm, DMPLEX);
1317:   DMGetDimension(dm, &dim);
1318:   DMSetDimension(sdm, dim);
1319:   switch (dim) {
1320:   case 2:
1321:   case 3:
1322:     DMPlexConstructCohesiveCells_Internal(dm, label, sdm);
1323:     break;
1324:   default:
1325:     SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cannot construct cohesive cells for dimension %d", dim);
1326:   }
1327:   *dmSplit = sdm;
1328:   return(0);
1329: }

1333: /* Returns the side of the surface for a given cell with a face on the surface */
1334: static PetscErrorCode GetSurfaceSide_Static(DM dm, DM subdm, PetscInt numSubpoints, const PetscInt *subpoints, PetscInt cell, PetscInt face, PetscBool *pos)
1335: {
1336:   const PetscInt *cone, *ornt;
1337:   PetscInt        dim, coneSize, c;
1338:   PetscErrorCode  ierr;

1341:   *pos = PETSC_TRUE;
1342:   DMGetDimension(dm, &dim);
1343:   DMPlexGetConeSize(dm, cell, &coneSize);
1344:   DMPlexGetCone(dm, cell, &cone);
1345:   DMPlexGetConeOrientation(dm, cell, &ornt);
1346:   for (c = 0; c < coneSize; ++c) {
1347:     if (cone[c] == face) {
1348:       PetscInt o = ornt[c];

1350:       if (subdm) {
1351:         const PetscInt *subcone, *subornt;
1352:         PetscInt        subpoint, subface, subconeSize, sc;

1354:         PetscFindInt(cell, numSubpoints, subpoints, &subpoint);
1355:         PetscFindInt(face, numSubpoints, subpoints, &subface);
1356:         DMPlexGetConeSize(subdm, subpoint, &subconeSize);
1357:         DMPlexGetCone(subdm, subpoint, &subcone);
1358:         DMPlexGetConeOrientation(subdm, subpoint, &subornt);
1359:         for (sc = 0; sc < subconeSize; ++sc) {
1360:           if (subcone[sc] == subface) {
1361:             o = subornt[0];
1362:             break;
1363:           }
1364:         }
1365:         if (sc >= subconeSize) SETERRQ4(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find subpoint %d (%d) in cone for subpoint %d (%d)", subface, face, subpoint, cell);
1366:       }
1367:       if (o >= 0) *pos = PETSC_TRUE;
1368:       else        *pos = PETSC_FALSE;
1369:       break;
1370:     }
1371:   }
1372:   if (c == coneSize) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Cell %d in split face %d support does not have it in the cone", cell, face);
1373:   return(0);
1374: }

1378: /*@
1379:   DMPlexLabelCohesiveComplete - Starting with a label marking points on an internal surface, we add all other mesh pieces
1380:   to complete the surface

1382:   Input Parameters:
1383: + dm     - The DM
1384: . label  - A DMLabel marking the surface
1385: . blabel - A DMLabel marking the vertices on the boundary which will not be duplicated, or NULL to find them automatically
1386: . flip   - Flag to flip the submesh normal and replace points on the other side
1387: - subdm  - The subDM associated with the label, or NULL

1389:   Output Parameter:
1390: . label - A DMLabel marking all surface points

1392:   Note: The vertices in blabel are called "unsplit" in the terminology from hybrid cell creation.

1394:   Level: developer

1396: .seealso: DMPlexConstructCohesiveCells(), DMPlexLabelComplete()
1397: @*/
1398: PetscErrorCode DMPlexLabelCohesiveComplete(DM dm, DMLabel label, DMLabel blabel, PetscBool flip, DM subdm)
1399: {
1400:   DMLabel         depthLabel;
1401:   IS              dimIS, subpointIS, facePosIS, faceNegIS, crossEdgeIS = NULL;
1402:   const PetscInt *points, *subpoints;
1403:   const PetscInt  rev   = flip ? -1 : 1;
1404:   PetscInt       *pMax;
1405:   PetscInt        shift = 100, shift2 = 200, dim, depth, pSize, dep, cStart, cEnd, cMax, fStart, fEnd, vStart, vEnd, numPoints, numSubpoints, p, val;
1406:   PetscErrorCode  ierr;

1409:   DMPlexGetDepth(dm, &depth);
1410:   DMGetDimension(dm, &dim);
1411:   pSize = PetscMax(depth, dim) + 1;
1412:   PetscMalloc1(pSize,&pMax);
1413:   DMPlexGetHybridBounds(dm, depth >= 0 ? &pMax[depth] : NULL, depth>1 ? &pMax[depth-1] : NULL, depth>2 ? &pMax[1] : NULL, &pMax[0]);
1414:   DMPlexGetDepthLabel(dm, &depthLabel);
1415:   DMGetDimension(dm, &dim);
1416:   if (subdm) {
1417:     DMPlexCreateSubpointIS(subdm, &subpointIS);
1418:     if (subpointIS) {
1419:       ISGetLocalSize(subpointIS, &numSubpoints);
1420:       ISGetIndices(subpointIS, &subpoints);
1421:     }
1422:   }
1423:   /* Mark cell on the fault, and its faces which touch the fault: cell orientation for face gives the side of the fault */
1424:   DMLabelGetStratumIS(label, dim-1, &dimIS);
1425:   if (!dimIS) {
1426:     PetscFree(pMax);
1427:     return(0);
1428:   }
1429:   ISGetLocalSize(dimIS, &numPoints);
1430:   ISGetIndices(dimIS, &points);
1431:   for (p = 0; p < numPoints; ++p) { /* Loop over fault faces */
1432:     const PetscInt *support;
1433:     PetscInt        supportSize, s;

1435:     DMPlexGetSupportSize(dm, points[p], &supportSize);
1436:     if (supportSize != 2) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Split face %d has %d != 2 supports", points[p], supportSize);
1437:     DMPlexGetSupport(dm, points[p], &support);
1438:     for (s = 0; s < supportSize; ++s) {
1439:       const PetscInt *cone;
1440:       PetscInt        coneSize, c;
1441:       PetscBool       pos;

1443:       GetSurfaceSide_Static(dm, subdm, numSubpoints, subpoints, support[s], points[p], &pos);
1444:       if (pos) {DMLabelSetValue(label, support[s],  rev*(shift+dim));}
1445:       else     {DMLabelSetValue(label, support[s], -rev*(shift+dim));}
1446:       if (rev < 0) pos = !pos ? PETSC_TRUE : PETSC_FALSE;
1447:       /* Put faces touching the fault in the label */
1448:       DMPlexGetConeSize(dm, support[s], &coneSize);
1449:       DMPlexGetCone(dm, support[s], &cone);
1450:       for (c = 0; c < coneSize; ++c) {
1451:         const PetscInt point = cone[c];

1453:         DMLabelGetValue(label, point, &val);
1454:         if (val == -1) {
1455:           PetscInt *closure = NULL;
1456:           PetscInt  closureSize, cl;

1458:           DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);
1459:           for (cl = 0; cl < closureSize*2; cl += 2) {
1460:             const PetscInt clp  = closure[cl];
1461:             PetscInt       bval = -1;

1463:             DMLabelGetValue(label, clp, &val);
1464:             if (blabel) {DMLabelGetValue(blabel, clp, &bval);}
1465:             if ((val >= 0) && (val < dim-1) && (bval < 0)) {
1466:               DMLabelSetValue(label, point, pos == PETSC_TRUE ? shift+dim-1 : -(shift+dim-1));
1467:               break;
1468:             }
1469:           }
1470:           DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);
1471:         }
1472:       }
1473:     }
1474:   }
1475:   ISRestoreIndices(dimIS, &points);
1476:   ISDestroy(&dimIS);
1477:   if (subdm) {
1478:     if (subpointIS) {ISRestoreIndices(subpointIS, &subpoints);}
1479:     ISDestroy(&subpointIS);
1480:   }
1481:   /* Mark boundary points as unsplit */
1482:   if (blabel) {
1483:     DMLabelGetStratumIS(blabel, 1, &dimIS);
1484:     ISGetLocalSize(dimIS, &numPoints);
1485:     ISGetIndices(dimIS, &points);
1486:     for (p = 0; p < numPoints; ++p) {
1487:       const PetscInt point = points[p];
1488:       PetscInt       val, bval;

1490:       DMLabelGetValue(blabel, point, &bval);
1491:       if (bval >= 0) {
1492:         DMLabelGetValue(label, point, &val);
1493:         if ((val < 0) || (val > dim)) {
1494:           /* This could be a point added from splitting a vertex on an adjacent fault, otherwise its just wrong */
1495:           DMLabelClearValue(blabel, point, bval);
1496:         }
1497:       }
1498:     }
1499:     for (p = 0; p < numPoints; ++p) {
1500:       const PetscInt point = points[p];
1501:       PetscInt       val, bval;

1503:       DMLabelGetValue(blabel, point, &bval);
1504:       if (bval >= 0) {
1505:         const PetscInt *cone,    *support;
1506:         PetscInt        coneSize, supportSize, s, valA, valB, valE;

1508:         /* Mark as unsplit */
1509:         DMLabelGetValue(label, point, &val);
1510:         if ((val < 0) || (val > dim)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %d has label value %d, should be part of the fault", point, val);
1511:         DMLabelClearValue(label, point, val);
1512:         DMLabelSetValue(label, point, shift2+val);
1513:         /* Check for cross-edge
1514:              A cross-edge has endpoints which are both on the boundary of the surface, but the edge itself is not. */
1515:         if (val != 0) continue;
1516:         DMPlexGetSupport(dm, point, &support);
1517:         DMPlexGetSupportSize(dm, point, &supportSize);
1518:         for (s = 0; s < supportSize; ++s) {
1519:           DMPlexGetCone(dm, support[s], &cone);
1520:           DMPlexGetConeSize(dm, support[s], &coneSize);
1521:           if (coneSize != 2) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Edge %D has %D vertices != 2", support[s], coneSize);
1522:           DMLabelGetValue(blabel, cone[0], &valA);
1523:           DMLabelGetValue(blabel, cone[1], &valB);
1524:           DMLabelGetValue(blabel, support[s], &valE);
1525:           if ((valE < 0) && (valA >= 0) && (valB >= 0) && (cone[0] != cone[1])) {DMLabelSetValue(blabel, support[s], 2);}
1526:         }
1527:       }
1528:     }
1529:     ISRestoreIndices(dimIS, &points);
1530:     ISDestroy(&dimIS);
1531:   }
1532:   /* Search for other cells/faces/edges connected to the fault by a vertex */
1533:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
1534:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
1535:   DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);
1536:   cMax = cMax < 0 ? cEnd : cMax;
1537:   DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
1538:   DMLabelGetStratumIS(label, 0, &dimIS);
1539:   if (blabel) {DMLabelGetStratumIS(blabel, 2, &crossEdgeIS);}
1540:   if (dimIS && crossEdgeIS) {
1541:     IS vertIS = dimIS;

1543:     ISExpand(vertIS, crossEdgeIS, &dimIS);
1544:     ISDestroy(&crossEdgeIS);
1545:     ISDestroy(&vertIS);
1546:   }
1547:   if (!dimIS) {
1548:     PetscFree(pMax);
1549:     return(0);
1550:   }
1551:   ISGetLocalSize(dimIS, &numPoints);
1552:   ISGetIndices(dimIS, &points);
1553:   for (p = 0; p < numPoints; ++p) { /* Loop over fault vertices */
1554:     PetscInt *star = NULL;
1555:     PetscInt  starSize, s;
1556:     PetscInt  again = 1;  /* 0: Finished 1: Keep iterating after a change 2: No change */

1558:     /* All points connected to the fault are inside a cell, so at the top level we will only check cells */
1559:     DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);
1560:     while (again) {
1561:       if (again > 1) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Could not classify all cells connected to the fault");
1562:       again = 0;
1563:       for (s = 0; s < starSize*2; s += 2) {
1564:         const PetscInt  point = star[s];
1565:         const PetscInt *cone;
1566:         PetscInt        coneSize, c;

1568:         if ((point < cStart) || (point >= cMax)) continue;
1569:         DMLabelGetValue(label, point, &val);
1570:         if (val != -1) continue;
1571:         again = again == 1 ? 1 : 2;
1572:         DMPlexGetConeSize(dm, point, &coneSize);
1573:         DMPlexGetCone(dm, point, &cone);
1574:         for (c = 0; c < coneSize; ++c) {
1575:           DMLabelGetValue(label, cone[c], &val);
1576:           if (val != -1) {
1577:             const PetscInt *ccone;
1578:             PetscInt        cconeSize, cc, side;

1580:             if (PetscAbs(val) < shift) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Face %d on cell %d has an invalid label %d", cone[c], point, val);
1581:             if (val > 0) side =  1;
1582:             else         side = -1;
1583:             DMLabelSetValue(label, point, side*(shift+dim));
1584:             /* Mark cell faces which touch the fault */
1585:             DMPlexGetConeSize(dm, point, &cconeSize);
1586:             DMPlexGetCone(dm, point, &ccone);
1587:             for (cc = 0; cc < cconeSize; ++cc) {
1588:               PetscInt *closure = NULL;
1589:               PetscInt  closureSize, cl;

1591:               DMLabelGetValue(label, ccone[cc], &val);
1592:               if (val != -1) continue;
1593:               DMPlexGetTransitiveClosure(dm, ccone[cc], PETSC_TRUE, &closureSize, &closure);
1594:               for (cl = 0; cl < closureSize*2; cl += 2) {
1595:                 const PetscInt clp = closure[cl];

1597:                 DMLabelGetValue(label, clp, &val);
1598:                 if (val == -1) continue;
1599:                 DMLabelSetValue(label, ccone[cc], side*(shift+dim-1));
1600:                 break;
1601:               }
1602:               DMPlexRestoreTransitiveClosure(dm, ccone[cc], PETSC_TRUE, &closureSize, &closure);
1603:             }
1604:             again = 1;
1605:             break;
1606:           }
1607:         }
1608:       }
1609:     }
1610:     /* Classify the rest by cell membership */
1611:     for (s = 0; s < starSize*2; s += 2) {
1612:       const PetscInt point = star[s];

1614:       DMLabelGetValue(label, point, &val);
1615:       if (val == -1) {
1616:         PetscInt  *sstar = NULL;
1617:         PetscInt   sstarSize, ss;
1618:         PetscBool  marked = PETSC_FALSE;

1620:         DMPlexGetTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);
1621:         for (ss = 0; ss < sstarSize*2; ss += 2) {
1622:           const PetscInt spoint = sstar[ss];

1624:           if ((spoint < cStart) || (spoint >= cMax)) continue;
1625:           DMLabelGetValue(label, spoint, &val);
1626:           if (val == -1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d in star of %d does not have a valid label", spoint, point);
1627:           DMLabelGetValue(depthLabel, point, &dep);
1628:           if (val > 0) {
1629:             DMLabelSetValue(label, point,   shift+dep);
1630:           } else {
1631:             DMLabelSetValue(label, point, -(shift+dep));
1632:           }
1633:           marked = PETSC_TRUE;
1634:           break;
1635:         }
1636:         DMPlexRestoreTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);
1637:         DMLabelGetValue(depthLabel, point, &dep);
1638:         if (point < pMax[dep] && !marked) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Point %d could not be classified", point);
1639:       }
1640:     }
1641:     DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);
1642:   }
1643:   ISRestoreIndices(dimIS, &points);
1644:   ISDestroy(&dimIS);
1645:   /* If any faces touching the fault divide cells on either side, split them */
1646:   DMLabelGetStratumIS(label,   shift+dim-1,  &facePosIS);
1647:   DMLabelGetStratumIS(label, -(shift+dim-1), &faceNegIS);
1648:   ISExpand(facePosIS, faceNegIS, &dimIS);
1649:   ISDestroy(&facePosIS);
1650:   ISDestroy(&faceNegIS);
1651:   ISGetLocalSize(dimIS, &numPoints);
1652:   ISGetIndices(dimIS, &points);
1653:   for (p = 0; p < numPoints; ++p) {
1654:     const PetscInt  point = points[p];
1655:     const PetscInt *support;
1656:     PetscInt        supportSize, valA, valB;

1658:     DMPlexGetSupportSize(dm, point, &supportSize);
1659:     if (supportSize != 2) continue;
1660:     DMPlexGetSupport(dm, point, &support);
1661:     DMLabelGetValue(label, support[0], &valA);
1662:     DMLabelGetValue(label, support[1], &valB);
1663:     if ((valA == -1) || (valB == -1)) continue;
1664:     if (valA*valB > 0) continue;
1665:     /* Split the face */
1666:     DMLabelGetValue(label, point, &valA);
1667:     DMLabelClearValue(label, point, valA);
1668:     DMLabelSetValue(label, point, dim-1);
1669:     /* Label its closure:
1670:       unmarked: label as unsplit
1671:       incident: relabel as split
1672:       split:    do nothing
1673:     */
1674:     {
1675:       PetscInt *closure = NULL;
1676:       PetscInt  closureSize, cl;

1678:       DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);
1679:       for (cl = 0; cl < closureSize*2; cl += 2) {
1680:         DMLabelGetValue(label, closure[cl], &valA);
1681:         if (valA == -1) { /* Mark as unsplit */
1682:           DMLabelGetValue(depthLabel, closure[cl], &dep);
1683:           DMLabelSetValue(label, closure[cl], shift2+dep);
1684:         } else if (((valA >= shift) && (valA < shift2)) || ((valA <= -shift) && (valA > -shift2))) {
1685:           DMLabelGetValue(depthLabel, closure[cl], &dep);
1686:           DMLabelClearValue(label, closure[cl], valA);
1687:           DMLabelSetValue(label, closure[cl], dep);
1688:         }
1689:       }
1690:       DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);
1691:     }
1692:   }
1693:   ISRestoreIndices(dimIS, &points);
1694:   ISDestroy(&dimIS);
1695:   PetscFree(pMax);
1696:   return(0);
1697: }

1701: /*@C
1702:   DMPlexCreateHybridMesh - Create a mesh with hybrid cells along an internal interface

1704:   Collective on dm

1706:   Input Parameters:
1707: + dm - The original DM
1708: - labelName - The label specifying the interface vertices

1710:   Output Parameters:
1711: + hybridLabel - The label fully marking the interface
1712: - dmHybrid - The new DM

1714:   Level: developer

1716: .seealso: DMPlexConstructCohesiveCells(), DMPlexLabelCohesiveComplete(), DMCreate()
1717: @*/
1718: PetscErrorCode DMPlexCreateHybridMesh(DM dm, DMLabel label, DMLabel *hybridLabel, DM *dmHybrid)
1719: {
1720:   DM             idm;
1721:   DMLabel        subpointMap, hlabel;
1722:   PetscInt       dim;

1729:   DMGetDimension(dm, &dim);
1730:   DMPlexCreateSubmesh(dm, label, 1, &idm);
1731:   DMPlexOrient(idm);
1732:   DMPlexGetSubpointMap(idm, &subpointMap);
1733:   DMLabelDuplicate(subpointMap, &hlabel);
1734:   DMLabelClearStratum(hlabel, dim);
1735:   DMPlexLabelCohesiveComplete(dm, hlabel, NULL, PETSC_FALSE, idm);
1736:   DMDestroy(&idm);
1737:   DMPlexConstructCohesiveCells(dm, hlabel, dmHybrid);
1738:   if (hybridLabel) *hybridLabel = hlabel;
1739:   else             {DMLabelDestroy(&hlabel);}
1740:   return(0);
1741: }

1745: /* Here we need the explicit assumption that:

1747:      For any marked cell, the marked vertices constitute a single face
1748: */
1749: static PetscErrorCode DMPlexMarkSubmesh_Uninterpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, DM subdm)
1750: {
1751:   IS               subvertexIS = NULL;
1752:   const PetscInt  *subvertices;
1753:   PetscInt        *pStart, *pEnd, *pMax, pSize;
1754:   PetscInt         depth, dim, d, numSubVerticesInitial = 0, v;
1755:   PetscErrorCode   ierr;

1758:   *numFaces = 0;
1759:   *nFV      = 0;
1760:   DMPlexGetDepth(dm, &depth);
1761:   DMGetDimension(dm, &dim);
1762:   pSize = PetscMax(depth, dim) + 1;
1763:   PetscMalloc3(pSize,&pStart,pSize,&pEnd,pSize,&pMax);
1764:   DMPlexGetHybridBounds(dm, depth >= 0 ? &pMax[depth] : NULL, depth>1 ? &pMax[depth-1] : NULL, depth>2 ? &pMax[1] : NULL, &pMax[0]);
1765:   for (d = 0; d <= depth; ++d) {
1766:     DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);
1767:     if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]);
1768:   }
1769:   /* Loop over initial vertices and mark all faces in the collective star() */
1770:   if (vertexLabel) {DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);}
1771:   if (subvertexIS) {
1772:     ISGetSize(subvertexIS, &numSubVerticesInitial);
1773:     ISGetIndices(subvertexIS, &subvertices);
1774:   }
1775:   for (v = 0; v < numSubVerticesInitial; ++v) {
1776:     const PetscInt vertex = subvertices[v];
1777:     PetscInt      *star   = NULL;
1778:     PetscInt       starSize, s, numCells = 0, c;

1780:     DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);
1781:     for (s = 0; s < starSize*2; s += 2) {
1782:       const PetscInt point = star[s];
1783:       if ((point >= pStart[depth]) && (point < pEnd[depth])) star[numCells++] = point;
1784:     }
1785:     for (c = 0; c < numCells; ++c) {
1786:       const PetscInt cell    = star[c];
1787:       PetscInt      *closure = NULL;
1788:       PetscInt       closureSize, cl;
1789:       PetscInt       cellLoc, numCorners = 0, faceSize = 0;

1791:       DMLabelGetValue(subpointMap, cell, &cellLoc);
1792:       if (cellLoc == 2) continue;
1793:       if (cellLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d has dimension %d in the surface label", cell, cellLoc);
1794:       DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);
1795:       for (cl = 0; cl < closureSize*2; cl += 2) {
1796:         const PetscInt point = closure[cl];
1797:         PetscInt       vertexLoc;

1799:         if ((point >= pStart[0]) && (point < pEnd[0])) {
1800:           ++numCorners;
1801:           DMLabelGetValue(vertexLabel, point, &vertexLoc);
1802:           if (vertexLoc == value) closure[faceSize++] = point;
1803:         }
1804:       }
1805:       if (!(*nFV)) {DMPlexGetNumFaceVertices(dm, dim, numCorners, nFV);}
1806:       if (faceSize > *nFV) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize);
1807:       if (faceSize == *nFV) {
1808:         const PetscInt *cells = NULL;
1809:         PetscInt        numCells, nc;

1811:         ++(*numFaces);
1812:         for (cl = 0; cl < faceSize; ++cl) {
1813:           DMLabelSetValue(subpointMap, closure[cl], 0);
1814:         }
1815:         DMPlexGetJoin(dm, faceSize, closure, &numCells, &cells);
1816:         for (nc = 0; nc < numCells; ++nc) {
1817:           DMLabelSetValue(subpointMap, cells[nc], 2);
1818:         }
1819:         DMPlexRestoreJoin(dm, faceSize, closure, &numCells, &cells);
1820:       }
1821:       DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);
1822:     }
1823:     DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);
1824:   }
1825:   if (subvertexIS) {
1826:     ISRestoreIndices(subvertexIS, &subvertices);
1827:   }
1828:   ISDestroy(&subvertexIS);
1829:   PetscFree3(pStart,pEnd,pMax);
1830:   return(0);
1831: }

1835: static PetscErrorCode DMPlexMarkSubmesh_Interpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, DM subdm)
1836: {
1837:   IS               subvertexIS = NULL;
1838:   const PetscInt  *subvertices;
1839:   PetscInt        *pStart, *pEnd, *pMax;
1840:   PetscInt         dim, d, numSubVerticesInitial = 0, v;
1841:   PetscErrorCode   ierr;

1844:   DMGetDimension(dm, &dim);
1845:   PetscMalloc3(dim+1,&pStart,dim+1,&pEnd,dim+1,&pMax);
1846:   DMPlexGetHybridBounds(dm, &pMax[dim], dim>1 ? &pMax[dim-1] : NULL, dim > 2 ? &pMax[1] : NULL, &pMax[0]);
1847:   for (d = 0; d <= dim; ++d) {
1848:     DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);
1849:     if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]);
1850:   }
1851:   /* Loop over initial vertices and mark all faces in the collective star() */
1852:   if (vertexLabel) {
1853:     DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);
1854:     if (subvertexIS) {
1855:       ISGetSize(subvertexIS, &numSubVerticesInitial);
1856:       ISGetIndices(subvertexIS, &subvertices);
1857:     }
1858:   }
1859:   for (v = 0; v < numSubVerticesInitial; ++v) {
1860:     const PetscInt vertex = subvertices[v];
1861:     PetscInt      *star   = NULL;
1862:     PetscInt       starSize, s, numFaces = 0, f;

1864:     DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);
1865:     for (s = 0; s < starSize*2; s += 2) {
1866:       const PetscInt point = star[s];
1867:       if ((point >= pStart[dim-1]) && (point < pEnd[dim-1])) star[numFaces++] = point;
1868:     }
1869:     for (f = 0; f < numFaces; ++f) {
1870:       const PetscInt face    = star[f];
1871:       PetscInt      *closure = NULL;
1872:       PetscInt       closureSize, c;
1873:       PetscInt       faceLoc;

1875:       DMLabelGetValue(subpointMap, face, &faceLoc);
1876:       if (faceLoc == dim-1) continue;
1877:       if (faceLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Face %d has dimension %d in the surface label", face, faceLoc);
1878:       DMPlexGetTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);
1879:       for (c = 0; c < closureSize*2; c += 2) {
1880:         const PetscInt point = closure[c];
1881:         PetscInt       vertexLoc;

1883:         if ((point >= pStart[0]) && (point < pEnd[0])) {
1884:           DMLabelGetValue(vertexLabel, point, &vertexLoc);
1885:           if (vertexLoc != value) break;
1886:         }
1887:       }
1888:       if (c == closureSize*2) {
1889:         const PetscInt *support;
1890:         PetscInt        supportSize, s;

1892:         for (c = 0; c < closureSize*2; c += 2) {
1893:           const PetscInt point = closure[c];

1895:           for (d = 0; d < dim; ++d) {
1896:             if ((point >= pStart[d]) && (point < pEnd[d])) {
1897:               DMLabelSetValue(subpointMap, point, d);
1898:               break;
1899:             }
1900:           }
1901:         }
1902:         DMPlexGetSupportSize(dm, face, &supportSize);
1903:         DMPlexGetSupport(dm, face, &support);
1904:         for (s = 0; s < supportSize; ++s) {
1905:           DMLabelSetValue(subpointMap, support[s], dim);
1906:         }
1907:       }
1908:       DMPlexRestoreTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);
1909:     }
1910:     DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);
1911:   }
1912:   if (subvertexIS) {ISRestoreIndices(subvertexIS, &subvertices);}
1913:   ISDestroy(&subvertexIS);
1914:   PetscFree3(pStart,pEnd,pMax);
1915:   return(0);
1916: }

1920: static PetscErrorCode DMPlexMarkCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, const char labelname[], PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, PetscInt *subCells[], DM subdm)
1921: {
1922:   DMLabel         label = NULL;
1923:   const PetscInt *cone;
1924:   PetscInt        dim, cMax, cEnd, c, subc = 0, p, coneSize;
1925:   PetscErrorCode  ierr;

1928:   *numFaces = 0;
1929:   *nFV = 0;
1930:   if (labelname) {DMPlexGetLabel(dm, labelname, &label);}
1931:   *subCells = NULL;
1932:   DMGetDimension(dm, &dim);
1933:   DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);
1934:   DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);
1935:   if (cMax < 0) return(0);
1936:   if (label) {
1937:     for (c = cMax; c < cEnd; ++c) {
1938:       PetscInt val;

1940:       DMLabelGetValue(label, c, &val);
1941:       if (val == value) {
1942:         ++(*numFaces);
1943:         DMPlexGetConeSize(dm, c, &coneSize);
1944:       }
1945:     }
1946:   } else {
1947:     *numFaces = cEnd - cMax;
1948:     DMPlexGetConeSize(dm, cMax, &coneSize);
1949:   }
1950:   *nFV = hasLagrange ? coneSize/3 : coneSize/2;
1951:   PetscMalloc1(*numFaces *2, subCells);
1952:   for (c = cMax; c < cEnd; ++c) {
1953:     const PetscInt *cells;
1954:     PetscInt        numCells;

1956:     if (label) {
1957:       PetscInt val;

1959:       DMLabelGetValue(label, c, &val);
1960:       if (val != value) continue;
1961:     }
1962:     DMPlexGetCone(dm, c, &cone);
1963:     for (p = 0; p < *nFV; ++p) {
1964:       DMLabelSetValue(subpointMap, cone[p], 0);
1965:     }
1966:     /* Negative face */
1967:     DMPlexGetJoin(dm, *nFV, cone, &numCells, &cells);
1968:     /* Not true in parallel
1969:     if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); */
1970:     for (p = 0; p < numCells; ++p) {
1971:       DMLabelSetValue(subpointMap, cells[p], 2);
1972:       (*subCells)[subc++] = cells[p];
1973:     }
1974:     DMPlexRestoreJoin(dm, *nFV, cone, &numCells, &cells);
1975:     /* Positive face is not included */
1976:   }
1977:   return(0);
1978: }

1982: static PetscErrorCode DMPlexMarkCohesiveSubmesh_Interpolated(DM dm, DMLabel label, PetscInt value, DMLabel subpointMap, DM subdm)
1983: {
1984:   PetscInt      *pStart, *pEnd;
1985:   PetscInt       dim, cMax, cEnd, c, d;

1989:   DMGetDimension(dm, &dim);
1990:   DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);
1991:   DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);
1992:   if (cMax < 0) return(0);
1993:   PetscMalloc2(dim+1,&pStart,dim+1,&pEnd);
1994:   for (d = 0; d <= dim; ++d) {DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);}
1995:   for (c = cMax; c < cEnd; ++c) {
1996:     const PetscInt *cone;
1997:     PetscInt       *closure = NULL;
1998:     PetscInt        fconeSize, coneSize, closureSize, cl, val;

2000:     if (label) {
2001:       DMLabelGetValue(label, c, &val);
2002:       if (val != value) continue;
2003:     }
2004:     DMPlexGetConeSize(dm, c, &coneSize);
2005:     DMPlexGetCone(dm, c, &cone);
2006:     DMPlexGetConeSize(dm, cone[0], &fconeSize);
2007:     if (coneSize != (fconeSize ? fconeSize : 1) + 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells");
2008:     /* Negative face */
2009:     DMPlexGetTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);
2010:     for (cl = 0; cl < closureSize*2; cl += 2) {
2011:       const PetscInt point = closure[cl];

2013:       for (d = 0; d <= dim; ++d) {
2014:         if ((point >= pStart[d]) && (point < pEnd[d])) {
2015:           DMLabelSetValue(subpointMap, point, d);
2016:           break;
2017:         }
2018:       }
2019:     }
2020:     DMPlexRestoreTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);
2021:     /* Cells -- positive face is not included */
2022:     for (cl = 0; cl < 1; ++cl) {
2023:       const PetscInt *support;
2024:       PetscInt        supportSize, s;

2026:       DMPlexGetSupportSize(dm, cone[cl], &supportSize);
2027:       /* if (supportSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive faces should separate two cells"); */
2028:       DMPlexGetSupport(dm, cone[cl], &support);
2029:       for (s = 0; s < supportSize; ++s) {
2030:         DMLabelSetValue(subpointMap, support[s], dim);
2031:       }
2032:     }
2033:   }
2034:   PetscFree2(pStart, pEnd);
2035:   return(0);
2036: }

2040: PetscErrorCode DMPlexGetFaceOrientation(DM dm, PetscInt cell, PetscInt numCorners, PetscInt indices[], PetscInt oppositeVertex, PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented)
2041: {
2042:   MPI_Comm       comm;
2043:   PetscBool      posOrient = PETSC_FALSE;
2044:   const PetscInt debug     = 0;
2045:   PetscInt       cellDim, faceSize, f;

2049:   PetscObjectGetComm((PetscObject)dm,&comm);
2050:   DMGetDimension(dm, &cellDim);
2051:   if (debug) {PetscPrintf(comm, "cellDim: %d numCorners: %d\n", cellDim, numCorners);}

2053:   if (cellDim == 1 && numCorners == 2) {
2054:     /* Triangle */
2055:     faceSize  = numCorners-1;
2056:     posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE;
2057:   } else if (cellDim == 2 && numCorners == 3) {
2058:     /* Triangle */
2059:     faceSize  = numCorners-1;
2060:     posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE;
2061:   } else if (cellDim == 3 && numCorners == 4) {
2062:     /* Tetrahedron */
2063:     faceSize  = numCorners-1;
2064:     posOrient = (oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE;
2065:   } else if (cellDim == 1 && numCorners == 3) {
2066:     /* Quadratic line */
2067:     faceSize  = 1;
2068:     posOrient = PETSC_TRUE;
2069:   } else if (cellDim == 2 && numCorners == 4) {
2070:     /* Quads */
2071:     faceSize = 2;
2072:     if ((indices[1] > indices[0]) && (indices[1] - indices[0] == 1)) {
2073:       posOrient = PETSC_TRUE;
2074:     } else if ((indices[0] == 3) && (indices[1] == 0)) {
2075:       posOrient = PETSC_TRUE;
2076:     } else {
2077:       if (((indices[0] > indices[1]) && (indices[0] - indices[1] == 1)) || ((indices[0] == 0) && (indices[1] == 3))) {
2078:         posOrient = PETSC_FALSE;
2079:       } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossedge");
2080:     }
2081:   } else if (cellDim == 2 && numCorners == 6) {
2082:     /* Quadratic triangle (I hate this) */
2083:     /* Edges are determined by the first 2 vertices (corners of edges) */
2084:     const PetscInt faceSizeTri = 3;
2085:     PetscInt       sortedIndices[3], i, iFace;
2086:     PetscBool      found                    = PETSC_FALSE;
2087:     PetscInt       faceVerticesTriSorted[9] = {
2088:       0, 3,  4, /* bottom */
2089:       1, 4,  5, /* right */
2090:       2, 3,  5, /* left */
2091:     };
2092:     PetscInt       faceVerticesTri[9] = {
2093:       0, 3,  4, /* bottom */
2094:       1, 4,  5, /* right */
2095:       2, 5,  3, /* left */
2096:     };

2098:     faceSize = faceSizeTri;
2099:     for (i = 0; i < faceSizeTri; ++i) sortedIndices[i] = indices[i];
2100:     PetscSortInt(faceSizeTri, sortedIndices);
2101:     for (iFace = 0; iFace < 3; ++iFace) {
2102:       const PetscInt ii = iFace*faceSizeTri;
2103:       PetscInt       fVertex, cVertex;

2105:       if ((sortedIndices[0] == faceVerticesTriSorted[ii+0]) &&
2106:           (sortedIndices[1] == faceVerticesTriSorted[ii+1])) {
2107:         for (fVertex = 0; fVertex < faceSizeTri; ++fVertex) {
2108:           for (cVertex = 0; cVertex < faceSizeTri; ++cVertex) {
2109:             if (indices[cVertex] == faceVerticesTri[ii+fVertex]) {
2110:               faceVertices[fVertex] = origVertices[cVertex];
2111:               break;
2112:             }
2113:           }
2114:         }
2115:         found = PETSC_TRUE;
2116:         break;
2117:       }
2118:     }
2119:     if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tri crossface");
2120:     if (posOriented) *posOriented = PETSC_TRUE;
2121:     return(0);
2122:   } else if (cellDim == 2 && numCorners == 9) {
2123:     /* Quadratic quad (I hate this) */
2124:     /* Edges are determined by the first 2 vertices (corners of edges) */
2125:     const PetscInt faceSizeQuad = 3;
2126:     PetscInt       sortedIndices[3], i, iFace;
2127:     PetscBool      found                      = PETSC_FALSE;
2128:     PetscInt       faceVerticesQuadSorted[12] = {
2129:       0, 1,  4, /* bottom */
2130:       1, 2,  5, /* right */
2131:       2, 3,  6, /* top */
2132:       0, 3,  7, /* left */
2133:     };
2134:     PetscInt       faceVerticesQuad[12] = {
2135:       0, 1,  4, /* bottom */
2136:       1, 2,  5, /* right */
2137:       2, 3,  6, /* top */
2138:       3, 0,  7, /* left */
2139:     };

2141:     faceSize = faceSizeQuad;
2142:     for (i = 0; i < faceSizeQuad; ++i) sortedIndices[i] = indices[i];
2143:     PetscSortInt(faceSizeQuad, sortedIndices);
2144:     for (iFace = 0; iFace < 4; ++iFace) {
2145:       const PetscInt ii = iFace*faceSizeQuad;
2146:       PetscInt       fVertex, cVertex;

2148:       if ((sortedIndices[0] == faceVerticesQuadSorted[ii+0]) &&
2149:           (sortedIndices[1] == faceVerticesQuadSorted[ii+1])) {
2150:         for (fVertex = 0; fVertex < faceSizeQuad; ++fVertex) {
2151:           for (cVertex = 0; cVertex < faceSizeQuad; ++cVertex) {
2152:             if (indices[cVertex] == faceVerticesQuad[ii+fVertex]) {
2153:               faceVertices[fVertex] = origVertices[cVertex];
2154:               break;
2155:             }
2156:           }
2157:         }
2158:         found = PETSC_TRUE;
2159:         break;
2160:       }
2161:     }
2162:     if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossface");
2163:     if (posOriented) *posOriented = PETSC_TRUE;
2164:     return(0);
2165:   } else if (cellDim == 3 && numCorners == 8) {
2166:     /* Hexes
2167:        A hex is two oriented quads with the normal of the first
2168:        pointing up at the second.

2170:           7---6
2171:          /|  /|
2172:         4---5 |
2173:         | 1-|-2
2174:         |/  |/
2175:         0---3

2177:         Faces are determined by the first 4 vertices (corners of faces) */
2178:     const PetscInt faceSizeHex = 4;
2179:     PetscInt       sortedIndices[4], i, iFace;
2180:     PetscBool      found                     = PETSC_FALSE;
2181:     PetscInt       faceVerticesHexSorted[24] = {
2182:       0, 1, 2, 3,  /* bottom */
2183:       4, 5, 6, 7,  /* top */
2184:       0, 3, 4, 5,  /* front */
2185:       2, 3, 5, 6,  /* right */
2186:       1, 2, 6, 7,  /* back */
2187:       0, 1, 4, 7,  /* left */
2188:     };
2189:     PetscInt       faceVerticesHex[24] = {
2190:       1, 2, 3, 0,  /* bottom */
2191:       4, 5, 6, 7,  /* top */
2192:       0, 3, 5, 4,  /* front */
2193:       3, 2, 6, 5,  /* right */
2194:       2, 1, 7, 6,  /* back */
2195:       1, 0, 4, 7,  /* left */
2196:     };

2198:     faceSize = faceSizeHex;
2199:     for (i = 0; i < faceSizeHex; ++i) sortedIndices[i] = indices[i];
2200:     PetscSortInt(faceSizeHex, sortedIndices);
2201:     for (iFace = 0; iFace < 6; ++iFace) {
2202:       const PetscInt ii = iFace*faceSizeHex;
2203:       PetscInt       fVertex, cVertex;

2205:       if ((sortedIndices[0] == faceVerticesHexSorted[ii+0]) &&
2206:           (sortedIndices[1] == faceVerticesHexSorted[ii+1]) &&
2207:           (sortedIndices[2] == faceVerticesHexSorted[ii+2]) &&
2208:           (sortedIndices[3] == faceVerticesHexSorted[ii+3])) {
2209:         for (fVertex = 0; fVertex < faceSizeHex; ++fVertex) {
2210:           for (cVertex = 0; cVertex < faceSizeHex; ++cVertex) {
2211:             if (indices[cVertex] == faceVerticesHex[ii+fVertex]) {
2212:               faceVertices[fVertex] = origVertices[cVertex];
2213:               break;
2214:             }
2215:           }
2216:         }
2217:         found = PETSC_TRUE;
2218:         break;
2219:       }
2220:     }
2221:     if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface");
2222:     if (posOriented) *posOriented = PETSC_TRUE;
2223:     return(0);
2224:   } else if (cellDim == 3 && numCorners == 10) {
2225:     /* Quadratic tet */
2226:     /* Faces are determined by the first 3 vertices (corners of faces) */
2227:     const PetscInt faceSizeTet = 6;
2228:     PetscInt       sortedIndices[6], i, iFace;
2229:     PetscBool      found                     = PETSC_FALSE;
2230:     PetscInt       faceVerticesTetSorted[24] = {
2231:       0, 1, 2,  6, 7, 8, /* bottom */
2232:       0, 3, 4,  6, 7, 9,  /* front */
2233:       1, 4, 5,  7, 8, 9,  /* right */
2234:       2, 3, 5,  6, 8, 9,  /* left */
2235:     };
2236:     PetscInt       faceVerticesTet[24] = {
2237:       0, 1, 2,  6, 7, 8, /* bottom */
2238:       0, 4, 3,  6, 7, 9,  /* front */
2239:       1, 5, 4,  7, 8, 9,  /* right */
2240:       2, 3, 5,  8, 6, 9,  /* left */
2241:     };

2243:     faceSize = faceSizeTet;
2244:     for (i = 0; i < faceSizeTet; ++i) sortedIndices[i] = indices[i];
2245:     PetscSortInt(faceSizeTet, sortedIndices);
2246:     for (iFace=0; iFace < 4; ++iFace) {
2247:       const PetscInt ii = iFace*faceSizeTet;
2248:       PetscInt       fVertex, cVertex;

2250:       if ((sortedIndices[0] == faceVerticesTetSorted[ii+0]) &&
2251:           (sortedIndices[1] == faceVerticesTetSorted[ii+1]) &&
2252:           (sortedIndices[2] == faceVerticesTetSorted[ii+2]) &&
2253:           (sortedIndices[3] == faceVerticesTetSorted[ii+3])) {
2254:         for (fVertex = 0; fVertex < faceSizeTet; ++fVertex) {
2255:           for (cVertex = 0; cVertex < faceSizeTet; ++cVertex) {
2256:             if (indices[cVertex] == faceVerticesTet[ii+fVertex]) {
2257:               faceVertices[fVertex] = origVertices[cVertex];
2258:               break;
2259:             }
2260:           }
2261:         }
2262:         found = PETSC_TRUE;
2263:         break;
2264:       }
2265:     }
2266:     if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tet crossface");
2267:     if (posOriented) *posOriented = PETSC_TRUE;
2268:     return(0);
2269:   } else if (cellDim == 3 && numCorners == 27) {
2270:     /* Quadratic hexes (I hate this)
2271:        A hex is two oriented quads with the normal of the first
2272:        pointing up at the second.

2274:          7---6
2275:         /|  /|
2276:        4---5 |
2277:        | 3-|-2
2278:        |/  |/
2279:        0---1

2281:        Faces are determined by the first 4 vertices (corners of faces) */
2282:     const PetscInt faceSizeQuadHex = 9;
2283:     PetscInt       sortedIndices[9], i, iFace;
2284:     PetscBool      found                         = PETSC_FALSE;
2285:     PetscInt       faceVerticesQuadHexSorted[54] = {
2286:       0, 1, 2, 3,  8, 9, 10, 11,  24, /* bottom */
2287:       4, 5, 6, 7,  12, 13, 14, 15,  25, /* top */
2288:       0, 1, 4, 5,  8, 12, 16, 17,  22, /* front */
2289:       1, 2, 5, 6,  9, 13, 17, 18,  21, /* right */
2290:       2, 3, 6, 7,  10, 14, 18, 19,  23, /* back */
2291:       0, 3, 4, 7,  11, 15, 16, 19,  20, /* left */
2292:     };
2293:     PetscInt       faceVerticesQuadHex[54] = {
2294:       3, 2, 1, 0,  10, 9, 8, 11,  24, /* bottom */
2295:       4, 5, 6, 7,  12, 13, 14, 15,  25, /* top */
2296:       0, 1, 5, 4,  8, 17, 12, 16,  22, /* front */
2297:       1, 2, 6, 5,  9, 18, 13, 17,  21, /* right */
2298:       2, 3, 7, 6,  10, 19, 14, 18,  23, /* back */
2299:       3, 0, 4, 7,  11, 16, 15, 19,  20 /* left */
2300:     };

2302:     faceSize = faceSizeQuadHex;
2303:     for (i = 0; i < faceSizeQuadHex; ++i) sortedIndices[i] = indices[i];
2304:     PetscSortInt(faceSizeQuadHex, sortedIndices);
2305:     for (iFace = 0; iFace < 6; ++iFace) {
2306:       const PetscInt ii = iFace*faceSizeQuadHex;
2307:       PetscInt       fVertex, cVertex;

2309:       if ((sortedIndices[0] == faceVerticesQuadHexSorted[ii+0]) &&
2310:           (sortedIndices[1] == faceVerticesQuadHexSorted[ii+1]) &&
2311:           (sortedIndices[2] == faceVerticesQuadHexSorted[ii+2]) &&
2312:           (sortedIndices[3] == faceVerticesQuadHexSorted[ii+3])) {
2313:         for (fVertex = 0; fVertex < faceSizeQuadHex; ++fVertex) {
2314:           for (cVertex = 0; cVertex < faceSizeQuadHex; ++cVertex) {
2315:             if (indices[cVertex] == faceVerticesQuadHex[ii+fVertex]) {
2316:               faceVertices[fVertex] = origVertices[cVertex];
2317:               break;
2318:             }
2319:           }
2320:         }
2321:         found = PETSC_TRUE;
2322:         break;
2323:       }
2324:     }
2325:     if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface");
2326:     if (posOriented) *posOriented = PETSC_TRUE;
2327:     return(0);
2328:   } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Unknown cell type for faceOrientation().");
2329:   if (!posOrient) {
2330:     if (debug) {PetscPrintf(comm, "  Reversing initial face orientation\n");}
2331:     for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[faceSize-1 - f];
2332:   } else {
2333:     if (debug) {PetscPrintf(comm, "  Keeping initial face orientation\n");}
2334:     for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[f];
2335:   }
2336:   if (posOriented) *posOriented = posOrient;
2337:   return(0);
2338: }

2342: /*
2343:     Given a cell and a face, as a set of vertices,
2344:       return the oriented face, as a set of vertices, in faceVertices
2345:     The orientation is such that the face normal points out of the cell
2346: */
2347: PetscErrorCode DMPlexGetOrientedFace(DM dm, PetscInt cell, PetscInt faceSize, const PetscInt face[], PetscInt numCorners, PetscInt indices[], PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented)
2348: {
2349:   const PetscInt *cone = NULL;
2350:   PetscInt        coneSize, v, f, v2;
2351:   PetscInt        oppositeVertex = -1;
2352:   PetscErrorCode  ierr;

2355:   DMPlexGetConeSize(dm, cell, &coneSize);
2356:   DMPlexGetCone(dm, cell, &cone);
2357:   for (v = 0, v2 = 0; v < coneSize; ++v) {
2358:     PetscBool found = PETSC_FALSE;

2360:     for (f = 0; f < faceSize; ++f) {
2361:       if (face[f] == cone[v]) {
2362:         found = PETSC_TRUE; break;
2363:       }
2364:     }
2365:     if (found) {
2366:       indices[v2]      = v;
2367:       origVertices[v2] = cone[v];
2368:       ++v2;
2369:     } else {
2370:       oppositeVertex = v;
2371:     }
2372:   }
2373:   DMPlexGetFaceOrientation(dm, cell, numCorners, indices, oppositeVertex, origVertices, faceVertices, posOriented);
2374:   return(0);
2375: }

2379: /*
2380:   DMPlexInsertFace_Internal - Puts a face into the mesh

2382:   Not collective

2384:   Input Parameters:
2385:   + dm              - The DMPlex
2386:   . numFaceVertex   - The number of vertices in the face
2387:   . faceVertices    - The vertices in the face for dm
2388:   . subfaceVertices - The vertices in the face for subdm
2389:   . numCorners      - The number of vertices in the cell
2390:   . cell            - A cell in dm containing the face
2391:   . subcell         - A cell in subdm containing the face
2392:   . firstFace       - First face in the mesh
2393:   - newFacePoint    - Next face in the mesh

2395:   Output Parameters:
2396:   . newFacePoint - Contains next face point number on input, updated on output

2398:   Level: developer
2399: */
2400: static PetscErrorCode DMPlexInsertFace_Internal(DM dm, DM subdm, PetscInt numFaceVertices, const PetscInt faceVertices[], const PetscInt subfaceVertices[], PetscInt numCorners, PetscInt cell, PetscInt subcell, PetscInt firstFace, PetscInt *newFacePoint)
2401: {
2402:   MPI_Comm        comm;
2403:   DM_Plex        *submesh = (DM_Plex*) subdm->data;
2404:   const PetscInt *faces;
2405:   PetscInt        numFaces, coneSize;
2406:   PetscErrorCode  ierr;

2409:   PetscObjectGetComm((PetscObject)dm,&comm);
2410:   DMPlexGetConeSize(subdm, subcell, &coneSize);
2411:   if (coneSize != 1) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone size of cell %d is %d != 1", cell, coneSize);
2412: #if 0
2413:   /* Cannot use this because support() has not been constructed yet */
2414:   DMPlexGetJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);
2415: #else
2416:   {
2417:     PetscInt f;

2419:     numFaces = 0;
2420:     DMGetWorkArray(subdm, 1, PETSC_INT, (void **) &faces);
2421:     for (f = firstFace; f < *newFacePoint; ++f) {
2422:       PetscInt dof, off, d;

2424:       PetscSectionGetDof(submesh->coneSection, f, &dof);
2425:       PetscSectionGetOffset(submesh->coneSection, f, &off);
2426:       /* Yes, I know this is quadratic, but I expect the sizes to be <5 */
2427:       for (d = 0; d < dof; ++d) {
2428:         const PetscInt p = submesh->cones[off+d];
2429:         PetscInt       v;

2431:         for (v = 0; v < numFaceVertices; ++v) {
2432:           if (subfaceVertices[v] == p) break;
2433:         }
2434:         if (v == numFaceVertices) break;
2435:       }
2436:       if (d == dof) {
2437:         numFaces               = 1;
2438:         ((PetscInt*) faces)[0] = f;
2439:       }
2440:     }
2441:   }
2442: #endif
2443:   if (numFaces > 1) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex set had %d faces, not one", numFaces);
2444:   else if (numFaces == 1) {
2445:     /* Add the other cell neighbor for this face */
2446:     DMPlexSetCone(subdm, subcell, faces);
2447:   } else {
2448:     PetscInt *indices, *origVertices, *orientedVertices, *orientedSubVertices, v, ov;
2449:     PetscBool posOriented;

2451:     DMGetWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);
2452:     origVertices        = &orientedVertices[numFaceVertices];
2453:     indices             = &orientedVertices[numFaceVertices*2];
2454:     orientedSubVertices = &orientedVertices[numFaceVertices*3];
2455:     DMPlexGetOrientedFace(dm, cell, numFaceVertices, faceVertices, numCorners, indices, origVertices, orientedVertices, &posOriented);
2456:     /* TODO: I know that routine should return a permutation, not the indices */
2457:     for (v = 0; v < numFaceVertices; ++v) {
2458:       const PetscInt vertex = faceVertices[v], subvertex = subfaceVertices[v];
2459:       for (ov = 0; ov < numFaceVertices; ++ov) {
2460:         if (orientedVertices[ov] == vertex) {
2461:           orientedSubVertices[ov] = subvertex;
2462:           break;
2463:         }
2464:       }
2465:       if (ov == numFaceVertices) SETERRQ1(comm, PETSC_ERR_PLIB, "Could not find face vertex %d in orientated set", vertex);
2466:     }
2467:     DMPlexSetCone(subdm, *newFacePoint, orientedSubVertices);
2468:     DMPlexSetCone(subdm, subcell, newFacePoint);
2469:     DMRestoreWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);
2470:     ++(*newFacePoint);
2471:   }
2472: #if 0
2473:   DMPlexRestoreJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);
2474: #else
2475:   DMRestoreWorkArray(subdm, 1, PETSC_INT, (void **) &faces);
2476: #endif
2477:   return(0);
2478: }

2482: static PetscErrorCode DMPlexCreateSubmesh_Uninterpolated(DM dm, DMLabel vertexLabel, PetscInt value, DM subdm)
2483: {
2484:   MPI_Comm        comm;
2485:   DMLabel         subpointMap;
2486:   IS              subvertexIS,  subcellIS;
2487:   const PetscInt *subVertices, *subCells;
2488:   PetscInt        numSubVertices, firstSubVertex, numSubCells;
2489:   PetscInt       *subface, maxConeSize, numSubFaces = 0, firstSubFace, newFacePoint, nFV = 0;
2490:   PetscInt        vStart, vEnd, c, f;
2491:   PetscErrorCode  ierr;

2494:   PetscObjectGetComm((PetscObject)dm,&comm);
2495:   /* Create subpointMap which marks the submesh */
2496:   DMLabelCreate("subpoint_map", &subpointMap);
2497:   DMPlexSetSubpointMap(subdm, subpointMap);
2498:   DMLabelDestroy(&subpointMap);
2499:   if (vertexLabel) {DMPlexMarkSubmesh_Uninterpolated(dm, vertexLabel, value, subpointMap, &numSubFaces, &nFV, subdm);}
2500:   /* Setup chart */
2501:   DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);
2502:   DMLabelGetStratumSize(subpointMap, 2, &numSubCells);
2503:   DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);
2504:   DMPlexSetVTKCellHeight(subdm, 1);
2505:   /* Set cone sizes */
2506:   firstSubVertex = numSubCells;
2507:   firstSubFace   = numSubCells+numSubVertices;
2508:   newFacePoint   = firstSubFace;
2509:   DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);
2510:   if (subvertexIS) {ISGetIndices(subvertexIS, &subVertices);}
2511:   DMLabelGetStratumIS(subpointMap, 2, &subcellIS);
2512:   if (subcellIS) {ISGetIndices(subcellIS, &subCells);}
2513:   for (c = 0; c < numSubCells; ++c) {
2514:     DMPlexSetConeSize(subdm, c, 1);
2515:   }
2516:   for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) {
2517:     DMPlexSetConeSize(subdm, f, nFV);
2518:   }
2519:   DMSetUp(subdm);
2520:   /* Create face cones */
2521:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
2522:   DMPlexGetMaxSizes(dm, &maxConeSize, NULL);
2523:   DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);
2524:   for (c = 0; c < numSubCells; ++c) {
2525:     const PetscInt cell    = subCells[c];
2526:     const PetscInt subcell = c;
2527:     PetscInt      *closure = NULL;
2528:     PetscInt       closureSize, cl, numCorners = 0, faceSize = 0;

2530:     DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);
2531:     for (cl = 0; cl < closureSize*2; cl += 2) {
2532:       const PetscInt point = closure[cl];
2533:       PetscInt       subVertex;

2535:       if ((point >= vStart) && (point < vEnd)) {
2536:         ++numCorners;
2537:         PetscFindInt(point, numSubVertices, subVertices, &subVertex);
2538:         if (subVertex >= 0) {
2539:           closure[faceSize] = point;
2540:           subface[faceSize] = firstSubVertex+subVertex;
2541:           ++faceSize;
2542:         }
2543:       }
2544:     }
2545:     if (faceSize > nFV) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize);
2546:     if (faceSize == nFV) {
2547:       DMPlexInsertFace_Internal(dm, subdm, faceSize, closure, subface, numCorners, cell, subcell, firstSubFace, &newFacePoint);
2548:     }
2549:     DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);
2550:   }
2551:   DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);
2552:   DMPlexSymmetrize(subdm);
2553:   DMPlexStratify(subdm);
2554:   /* Build coordinates */
2555:   {
2556:     PetscSection coordSection, subCoordSection;
2557:     Vec          coordinates, subCoordinates;
2558:     PetscScalar *coords, *subCoords;
2559:     PetscInt     numComp, coordSize, v;

2561:     DMGetCoordinateSection(dm, &coordSection);
2562:     DMGetCoordinatesLocal(dm, &coordinates);
2563:     DMGetCoordinateSection(subdm, &subCoordSection);
2564:     PetscSectionSetNumFields(subCoordSection, 1);
2565:     PetscSectionGetFieldComponents(coordSection, 0, &numComp);
2566:     PetscSectionSetFieldComponents(subCoordSection, 0, numComp);
2567:     PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);
2568:     for (v = 0; v < numSubVertices; ++v) {
2569:       const PetscInt vertex    = subVertices[v];
2570:       const PetscInt subvertex = firstSubVertex+v;
2571:       PetscInt       dof;

2573:       PetscSectionGetDof(coordSection, vertex, &dof);
2574:       PetscSectionSetDof(subCoordSection, subvertex, dof);
2575:       PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);
2576:     }
2577:     PetscSectionSetUp(subCoordSection);
2578:     PetscSectionGetStorageSize(subCoordSection, &coordSize);
2579:     VecCreate(comm, &subCoordinates);
2580:     VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);
2581:     VecSetType(subCoordinates,VECSTANDARD);
2582:     if (coordSize) {
2583:       VecGetArray(coordinates,    &coords);
2584:       VecGetArray(subCoordinates, &subCoords);
2585:       for (v = 0; v < numSubVertices; ++v) {
2586:         const PetscInt vertex    = subVertices[v];
2587:         const PetscInt subvertex = firstSubVertex+v;
2588:         PetscInt       dof, off, sdof, soff, d;

2590:         PetscSectionGetDof(coordSection, vertex, &dof);
2591:         PetscSectionGetOffset(coordSection, vertex, &off);
2592:         PetscSectionGetDof(subCoordSection, subvertex, &sdof);
2593:         PetscSectionGetOffset(subCoordSection, subvertex, &soff);
2594:         if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof);
2595:         for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d];
2596:       }
2597:       VecRestoreArray(coordinates,    &coords);
2598:       VecRestoreArray(subCoordinates, &subCoords);
2599:     }
2600:     DMSetCoordinatesLocal(subdm, subCoordinates);
2601:     VecDestroy(&subCoordinates);
2602:   }
2603:   /* Cleanup */
2604:   if (subvertexIS) {ISRestoreIndices(subvertexIS, &subVertices);}
2605:   ISDestroy(&subvertexIS);
2606:   if (subcellIS) {ISRestoreIndices(subcellIS, &subCells);}
2607:   ISDestroy(&subcellIS);
2608:   return(0);
2609: }

2613: PETSC_STATIC_INLINE PetscInt DMPlexFilterPoint_Internal(PetscInt point, PetscInt firstSubPoint, PetscInt numSubPoints, const PetscInt subPoints[])
2614: {
2615:   PetscInt       subPoint;

2618:   PetscFindInt(point, numSubPoints, subPoints, &subPoint); if (ierr < 0) return ierr;
2619:   return subPoint < 0 ? subPoint : firstSubPoint+subPoint;
2620: }

2624: static PetscErrorCode DMPlexCreateSubmeshGeneric_Interpolated(DM dm, DMLabel label, PetscInt value, PetscBool isCohesive, DM subdm)
2625: {
2626:   MPI_Comm         comm;
2627:   DMLabel          subpointMap;
2628:   IS              *subpointIS;
2629:   const PetscInt **subpoints;
2630:   PetscInt        *numSubPoints, *firstSubPoint, *coneNew, *orntNew;
2631:   PetscInt         totSubPoints = 0, maxConeSize, dim, p, d, v;
2632:   PetscErrorCode   ierr;

2635:   PetscObjectGetComm((PetscObject)dm,&comm);
2636:   /* Create subpointMap which marks the submesh */
2637:   DMLabelCreate("subpoint_map", &subpointMap);
2638:   DMPlexSetSubpointMap(subdm, subpointMap);
2639:   DMLabelDestroy(&subpointMap);
2640:   if (isCohesive) {DMPlexMarkCohesiveSubmesh_Interpolated(dm, label, value, subpointMap, subdm);}
2641:   else            {DMPlexMarkSubmesh_Interpolated(dm, label, value, subpointMap, subdm);}
2642:   /* Setup chart */
2643:   DMGetDimension(dm, &dim);
2644:   PetscMalloc4(dim+1,&numSubPoints,dim+1,&firstSubPoint,dim+1,&subpointIS,dim+1,&subpoints);
2645:   for (d = 0; d <= dim; ++d) {
2646:     DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);
2647:     totSubPoints += numSubPoints[d];
2648:   }
2649:   DMPlexSetChart(subdm, 0, totSubPoints);
2650:   DMPlexSetVTKCellHeight(subdm, 1);
2651:   /* Set cone sizes */
2652:   firstSubPoint[dim] = 0;
2653:   firstSubPoint[0]   = firstSubPoint[dim] + numSubPoints[dim];
2654:   if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0]     + numSubPoints[0];}
2655:   if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];}
2656:   for (d = 0; d <= dim; ++d) {
2657:     DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);
2658:     if (subpointIS[d]) {ISGetIndices(subpointIS[d], &subpoints[d]);}
2659:   }
2660:   for (d = 0; d <= dim; ++d) {
2661:     for (p = 0; p < numSubPoints[d]; ++p) {
2662:       const PetscInt  point    = subpoints[d][p];
2663:       const PetscInt  subpoint = firstSubPoint[d] + p;
2664:       const PetscInt *cone;
2665:       PetscInt        coneSize, coneSizeNew, c, val;

2667:       DMPlexGetConeSize(dm, point, &coneSize);
2668:       DMPlexSetConeSize(subdm, subpoint, coneSize);
2669:       if (d == dim) {
2670:         DMPlexGetCone(dm, point, &cone);
2671:         for (c = 0, coneSizeNew = 0; c < coneSize; ++c) {
2672:           DMLabelGetValue(subpointMap, cone[c], &val);
2673:           if (val >= 0) coneSizeNew++;
2674:         }
2675:         DMPlexSetConeSize(subdm, subpoint, coneSizeNew);
2676:       }
2677:     }
2678:   }
2679:   DMSetUp(subdm);
2680:   /* Set cones */
2681:   DMPlexGetMaxSizes(dm, &maxConeSize, NULL);
2682:   PetscMalloc2(maxConeSize,&coneNew,maxConeSize,&orntNew);
2683:   for (d = 0; d <= dim; ++d) {
2684:     for (p = 0; p < numSubPoints[d]; ++p) {
2685:       const PetscInt  point    = subpoints[d][p];
2686:       const PetscInt  subpoint = firstSubPoint[d] + p;
2687:       const PetscInt *cone, *ornt;
2688:       PetscInt        coneSize, subconeSize, coneSizeNew, c, subc;

2690:       DMPlexGetConeSize(dm, point, &coneSize);
2691:       DMPlexGetConeSize(subdm, subpoint, &subconeSize);
2692:       DMPlexGetCone(dm, point, &cone);
2693:       DMPlexGetConeOrientation(dm, point, &ornt);
2694:       for (c = 0, coneSizeNew = 0; c < coneSize; ++c) {
2695:         PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);
2696:         if (subc >= 0) {
2697:           coneNew[coneSizeNew] = firstSubPoint[d-1] + subc;
2698:           orntNew[coneSizeNew] = ornt[c];
2699:           ++coneSizeNew;
2700:         }
2701:       }
2702:       if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize);
2703:       DMPlexSetCone(subdm, subpoint, coneNew);
2704:       DMPlexSetConeOrientation(subdm, subpoint, orntNew);
2705:     }
2706:   }
2707:   PetscFree2(coneNew,orntNew);
2708:   DMPlexSymmetrize(subdm);
2709:   DMPlexStratify(subdm);
2710:   /* Build coordinates */
2711:   {
2712:     PetscSection coordSection, subCoordSection;
2713:     Vec          coordinates, subCoordinates;
2714:     PetscScalar *coords, *subCoords;
2715:     PetscInt     numComp, coordSize;

2717:     DMGetCoordinateSection(dm, &coordSection);
2718:     DMGetCoordinatesLocal(dm, &coordinates);
2719:     DMGetCoordinateSection(subdm, &subCoordSection);
2720:     PetscSectionSetNumFields(subCoordSection, 1);
2721:     PetscSectionGetFieldComponents(coordSection, 0, &numComp);
2722:     PetscSectionSetFieldComponents(subCoordSection, 0, numComp);
2723:     PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);
2724:     for (v = 0; v < numSubPoints[0]; ++v) {
2725:       const PetscInt vertex    = subpoints[0][v];
2726:       const PetscInt subvertex = firstSubPoint[0]+v;
2727:       PetscInt       dof;

2729:       PetscSectionGetDof(coordSection, vertex, &dof);
2730:       PetscSectionSetDof(subCoordSection, subvertex, dof);
2731:       PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);
2732:     }
2733:     PetscSectionSetUp(subCoordSection);
2734:     PetscSectionGetStorageSize(subCoordSection, &coordSize);
2735:     VecCreate(comm, &subCoordinates);
2736:     VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);
2737:     VecSetType(subCoordinates,VECSTANDARD);
2738:     VecGetArray(coordinates,    &coords);
2739:     VecGetArray(subCoordinates, &subCoords);
2740:     for (v = 0; v < numSubPoints[0]; ++v) {
2741:       const PetscInt vertex    = subpoints[0][v];
2742:       const PetscInt subvertex = firstSubPoint[0]+v;
2743:       PetscInt dof, off, sdof, soff, d;

2745:       PetscSectionGetDof(coordSection, vertex, &dof);
2746:       PetscSectionGetOffset(coordSection, vertex, &off);
2747:       PetscSectionGetDof(subCoordSection, subvertex, &sdof);
2748:       PetscSectionGetOffset(subCoordSection, subvertex, &soff);
2749:       if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof);
2750:       for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d];
2751:     }
2752:     VecRestoreArray(coordinates,    &coords);
2753:     VecRestoreArray(subCoordinates, &subCoords);
2754:     DMSetCoordinatesLocal(subdm, subCoordinates);
2755:     VecDestroy(&subCoordinates);
2756:   }
2757:   /* Build SF: We need this complexity because subpoints might not be selected on the owning process */
2758:   {
2759:     PetscSF            sfPoint, sfPointSub;
2760:     IS                 subpIS;
2761:     const PetscSFNode *remotePoints;
2762:     PetscSFNode       *sremotePoints, *newLocalPoints, *newOwners;
2763:     const PetscInt    *localPoints, *subpoints;
2764:     PetscInt          *slocalPoints;
2765:     PetscInt           numRoots, numLeaves, numSubpoints = 0, numSubroots, numSubleaves = 0, l, sl, ll, pStart, pEnd, p;
2766:     PetscMPIInt        rank;

2768:     MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
2769:     DMGetPointSF(dm, &sfPoint);
2770:     DMGetPointSF(subdm, &sfPointSub);
2771:     DMPlexGetChart(dm, &pStart, &pEnd);
2772:     DMPlexGetChart(subdm, NULL, &numSubroots);
2773:     DMPlexCreateSubpointIS(subdm, &subpIS);
2774:     if (subpIS) {
2775:       ISGetIndices(subpIS, &subpoints);
2776:       ISGetLocalSize(subpIS, &numSubpoints);
2777:     }
2778:     PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);
2779:     if (numRoots >= 0) {
2780:       PetscMalloc2(pEnd-pStart,&newLocalPoints,numRoots,&newOwners);
2781:       for (p = 0; p < pEnd-pStart; ++p) {
2782:         newLocalPoints[p].rank  = -2;
2783:         newLocalPoints[p].index = -2;
2784:       }
2785:       /* Set subleaves */
2786:       for (l = 0; l < numLeaves; ++l) {
2787:         const PetscInt point    = localPoints[l];
2788:         const PetscInt subpoint = DMPlexFilterPoint_Internal(point, 0, numSubpoints, subpoints);

2790:         if (subpoint < 0) continue;
2791:         newLocalPoints[point-pStart].rank  = rank;
2792:         newLocalPoints[point-pStart].index = subpoint;
2793:         ++numSubleaves;
2794:       }
2795:       /* Must put in owned subpoints */
2796:       for (p = pStart; p < pEnd; ++p) {
2797:         const PetscInt subpoint = DMPlexFilterPoint_Internal(p, 0, numSubpoints, subpoints);

2799:         if (subpoint < 0) {
2800:           newOwners[p-pStart].rank  = -3;
2801:           newOwners[p-pStart].index = -3;
2802:         } else {
2803:           newOwners[p-pStart].rank  = rank;
2804:           newOwners[p-pStart].index = subpoint;
2805:         }
2806:       }
2807:       PetscSFReduceBegin(sfPoint, MPIU_2INT, newLocalPoints, newOwners, MPI_MAXLOC);
2808:       PetscSFReduceEnd(sfPoint, MPIU_2INT, newLocalPoints, newOwners, MPI_MAXLOC);
2809:       PetscSFBcastBegin(sfPoint, MPIU_2INT, newOwners, newLocalPoints);
2810:       PetscSFBcastEnd(sfPoint, MPIU_2INT, newOwners, newLocalPoints);
2811:       PetscMalloc1(numSubleaves, &slocalPoints);
2812:       PetscMalloc1(numSubleaves, &sremotePoints);
2813:       for (l = 0, sl = 0, ll = 0; l < numLeaves; ++l) {
2814:         const PetscInt point    = localPoints[l];
2815:         const PetscInt subpoint = DMPlexFilterPoint_Internal(point, 0, numSubpoints, subpoints);

2817:         if (subpoint < 0) continue;
2818:         if (newLocalPoints[point].rank == rank) {++ll; continue;}
2819:         slocalPoints[sl]        = subpoint;
2820:         sremotePoints[sl].rank  = newLocalPoints[point].rank;
2821:         sremotePoints[sl].index = newLocalPoints[point].index;
2822:         if (sremotePoints[sl].rank  < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid remote rank for local point %d", point);
2823:         if (sremotePoints[sl].index < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid remote subpoint for local point %d", point);
2824:         ++sl;
2825:       }
2826:       if (sl + ll != numSubleaves) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatch in number of subleaves %d + %d != %d", sl, ll, numSubleaves);
2827:       PetscFree2(newLocalPoints,newOwners);
2828:       PetscSFSetGraph(sfPointSub, numSubroots, sl, slocalPoints, PETSC_OWN_POINTER, sremotePoints, PETSC_OWN_POINTER);
2829:     }
2830:     if (subpIS) {
2831:       ISRestoreIndices(subpIS, &subpoints);
2832:       ISDestroy(&subpIS);
2833:     }
2834:   }
2835:   /* Cleanup */
2836:   for (d = 0; d <= dim; ++d) {
2837:     if (subpointIS[d]) {ISRestoreIndices(subpointIS[d], &subpoints[d]);}
2838:     ISDestroy(&subpointIS[d]);
2839:   }
2840:   PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);
2841:   return(0);
2842: }

2846: static PetscErrorCode DMPlexCreateSubmesh_Interpolated(DM dm, DMLabel vertexLabel, PetscInt value, DM subdm)
2847: {

2851:   DMPlexCreateSubmeshGeneric_Interpolated(dm, vertexLabel, value, PETSC_FALSE, subdm);
2852:   return(0);
2853: }

2857: /*@
2858:   DMPlexCreateSubmesh - Extract a hypersurface from the mesh using vertices defined by a label

2860:   Input Parameters:
2861: + dm           - The original mesh
2862: . vertexLabel  - The DMLabel marking vertices contained in the surface
2863: - value        - The label value to use

2865:   Output Parameter:
2866: . subdm - The surface mesh

2868:   Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap().

2870:   Level: developer

2872: .seealso: DMPlexGetSubpointMap(), DMPlexGetLabel(), DMLabelSetValue()
2873: @*/
2874: PetscErrorCode DMPlexCreateSubmesh(DM dm, DMLabel vertexLabel, PetscInt value, DM *subdm)
2875: {
2876:   PetscInt       dim, depth;

2882:   DMGetDimension(dm, &dim);
2883:   DMPlexGetDepth(dm, &depth);
2884:   DMCreate(PetscObjectComm((PetscObject)dm), subdm);
2885:   DMSetType(*subdm, DMPLEX);
2886:   DMSetDimension(*subdm, dim-1);
2887:   if (depth == dim) {
2888:     DMPlexCreateSubmesh_Interpolated(dm, vertexLabel, value, *subdm);
2889:   } else {
2890:     DMPlexCreateSubmesh_Uninterpolated(dm, vertexLabel, value, *subdm);
2891:   }
2892:   return(0);
2893: }

2897: static PetscErrorCode DMPlexCreateCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM subdm)
2898: {
2899:   MPI_Comm        comm;
2900:   DMLabel         subpointMap;
2901:   IS              subvertexIS;
2902:   const PetscInt *subVertices;
2903:   PetscInt        numSubVertices, firstSubVertex, numSubCells, *subCells = NULL;
2904:   PetscInt       *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV;
2905:   PetscInt        cMax, c, f;
2906:   PetscErrorCode  ierr;

2909:   PetscObjectGetComm((PetscObject)dm, &comm);
2910:   /* Create subpointMap which marks the submesh */
2911:   DMLabelCreate("subpoint_map", &subpointMap);
2912:   DMPlexSetSubpointMap(subdm, subpointMap);
2913:   DMLabelDestroy(&subpointMap);
2914:   DMPlexMarkCohesiveSubmesh_Uninterpolated(dm, hasLagrange, label, value, subpointMap, &numSubFaces, &nFV, &subCells, subdm);
2915:   /* Setup chart */
2916:   DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);
2917:   DMLabelGetStratumSize(subpointMap, 2, &numSubCells);
2918:   DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);
2919:   DMPlexSetVTKCellHeight(subdm, 1);
2920:   /* Set cone sizes */
2921:   firstSubVertex = numSubCells;
2922:   firstSubFace   = numSubCells+numSubVertices;
2923:   newFacePoint   = firstSubFace;
2924:   DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);
2925:   if (subvertexIS) {ISGetIndices(subvertexIS, &subVertices);}
2926:   for (c = 0; c < numSubCells; ++c) {
2927:     DMPlexSetConeSize(subdm, c, 1);
2928:   }
2929:   for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) {
2930:     DMPlexSetConeSize(subdm, f, nFV);
2931:   }
2932:   DMSetUp(subdm);
2933:   /* Create face cones */
2934:   DMPlexGetMaxSizes(dm, &maxConeSize, NULL);
2935:   DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);
2936:   DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);
2937:   for (c = 0; c < numSubCells; ++c) {
2938:     const PetscInt  cell    = subCells[c];
2939:     const PetscInt  subcell = c;
2940:     const PetscInt *cone, *cells;
2941:     PetscInt        numCells, subVertex, p, v;

2943:     if (cell < cMax) continue;
2944:     DMPlexGetCone(dm, cell, &cone);
2945:     for (v = 0; v < nFV; ++v) {
2946:       PetscFindInt(cone[v], numSubVertices, subVertices, &subVertex);
2947:       subface[v] = firstSubVertex+subVertex;
2948:     }
2949:     DMPlexSetCone(subdm, newFacePoint, subface);
2950:     DMPlexSetCone(subdm, subcell, &newFacePoint);
2951:     DMPlexGetJoin(dm, nFV, cone, &numCells, &cells);
2952:     /* Not true in parallel
2953:     if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); */
2954:     for (p = 0; p < numCells; ++p) {
2955:       PetscInt negsubcell;

2957:       if (cells[p] >= cMax) continue;
2958:       /* I know this is a crap search */
2959:       for (negsubcell = 0; negsubcell < numSubCells; ++negsubcell) {
2960:         if (subCells[negsubcell] == cells[p]) break;
2961:       }
2962:       if (negsubcell == numSubCells) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find negative face neighbor for cohesive cell %d", cell);
2963:       DMPlexSetCone(subdm, negsubcell, &newFacePoint);
2964:     }
2965:     DMPlexRestoreJoin(dm, nFV, cone, &numCells, &cells);
2966:     ++newFacePoint;
2967:   }
2968:   DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);
2969:   DMPlexSymmetrize(subdm);
2970:   DMPlexStratify(subdm);
2971:   /* Build coordinates */
2972:   {
2973:     PetscSection coordSection, subCoordSection;
2974:     Vec          coordinates, subCoordinates;
2975:     PetscScalar *coords, *subCoords;
2976:     PetscInt     numComp, coordSize, v;

2978:     DMGetCoordinateSection(dm, &coordSection);
2979:     DMGetCoordinatesLocal(dm, &coordinates);
2980:     DMGetCoordinateSection(subdm, &subCoordSection);
2981:     PetscSectionSetNumFields(subCoordSection, 1);
2982:     PetscSectionGetFieldComponents(coordSection, 0, &numComp);
2983:     PetscSectionSetFieldComponents(subCoordSection, 0, numComp);
2984:     PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);
2985:     for (v = 0; v < numSubVertices; ++v) {
2986:       const PetscInt vertex    = subVertices[v];
2987:       const PetscInt subvertex = firstSubVertex+v;
2988:       PetscInt       dof;

2990:       PetscSectionGetDof(coordSection, vertex, &dof);
2991:       PetscSectionSetDof(subCoordSection, subvertex, dof);
2992:       PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);
2993:     }
2994:     PetscSectionSetUp(subCoordSection);
2995:     PetscSectionGetStorageSize(subCoordSection, &coordSize);
2996:     VecCreate(comm, &subCoordinates);
2997:     VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);
2998:     VecSetType(subCoordinates,VECSTANDARD);
2999:     VecGetArray(coordinates,    &coords);
3000:     VecGetArray(subCoordinates, &subCoords);
3001:     for (v = 0; v < numSubVertices; ++v) {
3002:       const PetscInt vertex    = subVertices[v];
3003:       const PetscInt subvertex = firstSubVertex+v;
3004:       PetscInt       dof, off, sdof, soff, d;

3006:       PetscSectionGetDof(coordSection, vertex, &dof);
3007:       PetscSectionGetOffset(coordSection, vertex, &off);
3008:       PetscSectionGetDof(subCoordSection, subvertex, &sdof);
3009:       PetscSectionGetOffset(subCoordSection, subvertex, &soff);
3010:       if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof);
3011:       for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d];
3012:     }
3013:     VecRestoreArray(coordinates,    &coords);
3014:     VecRestoreArray(subCoordinates, &subCoords);
3015:     DMSetCoordinatesLocal(subdm, subCoordinates);
3016:     VecDestroy(&subCoordinates);
3017:   }
3018:   /* Build SF */
3019:   CHKMEMQ;
3020:   {
3021:     PetscSF            sfPoint, sfPointSub;
3022:     const PetscSFNode *remotePoints;
3023:     PetscSFNode       *sremotePoints, *newLocalPoints, *newOwners;
3024:     const PetscInt    *localPoints;
3025:     PetscInt          *slocalPoints;
3026:     PetscInt           numRoots, numLeaves, numSubRoots = numSubCells+numSubFaces+numSubVertices, numSubLeaves = 0, l, sl, ll, pStart, pEnd, p, vStart, vEnd;
3027:     PetscMPIInt        rank;

3029:     MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
3030:     DMGetPointSF(dm, &sfPoint);
3031:     DMGetPointSF(subdm, &sfPointSub);
3032:     DMPlexGetChart(dm, &pStart, &pEnd);
3033:     DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
3034:     PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);
3035:     if (numRoots >= 0) {
3036:       /* Only vertices should be shared */
3037:       PetscMalloc2(pEnd-pStart,&newLocalPoints,numRoots,&newOwners);
3038:       for (p = 0; p < pEnd-pStart; ++p) {
3039:         newLocalPoints[p].rank  = -2;
3040:         newLocalPoints[p].index = -2;
3041:       }
3042:       /* Set subleaves */
3043:       for (l = 0; l < numLeaves; ++l) {
3044:         const PetscInt point    = localPoints[l];
3045:         const PetscInt subPoint = DMPlexFilterPoint_Internal(point, firstSubVertex, numSubVertices, subVertices);

3047:         if ((point < vStart) && (point >= vEnd)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Should not be mapping anything but vertices, %d", point);
3048:         if (subPoint < 0) continue;
3049:         newLocalPoints[point-pStart].rank  = rank;
3050:         newLocalPoints[point-pStart].index = subPoint;
3051:         ++numSubLeaves;
3052:       }
3053:       /* Must put in owned subpoints */
3054:       for (p = pStart; p < pEnd; ++p) {
3055:         const PetscInt subPoint = DMPlexFilterPoint_Internal(p, firstSubVertex, numSubVertices, subVertices);

3057:         if (subPoint < 0) {
3058:           newOwners[p-pStart].rank  = -3;
3059:           newOwners[p-pStart].index = -3;
3060:         } else {
3061:           newOwners[p-pStart].rank  = rank;
3062:           newOwners[p-pStart].index = subPoint;
3063:         }
3064:       }
3065:       PetscSFReduceBegin(sfPoint, MPIU_2INT, newLocalPoints, newOwners, MPI_MAXLOC);
3066:       PetscSFReduceEnd(sfPoint, MPIU_2INT, newLocalPoints, newOwners, MPI_MAXLOC);
3067:       PetscSFBcastBegin(sfPoint, MPIU_2INT, newOwners, newLocalPoints);
3068:       PetscSFBcastEnd(sfPoint, MPIU_2INT, newOwners, newLocalPoints);
3069:       PetscMalloc1(numSubLeaves,    &slocalPoints);
3070:       PetscMalloc1(numSubLeaves, &sremotePoints);
3071:       for (l = 0, sl = 0, ll = 0; l < numLeaves; ++l) {
3072:         const PetscInt point    = localPoints[l];
3073:         const PetscInt subPoint = DMPlexFilterPoint_Internal(point, firstSubVertex, numSubVertices, subVertices);

3075:         if (subPoint < 0) continue;
3076:         if (newLocalPoints[point].rank == rank) {++ll; continue;}
3077:         slocalPoints[sl]        = subPoint;
3078:         sremotePoints[sl].rank  = newLocalPoints[point].rank;
3079:         sremotePoints[sl].index = newLocalPoints[point].index;
3080:         if (sremotePoints[sl].rank  < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid remote rank for local point %d", point);
3081:         if (sremotePoints[sl].index < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid remote subpoint for local point %d", point);
3082:         ++sl;
3083:       }
3084:       PetscFree2(newLocalPoints,newOwners);
3085:       if (sl + ll != numSubLeaves) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatch in number of subleaves %d + %d != %d", sl, ll, numSubLeaves);
3086:       PetscSFSetGraph(sfPointSub, numSubRoots, sl, slocalPoints, PETSC_OWN_POINTER, sremotePoints, PETSC_OWN_POINTER);
3087:     }
3088:   }
3089:   CHKMEMQ;
3090:   /* Cleanup */
3091:   if (subvertexIS) {ISRestoreIndices(subvertexIS, &subVertices);}
3092:   ISDestroy(&subvertexIS);
3093:   PetscFree(subCells);
3094:   return(0);
3095: }

3099: static PetscErrorCode DMPlexCreateCohesiveSubmesh_Interpolated(DM dm, const char labelname[], PetscInt value, DM subdm)
3100: {
3101:   DMLabel        label = NULL;

3105:   if (labelname) {DMPlexGetLabel(dm, labelname, &label);}
3106:   DMPlexCreateSubmeshGeneric_Interpolated(dm, label, value, PETSC_TRUE, subdm);
3107:   return(0);
3108: }

3112: /*
3113:   DMPlexCreateCohesiveSubmesh - Extract from a mesh with cohesive cells the hypersurface defined by one face of the cells. Optionally, a Label an be given to restrict the cells.

3115:   Input Parameters:
3116: + dm          - The original mesh
3117: . hasLagrange - The mesh has Lagrange unknowns in the cohesive cells
3118: . label       - A label name, or NULL
3119: - value  - A label value

3121:   Output Parameter:
3122: . subdm - The surface mesh

3124:   Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap().

3126:   Level: developer

3128: .seealso: DMPlexGetSubpointMap(), DMPlexCreateSubmesh()
3129: */
3130: PetscErrorCode DMPlexCreateCohesiveSubmesh(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM *subdm)
3131: {
3132:   PetscInt       dim, depth;

3138:   DMGetDimension(dm, &dim);
3139:   DMPlexGetDepth(dm, &depth);
3140:   DMCreate(PetscObjectComm((PetscObject)dm), subdm);
3141:   DMSetType(*subdm, DMPLEX);
3142:   DMSetDimension(*subdm, dim-1);
3143:   if (depth == dim) {
3144:     DMPlexCreateCohesiveSubmesh_Interpolated(dm, label, value, *subdm);
3145:   } else {
3146:     DMPlexCreateCohesiveSubmesh_Uninterpolated(dm, hasLagrange, label, value, *subdm);
3147:   }
3148:   return(0);
3149: }

3153: /*@
3154:   DMPlexGetSubpointMap - Returns a DMLabel with point dimension as values

3156:   Input Parameter:
3157: . dm - The submesh DM

3159:   Output Parameter:
3160: . subpointMap - The DMLabel of all the points from the original mesh in this submesh, or NULL if this is not a submesh

3162:   Level: developer

3164: .seealso: DMPlexCreateSubmesh(), DMPlexCreateSubpointIS()
3165: @*/
3166: PetscErrorCode DMPlexGetSubpointMap(DM dm, DMLabel *subpointMap)
3167: {
3168:   DM_Plex *mesh = (DM_Plex*) dm->data;

3173:   *subpointMap = mesh->subpointMap;
3174:   return(0);
3175: }

3179: /* Note: Should normally not be called by the user, since it is set in DMPlexCreateSubmesh() */
3180: PetscErrorCode DMPlexSetSubpointMap(DM dm, DMLabel subpointMap)
3181: {
3182:   DM_Plex       *mesh = (DM_Plex *) dm->data;
3183:   DMLabel        tmp;

3188:   tmp  = mesh->subpointMap;
3189:   mesh->subpointMap = subpointMap;
3190:   ++mesh->subpointMap->refct;
3191:   DMLabelDestroy(&tmp);
3192:   return(0);
3193: }

3197: /*@
3198:   DMPlexCreateSubpointIS - Creates an IS covering the entire subdm chart with the original points as data

3200:   Input Parameter:
3201: . dm - The submesh DM

3203:   Output Parameter:
3204: . subpointIS - The IS of all the points from the original mesh in this submesh, or NULL if this is not a submesh

3206:   Note: This IS is guaranteed to be sorted by the construction of the submesh

3208:   Level: developer

3210: .seealso: DMPlexCreateSubmesh(), DMPlexGetSubpointMap()
3211: @*/
3212: PetscErrorCode DMPlexCreateSubpointIS(DM dm, IS *subpointIS)
3213: {
3214:   MPI_Comm        comm;
3215:   DMLabel         subpointMap;
3216:   IS              is;
3217:   const PetscInt *opoints;
3218:   PetscInt       *points, *depths;
3219:   PetscInt        depth, depStart, depEnd, d, pStart, pEnd, p, n, off;
3220:   PetscErrorCode  ierr;

3225:   PetscObjectGetComm((PetscObject)dm,&comm);
3226:   *subpointIS = NULL;
3227:   DMPlexGetSubpointMap(dm, &subpointMap);
3228:   DMPlexGetDepth(dm, &depth);
3229:   if (subpointMap && depth >= 0) {
3230:     DMPlexGetChart(dm, &pStart, &pEnd);
3231:     if (pStart) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Submeshes must start the point numbering at 0, not %d", pStart);
3232:     DMGetWorkArray(dm, depth+1, PETSC_INT, &depths);
3233:     depths[0] = depth;
3234:     depths[1] = 0;
3235:     for(d = 2; d <= depth; ++d) {depths[d] = depth+1 - d;}
3236:     PetscMalloc1(pEnd, &points);
3237:     for(d = 0, off = 0; d <= depth; ++d) {
3238:       const PetscInt dep = depths[d];

3240:       DMPlexGetDepthStratum(dm, dep, &depStart, &depEnd);
3241:       DMLabelGetStratumSize(subpointMap, dep, &n);
3242:       if (((d < 2) && (depth > 1)) || (d == 1)) { /* Only check vertices and cells for now since the map is broken for others */
3243:         if (n != depEnd-depStart) SETERRQ3(comm, PETSC_ERR_ARG_WRONG, "The number of mapped submesh points %d at depth %d should be %d", n, dep, depEnd-depStart);
3244:       } else {
3245:         if (!n) {
3246:           if (d == 0) {
3247:             /* Missing cells */
3248:             for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = -1;
3249:           } else {
3250:             /* Missing faces */
3251:             for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = PETSC_MAX_INT;
3252:           }
3253:         }
3254:       }
3255:       if (n) {
3256:         DMLabelGetStratumIS(subpointMap, dep, &is);
3257:         ISGetIndices(is, &opoints);
3258:         for(p = 0; p < n; ++p, ++off) points[off] = opoints[p];
3259:         ISRestoreIndices(is, &opoints);
3260:         ISDestroy(&is);
3261:       }
3262:     }
3263:     DMRestoreWorkArray(dm, depth+1, PETSC_INT, &depths);
3264:     if (off != pEnd) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "The number of mapped submesh points %d should be %d", off, pEnd);
3265:     ISCreateGeneral(PETSC_COMM_SELF, pEnd, points, PETSC_OWN_POINTER, subpointIS);
3266:   }
3267:   return(0);
3268: }