Actual source code: section.c

  1: /*
  2:    This file contains routines for basic section object implementation.
  3: */

  5: #include <petsc/private/sectionimpl.h>
  6: #include <petscsf.h>

  8: PetscClassId PETSC_SECTION_CLASSID;

 10: /*@
 11:   PetscSectionCreate - Allocates a `PetscSection` and sets the map contents to the default.

 13:   Collective

 15:   Input Parameters:
 16: + comm - the MPI communicator
 17: - s    - pointer to the section

 19:   Level: beginner

 21:   Notes:
 22:   Typical calling sequence
 23: .vb
 24:        PetscSectionCreate(MPI_Comm,PetscSection *);!
 25:        PetscSectionSetNumFields(PetscSection, numFields);
 26:        PetscSectionSetChart(PetscSection,low,high);
 27:        PetscSectionSetDof(PetscSection,point,numdof);
 28:        PetscSectionSetUp(PetscSection);
 29:        PetscSectionGetOffset(PetscSection,point,PetscInt *);
 30:        PetscSectionDestroy(PetscSection);
 31: .ve

 33:   The `PetscSection` object and methods are intended to be used in the PETSc `Vec` and `Mat` implementations. The indices returned by the `PetscSection` are appropriate for the kind of `Vec` it is associated with. For example, if the vector being indexed is a local vector, we call the section a local section. If the section indexes a global vector, we call it a global section. For parallel vectors, like global vectors, we use negative indices to indicate dofs owned by other processes.

 35: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionSetChart()`, `PetscSectionDestroy()`, `PetscSectionCreateGlobalSection()`
 36: @*/
 37: PetscErrorCode PetscSectionCreate(MPI_Comm comm, PetscSection *s)
 38: {
 39:   PetscFunctionBegin;
 40:   PetscAssertPointer(s, 2);
 41:   PetscCall(ISInitializePackage());

 43:   PetscCall(PetscHeaderCreate(*s, PETSC_SECTION_CLASSID, "PetscSection", "Section", "IS", comm, PetscSectionDestroy, PetscSectionView));
 44:   (*s)->pStart              = -1;
 45:   (*s)->pEnd                = -1;
 46:   (*s)->perm                = NULL;
 47:   (*s)->pointMajor          = PETSC_TRUE;
 48:   (*s)->includesConstraints = PETSC_TRUE;
 49:   (*s)->atlasDof            = NULL;
 50:   (*s)->atlasOff            = NULL;
 51:   (*s)->bc                  = NULL;
 52:   (*s)->bcIndices           = NULL;
 53:   (*s)->setup               = PETSC_FALSE;
 54:   (*s)->numFields           = 0;
 55:   (*s)->fieldNames          = NULL;
 56:   (*s)->field               = NULL;
 57:   (*s)->useFieldOff         = PETSC_FALSE;
 58:   (*s)->compNames           = NULL;
 59:   (*s)->clObj               = NULL;
 60:   (*s)->clHash              = NULL;
 61:   (*s)->clSection           = NULL;
 62:   (*s)->clPoints            = NULL;
 63:   PetscCall(PetscSectionInvalidateMaxDof_Internal(*s));
 64:   PetscFunctionReturn(PETSC_SUCCESS);
 65: }

 67: /*@
 68:   PetscSectionCopy - Creates a shallow (if possible) copy of the `PetscSection`

 70:   Collective

 72:   Input Parameter:
 73: . section - the `PetscSection`

 75:   Output Parameter:
 76: . newSection - the copy

 78:   Level: intermediate

 80:   Developer Notes:
 81:   What exactly does shallow mean in this context?

 83: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreate()`, `PetscSectionDestroy()`
 84: @*/
 85: PetscErrorCode PetscSectionCopy(PetscSection section, PetscSection newSection)
 86: {
 87:   PetscFunctionBegin;
 90:   PetscCall(PetscSectionCopy_Internal(section, newSection, NULL));
 91:   PetscFunctionReturn(PETSC_SUCCESS);
 92: }

 94: PetscErrorCode PetscSectionCopy_Internal(PetscSection section, PetscSection newSection, PetscBT constrained_dofs)
 95: {
 96:   PetscSectionSym sym;
 97:   IS              perm;
 98:   PetscInt        numFields, f, c, pStart, pEnd, p;

100:   PetscFunctionBegin;
103:   PetscCall(PetscSectionReset(newSection));
104:   PetscCall(PetscSectionGetNumFields(section, &numFields));
105:   if (numFields) PetscCall(PetscSectionSetNumFields(newSection, numFields));
106:   for (f = 0; f < numFields; ++f) {
107:     const char *fieldName = NULL, *compName = NULL;
108:     PetscInt    numComp = 0;

110:     PetscCall(PetscSectionGetFieldName(section, f, &fieldName));
111:     PetscCall(PetscSectionSetFieldName(newSection, f, fieldName));
112:     PetscCall(PetscSectionGetFieldComponents(section, f, &numComp));
113:     PetscCall(PetscSectionSetFieldComponents(newSection, f, numComp));
114:     for (c = 0; c < numComp; ++c) {
115:       PetscCall(PetscSectionGetComponentName(section, f, c, &compName));
116:       PetscCall(PetscSectionSetComponentName(newSection, f, c, compName));
117:     }
118:     PetscCall(PetscSectionGetFieldSym(section, f, &sym));
119:     PetscCall(PetscSectionSetFieldSym(newSection, f, sym));
120:   }
121:   PetscCall(PetscSectionGetChart(section, &pStart, &pEnd));
122:   PetscCall(PetscSectionSetChart(newSection, pStart, pEnd));
123:   PetscCall(PetscSectionGetPermutation(section, &perm));
124:   PetscCall(PetscSectionSetPermutation(newSection, perm));
125:   PetscCall(PetscSectionGetSym(section, &sym));
126:   PetscCall(PetscSectionSetSym(newSection, sym));
127:   for (p = pStart; p < pEnd; ++p) {
128:     PetscInt  dof, cdof, fcdof = 0;
129:     PetscBool force_constrained = (PetscBool)(constrained_dofs && PetscBTLookup(constrained_dofs, p - pStart));

131:     PetscCall(PetscSectionGetDof(section, p, &dof));
132:     PetscCall(PetscSectionSetDof(newSection, p, dof));
133:     if (force_constrained) cdof = dof;
134:     else PetscCall(PetscSectionGetConstraintDof(section, p, &cdof));
135:     if (cdof) PetscCall(PetscSectionSetConstraintDof(newSection, p, cdof));
136:     for (f = 0; f < numFields; ++f) {
137:       PetscCall(PetscSectionGetFieldDof(section, p, f, &dof));
138:       PetscCall(PetscSectionSetFieldDof(newSection, p, f, dof));
139:       if (cdof) {
140:         if (force_constrained) fcdof = dof;
141:         else PetscCall(PetscSectionGetFieldConstraintDof(section, p, f, &fcdof));
142:         if (fcdof) PetscCall(PetscSectionSetFieldConstraintDof(newSection, p, f, fcdof));
143:       }
144:     }
145:   }
146:   PetscCall(PetscSectionSetUp(newSection));
147:   for (p = pStart; p < pEnd; ++p) {
148:     PetscInt        off, cdof, fcdof = 0;
149:     const PetscInt *cInd;
150:     PetscBool       force_constrained = (PetscBool)(constrained_dofs && PetscBTLookup(constrained_dofs, p - pStart));

152:     /* Must set offsets in case they do not agree with the prefix sums */
153:     PetscCall(PetscSectionGetOffset(section, p, &off));
154:     PetscCall(PetscSectionSetOffset(newSection, p, off));
155:     PetscCall(PetscSectionGetConstraintDof(newSection, p, &cdof));
156:     if (cdof) {
157:       if (force_constrained) cInd = NULL;
158:       else PetscCall(PetscSectionGetConstraintIndices(section, p, &cInd));
159:       PetscCall(PetscSectionSetConstraintIndices(newSection, p, cInd));
160:       for (f = 0; f < numFields; ++f) {
161:         PetscCall(PetscSectionGetFieldOffset(section, p, f, &off));
162:         PetscCall(PetscSectionSetFieldOffset(newSection, p, f, off));
163:         PetscCall(PetscSectionGetFieldConstraintDof(newSection, p, f, &fcdof));
164:         if (fcdof) {
165:           if (force_constrained) cInd = NULL;
166:           else PetscCall(PetscSectionGetFieldConstraintIndices(section, p, f, &cInd));
167:           PetscCall(PetscSectionSetFieldConstraintIndices(newSection, p, f, cInd));
168:         }
169:       }
170:     }
171:   }
172:   PetscFunctionReturn(PETSC_SUCCESS);
173: }

175: /*@
176:   PetscSectionClone - Creates a shallow (if possible) copy of the `PetscSection`

178:   Collective

180:   Input Parameter:
181: . section - the `PetscSection`

183:   Output Parameter:
184: . newSection - the copy

186:   Level: beginner

188:   Developer Notes:
189:   With standard PETSc terminology this should be called `PetscSectionDuplicate()`

191: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreate()`, `PetscSectionDestroy()`, `PetscSectionCopy()`
192: @*/
193: PetscErrorCode PetscSectionClone(PetscSection section, PetscSection *newSection)
194: {
195:   PetscFunctionBegin;
197:   PetscAssertPointer(newSection, 2);
198:   PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)section), newSection));
199:   PetscCall(PetscSectionCopy(section, *newSection));
200:   PetscFunctionReturn(PETSC_SUCCESS);
201: }

203: /*@
204:   PetscSectionSetFromOptions - sets parameters in a `PetscSection` from the options database

206:   Collective

208:   Input Parameter:
209: . s - the `PetscSection`

211:   Options Database Key:
212: . -petscsection_point_major - `PETSC_TRUE` for point-major order

214:   Level: intermediate

216: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreate()`, `PetscSectionDestroy()`
217: @*/
218: PetscErrorCode PetscSectionSetFromOptions(PetscSection s)
219: {
220:   PetscFunctionBegin;
222:   PetscObjectOptionsBegin((PetscObject)s);
223:   PetscCall(PetscOptionsBool("-petscsection_point_major", "The for ordering, either point major or field major", "PetscSectionSetPointMajor", s->pointMajor, &s->pointMajor, NULL));
224:   /* process any options handlers added with PetscObjectAddOptionsHandler() */
225:   PetscCall(PetscObjectProcessOptionsHandlers((PetscObject)s, PetscOptionsObject));
226:   PetscOptionsEnd();
227:   PetscCall(PetscObjectViewFromOptions((PetscObject)s, NULL, "-petscsection_view"));
228:   PetscFunctionReturn(PETSC_SUCCESS);
229: }

231: /*@
232:   PetscSectionCompare - Compares two sections

234:   Collective

236:   Input Parameters:
237: + s1 - the first `PetscSection`
238: - s2 - the second `PetscSection`

240:   Output Parameter:
241: . congruent - `PETSC_TRUE` if the two sections are congruent, `PETSC_FALSE` otherwise

243:   Level: intermediate

245:   Note:
246:   Field names are disregarded.

248: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreate()`, `PetscSectionCopy()`, `PetscSectionClone()`
249: @*/
250: PetscErrorCode PetscSectionCompare(PetscSection s1, PetscSection s2, PetscBool *congruent)
251: {
252:   PetscInt        pStart, pEnd, nfields, ncdof, nfcdof, p, f, n1, n2;
253:   const PetscInt *idx1, *idx2;
254:   IS              perm1, perm2;
255:   PetscBool       flg;
256:   PetscMPIInt     mflg;

258:   PetscFunctionBegin;
261:   PetscAssertPointer(congruent, 3);
262:   flg = PETSC_FALSE;

264:   PetscCallMPI(MPI_Comm_compare(PetscObjectComm((PetscObject)s1), PetscObjectComm((PetscObject)s2), &mflg));
265:   if (mflg != MPI_CONGRUENT && mflg != MPI_IDENT) {
266:     *congruent = PETSC_FALSE;
267:     PetscFunctionReturn(PETSC_SUCCESS);
268:   }

270:   PetscCall(PetscSectionGetChart(s1, &pStart, &pEnd));
271:   PetscCall(PetscSectionGetChart(s2, &n1, &n2));
272:   if (pStart != n1 || pEnd != n2) goto not_congruent;

274:   PetscCall(PetscSectionGetPermutation(s1, &perm1));
275:   PetscCall(PetscSectionGetPermutation(s2, &perm2));
276:   if (perm1 && perm2) {
277:     PetscCall(ISEqual(perm1, perm2, congruent));
278:     if (!*congruent) goto not_congruent;
279:   } else if (perm1 != perm2) goto not_congruent;

281:   for (p = pStart; p < pEnd; ++p) {
282:     PetscCall(PetscSectionGetOffset(s1, p, &n1));
283:     PetscCall(PetscSectionGetOffset(s2, p, &n2));
284:     if (n1 != n2) goto not_congruent;

286:     PetscCall(PetscSectionGetDof(s1, p, &n1));
287:     PetscCall(PetscSectionGetDof(s2, p, &n2));
288:     if (n1 != n2) goto not_congruent;

290:     PetscCall(PetscSectionGetConstraintDof(s1, p, &ncdof));
291:     PetscCall(PetscSectionGetConstraintDof(s2, p, &n2));
292:     if (ncdof != n2) goto not_congruent;

294:     PetscCall(PetscSectionGetConstraintIndices(s1, p, &idx1));
295:     PetscCall(PetscSectionGetConstraintIndices(s2, p, &idx2));
296:     PetscCall(PetscArraycmp(idx1, idx2, ncdof, congruent));
297:     if (!*congruent) goto not_congruent;
298:   }

300:   PetscCall(PetscSectionGetNumFields(s1, &nfields));
301:   PetscCall(PetscSectionGetNumFields(s2, &n2));
302:   if (nfields != n2) goto not_congruent;

304:   for (f = 0; f < nfields; ++f) {
305:     PetscCall(PetscSectionGetFieldComponents(s1, f, &n1));
306:     PetscCall(PetscSectionGetFieldComponents(s2, f, &n2));
307:     if (n1 != n2) goto not_congruent;

309:     for (p = pStart; p < pEnd; ++p) {
310:       PetscCall(PetscSectionGetFieldOffset(s1, p, f, &n1));
311:       PetscCall(PetscSectionGetFieldOffset(s2, p, f, &n2));
312:       if (n1 != n2) goto not_congruent;

314:       PetscCall(PetscSectionGetFieldDof(s1, p, f, &n1));
315:       PetscCall(PetscSectionGetFieldDof(s2, p, f, &n2));
316:       if (n1 != n2) goto not_congruent;

318:       PetscCall(PetscSectionGetFieldConstraintDof(s1, p, f, &nfcdof));
319:       PetscCall(PetscSectionGetFieldConstraintDof(s2, p, f, &n2));
320:       if (nfcdof != n2) goto not_congruent;

322:       PetscCall(PetscSectionGetFieldConstraintIndices(s1, p, f, &idx1));
323:       PetscCall(PetscSectionGetFieldConstraintIndices(s2, p, f, &idx2));
324:       PetscCall(PetscArraycmp(idx1, idx2, nfcdof, congruent));
325:       if (!*congruent) goto not_congruent;
326:     }
327:   }

329:   flg = PETSC_TRUE;
330: not_congruent:
331:   PetscCallMPI(MPIU_Allreduce(&flg, congruent, 1, MPIU_BOOL, MPI_LAND, PetscObjectComm((PetscObject)s1)));
332:   PetscFunctionReturn(PETSC_SUCCESS);
333: }

335: /*@
336:   PetscSectionGetNumFields - Returns the number of fields in a `PetscSection`, or 0 if no fields were defined.

338:   Not Collective

340:   Input Parameter:
341: . s - the `PetscSection`

343:   Output Parameter:
344: . numFields - the number of fields defined, or 0 if none were defined

346:   Level: intermediate

348: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionSetNumFields()`
349: @*/
350: PetscErrorCode PetscSectionGetNumFields(PetscSection s, PetscInt *numFields)
351: {
352:   PetscFunctionBegin;
354:   PetscAssertPointer(numFields, 2);
355:   *numFields = s->numFields;
356:   PetscFunctionReturn(PETSC_SUCCESS);
357: }

359: /*@
360:   PetscSectionSetNumFields - Sets the number of fields in a `PetscSection`

362:   Not Collective

364:   Input Parameters:
365: + s         - the `PetscSection`
366: - numFields - the number of fields

368:   Level: intermediate

370:   Notes:
371:   Calling this destroys all the information in the `PetscSection` including the chart.

373:   You must call `PetscSectionSetChart()` after calling this.

375: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetNumFields()`, `PetscSectionSetChart()`, `PetscSectionReset()`
376: @*/
377: PetscErrorCode PetscSectionSetNumFields(PetscSection s, PetscInt numFields)
378: {
379:   PetscInt f;

381:   PetscFunctionBegin;
383:   PetscCheck(numFields > 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "The number of fields %" PetscInt_FMT " must be positive", numFields);
384:   PetscCall(PetscSectionReset(s));

386:   s->numFields = numFields;
387:   PetscCall(PetscMalloc1(s->numFields, &s->numFieldComponents));
388:   PetscCall(PetscMalloc1(s->numFields, &s->fieldNames));
389:   PetscCall(PetscMalloc1(s->numFields, &s->compNames));
390:   PetscCall(PetscMalloc1(s->numFields, &s->field));
391:   for (f = 0; f < s->numFields; ++f) {
392:     char name[64];

394:     s->numFieldComponents[f] = 1;

396:     PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)s), &s->field[f]));
397:     PetscCall(PetscSNPrintf(name, 64, "Field_%" PetscInt_FMT, f));
398:     PetscCall(PetscStrallocpy(name, &s->fieldNames[f]));
399:     PetscCall(PetscSNPrintf(name, 64, "Component_0"));
400:     PetscCall(PetscMalloc1(s->numFieldComponents[f], &s->compNames[f]));
401:     PetscCall(PetscStrallocpy(name, &s->compNames[f][0]));
402:   }
403:   PetscFunctionReturn(PETSC_SUCCESS);
404: }

406: /*@
407:   PetscSectionGetFieldName - Returns the name of a field in the `PetscSection`

409:   Not Collective

411:   Input Parameters:
412: + s     - the `PetscSection`
413: - field - the field number

415:   Output Parameter:
416: . fieldName - the field name

418:   Level: intermediate

420:   Note:
421:   Will error if the field number is out of range

423: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionSetFieldName()`, `PetscSectionSetNumFields()`, `PetscSectionGetNumFields()`
424: @*/
425: PetscErrorCode PetscSectionGetFieldName(PetscSection s, PetscInt field, const char *fieldName[])
426: {
427:   PetscFunctionBegin;
429:   PetscAssertPointer(fieldName, 3);
430:   PetscSectionCheckValidField(field, s->numFields);
431:   *fieldName = s->fieldNames[field];
432:   PetscFunctionReturn(PETSC_SUCCESS);
433: }

435: /*@
436:   PetscSectionSetFieldName - Sets the name of a field in the `PetscSection`

438:   Not Collective

440:   Input Parameters:
441: + s         - the `PetscSection`
442: . field     - the field number
443: - fieldName - the field name

445:   Level: intermediate

447:   Note:
448:   Will error if the field number is out of range

450: .seealso: [PetscSection](ch_petscsection), `PetscSectionGetFieldName()`, `PetscSectionSetNumFields()`, `PetscSectionGetNumFields()`
451: @*/
452: PetscErrorCode PetscSectionSetFieldName(PetscSection s, PetscInt field, const char fieldName[])
453: {
454:   PetscFunctionBegin;
456:   if (fieldName) PetscAssertPointer(fieldName, 3);
457:   PetscSectionCheckValidField(field, s->numFields);
458:   PetscCall(PetscFree(s->fieldNames[field]));
459:   PetscCall(PetscStrallocpy(fieldName, &s->fieldNames[field]));
460:   PetscFunctionReturn(PETSC_SUCCESS);
461: }

463: /*@
464:   PetscSectionGetComponentName - Gets the name of a field component in the `PetscSection`

466:   Not Collective

468:   Input Parameters:
469: + s     - the `PetscSection`
470: . field - the field number
471: - comp  - the component number

473:   Output Parameter:
474: . compName - the component name

476:   Level: intermediate

478:   Note:
479:   Will error if the field or component number do not exist

481:   Developer Notes:
482:   The function name should have Field in it since they are field components.

484: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetFieldName()`, `PetscSectionSetNumFields()`, `PetscSectionGetNumFields()`,
485:           `PetscSectionSetComponentName()`, `PetscSectionSetFieldName()`, `PetscSectionGetFieldComponents()`, `PetscSectionSetFieldComponents()`
486: @*/
487: PetscErrorCode PetscSectionGetComponentName(PetscSection s, PetscInt field, PetscInt comp, const char *compName[])
488: {
489:   PetscFunctionBegin;
491:   PetscAssertPointer(compName, 4);
492:   PetscSectionCheckValidField(field, s->numFields);
493:   PetscSectionCheckValidFieldComponent(comp, s->numFieldComponents[field]);
494:   *compName = s->compNames[field][comp];
495:   PetscFunctionReturn(PETSC_SUCCESS);
496: }

498: /*@
499:   PetscSectionSetComponentName - Sets the name of a field component in the `PetscSection`

501:   Not Collective

503:   Input Parameters:
504: + s        - the `PetscSection`
505: . field    - the field number
506: . comp     - the component number
507: - compName - the component name

509:   Level: advanced

511:   Note:
512:   Will error if the field or component number do not exist

514:   Developer Notes:
515:   The function name should have Field in it since they are field components.

517: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetComponentName()`, `PetscSectionSetNumFields()`, `PetscSectionGetNumFields()`,
518:           `PetscSectionSetFieldName()`, `PetscSectionGetFieldComponents()`, `PetscSectionSetFieldComponents()`
519: @*/
520: PetscErrorCode PetscSectionSetComponentName(PetscSection s, PetscInt field, PetscInt comp, const char compName[])
521: {
522:   PetscFunctionBegin;
524:   if (compName) PetscAssertPointer(compName, 4);
525:   PetscSectionCheckValidField(field, s->numFields);
526:   PetscSectionCheckValidFieldComponent(comp, s->numFieldComponents[field]);
527:   PetscCall(PetscFree(s->compNames[field][comp]));
528:   PetscCall(PetscStrallocpy(compName, &s->compNames[field][comp]));
529:   PetscFunctionReturn(PETSC_SUCCESS);
530: }

532: /*@
533:   PetscSectionGetFieldComponents - Returns the number of field components for the given field.

535:   Not Collective

537:   Input Parameters:
538: + s     - the `PetscSection`
539: - field - the field number

541:   Output Parameter:
542: . numComp - the number of field components

544:   Level: advanced

546:   Developer Notes:
547:   This function is misnamed. There is a Num in `PetscSectionGetNumFields()` but not in this name

549: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionSetFieldComponents()`, `PetscSectionGetNumFields()`,
550:           `PetscSectionSetComponentName()`, `PetscSectionGetComponentName()`
551: @*/
552: PetscErrorCode PetscSectionGetFieldComponents(PetscSection s, PetscInt field, PetscInt *numComp)
553: {
554:   PetscFunctionBegin;
556:   PetscAssertPointer(numComp, 3);
557:   PetscSectionCheckValidField(field, s->numFields);
558:   *numComp = s->numFieldComponents[field];
559:   PetscFunctionReturn(PETSC_SUCCESS);
560: }

562: /*@
563:   PetscSectionSetFieldComponents - Sets the number of field components for the given field.

565:   Not Collective

567:   Input Parameters:
568: + s       - the `PetscSection`
569: . field   - the field number
570: - numComp - the number of field components

572:   Level: advanced

574:   Note:
575:   This number can be different than the values set with `PetscSectionSetFieldDof()`. It can be used to indicate the number of
576:   components in the field of the underlying physical model which may be different than the number of degrees of freedom needed
577:   at a point in a discretization. For example, if in three dimensions the field is velocity, it will have 3 components, u, v, and w but
578:   an face based model for velocity (where the velocity normal to the face is stored) there is only 1 dof for each face point.

580:   The value set with this function are not needed or used in `PetscSectionSetUp()`.

582:   Developer Notes:
583:   This function is misnamed. There is a Num in `PetscSectionSetNumFields()` but not in this name

585: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetFieldComponents()`, `PetscSectionSetComponentName()`,
586:           `PetscSectionGetComponentName()`, `PetscSectionGetNumFields()`
587: @*/
588: PetscErrorCode PetscSectionSetFieldComponents(PetscSection s, PetscInt field, PetscInt numComp)
589: {
590:   PetscInt c;

592:   PetscFunctionBegin;
594:   PetscSectionCheckValidField(field, s->numFields);
595:   if (s->compNames) {
596:     for (c = 0; c < s->numFieldComponents[field]; ++c) PetscCall(PetscFree(s->compNames[field][c]));
597:     PetscCall(PetscFree(s->compNames[field]));
598:   }

600:   s->numFieldComponents[field] = numComp;
601:   if (numComp) {
602:     PetscCall(PetscMalloc1(numComp, &s->compNames[field]));
603:     for (c = 0; c < numComp; ++c) {
604:       char name[64];

606:       PetscCall(PetscSNPrintf(name, 64, "%" PetscInt_FMT, c));
607:       PetscCall(PetscStrallocpy(name, &s->compNames[field][c]));
608:     }
609:   }
610:   PetscFunctionReturn(PETSC_SUCCESS);
611: }

613: /*@
614:   PetscSectionGetChart - Returns the range [`pStart`, `pEnd`) in which points (indices) lie for this `PetscSection` on this MPI process

616:   Not Collective

618:   Input Parameter:
619: . s - the `PetscSection`

621:   Output Parameters:
622: + pStart - the first point
623: - pEnd   - one past the last point

625:   Level: intermediate

627: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionSetChart()`, `PetscSectionCreate()`
628: @*/
629: PetscErrorCode PetscSectionGetChart(PetscSection s, PetscInt *pStart, PetscInt *pEnd)
630: {
631:   PetscFunctionBegin;
633:   if (pStart) *pStart = s->pStart;
634:   if (pEnd) *pEnd = s->pEnd;
635:   PetscFunctionReturn(PETSC_SUCCESS);
636: }

638: /*@
639:   PetscSectionSetChart - Sets the range [`pStart`, `pEnd`) in which points (indices) lie for this `PetscSection` on this MPI process

641:   Not Collective

643:   Input Parameters:
644: + s      - the `PetscSection`
645: . pStart - the first point
646: - pEnd   - one past the last point, `pStart` $ \le $ `pEnd`

648:   Level: intermediate

650:   Notes:
651:   The charts on different MPI processes may (and often do) overlap

653:   If you intend to use `PetscSectionSetNumFields()` it must be called before this call.

655:   The chart for all fields created with `PetscSectionSetNumFields()` is the same as this chart.

657: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetChart()`, `PetscSectionCreate()`, `PetscSectionSetNumFields()`
658: @*/
659: PetscErrorCode PetscSectionSetChart(PetscSection s, PetscInt pStart, PetscInt pEnd)
660: {
661:   PetscInt f;

663:   PetscFunctionBegin;
665:   PetscCheck(pEnd >= pStart, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Chart pEnd %" PetscInt_FMT " cannot be smaller than chart pStart %" PetscInt_FMT, pEnd, pStart);
666:   if (pStart == s->pStart && pEnd == s->pEnd) PetscFunctionReturn(PETSC_SUCCESS);
667:   /* Cannot Reset() because it destroys field information */
668:   s->setup = PETSC_FALSE;
669:   PetscCall(PetscSectionDestroy(&s->bc));
670:   PetscCall(PetscFree(s->bcIndices));
671:   PetscCall(PetscFree2(s->atlasDof, s->atlasOff));

673:   s->pStart = pStart;
674:   s->pEnd   = pEnd;
675:   PetscCall(PetscMalloc2(pEnd - pStart, &s->atlasDof, pEnd - pStart, &s->atlasOff));
676:   PetscCall(PetscArrayzero(s->atlasDof, pEnd - pStart));
677:   for (f = 0; f < s->numFields; ++f) PetscCall(PetscSectionSetChart(s->field[f], pStart, pEnd));
678:   PetscFunctionReturn(PETSC_SUCCESS);
679: }

681: /*@
682:   PetscSectionGetPermutation - Returns the permutation of [0, `pEnd` - `pStart`) or `NULL` that was set with `PetscSectionSetPermutation()`

684:   Not Collective

686:   Input Parameter:
687: . s - the `PetscSection`

689:   Output Parameter:
690: . perm - The permutation as an `IS`

692:   Level: intermediate

694: .seealso: [](sec_scatter), `IS`, `PetscSection`, `PetscSectionSetPermutation()`, `PetscSectionCreate()`
695: @*/
696: PetscErrorCode PetscSectionGetPermutation(PetscSection s, IS *perm)
697: {
698:   PetscFunctionBegin;
700:   if (perm) {
701:     PetscAssertPointer(perm, 2);
702:     *perm = s->perm;
703:   }
704:   PetscFunctionReturn(PETSC_SUCCESS);
705: }

707: /*@
708:   PetscSectionSetPermutation - Sets a permutation of the chart for this section, [0, `pEnd` - `pStart`), which determines the order to store the `PetscSection` information

710:   Not Collective

712:   Input Parameters:
713: + s    - the `PetscSection`
714: - perm - the permutation of points

716:   Level: intermediate

718:   Notes:
719:   The permutation must be provided before `PetscSectionSetUp()`.

721:   The data in the `PetscSection` are permuted but the access via `PetscSectionGetFieldOffset()` and `PetscSectionGetOffset()` is not changed

723:   Compare to `PetscSectionPermute()`

725: .seealso: [](sec_scatter), `IS`, `PetscSection`, `PetscSectionSetUp()`, `PetscSectionGetPermutation()`, `PetscSectionPermute()`, `PetscSectionCreate()`
726: @*/
727: PetscErrorCode PetscSectionSetPermutation(PetscSection s, IS perm)
728: {
729:   PetscFunctionBegin;
732:   PetscCheck(!s->setup, PetscObjectComm((PetscObject)s), PETSC_ERR_ARG_WRONGSTATE, "Cannot set a permutation after the section is setup");
733:   if (s->perm != perm) {
734:     PetscCall(ISDestroy(&s->perm));
735:     if (perm) {
736:       s->perm = perm;
737:       PetscCall(PetscObjectReference((PetscObject)s->perm));
738:     }
739:   }
740:   PetscFunctionReturn(PETSC_SUCCESS);
741: }

743: /*@C
744:   PetscSectionGetBlockStarts - Returns a table indicating which points start new blocks

746:   Not Collective, No Fortran Support

748:   Input Parameter:
749: . s - the `PetscSection`

751:   Output Parameter:
752: . blockStarts - The `PetscBT` with a 1 for each point that begins a block

754:   Notes:
755:   The table is on [0, `pEnd` - `pStart`).

757:   This information is used by `DMCreateMatrix()` to create a variable block size description which is set using `MatSetVariableBlockSizes()`.

759:   Level: intermediate

761: .seealso: [](sec_scatter), `IS`, `PetscSection`, `PetscSectionSetBlockStarts()`, `PetscSectionCreate()`, `DMCreateMatrix()`, `MatSetVariableBlockSizes()`
762: @*/
763: PetscErrorCode PetscSectionGetBlockStarts(PetscSection s, PetscBT *blockStarts)
764: {
765:   PetscFunctionBegin;
767:   if (blockStarts) {
768:     PetscAssertPointer(blockStarts, 2);
769:     *blockStarts = s->blockStarts;
770:   }
771:   PetscFunctionReturn(PETSC_SUCCESS);
772: }

774: /*@C
775:   PetscSectionSetBlockStarts - Sets a table indicating which points start new blocks

777:   Not Collective, No Fortran Support

779:   Input Parameters:
780: + s           - the `PetscSection`
781: - blockStarts - The `PetscBT` with a 1 for each point that begins a block

783:   Level: intermediate

785:   Notes:
786:   The table is on [0, `pEnd` - `pStart`). PETSc takes ownership of the `PetscBT` when it is passed in and will destroy it. The user should not destroy it.

788:   This information is used by `DMCreateMatrix()` to create a variable block size description which is set using `MatSetVariableBlockSizes()`.

790: .seealso: [](sec_scatter), `IS`, `PetscSection`, `PetscSectionGetBlockStarts()`, `PetscSectionCreate()`, `DMCreateMatrix()`, `MatSetVariableBlockSizes()`
791: @*/
792: PetscErrorCode PetscSectionSetBlockStarts(PetscSection s, PetscBT blockStarts)
793: {
794:   PetscFunctionBegin;
796:   if (s->blockStarts != blockStarts) {
797:     PetscCall(PetscBTDestroy(&s->blockStarts));
798:     s->blockStarts = blockStarts;
799:   }
800:   PetscFunctionReturn(PETSC_SUCCESS);
801: }

803: /*@
804:   PetscSectionGetPointMajor - Returns the flag for dof ordering, `PETSC_TRUE` if it is point major, `PETSC_FALSE` if it is field major

806:   Not Collective

808:   Input Parameter:
809: . s - the `PetscSection`

811:   Output Parameter:
812: . pm - the flag for point major ordering

814:   Level: intermediate

816: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionSetPointMajor()`
817: @*/
818: PetscErrorCode PetscSectionGetPointMajor(PetscSection s, PetscBool *pm)
819: {
820:   PetscFunctionBegin;
822:   PetscAssertPointer(pm, 2);
823:   *pm = s->pointMajor;
824:   PetscFunctionReturn(PETSC_SUCCESS);
825: }

827: /*@
828:   PetscSectionSetPointMajor - Sets the flag for dof ordering, `PETSC_TRUE` for point major, otherwise it will be field major

830:   Not Collective

832:   Input Parameters:
833: + s  - the `PetscSection`
834: - pm - the flag for point major ordering

836:   Level: intermediate

838:   Note:
839:   Field-major order is not recommended unless you are managing the entire problem yourself, since many higher-level functions in PETSc depend on point-major order.

841:   Point major order means the degrees of freedom are stored as follows
842: .vb
843:     all the degrees of freedom for each point are stored contiguously, one point after another (respecting a permutation set with `PetscSectionSetPermutation()`)
844:     for each point
845:        the degrees of freedom for each field (starting with the unnamed default field) are listed in order by field
846: .ve

848:   Field major order means the degrees of freedom are stored as follows
849: .vb
850:     all degrees of freedom for each field (including the unnamed default field) are stored contiguously, one field after another
851:     for each field (started with unnamed default field)
852:       the degrees of freedom for each point are listed in order by point (respecting a permutation set with `PetscSectionSetPermutation()`)
853: .ve

855: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetPointMajor()`, `PetscSectionSetPermutation()`
856: @*/
857: PetscErrorCode PetscSectionSetPointMajor(PetscSection s, PetscBool pm)
858: {
859:   PetscFunctionBegin;
861:   PetscCheck(!s->setup, PetscObjectComm((PetscObject)s), PETSC_ERR_ARG_WRONGSTATE, "Cannot set the dof ordering after the section is setup");
862:   s->pointMajor = pm;
863:   PetscFunctionReturn(PETSC_SUCCESS);
864: }

866: /*@
867:   PetscSectionGetIncludesConstraints - Returns the flag indicating if constrained dofs were included when computing offsets in the `PetscSection`.
868:   The value is set with `PetscSectionSetIncludesConstraints()`

870:   Not Collective

872:   Input Parameter:
873: . s - the `PetscSection`

875:   Output Parameter:
876: . includesConstraints - the flag indicating if constrained dofs were included when computing offsets

878:   Level: intermediate

880: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionSetIncludesConstraints()`
881: @*/
882: PetscErrorCode PetscSectionGetIncludesConstraints(PetscSection s, PetscBool *includesConstraints)
883: {
884:   PetscFunctionBegin;
886:   PetscAssertPointer(includesConstraints, 2);
887:   *includesConstraints = s->includesConstraints;
888:   PetscFunctionReturn(PETSC_SUCCESS);
889: }

891: /*@
892:   PetscSectionSetIncludesConstraints - Sets the flag indicating if constrained dofs are to be included when computing offsets

894:   Not Collective

896:   Input Parameters:
897: + s                   - the `PetscSection`
898: - includesConstraints - the flag indicating if constrained dofs are to be included when computing offsets

900:   Level: intermediate

902: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetIncludesConstraints()`
903: @*/
904: PetscErrorCode PetscSectionSetIncludesConstraints(PetscSection s, PetscBool includesConstraints)
905: {
906:   PetscFunctionBegin;
908:   PetscCheck(!s->setup, PetscObjectComm((PetscObject)s), PETSC_ERR_ARG_WRONGSTATE, "Cannot set includesConstraints after the section is set up");
909:   s->includesConstraints = includesConstraints;
910:   PetscFunctionReturn(PETSC_SUCCESS);
911: }

913: /*@
914:   PetscSectionGetDof - Return the total number of degrees of freedom associated with a given point.

916:   Not Collective

918:   Input Parameters:
919: + s     - the `PetscSection`
920: - point - the point

922:   Output Parameter:
923: . numDof - the number of dof

925:   Level: intermediate

927:   Notes:
928:   In a global section, this size will be negative for points not owned by this process.

930:   This number is for the unnamed default field at the given point plus all degrees of freedom associated with all fields at that point

932: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionSetDof()`, `PetscSectionCreate()`
933: @*/
934: PetscErrorCode PetscSectionGetDof(PetscSection s, PetscInt point, PetscInt *numDof)
935: {
936:   PetscFunctionBeginHot;
938:   PetscAssertPointer(numDof, 3);
939:   PetscAssert(point >= s->pStart && point < s->pEnd, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Section point %" PetscInt_FMT " should be in [%" PetscInt_FMT ", %" PetscInt_FMT ")", point, s->pStart, s->pEnd);
940:   *numDof = s->atlasDof[point - s->pStart];
941:   PetscFunctionReturn(PETSC_SUCCESS);
942: }

944: /*@
945:   PetscSectionSetDof - Sets the total number of degrees of freedom associated with a given point.

947:   Not Collective

949:   Input Parameters:
950: + s      - the `PetscSection`
951: . point  - the point
952: - numDof - the number of dof, these values may be negative -(dof+1) to indicate they are off process

954:   Level: intermediate

956:   Note:
957:   This number is for the unnamed default field at the given point plus all degrees of freedom associated with all fields at that point

959: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetDof()`, `PetscSectionAddDof()`, `PetscSectionCreate()`
960: @*/
961: PetscErrorCode PetscSectionSetDof(PetscSection s, PetscInt point, PetscInt numDof)
962: {
963:   PetscFunctionBegin;
965:   PetscAssert(point >= s->pStart && point < s->pEnd, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Section point %" PetscInt_FMT " should be in [%" PetscInt_FMT ", %" PetscInt_FMT ")", point, s->pStart, s->pEnd);
966:   s->atlasDof[point - s->pStart] = numDof;
967:   PetscCall(PetscSectionInvalidateMaxDof_Internal(s));
968:   PetscFunctionReturn(PETSC_SUCCESS);
969: }

971: /*@
972:   PetscSectionAddDof - Adds to the total number of degrees of freedom associated with a given point.

974:   Not Collective

976:   Input Parameters:
977: + s      - the `PetscSection`
978: . point  - the point
979: - numDof - the number of additional dof

981:   Level: intermediate

983:   Note:
984:   This number is for the unnamed default field at the given point plus all degrees of freedom associated with all fields at that point

986: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetDof()`, `PetscSectionSetDof()`, `PetscSectionCreate()`
987: @*/
988: PetscErrorCode PetscSectionAddDof(PetscSection s, PetscInt point, PetscInt numDof)
989: {
990:   PetscFunctionBeginHot;
992:   PetscAssert(point >= s->pStart && point < s->pEnd, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Section point %" PetscInt_FMT " should be in [%" PetscInt_FMT ", %" PetscInt_FMT ")", point, s->pStart, s->pEnd);
993:   PetscCheck(numDof >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "numDof %" PetscInt_FMT " should not be negative", numDof);
994:   s->atlasDof[point - s->pStart] += numDof;
995:   PetscCall(PetscSectionInvalidateMaxDof_Internal(s));
996:   PetscFunctionReturn(PETSC_SUCCESS);
997: }

999: /*@
1000:   PetscSectionGetFieldDof - Return the number of degrees of freedom associated with a field on a given point.

1002:   Not Collective

1004:   Input Parameters:
1005: + s     - the `PetscSection`
1006: . point - the point
1007: - field - the field

1009:   Output Parameter:
1010: . numDof - the number of dof

1012:   Level: intermediate

1014: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionSetFieldDof()`, `PetscSectionCreate()`
1015: @*/
1016: PetscErrorCode PetscSectionGetFieldDof(PetscSection s, PetscInt point, PetscInt field, PetscInt *numDof)
1017: {
1018:   PetscFunctionBegin;
1020:   PetscAssertPointer(numDof, 4);
1021:   PetscSectionCheckValidField(field, s->numFields);
1022:   PetscCall(PetscSectionGetDof(s->field[field], point, numDof));
1023:   PetscFunctionReturn(PETSC_SUCCESS);
1024: }

1026: /*@
1027:   PetscSectionSetFieldDof - Sets the number of degrees of freedom associated with a field on a given point.

1029:   Not Collective

1031:   Input Parameters:
1032: + s      - the `PetscSection`
1033: . point  - the point
1034: . field  - the field
1035: - numDof - the number of dof, these values may be negative -(dof+1) to indicate they are off process

1037:   Level: intermediate

1039:   Note:
1040:   When setting the number of dof for a field at a point one must also ensure the count of the total number of dof at the point (summed over
1041:   the fields and the unnamed default field) is correct by also calling `PetscSectionAddDof()` or `PetscSectionSetDof()`

1043:   This is equivalent to
1044: .vb
1045:      PetscSection fs;
1046:      PetscSectionGetField(s,field,&fs)
1047:      PetscSectionSetDof(fs,numDof)
1048: .ve

1050: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetFieldDof()`, `PetscSectionCreate()`, `PetscSectionAddDof()`, `PetscSectionSetDof()`
1051: @*/
1052: PetscErrorCode PetscSectionSetFieldDof(PetscSection s, PetscInt point, PetscInt field, PetscInt numDof)
1053: {
1054:   PetscFunctionBegin;
1056:   PetscSectionCheckValidField(field, s->numFields);
1057:   PetscCall(PetscSectionSetDof(s->field[field], point, numDof));
1058:   PetscFunctionReturn(PETSC_SUCCESS);
1059: }

1061: /*@
1062:   PetscSectionAddFieldDof - Adds a number of degrees of freedom associated with a field on a given point.

1064:   Not Collective

1066:   Input Parameters:
1067: + s      - the `PetscSection`
1068: . point  - the point
1069: . field  - the field
1070: - numDof - the number of dof

1072:   Level: intermediate

1074:   Notes:
1075:   When adding to the number of dof for a field at a point one must also ensure the count of the total number of dof at the point (summed over
1076:   the fields and the unnamed default field) is correct by also calling `PetscSectionAddDof()` or `PetscSectionSetDof()`

1078:   This is equivalent to
1079: .vb
1080:      PetscSection fs;
1081:      PetscSectionGetField(s,field,&fs)
1082:      PetscSectionAddDof(fs,numDof)
1083: .ve

1085: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionSetFieldDof()`, `PetscSectionGetFieldDof()`, `PetscSectionCreate()`
1086: @*/
1087: PetscErrorCode PetscSectionAddFieldDof(PetscSection s, PetscInt point, PetscInt field, PetscInt numDof)
1088: {
1089:   PetscFunctionBegin;
1091:   PetscSectionCheckValidField(field, s->numFields);
1092:   PetscCall(PetscSectionAddDof(s->field[field], point, numDof));
1093:   PetscFunctionReturn(PETSC_SUCCESS);
1094: }

1096: /*@
1097:   PetscSectionGetConstraintDof - Return the number of constrained degrees of freedom associated with a given point.

1099:   Not Collective

1101:   Input Parameters:
1102: + s     - the `PetscSection`
1103: - point - the point

1105:   Output Parameter:
1106: . numDof - the number of dof which are fixed by constraints

1108:   Level: intermediate

1110: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetDof()`, `PetscSectionSetConstraintDof()`, `PetscSectionCreate()`
1111: @*/
1112: PetscErrorCode PetscSectionGetConstraintDof(PetscSection s, PetscInt point, PetscInt *numDof)
1113: {
1114:   PetscFunctionBegin;
1116:   PetscAssertPointer(numDof, 3);
1117:   if (s->bc) PetscCall(PetscSectionGetDof(s->bc, point, numDof));
1118:   else *numDof = 0;
1119:   PetscFunctionReturn(PETSC_SUCCESS);
1120: }

1122: /*@
1123:   PetscSectionSetConstraintDof - Set the number of constrained degrees of freedom associated with a given point.

1125:   Not Collective

1127:   Input Parameters:
1128: + s      - the `PetscSection`
1129: . point  - the point
1130: - numDof - the number of dof which are fixed by constraints

1132:   Level: intermediate

1134: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionSetDof()`, `PetscSectionGetConstraintDof()`, `PetscSectionCreate()`
1135: @*/
1136: PetscErrorCode PetscSectionSetConstraintDof(PetscSection s, PetscInt point, PetscInt numDof)
1137: {
1138:   PetscFunctionBegin;
1140:   if (numDof) {
1141:     PetscCall(PetscSectionCheckConstraints_Private(s));
1142:     PetscCall(PetscSectionSetDof(s->bc, point, numDof));
1143:   }
1144:   PetscFunctionReturn(PETSC_SUCCESS);
1145: }

1147: /*@
1148:   PetscSectionAddConstraintDof - Increment the number of constrained degrees of freedom associated with a given point.

1150:   Not Collective

1152:   Input Parameters:
1153: + s      - the `PetscSection`
1154: . point  - the point
1155: - numDof - the number of additional dof which are fixed by constraints

1157:   Level: intermediate

1159: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionAddDof()`, `PetscSectionGetConstraintDof()`, `PetscSectionCreate()`
1160: @*/
1161: PetscErrorCode PetscSectionAddConstraintDof(PetscSection s, PetscInt point, PetscInt numDof)
1162: {
1163:   PetscFunctionBegin;
1165:   if (numDof) {
1166:     PetscCall(PetscSectionCheckConstraints_Private(s));
1167:     PetscCall(PetscSectionAddDof(s->bc, point, numDof));
1168:   }
1169:   PetscFunctionReturn(PETSC_SUCCESS);
1170: }

1172: /*@
1173:   PetscSectionGetFieldConstraintDof - Return the number of constrained degrees of freedom associated with a given field on a point.

1175:   Not Collective

1177:   Input Parameters:
1178: + s     - the `PetscSection`
1179: . point - the point
1180: - field - the field

1182:   Output Parameter:
1183: . numDof - the number of dof which are fixed by constraints

1185:   Level: intermediate

1187: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetDof()`, `PetscSectionSetFieldConstraintDof()`, `PetscSectionCreate()`
1188: @*/
1189: PetscErrorCode PetscSectionGetFieldConstraintDof(PetscSection s, PetscInt point, PetscInt field, PetscInt *numDof)
1190: {
1191:   PetscFunctionBegin;
1193:   PetscAssertPointer(numDof, 4);
1194:   PetscSectionCheckValidField(field, s->numFields);
1195:   PetscCall(PetscSectionGetConstraintDof(s->field[field], point, numDof));
1196:   PetscFunctionReturn(PETSC_SUCCESS);
1197: }

1199: /*@
1200:   PetscSectionSetFieldConstraintDof - Set the number of constrained degrees of freedom associated with a given field on a point.

1202:   Not Collective

1204:   Input Parameters:
1205: + s      - the `PetscSection`
1206: . point  - the point
1207: . field  - the field
1208: - numDof - the number of dof which are fixed by constraints

1210:   Level: intermediate

1212: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionSetDof()`, `PetscSectionGetFieldConstraintDof()`, `PetscSectionCreate()`
1213: @*/
1214: PetscErrorCode PetscSectionSetFieldConstraintDof(PetscSection s, PetscInt point, PetscInt field, PetscInt numDof)
1215: {
1216:   PetscFunctionBegin;
1218:   PetscSectionCheckValidField(field, s->numFields);
1219:   PetscCall(PetscSectionSetConstraintDof(s->field[field], point, numDof));
1220:   PetscFunctionReturn(PETSC_SUCCESS);
1221: }

1223: /*@
1224:   PetscSectionAddFieldConstraintDof - Increment the number of constrained degrees of freedom associated with a given field on a point.

1226:   Not Collective

1228:   Input Parameters:
1229: + s      - the `PetscSection`
1230: . point  - the point
1231: . field  - the field
1232: - numDof - the number of additional dof which are fixed by constraints

1234:   Level: intermediate

1236: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionAddDof()`, `PetscSectionGetFieldConstraintDof()`, `PetscSectionCreate()`
1237: @*/
1238: PetscErrorCode PetscSectionAddFieldConstraintDof(PetscSection s, PetscInt point, PetscInt field, PetscInt numDof)
1239: {
1240:   PetscFunctionBegin;
1242:   PetscSectionCheckValidField(field, s->numFields);
1243:   PetscCall(PetscSectionAddConstraintDof(s->field[field], point, numDof));
1244:   PetscFunctionReturn(PETSC_SUCCESS);
1245: }

1247: /*@
1248:   PetscSectionSetUpBC - Setup the subsections describing boundary conditions.

1250:   Not Collective

1252:   Input Parameter:
1253: . s - the `PetscSection`

1255:   Level: advanced

1257: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionSetUp()`, `PetscSectionCreate()`
1258: @*/
1259: PetscErrorCode PetscSectionSetUpBC(PetscSection s)
1260: {
1261:   PetscFunctionBegin;
1263:   if (s->bc) {
1264:     const PetscInt last = (s->bc->pEnd - s->bc->pStart) - 1;

1266:     PetscCall(PetscSectionSetUp(s->bc));
1267:     if (last >= 0) PetscCall(PetscMalloc1(s->bc->atlasOff[last] + s->bc->atlasDof[last], &s->bcIndices));
1268:     else s->bcIndices = NULL;
1269:   }
1270:   PetscFunctionReturn(PETSC_SUCCESS);
1271: }

1273: /*@
1274:   PetscSectionSetUp - Calculate offsets based upon the number of degrees of freedom for each point in preparation for use of the `PetscSection`

1276:   Not Collective

1278:   Input Parameter:
1279: . s - the `PetscSection`

1281:   Level: intermediate

1283:   Notes:
1284:   If used, `PetscSectionSetPermutation()` must be called before this routine.

1286:   `PetscSectionSetPointMajor()`, cannot be called after this routine.

1288: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreate()`, `PetscSectionSetPermutation()`
1289: @*/
1290: PetscErrorCode PetscSectionSetUp(PetscSection s)
1291: {
1292:   PetscInt        f;
1293:   const PetscInt *pind   = NULL;
1294:   PetscCount      offset = 0;

1296:   PetscFunctionBegin;
1298:   if (s->setup) PetscFunctionReturn(PETSC_SUCCESS);
1299:   s->setup = PETSC_TRUE;
1300:   /* Set offsets and field offsets for all points */
1301:   /*   Assume that all fields have the same chart */
1302:   PetscCheck(s->includesConstraints, PETSC_COMM_SELF, PETSC_ERR_SUP, "PetscSectionSetUp is currently unsupported for includesConstraints = PETSC_TRUE");
1303:   if (s->perm) PetscCall(ISGetIndices(s->perm, &pind));
1304:   if (s->pointMajor) {
1305:     PetscCount foff;
1306:     for (PetscInt p = 0; p < s->pEnd - s->pStart; ++p) {
1307:       const PetscInt q = pind ? pind[p] : p;

1309:       /* Set point offset */
1310:       PetscCall(PetscIntCast(offset, &s->atlasOff[q]));
1311:       offset += s->atlasDof[q];
1312:       /* Set field offset */
1313:       for (f = 0, foff = s->atlasOff[q]; f < s->numFields; ++f) {
1314:         PetscSection sf = s->field[f];

1316:         PetscCall(PetscIntCast(foff, &sf->atlasOff[q]));
1317:         foff += sf->atlasDof[q];
1318:       }
1319:     }
1320:   } else {
1321:     /* Set field offsets for all points */
1322:     for (f = 0; f < s->numFields; ++f) {
1323:       PetscSection sf = s->field[f];

1325:       for (PetscInt p = 0; p < s->pEnd - s->pStart; ++p) {
1326:         const PetscInt q = pind ? pind[p] : p;

1328:         PetscCall(PetscIntCast(offset, &sf->atlasOff[q]));
1329:         offset += sf->atlasDof[q];
1330:       }
1331:     }
1332:     /* Disable point offsets since these are unused */
1333:     for (PetscInt p = 0; p < s->pEnd - s->pStart; ++p) s->atlasOff[p] = -1;
1334:   }
1335:   if (s->perm) PetscCall(ISRestoreIndices(s->perm, &pind));
1336:   /* Setup BC sections */
1337:   PetscCall(PetscSectionSetUpBC(s));
1338:   for (f = 0; f < s->numFields; ++f) PetscCall(PetscSectionSetUpBC(s->field[f]));
1339:   PetscFunctionReturn(PETSC_SUCCESS);
1340: }

1342: /*@
1343:   PetscSectionGetMaxDof - Return the maximum number of degrees of freedom on any point in the `PetscSection`

1345:   Not Collective

1347:   Input Parameter:
1348: . s - the `PetscSection`

1350:   Output Parameter:
1351: . maxDof - the maximum dof

1353:   Level: intermediate

1355:   Notes:
1356:   The returned number is up-to-date without need for `PetscSectionSetUp()`.

1358:   This is the maximum over all points of the sum of the number of dof in the unnamed default field plus all named fields. This is equivalent to
1359:   the maximum over all points of the value returned by `PetscSectionGetDof()` on this MPI process

1361:   Developer Notes:
1362:   The returned number is calculated lazily and stashed.

1364:   A call to `PetscSectionInvalidateMaxDof_Internal()` invalidates the stashed value.

1366:   `PetscSectionInvalidateMaxDof_Internal()` is called in `PetscSectionSetDof()`, `PetscSectionAddDof()` and `PetscSectionReset()`

1368:   It should also be called every time `atlasDof` is modified directly.

1370: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetDof()`, `PetscSectionSetDof()`, `PetscSectionAddDof()`, `PetscSectionCreate()`
1371: @*/
1372: PetscErrorCode PetscSectionGetMaxDof(PetscSection s, PetscInt *maxDof)
1373: {
1374:   PetscInt p;

1376:   PetscFunctionBegin;
1378:   PetscAssertPointer(maxDof, 2);
1379:   if (s->maxDof == PETSC_INT_MIN) {
1380:     s->maxDof = 0;
1381:     for (p = 0; p < s->pEnd - s->pStart; ++p) s->maxDof = PetscMax(s->maxDof, s->atlasDof[p]);
1382:   }
1383:   *maxDof = s->maxDof;
1384:   PetscFunctionReturn(PETSC_SUCCESS);
1385: }

1387: /*@
1388:   PetscSectionGetStorageSize - Return the size of an array or local `Vec` capable of holding all the degrees of freedom defined in a `PetscSection`

1390:   Not Collective

1392:   Input Parameter:
1393: . s - the `PetscSection`

1395:   Output Parameter:
1396: . size - the size of an array which can hold all the dofs

1398:   Level: intermediate

1400: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetOffset()`, `PetscSectionGetConstrainedStorageSize()`, `PetscSectionCreate()`
1401: @*/
1402: PetscErrorCode PetscSectionGetStorageSize(PetscSection s, PetscInt *size)
1403: {
1404:   PetscInt64 n = 0;

1406:   PetscFunctionBegin;
1408:   PetscAssertPointer(size, 2);
1409:   for (PetscInt p = 0; p < s->pEnd - s->pStart; ++p) n += s->atlasDof[p] > 0 ? s->atlasDof[p] : 0;
1410:   PetscCall(PetscIntCast(n, size));
1411:   PetscFunctionReturn(PETSC_SUCCESS);
1412: }

1414: /*@
1415:   PetscSectionGetConstrainedStorageSize - Return the size of an array or local `Vec` capable of holding all unconstrained degrees of freedom in a `PetscSection`

1417:   Not Collective

1419:   Input Parameter:
1420: . s - the `PetscSection`

1422:   Output Parameter:
1423: . size - the size of an array which can hold all unconstrained dofs

1425:   Level: intermediate

1427: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetStorageSize()`, `PetscSectionGetOffset()`, `PetscSectionCreate()`
1428: @*/
1429: PetscErrorCode PetscSectionGetConstrainedStorageSize(PetscSection s, PetscInt *size)
1430: {
1431:   PetscInt64 n = 0;

1433:   PetscFunctionBegin;
1435:   PetscAssertPointer(size, 2);
1436:   for (PetscInt p = 0; p < s->pEnd - s->pStart; ++p) {
1437:     const PetscInt cdof = s->bc ? s->bc->atlasDof[p] : 0;
1438:     n += s->atlasDof[p] > 0 ? s->atlasDof[p] - cdof : 0;
1439:   }
1440:   PetscCall(PetscIntCast(n, size));
1441:   PetscFunctionReturn(PETSC_SUCCESS);
1442: }

1444: /*@
1445:   PetscSectionCreateGlobalSection - Create a parallel section describing the global layout using
1446:   a local (sequential) `PetscSection` on each MPI process and a `PetscSF` describing the section point overlap.

1448:   Input Parameters:
1449: + s                  - The `PetscSection` for the local field layout
1450: . sf                 - The `PetscSF` describing parallel layout of the section points (leaves are unowned local points)
1451: . usePermutation     - By default this is `PETSC_TRUE`, meaning any permutation of the local section is transferred to the global section
1452: . includeConstraints - By default this is `PETSC_FALSE`, meaning that the global field vector will not possess constrained dofs
1453: - localOffsets       - If `PETSC_TRUE`, use local rather than global offsets for the points

1455:   Output Parameter:
1456: . gsection - The `PetscSection` for the global field layout

1458:   Level: intermediate

1460:   Notes:
1461:   On each MPI process `gsection` inherits the chart of the `s` on that process.

1463:   This sets negative sizes and offsets to points not owned by this process as defined by `sf` but that are within the local value of the chart of `gsection`.
1464:   In those locations the value of size is -(size+1) and the value of the offset on the remote process is -(off+1).

1466: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreate()`, `PetscSectionCreateGlobalSectionCensored()`
1467: @*/
1468: PetscErrorCode PetscSectionCreateGlobalSection(PetscSection s, PetscSF sf, PetscBool usePermutation, PetscBool includeConstraints, PetscBool localOffsets, PetscSection *gsection)
1469: {
1470:   PetscSection    gs;
1471:   const PetscInt *pind = NULL;
1472:   PetscInt       *recv = NULL, *neg = NULL;
1473:   PetscInt        pStart, pEnd, p, dof, cdof, off, globalOff = 0, nroots, nlocal, maxleaf;
1474:   PetscInt        numFields, f, numComponents;
1475:   PetscInt        foff;

1477:   PetscFunctionBegin;
1483:   PetscAssertPointer(gsection, 6);
1484:   PetscCheck(s->pointMajor, PETSC_COMM_SELF, PETSC_ERR_SUP, "No support for field major ordering");
1485:   PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)s), &gs));
1486:   PetscCall(PetscSectionGetNumFields(s, &numFields));
1487:   if (numFields > 0) PetscCall(PetscSectionSetNumFields(gs, numFields));
1488:   PetscCall(PetscSectionGetChart(s, &pStart, &pEnd));
1489:   PetscCall(PetscSectionSetChart(gs, pStart, pEnd));
1490:   gs->includesConstraints = includeConstraints;
1491:   PetscCall(PetscSFGetGraph(sf, &nroots, NULL, NULL, NULL));
1492:   nlocal = nroots; /* The local/leaf space matches global/root space */
1493:   /* Must allocate for all points visible to SF, which may be more than this section */
1494:   if (nroots >= 0) { /* nroots < 0 means that the graph has not been set, only happens in serial */
1495:     PetscCall(PetscSFGetLeafRange(sf, NULL, &maxleaf));
1496:     PetscCheck(nroots >= pEnd, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "SF roots %" PetscInt_FMT " < pEnd %" PetscInt_FMT, nroots, pEnd);
1497:     PetscCheck(maxleaf < nroots, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Max local leaf %" PetscInt_FMT " >= nroots %" PetscInt_FMT, maxleaf, nroots);
1498:     PetscCall(PetscMalloc2(nroots, &neg, nlocal, &recv));
1499:     PetscCall(PetscArrayzero(neg, nroots));
1500:   }
1501:   /* Mark all local points with negative dof */
1502:   for (p = pStart; p < pEnd; ++p) {
1503:     PetscCall(PetscSectionGetDof(s, p, &dof));
1504:     PetscCall(PetscSectionSetDof(gs, p, dof));
1505:     PetscCall(PetscSectionGetConstraintDof(s, p, &cdof));
1506:     if (!includeConstraints && cdof > 0) PetscCall(PetscSectionSetConstraintDof(gs, p, cdof));
1507:     if (neg) neg[p] = -(dof + 1);
1508:   }
1509:   PetscCall(PetscSectionSetUpBC(gs));
1510:   if (gs->bcIndices) PetscCall(PetscArraycpy(gs->bcIndices, s->bcIndices, gs->bc->atlasOff[gs->bc->pEnd - gs->bc->pStart - 1] + gs->bc->atlasDof[gs->bc->pEnd - gs->bc->pStart - 1]));
1511:   if (nroots >= 0) {
1512:     PetscCall(PetscArrayzero(recv, nlocal));
1513:     PetscCall(PetscSFBcastBegin(sf, MPIU_INT, neg, recv, MPI_REPLACE));
1514:     PetscCall(PetscSFBcastEnd(sf, MPIU_INT, neg, recv, MPI_REPLACE));
1515:     for (p = pStart; p < pEnd; ++p) {
1516:       if (recv[p] < 0) {
1517:         gs->atlasDof[p - pStart] = recv[p];
1518:         PetscCall(PetscSectionGetDof(s, p, &dof));
1519:         PetscCheck(-(recv[p] + 1) == dof, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Global dof %" PetscInt_FMT " for point %" PetscInt_FMT " is not the unconstrained %" PetscInt_FMT, -(recv[p] + 1), p, dof);
1520:       }
1521:     }
1522:   }
1523:   /* Calculate new sizes, get process offset, and calculate point offsets */
1524:   if (usePermutation && s->perm) PetscCall(ISGetIndices(s->perm, &pind));
1525:   for (p = 0, off = 0; p < pEnd - pStart; ++p) {
1526:     const PetscInt q = pind ? pind[p] : p;

1528:     cdof            = (!includeConstraints && s->bc) ? s->bc->atlasDof[q] : 0;
1529:     gs->atlasOff[q] = off;
1530:     off += gs->atlasDof[q] > 0 ? gs->atlasDof[q] - cdof : 0;
1531:   }
1532:   if (!localOffsets) {
1533:     PetscCallMPI(MPI_Scan(&off, &globalOff, 1, MPIU_INT, MPI_SUM, PetscObjectComm((PetscObject)sf)));
1534:     globalOff -= off;
1535:   }
1536:   for (p = pStart, off = 0; p < pEnd; ++p) {
1537:     gs->atlasOff[p - pStart] += globalOff;
1538:     if (neg) neg[p] = -(gs->atlasOff[p - pStart] + 1);
1539:   }
1540:   if (usePermutation && s->perm) PetscCall(ISRestoreIndices(s->perm, &pind));
1541:   /* Put in negative offsets for ghost points */
1542:   if (nroots >= 0) {
1543:     PetscCall(PetscArrayzero(recv, nlocal));
1544:     PetscCall(PetscSFBcastBegin(sf, MPIU_INT, neg, recv, MPI_REPLACE));
1545:     PetscCall(PetscSFBcastEnd(sf, MPIU_INT, neg, recv, MPI_REPLACE));
1546:     for (p = pStart; p < pEnd; ++p) {
1547:       if (recv[p] < 0) gs->atlasOff[p - pStart] = recv[p];
1548:     }
1549:   }
1550:   PetscCall(PetscFree2(neg, recv));
1551:   /* Set field dofs/offsets/constraints */
1552:   for (f = 0; f < numFields; ++f) {
1553:     const char *name;

1555:     gs->field[f]->includesConstraints = includeConstraints;
1556:     PetscCall(PetscSectionGetFieldComponents(s, f, &numComponents));
1557:     PetscCall(PetscSectionSetFieldComponents(gs, f, numComponents));
1558:     PetscCall(PetscSectionGetFieldName(s, f, &name));
1559:     PetscCall(PetscSectionSetFieldName(gs, f, name));
1560:   }
1561:   for (p = pStart; p < pEnd; ++p) {
1562:     PetscCall(PetscSectionGetOffset(gs, p, &off));
1563:     for (f = 0, foff = off; f < numFields; ++f) {
1564:       PetscCall(PetscSectionGetFieldConstraintDof(s, p, f, &cdof));
1565:       if (!includeConstraints && cdof > 0) PetscCall(PetscSectionSetFieldConstraintDof(gs, p, f, cdof));
1566:       PetscCall(PetscSectionGetFieldDof(s, p, f, &dof));
1567:       PetscCall(PetscSectionSetFieldDof(gs, p, f, off < 0 ? -(dof + 1) : dof));
1568:       PetscCall(PetscSectionSetFieldOffset(gs, p, f, foff));
1569:       PetscCall(PetscSectionGetFieldConstraintDof(gs, p, f, &cdof));
1570:       foff = off < 0 ? foff - (dof - cdof) : foff + (dof - cdof);
1571:     }
1572:   }
1573:   for (f = 0; f < numFields; ++f) {
1574:     PetscSection gfs = gs->field[f];

1576:     PetscCall(PetscSectionSetUpBC(gfs));
1577:     if (gfs->bcIndices) PetscCall(PetscArraycpy(gfs->bcIndices, s->field[f]->bcIndices, gfs->bc->atlasOff[gfs->bc->pEnd - gfs->bc->pStart - 1] + gfs->bc->atlasDof[gfs->bc->pEnd - gfs->bc->pStart - 1]));
1578:   }
1579:   gs->setup = PETSC_TRUE;
1580:   PetscCall(PetscSectionViewFromOptions(gs, NULL, "-global_section_view"));
1581:   *gsection = gs;
1582:   PetscFunctionReturn(PETSC_SUCCESS);
1583: }

1585: /*@
1586:   PetscSectionCreateGlobalSectionCensored - Create a `PetscSection` describing the globallayout using
1587:   a local (sequential) `PetscSection` on each MPI process and an `PetscSF` describing the section point overlap.

1589:   Input Parameters:
1590: + s                  - The `PetscSection` for the local field layout
1591: . sf                 - The `PetscSF` describing parallel layout of the section points
1592: . includeConstraints - By default this is `PETSC_FALSE`, meaning that the global vector will not possess constrained dofs
1593: . numExcludes        - The number of exclusion ranges, this must have the same value on all MPI processes
1594: - excludes           - An array [start_0, end_0, start_1, end_1, ...] where there are `numExcludes` pairs and must have the same values on all MPI processes

1596:   Output Parameter:
1597: . gsection - The `PetscSection` for the global field layout

1599:   Level: advanced

1601:   Notes:
1602:   On each MPI process `gsection` inherits the chart of the `s` on that process.

1604:   This sets negative sizes and offsets to points not owned by this process as defined by `sf` but that are within the local value of the chart of `gsection`.
1605:   In those locations the value of size is -(size+1) and the value of the offset on the remote process is -(off+1).

1607:   This routine augments `PetscSectionCreateGlobalSection()` by allowing one to exclude certain ranges in the chart of the `PetscSection`

1609:   Developer Notes:
1610:   This is a terrible function name

1612: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreate()`
1613: @*/
1614: PetscErrorCode PetscSectionCreateGlobalSectionCensored(PetscSection s, PetscSF sf, PetscBool includeConstraints, PetscInt numExcludes, const PetscInt excludes[], PetscSection *gsection)
1615: {
1616:   const PetscInt *pind = NULL;
1617:   PetscInt       *neg = NULL, *tmpOff = NULL;
1618:   PetscInt        pStart, pEnd, p, e, dof, cdof, globalOff = 0, nroots;
1619:   PetscInt        off;

1621:   PetscFunctionBegin;
1624:   PetscAssertPointer(gsection, 6);
1625:   PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)s), gsection));
1626:   PetscCall(PetscSectionGetChart(s, &pStart, &pEnd));
1627:   PetscCall(PetscSectionSetChart(*gsection, pStart, pEnd));
1628:   PetscCall(PetscSFGetGraph(sf, &nroots, NULL, NULL, NULL));
1629:   if (nroots >= 0) {
1630:     PetscCheck(nroots >= pEnd - pStart, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "PetscSF nroots %" PetscInt_FMT " < %" PetscInt_FMT " section size", nroots, pEnd - pStart);
1631:     PetscCall(PetscCalloc1(nroots, &neg));
1632:     if (nroots > pEnd - pStart) {
1633:       PetscCall(PetscCalloc1(nroots, &tmpOff));
1634:     } else {
1635:       tmpOff = &(*gsection)->atlasDof[-pStart];
1636:     }
1637:   }
1638:   /* Mark ghost points with negative dof */
1639:   for (p = pStart; p < pEnd; ++p) {
1640:     for (e = 0; e < numExcludes; ++e) {
1641:       if ((p >= excludes[e * 2 + 0]) && (p < excludes[e * 2 + 1])) {
1642:         PetscCall(PetscSectionSetDof(*gsection, p, 0));
1643:         break;
1644:       }
1645:     }
1646:     if (e < numExcludes) continue;
1647:     PetscCall(PetscSectionGetDof(s, p, &dof));
1648:     PetscCall(PetscSectionSetDof(*gsection, p, dof));
1649:     PetscCall(PetscSectionGetConstraintDof(s, p, &cdof));
1650:     if (!includeConstraints && cdof > 0) PetscCall(PetscSectionSetConstraintDof(*gsection, p, cdof));
1651:     if (neg) neg[p] = -(dof + 1);
1652:   }
1653:   PetscCall(PetscSectionSetUpBC(*gsection));
1654:   if (nroots >= 0) {
1655:     PetscCall(PetscSFBcastBegin(sf, MPIU_INT, neg, tmpOff, MPI_REPLACE));
1656:     PetscCall(PetscSFBcastEnd(sf, MPIU_INT, neg, tmpOff, MPI_REPLACE));
1657:     if (nroots > pEnd - pStart) {
1658:       for (p = pStart; p < pEnd; ++p) {
1659:         if (tmpOff[p] < 0) (*gsection)->atlasDof[p - pStart] = tmpOff[p];
1660:       }
1661:     }
1662:   }
1663:   /* Calculate new sizes, get process offset, and calculate point offsets */
1664:   if (s->perm) PetscCall(ISGetIndices(s->perm, &pind));
1665:   for (p = 0, off = 0; p < pEnd - pStart; ++p) {
1666:     const PetscInt q = pind ? pind[p] : p;

1668:     cdof                     = (!includeConstraints && s->bc) ? s->bc->atlasDof[q] : 0;
1669:     (*gsection)->atlasOff[q] = off;
1670:     off += (*gsection)->atlasDof[q] > 0 ? (*gsection)->atlasDof[q] - cdof : 0;
1671:   }
1672:   PetscCallMPI(MPI_Scan(&off, &globalOff, 1, MPIU_INT, MPI_SUM, PetscObjectComm((PetscObject)s)));
1673:   globalOff -= off;
1674:   for (p = 0, off = 0; p < pEnd - pStart; ++p) {
1675:     (*gsection)->atlasOff[p] += globalOff;
1676:     if (neg) neg[p + pStart] = -((*gsection)->atlasOff[p] + 1);
1677:   }
1678:   if (s->perm) PetscCall(ISRestoreIndices(s->perm, &pind));
1679:   /* Put in negative offsets for ghost points */
1680:   if (nroots >= 0) {
1681:     if (nroots == pEnd - pStart) tmpOff = &(*gsection)->atlasOff[-pStart];
1682:     PetscCall(PetscSFBcastBegin(sf, MPIU_INT, neg, tmpOff, MPI_REPLACE));
1683:     PetscCall(PetscSFBcastEnd(sf, MPIU_INT, neg, tmpOff, MPI_REPLACE));
1684:     if (nroots > pEnd - pStart) {
1685:       for (p = pStart; p < pEnd; ++p) {
1686:         if (tmpOff[p] < 0) (*gsection)->atlasOff[p - pStart] = tmpOff[p];
1687:       }
1688:     }
1689:   }
1690:   if (nroots >= 0 && nroots > pEnd - pStart) PetscCall(PetscFree(tmpOff));
1691:   PetscCall(PetscFree(neg));
1692:   PetscFunctionReturn(PETSC_SUCCESS);
1693: }

1695: /*@
1696:   PetscSectionGetPointLayout - Get a `PetscLayout` for the points with nonzero dof counts of the unnamed default field within this `PetscSection`s local chart

1698:   Collective

1700:   Input Parameters:
1701: + comm - The `MPI_Comm`
1702: - s    - The `PetscSection`

1704:   Output Parameter:
1705: . layout - The point layout for the data that defines the section

1707:   Level: advanced

1709:   Notes:
1710:   `PetscSectionGetValueLayout()` provides similar information but counting the total number of degrees of freedom on the MPI process (excluding constrained
1711:   degrees of freedom).

1713:   This count includes constrained degrees of freedom

1715:   This is usually called on the default global section.

1717:   Example:
1718: .vb
1719:      The chart is [2,5), point 2 has 2 dof, point 3 has 0 dof, point 4 has 1 dof
1720:      The local size of the `PetscLayout` is 2 since 2 points have a non-zero number of dof
1721: .ve

1723:   Developer Notes:
1724:   I find the names of these two functions extremely non-informative

1726: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetValueLayout()`, `PetscSectionCreate()`
1727: @*/
1728: PetscErrorCode PetscSectionGetPointLayout(MPI_Comm comm, PetscSection s, PetscLayout *layout)
1729: {
1730:   PetscInt pStart, pEnd, p, localSize = 0;

1732:   PetscFunctionBegin;
1733:   PetscCall(PetscSectionGetChart(s, &pStart, &pEnd));
1734:   for (p = pStart; p < pEnd; ++p) {
1735:     PetscInt dof;

1737:     PetscCall(PetscSectionGetDof(s, p, &dof));
1738:     if (dof >= 0) ++localSize;
1739:   }
1740:   PetscCall(PetscLayoutCreate(comm, layout));
1741:   PetscCall(PetscLayoutSetLocalSize(*layout, localSize));
1742:   PetscCall(PetscLayoutSetBlockSize(*layout, 1));
1743:   PetscCall(PetscLayoutSetUp(*layout));
1744:   PetscFunctionReturn(PETSC_SUCCESS);
1745: }

1747: /*@
1748:   PetscSectionGetValueLayout - Get the `PetscLayout` associated with the section dofs of a `PetscSection`

1750:   Collective

1752:   Input Parameters:
1753: + comm - The `MPI_Comm`
1754: - s    - The `PetscSection`

1756:   Output Parameter:
1757: . layout - The dof layout for the section

1759:   Level: advanced

1761:   Notes:
1762:   `PetscSectionGetPointLayout()` provides similar information but only counting the number of points with nonzero degrees of freedom and
1763:   including the constrained degrees of freedom

1765:   This is usually called for the default global section.

1767:   Example:
1768: .vb
1769:      The chart is [2,5), point 2 has 4 dof (2 constrained), point 3 has 0 dof, point 4 has 1 dof (not constrained)
1770:      The local size of the `PetscLayout` is 3 since there are 3 unconstrained degrees of freedom on this MPI process
1771: .ve

1773: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetPointLayout()`, `PetscSectionCreate()`
1774: @*/
1775: PetscErrorCode PetscSectionGetValueLayout(MPI_Comm comm, PetscSection s, PetscLayout *layout)
1776: {
1777:   PetscInt pStart, pEnd, p, localSize = 0;

1779:   PetscFunctionBegin;
1781:   PetscAssertPointer(layout, 3);
1782:   PetscCall(PetscSectionGetChart(s, &pStart, &pEnd));
1783:   for (p = pStart; p < pEnd; ++p) {
1784:     PetscInt dof, cdof;

1786:     PetscCall(PetscSectionGetDof(s, p, &dof));
1787:     PetscCall(PetscSectionGetConstraintDof(s, p, &cdof));
1788:     if (dof - cdof > 0) localSize += dof - cdof;
1789:   }
1790:   PetscCall(PetscLayoutCreate(comm, layout));
1791:   PetscCall(PetscLayoutSetLocalSize(*layout, localSize));
1792:   PetscCall(PetscLayoutSetBlockSize(*layout, 1));
1793:   PetscCall(PetscLayoutSetUp(*layout));
1794:   PetscFunctionReturn(PETSC_SUCCESS);
1795: }

1797: /*@
1798:   PetscSectionGetOffset - Return the offset into an array or `Vec` for the dof associated with the given point.

1800:   Not Collective

1802:   Input Parameters:
1803: + s     - the `PetscSection`
1804: - point - the point

1806:   Output Parameter:
1807: . offset - the offset

1809:   Level: intermediate

1811:   Notes:
1812:   In a global section, `offset` will be negative for points not owned by this process.

1814:   This is for the unnamed default field in the `PetscSection` not the named fields

1816:   The `offset` values are different depending on a value set with `PetscSectionSetPointMajor()`

1818: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetFieldOffset()`, `PetscSectionCreate()`, `PetscSectionSetPointMajor()`
1819: @*/
1820: PetscErrorCode PetscSectionGetOffset(PetscSection s, PetscInt point, PetscInt *offset)
1821: {
1822:   PetscFunctionBegin;
1824:   PetscAssertPointer(offset, 3);
1825:   PetscAssert(!(point < s->pStart) && !(point >= s->pEnd), PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Section point %" PetscInt_FMT " should be in [%" PetscInt_FMT ", %" PetscInt_FMT ")", point, s->pStart, s->pEnd);
1826:   *offset = s->atlasOff[point - s->pStart];
1827:   PetscFunctionReturn(PETSC_SUCCESS);
1828: }

1830: /*@
1831:   PetscSectionSetOffset - Set the offset into an array or `Vec` for the dof associated with the given point.

1833:   Not Collective

1835:   Input Parameters:
1836: + s      - the `PetscSection`
1837: . point  - the point
1838: - offset - the offset, these values may be negative indicating the values are off process

1840:   Level: developer

1842:   Note:
1843:   The user usually does not call this function, but uses `PetscSectionSetUp()`

1845: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetFieldOffset()`, `PetscSectionCreate()`, `PetscSectionSetUp()`
1846: @*/
1847: PetscErrorCode PetscSectionSetOffset(PetscSection s, PetscInt point, PetscInt offset)
1848: {
1849:   PetscFunctionBegin;
1851:   PetscCheck(!(point < s->pStart) && !(point >= s->pEnd), PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Section point %" PetscInt_FMT " should be in [%" PetscInt_FMT ", %" PetscInt_FMT ")", point, s->pStart, s->pEnd);
1852:   s->atlasOff[point - s->pStart] = offset;
1853:   PetscFunctionReturn(PETSC_SUCCESS);
1854: }

1856: /*@
1857:   PetscSectionGetFieldOffset - Return the offset into an array or `Vec` for the field dof associated with the given point.

1859:   Not Collective

1861:   Input Parameters:
1862: + s     - the `PetscSection`
1863: . point - the point
1864: - field - the field

1866:   Output Parameter:
1867: . offset - the offset

1869:   Level: intermediate

1871:   Notes:
1872:   In a global section, `offset` will be negative for points not owned by this process.

1874:   The `offset` values are different depending on a value set with `PetscSectionSetPointMajor()`

1876: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetOffset()`, `PetscSectionCreate()`, `PetscSectionGetFieldPointOffset()`
1877: @*/
1878: PetscErrorCode PetscSectionGetFieldOffset(PetscSection s, PetscInt point, PetscInt field, PetscInt *offset)
1879: {
1880:   PetscFunctionBegin;
1882:   PetscAssertPointer(offset, 4);
1883:   PetscSectionCheckValidField(field, s->numFields);
1884:   PetscCall(PetscSectionGetOffset(s->field[field], point, offset));
1885:   PetscFunctionReturn(PETSC_SUCCESS);
1886: }

1888: /*@
1889:   PetscSectionSetFieldOffset - Set the offset into an array or `Vec` for the dof associated with the given field at a point.

1891:   Not Collective

1893:   Input Parameters:
1894: + s      - the `PetscSection`
1895: . point  - the point
1896: . field  - the field
1897: - offset - the offset, these values may be negative indicating the values are off process

1899:   Level: developer

1901:   Note:
1902:   The user usually does not call this function, but uses `PetscSectionSetUp()`

1904: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetFieldOffset()`, `PetscSectionSetOffset()`, `PetscSectionCreate()`, `PetscSectionSetUp()`
1905: @*/
1906: PetscErrorCode PetscSectionSetFieldOffset(PetscSection s, PetscInt point, PetscInt field, PetscInt offset)
1907: {
1908:   PetscFunctionBegin;
1910:   PetscSectionCheckValidField(field, s->numFields);
1911:   PetscCall(PetscSectionSetOffset(s->field[field], point, offset));
1912:   PetscFunctionReturn(PETSC_SUCCESS);
1913: }

1915: /*@
1916:   PetscSectionGetFieldPointOffset - Return the offset for the first field dof associated with the given point relative to the offset for that point for the
1917:   unnamed default field's first dof

1919:   Not Collective

1921:   Input Parameters:
1922: + s     - the `PetscSection`
1923: . point - the point
1924: - field - the field

1926:   Output Parameter:
1927: . offset - the offset

1929:   Level: advanced

1931:   Note:
1932:   This ignores constraints

1934:   Example:
1935: .vb
1936:   if PetscSectionSetPointMajor(s,PETSC_TRUE)
1937:   The unnamed default field has 3 dof at `point`
1938:   Field 0 has 2 dof at `point`
1939:   Then PetscSectionGetFieldPointOffset(s,point,1,&offset) returns and offset of 5
1940: .ve

1942: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetOffset()`, `PetscSectionCreate()`, `PetscSectionGetFieldOffset()`
1943: @*/
1944: PetscErrorCode PetscSectionGetFieldPointOffset(PetscSection s, PetscInt point, PetscInt field, PetscInt *offset)
1945: {
1946:   PetscInt off, foff;

1948:   PetscFunctionBegin;
1950:   PetscAssertPointer(offset, 4);
1951:   PetscSectionCheckValidField(field, s->numFields);
1952:   PetscCall(PetscSectionGetOffset(s, point, &off));
1953:   PetscCall(PetscSectionGetOffset(s->field[field], point, &foff));
1954:   *offset = foff - off;
1955:   PetscFunctionReturn(PETSC_SUCCESS);
1956: }

1958: /*@
1959:   PetscSectionGetOffsetRange - Return the full range of offsets [`start`, `end`) for a `PetscSection`

1961:   Not Collective

1963:   Input Parameter:
1964: . s - the `PetscSection`

1966:   Output Parameters:
1967: + start - the minimum offset
1968: - end   - one more than the maximum offset

1970:   Level: intermediate

1972: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetOffset()`, `PetscSectionCreate()`
1973: @*/
1974: PetscErrorCode PetscSectionGetOffsetRange(PetscSection s, PetscInt *start, PetscInt *end)
1975: {
1976:   PetscInt os = 0, oe = 0, pStart, pEnd, p;

1978:   PetscFunctionBegin;
1980:   if (s->atlasOff) {
1981:     os = s->atlasOff[0];
1982:     oe = s->atlasOff[0];
1983:   }
1984:   PetscCall(PetscSectionGetChart(s, &pStart, &pEnd));
1985:   for (p = 0; p < pEnd - pStart; ++p) {
1986:     PetscInt dof = s->atlasDof[p], off = s->atlasOff[p];

1988:     if (off >= 0) {
1989:       os = PetscMin(os, off);
1990:       oe = PetscMax(oe, off + dof);
1991:     }
1992:   }
1993:   if (start) *start = os;
1994:   if (end) *end = oe;
1995:   PetscFunctionReturn(PETSC_SUCCESS);
1996: }

1998: /*@
1999:   PetscSectionCreateSubsection - Create a new, smaller `PetscSection` composed of only selected fields

2001:   Collective

2003:   Input Parameters:
2004: + s      - the `PetscSection`
2005: . len    - the number of subfields
2006: - fields - the subfield numbers

2008:   Output Parameter:
2009: . subs - the subsection

2011:   Level: advanced

2013:   Notes:
2014:   The chart of `subs` is the same as the chart of `s`

2016:   This will error if a fieldnumber is out of range

2018: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreateSupersection()`, `PetscSectionCreate()`
2019: @*/
2020: PetscErrorCode PetscSectionCreateSubsection(PetscSection s, PetscInt len, const PetscInt fields[], PetscSection *subs)
2021: {
2022:   PetscInt nF, f, c, pStart, pEnd, p, maxCdof = 0;

2024:   PetscFunctionBegin;
2025:   if (!len) PetscFunctionReturn(PETSC_SUCCESS);
2027:   PetscAssertPointer(fields, 3);
2028:   PetscAssertPointer(subs, 4);
2029:   PetscCall(PetscSectionGetNumFields(s, &nF));
2030:   PetscCheck(len <= nF, PetscObjectComm((PetscObject)s), PETSC_ERR_ARG_WRONG, "Number of requested fields %" PetscInt_FMT " greater than number of fields %" PetscInt_FMT, len, nF);
2031:   PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)s), subs));
2032:   PetscCall(PetscSectionSetNumFields(*subs, len));
2033:   for (f = 0; f < len; ++f) {
2034:     const char     *name    = NULL;
2035:     PetscInt        numComp = 0;
2036:     PetscSectionSym sym;

2038:     PetscCall(PetscSectionGetFieldName(s, fields[f], &name));
2039:     PetscCall(PetscSectionSetFieldName(*subs, f, name));
2040:     PetscCall(PetscSectionGetFieldComponents(s, fields[f], &numComp));
2041:     PetscCall(PetscSectionSetFieldComponents(*subs, f, numComp));
2042:     for (c = 0; c < s->numFieldComponents[fields[f]]; ++c) {
2043:       PetscCall(PetscSectionGetComponentName(s, fields[f], c, &name));
2044:       PetscCall(PetscSectionSetComponentName(*subs, f, c, name));
2045:     }
2046:     PetscCall(PetscSectionGetFieldSym(s, fields[f], &sym));
2047:     PetscCall(PetscSectionSetFieldSym(*subs, f, sym));
2048:   }
2049:   PetscCall(PetscSectionGetChart(s, &pStart, &pEnd));
2050:   PetscCall(PetscSectionSetChart(*subs, pStart, pEnd));
2051:   for (p = pStart; p < pEnd; ++p) {
2052:     PetscInt dof = 0, cdof = 0, fdof = 0, cfdof = 0;

2054:     for (f = 0; f < len; ++f) {
2055:       PetscCall(PetscSectionGetFieldDof(s, p, fields[f], &fdof));
2056:       PetscCall(PetscSectionSetFieldDof(*subs, p, f, fdof));
2057:       PetscCall(PetscSectionGetFieldConstraintDof(s, p, fields[f], &cfdof));
2058:       if (cfdof) PetscCall(PetscSectionSetFieldConstraintDof(*subs, p, f, cfdof));
2059:       dof += fdof;
2060:       cdof += cfdof;
2061:     }
2062:     PetscCall(PetscSectionSetDof(*subs, p, dof));
2063:     if (cdof) PetscCall(PetscSectionSetConstraintDof(*subs, p, cdof));
2064:     maxCdof = PetscMax(cdof, maxCdof);
2065:   }
2066:   PetscBT bst, subbst;

2068:   PetscCall(PetscSectionGetBlockStarts(s, &bst));
2069:   if (bst) {
2070:     PetscCall(PetscBTCreate(pEnd - pStart, &subbst));
2071:     PetscCall(PetscBTCopy(subbst, pEnd - pStart, bst));
2072:     PetscCall(PetscSectionSetBlockStarts(*subs, subbst));
2073:   }
2074:   PetscCall(PetscSectionSetUp(*subs));
2075:   if (maxCdof) {
2076:     PetscInt *indices;

2078:     PetscCall(PetscMalloc1(maxCdof, &indices));
2079:     for (p = pStart; p < pEnd; ++p) {
2080:       PetscInt cdof;

2082:       PetscCall(PetscSectionGetConstraintDof(*subs, p, &cdof));
2083:       if (cdof) {
2084:         const PetscInt *oldIndices = NULL;
2085:         PetscInt        fdof = 0, cfdof = 0, fc, numConst = 0, fOff = 0;

2087:         for (f = 0; f < len; ++f) {
2088:           PetscCall(PetscSectionGetFieldDof(s, p, fields[f], &fdof));
2089:           PetscCall(PetscSectionGetFieldConstraintDof(s, p, fields[f], &cfdof));
2090:           PetscCall(PetscSectionGetFieldConstraintIndices(s, p, fields[f], &oldIndices));
2091:           PetscCall(PetscSectionSetFieldConstraintIndices(*subs, p, f, oldIndices));
2092:           for (fc = 0; fc < cfdof; ++fc) indices[numConst + fc] = oldIndices[fc] + fOff;
2093:           numConst += cfdof;
2094:           fOff += fdof;
2095:         }
2096:         PetscCall(PetscSectionSetConstraintIndices(*subs, p, indices));
2097:       }
2098:     }
2099:     PetscCall(PetscFree(indices));
2100:   }
2101:   PetscFunctionReturn(PETSC_SUCCESS);
2102: }

2104: /*@
2105:   PetscSectionCreateComponentSubsection - Create a new, smaller `PetscSection` composed of only selected components

2107:   Collective

2109:   Input Parameters:
2110: + s     - the `PetscSection`
2111: . len   - the number of components
2112: - comps - the component numbers

2114:   Output Parameter:
2115: . subs - the subsection

2117:   Level: advanced

2119:   Notes:
2120:   The chart of `subs` is the same as the chart of `s`

2122:   This will error if the section has more than one field, or if a component number is out of range

2124: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreateSupersection()`, `PetscSectionCreate()`
2125: @*/
2126: PetscErrorCode PetscSectionCreateComponentSubsection(PetscSection s, PetscInt len, const PetscInt comps[], PetscSection *subs)
2127: {
2128:   PetscSectionSym sym;
2129:   const char     *name = NULL;
2130:   PetscInt        Nf, pStart, pEnd;

2132:   PetscFunctionBegin;
2133:   if (!len) PetscFunctionReturn(PETSC_SUCCESS);
2135:   PetscAssertPointer(comps, 3);
2136:   PetscAssertPointer(subs, 4);
2137:   PetscCall(PetscSectionGetNumFields(s, &Nf));
2138:   PetscCheck(Nf == 1, PetscObjectComm((PetscObject)s), PETSC_ERR_ARG_WRONG, "This method can only handle one field, not %" PetscInt_FMT, Nf);
2139:   PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)s), subs));
2140:   PetscCall(PetscSectionSetNumFields(*subs, 1));
2141:   PetscCall(PetscSectionGetFieldName(s, 0, &name));
2142:   PetscCall(PetscSectionSetFieldName(*subs, 0, name));
2143:   PetscCall(PetscSectionSetFieldComponents(*subs, 0, len));
2144:   PetscCall(PetscSectionGetFieldSym(s, 0, &sym));
2145:   PetscCall(PetscSectionSetFieldSym(*subs, 0, sym));
2146:   for (PetscInt c = 0; c < len; ++c) {
2147:     PetscCall(PetscSectionGetComponentName(s, 0, comps[c], &name));
2148:     PetscCall(PetscSectionSetComponentName(*subs, 0, c, name));
2149:   }
2150:   PetscCall(PetscSectionGetChart(s, &pStart, &pEnd));
2151:   PetscCall(PetscSectionSetChart(*subs, pStart, pEnd));
2152:   for (PetscInt p = pStart; p < pEnd; ++p) {
2153:     PetscInt dof, cdof, cfdof;

2155:     PetscCall(PetscSectionGetDof(s, p, &dof));
2156:     if (!dof) continue;
2157:     PetscCall(PetscSectionGetFieldConstraintDof(s, p, 0, &cfdof));
2158:     PetscCall(PetscSectionGetConstraintDof(s, p, &cdof));
2159:     PetscCheck(!cdof && !cfdof, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Component selection does not work with constraints");
2160:     PetscCall(PetscSectionSetFieldDof(*subs, p, 0, len));
2161:     PetscCall(PetscSectionSetDof(*subs, p, len));
2162:   }
2163:   PetscCall(PetscSectionSetUp(*subs));
2164:   PetscFunctionReturn(PETSC_SUCCESS);
2165: }

2167: /*@
2168:   PetscSectionCreateSupersection - Create a new, larger section composed of multiple `PetscSection`s

2170:   Collective

2172:   Input Parameters:
2173: + s   - the input sections
2174: - len - the number of input sections

2176:   Output Parameter:
2177: . supers - the supersection

2179:   Level: advanced

2181:   Notes:
2182:   The section offsets now refer to a new, larger vector.

2184:   Developer Notes:
2185:   Needs to explain how the sections are composed

2187: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreateSubsection()`, `PetscSectionCreate()`
2188: @*/
2189: PetscErrorCode PetscSectionCreateSupersection(PetscSection s[], PetscInt len, PetscSection *supers)
2190: {
2191:   PetscInt Nf = 0, f, pStart = PETSC_INT_MAX, pEnd = 0, p, maxCdof = 0, i;

2193:   PetscFunctionBegin;
2194:   if (!len) PetscFunctionReturn(PETSC_SUCCESS);
2195:   for (i = 0; i < len; ++i) {
2196:     PetscInt nf, pStarti, pEndi;

2198:     PetscCall(PetscSectionGetNumFields(s[i], &nf));
2199:     PetscCall(PetscSectionGetChart(s[i], &pStarti, &pEndi));
2200:     pStart = PetscMin(pStart, pStarti);
2201:     pEnd   = PetscMax(pEnd, pEndi);
2202:     Nf += nf;
2203:   }
2204:   PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)s[0]), supers));
2205:   PetscCall(PetscSectionSetNumFields(*supers, Nf));
2206:   for (i = 0, f = 0; i < len; ++i) {
2207:     PetscInt nf, fi, ci;

2209:     PetscCall(PetscSectionGetNumFields(s[i], &nf));
2210:     for (fi = 0; fi < nf; ++fi, ++f) {
2211:       const char *name    = NULL;
2212:       PetscInt    numComp = 0;

2214:       PetscCall(PetscSectionGetFieldName(s[i], fi, &name));
2215:       PetscCall(PetscSectionSetFieldName(*supers, f, name));
2216:       PetscCall(PetscSectionGetFieldComponents(s[i], fi, &numComp));
2217:       PetscCall(PetscSectionSetFieldComponents(*supers, f, numComp));
2218:       for (ci = 0; ci < s[i]->numFieldComponents[fi]; ++ci) {
2219:         PetscCall(PetscSectionGetComponentName(s[i], fi, ci, &name));
2220:         PetscCall(PetscSectionSetComponentName(*supers, f, ci, name));
2221:       }
2222:     }
2223:   }
2224:   PetscCall(PetscSectionSetChart(*supers, pStart, pEnd));
2225:   for (p = pStart; p < pEnd; ++p) {
2226:     PetscInt dof = 0, cdof = 0;

2228:     for (i = 0, f = 0; i < len; ++i) {
2229:       PetscInt nf, fi, pStarti, pEndi;
2230:       PetscInt fdof = 0, cfdof = 0;

2232:       PetscCall(PetscSectionGetNumFields(s[i], &nf));
2233:       PetscCall(PetscSectionGetChart(s[i], &pStarti, &pEndi));
2234:       if ((p < pStarti) || (p >= pEndi)) continue;
2235:       for (fi = 0; fi < nf; ++fi, ++f) {
2236:         PetscCall(PetscSectionGetFieldDof(s[i], p, fi, &fdof));
2237:         PetscCall(PetscSectionAddFieldDof(*supers, p, f, fdof));
2238:         PetscCall(PetscSectionGetFieldConstraintDof(s[i], p, fi, &cfdof));
2239:         if (cfdof) PetscCall(PetscSectionAddFieldConstraintDof(*supers, p, f, cfdof));
2240:         dof += fdof;
2241:         cdof += cfdof;
2242:       }
2243:     }
2244:     PetscCall(PetscSectionSetDof(*supers, p, dof));
2245:     if (cdof) PetscCall(PetscSectionSetConstraintDof(*supers, p, cdof));
2246:     maxCdof = PetscMax(cdof, maxCdof);
2247:   }
2248:   PetscCall(PetscSectionSetUp(*supers));
2249:   if (maxCdof) {
2250:     PetscInt *indices;

2252:     PetscCall(PetscMalloc1(maxCdof, &indices));
2253:     for (p = pStart; p < pEnd; ++p) {
2254:       PetscInt cdof;

2256:       PetscCall(PetscSectionGetConstraintDof(*supers, p, &cdof));
2257:       if (cdof) {
2258:         PetscInt dof, numConst = 0, fOff = 0;

2260:         for (i = 0, f = 0; i < len; ++i) {
2261:           const PetscInt *oldIndices = NULL;
2262:           PetscInt        nf, fi, pStarti, pEndi, fdof, cfdof, fc;

2264:           PetscCall(PetscSectionGetNumFields(s[i], &nf));
2265:           PetscCall(PetscSectionGetChart(s[i], &pStarti, &pEndi));
2266:           if ((p < pStarti) || (p >= pEndi)) continue;
2267:           for (fi = 0; fi < nf; ++fi, ++f) {
2268:             PetscCall(PetscSectionGetFieldDof(s[i], p, fi, &fdof));
2269:             PetscCall(PetscSectionGetFieldConstraintDof(s[i], p, fi, &cfdof));
2270:             PetscCall(PetscSectionGetFieldConstraintIndices(s[i], p, fi, &oldIndices));
2271:             for (fc = 0; fc < cfdof; ++fc) indices[numConst + fc] = oldIndices[fc];
2272:             PetscCall(PetscSectionSetFieldConstraintIndices(*supers, p, f, &indices[numConst]));
2273:             for (fc = 0; fc < cfdof; ++fc) indices[numConst + fc] += fOff;
2274:             numConst += cfdof;
2275:           }
2276:           PetscCall(PetscSectionGetDof(s[i], p, &dof));
2277:           fOff += dof;
2278:         }
2279:         PetscCall(PetscSectionSetConstraintIndices(*supers, p, indices));
2280:       }
2281:     }
2282:     PetscCall(PetscFree(indices));
2283:   }
2284:   PetscFunctionReturn(PETSC_SUCCESS);
2285: }

2287: static PetscErrorCode PetscSectionCreateSubplexSection_Private(PetscSection s, IS subpointIS, PetscBool renumberPoints, PetscSection *subs)
2288: {
2289:   const PetscInt *points = NULL, *indices = NULL;
2290:   PetscInt       *spoints = NULL, *order = NULL;
2291:   PetscInt        numFields, f, c, numSubpoints = 0, pStart, pEnd, p, spStart, spEnd, subp;

2293:   PetscFunctionBegin;
2296:   PetscAssertPointer(subs, 4);
2297:   PetscCall(PetscSectionGetNumFields(s, &numFields));
2298:   PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)s), subs));
2299:   if (numFields) PetscCall(PetscSectionSetNumFields(*subs, numFields));
2300:   for (f = 0; f < numFields; ++f) {
2301:     const char *name    = NULL;
2302:     PetscInt    numComp = 0;

2304:     PetscCall(PetscSectionGetFieldName(s, f, &name));
2305:     PetscCall(PetscSectionSetFieldName(*subs, f, name));
2306:     PetscCall(PetscSectionGetFieldComponents(s, f, &numComp));
2307:     PetscCall(PetscSectionSetFieldComponents(*subs, f, numComp));
2308:     for (c = 0; c < s->numFieldComponents[f]; ++c) {
2309:       PetscCall(PetscSectionGetComponentName(s, f, c, &name));
2310:       PetscCall(PetscSectionSetComponentName(*subs, f, c, name));
2311:     }
2312:   }
2313:   /* For right now, we do not try to squeeze the subchart */
2314:   if (subpointIS) {
2315:     PetscCall(ISGetLocalSize(subpointIS, &numSubpoints));
2316:     PetscCall(ISGetIndices(subpointIS, &points));
2317:   }
2318:   PetscCall(PetscSectionGetChart(s, &pStart, &pEnd));
2319:   if (renumberPoints) {
2320:     PetscBool sorted;

2322:     spStart = 0;
2323:     spEnd   = numSubpoints;
2324:     PetscCall(ISSorted(subpointIS, &sorted));
2325:     if (!sorted) {
2326:       PetscCall(PetscMalloc2(numSubpoints, &spoints, numSubpoints, &order));
2327:       PetscCall(PetscArraycpy(spoints, points, numSubpoints));
2328:       for (PetscInt i = 0; i < numSubpoints; ++i) order[i] = i;
2329:       PetscCall(PetscSortIntWithArray(numSubpoints, spoints, order));
2330:     }
2331:   } else {
2332:     PetscCall(ISGetMinMax(subpointIS, &spStart, &spEnd));
2333:     ++spEnd;
2334:   }
2335:   PetscCall(PetscSectionSetChart(*subs, spStart, spEnd));
2336:   for (p = pStart; p < pEnd; ++p) {
2337:     PetscInt dof, cdof, fdof = 0, cfdof = 0;

2339:     PetscCall(PetscFindInt(p, numSubpoints, spoints ? spoints : points, &subp));
2340:     if (subp < 0) continue;
2341:     if (!renumberPoints) subp = p;
2342:     else subp = order ? order[subp] : subp;
2343:     for (f = 0; f < numFields; ++f) {
2344:       PetscCall(PetscSectionGetFieldDof(s, p, f, &fdof));
2345:       PetscCall(PetscSectionSetFieldDof(*subs, subp, f, fdof));
2346:       PetscCall(PetscSectionGetFieldConstraintDof(s, p, f, &cfdof));
2347:       if (cfdof) PetscCall(PetscSectionSetFieldConstraintDof(*subs, subp, f, cfdof));
2348:     }
2349:     PetscCall(PetscSectionGetDof(s, p, &dof));
2350:     PetscCall(PetscSectionSetDof(*subs, subp, dof));
2351:     PetscCall(PetscSectionGetConstraintDof(s, p, &cdof));
2352:     if (cdof) PetscCall(PetscSectionSetConstraintDof(*subs, subp, cdof));
2353:   }
2354:   PetscCall(PetscSectionSetUp(*subs));
2355:   /* Change offsets to original offsets */
2356:   for (p = pStart; p < pEnd; ++p) {
2357:     PetscInt off, foff = 0;

2359:     PetscCall(PetscFindInt(p, numSubpoints, spoints ? spoints : points, &subp));
2360:     if (subp < 0) continue;
2361:     if (!renumberPoints) subp = p;
2362:     else subp = order ? order[subp] : subp;
2363:     for (f = 0; f < numFields; ++f) {
2364:       PetscCall(PetscSectionGetFieldOffset(s, p, f, &foff));
2365:       PetscCall(PetscSectionSetFieldOffset(*subs, subp, f, foff));
2366:     }
2367:     PetscCall(PetscSectionGetOffset(s, p, &off));
2368:     PetscCall(PetscSectionSetOffset(*subs, subp, off));
2369:   }
2370:   /* Copy constraint indices */
2371:   for (subp = spStart; subp < spEnd; ++subp) {
2372:     PetscInt cdof;

2374:     PetscCall(PetscSectionGetConstraintDof(*subs, subp, &cdof));
2375:     if (cdof) {
2376:       for (f = 0; f < numFields; ++f) {
2377:         PetscCall(PetscSectionGetFieldConstraintIndices(s, points[subp - spStart], f, &indices));
2378:         PetscCall(PetscSectionSetFieldConstraintIndices(*subs, subp, f, indices));
2379:       }
2380:       PetscCall(PetscSectionGetConstraintIndices(s, points[subp - spStart], &indices));
2381:       PetscCall(PetscSectionSetConstraintIndices(*subs, subp, indices));
2382:     }
2383:   }
2384:   if (subpointIS) PetscCall(ISRestoreIndices(subpointIS, &points));
2385:   PetscCall(PetscFree2(spoints, order));
2386:   PetscFunctionReturn(PETSC_SUCCESS);
2387: }

2389: /*@
2390:   PetscSectionCreateSubmeshSection - Create a new, smaller section with support on the submesh

2392:   Collective

2394:   Input Parameters:
2395: + s          - the `PetscSection`
2396: - subpointIS - a sorted list of points in the original mesh which are in the submesh

2398:   Output Parameter:
2399: . subs - the subsection

2401:   Level: advanced

2403:   Notes:
2404:   The points are renumbered from 0, and the section offsets now refer to a new, smaller vector. That is the chart of `subs` is `[0,sizeof(subpointmap))`

2406:   Compare this with `PetscSectionCreateSubdomainSection()` that does not map the points numbers to start at zero but leaves them as before

2408:   Developer Notes:
2409:   The use of the term Submesh is confusing and needs clarification, it is not specific to meshes. It appears to be just a subset of the chart of the original `PetscSection`

2411: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreateSubdomainSection()`, `PetscSectionCreateSubsection()`, `DMPlexGetSubpointMap()`, `PetscSectionCreate()`
2412: @*/
2413: PetscErrorCode PetscSectionCreateSubmeshSection(PetscSection s, IS subpointIS, PetscSection *subs)
2414: {
2415:   PetscFunctionBegin;
2416:   PetscCall(PetscSectionCreateSubplexSection_Private(s, subpointIS, PETSC_TRUE, subs));
2417:   PetscFunctionReturn(PETSC_SUCCESS);
2418: }

2420: /*@
2421:   PetscSectionCreateSubdomainSection - Create a new, smaller section with support on a subdomain of the mesh

2423:   Collective

2425:   Input Parameters:
2426: + s           - the `PetscSection`
2427: - subpointMap - a sorted list of points in the original mesh which are in the subdomain

2429:   Output Parameter:
2430: . subs - the subsection

2432:   Level: advanced

2434:   Notes:
2435:   The point numbers remain the same as in the larger `PetscSection`, but the section offsets now refer to a new, smaller vector. The chart of `subs`
2436:   is `[min(subpointMap),max(subpointMap)+1)`

2438:   Compare this with `PetscSectionCreateSubmeshSection()` that maps the point numbers to start at zero

2440:   Developer Notes:
2441:   The use of the term Subdomain is unneeded and needs clarification, it is not specific to meshes. It appears to be just a subset of the chart of the original `PetscSection`

2443: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreateSubmeshSection()`, `PetscSectionCreateSubsection()`, `DMPlexGetSubpointMap()`, `PetscSectionCreate()`
2444: @*/
2445: PetscErrorCode PetscSectionCreateSubdomainSection(PetscSection s, IS subpointMap, PetscSection *subs)
2446: {
2447:   PetscFunctionBegin;
2448:   PetscCall(PetscSectionCreateSubplexSection_Private(s, subpointMap, PETSC_FALSE, subs));
2449:   PetscFunctionReturn(PETSC_SUCCESS);
2450: }

2452: static PetscErrorCode PetscSectionView_ASCII(PetscSection s, PetscViewer viewer)
2453: {
2454:   PetscInt    p;
2455:   PetscMPIInt rank;

2457:   PetscFunctionBegin;
2458:   PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank));
2459:   PetscCall(PetscViewerASCIIPushSynchronized(viewer));
2460:   PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "Process %d:\n", rank));
2461:   for (p = 0; p < s->pEnd - s->pStart; ++p) {
2462:     if (s->bc && s->bc->atlasDof[p] > 0) {
2463:       PetscInt b;
2464:       PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "  (%4" PetscInt_FMT ") dof %2" PetscInt_FMT " offset %3" PetscInt_FMT " constrained", p + s->pStart, s->atlasDof[p], s->atlasOff[p]));
2465:       if (s->bcIndices) {
2466:         for (b = 0; b < s->bc->atlasDof[p]; ++b) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %" PetscInt_FMT, s->bcIndices[s->bc->atlasOff[p] + b]));
2467:       }
2468:       PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\n"));
2469:     } else {
2470:       PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "  (%4" PetscInt_FMT ") dof %2" PetscInt_FMT " offset %3" PetscInt_FMT "\n", p + s->pStart, s->atlasDof[p], s->atlasOff[p]));
2471:     }
2472:   }
2473:   PetscCall(PetscViewerFlush(viewer));
2474:   PetscCall(PetscViewerASCIIPopSynchronized(viewer));
2475:   if (s->sym) {
2476:     PetscCall(PetscViewerASCIIPushTab(viewer));
2477:     PetscCall(PetscSectionSymView(s->sym, viewer));
2478:     PetscCall(PetscViewerASCIIPopTab(viewer));
2479:   }
2480:   PetscFunctionReturn(PETSC_SUCCESS);
2481: }

2483: /*@
2484:   PetscSectionViewFromOptions - View the `PetscSection` based on values in the options database

2486:   Collective

2488:   Input Parameters:
2489: + A    - the `PetscSection` object to view
2490: . obj  - Optional object that provides the options prefix used for the options
2491: - name - command line option

2493:   Level: intermediate

2495:   Note:
2496:   See `PetscObjectViewFromOptions()` for available values of `PetscViewer` and `PetscViewerFormat`

2498: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionView`, `PetscObjectViewFromOptions()`, `PetscSectionCreate()`, `PetscSectionView()`
2499: @*/
2500: PetscErrorCode PetscSectionViewFromOptions(PetscSection A, PetscObject obj, const char name[])
2501: {
2502:   PetscFunctionBegin;
2504:   PetscCall(PetscObjectViewFromOptions((PetscObject)A, obj, name));
2505:   PetscFunctionReturn(PETSC_SUCCESS);
2506: }

2508: /*@
2509:   PetscSectionView - Views a `PetscSection`

2511:   Collective

2513:   Input Parameters:
2514: + s      - the `PetscSection` object to view
2515: - viewer - the viewer

2517:   Level: beginner

2519:   Note:
2520:   `PetscSectionView()`, when viewer is of type `PETSCVIEWERHDF5`, only saves
2521:   distribution independent data, such as dofs, offsets, constraint dofs,
2522:   and constraint indices. Points that have negative dofs, for instance,
2523:   are not saved as they represent points owned by other processes.
2524:   Point numbering and rank assignment is currently not stored.
2525:   The saved section can be loaded with `PetscSectionLoad()`.

2527: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreate()`, `PetscSectionDestroy()`, `PetscSectionLoad()`, `PetscViewer`
2528: @*/
2529: PetscErrorCode PetscSectionView(PetscSection s, PetscViewer viewer)
2530: {
2531:   PetscBool isascii, ishdf5;
2532:   PetscInt  f;

2534:   PetscFunctionBegin;
2536:   if (!viewer) PetscCall(PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)s), &viewer));
2538:   PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &isascii));
2539:   PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5));
2540:   if (isascii) {
2541:     PetscCall(PetscObjectPrintClassNamePrefixType((PetscObject)s, viewer));
2542:     if (s->numFields) {
2543:       PetscCall(PetscViewerASCIIPrintf(viewer, "%" PetscInt_FMT " fields\n", s->numFields));
2544:       for (f = 0; f < s->numFields; ++f) {
2545:         PetscCall(PetscViewerASCIIPrintf(viewer, "  field %" PetscInt_FMT " \"%s\" with %" PetscInt_FMT " components\n", f, s->fieldNames[f], s->numFieldComponents[f]));
2546:         PetscCall(PetscSectionView_ASCII(s->field[f], viewer));
2547:       }
2548:     } else {
2549:       PetscCall(PetscSectionView_ASCII(s, viewer));
2550:     }
2551:   } else if (ishdf5) {
2552: #if PetscDefined(HAVE_HDF5)
2553:     PetscCall(PetscSectionView_HDF5_Internal(s, viewer));
2554: #else
2555:     SETERRQ(PetscObjectComm((PetscObject)s), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
2556: #endif
2557:   }
2558:   PetscFunctionReturn(PETSC_SUCCESS);
2559: }

2561: /*@
2562:   PetscSectionLoad - Loads a `PetscSection`

2564:   Collective

2566:   Input Parameters:
2567: + s      - the `PetscSection` object to load
2568: - viewer - the viewer

2570:   Level: beginner

2572:   Note:
2573:   `PetscSectionLoad()`, when viewer is of type `PETSCVIEWERHDF5`, loads
2574:   a section saved with `PetscSectionView()`. The number of processes
2575:   used here (N) does not need to be the same as that used when saving.
2576:   After calling this function, the chart of s on rank i will be set
2577:   to [0, E_i), where \sum_{i=0}^{N-1}E_i equals to the total number of
2578:   saved section points.

2580: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreate()`, `PetscSectionDestroy()`, `PetscSectionView()`
2581: @*/
2582: PetscErrorCode PetscSectionLoad(PetscSection s, PetscViewer viewer)
2583: {
2584:   PetscBool ishdf5;

2586:   PetscFunctionBegin;
2589:   PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5));
2590:   PetscCheck(ishdf5, PetscObjectComm((PetscObject)s), PETSC_ERR_SUP, "Viewer type %s not yet supported for PetscSection loading", ((PetscObject)viewer)->type_name);
2591: #if PetscDefined(HAVE_HDF5)
2592:   PetscCall(PetscSectionLoad_HDF5_Internal(s, viewer));
2593:   PetscFunctionReturn(PETSC_SUCCESS);
2594: #else
2595:   SETERRQ(PetscObjectComm((PetscObject)s), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
2596: #endif
2597: }

2599: /*@
2600:   PetscSectionResetClosurePermutation - Remove any existing closure permutation

2602:   Input Parameter:
2603: . section - The `PetscSection`

2605:   Level: intermediate

2607: .seealso: `PetscSectionSetClosurePermutation()`, `PetscSectionSetClosureIndex()`, `PetscSectionReset()`
2608: @*/
2609: PetscErrorCode PetscSectionResetClosurePermutation(PetscSection section)
2610: {
2611:   PetscSectionClosurePermVal clVal;

2613:   PetscFunctionBegin;
2614:   if (!section->clHash) PetscFunctionReturn(PETSC_SUCCESS);
2615:   kh_foreach_value(section->clHash, clVal, {
2616:     PetscCall(PetscFree(clVal.perm));
2617:     PetscCall(PetscFree(clVal.invPerm));
2618:   });
2619:   kh_destroy(ClPerm, section->clHash);
2620:   section->clHash = NULL;
2621:   PetscFunctionReturn(PETSC_SUCCESS);
2622: }

2624: /*@
2625:   PetscSectionReset - Frees all section data, the section is then as if `PetscSectionCreate()` had just been called.

2627:   Not Collective

2629:   Input Parameter:
2630: . s - the `PetscSection`

2632:   Level: beginner

2634: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreate()`
2635: @*/
2636: PetscErrorCode PetscSectionReset(PetscSection s)
2637: {
2638:   PetscInt f, c;

2640:   PetscFunctionBegin;
2642:   for (f = 0; f < s->numFields; ++f) {
2643:     PetscCall(PetscSectionDestroy(&s->field[f]));
2644:     PetscCall(PetscFree(s->fieldNames[f]));
2645:     for (c = 0; c < s->numFieldComponents[f]; ++c) PetscCall(PetscFree(s->compNames[f][c]));
2646:     PetscCall(PetscFree(s->compNames[f]));
2647:   }
2648:   PetscCall(PetscFree(s->numFieldComponents));
2649:   PetscCall(PetscFree(s->fieldNames));
2650:   PetscCall(PetscFree(s->compNames));
2651:   PetscCall(PetscFree(s->field));
2652:   PetscCall(PetscSectionDestroy(&s->bc));
2653:   PetscCall(PetscFree(s->bcIndices));
2654:   PetscCall(PetscFree2(s->atlasDof, s->atlasOff));
2655:   PetscCall(PetscSectionDestroy(&s->clSection));
2656:   PetscCall(ISDestroy(&s->clPoints));
2657:   PetscCall(ISDestroy(&s->perm));
2658:   PetscCall(PetscBTDestroy(&s->blockStarts));
2659:   PetscCall(PetscSectionResetClosurePermutation(s));
2660:   PetscCall(PetscSectionSymDestroy(&s->sym));
2661:   PetscCall(PetscSectionDestroy(&s->clSection));
2662:   PetscCall(ISDestroy(&s->clPoints));
2663:   PetscCall(PetscSectionInvalidateMaxDof_Internal(s));
2664:   s->pStart    = -1;
2665:   s->pEnd      = -1;
2666:   s->maxDof    = 0;
2667:   s->setup     = PETSC_FALSE;
2668:   s->numFields = 0;
2669:   s->clObj     = NULL;
2670:   PetscFunctionReturn(PETSC_SUCCESS);
2671: }

2673: /*@
2674:   PetscSectionDestroy - Frees a `PetscSection`

2676:   Not Collective

2678:   Input Parameter:
2679: . s - the `PetscSection`

2681:   Level: beginner

2683: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreate()`, `PetscSectionReset()`
2684: @*/
2685: PetscErrorCode PetscSectionDestroy(PetscSection *s)
2686: {
2687:   PetscFunctionBegin;
2688:   if (!*s) PetscFunctionReturn(PETSC_SUCCESS);
2690:   if (--((PetscObject)*s)->refct > 0) {
2691:     *s = NULL;
2692:     PetscFunctionReturn(PETSC_SUCCESS);
2693:   }
2694:   PetscCall(PetscSectionReset(*s));
2695:   PetscCall(PetscHeaderDestroy(s));
2696:   PetscFunctionReturn(PETSC_SUCCESS);
2697: }

2699: static PetscErrorCode VecIntGetValuesSection_Private(const PetscInt *baseArray, PetscSection s, PetscInt point, const PetscInt **values)
2700: {
2701:   const PetscInt p = point - s->pStart;

2703:   PetscFunctionBegin;
2705:   *values = &baseArray[s->atlasOff[p]];
2706:   PetscFunctionReturn(PETSC_SUCCESS);
2707: }

2709: static PetscErrorCode VecIntSetValuesSection_Private(PetscInt *baseArray, PetscSection s, PetscInt point, const PetscInt values[], InsertMode mode)
2710: {
2711:   PetscInt      *array;
2712:   const PetscInt p           = point - s->pStart;
2713:   const PetscInt orientation = 0; /* Needs to be included for use in closure operations */
2714:   PetscInt       cDim        = 0;

2716:   PetscFunctionBegin;
2718:   PetscCall(PetscSectionGetConstraintDof(s, p, &cDim));
2719:   array = &baseArray[s->atlasOff[p]];
2720:   if (!cDim) {
2721:     if (orientation >= 0) {
2722:       const PetscInt dim = s->atlasDof[p];
2723:       PetscInt       i;

2725:       if (mode == INSERT_VALUES) {
2726:         for (i = 0; i < dim; ++i) array[i] = values ? values[i] : i;
2727:       } else {
2728:         for (i = 0; i < dim; ++i) array[i] += values[i];
2729:       }
2730:     } else {
2731:       PetscInt offset = 0;
2732:       PetscInt j      = -1, field, i;

2734:       for (field = 0; field < s->numFields; ++field) {
2735:         const PetscInt dim = s->field[field]->atlasDof[p];

2737:         for (i = dim - 1; i >= 0; --i) array[++j] = values ? values[i + offset] : i + offset;
2738:         offset += dim;
2739:       }
2740:     }
2741:   } else {
2742:     if (orientation >= 0) {
2743:       const PetscInt  dim  = s->atlasDof[p];
2744:       PetscInt        cInd = 0, i;
2745:       const PetscInt *cDof;

2747:       PetscCall(PetscSectionGetConstraintIndices(s, point, &cDof));
2748:       if (mode == INSERT_VALUES) {
2749:         for (i = 0; i < dim; ++i) {
2750:           if ((cInd < cDim) && (i == cDof[cInd])) {
2751:             ++cInd;
2752:             continue;
2753:           }
2754:           array[i] = values ? values[i] : i;
2755:         }
2756:       } else {
2757:         for (i = 0; i < dim; ++i) {
2758:           if ((cInd < cDim) && (i == cDof[cInd])) {
2759:             ++cInd;
2760:             continue;
2761:           }
2762:           array[i] += values[i];
2763:         }
2764:       }
2765:     } else {
2766:       const PetscInt *cDof;
2767:       PetscInt        offset  = 0;
2768:       PetscInt        cOffset = 0;
2769:       PetscInt        j       = 0, field;

2771:       PetscCall(PetscSectionGetConstraintIndices(s, point, &cDof));
2772:       for (field = 0; field < s->numFields; ++field) {
2773:         const PetscInt dim  = s->field[field]->atlasDof[p];     /* PetscSectionGetFieldDof() */
2774:         const PetscInt tDim = s->field[field]->bc->atlasDof[p]; /* PetscSectionGetFieldConstraintDof() */
2775:         const PetscInt sDim = dim - tDim;
2776:         PetscInt       cInd = 0, i, k;

2778:         for (i = 0, k = dim + offset - 1; i < dim; ++i, ++j, --k) {
2779:           if ((cInd < sDim) && (j == cDof[cInd + cOffset])) {
2780:             ++cInd;
2781:             continue;
2782:           }
2783:           array[j] = values ? values[k] : k;
2784:         }
2785:         offset += dim;
2786:         cOffset += dim - tDim;
2787:       }
2788:     }
2789:   }
2790:   PetscFunctionReturn(PETSC_SUCCESS);
2791: }

2793: /*@
2794:   PetscSectionHasConstraints - Determine whether a `PetscSection` has constrained dofs

2796:   Not Collective

2798:   Input Parameter:
2799: . s - The `PetscSection`

2801:   Output Parameter:
2802: . hasConstraints - flag indicating that the section has constrained dofs

2804:   Level: intermediate

2806: .seealso: [PetscSection](ch_petscsection), `PetscSectionSetConstraintIndices()`, `PetscSectionGetConstraintDof()`, `PetscSection`
2807: @*/
2808: PetscErrorCode PetscSectionHasConstraints(PetscSection s, PetscBool *hasConstraints)
2809: {
2810:   PetscFunctionBegin;
2812:   PetscAssertPointer(hasConstraints, 2);
2813:   *hasConstraints = s->bc ? PETSC_TRUE : PETSC_FALSE;
2814:   PetscFunctionReturn(PETSC_SUCCESS);
2815: }

2817: /*@C
2818:   PetscSectionGetConstraintIndices - Get the point dof numbers, in [0, dof), which are constrained for a given point

2820:   Not Collective

2822:   Input Parameters:
2823: + s     - The `PetscSection`
2824: - point - The point

2826:   Output Parameter:
2827: . indices - The constrained dofs

2829:   Level: intermediate

2831:   Fortran Notes:
2832:   Use `PetscSectionRestoreConstraintIndices()` when the indices are no longer needed

2834: .seealso: [PetscSection](ch_petscsection), `PetscSectionSetConstraintIndices()`, `PetscSectionGetConstraintDof()`, `PetscSection`
2835: @*/
2836: PetscErrorCode PetscSectionGetConstraintIndices(PetscSection s, PetscInt point, const PetscInt *indices[])
2837: {
2838:   PetscFunctionBegin;
2840:   if (s->bc) PetscCall(VecIntGetValuesSection_Private(s->bcIndices, s->bc, point, indices));
2841:   else *indices = NULL;
2842:   PetscFunctionReturn(PETSC_SUCCESS);
2843: }

2845: /*@
2846:   PetscSectionSetConstraintIndices - Set the point dof numbers, in [0, dof), which are constrained

2848:   Not Collective

2850:   Input Parameters:
2851: + s       - The `PetscSection`
2852: . point   - The point
2853: - indices - The constrained dofs

2855:   Level: intermediate

2857: .seealso: [PetscSection](ch_petscsection), `PetscSectionGetConstraintIndices()`, `PetscSectionGetConstraintDof()`, `PetscSection`
2858: @*/
2859: PetscErrorCode PetscSectionSetConstraintIndices(PetscSection s, PetscInt point, const PetscInt indices[])
2860: {
2861:   PetscFunctionBegin;
2863:   if (s->bc) {
2864:     const PetscInt dof  = s->atlasDof[point];
2865:     const PetscInt cdof = s->bc->atlasDof[point];
2866:     PetscInt       d;

2868:     if (indices)
2869:       for (d = 0; d < cdof; ++d) PetscCheck(indices[d] < dof, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Point %" PetscInt_FMT " dof %" PetscInt_FMT ", invalid constraint index[%" PetscInt_FMT "]: %" PetscInt_FMT, point, dof, d, indices[d]);
2870:     PetscCall(VecIntSetValuesSection_Private(s->bcIndices, s->bc, point, indices, INSERT_VALUES));
2871:   }
2872:   PetscFunctionReturn(PETSC_SUCCESS);
2873: }

2875: /*@C
2876:   PetscSectionGetFieldConstraintIndices - Get the field dof numbers, in [0, fdof), which are constrained

2878:   Not Collective

2880:   Input Parameters:
2881: + s     - The `PetscSection`
2882: . field - The field number
2883: - point - The point

2885:   Output Parameter:
2886: . indices - The constrained dofs sorted in ascending order, the length is returned by `PetscSectionGetConstraintDof()`.

2888:   Level: intermediate

2890:   Fortran Notes:
2891:   Use `PetscSectionRestoreFieldConstraintIndices()` to restore the indices when no longer needed

2893: .seealso: [PetscSection](ch_petscsection), `PetscSectionSetFieldConstraintIndices()`, `PetscSectionGetConstraintIndices()`, `PetscSectionGetConstraintDof()`, `PetscSection`
2894: @*/
2895: PetscErrorCode PetscSectionGetFieldConstraintIndices(PetscSection s, PetscInt point, PetscInt field, const PetscInt *indices[])
2896: {
2897:   PetscFunctionBegin;
2899:   PetscAssertPointer(indices, 4);
2900:   PetscSectionCheckValidField(field, s->numFields);
2901:   PetscCall(PetscSectionGetConstraintIndices(s->field[field], point, indices));
2902:   PetscFunctionReturn(PETSC_SUCCESS);
2903: }

2905: /*@
2906:   PetscSectionSetFieldConstraintIndices - Set the field dof numbers, in [0, fdof), which are constrained

2908:   Not Collective

2910:   Input Parameters:
2911: + s       - The `PetscSection`
2912: . point   - The point
2913: . field   - The field number
2914: - indices - The constrained dofs

2916:   Level: intermediate

2918: .seealso: [PetscSection](ch_petscsection), `PetscSectionSetConstraintIndices()`, `PetscSectionGetFieldConstraintIndices()`, `PetscSectionGetConstraintDof()`, `PetscSection`
2919: @*/
2920: PetscErrorCode PetscSectionSetFieldConstraintIndices(PetscSection s, PetscInt point, PetscInt field, const PetscInt indices[])
2921: {
2922:   PetscFunctionBegin;
2924:   PetscSectionCheckValidField(field, s->numFields);
2925:   PetscCall(PetscSectionSetConstraintIndices(s->field[field], point, indices));
2926:   PetscFunctionReturn(PETSC_SUCCESS);
2927: }

2929: /*@
2930:   PetscSectionPermute - Reorder the section according to the input point permutation

2932:   Collective

2934:   Input Parameters:
2935: + section     - The `PetscSection` object
2936: - permutation - The point permutation, old point p becomes new point perm[p]

2938:   Output Parameter:
2939: . sectionNew - The permuted `PetscSection`

2941:   Level: intermediate

2943:   Note:
2944:   The data and the access to the data via `PetscSectionGetFieldOffset()` and `PetscSectionGetOffset()` are both changed in `sectionNew`

2946:   Compare to `PetscSectionSetPermutation()`

2948: .seealso: [PetscSection](ch_petscsection), `IS`, `PetscSection`, `MatPermute()`, `PetscSectionSetPermutation()`
2949: @*/
2950: PetscErrorCode PetscSectionPermute(PetscSection section, IS permutation, PetscSection *sectionNew)
2951: {
2952:   PetscSection    s = section, sNew;
2953:   const PetscInt *perm;
2954:   PetscInt        numFields, f, c, numPoints, pStart, pEnd, p;

2956:   PetscFunctionBegin;
2959:   PetscAssertPointer(sectionNew, 3);
2960:   PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)s), &sNew));
2961:   PetscCall(PetscSectionGetNumFields(s, &numFields));
2962:   if (numFields) PetscCall(PetscSectionSetNumFields(sNew, numFields));
2963:   for (f = 0; f < numFields; ++f) {
2964:     const char *name;
2965:     PetscInt    numComp;

2967:     PetscCall(PetscSectionGetFieldName(s, f, &name));
2968:     PetscCall(PetscSectionSetFieldName(sNew, f, name));
2969:     PetscCall(PetscSectionGetFieldComponents(s, f, &numComp));
2970:     PetscCall(PetscSectionSetFieldComponents(sNew, f, numComp));
2971:     for (c = 0; c < s->numFieldComponents[f]; ++c) {
2972:       PetscCall(PetscSectionGetComponentName(s, f, c, &name));
2973:       PetscCall(PetscSectionSetComponentName(sNew, f, c, name));
2974:     }
2975:   }
2976:   PetscCall(ISGetLocalSize(permutation, &numPoints));
2977:   PetscCall(ISGetIndices(permutation, &perm));
2978:   PetscCall(PetscSectionGetChart(s, &pStart, &pEnd));
2979:   PetscCall(PetscSectionSetChart(sNew, pStart, pEnd));
2980:   PetscCheck(numPoints >= pEnd, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Permutation size %" PetscInt_FMT " is less than largest Section point %" PetscInt_FMT, numPoints, pEnd);
2981:   for (p = pStart; p < pEnd; ++p) {
2982:     PetscInt dof, cdof;

2984:     PetscCall(PetscSectionGetDof(s, p, &dof));
2985:     PetscCall(PetscSectionSetDof(sNew, perm[p], dof));
2986:     PetscCall(PetscSectionGetConstraintDof(s, p, &cdof));
2987:     if (cdof) PetscCall(PetscSectionSetConstraintDof(sNew, perm[p], cdof));
2988:     for (f = 0; f < numFields; ++f) {
2989:       PetscCall(PetscSectionGetFieldDof(s, p, f, &dof));
2990:       PetscCall(PetscSectionSetFieldDof(sNew, perm[p], f, dof));
2991:       PetscCall(PetscSectionGetFieldConstraintDof(s, p, f, &cdof));
2992:       if (cdof) PetscCall(PetscSectionSetFieldConstraintDof(sNew, perm[p], f, cdof));
2993:     }
2994:   }
2995:   PetscCall(PetscSectionSetUp(sNew));
2996:   for (p = pStart; p < pEnd; ++p) {
2997:     const PetscInt *cind;
2998:     PetscInt        cdof;

3000:     PetscCall(PetscSectionGetConstraintDof(s, p, &cdof));
3001:     if (cdof) {
3002:       PetscCall(PetscSectionGetConstraintIndices(s, p, &cind));
3003:       PetscCall(PetscSectionSetConstraintIndices(sNew, perm[p], cind));
3004:     }
3005:     for (f = 0; f < numFields; ++f) {
3006:       PetscCall(PetscSectionGetFieldConstraintDof(s, p, f, &cdof));
3007:       if (cdof) {
3008:         PetscCall(PetscSectionGetFieldConstraintIndices(s, p, f, &cind));
3009:         PetscCall(PetscSectionSetFieldConstraintIndices(sNew, perm[p], f, cind));
3010:       }
3011:     }
3012:   }
3013:   PetscCall(ISRestoreIndices(permutation, &perm));
3014:   *sectionNew = sNew;
3015:   PetscFunctionReturn(PETSC_SUCCESS);
3016: }

3018: /*@
3019:   PetscSectionSetClosureIndex - Create an internal data structure to speed up closure queries.

3021:   Collective

3023:   Input Parameters:
3024: + section   - The `PetscSection`
3025: . obj       - A `PetscObject` which serves as the key for this index
3026: . clSection - `PetscSection` giving the size of the closure of each point
3027: - clPoints  - `IS` giving the points in each closure

3029:   Level: advanced

3031:   Note:
3032:   This function creates an internal map from each point to its closure. We compress out closure points with no dofs in this section.

3034:   Developer Notes:
3035:   The information provided here is completely opaque

3037: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetClosureIndex()`, `DMPlexCreateClosureIndex()`
3038: @*/
3039: PetscErrorCode PetscSectionSetClosureIndex(PetscSection section, PetscObject obj, PetscSection clSection, IS clPoints)
3040: {
3041:   PetscFunctionBegin;
3045:   if (section->clObj != obj) PetscCall(PetscSectionResetClosurePermutation(section));
3046:   section->clObj = obj;
3047:   PetscCall(PetscObjectReference((PetscObject)clSection));
3048:   PetscCall(PetscObjectReference((PetscObject)clPoints));
3049:   PetscCall(PetscSectionDestroy(&section->clSection));
3050:   PetscCall(ISDestroy(&section->clPoints));
3051:   section->clSection = clSection;
3052:   section->clPoints  = clPoints;
3053:   PetscFunctionReturn(PETSC_SUCCESS);
3054: }

3056: /*@
3057:   PetscSectionGetClosureIndex - Get the cache of points in the closure of each point in the section set with `PetscSectionSetClosureIndex()`

3059:   Collective

3061:   Input Parameters:
3062: + section - The `PetscSection`
3063: - obj     - A `PetscObject` which serves as the key for this index

3065:   Output Parameters:
3066: + clSection - `PetscSection` giving the size of the closure of each point
3067: - clPoints  - `IS` giving the points in each closure

3069:   Level: advanced

3071: .seealso: [PetscSection](ch_petscsection), `PetscSectionSetClosureIndex()`, `DMPlexCreateClosureIndex()`
3072: @*/
3073: PetscErrorCode PetscSectionGetClosureIndex(PetscSection section, PetscObject obj, PetscSection *clSection, IS *clPoints)
3074: {
3075:   PetscFunctionBegin;
3076:   if (section->clObj == obj) {
3077:     if (clSection) *clSection = section->clSection;
3078:     if (clPoints) *clPoints = section->clPoints;
3079:   } else {
3080:     if (clSection) *clSection = NULL;
3081:     if (clPoints) *clPoints = NULL;
3082:   }
3083:   PetscFunctionReturn(PETSC_SUCCESS);
3084: }

3086: PetscErrorCode PetscSectionSetClosurePermutation_Internal(PetscSection section, PetscObject obj, PetscInt depth, PetscInt clSize, PetscCopyMode mode, PetscInt *clPerm)
3087: {
3088:   PetscInt                    i;
3089:   khiter_t                    iter;
3090:   int                         new_entry;
3091:   PetscSectionClosurePermKey  key = {depth, clSize};
3092:   PetscSectionClosurePermVal *val;

3094:   PetscFunctionBegin;
3095:   if (section->clObj != obj) {
3096:     PetscCall(PetscSectionDestroy(&section->clSection));
3097:     PetscCall(ISDestroy(&section->clPoints));
3098:   }
3099:   section->clObj = obj;
3100:   if (!section->clHash) PetscCall(PetscClPermCreate(&section->clHash));
3101:   iter = kh_put(ClPerm, section->clHash, key, &new_entry);
3102:   val  = &kh_val(section->clHash, iter);
3103:   if (!new_entry) {
3104:     PetscCall(PetscFree(val->perm));
3105:     PetscCall(PetscFree(val->invPerm));
3106:   }
3107:   if (mode == PETSC_COPY_VALUES) {
3108:     PetscCall(PetscMalloc1(clSize, &val->perm));
3109:     PetscCall(PetscArraycpy(val->perm, clPerm, clSize));
3110:   } else if (mode == PETSC_OWN_POINTER) {
3111:     val->perm = clPerm;
3112:   } else SETERRQ(PetscObjectComm(obj), PETSC_ERR_SUP, "Do not support borrowed arrays");
3113:   PetscCall(PetscMalloc1(clSize, &val->invPerm));
3114:   for (i = 0; i < clSize; ++i) val->invPerm[clPerm[i]] = i;
3115:   PetscFunctionReturn(PETSC_SUCCESS);
3116: }

3118: /*@
3119:   PetscSectionSetClosurePermutation - Set the dof permutation for the closure of each cell in the section, meaning clPerm[newIndex] = oldIndex.

3121:   Not Collective

3123:   Input Parameters:
3124: + section - The `PetscSection`
3125: . obj     - A `PetscObject` which serves as the key for this index (usually a `DM`)
3126: . depth   - Depth of points on which to apply the given permutation
3127: - perm    - Permutation of the cell dof closure

3129:   Level: intermediate

3131:   Notes:
3132:   The specified permutation will only be applied to points at depth whose closure size matches the length of perm.  In a
3133:   mixed-topology or variable-degree finite element space, this function can be called multiple times at each depth for
3134:   each topology and degree.

3136:   This approach assumes that (depth, len(perm)) uniquely identifies the desired permutation; this might not be true for
3137:   exotic/enriched spaces on mixed topology meshes.

3139: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `IS`, `PetscSectionGetClosurePermutation()`, `PetscSectionGetClosureIndex()`, `DMPlexCreateClosureIndex()`, `PetscCopyMode`
3140: @*/
3141: PetscErrorCode PetscSectionSetClosurePermutation(PetscSection section, PetscObject obj, PetscInt depth, IS perm)
3142: {
3143:   const PetscInt *clPerm = NULL;
3144:   PetscInt        clSize = 0;

3146:   PetscFunctionBegin;
3147:   if (perm) {
3148:     PetscCall(ISGetLocalSize(perm, &clSize));
3149:     PetscCall(ISGetIndices(perm, &clPerm));
3150:   }
3151:   PetscCall(PetscSectionSetClosurePermutation_Internal(section, obj, depth, clSize, PETSC_COPY_VALUES, (PetscInt *)clPerm));
3152:   if (perm) PetscCall(ISRestoreIndices(perm, &clPerm));
3153:   PetscFunctionReturn(PETSC_SUCCESS);
3154: }

3156: static PetscErrorCode PetscSectionGetClosurePermutation_Private(PetscSection section, PetscObject obj, PetscInt depth, PetscInt size, const PetscInt *perm[])
3157: {
3158:   PetscFunctionBegin;
3159:   if (section->clObj == obj) {
3160:     PetscSectionClosurePermKey k = {depth, size};
3161:     PetscSectionClosurePermVal v;

3163:     PetscCall(PetscClPermGet(section->clHash, k, &v));
3164:     if (perm) *perm = v.perm;
3165:   } else {
3166:     if (perm) *perm = NULL;
3167:   }
3168:   PetscFunctionReturn(PETSC_SUCCESS);
3169: }

3171: /*@
3172:   PetscSectionGetClosurePermutation - Get the dof permutation for the closure of each cell in the section, meaning clPerm[newIndex] = oldIndex.

3174:   Not Collective

3176:   Input Parameters:
3177: + section - The `PetscSection`
3178: . obj     - A `PetscObject` which serves as the key for this index (usually a DM)
3179: . depth   - Depth stratum on which to obtain closure permutation
3180: - clSize  - Closure size to be permuted (e.g., may vary with element topology and degree)

3182:   Output Parameter:
3183: . perm - The dof closure permutation

3185:   Level: intermediate

3187:   Note:
3188:   The user must destroy the `IS` that is returned.

3190: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `IS`, `PetscSectionSetClosurePermutation()`, `PetscSectionGetClosureInversePermutation()`, `PetscSectionGetClosureIndex()`, `PetscSectionSetClosureIndex()`, `DMPlexCreateClosureIndex()`
3191: @*/
3192: PetscErrorCode PetscSectionGetClosurePermutation(PetscSection section, PetscObject obj, PetscInt depth, PetscInt clSize, IS *perm)
3193: {
3194:   const PetscInt *clPerm = NULL;

3196:   PetscFunctionBegin;
3197:   PetscCall(PetscSectionGetClosurePermutation_Private(section, obj, depth, clSize, &clPerm));
3198:   PetscCheck(clPerm, PetscObjectComm(obj), PETSC_ERR_ARG_WRONG, "There is no closure permutation associated with this object for depth %" PetscInt_FMT " of size %" PetscInt_FMT, depth, clSize);
3199:   PetscCall(ISCreateGeneral(PETSC_COMM_SELF, clSize, clPerm, PETSC_USE_POINTER, perm));
3200:   PetscFunctionReturn(PETSC_SUCCESS);
3201: }

3203: PetscErrorCode PetscSectionGetClosureInversePermutation_Internal(PetscSection section, PetscObject obj, PetscInt depth, PetscInt size, const PetscInt *perm[])
3204: {
3205:   PetscFunctionBegin;
3206:   if (section->clObj == obj && section->clHash) {
3207:     PetscSectionClosurePermKey k = {depth, size};
3208:     PetscSectionClosurePermVal v;
3209:     PetscCall(PetscClPermGet(section->clHash, k, &v));
3210:     if (perm) *perm = v.invPerm;
3211:   } else {
3212:     if (perm) *perm = NULL;
3213:   }
3214:   PetscFunctionReturn(PETSC_SUCCESS);
3215: }

3217: /*@
3218:   PetscSectionGetClosureInversePermutation - Get the inverse dof permutation for the closure of each cell in the section, meaning clPerm[oldIndex] = newIndex.

3220:   Not Collective

3222:   Input Parameters:
3223: + section - The `PetscSection`
3224: . obj     - A `PetscObject` which serves as the key for this index (usually a `DM`)
3225: . depth   - Depth stratum on which to obtain closure permutation
3226: - clSize  - Closure size to be permuted (e.g., may vary with element topology and degree)

3228:   Output Parameter:
3229: . perm - The dof closure permutation

3231:   Level: intermediate

3233:   Note:
3234:   The user must destroy the `IS` that is returned.

3236: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `IS`, `PetscSectionSetClosurePermutation()`, `PetscSectionGetClosureIndex()`, `PetscSectionSetClosureIndex()`, `DMPlexCreateClosureIndex()`
3237: @*/
3238: PetscErrorCode PetscSectionGetClosureInversePermutation(PetscSection section, PetscObject obj, PetscInt depth, PetscInt clSize, IS *perm)
3239: {
3240:   const PetscInt *clPerm = NULL;

3242:   PetscFunctionBegin;
3243:   PetscCall(PetscSectionGetClosureInversePermutation_Internal(section, obj, depth, clSize, &clPerm));
3244:   PetscCall(ISCreateGeneral(PETSC_COMM_SELF, clSize, clPerm, PETSC_USE_POINTER, perm));
3245:   PetscFunctionReturn(PETSC_SUCCESS);
3246: }

3248: /*@
3249:   PetscSectionGetField - Get the `PetscSection` associated with a single field

3251:   Input Parameters:
3252: + s     - The `PetscSection`
3253: - field - The field number

3255:   Output Parameter:
3256: . subs - The `PetscSection` for the given field, note the chart of `subs` is not set

3258:   Level: intermediate

3260:   Note:
3261:   Does not increase the reference count of the selected sub-section. There is no matching `PetscSectionRestoreField()`

3263: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `IS`, `PetscSectionSetNumFields()`
3264: @*/
3265: PetscErrorCode PetscSectionGetField(PetscSection s, PetscInt field, PetscSection *subs)
3266: {
3267:   PetscFunctionBegin;
3269:   PetscAssertPointer(subs, 3);
3270:   PetscSectionCheckValidField(field, s->numFields);
3271:   *subs = s->field[field];
3272:   PetscFunctionReturn(PETSC_SUCCESS);
3273: }

3275: PetscClassId      PETSC_SECTION_SYM_CLASSID;
3276: PetscFunctionList PetscSectionSymList = NULL;

3278: /*@
3279:   PetscSectionSymCreate - Creates an empty `PetscSectionSym` object.

3281:   Collective

3283:   Input Parameter:
3284: . comm - the MPI communicator

3286:   Output Parameter:
3287: . sym - pointer to the new set of symmetries

3289:   Level: developer

3291: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionSym`, `PetscSectionSymDestroy()`
3292: @*/
3293: PetscErrorCode PetscSectionSymCreate(MPI_Comm comm, PetscSectionSym *sym)
3294: {
3295:   PetscFunctionBegin;
3296:   PetscAssertPointer(sym, 2);
3297:   PetscCall(ISInitializePackage());

3299:   PetscCall(PetscHeaderCreate(*sym, PETSC_SECTION_SYM_CLASSID, "PetscSectionSym", "Section Symmetry", "IS", comm, PetscSectionSymDestroy, PetscSectionSymView));
3300:   PetscFunctionReturn(PETSC_SUCCESS);
3301: }

3303: /*@
3304:   PetscSectionSymSetType - Builds a `PetscSectionSym`, for a particular implementation.

3306:   Collective

3308:   Input Parameters:
3309: + sym    - The section symmetry object
3310: - method - The name of the section symmetry type

3312:   Level: developer

3314: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSymType`, `PetscSectionSymGetType()`, `PetscSectionSymCreate()`
3315: @*/
3316: PetscErrorCode PetscSectionSymSetType(PetscSectionSym sym, PetscSectionSymType method)
3317: {
3318:   PetscErrorCode (*r)(PetscSectionSym);
3319:   PetscBool match;

3321:   PetscFunctionBegin;
3323:   PetscCall(PetscObjectTypeCompare((PetscObject)sym, method, &match));
3324:   if (match) PetscFunctionReturn(PETSC_SUCCESS);

3326:   PetscCall(PetscFunctionListFind(PetscSectionSymList, method, &r));
3327:   PetscCheck(r, PetscObjectComm((PetscObject)sym), PETSC_ERR_ARG_UNKNOWN_TYPE, "Unknown PetscSectionSym type: %s", method);
3328:   PetscTryTypeMethod(sym, destroy);
3329:   sym->ops->destroy = NULL;

3331:   PetscCall((*r)(sym));
3332:   PetscCall(PetscObjectChangeTypeName((PetscObject)sym, method));
3333:   PetscFunctionReturn(PETSC_SUCCESS);
3334: }

3336: /*@
3337:   PetscSectionSymGetType - Gets the section symmetry type name (as a string) from the `PetscSectionSym`.

3339:   Not Collective

3341:   Input Parameter:
3342: . sym - The section symmetry

3344:   Output Parameter:
3345: . type - The index set type name

3347:   Level: developer

3349: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSymType`, `PetscSectionSymSetType()`, `PetscSectionSymCreate()`
3350: @*/
3351: PetscErrorCode PetscSectionSymGetType(PetscSectionSym sym, PetscSectionSymType *type)
3352: {
3353:   PetscFunctionBegin;
3355:   PetscAssertPointer(type, 2);
3356:   *type = ((PetscObject)sym)->type_name;
3357:   PetscFunctionReturn(PETSC_SUCCESS);
3358: }

3360: /*@C
3361:   PetscSectionSymRegister - Registers a new section symmetry implementation

3363:   Not Collective, No Fortran Support

3365:   Input Parameters:
3366: + sname    - The name of a new user-defined creation routine
3367: - function - The creation routine itself

3369:   Level: developer

3371:   Notes:
3372:   `PetscSectionSymRegister()` may be called multiple times to add several user-defined vectors

3374: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSymType`, `PetscSectionSymCreate()`, `PetscSectionSymSetType()`
3375: @*/
3376: PetscErrorCode PetscSectionSymRegister(const char sname[], PetscErrorCode (*function)(PetscSectionSym))
3377: {
3378:   PetscFunctionBegin;
3379:   PetscCall(ISInitializePackage());
3380:   PetscCall(PetscFunctionListAdd(&PetscSectionSymList, sname, function));
3381:   PetscFunctionReturn(PETSC_SUCCESS);
3382: }

3384: /*@
3385:   PetscSectionSymDestroy - Destroys a section symmetry.

3387:   Collective

3389:   Input Parameter:
3390: . sym - the section symmetry

3392:   Level: developer

3394: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSymCreate()`
3395: @*/
3396: PetscErrorCode PetscSectionSymDestroy(PetscSectionSym *sym)
3397: {
3398:   SymWorkLink link, next;

3400:   PetscFunctionBegin;
3401:   if (!*sym) PetscFunctionReturn(PETSC_SUCCESS);
3403:   if (--((PetscObject)*sym)->refct > 0) {
3404:     *sym = NULL;
3405:     PetscFunctionReturn(PETSC_SUCCESS);
3406:   }
3407:   PetscTryTypeMethod(*sym, destroy);
3408:   PetscCheck(!(*sym)->workout, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Work array still checked out");
3409:   for (link = (*sym)->workin; link; link = next) {
3410:     PetscInt    **perms = (PetscInt **)link->perms;
3411:     PetscScalar **rots  = (PetscScalar **)link->rots;
3412:     PetscCall(PetscFree2(perms, rots));
3413:     next = link->next;
3414:     PetscCall(PetscFree(link));
3415:   }
3416:   (*sym)->workin = NULL;
3417:   PetscCall(PetscHeaderDestroy(sym));
3418:   PetscFunctionReturn(PETSC_SUCCESS);
3419: }

3421: /*@
3422:   PetscSectionSymView - Displays a section symmetry

3424:   Collective

3426:   Input Parameters:
3427: + sym    - the index set
3428: - viewer - viewer used to display the set, for example `PETSC_VIEWER_STDOUT_SELF`.

3430:   Level: developer

3432: .seealso: `PetscSectionSym`, `PetscViewer`, `PetscViewerASCIIOpen()`
3433: @*/
3434: PetscErrorCode PetscSectionSymView(PetscSectionSym sym, PetscViewer viewer)
3435: {
3436:   PetscFunctionBegin;
3438:   if (!viewer) PetscCall(PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)sym), &viewer));
3440:   PetscCheckSameComm(sym, 1, viewer, 2);
3441:   PetscCall(PetscObjectPrintClassNamePrefixType((PetscObject)sym, viewer));
3442:   PetscTryTypeMethod(sym, view, viewer);
3443:   PetscFunctionReturn(PETSC_SUCCESS);
3444: }

3446: /*@
3447:   PetscSectionSetSym - Set the symmetries for the data referred to by the section

3449:   Collective

3451:   Input Parameters:
3452: + section - the section describing data layout
3453: - sym     - the symmetry describing the affect of orientation on the access of the data

3455:   Level: developer

3457: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionGetSym()`, `PetscSectionSymCreate()`
3458: @*/
3459: PetscErrorCode PetscSectionSetSym(PetscSection section, PetscSectionSym sym)
3460: {
3461:   PetscFunctionBegin;
3463:   PetscCall(PetscSectionSymDestroy(&section->sym));
3464:   if (sym) {
3466:     PetscCheckSameComm(section, 1, sym, 2);
3467:     PetscCall(PetscObjectReference((PetscObject)sym));
3468:   }
3469:   section->sym = sym;
3470:   PetscFunctionReturn(PETSC_SUCCESS);
3471: }

3473: /*@
3474:   PetscSectionGetSym - Get the symmetries for the data referred to by the section

3476:   Not Collective

3478:   Input Parameter:
3479: . section - the section describing data layout

3481:   Output Parameter:
3482: . sym - the symmetry describing the affect of orientation on the access of the data, provided previously by `PetscSectionSetSym()`

3484:   Level: developer

3486: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSetSym()`, `PetscSectionSymCreate()`
3487: @*/
3488: PetscErrorCode PetscSectionGetSym(PetscSection section, PetscSectionSym *sym)
3489: {
3490:   PetscFunctionBegin;
3492:   *sym = section->sym;
3493:   PetscFunctionReturn(PETSC_SUCCESS);
3494: }

3496: /*@
3497:   PetscSectionSetFieldSym - Set the symmetries for the data referred to by a field of the section

3499:   Collective

3501:   Input Parameters:
3502: + section - the section describing data layout
3503: . field   - the field number
3504: - sym     - the symmetry describing the affect of orientation on the access of the data

3506:   Level: developer

3508: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionGetFieldSym()`, `PetscSectionSymCreate()`
3509: @*/
3510: PetscErrorCode PetscSectionSetFieldSym(PetscSection section, PetscInt field, PetscSectionSym sym)
3511: {
3512:   PetscFunctionBegin;
3514:   PetscSectionCheckValidField(field, section->numFields);
3515:   PetscCall(PetscSectionSetSym(section->field[field], sym));
3516:   PetscFunctionReturn(PETSC_SUCCESS);
3517: }

3519: /*@
3520:   PetscSectionGetFieldSym - Get the symmetries for the data referred to by a field of the section

3522:   Collective

3524:   Input Parameters:
3525: + section - the section describing data layout
3526: - field   - the field number

3528:   Output Parameter:
3529: . sym - the symmetry describing the affect of orientation on the access of the data

3531:   Level: developer

3533: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSetFieldSym()`, `PetscSectionSymCreate()`
3534: @*/
3535: PetscErrorCode PetscSectionGetFieldSym(PetscSection section, PetscInt field, PetscSectionSym *sym)
3536: {
3537:   PetscFunctionBegin;
3539:   PetscSectionCheckValidField(field, section->numFields);
3540:   *sym = section->field[field]->sym;
3541:   PetscFunctionReturn(PETSC_SUCCESS);
3542: }

3544: /*@C
3545:   PetscSectionGetPointSyms - Get the symmetries for a set of points in a `PetscSection` under specific orientations.

3547:   Not Collective

3549:   Input Parameters:
3550: + section   - the section
3551: . numPoints - the number of points
3552: - points    - an array of size 2 * `numPoints`, containing a list of (point, orientation) pairs. (An orientation is an
3553:               arbitrary integer: its interpretation is up to sym.  Orientations are used by `DM`: for their interpretation in that
3554:               context, see `DMPlexGetConeOrientation()`).

3556:   Output Parameters:
3557: + perms - The permutations for the given orientations (or `NULL` if there is no symmetry or the permutation is the identity).
3558: - rots  - The field rotations symmetries for the given orientations (or `NULL` if there is no symmetry or the rotations are all
3559:     identity).

3561:   Example of usage, gathering dofs into a local array (lArray) from a section array (sArray):
3562: .vb
3563:      const PetscInt    **perms;
3564:      const PetscScalar **rots;
3565:      PetscInt            lOffset;

3567:      PetscSectionGetPointSyms(section,numPoints,points,&perms,&rots);
3568:      for (i = 0, lOffset = 0; i < numPoints; i++) {
3569:        PetscInt           point = points[2*i], dof, sOffset;
3570:        const PetscInt    *perm  = perms ? perms[i] : NULL;
3571:        const PetscScalar *rot   = rots  ? rots[i]  : NULL;

3573:        PetscSectionGetDof(section,point,&dof);
3574:        PetscSectionGetOffset(section,point,&sOffset);

3576:        if (perm) { for (j = 0; j < dof; j++) lArray[lOffset + perm[j]]  = sArray[sOffset + j]; }
3577:        else      { for (j = 0; j < dof; j++) lArray[lOffset +      j ]  = sArray[sOffset + j]; }
3578:        if (rot)  { for (j = 0; j < dof; j++) lArray[lOffset +      j ] *= rot[j];              }
3579:        lOffset += dof;
3580:      }
3581:      PetscSectionRestorePointSyms(section,numPoints,points,&perms,&rots);
3582: .ve

3584:   Example of usage, adding dofs into a section array (sArray) from a local array (lArray):
3585: .vb
3586:      const PetscInt    **perms;
3587:      const PetscScalar **rots;
3588:      PetscInt            lOffset;

3590:      PetscSectionGetPointSyms(section,numPoints,points,&perms,&rots);
3591:      for (i = 0, lOffset = 0; i < numPoints; i++) {
3592:        PetscInt           point = points[2*i], dof, sOffset;
3593:        const PetscInt    *perm  = perms ? perms[i] : NULL;
3594:        const PetscScalar *rot   = rots  ? rots[i]  : NULL;

3596:        PetscSectionGetDof(section,point,&dof);
3597:        PetscSectionGetOffset(section,point,&sOff);

3599:        if (perm) { for (j = 0; j < dof; j++) sArray[sOffset + j] += lArray[lOffset + perm[j]] * (rot ? PetscConj(rot[perm[j]]) : 1.); }
3600:        else      { for (j = 0; j < dof; j++) sArray[sOffset + j] += lArray[lOffset +      j ] * (rot ? PetscConj(rot[     j ]) : 1.); }
3601:        offset += dof;
3602:      }
3603:      PetscSectionRestorePointSyms(section,numPoints,points,&perms,&rots);
3604: .ve

3606:   Level: developer

3608:   Notes:
3609:   `PetscSectionSetSym()` must have been previously called to provide the symmetries to the `PetscSection`

3611:   Use `PetscSectionRestorePointSyms()` when finished with the data

3613: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionRestorePointSyms()`, `PetscSectionSymCreate()`, `PetscSectionSetSym()`, `PetscSectionGetSym()`
3614: @*/
3615: PetscErrorCode PetscSectionGetPointSyms(PetscSection section, PetscInt numPoints, const PetscInt *points, const PetscInt ***perms, const PetscScalar ***rots)
3616: {
3617:   PetscSectionSym sym;

3619:   PetscFunctionBegin;
3621:   if (numPoints) PetscAssertPointer(points, 3);
3622:   if (perms) *perms = NULL;
3623:   if (rots) *rots = NULL;
3624:   sym = section->sym;
3625:   if (sym && (perms || rots)) {
3626:     SymWorkLink link;

3628:     if (sym->workin) {
3629:       link        = sym->workin;
3630:       sym->workin = sym->workin->next;
3631:     } else {
3632:       PetscCall(PetscNew(&link));
3633:     }
3634:     if (numPoints > link->numPoints) {
3635:       PetscInt    **perms = (PetscInt **)link->perms;
3636:       PetscScalar **rots  = (PetscScalar **)link->rots;
3637:       PetscCall(PetscFree2(perms, rots));
3638:       PetscCall(PetscMalloc2(numPoints, (PetscInt ***)&link->perms, numPoints, (PetscScalar ***)&link->rots));
3639:       link->numPoints = numPoints;
3640:     }
3641:     link->next   = sym->workout;
3642:     sym->workout = link;
3643:     PetscCall(PetscArrayzero((PetscInt **)link->perms, numPoints));
3644:     PetscCall(PetscArrayzero((PetscInt **)link->rots, numPoints));
3645:     PetscUseTypeMethod(sym, getpoints, section, numPoints, points, link->perms, link->rots);
3646:     if (perms) *perms = link->perms;
3647:     if (rots) *rots = link->rots;
3648:   }
3649:   PetscFunctionReturn(PETSC_SUCCESS);
3650: }

3652: /*@C
3653:   PetscSectionRestorePointSyms - Restore the symmetries returned by `PetscSectionGetPointSyms()`

3655:   Not Collective

3657:   Input Parameters:
3658: + section   - the section
3659: . numPoints - the number of points
3660: . points    - an array of size 2 * `numPoints`, containing a list of (point, orientation) pairs. (An orientation is an
3661:               arbitrary integer: its interpretation is up to sym.  Orientations are used by `DM`: for their interpretation in that
3662:               context, see `DMPlexGetConeOrientation()`).
3663: . perms     - The permutations for the given orientations: set to `NULL` at conclusion
3664: - rots      - The field rotations symmetries for the given orientations: set to `NULL` at conclusion

3666:   Level: developer

3668: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionGetPointSyms()`, `PetscSectionSymCreate()`, `PetscSectionSetSym()`, `PetscSectionGetSym()`
3669: @*/
3670: PetscErrorCode PetscSectionRestorePointSyms(PetscSection section, PetscInt numPoints, const PetscInt *points, const PetscInt ***perms, const PetscScalar ***rots)
3671: {
3672:   PetscSectionSym sym;

3674:   PetscFunctionBegin;
3676:   sym = section->sym;
3677:   if (sym && (perms || rots)) {
3678:     SymWorkLink *p, link;

3680:     for (p = &sym->workout; (link = *p); p = &link->next) {
3681:       if ((perms && link->perms == *perms) || (rots && link->rots == *rots)) {
3682:         *p          = link->next;
3683:         link->next  = sym->workin;
3684:         sym->workin = link;
3685:         if (perms) *perms = NULL;
3686:         if (rots) *rots = NULL;
3687:         PetscFunctionReturn(PETSC_SUCCESS);
3688:       }
3689:     }
3690:     SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Array was not checked out");
3691:   }
3692:   PetscFunctionReturn(PETSC_SUCCESS);
3693: }

3695: /*@C
3696:   PetscSectionGetFieldPointSyms - Get the symmetries for a set of points in a field of a `PetscSection` under specific orientations.

3698:   Not Collective

3700:   Input Parameters:
3701: + section   - the section
3702: . field     - the field of the section
3703: . numPoints - the number of points
3704: - points    - an array of size 2 * `numPoints`, containing a list of (point, orientation) pairs. (An orientation is an
3705:     arbitrary integer: its interpretation is up to sym.  Orientations are used by `DM`: for their interpretation in that
3706:     context, see `DMPlexGetConeOrientation()`).

3708:   Output Parameters:
3709: + perms - The permutations for the given orientations (or `NULL` if there is no symmetry or the permutation is the identity).
3710: - rots  - The field rotations symmetries for the given orientations (or `NULL` if there is no symmetry or the rotations are all
3711:     identity).

3713:   Level: developer

3715:   Notes:
3716:   `PetscSectionSetFieldSym()` must have been previously called to provide the symmetries to the `PetscSection`

3718:   Use `PetscSectionRestoreFieldPointSyms()` when finished with the data

3720: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionGetPointSyms()`, `PetscSectionRestoreFieldPointSyms()`
3721: @*/
3722: PetscErrorCode PetscSectionGetFieldPointSyms(PetscSection section, PetscInt field, PetscInt numPoints, const PetscInt *points, const PetscInt ***perms, const PetscScalar ***rots)
3723: {
3724:   PetscFunctionBegin;
3726:   PetscCheck(field <= section->numFields, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "field %" PetscInt_FMT " greater than number of fields (%" PetscInt_FMT ") in section", field, section->numFields);
3727:   PetscCall(PetscSectionGetPointSyms(section->field[field], numPoints, points, perms, rots));
3728:   PetscFunctionReturn(PETSC_SUCCESS);
3729: }

3731: /*@C
3732:   PetscSectionRestoreFieldPointSyms - Restore the symmetries returned by `PetscSectionGetFieldPointSyms()`

3734:   Not Collective

3736:   Input Parameters:
3737: + section   - the section
3738: . field     - the field number
3739: . numPoints - the number of points
3740: . points    - an array of size 2 * `numPoints`, containing a list of (point, orientation) pairs. (An orientation is an
3741:     arbitrary integer: its interpretation is up to sym.  Orientations are used by `DM`: for their interpretation in that
3742:     context, see `DMPlexGetConeOrientation()`).
3743: . perms     - The permutations for the given orientations: set to NULL at conclusion
3744: - rots      - The field rotations symmetries for the given orientations: set to NULL at conclusion

3746:   Level: developer

3748: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionRestorePointSyms()`, `petscSectionGetFieldPointSyms()`, `PetscSectionSymCreate()`, `PetscSectionSetSym()`, `PetscSectionGetSym()`
3749: @*/
3750: PetscErrorCode PetscSectionRestoreFieldPointSyms(PetscSection section, PetscInt field, PetscInt numPoints, const PetscInt *points, const PetscInt ***perms, const PetscScalar ***rots)
3751: {
3752:   PetscFunctionBegin;
3754:   PetscCheck(field <= section->numFields, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "field %" PetscInt_FMT " greater than number of fields (%" PetscInt_FMT ") in section", field, section->numFields);
3755:   PetscCall(PetscSectionRestorePointSyms(section->field[field], numPoints, points, perms, rots));
3756:   PetscFunctionReturn(PETSC_SUCCESS);
3757: }

3759: /*@
3760:   PetscSectionSymCopy - Copy the symmetries, assuming that the point structure is compatible

3762:   Not Collective

3764:   Input Parameter:
3765: . sym - the `PetscSectionSym`

3767:   Output Parameter:
3768: . nsym - the equivalent symmetries

3770:   Level: developer

3772: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSymCreate()`, `PetscSectionSetSym()`, `PetscSectionGetSym()`, `PetscSectionSymLabelSetStratum()`, `PetscSectionGetPointSyms()`
3773: @*/
3774: PetscErrorCode PetscSectionSymCopy(PetscSectionSym sym, PetscSectionSym nsym)
3775: {
3776:   PetscFunctionBegin;
3779:   PetscTryTypeMethod(sym, copy, nsym);
3780:   PetscFunctionReturn(PETSC_SUCCESS);
3781: }

3783: /*@
3784:   PetscSectionSymDistribute - Distribute the symmetries in accordance with the input `PetscSF`

3786:   Collective

3788:   Input Parameters:
3789: + sym         - the `PetscSectionSym`
3790: - migrationSF - the distribution map from roots to leaves

3792:   Output Parameter:
3793: . dsym - the redistributed symmetries

3795:   Level: developer

3797: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSymCreate()`, `PetscSectionSetSym()`, `PetscSectionGetSym()`, `PetscSectionSymLabelSetStratum()`, `PetscSectionGetPointSyms()`
3798: @*/
3799: PetscErrorCode PetscSectionSymDistribute(PetscSectionSym sym, PetscSF migrationSF, PetscSectionSym *dsym)
3800: {
3801:   PetscFunctionBegin;
3804:   PetscAssertPointer(dsym, 3);
3805:   PetscTryTypeMethod(sym, distribute, migrationSF, dsym);
3806:   PetscFunctionReturn(PETSC_SUCCESS);
3807: }

3809: /*@
3810:   PetscSectionGetUseFieldOffsets - Get the flag indicating if field offsets are used directly in a global section, rather than just the point offset

3812:   Not Collective

3814:   Input Parameter:
3815: . s - the global `PetscSection`

3817:   Output Parameter:
3818: . flg - the flag

3820:   Level: developer

3822: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSetChart()`, `PetscSectionCreate()`
3823: @*/
3824: PetscErrorCode PetscSectionGetUseFieldOffsets(PetscSection s, PetscBool *flg)
3825: {
3826:   PetscFunctionBegin;
3828:   *flg = s->useFieldOff;
3829:   PetscFunctionReturn(PETSC_SUCCESS);
3830: }

3832: /*@
3833:   PetscSectionSetUseFieldOffsets - Set the flag to use field offsets directly in a global section, rather than just the point offset

3835:   Not Collective

3837:   Input Parameters:
3838: + s   - the global `PetscSection`
3839: - flg - the flag

3841:   Level: developer

3843: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionGetUseFieldOffsets()`, `PetscSectionSetChart()`, `PetscSectionCreate()`
3844: @*/
3845: PetscErrorCode PetscSectionSetUseFieldOffsets(PetscSection s, PetscBool flg)
3846: {
3847:   PetscFunctionBegin;
3849:   s->useFieldOff = flg;
3850:   PetscFunctionReturn(PETSC_SUCCESS);
3851: }

3853: #define PetscSectionExpandPoints_Loop(TYPE) \
3854:   do { \
3855:     PetscInt i, n, o0, o1, size; \
3856:     TYPE    *a0 = (TYPE *)origArray, *a1; \
3857:     PetscCall(PetscSectionGetStorageSize(s, &size)); \
3858:     PetscCall(PetscMalloc1(size, &a1)); \
3859:     for (i = 0; i < npoints; i++) { \
3860:       PetscCall(PetscSectionGetOffset(origSection, points_[i], &o0)); \
3861:       PetscCall(PetscSectionGetOffset(s, i, &o1)); \
3862:       PetscCall(PetscSectionGetDof(s, i, &n)); \
3863:       PetscCall(PetscMemcpy(&a1[o1], &a0[o0], n * unitsize)); \
3864:     } \
3865:     *newArray = (void *)a1; \
3866:   } while (0)

3868: /*@
3869:   PetscSectionExtractDofsFromArray - Extracts elements of an array corresponding to DOFs of specified points.

3871:   Not Collective

3873:   Input Parameters:
3874: + origSection - the `PetscSection` describing the layout of the array
3875: . dataType    - `MPI_Datatype` describing the data type of the array (currently only `MPIU_INT`, `MPIU_SCALAR`, `MPIU_REAL`)
3876: . origArray   - the array; its size must be equal to the storage size of `origSection`
3877: - points      - `IS` with points to extract; its indices must lie in the chart of `origSection`

3879:   Output Parameters:
3880: + newSection - the new `PetscSection` describing the layout of the new array (with points renumbered 0,1,... but preserving numbers of DOFs)
3881: - newArray   - the array of the extracted DOFs; its size is the storage size of `newSection`

3883:   Level: developer

3885: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionGetChart()`, `PetscSectionGetDof()`, `PetscSectionGetStorageSize()`, `PetscSectionCreate()`
3886: @*/
3887: PetscErrorCode PetscSectionExtractDofsFromArray(PetscSection origSection, MPI_Datatype dataType, const void *origArray, IS points, PetscSection *newSection, void *newArray[])
3888: {
3889:   PetscSection    s;
3890:   const PetscInt *points_;
3891:   PetscInt        i, n, npoints, pStart, pEnd;
3892:   PetscMPIInt     unitsize;

3894:   PetscFunctionBegin;
3896:   PetscAssertPointer(origArray, 3);
3898:   if (newSection) PetscAssertPointer(newSection, 5);
3899:   if (newArray) PetscAssertPointer(newArray, 6);
3900:   PetscCallMPI(MPI_Type_size(dataType, &unitsize));
3901:   PetscCall(ISGetLocalSize(points, &npoints));
3902:   PetscCall(ISGetIndices(points, &points_));
3903:   PetscCall(PetscSectionGetChart(origSection, &pStart, &pEnd));
3904:   PetscCall(PetscSectionCreate(PETSC_COMM_SELF, &s));
3905:   PetscCall(PetscSectionSetChart(s, 0, npoints));
3906:   for (i = 0; i < npoints; i++) {
3907:     PetscCheck(points_[i] >= pStart && points_[i] < pEnd, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "point %" PetscInt_FMT " (index %" PetscInt_FMT ") in input IS out of input section's chart", points_[i], i);
3908:     PetscCall(PetscSectionGetDof(origSection, points_[i], &n));
3909:     PetscCall(PetscSectionSetDof(s, i, n));
3910:   }
3911:   PetscCall(PetscSectionSetUp(s));
3912:   if (newArray) {
3913:     if (dataType == MPIU_INT) {
3914:       PetscSectionExpandPoints_Loop(PetscInt);
3915:     } else if (dataType == MPIU_SCALAR) {
3916:       PetscSectionExpandPoints_Loop(PetscScalar);
3917:     } else if (dataType == MPIU_REAL) {
3918:       PetscSectionExpandPoints_Loop(PetscReal);
3919:     } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "not implemented for this MPI_Datatype");
3920:   }
3921:   if (newSection) {
3922:     *newSection = s;
3923:   } else {
3924:     PetscCall(PetscSectionDestroy(&s));
3925:   }
3926:   PetscCall(ISRestoreIndices(points, &points_));
3927:   PetscFunctionReturn(PETSC_SUCCESS);
3928: }