Actual source code: plextree.c
petsc-3.10.5 2019-03-28
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      1:  #include <petsc/private/dmpleximpl.h>
      2:  #include <petsc/private/isimpl.h>
      3:  #include <petsc/private/petscfeimpl.h>
      4:  #include <petscsf.h>
      5:  #include <petscds.h>

      7: /** hierarchy routines */

      9: /*@
     10:   DMPlexSetReferenceTree - set the reference tree for hierarchically non-conforming meshes.

     12:   Not collective

     14:   Input Parameters:
     15: + dm - The DMPlex object
     16: - ref - The reference tree DMPlex object

     18:   Level: intermediate

     20: .seealso: DMPlexGetReferenceTree(), DMPlexCreateDefaultReferenceTree()
     21: @*/
     22: PetscErrorCode DMPlexSetReferenceTree(DM dm, DM ref)
     23: {
     24:   DM_Plex        *mesh = (DM_Plex *)dm->data;
     25:   PetscErrorCode  ierr;

     30:   PetscObjectReference((PetscObject)ref);
     31:   DMDestroy(&mesh->referenceTree);
     32:   mesh->referenceTree = ref;
     33:   return(0);
     34: }

     36: /*@
     37:   DMPlexGetReferenceTree - get the reference tree for hierarchically non-conforming meshes.

     39:   Not collective

     41:   Input Parameters:
     42: . dm - The DMPlex object

     44:   Output Parameters
     45: . ref - The reference tree DMPlex object

     47:   Level: intermediate

     49: .seealso: DMPlexSetReferenceTree(), DMPlexCreateDefaultReferenceTree()
     50: @*/
     51: PetscErrorCode DMPlexGetReferenceTree(DM dm, DM *ref)
     52: {
     53:   DM_Plex        *mesh = (DM_Plex *)dm->data;

     58:   *ref = mesh->referenceTree;
     59:   return(0);
     60: }

     62: static PetscErrorCode DMPlexReferenceTreeGetChildSymmetry_Default(DM dm, PetscInt parent, PetscInt parentOrientA, PetscInt childOrientA, PetscInt childA, PetscInt parentOrientB, PetscInt *childOrientB, PetscInt *childB)
     63: {
     64:   PetscInt       coneSize, dStart, dEnd, dim, ABswap, oAvert, oBvert, ABswapVert;

     68:   if (parentOrientA == parentOrientB) {
     69:     if (childOrientB) *childOrientB = childOrientA;
     70:     if (childB) *childB = childA;
     71:     return(0);
     72:   }
     73:   for (dim = 0; dim < 3; dim++) {
     74:     DMPlexGetDepthStratum(dm,dim,&dStart,&dEnd);
     75:     if (parent >= dStart && parent <= dEnd) {
     76:       break;
     77:     }
     78:   }
     79:   if (dim > 2) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot perform child symmetry for %d-cells",dim);
     80:   if (!dim) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"A vertex has no children");
     81:   if (childA < dStart || childA >= dEnd) {
     82:     /* this is a lower-dimensional child: bootstrap */
     83:     PetscInt size, i, sA = -1, sB, sOrientB, sConeSize;
     84:     const PetscInt *supp, *coneA, *coneB, *oA, *oB;

     86:     DMPlexGetSupportSize(dm,childA,&size);
     87:     DMPlexGetSupport(dm,childA,&supp);

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

     93:       sA   = supp[i];
     94:       if (sA == parent) continue;
     95:       DMPlexGetTreeParent(dm,sA,&sParent,NULL);
     96:       if (sParent == parent) {
     97:         break;
     98:       }
     99:     }
    100:     if (i == size) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"could not find support in children");
    101:     /* find out which point sB is in an equivalent position to sA under
    102:      * parentOrientB */
    103:     DMPlexReferenceTreeGetChildSymmetry_Default(dm,parent,parentOrientA,0,sA,parentOrientB,&sOrientB,&sB);
    104:     DMPlexGetConeSize(dm,sA,&sConeSize);
    105:     DMPlexGetCone(dm,sA,&coneA);
    106:     DMPlexGetCone(dm,sB,&coneB);
    107:     DMPlexGetConeOrientation(dm,sA,&oA);
    108:     DMPlexGetConeOrientation(dm,sB,&oB);
    109:     /* step through the cone of sA in natural order */
    110:     for (i = 0; i < sConeSize; i++) {
    111:       if (coneA[i] == childA) {
    112:         /* if childA is at position i in coneA,
    113:          * then we want the point that is at sOrientB*i in coneB */
    114:         PetscInt j = (sOrientB >= 0) ? ((sOrientB + i) % sConeSize) : ((sConeSize -(sOrientB+1) - i) % sConeSize);
    115:         if (childB) *childB = coneB[j];
    116:         if (childOrientB) {
    117:           PetscInt oBtrue;

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

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

    170:       posB = (ABswapVert >= 0) ? ((ABswapVert + posA) % coneSize) : ((coneSize -(ABswapVert + 1) - posA) % coneSize);
    171:       if (childB) *childB = children[posB];
    172:     }
    173:   }
    174:   if (childOrientB) *childOrientB = DihedralCompose(coneSize,childOrientA,ABswap);
    175:   return(0);
    176: }

    178: /*@
    179:   DMPlexReferenceTreeGetChildSymmetry - Given a reference tree, transform a childid and orientation from one parent frame to another

    181:   Input Parameters:
    182: + dm - the reference tree DMPlex object
    183: . parent - the parent point
    184: . parentOrientA - the reference orientation for describing the parent
    185: . childOrientA - the reference orientation for describing the child
    186: . childA - the reference childID for describing the child
    187: - parentOrientB - the new orientation for describing the parent

    189:   Output Parameters:
    190: + childOrientB - if not NULL, set to the new oreintation for describing the child
    191: - childB - if not NULL, the new childID for describing the child

    193:   Level: developer

    195: .seealso: DMPlexGetReferenceTree(), DMPlexSetReferenceTree(), DMPlexSetTree()
    196: @*/
    197: PetscErrorCode DMPlexReferenceTreeGetChildSymmetry(DM dm, PetscInt parent, PetscInt parentOrientA, PetscInt childOrientA, PetscInt childA, PetscInt parentOrientB, PetscInt *childOrientB, PetscInt *childB)
    198: {
    199:   DM_Plex        *mesh = (DM_Plex *)dm->data;

    204:   if (!mesh->getchildsymmetry) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"DMPlexReferenceTreeGetChildSymmetry not implemented");
    205:   mesh->getchildsymmetry(dm,parent,parentOrientA,childOrientA,childA,parentOrientB,childOrientB,childB);
    206:   return(0);
    207: }

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

    211: PetscErrorCode DMPlexCreateReferenceTree_Union(DM K, DM Kref, const char *labelName, DM *ref)
    212: {
    213:   MPI_Comm       comm;
    214:   PetscInt       dim, p, pStart, pEnd, pRefStart, pRefEnd, d, offset, parentSize, *parents, *childIDs;
    215:   PetscInt      *permvals, *unionCones, *coneSizes, *unionOrientations, numUnionPoints, *numDimPoints, numCones, numVerts;
    216:   DMLabel        identity, identityRef;
    217:   PetscSection   unionSection, unionConeSection, parentSection;
    218:   PetscScalar   *unionCoords;
    219:   IS             perm;

    223:   comm = PetscObjectComm((PetscObject)K);
    224:   DMGetDimension(K, &dim);
    225:   DMPlexGetChart(K, &pStart, &pEnd);
    226:   DMGetLabel(K, labelName, &identity);
    227:   DMGetLabel(Kref, labelName, &identityRef);
    228:   DMPlexGetChart(Kref, &pRefStart, &pRefEnd);
    229:   PetscSectionCreate(comm, &unionSection);
    230:   PetscSectionSetChart(unionSection, 0, (pEnd - pStart) + (pRefEnd - pRefStart));
    231:   /* count points that will go in the union */
    232:   for (p = pStart; p < pEnd; p++) {
    233:     PetscSectionSetDof(unionSection, p - pStart, 1);
    234:   }
    235:   for (p = pRefStart; p < pRefEnd; p++) {
    236:     PetscInt q, qSize;
    237:     DMLabelGetValue(identityRef, p, &q);
    238:     DMLabelGetStratumSize(identityRef, q, &qSize);
    239:     if (qSize > 1) {
    240:       PetscSectionSetDof(unionSection, p - pRefStart + (pEnd - pStart), 1);
    241:     }
    242:   }
    243:   PetscMalloc1(pEnd - pStart + pRefEnd - pRefStart,&permvals);
    244:   offset = 0;
    245:   /* stratify points in the union by topological dimension */
    246:   for (d = 0; d <= dim; d++) {
    247:     PetscInt cStart, cEnd, c;

    249:     DMPlexGetHeightStratum(K, d, &cStart, &cEnd);
    250:     for (c = cStart; c < cEnd; c++) {
    251:       permvals[offset++] = c;
    252:     }

    254:     DMPlexGetHeightStratum(Kref, d, &cStart, &cEnd);
    255:     for (c = cStart; c < cEnd; c++) {
    256:       permvals[offset++] = c + (pEnd - pStart);
    257:     }
    258:   }
    259:   ISCreateGeneral(comm, (pEnd - pStart) + (pRefEnd - pRefStart), permvals, PETSC_OWN_POINTER, &perm);
    260:   PetscSectionSetPermutation(unionSection,perm);
    261:   PetscSectionSetUp(unionSection);
    262:   PetscSectionGetStorageSize(unionSection,&numUnionPoints);
    263:   PetscMalloc2(numUnionPoints,&coneSizes,dim+1,&numDimPoints);
    264:   /* count dimension points */
    265:   for (d = 0; d <= dim; d++) {
    266:     PetscInt cStart, cOff, cOff2;
    267:     DMPlexGetHeightStratum(K,d,&cStart,NULL);
    268:     PetscSectionGetOffset(unionSection,cStart-pStart,&cOff);
    269:     if (d < dim) {
    270:       DMPlexGetHeightStratum(K,d+1,&cStart,NULL);
    271:       PetscSectionGetOffset(unionSection,cStart-pStart,&cOff2);
    272:     }
    273:     else {
    274:       cOff2 = numUnionPoints;
    275:     }
    276:     numDimPoints[dim - d] = cOff2 - cOff;
    277:   }
    278:   PetscSectionCreate(comm, &unionConeSection);
    279:   PetscSectionSetChart(unionConeSection, 0, numUnionPoints);
    280:   /* count the cones in the union */
    281:   for (p = pStart; p < pEnd; p++) {
    282:     PetscInt dof, uOff;

    284:     DMPlexGetConeSize(K, p, &dof);
    285:     PetscSectionGetOffset(unionSection, p - pStart,&uOff);
    286:     PetscSectionSetDof(unionConeSection, uOff, dof);
    287:     coneSizes[uOff] = dof;
    288:   }
    289:   for (p = pRefStart; p < pRefEnd; p++) {
    290:     PetscInt dof, uDof, uOff;

    292:     DMPlexGetConeSize(Kref, p, &dof);
    293:     PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);
    294:     PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);
    295:     if (uDof) {
    296:       PetscSectionSetDof(unionConeSection, uOff, dof);
    297:       coneSizes[uOff] = dof;
    298:     }
    299:   }
    300:   PetscSectionSetUp(unionConeSection);
    301:   PetscSectionGetStorageSize(unionConeSection,&numCones);
    302:   PetscMalloc2(numCones,&unionCones,numCones,&unionOrientations);
    303:   /* write the cones in the union */
    304:   for (p = pStart; p < pEnd; p++) {
    305:     PetscInt dof, uOff, c, cOff;
    306:     const PetscInt *cone, *orientation;

    308:     DMPlexGetConeSize(K, p, &dof);
    309:     DMPlexGetCone(K, p, &cone);
    310:     DMPlexGetConeOrientation(K, p, &orientation);
    311:     PetscSectionGetOffset(unionSection, p - pStart,&uOff);
    312:     PetscSectionGetOffset(unionConeSection,uOff,&cOff);
    313:     for (c = 0; c < dof; c++) {
    314:       PetscInt e, eOff;
    315:       e                           = cone[c];
    316:       PetscSectionGetOffset(unionSection, e - pStart, &eOff);
    317:       unionCones[cOff + c]        = eOff;
    318:       unionOrientations[cOff + c] = orientation[c];
    319:     }
    320:   }
    321:   for (p = pRefStart; p < pRefEnd; p++) {
    322:     PetscInt dof, uDof, uOff, c, cOff;
    323:     const PetscInt *cone, *orientation;

    325:     DMPlexGetConeSize(Kref, p, &dof);
    326:     DMPlexGetCone(Kref, p, &cone);
    327:     DMPlexGetConeOrientation(Kref, p, &orientation);
    328:     PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);
    329:     PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);
    330:     if (uDof) {
    331:       PetscSectionGetOffset(unionConeSection,uOff,&cOff);
    332:       for (c = 0; c < dof; c++) {
    333:         PetscInt e, eOff, eDof;

    335:         e    = cone[c];
    336:         PetscSectionGetDof(unionSection, e - pRefStart + (pEnd - pStart),&eDof);
    337:         if (eDof) {
    338:           PetscSectionGetOffset(unionSection, e - pRefStart + (pEnd - pStart), &eOff);
    339:         }
    340:         else {
    341:           DMLabelGetValue(identityRef, e, &e);
    342:           PetscSectionGetOffset(unionSection, e - pStart, &eOff);
    343:         }
    344:         unionCones[cOff + c]        = eOff;
    345:         unionOrientations[cOff + c] = orientation[c];
    346:       }
    347:     }
    348:   }
    349:   /* get the coordinates */
    350:   {
    351:     PetscInt vStart, vEnd, vRefStart, vRefEnd, v, vDof, vOff;
    352:     PetscSection KcoordsSec, KrefCoordsSec;
    353:     Vec      KcoordsVec, KrefCoordsVec;
    354:     PetscScalar *Kcoords;

    356:     DMGetCoordinateSection(K, &KcoordsSec);
    357:     DMGetCoordinatesLocal(K, &KcoordsVec);
    358:     DMGetCoordinateSection(Kref, &KrefCoordsSec);
    359:     DMGetCoordinatesLocal(Kref, &KrefCoordsVec);

    361:     numVerts = numDimPoints[0];
    362:     PetscMalloc1(numVerts * dim,&unionCoords);
    363:     DMPlexGetDepthStratum(K,0,&vStart,&vEnd);

    365:     offset = 0;
    366:     for (v = vStart; v < vEnd; v++) {
    367:       PetscSectionGetOffset(unionSection,v - pStart,&vOff);
    368:       VecGetValuesSection(KcoordsVec, KcoordsSec, v, &Kcoords);
    369:       for (d = 0; d < dim; d++) {
    370:         unionCoords[offset * dim + d] = Kcoords[d];
    371:       }
    372:       offset++;
    373:     }
    374:     DMPlexGetDepthStratum(Kref,0,&vRefStart,&vRefEnd);
    375:     for (v = vRefStart; v < vRefEnd; v++) {
    376:       PetscSectionGetDof(unionSection,v - pRefStart + (pEnd - pStart),&vDof);
    377:       PetscSectionGetOffset(unionSection,v - pRefStart + (pEnd - pStart),&vOff);
    378:       VecGetValuesSection(KrefCoordsVec, KrefCoordsSec, v, &Kcoords);
    379:       if (vDof) {
    380:         for (d = 0; d < dim; d++) {
    381:           unionCoords[offset * dim + d] = Kcoords[d];
    382:         }
    383:         offset++;
    384:       }
    385:     }
    386:   }
    387:   DMCreate(comm,ref);
    388:   DMSetType(*ref,DMPLEX);
    389:   DMSetDimension(*ref,dim);
    390:   DMPlexCreateFromDAG(*ref,dim,numDimPoints,coneSizes,unionCones,unionOrientations,unionCoords);
    391:   /* set the tree */
    392:   PetscSectionCreate(comm,&parentSection);
    393:   PetscSectionSetChart(parentSection,0,numUnionPoints);
    394:   for (p = pRefStart; p < pRefEnd; p++) {
    395:     PetscInt uDof, uOff;

    397:     PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);
    398:     PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);
    399:     if (uDof) {
    400:       PetscSectionSetDof(parentSection,uOff,1);
    401:     }
    402:   }
    403:   PetscSectionSetUp(parentSection);
    404:   PetscSectionGetStorageSize(parentSection,&parentSize);
    405:   PetscMalloc2(parentSize,&parents,parentSize,&childIDs);
    406:   for (p = pRefStart; p < pRefEnd; p++) {
    407:     PetscInt uDof, uOff;

    409:     PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);
    410:     PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);
    411:     if (uDof) {
    412:       PetscInt pOff, parent, parentU;
    413:       PetscSectionGetOffset(parentSection,uOff,&pOff);
    414:       DMLabelGetValue(identityRef,p,&parent);
    415:       PetscSectionGetOffset(unionSection, parent - pStart,&parentU);
    416:       parents[pOff] = parentU;
    417:       childIDs[pOff] = uOff;
    418:     }
    419:   }
    420:   DMPlexSetTree_Internal(*ref,parentSection,parents,childIDs,PETSC_TRUE,PETSC_FALSE);
    421:   PetscSectionDestroy(&parentSection);
    422:   PetscFree2(parents,childIDs);

    424:   /* clean up */
    425:   PetscSectionDestroy(&unionSection);
    426:   PetscSectionDestroy(&unionConeSection);
    427:   ISDestroy(&perm);
    428:   PetscFree(unionCoords);
    429:   PetscFree2(unionCones,unionOrientations);
    430:   PetscFree2(coneSizes,numDimPoints);
    431:   return(0);
    432: }

    434: /*@
    435:   DMPlexCreateDefaultReferenceTree - create a reference tree for isotropic hierarchical mesh refinement.

    437:   Collective on comm

    439:   Input Parameters:
    440: + comm    - the MPI communicator
    441: . dim     - the spatial dimension
    442: - simplex - Flag for simplex, otherwise use a tensor-product cell

    444:   Output Parameters:
    445: . ref     - the reference tree DMPlex object

    447:   Level: intermediate

    449: .keywords: reference cell
    450: .seealso: DMPlexSetReferenceTree(), DMPlexGetReferenceTree()
    451: @*/
    452: PetscErrorCode DMPlexCreateDefaultReferenceTree(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *ref)
    453: {
    454:   DM_Plex       *mesh;
    455:   DM             K, Kref;
    456:   PetscInt       p, pStart, pEnd;
    457:   DMLabel        identity;

    461: #if 1
    462:   comm = PETSC_COMM_SELF;
    463: #endif
    464:   /* create a reference element */
    465:   DMPlexCreateReferenceCell(comm, dim, simplex, &K);
    466:   DMCreateLabel(K, "identity");
    467:   DMGetLabel(K, "identity", &identity);
    468:   DMPlexGetChart(K, &pStart, &pEnd);
    469:   for (p = pStart; p < pEnd; p++) {
    470:     DMLabelSetValue(identity, p, p);
    471:   }
    472:   /* refine it */
    473:   DMRefine(K,comm,&Kref);

    475:   /* the reference tree is the union of these two, without duplicating
    476:    * points that appear in both */
    477:   DMPlexCreateReferenceTree_Union(K, Kref, "identity", ref);
    478:   mesh = (DM_Plex *) (*ref)->data;
    479:   mesh->getchildsymmetry = DMPlexReferenceTreeGetChildSymmetry_Default;
    480:   DMDestroy(&K);
    481:   DMDestroy(&Kref);
    482:   return(0);
    483: }

    485: static PetscErrorCode DMPlexTreeSymmetrize(DM dm)
    486: {
    487:   DM_Plex        *mesh = (DM_Plex *)dm->data;
    488:   PetscSection   childSec, pSec;
    489:   PetscInt       p, pSize, cSize, parMax = PETSC_MIN_INT, parMin = PETSC_MAX_INT;
    490:   PetscInt       *offsets, *children, pStart, pEnd;

    495:   PetscSectionDestroy(&mesh->childSection);
    496:   PetscFree(mesh->children);
    497:   pSec = mesh->parentSection;
    498:   if (!pSec) return(0);
    499:   PetscSectionGetStorageSize(pSec,&pSize);
    500:   for (p = 0; p < pSize; p++) {
    501:     PetscInt par = mesh->parents[p];

    503:     parMax = PetscMax(parMax,par+1);
    504:     parMin = PetscMin(parMin,par);
    505:   }
    506:   if (parMin > parMax) {
    507:     parMin = -1;
    508:     parMax = -1;
    509:   }
    510:   PetscSectionCreate(PetscObjectComm((PetscObject)pSec),&childSec);
    511:   PetscSectionSetChart(childSec,parMin,parMax);
    512:   for (p = 0; p < pSize; p++) {
    513:     PetscInt par = mesh->parents[p];

    515:     PetscSectionAddDof(childSec,par,1);
    516:   }
    517:   PetscSectionSetUp(childSec);
    518:   PetscSectionGetStorageSize(childSec,&cSize);
    519:   PetscMalloc1(cSize,&children);
    520:   PetscCalloc1(parMax-parMin,&offsets);
    521:   PetscSectionGetChart(pSec,&pStart,&pEnd);
    522:   for (p = pStart; p < pEnd; p++) {
    523:     PetscInt dof, off, i;

    525:     PetscSectionGetDof(pSec,p,&dof);
    526:     PetscSectionGetOffset(pSec,p,&off);
    527:     for (i = 0; i < dof; i++) {
    528:       PetscInt par = mesh->parents[off + i], cOff;

    530:       PetscSectionGetOffset(childSec,par,&cOff);
    531:       children[cOff + offsets[par-parMin]++] = p;
    532:     }
    533:   }
    534:   mesh->childSection = childSec;
    535:   mesh->children = children;
    536:   PetscFree(offsets);
    537:   return(0);
    538: }

    540: static PetscErrorCode AnchorsFlatten (PetscSection section, IS is, PetscSection *sectionNew, IS *isNew)
    541: {
    542:   PetscInt       pStart, pEnd, size, sizeNew, i, p, *valsNew = NULL;
    543:   const PetscInt *vals;
    544:   PetscSection   secNew;
    545:   PetscBool      anyNew, globalAnyNew;
    546:   PetscBool      compress;

    550:   PetscSectionGetChart(section,&pStart,&pEnd);
    551:   ISGetLocalSize(is,&size);
    552:   ISGetIndices(is,&vals);
    553:   PetscSectionCreate(PetscObjectComm((PetscObject)section),&secNew);
    554:   PetscSectionSetChart(secNew,pStart,pEnd);
    555:   for (i = 0; i < size; i++) {
    556:     PetscInt dof;

    558:     p = vals[i];
    559:     if (p < pStart || p >= pEnd) continue;
    560:     PetscSectionGetDof(section, p, &dof);
    561:     if (dof) break;
    562:   }
    563:   if (i == size) {
    564:     PetscSectionSetUp(secNew);
    565:     anyNew   = PETSC_FALSE;
    566:     compress = PETSC_FALSE;
    567:     sizeNew  = 0;
    568:   }
    569:   else {
    570:     anyNew = PETSC_TRUE;
    571:     for (p = pStart; p < pEnd; p++) {
    572:       PetscInt dof, off;

    574:       PetscSectionGetDof(section, p, &dof);
    575:       PetscSectionGetOffset(section, p, &off);
    576:       for (i = 0; i < dof; i++) {
    577:         PetscInt q = vals[off + i], qDof = 0;

    579:         if (q >= pStart && q < pEnd) {
    580:           PetscSectionGetDof(section, q, &qDof);
    581:         }
    582:         if (qDof) {
    583:           PetscSectionAddDof(secNew, p, qDof);
    584:         }
    585:         else {
    586:           PetscSectionAddDof(secNew, p, 1);
    587:         }
    588:       }
    589:     }
    590:     PetscSectionSetUp(secNew);
    591:     PetscSectionGetStorageSize(secNew,&sizeNew);
    592:     PetscMalloc1(sizeNew,&valsNew);
    593:     compress = PETSC_FALSE;
    594:     for (p = pStart; p < pEnd; p++) {
    595:       PetscInt dof, off, count, offNew, dofNew;

    597:       PetscSectionGetDof(section, p, &dof);
    598:       PetscSectionGetOffset(section, p, &off);
    599:       PetscSectionGetDof(secNew, p, &dofNew);
    600:       PetscSectionGetOffset(secNew, p, &offNew);
    601:       count = 0;
    602:       for (i = 0; i < dof; i++) {
    603:         PetscInt q = vals[off + i], qDof = 0, qOff = 0, j;

    605:         if (q >= pStart && q < pEnd) {
    606:           PetscSectionGetDof(section, q, &qDof);
    607:           PetscSectionGetOffset(section, q, &qOff);
    608:         }
    609:         if (qDof) {
    610:           PetscInt oldCount = count;

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

    615:             for (k = 0; k < oldCount; k++) {
    616:               if (valsNew[offNew + k] == r) {
    617:                 break;
    618:               }
    619:             }
    620:             if (k == oldCount) {
    621:               valsNew[offNew + count++] = r;
    622:             }
    623:           }
    624:         }
    625:         else {
    626:           PetscInt k, oldCount = count;

    628:           for (k = 0; k < oldCount; k++) {
    629:             if (valsNew[offNew + k] == q) {
    630:               break;
    631:             }
    632:           }
    633:           if (k == oldCount) {
    634:             valsNew[offNew + count++] = q;
    635:           }
    636:         }
    637:       }
    638:       if (count < dofNew) {
    639:         PetscSectionSetDof(secNew, p, count);
    640:         compress = PETSC_TRUE;
    641:       }
    642:     }
    643:   }
    644:   ISRestoreIndices(is,&vals);
    645:   MPIU_Allreduce(&anyNew,&globalAnyNew,1,MPIU_BOOL,MPI_LOR,PetscObjectComm((PetscObject)secNew));
    646:   if (!globalAnyNew) {
    647:     PetscSectionDestroy(&secNew);
    648:     *sectionNew = NULL;
    649:     *isNew = NULL;
    650:   }
    651:   else {
    652:     PetscBool globalCompress;

    654:     MPIU_Allreduce(&compress,&globalCompress,1,MPIU_BOOL,MPI_LOR,PetscObjectComm((PetscObject)secNew));
    655:     if (compress) {
    656:       PetscSection secComp;
    657:       PetscInt *valsComp = NULL;

    659:       PetscSectionCreate(PetscObjectComm((PetscObject)section),&secComp);
    660:       PetscSectionSetChart(secComp,pStart,pEnd);
    661:       for (p = pStart; p < pEnd; p++) {
    662:         PetscInt dof;

    664:         PetscSectionGetDof(secNew, p, &dof);
    665:         PetscSectionSetDof(secComp, p, dof);
    666:       }
    667:       PetscSectionSetUp(secComp);
    668:       PetscSectionGetStorageSize(secComp,&sizeNew);
    669:       PetscMalloc1(sizeNew,&valsComp);
    670:       for (p = pStart; p < pEnd; p++) {
    671:         PetscInt dof, off, offNew, j;

    673:         PetscSectionGetDof(secNew, p, &dof);
    674:         PetscSectionGetOffset(secNew, p, &off);
    675:         PetscSectionGetOffset(secComp, p, &offNew);
    676:         for (j = 0; j < dof; j++) {
    677:           valsComp[offNew + j] = valsNew[off + j];
    678:         }
    679:       }
    680:       PetscSectionDestroy(&secNew);
    681:       secNew  = secComp;
    682:       PetscFree(valsNew);
    683:       valsNew = valsComp;
    684:     }
    685:     ISCreateGeneral(PetscObjectComm((PetscObject)is),sizeNew,valsNew,PETSC_OWN_POINTER,isNew);
    686:   }
    687:   return(0);
    688: }

    690: static PetscErrorCode DMPlexCreateAnchors_Tree(DM dm)
    691: {
    692:   PetscInt       p, pStart, pEnd, *anchors, size;
    693:   PetscInt       aMin = PETSC_MAX_INT, aMax = PETSC_MIN_INT;
    694:   PetscSection   aSec;
    695:   DMLabel        canonLabel;
    696:   IS             aIS;

    701:   DMPlexGetChart(dm,&pStart,&pEnd);
    702:   DMGetLabel(dm,"canonical",&canonLabel);
    703:   for (p = pStart; p < pEnd; p++) {
    704:     PetscInt parent;

    706:     if (canonLabel) {
    707:       PetscInt canon;

    709:       DMLabelGetValue(canonLabel,p,&canon);
    710:       if (p != canon) continue;
    711:     }
    712:     DMPlexGetTreeParent(dm,p,&parent,NULL);
    713:     if (parent != p) {
    714:       aMin = PetscMin(aMin,p);
    715:       aMax = PetscMax(aMax,p+1);
    716:     }
    717:   }
    718:   if (aMin > aMax) {
    719:     aMin = -1;
    720:     aMax = -1;
    721:   }
    722:   PetscSectionCreate(PETSC_COMM_SELF,&aSec);
    723:   PetscSectionSetChart(aSec,aMin,aMax);
    724:   for (p = aMin; p < aMax; p++) {
    725:     PetscInt parent, ancestor = p;

    727:     if (canonLabel) {
    728:       PetscInt canon;

    730:       DMLabelGetValue(canonLabel,p,&canon);
    731:       if (p != canon) continue;
    732:     }
    733:     DMPlexGetTreeParent(dm,p,&parent,NULL);
    734:     while (parent != ancestor) {
    735:       ancestor = parent;
    736:       DMPlexGetTreeParent(dm,ancestor,&parent,NULL);
    737:     }
    738:     if (ancestor != p) {
    739:       PetscInt closureSize, *closure = NULL;

    741:       DMPlexGetTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);
    742:       PetscSectionSetDof(aSec,p,closureSize);
    743:       DMPlexRestoreTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);
    744:     }
    745:   }
    746:   PetscSectionSetUp(aSec);
    747:   PetscSectionGetStorageSize(aSec,&size);
    748:   PetscMalloc1(size,&anchors);
    749:   for (p = aMin; p < aMax; p++) {
    750:     PetscInt parent, ancestor = p;

    752:     if (canonLabel) {
    753:       PetscInt canon;

    755:       DMLabelGetValue(canonLabel,p,&canon);
    756:       if (p != canon) continue;
    757:     }
    758:     DMPlexGetTreeParent(dm,p,&parent,NULL);
    759:     while (parent != ancestor) {
    760:       ancestor = parent;
    761:       DMPlexGetTreeParent(dm,ancestor,&parent,NULL);
    762:     }
    763:     if (ancestor != p) {
    764:       PetscInt j, closureSize, *closure = NULL, aOff;

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

    768:       DMPlexGetTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);
    769:       for (j = 0; j < closureSize; j++) {
    770:         anchors[aOff + j] = closure[2*j];
    771:       }
    772:       DMPlexRestoreTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);
    773:     }
    774:   }
    775:   ISCreateGeneral(PETSC_COMM_SELF,size,anchors,PETSC_OWN_POINTER,&aIS);
    776:   {
    777:     PetscSection aSecNew = aSec;
    778:     IS           aISNew  = aIS;

    780:     PetscObjectReference((PetscObject)aSec);
    781:     PetscObjectReference((PetscObject)aIS);
    782:     while (aSecNew) {
    783:       PetscSectionDestroy(&aSec);
    784:       ISDestroy(&aIS);
    785:       aSec    = aSecNew;
    786:       aIS     = aISNew;
    787:       aSecNew = NULL;
    788:       aISNew  = NULL;
    789:       AnchorsFlatten(aSec,aIS,&aSecNew,&aISNew);
    790:     }
    791:   }
    792:   DMPlexSetAnchors(dm,aSec,aIS);
    793:   PetscSectionDestroy(&aSec);
    794:   ISDestroy(&aIS);
    795:   return(0);
    796: }

    798: static PetscErrorCode DMPlexGetTrueSupportSize(DM dm,PetscInt p,PetscInt *dof,PetscInt *numTrueSupp)
    799: {

    803:   if (numTrueSupp[p] == -1) {
    804:     PetscInt i, alldof;
    805:     const PetscInt *supp;
    806:     PetscInt count = 0;

    808:     DMPlexGetSupportSize(dm,p,&alldof);
    809:     DMPlexGetSupport(dm,p,&supp);
    810:     for (i = 0; i < alldof; i++) {
    811:       PetscInt q = supp[i], numCones, j;
    812:       const PetscInt *cone;

    814:       DMPlexGetConeSize(dm,q,&numCones);
    815:       DMPlexGetCone(dm,q,&cone);
    816:       for (j = 0; j < numCones; j++) {
    817:         if (cone[j] == p) break;
    818:       }
    819:       if (j < numCones) count++;
    820:     }
    821:     numTrueSupp[p] = count;
    822:   }
    823:   *dof = numTrueSupp[p];
    824:   return(0);
    825: }

    827: static PetscErrorCode DMPlexTreeExchangeSupports(DM dm)
    828: {
    829:   DM_Plex *mesh = (DM_Plex *)dm->data;
    830:   PetscSection newSupportSection;
    831:   PetscInt newSize, *newSupports, pStart, pEnd, p, d, depth;
    832:   PetscInt *numTrueSupp;
    833:   PetscInt *offsets;

    838:   /* symmetrize the hierarchy */
    839:   DMPlexGetDepth(dm,&depth);
    840:   PetscSectionCreate(PetscObjectComm((PetscObject)(mesh->supportSection)),&newSupportSection);
    841:   DMPlexGetChart(dm,&pStart,&pEnd);
    842:   PetscSectionSetChart(newSupportSection,pStart,pEnd);
    843:   PetscCalloc1(pEnd,&offsets);
    844:   PetscMalloc1(pEnd,&numTrueSupp);
    845:   for (p = 0; p < pEnd; p++) numTrueSupp[p] = -1;
    846:   /* if a point is in the (true) support of q, it should be in the support of
    847:    * parent(q) */
    848:   for (d = 0; d <= depth; d++) {
    849:     DMPlexGetHeightStratum(dm,d,&pStart,&pEnd);
    850:     for (p = pStart; p < pEnd; ++p) {
    851:       PetscInt dof, q, qdof, parent;

    853:       DMPlexGetTrueSupportSize(dm,p,&dof,numTrueSupp);
    854:       PetscSectionAddDof(newSupportSection, p, dof);
    855:       q    = p;
    856:       DMPlexGetTreeParent(dm,q,&parent,NULL);
    857:       while (parent != q && parent >= pStart && parent < pEnd) {
    858:         q = parent;

    860:         DMPlexGetTrueSupportSize(dm,q,&qdof,numTrueSupp);
    861:         PetscSectionAddDof(newSupportSection,p,qdof);
    862:         PetscSectionAddDof(newSupportSection,q,dof);
    863:         DMPlexGetTreeParent(dm,q,&parent,NULL);
    864:       }
    865:     }
    866:   }
    867:   PetscSectionSetUp(newSupportSection);
    868:   PetscSectionGetStorageSize(newSupportSection,&newSize);
    869:   PetscMalloc1(newSize,&newSupports);
    870:   for (d = 0; d <= depth; d++) {
    871:     DMPlexGetHeightStratum(dm,d,&pStart,&pEnd);
    872:     for (p = pStart; p < pEnd; p++) {
    873:       PetscInt dof, off, q, qdof, qoff, newDof, newOff, newqOff, i, parent;

    875:       PetscSectionGetDof(mesh->supportSection, p, &dof);
    876:       PetscSectionGetOffset(mesh->supportSection, p, &off);
    877:       PetscSectionGetDof(newSupportSection, p, &newDof);
    878:       PetscSectionGetOffset(newSupportSection, p, &newOff);
    879:       for (i = 0; i < dof; i++) {
    880:         PetscInt numCones, j;
    881:         const PetscInt *cone;
    882:         PetscInt q = mesh->supports[off + i];

    884:         DMPlexGetConeSize(dm,q,&numCones);
    885:         DMPlexGetCone(dm,q,&cone);
    886:         for (j = 0; j < numCones; j++) {
    887:           if (cone[j] == p) break;
    888:         }
    889:         if (j < numCones) newSupports[newOff+offsets[p]++] = q;
    890:       }
    891:       mesh->maxSupportSize = PetscMax(mesh->maxSupportSize,newDof);

    893:       q    = p;
    894:       DMPlexGetTreeParent(dm,q,&parent,NULL);
    895:       while (parent != q && parent >= pStart && parent < pEnd) {
    896:         q = parent;
    897:         PetscSectionGetDof(mesh->supportSection, q, &qdof);
    898:         PetscSectionGetOffset(mesh->supportSection, q, &qoff);
    899:         PetscSectionGetOffset(newSupportSection, q, &newqOff);
    900:         for (i = 0; i < qdof; i++) {
    901:           PetscInt numCones, j;
    902:           const PetscInt *cone;
    903:           PetscInt r = mesh->supports[qoff + i];

    905:           DMPlexGetConeSize(dm,r,&numCones);
    906:           DMPlexGetCone(dm,r,&cone);
    907:           for (j = 0; j < numCones; j++) {
    908:             if (cone[j] == q) break;
    909:           }
    910:           if (j < numCones) newSupports[newOff+offsets[p]++] = r;
    911:         }
    912:         for (i = 0; i < dof; i++) {
    913:           PetscInt numCones, j;
    914:           const PetscInt *cone;
    915:           PetscInt r = mesh->supports[off + i];

    917:           DMPlexGetConeSize(dm,r,&numCones);
    918:           DMPlexGetCone(dm,r,&cone);
    919:           for (j = 0; j < numCones; j++) {
    920:             if (cone[j] == p) break;
    921:           }
    922:           if (j < numCones) newSupports[newqOff+offsets[q]++] = r;
    923:         }
    924:         DMPlexGetTreeParent(dm,q,&parent,NULL);
    925:       }
    926:     }
    927:   }
    928:   PetscSectionDestroy(&mesh->supportSection);
    929:   mesh->supportSection = newSupportSection;
    930:   PetscFree(mesh->supports);
    931:   mesh->supports = newSupports;
    932:   PetscFree(offsets);
    933:   PetscFree(numTrueSupp);

    935:   return(0);
    936: }

    938: static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_Direct(DM,PetscSection,PetscSection,Mat);
    939: static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_FromReference(DM,PetscSection,PetscSection,Mat);

    941: static PetscErrorCode DMPlexSetTree_Internal(DM dm, PetscSection parentSection, PetscInt *parents, PetscInt *childIDs, PetscBool computeCanonical, PetscBool exchangeSupports)
    942: {
    943:   DM_Plex       *mesh = (DM_Plex *)dm->data;
    944:   DM             refTree;
    945:   PetscInt       size;

    951:   PetscObjectReference((PetscObject)parentSection);
    952:   PetscSectionDestroy(&mesh->parentSection);
    953:   mesh->parentSection = parentSection;
    954:   PetscSectionGetStorageSize(parentSection,&size);
    955:   if (parents != mesh->parents) {
    956:     PetscFree(mesh->parents);
    957:     PetscMalloc1(size,&mesh->parents);
    958:     PetscMemcpy(mesh->parents, parents, size * sizeof(*parents));
    959:   }
    960:   if (childIDs != mesh->childIDs) {
    961:     PetscFree(mesh->childIDs);
    962:     PetscMalloc1(size,&mesh->childIDs);
    963:     PetscMemcpy(mesh->childIDs, childIDs, size * sizeof(*childIDs));
    964:   }
    965:   DMPlexGetReferenceTree(dm,&refTree);
    966:   if (refTree) {
    967:     DMLabel canonLabel;

    969:     DMGetLabel(refTree,"canonical",&canonLabel);
    970:     if (canonLabel) {
    971:       PetscInt i;

    973:       for (i = 0; i < size; i++) {
    974:         PetscInt canon;
    975:         DMLabelGetValue(canonLabel, mesh->childIDs[i], &canon);
    976:         if (canon >= 0) {
    977:           mesh->childIDs[i] = canon;
    978:         }
    979:       }
    980:     }
    981:     mesh->computeanchormatrix = DMPlexComputeAnchorMatrix_Tree_FromReference;
    982:   }
    983:   else {
    984:     mesh->computeanchormatrix = DMPlexComputeAnchorMatrix_Tree_Direct;
    985:   }
    986:   DMPlexTreeSymmetrize(dm);
    987:   if (computeCanonical) {
    988:     PetscInt d, dim;

    990:     /* add the canonical label */
    991:     DMGetDimension(dm,&dim);
    992:     DMCreateLabel(dm,"canonical");
    993:     for (d = 0; d <= dim; d++) {
    994:       PetscInt p, dStart, dEnd, canon = -1, cNumChildren;
    995:       const PetscInt *cChildren;

    997:       DMPlexGetDepthStratum(dm,d,&dStart,&dEnd);
    998:       for (p = dStart; p < dEnd; p++) {
    999:         DMPlexGetTreeChildren(dm,p,&cNumChildren,&cChildren);
    1000:         if (cNumChildren) {
    1001:           canon = p;
    1002:           break;
    1003:         }
    1004:       }
    1005:       if (canon == -1) continue;
    1006:       for (p = dStart; p < dEnd; p++) {
    1007:         PetscInt numChildren, i;
    1008:         const PetscInt *children;

    1010:         DMPlexGetTreeChildren(dm,p,&numChildren,&children);
    1011:         if (numChildren) {
    1012:           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);
    1013:           DMSetLabelValue(dm,"canonical",p,canon);
    1014:           for (i = 0; i < numChildren; i++) {
    1015:             DMSetLabelValue(dm,"canonical",children[i],cChildren[i]);
    1016:           }
    1017:         }
    1018:       }
    1019:     }
    1020:   }
    1021:   if (exchangeSupports) {
    1022:     DMPlexTreeExchangeSupports(dm);
    1023:   }
    1024:   mesh->createanchors = DMPlexCreateAnchors_Tree;
    1025:   /* reset anchors */
    1026:   DMPlexSetAnchors(dm,NULL,NULL);
    1027:   return(0);
    1028: }

    1030: /*@
    1031:   DMPlexSetTree - set the tree that describes the hierarchy of non-conforming mesh points.  This routine also creates
    1032:   the point-to-point constraints determined by the tree: a point is constained to the points in the closure of its
    1033:   tree root.

    1035:   Collective on dm

    1037:   Input Parameters:
    1038: + dm - the DMPlex object
    1039: . parentSection - a section describing the tree: a point has a parent if it has 1 dof in the section; the section
    1040:                   offset indexes the parent and childID list; the reference count of parentSection is incremented
    1041: . parents - a list of the point parents; copied, can be destroyed
    1042: - childIDs - identifies the relationship of the child point to the parent point; if there is a reference tree, then
    1043:              the child corresponds to the point in the reference tree with index childIDs; copied, can be destroyed

    1045:   Level: intermediate

    1047: .seealso: DMPlexGetTree(), DMPlexSetReferenceTree(), DMPlexSetAnchors(), DMPlexGetTreeParent(), DMPlexGetTreeChildren()
    1048: @*/
    1049: PetscErrorCode DMPlexSetTree(DM dm, PetscSection parentSection, PetscInt parents[], PetscInt childIDs[])
    1050: {

    1054:   DMPlexSetTree_Internal(dm,parentSection,parents,childIDs,PETSC_FALSE,PETSC_TRUE);
    1055:   return(0);
    1056: }

    1058: /*@
    1059:   DMPlexGetTree - get the tree that describes the hierarchy of non-conforming mesh points.
    1060:   Collective on dm

    1062:   Input Parameters:
    1063: . dm - the DMPlex object

    1065:   Output Parameters:
    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
    1068: . parents - a list of the point parents
    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 childID
    1071: . childSection - the inverse of the parent section
    1072: - children - a list of the point children

    1074:   Level: intermediate

    1076: .seealso: DMPlexSetTree(), DMPlexSetReferenceTree(), DMPlexSetAnchors(), DMPlexGetTreeParent(), DMPlexGetTreeChildren()
    1077: @*/
    1078: PetscErrorCode DMPlexGetTree(DM dm, PetscSection *parentSection, PetscInt *parents[], PetscInt *childIDs[], PetscSection *childSection, PetscInt *children[])
    1079: {
    1080:   DM_Plex        *mesh = (DM_Plex *)dm->data;

    1084:   if (parentSection) *parentSection = mesh->parentSection;
    1085:   if (parents)       *parents       = mesh->parents;
    1086:   if (childIDs)      *childIDs      = mesh->childIDs;
    1087:   if (childSection)  *childSection  = mesh->childSection;
    1088:   if (children)      *children      = mesh->children;
    1089:   return(0);
    1090: }

    1092: /*@
    1093:   DMPlexGetTreeParent - get the parent of a point in the tree describing the point hierarchy (not the DAG)

    1095:   Input Parameters:
    1096: + dm - the DMPlex object
    1097: - point - the query point

    1099:   Output Parameters:
    1100: + parent - if not NULL, set to the parent of the point, or the point itself if the point does not have a parent
    1101: - childID - if not NULL, set to the child ID of the point with respect to its parent, or 0 if the point
    1102:             does not have a parent

    1104:   Level: intermediate

    1106: .seealso: DMPlexSetTree(), DMPlexGetTree(), DMPlexGetTreeChildren()
    1107: @*/
    1108: PetscErrorCode DMPlexGetTreeParent(DM dm, PetscInt point, PetscInt *parent, PetscInt *childID)
    1109: {
    1110:   DM_Plex       *mesh = (DM_Plex *)dm->data;
    1111:   PetscSection   pSec;

    1116:   pSec = mesh->parentSection;
    1117:   if (pSec && point >= pSec->pStart && point < pSec->pEnd) {
    1118:     PetscInt dof;

    1120:     PetscSectionGetDof (pSec, point, &dof);
    1121:     if (dof) {
    1122:       PetscInt off;

    1124:       PetscSectionGetOffset (pSec, point, &off);
    1125:       if (parent)  *parent = mesh->parents[off];
    1126:       if (childID) *childID = mesh->childIDs[off];
    1127:       return(0);
    1128:     }
    1129:   }
    1130:   if (parent) {
    1131:     *parent = point;
    1132:   }
    1133:   if (childID) {
    1134:     *childID = 0;
    1135:   }
    1136:   return(0);
    1137: }

    1139: /*@C
    1140:   DMPlexGetTreeChildren - get the children of a point in the tree describing the point hierarchy (not the DAG)

    1142:   Input Parameters:
    1143: + dm - the DMPlex object
    1144: - point - the query point

    1146:   Output Parameters:
    1147: + numChildren - if not NULL, set to the number of children
    1148: - children - if not NULL, set to a list children, or set to NULL if the point has no children

    1150:   Level: intermediate

    1152:   Fortran Notes:
    1153:   Since it returns an array, this routine is only available in Fortran 90, and you must
    1154:   include petsc.h90 in your code.

    1156: .seealso: DMPlexSetTree(), DMPlexGetTree(), DMPlexGetTreeParent()
    1157: @*/
    1158: PetscErrorCode DMPlexGetTreeChildren(DM dm, PetscInt point, PetscInt *numChildren, const PetscInt *children[])
    1159: {
    1160:   DM_Plex       *mesh = (DM_Plex *)dm->data;
    1161:   PetscSection   childSec;
    1162:   PetscInt       dof = 0;

    1167:   childSec = mesh->childSection;
    1168:   if (childSec && point >= childSec->pStart && point < childSec->pEnd) {
    1169:     PetscSectionGetDof (childSec, point, &dof);
    1170:   }
    1171:   if (numChildren) *numChildren = dof;
    1172:   if (children) {
    1173:     if (dof) {
    1174:       PetscInt off;

    1176:       PetscSectionGetOffset (childSec, point, &off);
    1177:       *children = &mesh->children[off];
    1178:     }
    1179:     else {
    1180:       *children = NULL;
    1181:     }
    1182:   }
    1183:   return(0);
    1184: }

    1186: static PetscErrorCode EvaluateBasis(PetscSpace space, PetscInt nBasis, PetscInt nFunctionals, PetscInt nComps, PetscInt nPoints, const PetscInt *pointsPerFn, const PetscReal *points, const PetscReal *weights, PetscReal *work, Mat basisAtPoints)
    1187: {
    1188:   PetscInt       f, b, p, c, offset, qPoints;

    1192:   PetscSpaceEvaluate(space,nPoints,points,work,NULL,NULL);
    1193:   for (f = 0, offset = 0; f < nFunctionals; f++) {
    1194:     qPoints = pointsPerFn[f];
    1195:     for (b = 0; b < nBasis; b++) {
    1196:       PetscScalar val = 0.;

    1198:       for (p = 0; p < qPoints; p++) {
    1199:         for (c = 0; c < nComps; c++) {
    1200:           val += work[((offset + p) * nBasis + b) * nComps + c] * weights[(offset + p) * nComps + c];
    1201:         }
    1202:       }
    1203:       MatSetValue(basisAtPoints,b,f,val,INSERT_VALUES);
    1204:     }
    1205:     offset += qPoints;
    1206:   }
    1207:   MatAssemblyBegin(basisAtPoints,MAT_FINAL_ASSEMBLY);
    1208:   MatAssemblyEnd(basisAtPoints,MAT_FINAL_ASSEMBLY);
    1209:   return(0);
    1210: }

    1212: static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_Direct(DM dm, PetscSection section, PetscSection cSec, Mat cMat)
    1213: {
    1214:   PetscDS        ds;
    1215:   PetscInt       spdim;
    1216:   PetscInt       numFields, f, c, cStart, cEnd, pStart, pEnd, conStart, conEnd;
    1217:   const PetscInt *anchors;
    1218:   PetscSection   aSec;
    1219:   PetscReal      *v0, *v0parent, *vtmp, *J, *Jparent, *invJparent, detJ, detJparent;
    1220:   IS             aIS;

    1224:   DMPlexGetChart(dm,&pStart,&pEnd);
    1225:   DMGetDS(dm,&ds);
    1226:   PetscDSGetNumFields(ds,&numFields);
    1227:   DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);
    1228:   DMPlexGetAnchors(dm,&aSec,&aIS);
    1229:   ISGetIndices(aIS,&anchors);
    1230:   PetscSectionGetChart(cSec,&conStart,&conEnd);
    1231:   DMGetDimension(dm,&spdim);
    1232:   PetscMalloc6(spdim,&v0,spdim,&v0parent,spdim,&vtmp,spdim*spdim,&J,spdim*spdim,&Jparent,spdim*spdim,&invJparent);

    1234:   for (f = 0; f < numFields; f++) {
    1235:     PetscObject disc;
    1236:     PetscClassId id;
    1237:     PetscSpace     bspace;
    1238:     PetscDualSpace dspace;
    1239:     PetscInt i, j, k, nPoints, Nc, offset;
    1240:     PetscInt fSize, maxDof;
    1241:     PetscReal   *weights, *pointsRef, *pointsReal, *work;
    1242:     PetscScalar *scwork, *X;
    1243:     PetscInt  *sizes, *workIndRow, *workIndCol;
    1244:     Mat Amat, Bmat, Xmat;
    1245:     const PetscInt    *numDof  = NULL;
    1246:     const PetscInt    ***perms = NULL;
    1247:     const PetscScalar ***flips = NULL;

    1249:     PetscDSGetDiscretization(ds,f,&disc);
    1250:     PetscObjectGetClassId(disc,&id);
    1251:     if (id == PETSCFE_CLASSID) {
    1252:       PetscFE fe = (PetscFE) disc;

    1254:       PetscFEGetBasisSpace(fe,&bspace);
    1255:       PetscFEGetDualSpace(fe,&dspace);
    1256:       PetscDualSpaceGetDimension(dspace,&fSize);
    1257:       PetscFEGetNumComponents(fe,&Nc);
    1258:     }
    1259:     else if (id == PETSCFV_CLASSID) {
    1260:       PetscFV fv = (PetscFV) disc;

    1262:       PetscFVGetNumComponents(fv,&Nc);
    1263:       PetscSpaceCreate(PetscObjectComm((PetscObject)fv),&bspace);
    1264:       PetscSpaceSetType(bspace,PETSCSPACEPOLYNOMIAL);
    1265:       PetscSpaceSetDegree(bspace,0,PETSC_DETERMINE);
    1266:       PetscSpaceSetNumComponents(bspace,Nc);
    1267:       PetscSpaceSetNumVariables(bspace,spdim);
    1268:       PetscSpaceSetUp(bspace);
    1269:       PetscFVGetDualSpace(fv,&dspace);
    1270:       PetscDualSpaceGetDimension(dspace,&fSize);
    1271:     }
    1272:     else SETERRQ1(PetscObjectComm(disc),PETSC_ERR_ARG_UNKNOWN_TYPE, "PetscDS discretization id %d not recognized.", id);
    1273:     PetscDualSpaceGetNumDof(dspace,&numDof);
    1274:     for (i = 0, maxDof = 0; i <= spdim; i++) {maxDof = PetscMax(maxDof,numDof[i]);}
    1275:     PetscDualSpaceGetSymmetries(dspace,&perms,&flips);

    1277:     MatCreate(PETSC_COMM_SELF,&Amat);
    1278:     MatSetSizes(Amat,fSize,fSize,fSize,fSize);
    1279:     MatSetType(Amat,MATSEQDENSE);
    1280:     MatSetUp(Amat);
    1281:     MatDuplicate(Amat,MAT_DO_NOT_COPY_VALUES,&Bmat);
    1282:     MatDuplicate(Amat,MAT_DO_NOT_COPY_VALUES,&Xmat);
    1283:     nPoints = 0;
    1284:     for (i = 0; i < fSize; i++) {
    1285:       PetscInt        qPoints, thisNc;
    1286:       PetscQuadrature quad;

    1288:       PetscDualSpaceGetFunctional(dspace,i,&quad);
    1289:       PetscQuadratureGetData(quad,NULL,&thisNc,&qPoints,NULL,NULL);
    1290:       if (thisNc != Nc) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Functional dim %D does not much basis dim %D\n",thisNc,Nc);
    1291:       nPoints += qPoints;
    1292:     }
    1293:     PetscMalloc7(fSize,&sizes,nPoints*Nc,&weights,spdim*nPoints,&pointsRef,spdim*nPoints,&pointsReal,nPoints*fSize*Nc,&work,maxDof,&workIndRow,maxDof,&workIndCol);
    1294:     PetscMalloc1(maxDof * maxDof,&scwork);
    1295:     offset = 0;
    1296:     for (i = 0; i < fSize; i++) {
    1297:       PetscInt        qPoints;
    1298:       const PetscReal    *p, *w;
    1299:       PetscQuadrature quad;

    1301:       PetscDualSpaceGetFunctional(dspace,i,&quad);
    1302:       PetscQuadratureGetData(quad,NULL,NULL,&qPoints,&p,&w);
    1303:       PetscMemcpy(weights+Nc*offset,w,Nc*qPoints*sizeof(*w));
    1304:       PetscMemcpy(pointsRef+spdim*offset,p,spdim*qPoints*sizeof(*p));
    1305:       sizes[i] = qPoints;
    1306:       offset  += qPoints;
    1307:     }
    1308:     EvaluateBasis(bspace,fSize,fSize,Nc,nPoints,sizes,pointsRef,weights,work,Amat);
    1309:     MatLUFactor(Amat,NULL,NULL,NULL);
    1310:     for (c = cStart; c < cEnd; c++) {
    1311:       PetscInt        parent;
    1312:       PetscInt        closureSize, closureSizeP, *closure = NULL, *closureP = NULL;
    1313:       PetscInt        *childOffsets, *parentOffsets;

    1315:       DMPlexGetTreeParent(dm,c,&parent,NULL);
    1316:       if (parent == c) continue;
    1317:       DMPlexGetTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);
    1318:       for (i = 0; i < closureSize; i++) {
    1319:         PetscInt p = closure[2*i];
    1320:         PetscInt conDof;

    1322:         if (p < conStart || p >= conEnd) continue;
    1323:         if (numFields) {
    1324:           PetscSectionGetFieldDof(cSec,p,f,&conDof);
    1325:         }
    1326:         else {
    1327:           PetscSectionGetDof(cSec,p,&conDof);
    1328:         }
    1329:         if (conDof) break;
    1330:       }
    1331:       if (i == closureSize) {
    1332:         DMPlexRestoreTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);
    1333:         continue;
    1334:       }

    1336:       DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, NULL, &detJ);
    1337:       DMPlexComputeCellGeometryFEM(dm, parent, NULL, v0parent, Jparent, invJparent, &detJparent);
    1338:       for (i = 0; i < nPoints; i++) {
    1339:         const PetscReal xi0[3] = {-1.,-1.,-1.};

    1341:         CoordinatesRefToReal(spdim, spdim, xi0, v0, J, &pointsRef[i*spdim],vtmp);
    1342:         CoordinatesRealToRef(spdim, spdim, xi0, v0parent, invJparent, vtmp, &pointsReal[i*spdim]);
    1343:       }
    1344:       EvaluateBasis(bspace,fSize,fSize,Nc,nPoints,sizes,pointsReal,weights,work,Bmat);
    1345:       MatMatSolve(Amat,Bmat,Xmat);
    1346:       MatDenseGetArray(Xmat,&X);
    1347:       DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSizeP,&closureP);
    1348:       PetscMalloc2(closureSize+1,&childOffsets,closureSizeP+1,&parentOffsets);
    1349:       childOffsets[0] = 0;
    1350:       for (i = 0; i < closureSize; i++) {
    1351:         PetscInt p = closure[2*i];
    1352:         PetscInt dof;

    1354:         if (numFields) {
    1355:           PetscSectionGetFieldDof(section,p,f,&dof);
    1356:         }
    1357:         else {
    1358:           PetscSectionGetDof(section,p,&dof);
    1359:         }
    1360:         childOffsets[i+1]=childOffsets[i]+dof;
    1361:       }
    1362:       parentOffsets[0] = 0;
    1363:       for (i = 0; i < closureSizeP; i++) {
    1364:         PetscInt p = closureP[2*i];
    1365:         PetscInt dof;

    1367:         if (numFields) {
    1368:           PetscSectionGetFieldDof(section,p,f,&dof);
    1369:         }
    1370:         else {
    1371:           PetscSectionGetDof(section,p,&dof);
    1372:         }
    1373:         parentOffsets[i+1]=parentOffsets[i]+dof;
    1374:       }
    1375:       for (i = 0; i < closureSize; i++) {
    1376:         PetscInt conDof, conOff, aDof, aOff, nWork;
    1377:         PetscInt p = closure[2*i];
    1378:         PetscInt o = closure[2*i+1];
    1379:         const PetscInt    *perm;
    1380:         const PetscScalar *flip;

    1382:         if (p < conStart || p >= conEnd) continue;
    1383:         if (numFields) {
    1384:           PetscSectionGetFieldDof(cSec,p,f,&conDof);
    1385:           PetscSectionGetFieldOffset(cSec,p,f,&conOff);
    1386:         }
    1387:         else {
    1388:           PetscSectionGetDof(cSec,p,&conDof);
    1389:           PetscSectionGetOffset(cSec,p,&conOff);
    1390:         }
    1391:         if (!conDof) continue;
    1392:         perm  = (perms && perms[i]) ? perms[i][o] : NULL;
    1393:         flip  = (flips && flips[i]) ? flips[i][o] : NULL;
    1394:         PetscSectionGetDof(aSec,p,&aDof);
    1395:         PetscSectionGetOffset(aSec,p,&aOff);
    1396:         nWork = childOffsets[i+1]-childOffsets[i];
    1397:         for (k = 0; k < aDof; k++) {
    1398:           PetscInt a = anchors[aOff + k];
    1399:           PetscInt aSecDof, aSecOff;

    1401:           if (numFields) {
    1402:             PetscSectionGetFieldDof(section,a,f,&aSecDof);
    1403:             PetscSectionGetFieldOffset(section,a,f,&aSecOff);
    1404:           }
    1405:           else {
    1406:             PetscSectionGetDof(section,a,&aSecDof);
    1407:             PetscSectionGetOffset(section,a,&aSecOff);
    1408:           }
    1409:           if (!aSecDof) continue;

    1411:           for (j = 0; j < closureSizeP; j++) {
    1412:             PetscInt q = closureP[2*j];
    1413:             PetscInt oq = closureP[2*j+1];

    1415:             if (q == a) {
    1416:               PetscInt           r, s, nWorkP;
    1417:               const PetscInt    *permP;
    1418:               const PetscScalar *flipP;

    1420:               permP  = (perms && perms[j]) ? perms[j][oq] : NULL;
    1421:               flipP  = (flips && flips[j]) ? flips[j][oq] : NULL;
    1422:               nWorkP = parentOffsets[j+1]-parentOffsets[j];
    1423:               /* get a copy of the child-to-anchor portion of the matrix, and transpose so that rows correspond to the
    1424:                * child and columns correspond to the anchor: BUT the maxrix returned by MatDenseGetArray is
    1425:                * column-major, so transpose-transpose = do nothing */
    1426:               for (r = 0; r < nWork; r++) {
    1427:                 for (s = 0; s < nWorkP; s++) {
    1428:                   scwork[r * nWorkP + s] = X[fSize * (r + childOffsets[i]) + (s + parentOffsets[j])];
    1429:                 }
    1430:               }
    1431:               for (r = 0; r < nWork; r++)  {workIndRow[perm  ? perm[r]  : r] = conOff  + r;}
    1432:               for (s = 0; s < nWorkP; s++) {workIndCol[permP ? permP[s] : s] = aSecOff + s;}
    1433:               if (flip) {
    1434:                 for (r = 0; r < nWork; r++) {
    1435:                   for (s = 0; s < nWorkP; s++) {
    1436:                     scwork[r * nWorkP + s] *= flip[r];
    1437:                   }
    1438:                 }
    1439:               }
    1440:               if (flipP) {
    1441:                 for (r = 0; r < nWork; r++) {
    1442:                   for (s = 0; s < nWorkP; s++) {
    1443:                     scwork[r * nWorkP + s] *= flipP[s];
    1444:                   }
    1445:                 }
    1446:               }
    1447:               MatSetValues(cMat,nWork,workIndRow,nWorkP,workIndCol,scwork,INSERT_VALUES);
    1448:               break;
    1449:             }
    1450:           }
    1451:         }
    1452:       }
    1453:       MatDenseRestoreArray(Xmat,&X);
    1454:       PetscFree2(childOffsets,parentOffsets);
    1455:       DMPlexRestoreTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);
    1456:       DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSizeP,&closureP);
    1457:     }
    1458:     MatDestroy(&Amat);
    1459:     MatDestroy(&Bmat);
    1460:     MatDestroy(&Xmat);
    1461:     PetscFree(scwork);
    1462:     PetscFree7(sizes,weights,pointsRef,pointsReal,work,workIndRow,workIndCol);
    1463:     if (id == PETSCFV_CLASSID) {
    1464:       PetscSpaceDestroy(&bspace);
    1465:     }
    1466:   }
    1467:   MatAssemblyBegin(cMat,MAT_FINAL_ASSEMBLY);
    1468:   MatAssemblyEnd(cMat,MAT_FINAL_ASSEMBLY);
    1469:   PetscFree6(v0,v0parent,vtmp,J,Jparent,invJparent);
    1470:   ISRestoreIndices(aIS,&anchors);

    1472:   return(0);
    1473: }

    1475: static PetscErrorCode DMPlexReferenceTreeGetChildrenMatrices(DM refTree, PetscScalar ****childrenMats, PetscInt ***childrenN)
    1476: {
    1477:   Mat               refCmat;
    1478:   PetscDS           ds;
    1479:   PetscInt          numFields, maxFields, f, pRefStart, pRefEnd, p, *rows, *cols, maxDof, maxAnDof, **refPointFieldN;
    1480:   PetscScalar       ***refPointFieldMats;
    1481:   PetscSection      refConSec, refAnSec, refSection;
    1482:   IS                refAnIS;
    1483:   const PetscInt    *refAnchors;
    1484:   const PetscInt    **perms;
    1485:   const PetscScalar **flips;
    1486:   PetscErrorCode    ierr;

    1489:   DMGetDS(refTree,&ds);
    1490:   PetscDSGetNumFields(ds,&numFields);
    1491:   maxFields = PetscMax(1,numFields);
    1492:   DMGetDefaultConstraints(refTree,&refConSec,&refCmat);
    1493:   DMPlexGetAnchors(refTree,&refAnSec,&refAnIS);
    1494:   ISGetIndices(refAnIS,&refAnchors);
    1495:   DMGetSection(refTree,&refSection);
    1496:   PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
    1497:   PetscMalloc1(pRefEnd-pRefStart,&refPointFieldMats);
    1498:   PetscMalloc1(pRefEnd-pRefStart,&refPointFieldN);
    1499:   PetscSectionGetMaxDof(refConSec,&maxDof);
    1500:   PetscSectionGetMaxDof(refAnSec,&maxAnDof);
    1501:   PetscMalloc1(maxDof,&rows);
    1502:   PetscMalloc1(maxDof*maxAnDof,&cols);
    1503:   for (p = pRefStart; p < pRefEnd; p++) {
    1504:     PetscInt parent, closureSize, *closure = NULL, pDof;

    1506:     DMPlexGetTreeParent(refTree,p,&parent,NULL);
    1507:     PetscSectionGetDof(refConSec,p,&pDof);
    1508:     if (!pDof || parent == p) continue;

    1510:     PetscMalloc1(maxFields,&refPointFieldMats[p-pRefStart]);
    1511:     PetscCalloc1(maxFields,&refPointFieldN[p-pRefStart]);
    1512:     DMPlexGetTransitiveClosure(refTree,parent,PETSC_TRUE,&closureSize,&closure);
    1513:     for (f = 0; f < maxFields; f++) {
    1514:       PetscInt cDof, cOff, numCols, r, i;

    1516:       if (f < numFields) {
    1517:         PetscSectionGetFieldDof(refConSec,p,f,&cDof);
    1518:         PetscSectionGetFieldOffset(refConSec,p,f,&cOff);
    1519:         PetscSectionGetFieldPointSyms(refSection,f,closureSize,closure,&perms,&flips);
    1520:       } else {
    1521:         PetscSectionGetDof(refConSec,p,&cDof);
    1522:         PetscSectionGetOffset(refConSec,p,&cOff);
    1523:         PetscSectionGetPointSyms(refSection,closureSize,closure,&perms,&flips);
    1524:       }

    1526:       for (r = 0; r < cDof; r++) {
    1527:         rows[r] = cOff + r;
    1528:       }
    1529:       numCols = 0;
    1530:       for (i = 0; i < closureSize; i++) {
    1531:         PetscInt          q = closure[2*i];
    1532:         PetscInt          aDof, aOff, j;
    1533:         const PetscInt    *perm = perms ? perms[i] : NULL;

    1535:         if (numFields) {
    1536:           PetscSectionGetFieldDof(refSection,q,f,&aDof);
    1537:           PetscSectionGetFieldOffset(refSection,q,f,&aOff);
    1538:         }
    1539:         else {
    1540:           PetscSectionGetDof(refSection,q,&aDof);
    1541:           PetscSectionGetOffset(refSection,q,&aOff);
    1542:         }

    1544:         for (j = 0; j < aDof; j++) {
    1545:           cols[numCols++] = aOff + (perm ? perm[j] : j);
    1546:         }
    1547:       }
    1548:       refPointFieldN[p-pRefStart][f] = numCols;
    1549:       PetscMalloc1(cDof*numCols,&refPointFieldMats[p-pRefStart][f]);
    1550:       MatGetValues(refCmat,cDof,rows,numCols,cols,refPointFieldMats[p-pRefStart][f]);
    1551:       if (flips) {
    1552:         PetscInt colOff = 0;

    1554:         for (i = 0; i < closureSize; i++) {
    1555:           PetscInt          q = closure[2*i];
    1556:           PetscInt          aDof, aOff, j;
    1557:           const PetscScalar *flip = flips ? flips[i] : NULL;

    1559:           if (numFields) {
    1560:             PetscSectionGetFieldDof(refSection,q,f,&aDof);
    1561:             PetscSectionGetFieldOffset(refSection,q,f,&aOff);
    1562:           }
    1563:           else {
    1564:             PetscSectionGetDof(refSection,q,&aDof);
    1565:             PetscSectionGetOffset(refSection,q,&aOff);
    1566:           }
    1567:           if (flip) {
    1568:             PetscInt k;
    1569:             for (k = 0; k < cDof; k++) {
    1570:               for (j = 0; j < aDof; j++) {
    1571:                 refPointFieldMats[p-pRefStart][f][k * numCols + colOff + j] *= flip[j];
    1572:               }
    1573:             }
    1574:           }
    1575:           colOff += aDof;
    1576:         }
    1577:       }
    1578:       if (numFields) {
    1579:         PetscSectionRestoreFieldPointSyms(refSection,f,closureSize,closure,&perms,&flips);
    1580:       } else {
    1581:         PetscSectionRestorePointSyms(refSection,closureSize,closure,&perms,&flips);
    1582:       }
    1583:     }
    1584:     DMPlexRestoreTransitiveClosure(refTree,parent,PETSC_TRUE,&closureSize,&closure);
    1585:   }
    1586:   *childrenMats = refPointFieldMats;
    1587:   *childrenN = refPointFieldN;
    1588:   ISRestoreIndices(refAnIS,&refAnchors);
    1589:   PetscFree(rows);
    1590:   PetscFree(cols);
    1591:   return(0);
    1592: }

    1594: static PetscErrorCode DMPlexReferenceTreeRestoreChildrenMatrices(DM refTree, PetscScalar ****childrenMats, PetscInt ***childrenN)
    1595: {
    1596:   PetscDS        ds;
    1597:   PetscInt       **refPointFieldN;
    1598:   PetscScalar    ***refPointFieldMats;
    1599:   PetscInt       numFields, maxFields, pRefStart, pRefEnd, p, f;
    1600:   PetscSection   refConSec;

    1604:   refPointFieldN = *childrenN;
    1605:   *childrenN = NULL;
    1606:   refPointFieldMats = *childrenMats;
    1607:   *childrenMats = NULL;
    1608:   DMGetDS(refTree,&ds);
    1609:   PetscDSGetNumFields(ds,&numFields);
    1610:   maxFields = PetscMax(1,numFields);
    1611:   DMGetDefaultConstraints(refTree,&refConSec,NULL);
    1612:   PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
    1613:   for (p = pRefStart; p < pRefEnd; p++) {
    1614:     PetscInt parent, pDof;

    1616:     DMPlexGetTreeParent(refTree,p,&parent,NULL);
    1617:     PetscSectionGetDof(refConSec,p,&pDof);
    1618:     if (!pDof || parent == p) continue;

    1620:     for (f = 0; f < maxFields; f++) {
    1621:       PetscInt cDof;

    1623:       if (numFields) {
    1624:         PetscSectionGetFieldDof(refConSec,p,f,&cDof);
    1625:       }
    1626:       else {
    1627:         PetscSectionGetDof(refConSec,p,&cDof);
    1628:       }

    1630:       PetscFree(refPointFieldMats[p - pRefStart][f]);
    1631:     }
    1632:     PetscFree(refPointFieldMats[p - pRefStart]);
    1633:     PetscFree(refPointFieldN[p - pRefStart]);
    1634:   }
    1635:   PetscFree(refPointFieldMats);
    1636:   PetscFree(refPointFieldN);
    1637:   return(0);
    1638: }

    1640: static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_FromReference(DM dm, PetscSection section, PetscSection conSec, Mat cMat)
    1641: {
    1642:   DM             refTree;
    1643:   PetscDS        ds;
    1644:   Mat            refCmat;
    1645:   PetscInt       numFields, maxFields, f, pRefStart, pRefEnd, p, maxDof, maxAnDof, *perm, *iperm, pStart, pEnd, conStart, conEnd, **refPointFieldN;
    1646:   PetscScalar ***refPointFieldMats, *pointWork;
    1647:   PetscSection   refConSec, refAnSec, anSec;
    1648:   IS             refAnIS, anIS;
    1649:   const PetscInt *anchors;

    1654:   DMGetDS(dm,&ds);
    1655:   PetscDSGetNumFields(ds,&numFields);
    1656:   maxFields = PetscMax(1,numFields);
    1657:   DMPlexGetReferenceTree(dm,&refTree);
    1658:   DMSetDS(refTree,ds);
    1659:   DMGetDefaultConstraints(refTree,&refConSec,&refCmat);
    1660:   DMPlexGetAnchors(refTree,&refAnSec,&refAnIS);
    1661:   DMPlexGetAnchors(dm,&anSec,&anIS);
    1662:   ISGetIndices(anIS,&anchors);
    1663:   PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
    1664:   PetscSectionGetChart(conSec,&conStart,&conEnd);
    1665:   PetscSectionGetMaxDof(refConSec,&maxDof);
    1666:   PetscSectionGetMaxDof(refAnSec,&maxAnDof);
    1667:   PetscMalloc1(maxDof*maxDof*maxAnDof,&pointWork);

    1669:   /* step 1: get submats for every constrained point in the reference tree */
    1670:   DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);

    1672:   /* step 2: compute the preorder */
    1673:   DMPlexGetChart(dm,&pStart,&pEnd);
    1674:   PetscMalloc2(pEnd-pStart,&perm,pEnd-pStart,&iperm);
    1675:   for (p = pStart; p < pEnd; p++) {
    1676:     perm[p - pStart] = p;
    1677:     iperm[p - pStart] = p-pStart;
    1678:   }
    1679:   for (p = 0; p < pEnd - pStart;) {
    1680:     PetscInt point = perm[p];
    1681:     PetscInt parent;

    1683:     DMPlexGetTreeParent(dm,point,&parent,NULL);
    1684:     if (parent == point) {
    1685:       p++;
    1686:     }
    1687:     else {
    1688:       PetscInt size, closureSize, *closure = NULL, i;

    1690:       DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
    1691:       for (i = 0; i < closureSize; i++) {
    1692:         PetscInt q = closure[2*i];
    1693:         if (iperm[q-pStart] > iperm[point-pStart]) {
    1694:           /* swap */
    1695:           perm[p]               = q;
    1696:           perm[iperm[q-pStart]] = point;
    1697:           iperm[point-pStart]   = iperm[q-pStart];
    1698:           iperm[q-pStart]       = p;
    1699:           break;
    1700:         }
    1701:       }
    1702:       size = closureSize;
    1703:       DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
    1704:       if (i == size) {
    1705:         p++;
    1706:       }
    1707:     }
    1708:   }

    1710:   /* step 3: fill the constraint matrix */
    1711:   /* we are going to use a preorder progressive fill strategy.  Mat doesn't
    1712:    * allow progressive fill without assembly, so we are going to set up the
    1713:    * values outside of the Mat first.
    1714:    */
    1715:   {
    1716:     PetscInt nRows, row, nnz;
    1717:     PetscBool done;
    1718:     const PetscInt *ia, *ja;
    1719:     PetscScalar *vals;

    1721:     MatGetRowIJ(cMat,0,PETSC_FALSE,PETSC_FALSE,&nRows,&ia,&ja,&done);
    1722:     if (!done) SETERRQ(PetscObjectComm((PetscObject)cMat),PETSC_ERR_PLIB,"Could not get RowIJ of constraint matrix");
    1723:     nnz  = ia[nRows];
    1724:     /* malloc and then zero rows right before we fill them: this way valgrind
    1725:      * can tell if we are doing progressive fill in the wrong order */
    1726:     PetscMalloc1(nnz,&vals);
    1727:     for (p = 0; p < pEnd - pStart; p++) {
    1728:       PetscInt        parent, childid, closureSize, *closure = NULL;
    1729:       PetscInt        point = perm[p], pointDof;

    1731:       DMPlexGetTreeParent(dm,point,&parent,&childid);
    1732:       if ((point < conStart) || (point >= conEnd) || (parent == point)) continue;
    1733:       PetscSectionGetDof(conSec,point,&pointDof);
    1734:       if (!pointDof) continue;
    1735:       DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
    1736:       for (f = 0; f < maxFields; f++) {
    1737:         PetscInt cDof, cOff, numCols, numFillCols, i, r, matOffset, offset;
    1738:         PetscScalar *pointMat;
    1739:         const PetscInt    **perms;
    1740:         const PetscScalar **flips;

    1742:         if (numFields) {
    1743:           PetscSectionGetFieldDof(conSec,point,f,&cDof);
    1744:           PetscSectionGetFieldOffset(conSec,point,f,&cOff);
    1745:         }
    1746:         else {
    1747:           PetscSectionGetDof(conSec,point,&cDof);
    1748:           PetscSectionGetOffset(conSec,point,&cOff);
    1749:         }
    1750:         if (!cDof) continue;
    1751:         if (numFields) {PetscSectionGetFieldPointSyms(section,f,closureSize,closure,&perms,&flips);}
    1752:         else           {PetscSectionGetPointSyms(section,closureSize,closure,&perms,&flips);}

    1754:         /* make sure that every row for this point is the same size */
    1755: #if defined(PETSC_USE_DEBUG)
    1756:         for (r = 0; r < cDof; r++) {
    1757:           if (cDof > 1 && r) {
    1758:             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]));
    1759:           }
    1760:         }
    1761: #endif
    1762:         /* zero rows */
    1763:         for (i = ia[cOff] ; i< ia[cOff+cDof];i++) {
    1764:           vals[i] = 0.;
    1765:         }
    1766:         matOffset = ia[cOff];
    1767:         numFillCols = ia[cOff+1] - matOffset;
    1768:         pointMat = refPointFieldMats[childid-pRefStart][f];
    1769:         numCols = refPointFieldN[childid-pRefStart][f];
    1770:         offset = 0;
    1771:         for (i = 0; i < closureSize; i++) {
    1772:           PetscInt q = closure[2*i];
    1773:           PetscInt aDof, aOff, j, k, qConDof, qConOff;
    1774:           const PetscInt    *perm = perms ? perms[i] : NULL;
    1775:           const PetscScalar *flip = flips ? flips[i] : NULL;

    1777:           qConDof = qConOff = 0;
    1778:           if (numFields) {
    1779:             PetscSectionGetFieldDof(section,q,f,&aDof);
    1780:             PetscSectionGetFieldOffset(section,q,f,&aOff);
    1781:             if (q >= conStart && q < conEnd) {
    1782:               PetscSectionGetFieldDof(conSec,q,f,&qConDof);
    1783:               PetscSectionGetFieldOffset(conSec,q,f,&qConOff);
    1784:             }
    1785:           }
    1786:           else {
    1787:             PetscSectionGetDof(section,q,&aDof);
    1788:             PetscSectionGetOffset(section,q,&aOff);
    1789:             if (q >= conStart && q < conEnd) {
    1790:               PetscSectionGetDof(conSec,q,&qConDof);
    1791:               PetscSectionGetOffset(conSec,q,&qConOff);
    1792:             }
    1793:           }
    1794:           if (!aDof) continue;
    1795:           if (qConDof) {
    1796:             /* this point has anchors: its rows of the matrix should already
    1797:              * be filled, thanks to preordering */
    1798:             /* first multiply into pointWork, then set in matrix */
    1799:             PetscInt aMatOffset = ia[qConOff];
    1800:             PetscInt aNumFillCols = ia[qConOff + 1] - aMatOffset;
    1801:             for (r = 0; r < cDof; r++) {
    1802:               for (j = 0; j < aNumFillCols; j++) {
    1803:                 PetscScalar inVal = 0;
    1804:                 for (k = 0; k < aDof; k++) {
    1805:                   PetscInt col = perm ? perm[k] : k;

    1807:                   inVal += pointMat[r * numCols + offset + col] * vals[aMatOffset + aNumFillCols * k + j] * (flip ? flip[col] : 1.);
    1808:                 }
    1809:                 pointWork[r * aNumFillCols + j] = inVal;
    1810:               }
    1811:             }
    1812:             /* assume that the columns are sorted, spend less time searching */
    1813:             for (j = 0, k = 0; j < aNumFillCols; j++) {
    1814:               PetscInt col = ja[aMatOffset + j];
    1815:               for (;k < numFillCols; k++) {
    1816:                 if (ja[matOffset + k] == col) {
    1817:                   break;
    1818:                 }
    1819:               }
    1820:               if (k == numFillCols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"No nonzero space for (%d, %d)", cOff, col);
    1821:               for (r = 0; r < cDof; r++) {
    1822:                 vals[matOffset + numFillCols * r + k] = pointWork[r * aNumFillCols + j];
    1823:               }
    1824:             }
    1825:           }
    1826:           else {
    1827:             /* find where to put this portion of pointMat into the matrix */
    1828:             for (k = 0; k < numFillCols; k++) {
    1829:               if (ja[matOffset + k] == aOff) {
    1830:                 break;
    1831:               }
    1832:             }
    1833:             if (k == numFillCols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"No nonzero space for (%d, %d)", cOff, aOff);
    1834:             for (r = 0; r < cDof; r++) {
    1835:               for (j = 0; j < aDof; j++) {
    1836:                 PetscInt col = perm ? perm[j] : j;

    1838:                 vals[matOffset + numFillCols * r + k + col] += pointMat[r * numCols + offset + j] * (flip ? flip[col] : 1.);
    1839:               }
    1840:             }
    1841:           }
    1842:           offset += aDof;
    1843:         }
    1844:         if (numFields) {
    1845:           PetscSectionRestoreFieldPointSyms(section,f,closureSize,closure,&perms,&flips);
    1846:         } else {
    1847:           PetscSectionRestorePointSyms(section,closureSize,closure,&perms,&flips);
    1848:         }
    1849:       }
    1850:       DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
    1851:     }
    1852:     for (row = 0; row < nRows; row++) {
    1853:       MatSetValues(cMat,1,&row,ia[row+1]-ia[row],&ja[ia[row]],&vals[ia[row]],INSERT_VALUES);
    1854:     }
    1855:     MatRestoreRowIJ(cMat,0,PETSC_FALSE,PETSC_FALSE,&nRows,&ia,&ja,&done);
    1856:     if (!done) SETERRQ(PetscObjectComm((PetscObject)cMat),PETSC_ERR_PLIB,"Could not restore RowIJ of constraint matrix");
    1857:     MatAssemblyBegin(cMat,MAT_FINAL_ASSEMBLY);
    1858:     MatAssemblyEnd(cMat,MAT_FINAL_ASSEMBLY);
    1859:     PetscFree(vals);
    1860:   }

    1862:   /* clean up */
    1863:   ISRestoreIndices(anIS,&anchors);
    1864:   PetscFree2(perm,iperm);
    1865:   PetscFree(pointWork);
    1866:   DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
    1867:   return(0);
    1868: }

    1870: /* refine a single cell on rank 0: this is not intended to provide good local refinement, only to create an example of
    1871:  * a non-conforming mesh.  Local refinement comes later */
    1872: PetscErrorCode DMPlexTreeRefineCell (DM dm, PetscInt cell, DM *ncdm)
    1873: {
    1874:   DM K;
    1875:   PetscMPIInt rank;
    1876:   PetscInt dim, *pNewStart, *pNewEnd, *pNewCount, *pOldStart, *pOldEnd, offset, d, pStart, pEnd;
    1877:   PetscInt numNewCones, *newConeSizes, *newCones, *newOrientations;
    1878:   PetscInt *Kembedding;
    1879:   PetscInt *cellClosure=NULL, nc;
    1880:   PetscScalar *newVertexCoords;
    1881:   PetscInt numPointsWithParents, *parents, *childIDs, *perm, *iperm, *preOrient, pOffset;
    1882:   PetscSection parentSection;

    1886:   MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);
    1887:   DMGetDimension(dm,&dim);
    1888:   DMPlexCreate(PetscObjectComm((PetscObject)dm), ncdm);
    1889:   DMSetDimension(*ncdm,dim);

    1891:   DMPlexGetChart(dm, &pStart, &pEnd);
    1892:   PetscSectionCreate(PetscObjectComm((PetscObject)dm),&parentSection);
    1893:   DMPlexGetReferenceTree(dm,&K);
    1894:   if (!rank) {
    1895:     /* compute the new charts */
    1896:     PetscMalloc5(dim+1,&pNewCount,dim+1,&pNewStart,dim+1,&pNewEnd,dim+1,&pOldStart,dim+1,&pOldEnd);
    1897:     offset = 0;
    1898:     for (d = 0; d <= dim; d++) {
    1899:       PetscInt pOldCount, kStart, kEnd, k;

    1901:       pNewStart[d] = offset;
    1902:       DMPlexGetHeightStratum(dm,d,&pOldStart[d],&pOldEnd[d]);
    1903:       DMPlexGetHeightStratum(K,d,&kStart,&kEnd);
    1904:       pOldCount = pOldEnd[d] - pOldStart[d];
    1905:       /* adding the new points */
    1906:       pNewCount[d] = pOldCount + kEnd - kStart;
    1907:       if (!d) {
    1908:         /* removing the cell */
    1909:         pNewCount[d]--;
    1910:       }
    1911:       for (k = kStart; k < kEnd; k++) {
    1912:         PetscInt parent;
    1913:         DMPlexGetTreeParent(K,k,&parent,NULL);
    1914:         if (parent == k) {
    1915:           /* avoid double counting points that won't actually be new */
    1916:           pNewCount[d]--;
    1917:         }
    1918:       }
    1919:       pNewEnd[d] = pNewStart[d] + pNewCount[d];
    1920:       offset = pNewEnd[d];

    1922:     }
    1923:     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]);
    1924:     /* get the current closure of the cell that we are removing */
    1925:     DMPlexGetTransitiveClosure(dm,cell,PETSC_TRUE,&nc,&cellClosure);

    1927:     PetscMalloc1(pNewEnd[dim],&newConeSizes);
    1928:     {
    1929:       PetscInt kStart, kEnd, k, closureSizeK, *closureK = NULL, j;

    1931:       DMPlexGetChart(K,&kStart,&kEnd);
    1932:       PetscMalloc4(kEnd-kStart,&Kembedding,kEnd-kStart,&perm,kEnd-kStart,&iperm,kEnd-kStart,&preOrient);

    1934:       for (k = kStart; k < kEnd; k++) {
    1935:         perm[k - kStart] = k;
    1936:         iperm [k - kStart] = k - kStart;
    1937:         preOrient[k - kStart] = 0;
    1938:       }

    1940:       DMPlexGetTransitiveClosure(K,0,PETSC_TRUE,&closureSizeK,&closureK);
    1941:       for (j = 1; j < closureSizeK; j++) {
    1942:         PetscInt parentOrientA = closureK[2*j+1];
    1943:         PetscInt parentOrientB = cellClosure[2*j+1];
    1944:         PetscInt p, q;

    1946:         p = closureK[2*j];
    1947:         q = cellClosure[2*j];
    1948:         for (d = 0; d <= dim; d++) {
    1949:           if (q >= pOldStart[d] && q < pOldEnd[d]) {
    1950:             Kembedding[p] = (q - pOldStart[d]) + pNewStart[d];
    1951:           }
    1952:         }
    1953:         if (parentOrientA != parentOrientB) {
    1954:           PetscInt numChildren, i;
    1955:           const PetscInt *children;

    1957:           DMPlexGetTreeChildren(K,p,&numChildren,&children);
    1958:           for (i = 0; i < numChildren; i++) {
    1959:             PetscInt kPerm, oPerm;

    1961:             k    = children[i];
    1962:             DMPlexReferenceTreeGetChildSymmetry(K,p,parentOrientA,0,k,parentOrientB,&oPerm,&kPerm);
    1963:             /* perm = what refTree position I'm in */
    1964:             perm[kPerm-kStart]      = k;
    1965:             /* iperm = who is at this position */
    1966:             iperm[k-kStart]         = kPerm-kStart;
    1967:             preOrient[kPerm-kStart] = oPerm;
    1968:           }
    1969:         }
    1970:       }
    1971:       DMPlexRestoreTransitiveClosure(K,0,PETSC_TRUE,&closureSizeK,&closureK);
    1972:     }
    1973:     PetscSectionSetChart(parentSection,0,pNewEnd[dim]);
    1974:     offset = 0;
    1975:     numNewCones = 0;
    1976:     for (d = 0; d <= dim; d++) {
    1977:       PetscInt kStart, kEnd, k;
    1978:       PetscInt p;
    1979:       PetscInt size;

    1981:       for (p = pOldStart[d]; p < pOldEnd[d]; p++) {
    1982:         /* skip cell 0 */
    1983:         if (p == cell) continue;
    1984:         /* old cones to new cones */
    1985:         DMPlexGetConeSize(dm,p,&size);
    1986:         newConeSizes[offset++] = size;
    1987:         numNewCones += size;
    1988:       }

    1990:       DMPlexGetHeightStratum(K,d,&kStart,&kEnd);
    1991:       for (k = kStart; k < kEnd; k++) {
    1992:         PetscInt kParent;

    1994:         DMPlexGetTreeParent(K,k,&kParent,NULL);
    1995:         if (kParent != k) {
    1996:           Kembedding[k] = offset;
    1997:           DMPlexGetConeSize(K,k,&size);
    1998:           newConeSizes[offset++] = size;
    1999:           numNewCones += size;
    2000:           if (kParent != 0) {
    2001:             PetscSectionSetDof(parentSection,Kembedding[k],1);
    2002:           }
    2003:         }
    2004:       }
    2005:     }

    2007:     PetscSectionSetUp(parentSection);
    2008:     PetscSectionGetStorageSize(parentSection,&numPointsWithParents);
    2009:     PetscMalloc2(numNewCones,&newCones,numNewCones,&newOrientations);
    2010:     PetscMalloc2(numPointsWithParents,&parents,numPointsWithParents,&childIDs);

    2012:     /* fill new cones */
    2013:     offset = 0;
    2014:     for (d = 0; d <= dim; d++) {
    2015:       PetscInt kStart, kEnd, k, l;
    2016:       PetscInt p;
    2017:       PetscInt size;
    2018:       const PetscInt *cone, *orientation;

    2020:       for (p = pOldStart[d]; p < pOldEnd[d]; p++) {
    2021:         /* skip cell 0 */
    2022:         if (p == cell) continue;
    2023:         /* old cones to new cones */
    2024:         DMPlexGetConeSize(dm,p,&size);
    2025:         DMPlexGetCone(dm,p,&cone);
    2026:         DMPlexGetConeOrientation(dm,p,&orientation);
    2027:         for (l = 0; l < size; l++) {
    2028:           newCones[offset]          = (cone[l] - pOldStart[d + 1]) + pNewStart[d + 1];
    2029:           newOrientations[offset++] = orientation[l];
    2030:         }
    2031:       }

    2033:       DMPlexGetHeightStratum(K,d,&kStart,&kEnd);
    2034:       for (k = kStart; k < kEnd; k++) {
    2035:         PetscInt kPerm = perm[k], kParent;
    2036:         PetscInt preO  = preOrient[k];

    2038:         DMPlexGetTreeParent(K,k,&kParent,NULL);
    2039:         if (kParent != k) {
    2040:           /* embed new cones */
    2041:           DMPlexGetConeSize(K,k,&size);
    2042:           DMPlexGetCone(K,kPerm,&cone);
    2043:           DMPlexGetConeOrientation(K,kPerm,&orientation);
    2044:           for (l = 0; l < size; l++) {
    2045:             PetscInt q, m = (preO >= 0) ? ((preO + l) % size) : ((size -(preO + 1) - l) % size);
    2046:             PetscInt newO, lSize, oTrue;

    2048:             q                         = iperm[cone[m]];
    2049:             newCones[offset]          = Kembedding[q];
    2050:             DMPlexGetConeSize(K,q,&lSize);
    2051:             oTrue                     = orientation[m];
    2052:             oTrue                     = ((!lSize) || (preOrient[k] >= 0)) ? oTrue : -(oTrue + 2);
    2053:             newO                      = DihedralCompose(lSize,oTrue,preOrient[q]);
    2054:             newOrientations[offset++] = newO;
    2055:           }
    2056:           if (kParent != 0) {
    2057:             PetscInt newPoint = Kembedding[kParent];
    2058:             PetscSectionGetOffset(parentSection,Kembedding[k],&pOffset);
    2059:             parents[pOffset]  = newPoint;
    2060:             childIDs[pOffset] = k;
    2061:           }
    2062:         }
    2063:       }
    2064:     }

    2066:     PetscMalloc1(dim*(pNewEnd[dim]-pNewStart[dim]),&newVertexCoords);

    2068:     /* fill coordinates */
    2069:     offset = 0;
    2070:     {
    2071:       PetscInt kStart, kEnd, l;
    2072:       PetscSection vSection;
    2073:       PetscInt v;
    2074:       Vec coords;
    2075:       PetscScalar *coordvals;
    2076:       PetscInt dof, off;
    2077:       PetscReal v0[3], J[9], detJ;

    2079: #if defined(PETSC_USE_DEBUG)
    2080:       {
    2081:         PetscInt k;
    2082:         DMPlexGetHeightStratum(K,0,&kStart,&kEnd);
    2083:         for (k = kStart; k < kEnd; k++) {
    2084:           DMPlexComputeCellGeometryFEM(K, k, NULL, v0, J, NULL, &detJ);
    2085:           if (detJ <= 0.) SETERRQ1 (PETSC_COMM_SELF,PETSC_ERR_PLIB,"reference tree cell %d has bad determinant",k);
    2086:         }
    2087:       }
    2088: #endif
    2089:       DMPlexComputeCellGeometryFEM(dm, cell, NULL, v0, J, NULL, &detJ);
    2090:       DMGetCoordinateSection(dm,&vSection);
    2091:       DMGetCoordinatesLocal(dm,&coords);
    2092:       VecGetArray(coords,&coordvals);
    2093:       for (v = pOldStart[dim]; v < pOldEnd[dim]; v++) {

    2095:         PetscSectionGetDof(vSection,v,&dof);
    2096:         PetscSectionGetOffset(vSection,v,&off);
    2097:         for (l = 0; l < dof; l++) {
    2098:           newVertexCoords[offset++] = coordvals[off + l];
    2099:         }
    2100:       }
    2101:       VecRestoreArray(coords,&coordvals);

    2103:       DMGetCoordinateSection(K,&vSection);
    2104:       DMGetCoordinatesLocal(K,&coords);
    2105:       VecGetArray(coords,&coordvals);
    2106:       DMPlexGetDepthStratum(K,0,&kStart,&kEnd);
    2107:       for (v = kStart; v < kEnd; v++) {
    2108:         PetscReal coord[3], newCoord[3];
    2109:         PetscInt  vPerm = perm[v];
    2110:         PetscInt  kParent;
    2111:         const PetscReal xi0[3] = {-1.,-1.,-1.};

    2113:         DMPlexGetTreeParent(K,v,&kParent,NULL);
    2114:         if (kParent != v) {
    2115:           /* this is a new vertex */
    2116:           PetscSectionGetOffset(vSection,vPerm,&off);
    2117:           for (l = 0; l < dim; ++l) coord[l] = PetscRealPart(coordvals[off+l]);
    2118:           CoordinatesRefToReal(dim, dim, xi0, v0, J, coord, newCoord);
    2119:           for (l = 0; l < dim; ++l) newVertexCoords[offset+l] = newCoord[l];
    2120:           offset += dim;
    2121:         }
    2122:       }
    2123:       VecRestoreArray(coords,&coordvals);
    2124:     }

    2126:     /* need to reverse the order of pNewCount: vertices first, cells last */
    2127:     for (d = 0; d < (dim + 1) / 2; d++) {
    2128:       PetscInt tmp;

    2130:       tmp = pNewCount[d];
    2131:       pNewCount[d] = pNewCount[dim - d];
    2132:       pNewCount[dim - d] = tmp;
    2133:     }

    2135:     DMPlexCreateFromDAG(*ncdm,dim,pNewCount,newConeSizes,newCones,newOrientations,newVertexCoords);
    2136:     DMPlexSetReferenceTree(*ncdm,K);
    2137:     DMPlexSetTree(*ncdm,parentSection,parents,childIDs);

    2139:     /* clean up */
    2140:     DMPlexRestoreTransitiveClosure(dm,cell,PETSC_TRUE,&nc,&cellClosure);
    2141:     PetscFree5(pNewCount,pNewStart,pNewEnd,pOldStart,pOldEnd);
    2142:     PetscFree(newConeSizes);
    2143:     PetscFree2(newCones,newOrientations);
    2144:     PetscFree(newVertexCoords);
    2145:     PetscFree2(parents,childIDs);
    2146:     PetscFree4(Kembedding,perm,iperm,preOrient);
    2147:   }
    2148:   else {
    2149:     PetscInt    p, counts[4];
    2150:     PetscInt    *coneSizes, *cones, *orientations;
    2151:     Vec         coordVec;
    2152:     PetscScalar *coords;

    2154:     for (d = 0; d <= dim; d++) {
    2155:       PetscInt dStart, dEnd;

    2157:       DMPlexGetDepthStratum(dm,d,&dStart,&dEnd);
    2158:       counts[d] = dEnd - dStart;
    2159:     }
    2160:     PetscMalloc1(pEnd-pStart,&coneSizes);
    2161:     for (p = pStart; p < pEnd; p++) {
    2162:       DMPlexGetConeSize(dm,p,&coneSizes[p-pStart]);
    2163:     }
    2164:     DMPlexGetCones(dm, &cones);
    2165:     DMPlexGetConeOrientations(dm, &orientations);
    2166:     DMGetCoordinatesLocal(dm,&coordVec);
    2167:     VecGetArray(coordVec,&coords);

    2169:     PetscSectionSetChart(parentSection,pStart,pEnd);
    2170:     PetscSectionSetUp(parentSection);
    2171:     DMPlexCreateFromDAG(*ncdm,dim,counts,coneSizes,cones,orientations,NULL);
    2172:     DMPlexSetReferenceTree(*ncdm,K);
    2173:     DMPlexSetTree(*ncdm,parentSection,NULL,NULL);
    2174:     VecRestoreArray(coordVec,&coords);
    2175:   }
    2176:   PetscSectionDestroy(&parentSection);

    2178:   return(0);
    2179: }

    2181: PetscErrorCode DMPlexComputeInterpolatorTree(DM coarse, DM fine, PetscSF coarseToFine, PetscInt *childIds, Mat mat)
    2182: {
    2183:   PetscSF           coarseToFineEmbedded;
    2184:   PetscSection      globalCoarse, globalFine;
    2185:   PetscSection      localCoarse, localFine;
    2186:   PetscSection      aSec, cSec;
    2187:   PetscSection      rootIndicesSec, rootMatricesSec;
    2188:   PetscSection      leafIndicesSec, leafMatricesSec;
    2189:   PetscInt          *rootIndices, *leafIndices;
    2190:   PetscScalar       *rootMatrices, *leafMatrices;
    2191:   IS                aIS;
    2192:   const PetscInt    *anchors;
    2193:   Mat               cMat;
    2194:   PetscInt          numFields, maxFields;
    2195:   PetscInt          pStartC, pEndC, pStartF, pEndF, p;
    2196:   PetscInt          aStart, aEnd, cStart, cEnd;
    2197:   PetscInt          *maxChildIds;
    2198:   PetscInt          *offsets, *newOffsets, *offsetsCopy, *newOffsetsCopy, *rowOffsets, *numD, *numO;
    2199:   const PetscInt    ***perms;
    2200:   const PetscScalar ***flips;
    2201:   PetscErrorCode    ierr;

    2204:   DMPlexGetChart(coarse,&pStartC,&pEndC);
    2205:   DMPlexGetChart(fine,&pStartF,&pEndF);
    2206:   DMGetGlobalSection(fine,&globalFine);
    2207:   { /* winnow fine points that don't have global dofs out of the sf */
    2208:     PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs, nleaves, l;
    2209:     const PetscInt *leaves;

    2211:     PetscSFGetGraph(coarseToFine,NULL,&nleaves,&leaves,NULL);
    2212:     for (l = 0, numPointsWithDofs = 0; l < nleaves; l++) {
    2213:       p = leaves ? leaves[l] : l;
    2214:       PetscSectionGetDof(globalFine,p,&dof);
    2215:       PetscSectionGetConstraintDof(globalFine,p,&cdof);
    2216:       if ((dof - cdof) > 0) {
    2217:         numPointsWithDofs++;
    2218:       }
    2219:     }
    2220:     PetscMalloc1(numPointsWithDofs,&pointsWithDofs);
    2221:     for (l = 0, offset = 0; l < nleaves; l++) {
    2222:       p = leaves ? leaves[l] : l;
    2223:       PetscSectionGetDof(globalFine,p,&dof);
    2224:       PetscSectionGetConstraintDof(globalFine,p,&cdof);
    2225:       if ((dof - cdof) > 0) {
    2226:         pointsWithDofs[offset++] = l;
    2227:       }
    2228:     }
    2229:     PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);
    2230:     PetscFree(pointsWithDofs);
    2231:   }
    2232:   /* communicate back to the coarse mesh which coarse points have children (that may require interpolation) */
    2233:   PetscMalloc1(pEndC-pStartC,&maxChildIds);
    2234:   for (p = pStartC; p < pEndC; p++) {
    2235:     maxChildIds[p - pStartC] = -2;
    2236:   }
    2237:   PetscSFReduceBegin(coarseToFineEmbedded,MPIU_INT,childIds,maxChildIds,MPIU_MAX);
    2238:   PetscSFReduceEnd(coarseToFineEmbedded,MPIU_INT,childIds,maxChildIds,MPIU_MAX);

    2240:   DMGetSection(coarse,&localCoarse);
    2241:   DMGetGlobalSection(coarse,&globalCoarse);

    2243:   DMPlexGetAnchors(coarse,&aSec,&aIS);
    2244:   ISGetIndices(aIS,&anchors);
    2245:   PetscSectionGetChart(aSec,&aStart,&aEnd);

    2247:   DMGetDefaultConstraints(coarse,&cSec,&cMat);
    2248:   PetscSectionGetChart(cSec,&cStart,&cEnd);

    2250:   /* create sections that will send to children the indices and matrices they will need to construct the interpolator */
    2251:   PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootIndicesSec);
    2252:   PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootMatricesSec);
    2253:   PetscSectionSetChart(rootIndicesSec,pStartC,pEndC);
    2254:   PetscSectionSetChart(rootMatricesSec,pStartC,pEndC);
    2255:   PetscSectionGetNumFields(localCoarse,&numFields);
    2256:   maxFields = PetscMax(1,numFields);
    2257:   PetscMalloc7(maxFields+1,&offsets,maxFields+1,&offsetsCopy,maxFields+1,&newOffsets,maxFields+1,&newOffsetsCopy,maxFields+1,&rowOffsets,maxFields+1,&numD,maxFields+1,&numO);
    2258:   PetscMalloc2(maxFields+1,(PetscInt****)&perms,maxFields+1,(PetscScalar****)&flips);
    2259:   PetscMemzero((void *) perms, (maxFields+1) * sizeof(const PetscInt **));
    2260:   PetscMemzero((void *) flips, (maxFields+1) * sizeof(const PetscScalar **));

    2262:   for (p = pStartC; p < pEndC; p++) { /* count the sizes of the indices and matrices */
    2263:     PetscInt dof, matSize   = 0;
    2264:     PetscInt aDof           = 0;
    2265:     PetscInt cDof           = 0;
    2266:     PetscInt maxChildId     = maxChildIds[p - pStartC];
    2267:     PetscInt numRowIndices  = 0;
    2268:     PetscInt numColIndices  = 0;
    2269:     PetscInt f;

    2271:     PetscSectionGetDof(globalCoarse,p,&dof);
    2272:     if (dof < 0) {
    2273:       dof = -(dof + 1);
    2274:     }
    2275:     if (p >= aStart && p < aEnd) {
    2276:       PetscSectionGetDof(aSec,p,&aDof);
    2277:     }
    2278:     if (p >= cStart && p < cEnd) {
    2279:       PetscSectionGetDof(cSec,p,&cDof);
    2280:     }
    2281:     for (f = 0; f <= numFields; f++) offsets[f] = 0;
    2282:     for (f = 0; f <= numFields; f++) newOffsets[f] = 0;
    2283:     if (maxChildId >= 0) { /* this point has children (with dofs) that will need to be interpolated from the closure of p */
    2284:       PetscInt *closure = NULL, closureSize, cl;

    2286:       DMPlexGetTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);
    2287:       for (cl = 0; cl < closureSize; cl++) { /* get the closure */
    2288:         PetscInt c = closure[2 * cl], clDof;

    2290:         PetscSectionGetDof(localCoarse,c,&clDof);
    2291:         numRowIndices += clDof;
    2292:         for (f = 0; f < numFields; f++) {
    2293:           PetscSectionGetFieldDof(localCoarse,c,f,&clDof);
    2294:           offsets[f + 1] += clDof;
    2295:         }
    2296:       }
    2297:       for (f = 0; f < numFields; f++) {
    2298:         offsets[f + 1]   += offsets[f];
    2299:         newOffsets[f + 1] = offsets[f + 1];
    2300:       }
    2301:       /* get the number of indices needed and their field offsets */
    2302:       DMPlexAnchorsModifyMat(coarse,localCoarse,closureSize,numRowIndices,closure,NULL,NULL,NULL,&numColIndices,NULL,NULL,newOffsets,PETSC_FALSE);
    2303:       DMPlexRestoreTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);
    2304:       if (!numColIndices) { /* there are no hanging constraint modifications, so the matrix is just the identity: do not send it */
    2305:         numColIndices = numRowIndices;
    2306:         matSize = 0;
    2307:       }
    2308:       else if (numFields) { /* we send one submat for each field: sum their sizes */
    2309:         matSize = 0;
    2310:         for (f = 0; f < numFields; f++) {
    2311:           PetscInt numRow, numCol;

    2313:           numRow = offsets[f + 1] - offsets[f];
    2314:           numCol = newOffsets[f + 1] - newOffsets[f];
    2315:           matSize += numRow * numCol;
    2316:         }
    2317:       }
    2318:       else {
    2319:         matSize = numRowIndices * numColIndices;
    2320:       }
    2321:     } else if (maxChildId == -1) {
    2322:       if (cDof > 0) { /* this point's dofs are interpolated via cMat: get the submatrix of cMat */
    2323:         PetscInt aOff, a;

    2325:         PetscSectionGetOffset(aSec,p,&aOff);
    2326:         for (f = 0; f < numFields; f++) {
    2327:           PetscInt fDof;

    2329:           PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
    2330:           offsets[f+1] = fDof;
    2331:         }
    2332:         for (a = 0; a < aDof; a++) {
    2333:           PetscInt anchor = anchors[a + aOff], aLocalDof;

    2335:           PetscSectionGetDof(localCoarse,anchor,&aLocalDof);
    2336:           numColIndices += aLocalDof;
    2337:           for (f = 0; f < numFields; f++) {
    2338:             PetscInt fDof;

    2340:             PetscSectionGetFieldDof(localCoarse,anchor,f,&fDof);
    2341:             newOffsets[f+1] += fDof;
    2342:           }
    2343:         }
    2344:         if (numFields) {
    2345:           matSize = 0;
    2346:           for (f = 0; f < numFields; f++) {
    2347:             matSize += offsets[f+1] * newOffsets[f+1];
    2348:           }
    2349:         }
    2350:         else {
    2351:           matSize = numColIndices * dof;
    2352:         }
    2353:       }
    2354:       else { /* no children, and no constraints on dofs: just get the global indices */
    2355:         numColIndices = dof;
    2356:         matSize       = 0;
    2357:       }
    2358:     }
    2359:     /* we will pack the column indices with the field offsets */
    2360:     PetscSectionSetDof(rootIndicesSec,p,numColIndices ? numColIndices+2*numFields : 0);
    2361:     PetscSectionSetDof(rootMatricesSec,p,matSize);
    2362:   }
    2363:   PetscSectionSetUp(rootIndicesSec);
    2364:   PetscSectionSetUp(rootMatricesSec);
    2365:   {
    2366:     PetscInt numRootIndices, numRootMatrices;

    2368:     PetscSectionGetStorageSize(rootIndicesSec,&numRootIndices);
    2369:     PetscSectionGetStorageSize(rootMatricesSec,&numRootMatrices);
    2370:     PetscMalloc2(numRootIndices,&rootIndices,numRootMatrices,&rootMatrices);
    2371:     for (p = pStartC; p < pEndC; p++) {
    2372:       PetscInt    numRowIndices, numColIndices, matSize, dof;
    2373:       PetscInt    pIndOff, pMatOff, f;
    2374:       PetscInt    *pInd;
    2375:       PetscInt    maxChildId = maxChildIds[p - pStartC];
    2376:       PetscScalar *pMat = NULL;

    2378:       PetscSectionGetDof(rootIndicesSec,p,&numColIndices);
    2379:       if (!numColIndices) {
    2380:         continue;
    2381:       }
    2382:       for (f = 0; f <= numFields; f++) {
    2383:         offsets[f]        = 0;
    2384:         newOffsets[f]     = 0;
    2385:         offsetsCopy[f]    = 0;
    2386:         newOffsetsCopy[f] = 0;
    2387:       }
    2388:       numColIndices -= 2 * numFields;
    2389:       PetscSectionGetOffset(rootIndicesSec,p,&pIndOff);
    2390:       pInd = &(rootIndices[pIndOff]);
    2391:       PetscSectionGetDof(rootMatricesSec,p,&matSize);
    2392:       if (matSize) {
    2393:         PetscSectionGetOffset(rootMatricesSec,p,&pMatOff);
    2394:         pMat = &rootMatrices[pMatOff];
    2395:       }
    2396:       PetscSectionGetDof(globalCoarse,p,&dof);
    2397:       if (dof < 0) {
    2398:         dof = -(dof + 1);
    2399:       }
    2400:       if (maxChildId >= 0) { /* build an identity matrix, apply matrix constraints on the right */
    2401:         PetscInt i, j;
    2402:         PetscInt numRowIndices = matSize / numColIndices;

    2404:         if (!numRowIndices) { /* don't need to calculate the mat, just the indices */
    2405:           PetscInt numIndices, *indices;
    2406:           DMPlexGetClosureIndices(coarse,localCoarse,globalCoarse,p,&numIndices,&indices,offsets);
    2407:           if (numIndices != numColIndices) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"mismatching constraint indices calculations");
    2408:           for (i = 0; i < numColIndices; i++) {
    2409:             pInd[i] = indices[i];
    2410:           }
    2411:           for (i = 0; i < numFields; i++) {
    2412:             pInd[numColIndices + i]             = offsets[i+1];
    2413:             pInd[numColIndices + numFields + i] = offsets[i+1];
    2414:           }
    2415:           DMPlexRestoreClosureIndices(coarse,localCoarse,globalCoarse,p,&numIndices,&indices,offsets);
    2416:         }
    2417:         else {
    2418:           PetscInt closureSize, *closure = NULL, cl;
    2419:           PetscScalar *pMatIn, *pMatModified;
    2420:           PetscInt numPoints,*points;

    2422:           DMGetWorkArray(coarse,numRowIndices * numRowIndices,MPIU_SCALAR,&pMatIn);
    2423:           for (i = 0; i < numRowIndices; i++) { /* initialize to the identity */
    2424:             for (j = 0; j < numRowIndices; j++) {
    2425:               pMatIn[i * numRowIndices + j] = (i == j) ? 1. : 0.;
    2426:             }
    2427:           }
    2428:           DMPlexGetTransitiveClosure(coarse, p, PETSC_TRUE, &closureSize, &closure);
    2429:           for (f = 0; f < maxFields; f++) {
    2430:             if (numFields) {PetscSectionGetFieldPointSyms(localCoarse,f,closureSize,closure,&perms[f],&flips[f]);}
    2431:             else           {PetscSectionGetPointSyms(localCoarse,closureSize,closure,&perms[f],&flips[f]);}
    2432:           }
    2433:           if (numFields) {
    2434:             for (cl = 0; cl < closureSize; cl++) {
    2435:               PetscInt c = closure[2 * cl];

    2437:               for (f = 0; f < numFields; f++) {
    2438:                 PetscInt fDof;

    2440:                 PetscSectionGetFieldDof(localCoarse,c,f,&fDof);
    2441:                 offsets[f + 1] += fDof;
    2442:               }
    2443:             }
    2444:             for (f = 0; f < numFields; f++) {
    2445:               offsets[f + 1]   += offsets[f];
    2446:               newOffsets[f + 1] = offsets[f + 1];
    2447:             }
    2448:           }
    2449:           /* TODO : flips here ? */
    2450:           /* apply hanging node constraints on the right, get the new points and the new offsets */
    2451:           DMPlexAnchorsModifyMat(coarse,localCoarse,closureSize,numRowIndices,closure,perms,pMatIn,&numPoints,NULL,&points,&pMatModified,newOffsets,PETSC_FALSE);
    2452:           for (f = 0; f < maxFields; f++) {
    2453:             if (numFields) {PetscSectionRestoreFieldPointSyms(localCoarse,f,closureSize,closure,&perms[f],&flips[f]);}
    2454:             else           {PetscSectionRestorePointSyms(localCoarse,closureSize,closure,&perms[f],&flips[f]);}
    2455:           }
    2456:           for (f = 0; f < maxFields; f++) {
    2457:             if (numFields) {PetscSectionGetFieldPointSyms(localCoarse,f,numPoints,points,&perms[f],&flips[f]);}
    2458:             else           {PetscSectionGetPointSyms(localCoarse,numPoints,points,&perms[f],&flips[f]);}
    2459:           }
    2460:           if (!numFields) {
    2461:             for (i = 0; i < numRowIndices * numColIndices; i++) {
    2462:               pMat[i] = pMatModified[i];
    2463:             }
    2464:           }
    2465:           else {
    2466:             PetscInt i, j, count;
    2467:             for (f = 0, count = 0; f < numFields; f++) {
    2468:               for (i = offsets[f]; i < offsets[f+1]; i++) {
    2469:                 for (j = newOffsets[f]; j < newOffsets[f+1]; j++, count++) {
    2470:                   pMat[count] = pMatModified[i * numColIndices + j];
    2471:                 }
    2472:               }
    2473:             }
    2474:           }
    2475:           DMRestoreWorkArray(coarse,numRowIndices * numColIndices,MPIU_SCALAR,&pMatModified);
    2476:           DMPlexRestoreTransitiveClosure(coarse, p, PETSC_TRUE, &closureSize, &closure);
    2477:           DMRestoreWorkArray(coarse,numRowIndices * numColIndices,MPIU_SCALAR,&pMatIn);
    2478:           if (numFields) {
    2479:             for (f = 0; f < numFields; f++) {
    2480:               pInd[numColIndices + f]             = offsets[f+1];
    2481:               pInd[numColIndices + numFields + f] = newOffsets[f+1];
    2482:             }
    2483:             for (cl = 0; cl < numPoints; cl++) {
    2484:               PetscInt globalOff, c = points[2*cl];
    2485:               PetscSectionGetOffset(globalCoarse, c, &globalOff);
    2486:               DMPlexGetIndicesPointFields_Internal(localCoarse, c, globalOff < 0 ? -(globalOff+1) : globalOff, newOffsets, PETSC_FALSE, perms, cl, pInd);
    2487:             }
    2488:           } else {
    2489:             for (cl = 0; cl < numPoints; cl++) {
    2490:               PetscInt c = points[2*cl], globalOff;
    2491:               const PetscInt *perm = perms[0] ? perms[0][cl] : NULL;

    2493:               PetscSectionGetOffset(globalCoarse, c, &globalOff);
    2494:               DMPlexGetIndicesPoint_Internal(localCoarse, c, globalOff < 0 ? -(globalOff+1) : globalOff, newOffsets, PETSC_FALSE, perm, pInd);
    2495:             }
    2496:           }
    2497:           for (f = 0; f < maxFields; f++) {
    2498:             if (numFields) {PetscSectionRestoreFieldPointSyms(localCoarse,f,numPoints,points,&perms[f],&flips[f]);}
    2499:             else           {PetscSectionRestorePointSyms(localCoarse,numPoints,points,&perms[f],&flips[f]);}
    2500:           }
    2501:           DMRestoreWorkArray(coarse,numPoints,MPIU_SCALAR,&points);
    2502:         }
    2503:       }
    2504:       else if (matSize) {
    2505:         PetscInt cOff;
    2506:         PetscInt *rowIndices, *colIndices, a, aDof, aOff;

    2508:         numRowIndices = matSize / numColIndices;
    2509:         if (numRowIndices != dof) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Miscounted dofs");
    2510:         DMGetWorkArray(coarse,numRowIndices,MPIU_INT,&rowIndices);
    2511:         DMGetWorkArray(coarse,numColIndices,MPIU_INT,&colIndices);
    2512:         PetscSectionGetOffset(cSec,p,&cOff);
    2513:         PetscSectionGetDof(aSec,p,&aDof);
    2514:         PetscSectionGetOffset(aSec,p,&aOff);
    2515:         if (numFields) {
    2516:           for (f = 0; f < numFields; f++) {
    2517:             PetscInt fDof;

    2519:             PetscSectionGetFieldDof(cSec,p,f,&fDof);
    2520:             offsets[f + 1] = fDof;
    2521:             for (a = 0; a < aDof; a++) {
    2522:               PetscInt anchor = anchors[a + aOff];
    2523:               PetscSectionGetFieldDof(localCoarse,anchor,f,&fDof);
    2524:               newOffsets[f + 1] += fDof;
    2525:             }
    2526:           }
    2527:           for (f = 0; f < numFields; f++) {
    2528:             offsets[f + 1]       += offsets[f];
    2529:             offsetsCopy[f + 1]    = offsets[f + 1];
    2530:             newOffsets[f + 1]    += newOffsets[f];
    2531:             newOffsetsCopy[f + 1] = newOffsets[f + 1];
    2532:           }
    2533:           DMPlexGetIndicesPointFields_Internal(cSec,p,cOff,offsetsCopy,PETSC_TRUE,NULL,-1,rowIndices);
    2534:           for (a = 0; a < aDof; a++) {
    2535:             PetscInt anchor = anchors[a + aOff], lOff;
    2536:             PetscSectionGetOffset(localCoarse,anchor,&lOff);
    2537:             DMPlexGetIndicesPointFields_Internal(localCoarse,anchor,lOff,newOffsetsCopy,PETSC_TRUE,NULL,-1,colIndices);
    2538:           }
    2539:         }
    2540:         else {
    2541:           DMPlexGetIndicesPoint_Internal(cSec,p,cOff,offsetsCopy,PETSC_TRUE,NULL,rowIndices);
    2542:           for (a = 0; a < aDof; a++) {
    2543:             PetscInt anchor = anchors[a + aOff], lOff;
    2544:             PetscSectionGetOffset(localCoarse,anchor,&lOff);
    2545:             DMPlexGetIndicesPoint_Internal(localCoarse,anchor,lOff,newOffsetsCopy,PETSC_TRUE,NULL,colIndices);
    2546:           }
    2547:         }
    2548:         if (numFields) {
    2549:           PetscInt count, a;

    2551:           for (f = 0, count = 0; f < numFields; f++) {
    2552:             PetscInt iSize = offsets[f + 1] - offsets[f];
    2553:             PetscInt jSize = newOffsets[f + 1] - newOffsets[f];
    2554:             MatGetValues(cMat,iSize,&rowIndices[offsets[f]],jSize,&colIndices[newOffsets[f]],&pMat[count]);
    2555:             count += iSize * jSize;
    2556:             pInd[numColIndices + f]             = offsets[f+1];
    2557:             pInd[numColIndices + numFields + f] = newOffsets[f+1];
    2558:           }
    2559:           for (a = 0; a < aDof; a++) {
    2560:             PetscInt anchor = anchors[a + aOff];
    2561:             PetscInt gOff;
    2562:             PetscSectionGetOffset(globalCoarse,anchor,&gOff);
    2563:             DMPlexGetIndicesPointFields_Internal(localCoarse,anchor,gOff < 0 ? -(gOff + 1) : gOff,newOffsets,PETSC_FALSE,NULL,-1,pInd);
    2564:           }
    2565:         }
    2566:         else {
    2567:           PetscInt a;
    2568:           MatGetValues(cMat,numRowIndices,rowIndices,numColIndices,colIndices,pMat);
    2569:           for (a = 0; a < aDof; a++) {
    2570:             PetscInt anchor = anchors[a + aOff];
    2571:             PetscInt gOff;
    2572:             PetscSectionGetOffset(globalCoarse,anchor,&gOff);
    2573:             DMPlexGetIndicesPoint_Internal(localCoarse,anchor,gOff < 0 ? -(gOff + 1) : gOff,newOffsets,PETSC_FALSE,NULL,pInd);
    2574:           }
    2575:         }
    2576:         DMRestoreWorkArray(coarse,numColIndices,MPIU_INT,&colIndices);
    2577:         DMRestoreWorkArray(coarse,numRowIndices,MPIU_INT,&rowIndices);
    2578:       }
    2579:       else {
    2580:         PetscInt gOff;

    2582:         PetscSectionGetOffset(globalCoarse,p,&gOff);
    2583:         if (numFields) {
    2584:           for (f = 0; f < numFields; f++) {
    2585:             PetscInt fDof;
    2586:             PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
    2587:             offsets[f + 1] = fDof + offsets[f];
    2588:           }
    2589:           for (f = 0; f < numFields; f++) {
    2590:             pInd[numColIndices + f]             = offsets[f+1];
    2591:             pInd[numColIndices + numFields + f] = offsets[f+1];
    2592:           }
    2593:           DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,NULL,-1,pInd);
    2594:         }
    2595:         else {
    2596:           DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,NULL,pInd);
    2597:         }
    2598:       }
    2599:     }
    2600:     PetscFree(maxChildIds);
    2601:   }
    2602:   {
    2603:     PetscSF  indicesSF, matricesSF;
    2604:     PetscInt *remoteOffsetsIndices, *remoteOffsetsMatrices, numLeafIndices, numLeafMatrices;

    2606:     PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafIndicesSec);
    2607:     PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafMatricesSec);
    2608:     PetscSFDistributeSection(coarseToFineEmbedded,rootIndicesSec,&remoteOffsetsIndices,leafIndicesSec);
    2609:     PetscSFDistributeSection(coarseToFineEmbedded,rootMatricesSec,&remoteOffsetsMatrices,leafMatricesSec);
    2610:     PetscSFCreateSectionSF(coarseToFineEmbedded,rootIndicesSec,remoteOffsetsIndices,leafIndicesSec,&indicesSF);
    2611:     PetscSFCreateSectionSF(coarseToFineEmbedded,rootMatricesSec,remoteOffsetsMatrices,leafMatricesSec,&matricesSF);
    2612:     PetscSFDestroy(&coarseToFineEmbedded);
    2613:     PetscFree(remoteOffsetsIndices);
    2614:     PetscFree(remoteOffsetsMatrices);
    2615:     PetscSectionGetStorageSize(leafIndicesSec,&numLeafIndices);
    2616:     PetscSectionGetStorageSize(leafMatricesSec,&numLeafMatrices);
    2617:     PetscMalloc2(numLeafIndices,&leafIndices,numLeafMatrices,&leafMatrices);
    2618:     PetscSFBcastBegin(indicesSF,MPIU_INT,rootIndices,leafIndices);
    2619:     PetscSFBcastBegin(matricesSF,MPIU_SCALAR,rootMatrices,leafMatrices);
    2620:     PetscSFBcastEnd(indicesSF,MPIU_INT,rootIndices,leafIndices);
    2621:     PetscSFBcastEnd(matricesSF,MPIU_SCALAR,rootMatrices,leafMatrices);
    2622:     PetscSFDestroy(&matricesSF);
    2623:     PetscSFDestroy(&indicesSF);
    2624:     PetscFree2(rootIndices,rootMatrices);
    2625:     PetscSectionDestroy(&rootIndicesSec);
    2626:     PetscSectionDestroy(&rootMatricesSec);
    2627:   }
    2628:   /* count to preallocate */
    2629:   DMGetSection(fine,&localFine);
    2630:   {
    2631:     PetscInt    nGlobal;
    2632:     PetscInt    *dnnz, *onnz;
    2633:     PetscLayout rowMap, colMap;
    2634:     PetscInt    rowStart, rowEnd, colStart, colEnd;
    2635:     PetscInt    maxDof;
    2636:     PetscInt    *rowIndices;
    2637:     DM           refTree;
    2638:     PetscInt     **refPointFieldN;
    2639:     PetscScalar  ***refPointFieldMats;
    2640:     PetscSection refConSec, refAnSec;
    2641:     PetscInt     pRefStart,pRefEnd,maxConDof,maxColumns,leafStart,leafEnd;
    2642:     PetscScalar  *pointWork;

    2644:     PetscSectionGetConstrainedStorageSize(globalFine,&nGlobal);
    2645:     PetscCalloc2(nGlobal,&dnnz,nGlobal,&onnz);
    2646:     MatGetLayouts(mat,&rowMap,&colMap);
    2647:     PetscLayoutSetUp(rowMap);
    2648:     PetscLayoutSetUp(colMap);
    2649:     PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);
    2650:     PetscLayoutGetRange(colMap,&colStart,&colEnd);
    2651:     PetscSectionGetMaxDof(globalFine,&maxDof);
    2652:     PetscSectionGetChart(leafIndicesSec,&leafStart,&leafEnd);
    2653:     DMGetWorkArray(fine,maxDof,MPIU_INT,&rowIndices);
    2654:     for (p = leafStart; p < leafEnd; p++) {
    2655:       PetscInt    gDof, gcDof, gOff;
    2656:       PetscInt    numColIndices, pIndOff, *pInd;
    2657:       PetscInt    matSize;
    2658:       PetscInt    i;

    2660:       PetscSectionGetDof(globalFine,p,&gDof);
    2661:       PetscSectionGetConstraintDof(globalFine,p,&gcDof);
    2662:       if ((gDof - gcDof) <= 0) {
    2663:         continue;
    2664:       }
    2665:       PetscSectionGetOffset(globalFine,p,&gOff);
    2666:       if (gOff < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"I though having global dofs meant a non-negative offset");
    2667:       if ((gOff < rowStart) || ((gOff + gDof - gcDof) > rowEnd)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"I thought the row map would constrain the global dofs");
    2668:       PetscSectionGetDof(leafIndicesSec,p,&numColIndices);
    2669:       PetscSectionGetOffset(leafIndicesSec,p,&pIndOff);
    2670:       numColIndices -= 2 * numFields;
    2671:       if (numColIndices <= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"global fine dof with no dofs to interpolate from");
    2672:       pInd = &leafIndices[pIndOff];
    2673:       offsets[0]        = 0;
    2674:       offsetsCopy[0]    = 0;
    2675:       newOffsets[0]     = 0;
    2676:       newOffsetsCopy[0] = 0;
    2677:       if (numFields) {
    2678:         PetscInt f;
    2679:         for (f = 0; f < numFields; f++) {
    2680:           PetscInt rowDof;

    2682:           PetscSectionGetFieldDof(localFine,p,f,&rowDof);
    2683:           offsets[f + 1]        = offsets[f] + rowDof;
    2684:           offsetsCopy[f + 1]    = offsets[f + 1];
    2685:           newOffsets[f + 1]     = pInd[numColIndices + numFields + f];
    2686:           numD[f] = 0;
    2687:           numO[f] = 0;
    2688:         }
    2689:         DMPlexGetIndicesPointFields_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,NULL,-1,rowIndices);
    2690:         for (f = 0; f < numFields; f++) {
    2691:           PetscInt colOffset    = newOffsets[f];
    2692:           PetscInt numFieldCols = newOffsets[f + 1] - newOffsets[f];

    2694:           for (i = 0; i < numFieldCols; i++) {
    2695:             PetscInt gInd = pInd[i + colOffset];

    2697:             if (gInd >= colStart && gInd < colEnd) {
    2698:               numD[f]++;
    2699:             }
    2700:             else if (gInd >= 0) { /* negative means non-entry */
    2701:               numO[f]++;
    2702:             }
    2703:           }
    2704:         }
    2705:       }
    2706:       else {
    2707:         DMPlexGetIndicesPoint_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,NULL,rowIndices);
    2708:         numD[0] = 0;
    2709:         numO[0] = 0;
    2710:         for (i = 0; i < numColIndices; i++) {
    2711:           PetscInt gInd = pInd[i];

    2713:           if (gInd >= colStart && gInd < colEnd) {
    2714:             numD[0]++;
    2715:           }
    2716:           else if (gInd >= 0) { /* negative means non-entry */
    2717:             numO[0]++;
    2718:           }
    2719:         }
    2720:       }
    2721:       PetscSectionGetDof(leafMatricesSec,p,&matSize);
    2722:       if (!matSize) { /* incoming matrix is identity */
    2723:         PetscInt childId;

    2725:         childId = childIds[p-pStartF];
    2726:         if (childId < 0) { /* no child interpolation: one nnz per */
    2727:           if (numFields) {
    2728:             PetscInt f;
    2729:             for (f = 0; f < numFields; f++) {
    2730:               PetscInt numRows = offsets[f+1] - offsets[f], row;
    2731:               for (row = 0; row < numRows; row++) {
    2732:                 PetscInt gIndCoarse = pInd[newOffsets[f] + row];
    2733:                 PetscInt gIndFine   = rowIndices[offsets[f] + row];
    2734:                 if (gIndCoarse >= colStart && gIndCoarse < colEnd) { /* local */
    2735:                   if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2736:                   dnnz[gIndFine - rowStart] = 1;
    2737:                 }
    2738:                 else if (gIndCoarse >= 0) { /* remote */
    2739:                   if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2740:                   onnz[gIndFine - rowStart] = 1;
    2741:                 }
    2742:                 else { /* constrained */
    2743:                   if (gIndFine >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2744:                 }
    2745:               }
    2746:             }
    2747:           }
    2748:           else {
    2749:             PetscInt i;
    2750:             for (i = 0; i < gDof; i++) {
    2751:               PetscInt gIndCoarse = pInd[i];
    2752:               PetscInt gIndFine   = rowIndices[i];
    2753:               if (gIndCoarse >= colStart && gIndCoarse < colEnd) { /* local */
    2754:                 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2755:                 dnnz[gIndFine - rowStart] = 1;
    2756:               }
    2757:               else if (gIndCoarse >= 0) { /* remote */
    2758:                 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2759:                 onnz[gIndFine - rowStart] = 1;
    2760:               }
    2761:               else { /* constrained */
    2762:                 if (gIndFine >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2763:               }
    2764:             }
    2765:           }
    2766:         }
    2767:         else { /* interpolate from all */
    2768:           if (numFields) {
    2769:             PetscInt f;
    2770:             for (f = 0; f < numFields; f++) {
    2771:               PetscInt numRows = offsets[f+1] - offsets[f], row;
    2772:               for (row = 0; row < numRows; row++) {
    2773:                 PetscInt gIndFine = rowIndices[offsets[f] + row];
    2774:                 if (gIndFine >= 0) {
    2775:                   if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2776:                   dnnz[gIndFine - rowStart] = numD[f];
    2777:                   onnz[gIndFine - rowStart] = numO[f];
    2778:                 }
    2779:               }
    2780:             }
    2781:           }
    2782:           else {
    2783:             PetscInt i;
    2784:             for (i = 0; i < gDof; i++) {
    2785:               PetscInt gIndFine = rowIndices[i];
    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[0];
    2789:                 onnz[gIndFine - rowStart] = numO[0];
    2790:               }
    2791:             }
    2792:           }
    2793:         }
    2794:       }
    2795:       else { /* interpolate from all */
    2796:         if (numFields) {
    2797:           PetscInt f;
    2798:           for (f = 0; f < numFields; f++) {
    2799:             PetscInt numRows = offsets[f+1] - offsets[f], row;
    2800:             for (row = 0; row < numRows; row++) {
    2801:               PetscInt gIndFine = rowIndices[offsets[f] + row];
    2802:               if (gIndFine >= 0) {
    2803:                 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
    2804:                 dnnz[gIndFine - rowStart] = numD[f];
    2805:                 onnz[gIndFine - rowStart] = numO[f];
    2806:               }
    2807:             }
    2808:           }
    2809:         }
    2810:         else { /* every dof get a full row */
    2811:           PetscInt i;
    2812:           for (i = 0; i < gDof; i++) {
    2813:             PetscInt gIndFine = rowIndices[i];
    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[0];
    2817:               onnz[gIndFine - rowStart] = numO[0];
    2818:             }
    2819:           }
    2820:         }
    2821:       }
    2822:     }
    2823:     MatXAIJSetPreallocation(mat,1,dnnz,onnz,NULL,NULL);
    2824:     PetscFree2(dnnz,onnz);

    2826:     DMPlexGetReferenceTree(fine,&refTree);
    2827:     DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
    2828:     DMGetDefaultConstraints(refTree,&refConSec,NULL);
    2829:     DMPlexGetAnchors(refTree,&refAnSec,NULL);
    2830:     PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
    2831:     PetscSectionGetMaxDof(refConSec,&maxConDof);
    2832:     PetscSectionGetMaxDof(leafIndicesSec,&maxColumns);
    2833:     PetscMalloc1(maxConDof*maxColumns,&pointWork);
    2834:     for (p = leafStart; p < leafEnd; p++) {
    2835:       PetscInt    gDof, gcDof, gOff;
    2836:       PetscInt    numColIndices, pIndOff, *pInd;
    2837:       PetscInt    matSize;
    2838:       PetscInt    childId;

    2841:       PetscSectionGetDof(globalFine,p,&gDof);
    2842:       PetscSectionGetConstraintDof(globalFine,p,&gcDof);
    2843:       if ((gDof - gcDof) <= 0) {
    2844:         continue;
    2845:       }
    2846:       childId = childIds[p-pStartF];
    2847:       PetscSectionGetOffset(globalFine,p,&gOff);
    2848:       PetscSectionGetDof(leafIndicesSec,p,&numColIndices);
    2849:       PetscSectionGetOffset(leafIndicesSec,p,&pIndOff);
    2850:       numColIndices -= 2 * numFields;
    2851:       pInd = &leafIndices[pIndOff];
    2852:       offsets[0]        = 0;
    2853:       offsetsCopy[0]    = 0;
    2854:       newOffsets[0]     = 0;
    2855:       newOffsetsCopy[0] = 0;
    2856:       rowOffsets[0]     = 0;
    2857:       if (numFields) {
    2858:         PetscInt f;
    2859:         for (f = 0; f < numFields; f++) {
    2860:           PetscInt rowDof;

    2862:           PetscSectionGetFieldDof(localFine,p,f,&rowDof);
    2863:           offsets[f + 1]     = offsets[f] + rowDof;
    2864:           offsetsCopy[f + 1] = offsets[f + 1];
    2865:           rowOffsets[f + 1]  = pInd[numColIndices + f];
    2866:           newOffsets[f + 1]  = pInd[numColIndices + numFields + f];
    2867:         }
    2868:         DMPlexGetIndicesPointFields_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,NULL,-1,rowIndices);
    2869:       }
    2870:       else {
    2871:         DMPlexGetIndicesPoint_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,NULL,rowIndices);
    2872:       }
    2873:       PetscSectionGetDof(leafMatricesSec,p,&matSize);
    2874:       if (!matSize) { /* incoming matrix is identity */
    2875:         if (childId < 0) { /* no child interpolation: scatter */
    2876:           if (numFields) {
    2877:             PetscInt f;
    2878:             for (f = 0; f < numFields; f++) {
    2879:               PetscInt numRows = offsets[f+1] - offsets[f], row;
    2880:               for (row = 0; row < numRows; row++) {
    2881:                 MatSetValue(mat,rowIndices[offsets[f]+row],pInd[newOffsets[f]+row],1.,INSERT_VALUES);
    2882:               }
    2883:             }
    2884:           }
    2885:           else {
    2886:             PetscInt numRows = gDof, row;
    2887:             for (row = 0; row < numRows; row++) {
    2888:               MatSetValue(mat,rowIndices[row],pInd[row],1.,INSERT_VALUES);
    2889:             }
    2890:           }
    2891:         }
    2892:         else { /* interpolate from all */
    2893:           if (numFields) {
    2894:             PetscInt f;
    2895:             for (f = 0; f < numFields; f++) {
    2896:               PetscInt numRows = offsets[f+1] - offsets[f];
    2897:               PetscInt numCols = newOffsets[f + 1] - newOffsets[f];
    2898:               MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],refPointFieldMats[childId - pRefStart][f],INSERT_VALUES);
    2899:             }
    2900:           }
    2901:           else {
    2902:             MatSetValues(mat,gDof,rowIndices,numColIndices,pInd,refPointFieldMats[childId - pRefStart][0],INSERT_VALUES);
    2903:           }
    2904:         }
    2905:       }
    2906:       else { /* interpolate from all */
    2907:         PetscInt    pMatOff;
    2908:         PetscScalar *pMat;

    2910:         PetscSectionGetOffset(leafMatricesSec,p,&pMatOff);
    2911:         pMat = &leafMatrices[pMatOff];
    2912:         if (childId < 0) { /* copy the incoming matrix */
    2913:           if (numFields) {
    2914:             PetscInt f, count;
    2915:             for (f = 0, count = 0; f < numFields; f++) {
    2916:               PetscInt numRows = offsets[f+1]-offsets[f];
    2917:               PetscInt numCols = newOffsets[f+1]-newOffsets[f];
    2918:               PetscInt numInRows = rowOffsets[f+1]-rowOffsets[f];
    2919:               PetscScalar *inMat = &pMat[count];

    2921:               MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],inMat,INSERT_VALUES);
    2922:               count += numCols * numInRows;
    2923:             }
    2924:           }
    2925:           else {
    2926:             MatSetValues(mat,gDof,rowIndices,numColIndices,pInd,pMat,INSERT_VALUES);
    2927:           }
    2928:         }
    2929:         else { /* multiply the incoming matrix by the child interpolation */
    2930:           if (numFields) {
    2931:             PetscInt f, count;
    2932:             for (f = 0, count = 0; f < numFields; f++) {
    2933:               PetscInt numRows = offsets[f+1]-offsets[f];
    2934:               PetscInt numCols = newOffsets[f+1]-newOffsets[f];
    2935:               PetscInt numInRows = rowOffsets[f+1]-rowOffsets[f];
    2936:               PetscScalar *inMat = &pMat[count];
    2937:               PetscInt i, j, k;
    2938:               if (refPointFieldN[childId - pRefStart][f] != numInRows) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Point constraint matrix multiply dimension mismatch");
    2939:               for (i = 0; i < numRows; i++) {
    2940:                 for (j = 0; j < numCols; j++) {
    2941:                   PetscScalar val = 0.;
    2942:                   for (k = 0; k < numInRows; k++) {
    2943:                     val += refPointFieldMats[childId - pRefStart][f][i * numInRows + k] * inMat[k * numCols + j];
    2944:                   }
    2945:                   pointWork[i * numCols + j] = val;
    2946:                 }
    2947:               }
    2948:               MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],pointWork,INSERT_VALUES);
    2949:               count += numCols * numInRows;
    2950:             }
    2951:           }
    2952:           else { /* every dof gets a full row */
    2953:             PetscInt numRows   = gDof;
    2954:             PetscInt numCols   = numColIndices;
    2955:             PetscInt numInRows = matSize / numColIndices;
    2956:             PetscInt i, j, k;
    2957:             if (refPointFieldN[childId - pRefStart][0] != numInRows) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Point constraint matrix multiply dimension mismatch");
    2958:             for (i = 0; i < numRows; i++) {
    2959:               for (j = 0; j < numCols; j++) {
    2960:                 PetscScalar val = 0.;
    2961:                 for (k = 0; k < numInRows; k++) {
    2962:                   val += refPointFieldMats[childId - pRefStart][0][i * numInRows + k] * pMat[k * numCols + j];
    2963:                 }
    2964:                 pointWork[i * numCols + j] = val;
    2965:               }
    2966:             }
    2967:             MatSetValues(mat,numRows,rowIndices,numCols,pInd,pointWork,INSERT_VALUES);
    2968:           }
    2969:         }
    2970:       }
    2971:     }
    2972:     DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
    2973:     DMRestoreWorkArray(fine,maxDof,MPIU_INT,&rowIndices);
    2974:     PetscFree(pointWork);
    2975:   }
    2976:   MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);
    2977:   MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);
    2978:   PetscSectionDestroy(&leafIndicesSec);
    2979:   PetscSectionDestroy(&leafMatricesSec);
    2980:   PetscFree2(leafIndices,leafMatrices);
    2981:   PetscFree2(*(PetscInt****)&perms,*(PetscScalar****)&flips);
    2982:   PetscFree7(offsets,offsetsCopy,newOffsets,newOffsetsCopy,rowOffsets,numD,numO);
    2983:   ISRestoreIndices(aIS,&anchors);
    2984:   return(0);
    2985: }

    2987: /*
    2988:  * Assuming a nodal basis (w.r.t. the dual basis) basis:
    2989:  *
    2990:  * for each coarse dof \phi^c_i:
    2991:  *   for each quadrature point (w_l,x_l) in the dual basis definition of \phi^c_i:
    2992:  *     for each fine dof \phi^f_j;
    2993:  *       a_{i,j} = 0;
    2994:  *       for each fine dof \phi^f_k:
    2995:  *         a_{i,j} += interp_{i,k} * \phi^f_k(x_l) * \phi^f_j(x_l) * w_l
    2996:  *                    [^^^ this is = \phi^c_i ^^^]
    2997:  */
    2998: PetscErrorCode DMPlexComputeInjectorReferenceTree(DM refTree, Mat *inj)
    2999: {
    3000:   PetscDS        ds;
    3001:   PetscSection   section, cSection;
    3002:   DMLabel        canonical, depth;
    3003:   Mat            cMat, mat;
    3004:   PetscInt       *nnz;
    3005:   PetscInt       f, dim, numFields, numSecFields, p, pStart, pEnd, cStart, cEnd;
    3006:   PetscInt       m, n;
    3007:   PetscScalar    *pointScalar;
    3008:   PetscReal      *v0, *v0parent, *vtmp, *J, *Jparent, *invJ, *pointRef, detJ, detJparent;

    3012:   DMGetSection(refTree,&section);
    3013:   DMGetDimension(refTree, &dim);
    3014:   PetscMalloc6(dim,&v0,dim,&v0parent,dim,&vtmp,dim*dim,&J,dim*dim,&Jparent,dim*dim,&invJ);
    3015:   PetscMalloc2(dim,&pointScalar,dim,&pointRef);
    3016:   DMGetDS(refTree,&ds);
    3017:   PetscDSGetNumFields(ds,&numFields);
    3018:   PetscSectionGetNumFields(section,&numSecFields);
    3019:   DMGetLabel(refTree,"canonical",&canonical);
    3020:   DMGetLabel(refTree,"depth",&depth);
    3021:   DMGetDefaultConstraints(refTree,&cSection,&cMat);
    3022:   DMPlexGetChart(refTree, &pStart, &pEnd);
    3023:   DMPlexGetHeightStratum(refTree, 0, &cStart, &cEnd);
    3024:   MatGetSize(cMat,&n,&m); /* the injector has transpose sizes from the constraint matrix */
    3025:   /* Step 1: compute non-zero pattern.  A proper subset of constraint matrix non-zero */
    3026:   PetscCalloc1(m,&nnz);
    3027:   for (p = pStart; p < pEnd; p++) { /* a point will have non-zeros if it is canonical, it has dofs, and its children have dofs */
    3028:     const PetscInt *children;
    3029:     PetscInt numChildren;
    3030:     PetscInt i, numChildDof, numSelfDof;

    3032:     if (canonical) {
    3033:       PetscInt pCanonical;
    3034:       DMLabelGetValue(canonical,p,&pCanonical);
    3035:       if (p != pCanonical) continue;
    3036:     }
    3037:     DMPlexGetTreeChildren(refTree,p,&numChildren,&children);
    3038:     if (!numChildren) continue;
    3039:     for (i = 0, numChildDof = 0; i < numChildren; i++) {
    3040:       PetscInt child = children[i];
    3041:       PetscInt dof;

    3043:       PetscSectionGetDof(section,child,&dof);
    3044:       numChildDof += dof;
    3045:     }
    3046:     PetscSectionGetDof(section,p,&numSelfDof);
    3047:     if (!numChildDof || !numSelfDof) continue;
    3048:     for (f = 0; f < numFields; f++) {
    3049:       PetscInt selfOff;

    3051:       if (numSecFields) { /* count the dofs for just this field */
    3052:         for (i = 0, numChildDof = 0; i < numChildren; i++) {
    3053:           PetscInt child = children[i];
    3054:           PetscInt dof;

    3056:           PetscSectionGetFieldDof(section,child,f,&dof);
    3057:           numChildDof += dof;
    3058:         }
    3059:         PetscSectionGetFieldDof(section,p,f,&numSelfDof);
    3060:         PetscSectionGetFieldOffset(section,p,f,&selfOff);
    3061:       }
    3062:       else {
    3063:         PetscSectionGetOffset(section,p,&selfOff);
    3064:       }
    3065:       for (i = 0; i < numSelfDof; i++) {
    3066:         nnz[selfOff + i] = numChildDof;
    3067:       }
    3068:     }
    3069:   }
    3070:   MatCreateAIJ(PETSC_COMM_SELF,m,n,m,n,-1,nnz,-1,NULL,&mat);
    3071:   PetscFree(nnz);
    3072:   /* Setp 2: compute entries */
    3073:   for (p = pStart; p < pEnd; p++) {
    3074:     const PetscInt *children;
    3075:     PetscInt numChildren;
    3076:     PetscInt i, numChildDof, numSelfDof;

    3078:     /* same conditions about when entries occur */
    3079:     if (canonical) {
    3080:       PetscInt pCanonical;
    3081:       DMLabelGetValue(canonical,p,&pCanonical);
    3082:       if (p != pCanonical) continue;
    3083:     }
    3084:     DMPlexGetTreeChildren(refTree,p,&numChildren,&children);
    3085:     if (!numChildren) continue;
    3086:     for (i = 0, numChildDof = 0; i < numChildren; i++) {
    3087:       PetscInt child = children[i];
    3088:       PetscInt dof;

    3090:       PetscSectionGetDof(section,child,&dof);
    3091:       numChildDof += dof;
    3092:     }
    3093:     PetscSectionGetDof(section,p,&numSelfDof);
    3094:     if (!numChildDof || !numSelfDof) continue;

    3096:     for (f = 0; f < numFields; f++) {
    3097:       PetscInt       selfOff, Nc, parentCell;
    3098:       PetscInt       cellShapeOff;
    3099:       PetscObject    disc;
    3100:       PetscDualSpace dsp;
    3101:       PetscClassId   classId;
    3102:       PetscScalar    *pointMat;
    3103:       PetscInt       *matRows, *matCols;
    3104:       PetscInt       pO = PETSC_MIN_INT;
    3105:       const PetscInt *depthNumDof;

    3107:       if (numSecFields) {
    3108:         for (i = 0, numChildDof = 0; i < numChildren; i++) {
    3109:           PetscInt child = children[i];
    3110:           PetscInt dof;

    3112:           PetscSectionGetFieldDof(section,child,f,&dof);
    3113:           numChildDof += dof;
    3114:         }
    3115:         PetscSectionGetFieldDof(section,p,f,&numSelfDof);
    3116:         PetscSectionGetFieldOffset(section,p,f,&selfOff);
    3117:       }
    3118:       else {
    3119:         PetscSectionGetOffset(section,p,&selfOff);
    3120:       }

    3122:       /* find a cell whose closure contains p */
    3123:       if (p >= cStart && p < cEnd) {
    3124:         parentCell = p;
    3125:       }
    3126:       else {
    3127:         PetscInt *star = NULL;
    3128:         PetscInt numStar;

    3130:         parentCell = -1;
    3131:         DMPlexGetTransitiveClosure(refTree,p,PETSC_FALSE,&numStar,&star);
    3132:         for (i = numStar - 1; i >= 0; i--) {
    3133:           PetscInt c = star[2 * i];

    3135:           if (c >= cStart && c < cEnd) {
    3136:             parentCell = c;
    3137:             break;
    3138:           }
    3139:         }
    3140:         DMPlexRestoreTransitiveClosure(refTree,p,PETSC_FALSE,&numStar,&star);
    3141:       }
    3142:       /* determine the offset of p's shape functions withing parentCell's shape functions */
    3143:       PetscDSGetDiscretization(ds,f,&disc);
    3144:       PetscObjectGetClassId(disc,&classId);
    3145:       if (classId == PETSCFE_CLASSID) {
    3146:         PetscFEGetDualSpace((PetscFE)disc,&dsp);
    3147:       }
    3148:       else if (classId == PETSCFV_CLASSID) {
    3149:         PetscFVGetDualSpace((PetscFV)disc,&dsp);
    3150:       }
    3151:       else {
    3152:         SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unsupported discretization object");
    3153:       }
    3154:       PetscDualSpaceGetNumDof(dsp,&depthNumDof);
    3155:       PetscDualSpaceGetNumComponents(dsp,&Nc);
    3156:       {
    3157:         PetscInt *closure = NULL;
    3158:         PetscInt numClosure;

    3160:         DMPlexGetTransitiveClosure(refTree,parentCell,PETSC_TRUE,&numClosure,&closure);
    3161:         for (i = 0, cellShapeOff = 0; i < numClosure; i++) {
    3162:           PetscInt point = closure[2 * i], pointDepth;

    3164:           pO = closure[2 * i + 1];
    3165:           if (point == p) break;
    3166:           DMLabelGetValue(depth,point,&pointDepth);
    3167:           cellShapeOff += depthNumDof[pointDepth];
    3168:         }
    3169:         DMPlexRestoreTransitiveClosure(refTree,parentCell,PETSC_TRUE,&numClosure,&closure);
    3170:       }

    3172:       DMGetWorkArray(refTree, numSelfDof * numChildDof, MPIU_SCALAR,&pointMat);
    3173:       DMGetWorkArray(refTree, numSelfDof + numChildDof, MPIU_INT,&matRows);
    3174:       matCols = matRows + numSelfDof;
    3175:       for (i = 0; i < numSelfDof; i++) {
    3176:         matRows[i] = selfOff + i;
    3177:       }
    3178:       for (i = 0; i < numSelfDof * numChildDof; i++) pointMat[i] = 0.;
    3179:       {
    3180:         PetscInt colOff = 0;

    3182:         for (i = 0; i < numChildren; i++) {
    3183:           PetscInt child = children[i];
    3184:           PetscInt dof, off, j;

    3186:           if (numSecFields) {
    3187:             PetscSectionGetFieldDof(cSection,child,f,&dof);
    3188:             PetscSectionGetFieldOffset(cSection,child,f,&off);
    3189:           }
    3190:           else {
    3191:             PetscSectionGetDof(cSection,child,&dof);
    3192:             PetscSectionGetOffset(cSection,child,&off);
    3193:           }

    3195:           for (j = 0; j < dof; j++) {
    3196:             matCols[colOff++] = off + j;
    3197:           }
    3198:         }
    3199:       }
    3200:       if (classId == PETSCFE_CLASSID) {
    3201:         PetscFE        fe = (PetscFE) disc;
    3202:         PetscInt       fSize;

    3204:         PetscFEGetDualSpace(fe,&dsp);
    3205:         PetscDualSpaceGetDimension(dsp,&fSize);
    3206:         for (i = 0; i < numSelfDof; i++) { /* for every shape function */
    3207:           PetscQuadrature q;
    3208:           PetscInt        dim, thisNc, numPoints, j, k;
    3209:           const PetscReal *points;
    3210:           const PetscReal *weights;
    3211:           PetscInt        *closure = NULL;
    3212:           PetscInt        numClosure;
    3213:           PetscInt        parentCellShapeDof = cellShapeOff + (pO < 0 ? (numSelfDof - 1 - i) : i);
    3214:           PetscReal       *Bparent;

    3216:           PetscDualSpaceGetFunctional(dsp,parentCellShapeDof,&q);
    3217:           PetscQuadratureGetData(q,&dim,&thisNc,&numPoints,&points,&weights);
    3218:           if (thisNc != Nc) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Functional dim %D does not much basis dim %D\n",thisNc,Nc);
    3219:           PetscFEGetTabulation(fe,numPoints,points,&Bparent,NULL,NULL); /* I'm expecting a nodal basis: weights[:]' * Bparent[:,cellShapeDof] = 1. */
    3220:           for (j = 0; j < numPoints; j++) {
    3221:             PetscInt          childCell = -1;
    3222:             PetscReal         *parentValAtPoint;
    3223:             const PetscReal   xi0[3] = {-1.,-1.,-1.};
    3224:             const PetscReal   *pointReal = &points[dim * j];
    3225:             const PetscScalar *point;
    3226:             PetscReal         *Bchild;
    3227:             PetscInt          childCellShapeOff, pointMatOff;
    3228: #if defined(PETSC_USE_COMPLEX)
    3229:             PetscInt          d;

    3231:             for (d = 0; d < dim; d++) {
    3232:               pointScalar[d] = points[dim * j + d];
    3233:             }
    3234:             point = pointScalar;
    3235: #else
    3236:             point = pointReal;
    3237: #endif

    3239:             parentValAtPoint = &Bparent[(fSize * j + parentCellShapeDof) * Nc];

    3241:             for (k = 0; k < numChildren; k++) { /* locate the point in a child's star cell*/
    3242:               PetscInt child = children[k];
    3243:               PetscInt *star = NULL;
    3244:               PetscInt numStar, s;

    3246:               DMPlexGetTransitiveClosure(refTree,child,PETSC_FALSE,&numStar,&star);
    3247:               for (s = numStar - 1; s >= 0; s--) {
    3248:                 PetscInt c = star[2 * s];

    3250:                 if (c < cStart || c >= cEnd) continue;
    3251:                 DMPlexLocatePoint_Internal(refTree,dim,point,c,&childCell);
    3252:                 if (childCell >= 0) break;
    3253:               }
    3254:               DMPlexRestoreTransitiveClosure(refTree,child,PETSC_FALSE,&numStar,&star);
    3255:               if (childCell >= 0) break;
    3256:             }
    3257:             if (childCell < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Could not locate quadrature point");
    3258:             DMPlexComputeCellGeometryFEM(refTree, childCell, NULL, v0, J, invJ, &detJ);
    3259:             DMPlexComputeCellGeometryFEM(refTree, parentCell, NULL, v0parent, Jparent, NULL, &detJparent);
    3260:             CoordinatesRefToReal(dim, dim, xi0, v0parent, Jparent, pointReal, vtmp);
    3261:             CoordinatesRealToRef(dim, dim, xi0, v0, invJ, vtmp, pointRef);

    3263:             PetscFEGetTabulation(fe,1,pointRef,&Bchild,NULL,NULL);
    3264:             DMPlexGetTransitiveClosure(refTree,childCell,PETSC_TRUE,&numClosure,&closure);
    3265:             for (k = 0, pointMatOff = 0; k < numChildren; k++) { /* point is located in cell => child dofs support at point are in closure of cell */
    3266:               PetscInt child = children[k], childDepth, childDof, childO = PETSC_MIN_INT;
    3267:               PetscInt l;

    3269:               DMLabelGetValue(depth,child,&childDepth);
    3270:               childDof = depthNumDof[childDepth];
    3271:               for (l = 0, childCellShapeOff = 0; l < numClosure; l++) {
    3272:                 PetscInt point = closure[2 * l];
    3273:                 PetscInt pointDepth;

    3275:                 childO = closure[2 * l + 1];
    3276:                 if (point == child) break;
    3277:                 DMLabelGetValue(depth,point,&pointDepth);
    3278:                 childCellShapeOff += depthNumDof[pointDepth];
    3279:               }
    3280:               if (l == numClosure) {
    3281:                 pointMatOff += childDof;
    3282:                 continue; /* child is not in the closure of the cell: has nothing to contribute to this point */
    3283:               }
    3284:               for (l = 0; l < childDof; l++) {
    3285:                 PetscInt    childCellDof = childCellShapeOff + (childO ? (childDof - 1 - l) : l), m;
    3286:                 PetscReal   *childValAtPoint;
    3287:                 PetscReal   val = 0.;

    3289:                 childValAtPoint = &Bchild[childCellDof * Nc];
    3290:                 for (m = 0; m < Nc; m++) {
    3291:                   val += weights[j * Nc + m] * parentValAtPoint[m] * childValAtPoint[m];
    3292:                 }

    3294:                 pointMat[i * numChildDof + pointMatOff + l] += val;
    3295:               }
    3296:               pointMatOff += childDof;
    3297:             }
    3298:             DMPlexRestoreTransitiveClosure(refTree,childCell,PETSC_TRUE,&numClosure,&closure);
    3299:             PetscFERestoreTabulation(fe,1,pointRef,&Bchild,NULL,NULL);
    3300:           }
    3301:           PetscFERestoreTabulation(fe,numPoints,points,&Bparent,NULL,NULL);
    3302:         }
    3303:       }
    3304:       else { /* just the volume-weighted averages of the children */
    3305:         PetscReal parentVol;
    3306:         PetscInt  childCell;

    3308:         DMPlexComputeCellGeometryFVM(refTree, p, &parentVol, NULL, NULL);
    3309:         for (i = 0, childCell = 0; i < numChildren; i++) {
    3310:           PetscInt  child = children[i], j;
    3311:           PetscReal childVol;

    3313:           if (child < cStart || child >= cEnd) continue;
    3314:           DMPlexComputeCellGeometryFVM(refTree, child, &childVol, NULL, NULL);
    3315:           for (j = 0; j < Nc; j++) {
    3316:             pointMat[j * numChildDof + Nc * childCell + j] = childVol / parentVol;
    3317:           }
    3318:           childCell++;
    3319:         }
    3320:       }
    3321:       /* Insert pointMat into mat */
    3322:       MatSetValues(mat,numSelfDof,matRows,numChildDof,matCols,pointMat,INSERT_VALUES);
    3323:       DMRestoreWorkArray(refTree, numSelfDof + numChildDof, MPIU_INT,&matRows);
    3324:       DMRestoreWorkArray(refTree, numSelfDof * numChildDof, MPIU_SCALAR,&pointMat);
    3325:     }
    3326:   }
    3327:   PetscFree6(v0,v0parent,vtmp,J,Jparent,invJ);
    3328:   PetscFree2(pointScalar,pointRef);
    3329:   MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);
    3330:   MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);
    3331:   *inj = mat;
    3332:   return(0);
    3333: }

    3335: static PetscErrorCode DMPlexReferenceTreeGetChildrenMatrices_Injection(DM refTree, Mat inj, PetscScalar ****childrenMats)
    3336: {
    3337:   PetscDS        ds;
    3338:   PetscInt       numFields, f, pRefStart, pRefEnd, p, *rows, *cols, maxDof;
    3339:   PetscScalar    ***refPointFieldMats;
    3340:   PetscSection   refConSec, refSection;

    3344:   DMGetDS(refTree,&ds);
    3345:   PetscDSGetNumFields(ds,&numFields);
    3346:   DMGetDefaultConstraints(refTree,&refConSec,NULL);
    3347:   DMGetSection(refTree,&refSection);
    3348:   PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
    3349:   PetscMalloc1(pRefEnd-pRefStart,&refPointFieldMats);
    3350:   PetscSectionGetMaxDof(refConSec,&maxDof);
    3351:   PetscMalloc1(maxDof,&rows);
    3352:   PetscMalloc1(maxDof*maxDof,&cols);
    3353:   for (p = pRefStart; p < pRefEnd; p++) {
    3354:     PetscInt parent, pDof, parentDof;

    3356:     DMPlexGetTreeParent(refTree,p,&parent,NULL);
    3357:     PetscSectionGetDof(refConSec,p,&pDof);
    3358:     PetscSectionGetDof(refSection,parent,&parentDof);
    3359:     if (!pDof || !parentDof || parent == p) continue;

    3361:     PetscMalloc1(numFields,&refPointFieldMats[p-pRefStart]);
    3362:     for (f = 0; f < numFields; f++) {
    3363:       PetscInt cDof, cOff, numCols, r;

    3365:       if (numFields > 1) {
    3366:         PetscSectionGetFieldDof(refConSec,p,f,&cDof);
    3367:         PetscSectionGetFieldOffset(refConSec,p,f,&cOff);
    3368:       }
    3369:       else {
    3370:         PetscSectionGetDof(refConSec,p,&cDof);
    3371:         PetscSectionGetOffset(refConSec,p,&cOff);
    3372:       }

    3374:       for (r = 0; r < cDof; r++) {
    3375:         rows[r] = cOff + r;
    3376:       }
    3377:       numCols = 0;
    3378:       {
    3379:         PetscInt aDof, aOff, j;

    3381:         if (numFields > 1) {
    3382:           PetscSectionGetFieldDof(refSection,parent,f,&aDof);
    3383:           PetscSectionGetFieldOffset(refSection,parent,f,&aOff);
    3384:         }
    3385:         else {
    3386:           PetscSectionGetDof(refSection,parent,&aDof);
    3387:           PetscSectionGetOffset(refSection,parent,&aOff);
    3388:         }

    3390:         for (j = 0; j < aDof; j++) {
    3391:           cols[numCols++] = aOff + j;
    3392:         }
    3393:       }
    3394:       PetscMalloc1(cDof*numCols,&refPointFieldMats[p-pRefStart][f]);
    3395:       /* transpose of constraint matrix */
    3396:       MatGetValues(inj,numCols,cols,cDof,rows,refPointFieldMats[p-pRefStart][f]);
    3397:     }
    3398:   }
    3399:   *childrenMats = refPointFieldMats;
    3400:   PetscFree(rows);
    3401:   PetscFree(cols);
    3402:   return(0);
    3403: }

    3405: static PetscErrorCode DMPlexReferenceTreeRestoreChildrenMatrices_Injection(DM refTree, Mat inj, PetscScalar ****childrenMats)
    3406: {
    3407:   PetscDS        ds;
    3408:   PetscScalar    ***refPointFieldMats;
    3409:   PetscInt       numFields, pRefStart, pRefEnd, p, f;
    3410:   PetscSection   refConSec, refSection;

    3414:   refPointFieldMats = *childrenMats;
    3415:   *childrenMats = NULL;
    3416:   DMGetDS(refTree,&ds);
    3417:   DMGetSection(refTree,&refSection);
    3418:   PetscDSGetNumFields(ds,&numFields);
    3419:   DMGetDefaultConstraints(refTree,&refConSec,NULL);
    3420:   PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
    3421:   for (p = pRefStart; p < pRefEnd; p++) {
    3422:     PetscInt parent, pDof, parentDof;

    3424:     DMPlexGetTreeParent(refTree,p,&parent,NULL);
    3425:     PetscSectionGetDof(refConSec,p,&pDof);
    3426:     PetscSectionGetDof(refSection,parent,&parentDof);
    3427:     if (!pDof || !parentDof || parent == p) continue;

    3429:     for (f = 0; f < numFields; f++) {
    3430:       PetscInt cDof;

    3432:       if (numFields > 1) {
    3433:         PetscSectionGetFieldDof(refConSec,p,f,&cDof);
    3434:       }
    3435:       else {
    3436:         PetscSectionGetDof(refConSec,p,&cDof);
    3437:       }

    3439:       PetscFree(refPointFieldMats[p - pRefStart][f]);
    3440:     }
    3441:     PetscFree(refPointFieldMats[p - pRefStart]);
    3442:   }
    3443:   PetscFree(refPointFieldMats);
    3444:   return(0);
    3445: }

    3447: static PetscErrorCode DMPlexReferenceTreeGetInjector(DM refTree,Mat *injRef)
    3448: {
    3449:   Mat            cMatRef;
    3450:   PetscObject    injRefObj;

    3454:   DMGetDefaultConstraints(refTree,NULL,&cMatRef);
    3455:   PetscObjectQuery((PetscObject)cMatRef,"DMPlexComputeInjectorTree_refTree",&injRefObj);
    3456:   *injRef = (Mat) injRefObj;
    3457:   if (!*injRef) {
    3458:     DMPlexComputeInjectorReferenceTree(refTree,injRef);
    3459:     PetscObjectCompose((PetscObject)cMatRef,"DMPlexComputeInjectorTree_refTree",(PetscObject)*injRef);
    3460:     /* there is now a reference in cMatRef, which should be the only one for symmetry with the above case */
    3461:     PetscObjectDereference((PetscObject)*injRef);
    3462:   }
    3463:   return(0);
    3464: }

    3466: static PetscErrorCode DMPlexTransferInjectorTree(DM coarse, DM fine, PetscSF coarseToFine, const PetscInt *childIds, Vec fineVec, PetscInt numFields, PetscInt *offsets, PetscSection *rootMultiSec, PetscSection *multiLeafSec, PetscInt **gatheredIndices, PetscScalar **gatheredValues)
    3467: {
    3468:   PetscInt       pStartF, pEndF, pStartC, pEndC, p, maxDof, numMulti;
    3469:   PetscSection   globalCoarse, globalFine;
    3470:   PetscSection   localCoarse, localFine, leafIndicesSec;
    3471:   PetscSection   multiRootSec, rootIndicesSec;
    3472:   PetscInt       *leafInds, *rootInds = NULL;
    3473:   const PetscInt *rootDegrees;
    3474:   PetscScalar    *leafVals = NULL, *rootVals = NULL;
    3475:   PetscSF        coarseToFineEmbedded;

    3479:   DMPlexGetChart(coarse,&pStartC,&pEndC);
    3480:   DMPlexGetChart(fine,&pStartF,&pEndF);
    3481:   DMGetSection(fine,&localFine);
    3482:   DMGetGlobalSection(fine,&globalFine);
    3483:   PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafIndicesSec);
    3484:   PetscSectionSetChart(leafIndicesSec,pStartF, pEndF);
    3485:   PetscSectionGetMaxDof(localFine,&maxDof);
    3486:   { /* winnow fine points that don't have global dofs out of the sf */
    3487:     PetscInt l, nleaves, dof, cdof, numPointsWithDofs, offset, *pointsWithDofs, numIndices;
    3488:     const PetscInt *leaves;

    3490:     PetscSFGetGraph(coarseToFine,NULL,&nleaves,&leaves,NULL);
    3491:     for (l = 0, numPointsWithDofs = 0; l < nleaves; l++) {
    3492:       p    = leaves ? leaves[l] : l;
    3493:       PetscSectionGetDof(globalFine,p,&dof);
    3494:       PetscSectionGetConstraintDof(globalFine,p,&cdof);
    3495:       if ((dof - cdof) > 0) {
    3496:         numPointsWithDofs++;

    3498:         PetscSectionGetDof(localFine,p,&dof);
    3499:         PetscSectionSetDof(leafIndicesSec,p,dof + 1);
    3500:       }
    3501:     }
    3502:     PetscMalloc1(numPointsWithDofs,&pointsWithDofs);
    3503:     PetscSectionSetUp(leafIndicesSec);
    3504:     PetscSectionGetStorageSize(leafIndicesSec,&numIndices);
    3505:     PetscMalloc1(gatheredIndices ? numIndices : (maxDof + 1),&leafInds);
    3506:     if (gatheredValues)  {PetscMalloc1(numIndices,&leafVals);}
    3507:     for (l = 0, offset = 0; l < nleaves; l++) {
    3508:       p    = leaves ? leaves[l] : l;
    3509:       PetscSectionGetDof(globalFine,p,&dof);
    3510:       PetscSectionGetConstraintDof(globalFine,p,&cdof);
    3511:       if ((dof - cdof) > 0) {
    3512:         PetscInt    off, gOff;
    3513:         PetscInt    *pInd;
    3514:         PetscScalar *pVal = NULL;

    3516:         pointsWithDofs[offset++] = l;

    3518:         PetscSectionGetOffset(leafIndicesSec,p,&off);

    3520:         pInd = gatheredIndices ? (&leafInds[off + 1]) : leafInds;
    3521:         if (gatheredValues) {
    3522:           PetscInt i;

    3524:           pVal = &leafVals[off + 1];
    3525:           for (i = 0; i < dof; i++) pVal[i] = 0.;
    3526:         }
    3527:         PetscSectionGetOffset(globalFine,p,&gOff);

    3529:         offsets[0] = 0;
    3530:         if (numFields) {
    3531:           PetscInt f;

    3533:           for (f = 0; f < numFields; f++) {
    3534:             PetscInt fDof;
    3535:             PetscSectionGetFieldDof(localFine,p,f,&fDof);
    3536:             offsets[f + 1] = fDof + offsets[f];
    3537:           }
    3538:           DMPlexGetIndicesPointFields_Internal(localFine,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,NULL,-1,pInd);
    3539:         }
    3540:         else {
    3541:           DMPlexGetIndicesPoint_Internal(localFine,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,NULL,pInd);
    3542:         }
    3543:         if (gatheredValues) {VecGetValues(fineVec,dof,pInd,pVal);}
    3544:       }
    3545:     }
    3546:     PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);
    3547:     PetscFree(pointsWithDofs);
    3548:   }

    3550:   DMPlexGetChart(coarse,&pStartC,&pEndC);
    3551:   DMGetSection(coarse,&localCoarse);
    3552:   DMGetGlobalSection(coarse,&globalCoarse);

    3554:   { /* there may be the case where an sf root has a parent: broadcast parents back to children */
    3555:     MPI_Datatype threeInt;
    3556:     PetscMPIInt  rank;
    3557:     PetscInt     (*parentNodeAndIdCoarse)[3];
    3558:     PetscInt     (*parentNodeAndIdFine)[3];
    3559:     PetscInt     p, nleaves, nleavesToParents;
    3560:     PetscSF      pointSF, sfToParents;
    3561:     const PetscInt *ilocal;
    3562:     const PetscSFNode *iremote;
    3563:     PetscSFNode  *iremoteToParents;
    3564:     PetscInt     *ilocalToParents;

    3566:     MPI_Comm_rank(PetscObjectComm((PetscObject)coarse),&rank);
    3567:     MPI_Type_contiguous(3,MPIU_INT,&threeInt);
    3568:     MPI_Type_commit(&threeInt);
    3569:     PetscMalloc2(pEndC-pStartC,&parentNodeAndIdCoarse,pEndF-pStartF,&parentNodeAndIdFine);
    3570:     DMGetPointSF(coarse,&pointSF);
    3571:     PetscSFGetGraph(pointSF,NULL,&nleaves,&ilocal,&iremote);
    3572:     for (p = pStartC; p < pEndC; p++) {
    3573:       PetscInt parent, childId;
    3574:       DMPlexGetTreeParent(coarse,p,&parent,&childId);
    3575:       parentNodeAndIdCoarse[p - pStartC][0] = rank;
    3576:       parentNodeAndIdCoarse[p - pStartC][1] = parent - pStartC;
    3577:       parentNodeAndIdCoarse[p - pStartC][2] = (p == parent) ? -1 : childId;
    3578:       if (nleaves > 0) {
    3579:         PetscInt leaf = -1;

    3581:         if (ilocal) {
    3582:           PetscFindInt(parent,nleaves,ilocal,&leaf);
    3583:         }
    3584:         else {
    3585:           leaf = p - pStartC;
    3586:         }
    3587:         if (leaf >= 0) {
    3588:           parentNodeAndIdCoarse[p - pStartC][0] = iremote[leaf].rank;
    3589:           parentNodeAndIdCoarse[p - pStartC][1] = iremote[leaf].index;
    3590:         }
    3591:       }
    3592:     }
    3593:     for (p = pStartF; p < pEndF; p++) {
    3594:       parentNodeAndIdFine[p - pStartF][0] = -1;
    3595:       parentNodeAndIdFine[p - pStartF][1] = -1;
    3596:       parentNodeAndIdFine[p - pStartF][2] = -1;
    3597:     }
    3598:     PetscSFBcastBegin(coarseToFineEmbedded,threeInt,parentNodeAndIdCoarse,parentNodeAndIdFine);
    3599:     PetscSFBcastEnd(coarseToFineEmbedded,threeInt,parentNodeAndIdCoarse,parentNodeAndIdFine);
    3600:     for (p = pStartF, nleavesToParents = 0; p < pEndF; p++) {
    3601:       PetscInt dof;

    3603:       PetscSectionGetDof(leafIndicesSec,p,&dof);
    3604:       if (dof) {
    3605:         PetscInt off;

    3607:         PetscSectionGetOffset(leafIndicesSec,p,&off);
    3608:         if (gatheredIndices) {
    3609:           leafInds[off] = PetscMax(childIds[p-pStartF],parentNodeAndIdFine[p-pStartF][2]);
    3610:         } else if (gatheredValues) {
    3611:           leafVals[off] = (PetscScalar) PetscMax(childIds[p-pStartF],parentNodeAndIdFine[p-pStartF][2]);
    3612:         }
    3613:       }
    3614:       if (parentNodeAndIdFine[p-pStartF][0] >= 0) {
    3615:         nleavesToParents++;
    3616:       }
    3617:     }
    3618:     PetscMalloc1(nleavesToParents,&ilocalToParents);
    3619:     PetscMalloc1(nleavesToParents,&iremoteToParents);
    3620:     for (p = pStartF, nleavesToParents = 0; p < pEndF; p++) {
    3621:       if (parentNodeAndIdFine[p-pStartF][0] >= 0) {
    3622:         ilocalToParents[nleavesToParents] = p - pStartF;
    3623:         iremoteToParents[nleavesToParents].rank  = parentNodeAndIdFine[p-pStartF][0];
    3624:         iremoteToParents[nleavesToParents].index = parentNodeAndIdFine[p-pStartF][1];
    3625:         nleavesToParents++;
    3626:       }
    3627:     }
    3628:     PetscSFCreate(PetscObjectComm((PetscObject)coarse),&sfToParents);
    3629:     PetscSFSetGraph(sfToParents,pEndC-pStartC,nleavesToParents,ilocalToParents,PETSC_OWN_POINTER,iremoteToParents,PETSC_OWN_POINTER);
    3630:     PetscSFDestroy(&coarseToFineEmbedded);

    3632:     coarseToFineEmbedded = sfToParents;

    3634:     PetscFree2(parentNodeAndIdCoarse,parentNodeAndIdFine);
    3635:     MPI_Type_free(&threeInt);
    3636:   }

    3638:   { /* winnow out coarse points that don't have dofs */
    3639:     PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs;
    3640:     PetscSF  sfDofsOnly;

    3642:     for (p = pStartC, numPointsWithDofs = 0; p < pEndC; p++) {
    3643:       PetscSectionGetDof(globalCoarse,p,&dof);
    3644:       PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
    3645:       if ((dof - cdof) > 0) {
    3646:         numPointsWithDofs++;
    3647:       }
    3648:     }
    3649:     PetscMalloc1(numPointsWithDofs,&pointsWithDofs);
    3650:     for (p = pStartC, offset = 0; p < pEndC; p++) {
    3651:       PetscSectionGetDof(globalCoarse,p,&dof);
    3652:       PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
    3653:       if ((dof - cdof) > 0) {
    3654:         pointsWithDofs[offset++] = p - pStartC;
    3655:       }
    3656:     }
    3657:     PetscSFCreateEmbeddedSF(coarseToFineEmbedded, numPointsWithDofs, pointsWithDofs, &sfDofsOnly);
    3658:     PetscSFDestroy(&coarseToFineEmbedded);
    3659:     PetscFree(pointsWithDofs);
    3660:     coarseToFineEmbedded = sfDofsOnly;
    3661:   }

    3663:   /* communicate back to the coarse mesh which coarse points have children (that may require injection) */
    3664:   PetscSFComputeDegreeBegin(coarseToFineEmbedded,&rootDegrees);
    3665:   PetscSFComputeDegreeEnd(coarseToFineEmbedded,&rootDegrees);
    3666:   PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&multiRootSec);
    3667:   PetscSectionSetChart(multiRootSec,pStartC,pEndC);
    3668:   for (p = pStartC; p < pEndC; p++) {
    3669:     PetscSectionSetDof(multiRootSec,p,rootDegrees[p-pStartC]);
    3670:   }
    3671:   PetscSectionSetUp(multiRootSec);
    3672:   PetscSectionGetStorageSize(multiRootSec,&numMulti);
    3673:   PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootIndicesSec);
    3674:   { /* distribute the leaf section */
    3675:     PetscSF multi, multiInv, indicesSF;
    3676:     PetscInt *remoteOffsets, numRootIndices;

    3678:     PetscSFGetMultiSF(coarseToFineEmbedded,&multi);
    3679:     PetscSFCreateInverseSF(multi,&multiInv);
    3680:     PetscSFDistributeSection(multiInv,leafIndicesSec,&remoteOffsets,rootIndicesSec);
    3681:     PetscSFCreateSectionSF(multiInv,leafIndicesSec,remoteOffsets,rootIndicesSec,&indicesSF);
    3682:     PetscFree(remoteOffsets);
    3683:     PetscSFDestroy(&multiInv);
    3684:     PetscSectionGetStorageSize(rootIndicesSec,&numRootIndices);
    3685:     if (gatheredIndices) {
    3686:       PetscMalloc1(numRootIndices,&rootInds);
    3687:       PetscSFBcastBegin(indicesSF,MPIU_INT,leafInds,rootInds);
    3688:       PetscSFBcastEnd(indicesSF,MPIU_INT,leafInds,rootInds);
    3689:     }
    3690:     if (gatheredValues) {
    3691:       PetscMalloc1(numRootIndices,&rootVals);
    3692:       PetscSFBcastBegin(indicesSF,MPIU_SCALAR,leafVals,rootVals);
    3693:       PetscSFBcastEnd(indicesSF,MPIU_SCALAR,leafVals,rootVals);
    3694:     }
    3695:     PetscSFDestroy(&indicesSF);
    3696:   }
    3697:   PetscSectionDestroy(&leafIndicesSec);
    3698:   PetscFree(leafInds);
    3699:   PetscFree(leafVals);
    3700:   PetscSFDestroy(&coarseToFineEmbedded);
    3701:   *rootMultiSec = multiRootSec;
    3702:   *multiLeafSec = rootIndicesSec;
    3703:   if (gatheredIndices) *gatheredIndices = rootInds;
    3704:   if (gatheredValues)  *gatheredValues  = rootVals;
    3705:   return(0);
    3706: }

    3708: PetscErrorCode DMPlexComputeInjectorTree(DM coarse, DM fine, PetscSF coarseToFine, PetscInt *childIds, Mat mat)
    3709: {
    3710:   DM             refTree;
    3711:   PetscSection   multiRootSec, rootIndicesSec;
    3712:   PetscSection   globalCoarse, globalFine;
    3713:   PetscSection   localCoarse, localFine;
    3714:   PetscSection   cSecRef;
    3715:   PetscInt       *rootIndices, *parentIndices, pRefStart, pRefEnd;
    3716:   Mat            injRef;
    3717:   PetscInt       numFields, maxDof;
    3718:   PetscInt       pStartC, pEndC, pStartF, pEndF, p;
    3719:   PetscInt       *offsets, *offsetsCopy, *rowOffsets;
    3720:   PetscLayout    rowMap, colMap;
    3721:   PetscInt       rowStart, rowEnd, colStart, colEnd, *nnzD, *nnzO;
    3722:   PetscScalar    ***childrenMats=NULL ; /* gcc -O gives 'may be used uninitialized' warning'. Initializing to suppress this warning */

    3727:   /* get the templates for the fine-to-coarse injection from the reference tree */
    3728:   DMPlexGetReferenceTree(coarse,&refTree);
    3729:   DMGetDefaultConstraints(refTree,&cSecRef,NULL);
    3730:   PetscSectionGetChart(cSecRef,&pRefStart,&pRefEnd);
    3731:   DMPlexReferenceTreeGetInjector(refTree,&injRef);

    3733:   DMPlexGetChart(fine,&pStartF,&pEndF);
    3734:   DMGetSection(fine,&localFine);
    3735:   DMGetGlobalSection(fine,&globalFine);
    3736:   PetscSectionGetNumFields(localFine,&numFields);
    3737:   DMPlexGetChart(coarse,&pStartC,&pEndC);
    3738:   DMGetSection(coarse,&localCoarse);
    3739:   DMGetGlobalSection(coarse,&globalCoarse);
    3740:   PetscSectionGetMaxDof(localCoarse,&maxDof);
    3741:   {
    3742:     PetscInt maxFields = PetscMax(1,numFields) + 1;
    3743:     PetscMalloc3(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&rowOffsets);
    3744:   }

    3746:   DMPlexTransferInjectorTree(coarse,fine,coarseToFine,childIds,NULL,numFields,offsets,&multiRootSec,&rootIndicesSec,&rootIndices,NULL);

    3748:   PetscMalloc1(maxDof,&parentIndices);

    3750:   /* count indices */
    3751:   MatGetLayouts(mat,&rowMap,&colMap);
    3752:   PetscLayoutSetUp(rowMap);
    3753:   PetscLayoutSetUp(colMap);
    3754:   PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);
    3755:   PetscLayoutGetRange(colMap,&colStart,&colEnd);
    3756:   PetscCalloc2(rowEnd-rowStart,&nnzD,rowEnd-rowStart,&nnzO);
    3757:   for (p = pStartC; p < pEndC; p++) {
    3758:     PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff;

    3760:     PetscSectionGetDof(globalCoarse,p,&dof);
    3761:     PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
    3762:     if ((dof - cdof) <= 0) continue;
    3763:     PetscSectionGetOffset(globalCoarse,p,&gOff);

    3765:     rowOffsets[0] = 0;
    3766:     offsetsCopy[0] = 0;
    3767:     if (numFields) {
    3768:       PetscInt f;

    3770:       for (f = 0; f < numFields; f++) {
    3771:         PetscInt fDof;
    3772:         PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
    3773:         rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f];
    3774:       }
    3775:       DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL,-1,parentIndices);
    3776:     }
    3777:     else {
    3778:       DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL,parentIndices);
    3779:       rowOffsets[1] = offsetsCopy[0];
    3780:     }

    3782:     PetscSectionGetDof(multiRootSec,p,&numLeaves);
    3783:     PetscSectionGetOffset(multiRootSec,p,&leafStart);
    3784:     leafEnd = leafStart + numLeaves;
    3785:     for (l = leafStart; l < leafEnd; l++) {
    3786:       PetscInt numIndices, childId, offset;
    3787:       const PetscInt *childIndices;

    3789:       PetscSectionGetDof(rootIndicesSec,l,&numIndices);
    3790:       PetscSectionGetOffset(rootIndicesSec,l,&offset);
    3791:       childId = rootIndices[offset++];
    3792:       childIndices = &rootIndices[offset];
    3793:       numIndices--;

    3795:       if (childId == -1) { /* equivalent points: scatter */
    3796:         PetscInt i;

    3798:         for (i = 0; i < numIndices; i++) {
    3799:           PetscInt colIndex = childIndices[i];
    3800:           PetscInt rowIndex = parentIndices[i];
    3801:           if (rowIndex < 0) continue;
    3802:           if (colIndex < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Unconstrained fine and constrained coarse");
    3803:           if (colIndex >= colStart && colIndex < colEnd) {
    3804:             nnzD[rowIndex - rowStart] = 1;
    3805:           }
    3806:           else {
    3807:             nnzO[rowIndex - rowStart] = 1;
    3808:           }
    3809:         }
    3810:       }
    3811:       else {
    3812:         PetscInt parentId, f, lim;

    3814:         DMPlexGetTreeParent(refTree,childId,&parentId,NULL);

    3816:         lim = PetscMax(1,numFields);
    3817:         offsets[0] = 0;
    3818:         if (numFields) {
    3819:           PetscInt f;

    3821:           for (f = 0; f < numFields; f++) {
    3822:             PetscInt fDof;
    3823:             PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);

    3825:             offsets[f + 1] = fDof + offsets[f];
    3826:           }
    3827:         }
    3828:         else {
    3829:           PetscInt cDof;

    3831:           PetscSectionGetDof(cSecRef,childId,&cDof);
    3832:           offsets[1] = cDof;
    3833:         }
    3834:         for (f = 0; f < lim; f++) {
    3835:           PetscInt parentStart = rowOffsets[f], parentEnd = rowOffsets[f + 1];
    3836:           PetscInt childStart = offsets[f], childEnd = offsets[f + 1];
    3837:           PetscInt i, numD = 0, numO = 0;

    3839:           for (i = childStart; i < childEnd; i++) {
    3840:             PetscInt colIndex = childIndices[i];

    3842:             if (colIndex < 0) continue;
    3843:             if (colIndex >= colStart && colIndex < colEnd) {
    3844:               numD++;
    3845:             }
    3846:             else {
    3847:               numO++;
    3848:             }
    3849:           }
    3850:           for (i = parentStart; i < parentEnd; i++) {
    3851:             PetscInt rowIndex = parentIndices[i];

    3853:             if (rowIndex < 0) continue;
    3854:             nnzD[rowIndex - rowStart] += numD;
    3855:             nnzO[rowIndex - rowStart] += numO;
    3856:           }
    3857:         }
    3858:       }
    3859:     }
    3860:   }
    3861:   /* preallocate */
    3862:   MatXAIJSetPreallocation(mat,1,nnzD,nnzO,NULL,NULL);
    3863:   PetscFree2(nnzD,nnzO);
    3864:   /* insert values */
    3865:   DMPlexReferenceTreeGetChildrenMatrices_Injection(refTree,injRef,&childrenMats);
    3866:   for (p = pStartC; p < pEndC; p++) {
    3867:     PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff;

    3869:     PetscSectionGetDof(globalCoarse,p,&dof);
    3870:     PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
    3871:     if ((dof - cdof) <= 0) continue;
    3872:     PetscSectionGetOffset(globalCoarse,p,&gOff);

    3874:     rowOffsets[0] = 0;
    3875:     offsetsCopy[0] = 0;
    3876:     if (numFields) {
    3877:       PetscInt f;

    3879:       for (f = 0; f < numFields; f++) {
    3880:         PetscInt fDof;
    3881:         PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
    3882:         rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f];
    3883:       }
    3884:       DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL,-1,parentIndices);
    3885:     }
    3886:     else {
    3887:       DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL,parentIndices);
    3888:       rowOffsets[1] = offsetsCopy[0];
    3889:     }

    3891:     PetscSectionGetDof(multiRootSec,p,&numLeaves);
    3892:     PetscSectionGetOffset(multiRootSec,p,&leafStart);
    3893:     leafEnd = leafStart + numLeaves;
    3894:     for (l = leafStart; l < leafEnd; l++) {
    3895:       PetscInt numIndices, childId, offset;
    3896:       const PetscInt *childIndices;

    3898:       PetscSectionGetDof(rootIndicesSec,l,&numIndices);
    3899:       PetscSectionGetOffset(rootIndicesSec,l,&offset);
    3900:       childId = rootIndices[offset++];
    3901:       childIndices = &rootIndices[offset];
    3902:       numIndices--;

    3904:       if (childId == -1) { /* equivalent points: scatter */
    3905:         PetscInt i;

    3907:         for (i = 0; i < numIndices; i++) {
    3908:           MatSetValue(mat,parentIndices[i],childIndices[i],1.,INSERT_VALUES);
    3909:         }
    3910:       }
    3911:       else {
    3912:         PetscInt parentId, f, lim;

    3914:         DMPlexGetTreeParent(refTree,childId,&parentId,NULL);

    3916:         lim = PetscMax(1,numFields);
    3917:         offsets[0] = 0;
    3918:         if (numFields) {
    3919:           PetscInt f;

    3921:           for (f = 0; f < numFields; f++) {
    3922:             PetscInt fDof;
    3923:             PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);

    3925:             offsets[f + 1] = fDof + offsets[f];
    3926:           }
    3927:         }
    3928:         else {
    3929:           PetscInt cDof;

    3931:           PetscSectionGetDof(cSecRef,childId,&cDof);
    3932:           offsets[1] = cDof;
    3933:         }
    3934:         for (f = 0; f < lim; f++) {
    3935:           PetscScalar    *childMat   = &childrenMats[childId - pRefStart][f][0];
    3936:           PetscInt       *rowIndices = &parentIndices[rowOffsets[f]];
    3937:           const PetscInt *colIndices = &childIndices[offsets[f]];

    3939:           MatSetValues(mat,rowOffsets[f+1]-rowOffsets[f],rowIndices,offsets[f+1]-offsets[f],colIndices,childMat,INSERT_VALUES);
    3940:         }
    3941:       }
    3942:     }
    3943:   }
    3944:   PetscSectionDestroy(&multiRootSec);
    3945:   PetscSectionDestroy(&rootIndicesSec);
    3946:   PetscFree(parentIndices);
    3947:   DMPlexReferenceTreeRestoreChildrenMatrices_Injection(refTree,injRef,&childrenMats);
    3948:   PetscFree(rootIndices);
    3949:   PetscFree3(offsets,offsetsCopy,rowOffsets);

    3951:   MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);
    3952:   MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);
    3953:   return(0);
    3954: }

    3956: static PetscErrorCode DMPlexTransferVecTree_Interpolate(DM coarse, Vec vecCoarseLocal, DM fine, Vec vecFine, PetscSF coarseToFine, PetscInt *cids, Vec grad, Vec cellGeom)
    3957: {
    3958:   PetscDS           ds;
    3959:   PetscSF           coarseToFineEmbedded;
    3960:   PetscSection      globalCoarse, globalFine;
    3961:   PetscSection      localCoarse, localFine;
    3962:   PetscSection      aSec, cSec;
    3963:   PetscSection      rootValuesSec;
    3964:   PetscSection      leafValuesSec;
    3965:   PetscScalar       *rootValues, *leafValues;
    3966:   IS                aIS;
    3967:   const PetscInt    *anchors;
    3968:   Mat               cMat;
    3969:   PetscInt          numFields;
    3970:   PetscInt          pStartC, pEndC, pStartF, pEndF, p, cellStart, cellEnd, cellEndInterior;
    3971:   PetscInt          aStart, aEnd, cStart, cEnd;
    3972:   PetscInt          *maxChildIds;
    3973:   PetscInt          *offsets, *newOffsets, *offsetsCopy, *newOffsetsCopy, *rowOffsets, *numD, *numO;
    3974:   PetscFV           fv = NULL;
    3975:   PetscInt          dim, numFVcomps = -1, fvField = -1;
    3976:   DM                cellDM = NULL, gradDM = NULL;
    3977:   const PetscScalar *cellGeomArray = NULL;
    3978:   const PetscScalar *gradArray = NULL;
    3979:   PetscErrorCode    ierr;

    3982:   VecSetOption(vecFine,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);
    3983:   DMPlexGetChart(coarse,&pStartC,&pEndC);
    3984:   DMPlexGetHeightStratum(coarse,0,&cellStart,&cellEnd);
    3985:   DMPlexGetHybridBounds(coarse,&cellEndInterior,NULL,NULL,NULL);
    3986:   cellEnd = (cellEndInterior < 0) ? cellEnd : cellEndInterior;
    3987:   DMPlexGetChart(fine,&pStartF,&pEndF);
    3988:   DMGetGlobalSection(fine,&globalFine);
    3989:   DMGetCoordinateDim(coarse,&dim);
    3990:   { /* winnow fine points that don't have global dofs out of the sf */
    3991:     PetscInt       nleaves, l;
    3992:     const PetscInt *leaves;
    3993:     PetscInt       dof, cdof, numPointsWithDofs, offset, *pointsWithDofs;

    3995:     PetscSFGetGraph(coarseToFine,NULL,&nleaves,&leaves,NULL);

    3997:     for (l = 0, numPointsWithDofs = 0; l < nleaves; l++) {
    3998:       PetscInt p = leaves ? leaves[l] : l;

    4000:       PetscSectionGetDof(globalFine,p,&dof);
    4001:       PetscSectionGetConstraintDof(globalFine,p,&cdof);
    4002:       if ((dof - cdof) > 0) {
    4003:         numPointsWithDofs++;
    4004:       }
    4005:     }
    4006:     PetscMalloc1(numPointsWithDofs,&pointsWithDofs);
    4007:     for (l = 0, offset = 0; l < nleaves; l++) {
    4008:       PetscInt p = leaves ? leaves[l] : l;

    4010:       PetscSectionGetDof(globalFine,p,&dof);
    4011:       PetscSectionGetConstraintDof(globalFine,p,&cdof);
    4012:       if ((dof - cdof) > 0) {
    4013:         pointsWithDofs[offset++] = l;
    4014:       }
    4015:     }
    4016:     PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);
    4017:     PetscFree(pointsWithDofs);
    4018:   }
    4019:   /* communicate back to the coarse mesh which coarse points have children (that may require interpolation) */
    4020:   PetscMalloc1(pEndC-pStartC,&maxChildIds);
    4021:   for (p = pStartC; p < pEndC; p++) {
    4022:     maxChildIds[p - pStartC] = -2;
    4023:   }
    4024:   PetscSFReduceBegin(coarseToFineEmbedded,MPIU_INT,cids,maxChildIds,MPIU_MAX);
    4025:   PetscSFReduceEnd(coarseToFineEmbedded,MPIU_INT,cids,maxChildIds,MPIU_MAX);

    4027:   DMGetSection(coarse,&localCoarse);
    4028:   DMGetGlobalSection(coarse,&globalCoarse);

    4030:   DMPlexGetAnchors(coarse,&aSec,&aIS);
    4031:   ISGetIndices(aIS,&anchors);
    4032:   PetscSectionGetChart(aSec,&aStart,&aEnd);

    4034:   DMGetDefaultConstraints(coarse,&cSec,&cMat);
    4035:   PetscSectionGetChart(cSec,&cStart,&cEnd);

    4037:   /* create sections that will send to children the indices and matrices they will need to construct the interpolator */
    4038:   PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootValuesSec);
    4039:   PetscSectionSetChart(rootValuesSec,pStartC,pEndC);
    4040:   PetscSectionGetNumFields(localCoarse,&numFields);
    4041:   {
    4042:     PetscInt maxFields = PetscMax(1,numFields) + 1;
    4043:     PetscMalloc7(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&newOffsets,maxFields,&newOffsetsCopy,maxFields,&rowOffsets,maxFields,&numD,maxFields,&numO);
    4044:   }
    4045:   if (grad) {
    4046:     PetscInt i;

    4048:     VecGetDM(cellGeom,&cellDM);
    4049:     VecGetArrayRead(cellGeom,&cellGeomArray);
    4050:     VecGetDM(grad,&gradDM);
    4051:     VecGetArrayRead(grad,&gradArray);
    4052:     for (i = 0; i < PetscMax(1,numFields); i++) {
    4053:       PetscObject  obj;
    4054:       PetscClassId id;

    4056:       DMGetField(coarse, i, &obj);
    4057:       PetscObjectGetClassId(obj,&id);
    4058:       if (id == PETSCFV_CLASSID) {
    4059:         fv      = (PetscFV) obj;
    4060:         PetscFVGetNumComponents(fv,&numFVcomps);
    4061:         fvField = i;
    4062:         break;
    4063:       }
    4064:     }
    4065:   }

    4067:   for (p = pStartC; p < pEndC; p++) { /* count the sizes of the indices and matrices */
    4068:     PetscInt dof;
    4069:     PetscInt maxChildId     = maxChildIds[p - pStartC];
    4070:     PetscInt numValues      = 0;

    4072:     PetscSectionGetDof(globalCoarse,p,&dof);
    4073:     if (dof < 0) {
    4074:       dof = -(dof + 1);
    4075:     }
    4076:     offsets[0]    = 0;
    4077:     newOffsets[0] = 0;
    4078:     if (maxChildId >= 0) { /* this point has children (with dofs) that will need to be interpolated from the closure of p */
    4079:       PetscInt *closure = NULL, closureSize, cl;

    4081:       DMPlexGetTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);
    4082:       for (cl = 0; cl < closureSize; cl++) { /* get the closure */
    4083:         PetscInt c = closure[2 * cl], clDof;

    4085:         PetscSectionGetDof(localCoarse,c,&clDof);
    4086:         numValues += clDof;
    4087:       }
    4088:       DMPlexRestoreTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);
    4089:     }
    4090:     else if (maxChildId == -1) {
    4091:       PetscSectionGetDof(localCoarse,p,&numValues);
    4092:     }
    4093:     /* we will pack the column indices with the field offsets */
    4094:     if (maxChildId >= 0 && grad && p >= cellStart && p < cellEnd) {
    4095:       /* also send the centroid, and the gradient */
    4096:       numValues += dim * (1 + numFVcomps);
    4097:     }
    4098:     PetscSectionSetDof(rootValuesSec,p,numValues);
    4099:   }
    4100:   PetscSectionSetUp(rootValuesSec);
    4101:   {
    4102:     PetscInt          numRootValues;
    4103:     const PetscScalar *coarseArray;

    4105:     PetscSectionGetStorageSize(rootValuesSec,&numRootValues);
    4106:     PetscMalloc1(numRootValues,&rootValues);
    4107:     VecGetArrayRead(vecCoarseLocal,&coarseArray);
    4108:     for (p = pStartC; p < pEndC; p++) {
    4109:       PetscInt    numValues;
    4110:       PetscInt    pValOff;
    4111:       PetscScalar *pVal;
    4112:       PetscInt    maxChildId = maxChildIds[p - pStartC];

    4114:       PetscSectionGetDof(rootValuesSec,p,&numValues);
    4115:       if (!numValues) {
    4116:         continue;
    4117:       }
    4118:       PetscSectionGetOffset(rootValuesSec,p,&pValOff);
    4119:       pVal = &(rootValues[pValOff]);
    4120:       if (maxChildId >= 0) { /* build an identity matrix, apply matrix constraints on the right */
    4121:         PetscInt closureSize = numValues;
    4122:         DMPlexVecGetClosure(coarse,NULL,vecCoarseLocal,p,&closureSize,&pVal);
    4123:         if (grad && p >= cellStart && p < cellEnd) {
    4124:           PetscFVCellGeom *cg;
    4125:           PetscScalar     *gradVals = NULL;
    4126:           PetscInt        i;

    4128:           pVal += (numValues - dim * (1 + numFVcomps));

    4130:           DMPlexPointLocalRead(cellDM,p,cellGeomArray,(void *) &cg);
    4131:           for (i = 0; i < dim; i++) pVal[i] = cg->centroid[i];
    4132:           pVal += dim;
    4133:           DMPlexPointGlobalRead(gradDM,p,gradArray,(void *) &gradVals);
    4134:           for (i = 0; i < dim * numFVcomps; i++) pVal[i] = gradVals[i];
    4135:         }
    4136:       }
    4137:       else if (maxChildId == -1) {
    4138:         PetscInt lDof, lOff, i;

    4140:         PetscSectionGetDof(localCoarse,p,&lDof);
    4141:         PetscSectionGetOffset(localCoarse,p,&lOff);
    4142:         for (i = 0; i < lDof; i++) pVal[i] = coarseArray[lOff + i];
    4143:       }
    4144:     }
    4145:     VecRestoreArrayRead(vecCoarseLocal,&coarseArray);
    4146:     PetscFree(maxChildIds);
    4147:   }
    4148:   {
    4149:     PetscSF  valuesSF;
    4150:     PetscInt *remoteOffsetsValues, numLeafValues;

    4152:     PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafValuesSec);
    4153:     PetscSFDistributeSection(coarseToFineEmbedded,rootValuesSec,&remoteOffsetsValues,leafValuesSec);
    4154:     PetscSFCreateSectionSF(coarseToFineEmbedded,rootValuesSec,remoteOffsetsValues,leafValuesSec,&valuesSF);
    4155:     PetscSFDestroy(&coarseToFineEmbedded);
    4156:     PetscFree(remoteOffsetsValues);
    4157:     PetscSectionGetStorageSize(leafValuesSec,&numLeafValues);
    4158:     PetscMalloc1(numLeafValues,&leafValues);
    4159:     PetscSFBcastBegin(valuesSF,MPIU_SCALAR,rootValues,leafValues);
    4160:     PetscSFBcastEnd(valuesSF,MPIU_SCALAR,rootValues,leafValues);
    4161:     PetscSFDestroy(&valuesSF);
    4162:     PetscFree(rootValues);
    4163:     PetscSectionDestroy(&rootValuesSec);
    4164:   }
    4165:   DMGetSection(fine,&localFine);
    4166:   {
    4167:     PetscInt    maxDof;
    4168:     PetscInt    *rowIndices;
    4169:     DM           refTree;
    4170:     PetscInt     **refPointFieldN;
    4171:     PetscScalar  ***refPointFieldMats;
    4172:     PetscSection refConSec, refAnSec;
    4173:     PetscInt     pRefStart,pRefEnd,leafStart,leafEnd;
    4174:     PetscScalar  *pointWork;

    4176:     PetscSectionGetMaxDof(globalFine,&maxDof);
    4177:     DMGetWorkArray(fine,maxDof,MPIU_INT,&rowIndices);
    4178:     DMGetWorkArray(fine,maxDof,MPIU_SCALAR,&pointWork);
    4179:     DMPlexGetReferenceTree(fine,&refTree);
    4180:     DMGetDS(fine,&ds);
    4181:     DMSetDS(refTree,ds);
    4182:     DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
    4183:     DMGetDefaultConstraints(refTree,&refConSec,NULL);
    4184:     DMPlexGetAnchors(refTree,&refAnSec,NULL);
    4185:     PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
    4186:     PetscSectionGetChart(leafValuesSec,&leafStart,&leafEnd);
    4187:     DMPlexGetHeightStratum(fine,0,&cellStart,&cellEnd);
    4188:     DMPlexGetHybridBounds(fine,&cellEndInterior,NULL,NULL,NULL);
    4189:     cellEnd = (cellEndInterior < 0) ? cellEnd : cellEndInterior;
    4190:     for (p = leafStart; p < leafEnd; p++) {
    4191:       PetscInt          gDof, gcDof, gOff, lDof;
    4192:       PetscInt          numValues, pValOff;
    4193:       PetscInt          childId;
    4194:       const PetscScalar *pVal;
    4195:       const PetscScalar *fvGradData = NULL;

    4197:       PetscSectionGetDof(globalFine,p,&gDof);
    4198:       PetscSectionGetDof(localFine,p,&lDof);
    4199:       PetscSectionGetConstraintDof(globalFine,p,&gcDof);
    4200:       if ((gDof - gcDof) <= 0) {
    4201:         continue;
    4202:       }
    4203:       PetscSectionGetOffset(globalFine,p,&gOff);
    4204:       PetscSectionGetDof(leafValuesSec,p,&numValues);
    4205:       if (!numValues) continue;
    4206:       PetscSectionGetOffset(leafValuesSec,p,&pValOff);
    4207:       pVal = &leafValues[pValOff];
    4208:       offsets[0]        = 0;
    4209:       offsetsCopy[0]    = 0;
    4210:       newOffsets[0]     = 0;
    4211:       newOffsetsCopy[0] = 0;
    4212:       childId           = cids[p - pStartF];
    4213:       if (numFields) {
    4214:         PetscInt f;
    4215:         for (f = 0; f < numFields; f++) {
    4216:           PetscInt rowDof;

    4218:           PetscSectionGetFieldDof(localFine,p,f,&rowDof);
    4219:           offsets[f + 1]        = offsets[f] + rowDof;
    4220:           offsetsCopy[f + 1]    = offsets[f + 1];
    4221:           /* TODO: closure indices */
    4222:           newOffsets[f + 1]     = newOffsets[f] + ((childId == -1) ? rowDof : refPointFieldN[childId - pRefStart][f]);
    4223:         }
    4224:         DMPlexGetIndicesPointFields_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,NULL,-1,rowIndices);
    4225:       }
    4226:       else {
    4227:         offsets[0]    = 0;
    4228:         offsets[1]    = lDof;
    4229:         newOffsets[0] = 0;
    4230:         newOffsets[1] = (childId == -1) ? lDof : refPointFieldN[childId - pRefStart][0];
    4231:         DMPlexGetIndicesPoint_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,NULL,rowIndices);
    4232:       }
    4233:       if (childId == -1) { /* no child interpolation: one nnz per */
    4234:         VecSetValues(vecFine,numValues,rowIndices,pVal,INSERT_VALUES);
    4235:       } else {
    4236:         PetscInt f;

    4238:         if (grad && p >= cellStart && p < cellEnd) {
    4239:           numValues -= (dim * (1 + numFVcomps));
    4240:           fvGradData = &pVal[numValues];
    4241:         }
    4242:         for (f = 0; f < PetscMax(1,numFields); f++) {
    4243:           const PetscScalar *childMat = refPointFieldMats[childId - pRefStart][f];
    4244:           PetscInt numRows = offsets[f+1] - offsets[f];
    4245:           PetscInt numCols = newOffsets[f + 1] - newOffsets[f];
    4246:           const PetscScalar *cVal = &pVal[newOffsets[f]];
    4247:           PetscScalar *rVal = &pointWork[offsets[f]];
    4248:           PetscInt i, j;

    4250: #if 0
    4251:           PetscInfo6(coarse,"field %D, numFields %D, childId %D, numRows %D, numCols %D, refPointFieldN %D\n",f,numFields,childId,numRows,numCols,refPointFieldN[childId - pRefStart][f]);
    4252: #endif
    4253:           for (i = 0; i < numRows; i++) {
    4254:             PetscScalar val = 0.;
    4255:             for (j = 0; j < numCols; j++) {
    4256:               val += childMat[i * numCols + j] * cVal[j];
    4257:             }
    4258:             rVal[i] = val;
    4259:           }
    4260:           if (f == fvField && p >= cellStart && p < cellEnd) {
    4261:             PetscReal   centroid[3];
    4262:             PetscScalar diff[3];
    4263:             const PetscScalar *parentCentroid = &fvGradData[0];
    4264:             const PetscScalar *gradient       = &fvGradData[dim];

    4266:             DMPlexComputeCellGeometryFVM(fine,p,NULL,centroid,NULL);
    4267:             for (i = 0; i < dim; i++) {
    4268:               diff[i] = centroid[i] - parentCentroid[i];
    4269:             }
    4270:             for (i = 0; i < numFVcomps; i++) {
    4271:               PetscScalar val = 0.;

    4273:               for (j = 0; j < dim; j++) {
    4274:                 val += gradient[dim * i + j] * diff[j];
    4275:               }
    4276:               rVal[i] += val;
    4277:             }
    4278:           }
    4279:           VecSetValues(vecFine,numRows,&rowIndices[offsets[f]],rVal,INSERT_VALUES);
    4280:         }
    4281:       }
    4282:     }
    4283:     DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
    4284:     DMRestoreWorkArray(fine,maxDof,MPIU_INT,&rowIndices);
    4285:     DMRestoreWorkArray(fine,maxDof,MPIU_SCALAR,&pointWork);
    4286:   }
    4287:   PetscFree(leafValues);
    4288:   PetscSectionDestroy(&leafValuesSec);
    4289:   PetscFree7(offsets,offsetsCopy,newOffsets,newOffsetsCopy,rowOffsets,numD,numO);
    4290:   ISRestoreIndices(aIS,&anchors);
    4291:   return(0);
    4292: }

    4294: static PetscErrorCode DMPlexTransferVecTree_Inject(DM fine, Vec vecFine, DM coarse, Vec vecCoarse, PetscSF coarseToFine, PetscInt *cids)
    4295: {
    4296:   PetscDS        ds;
    4297:   DM             refTree;
    4298:   PetscSection   multiRootSec, rootIndicesSec;
    4299:   PetscSection   globalCoarse, globalFine;
    4300:   PetscSection   localCoarse, localFine;
    4301:   PetscSection   cSecRef;
    4302:   PetscInt       *parentIndices, pRefStart, pRefEnd;
    4303:   PetscScalar    *rootValues, *parentValues;
    4304:   Mat            injRef;
    4305:   PetscInt       numFields, maxDof;
    4306:   PetscInt       pStartC, pEndC, pStartF, pEndF, p;
    4307:   PetscInt       *offsets, *offsetsCopy, *rowOffsets;
    4308:   PetscLayout    rowMap, colMap;
    4309:   PetscInt       rowStart, rowEnd, colStart, colEnd;
    4310:   PetscScalar    ***childrenMats=NULL ; /* gcc -O gives 'may be used uninitialized' warning'. Initializing to suppress this warning */

    4315:   /* get the templates for the fine-to-coarse injection from the reference tree */
    4316:   VecSetOption(vecFine,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);
    4317:   VecSetOption(vecCoarse,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);
    4318:   DMPlexGetReferenceTree(coarse,&refTree);
    4319:   DMGetDS(coarse,&ds);
    4320:   DMSetDS(refTree,ds);
    4321:   DMGetDefaultConstraints(refTree,&cSecRef,NULL);
    4322:   PetscSectionGetChart(cSecRef,&pRefStart,&pRefEnd);
    4323:   DMPlexReferenceTreeGetInjector(refTree,&injRef);

    4325:   DMPlexGetChart(fine,&pStartF,&pEndF);
    4326:   DMGetSection(fine,&localFine);
    4327:   DMGetGlobalSection(fine,&globalFine);
    4328:   PetscSectionGetNumFields(localFine,&numFields);
    4329:   DMPlexGetChart(coarse,&pStartC,&pEndC);
    4330:   DMGetSection(coarse,&localCoarse);
    4331:   DMGetGlobalSection(coarse,&globalCoarse);
    4332:   PetscSectionGetMaxDof(localCoarse,&maxDof);
    4333:   {
    4334:     PetscInt maxFields = PetscMax(1,numFields) + 1;
    4335:     PetscMalloc3(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&rowOffsets);
    4336:   }

    4338:   DMPlexTransferInjectorTree(coarse,fine,coarseToFine,cids,vecFine,numFields,offsets,&multiRootSec,&rootIndicesSec,NULL,&rootValues);

    4340:   PetscMalloc2(maxDof,&parentIndices,maxDof,&parentValues);

    4342:   /* count indices */
    4343:   VecGetLayout(vecFine,&colMap);
    4344:   VecGetLayout(vecCoarse,&rowMap);
    4345:   PetscLayoutSetUp(rowMap);
    4346:   PetscLayoutSetUp(colMap);
    4347:   PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);
    4348:   PetscLayoutGetRange(colMap,&colStart,&colEnd);
    4349:   /* insert values */
    4350:   DMPlexReferenceTreeGetChildrenMatrices_Injection(refTree,injRef,&childrenMats);
    4351:   for (p = pStartC; p < pEndC; p++) {
    4352:     PetscInt  numLeaves, leafStart, leafEnd, l, dof, cdof, gOff;
    4353:     PetscBool contribute = PETSC_FALSE;

    4355:     PetscSectionGetDof(globalCoarse,p,&dof);
    4356:     PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
    4357:     if ((dof - cdof) <= 0) continue;
    4358:     PetscSectionGetDof(localCoarse,p,&dof);
    4359:     PetscSectionGetOffset(globalCoarse,p,&gOff);

    4361:     rowOffsets[0] = 0;
    4362:     offsetsCopy[0] = 0;
    4363:     if (numFields) {
    4364:       PetscInt f;

    4366:       for (f = 0; f < numFields; f++) {
    4367:         PetscInt fDof;
    4368:         PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
    4369:         rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f];
    4370:       }
    4371:       DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL,-1,parentIndices);
    4372:     }
    4373:     else {
    4374:       DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL,parentIndices);
    4375:       rowOffsets[1] = offsetsCopy[0];
    4376:     }

    4378:     PetscSectionGetDof(multiRootSec,p,&numLeaves);
    4379:     PetscSectionGetOffset(multiRootSec,p,&leafStart);
    4380:     leafEnd = leafStart + numLeaves;
    4381:     for (l = 0; l < dof; l++) parentValues[l] = 0.;
    4382:     for (l = leafStart; l < leafEnd; l++) {
    4383:       PetscInt numIndices, childId, offset;
    4384:       const PetscScalar *childValues;

    4386:       PetscSectionGetDof(rootIndicesSec,l,&numIndices);
    4387:       PetscSectionGetOffset(rootIndicesSec,l,&offset);
    4388:       childId = (PetscInt) PetscRealPart(rootValues[offset++]);
    4389:       childValues = &rootValues[offset];
    4390:       numIndices--;

    4392:       if (childId == -2) { /* skip */
    4393:         continue;
    4394:       } else if (childId == -1) { /* equivalent points: scatter */
    4395:         PetscInt m;

    4397:         contribute = PETSC_TRUE;
    4398:         for (m = 0; m < numIndices; m++) parentValues[m] = childValues[m];
    4399:       } else { /* contributions from children: sum with injectors from reference tree */
    4400:         PetscInt parentId, f, lim;

    4402:         contribute = PETSC_TRUE;
    4403:         DMPlexGetTreeParent(refTree,childId,&parentId,NULL);

    4405:         lim = PetscMax(1,numFields);
    4406:         offsets[0] = 0;
    4407:         if (numFields) {
    4408:           PetscInt f;

    4410:           for (f = 0; f < numFields; f++) {
    4411:             PetscInt fDof;
    4412:             PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);

    4414:             offsets[f + 1] = fDof + offsets[f];
    4415:           }
    4416:         }
    4417:         else {
    4418:           PetscInt cDof;

    4420:           PetscSectionGetDof(cSecRef,childId,&cDof);
    4421:           offsets[1] = cDof;
    4422:         }
    4423:         for (f = 0; f < lim; f++) {
    4424:           PetscScalar       *childMat   = &childrenMats[childId - pRefStart][f][0];
    4425:           PetscInt          n           = offsets[f+1]-offsets[f];
    4426:           PetscInt          m           = rowOffsets[f+1]-rowOffsets[f];
    4427:           PetscInt          i, j;
    4428:           const PetscScalar *colValues  = &childValues[offsets[f]];

    4430:           for (i = 0; i < m; i++) {
    4431:             PetscScalar val = 0.;
    4432:             for (j = 0; j < n; j++) {
    4433:               val += childMat[n * i + j] * colValues[j];
    4434:             }
    4435:             parentValues[rowOffsets[f] + i] += val;
    4436:           }
    4437:         }
    4438:       }
    4439:     }
    4440:     if (contribute) {VecSetValues(vecCoarse,dof,parentIndices,parentValues,INSERT_VALUES);}
    4441:   }
    4442:   PetscSectionDestroy(&multiRootSec);
    4443:   PetscSectionDestroy(&rootIndicesSec);
    4444:   PetscFree2(parentIndices,parentValues);
    4445:   DMPlexReferenceTreeRestoreChildrenMatrices_Injection(refTree,injRef,&childrenMats);
    4446:   PetscFree(rootValues);
    4447:   PetscFree3(offsets,offsetsCopy,rowOffsets);
    4448:   return(0);
    4449: }

    4451: /*@
    4452:   DMPlexTransferVecTree - transfer a vector between two meshes that differ from each other by refinement/coarsening
    4453:   that can be represented by a common reference tree used by both.  This routine can be used for a combination of
    4454:   coarsening and refinement at the same time.

    4456:   collective

    4458:   Input Parameters:
    4459: + dmIn        - The DMPlex mesh for the input vector
    4460: . vecIn       - The input vector
    4461: . sfRefine    - A star forest indicating points in the mesh dmIn (roots in the star forest) that are parents to points in
    4462:                 the mesh dmOut (leaves in the star forest), i.e. where dmOut is more refined than dmIn
    4463: . sfCoarsen   - A star forest indicating points in the mesh dmOut (roots in the star forest) that are parents to points in
    4464:                 the mesh dmIn (leaves in the star forest), i.e. where dmOut is more coarsened than dmIn
    4465: . cidsRefine  - The childIds of the points in dmOut.  These childIds relate back to the reference tree: childid[j] = k implies
    4466:                 that mesh point j of dmOut was refined from a point in dmIn just as the mesh point k in the reference
    4467:                 tree was refined from its parent.  childid[j] = -1 indicates that the point j in dmOut is exactly
    4468:                 equivalent to its root in dmIn, so no interpolation is necessary.  childid[j] = -2 indicates that this
    4469:                 point j in dmOut is not a leaf of sfRefine.
    4470: . cidsCoarsen - The childIds of the points in dmIn.  These childIds relate back to the reference tree: childid[j] = k implies
    4471:                 that mesh point j of dmIn coarsens to a point in dmOut just as the mesh point k in the reference
    4472:                 tree coarsens to its parent.  childid[j] = -2 indicates that point j in dmOut is not a leaf in sfCoarsen.
    4473: . useBCs      - PETSC_TRUE indicates that boundary values should be inserted into vecIn before transfer.
    4474: - time        - Used if boundary values are time dependent.

    4476:   Output Parameters:
    4477: . vecOut      - Using interpolation and injection operators calculated on the reference tree, the transfered
    4478:                 projection of vecIn from dmIn to dmOut.  Note that any field discretized with a PetscFV finite volume
    4479:                 method that uses gradient reconstruction will use reconstructed gradients when interpolating from
    4480:                 coarse points to fine points.

    4482:   Level: developer

    4484: .seealso(): DMPlexSetReferenceTree(), DMPlexGetReferenceTree(), PetscFVGetComputeGradients()
    4485: @*/
    4486: PetscErrorCode DMPlexTransferVecTree(DM dmIn, Vec vecIn, DM dmOut, Vec vecOut, PetscSF sfRefine, PetscSF sfCoarsen, PetscInt *cidsRefine, PetscInt *cidsCoarsen, PetscBool useBCs, PetscReal time)
    4487: {

    4491:   VecSet(vecOut,0.0);
    4492:   if (sfRefine) {
    4493:     Vec vecInLocal;
    4494:     DM  dmGrad = NULL;
    4495:     Vec faceGeom = NULL, cellGeom = NULL, grad = NULL;

    4497:     DMGetLocalVector(dmIn,&vecInLocal);
    4498:     VecSet(vecInLocal,0.0);
    4499:     {
    4500:       PetscInt  numFields, i;

    4502:       DMGetNumFields(dmIn, &numFields);
    4503:       for (i = 0; i < numFields; i++) {
    4504:         PetscObject  obj;
    4505:         PetscClassId classid;

    4507:         DMGetField(dmIn, i, &obj);
    4508:         PetscObjectGetClassId(obj, &classid);
    4509:         if (classid == PETSCFV_CLASSID) {
    4510:           DMPlexGetDataFVM(dmIn,(PetscFV)obj,&cellGeom,&faceGeom,&dmGrad);
    4511:           break;
    4512:         }
    4513:       }
    4514:     }
    4515:     if (useBCs) {
    4516:       DMPlexInsertBoundaryValues(dmIn,PETSC_TRUE,vecInLocal,time,faceGeom,cellGeom,NULL);
    4517:     }
    4518:     DMGlobalToLocalBegin(dmIn,vecIn,INSERT_VALUES,vecInLocal);
    4519:     DMGlobalToLocalEnd(dmIn,vecIn,INSERT_VALUES,vecInLocal);
    4520:     if (dmGrad) {
    4521:       DMGetGlobalVector(dmGrad,&grad);
    4522:       DMPlexReconstructGradientsFVM(dmIn,vecInLocal,grad);
    4523:     }
    4524:     DMPlexTransferVecTree_Interpolate(dmIn,vecInLocal,dmOut,vecOut,sfRefine,cidsRefine,grad,cellGeom);
    4525:     DMRestoreLocalVector(dmIn,&vecInLocal);
    4526:     if (dmGrad) {
    4527:       DMRestoreGlobalVector(dmGrad,&grad);
    4528:     }
    4529:   }
    4530:   if (sfCoarsen) {
    4531:     DMPlexTransferVecTree_Inject(dmIn,vecIn,dmOut,vecOut,sfCoarsen,cidsCoarsen);
    4532:   }
    4533:   VecAssemblyBegin(vecOut);
    4534:   VecAssemblyEnd(vecOut);
    4535:   return(0);
    4536: }