Actual source code: plex.c

petsc-3.12.0 2019-09-29
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  1:  #include <petsc/private/dmpleximpl.h>
  2:  #include <petsc/private/isimpl.h>
  3:  #include <petsc/private/vecimpl.h>
  4:  #include <petsc/private/glvisvecimpl.h>
  5:  #include <petscsf.h>
  6:  #include <petscds.h>
  7:  #include <petscdraw.h>
  8:  #include <petscdmfield.h>

 10: /* Logging support */
 11: PetscLogEvent DMPLEX_Interpolate, DMPLEX_Partition, DMPLEX_Distribute, DMPLEX_DistributeCones, DMPLEX_DistributeLabels, DMPLEX_DistributeSF, DMPLEX_DistributeOverlap, DMPLEX_DistributeField, DMPLEX_DistributeData, DMPLEX_Migrate, DMPLEX_InterpolateSF, DMPLEX_GlobalToNaturalBegin, DMPLEX_GlobalToNaturalEnd, DMPLEX_NaturalToGlobalBegin, DMPLEX_NaturalToGlobalEnd, DMPLEX_Stratify, DMPLEX_Symmetrize, DMPLEX_Preallocate, DMPLEX_ResidualFEM, DMPLEX_JacobianFEM, DMPLEX_InterpolatorFEM, DMPLEX_InjectorFEM, DMPLEX_IntegralFEM, DMPLEX_CreateGmsh, DMPLEX_RebalanceSharedPoints, DMPLEX_PartSelf, DMPLEX_PartLabelInvert, DMPLEX_PartLabelCreateSF, DMPLEX_PartStratSF, DMPLEX_CreatePointSF;

 13: PETSC_EXTERN PetscErrorCode VecView_MPI(Vec, PetscViewer);

 15: /*@
 16:   DMPlexRefineSimplexToTensor - Uniformly refines simplicial cells into tensor product cells.
 17:   3 quadrilaterals per triangle in 2D and 4 hexahedra per tetrahedron in 3D.

 19:   Collective

 21:   Input Parameters:
 22: . dm - The DMPlex object

 24:   Output Parameters:
 25: . dmRefined - The refined DMPlex object

 27:   Note: Returns NULL if the mesh is already a tensor product mesh.

 29:   Level: intermediate

 31: .seealso: DMPlexCreate(), DMPlexSetRefinementUniform()
 32: @*/
 33: PetscErrorCode DMPlexRefineSimplexToTensor(DM dm, DM *dmRefined)
 34: {
 35:   PetscInt         dim, cMax, fMax, cStart, cEnd, coneSize;
 36:   CellRefiner      cellRefiner;
 37:   PetscBool        lop, allnoop, localized;
 38:   PetscErrorCode   ierr;

 43:   DMGetDimension(dm, &dim);
 44:   DMPlexGetHybridBounds(dm,&cMax,&fMax,NULL,NULL);
 45:   DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);
 46:   if (!(cEnd - cStart)) cellRefiner = REFINER_NOOP;
 47:   else {
 48:     DMPlexGetConeSize(dm,cStart,&coneSize);
 49:     switch (dim) {
 50:     case 1:
 51:       cellRefiner = REFINER_NOOP;
 52:     break;
 53:     case 2:
 54:       switch (coneSize) {
 55:       case 3:
 56:         if (cMax >= 0) cellRefiner = REFINER_HYBRID_SIMPLEX_TO_HEX_2D;
 57:         else cellRefiner = REFINER_SIMPLEX_TO_HEX_2D;
 58:       break;
 59:       case 4:
 60:         if (cMax >= 0) cellRefiner = REFINER_HYBRID_SIMPLEX_TO_HEX_2D;
 61:         else cellRefiner = REFINER_NOOP;
 62:       break;
 63:       default: SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot handle coneSize %D with dimension %D",coneSize,dim);
 64:       }
 65:     break;
 66:     case 3:
 67:       switch (coneSize) {
 68:       case 4:
 69:         if (cMax >= 0) cellRefiner = REFINER_HYBRID_SIMPLEX_TO_HEX_3D;
 70:         else cellRefiner = REFINER_SIMPLEX_TO_HEX_3D;
 71:       break;
 72:       case 5:
 73:         if (cMax >= 0) cellRefiner = REFINER_HYBRID_SIMPLEX_TO_HEX_3D;
 74:         else cellRefiner = REFINER_NOOP;
 75:       break;
 76:       case 6:
 77:         if (cMax >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Simplex2Tensor in 3D with Hybrid mesh not yet done");
 78:         cellRefiner = REFINER_NOOP;
 79:       break;
 80:       default: SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot handle coneSize %D with dimension %D",coneSize,dim);
 81:       }
 82:     break;
 83:     default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot handle dimension %D",dim);
 84:     }
 85:   }
 86:   /* return if we don't need to refine */
 87:   lop = (cellRefiner == REFINER_NOOP) ? PETSC_TRUE : PETSC_FALSE;
 88:   MPIU_Allreduce(&lop,&allnoop,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)dm));
 89:   if (allnoop) {
 90:     *dmRefined = NULL;
 91:     return(0);
 92:   }
 93:   DMPlexRefineUniform_Internal(dm, cellRefiner, dmRefined);
 94:   DMCopyBoundary(dm, *dmRefined);
 95:   DMGetCoordinatesLocalized(dm, &localized);
 96:   if (localized) {
 97:     DMLocalizeCoordinates(*dmRefined);
 98:   }
 99:   return(0);
100: }

102: PetscErrorCode DMPlexGetFieldType_Internal(DM dm, PetscSection section, PetscInt field, PetscInt *sStart, PetscInt *sEnd, PetscViewerVTKFieldType *ft)
103: {
104:   PetscInt       dim, pStart, pEnd, vStart, vEnd, cStart, cEnd, cEndInterior;
105:   PetscInt       vcdof[2] = {0,0}, globalvcdof[2];

109:   *ft  = PETSC_VTK_POINT_FIELD;
110:   DMGetDimension(dm, &dim);
111:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
112:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
113:   DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);
114:   cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
115:   PetscSectionGetChart(section, &pStart, &pEnd);
116:   if (field >= 0) {
117:     if ((vStart >= pStart) && (vStart < pEnd)) {PetscSectionGetFieldDof(section, vStart, field, &vcdof[0]);}
118:     if ((cStart >= pStart) && (cStart < pEnd)) {PetscSectionGetFieldDof(section, cStart, field, &vcdof[1]);}
119:   } else {
120:     if ((vStart >= pStart) && (vStart < pEnd)) {PetscSectionGetDof(section, vStart, &vcdof[0]);}
121:     if ((cStart >= pStart) && (cStart < pEnd)) {PetscSectionGetDof(section, cStart, &vcdof[1]);}
122:   }
123:   MPI_Allreduce(vcdof, globalvcdof, 2, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm));
124:   if (globalvcdof[0]) {
125:     *sStart = vStart;
126:     *sEnd   = vEnd;
127:     if (globalvcdof[0] == dim) *ft = PETSC_VTK_POINT_VECTOR_FIELD;
128:     else                       *ft = PETSC_VTK_POINT_FIELD;
129:   } else if (globalvcdof[1]) {
130:     *sStart = cStart;
131:     *sEnd   = cEnd;
132:     if (globalvcdof[1] == dim) *ft = PETSC_VTK_CELL_VECTOR_FIELD;
133:     else                       *ft = PETSC_VTK_CELL_FIELD;
134:   } else SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Could not classify input Vec for VTK");
135:   return(0);
136: }

138: static PetscErrorCode VecView_Plex_Local_Draw(Vec v, PetscViewer viewer)
139: {
140:   DM                 dm;
141:   PetscSection       s;
142:   PetscDraw          draw, popup;
143:   DM                 cdm;
144:   PetscSection       coordSection;
145:   Vec                coordinates;
146:   const PetscScalar *coords, *array;
147:   PetscReal          bound[4] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL};
148:   PetscReal          vbound[2], time;
149:   PetscBool          isnull, flg;
150:   PetscInt           dim, Nf, f, Nc, comp, vStart, vEnd, cStart, cEnd, c, N, level, step, w = 0;
151:   const char        *name;
152:   char               title[PETSC_MAX_PATH_LEN];
153:   PetscErrorCode     ierr;

156:   PetscViewerDrawGetDraw(viewer, 0, &draw);
157:   PetscDrawIsNull(draw, &isnull);
158:   if (isnull) return(0);

160:   VecGetDM(v, &dm);
161:   DMGetCoordinateDim(dm, &dim);
162:   if (dim != 2) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Cannot draw meshes of dimension %D. Use PETSCVIEWERGLVIS", dim);
163:   DMGetLocalSection(dm, &s);
164:   PetscSectionGetNumFields(s, &Nf);
165:   DMGetCoarsenLevel(dm, &level);
166:   DMGetCoordinateDM(dm, &cdm);
167:   DMGetLocalSection(cdm, &coordSection);
168:   DMGetCoordinatesLocal(dm, &coordinates);
169:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
170:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);

172:   PetscObjectGetName((PetscObject) v, &name);
173:   DMGetOutputSequenceNumber(dm, &step, &time);

175:   VecGetLocalSize(coordinates, &N);
176:   VecGetArrayRead(coordinates, &coords);
177:   for (c = 0; c < N; c += dim) {
178:     bound[0] = PetscMin(bound[0], PetscRealPart(coords[c]));   bound[2] = PetscMax(bound[2], PetscRealPart(coords[c]));
179:     bound[1] = PetscMin(bound[1], PetscRealPart(coords[c+1])); bound[3] = PetscMax(bound[3], PetscRealPart(coords[c+1]));
180:   }
181:   VecRestoreArrayRead(coordinates, &coords);
182:   PetscDrawClear(draw);

184:   /* Could implement something like DMDASelectFields() */
185:   for (f = 0; f < Nf; ++f) {
186:     DM   fdm = dm;
187:     Vec  fv  = v;
188:     IS   fis;
189:     char prefix[PETSC_MAX_PATH_LEN];
190:     const char *fname;

192:     PetscSectionGetFieldComponents(s, f, &Nc);
193:     PetscSectionGetFieldName(s, f, &fname);

195:     if (v->hdr.prefix) {PetscStrncpy(prefix, v->hdr.prefix,sizeof(prefix));}
196:     else               {prefix[0] = '\0';}
197:     if (Nf > 1) {
198:       DMCreateSubDM(dm, 1, &f, &fis, &fdm);
199:       VecGetSubVector(v, fis, &fv);
200:       PetscStrlcat(prefix, fname,sizeof(prefix));
201:       PetscStrlcat(prefix, "_",sizeof(prefix));
202:     }
203:     for (comp = 0; comp < Nc; ++comp, ++w) {
204:       PetscInt nmax = 2;

206:       PetscViewerDrawGetDraw(viewer, w, &draw);
207:       if (Nc > 1) {PetscSNPrintf(title, sizeof(title), "%s:%s_%D Step: %D Time: %.4g", name, fname, comp, step, time);}
208:       else        {PetscSNPrintf(title, sizeof(title), "%s:%s Step: %D Time: %.4g", name, fname, step, time);}
209:       PetscDrawSetTitle(draw, title);

211:       /* TODO Get max and min only for this component */
212:       PetscOptionsGetRealArray(NULL, prefix, "-vec_view_bounds", vbound, &nmax, &flg);
213:       if (!flg) {
214:         VecMin(fv, NULL, &vbound[0]);
215:         VecMax(fv, NULL, &vbound[1]);
216:         if (vbound[1] <= vbound[0]) vbound[1] = vbound[0] + 1.0;
217:       }
218:       PetscDrawGetPopup(draw, &popup);
219:       PetscDrawScalePopup(popup, vbound[0], vbound[1]);
220:       PetscDrawSetCoordinates(draw, bound[0], bound[1], bound[2], bound[3]);

222:       VecGetArrayRead(fv, &array);
223:       for (c = cStart; c < cEnd; ++c) {
224:         PetscScalar *coords = NULL, *a = NULL;
225:         PetscInt     numCoords, color[4] = {-1,-1,-1,-1};

227:         DMPlexPointLocalRead(fdm, c, array, &a);
228:         if (a) {
229:           color[0] = PetscDrawRealToColor(PetscRealPart(a[comp]), vbound[0], vbound[1]);
230:           color[1] = color[2] = color[3] = color[0];
231:         } else {
232:           PetscScalar *vals = NULL;
233:           PetscInt     numVals, va;

235:           DMPlexVecGetClosure(fdm, NULL, fv, c, &numVals, &vals);
236:           if (numVals % Nc) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of components %D does not divide the number of values in the closure %D", Nc, numVals);
237:           switch (numVals/Nc) {
238:           case 3: /* P1 Triangle */
239:           case 4: /* P1 Quadrangle */
240:             for (va = 0; va < numVals/Nc; ++va) color[va] = PetscDrawRealToColor(PetscRealPart(vals[va*Nc+comp]), vbound[0], vbound[1]);
241:             break;
242:           case 6: /* P2 Triangle */
243:           case 8: /* P2 Quadrangle */
244:             for (va = 0; va < numVals/(Nc*2); ++va) color[va] = PetscDrawRealToColor(PetscRealPart(vals[va*Nc+comp + numVals/(Nc*2)]), vbound[0], vbound[1]);
245:             break;
246:           default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of values for cell closure %D cannot be handled", numVals/Nc);
247:           }
248:           DMPlexVecRestoreClosure(fdm, NULL, fv, c, &numVals, &vals);
249:         }
250:         DMPlexVecGetClosure(dm, coordSection, coordinates, c, &numCoords, &coords);
251:         switch (numCoords) {
252:         case 6:
253:           PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), color[0], color[1], color[2]);
254:           break;
255:         case 8:
256:           PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), color[0], color[1], color[2]);
257:           PetscDrawTriangle(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[6]), PetscRealPart(coords[7]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), color[2], color[3], color[0]);
258:           break;
259:         default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells with %D coordinates", numCoords);
260:         }
261:         DMPlexVecRestoreClosure(dm, coordSection, coordinates, c, &numCoords, &coords);
262:       }
263:       VecRestoreArrayRead(fv, &array);
264:       PetscDrawFlush(draw);
265:       PetscDrawPause(draw);
266:       PetscDrawSave(draw);
267:     }
268:     if (Nf > 1) {
269:       VecRestoreSubVector(v, fis, &fv);
270:       ISDestroy(&fis);
271:       DMDestroy(&fdm);
272:     }
273:   }
274:   return(0);
275: }

277: static PetscErrorCode VecView_Plex_Local_VTK(Vec v, PetscViewer viewer)
278: {
279:   DM                      dm;
280:   Vec                     locv;
281:   const char              *name;
282:   PetscSection            section;
283:   PetscInt                pStart, pEnd;
284:   PetscViewerVTKFieldType ft;
285:   PetscErrorCode          ierr;

288:   VecGetDM(v, &dm);
289:   DMCreateLocalVector(dm, &locv); /* VTK viewer requires exclusive ownership of the vector */
290:   PetscObjectGetName((PetscObject) v, &name);
291:   PetscObjectSetName((PetscObject) locv, name);
292:   VecCopy(v, locv);
293:   DMGetLocalSection(dm, &section);
294:   DMPlexGetFieldType_Internal(dm, section, PETSC_DETERMINE, &pStart, &pEnd, &ft);
295:   PetscViewerVTKAddField(viewer, (PetscObject) dm, DMPlexVTKWriteAll, ft, PETSC_TRUE,(PetscObject) locv);
296:   return(0);
297: }

299: PetscErrorCode VecView_Plex_Local(Vec v, PetscViewer viewer)
300: {
301:   DM             dm;
302:   PetscBool      isvtk, ishdf5, isdraw, isglvis;

306:   VecGetDM(v, &dm);
307:   if (!dm) SETERRQ(PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM");
308:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK,   &isvtk);
309:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5,  &ishdf5);
310:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERDRAW,  &isdraw);
311:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERGLVIS, &isglvis);
312:   if (isvtk || ishdf5 || isdraw || isglvis) {
313:     PetscInt    i,numFields;
314:     PetscObject fe;
315:     PetscBool   fem = PETSC_FALSE;
316:     Vec         locv = v;
317:     const char  *name;
318:     PetscInt    step;
319:     PetscReal   time;

321:     DMGetNumFields(dm, &numFields);
322:     for (i=0; i<numFields; i++) {
323:       DMGetField(dm, i, NULL, &fe);
324:       if (fe->classid == PETSCFE_CLASSID) { fem = PETSC_TRUE; break; }
325:     }
326:     if (fem) {
327:       DMGetLocalVector(dm, &locv);
328:       PetscObjectGetName((PetscObject) v, &name);
329:       PetscObjectSetName((PetscObject) locv, name);
330:       VecCopy(v, locv);
331:       DMGetOutputSequenceNumber(dm, NULL, &time);
332:       DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locv, time, NULL, NULL, NULL);
333:     }
334:     if (isvtk) {
335:       VecView_Plex_Local_VTK(locv, viewer);
336:     } else if (ishdf5) {
337: #if defined(PETSC_HAVE_HDF5)
338:       VecView_Plex_Local_HDF5_Internal(locv, viewer);
339: #else
340:       SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
341: #endif
342:     } else if (isdraw) {
343:       VecView_Plex_Local_Draw(locv, viewer);
344:     } else if (isglvis) {
345:       DMGetOutputSequenceNumber(dm, &step, NULL);
346:       PetscViewerGLVisSetSnapId(viewer, step);
347:       VecView_GLVis(locv, viewer);
348:     }
349:     if (fem) {DMRestoreLocalVector(dm, &locv);}
350:   } else {
351:     PetscBool isseq;

353:     PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);
354:     if (isseq) {VecView_Seq(v, viewer);}
355:     else       {VecView_MPI(v, viewer);}
356:   }
357:   return(0);
358: }

360: PetscErrorCode VecView_Plex(Vec v, PetscViewer viewer)
361: {
362:   DM             dm;
363:   PetscBool      isvtk, ishdf5, isdraw, isglvis;

367:   VecGetDM(v, &dm);
368:   if (!dm) SETERRQ(PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM");
369:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK,   &isvtk);
370:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5,  &ishdf5);
371:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERDRAW,  &isdraw);
372:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERGLVIS, &isglvis);
373:   if (isvtk || isdraw || isglvis) {
374:     Vec         locv;
375:     const char *name;

377:     DMGetLocalVector(dm, &locv);
378:     PetscObjectGetName((PetscObject) v, &name);
379:     PetscObjectSetName((PetscObject) locv, name);
380:     DMGlobalToLocalBegin(dm, v, INSERT_VALUES, locv);
381:     DMGlobalToLocalEnd(dm, v, INSERT_VALUES, locv);
382:     VecView_Plex_Local(locv, viewer);
383:     DMRestoreLocalVector(dm, &locv);
384:   } else if (ishdf5) {
385: #if defined(PETSC_HAVE_HDF5)
386:     VecView_Plex_HDF5_Internal(v, viewer);
387: #else
388:     SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
389: #endif
390:   } else {
391:     PetscBool isseq;

393:     PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);
394:     if (isseq) {VecView_Seq(v, viewer);}
395:     else       {VecView_MPI(v, viewer);}
396:   }
397:   return(0);
398: }

400: PetscErrorCode VecView_Plex_Native(Vec originalv, PetscViewer viewer)
401: {
402:   DM                dm;
403:   MPI_Comm          comm;
404:   PetscViewerFormat format;
405:   Vec               v;
406:   PetscBool         isvtk, ishdf5;
407:   PetscErrorCode    ierr;

410:   VecGetDM(originalv, &dm);
411:   PetscObjectGetComm((PetscObject) originalv, &comm);
412:   if (!dm) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Vector not generated from a DM");
413:   PetscViewerGetFormat(viewer, &format);
414:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
415:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK,  &isvtk);
416:   if (format == PETSC_VIEWER_NATIVE) {
417:     /* Natural ordering is the common case for DMDA, NATIVE means plain vector, for PLEX is the opposite */
418:     /* this need a better fix */
419:     if (dm->useNatural) {
420:       if (dm->sfNatural) {
421:         const char *vecname;
422:         PetscInt    n, nroots;

424:         VecGetLocalSize(originalv, &n);
425:         PetscSFGetGraph(dm->sfNatural, &nroots, NULL, NULL, NULL);
426:         if (n == nroots) {
427:           DMGetGlobalVector(dm, &v);
428:           DMPlexGlobalToNaturalBegin(dm, originalv, v);
429:           DMPlexGlobalToNaturalEnd(dm, originalv, v);
430:           PetscObjectGetName((PetscObject) originalv, &vecname);
431:           PetscObjectSetName((PetscObject) v, vecname);
432:         } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "DM global to natural SF only handles global vectors");
433:       } else SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "DM global to natural SF was not created");
434:     } else v = originalv;
435:   } else v = originalv;

437:   if (ishdf5) {
438: #if defined(PETSC_HAVE_HDF5)
439:     VecView_Plex_HDF5_Native_Internal(v, viewer);
440: #else
441:     SETERRQ(comm, PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
442: #endif
443:   } else if (isvtk) {
444:     SETERRQ(comm, PETSC_ERR_SUP, "VTK format does not support viewing in natural order. Please switch to HDF5.");
445:   } else {
446:     PetscBool isseq;

448:     PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);
449:     if (isseq) {VecView_Seq(v, viewer);}
450:     else       {VecView_MPI(v, viewer);}
451:   }
452:   if (v != originalv) {DMRestoreGlobalVector(dm, &v);}
453:   return(0);
454: }

456: PetscErrorCode VecLoad_Plex_Local(Vec v, PetscViewer viewer)
457: {
458:   DM             dm;
459:   PetscBool      ishdf5;

463:   VecGetDM(v, &dm);
464:   if (!dm) SETERRQ(PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM");
465:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
466:   if (ishdf5) {
467:     DM          dmBC;
468:     Vec         gv;
469:     const char *name;

471:     DMGetOutputDM(dm, &dmBC);
472:     DMGetGlobalVector(dmBC, &gv);
473:     PetscObjectGetName((PetscObject) v, &name);
474:     PetscObjectSetName((PetscObject) gv, name);
475:     VecLoad_Default(gv, viewer);
476:     DMGlobalToLocalBegin(dmBC, gv, INSERT_VALUES, v);
477:     DMGlobalToLocalEnd(dmBC, gv, INSERT_VALUES, v);
478:     DMRestoreGlobalVector(dmBC, &gv);
479:   } else {
480:     VecLoad_Default(v, viewer);
481:   }
482:   return(0);
483: }

485: PetscErrorCode VecLoad_Plex(Vec v, PetscViewer viewer)
486: {
487:   DM             dm;
488:   PetscBool      ishdf5;

492:   VecGetDM(v, &dm);
493:   if (!dm) SETERRQ(PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM");
494:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
495:   if (ishdf5) {
496: #if defined(PETSC_HAVE_HDF5)
497:     VecLoad_Plex_HDF5_Internal(v, viewer);
498: #else
499:     SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
500: #endif
501:   } else {
502:     VecLoad_Default(v, viewer);
503:   }
504:   return(0);
505: }

507: PetscErrorCode VecLoad_Plex_Native(Vec originalv, PetscViewer viewer)
508: {
509:   DM                dm;
510:   PetscViewerFormat format;
511:   PetscBool         ishdf5;
512:   PetscErrorCode    ierr;

515:   VecGetDM(originalv, &dm);
516:   if (!dm) SETERRQ(PetscObjectComm((PetscObject) originalv), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM");
517:   PetscViewerGetFormat(viewer, &format);
518:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
519:   if (format == PETSC_VIEWER_NATIVE) {
520:     if (dm->useNatural) {
521:       if (dm->sfNatural) {
522:         if (ishdf5) {
523: #if defined(PETSC_HAVE_HDF5)
524:           Vec         v;
525:           const char *vecname;

527:           DMGetGlobalVector(dm, &v);
528:           PetscObjectGetName((PetscObject) originalv, &vecname);
529:           PetscObjectSetName((PetscObject) v, vecname);
530:           VecLoad_Plex_HDF5_Native_Internal(v, viewer);
531:           DMPlexNaturalToGlobalBegin(dm, v, originalv);
532:           DMPlexNaturalToGlobalEnd(dm, v, originalv);
533:           DMRestoreGlobalVector(dm, &v);
534: #else
535:           SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
536: #endif
537:         } else SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Reading in natural order is not supported for anything but HDF5.");
538:       }
539:     } else {
540:       VecLoad_Default(originalv, viewer);
541:     }
542:   }
543:   return(0);
544: }

546: PETSC_UNUSED static PetscErrorCode DMPlexView_Ascii_Geometry(DM dm, PetscViewer viewer)
547: {
548:   PetscSection       coordSection;
549:   Vec                coordinates;
550:   DMLabel            depthLabel;
551:   const char        *name[4];
552:   const PetscScalar *a;
553:   PetscInt           dim, pStart, pEnd, cStart, cEnd, c;
554:   PetscErrorCode     ierr;

557:   DMGetDimension(dm, &dim);
558:   DMGetCoordinatesLocal(dm, &coordinates);
559:   DMGetCoordinateSection(dm, &coordSection);
560:   DMPlexGetDepthLabel(dm, &depthLabel);
561:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
562:   PetscSectionGetChart(coordSection, &pStart, &pEnd);
563:   VecGetArrayRead(coordinates, &a);
564:   name[0]     = "vertex";
565:   name[1]     = "edge";
566:   name[dim-1] = "face";
567:   name[dim]   = "cell";
568:   for (c = cStart; c < cEnd; ++c) {
569:     PetscInt *closure = NULL;
570:     PetscInt  closureSize, cl;

572:     PetscViewerASCIIPrintf(viewer, "Geometry for cell %D:\n", c);
573:     DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
574:     PetscViewerASCIIPushTab(viewer);
575:     for (cl = 0; cl < closureSize*2; cl += 2) {
576:       PetscInt point = closure[cl], depth, dof, off, d, p;

578:       if ((point < pStart) || (point >= pEnd)) continue;
579:       PetscSectionGetDof(coordSection, point, &dof);
580:       if (!dof) continue;
581:       DMLabelGetValue(depthLabel, point, &depth);
582:       PetscSectionGetOffset(coordSection, point, &off);
583:       PetscViewerASCIIPrintf(viewer, "%s %D coords:", name[depth], point);
584:       for (p = 0; p < dof/dim; ++p) {
585:         PetscViewerASCIIPrintf(viewer, " (");
586:         for (d = 0; d < dim; ++d) {
587:           if (d > 0) {PetscViewerASCIIPrintf(viewer, ", ");}
588:           PetscViewerASCIIPrintf(viewer, "%g", (double) PetscRealPart(a[off+p*dim+d]));
589:         }
590:         PetscViewerASCIIPrintf(viewer, ")");
591:       }
592:       PetscViewerASCIIPrintf(viewer, "\n");
593:     }
594:     DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
595:     PetscViewerASCIIPopTab(viewer);
596:   }
597:   VecRestoreArrayRead(coordinates, &a);
598:   return(0);
599: }

601: static PetscErrorCode DMPlexView_Ascii(DM dm, PetscViewer viewer)
602: {
603:   DM_Plex          *mesh = (DM_Plex*) dm->data;
604:   DM                cdm;
605:   DMLabel           markers;
606:   PetscSection      coordSection;
607:   Vec               coordinates;
608:   PetscViewerFormat format;
609:   PetscErrorCode    ierr;

612:   DMGetCoordinateDM(dm, &cdm);
613:   DMGetLocalSection(cdm, &coordSection);
614:   DMGetCoordinatesLocal(dm, &coordinates);
615:   PetscViewerGetFormat(viewer, &format);
616:   if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) {
617:     const char *name;
618:     PetscInt    dim, cellHeight, maxConeSize, maxSupportSize;
619:     PetscInt    pStart, pEnd, p;
620:     PetscMPIInt rank, size;

622:     MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
623:     MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size);
624:     PetscObjectGetName((PetscObject) dm, &name);
625:     DMPlexGetChart(dm, &pStart, &pEnd);
626:     DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);
627:     DMGetDimension(dm, &dim);
628:     DMPlexGetVTKCellHeight(dm, &cellHeight);
629:     if (name) {PetscViewerASCIIPrintf(viewer, "%s in %D dimension%s:\n", name, dim, dim == 1 ? "" : "s");}
630:     else      {PetscViewerASCIIPrintf(viewer, "Mesh in %D dimension%s:\n", dim, dim == 1 ? "" : "s");}
631:     if (cellHeight) {PetscViewerASCIIPrintf(viewer, "  Cells are at height %D\n", cellHeight);}
632:     PetscViewerASCIIPrintf(viewer, "Supports:\n", name);
633:     PetscViewerASCIIPushSynchronized(viewer);
634:     PetscViewerASCIISynchronizedPrintf(viewer, "[%d] Max support size: %D\n", rank, maxSupportSize);
635:     for (p = pStart; p < pEnd; ++p) {
636:       PetscInt dof, off, s;

638:       PetscSectionGetDof(mesh->supportSection, p, &dof);
639:       PetscSectionGetOffset(mesh->supportSection, p, &off);
640:       for (s = off; s < off+dof; ++s) {
641:         PetscViewerASCIISynchronizedPrintf(viewer, "[%d]: %D ----> %D\n", rank, p, mesh->supports[s]);
642:       }
643:     }
644:     PetscViewerFlush(viewer);
645:     PetscViewerASCIIPrintf(viewer, "Cones:\n", name);
646:     PetscViewerASCIISynchronizedPrintf(viewer, "[%d] Max cone size: %D\n", rank, maxConeSize);
647:     for (p = pStart; p < pEnd; ++p) {
648:       PetscInt dof, off, c;

650:       PetscSectionGetDof(mesh->coneSection, p, &dof);
651:       PetscSectionGetOffset(mesh->coneSection, p, &off);
652:       for (c = off; c < off+dof; ++c) {
653:         PetscViewerASCIISynchronizedPrintf(viewer, "[%d]: %D <---- %D (%D)\n", rank, p, mesh->cones[c], mesh->coneOrientations[c]);
654:       }
655:     }
656:     PetscViewerFlush(viewer);
657:     PetscViewerASCIIPopSynchronized(viewer);
658:     if (coordSection && coordinates) {
659:       PetscSectionVecView(coordSection, coordinates, viewer);
660:     }
661:     DMGetLabel(dm, "marker", &markers);
662:     if (markers) {DMLabelView(markers,viewer);}
663:     if (size > 1) {
664:       PetscSF sf;

666:       DMGetPointSF(dm, &sf);
667:       PetscSFView(sf, viewer);
668:     }
669:     PetscViewerFlush(viewer);
670:   } else if (format == PETSC_VIEWER_ASCII_LATEX) {
671:     const char  *name, *color;
672:     const char  *defcolors[3]  = {"gray", "orange", "green"};
673:     const char  *deflcolors[4] = {"blue", "cyan", "red", "magenta"};
674:     char         lname[PETSC_MAX_PATH_LEN];
675:     PetscReal    scale         = 2.0;
676:     PetscReal    tikzscale     = 1.0;
677:     PetscBool    useNumbers    = PETSC_TRUE, useLabels, useColors;
678:     double       tcoords[3];
679:     PetscScalar *coords;
680:     PetscInt     numLabels, l, numColors, numLColors, dim, depth, cStart, cEnd, c, vStart, vEnd, v, eStart = 0, eEnd = 0, e, p;
681:     PetscMPIInt  rank, size;
682:     char         **names, **colors, **lcolors;
683:     PetscBool    plotEdges, flg, lflg;
684:     PetscBT      wp = NULL;
685:     PetscInt     pEnd, pStart;

687:     DMGetDimension(dm, &dim);
688:     DMPlexGetDepth(dm, &depth);
689:     DMGetNumLabels(dm, &numLabels);
690:     numLabels  = PetscMax(numLabels, 10);
691:     numColors  = 10;
692:     numLColors = 10;
693:     PetscCalloc3(numLabels, &names, numColors, &colors, numLColors, &lcolors);
694:     PetscOptionsGetReal(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_scale", &scale, NULL);
695:     PetscOptionsGetReal(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_tikzscale", &tikzscale, NULL);
696:     PetscOptionsGetBool(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_numbers", &useNumbers, NULL);
697:     PetscOptionsGetStringArray(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_labels", names, &numLabels, &useLabels);
698:     if (!useLabels) numLabels = 0;
699:     PetscOptionsGetStringArray(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_colors", colors, &numColors, &useColors);
700:     if (!useColors) {
701:       numColors = 3;
702:       for (c = 0; c < numColors; ++c) {PetscStrallocpy(defcolors[c], &colors[c]);}
703:     }
704:     PetscOptionsGetStringArray(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_lcolors", lcolors, &numLColors, &useColors);
705:     if (!useColors) {
706:       numLColors = 4;
707:       for (c = 0; c < numLColors; ++c) {PetscStrallocpy(deflcolors[c], &lcolors[c]);}
708:     }
709:     PetscOptionsGetString(((PetscObject) viewer)->options, ((PetscObject) viewer)->prefix, "-dm_plex_view_label_filter", lname, PETSC_MAX_PATH_LEN, &lflg);
710:     plotEdges = (PetscBool)(depth > 1 && useNumbers && dim < 3);
711:     PetscOptionsGetBool(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_edges", &plotEdges, &flg);
712:     if (flg && plotEdges && depth < dim) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Mesh must be interpolated");
713:     if (depth < dim) plotEdges = PETSC_FALSE;

715:     /* filter points with labelvalue != labeldefaultvalue */
716:     DMPlexGetChart(dm, &pStart, &pEnd);
717:     if (lflg) {
718:       DMLabel lbl;

720:       DMGetLabel(dm, lname, &lbl);
721:       if (lbl) {
722:         PetscInt val, defval;

724:         DMLabelGetDefaultValue(lbl, &defval);
725:         PetscBTCreate(pEnd-pStart, &wp);
726:         for (c = pStart;  c < pEnd; c++) {
727:           PetscInt *closure = NULL;
728:           PetscInt  closureSize;

730:           DMLabelGetValue(lbl, c, &val);
731:           if (val == defval) continue;

733:           DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
734:           for (p = 0; p < closureSize*2; p += 2) {
735:             PetscBTSet(wp, closure[p] - pStart);
736:           }
737:           DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
738:         }
739:       }
740:     }

742:     MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
743:     MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size);
744:     PetscObjectGetName((PetscObject) dm, &name);
745:     PetscViewerASCIIPrintf(viewer, "\
746: \\documentclass[tikz]{standalone}\n\n\
747: \\usepackage{pgflibraryshapes}\n\
748: \\usetikzlibrary{backgrounds}\n\
749: \\usetikzlibrary{arrows}\n\
750: \\begin{document}\n");
751:     if (size > 1) {
752:       PetscViewerASCIIPrintf(viewer, "%s for process ", name);
753:       for (p = 0; p < size; ++p) {
754:         if (p > 0 && p == size-1) {
755:           PetscViewerASCIIPrintf(viewer, ", and ", colors[p%numColors], p);
756:         } else if (p > 0) {
757:           PetscViewerASCIIPrintf(viewer, ", ", colors[p%numColors], p);
758:         }
759:         PetscViewerASCIIPrintf(viewer, "{\\textcolor{%s}%D}", colors[p%numColors], p);
760:       }
761:       PetscViewerASCIIPrintf(viewer, ".\n\n\n");
762:     }
763:     PetscViewerASCIIPrintf(viewer, "\\begin{tikzpicture}[scale = %g,font=\\fontsize{8}{8}\\selectfont]\n", (double) tikzscale);

765:     /* Plot vertices */
766:     DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
767:     VecGetArray(coordinates, &coords);
768:     PetscViewerASCIIPushSynchronized(viewer);
769:     for (v = vStart; v < vEnd; ++v) {
770:       PetscInt  off, dof, d;
771:       PetscBool isLabeled = PETSC_FALSE;

773:       if (wp && !PetscBTLookup(wp,v - pStart)) continue;
774:       PetscSectionGetDof(coordSection, v, &dof);
775:       PetscSectionGetOffset(coordSection, v, &off);
776:       PetscViewerASCIISynchronizedPrintf(viewer, "\\path (");
777:       if (PetscUnlikely(dof > 3)) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"coordSection vertex %D has dof %D > 3",v,dof);
778:       for (d = 0; d < dof; ++d) {
779:         tcoords[d] = (double) (scale*PetscRealPart(coords[off+d]));
780:         tcoords[d] = PetscAbs(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d];
781:       }
782:       /* Rotate coordinates since PGF makes z point out of the page instead of up */
783:       if (dim == 3) {PetscReal tmp = tcoords[1]; tcoords[1] = tcoords[2]; tcoords[2] = -tmp;}
784:       for (d = 0; d < dof; ++d) {
785:         if (d > 0) {PetscViewerASCIISynchronizedPrintf(viewer, ",");}
786:         PetscViewerASCIISynchronizedPrintf(viewer, "%g", (double) tcoords[d]);
787:       }
788:       color = colors[rank%numColors];
789:       for (l = 0; l < numLabels; ++l) {
790:         PetscInt val;
791:         DMGetLabelValue(dm, names[l], v, &val);
792:         if (val >= 0) {color = lcolors[l%numLColors]; isLabeled = PETSC_TRUE; break;}
793:       }
794:       if (useNumbers) {
795:         PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [draw,shape=circle,color=%s] {%D};\n", v, rank, color, v);
796:       } else {
797:         PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [fill,inner sep=%dpt,shape=circle,color=%s] {};\n", v, rank, !isLabeled ? 1 : 2, color);
798:       }
799:     }
800:     VecRestoreArray(coordinates, &coords);
801:     PetscViewerFlush(viewer);
802:     /* Plot cells */
803:     DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
804:     DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd);
805:     if (dim == 3 || !useNumbers) {
806:       for (e = eStart; e < eEnd; ++e) {
807:         const PetscInt *cone;

809:         if (wp && !PetscBTLookup(wp,e - pStart)) continue;
810:         color = colors[rank%numColors];
811:         for (l = 0; l < numLabels; ++l) {
812:           PetscInt val;
813:           DMGetLabelValue(dm, names[l], e, &val);
814:           if (val >= 0) {color = lcolors[l%numLColors]; break;}
815:         }
816:         DMPlexGetCone(dm, e, &cone);
817:         PetscViewerASCIISynchronizedPrintf(viewer, "\\draw[color=%s] (%D_%d) -- (%D_%d);\n", color, cone[0], rank, cone[1], rank);
818:       }
819:     } else {
820:       for (c = cStart; c < cEnd; ++c) {
821:         PetscInt *closure = NULL;
822:         PetscInt  closureSize, firstPoint = -1;

824:         if (wp && !PetscBTLookup(wp,c - pStart)) continue;
825:         DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
826:         PetscViewerASCIISynchronizedPrintf(viewer, "\\draw[color=%s] ", colors[rank%numColors]);
827:         for (p = 0; p < closureSize*2; p += 2) {
828:           const PetscInt point = closure[p];

830:           if ((point < vStart) || (point >= vEnd)) continue;
831:           if (firstPoint >= 0) {PetscViewerASCIISynchronizedPrintf(viewer, " -- ");}
832:           PetscViewerASCIISynchronizedPrintf(viewer, "(%D_%d)", point, rank);
833:           if (firstPoint < 0) firstPoint = point;
834:         }
835:         /* Why doesn't this work? PetscViewerASCIISynchronizedPrintf(viewer, " -- cycle;\n"); */
836:         PetscViewerASCIISynchronizedPrintf(viewer, " -- (%D_%d);\n", firstPoint, rank);
837:         DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
838:       }
839:     }
840:     VecGetArray(coordinates, &coords);
841:     for (c = cStart; c < cEnd; ++c) {
842:       double    ccoords[3] = {0.0, 0.0, 0.0};
843:       PetscBool isLabeled  = PETSC_FALSE;
844:       PetscInt *closure    = NULL;
845:       PetscInt  closureSize, dof, d, n = 0;

847:       if (wp && !PetscBTLookup(wp,c - pStart)) continue;
848:       DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
849:       PetscViewerASCIISynchronizedPrintf(viewer, "\\path (");
850:       for (p = 0; p < closureSize*2; p += 2) {
851:         const PetscInt point = closure[p];
852:         PetscInt       off;

854:         if ((point < vStart) || (point >= vEnd)) continue;
855:         PetscSectionGetDof(coordSection, point, &dof);
856:         PetscSectionGetOffset(coordSection, point, &off);
857:         for (d = 0; d < dof; ++d) {
858:           tcoords[d] = (double) (scale*PetscRealPart(coords[off+d]));
859:           tcoords[d] = PetscAbs(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d];
860:         }
861:         /* Rotate coordinates since PGF makes z point out of the page instead of up */
862:         if (dof == 3) {PetscReal tmp = tcoords[1]; tcoords[1] = tcoords[2]; tcoords[2] = -tmp;}
863:         for (d = 0; d < dof; ++d) {ccoords[d] += tcoords[d];}
864:         ++n;
865:       }
866:       for (d = 0; d < dof; ++d) {ccoords[d] /= n;}
867:       DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
868:       for (d = 0; d < dof; ++d) {
869:         if (d > 0) {PetscViewerASCIISynchronizedPrintf(viewer, ",");}
870:         PetscViewerASCIISynchronizedPrintf(viewer, "%g", (double) ccoords[d]);
871:       }
872:       color = colors[rank%numColors];
873:       for (l = 0; l < numLabels; ++l) {
874:         PetscInt val;
875:         DMGetLabelValue(dm, names[l], c, &val);
876:         if (val >= 0) {color = lcolors[l%numLColors]; isLabeled = PETSC_TRUE; break;}
877:       }
878:       if (useNumbers) {
879:         PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [draw,shape=circle,color=%s] {%D};\n", c, rank, color, c);
880:       } else {
881:         PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [fill,inner sep=%dpt,shape=circle,color=%s] {};\n", c, rank, !isLabeled ? 1 : 2, color);
882:       }
883:     }
884:     VecRestoreArray(coordinates, &coords);
885:     /* Plot edges */
886:     if (plotEdges) {
887:       VecGetArray(coordinates, &coords);
888:       PetscViewerASCIIPrintf(viewer, "\\path\n");
889:       for (e = eStart; e < eEnd; ++e) {
890:         const PetscInt *cone;
891:         PetscInt        coneSize, offA, offB, dof, d;

893:         if (wp && !PetscBTLookup(wp,e - pStart)) continue;
894:         DMPlexGetConeSize(dm, e, &coneSize);
895:         if (coneSize != 2) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Edge %D cone should have two vertices, not %D", e, coneSize);
896:         DMPlexGetCone(dm, e, &cone);
897:         PetscSectionGetDof(coordSection, cone[0], &dof);
898:         PetscSectionGetOffset(coordSection, cone[0], &offA);
899:         PetscSectionGetOffset(coordSection, cone[1], &offB);
900:         PetscViewerASCIISynchronizedPrintf(viewer, "(");
901:         for (d = 0; d < dof; ++d) {
902:           tcoords[d] = (double) (0.5*scale*PetscRealPart(coords[offA+d]+coords[offB+d]));
903:           tcoords[d] = PetscAbs(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d];
904:         }
905:         /* Rotate coordinates since PGF makes z point out of the page instead of up */
906:         if (dim == 3) {PetscReal tmp = tcoords[1]; tcoords[1] = tcoords[2]; tcoords[2] = -tmp;}
907:         for (d = 0; d < dof; ++d) {
908:           if (d > 0) {PetscViewerASCIISynchronizedPrintf(viewer, ",");}
909:           PetscViewerASCIISynchronizedPrintf(viewer, "%g", (double)tcoords[d]);
910:         }
911:         color = colors[rank%numColors];
912:         for (l = 0; l < numLabels; ++l) {
913:           PetscInt val;
914:           DMGetLabelValue(dm, names[l], v, &val);
915:           if (val >= 0) {color = lcolors[l%numLColors]; break;}
916:         }
917:         PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [draw,shape=circle,color=%s] {%D} --\n", e, rank, color, e);
918:       }
919:       VecRestoreArray(coordinates, &coords);
920:       PetscViewerFlush(viewer);
921:       PetscViewerASCIIPrintf(viewer, "(0,0);\n");
922:     }
923:     PetscViewerFlush(viewer);
924:     PetscViewerASCIIPopSynchronized(viewer);
925:     PetscViewerASCIIPrintf(viewer, "\\end{tikzpicture}\n");
926:     PetscViewerASCIIPrintf(viewer, "\\end{document}\n", name);
927:     for (l = 0; l < numLabels;  ++l) {PetscFree(names[l]);}
928:     for (c = 0; c < numColors;  ++c) {PetscFree(colors[c]);}
929:     for (c = 0; c < numLColors; ++c) {PetscFree(lcolors[c]);}
930:     PetscFree3(names, colors, lcolors);
931:     PetscBTDestroy(&wp);
932:   } else if (format == PETSC_VIEWER_LOAD_BALANCE) {
933:     Vec                    cown,acown;
934:     VecScatter             sct;
935:     ISLocalToGlobalMapping g2l;
936:     IS                     gid,acis;
937:     MPI_Comm               comm,ncomm = MPI_COMM_NULL;
938:     MPI_Group              ggroup,ngroup;
939:     PetscScalar            *array,nid;
940:     const PetscInt         *idxs;
941:     PetscInt               *idxs2,*start,*adjacency,*work;
942:     PetscInt64             lm[3],gm[3];
943:     PetscInt               i,c,cStart,cEnd,cum,numVertices,ect,ectn,cellHeight;
944:     PetscMPIInt            d1,d2,rank;

946:     PetscObjectGetComm((PetscObject)dm,&comm);
947:     MPI_Comm_rank(comm,&rank);
948: #if defined(PETSC_HAVE_MPI_PROCESS_SHARED_MEMORY)
949:     MPI_Comm_split_type(comm,MPI_COMM_TYPE_SHARED,rank,MPI_INFO_NULL,&ncomm);
950: #endif
951:     if (ncomm != MPI_COMM_NULL) {
952:       MPI_Comm_group(comm,&ggroup);
953:       MPI_Comm_group(ncomm,&ngroup);
954:       d1   = 0;
955:       MPI_Group_translate_ranks(ngroup,1,&d1,ggroup,&d2);
956:       nid  = d2;
957:       MPI_Group_free(&ggroup);
958:       MPI_Group_free(&ngroup);
959:       MPI_Comm_free(&ncomm);
960:     } else nid = 0.0;

962:     /* Get connectivity */
963:     DMPlexGetVTKCellHeight(dm,&cellHeight);
964:     DMPlexCreatePartitionerGraph(dm,cellHeight,&numVertices,&start,&adjacency,&gid);

966:     /* filter overlapped local cells */
967:     DMPlexGetHeightStratum(dm,cellHeight,&cStart,&cEnd);
968:     ISGetIndices(gid,&idxs);
969:     ISGetLocalSize(gid,&cum);
970:     PetscMalloc1(cum,&idxs2);
971:     for (c = cStart, cum = 0; c < cEnd; c++) {
972:       if (idxs[c-cStart] < 0) continue;
973:       idxs2[cum++] = idxs[c-cStart];
974:     }
975:     ISRestoreIndices(gid,&idxs);
976:     if (numVertices != cum) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Unexpected %D != %D",numVertices,cum);
977:     ISDestroy(&gid);
978:     ISCreateGeneral(comm,numVertices,idxs2,PETSC_OWN_POINTER,&gid);

980:     /* support for node-aware cell locality */
981:     ISCreateGeneral(comm,start[numVertices],adjacency,PETSC_USE_POINTER,&acis);
982:     VecCreateSeq(PETSC_COMM_SELF,start[numVertices],&acown);
983:     VecCreateMPI(comm,numVertices,PETSC_DECIDE,&cown);
984:     VecGetArray(cown,&array);
985:     for (c = 0; c < numVertices; c++) array[c] = nid;
986:     VecRestoreArray(cown,&array);
987:     VecScatterCreate(cown,acis,acown,NULL,&sct);
988:     VecScatterBegin(sct,cown,acown,INSERT_VALUES,SCATTER_FORWARD);
989:     VecScatterEnd(sct,cown,acown,INSERT_VALUES,SCATTER_FORWARD);
990:     ISDestroy(&acis);
991:     VecScatterDestroy(&sct);
992:     VecDestroy(&cown);

994:     /* compute edgeCut */
995:     for (c = 0, cum = 0; c < numVertices; c++) cum = PetscMax(cum,start[c+1]-start[c]);
996:     PetscMalloc1(cum,&work);
997:     ISLocalToGlobalMappingCreateIS(gid,&g2l);
998:     ISLocalToGlobalMappingSetType(g2l,ISLOCALTOGLOBALMAPPINGHASH);
999:     ISDestroy(&gid);
1000:     VecGetArray(acown,&array);
1001:     for (c = 0, ect = 0, ectn = 0; c < numVertices; c++) {
1002:       PetscInt totl;

1004:       totl = start[c+1]-start[c];
1005:       ISGlobalToLocalMappingApply(g2l,IS_GTOLM_MASK,totl,adjacency+start[c],NULL,work);
1006:       for (i = 0; i < totl; i++) {
1007:         if (work[i] < 0) {
1008:           ect  += 1;
1009:           ectn += (array[i + start[c]] != nid) ? 0 : 1;
1010:         }
1011:       }
1012:     }
1013:     PetscFree(work);
1014:     VecRestoreArray(acown,&array);
1015:     lm[0] = numVertices > 0 ?  numVertices : PETSC_MAX_INT;
1016:     lm[1] = -numVertices;
1017:     MPIU_Allreduce(lm,gm,2,MPIU_INT64,MPI_MIN,comm);
1018:     PetscViewerASCIIPrintf(viewer,"  Cell balance: %.2f (max %D, min %D",-((double)gm[1])/((double)gm[0]),-(PetscInt)gm[1],(PetscInt)gm[0]);
1019:     lm[0] = ect; /* edgeCut */
1020:     lm[1] = ectn; /* node-aware edgeCut */
1021:     lm[2] = numVertices > 0 ? 0 : 1; /* empty processes */
1022:     MPIU_Allreduce(lm,gm,3,MPIU_INT64,MPI_SUM,comm);
1023:     PetscViewerASCIIPrintf(viewer,", empty %D)\n",(PetscInt)gm[2]);
1024: #if defined(PETSC_HAVE_MPI_PROCESS_SHARED_MEMORY)
1025:     PetscViewerASCIIPrintf(viewer,"  Edge Cut: %D (on node %.3f)\n",(PetscInt)(gm[0]/2),gm[0] ? ((double)(gm[1]))/((double)gm[0]) : 1.);
1026: #else
1027:     PetscViewerASCIIPrintf(viewer,"  Edge Cut: %D (on node %.3f)\n",(PetscInt)(gm[0]/2),0.0);
1028: #endif
1029:     ISLocalToGlobalMappingDestroy(&g2l);
1030:     PetscFree(start);
1031:     PetscFree(adjacency);
1032:     VecDestroy(&acown);
1033:   } else {
1034:     MPI_Comm    comm;
1035:     PetscInt   *sizes, *hybsizes;
1036:     PetscInt    locDepth, depth, cellHeight, dim, d, pMax[4];
1037:     PetscInt    pStart, pEnd, p;
1038:     PetscInt    numLabels, l;
1039:     const char *name;
1040:     PetscMPIInt size;

1042:     PetscObjectGetComm((PetscObject)dm,&comm);
1043:     MPI_Comm_size(comm, &size);
1044:     DMGetDimension(dm, &dim);
1045:     DMPlexGetVTKCellHeight(dm, &cellHeight);
1046:     PetscObjectGetName((PetscObject) dm, &name);
1047:     if (name) {PetscViewerASCIIPrintf(viewer, "%s in %D dimension%s:\n", name, dim, dim == 1 ? "" : "s");}
1048:     else      {PetscViewerASCIIPrintf(viewer, "Mesh in %D dimension%s:\n", dim, dim == 1 ? "" : "s");}
1049:     if (cellHeight) {PetscViewerASCIIPrintf(viewer, "  Cells are at height %D\n", cellHeight);}
1050:     DMPlexGetDepth(dm, &locDepth);
1051:     MPIU_Allreduce(&locDepth, &depth, 1, MPIU_INT, MPI_MAX, comm);
1052:     DMPlexGetHybridBounds(dm, &pMax[depth], depth > 0 ? &pMax[depth-1] : NULL, depth > 1 ? &pMax[depth - 2] : NULL, &pMax[0]);
1053:     PetscCalloc2(size,&sizes,size,&hybsizes);
1054:     if (depth == 1) {
1055:       DMPlexGetDepthStratum(dm, 0, &pStart, &pEnd);
1056:       pEnd = pEnd - pStart;
1057:       pMax[0] -= pStart;
1058:       MPI_Gather(&pEnd, 1, MPIU_INT, sizes, 1, MPIU_INT, 0, comm);
1059:       MPI_Gather(&pMax[0], 1, MPIU_INT, hybsizes, 1, MPIU_INT, 0, comm);
1060:       PetscViewerASCIIPrintf(viewer, "  %d-cells:", 0);
1061:       for (p = 0; p < size; ++p) {
1062:         if (hybsizes[p] >= 0) {PetscViewerASCIIPrintf(viewer, " %D (%D)", sizes[p], sizes[p] - hybsizes[p]);}
1063:         else                  {PetscViewerASCIIPrintf(viewer, " %D", sizes[p]);}
1064:       }
1065:       PetscViewerASCIIPrintf(viewer, "\n");
1066:       DMPlexGetHeightStratum(dm, 0, &pStart, &pEnd);
1067:       pEnd = pEnd - pStart;
1068:       pMax[depth] -= pStart;
1069:       MPI_Gather(&pEnd, 1, MPIU_INT, sizes, 1, MPIU_INT, 0, comm);
1070:       MPI_Gather(&pMax[depth], 1, MPIU_INT, hybsizes, 1, MPIU_INT, 0, comm);
1071:       PetscViewerASCIIPrintf(viewer, "  %D-cells:", dim);
1072:       for (p = 0; p < size; ++p) {
1073:         if (hybsizes[p] >= 0) {PetscViewerASCIIPrintf(viewer, " %D (%D)", sizes[p], sizes[p] - hybsizes[p]);}
1074:         else                  {PetscViewerASCIIPrintf(viewer, " %D", sizes[p]);}
1075:       }
1076:       PetscViewerASCIIPrintf(viewer, "\n");
1077:     } else {
1078:       PetscMPIInt rank;
1079:       MPI_Comm_rank(comm, &rank);
1080:       for (d = 0; d <= dim; d++) {
1081:         DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
1082:         pEnd    -= pStart;
1083:         pMax[d] -= pStart;
1084:         MPI_Gather(&pEnd, 1, MPIU_INT, sizes, 1, MPIU_INT, 0, comm);
1085:         MPI_Gather(&pMax[d], 1, MPIU_INT, hybsizes, 1, MPIU_INT, 0, comm);
1086:         PetscViewerASCIIPrintf(viewer, "  %D-cells:", d);
1087:         for (p = 0; p < size; ++p) {
1088:           if (!rank) {
1089:             if (hybsizes[p] >= 0) {PetscViewerASCIIPrintf(viewer, " %D (%D)", sizes[p], sizes[p] - hybsizes[p]);}
1090:             else                  {PetscViewerASCIIPrintf(viewer, " %D", sizes[p]);}
1091:           }
1092:         }
1093:         PetscViewerASCIIPrintf(viewer, "\n");
1094:       }
1095:     }
1096:     PetscFree2(sizes,hybsizes);
1097:     DMGetNumLabels(dm, &numLabels);
1098:     if (numLabels) {PetscViewerASCIIPrintf(viewer, "Labels:\n");}
1099:     for (l = 0; l < numLabels; ++l) {
1100:       DMLabel         label;
1101:       const char     *name;
1102:       IS              valueIS;
1103:       const PetscInt *values;
1104:       PetscInt        numValues, v;

1106:       DMGetLabelName(dm, l, &name);
1107:       DMGetLabel(dm, name, &label);
1108:       DMLabelGetNumValues(label, &numValues);
1109:       PetscViewerASCIIPrintf(viewer, "  %s: %D strata with value/size (", name, numValues);
1110:       DMLabelGetValueIS(label, &valueIS);
1111:       ISGetIndices(valueIS, &values);
1112:       PetscViewerASCIIUseTabs(viewer, PETSC_FALSE);
1113:       for (v = 0; v < numValues; ++v) {
1114:         PetscInt size;

1116:         DMLabelGetStratumSize(label, values[v], &size);
1117:         if (v > 0) {PetscViewerASCIIPrintf(viewer, ", ");}
1118:         PetscViewerASCIIPrintf(viewer, "%D (%D)", values[v], size);
1119:       }
1120:       PetscViewerASCIIPrintf(viewer, ")\n");
1121:       PetscViewerASCIIUseTabs(viewer, PETSC_TRUE);
1122:       ISRestoreIndices(valueIS, &values);
1123:       ISDestroy(&valueIS);
1124:     }
1125:     /* If no fields are specified, people do not want to see adjacency */
1126:     if (dm->Nf) {
1127:       PetscInt f;

1129:       for (f = 0; f < dm->Nf; ++f) {
1130:         const char *name;

1132:         PetscObjectGetName(dm->fields[f].disc, &name);
1133:         if (numLabels) {PetscViewerASCIIPrintf(viewer, "Field %s:\n", name);}
1134:         PetscViewerASCIIPushTab(viewer);
1135:         if (dm->fields[f].label) {DMLabelView(dm->fields[f].label, viewer);}
1136:         if (dm->fields[f].adjacency[0]) {
1137:           if (dm->fields[f].adjacency[1]) {PetscViewerASCIIPrintf(viewer, "adjacency FVM++\n");}
1138:           else                            {PetscViewerASCIIPrintf(viewer, "adjacency FVM\n");}
1139:         } else {
1140:           if (dm->fields[f].adjacency[1]) {PetscViewerASCIIPrintf(viewer, "adjacency FEM\n");}
1141:           else                            {PetscViewerASCIIPrintf(viewer, "adjacency FUNKY\n");}
1142:         }
1143:         PetscViewerASCIIPopTab(viewer);
1144:       }
1145:     }
1146:     DMGetCoarseDM(dm, &cdm);
1147:     if (cdm) {
1148:       PetscViewerASCIIPushTab(viewer);
1149:       DMPlexView_Ascii(cdm, viewer);
1150:       PetscViewerASCIIPopTab(viewer);
1151:     }
1152:   }
1153:   return(0);
1154: }

1156: static PetscErrorCode DMPlexView_Draw(DM dm, PetscViewer viewer)
1157: {
1158:   PetscDraw          draw;
1159:   DM                 cdm;
1160:   PetscSection       coordSection;
1161:   Vec                coordinates;
1162:   const PetscScalar *coords;
1163:   PetscReal          xyl[2],xyr[2],bound[4] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL};
1164:   PetscBool          isnull;
1165:   PetscInt           dim, vStart, vEnd, cStart, cEnd, c, N;
1166:   PetscMPIInt        rank;
1167:   PetscErrorCode     ierr;

1170:   DMGetCoordinateDim(dm, &dim);
1171:   if (dim != 2) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Cannot draw meshes of dimension %D", dim);
1172:   DMGetCoordinateDM(dm, &cdm);
1173:   DMGetLocalSection(cdm, &coordSection);
1174:   DMGetCoordinatesLocal(dm, &coordinates);
1175:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
1176:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);

1178:   PetscViewerDrawGetDraw(viewer, 0, &draw);
1179:   PetscDrawIsNull(draw, &isnull);
1180:   if (isnull) return(0);
1181:   PetscDrawSetTitle(draw, "Mesh");

1183:   VecGetLocalSize(coordinates, &N);
1184:   VecGetArrayRead(coordinates, &coords);
1185:   for (c = 0; c < N; c += dim) {
1186:     bound[0] = PetscMin(bound[0], PetscRealPart(coords[c]));   bound[2] = PetscMax(bound[2], PetscRealPart(coords[c]));
1187:     bound[1] = PetscMin(bound[1], PetscRealPart(coords[c+1])); bound[3] = PetscMax(bound[3], PetscRealPart(coords[c+1]));
1188:   }
1189:   VecRestoreArrayRead(coordinates, &coords);
1190:   MPIU_Allreduce(&bound[0],xyl,2,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)dm));
1191:   MPIU_Allreduce(&bound[2],xyr,2,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)dm));
1192:   PetscDrawSetCoordinates(draw, xyl[0], xyl[1], xyr[0], xyr[1]);
1193:   PetscDrawClear(draw);

1195:   MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
1196:   for (c = cStart; c < cEnd; ++c) {
1197:     PetscScalar *coords = NULL;
1198:     PetscInt     numCoords,coneSize;

1200:     DMPlexGetConeSize(dm, c, &coneSize);
1201:     DMPlexVecGetClosure(dm, coordSection, coordinates, c, &numCoords, &coords);
1202:     switch (coneSize) {
1203:     case 3:
1204:       PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]),
1205:                                PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2,
1206:                                PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2,
1207:                                PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2);
1208:       break;
1209:     case 4:
1210:       PetscDrawRectangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[4]), PetscRealPart(coords[5]),
1211:                                 PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2,
1212:                                 PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2,
1213:                                 PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2,
1214:                                 PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2);
1215:       break;
1216:     default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells with %D facets", coneSize);
1217:     }
1218:     DMPlexVecRestoreClosure(dm, coordSection, coordinates, c, &numCoords, &coords);
1219:   }
1220:   for (c = cStart; c < cEnd; ++c) {
1221:     PetscScalar *coords = NULL;
1222:     PetscInt     numCoords,coneSize;

1224:     DMPlexGetConeSize(dm, c, &coneSize);
1225:     DMPlexVecGetClosure(dm, coordSection, coordinates, c, &numCoords, &coords);
1226:     switch (coneSize) {
1227:     case 3:
1228:       PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK);
1229:       PetscDrawLine(draw, PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_BLACK);
1230:       PetscDrawLine(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), PETSC_DRAW_BLACK);
1231:       break;
1232:     case 4:
1233:       PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK);
1234:       PetscDrawLine(draw, PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_BLACK);
1235:       PetscDrawLine(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[6]), PetscRealPart(coords[7]), PETSC_DRAW_BLACK);
1236:       PetscDrawLine(draw, PetscRealPart(coords[6]), PetscRealPart(coords[7]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), PETSC_DRAW_BLACK);
1237:       break;
1238:     default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells with %D facets", coneSize);
1239:     }
1240:     DMPlexVecRestoreClosure(dm, coordSection, coordinates, c, &numCoords, &coords);
1241:   }
1242:   PetscDrawFlush(draw);
1243:   PetscDrawPause(draw);
1244:   PetscDrawSave(draw);
1245:   return(0);
1246: }

1248: PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer)
1249: {
1250:   PetscBool      iascii, ishdf5, isvtk, isdraw, flg, isglvis;
1251:   char           name[PETSC_MAX_PATH_LEN];

1257:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);
1258:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK,   &isvtk);
1259:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5,  &ishdf5);
1260:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERDRAW,  &isdraw);
1261:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERGLVIS, &isglvis);
1262:   if (iascii) {
1263:     PetscViewerFormat format;
1264:     PetscViewerGetFormat(viewer, &format);
1265:     if (format == PETSC_VIEWER_ASCII_GLVIS) {
1266:       DMPlexView_GLVis(dm, viewer);
1267:     } else {
1268:       DMPlexView_Ascii(dm, viewer);
1269:     }
1270:   } else if (ishdf5) {
1271: #if defined(PETSC_HAVE_HDF5)
1272:     DMPlexView_HDF5_Internal(dm, viewer);
1273: #else
1274:     SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
1275: #endif
1276:   } else if (isvtk) {
1277:     DMPlexVTKWriteAll((PetscObject) dm,viewer);
1278:   } else if (isdraw) {
1279:     DMPlexView_Draw(dm, viewer);
1280:   } else if (isglvis) {
1281:     DMPlexView_GLVis(dm, viewer);
1282:   } else {
1283:     SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Viewer type %s not yet supported for DMPlex writing", ((PetscObject)viewer)->type_name);
1284:   }
1285:   /* Optionally view the partition */
1286:   PetscOptionsHasName(((PetscObject) dm)->options, ((PetscObject) dm)->prefix, "-dm_partition_view", &flg);
1287:   if (flg) {
1288:     Vec ranks;
1289:     DMPlexCreateRankField(dm, &ranks);
1290:     VecView(ranks, viewer);
1291:     VecDestroy(&ranks);
1292:   }
1293:   /* Optionally view a label */
1294:   PetscOptionsGetString(((PetscObject) dm)->options, ((PetscObject) dm)->prefix, "-dm_label_view", name, PETSC_MAX_PATH_LEN, &flg);
1295:   if (flg) {
1296:     DMLabel label;
1297:     Vec     val;

1299:     DMGetLabel(dm, name, &label);
1300:     if (!label) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Label %s provided to -dm_label_view does not exist in this DM", name);
1301:     DMPlexCreateLabelField(dm, label, &val);
1302:     VecView(val, viewer);
1303:     VecDestroy(&val);
1304:   }
1305:   return(0);
1306: }

1308: PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer)
1309: {
1310:   PetscBool      ishdf5;

1316:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5,   &ishdf5);
1317:   if (ishdf5) {
1318: #if defined(PETSC_HAVE_HDF5)
1319:     PetscViewerFormat format;
1320:     PetscViewerGetFormat(viewer, &format);
1321:     if (format == PETSC_VIEWER_HDF5_XDMF || format == PETSC_VIEWER_HDF5_VIZ) {
1322:       DMPlexLoad_HDF5_Xdmf_Internal(dm, viewer);
1323:     } else if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) {
1324:       DMPlexLoad_HDF5_Internal(dm, viewer);
1325:     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]);
1326: #else
1327:     SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
1328: #endif
1329:   } else {
1330:     SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Viewer type %s not yet supported for DMPlex loading", ((PetscObject)viewer)->type_name);
1331:   }
1332:   return(0);
1333: }

1335: PetscErrorCode DMDestroy_Plex(DM dm)
1336: {
1337:   DM_Plex       *mesh = (DM_Plex*) dm->data;

1341:   PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",NULL);
1342:   PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C", NULL);
1343:   PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C", NULL);
1344:   if (--mesh->refct > 0) return(0);
1345:   PetscSectionDestroy(&mesh->coneSection);
1346:   PetscFree(mesh->cones);
1347:   PetscFree(mesh->coneOrientations);
1348:   PetscSectionDestroy(&mesh->supportSection);
1349:   PetscSectionDestroy(&mesh->subdomainSection);
1350:   PetscFree(mesh->supports);
1351:   PetscFree(mesh->facesTmp);
1352:   PetscFree(mesh->tetgenOpts);
1353:   PetscFree(mesh->triangleOpts);
1354:   PetscPartitionerDestroy(&mesh->partitioner);
1355:   DMLabelDestroy(&mesh->subpointMap);
1356:   ISDestroy(&mesh->globalVertexNumbers);
1357:   ISDestroy(&mesh->globalCellNumbers);
1358:   PetscSectionDestroy(&mesh->anchorSection);
1359:   ISDestroy(&mesh->anchorIS);
1360:   PetscSectionDestroy(&mesh->parentSection);
1361:   PetscFree(mesh->parents);
1362:   PetscFree(mesh->childIDs);
1363:   PetscSectionDestroy(&mesh->childSection);
1364:   PetscFree(mesh->children);
1365:   DMDestroy(&mesh->referenceTree);
1366:   PetscGridHashDestroy(&mesh->lbox);
1367:   /* This was originally freed in DMDestroy(), but that prevents reference counting of backend objects */
1368:   PetscFree(mesh);
1369:   return(0);
1370: }

1372: PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J)
1373: {
1374:   PetscSection           sectionGlobal;
1375:   PetscInt               bs = -1, mbs;
1376:   PetscInt               localSize;
1377:   PetscBool              isShell, isBlock, isSeqBlock, isMPIBlock, isSymBlock, isSymSeqBlock, isSymMPIBlock, isMatIS;
1378:   PetscErrorCode         ierr;
1379:   MatType                mtype;
1380:   ISLocalToGlobalMapping ltog;

1383:   MatInitializePackage();
1384:   mtype = dm->mattype;
1385:   DMGetGlobalSection(dm, &sectionGlobal);
1386:   /* PetscSectionGetStorageSize(sectionGlobal, &localSize); */
1387:   PetscSectionGetConstrainedStorageSize(sectionGlobal, &localSize);
1388:   MatCreate(PetscObjectComm((PetscObject)dm), J);
1389:   MatSetSizes(*J, localSize, localSize, PETSC_DETERMINE, PETSC_DETERMINE);
1390:   MatSetType(*J, mtype);
1391:   MatSetFromOptions(*J);
1392:   MatGetBlockSize(*J, &mbs);
1393:   if (mbs > 1) bs = mbs;
1394:   PetscStrcmp(mtype, MATSHELL, &isShell);
1395:   PetscStrcmp(mtype, MATBAIJ, &isBlock);
1396:   PetscStrcmp(mtype, MATSEQBAIJ, &isSeqBlock);
1397:   PetscStrcmp(mtype, MATMPIBAIJ, &isMPIBlock);
1398:   PetscStrcmp(mtype, MATSBAIJ, &isSymBlock);
1399:   PetscStrcmp(mtype, MATSEQSBAIJ, &isSymSeqBlock);
1400:   PetscStrcmp(mtype, MATMPISBAIJ, &isSymMPIBlock);
1401:   PetscStrcmp(mtype, MATIS, &isMatIS);
1402:   if (!isShell) {
1403:     PetscSection subSection;
1404:     PetscBool    fillMatrix = (PetscBool)(!dm->prealloc_only && !isMatIS);
1405:     PetscInt    *dnz, *onz, *dnzu, *onzu, bsLocal[2], bsMinMax[2], *ltogidx, lsize;
1406:     PetscInt     pStart, pEnd, p, dof, cdof;

1408:     /* Set localtoglobalmapping on the matrix for MatSetValuesLocal() to work (it also creates the local matrices in case of MATIS) */
1409:     if (isMatIS) { /* need a different l2g map than the one computed by DMGetLocalToGlobalMapping */
1410:       PetscSection section;
1411:       PetscInt     size;

1413:       DMGetLocalSection(dm, &section);
1414:       PetscSectionGetStorageSize(section, &size);
1415:       PetscMalloc1(size,&ltogidx);
1416:       DMPlexGetSubdomainSection(dm, &subSection);
1417:     } else {
1418:       DMGetLocalToGlobalMapping(dm,&ltog);
1419:     }
1420:     PetscSectionGetChart(sectionGlobal, &pStart, &pEnd);
1421:     for (p = pStart, lsize = 0; p < pEnd; ++p) {
1422:       PetscInt bdof;

1424:       PetscSectionGetDof(sectionGlobal, p, &dof);
1425:       PetscSectionGetConstraintDof(sectionGlobal, p, &cdof);
1426:       dof  = dof < 0 ? -(dof+1) : dof;
1427:       bdof = cdof && (dof-cdof) ? 1 : dof;
1428:       if (dof) {
1429:         if (bs < 0)          {bs = bdof;}
1430:         else if (bs != bdof) {bs = 1; if (!isMatIS) break;}
1431:       }
1432:       if (isMatIS) {
1433:         PetscInt loff,c,off;
1434:         PetscSectionGetOffset(subSection, p, &loff);
1435:         PetscSectionGetOffset(sectionGlobal, p, &off);
1436:         for (c = 0; c < dof-cdof; ++c, ++lsize) ltogidx[loff+c] = off > -1 ? off+c : -(off+1)+c;
1437:       }
1438:     }
1439:     /* Must have same blocksize on all procs (some might have no points) */
1440:     bsLocal[0] = bs < 0 ? PETSC_MAX_INT : bs; bsLocal[1] = bs;
1441:     PetscGlobalMinMaxInt(PetscObjectComm((PetscObject) dm), bsLocal, bsMinMax);
1442:     if (bsMinMax[0] != bsMinMax[1]) {bs = 1;}
1443:     else                            {bs = bsMinMax[0];}
1444:     bs = PetscMax(1,bs);
1445:     if (isMatIS) { /* Must reduce indices by blocksize */
1446:       PetscInt l;

1448:       lsize = lsize/bs;
1449:       if (bs > 1) for (l = 0; l < lsize; ++l) ltogidx[l] = ltogidx[l*bs]/bs;
1450:       ISLocalToGlobalMappingCreate(PetscObjectComm((PetscObject)dm), bs, lsize, ltogidx, PETSC_OWN_POINTER, &ltog);
1451:     }
1452:     MatSetLocalToGlobalMapping(*J,ltog,ltog);
1453:     if (isMatIS) {
1454:       ISLocalToGlobalMappingDestroy(&ltog);
1455:     }
1456:     PetscCalloc4(localSize/bs, &dnz, localSize/bs, &onz, localSize/bs, &dnzu, localSize/bs, &onzu);
1457:     DMPlexPreallocateOperator(dm, bs, dnz, onz, dnzu, onzu, *J, fillMatrix);
1458:     PetscFree4(dnz, onz, dnzu, onzu);
1459:   }
1460:   MatSetDM(*J, dm);
1461:   return(0);
1462: }

1464: /*@
1465:   DMPlexGetSubdomainSection - Returns the section associated with the subdomain

1467:   Not collective

1469:   Input Parameter:
1470: . mesh - The DMPlex

1472:   Output Parameters:
1473: . subsection - The subdomain section

1475:   Level: developer

1477: .seealso:
1478: @*/
1479: PetscErrorCode DMPlexGetSubdomainSection(DM dm, PetscSection *subsection)
1480: {
1481:   DM_Plex       *mesh = (DM_Plex*) dm->data;

1486:   if (!mesh->subdomainSection) {
1487:     PetscSection section;
1488:     PetscSF      sf;

1490:     PetscSFCreate(PETSC_COMM_SELF,&sf);
1491:     DMGetLocalSection(dm,&section);
1492:     PetscSectionCreateGlobalSection(section,sf,PETSC_FALSE,PETSC_TRUE,&mesh->subdomainSection);
1493:     PetscSFDestroy(&sf);
1494:   }
1495:   *subsection = mesh->subdomainSection;
1496:   return(0);
1497: }

1499: /*@
1500:   DMPlexGetChart - Return the interval for all mesh points [pStart, pEnd)

1502:   Not collective

1504:   Input Parameter:
1505: . mesh - The DMPlex

1507:   Output Parameters:
1508: + pStart - The first mesh point
1509: - pEnd   - The upper bound for mesh points

1511:   Level: beginner

1513: .seealso: DMPlexCreate(), DMPlexSetChart()
1514: @*/
1515: PetscErrorCode DMPlexGetChart(DM dm, PetscInt *pStart, PetscInt *pEnd)
1516: {
1517:   DM_Plex       *mesh = (DM_Plex*) dm->data;

1522:   PetscSectionGetChart(mesh->coneSection, pStart, pEnd);
1523:   return(0);
1524: }

1526: /*@
1527:   DMPlexSetChart - Set the interval for all mesh points [pStart, pEnd)

1529:   Not collective

1531:   Input Parameters:
1532: + mesh - The DMPlex
1533: . pStart - The first mesh point
1534: - pEnd   - The upper bound for mesh points

1536:   Output Parameters:

1538:   Level: beginner

1540: .seealso: DMPlexCreate(), DMPlexGetChart()
1541: @*/
1542: PetscErrorCode DMPlexSetChart(DM dm, PetscInt pStart, PetscInt pEnd)
1543: {
1544:   DM_Plex       *mesh = (DM_Plex*) dm->data;

1549:   PetscSectionSetChart(mesh->coneSection, pStart, pEnd);
1550:   PetscSectionSetChart(mesh->supportSection, pStart, pEnd);
1551:   return(0);
1552: }

1554: /*@
1555:   DMPlexGetConeSize - Return the number of in-edges for this point in the DAG

1557:   Not collective

1559:   Input Parameters:
1560: + mesh - The DMPlex
1561: - p - The point, which must lie in the chart set with DMPlexSetChart()

1563:   Output Parameter:
1564: . size - The cone size for point p

1566:   Level: beginner

1568: .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexSetChart()
1569: @*/
1570: PetscErrorCode DMPlexGetConeSize(DM dm, PetscInt p, PetscInt *size)
1571: {
1572:   DM_Plex       *mesh = (DM_Plex*) dm->data;

1578:   PetscSectionGetDof(mesh->coneSection, p, size);
1579:   return(0);
1580: }

1582: /*@
1583:   DMPlexSetConeSize - Set the number of in-edges for this point in the DAG

1585:   Not collective

1587:   Input Parameters:
1588: + mesh - The DMPlex
1589: . p - The point, which must lie in the chart set with DMPlexSetChart()
1590: - size - The cone size for point p

1592:   Output Parameter:

1594:   Note:
1595:   This should be called after DMPlexSetChart().

1597:   Level: beginner

1599: .seealso: DMPlexCreate(), DMPlexGetConeSize(), DMPlexSetChart()
1600: @*/
1601: PetscErrorCode DMPlexSetConeSize(DM dm, PetscInt p, PetscInt size)
1602: {
1603:   DM_Plex       *mesh = (DM_Plex*) dm->data;

1608:   PetscSectionSetDof(mesh->coneSection, p, size);

1610:   mesh->maxConeSize = PetscMax(mesh->maxConeSize, size);
1611:   return(0);
1612: }

1614: /*@
1615:   DMPlexAddConeSize - Add the given number of in-edges to this point in the DAG

1617:   Not collective

1619:   Input Parameters:
1620: + mesh - The DMPlex
1621: . p - The point, which must lie in the chart set with DMPlexSetChart()
1622: - size - The additional cone size for point p

1624:   Output Parameter:

1626:   Note:
1627:   This should be called after DMPlexSetChart().

1629:   Level: beginner

1631: .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexGetConeSize(), DMPlexSetChart()
1632: @*/
1633: PetscErrorCode DMPlexAddConeSize(DM dm, PetscInt p, PetscInt size)
1634: {
1635:   DM_Plex       *mesh = (DM_Plex*) dm->data;
1636:   PetscInt       csize;

1641:   PetscSectionAddDof(mesh->coneSection, p, size);
1642:   PetscSectionGetDof(mesh->coneSection, p, &csize);

1644:   mesh->maxConeSize = PetscMax(mesh->maxConeSize, csize);
1645:   return(0);
1646: }

1648: /*@C
1649:   DMPlexGetCone - Return the points on the in-edges for this point in the DAG

1651:   Not collective

1653:   Input Parameters:
1654: + dm - The DMPlex
1655: - p - The point, which must lie in the chart set with DMPlexSetChart()

1657:   Output Parameter:
1658: . cone - An array of points which are on the in-edges for point p

1660:   Level: beginner

1662:   Fortran Notes:
1663:   Since it returns an array, this routine is only available in Fortran 90, and you must
1664:   include petsc.h90 in your code.
1665:   You must also call DMPlexRestoreCone() after you finish using the returned array.
1666:   DMPlexRestoreCone() is not needed/available in C.

1668: .seealso: DMPlexCreate(), DMPlexSetCone(), DMPlexGetConeTuple(), DMPlexSetChart()
1669: @*/
1670: PetscErrorCode DMPlexGetCone(DM dm, PetscInt p, const PetscInt *cone[])
1671: {
1672:   DM_Plex       *mesh = (DM_Plex*) dm->data;
1673:   PetscInt       off;

1679:   PetscSectionGetOffset(mesh->coneSection, p, &off);
1680:   *cone = &mesh->cones[off];
1681:   return(0);
1682: }

1684: /*@C
1685:   DMPlexGetConeTuple - Return the points on the in-edges of several points in the DAG

1687:   Not collective

1689:   Input Parameters:
1690: + dm - The DMPlex
1691: - p - The IS of points, which must lie in the chart set with DMPlexSetChart()

1693:   Output Parameter:
1694: + pConesSection - PetscSection describing the layout of pCones
1695: - pCones - An array of points which are on the in-edges for the point set p

1697:   Level: intermediate

1699: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexGetConeRecursive(), DMPlexSetChart()
1700: @*/
1701: PetscErrorCode DMPlexGetConeTuple(DM dm, IS p, PetscSection *pConesSection, IS *pCones)
1702: {
1703:   PetscSection        cs, newcs;
1704:   PetscInt            *cones;
1705:   PetscInt            *newarr=NULL;
1706:   PetscInt            n;
1707:   PetscErrorCode      ierr;

1710:   DMPlexGetCones(dm, &cones);
1711:   DMPlexGetConeSection(dm, &cs);
1712:   PetscSectionExtractDofsFromArray(cs, MPIU_INT, cones, p, &newcs, pCones ? ((void**)&newarr) : NULL);
1713:   if (pConesSection) *pConesSection = newcs;
1714:   if (pCones) {
1715:     PetscSectionGetStorageSize(newcs, &n);
1716:     ISCreateGeneral(PetscObjectComm((PetscObject)p), n, newarr, PETSC_OWN_POINTER, pCones);
1717:   }
1718:   return(0);
1719: }

1721: /*@
1722:   DMPlexGetConeRecursiveVertices - Expand each given point into its cone points and do that recursively until we end up just with vertices.

1724:   Not collective

1726:   Input Parameters:
1727: + dm - The DMPlex
1728: - points - The IS of points, which must lie in the chart set with DMPlexSetChart()

1730:   Output Parameter:
1731: . expandedPoints - An array of vertices recursively expanded from input points

1733:   Level: advanced

1735:   Notes:
1736:   Like DMPlexGetConeRecursive but returns only the 0-depth IS (i.e. vertices only) and no sections.
1737:   There is no corresponding Restore function, just call ISDestroy() on the returned IS to deallocate.

1739: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexGetConeTuple(), DMPlexGetConeRecursive(), DMPlexRestoreConeRecursive(), DMPlexGetDepth()
1740: @*/
1741: PetscErrorCode DMPlexGetConeRecursiveVertices(DM dm, IS points, IS *expandedPoints)
1742: {
1743:   IS                  *expandedPointsAll;
1744:   PetscInt            depth;
1745:   PetscErrorCode      ierr;

1751:   DMPlexGetConeRecursive(dm, points, &depth, &expandedPointsAll, NULL);
1752:   *expandedPoints = expandedPointsAll[0];
1753:   PetscObjectReference((PetscObject)expandedPointsAll[0]);
1754:   DMPlexRestoreConeRecursive(dm, points, &depth, &expandedPointsAll, NULL);
1755:   return(0);
1756: }

1758: /*@
1759:   DMPlexGetConeRecursive - Expand each given point into its cone points and do that recursively until we end up just with vertices (DAG points of depth 0, i.e. without cones).

1761:   Not collective

1763:   Input Parameters:
1764: + dm - The DMPlex
1765: - points - The IS of points, which must lie in the chart set with DMPlexSetChart()

1767:   Output Parameter:
1768: + depth - (optional) Size of the output arrays, equal to DMPlex depth, returned by DMPlexGetDepth()
1769: . expandedPoints - (optional) An array of index sets with recursively expanded cones
1770: - sections - (optional) An array of sections which describe mappings from points to their cone points

1772:   Level: advanced

1774:   Notes:
1775:   Like DMPlexGetConeTuple() but recursive.

1777:   Array expandedPoints has size equal to depth. Each expandedPoints[d] contains DAG points with maximum depth d, recursively cone-wise expanded from the input points.
1778:   For example, for d=0 it contains only vertices, for d=1 it can contain vertices and edges, etc.

1780:   Array section has size equal to depth.  Each PetscSection sections[d] realizes mapping from expandedPoints[d+1] (section points) to expandedPoints[d] (section dofs) as follows:
1781:   (1) DAG points in expandedPoints[d+1] with depth d+1 to their cone points in expandedPoints[d];
1782:   (2) DAG points in expandedPoints[d+1] with depth in [0,d] to the same points in expandedPoints[d].

1784: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexGetConeTuple(), DMPlexRestoreConeRecursive(), DMPlexGetConeRecursiveVertices(), DMPlexGetDepth()
1785: @*/
1786: PetscErrorCode DMPlexGetConeRecursive(DM dm, IS points, PetscInt *depth, IS *expandedPoints[], PetscSection *sections[])
1787: {
1788:   const PetscInt      *arr0=NULL, *cone=NULL;
1789:   PetscInt            *arr=NULL, *newarr=NULL;
1790:   PetscInt            d, depth_, i, n, newn, cn, co, start, end;
1791:   IS                  *expandedPoints_;
1792:   PetscSection        *sections_;
1793:   PetscErrorCode      ierr;

1801:   ISGetLocalSize(points, &n);
1802:   ISGetIndices(points, &arr0);
1803:   DMPlexGetDepth(dm, &depth_);
1804:   PetscCalloc1(depth_, &expandedPoints_);
1805:   PetscCalloc1(depth_, &sections_);
1806:   arr = (PetscInt*) arr0; /* this is ok because first generation of arr is not modified */
1807:   for (d=depth_-1; d>=0; d--) {
1808:     PetscSectionCreate(PETSC_COMM_SELF, &sections_[d]);
1809:     PetscSectionSetChart(sections_[d], 0, n);
1810:     for (i=0; i<n; i++) {
1811:       DMPlexGetDepthStratum(dm, d+1, &start, &end);
1812:       if (arr[i] >= start && arr[i] < end) {
1813:         DMPlexGetConeSize(dm, arr[i], &cn);
1814:         PetscSectionSetDof(sections_[d], i, cn);
1815:       } else {
1816:         PetscSectionSetDof(sections_[d], i, 1);
1817:       }
1818:     }
1819:     PetscSectionSetUp(sections_[d]);
1820:     PetscSectionGetStorageSize(sections_[d], &newn);
1821:     PetscMalloc1(newn, &newarr);
1822:     for (i=0; i<n; i++) {
1823:       PetscSectionGetDof(sections_[d], i, &cn);
1824:       PetscSectionGetOffset(sections_[d], i, &co);
1825:       if (cn > 1) {
1826:         DMPlexGetCone(dm, arr[i], &cone);
1827:         PetscMemcpy(&newarr[co], cone, cn*sizeof(PetscInt));
1828:       } else {
1829:         newarr[co] = arr[i];
1830:       }
1831:     }
1832:     ISCreateGeneral(PETSC_COMM_SELF, newn, newarr, PETSC_OWN_POINTER, &expandedPoints_[d]);
1833:     arr = newarr;
1834:     n = newn;
1835:   }
1836:   *depth = depth_;
1837:   if (expandedPoints) *expandedPoints = expandedPoints_;
1838:   else {
1839:     for (d=0; d<depth_; d++) {ISDestroy(&expandedPoints_[d]);}
1840:     PetscFree(expandedPoints_);
1841:   }
1842:   if (sections) *sections = sections_;
1843:   else {
1844:     for (d=0; d<depth_; d++) {PetscSectionDestroy(&sections_[d]);}
1845:     PetscFree(sections_);
1846:   }
1847:   return(0);
1848: }

1850: /*@
1851:   DMPlexRestoreConeRecursive - Deallocates arrays created by DMPlexGetConeRecursive

1853:   Not collective

1855:   Input Parameters:
1856: + dm - The DMPlex
1857: - points - The IS of points, which must lie in the chart set with DMPlexSetChart()

1859:   Output Parameter:
1860: + depth - (optional) Size of the output arrays, equal to DMPlex depth, returned by DMPlexGetDepth()
1861: . expandedPoints - (optional) An array of recursively expanded cones
1862: - sections - (optional) An array of sections which describe mappings from points to their cone points

1864:   Level: advanced

1866:   Notes:
1867:   See DMPlexGetConeRecursive() for details.

1869: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexGetConeTuple(), DMPlexGetConeRecursive(), DMPlexGetConeRecursiveVertices(), DMPlexGetDepth()
1870: @*/
1871: PetscErrorCode DMPlexRestoreConeRecursive(DM dm, IS points, PetscInt *depth, IS *expandedPoints[], PetscSection *sections[])
1872: {
1873:   PetscInt            d, depth_;
1874:   PetscErrorCode      ierr;

1877:   DMPlexGetDepth(dm, &depth_);
1878:   if (depth && *depth != depth_) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "depth changed since last call to DMPlexGetConeRecursive");
1879:   if (depth) *depth = 0;
1880:   if (expandedPoints) {
1881:     for (d=0; d<depth_; d++) {ISDestroy(&((*expandedPoints)[d]));}
1882:     PetscFree(*expandedPoints);
1883:   }
1884:   if (sections)  {
1885:     for (d=0; d<depth_; d++) {PetscSectionDestroy(&((*sections)[d]));}
1886:     PetscFree(*sections);
1887:   }
1888:   return(0);
1889: }

1891: /*@
1892:   DMPlexSetCone - Set the points on the in-edges for this point in the DAG; that is these are the points that cover the specific point

1894:   Not collective

1896:   Input Parameters:
1897: + mesh - The DMPlex
1898: . p - The point, which must lie in the chart set with DMPlexSetChart()
1899: - cone - An array of points which are on the in-edges for point p

1901:   Output Parameter:

1903:   Note:
1904:   This should be called after all calls to DMPlexSetConeSize() and DMSetUp().

1906:   Developer Note: Why not call this DMPlexSetCover()

1908:   Level: beginner

1910: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp(), DMPlexSetSupport(), DMPlexSetSupportSize()
1911: @*/
1912: PetscErrorCode DMPlexSetCone(DM dm, PetscInt p, const PetscInt cone[])
1913: {
1914:   DM_Plex       *mesh = (DM_Plex*) dm->data;
1915:   PetscInt       pStart, pEnd;
1916:   PetscInt       dof, off, c;

1921:   PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);
1922:   PetscSectionGetDof(mesh->coneSection, p, &dof);
1924:   PetscSectionGetOffset(mesh->coneSection, p, &off);
1925:   if ((p < pStart) || (p >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd);
1926:   for (c = 0; c < dof; ++c) {
1927:     if ((cone[c] < pStart) || (cone[c] >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cone point %D is not in the valid range [%D, %D)", cone[c], pStart, pEnd);
1928:     mesh->cones[off+c] = cone[c];
1929:   }
1930:   return(0);
1931: }

1933: /*@C
1934:   DMPlexGetConeOrientation - Return the orientations on the in-edges for this point in the DAG

1936:   Not collective

1938:   Input Parameters:
1939: + mesh - The DMPlex
1940: - p - The point, which must lie in the chart set with DMPlexSetChart()

1942:   Output Parameter:
1943: . coneOrientation - An array of orientations which are on the in-edges for point p. An orientation is an
1944:                     integer giving the prescription for cone traversal. If it is negative, the cone is
1945:                     traversed in the opposite direction. Its value 'o', or if negative '-(o+1)', gives
1946:                     the index of the cone point on which to start.

1948:   Level: beginner

1950:   Fortran Notes:
1951:   Since it returns an array, this routine is only available in Fortran 90, and you must
1952:   include petsc.h90 in your code.
1953:   You must also call DMPlexRestoreConeOrientation() after you finish using the returned array.
1954:   DMPlexRestoreConeOrientation() is not needed/available in C.

1956: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetCone(), DMPlexSetChart()
1957: @*/
1958: PetscErrorCode DMPlexGetConeOrientation(DM dm, PetscInt p, const PetscInt *coneOrientation[])
1959: {
1960:   DM_Plex       *mesh = (DM_Plex*) dm->data;
1961:   PetscInt       off;

1966: #if defined(PETSC_USE_DEBUG)
1967:   {
1968:     PetscInt dof;
1969:     PetscSectionGetDof(mesh->coneSection, p, &dof);
1971:   }
1972: #endif
1973:   PetscSectionGetOffset(mesh->coneSection, p, &off);

1975:   *coneOrientation = &mesh->coneOrientations[off];
1976:   return(0);
1977: }

1979: /*@
1980:   DMPlexSetConeOrientation - Set the orientations on the in-edges for this point in the DAG

1982:   Not collective

1984:   Input Parameters:
1985: + mesh - The DMPlex
1986: . p - The point, which must lie in the chart set with DMPlexSetChart()
1987: - coneOrientation - An array of orientations which are on the in-edges for point p. An orientation is an
1988:                     integer giving the prescription for cone traversal. If it is negative, the cone is
1989:                     traversed in the opposite direction. Its value 'o', or if negative '-(o+1)', gives
1990:                     the index of the cone point on which to start.

1992:   Output Parameter:

1994:   Note:
1995:   This should be called after all calls to DMPlexSetConeSize() and DMSetUp().

1997:   Level: beginner

1999: .seealso: DMPlexCreate(), DMPlexGetConeOrientation(), DMPlexSetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp()
2000: @*/
2001: PetscErrorCode DMPlexSetConeOrientation(DM dm, PetscInt p, const PetscInt coneOrientation[])
2002: {
2003:   DM_Plex       *mesh = (DM_Plex*) dm->data;
2004:   PetscInt       pStart, pEnd;
2005:   PetscInt       dof, off, c;

2010:   PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);
2011:   PetscSectionGetDof(mesh->coneSection, p, &dof);
2013:   PetscSectionGetOffset(mesh->coneSection, p, &off);
2014:   if ((p < pStart) || (p >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd);
2015:   for (c = 0; c < dof; ++c) {
2016:     PetscInt cdof, o = coneOrientation[c];

2018:     PetscSectionGetDof(mesh->coneSection, mesh->cones[off+c], &cdof);
2019:     if (o && ((o < -(cdof+1)) || (o >= cdof))) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cone orientation %D is not in the valid range [%D. %D)", o, -(cdof+1), cdof);
2020:     mesh->coneOrientations[off+c] = o;
2021:   }
2022:   return(0);
2023: }

2025: /*@
2026:   DMPlexInsertCone - Insert a point into the in-edges for the point p in the DAG

2028:   Not collective

2030:   Input Parameters:
2031: + mesh - The DMPlex
2032: . p - The point, which must lie in the chart set with DMPlexSetChart()
2033: . conePos - The local index in the cone where the point should be put
2034: - conePoint - The mesh point to insert

2036:   Level: beginner

2038: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp()
2039: @*/
2040: PetscErrorCode DMPlexInsertCone(DM dm, PetscInt p, PetscInt conePos, PetscInt conePoint)
2041: {
2042:   DM_Plex       *mesh = (DM_Plex*) dm->data;
2043:   PetscInt       pStart, pEnd;
2044:   PetscInt       dof, off;

2049:   PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);
2050:   if ((p < pStart) || (p >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd);
2051:   if ((conePoint < pStart) || (conePoint >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cone point %D is not in the valid range [%D, %D)", conePoint, pStart, pEnd);
2052:   PetscSectionGetDof(mesh->coneSection, p, &dof);
2053:   PetscSectionGetOffset(mesh->coneSection, p, &off);
2054:   if ((conePos < 0) || (conePos >= dof)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cone position %D of point %D is not in the valid range [0, %D)", conePos, p, dof);
2055:   mesh->cones[off+conePos] = conePoint;
2056:   return(0);
2057: }

2059: /*@
2060:   DMPlexInsertConeOrientation - Insert a point orientation for the in-edge for the point p in the DAG

2062:   Not collective

2064:   Input Parameters:
2065: + mesh - The DMPlex
2066: . p - The point, which must lie in the chart set with DMPlexSetChart()
2067: . conePos - The local index in the cone where the point should be put
2068: - coneOrientation - The point orientation to insert

2070:   Level: beginner

2072: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp()
2073: @*/
2074: PetscErrorCode DMPlexInsertConeOrientation(DM dm, PetscInt p, PetscInt conePos, PetscInt coneOrientation)
2075: {
2076:   DM_Plex       *mesh = (DM_Plex*) dm->data;
2077:   PetscInt       pStart, pEnd;
2078:   PetscInt       dof, off;

2083:   PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);
2084:   if ((p < pStart) || (p >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd);
2085:   PetscSectionGetDof(mesh->coneSection, p, &dof);
2086:   PetscSectionGetOffset(mesh->coneSection, p, &off);
2087:   if ((conePos < 0) || (conePos >= dof)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cone position %D of point %D is not in the valid range [0, %D)", conePos, p, dof);
2088:   mesh->coneOrientations[off+conePos] = coneOrientation;
2089:   return(0);
2090: }

2092: /*@
2093:   DMPlexGetSupportSize - Return the number of out-edges for this point in the DAG

2095:   Not collective

2097:   Input Parameters:
2098: + mesh - The DMPlex
2099: - p - The point, which must lie in the chart set with DMPlexSetChart()

2101:   Output Parameter:
2102: . size - The support size for point p

2104:   Level: beginner

2106: .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexSetChart(), DMPlexGetConeSize()
2107: @*/
2108: PetscErrorCode DMPlexGetSupportSize(DM dm, PetscInt p, PetscInt *size)
2109: {
2110:   DM_Plex       *mesh = (DM_Plex*) dm->data;

2116:   PetscSectionGetDof(mesh->supportSection, p, size);
2117:   return(0);
2118: }

2120: /*@
2121:   DMPlexSetSupportSize - Set the number of out-edges for this point in the DAG

2123:   Not collective

2125:   Input Parameters:
2126: + mesh - The DMPlex
2127: . p - The point, which must lie in the chart set with DMPlexSetChart()
2128: - size - The support size for point p

2130:   Output Parameter:

2132:   Note:
2133:   This should be called after DMPlexSetChart().

2135:   Level: beginner

2137: .seealso: DMPlexCreate(), DMPlexGetSupportSize(), DMPlexSetChart()
2138: @*/
2139: PetscErrorCode DMPlexSetSupportSize(DM dm, PetscInt p, PetscInt size)
2140: {
2141:   DM_Plex       *mesh = (DM_Plex*) dm->data;

2146:   PetscSectionSetDof(mesh->supportSection, p, size);

2148:   mesh->maxSupportSize = PetscMax(mesh->maxSupportSize, size);
2149:   return(0);
2150: }

2152: /*@C
2153:   DMPlexGetSupport - Return the points on the out-edges for this point in the DAG

2155:   Not collective

2157:   Input Parameters:
2158: + mesh - The DMPlex
2159: - p - The point, which must lie in the chart set with DMPlexSetChart()

2161:   Output Parameter:
2162: . support - An array of points which are on the out-edges for point p

2164:   Level: beginner

2166:   Fortran Notes:
2167:   Since it returns an array, this routine is only available in Fortran 90, and you must
2168:   include petsc.h90 in your code.
2169:   You must also call DMPlexRestoreSupport() after you finish using the returned array.
2170:   DMPlexRestoreSupport() is not needed/available in C.

2172: .seealso: DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone()
2173: @*/
2174: PetscErrorCode DMPlexGetSupport(DM dm, PetscInt p, const PetscInt *support[])
2175: {
2176:   DM_Plex       *mesh = (DM_Plex*) dm->data;
2177:   PetscInt       off;

2183:   PetscSectionGetOffset(mesh->supportSection, p, &off);
2184:   *support = &mesh->supports[off];
2185:   return(0);
2186: }

2188: /*@
2189:   DMPlexSetSupport - Set the points on the out-edges for this point in the DAG, that is the list of points that this point covers

2191:   Not collective

2193:   Input Parameters:
2194: + mesh - The DMPlex
2195: . p - The point, which must lie in the chart set with DMPlexSetChart()
2196: - support - An array of points which are on the out-edges for point p

2198:   Output Parameter:

2200:   Note:
2201:   This should be called after all calls to DMPlexSetSupportSize() and DMSetUp().

2203:   Level: beginner

2205: .seealso: DMPlexSetCone(), DMPlexSetConeSize(), DMPlexCreate(), DMPlexGetSupport(), DMPlexSetChart(), DMPlexSetSupportSize(), DMSetUp()
2206: @*/
2207: PetscErrorCode DMPlexSetSupport(DM dm, PetscInt p, const PetscInt support[])
2208: {
2209:   DM_Plex       *mesh = (DM_Plex*) dm->data;
2210:   PetscInt       pStart, pEnd;
2211:   PetscInt       dof, off, c;

2216:   PetscSectionGetChart(mesh->supportSection, &pStart, &pEnd);
2217:   PetscSectionGetDof(mesh->supportSection, p, &dof);
2219:   PetscSectionGetOffset(mesh->supportSection, p, &off);
2220:   if ((p < pStart) || (p >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd);
2221:   for (c = 0; c < dof; ++c) {
2222:     if ((support[c] < pStart) || (support[c] >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Support point %D is not in the valid range [%D, %D)", support[c], pStart, pEnd);
2223:     mesh->supports[off+c] = support[c];
2224:   }
2225:   return(0);
2226: }

2228: /*@
2229:   DMPlexInsertSupport - Insert a point into the out-edges for the point p in the DAG

2231:   Not collective

2233:   Input Parameters:
2234: + mesh - The DMPlex
2235: . p - The point, which must lie in the chart set with DMPlexSetChart()
2236: . supportPos - The local index in the cone where the point should be put
2237: - supportPoint - The mesh point to insert

2239:   Level: beginner

2241: .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp()
2242: @*/
2243: PetscErrorCode DMPlexInsertSupport(DM dm, PetscInt p, PetscInt supportPos, PetscInt supportPoint)
2244: {
2245:   DM_Plex       *mesh = (DM_Plex*) dm->data;
2246:   PetscInt       pStart, pEnd;
2247:   PetscInt       dof, off;

2252:   PetscSectionGetChart(mesh->supportSection, &pStart, &pEnd);
2253:   PetscSectionGetDof(mesh->supportSection, p, &dof);
2254:   PetscSectionGetOffset(mesh->supportSection, p, &off);
2255:   if ((p < pStart) || (p >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd);
2256:   if ((supportPoint < pStart) || (supportPoint >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Support point %D is not in the valid range [%D, %D)", supportPoint, pStart, pEnd);
2257:   if (supportPos >= dof) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Support position %D of point %D is not in the valid range [0, %D)", supportPos, p, dof);
2258:   mesh->supports[off+supportPos] = supportPoint;
2259:   return(0);
2260: }

2262: /*@C
2263:   DMPlexGetTransitiveClosure - Return the points on the transitive closure of the in-edges or out-edges for this point in the DAG

2265:   Not collective

2267:   Input Parameters:
2268: + mesh - The DMPlex
2269: . p - The point, which must lie in the chart set with DMPlexSetChart()
2270: . useCone - PETSC_TRUE for in-edges,  otherwise use out-edges
2271: - points - If points is NULL on input, internal storage will be returned, otherwise the provided array is used

2273:   Output Parameters:
2274: + numPoints - The number of points in the closure, so points[] is of size 2*numPoints
2275: - points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...]

2277:   Note:
2278:   If using internal storage (points is NULL on input), each call overwrites the last output.

2280:   Fortran Notes:
2281:   Since it returns an array, this routine is only available in Fortran 90, and you must
2282:   include petsc.h90 in your code.

2284:   The numPoints argument is not present in the Fortran 90 binding since it is internal to the array.

2286:   Level: beginner

2288: .seealso: DMPlexRestoreTransitiveClosure(), DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone()
2289: @*/
2290: PetscErrorCode DMPlexGetTransitiveClosure(DM dm, PetscInt p, PetscBool useCone, PetscInt *numPoints, PetscInt *points[])
2291: {
2292:   DM_Plex        *mesh = (DM_Plex*) dm->data;
2293:   PetscInt       *closure, *fifo;
2294:   const PetscInt *tmp = NULL, *tmpO = NULL;
2295:   PetscInt        tmpSize, t;
2296:   PetscInt        depth       = 0, maxSize;
2297:   PetscInt        closureSize = 2, fifoSize = 0, fifoStart = 0;
2298:   PetscErrorCode  ierr;

2302:   DMPlexGetDepth(dm, &depth);
2303:   /* This is only 1-level */
2304:   if (useCone) {
2305:     DMPlexGetConeSize(dm, p, &tmpSize);
2306:     DMPlexGetCone(dm, p, &tmp);
2307:     DMPlexGetConeOrientation(dm, p, &tmpO);
2308:   } else {
2309:     DMPlexGetSupportSize(dm, p, &tmpSize);
2310:     DMPlexGetSupport(dm, p, &tmp);
2311:   }
2312:   if (depth == 1) {
2313:     if (*points) {
2314:       closure = *points;
2315:     } else {
2316:       maxSize = 2*(PetscMax(mesh->maxConeSize, mesh->maxSupportSize)+1);
2317:       DMGetWorkArray(dm, maxSize, MPIU_INT, &closure);
2318:     }
2319:     closure[0] = p; closure[1] = 0;
2320:     for (t = 0; t < tmpSize; ++t, closureSize += 2) {
2321:       closure[closureSize]   = tmp[t];
2322:       closure[closureSize+1] = tmpO ? tmpO[t] : 0;
2323:     }
2324:     if (numPoints) *numPoints = closureSize/2;
2325:     if (points)    *points    = closure;
2326:     return(0);
2327:   }
2328:   {
2329:     PetscInt c, coneSeries, s,supportSeries;

2331:     c = mesh->maxConeSize;
2332:     coneSeries = (c > 1) ? ((PetscPowInt(c,depth+1)-1)/(c-1)) : depth+1;
2333:     s = mesh->maxSupportSize;
2334:     supportSeries = (s > 1) ? ((PetscPowInt(s,depth+1)-1)/(s-1)) : depth+1;
2335:     maxSize = 2*PetscMax(coneSeries,supportSeries);
2336:   }
2337:   DMGetWorkArray(dm, maxSize, MPIU_INT, &fifo);
2338:   if (*points) {
2339:     closure = *points;
2340:   } else {
2341:     DMGetWorkArray(dm, maxSize, MPIU_INT, &closure);
2342:   }
2343:   closure[0] = p; closure[1] = 0;
2344:   for (t = 0; t < tmpSize; ++t, closureSize += 2, fifoSize += 2) {
2345:     const PetscInt cp = tmp[t];
2346:     const PetscInt co = tmpO ? tmpO[t] : 0;

2348:     closure[closureSize]   = cp;
2349:     closure[closureSize+1] = co;
2350:     fifo[fifoSize]         = cp;
2351:     fifo[fifoSize+1]       = co;
2352:   }
2353:   /* Should kick out early when depth is reached, rather than checking all vertices for empty cones */
2354:   while (fifoSize - fifoStart) {
2355:     const PetscInt q   = fifo[fifoStart];
2356:     const PetscInt o   = fifo[fifoStart+1];
2357:     const PetscInt rev = o >= 0 ? 0 : 1;
2358:     const PetscInt off = rev ? -(o+1) : o;

2360:     if (useCone) {
2361:       DMPlexGetConeSize(dm, q, &tmpSize);
2362:       DMPlexGetCone(dm, q, &tmp);
2363:       DMPlexGetConeOrientation(dm, q, &tmpO);
2364:     } else {
2365:       DMPlexGetSupportSize(dm, q, &tmpSize);
2366:       DMPlexGetSupport(dm, q, &tmp);
2367:       tmpO = NULL;
2368:     }
2369:     for (t = 0; t < tmpSize; ++t) {
2370:       const PetscInt i  = ((rev ? tmpSize-t : t) + off)%tmpSize;
2371:       const PetscInt cp = tmp[i];
2372:       /* Must propogate orientation: When we reverse orientation, we both reverse the direction of iteration and start at the other end of the chain. */
2373:       /* HACK: It is worse to get the size here, than to change the interpretation of -(*+1)
2374:        const PetscInt co = tmpO ? (rev ? -(tmpO[i]+1) : tmpO[i]) : 0; */
2375:       PetscInt       co = tmpO ? tmpO[i] : 0;
2376:       PetscInt       c;

2378:       if (rev) {
2379:         PetscInt childSize, coff;
2380:         DMPlexGetConeSize(dm, cp, &childSize);
2381:         coff = tmpO[i] < 0 ? -(tmpO[i]+1) : tmpO[i];
2382:         co   = childSize ? -(((coff+childSize-1)%childSize)+1) : 0;
2383:       }
2384:       /* Check for duplicate */
2385:       for (c = 0; c < closureSize; c += 2) {
2386:         if (closure[c] == cp) break;
2387:       }
2388:       if (c == closureSize) {
2389:         closure[closureSize]   = cp;
2390:         closure[closureSize+1] = co;
2391:         fifo[fifoSize]         = cp;
2392:         fifo[fifoSize+1]       = co;
2393:         closureSize           += 2;
2394:         fifoSize              += 2;
2395:       }
2396:     }
2397:     fifoStart += 2;
2398:   }
2399:   if (numPoints) *numPoints = closureSize/2;
2400:   if (points)    *points    = closure;
2401:   DMRestoreWorkArray(dm, maxSize, MPIU_INT, &fifo);
2402:   return(0);
2403: }

2405: /*@C
2406:   DMPlexGetTransitiveClosure_Internal - Return the points on the transitive closure of the in-edges or out-edges for this point in the DAG with a specified initial orientation

2408:   Not collective

2410:   Input Parameters:
2411: + mesh - The DMPlex
2412: . p - The point, which must lie in the chart set with DMPlexSetChart()
2413: . orientation - The orientation of the point
2414: . useCone - PETSC_TRUE for in-edges,  otherwise use out-edges
2415: - points - If points is NULL on input, internal storage will be returned, otherwise the provided array is used

2417:   Output Parameters:
2418: + numPoints - The number of points in the closure, so points[] is of size 2*numPoints
2419: - points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...]

2421:   Note:
2422:   If using internal storage (points is NULL on input), each call overwrites the last output.

2424:   Fortran Notes:
2425:   Since it returns an array, this routine is only available in Fortran 90, and you must
2426:   include petsc.h90 in your code.

2428:   The numPoints argument is not present in the Fortran 90 binding since it is internal to the array.

2430:   Level: beginner

2432: .seealso: DMPlexRestoreTransitiveClosure(), DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone()
2433: @*/
2434: PetscErrorCode DMPlexGetTransitiveClosure_Internal(DM dm, PetscInt p, PetscInt ornt, PetscBool useCone, PetscInt *numPoints, PetscInt *points[])
2435: {
2436:   DM_Plex        *mesh = (DM_Plex*) dm->data;
2437:   PetscInt       *closure, *fifo;
2438:   const PetscInt *tmp = NULL, *tmpO = NULL;
2439:   PetscInt        tmpSize, t;
2440:   PetscInt        depth       = 0, maxSize;
2441:   PetscInt        closureSize = 2, fifoSize = 0, fifoStart = 0;
2442:   PetscErrorCode  ierr;

2446:   DMPlexGetDepth(dm, &depth);
2447:   /* This is only 1-level */
2448:   if (useCone) {
2449:     DMPlexGetConeSize(dm, p, &tmpSize);
2450:     DMPlexGetCone(dm, p, &tmp);
2451:     DMPlexGetConeOrientation(dm, p, &tmpO);
2452:   } else {
2453:     DMPlexGetSupportSize(dm, p, &tmpSize);
2454:     DMPlexGetSupport(dm, p, &tmp);
2455:   }
2456:   if (depth == 1) {
2457:     if (*points) {
2458:       closure = *points;
2459:     } else {
2460:       maxSize = 2*(PetscMax(mesh->maxConeSize, mesh->maxSupportSize)+1);
2461:       DMGetWorkArray(dm, maxSize, MPIU_INT, &closure);
2462:     }
2463:     closure[0] = p; closure[1] = ornt;
2464:     for (t = 0; t < tmpSize; ++t, closureSize += 2) {
2465:       const PetscInt i = ornt >= 0 ? (t+ornt)%tmpSize : (-(ornt+1) + tmpSize-t)%tmpSize;
2466:       closure[closureSize]   = tmp[i];
2467:       closure[closureSize+1] = tmpO ? tmpO[i] : 0;
2468:     }
2469:     if (numPoints) *numPoints = closureSize/2;
2470:     if (points)    *points    = closure;
2471:     return(0);
2472:   }
2473:   {
2474:     PetscInt c, coneSeries, s,supportSeries;

2476:     c = mesh->maxConeSize;
2477:     coneSeries = (c > 1) ? ((PetscPowInt(c,depth+1)-1)/(c-1)) : depth+1;
2478:     s = mesh->maxSupportSize;
2479:     supportSeries = (s > 1) ? ((PetscPowInt(s,depth+1)-1)/(s-1)) : depth+1;
2480:     maxSize = 2*PetscMax(coneSeries,supportSeries);
2481:   }
2482:   DMGetWorkArray(dm, maxSize, MPIU_INT, &fifo);
2483:   if (*points) {
2484:     closure = *points;
2485:   } else {
2486:     DMGetWorkArray(dm, maxSize, MPIU_INT, &closure);
2487:   }
2488:   closure[0] = p; closure[1] = ornt;
2489:   for (t = 0; t < tmpSize; ++t, closureSize += 2, fifoSize += 2) {
2490:     const PetscInt i  = ornt >= 0 ? (t+ornt)%tmpSize : (-(ornt+1) + tmpSize-t)%tmpSize;
2491:     const PetscInt cp = tmp[i];
2492:     PetscInt       co = tmpO ? tmpO[i] : 0;

2494:     if (ornt < 0) {
2495:       PetscInt childSize, coff;
2496:       DMPlexGetConeSize(dm, cp, &childSize);
2497:       coff = co < 0 ? -(tmpO[i]+1) : tmpO[i];
2498:       co   = childSize ? -(((coff+childSize-1)%childSize)+1) : 0;
2499:     }
2500:     closure[closureSize]   = cp;
2501:     closure[closureSize+1] = co;
2502:     fifo[fifoSize]         = cp;
2503:     fifo[fifoSize+1]       = co;
2504:   }
2505:   /* Should kick out early when depth is reached, rather than checking all vertices for empty cones */
2506:   while (fifoSize - fifoStart) {
2507:     const PetscInt q   = fifo[fifoStart];
2508:     const PetscInt o   = fifo[fifoStart+1];
2509:     const PetscInt rev = o >= 0 ? 0 : 1;
2510:     const PetscInt off = rev ? -(o+1) : o;

2512:     if (useCone) {
2513:       DMPlexGetConeSize(dm, q, &tmpSize);
2514:       DMPlexGetCone(dm, q, &tmp);
2515:       DMPlexGetConeOrientation(dm, q, &tmpO);
2516:     } else {
2517:       DMPlexGetSupportSize(dm, q, &tmpSize);
2518:       DMPlexGetSupport(dm, q, &tmp);
2519:       tmpO = NULL;
2520:     }
2521:     for (t = 0; t < tmpSize; ++t) {
2522:       const PetscInt i  = ((rev ? tmpSize-t : t) + off)%tmpSize;
2523:       const PetscInt cp = tmp[i];
2524:       /* Must propogate orientation: When we reverse orientation, we both reverse the direction of iteration and start at the other end of the chain. */
2525:       /* HACK: It is worse to get the size here, than to change the interpretation of -(*+1)
2526:        const PetscInt co = tmpO ? (rev ? -(tmpO[i]+1) : tmpO[i]) : 0; */
2527:       PetscInt       co = tmpO ? tmpO[i] : 0;
2528:       PetscInt       c;

2530:       if (rev) {
2531:         PetscInt childSize, coff;
2532:         DMPlexGetConeSize(dm, cp, &childSize);
2533:         coff = tmpO[i] < 0 ? -(tmpO[i]+1) : tmpO[i];
2534:         co   = childSize ? -(((coff+childSize-1)%childSize)+1) : 0;
2535:       }
2536:       /* Check for duplicate */
2537:       for (c = 0; c < closureSize; c += 2) {
2538:         if (closure[c] == cp) break;
2539:       }
2540:       if (c == closureSize) {
2541:         closure[closureSize]   = cp;
2542:         closure[closureSize+1] = co;
2543:         fifo[fifoSize]         = cp;
2544:         fifo[fifoSize+1]       = co;
2545:         closureSize           += 2;
2546:         fifoSize              += 2;
2547:       }
2548:     }
2549:     fifoStart += 2;
2550:   }
2551:   if (numPoints) *numPoints = closureSize/2;
2552:   if (points)    *points    = closure;
2553:   DMRestoreWorkArray(dm, maxSize, MPIU_INT, &fifo);
2554:   return(0);
2555: }

2557: /*@C
2558:   DMPlexRestoreTransitiveClosure - Restore the array of points on the transitive closure of the in-edges or out-edges for this point in the DAG

2560:   Not collective

2562:   Input Parameters:
2563: + mesh - The DMPlex
2564: . p - The point, which must lie in the chart set with DMPlexSetChart()
2565: . useCone - PETSC_TRUE for in-edges,  otherwise use out-edges
2566: . numPoints - The number of points in the closure, so points[] is of size 2*numPoints, zeroed on exit
2567: - points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...], zeroed on exit

2569:   Note:
2570:   If not using internal storage (points is not NULL on input), this call is unnecessary

2572:   Fortran Notes:
2573:   Since it returns an array, this routine is only available in Fortran 90, and you must
2574:   include petsc.h90 in your code.

2576:   The numPoints argument is not present in the Fortran 90 binding since it is internal to the array.

2578:   Level: beginner

2580: .seealso: DMPlexGetTransitiveClosure(), DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone()
2581: @*/
2582: PetscErrorCode DMPlexRestoreTransitiveClosure(DM dm, PetscInt p, PetscBool useCone, PetscInt *numPoints, PetscInt *points[])
2583: {

2590:   DMRestoreWorkArray(dm, 0, MPIU_INT, points);
2591:   if (numPoints) *numPoints = 0;
2592:   return(0);
2593: }

2595: /*@
2596:   DMPlexGetMaxSizes - Return the maximum number of in-edges (cone) and out-edges (support) for any point in the DAG

2598:   Not collective

2600:   Input Parameter:
2601: . mesh - The DMPlex

2603:   Output Parameters:
2604: + maxConeSize - The maximum number of in-edges
2605: - maxSupportSize - The maximum number of out-edges

2607:   Level: beginner

2609: .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexSetChart()
2610: @*/
2611: PetscErrorCode DMPlexGetMaxSizes(DM dm, PetscInt *maxConeSize, PetscInt *maxSupportSize)
2612: {
2613:   DM_Plex *mesh = (DM_Plex*) dm->data;

2617:   if (maxConeSize)    *maxConeSize    = mesh->maxConeSize;
2618:   if (maxSupportSize) *maxSupportSize = mesh->maxSupportSize;
2619:   return(0);
2620: }

2622: PetscErrorCode DMSetUp_Plex(DM dm)
2623: {
2624:   DM_Plex       *mesh = (DM_Plex*) dm->data;
2625:   PetscInt       size;

2630:   PetscSectionSetUp(mesh->coneSection);
2631:   PetscSectionGetStorageSize(mesh->coneSection, &size);
2632:   PetscMalloc1(size, &mesh->cones);
2633:   PetscCalloc1(size, &mesh->coneOrientations);
2634:   if (mesh->maxSupportSize) {
2635:     PetscSectionSetUp(mesh->supportSection);
2636:     PetscSectionGetStorageSize(mesh->supportSection, &size);
2637:     PetscMalloc1(size, &mesh->supports);
2638:   }
2639:   return(0);
2640: }

2642: PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm)
2643: {

2647:   if (subdm) {DMClone(dm, subdm);}
2648:   DMCreateSectionSubDM(dm, numFields, fields, is, subdm);
2649:   if (subdm) {(*subdm)->useNatural = dm->useNatural;}
2650:   if (dm->useNatural && dm->sfMigration) {
2651:     PetscSF        sfMigrationInv,sfNatural;
2652:     PetscSection   section, sectionSeq;

2654:     (*subdm)->sfMigration = dm->sfMigration;
2655:     PetscObjectReference((PetscObject) dm->sfMigration);
2656:     DMGetLocalSection((*subdm), &section);
2657:     PetscSFCreateInverseSF((*subdm)->sfMigration, &sfMigrationInv);
2658:     PetscSectionCreate(PetscObjectComm((PetscObject) (*subdm)), &sectionSeq);
2659:     PetscSFDistributeSection(sfMigrationInv, section, NULL, sectionSeq);

2661:     DMPlexCreateGlobalToNaturalSF(*subdm, sectionSeq, (*subdm)->sfMigration, &sfNatural);
2662:     (*subdm)->sfNatural = sfNatural;
2663:     PetscSectionDestroy(&sectionSeq);
2664:     PetscSFDestroy(&sfMigrationInv);
2665:   }
2666:   return(0);
2667: }

2669: PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm)
2670: {
2672:   PetscInt       i = 0;

2675:   DMClone(dms[0], superdm);
2676:   DMCreateSectionSuperDM(dms, len, is, superdm);
2677:   (*superdm)->useNatural = PETSC_FALSE;
2678:   for (i = 0; i < len; i++){
2679:     if (dms[i]->useNatural && dms[i]->sfMigration) {
2680:       PetscSF        sfMigrationInv,sfNatural;
2681:       PetscSection   section, sectionSeq;

2683:       (*superdm)->sfMigration = dms[i]->sfMigration;
2684:       PetscObjectReference((PetscObject) dms[i]->sfMigration);
2685:       (*superdm)->useNatural = PETSC_TRUE;
2686:       DMGetLocalSection((*superdm), &section);
2687:       PetscSFCreateInverseSF((*superdm)->sfMigration, &sfMigrationInv);
2688:       PetscSectionCreate(PetscObjectComm((PetscObject) (*superdm)), &sectionSeq);
2689:       PetscSFDistributeSection(sfMigrationInv, section, NULL, sectionSeq);

2691:       DMPlexCreateGlobalToNaturalSF(*superdm, sectionSeq, (*superdm)->sfMigration, &sfNatural);
2692:       (*superdm)->sfNatural = sfNatural;
2693:       PetscSectionDestroy(&sectionSeq);
2694:       PetscSFDestroy(&sfMigrationInv);
2695:       break;
2696:     }
2697:   }
2698:   return(0);
2699: }

2701: /*@
2702:   DMPlexSymmetrize - Create support (out-edge) information from cone (in-edge) information

2704:   Not collective

2706:   Input Parameter:
2707: . mesh - The DMPlex

2709:   Output Parameter:

2711:   Note:
2712:   This should be called after all calls to DMPlexSetCone()

2714:   Level: beginner

2716: .seealso: DMPlexCreate(), DMPlexSetChart(), DMPlexSetConeSize(), DMPlexSetCone()
2717: @*/
2718: PetscErrorCode DMPlexSymmetrize(DM dm)
2719: {
2720:   DM_Plex       *mesh = (DM_Plex*) dm->data;
2721:   PetscInt      *offsets;
2722:   PetscInt       supportSize;
2723:   PetscInt       pStart, pEnd, p;

2728:   if (mesh->supports) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE, "Supports were already setup in this DMPlex");
2729:   PetscLogEventBegin(DMPLEX_Symmetrize,dm,0,0,0);
2730:   /* Calculate support sizes */
2731:   DMPlexGetChart(dm, &pStart, &pEnd);
2732:   for (p = pStart; p < pEnd; ++p) {
2733:     PetscInt dof, off, c;

2735:     PetscSectionGetDof(mesh->coneSection, p, &dof);
2736:     PetscSectionGetOffset(mesh->coneSection, p, &off);
2737:     for (c = off; c < off+dof; ++c) {
2738:       PetscSectionAddDof(mesh->supportSection, mesh->cones[c], 1);
2739:     }
2740:   }
2741:   for (p = pStart; p < pEnd; ++p) {
2742:     PetscInt dof;

2744:     PetscSectionGetDof(mesh->supportSection, p, &dof);

2746:     mesh->maxSupportSize = PetscMax(mesh->maxSupportSize, dof);
2747:   }
2748:   PetscSectionSetUp(mesh->supportSection);
2749:   /* Calculate supports */
2750:   PetscSectionGetStorageSize(mesh->supportSection, &supportSize);
2751:   PetscMalloc1(supportSize, &mesh->supports);
2752:   PetscCalloc1(pEnd - pStart, &offsets);
2753:   for (p = pStart; p < pEnd; ++p) {
2754:     PetscInt dof, off, c;

2756:     PetscSectionGetDof(mesh->coneSection, p, &dof);
2757:     PetscSectionGetOffset(mesh->coneSection, p, &off);
2758:     for (c = off; c < off+dof; ++c) {
2759:       const PetscInt q = mesh->cones[c];
2760:       PetscInt       offS;

2762:       PetscSectionGetOffset(mesh->supportSection, q, &offS);

2764:       mesh->supports[offS+offsets[q]] = p;
2765:       ++offsets[q];
2766:     }
2767:   }
2768:   PetscFree(offsets);
2769:   PetscLogEventEnd(DMPLEX_Symmetrize,dm,0,0,0);
2770:   return(0);
2771: }

2773: static PetscErrorCode DMPlexCreateDepthStratum(DM dm, DMLabel label, PetscInt depth, PetscInt pStart, PetscInt pEnd)
2774: {
2775:   IS             stratumIS;

2779:   if (pStart >= pEnd) return(0);
2780: #if defined(PETSC_USE_DEBUG)
2781:   {
2782:     PetscInt  qStart, qEnd, numLevels, level;
2783:     PetscBool overlap = PETSC_FALSE;
2784:     DMLabelGetNumValues(label, &numLevels);
2785:     for (level = 0; level < numLevels; level++) {
2786:       DMLabelGetStratumBounds(label, level, &qStart, &qEnd);
2787:       if ((pStart >= qStart && pStart < qEnd) || (pEnd > qStart && pEnd <= qEnd)) {overlap = PETSC_TRUE; break;}
2788:     }
2789:     if (overlap) SETERRQ6(PETSC_COMM_SELF, PETSC_ERR_PLIB, "New depth %D range [%D,%D) overlaps with depth %D range [%D,%D)", depth, pStart, pEnd, level, qStart, qEnd);
2790:   }
2791: #endif
2792:   ISCreateStride(PETSC_COMM_SELF, pEnd-pStart, pStart, 1, &stratumIS);
2793:   DMLabelSetStratumIS(label, depth, stratumIS);
2794:   ISDestroy(&stratumIS);
2795:   return(0);
2796: }

2798: static PetscErrorCode DMPlexCreateDimStratum(DM,DMLabel,DMLabel,PetscInt,PetscInt);

2800: /*@
2801:   DMPlexStratify - The DAG for most topologies is a graded poset (https://en.wikipedia.org/wiki/Graded_poset), and
2802:   can be illustrated by a Hasse Diagram (https://en.wikipedia.org/wiki/Hasse_diagram). The strata group all points of the
2803:   same grade, and this function calculates the strata. This grade can be seen as the height (or depth) of the point in
2804:   the DAG.

2806:   Collective on dm

2808:   Input Parameter:
2809: . mesh - The DMPlex

2811:   Output Parameter:

2813:   Notes:
2814:   Concretely, DMPlexStratify() creates a new label named "depth" containing the dimension of each element: 0 for vertices,
2815:   1 for edges, and so on.  The depth label can be accessed through DMPlexGetDepthLabel() or DMPlexGetDepthStratum(), or
2816:   manually via DMGetLabel().  The height is defined implicitly by height = maxDimension - depth, and can be accessed
2817:   via DMPlexGetHeightStratum().  For example, cells have height 0 and faces have height 1.

2819:   DMPlexStratify() should be called after all calls to DMPlexSymmetrize()

2821:   Level: beginner

2823: .seealso: DMPlexCreate(), DMPlexSymmetrize()
2824: @*/
2825: PetscErrorCode DMPlexStratify(DM dm)
2826: {
2827:   DM_Plex       *mesh = (DM_Plex*) dm->data;
2828:   DMLabel        label;
2829:   PetscInt       pStart, pEnd, p;
2830:   PetscInt       numRoots = 0, numLeaves = 0;
2831:   PetscInt       cMax, fMax, eMax, vMax;

2836:   PetscLogEventBegin(DMPLEX_Stratify,dm,0,0,0);

2838:   /* Create depth label */
2839:   DMPlexGetChart(dm, &pStart, &pEnd);
2840:   DMCreateLabel(dm, "depth");
2841:   DMPlexGetDepthLabel(dm, &label);

2843:   {
2844:     /* Initialize roots and count leaves */
2845:     PetscInt sMin = PETSC_MAX_INT;
2846:     PetscInt sMax = PETSC_MIN_INT;
2847:     PetscInt coneSize, supportSize;

2849:     for (p = pStart; p < pEnd; ++p) {
2850:       DMPlexGetConeSize(dm, p, &coneSize);
2851:       DMPlexGetSupportSize(dm, p, &supportSize);
2852:       if (!coneSize && supportSize) {
2853:         sMin = PetscMin(p, sMin);
2854:         sMax = PetscMax(p, sMax);
2855:         ++numRoots;
2856:       } else if (!supportSize && coneSize) {
2857:         ++numLeaves;
2858:       } else if (!supportSize && !coneSize) {
2859:         /* Isolated points */
2860:         sMin = PetscMin(p, sMin);
2861:         sMax = PetscMax(p, sMax);
2862:       }
2863:     }
2864:     DMPlexCreateDepthStratum(dm, label, 0, sMin, sMax+1);
2865:   }

2867:   if (numRoots + numLeaves == (pEnd - pStart)) {
2868:     PetscInt sMin = PETSC_MAX_INT;
2869:     PetscInt sMax = PETSC_MIN_INT;
2870:     PetscInt coneSize, supportSize;

2872:     for (p = pStart; p < pEnd; ++p) {
2873:       DMPlexGetConeSize(dm, p, &coneSize);
2874:       DMPlexGetSupportSize(dm, p, &supportSize);
2875:       if (!supportSize && coneSize) {
2876:         sMin = PetscMin(p, sMin);
2877:         sMax = PetscMax(p, sMax);
2878:       }
2879:     }
2880:     DMPlexCreateDepthStratum(dm, label, 1, sMin, sMax+1);
2881:   } else {
2882:     PetscInt level = 0;
2883:     PetscInt qStart, qEnd, q;

2885:     DMLabelGetStratumBounds(label, level, &qStart, &qEnd);
2886:     while (qEnd > qStart) {
2887:       PetscInt sMin = PETSC_MAX_INT;
2888:       PetscInt sMax = PETSC_MIN_INT;

2890:       for (q = qStart; q < qEnd; ++q) {
2891:         const PetscInt *support;
2892:         PetscInt        supportSize, s;

2894:         DMPlexGetSupportSize(dm, q, &supportSize);
2895:         DMPlexGetSupport(dm, q, &support);
2896:         for (s = 0; s < supportSize; ++s) {
2897:           sMin = PetscMin(support[s], sMin);
2898:           sMax = PetscMax(support[s], sMax);
2899:         }
2900:       }
2901:       DMLabelGetNumValues(label, &level);
2902:       DMPlexCreateDepthStratum(dm, label, level, sMin, sMax+1);
2903:       DMLabelGetStratumBounds(label, level, &qStart, &qEnd);
2904:     }
2905:   }
2906:   { /* just in case there is an empty process */
2907:     PetscInt numValues, maxValues = 0, v;

2909:     DMLabelGetNumValues(label, &numValues);
2910:     MPI_Allreduce(&numValues,&maxValues,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)dm));
2911:     for (v = numValues; v < maxValues; v++) {
2912:       DMLabelAddStratum(label, v);
2913:     }
2914:   }
2915:   PetscObjectStateGet((PetscObject) label, &mesh->depthState);

2917:   DMPlexGetHybridBounds(dm, &cMax, &fMax, &eMax, &vMax);
2918:   if (cMax >= 0 || fMax >= 0 || eMax >= 0 || vMax >= 0) {
2919:     PetscInt dim;
2920:     DMLabel  dimLabel;

2922:     DMGetDimension(dm, &dim);
2923:     DMCreateLabel(dm, "dim");
2924:     DMGetLabel(dm, "dim", &dimLabel);
2925:     if (cMax >= 0) {DMPlexCreateDimStratum(dm, label, dimLabel, dim, cMax);}
2926:     if (fMax >= 0) {DMPlexCreateDimStratum(dm, label, dimLabel, dim - 1, fMax);}
2927:     if (eMax >= 0) {DMPlexCreateDimStratum(dm, label, dimLabel, 1, eMax);}
2928:     if (vMax >= 0) {DMPlexCreateDimStratum(dm, label, dimLabel, 0, vMax);}
2929:   }
2930:   PetscLogEventEnd(DMPLEX_Stratify,dm,0,0,0);
2931:   return(0);
2932: }

2934: /*@C
2935:   DMPlexGetJoin - Get an array for the join of the set of points

2937:   Not Collective

2939:   Input Parameters:
2940: + dm - The DMPlex object
2941: . numPoints - The number of input points for the join
2942: - points - The input points

2944:   Output Parameters:
2945: + numCoveredPoints - The number of points in the join
2946: - coveredPoints - The points in the join

2948:   Level: intermediate

2950:   Note: Currently, this is restricted to a single level join

2952:   Fortran Notes:
2953:   Since it returns an array, this routine is only available in Fortran 90, and you must
2954:   include petsc.h90 in your code.

2956:   The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array.

2958: .seealso: DMPlexRestoreJoin(), DMPlexGetMeet()
2959: @*/
2960: PetscErrorCode DMPlexGetJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints)
2961: {
2962:   DM_Plex       *mesh = (DM_Plex*) dm->data;
2963:   PetscInt      *join[2];
2964:   PetscInt       joinSize, i = 0;
2965:   PetscInt       dof, off, p, c, m;

2973:   DMGetWorkArray(dm, mesh->maxSupportSize, MPIU_INT, &join[0]);
2974:   DMGetWorkArray(dm, mesh->maxSupportSize, MPIU_INT, &join[1]);
2975:   /* Copy in support of first point */
2976:   PetscSectionGetDof(mesh->supportSection, points[0], &dof);
2977:   PetscSectionGetOffset(mesh->supportSection, points[0], &off);
2978:   for (joinSize = 0; joinSize < dof; ++joinSize) {
2979:     join[i][joinSize] = mesh->supports[off+joinSize];
2980:   }
2981:   /* Check each successive support */
2982:   for (p = 1; p < numPoints; ++p) {
2983:     PetscInt newJoinSize = 0;

2985:     PetscSectionGetDof(mesh->supportSection, points[p], &dof);
2986:     PetscSectionGetOffset(mesh->supportSection, points[p], &off);
2987:     for (c = 0; c < dof; ++c) {
2988:       const PetscInt point = mesh->supports[off+c];

2990:       for (m = 0; m < joinSize; ++m) {
2991:         if (point == join[i][m]) {
2992:           join[1-i][newJoinSize++] = point;
2993:           break;
2994:         }
2995:       }
2996:     }
2997:     joinSize = newJoinSize;
2998:     i        = 1-i;
2999:   }
3000:   *numCoveredPoints = joinSize;
3001:   *coveredPoints    = join[i];
3002:   DMRestoreWorkArray(dm, mesh->maxSupportSize, MPIU_INT, &join[1-i]);
3003:   return(0);
3004: }

3006: /*@C
3007:   DMPlexRestoreJoin - Restore an array for the join of the set of points

3009:   Not Collective

3011:   Input Parameters:
3012: + dm - The DMPlex object
3013: . numPoints - The number of input points for the join
3014: - points - The input points

3016:   Output Parameters:
3017: + numCoveredPoints - The number of points in the join
3018: - coveredPoints - The points in the join

3020:   Fortran Notes:
3021:   Since it returns an array, this routine is only available in Fortran 90, and you must
3022:   include petsc.h90 in your code.

3024:   The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array.

3026:   Level: intermediate

3028: .seealso: DMPlexGetJoin(), DMPlexGetFullJoin(), DMPlexGetMeet()
3029: @*/
3030: PetscErrorCode DMPlexRestoreJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints)
3031: {

3039:   DMRestoreWorkArray(dm, 0, MPIU_INT, (void*) coveredPoints);
3040:   if (numCoveredPoints) *numCoveredPoints = 0;
3041:   return(0);
3042: }

3044: /*@C
3045:   DMPlexGetFullJoin - Get an array for the join of the set of points

3047:   Not Collective

3049:   Input Parameters:
3050: + dm - The DMPlex object
3051: . numPoints - The number of input points for the join
3052: - points - The input points

3054:   Output Parameters:
3055: + numCoveredPoints - The number of points in the join
3056: - coveredPoints - The points in the join

3058:   Fortran Notes:
3059:   Since it returns an array, this routine is only available in Fortran 90, and you must
3060:   include petsc.h90 in your code.

3062:   The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array.

3064:   Level: intermediate

3066: .seealso: DMPlexGetJoin(), DMPlexRestoreJoin(), DMPlexGetMeet()
3067: @*/
3068: PetscErrorCode DMPlexGetFullJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints)
3069: {
3070:   DM_Plex       *mesh = (DM_Plex*) dm->data;
3071:   PetscInt      *offsets, **closures;
3072:   PetscInt      *join[2];
3073:   PetscInt       depth = 0, maxSize, joinSize = 0, i = 0;
3074:   PetscInt       p, d, c, m, ms;


3083:   DMPlexGetDepth(dm, &depth);
3084:   PetscCalloc1(numPoints, &closures);
3085:   DMGetWorkArray(dm, numPoints*(depth+2), MPIU_INT, &offsets);
3086:   ms      = mesh->maxSupportSize;
3087:   maxSize = (ms > 1) ? ((PetscPowInt(ms,depth+1)-1)/(ms-1)) : depth + 1;
3088:   DMGetWorkArray(dm, maxSize, MPIU_INT, &join[0]);
3089:   DMGetWorkArray(dm, maxSize, MPIU_INT, &join[1]);

3091:   for (p = 0; p < numPoints; ++p) {
3092:     PetscInt closureSize;

3094:     DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &closureSize, &closures[p]);

3096:     offsets[p*(depth+2)+0] = 0;
3097:     for (d = 0; d < depth+1; ++d) {
3098:       PetscInt pStart, pEnd, i;

3100:       DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
3101:       for (i = offsets[p*(depth+2)+d]; i < closureSize; ++i) {
3102:         if ((pStart > closures[p][i*2]) || (pEnd <= closures[p][i*2])) {
3103:           offsets[p*(depth+2)+d+1] = i;
3104:           break;
3105:         }
3106:       }
3107:       if (i == closureSize) offsets[p*(depth+2)+d+1] = i;
3108:     }
3109:     if (offsets[p*(depth+2)+depth+1] != closureSize) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Total size of closure %D should be %D", offsets[p*(depth+2)+depth+1], closureSize);
3110:   }
3111:   for (d = 0; d < depth+1; ++d) {
3112:     PetscInt dof;

3114:     /* Copy in support of first point */
3115:     dof = offsets[d+1] - offsets[d];
3116:     for (joinSize = 0; joinSize < dof; ++joinSize) {
3117:       join[i][joinSize] = closures[0][(offsets[d]+joinSize)*2];
3118:     }
3119:     /* Check each successive cone */
3120:     for (p = 1; p < numPoints && joinSize; ++p) {
3121:       PetscInt newJoinSize = 0;

3123:       dof = offsets[p*(depth+2)+d+1] - offsets[p*(depth+2)+d];
3124:       for (c = 0; c < dof; ++c) {
3125:         const PetscInt point = closures[p][(offsets[p*(depth+2)+d]+c)*2];

3127:         for (m = 0; m < joinSize; ++m) {
3128:           if (point == join[i][m]) {
3129:             join[1-i][newJoinSize++] = point;
3130:             break;
3131:           }
3132:         }
3133:       }
3134:       joinSize = newJoinSize;
3135:       i        = 1-i;
3136:     }
3137:     if (joinSize) break;
3138:   }
3139:   *numCoveredPoints = joinSize;
3140:   *coveredPoints    = join[i];
3141:   for (p = 0; p < numPoints; ++p) {
3142:     DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, NULL, &closures[p]);
3143:   }
3144:   PetscFree(closures);
3145:   DMRestoreWorkArray(dm, numPoints*(depth+2), MPIU_INT, &offsets);
3146:   DMRestoreWorkArray(dm, mesh->maxSupportSize, MPIU_INT, &join[1-i]);
3147:   return(0);
3148: }

3150: /*@C
3151:   DMPlexGetMeet - Get an array for the meet of the set of points

3153:   Not Collective

3155:   Input Parameters:
3156: + dm - The DMPlex object
3157: . numPoints - The number of input points for the meet
3158: - points - The input points

3160:   Output Parameters:
3161: + numCoveredPoints - The number of points in the meet
3162: - coveredPoints - The points in the meet

3164:   Level: intermediate

3166:   Note: Currently, this is restricted to a single level meet

3168:   Fortran Notes:
3169:   Since it returns an array, this routine is only available in Fortran 90, and you must
3170:   include petsc.h90 in your code.

3172:   The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array.

3174: .seealso: DMPlexRestoreMeet(), DMPlexGetJoin()
3175: @*/
3176: PetscErrorCode DMPlexGetMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveringPoints, const PetscInt **coveringPoints)
3177: {
3178:   DM_Plex       *mesh = (DM_Plex*) dm->data;
3179:   PetscInt      *meet[2];
3180:   PetscInt       meetSize, i = 0;
3181:   PetscInt       dof, off, p, c, m;

3189:   DMGetWorkArray(dm, mesh->maxConeSize, MPIU_INT, &meet[0]);
3190:   DMGetWorkArray(dm, mesh->maxConeSize, MPIU_INT, &meet[1]);
3191:   /* Copy in cone of first point */
3192:   PetscSectionGetDof(mesh->coneSection, points[0], &dof);
3193:   PetscSectionGetOffset(mesh->coneSection, points[0], &off);
3194:   for (meetSize = 0; meetSize < dof; ++meetSize) {
3195:     meet[i][meetSize] = mesh->cones[off+meetSize];
3196:   }
3197:   /* Check each successive cone */
3198:   for (p = 1; p < numPoints; ++p) {
3199:     PetscInt newMeetSize = 0;

3201:     PetscSectionGetDof(mesh->coneSection, points[p], &dof);
3202:     PetscSectionGetOffset(mesh->coneSection, points[p], &off);
3203:     for (c = 0; c < dof; ++c) {
3204:       const PetscInt point = mesh->cones[off+c];

3206:       for (m = 0; m < meetSize; ++m) {
3207:         if (point == meet[i][m]) {
3208:           meet[1-i][newMeetSize++] = point;
3209:           break;
3210:         }
3211:       }
3212:     }
3213:     meetSize = newMeetSize;
3214:     i        = 1-i;
3215:   }
3216:   *numCoveringPoints = meetSize;
3217:   *coveringPoints    = meet[i];
3218:   DMRestoreWorkArray(dm, mesh->maxConeSize, MPIU_INT, &meet[1-i]);
3219:   return(0);
3220: }

3222: /*@C
3223:   DMPlexRestoreMeet - Restore an array for the meet of the set of points

3225:   Not Collective

3227:   Input Parameters:
3228: + dm - The DMPlex object
3229: . numPoints - The number of input points for the meet
3230: - points - The input points

3232:   Output Parameters:
3233: + numCoveredPoints - The number of points in the meet
3234: - coveredPoints - The points in the meet

3236:   Level: intermediate

3238:   Fortran Notes:
3239:   Since it returns an array, this routine is only available in Fortran 90, and you must
3240:   include petsc.h90 in your code.

3242:   The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array.

3244: .seealso: DMPlexGetMeet(), DMPlexGetFullMeet(), DMPlexGetJoin()
3245: @*/
3246: PetscErrorCode DMPlexRestoreMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints)
3247: {

3255:   DMRestoreWorkArray(dm, 0, MPIU_INT, (void*) coveredPoints);
3256:   if (numCoveredPoints) *numCoveredPoints = 0;
3257:   return(0);
3258: }

3260: /*@C
3261:   DMPlexGetFullMeet - Get an array for the meet of the set of points

3263:   Not Collective

3265:   Input Parameters:
3266: + dm - The DMPlex object
3267: . numPoints - The number of input points for the meet
3268: - points - The input points

3270:   Output Parameters:
3271: + numCoveredPoints - The number of points in the meet
3272: - coveredPoints - The points in the meet

3274:   Level: intermediate

3276:   Fortran Notes:
3277:   Since it returns an array, this routine is only available in Fortran 90, and you must
3278:   include petsc.h90 in your code.

3280:   The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array.

3282: .seealso: DMPlexGetMeet(), DMPlexRestoreMeet(), DMPlexGetJoin()
3283: @*/
3284: PetscErrorCode DMPlexGetFullMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints)
3285: {
3286:   DM_Plex       *mesh = (DM_Plex*) dm->data;
3287:   PetscInt      *offsets, **closures;
3288:   PetscInt      *meet[2];
3289:   PetscInt       height = 0, maxSize, meetSize = 0, i = 0;
3290:   PetscInt       p, h, c, m, mc;


3299:   DMPlexGetDepth(dm, &height);
3300:   PetscMalloc1(numPoints, &closures);
3301:   DMGetWorkArray(dm, numPoints*(height+2), MPIU_INT, &offsets);
3302:   mc      = mesh->maxConeSize;
3303:   maxSize = (mc > 1) ? ((PetscPowInt(mc,height+1)-1)/(mc-1)) : height + 1;
3304:   DMGetWorkArray(dm, maxSize, MPIU_INT, &meet[0]);
3305:   DMGetWorkArray(dm, maxSize, MPIU_INT, &meet[1]);

3307:   for (p = 0; p < numPoints; ++p) {
3308:     PetscInt closureSize;

3310:     DMPlexGetTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closures[p]);

3312:     offsets[p*(height+2)+0] = 0;
3313:     for (h = 0; h < height+1; ++h) {
3314:       PetscInt pStart, pEnd, i;

3316:       DMPlexGetHeightStratum(dm, h, &pStart, &pEnd);
3317:       for (i = offsets[p*(height+2)+h]; i < closureSize; ++i) {
3318:         if ((pStart > closures[p][i*2]) || (pEnd <= closures[p][i*2])) {
3319:           offsets[p*(height+2)+h+1] = i;
3320:           break;
3321:         }
3322:       }
3323:       if (i == closureSize) offsets[p*(height+2)+h+1] = i;
3324:     }
3325:     if (offsets[p*(height+2)+height+1] != closureSize) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Total size of closure %D should be %D", offsets[p*(height+2)+height+1], closureSize);
3326:   }
3327:   for (h = 0; h < height+1; ++h) {
3328:     PetscInt dof;

3330:     /* Copy in cone of first point */
3331:     dof = offsets[h+1] - offsets[h];
3332:     for (meetSize = 0; meetSize < dof; ++meetSize) {
3333:       meet[i][meetSize] = closures[0][(offsets[h]+meetSize)*2];
3334:     }
3335:     /* Check each successive cone */
3336:     for (p = 1; p < numPoints && meetSize; ++p) {
3337:       PetscInt newMeetSize = 0;

3339:       dof = offsets[p*(height+2)+h+1] - offsets[p*(height+2)+h];
3340:       for (c = 0; c < dof; ++c) {
3341:         const PetscInt point = closures[p][(offsets[p*(height+2)+h]+c)*2];

3343:         for (m = 0; m < meetSize; ++m) {
3344:           if (point == meet[i][m]) {
3345:             meet[1-i][newMeetSize++] = point;
3346:             break;
3347:           }
3348:         }
3349:       }
3350:       meetSize = newMeetSize;
3351:       i        = 1-i;
3352:     }
3353:     if (meetSize) break;
3354:   }
3355:   *numCoveredPoints = meetSize;
3356:   *coveredPoints    = meet[i];
3357:   for (p = 0; p < numPoints; ++p) {
3358:     DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_TRUE, NULL, &closures[p]);
3359:   }
3360:   PetscFree(closures);
3361:   DMRestoreWorkArray(dm, numPoints*(height+2), MPIU_INT, &offsets);
3362:   DMRestoreWorkArray(dm, mesh->maxConeSize, MPIU_INT, &meet[1-i]);
3363:   return(0);
3364: }

3366: /*@C
3367:   DMPlexEqual - Determine if two DMs have the same topology

3369:   Not Collective

3371:   Input Parameters:
3372: + dmA - A DMPlex object
3373: - dmB - A DMPlex object

3375:   Output Parameters:
3376: . equal - PETSC_TRUE if the topologies are identical

3378:   Level: intermediate

3380:   Notes:
3381:   We are not solving graph isomorphism, so we do not permutation.

3383: .seealso: DMPlexGetCone()
3384: @*/
3385: PetscErrorCode DMPlexEqual(DM dmA, DM dmB, PetscBool *equal)
3386: {
3387:   PetscInt       depth, depthB, pStart, pEnd, pStartB, pEndB, p;


3395:   *equal = PETSC_FALSE;
3396:   DMPlexGetDepth(dmA, &depth);
3397:   DMPlexGetDepth(dmB, &depthB);
3398:   if (depth != depthB) return(0);
3399:   DMPlexGetChart(dmA, &pStart,  &pEnd);
3400:   DMPlexGetChart(dmB, &pStartB, &pEndB);
3401:   if ((pStart != pStartB) || (pEnd != pEndB)) return(0);
3402:   for (p = pStart; p < pEnd; ++p) {
3403:     const PetscInt *cone, *coneB, *ornt, *orntB, *support, *supportB;
3404:     PetscInt        coneSize, coneSizeB, c, supportSize, supportSizeB, s;

3406:     DMPlexGetConeSize(dmA, p, &coneSize);
3407:     DMPlexGetCone(dmA, p, &cone);
3408:     DMPlexGetConeOrientation(dmA, p, &ornt);
3409:     DMPlexGetConeSize(dmB, p, &coneSizeB);
3410:     DMPlexGetCone(dmB, p, &coneB);
3411:     DMPlexGetConeOrientation(dmB, p, &orntB);
3412:     if (coneSize != coneSizeB) return(0);
3413:     for (c = 0; c < coneSize; ++c) {
3414:       if (cone[c] != coneB[c]) return(0);
3415:       if (ornt[c] != orntB[c]) return(0);
3416:     }
3417:     DMPlexGetSupportSize(dmA, p, &supportSize);
3418:     DMPlexGetSupport(dmA, p, &support);
3419:     DMPlexGetSupportSize(dmB, p, &supportSizeB);
3420:     DMPlexGetSupport(dmB, p, &supportB);
3421:     if (supportSize != supportSizeB) return(0);
3422:     for (s = 0; s < supportSize; ++s) {
3423:       if (support[s] != supportB[s]) return(0);
3424:     }
3425:   }
3426:   *equal = PETSC_TRUE;
3427:   return(0);
3428: }

3430: /*@C
3431:   DMPlexGetNumFaceVertices - Returns the number of vertices on a face

3433:   Not Collective

3435:   Input Parameters:
3436: + dm         - The DMPlex
3437: . cellDim    - The cell dimension
3438: - numCorners - The number of vertices on a cell

3440:   Output Parameters:
3441: . numFaceVertices - The number of vertices on a face

3443:   Level: developer

3445:   Notes:
3446:   Of course this can only work for a restricted set of symmetric shapes

3448: .seealso: DMPlexGetCone()
3449: @*/
3450: PetscErrorCode DMPlexGetNumFaceVertices(DM dm, PetscInt cellDim, PetscInt numCorners, PetscInt *numFaceVertices)
3451: {
3452:   MPI_Comm       comm;

3456:   PetscObjectGetComm((PetscObject)dm,&comm);
3458:   switch (cellDim) {
3459:   case 0:
3460:     *numFaceVertices = 0;
3461:     break;
3462:   case 1:
3463:     *numFaceVertices = 1;
3464:     break;
3465:   case 2:
3466:     switch (numCorners) {
3467:     case 3: /* triangle */
3468:       *numFaceVertices = 2; /* Edge has 2 vertices */
3469:       break;
3470:     case 4: /* quadrilateral */
3471:       *numFaceVertices = 2; /* Edge has 2 vertices */
3472:       break;
3473:     case 6: /* quadratic triangle, tri and quad cohesive Lagrange cells */
3474:       *numFaceVertices = 3; /* Edge has 3 vertices */
3475:       break;
3476:     case 9: /* quadratic quadrilateral, quadratic quad cohesive Lagrange cells */
3477:       *numFaceVertices = 3; /* Edge has 3 vertices */
3478:       break;
3479:     default:
3480:       SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of face corners %D for dimension %D", numCorners, cellDim);
3481:     }
3482:     break;
3483:   case 3:
3484:     switch (numCorners) {
3485:     case 4: /* tetradehdron */
3486:       *numFaceVertices = 3; /* Face has 3 vertices */
3487:       break;
3488:     case 6: /* tet cohesive cells */
3489:       *numFaceVertices = 4; /* Face has 4 vertices */
3490:       break;
3491:     case 8: /* hexahedron */
3492:       *numFaceVertices = 4; /* Face has 4 vertices */
3493:       break;
3494:     case 9: /* tet cohesive Lagrange cells */
3495:       *numFaceVertices = 6; /* Face has 6 vertices */
3496:       break;
3497:     case 10: /* quadratic tetrahedron */
3498:       *numFaceVertices = 6; /* Face has 6 vertices */
3499:       break;
3500:     case 12: /* hex cohesive Lagrange cells */
3501:       *numFaceVertices = 6; /* Face has 6 vertices */
3502:       break;
3503:     case 18: /* quadratic tet cohesive Lagrange cells */
3504:       *numFaceVertices = 6; /* Face has 6 vertices */
3505:       break;
3506:     case 27: /* quadratic hexahedron, quadratic hex cohesive Lagrange cells */
3507:       *numFaceVertices = 9; /* Face has 9 vertices */
3508:       break;
3509:     default:
3510:       SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of face corners %D for dimension %D", numCorners, cellDim);
3511:     }
3512:     break;
3513:   default:
3514:     SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid cell dimension %D", cellDim);
3515:   }
3516:   return(0);
3517: }

3519: /*@
3520:   DMPlexGetDepthLabel - Get the DMLabel recording the depth of each point

3522:   Not Collective

3524:   Input Parameter:
3525: . dm    - The DMPlex object

3527:   Output Parameter:
3528: . depthLabel - The DMLabel recording point depth

3530:   Level: developer

3532: .seealso: DMPlexGetDepth(), DMPlexGetHeightStratum(), DMPlexGetDepthStratum()
3533: @*/
3534: PetscErrorCode DMPlexGetDepthLabel(DM dm, DMLabel *depthLabel)
3535: {

3541:   if (!dm->depthLabel) {DMGetLabel(dm, "depth", &dm->depthLabel);}
3542:   *depthLabel = dm->depthLabel;
3543:   return(0);
3544: }

3546: /*@
3547:   DMPlexGetDepth - Get the depth of the DAG representing this mesh

3549:   Not Collective

3551:   Input Parameter:
3552: . dm    - The DMPlex object

3554:   Output Parameter:
3555: . depth - The number of strata (breadth first levels) in the DAG

3557:   Level: developer

3559: .seealso: DMPlexGetDepthLabel(), DMPlexGetHeightStratum(), DMPlexGetDepthStratum()
3560: @*/
3561: PetscErrorCode DMPlexGetDepth(DM dm, PetscInt *depth)
3562: {
3563:   DMLabel        label;
3564:   PetscInt       d = 0;

3570:   DMPlexGetDepthLabel(dm, &label);
3571:   if (label) {DMLabelGetNumValues(label, &d);}
3572:   *depth = d-1;
3573:   return(0);
3574: }

3576: /*@
3577:   DMPlexGetDepthStratum - Get the bounds [start, end) for all points at a certain depth.

3579:   Not Collective

3581:   Input Parameters:
3582: + dm           - The DMPlex object
3583: - stratumValue - The requested depth

3585:   Output Parameters:
3586: + start - The first point at this depth
3587: - end   - One beyond the last point at this depth

3589:   Notes:
3590:   Depth indexing is related to topological dimension.  Depth stratum 0 contains the lowest topological dimension points,
3591:   often "vertices".  If the mesh is "interpolated" (see DMPlexInterpolate()), then depth stratum 1 contains the next
3592:   higher dimension, e.g., "edges".

3594:   Level: developer

3596: .seealso: DMPlexGetHeightStratum(), DMPlexGetDepth()
3597: @*/
3598: PetscErrorCode DMPlexGetDepthStratum(DM dm, PetscInt stratumValue, PetscInt *start, PetscInt *end)
3599: {
3600:   DMLabel        label;
3601:   PetscInt       pStart, pEnd;

3608:   DMPlexGetChart(dm, &pStart, &pEnd);
3609:   if (pStart == pEnd) return(0);
3610:   if (stratumValue < 0) {
3611:     if (start) *start = pStart;
3612:     if (end)   *end   = pEnd;
3613:     return(0);
3614:   }
3615:   DMPlexGetDepthLabel(dm, &label);
3616:   if (!label) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "No label named depth was found");
3617:   DMLabelGetStratumBounds(label, stratumValue, start, end);
3618:   return(0);
3619: }

3621: /*@
3622:   DMPlexGetHeightStratum - Get the bounds [start, end) for all points at a certain height.

3624:   Not Collective

3626:   Input Parameters:
3627: + dm           - The DMPlex object
3628: - stratumValue - The requested height

3630:   Output Parameters:
3631: + start - The first point at this height
3632: - end   - One beyond the last point at this height

3634:   Notes:
3635:   Height indexing is related to topological codimension.  Height stratum 0 contains the highest topological dimension
3636:   points, often called "cells" or "elements".  If the mesh is "interpolated" (see DMPlexInterpolate()), then height
3637:   stratum 1 contains the boundary of these "cells", often called "faces" or "facets".

3639:   Level: developer

3641: .seealso: DMPlexGetDepthStratum(), DMPlexGetDepth()
3642: @*/
3643: PetscErrorCode DMPlexGetHeightStratum(DM dm, PetscInt stratumValue, PetscInt *start, PetscInt *end)
3644: {
3645:   DMLabel        label;
3646:   PetscInt       depth, pStart, pEnd;

3653:   DMPlexGetChart(dm, &pStart, &pEnd);
3654:   if (pStart == pEnd) return(0);
3655:   if (stratumValue < 0) {
3656:     if (start) *start = pStart;
3657:     if (end)   *end   = pEnd;
3658:     return(0);
3659:   }
3660:   DMPlexGetDepthLabel(dm, &label);
3661:   if (!label) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "No label named depth was found");
3662:   DMLabelGetNumValues(label, &depth);
3663:   DMLabelGetStratumBounds(label, depth-1-stratumValue, start, end);
3664:   return(0);
3665: }

3667: PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm)
3668: {
3669:   PetscSection   section, s;
3670:   Mat            m;
3671:   PetscInt       maxHeight;

3675:   DMClone(dm, cdm);
3676:   DMPlexGetMaxProjectionHeight(dm, &maxHeight);
3677:   DMPlexSetMaxProjectionHeight(*cdm, maxHeight);
3678:   PetscSectionCreate(PetscObjectComm((PetscObject)dm), &section);
3679:   DMSetLocalSection(*cdm, section);
3680:   PetscSectionDestroy(&section);
3681:   PetscSectionCreate(PETSC_COMM_SELF, &s);
3682:   MatCreate(PETSC_COMM_SELF, &m);
3683:   DMSetDefaultConstraints(*cdm, s, m);
3684:   PetscSectionDestroy(&s);
3685:   MatDestroy(&m);

3687:   DMSetNumFields(*cdm, 1);
3688:   DMCreateDS(*cdm);
3689:   return(0);
3690: }

3692: PetscErrorCode DMCreateCoordinateField_Plex(DM dm, DMField *field)
3693: {
3694:   Vec            coordsLocal;
3695:   DM             coordsDM;

3699:   *field = NULL;
3700:   DMGetCoordinatesLocal(dm,&coordsLocal);
3701:   DMGetCoordinateDM(dm,&coordsDM);
3702:   if (coordsLocal && coordsDM) {
3703:     DMFieldCreateDS(coordsDM, 0, coordsLocal, field);
3704:   }
3705:   return(0);
3706: }

3708: /*@C
3709:   DMPlexGetConeSection - Return a section which describes the layout of cone data

3711:   Not Collective

3713:   Input Parameters:
3714: . dm        - The DMPlex object

3716:   Output Parameter:
3717: . section - The PetscSection object

3719:   Level: developer

3721: .seealso: DMPlexGetSupportSection(), DMPlexGetCones(), DMPlexGetConeOrientations()
3722: @*/
3723: PetscErrorCode DMPlexGetConeSection(DM dm, PetscSection *section)
3724: {
3725:   DM_Plex *mesh = (DM_Plex*) dm->data;

3729:   if (section) *section = mesh->coneSection;
3730:   return(0);
3731: }

3733: /*@C
3734:   DMPlexGetSupportSection - Return a section which describes the layout of support data

3736:   Not Collective

3738:   Input Parameters:
3739: . dm        - The DMPlex object

3741:   Output Parameter:
3742: . section - The PetscSection object

3744:   Level: developer

3746: .seealso: DMPlexGetConeSection()
3747: @*/
3748: PetscErrorCode DMPlexGetSupportSection(DM dm, PetscSection *section)
3749: {
3750:   DM_Plex *mesh = (DM_Plex*) dm->data;

3754:   if (section) *section = mesh->supportSection;
3755:   return(0);
3756: }

3758: /*@C
3759:   DMPlexGetCones - Return cone data

3761:   Not Collective

3763:   Input Parameters:
3764: . dm        - The DMPlex object

3766:   Output Parameter:
3767: . cones - The cone for each point

3769:   Level: developer

3771: .seealso: DMPlexGetConeSection()
3772: @*/
3773: PetscErrorCode DMPlexGetCones(DM dm, PetscInt *cones[])
3774: {
3775:   DM_Plex *mesh = (DM_Plex*) dm->data;

3779:   if (cones) *cones = mesh->cones;
3780:   return(0);
3781: }

3783: /*@C
3784:   DMPlexGetConeOrientations - Return cone orientation data

3786:   Not Collective

3788:   Input Parameters:
3789: . dm        - The DMPlex object

3791:   Output Parameter:
3792: . coneOrientations - The cone orientation for each point

3794:   Level: developer

3796: .seealso: DMPlexGetConeSection()
3797: @*/
3798: PetscErrorCode DMPlexGetConeOrientations(DM dm, PetscInt *coneOrientations[])
3799: {
3800:   DM_Plex *mesh = (DM_Plex*) dm->data;

3804:   if (coneOrientations) *coneOrientations = mesh->coneOrientations;
3805:   return(0);
3806: }

3808: /******************************** FEM Support **********************************/

3810: /*
3811:  Returns number of components and tensor degree for the field.  For interpolated meshes, line should be a point
3812:  representing a line in the section.
3813: */
3814: static PetscErrorCode PetscSectionFieldGetTensorDegree_Private(PetscSection section,PetscInt field,PetscInt line,PetscBool vertexchart,PetscInt *Nc,PetscInt *k)
3815: {

3819:   PetscSectionGetFieldComponents(section, field, Nc);
3820:   if (vertexchart) {            /* If we only have a vertex chart, we must have degree k=1 */
3821:     *k = 1;
3822:   } else {                      /* Assume the full interpolated mesh is in the chart; lines in particular */
3823:     /* An order k SEM disc has k-1 dofs on an edge */
3824:     PetscSectionGetFieldDof(section, line, field, k);
3825:     *k = *k / *Nc + 1;
3826:   }
3827:   return(0);
3828: }

3830: /*@

3832:   DMPlexSetClosurePermutationTensor - Create a permutation from the default (BFS) point ordering in the closure, to a
3833:   lexicographic ordering over the tensor product cell (i.e., line, quad, hex, etc.), and set this permutation in the
3834:   section provided (or the section of the DM).

3836:   Input Parameters:
3837: + dm      - The DM
3838: . point   - Either a cell (highest dim point) or an edge (dim 1 point), or PETSC_DETERMINE
3839: - section - The PetscSection to reorder, or NULL for the default section

3841:   Note: The point is used to determine the number of dofs/field on an edge. For SEM, this is related to the polynomial
3842:   degree of the basis.

3844:   Example:
3845:   A typical interpolated single-quad mesh might order points as
3846: .vb
3847:   [c0, v1, v2, v3, v4, e5, e6, e7, e8]

3849:   v4 -- e6 -- v3
3850:   |           |
3851:   e7    c0    e8
3852:   |           |
3853:   v1 -- e5 -- v2
3854: .ve

3856:   (There is no significance to the ordering described here.)  The default section for a Q3 quad might typically assign
3857:   dofs in the order of points, e.g.,
3858: .vb
3859:     c0 -> [0,1,2,3]
3860:     v1 -> [4]
3861:     ...
3862:     e5 -> [8, 9]
3863: .ve

3865:   which corresponds to the dofs
3866: .vb
3867:     6   10  11  7
3868:     13  2   3   15
3869:     12  0   1   14
3870:     4   8   9   5
3871: .ve

3873:   The closure in BFS ordering works through height strata (cells, edges, vertices) to produce the ordering
3874: .vb
3875:   0 1 2 3 8 9 14 15 11 10 13 12 4 5 7 6
3876: .ve

3878:   After calling DMPlexSetClosurePermutationTensor(), the closure will be ordered lexicographically,
3879: .vb
3880:    4 8 9 5 12 0 1 14 13 2 3 15 6 10 11 7
3881: .ve

3883:   Level: developer

3885: .seealso: DMGetLocalSection(), PetscSectionSetClosurePermutation(), DMSetGlocalSection()
3886: @*/
3887: PetscErrorCode DMPlexSetClosurePermutationTensor(DM dm, PetscInt point, PetscSection section)
3888: {
3889:   DMLabel        label;
3890:   PetscInt      *perm;
3891:   PetscInt       dim, depth, eStart, k, Nf, f, Nc, c, i, j, size = 0, offset = 0, foffset = 0;
3892:   PetscBool      vertexchart;

3896:   if (point < 0) {DMPlexGetDepthStratum(dm, 1, &point, NULL);}
3897:   DMGetDimension(dm, &dim);
3898:   DMPlexGetDepthLabel(dm, &label);
3899:   DMLabelGetValue(label, point, &depth);
3900:   if (depth == 1) {eStart = point;}
3901:   else if  (depth == dim) {
3902:     const PetscInt *cone;

3904:     DMPlexGetCone(dm, point, &cone);
3905:     if (dim == 2) eStart = cone[0];
3906:     else if (dim == 3) {
3907:       const PetscInt *cone2;
3908:       DMPlexGetCone(dm, cone[0], &cone2);
3909:       eStart = cone2[0];
3910:     } else SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Point %D of depth %D cannot be used to bootstrap spectral ordering for dim %D", point, depth, dim);
3911:   } else SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Point %D of depth %D cannot be used to bootstrap spectral ordering for dim %D", point, depth, dim);
3912:   if (!section) {DMGetLocalSection(dm, &section);}
3913:   {                             /* Determine whether the chart covers all points or just vertices. */
3914:     PetscInt pStart,pEnd,cStart,cEnd;
3915:     DMPlexGetDepthStratum(dm,0,&pStart,&pEnd);
3916:     PetscSectionGetChart(section,&cStart,&cEnd);
3917:     if (pStart == cStart && pEnd == cEnd) vertexchart = PETSC_TRUE; /* Just vertices */
3918:     else vertexchart = PETSC_FALSE;                                 /* Assume all interpolated points are in chart */
3919:   }
3920:   PetscSectionGetNumFields(section, &Nf);
3921:   if (dim < 1) return(0);
3922:   for (f = 0; f < Nf; ++f) {
3923:     PetscSectionFieldGetTensorDegree_Private(section,f,eStart,vertexchart,&Nc,&k);
3924:     size += PetscPowInt(k+1, dim)*Nc;
3925:   }
3926:   PetscMalloc1(size, &perm);
3927:   for (f = 0; f < Nf; ++f) {
3928:     switch (dim) {
3929:     case 1:
3930:       PetscSectionFieldGetTensorDegree_Private(section,f,eStart,vertexchart,&Nc,&k);
3931:       /*
3932:         Original ordering is [ edge of length k-1; vtx0; vtx1 ]
3933:         We want              [ vtx0; edge of length k-1; vtx1 ]
3934:       */
3935:       for (c=0; c<Nc; c++,offset++) perm[offset] = (k-1)*Nc + c + foffset;
3936:       for (i=0; i<k-1; i++) for (c=0; c<Nc; c++,offset++) perm[offset] = i*Nc + c + foffset;
3937:       for (c=0; c<Nc; c++,offset++) perm[offset] = k*Nc + c + foffset;
3938:       foffset = offset;
3939:       break;
3940:     case 2:
3941:       /* The original quad closure is oriented clockwise, {f, e_b, e_r, e_t, e_l, v_lb, v_rb, v_tr, v_tl} */
3942:       PetscSectionFieldGetTensorDegree_Private(section,f,eStart,vertexchart,&Nc,&k);
3943:       /* The SEM order is

3945:          v_lb, {e_b}, v_rb,
3946:          e^{(k-1)-i}_l, {f^{i*(k-1)}}, e^i_r,
3947:          v_lt, reverse {e_t}, v_rt
3948:       */
3949:       {
3950:         const PetscInt of   = 0;
3951:         const PetscInt oeb  = of   + PetscSqr(k-1);
3952:         const PetscInt oer  = oeb  + (k-1);
3953:         const PetscInt oet  = oer  + (k-1);
3954:         const PetscInt oel  = oet  + (k-1);
3955:         const PetscInt ovlb = oel  + (k-1);
3956:         const PetscInt ovrb = ovlb + 1;
3957:         const PetscInt ovrt = ovrb + 1;
3958:         const PetscInt ovlt = ovrt + 1;
3959:         PetscInt       o;

3961:         /* bottom */
3962:         for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovlb*Nc + c + foffset;
3963:         for (o = oeb; o < oer; ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
3964:         for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovrb*Nc + c + foffset;
3965:         /* middle */
3966:         for (i = 0; i < k-1; ++i) {
3967:           for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oel+(k-2)-i)*Nc + c + foffset;
3968:           for (o = of+(k-1)*i; o < of+(k-1)*(i+1); ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
3969:           for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oer+i)*Nc + c + foffset;
3970:         }
3971:         /* top */
3972:         for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovlt*Nc + c + foffset;
3973:         for (o = oel-1; o >= oet; --o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
3974:         for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovrt*Nc + c + foffset;
3975:         foffset = offset;
3976:       }
3977:       break;
3978:     case 3:
3979:       /* The original hex closure is

3981:          {c,
3982:           f_b, f_t, f_f, f_b, f_r, f_l,
3983:           e_bl, e_bb, e_br, e_bf,  e_tf, e_tr, e_tb, e_tl,  e_rf, e_lf, e_lb, e_rb,
3984:           v_blf, v_blb, v_brb, v_brf, v_tlf, v_trf, v_trb, v_tlb}
3985:       */
3986:       PetscSectionFieldGetTensorDegree_Private(section,f,eStart,vertexchart,&Nc,&k);
3987:       /* The SEM order is
3988:          Bottom Slice
3989:          v_blf, {e^{(k-1)-n}_bf}, v_brf,
3990:          e^{i}_bl, f^{n*(k-1)+(k-1)-i}_b, e^{(k-1)-i}_br,
3991:          v_blb, {e_bb}, v_brb,

3993:          Middle Slice (j)
3994:          {e^{(k-1)-j}_lf}, {f^{j*(k-1)+n}_f}, e^j_rf,
3995:          f^{i*(k-1)+j}_l, {c^{(j*(k-1) + i)*(k-1)+n}_t}, f^{j*(k-1)+i}_r,
3996:          e^j_lb, {f^{j*(k-1)+(k-1)-n}_b}, e^{(k-1)-j}_rb,

3998:          Top Slice
3999:          v_tlf, {e_tf}, v_trf,
4000:          e^{(k-1)-i}_tl, {f^{i*(k-1)}_t}, e^{i}_tr,
4001:          v_tlb, {e^{(k-1)-n}_tb}, v_trb,
4002:       */
4003:       {
4004:         const PetscInt oc    = 0;
4005:         const PetscInt ofb   = oc    + PetscSqr(k-1)*(k-1);
4006:         const PetscInt oft   = ofb   + PetscSqr(k-1);
4007:         const PetscInt off   = oft   + PetscSqr(k-1);
4008:         const PetscInt ofk   = off   + PetscSqr(k-1);
4009:         const PetscInt ofr   = ofk   + PetscSqr(k-1);
4010:         const PetscInt ofl   = ofr   + PetscSqr(k-1);
4011:         const PetscInt oebl  = ofl   + PetscSqr(k-1);
4012:         const PetscInt oebb  = oebl  + (k-1);
4013:         const PetscInt oebr  = oebb  + (k-1);
4014:         const PetscInt oebf  = oebr  + (k-1);
4015:         const PetscInt oetf  = oebf  + (k-1);
4016:         const PetscInt oetr  = oetf  + (k-1);
4017:         const PetscInt oetb  = oetr  + (k-1);
4018:         const PetscInt oetl  = oetb  + (k-1);
4019:         const PetscInt oerf  = oetl  + (k-1);
4020:         const PetscInt oelf  = oerf  + (k-1);
4021:         const PetscInt oelb  = oelf  + (k-1);
4022:         const PetscInt oerb  = oelb  + (k-1);
4023:         const PetscInt ovblf = oerb  + (k-1);
4024:         const PetscInt ovblb = ovblf + 1;
4025:         const PetscInt ovbrb = ovblb + 1;
4026:         const PetscInt ovbrf = ovbrb + 1;
4027:         const PetscInt ovtlf = ovbrf + 1;
4028:         const PetscInt ovtrf = ovtlf + 1;
4029:         const PetscInt ovtrb = ovtrf + 1;
4030:         const PetscInt ovtlb = ovtrb + 1;
4031:         PetscInt       o, n;

4033:         /* Bottom Slice */
4034:         /*   bottom */
4035:         for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovblf*Nc + c + foffset;
4036:         for (o = oetf-1; o >= oebf; --o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
4037:         for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovbrf*Nc + c + foffset;
4038:         /*   middle */
4039:         for (i = 0; i < k-1; ++i) {
4040:           for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oebl+i)*Nc + c + foffset;
4041:           for (n = 0; n < k-1; ++n) {o = ofb+n*(k-1)+i; for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;}
4042:           for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oebr+(k-2)-i)*Nc + c + foffset;
4043:         }
4044:         /*   top */
4045:         for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovblb*Nc + c + foffset;
4046:         for (o = oebb; o < oebr; ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
4047:         for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovbrb*Nc + c + foffset;

4049:         /* Middle Slice */
4050:         for (j = 0; j < k-1; ++j) {
4051:           /*   bottom */
4052:           for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oelf+(k-2)-j)*Nc + c + foffset;
4053:           for (o = off+j*(k-1); o < off+(j+1)*(k-1); ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
4054:           for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oerf+j)*Nc + c + foffset;
4055:           /*   middle */
4056:           for (i = 0; i < k-1; ++i) {
4057:             for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (ofl+i*(k-1)+j)*Nc + c + foffset;
4058:             for (n = 0; n < k-1; ++n) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oc+(j*(k-1)+i)*(k-1)+n)*Nc + c + foffset;
4059:             for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (ofr+j*(k-1)+i)*Nc + c + foffset;
4060:           }
4061:           /*   top */
4062:           for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oelb+j)*Nc + c + foffset;
4063:           for (o = ofk+j*(k-1)+(k-2); o >= ofk+j*(k-1); --o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
4064:           for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oerb+(k-2)-j)*Nc + c + foffset;
4065:         }

4067:         /* Top Slice */
4068:         /*   bottom */
4069:         for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtlf*Nc + c + foffset;
4070:         for (o = oetf; o < oetr; ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
4071:         for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtrf*Nc + c + foffset;
4072:         /*   middle */
4073:         for (i = 0; i < k-1; ++i) {
4074:           for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oetl+(k-2)-i)*Nc + c + foffset;
4075:           for (n = 0; n < k-1; ++n) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oft+i*(k-1)+n)*Nc + c + foffset;
4076:           for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oetr+i)*Nc + c + foffset;
4077:         }
4078:         /*   top */
4079:         for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtlb*Nc + c + foffset;
4080:         for (o = oetl-1; o >= oetb; --o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;
4081:         for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtrb*Nc + c + foffset;

4083:         foffset = offset;
4084:       }
4085:       break;
4086:     default: SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "No spectral ordering for dimension %D", dim);
4087:     }
4088:   }
4089:   if (offset != size) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Number of permutation entries %D != %D", offset, size);
4090:   /* Check permutation */
4091:   {
4092:     PetscInt *check;

4094:     PetscMalloc1(size, &check);
4095:     for (i = 0; i < size; ++i) {check[i] = -1; if (perm[i] < 0 || perm[i] >= size) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid permutation index p[%D] = %D", i, perm[i]);}
4096:     for (i = 0; i < size; ++i) check[perm[i]] = i;
4097:     for (i = 0; i < size; ++i) {if (check[i] < 0) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Missing permutation index %D", i);}
4098:     PetscFree(check);
4099:   }
4100:   PetscSectionSetClosurePermutation_Internal(section, (PetscObject) dm, size, PETSC_OWN_POINTER, perm);
4101:   return(0);
4102: }

4104: PetscErrorCode DMPlexGetPointDualSpaceFEM(DM dm, PetscInt point, PetscInt field, PetscDualSpace *dspace)
4105: {
4106:   PetscDS        prob;
4107:   PetscInt       depth, Nf, h;
4108:   DMLabel        label;

4112:   DMGetDS(dm, &prob);
4113:   Nf      = prob->Nf;
4114:   label   = dm->depthLabel;
4115:   *dspace = NULL;
4116:   if (field < Nf) {
4117:     PetscObject disc = prob->disc[field];

4119:     if (disc->classid == PETSCFE_CLASSID) {
4120:       PetscDualSpace dsp;

4122:       PetscFEGetDualSpace((PetscFE)disc,&dsp);
4123:       DMLabelGetNumValues(label,&depth);
4124:       DMLabelGetValue(label,point,&h);
4125:       h    = depth - 1 - h;
4126:       if (h) {
4127:         PetscDualSpaceGetHeightSubspace(dsp,h,dspace);
4128:       } else {
4129:         *dspace = dsp;
4130:       }
4131:     }
4132:   }
4133:   return(0);
4134: }


4137: PETSC_STATIC_INLINE PetscErrorCode DMPlexVecGetClosure_Depth1_Static(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[])
4138: {
4139:   PetscScalar    *array, *vArray;
4140:   const PetscInt *cone, *coneO;
4141:   PetscInt        pStart, pEnd, p, numPoints, size = 0, offset = 0;
4142:   PetscErrorCode  ierr;

4145:   PetscSectionGetChart(section, &pStart, &pEnd);
4146:   DMPlexGetConeSize(dm, point, &numPoints);
4147:   DMPlexGetCone(dm, point, &cone);
4148:   DMPlexGetConeOrientation(dm, point, &coneO);
4149:   if (!values || !*values) {
4150:     if ((point >= pStart) && (point < pEnd)) {
4151:       PetscInt dof;

4153:       PetscSectionGetDof(section, point, &dof);
4154:       size += dof;
4155:     }
4156:     for (p = 0; p < numPoints; ++p) {
4157:       const PetscInt cp = cone[p];
4158:       PetscInt       dof;

4160:       if ((cp < pStart) || (cp >= pEnd)) continue;
4161:       PetscSectionGetDof(section, cp, &dof);
4162:       size += dof;
4163:     }
4164:     if (!values) {
4165:       if (csize) *csize = size;
4166:       return(0);
4167:     }
4168:     DMGetWorkArray(dm, size, MPIU_SCALAR, &array);
4169:   } else {
4170:     array = *values;
4171:   }
4172:   size = 0;
4173:   VecGetArray(v, &vArray);
4174:   if ((point >= pStart) && (point < pEnd)) {
4175:     PetscInt     dof, off, d;
4176:     PetscScalar *varr;

4178:     PetscSectionGetDof(section, point, &dof);
4179:     PetscSectionGetOffset(section, point, &off);
4180:     varr = &vArray[off];
4181:     for (d = 0; d < dof; ++d, ++offset) {
4182:       array[offset] = varr[d];
4183:     }
4184:     size += dof;
4185:   }
4186:   for (p = 0; p < numPoints; ++p) {
4187:     const PetscInt cp = cone[p];
4188:     PetscInt       o  = coneO[p];
4189:     PetscInt       dof, off, d;
4190:     PetscScalar   *varr;

4192:     if ((cp < pStart) || (cp >= pEnd)) continue;
4193:     PetscSectionGetDof(section, cp, &dof);
4194:     PetscSectionGetOffset(section, cp, &off);
4195:     varr = &vArray[off];
4196:     if (o >= 0) {
4197:       for (d = 0; d < dof; ++d, ++offset) {
4198:         array[offset] = varr[d];
4199:       }
4200:     } else {
4201:       for (d = dof-1; d >= 0; --d, ++offset) {
4202:         array[offset] = varr[d];
4203:       }
4204:     }
4205:     size += dof;
4206:   }
4207:   VecRestoreArray(v, &vArray);
4208:   if (!*values) {
4209:     if (csize) *csize = size;
4210:     *values = array;
4211:   } else {
4212:     if (size > *csize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Size of input array %D < actual size %D", *csize, size);
4213:     *csize = size;
4214:   }
4215:   return(0);
4216: }

4218: PetscErrorCode DMPlexGetCompressedClosure(DM dm, PetscSection section, PetscInt point, PetscInt *numPoints, PetscInt **points, PetscSection *clSec, IS *clPoints, const PetscInt **clp)
4219: {
4220:   const PetscInt *cla;
4221:   PetscInt       np, *pts = NULL;

4225:   PetscSectionGetClosureIndex(section, (PetscObject) dm, clSec, clPoints);
4226:   if (!*clPoints) {
4227:     PetscInt pStart, pEnd, p, q;

4229:     PetscSectionGetChart(section, &pStart, &pEnd);
4230:     DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &np, &pts);
4231:     /* Compress out points not in the section */
4232:     for (p = 0, q = 0; p < np; p++) {
4233:       PetscInt r = pts[2*p];
4234:       if ((r >= pStart) && (r < pEnd)) {
4235:         pts[q*2]   = r;
4236:         pts[q*2+1] = pts[2*p+1];
4237:         ++q;
4238:       }
4239:     }
4240:     np = q;
4241:     cla = NULL;
4242:   } else {
4243:     PetscInt dof, off;

4245:     PetscSectionGetDof(*clSec, point, &dof);
4246:     PetscSectionGetOffset(*clSec, point, &off);
4247:     ISGetIndices(*clPoints, &cla);
4248:     np   = dof/2;
4249:     pts  = (PetscInt *) &cla[off];
4250:   }
4251:   *numPoints = np;
4252:   *points    = pts;
4253:   *clp       = cla;

4255:   return(0);
4256: }

4258: PetscErrorCode DMPlexRestoreCompressedClosure(DM dm, PetscSection section, PetscInt point, PetscInt *numPoints, PetscInt **points, PetscSection *clSec, IS *clPoints, const PetscInt **clp)
4259: {

4263:   if (!*clPoints) {
4264:     DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, numPoints, points);
4265:   } else {
4266:     ISRestoreIndices(*clPoints, clp);
4267:   }
4268:   *numPoints = 0;
4269:   *points    = NULL;
4270:   *clSec     = NULL;
4271:   *clPoints  = NULL;
4272:   *clp       = NULL;
4273:   return(0);
4274: }

4276: PETSC_STATIC_INLINE PetscErrorCode DMPlexVecGetClosure_Static(DM dm, PetscSection section, PetscInt numPoints, const PetscInt points[], const PetscInt clperm[], const PetscScalar vArray[], PetscInt *size, PetscScalar array[])
4277: {
4278:   PetscInt          offset = 0, p;
4279:   const PetscInt    **perms = NULL;
4280:   const PetscScalar **flips = NULL;
4281:   PetscErrorCode    ierr;

4284:   *size = 0;
4285:   PetscSectionGetPointSyms(section,numPoints,points,&perms,&flips);
4286:   for (p = 0; p < numPoints; p++) {
4287:     const PetscInt    point = points[2*p];
4288:     const PetscInt    *perm = perms ? perms[p] : NULL;
4289:     const PetscScalar *flip = flips ? flips[p] : NULL;
4290:     PetscInt          dof, off, d;
4291:     const PetscScalar *varr;

4293:     PetscSectionGetDof(section, point, &dof);
4294:     PetscSectionGetOffset(section, point, &off);
4295:     varr = &vArray[off];
4296:     if (clperm) {
4297:       if (perm) {
4298:         for (d = 0; d < dof; d++) array[clperm[offset + perm[d]]]  = varr[d];
4299:       } else {
4300:         for (d = 0; d < dof; d++) array[clperm[offset +      d ]]  = varr[d];
4301:       }
4302:       if (flip) {
4303:         for (d = 0; d < dof; d++) array[clperm[offset +      d ]] *= flip[d];
4304:       }
4305:     } else {
4306:       if (perm) {
4307:         for (d = 0; d < dof; d++) array[offset + perm[d]]  = varr[d];
4308:       } else {
4309:         for (d = 0; d < dof; d++) array[offset +      d ]  = varr[d];
4310:       }
4311:       if (flip) {
4312:         for (d = 0; d < dof; d++) array[offset +      d ] *= flip[d];
4313:       }
4314:     }
4315:     offset += dof;
4316:   }
4317:   PetscSectionRestorePointSyms(section,numPoints,points,&perms,&flips);
4318:   *size = offset;
4319:   return(0);
4320: }

4322: PETSC_STATIC_INLINE PetscErrorCode DMPlexVecGetClosure_Fields_Static(DM dm, PetscSection section, PetscInt numPoints, const PetscInt points[], PetscInt numFields, const PetscInt clperm[], const PetscScalar vArray[], PetscInt *size, PetscScalar array[])
4323: {
4324:   PetscInt          offset = 0, f;
4325:   PetscErrorCode    ierr;

4328:   *size = 0;
4329:   for (f = 0; f < numFields; ++f) {
4330:     PetscInt          p;
4331:     const PetscInt    **perms = NULL;
4332:     const PetscScalar **flips = NULL;

4334:     PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms,&flips);
4335:     for (p = 0; p < numPoints; p++) {
4336:       const PetscInt    point = points[2*p];
4337:       PetscInt          fdof, foff, b;
4338:       const PetscScalar *varr;
4339:       const PetscInt    *perm = perms ? perms[p] : NULL;
4340:       const PetscScalar *flip = flips ? flips[p] : NULL;

4342:       PetscSectionGetFieldDof(section, point, f, &fdof);
4343:       PetscSectionGetFieldOffset(section, point, f, &foff);
4344:       varr = &vArray[foff];
4345:       if (clperm) {
4346:         if (perm) {for (b = 0; b < fdof; b++) {array[clperm[offset + perm[b]]]  = varr[b];}}
4347:         else      {for (b = 0; b < fdof; b++) {array[clperm[offset +      b ]]  = varr[b];}}
4348:         if (flip) {for (b = 0; b < fdof; b++) {array[clperm[offset +      b ]] *= flip[b];}}
4349:       } else {
4350:         if (perm) {for (b = 0; b < fdof; b++) {array[offset + perm[b]]  = varr[b];}}
4351:         else      {for (b = 0; b < fdof; b++) {array[offset +      b ]  = varr[b];}}
4352:         if (flip) {for (b = 0; b < fdof; b++) {array[offset +      b ] *= flip[b];}}
4353:       }
4354:       offset += fdof;
4355:     }
4356:     PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms,&flips);
4357:   }
4358:   *size = offset;
4359:   return(0);
4360: }

4362: /*@C
4363:   DMPlexVecGetClosure - Get an array of the values on the closure of 'point'

4365:   Not collective

4367:   Input Parameters:
4368: + dm - The DM
4369: . section - The section describing the layout in v, or NULL to use the default section
4370: . v - The local vector
4371: . point - The point in the DM
4372: . csize - The size of the input values array, or NULL
4373: - values - An array to use for the values, or NULL to have it allocated automatically

4375:   Output Parameters:
4376: + csize - The number of values in the closure
4377: - values - The array of values. If the user provided NULL, it is a borrowed array and should not be freed

4379: $ Note that DMPlexVecGetClosure/DMPlexVecRestoreClosure only allocates the values array if it set to NULL in the
4380: $ calling function. This is because DMPlexVecGetClosure() is typically called in the inner loop of a Vec or Mat
4381: $ assembly function, and a user may already have allocated storage for this operation.
4382: $
4383: $ A typical use could be
4384: $
4385: $  values = NULL;
4386: $  DMPlexVecGetClosure(dm, NULL, v, p, &clSize, &values);
4387: $  for (cl = 0; cl < clSize; ++cl) {
4388: $    <Compute on closure>
4389: $  }
4390: $  DMPlexVecRestoreClosure(dm, NULL, v, p, &clSize, &values);
4391: $
4392: $ or
4393: $
4394: $  PetscMalloc1(clMaxSize, &values);
4395: $  for (p = pStart; p < pEnd; ++p) {
4396: $    clSize = clMaxSize;
4397: $    DMPlexVecGetClosure(dm, NULL, v, p, &clSize, &values);
4398: $    for (cl = 0; cl < clSize; ++cl) {
4399: $      <Compute on closure>
4400: $    }
4401: $  }
4402: $  PetscFree(values);

4404:   Fortran Notes:
4405:   Since it returns an array, this routine is only available in Fortran 90, and you must
4406:   include petsc.h90 in your code.

4408:   The csize argument is not present in the Fortran 90 binding since it is internal to the array.

4410:   Level: intermediate

4412: .seealso DMPlexVecRestoreClosure(), DMPlexVecSetClosure(), DMPlexMatSetClosure()
4413: @*/
4414: PetscErrorCode DMPlexVecGetClosure(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[])
4415: {
4416:   PetscSection       clSection;
4417:   IS                 clPoints;
4418:   PetscScalar       *array;
4419:   const PetscScalar *vArray;
4420:   PetscInt          *points = NULL;
4421:   const PetscInt    *clp, *perm;
4422:   PetscInt           depth, numFields, numPoints, size;
4423:   PetscErrorCode     ierr;

4427:   if (!section) {DMGetLocalSection(dm, &section);}
4430:   DMPlexGetDepth(dm, &depth);
4431:   PetscSectionGetNumFields(section, &numFields);
4432:   if (depth == 1 && numFields < 2) {
4433:     DMPlexVecGetClosure_Depth1_Static(dm, section, v, point, csize, values);
4434:     return(0);
4435:   }
4436:   /* Get points */
4437:   DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
4438:   PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, NULL, &perm);
4439:   /* Get array */
4440:   if (!values || !*values) {
4441:     PetscInt asize = 0, dof, p;

4443:     for (p = 0; p < numPoints*2; p += 2) {
4444:       PetscSectionGetDof(section, points[p], &dof);
4445:       asize += dof;
4446:     }
4447:     if (!values) {
4448:       DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
4449:       if (csize) *csize = asize;
4450:       return(0);
4451:     }
4452:     DMGetWorkArray(dm, asize, MPIU_SCALAR, &array);
4453:   } else {
4454:     array = *values;
4455:   }
4456:   VecGetArrayRead(v, &vArray);
4457:   /* Get values */
4458:   if (numFields > 0) {DMPlexVecGetClosure_Fields_Static(dm, section, numPoints, points, numFields, perm, vArray, &size, array);}
4459:   else               {DMPlexVecGetClosure_Static(dm, section, numPoints, points, perm, vArray, &size, array);}
4460:   /* Cleanup points */
4461:   DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
4462:   /* Cleanup array */
4463:   VecRestoreArrayRead(v, &vArray);
4464:   if (!*values) {
4465:     if (csize) *csize = size;
4466:     *values = array;
4467:   } else {
4468:     if (size > *csize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Size of input array %D < actual size %D", *csize, size);
4469:     *csize = size;
4470:   }
4471:   return(0);
4472: }

4474: /*@C
4475:   DMPlexVecRestoreClosure - Restore the array of the values on the closure of 'point'

4477:   Not collective

4479:   Input Parameters:
4480: + dm - The DM
4481: . section - The section describing the layout in v, or NULL to use the default section
4482: . v - The local vector
4483: . point - The point in the DM
4484: . csize - The number of values in the closure, or NULL
4485: - values - The array of values, which is a borrowed array and should not be freed

4487:   Note that the array values are discarded and not copied back into v. In order to copy values back to v, use DMPlexVecSetClosure()

4489:   Fortran Notes:
4490:   Since it returns an array, this routine is only available in Fortran 90, and you must
4491:   include petsc.h90 in your code.

4493:   The csize argument is not present in the Fortran 90 binding since it is internal to the array.

4495:   Level: intermediate

4497: .seealso DMPlexVecGetClosure(), DMPlexVecSetClosure(), DMPlexMatSetClosure()
4498: @*/
4499: PetscErrorCode DMPlexVecRestoreClosure(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[])
4500: {
4501:   PetscInt       size = 0;

4505:   /* Should work without recalculating size */
4506:   DMRestoreWorkArray(dm, size, MPIU_SCALAR, (void*) values);
4507:   *values = NULL;
4508:   return(0);
4509: }

4511: PETSC_STATIC_INLINE void add   (PetscScalar *x, PetscScalar y) {*x += y;}
4512: PETSC_STATIC_INLINE void insert(PetscScalar *x, PetscScalar y) {*x  = y;}

4514: PETSC_STATIC_INLINE PetscErrorCode updatePoint_private(PetscSection section, PetscInt point, PetscInt dof, void (*fuse)(PetscScalar*, PetscScalar), PetscBool setBC, const PetscInt perm[], const PetscScalar flip[], const PetscInt clperm[], const PetscScalar values[], PetscInt offset, PetscScalar array[])
4515: {
4516:   PetscInt        cdof;   /* The number of constraints on this point */
4517:   const PetscInt *cdofs; /* The indices of the constrained dofs on this point */
4518:   PetscScalar    *a;
4519:   PetscInt        off, cind = 0, k;
4520:   PetscErrorCode  ierr;

4523:   PetscSectionGetConstraintDof(section, point, &cdof);
4524:   PetscSectionGetOffset(section, point, &off);
4525:   a    = &array[off];
4526:   if (!cdof || setBC) {
4527:     if (clperm) {
4528:       if (perm) {for (k = 0; k < dof; ++k) {fuse(&a[k], values[clperm[offset+perm[k]]] * (flip ? flip[perm[k]] : 1.));}}
4529:       else      {for (k = 0; k < dof; ++k) {fuse(&a[k], values[clperm[offset+     k ]] * (flip ? flip[     k ] : 1.));}}
4530:     } else {
4531:       if (perm) {for (k = 0; k < dof; ++k) {fuse(&a[k], values[offset+perm[k]] * (flip ? flip[perm[k]] : 1.));}}
4532:       else      {for (k = 0; k < dof; ++k) {fuse(&a[k], values[offset+     k ] * (flip ? flip[     k ] : 1.));}}
4533:     }
4534:   } else {
4535:     PetscSectionGetConstraintIndices(section, point, &cdofs);
4536:     if (clperm) {
4537:       if (perm) {for (k = 0; k < dof; ++k) {
4538:           if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;}
4539:           fuse(&a[k], values[clperm[offset+perm[k]]] * (flip ? flip[perm[k]] : 1.));
4540:         }
4541:       } else {
4542:         for (k = 0; k < dof; ++k) {
4543:           if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;}
4544:           fuse(&a[k], values[clperm[offset+     k ]] * (flip ? flip[     k ] : 1.));
4545:         }
4546:       }
4547:     } else {
4548:       if (perm) {
4549:         for (k = 0; k < dof; ++k) {
4550:           if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;}
4551:           fuse(&a[k], values[offset+perm[k]] * (flip ? flip[perm[k]] : 1.));
4552:         }
4553:       } else {
4554:         for (k = 0; k < dof; ++k) {
4555:           if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;}
4556:           fuse(&a[k], values[offset+     k ] * (flip ? flip[     k ] : 1.));
4557:         }
4558:       }
4559:     }
4560:   }
4561:   return(0);
4562: }

4564: PETSC_STATIC_INLINE PetscErrorCode updatePointBC_private(PetscSection section, PetscInt point, PetscInt dof, void (*fuse)(PetscScalar*, PetscScalar), const PetscInt perm[], const PetscScalar flip[], const PetscInt clperm[], const PetscScalar values[], PetscInt offset, PetscScalar array[])
4565: {
4566:   PetscInt        cdof;   /* The number of constraints on this point */
4567:   const PetscInt *cdofs; /* The indices of the constrained dofs on this point */
4568:   PetscScalar    *a;
4569:   PetscInt        off, cind = 0, k;
4570:   PetscErrorCode  ierr;

4573:   PetscSectionGetConstraintDof(section, point, &cdof);
4574:   PetscSectionGetOffset(section, point, &off);
4575:   a    = &array[off];
4576:   if (cdof) {
4577:     PetscSectionGetConstraintIndices(section, point, &cdofs);
4578:     if (clperm) {
4579:       if (perm) {
4580:         for (k = 0; k < dof; ++k) {
4581:           if ((cind < cdof) && (k == cdofs[cind])) {
4582:             fuse(&a[k], values[clperm[offset+perm[k]]] * (flip ? flip[perm[k]] : 1.));
4583:             cind++;
4584:           }
4585:         }
4586:       } else {
4587:         for (k = 0; k < dof; ++k) {
4588:           if ((cind < cdof) && (k == cdofs[cind])) {
4589:             fuse(&a[k], values[clperm[offset+     k ]] * (flip ? flip[     k ] : 1.));
4590:             cind++;
4591:           }
4592:         }
4593:       }
4594:     } else {
4595:       if (perm) {
4596:         for (k = 0; k < dof; ++k) {
4597:           if ((cind < cdof) && (k == cdofs[cind])) {
4598:             fuse(&a[k], values[offset+perm[k]] * (flip ? flip[perm[k]] : 1.));
4599:             cind++;
4600:           }
4601:         }
4602:       } else {
4603:         for (k = 0; k < dof; ++k) {
4604:           if ((cind < cdof) && (k == cdofs[cind])) {
4605:             fuse(&a[k], values[offset+     k ] * (flip ? flip[     k ] : 1.));
4606:             cind++;
4607:           }
4608:         }
4609:       }
4610:     }
4611:   }
4612:   return(0);
4613: }

4615: PETSC_STATIC_INLINE PetscErrorCode updatePointFields_private(PetscSection section, PetscInt point, const PetscInt *perm, const PetscScalar *flip, PetscInt f, void (*fuse)(PetscScalar*, PetscScalar), PetscBool setBC, const PetscInt clperm[], const PetscScalar values[], PetscInt *offset, PetscScalar array[])
4616: {
4617:   PetscScalar    *a;
4618:   PetscInt        fdof, foff, fcdof, foffset = *offset;
4619:   const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */
4620:   PetscInt        cind = 0, b;
4621:   PetscErrorCode  ierr;

4624:   PetscSectionGetFieldDof(section, point, f, &fdof);
4625:   PetscSectionGetFieldConstraintDof(section, point, f, &fcdof);
4626:   PetscSectionGetFieldOffset(section, point, f, &foff);
4627:   a    = &array[foff];
4628:   if (!fcdof || setBC) {
4629:     if (clperm) {
4630:       if (perm) {for (b = 0; b < fdof; b++) {fuse(&a[b], values[clperm[foffset+perm[b]]] * (flip ? flip[perm[b]] : 1.));}}
4631:       else      {for (b = 0; b < fdof; b++) {fuse(&a[b], values[clperm[foffset+     b ]] * (flip ? flip[     b ] : 1.));}}
4632:     } else {
4633:       if (perm) {for (b = 0; b < fdof; b++) {fuse(&a[b], values[foffset+perm[b]] * (flip ? flip[perm[b]] : 1.));}}
4634:       else      {for (b = 0; b < fdof; b++) {fuse(&a[b], values[foffset+     b ] * (flip ? flip[     b ] : 1.));}}
4635:     }
4636:   } else {
4637:     PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);
4638:     if (clperm) {
4639:       if (perm) {
4640:         for (b = 0; b < fdof; b++) {
4641:           if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; continue;}
4642:           fuse(&a[b], values[clperm[foffset+perm[b]]] * (flip ? flip[perm[b]] : 1.));
4643:         }
4644:       } else {
4645:         for (b = 0; b < fdof; b++) {
4646:           if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; continue;}
4647:           fuse(&a[b], values[clperm[foffset+     b ]] * (flip ? flip[     b ] : 1.));
4648:         }
4649:       }
4650:     } else {
4651:       if (perm) {
4652:         for (b = 0; b < fdof; b++) {
4653:           if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; continue;}
4654:           fuse(&a[b], values[foffset+perm[b]] * (flip ? flip[perm[b]] : 1.));
4655:         }
4656:       } else {
4657:         for (b = 0; b < fdof; b++) {
4658:           if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; continue;}
4659:           fuse(&a[b], values[foffset+     b ] * (flip ? flip[     b ] : 1.));
4660:         }
4661:       }
4662:     }
4663:   }
4664:   *offset += fdof;
4665:   return(0);
4666: }

4668: PETSC_STATIC_INLINE PetscErrorCode updatePointFieldsBC_private(PetscSection section, PetscInt point, const PetscInt perm[], const PetscScalar flip[], PetscInt f, PetscInt Ncc, const PetscInt comps[], void (*fuse)(PetscScalar*, PetscScalar), const PetscInt clperm[], const PetscScalar values[], PetscInt *offset, PetscScalar array[])
4669: {
4670:   PetscScalar    *a;
4671:   PetscInt        fdof, foff, fcdof, foffset = *offset;
4672:   const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */
4673:   PetscInt        cind = 0, ncind = 0, b;
4674:   PetscBool       ncSet, fcSet;
4675:   PetscErrorCode  ierr;

4678:   PetscSectionGetFieldDof(section, point, f, &fdof);
4679:   PetscSectionGetFieldConstraintDof(section, point, f, &fcdof);
4680:   PetscSectionGetFieldOffset(section, point, f, &foff);
4681:   a    = &array[foff];
4682:   if (fcdof) {
4683:     /* We just override fcdof and fcdofs with Ncc and comps */
4684:     PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);
4685:     if (clperm) {
4686:       if (perm) {
4687:         if (comps) {
4688:           for (b = 0; b < fdof; b++) {
4689:             ncSet = fcSet = PETSC_FALSE;
4690:             if ((ncind < Ncc)  && (b == comps[ncind])) {++ncind; ncSet = PETSC_TRUE;}
4691:             if ((cind < fcdof) && (b == fcdofs[cind])) {++cind;  fcSet = PETSC_TRUE;}
4692:             if (ncSet && fcSet) {fuse(&a[b], values[clperm[foffset+perm[b]]] * (flip ? flip[perm[b]] : 1.));}
4693:           }
4694:         } else {
4695:           for (b = 0; b < fdof; b++) {
4696:             if ((cind < fcdof) && (b == fcdofs[cind])) {
4697:               fuse(&a[b], values[clperm[foffset+perm[b]]] * (flip ? flip[perm[b]] : 1.));
4698:               ++cind;
4699:             }
4700:           }
4701:         }
4702:       } else {
4703:         if (comps) {
4704:           for (b = 0; b < fdof; b++) {
4705:             ncSet = fcSet = PETSC_FALSE;
4706:             if ((ncind < Ncc)  && (b == comps[ncind])) {++ncind; ncSet = PETSC_TRUE;}
4707:             if ((cind < fcdof) && (b == fcdofs[cind])) {++cind;  fcSet = PETSC_TRUE;}
4708:             if (ncSet && fcSet) {fuse(&a[b], values[clperm[foffset+     b ]] * (flip ? flip[     b ] : 1.));}
4709:           }
4710:         } else {
4711:           for (b = 0; b < fdof; b++) {
4712:             if ((cind < fcdof) && (b == fcdofs[cind])) {
4713:               fuse(&a[b], values[clperm[foffset+     b ]] * (flip ? flip[     b ] : 1.));
4714:               ++cind;
4715:             }
4716:           }
4717:         }
4718:       }
4719:     } else {
4720:       if (perm) {
4721:         if (comps) {
4722:           for (b = 0; b < fdof; b++) {
4723:             ncSet = fcSet = PETSC_FALSE;
4724:             if ((ncind < Ncc)  && (b == comps[ncind])) {++ncind; ncSet = PETSC_TRUE;}
4725:             if ((cind < fcdof) && (b == fcdofs[cind])) {++cind;  fcSet = PETSC_TRUE;}
4726:             if (ncSet && fcSet) {fuse(&a[b], values[foffset+perm[b]] * (flip ? flip[perm[b]] : 1.));}
4727:           }
4728:         } else {
4729:           for (b = 0; b < fdof; b++) {
4730:             if ((cind < fcdof) && (b == fcdofs[cind])) {
4731:               fuse(&a[b], values[foffset+perm[b]] * (flip ? flip[perm[b]] : 1.));
4732:               ++cind;
4733:             }
4734:           }
4735:         }
4736:       } else {
4737:         if (comps) {
4738:           for (b = 0; b < fdof; b++) {
4739:             ncSet = fcSet = PETSC_FALSE;
4740:             if ((ncind < Ncc)  && (b == comps[ncind])) {++ncind; ncSet = PETSC_TRUE;}
4741:             if ((cind < fcdof) && (b == fcdofs[cind])) {++cind;  fcSet = PETSC_TRUE;}
4742:             if (ncSet && fcSet) {fuse(&a[b], values[foffset+     b ] * (flip ? flip[     b ] : 1.));}
4743:           }
4744:         } else {
4745:           for (b = 0; b < fdof; b++) {
4746:             if ((cind < fcdof) && (b == fcdofs[cind])) {
4747:               fuse(&a[b], values[foffset+     b ] * (flip ? flip[     b ] : 1.));
4748:               ++cind;
4749:             }
4750:           }
4751:         }
4752:       }
4753:     }
4754:   }
4755:   *offset += fdof;
4756:   return(0);
4757: }

4759: PETSC_STATIC_INLINE PetscErrorCode DMPlexVecSetClosure_Depth1_Static(DM dm, PetscSection section, Vec v, PetscInt point, const PetscScalar values[], InsertMode mode)
4760: {
4761:   PetscScalar    *array;
4762:   const PetscInt *cone, *coneO;
4763:   PetscInt        pStart, pEnd, p, numPoints, off, dof;
4764:   PetscErrorCode  ierr;

4767:   PetscSectionGetChart(section, &pStart, &pEnd);
4768:   DMPlexGetConeSize(dm, point, &numPoints);
4769:   DMPlexGetCone(dm, point, &cone);
4770:   DMPlexGetConeOrientation(dm, point, &coneO);
4771:   VecGetArray(v, &array);
4772:   for (p = 0, off = 0; p <= numPoints; ++p, off += dof) {
4773:     const PetscInt cp = !p ? point : cone[p-1];
4774:     const PetscInt o  = !p ? 0     : coneO[p-1];

4776:     if ((cp < pStart) || (cp >= pEnd)) {dof = 0; continue;}
4777:     PetscSectionGetDof(section, cp, &dof);
4778:     /* ADD_VALUES */
4779:     {
4780:       const PetscInt *cdofs; /* The indices of the constrained dofs on this point */
4781:       PetscScalar    *a;
4782:       PetscInt        cdof, coff, cind = 0, k;

4784:       PetscSectionGetConstraintDof(section, cp, &cdof);
4785:       PetscSectionGetOffset(section, cp, &coff);
4786:       a    = &array[coff];
4787:       if (!cdof) {
4788:         if (o >= 0) {
4789:           for (k = 0; k < dof; ++k) {
4790:             a[k] += values[off+k];
4791:           }
4792:         } else {
4793:           for (k = 0; k < dof; ++k) {
4794:             a[k] += values[off+dof-k-1];
4795:           }
4796:         }
4797:       } else {
4798:         PetscSectionGetConstraintIndices(section, cp, &cdofs);
4799:         if (o >= 0) {
4800:           for (k = 0; k < dof; ++k) {
4801:             if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;}
4802:             a[k] += values[off+k];
4803:           }
4804:         } else {
4805:           for (k = 0; k < dof; ++k) {
4806:             if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;}
4807:             a[k] += values[off+dof-k-1];
4808:           }
4809:         }
4810:       }
4811:     }
4812:   }
4813:   VecRestoreArray(v, &array);
4814:   return(0);
4815: }

4817: /*@C
4818:   DMPlexVecSetClosure - Set an array of the values on the closure of 'point'

4820:   Not collective

4822:   Input Parameters:
4823: + dm - The DM
4824: . section - The section describing the layout in v, or NULL to use the default section
4825: . v - The local vector
4826: . point - The point in the DM
4827: . values - The array of values
4828: - mode - The insert mode. One of INSERT_ALL_VALUES, ADD_ALL_VALUES, INSERT_VALUES, ADD_VALUES, INSERT_BC_VALUES, and ADD_BC_VALUES,
4829:          where INSERT_ALL_VALUES and ADD_ALL_VALUES also overwrite boundary conditions.

4831:   Fortran Notes:
4832:   This routine is only available in Fortran 90, and you must include petsc.h90 in your code.

4834:   Level: intermediate

4836: .seealso DMPlexVecGetClosure(), DMPlexMatSetClosure()
4837: @*/
4838: PetscErrorCode DMPlexVecSetClosure(DM dm, PetscSection section, Vec v, PetscInt point, const PetscScalar values[], InsertMode mode)
4839: {
4840:   PetscSection    clSection;
4841:   IS              clPoints;
4842:   PetscScalar    *array;
4843:   PetscInt       *points = NULL;
4844:   const PetscInt *clp, *clperm;
4845:   PetscInt        depth, numFields, numPoints, p;
4846:   PetscErrorCode  ierr;

4850:   if (!section) {DMGetLocalSection(dm, &section);}
4853:   DMPlexGetDepth(dm, &depth);
4854:   PetscSectionGetNumFields(section, &numFields);
4855:   if (depth == 1 && numFields < 2 && mode == ADD_VALUES) {
4856:     DMPlexVecSetClosure_Depth1_Static(dm, section, v, point, values, mode);
4857:     return(0);
4858:   }
4859:   /* Get points */
4860:   PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, NULL, &clperm);
4861:   DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
4862:   /* Get array */
4863:   VecGetArray(v, &array);
4864:   /* Get values */
4865:   if (numFields > 0) {
4866:     PetscInt offset = 0, f;
4867:     for (f = 0; f < numFields; ++f) {
4868:       const PetscInt    **perms = NULL;
4869:       const PetscScalar **flips = NULL;

4871:       PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms,&flips);
4872:       switch (mode) {
4873:       case INSERT_VALUES:
4874:         for (p = 0; p < numPoints; p++) {
4875:           const PetscInt    point = points[2*p];
4876:           const PetscInt    *perm = perms ? perms[p] : NULL;
4877:           const PetscScalar *flip = flips ? flips[p] : NULL;
4878:           updatePointFields_private(section, point, perm, flip, f, insert, PETSC_FALSE, clperm, values, &offset, array);
4879:         } break;
4880:       case INSERT_ALL_VALUES:
4881:         for (p = 0; p < numPoints; p++) {
4882:           const PetscInt    point = points[2*p];
4883:           const PetscInt    *perm = perms ? perms[p] : NULL;
4884:           const PetscScalar *flip = flips ? flips[p] : NULL;
4885:           updatePointFields_private(section, point, perm, flip, f, insert, PETSC_TRUE, clperm, values, &offset, array);
4886:         } break;
4887:       case INSERT_BC_VALUES:
4888:         for (p = 0; p < numPoints; p++) {
4889:           const PetscInt    point = points[2*p];
4890:           const PetscInt    *perm = perms ? perms[p] : NULL;
4891:           const PetscScalar *flip = flips ? flips[p] : NULL;
4892:           updatePointFieldsBC_private(section, point, perm, flip, f, -1, NULL, insert, clperm, values, &offset, array);
4893:         } break;
4894:       case ADD_VALUES:
4895:         for (p = 0; p < numPoints; p++) {
4896:           const PetscInt    point = points[2*p];
4897:           const PetscInt    *perm = perms ? perms[p] : NULL;
4898:           const PetscScalar *flip = flips ? flips[p] : NULL;
4899:           updatePointFields_private(section, point, perm, flip, f, add, PETSC_FALSE, clperm, values, &offset, array);
4900:         } break;
4901:       case ADD_ALL_VALUES:
4902:         for (p = 0; p < numPoints; p++) {
4903:           const PetscInt    point = points[2*p];
4904:           const PetscInt    *perm = perms ? perms[p] : NULL;
4905:           const PetscScalar *flip = flips ? flips[p] : NULL;
4906:           updatePointFields_private(section, point, perm, flip, f, add, PETSC_TRUE, clperm, values, &offset, array);
4907:         } break;
4908:       case ADD_BC_VALUES:
4909:         for (p = 0; p < numPoints; p++) {
4910:           const PetscInt    point = points[2*p];
4911:           const PetscInt    *perm = perms ? perms[p] : NULL;
4912:           const PetscScalar *flip = flips ? flips[p] : NULL;
4913:           updatePointFieldsBC_private(section, point, perm, flip, f, -1, NULL, add, clperm, values, &offset, array);
4914:         } break;
4915:       default:
4916:         SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode);
4917:       }
4918:       PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms,&flips);
4919:     }
4920:   } else {
4921:     PetscInt dof, off;
4922:     const PetscInt    **perms = NULL;
4923:     const PetscScalar **flips = NULL;

4925:     PetscSectionGetPointSyms(section,numPoints,points,&perms,&flips);
4926:     switch (mode) {
4927:     case INSERT_VALUES:
4928:       for (p = 0, off = 0; p < numPoints; p++, off += dof) {
4929:         const PetscInt    point = points[2*p];
4930:         const PetscInt    *perm = perms ? perms[p] : NULL;
4931:         const PetscScalar *flip = flips ? flips[p] : NULL;
4932:         PetscSectionGetDof(section, point, &dof);
4933:         updatePoint_private(section, point, dof, insert, PETSC_FALSE, perm, flip, clperm, values, off, array);
4934:       } break;
4935:     case INSERT_ALL_VALUES:
4936:       for (p = 0, off = 0; p < numPoints; p++, off += dof) {
4937:         const PetscInt    point = points[2*p];
4938:         const PetscInt    *perm = perms ? perms[p] : NULL;
4939:         const PetscScalar *flip = flips ? flips[p] : NULL;
4940:         PetscSectionGetDof(section, point, &dof);
4941:         updatePoint_private(section, point, dof, insert, PETSC_TRUE,  perm, flip, clperm, values, off, array);
4942:       } break;
4943:     case INSERT_BC_VALUES:
4944:       for (p = 0, off = 0; p < numPoints; p++, off += dof) {
4945:         const PetscInt    point = points[2*p];
4946:         const PetscInt    *perm = perms ? perms[p] : NULL;
4947:         const PetscScalar *flip = flips ? flips[p] : NULL;
4948:         PetscSectionGetDof(section, point, &dof);
4949:         updatePointBC_private(section, point, dof, insert,  perm, flip, clperm, values, off, array);
4950:       } break;
4951:     case ADD_VALUES:
4952:       for (p = 0, off = 0; p < numPoints; p++, off += dof) {
4953:         const PetscInt    point = points[2*p];
4954:         const PetscInt    *perm = perms ? perms[p] : NULL;
4955:         const PetscScalar *flip = flips ? flips[p] : NULL;
4956:         PetscSectionGetDof(section, point, &dof);
4957:         updatePoint_private(section, point, dof, add,    PETSC_FALSE, perm, flip, clperm, values, off, array);
4958:       } break;
4959:     case ADD_ALL_VALUES:
4960:       for (p = 0, off = 0; p < numPoints; p++, off += dof) {
4961:         const PetscInt    point = points[2*p];
4962:         const PetscInt    *perm = perms ? perms[p] : NULL;
4963:         const PetscScalar *flip = flips ? flips[p] : NULL;
4964:         PetscSectionGetDof(section, point, &dof);
4965:         updatePoint_private(section, point, dof, add,    PETSC_TRUE,  perm, flip, clperm, values, off, array);
4966:       } break;
4967:     case ADD_BC_VALUES:
4968:       for (p = 0, off = 0; p < numPoints; p++, off += dof) {
4969:         const PetscInt    point = points[2*p];
4970:         const PetscInt    *perm = perms ? perms[p] : NULL;
4971:         const PetscScalar *flip = flips ? flips[p] : NULL;
4972:         PetscSectionGetDof(section, point, &dof);
4973:         updatePointBC_private(section, point, dof, add,  perm, flip, clperm, values, off, array);
4974:       } break;
4975:     default:
4976:       SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode);
4977:     }
4978:     PetscSectionRestorePointSyms(section,numPoints,points,&perms,&flips);
4979:   }
4980:   /* Cleanup points */
4981:   DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
4982:   /* Cleanup array */
4983:   VecRestoreArray(v, &array);
4984:   return(0);
4985: }

4987: PetscErrorCode DMPlexVecSetFieldClosure_Internal(DM dm, PetscSection section, Vec v, PetscBool fieldActive[], PetscInt point, PetscInt Ncc, const PetscInt comps[], const PetscScalar values[], InsertMode mode)
4988: {
4989:   PetscSection      clSection;
4990:   IS                clPoints;
4991:   PetscScalar       *array;
4992:   PetscInt          *points = NULL;
4993:   const PetscInt    *clp, *clperm;
4994:   PetscInt          numFields, numPoints, p;
4995:   PetscInt          offset = 0, f;
4996:   PetscErrorCode    ierr;

5000:   if (!section) {DMGetLocalSection(dm, &section);}
5003:   PetscSectionGetNumFields(section, &numFields);
5004:   /* Get points */
5005:   PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, NULL, &clperm);
5006:   DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
5007:   /* Get array */
5008:   VecGetArray(v, &array);
5009:   /* Get values */
5010:   for (f = 0; f < numFields; ++f) {
5011:     const PetscInt    **perms = NULL;
5012:     const PetscScalar **flips = NULL;

5014:     if (!fieldActive[f]) {
5015:       for (p = 0; p < numPoints*2; p += 2) {
5016:         PetscInt fdof;
5017:         PetscSectionGetFieldDof(section, points[p], f, &fdof);
5018:         offset += fdof;
5019:       }
5020:       continue;
5021:     }
5022:     PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms,&flips);
5023:     switch (mode) {
5024:     case INSERT_VALUES:
5025:       for (p = 0; p < numPoints; p++) {
5026:         const PetscInt    point = points[2*p];
5027:         const PetscInt    *perm = perms ? perms[p] : NULL;
5028:         const PetscScalar *flip = flips ? flips[p] : NULL;
5029:         updatePointFields_private(section, point, perm, flip, f, insert, PETSC_FALSE, clperm, values, &offset, array);
5030:       } break;
5031:     case INSERT_ALL_VALUES:
5032:       for (p = 0; p < numPoints; p++) {
5033:         const PetscInt    point = points[2*p];
5034:         const PetscInt    *perm = perms ? perms[p] : NULL;
5035:         const PetscScalar *flip = flips ? flips[p] : NULL;
5036:         updatePointFields_private(section, point, perm, flip, f, insert, PETSC_TRUE, clperm, values, &offset, array);
5037:         } break;
5038:     case INSERT_BC_VALUES:
5039:       for (p = 0; p < numPoints; p++) {
5040:         const PetscInt    point = points[2*p];
5041:         const PetscInt    *perm = perms ? perms[p] : NULL;
5042:         const PetscScalar *flip = flips ? flips[p] : NULL;
5043:         updatePointFieldsBC_private(section, point, perm, flip, f, Ncc, comps, insert, clperm, values, &offset, array);
5044:       } break;
5045:     case ADD_VALUES:
5046:       for (p = 0; p < numPoints; p++) {
5047:         const PetscInt    point = points[2*p];
5048:         const PetscInt    *perm = perms ? perms[p] : NULL;
5049:         const PetscScalar *flip = flips ? flips[p] : NULL;
5050:         updatePointFields_private(section, point, perm, flip, f, add, PETSC_FALSE, clperm, values, &offset, array);
5051:       } break;
5052:     case ADD_ALL_VALUES:
5053:       for (p = 0; p < numPoints; p++) {
5054:         const PetscInt    point = points[2*p];
5055:         const PetscInt    *perm = perms ? perms[p] : NULL;
5056:         const PetscScalar *flip = flips ? flips[p] : NULL;
5057:         updatePointFields_private(section, point, perm, flip, f, add, PETSC_TRUE, clperm, values, &offset, array);
5058:       } break;
5059:     default:
5060:       SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode);
5061:     }
5062:     PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms,&flips);
5063:   }
5064:   /* Cleanup points */
5065:   DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
5066:   /* Cleanup array */
5067:   VecRestoreArray(v, &array);
5068:   return(0);
5069: }

5071: static PetscErrorCode DMPlexPrintMatSetValues(PetscViewer viewer, Mat A, PetscInt point, PetscInt numRIndices, const PetscInt rindices[], PetscInt numCIndices, const PetscInt cindices[], const PetscScalar values[])
5072: {
5073:   PetscMPIInt    rank;
5074:   PetscInt       i, j;

5078:   MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank);
5079:   PetscViewerASCIIPrintf(viewer, "[%d]mat for point %D\n", rank, point);
5080:   for (i = 0; i < numRIndices; i++) {PetscViewerASCIIPrintf(viewer, "[%d]mat row indices[%D] = %D\n", rank, i, rindices[i]);}
5081:   for (i = 0; i < numCIndices; i++) {PetscViewerASCIIPrintf(viewer, "[%d]mat col indices[%D] = %D\n", rank, i, cindices[i]);}
5082:   numCIndices = numCIndices ? numCIndices : numRIndices;
5083:   for (i = 0; i < numRIndices; i++) {
5084:     PetscViewerASCIIPrintf(viewer, "[%d]", rank);
5085:     for (j = 0; j < numCIndices; j++) {
5086: #if defined(PETSC_USE_COMPLEX)
5087:       PetscViewerASCIIPrintf(viewer, " (%g,%g)", (double)PetscRealPart(values[i*numCIndices+j]), (double)PetscImaginaryPart(values[i*numCIndices+j]));
5088: #else
5089:       PetscViewerASCIIPrintf(viewer, " %g", (double)values[i*numCIndices+j]);
5090: #endif
5091:     }
5092:     PetscViewerASCIIPrintf(viewer, "\n");
5093:   }
5094:   return(0);
5095: }

5097: /*
5098:   DMPlexGetIndicesPoint_Internal - Add the indices for dofs on a point to an index array

5100:   Input Parameters:
5101: + section - The section for this data layout
5102: . point   - The point contributing dofs with these indices
5103: . off     - The global offset of this point
5104: . loff    - The local offset of each field
5105: . setBC   - The flag determining whether to include indices of bounsary values
5106: . perm    - A permutation of the dofs on this point, or NULL
5107: - indperm - A permutation of the entire indices array, or NULL

5109:   Output Parameter:
5110: . indices - Indices for dofs on this point

5112:   Level: developer

5114:   Note: The indices could be local or global, depending on the value of 'off'.
5115: */
5116: PetscErrorCode DMPlexGetIndicesPoint_Internal(PetscSection section, PetscInt point, PetscInt off, PetscInt *loff, PetscBool setBC, const PetscInt perm[], const PetscInt indperm[], PetscInt indices[])
5117: {
5118:   PetscInt        dof;   /* The number of unknowns on this point */
5119:   PetscInt        cdof;  /* The number of constraints on this point */
5120:   const PetscInt *cdofs; /* The indices of the constrained dofs on this point */
5121:   PetscInt        cind = 0, k;
5122:   PetscErrorCode  ierr;

5125:   PetscSectionGetDof(section, point, &dof);
5126:   PetscSectionGetConstraintDof(section, point, &cdof);
5127:   if (!cdof || setBC) {
5128:     for (k = 0; k < dof; ++k) {
5129:       const PetscInt preind = perm ? *loff+perm[k] : *loff+k;
5130:       const PetscInt ind    = indperm ? indperm[preind] : preind;

5132:       indices[ind] = off + k;
5133:     }
5134:   } else {
5135:     PetscSectionGetConstraintIndices(section, point, &cdofs);
5136:     for (k = 0; k < dof; ++k) {
5137:       const PetscInt preind = perm ? *loff+perm[k] : *loff+k;
5138:       const PetscInt ind    = indperm ? indperm[preind] : preind;

5140:       if ((cind < cdof) && (k == cdofs[cind])) {
5141:         /* Insert check for returning constrained indices */
5142:         indices[ind] = -(off+k+1);
5143:         ++cind;
5144:       } else {
5145:         indices[ind] = off+k-cind;
5146:       }
5147:     }
5148:   }
5149:   *loff += dof;
5150:   return(0);
5151: }

5153: /*
5154:   This version only believes the point offset from the globalSection

5156:  . off - The global offset of this point
5157: */
5158: PetscErrorCode DMPlexGetIndicesPointFields_Internal(PetscSection section, PetscInt point, PetscInt off, PetscInt foffs[], PetscBool setBC, const PetscInt ***perms, PetscInt permsoff, const PetscInt indperm[], PetscInt indices[])
5159: {
5160:   PetscInt       numFields, foff, f;

5164:   PetscSectionGetNumFields(section, &numFields);
5165:   for (f = 0, foff = 0; f < numFields; ++f) {
5166:     PetscInt        fdof, cfdof;
5167:     const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */
5168:     PetscInt        cind = 0, b;
5169:     const PetscInt  *perm = (perms && perms[f]) ? perms[f][permsoff] : NULL;

5171:     PetscSectionGetFieldDof(section, point, f, &fdof);
5172:     PetscSectionGetFieldConstraintDof(section, point, f, &cfdof);
5173:     if (!cfdof || setBC) {
5174:       for (b = 0; b < fdof; ++b) {
5175:         const PetscInt preind = perm ? foffs[f]+perm[b] : foffs[f]+b;
5176:         const PetscInt ind    = indperm ? indperm[preind] : preind;

5178:         indices[ind] = off+foff+b;
5179:       }
5180:     } else {
5181:       PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);
5182:       for (b = 0; b < fdof; ++b) {
5183:         const PetscInt preind = perm ? foffs[f]+perm[b] : foffs[f]+b;
5184:         const PetscInt ind    = indperm ? indperm[preind] : preind;

5186:         if ((cind < cfdof) && (b == fcdofs[cind])) {
5187:           indices[ind] = -(off+foff+b+1);
5188:           ++cind;
5189:         } else {
5190:           indices[ind] = off+foff+b-cind;
5191:         }
5192:       }
5193:     }
5194:     foff     += (setBC ? fdof : (fdof - cfdof));
5195:     foffs[f] += fdof;
5196:   }
5197:   return(0);
5198: }

5200: /*
5201:   This version believes the globalSection offsets for each field, rather than just the point offset

5203:  . foffs - The offset into 'indices' for each field, since it is segregated by field
5204: */
5205: PetscErrorCode DMPlexGetIndicesPointFieldsSplit_Internal(PetscSection section, PetscSection globalSection, PetscInt point, PetscInt foffs[], PetscBool setBC, const PetscInt ***perms, PetscInt permsoff, const PetscInt indperm[], PetscInt indices[])
5206: {
5207:   PetscInt       numFields, foff, f;

5211:   PetscSectionGetNumFields(section, &numFields);
5212:   for (f = 0; f < numFields; ++f) {
5213:     PetscInt        fdof, cfdof;
5214:     const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */
5215:     PetscInt        cind = 0, b;
5216:     const PetscInt  *perm = (perms && perms[f]) ? perms[f][permsoff] : NULL;

5218:     PetscSectionGetFieldDof(section, point, f, &fdof);
5219:     PetscSectionGetFieldConstraintDof(section, point, f, &cfdof);
5220:     PetscSectionGetFieldOffset(globalSection, point, f, &foff);
5221:     if (!cfdof || setBC) {
5222:       for (b = 0; b < fdof; ++b) {
5223:         const PetscInt preind = perm ? foffs[f]+perm[b] : foffs[f]+b;
5224:         const PetscInt ind    = indperm ? indperm[preind] : preind;

5226:         indices[ind] = foff+b;
5227:       }
5228:     } else {
5229:       PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);
5230:       for (b = 0; b < fdof; ++b) {
5231:         const PetscInt preind = perm ? foffs[f]+perm[b] : foffs[f]+b;
5232:         const PetscInt ind    = indperm ? indperm[preind] : preind;

5234:         if ((cind < cfdof) && (b == fcdofs[cind])) {
5235:           indices[ind] = -(foff+b+1);
5236:           ++cind;
5237:         } else {
5238:           indices[ind] = foff+b-cind;
5239:         }
5240:       }
5241:     }
5242:     foffs[f] += fdof;
5243:   }
5244:   return(0);
5245: }

5247: PetscErrorCode DMPlexAnchorsModifyMat(DM dm, PetscSection section, PetscInt numPoints, PetscInt numIndices, const PetscInt points[], const PetscInt ***perms, const PetscScalar values[], PetscInt *outNumPoints, PetscInt *outNumIndices, PetscInt *outPoints[], PetscScalar *outValues[], PetscInt offsets[], PetscBool multiplyLeft)
5248: {
5249:   Mat             cMat;
5250:   PetscSection    aSec, cSec;
5251:   IS              aIS;
5252:   PetscInt        aStart = -1, aEnd = -1;
5253:   const PetscInt  *anchors;
5254:   PetscInt        numFields, f, p, q, newP = 0;
5255:   PetscInt        newNumPoints = 0, newNumIndices = 0;
5256:   PetscInt        *newPoints, *indices, *newIndices;
5257:   PetscInt        maxAnchor, maxDof;
5258:   PetscInt        newOffsets[32];
5259:   PetscInt        *pointMatOffsets[32];
5260:   PetscInt        *newPointOffsets[32];
5261:   PetscScalar     *pointMat[32];
5262:   PetscScalar     *newValues=NULL,*tmpValues;
5263:   PetscBool       anyConstrained = PETSC_FALSE;
5264:   PetscErrorCode  ierr;

5269:   PetscSectionGetNumFields(section, &numFields);

5271:   DMPlexGetAnchors(dm,&aSec,&aIS);
5272:   /* if there are point-to-point constraints */
5273:   if (aSec) {
5274:     PetscArrayzero(newOffsets, 32);
5275:     ISGetIndices(aIS,&anchors);
5276:     PetscSectionGetChart(aSec,&aStart,&aEnd);
5277:     /* figure out how many points are going to be in the new element matrix
5278:      * (we allow double counting, because it's all just going to be summed
5279:      * into the global matrix anyway) */
5280:     for (p = 0; p < 2*numPoints; p+=2) {
5281:       PetscInt b    = points[p];
5282:       PetscInt bDof = 0, bSecDof;

5284:       PetscSectionGetDof(section,b,&bSecDof);
5285:       if (!bSecDof) {
5286:         continue;
5287:       }
5288:       if (b >= aStart && b < aEnd) {
5289:         PetscSectionGetDof(aSec,b,&bDof);
5290:       }
5291:       if (bDof) {
5292:         /* this point is constrained */
5293:         /* it is going to be replaced by its anchors */
5294:         PetscInt bOff, q;

5296:         anyConstrained = PETSC_TRUE;
5297:         newNumPoints  += bDof;
5298:         PetscSectionGetOffset(aSec,b,&bOff);
5299:         for (q = 0; q < bDof; q++) {
5300:           PetscInt a = anchors[bOff + q];
5301:           PetscInt aDof;

5303:           PetscSectionGetDof(section,a,&aDof);
5304:           newNumIndices += aDof;
5305:           for (f = 0; f < numFields; ++f) {
5306:             PetscInt fDof;

5308:             PetscSectionGetFieldDof(section, a, f, &fDof);
5309:             newOffsets[f+1] += fDof;
5310:           }
5311:         }
5312:       }
5313:       else {
5314:         /* this point is not constrained */
5315:         newNumPoints++;
5316:         newNumIndices += bSecDof;
5317:         for (f = 0; f < numFields; ++f) {
5318:           PetscInt fDof;

5320:           PetscSectionGetFieldDof(section, b, f, &fDof);
5321:           newOffsets[f+1] += fDof;
5322:         }
5323:       }
5324:     }
5325:   }
5326:   if (!anyConstrained) {
5327:     if (outNumPoints)  *outNumPoints  = 0;
5328:     if (outNumIndices) *outNumIndices = 0;
5329:     if (outPoints)     *outPoints     = NULL;
5330:     if (outValues)     *outValues     = NULL;
5331:     if (aSec) {ISRestoreIndices(aIS,&anchors);}
5332:     return(0);
5333:   }

5335:   if (outNumPoints)  *outNumPoints  = newNumPoints;
5336:   if (outNumIndices) *outNumIndices = newNumIndices;

5338:   for (f = 0; f < numFields; ++f) newOffsets[f+1] += newOffsets[f];

5340:   if (!outPoints && !outValues) {
5341:     if (offsets) {
5342:       for (f = 0; f <= numFields; f++) {
5343:         offsets[f] = newOffsets[f];
5344:       }
5345:     }
5346:     if (aSec) {ISRestoreIndices(aIS,&anchors);}
5347:     return(0);
5348:   }

5350:   if (numFields && newOffsets[numFields] != newNumIndices) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", newOffsets[numFields], newNumIndices);

5352:   DMGetDefaultConstraints(dm, &cSec, &cMat);

5354:   /* workspaces */
5355:   if (numFields) {
5356:     for (f = 0; f < numFields; f++) {
5357:       DMGetWorkArray(dm,numPoints+1,MPIU_INT,&pointMatOffsets[f]);
5358:       DMGetWorkArray(dm,numPoints+1,MPIU_INT,&newPointOffsets[f]);
5359:     }
5360:   }
5361:   else {
5362:     DMGetWorkArray(dm,numPoints+1,MPIU_INT,&pointMatOffsets[0]);
5363:     DMGetWorkArray(dm,numPoints,MPIU_INT,&newPointOffsets[0]);
5364:   }

5366:   /* get workspaces for the point-to-point matrices */
5367:   if (numFields) {
5368:     PetscInt totalOffset, totalMatOffset;

5370:     for (p = 0; p < numPoints; p++) {
5371:       PetscInt b    = points[2*p];
5372:       PetscInt bDof = 0, bSecDof;

5374:       PetscSectionGetDof(section,b,&bSecDof);
5375:       if (!bSecDof) {
5376:         for (f = 0; f < numFields; f++) {
5377:           newPointOffsets[f][p + 1] = 0;
5378:           pointMatOffsets[f][p + 1] = 0;
5379:         }
5380:         continue;
5381:       }
5382:       if (b >= aStart && b < aEnd) {
5383:         PetscSectionGetDof(aSec, b, &bDof);
5384:       }
5385:       if (bDof) {
5386:         for (f = 0; f < numFields; f++) {
5387:           PetscInt fDof, q, bOff, allFDof = 0;

5389:           PetscSectionGetFieldDof(section, b, f, &fDof);
5390:           PetscSectionGetOffset(aSec, b, &bOff);
5391:           for (q = 0; q < bDof; q++) {
5392:             PetscInt a = anchors[bOff + q];
5393:             PetscInt aFDof;

5395:             PetscSectionGetFieldDof(section, a, f, &aFDof);
5396:             allFDof += aFDof;
5397:           }
5398:           newPointOffsets[f][p+1] = allFDof;
5399:           pointMatOffsets[f][p+1] = fDof * allFDof;
5400:         }
5401:       }
5402:       else {
5403:         for (f = 0; f < numFields; f++) {
5404:           PetscInt fDof;

5406:           PetscSectionGetFieldDof(section, b, f, &fDof);
5407:           newPointOffsets[f][p+1] = fDof;
5408:           pointMatOffsets[f][p+1] = 0;
5409:         }
5410:       }
5411:     }
5412:     for (f = 0, totalOffset = 0, totalMatOffset = 0; f < numFields; f++) {
5413:       newPointOffsets[f][0] = totalOffset;
5414:       pointMatOffsets[f][0] = totalMatOffset;
5415:       for (p = 0; p < numPoints; p++) {
5416:         newPointOffsets[f][p+1] += newPointOffsets[f][p];
5417:         pointMatOffsets[f][p+1] += pointMatOffsets[f][p];
5418:       }
5419:       totalOffset    = newPointOffsets[f][numPoints];
5420:       totalMatOffset = pointMatOffsets[f][numPoints];
5421:       DMGetWorkArray(dm,pointMatOffsets[f][numPoints],MPIU_SCALAR,&pointMat[f]);
5422:     }
5423:   }
5424:   else {
5425:     for (p = 0; p < numPoints; p++) {
5426:       PetscInt b    = points[2*p];
5427:       PetscInt bDof = 0, bSecDof;

5429:       PetscSectionGetDof(section,b,&bSecDof);
5430:       if (!bSecDof) {
5431:         newPointOffsets[0][p + 1] = 0;
5432:         pointMatOffsets[0][p + 1] = 0;
5433:         continue;
5434:       }
5435:       if (b >= aStart && b < aEnd) {
5436:         PetscSectionGetDof(aSec, b, &bDof);
5437:       }
5438:       if (bDof) {
5439:         PetscInt bOff, q, allDof = 0;

5441:         PetscSectionGetOffset(aSec, b, &bOff);
5442:         for (q = 0; q < bDof; q++) {
5443:           PetscInt a = anchors[bOff + q], aDof;

5445:           PetscSectionGetDof(section, a, &aDof);
5446:           allDof += aDof;
5447:         }
5448:         newPointOffsets[0][p+1] = allDof;
5449:         pointMatOffsets[0][p+1] = bSecDof * allDof;
5450:       }
5451:       else {
5452:         newPointOffsets[0][p+1] = bSecDof;
5453:         pointMatOffsets[0][p+1] = 0;
5454:       }
5455:     }
5456:     newPointOffsets[0][0] = 0;
5457:     pointMatOffsets[0][0] = 0;
5458:     for (p = 0; p < numPoints; p++) {
5459:       newPointOffsets[0][p+1] += newPointOffsets[0][p];
5460:       pointMatOffsets[0][p+1] += pointMatOffsets[0][p];
5461:     }
5462:     DMGetWorkArray(dm,pointMatOffsets[0][numPoints],MPIU_SCALAR,&pointMat[0]);
5463:   }

5465:   /* output arrays */
5466:   DMGetWorkArray(dm,2*newNumPoints,MPIU_INT,&newPoints);

5468:   /* get the point-to-point matrices; construct newPoints */
5469:   PetscSectionGetMaxDof(aSec, &maxAnchor);
5470:   PetscSectionGetMaxDof(section, &maxDof);
5471:   DMGetWorkArray(dm,maxDof,MPIU_INT,&indices);
5472:   DMGetWorkArray(dm,maxAnchor*maxDof,MPIU_INT,&newIndices);
5473:   if (numFields) {
5474:     for (p = 0, newP = 0; p < numPoints; p++) {
5475:       PetscInt b    = points[2*p];
5476:       PetscInt o    = points[2*p+1];
5477:       PetscInt bDof = 0, bSecDof;

5479:       PetscSectionGetDof(section, b, &bSecDof);
5480:       if (!bSecDof) {
5481:         continue;
5482:       }
5483:       if (b >= aStart && b < aEnd) {
5484:         PetscSectionGetDof(aSec, b, &bDof);
5485:       }
5486:       if (bDof) {
5487:         PetscInt fStart[32], fEnd[32], fAnchorStart[32], fAnchorEnd[32], bOff, q;

5489:         fStart[0] = 0;
5490:         fEnd[0]   = 0;
5491:         for (f = 0; f < numFields; f++) {
5492:           PetscInt fDof;

5494:           PetscSectionGetFieldDof(cSec, b, f, &fDof);
5495:           fStart[f+1] = fStart[f] + fDof;
5496:           fEnd[f+1]   = fStart[f+1];
5497:         }
5498:         PetscSectionGetOffset(cSec, b, &bOff);
5499:         DMPlexGetIndicesPointFields_Internal(cSec, b, bOff, fEnd, PETSC_TRUE, perms, p, NULL, indices);

5501:         fAnchorStart[0] = 0;
5502:         fAnchorEnd[0]   = 0;
5503:         for (f = 0; f < numFields; f++) {
5504:           PetscInt fDof = newPointOffsets[f][p + 1] - newPointOffsets[f][p];

5506:           fAnchorStart[f+1] = fAnchorStart[f] + fDof;
5507:           fAnchorEnd[f+1]   = fAnchorStart[f + 1];
5508:         }
5509:         PetscSectionGetOffset(aSec, b, &bOff);
5510:         for (q = 0; q < bDof; q++) {
5511:           PetscInt a = anchors[bOff + q], aOff;

5513:           /* we take the orientation of ap into account in the order that we constructed the indices above: the newly added points have no orientation */
5514:           newPoints[2*(newP + q)]     = a;
5515:           newPoints[2*(newP + q) + 1] = 0;
5516:           PetscSectionGetOffset(section, a, &aOff);
5517:           DMPlexGetIndicesPointFields_Internal(section, a, aOff, fAnchorEnd, PETSC_TRUE, NULL, -1, NULL, newIndices);
5518:         }
5519:         newP += bDof;

5521:         if (outValues) {
5522:           /* get the point-to-point submatrix */
5523:           for (f = 0; f < numFields; f++) {
5524:             MatGetValues(cMat,fEnd[f]-fStart[f],indices + fStart[f],fAnchorEnd[f] - fAnchorStart[f],newIndices + fAnchorStart[f],pointMat[f] + pointMatOffsets[f][p]);
5525:           }
5526:         }
5527:       }
5528:       else {
5529:         newPoints[2 * newP]     = b;
5530:         newPoints[2 * newP + 1] = o;
5531:         newP++;
5532:       }
5533:     }
5534:   } else {
5535:     for (p = 0; p < numPoints; p++) {
5536:       PetscInt b    = points[2*p];
5537:       PetscInt o    = points[2*p+1];
5538:       PetscInt bDof = 0, bSecDof;

5540:       PetscSectionGetDof(section, b, &bSecDof);
5541:       if (!bSecDof) {
5542:         continue;
5543:       }
5544:       if (b >= aStart && b < aEnd) {
5545:         PetscSectionGetDof(aSec, b, &bDof);
5546:       }
5547:       if (bDof) {
5548:         PetscInt bEnd = 0, bAnchorEnd = 0, bOff;

5550:         PetscSectionGetOffset(cSec, b, &bOff);
5551:         DMPlexGetIndicesPoint_Internal(cSec, b, bOff, &bEnd, PETSC_TRUE, (perms && perms[0]) ? perms[0][p] : NULL, NULL, indices);

5553:         PetscSectionGetOffset (aSec, b, &bOff);
5554:         for (q = 0; q < bDof; q++) {
5555:           PetscInt a = anchors[bOff + q], aOff;

5557:           /* we take the orientation of ap into account in the order that we constructed the indices above: the newly added points have no orientation */

5559:           newPoints[2*(newP + q)]     = a;
5560:           newPoints[2*(newP + q) + 1] = 0;
5561:           PetscSectionGetOffset(section, a, &aOff);
5562:           DMPlexGetIndicesPoint_Internal(section, a, aOff, &bAnchorEnd, PETSC_TRUE, NULL, NULL, newIndices);
5563:         }
5564:         newP += bDof;

5566:         /* get the point-to-point submatrix */
5567:         if (outValues) {
5568:           MatGetValues(cMat,bEnd,indices,bAnchorEnd,newIndices,pointMat[0] + pointMatOffsets[0][p]);
5569:         }
5570:       }
5571:       else {
5572:         newPoints[2 * newP]     = b;
5573:         newPoints[2 * newP + 1] = o;
5574:         newP++;
5575:       }
5576:     }
5577:   }

5579:   if (outValues) {
5580:     DMGetWorkArray(dm,newNumIndices*numIndices,MPIU_SCALAR,&tmpValues);
5581:     PetscArrayzero(tmpValues,newNumIndices*numIndices);
5582:     /* multiply constraints on the right */
5583:     if (numFields) {
5584:       for (f = 0; f < numFields; f++) {
5585:         PetscInt oldOff = offsets[f];

5587:         for (p = 0; p < numPoints; p++) {
5588:           PetscInt cStart = newPointOffsets[f][p];
5589:           PetscInt b      = points[2 * p];
5590:           PetscInt c, r, k;
5591:           PetscInt dof;

5593:           PetscSectionGetFieldDof(section,b,f,&dof);
5594:           if (!dof) {
5595:             continue;
5596:           }
5597:           if (pointMatOffsets[f][p] < pointMatOffsets[f][p + 1]) {
5598:             PetscInt nCols         = newPointOffsets[f][p+1]-cStart;
5599:             const PetscScalar *mat = pointMat[f] + pointMatOffsets[f][p];

5601:             for (r = 0; r < numIndices; r++) {
5602:               for (c = 0; c < nCols; c++) {
5603:                 for (k = 0; k < dof; k++) {
5604:                   tmpValues[r * newNumIndices + cStart + c] += values[r * numIndices + oldOff + k] * mat[k * nCols + c];
5605:                 }
5606:               }
5607:             }
5608:           }
5609:           else {
5610:             /* copy this column as is */
5611:             for (r = 0; r < numIndices; r++) {
5612:               for (c = 0; c < dof; c++) {
5613:                 tmpValues[r * newNumIndices + cStart + c] = values[r * numIndices + oldOff + c];
5614:               }
5615:             }
5616:           }
5617:           oldOff += dof;
5618:         }
5619:       }
5620:     }
5621:     else {
5622:       PetscInt oldOff = 0;
5623:       for (p = 0; p < numPoints; p++) {
5624:         PetscInt cStart = newPointOffsets[0][p];
5625:         PetscInt b      = points[2 * p];
5626:         PetscInt c, r, k;
5627:         PetscInt dof;

5629:         PetscSectionGetDof(section,b,&dof);
5630:         if (!dof) {
5631:           continue;
5632:         }
5633:         if (pointMatOffsets[0][p] < pointMatOffsets[0][p + 1]) {
5634:           PetscInt nCols         = newPointOffsets[0][p+1]-cStart;
5635:           const PetscScalar *mat = pointMat[0] + pointMatOffsets[0][p];

5637:           for (r = 0; r < numIndices; r++) {
5638:             for (c = 0; c < nCols; c++) {
5639:               for (k = 0; k < dof; k++) {
5640:                 tmpValues[r * newNumIndices + cStart + c] += mat[k * nCols + c] * values[r * numIndices + oldOff + k];
5641:               }
5642:             }
5643:           }
5644:         }
5645:         else {
5646:           /* copy this column as is */
5647:           for (r = 0; r < numIndices; r++) {
5648:             for (c = 0; c < dof; c++) {
5649:               tmpValues[r * newNumIndices + cStart + c] = values[r * numIndices + oldOff + c];
5650:             }
5651:           }
5652:         }
5653:         oldOff += dof;
5654:       }
5655:     }

5657:     if (multiplyLeft) {
5658:       DMGetWorkArray(dm,newNumIndices*newNumIndices,MPIU_SCALAR,&newValues);
5659:       PetscArrayzero(newValues,newNumIndices*newNumIndices);
5660:       /* multiply constraints transpose on the left */
5661:       if (numFields) {
5662:         for (f = 0; f < numFields; f++) {
5663:           PetscInt oldOff = offsets[f];

5665:           for (p = 0; p < numPoints; p++) {
5666:             PetscInt rStart = newPointOffsets[f][p];
5667:             PetscInt b      = points[2 * p];
5668:             PetscInt c, r, k;
5669:             PetscInt dof;

5671:             PetscSectionGetFieldDof(section,b,f,&dof);
5672:             if (pointMatOffsets[f][p] < pointMatOffsets[f][p + 1]) {
5673:               PetscInt nRows                        = newPointOffsets[f][p+1]-rStart;
5674:               const PetscScalar *PETSC_RESTRICT mat = pointMat[f] + pointMatOffsets[f][p];

5676:               for (r = 0; r < nRows; r++) {
5677:                 for (c = 0; c < newNumIndices; c++) {
5678:                   for (k = 0; k < dof; k++) {
5679:                     newValues[(rStart + r) * newNumIndices + c] += mat[k * nRows + r] * tmpValues[(oldOff + k) * newNumIndices + c];
5680:                   }
5681:                 }
5682:               }
5683:             }
5684:             else {
5685:               /* copy this row as is */
5686:               for (r = 0; r < dof; r++) {
5687:                 for (c = 0; c < newNumIndices; c++) {
5688:                   newValues[(rStart + r) * newNumIndices + c] = tmpValues[(oldOff + r) * newNumIndices + c];
5689:                 }
5690:               }
5691:             }
5692:             oldOff += dof;
5693:           }
5694:         }
5695:       }
5696:       else {
5697:         PetscInt oldOff = 0;

5699:         for (p = 0; p < numPoints; p++) {
5700:           PetscInt rStart = newPointOffsets[0][p];
5701:           PetscInt b      = points[2 * p];
5702:           PetscInt c, r, k;
5703:           PetscInt dof;

5705:           PetscSectionGetDof(section,b,&dof);
5706:           if (pointMatOffsets[0][p] < pointMatOffsets[0][p + 1]) {
5707:             PetscInt nRows                        = newPointOffsets[0][p+1]-rStart;
5708:             const PetscScalar *PETSC_RESTRICT mat = pointMat[0] + pointMatOffsets[0][p];

5710:             for (r = 0; r < nRows; r++) {
5711:               for (c = 0; c < newNumIndices; c++) {
5712:                 for (k = 0; k < dof; k++) {
5713:                   newValues[(rStart + r) * newNumIndices + c] += mat[k * nRows + r] * tmpValues[(oldOff + k) * newNumIndices + c];
5714:                 }
5715:               }
5716:             }
5717:           }
5718:           else {
5719:             /* copy this row as is */
5720:             for (r = 0; r < dof; r++) {
5721:               for (c = 0; c < newNumIndices; c++) {
5722:                 newValues[(rStart + r) * newNumIndices + c] = tmpValues[(oldOff + r) * newNumIndices + c];
5723:               }
5724:             }
5725:           }
5726:           oldOff += dof;
5727:         }
5728:       }

5730:       DMRestoreWorkArray(dm,newNumIndices*numIndices,MPIU_SCALAR,&tmpValues);
5731:     }
5732:     else {
5733:       newValues = tmpValues;
5734:     }
5735:   }

5737:   /* clean up */
5738:   DMRestoreWorkArray(dm,maxDof,MPIU_INT,&indices);
5739:   DMRestoreWorkArray(dm,maxAnchor*maxDof,MPIU_INT,&newIndices);

5741:   if (numFields) {
5742:     for (f = 0; f < numFields; f++) {
5743:       DMRestoreWorkArray(dm,pointMatOffsets[f][numPoints],MPIU_SCALAR,&pointMat[f]);
5744:       DMRestoreWorkArray(dm,numPoints+1,MPIU_INT,&pointMatOffsets[f]);
5745:       DMRestoreWorkArray(dm,numPoints+1,MPIU_INT,&newPointOffsets[f]);
5746:     }
5747:   }
5748:   else {
5749:     DMRestoreWorkArray(dm,pointMatOffsets[0][numPoints],MPIU_SCALAR,&pointMat[0]);
5750:     DMRestoreWorkArray(dm,numPoints+1,MPIU_INT,&pointMatOffsets[0]);
5751:     DMRestoreWorkArray(dm,numPoints+1,MPIU_INT,&newPointOffsets[0]);
5752:   }
5753:   ISRestoreIndices(aIS,&anchors);

5755:   /* output */
5756:   if (outPoints) {
5757:     *outPoints = newPoints;
5758:   }
5759:   else {
5760:     DMRestoreWorkArray(dm,2*newNumPoints,MPIU_INT,&newPoints);
5761:   }
5762:   if (outValues) {
5763:     *outValues = newValues;
5764:   }
5765:   for (f = 0; f <= numFields; f++) {
5766:     offsets[f] = newOffsets[f];
5767:   }
5768:   return(0);
5769: }

5771: /*@C
5772:   DMPlexGetClosureIndices - Get the global indices in a vector v for all points in the closure of the given point

5774:   Not collective

5776:   Input Parameters:
5777: + dm - The DM
5778: . section - The section describing the layout in v, or NULL to use the default section
5779: . globalSection - The section describing the parallel layout in v, or NULL to use the default section
5780: - point - The mesh point

5782:   Output parameters:
5783: + numIndices - The number of indices
5784: . indices - The indices
5785: - outOffsets - Field offset if not NULL

5787:   Note: Must call DMPlexRestoreClosureIndices() to free allocated memory

5789:   Level: advanced

5791: .seealso DMPlexRestoreClosureIndices(), DMPlexVecGetClosure(), DMPlexMatSetClosure()
5792: @*/
5793: PetscErrorCode DMPlexGetClosureIndices(DM dm, PetscSection section, PetscSection globalSection, PetscInt point, PetscInt *numIndices, PetscInt **indices, PetscInt *outOffsets)
5794: {
5795:   PetscSection    clSection;
5796:   IS              clPoints;
5797:   const PetscInt *clp, *clperm;
5798:   const PetscInt  **perms[32] = {NULL};
5799:   PetscInt       *points = NULL, *pointsNew;
5800:   PetscInt        numPoints, numPointsNew;
5801:   PetscInt        offsets[32];
5802:   PetscInt        Nf, Nind, NindNew, off, globalOff, f, p;
5803:   PetscErrorCode  ierr;

5811:   PetscSectionGetNumFields(section, &Nf);
5812:   if (Nf > 31) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %D limited to 31", Nf);
5813:   PetscArrayzero(offsets, 32);
5814:   /* Get points in closure */
5815:   DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
5816:   PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, NULL, &clperm);
5817:   /* Get number of indices and indices per field */
5818:   for (p = 0, Nind = 0; p < numPoints*2; p += 2) {
5819:     PetscInt dof, fdof;

5821:     PetscSectionGetDof(section, points[p], &dof);
5822:     for (f = 0; f < Nf; ++f) {
5823:       PetscSectionGetFieldDof(section, points[p], f, &fdof);
5824:       offsets[f+1] += fdof;
5825:     }
5826:     Nind += dof;
5827:   }
5828:   for (f = 1; f < Nf; ++f) offsets[f+1] += offsets[f];
5829:   if (Nf && offsets[Nf] != Nind) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", offsets[Nf], Nind);
5830:   if (!Nf) offsets[1] = Nind;
5831:   /* Get dual space symmetries */
5832:   for (f = 0; f < PetscMax(1,Nf); f++) {
5833:     if (Nf) {PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms[f],NULL);}
5834:     else    {PetscSectionGetPointSyms(section,numPoints,points,&perms[f],NULL);}
5835:   }
5836:   /* Correct for hanging node constraints */
5837:   {
5838:     DMPlexAnchorsModifyMat(dm, section, numPoints, Nind, points, perms, NULL, &numPointsNew, &NindNew, &pointsNew, NULL, offsets, PETSC_TRUE);
5839:     if (numPointsNew) {
5840:       for (f = 0; f < PetscMax(1,Nf); f++) {
5841:         if (Nf) {PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms[f],NULL);}
5842:         else    {PetscSectionRestorePointSyms(section,numPoints,points,&perms[f],NULL);}
5843:       }
5844:       for (f = 0; f < PetscMax(1,Nf); f++) {
5845:         if (Nf) {PetscSectionGetFieldPointSyms(section,f,numPointsNew,pointsNew,&perms[f],NULL);}
5846:         else    {PetscSectionGetPointSyms(section,numPointsNew,pointsNew,&perms[f],NULL);}
5847:       }
5848:       DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
5849:       numPoints = numPointsNew;
5850:       Nind      = NindNew;
5851:       points    = pointsNew;
5852:     }
5853:   }
5854:   /* Calculate indices */
5855:   DMGetWorkArray(dm, Nind, MPIU_INT, indices);
5856:   if (Nf) {
5857:     if (outOffsets) {
5858:       PetscInt f;

5860:       for (f = 0; f <= Nf; f++) {
5861:         outOffsets[f] = offsets[f];
5862:       }
5863:     }
5864:     for (p = 0; p < numPoints; p++) {
5865:       PetscSectionGetOffset(globalSection, points[2*p], &globalOff);
5866:       DMPlexGetIndicesPointFields_Internal(section, points[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, offsets, PETSC_FALSE, perms, p, clperm, *indices);
5867:     }
5868:   } else {
5869:     for (p = 0, off = 0; p < numPoints; p++) {
5870:       const PetscInt *perm = perms[0] ? perms[0][p] : NULL;

5872:       PetscSectionGetOffset(globalSection, points[2*p], &globalOff);
5873:       DMPlexGetIndicesPoint_Internal(section, points[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, clperm, *indices);
5874:     }
5875:   }
5876:   /* Cleanup points */
5877:   for (f = 0; f < PetscMax(1,Nf); f++) {
5878:     if (Nf) {PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms[f],NULL);}
5879:     else    {PetscSectionRestorePointSyms(section,numPoints,points,&perms[f],NULL);}
5880:   }
5881:   if (numPointsNew) {
5882:     DMRestoreWorkArray(dm, 2*numPointsNew, MPIU_INT, &pointsNew);
5883:   } else {
5884:     DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
5885:   }
5886:   if (numIndices) *numIndices = Nind;
5887:   return(0);
5888: }

5890: /*@C
5891:   DMPlexRestoreClosureIndices - Restore the indices in a vector v for all points in the closure of the given point

5893:   Not collective

5895:   Input Parameters:
5896: + dm - The DM
5897: . section - The section describing the layout in v, or NULL to use the default section
5898: . globalSection - The section describing the parallel layout in v, or NULL to use the default section
5899: . point - The mesh point
5900: . numIndices - The number of indices
5901: . indices - The indices
5902: - outOffsets - Field offset if not NULL

5904:   Level: advanced

5906: .seealso DMPlexGetClosureIndices(), DMPlexVecGetClosure(), DMPlexMatSetClosure()
5907: @*/
5908: PetscErrorCode DMPlexRestoreClosureIndices(DM dm, PetscSection section, PetscSection globalSection, PetscInt point, PetscInt *numIndices, PetscInt **indices,PetscInt *outOffsets)
5909: {

5915:   DMRestoreWorkArray(dm, 0, MPIU_INT, indices);
5916:   return(0);
5917: }

5919: /*@C
5920:   DMPlexMatSetClosure - Set an array of the values on the closure of 'point'

5922:   Not collective

5924:   Input Parameters:
5925: + dm - The DM
5926: . section - The section describing the layout in v, or NULL to use the default section
5927: . globalSection - The section describing the layout in v, or NULL to use the default global section
5928: . A - The matrix
5929: . point - The point in the DM
5930: . values - The array of values
5931: - mode - The insert mode, where INSERT_ALL_VALUES and ADD_ALL_VALUES also overwrite boundary conditions

5933:   Fortran Notes:
5934:   This routine is only available in Fortran 90, and you must include petsc.h90 in your code.

5936:   Level: intermediate

5938: .seealso DMPlexVecGetClosure(), DMPlexVecSetClosure()
5939: @*/
5940: PetscErrorCode DMPlexMatSetClosure(DM dm, PetscSection section, PetscSection globalSection, Mat A, PetscInt point, const PetscScalar values[], InsertMode mode)
5941: {
5942:   DM_Plex            *mesh   = (DM_Plex*) dm->data;
5943:   PetscSection        clSection;
5944:   IS                  clPoints;
5945:   PetscInt           *points = NULL, *newPoints;
5946:   const PetscInt     *clp, *clperm;
5947:   PetscInt           *indices;
5948:   PetscInt            offsets[32];
5949:   const PetscInt    **perms[32] = {NULL};
5950:   const PetscScalar **flips[32] = {NULL};
5951:   PetscInt            numFields, numPoints, newNumPoints, numIndices, newNumIndices, dof, off, globalOff, p, f;
5952:   PetscScalar        *valCopy = NULL;
5953:   PetscScalar        *newValues;
5954:   PetscErrorCode      ierr;

5958:   if (!section) {DMGetLocalSection(dm, &section);}
5960:   if (!globalSection) {DMGetGlobalSection(dm, &globalSection);}
5963:   PetscSectionGetNumFields(section, &numFields);
5964:   if (numFields > 31) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %D limited to 31", numFields);
5965:   PetscArrayzero(offsets, 32);
5966:   PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, NULL, &clperm);
5967:   DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
5968:   for (p = 0, numIndices = 0; p < numPoints*2; p += 2) {
5969:     PetscInt fdof;

5971:     PetscSectionGetDof(section, points[p], &dof);
5972:     for (f = 0; f < numFields; ++f) {
5973:       PetscSectionGetFieldDof(section, points[p], f, &fdof);
5974:       offsets[f+1] += fdof;
5975:     }
5976:     numIndices += dof;
5977:   }
5978:   for (f = 1; f < numFields; ++f) offsets[f+1] += offsets[f];

5980:   if (numFields && offsets[numFields] != numIndices) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", offsets[numFields], numIndices);
5981:   /* Get symmetries */
5982:   for (f = 0; f < PetscMax(1,numFields); f++) {
5983:     if (numFields) {PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms[f],&flips[f]);}
5984:     else           {PetscSectionGetPointSyms(section,numPoints,points,&perms[f],&flips[f]);}
5985:     if (values && flips[f]) { /* may need to apply sign changes to the element matrix */
5986:       PetscInt foffset = offsets[f];

5988:       for (p = 0; p < numPoints; p++) {
5989:         PetscInt point          = points[2*p], fdof;
5990:         const PetscScalar *flip = flips[f] ? flips[f][p] : NULL;

5992:         if (!numFields) {
5993:           PetscSectionGetDof(section,point,&fdof);
5994:         } else {
5995:           PetscSectionGetFieldDof(section,point,f,&fdof);
5996:         }
5997:         if (flip) {
5998:           PetscInt i, j, k;

6000:           if (!valCopy) {
6001:             DMGetWorkArray(dm,numIndices*numIndices,MPIU_SCALAR,&valCopy);
6002:             for (j = 0; j < numIndices * numIndices; j++) valCopy[j] = values[j];
6003:             values = valCopy;
6004:           }
6005:           for (i = 0; i < fdof; i++) {
6006:             PetscScalar fval = flip[i];

6008:             for (k = 0; k < numIndices; k++) {
6009:               valCopy[numIndices * (foffset + i) + k] *= fval;
6010:               valCopy[numIndices * k + (foffset + i)] *= fval;
6011:             }
6012:           }
6013:         }
6014:         foffset += fdof;
6015:       }
6016:     }
6017:   }
6018:   DMPlexAnchorsModifyMat(dm,section,numPoints,numIndices,points,perms,values,&newNumPoints,&newNumIndices,&newPoints,&newValues,offsets,PETSC_TRUE);
6019:   if (newNumPoints) {
6020:     if (valCopy) {
6021:       DMRestoreWorkArray(dm,numIndices*numIndices,MPIU_SCALAR,&valCopy);
6022:     }
6023:     for (f = 0; f < PetscMax(1,numFields); f++) {
6024:       if (numFields) {PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms[f],&flips[f]);}
6025:       else           {PetscSectionRestorePointSyms(section,numPoints,points,&perms[f],&flips[f]);}
6026:     }
6027:     for (f = 0; f < PetscMax(1,numFields); f++) {
6028:       if (numFields) {PetscSectionGetFieldPointSyms(section,f,newNumPoints,newPoints,&perms[f],&flips[f]);}
6029:       else           {PetscSectionGetPointSyms(section,newNumPoints,newPoints,&perms[f],&flips[f]);}
6030:     }
6031:     DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
6032:     numPoints  = newNumPoints;
6033:     numIndices = newNumIndices;
6034:     points     = newPoints;
6035:     values     = newValues;
6036:   }
6037:   DMGetWorkArray(dm, numIndices, MPIU_INT, &indices);
6038:   if (numFields) {
6039:     PetscBool useFieldOffsets;

6041:     PetscSectionGetUseFieldOffsets(globalSection, &useFieldOffsets);
6042:     if (useFieldOffsets) {
6043:       for (p = 0; p < numPoints; p++) {
6044:         DMPlexGetIndicesPointFieldsSplit_Internal(section, globalSection, points[2*p], offsets, PETSC_FALSE, perms, p, clperm, indices);
6045:       }
6046:     } else {
6047:       for (p = 0; p < numPoints; p++) {
6048:         PetscSectionGetOffset(globalSection, points[2*p], &globalOff);
6049:         DMPlexGetIndicesPointFields_Internal(section, points[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, offsets, PETSC_FALSE, perms, p, clperm, indices);
6050:       }
6051:     }
6052:   } else {
6053:     for (p = 0, off = 0; p < numPoints; p++) {
6054:       const PetscInt *perm = perms[0] ? perms[0][p] : NULL;
6055:       PetscSectionGetOffset(globalSection, points[2*p], &globalOff);
6056:       DMPlexGetIndicesPoint_Internal(section, points[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, clperm, indices);
6057:     }
6058:   }
6059:   if (mesh->printSetValues) {DMPlexPrintMatSetValues(PETSC_VIEWER_STDOUT_SELF, A, point, numIndices, indices, 0, NULL, values);}
6060:   MatSetValues(A, numIndices, indices, numIndices, indices, values, mode);
6061:   if (mesh->printFEM > 1) {
6062:     PetscInt i;
6063:     PetscPrintf(PETSC_COMM_SELF, "  Indices:");
6064:     for (i = 0; i < numIndices; ++i) {PetscPrintf(PETSC_COMM_SELF, " %D", indices[i]);}
6065:     PetscPrintf(PETSC_COMM_SELF, "\n");
6066:   }
6067:   if (ierr) {
6068:     PetscMPIInt    rank;
6069:     PetscErrorCode ierr2;

6071:     ierr2 = MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank);CHKERRQ(ierr2);
6072:     ierr2 = (*PetscErrorPrintf)("[%d]ERROR in DMPlexMatSetClosure\n", rank);CHKERRQ(ierr2);
6073:     ierr2 = DMPlexPrintMatSetValues(PETSC_VIEWER_STDERR_SELF, A, point, numIndices, indices, 0, NULL, values);CHKERRQ(ierr2);
6074:     ierr2 = DMRestoreWorkArray(dm, numIndices, MPIU_INT, &indices);CHKERRQ(ierr2);
6075: 
6076:   }
6077:   for (f = 0; f < PetscMax(1,numFields); f++) {
6078:     if (numFields) {PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms[f],&flips[f]);}
6079:     else           {PetscSectionRestorePointSyms(section,numPoints,points,&perms[f],&flips[f]);}
6080:   }
6081:   if (newNumPoints) {
6082:     DMRestoreWorkArray(dm,newNumIndices*newNumIndices,MPIU_SCALAR,&newValues);
6083:     DMRestoreWorkArray(dm,2*newNumPoints,MPIU_INT,&newPoints);
6084:   }
6085:   else {
6086:     if (valCopy) {
6087:       DMRestoreWorkArray(dm,numIndices*numIndices,MPIU_SCALAR,&valCopy);
6088:     }
6089:     DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);
6090:   }
6091:   DMRestoreWorkArray(dm, numIndices, MPIU_INT, &indices);
6092:   return(0);
6093: }

6095: PetscErrorCode DMPlexMatSetClosureRefined(DM dmf, PetscSection fsection, PetscSection globalFSection, DM dmc, PetscSection csection, PetscSection globalCSection, Mat A, PetscInt point, const PetscScalar values[], InsertMode mode)
6096: {
6097:   DM_Plex        *mesh   = (DM_Plex*) dmf->data;
6098:   PetscInt       *fpoints = NULL, *ftotpoints = NULL;
6099:   PetscInt       *cpoints = NULL;
6100:   PetscInt       *findices, *cindices;
6101:   const PetscInt *fclperm, *cclperm;
6102:   PetscInt        foffsets[32], coffsets[32];
6103:   CellRefiner     cellRefiner;
6104:   PetscInt        numFields, numSubcells, maxFPoints, numFPoints, numCPoints, numFIndices, numCIndices, dof, off, globalOff, pStart, pEnd, p, q, r, s, f;
6105:   PetscErrorCode  ierr;

6110:   if (!fsection) {DMGetLocalSection(dmf, &fsection);}
6112:   if (!csection) {DMGetLocalSection(dmc, &csection);}
6114:   if (!globalFSection) {DMGetGlobalSection(dmf, &globalFSection);}
6116:   if (!globalCSection) {DMGetGlobalSection(dmc, &globalCSection);}
6119:   PetscSectionGetNumFields(fsection, &numFields);
6120:   if (numFields > 31) SETERRQ1(PetscObjectComm((PetscObject)dmf), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %D limited to 31", numFields);
6121:   PetscArrayzero(foffsets, 32);
6122:   PetscArrayzero(coffsets, 32);
6123:   PetscSectionGetClosureInversePermutation_Internal(fsection, (PetscObject) dmf, NULL, &fclperm);
6124:   PetscSectionGetClosureInversePermutation_Internal(csection, (PetscObject) dmc, NULL, &cclperm);
6125:   /* Column indices */
6126:   DMPlexGetTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints);
6127:   maxFPoints = numCPoints;
6128:   /* Compress out points not in the section */
6129:   /*   TODO: Squeeze out points with 0 dof as well */
6130:   PetscSectionGetChart(csection, &pStart, &pEnd);
6131:   for (p = 0, q = 0; p < numCPoints*2; p += 2) {
6132:     if ((cpoints[p] >= pStart) && (cpoints[p] < pEnd)) {
6133:       cpoints[q*2]   = cpoints[p];
6134:       cpoints[q*2+1] = cpoints[p+1];
6135:       ++q;
6136:     }
6137:   }
6138:   numCPoints = q;
6139:   for (p = 0, numCIndices = 0; p < numCPoints*2; p += 2) {
6140:     PetscInt fdof;

6142:     PetscSectionGetDof(csection, cpoints[p], &dof);
6143:     if (!dof) continue;
6144:     for (f = 0; f < numFields; ++f) {
6145:       PetscSectionGetFieldDof(csection, cpoints[p], f, &fdof);
6146:       coffsets[f+1] += fdof;
6147:     }
6148:     numCIndices += dof;
6149:   }
6150:   for (f = 1; f < numFields; ++f) coffsets[f+1] += coffsets[f];
6151:   /* Row indices */
6152:   DMPlexGetCellRefiner_Internal(dmc, &cellRefiner);
6153:   CellRefinerGetAffineTransforms_Internal(cellRefiner, &numSubcells, NULL, NULL, NULL);
6154:   DMGetWorkArray(dmf, maxFPoints*2*numSubcells, MPIU_INT, &ftotpoints);
6155:   for (r = 0, q = 0; r < numSubcells; ++r) {
6156:     /* TODO Map from coarse to fine cells */
6157:     DMPlexGetTransitiveClosure(dmf, point*numSubcells + r, PETSC_TRUE, &numFPoints, &fpoints);
6158:     /* Compress out points not in the section */
6159:     PetscSectionGetChart(fsection, &pStart, &pEnd);
6160:     for (p = 0; p < numFPoints*2; p += 2) {
6161:       if ((fpoints[p] >= pStart) && (fpoints[p] < pEnd)) {
6162:         PetscSectionGetDof(fsection, fpoints[p], &dof);
6163:         if (!dof) continue;
6164:         for (s = 0; s < q; ++s) if (fpoints[p] == ftotpoints[s*2]) break;
6165:         if (s < q) continue;
6166:         ftotpoints[q*2]   = fpoints[p];
6167:         ftotpoints[q*2+1] = fpoints[p+1];
6168:         ++q;
6169:       }
6170:     }
6171:     DMPlexRestoreTransitiveClosure(dmf, point, PETSC_TRUE, &numFPoints, &fpoints);
6172:   }
6173:   numFPoints = q;
6174:   for (p = 0, numFIndices = 0; p < numFPoints*2; p += 2) {
6175:     PetscInt fdof;

6177:     PetscSectionGetDof(fsection, ftotpoints[p], &dof);
6178:     if (!dof) continue;
6179:     for (f = 0; f < numFields; ++f) {
6180:       PetscSectionGetFieldDof(fsection, ftotpoints[p], f, &fdof);
6181:       foffsets[f+1] += fdof;
6182:     }
6183:     numFIndices += dof;
6184:   }
6185:   for (f = 1; f < numFields; ++f) foffsets[f+1] += foffsets[f];

6187:   if (numFields && foffsets[numFields] != numFIndices) SETERRQ2(PetscObjectComm((PetscObject)dmf), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", foffsets[numFields], numFIndices);
6188:   if (numFields && coffsets[numFields] != numCIndices) SETERRQ2(PetscObjectComm((PetscObject)dmc), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", coffsets[numFields], numCIndices);
6189:   DMGetWorkArray(dmf, numFIndices, MPIU_INT, &findices);
6190:   DMGetWorkArray(dmc, numCIndices, MPIU_INT, &cindices);
6191:   if (numFields) {
6192:     const PetscInt **permsF[32] = {NULL};
6193:     const PetscInt **permsC[32] = {NULL};

6195:     for (f = 0; f < numFields; f++) {
6196:       PetscSectionGetFieldPointSyms(fsection,f,numFPoints,ftotpoints,&permsF[f],NULL);
6197:       PetscSectionGetFieldPointSyms(csection,f,numCPoints,cpoints,&permsC[f],NULL);
6198:     }
6199:     for (p = 0; p < numFPoints; p++) {
6200:       PetscSectionGetOffset(globalFSection, ftotpoints[2*p], &globalOff);
6201:       DMPlexGetIndicesPointFields_Internal(fsection, ftotpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, foffsets, PETSC_FALSE, permsF, p, fclperm, findices);
6202:     }
6203:     for (p = 0; p < numCPoints; p++) {
6204:       PetscSectionGetOffset(globalCSection, cpoints[2*p], &globalOff);
6205:       DMPlexGetIndicesPointFields_Internal(csection, cpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, coffsets, PETSC_FALSE, permsC, p, cclperm, cindices);
6206:     }
6207:     for (f = 0; f < numFields; f++) {
6208:       PetscSectionRestoreFieldPointSyms(fsection,f,numFPoints,ftotpoints,&permsF[f],NULL);
6209:       PetscSectionRestoreFieldPointSyms(csection,f,numCPoints,cpoints,&permsC[f],NULL);
6210:     }
6211:   } else {
6212:     const PetscInt **permsF = NULL;
6213:     const PetscInt **permsC = NULL;

6215:     PetscSectionGetPointSyms(fsection,numFPoints,ftotpoints,&permsF,NULL);
6216:     PetscSectionGetPointSyms(csection,numCPoints,cpoints,&permsC,NULL);
6217:     for (p = 0, off = 0; p < numFPoints; p++) {
6218:       const PetscInt *perm = permsF ? permsF[p] : NULL;

6220:       PetscSectionGetOffset(globalFSection, ftotpoints[2*p], &globalOff);
6221:       DMPlexGetIndicesPoint_Internal(fsection, ftotpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, fclperm, findices);
6222:     }
6223:     for (p = 0, off = 0; p < numCPoints; p++) {
6224:       const PetscInt *perm = permsC ? permsC[p] : NULL;

6226:       PetscSectionGetOffset(globalCSection, cpoints[2*p], &globalOff);
6227:       DMPlexGetIndicesPoint_Internal(csection, cpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, cclperm, cindices);
6228:     }
6229:     PetscSectionRestorePointSyms(fsection,numFPoints,ftotpoints,&permsF,NULL);
6230:     PetscSectionRestorePointSyms(csection,numCPoints,cpoints,&permsC,NULL);
6231:   }
6232:   if (mesh->printSetValues) {DMPlexPrintMatSetValues(PETSC_VIEWER_STDOUT_SELF, A, point, numFIndices, findices, numCIndices, cindices, values);}
6233:   /* TODO: flips */
6234:   MatSetValues(A, numFIndices, findices, numCIndices, cindices, values, mode);
6235:   if (ierr) {
6236:     PetscMPIInt    rank;
6237:     PetscErrorCode ierr2;

6239:     ierr2 = MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank);CHKERRQ(ierr2);
6240:     ierr2 = (*PetscErrorPrintf)("[%d]ERROR in DMPlexMatSetClosure\n", rank);CHKERRQ(ierr2);
6241:     ierr2 = DMPlexPrintMatSetValues(PETSC_VIEWER_STDERR_SELF, A, point, numFIndices, findices, numCIndices, cindices, values);CHKERRQ(ierr2);
6242:     ierr2 = DMRestoreWorkArray(dmf, numFIndices, MPIU_INT, &findices);CHKERRQ(ierr2);
6243:     ierr2 = DMRestoreWorkArray(dmc, numCIndices, MPIU_INT, &cindices);CHKERRQ(ierr2);
6244: 
6245:   }
6246:   DMRestoreWorkArray(dmf, numCPoints*2*4, MPIU_INT, &ftotpoints);
6247:   DMPlexRestoreTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints);
6248:   DMRestoreWorkArray(dmf, numFIndices, MPIU_INT, &findices);
6249:   DMRestoreWorkArray(dmc, numCIndices, MPIU_INT, &cindices);
6250:   return(0);
6251: }

6253: PetscErrorCode DMPlexMatGetClosureIndicesRefined(DM dmf, PetscSection fsection, PetscSection globalFSection, DM dmc, PetscSection csection, PetscSection globalCSection, PetscInt point, PetscInt cindices[], PetscInt findices[])
6254: {
6255:   PetscInt      *fpoints = NULL, *ftotpoints = NULL;
6256:   PetscInt      *cpoints = NULL;
6257:   PetscInt       foffsets[32], coffsets[32];
6258:   const PetscInt *fclperm, *cclperm;
6259:   CellRefiner    cellRefiner;
6260:   PetscInt       numFields, numSubcells, maxFPoints, numFPoints, numCPoints, numFIndices, numCIndices, dof, off, globalOff, pStart, pEnd, p, q, r, s, f;

6266:   if (!fsection) {DMGetLocalSection(dmf, &fsection);}
6268:   if (!csection) {DMGetLocalSection(dmc, &csection);}
6270:   if (!globalFSection) {DMGetGlobalSection(dmf, &globalFSection);}
6272:   if (!globalCSection) {DMGetGlobalSection(dmc, &globalCSection);}
6274:   PetscSectionGetNumFields(fsection, &numFields);
6275:   if (numFields > 31) SETERRQ1(PetscObjectComm((PetscObject)dmf), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %D limited to 31", numFields);
6276:   PetscArrayzero(foffsets, 32);
6277:   PetscArrayzero(coffsets, 32);
6278:   PetscSectionGetClosureInversePermutation_Internal(fsection, (PetscObject) dmf, NULL, &fclperm);
6279:   PetscSectionGetClosureInversePermutation_Internal(csection, (PetscObject) dmc, NULL, &cclperm);
6280:   /* Column indices */
6281:   DMPlexGetTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints);
6282:   maxFPoints = numCPoints;
6283:   /* Compress out points not in the section */
6284:   /*   TODO: Squeeze out points with 0 dof as well */
6285:   PetscSectionGetChart(csection, &pStart, &pEnd);
6286:   for (p = 0, q = 0; p < numCPoints*2; p += 2) {
6287:     if ((cpoints[p] >= pStart) && (cpoints[p] < pEnd)) {
6288:       cpoints[q*2]   = cpoints[p];
6289:       cpoints[q*2+1] = cpoints[p+1];
6290:       ++q;
6291:     }
6292:   }
6293:   numCPoints = q;
6294:   for (p = 0, numCIndices = 0; p < numCPoints*2; p += 2) {
6295:     PetscInt fdof;

6297:     PetscSectionGetDof(csection, cpoints[p], &dof);
6298:     if (!dof) continue;
6299:     for (f = 0; f < numFields; ++f) {
6300:       PetscSectionGetFieldDof(csection, cpoints[p], f, &fdof);
6301:       coffsets[f+1] += fdof;
6302:     }
6303:     numCIndices += dof;
6304:   }
6305:   for (f = 1; f < numFields; ++f) coffsets[f+1] += coffsets[f];
6306:   /* Row indices */
6307:   DMPlexGetCellRefiner_Internal(dmc, &cellRefiner);
6308:   CellRefinerGetAffineTransforms_Internal(cellRefiner, &numSubcells, NULL, NULL, NULL);
6309:   DMGetWorkArray(dmf, maxFPoints*2*numSubcells, MPIU_INT, &ftotpoints);
6310:   for (r = 0, q = 0; r < numSubcells; ++r) {
6311:     /* TODO Map from coarse to fine cells */
6312:     DMPlexGetTransitiveClosure(dmf, point*numSubcells + r, PETSC_TRUE, &numFPoints, &fpoints);
6313:     /* Compress out points not in the section */
6314:     PetscSectionGetChart(fsection, &pStart, &pEnd);
6315:     for (p = 0; p < numFPoints*2; p += 2) {
6316:       if ((fpoints[p] >= pStart) && (fpoints[p] < pEnd)) {
6317:         PetscSectionGetDof(fsection, fpoints[p], &dof);
6318:         if (!dof) continue;
6319:         for (s = 0; s < q; ++s) if (fpoints[p] == ftotpoints[s*2]) break;
6320:         if (s < q) continue;
6321:         ftotpoints[q*2]   = fpoints[p];
6322:         ftotpoints[q*2+1] = fpoints[p+1];
6323:         ++q;
6324:       }
6325:     }
6326:     DMPlexRestoreTransitiveClosure(dmf, point, PETSC_TRUE, &numFPoints, &fpoints);
6327:   }
6328:   numFPoints = q;
6329:   for (p = 0, numFIndices = 0; p < numFPoints*2; p += 2) {
6330:     PetscInt fdof;

6332:     PetscSectionGetDof(fsection, ftotpoints[p], &dof);
6333:     if (!dof) continue;
6334:     for (f = 0; f < numFields; ++f) {
6335:       PetscSectionGetFieldDof(fsection, ftotpoints[p], f, &fdof);
6336:       foffsets[f+1] += fdof;
6337:     }
6338:     numFIndices += dof;
6339:   }
6340:   for (f = 1; f < numFields; ++f) foffsets[f+1] += foffsets[f];

6342:   if (numFields && foffsets[numFields] != numFIndices) SETERRQ2(PetscObjectComm((PetscObject)dmf), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", foffsets[numFields], numFIndices);
6343:   if (numFields && coffsets[numFields] != numCIndices) SETERRQ2(PetscObjectComm((PetscObject)dmc), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", coffsets[numFields], numCIndices);
6344:   if (numFields) {
6345:     const PetscInt **permsF[32] = {NULL};
6346:     const PetscInt **permsC[32] = {NULL};

6348:     for (f = 0; f < numFields; f++) {
6349:       PetscSectionGetFieldPointSyms(fsection,f,numFPoints,ftotpoints,&permsF[f],NULL);
6350:       PetscSectionGetFieldPointSyms(csection,f,numCPoints,cpoints,&permsC[f],NULL);
6351:     }
6352:     for (p = 0; p < numFPoints; p++) {
6353:       PetscSectionGetOffset(globalFSection, ftotpoints[2*p], &globalOff);
6354:       DMPlexGetIndicesPointFields_Internal(fsection, ftotpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, foffsets, PETSC_FALSE, permsF, p, fclperm, findices);
6355:     }
6356:     for (p = 0; p < numCPoints; p++) {
6357:       PetscSectionGetOffset(globalCSection, cpoints[2*p], &globalOff);
6358:       DMPlexGetIndicesPointFields_Internal(csection, cpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, coffsets, PETSC_FALSE, permsC, p, cclperm, cindices);
6359:     }
6360:     for (f = 0; f < numFields; f++) {
6361:       PetscSectionRestoreFieldPointSyms(fsection,f,numFPoints,ftotpoints,&permsF[f],NULL);
6362:       PetscSectionRestoreFieldPointSyms(csection,f,numCPoints,cpoints,&permsC[f],NULL);
6363:     }
6364:   } else {
6365:     const PetscInt **permsF = NULL;
6366:     const PetscInt **permsC = NULL;

6368:     PetscSectionGetPointSyms(fsection,numFPoints,ftotpoints,&permsF,NULL);
6369:     PetscSectionGetPointSyms(csection,numCPoints,cpoints,&permsC,NULL);
6370:     for (p = 0, off = 0; p < numFPoints; p++) {
6371:       const PetscInt *perm = permsF ? permsF[p] : NULL;

6373:       PetscSectionGetOffset(globalFSection, ftotpoints[2*p], &globalOff);
6374:       DMPlexGetIndicesPoint_Internal(fsection, ftotpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, fclperm, findices);
6375:     }
6376:     for (p = 0, off = 0; p < numCPoints; p++) {
6377:       const PetscInt *perm = permsC ? permsC[p] : NULL;

6379:       PetscSectionGetOffset(globalCSection, cpoints[2*p], &globalOff);
6380:       DMPlexGetIndicesPoint_Internal(csection, cpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, cclperm, cindices);
6381:     }
6382:     PetscSectionRestorePointSyms(fsection,numFPoints,ftotpoints,&permsF,NULL);
6383:     PetscSectionRestorePointSyms(csection,numCPoints,cpoints,&permsC,NULL);
6384:   }
6385:   DMRestoreWorkArray(dmf, numCPoints*2*4, MPIU_INT, &ftotpoints);
6386:   DMPlexRestoreTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints);
6387:   return(0);
6388: }

6390: /*@
6391:   DMPlexGetHybridBounds - Get the first mesh point of each dimension which is a hybrid

6393:   Input Parameter:
6394: . dm - The DMPlex object

6396:   Output Parameters:
6397: + cMax - The first hybrid cell
6398: . fMax - The first hybrid face
6399: . eMax - The first hybrid edge
6400: - vMax - The first hybrid vertex

6402:   Level: developer

6404: .seealso DMPlexCreateHybridMesh(), DMPlexSetHybridBounds()
6405: @*/
6406: PetscErrorCode DMPlexGetHybridBounds(DM dm, PetscInt *cMax, PetscInt *fMax, PetscInt *eMax, PetscInt *vMax)
6407: {
6408:   DM_Plex       *mesh = (DM_Plex*) dm->data;
6409:   PetscInt       dim;

6414:   DMGetDimension(dm, &dim);
6415:   if (dim < 0) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE, "DM dimension not yet set");
6416:   if (cMax) *cMax = mesh->hybridPointMax[dim];
6417:   if (fMax) *fMax = mesh->hybridPointMax[PetscMax(dim-1,0)];
6418:   if (eMax) *eMax = mesh->hybridPointMax[1];
6419:   if (vMax) *vMax = mesh->hybridPointMax[0];
6420:   return(0);
6421: }

6423: static PetscErrorCode DMPlexCreateDimStratum(DM dm, DMLabel depthLabel, DMLabel dimLabel, PetscInt d, PetscInt dMax)
6424: {
6425:   IS             is, his;
6426:   PetscInt       first = 0, stride;
6427:   PetscBool      isStride;

6431:   DMLabelGetStratumIS(depthLabel, d, &is);
6432:   PetscObjectTypeCompare((PetscObject) is, ISSTRIDE, &isStride);
6433:   if (isStride) {
6434:     ISStrideGetInfo(is, &first, &stride);
6435:   }
6436:   if (is && (!isStride || stride != 1)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "DM is not stratified: depth %D IS is not contiguous", d);
6437:   ISCreateStride(PETSC_COMM_SELF, (dMax - first), first, 1, &his);
6438:   DMLabelSetStratumIS(dimLabel, d, his);
6439:   ISDestroy(&his);
6440:   ISDestroy(&is);
6441:   return(0);
6442: }

6444: /*@
6445:   DMPlexSetHybridBounds - Set the first mesh point of each dimension which is a hybrid

6447:   Input Parameters:
6448: + dm   - The DMPlex object
6449: . cMax - The first hybrid cell
6450: . fMax - The first hybrid face
6451: . eMax - The first hybrid edge
6452: - vMax - The first hybrid vertex

6454:   Level: developer

6456: .seealso DMPlexCreateHybridMesh(), DMPlexGetHybridBounds()
6457: @*/
6458: PetscErrorCode DMPlexSetHybridBounds(DM dm, PetscInt cMax, PetscInt fMax, PetscInt eMax, PetscInt vMax)
6459: {
6460:   DM_Plex       *mesh = (DM_Plex*) dm->data;
6461:   PetscInt       dim;

6466:   DMGetDimension(dm, &dim);
6467:   if (dim < 0) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE, "DM dimension not yet set");
6468:   if (cMax >= 0) mesh->hybridPointMax[dim]               = cMax;
6469:   if (fMax >= 0) mesh->hybridPointMax[PetscMax(dim-1,0)] = fMax;
6470:   if (eMax >= 0) mesh->hybridPointMax[1]                 = eMax;
6471:   if (vMax >= 0) mesh->hybridPointMax[0]                 = vMax;
6472:   return(0);
6473: }

6475: /*@C
6476:   DMPlexGetVTKCellHeight - Returns the height in the DAG used to determine which points are cells (normally 0)

6478:   Input Parameter:
6479: . dm   - The DMPlex object

6481:   Output Parameter:
6482: . cellHeight - The height of a cell

6484:   Level: developer

6486: .seealso DMPlexSetVTKCellHeight()
6487: @*/
6488: PetscErrorCode DMPlexGetVTKCellHeight(DM dm, PetscInt *cellHeight)
6489: {
6490:   DM_Plex *mesh = (DM_Plex*) dm->data;

6495:   *cellHeight = mesh->vtkCellHeight;
6496:   return(0);
6497: }

6499: /*@C
6500:   DMPlexSetVTKCellHeight - Sets the height in the DAG used to determine which points are cells (normally 0)

6502:   Input Parameters:
6503: + dm   - The DMPlex object
6504: - cellHeight - The height of a cell

6506:   Level: developer

6508: .seealso DMPlexGetVTKCellHeight()
6509: @*/
6510: PetscErrorCode DMPlexSetVTKCellHeight(DM dm, PetscInt cellHeight)
6511: {
6512:   DM_Plex *mesh = (DM_Plex*) dm->data;

6516:   mesh->vtkCellHeight = cellHeight;
6517:   return(0);
6518: }

6520: /* We can easily have a form that takes an IS instead */
6521: PetscErrorCode DMPlexCreateNumbering_Internal(DM dm, PetscInt pStart, PetscInt pEnd, PetscInt shift, PetscInt *globalSize, PetscSF sf, IS *numbering)
6522: {
6523:   PetscSection   section, globalSection;
6524:   PetscInt      *numbers, p;

6528:   PetscSectionCreate(PetscObjectComm((PetscObject)dm), &section);
6529:   PetscSectionSetChart(section, pStart, pEnd);
6530:   for (p = pStart; p < pEnd; ++p) {
6531:     PetscSectionSetDof(section, p, 1);
6532:   }
6533:   PetscSectionSetUp(section);
6534:   PetscSectionCreateGlobalSection(section, sf, PETSC_FALSE, PETSC_FALSE, &globalSection);
6535:   PetscMalloc1(pEnd - pStart, &numbers);
6536:   for (p = pStart; p < pEnd; ++p) {
6537:     PetscSectionGetOffset(globalSection, p, &numbers[p-pStart]);
6538:     if (numbers[p-pStart] < 0) numbers[p-pStart] -= shift;
6539:     else                       numbers[p-pStart] += shift;
6540:   }
6541:   ISCreateGeneral(PetscObjectComm((PetscObject) dm), pEnd - pStart, numbers, PETSC_OWN_POINTER, numbering);
6542:   if (globalSize) {
6543:     PetscLayout layout;
6544:     PetscSectionGetPointLayout(PetscObjectComm((PetscObject) dm), globalSection, &layout);
6545:     PetscLayoutGetSize(layout, globalSize);
6546:     PetscLayoutDestroy(&layout);
6547:   }
6548:   PetscSectionDestroy(&section);
6549:   PetscSectionDestroy(&globalSection);
6550:   return(0);
6551: }

6553: PetscErrorCode DMPlexCreateCellNumbering_Internal(DM dm, PetscBool includeHybrid, IS *globalCellNumbers)
6554: {
6555:   PetscInt       cellHeight, cStart, cEnd, cMax;

6559:   DMPlexGetVTKCellHeight(dm, &cellHeight);
6560:   DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);
6561:   DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);
6562:   if (cMax >= 0 && !includeHybrid) cEnd = PetscMin(cEnd, cMax);
6563:   DMPlexCreateNumbering_Internal(dm, cStart, cEnd, 0, NULL, dm->sf, globalCellNumbers);
6564:   return(0);
6565: }

6567: /*@
6568:   DMPlexGetCellNumbering - Get a global cell numbering for all cells on this process

6570:   Input Parameter:
6571: . dm   - The DMPlex object

6573:   Output Parameter:
6574: . globalCellNumbers - Global cell numbers for all cells on this process

6576:   Level: developer

6578: .seealso DMPlexGetVertexNumbering()
6579: @*/
6580: PetscErrorCode DMPlexGetCellNumbering(DM dm, IS *globalCellNumbers)
6581: {
6582:   DM_Plex       *mesh = (DM_Plex*) dm->data;

6587:   if (!mesh->globalCellNumbers) {DMPlexCreateCellNumbering_Internal(dm, PETSC_FALSE, &mesh->globalCellNumbers);}
6588:   *globalCellNumbers = mesh->globalCellNumbers;
6589:   return(0);
6590: }

6592: PetscErrorCode DMPlexCreateVertexNumbering_Internal(DM dm, PetscBool includeHybrid, IS *globalVertexNumbers)
6593: {
6594:   PetscInt       vStart, vEnd, vMax;

6599:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
6600:   DMPlexGetHybridBounds(dm, NULL, NULL, NULL, &vMax);
6601:   if (vMax >= 0 && !includeHybrid) vEnd = PetscMin(vEnd, vMax);
6602:   DMPlexCreateNumbering_Internal(dm, vStart, vEnd, 0, NULL, dm->sf, globalVertexNumbers);
6603:   return(0);
6604: }

6606: /*@
6607:   DMPlexGetVertexNumbering - Get a global vertex numbering for all vertices on this process

6609:   Input Parameter:
6610: . dm   - The DMPlex object

6612:   Output Parameter:
6613: . globalVertexNumbers - Global vertex numbers for all vertices on this process

6615:   Level: developer

6617: .seealso DMPlexGetCellNumbering()
6618: @*/
6619: PetscErrorCode DMPlexGetVertexNumbering(DM dm, IS *globalVertexNumbers)
6620: {
6621:   DM_Plex       *mesh = (DM_Plex*) dm->data;

6626:   if (!mesh->globalVertexNumbers) {DMPlexCreateVertexNumbering_Internal(dm, PETSC_FALSE, &mesh->globalVertexNumbers);}
6627:   *globalVertexNumbers = mesh->globalVertexNumbers;
6628:   return(0);
6629: }

6631: /*@
6632:   DMPlexCreatePointNumbering - Create a global numbering for all points on this process

6634:   Input Parameter:
6635: . dm   - The DMPlex object

6637:   Output Parameter:
6638: . globalPointNumbers - Global numbers for all points on this process

6640:   Level: developer

6642: .seealso DMPlexGetCellNumbering()
6643: @*/
6644: PetscErrorCode DMPlexCreatePointNumbering(DM dm, IS *globalPointNumbers)
6645: {
6646:   IS             nums[4];
6647:   PetscInt       depths[4], gdepths[4], starts[4];
6648:   PetscInt       depth, d, shift = 0;

6653:   DMPlexGetDepth(dm, &depth);
6654:   /* For unstratified meshes use dim instead of depth */
6655:   if (depth < 0) {DMGetDimension(dm, &depth);}
6656:   for (d = 0; d <= depth; ++d) {
6657:     PetscInt end;

6659:     depths[d] = depth-d;
6660:     DMPlexGetDepthStratum(dm, depths[d], &starts[d], &end);
6661:     if (!(starts[d]-end)) { starts[d] = depths[d] = -1; }
6662:   }
6663:   PetscSortIntWithArray(depth+1, starts, depths);
6664:   MPIU_Allreduce(depths, gdepths, depth+1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject) dm));
6665:   for (d = 0; d <= depth; ++d) {
6666:     if (starts[d] >= 0 && depths[d] != gdepths[d]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Expected depth %D, found %D",depths[d],gdepths[d]);
6667:   }
6668:   for (d = 0; d <= depth; ++d) {
6669:     PetscInt pStart, pEnd, gsize;

6671:     DMPlexGetDepthStratum(dm, gdepths[d], &pStart, &pEnd);
6672:     DMPlexCreateNumbering_Internal(dm, pStart, pEnd, shift, &gsize, dm->sf, &nums[d]);
6673:     shift += gsize;
6674:   }
6675:   ISConcatenate(PetscObjectComm((PetscObject) dm), depth+1, nums, globalPointNumbers);
6676:   for (d = 0; d <= depth; ++d) {ISDestroy(&nums[d]);}
6677:   return(0);
6678: }


6681: /*@
6682:   DMPlexCreateRankField - Create a cell field whose value is the rank of the owner

6684:   Input Parameter:
6685: . dm - The DMPlex object

6687:   Output Parameter:
6688: . ranks - The rank field

6690:   Options Database Keys:
6691: . -dm_partition_view - Adds the rank field into the DM output from -dm_view using the same viewer

6693:   Level: intermediate

6695: .seealso: DMView()
6696: @*/
6697: PetscErrorCode DMPlexCreateRankField(DM dm, Vec *ranks)
6698: {
6699:   DM             rdm;
6700:   PetscFE        fe;
6701:   PetscScalar   *r;
6702:   PetscMPIInt    rank;
6703:   PetscInt       dim, cStart, cEnd, c;

6709:   MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
6710:   DMClone(dm, &rdm);
6711:   DMGetDimension(rdm, &dim);
6712:   PetscFECreateDefault(PetscObjectComm((PetscObject) rdm), dim, 1, PETSC_TRUE, "PETSc___rank_", -1, &fe);
6713:   PetscObjectSetName((PetscObject) fe, "rank");
6714:   DMSetField(rdm, 0, NULL, (PetscObject) fe);
6715:   PetscFEDestroy(&fe);
6716:   DMCreateDS(rdm);
6717:   DMPlexGetHeightStratum(rdm, 0, &cStart, &cEnd);
6718:   DMCreateGlobalVector(rdm, ranks);
6719:   PetscObjectSetName((PetscObject) *ranks, "partition");
6720:   VecGetArray(*ranks, &r);
6721:   for (c = cStart; c < cEnd; ++c) {
6722:     PetscScalar *lr;

6724:     DMPlexPointGlobalRef(rdm, c, r, &lr);
6725:     *lr = rank;
6726:   }
6727:   VecRestoreArray(*ranks, &r);
6728:   DMDestroy(&rdm);
6729:   return(0);
6730: }

6732: /*@
6733:   DMPlexCreateLabelField - Create a cell field whose value is the label value for that cell

6735:   Input Parameters:
6736: + dm    - The DMPlex
6737: - label - The DMLabel

6739:   Output Parameter:
6740: . val - The label value field

6742:   Options Database Keys:
6743: . -dm_label_view - Adds the label value field into the DM output from -dm_view using the same viewer

6745:   Level: intermediate

6747: .seealso: DMView()
6748: @*/
6749: PetscErrorCode DMPlexCreateLabelField(DM dm, DMLabel label, Vec *val)
6750: {
6751:   DM             rdm;
6752:   PetscFE        fe;
6753:   PetscScalar   *v;
6754:   PetscInt       dim, cStart, cEnd, c;

6761:   DMClone(dm, &rdm);
6762:   DMGetDimension(rdm, &dim);
6763:   PetscFECreateDefault(PetscObjectComm((PetscObject) rdm), dim, 1, PETSC_TRUE, "PETSc___label_value_", -1, &fe);
6764:   PetscObjectSetName((PetscObject) fe, "label_value");
6765:   DMSetField(rdm, 0, NULL, (PetscObject) fe);
6766:   PetscFEDestroy(&fe);
6767:   DMCreateDS(rdm);
6768:   DMPlexGetHeightStratum(rdm, 0, &cStart, &cEnd);
6769:   DMCreateGlobalVector(rdm, val);
6770:   PetscObjectSetName((PetscObject) *val, "label_value");
6771:   VecGetArray(*val, &v);
6772:   for (c = cStart; c < cEnd; ++c) {
6773:     PetscScalar *lv;
6774:     PetscInt     cval;

6776:     DMPlexPointGlobalRef(rdm, c, v, &lv);
6777:     DMLabelGetValue(label, c, &cval);
6778:     *lv = cval;
6779:   }
6780:   VecRestoreArray(*val, &v);
6781:   DMDestroy(&rdm);
6782:   return(0);
6783: }

6785: /*@
6786:   DMPlexCheckSymmetry - Check that the adjacency information in the mesh is symmetric.

6788:   Input Parameter:
6789: . dm - The DMPlex object

6791:   Note: This is a useful diagnostic when creating meshes programmatically.

6793:   Level: developer

6795: .seealso: DMCreate(), DMPlexCheckSkeleton(), DMPlexCheckFaces()
6796: @*/
6797: PetscErrorCode DMPlexCheckSymmetry(DM dm)
6798: {
6799:   PetscSection    coneSection, supportSection;
6800:   const PetscInt *cone, *support;
6801:   PetscInt        coneSize, c, supportSize, s;
6802:   PetscInt        pStart, pEnd, p, pp, csize, ssize;
6803:   PetscBool       storagecheck = PETSC_TRUE;
6804:   PetscErrorCode  ierr;

6808:   DMPlexGetConeSection(dm, &coneSection);
6809:   DMPlexGetSupportSection(dm, &supportSection);
6810:   /* Check that point p is found in the support of its cone points, and vice versa */
6811:   DMPlexGetChart(dm, &pStart, &pEnd);
6812:   for (p = pStart; p < pEnd; ++p) {
6813:     DMPlexGetConeSize(dm, p, &coneSize);
6814:     DMPlexGetCone(dm, p, &cone);
6815:     for (c = 0; c < coneSize; ++c) {
6816:       PetscBool dup = PETSC_FALSE;
6817:       PetscInt  d;
6818:       for (d = c-1; d >= 0; --d) {
6819:         if (cone[c] == cone[d]) {dup = PETSC_TRUE; break;}
6820:       }
6821:       DMPlexGetSupportSize(dm, cone[c], &supportSize);
6822:       DMPlexGetSupport(dm, cone[c], &support);
6823:       for (s = 0; s < supportSize; ++s) {
6824:         if (support[s] == p) break;
6825:       }
6826:       if ((s >= supportSize) || (dup && (support[s+1] != p))) {
6827:         PetscPrintf(PETSC_COMM_SELF, "p: %D cone: ", p);
6828:         for (s = 0; s < coneSize; ++s) {
6829:           PetscPrintf(PETSC_COMM_SELF, "%D, ", cone[s]);
6830:         }
6831:         PetscPrintf(PETSC_COMM_SELF, "\n");
6832:         PetscPrintf(PETSC_COMM_SELF, "p: %D support: ", cone[c]);
6833:         for (s = 0; s < supportSize; ++s) {
6834:           PetscPrintf(PETSC_COMM_SELF, "%D, ", support[s]);
6835:         }
6836:         PetscPrintf(PETSC_COMM_SELF, "\n");
6837:         if (dup) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %D not repeatedly found in support of repeated cone point %D", p, cone[c]);
6838:         else SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %D not found in support of cone point %D", p, cone[c]);
6839:       }
6840:     }
6841:     DMPlexGetTreeParent(dm, p, &pp, NULL);
6842:     if (p != pp) { storagecheck = PETSC_FALSE; continue; }
6843:     DMPlexGetSupportSize(dm, p, &supportSize);
6844:     DMPlexGetSupport(dm, p, &support);
6845:     for (s = 0; s < supportSize; ++s) {
6846:       DMPlexGetConeSize(dm, support[s], &coneSize);
6847:       DMPlexGetCone(dm, support[s], &cone);
6848:       for (c = 0; c < coneSize; ++c) {
6849:         DMPlexGetTreeParent(dm, cone[c], &pp, NULL);
6850:         if (cone[c] != pp) { c = 0; break; }
6851:         if (cone[c] == p) break;
6852:       }
6853:       if (c >= coneSize) {
6854:         PetscPrintf(PETSC_COMM_SELF, "p: %D support: ", p);
6855:         for (c = 0; c < supportSize; ++c) {
6856:           PetscPrintf(PETSC_COMM_SELF, "%D, ", support[c]);
6857:         }
6858:         PetscPrintf(PETSC_COMM_SELF, "\n");
6859:         PetscPrintf(PETSC_COMM_SELF, "p: %D cone: ", support[s]);
6860:         for (c = 0; c < coneSize; ++c) {
6861:           PetscPrintf(PETSC_COMM_SELF, "%D, ", cone[c]);
6862:         }
6863:         PetscPrintf(PETSC_COMM_SELF, "\n");
6864:         SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %D not found in cone of support point %D", p, support[s]);
6865:       }
6866:     }
6867:   }
6868:   if (storagecheck) {
6869:     PetscSectionGetStorageSize(coneSection, &csize);
6870:     PetscSectionGetStorageSize(supportSection, &ssize);
6871:     if (csize != ssize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Total cone size %D != Total support size %D", csize, ssize);
6872:   }
6873:   return(0);
6874: }

6876: /*@
6877:   DMPlexCheckSkeleton - Check that each cell has the correct number of vertices

6879:   Input Parameters:
6880: + dm - The DMPlex object
6881: - cellHeight - Normally 0

6883:   Note: This is a useful diagnostic when creating meshes programmatically.
6884:   Currently applicable only to homogeneous simplex or tensor meshes.

6886:   Level: developer

6888: .seealso: DMCreate(), DMPlexCheckSymmetry(), DMPlexCheckFaces()
6889: @*/
6890: PetscErrorCode DMPlexCheckSkeleton(DM dm, PetscInt cellHeight)
6891: {
6892:   PetscInt       dim, numCorners, numHybridCorners, vStart, vEnd, cStart, cEnd, cMax, c;
6893:   PetscBool      isSimplex = PETSC_FALSE;

6898:   DMGetDimension(dm, &dim);
6899:   DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);
6900:   if (cStart < cEnd) {
6901:     DMPlexGetConeSize(dm, cStart, &c);
6902:     isSimplex = c == dim+1 ? PETSC_TRUE : PETSC_FALSE;
6903:   }
6904:   switch (dim) {
6905:   case 1: numCorners = isSimplex ? 2 : 2; numHybridCorners = isSimplex ? 2 : 2; break;
6906:   case 2: numCorners = isSimplex ? 3 : 4; numHybridCorners = isSimplex ? 4 : 4; break;
6907:   case 3: numCorners = isSimplex ? 4 : 8; numHybridCorners = isSimplex ? 6 : 8; break;
6908:   default:
6909:     SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Cannot handle meshes of dimension %D", dim);
6910:   }
6911:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
6912:   DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);
6913:   cMax = cMax >= 0 ? cMax : cEnd;
6914:   for (c = cStart; c < cMax; ++c) {
6915:     PetscInt *closure = NULL, closureSize, cl, coneSize = 0;

6917:     DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
6918:     for (cl = 0; cl < closureSize*2; cl += 2) {
6919:       const PetscInt p = closure[cl];
6920:       if ((p >= vStart) && (p < vEnd)) ++coneSize;
6921:     }
6922:     DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
6923:     if (coneSize != numCorners) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %D has  %D vertices != %D", c, coneSize, numCorners);
6924:   }
6925:   for (c = cMax; c < cEnd; ++c) {
6926:     PetscInt *closure = NULL, closureSize, cl, coneSize = 0;

6928:     DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
6929:     for (cl = 0; cl < closureSize*2; cl += 2) {
6930:       const PetscInt p = closure[cl];
6931:       if ((p >= vStart) && (p < vEnd)) ++coneSize;
6932:     }
6933:     DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
6934:     if (coneSize > numHybridCorners) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Hybrid cell %D has  %D vertices > %D", c, coneSize, numHybridCorners);
6935:   }
6936:   return(0);
6937: }

6939: /*@
6940:   DMPlexCheckFaces - Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type

6942:   Input Parameters:
6943: + dm - The DMPlex object
6944: - cellHeight - Normally 0

6946:   Note: This is a useful diagnostic when creating meshes programmatically.

6948:   Level: developer

6950: .seealso: DMCreate(), DMPlexCheckSymmetry(), DMPlexCheckSkeleton()
6951: @*/
6952: PetscErrorCode DMPlexCheckFaces(DM dm, PetscInt cellHeight)
6953: {
6954:   PetscInt       pMax[4];
6955:   PetscInt       dim, depth, vStart, vEnd, cStart, cEnd, c, h;

6960:   DMGetDimension(dm, &dim);
6961:   DMPlexGetDepth(dm, &depth);
6962:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
6963:   DMPlexGetHybridBounds(dm, &pMax[dim], &pMax[dim-1], &pMax[1], &pMax[0]);
6964:   for (h = cellHeight; h < PetscMin(depth, dim); ++h) {
6965:     DMPlexGetHeightStratum(dm, h, &cStart, &cEnd);
6966:     for (c = cStart; c < cEnd; ++c) {
6967:       const PetscInt *cone, *ornt, *faces;
6968:       PetscInt        numFaces, faceSize, coneSize,f;
6969:       PetscInt       *closure = NULL, closureSize, cl, numCorners = 0;

6971:       if (pMax[dim-h] >= 0 && c >= pMax[dim-h]) continue;
6972:       DMPlexGetConeSize(dm, c, &coneSize);
6973:       DMPlexGetCone(dm, c, &cone);
6974:       DMPlexGetConeOrientation(dm, c, &ornt);
6975:       DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
6976:       for (cl = 0; cl < closureSize*2; cl += 2) {
6977:         const PetscInt p = closure[cl];
6978:         if ((p >= vStart) && (p < vEnd)) closure[numCorners++] = p;
6979:       }
6980:       DMPlexGetRawFaces_Internal(dm, dim-h, numCorners, closure, &numFaces, &faceSize, &faces);
6981:       if (coneSize != numFaces) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %D has %D faces but should have %D", c, coneSize, numFaces);
6982:       for (f = 0; f < numFaces; ++f) {
6983:         PetscInt *fclosure = NULL, fclosureSize, cl, fnumCorners = 0, v;

6985:         DMPlexGetTransitiveClosure_Internal(dm, cone[f], ornt[f], PETSC_TRUE, &fclosureSize, &fclosure);
6986:         for (cl = 0; cl < fclosureSize*2; cl += 2) {
6987:           const PetscInt p = fclosure[cl];
6988:           if ((p >= vStart) && (p < vEnd)) fclosure[fnumCorners++] = p;
6989:         }
6990:         if (fnumCorners != faceSize) SETERRQ5(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %D (%D) of cell %D has %D vertices but should have %D", cone[f], f, c, fnumCorners, faceSize);
6991:         for (v = 0; v < fnumCorners; ++v) {
6992:           if (fclosure[v] != faces[f*faceSize+v]) SETERRQ6(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %D (%d) of cell %D vertex %D, %D != %D", cone[f], f, c, v, fclosure[v], faces[f*faceSize+v]);
6993:         }
6994:         DMPlexRestoreTransitiveClosure(dm, cone[f], PETSC_TRUE, &fclosureSize, &fclosure);
6995:       }
6996:       DMPlexRestoreFaces_Internal(dm, dim, c, &numFaces, &faceSize, &faces);
6997:       DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
6998:     }
6999:   }
7000:   return(0);
7001: }

7003: /*@
7004:   DMPlexCheckGeometry - Check the geometry of mesh cells

7006:   Input Parameter:
7007: . dm - The DMPlex object

7009:   Note: This is a useful diagnostic when creating meshes programmatically.

7011:   Level: developer

7013: .seealso: DMCreate(), DMCheckSymmetry(), DMCheckSkeleton(), DMCheckFaces()
7014: @*/
7015: PetscErrorCode DMPlexCheckGeometry(DM dm)
7016: {
7017:   PetscReal      detJ, J[9], refVol = 1.0;
7018:   PetscReal      vol;
7019:   PetscInt       dim, depth, d, cStart, cEnd, c, cMax;

7023:   DMGetDimension(dm, &dim);
7024:   DMPlexGetDepth(dm, &depth);
7025:   for (d = 0; d < dim; ++d) refVol *= 2.0;
7026:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
7027:   DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);
7028:   cMax = cMax < 0 ? cEnd : cMax;
7029:   for (c = cStart; c < cMax; ++c) {
7030:     DMPlexComputeCellGeometryFEM(dm, c, NULL, NULL, J, NULL, &detJ);
7031:     if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh cell %D is inverted, |J| = %g", c, (double) detJ);
7032:     PetscInfo2(dm, "Cell %D FEM Volume %g\n", c, (double) detJ*refVol);
7033:     if (depth > 1) {
7034:       DMPlexComputeCellGeometryFVM(dm, c, &vol, NULL, NULL);
7035:       if (vol <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh cell %d is inverted, vol = %g", c, (double) vol);
7036:       PetscInfo2(dm, "Cell %D FVM Volume %g\n", c, (double) vol);
7037:     }
7038:   }
7039:   return(0);
7040: }

7042: static PetscErrorCode DMPlexAreAllConePointsInArray_Private(DM dm, PetscInt p, PetscInt npoints, const PetscInt *points, PetscInt *missingPoint)
7043: {
7044:   PetscInt i,l,n;
7045:   const PetscInt *cone;

7049:   *missingPoint = -1;
7050:   DMPlexGetConeSize(dm, p, &n);
7051:   DMPlexGetCone(dm, p, &cone);
7052:   for (i=0; i<n; i++) {
7053:     PetscFindInt(cone[i], npoints, points, &l);
7054:     if (l < 0) {
7055:       *missingPoint = cone[i];
7056:       break;
7057:     }
7058:   }
7059:   return(0);
7060: }

7062: /*@
7063:   DMPlexCheckPointSF - Check that several necessary conditions are met for the point SF of this plex.

7065:   Input Parameters:
7066: . dm - The DMPlex object

7068:   Notes:
7069:   This is mainly intended for debugging/testing purposes.
7070:   It currently checks only meshes with no partition overlapping.

7072:   Level: developer

7074: .seealso: DMGetPointSF(), DMPlexCheckSymmetry(), DMPlexCheckSkeleton(), DMPlexCheckFaces()
7075: @*/
7076: PetscErrorCode DMPlexCheckPointSF(DM dm)
7077: {
7078:   PetscSF         sf;
7079:   PetscInt        d,depth,i,nleaves,p,plo,phi,missingPoint;
7080:   const PetscInt *locals;
7081:   PetscErrorCode  ierr;

7085:   DMPlexGetDepth(dm, &depth);
7086:   DMGetPointSF(dm, &sf);
7087:   DMPlexGetOverlap(dm, &d);
7088:   if (d) {
7089:     PetscPrintf(PetscObjectComm((PetscObject)dm), "Warning: DMPlexCheckPointSF() is currently not implemented for meshes with partition overlapping");
7090:     return(0);
7091:   }
7092:   PetscSFGetGraph(sf, NULL, &nleaves, &locals, NULL);

7094:   /* 1) check there are no faces in 2D, cells in 3D, in interface */
7095:   DMPlexGetVTKCellHeight(dm, &d);
7096:   DMPlexGetHeightStratum(dm, d, &plo, &phi);
7097:   for (i=0; i<nleaves; i++) {
7098:     p = locals[i];
7099:     if (p >= plo && p < phi) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "point SF contains %d which is a cell",p);
7100:   }

7102:   /* 2) if some point is in interface, then all its cone points must be also in interface  */
7103:   for (i=0; i<nleaves; i++) {
7104:     p = locals[i];
7105:     DMPlexAreAllConePointsInArray_Private(dm, p, nleaves, locals, &missingPoint);
7106:     if (missingPoint >= 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "point SF contains %d but not %d from its cone",p,missingPoint);
7107:   }
7108:   return(0);
7109: }

7111: typedef struct cell_stats
7112: {
7113:   PetscReal min, max, sum, squaresum;
7114:   PetscInt  count;
7115: } cell_stats_t;

7117: static void MPIAPI cell_stats_reduce(void *a, void *b, int * len, MPI_Datatype *datatype)
7118: {
7119:   PetscInt i, N = *len;

7121:   for (i = 0; i < N; i++) {
7122:     cell_stats_t *A = (cell_stats_t *) a;
7123:     cell_stats_t *B = (cell_stats_t *) b;

7125:     B->min = PetscMin(A->min,B->min);
7126:     B->max = PetscMax(A->max,B->max);
7127:     B->sum += A->sum;
7128:     B->squaresum += A->squaresum;
7129:     B->count += A->count;
7130:   }
7131: }

7133: /*@
7134:   DMPlexCheckCellShape - Checks the Jacobian of the mapping from reference to real cells and computes some minimal statistics.

7136:   Collective on dm

7138:   Input Parameters:
7139: + dm        - The DMPlex object
7140: . output    - If true, statistics will be displayed on stdout
7141: - condLimit - Display all cells above this condition number, or PETSC_DETERMINE for no cell output

7143:   Note: This is mainly intended for debugging/testing purposes.

7145:   Level: developer

7147: .seealso: DMPlexCheckSymmetry(), DMPlexCheckSkeleton(), DMPlexCheckFaces()
7148: @*/
7149: PetscErrorCode DMPlexCheckCellShape(DM dm, PetscBool output, PetscReal condLimit)
7150: {
7151:   DM             dmCoarse;
7152:   cell_stats_t   stats, globalStats;
7153:   MPI_Comm       comm = PetscObjectComm((PetscObject)dm);
7154:   PetscReal      *J, *invJ, min = 0, max = 0, mean = 0, stdev = 0;
7155:   PetscReal      limit = condLimit > 0 ? condLimit : PETSC_MAX_REAL;
7156:   PetscInt       cdim, cStart, cEnd, cMax, c, eStart, eEnd, count = 0;
7157:   PetscMPIInt    rank,size;

7162:   stats.min   = PETSC_MAX_REAL;
7163:   stats.max   = PETSC_MIN_REAL;
7164:   stats.sum   = stats.squaresum = 0.;
7165:   stats.count = 0;

7167:   MPI_Comm_size(comm, &size);
7168:   MPI_Comm_rank(comm, &rank);
7169:   DMGetCoordinateDim(dm,&cdim);
7170:   PetscMalloc2(PetscSqr(cdim), &J, PetscSqr(cdim), &invJ);
7171:   DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);
7172:   DMPlexGetDepthStratum(dm,1,&eStart,&eEnd);
7173:   DMPlexGetHybridBounds(dm,&cMax,NULL,NULL,NULL);
7174:   cMax = cMax < 0 ? cEnd : cMax;
7175:   for (c = cStart; c < cMax; c++) {
7176:     PetscInt  i;
7177:     PetscReal frobJ = 0., frobInvJ = 0., cond2, cond, detJ;

7179:     DMPlexComputeCellGeometryAffineFEM(dm,c,NULL,J,invJ,&detJ);
7180:     if (detJ < 0.0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh cell %D is inverted", c);
7181:     for (i = 0; i < PetscSqr(cdim); ++i) {
7182:       frobJ    += J[i] * J[i];
7183:       frobInvJ += invJ[i] * invJ[i];
7184:     }
7185:     cond2 = frobJ * frobInvJ;
7186:     cond  = PetscSqrtReal(cond2);

7188:     stats.min        = PetscMin(stats.min,cond);
7189:     stats.max        = PetscMax(stats.max,cond);
7190:     stats.sum       += cond;
7191:     stats.squaresum += cond2;
7192:     stats.count++;
7193:     if (output && cond > limit) {
7194:       PetscSection coordSection;
7195:       Vec          coordsLocal;
7196:       PetscScalar *coords = NULL;
7197:       PetscInt     Nv, d, clSize, cl, *closure = NULL;

7199:       DMGetCoordinatesLocal(dm, &coordsLocal);
7200:       DMGetCoordinateSection(dm, &coordSection);
7201:       DMPlexVecGetClosure(dm, coordSection, coordsLocal, c, &Nv, &coords);
7202:       PetscSynchronizedPrintf(comm, "[%d] Cell %D cond %g\n", rank, c, (double) cond);
7203:       for (i = 0; i < Nv/cdim; ++i) {
7204:         PetscSynchronizedPrintf(comm, "  Vertex %D: (", i);
7205:         for (d = 0; d < cdim; ++d) {
7206:           if (d > 0) {PetscSynchronizedPrintf(comm, ", ");}
7207:           PetscSynchronizedPrintf(comm, "%g", (double) PetscRealPart(coords[i*cdim+d]));
7208:         }
7209:         PetscSynchronizedPrintf(comm, ")\n");
7210:       }
7211:       DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &clSize, &closure);
7212:       for (cl = 0; cl < clSize*2; cl += 2) {
7213:         const PetscInt edge = closure[cl];

7215:         if ((edge >= eStart) && (edge < eEnd)) {
7216:           PetscReal len;

7218:           DMPlexComputeCellGeometryFVM(dm, edge, &len, NULL, NULL);
7219:           PetscSynchronizedPrintf(comm, "  Edge %D: length %g\n", edge, (double) len);
7220:         }
7221:       }
7222:       DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &clSize, &closure);
7223:       DMPlexVecRestoreClosure(dm, coordSection, coordsLocal, c, &Nv, &coords);
7224:     }
7225:   }
7226:   if (output) {PetscSynchronizedFlush(comm, NULL);}

7228:   if (size > 1) {
7229:     PetscMPIInt   blockLengths[2] = {4,1};
7230:     MPI_Aint      blockOffsets[2] = {offsetof(cell_stats_t,min),offsetof(cell_stats_t,count)};
7231:     MPI_Datatype  blockTypes[2]   = {MPIU_REAL,MPIU_INT}, statType;
7232:     MPI_Op        statReduce;

7234:     MPI_Type_create_struct(2,blockLengths,blockOffsets,blockTypes,&statType);
7235:     MPI_Type_commit(&statType);
7236:     MPI_Op_create(cell_stats_reduce, PETSC_TRUE, &statReduce);
7237:     MPI_Reduce(&stats,&globalStats,1,statType,statReduce,0,comm);
7238:     MPI_Op_free(&statReduce);
7239:     MPI_Type_free(&statType);
7240:   } else {
7241:     PetscArraycpy(&globalStats,&stats,1);
7242:   }
7243:   if (!rank) {
7244:     count = globalStats.count;
7245:     min   = globalStats.min;
7246:     max   = globalStats.max;
7247:     mean  = globalStats.sum / globalStats.count;
7248:     stdev = globalStats.count > 1 ? PetscSqrtReal(PetscMax((globalStats.squaresum - globalStats.count * mean * mean) / (globalStats.count - 1),0)) : 0.0;
7249:   }

7251:   if (output) {
7252:     PetscPrintf(comm,"Mesh with %D cells, shape condition numbers: min = %g, max = %g, mean = %g, stddev = %g\n", count, (double) min, (double) max, (double) mean, (double) stdev);
7253:   }
7254:   PetscFree2(J,invJ);

7256:   DMGetCoarseDM(dm,&dmCoarse);
7257:   if (dmCoarse) {
7258:     PetscBool isplex;

7260:     PetscObjectTypeCompare((PetscObject)dmCoarse,DMPLEX,&isplex);
7261:     if (isplex) {
7262:       DMPlexCheckCellShape(dmCoarse,output,condLimit);
7263:     }
7264:   }
7265:   return(0);
7266: }

7268: /* Pointwise interpolation
7269:      Just code FEM for now
7270:      u^f = I u^c
7271:      sum_k u^f_k phi^f_k = I sum_j u^c_j phi^c_j
7272:      u^f_i = sum_j psi^f_i I phi^c_j u^c_j
7273:      I_{ij} = psi^f_i phi^c_j
7274: */
7275: PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling)
7276: {
7277:   PetscSection   gsc, gsf;
7278:   PetscInt       m, n;
7279:   void          *ctx;
7280:   DM             cdm;
7281:   PetscBool      regular, ismatis;

7285:   DMGetGlobalSection(dmFine, &gsf);
7286:   PetscSectionGetConstrainedStorageSize(gsf, &m);
7287:   DMGetGlobalSection(dmCoarse, &gsc);
7288:   PetscSectionGetConstrainedStorageSize(gsc, &n);

7290:   PetscStrcmp(dmCoarse->mattype, MATIS, &ismatis);
7291:   MatCreate(PetscObjectComm((PetscObject) dmCoarse), interpolation);
7292:   MatSetSizes(*interpolation, m, n, PETSC_DETERMINE, PETSC_DETERMINE);
7293:   MatSetType(*interpolation, ismatis ? MATAIJ : dmCoarse->mattype);
7294:   DMGetApplicationContext(dmFine, &ctx);

7296:   DMGetCoarseDM(dmFine, &cdm);
7297:   DMPlexGetRegularRefinement(dmFine, &regular);
7298:   if (regular && cdm == dmCoarse) {DMPlexComputeInterpolatorNested(dmCoarse, dmFine, *interpolation, ctx);}
7299:   else                            {DMPlexComputeInterpolatorGeneral(dmCoarse, dmFine, *interpolation, ctx);}
7300:   MatViewFromOptions(*interpolation, NULL, "-interp_mat_view");
7301:   if (scaling) {
7302:     /* Use naive scaling */
7303:     DMCreateInterpolationScale(dmCoarse, dmFine, *interpolation, scaling);
7304:   }
7305:   return(0);
7306: }

7308: PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat)
7309: {
7311:   VecScatter     ctx;

7314:   DMPlexComputeInjectorFEM(dmCoarse, dmFine, &ctx, NULL);
7315:   MatCreateScatter(PetscObjectComm((PetscObject)ctx), ctx, mat);
7316:   VecScatterDestroy(&ctx);
7317:   return(0);
7318: }

7320: PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mass)
7321: {
7322:   PetscSection   gsc, gsf;
7323:   PetscInt       m, n;
7324:   void          *ctx;
7325:   DM             cdm;
7326:   PetscBool      regular;

7330:   DMGetGlobalSection(dmFine, &gsf);
7331:   PetscSectionGetConstrainedStorageSize(gsf, &m);
7332:   DMGetGlobalSection(dmCoarse, &gsc);
7333:   PetscSectionGetConstrainedStorageSize(gsc, &n);

7335:   MatCreate(PetscObjectComm((PetscObject) dmCoarse), mass);
7336:   MatSetSizes(*mass, m, n, PETSC_DETERMINE, PETSC_DETERMINE);
7337:   MatSetType(*mass, dmCoarse->mattype);
7338:   DMGetApplicationContext(dmFine, &ctx);

7340:   DMGetCoarseDM(dmFine, &cdm);
7341:   DMPlexGetRegularRefinement(dmFine, &regular);
7342:   if (regular && cdm == dmCoarse) {DMPlexComputeMassMatrixNested(dmCoarse, dmFine, *mass, ctx);}
7343:   else                            {DMPlexComputeMassMatrixGeneral(dmCoarse, dmFine, *mass, ctx);}
7344:   MatViewFromOptions(*mass, NULL, "-mass_mat_view");
7345:   return(0);
7346: }

7348: /*@
7349:   DMPlexGetRegularRefinement - Get the flag indicating that this mesh was obtained by regular refinement from its coarse mesh

7351:   Input Parameter:
7352: . dm - The DMPlex object

7354:   Output Parameter:
7355: . regular - The flag

7357:   Level: intermediate

7359: .seealso: DMPlexSetRegularRefinement()
7360: @*/
7361: PetscErrorCode DMPlexGetRegularRefinement(DM dm, PetscBool *regular)
7362: {
7366:   *regular = ((DM_Plex *) dm->data)->regularRefinement;
7367:   return(0);
7368: }

7370: /*@
7371:   DMPlexSetRegularRefinement - Set the flag indicating that this mesh was obtained by regular refinement from its coarse mesh

7373:   Input Parameters:
7374: + dm - The DMPlex object
7375: - regular - The flag

7377:   Level: intermediate

7379: .seealso: DMPlexGetRegularRefinement()
7380: @*/
7381: PetscErrorCode DMPlexSetRegularRefinement(DM dm, PetscBool regular)
7382: {
7385:   ((DM_Plex *) dm->data)->regularRefinement = regular;
7386:   return(0);
7387: }

7389: /* anchors */
7390: /*@
7391:   DMPlexGetAnchors - Get the layout of the anchor (point-to-point) constraints.  Typically, the user will not have to
7392:   call DMPlexGetAnchors() directly: if there are anchors, then DMPlexGetAnchors() is called during DMGetConstraints().

7394:   not collective

7396:   Input Parameters:
7397: . dm - The DMPlex object

7399:   Output Parameters:
7400: + anchorSection - If not NULL, set to the section describing which points anchor the constrained points.
7401: - anchorIS - If not NULL, set to the list of anchors indexed by anchorSection


7404:   Level: intermediate

7406: .seealso: DMPlexSetAnchors(), DMGetConstraints(), DMSetConstraints()
7407: @*/
7408: PetscErrorCode DMPlexGetAnchors(DM dm, PetscSection *anchorSection, IS *anchorIS)
7409: {
7410:   DM_Plex *plex = (DM_Plex *)dm->data;

7415:   if (!plex->anchorSection && !plex->anchorIS && plex->createanchors) {(*plex->createanchors)(dm);}
7416:   if (anchorSection) *anchorSection = plex->anchorSection;
7417:   if (anchorIS) *anchorIS = plex->anchorIS;
7418:   return(0);
7419: }

7421: /*@
7422:   DMPlexSetAnchors - Set the layout of the local anchor (point-to-point) constraints.  Unlike boundary conditions,
7423:   when a point's degrees of freedom in a section are constrained to an outside value, the anchor constraints set a
7424:   point's degrees of freedom to be a linear combination of other points' degrees of freedom.

7426:   After specifying the layout of constraints with DMPlexSetAnchors(), one specifies the constraints by calling
7427:   DMGetConstraints() and filling in the entries in the constraint matrix.

7429:   collective on dm

7431:   Input Parameters:
7432: + dm - The DMPlex object
7433: . anchorSection - The section that describes the mapping from constrained points to the anchor points listed in anchorIS.  Must have a local communicator (PETSC_COMM_SELF or derivative).
7434: - anchorIS - The list of all anchor points.  Must have a local communicator (PETSC_COMM_SELF or derivative).

7436:   The reference counts of anchorSection and anchorIS are incremented.

7438:   Level: intermediate

7440: .seealso: DMPlexGetAnchors(), DMGetConstraints(), DMSetConstraints()
7441: @*/
7442: PetscErrorCode DMPlexSetAnchors(DM dm, PetscSection anchorSection, IS anchorIS)
7443: {
7444:   DM_Plex        *plex = (DM_Plex *)dm->data;
7445:   PetscMPIInt    result;

7450:   if (anchorSection) {
7452:     MPI_Comm_compare(PETSC_COMM_SELF,PetscObjectComm((PetscObject)anchorSection),&result);
7453:     if (result != MPI_CONGRUENT && result != MPI_IDENT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMECOMM,"anchor section must have local communicator");
7454:   }
7455:   if (anchorIS) {
7457:     MPI_Comm_compare(PETSC_COMM_SELF,PetscObjectComm((PetscObject)anchorIS),&result);
7458:     if (result != MPI_CONGRUENT && result != MPI_IDENT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMECOMM,"anchor IS must have local communicator");
7459:   }

7461:   PetscObjectReference((PetscObject)anchorSection);
7462:   PetscSectionDestroy(&plex->anchorSection);
7463:   plex->anchorSection = anchorSection;

7465:   PetscObjectReference((PetscObject)anchorIS);
7466:   ISDestroy(&plex->anchorIS);
7467:   plex->anchorIS = anchorIS;

7469: #if defined(PETSC_USE_DEBUG)
7470:   if (anchorIS && anchorSection) {
7471:     PetscInt size, a, pStart, pEnd;
7472:     const PetscInt *anchors;

7474:     PetscSectionGetChart(anchorSection,&pStart,&pEnd);
7475:     ISGetLocalSize(anchorIS,&size);
7476:     ISGetIndices(anchorIS,&anchors);
7477:     for (a = 0; a < size; a++) {
7478:       PetscInt p;

7480:       p = anchors[a];
7481:       if (p >= pStart && p < pEnd) {
7482:         PetscInt dof;

7484:         PetscSectionGetDof(anchorSection,p,&dof);
7485:         if (dof) {
7486:           PetscErrorCode ierr2;

7488:           ierr2 = ISRestoreIndices(anchorIS,&anchors);CHKERRQ(ierr2);
7489:           SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Point %D cannot be constrained and an anchor",p);
7490:         }
7491:       }
7492:     }
7493:     ISRestoreIndices(anchorIS,&anchors);
7494:   }
7495: #endif
7496:   /* reset the generic constraints */
7497:   DMSetDefaultConstraints(dm,NULL,NULL);
7498:   return(0);
7499: }

7501: static PetscErrorCode DMPlexCreateConstraintSection_Anchors(DM dm, PetscSection section, PetscSection *cSec)
7502: {
7503:   PetscSection anchorSection;
7504:   PetscInt pStart, pEnd, sStart, sEnd, p, dof, numFields, f;

7509:   DMPlexGetAnchors(dm,&anchorSection,NULL);
7510:   PetscSectionCreate(PETSC_COMM_SELF,cSec);
7511:   PetscSectionGetNumFields(section,&numFields);
7512:   if (numFields) {
7513:     PetscInt f;
7514:     PetscSectionSetNumFields(*cSec,numFields);

7516:     for (f = 0; f < numFields; f++) {
7517:       PetscInt numComp;

7519:       PetscSectionGetFieldComponents(section,f,&numComp);
7520:       PetscSectionSetFieldComponents(*cSec,f,numComp);
7521:     }
7522:   }
7523:   PetscSectionGetChart(anchorSection,&pStart,&pEnd);
7524:   PetscSectionGetChart(section,&sStart,&sEnd);
7525:   pStart = PetscMax(pStart,sStart);
7526:   pEnd   = PetscMin(pEnd,sEnd);
7527:   pEnd   = PetscMax(pStart,pEnd);
7528:   PetscSectionSetChart(*cSec,pStart,pEnd);
7529:   for (p = pStart; p < pEnd; p++) {
7530:     PetscSectionGetDof(anchorSection,p,&dof);
7531:     if (dof) {
7532:       PetscSectionGetDof(section,p,&dof);
7533:       PetscSectionSetDof(*cSec,p,dof);
7534:       for (f = 0; f < numFields; f++) {
7535:         PetscSectionGetFieldDof(section,p,f,&dof);
7536:         PetscSectionSetFieldDof(*cSec,p,f,dof);
7537:       }
7538:     }
7539:   }
7540:   PetscSectionSetUp(*cSec);
7541:   return(0);
7542: }

7544: static PetscErrorCode DMPlexCreateConstraintMatrix_Anchors(DM dm, PetscSection section, PetscSection cSec, Mat *cMat)
7545: {
7546:   PetscSection aSec;
7547:   PetscInt pStart, pEnd, p, dof, aDof, aOff, off, nnz, annz, m, n, q, a, offset, *i, *j;
7548:   const PetscInt *anchors;
7549:   PetscInt numFields, f;
7550:   IS aIS;

7555:   PetscSectionGetStorageSize(cSec, &m);
7556:   PetscSectionGetStorageSize(section, &n);
7557:   MatCreate(PETSC_COMM_SELF,cMat);
7558:   MatSetSizes(*cMat,m,n,m,n);
7559:   MatSetType(*cMat,MATSEQAIJ);
7560:   DMPlexGetAnchors(dm,&aSec,&aIS);
7561:   ISGetIndices(aIS,&anchors);
7562:   /* cSec will be a subset of aSec and section */
7563:   PetscSectionGetChart(cSec,&pStart,&pEnd);
7564:   PetscMalloc1(m+1,&i);
7565:   i[0] = 0;
7566:   PetscSectionGetNumFields(section,&numFields);
7567:   for (p = pStart; p < pEnd; p++) {
7568:     PetscInt rDof, rOff, r;

7570:     PetscSectionGetDof(aSec,p,&rDof);
7571:     if (!rDof) continue;
7572:     PetscSectionGetOffset(aSec,p,&rOff);
7573:     if (numFields) {
7574:       for (f = 0; f < numFields; f++) {
7575:         annz = 0;
7576:         for (r = 0; r < rDof; r++) {
7577:           a = anchors[rOff + r];
7578:           PetscSectionGetFieldDof(section,a,f,&aDof);
7579:           annz += aDof;
7580:         }
7581:         PetscSectionGetFieldDof(cSec,p,f,&dof);
7582:         PetscSectionGetFieldOffset(cSec,p,f,&off);
7583:         for (q = 0; q < dof; q++) {
7584:           i[off + q + 1] = i[off + q] + annz;
7585:         }
7586:       }
7587:     }
7588:     else {
7589:       annz = 0;
7590:       for (q = 0; q < dof; q++) {
7591:         a = anchors[off + q];
7592:         PetscSectionGetDof(section,a,&aDof);
7593:         annz += aDof;
7594:       }
7595:       PetscSectionGetDof(cSec,p,&dof);
7596:       PetscSectionGetOffset(cSec,p,&off);
7597:       for (q = 0; q < dof; q++) {
7598:         i[off + q + 1] = i[off + q] + annz;
7599:       }
7600:     }
7601:   }
7602:   nnz = i[m];
7603:   PetscMalloc1(nnz,&j);
7604:   offset = 0;
7605:   for (p = pStart; p < pEnd; p++) {
7606:     if (numFields) {
7607:       for (f = 0; f < numFields; f++) {
7608:         PetscSectionGetFieldDof(cSec,p,f,&dof);
7609:         for (q = 0; q < dof; q++) {
7610:           PetscInt rDof, rOff, r;
7611:           PetscSectionGetDof(aSec,p,&rDof);
7612:           PetscSectionGetOffset(aSec,p,&rOff);
7613:           for (r = 0; r < rDof; r++) {
7614:             PetscInt s;

7616:             a = anchors[rOff + r];
7617:             PetscSectionGetFieldDof(section,a,f,&aDof);
7618:             PetscSectionGetFieldOffset(section,a,f,&aOff);
7619:             for (s = 0; s < aDof; s++) {
7620:               j[offset++] = aOff + s;
7621:             }
7622:           }
7623:         }
7624:       }
7625:     }
7626:     else {
7627:       PetscSectionGetDof(cSec,p,&dof);
7628:       for (q = 0; q < dof; q++) {
7629:         PetscInt rDof, rOff, r;
7630:         PetscSectionGetDof(aSec,p,&rDof);
7631:         PetscSectionGetOffset(aSec,p,&rOff);
7632:         for (r = 0; r < rDof; r++) {
7633:           PetscInt s;

7635:           a = anchors[rOff + r];
7636:           PetscSectionGetDof(section,a,&aDof);
7637:           PetscSectionGetOffset(section,a,&aOff);
7638:           for (s = 0; s < aDof; s++) {
7639:             j[offset++] = aOff + s;
7640:           }
7641:         }
7642:       }
7643:     }
7644:   }
7645:   MatSeqAIJSetPreallocationCSR(*cMat,i,j,NULL);
7646:   PetscFree(i);
7647:   PetscFree(j);
7648:   ISRestoreIndices(aIS,&anchors);
7649:   return(0);
7650: }

7652: PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm)
7653: {
7654:   DM_Plex        *plex = (DM_Plex *)dm->data;
7655:   PetscSection   anchorSection, section, cSec;
7656:   Mat            cMat;

7661:   DMPlexGetAnchors(dm,&anchorSection,NULL);
7662:   if (anchorSection) {
7663:     PetscInt Nf;

7665:     DMGetLocalSection(dm,&section);
7666:     DMPlexCreateConstraintSection_Anchors(dm,section,&cSec);
7667:     DMPlexCreateConstraintMatrix_Anchors(dm,section,cSec,&cMat);
7668:     DMGetNumFields(dm,&Nf);
7669:     if (Nf && plex->computeanchormatrix) {(*plex->computeanchormatrix)(dm,section,cSec,cMat);}
7670:     DMSetDefaultConstraints(dm,cSec,cMat);
7671:     PetscSectionDestroy(&cSec);
7672:     MatDestroy(&cMat);
7673:   }
7674:   return(0);
7675: }

7677: PetscErrorCode DMCreateSubDomainDM_Plex(DM dm, DMLabel label, PetscInt value, IS *is, DM *subdm)
7678: {
7679:   IS             subis;
7680:   PetscSection   section, subsection;

7684:   DMGetLocalSection(dm, &section);
7685:   if (!section) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Must set default section for DM before splitting subdomain");
7686:   if (!subdm)   SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Must set output subDM for splitting subdomain");
7687:   /* Create subdomain */
7688:   DMPlexFilter(dm, label, value, subdm);
7689:   /* Create submodel */
7690:   DMPlexCreateSubpointIS(*subdm, &subis);
7691:   PetscSectionCreateSubmeshSection(section, subis, &subsection);
7692:   ISDestroy(&subis);
7693:   DMSetLocalSection(*subdm, subsection);
7694:   PetscSectionDestroy(&subsection);
7695:   DMCopyDisc(dm, *subdm);
7696:   /* Create map from submodel to global model */
7697:   if (is) {
7698:     PetscSection    sectionGlobal, subsectionGlobal;
7699:     IS              spIS;
7700:     const PetscInt *spmap;
7701:     PetscInt       *subIndices;
7702:     PetscInt        subSize = 0, subOff = 0, pStart, pEnd, p;
7703:     PetscInt        Nf, f, bs = -1, bsLocal[2], bsMinMax[2];

7705:     DMPlexCreateSubpointIS(*subdm, &spIS);
7706:     ISGetIndices(spIS, &spmap);
7707:     PetscSectionGetNumFields(section, &Nf);
7708:     DMGetGlobalSection(dm, &sectionGlobal);
7709:     DMGetGlobalSection(*subdm, &subsectionGlobal);
7710:     PetscSectionGetChart(subsection, &pStart, &pEnd);
7711:     for (p = pStart; p < pEnd; ++p) {
7712:       PetscInt gdof, pSubSize  = 0;

7714:       PetscSectionGetDof(sectionGlobal, p, &gdof);
7715:       if (gdof > 0) {
7716:         for (f = 0; f < Nf; ++f) {
7717:           PetscInt fdof, fcdof;

7719:           PetscSectionGetFieldDof(subsection, p, f, &fdof);
7720:           PetscSectionGetFieldConstraintDof(subsection, p, f, &fcdof);
7721:           pSubSize += fdof-fcdof;
7722:         }
7723:         subSize += pSubSize;
7724:         if (pSubSize) {
7725:           if (bs < 0) {
7726:             bs = pSubSize;
7727:           } else if (bs != pSubSize) {
7728:             /* Layout does not admit a pointwise block size */
7729:             bs = 1;
7730:           }
7731:         }
7732:       }
7733:     }
7734:     /* Must have same blocksize on all procs (some might have no points) */
7735:     bsLocal[0] = bs < 0 ? PETSC_MAX_INT : bs; bsLocal[1] = bs;
7736:     PetscGlobalMinMaxInt(PetscObjectComm((PetscObject) dm), bsLocal, bsMinMax);
7737:     if (bsMinMax[0] != bsMinMax[1]) {bs = 1;}
7738:     else                            {bs = bsMinMax[0];}
7739:     PetscMalloc1(subSize, &subIndices);
7740:     for (p = pStart; p < pEnd; ++p) {
7741:       PetscInt gdof, goff;

7743:       PetscSectionGetDof(subsectionGlobal, p, &gdof);
7744:       if (gdof > 0) {
7745:         const PetscInt point = spmap[p];

7747:         PetscSectionGetOffset(sectionGlobal, point, &goff);
7748:         for (f = 0; f < Nf; ++f) {
7749:           PetscInt fdof, fcdof, fc, f2, poff = 0;

7751:           /* Can get rid of this loop by storing field information in the global section */
7752:           for (f2 = 0; f2 < f; ++f2) {
7753:             PetscSectionGetFieldDof(section, p, f2, &fdof);
7754:             PetscSectionGetFieldConstraintDof(section, p, f2, &fcdof);
7755:             poff += fdof-fcdof;
7756:           }
7757:           PetscSectionGetFieldDof(section, p, f, &fdof);
7758:           PetscSectionGetFieldConstraintDof(section, p, f, &fcdof);
7759:           for (fc = 0; fc < fdof-fcdof; ++fc, ++subOff) {
7760:             subIndices[subOff] = goff+poff+fc;
7761:           }
7762:         }
7763:       }
7764:     }
7765:     ISRestoreIndices(spIS, &spmap);
7766:     ISDestroy(&spIS);
7767:     ISCreateGeneral(PetscObjectComm((PetscObject)dm), subSize, subIndices, PETSC_OWN_POINTER, is);
7768:     if (bs > 1) {
7769:       /* We need to check that the block size does not come from non-contiguous fields */
7770:       PetscInt i, j, set = 1;
7771:       for (i = 0; i < subSize; i += bs) {
7772:         for (j = 0; j < bs; ++j) {
7773:           if (subIndices[i+j] != subIndices[i]+j) {set = 0; break;}
7774:         }
7775:       }
7776:       if (set) {ISSetBlockSize(*is, bs);}
7777:     }
7778:     /* Attach nullspace */
7779:     for (f = 0; f < Nf; ++f) {
7780:       (*subdm)->nullspaceConstructors[f] = dm->nullspaceConstructors[f];
7781:       if ((*subdm)->nullspaceConstructors[f]) break;
7782:     }
7783:     if (f < Nf) {
7784:       MatNullSpace nullSpace;

7786:       (*(*subdm)->nullspaceConstructors[f])(*subdm, f, &nullSpace);
7787:       PetscObjectCompose((PetscObject) *is, "nullspace", (PetscObject) nullSpace);
7788:       MatNullSpaceDestroy(&nullSpace);
7789:     }
7790:   }
7791:   return(0);
7792: }