Date: 2016-07-24T17:01:03+00:00

Actual source code: plextree.c
petsc-3.7.3 2016-07-24
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      1: #include <petsc/private/dmpleximpl.h>   /*I      "petscdmplex.h"   I*/
      2: #include <../src/sys/utils/hash.h>
      3: #include <petsc/private/isimpl.h>
      4: #include <petsc/private/petscfeimpl.h>
      5: #include <petscsf.h>
      6: #include <petscds.h>

      8: /** hierarchy routines */

     12: /*@
     13:   DMPlexSetReferenceTree - set the reference tree for hierarchically non-conforming meshes.

     15:   Not collective

     17:   Input Parameters:
     18: + dm - The DMPlex object
     19: - ref - The reference tree DMPlex object

     21:   Level: intermediate

     23: .seealso: DMPlexGetReferenceTree(), DMPlexCreateDefaultReferenceTree()
     24: @*/
     25: PetscErrorCode DMPlexSetReferenceTree(DM dm, DM ref)
     26: {
     27:   DM_Plex        *mesh = (DM_Plex *)dm->data;
     28:   PetscErrorCode  ierr;

     33:   PetscObjectReference((PetscObject)ref);
     34:   DMDestroy(&mesh->referenceTree);
     35:   mesh->referenceTree = ref;
     36:   return(0);
     37: }

     41: /*@
     42:   DMPlexGetReferenceTree - get the reference tree for hierarchically non-conforming meshes.

     44:   Not collective

     46:   Input Parameters:
     47: . dm - The DMPlex object

     49:   Output Parameters
     50: . ref - The reference tree DMPlex object

     52:   Level: intermediate

     54: .seealso: DMPlexSetReferenceTree(), DMPlexCreateDefaultReferenceTree()
     55: @*/
     56: PetscErrorCode DMPlexGetReferenceTree(DM dm, DM *ref)
     57: {
     58:   DM_Plex        *mesh = (DM_Plex *)dm->data;

     63:   *ref = mesh->referenceTree;
     64:   return(0);
     65: }

     69: static PetscErrorCode DMPlexReferenceTreeGetChildSymmetry_Default(DM dm, PetscInt parent, PetscInt parentOrientA, PetscInt childOrientA, PetscInt childA, PetscInt parentOrientB, PetscInt *childOrientB, PetscInt *childB)
     70: {
     71:   PetscInt       coneSize, dStart, dEnd, dim, ABswap, oAvert, oBvert, ABswapVert;

     75:   if (parentOrientA == parentOrientB) {
     76:     if (childOrientB) *childOrientB = childOrientA;
     77:     if (childB) *childB = childA;
     78:     return(0);
     79:   }
     80:   for (dim = 0; dim < 3; dim++) {
     81:     DMPlexGetDepthStratum(dm,dim,&dStart,&dEnd);
     82:     if (parent >= dStart && parent <= dEnd) {
     83:       break;
     84:     }
     85:   }
     86:   if (dim > 2) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot perform child symmetry for %d-cells",dim);
     87:   if (!dim) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"A vertex has no children");
     88:   if (childA < dStart || childA >= dEnd) {
     89:     /* this is a lower-dimensional child: bootstrap */
     90:     PetscInt size, i, sA = -1, sB, sOrientB, sConeSize;
     91:     const PetscInt *supp, *coneA, *coneB, *oA, *oB;

     93:     DMPlexGetSupportSize(dm,childA,&size);
     94:     DMPlexGetSupport(dm,childA,&supp);

     96:     /* find a point sA in supp(childA) that has the same parent */
     97:     for (i = 0; i < size; i++) {
     98:       PetscInt sParent;

    100:       sA   = supp[i];
    101:       if (sA == parent) continue;
    102:       DMPlexGetTreeParent(dm,sA,&sParent,NULL);
    103:       if (sParent == parent) {
    104:         break;
    105:       }
    106:     }
    107:     if (i == size) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"could not find support in children");
    108:     /* find out which point sB is in an equivalent position to sA under
    109:      * parentOrientB */
    110:     DMPlexReferenceTreeGetChildSymmetry_Default(dm,parent,parentOrientA,0,sA,parentOrientB,&sOrientB,&sB);
    111:     DMPlexGetConeSize(dm,sA,&sConeSize);
    112:     DMPlexGetCone(dm,sA,&coneA);
    113:     DMPlexGetCone(dm,sB,&coneB);
    114:     DMPlexGetConeOrientation(dm,sA,&oA);
    115:     DMPlexGetConeOrientation(dm,sB,&oB);
    116:     /* step through the cone of sA in natural order */
    117:     for (i = 0; i < sConeSize; i++) {
    118:       if (coneA[i] == childA) {
    119:         /* if childA is at position i in coneA,
    120:          * then we want the point that is at sOrientB*i in coneB */
    121:         PetscInt j = (sOrientB >= 0) ? ((sOrientB + i) % sConeSize) : ((sConeSize -(sOrientB+1) - i) % sConeSize);
    122:         if (childB) *childB = coneB[j];
    123:         if (childOrientB) {
    124:           PetscInt oBtrue;

    126:           DMPlexGetConeSize(dm,childA,&coneSize);
    127:           /* compose sOrientB and oB[j] */
    128:           if (coneSize != 0 && coneSize != 2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Expected a vertex or an edge");
    129:           /* we may have to flip an edge */
    130:           oBtrue        = coneSize ? ((sOrientB >= 0) ? oB[j] : -(oB[j] + 2)) : 0;
    131:           ABswap        = DihedralSwap(coneSize,oA[i],oBtrue);
    132:           *childOrientB = DihedralCompose(coneSize,childOrientA,ABswap);
    133:         }
    134:         break;
    135:       }
    136:     }
    137:     if (i == sConeSize) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"support cone mismatch");
    138:     return(0);
    139:   }
    140:   /* get the cone size and symmetry swap */
    141:   DMPlexGetConeSize(dm,parent,&coneSize);
    142:   ABswap = DihedralSwap(coneSize, parentOrientA, parentOrientB);
    143:   if (dim == 2) {
    144:     /* orientations refer to cones: we want them to refer to vertices:
    145:      * if it's a rotation, they are the same, but if the order is reversed, a
    146:      * permutation that puts side i first does *not* put vertex i first */
    147:     oAvert     = (parentOrientA >= 0) ? parentOrientA : -((-parentOrientA % coneSize) + 1);
    148:     oBvert     = (parentOrientB >= 0) ? parentOrientB : -((-parentOrientB % coneSize) + 1);
    149:     ABswapVert = DihedralSwap(coneSize, oAvert, oBvert);
    150:   } else {
    151:     ABswapVert = ABswap;
    152:   }
    153:   if (childB) {
    154:     /* assume that each child corresponds to a vertex, in the same order */
    155:     PetscInt p, posA = -1, numChildren, i;
    156:     const PetscInt *children;

    158:     /* count which position the child is in */
    159:     DMPlexGetTreeChildren(dm,parent,&numChildren,&children);
    160:     for (i = 0; i < numChildren; i++) {
    161:       p = children[i];
    162:       if (p == childA) {
    163:         posA = i;
    164:         break;
    165:       }
    166:     }
    167:     if (posA >= coneSize) {
    168:       /* this is the triangle in the middle of a uniformly refined triangle: it
    169:        * is invariant */
    170:       if (dim != 2 || posA != 3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Expected a middle triangle, got something else");
    171:       *childB = childA;
    172:     }
    173:     else {
    174:       /* figure out position B by applying ABswapVert */
    175:       PetscInt posB;

    177:       posB = (ABswapVert >= 0) ? ((ABswapVert + posA) % coneSize) : ((coneSize -(ABswapVert + 1) - posA) % coneSize);
    178:       if (childB) *childB = children[posB];
    179:     }
    180:   }
    181:   if (childOrientB) *childOrientB = DihedralCompose(coneSize,childOrientA,ABswap);
    182:   return(0);
    183: }

    187: /*@
    188:   DMPlexReferenceTreeGetChildSymmetry - Given a reference tree, transform a childid and orientation from one parent frame to another

    190:   Input Parameters:
    191: + dm - the reference tree DMPlex object
    192: . parent - the parent point
    193: . parentOrientA - the reference orientation for describing the parent
    194: . childOrientA - the reference orientation for describing the child
    195: . childA - the reference childID for describing the child
    196: - parentOrientB - the new orientation for describing the parent

    198:   Output Parameters:
    199: + childOrientB - if not NULL, set to the new oreintation for describing the child
    200: . childB - if not NULL, the new childID for describing the child

    202:   Level: developer

    204: .seealso: DMPlexGetReferenceTree(), DMPlexSetReferenceTree(), DMPlexSetTree()
    205: @*/
    206: PetscErrorCode DMPlexReferenceTreeGetChildSymmetry(DM dm, PetscInt parent, PetscInt parentOrientA, PetscInt childOrientA, PetscInt childA, PetscInt parentOrientB, PetscInt *childOrientB, PetscInt *childB)
    207: {
    208:   DM_Plex        *mesh = (DM_Plex *)dm->data;

    213:   if (!mesh->getchildsymmetry) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"DMPlexReferenceTreeGetChildSymmetry not implemented");
    214:   mesh->getchildsymmetry(dm,parent,parentOrientA,childOrientA,childA,parentOrientB,childOrientB,childB);
    215:   return(0);
    216: }

    218: static PetscErrorCode DMPlexSetTree_Internal(DM,PetscSection,PetscInt*,PetscInt*,PetscBool,PetscBool);

    222: PetscErrorCode DMPlexCreateReferenceTree_Union(DM K, DM Kref, const char *labelName, DM *ref)
    223: {
    224:   MPI_Comm       comm;
    225:   PetscInt       dim, p, pStart, pEnd, pRefStart, pRefEnd, d, offset, parentSize, *parents, *childIDs;
    226:   PetscInt      *permvals, *unionCones, *coneSizes, *unionOrientations, numUnionPoints, *numDimPoints, numCones, numVerts;
    227:   DMLabel        identity, identityRef;
    228:   PetscSection   unionSection, unionConeSection, parentSection;
    229:   PetscScalar   *unionCoords;
    230:   IS             perm;

    234:   comm = PetscObjectComm((PetscObject)K);
    235:   DMGetDimension(K, &dim);
    236:   DMPlexGetChart(K, &pStart, &pEnd);
    237:   DMGetLabel(K, labelName, &identity);
    238:   DMGetLabel(Kref, labelName, &identityRef);
    239:   DMPlexGetChart(Kref, &pRefStart, &pRefEnd);
    240:   PetscSectionCreate(comm, &unionSection);
    241:   PetscSectionSetChart(unionSection, 0, (pEnd - pStart) + (pRefEnd - pRefStart));
    242:   /* count points that will go in the union */
    243:   for (p = pStart; p < pEnd; p++) {
    244:     PetscSectionSetDof(unionSection, p - pStart, 1);
    245:   }
    246:   for (p = pRefStart; p < pRefEnd; p++) {
    247:     PetscInt q, qSize;
    248:     DMLabelGetValue(identityRef, p, &q);
    249:     DMLabelGetStratumSize(identityRef, q, &qSize);
    250:     if (qSize > 1) {
    251:       PetscSectionSetDof(unionSection, p - pRefStart + (pEnd - pStart), 1);
    252:     }
    253:   }
    254:   PetscMalloc1(pEnd - pStart + pRefEnd - pRefStart,&permvals);
    255:   offset = 0;
    256:   /* stratify points in the union by topological dimension */
    257:   for (d = 0; d <= dim; d++) {
    258:     PetscInt cStart, cEnd, c;

    260:     DMPlexGetHeightStratum(K, d, &cStart, &cEnd);
    261:     for (c = cStart; c < cEnd; c++) {
    262:       permvals[offset++] = c;
    263:     }

    265:     DMPlexGetHeightStratum(Kref, d, &cStart, &cEnd);
    266:     for (c = cStart; c < cEnd; c++) {
    267:       permvals[offset++] = c + (pEnd - pStart);
    268:     }
    269:   }
    270:   ISCreateGeneral(comm, (pEnd - pStart) + (pRefEnd - pRefStart), permvals, PETSC_OWN_POINTER, &perm);
    271:   PetscSectionSetPermutation(unionSection,perm);
    272:   PetscSectionSetUp(unionSection);
    273:   PetscSectionGetStorageSize(unionSection,&numUnionPoints);
    274:   PetscMalloc2(numUnionPoints,&coneSizes,dim+1,&numDimPoints);
    275:   /* count dimension points */
    276:   for (d = 0; d <= dim; d++) {
    277:     PetscInt cStart, cOff, cOff2;
    278:     DMPlexGetHeightStratum(K,d,&cStart,NULL);
    279:     PetscSectionGetOffset(unionSection,cStart-pStart,&cOff);
    280:     if (d < dim) {
    281:       DMPlexGetHeightStratum(K,d+1,&cStart,NULL);
    282:       PetscSectionGetOffset(unionSection,cStart-pStart,&cOff2);
    283:     }
    284:     else {
    285:       cOff2 = numUnionPoints;
    286:     }
    287:     numDimPoints[dim - d] = cOff2 - cOff;
    288:   }
    289:   PetscSectionCreate(comm, &unionConeSection);
    290:   PetscSectionSetChart(unionConeSection, 0, numUnionPoints);
    291:   /* count the cones in the union */
    292:   for (p = pStart; p < pEnd; p++) {
    293:     PetscInt dof, uOff;

    295:     DMPlexGetConeSize(K, p, &dof);
    296:     PetscSectionGetOffset(unionSection, p - pStart,&uOff);
    297:     PetscSectionSetDof(unionConeSection, uOff, dof);
    298:     coneSizes[uOff] = dof;
    299:   }
    300:   for (p = pRefStart; p < pRefEnd; p++) {
    301:     PetscInt dof, uDof, uOff;

    303:     DMPlexGetConeSize(Kref, p, &dof);
    304:     PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);
    305:     PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);
    306:     if (uDof) {
    307:       PetscSectionSetDof(unionConeSection, uOff, dof);
    308:       coneSizes[uOff] = dof;
    309:     }
    310:   }
    311:   PetscSectionSetUp(unionConeSection);
    312:   PetscSectionGetStorageSize(unionConeSection,&numCones);
    313:   PetscMalloc2(numCones,&unionCones,numCones,&unionOrientations);
    314:   /* write the cones in the union */
    315:   for (p = pStart; p < pEnd; p++) {
    316:     PetscInt dof, uOff, c, cOff;
    317:     const PetscInt *cone, *orientation;

    319:     DMPlexGetConeSize(K, p, &dof);
    320:     DMPlexGetCone(K, p, &cone);
    321:     DMPlexGetConeOrientation(K, p, &orientation);
    322:     PetscSectionGetOffset(unionSection, p - pStart,&uOff);
    323:     PetscSectionGetOffset(unionConeSection,uOff,&cOff);
    324:     for (c = 0; c < dof; c++) {
    325:       PetscInt e, eOff;
    326:       e                           = cone[c];
    327:       PetscSectionGetOffset(unionSection, e - pStart, &eOff);
    328:       unionCones[cOff + c]        = eOff;
    329:       unionOrientations[cOff + c] = orientation[c];
    330:     }
    331:   }
    332:   for (p = pRefStart; p < pRefEnd; p++) {
    333:     PetscInt dof, uDof, uOff, c, cOff;
    334:     const PetscInt *cone, *orientation;

    336:     DMPlexGetConeSize(Kref, p, &dof);
    337:     DMPlexGetCone(Kref, p, &cone);
    338:     DMPlexGetConeOrientation(Kref, p, &orientation);
    339:     PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);
    340:     PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);
    341:     if (uDof) {
    342:       PetscSectionGetOffset(unionConeSection,uOff,&cOff);
    343:       for (c = 0; c < dof; c++) {
    344:         PetscInt e, eOff, eDof;

    346:         e    = cone[c];
    347:         PetscSectionGetDof(unionSection, e - pRefStart + (pEnd - pStart),&eDof);
    348:         if (eDof) {
    349:           PetscSectionGetOffset(unionSection, e - pRefStart + (pEnd - pStart), &eOff);
    350:         }
    351:         else {
    352:           DMLabelGetValue(identityRef, e, &e);
    353:           PetscSectionGetOffset(unionSection, e - pStart, &eOff);
    354:         }
    355:         unionCones[cOff + c]        = eOff;
    356:         unionOrientations[cOff + c] = orientation[c];
    357:       }
    358:     }
    359:   }
    360:   /* get the coordinates */
    361:   {
    362:     PetscInt vStart, vEnd, vRefStart, vRefEnd, v, vDof, vOff;
    363:     PetscSection KcoordsSec, KrefCoordsSec;
    364:     Vec      KcoordsVec, KrefCoordsVec;
    365:     PetscScalar *Kcoords;

    367:     DMGetCoordinateSection(K, &KcoordsSec);
    368:     DMGetCoordinatesLocal(K, &KcoordsVec);
    369:     DMGetCoordinateSection(Kref, &KrefCoordsSec);
    370:     DMGetCoordinatesLocal(Kref, &KrefCoordsVec);

    372:     numVerts = numDimPoints[0];
    373:     PetscMalloc1(numVerts * dim,&unionCoords);
    374:     DMPlexGetDepthStratum(K,0,&vStart,&vEnd);

    376:     offset = 0;
    377:     for (v = vStart; v < vEnd; v++) {
    378:       PetscSectionGetOffset(unionSection,v - pStart,&vOff);
    379:       VecGetValuesSection(KcoordsVec, KcoordsSec, v, &Kcoords);
    380:       for (d = 0; d < dim; d++) {
    381:         unionCoords[offset * dim + d] = Kcoords[d];
    382:       }
    383:       offset++;
    384:     }
    385:     DMPlexGetDepthStratum(Kref,0,&vRefStart,&vRefEnd);
    386:     for (v = vRefStart; v < vRefEnd; v++) {
    387:       PetscSectionGetDof(unionSection,v - pRefStart + (pEnd - pStart),&vDof);
    388:       PetscSectionGetOffset(unionSection,v - pRefStart + (pEnd - pStart),&vOff);
    389:       VecGetValuesSection(KrefCoordsVec, KrefCoordsSec, v, &Kcoords);
    390:       if (vDof) {
    391:         for (d = 0; d < dim; d++) {
    392:           unionCoords[offset * dim + d] = Kcoords[d];
    393:         }
    394:         offset++;
    395:       }
    396:     }
    397:   }
    398:   DMCreate(comm,ref);
    399:   DMSetType(*ref,DMPLEX);
    400:   DMSetDimension(*ref,dim);
    401:   DMPlexCreateFromDAG(*ref,dim,numDimPoints,coneSizes,unionCones,unionOrientations,unionCoords);
    402:   /* set the tree */
    403:   PetscSectionCreate(comm,&parentSection);
    404:   PetscSectionSetChart(parentSection,0,numUnionPoints);
    405:   for (p = pRefStart; p < pRefEnd; p++) {
    406:     PetscInt uDof, uOff;

    408:     PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);
    409:     PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);
    410:     if (uDof) {
    411:       PetscSectionSetDof(parentSection,uOff,1);
    412:     }
    413:   }
    414:   PetscSectionSetUp(parentSection);
    415:   PetscSectionGetStorageSize(parentSection,&parentSize);
    416:   PetscMalloc2(parentSize,&parents,parentSize,&childIDs);
    417:   for (p = pRefStart; p < pRefEnd; p++) {
    418:     PetscInt uDof, uOff;

    420:     PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);
    421:     PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);
    422:     if (uDof) {
    423:       PetscInt pOff, parent, parentU;
    424:       PetscSectionGetOffset(parentSection,uOff,&pOff);
    425:       DMLabelGetValue(identityRef,p,&parent);
    426:       PetscSectionGetOffset(unionSection, parent - pStart,&parentU);
    427:       parents[pOff] = parentU;
    428:       childIDs[pOff] = uOff;
    429:     }
    430:   }
    431:   DMPlexSetTree_Internal(*ref,parentSection,parents,childIDs,PETSC_TRUE,PETSC_FALSE);
    432:   PetscSectionDestroy(&parentSection);
    433:   PetscFree2(parents,childIDs);

    435:   /* clean up */
    436:   PetscSectionDestroy(&unionSection);
    437:   PetscSectionDestroy(&unionConeSection);
    438:   ISDestroy(&perm);
    439:   PetscFree(unionCoords);
    440:   PetscFree2(unionCones,unionOrientations);
    441:   PetscFree2(coneSizes,numDimPoints);
    442:   return(0);
    443: }

    447: /*@
    448:   DMPlexCreateDefaultReferenceTree - create a reference tree for isotropic hierarchical mesh refinement.

    450:   Collective on comm

    452:   Input Parameters:
    453: + comm    - the MPI communicator
    454: . dim     - the spatial dimension
    455: - simplex - Flag for simplex, otherwise use a tensor-product cell

    457:   Output Parameters:
    458: . ref     - the reference tree DMPlex object

    460:   Level: intermediate

    462: .keywords: reference cell
    463: .seealso: DMPlexSetReferenceTree(), DMPlexGetReferenceTree()
    464: @*/
    465: PetscErrorCode DMPlexCreateDefaultReferenceTree(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *ref)
    466: {
    467:   DM_Plex       *mesh;
    468:   DM             K, Kref;
    469:   PetscInt       p, pStart, pEnd;
    470:   DMLabel        identity;

    474: #if 1
    475:   comm = PETSC_COMM_SELF;
    476: #endif
    477:   /* create a reference element */
    478:   DMPlexCreateReferenceCell(comm, dim, simplex, &K);
    479:   DMCreateLabel(K, "identity");
    480:   DMGetLabel(K, "identity", &identity);
    481:   DMPlexGetChart(K, &pStart, &pEnd);
    482:   for (p = pStart; p < pEnd; p++) {
    483:     DMLabelSetValue(identity, p, p);
    484:   }
    485:   /* refine it */
    486:   DMRefine(K,comm,&Kref);

    488:   /* the reference tree is the union of these two, without duplicating
    489:    * points that appear in both */
    490:   DMPlexCreateReferenceTree_Union(K, Kref, "identity", ref);
    491:   mesh = (DM_Plex *) (*ref)->data;
    492:   mesh->getchildsymmetry = DMPlexReferenceTreeGetChildSymmetry_Default;
    493:   DMDestroy(&K);
    494:   DMDestroy(&Kref);
    495:   return(0);
    496: }

    500: static PetscErrorCode DMPlexTreeSymmetrize(DM dm)
    501: {
    502:   DM_Plex        *mesh = (DM_Plex *)dm->data;
    503:   PetscSection   childSec, pSec;
    504:   PetscInt       p, pSize, cSize, parMax = PETSC_MIN_INT, parMin = PETSC_MAX_INT;
    505:   PetscInt       *offsets, *children, pStart, pEnd;

    510:   PetscSectionDestroy(&mesh->childSection);
    511:   PetscFree(mesh->children);
    512:   pSec = mesh->parentSection;
    513:   if (!pSec) return(0);
    514:   PetscSectionGetStorageSize(pSec,&pSize);
    515:   for (p = 0; p < pSize; p++) {
    516:     PetscInt par = mesh->parents[p];

    518:     parMax = PetscMax(parMax,par+1);
    519:     parMin = PetscMin(parMin,par);
    520:   }
    521:   if (parMin > parMax) {
    522:     parMin = -1;
    523:     parMax = -1;
    524:   }
    525:   PetscSectionCreate(PetscObjectComm((PetscObject)pSec),&childSec);
    526:   PetscSectionSetChart(childSec,parMin,parMax);
    527:   for (p = 0; p < pSize; p++) {
    528:     PetscInt par = mesh->parents[p];

    530:     PetscSectionAddDof(childSec,par,1);
    531:   }
    532:   PetscSectionSetUp(childSec);
    533:   PetscSectionGetStorageSize(childSec,&cSize);
    534:   PetscMalloc1(cSize,&children);
    535:   PetscCalloc1(parMax-parMin,&offsets);
    536:   PetscSectionGetChart(pSec,&pStart,&pEnd);
    537:   for (p = pStart; p < pEnd; p++) {
    538:     PetscInt dof, off, i;

    540:     PetscSectionGetDof(pSec,p,&dof);
    541:     PetscSectionGetOffset(pSec,p,&off);
    542:     for (i = 0; i < dof; i++) {
    543:       PetscInt par = mesh->parents[off + i], cOff;

    545:       PetscSectionGetOffset(childSec,par,&cOff);
    546:       children[cOff + offsets[par-parMin]++] = p;
    547:     }
    548:   }
    549:   mesh->childSection = childSec;
    550:   mesh->children = children;
    551:   PetscFree(offsets);
    552:   return(0);
    553: }

    557: static PetscErrorCode AnchorsFlatten (PetscSection section, IS is, PetscSection *sectionNew, IS *isNew)
    558: {
    559:   PetscInt       pStart, pEnd, size, sizeNew, i, p, *valsNew = NULL;
    560:   const PetscInt *vals;
    561:   PetscSection   secNew;
    562:   PetscBool      anyNew, globalAnyNew;
    563:   PetscBool      compress;

    567:   PetscSectionGetChart(section,&pStart,&pEnd);
    568:   ISGetLocalSize(is,&size);
    569:   ISGetIndices(is,&vals);
    570:   PetscSectionCreate(PetscObjectComm((PetscObject)section),&secNew);
    571:   PetscSectionSetChart(secNew,pStart,pEnd);
    572:   for (i = 0; i < size; i++) {
    573:     PetscInt dof;

    575:     p = vals[i];
    576:     if (p < pStart || p >= pEnd) continue;
    577:     PetscSectionGetDof(section, p, &dof);
    578:     if (dof) break;
    579:   }
    580:   if (i == size) {
    581:     PetscSectionSetUp(secNew);
    582:     anyNew   = PETSC_FALSE;
    583:     compress = PETSC_FALSE;
    584:     sizeNew  = 0;
    585:   }
    586:   else {
    587:     anyNew = PETSC_TRUE;
    588:     for (p = pStart; p < pEnd; p++) {
    589:       PetscInt dof, off;

    591:       PetscSectionGetDof(section, p, &dof);
    592:       PetscSectionGetOffset(section, p, &off);
    593:       for (i = 0; i < dof; i++) {
    594:         PetscInt q = vals[off + i], qDof = 0;

    596:         if (q >= pStart && q < pEnd) {
    597:           PetscSectionGetDof(section, q, &qDof);
    598:         }
    599:         if (qDof) {
    600:           PetscSectionAddDof(secNew, p, qDof);
    601:         }
    602:         else {
    603:           PetscSectionAddDof(secNew, p, 1);
    604:         }
    605:       }
    606:     }
    607:     PetscSectionSetUp(secNew);
    608:     PetscSectionGetStorageSize(secNew,&sizeNew);
    609:     PetscMalloc1(sizeNew,&valsNew);
    610:     compress = PETSC_FALSE;
    611:     for (p = pStart; p < pEnd; p++) {
    612:       PetscInt dof, off, count, offNew, dofNew;

    614:       PetscSectionGetDof(section, p, &dof);
    615:       PetscSectionGetOffset(section, p, &off);
    616:       PetscSectionGetDof(secNew, p, &dofNew);
    617:       PetscSectionGetOffset(secNew, p, &offNew);
    618:       count = 0;
    619:       for (i = 0; i < dof; i++) {
    620:         PetscInt q = vals[off + i], qDof = 0, qOff = 0, j;

    622:         if (q >= pStart && q < pEnd) {
    623:           PetscSectionGetDof(section, q, &qDof);
    624:           PetscSectionGetOffset(section, q, &qOff);
    625:         }
    626:         if (qDof) {
    627:           PetscInt oldCount = count;

    629:           for (j = 0; j < qDof; j++) {
    630:             PetscInt k, r = vals[qOff + j];

    632:             for (k = 0; k < oldCount; k++) {
    633:               if (valsNew[offNew + k] == r) {
    634:                 break;
    635:               }
    636:             }
    637:             if (k == oldCount) {
    638:               valsNew[offNew + count++] = r;
    639:             }
    640:           }
    641:         }
    642:         else {
    643:           PetscInt k, oldCount = count;

    645:           for (k = 0; k < oldCount; k++) {
    646:             if (valsNew[offNew + k] == q) {
    647:               break;
    648:             }
    649:           }
    650:           if (k == oldCount) {
    651:             valsNew[offNew + count++] = q;
    652:           }
    653:         }
    654:       }
    655:       if (count < dofNew) {
    656:         PetscSectionSetDof(secNew, p, count);
    657:         compress = PETSC_TRUE;
    658:       }
    659:     }
    660:   }
    661:   ISRestoreIndices(is,&vals);
    662:   MPIU_Allreduce(&anyNew,&globalAnyNew,1,MPIU_BOOL,MPI_LOR,PetscObjectComm((PetscObject)secNew));
    663:   if (!globalAnyNew) {
    664:     PetscSectionDestroy(&secNew);
    665:     *sectionNew = NULL;
    666:     *isNew = NULL;
    667:   }
    668:   else {
    669:     PetscBool globalCompress;

    671:     MPIU_Allreduce(&compress,&globalCompress,1,MPIU_BOOL,MPI_LOR,PetscObjectComm((PetscObject)secNew));
    672:     if (compress) {
    673:       PetscSection secComp;
    674:       PetscInt *valsComp = NULL;

    676:       PetscSectionCreate(PetscObjectComm((PetscObject)section),&secComp);
    677:       PetscSectionSetChart(secComp,pStart,pEnd);
    678:       for (p = pStart; p < pEnd; p++) {
    679:         PetscInt dof;

    681:         PetscSectionGetDof(secNew, p, &dof);
    682:         PetscSectionSetDof(secComp, p, dof);
    683:       }
    684:       PetscSectionSetUp(secComp);
    685:       PetscSectionGetStorageSize(secComp,&sizeNew);
    686:       PetscMalloc1(sizeNew,&valsComp);
    687:       for (p = pStart; p < pEnd; p++) {
    688:         PetscInt dof, off, offNew, j;

    690:         PetscSectionGetDof(secNew, p, &dof);
    691:         PetscSectionGetOffset(secNew, p, &off);
    692:         PetscSectionGetOffset(secComp, p, &offNew);
    693:         for (j = 0; j < dof; j++) {
    694:           valsComp[offNew + j] = valsNew[off + j];
    695:         }
    696:       }
    697:       PetscSectionDestroy(&secNew);
    698:       secNew  = secComp;
    699:       PetscFree(valsNew);
    700:       valsNew = valsComp;
    701:     }
    702:     ISCreateGeneral(PetscObjectComm((PetscObject)is),sizeNew,valsNew,PETSC_OWN_POINTER,isNew);
    703:   }
    704:   return(0);
    705: }

    709: static PetscErrorCode DMPlexCreateAnchors_Tree(DM dm)
    710: {
    711:   PetscInt       p, pStart, pEnd, *anchors, size;
    712:   PetscInt       aMin = PETSC_MAX_INT, aMax = PETSC_MIN_INT;
    713:   PetscSection   aSec;
    714:   DMLabel        canonLabel;
    715:   IS             aIS;

    720:   DMPlexGetChart(dm,&pStart,&pEnd);
    721:   DMGetLabel(dm,"canonical",&canonLabel);
    722:   for (p = pStart; p < pEnd; p++) {
    723:     PetscInt parent;

    725:     if (canonLabel) {
    726:       PetscInt canon;

    728:       DMLabelGetValue(canonLabel,p,&canon);
    729:       if (p != canon) continue;
    730:     }
    731:     DMPlexGetTreeParent(dm,p,&parent,NULL);
    732:     if (parent != p) {
    733:       aMin = PetscMin(aMin,p);
    734:       aMax = PetscMax(aMax,p+1);
    735:     }
    736:   }
    737:   if (aMin > aMax) {
    738:     aMin = -1;
    739:     aMax = -1;
    740:   }
    741:   PetscSectionCreate(PETSC_COMM_SELF,&aSec);
    742:   PetscSectionSetChart(aSec,aMin,aMax);
    743:   for (p = aMin; p < aMax; p++) {
    744:     PetscInt parent, ancestor = p;

    746:     if (canonLabel) {
    747:       PetscInt canon;

    749:       DMLabelGetValue(canonLabel,p,&canon);
    750:       if (p != canon) continue;
    751:     }
    752:     DMPlexGetTreeParent(dm,p,&parent,NULL);
    753:     while (parent != ancestor) {
    754:       ancestor = parent;
    755:       DMPlexGetTreeParent(dm,ancestor,&parent,NULL);
    756:     }
    757:     if (ancestor != p) {
    758:       PetscInt closureSize, *closure = NULL;

    760:       DMPlexGetTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);
    761:       PetscSectionSetDof(aSec,p,closureSize);
    762:       DMPlexRestoreTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);
    763:     }
    764:   }
    765:   PetscSectionSetUp(aSec);
    766:   PetscSectionGetStorageSize(aSec,&size);
    767:   PetscMalloc1(size,&anchors);
    768:   for (p = aMin; p < aMax; p++) {
    769:     PetscInt parent, ancestor = p;

    771:     if (canonLabel) {
    772:       PetscInt canon;

    774:       DMLabelGetValue(canonLabel,p,&canon);
    775:       if (p != canon) continue;
    776:     }
    777:     DMPlexGetTreeParent(dm,p,&parent,NULL);
    778:     while (parent != ancestor) {
    779:       ancestor = parent;
    780:       DMPlexGetTreeParent(dm,ancestor,&parent,NULL);
    781:     }
    782:     if (ancestor != p) {
    783:       PetscInt j, closureSize, *closure = NULL, aOff;

    785:       PetscSectionGetOffset(aSec,p,&aOff);

    787:       DMPlexGetTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);
    788:       for (j = 0; j < closureSize; j++) {
    789:         anchors[aOff + j] = closure[2*j];
    790:       }
    791:       DMPlexRestoreTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);
    792:     }
    793:   }
    794:   ISCreateGeneral(PETSC_COMM_SELF,size,anchors,PETSC_OWN_POINTER,&aIS);
    795:   {
    796:     PetscSection aSecNew = aSec;
    797:     IS           aISNew  = aIS;

    799:     PetscObjectReference((PetscObject)aSec);
    800:     PetscObjectReference((PetscObject)aIS);
    801:     while (aSecNew) {
    802:       PetscSectionDestroy(&aSec);
    803:       ISDestroy(&aIS);
    804:       aSec    = aSecNew;
    805:       aIS     = aISNew;
    806:       aSecNew = NULL;
    807:       aISNew  = NULL;
    808:       AnchorsFlatten(aSec,aIS,&aSecNew,&aISNew);
    809:     }
    810:   }
    811:   DMPlexSetAnchors(dm,aSec,aIS);
    812:   PetscSectionDestroy(&aSec);
    813:   ISDestroy(&aIS);
    814:   return(0);
    815: }

    819: static PetscErrorCode DMPlexGetTrueSupportSize(DM dm,PetscInt p,PetscInt *dof,PetscInt *numTrueSupp)
    820: {

    824:   if (numTrueSupp[p] == -1) {
    825:     PetscInt i, alldof;
    826:     const PetscInt *supp;
    827:     PetscInt count = 0;

    829:     DMPlexGetSupportSize(dm,p,&alldof);
    830:     DMPlexGetSupport(dm,p,&supp);
    831:     for (i = 0; i < alldof; i++) {
    832:       PetscInt q = supp[i], numCones, j;
    833:       const PetscInt *cone;

    835:       DMPlexGetConeSize(dm,q,&numCones);
    836:       DMPlexGetCone(dm,q,&cone);
    837:       for (j = 0; j < numCones; j++) {
    838:         if (cone[j] == p) break;
    839:       }
    840:       if (j < numCones) count++;
    841:     }
    842:     numTrueSupp[p] = count;
    843:   }
    844:   *dof = numTrueSupp[p];
    845:   return(0);
    846: }

    850: static PetscErrorCode DMPlexTreeExchangeSupports(DM dm)
    851: {
    852:   DM_Plex *mesh = (DM_Plex *)dm->data;
    853:   PetscSection newSupportSection;
    854:   PetscInt newSize, *newSupports, pStart, pEnd, p, d, depth;
    855:   PetscInt *numTrueSupp;
    856:   PetscInt *offsets;

    861:   /* symmetrize the hierarchy */
    862:   DMPlexGetDepth(dm,&depth);
    863:   PetscSectionCreate(PetscObjectComm((PetscObject)(mesh->supportSection)),&newSupportSection);
    864:   DMPlexGetChart(dm,&pStart,&pEnd);
    865:   PetscSectionSetChart(newSupportSection,pStart,pEnd);
    866:   PetscCalloc1(pEnd,&offsets);
    867:   PetscMalloc1(pEnd,&numTrueSupp);
    868:   for (p = 0; p < pEnd; p++) numTrueSupp[p] = -1;
    869:   /* if a point is in the (true) support of q, it should be in the support of
    870:    * parent(q) */
    871:   for (d = 0; d <= depth; d++) {
    872:     DMPlexGetHeightStratum(dm,d,&pStart,&pEnd);
    873:     for (p = pStart; p < pEnd; ++p) {
    874:       PetscInt dof, q, qdof, parent;

    876:       DMPlexGetTrueSupportSize(dm,p,&dof,numTrueSupp);
    877:       PetscSectionAddDof(newSupportSection, p, dof);
    878:       q    = p;
    879:       DMPlexGetTreeParent(dm,q,&parent,NULL);
    880:       while (parent != q && parent >= pStart && parent < pEnd) {
    881:         q = parent;

    883:         DMPlexGetTrueSupportSize(dm,q,&qdof,numTrueSupp);
    884:         PetscSectionAddDof(newSupportSection,p,qdof);
    885:         PetscSectionAddDof(newSupportSection,q,dof);
    886:         DMPlexGetTreeParent(dm,q,&parent,NULL);
    887:       }
    888:     }
    889:   }
    890:   PetscSectionSetUp(newSupportSection);
    891:   PetscSectionGetStorageSize(newSupportSection,&newSize);
    892:   PetscMalloc1(newSize,&newSupports);
    893:   for (d = 0; d <= depth; d++) {
    894:     DMPlexGetHeightStratum(dm,d,&pStart,&pEnd);
    895:     for (p = pStart; p < pEnd; p++) {
    896:       PetscInt dof, off, q, qdof, qoff, newDof, newOff, newqOff, i, parent;

    898:       PetscSectionGetDof(mesh->supportSection, p, &dof);
    899:       PetscSectionGetOffset(mesh->supportSection, p, &off);
    900:       PetscSectionGetDof(newSupportSection, p, &newDof);
    901:       PetscSectionGetOffset(newSupportSection, p, &newOff);
    902:       for (i = 0; i < dof; i++) {
    903:         PetscInt numCones, j;
    904:         const PetscInt *cone;
    905:         PetscInt q = mesh->supports[off + i];

    907:         DMPlexGetConeSize(dm,q,&numCones);
    908:         DMPlexGetCone(dm,q,&cone);
    909:         for (j = 0; j < numCones; j++) {
    910:           if (cone[j] == p) break;
    911:         }
    912:         if (j < numCones) newSupports[newOff+offsets[p]++] = q;
    913:       }
    914:       mesh->maxSupportSize = PetscMax(mesh->maxSupportSize,newDof);

    916:       q    = p;
    917:       DMPlexGetTreeParent(dm,q,&parent,NULL);
    918:       while (parent != q && parent >= pStart && parent < pEnd) {
    919:         q = parent;
    920:         PetscSectionGetDof(mesh->supportSection, q, &qdof);
    921:         PetscSectionGetOffset(mesh->supportSection, q, &qoff);
    922:         PetscSectionGetOffset(newSupportSection, q, &newqOff);
    923:         for (i = 0; i < qdof; i++) {
    924:           PetscInt numCones, j;
    925:           const PetscInt *cone;
    926:           PetscInt r = mesh->supports[qoff + i];

    928:           DMPlexGetConeSize(dm,r,&numCones);
    929:           DMPlexGetCone(dm,r,&cone);
    930:           for (j = 0; j < numCones; j++) {
    931:             if (cone[j] == q) break;
    932:           }
    933:           if (j < numCones) newSupports[newOff+offsets[p]++] = r;
    934:         }
    935:         for (i = 0; i < dof; i++) {
    936:           PetscInt numCones, j;
    937:           const PetscInt *cone;
    938:           PetscInt r = mesh->supports[off + i];

    940:           DMPlexGetConeSize(dm,r,&numCones);
    941:           DMPlexGetCone(dm,r,&cone);
    942:           for (j = 0; j < numCones; j++) {
    943:             if (cone[j] == p) break;
    944:           }
    945:           if (j < numCones) newSupports[newqOff+offsets[q]++] = r;
    946:         }
    947:         DMPlexGetTreeParent(dm,q,&parent,NULL);
    948:       }
    949:     }
    950:   }
    951:   PetscSectionDestroy(&mesh->supportSection);
    952:   mesh->supportSection = newSupportSection;
    953:   PetscFree(mesh->supports);
    954:   mesh->supports = newSupports;
    955:   PetscFree(offsets);
    956:   PetscFree(numTrueSupp);

    958:   return(0);
    959: }

    961: static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_Direct(DM,PetscSection,PetscSection,Mat);
    962: static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_FromReference(DM,PetscSection,PetscSection,Mat);

    966: static PetscErrorCode DMPlexSetTree_Internal(DM dm, PetscSection parentSection, PetscInt *parents, PetscInt *childIDs, PetscBool computeCanonical, PetscBool exchangeSupports)
    967: {
    968:   DM_Plex       *mesh = (DM_Plex *)dm->data;
    969:   DM             refTree;
    970:   PetscInt       size;

    976:   PetscObjectReference((PetscObject)parentSection);
    977:   PetscSectionDestroy(&mesh->parentSection);
    978:   mesh->parentSection = parentSection;
    979:   PetscSectionGetStorageSize(parentSection,&size);
    980:   if (parents != mesh->parents) {
    981:     PetscFree(mesh->parents);
    982:     PetscMalloc1(size,&mesh->parents);
    983:     PetscMemcpy(mesh->parents, parents, size * sizeof(*parents));
    984:   }
    985:   if (childIDs != mesh->childIDs) {
    986:     PetscFree(mesh->childIDs);
    987:     PetscMalloc1(size,&mesh->childIDs);
    988:     PetscMemcpy(mesh->childIDs, childIDs, size * sizeof(*childIDs));
    989:   }
    990:   DMPlexGetReferenceTree(dm,&refTree);
    991:   if (refTree) {
    992:     DMLabel canonLabel;

    994:     DMGetLabel(refTree,"canonical",&canonLabel);
    995:     if (canonLabel) {
    996:       PetscInt i;

    998:       for (i = 0; i < size; i++) {
    999:         PetscInt canon;
    1000:         DMLabelGetValue(canonLabel, mesh->childIDs[i], &canon);
    1001:         if (canon >= 0) {
    1002:           mesh->childIDs[i] = canon;
    1003:         }
    1004:       }
    1005:     }
    1006:     mesh->computeanchormatrix = DMPlexComputeAnchorMatrix_Tree_FromReference;
    1007:   }
    1008:   else {
    1009:     mesh->computeanchormatrix = DMPlexComputeAnchorMatrix_Tree_Direct;
    1010:   }
    1011:   DMPlexTreeSymmetrize(dm);
    1012:   if (computeCanonical) {
    1013:     PetscInt d, dim;

    1015:     /* add the canonical label */
    1016:     DMGetDimension(dm,&dim);
    1017:     DMCreateLabel(dm,"canonical");
    1018:     for (d = 0; d <= dim; d++) {
    1019:       PetscInt p, dStart, dEnd, canon = -1, cNumChildren;
    1020:       const PetscInt *cChildren;

    1022:       DMPlexGetDepthStratum(dm,d,&dStart,&dEnd);
    1023:       for (p = dStart; p < dEnd; p++) {
    1024:         DMPlexGetTreeChildren(dm,p,&cNumChildren,&cChildren);
    1025:         if (cNumChildren) {
    1026:           canon = p;
    1027:           break;
    1028:         }
    1029:       }
    1030:       if (canon == -1) continue;
    1031:       for (p = dStart; p < dEnd; p++) {
    1032:         PetscInt numChildren, i;
    1033:         const PetscInt *children;

    1035:         DMPlexGetTreeChildren(dm,p,&numChildren,&children);
    1036:         if (numChildren) {
    1037:           if (numChildren != cNumChildren) SETERRQ2(PetscObjectComm((PetscObject)dm),PETSC_ERR_PLIB,"All parent points in a stratum should have the same number of children: %d != %d", numChildren, cNumChildren);
    1038:           DMSetLabelValue(dm,"canonical",p,canon);
    1039:           for (i = 0; i < numChildren; i++) {
    1040:             DMSetLabelValue(dm,"canonical",children[i],cChildren[i]);
    1041:           }
    1042:         }
    1043:       }
    1044:     }
    1045:   }
    1046:   if (exchangeSupports) {
    1047:     DMPlexTreeExchangeSupports(dm);
    1048:   }
    1049:   mesh->createanchors = DMPlexCreateAnchors_Tree;
    1050:   /* reset anchors */
    1051:   DMPlexSetAnchors(dm,NULL,NULL);
    1052:   return(0);
    1053: }

    1057: /*@
    1058:   DMPlexSetTree - set the tree that describes the hierarchy of non-conforming mesh points.  This routine also creates
    1059:   the point-to-point constraints determined by the tree: a point is constained to the points in the closure of its
    1060:   tree root.

    1062:   Collective on dm

    1064:   Input Parameters:
    1065: + dm - the DMPlex object
    1066: . parentSection - a section describing the tree: a point has a parent if it has 1 dof in the section; the section
    1067:                   offset indexes the parent and childID list; the reference count of parentSection is incremented
    1068: . parents - a list of the point parents; copied, can be destroyed
    1069: - childIDs - identifies the relationship of the child point to the parent point; if there is a reference tree, then
    1070:              the child corresponds to the point in the reference tree with index childIDs; copied, can be destroyed

    1072:   Level: intermediate

    1074: .seealso: DMPlexGetTree(), DMPlexSetReferenceTree(), DMPlexSetAnchors(), DMPlexGetTreeParent(), DMPlexGetTreeChildren()
    1075: @*/
    1076: PetscErrorCode DMPlexSetTree(DM dm, PetscSection parentSection, PetscInt parents[], PetscInt childIDs[])
    1077: {

    1081:   DMPlexSetTree_Internal(dm,parentSection,parents,childIDs,PETSC_FALSE,PETSC_TRUE);
    1082:   return(0);
    1083: }

    1087: /*@
    1088:   DMPlexGetTree - get the tree that describes the hierarchy of non-conforming mesh points.
    1089:   Collective on dm

    1091:   Input Parameters:
    1092: . dm - the DMPlex object

    1094:   Output Parameters:
    1095: + parentSection - a section describing the tree: a point has a parent if it has 1 dof in the section; the section
    1096:                   offset indexes the parent and childID list
    1097: . parents - a list of the point parents
    1098: . childIDs - identifies the relationship of the child point to the parent point; if there is a reference tree, then
    1099:              the child corresponds to the point in the reference tree with index childID
    1100: . childSection - the inverse of the parent section
    1101: - children - a list of the point children

    1103:   Level: intermediate

    1105: .seealso: DMPlexSetTree(), DMPlexSetReferenceTree(), DMPlexSetAnchors(), DMPlexGetTreeParent(), DMPlexGetTreeChildren()
    1106: @*/
    1107: PetscErrorCode DMPlexGetTree(DM dm, PetscSection *parentSection, PetscInt *parents[], PetscInt *childIDs[], PetscSection *childSection, PetscInt *children[])
    1108: {
    1109:   DM_Plex        *mesh = (DM_Plex *)dm->data;

    1113:   if (parentSection) *parentSection = mesh->parentSection;
    1114:   if (parents)       *parents       = mesh->parents;
    1115:   if (childIDs)      *childIDs      = mesh->childIDs;
    1116:   if (childSection)  *childSection  = mesh->childSection;
    1117:   if (children)      *children      = mesh->children;
    1118:   return(0);
    1119: }

    1123: /*@
    1124:   DMPlexGetTreeParent - get the parent of a point in the tree describing the point hierarchy (not the Sieve DAG)

    1126:   Input Parameters:
    1127: + dm - the DMPlex object
    1128: - point - the query point

    1130:   Output Parameters:
    1131: + parent - if not NULL, set to the parent of the point, or the point itself if the point does not have a parent
    1132: - childID - if not NULL, set to the child ID of the point with respect to its parent, or 0 if the point
    1133:             does not have a parent

    1135:   Level: intermediate

    1137: .seealso: DMPlexSetTree(), DMPlexGetTree(), DMPlexGetTreeChildren()
    1138: @*/
    1139: PetscErrorCode DMPlexGetTreeParent(DM dm, PetscInt point, PetscInt *parent, PetscInt *childID)
    1140: {
    1141:   DM_Plex       *mesh = (DM_Plex *)dm->data;
    1142:   PetscSection   pSec;

    1147:   pSec = mesh->parentSection;
    1148:   if (pSec && point >= pSec->pStart && point < pSec->pEnd) {
    1149:     PetscInt dof;

    1151:     PetscSectionGetDof (pSec, point, &dof);
    1152:     if (dof) {
    1153:       PetscInt off;

    1155:       PetscSectionGetOffset (pSec, point, &off);
    1156:       if (parent)  *parent = mesh->parents[off];
    1157:       if (childID) *childID = mesh->childIDs[off];
    1158:       return(0);
    1159:     }
    1160:   }
    1161:   if (parent) {
    1162:     *parent = point;
    1163:   }
    1164:   if (childID) {
    1165:     *childID = 0;
    1166:   }
    1167:   return(0);
    1168: }

    1172: /*@C
    1173:   DMPlexGetTreeChildren - get the children of a point in the tree describing the point hierarchy (not the Sieve DAG)

    1175:   Input Parameters:
    1176: + dm - the DMPlex object
    1177: - point - the query point

    1179:   Output Parameters:
    1180: + numChildren - if not NULL, set to the number of children
    1181: - children - if not NULL, set to a list children, or set to NULL if the point has no children

    1183:   Level: intermediate

    1185:   Fortran Notes:
    1186:   Since it returns an array, this routine is only available in Fortran 90, and you must
    1187:   include petsc.h90 in your code.

    1189: .seealso: DMPlexSetTree(), DMPlexGetTree(), DMPlexGetTreeParent()
    1190: @*/
    1191: PetscErrorCode DMPlexGetTreeChildren(DM dm, PetscInt point, PetscInt *numChildren, const PetscInt *children[])
    1192: {
    1193:   DM_Plex       *mesh = (DM_Plex *)dm->data;
    1194:   PetscSection   childSec;
    1195:   PetscInt       dof = 0;

    1200:   childSec = mesh->childSection;
    1201:   if (childSec && point >= childSec->pStart && point < childSec->pEnd) {
    1202:     PetscSectionGetDof (childSec, point, &dof);
    1203:   }
    1204:   if (numChildren) *numChildren = dof;
    1205:   if (children) {
    1206:     if (dof) {
    1207:       PetscInt off;

    1209:       PetscSectionGetOffset (childSec, point, &off);
    1210:       *children = &mesh->children[off];
    1211:     }
    1212:     else {
    1213:       *children = NULL;
    1214:     }
    1215:   }
    1216:   return(0);
    1217: }

    1221: static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_Direct(DM dm, PetscSection section, PetscSection cSec, Mat cMat)
    1222: {
    1223:   PetscDS        ds;
    1224:   PetscInt       spdim;
    1225:   PetscInt       numFields, f, c, cStart, cEnd, pStart, pEnd, conStart, conEnd;
    1226:   const PetscInt *anchors;
    1227:   PetscSection   aSec;
    1228:   PetscReal      *v0, *v0parent, *vtmp, *J, *Jparent, *invJparent, detJ, detJparent;
    1229:   IS             aIS;

    1233:   DMPlexGetChart(dm,&pStart,&pEnd);
    1234:   DMGetDS(dm,&ds);
    1235:   PetscDSGetNumFields(ds,&numFields);
    1236:   DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);
    1237:   DMPlexGetAnchors(dm,&aSec,&aIS);
    1238:   ISGetIndices(aIS,&anchors);
    1239:   PetscSectionGetChart(cSec,&conStart,&conEnd);
    1240:   DMGetDimension(dm,&spdim);
    1241:   PetscMalloc6(spdim,&v0,spdim,&v0parent,spdim,&vtmp,spdim*spdim,&J,spdim*spdim,&Jparent,spdim*spdim,&invJparent);

    1243:   for (f = 0; f < numFields; f++) {
    1244:     PetscObject disc;
    1245:     PetscFE fe = NULL;
    1246:     PetscFV fv = NULL;
    1247:     PetscClassId id;
    1248:     PetscDualSpace space;
    1249:     PetscInt i, j, k, nPoints, offset;
    1250:     PetscInt fSize, fComp;
    1251:     PetscReal *B = NULL;
    1252:     PetscReal *weights, *pointsRef, *pointsReal;
    1253:     Mat Amat, Bmat, Xmat;

    1255:     PetscDSGetDiscretization(ds,f,&disc);
    1256:     PetscObjectGetClassId(disc,&id);
    1257:     if (id == PETSCFE_CLASSID) {
    1258:       fe = (PetscFE) disc;
    1259:       PetscFEGetDualSpace(fe,&space);
    1260:       PetscDualSpaceGetDimension(space,&fSize);
    1261:       PetscFEGetNumComponents(fe,&fComp);
    1262:     }
    1263:     else if (id == PETSCFV_CLASSID) {
    1264:       fv = (PetscFV) disc;
    1265:       PetscFVGetDualSpace(fv,&space);
    1266:       PetscDualSpaceGetDimension(space,&fSize);
    1267:       PetscFVGetNumComponents(fv,&fComp);
    1268:     }
    1269:     else SETERRQ1(PetscObjectComm(disc),PETSC_ERR_ARG_UNKNOWN_TYPE, "PetscDS discretization id %d not recognized.", id);

    1271:     MatCreate(PETSC_COMM_SELF,&Amat);
    1272:     MatSetSizes(Amat,fSize,fSize,fSize,fSize);
    1273:     MatSetType(Amat,MATSEQDENSE);
    1274:     MatSetUp(Amat);
    1275:     MatDuplicate(Amat,MAT_DO_NOT_COPY_VALUES,&Bmat);
    1276:     MatDuplicate(Amat,MAT_DO_NOT_COPY_VALUES,&Xmat);
    1277:     nPoints = 0;
    1278:     for (i = 0; i < fSize; i++) {
    1279:       PetscInt        qPoints;
    1280:       PetscQuadrature quad;

    1282:       PetscDualSpaceGetFunctional(space,i,&quad);
    1283:       PetscQuadratureGetData(quad,NULL,&qPoints,NULL,NULL);
    1284:       nPoints += qPoints;
    1285:     }
    1286:     PetscMalloc3(nPoints,&weights,spdim*nPoints,&pointsRef,spdim*nPoints,&pointsReal);
    1287:     offset = 0;
    1288:     for (i = 0; i < fSize; i++) {
    1289:       PetscInt        qPoints;
    1290:       const PetscReal    *p, *w;
    1291:       PetscQuadrature quad;

    1293:       PetscDualSpaceGetFunctional(space,i,&quad);
    1294:       PetscQuadratureGetData(quad,NULL,&qPoints,&p,&w);
    1295:       PetscMemcpy(weights+offset,w,qPoints*sizeof(*w));
    1296:       PetscMemcpy(pointsRef+spdim*offset,p,spdim*qPoints*sizeof(*p));
    1297:       offset += qPoints;
    1298:     }
    1299:     if (id == PETSCFE_CLASSID) {
    1300:       PetscFEGetTabulation(fe,nPoints,pointsRef,&B,NULL,NULL);
    1301:     }
    1302:     else {
    1303:       PetscFVGetTabulation(fv,nPoints,pointsRef,&B,NULL,NULL);
    1304:     }
    1305:     offset = 0;
    1306:     for (i = 0; i < fSize; i++) {
    1307:       PetscInt        qPoints;
    1308:       PetscQuadrature quad;

    1310:       PetscDualSpaceGetFunctional(space,i,&quad);
    1311:       PetscQuadratureGetData(quad,NULL,&qPoints,NULL,NULL);
    1312:       for (j = 0; j < fSize; j++) {
    1313:         PetscScalar val = 0.;

    1315:         for (k = 0; k < qPoints; k++) {
    1316:           val += B[((offset + k) * fSize + j) * fComp] * weights[k];
    1317:         }
    1318:         MatSetValue(Amat,i,j,val,INSERT_VALUES);
    1319:       }
    1320:       offset += qPoints;
    1321:     }
    1322:     if (id == PETSCFE_CLASSID) {
    1323:       PetscFERestoreTabulation(fe,nPoints,pointsRef,&B,NULL,NULL);
    1324:     }
    1325:     else {
    1326:       PetscFVRestoreTabulation(fv,nPoints,pointsRef,&B,NULL,NULL);
    1327:     }
    1328:     MatAssemblyBegin(Amat,MAT_FINAL_ASSEMBLY);
    1329:     MatAssemblyEnd(Amat,MAT_FINAL_ASSEMBLY);
    1330:     MatLUFactor(Amat,NULL,NULL,NULL);
    1331:     for (c = cStart; c < cEnd; c++) {
    1332:       PetscInt parent;
    1333:       PetscInt closureSize, closureSizeP, *closure = NULL, *closureP = NULL;
    1334:       PetscInt *childOffsets, *parentOffsets;

    1336:       DMPlexGetTreeParent(dm,c,&parent,NULL);
    1337:       if (parent == c) continue;
    1338:       DMPlexGetTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);
    1339:       for (i = 0; i < closureSize; i++) {
    1340:         PetscInt p = closure[2*i];
    1341:         PetscInt conDof;

    1343:         if (p < conStart || p >= conEnd) continue;
    1344:         if (numFields > 1) {
    1345:           PetscSectionGetFieldDof(cSec,p,f,&conDof);
    1346:         }
    1347:         else {
    1348:           PetscSectionGetDof(cSec,p,&conDof);
    1349:         }
    1350:         if (conDof) break;
    1351:       }
    1352:       if (i == closureSize) {
    1353:         DMPlexRestoreTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);
    1354:         continue;
    1355:       }

    1357:       DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, NULL, &detJ);
    1358:       DMPlexComputeCellGeometryFEM(dm, parent, NULL, v0parent, Jparent, invJparent, &detJparent);
    1359:       for (i = 0; i < nPoints; i++) {
    1360:         CoordinatesRefToReal(spdim, spdim, v0, J, &pointsRef[i*spdim],vtmp);
    1361:         CoordinatesRealToRef(spdim, spdim, v0parent, invJparent, vtmp, &pointsReal[i*spdim]);
    1362:       }
    1363:       if (id == PETSCFE_CLASSID) {
    1364:         PetscFEGetTabulation(fe,nPoints,pointsReal,&B,NULL,NULL);
    1365:       }
    1366:       else {
    1367:         PetscFVGetTabulation(fv,nPoints,pointsReal,&B,NULL,NULL);
    1368:       }
    1369:       offset = 0;
    1370:       for (i = 0; i < fSize; i++) {
    1371:         PetscInt        qPoints;
    1372:         PetscQuadrature quad;

    1374:         PetscDualSpaceGetFunctional(space,i,&quad);
    1375:         PetscQuadratureGetData(quad,NULL,&qPoints,NULL,NULL);
    1376:         for (j = 0; j < fSize; j++) {
    1377:           PetscScalar val = 0.;

    1379:           for (k = 0; k < qPoints; k++) {
    1380:             val += B[((offset + k) * fSize + j) * fComp] * weights[k];
    1381:           }
    1382:           MatSetValue(Bmat,i,j,val,INSERT_VALUES);
    1383:         }
    1384:         offset += qPoints;
    1385:       }
    1386:       if (id == PETSCFE_CLASSID) {
    1387:         PetscFERestoreTabulation(fe,nPoints,pointsReal,&B,NULL,NULL);
    1388:       }
    1389:       else {
    1390:         PetscFVRestoreTabulation(fv,nPoints,pointsReal,&B,NULL,NULL);
    1391:       }
    1392:       MatAssemblyBegin(Bmat,MAT_FINAL_ASSEMBLY);
    1393:       MatAssemblyEnd(Bmat,MAT_FINAL_ASSEMBLY);
    1394:       MatMatSolve(Amat,Bmat,Xmat);
    1395:       DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSizeP,&closureP);
    1396:       PetscMalloc2(closureSize+1,&childOffsets,closureSizeP+1,&parentOffsets);
    1397:       childOffsets[0] = 0;
    1398:       for (i = 0; i < closureSize; i++) {
    1399:         PetscInt p = closure[2*i];
    1400:         PetscInt dof;

    1402:         if (numFields > 1) {
    1403:           PetscSectionGetFieldDof(section,p,f,&dof);
    1404:         }
    1405:         else {
    1406:           PetscSectionGetDof(section,p,&dof);
    1407:         }
    1408:         childOffsets[i+1]=childOffsets[i]+dof / fComp;
    1409:       }
    1410:       parentOffsets[0] = 0;
    1411:       for (i = 0; i < closureSizeP; i++) {
    1412:         PetscInt p = closureP[2*i];
    1413:         PetscInt dof;

    1415:         if (numFields > 1) {
    1416:           PetscSectionGetFieldDof(section,p,f,&dof);
    1417:         }
    1418:         else {
    1419:           PetscSectionGetDof(section,p,&dof);
    1420:         }
    1421:         parentOffsets[i+1]=parentOffsets[i]+dof / fComp;
    1422:       }
    1423:       for (i = 0; i < closureSize; i++) {
    1424:         PetscInt conDof, conOff, aDof, aOff;
    1425:         PetscInt p = closure[2*i];
    1426:         PetscInt o = closure[2*i+1];

    1428:         if (p < conStart || p >= conEnd) continue;
    1429:         if (numFields > 1) {
    1430:           PetscSectionGetFieldDof(cSec,p,f,&conDof);
    1431:           PetscSectionGetFieldOffset(cSec,p,f,&conOff);
    1432:         }
    1433:         else {
    1434:           PetscSectionGetDof(cSec,p,&conDof);
    1435:           PetscSectionGetOffset(cSec,p,&conOff);
    1436:         }
    1437:         if (!conDof) continue;
    1438:         PetscSectionGetDof(aSec,p,&aDof);
    1439:         PetscSectionGetOffset(aSec,p,&aOff);
    1440:         for (k = 0; k < aDof; k++) {
    1441:           PetscInt a = anchors[aOff + k];
    1442:           PetscInt aSecDof, aSecOff;

    1444:           if (numFields > 1) {
    1445:             PetscSectionGetFieldDof(section,a,f,&aSecDof);
    1446:             PetscSectionGetFieldOffset(section,a,f,&aSecOff);
    1447:           }
    1448:           else {
    1449:             PetscSectionGetDof(section,a,&aSecDof);
    1450:             PetscSectionGetOffset(section,a,&aSecOff);
    1451:           }
    1452:           if (!aSecDof) continue;

    1454:           for (j = 0; j < closureSizeP; j++) {
    1455:             PetscInt q = closureP[2*j];
    1456:             PetscInt oq = closureP[2*j+1];

    1458:             if (q == a) {
    1459:               PetscInt r, s, t;

    1461:               for (r = childOffsets[i]; r < childOffsets[i+1]; r++) {
    1462:                 for (s = parentOffsets[j]; s < parentOffsets[j+1]; s++) {
    1463:                   PetscScalar val;
    1464:                   PetscInt insertCol, insertRow;

    1466:                   MatGetValue(Xmat,r,s,&val);
    1467:                   if (o >= 0) {
    1468:                     insertRow = conOff + fComp * (r - childOffsets[i]);
    1469:                   }
    1470:                   else {
    1471:                     insertRow = conOff + fComp * (childOffsets[i + 1] - 1 - r);
    1472:                   }
    1473:                   if (oq >= 0) {
    1474:                     insertCol = aSecOff + fComp * (s - parentOffsets[j]);
    1475:                   }
    1476:                   else {
    1477:                     insertCol = aSecOff + fComp * (parentOffsets[j + 1] - 1 - s);
    1478:                   }
    1479:                   for (t = 0; t < fComp; t++) {
    1480:                     MatSetValue(cMat,insertRow + t,insertCol + t,val,INSERT_VALUES);
    1481:                   }
    1482:                 }
    1483:               }
    1484:             }
    1485:           }
    1486:         }
    1487:       }
    1488:       PetscFree2(childOffsets,parentOffsets);
    1489:       DMPlexRestoreTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);
    1490:       DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSizeP,&closureP);
    1491:     }
    1492:     MatDestroy(&Amat);
    1493:     MatDestroy(&Bmat);
    1494:     MatDestroy(&Xmat);
    1495:     PetscFree3(weights,pointsRef,pointsReal);
    1496:   }
    1497:   MatAssemblyBegin(cMat,MAT_FINAL_ASSEMBLY);
    1498:   MatAssemblyEnd(cMat,MAT_FINAL_ASSEMBLY);
    1499:   PetscFree6(v0,v0parent,vtmp,J,Jparent,invJparent);
    1500:   ISRestoreIndices(aIS,&anchors);

    1502:   return(0);
    1503: }

    1507: static PetscErrorCode DMPlexReferenceTreeGetChildrenMatrices(DM refTree, PetscScalar ****childrenMats, PetscInt ***childrenN)
    1508: {
    1509:   Mat            refCmat;
    1510:   PetscDS        ds;
    1511:   PetscInt       numFields, f, pRefStart, pRefEnd, p, *rows, *cols, maxDof, maxAnDof, **refPointFieldN;
    1512:   PetscScalar    ***refPointFieldMats;
    1513:   PetscSection   refConSec, refAnSec, refSection;
    1514:   IS             refAnIS;
    1515:   const PetscInt *refAnchors;

    1519:   DMGetDS(refTree,&ds);
    1520:   PetscDSGetNumFields(ds,&numFields);
    1521:   DMGetDefaultConstraints(refTree,&refConSec,&refCmat);
    1522:   DMPlexGetAnchors(refTree,&refAnSec,&refAnIS);
    1523:   ISGetIndices(refAnIS,&refAnchors);
    1524:   DMGetDefaultSection(refTree,&refSection);
    1525:   PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
    1526:   PetscMalloc1(pRefEnd-pRefStart,&refPointFieldMats);
    1527:   PetscMalloc1(pRefEnd-pRefStart,&refPointFieldN);
    1528:   PetscSectionGetMaxDof(refConSec,&maxDof);
    1529:   PetscSectionGetMaxDof(refAnSec,&maxAnDof);
    1530:   PetscMalloc1(maxDof,&rows);
    1531:   PetscMalloc1(maxDof*maxAnDof,&cols);
    1532:   for (p = pRefStart; p < pRefEnd; p++) {
    1533:     PetscInt parent, closureSize, *closure = NULL, pDof;

    1535:     DMPlexGetTreeParent(refTree,p,&parent,NULL);
    1536:     PetscSectionGetDof(refConSec,p,&pDof);
    1537:     if (!pDof || parent == p) continue;

    1539:     PetscMalloc1(numFields,&refPointFieldMats[p-pRefStart]);
    1540:     PetscCalloc1(numFields,&refPointFieldN[p-pRefStart]);
    1541:     DMPlexGetTransitiveClosure(refTree,parent,PETSC_TRUE,&closureSize,&closure);
    1542:     for (f = 0; f < numFields; f++) {
    1543:       PetscInt cDof, cOff, numCols, r, i, fComp;
    1544:       PetscObject disc;
    1545:       PetscClassId id;
    1546:       PetscFE fe = NULL;
    1547:       PetscFV fv = NULL;

    1549:       PetscDSGetDiscretization(ds,f,&disc);
    1550:       PetscObjectGetClassId(disc,&id);
    1551:       if (id == PETSCFE_CLASSID) {
    1552:         fe = (PetscFE) disc;
    1553:         PetscFEGetNumComponents(fe,&fComp);
    1554:       }
    1555:       else if (id == PETSCFV_CLASSID) {
    1556:         fv = (PetscFV) disc;
    1557:         PetscFVGetNumComponents(fv,&fComp);
    1558:       }
    1559:       else SETERRQ1(PetscObjectComm(disc),PETSC_ERR_ARG_UNKNOWN_TYPE, "PetscDS discretization id %d not recognized.", id);

    1561:       if (numFields > 1) {
    1562:         PetscSectionGetFieldDof(refConSec,p,f,&cDof);
    1563:         PetscSectionGetFieldOffset(refConSec,p,f,&cOff);
    1564:       }
    1565:       else {
    1566:         PetscSectionGetDof(refConSec,p,&cDof);
    1567:         PetscSectionGetOffset(refConSec,p,&cOff);
    1568:       }

    1570:       if (!cDof) continue;
    1571:       for (r = 0; r < cDof; r++) {
    1572:         rows[r] = cOff + r;
    1573:       }
    1574:       numCols = 0;
    1575:       for (i = 0; i < closureSize; i++) {
    1576:         PetscInt q = closure[2*i];
    1577:         PetscInt o = closure[2*i+1];
    1578:         PetscInt aDof, aOff, j;

    1580:         if (numFields > 1) {
    1581:           PetscSectionGetFieldDof(refSection,q,f,&aDof);
    1582:           PetscSectionGetFieldOffset(refSection,q,f,&aOff);
    1583:         }
    1584:         else {
    1585:           PetscSectionGetDof(refSection,q,&aDof);
    1586:           PetscSectionGetOffset(refSection,q,&aOff);
    1587:         }

    1589:         for (j = 0; j < aDof; j++) {
    1590:           PetscInt node = (o >= 0) ? (j / fComp) : ((aDof - 1 - j) / fComp);
    1591:           PetscInt comp = (j % fComp);

    1593:           cols[numCols++] = aOff + node * fComp + comp;
    1594:         }
    1595:       }
    1596:       refPointFieldN[p-pRefStart][f] = numCols;
    1597:       PetscMalloc1(cDof*numCols,&refPointFieldMats[p-pRefStart][f]);
    1598:       MatGetValues(refCmat,cDof,rows,numCols,cols,refPointFieldMats[p-pRefStart][f]);
    1599:     }
    1600:     DMPlexRestoreTransitiveClosure(refTree,parent,PETSC_TRUE,&closureSize,&closure);
    1601:   }
    1602:   *childrenMats = refPointFieldMats;
    1603:   *childrenN = refPointFieldN;
    1604:   ISRestoreIndices(refAnIS,&refAnchors);
    1605:   PetscFree(rows);
    1606:   PetscFree(cols);
    1607:   return(0);
    1608: }

    1612: static PetscErrorCode DMPlexReferenceTreeRestoreChildrenMatrices(DM refTree, PetscScalar ****childrenMats, PetscInt ***childrenN)
    1613: {
    1614:   PetscDS        ds;
    1615:   PetscInt       **refPointFieldN;
    1616:   PetscScalar    ***refPointFieldMats;
    1617:   PetscInt       numFields, pRefStart, pRefEnd, p, f;
    1618:   PetscSection   refConSec;

    1622:   refPointFieldN = *childrenN;
    1623:   *childrenN = NULL;
    1624:   refPointFieldMats = *childrenMats;
    1625:   *childrenMats = NULL;
    1626:   DMGetDS(refTree,&ds);
    1627:   PetscDSGetNumFields(ds,&numFields);
    1628:   DMGetDefaultConstraints(refTree,&refConSec,NULL);
    1629:   PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
    1630:   for (p = pRefStart; p < pRefEnd; p++) {
    1631:     PetscInt parent, pDof;

    1633:     DMPlexGetTreeParent(refTree,p,&parent,NULL);
    1634:     PetscSectionGetDof(refConSec,p,&pDof);
    1635:     if (!pDof || parent == p) continue;

    1637:     for (f = 0; f < numFields; f++) {
    1638:       PetscInt cDof;

    1640:       if (numFields > 1) {
    1641:         PetscSectionGetFieldDof(refConSec,p,f,&cDof);
    1642:       }
    1643:       else {
    1644:         PetscSectionGetDof(refConSec,p,&cDof);
    1645:       }

    1647:       if (!cDof) continue;
    1648:       PetscFree(refPointFieldMats[p - pRefStart][f]);
    1649:     }
    1650:     PetscFree(refPointFieldMats[p - pRefStart]);
    1651:     PetscFree(refPointFieldN[p - pRefStart]);
    1652:   }
    1653:   PetscFree(refPointFieldMats);
    1654:   PetscFree(refPointFieldN);
    1655:   return(0);
    1656: }

    1660: static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_FromReference(DM dm, PetscSection section, PetscSection conSec, Mat cMat)
    1661: {
    1662:   DM             refTree;
    1663:   PetscDS        ds;
    1664:   Mat            refCmat;
    1665:   PetscInt       numFields, f, pRefStart, pRefEnd, p, maxDof, maxAnDof, *perm, *iperm, pStart, pEnd, conStart, conEnd, **refPointFieldN;
    1666:   PetscScalar ***refPointFieldMats, *pointWork;
    1667:   PetscSection   refConSec, refAnSec, anSec;
    1668:   IS             refAnIS, anIS;
    1669:   const PetscInt *anchors;

    1674:   DMGetDS(dm,&ds);
    1675:   PetscDSGetNumFields(ds,&numFields);
    1676:   DMPlexGetReferenceTree(dm,&refTree);
    1677:   DMSetDS(refTree,ds);
    1678:   DMGetDefaultConstraints(refTree,&refConSec,&refCmat);
    1679:   DMPlexGetAnchors(refTree,&refAnSec,&refAnIS);
    1680:   DMPlexGetAnchors(dm,&anSec,&anIS);
    1681:   ISGetIndices(anIS,&anchors);
    1682:   PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
    1683:   PetscSectionGetChart(conSec,&conStart,&conEnd);
    1684:   PetscSectionGetMaxDof(refConSec,&maxDof);
    1685:   PetscSectionGetMaxDof(refAnSec,&maxAnDof);
    1686:   PetscMalloc1(maxDof*maxDof*maxAnDof,&pointWork);

    1688:   /* step 1: get submats for every constrained point in the reference tree */
    1689:   DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);

    1691:   /* step 2: compute the preorder */
    1692:   DMPlexGetChart(dm,&pStart,&pEnd);
    1693:   PetscMalloc2(pEnd-pStart,&perm,pEnd-pStart,&iperm);
    1694:   for (p = pStart; p < pEnd; p++) {
    1695:     perm[p - pStart] = p;
    1696:     iperm[p - pStart] = p-pStart;
    1697:   }
    1698:   for (p = 0; p < pEnd - pStart;) {
    1699:     PetscInt point = perm[p];
    1700:     PetscInt parent;

    1702:     DMPlexGetTreeParent(dm,point,&parent,NULL);
    1703:     if (parent == point) {
    1704:       p++;
    1705:     }
    1706:     else {
    1707:       PetscInt size, closureSize, *closure = NULL, i;

    1709:       DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
    1710:       for (i = 0; i < closureSize; i++) {
    1711:         PetscInt q = closure[2*i];
    1712:         if (iperm[q-pStart] > iperm[point-pStart]) {
    1713:           /* swap */
    1714:           perm[p]               = q;
    1715:           perm[iperm[q-pStart]] = point;
    1716:           iperm[point-pStart]   = iperm[q-pStart];
    1717:           iperm[q-pStart]       = p;
    1718:           break;
    1719:         }
    1720:       }
    1721:       size = closureSize;
    1722:       DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
    1723:       if (i == size) {
    1724:         p++;
    1725:       }
    1726:     }
    1727:   }

    1729:   /* step 3: fill the constraint matrix */
    1730:   /* we are going to use a preorder progressive fill strategy.  Mat doesn't
    1731:    * allow progressive fill without assembly, so we are going to set up the
    1732:    * values outside of the Mat first.
    1733:    */
    1734:   {
    1735:     PetscInt nRows, row, nnz;
    1736:     PetscBool done;
    1737:     const PetscInt *ia, *ja;
    1738:     PetscScalar *vals;

    1740:     MatGetRowIJ(cMat,0,PETSC_FALSE,PETSC_FALSE,&nRows,&ia,&ja,&done);
    1741:     if (!done) SETERRQ(PetscObjectComm((PetscObject)cMat),PETSC_ERR_PLIB,"Could not get RowIJ of constraint matrix");
    1742:     nnz  = ia[nRows];
    1743:     /* malloc and then zero rows right before we fill them: this way valgrind
    1744:      * can tell if we are doing progressive fill in the wrong order */
    1745:     PetscMalloc1(nnz,&vals);
    1746:     for (p = 0; p < pEnd - pStart; p++) {
    1747:       PetscInt parent, childid, closureSize, *closure = NULL;
    1748:       PetscInt point = perm[p], pointDof;

    1750:       DMPlexGetTreeParent(dm,point,&parent,&childid);
    1751:       if ((point < conStart) || (point >= conEnd) || (parent == point)) continue;
    1752:       PetscSectionGetDof(conSec,point,&pointDof);
    1753:       if (!pointDof) continue;
    1754:       DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
    1755:       for (f = 0; f < numFields; f++) {
    1756:         PetscInt cDof, cOff, numCols, numFillCols, i, r, fComp = -1, matOffset, offset;
    1757:         PetscScalar *pointMat;
    1758:         PetscObject disc;
    1759:         PetscClassId id;
    1760:         PetscFE fe = NULL;
    1761:         PetscFV fv = NULL;

    1763:         PetscDSGetDiscretization(ds,f,&disc);
    1764:         PetscObjectGetClassId(disc,&id);
    1765:         if (id == PETSCFE_CLASSID) {
    1766:           fe = (PetscFE) disc;
    1767:           PetscFEGetNumComponents(fe,&fComp);
    1768:         }
    1769:         else if (id == PETSCFV_CLASSID) {
    1770:           fv = (PetscFV) disc;
    1771:           PetscFVGetNumComponents(fv,&fComp);
    1772:         }
    1773:         else {
    1774:           SETERRQ(PetscObjectComm((PetscObject)disc),PETSC_ERR_SUP,"Unsupported discretization");
    1775:         }

    1777:         if (numFields > 1) {
    1778:           PetscSectionGetFieldDof(conSec,point,f,&cDof);
    1779:           PetscSectionGetFieldOffset(conSec,point,f,&cOff);
    1780:         }
    1781:         else {
    1782:           PetscSectionGetDof(conSec,point,&cDof);
    1783:           PetscSectionGetOffset(conSec,point,&cOff);
    1784:         }
    1785:         if (!cDof) continue;

    1787:         /* make sure that every row for this point is the same size */
    1788: #if defined(PETSC_USE_DEBUG)
    1789:         for (r = 0; r < cDof; r++) {
    1790:           if (cDof > 1 && r) {
    1791:             if ((ia[cOff+r+1]-ia[cOff+r]) != (ia[cOff+r]-ia[cOff+r-1])) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Two point rows have different nnz: %D vs. %D", (ia[cOff+r+1]-ia[cOff+r]), (ia[cOff+r]-ia[cOff+r-1]));
    1792:           }
    1793:         }
    1794: #endif
    1795:         /* zero rows */
    1796:         for (i = ia[cOff] ; i< ia[cOff+cDof];i++) {
    1797:           vals[i] = 0.;
    1798:         }
    1799:         matOffset = ia[cOff];
    1800:         numFillCols = ia[cOff+1] - matOffset;
    1801:         pointMat = refPointFieldMats[childid-pRefStart][f];
    1802:         numCols = refPointFieldN[childid-pRefStart][f];
    1803:         offset = 0;
    1804:         for (i = 0; i < closureSize; i++) {
    1805:           PetscInt q = closure[2*i];
    1806:           PetscInt o = closure[2*i+1];
    1807:           PetscInt aDof, aOff, j, k, qConDof, qConOff;

    1809:           qConDof = qConOff = 0;
    1810:           if (numFields > 1) {
    1811:             PetscSectionGetFieldDof(section,q,f,&aDof);
    1812:             PetscSectionGetFieldOffset(section,q,f,&aOff);
    1813:             if (q >= conStart && q < conEnd) {
    1814:               PetscSectionGetFieldDof(conSec,q,f,&qConDof);
    1815:               PetscSectionGetFieldOffset(conSec,q,f,&qConOff);
    1816:             }
    1817:           }
    1818:           else {
    1819:             PetscSectionGetDof(section,q,&aDof);
    1820:             PetscSectionGetOffset(section,q,&aOff);
    1821:             if (q >= conStart && q < conEnd) {
    1822:               PetscSectionGetDof(conSec,q,&qConDof);
    1823:               PetscSectionGetOffset(conSec,q,&qConOff);
    1824:             }
    1825:           }
    1826:           if (!aDof) continue;
    1827:           if (qConDof) {
    1828:             /* this point has anchors: its rows of the matrix should already
    1829:              * be filled, thanks to preordering */
    1830:             /* first multiply into pointWork, then set in matrix */
    1831:             PetscInt aMatOffset = ia[qConOff];
    1832:             PetscInt aNumFillCols = ia[qConOff + 1] - aMatOffset;
    1833:             for (r = 0; r < cDof; r++) {
    1834:               for (j = 0; j < aNumFillCols; j++) {
    1835:                 PetscScalar inVal = 0;
    1836:                 for (k = 0; k < aDof; k++) {
    1837:                   PetscInt node = (o >= 0) ? (k / fComp) : ((aDof - 1 - k) / fComp);
    1838:                   PetscInt comp = (k % fComp);
    1839:                   PetscInt col  = node * fComp + comp;

    1841:                   inVal += pointMat[r * numCols + offset + col] * vals[aMatOffset + aNumFillCols * k + j];
    1842:                 }
    1843:                 pointWork[r * aNumFillCols + j] = inVal;
    1844:               }
    1845:             }
    1846:             /* assume that the columns are sorted, spend less time searching */
    1847:             for (j = 0, k = 0; j < aNumFillCols; j++) {
    1848:               PetscInt col = ja[aMatOffset + j];
    1849:               for (;k < numFillCols; k++) {
    1850:                 if (ja[matOffset + k] == col) {
    1851:                   break;
    1852:                 }
    1853:               }
    1854:               if (k == numFillCols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"No nonzero space for (%d, %d)", cOff, col);
    1855:               for (r = 0; r < cDof; r++) {
    1856:                 vals[matOffset + numFillCols * r + k] = pointWork[r * aNumFillCols + j];
    1857:               }
    1858:             }
    1859:           }
    1860:           else {
    1861:             /* find where to put this portion of pointMat into the matrix */
    1862:             for (k = 0; k < numFillCols; k++) {
    1863:               if (ja[matOffset + k] == aOff) {
    1864:                 break;
    1865:               }
    1866:             }
    1867:             if (k == numFillCols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"No nonzero space for (%d, %d)", cOff, aOff);
    1868:             for (j = 0; j < aDof; j++) {
    1869:               PetscInt node = (o >= 0) ? (j / fComp) : ((aDof - 1 - j) / fComp);
    1870:               PetscInt comp = (j % fComp);
    1871:               PetscInt col  = node * fComp + comp;
    1872:               for (r = 0; r < cDof; r++) {
    1873:                 vals[matOffset + numFillCols * r + k + col] += pointMat[r * numCols + offset + col];
    1874:               }
    1875:             }
    1876:           }
    1877:           offset += aDof;
    1878:         }
    1879:       }
    1880:       DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
    1881:     }
    1882:     for (row = 0; row < nRows; row++) {
    1883:       MatSetValues(cMat,1,&row,ia[row+1]-ia[row],&ja[ia[row]],&vals[ia[row]],INSERT_VALUES);
    1884:     }
    1885:     MatRestoreRowIJ(cMat,0,PETSC_FALSE,PETSC_FALSE,&nRows,&ia,&ja,&done);
    1886:     if (!done) SETERRQ(PetscObjectComm((PetscObject)cMat),PETSC_ERR_PLIB,"Could not restore RowIJ of constraint matrix");
    1887:     MatAssemblyBegin(cMat,MAT_FINAL_ASSEMBLY);
    1888:     MatAssemblyEnd(cMat,MAT_FINAL_ASSEMBLY);
    1889:     PetscFree(vals);
    1890:   }

    1892:   /* clean up */
    1893:   ISRestoreIndices(anIS,&anchors);
    1894:   PetscFree2(perm,iperm);
    1895:   PetscFree(pointWork);
    1896:   DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
    1897:   return(0);
    1898: }

    1902: /* refine a single cell on rank 0: this is not intended to provide good local refinement, only to create an example of
    1903:  * a non-conforming mesh.  Local refinement comes later */
    1904: PetscErrorCode DMPlexTreeRefineCell (DM dm, PetscInt cell, DM *ncdm)
    1905: {
    1906:   DM K;
    1907:   PetscMPIInt rank;
    1908:   PetscInt dim, *pNewStart, *pNewEnd, *pNewCount, *pOldStart, *pOldEnd, offset, d, pStart, pEnd;
    1909:   PetscInt numNewCones, *newConeSizes, *newCones, *newOrientations;
    1910:   PetscInt *Kembedding;
    1911:   PetscInt *cellClosure=NULL, nc;
    1912:   PetscScalar *newVertexCoords;
    1913:   PetscInt numPointsWithParents, *parents, *childIDs, *perm, *iperm, *preOrient, pOffset;
    1914:   PetscSection parentSection;

    1918:   MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);
    1919:   DMGetDimension(dm,&dim);
    1920:   DMPlexCreate(PetscObjectComm((PetscObject)dm), ncdm);
    1921:   DMSetDimension(*ncdm,dim);

    1923:   DMPlexGetChart(dm, &pStart, &pEnd);
    1924:   PetscSectionCreate(PetscObjectComm((PetscObject)dm),&parentSection);
    1925:   DMPlexGetReferenceTree(dm,&K);
    1926:   if (!rank) {
    1927:     /* compute the new charts */
    1928:     PetscMalloc5(dim+1,&pNewCount,dim+1,&pNewStart,dim+1,&pNewEnd,dim+1,&pOldStart,dim+1,&pOldEnd);
    1929:     offset = 0;
    1930:     for (d = 0; d <= dim; d++) {
    1931:       PetscInt pOldCount, kStart, kEnd, k;

    1933:       pNewStart[d] = offset;
    1934:       DMPlexGetHeightStratum(dm,d,&pOldStart[d],&pOldEnd[d]);
    1935:       DMPlexGetHeightStratum(K,d,&kStart,&kEnd);
    1936:       pOldCount = pOldEnd[d] - pOldStart[d];
    1937:       /* adding the new points */
    1938:       pNewCount[d] = pOldCount + kEnd - kStart;
    1939:       if (!d) {
    1940:         /* removing the cell */
    1941:         pNewCount[d]--;
    1942:       }
    1943:       for (k = kStart; k < kEnd; k++) {
    1944:         PetscInt parent;
    1945:         DMPlexGetTreeParent(K,k,&parent,NULL);
    1946:         if (parent == k) {
    1947:           /* avoid double counting points that won't actually be new */
    1948:           pNewCount[d]--;
    1949:         }
    1950:       }
    1951:       pNewEnd[d] = pNewStart[d] + pNewCount[d];
    1952:       offset = pNewEnd[d];

    1954:     }
    1955:     if (cell < pOldStart[0] || cell >= pOldEnd[0]) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"%d not in cell range [%d, %d)", cell, pOldStart[0], pOldEnd[0]);
    1956:     /* get the current closure of the cell that we are removing */
    1957:     DMPlexGetTransitiveClosure(dm,cell,PETSC_TRUE,&nc,&cellClosure);

    1959:     PetscMalloc1(pNewEnd[dim],&newConeSizes);
    1960:     {
    1961:       PetscInt kStart, kEnd, k, closureSizeK, *closureK = NULL, j;

    1963:       DMPlexGetChart(K,&kStart,&kEnd);
    1964:       PetscMalloc4(kEnd-kStart,&Kembedding,kEnd-kStart,&perm,kEnd-kStart,&iperm,kEnd-kStart,&preOrient);

    1966:       for (k = kStart; k < kEnd; k++) {
    1967:         perm[k - kStart] = k;
    1968:         iperm [k - kStart] = k - kStart;
    1969:         preOrient[k - kStart] = 0;
    1970:       }

    1972:       DMPlexGetTransitiveClosure(K,0,PETSC_TRUE,&closureSizeK,&closureK);
    1973:       for (j = 1; j < closureSizeK; j++) {
    1974:         PetscInt parentOrientA = closureK[2*j+1];
    1975:         PetscInt parentOrientB = cellClosure[2*j+1];
    1976:         PetscInt p, q;

    1978:         p = closureK[2*j];
    1979:         q = cellClosure[2*j];
    1980:         for (d = 0; d <= dim; d++) {
    1981:           if (q >= pOldStart[d] && q < pOldEnd[d]) {
    1982:             Kembedding[p] = (q - pOldStart[d]) + pNewStart[d];
    1983:           }
    1984:         }
    1985:         if (parentOrientA != parentOrientB) {
    1986:           PetscInt numChildren, i;
    1987:           const PetscInt *children;

    1989:           DMPlexGetTreeChildren(K,p,&numChildren,&children);
    1990:           for (i = 0; i < numChildren; i++) {
    1991:             PetscInt kPerm, oPerm;

    1993:             k    = children[i];
    1994:             DMPlexReferenceTreeGetChildSymmetry(K,p,parentOrientA,0,k,parentOrientB,&oPerm,&kPerm);
    1995:             /* perm = what refTree position I'm in */
    1996:             perm[kPerm-kStart]      = k;
    1997:             /* iperm = who is at this position */
    1998:             iperm[k-kStart]         = kPerm-kStart;
    1999:             preOrient[kPerm-kStart] = oPerm;
    2000:           }
    2001:         }
    2002:       }
    2003:       DMPlexRestoreTransitiveClosure(K,0,PETSC_TRUE,&closureSizeK,&closureK);
    2004:     }
    2005:     PetscSectionSetChart(parentSection,0,pNewEnd[dim]);
    2006:     offset = 0;
    2007:     numNewCones = 0;
    2008:     for (d = 0; d <= dim; d++) {
    2009:       PetscInt kStart, kEnd, k;
    2010:       PetscInt p;
    2011:       PetscInt size;

    2013:       for (p = pOldStart[d]; p < pOldEnd[d]; p++) {
    2014:         /* skip cell 0 */
    2015:         if (p == cell) continue;
    2016:         /* old cones to new cones */
    2017:         DMPlexGetConeSize(dm,p,&size);
    2018:         newConeSizes[offset++] = size;
    2019:         numNewCones += size;
    2020:       }

    2022:       DMPlexGetHeightStratum(K,d,&kStart,&kEnd);
    2023:       for (k = kStart; k < kEnd; k++) {
    2024:         PetscInt kParent;

    2026:         DMPlexGetTreeParent(K,k,&kParent,NULL);
    2027:         if (kParent != k) {
    2028:           Kembedding[k] = offset;
    2029:           DMPlexGetConeSize(K,k,&size);
    2030:           newConeSizes[offset++] = size;
    2031:           numNewCones += size;
    2032:           if (kParent != 0) {
    2033:             PetscSectionSetDof(parentSection,Kembedding[k],1);
    2034:           }
    2035:         }
    2036:       }
    2037:     }

    2039:     PetscSectionSetUp(parentSection);
    2040:     PetscSectionGetStorageSize(parentSection,&numPointsWithParents);
    2041:     PetscMalloc2(numNewCones,&newCones,numNewCones,&newOrientations);
    2042:     PetscMalloc2(numPointsWithParents,&parents,numPointsWithParents,&childIDs);

    2044:     /* fill new cones */
    2045:     offset = 0;
    2046:     for (d = 0; d <= dim; d++) {
    2047:       PetscInt kStart, kEnd, k, l;
    2048:       PetscInt p;
    2049:       PetscInt size;
    2050:       const PetscInt *cone, *orientation;

    2052:       for (p = pOldStart[d]; p < pOldEnd[d]; p++) {
    2053:         /* skip cell 0 */
    2054:         if (p == cell) continue;
    2055:         /* old cones to new cones */
    2056:         DMPlexGetConeSize(dm,p,&size);
    2057:         DMPlexGetCone(dm,p,&cone);
    2058:         DMPlexGetConeOrientation(dm,p,&orientation);
    2059:         for (l = 0; l < size; l++) {
    2060:           newCones[offset]          = (cone[l] - pOldStart[d + 1]) + pNewStart[d + 1];
    2061:           newOrientations[offset++] = orientation[l];
    2062:         }
    2063:       }

    2065:       DMPlexGetHeightStratum(K,d,&kStart,&kEnd);
    2066:       for (k = kStart; k < kEnd; k++) {
    2067:         PetscInt kPerm = perm[k], kParent;
    2068:         PetscInt preO  = preOrient[k];

    2070:         DMPlexGetTreeParent(K,k,&kParent,NULL);
    2071:         if (kParent != k) {
    2072:           /* embed new cones */
    2073:           DMPlexGetConeSize(K,k,&size);
    2074:           DMPlexGetCone(K,kPerm,&cone);
    2075:           DMPlexGetConeOrientation(K,kPerm,&orientation);
    2076:           for (l = 0; l < size; l++) {
    2077:             PetscInt q, m = (preO >= 0) ? ((preO + l) % size) : ((size -(preO + 1) - l) % size);
    2078:             PetscInt newO, lSize, oTrue;

    2080:             q                         = iperm[cone[m]];
    2081:             newCones[offset]          = Kembedding[q];
    2082:             DMPlexGetConeSize(K,q,&lSize);
    2083:             oTrue                     = orientation[m];
    2084:             oTrue                     = ((!lSize) || (preOrient[k] >= 0)) ? oTrue : -(oTrue + 2);
    2085:             newO                      = DihedralCompose(lSize,oTrue,preOrient[q]);
    2086:             newOrientations[offset++] = newO;
    2087:           }
    2088:           if (kParent != 0) {
    2089:             PetscInt newPoint = Kembedding[kParent];
    2090:             PetscSectionGetOffset(parentSection,Kembedding[k],&pOffset);
    2091:             parents[pOffset]  = newPoint;
    2092:             childIDs[pOffset] = k;
    2093:           }
    2094:         }
    2095:       }
    2096:     }

    2098:     PetscMalloc1(dim*(pNewEnd[dim]-pNewStart[dim]),&newVertexCoords);

    2100:     /* fill coordinates */
    2101:     offset = 0;
    2102:     {
    2103:       PetscInt kStart, kEnd, l;
    2104:       PetscSection vSection;
    2105:       PetscInt v;
    2106:       Vec coords;
    2107:       PetscScalar *coordvals;
    2108:       PetscInt dof, off;
    2109:       PetscReal v0[3], J[9], detJ;

    2111: #if defined(PETSC_USE_DEBUG)
    2112:       {
    2113:         PetscInt k;
    2114:         DMPlexGetHeightStratum(K,0,&kStart,&kEnd);
    2115:         for (k = kStart; k < kEnd; k++) {
    2116:           DMPlexComputeCellGeometryFEM(K, k, NULL, v0, J, NULL, &detJ);
    2117:           if (detJ <= 0.) SETERRQ1 (PETSC_COMM_SELF,PETSC_ERR_PLIB,"reference tree cell %d has bad determinant",k);
    2118:         }
    2119:       }
    2120: #endif
    2121:       DMPlexComputeCellGeometryFEM(dm, cell, NULL, v0, J, NULL, &detJ);
    2122:       DMGetCoordinateSection(dm,&vSection);
    2123:       DMGetCoordinatesLocal(dm,&coords);
    2124:       VecGetArray(coords,&coordvals);
    2125:       for (v = pOldStart[dim]; v < pOldEnd[dim]; v++) {

    2127:         PetscSectionGetDof(vSection,v,&dof);
    2128:         PetscSectionGetOffset(vSection,v,&off);
    2129:         for (l = 0; l < dof; l++) {
    2130:           newVertexCoords[offset++] = coordvals[off + l];
    2131:         }
    2132:       }
    2133:       VecRestoreArray(coords,&coordvals);

    2135:       DMGetCoordinateSection(K,&vSection);
    2136:       DMGetCoordinatesLocal(K,&coords);
    2137:       VecGetArray(coords,&coordvals);
    2138:       DMPlexGetDepthStratum(K,0,&kStart,&kEnd);
    2139:       for (v = kStart; v < kEnd; v++) {
    2140:         PetscReal coord[3], newCoord[3];
    2141:         PetscInt  vPerm = perm[v];
    2142:         PetscInt  kParent;

    2144:         DMPlexGetTreeParent(K,v,&kParent,NULL);
    2145:         if (kParent != v) {
    2146:           /* this is a new vertex */
    2147:           PetscSectionGetOffset(vSection,vPerm,&off);
    2148:           for (l = 0; l < dim; ++l) coord[l] = PetscRealPart(coordvals[off+l]);
    2149:           CoordinatesRefToReal(dim, dim, v0, J, coord, newCoord);
    2150:           for (l = 0; l < dim; ++l) newVertexCoords[offset+l] = newCoord[l];
    2151:           offset += dim;
    2152:         }
    2153:       }
    2154:       VecRestoreArray(coords,&coordvals);
    2155:     }

    2157:     /* need to reverse the order of pNewCount: vertices first, cells last */
    2158:     for (d = 0; d < (dim + 1) / 2; d++) {
    2159:       PetscInt tmp;

    2161:       tmp = pNewCount[d];
    2162:       pNewCount[d] = pNewCount[dim - d];
    2163:       pNewCount[dim - d] = tmp;
    2164:     }

    2166:     DMPlexCreateFromDAG(*ncdm,dim,pNewCount,newConeSizes,newCones,newOrientations,newVertexCoords);
    2167:     DMPlexSetReferenceTree(*ncdm,K);
    2168:     DMPlexSetTree(*ncdm,parentSection,parents,childIDs);

    2170:     /* clean up */
    2171:     DMPlexRestoreTransitiveClosure(dm,cell,PETSC_TRUE,&nc,&cellClosure);
    2172:     PetscFree5(pNewCount,pNewStart,pNewEnd,pOldStart,pOldEnd);
    2173:     PetscFree(newConeSizes);
    2174:     PetscFree2(newCones,newOrientations);
    2175:     PetscFree(newVertexCoords);
    2176:     PetscFree2(parents,childIDs);
    2177:     PetscFree4(Kembedding,perm,iperm,preOrient);
    2178:   }
    2179:   else {
    2180:     PetscInt    p, counts[4];
    2181:     PetscInt    *coneSizes, *cones, *orientations;
    2182:     Vec         coordVec;
    2183:     PetscScalar *coords;

    2185:     for (d = 0; d <= dim; d++) {
    2186:       PetscInt dStart, dEnd;

    2188:       DMPlexGetDepthStratum(dm,d,&dStart,&dEnd);
    2189:       counts[d] = dEnd - dStart;
    2190:     }
    2191:     PetscMalloc1(pEnd-pStart,&coneSizes);
    2192:     for (p = pStart; p < pEnd; p++) {
    2193:       DMPlexGetConeSize(dm,p,&coneSizes[p-pStart]);
    2194:     }
    2195:     DMPlexGetCones(dm, &cones);
    2196:     DMPlexGetConeOrientations(dm, &orientations);
    2197:     DMGetCoordinatesLocal(dm,&coordVec);
    2198:     VecGetArray(coordVec,&coords);

    2200:     PetscSectionSetChart(parentSection,pStart,pEnd);
    2201:     PetscSectionSetUp(parentSection);
    2202:     DMPlexCreateFromDAG(*ncdm,dim,counts,coneSizes,cones,orientations,NULL);
    2203:     DMPlexSetReferenceTree(*ncdm,K);
    2204:     DMPlexSetTree(*ncdm,parentSection,NULL,NULL);
    2205:     VecRestoreArray(coordVec,&coords);
    2206:   }
    2207:   PetscSectionDestroy(&parentSection);

    2209:   return(0);
    2210: }

    2212: PETSC_EXTERN PetscErrorCode indicesPointFields_private(PetscSection,PetscInt,PetscInt,PetscInt[],PetscBool,PetscInt,PetscInt[]);
    2213: PETSC_EXTERN PetscErrorCode indicesPoint_private(PetscSection,PetscInt,PetscInt,PetscInt *,PetscBool,PetscInt,PetscInt[]);

    2217: PetscErrorCode DMPlexComputeInterpolatorTree(DM coarse, DM fine, PetscSF coarseToFine, PetscInt *childIds, Mat mat)
    2218: {
    2219:   PetscSF        coarseToFineEmbedded;
    2220:   PetscSection   globalCoarse, globalFine;
    2221:   PetscSection   localCoarse, localFine;
    2222:   PetscSection   aSec, cSec;
    2223:   PetscSection   rootIndicesSec, rootMatricesSec;
    2224:   PetscSection   leafIndicesSec, leafMatricesSec;
    2225:   PetscInt       *rootIndices, *leafIndices;
    2226:   PetscScalar    *rootMatrices, *leafMatrices;
    2227:   IS             aIS;
    2228:   const PetscInt *anchors;
    2229:   Mat            cMat;
    2230:   PetscInt       numFields;
    2231:   PetscInt       pStartC, pEndC, pStartF, pEndF, p;
    2232:   PetscInt       aStart, aEnd, cStart, cEnd;
    2233:   PetscInt       *maxChildIds;
    2234:   PetscInt       *offsets, *newOffsets, *offsetsCopy, *newOffsetsCopy, *rowOffsets, *numD, *numO;

    2238:   DMPlexGetChart(coarse,&pStartC,&pEndC);
    2239:   DMPlexGetChart(fine,&pStartF,&pEndF);
    2240:   DMGetDefaultGlobalSection(fine,&globalFine);
    2241:   { /* winnow fine points that don't have global dofs out of the sf */
    2242:     PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs;

    2244:     for (p = pStartF, numPointsWithDofs = 0; p < pEndF; p++) {
    2245:       PetscSectionGetDof(globalFine,p,&dof);
    2246:       PetscSectionGetConstraintDof(globalFine,p,&cdof);
    2247:       if ((dof - cdof) > 0) {
    2248:         numPointsWithDofs++;
    2249:       }
    2250:     }
    2251:     PetscMalloc1(numPointsWithDofs,&pointsWithDofs);
    2252:     for (p = pStartF, offset = 0; p < pEndF; p++) {
    2253:       PetscSectionGetDof(globalFine,p,&dof);
    2254:       PetscSectionGetConstraintDof(globalFine,p,&cdof);
    2255:       if ((dof - cdof) > 0) {
    2256:         pointsWithDofs[offset++] = p - pStartF;
    2257:       }
    2258:     }
    2259:     PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);
    2260:     PetscFree(pointsWithDofs);
    2261:   }
    2262:   /* communicate back to the coarse mesh which coarse points have children (that may require interpolation) */
    2263:   PetscMalloc1(pEndC-pStartC,&maxChildIds);
    2264:   for (p = pStartC; p < pEndC; p++) {
    2265:     maxChildIds[p - pStartC] = -2;
    2266:   }
    2267:   PetscSFReduceBegin(coarseToFineEmbedded,MPIU_INT,childIds,maxChildIds,MPIU_MAX);
    2268:   PetscSFReduceEnd(coarseToFineEmbedded,MPIU_INT,childIds,maxChildIds,MPIU_MAX);

    2270:   DMGetDefaultSection(coarse,&localCoarse);
    2271:   DMGetDefaultGlobalSection(coarse,&globalCoarse);

    2273:   DMPlexGetAnchors(coarse,&aSec,&aIS);
    2274:   ISGetIndices(aIS,&anchors);
    2275:   PetscSectionGetChart(aSec,&aStart,&aEnd);

    2277:   DMGetDefaultConstraints(coarse,&cSec,&cMat);
    2278:   PetscSectionGetChart(cSec,&cStart,&cEnd);

    2280:   /* create sections that will send to children the indices and matrices they will need to construct the interpolator */
    2281:   PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootIndicesSec);
    2282:   PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootMatricesSec);
    2283:   PetscSectionSetChart(rootIndicesSec,pStartC,pEndC);
    2284:   PetscSectionSetChart(rootMatricesSec,pStartC,pEndC);
    2285:   PetscSectionGetNumFields(globalCoarse,&numFields);
    2286:   {
    2287:     PetscInt maxFields = PetscMax(1,numFields) + 1;
    2288:     PetscMalloc7(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&newOffsets,maxFields,&newOffsetsCopy,maxFields,&rowOffsets,maxFields,&numD,maxFields,&numO);
    2289:   }

    2291:   for (p = pStartC; p < pEndC; p++) { /* count the sizes of the indices and matrices */
    2292:     PetscInt dof, matSize   = 0;
    2293:     PetscInt aDof           = 0;
    2294:     PetscInt cDof           = 0;
    2295:     PetscInt maxChildId     = maxChildIds[p - pStartC];
    2296:     PetscInt numRowIndices  = 0;
    2297:     PetscInt numColIndices  = 0;

    2299:     PetscSectionGetDof(globalCoarse,p,&dof);
    2300:     if (dof < 0) {
    2301:       dof = -(dof + 1);
    2302:     }
    2303:     if (p >= aStart && p < aEnd) {
    2304:       PetscSectionGetDof(aSec,p,&aDof);
    2305:     }
    2306:     if (p >= cStart && p < cEnd) {
    2307:       PetscSectionGetDof(cSec,p,&cDof);
    2308:     }
    2309:     offsets[0]    = 0;
    2310:     newOffsets[0] = 0;
    2311:     if (maxChildId >= 0) { /* this point has children (with dofs) that will need to be interpolated from the closure of p */
    2312:       PetscInt *closure = NULL, closureSize, cl, f;

    2314:       DMPlexGetTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);
    2315:       for (cl = 0; cl < closureSize; cl++) { /* get the closure */
    2316:         PetscInt c = closure[2 * cl], clDof;

    2318:         PetscSectionGetDof(localCoarse,c,&clDof);
    2319:         numRowIndices += clDof;
    2320:         for (f = 0; f < numFields; f++) {
    2321:           PetscSectionGetFieldDof(localCoarse,c,f,&clDof);
    2322:           offsets[f + 1] += clDof;
    2323:         }
    2324:       }
    2325:       for (f = 0; f < numFields; f++) {
    2326:         offsets[f + 1]   += offsets[f];
    2327:         newOffsets[f + 1] = offsets[f + 1];
    2328:       }
    2329:       /* get the number of indices needed and their field offsets */
    2330:       DMPlexAnchorsModifyMat(coarse,localCoarse,closureSize,numRowIndices,closure,NULL,NULL,&numColIndices,NULL,NULL,newOffsets,PETSC_FALSE);
    2331:       DMPlexRestoreTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);
    2332:       if (!numColIndices) { /* there are no hanging constraint modifications, so the matrix is just the identity: do not send it */
    2333:         numColIndices = numRowIndices;
    2334:         matSize = 0;
    2335:       }
    2336:       else if (numFields) { /* we send one submat for each field: sum their sizes */
    2337:         matSize = 0;
    2338:         for (f = 0; f < numFields; f++) {
    2339:           PetscInt numRow, numCol;

    2341:           numRow = offsets[f + 1] - offsets[f];
    2342:           numCol = newOffsets[f + 1] - newOffsets[f + 1];
    2343:           matSize += numRow * numCol;
    2344:         }
    2345:       }
    2346:       else {
    2347:         matSize = numRowIndices * numColIndices;
    2348:       }
    2349:     }
    2350:     else if (maxChildId == -1) {
    2351:       if (cDof > 0) { /* this point's dofs are interpolated via cMat: get the submatrix of cMat */
    2352:         PetscInt aOff, a, f;

    2354:         PetscSectionGetOffset(aSec,p,&aOff);
    2355:         for (f = 0; f < numFields; f++) {
    2356:           PetscInt fDof;

    2358:           PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
    2359:           offsets[f+1] = fDof;
    2360:         }
    2361:         for (a = 0; a < aDof; a++) {
    2362:           PetscInt anchor = anchors[a + aOff], aLocalDof;

    2364:           PetscSectionGetDof(localCoarse,anchor,&aLocalDof);
    2365:           numColIndices += aLocalDof;
    2366:           for (f = 0; f < numFields; f++) {
    2367:             PetscInt fDof;

    2369:             PetscSectionGetFieldDof(localCoarse,anchor,f,&fDof);
    2370:             newOffsets[f+1] += fDof;
    2371:           }
    2372:         }
    2373:         if (numFields) {
    2374:           matSize = 0;
    2375:           for (f = 0; f < numFields; f++) {
    2376:             matSize += offsets[f+1] * newOffsets[f+1];
    2377:           }
    2378:         }
    2379:         else {
    2380:           matSize = numColIndices * dof;
    2381:         }
    2382:       }
    2383:       else { /* no children, and no constraints on dofs: just get the global indices */
    2384:         numColIndices = dof;
    2385:         matSize       = 0;
    2386:       }
    2387:     }
    2388:     /* we will pack the column indices with the field offsets */
    2389:     PetscSectionSetDof(rootIndicesSec,p,numColIndices ? numColIndices+2*numFields : 0);
    2390:     PetscSectionSetDof(rootMatricesSec,p,matSize);
    2391:   }
    2392:   PetscSectionSetUp(rootIndicesSec);
    2393:   PetscSectionSetUp(rootMatricesSec);
    2394:   {
    2395:     PetscInt    numRootIndices, numRootMatrices;

    2397:     PetscSectionGetStorageSize(rootIndicesSec,&numRootIndices);
    2398:     PetscSectionGetStorageSize(rootMatricesSec,&numRootMatrices);
    2399:     PetscMalloc2(numRootIndices,&rootIndices,numRootMatrices,&rootMatrices);
    2400:     for (p = pStartC; p < pEndC; p++) {
    2401:       PetscInt    numRowIndices, numColIndices, matSize, dof;
    2402:       PetscInt    pIndOff, pMatOff;
    2403:       PetscInt    *pInd;
    2404:       PetscInt    maxChildId = maxChildIds[p - pStartC];
    2405:       PetscScalar *pMat = NULL;

    2407:       PetscSectionGetDof(rootIndicesSec,p,&numColIndices);
    2408:       if (!numColIndices) {
    2409:         continue;
    2410:       }
    2411:       offsets[0]        = 0;
    2412:       newOffsets[0]     = 0;
    2413:       offsetsCopy[0]    = 0;
    2414:       newOffsetsCopy[0] = 0;
    2415:       numColIndices -= 2 * numFields;
    2416:       PetscSectionGetOffset(rootIndicesSec,p,&pIndOff);
    2417:       pInd = &(rootIndices[pIndOff]);
    2418:       PetscSectionGetDof(rootMatricesSec,p,&matSize);
    2419:       if (matSize) {
    2420:         PetscSectionGetOffset(rootMatricesSec,p,&pMatOff);
    2421:         pMat = &rootMatrices[pMatOff];
    2422:       }
    2423:       PetscSectionGetDof(globalCoarse,p,&dof);
    2424:       if (dof < 0) {
    2425:         dof = -(dof + 1);
    2426:       }
    2427:       if (maxChildId >= 0) { /* build an identity matrix, apply matrix constraints on the right */
    2428:         PetscInt i, j;
    2429:         PetscInt numRowIndices = matSize / numColIndices;

    2431:         if (!numRowIndices) { /* don't need to calculate the mat, just the indices */
    2432:           PetscInt numIndices, *indices;
    2433:           DMPlexGetClosureIndices(coarse,localCoarse,globalCoarse,p,&numIndices,&indices,offsets);
    2434:           if (numIndices != numColIndices) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"mismatching constraint indices calculations");
    2435:           for (i = 0; i < numColIndices; i++) {
    2436:             pInd[i] = indices[i];
    2437:           }
    2438:           for (i = 0; i < numFields; i++) {
    2439:             pInd[numColIndices + i]             = offsets[i+1];
    2440:             pInd[numColIndices + numFields + i] = offsets[i+1];
    2441:           }
    2442:           DMPlexRestoreClosureIndices(coarse,localCoarse,globalCoarse,p,&numIndices,&indices,offsets);
    2443:         }
    2444:         else {
    2445:           PetscInt closureSize, *closure = NULL, cl;
    2446:           PetscScalar *pMatIn, *pMatModified;
    2447:           PetscInt numPoints,*points;

    2449:           DMGetWorkArray(coarse,numRowIndices * numRowIndices,PETSC_SCALAR,&pMatIn);
    2450:           for (i = 0; i < numRowIndices; i++) { /* initialize to the identity */
    2451:             for (j = 0; j < numRowIndices; j++) {
    2452:               pMatIn[i * numRowIndices + j] = (i == j) ? 1. : 0.;
    2453:             }
    2454:           }
    2455:           DMPlexGetTransitiveClosure(coarse, p, PETSC_TRUE, &closureSize, &closure);
    2456:           if (numFields) {
    2457:             PetscInt f;

    2459:             for (cl = 0; cl < closureSize; cl++) {
    2460:               PetscInt c = closure[2 * cl];

    2462:               for (f = 0; f < numFields; f++) {
    2463:                 PetscInt fDof;

    2465:                 PetscSectionGetFieldDof(localCoarse,c,f,&fDof);
    2466:                 offsets[f + 1] += fDof;
    2467:               }
    2468:             }
    2469:             for (f = 0; f < numFields; f++) {
    2470:               offsets[f + 1]   += offsets[f];
    2471:               newOffsets[f + 1] = offsets[f + 1];
    2472:             }
    2473:           }
    2474:           /* apply hanging node constraints on the right, get the new points and the new offsets */
    2475:           DMPlexAnchorsModifyMat(coarse,localCoarse,closureSize,numRowIndices,closure,pMatIn,&numPoints,NULL,&points,&pMatModified,newOffsets,PETSC_FALSE);
    2476:           if (!numFields) {
    2477:             for (i = 0; i < numRowIndices * numColIndices; i++) {
    2478:               pMat[i] = pMatModified[i];
    2479:             }
    2480:           }
    2481:           else {
    2482:             PetscInt f, i, j, count;
    2483:             for (f = 0, count = 0; f < numFields; f++) {
    2484:               for (i = offsets[f]; i < offsets[f+1]; i++) {
    2485:                 for (j = newOffsets[f]; j < newOffsets[f+1]; j++, count++) {
    2486:                   pMat[count] = pMatModified[i * numColIndices + j];
    2487:                 }
    2488:               }
    2489:             }
    2490:           }
    2491:           DMRestoreWorkArray(coarse,numRowIndices * numColIndices,PETSC_SCALAR,&pMatModified);
    2492:           DMPlexRestoreTransitiveClosure(coarse, p, PETSC_TRUE, &closureSize, &closure);
    2493:           DMRestoreWorkArray(coarse,numRowIndices * numColIndices,PETSC_SCALAR,&pMatIn);
    2494:           if (numFields) {
    2495:             PetscInt f;
    2496:             for (f = 0; f < numFields; f++) {
    2497:               pInd[numColIndices + f]             = offsets[f+1];
    2498:               pInd[numColIndices + numFields + f] = newOffsets[f+1];
    2499:             }
    2500:             for (cl = 0; cl < numPoints*2; cl += 2) {
    2501:               PetscInt o = points[cl+1], globalOff, c = points[cl];
    2502:               PetscSectionGetOffset(globalCoarse, c, &globalOff);
    2503:               indicesPointFields_private(localCoarse, c, globalOff < 0 ? -(globalOff+1) : globalOff, newOffsets, PETSC_FALSE, o, pInd);
    2504:             }
    2505:           } else {
    2506:             for (cl = 0; cl < numPoints*2; cl += 2) {
    2507:               PetscInt o = points[cl+1], c = points[cl], globalOff;
    2508:               PetscSectionGetOffset(globalCoarse, c, &globalOff);
    2509:               indicesPoint_private(localCoarse, c, globalOff < 0 ? -(globalOff+1) : globalOff, newOffsets, PETSC_FALSE, o, pInd);
    2510:             }
    2511:           }
    2512:           DMRestoreWorkArray(coarse,numPoints,PETSC_SCALAR,&points);
    2513:         }
    2514:       }
    2515:       else if (matSize) {
    2516:         PetscInt cOff;
    2517:         PetscInt *rowIndices, *colIndices, a, aDof, aOff;

    2519:         numRowIndices = matSize / numColIndices;
    2520:         if (numRowIndices != dof) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Miscounted dofs");
    2521:         DMGetWorkArray(coarse,numRowIndices,PETSC_INT,&rowIndices);
    2522:         DMGetWorkArray(coarse,numColIndices,PETSC_INT,&colIndices);
    2523:         PetscSectionGetOffset(cSec,p,&cOff);
    2524:         PetscSectionGetDof(aSec,p,&aDof);
    2525:         PetscSectionGetOffset(aSec,p,&aOff);
    2526:         if (numFields) {
    2527:           PetscInt f;

    2529:           for (f = 0; f < numFields; f++) {
    2530:             PetscInt fDof;
    2531:             PetscSectionGetFieldDof(cSec,p,f,&fDof);
    2532:             offsets[f + 1] = fDof;
    2533:             for (a = 0; a < aDof; a++) {
    2534:               PetscInt anchor = anchors[a + aOff];
    2535:               PetscSectionGetFieldDof(localCoarse,anchor,f,&fDof);
    2536:               newOffsets[f + 1] += fDof;
    2537:             }
    2538:           }
    2539:           for (f = 0; f < numFields; f++) {
    2540:             offsets[f + 1]       += offsets[f];
    2541:             offsetsCopy[f + 1]    = offsets[f + 1];
    2542:             newOffsets[f + 1]    += newOffsets[f];
    2543:             newOffsetsCopy[f + 1] = newOffsets[f + 1];
    2544:           }
    2545:           indicesPointFields_private(cSec,p,cOff,offsetsCopy,PETSC_TRUE,0,rowIndices);
    2546:           for (a = 0; a < aDof; a++) {
    2547:             PetscInt anchor = anchors[a + aOff], lOff;
    2548:             PetscSectionGetOffset(localCoarse,anchor,&lOff);
    2549:             indicesPointFields_private(localCoarse,anchor,lOff,newOffsetsCopy,PETSC_TRUE,0,colIndices);
    2550:           }
    2551:         }
    2552:         else {
    2553:           indicesPoint_private(cSec,p,cOff,offsetsCopy,PETSC_TRUE,0,rowIndices);
    2554:           for (a = 0; a < aDof; a++) {
    2555:             PetscInt anchor = anchors[a + aOff], lOff;
    2556:             PetscSectionGetOffset(localCoarse,anchor,&lOff);
    2557:             indicesPoint_private(localCoarse,anchor,lOff,newOffsetsCopy,PETSC_TRUE,0,colIndices);
    2558:           }
    2559:         }
    2560:         if (numFields) {
    2561:           PetscInt count, f, a;
    2562:           for (f = 0, count = 0; f < numFields; f++) {
    2563:             PetscInt iSize = offsets[f + 1] - offsets[f];
    2564:             PetscInt jSize = newOffsets[f + 1] - newOffsets[f];
    2565:             MatGetValues(cMat,iSize,&rowIndices[offsets[f]],jSize,&colIndices[newOffsets[f]],&pMat[count]);
    2566:             count += iSize * jSize;
    2567:             pInd[numColIndices + f]             = offsets[f+1];
    2568:             pInd[numColIndices + numFields + f] = newOffsets[f+1];
    2569:           }
    2570:           for (a = 0; a < aDof; a++) {
    2571:             PetscInt anchor = anchors[a + aOff];
    2572:             PetscInt gOff;
    2573:             PetscSectionGetOffset(globalCoarse,anchor,&gOff);
    2574:             indicesPointFields_private(localCoarse,anchor,gOff < 0 ? -(gOff + 1) : gOff,newOffsets,PETSC_FALSE,0,pInd);
    2575:           }
    2576:         }
    2577:         else {
    2578:           PetscInt a;
    2579:           MatGetValues(cMat,numRowIndices,rowIndices,numColIndices,colIndices,pMat);
    2580:           for (a = 0; a < aDof; a++) {
    2581:             PetscInt anchor = anchors[a + aOff];
    2582:             PetscInt gOff;
    2583:             PetscSectionGetOffset(globalCoarse,anchor,&gOff);
    2584:             indicesPoint_private(localCoarse,anchor,gOff < 0 ? -(gOff + 1) : gOff,newOffsets,PETSC_FALSE,0,pInd);
    2585:           }
    2586:         }
    2587:         DMRestoreWorkArray(coarse,numColIndices,PETSC_INT,&colIndices);
    2588:         DMRestoreWorkArray(coarse,numRowIndices,PETSC_INT,&rowIndices);
    2589:       }
    2590:       else {
    2591:         PetscInt gOff;

    2593:         PetscSectionGetOffset(globalCoarse,p,&gOff);
    2594:         if (numFields) {
    2595:           PetscInt f;

    2597:           for (f = 0; f < numFields; f++) {
    2598:             PetscInt fDof;
    2599:             PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
    2600:             offsets[f + 1] = fDof + offsets[f];
    2601:           }
    2602:           for (f = 0; f < numFields; f++) {
    2603:             pInd[numColIndices + f]             = offsets[f+1];
    2604:             pInd[numColIndices + numFields + f] = offsets[f+1];
    2605:           }
    2606:           indicesPointFields_private(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,0,pInd);
    2607:         }
    2608:         else {
    2609:           indicesPoint_private(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,0,pInd);
    2610:         }
    2611:       }
    2612:     }
    2613:     PetscFree(maxChildIds);
    2614:   }
    2615:   {
    2616:     PetscSF  indicesSF, matricesSF;
    2617:     PetscInt *remoteOffsetsIndices, *remoteOffsetsMatrices, numLeafIndices, numLeafMatrices;

    2619:     PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafIndicesSec);
    2620:     PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafMatricesSec);
    2621:     PetscSFDistributeSection(coarseToFineEmbedded,rootIndicesSec,&remoteOffsetsIndices,leafIndicesSec);
    2622:     PetscSFDistributeSection(coarseToFineEmbedded,rootMatricesSec,&remoteOffsetsMatrices,leafMatricesSec);
    2623:     PetscSFCreateSectionSF(coarseToFineEmbedded,rootIndicesSec,remoteOffsetsIndices,leafIndicesSec,&indicesSF);
    2624:     PetscSFCreateSectionSF(coarseToFineEmbedded,rootMatricesSec,remoteOffsetsMatrices,leafMatricesSec,&matricesSF);
    2625:     PetscSFDestroy(&coarseToFineEmbedded);
    2626:     PetscFree(remoteOffsetsIndices);
    2627:     PetscFree(remoteOffsetsMatrices);
    2628:     PetscSectionGetStorageSize(leafIndicesSec,&numLeafIndices);
    2629:     PetscSectionGetStorageSize(leafMatricesSec,&numLeafMatrices);
    2630:     PetscMalloc2(numLeafIndices,&leafIndices,numLeafMatrices,&leafMatrices);
    2631:     PetscSFBcastBegin(indicesSF,MPIU_INT,rootIndices,leafIndices);
    2632:     PetscSFBcastBegin(matricesSF,MPIU_SCALAR,rootMatrices,leafMatrices);
    2633:     PetscSFBcastEnd(indicesSF,MPIU_INT,rootIndices,leafIndices);
    2634:     PetscSFBcastEnd(matricesSF,MPIU_SCALAR,rootMatrices,leafMatrices);
    2635:     PetscSFDestroy(&matricesSF);
    2636:     PetscSFDestroy(&indicesSF);
    2637:     PetscFree2(rootIndices,rootMatrices);
    2638:     PetscSectionDestroy(&rootIndicesSec);
    2639:     PetscSectionDestroy(&rootMatricesSec);
    2640:   }
    2641:   /* count to preallocate */
    2642:   DMGetDefaultSection(fine,&localFine);
    2643:   {
    2644:     PetscInt    nGlobal;
    2645:     PetscInt    *dnnz, *onnz;
    2646:     PetscLayout rowMap, colMap;
    2647:     PetscInt    rowStart, rowEnd, colStart, colEnd;
    2648:     PetscInt    maxDof;
    2649:     PetscInt    *rowIndices;
    2650:     DM           refTree;
    2651:     PetscInt     **refPointFieldN;
    2652:     PetscScalar  ***refPointFieldMats;
    2653:     PetscSection refConSec, refAnSec;
    2654:     PetscInt     pRefStart,pRefEnd,maxConDof,maxColumns;
    2655:     PetscScalar  *pointWork;

    2657:     PetscSectionGetConstrainedStorageSize(globalFine,&nGlobal);
    2658:     PetscCalloc2(nGlobal,&dnnz,nGlobal,&onnz);
    2659:     MatGetLayouts(mat,&rowMap,&colMap);
    2660:     PetscLayoutSetUp(rowMap);
    2661:     PetscLayoutSetUp(colMap);
    2662:     PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);
    2663:     PetscLayoutGetRange(colMap,&colStart,&colEnd);
    2664:     PetscSectionGetMaxDof(globalFine,&maxDof);
    2665:     DMGetWorkArray(fine,maxDof,PETSC_INT,&rowIndices);
    2666:     for (p = pStartF; p < pEndF; p++) {
    2667:       PetscInt    gDof, gcDof, gOff;
    2668:       PetscInt    numColIndices, pIndOff, *pInd;
    2669:       PetscInt    matSize;
    2670:       PetscInt    i;

    2672:       PetscSectionGetDof(globalFine,p,&gDof);
    2673:       PetscSectionGetConstraintDof(globalFine,p,&gcDof);
    2674:       if ((gDof - gcDof) <= 0) {
    2675:         continue;
    2676:       }
    2677:       PetscSectionGetOffset(globalFine,p,&gOff);
    2678:       if (gOff < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"I though having global dofs meant a non-negative offset");
    2679:       if ((gOff < rowStart) || ((gOff + gDof - gcDof) > rowEnd)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"I thought the row map would constrain the global dofs");
    2680:       PetscSectionGetDof(leafIndicesSec,p,&numColIndices);
    2681:       PetscSectionGetOffset(leafIndicesSec,p,&pIndOff);
    2682:       numColIndices -= 2 * numFields;
    2683:       if (numColIndices <= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"global fine dof with no dofs to interpolate from");
    2684:       pInd = &leafIndices[pIndOff];
    2685:       offsets[0]        = 0;
    2686:       offsetsCopy[0]    = 0;
    2687:       newOffsets[0]     = 0;
    2688:       newOffsetsCopy[0] = 0;
    2689:       if (numFields) {
    2690:         PetscInt f;
    2691:         for (f = 0; f < numFields; f++) {
    2692:           PetscInt rowDof;

    2694:           PetscSectionGetFieldDof(localFine,p,f,&rowDof);
    2695:           offsets[f + 1]        = offsets[f] + rowDof;
    2696:           offsetsCopy[f + 1]    = offsets[f + 1];
    2697:           newOffsets[f + 1]     = pInd[numColIndices + numFields + f];
    2698:           numD[f] = 0;
    2699:           numO[f] = 0;
    2700:         }
    2701:         indicesPointFields_private(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);
    2702:         for (f = 0; f < numFields; f++) {
    2703:           PetscInt colOffset    = newOffsets[f];
    2704:           PetscInt numFieldCols = newOffsets[f + 1] - newOffsets[f];

    2706:           for (i = 0; i < numFieldCols; i++) {
    2707:             PetscInt gInd = pInd[i + colOffset];

    2709:             if (gInd >= colStart && gInd < colEnd) {
    2710:               numD[f]++;
    2711:             }
    2712:             else if (gInd >= 0) { /* negative means non-entry */
    2713:               numO[f]++;
    2714:             }
    2715:           }
    2716:         }
    2717:       }
    2718:       else {
    2719:         indicesPoint_private(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);
    2720:         numD[0] = 0;
    2721:         numO[0] = 0;
    2722:         for (i = 0; i < numColIndices; i++) {
    2723:           PetscInt gInd = pInd[i];

    2725:           if (gInd >= colStart && gInd < colEnd) {
    2726:             numD[0]++;
    2727:           }
    2728:           else if (gInd >= 0) { /* negative means non-entry */
    2729:             numO[0]++;
    2730:           }
    2731:         }
    2732:       }
    2733:       PetscSectionGetDof(leafMatricesSec,p,&matSize);
    2734:       if (!matSize) { /* incoming matrix is identity */
    2735:         PetscInt childId;

    2737:         childId = childIds[p-pStartF];
    2738:         if (childId < 0) { /* no child interpolation: one nnz per */
    2739:           if (numFields) {
    2740:             PetscInt f;
    2741:             for (f = 0; f < numFields; f++) {
    2742:               PetscInt numRows = offsets[f+1] - offsets[f], row;
    2743:               for (row = 0; row < numRows; row++) {
    2744:                 PetscInt gIndCoarse = pInd[newOffsets[f] + row];
    2745:                 PetscInt gIndFine   = rowIndices[offsets[f] + row];
    2746:                 if (gIndCoarse >= colStart && gIndCoarse < colEnd) { /* local */
    2747:                   if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2748:                   dnnz[gIndFine - rowStart] = 1;
    2749:                 }
    2750:                 else if (gIndCoarse >= 0) { /* remote */
    2751:                   if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2752:                   onnz[gIndFine - rowStart] = 1;
    2753:                 }
    2754:                 else { /* constrained */
    2755:                   if (gIndFine >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2756:                 }
    2757:               }
    2758:             }
    2759:           }
    2760:           else {
    2761:             PetscInt i;
    2762:             for (i = 0; i < gDof; i++) {
    2763:               PetscInt gIndCoarse = pInd[i];
    2764:               PetscInt gIndFine   = rowIndices[i];
    2765:               if (gIndCoarse >= colStart && gIndCoarse < colEnd) { /* local */
    2766:                 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2767:                 dnnz[gIndFine - rowStart] = 1;
    2768:               }
    2769:               else if (gIndCoarse >= 0) { /* remote */
    2770:                 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2771:                 onnz[gIndFine - rowStart] = 1;
    2772:               }
    2773:               else { /* constrained */
    2774:                 if (gIndFine >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2775:               }
    2776:             }
    2777:           }
    2778:         }
    2779:         else { /* interpolate from all */
    2780:           if (numFields) {
    2781:             PetscInt f;
    2782:             for (f = 0; f < numFields; f++) {
    2783:               PetscInt numRows = offsets[f+1] - offsets[f], row;
    2784:               for (row = 0; row < numRows; row++) {
    2785:                 PetscInt gIndFine = rowIndices[offsets[f] + row];
    2786:                 if (gIndFine >= 0) {
    2787:                   if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2788:                   dnnz[gIndFine - rowStart] = numD[f];
    2789:                   onnz[gIndFine - rowStart] = numO[f];
    2790:                 }
    2791:               }
    2792:             }
    2793:           }
    2794:           else {
    2795:             PetscInt i;
    2796:             for (i = 0; i < gDof; i++) {
    2797:               PetscInt gIndFine = rowIndices[i];
    2798:               if (gIndFine >= 0) {
    2799:                 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2800:                 dnnz[gIndFine - rowStart] = numD[0];
    2801:                 onnz[gIndFine - rowStart] = numO[0];
    2802:               }
    2803:             }
    2804:           }
    2805:         }
    2806:       }
    2807:       else { /* interpolate from all */
    2808:         if (numFields) {
    2809:           PetscInt f;
    2810:           for (f = 0; f < numFields; f++) {
    2811:             PetscInt numRows = offsets[f+1] - offsets[f], row;
    2812:             for (row = 0; row < numRows; row++) {
    2813:               PetscInt gIndFine = rowIndices[offsets[f] + row];
    2814:               if (gIndFine >= 0) {
    2815:                 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2816:                 dnnz[gIndFine - rowStart] = numD[f];
    2817:                 onnz[gIndFine - rowStart] = numO[f];
    2818:               }
    2819:             }
    2820:           }
    2821:         }
    2822:         else { /* every dof get a full row */
    2823:           PetscInt i;
    2824:           for (i = 0; i < gDof; i++) {
    2825:             PetscInt gIndFine = rowIndices[i];
    2826:             if (gIndFine >= 0) {
    2827:               if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2828:               dnnz[gIndFine - rowStart] = numD[0];
    2829:               onnz[gIndFine - rowStart] = numO[0];
    2830:             }
    2831:           }
    2832:         }
    2833:       }
    2834:     }
    2835:     MatXAIJSetPreallocation(mat,1,dnnz,onnz,NULL,NULL);
    2836:     PetscFree2(dnnz,onnz);

    2838:     DMPlexGetReferenceTree(fine,&refTree);
    2839:     DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
    2840:     DMGetDefaultConstraints(refTree,&refConSec,NULL);
    2841:     DMPlexGetAnchors(refTree,&refAnSec,NULL);
    2842:     PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
    2843:     PetscSectionGetMaxDof(refConSec,&maxConDof);
    2844:     PetscSectionGetMaxDof(leafIndicesSec,&maxColumns);
    2845:     PetscMalloc1(maxConDof*maxColumns,&pointWork);
    2846:     for (p = pStartF; p < pEndF; p++) {
    2847:       PetscInt    gDof, gcDof, gOff;
    2848:       PetscInt    numColIndices, pIndOff, *pInd;
    2849:       PetscInt    matSize;
    2850:       PetscInt    childId;

    2853:       PetscSectionGetDof(globalFine,p,&gDof);
    2854:       PetscSectionGetConstraintDof(globalFine,p,&gcDof);
    2855:       if ((gDof - gcDof) <= 0) {
    2856:         continue;
    2857:       }
    2858:       childId = childIds[p-pStartF];
    2859:       PetscSectionGetOffset(globalFine,p,&gOff);
    2860:       PetscSectionGetDof(leafIndicesSec,p,&numColIndices);
    2861:       PetscSectionGetOffset(leafIndicesSec,p,&pIndOff);
    2862:       numColIndices -= 2 * numFields;
    2863:       pInd = &leafIndices[pIndOff];
    2864:       offsets[0]        = 0;
    2865:       offsetsCopy[0]    = 0;
    2866:       newOffsets[0]     = 0;
    2867:       newOffsetsCopy[0] = 0;
    2868:       rowOffsets[0]     = 0;
    2869:       if (numFields) {
    2870:         PetscInt f;
    2871:         for (f = 0; f < numFields; f++) {
    2872:           PetscInt rowDof;

    2874:           PetscSectionGetFieldDof(localFine,p,f,&rowDof);
    2875:           offsets[f + 1]     = offsets[f] + rowDof;
    2876:           offsetsCopy[f + 1] = offsets[f + 1];
    2877:           rowOffsets[f + 1]  = pInd[numColIndices + f];
    2878:           newOffsets[f + 1]  = pInd[numColIndices + numFields + f];
    2879:         }
    2880:         indicesPointFields_private(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);
    2881:       }
    2882:       else {
    2883:         indicesPoint_private(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);
    2884:       }
    2885:       PetscSectionGetDof(leafMatricesSec,p,&matSize);
    2886:       if (!matSize) { /* incoming matrix is identity */
    2887:         if (childId < 0) { /* no child interpolation: scatter */
    2888:           if (numFields) {
    2889:             PetscInt f;
    2890:             for (f = 0; f < numFields; f++) {
    2891:               PetscInt numRows = offsets[f+1] - offsets[f], row;
    2892:               for (row = 0; row < numRows; row++) {
    2893:                 MatSetValue(mat,rowIndices[offsets[f]+row],pInd[newOffsets[f]+row],1.,INSERT_VALUES);
    2894:               }
    2895:             }
    2896:           }
    2897:           else {
    2898:             PetscInt numRows = gDof, row;
    2899:             for (row = 0; row < numRows; row++) {
    2900:               MatSetValue(mat,rowIndices[row],pInd[row],1.,INSERT_VALUES);
    2901:             }
    2902:           }
    2903:         }
    2904:         else { /* interpolate from all */
    2905:           if (numFields) {
    2906:             PetscInt f;
    2907:             for (f = 0; f < numFields; f++) {
    2908:               PetscInt numRows = offsets[f+1] - offsets[f];
    2909:               PetscInt numCols = newOffsets[f + 1] - newOffsets[f];
    2910:               MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],refPointFieldMats[childId - pRefStart][f],INSERT_VALUES);
    2911:             }
    2912:           }
    2913:           else {
    2914:             MatSetValues(mat,gDof,rowIndices,numColIndices,pInd,refPointFieldMats[childId - pRefStart][0],INSERT_VALUES);
    2915:           }
    2916:         }
    2917:       }
    2918:       else { /* interpolate from all */
    2919:         PetscInt    pMatOff;
    2920:         PetscScalar *pMat;

    2922:         PetscSectionGetOffset(leafMatricesSec,p,&pMatOff);
    2923:         pMat = &leafMatrices[pMatOff];
    2924:         if (childId < 0) { /* copy the incoming matrix */
    2925:           if (numFields) {
    2926:             PetscInt f, count;
    2927:             for (f = 0, count = 0; f < numFields; f++) {
    2928:               PetscInt numRows = offsets[f+1]-offsets[f];
    2929:               PetscInt numCols = newOffsets[f+1]-newOffsets[f];
    2930:               PetscInt numInRows = rowOffsets[f+1]-rowOffsets[f];
    2931:               PetscScalar *inMat = &pMat[count];

    2933:               MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],inMat,INSERT_VALUES);
    2934:               count += numCols * numInRows;
    2935:             }
    2936:           }
    2937:           else {
    2938:             MatSetValues(mat,gDof,rowIndices,numColIndices,pInd,pMat,INSERT_VALUES);
    2939:           }
    2940:         }
    2941:         else { /* multiply the incoming matrix by the child interpolation */
    2942:           if (numFields) {
    2943:             PetscInt f, count;
    2944:             for (f = 0, count = 0; f < numFields; f++) {
    2945:               PetscInt numRows = offsets[f+1]-offsets[f];
    2946:               PetscInt numCols = newOffsets[f+1]-newOffsets[f];
    2947:               PetscInt numInRows = rowOffsets[f+1]-rowOffsets[f];
    2948:               PetscScalar *inMat = &pMat[count];
    2949:               PetscInt i, j, k;
    2950:               if (refPointFieldN[childId - pRefStart][f] != numInRows) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Point constraint matrix multiply dimension mismatch");
    2951:               for (i = 0; i < numRows; i++) {
    2952:                 for (j = 0; j < numCols; j++) {
    2953:                   PetscScalar val = 0.;
    2954:                   for (k = 0; k < numInRows; k++) {
    2955:                     val += refPointFieldMats[childId - pRefStart][f][i * numInRows + k] * inMat[k * numCols + j];
    2956:                   }
    2957:                   pointWork[i * numCols + j] = val;
    2958:                 }
    2959:               }
    2960:               MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],pointWork,INSERT_VALUES);
    2961:               count += numCols * numInRows;
    2962:             }
    2963:           }
    2964:           else { /* every dof gets a full row */
    2965:             PetscInt numRows   = gDof;
    2966:             PetscInt numCols   = numColIndices;
    2967:             PetscInt numInRows = matSize / numColIndices;
    2968:             PetscInt i, j, k;
    2969:             if (refPointFieldN[childId - pRefStart][0] != numInRows) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Point constraint matrix multiply dimension mismatch");
    2970:             for (i = 0; i < numRows; i++) {
    2971:               for (j = 0; j < numCols; j++) {
    2972:                 PetscScalar val = 0.;
    2973:                 for (k = 0; k < numInRows; k++) {
    2974:                   val += refPointFieldMats[childId - pRefStart][0][i * numInRows + k] * pMat[k * numCols + j];
    2975:                 }
    2976:                 pointWork[i * numCols + j] = val;
    2977:               }
    2978:             }
    2979:             MatSetValues(mat,numRows,rowIndices,numCols,pInd,pointWork,INSERT_VALUES);
    2980:           }
    2981:         }
    2982:       }
    2983:     }
    2984:     DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
    2985:     DMRestoreWorkArray(fine,maxDof,PETSC_INT,&rowIndices);
    2986:     PetscFree(pointWork);
    2987:   }
    2988:   MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);
    2989:   MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);
    2990:   PetscSectionDestroy(&leafIndicesSec);
    2991:   PetscSectionDestroy(&leafMatricesSec);
    2992:   PetscFree2(leafIndices,leafMatrices);
    2993:   PetscFree7(offsets,offsetsCopy,newOffsets,newOffsetsCopy,rowOffsets,numD,numO);
    2994:   ISRestoreIndices(aIS,&anchors);
    2995:   return(0);
    2996: }

    3000: /*
    3001:  * Assuming a nodal basis (w.r.t. the dual basis) basis:
    3002:  *
    3003:  * for each coarse dof \phi^c_i:
    3004:  *   for each quadrature point (w_l,x_l) in the dual basis definition of \phi^c_i:
    3005:  *     for each fine dof \phi^f_j;
    3006:  *       a_{i,j} = 0;
    3007:  *       for each fine dof \phi^f_k:
    3008:  *         a_{i,j} += interp_{i,k} * \phi^f_k(x_l) * \phi^f_j(x_l) * w_l
    3009:  *                    [^^^ this is = \phi^c_i ^^^]
    3010:  */
    3011: PetscErrorCode DMPlexComputeInjectorReferenceTree(DM refTree, Mat *inj)
    3012: {
    3013:   PetscDS        ds;
    3014:   PetscSection   section, cSection;
    3015:   DMLabel        canonical, depth;
    3016:   Mat            cMat, mat;
    3017:   PetscInt       *nnz;
    3018:   PetscInt       f, dim, numFields, numSecFields, p, pStart, pEnd, cStart, cEnd;
    3019:   PetscInt       m, n;
    3020:   PetscScalar    *pointScalar;
    3021:   PetscReal      *v0, *v0parent, *vtmp, *J, *Jparent, *invJ, *pointRef, detJ, detJparent;

    3025:   DMGetDefaultSection(refTree,&section);
    3026:   DMGetDimension(refTree, &dim);
    3027:   PetscMalloc6(dim,&v0,dim,&v0parent,dim,&vtmp,dim*dim,&J,dim*dim,&Jparent,dim*dim,&invJ);
    3028:   PetscMalloc2(dim,&pointScalar,dim,&pointRef);
    3029:   DMGetDS(refTree,&ds);
    3030:   PetscDSGetNumFields(ds,&numFields);
    3031:   PetscSectionGetNumFields(section,&numSecFields);
    3032:   DMGetLabel(refTree,"canonical",&canonical);
    3033:   DMGetLabel(refTree,"depth",&depth);
    3034:   DMGetDefaultConstraints(refTree,&cSection,&cMat);
    3035:   DMPlexGetChart(refTree, &pStart, &pEnd);
    3036:   DMPlexGetHeightStratum(refTree, 0, &cStart, &cEnd);
    3037:   MatGetSize(cMat,&n,&m); /* the injector has transpose sizes from the constraint matrix */
    3038:   /* Step 1: compute non-zero pattern.  A proper subset of constraint matrix non-zero */
    3039:   PetscCalloc1(m,&nnz);
    3040:   for (p = pStart; p < pEnd; p++) { /* a point will have non-zeros if it is canonical, it has dofs, and its children have dofs */
    3041:     const PetscInt *children;
    3042:     PetscInt numChildren;
    3043:     PetscInt i, numChildDof, numSelfDof;

    3045:     if (canonical) {
    3046:       PetscInt pCanonical;
    3047:       DMLabelGetValue(canonical,p,&pCanonical);
    3048:       if (p != pCanonical) continue;
    3049:     }
    3050:     DMPlexGetTreeChildren(refTree,p,&numChildren,&children);
    3051:     if (!numChildren) continue;
    3052:     for (i = 0, numChildDof = 0; i < numChildren; i++) {
    3053:       PetscInt child = children[i];
    3054:       PetscInt dof;

    3056:       PetscSectionGetDof(section,child,&dof);
    3057:       numChildDof += dof;
    3058:     }
    3059:     PetscSectionGetDof(section,p,&numSelfDof);
    3060:     if (!numChildDof || !numSelfDof) continue;
    3061:     for (f = 0; f < numFields; f++) {
    3062:       PetscInt selfOff;

    3064:       if (numSecFields) { /* count the dofs for just this field */
    3065:         for (i = 0, numChildDof = 0; i < numChildren; i++) {
    3066:           PetscInt child = children[i];
    3067:           PetscInt dof;

    3069:           PetscSectionGetFieldDof(section,child,f,&dof);
    3070:           numChildDof += dof;
    3071:         }
    3072:         PetscSectionGetFieldDof(section,p,f,&numSelfDof);
    3073:         PetscSectionGetFieldOffset(section,p,f,&selfOff);
    3074:       }
    3075:       else {
    3076:         PetscSectionGetOffset(section,p,&selfOff);
    3077:       }
    3078:       for (i = 0; i < numSelfDof; i++) {
    3079:         nnz[selfOff + i] = numChildDof;
    3080:       }
    3081:     }
    3082:   }
    3083:   MatCreateAIJ(PETSC_COMM_SELF,m,n,m,n,-1,nnz,-1,NULL,&mat);
    3084:   PetscFree(nnz);
    3085:   /* Setp 2: compute entries */
    3086:   for (p = pStart; p < pEnd; p++) {
    3087:     const PetscInt *children;
    3088:     PetscInt numChildren;
    3089:     PetscInt i, numChildDof, numSelfDof;

    3091:     /* same conditions about when entries occur */
    3092:     if (canonical) {
    3093:       PetscInt pCanonical;
    3094:       DMLabelGetValue(canonical,p,&pCanonical);
    3095:       if (p != pCanonical) continue;
    3096:     }
    3097:     DMPlexGetTreeChildren(refTree,p,&numChildren,&children);
    3098:     if (!numChildren) continue;
    3099:     for (i = 0, numChildDof = 0; i < numChildren; i++) {
    3100:       PetscInt child = children[i];
    3101:       PetscInt dof;

    3103:       PetscSectionGetDof(section,child,&dof);
    3104:       numChildDof += dof;
    3105:     }
    3106:     PetscSectionGetDof(section,p,&numSelfDof);
    3107:     if (!numChildDof || !numSelfDof) continue;

    3109:     for (f = 0; f < numFields; f++) {
    3110:       PetscInt       selfOff, fComp, numSelfShapes, numChildShapes, parentCell;
    3111:       PetscInt       cellShapeOff;
    3112:       PetscObject    disc;
    3113:       PetscDualSpace dsp;
    3114:       PetscClassId   classId;
    3115:       PetscScalar    *pointMat;
    3116:       PetscInt       *matRows, *matCols;
    3117:       PetscInt       pO = PETSC_MIN_INT;
    3118:       const PetscInt *depthNumDof;

    3120:       if (numSecFields) {
    3121:         for (i = 0, numChildDof = 0; i < numChildren; i++) {
    3122:           PetscInt child = children[i];
    3123:           PetscInt dof;

    3125:           PetscSectionGetFieldDof(section,child,f,&dof);
    3126:           numChildDof += dof;
    3127:         }
    3128:         PetscSectionGetFieldDof(section,p,f,&numSelfDof);
    3129:         PetscSectionGetFieldOffset(section,p,f,&selfOff);
    3130:         PetscSectionGetFieldComponents(section,f,&fComp);
    3131:       }
    3132:       else {
    3133:         PetscSectionGetOffset(section,p,&selfOff);
    3134:         fComp = 1;
    3135:       }
    3136:       numSelfShapes  = numSelfDof  / fComp;
    3137:       numChildShapes = numChildDof / fComp;

    3139:       /* find a cell whose closure contains p */
    3140:       if (p >= cStart && p < cEnd) {
    3141:         parentCell = p;
    3142:       }
    3143:       else {
    3144:         PetscInt *star = NULL;
    3145:         PetscInt numStar;

    3147:         parentCell = -1;
    3148:         DMPlexGetTransitiveClosure(refTree,p,PETSC_FALSE,&numStar,&star);
    3149:         for (i = numStar - 1; i >= 0; i--) {
    3150:           PetscInt c = star[2 * i];

    3152:           if (c >= cStart && c < cEnd) {
    3153:             parentCell = c;
    3154:             break;
    3155:           }
    3156:         }
    3157:         DMPlexRestoreTransitiveClosure(refTree,p,PETSC_FALSE,&numStar,&star);
    3158:       }
    3159:       /* determine the offset of p's shape functions withing parentCell's shape functions */
    3160:       PetscDSGetDiscretization(ds,f,&disc);
    3161:       PetscObjectGetClassId(disc,&classId);
    3162:       if (classId == PETSCFE_CLASSID) {
    3163:         PetscFEGetDualSpace((PetscFE)disc,&dsp);
    3164:       }
    3165:       else if (classId == PETSCFV_CLASSID) {
    3166:         PetscFVGetDualSpace((PetscFV)disc,&dsp);
    3167:       }
    3168:       else {
    3169:         SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unsupported discretization object");
    3170:       }
    3171:       PetscDualSpaceGetNumDof(dsp,&depthNumDof);
    3172:       {
    3173:         PetscInt *closure = NULL;
    3174:         PetscInt numClosure;

    3176:         DMPlexGetTransitiveClosure(refTree,parentCell,PETSC_TRUE,&numClosure,&closure);
    3177:         for (i = 0, cellShapeOff = 0; i < numClosure; i++) {
    3178:           PetscInt point = closure[2 * i], pointDepth;

    3180:           pO = closure[2 * i + 1];
    3181:           if (point == p) break;
    3182:           DMLabelGetValue(depth,point,&pointDepth);
    3183:           cellShapeOff += depthNumDof[pointDepth];
    3184:         }
    3185:         DMPlexRestoreTransitiveClosure(refTree,parentCell,PETSC_TRUE,&numClosure,&closure);
    3186:       }

    3188:       DMGetWorkArray(refTree, numSelfShapes * numChildShapes, PETSC_SCALAR,&pointMat);
    3189:       DMGetWorkArray(refTree, numSelfShapes + numChildShapes, PETSC_INT,&matRows);
    3190:       matCols = matRows + numSelfShapes;
    3191:       for (i = 0; i < numSelfShapes; i++) {
    3192:         matRows[i] = selfOff + i * fComp;
    3193:       }
    3194:       {
    3195:         PetscInt colOff = 0;

    3197:         for (i = 0; i < numChildren; i++) {
    3198:           PetscInt child = children[i];
    3199:           PetscInt dof, off, j;

    3201:           if (numSecFields) {
    3202:             PetscSectionGetFieldDof(cSection,child,f,&dof);
    3203:             PetscSectionGetFieldOffset(cSection,child,f,&off);
    3204:           }
    3205:           else {
    3206:             PetscSectionGetDof(cSection,child,&dof);
    3207:             PetscSectionGetOffset(cSection,child,&off);
    3208:           }

    3210:           for (j = 0; j < dof / fComp; j++) {
    3211:             matCols[colOff++] = off + j * fComp;
    3212:           }
    3213:         }
    3214:       }
    3215:       if (classId == PETSCFE_CLASSID) {
    3216:         PetscFE        fe = (PetscFE) disc;
    3217:         PetscInt       fSize;

    3219:         PetscFEGetDualSpace(fe,&dsp);
    3220:         PetscDualSpaceGetDimension(dsp,&fSize);
    3221:         for (i = 0; i < numSelfShapes; i++) { /* for every shape function */
    3222:           PetscQuadrature q;
    3223:           PetscInt        dim, numPoints, j, k;
    3224:           const PetscReal *points;
    3225:           const PetscReal *weights;
    3226:           PetscInt        *closure = NULL;
    3227:           PetscInt        numClosure;
    3228:           PetscInt        parentCellShapeDof = cellShapeOff + (pO < 0 ? (numSelfShapes - 1 - i) : i);
    3229:           PetscReal       *Bparent;

    3231:           PetscDualSpaceGetFunctional(dsp,parentCellShapeDof,&q);
    3232:           PetscQuadratureGetData(q,&dim,&numPoints,&points,&weights);
    3233:           PetscFEGetTabulation(fe,numPoints,points,&Bparent,NULL,NULL); /* I'm expecting a nodal basis: weights[:]' * Bparent[:,cellShapeDof] = 1. */
    3234:           for (k = 0; k < numChildShapes; k++) {
    3235:             pointMat[numChildShapes * i + k] = 0.;
    3236:           }
    3237:           for (j = 0; j < numPoints; j++) {
    3238:             PetscInt          childCell = -1;
    3239:             PetscReal         parentValAtPoint;
    3240:             const PetscReal   *pointReal = &points[dim * j];
    3241:             const PetscScalar *point;
    3242:             PetscReal         *Bchild;
    3243:             PetscInt          childCellShapeOff, pointMatOff;
    3244: #if defined(PETSC_USE_COMPLEX)
    3245:             PetscInt          d;

    3247:             for (d = 0; d < dim; d++) {
    3248:               pointScalar[d] = points[dim * j + d];
    3249:             }
    3250:             point = pointScalar;
    3251: #else
    3252:             point = pointReal;
    3253: #endif

    3255:             parentValAtPoint = Bparent[(fSize * j + parentCellShapeDof) * fComp];

    3257:             for (k = 0; k < numChildren; k++) { /* locate the point in a child's star cell*/
    3258:               PetscInt child = children[k];
    3259:               PetscInt *star = NULL;
    3260:               PetscInt numStar, s;

    3262:               DMPlexGetTransitiveClosure(refTree,child,PETSC_FALSE,&numStar,&star);
    3263:               for (s = numStar - 1; s >= 0; s--) {
    3264:                 PetscInt c = star[2 * s];

    3266:                 if (c < cStart || c >= cEnd) continue;
    3267:                 DMPlexLocatePoint_Internal(refTree,dim,point,c,&childCell);
    3268:                 if (childCell >= 0) break;
    3269:               }
    3270:               DMPlexRestoreTransitiveClosure(refTree,child,PETSC_FALSE,&numStar,&star);
    3271:               if (childCell >= 0) break;
    3272:             }
    3273:             if (childCell < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Could not locate quadrature point");
    3274:             DMPlexComputeCellGeometryFEM(refTree, childCell, NULL, v0, J, invJ, &detJ);
    3275:             DMPlexComputeCellGeometryFEM(refTree, parentCell, NULL, v0parent, Jparent, NULL, &detJparent);
    3276:             CoordinatesRefToReal(dim, dim, v0parent, Jparent, pointReal, vtmp);
    3277:             CoordinatesRealToRef(dim, dim, v0, invJ, vtmp, pointRef);

    3279:             PetscFEGetTabulation(fe,1,pointRef,&Bchild,NULL,NULL);
    3280:             DMPlexGetTransitiveClosure(refTree,childCell,PETSC_TRUE,&numClosure,&closure);
    3281:             for (k = 0, pointMatOff = 0; k < numChildren; k++) { /* point is located in cell => child dofs support at point are in closure of cell */
    3282:               PetscInt child = children[k], childDepth, childDof, childO = PETSC_MIN_INT;
    3283:               PetscInt l;

    3285:               DMLabelGetValue(depth,child,&childDepth);
    3286:               childDof = depthNumDof[childDepth];
    3287:               for (l = 0, childCellShapeOff = 0; l < numClosure; l++) {
    3288:                 PetscInt point = closure[2 * l];
    3289:                 PetscInt pointDepth;

    3291:                 childO = closure[2 * l + 1];
    3292:                 if (point == child) break;
    3293:                 DMLabelGetValue(depth,point,&pointDepth);
    3294:                 childCellShapeOff += depthNumDof[pointDepth];
    3295:               }
    3296:               if (l == numClosure) {
    3297:                 pointMatOff += childDof;
    3298:                 continue; /* child is not in the closure of the cell: has nothing to contribute to this point */
    3299:               }
    3300:               for (l = 0; l < childDof; l++) {
    3301:                 PetscInt    childCellDof    = childCellShapeOff + (childO ? (childDof - 1 - l) : l);
    3302:                 PetscReal   childValAtPoint = Bchild[childCellDof * fComp];

    3304:                 pointMat[i * numChildShapes + pointMatOff + l] += weights[j] * parentValAtPoint * childValAtPoint;
    3305:               }
    3306:               pointMatOff += childDof;
    3307:             }
    3308:             DMPlexRestoreTransitiveClosure(refTree,childCell,PETSC_TRUE,&numClosure,&closure);
    3309:             PetscFERestoreTabulation(fe,1,pointRef,&Bchild,NULL,NULL);
    3310:           }
    3311:           PetscFERestoreTabulation(fe,numPoints,points,&Bparent,NULL,NULL);
    3312:         }
    3313:       }
    3314:       else { /* just the volume-weighted averages of the children */
    3315:         PetscInt  childShapeOff;
    3316:         PetscReal parentVol;

    3318:         DMPlexComputeCellGeometryFVM(refTree, p, &parentVol, NULL, NULL);
    3319:         for (i = 0, childShapeOff = 0; i < numChildren; i++) {
    3320:           PetscInt  child = children[i];
    3321:           PetscReal childVol;

    3323:           if (child < cStart || child >= cEnd) continue;
    3324:           DMPlexComputeCellGeometryFVM(refTree, child, &childVol, NULL, NULL);
    3325:           pointMat[childShapeOff] = childVol / parentVol;
    3326:           childShapeOff++;
    3327:         }
    3328:       }
    3329:       /* Insert pointMat into mat */
    3330:       for (i = 0; i < fComp; i++) {
    3331:         PetscInt j;
    3332:         MatSetValues(mat,numSelfShapes,matRows,numChildShapes,matCols,pointMat,INSERT_VALUES);

    3334:         for (j = 0; j < numSelfShapes; j++) {
    3335:           matRows[j]++;
    3336:         }
    3337:         for (j = 0; j < numChildShapes; j++) {
    3338:           matCols[j]++;
    3339:         }
    3340:       }
    3341:       DMRestoreWorkArray(refTree, numSelfShapes + numChildShapes, PETSC_INT,&matRows);
    3342:       DMRestoreWorkArray(refTree, numSelfShapes * numChildShapes, PETSC_SCALAR,&pointMat);
    3343:     }
    3344:   }
    3345:   PetscFree6(v0,v0parent,vtmp,J,Jparent,invJ);
    3346:   PetscFree2(pointScalar,pointRef);
    3347:   MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);
    3348:   MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);
    3349:   *inj = mat;
    3350:   return(0);
    3351: }

    3355: static PetscErrorCode DMPlexReferenceTreeGetChildrenMatrices_Injection(DM refTree, Mat inj, PetscScalar ****childrenMats)
    3356: {
    3357:   PetscDS        ds;
    3358:   PetscInt       numFields, f, pRefStart, pRefEnd, p, *rows, *cols, maxDof;
    3359:   PetscScalar    ***refPointFieldMats;
    3360:   PetscSection   refConSec, refSection;

    3364:   DMGetDS(refTree,&ds);
    3365:   PetscDSGetNumFields(ds,&numFields);
    3366:   DMGetDefaultConstraints(refTree,&refConSec,NULL);
    3367:   DMGetDefaultSection(refTree,&refSection);
    3368:   PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
    3369:   PetscMalloc1(pRefEnd-pRefStart,&refPointFieldMats);
    3370:   PetscSectionGetMaxDof(refConSec,&maxDof);
    3371:   PetscMalloc1(maxDof,&rows);
    3372:   PetscMalloc1(maxDof*maxDof,&cols);
    3373:   for (p = pRefStart; p < pRefEnd; p++) {
    3374:     PetscInt parent, pDof, parentDof;

    3376:     DMPlexGetTreeParent(refTree,p,&parent,NULL);
    3377:     PetscSectionGetDof(refConSec,p,&pDof);
    3378:     PetscSectionGetDof(refSection,parent,&parentDof);
    3379:     if (!pDof || !parentDof || parent == p) continue;

    3381:     PetscMalloc1(numFields,&refPointFieldMats[p-pRefStart]);
    3382:     for (f = 0; f < numFields; f++) {
    3383:       PetscInt cDof, cOff, numCols, r, fComp;
    3384:       PetscObject disc;
    3385:       PetscClassId id;
    3386:       PetscFE fe = NULL;
    3387:       PetscFV fv = NULL;

    3389:       PetscDSGetDiscretization(ds,f,&disc);
    3390:       PetscObjectGetClassId(disc,&id);
    3391:       if (id == PETSCFE_CLASSID) {
    3392:         fe = (PetscFE) disc;
    3393:         PetscFEGetNumComponents(fe,&fComp);
    3394:       }
    3395:       else if (id == PETSCFV_CLASSID) {
    3396:         fv = (PetscFV) disc;
    3397:         PetscFVGetNumComponents(fv,&fComp);
    3398:       }
    3399:       else SETERRQ1(PetscObjectComm(disc),PETSC_ERR_ARG_UNKNOWN_TYPE, "PetscDS discretization id %d not recognized.", id);

    3401:       if (numFields > 1) {
    3402:         PetscSectionGetFieldDof(refConSec,p,f,&cDof);
    3403:         PetscSectionGetFieldOffset(refConSec,p,f,&cOff);
    3404:       }
    3405:       else {
    3406:         PetscSectionGetDof(refConSec,p,&cDof);
    3407:         PetscSectionGetOffset(refConSec,p,&cOff);
    3408:       }

    3410:       if (!cDof) continue;
    3411:       for (r = 0; r < cDof; r++) {
    3412:         rows[r] = cOff + r;
    3413:       }
    3414:       numCols = 0;
    3415:       {
    3416:         PetscInt aDof, aOff, j;

    3418:         if (numFields > 1) {
    3419:           PetscSectionGetFieldDof(refSection,parent,f,&aDof);
    3420:           PetscSectionGetFieldOffset(refSection,parent,f,&aOff);
    3421:         }
    3422:         else {
    3423:           PetscSectionGetDof(refSection,parent,&aDof);
    3424:           PetscSectionGetOffset(refSection,parent,&aOff);
    3425:         }

    3427:         for (j = 0; j < aDof; j++) {
    3428:           cols[numCols++] = aOff + j;
    3429:         }
    3430:       }
    3431:       PetscMalloc1(cDof*numCols,&refPointFieldMats[p-pRefStart][f]);
    3432:       /* transpose of constraint matrix */
    3433:       MatGetValues(inj,numCols,cols,cDof,rows,refPointFieldMats[p-pRefStart][f]);
    3434:     }
    3435:   }
    3436:   *childrenMats = refPointFieldMats;
    3437:   PetscFree(rows);
    3438:   PetscFree(cols);
    3439:   return(0);
    3440: }

    3444: static PetscErrorCode DMPlexReferenceTreeRestoreChildrenMatrices_Injection(DM refTree, Mat inj, PetscScalar ****childrenMats)
    3445: {
    3446:   PetscDS        ds;
    3447:   PetscScalar    ***refPointFieldMats;
    3448:   PetscInt       numFields, pRefStart, pRefEnd, p, f;
    3449:   PetscSection   refConSec, refSection;

    3453:   refPointFieldMats = *childrenMats;
    3454:   *childrenMats = NULL;
    3455:   DMGetDS(refTree,&ds);
    3456:   DMGetDefaultSection(refTree,&refSection);
    3457:   PetscDSGetNumFields(ds,&numFields);
    3458:   DMGetDefaultConstraints(refTree,&refConSec,NULL);
    3459:   PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
    3460:   for (p = pRefStart; p < pRefEnd; p++) {
    3461:     PetscInt parent, pDof, parentDof;

    3463:     DMPlexGetTreeParent(refTree,p,&parent,NULL);
    3464:     PetscSectionGetDof(refConSec,p,&pDof);
    3465:     PetscSectionGetDof(refSection,parent,&parentDof);
    3466:     if (!pDof || !parentDof || parent == p) continue;

    3468:     for (f = 0; f < numFields; f++) {
    3469:       PetscInt cDof;

    3471:       if (numFields > 1) {
    3472:         PetscSectionGetFieldDof(refConSec,p,f,&cDof);
    3473:       }
    3474:       else {
    3475:         PetscSectionGetDof(refConSec,p,&cDof);
    3476:       }

    3478:       if (!cDof) continue;
    3479:       PetscFree(refPointFieldMats[p - pRefStart][f]);
    3480:     }
    3481:     PetscFree(refPointFieldMats[p - pRefStart]);
    3482:   }
    3483:   PetscFree(refPointFieldMats);
    3484:   return(0);
    3485: }

    3489: PetscErrorCode DMPlexComputeInjectorTree(DM coarse, DM fine, PetscSF coarseToFine, PetscInt *childIds, Mat mat)
    3490: {
    3491:   DM             refTree;
    3492:   PetscSF        coarseToFineEmbedded;
    3493:   const PetscInt *rootDegrees;
    3494:   PetscSection   multiRootSec, rootIndicesSec, leafIndicesSec;
    3495:   PetscSection   globalCoarse, globalFine;
    3496:   PetscSection   localCoarse, localFine;
    3497:   PetscSection   cSecRef;
    3498:   PetscInt       *rootIndices, *leafIndices, *parentIndices, pRefStart, pRefEnd;
    3499:   Mat            cMatRef, injRef;
    3500:   PetscInt       numFields, numMulti, maxDof;
    3501:   PetscInt       pStartC, pEndC, pStartF, pEndF, p;
    3502:   PetscInt       *offsets, *offsetsCopy, *rowOffsets;
    3503:   PetscLayout    rowMap, colMap;
    3504:   PetscInt       rowStart, rowEnd, colStart, colEnd, *nnzD, *nnzO;
    3505:   PetscObject    injRefObj;
    3506:   PetscScalar    ***childrenMats=NULL ; /* gcc -O gives 'may be used uninitialized' warning'. Initializing to suppress this warning */

    3511:   /* get the templates for the fine-to-coarse injection from the reference tree */
    3512:   DMPlexGetReferenceTree(coarse,&refTree);
    3513:   DMGetDefaultConstraints(refTree,&cSecRef,&cMatRef);
    3514:   PetscSectionGetChart(cSecRef,&pRefStart,&pRefEnd);
    3515:   PetscObjectQuery((PetscObject)cMatRef,"DMPlexComputeInjectorTree_refTree",&injRefObj);
    3516:   injRef = (Mat) injRefObj;
    3517:   if (!injRef) {
    3518:     DMPlexComputeInjectorReferenceTree(refTree,&injRef);
    3519:     PetscObjectCompose((PetscObject)cMatRef,"DMPlexComputeInjectorTree_refTree",(PetscObject)injRef);
    3520:     /* there is now a reference in cMatRef, which should be the only one for symmetry with the above case */
    3521:     PetscObjectDereference((PetscObject)injRef);
    3522:   }

    3524:   DMPlexGetChart(fine,&pStartF,&pEndF);
    3525:   DMGetDefaultSection(fine,&localFine);
    3526:   DMGetDefaultGlobalSection(fine,&globalFine);

    3528:   PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafIndicesSec);
    3529:   PetscSectionSetChart(leafIndicesSec,pStartF, pEndF);

    3531:   PetscSectionGetNumFields(localFine,&numFields);
    3532:   {
    3533:     PetscInt maxFields = PetscMax(1,numFields) + 1;
    3534:     PetscMalloc3(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&rowOffsets);
    3535:   }

    3537:   { /* winnow fine points that don't have global dofs out of the sf */
    3538:     PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs, numIndices;

    3540:     for (p = pStartF, numPointsWithDofs = 0; p < pEndF; p++) {
    3541:       PetscSectionGetDof(globalFine,p,&dof);
    3542:       PetscSectionGetConstraintDof(globalFine,p,&cdof);
    3543:       if ((dof - cdof) > 0) {
    3544:         numPointsWithDofs++;

    3546:         PetscSectionGetDof(localFine,p,&dof);
    3547:         PetscSectionSetDof(leafIndicesSec,p,dof + 1);
    3548:       }
    3549:     }
    3550:     PetscMalloc1(numPointsWithDofs,&pointsWithDofs);
    3551:     PetscSectionSetUp(leafIndicesSec);
    3552:     PetscSectionGetStorageSize(leafIndicesSec,&numIndices);
    3553:     PetscMalloc1(numIndices,&leafIndices);
    3554:     for (p = pStartF, offset = 0; p < pEndF; p++) {
    3555:       PetscSectionGetDof(globalFine,p,&dof);
    3556:       PetscSectionGetConstraintDof(globalFine,p,&cdof);
    3557:       if ((dof - cdof) > 0) {
    3558:         PetscInt off, gOff;
    3559:         PetscInt *pInd;

    3561:         pointsWithDofs[offset++] = p - pStartF;

    3563:         PetscSectionGetOffset(leafIndicesSec,p,&off);

    3565:         pInd = &leafIndices[off + 1];
    3566:         PetscSectionGetOffset(globalFine,p,&gOff);

    3568:         offsets[0] = 0;
    3569:         if (numFields) {
    3570:           PetscInt f;

    3572:           for (f = 0; f < numFields; f++) {
    3573:             PetscInt fDof;
    3574:             PetscSectionGetFieldDof(localFine,p,f,&fDof);
    3575:             offsets[f + 1] = fDof + offsets[f];
    3576:           }
    3577:           indicesPointFields_private(localFine,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,0,pInd);
    3578:         }
    3579:         else {
    3580:           indicesPoint_private(localFine,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,0,pInd);
    3581:         }
    3582:       }
    3583:     }
    3584:     PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);
    3585:     PetscFree(pointsWithDofs);
    3586:   }

    3588:   DMPlexGetChart(coarse,&pStartC,&pEndC);
    3589:   DMGetDefaultSection(coarse,&localCoarse);
    3590:   DMGetDefaultGlobalSection(coarse,&globalCoarse);
    3591:   PetscSectionGetMaxDof(localCoarse,&maxDof);

    3593:   { /* there may be the case where an sf root has a parent: broadcast parents back to children */
    3594:     MPI_Datatype threeInt;
    3595:     PetscMPIInt  rank;
    3596:     PetscInt     (*parentNodeAndIdCoarse)[3];
    3597:     PetscInt     (*parentNodeAndIdFine)[3];
    3598:     PetscInt     p, nleaves, nleavesToParents;
    3599:     PetscSF      pointSF, sfToParents;
    3600:     const PetscInt *ilocal;
    3601:     const PetscSFNode *iremote;
    3602:     PetscSFNode  *iremoteToParents;
    3603:     PetscInt     *ilocalToParents;

    3605:     MPI_Comm_rank(PetscObjectComm((PetscObject)coarse),&rank);
    3606:     MPI_Type_contiguous(3,MPIU_INT,&threeInt);
    3607:     MPI_Type_commit(&threeInt);
    3608:     PetscMalloc2(pEndC-pStartC,&parentNodeAndIdCoarse,pEndF-pStartF,&parentNodeAndIdFine);
    3609:     DMGetPointSF(coarse,&pointSF);
    3610:     PetscSFGetGraph(pointSF,NULL,&nleaves,&ilocal,&iremote);
    3611:     for (p = pStartC; p < pEndC; p++) {
    3612:       PetscInt parent, childId;
    3613:       DMPlexGetTreeParent(coarse,p,&parent,&childId);
    3614:       parentNodeAndIdCoarse[p - pStartC][0] = rank;
    3615:       parentNodeAndIdCoarse[p - pStartC][1] = parent - pStartC;
    3616:       parentNodeAndIdCoarse[p - pStartC][2] = (p == parent) ? -1 : childId;
    3617:       if (nleaves > 0) {
    3618:         PetscInt leaf = -1;

    3620:         if (ilocal) {
    3621:           PetscFindInt(parent,nleaves,ilocal,&leaf);
    3622:         }
    3623:         else {
    3624:           leaf = p - pStartC;
    3625:         }
    3626:         if (leaf >= 0) {
    3627:           parentNodeAndIdCoarse[p - pStartC][0] = iremote[leaf].rank;
    3628:           parentNodeAndIdCoarse[p - pStartC][1] = iremote[leaf].index;
    3629:         }
    3630:       }
    3631:     }
    3632:     for (p = pStartF; p < pEndF; p++) {
    3633:       parentNodeAndIdFine[p - pStartF][0] = -1;
    3634:       parentNodeAndIdFine[p - pStartF][1] = -1;
    3635:       parentNodeAndIdFine[p - pStartF][2] = -1;
    3636:     }
    3637:     PetscSFBcastBegin(coarseToFineEmbedded,threeInt,parentNodeAndIdCoarse,parentNodeAndIdFine);
    3638:     PetscSFBcastEnd(coarseToFineEmbedded,threeInt,parentNodeAndIdCoarse,parentNodeAndIdFine);
    3639:     for (p = pStartF, nleavesToParents = 0; p < pEndF; p++) {
    3640:       PetscInt dof;

    3642:       PetscSectionGetDof(leafIndicesSec,p,&dof);
    3643:       if (dof) {
    3644:         PetscInt off;

    3646:         PetscSectionGetOffset(leafIndicesSec,p,&off);
    3647:         leafIndices[off] = PetscMax(childIds[p-pStartF],parentNodeAndIdFine[p-pStartF][2]);
    3648:       }
    3649:       if (parentNodeAndIdFine[p-pStartF][0] >= 0) {
    3650:         nleavesToParents++;
    3651:       }
    3652:     }
    3653:     PetscMalloc1(nleavesToParents,&ilocalToParents);
    3654:     PetscMalloc1(nleavesToParents,&iremoteToParents);
    3655:     for (p = pStartF, nleavesToParents = 0; p < pEndF; p++) {
    3656:       if (parentNodeAndIdFine[p-pStartF][0] >= 0) {
    3657:         ilocalToParents[nleavesToParents] = p - pStartF;
    3658:         iremoteToParents[nleavesToParents].rank  = parentNodeAndIdFine[p-pStartF][0];
    3659:         iremoteToParents[nleavesToParents].index = parentNodeAndIdFine[p-pStartF][1];
    3660:         nleavesToParents++;
    3661:       }
    3662:     }
    3663:     PetscSFCreate(PetscObjectComm((PetscObject)coarse),&sfToParents);
    3664:     PetscSFSetGraph(sfToParents,pEndC-pStartC,nleavesToParents,ilocalToParents,PETSC_OWN_POINTER,iremoteToParents,PETSC_OWN_POINTER);
    3665:     PetscSFDestroy(&coarseToFineEmbedded);

    3667:     coarseToFineEmbedded = sfToParents;

    3669:     PetscFree2(parentNodeAndIdCoarse,parentNodeAndIdFine);
    3670:     MPI_Type_free(&threeInt);
    3671:   }

    3673:   { /* winnow out coarse points that don't have dofs */
    3674:     PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs;
    3675:     PetscSF  sfDofsOnly;

    3677:     for (p = pStartC, numPointsWithDofs = 0; p < pEndC; p++) {
    3678:       PetscSectionGetDof(globalCoarse,p,&dof);
    3679:       PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
    3680:       if ((dof - cdof) > 0) {
    3681:         numPointsWithDofs++;
    3682:       }
    3683:     }
    3684:     PetscMalloc1(numPointsWithDofs,&pointsWithDofs);
    3685:     for (p = pStartC, offset = 0; p < pEndC; p++) {
    3686:       PetscSectionGetDof(globalCoarse,p,&dof);
    3687:       PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
    3688:       if ((dof - cdof) > 0) {
    3689:         pointsWithDofs[offset++] = p - pStartC;
    3690:       }
    3691:     }
    3692:     PetscSFCreateEmbeddedSF(coarseToFineEmbedded, numPointsWithDofs, pointsWithDofs, &sfDofsOnly);
    3693:     PetscSFDestroy(&coarseToFineEmbedded);
    3694:     PetscFree(pointsWithDofs);
    3695:     coarseToFineEmbedded = sfDofsOnly;
    3696:   }

    3698:   /* communicate back to the coarse mesh which coarse points have children (that may require injection) */
    3699:   PetscSFComputeDegreeBegin(coarseToFineEmbedded,&rootDegrees);
    3700:   PetscSFComputeDegreeEnd(coarseToFineEmbedded,&rootDegrees);
    3701:   PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&multiRootSec);
    3702:   PetscSectionSetChart(multiRootSec,pStartC,pEndC);
    3703:   for (p = pStartC; p < pEndC; p++) {
    3704:     PetscSectionSetDof(multiRootSec,p,rootDegrees[p-pStartC]);
    3705:   }
    3706:   PetscSectionSetUp(multiRootSec);
    3707:   PetscSectionGetStorageSize(multiRootSec,&numMulti);
    3708:   PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootIndicesSec);
    3709:   { /* distribute the leaf section */
    3710:     PetscSF multi, multiInv, indicesSF;
    3711:     PetscInt *remoteOffsets, numRootIndices;

    3713:     PetscSFGetMultiSF(coarseToFineEmbedded,&multi);
    3714:     PetscSFCreateInverseSF(multi,&multiInv);
    3715:     PetscSFDistributeSection(multiInv,leafIndicesSec,&remoteOffsets,rootIndicesSec);
    3716:     PetscSFCreateSectionSF(multiInv,leafIndicesSec,remoteOffsets,rootIndicesSec,&indicesSF);
    3717:     PetscFree(remoteOffsets);
    3718:     PetscSFDestroy(&multiInv);
    3719:     PetscSectionGetStorageSize(rootIndicesSec,&numRootIndices);
    3720:     PetscMalloc1(numRootIndices,&rootIndices);
    3721:     PetscSFBcastBegin(indicesSF,MPIU_INT,leafIndices,rootIndices);
    3722:     PetscSFBcastEnd(indicesSF,MPIU_INT,leafIndices,rootIndices);
    3723:     PetscSFDestroy(&indicesSF);
    3724:   }
    3725:   PetscSectionDestroy(&leafIndicesSec);
    3726:   PetscFree(leafIndices);
    3727:   PetscSFDestroy(&coarseToFineEmbedded);

    3729:   PetscMalloc1(maxDof,&parentIndices);

    3731:   /* count indices */
    3732:   MatGetLayouts(mat,&rowMap,&colMap);
    3733:   PetscLayoutSetUp(rowMap);
    3734:   PetscLayoutSetUp(colMap);
    3735:   PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);
    3736:   PetscLayoutGetRange(colMap,&colStart,&colEnd);
    3737:   PetscCalloc2(rowEnd-rowStart,&nnzD,rowEnd-rowStart,&nnzO);
    3738:   for (p = pStartC; p < pEndC; p++) {
    3739:     PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff;

    3741:     PetscSectionGetDof(globalCoarse,p,&dof);
    3742:     PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
    3743:     if ((dof - cdof) <= 0) continue;
    3744:     PetscSectionGetOffset(globalCoarse,p,&gOff);

    3746:     rowOffsets[0] = 0;
    3747:     offsetsCopy[0] = 0;
    3748:     if (numFields) {
    3749:       PetscInt f;

    3751:       for (f = 0; f < numFields; f++) {
    3752:         PetscInt fDof;
    3753:         PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
    3754:         rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f];
    3755:       }
    3756:       indicesPointFields_private(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);
    3757:     }
    3758:     else {
    3759:       indicesPoint_private(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);
    3760:       rowOffsets[1] = offsetsCopy[0];
    3761:     }

    3763:     PetscSectionGetDof(multiRootSec,p,&numLeaves);
    3764:     PetscSectionGetOffset(multiRootSec,p,&leafStart);
    3765:     leafEnd = leafStart + numLeaves;
    3766:     for (l = leafStart; l < leafEnd; l++) {
    3767:       PetscInt numIndices, childId, offset;
    3768:       const PetscInt *childIndices;

    3770:       PetscSectionGetDof(rootIndicesSec,l,&numIndices);
    3771:       PetscSectionGetOffset(rootIndicesSec,l,&offset);
    3772:       childId = rootIndices[offset++];
    3773:       childIndices = &rootIndices[offset];
    3774:       numIndices--;

    3776:       if (childId == -1) { /* equivalent points: scatter */
    3777:         PetscInt i;

    3779:         for (i = 0; i < numIndices; i++) {
    3780:           PetscInt colIndex = childIndices[i];
    3781:           PetscInt rowIndex = parentIndices[i];
    3782:           if (rowIndex < 0) continue;
    3783:           if (colIndex < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Unconstrained fine and constrained coarse");
    3784:           if (colIndex >= colStart && colIndex < colEnd) {
    3785:             nnzD[rowIndex - rowStart] = 1;
    3786:           }
    3787:           else {
    3788:             nnzO[rowIndex - rowStart] = 1;
    3789:           }
    3790:         }
    3791:       }
    3792:       else {
    3793:         PetscInt parentId, f, lim;

    3795:         DMPlexGetTreeParent(refTree,childId,&parentId,NULL);

    3797:         lim = PetscMax(1,numFields);
    3798:         offsets[0] = 0;
    3799:         if (numFields) {
    3800:           PetscInt f;

    3802:           for (f = 0; f < numFields; f++) {
    3803:             PetscInt fDof;
    3804:             PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);

    3806:             offsets[f + 1] = fDof + offsets[f];
    3807:           }
    3808:         }
    3809:         else {
    3810:           PetscInt cDof;

    3812:           PetscSectionGetDof(cSecRef,childId,&cDof);
    3813:           offsets[1] = cDof;
    3814:         }
    3815:         for (f = 0; f < lim; f++) {
    3816:           PetscInt parentStart = rowOffsets[f], parentEnd = rowOffsets[f + 1];
    3817:           PetscInt childStart = offsets[f], childEnd = offsets[f + 1];
    3818:           PetscInt i, numD = 0, numO = 0;

    3820:           for (i = childStart; i < childEnd; i++) {
    3821:             PetscInt colIndex = childIndices[i];

    3823:             if (colIndex < 0) continue;
    3824:             if (colIndex >= colStart && colIndex < colEnd) {
    3825:               numD++;
    3826:             }
    3827:             else {
    3828:               numO++;
    3829:             }
    3830:           }
    3831:           for (i = parentStart; i < parentEnd; i++) {
    3832:             PetscInt rowIndex = parentIndices[i];

    3834:             if (rowIndex < 0) continue;
    3835:             nnzD[rowIndex - rowStart] += numD;
    3836:             nnzO[rowIndex - rowStart] += numO;
    3837:           }
    3838:         }
    3839:       }
    3840:     }
    3841:   }
    3842:   /* preallocate */
    3843:   MatXAIJSetPreallocation(mat,1,nnzD,nnzO,NULL,NULL);
    3844:   PetscFree2(nnzD,nnzO);
    3845:   /* insert values */
    3846:   DMPlexReferenceTreeGetChildrenMatrices_Injection(refTree,injRef,&childrenMats);
    3847:   for (p = pStartC; p < pEndC; p++) {
    3848:     PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff;

    3850:     PetscSectionGetDof(globalCoarse,p,&dof);
    3851:     PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
    3852:     if ((dof - cdof) <= 0) continue;
    3853:     PetscSectionGetOffset(globalCoarse,p,&gOff);

    3855:     rowOffsets[0] = 0;
    3856:     offsetsCopy[0] = 0;
    3857:     if (numFields) {
    3858:       PetscInt f;

    3860:       for (f = 0; f < numFields; f++) {
    3861:         PetscInt fDof;
    3862:         PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
    3863:         rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f];
    3864:       }
    3865:       indicesPointFields_private(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);
    3866:     }
    3867:     else {
    3868:       indicesPoint_private(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);
    3869:       rowOffsets[1] = offsetsCopy[0];
    3870:     }

    3872:     PetscSectionGetDof(multiRootSec,p,&numLeaves);
    3873:     PetscSectionGetOffset(multiRootSec,p,&leafStart);
    3874:     leafEnd = leafStart + numLeaves;
    3875:     for (l = leafStart; l < leafEnd; l++) {
    3876:       PetscInt numIndices, childId, offset;
    3877:       const PetscInt *childIndices;

    3879:       PetscSectionGetDof(rootIndicesSec,l,&numIndices);
    3880:       PetscSectionGetOffset(rootIndicesSec,l,&offset);
    3881:       childId = rootIndices[offset++];
    3882:       childIndices = &rootIndices[offset];
    3883:       numIndices--;

    3885:       if (childId == -1) { /* equivalent points: scatter */
    3886:         PetscInt i;

    3888:         for (i = 0; i < numIndices; i++) {
    3889:           MatSetValue(mat,parentIndices[i],childIndices[i],1.,INSERT_VALUES);
    3890:         }
    3891:       }
    3892:       else {
    3893:         PetscInt parentId, f, lim;

    3895:         DMPlexGetTreeParent(refTree,childId,&parentId,NULL);

    3897:         lim = PetscMax(1,numFields);
    3898:         offsets[0] = 0;
    3899:         if (numFields) {
    3900:           PetscInt f;

    3902:           for (f = 0; f < numFields; f++) {
    3903:             PetscInt fDof;
    3904:             PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);

    3906:             offsets[f + 1] = fDof + offsets[f];
    3907:           }
    3908:         }
    3909:         else {
    3910:           PetscInt cDof;

    3912:           PetscSectionGetDof(cSecRef,childId,&cDof);
    3913:           offsets[1] = cDof;
    3914:         }
    3915:         for (f = 0; f < lim; f++) {
    3916:           PetscScalar    *childMat   = &childrenMats[childId - pRefStart][f][0];
    3917:           PetscInt       *rowIndices = &parentIndices[rowOffsets[f]];
    3918:           const PetscInt *colIndices = &childIndices[offsets[f]];

    3920:           MatSetValues(mat,rowOffsets[f+1]-rowOffsets[f],rowIndices,offsets[f+1]-offsets[f],colIndices,childMat,INSERT_VALUES);
    3921:         }
    3922:       }
    3923:     }
    3924:   }
    3925:   PetscSectionDestroy(&multiRootSec);
    3926:   PetscSectionDestroy(&rootIndicesSec);
    3927:   PetscFree(parentIndices);
    3928:   DMPlexReferenceTreeRestoreChildrenMatrices_Injection(refTree,injRef,&childrenMats);
    3929:   PetscFree(rootIndices);
    3930:   PetscFree3(offsets,offsetsCopy,rowOffsets);

    3932:   MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);
    3933:   MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);
    3934:   return(0);
    3935: }