Actual source code: dm.c

petsc-3.7.6 2017-04-24
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  1: #include <petsc/private/dmimpl.h>           /*I      "petscdm.h"          I*/
  2: #include <petsc/private/dmlabelimpl.h>      /*I      "petscdmlabel.h"     I*/
  3: #include <petscsf.h>
  4: #include <petscds.h>

  6: PetscClassId  DM_CLASSID;
  7: PetscLogEvent DM_Convert, DM_GlobalToLocal, DM_LocalToGlobal, DM_LocalToLocal, DM_LocatePoints, DM_Coarsen, DM_CreateInterpolation, DM_CreateRestriction;

  9: const char *const DMBoundaryTypes[] = {"NONE","GHOSTED","MIRROR","PERIODIC","TWIST","DM_BOUNDARY_",0};

 13: /*@
 14:   DMCreate - Creates an empty DM object. The type can then be set with DMSetType().

 16:    If you never  call DMSetType()  it will generate an
 17:    error when you try to use the vector.

 19:   Collective on MPI_Comm

 21:   Input Parameter:
 22: . comm - The communicator for the DM object

 24:   Output Parameter:
 25: . dm - The DM object

 27:   Level: beginner

 29: .seealso: DMSetType(), DMDA, DMSLICED, DMCOMPOSITE, DMPLEX, DMMOAB, DMNETWORK
 30: @*/
 31: PetscErrorCode  DMCreate(MPI_Comm comm,DM *dm)
 32: {
 33:   DM             v;

 38:   *dm = NULL;
 39:   PetscSysInitializePackage();
 40:   VecInitializePackage();
 41:   MatInitializePackage();
 42:   DMInitializePackage();

 44:   PetscHeaderCreate(v, DM_CLASSID, "DM", "Distribution Manager", "DM", comm, DMDestroy, DMView);

 46:   v->ltogmap                  = NULL;
 47:   v->bs                       = 1;
 48:   v->coloringtype             = IS_COLORING_GLOBAL;
 49:   PetscSFCreate(comm, &v->sf);
 50:   PetscSFCreate(comm, &v->defaultSF);
 51:   v->labels                   = NULL;
 52:   v->depthLabel               = NULL;
 53:   v->defaultSection           = NULL;
 54:   v->defaultGlobalSection     = NULL;
 55:   v->defaultConstraintSection = NULL;
 56:   v->defaultConstraintMat     = NULL;
 57:   v->L                        = NULL;
 58:   v->maxCell                  = NULL;
 59:   v->bdtype                   = NULL;
 60:   v->dimEmbed                 = PETSC_DEFAULT;
 61:   {
 62:     PetscInt i;
 63:     for (i = 0; i < 10; ++i) {
 64:       v->nullspaceConstructors[i] = NULL;
 65:     }
 66:   }
 67:   PetscDSCreate(comm, &v->prob);
 68:   v->dmBC = NULL;
 69:   v->coarseMesh = NULL;
 70:   v->outputSequenceNum = -1;
 71:   v->outputSequenceVal = 0.0;
 72:   DMSetVecType(v,VECSTANDARD);
 73:   DMSetMatType(v,MATAIJ);
 74:   PetscNew(&(v->labels));
 75:   v->labels->refct = 1;
 76:   PetscNew(&(v->boundary));
 77:   v->boundary->refct = 1;
 78:   *dm = v;
 79:   return(0);
 80: }

 84: /*@
 85:   DMClone - Creates a DM object with the same topology as the original.

 87:   Collective on MPI_Comm

 89:   Input Parameter:
 90: . dm - The original DM object

 92:   Output Parameter:
 93: . newdm  - The new DM object

 95:   Level: beginner

 97: .keywords: DM, topology, create
 98: @*/
 99: PetscErrorCode DMClone(DM dm, DM *newdm)
100: {
101:   PetscSF        sf;
102:   Vec            coords;
103:   void          *ctx;
104:   PetscInt       dim;

110:   DMCreate(PetscObjectComm((PetscObject) dm), newdm);
111:   PetscFree((*newdm)->labels);
112:   dm->labels->refct++;
113:   (*newdm)->labels = dm->labels;
114:   (*newdm)->depthLabel = dm->depthLabel;
115:   DMGetDimension(dm, &dim);
116:   DMSetDimension(*newdm, dim);
117:   if (dm->ops->clone) {
118:     (*dm->ops->clone)(dm, newdm);
119:   }
120:   (*newdm)->setupcalled = dm->setupcalled;
121:   DMGetPointSF(dm, &sf);
122:   DMSetPointSF(*newdm, sf);
123:   DMGetApplicationContext(dm, &ctx);
124:   DMSetApplicationContext(*newdm, ctx);
125:   if (dm->coordinateDM) {
126:     DM           ncdm;
127:     PetscSection cs;
128:     PetscInt     pEnd = -1, pEndMax = -1;

130:     DMGetDefaultSection(dm->coordinateDM, &cs);
131:     if (cs) {PetscSectionGetChart(cs, NULL, &pEnd);}
132:     MPI_Allreduce(&pEnd,&pEndMax,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)dm));
133:     if (pEndMax >= 0) {
134:       DMClone(dm->coordinateDM, &ncdm);
135:       DMSetDefaultSection(ncdm, cs);
136:       DMSetCoordinateDM(*newdm, ncdm);
137:       DMDestroy(&ncdm);
138:     }
139:   }
140:   DMGetCoordinatesLocal(dm, &coords);
141:   if (coords) {
142:     DMSetCoordinatesLocal(*newdm, coords);
143:   } else {
144:     DMGetCoordinates(dm, &coords);
145:     if (coords) {DMSetCoordinates(*newdm, coords);}
146:   }
147:   if (dm->maxCell) {
148:     const PetscReal *maxCell, *L;
149:     const DMBoundaryType *bd;
150:     DMGetPeriodicity(dm,     &maxCell, &L, &bd);
151:     DMSetPeriodicity(*newdm,  maxCell,  L,  bd);
152:   }
153:   return(0);
154: }

158: /*@C
159:        DMSetVecType - Sets the type of vector created with DMCreateLocalVector() and DMCreateGlobalVector()

161:    Logically Collective on DM

163:    Input Parameter:
164: +  da - initial distributed array
165: .  ctype - the vector type, currently either VECSTANDARD or VECCUSP

167:    Options Database:
168: .   -dm_vec_type ctype

170:    Level: intermediate

172: .seealso: DMCreate(), DMDestroy(), DM, DMDAInterpolationType, VecType, DMGetVecType()
173: @*/
174: PetscErrorCode  DMSetVecType(DM da,VecType ctype)
175: {

180:   PetscFree(da->vectype);
181:   PetscStrallocpy(ctype,(char**)&da->vectype);
182:   return(0);
183: }

187: /*@C
188:        DMGetVecType - Gets the type of vector created with DMCreateLocalVector() and DMCreateGlobalVector()

190:    Logically Collective on DM

192:    Input Parameter:
193: .  da - initial distributed array

195:    Output Parameter:
196: .  ctype - the vector type

198:    Level: intermediate

200: .seealso: DMCreate(), DMDestroy(), DM, DMDAInterpolationType, VecType
201: @*/
202: PetscErrorCode  DMGetVecType(DM da,VecType *ctype)
203: {
206:   *ctype = da->vectype;
207:   return(0);
208: }

212: /*@
213:   VecGetDM - Gets the DM defining the data layout of the vector

215:   Not collective

217:   Input Parameter:
218: . v - The Vec

220:   Output Parameter:
221: . dm - The DM

223:   Level: intermediate

225: .seealso: VecSetDM(), DMGetLocalVector(), DMGetGlobalVector(), DMSetVecType()
226: @*/
227: PetscErrorCode VecGetDM(Vec v, DM *dm)
228: {

234:   PetscObjectQuery((PetscObject) v, "__PETSc_dm", (PetscObject*) dm);
235:   return(0);
236: }

240: /*@
241:   VecSetDM - Sets the DM defining the data layout of the vector.

243:   Not collective

245:   Input Parameters:
246: + v - The Vec
247: - dm - The DM

249:   Note: This is NOT the same as DMCreateGlobalVector() since it does not change the view methods or perform other customization, but merely sets the DM member.

251:   Level: intermediate

253: .seealso: VecGetDM(), DMGetLocalVector(), DMGetGlobalVector(), DMSetVecType()
254: @*/
255: PetscErrorCode VecSetDM(Vec v, DM dm)
256: {

262:   PetscObjectCompose((PetscObject) v, "__PETSc_dm", (PetscObject) dm);
263:   return(0);
264: }

268: /*@C
269:        DMSetMatType - Sets the type of matrix created with DMCreateMatrix()

271:    Logically Collective on DM

273:    Input Parameter:
274: +  dm - the DM context
275: .  ctype - the matrix type

277:    Options Database:
278: .   -dm_mat_type ctype

280:    Level: intermediate

282: .seealso: DMDACreate1d(), DMDACreate2d(), DMDACreate3d(), DMCreateMatrix(), DMSetMatrixPreallocateOnly(), MatType, DMGetMatType()
283: @*/
284: PetscErrorCode  DMSetMatType(DM dm,MatType ctype)
285: {

290:   PetscFree(dm->mattype);
291:   PetscStrallocpy(ctype,(char**)&dm->mattype);
292:   return(0);
293: }

297: /*@C
298:        DMGetMatType - Gets the type of matrix created with DMCreateMatrix()

300:    Logically Collective on DM

302:    Input Parameter:
303: .  dm - the DM context

305:    Output Parameter:
306: .  ctype - the matrix type

308:    Options Database:
309: .   -dm_mat_type ctype

311:    Level: intermediate

313: .seealso: DMDACreate1d(), DMDACreate2d(), DMDACreate3d(), DMCreateMatrix(), DMSetMatrixPreallocateOnly(), MatType, DMSetMatType()
314: @*/
315: PetscErrorCode  DMGetMatType(DM dm,MatType *ctype)
316: {
319:   *ctype = dm->mattype;
320:   return(0);
321: }

325: /*@
326:   MatGetDM - Gets the DM defining the data layout of the matrix

328:   Not collective

330:   Input Parameter:
331: . A - The Mat

333:   Output Parameter:
334: . dm - The DM

336:   Level: intermediate

338: .seealso: MatSetDM(), DMCreateMatrix(), DMSetMatType()
339: @*/
340: PetscErrorCode MatGetDM(Mat A, DM *dm)
341: {

347:   PetscObjectQuery((PetscObject) A, "__PETSc_dm", (PetscObject*) dm);
348:   return(0);
349: }

353: /*@
354:   MatSetDM - Sets the DM defining the data layout of the matrix

356:   Not collective

358:   Input Parameters:
359: + A - The Mat
360: - dm - The DM

362:   Level: intermediate

364: .seealso: MatGetDM(), DMCreateMatrix(), DMSetMatType()
365: @*/
366: PetscErrorCode MatSetDM(Mat A, DM dm)
367: {

373:   PetscObjectCompose((PetscObject) A, "__PETSc_dm", (PetscObject) dm);
374:   return(0);
375: }

379: /*@C
380:    DMSetOptionsPrefix - Sets the prefix used for searching for all
381:    DM options in the database.

383:    Logically Collective on DM

385:    Input Parameter:
386: +  da - the DM context
387: -  prefix - the prefix to prepend to all option names

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

393:    Level: advanced

395: .keywords: DM, set, options, prefix, database

397: .seealso: DMSetFromOptions()
398: @*/
399: PetscErrorCode  DMSetOptionsPrefix(DM dm,const char prefix[])
400: {

405:   PetscObjectSetOptionsPrefix((PetscObject)dm,prefix);
406:   if (dm->sf) {
407:     PetscObjectSetOptionsPrefix((PetscObject)dm->sf,prefix);
408:   }
409:   if (dm->defaultSF) {
410:     PetscObjectSetOptionsPrefix((PetscObject)dm->defaultSF,prefix);
411:   }
412:   return(0);
413: }

417: /*@C
418:    DMAppendOptionsPrefix - Appends to the prefix used for searching for all
419:    DM options in the database.

421:    Logically Collective on DM

423:    Input Parameters:
424: +  dm - the DM context
425: -  prefix - the prefix string to prepend to all DM option requests

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

431:    Level: advanced

433: .keywords: DM, append, options, prefix, database

435: .seealso: DMSetOptionsPrefix(), DMGetOptionsPrefix()
436: @*/
437: PetscErrorCode  DMAppendOptionsPrefix(DM dm,const char prefix[])
438: {

443:   PetscObjectAppendOptionsPrefix((PetscObject)dm,prefix);
444:   return(0);
445: }

449: /*@C
450:    DMGetOptionsPrefix - Gets the prefix used for searching for all
451:    DM options in the database.

453:    Not Collective

455:    Input Parameters:
456: .  dm - the DM context

458:    Output Parameters:
459: .  prefix - pointer to the prefix string used is returned

461:    Notes: On the fortran side, the user should pass in a string 'prefix' of
462:    sufficient length to hold the prefix.

464:    Level: advanced

466: .keywords: DM, set, options, prefix, database

468: .seealso: DMSetOptionsPrefix(), DMAppendOptionsPrefix()
469: @*/
470: PetscErrorCode  DMGetOptionsPrefix(DM dm,const char *prefix[])
471: {

476:   PetscObjectGetOptionsPrefix((PetscObject)dm,prefix);
477:   return(0);
478: }

482: static PetscErrorCode DMCountNonCyclicReferences(DM dm, PetscBool recurseCoarse, PetscBool recurseFine, PetscInt *ncrefct)
483: {
484:   PetscInt i, refct = ((PetscObject) dm)->refct;
485:   DMNamedVecLink nlink;

489:   /* count all the circular references of DM and its contained Vecs */
490:   for (i=0; i<DM_MAX_WORK_VECTORS; i++) {
491:     if (dm->localin[i])  refct--;
492:     if (dm->globalin[i]) refct--;
493:   }
494:   for (nlink=dm->namedglobal; nlink; nlink=nlink->next) refct--;
495:   for (nlink=dm->namedlocal; nlink; nlink=nlink->next) refct--;
496:   if (dm->x) {
497:     DM obj;
498:     VecGetDM(dm->x, &obj);
499:     if (obj == dm) refct--;
500:   }
501:   if (dm->coarseMesh && dm->coarseMesh->fineMesh == dm) {
502:     refct--;
503:     if (recurseCoarse) {
504:       PetscInt coarseCount;

506:       DMCountNonCyclicReferences(dm->coarseMesh, PETSC_TRUE, PETSC_FALSE,&coarseCount);
507:       refct += coarseCount;
508:     }
509:   }
510:   if (dm->fineMesh && dm->fineMesh->coarseMesh == dm) {
511:     refct--;
512:     if (recurseFine) {
513:       PetscInt fineCount;

515:       DMCountNonCyclicReferences(dm->fineMesh, PETSC_FALSE, PETSC_TRUE,&fineCount);
516:       refct += fineCount;
517:     }
518:   }
519:   *ncrefct = refct;
520:   return(0);
521: }

523: PetscErrorCode DMBoundaryDestroy(DMBoundaryLinkList *boundary);

527: PetscErrorCode DMDestroyLabelLinkList(DM dm)
528: {

532:   if (!--(dm->labels->refct)) {
533:     DMLabelLink next = dm->labels->next;

535:     /* destroy the labels */
536:     while (next) {
537:       DMLabelLink tmp = next->next;

539:       DMLabelDestroy(&next->label);
540:       PetscFree(next);
541:       next = tmp;
542:     }
543:     PetscFree(dm->labels);
544:   }
545:   return(0);
546: }

550: /*@
551:     DMDestroy - Destroys a vector packer or DM.

553:     Collective on DM

555:     Input Parameter:
556: .   dm - the DM object to destroy

558:     Level: developer

560: .seealso DMView(), DMCreateGlobalVector(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix()

562: @*/
563: PetscErrorCode  DMDestroy(DM *dm)
564: {
565:   PetscInt       i, cnt;
566:   DMNamedVecLink nlink,nnext;

570:   if (!*dm) return(0);

573:   /* count all non-cyclic references in the doubly-linked list of coarse<->fine meshes */
574:   DMCountNonCyclicReferences(*dm,PETSC_TRUE,PETSC_TRUE,&cnt);
575:   --((PetscObject)(*dm))->refct;
576:   if (--cnt > 0) {*dm = 0; return(0);}
577:   /*
578:      Need this test because the dm references the vectors that
579:      reference the dm, so destroying the dm calls destroy on the
580:      vectors that cause another destroy on the dm
581:   */
582:   if (((PetscObject)(*dm))->refct < 0) return(0);
583:   ((PetscObject) (*dm))->refct = 0;
584:   for (i=0; i<DM_MAX_WORK_VECTORS; i++) {
585:     if ((*dm)->localout[i]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Destroying a DM that has a local vector obtained with DMGetLocalVector()");
586:     VecDestroy(&(*dm)->localin[i]);
587:   }
588:   nnext=(*dm)->namedglobal;
589:   (*dm)->namedglobal = NULL;
590:   for (nlink=nnext; nlink; nlink=nnext) { /* Destroy the named vectors */
591:     nnext = nlink->next;
592:     if (nlink->status != DMVEC_STATUS_IN) SETERRQ1(((PetscObject)*dm)->comm,PETSC_ERR_ARG_WRONGSTATE,"DM still has Vec named '%s' checked out",nlink->name);
593:     PetscFree(nlink->name);
594:     VecDestroy(&nlink->X);
595:     PetscFree(nlink);
596:   }
597:   nnext=(*dm)->namedlocal;
598:   (*dm)->namedlocal = NULL;
599:   for (nlink=nnext; nlink; nlink=nnext) { /* Destroy the named local vectors */
600:     nnext = nlink->next;
601:     if (nlink->status != DMVEC_STATUS_IN) SETERRQ1(((PetscObject)*dm)->comm,PETSC_ERR_ARG_WRONGSTATE,"DM still has Vec named '%s' checked out",nlink->name);
602:     PetscFree(nlink->name);
603:     VecDestroy(&nlink->X);
604:     PetscFree(nlink);
605:   }

607:   /* Destroy the list of hooks */
608:   {
609:     DMCoarsenHookLink link,next;
610:     for (link=(*dm)->coarsenhook; link; link=next) {
611:       next = link->next;
612:       PetscFree(link);
613:     }
614:     (*dm)->coarsenhook = NULL;
615:   }
616:   {
617:     DMRefineHookLink link,next;
618:     for (link=(*dm)->refinehook; link; link=next) {
619:       next = link->next;
620:       PetscFree(link);
621:     }
622:     (*dm)->refinehook = NULL;
623:   }
624:   {
625:     DMSubDomainHookLink link,next;
626:     for (link=(*dm)->subdomainhook; link; link=next) {
627:       next = link->next;
628:       PetscFree(link);
629:     }
630:     (*dm)->subdomainhook = NULL;
631:   }
632:   {
633:     DMGlobalToLocalHookLink link,next;
634:     for (link=(*dm)->gtolhook; link; link=next) {
635:       next = link->next;
636:       PetscFree(link);
637:     }
638:     (*dm)->gtolhook = NULL;
639:   }
640:   {
641:     DMLocalToGlobalHookLink link,next;
642:     for (link=(*dm)->ltoghook; link; link=next) {
643:       next = link->next;
644:       PetscFree(link);
645:     }
646:     (*dm)->ltoghook = NULL;
647:   }
648:   /* Destroy the work arrays */
649:   {
650:     DMWorkLink link,next;
651:     if ((*dm)->workout) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Work array still checked out");
652:     for (link=(*dm)->workin; link; link=next) {
653:       next = link->next;
654:       PetscFree(link->mem);
655:       PetscFree(link);
656:     }
657:     (*dm)->workin = NULL;
658:   }
659:   if (!--((*dm)->labels->refct)) {
660:     DMLabelLink next = (*dm)->labels->next;

662:     /* destroy the labels */
663:     while (next) {
664:       DMLabelLink tmp = next->next;

666:       DMLabelDestroy(&next->label);
667:       PetscFree(next);
668:       next = tmp;
669:     }
670:     PetscFree((*dm)->labels);
671:   }
672:   DMBoundaryDestroy(&(*dm)->boundary);

674:   PetscObjectDestroy(&(*dm)->dmksp);
675:   PetscObjectDestroy(&(*dm)->dmsnes);
676:   PetscObjectDestroy(&(*dm)->dmts);

678:   if ((*dm)->ctx && (*dm)->ctxdestroy) {
679:     (*(*dm)->ctxdestroy)(&(*dm)->ctx);
680:   }
681:   VecDestroy(&(*dm)->x);
682:   MatFDColoringDestroy(&(*dm)->fd);
683:   DMClearGlobalVectors(*dm);
684:   ISLocalToGlobalMappingDestroy(&(*dm)->ltogmap);
685:   PetscFree((*dm)->vectype);
686:   PetscFree((*dm)->mattype);

688:   PetscSectionDestroy(&(*dm)->defaultSection);
689:   PetscSectionDestroy(&(*dm)->defaultGlobalSection);
690:   PetscLayoutDestroy(&(*dm)->map);
691:   PetscSectionDestroy(&(*dm)->defaultConstraintSection);
692:   MatDestroy(&(*dm)->defaultConstraintMat);
693:   PetscSFDestroy(&(*dm)->sf);
694:   PetscSFDestroy(&(*dm)->defaultSF);
695:   PetscSFDestroy(&(*dm)->sfNatural);

697:   if ((*dm)->coarseMesh && (*dm)->coarseMesh->fineMesh == *dm) {
698:     DMSetFineDM((*dm)->coarseMesh,NULL);
699:   }
700:   DMDestroy(&(*dm)->coarseMesh);
701:   if ((*dm)->fineMesh && (*dm)->fineMesh->coarseMesh == *dm) {
702:     DMSetCoarseDM((*dm)->fineMesh,NULL);
703:   }
704:   DMDestroy(&(*dm)->fineMesh);
705:   DMDestroy(&(*dm)->coordinateDM);
706:   VecDestroy(&(*dm)->coordinates);
707:   VecDestroy(&(*dm)->coordinatesLocal);
708:   PetscFree3((*dm)->L,(*dm)->maxCell,(*dm)->bdtype);

710:   PetscDSDestroy(&(*dm)->prob);
711:   DMDestroy(&(*dm)->dmBC);
712:   /* if memory was published with SAWs then destroy it */
713:   PetscObjectSAWsViewOff((PetscObject)*dm);

715:   (*(*dm)->ops->destroy)(*dm);
716:   /* We do not destroy (*dm)->data here so that we can reference count backend objects */
717:   PetscHeaderDestroy(dm);
718:   return(0);
719: }

723: /*@
724:     DMSetUp - sets up the data structures inside a DM object

726:     Collective on DM

728:     Input Parameter:
729: .   dm - the DM object to setup

731:     Level: developer

733: .seealso DMView(), DMCreateGlobalVector(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix()

735: @*/
736: PetscErrorCode  DMSetUp(DM dm)
737: {

742:   if (dm->setupcalled) return(0);
743:   if (dm->ops->setup) {
744:     (*dm->ops->setup)(dm);
745:   }
746:   dm->setupcalled = PETSC_TRUE;
747:   return(0);
748: }

752: /*@
753:     DMSetFromOptions - sets parameters in a DM from the options database

755:     Collective on DM

757:     Input Parameter:
758: .   dm - the DM object to set options for

760:     Options Database:
761: +   -dm_preallocate_only - Only preallocate the matrix for DMCreateMatrix(), but do not fill it with zeros
762: .   -dm_vec_type <type>  - type of vector to create inside DM
763: .   -dm_mat_type <type>  - type of matrix to create inside DM
764: -   -dm_coloring_type    - <global or ghosted>

766:     Level: developer

768: .seealso DMView(), DMCreateGlobalVector(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix()

770: @*/
771: PetscErrorCode  DMSetFromOptions(DM dm)
772: {
773:   char           typeName[256];
774:   PetscBool      flg;

779:   if (dm->sf) {
780:     PetscSFSetFromOptions(dm->sf);
781:   }
782:   if (dm->defaultSF) {
783:     PetscSFSetFromOptions(dm->defaultSF);
784:   }
785:   PetscObjectOptionsBegin((PetscObject)dm);
786:   PetscOptionsBool("-dm_preallocate_only","only preallocate matrix, but do not set column indices","DMSetMatrixPreallocateOnly",dm->prealloc_only,&dm->prealloc_only,NULL);
787:   PetscOptionsFList("-dm_vec_type","Vector type used for created vectors","DMSetVecType",VecList,dm->vectype,typeName,256,&flg);
788:   if (flg) {
789:     DMSetVecType(dm,typeName);
790:   }
791:   PetscOptionsFList("-dm_mat_type","Matrix type used for created matrices","DMSetMatType",MatList,dm->mattype ? dm->mattype : typeName,typeName,sizeof(typeName),&flg);
792:   if (flg) {
793:     DMSetMatType(dm,typeName);
794:   }
795:   PetscOptionsEnum("-dm_is_coloring_type","Global or local coloring of Jacobian","ISColoringType",ISColoringTypes,(PetscEnum)dm->coloringtype,(PetscEnum*)&dm->coloringtype,NULL);
796:   if (dm->ops->setfromoptions) {
797:     (*dm->ops->setfromoptions)(PetscOptionsObject,dm);
798:   }
799:   /* process any options handlers added with PetscObjectAddOptionsHandler() */
800:   PetscObjectProcessOptionsHandlers(PetscOptionsObject,(PetscObject) dm);
801:   PetscOptionsEnd();
802:   return(0);
803: }

807: /*@C
808:     DMView - Views a DM

810:     Collective on DM

812:     Input Parameter:
813: +   dm - the DM object to view
814: -   v - the viewer

816:     Level: beginner

818: .seealso DMDestroy(), DMCreateGlobalVector(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix()

820: @*/
821: PetscErrorCode  DMView(DM dm,PetscViewer v)
822: {
824:   PetscBool      isbinary;

828:   if (!v) {
829:     PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)dm),&v);
830:   }
831:   PetscObjectPrintClassNamePrefixType((PetscObject)dm,v);
832:   PetscObjectTypeCompare((PetscObject)v,PETSCVIEWERBINARY,&isbinary);
833:   if (isbinary) {
834:     PetscInt classid = DM_FILE_CLASSID;
835:     char     type[256];

837:     PetscViewerBinaryWrite(v,&classid,1,PETSC_INT,PETSC_FALSE);
838:     PetscStrncpy(type,((PetscObject)dm)->type_name,256);
839:     PetscViewerBinaryWrite(v,type,256,PETSC_CHAR,PETSC_FALSE);
840:   }
841:   if (dm->ops->view) {
842:     (*dm->ops->view)(dm,v);
843:   }
844:   return(0);
845: }

849: /*@
850:     DMCreateGlobalVector - Creates a global vector from a DM object

852:     Collective on DM

854:     Input Parameter:
855: .   dm - the DM object

857:     Output Parameter:
858: .   vec - the global vector

860:     Level: beginner

862: .seealso DMDestroy(), DMView(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix()

864: @*/
865: PetscErrorCode  DMCreateGlobalVector(DM dm,Vec *vec)
866: {

871:   (*dm->ops->createglobalvector)(dm,vec);
872:   return(0);
873: }

877: /*@
878:     DMCreateLocalVector - Creates a local vector from a DM object

880:     Not Collective

882:     Input Parameter:
883: .   dm - the DM object

885:     Output Parameter:
886: .   vec - the local vector

888:     Level: beginner

890: .seealso DMDestroy(), DMView(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix()

892: @*/
893: PetscErrorCode  DMCreateLocalVector(DM dm,Vec *vec)
894: {

899:   (*dm->ops->createlocalvector)(dm,vec);
900:   return(0);
901: }

905: /*@
906:    DMGetLocalToGlobalMapping - Accesses the local-to-global mapping in a DM.

908:    Collective on DM

910:    Input Parameter:
911: .  dm - the DM that provides the mapping

913:    Output Parameter:
914: .  ltog - the mapping

916:    Level: intermediate

918:    Notes:
919:    This mapping can then be used by VecSetLocalToGlobalMapping() or
920:    MatSetLocalToGlobalMapping().

922: .seealso: DMCreateLocalVector()
923: @*/
924: PetscErrorCode  DMGetLocalToGlobalMapping(DM dm,ISLocalToGlobalMapping *ltog)
925: {
926:   PetscInt       bs = -1;

932:   if (!dm->ltogmap) {
933:     PetscSection section, sectionGlobal;

935:     DMGetDefaultSection(dm, &section);
936:     if (section) {
937:       PetscInt *ltog;
938:       PetscInt pStart, pEnd, size, p, l;

940:       DMGetDefaultGlobalSection(dm, &sectionGlobal);
941:       PetscSectionGetChart(section, &pStart, &pEnd);
942:       PetscSectionGetStorageSize(section, &size);
943:       PetscMalloc1(size, &ltog); /* We want the local+overlap size */
944:       for (p = pStart, l = 0; p < pEnd; ++p) {
945:         PetscInt bdof, cdof, dof, off, c;

947:         /* Should probably use constrained dofs */
948:         PetscSectionGetDof(section, p, &dof);
949:         PetscSectionGetOffset(sectionGlobal, p, &off);
950:         PetscSectionGetConstraintDof(sectionGlobal, p, &cdof);
951:         bdof = cdof ? 1 : dof;
952:         if (bs < 0)          {bs = bdof;}
953:         else if (bs != bdof) {bs = 1;}
954:         for (c = 0; c < dof; ++c, ++l) {
955:           ltog[l] = off+c;
956:         }
957:       }
958:       ISLocalToGlobalMappingCreate(PETSC_COMM_SELF, bs < 0 ? 1 : bs, size, ltog, PETSC_OWN_POINTER, &dm->ltogmap);
959:       PetscLogObjectParent((PetscObject)dm, (PetscObject)dm->ltogmap);
960:     } else {
961:       if (!dm->ops->getlocaltoglobalmapping) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"DM can not create LocalToGlobalMapping");
962:       (*dm->ops->getlocaltoglobalmapping)(dm);
963:     }
964:   }
965:   *ltog = dm->ltogmap;
966:   return(0);
967: }

971: /*@
972:    DMGetBlockSize - Gets the inherent block size associated with a DM

974:    Not Collective

976:    Input Parameter:
977: .  dm - the DM with block structure

979:    Output Parameter:
980: .  bs - the block size, 1 implies no exploitable block structure

982:    Level: intermediate

984: .seealso: ISCreateBlock(), VecSetBlockSize(), MatSetBlockSize(), DMGetLocalToGlobalMapping()
985: @*/
986: PetscErrorCode  DMGetBlockSize(DM dm,PetscInt *bs)
987: {
991:   if (dm->bs < 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"DM does not have enough information to provide a block size yet");
992:   *bs = dm->bs;
993:   return(0);
994: }

998: /*@
999:     DMCreateInterpolation - Gets interpolation matrix between two DM objects

1001:     Collective on DM

1003:     Input Parameter:
1004: +   dm1 - the DM object
1005: -   dm2 - the second, finer DM object

1007:     Output Parameter:
1008: +  mat - the interpolation
1009: -  vec - the scaling (optional)

1011:     Level: developer

1013:     Notes:  For DMDA objects this only works for "uniform refinement", that is the refined mesh was obtained DMRefine() or the coarse mesh was obtained by
1014:         DMCoarsen(). The coordinates set into the DMDA are completely ignored in computing the interpolation.

1016:         For DMDA objects you can use this interpolation (more precisely the interpolation from the DMGetCoordinateDM()) to interpolate the mesh coordinate vectors
1017:         EXCEPT in the periodic case where it does not make sense since the coordinate vectors are not periodic.


1020: .seealso DMDestroy(), DMView(), DMCreateGlobalVector(), DMCreateColoring(), DMCreateMatrix(), DMRefine(), DMCoarsen(), DMCreateRestriction()

1022: @*/
1023: PetscErrorCode  DMCreateInterpolation(DM dm1,DM dm2,Mat *mat,Vec *vec)
1024: {

1030:   PetscLogEventBegin(DM_CreateInterpolation,dm1,dm2,0,0);
1031:   (*dm1->ops->createinterpolation)(dm1,dm2,mat,vec);
1032:   PetscLogEventEnd(DM_CreateInterpolation,dm1,dm2,0,0);
1033:   return(0);
1034: }

1038: /*@
1039:     DMCreateRestriction - Gets restriction matrix between two DM objects

1041:     Collective on DM

1043:     Input Parameter:
1044: +   dm1 - the DM object
1045: -   dm2 - the second, finer DM object

1047:     Output Parameter:
1048: .  mat - the restriction


1051:     Level: developer

1053:     Notes:  For DMDA objects this only works for "uniform refinement", that is the refined mesh was obtained DMRefine() or the coarse mesh was obtained by
1054:         DMCoarsen(). The coordinates set into the DMDA are completely ignored in computing the interpolation.

1056:  
1057: .seealso DMDestroy(), DMView(), DMCreateGlobalVector(), DMCreateColoring(), DMCreateMatrix(), DMRefine(), DMCoarsen(), DMCreateInterpolation()

1059: @*/
1060: PetscErrorCode  DMCreateRestriction(DM dm1,DM dm2,Mat *mat)
1061: {

1067:   PetscLogEventBegin(DM_CreateRestriction,dm1,dm2,0,0);
1068:   (*dm1->ops->createrestriction)(dm1,dm2,mat);
1069:   PetscLogEventEnd(DM_CreateRestriction,dm1,dm2,0,0);
1070:   return(0);
1071: }

1075: /*@
1076:     DMCreateInjection - Gets injection matrix between two DM objects

1078:     Collective on DM

1080:     Input Parameter:
1081: +   dm1 - the DM object
1082: -   dm2 - the second, finer DM object

1084:     Output Parameter:
1085: .   mat - the injection

1087:     Level: developer

1089:    Notes:  For DMDA objects this only works for "uniform refinement", that is the refined mesh was obtained DMRefine() or the coarse mesh was obtained by
1090:         DMCoarsen(). The coordinates set into the DMDA are completely ignored in computing the injection.

1092: .seealso DMDestroy(), DMView(), DMCreateGlobalVector(), DMCreateColoring(), DMCreateMatrix(), DMCreateInterpolation()

1094: @*/
1095: PetscErrorCode  DMCreateInjection(DM dm1,DM dm2,Mat *mat)
1096: {

1102:   if (!*dm1->ops->getinjection) SETERRQ(PetscObjectComm((PetscObject)dm1),PETSC_ERR_SUP,"DMCreateInjection not implemented for this type");
1103:   (*dm1->ops->getinjection)(dm1,dm2,mat);
1104:   return(0);
1105: }

1109: /*@
1110:     DMCreateColoring - Gets coloring for a DM

1112:     Collective on DM

1114:     Input Parameter:
1115: +   dm - the DM object
1116: -   ctype - IS_COLORING_GHOSTED or IS_COLORING_GLOBAL

1118:     Output Parameter:
1119: .   coloring - the coloring

1121:     Level: developer

1123: .seealso DMDestroy(), DMView(), DMCreateGlobalVector(), DMCreateInterpolation(), DMCreateMatrix(), DMSetMatType()

1125: @*/
1126: PetscErrorCode  DMCreateColoring(DM dm,ISColoringType ctype,ISColoring *coloring)
1127: {

1132:   if (!dm->ops->getcoloring) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"No coloring for this type of DM yet");
1133:   (*dm->ops->getcoloring)(dm,ctype,coloring);
1134:   return(0);
1135: }

1139: /*@
1140:     DMCreateMatrix - Gets empty Jacobian for a DM

1142:     Collective on DM

1144:     Input Parameter:
1145: .   dm - the DM object

1147:     Output Parameter:
1148: .   mat - the empty Jacobian

1150:     Level: beginner

1152:     Notes: This properly preallocates the number of nonzeros in the sparse matrix so you
1153:        do not need to do it yourself.

1155:        By default it also sets the nonzero structure and puts in the zero entries. To prevent setting
1156:        the nonzero pattern call DMDASetMatPreallocateOnly()

1158:        For structured grid problems, when you call MatView() on this matrix it is displayed using the global natural ordering, NOT in the ordering used
1159:        internally by PETSc.

1161:        For structured grid problems, in general it is easiest to use MatSetValuesStencil() or MatSetValuesLocal() to put values into the matrix because MatSetValues() requires
1162:        the indices for the global numbering for DMDAs which is complicated.

1164: .seealso DMDestroy(), DMView(), DMCreateGlobalVector(), DMCreateInterpolation(), DMSetMatType()

1166: @*/
1167: PetscErrorCode  DMCreateMatrix(DM dm,Mat *mat)
1168: {

1173:   MatInitializePackage();
1176:   (*dm->ops->creatematrix)(dm,mat);
1177:   return(0);
1178: }

1182: /*@
1183:   DMSetMatrixPreallocateOnly - When DMCreateMatrix() is called the matrix will be properly
1184:     preallocated but the nonzero structure and zero values will not be set.

1186:   Logically Collective on DM

1188:   Input Parameter:
1189: + dm - the DM
1190: - only - PETSC_TRUE if only want preallocation

1192:   Level: developer
1193: .seealso DMCreateMatrix()
1194: @*/
1195: PetscErrorCode DMSetMatrixPreallocateOnly(DM dm, PetscBool only)
1196: {
1199:   dm->prealloc_only = only;
1200:   return(0);
1201: }

1205: /*@C
1206:   DMGetWorkArray - Gets a work array guaranteed to be at least the input size, restore with DMRestoreWorkArray()

1208:   Not Collective

1210:   Input Parameters:
1211: + dm - the DM object
1212: . count - The minium size
1213: - dtype - data type (PETSC_REAL, PETSC_SCALAR, PETSC_INT)

1215:   Output Parameter:
1216: . array - the work array

1218:   Level: developer

1220: .seealso DMDestroy(), DMCreate()
1221: @*/
1222: PetscErrorCode DMGetWorkArray(DM dm,PetscInt count,PetscDataType dtype,void *mem)
1223: {
1225:   DMWorkLink     link;
1226:   size_t         dsize;

1231:   if (dm->workin) {
1232:     link       = dm->workin;
1233:     dm->workin = dm->workin->next;
1234:   } else {
1235:     PetscNewLog(dm,&link);
1236:   }
1237:   PetscDataTypeGetSize(dtype,&dsize);
1238:   if (dsize*count > link->bytes) {
1239:     PetscFree(link->mem);
1240:     PetscMalloc(dsize*count,&link->mem);
1241:     link->bytes = dsize*count;
1242:   }
1243:   link->next   = dm->workout;
1244:   dm->workout  = link;
1245:   *(void**)mem = link->mem;
1246:   return(0);
1247: }

1251: /*@C
1252:   DMRestoreWorkArray - Restores a work array guaranteed to be at least the input size, restore with DMRestoreWorkArray()

1254:   Not Collective

1256:   Input Parameters:
1257: + dm - the DM object
1258: . count - The minium size
1259: - dtype - data type (PETSC_REAL, PETSC_SCALAR, PETSC_INT)

1261:   Output Parameter:
1262: . array - the work array

1264:   Level: developer

1266: .seealso DMDestroy(), DMCreate()
1267: @*/
1268: PetscErrorCode DMRestoreWorkArray(DM dm,PetscInt count,PetscDataType dtype,void *mem)
1269: {
1270:   DMWorkLink *p,link;

1275:   for (p=&dm->workout; (link=*p); p=&link->next) {
1276:     if (link->mem == *(void**)mem) {
1277:       *p           = link->next;
1278:       link->next   = dm->workin;
1279:       dm->workin   = link;
1280:       *(void**)mem = NULL;
1281:       return(0);
1282:     }
1283:   }
1284:   SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Array was not checked out");
1285: }

1289: PetscErrorCode DMSetNullSpaceConstructor(DM dm, PetscInt field, PetscErrorCode (*nullsp)(DM dm, PetscInt field, MatNullSpace *nullSpace))
1290: {
1293:   if (field >= 10) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cannot handle %d >= 10 fields", field);
1294:   dm->nullspaceConstructors[field] = nullsp;
1295:   return(0);
1296: }

1300: /*@C
1301:   DMCreateFieldIS - Creates a set of IS objects with the global indices of dofs for each field

1303:   Not collective

1305:   Input Parameter:
1306: . dm - the DM object

1308:   Output Parameters:
1309: + numFields  - The number of fields (or NULL if not requested)
1310: . fieldNames - The name for each field (or NULL if not requested)
1311: - fields     - The global indices for each field (or NULL if not requested)

1313:   Level: intermediate

1315:   Notes:
1316:   The user is responsible for freeing all requested arrays. In particular, every entry of names should be freed with
1317:   PetscFree(), every entry of fields should be destroyed with ISDestroy(), and both arrays should be freed with
1318:   PetscFree().

1320: .seealso DMDestroy(), DMView(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix()
1321: @*/
1322: PetscErrorCode DMCreateFieldIS(DM dm, PetscInt *numFields, char ***fieldNames, IS **fields)
1323: {
1324:   PetscSection   section, sectionGlobal;

1329:   if (numFields) {
1331:     *numFields = 0;
1332:   }
1333:   if (fieldNames) {
1335:     *fieldNames = NULL;
1336:   }
1337:   if (fields) {
1339:     *fields = NULL;
1340:   }
1341:   DMGetDefaultSection(dm, &section);
1342:   if (section) {
1343:     PetscInt *fieldSizes, **fieldIndices;
1344:     PetscInt nF, f, pStart, pEnd, p;

1346:     DMGetDefaultGlobalSection(dm, &sectionGlobal);
1347:     PetscSectionGetNumFields(section, &nF);
1348:     PetscMalloc2(nF,&fieldSizes,nF,&fieldIndices);
1349:     PetscSectionGetChart(sectionGlobal, &pStart, &pEnd);
1350:     for (f = 0; f < nF; ++f) {
1351:       fieldSizes[f] = 0;
1352:     }
1353:     for (p = pStart; p < pEnd; ++p) {
1354:       PetscInt gdof;

1356:       PetscSectionGetDof(sectionGlobal, p, &gdof);
1357:       if (gdof > 0) {
1358:         for (f = 0; f < nF; ++f) {
1359:           PetscInt fdof, fcdof;

1361:           PetscSectionGetFieldDof(section, p, f, &fdof);
1362:           PetscSectionGetFieldConstraintDof(section, p, f, &fcdof);
1363:           fieldSizes[f] += fdof-fcdof;
1364:         }
1365:       }
1366:     }
1367:     for (f = 0; f < nF; ++f) {
1368:       PetscMalloc1(fieldSizes[f], &fieldIndices[f]);
1369:       fieldSizes[f] = 0;
1370:     }
1371:     for (p = pStart; p < pEnd; ++p) {
1372:       PetscInt gdof, goff;

1374:       PetscSectionGetDof(sectionGlobal, p, &gdof);
1375:       if (gdof > 0) {
1376:         PetscSectionGetOffset(sectionGlobal, p, &goff);
1377:         for (f = 0; f < nF; ++f) {
1378:           PetscInt fdof, fcdof, fc;

1380:           PetscSectionGetFieldDof(section, p, f, &fdof);
1381:           PetscSectionGetFieldConstraintDof(section, p, f, &fcdof);
1382:           for (fc = 0; fc < fdof-fcdof; ++fc, ++fieldSizes[f]) {
1383:             fieldIndices[f][fieldSizes[f]] = goff++;
1384:           }
1385:         }
1386:       }
1387:     }
1388:     if (numFields) *numFields = nF;
1389:     if (fieldNames) {
1390:       PetscMalloc1(nF, fieldNames);
1391:       for (f = 0; f < nF; ++f) {
1392:         const char *fieldName;

1394:         PetscSectionGetFieldName(section, f, &fieldName);
1395:         PetscStrallocpy(fieldName, (char**) &(*fieldNames)[f]);
1396:       }
1397:     }
1398:     if (fields) {
1399:       PetscMalloc1(nF, fields);
1400:       for (f = 0; f < nF; ++f) {
1401:         ISCreateGeneral(PetscObjectComm((PetscObject)dm), fieldSizes[f], fieldIndices[f], PETSC_OWN_POINTER, &(*fields)[f]);
1402:       }
1403:     }
1404:     PetscFree2(fieldSizes,fieldIndices);
1405:   } else if (dm->ops->createfieldis) {
1406:     (*dm->ops->createfieldis)(dm, numFields, fieldNames, fields);
1407:   }
1408:   return(0);
1409: }


1414: /*@C
1415:   DMCreateFieldDecomposition - Returns a list of IS objects defining a decomposition of a problem into subproblems
1416:                           corresponding to different fields: each IS contains the global indices of the dofs of the
1417:                           corresponding field. The optional list of DMs define the DM for each subproblem.
1418:                           Generalizes DMCreateFieldIS().

1420:   Not collective

1422:   Input Parameter:
1423: . dm - the DM object

1425:   Output Parameters:
1426: + len       - The number of subproblems in the field decomposition (or NULL if not requested)
1427: . namelist  - The name for each field (or NULL if not requested)
1428: . islist    - The global indices for each field (or NULL if not requested)
1429: - dmlist    - The DMs for each field subproblem (or NULL, if not requested; if NULL is returned, no DMs are defined)

1431:   Level: intermediate

1433:   Notes:
1434:   The user is responsible for freeing all requested arrays. In particular, every entry of names should be freed with
1435:   PetscFree(), every entry of is should be destroyed with ISDestroy(), every entry of dm should be destroyed with DMDestroy(),
1436:   and all of the arrays should be freed with PetscFree().

1438: .seealso DMDestroy(), DMView(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix(), DMCreateFieldIS()
1439: @*/
1440: PetscErrorCode DMCreateFieldDecomposition(DM dm, PetscInt *len, char ***namelist, IS **islist, DM **dmlist)
1441: {

1446:   if (len) {
1448:     *len = 0;
1449:   }
1450:   if (namelist) {
1452:     *namelist = 0;
1453:   }
1454:   if (islist) {
1456:     *islist = 0;
1457:   }
1458:   if (dmlist) {
1460:     *dmlist = 0;
1461:   }
1462:   /*
1463:    Is it a good idea to apply the following check across all impls?
1464:    Perhaps some impls can have a well-defined decomposition before DMSetUp?
1465:    This, however, follows the general principle that accessors are not well-behaved until the object is set up.
1466:    */
1467:   if (!dm->setupcalled) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_ARG_WRONGSTATE, "Decomposition defined only after DMSetUp");
1468:   if (!dm->ops->createfielddecomposition) {
1469:     PetscSection section;
1470:     PetscInt     numFields, f;

1472:     DMGetDefaultSection(dm, &section);
1473:     if (section) {PetscSectionGetNumFields(section, &numFields);}
1474:     if (section && numFields && dm->ops->createsubdm) {
1475:       if (len) *len = numFields;
1476:       if (namelist) {PetscMalloc1(numFields,namelist);}
1477:       if (islist)   {PetscMalloc1(numFields,islist);}
1478:       if (dmlist)   {PetscMalloc1(numFields,dmlist);}
1479:       for (f = 0; f < numFields; ++f) {
1480:         const char *fieldName;

1482:         DMCreateSubDM(dm, 1, &f, islist ? &(*islist)[f] : NULL, dmlist ? &(*dmlist)[f] : NULL);
1483:         if (namelist) {
1484:           PetscSectionGetFieldName(section, f, &fieldName);
1485:           PetscStrallocpy(fieldName, (char**) &(*namelist)[f]);
1486:         }
1487:       }
1488:     } else {
1489:       DMCreateFieldIS(dm, len, namelist, islist);
1490:       /* By default there are no DMs associated with subproblems. */
1491:       if (dmlist) *dmlist = NULL;
1492:     }
1493:   } else {
1494:     (*dm->ops->createfielddecomposition)(dm,len,namelist,islist,dmlist);
1495:   }
1496:   return(0);
1497: }

1501: /*@
1502:   DMCreateSubDM - Returns an IS and DM encapsulating a subproblem defined by the fields passed in.
1503:                   The fields are defined by DMCreateFieldIS().

1505:   Not collective

1507:   Input Parameters:
1508: + dm - the DM object
1509: . numFields - number of fields in this subproblem
1510: - len       - The number of subproblems in the decomposition (or NULL if not requested)

1512:   Output Parameters:
1513: . is - The global indices for the subproblem
1514: - dm - The DM for the subproblem

1516:   Level: intermediate

1518: .seealso DMDestroy(), DMView(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix(), DMCreateFieldIS()
1519: @*/
1520: PetscErrorCode DMCreateSubDM(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm)
1521: {

1529:   if (dm->ops->createsubdm) {
1530:     (*dm->ops->createsubdm)(dm, numFields, fields, is, subdm);
1531:   } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "This type has no DMCreateSubDM implementation defined");
1532:   return(0);
1533: }


1538: /*@C
1539:   DMCreateDomainDecomposition - Returns lists of IS objects defining a decomposition of a problem into subproblems
1540:                           corresponding to restrictions to pairs nested subdomains: each IS contains the global
1541:                           indices of the dofs of the corresponding subdomains.  The inner subdomains conceptually
1542:                           define a nonoverlapping covering, while outer subdomains can overlap.
1543:                           The optional list of DMs define the DM for each subproblem.

1545:   Not collective

1547:   Input Parameter:
1548: . dm - the DM object

1550:   Output Parameters:
1551: + len         - The number of subproblems in the domain decomposition (or NULL if not requested)
1552: . namelist    - The name for each subdomain (or NULL if not requested)
1553: . innerislist - The global indices for each inner subdomain (or NULL, if not requested)
1554: . outerislist - The global indices for each outer subdomain (or NULL, if not requested)
1555: - dmlist      - The DMs for each subdomain subproblem (or NULL, if not requested; if NULL is returned, no DMs are defined)

1557:   Level: intermediate

1559:   Notes:
1560:   The user is responsible for freeing all requested arrays. In particular, every entry of names should be freed with
1561:   PetscFree(), every entry of is should be destroyed with ISDestroy(), every entry of dm should be destroyed with DMDestroy(),
1562:   and all of the arrays should be freed with PetscFree().

1564: .seealso DMDestroy(), DMView(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix(), DMCreateDomainDecompositionDM(), DMCreateFieldDecomposition()
1565: @*/
1566: PetscErrorCode DMCreateDomainDecomposition(DM dm, PetscInt *len, char ***namelist, IS **innerislist, IS **outerislist, DM **dmlist)
1567: {
1568:   PetscErrorCode      ierr;
1569:   DMSubDomainHookLink link;
1570:   PetscInt            i,l;

1579:   /*
1580:    Is it a good idea to apply the following check across all impls?
1581:    Perhaps some impls can have a well-defined decomposition before DMSetUp?
1582:    This, however, follows the general principle that accessors are not well-behaved until the object is set up.
1583:    */
1584:   if (!dm->setupcalled) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_ARG_WRONGSTATE, "Decomposition defined only after DMSetUp");
1585:   if (dm->ops->createdomaindecomposition) {
1586:     (*dm->ops->createdomaindecomposition)(dm,&l,namelist,innerislist,outerislist,dmlist);
1587:     /* copy subdomain hooks and context over to the subdomain DMs */
1588:     if (dmlist && *dmlist) {
1589:       for (i = 0; i < l; i++) {
1590:         for (link=dm->subdomainhook; link; link=link->next) {
1591:           if (link->ddhook) {(*link->ddhook)(dm,(*dmlist)[i],link->ctx);}
1592:         }
1593:         (*dmlist)[i]->ctx = dm->ctx;
1594:       }
1595:     }
1596:     if (len) *len = l;
1597:   }
1598:   return(0);
1599: }


1604: /*@C
1605:   DMCreateDomainDecompositionScatters - Returns scatters to the subdomain vectors from the global vector

1607:   Not collective

1609:   Input Parameters:
1610: + dm - the DM object
1611: . n  - the number of subdomain scatters
1612: - subdms - the local subdomains

1614:   Output Parameters:
1615: + n     - the number of scatters returned
1616: . iscat - scatter from global vector to nonoverlapping global vector entries on subdomain
1617: . oscat - scatter from global vector to overlapping global vector entries on subdomain
1618: - gscat - scatter from global vector to local vector on subdomain (fills in ghosts)

1620:   Notes: This is an alternative to the iis and ois arguments in DMCreateDomainDecomposition that allow for the solution
1621:   of general nonlinear problems with overlapping subdomain methods.  While merely having index sets that enable subsets
1622:   of the residual equations to be created is fine for linear problems, nonlinear problems require local assembly of
1623:   solution and residual data.

1625:   Level: developer

1627: .seealso DMDestroy(), DMView(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix(), DMCreateFieldIS()
1628: @*/
1629: PetscErrorCode DMCreateDomainDecompositionScatters(DM dm,PetscInt n,DM *subdms,VecScatter **iscat,VecScatter **oscat,VecScatter **gscat)
1630: {

1636:   if (dm->ops->createddscatters) {
1637:     (*dm->ops->createddscatters)(dm,n,subdms,iscat,oscat,gscat);
1638:   } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "This type has no DMCreateDomainDecompositionScatter implementation defined");
1639:   return(0);
1640: }

1644: /*@
1645:   DMRefine - Refines a DM object

1647:   Collective on DM

1649:   Input Parameter:
1650: + dm   - the DM object
1651: - comm - the communicator to contain the new DM object (or MPI_COMM_NULL)

1653:   Output Parameter:
1654: . dmf - the refined DM, or NULL

1656:   Note: If no refinement was done, the return value is NULL

1658:   Level: developer

1660: .seealso DMCoarsen(), DMDestroy(), DMView(), DMCreateGlobalVector(), DMCreateInterpolation()
1661: @*/
1662: PetscErrorCode  DMRefine(DM dm,MPI_Comm comm,DM *dmf)
1663: {
1664:   PetscErrorCode   ierr;
1665:   DMRefineHookLink link;

1669:   if (!dm->ops->refine) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"This DM cannot refine");
1670:   (*dm->ops->refine)(dm,comm,dmf);
1671:   if (*dmf) {
1672:     (*dmf)->ops->creatematrix = dm->ops->creatematrix;

1674:     PetscObjectCopyFortranFunctionPointers((PetscObject)dm,(PetscObject)*dmf);

1676:     (*dmf)->ctx       = dm->ctx;
1677:     (*dmf)->leveldown = dm->leveldown;
1678:     (*dmf)->levelup   = dm->levelup + 1;

1680:     DMSetMatType(*dmf,dm->mattype);
1681:     for (link=dm->refinehook; link; link=link->next) {
1682:       if (link->refinehook) {
1683:         (*link->refinehook)(dm,*dmf,link->ctx);
1684:       }
1685:     }
1686:   }
1687:   return(0);
1688: }

1692: /*@C
1693:    DMRefineHookAdd - adds a callback to be run when interpolating a nonlinear problem to a finer grid

1695:    Logically Collective

1697:    Input Arguments:
1698: +  coarse - nonlinear solver context on which to run a hook when restricting to a coarser level
1699: .  refinehook - function to run when setting up a coarser level
1700: .  interphook - function to run to update data on finer levels (once per SNESSolve())
1701: -  ctx - [optional] user-defined context for provide data for the hooks (may be NULL)

1703:    Calling sequence of refinehook:
1704: $    refinehook(DM coarse,DM fine,void *ctx);

1706: +  coarse - coarse level DM
1707: .  fine - fine level DM to interpolate problem to
1708: -  ctx - optional user-defined function context

1710:    Calling sequence for interphook:
1711: $    interphook(DM coarse,Mat interp,DM fine,void *ctx)

1713: +  coarse - coarse level DM
1714: .  interp - matrix interpolating a coarse-level solution to the finer grid
1715: .  fine - fine level DM to update
1716: -  ctx - optional user-defined function context

1718:    Level: advanced

1720:    Notes:
1721:    This function is only needed if auxiliary data needs to be passed to fine grids while grid sequencing

1723:    If this function is called multiple times, the hooks will be run in the order they are added.

1725:    This function is currently not available from Fortran.

1727: .seealso: DMCoarsenHookAdd(), SNESFASGetInterpolation(), SNESFASGetInjection(), PetscObjectCompose(), PetscContainerCreate()
1728: @*/
1729: PetscErrorCode DMRefineHookAdd(DM coarse,PetscErrorCode (*refinehook)(DM,DM,void*),PetscErrorCode (*interphook)(DM,Mat,DM,void*),void *ctx)
1730: {
1731:   PetscErrorCode   ierr;
1732:   DMRefineHookLink link,*p;

1736:   for (p=&coarse->refinehook; *p; p=&(*p)->next) {} /* Scan to the end of the current list of hooks */
1737:   PetscMalloc(sizeof(struct _DMRefineHookLink),&link);
1738:   link->refinehook = refinehook;
1739:   link->interphook = interphook;
1740:   link->ctx        = ctx;
1741:   link->next       = NULL;
1742:   *p               = link;
1743:   return(0);
1744: }

1748: /*@
1749:    DMInterpolate - interpolates user-defined problem data to a finer DM by running hooks registered by DMRefineHookAdd()

1751:    Collective if any hooks are

1753:    Input Arguments:
1754: +  coarse - coarser DM to use as a base
1755: .  restrct - interpolation matrix, apply using MatInterpolate()
1756: -  fine - finer DM to update

1758:    Level: developer

1760: .seealso: DMRefineHookAdd(), MatInterpolate()
1761: @*/
1762: PetscErrorCode DMInterpolate(DM coarse,Mat interp,DM fine)
1763: {
1764:   PetscErrorCode   ierr;
1765:   DMRefineHookLink link;

1768:   for (link=fine->refinehook; link; link=link->next) {
1769:     if (link->interphook) {
1770:       (*link->interphook)(coarse,interp,fine,link->ctx);
1771:     }
1772:   }
1773:   return(0);
1774: }

1778: /*@
1779:     DMGetRefineLevel - Get's the number of refinements that have generated this DM.

1781:     Not Collective

1783:     Input Parameter:
1784: .   dm - the DM object

1786:     Output Parameter:
1787: .   level - number of refinements

1789:     Level: developer

1791: .seealso DMCoarsen(), DMGetCoarsenLevel(), DMDestroy(), DMView(), DMCreateGlobalVector(), DMCreateInterpolation()

1793: @*/
1794: PetscErrorCode  DMGetRefineLevel(DM dm,PetscInt *level)
1795: {
1798:   *level = dm->levelup;
1799:   return(0);
1800: }

1804: /*@
1805:     DMSetRefineLevel - Set's the number of refinements that have generated this DM.

1807:     Not Collective

1809:     Input Parameter:
1810: +   dm - the DM object
1811: -   level - number of refinements

1813:     Level: advanced

1815:     Notes: This value is used by PCMG to determine how many multigrid levels to use

1817: .seealso DMCoarsen(), DMGetCoarsenLevel(), DMDestroy(), DMView(), DMCreateGlobalVector(), DMCreateInterpolation()

1819: @*/
1820: PetscErrorCode  DMSetRefineLevel(DM dm,PetscInt level)
1821: {
1824:   dm->levelup = level;
1825:   return(0);
1826: }

1830: /*@C
1831:    DMGlobalToLocalHookAdd - adds a callback to be run when global to local is called

1833:    Logically Collective

1835:    Input Arguments:
1836: +  dm - the DM
1837: .  beginhook - function to run at the beginning of DMGlobalToLocalBegin()
1838: .  endhook - function to run after DMGlobalToLocalEnd() has completed
1839: -  ctx - [optional] user-defined context for provide data for the hooks (may be NULL)

1841:    Calling sequence for beginhook:
1842: $    beginhook(DM fine,VecScatter out,VecScatter in,DM coarse,void *ctx)

1844: +  dm - global DM
1845: .  g - global vector
1846: .  mode - mode
1847: .  l - local vector
1848: -  ctx - optional user-defined function context


1851:    Calling sequence for endhook:
1852: $    endhook(DM fine,VecScatter out,VecScatter in,DM coarse,void *ctx)

1854: +  global - global DM
1855: -  ctx - optional user-defined function context

1857:    Level: advanced

1859: .seealso: DMRefineHookAdd(), SNESFASGetInterpolation(), SNESFASGetInjection(), PetscObjectCompose(), PetscContainerCreate()
1860: @*/
1861: PetscErrorCode DMGlobalToLocalHookAdd(DM dm,PetscErrorCode (*beginhook)(DM,Vec,InsertMode,Vec,void*),PetscErrorCode (*endhook)(DM,Vec,InsertMode,Vec,void*),void *ctx)
1862: {
1863:   PetscErrorCode          ierr;
1864:   DMGlobalToLocalHookLink link,*p;

1868:   for (p=&dm->gtolhook; *p; p=&(*p)->next) {} /* Scan to the end of the current list of hooks */
1869:   PetscMalloc(sizeof(struct _DMGlobalToLocalHookLink),&link);
1870:   link->beginhook = beginhook;
1871:   link->endhook   = endhook;
1872:   link->ctx       = ctx;
1873:   link->next      = NULL;
1874:   *p              = link;
1875:   return(0);
1876: }

1880: static PetscErrorCode DMGlobalToLocalHook_Constraints(DM dm, Vec g, InsertMode mode, Vec l, void *ctx)
1881: {
1882:   Mat cMat;
1883:   Vec cVec;
1884:   PetscSection section, cSec;
1885:   PetscInt pStart, pEnd, p, dof;

1890:   DMGetDefaultConstraints(dm,&cSec,&cMat);
1891:   if (cMat && (mode == INSERT_VALUES || mode == INSERT_ALL_VALUES || mode == INSERT_BC_VALUES)) {
1892:     PetscInt nRows;

1894:     MatGetSize(cMat,&nRows,NULL);
1895:     if (nRows <= 0) return(0);
1896:     DMGetDefaultSection(dm,&section);
1897:     MatCreateVecs(cMat,NULL,&cVec);
1898:     MatMult(cMat,l,cVec);
1899:     PetscSectionGetChart(cSec,&pStart,&pEnd);
1900:     for (p = pStart; p < pEnd; p++) {
1901:       PetscSectionGetDof(cSec,p,&dof);
1902:       if (dof) {
1903:         PetscScalar *vals;
1904:         VecGetValuesSection(cVec,cSec,p,&vals);
1905:         VecSetValuesSection(l,section,p,vals,INSERT_ALL_VALUES);
1906:       }
1907:     }
1908:     VecDestroy(&cVec);
1909:   }
1910:   return(0);
1911: }

1915: /*@
1916:     DMGlobalToLocalBegin - Begins updating local vectors from global vector

1918:     Neighbor-wise Collective on DM

1920:     Input Parameters:
1921: +   dm - the DM object
1922: .   g - the global vector
1923: .   mode - INSERT_VALUES or ADD_VALUES
1924: -   l - the local vector


1927:     Level: beginner

1929: .seealso DMCoarsen(), DMDestroy(), DMView(), DMCreateGlobalVector(), DMCreateInterpolation(), DMGlobalToLocalEnd(), DMLocalToGlobalBegin()

1931: @*/
1932: PetscErrorCode  DMGlobalToLocalBegin(DM dm,Vec g,InsertMode mode,Vec l)
1933: {
1934:   PetscSF                 sf;
1935:   PetscErrorCode          ierr;
1936:   DMGlobalToLocalHookLink link;

1940:   for (link=dm->gtolhook; link; link=link->next) {
1941:     if (link->beginhook) {
1942:       (*link->beginhook)(dm,g,mode,l,link->ctx);
1943:     }
1944:   }
1945:   DMGetDefaultSF(dm, &sf);
1946:   if (sf) {
1947:     const PetscScalar *gArray;
1948:     PetscScalar       *lArray;

1950:     if (mode == ADD_VALUES) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insertion mode %D", mode);
1951:     VecGetArray(l, &lArray);
1952:     VecGetArrayRead(g, &gArray);
1953:     PetscSFBcastBegin(sf, MPIU_SCALAR, gArray, lArray);
1954:     VecRestoreArray(l, &lArray);
1955:     VecRestoreArrayRead(g, &gArray);
1956:   } else {
1957:     (*dm->ops->globaltolocalbegin)(dm,g,mode == INSERT_ALL_VALUES ? INSERT_VALUES : (mode == ADD_ALL_VALUES ? ADD_VALUES : mode),l);
1958:   }
1959:   return(0);
1960: }

1964: /*@
1965:     DMGlobalToLocalEnd - Ends updating local vectors from global vector

1967:     Neighbor-wise Collective on DM

1969:     Input Parameters:
1970: +   dm - the DM object
1971: .   g - the global vector
1972: .   mode - INSERT_VALUES or ADD_VALUES
1973: -   l - the local vector


1976:     Level: beginner

1978: .seealso DMCoarsen(), DMDestroy(), DMView(), DMCreateGlobalVector(), DMCreateInterpolation(), DMGlobalToLocalEnd(), DMLocalToGlobalBegin()

1980: @*/
1981: PetscErrorCode  DMGlobalToLocalEnd(DM dm,Vec g,InsertMode mode,Vec l)
1982: {
1983:   PetscSF                 sf;
1984:   PetscErrorCode          ierr;
1985:   const PetscScalar      *gArray;
1986:   PetscScalar            *lArray;
1987:   DMGlobalToLocalHookLink link;

1991:   DMGetDefaultSF(dm, &sf);
1992:   if (sf) {
1993:     if (mode == ADD_VALUES) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insertion mode %D", mode);

1995:     VecGetArray(l, &lArray);
1996:     VecGetArrayRead(g, &gArray);
1997:     PetscSFBcastEnd(sf, MPIU_SCALAR, gArray, lArray);
1998:     VecRestoreArray(l, &lArray);
1999:     VecRestoreArrayRead(g, &gArray);
2000:   } else {
2001:     (*dm->ops->globaltolocalend)(dm,g,mode == INSERT_ALL_VALUES ? INSERT_VALUES : (mode == ADD_ALL_VALUES ? ADD_VALUES : mode),l);
2002:   }
2003:   DMGlobalToLocalHook_Constraints(dm,g,mode,l,NULL);
2004:   for (link=dm->gtolhook; link; link=link->next) {
2005:     if (link->endhook) {(*link->endhook)(dm,g,mode,l,link->ctx);}
2006:   }
2007:   return(0);
2008: }

2012: /*@C
2013:    DMLocalToGlobalHookAdd - adds a callback to be run when a local to global is called

2015:    Logically Collective

2017:    Input Arguments:
2018: +  dm - the DM
2019: .  beginhook - function to run at the beginning of DMLocalToGlobalBegin()
2020: .  endhook - function to run after DMLocalToGlobalEnd() has completed
2021: -  ctx - [optional] user-defined context for provide data for the hooks (may be NULL)

2023:    Calling sequence for beginhook:
2024: $    beginhook(DM fine,Vec l,InsertMode mode,Vec g,void *ctx)

2026: +  dm - global DM
2027: .  l - local vector
2028: .  mode - mode
2029: .  g - global vector
2030: -  ctx - optional user-defined function context


2033:    Calling sequence for endhook:
2034: $    endhook(DM fine,Vec l,InsertMode mode,Vec g,void *ctx)

2036: +  global - global DM
2037: .  l - local vector
2038: .  mode - mode
2039: .  g - global vector
2040: -  ctx - optional user-defined function context

2042:    Level: advanced

2044: .seealso: DMRefineHookAdd(), SNESFASGetInterpolation(), SNESFASGetInjection(), PetscObjectCompose(), PetscContainerCreate()
2045: @*/
2046: PetscErrorCode DMLocalToGlobalHookAdd(DM dm,PetscErrorCode (*beginhook)(DM,Vec,InsertMode,Vec,void*),PetscErrorCode (*endhook)(DM,Vec,InsertMode,Vec,void*),void *ctx)
2047: {
2048:   PetscErrorCode          ierr;
2049:   DMLocalToGlobalHookLink link,*p;

2053:   for (p=&dm->ltoghook; *p; p=&(*p)->next) {} /* Scan to the end of the current list of hooks */
2054:   PetscMalloc(sizeof(struct _DMLocalToGlobalHookLink),&link);
2055:   link->beginhook = beginhook;
2056:   link->endhook   = endhook;
2057:   link->ctx       = ctx;
2058:   link->next      = NULL;
2059:   *p              = link;
2060:   return(0);
2061: }

2065: static PetscErrorCode DMLocalToGlobalHook_Constraints(DM dm, Vec l, InsertMode mode, Vec g, void *ctx)
2066: {
2067:   Mat cMat;
2068:   Vec cVec;
2069:   PetscSection section, cSec;
2070:   PetscInt pStart, pEnd, p, dof;

2075:   DMGetDefaultConstraints(dm,&cSec,&cMat);
2076:   if (cMat && (mode == ADD_VALUES || mode == ADD_ALL_VALUES || mode == ADD_BC_VALUES)) {
2077:     PetscInt nRows;

2079:     MatGetSize(cMat,&nRows,NULL);
2080:     if (nRows <= 0) return(0);
2081:     DMGetDefaultSection(dm,&section);
2082:     MatCreateVecs(cMat,NULL,&cVec);
2083:     PetscSectionGetChart(cSec,&pStart,&pEnd);
2084:     for (p = pStart; p < pEnd; p++) {
2085:       PetscSectionGetDof(cSec,p,&dof);
2086:       if (dof) {
2087:         PetscInt d;
2088:         PetscScalar *vals;
2089:         VecGetValuesSection(l,section,p,&vals);
2090:         VecSetValuesSection(cVec,cSec,p,vals,mode);
2091:         /* for this to be the true transpose, we have to zero the values that
2092:          * we just extracted */
2093:         for (d = 0; d < dof; d++) {
2094:           vals[d] = 0.;
2095:         }
2096:       }
2097:     }
2098:     MatMultTransposeAdd(cMat,cVec,l,l);
2099:     VecDestroy(&cVec);
2100:   }
2101:   return(0);
2102: }

2106: /*@
2107:     DMLocalToGlobalBegin - updates global vectors from local vectors

2109:     Neighbor-wise Collective on DM

2111:     Input Parameters:
2112: +   dm - the DM object
2113: .   l - the local vector
2114: .   mode - if INSERT_VALUES then no parallel communication is used, if ADD_VALUES then all ghost points from the same base point accumulate into that base point.
2115: -   g - the global vector

2117:     Notes: In the ADD_VALUES case you normally would zero the receiving vector before beginning this operation.
2118:            INSERT_VALUES is not supported for DMDA, in that case simply compute the values directly into a global vector instead of a local one.

2120:     Level: beginner

2122: .seealso DMCoarsen(), DMDestroy(), DMView(), DMCreateGlobalVector(), DMCreateInterpolation(), DMGlobalToLocalEnd(), DMGlobalToLocalBegin()

2124: @*/
2125: PetscErrorCode  DMLocalToGlobalBegin(DM dm,Vec l,InsertMode mode,Vec g)
2126: {
2127:   PetscSF                 sf;
2128:   PetscSection            s, gs;
2129:   DMLocalToGlobalHookLink link;
2130:   const PetscScalar      *lArray;
2131:   PetscScalar            *gArray;
2132:   PetscBool               isInsert;
2133:   PetscErrorCode          ierr;

2137:   for (link=dm->ltoghook; link; link=link->next) {
2138:     if (link->beginhook) {
2139:       (*link->beginhook)(dm,l,mode,g,link->ctx);
2140:     }
2141:   }
2142:   DMLocalToGlobalHook_Constraints(dm,l,mode,g,NULL);
2143:   DMGetDefaultSF(dm, &sf);
2144:   DMGetDefaultSection(dm, &s);
2145:   switch (mode) {
2146:   case INSERT_VALUES:
2147:   case INSERT_ALL_VALUES:
2148:     isInsert = PETSC_TRUE; break;
2149:   case ADD_VALUES:
2150:   case ADD_ALL_VALUES:
2151:     isInsert = PETSC_FALSE; break;
2152:   default:
2153:     SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insertion mode %D", mode);
2154:   }
2155:   if (sf && !isInsert) {
2156:     VecGetArrayRead(l, &lArray);
2157:     VecGetArray(g, &gArray);
2158:     PetscSFReduceBegin(sf, MPIU_SCALAR, lArray, gArray, MPIU_SUM);
2159:     VecRestoreArrayRead(l, &lArray);
2160:     VecRestoreArray(g, &gArray);
2161:   } else if (s && isInsert) {
2162:     PetscInt gStart, pStart, pEnd, p;

2164:     DMGetDefaultGlobalSection(dm, &gs);
2165:     PetscSectionGetChart(s, &pStart, &pEnd);
2166:     VecGetOwnershipRange(g, &gStart, NULL);
2167:     VecGetArrayRead(l, &lArray);
2168:     VecGetArray(g, &gArray);
2169:     for (p = pStart; p < pEnd; ++p) {
2170:       PetscInt dof, gdof, cdof, gcdof, off, goff, d, e;

2172:       PetscSectionGetDof(s, p, &dof);
2173:       PetscSectionGetDof(gs, p, &gdof);
2174:       PetscSectionGetConstraintDof(s, p, &cdof);
2175:       PetscSectionGetConstraintDof(gs, p, &gcdof);
2176:       PetscSectionGetOffset(s, p, &off);
2177:       PetscSectionGetOffset(gs, p, &goff);
2178:       /* Ignore off-process data and points with no global data */
2179:       if (!gdof || goff < 0) continue;
2180:       if (dof != gdof) SETERRQ5(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Inconsistent sizes, p: %d dof: %d gdof: %d cdof: %d gcdof: %d", p, dof, gdof, cdof, gcdof);
2181:       /* If no constraints are enforced in the global vector */
2182:       if (!gcdof) {
2183:         for (d = 0; d < dof; ++d) gArray[goff-gStart+d] = lArray[off+d];
2184:       /* If constraints are enforced in the global vector */
2185:       } else if (cdof == gcdof) {
2186:         const PetscInt *cdofs;
2187:         PetscInt        cind = 0;

2189:         PetscSectionGetConstraintIndices(s, p, &cdofs);
2190:         for (d = 0, e = 0; d < dof; ++d) {
2191:           if ((cind < cdof) && (d == cdofs[cind])) {++cind; continue;}
2192:           gArray[goff-gStart+e++] = lArray[off+d];
2193:         }
2194:       } else SETERRQ5(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Inconsistent sizes, p: %d dof: %d gdof: %d cdof: %d gcdof: %d", p, dof, gdof, cdof, gcdof);
2195:     }
2196:     VecRestoreArrayRead(l, &lArray);
2197:     VecRestoreArray(g, &gArray);
2198:   } else {
2199:     (*dm->ops->localtoglobalbegin)(dm,l,mode == INSERT_ALL_VALUES ? INSERT_VALUES : (mode == ADD_ALL_VALUES ? ADD_VALUES : mode),g);
2200:   }
2201:   return(0);
2202: }

2206: /*@
2207:     DMLocalToGlobalEnd - updates global vectors from local vectors

2209:     Neighbor-wise Collective on DM

2211:     Input Parameters:
2212: +   dm - the DM object
2213: .   l - the local vector
2214: .   mode - INSERT_VALUES or ADD_VALUES
2215: -   g - the global vector


2218:     Level: beginner

2220: .seealso DMCoarsen(), DMDestroy(), DMView(), DMCreateGlobalVector(), DMCreateInterpolation(), DMGlobalToLocalEnd(), DMGlobalToLocalEnd()

2222: @*/
2223: PetscErrorCode  DMLocalToGlobalEnd(DM dm,Vec l,InsertMode mode,Vec g)
2224: {
2225:   PetscSF                 sf;
2226:   PetscSection            s;
2227:   DMLocalToGlobalHookLink link;
2228:   PetscBool               isInsert;
2229:   PetscErrorCode          ierr;

2233:   DMGetDefaultSF(dm, &sf);
2234:   DMGetDefaultSection(dm, &s);
2235:   switch (mode) {
2236:   case INSERT_VALUES:
2237:   case INSERT_ALL_VALUES:
2238:     isInsert = PETSC_TRUE; break;
2239:   case ADD_VALUES:
2240:   case ADD_ALL_VALUES:
2241:     isInsert = PETSC_FALSE; break;
2242:   default:
2243:     SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insertion mode %D", mode);
2244:   }
2245:   if (sf && !isInsert) {
2246:     const PetscScalar *lArray;
2247:     PetscScalar       *gArray;

2249:     VecGetArrayRead(l, &lArray);
2250:     VecGetArray(g, &gArray);
2251:     PetscSFReduceEnd(sf, MPIU_SCALAR, lArray, gArray, MPIU_SUM);
2252:     VecRestoreArrayRead(l, &lArray);
2253:     VecRestoreArray(g, &gArray);
2254:   } else if (s && isInsert) {
2255:   } else {
2256:     (*dm->ops->localtoglobalend)(dm,l,mode == INSERT_ALL_VALUES ? INSERT_VALUES : (mode == ADD_ALL_VALUES ? ADD_VALUES : mode),g);
2257:   }
2258:   for (link=dm->ltoghook; link; link=link->next) {
2259:     if (link->endhook) {(*link->endhook)(dm,g,mode,l,link->ctx);}
2260:   }
2261:   return(0);
2262: }

2266: /*@
2267:    DMLocalToLocalBegin - Maps from a local vector (including ghost points
2268:    that contain irrelevant values) to another local vector where the ghost
2269:    points in the second are set correctly. Must be followed by DMLocalToLocalEnd().

2271:    Neighbor-wise Collective on DM and Vec

2273:    Input Parameters:
2274: +  dm - the DM object
2275: .  g - the original local vector
2276: -  mode - one of INSERT_VALUES or ADD_VALUES

2278:    Output Parameter:
2279: .  l  - the local vector with correct ghost values

2281:    Level: intermediate

2283:    Notes:
2284:    The local vectors used here need not be the same as those
2285:    obtained from DMCreateLocalVector(), BUT they
2286:    must have the same parallel data layout; they could, for example, be
2287:    obtained with VecDuplicate() from the DM originating vectors.

2289: .keywords: DM, local-to-local, begin
2290: .seealso DMCoarsen(), DMDestroy(), DMView(), DMCreateLocalVector(), DMCreateGlobalVector(), DMCreateInterpolation(), DMLocalToLocalEnd(), DMGlobalToLocalEnd(), DMLocalToGlobalBegin()

2292: @*/
2293: PetscErrorCode  DMLocalToLocalBegin(DM dm,Vec g,InsertMode mode,Vec l)
2294: {
2295:   PetscErrorCode          ierr;

2299:   (*dm->ops->localtolocalbegin)(dm,g,mode == INSERT_ALL_VALUES ? INSERT_VALUES : (mode == ADD_ALL_VALUES ? ADD_VALUES : mode),l);
2300:   return(0);
2301: }

2305: /*@
2306:    DMLocalToLocalEnd - Maps from a local vector (including ghost points
2307:    that contain irrelevant values) to another local vector where the ghost
2308:    points in the second are set correctly. Must be preceded by DMLocalToLocalBegin().

2310:    Neighbor-wise Collective on DM and Vec

2312:    Input Parameters:
2313: +  da - the DM object
2314: .  g - the original local vector
2315: -  mode - one of INSERT_VALUES or ADD_VALUES

2317:    Output Parameter:
2318: .  l  - the local vector with correct ghost values

2320:    Level: intermediate

2322:    Notes:
2323:    The local vectors used here need not be the same as those
2324:    obtained from DMCreateLocalVector(), BUT they
2325:    must have the same parallel data layout; they could, for example, be
2326:    obtained with VecDuplicate() from the DM originating vectors.

2328: .keywords: DM, local-to-local, end
2329: .seealso DMCoarsen(), DMDestroy(), DMView(), DMCreateLocalVector(), DMCreateGlobalVector(), DMCreateInterpolation(), DMLocalToLocalBegin(), DMGlobalToLocalEnd(), DMLocalToGlobalBegin()

2331: @*/
2332: PetscErrorCode  DMLocalToLocalEnd(DM dm,Vec g,InsertMode mode,Vec l)
2333: {
2334:   PetscErrorCode          ierr;

2338:   (*dm->ops->localtolocalend)(dm,g,mode == INSERT_ALL_VALUES ? INSERT_VALUES : (mode == ADD_ALL_VALUES ? ADD_VALUES : mode),l);
2339:   return(0);
2340: }


2345: /*@
2346:     DMCoarsen - Coarsens a DM object

2348:     Collective on DM

2350:     Input Parameter:
2351: +   dm - the DM object
2352: -   comm - the communicator to contain the new DM object (or MPI_COMM_NULL)

2354:     Output Parameter:
2355: .   dmc - the coarsened DM

2357:     Level: developer

2359: .seealso DMRefine(), DMDestroy(), DMView(), DMCreateGlobalVector(), DMCreateInterpolation()

2361: @*/
2362: PetscErrorCode DMCoarsen(DM dm, MPI_Comm comm, DM *dmc)
2363: {
2364:   PetscErrorCode    ierr;
2365:   DMCoarsenHookLink link;

2369:   if (!dm->ops->coarsen) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"This DM cannot coarsen");
2370:   PetscLogEventBegin(DM_Coarsen,dm,0,0,0);
2371:   (*dm->ops->coarsen)(dm, comm, dmc);
2372:   if (!(*dmc)) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "NULL coarse mesh produced");
2373:   DMSetCoarseDM(dm,*dmc);
2374:   (*dmc)->ops->creatematrix = dm->ops->creatematrix;
2375:   PetscObjectCopyFortranFunctionPointers((PetscObject)dm,(PetscObject)*dmc);
2376:   (*dmc)->ctx               = dm->ctx;
2377:   (*dmc)->levelup           = dm->levelup;
2378:   (*dmc)->leveldown         = dm->leveldown + 1;
2379:   DMSetMatType(*dmc,dm->mattype);
2380:   for (link=dm->coarsenhook; link; link=link->next) {
2381:     if (link->coarsenhook) {(*link->coarsenhook)(dm,*dmc,link->ctx);}
2382:   }
2383:   PetscLogEventEnd(DM_Coarsen,dm,0,0,0);
2384:   return(0);
2385: }

2389: /*@C
2390:    DMCoarsenHookAdd - adds a callback to be run when restricting a nonlinear problem to the coarse grid

2392:    Logically Collective

2394:    Input Arguments:
2395: +  fine - nonlinear solver context on which to run a hook when restricting to a coarser level
2396: .  coarsenhook - function to run when setting up a coarser level
2397: .  restricthook - function to run to update data on coarser levels (once per SNESSolve())
2398: -  ctx - [optional] user-defined context for provide data for the hooks (may be NULL)

2400:    Calling sequence of coarsenhook:
2401: $    coarsenhook(DM fine,DM coarse,void *ctx);

2403: +  fine - fine level DM
2404: .  coarse - coarse level DM to restrict problem to
2405: -  ctx - optional user-defined function context

2407:    Calling sequence for restricthook:
2408: $    restricthook(DM fine,Mat mrestrict,Vec rscale,Mat inject,DM coarse,void *ctx)

2410: +  fine - fine level DM
2411: .  mrestrict - matrix restricting a fine-level solution to the coarse grid
2412: .  rscale - scaling vector for restriction
2413: .  inject - matrix restricting by injection
2414: .  coarse - coarse level DM to update
2415: -  ctx - optional user-defined function context

2417:    Level: advanced

2419:    Notes:
2420:    This function is only needed if auxiliary data needs to be set up on coarse grids.

2422:    If this function is called multiple times, the hooks will be run in the order they are added.

2424:    In order to compose with nonlinear preconditioning without duplicating storage, the hook should be implemented to
2425:    extract the finest level information from its context (instead of from the SNES).

2427:    This function is currently not available from Fortran.

2429: .seealso: DMRefineHookAdd(), SNESFASGetInterpolation(), SNESFASGetInjection(), PetscObjectCompose(), PetscContainerCreate()
2430: @*/
2431: PetscErrorCode DMCoarsenHookAdd(DM fine,PetscErrorCode (*coarsenhook)(DM,DM,void*),PetscErrorCode (*restricthook)(DM,Mat,Vec,Mat,DM,void*),void *ctx)
2432: {
2433:   PetscErrorCode    ierr;
2434:   DMCoarsenHookLink link,*p;

2438:   for (p=&fine->coarsenhook; *p; p=&(*p)->next) {} /* Scan to the end of the current list of hooks */
2439:   PetscMalloc(sizeof(struct _DMCoarsenHookLink),&link);
2440:   link->coarsenhook  = coarsenhook;
2441:   link->restricthook = restricthook;
2442:   link->ctx          = ctx;
2443:   link->next         = NULL;
2444:   *p                 = link;
2445:   return(0);
2446: }

2450: /*@
2451:    DMRestrict - restricts user-defined problem data to a coarser DM by running hooks registered by DMCoarsenHookAdd()

2453:    Collective if any hooks are

2455:    Input Arguments:
2456: +  fine - finer DM to use as a base
2457: .  restrct - restriction matrix, apply using MatRestrict()
2458: .  inject - injection matrix, also use MatRestrict()
2459: -  coarse - coarer DM to update

2461:    Level: developer

2463: .seealso: DMCoarsenHookAdd(), MatRestrict()
2464: @*/
2465: PetscErrorCode DMRestrict(DM fine,Mat restrct,Vec rscale,Mat inject,DM coarse)
2466: {
2467:   PetscErrorCode    ierr;
2468:   DMCoarsenHookLink link;

2471:   for (link=fine->coarsenhook; link; link=link->next) {
2472:     if (link->restricthook) {
2473:       (*link->restricthook)(fine,restrct,rscale,inject,coarse,link->ctx);
2474:     }
2475:   }
2476:   return(0);
2477: }

2481: /*@C
2482:    DMSubDomainHookAdd - adds a callback to be run when restricting a problem to the coarse grid

2484:    Logically Collective

2486:    Input Arguments:
2487: +  global - global DM
2488: .  ddhook - function to run to pass data to the decomposition DM upon its creation
2489: .  restricthook - function to run to update data on block solve (at the beginning of the block solve)
2490: -  ctx - [optional] user-defined context for provide data for the hooks (may be NULL)


2493:    Calling sequence for ddhook:
2494: $    ddhook(DM global,DM block,void *ctx)

2496: +  global - global DM
2497: .  block  - block DM
2498: -  ctx - optional user-defined function context

2500:    Calling sequence for restricthook:
2501: $    restricthook(DM global,VecScatter out,VecScatter in,DM block,void *ctx)

2503: +  global - global DM
2504: .  out    - scatter to the outer (with ghost and overlap points) block vector
2505: .  in     - scatter to block vector values only owned locally
2506: .  block  - block DM
2507: -  ctx - optional user-defined function context

2509:    Level: advanced

2511:    Notes:
2512:    This function is only needed if auxiliary data needs to be set up on subdomain DMs.

2514:    If this function is called multiple times, the hooks will be run in the order they are added.

2516:    In order to compose with nonlinear preconditioning without duplicating storage, the hook should be implemented to
2517:    extract the global information from its context (instead of from the SNES).

2519:    This function is currently not available from Fortran.

2521: .seealso: DMRefineHookAdd(), SNESFASGetInterpolation(), SNESFASGetInjection(), PetscObjectCompose(), PetscContainerCreate()
2522: @*/
2523: PetscErrorCode DMSubDomainHookAdd(DM global,PetscErrorCode (*ddhook)(DM,DM,void*),PetscErrorCode (*restricthook)(DM,VecScatter,VecScatter,DM,void*),void *ctx)
2524: {
2525:   PetscErrorCode      ierr;
2526:   DMSubDomainHookLink link,*p;

2530:   for (p=&global->subdomainhook; *p; p=&(*p)->next) {} /* Scan to the end of the current list of hooks */
2531:   PetscMalloc(sizeof(struct _DMSubDomainHookLink),&link);
2532:   link->restricthook = restricthook;
2533:   link->ddhook       = ddhook;
2534:   link->ctx          = ctx;
2535:   link->next         = NULL;
2536:   *p                 = link;
2537:   return(0);
2538: }

2542: /*@
2543:    DMSubDomainRestrict - restricts user-defined problem data to a block DM by running hooks registered by DMSubDomainHookAdd()

2545:    Collective if any hooks are

2547:    Input Arguments:
2548: +  fine - finer DM to use as a base
2549: .  oscatter - scatter from domain global vector filling subdomain global vector with overlap
2550: .  gscatter - scatter from domain global vector filling subdomain local vector with ghosts
2551: -  coarse - coarer DM to update

2553:    Level: developer

2555: .seealso: DMCoarsenHookAdd(), MatRestrict()
2556: @*/
2557: PetscErrorCode DMSubDomainRestrict(DM global,VecScatter oscatter,VecScatter gscatter,DM subdm)
2558: {
2559:   PetscErrorCode      ierr;
2560:   DMSubDomainHookLink link;

2563:   for (link=global->subdomainhook; link; link=link->next) {
2564:     if (link->restricthook) {
2565:       (*link->restricthook)(global,oscatter,gscatter,subdm,link->ctx);
2566:     }
2567:   }
2568:   return(0);
2569: }

2573: /*@
2574:     DMGetCoarsenLevel - Get's the number of coarsenings that have generated this DM.

2576:     Not Collective

2578:     Input Parameter:
2579: .   dm - the DM object

2581:     Output Parameter:
2582: .   level - number of coarsenings

2584:     Level: developer

2586: .seealso DMCoarsen(), DMGetRefineLevel(), DMDestroy(), DMView(), DMCreateGlobalVector(), DMCreateInterpolation()

2588: @*/
2589: PetscErrorCode  DMGetCoarsenLevel(DM dm,PetscInt *level)
2590: {
2593:   *level = dm->leveldown;
2594:   return(0);
2595: }



2601: /*@C
2602:     DMRefineHierarchy - Refines a DM object, all levels at once

2604:     Collective on DM

2606:     Input Parameter:
2607: +   dm - the DM object
2608: -   nlevels - the number of levels of refinement

2610:     Output Parameter:
2611: .   dmf - the refined DM hierarchy

2613:     Level: developer

2615: .seealso DMCoarsenHierarchy(), DMDestroy(), DMView(), DMCreateGlobalVector(), DMCreateInterpolation()

2617: @*/
2618: PetscErrorCode  DMRefineHierarchy(DM dm,PetscInt nlevels,DM dmf[])
2619: {

2624:   if (nlevels < 0) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_ARG_OUTOFRANGE,"nlevels cannot be negative");
2625:   if (nlevels == 0) return(0);
2626:   if (dm->ops->refinehierarchy) {
2627:     (*dm->ops->refinehierarchy)(dm,nlevels,dmf);
2628:   } else if (dm->ops->refine) {
2629:     PetscInt i;

2631:     DMRefine(dm,PetscObjectComm((PetscObject)dm),&dmf[0]);
2632:     for (i=1; i<nlevels; i++) {
2633:       DMRefine(dmf[i-1],PetscObjectComm((PetscObject)dm),&dmf[i]);
2634:     }
2635:   } else SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"No RefineHierarchy for this DM yet");
2636:   return(0);
2637: }

2641: /*@C
2642:     DMCoarsenHierarchy - Coarsens a DM object, all levels at once

2644:     Collective on DM

2646:     Input Parameter:
2647: +   dm - the DM object
2648: -   nlevels - the number of levels of coarsening

2650:     Output Parameter:
2651: .   dmc - the coarsened DM hierarchy

2653:     Level: developer

2655: .seealso DMRefineHierarchy(), DMDestroy(), DMView(), DMCreateGlobalVector(), DMCreateInterpolation()

2657: @*/
2658: PetscErrorCode  DMCoarsenHierarchy(DM dm, PetscInt nlevels, DM dmc[])
2659: {

2664:   if (nlevels < 0) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_ARG_OUTOFRANGE,"nlevels cannot be negative");
2665:   if (nlevels == 0) return(0);
2667:   if (dm->ops->coarsenhierarchy) {
2668:     (*dm->ops->coarsenhierarchy)(dm, nlevels, dmc);
2669:   } else if (dm->ops->coarsen) {
2670:     PetscInt i;

2672:     DMCoarsen(dm,PetscObjectComm((PetscObject)dm),&dmc[0]);
2673:     for (i=1; i<nlevels; i++) {
2674:       DMCoarsen(dmc[i-1],PetscObjectComm((PetscObject)dm),&dmc[i]);
2675:     }
2676:   } else SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"No CoarsenHierarchy for this DM yet");
2677:   return(0);
2678: }

2682: /*@
2683:    DMCreateAggregates - Gets the aggregates that map between
2684:    grids associated with two DMs.

2686:    Collective on DM

2688:    Input Parameters:
2689: +  dmc - the coarse grid DM
2690: -  dmf - the fine grid DM

2692:    Output Parameters:
2693: .  rest - the restriction matrix (transpose of the projection matrix)

2695:    Level: intermediate

2697: .keywords: interpolation, restriction, multigrid

2699: .seealso: DMRefine(), DMCreateInjection(), DMCreateInterpolation()
2700: @*/
2701: PetscErrorCode  DMCreateAggregates(DM dmc, DM dmf, Mat *rest)
2702: {

2708:   (*dmc->ops->getaggregates)(dmc, dmf, rest);
2709:   return(0);
2710: }

2714: /*@C
2715:     DMSetApplicationContextDestroy - Sets a user function that will be called to destroy the application context when the DM is destroyed

2717:     Not Collective

2719:     Input Parameters:
2720: +   dm - the DM object
2721: -   destroy - the destroy function

2723:     Level: intermediate

2725: .seealso DMView(), DMCreateGlobalVector(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix(), DMGetApplicationContext()

2727: @*/
2728: PetscErrorCode  DMSetApplicationContextDestroy(DM dm,PetscErrorCode (*destroy)(void**))
2729: {
2732:   dm->ctxdestroy = destroy;
2733:   return(0);
2734: }

2738: /*@
2739:     DMSetApplicationContext - Set a user context into a DM object

2741:     Not Collective

2743:     Input Parameters:
2744: +   dm - the DM object
2745: -   ctx - the user context

2747:     Level: intermediate

2749: .seealso DMView(), DMCreateGlobalVector(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix(), DMGetApplicationContext()

2751: @*/
2752: PetscErrorCode  DMSetApplicationContext(DM dm,void *ctx)
2753: {
2756:   dm->ctx = ctx;
2757:   return(0);
2758: }

2762: /*@
2763:     DMGetApplicationContext - Gets a user context from a DM object

2765:     Not Collective

2767:     Input Parameter:
2768: .   dm - the DM object

2770:     Output Parameter:
2771: .   ctx - the user context

2773:     Level: intermediate

2775: .seealso DMView(), DMCreateGlobalVector(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix(), DMGetApplicationContext()

2777: @*/
2778: PetscErrorCode  DMGetApplicationContext(DM dm,void *ctx)
2779: {
2782:   *(void**)ctx = dm->ctx;
2783:   return(0);
2784: }

2788: /*@C
2789:     DMSetVariableBounds - sets a function to compute the lower and upper bound vectors for SNESVI.

2791:     Logically Collective on DM

2793:     Input Parameter:
2794: +   dm - the DM object
2795: -   f - the function that computes variable bounds used by SNESVI (use NULL to cancel a previous function that was set)

2797:     Level: intermediate

2799: .seealso DMView(), DMCreateGlobalVector(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix(), DMGetApplicationContext(),
2800:          DMSetJacobian()

2802: @*/
2803: PetscErrorCode  DMSetVariableBounds(DM dm,PetscErrorCode (*f)(DM,Vec,Vec))
2804: {
2806:   dm->ops->computevariablebounds = f;
2807:   return(0);
2808: }

2812: /*@
2813:     DMHasVariableBounds - does the DM object have a variable bounds function?

2815:     Not Collective

2817:     Input Parameter:
2818: .   dm - the DM object to destroy

2820:     Output Parameter:
2821: .   flg - PETSC_TRUE if the variable bounds function exists

2823:     Level: developer

2825: .seealso DMView(), DMCreateGlobalVector(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix(), DMGetApplicationContext()

2827: @*/
2828: PetscErrorCode  DMHasVariableBounds(DM dm,PetscBool  *flg)
2829: {
2831:   *flg =  (dm->ops->computevariablebounds) ? PETSC_TRUE : PETSC_FALSE;
2832:   return(0);
2833: }

2837: /*@C
2838:     DMComputeVariableBounds - compute variable bounds used by SNESVI.

2840:     Logically Collective on DM

2842:     Input Parameters:
2843: .   dm - the DM object

2845:     Output parameters:
2846: +   xl - lower bound
2847: -   xu - upper bound

2849:     Level: advanced

2851:     Notes: This is generally not called by users. It calls the function provided by the user with DMSetVariableBounds()

2853: .seealso DMView(), DMCreateGlobalVector(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix(), DMGetApplicationContext()

2855: @*/
2856: PetscErrorCode  DMComputeVariableBounds(DM dm, Vec xl, Vec xu)
2857: {

2863:   if (dm->ops->computevariablebounds) {
2864:     (*dm->ops->computevariablebounds)(dm, xl,xu);
2865:   } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "This DM is incapable of computing variable bounds.");
2866:   return(0);
2867: }

2871: /*@
2872:     DMHasColoring - does the DM object have a method of providing a coloring?

2874:     Not Collective

2876:     Input Parameter:
2877: .   dm - the DM object

2879:     Output Parameter:
2880: .   flg - PETSC_TRUE if the DM has facilities for DMCreateColoring().

2882:     Level: developer

2884: .seealso DMHasFunction(), DMCreateColoring()

2886: @*/
2887: PetscErrorCode  DMHasColoring(DM dm,PetscBool  *flg)
2888: {
2890:   *flg =  (dm->ops->getcoloring) ? PETSC_TRUE : PETSC_FALSE;
2891:   return(0);
2892: }

2896: /*@
2897:     DMHasCreateRestriction - does the DM object have a method of providing a restriction?

2899:     Not Collective

2901:     Input Parameter:
2902: .   dm - the DM object

2904:     Output Parameter:
2905: .   flg - PETSC_TRUE if the DM has facilities for DMCreateRestriction().

2907:     Level: developer

2909: .seealso DMHasFunction(), DMCreateRestriction()

2911: @*/
2912: PetscErrorCode  DMHasCreateRestriction(DM dm,PetscBool  *flg)
2913: {
2915:   *flg =  (dm->ops->createrestriction) ? PETSC_TRUE : PETSC_FALSE;
2916:   return(0);
2917: }

2919: #undef  __FUNCT__
2921: /*@C
2922:     DMSetVec - set the vector at which to compute residual, Jacobian and VI bounds, if the problem is nonlinear.

2924:     Collective on DM

2926:     Input Parameter:
2927: +   dm - the DM object
2928: -   x - location to compute residual and Jacobian, if NULL is passed to those routines; will be NULL for linear problems.

2930:     Level: developer

2932: .seealso DMView(), DMCreateGlobalVector(), DMCreateInterpolation(), DMCreateColoring(), DMCreateMatrix(), DMGetApplicationContext()

2934: @*/
2935: PetscErrorCode  DMSetVec(DM dm,Vec x)
2936: {

2940:   if (x) {
2941:     if (!dm->x) {
2942:       DMCreateGlobalVector(dm,&dm->x);
2943:     }
2944:     VecCopy(x,dm->x);
2945:   } else if (dm->x) {
2946:     VecDestroy(&dm->x);
2947:   }
2948:   return(0);
2949: }

2951: PetscFunctionList DMList              = NULL;
2952: PetscBool         DMRegisterAllCalled = PETSC_FALSE;

2956: /*@C
2957:   DMSetType - Builds a DM, for a particular DM implementation.

2959:   Collective on DM

2961:   Input Parameters:
2962: + dm     - The DM object
2963: - method - The name of the DM type

2965:   Options Database Key:
2966: . -dm_type <type> - Sets the DM type; use -help for a list of available types

2968:   Notes:
2969:   See "petsc/include/petscdm.h" for available DM types (for instance, DM1D, DM2D, or DM3D).

2971:   Level: intermediate

2973: .keywords: DM, set, type
2974: .seealso: DMGetType(), DMCreate()
2975: @*/
2976: PetscErrorCode  DMSetType(DM dm, DMType method)
2977: {
2978:   PetscErrorCode (*r)(DM);
2979:   PetscBool      match;

2984:   PetscObjectTypeCompare((PetscObject) dm, method, &match);
2985:   if (match) return(0);

2987:   DMRegisterAll();
2988:   PetscFunctionListFind(DMList,method,&r);
2989:   if (!r) SETERRQ1(PetscObjectComm((PetscObject)dm),PETSC_ERR_ARG_UNKNOWN_TYPE, "Unknown DM type: %s", method);

2991:   if (dm->ops->destroy) {
2992:     (*dm->ops->destroy)(dm);
2993:     dm->ops->destroy = NULL;
2994:   }
2995:   (*r)(dm);
2996:   PetscObjectChangeTypeName((PetscObject)dm,method);
2997:   return(0);
2998: }

3002: /*@C
3003:   DMGetType - Gets the DM type name (as a string) from the DM.

3005:   Not Collective

3007:   Input Parameter:
3008: . dm  - The DM

3010:   Output Parameter:
3011: . type - The DM type name

3013:   Level: intermediate

3015: .keywords: DM, get, type, name
3016: .seealso: DMSetType(), DMCreate()
3017: @*/
3018: PetscErrorCode  DMGetType(DM dm, DMType *type)
3019: {

3025:   DMRegisterAll();
3026:   *type = ((PetscObject)dm)->type_name;
3027:   return(0);
3028: }

3032: /*@C
3033:   DMConvert - Converts a DM to another DM, either of the same or different type.

3035:   Collective on DM

3037:   Input Parameters:
3038: + dm - the DM
3039: - newtype - new DM type (use "same" for the same type)

3041:   Output Parameter:
3042: . M - pointer to new DM

3044:   Notes:
3045:   Cannot be used to convert a sequential DM to parallel or parallel to sequential,
3046:   the MPI communicator of the generated DM is always the same as the communicator
3047:   of the input DM.

3049:   Level: intermediate

3051: .seealso: DMCreate()
3052: @*/
3053: PetscErrorCode DMConvert(DM dm, DMType newtype, DM *M)
3054: {
3055:   DM             B;
3056:   char           convname[256];
3057:   PetscBool      sametype/*, issame */;

3064:   PetscObjectTypeCompare((PetscObject) dm, newtype, &sametype);
3065:   /* PetscStrcmp(newtype, "same", &issame); */
3066:   if (sametype) {
3067:     *M   = dm;
3068:     PetscObjectReference((PetscObject) dm);
3069:     return(0);
3070:   } else {
3071:     PetscErrorCode (*conv)(DM, DMType, DM*) = NULL;

3073:     /*
3074:        Order of precedence:
3075:        1) See if a specialized converter is known to the current DM.
3076:        2) See if a specialized converter is known to the desired DM class.
3077:        3) See if a good general converter is registered for the desired class
3078:        4) See if a good general converter is known for the current matrix.
3079:        5) Use a really basic converter.
3080:     */

3082:     /* 1) See if a specialized converter is known to the current DM and the desired class */
3083:     PetscStrcpy(convname,"DMConvert_");
3084:     PetscStrcat(convname,((PetscObject) dm)->type_name);
3085:     PetscStrcat(convname,"_");
3086:     PetscStrcat(convname,newtype);
3087:     PetscStrcat(convname,"_C");
3088:     PetscObjectQueryFunction((PetscObject)dm,convname,&conv);
3089:     if (conv) goto foundconv;

3091:     /* 2)  See if a specialized converter is known to the desired DM class. */
3092:     DMCreate(PetscObjectComm((PetscObject)dm), &B);
3093:     DMSetType(B, newtype);
3094:     PetscStrcpy(convname,"DMConvert_");
3095:     PetscStrcat(convname,((PetscObject) dm)->type_name);
3096:     PetscStrcat(convname,"_");
3097:     PetscStrcat(convname,newtype);
3098:     PetscStrcat(convname,"_C");
3099:     PetscObjectQueryFunction((PetscObject)B,convname,&conv);
3100:     if (conv) {
3101:       DMDestroy(&B);
3102:       goto foundconv;
3103:     }

3105: #if 0
3106:     /* 3) See if a good general converter is registered for the desired class */
3107:     conv = B->ops->convertfrom;
3108:     DMDestroy(&B);
3109:     if (conv) goto foundconv;

3111:     /* 4) See if a good general converter is known for the current matrix */
3112:     if (dm->ops->convert) {
3113:       conv = dm->ops->convert;
3114:     }
3115:     if (conv) goto foundconv;
3116: #endif

3118:     /* 5) Use a really basic converter. */
3119:     SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "No conversion possible between DM types %s and %s", ((PetscObject) dm)->type_name, newtype);

3121: foundconv:
3122:     PetscLogEventBegin(DM_Convert,dm,0,0,0);
3123:     (*conv)(dm,newtype,M);
3124:     /* Things that are independent of DM type: We should consult DMClone() here */
3125:     if (dm->maxCell) {
3126:       const PetscReal *maxCell, *L;
3127:       const DMBoundaryType *bd;
3128:       DMGetPeriodicity(dm, &maxCell, &L, &bd);
3129:       DMSetPeriodicity(*M,  maxCell,  L,  bd);
3130:     }
3131:     PetscLogEventEnd(DM_Convert,dm,0,0,0);
3132:   }
3133:   PetscObjectStateIncrease((PetscObject) *M);
3134:   return(0);
3135: }

3137: /*--------------------------------------------------------------------------------------------------------------------*/

3141: /*@C
3142:   DMRegister -  Adds a new DM component implementation

3144:   Not Collective

3146:   Input Parameters:
3147: + name        - The name of a new user-defined creation routine
3148: - create_func - The creation routine itself

3150:   Notes:
3151:   DMRegister() may be called multiple times to add several user-defined DMs


3154:   Sample usage:
3155: .vb
3156:     DMRegister("my_da", MyDMCreate);
3157: .ve

3159:   Then, your DM type can be chosen with the procedural interface via
3160: .vb
3161:     DMCreate(MPI_Comm, DM *);
3162:     DMSetType(DM,"my_da");
3163: .ve
3164:    or at runtime via the option
3165: .vb
3166:     -da_type my_da
3167: .ve

3169:   Level: advanced

3171: .keywords: DM, register
3172: .seealso: DMRegisterAll(), DMRegisterDestroy()

3174: @*/
3175: PetscErrorCode  DMRegister(const char sname[],PetscErrorCode (*function)(DM))
3176: {

3180:   PetscFunctionListAdd(&DMList,sname,function);
3181:   return(0);
3182: }

3186: /*@C
3187:   DMLoad - Loads a DM that has been stored in binary  with DMView().

3189:   Collective on PetscViewer

3191:   Input Parameters:
3192: + newdm - the newly loaded DM, this needs to have been created with DMCreate() or
3193:            some related function before a call to DMLoad().
3194: - viewer - binary file viewer, obtained from PetscViewerBinaryOpen() or
3195:            HDF5 file viewer, obtained from PetscViewerHDF5Open()

3197:    Level: intermediate

3199:   Notes:
3200:    The type is determined by the data in the file, any type set into the DM before this call is ignored.

3202:   Notes for advanced users:
3203:   Most users should not need to know the details of the binary storage
3204:   format, since DMLoad() and DMView() completely hide these details.
3205:   But for anyone who's interested, the standard binary matrix storage
3206:   format is
3207: .vb
3208:      has not yet been determined
3209: .ve

3211: .seealso: PetscViewerBinaryOpen(), DMView(), MatLoad(), VecLoad()
3212: @*/
3213: PetscErrorCode  DMLoad(DM newdm, PetscViewer viewer)
3214: {
3215:   PetscBool      isbinary, ishdf5;

3221:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
3222:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);
3223:   if (isbinary) {
3224:     PetscInt classid;
3225:     char     type[256];

3227:     PetscViewerBinaryRead(viewer,&classid,1,NULL,PETSC_INT);
3228:     if (classid != DM_FILE_CLASSID) SETERRQ1(PetscObjectComm((PetscObject)newdm),PETSC_ERR_ARG_WRONG,"Not DM next in file, classid found %d",(int)classid);
3229:     PetscViewerBinaryRead(viewer,type,256,NULL,PETSC_CHAR);
3230:     DMSetType(newdm, type);
3231:     if (newdm->ops->load) {(*newdm->ops->load)(newdm,viewer);}
3232:   } else if (ishdf5) {
3233:     if (newdm->ops->load) {(*newdm->ops->load)(newdm,viewer);}
3234:   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid viewer; open viewer with PetscViewerBinaryOpen() or PetscViewerHDF5Open()");
3235:   return(0);
3236: }

3238: /******************************** FEM Support **********************************/

3242: PetscErrorCode DMPrintCellVector(PetscInt c, const char name[], PetscInt len, const PetscScalar x[])
3243: {
3244:   PetscInt       f;

3248:   PetscPrintf(PETSC_COMM_SELF, "Cell %D Element %s\n", c, name);
3249:   for (f = 0; f < len; ++f) {
3250:     PetscPrintf(PETSC_COMM_SELF, "  | %g |\n", (double)PetscRealPart(x[f]));
3251:   }
3252:   return(0);
3253: }

3257: PetscErrorCode DMPrintCellMatrix(PetscInt c, const char name[], PetscInt rows, PetscInt cols, const PetscScalar A[])
3258: {
3259:   PetscInt       f, g;

3263:   PetscPrintf(PETSC_COMM_SELF, "Cell %D Element %s\n", c, name);
3264:   for (f = 0; f < rows; ++f) {
3265:     PetscPrintf(PETSC_COMM_SELF, "  |");
3266:     for (g = 0; g < cols; ++g) {
3267:       PetscPrintf(PETSC_COMM_SELF, " % 9.5g", PetscRealPart(A[f*cols+g]));
3268:     }
3269:     PetscPrintf(PETSC_COMM_SELF, " |\n");
3270:   }
3271:   return(0);
3272: }

3276: PetscErrorCode DMPrintLocalVec(DM dm, const char name[], PetscReal tol, Vec X)
3277: {
3278:   PetscMPIInt    rank, numProcs;
3279:   PetscInt       p;

3283:   MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
3284:   MPI_Comm_size(PetscObjectComm((PetscObject) dm), &numProcs);
3285:   PetscPrintf(PetscObjectComm((PetscObject) dm), "%s:\n", name);
3286:   for (p = 0; p < numProcs; ++p) {
3287:     if (p == rank) {
3288:       Vec x;

3290:       VecDuplicate(X, &x);
3291:       VecCopy(X, x);
3292:       VecChop(x, tol);
3293:       VecView(x, PETSC_VIEWER_STDOUT_SELF);
3294:       VecDestroy(&x);
3295:       PetscViewerFlush(PETSC_VIEWER_STDOUT_SELF);
3296:     }
3297:     PetscBarrier((PetscObject) dm);
3298:   }
3299:   return(0);
3300: }

3304: /*@
3305:   DMGetDefaultSection - Get the PetscSection encoding the local data layout for the DM.

3307:   Input Parameter:
3308: . dm - The DM

3310:   Output Parameter:
3311: . section - The PetscSection

3313:   Level: intermediate

3315:   Note: This gets a borrowed reference, so the user should not destroy this PetscSection.

3317: .seealso: DMSetDefaultSection(), DMGetDefaultGlobalSection()
3318: @*/
3319: PetscErrorCode DMGetDefaultSection(DM dm, PetscSection *section)
3320: {

3326:   if (!dm->defaultSection && dm->ops->createdefaultsection) {
3327:     (*dm->ops->createdefaultsection)(dm);
3328:     if (dm->defaultSection) {PetscObjectViewFromOptions((PetscObject) dm->defaultSection, NULL, "-dm_petscsection_view");}
3329:   }
3330:   *section = dm->defaultSection;
3331:   return(0);
3332: }

3336: /*@
3337:   DMSetDefaultSection - Set the PetscSection encoding the local data layout for the DM.

3339:   Input Parameters:
3340: + dm - The DM
3341: - section - The PetscSection

3343:   Level: intermediate

3345:   Note: Any existing Section will be destroyed

3347: .seealso: DMSetDefaultSection(), DMGetDefaultGlobalSection()
3348: @*/
3349: PetscErrorCode DMSetDefaultSection(DM dm, PetscSection section)
3350: {
3351:   PetscInt       numFields = 0;
3352:   PetscInt       f;

3357:   if (section) {
3359:     PetscObjectReference((PetscObject)section);
3360:   }
3361:   PetscSectionDestroy(&dm->defaultSection);
3362:   dm->defaultSection = section;
3363:   if (section) {PetscSectionGetNumFields(dm->defaultSection, &numFields);}
3364:   if (numFields) {
3365:     DMSetNumFields(dm, numFields);
3366:     for (f = 0; f < numFields; ++f) {
3367:       PetscObject disc;
3368:       const char *name;

3370:       PetscSectionGetFieldName(dm->defaultSection, f, &name);
3371:       DMGetField(dm, f, &disc);
3372:       PetscObjectSetName(disc, name);
3373:     }
3374:   }
3375:   /* The global section will be rebuilt in the next call to DMGetDefaultGlobalSection(). */
3376:   PetscSectionDestroy(&dm->defaultGlobalSection);
3377:   return(0);
3378: }

3382: /*@
3383:   DMGetDefaultConstraints - Get the PetscSection and Mat the specify the local constraint interpolation. See DMSetDefaultConstraints() for a description of the purpose of constraint interpolation.

3385:   not collective

3387:   Input Parameter:
3388: . dm - The DM

3390:   Output Parameter:
3391: + section - The PetscSection describing the range of the constraint matrix: relates rows of the constraint matrix to dofs of the default section.  Returns NULL if there are no local constraints.
3392: - mat - The Mat that interpolates local constraints: its width should be the layout size of the default section.  Returns NULL if there are no local constraints.

3394:   Level: advanced

3396:   Note: This gets borrowed references, so the user should not destroy the PetscSection or the Mat.

3398: .seealso: DMSetDefaultConstraints()
3399: @*/
3400: PetscErrorCode DMGetDefaultConstraints(DM dm, PetscSection *section, Mat *mat)
3401: {

3406:   if (!dm->defaultConstraintSection && !dm->defaultConstraintMat && dm->ops->createdefaultconstraints) {(*dm->ops->createdefaultconstraints)(dm);}
3407:   if (section) {*section = dm->defaultConstraintSection;}
3408:   if (mat) {*mat = dm->defaultConstraintMat;}
3409:   return(0);
3410: }

3414: /*@
3415:   DMSetDefaultConstraints - Set the PetscSection and Mat the specify the local constraint interpolation.

3417:   If a constraint matrix is specified, then it is applied during DMGlobalToLocalEnd() when mode is INSERT_VALUES, INSERT_BC_VALUES, or INSERT_ALL_VALUES.  Without a constraint matrix, the local vector l returned by DMGlobalToLocalEnd() contains values that have been scattered from a global vector without modification; with a constraint matrix A, l is modified by computing c = A * l, l[s[i]] = c[i], where the scatter s is defined by the PetscSection returned by DMGetDefaultConstraintMatrix().

3419:   If a constraint matrix is specified, then its adjoint is applied during DMLocalToGlobalBegin() when mode is ADD_VALUES, ADD_BC_VALUES, or ADD_ALL_VALUES.  Without a constraint matrix, the local vector l is accumulated into a global vector without modification; with a constraint matrix A, l is first modified by computing c[i] = l[s[i]], l[s[i]] = 0, l = l + A'*c, which is the adjoint of the operation described above.

3421:   collective on dm

3423:   Input Parameters:
3424: + dm - The DM
3425: + section - The PetscSection describing the range of the constraint matrix: relates rows of the constraint matrix to dofs of the default section.  Must have a local communicator (PETSC_COMM_SELF or derivative).
3426: - mat - The Mat that interpolates local constraints: its width should be the layout size of the default section:  NULL indicates no constraints.  Must have a local communicator (PETSC_COMM_SELF or derivative).

3428:   Level: advanced

3430:   Note: This increments the references of the PetscSection and the Mat, so they user can destroy them

3432: .seealso: DMGetDefaultConstraints()
3433: @*/
3434: PetscErrorCode DMSetDefaultConstraints(DM dm, PetscSection section, Mat mat)
3435: {
3436:   PetscMPIInt result;

3441:   if (section) {
3443:     MPI_Comm_compare(PETSC_COMM_SELF,PetscObjectComm((PetscObject)section),&result);
3444:     if (result != MPI_CONGRUENT && result != MPI_IDENT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMECOMM,"constraint section must have local communicator");
3445:   }
3446:   if (mat) {
3448:     MPI_Comm_compare(PETSC_COMM_SELF,PetscObjectComm((PetscObject)mat),&result);
3449:     if (result != MPI_CONGRUENT && result != MPI_IDENT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMECOMM,"constraint matrix must have local communicator");
3450:   }
3451:   PetscObjectReference((PetscObject)section);
3452:   PetscSectionDestroy(&dm->defaultConstraintSection);
3453:   dm->defaultConstraintSection = section;
3454:   PetscObjectReference((PetscObject)mat);
3455:   MatDestroy(&dm->defaultConstraintMat);
3456:   dm->defaultConstraintMat = mat;
3457:   return(0);
3458: }

3460: #ifdef PETSC_USE_DEBUG
3463: /*
3464:   DMDefaultSectionCheckConsistency - Check the consistentcy of the global and local sections.

3466:   Input Parameters:
3467: + dm - The DM
3468: . localSection - PetscSection describing the local data layout
3469: - globalSection - PetscSection describing the global data layout

3471:   Level: intermediate

3473: .seealso: DMGetDefaultSF(), DMSetDefaultSF()
3474: */
3475: static PetscErrorCode DMDefaultSectionCheckConsistency_Internal(DM dm, PetscSection localSection, PetscSection globalSection)
3476: {
3477:   MPI_Comm        comm;
3478:   PetscLayout     layout;
3479:   const PetscInt *ranges;
3480:   PetscInt        pStart, pEnd, p, nroots;
3481:   PetscMPIInt     size, rank;
3482:   PetscBool       valid = PETSC_TRUE, gvalid;
3483:   PetscErrorCode  ierr;

3486:   PetscObjectGetComm((PetscObject)dm,&comm);
3488:   MPI_Comm_size(comm, &size);
3489:   MPI_Comm_rank(comm, &rank);
3490:   PetscSectionGetChart(globalSection, &pStart, &pEnd);
3491:   PetscSectionGetConstrainedStorageSize(globalSection, &nroots);
3492:   PetscLayoutCreate(comm, &layout);
3493:   PetscLayoutSetBlockSize(layout, 1);
3494:   PetscLayoutSetLocalSize(layout, nroots);
3495:   PetscLayoutSetUp(layout);
3496:   PetscLayoutGetRanges(layout, &ranges);
3497:   for (p = pStart; p < pEnd; ++p) {
3498:     PetscInt       dof, cdof, off, gdof, gcdof, goff, gsize, d;

3500:     PetscSectionGetDof(localSection, p, &dof);
3501:     PetscSectionGetOffset(localSection, p, &off);
3502:     PetscSectionGetConstraintDof(localSection, p, &cdof);
3503:     PetscSectionGetDof(globalSection, p, &gdof);
3504:     PetscSectionGetConstraintDof(globalSection, p, &gcdof);
3505:     PetscSectionGetOffset(globalSection, p, &goff);
3506:     if (!gdof) continue; /* Censored point */
3507:     if ((gdof < 0 ? -(gdof+1) : gdof) != dof) {PetscSynchronizedPrintf(comm, "[%d]Global dof %d for point %d not equal to local dof %d\n", rank, gdof, p, dof); valid = PETSC_FALSE;}
3508:     if (gcdof && (gcdof != cdof)) {PetscSynchronizedPrintf(comm, "[%d]Global constraints %d for point %d not equal to local constraints %d\n", rank, gcdof, p, cdof); valid = PETSC_FALSE;}
3509:     if (gdof < 0) {
3510:       gsize = gdof < 0 ? -(gdof+1)-gcdof : gdof-gcdof;
3511:       for (d = 0; d < gsize; ++d) {
3512:         PetscInt offset = -(goff+1) + d, r;

3514:         PetscFindInt(offset,size+1,ranges,&r);
3515:         if (r < 0) r = -(r+2);
3516:         if ((r < 0) || (r >= size)) {PetscSynchronizedPrintf(comm, "[%d]Point %d mapped to invalid process %d (%d, %d)\n", rank, p, r, gdof, goff); valid = PETSC_FALSE;break;}
3517:       }
3518:     }
3519:   }
3520:   PetscLayoutDestroy(&layout);
3521:   PetscSynchronizedFlush(comm, NULL);
3522:   MPIU_Allreduce(&valid, &gvalid, 1, MPIU_BOOL, MPI_LAND, comm);
3523:   if (!gvalid) {
3524:     DMView(dm, NULL);
3525:     SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Inconsistent local and global sections");
3526:   }
3527:   return(0);
3528: }
3529: #endif

3533: /*@
3534:   DMGetDefaultGlobalSection - Get the PetscSection encoding the global data layout for the DM.

3536:   Collective on DM

3538:   Input Parameter:
3539: . dm - The DM

3541:   Output Parameter:
3542: . section - The PetscSection

3544:   Level: intermediate

3546:   Note: This gets a borrowed reference, so the user should not destroy this PetscSection.

3548: .seealso: DMSetDefaultSection(), DMGetDefaultSection()
3549: @*/
3550: PetscErrorCode DMGetDefaultGlobalSection(DM dm, PetscSection *section)
3551: {

3557:   if (!dm->defaultGlobalSection) {
3558:     PetscSection s;

3560:     DMGetDefaultSection(dm, &s);
3561:     if (!s)  SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONGSTATE, "DM must have a default PetscSection in order to create a global PetscSection");
3562:     if (!dm->sf) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE, "DM must have a default PetscSF in order to create a global PetscSection");
3563:     PetscSectionCreateGlobalSection(s, dm->sf, PETSC_FALSE, PETSC_FALSE, &dm->defaultGlobalSection);
3564:     PetscLayoutDestroy(&dm->map);
3565:     PetscSectionGetValueLayout(PetscObjectComm((PetscObject)dm), dm->defaultGlobalSection, &dm->map);
3566:     PetscSectionViewFromOptions(dm->defaultGlobalSection, NULL, "-global_section_view");
3567:   }
3568:   *section = dm->defaultGlobalSection;
3569:   return(0);
3570: }

3574: /*@
3575:   DMSetDefaultGlobalSection - Set the PetscSection encoding the global data layout for the DM.

3577:   Input Parameters:
3578: + dm - The DM
3579: - section - The PetscSection, or NULL

3581:   Level: intermediate

3583:   Note: Any existing Section will be destroyed

3585: .seealso: DMGetDefaultGlobalSection(), DMSetDefaultSection()
3586: @*/
3587: PetscErrorCode DMSetDefaultGlobalSection(DM dm, PetscSection section)
3588: {

3594:   PetscObjectReference((PetscObject)section);
3595:   PetscSectionDestroy(&dm->defaultGlobalSection);
3596:   dm->defaultGlobalSection = section;
3597: #ifdef PETSC_USE_DEBUG
3598:   if (section) {DMDefaultSectionCheckConsistency_Internal(dm, dm->defaultSection, section);}
3599: #endif
3600:   return(0);
3601: }

3605: /*@
3606:   DMGetDefaultSF - Get the PetscSF encoding the parallel dof overlap for the DM. If it has not been set,
3607:   it is created from the default PetscSection layouts in the DM.

3609:   Input Parameter:
3610: . dm - The DM

3612:   Output Parameter:
3613: . sf - The PetscSF

3615:   Level: intermediate

3617:   Note: This gets a borrowed reference, so the user should not destroy this PetscSF.

3619: .seealso: DMSetDefaultSF(), DMCreateDefaultSF()
3620: @*/
3621: PetscErrorCode DMGetDefaultSF(DM dm, PetscSF *sf)
3622: {
3623:   PetscInt       nroots;

3629:   PetscSFGetGraph(dm->defaultSF, &nroots, NULL, NULL, NULL);
3630:   if (nroots < 0) {
3631:     PetscSection section, gSection;

3633:     DMGetDefaultSection(dm, &section);
3634:     if (section) {
3635:       DMGetDefaultGlobalSection(dm, &gSection);
3636:       DMCreateDefaultSF(dm, section, gSection);
3637:     } else {
3638:       *sf = NULL;
3639:       return(0);
3640:     }
3641:   }
3642:   *sf = dm->defaultSF;
3643:   return(0);
3644: }

3648: /*@
3649:   DMSetDefaultSF - Set the PetscSF encoding the parallel dof overlap for the DM

3651:   Input Parameters:
3652: + dm - The DM
3653: - sf - The PetscSF

3655:   Level: intermediate

3657:   Note: Any previous SF is destroyed

3659: .seealso: DMGetDefaultSF(), DMCreateDefaultSF()
3660: @*/
3661: PetscErrorCode DMSetDefaultSF(DM dm, PetscSF sf)
3662: {

3668:   PetscSFDestroy(&dm->defaultSF);
3669:   dm->defaultSF = sf;
3670:   return(0);
3671: }

3675: /*@C
3676:   DMCreateDefaultSF - Create the PetscSF encoding the parallel dof overlap for the DM based upon the PetscSections
3677:   describing the data layout.

3679:   Input Parameters:
3680: + dm - The DM
3681: . localSection - PetscSection describing the local data layout
3682: - globalSection - PetscSection describing the global data layout

3684:   Level: intermediate

3686: .seealso: DMGetDefaultSF(), DMSetDefaultSF()
3687: @*/
3688: PetscErrorCode DMCreateDefaultSF(DM dm, PetscSection localSection, PetscSection globalSection)
3689: {
3690:   MPI_Comm       comm;
3691:   PetscLayout    layout;
3692:   const PetscInt *ranges;
3693:   PetscInt       *local;
3694:   PetscSFNode    *remote;
3695:   PetscInt       pStart, pEnd, p, nroots, nleaves = 0, l;
3696:   PetscMPIInt    size, rank;

3700:   PetscObjectGetComm((PetscObject)dm,&comm);
3702:   MPI_Comm_size(comm, &size);
3703:   MPI_Comm_rank(comm, &rank);
3704:   PetscSectionGetChart(globalSection, &pStart, &pEnd);
3705:   PetscSectionGetConstrainedStorageSize(globalSection, &nroots);
3706:   PetscLayoutCreate(comm, &layout);
3707:   PetscLayoutSetBlockSize(layout, 1);
3708:   PetscLayoutSetLocalSize(layout, nroots);
3709:   PetscLayoutSetUp(layout);
3710:   PetscLayoutGetRanges(layout, &ranges);
3711:   for (p = pStart; p < pEnd; ++p) {
3712:     PetscInt gdof, gcdof;

3714:     PetscSectionGetDof(globalSection, p, &gdof);
3715:     PetscSectionGetConstraintDof(globalSection, p, &gcdof);
3716:     if (gcdof > (gdof < 0 ? -(gdof+1) : gdof)) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Point %d has %d constraints > %d dof", p, gcdof, (gdof < 0 ? -(gdof+1) : gdof));
3717:     nleaves += gdof < 0 ? -(gdof+1)-gcdof : gdof-gcdof;
3718:   }
3719:   PetscMalloc1(nleaves, &local);
3720:   PetscMalloc1(nleaves, &remote);
3721:   for (p = pStart, l = 0; p < pEnd; ++p) {
3722:     const PetscInt *cind;
3723:     PetscInt       dof, cdof, off, gdof, gcdof, goff, gsize, d, c;

3725:     PetscSectionGetDof(localSection, p, &dof);
3726:     PetscSectionGetOffset(localSection, p, &off);
3727:     PetscSectionGetConstraintDof(localSection, p, &cdof);
3728:     PetscSectionGetConstraintIndices(localSection, p, &cind);
3729:     PetscSectionGetDof(globalSection, p, &gdof);
3730:     PetscSectionGetConstraintDof(globalSection, p, &gcdof);
3731:     PetscSectionGetOffset(globalSection, p, &goff);
3732:     if (!gdof) continue; /* Censored point */
3733:     gsize = gdof < 0 ? -(gdof+1)-gcdof : gdof-gcdof;
3734:     if (gsize != dof-cdof) {
3735:       if (gsize != dof) SETERRQ4(comm, PETSC_ERR_ARG_WRONG, "Global dof %d for point %d is neither the constrained size %d, nor the unconstrained %d", gsize, p, dof-cdof, dof);
3736:       cdof = 0; /* Ignore constraints */
3737:     }
3738:     for (d = 0, c = 0; d < dof; ++d) {
3739:       if ((c < cdof) && (cind[c] == d)) {++c; continue;}
3740:       local[l+d-c] = off+d;
3741:     }
3742:     if (gdof < 0) {
3743:       for (d = 0; d < gsize; ++d, ++l) {
3744:         PetscInt offset = -(goff+1) + d, r;

3746:         PetscFindInt(offset,size+1,ranges,&r);
3747:         if (r < 0) r = -(r+2);
3748:         if ((r < 0) || (r >= size)) SETERRQ4(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Point %d mapped to invalid process %d (%d, %d)", p, r, gdof, goff);
3749:         remote[l].rank  = r;
3750:         remote[l].index = offset - ranges[r];
3751:       }
3752:     } else {
3753:       for (d = 0; d < gsize; ++d, ++l) {
3754:         remote[l].rank  = rank;
3755:         remote[l].index = goff+d - ranges[rank];
3756:       }
3757:     }
3758:   }
3759:   if (l != nleaves) SETERRQ2(comm, PETSC_ERR_PLIB, "Iteration error, l %d != nleaves %d", l, nleaves);
3760:   PetscLayoutDestroy(&layout);
3761:   PetscSFSetGraph(dm->defaultSF, nroots, nleaves, local, PETSC_OWN_POINTER, remote, PETSC_OWN_POINTER);
3762:   return(0);
3763: }

3767: /*@
3768:   DMGetPointSF - Get the PetscSF encoding the parallel section point overlap for the DM.

3770:   Input Parameter:
3771: . dm - The DM

3773:   Output Parameter:
3774: . sf - The PetscSF

3776:   Level: intermediate

3778:   Note: This gets a borrowed reference, so the user should not destroy this PetscSF.

3780: .seealso: DMSetPointSF(), DMGetDefaultSF(), DMSetDefaultSF(), DMCreateDefaultSF()
3781: @*/
3782: PetscErrorCode DMGetPointSF(DM dm, PetscSF *sf)
3783: {
3787:   *sf = dm->sf;
3788:   return(0);
3789: }

3793: /*@
3794:   DMSetPointSF - Set the PetscSF encoding the parallel section point overlap for the DM.

3796:   Input Parameters:
3797: + dm - The DM
3798: - sf - The PetscSF

3800:   Level: intermediate

3802: .seealso: DMGetPointSF(), DMGetDefaultSF(), DMSetDefaultSF(), DMCreateDefaultSF()
3803: @*/
3804: PetscErrorCode DMSetPointSF(DM dm, PetscSF sf)
3805: {

3811:   PetscSFDestroy(&dm->sf);
3812:   PetscObjectReference((PetscObject) sf);
3813:   dm->sf = sf;
3814:   return(0);
3815: }

3819: /*@
3820:   DMGetDS - Get the PetscDS

3822:   Input Parameter:
3823: . dm - The DM

3825:   Output Parameter:
3826: . prob - The PetscDS

3828:   Level: developer

3830: .seealso: DMSetDS()
3831: @*/
3832: PetscErrorCode DMGetDS(DM dm, PetscDS *prob)
3833: {
3837:   *prob = dm->prob;
3838:   return(0);
3839: }

3843: /*@
3844:   DMSetDS - Set the PetscDS

3846:   Input Parameters:
3847: + dm - The DM
3848: - prob - The PetscDS

3850:   Level: developer

3852: .seealso: DMGetDS()
3853: @*/
3854: PetscErrorCode DMSetDS(DM dm, PetscDS prob)
3855: {

3861:   PetscDSDestroy(&dm->prob);
3862:   dm->prob = prob;
3863:   PetscObjectReference((PetscObject) dm->prob);
3864:   return(0);
3865: }

3869: PetscErrorCode DMGetNumFields(DM dm, PetscInt *numFields)
3870: {

3875:   PetscDSGetNumFields(dm->prob, numFields);
3876:   return(0);
3877: }

3881: PetscErrorCode DMSetNumFields(DM dm, PetscInt numFields)
3882: {
3883:   PetscInt       Nf, f;

3888:   PetscDSGetNumFields(dm->prob, &Nf);
3889:   for (f = Nf; f < numFields; ++f) {
3890:     PetscContainer obj;

3892:     PetscContainerCreate(PetscObjectComm((PetscObject) dm), &obj);
3893:     PetscDSSetDiscretization(dm->prob, f, (PetscObject) obj);
3894:     PetscContainerDestroy(&obj);
3895:   }
3896:   return(0);
3897: }

3901: /*@
3902:   DMGetField - Return the discretization object for a given DM field

3904:   Not collective

3906:   Input Parameters:
3907: + dm - The DM
3908: - f  - The field number

3910:   Output Parameter:
3911: . field - The discretization object

3913:   Level: developer

3915: .seealso: DMSetField()
3916: @*/
3917: PetscErrorCode DMGetField(DM dm, PetscInt f, PetscObject *field)
3918: {

3923:   PetscDSGetDiscretization(dm->prob, f, field);
3924:   return(0);
3925: }

3929: /*@
3930:   DMSetField - Set the discretization object for a given DM field

3932:   Logically collective on DM

3934:   Input Parameters:
3935: + dm - The DM
3936: . f  - The field number
3937: - field - The discretization object

3939:   Level: developer

3941: .seealso: DMGetField()
3942: @*/
3943: PetscErrorCode DMSetField(DM dm, PetscInt f, PetscObject field)
3944: {

3949:   PetscDSSetDiscretization(dm->prob, f, field);
3950:   return(0);
3951: }

3955: PetscErrorCode DMRestrictHook_Coordinates(DM dm,DM dmc,void *ctx)
3956: {
3957:   DM dm_coord,dmc_coord;
3959:   Vec coords,ccoords;
3960:   Mat inject;
3962:   DMGetCoordinateDM(dm,&dm_coord);
3963:   DMGetCoordinateDM(dmc,&dmc_coord);
3964:   DMGetCoordinates(dm,&coords);
3965:   DMGetCoordinates(dmc,&ccoords);
3966:   if (coords && !ccoords) {
3967:     DMCreateGlobalVector(dmc_coord,&ccoords);
3968:     PetscObjectSetName((PetscObject)ccoords,"coordinates");
3969:     DMCreateInjection(dmc_coord,dm_coord,&inject);
3970:     MatRestrict(inject,coords,ccoords);
3971:     MatDestroy(&inject);
3972:     DMSetCoordinates(dmc,ccoords);
3973:     VecDestroy(&ccoords);
3974:   }
3975:   return(0);
3976: }

3980: static PetscErrorCode DMSubDomainHook_Coordinates(DM dm,DM subdm,void *ctx)
3981: {
3982:   DM dm_coord,subdm_coord;
3984:   Vec coords,ccoords,clcoords;
3985:   VecScatter *scat_i,*scat_g;
3987:   DMGetCoordinateDM(dm,&dm_coord);
3988:   DMGetCoordinateDM(subdm,&subdm_coord);
3989:   DMGetCoordinates(dm,&coords);
3990:   DMGetCoordinates(subdm,&ccoords);
3991:   if (coords && !ccoords) {
3992:     DMCreateGlobalVector(subdm_coord,&ccoords);
3993:     PetscObjectSetName((PetscObject)ccoords,"coordinates");
3994:     DMCreateLocalVector(subdm_coord,&clcoords);
3995:     PetscObjectSetName((PetscObject)clcoords,"coordinates");
3996:     DMCreateDomainDecompositionScatters(dm_coord,1,&subdm_coord,NULL,&scat_i,&scat_g);
3997:     VecScatterBegin(scat_i[0],coords,ccoords,INSERT_VALUES,SCATTER_FORWARD);
3998:     VecScatterBegin(scat_g[0],coords,clcoords,INSERT_VALUES,SCATTER_FORWARD);
3999:     VecScatterEnd(scat_i[0],coords,ccoords,INSERT_VALUES,SCATTER_FORWARD);
4000:     VecScatterEnd(scat_g[0],coords,clcoords,INSERT_VALUES,SCATTER_FORWARD);
4001:     DMSetCoordinates(subdm,ccoords);
4002:     DMSetCoordinatesLocal(subdm,clcoords);
4003:     VecScatterDestroy(&scat_i[0]);
4004:     VecScatterDestroy(&scat_g[0]);
4005:     VecDestroy(&ccoords);
4006:     VecDestroy(&clcoords);
4007:     PetscFree(scat_i);
4008:     PetscFree(scat_g);
4009:   }
4010:   return(0);
4011: }

4015: /*@
4016:   DMGetDimension - Return the topological dimension of the DM

4018:   Not collective

4020:   Input Parameter:
4021: . dm - The DM

4023:   Output Parameter:
4024: . dim - The topological dimension

4026:   Level: beginner

4028: .seealso: DMSetDimension(), DMCreate()
4029: @*/
4030: PetscErrorCode DMGetDimension(DM dm, PetscInt *dim)
4031: {
4035:   *dim = dm->dim;
4036:   return(0);
4037: }

4041: /*@
4042:   DMSetDimension - Set the topological dimension of the DM

4044:   Collective on dm

4046:   Input Parameters:
4047: + dm - The DM
4048: - dim - The topological dimension

4050:   Level: beginner

4052: .seealso: DMGetDimension(), DMCreate()
4053: @*/
4054: PetscErrorCode DMSetDimension(DM dm, PetscInt dim)
4055: {
4059:   dm->dim = dim;
4060:   return(0);
4061: }

4065: /*@
4066:   DMGetDimPoints - Get the half-open interval for all points of a given dimension

4068:   Collective on DM

4070:   Input Parameters:
4071: + dm - the DM
4072: - dim - the dimension

4074:   Output Parameters:
4075: + pStart - The first point of the given dimension
4076: . pEnd - The first point following points of the given dimension

4078:   Note:
4079:   The points are vertices in the Hasse diagram encoding the topology. This is explained in
4080:   http://arxiv.org/abs/0908.4427. If not points exist of this dimension in the storage scheme,
4081:   then the interval is empty.

4083:   Level: intermediate

4085: .keywords: point, Hasse Diagram, dimension
4086: .seealso: DMPLEX, DMPlexGetDepthStratum(), DMPlexGetHeightStratum()
4087: @*/
4088: PetscErrorCode DMGetDimPoints(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd)
4089: {
4090:   PetscInt       d;

4095:   DMGetDimension(dm, &d);
4096:   if ((dim < 0) || (dim > d)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid dimension %d 1", dim, d);
4097:   (*dm->ops->getdimpoints)(dm, dim, pStart, pEnd);
4098:   return(0);
4099: }

4103: /*@
4104:   DMSetCoordinates - Sets into the DM a global vector that holds the coordinates

4106:   Collective on DM

4108:   Input Parameters:
4109: + dm - the DM
4110: - c - coordinate vector

4112:   Note:
4113:   The coordinates do include those for ghost points, which are in the local vector

4115:   Level: intermediate

4117: .keywords: distributed array, get, corners, nodes, local indices, coordinates
4118: .seealso: DMSetCoordinatesLocal(), DMGetCoordinates(), DMGetCoordinatesLoca(), DMGetCoordinateDM()
4119: @*/
4120: PetscErrorCode DMSetCoordinates(DM dm, Vec c)
4121: {

4127:   PetscObjectReference((PetscObject) c);
4128:   VecDestroy(&dm->coordinates);
4129:   dm->coordinates = c;
4130:   VecDestroy(&dm->coordinatesLocal);
4131:   DMCoarsenHookAdd(dm,DMRestrictHook_Coordinates,NULL,NULL);
4132:   DMSubDomainHookAdd(dm,DMSubDomainHook_Coordinates,NULL,NULL);
4133:   return(0);
4134: }

4138: /*@
4139:   DMSetCoordinatesLocal - Sets into the DM a local vector that holds the coordinates

4141:   Collective on DM

4143:    Input Parameters:
4144: +  dm - the DM
4145: -  c - coordinate vector

4147:   Note:
4148:   The coordinates of ghost points can be set using DMSetCoordinates()
4149:   followed by DMGetCoordinatesLocal(). This is intended to enable the
4150:   setting of ghost coordinates outside of the domain.

4152:   Level: intermediate

4154: .keywords: distributed array, get, corners, nodes, local indices, coordinates
4155: .seealso: DMGetCoordinatesLocal(), DMSetCoordinates(), DMGetCoordinates(), DMGetCoordinateDM()
4156: @*/
4157: PetscErrorCode DMSetCoordinatesLocal(DM dm, Vec c)
4158: {

4164:   PetscObjectReference((PetscObject) c);
4165:   VecDestroy(&dm->coordinatesLocal);

4167:   dm->coordinatesLocal = c;

4169:   VecDestroy(&dm->coordinates);
4170:   return(0);
4171: }

4175: /*@
4176:   DMGetCoordinates - Gets a global vector with the coordinates associated with the DM.

4178:   Not Collective

4180:   Input Parameter:
4181: . dm - the DM

4183:   Output Parameter:
4184: . c - global coordinate vector

4186:   Note:
4187:   This is a borrowed reference, so the user should NOT destroy this vector

4189:   Each process has only the local coordinates (does NOT have the ghost coordinates).

4191:   For DMDA, in two and three dimensions coordinates are interlaced (x_0,y_0,x_1,y_1,...)
4192:   and (x_0,y_0,z_0,x_1,y_1,z_1...)

4194:   Level: intermediate

4196: .keywords: distributed array, get, corners, nodes, local indices, coordinates
4197: .seealso: DMSetCoordinates(), DMGetCoordinatesLocal(), DMGetCoordinateDM()
4198: @*/
4199: PetscErrorCode DMGetCoordinates(DM dm, Vec *c)
4200: {

4206:   if (!dm->coordinates && dm->coordinatesLocal) {
4207:     DM cdm = NULL;

4209:     DMGetCoordinateDM(dm, &cdm);
4210:     DMCreateGlobalVector(cdm, &dm->coordinates);
4211:     PetscObjectSetName((PetscObject) dm->coordinates, "coordinates");
4212:     DMLocalToGlobalBegin(cdm, dm->coordinatesLocal, INSERT_VALUES, dm->coordinates);
4213:     DMLocalToGlobalEnd(cdm, dm->coordinatesLocal, INSERT_VALUES, dm->coordinates);
4214:   }
4215:   *c = dm->coordinates;
4216:   return(0);
4217: }

4221: /*@
4222:   DMGetCoordinatesLocal - Gets a local vector with the coordinates associated with the DM.

4224:   Collective on DM

4226:   Input Parameter:
4227: . dm - the DM

4229:   Output Parameter:
4230: . c - coordinate vector

4232:   Note:
4233:   This is a borrowed reference, so the user should NOT destroy this vector

4235:   Each process has the local and ghost coordinates

4237:   For DMDA, in two and three dimensions coordinates are interlaced (x_0,y_0,x_1,y_1,...)
4238:   and (x_0,y_0,z_0,x_1,y_1,z_1...)

4240:   Level: intermediate

4242: .keywords: distributed array, get, corners, nodes, local indices, coordinates
4243: .seealso: DMSetCoordinatesLocal(), DMGetCoordinates(), DMSetCoordinates(), DMGetCoordinateDM()
4244: @*/
4245: PetscErrorCode DMGetCoordinatesLocal(DM dm, Vec *c)
4246: {

4252:   if (!dm->coordinatesLocal && dm->coordinates) {
4253:     DM cdm = NULL;

4255:     DMGetCoordinateDM(dm, &cdm);
4256:     DMCreateLocalVector(cdm, &dm->coordinatesLocal);
4257:     PetscObjectSetName((PetscObject) dm->coordinatesLocal, "coordinates");
4258:     DMGlobalToLocalBegin(cdm, dm->coordinates, INSERT_VALUES, dm->coordinatesLocal);
4259:     DMGlobalToLocalEnd(cdm, dm->coordinates, INSERT_VALUES, dm->coordinatesLocal);
4260:   }
4261:   *c = dm->coordinatesLocal;
4262:   return(0);
4263: }

4267: /*@
4268:   DMGetCoordinateDM - Gets the DM that prescribes coordinate layout and scatters between global and local coordinates

4270:   Collective on DM

4272:   Input Parameter:
4273: . dm - the DM

4275:   Output Parameter:
4276: . cdm - coordinate DM

4278:   Level: intermediate

4280: .keywords: distributed array, get, corners, nodes, local indices, coordinates
4281: .seealso: DMSetCoordinateDM(), DMSetCoordinates(), DMSetCoordinatesLocal(), DMGetCoordinates(), DMGetCoordinatesLocal()
4282: @*/
4283: PetscErrorCode DMGetCoordinateDM(DM dm, DM *cdm)
4284: {

4290:   if (!dm->coordinateDM) {
4291:     if (!dm->ops->createcoordinatedm) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unable to create coordinates for this DM");
4292:     (*dm->ops->createcoordinatedm)(dm, &dm->coordinateDM);
4293:   }
4294:   *cdm = dm->coordinateDM;
4295:   return(0);
4296: }

4300: /*@
4301:   DMSetCoordinateDM - Sets the DM that prescribes coordinate layout and scatters between global and local coordinates

4303:   Logically Collective on DM

4305:   Input Parameters:
4306: + dm - the DM
4307: - cdm - coordinate DM

4309:   Level: intermediate

4311: .keywords: distributed array, get, corners, nodes, local indices, coordinates
4312: .seealso: DMGetCoordinateDM(), DMSetCoordinates(), DMSetCoordinatesLocal(), DMGetCoordinates(), DMGetCoordinatesLocal()
4313: @*/
4314: PetscErrorCode DMSetCoordinateDM(DM dm, DM cdm)
4315: {

4321:   DMDestroy(&dm->coordinateDM);
4322:   dm->coordinateDM = cdm;
4323:   PetscObjectReference((PetscObject) dm->coordinateDM);
4324:   return(0);
4325: }

4329: /*@
4330:   DMGetCoordinateDim - Retrieve the dimension of embedding space for coordinate values.

4332:   Not Collective

4334:   Input Parameter:
4335: . dm - The DM object

4337:   Output Parameter:
4338: . dim - The embedding dimension

4340:   Level: intermediate

4342: .keywords: mesh, coordinates
4343: .seealso: DMSetCoordinateDim(), DMGetCoordinateSection(), DMGetCoordinateDM(), DMGetDefaultSection(), DMSetDefaultSection()
4344: @*/
4345: PetscErrorCode DMGetCoordinateDim(DM dm, PetscInt *dim)
4346: {
4350:   if (dm->dimEmbed == PETSC_DEFAULT) {
4351:     dm->dimEmbed = dm->dim;
4352:   }
4353:   *dim = dm->dimEmbed;
4354:   return(0);
4355: }

4359: /*@
4360:   DMSetCoordinateDim - Set the dimension of the embedding space for coordinate values.

4362:   Not Collective

4364:   Input Parameters:
4365: + dm  - The DM object
4366: - dim - The embedding dimension

4368:   Level: intermediate

4370: .keywords: mesh, coordinates
4371: .seealso: DMGetCoordinateDim(), DMSetCoordinateSection(), DMGetCoordinateSection(), DMGetDefaultSection(), DMSetDefaultSection()
4372: @*/
4373: PetscErrorCode DMSetCoordinateDim(DM dm, PetscInt dim)
4374: {
4377:   dm->dimEmbed = dim;
4378:   return(0);
4379: }

4383: /*@
4384:   DMGetCoordinateSection - Retrieve the layout of coordinate values over the mesh.

4386:   Not Collective

4388:   Input Parameter:
4389: . dm - The DM object

4391:   Output Parameter:
4392: . section - The PetscSection object

4394:   Level: intermediate

4396: .keywords: mesh, coordinates
4397: .seealso: DMGetCoordinateDM(), DMGetDefaultSection(), DMSetDefaultSection()
4398: @*/
4399: PetscErrorCode DMGetCoordinateSection(DM dm, PetscSection *section)
4400: {
4401:   DM             cdm;

4407:   DMGetCoordinateDM(dm, &cdm);
4408:   DMGetDefaultSection(cdm, section);
4409:   return(0);
4410: }

4414: /*@
4415:   DMSetCoordinateSection - Set the layout of coordinate values over the mesh.

4417:   Not Collective

4419:   Input Parameters:
4420: + dm      - The DM object
4421: . dim     - The embedding dimension, or PETSC_DETERMINE
4422: - section - The PetscSection object

4424:   Level: intermediate

4426: .keywords: mesh, coordinates
4427: .seealso: DMGetCoordinateSection(), DMGetDefaultSection(), DMSetDefaultSection()
4428: @*/
4429: PetscErrorCode DMSetCoordinateSection(DM dm, PetscInt dim, PetscSection section)
4430: {
4431:   DM             cdm;

4437:   DMGetCoordinateDM(dm, &cdm);
4438:   DMSetDefaultSection(cdm, section);
4439:   if (dim == PETSC_DETERMINE) {
4440:     PetscInt d = dim;
4441:     PetscInt pStart, pEnd, vStart, vEnd, v, dd;

4443:     PetscSectionGetChart(section, &pStart, &pEnd);
4444:     DMGetDimPoints(dm, 0, &vStart, &vEnd);
4445:     pStart = PetscMax(vStart, pStart);
4446:     pEnd   = PetscMin(vEnd, pEnd);
4447:     for (v = pStart; v < pEnd; ++v) {
4448:       PetscSectionGetDof(section, v, &dd);
4449:       if (dd) {d = dd; break;}
4450:     }
4451:     DMSetCoordinateDim(dm, d);
4452:   }
4453:   return(0);
4454: }

4458: /*@C
4459:   DMSetPeriodicity - Set the description of mesh periodicity

4461:   Input Parameters:
4462: + dm      - The DM object
4463: . maxCell - Over distances greater than this, we can assume a point has crossed over to another sheet, when trying to localize cell coordinates
4464: . L       - If we assume the mesh is a torus, this is the length of each coordinate
4465: - bd      - This describes the type of periodicity in each topological dimension

4467:   Level: developer

4469: .seealso: DMGetPeriodicity()
4470: @*/
4471: PetscErrorCode DMGetPeriodicity(DM dm, const PetscReal **maxCell, const PetscReal **L, const DMBoundaryType **bd)
4472: {
4475:   if (L)       *L       = dm->L;
4476:   if (maxCell) *maxCell = dm->maxCell;
4477:   if (bd)      *bd      = dm->bdtype;
4478:   return(0);
4479: }

4483: /*@C
4484:   DMSetPeriodicity - Set the description of mesh periodicity

4486:   Input Parameters:
4487: + dm      - The DM object
4488: . maxCell - Over distances greater than this, we can assume a point has crossed over to another sheet, when trying to localize cell coordinates
4489: . L       - If we assume the mesh is a torus, this is the length of each coordinate
4490: - bd      - This describes the type of periodicity in each topological dimension

4492:   Level: developer

4494: .seealso: DMGetPeriodicity()
4495: @*/
4496: PetscErrorCode DMSetPeriodicity(DM dm, const PetscReal maxCell[], const PetscReal L[], const DMBoundaryType bd[])
4497: {
4498:   PetscInt       dim, d;

4504:   PetscFree3(dm->L,dm->maxCell,dm->bdtype);
4505:   DMGetDimension(dm, &dim);
4506:   PetscMalloc3(dim,&dm->L,dim,&dm->maxCell,dim,&dm->bdtype);
4507:   for (d = 0; d < dim; ++d) {dm->L[d] = L[d]; dm->maxCell[d] = maxCell[d]; dm->bdtype[d] = bd[d];}
4508:   return(0);
4509: }

4513: /*@
4514:   DMLocalizeCoordinate - If a mesh is periodic (a torus with lengths L_i, some of which can be infinite), project the coordinate onto [0, L_i) in each dimension.

4516:   Input Parameters:
4517: + dm     - The DM
4518: - in     - The input coordinate point (dim numbers)

4520:   Output Parameter:
4521: . out - The localized coordinate point

4523:   Level: developer

4525: .seealso: DMLocalizeCoordinates(), DMLocalizeAddCoordinate()
4526: @*/
4527: PetscErrorCode DMLocalizeCoordinate(DM dm, const PetscScalar in[], PetscScalar out[])
4528: {
4529:   PetscInt       dim, d;

4533:   DMGetCoordinateDim(dm, &dim);
4534:   if (!dm->maxCell) {
4535:     for (d = 0; d < dim; ++d) out[d] = in[d];
4536:   } else {
4537:     for (d = 0; d < dim; ++d) {
4538:       out[d] = in[d] - dm->L[d]*floor(PetscRealPart(in[d])/dm->L[d]);
4539:     }
4540:   }
4541:   return(0);
4542: }

4546: /*
4547:   DMLocalizeCoordinate_Internal - If a mesh is periodic, and the input point is far from the anchor, pick the coordinate sheet of the torus which moves it closer.

4549:   Input Parameters:
4550: + dm     - The DM
4551: . dim    - The spatial dimension
4552: . anchor - The anchor point, the input point can be no more than maxCell away from it
4553: - in     - The input coordinate point (dim numbers)

4555:   Output Parameter:
4556: . out - The localized coordinate point

4558:   Level: developer

4560:   Note: This is meant to get a set of coordinates close to each other, as in a cell. The anchor is usually the one of the vertices on a containing cell

4562: .seealso: DMLocalizeCoordinates(), DMLocalizeAddCoordinate()
4563: */
4564: PetscErrorCode DMLocalizeCoordinate_Internal(DM dm, PetscInt dim, const PetscScalar anchor[], const PetscScalar in[], PetscScalar out[])
4565: {
4566:   PetscInt d;

4569:   if (!dm->maxCell) {
4570:     for (d = 0; d < dim; ++d) out[d] = in[d];
4571:   } else {
4572:     for (d = 0; d < dim; ++d) {
4573:       if (PetscAbsScalar(anchor[d] - in[d]) > dm->maxCell[d]) {
4574:         out[d] = PetscRealPart(anchor[d]) > PetscRealPart(in[d]) ? dm->L[d] + in[d] : in[d] - dm->L[d];
4575:       } else {
4576:         out[d] = in[d];
4577:       }
4578:     }
4579:   }
4580:   return(0);
4581: }
4584: PetscErrorCode DMLocalizeCoordinateReal_Internal(DM dm, PetscInt dim, const PetscReal anchor[], const PetscReal in[], PetscReal out[])
4585: {
4586:   PetscInt d;

4589:   if (!dm->maxCell) {
4590:     for (d = 0; d < dim; ++d) out[d] = in[d];
4591:   } else {
4592:     for (d = 0; d < dim; ++d) {
4593:       if (PetscAbsReal(anchor[d] - in[d]) > dm->maxCell[d]) {
4594:         out[d] = anchor[d] > in[d] ? dm->L[d] + in[d] : in[d] - dm->L[d];
4595:       } else {
4596:         out[d] = in[d];
4597:       }
4598:     }
4599:   }
4600:   return(0);
4601: }

4605: /*
4606:   DMLocalizeAddCoordinate_Internal - If a mesh is periodic, and the input point is far from the anchor, pick the coordinate sheet of the torus which moves it closer.

4608:   Input Parameters:
4609: + dm     - The DM
4610: . dim    - The spatial dimension
4611: . anchor - The anchor point, the input point can be no more than maxCell away from it
4612: . in     - The input coordinate delta (dim numbers)
4613: - out    - The input coordinate point (dim numbers)

4615:   Output Parameter:
4616: . out    - The localized coordinate in + out

4618:   Level: developer

4620:   Note: This is meant to get a set of coordinates close to each other, as in a cell. The anchor is usually the one of the vertices on a containing cell

4622: .seealso: DMLocalizeCoordinates(), DMLocalizeCoordinate()
4623: */
4624: PetscErrorCode DMLocalizeAddCoordinate_Internal(DM dm, PetscInt dim, const PetscScalar anchor[], const PetscScalar in[], PetscScalar out[])
4625: {
4626:   PetscInt d;

4629:   if (!dm->maxCell) {
4630:     for (d = 0; d < dim; ++d) out[d] += in[d];
4631:   } else {
4632:     for (d = 0; d < dim; ++d) {
4633:       if (PetscAbsScalar(anchor[d] - in[d]) > dm->maxCell[d]) {
4634:         out[d] += PetscRealPart(anchor[d]) > PetscRealPart(in[d]) ? dm->L[d] + in[d] : in[d] - dm->L[d];
4635:       } else {
4636:         out[d] += in[d];
4637:       }
4638:     }
4639:   }
4640:   return(0);
4641: }

4643: PETSC_EXTERN PetscErrorCode DMPlexGetDepthStratum(DM, PetscInt, PetscInt *, PetscInt *);
4644: PETSC_EXTERN PetscErrorCode DMPlexGetHeightStratum(DM, PetscInt, PetscInt *, PetscInt *);
4645: PETSC_EXTERN PetscErrorCode DMPlexVecGetClosure(DM, PetscSection, Vec, PetscInt, PetscInt *, PetscScalar *[]);
4646: PETSC_EXTERN PetscErrorCode DMPlexVecRestoreClosure(DM, PetscSection, Vec, PetscInt, PetscInt *, PetscScalar *[]);

4650: /*@
4651:   DMGetCoordinatesLocalized - Check if the DM coordinates have been localized for cells

4653:   Input Parameter:
4654: . dm - The DM

4656:   Output Parameter:
4657:   areLocalized - True if localized

4659:   Level: developer

4661: .seealso: DMLocalizeCoordinates()
4662: @*/
4663: PetscErrorCode DMGetCoordinatesLocalized(DM dm,PetscBool *areLocalized)
4664: {
4665:   DM             cdm;
4666:   PetscSection   coordSection;
4667:   PetscInt       cStart, cEnd, c, sStart, sEnd, dof;
4668:   PetscBool      alreadyLocalized, alreadyLocalizedGlobal;

4673:   if (!dm->maxCell) {
4674:     *areLocalized = PETSC_FALSE;
4675:     return(0);
4676:   }
4677:   /* We need some generic way of refering to cells/vertices */
4678:   DMGetCoordinateDM(dm, &cdm);
4679:   {
4680:     PetscBool isplex;

4682:     PetscObjectTypeCompare((PetscObject) cdm, DMPLEX, &isplex);
4683:     if (isplex) {
4684:       DMPlexGetHeightStratum(cdm, 0, &cStart, &cEnd);
4685:     } else SETERRQ(PetscObjectComm((PetscObject) cdm), PETSC_ERR_ARG_WRONG, "Coordinate localization requires a DMPLEX coordinate DM");
4686:   }
4687:   DMGetCoordinateSection(dm, &coordSection);
4688:   PetscSectionGetChart(coordSection,&sStart,&sEnd);
4689:   alreadyLocalized = alreadyLocalizedGlobal = PETSC_TRUE;
4690:   for (c = cStart; c < cEnd; ++c) {
4691:     if (c < sStart || c >= sEnd) {
4692:       alreadyLocalized = PETSC_FALSE;
4693:       break;
4694:     }
4695:     PetscSectionGetDof(coordSection, c, &dof);
4696:     if (!dof) {
4697:       alreadyLocalized = PETSC_FALSE;
4698:       break;
4699:     }
4700:   }
4701:   MPI_Allreduce(&alreadyLocalized,&alreadyLocalizedGlobal,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)dm));
4702:   *areLocalized = alreadyLocalizedGlobal;
4703:   return(0);
4704: }


4709: /*@
4710:   DMLocalizeCoordinates - If a mesh is periodic, create local coordinates for each cell

4712:   Input Parameter:
4713: . dm - The DM

4715:   Level: developer

4717: .seealso: DMLocalizeCoordinate(), DMLocalizeAddCoordinate()
4718: @*/
4719: PetscErrorCode DMLocalizeCoordinates(DM dm)
4720: {
4721:   DM             cdm;
4722:   PetscSection   coordSection, cSection;
4723:   Vec            coordinates,  cVec;
4724:   PetscScalar   *coords, *coords2, *anchor;
4725:   PetscInt       Nc, cStart, cEnd, c, vStart, vEnd, v, sStart, sEnd, dof, d, off, off2, bs, coordSize;
4726:   PetscBool      alreadyLocalized, alreadyLocalizedGlobal;

4731:   if (!dm->maxCell) return(0);
4732:   /* We need some generic way of refering to cells/vertices */
4733:   DMGetCoordinateDM(dm, &cdm);
4734:   {
4735:     PetscBool isplex;

4737:     PetscObjectTypeCompare((PetscObject) cdm, DMPLEX, &isplex);
4738:     if (isplex) {
4739:       DMPlexGetHeightStratum(cdm, 0, &cStart, &cEnd);
4740:       DMPlexGetDepthStratum(cdm, 0, &vStart, &vEnd);
4741:     } else SETERRQ(PetscObjectComm((PetscObject) cdm), PETSC_ERR_ARG_WRONG, "Coordinate localization requires a DMPLEX coordinate DM");
4742:   }
4743:   DMGetCoordinatesLocal(dm, &coordinates);
4744:   DMGetCoordinateSection(dm, &coordSection);
4745:   PetscSectionGetChart(coordSection,&sStart,&sEnd);
4746:   alreadyLocalized = alreadyLocalizedGlobal = PETSC_TRUE;
4747:   for (c = cStart; c < cEnd; ++c) {
4748:     if (c < sStart || c >= sEnd) {
4749:       alreadyLocalized = PETSC_FALSE;
4750:       break;
4751:     }
4752:     PetscSectionGetDof(coordSection, c, &dof);
4753:     if (!dof) {
4754:       alreadyLocalized = PETSC_FALSE;
4755:       break;
4756:     }
4757:   }
4758:   MPI_Allreduce(&alreadyLocalized,&alreadyLocalizedGlobal,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)dm));
4759:   if (alreadyLocalizedGlobal) return(0);
4760:   PetscSectionCreate(PetscObjectComm((PetscObject) dm), &cSection);
4761:   PetscSectionSetNumFields(cSection, 1);
4762:   PetscSectionGetFieldComponents(coordSection, 0, &Nc);
4763:   PetscSectionSetFieldComponents(cSection, 0, Nc);
4764:   PetscSectionSetChart(cSection, cStart, vEnd);
4765:   for (v = vStart; v < vEnd; ++v) {
4766:     PetscSectionGetDof(coordSection, v, &dof);
4767:     PetscSectionSetDof(cSection,     v,  dof);
4768:     PetscSectionSetFieldDof(cSection, v, 0, dof);
4769:   }
4770:   for (c = cStart; c < cEnd; ++c) {
4771:     DMPlexVecGetClosure(cdm, coordSection, coordinates, c, &dof, NULL);
4772:     PetscSectionSetDof(cSection, c, dof);
4773:     PetscSectionSetFieldDof(cSection, c, 0, dof);
4774:   }
4775:   PetscSectionSetUp(cSection);
4776:   PetscSectionGetStorageSize(cSection, &coordSize);
4777:   VecCreate(PETSC_COMM_SELF, &cVec);
4778:   PetscObjectSetName((PetscObject)cVec,"coordinates");
4779:   VecGetBlockSize(coordinates, &bs);
4780:   VecSetBlockSize(cVec,         bs);
4781:   VecSetSizes(cVec, coordSize, PETSC_DETERMINE);
4782:   VecSetType(cVec, VECSTANDARD);
4783:   VecGetArrayRead(coordinates, (const PetscScalar**)&coords);
4784:   VecGetArray(cVec, &coords2);
4785:   for (v = vStart; v < vEnd; ++v) {
4786:     PetscSectionGetDof(coordSection, v, &dof);
4787:     PetscSectionGetOffset(coordSection, v, &off);
4788:     PetscSectionGetOffset(cSection,     v, &off2);
4789:     for (d = 0; d < dof; ++d) coords2[off2+d] = coords[off+d];
4790:   }
4791:   DMGetWorkArray(dm, 3, PETSC_SCALAR, &anchor);
4792:   for (c = cStart; c < cEnd; ++c) {
4793:     PetscScalar *cellCoords = NULL;
4794:     PetscInt     b;

4796:     DMPlexVecGetClosure(cdm, coordSection, coordinates, c, &dof, &cellCoords);
4797:     PetscSectionGetOffset(cSection, c, &off2);
4798:     for (b = 0; b < bs; ++b) anchor[b] = cellCoords[b];
4799:     for (d = 0; d < dof/bs; ++d) {DMLocalizeCoordinate_Internal(dm, bs, anchor, &cellCoords[d*bs], &coords2[off2+d*bs]);}
4800:     DMPlexVecRestoreClosure(cdm, coordSection, coordinates, c, &dof, &cellCoords);
4801:   }
4802:   DMRestoreWorkArray(dm, 3, PETSC_SCALAR, &anchor);
4803:   VecRestoreArrayRead(coordinates, (const PetscScalar**)&coords);
4804:   VecRestoreArray(cVec, &coords2);
4805:   DMSetCoordinateSection(dm, PETSC_DETERMINE, cSection);
4806:   DMSetCoordinatesLocal(dm, cVec);
4807:   VecDestroy(&cVec);
4808:   PetscSectionDestroy(&cSection);
4809:   return(0);
4810: }

4814: /*@
4815:   DMLocatePoints - Locate the points in v in the mesh and return a PetscSF of the containing cells

4817:   Collective on Vec v (see explanation below)

4819:   Input Parameters:
4820: + dm - The DM
4821: . v - The Vec of points
4822: - cells - Points to either NULL, or a PetscSF with guesses for which cells contain each point.

4824:   Output Parameter:
4825: . cells - The PetscSF containing the ranks and local indices of the containing points.


4828:   Level: developer

4830:   To do a search of the local cells of the mesh, v should have PETSC_COMM_SELF as its communicator.

4832:   To do a search of all the cells in the distributed mesh, v should have the same communicator as
4833:   dm.

4835:   If *cellSF is NULL on input, a PetscSF will be created.

4837:   If *cellSF is not NULL on input, it should point to an existing PetscSF, whose graph will be used as initial
4838:   guesses.

4840:   An array that maps each point to its containing cell can be obtained with

4842:     const PetscSFNode *cells;
4843:     PetscInt           nFound;
4844:     const PetscSFNode *found;

4846:     PetscSFGetGraph(cells,NULL,&nFound,&found,&cells);

4848:   Where cells[i].rank is the rank of the cell containing point found[i] (or i if found == NULL), and cells[i].index is
4849:   the index of the cell in its rank's local numbering.

4851: .keywords: point location, mesh
4852: .seealso: DMSetCoordinates(), DMSetCoordinatesLocal(), DMGetCoordinates(), DMGetCoordinatesLocal()
4853: @*/
4854: PetscErrorCode DMLocatePoints(DM dm, Vec v, PetscSF *cellSF)
4855: {

4862:   if (*cellSF) {
4863:     PetscMPIInt result;

4866:     MPI_Comm_compare(PetscObjectComm((PetscObject)v),PetscObjectComm((PetscObject)cellSF),&result);
4867:     if (result != MPI_IDENT && result != MPI_CONGRUENT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"cellSF must have a communicator congruent to v's");
4868:   }
4869:   else {
4870:     PetscSFCreate(PetscObjectComm((PetscObject)v),cellSF);
4871:   }
4872:   PetscLogEventBegin(DM_LocatePoints,dm,0,0,0);
4873:   if (dm->ops->locatepoints) {
4874:     (*dm->ops->locatepoints)(dm,v,*cellSF);
4875:   } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Point location not available for this DM");
4876:   PetscLogEventEnd(DM_LocatePoints,dm,0,0,0);
4877:   return(0);
4878: }

4882: /*@
4883:   DMGetOutputDM - Retrieve the DM associated with the layout for output

4885:   Input Parameter:
4886: . dm - The original DM

4888:   Output Parameter:
4889: . odm - The DM which provides the layout for output

4891:   Level: intermediate

4893: .seealso: VecView(), DMGetDefaultGlobalSection()
4894: @*/
4895: PetscErrorCode DMGetOutputDM(DM dm, DM *odm)
4896: {
4897:   PetscSection   section;
4898:   PetscBool      hasConstraints;

4904:   DMGetDefaultSection(dm, &section);
4905:   PetscSectionHasConstraints(section, &hasConstraints);
4906:   if (!hasConstraints) {
4907:     *odm = dm;
4908:     return(0);
4909:   }
4910:   if (!dm->dmBC) {
4911:     PetscDS      ds;
4912:     PetscSection newSection, gsection;
4913:     PetscSF      sf;

4915:     DMClone(dm, &dm->dmBC);
4916:     DMGetDS(dm, &ds);
4917:     DMSetDS(dm->dmBC, ds);
4918:     PetscSectionClone(section, &newSection);
4919:     DMSetDefaultSection(dm->dmBC, newSection);
4920:     PetscSectionDestroy(&newSection);
4921:     DMGetPointSF(dm->dmBC, &sf);
4922:     PetscSectionCreateGlobalSection(section, sf, PETSC_TRUE, PETSC_FALSE, &gsection);
4923:     DMSetDefaultGlobalSection(dm->dmBC, gsection);
4924:     PetscSectionDestroy(&gsection);
4925:   }
4926:   *odm = dm->dmBC;
4927:   return(0);
4928: }

4932: /*@
4933:   DMGetOutputSequenceNumber - Retrieve the sequence number/value for output

4935:   Input Parameter:
4936: . dm - The original DM

4938:   Output Parameters:
4939: + num - The output sequence number
4940: - val - The output sequence value

4942:   Level: intermediate

4944:   Note: This is intended for output that should appear in sequence, for instance
4945:   a set of timesteps in an HDF5 file, or a set of realizations of a stochastic system.

4947: .seealso: VecView()
4948: @*/
4949: PetscErrorCode DMGetOutputSequenceNumber(DM dm, PetscInt *num, PetscReal *val)
4950: {
4955:   return(0);
4956: }

4960: /*@
4961:   DMSetOutputSequenceNumber - Set the sequence number/value for output

4963:   Input Parameters:
4964: + dm - The original DM
4965: . num - The output sequence number
4966: - val - The output sequence value

4968:   Level: intermediate

4970:   Note: This is intended for output that should appear in sequence, for instance
4971:   a set of timesteps in an HDF5 file, or a set of realizations of a stochastic system.

4973: .seealso: VecView()
4974: @*/
4975: PetscErrorCode DMSetOutputSequenceNumber(DM dm, PetscInt num, PetscReal val)
4976: {
4979:   dm->outputSequenceNum = num;
4980:   dm->outputSequenceVal = val;
4981:   return(0);
4982: }

4986: /*@C
4987:   DMOutputSequenceLoad - Retrieve the sequence value from a Viewer

4989:   Input Parameters:
4990: + dm   - The original DM
4991: . name - The sequence name
4992: - num  - The output sequence number

4994:   Output Parameter:
4995: . val  - The output sequence value

4997:   Level: intermediate

4999:   Note: This is intended for output that should appear in sequence, for instance
5000:   a set of timesteps in an HDF5 file, or a set of realizations of a stochastic system.

5002: .seealso: DMGetOutputSequenceNumber(), DMSetOutputSequenceNumber(), VecView()
5003: @*/
5004: PetscErrorCode DMOutputSequenceLoad(DM dm, PetscViewer viewer, const char *name, PetscInt num, PetscReal *val)
5005: {
5006:   PetscBool      ishdf5;

5013:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);
5014:   if (ishdf5) {
5015: #if defined(PETSC_HAVE_HDF5)
5016:     PetscScalar value;

5018:     DMSequenceLoad_HDF5(dm, name, num, &value, viewer);
5019:     *val = PetscRealPart(value);
5020: #endif
5021:   } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid viewer; open viewer with PetscViewerHDF5Open()");
5022:   return(0);
5023: }

5027: /*@
5028:   DMGetUseNatural - Get the flag for creating a mapping to the natural order on distribution

5030:   Not collective

5032:   Input Parameter:
5033: . dm - The DM

5035:   Output Parameter:
5036: . useNatural - The flag to build the mapping to a natural order during distribution

5038:   Level: beginner

5040: .seealso: DMSetUseNatural(), DMCreate()
5041: @*/
5042: PetscErrorCode DMGetUseNatural(DM dm, PetscBool *useNatural)
5043: {
5047:   *useNatural = dm->useNatural;
5048:   return(0);
5049: }

5053: /*@
5054:   DMSetUseNatural - Set the flag for creating a mapping to the natural order on distribution

5056:   Collective on dm

5058:   Input Parameters:
5059: + dm - The DM
5060: - useNatural - The flag to build the mapping to a natural order during distribution

5062:   Level: beginner

5064: .seealso: DMGetUseNatural(), DMCreate()
5065: @*/
5066: PetscErrorCode DMSetUseNatural(DM dm, PetscBool useNatural)
5067: {
5071:   dm->useNatural = useNatural;
5072:   return(0);
5073: }


5080: /*@C
5081:   DMCreateLabel - Create a label of the given name if it does not already exist

5083:   Not Collective

5085:   Input Parameters:
5086: + dm   - The DM object
5087: - name - The label name

5089:   Level: intermediate

5091: .keywords: mesh
5092: .seealso: DMLabelCreate(), DMHasLabel(), DMGetLabelValue(), DMSetLabelValue(), DMGetStratumIS()
5093: @*/
5094: PetscErrorCode DMCreateLabel(DM dm, const char name[])
5095: {
5096:   DMLabelLink    next  = dm->labels->next;
5097:   PetscBool      flg   = PETSC_FALSE;

5103:   while (next) {
5104:     PetscStrcmp(name, next->label->name, &flg);
5105:     if (flg) break;
5106:     next = next->next;
5107:   }
5108:   if (!flg) {
5109:     DMLabelLink tmpLabel;

5111:     PetscCalloc1(1, &tmpLabel);
5112:     DMLabelCreate(name, &tmpLabel->label);
5113:     tmpLabel->output = PETSC_TRUE;
5114:     tmpLabel->next   = dm->labels->next;
5115:     dm->labels->next = tmpLabel;
5116:   }
5117:   return(0);
5118: }

5122: /*@C
5123:   DMGetLabelValue - Get the value in a Sieve Label for the given point, with 0 as the default

5125:   Not Collective

5127:   Input Parameters:
5128: + dm   - The DM object
5129: . name - The label name
5130: - point - The mesh point

5132:   Output Parameter:
5133: . value - The label value for this point, or -1 if the point is not in the label

5135:   Level: beginner

5137: .keywords: mesh
5138: .seealso: DMLabelGetValue(), DMSetLabelValue(), DMGetStratumIS()
5139: @*/
5140: PetscErrorCode DMGetLabelValue(DM dm, const char name[], PetscInt point, PetscInt *value)
5141: {
5142:   DMLabel        label;

5148:   DMGetLabel(dm, name, &label);
5149:   if (!label) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No label named %s was found", name);
5150:   DMLabelGetValue(label, point, value);
5151:   return(0);
5152: }

5156: /*@C
5157:   DMSetLabelValue - Add a point to a Sieve Label with given value

5159:   Not Collective

5161:   Input Parameters:
5162: + dm   - The DM object
5163: . name - The label name
5164: . point - The mesh point
5165: - value - The label value for this point

5167:   Output Parameter:

5169:   Level: beginner

5171: .keywords: mesh
5172: .seealso: DMLabelSetValue(), DMGetStratumIS(), DMClearLabelValue()
5173: @*/
5174: PetscErrorCode DMSetLabelValue(DM dm, const char name[], PetscInt point, PetscInt value)
5175: {
5176:   DMLabel        label;

5182:   DMGetLabel(dm, name, &label);
5183:   if (!label) {
5184:     DMCreateLabel(dm, name);
5185:     DMGetLabel(dm, name, &label);
5186:   }
5187:   DMLabelSetValue(label, point, value);
5188:   return(0);
5189: }

5193: /*@C
5194:   DMClearLabelValue - Remove a point from a Sieve Label with given value

5196:   Not Collective

5198:   Input Parameters:
5199: + dm   - The DM object
5200: . name - The label name
5201: . point - The mesh point
5202: - value - The label value for this point

5204:   Output Parameter:

5206:   Level: beginner

5208: .keywords: mesh
5209: .seealso: DMLabelClearValue(), DMSetLabelValue(), DMGetStratumIS()
5210: @*/
5211: PetscErrorCode DMClearLabelValue(DM dm, const char name[], PetscInt point, PetscInt value)
5212: {
5213:   DMLabel        label;

5219:   DMGetLabel(dm, name, &label);
5220:   if (!label) return(0);
5221:   DMLabelClearValue(label, point, value);
5222:   return(0);
5223: }

5227: /*@C
5228:   DMGetLabelSize - Get the number of different integer ids in a Label

5230:   Not Collective

5232:   Input Parameters:
5233: + dm   - The DM object
5234: - name - The label name

5236:   Output Parameter:
5237: . size - The number of different integer ids, or 0 if the label does not exist

5239:   Level: beginner

5241: .keywords: mesh
5242: .seealso: DMLabeGetNumValues(), DMSetLabelValue()
5243: @*/
5244: PetscErrorCode DMGetLabelSize(DM dm, const char name[], PetscInt *size)
5245: {
5246:   DMLabel        label;

5253:   DMGetLabel(dm, name, &label);
5254:   *size = 0;
5255:   if (!label) return(0);
5256:   DMLabelGetNumValues(label, size);
5257:   return(0);
5258: }

5262: /*@C
5263:   DMGetLabelIdIS - Get the integer ids in a label

5265:   Not Collective

5267:   Input Parameters:
5268: + mesh - The DM object
5269: - name - The label name

5271:   Output Parameter:
5272: . ids - The integer ids, or NULL if the label does not exist

5274:   Level: beginner

5276: .keywords: mesh
5277: .seealso: DMLabelGetValueIS(), DMGetLabelSize()
5278: @*/
5279: PetscErrorCode DMGetLabelIdIS(DM dm, const char name[], IS *ids)
5280: {
5281:   DMLabel        label;

5288:   DMGetLabel(dm, name, &label);
5289:   *ids = NULL;
5290:   if (!label) return(0);
5291:   DMLabelGetValueIS(label, ids);
5292:   return(0);
5293: }

5297: /*@C
5298:   DMGetStratumSize - Get the number of points in a label stratum

5300:   Not Collective

5302:   Input Parameters:
5303: + dm - The DM object
5304: . name - The label name
5305: - value - The stratum value

5307:   Output Parameter:
5308: . size - The stratum size

5310:   Level: beginner

5312: .keywords: mesh
5313: .seealso: DMLabelGetStratumSize(), DMGetLabelSize(), DMGetLabelIds()
5314: @*/
5315: PetscErrorCode DMGetStratumSize(DM dm, const char name[], PetscInt value, PetscInt *size)
5316: {
5317:   DMLabel        label;

5324:   DMGetLabel(dm, name, &label);
5325:   *size = 0;
5326:   if (!label) return(0);
5327:   DMLabelGetStratumSize(label, value, size);
5328:   return(0);
5329: }

5333: /*@C
5334:   DMGetStratumIS - Get the points in a label stratum

5336:   Not Collective

5338:   Input Parameters:
5339: + dm - The DM object
5340: . name - The label name
5341: - value - The stratum value

5343:   Output Parameter:
5344: . points - The stratum points, or NULL if the label does not exist or does not have that value

5346:   Level: beginner

5348: .keywords: mesh
5349: .seealso: DMLabelGetStratumIS(), DMGetStratumSize()
5350: @*/
5351: PetscErrorCode DMGetStratumIS(DM dm, const char name[], PetscInt value, IS *points)
5352: {
5353:   DMLabel        label;

5360:   DMGetLabel(dm, name, &label);
5361:   *points = NULL;
5362:   if (!label) return(0);
5363:   DMLabelGetStratumIS(label, value, points);
5364:   return(0);
5365: }

5369: /*@C
5370:   DMClearLabelStratum - Remove all points from a stratum from a Sieve Label

5372:   Not Collective

5374:   Input Parameters:
5375: + dm   - The DM object
5376: . name - The label name
5377: - value - The label value for this point

5379:   Output Parameter:

5381:   Level: beginner

5383: .keywords: mesh
5384: .seealso: DMLabelClearStratum(), DMSetLabelValue(), DMGetStratumIS(), DMClearLabelValue()
5385: @*/
5386: PetscErrorCode DMClearLabelStratum(DM dm, const char name[], PetscInt value)
5387: {
5388:   DMLabel        label;

5394:   DMGetLabel(dm, name, &label);
5395:   if (!label) return(0);
5396:   DMLabelClearStratum(label, value);
5397:   return(0);
5398: }

5402: /*@
5403:   DMGetNumLabels - Return the number of labels defined by the mesh

5405:   Not Collective

5407:   Input Parameter:
5408: . dm   - The DM object

5410:   Output Parameter:
5411: . numLabels - the number of Labels

5413:   Level: intermediate

5415: .keywords: mesh
5416: .seealso: DMGetLabelValue(), DMSetLabelValue(), DMGetStratumIS()
5417: @*/
5418: PetscErrorCode DMGetNumLabels(DM dm, PetscInt *numLabels)
5419: {
5420:   DMLabelLink next = dm->labels->next;
5421:   PetscInt  n    = 0;

5426:   while (next) {++n; next = next->next;}
5427:   *numLabels = n;
5428:   return(0);
5429: }

5433: /*@C
5434:   DMGetLabelName - Return the name of nth label

5436:   Not Collective

5438:   Input Parameters:
5439: + dm - The DM object
5440: - n  - the label number

5442:   Output Parameter:
5443: . name - the label name

5445:   Level: intermediate

5447: .keywords: mesh
5448: .seealso: DMGetLabelValue(), DMSetLabelValue(), DMGetStratumIS()
5449: @*/
5450: PetscErrorCode DMGetLabelName(DM dm, PetscInt n, const char **name)
5451: {
5452:   DMLabelLink next = dm->labels->next;
5453:   PetscInt  l    = 0;

5458:   while (next) {
5459:     if (l == n) {
5460:       *name = next->label->name;
5461:       return(0);
5462:     }
5463:     ++l;
5464:     next = next->next;
5465:   }
5466:   SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Label %D does not exist in this DM", n);
5467: }

5471: /*@C
5472:   DMHasLabel - Determine whether the mesh has a label of a given name

5474:   Not Collective

5476:   Input Parameters:
5477: + dm   - The DM object
5478: - name - The label name

5480:   Output Parameter:
5481: . hasLabel - PETSC_TRUE if the label is present

5483:   Level: intermediate

5485: .keywords: mesh
5486: .seealso: DMCreateLabel(), DMGetLabelValue(), DMSetLabelValue(), DMGetStratumIS()
5487: @*/
5488: PetscErrorCode DMHasLabel(DM dm, const char name[], PetscBool *hasLabel)
5489: {
5490:   DMLabelLink    next = dm->labels->next;

5497:   *hasLabel = PETSC_FALSE;
5498:   while (next) {
5499:     PetscStrcmp(name, next->label->name, hasLabel);
5500:     if (*hasLabel) break;
5501:     next = next->next;
5502:   }
5503:   return(0);
5504: }

5508: /*@C
5509:   DMGetLabel - Return the label of a given name, or NULL

5511:   Not Collective

5513:   Input Parameters:
5514: + dm   - The DM object
5515: - name - The label name

5517:   Output Parameter:
5518: . label - The DMLabel, or NULL if the label is absent

5520:   Level: intermediate

5522: .keywords: mesh
5523: .seealso: DMCreateLabel(), DMHasLabel(), DMGetLabelValue(), DMSetLabelValue(), DMGetStratumIS()
5524: @*/
5525: PetscErrorCode DMGetLabel(DM dm, const char name[], DMLabel *label)
5526: {
5527:   DMLabelLink    next = dm->labels->next;
5528:   PetscBool      hasLabel;

5535:   *label = NULL;
5536:   while (next) {
5537:     PetscStrcmp(name, next->label->name, &hasLabel);
5538:     if (hasLabel) {
5539:       *label = next->label;
5540:       break;
5541:     }
5542:     next = next->next;
5543:   }
5544:   return(0);
5545: }

5549: /*@C
5550:   DMGetLabelByNum - Return the nth label

5552:   Not Collective

5554:   Input Parameters:
5555: + dm - The DM object
5556: - n  - the label number

5558:   Output Parameter:
5559: . label - the label

5561:   Level: intermediate

5563: .keywords: mesh
5564: .seealso: DMGetLabelValue(), DMSetLabelValue(), DMGetStratumIS()
5565: @*/
5566: PetscErrorCode DMGetLabelByNum(DM dm, PetscInt n, DMLabel *label)
5567: {
5568:   DMLabelLink next = dm->labels->next;
5569:   PetscInt    l    = 0;

5574:   while (next) {
5575:     if (l == n) {
5576:       *label = next->label;
5577:       return(0);
5578:     }
5579:     ++l;
5580:     next = next->next;
5581:   }
5582:   SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Label %D does not exist in this DM", n);
5583: }

5587: /*@C
5588:   DMAddLabel - Add the label to this mesh

5590:   Not Collective

5592:   Input Parameters:
5593: + dm   - The DM object
5594: - label - The DMLabel

5596:   Level: developer

5598: .keywords: mesh
5599: .seealso: DMCreateLabel(), DMHasLabel(), DMGetLabelValue(), DMSetLabelValue(), DMGetStratumIS()
5600: @*/
5601: PetscErrorCode DMAddLabel(DM dm, DMLabel label)
5602: {
5603:   DMLabelLink    tmpLabel;
5604:   PetscBool      hasLabel;

5609:   DMHasLabel(dm, label->name, &hasLabel);
5610:   if (hasLabel) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Label %s already exists in this DM", label->name);
5611:   PetscCalloc1(1, &tmpLabel);
5612:   tmpLabel->label  = label;
5613:   tmpLabel->output = PETSC_TRUE;
5614:   tmpLabel->next   = dm->labels->next;
5615:   dm->labels->next = tmpLabel;
5616:   return(0);
5617: }

5621: /*@C
5622:   DMRemoveLabel - Remove the label from this mesh

5624:   Not Collective

5626:   Input Parameters:
5627: + dm   - The DM object
5628: - name - The label name

5630:   Output Parameter:
5631: . label - The DMLabel, or NULL if the label is absent

5633:   Level: developer

5635: .keywords: mesh
5636: .seealso: DMCreateLabel(), DMHasLabel(), DMGetLabelValue(), DMSetLabelValue(), DMGetStratumIS()
5637: @*/
5638: PetscErrorCode DMRemoveLabel(DM dm, const char name[], DMLabel *label)
5639: {
5640:   DMLabelLink    next = dm->labels->next;
5641:   DMLabelLink    last = NULL;
5642:   PetscBool      hasLabel;

5647:   DMHasLabel(dm, name, &hasLabel);
5648:   *label = NULL;
5649:   if (!hasLabel) return(0);
5650:   while (next) {
5651:     PetscStrcmp(name, next->label->name, &hasLabel);
5652:     if (hasLabel) {
5653:       if (last) last->next       = next->next;
5654:       else      dm->labels->next = next->next;
5655:       next->next = NULL;
5656:       *label     = next->label;
5657:       PetscStrcmp(name, "depth", &hasLabel);
5658:       if (hasLabel) {
5659:         dm->depthLabel = NULL;
5660:       }
5661:       PetscFree(next);
5662:       break;
5663:     }
5664:     last = next;
5665:     next = next->next;
5666:   }
5667:   return(0);
5668: }

5672: /*@C
5673:   DMGetLabelOutput - Get the output flag for a given label

5675:   Not Collective

5677:   Input Parameters:
5678: + dm   - The DM object
5679: - name - The label name

5681:   Output Parameter:
5682: . output - The flag for output

5684:   Level: developer

5686: .keywords: mesh
5687: .seealso: DMSetLabelOutput(), DMCreateLabel(), DMHasLabel(), DMGetLabelValue(), DMSetLabelValue(), DMGetStratumIS()
5688: @*/
5689: PetscErrorCode DMGetLabelOutput(DM dm, const char name[], PetscBool *output)
5690: {
5691:   DMLabelLink    next = dm->labels->next;

5698:   while (next) {
5699:     PetscBool flg;

5701:     PetscStrcmp(name, next->label->name, &flg);
5702:     if (flg) {*output = next->output; return(0);}
5703:     next = next->next;
5704:   }
5705:   SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "No label named %s was present in this dm", name);
5706: }

5710: /*@C
5711:   DMSetLabelOutput - Set the output flag for a given label

5713:   Not Collective

5715:   Input Parameters:
5716: + dm     - The DM object
5717: . name   - The label name
5718: - output - The flag for output

5720:   Level: developer

5722: .keywords: mesh
5723: .seealso: DMGetLabelOutput(), DMCreateLabel(), DMHasLabel(), DMGetLabelValue(), DMSetLabelValue(), DMGetStratumIS()
5724: @*/
5725: PetscErrorCode DMSetLabelOutput(DM dm, const char name[], PetscBool output)
5726: {
5727:   DMLabelLink    next = dm->labels->next;

5733:   while (next) {
5734:     PetscBool flg;

5736:     PetscStrcmp(name, next->label->name, &flg);
5737:     if (flg) {next->output = output; return(0);}
5738:     next = next->next;
5739:   }
5740:   SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "No label named %s was present in this dm", name);
5741: }


5746: /*@
5747:   DMCopyLabels - Copy labels from one mesh to another with a superset of the points

5749:   Collective on DM

5751:   Input Parameter:
5752: . dmA - The DM object with initial labels

5754:   Output Parameter:
5755: . dmB - The DM object with copied labels

5757:   Level: intermediate

5759:   Note: This is typically used when interpolating or otherwise adding to a mesh

5761: .keywords: mesh
5762: .seealso: DMCopyCoordinates(), DMGetCoordinates(), DMGetCoordinatesLocal(), DMGetCoordinateDM(), DMGetCoordinateSection()
5763: @*/
5764: PetscErrorCode DMCopyLabels(DM dmA, DM dmB)
5765: {
5766:   PetscInt       numLabels, l;

5770:   if (dmA == dmB) return(0);
5771:   DMGetNumLabels(dmA, &numLabels);
5772:   for (l = 0; l < numLabels; ++l) {
5773:     DMLabel     label, labelNew;
5774:     const char *name;
5775:     PetscBool   flg;

5777:     DMGetLabelName(dmA, l, &name);
5778:     PetscStrcmp(name, "depth", &flg);
5779:     if (flg) continue;
5780:     DMGetLabel(dmA, name, &label);
5781:     DMLabelDuplicate(label, &labelNew);
5782:     DMAddLabel(dmB, labelNew);
5783:   }
5784:   return(0);
5785: }

5789: /*@
5790:   DMGetCoarseDM - Get the coarse mesh from which this was obtained by refinement

5792:   Input Parameter:
5793: . dm - The DM object

5795:   Output Parameter:
5796: . cdm - The coarse DM

5798:   Level: intermediate

5800: .seealso: DMSetCoarseDM()
5801: @*/
5802: PetscErrorCode DMGetCoarseDM(DM dm, DM *cdm)
5803: {
5807:   *cdm = dm->coarseMesh;
5808:   return(0);
5809: }

5813: /*@
5814:   DMSetCoarseDM - Set the coarse mesh from which this was obtained by refinement

5816:   Input Parameters:
5817: + dm - The DM object
5818: - cdm - The coarse DM

5820:   Level: intermediate

5822: .seealso: DMGetCoarseDM()
5823: @*/
5824: PetscErrorCode DMSetCoarseDM(DM dm, DM cdm)
5825: {

5831:   PetscObjectReference((PetscObject)cdm);
5832:   DMDestroy(&dm->coarseMesh);
5833:   dm->coarseMesh = cdm;
5834:   return(0);
5835: }

5839: /*@
5840:   DMGetFineDM - Get the fine mesh from which this was obtained by refinement

5842:   Input Parameter:
5843: . dm - The DM object

5845:   Output Parameter:
5846: . fdm - The fine DM

5848:   Level: intermediate

5850: .seealso: DMSetFineDM()
5851: @*/
5852: PetscErrorCode DMGetFineDM(DM dm, DM *fdm)
5853: {
5857:   *fdm = dm->fineMesh;
5858:   return(0);
5859: }

5863: /*@
5864:   DMSetFineDM - Set the fine mesh from which this was obtained by refinement

5866:   Input Parameters:
5867: + dm - The DM object
5868: - fdm - The fine DM

5870:   Level: intermediate

5872: .seealso: DMGetFineDM()
5873: @*/
5874: PetscErrorCode DMSetFineDM(DM dm, DM fdm)
5875: {

5881:   PetscObjectReference((PetscObject)fdm);
5882:   DMDestroy(&dm->fineMesh);
5883:   dm->fineMesh = fdm;
5884:   return(0);
5885: }

5887: /*=== DMBoundary code ===*/

5891: PetscErrorCode DMBoundaryDuplicate(DMBoundaryLinkList bd, DMBoundaryLinkList *boundary)
5892: {
5893:   DMBoundary     b = bd->next, b2, bold = NULL;

5897:   PetscNew(boundary);
5898:   (*boundary)->refct = 1;
5899:   (*boundary)->next = NULL;
5900:   for (; b; b = b->next, bold = b2) {
5901:     PetscNew(&b2);
5902:     PetscStrallocpy(b->name, (char **) &b2->name);
5903:     PetscStrallocpy(b->labelname, (char **) &b2->labelname);
5904:     PetscMalloc1(b->numids, &b2->ids);
5905:     PetscMemcpy(b2->ids, b->ids, b->numids*sizeof(PetscInt));
5906:     PetscMalloc1(b->numcomps, &b2->comps);
5907:     PetscMemcpy(b2->comps, b->comps, b->numcomps*sizeof(PetscInt));
5908:     b2->label     = NULL;
5909:     b2->essential = b->essential;
5910:     b2->field     = b->field;
5911:     b2->numcomps  = b->numcomps;
5912:     b2->func      = b->func;
5913:     b2->numids    = b->numids;
5914:     b2->ctx       = b->ctx;
5915:     b2->next      = NULL;
5916:     if (!(*boundary)->next) (*boundary)->next   = b2;
5917:     if (bold)        bold->next = b2;
5918:   }
5919:   return(0);
5920: }

5924: PetscErrorCode DMBoundaryDestroy(DMBoundaryLinkList *boundary)
5925: {
5926:   DMBoundary     b, next;

5930:   if (!boundary) return(0);
5931:   if (--((*boundary)->refct)) {
5932:     *boundary = NULL;
5933:     return(0);
5934:   }
5935:   b = (*boundary)->next;
5936:   for (; b; b = next) {
5937:     next = b->next;
5938:     PetscFree(b->comps);
5939:     PetscFree(b->ids);
5940:     PetscFree(b->name);
5941:     PetscFree(b->labelname);
5942:     PetscFree(b);
5943:   }
5944:   PetscFree(*boundary);
5945:   return(0);
5946: }

5950: PetscErrorCode DMCopyBoundary(DM dm, DM dmNew)
5951: {
5952:   DMBoundary     b;

5956:   DMBoundaryDestroy(&dmNew->boundary);
5957:   DMBoundaryDuplicate(dm->boundary, &dmNew->boundary);
5958:   for (b = dmNew->boundary->next; b; b = b->next) {
5959:     if (b->labelname) {
5960:       DMGetLabel(dmNew, b->labelname, &b->label);
5961:       if (!b->label) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Label %s does not exist in this DM", b->labelname);
5962:     }
5963:   }
5964:   return(0);
5965: }

5969: /*@C
5970:   DMAddBoundary - Add a boundary condition to the model

5972:   Input Parameters:
5973: + dm          - The mesh object
5974: . isEssential - Flag for an essential (Dirichlet) condition, as opposed to a natural (Neumann) condition
5975: . name        - The BC name
5976: . labelname   - The label defining constrained points
5977: . field       - The field to constrain
5978: . numcomps    - The number of constrained field components
5979: . comps       - An array of constrained component numbers
5980: . bcFunc      - A pointwise function giving boundary values
5981: . numids      - The number of DMLabel ids for constrained points
5982: . ids         - An array of ids for constrained points
5983: - ctx         - An optional user context for bcFunc

5985:   Options Database Keys:
5986: + -bc_<boundary name> <num> - Overrides the boundary ids
5987: - -bc_<boundary name>_comp <num> - Overrides the boundary components

5989:   Level: developer

5991: .seealso: DMGetBoundary()
5992: @*/
5993: PetscErrorCode DMAddBoundary(DM dm, PetscBool isEssential, const char name[], const char labelname[], PetscInt field, PetscInt numcomps, const PetscInt *comps, void (*bcFunc)(), PetscInt numids, const PetscInt *ids, void *ctx)
5994: {
5995:   DMBoundary     b;

6000:   PetscNew(&b);
6001:   PetscStrallocpy(name, (char **) &b->name);
6002:   PetscStrallocpy(labelname, (char **) &b->labelname);
6003:   PetscMalloc1(numcomps, &b->comps);
6004:   if (numcomps) {PetscMemcpy(b->comps, comps, numcomps*sizeof(PetscInt));}
6005:   PetscMalloc1(numids, &b->ids);
6006:   if (numids) {PetscMemcpy(b->ids, ids, numids*sizeof(PetscInt));}
6007:   if (b->labelname) {
6008:     DMGetLabel(dm, b->labelname, &b->label);
6009:     if (!b->label) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Label %s does not exist in this DM", b->labelname);
6010:   }
6011:   b->essential       = isEssential;
6012:   b->field           = field;
6013:   b->numcomps        = numcomps;
6014:   b->func            = bcFunc;
6015:   b->numids          = numids;
6016:   b->ctx             = ctx;
6017:   b->next            = dm->boundary->next;
6018:   dm->boundary->next = b;
6019:   return(0);
6020: }

6024: /*@
6025:   DMGetNumBoundary - Get the number of registered BC

6027:   Input Parameters:
6028: . dm - The mesh object

6030:   Output Parameters:
6031: . numBd - The number of BC

6033:   Level: intermediate

6035: .seealso: DMAddBoundary(), DMGetBoundary()
6036: @*/
6037: PetscErrorCode DMGetNumBoundary(DM dm, PetscInt *numBd)
6038: {
6039:   DMBoundary b = dm->boundary->next;

6044:   *numBd = 0;
6045:   while (b) {++(*numBd); b = b->next;}
6046:   return(0);
6047: }

6051: /*@C
6052:   DMGetBoundary - Add a boundary condition to the model

6054:   Input Parameters:
6055: + dm          - The mesh object
6056: - bd          - The BC number

6058:   Output Parameters:
6059: + isEssential - Flag for an essential (Dirichlet) condition, as opposed to a natural (Neumann) condition
6060: . name        - The BC name
6061: . labelname   - The label defining constrained points
6062: . field       - The field to constrain
6063: . numcomps    - The number of constrained field components
6064: . comps       - An array of constrained component numbers
6065: . bcFunc      - A pointwise function giving boundary values
6066: . numids      - The number of DMLabel ids for constrained points
6067: . ids         - An array of ids for constrained points
6068: - ctx         - An optional user context for bcFunc

6070:   Options Database Keys:
6071: + -bc_<boundary name> <num> - Overrides the boundary ids
6072: - -bc_<boundary name>_comp <num> - Overrides the boundary components

6074:   Level: developer

6076: .seealso: DMAddBoundary()
6077: @*/
6078: PetscErrorCode DMGetBoundary(DM dm, PetscInt bd, PetscBool *isEssential, const char **name, const char **labelname, PetscInt *field, PetscInt *numcomps, const PetscInt **comps, void (**func)(), PetscInt *numids, const PetscInt **ids, void **ctx)
6079: {
6080:   DMBoundary b    = dm->boundary->next;
6081:   PetscInt   n    = 0;

6085:   while (b) {
6086:     if (n == bd) break;
6087:     b = b->next;
6088:     ++n;
6089:   }
6090:   if (!b) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Boundary %d is not in [0, %d)", bd, n);
6091:   if (isEssential) {
6093:     *isEssential = b->essential;
6094:   }
6095:   if (name) {
6097:     *name = b->name;
6098:   }
6099:   if (labelname) {
6101:     *labelname = b->labelname;
6102:   }
6103:   if (field) {
6105:     *field = b->field;
6106:   }
6107:   if (numcomps) {
6109:     *numcomps = b->numcomps;
6110:   }
6111:   if (comps) {
6113:     *comps = b->comps;
6114:   }
6115:   if (func) {
6117:     *func = b->func;
6118:   }
6119:   if (numids) {
6121:     *numids = b->numids;
6122:   }
6123:   if (ids) {
6125:     *ids = b->ids;
6126:   }
6127:   if (ctx) {
6129:     *ctx = b->ctx;
6130:   }
6131:   return(0);
6132: }

6136: PetscErrorCode DMIsBoundaryPoint(DM dm, PetscInt point, PetscBool *isBd)
6137: {
6138:   DMBoundary     b    = dm->boundary->next;

6144:   *isBd = PETSC_FALSE;
6145:   while (b && !(*isBd)) {
6146:     if (b->label) {
6147:       PetscInt i;

6149:       for (i = 0; i < b->numids && !(*isBd); ++i) {
6150:         DMLabelStratumHasPoint(b->label, b->ids[i], point, isBd);
6151:       }
6152:     }
6153:     b = b->next;
6154:   }
6155:   return(0);
6156: }

6160: /*@C
6161:   DMProjectFunction - This projects the given function into the function space provided.

6163:   Input Parameters:
6164: + dm      - The DM
6165: . time    - The time
6166: . funcs   - The coordinate functions to evaluate, one per field
6167: . ctxs    - Optional array of contexts to pass to each coordinate function.  ctxs itself may be null.
6168: - mode    - The insertion mode for values

6170:   Output Parameter:
6171: . X - vector

6173:    Calling sequence of func:
6174: $    func(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar u[], void *ctx);

6176: +  dim - The spatial dimension
6177: .  x   - The coordinates
6178: .  Nf  - The number of fields
6179: .  u   - The output field values
6180: -  ctx - optional user-defined function context

6182:   Level: developer

6184: .seealso: DMComputeL2Diff()
6185: @*/
6186: PetscErrorCode DMProjectFunction(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, InsertMode mode, Vec X)
6187: {
6188:   Vec            localX;

6193:   DMGetLocalVector(dm, &localX);
6194:   DMProjectFunctionLocal(dm, time, funcs, ctxs, mode, localX);
6195:   DMLocalToGlobalBegin(dm, localX, mode, X);
6196:   DMLocalToGlobalEnd(dm, localX, mode, X);
6197:   DMRestoreLocalVector(dm, &localX);
6198:   return(0);
6199: }

6203: PetscErrorCode DMProjectFunctionLocal(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, InsertMode mode, Vec localX)
6204: {

6210:   if (!dm->ops->projectfunctionlocal) SETERRQ1(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"DM type %s does not implemnt DMProjectFunctionLocal",((PetscObject)dm)->type_name);
6211:   (dm->ops->projectfunctionlocal) (dm, time, funcs, ctxs, mode, localX);
6212:   return(0);
6213: }

6217: PetscErrorCode DMProjectFieldLocal(DM dm, Vec localU,
6218:                                    void (**funcs)(PetscInt, PetscInt, PetscInt,
6219:                                                   const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
6220:                                                   const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
6221:                                                   PetscReal, const PetscReal[], PetscScalar[]),
6222:                                    InsertMode mode, Vec localX)
6223: {

6230:   if (!dm->ops->projectfieldlocal) SETERRQ1(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"DM type %s does not implemnt DMProjectFieldLocal",((PetscObject)dm)->type_name);
6231:   (dm->ops->projectfieldlocal) (dm, localU, funcs, mode, localX);
6232:   return(0);
6233: }

6237: PetscErrorCode DMProjectFunctionLabelLocal(DM dm, PetscReal time, DMLabel label, PetscInt numIds, const PetscInt ids[], PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, InsertMode mode, Vec localX)
6238: {

6244:   if (!dm->ops->projectfunctionlabellocal) SETERRQ1(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"DM type %s does not implemnt DMProjectFunctionLabelLocal",((PetscObject)dm)->type_name);
6245:   (dm->ops->projectfunctionlabellocal) (dm, time, label, numIds, ids, funcs, ctxs, mode, localX);
6246:   return(0);
6247: }

6251: /*@C
6252:   DMComputeL2Diff - This function computes the L_2 difference between a function u and an FEM interpolant solution u_h.

6254:   Input Parameters:
6255: + dm    - The DM
6256: . time  - The time
6257: . funcs - The functions to evaluate for each field component
6258: . ctxs  - Optional array of contexts to pass to each function, or NULL.
6259: - X     - The coefficient vector u_h

6261:   Output Parameter:
6262: . diff - The diff ||u - u_h||_2

6264:   Level: developer

6266: .seealso: DMProjectFunction(), DMComputeL2FieldDiff(), DMComputeL2GradientDiff()
6267: @*/
6268: PetscErrorCode DMComputeL2Diff(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, PetscReal *diff)
6269: {

6275:   if (!dm->ops->computel2diff) SETERRQ1(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"DM type %s does not implemnt DMComputeL2Diff",((PetscObject)dm)->type_name);
6276:   (dm->ops->computel2diff)(dm,time,funcs,ctxs,X,diff);
6277:   return(0);
6278: }

6282: /*@C
6283:   DMComputeL2GradientDiff - This function computes the L_2 difference between the gradient of a function u and an FEM interpolant solution grad u_h.

6285:   Input Parameters:
6286: + dm    - The DM
6287: , time  - The time
6288: . funcs - The gradient functions to evaluate for each field component
6289: . ctxs  - Optional array of contexts to pass to each function, or NULL.
6290: . X     - The coefficient vector u_h
6291: - n     - The vector to project along

6293:   Output Parameter:
6294: . diff - The diff ||(grad u - grad u_h) . n||_2

6296:   Level: developer

6298: .seealso: DMProjectFunction(), DMComputeL2Diff()
6299: @*/
6300: PetscErrorCode DMComputeL2GradientDiff(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], const PetscReal[], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, const PetscReal n[], PetscReal *diff)
6301: {

6307:   if (!dm->ops->computel2gradientdiff) SETERRQ1(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"DM type %s does not implement DMComputeL2GradientDiff",((PetscObject)dm)->type_name);
6308:   (dm->ops->computel2gradientdiff)(dm,time,funcs,ctxs,X,n,diff);
6309:   return(0);
6310: }

6314: /*@C
6315:   DMComputeL2FieldDiff - This function computes the L_2 difference between a function u and an FEM interpolant solution u_h, separated into field components.

6317:   Input Parameters:
6318: + dm    - The DM
6319: . time  - The time
6320: . funcs - The functions to evaluate for each field component
6321: . ctxs  - Optional array of contexts to pass to each function, or NULL.
6322: - X     - The coefficient vector u_h

6324:   Output Parameter:
6325: . diff - The array of differences, ||u^f - u^f_h||_2

6327:   Level: developer

6329: .seealso: DMProjectFunction(), DMComputeL2FieldDiff(), DMComputeL2GradientDiff()
6330: @*/
6331: PetscErrorCode DMComputeL2FieldDiff(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, PetscReal diff[])
6332: {

6338:   if (!dm->ops->computel2fielddiff) SETERRQ1(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"DM type %s does not implemnt DMComputeL2FieldDiff",((PetscObject)dm)->type_name);
6339:   (dm->ops->computel2fielddiff)(dm,time,funcs,ctxs,X,diff);
6340:   return(0);
6341: }