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, MPI_C_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: static inline PetscErrorCode PrintArrayElement(void *array, PetscDataType data_type, PetscCount index, PetscViewer viewer)
    2600: {
    2601:   PetscFunctionBeginUser;
    2602:   switch (data_type) {
    2603:   case PETSC_INT: {
    2604:     PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %2" PetscInt_FMT, ((PetscInt *)array)[index]));
    2605:     break;
    2606:   }
    2607:   case PETSC_INT32: {
    2608:     PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %2" PetscInt32_FMT, ((PetscInt32 *)array)[index]));
    2609:     break;
    2610:   }
    2611:   case PETSC_INT64: {
    2612:     PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %2" PetscInt64_FMT, ((PetscInt64 *)array)[index]));
    2613:     break;
    2614:   }
    2615:   case PETSC_COUNT: {
    2616:     PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %2" PetscCount_FMT, ((PetscCount *)array)[index]));
    2617:     break;
    2618:   }
    2619:   // PETSC_SCALAR is set to the appropriate type
    2620:   case PETSC_DOUBLE: {
    2621:     PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %g", ((double *)array)[index]));
    2622:     break;
    2623:   }
    2624:   case PETSC_FLOAT: {
    2625:     PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %g", (double)((float *)array)[index]));
    2626:     break;
    2627:   }
    2628: #if defined(PETSC_USE_REAL___FLOAT128)
    2629:   case PETSC___FLOAT128: {
    2630:     PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %g", (double)((PetscReal *)array)[index]));
    2631:     break;
    2632:   }
    2633: #endif
    2634: #if defined(PETSC_USE_REAL___FP16)
    2635:   case PETSC___FP16: {
    2636:     PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %g", (double)((PetscReal *)array)[index]));
    2637:     break;
    2638:   }
    2639: #endif
    2640: #if defined(PETSC_HAVE_COMPLEX)
    2641:   case PETSC_COMPLEX: {
    2642:     PetscComplex v = ((PetscComplex *)array)[index];
    2643:     if (PetscImaginaryPartComplex(v) > 0.0) {
    2644:       PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %g + %g i", (double)PetscRealPartComplex(v), (double)PetscImaginaryPartComplex(v)));
    2645:     } else if (PetscImaginaryPartComplex(v) < 0.0) {
    2646:       PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %g - %g i", (double)PetscRealPartComplex(v), (double)(-PetscImaginaryPartComplex(v))));
    2647:     } else {
    2648:       PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %g", (double)PetscRealPartComplex(v)));
    2649:     }
    2650:     break;
    2651:   }
    2652: #endif
    2653:   default:
    2654:     SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_SUP, "PetscDataType %d (%s) not supported", data_type, PetscDataTypes[data_type]);
    2655:   }
    2656:   PetscFunctionReturn(PETSC_SUCCESS);
    2657: }

    2659: PetscErrorCode PetscSectionArrayView_ASCII_Internal(PetscSection s, void *array, PetscDataType data_type, PetscViewer viewer)
    2660: {
    2661:   PetscInt    p, i;
    2662:   PetscMPIInt rank;

    2664:   PetscFunctionBegin;
    2665:   PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank));
    2666:   PetscCall(PetscViewerASCIIPushSynchronized(viewer));
    2667:   PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "Process %d:\n", rank));
    2668:   for (p = 0; p < s->pEnd - s->pStart; ++p) {
    2669:     if (s->bc && (s->bc->atlasDof[p] > 0)) {
    2670:       PetscInt b;

    2672:       PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "  (%4" PetscInt_FMT ") dof %2" PetscInt_FMT " offset %3" PetscInt_FMT, p + s->pStart, s->atlasDof[p], s->atlasOff[p]));
    2673:       for (i = s->atlasOff[p]; i < s->atlasOff[p] + s->atlasDof[p]; ++i) PetscCall(PrintArrayElement(array, data_type, i, viewer));
    2674:       PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " constrained"));
    2675:       for (b = 0; b < s->bc->atlasDof[p]; ++b) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %" PetscInt_FMT, s->bcIndices[s->bc->atlasOff[p] + b]));
    2676:       PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\n"));
    2677:     } else {
    2678:       PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "  (%4" PetscInt_FMT ") dof %2" PetscInt_FMT " offset %3" PetscInt_FMT, p + s->pStart, s->atlasDof[p], s->atlasOff[p]));
    2679:       for (i = s->atlasOff[p]; i < s->atlasOff[p] + s->atlasDof[p]; ++i) PetscCall(PrintArrayElement(array, data_type, i, viewer));
    2680:       PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\n"));
    2681:     }
    2682:   }
    2683:   PetscCall(PetscViewerFlush(viewer));
    2684:   PetscCall(PetscViewerASCIIPopSynchronized(viewer));
    2685:   PetscFunctionReturn(PETSC_SUCCESS);
    2686: }

    2688: /*@
    2689:   PetscSectionArrayView - View an array, using the section to structure the values

    2691:   Collective

    2693:   Input Parameters:
    2694: + s         - the organizing `PetscSection`
    2695: . array     - the array of values
    2696: . data_type - the `PetscDataType` of the array
    2697: - viewer    - the `PetscViewer`

    2699:   Level: developer

    2701: .seealso: `PetscSection`, `PetscViewer`, `PetscSectionCreate()`, `VecSetValuesSection()`, `PetscSectionVecView()`
    2702: @*/
    2703: PetscErrorCode PetscSectionArrayView(PetscSection s, void *array, PetscDataType data_type, PetscViewer viewer)
    2704: {
    2705:   PetscBool isascii;
    2706:   PetscInt  f;

    2708:   PetscFunctionBegin;
    2710:   if (!array) {
    2711:     PetscInt size;
    2712:     PetscCall(PetscSectionGetStorageSize(s, &size));
    2713:     PetscCheck(size == 0, PetscObjectComm((PetscObject)s), PETSC_ERR_ARG_SIZ, "NULL array passed, but section's storage size is non-zero");
    2714:   } else PetscAssertPointer(array, 2);
    2715:   if (!viewer) PetscCall(PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)s), &viewer));
    2717:   PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &isascii));
    2718:   if (isascii) {
    2719:     if (s->numFields) {
    2720:       PetscCall(PetscViewerASCIIPrintf(viewer, "Array with %" PetscInt_FMT " fields\n", s->numFields));
    2721:       for (f = 0; f < s->numFields; ++f) {
    2722:         PetscCall(PetscViewerASCIIPrintf(viewer, "  field %" PetscInt_FMT " with %" PetscInt_FMT " components\n", f, s->numFieldComponents[f]));
    2723:         PetscCall(PetscSectionArrayView_ASCII_Internal(s->field[f], array, data_type, viewer));
    2724:       }
    2725:     } else {
    2726:       PetscCall(PetscSectionArrayView_ASCII_Internal(s, array, data_type, viewer));
    2727:     }
    2728:   }
    2729:   PetscFunctionReturn(PETSC_SUCCESS);
    2730: }

    2732: /*@
    2733:   PetscSectionResetClosurePermutation - Remove any existing closure permutation

    2735:   Input Parameter:
    2736: . section - The `PetscSection`

    2738:   Level: intermediate

    2740: .seealso: `PetscSectionSetClosurePermutation()`, `PetscSectionSetClosureIndex()`, `PetscSectionReset()`
    2741: @*/
    2742: PetscErrorCode PetscSectionResetClosurePermutation(PetscSection section)
    2743: {
    2744:   PetscSectionClosurePermVal clVal;

    2746:   PetscFunctionBegin;
    2747:   if (!section->clHash) PetscFunctionReturn(PETSC_SUCCESS);
    2748:   kh_foreach_value(section->clHash, clVal, {
    2749:     PetscCall(PetscFree(clVal.perm));
    2750:     PetscCall(PetscFree(clVal.invPerm));
    2751:   });
    2752:   kh_destroy(ClPerm, section->clHash);
    2753:   section->clHash = NULL;
    2754:   PetscFunctionReturn(PETSC_SUCCESS);
    2755: }

    2757: /*@
    2758:   PetscSectionReset - Frees all section data, the section is then as if `PetscSectionCreate()` had just been called.

    2760:   Not Collective

    2762:   Input Parameter:
    2763: . s - the `PetscSection`

    2765:   Level: beginner

    2767: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreate()`
    2768: @*/
    2769: PetscErrorCode PetscSectionReset(PetscSection s)
    2770: {
    2771:   PetscInt f, c;

    2773:   PetscFunctionBegin;
    2775:   for (f = 0; f < s->numFields; ++f) {
    2776:     PetscCall(PetscSectionDestroy(&s->field[f]));
    2777:     PetscCall(PetscFree(s->fieldNames[f]));
    2778:     for (c = 0; c < s->numFieldComponents[f]; ++c) PetscCall(PetscFree(s->compNames[f][c]));
    2779:     PetscCall(PetscFree(s->compNames[f]));
    2780:   }
    2781:   PetscCall(PetscFree(s->numFieldComponents));
    2782:   PetscCall(PetscFree(s->fieldNames));
    2783:   PetscCall(PetscFree(s->compNames));
    2784:   PetscCall(PetscFree(s->field));
    2785:   PetscCall(PetscSectionDestroy(&s->bc));
    2786:   PetscCall(PetscFree(s->bcIndices));
    2787:   PetscCall(PetscFree2(s->atlasDof, s->atlasOff));
    2788:   PetscCall(PetscSectionDestroy(&s->clSection));
    2789:   PetscCall(ISDestroy(&s->clPoints));
    2790:   PetscCall(ISDestroy(&s->perm));
    2791:   PetscCall(PetscBTDestroy(&s->blockStarts));
    2792:   PetscCall(PetscSectionResetClosurePermutation(s));
    2793:   PetscCall(PetscSectionSymDestroy(&s->sym));
    2794:   PetscCall(PetscSectionDestroy(&s->clSection));
    2795:   PetscCall(ISDestroy(&s->clPoints));
    2796:   PetscCall(PetscSectionInvalidateMaxDof_Internal(s));
    2797:   s->pStart    = -1;
    2798:   s->pEnd      = -1;
    2799:   s->maxDof    = 0;
    2800:   s->setup     = PETSC_FALSE;
    2801:   s->numFields = 0;
    2802:   s->clObj     = NULL;
    2803:   PetscFunctionReturn(PETSC_SUCCESS);
    2804: }

    2806: /*@
    2807:   PetscSectionDestroy - Frees a `PetscSection`

    2809:   Not Collective

    2811:   Input Parameter:
    2812: . s - the `PetscSection`

    2814:   Level: beginner

    2816: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionCreate()`, `PetscSectionReset()`
    2817: @*/
    2818: PetscErrorCode PetscSectionDestroy(PetscSection *s)
    2819: {
    2820:   PetscFunctionBegin;
    2821:   if (!*s) PetscFunctionReturn(PETSC_SUCCESS);
    2823:   if (--((PetscObject)*s)->refct > 0) {
    2824:     *s = NULL;
    2825:     PetscFunctionReturn(PETSC_SUCCESS);
    2826:   }
    2827:   PetscCall(PetscSectionReset(*s));
    2828:   PetscCall(PetscHeaderDestroy(s));
    2829:   PetscFunctionReturn(PETSC_SUCCESS);
    2830: }

    2832: static PetscErrorCode VecIntGetValuesSection_Private(const PetscInt *baseArray, PetscSection s, PetscInt point, const PetscInt **values)
    2833: {
    2834:   const PetscInt p = point - s->pStart;

    2836:   PetscFunctionBegin;
    2838:   *values = &baseArray[s->atlasOff[p]];
    2839:   PetscFunctionReturn(PETSC_SUCCESS);
    2840: }

    2842: static PetscErrorCode VecIntSetValuesSection_Private(PetscInt *baseArray, PetscSection s, PetscInt point, const PetscInt values[], InsertMode mode)
    2843: {
    2844:   PetscInt      *array;
    2845:   const PetscInt p           = point - s->pStart;
    2846:   const PetscInt orientation = 0; /* Needs to be included for use in closure operations */
    2847:   PetscInt       cDim        = 0;

    2849:   PetscFunctionBegin;
    2851:   PetscCall(PetscSectionGetConstraintDof(s, p, &cDim));
    2852:   array = &baseArray[s->atlasOff[p]];
    2853:   if (!cDim) {
    2854:     if (orientation >= 0) {
    2855:       const PetscInt dim = s->atlasDof[p];
    2856:       PetscInt       i;

    2858:       if (mode == INSERT_VALUES) {
    2859:         for (i = 0; i < dim; ++i) array[i] = values ? values[i] : i;
    2860:       } else {
    2861:         for (i = 0; i < dim; ++i) array[i] += values[i];
    2862:       }
    2863:     } else {
    2864:       PetscInt offset = 0;
    2865:       PetscInt j      = -1, field, i;

    2867:       for (field = 0; field < s->numFields; ++field) {
    2868:         const PetscInt dim = s->field[field]->atlasDof[p];

    2870:         for (i = dim - 1; i >= 0; --i) array[++j] = values ? values[i + offset] : i + offset;
    2871:         offset += dim;
    2872:       }
    2873:     }
    2874:   } else {
    2875:     if (orientation >= 0) {
    2876:       const PetscInt  dim  = s->atlasDof[p];
    2877:       PetscInt        cInd = 0, i;
    2878:       const PetscInt *cDof;

    2880:       PetscCall(PetscSectionGetConstraintIndices(s, point, &cDof));
    2881:       if (mode == INSERT_VALUES) {
    2882:         for (i = 0; i < dim; ++i) {
    2883:           if ((cInd < cDim) && (i == cDof[cInd])) {
    2884:             ++cInd;
    2885:             continue;
    2886:           }
    2887:           array[i] = values ? values[i] : i;
    2888:         }
    2889:       } else {
    2890:         for (i = 0; i < dim; ++i) {
    2891:           if ((cInd < cDim) && (i == cDof[cInd])) {
    2892:             ++cInd;
    2893:             continue;
    2894:           }
    2895:           array[i] += values[i];
    2896:         }
    2897:       }
    2898:     } else {
    2899:       const PetscInt *cDof;
    2900:       PetscInt        offset  = 0;
    2901:       PetscInt        cOffset = 0;
    2902:       PetscInt        j       = 0, field;

    2904:       PetscCall(PetscSectionGetConstraintIndices(s, point, &cDof));
    2905:       for (field = 0; field < s->numFields; ++field) {
    2906:         const PetscInt dim  = s->field[field]->atlasDof[p];     /* PetscSectionGetFieldDof() */
    2907:         const PetscInt tDim = s->field[field]->bc->atlasDof[p]; /* PetscSectionGetFieldConstraintDof() */
    2908:         const PetscInt sDim = dim - tDim;
    2909:         PetscInt       cInd = 0, i, k;

    2911:         for (i = 0, k = dim + offset - 1; i < dim; ++i, ++j, --k) {
    2912:           if ((cInd < sDim) && (j == cDof[cInd + cOffset])) {
    2913:             ++cInd;
    2914:             continue;
    2915:           }
    2916:           array[j] = values ? values[k] : k;
    2917:         }
    2918:         offset += dim;
    2919:         cOffset += dim - tDim;
    2920:       }
    2921:     }
    2922:   }
    2923:   PetscFunctionReturn(PETSC_SUCCESS);
    2924: }

    2926: /*@
    2927:   PetscSectionHasConstraints - Determine whether a `PetscSection` has constrained dofs

    2929:   Not Collective

    2931:   Input Parameter:
    2932: . s - The `PetscSection`

    2934:   Output Parameter:
    2935: . hasConstraints - flag indicating that the section has constrained dofs

    2937:   Level: intermediate

    2939: .seealso: [PetscSection](ch_petscsection), `PetscSectionSetConstraintIndices()`, `PetscSectionGetConstraintDof()`, `PetscSection`
    2940: @*/
    2941: PetscErrorCode PetscSectionHasConstraints(PetscSection s, PetscBool *hasConstraints)
    2942: {
    2943:   PetscFunctionBegin;
    2945:   PetscAssertPointer(hasConstraints, 2);
    2946:   *hasConstraints = s->bc ? PETSC_TRUE : PETSC_FALSE;
    2947:   PetscFunctionReturn(PETSC_SUCCESS);
    2948: }

    2950: /*@C
    2951:   PetscSectionGetConstraintIndices - Get the point dof numbers, in [0, dof), which are constrained for a given point

    2953:   Not Collective

    2955:   Input Parameters:
    2956: + s     - The `PetscSection`
    2957: - point - The point

    2959:   Output Parameter:
    2960: . indices - The constrained dofs

    2962:   Level: intermediate

    2964:   Fortran Notes:
    2965:   Use `PetscSectionRestoreConstraintIndices()` when the indices are no longer needed

    2967: .seealso: [PetscSection](ch_petscsection), `PetscSectionSetConstraintIndices()`, `PetscSectionGetConstraintDof()`, `PetscSection`
    2968: @*/
    2969: PetscErrorCode PetscSectionGetConstraintIndices(PetscSection s, PetscInt point, const PetscInt *indices[])
    2970: {
    2971:   PetscFunctionBegin;
    2973:   if (s->bc) PetscCall(VecIntGetValuesSection_Private(s->bcIndices, s->bc, point, indices));
    2974:   else *indices = NULL;
    2975:   PetscFunctionReturn(PETSC_SUCCESS);
    2976: }

    2978: /*@
    2979:   PetscSectionSetConstraintIndices - Set the point dof numbers, in [0, dof), which are constrained

    2981:   Not Collective

    2983:   Input Parameters:
    2984: + s       - The `PetscSection`
    2985: . point   - The point
    2986: - indices - The constrained dofs

    2988:   Level: intermediate

    2990: .seealso: [PetscSection](ch_petscsection), `PetscSectionGetConstraintIndices()`, `PetscSectionGetConstraintDof()`, `PetscSection`
    2991: @*/
    2992: PetscErrorCode PetscSectionSetConstraintIndices(PetscSection s, PetscInt point, const PetscInt indices[])
    2993: {
    2994:   PetscFunctionBegin;
    2996:   if (s->bc) {
    2997:     const PetscInt dof  = s->atlasDof[point];
    2998:     const PetscInt cdof = s->bc->atlasDof[point];
    2999:     PetscInt       d;

    3001:     if (indices)
    3002:       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]);
    3003:     PetscCall(VecIntSetValuesSection_Private(s->bcIndices, s->bc, point, indices, INSERT_VALUES));
    3004:   }
    3005:   PetscFunctionReturn(PETSC_SUCCESS);
    3006: }

    3008: /*@C
    3009:   PetscSectionGetFieldConstraintIndices - Get the field dof numbers, in [0, fdof), which are constrained

    3011:   Not Collective

    3013:   Input Parameters:
    3014: + s     - The `PetscSection`
    3015: . field - The field number
    3016: - point - The point

    3018:   Output Parameter:
    3019: . indices - The constrained dofs sorted in ascending order, the length is returned by `PetscSectionGetConstraintDof()`.

    3021:   Level: intermediate

    3023:   Fortran Notes:
    3024:   Use `PetscSectionRestoreFieldConstraintIndices()` to restore the indices when no longer needed

    3026: .seealso: [PetscSection](ch_petscsection), `PetscSectionSetFieldConstraintIndices()`, `PetscSectionGetConstraintIndices()`, `PetscSectionGetConstraintDof()`, `PetscSection`
    3027: @*/
    3028: PetscErrorCode PetscSectionGetFieldConstraintIndices(PetscSection s, PetscInt point, PetscInt field, const PetscInt *indices[])
    3029: {
    3030:   PetscFunctionBegin;
    3032:   PetscAssertPointer(indices, 4);
    3033:   PetscSectionCheckValidField(field, s->numFields);
    3034:   PetscCall(PetscSectionGetConstraintIndices(s->field[field], point, indices));
    3035:   PetscFunctionReturn(PETSC_SUCCESS);
    3036: }

    3038: /*@
    3039:   PetscSectionSetFieldConstraintIndices - Set the field dof numbers, in [0, fdof), which are constrained

    3041:   Not Collective

    3043:   Input Parameters:
    3044: + s       - The `PetscSection`
    3045: . point   - The point
    3046: . field   - The field number
    3047: - indices - The constrained dofs

    3049:   Level: intermediate

    3051: .seealso: [PetscSection](ch_petscsection), `PetscSectionSetConstraintIndices()`, `PetscSectionGetFieldConstraintIndices()`, `PetscSectionGetConstraintDof()`, `PetscSection`
    3052: @*/
    3053: PetscErrorCode PetscSectionSetFieldConstraintIndices(PetscSection s, PetscInt point, PetscInt field, const PetscInt indices[])
    3054: {
    3055:   PetscFunctionBegin;
    3057:   PetscSectionCheckValidField(field, s->numFields);
    3058:   PetscCall(PetscSectionSetConstraintIndices(s->field[field], point, indices));
    3059:   PetscFunctionReturn(PETSC_SUCCESS);
    3060: }

    3062: /*@
    3063:   PetscSectionPermute - Reorder the section according to the input point permutation

    3065:   Collective

    3067:   Input Parameters:
    3068: + section     - The `PetscSection` object
    3069: - permutation - The point permutation, old point p becomes new point perm[p]

    3071:   Output Parameter:
    3072: . sectionNew - The permuted `PetscSection`

    3074:   Level: intermediate

    3076:   Note:
    3077:   The data and the access to the data via `PetscSectionGetFieldOffset()` and `PetscSectionGetOffset()` are both changed in `sectionNew`

    3079:   Compare to `PetscSectionSetPermutation()`

    3081: .seealso: [PetscSection](ch_petscsection), `IS`, `PetscSection`, `MatPermute()`, `PetscSectionSetPermutation()`
    3082: @*/
    3083: PetscErrorCode PetscSectionPermute(PetscSection section, IS permutation, PetscSection *sectionNew)
    3084: {
    3085:   PetscSection    s = section, sNew;
    3086:   const PetscInt *perm;
    3087:   PetscInt        numFields, f, c, numPoints, pStart, pEnd, p;

    3089:   PetscFunctionBegin;
    3092:   PetscAssertPointer(sectionNew, 3);
    3093:   PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)s), &sNew));
    3094:   PetscCall(PetscSectionGetNumFields(s, &numFields));
    3095:   if (numFields) PetscCall(PetscSectionSetNumFields(sNew, numFields));
    3096:   for (f = 0; f < numFields; ++f) {
    3097:     const char *name;
    3098:     PetscInt    numComp;

    3100:     PetscCall(PetscSectionGetFieldName(s, f, &name));
    3101:     PetscCall(PetscSectionSetFieldName(sNew, f, name));
    3102:     PetscCall(PetscSectionGetFieldComponents(s, f, &numComp));
    3103:     PetscCall(PetscSectionSetFieldComponents(sNew, f, numComp));
    3104:     for (c = 0; c < s->numFieldComponents[f]; ++c) {
    3105:       PetscCall(PetscSectionGetComponentName(s, f, c, &name));
    3106:       PetscCall(PetscSectionSetComponentName(sNew, f, c, name));
    3107:     }
    3108:   }
    3109:   PetscCall(ISGetLocalSize(permutation, &numPoints));
    3110:   PetscCall(ISGetIndices(permutation, &perm));
    3111:   PetscCall(PetscSectionGetChart(s, &pStart, &pEnd));
    3112:   PetscCall(PetscSectionSetChart(sNew, pStart, pEnd));
    3113:   PetscCheck(numPoints >= pEnd, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Permutation size %" PetscInt_FMT " is less than largest Section point %" PetscInt_FMT, numPoints, pEnd);
    3114:   for (p = pStart; p < pEnd; ++p) {
    3115:     PetscInt dof, cdof;

    3117:     PetscCall(PetscSectionGetDof(s, p, &dof));
    3118:     PetscCall(PetscSectionSetDof(sNew, perm[p], dof));
    3119:     PetscCall(PetscSectionGetConstraintDof(s, p, &cdof));
    3120:     if (cdof) PetscCall(PetscSectionSetConstraintDof(sNew, perm[p], cdof));
    3121:     for (f = 0; f < numFields; ++f) {
    3122:       PetscCall(PetscSectionGetFieldDof(s, p, f, &dof));
    3123:       PetscCall(PetscSectionSetFieldDof(sNew, perm[p], f, dof));
    3124:       PetscCall(PetscSectionGetFieldConstraintDof(s, p, f, &cdof));
    3125:       if (cdof) PetscCall(PetscSectionSetFieldConstraintDof(sNew, perm[p], f, cdof));
    3126:     }
    3127:   }
    3128:   PetscCall(PetscSectionSetUp(sNew));
    3129:   for (p = pStart; p < pEnd; ++p) {
    3130:     const PetscInt *cind;
    3131:     PetscInt        cdof;

    3133:     PetscCall(PetscSectionGetConstraintDof(s, p, &cdof));
    3134:     if (cdof) {
    3135:       PetscCall(PetscSectionGetConstraintIndices(s, p, &cind));
    3136:       PetscCall(PetscSectionSetConstraintIndices(sNew, perm[p], cind));
    3137:     }
    3138:     for (f = 0; f < numFields; ++f) {
    3139:       PetscCall(PetscSectionGetFieldConstraintDof(s, p, f, &cdof));
    3140:       if (cdof) {
    3141:         PetscCall(PetscSectionGetFieldConstraintIndices(s, p, f, &cind));
    3142:         PetscCall(PetscSectionSetFieldConstraintIndices(sNew, perm[p], f, cind));
    3143:       }
    3144:     }
    3145:   }
    3146:   PetscCall(ISRestoreIndices(permutation, &perm));
    3147:   *sectionNew = sNew;
    3148:   PetscFunctionReturn(PETSC_SUCCESS);
    3149: }

    3151: /*@
    3152:   PetscSectionSetClosureIndex - Create an internal data structure to speed up closure queries.

    3154:   Collective

    3156:   Input Parameters:
    3157: + section   - The `PetscSection`
    3158: . obj       - A `PetscObject` which serves as the key for this index
    3159: . clSection - `PetscSection` giving the size of the closure of each point
    3160: - clPoints  - `IS` giving the points in each closure

    3162:   Level: advanced

    3164:   Note:
    3165:   This function creates an internal map from each point to its closure. We compress out closure points with no dofs in this section.

    3167:   Developer Notes:
    3168:   The information provided here is completely opaque

    3170: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionGetClosureIndex()`, `DMPlexCreateClosureIndex()`
    3171: @*/
    3172: PetscErrorCode PetscSectionSetClosureIndex(PetscSection section, PetscObject obj, PetscSection clSection, IS clPoints)
    3173: {
    3174:   PetscFunctionBegin;
    3178:   if (section->clObj != obj) PetscCall(PetscSectionResetClosurePermutation(section));
    3179:   section->clObj = obj;
    3180:   PetscCall(PetscObjectReference((PetscObject)clSection));
    3181:   PetscCall(PetscObjectReference((PetscObject)clPoints));
    3182:   PetscCall(PetscSectionDestroy(&section->clSection));
    3183:   PetscCall(ISDestroy(&section->clPoints));
    3184:   section->clSection = clSection;
    3185:   section->clPoints  = clPoints;
    3186:   PetscFunctionReturn(PETSC_SUCCESS);
    3187: }

    3189: /*@
    3190:   PetscSectionGetClosureIndex - Get the cache of points in the closure of each point in the section set with `PetscSectionSetClosureIndex()`

    3192:   Collective

    3194:   Input Parameters:
    3195: + section - The `PetscSection`
    3196: - obj     - A `PetscObject` which serves as the key for this index

    3198:   Output Parameters:
    3199: + clSection - `PetscSection` giving the size of the closure of each point
    3200: - clPoints  - `IS` giving the points in each closure

    3202:   Level: advanced

    3204: .seealso: [PetscSection](ch_petscsection), `PetscSectionSetClosureIndex()`, `DMPlexCreateClosureIndex()`
    3205: @*/
    3206: PetscErrorCode PetscSectionGetClosureIndex(PetscSection section, PetscObject obj, PetscSection *clSection, IS *clPoints)
    3207: {
    3208:   PetscFunctionBegin;
    3209:   if (section->clObj == obj) {
    3210:     if (clSection) *clSection = section->clSection;
    3211:     if (clPoints) *clPoints = section->clPoints;
    3212:   } else {
    3213:     if (clSection) *clSection = NULL;
    3214:     if (clPoints) *clPoints = NULL;
    3215:   }
    3216:   PetscFunctionReturn(PETSC_SUCCESS);
    3217: }

    3219: PetscErrorCode PetscSectionSetClosurePermutation_Internal(PetscSection section, PetscObject obj, PetscInt depth, PetscInt clSize, PetscCopyMode mode, PetscInt *clPerm)
    3220: {
    3221:   PetscInt                    i;
    3222:   khiter_t                    iter;
    3223:   int                         new_entry;
    3224:   PetscSectionClosurePermKey  key = {depth, clSize};
    3225:   PetscSectionClosurePermVal *val;

    3227:   PetscFunctionBegin;
    3228:   if (section->clObj != obj) {
    3229:     PetscCall(PetscSectionDestroy(&section->clSection));
    3230:     PetscCall(ISDestroy(&section->clPoints));
    3231:   }
    3232:   section->clObj = obj;
    3233:   if (!section->clHash) PetscCall(PetscClPermCreate(&section->clHash));
    3234:   iter = kh_put(ClPerm, section->clHash, key, &new_entry);
    3235:   val  = &kh_val(section->clHash, iter);
    3236:   if (!new_entry) {
    3237:     PetscCall(PetscFree(val->perm));
    3238:     PetscCall(PetscFree(val->invPerm));
    3239:   }
    3240:   if (mode == PETSC_COPY_VALUES) {
    3241:     PetscCall(PetscMalloc1(clSize, &val->perm));
    3242:     PetscCall(PetscArraycpy(val->perm, clPerm, clSize));
    3243:   } else if (mode == PETSC_OWN_POINTER) {
    3244:     val->perm = clPerm;
    3245:   } else SETERRQ(PetscObjectComm(obj), PETSC_ERR_SUP, "Do not support borrowed arrays");
    3246:   PetscCall(PetscMalloc1(clSize, &val->invPerm));
    3247:   for (i = 0; i < clSize; ++i) val->invPerm[clPerm[i]] = i;
    3248:   PetscFunctionReturn(PETSC_SUCCESS);
    3249: }

    3251: /*@
    3252:   PetscSectionSetClosurePermutation - Set the dof permutation for the closure of each cell in the section, meaning clPerm[newIndex] = oldIndex.

    3254:   Not Collective

    3256:   Input Parameters:
    3257: + section - The `PetscSection`
    3258: . obj     - A `PetscObject` which serves as the key for this index (usually a `DM`)
    3259: . depth   - Depth of points on which to apply the given permutation
    3260: - perm    - Permutation of the cell dof closure

    3262:   Level: intermediate

    3264:   Notes:
    3265:   The specified permutation will only be applied to points at depth whose closure size matches the length of perm.  In a
    3266:   mixed-topology or variable-degree finite element space, this function can be called multiple times at each depth for
    3267:   each topology and degree.

    3269:   This approach assumes that (depth, len(perm)) uniquely identifies the desired permutation; this might not be true for
    3270:   exotic/enriched spaces on mixed topology meshes.

    3272: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `IS`, `PetscSectionGetClosurePermutation()`, `PetscSectionGetClosureIndex()`, `DMPlexCreateClosureIndex()`, `PetscCopyMode`
    3273: @*/
    3274: PetscErrorCode PetscSectionSetClosurePermutation(PetscSection section, PetscObject obj, PetscInt depth, IS perm)
    3275: {
    3276:   const PetscInt *clPerm = NULL;
    3277:   PetscInt        clSize = 0;

    3279:   PetscFunctionBegin;
    3280:   if (perm) {
    3281:     PetscCall(ISGetLocalSize(perm, &clSize));
    3282:     PetscCall(ISGetIndices(perm, &clPerm));
    3283:   }
    3284:   PetscCall(PetscSectionSetClosurePermutation_Internal(section, obj, depth, clSize, PETSC_COPY_VALUES, (PetscInt *)clPerm));
    3285:   if (perm) PetscCall(ISRestoreIndices(perm, &clPerm));
    3286:   PetscFunctionReturn(PETSC_SUCCESS);
    3287: }

    3289: static PetscErrorCode PetscSectionGetClosurePermutation_Private(PetscSection section, PetscObject obj, PetscInt depth, PetscInt size, const PetscInt *perm[])
    3290: {
    3291:   PetscFunctionBegin;
    3292:   if (section->clObj == obj) {
    3293:     PetscSectionClosurePermKey k = {depth, size};
    3294:     PetscSectionClosurePermVal v;

    3296:     PetscCall(PetscClPermGet(section->clHash, k, &v));
    3297:     if (perm) *perm = v.perm;
    3298:   } else {
    3299:     if (perm) *perm = NULL;
    3300:   }
    3301:   PetscFunctionReturn(PETSC_SUCCESS);
    3302: }

    3304: /*@
    3305:   PetscSectionGetClosurePermutation - Get the dof permutation for the closure of each cell in the section, meaning clPerm[newIndex] = oldIndex.

    3307:   Not Collective

    3309:   Input Parameters:
    3310: + section - The `PetscSection`
    3311: . obj     - A `PetscObject` which serves as the key for this index (usually a DM)
    3312: . depth   - Depth stratum on which to obtain closure permutation
    3313: - clSize  - Closure size to be permuted (e.g., may vary with element topology and degree)

    3315:   Output Parameter:
    3316: . perm - The dof closure permutation

    3318:   Level: intermediate

    3320:   Note:
    3321:   The user must destroy the `IS` that is returned.

    3323: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `IS`, `PetscSectionSetClosurePermutation()`, `PetscSectionGetClosureInversePermutation()`, `PetscSectionGetClosureIndex()`, `PetscSectionSetClosureIndex()`, `DMPlexCreateClosureIndex()`
    3324: @*/
    3325: PetscErrorCode PetscSectionGetClosurePermutation(PetscSection section, PetscObject obj, PetscInt depth, PetscInt clSize, IS *perm)
    3326: {
    3327:   const PetscInt *clPerm = NULL;

    3329:   PetscFunctionBegin;
    3330:   PetscCall(PetscSectionGetClosurePermutation_Private(section, obj, depth, clSize, &clPerm));
    3331:   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);
    3332:   PetscCall(ISCreateGeneral(PETSC_COMM_SELF, clSize, clPerm, PETSC_USE_POINTER, perm));
    3333:   PetscFunctionReturn(PETSC_SUCCESS);
    3334: }

    3336: PetscErrorCode PetscSectionGetClosureInversePermutation_Internal(PetscSection section, PetscObject obj, PetscInt depth, PetscInt size, const PetscInt *perm[])
    3337: {
    3338:   PetscFunctionBegin;
    3339:   if (section->clObj == obj && section->clHash) {
    3340:     PetscSectionClosurePermKey k = {depth, size};
    3341:     PetscSectionClosurePermVal v;
    3342:     PetscCall(PetscClPermGet(section->clHash, k, &v));
    3343:     if (perm) *perm = v.invPerm;
    3344:   } else {
    3345:     if (perm) *perm = NULL;
    3346:   }
    3347:   PetscFunctionReturn(PETSC_SUCCESS);
    3348: }

    3350: /*@
    3351:   PetscSectionGetClosureInversePermutation - Get the inverse dof permutation for the closure of each cell in the section, meaning clPerm[oldIndex] = newIndex.

    3353:   Not Collective

    3355:   Input Parameters:
    3356: + section - The `PetscSection`
    3357: . obj     - A `PetscObject` which serves as the key for this index (usually a `DM`)
    3358: . depth   - Depth stratum on which to obtain closure permutation
    3359: - clSize  - Closure size to be permuted (e.g., may vary with element topology and degree)

    3361:   Output Parameter:
    3362: . perm - The dof closure permutation

    3364:   Level: intermediate

    3366:   Note:
    3367:   The user must destroy the `IS` that is returned.

    3369: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `IS`, `PetscSectionSetClosurePermutation()`, `PetscSectionGetClosureIndex()`, `PetscSectionSetClosureIndex()`, `DMPlexCreateClosureIndex()`
    3370: @*/
    3371: PetscErrorCode PetscSectionGetClosureInversePermutation(PetscSection section, PetscObject obj, PetscInt depth, PetscInt clSize, IS *perm)
    3372: {
    3373:   const PetscInt *clPerm = NULL;

    3375:   PetscFunctionBegin;
    3376:   PetscCall(PetscSectionGetClosureInversePermutation_Internal(section, obj, depth, clSize, &clPerm));
    3377:   PetscCall(ISCreateGeneral(PETSC_COMM_SELF, clSize, clPerm, PETSC_USE_POINTER, perm));
    3378:   PetscFunctionReturn(PETSC_SUCCESS);
    3379: }

    3381: /*@
    3382:   PetscSectionGetField - Get the `PetscSection` associated with a single field

    3384:   Input Parameters:
    3385: + s     - The `PetscSection`
    3386: - field - The field number

    3388:   Output Parameter:
    3389: . subs - The `PetscSection` for the given field, note the chart of `subs` is not set

    3391:   Level: intermediate

    3393:   Note:
    3394:   Does not increase the reference count of the selected sub-section. There is no matching `PetscSectionRestoreField()`

    3396: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `IS`, `PetscSectionSetNumFields()`
    3397: @*/
    3398: PetscErrorCode PetscSectionGetField(PetscSection s, PetscInt field, PetscSection *subs)
    3399: {
    3400:   PetscFunctionBegin;
    3402:   PetscAssertPointer(subs, 3);
    3403:   PetscSectionCheckValidField(field, s->numFields);
    3404:   *subs = s->field[field];
    3405:   PetscFunctionReturn(PETSC_SUCCESS);
    3406: }

    3408: PetscClassId      PETSC_SECTION_SYM_CLASSID;
    3409: PetscFunctionList PetscSectionSymList = NULL;

    3411: /*@
    3412:   PetscSectionSymCreate - Creates an empty `PetscSectionSym` object.

    3414:   Collective

    3416:   Input Parameter:
    3417: . comm - the MPI communicator

    3419:   Output Parameter:
    3420: . sym - pointer to the new set of symmetries

    3422:   Level: developer

    3424: .seealso: [PetscSection](ch_petscsection), `PetscSection`, `PetscSectionSym`, `PetscSectionSymDestroy()`
    3425: @*/
    3426: PetscErrorCode PetscSectionSymCreate(MPI_Comm comm, PetscSectionSym *sym)
    3427: {
    3428:   PetscFunctionBegin;
    3429:   PetscAssertPointer(sym, 2);
    3430:   PetscCall(ISInitializePackage());

    3432:   PetscCall(PetscHeaderCreate(*sym, PETSC_SECTION_SYM_CLASSID, "PetscSectionSym", "Section Symmetry", "IS", comm, PetscSectionSymDestroy, PetscSectionSymView));
    3433:   PetscFunctionReturn(PETSC_SUCCESS);
    3434: }

    3436: /*@
    3437:   PetscSectionSymSetType - Builds a `PetscSectionSym`, for a particular implementation.

    3439:   Collective

    3441:   Input Parameters:
    3442: + sym    - The section symmetry object
    3443: - method - The name of the section symmetry type

    3445:   Level: developer

    3447: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSymType`, `PetscSectionSymGetType()`, `PetscSectionSymCreate()`
    3448: @*/
    3449: PetscErrorCode PetscSectionSymSetType(PetscSectionSym sym, PetscSectionSymType method)
    3450: {
    3451:   PetscErrorCode (*r)(PetscSectionSym);
    3452:   PetscBool match;

    3454:   PetscFunctionBegin;
    3456:   PetscCall(PetscObjectTypeCompare((PetscObject)sym, method, &match));
    3457:   if (match) PetscFunctionReturn(PETSC_SUCCESS);

    3459:   PetscCall(PetscFunctionListFind(PetscSectionSymList, method, &r));
    3460:   PetscCheck(r, PetscObjectComm((PetscObject)sym), PETSC_ERR_ARG_UNKNOWN_TYPE, "Unknown PetscSectionSym type: %s", method);
    3461:   PetscTryTypeMethod(sym, destroy);
    3462:   sym->ops->destroy = NULL;

    3464:   PetscCall((*r)(sym));
    3465:   PetscCall(PetscObjectChangeTypeName((PetscObject)sym, method));
    3466:   PetscFunctionReturn(PETSC_SUCCESS);
    3467: }

    3469: /*@
    3470:   PetscSectionSymGetType - Gets the section symmetry type name (as a string) from the `PetscSectionSym`.

    3472:   Not Collective

    3474:   Input Parameter:
    3475: . sym - The section symmetry

    3477:   Output Parameter:
    3478: . type - The index set type name

    3480:   Level: developer

    3482: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSymType`, `PetscSectionSymSetType()`, `PetscSectionSymCreate()`
    3483: @*/
    3484: PetscErrorCode PetscSectionSymGetType(PetscSectionSym sym, PetscSectionSymType *type)
    3485: {
    3486:   PetscFunctionBegin;
    3488:   PetscAssertPointer(type, 2);
    3489:   *type = ((PetscObject)sym)->type_name;
    3490:   PetscFunctionReturn(PETSC_SUCCESS);
    3491: }

    3493: /*@C
    3494:   PetscSectionSymRegister - Registers a new section symmetry implementation

    3496:   Not Collective, No Fortran Support

    3498:   Input Parameters:
    3499: + sname    - The name of a new user-defined creation routine
    3500: - function - The creation routine itself

    3502:   Level: developer

    3504:   Notes:
    3505:   `PetscSectionSymRegister()` may be called multiple times to add several user-defined vectors

    3507: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSymType`, `PetscSectionSymCreate()`, `PetscSectionSymSetType()`
    3508: @*/
    3509: PetscErrorCode PetscSectionSymRegister(const char sname[], PetscErrorCode (*function)(PetscSectionSym))
    3510: {
    3511:   PetscFunctionBegin;
    3512:   PetscCall(ISInitializePackage());
    3513:   PetscCall(PetscFunctionListAdd(&PetscSectionSymList, sname, function));
    3514:   PetscFunctionReturn(PETSC_SUCCESS);
    3515: }

    3517: /*@
    3518:   PetscSectionSymDestroy - Destroys a section symmetry.

    3520:   Collective

    3522:   Input Parameter:
    3523: . sym - the section symmetry

    3525:   Level: developer

    3527: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSymCreate()`
    3528: @*/
    3529: PetscErrorCode PetscSectionSymDestroy(PetscSectionSym *sym)
    3530: {
    3531:   SymWorkLink link, next;

    3533:   PetscFunctionBegin;
    3534:   if (!*sym) PetscFunctionReturn(PETSC_SUCCESS);
    3536:   if (--((PetscObject)*sym)->refct > 0) {
    3537:     *sym = NULL;
    3538:     PetscFunctionReturn(PETSC_SUCCESS);
    3539:   }
    3540:   PetscTryTypeMethod(*sym, destroy);
    3541:   PetscCheck(!(*sym)->workout, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Work array still checked out");
    3542:   for (link = (*sym)->workin; link; link = next) {
    3543:     PetscInt    **perms = (PetscInt **)link->perms;
    3544:     PetscScalar **rots  = (PetscScalar **)link->rots;
    3545:     PetscCall(PetscFree2(perms, rots));
    3546:     next = link->next;
    3547:     PetscCall(PetscFree(link));
    3548:   }
    3549:   (*sym)->workin = NULL;
    3550:   PetscCall(PetscHeaderDestroy(sym));
    3551:   PetscFunctionReturn(PETSC_SUCCESS);
    3552: }

    3554: /*@
    3555:   PetscSectionSymView - Displays a section symmetry

    3557:   Collective

    3559:   Input Parameters:
    3560: + sym    - the index set
    3561: - viewer - viewer used to display the set, for example `PETSC_VIEWER_STDOUT_SELF`.

    3563:   Level: developer

    3565: .seealso: `PetscSectionSym`, `PetscViewer`, `PetscViewerASCIIOpen()`
    3566: @*/
    3567: PetscErrorCode PetscSectionSymView(PetscSectionSym sym, PetscViewer viewer)
    3568: {
    3569:   PetscFunctionBegin;
    3571:   if (!viewer) PetscCall(PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)sym), &viewer));
    3573:   PetscCheckSameComm(sym, 1, viewer, 2);
    3574:   PetscCall(PetscObjectPrintClassNamePrefixType((PetscObject)sym, viewer));
    3575:   PetscTryTypeMethod(sym, view, viewer);
    3576:   PetscFunctionReturn(PETSC_SUCCESS);
    3577: }

    3579: /*@
    3580:   PetscSectionSetSym - Set the symmetries for the data referred to by the section

    3582:   Collective

    3584:   Input Parameters:
    3585: + section - the section describing data layout
    3586: - sym     - the symmetry describing the affect of orientation on the access of the data

    3588:   Level: developer

    3590: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionGetSym()`, `PetscSectionSymCreate()`
    3591: @*/
    3592: PetscErrorCode PetscSectionSetSym(PetscSection section, PetscSectionSym sym)
    3593: {
    3594:   PetscFunctionBegin;
    3596:   PetscCall(PetscSectionSymDestroy(&section->sym));
    3597:   if (sym) {
    3599:     PetscCheckSameComm(section, 1, sym, 2);
    3600:     PetscCall(PetscObjectReference((PetscObject)sym));
    3601:   }
    3602:   section->sym = sym;
    3603:   PetscFunctionReturn(PETSC_SUCCESS);
    3604: }

    3606: /*@
    3607:   PetscSectionGetSym - Get the symmetries for the data referred to by the section

    3609:   Not Collective

    3611:   Input Parameter:
    3612: . section - the section describing data layout

    3614:   Output Parameter:
    3615: . sym - the symmetry describing the affect of orientation on the access of the data, provided previously by `PetscSectionSetSym()`

    3617:   Level: developer

    3619: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSetSym()`, `PetscSectionSymCreate()`
    3620: @*/
    3621: PetscErrorCode PetscSectionGetSym(PetscSection section, PetscSectionSym *sym)
    3622: {
    3623:   PetscFunctionBegin;
    3625:   *sym = section->sym;
    3626:   PetscFunctionReturn(PETSC_SUCCESS);
    3627: }

    3629: /*@
    3630:   PetscSectionSetFieldSym - Set the symmetries for the data referred to by a field of the section

    3632:   Collective

    3634:   Input Parameters:
    3635: + section - the section describing data layout
    3636: . field   - the field number
    3637: - sym     - the symmetry describing the affect of orientation on the access of the data

    3639:   Level: developer

    3641: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionGetFieldSym()`, `PetscSectionSymCreate()`
    3642: @*/
    3643: PetscErrorCode PetscSectionSetFieldSym(PetscSection section, PetscInt field, PetscSectionSym sym)
    3644: {
    3645:   PetscFunctionBegin;
    3647:   PetscSectionCheckValidField(field, section->numFields);
    3648:   PetscCall(PetscSectionSetSym(section->field[field], sym));
    3649:   PetscFunctionReturn(PETSC_SUCCESS);
    3650: }

    3652: /*@
    3653:   PetscSectionGetFieldSym - Get the symmetries for the data referred to by a field of the section

    3655:   Collective

    3657:   Input Parameters:
    3658: + section - the section describing data layout
    3659: - field   - the field number

    3661:   Output Parameter:
    3662: . sym - the symmetry describing the affect of orientation on the access of the data

    3664:   Level: developer

    3666: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSetFieldSym()`, `PetscSectionSymCreate()`
    3667: @*/
    3668: PetscErrorCode PetscSectionGetFieldSym(PetscSection section, PetscInt field, PetscSectionSym *sym)
    3669: {
    3670:   PetscFunctionBegin;
    3672:   PetscSectionCheckValidField(field, section->numFields);
    3673:   *sym = section->field[field]->sym;
    3674:   PetscFunctionReturn(PETSC_SUCCESS);
    3675: }

    3677: /*@C
    3678:   PetscSectionGetPointSyms - Get the symmetries for a set of points in a `PetscSection` under specific orientations.

    3680:   Not Collective

    3682:   Input Parameters:
    3683: + section   - the section
    3684: . numPoints - the number of points
    3685: - points    - an array of size 2 * `numPoints`, containing a list of (point, orientation) pairs. (An orientation is an
    3686:               arbitrary integer: its interpretation is up to sym.  Orientations are used by `DM`: for their interpretation in that
    3687:               context, see `DMPlexGetConeOrientation()`).

    3689:   Output Parameters:
    3690: + perms - The permutations for the given orientations (or `NULL` if there is no symmetry or the permutation is the identity).
    3691: - rots  - The field rotations symmetries for the given orientations (or `NULL` if there is no symmetry or the rotations are all
    3692:     identity).

    3694:   Example of usage, gathering dofs into a local array (lArray) from a section array (sArray):
    3695: .vb
    3696:      const PetscInt    **perms;
    3697:      const PetscScalar **rots;
    3698:      PetscInt            lOffset;

    3700:      PetscSectionGetPointSyms(section,numPoints,points,&perms,&rots);
    3701:      for (i = 0, lOffset = 0; i < numPoints; i++) {
    3702:        PetscInt           point = points[2*i], dof, sOffset;
    3703:        const PetscInt    *perm  = perms ? perms[i] : NULL;
    3704:        const PetscScalar *rot   = rots  ? rots[i]  : NULL;

    3706:        PetscSectionGetDof(section,point,&dof);
    3707:        PetscSectionGetOffset(section,point,&sOffset);

    3709:        if (perm) { for (j = 0; j < dof; j++) lArray[lOffset + perm[j]]  = sArray[sOffset + j]; }
    3710:        else      { for (j = 0; j < dof; j++) lArray[lOffset +      j ]  = sArray[sOffset + j]; }
    3711:        if (rot)  { for (j = 0; j < dof; j++) lArray[lOffset +      j ] *= rot[j];              }
    3712:        lOffset += dof;
    3713:      }
    3714:      PetscSectionRestorePointSyms(section,numPoints,points,&perms,&rots);
    3715: .ve

    3717:   Example of usage, adding dofs into a section array (sArray) from a local array (lArray):
    3718: .vb
    3719:      const PetscInt    **perms;
    3720:      const PetscScalar **rots;
    3721:      PetscInt            lOffset;

    3723:      PetscSectionGetPointSyms(section,numPoints,points,&perms,&rots);
    3724:      for (i = 0, lOffset = 0; i < numPoints; i++) {
    3725:        PetscInt           point = points[2*i], dof, sOffset;
    3726:        const PetscInt    *perm  = perms ? perms[i] : NULL;
    3727:        const PetscScalar *rot   = rots  ? rots[i]  : NULL;

    3729:        PetscSectionGetDof(section,point,&dof);
    3730:        PetscSectionGetOffset(section,point,&sOff);

    3732:        if (perm) { for (j = 0; j < dof; j++) sArray[sOffset + j] += lArray[lOffset + perm[j]] * (rot ? PetscConj(rot[perm[j]]) : 1.); }
    3733:        else      { for (j = 0; j < dof; j++) sArray[sOffset + j] += lArray[lOffset +      j ] * (rot ? PetscConj(rot[     j ]) : 1.); }
    3734:        offset += dof;
    3735:      }
    3736:      PetscSectionRestorePointSyms(section,numPoints,points,&perms,&rots);
    3737: .ve

    3739:   Level: developer

    3741:   Notes:
    3742:   `PetscSectionSetSym()` must have been previously called to provide the symmetries to the `PetscSection`

    3744:   Use `PetscSectionRestorePointSyms()` when finished with the data

    3746: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionRestorePointSyms()`, `PetscSectionSymCreate()`, `PetscSectionSetSym()`, `PetscSectionGetSym()`
    3747: @*/
    3748: PetscErrorCode PetscSectionGetPointSyms(PetscSection section, PetscInt numPoints, const PetscInt *points, const PetscInt ***perms, const PetscScalar ***rots)
    3749: {
    3750:   PetscSectionSym sym;

    3752:   PetscFunctionBegin;
    3754:   if (numPoints) PetscAssertPointer(points, 3);
    3755:   if (perms) *perms = NULL;
    3756:   if (rots) *rots = NULL;
    3757:   sym = section->sym;
    3758:   if (sym && (perms || rots)) {
    3759:     SymWorkLink link;

    3761:     if (sym->workin) {
    3762:       link        = sym->workin;
    3763:       sym->workin = sym->workin->next;
    3764:     } else {
    3765:       PetscCall(PetscNew(&link));
    3766:     }
    3767:     if (numPoints > link->numPoints) {
    3768:       PetscInt    **perms = (PetscInt **)link->perms;
    3769:       PetscScalar **rots  = (PetscScalar **)link->rots;
    3770:       PetscCall(PetscFree2(perms, rots));
    3771:       PetscCall(PetscMalloc2(numPoints, (PetscInt ***)&link->perms, numPoints, (PetscScalar ***)&link->rots));
    3772:       link->numPoints = numPoints;
    3773:     }
    3774:     link->next   = sym->workout;
    3775:     sym->workout = link;
    3776:     PetscCall(PetscArrayzero((PetscInt **)link->perms, numPoints));
    3777:     PetscCall(PetscArrayzero((PetscInt **)link->rots, numPoints));
    3778:     PetscUseTypeMethod(sym, getpoints, section, numPoints, points, link->perms, link->rots);
    3779:     if (perms) *perms = link->perms;
    3780:     if (rots) *rots = link->rots;
    3781:   }
    3782:   PetscFunctionReturn(PETSC_SUCCESS);
    3783: }

    3785: /*@C
    3786:   PetscSectionRestorePointSyms - Restore the symmetries returned by `PetscSectionGetPointSyms()`

    3788:   Not Collective

    3790:   Input Parameters:
    3791: + section   - the section
    3792: . numPoints - the number of points
    3793: . points    - an array of size 2 * `numPoints`, containing a list of (point, orientation) pairs. (An orientation is an
    3794:               arbitrary integer: its interpretation is up to sym.  Orientations are used by `DM`: for their interpretation in that
    3795:               context, see `DMPlexGetConeOrientation()`).
    3796: . perms     - The permutations for the given orientations: set to `NULL` at conclusion
    3797: - rots      - The field rotations symmetries for the given orientations: set to `NULL` at conclusion

    3799:   Level: developer

    3801: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionGetPointSyms()`, `PetscSectionSymCreate()`, `PetscSectionSetSym()`, `PetscSectionGetSym()`
    3802: @*/
    3803: PetscErrorCode PetscSectionRestorePointSyms(PetscSection section, PetscInt numPoints, const PetscInt *points, const PetscInt ***perms, const PetscScalar ***rots)
    3804: {
    3805:   PetscSectionSym sym;

    3807:   PetscFunctionBegin;
    3809:   sym = section->sym;
    3810:   if (sym && (perms || rots)) {
    3811:     SymWorkLink *p, link;

    3813:     for (p = &sym->workout; (link = *p); p = &link->next) {
    3814:       if ((perms && link->perms == *perms) || (rots && link->rots == *rots)) {
    3815:         *p          = link->next;
    3816:         link->next  = sym->workin;
    3817:         sym->workin = link;
    3818:         if (perms) *perms = NULL;
    3819:         if (rots) *rots = NULL;
    3820:         PetscFunctionReturn(PETSC_SUCCESS);
    3821:       }
    3822:     }
    3823:     SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Array was not checked out");
    3824:   }
    3825:   PetscFunctionReturn(PETSC_SUCCESS);
    3826: }

    3828: /*@C
    3829:   PetscSectionGetFieldPointSyms - Get the symmetries for a set of points in a field of a `PetscSection` under specific orientations.

    3831:   Not Collective

    3833:   Input Parameters:
    3834: + section   - the section
    3835: . field     - the field of the section
    3836: . numPoints - the number of points
    3837: - points    - an array of size 2 * `numPoints`, containing a list of (point, orientation) pairs. (An orientation is an
    3838:     arbitrary integer: its interpretation is up to sym.  Orientations are used by `DM`: for their interpretation in that
    3839:     context, see `DMPlexGetConeOrientation()`).

    3841:   Output Parameters:
    3842: + perms - The permutations for the given orientations (or `NULL` if there is no symmetry or the permutation is the identity).
    3843: - rots  - The field rotations symmetries for the given orientations (or `NULL` if there is no symmetry or the rotations are all
    3844:     identity).

    3846:   Level: developer

    3848:   Notes:
    3849:   `PetscSectionSetFieldSym()` must have been previously called to provide the symmetries to the `PetscSection`

    3851:   Use `PetscSectionRestoreFieldPointSyms()` when finished with the data

    3853: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionGetPointSyms()`, `PetscSectionRestoreFieldPointSyms()`
    3854: @*/
    3855: PetscErrorCode PetscSectionGetFieldPointSyms(PetscSection section, PetscInt field, PetscInt numPoints, const PetscInt *points, const PetscInt ***perms, const PetscScalar ***rots)
    3856: {
    3857:   PetscFunctionBegin;
    3859:   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);
    3860:   PetscCall(PetscSectionGetPointSyms(section->field[field], numPoints, points, perms, rots));
    3861:   PetscFunctionReturn(PETSC_SUCCESS);
    3862: }

    3864: /*@C
    3865:   PetscSectionRestoreFieldPointSyms - Restore the symmetries returned by `PetscSectionGetFieldPointSyms()`

    3867:   Not Collective

    3869:   Input Parameters:
    3870: + section   - the section
    3871: . field     - the field number
    3872: . numPoints - the number of points
    3873: . points    - an array of size 2 * `numPoints`, containing a list of (point, orientation) pairs. (An orientation is an
    3874:     arbitrary integer: its interpretation is up to sym.  Orientations are used by `DM`: for their interpretation in that
    3875:     context, see `DMPlexGetConeOrientation()`).
    3876: . perms     - The permutations for the given orientations: set to NULL at conclusion
    3877: - rots      - The field rotations symmetries for the given orientations: set to NULL at conclusion

    3879:   Level: developer

    3881: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionRestorePointSyms()`, `petscSectionGetFieldPointSyms()`, `PetscSectionSymCreate()`, `PetscSectionSetSym()`, `PetscSectionGetSym()`
    3882: @*/
    3883: PetscErrorCode PetscSectionRestoreFieldPointSyms(PetscSection section, PetscInt field, PetscInt numPoints, const PetscInt *points, const PetscInt ***perms, const PetscScalar ***rots)
    3884: {
    3885:   PetscFunctionBegin;
    3887:   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);
    3888:   PetscCall(PetscSectionRestorePointSyms(section->field[field], numPoints, points, perms, rots));
    3889:   PetscFunctionReturn(PETSC_SUCCESS);
    3890: }

    3892: /*@
    3893:   PetscSectionSymCopy - Copy the symmetries, assuming that the point structure is compatible

    3895:   Not Collective

    3897:   Input Parameter:
    3898: . sym - the `PetscSectionSym`

    3900:   Output Parameter:
    3901: . nsym - the equivalent symmetries

    3903:   Level: developer

    3905: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSymCreate()`, `PetscSectionSetSym()`, `PetscSectionGetSym()`, `PetscSectionSymLabelSetStratum()`, `PetscSectionGetPointSyms()`
    3906: @*/
    3907: PetscErrorCode PetscSectionSymCopy(PetscSectionSym sym, PetscSectionSym nsym)
    3908: {
    3909:   PetscFunctionBegin;
    3912:   PetscTryTypeMethod(sym, copy, nsym);
    3913:   PetscFunctionReturn(PETSC_SUCCESS);
    3914: }

    3916: /*@
    3917:   PetscSectionSymDistribute - Distribute the symmetries in accordance with the input `PetscSF`

    3919:   Collective

    3921:   Input Parameters:
    3922: + sym         - the `PetscSectionSym`
    3923: - migrationSF - the distribution map from roots to leaves

    3925:   Output Parameter:
    3926: . dsym - the redistributed symmetries

    3928:   Level: developer

    3930: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSymCreate()`, `PetscSectionSetSym()`, `PetscSectionGetSym()`, `PetscSectionSymLabelSetStratum()`, `PetscSectionGetPointSyms()`
    3931: @*/
    3932: PetscErrorCode PetscSectionSymDistribute(PetscSectionSym sym, PetscSF migrationSF, PetscSectionSym *dsym)
    3933: {
    3934:   PetscFunctionBegin;
    3937:   PetscAssertPointer(dsym, 3);
    3938:   PetscTryTypeMethod(sym, distribute, migrationSF, dsym);
    3939:   PetscFunctionReturn(PETSC_SUCCESS);
    3940: }

    3942: /*@
    3943:   PetscSectionGetUseFieldOffsets - Get the flag indicating if field offsets are used directly in a global section, rather than just the point offset

    3945:   Not Collective

    3947:   Input Parameter:
    3948: . s - the global `PetscSection`

    3950:   Output Parameter:
    3951: . flg - the flag

    3953:   Level: developer

    3955: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionSetChart()`, `PetscSectionCreate()`
    3956: @*/
    3957: PetscErrorCode PetscSectionGetUseFieldOffsets(PetscSection s, PetscBool *flg)
    3958: {
    3959:   PetscFunctionBegin;
    3961:   *flg = s->useFieldOff;
    3962:   PetscFunctionReturn(PETSC_SUCCESS);
    3963: }

    3965: /*@
    3966:   PetscSectionSetUseFieldOffsets - Set the flag to use field offsets directly in a global section, rather than just the point offset

    3968:   Not Collective

    3970:   Input Parameters:
    3971: + s   - the global `PetscSection`
    3972: - flg - the flag

    3974:   Level: developer

    3976: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionGetUseFieldOffsets()`, `PetscSectionSetChart()`, `PetscSectionCreate()`
    3977: @*/
    3978: PetscErrorCode PetscSectionSetUseFieldOffsets(PetscSection s, PetscBool flg)
    3979: {
    3980:   PetscFunctionBegin;
    3982:   s->useFieldOff = flg;
    3983:   PetscFunctionReturn(PETSC_SUCCESS);
    3984: }

    3986: #define PetscSectionExpandPoints_Loop(TYPE) \
    3987:   do { \
    3988:     PetscInt i, n, o0, o1, size; \
    3989:     TYPE    *a0 = (TYPE *)origArray, *a1; \
    3990:     PetscCall(PetscSectionGetStorageSize(s, &size)); \
    3991:     PetscCall(PetscMalloc1(size, &a1)); \
    3992:     for (i = 0; i < npoints; i++) { \
    3993:       PetscCall(PetscSectionGetOffset(origSection, points_[i], &o0)); \
    3994:       PetscCall(PetscSectionGetOffset(s, i, &o1)); \
    3995:       PetscCall(PetscSectionGetDof(s, i, &n)); \
    3996:       PetscCall(PetscMemcpy(&a1[o1], &a0[o0], n * unitsize)); \
    3997:     } \
    3998:     *newArray = (void *)a1; \
    3999:   } while (0)

    4001: /*@
    4002:   PetscSectionExtractDofsFromArray - Extracts elements of an array corresponding to DOFs of specified points.

    4004:   Not Collective

    4006:   Input Parameters:
    4007: + origSection - the `PetscSection` describing the layout of the array
    4008: . dataType    - `MPI_Datatype` describing the data type of the array (currently only `MPIU_INT`, `MPIU_SCALAR`, `MPIU_REAL`)
    4009: . origArray   - the array; its size must be equal to the storage size of `origSection`
    4010: - points      - `IS` with points to extract; its indices must lie in the chart of `origSection`

    4012:   Output Parameters:
    4013: + newSection - the new `PetscSection` describing the layout of the new array (with points renumbered 0,1,... but preserving numbers of DOFs)
    4014: - newArray   - the array of the extracted DOFs; its size is the storage size of `newSection`

    4016:   Level: developer

    4018: .seealso: [PetscSection](ch_petscsection), `PetscSectionSym`, `PetscSectionGetChart()`, `PetscSectionGetDof()`, `PetscSectionGetStorageSize()`, `PetscSectionCreate()`
    4019: @*/
    4020: PetscErrorCode PetscSectionExtractDofsFromArray(PetscSection origSection, MPI_Datatype dataType, const void *origArray, IS points, PetscSection *newSection, void *newArray[])
    4021: {
    4022:   PetscSection    s;
    4023:   const PetscInt *points_;
    4024:   PetscInt        i, n, npoints, pStart, pEnd;
    4025:   PetscMPIInt     unitsize;

    4027:   PetscFunctionBegin;
    4029:   PetscAssertPointer(origArray, 3);
    4031:   if (newSection) PetscAssertPointer(newSection, 5);
    4032:   if (newArray) PetscAssertPointer(newArray, 6);
    4033:   PetscCallMPI(MPI_Type_size(dataType, &unitsize));
    4034:   PetscCall(ISGetLocalSize(points, &npoints));
    4035:   PetscCall(ISGetIndices(points, &points_));
    4036:   PetscCall(PetscSectionGetChart(origSection, &pStart, &pEnd));
    4037:   PetscCall(PetscSectionCreate(PETSC_COMM_SELF, &s));
    4038:   PetscCall(PetscSectionSetChart(s, 0, npoints));
    4039:   for (i = 0; i < npoints; i++) {
    4040:     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);
    4041:     PetscCall(PetscSectionGetDof(origSection, points_[i], &n));
    4042:     PetscCall(PetscSectionSetDof(s, i, n));
    4043:   }
    4044:   PetscCall(PetscSectionSetUp(s));
    4045:   if (newArray) {
    4046:     if (dataType == MPIU_INT) {
    4047:       PetscSectionExpandPoints_Loop(PetscInt);
    4048:     } else if (dataType == MPIU_SCALAR) {
    4049:       PetscSectionExpandPoints_Loop(PetscScalar);
    4050:     } else if (dataType == MPIU_REAL) {
    4051:       PetscSectionExpandPoints_Loop(PetscReal);
    4052:     } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "not implemented for this MPI_Datatype");
    4053:   }
    4054:   if (newSection) {
    4055:     *newSection = s;
    4056:   } else {
    4057:     PetscCall(PetscSectionDestroy(&s));
    4058:   }
    4059:   PetscCall(ISRestoreIndices(points, &points_));
    4060:   PetscFunctionReturn(PETSC_SUCCESS);
    4061: }