Actual source code: pcpatch.c
petsc-3.13.6 2020-09-29
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      1:  #include <petsc/private/pcpatchimpl.h>
      2:  #include <petsc/private/kspimpl.h>
      3:  #include <petsc/private/vecimpl.h>
      4:  #include <petsc/private/dmpleximpl.h>
      5:  #include <petscsf.h>
      6:  #include <petscbt.h>
      7:  #include <petscds.h>
      8:  #include <../src/mat/impls/dense/seq/dense.h>

     10: PetscLogEvent PC_Patch_CreatePatches, PC_Patch_ComputeOp, PC_Patch_Solve, PC_Patch_Apply, PC_Patch_Prealloc;

     12: PETSC_STATIC_INLINE PetscErrorCode ObjectView(PetscObject obj, PetscViewer viewer, PetscViewerFormat format)
     13: {

     16:   PetscViewerPushFormat(viewer, format);
     17:   PetscObjectView(obj, viewer);
     18:   PetscViewerPopFormat(viewer);
     19:   return(0);
     20: }

     22: static PetscErrorCode PCPatchConstruct_Star(void *vpatch, DM dm, PetscInt point, PetscHSetI ht)
     23: {
     24:   PetscInt       starSize;
     25:   PetscInt      *star = NULL, si;

     29:   PetscHSetIClear(ht);
     30:   /* To start with, add the point we care about */
     31:   PetscHSetIAdd(ht, point);
     32:   /* Loop over all the points that this point connects to */
     33:   DMPlexGetTransitiveClosure(dm, point, PETSC_FALSE, &starSize, &star);
     34:   for (si = 0; si < starSize*2; si += 2) {PetscHSetIAdd(ht, star[si]);}
     35:   DMPlexRestoreTransitiveClosure(dm, point, PETSC_FALSE, &starSize, &star);
     36:   return(0);
     37: }

     39: static PetscErrorCode PCPatchConstruct_Vanka(void *vpatch, DM dm, PetscInt point, PetscHSetI ht)
     40: {
     41:   PC_PATCH      *patch = (PC_PATCH *) vpatch;
     42:   PetscInt       starSize;
     43:   PetscInt      *star = NULL;
     44:   PetscBool      shouldIgnore = PETSC_FALSE;
     45:   PetscInt       cStart, cEnd, iStart, iEnd, si;

     49:   PetscHSetIClear(ht);
     50:   /* To start with, add the point we care about */
     51:   PetscHSetIAdd(ht, point);
     52:   /* Should we ignore any points of a certain dimension? */
     53:   if (patch->vankadim >= 0) {
     54:     shouldIgnore = PETSC_TRUE;
     55:     DMPlexGetDepthStratum(dm, patch->vankadim, &iStart, &iEnd);
     56:   }
     57:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
     58:   /* Loop over all the cells that this point connects to */
     59:   DMPlexGetTransitiveClosure(dm, point, PETSC_FALSE, &starSize, &star);
     60:   for (si = 0; si < starSize*2; si += 2) {
     61:     const PetscInt cell = star[si];
     62:     PetscInt       closureSize;
     63:     PetscInt      *closure = NULL, ci;

     65:     if (cell < cStart || cell >= cEnd) continue;
     66:     /* now loop over all entities in the closure of that cell */
     67:     DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);
     68:     for (ci = 0; ci < closureSize*2; ci += 2) {
     69:       const PetscInt newpoint = closure[ci];

     71:       /* We've been told to ignore entities of this type.*/
     72:       if (shouldIgnore && newpoint >= iStart && newpoint < iEnd) continue;
     73:       PetscHSetIAdd(ht, newpoint);
     74:     }
     75:     DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);
     76:   }
     77:   DMPlexRestoreTransitiveClosure(dm, point, PETSC_FALSE, &starSize, &star);
     78:   return(0);
     79: }

     81: static PetscErrorCode PCPatchConstruct_Pardecomp(void *vpatch, DM dm, PetscInt point, PetscHSetI ht)
     82: {
     83:   PC_PATCH       *patch = (PC_PATCH *) vpatch;
     84:   DMLabel         ghost = NULL;
     85:   const PetscInt *leaves;
     86:   PetscInt        nleaves, pStart, pEnd, loc;
     87:   PetscBool       isFiredrake;
     88:   PetscBool       flg;
     89:   PetscInt        starSize;
     90:   PetscInt       *star = NULL;
     91:   PetscInt        opoint, overlapi;
     92:   PetscErrorCode  ierr;

     95:   PetscHSetIClear(ht);

     97:   DMPlexGetChart(dm, &pStart, &pEnd);

     99:   DMHasLabel(dm, "pyop2_ghost", &isFiredrake);
    100:   if (isFiredrake) {
    101:     DMGetLabel(dm, "pyop2_ghost", &ghost);
    102:     DMLabelCreateIndex(ghost, pStart, pEnd);
    103:   } else {
    104:     PetscSF sf;
    105:     DMGetPointSF(dm, &sf);
    106:     PetscSFGetGraph(sf, NULL, &nleaves, &leaves, NULL);
    107:     nleaves = PetscMax(nleaves, 0);
    108:   }

    110:   for (opoint = pStart; opoint < pEnd; ++opoint) {
    111:     if (ghost) {DMLabelHasPoint(ghost, opoint, &flg);}
    112:     else       {PetscFindInt(opoint, nleaves, leaves, &loc); flg = loc >=0 ? PETSC_TRUE : PETSC_FALSE;}
    113:     /* Not an owned entity, don't make a cell patch. */
    114:     if (flg) continue;
    115:     PetscHSetIAdd(ht, opoint);
    116:   }

    118:   /* Now build the overlap for the patch */
    119:   for (overlapi = 0; overlapi < patch->pardecomp_overlap; ++overlapi) {
    120:     PetscInt index = 0;
    121:     PetscInt *htpoints = NULL;
    122:     PetscInt htsize;
    123:     PetscInt i;

    125:     PetscHSetIGetSize(ht, &htsize);
    126:     PetscMalloc1(htsize, &htpoints);
    127:     PetscHSetIGetElems(ht, &index, htpoints);

    129:     for (i = 0; i < htsize; ++i) {
    130:       PetscInt hpoint = htpoints[i];
    131:       PetscInt si;

    133:       DMPlexGetTransitiveClosure(dm, hpoint, PETSC_FALSE, &starSize, &star);
    134:       for (si = 0; si < starSize*2; si += 2) {
    135:         const PetscInt starp = star[si];
    136:         PetscInt       closureSize;
    137:         PetscInt      *closure = NULL, ci;

    139:         /* now loop over all entities in the closure of starp */
    140:         DMPlexGetTransitiveClosure(dm, starp, PETSC_TRUE, &closureSize, &closure);
    141:         for (ci = 0; ci < closureSize*2; ci += 2) {
    142:           const PetscInt closstarp = closure[ci];
    143:           PetscHSetIAdd(ht, closstarp);
    144:         }
    145:         DMPlexRestoreTransitiveClosure(dm, starp, PETSC_TRUE, &closureSize, &closure);
    146:       }
    147:       DMPlexRestoreTransitiveClosure(dm, hpoint, PETSC_FALSE, &starSize, &star);
    148:     }
    149:     PetscFree(htpoints);
    150:   }

    152:   return(0);
    153: }

    155: /* The user's already set the patches in patch->userIS. Build the hash tables */
    156: static PetscErrorCode PCPatchConstruct_User(void *vpatch, DM dm, PetscInt point, PetscHSetI ht)
    157: {
    158:   PC_PATCH       *patch   = (PC_PATCH *) vpatch;
    159:   IS              patchis = patch->userIS[point];
    160:   PetscInt        n;
    161:   const PetscInt *patchdata;
    162:   PetscInt        pStart, pEnd, i;
    163:   PetscErrorCode  ierr;

    166:   PetscHSetIClear(ht);
    167:   DMPlexGetChart(dm, &pStart, &pEnd);
    168:   ISGetLocalSize(patchis, &n);
    169:   ISGetIndices(patchis, &patchdata);
    170:   for (i = 0; i < n; ++i) {
    171:     const PetscInt ownedpoint = patchdata[i];

    173:     if (ownedpoint < pStart || ownedpoint >= pEnd) {
    174:       SETERRQ3(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D was not in [%D, %D)", ownedpoint, pStart, pEnd);
    175:     }
    176:     PetscHSetIAdd(ht, ownedpoint);
    177:   }
    178:   ISRestoreIndices(patchis, &patchdata);
    179:   return(0);
    180: }

    182: static PetscErrorCode PCPatchCreateDefaultSF_Private(PC pc, PetscInt n, const PetscSF *sf, const PetscInt *bs)
    183: {
    184:   PC_PATCH      *patch = (PC_PATCH *) pc->data;
    185:   PetscInt       i;

    189:   if (n == 1 && bs[0] == 1) {
    190:     patch->sectionSF = sf[0];
    191:     PetscObjectReference((PetscObject) patch->sectionSF);
    192:   } else {
    193:     PetscInt     allRoots = 0, allLeaves = 0;
    194:     PetscInt     leafOffset = 0;
    195:     PetscInt    *ilocal = NULL;
    196:     PetscSFNode *iremote = NULL;
    197:     PetscInt    *remoteOffsets = NULL;
    198:     PetscInt     index = 0;
    199:     PetscHMapI   rankToIndex;
    200:     PetscInt     numRanks = 0;
    201:     PetscSFNode *remote = NULL;
    202:     PetscSF      rankSF;
    203:     PetscInt    *ranks = NULL;
    204:     PetscInt    *offsets = NULL;
    205:     MPI_Datatype contig;
    206:     PetscHSetI   ranksUniq;

    208:     /* First figure out how many dofs there are in the concatenated numbering.
    209:      * allRoots: number of owned global dofs;
    210:      * allLeaves: number of visible dofs (global + ghosted).
    211:      */
    212:     for (i = 0; i < n; ++i) {
    213:       PetscInt nroots, nleaves;

    215:       PetscSFGetGraph(sf[i], &nroots, &nleaves, NULL, NULL);
    216:       allRoots  += nroots * bs[i];
    217:       allLeaves += nleaves * bs[i];
    218:     }
    219:     PetscMalloc1(allLeaves, &ilocal);
    220:     PetscMalloc1(allLeaves, &iremote);
    221:     /* Now build an SF that just contains process connectivity. */
    222:     PetscHSetICreate(&ranksUniq);
    223:     for (i = 0; i < n; ++i) {
    224:       const PetscMPIInt *ranks = NULL;
    225:       PetscInt           nranks, j;

    227:       PetscSFSetUp(sf[i]);
    228:       PetscSFGetRootRanks(sf[i], &nranks, &ranks, NULL, NULL, NULL);
    229:       /* These are all the ranks who communicate with me. */
    230:       for (j = 0; j < nranks; ++j) {
    231:         PetscHSetIAdd(ranksUniq, (PetscInt) ranks[j]);
    232:       }
    233:     }
    234:     PetscHSetIGetSize(ranksUniq, &numRanks);
    235:     PetscMalloc1(numRanks, &remote);
    236:     PetscMalloc1(numRanks, &ranks);
    237:     PetscHSetIGetElems(ranksUniq, &index, ranks);

    239:     PetscHMapICreate(&rankToIndex);
    240:     for (i = 0; i < numRanks; ++i) {
    241:       remote[i].rank  = ranks[i];
    242:       remote[i].index = 0;
    243:       PetscHMapISet(rankToIndex, ranks[i], i);
    244:     }
    245:     PetscFree(ranks);
    246:     PetscHSetIDestroy(&ranksUniq);
    247:     PetscSFCreate(PetscObjectComm((PetscObject) pc), &rankSF);
    248:     PetscSFSetGraph(rankSF, 1, numRanks, NULL, PETSC_OWN_POINTER, remote, PETSC_OWN_POINTER);
    249:     PetscSFSetUp(rankSF);
    250:     /* OK, use it to communicate the root offset on the remote
    251:      * processes for each subspace. */
    252:     PetscMalloc1(n, &offsets);
    253:     PetscMalloc1(n*numRanks, &remoteOffsets);

    255:     offsets[0] = 0;
    256:     for (i = 1; i < n; ++i) {
    257:       PetscInt nroots;

    259:       PetscSFGetGraph(sf[i-1], &nroots, NULL, NULL, NULL);
    260:       offsets[i] = offsets[i-1] + nroots*bs[i-1];
    261:     }
    262:     /* Offsets are the offsets on the current process of the
    263:      * global dof numbering for the subspaces. */
    264:     MPI_Type_contiguous(n, MPIU_INT, &contig);
    265:     MPI_Type_commit(&contig);

    267:     PetscSFBcastBegin(rankSF, contig, offsets, remoteOffsets);
    268:     PetscSFBcastEnd(rankSF, contig, offsets, remoteOffsets);
    269:     MPI_Type_free(&contig);
    270:     PetscFree(offsets);
    271:     PetscSFDestroy(&rankSF);
    272:     /* Now remoteOffsets contains the offsets on the remote
    273:      * processes who communicate with me.  So now we can
    274:      * concatenate the list of SFs into a single one. */
    275:     index = 0;
    276:     for (i = 0; i < n; ++i) {
    277:       const PetscSFNode *remote = NULL;
    278:       const PetscInt    *local  = NULL;
    279:       PetscInt           nroots, nleaves, j;

    281:       PetscSFGetGraph(sf[i], &nroots, &nleaves, &local, &remote);
    282:       for (j = 0; j < nleaves; ++j) {
    283:         PetscInt rank = remote[j].rank;
    284:         PetscInt idx, rootOffset, k;

    286:         PetscHMapIGet(rankToIndex, rank, &idx);
    287:         if (idx == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Didn't find rank, huh?");
    288:         /* Offset on given rank for ith subspace */
    289:         rootOffset = remoteOffsets[n*idx + i];
    290:         for (k = 0; k < bs[i]; ++k) {
    291:           ilocal[index]        = (local ? local[j] : j)*bs[i] + k + leafOffset;
    292:           iremote[index].rank  = remote[j].rank;
    293:           iremote[index].index = remote[j].index*bs[i] + k + rootOffset;
    294:           ++index;
    295:         }
    296:       }
    297:       leafOffset += nleaves * bs[i];
    298:     }
    299:     PetscHMapIDestroy(&rankToIndex);
    300:     PetscFree(remoteOffsets);
    301:     PetscSFCreate(PetscObjectComm((PetscObject)pc), &patch->sectionSF);
    302:     PetscSFSetGraph(patch->sectionSF, allRoots, allLeaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER);
    303:   }
    304:   return(0);
    305: }

    307: PetscErrorCode PCPatchSetDenseInverse(PC pc, PetscBool flg)
    308: {
    309:   PC_PATCH *patch = (PC_PATCH *) pc->data;
    311:   patch->denseinverse = flg;
    312:   return(0);
    313: }

    315: PetscErrorCode PCPatchGetDenseInverse(PC pc, PetscBool *flg)
    316: {
    317:   PC_PATCH *patch = (PC_PATCH *) pc->data;
    319:   *flg = patch->denseinverse;
    320:   return(0);
    321: }

    323: /* TODO: Docs */
    324: PetscErrorCode PCPatchSetIgnoreDim(PC pc, PetscInt dim)
    325: {
    326:   PC_PATCH *patch = (PC_PATCH *) pc->data;
    328:   patch->ignoredim = dim;
    329:   return(0);
    330: }

    332: /* TODO: Docs */
    333: PetscErrorCode PCPatchGetIgnoreDim(PC pc, PetscInt *dim)
    334: {
    335:   PC_PATCH *patch = (PC_PATCH *) pc->data;
    337:   *dim = patch->ignoredim;
    338:   return(0);
    339: }

    341: /* TODO: Docs */
    342: PetscErrorCode PCPatchSetSaveOperators(PC pc, PetscBool flg)
    343: {
    344:   PC_PATCH *patch = (PC_PATCH *) pc->data;
    346:   patch->save_operators = flg;
    347:   return(0);
    348: }

    350: /* TODO: Docs */
    351: PetscErrorCode PCPatchGetSaveOperators(PC pc, PetscBool *flg)
    352: {
    353:   PC_PATCH *patch = (PC_PATCH *) pc->data;
    355:   *flg = patch->save_operators;
    356:   return(0);
    357: }

    359: /* TODO: Docs */
    360: PetscErrorCode PCPatchSetPrecomputeElementTensors(PC pc, PetscBool flg)
    361: {
    362:   PC_PATCH *patch = (PC_PATCH *) pc->data;
    364:   patch->precomputeElementTensors = flg;
    365:   return(0);
    366: }

    368: /* TODO: Docs */
    369: PetscErrorCode PCPatchGetPrecomputeElementTensors(PC pc, PetscBool *flg)
    370: {
    371:   PC_PATCH *patch = (PC_PATCH *) pc->data;
    373:   *flg = patch->precomputeElementTensors;
    374:   return(0);
    375: }

    377: /* TODO: Docs */
    378: PetscErrorCode PCPatchSetPartitionOfUnity(PC pc, PetscBool flg)
    379: {
    380:   PC_PATCH *patch = (PC_PATCH *) pc->data;
    382:   patch->partition_of_unity = flg;
    383:   return(0);
    384: }

    386: /* TODO: Docs */
    387: PetscErrorCode PCPatchGetPartitionOfUnity(PC pc, PetscBool *flg)
    388: {
    389:   PC_PATCH *patch = (PC_PATCH *) pc->data;
    391:   *flg = patch->partition_of_unity;
    392:   return(0);
    393: }

    395: /* TODO: Docs */
    396: PetscErrorCode PCPatchSetLocalComposition(PC pc, PCCompositeType type)
    397: {
    398:   PC_PATCH *patch = (PC_PATCH *) pc->data;
    400:   if (type != PC_COMPOSITE_ADDITIVE && type != PC_COMPOSITE_MULTIPLICATIVE) SETERRQ(PetscObjectComm((PetscObject)pc),PETSC_ERR_SUP,"Only supports additive or multiplicative as the local type");
    401:   patch->local_composition_type = type;
    402:   return(0);
    403: }

    405: /* TODO: Docs */
    406: PetscErrorCode PCPatchGetLocalComposition(PC pc, PCCompositeType *type)
    407: {
    408:   PC_PATCH *patch = (PC_PATCH *) pc->data;
    410:   *type = patch->local_composition_type;
    411:   return(0);
    412: }

    414: /* TODO: Docs */
    415: PetscErrorCode PCPatchSetSubMatType(PC pc, MatType sub_mat_type)
    416: {
    417:   PC_PATCH      *patch = (PC_PATCH *) pc->data;

    421:   if (patch->sub_mat_type) {PetscFree(patch->sub_mat_type);}
    422:   PetscStrallocpy(sub_mat_type, (char **) &patch->sub_mat_type);
    423:   return(0);
    424: }

    426: /* TODO: Docs */
    427: PetscErrorCode PCPatchGetSubMatType(PC pc, MatType *sub_mat_type)
    428: {
    429:   PC_PATCH *patch = (PC_PATCH *) pc->data;
    431:   *sub_mat_type = patch->sub_mat_type;
    432:   return(0);
    433: }

    435: /* TODO: Docs */
    436: PetscErrorCode PCPatchSetCellNumbering(PC pc, PetscSection cellNumbering)
    437: {
    438:   PC_PATCH      *patch = (PC_PATCH *) pc->data;

    442:   patch->cellNumbering = cellNumbering;
    443:   PetscObjectReference((PetscObject) cellNumbering);
    444:   return(0);
    445: }

    447: /* TODO: Docs */
    448: PetscErrorCode PCPatchGetCellNumbering(PC pc, PetscSection *cellNumbering)
    449: {
    450:   PC_PATCH *patch = (PC_PATCH *) pc->data;
    452:   *cellNumbering = patch->cellNumbering;
    453:   return(0);
    454: }

    456: /* TODO: Docs */
    457: PetscErrorCode PCPatchSetConstructType(PC pc, PCPatchConstructType ctype, PetscErrorCode (*func)(PC, PetscInt *, IS **, IS *, void *), void *ctx)
    458: {
    459:   PC_PATCH *patch = (PC_PATCH *) pc->data;

    462:   patch->ctype = ctype;
    463:   switch (ctype) {
    464:   case PC_PATCH_STAR:
    465:     patch->user_patches     = PETSC_FALSE;
    466:     patch->patchconstructop = PCPatchConstruct_Star;
    467:     break;
    468:   case PC_PATCH_VANKA:
    469:     patch->user_patches     = PETSC_FALSE;
    470:     patch->patchconstructop = PCPatchConstruct_Vanka;
    471:     break;
    472:   case PC_PATCH_PARDECOMP:
    473:     patch->user_patches     = PETSC_FALSE;
    474:     patch->patchconstructop = PCPatchConstruct_Pardecomp;
    475:     break;
    476:   case PC_PATCH_USER:
    477:   case PC_PATCH_PYTHON:
    478:     patch->user_patches     = PETSC_TRUE;
    479:     patch->patchconstructop = PCPatchConstruct_User;
    480:     if (func) {
    481:       patch->userpatchconstructionop = func;
    482:       patch->userpatchconstructctx   = ctx;
    483:     }
    484:     break;
    485:   default:
    486:     SETERRQ1(PetscObjectComm((PetscObject) pc), PETSC_ERR_USER, "Unknown patch construction type %D", (PetscInt) patch->ctype);
    487:   }
    488:   return(0);
    489: }

    491: /* TODO: Docs */
    492: PetscErrorCode PCPatchGetConstructType(PC pc, PCPatchConstructType *ctype, PetscErrorCode (**func)(PC, PetscInt *, IS **, IS *, void *), void **ctx)
    493: {
    494:   PC_PATCH *patch = (PC_PATCH *) pc->data;

    497:   *ctype = patch->ctype;
    498:   switch (patch->ctype) {
    499:   case PC_PATCH_STAR:
    500:   case PC_PATCH_VANKA:
    501:   case PC_PATCH_PARDECOMP:
    502:     break;
    503:   case PC_PATCH_USER:
    504:   case PC_PATCH_PYTHON:
    505:     *func = patch->userpatchconstructionop;
    506:     *ctx  = patch->userpatchconstructctx;
    507:     break;
    508:   default:
    509:     SETERRQ1(PetscObjectComm((PetscObject) pc), PETSC_ERR_USER, "Unknown patch construction type %D", (PetscInt) patch->ctype);
    510:   }
    511:   return(0);
    512: }

    514: /* TODO: Docs */
    515: PetscErrorCode PCPatchSetDiscretisationInfo(PC pc, PetscInt nsubspaces, DM *dms, PetscInt *bs, PetscInt *nodesPerCell, const PetscInt **cellNodeMap,
    516:                                             const PetscInt *subspaceOffsets, PetscInt numGhostBcs, const PetscInt *ghostBcNodes, PetscInt numGlobalBcs, const PetscInt *globalBcNodes)
    517: {
    518:   PC_PATCH      *patch = (PC_PATCH *) pc->data;
    519:   DM             dm, plex;
    520:   PetscSF       *sfs;
    521:   PetscInt       cStart, cEnd, i, j;

    525:   PCGetDM(pc, &dm);
    526:   DMConvert(dm, DMPLEX, &plex);
    527:   dm = plex;
    528:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
    529:   PetscMalloc1(nsubspaces, &sfs);
    530:   PetscMalloc1(nsubspaces, &patch->dofSection);
    531:   PetscMalloc1(nsubspaces, &patch->bs);
    532:   PetscMalloc1(nsubspaces, &patch->nodesPerCell);
    533:   PetscMalloc1(nsubspaces, &patch->cellNodeMap);
    534:   PetscMalloc1(nsubspaces+1, &patch->subspaceOffsets);

    536:   patch->nsubspaces       = nsubspaces;
    537:   patch->totalDofsPerCell = 0;
    538:   for (i = 0; i < nsubspaces; ++i) {
    539:     DMGetLocalSection(dms[i], &patch->dofSection[i]);
    540:     PetscObjectReference((PetscObject) patch->dofSection[i]);
    541:     DMGetSectionSF(dms[i], &sfs[i]);
    542:     patch->bs[i]              = bs[i];
    543:     patch->nodesPerCell[i]    = nodesPerCell[i];
    544:     patch->totalDofsPerCell  += nodesPerCell[i]*bs[i];
    545:     PetscMalloc1((cEnd-cStart)*nodesPerCell[i], &patch->cellNodeMap[i]);
    546:     for (j = 0; j < (cEnd-cStart)*nodesPerCell[i]; ++j) patch->cellNodeMap[i][j] = cellNodeMap[i][j];
    547:     patch->subspaceOffsets[i] = subspaceOffsets[i];
    548:   }
    549:   PCPatchCreateDefaultSF_Private(pc, nsubspaces, sfs, patch->bs);
    550:   PetscFree(sfs);

    552:   patch->subspaceOffsets[nsubspaces] = subspaceOffsets[nsubspaces];
    553:   ISCreateGeneral(PETSC_COMM_SELF, numGhostBcs, ghostBcNodes, PETSC_COPY_VALUES, &patch->ghostBcNodes);
    554:   ISCreateGeneral(PETSC_COMM_SELF, numGlobalBcs, globalBcNodes, PETSC_COPY_VALUES, &patch->globalBcNodes);
    555:   DMDestroy(&dm);
    556:   return(0);
    557: }

    559: /* TODO: Docs */
    560: PetscErrorCode PCPatchSetDiscretisationInfoCombined(PC pc, DM dm, PetscInt *nodesPerCell, const PetscInt **cellNodeMap, PetscInt numGhostBcs, const PetscInt *ghostBcNodes, PetscInt numGlobalBcs, const PetscInt *globalBcNodes)
    561: {
    562:   PC_PATCH      *patch = (PC_PATCH *) pc->data;
    563:   PetscInt       cStart, cEnd, i, j;

    567:   patch->combined = PETSC_TRUE;
    568:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
    569:   DMGetNumFields(dm, &patch->nsubspaces);
    570:   PetscCalloc1(patch->nsubspaces, &patch->dofSection);
    571:   PetscMalloc1(patch->nsubspaces, &patch->bs);
    572:   PetscMalloc1(patch->nsubspaces, &patch->nodesPerCell);
    573:   PetscMalloc1(patch->nsubspaces, &patch->cellNodeMap);
    574:   PetscCalloc1(patch->nsubspaces+1, &patch->subspaceOffsets);
    575:   DMGetLocalSection(dm, &patch->dofSection[0]);
    576:   PetscObjectReference((PetscObject) patch->dofSection[0]);
    577:   PetscSectionGetStorageSize(patch->dofSection[0], &patch->subspaceOffsets[patch->nsubspaces]);
    578:   patch->totalDofsPerCell = 0;
    579:   for (i = 0; i < patch->nsubspaces; ++i) {
    580:     patch->bs[i]             = 1;
    581:     patch->nodesPerCell[i]   = nodesPerCell[i];
    582:     patch->totalDofsPerCell += nodesPerCell[i];
    583:     PetscMalloc1((cEnd-cStart)*nodesPerCell[i], &patch->cellNodeMap[i]);
    584:     for (j = 0; j < (cEnd-cStart)*nodesPerCell[i]; ++j) patch->cellNodeMap[i][j] = cellNodeMap[i][j];
    585:   }
    586:   DMGetSectionSF(dm, &patch->sectionSF);
    587:   PetscObjectReference((PetscObject) patch->sectionSF);
    588:   ISCreateGeneral(PETSC_COMM_SELF, numGhostBcs, ghostBcNodes, PETSC_COPY_VALUES, &patch->ghostBcNodes);
    589:   ISCreateGeneral(PETSC_COMM_SELF, numGlobalBcs, globalBcNodes, PETSC_COPY_VALUES, &patch->globalBcNodes);
    590:   return(0);
    591: }

    593: /*@C

    595:   PCPatchSetComputeFunction - Set the callback used to compute patch residuals

    597:   Logically collective on PC

    599:   Input Parameters:
    600: + pc   - The PC
    601: . func - The callback
    602: - ctx  - The user context

    604:   Calling sequence of func:
    605: $   func (PC pc,PetscInt point,Vec x,Vec f,IS cellIS,PetscInt n,const PetscInt* dofsArray,const PetscInt* dofsArrayWithAll,void* ctx)

    607: +  pc               - The PC
    608: .  point            - The point
    609: .  x                - The input solution (not used in linear problems)
    610: .  f                - The patch residual vector
    611: .  cellIS           - An array of the cell numbers
    612: .  n                - The size of dofsArray
    613: .  dofsArray        - The dofmap for the dofs to be solved for
    614: .  dofsArrayWithAll - The dofmap for all dofs on the patch
    615: -  ctx              - The user context

    617:   Level: advanced

    619:   Notes:
    620:   The entries of F (the output residual vector) have been set to zero before the call.

    622: .seealso: PCPatchSetComputeOperator(), PCPatchGetComputeOperator(), PCPatchSetDiscretisationInfo(), PCPatchSetComputeFunctionInteriorFacets()
    623: @*/
    624: PetscErrorCode PCPatchSetComputeFunction(PC pc, PetscErrorCode (*func)(PC, PetscInt, Vec, Vec, IS, PetscInt, const PetscInt *, const PetscInt *, void *), void *ctx)
    625: {
    626:   PC_PATCH *patch = (PC_PATCH *) pc->data;

    629:   patch->usercomputef    = func;
    630:   patch->usercomputefctx = ctx;
    631:   return(0);
    632: }

    634: /*@C

    636:   PCPatchSetComputeFunctionInteriorFacets - Set the callback used to compute facet integrals for patch residuals

    638:   Logically collective on PC

    640:   Input Parameters:
    641: + pc   - The PC
    642: . func - The callback
    643: - ctx  - The user context

    645:   Calling sequence of func:
    646: $   func (PC pc,PetscInt point,Vec x,Vec f,IS facetIS,PetscInt n,const PetscInt* dofsArray,const PetscInt* dofsArrayWithAll,void* ctx)

    648: +  pc               - The PC
    649: .  point            - The point
    650: .  x                - The input solution (not used in linear problems)
    651: .  f                - The patch residual vector
    652: .  facetIS          - An array of the facet numbers
    653: .  n                - The size of dofsArray
    654: .  dofsArray        - The dofmap for the dofs to be solved for
    655: .  dofsArrayWithAll - The dofmap for all dofs on the patch
    656: -  ctx              - The user context

    658:   Level: advanced

    660:   Notes:
    661:   The entries of F (the output residual vector) have been set to zero before the call.

    663: .seealso: PCPatchSetComputeOperator(), PCPatchGetComputeOperator(), PCPatchSetDiscretisationInfo(), PCPatchSetComputeFunction()
    664: @*/
    665: PetscErrorCode PCPatchSetComputeFunctionInteriorFacets(PC pc, PetscErrorCode (*func)(PC, PetscInt, Vec, Vec, IS, PetscInt, const PetscInt *, const PetscInt *, void *), void *ctx)
    666: {
    667:   PC_PATCH *patch = (PC_PATCH *) pc->data;

    670:   patch->usercomputefintfacet    = func;
    671:   patch->usercomputefintfacetctx = ctx;
    672:   return(0);
    673: }

    675: /*@C

    677:   PCPatchSetComputeOperator - Set the callback used to compute patch matrices

    679:   Logically collective on PC

    681:   Input Parameters:
    682: + pc   - The PC
    683: . func - The callback
    684: - ctx  - The user context

    686:   Calling sequence of func:
    687: $   func (PC pc,PetscInt point,Vec x,Mat mat,IS facetIS,PetscInt n,const PetscInt* dofsArray,const PetscInt* dofsArrayWithAll,void* ctx)

    689: +  pc               - The PC
    690: .  point            - The point
    691: .  x                - The input solution (not used in linear problems)
    692: .  mat              - The patch matrix
    693: .  cellIS           - An array of the cell numbers
    694: .  n                - The size of dofsArray
    695: .  dofsArray        - The dofmap for the dofs to be solved for
    696: .  dofsArrayWithAll - The dofmap for all dofs on the patch
    697: -  ctx              - The user context

    699:   Level: advanced

    701:   Notes:
    702:   The matrix entries have been set to zero before the call.

    704: .seealso: PCPatchGetComputeOperator(), PCPatchSetComputeFunction(), PCPatchSetDiscretisationInfo()
    705: @*/
    706: PetscErrorCode PCPatchSetComputeOperator(PC pc, PetscErrorCode (*func)(PC, PetscInt, Vec, Mat, IS, PetscInt, const PetscInt *, const PetscInt *, void *), void *ctx)
    707: {
    708:   PC_PATCH *patch = (PC_PATCH *) pc->data;

    711:   patch->usercomputeop    = func;
    712:   patch->usercomputeopctx = ctx;
    713:   return(0);
    714: }

    716: /*@C

    718:   PCPatchSetComputeOperatorInteriorFacets - Set the callback used to compute facet integrals for patch matrices

    720:   Logically collective on PC

    722:   Input Parameters:
    723: + pc   - The PC
    724: . func - The callback
    725: - ctx  - The user context

    727:   Calling sequence of func:
    728: $   func (PC pc,PetscInt point,Vec x,Mat mat,IS facetIS,PetscInt n,const PetscInt* dofsArray,const PetscInt* dofsArrayWithAll,void* ctx)

    730: +  pc               - The PC
    731: .  point            - The point
    732: .  x                - The input solution (not used in linear problems)
    733: .  mat              - The patch matrix
    734: .  facetIS          - An array of the facet numbers
    735: .  n                - The size of dofsArray
    736: .  dofsArray        - The dofmap for the dofs to be solved for
    737: .  dofsArrayWithAll - The dofmap for all dofs on the patch
    738: -  ctx              - The user context

    740:   Level: advanced

    742:   Notes:
    743:   The matrix entries have been set to zero before the call.

    745: .seealso: PCPatchGetComputeOperator(), PCPatchSetComputeFunction(), PCPatchSetDiscretisationInfo()
    746: @*/
    747: PetscErrorCode PCPatchSetComputeOperatorInteriorFacets(PC pc, PetscErrorCode (*func)(PC, PetscInt, Vec, Mat, IS, PetscInt, const PetscInt *, const PetscInt *, void *), void *ctx)
    748: {
    749:   PC_PATCH *patch = (PC_PATCH *) pc->data;

    752:   patch->usercomputeopintfacet    = func;
    753:   patch->usercomputeopintfacetctx = ctx;
    754:   return(0);
    755: }

    757: /* On entry, ht contains the topological entities whose dofs we are responsible for solving for;
    758:    on exit, cht contains all the topological entities we need to compute their residuals.
    759:    In full generality this should incorporate knowledge of the sparsity pattern of the matrix;
    760:    here we assume a standard FE sparsity pattern.*/
    761: /* TODO: Use DMPlexGetAdjacency() */
    762: static PetscErrorCode PCPatchCompleteCellPatch(PC pc, PetscHSetI ht, PetscHSetI cht)
    763: {
    764:   DM             dm, plex;
    765:   PC_PATCH      *patch = (PC_PATCH *) pc->data;
    766:   PetscHashIter  hi;
    767:   PetscInt       point;
    768:   PetscInt      *star = NULL, *closure = NULL;
    769:   PetscInt       ignoredim, iStart = 0, iEnd = -1, starSize, closureSize, si, ci;
    770:   PetscInt      *fStar = NULL, *fClosure = NULL;
    771:   PetscInt       fBegin, fEnd, fsi, fci, fStarSize, fClosureSize;

    775:   PCGetDM(pc, &dm);
    776:   DMConvert(dm, DMPLEX, &plex);
    777:   dm = plex;
    778:   DMPlexGetHeightStratum(dm, 1, &fBegin, &fEnd);
    779:   PCPatchGetIgnoreDim(pc, &ignoredim);
    780:   if (ignoredim >= 0) {DMPlexGetDepthStratum(dm, ignoredim, &iStart, &iEnd);}
    781:   PetscHSetIClear(cht);
    782:   PetscHashIterBegin(ht, hi);
    783:   while (!PetscHashIterAtEnd(ht, hi)) {

    785:     PetscHashIterGetKey(ht, hi, point);
    786:     PetscHashIterNext(ht, hi);

    788:     /* Loop over all the cells that this point connects to */
    789:     DMPlexGetTransitiveClosure(dm, point, PETSC_FALSE, &starSize, &star);
    790:     for (si = 0; si < starSize*2; si += 2) {
    791:       const PetscInt ownedpoint = star[si];
    792:       /* TODO Check for point in cht before running through closure again */
    793:       /* now loop over all entities in the closure of that cell */
    794:       DMPlexGetTransitiveClosure(dm, ownedpoint, PETSC_TRUE, &closureSize, &closure);
    795:       for (ci = 0; ci < closureSize*2; ci += 2) {
    796:         const PetscInt seenpoint = closure[ci];
    797:         if (ignoredim >= 0 && seenpoint >= iStart && seenpoint < iEnd) continue;
    798:         PetscHSetIAdd(cht, seenpoint);
    799:         /* Facet integrals couple dofs across facets, so in that case for each of
    800:          * the facets we need to add all dofs on the other side of the facet to
    801:          * the seen dofs. */
    802:         if(patch->usercomputeopintfacet){
    803:           if(fBegin <= seenpoint && seenpoint < fEnd){
    804:             DMPlexGetTransitiveClosure(dm, seenpoint, PETSC_FALSE, &fStarSize, &fStar);
    805:             for (fsi = 0; fsi < fStarSize*2; fsi += 2) {
    806:               DMPlexGetTransitiveClosure(dm, fStar[fsi], PETSC_TRUE, &fClosureSize, &fClosure);
    807:               for (fci = 0; fci < fClosureSize*2; fci += 2) {
    808:                 PetscHSetIAdd(cht, fClosure[fci]);
    809:               }
    810:               DMPlexRestoreTransitiveClosure(dm, fStar[fsi], PETSC_TRUE, NULL, &fClosure);
    811:             }
    812:             DMPlexRestoreTransitiveClosure(dm, seenpoint, PETSC_FALSE, NULL, &fStar);
    813:           }
    814:         }
    815:       }
    816:       DMPlexRestoreTransitiveClosure(dm, ownedpoint, PETSC_TRUE, NULL, &closure);
    817:     }
    818:     DMPlexRestoreTransitiveClosure(dm, point, PETSC_FALSE, NULL, &star);
    819:   }
    820:   DMDestroy(&dm);
    821:   return(0);
    822: }

    824: static PetscErrorCode PCPatchGetGlobalDofs(PC pc, PetscSection dofSection[], PetscInt f, PetscBool combined, PetscInt p, PetscInt *dof, PetscInt *off)
    825: {

    829:   if (combined) {
    830:     if (f < 0) {
    831:       if (dof) {PetscSectionGetDof(dofSection[0], p, dof);}
    832:       if (off) {PetscSectionGetOffset(dofSection[0], p, off);}
    833:     } else {
    834:       if (dof) {PetscSectionGetFieldDof(dofSection[0], p, f, dof);}
    835:       if (off) {PetscSectionGetFieldOffset(dofSection[0], p, f, off);}
    836:     }
    837:   } else {
    838:     if (f < 0) {
    839:       PC_PATCH *patch = (PC_PATCH *) pc->data;
    840:       PetscInt  fdof, g;

    842:       if (dof) {
    843:         *dof = 0;
    844:         for (g = 0; g < patch->nsubspaces; ++g) {
    845:           PetscSectionGetDof(dofSection[g], p, &fdof);
    846:           *dof += fdof;
    847:         }
    848:       }
    849:       if (off) {
    850:         *off = 0;
    851:         for (g = 0; g < patch->nsubspaces; ++g) {
    852:           PetscSectionGetOffset(dofSection[g], p, &fdof);
    853:           *off += fdof;
    854:         }
    855:       }
    856:     } else {
    857:       if (dof) {PetscSectionGetDof(dofSection[f], p, dof);}
    858:       if (off) {PetscSectionGetOffset(dofSection[f], p, off);}
    859:     }
    860:   }
    861:   return(0);
    862: }

    864: /* Given a hash table with a set of topological entities (pts), compute the degrees of
    865:    freedom in global concatenated numbering on those entities.
    866:    For Vanka smoothing, this needs to do something special: ignore dofs of the
    867:    constraint subspace on entities that aren't the base entity we're building the patch
    868:    around. */
    869: static PetscErrorCode PCPatchGetPointDofs(PC pc, PetscHSetI pts, PetscHSetI dofs, PetscInt base, PetscHSetI* subspaces_to_exclude)
    870: {
    871:   PC_PATCH      *patch = (PC_PATCH *) pc->data;
    872:   PetscHashIter  hi;
    873:   PetscInt       ldof, loff;
    874:   PetscInt       k, p;

    878:   PetscHSetIClear(dofs);
    879:   for (k = 0; k < patch->nsubspaces; ++k) {
    880:     PetscInt subspaceOffset = patch->subspaceOffsets[k];
    881:     PetscInt bs             = patch->bs[k];
    882:     PetscInt j, l;

    884:     if (subspaces_to_exclude != NULL) {
    885:       PetscBool should_exclude_k = PETSC_FALSE;
    886:       PetscHSetIHas(*subspaces_to_exclude, k, &should_exclude_k);
    887:       if (should_exclude_k) {
    888:         /* only get this subspace dofs at the base entity, not any others */
    889:         PCPatchGetGlobalDofs(pc, patch->dofSection, k, patch->combined, base, &ldof, &loff);
    890:         if (0 == ldof) continue;
    891:         for (j = loff; j < ldof + loff; ++j) {
    892:           for (l = 0; l < bs; ++l) {
    893:             PetscInt dof = bs*j + l + subspaceOffset;
    894:             PetscHSetIAdd(dofs, dof);
    895:           }
    896:         }
    897:         continue; /* skip the other dofs of this subspace */
    898:       }
    899:     }

    901:     PetscHashIterBegin(pts, hi);
    902:     while (!PetscHashIterAtEnd(pts, hi)) {
    903:       PetscHashIterGetKey(pts, hi, p);
    904:       PetscHashIterNext(pts, hi);
    905:       PCPatchGetGlobalDofs(pc, patch->dofSection, k, patch->combined, p, &ldof, &loff);
    906:       if (0 == ldof) continue;
    907:       for (j = loff; j < ldof + loff; ++j) {
    908:         for (l = 0; l < bs; ++l) {
    909:           PetscInt dof = bs*j + l + subspaceOffset;
    910:           PetscHSetIAdd(dofs, dof);
    911:         }
    912:       }
    913:     }
    914:   }
    915:   return(0);
    916: }

    918: /* Given two hash tables A and B, compute the keys in B that are not in A, and put them in C */
    919: static PetscErrorCode PCPatchComputeSetDifference_Private(PetscHSetI A, PetscHSetI B, PetscHSetI C)
    920: {
    921:   PetscHashIter  hi;
    922:   PetscInt       key;
    923:   PetscBool      flg;

    927:   PetscHSetIClear(C);
    928:   PetscHashIterBegin(B, hi);
    929:   while (!PetscHashIterAtEnd(B, hi)) {
    930:     PetscHashIterGetKey(B, hi, key);
    931:     PetscHashIterNext(B, hi);
    932:     PetscHSetIHas(A, key, &flg);
    933:     if (!flg) {PetscHSetIAdd(C, key);}
    934:   }
    935:   return(0);
    936: }

    938: /*
    939:  * PCPatchCreateCellPatches - create patches.
    940:  *
    941:  * Input Parameters:
    942:  * + dm - The DMPlex object defining the mesh
    943:  *
    944:  * Output Parameters:
    945:  * + cellCounts  - Section with counts of cells around each vertex
    946:  * . cells       - IS of the cell point indices of cells in each patch
    947:  * . pointCounts - Section with counts of cells around each vertex
    948:  * - point       - IS of the cell point indices of cells in each patch
    949:  */
    950: static PetscErrorCode PCPatchCreateCellPatches(PC pc)
    951: {
    952:   PC_PATCH       *patch = (PC_PATCH *) pc->data;
    953:   DMLabel         ghost = NULL;
    954:   DM              dm, plex;
    955:   PetscHSetI      ht, cht;
    956:   PetscSection    cellCounts,  pointCounts, intFacetCounts, extFacetCounts;
    957:   PetscInt       *cellsArray, *pointsArray, *intFacetsArray, *extFacetsArray, *intFacetsToPatchCell;
    958:   PetscInt        numCells, numPoints, numIntFacets, numExtFacets;
    959:   const PetscInt *leaves;
    960:   PetscInt        nleaves, pStart, pEnd, cStart, cEnd, vStart, vEnd, fStart, fEnd, v;
    961:   PetscBool       isFiredrake;
    962:   PetscErrorCode  ierr;

    965:   /* Used to keep track of the cells in the patch. */
    966:   PetscHSetICreate(&ht);
    967:   PetscHSetICreate(&cht);

    969:   PCGetDM(pc, &dm);
    970:   if (!dm) SETERRQ(PetscObjectComm((PetscObject) pc), PETSC_ERR_ARG_WRONGSTATE, "DM not yet set on patch PC\n");
    971:   DMConvert(dm, DMPLEX, &plex);
    972:   dm = plex;
    973:   DMPlexGetChart(dm, &pStart, &pEnd);
    974:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);

    976:   if (patch->user_patches) {
    977:     patch->userpatchconstructionop(pc, &patch->npatch, &patch->userIS, &patch->iterationSet, patch->userpatchconstructctx);
    978:     vStart = 0; vEnd = patch->npatch;
    979:   } else if (patch->ctype == PC_PATCH_PARDECOMP) {
    980:     vStart = 0; vEnd = 1;
    981:   } else if (patch->codim < 0) {
    982:     if (patch->dim < 0) {DMPlexGetDepthStratum(dm,  0,            &vStart, &vEnd);}
    983:     else                {DMPlexGetDepthStratum(dm,  patch->dim,   &vStart, &vEnd);}
    984:   } else                {DMPlexGetHeightStratum(dm, patch->codim, &vStart, &vEnd);}
    985:   patch->npatch = vEnd - vStart;

    987:   /* These labels mark the owned points.  We only create patches around points that this process owns. */
    988:   DMHasLabel(dm, "pyop2_ghost", &isFiredrake);
    989:   if (isFiredrake) {
    990:     DMGetLabel(dm, "pyop2_ghost", &ghost);
    991:     DMLabelCreateIndex(ghost, pStart, pEnd);
    992:   } else {
    993:     PetscSF sf;

    995:     DMGetPointSF(dm, &sf);
    996:     PetscSFGetGraph(sf, NULL, &nleaves, &leaves, NULL);
    997:     nleaves = PetscMax(nleaves, 0);
    998:   }

    1000:   PetscSectionCreate(PETSC_COMM_SELF, &patch->cellCounts);
    1001:   PetscObjectSetName((PetscObject) patch->cellCounts, "Patch Cell Layout");
    1002:   cellCounts = patch->cellCounts;
    1003:   PetscSectionSetChart(cellCounts, vStart, vEnd);
    1004:   PetscSectionCreate(PETSC_COMM_SELF, &patch->pointCounts);
    1005:   PetscObjectSetName((PetscObject) patch->pointCounts, "Patch Point Layout");
    1006:   pointCounts = patch->pointCounts;
    1007:   PetscSectionSetChart(pointCounts, vStart, vEnd);
    1008:   PetscSectionCreate(PETSC_COMM_SELF, &patch->extFacetCounts);
    1009:   PetscObjectSetName((PetscObject) patch->extFacetCounts, "Patch Exterior Facet Layout");
    1010:   extFacetCounts = patch->extFacetCounts;
    1011:   PetscSectionSetChart(extFacetCounts, vStart, vEnd);
    1012:   PetscSectionCreate(PETSC_COMM_SELF, &patch->intFacetCounts);
    1013:   PetscObjectSetName((PetscObject) patch->intFacetCounts, "Patch Interior Facet Layout");
    1014:   intFacetCounts = patch->intFacetCounts;
    1015:   PetscSectionSetChart(intFacetCounts, vStart, vEnd);
    1016:   /* Count cells and points in the patch surrounding each entity */
    1017:   DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
    1018:   for (v = vStart; v < vEnd; ++v) {
    1019:     PetscHashIter hi;
    1020:     PetscInt       chtSize, loc = -1;
    1021:     PetscBool      flg;

    1023:     if (!patch->user_patches && patch->ctype != PC_PATCH_PARDECOMP) {
    1024:       if (ghost) {DMLabelHasPoint(ghost, v, &flg);}
    1025:       else       {PetscFindInt(v, nleaves, leaves, &loc); flg = loc >=0 ? PETSC_TRUE : PETSC_FALSE;}
    1026:       /* Not an owned entity, don't make a cell patch. */
    1027:       if (flg) continue;
    1028:     }

    1030:     patch->patchconstructop((void *) patch, dm, v, ht);
    1031:     PCPatchCompleteCellPatch(pc, ht, cht);
    1032:     PetscHSetIGetSize(cht, &chtSize);
    1033:     /* empty patch, continue */
    1034:     if (chtSize == 0) continue;

    1036:     /* safe because size(cht) > 0 from above */
    1037:     PetscHashIterBegin(cht, hi);
    1038:     while (!PetscHashIterAtEnd(cht, hi)) {
    1039:       PetscInt point, pdof;

    1041:       PetscHashIterGetKey(cht, hi, point);
    1042:       if (fStart <= point && point < fEnd) {
    1043:         const PetscInt *support;
    1044:         PetscInt supportSize, p;
    1045:         PetscBool interior = PETSC_TRUE;
    1046:         DMPlexGetSupport(dm, point, &support);
    1047:         DMPlexGetSupportSize(dm, point, &supportSize);
    1048:         if (supportSize == 1) {
    1049:           interior = PETSC_FALSE;
    1050:         } else {
    1051:           for (p = 0; p < supportSize; p++) {
    1052:             PetscBool found;
    1053:             /* FIXME: can I do this while iterating over cht? */
    1054:             PetscHSetIHas(cht, support[p], &found);
    1055:             if (!found) {
    1056:               interior = PETSC_FALSE;
    1057:               break;
    1058:             }
    1059:           }
    1060:         }
    1061:         if (interior) {
    1062:           PetscSectionAddDof(intFacetCounts, v, 1);
    1063:         } else {
    1064:           PetscSectionAddDof(extFacetCounts, v, 1);
    1065:         }
    1066:       }
    1067:       PCPatchGetGlobalDofs(pc, patch->dofSection, -1, patch->combined, point, &pdof, NULL);
    1068:       if (pdof)                            {PetscSectionAddDof(pointCounts, v, 1);}
    1069:       if (point >= cStart && point < cEnd) {PetscSectionAddDof(cellCounts, v, 1);}
    1070:       PetscHashIterNext(cht, hi);
    1071:     }
    1072:   }
    1073:   if (isFiredrake) {DMLabelDestroyIndex(ghost);}

    1075:   PetscSectionSetUp(cellCounts);
    1076:   PetscSectionGetStorageSize(cellCounts, &numCells);
    1077:   PetscMalloc1(numCells, &cellsArray);
    1078:   PetscSectionSetUp(pointCounts);
    1079:   PetscSectionGetStorageSize(pointCounts, &numPoints);
    1080:   PetscMalloc1(numPoints, &pointsArray);

    1082:   PetscSectionSetUp(intFacetCounts);
    1083:   PetscSectionSetUp(extFacetCounts);
    1084:   PetscSectionGetStorageSize(intFacetCounts, &numIntFacets);
    1085:   PetscSectionGetStorageSize(extFacetCounts, &numExtFacets);
    1086:   PetscMalloc1(numIntFacets, &intFacetsArray);
    1087:   PetscMalloc1(numIntFacets*2, &intFacetsToPatchCell);
    1088:   PetscMalloc1(numExtFacets, &extFacetsArray);

    1091:   /* Now that we know how much space we need, run through again and actually remember the cells. */
    1092:   for (v = vStart; v < vEnd; v++ ) {
    1093:     PetscHashIter hi;
    1094:     PetscInt       dof, off, cdof, coff, efdof, efoff, ifdof, ifoff, pdof, n = 0, cn = 0, ifn = 0, efn = 0;

    1096:     PetscSectionGetDof(pointCounts, v, &dof);
    1097:     PetscSectionGetOffset(pointCounts, v, &off);
    1098:     PetscSectionGetDof(cellCounts, v, &cdof);
    1099:     PetscSectionGetOffset(cellCounts, v, &coff);
    1100:     PetscSectionGetDof(intFacetCounts, v, &ifdof);
    1101:     PetscSectionGetOffset(intFacetCounts, v, &ifoff);
    1102:     PetscSectionGetDof(extFacetCounts, v, &efdof);
    1103:     PetscSectionGetOffset(extFacetCounts, v, &efoff);
    1104:     if (dof <= 0) continue;
    1105:     patch->patchconstructop((void *) patch, dm, v, ht);
    1106:     PCPatchCompleteCellPatch(pc, ht, cht);
    1107:     PetscHashIterBegin(cht, hi);
    1108:     while (!PetscHashIterAtEnd(cht, hi)) {
    1109:       PetscInt point;

    1111:       PetscHashIterGetKey(cht, hi, point);
    1112:       if (fStart <= point && point < fEnd) {
    1113:         const PetscInt *support;
    1114:         PetscInt supportSize, p;
    1115:         PetscBool interior = PETSC_TRUE;
    1116:         DMPlexGetSupport(dm, point, &support);
    1117:         DMPlexGetSupportSize(dm, point, &supportSize);
    1118:         if (supportSize == 1) {
    1119:           interior = PETSC_FALSE;
    1120:         } else {
    1121:           for (p = 0; p < supportSize; p++) {
    1122:             PetscBool found;
    1123:             /* FIXME: can I do this while iterating over cht? */
    1124:             PetscHSetIHas(cht, support[p], &found);
    1125:             if (!found) {
    1126:               interior = PETSC_FALSE;
    1127:               break;
    1128:             }
    1129:           }
    1130:         }
    1131:         if (interior) {
    1132:           intFacetsToPatchCell[2*(ifoff + ifn)] = support[0];
    1133:           intFacetsToPatchCell[2*(ifoff + ifn) + 1] = support[1];
    1134:           intFacetsArray[ifoff + ifn++] = point;
    1135:         } else {
    1136:           extFacetsArray[efoff + efn++] = point;
    1137:         }
    1138:       }
    1139:       PCPatchGetGlobalDofs(pc, patch->dofSection, -1, patch->combined, point, &pdof, NULL);
    1140:       if (pdof)                            {pointsArray[off + n++] = point;}
    1141:       if (point >= cStart && point < cEnd) {cellsArray[coff + cn++] = point;}
    1142:       PetscHashIterNext(cht, hi);
    1143:     }
    1144:     if (ifn != ifdof) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Number of interior facets in patch %D is %D, but should be %D", v, ifn, ifdof);
    1145:     if (efn != efdof) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Number of exterior facets in patch %D is %D, but should be %D", v, efn, efdof);
    1146:     if (cn != cdof) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Number of cells in patch %D is %D, but should be %D", v, cn, cdof);
    1147:     if (n  != dof)  SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Number of points in patch %D is %D, but should be %D", v, n, dof);

    1149:     for (ifn = 0; ifn < ifdof; ifn++) {
    1150:       PetscInt cell0 = intFacetsToPatchCell[2*(ifoff + ifn)];
    1151:       PetscInt cell1 = intFacetsToPatchCell[2*(ifoff + ifn) + 1];
    1152:       PetscBool found0 = PETSC_FALSE, found1 = PETSC_FALSE;
    1153:       for (n = 0; n < cdof; n++) {
    1154:         if (!found0 && cell0 == cellsArray[coff + n]) {
    1155:           intFacetsToPatchCell[2*(ifoff + ifn)] = n;
    1156:           found0 = PETSC_TRUE;
    1157:         }
    1158:         if (!found1 && cell1 == cellsArray[coff + n]) {
    1159:           intFacetsToPatchCell[2*(ifoff + ifn) + 1] = n;
    1160:           found1 = PETSC_TRUE;
    1161:         }
    1162:         if (found0 && found1) break;
    1163:       }
    1164:       if (!(found0 && found1)) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Didn't manage to find local point numbers for facet support");
    1165:     }
    1166:   }
    1167:   PetscHSetIDestroy(&ht);
    1168:   PetscHSetIDestroy(&cht);

    1170:   ISCreateGeneral(PETSC_COMM_SELF, numCells,  cellsArray,  PETSC_OWN_POINTER, &patch->cells);
    1171:   PetscObjectSetName((PetscObject) patch->cells,  "Patch Cells");
    1172:   if (patch->viewCells) {
    1173:     ObjectView((PetscObject) patch->cellCounts, patch->viewerCells, patch->formatCells);
    1174:     ObjectView((PetscObject) patch->cells,      patch->viewerCells, patch->formatCells);
    1175:   }
    1176:   ISCreateGeneral(PETSC_COMM_SELF, numIntFacets,  intFacetsArray,  PETSC_OWN_POINTER, &patch->intFacets);
    1177:   PetscObjectSetName((PetscObject) patch->intFacets,  "Patch Interior Facets");
    1178:   ISCreateGeneral(PETSC_COMM_SELF, 2*numIntFacets, intFacetsToPatchCell, PETSC_OWN_POINTER, &patch->intFacetsToPatchCell);
    1179:   PetscObjectSetName((PetscObject) patch->intFacetsToPatchCell,  "Patch Interior Facets local support");
    1180:   if (patch->viewIntFacets) {
    1181:     ObjectView((PetscObject) patch->intFacetCounts,       patch->viewerIntFacets, patch->formatIntFacets);
    1182:     ObjectView((PetscObject) patch->intFacets,            patch->viewerIntFacets, patch->formatIntFacets);
    1183:     ObjectView((PetscObject) patch->intFacetsToPatchCell, patch->viewerIntFacets, patch->formatIntFacets);
    1184:   }
    1185:   ISCreateGeneral(PETSC_COMM_SELF, numExtFacets,  extFacetsArray,  PETSC_OWN_POINTER, &patch->extFacets);
    1186:   PetscObjectSetName((PetscObject) patch->extFacets,  "Patch Exterior Facets");
    1187:   if (patch->viewExtFacets) {
    1188:     ObjectView((PetscObject) patch->extFacetCounts, patch->viewerExtFacets, patch->formatExtFacets);
    1189:     ObjectView((PetscObject) patch->extFacets,      patch->viewerExtFacets, patch->formatExtFacets);
    1190:   }
    1191:   ISCreateGeneral(PETSC_COMM_SELF, numPoints, pointsArray, PETSC_OWN_POINTER, &patch->points);
    1192:   PetscObjectSetName((PetscObject) patch->points, "Patch Points");
    1193:   if (patch->viewPoints) {
    1194:     ObjectView((PetscObject) patch->pointCounts, patch->viewerPoints, patch->formatPoints);
    1195:     ObjectView((PetscObject) patch->points,      patch->viewerPoints, patch->formatPoints);
    1196:   }
    1197:   DMDestroy(&dm);
    1198:   return(0);
    1199: }

    1201: /*
    1202:  * PCPatchCreateCellPatchDiscretisationInfo - Build the dof maps for cell patches
    1203:  *
    1204:  * Input Parameters:
    1205:  * + dm - The DMPlex object defining the mesh
    1206:  * . cellCounts - Section with counts of cells around each vertex
    1207:  * . cells - IS of the cell point indices of cells in each patch
    1208:  * . cellNumbering - Section mapping plex cell points to Firedrake cell indices.
    1209:  * . nodesPerCell - number of nodes per cell.
    1210:  * - cellNodeMap - map from cells to node indices (nodesPerCell * numCells)
    1211:  *
    1212:  * Output Parameters:
    1213:  * + dofs - IS of local dof numbers of each cell in the patch, where local is a patch local numbering
    1214:  * . gtolCounts - Section with counts of dofs per cell patch
    1215:  * - gtol - IS mapping from global dofs to local dofs for each patch.
    1216:  */
    1217: static PetscErrorCode PCPatchCreateCellPatchDiscretisationInfo(PC pc)
    1218: {
    1219:   PC_PATCH       *patch           = (PC_PATCH *) pc->data;
    1220:   PetscSection    cellCounts      = patch->cellCounts;
    1221:   PetscSection    pointCounts     = patch->pointCounts;
    1222:   PetscSection    gtolCounts, gtolCountsWithArtificial = NULL, gtolCountsWithAll = NULL;
    1223:   IS              cells           = patch->cells;
    1224:   IS              points          = patch->points;
    1225:   PetscSection    cellNumbering   = patch->cellNumbering;
    1226:   PetscInt        Nf              = patch->nsubspaces;
    1227:   PetscInt        numCells, numPoints;
    1228:   PetscInt        numDofs;
    1229:   PetscInt        numGlobalDofs, numGlobalDofsWithArtificial, numGlobalDofsWithAll;
    1230:   PetscInt        totalDofsPerCell = patch->totalDofsPerCell;
    1231:   PetscInt        vStart, vEnd, v;
    1232:   const PetscInt *cellsArray, *pointsArray;
    1233:   PetscInt       *newCellsArray   = NULL;
    1234:   PetscInt       *dofsArray       = NULL;
    1235:   PetscInt       *dofsArrayWithArtificial = NULL;
    1236:   PetscInt       *dofsArrayWithAll = NULL;
    1237:   PetscInt       *offsArray       = NULL;
    1238:   PetscInt       *offsArrayWithArtificial = NULL;
    1239:   PetscInt       *offsArrayWithAll = NULL;
    1240:   PetscInt       *asmArray        = NULL;
    1241:   PetscInt       *asmArrayWithArtificial = NULL;
    1242:   PetscInt       *asmArrayWithAll = NULL;
    1243:   PetscInt       *globalDofsArray = NULL;
    1244:   PetscInt       *globalDofsArrayWithArtificial = NULL;
    1245:   PetscInt       *globalDofsArrayWithAll = NULL;
    1246:   PetscInt        globalIndex     = 0;
    1247:   PetscInt        key             = 0;
    1248:   PetscInt        asmKey          = 0;
    1249:   DM              dm              = NULL, plex;
    1250:   const PetscInt *bcNodes         = NULL;
    1251:   PetscHMapI      ht;
    1252:   PetscHMapI      htWithArtificial;
    1253:   PetscHMapI      htWithAll;
    1254:   PetscHSetI      globalBcs;
    1255:   PetscInt        numBcs;
    1256:   PetscHSetI      ownedpts, seenpts, owneddofs, seendofs, artificialbcs;
    1257:   PetscInt        pStart, pEnd, p, i;
    1258:   char            option[PETSC_MAX_PATH_LEN];
    1259:   PetscBool       isNonlinear;
    1260:   PetscErrorCode  ierr;

    1264:   PCGetDM(pc, &dm);
    1265:   DMConvert(dm, DMPLEX, &plex);
    1266:   dm = plex;
    1267:   /* dofcounts section is cellcounts section * dofPerCell */
    1268:   PetscSectionGetStorageSize(cellCounts, &numCells);
    1269:   PetscSectionGetStorageSize(patch->pointCounts, &numPoints);
    1270:   numDofs = numCells * totalDofsPerCell;
    1271:   PetscMalloc1(numDofs, &dofsArray);
    1272:   PetscMalloc1(numPoints*Nf, &offsArray);
    1273:   PetscMalloc1(numDofs, &asmArray);
    1274:   PetscMalloc1(numCells, &newCellsArray);
    1275:   PetscSectionGetChart(cellCounts, &vStart, &vEnd);
    1276:   PetscSectionCreate(PETSC_COMM_SELF, &patch->gtolCounts);
    1277:   gtolCounts = patch->gtolCounts;
    1278:   PetscSectionSetChart(gtolCounts, vStart, vEnd);
    1279:   PetscObjectSetName((PetscObject) patch->gtolCounts, "Patch Global Index Section");

    1281:   if (patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    1282:     PetscMalloc1(numPoints*Nf, &offsArrayWithArtificial);
    1283:     PetscMalloc1(numDofs, &asmArrayWithArtificial);
    1284:     PetscMalloc1(numDofs, &dofsArrayWithArtificial);
    1285:     PetscSectionCreate(PETSC_COMM_SELF, &patch->gtolCountsWithArtificial);
    1286:     gtolCountsWithArtificial = patch->gtolCountsWithArtificial;
    1287:     PetscSectionSetChart(gtolCountsWithArtificial, vStart, vEnd);
    1288:     PetscObjectSetName((PetscObject) patch->gtolCountsWithArtificial, "Patch Global Index Section Including Artificial BCs");
    1289:   }

    1291:   isNonlinear = patch->isNonlinear;
    1292:   if (isNonlinear) {
    1293:     PetscMalloc1(numPoints*Nf, &offsArrayWithAll);
    1294:     PetscMalloc1(numDofs, &asmArrayWithAll);
    1295:     PetscMalloc1(numDofs, &dofsArrayWithAll);
    1296:     PetscSectionCreate(PETSC_COMM_SELF, &patch->gtolCountsWithAll);
    1297:     gtolCountsWithAll = patch->gtolCountsWithAll;
    1298:     PetscSectionSetChart(gtolCountsWithAll, vStart, vEnd);
    1299:     PetscObjectSetName((PetscObject) patch->gtolCountsWithAll, "Patch Global Index Section Including All BCs");
    1300:   }

    1302:   /* Outside the patch loop, get the dofs that are globally-enforced Dirichlet
    1303:    conditions */
    1304:   PetscHSetICreate(&globalBcs);
    1305:   ISGetIndices(patch->ghostBcNodes, &bcNodes);
    1306:   ISGetSize(patch->ghostBcNodes, &numBcs);
    1307:   for (i = 0; i < numBcs; ++i) {
    1308:     PetscHSetIAdd(globalBcs, bcNodes[i]); /* these are already in concatenated numbering */
    1309:   }
    1310:   ISRestoreIndices(patch->ghostBcNodes, &bcNodes);
    1311:   ISDestroy(&patch->ghostBcNodes);  /* memory optimisation */

    1313:   /* Hash tables for artificial BC construction */
    1314:   PetscHSetICreate(&ownedpts);
    1315:   PetscHSetICreate(&seenpts);
    1316:   PetscHSetICreate(&owneddofs);
    1317:   PetscHSetICreate(&seendofs);
    1318:   PetscHSetICreate(&artificialbcs);

    1320:   ISGetIndices(cells, &cellsArray);
    1321:   ISGetIndices(points, &pointsArray);
    1322:   PetscHMapICreate(&ht);
    1323:   PetscHMapICreate(&htWithArtificial);
    1324:   PetscHMapICreate(&htWithAll);
    1325:   for (v = vStart; v < vEnd; ++v) {
    1326:     PetscInt localIndex = 0;
    1327:     PetscInt localIndexWithArtificial = 0;
    1328:     PetscInt localIndexWithAll = 0;
    1329:     PetscInt dof, off, i, j, k, l;

    1331:     PetscHMapIClear(ht);
    1332:     PetscHMapIClear(htWithArtificial);
    1333:     PetscHMapIClear(htWithAll);
    1334:     PetscSectionGetDof(cellCounts, v, &dof);
    1335:     PetscSectionGetOffset(cellCounts, v, &off);
    1336:     if (dof <= 0) continue;

    1338:     /* Calculate the global numbers of the artificial BC dofs here first */
    1339:     patch->patchconstructop((void*)patch, dm, v, ownedpts);
    1340:     PCPatchCompleteCellPatch(pc, ownedpts, seenpts);
    1341:     PCPatchGetPointDofs(pc, ownedpts, owneddofs, v, &patch->subspaces_to_exclude);
    1342:     PCPatchGetPointDofs(pc, seenpts, seendofs, v, NULL);
    1343:     PCPatchComputeSetDifference_Private(owneddofs, seendofs, artificialbcs);
    1344:     if (patch->viewPatches) {
    1345:       PetscHSetI globalbcdofs;
    1346:       PetscHashIter hi;
    1347:       MPI_Comm comm = PetscObjectComm((PetscObject)pc);

    1349:       PetscHSetICreate(&globalbcdofs);
    1350:       PetscSynchronizedPrintf(comm, "Patch %d: owned dofs:\n", v);
    1351:       PetscHashIterBegin(owneddofs, hi);
    1352:       while (!PetscHashIterAtEnd(owneddofs, hi)) {
    1353:         PetscInt globalDof;

    1355:         PetscHashIterGetKey(owneddofs, hi, globalDof);
    1356:         PetscHashIterNext(owneddofs, hi);
    1357:         PetscSynchronizedPrintf(comm, "%d ", globalDof);
    1358:       }
    1359:       PetscSynchronizedPrintf(comm, "\n");
    1360:       PetscSynchronizedPrintf(comm, "Patch %d: seen dofs:\n", v);
    1361:       PetscHashIterBegin(seendofs, hi);
    1362:       while (!PetscHashIterAtEnd(seendofs, hi)) {
    1363:         PetscInt globalDof;
    1364:         PetscBool flg;

    1366:         PetscHashIterGetKey(seendofs, hi, globalDof);
    1367:         PetscHashIterNext(seendofs, hi);
    1368:         PetscSynchronizedPrintf(comm, "%d ", globalDof);

    1370:         PetscHSetIHas(globalBcs, globalDof, &flg);
    1371:         if (flg) {PetscHSetIAdd(globalbcdofs, globalDof);}
    1372:       }
    1373:       PetscSynchronizedPrintf(comm, "\n");
    1374:       PetscSynchronizedPrintf(comm, "Patch %d: global BCs:\n", v);
    1375:       PetscHSetIGetSize(globalbcdofs, &numBcs);
    1376:       if (numBcs > 0) {
    1377:         PetscHashIterBegin(globalbcdofs, hi);
    1378:         while (!PetscHashIterAtEnd(globalbcdofs, hi)) {
    1379:           PetscInt globalDof;
    1380:           PetscHashIterGetKey(globalbcdofs, hi, globalDof);
    1381:           PetscHashIterNext(globalbcdofs, hi);
    1382:           PetscSynchronizedPrintf(comm, "%d ", globalDof);
    1383:         }
    1384:       }
    1385:       PetscSynchronizedPrintf(comm, "\n");
    1386:       PetscSynchronizedPrintf(comm, "Patch %d: artificial BCs:\n", v);
    1387:       PetscHSetIGetSize(artificialbcs, &numBcs);
    1388:       if (numBcs > 0) {
    1389:         PetscHashIterBegin(artificialbcs, hi);
    1390:         while (!PetscHashIterAtEnd(artificialbcs, hi)) {
    1391:           PetscInt globalDof;
    1392:           PetscHashIterGetKey(artificialbcs, hi, globalDof);
    1393:           PetscHashIterNext(artificialbcs, hi);
    1394:           PetscSynchronizedPrintf(comm, "%d ", globalDof);
    1395:         }
    1396:       }
    1397:       PetscSynchronizedPrintf(comm, "\n\n");
    1398:       PetscHSetIDestroy(&globalbcdofs);
    1399:     }
    1400:    for (k = 0; k < patch->nsubspaces; ++k) {
    1401:       const PetscInt *cellNodeMap    = patch->cellNodeMap[k];
    1402:       PetscInt        nodesPerCell   = patch->nodesPerCell[k];
    1403:       PetscInt        subspaceOffset = patch->subspaceOffsets[k];
    1404:       PetscInt        bs             = patch->bs[k];

    1406:       for (i = off; i < off + dof; ++i) {
    1407:         /* Walk over the cells in this patch. */
    1408:         const PetscInt c    = cellsArray[i];
    1409:         PetscInt       cell = c;

    1411:         /* TODO Change this to an IS */
    1412:         if (cellNumbering) {
    1413:           PetscSectionGetDof(cellNumbering, c, &cell);
    1414:           if (cell <= 0) SETERRQ1(PetscObjectComm((PetscObject) pc), PETSC_ERR_ARG_OUTOFRANGE, "Cell %D doesn't appear in cell numbering map", c);
    1415:           PetscSectionGetOffset(cellNumbering, c, &cell);
    1416:         }
    1417:         newCellsArray[i] = cell;
    1418:         for (j = 0; j < nodesPerCell; ++j) {
    1419:           /* For each global dof, map it into contiguous local storage. */
    1420:           const PetscInt globalDof = cellNodeMap[cell*nodesPerCell + j]*bs + subspaceOffset;
    1421:           /* finally, loop over block size */
    1422:           for (l = 0; l < bs; ++l) {
    1423:             PetscInt  localDof;
    1424:             PetscBool isGlobalBcDof, isArtificialBcDof;

    1426:             /* first, check if this is either a globally enforced or locally enforced BC dof */
    1427:             PetscHSetIHas(globalBcs, globalDof + l, &isGlobalBcDof);
    1428:             PetscHSetIHas(artificialbcs, globalDof + l, &isArtificialBcDof);

    1430:             /* if it's either, don't ever give it a local dof number */
    1431:             if (isGlobalBcDof || isArtificialBcDof) {
    1432:               dofsArray[globalIndex] = -1; /* don't use this in assembly in this patch */
    1433:             } else {
    1434:               PetscHMapIGet(ht, globalDof + l, &localDof);
    1435:               if (localDof == -1) {
    1436:                 localDof = localIndex++;
    1437:                 PetscHMapISet(ht, globalDof + l, localDof);
    1438:               }
    1439:               if ( globalIndex >= numDofs ) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Found more dofs %D than expected %D", globalIndex+1, numDofs);
    1440:               /* And store. */
    1441:               dofsArray[globalIndex] = localDof;
    1442:             }

    1444:             if(patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    1445:               if (isGlobalBcDof) {
    1446:                 dofsArrayWithArtificial[globalIndex] = -1; /* don't use this in assembly in this patch */
    1447:               } else {
    1448:                 PetscHMapIGet(htWithArtificial, globalDof + l, &localDof);
    1449:                 if (localDof == -1) {
    1450:                   localDof = localIndexWithArtificial++;
    1451:                   PetscHMapISet(htWithArtificial, globalDof + l, localDof);
    1452:                 }
    1453:                 if ( globalIndex >= numDofs ) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Found more dofs %D than expected %D", globalIndex+1, numDofs);
    1454:                 /* And store.*/
    1455:                 dofsArrayWithArtificial[globalIndex] = localDof;
    1456:               }
    1457:             }

    1459:             if(isNonlinear) {
    1460:               /* Build the dofmap for the function space with _all_ dofs,
    1461:                  including those in any kind of boundary condition */
    1462:               PetscHMapIGet(htWithAll, globalDof + l, &localDof);
    1463:               if (localDof == -1) {
    1464:                 localDof = localIndexWithAll++;
    1465:                 PetscHMapISet(htWithAll, globalDof + l, localDof);
    1466:               }
    1467:               if ( globalIndex >= numDofs ) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Found more dofs %D than expected %D", globalIndex+1, numDofs);
    1468:               /* And store.*/
    1469:               dofsArrayWithAll[globalIndex] = localDof;
    1470:             }
    1471:             globalIndex++;
    1472:           }
    1473:         }
    1474:       }
    1475:     }
    1476:      /*How many local dofs in this patch? */
    1477:    if (patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    1478:      PetscHMapIGetSize(htWithArtificial, &dof);
    1479:      PetscSectionSetDof(gtolCountsWithArtificial, v, dof);
    1480:    }
    1481:    if (isNonlinear) {
    1482:      PetscHMapIGetSize(htWithAll, &dof);
    1483:      PetscSectionSetDof(gtolCountsWithAll, v, dof);
    1484:    }
    1485:     PetscHMapIGetSize(ht, &dof);
    1486:     PetscSectionSetDof(gtolCounts, v, dof);
    1487:   }

    1489:   DMDestroy(&dm);
    1490:   if (globalIndex != numDofs) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Expected number of dofs (%d) doesn't match found number (%d)", numDofs, globalIndex);
    1491:   PetscSectionSetUp(gtolCounts);
    1492:   PetscSectionGetStorageSize(gtolCounts, &numGlobalDofs);
    1493:   PetscMalloc1(numGlobalDofs, &globalDofsArray);

    1495:   if (patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    1496:     PetscSectionSetUp(gtolCountsWithArtificial);
    1497:     PetscSectionGetStorageSize(gtolCountsWithArtificial, &numGlobalDofsWithArtificial);
    1498:     PetscMalloc1(numGlobalDofsWithArtificial, &globalDofsArrayWithArtificial);
    1499:   }
    1500:   if (isNonlinear) {
    1501:     PetscSectionSetUp(gtolCountsWithAll);
    1502:     PetscSectionGetStorageSize(gtolCountsWithAll, &numGlobalDofsWithAll);
    1503:     PetscMalloc1(numGlobalDofsWithAll, &globalDofsArrayWithAll);
    1504:   }
    1505:   /* Now populate the global to local map.  This could be merged into the above loop if we were willing to deal with reallocs. */
    1506:   for (v = vStart; v < vEnd; ++v) {
    1507:     PetscHashIter hi;
    1508:     PetscInt      dof, off, Np, ooff, i, j, k, l;

    1510:     PetscHMapIClear(ht);
    1511:     PetscHMapIClear(htWithArtificial);
    1512:     PetscHMapIClear(htWithAll);
    1513:     PetscSectionGetDof(cellCounts, v, &dof);
    1514:     PetscSectionGetOffset(cellCounts, v, &off);
    1515:     PetscSectionGetDof(pointCounts, v, &Np);
    1516:     PetscSectionGetOffset(pointCounts, v, &ooff);
    1517:     if (dof <= 0) continue;

    1519:     for (k = 0; k < patch->nsubspaces; ++k) {
    1520:       const PetscInt *cellNodeMap    = patch->cellNodeMap[k];
    1521:       PetscInt        nodesPerCell   = patch->nodesPerCell[k];
    1522:       PetscInt        subspaceOffset = patch->subspaceOffsets[k];
    1523:       PetscInt        bs             = patch->bs[k];
    1524:       PetscInt        goff;

    1526:       for (i = off; i < off + dof; ++i) {
    1527:         /* Reconstruct mapping of global-to-local on this patch. */
    1528:         const PetscInt c    = cellsArray[i];
    1529:         PetscInt       cell = c;

    1531:         if (cellNumbering) {PetscSectionGetOffset(cellNumbering, c, &cell);}
    1532:         for (j = 0; j < nodesPerCell; ++j) {
    1533:           for (l = 0; l < bs; ++l) {
    1534:             const PetscInt globalDof = cellNodeMap[cell*nodesPerCell + j]*bs + l + subspaceOffset;
    1535:             const PetscInt localDof  = dofsArray[key];
    1536:             if (localDof >= 0) {PetscHMapISet(ht, globalDof, localDof);}
    1537:             if (patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    1538:               const PetscInt localDofWithArtificial = dofsArrayWithArtificial[key];
    1539:               if (localDofWithArtificial >= 0) {
    1540:                 PetscHMapISet(htWithArtificial, globalDof, localDofWithArtificial);
    1541:               }
    1542:             }
    1543:             if (isNonlinear) {
    1544:               const PetscInt localDofWithAll = dofsArrayWithAll[key];
    1545:               if (localDofWithAll >= 0) {
    1546:                 PetscHMapISet(htWithAll, globalDof, localDofWithAll);
    1547:               }
    1548:             }
    1549:             key++;
    1550:           }
    1551:         }
    1552:       }

    1554:       /* Shove it in the output data structure. */
    1555:       PetscSectionGetOffset(gtolCounts, v, &goff);
    1556:       PetscHashIterBegin(ht, hi);
    1557:       while (!PetscHashIterAtEnd(ht, hi)) {
    1558:         PetscInt globalDof, localDof;

    1560:         PetscHashIterGetKey(ht, hi, globalDof);
    1561:         PetscHashIterGetVal(ht, hi, localDof);
    1562:         if (globalDof >= 0) globalDofsArray[goff + localDof] = globalDof;
    1563:         PetscHashIterNext(ht, hi);
    1564:       }

    1566:       if (patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    1567:         PetscSectionGetOffset(gtolCountsWithArtificial, v, &goff);
    1568:         PetscHashIterBegin(htWithArtificial, hi);
    1569:         while (!PetscHashIterAtEnd(htWithArtificial, hi)) {
    1570:           PetscInt globalDof, localDof;
    1571:           PetscHashIterGetKey(htWithArtificial, hi, globalDof);
    1572:           PetscHashIterGetVal(htWithArtificial, hi, localDof);
    1573:           if (globalDof >= 0) globalDofsArrayWithArtificial[goff + localDof] = globalDof;
    1574:           PetscHashIterNext(htWithArtificial, hi);
    1575:         }
    1576:       }
    1577:       if (isNonlinear) {
    1578:         PetscSectionGetOffset(gtolCountsWithAll, v, &goff);
    1579:         PetscHashIterBegin(htWithAll, hi);
    1580:         while (!PetscHashIterAtEnd(htWithAll, hi)) {
    1581:           PetscInt globalDof, localDof;
    1582:           PetscHashIterGetKey(htWithAll, hi, globalDof);
    1583:           PetscHashIterGetVal(htWithAll, hi, localDof);
    1584:           if (globalDof >= 0) globalDofsArrayWithAll[goff + localDof] = globalDof;
    1585:           PetscHashIterNext(htWithAll, hi);
    1586:         }
    1587:       }

    1589:       for (p = 0; p < Np; ++p) {
    1590:         const PetscInt point = pointsArray[ooff + p];
    1591:         PetscInt       globalDof, localDof;

    1593:         PCPatchGetGlobalDofs(pc, patch->dofSection, k, patch->combined, point, NULL, &globalDof);
    1594:         PetscHMapIGet(ht, globalDof, &localDof);
    1595:         offsArray[(ooff + p)*Nf + k] = localDof;
    1596:         if (patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    1597:           PetscHMapIGet(htWithArtificial, globalDof, &localDof);
    1598:           offsArrayWithArtificial[(ooff + p)*Nf + k] = localDof;
    1599:         }
    1600:         if (isNonlinear) {
    1601:           PetscHMapIGet(htWithAll, globalDof, &localDof);
    1602:           offsArrayWithAll[(ooff + p)*Nf + k] = localDof;
    1603:         }
    1604:       }
    1605:     }

    1607:     PetscHSetIDestroy(&globalBcs);
    1608:     PetscHSetIDestroy(&ownedpts);
    1609:     PetscHSetIDestroy(&seenpts);
    1610:     PetscHSetIDestroy(&owneddofs);
    1611:     PetscHSetIDestroy(&seendofs);
    1612:     PetscHSetIDestroy(&artificialbcs);

    1614:       /* At this point, we have a hash table ht built that maps globalDof -> localDof.
    1615:      We need to create the dof table laid out cellwise first, then by subspace,
    1616:      as the assembler assembles cell-wise and we need to stuff the different
    1617:      contributions of the different function spaces to the right places. So we loop
    1618:      over cells, then over subspaces. */
    1619:     if (patch->nsubspaces > 1) { /* for nsubspaces = 1, data we need is already in dofsArray */
    1620:       for (i = off; i < off + dof; ++i) {
    1621:         const PetscInt c    = cellsArray[i];
    1622:         PetscInt       cell = c;

    1624:         if (cellNumbering) {PetscSectionGetOffset(cellNumbering, c, &cell);}
    1625:         for (k = 0; k < patch->nsubspaces; ++k) {
    1626:           const PetscInt *cellNodeMap    = patch->cellNodeMap[k];
    1627:           PetscInt        nodesPerCell   = patch->nodesPerCell[k];
    1628:           PetscInt        subspaceOffset = patch->subspaceOffsets[k];
    1629:           PetscInt        bs             = patch->bs[k];

    1631:           for (j = 0; j < nodesPerCell; ++j) {
    1632:             for (l = 0; l < bs; ++l) {
    1633:               const PetscInt globalDof = cellNodeMap[cell*nodesPerCell + j]*bs + l + subspaceOffset;
    1634:               PetscInt       localDof;

    1636:               PetscHMapIGet(ht, globalDof, &localDof);
    1637:               /* If it's not in the hash table, i.e. is a BC dof,
    1638:                then the PetscHSetIMap above gives -1, which matches
    1639:                exactly the convention for PETSc's matrix assembly to
    1640:                ignore the dof. So we don't need to do anything here */
    1641:               asmArray[asmKey] = localDof;
    1642:               if (patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    1643:                 PetscHMapIGet(htWithArtificial, globalDof, &localDof);
    1644:                 asmArrayWithArtificial[asmKey] = localDof;
    1645:               }
    1646:               if (isNonlinear) {
    1647:                 PetscHMapIGet(htWithAll, globalDof, &localDof);
    1648:                 asmArrayWithAll[asmKey] = localDof;
    1649:               }
    1650:               asmKey++;
    1651:             }
    1652:           }
    1653:         }
    1654:       }
    1655:     }
    1656:   }
    1657:   if (1 == patch->nsubspaces) {
    1658:     PetscArraycpy(asmArray, dofsArray, numDofs);
    1659:     if (patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    1660:       PetscArraycpy(asmArrayWithArtificial, dofsArrayWithArtificial, numDofs);
    1661:     }
    1662:     if (isNonlinear) {
    1663:       PetscArraycpy(asmArrayWithAll, dofsArrayWithAll, numDofs);
    1664:     }
    1665:   }

    1667:   PetscHMapIDestroy(&ht);
    1668:   PetscHMapIDestroy(&htWithArtificial);
    1669:   PetscHMapIDestroy(&htWithAll);
    1670:   ISRestoreIndices(cells, &cellsArray);
    1671:   ISRestoreIndices(points, &pointsArray);
    1672:   PetscFree(dofsArray);
    1673:   if (patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    1674:     PetscFree(dofsArrayWithArtificial);
    1675:   }
    1676:   if (isNonlinear) {
    1677:     PetscFree(dofsArrayWithAll);
    1678:   }
    1679:   /* Create placeholder section for map from points to patch dofs */
    1680:   PetscSectionCreate(PETSC_COMM_SELF, &patch->patchSection);
    1681:   PetscSectionSetNumFields(patch->patchSection, patch->nsubspaces);
    1682:   if (patch->combined) {
    1683:     PetscInt numFields;
    1684:     PetscSectionGetNumFields(patch->dofSection[0], &numFields);
    1685:     if (numFields != patch->nsubspaces) SETERRQ2(PetscObjectComm((PetscObject)pc), PETSC_ERR_ARG_WRONG, "Mismatch between number of section fields %D and number of subspaces %D", numFields, patch->nsubspaces);
    1686:     PetscSectionGetChart(patch->dofSection[0], &pStart, &pEnd);
    1687:     PetscSectionSetChart(patch->patchSection, pStart, pEnd);
    1688:     for (p = pStart; p < pEnd; ++p) {
    1689:       PetscInt dof, fdof, f;

    1691:       PetscSectionGetDof(patch->dofSection[0], p, &dof);
    1692:       PetscSectionSetDof(patch->patchSection, p, dof);
    1693:       for (f = 0; f < patch->nsubspaces; ++f) {
    1694:         PetscSectionGetFieldDof(patch->dofSection[0], p, f, &fdof);
    1695:         PetscSectionSetFieldDof(patch->patchSection, p, f, fdof);
    1696:       }
    1697:     }
    1698:   } else {
    1699:     PetscInt pStartf, pEndf, f;
    1700:     pStart = PETSC_MAX_INT;
    1701:     pEnd = PETSC_MIN_INT;
    1702:     for (f = 0; f < patch->nsubspaces; ++f) {
    1703:       PetscSectionGetChart(patch->dofSection[f], &pStartf, &pEndf);
    1704:       pStart = PetscMin(pStart, pStartf);
    1705:       pEnd = PetscMax(pEnd, pEndf);
    1706:     }
    1707:     PetscSectionSetChart(patch->patchSection, pStart, pEnd);
    1708:     for (f = 0; f < patch->nsubspaces; ++f) {
    1709:       PetscSectionGetChart(patch->dofSection[f], &pStartf, &pEndf);
    1710:       for (p = pStartf; p < pEndf; ++p) {
    1711:         PetscInt fdof;
    1712:         PetscSectionGetDof(patch->dofSection[f], p, &fdof);
    1713:         PetscSectionAddDof(patch->patchSection, p, fdof);
    1714:         PetscSectionSetFieldDof(patch->patchSection, p, f, fdof);
    1715:       }
    1716:     }
    1717:   }
    1718:   PetscSectionSetUp(patch->patchSection);
    1719:   PetscSectionSetUseFieldOffsets(patch->patchSection, PETSC_TRUE);
    1720:   /* Replace cell indices with firedrake-numbered ones. */
    1721:   ISGeneralSetIndices(cells, numCells, (const PetscInt *) newCellsArray, PETSC_OWN_POINTER);
    1722:   ISCreateGeneral(PETSC_COMM_SELF, numGlobalDofs, globalDofsArray, PETSC_OWN_POINTER, &patch->gtol);
    1723:   PetscObjectSetName((PetscObject) patch->gtol, "Global Indices");
    1724:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_g2l_view", patch->classname);
    1725:   PetscSectionViewFromOptions(patch->gtolCounts, (PetscObject) pc, option);
    1726:   ISViewFromOptions(patch->gtol, (PetscObject) pc, option);
    1727:   ISCreateGeneral(PETSC_COMM_SELF, numDofs, asmArray, PETSC_OWN_POINTER, &patch->dofs);
    1728:   ISCreateGeneral(PETSC_COMM_SELF, numPoints*Nf, offsArray, PETSC_OWN_POINTER, &patch->offs);
    1729:   if (patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    1730:     ISCreateGeneral(PETSC_COMM_SELF, numGlobalDofsWithArtificial, globalDofsArrayWithArtificial, PETSC_OWN_POINTER, &patch->gtolWithArtificial);
    1731:     ISCreateGeneral(PETSC_COMM_SELF, numDofs, asmArrayWithArtificial, PETSC_OWN_POINTER, &patch->dofsWithArtificial);
    1732:     ISCreateGeneral(PETSC_COMM_SELF, numPoints*Nf, offsArrayWithArtificial, PETSC_OWN_POINTER, &patch->offsWithArtificial);
    1733:   }
    1734:   if (isNonlinear) {
    1735:     ISCreateGeneral(PETSC_COMM_SELF, numGlobalDofsWithAll, globalDofsArrayWithAll, PETSC_OWN_POINTER, &patch->gtolWithAll);
    1736:     ISCreateGeneral(PETSC_COMM_SELF, numDofs, asmArrayWithAll, PETSC_OWN_POINTER, &patch->dofsWithAll);
    1737:     ISCreateGeneral(PETSC_COMM_SELF, numPoints*Nf, offsArrayWithAll, PETSC_OWN_POINTER, &patch->offsWithAll);
    1738:   }
    1739:   return(0);
    1740: }

    1742: static PetscErrorCode PCPatchCreateMatrix_Private(PC pc, PetscInt point, Mat *mat, PetscBool withArtificial)
    1743: {
    1744:   PC_PATCH      *patch = (PC_PATCH *) pc->data;
    1745:   PetscBool      flg;
    1746:   PetscInt       csize, rsize;
    1747:   const char    *prefix = NULL;

    1751:   if(withArtificial) {
    1752:     /* would be nice if we could create a rectangular matrix of size numDofsWithArtificial x numDofs here */
    1753:     PetscInt pStart;
    1754:     PetscSectionGetChart(patch->gtolCountsWithArtificial, &pStart, NULL);
    1755:     PetscSectionGetDof(patch->gtolCountsWithArtificial, point + pStart, &rsize);
    1756:     csize = rsize;
    1757:   } else {
    1758:     PetscInt pStart;
    1759:     PetscSectionGetChart(patch->gtolCounts, &pStart, NULL);
    1760:     PetscSectionGetDof(patch->gtolCounts, point + pStart, &rsize);
    1761:     csize = rsize;
    1762:   }

    1764:   MatCreate(PETSC_COMM_SELF, mat);
    1765:   PCGetOptionsPrefix(pc, &prefix);
    1766:   MatSetOptionsPrefix(*mat, prefix);
    1767:   MatAppendOptionsPrefix(*mat, "pc_patch_sub_");
    1768:   if (patch->sub_mat_type)       {MatSetType(*mat, patch->sub_mat_type);}
    1769:   else if (!patch->sub_mat_type) {MatSetType(*mat, MATDENSE);}
    1770:   MatSetSizes(*mat, rsize, csize, rsize, csize);
    1771:   PetscObjectTypeCompare((PetscObject) *mat, MATDENSE, &flg);
    1772:   if (!flg) {PetscObjectTypeCompare((PetscObject)*mat, MATSEQDENSE, &flg);}
    1773:   /* Sparse patch matrices */
    1774:   if (!flg) {
    1775:     PetscBT         bt;
    1776:     PetscInt       *dnnz      = NULL;
    1777:     const PetscInt *dofsArray = NULL;
    1778:     PetscInt        pStart, pEnd, ncell, offset, c, i, j;

    1780:     if(withArtificial) {
    1781:       ISGetIndices(patch->dofsWithArtificial, &dofsArray);
    1782:     } else {
    1783:       ISGetIndices(patch->dofs, &dofsArray);
    1784:     }
    1785:     PetscSectionGetChart(patch->cellCounts, &pStart, &pEnd);
    1786:     point += pStart;
    1787:     if (point >= pEnd) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Operator point %D not in [%D, %D)\n", point, pStart, pEnd);
    1788:     PetscSectionGetDof(patch->cellCounts, point, &ncell);
    1789:     PetscSectionGetOffset(patch->cellCounts, point, &offset);
    1790:     PetscLogEventBegin(PC_Patch_Prealloc, pc, 0, 0, 0);
    1791:     /* A PetscBT uses N^2 bits to store the sparsity pattern on a
    1792:      * patch. This is probably OK if the patches are not too big,
    1793:      * but uses too much memory. We therefore switch based on rsize. */
    1794:     if (rsize < 3000) { /* FIXME: I picked this switch value out of my hat */
    1795:       PetscScalar *zeroes;
    1796:       PetscInt rows;

    1798:       PetscCalloc1(rsize, &dnnz);
    1799:       PetscBTCreate(rsize*rsize, &bt);
    1800:       for (c = 0; c < ncell; ++c) {
    1801:         const PetscInt *idx = dofsArray + (offset + c)*patch->totalDofsPerCell;
    1802:         for (i = 0; i < patch->totalDofsPerCell; ++i) {
    1803:           const PetscInt row = idx[i];
    1804:           if (row < 0) continue;
    1805:           for (j = 0; j < patch->totalDofsPerCell; ++j) {
    1806:             const PetscInt col = idx[j];
    1807:             const PetscInt key = row*rsize + col;
    1808:             if (col < 0) continue;
    1809:             if (!PetscBTLookupSet(bt, key)) ++dnnz[row];
    1810:           }
    1811:         }
    1812:       }

    1814:       if (patch->usercomputeopintfacet) {
    1815:         const PetscInt *intFacetsArray = NULL;
    1816:         PetscInt        i, numIntFacets, intFacetOffset;
    1817:         const PetscInt *facetCells = NULL;

    1819:         PetscSectionGetDof(patch->intFacetCounts, point, &numIntFacets);
    1820:         PetscSectionGetOffset(patch->intFacetCounts, point, &intFacetOffset);
    1821:         ISGetIndices(patch->intFacetsToPatchCell, &facetCells);
    1822:         ISGetIndices(patch->intFacets, &intFacetsArray);
    1823:         for (i = 0; i < numIntFacets; i++) {
    1824:           const PetscInt cell0 = facetCells[2*(intFacetOffset + i) + 0];
    1825:           const PetscInt cell1 = facetCells[2*(intFacetOffset + i) + 1];
    1826:           PetscInt       celli, cellj;

    1828:           for (celli = 0; celli < patch->totalDofsPerCell; celli++) {
    1829:             const PetscInt row = dofsArray[(offset + cell0)*patch->totalDofsPerCell + celli];
    1830:             if (row < 0) continue;
    1831:             for (cellj = 0; cellj < patch->totalDofsPerCell; cellj++) {
    1832:               const PetscInt col = dofsArray[(offset + cell1)*patch->totalDofsPerCell + cellj];
    1833:               const PetscInt key = row*rsize + col;
    1834:               if (col < 0) continue;
    1835:               if (!PetscBTLookupSet(bt, key)) ++dnnz[row];
    1836:             }
    1837:           }

    1839:           for (celli = 0; celli < patch->totalDofsPerCell; celli++) {
    1840:             const PetscInt row = dofsArray[(offset + cell1)*patch->totalDofsPerCell + celli];
    1841:             if (row < 0) continue;
    1842:             for (cellj = 0; cellj < patch->totalDofsPerCell; cellj++) {
    1843:               const PetscInt col = dofsArray[(offset + cell0)*patch->totalDofsPerCell + cellj];
    1844:               const PetscInt key = row*rsize + col;
    1845:               if (col < 0) continue;
    1846:               if (!PetscBTLookupSet(bt, key)) ++dnnz[row];
    1847:             }
    1848:           }
    1849:         }
    1850:       }
    1851:       PetscBTDestroy(&bt);
    1852:       MatXAIJSetPreallocation(*mat, 1, dnnz, NULL, NULL, NULL);
    1853:       PetscFree(dnnz);

    1855:       PetscCalloc1(patch->totalDofsPerCell*patch->totalDofsPerCell, &zeroes);
    1856:       for (c = 0; c < ncell; ++c) {
    1857:         const PetscInt *idx = &dofsArray[(offset + c)*patch->totalDofsPerCell];
    1858:         MatSetValues(*mat, patch->totalDofsPerCell, idx, patch->totalDofsPerCell, idx, zeroes, INSERT_VALUES);
    1859:       }
    1860:       MatGetLocalSize(*mat, &rows, NULL);
    1861:       for (i = 0; i < rows; ++i) {
    1862:         MatSetValues(*mat, 1, &i, 1, &i, zeroes, INSERT_VALUES);
    1863:       }

    1865:       if (patch->usercomputeopintfacet) {
    1866:         const PetscInt *intFacetsArray = NULL;
    1867:         PetscInt i, numIntFacets, intFacetOffset;
    1868:         const PetscInt *facetCells = NULL;

    1870:         PetscSectionGetDof(patch->intFacetCounts, point, &numIntFacets);
    1871:         PetscSectionGetOffset(patch->intFacetCounts, point, &intFacetOffset);
    1872:         ISGetIndices(patch->intFacetsToPatchCell, &facetCells);
    1873:         ISGetIndices(patch->intFacets, &intFacetsArray);
    1874:         for (i = 0; i < numIntFacets; i++) {
    1875:           const PetscInt cell0 = facetCells[2*(intFacetOffset + i) + 0];
    1876:           const PetscInt cell1 = facetCells[2*(intFacetOffset + i) + 1];
    1877:           const PetscInt *cell0idx = &dofsArray[(offset + cell0)*patch->totalDofsPerCell];
    1878:           const PetscInt *cell1idx = &dofsArray[(offset + cell1)*patch->totalDofsPerCell];
    1879:           MatSetValues(*mat, patch->totalDofsPerCell, cell0idx, patch->totalDofsPerCell, cell1idx, zeroes, INSERT_VALUES);
    1880:           MatSetValues(*mat, patch->totalDofsPerCell, cell1idx, patch->totalDofsPerCell, cell0idx, zeroes, INSERT_VALUES);
    1881:         }
    1882:       }

    1884:       MatAssemblyBegin(*mat, MAT_FINAL_ASSEMBLY);
    1885:       MatAssemblyEnd(*mat, MAT_FINAL_ASSEMBLY);

    1887:       PetscFree(zeroes);

    1889:     } else { /* rsize too big, use MATPREALLOCATOR */
    1890:       Mat preallocator;
    1891:       PetscScalar* vals;

    1893:       PetscCalloc1(patch->totalDofsPerCell*patch->totalDofsPerCell, &vals);
    1894:       MatCreate(PETSC_COMM_SELF, &preallocator);
    1895:       MatSetType(preallocator, MATPREALLOCATOR);
    1896:       MatSetSizes(preallocator, rsize, rsize, rsize, rsize);
    1897:       MatSetUp(preallocator);

    1899:       for (c = 0; c < ncell; ++c) {
    1900:         const PetscInt *idx = dofsArray + (offset + c)*patch->totalDofsPerCell;
    1901:         MatSetValues(preallocator, patch->totalDofsPerCell, idx, patch->totalDofsPerCell, idx, vals, INSERT_VALUES);
    1902:       }

    1904:       if (patch->usercomputeopintfacet) {
    1905:         const PetscInt *intFacetsArray = NULL;
    1906:         PetscInt        i, numIntFacets, intFacetOffset;
    1907:         const PetscInt *facetCells = NULL;

    1909:         PetscSectionGetDof(patch->intFacetCounts, point, &numIntFacets);
    1910:         PetscSectionGetOffset(patch->intFacetCounts, point, &intFacetOffset);
    1911:         ISGetIndices(patch->intFacetsToPatchCell, &facetCells);
    1912:         ISGetIndices(patch->intFacets, &intFacetsArray);
    1913:         for (i = 0; i < numIntFacets; i++) {
    1914:           const PetscInt cell0 = facetCells[2*(intFacetOffset + i) + 0];
    1915:           const PetscInt cell1 = facetCells[2*(intFacetOffset + i) + 1];
    1916:           const PetscInt *cell0idx = &dofsArray[(offset + cell0)*patch->totalDofsPerCell];
    1917:           const PetscInt *cell1idx = &dofsArray[(offset + cell1)*patch->totalDofsPerCell];
    1918:           MatSetValues(preallocator, patch->totalDofsPerCell, cell0idx, patch->totalDofsPerCell, cell1idx, vals, INSERT_VALUES);
    1919:           MatSetValues(preallocator, patch->totalDofsPerCell, cell1idx, patch->totalDofsPerCell, cell0idx, vals, INSERT_VALUES);
    1920:         }
    1921:       }

    1923:       PetscFree(vals);
    1924:       MatAssemblyBegin(preallocator, MAT_FINAL_ASSEMBLY);
    1925:       MatAssemblyEnd(preallocator, MAT_FINAL_ASSEMBLY);
    1926:       MatPreallocatorPreallocate(preallocator, PETSC_TRUE, *mat);
    1927:       MatDestroy(&preallocator);
    1928:     }
    1929:     PetscLogEventEnd(PC_Patch_Prealloc, pc, 0, 0, 0);
    1930:     if(withArtificial) {
    1931:       ISRestoreIndices(patch->dofsWithArtificial, &dofsArray);
    1932:     } else {
    1933:       ISRestoreIndices(patch->dofs, &dofsArray);
    1934:     }
    1935:   }
    1936:   MatSetUp(*mat);
    1937:   return(0);
    1938: }

    1940: static PetscErrorCode PCPatchComputeFunction_DMPlex_Private(PC pc, PetscInt patchNum, Vec x, Vec F, IS cellIS, PetscInt n, const PetscInt *l2p, const PetscInt *l2pWithAll, void *ctx)
    1941: {
    1942:   PC_PATCH       *patch = (PC_PATCH *) pc->data;
    1943:   DM              dm, plex;
    1944:   PetscSection    s;
    1945:   const PetscInt *parray, *oarray;
    1946:   PetscInt        Nf = patch->nsubspaces, Np, poff, p, f;
    1947:   PetscErrorCode  ierr;

    1950:   if (patch->precomputeElementTensors) SETERRQ(PetscObjectComm((PetscObject)pc), PETSC_ERR_ARG_WRONGSTATE, "Precomputing element tensors not implemented with DMPlex compute operator");
    1951:   PCGetDM(pc, &dm);
    1952:   DMConvert(dm, DMPLEX, &plex);
    1953:   dm = plex;
    1954:   DMGetLocalSection(dm, &s);
    1955:   /* Set offset into patch */
    1956:   PetscSectionGetDof(patch->pointCounts, patchNum, &Np);
    1957:   PetscSectionGetOffset(patch->pointCounts, patchNum, &poff);
    1958:   ISGetIndices(patch->points, &parray);
    1959:   ISGetIndices(patch->offs,   &oarray);
    1960:   for (f = 0; f < Nf; ++f) {
    1961:     for (p = 0; p < Np; ++p) {
    1962:       const PetscInt point = parray[poff+p];
    1963:       PetscInt       dof;

    1965:       PetscSectionGetFieldDof(patch->patchSection, point, f, &dof);
    1966:       PetscSectionSetFieldOffset(patch->patchSection, point, f, oarray[(poff+p)*Nf+f]);
    1967:       if (patch->nsubspaces == 1) {PetscSectionSetOffset(patch->patchSection, point, oarray[(poff+p)*Nf+f]);}
    1968:       else                        {PetscSectionSetOffset(patch->patchSection, point, -1);}
    1969:     }
    1970:   }
    1971:   ISRestoreIndices(patch->points, &parray);
    1972:   ISRestoreIndices(patch->offs,   &oarray);
    1973:   if (patch->viewSection) {ObjectView((PetscObject) patch->patchSection, patch->viewerSection, patch->formatSection);}
    1974:   DMPlexComputeResidual_Patch_Internal(dm, patch->patchSection, cellIS, 0.0, x, NULL, F, ctx);
    1975:   DMDestroy(&dm);
    1976:   return(0);
    1977: }

    1979: PetscErrorCode PCPatchComputeFunction_Internal(PC pc, Vec x, Vec F, PetscInt point)
    1980: {
    1981:   PC_PATCH       *patch = (PC_PATCH *) pc->data;
    1982:   const PetscInt *dofsArray;
    1983:   const PetscInt *dofsArrayWithAll;
    1984:   const PetscInt *cellsArray;
    1985:   PetscInt        ncell, offset, pStart, pEnd;
    1986:   PetscErrorCode  ierr;

    1989:   PetscLogEventBegin(PC_Patch_ComputeOp, pc, 0, 0, 0);
    1990:   if (!patch->usercomputeop) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Must call PCPatchSetComputeOperator() to set user callback\n");
    1991:   ISGetIndices(patch->dofs, &dofsArray);
    1992:   ISGetIndices(patch->dofsWithAll, &dofsArrayWithAll);
    1993:   ISGetIndices(patch->cells, &cellsArray);
    1994:   PetscSectionGetChart(patch->cellCounts, &pStart, &pEnd);

    1996:   point += pStart;
    1997:   if (point >= pEnd) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Operator point %D not in [%D, %D)\n", point, pStart, pEnd);

    1999:   PetscSectionGetDof(patch->cellCounts, point, &ncell);
    2000:   PetscSectionGetOffset(patch->cellCounts, point, &offset);
    2001:   if (ncell <= 0) {
    2002:     PetscLogEventEnd(PC_Patch_ComputeOp, pc, 0, 0, 0);
    2003:     return(0);
    2004:   }
    2005:   VecSet(F, 0.0);
    2006:   PetscStackPush("PCPatch user callback");
    2007:   /* Cannot reuse the same IS because the geometry info is being cached in it */
    2008:   ISCreateGeneral(PETSC_COMM_SELF, ncell, cellsArray + offset, PETSC_USE_POINTER, &patch->cellIS);
    2009:   patch->usercomputef(pc, point, x, F, patch->cellIS, ncell*patch->totalDofsPerCell, dofsArray + offset*patch->totalDofsPerCell,
    2010:                                                                                             dofsArrayWithAll + offset*patch->totalDofsPerCell,
    2011:                                                                                             patch->usercomputefctx);
    2012:   PetscStackPop;
    2013:   ISDestroy(&patch->cellIS);
    2014:   ISRestoreIndices(patch->dofs, &dofsArray);
    2015:   ISRestoreIndices(patch->dofsWithAll, &dofsArrayWithAll);
    2016:   ISRestoreIndices(patch->cells, &cellsArray);
    2017:   if (patch->viewMatrix) {
    2018:     char name[PETSC_MAX_PATH_LEN];

    2020:     PetscSNPrintf(name, PETSC_MAX_PATH_LEN-1, "Patch vector for Point %D", point);
    2021:     PetscObjectSetName((PetscObject) F, name);
    2022:     ObjectView((PetscObject) F, patch->viewerMatrix, patch->formatMatrix);
    2023:   }
    2024:   PetscLogEventEnd(PC_Patch_ComputeOp, pc, 0, 0, 0);
    2025:   return(0);
    2026: }

    2028: static PetscErrorCode PCPatchComputeOperator_DMPlex_Private(PC pc, PetscInt patchNum, Vec x, Mat J, IS cellIS, PetscInt n, const PetscInt *l2p, const PetscInt *l2pWithAll, void *ctx)
    2029: {
    2030:   PC_PATCH       *patch = (PC_PATCH *) pc->data;
    2031:   DM              dm, plex;
    2032:   PetscSection    s;
    2033:   const PetscInt *parray, *oarray;
    2034:   PetscInt        Nf = patch->nsubspaces, Np, poff, p, f;
    2035:   PetscErrorCode  ierr;

    2038:   PCGetDM(pc, &dm);
    2039:   DMConvert(dm, DMPLEX, &plex);
    2040:   dm = plex;
    2041:   DMGetLocalSection(dm, &s);
    2042:   /* Set offset into patch */
    2043:   PetscSectionGetDof(patch->pointCounts, patchNum, &Np);
    2044:   PetscSectionGetOffset(patch->pointCounts, patchNum, &poff);
    2045:   ISGetIndices(patch->points, &parray);
    2046:   ISGetIndices(patch->offs,   &oarray);
    2047:   for (f = 0; f < Nf; ++f) {
    2048:     for (p = 0; p < Np; ++p) {
    2049:       const PetscInt point = parray[poff+p];
    2050:       PetscInt       dof;

    2052:       PetscSectionGetFieldDof(patch->patchSection, point, f, &dof);
    2053:       PetscSectionSetFieldOffset(patch->patchSection, point, f, oarray[(poff+p)*Nf+f]);
    2054:       if (patch->nsubspaces == 1) {PetscSectionSetOffset(patch->patchSection, point, oarray[(poff+p)*Nf+f]);}
    2055:       else                        {PetscSectionSetOffset(patch->patchSection, point, -1);}
    2056:     }
    2057:   }
    2058:   ISRestoreIndices(patch->points, &parray);
    2059:   ISRestoreIndices(patch->offs,   &oarray);
    2060:   if (patch->viewSection) {ObjectView((PetscObject) patch->patchSection, patch->viewerSection, patch->formatSection);}
    2061:   /* TODO Shut off MatViewFromOptions() in MatAssemblyEnd() here */
    2062:   DMPlexComputeJacobian_Patch_Internal(dm, patch->patchSection, patch->patchSection, cellIS, 0.0, 0.0, x, NULL, J, J, ctx);
    2063:   DMDestroy(&dm);
    2064:   return(0);
    2065: }

    2067: /* This function zeros mat on entry */
    2068: PetscErrorCode PCPatchComputeOperator_Internal(PC pc, Vec x, Mat mat, PetscInt point, PetscBool withArtificial)
    2069: {
    2070:   PC_PATCH       *patch = (PC_PATCH *) pc->data;
    2071:   const PetscInt *dofsArray;
    2072:   const PetscInt *dofsArrayWithAll = NULL;
    2073:   const PetscInt *cellsArray;
    2074:   PetscInt        ncell, offset, pStart, pEnd, numIntFacets, intFacetOffset;
    2075:   PetscBool       isNonlinear;
    2076:   PetscErrorCode  ierr;

    2079:   PetscLogEventBegin(PC_Patch_ComputeOp, pc, 0, 0, 0);
    2080:   isNonlinear = patch->isNonlinear;
    2081:   if (!patch->usercomputeop) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Must call PCPatchSetComputeOperator() to set user callback\n");
    2082:   if(withArtificial) {
    2083:     ISGetIndices(patch->dofsWithArtificial, &dofsArray);
    2084:   } else {
    2085:     ISGetIndices(patch->dofs, &dofsArray);
    2086:   }
    2087:   if (isNonlinear) {
    2088:     ISGetIndices(patch->dofsWithAll, &dofsArrayWithAll);
    2089:   }
    2090:   ISGetIndices(patch->cells, &cellsArray);
    2091:   PetscSectionGetChart(patch->cellCounts, &pStart, &pEnd);

    2093:   point += pStart;
    2094:   if (point >= pEnd) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Operator point %D not in [%D, %D)\n", point, pStart, pEnd);

    2096:   PetscSectionGetDof(patch->cellCounts, point, &ncell);
    2097:   PetscSectionGetOffset(patch->cellCounts, point, &offset);
    2098:   if (ncell <= 0) {
    2099:     PetscLogEventEnd(PC_Patch_ComputeOp, pc, 0, 0, 0);
    2100:     return(0);
    2101:   }
    2102:   MatZeroEntries(mat);
    2103:   if (patch->precomputeElementTensors) {
    2104:     PetscInt           i;
    2105:     PetscInt           ndof = patch->totalDofsPerCell;
    2106:     const PetscScalar *elementTensors;

    2108:     VecGetArrayRead(patch->cellMats, &elementTensors);
    2109:     for (i = 0; i < ncell; i++) {
    2110:       const PetscInt     cell = cellsArray[i + offset];
    2111:       const PetscInt    *idx  = dofsArray + (offset + i)*ndof;
    2112:       const PetscScalar *v    = elementTensors + patch->precomputedTensorLocations[cell]*ndof*ndof;
    2113:       MatSetValues(mat, ndof, idx, ndof, idx, v, ADD_VALUES);
    2114:     }
    2115:     VecRestoreArrayRead(patch->cellMats, &elementTensors);
    2116:     MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY);
    2117:     MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY);
    2118:   } else {
    2119:     PetscStackPush("PCPatch user callback");
    2120:     /* Cannot reuse the same IS because the geometry info is being cached in it */
    2121:     ISCreateGeneral(PETSC_COMM_SELF, ncell, cellsArray + offset, PETSC_USE_POINTER, &patch->cellIS);
    2122:     patch->usercomputeop(pc, point, x, mat, patch->cellIS, ncell*patch->totalDofsPerCell, dofsArray + offset*patch->totalDofsPerCell, dofsArrayWithAll ? dofsArrayWithAll + offset*patch->totalDofsPerCell : NULL, patch->usercomputeopctx);
    2123:   }
    2124:   if (patch->usercomputeopintfacet) {
    2125:     PetscSectionGetDof(patch->intFacetCounts, point, &numIntFacets);
    2126:     PetscSectionGetOffset(patch->intFacetCounts, point, &intFacetOffset);
    2127:     if (numIntFacets > 0) {
    2128:       /* For each interior facet, grab the two cells (in local numbering, and concatenate dof numberings for those cells) */
    2129:       PetscInt       *facetDofs = NULL, *facetDofsWithAll = NULL;
    2130:       const PetscInt *intFacetsArray = NULL;
    2131:       PetscInt        idx = 0;
    2132:       PetscInt        i, c, d;
    2133:       PetscInt        fStart;
    2134:       DM              dm, plex;
    2135:       IS              facetIS = NULL;
    2136:       const PetscInt *facetCells = NULL;

    2138:       ISGetIndices(patch->intFacetsToPatchCell, &facetCells);
    2139:       ISGetIndices(patch->intFacets, &intFacetsArray);
    2140:       PCGetDM(pc, &dm);
    2141:       DMConvert(dm, DMPLEX, &plex);
    2142:       dm = plex;
    2143:       DMPlexGetHeightStratum(dm, 1, &fStart, NULL);
    2144:       /* FIXME: Pull this malloc out. */
    2145:       PetscMalloc1(2 * patch->totalDofsPerCell * numIntFacets, &facetDofs);
    2146:       if (dofsArrayWithAll) {
    2147:         PetscMalloc1(2 * patch->totalDofsPerCell * numIntFacets, &facetDofsWithAll);
    2148:       }
    2149:       if (patch->precomputeElementTensors) {
    2150:         PetscInt           nFacetDof = 2*patch->totalDofsPerCell;
    2151:         const PetscScalar *elementTensors;

    2153:         VecGetArrayRead(patch->intFacetMats, &elementTensors);

    2155:         for (i = 0; i < numIntFacets; i++) {
    2156:           const PetscInt     facet = intFacetsArray[i + intFacetOffset];
    2157:           const PetscScalar *v     = elementTensors + patch->precomputedIntFacetTensorLocations[facet - fStart]*nFacetDof*nFacetDof;
    2158:           idx = 0;
    2159:           /*
    2160:            * 0--1
    2161:            * |\-|
    2162:            * |+\|
    2163:            * 2--3
    2164:            * [0, 2, 3, 0, 1, 3]
    2165:            */
    2166:           for (c = 0; c < 2; c++) {
    2167:             const PetscInt cell = facetCells[2*(intFacetOffset + i) + c];
    2168:             for (d = 0; d < patch->totalDofsPerCell; d++) {
    2169:               facetDofs[idx] = dofsArray[(offset + cell)*patch->totalDofsPerCell + d];
    2170:               idx++;
    2171:             }
    2172:           }
    2173:           MatSetValues(mat, nFacetDof, facetDofs, nFacetDof, facetDofs, v, ADD_VALUES);
    2174:         }
    2175:         VecRestoreArrayRead(patch->intFacetMats, &elementTensors);
    2176:       } else {
    2177:         /*
    2178:          * 0--1
    2179:          * |\-|
    2180:          * |+\|
    2181:          * 2--3
    2182:          * [0, 2, 3, 0, 1, 3]
    2183:          */
    2184:         for (i = 0; i < numIntFacets; i++) {
    2185:           for (c = 0; c < 2; c++) {
    2186:             const PetscInt cell = facetCells[2*(intFacetOffset + i) + c];
    2187:             for (d = 0; d < patch->totalDofsPerCell; d++) {
    2188:               facetDofs[idx] = dofsArray[(offset + cell)*patch->totalDofsPerCell + d];
    2189:               if (dofsArrayWithAll) {
    2190:                 facetDofsWithAll[idx] = dofsArrayWithAll[(offset + cell)*patch->totalDofsPerCell + d];
    2191:               }
    2192:               idx++;
    2193:             }
    2194:           }
    2195:         }
    2196:         ISCreateGeneral(PETSC_COMM_SELF, numIntFacets, intFacetsArray + intFacetOffset, PETSC_USE_POINTER, &facetIS);
    2197:         patch->usercomputeopintfacet(pc, point, x, mat, facetIS, 2*numIntFacets*patch->totalDofsPerCell, facetDofs, facetDofsWithAll, patch->usercomputeopintfacetctx);
    2198:         ISDestroy(&facetIS);
    2199:       }
    2200:       ISRestoreIndices(patch->intFacetsToPatchCell, &facetCells);
    2201:       ISRestoreIndices(patch->intFacets, &intFacetsArray);
    2202:       PetscFree(facetDofs);
    2203:       PetscFree(facetDofsWithAll);
    2204:       DMDestroy(&dm);
    2205:     }
    2206:   }

    2208:   MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY);
    2209:   MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY);

    2211:   if (!(withArtificial || isNonlinear) && patch->denseinverse) {
    2212:     MatFactorInfo info;
    2213:     PetscBool     flg;
    2214:     PetscObjectTypeCompare((PetscObject)mat, MATSEQDENSE, &flg);
    2215:     if (!flg) SETERRQ(PetscObjectComm((PetscObject)pc), PETSC_ERR_ARG_WRONGSTATE, "Invalid Mat type for dense inverse");
    2216:     MatFactorInfoInitialize(&info);
    2217:     MatLUFactor(mat, NULL, NULL, &info);
    2218:     MatSeqDenseInvertFactors_Private(mat);
    2219:   }
    2220:   PetscStackPop;
    2221:   ISDestroy(&patch->cellIS);
    2222:   if(withArtificial) {
    2223:     ISRestoreIndices(patch->dofsWithArtificial, &dofsArray);
    2224:   } else {
    2225:     ISRestoreIndices(patch->dofs, &dofsArray);
    2226:   }
    2227:   if (isNonlinear) {
    2228:     ISRestoreIndices(patch->dofsWithAll, &dofsArrayWithAll);
    2229:   }
    2230:   ISRestoreIndices(patch->cells, &cellsArray);
    2231:   if (patch->viewMatrix) {
    2232:     char name[PETSC_MAX_PATH_LEN];

    2234:     PetscSNPrintf(name, PETSC_MAX_PATH_LEN-1, "Patch matrix for Point %D", point);
    2235:     PetscObjectSetName((PetscObject) mat, name);
    2236:     ObjectView((PetscObject) mat, patch->viewerMatrix, patch->formatMatrix);
    2237:   }
    2238:   PetscLogEventEnd(PC_Patch_ComputeOp, pc, 0, 0, 0);
    2239:   return(0);
    2240: }

    2242: static PetscErrorCode MatSetValues_PCPatch_Private(Mat mat, PetscInt m, const PetscInt idxm[],
    2243:                                                    PetscInt n, const PetscInt idxn[], const PetscScalar *v, InsertMode addv)
    2244: {
    2245:   Vec            data;
    2246:   PetscScalar   *array;
    2247:   PetscInt       bs, nz, i, j, cell;

    2250:   MatShellGetContext(mat, &data);
    2251:   VecGetBlockSize(data, &bs);
    2252:   VecGetSize(data, &nz);
    2253:   VecGetArray(data, &array);
    2254:   if (m != n) SETERRQ(PetscObjectComm((PetscObject)mat), PETSC_ERR_ARG_WRONG, "Only for square insertion");
    2255:   cell = (PetscInt)(idxm[0]/bs); /* use the fact that this is called once per cell */
    2256:   for (i = 0; i < m; i++) {
    2257:     if (idxm[i] != idxn[i]) SETERRQ(PetscObjectComm((PetscObject)mat), PETSC_ERR_ARG_WRONG, "Row and column indices must match!");
    2258:     for (j = 0; j < n; j++) {
    2259:       const PetscScalar v_ = v[i*bs + j];
    2260:       /* Indexing is special to the data structure we have! */
    2261:       if (addv == INSERT_VALUES) {
    2262:         array[cell*bs*bs + i*bs + j] = v_;
    2263:       } else {
    2264:         array[cell*bs*bs + i*bs + j] += v_;
    2265:       }
    2266:     }
    2267:   }
    2268:   VecRestoreArray(data, &array);
    2269:   return(0);
    2270: }

    2272: static PetscErrorCode PCPatchPrecomputePatchTensors_Private(PC pc)
    2273: {
    2274:   PC_PATCH       *patch = (PC_PATCH *)pc->data;
    2275:   const PetscInt *cellsArray;
    2276:   PetscInt        ncell, offset;
    2277:   const PetscInt *dofMapArray;
    2278:   PetscInt        i, j;
    2279:   IS              dofMap;
    2280:   IS              cellIS;
    2281:   const PetscInt  ndof  = patch->totalDofsPerCell;
    2282:   PetscErrorCode  ierr;
    2283:   Mat             vecMat;
    2284:   PetscInt        cStart, cEnd;
    2285:   DM              dm, plex;

    2288:   ISGetSize(patch->cells, &ncell);
    2289:   if (!ncell) { /* No cells to assemble over -> skip */
    2290:     return(0);
    2291:   }

    2293:   PetscLogEventBegin(PC_Patch_ComputeOp, pc, 0, 0, 0);

    2295:   PCGetDM(pc, &dm);
    2296:   DMConvert(dm, DMPLEX, &plex);
    2297:   dm = plex;
    2298:   if (!patch->allCells) {
    2299:     PetscHSetI      cells;
    2300:     PetscHashIter   hi;
    2301:     PetscInt pStart, pEnd;
    2302:     PetscInt *allCells = NULL;
    2303:     PetscHSetICreate(&cells);
    2304:     ISGetIndices(patch->cells, &cellsArray);
    2305:     PetscSectionGetChart(patch->cellCounts, &pStart, &pEnd);
    2306:     for (i = pStart; i < pEnd; i++) {
    2307:       PetscSectionGetDof(patch->cellCounts, i, &ncell);
    2308:       PetscSectionGetOffset(patch->cellCounts, i, &offset);
    2309:       if (ncell <= 0) continue;
    2310:       for (j = 0; j < ncell; j++) {
    2311:         PetscHSetIAdd(cells, cellsArray[offset + j]);
    2312:       }
    2313:     }
    2314:     ISRestoreIndices(patch->cells, &cellsArray);
    2315:     PetscHSetIGetSize(cells, &ncell);
    2316:     PetscMalloc1(ncell, &allCells);
    2317:     DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
    2318:     PetscMalloc1(cEnd-cStart, &patch->precomputedTensorLocations);
    2319:     i = 0;
    2320:     PetscHashIterBegin(cells, hi);
    2321:     while (!PetscHashIterAtEnd(cells, hi)) {
    2322:       PetscHashIterGetKey(cells, hi, allCells[i]);
    2323:       patch->precomputedTensorLocations[allCells[i]] = i;
    2324:       PetscHashIterNext(cells, hi);
    2325:       i++;
    2326:     }
    2327:     PetscHSetIDestroy(&cells);
    2328:     ISCreateGeneral(PETSC_COMM_SELF, ncell, allCells, PETSC_OWN_POINTER, &patch->allCells);
    2329:   }
    2330:   ISGetSize(patch->allCells, &ncell);
    2331:   if (!patch->cellMats) {
    2332:     VecCreateSeq(PETSC_COMM_SELF, ncell*ndof*ndof, &patch->cellMats);
    2333:     VecSetBlockSize(patch->cellMats, ndof);
    2334:   }
    2335:   VecSet(patch->cellMats, 0);

    2337:   MatCreateShell(PETSC_COMM_SELF, ncell*ndof, ncell*ndof, ncell*ndof, ncell*ndof,
    2338:                         (void*)patch->cellMats, &vecMat);
    2339:   MatShellSetOperation(vecMat, MATOP_SET_VALUES, (void(*)(void))&MatSetValues_PCPatch_Private);
    2340:   ISGetSize(patch->allCells, &ncell);
    2341:   ISCreateStride(PETSC_COMM_SELF, ndof*ncell, 0, 1, &dofMap);
    2342:   ISGetIndices(dofMap, &dofMapArray);
    2343:   ISGetIndices(patch->allCells, &cellsArray);
    2344:   ISCreateGeneral(PETSC_COMM_SELF, ncell, cellsArray, PETSC_USE_POINTER, &cellIS);
    2345:   PetscStackPush("PCPatch user callback");
    2346:   /* TODO: Fix for DMPlex compute op, this bypasses a lot of the machinery and just assembles every element tensor. */
    2347:   patch->usercomputeop(pc, -1, NULL, vecMat, cellIS, ndof*ncell, dofMapArray, NULL, patch->usercomputeopctx);
    2348:   PetscStackPop;
    2349:   ISDestroy(&cellIS);
    2350:   MatDestroy(&vecMat);
    2351:   ISRestoreIndices(patch->allCells, &cellsArray);
    2352:   ISRestoreIndices(dofMap, &dofMapArray);
    2353:   ISDestroy(&dofMap);

    2355:   if (patch->usercomputeopintfacet) {
    2356:     PetscInt nIntFacets;
    2357:     IS       intFacetsIS;
    2358:     const PetscInt *intFacetsArray = NULL;
    2359:     if (!patch->allIntFacets) {
    2360:       PetscHSetI      facets;
    2361:       PetscHashIter   hi;
    2362:       PetscInt pStart, pEnd, fStart, fEnd;
    2363:       PetscInt *allIntFacets = NULL;
    2364:       PetscHSetICreate(&facets);
    2365:       ISGetIndices(patch->intFacets, &intFacetsArray);
    2366:       PetscSectionGetChart(patch->intFacetCounts, &pStart, &pEnd);
    2367:       DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
    2368:       for (i = pStart; i < pEnd; i++) {
    2369:         PetscSectionGetDof(patch->intFacetCounts, i, &nIntFacets);
    2370:         PetscSectionGetOffset(patch->intFacetCounts, i, &offset);
    2371:         if (nIntFacets <= 0) continue;
    2372:         for (j = 0; j < nIntFacets; j++) {
    2373:           PetscHSetIAdd(facets, intFacetsArray[offset + j]);
    2374:         }
    2375:       }
    2376:       ISRestoreIndices(patch->intFacets, &intFacetsArray);
    2377:       PetscHSetIGetSize(facets, &nIntFacets);
    2378:       PetscMalloc1(nIntFacets, &allIntFacets);
    2379:       PetscMalloc1(fEnd-fStart, &patch->precomputedIntFacetTensorLocations);
    2380:       i = 0;
    2381:       PetscHashIterBegin(facets, hi);
    2382:       while (!PetscHashIterAtEnd(facets, hi)) {
    2383:         PetscHashIterGetKey(facets, hi, allIntFacets[i]);
    2384:         patch->precomputedIntFacetTensorLocations[allIntFacets[i] - fStart] = i;
    2385:         PetscHashIterNext(facets, hi);
    2386:         i++;
    2387:       }
    2388:       PetscHSetIDestroy(&facets);
    2389:       ISCreateGeneral(PETSC_COMM_SELF, nIntFacets, allIntFacets, PETSC_OWN_POINTER, &patch->allIntFacets);
    2390:     }
    2391:     ISGetSize(patch->allIntFacets, &nIntFacets);
    2392:     if (!patch->intFacetMats) {
    2393:       VecCreateSeq(PETSC_COMM_SELF, nIntFacets*ndof*ndof*4, &patch->intFacetMats);
    2394:       VecSetBlockSize(patch->intFacetMats, ndof*2);
    2395:     }
    2396:     VecSet(patch->intFacetMats, 0);

    2398:     MatCreateShell(PETSC_COMM_SELF, nIntFacets*ndof*2, nIntFacets*ndof*2, nIntFacets*ndof*2, nIntFacets*ndof*2,
    2399:                           (void*)patch->intFacetMats, &vecMat);
    2400:     MatShellSetOperation(vecMat, MATOP_SET_VALUES, (void(*)(void))&MatSetValues_PCPatch_Private);
    2401:     ISCreateStride(PETSC_COMM_SELF, 2*ndof*nIntFacets, 0, 1, &dofMap);
    2402:     ISGetIndices(dofMap, &dofMapArray);
    2403:     ISGetIndices(patch->allIntFacets, &intFacetsArray);
    2404:     ISCreateGeneral(PETSC_COMM_SELF, nIntFacets, intFacetsArray, PETSC_USE_POINTER, &intFacetsIS);
    2405:     PetscStackPush("PCPatch user callback (interior facets)");
    2406:     /* TODO: Fix for DMPlex compute op, this bypasses a lot of the machinery and just assembles every element tensor. */
    2407:     patch->usercomputeopintfacet(pc, -1, NULL, vecMat, intFacetsIS, 2*ndof*nIntFacets, dofMapArray, NULL, patch->usercomputeopintfacetctx);
    2408:     PetscStackPop;
    2409:     ISDestroy(&intFacetsIS);
    2410:     MatDestroy(&vecMat);
    2411:     ISRestoreIndices(patch->allIntFacets, &intFacetsArray);
    2412:     ISRestoreIndices(dofMap, &dofMapArray);
    2413:     ISDestroy(&dofMap);
    2414:   }
    2415:   DMDestroy(&dm);
    2416:   PetscLogEventEnd(PC_Patch_ComputeOp, pc, 0, 0, 0);

    2418:   return(0);
    2419: }

    2421: PetscErrorCode PCPatch_ScatterLocal_Private(PC pc, PetscInt p, Vec x, Vec y, InsertMode mode, ScatterMode scat, PatchScatterType scattertype)
    2422: {
    2423:   PC_PATCH          *patch     = (PC_PATCH *) pc->data;
    2424:   const PetscScalar *xArray    = NULL;
    2425:   PetscScalar       *yArray    = NULL;
    2426:   const PetscInt    *gtolArray = NULL;
    2427:   PetscInt           dof, offset, lidx;
    2428:   PetscErrorCode     ierr;

    2431:   VecGetArrayRead(x, &xArray);
    2432:   VecGetArray(y, &yArray);
    2433:   if (scattertype == SCATTER_WITHARTIFICIAL) {
    2434:     PetscSectionGetDof(patch->gtolCountsWithArtificial, p, &dof);
    2435:     PetscSectionGetOffset(patch->gtolCountsWithArtificial, p, &offset);
    2436:     ISGetIndices(patch->gtolWithArtificial, &gtolArray);
    2437:   } else if (scattertype == SCATTER_WITHALL) {
    2438:     PetscSectionGetDof(patch->gtolCountsWithAll, p, &dof);
    2439:     PetscSectionGetOffset(patch->gtolCountsWithAll, p, &offset);
    2440:     ISGetIndices(patch->gtolWithAll, &gtolArray);
    2441:   } else {
    2442:     PetscSectionGetDof(patch->gtolCounts, p, &dof);
    2443:     PetscSectionGetOffset(patch->gtolCounts, p, &offset);
    2444:     ISGetIndices(patch->gtol, &gtolArray);
    2445:   }
    2446:   if (mode == INSERT_VALUES && scat != SCATTER_FORWARD) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Can't insert if not scattering forward\n");
    2447:   if (mode == ADD_VALUES    && scat != SCATTER_REVERSE) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Can't add if not scattering reverse\n");
    2448:   for (lidx = 0; lidx < dof; ++lidx) {
    2449:     const PetscInt gidx = gtolArray[offset+lidx];

    2451:     if (mode == INSERT_VALUES) yArray[lidx]  = xArray[gidx]; /* Forward */
    2452:     else                       yArray[gidx] += xArray[lidx]; /* Reverse */
    2453:   }
    2454:   if (scattertype == SCATTER_WITHARTIFICIAL) {
    2455:     ISRestoreIndices(patch->gtolWithArtificial, &gtolArray);
    2456:   } else if (scattertype == SCATTER_WITHALL) {
    2457:     ISRestoreIndices(patch->gtolWithAll, &gtolArray);
    2458:   } else {
    2459:     ISRestoreIndices(patch->gtol, &gtolArray);
    2460:   }
    2461:   VecRestoreArrayRead(x, &xArray);
    2462:   VecRestoreArray(y, &yArray);
    2463:   return(0);
    2464: }

    2466: static PetscErrorCode PCSetUp_PATCH_Linear(PC pc)
    2467: {
    2468:   PC_PATCH      *patch = (PC_PATCH *) pc->data;
    2469:   const char    *prefix;
    2470:   PetscInt       i;

    2474:   if (!pc->setupcalled) {
    2475:     if (!patch->save_operators && patch->denseinverse) SETERRQ(PetscObjectComm((PetscObject)pc), PETSC_ERR_ARG_WRONGSTATE, "Can't have dense inverse without save operators");
    2476:     if (!patch->denseinverse) {
    2477:       PetscMalloc1(patch->npatch, &patch->solver);
    2478:       PCGetOptionsPrefix(pc, &prefix);
    2479:       for (i = 0; i < patch->npatch; ++i) {
    2480:         KSP ksp;
    2481:         PC  subpc;

    2483:         KSPCreate(PETSC_COMM_SELF, &ksp);
    2484:         KSPSetErrorIfNotConverged(ksp, pc->erroriffailure);
    2485:         KSPSetOptionsPrefix(ksp, prefix);
    2486:         KSPAppendOptionsPrefix(ksp, "sub_");
    2487:         PetscObjectIncrementTabLevel((PetscObject) ksp, (PetscObject) pc, 1);
    2488:         KSPGetPC(ksp, &subpc);
    2489:         PetscObjectIncrementTabLevel((PetscObject) subpc, (PetscObject) pc, 1);
    2490:         PetscLogObjectParent((PetscObject) pc, (PetscObject) ksp);
    2491:         patch->solver[i] = (PetscObject) ksp;
    2492:       }
    2493:     }
    2494:   }
    2495:   if (patch->save_operators) {
    2496:     if (patch->precomputeElementTensors) {
    2497:       PCPatchPrecomputePatchTensors_Private(pc);
    2498:     }
    2499:     for (i = 0; i < patch->npatch; ++i) {
    2500:       PCPatchComputeOperator_Internal(pc, NULL, patch->mat[i], i, PETSC_FALSE);
    2501:       if (!patch->denseinverse) {
    2502:         KSPSetOperators((KSP) patch->solver[i], patch->mat[i], patch->mat[i]);
    2503:       } else if (patch->mat[i] && !patch->densesolve) {
    2504:         /* Setup matmult callback */
    2505:         MatGetOperation(patch->mat[i], MATOP_MULT, (void (**)(void))&patch->densesolve);
    2506:       }
    2507:     }
    2508:   }
    2509:   if(patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    2510:     for (i = 0; i < patch->npatch; ++i) {
    2511:       /* Instead of padding patch->patchUpdate with zeros to get */
    2512:       /* patch->patchUpdateWithArtificial and then multiplying with the matrix, */
    2513:       /* just get rid of the columns that correspond to the dofs with */
    2514:       /* artificial bcs. That's of course fairly inefficient, hopefully we */
    2515:       /* can just assemble the rectangular matrix in the first place. */
    2516:       Mat matSquare;
    2517:       IS rowis;
    2518:       PetscInt dof;

    2520:       MatGetSize(patch->mat[i], &dof, NULL);
    2521:       if (dof == 0) {
    2522:         patch->matWithArtificial[i] = NULL;
    2523:         continue;
    2524:       }

    2526:       PCPatchCreateMatrix_Private(pc, i, &matSquare, PETSC_TRUE);
    2527:       PCPatchComputeOperator_Internal(pc, NULL, matSquare, i, PETSC_TRUE);

    2529:       MatGetSize(matSquare, &dof, NULL);
    2530:       ISCreateStride(PETSC_COMM_SELF, dof, 0, 1, &rowis);
    2531:       if (pc->setupcalled) {
    2532:         MatCreateSubMatrix(matSquare, rowis, patch->dofMappingWithoutToWithArtificial[i], MAT_REUSE_MATRIX, &patch->matWithArtificial[i]);
    2533:       } else {
    2534:         MatCreateSubMatrix(matSquare, rowis, patch->dofMappingWithoutToWithArtificial[i], MAT_INITIAL_MATRIX, &patch->matWithArtificial[i]);
    2535:       }
    2536:       ISDestroy(&rowis);
    2537:       MatDestroy(&matSquare);
    2538:     }
    2539:   }
    2540:   return(0);
    2541: }

    2543: static PetscErrorCode PCSetUp_PATCH(PC pc)
    2544: {
    2545:   PC_PATCH      *patch = (PC_PATCH *) pc->data;
    2546:   PetscInt       i;
    2547:   PetscBool      isNonlinear;
    2548:   PetscInt       maxDof = -1, maxDofWithArtificial = -1;

    2552:   if (!pc->setupcalled) {
    2553:     PetscInt pStart, pEnd, p;
    2554:     PetscInt localSize;

    2556:     PetscLogEventBegin(PC_Patch_CreatePatches, pc, 0, 0, 0);

    2558:     isNonlinear = patch->isNonlinear;
    2559:     if (!patch->nsubspaces) {
    2560:       DM           dm, plex;
    2561:       PetscSection s;
    2562:       PetscInt     cStart, cEnd, c, Nf, f, numGlobalBcs = 0, *globalBcs, *Nb, totNb = 0, **cellDofs;

    2564:       PCGetDM(pc, &dm);
    2565:       if (!dm) SETERRQ(PetscObjectComm((PetscObject) pc), PETSC_ERR_ARG_WRONG, "Must set DM for PCPATCH or call PCPatchSetDiscretisationInfo()");
    2566:       DMConvert(dm, DMPLEX, &plex);
    2567:       dm = plex;
    2568:       DMGetLocalSection(dm, &s);
    2569:       PetscSectionGetNumFields(s, &Nf);
    2570:       PetscSectionGetChart(s, &pStart, &pEnd);
    2571:       for (p = pStart; p < pEnd; ++p) {
    2572:         PetscInt cdof;
    2573:         PetscSectionGetConstraintDof(s, p, &cdof);
    2574:         numGlobalBcs += cdof;
    2575:       }
    2576:       DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
    2577:       PetscMalloc3(Nf, &Nb, Nf, &cellDofs, numGlobalBcs, &globalBcs);
    2578:       for (f = 0; f < Nf; ++f) {
    2579:         PetscFE        fe;
    2580:         PetscDualSpace sp;
    2581:         PetscInt       cdoff = 0;

    2583:         DMGetField(dm, f, NULL, (PetscObject *) &fe);
    2584:         /* PetscFEGetNumComponents(fe, &Nc[f]); */
    2585:         PetscFEGetDualSpace(fe, &sp);
    2586:         PetscDualSpaceGetDimension(sp, &Nb[f]);
    2587:         totNb += Nb[f];

    2589:         PetscMalloc1((cEnd-cStart)*Nb[f], &cellDofs[f]);
    2590:         for (c = cStart; c < cEnd; ++c) {
    2591:           PetscInt *closure = NULL;
    2592:           PetscInt  clSize  = 0, cl;

    2594:           DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &clSize, &closure);
    2595:           for (cl = 0; cl < clSize*2; cl += 2) {
    2596:             const PetscInt p = closure[cl];
    2597:             PetscInt       fdof, d, foff;

    2599:             PetscSectionGetFieldDof(s, p, f, &fdof);
    2600:             PetscSectionGetFieldOffset(s, p, f, &foff);
    2601:             for (d = 0; d < fdof; ++d, ++cdoff) cellDofs[f][cdoff] = foff + d;
    2602:           }
    2603:           DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &clSize, &closure);
    2604:         }
    2605:         if (cdoff != (cEnd-cStart)*Nb[f]) SETERRQ4(PetscObjectComm((PetscObject) pc), PETSC_ERR_ARG_SIZ, "Total number of cellDofs %D for field %D should be Nc (%D) * cellDof (%D)", cdoff, f, cEnd-cStart, Nb[f]);
    2606:       }
    2607:       numGlobalBcs = 0;
    2608:       for (p = pStart; p < pEnd; ++p) {
    2609:         const PetscInt *ind;
    2610:         PetscInt        off, cdof, d;

    2612:         PetscSectionGetOffset(s, p, &off);
    2613:         PetscSectionGetConstraintDof(s, p, &cdof);
    2614:         PetscSectionGetConstraintIndices(s, p, &ind);
    2615:         for (d = 0; d < cdof; ++d) globalBcs[numGlobalBcs++] = off + ind[d];
    2616:       }

    2618:       PCPatchSetDiscretisationInfoCombined(pc, dm, Nb, (const PetscInt **) cellDofs, numGlobalBcs, globalBcs, numGlobalBcs, globalBcs);
    2619:       for (f = 0; f < Nf; ++f) {
    2620:         PetscFree(cellDofs[f]);
    2621:       }
    2622:       PetscFree3(Nb, cellDofs, globalBcs);
    2623:       PCPatchSetComputeFunction(pc, PCPatchComputeFunction_DMPlex_Private, NULL);
    2624:       PCPatchSetComputeOperator(pc, PCPatchComputeOperator_DMPlex_Private, NULL);
    2625:       DMDestroy(&dm);
    2626:     }

    2628:     localSize = patch->subspaceOffsets[patch->nsubspaces];
    2629:     VecCreateSeq(PETSC_COMM_SELF, localSize, &patch->localRHS);
    2630:     VecSetUp(patch->localRHS);
    2631:     VecDuplicate(patch->localRHS, &patch->localUpdate);
    2632:     PCPatchCreateCellPatches(pc);
    2633:     PCPatchCreateCellPatchDiscretisationInfo(pc);

    2635:     /* OK, now build the work vectors */
    2636:     PetscSectionGetChart(patch->gtolCounts, &pStart, &pEnd);

    2638:     if (patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    2639:       PetscMalloc1(patch->npatch, &patch->dofMappingWithoutToWithArtificial);
    2640:     }
    2641:     if (isNonlinear) {
    2642:       PetscMalloc1(patch->npatch, &patch->dofMappingWithoutToWithAll);
    2643:     }
    2644:     for (p = pStart; p < pEnd; ++p) {
    2645:       PetscInt dof;

    2647:       PetscSectionGetDof(patch->gtolCounts, p, &dof);
    2648:       maxDof = PetscMax(maxDof, dof);
    2649:       if (patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    2650:         const PetscInt    *gtolArray, *gtolArrayWithArtificial = NULL;
    2651:         PetscInt           numPatchDofs, offset;
    2652:         PetscInt           numPatchDofsWithArtificial, offsetWithArtificial;
    2653:         PetscInt           dofWithoutArtificialCounter = 0;
    2654:         PetscInt          *patchWithoutArtificialToWithArtificialArray;

    2656:         PetscSectionGetDof(patch->gtolCountsWithArtificial, p, &dof);
    2657:         maxDofWithArtificial = PetscMax(maxDofWithArtificial, dof);

    2659:         /* Now build the mapping that for a dof in a patch WITHOUT dofs that have artificial bcs gives the */
    2660:         /* the index in the patch with all dofs */
    2661:         ISGetIndices(patch->gtol, &gtolArray);

    2663:         PetscSectionGetDof(patch->gtolCounts, p, &numPatchDofs);
    2664:         if (numPatchDofs == 0) {
    2665:           patch->dofMappingWithoutToWithArtificial[p-pStart] = NULL;
    2666:           continue;
    2667:         }

    2669:         PetscSectionGetOffset(patch->gtolCounts, p, &offset);
    2670:         ISGetIndices(patch->gtolWithArtificial, &gtolArrayWithArtificial);
    2671:         PetscSectionGetDof(patch->gtolCountsWithArtificial, p, &numPatchDofsWithArtificial);
    2672:         PetscSectionGetOffset(patch->gtolCountsWithArtificial, p, &offsetWithArtificial);

    2674:         PetscMalloc1(numPatchDofs, &patchWithoutArtificialToWithArtificialArray);
    2675:         for (i=0; i<numPatchDofsWithArtificial; i++) {
    2676:           if (gtolArrayWithArtificial[i+offsetWithArtificial] == gtolArray[offset+dofWithoutArtificialCounter]) {
    2677:             patchWithoutArtificialToWithArtificialArray[dofWithoutArtificialCounter] = i;
    2678:             dofWithoutArtificialCounter++;
    2679:             if (dofWithoutArtificialCounter == numPatchDofs)
    2680:               break;
    2681:           }
    2682:         }
    2683:         ISCreateGeneral(PETSC_COMM_SELF, numPatchDofs, patchWithoutArtificialToWithArtificialArray, PETSC_OWN_POINTER, &patch->dofMappingWithoutToWithArtificial[p-pStart]);
    2684:         ISRestoreIndices(patch->gtol, &gtolArray);
    2685:         ISRestoreIndices(patch->gtolWithArtificial, &gtolArrayWithArtificial);
    2686:       }
    2687:       if (isNonlinear) {
    2688:         const PetscInt    *gtolArray, *gtolArrayWithAll = NULL;
    2689:         PetscInt           numPatchDofs, offset;
    2690:         PetscInt           numPatchDofsWithAll, offsetWithAll;
    2691:         PetscInt           dofWithoutAllCounter = 0;
    2692:         PetscInt          *patchWithoutAllToWithAllArray;

    2694:         /* Now build the mapping that for a dof in a patch WITHOUT dofs that have artificial bcs gives the */
    2695:         /* the index in the patch with all dofs */
    2696:         ISGetIndices(patch->gtol, &gtolArray);

    2698:         PetscSectionGetDof(patch->gtolCounts, p, &numPatchDofs);
    2699:         if (numPatchDofs == 0) {
    2700:           patch->dofMappingWithoutToWithAll[p-pStart] = NULL;
    2701:           continue;
    2702:         }

    2704:         PetscSectionGetOffset(patch->gtolCounts, p, &offset);
    2705:         ISGetIndices(patch->gtolWithAll, &gtolArrayWithAll);
    2706:         PetscSectionGetDof(patch->gtolCountsWithAll, p, &numPatchDofsWithAll);
    2707:         PetscSectionGetOffset(patch->gtolCountsWithAll, p, &offsetWithAll);

    2709:         PetscMalloc1(numPatchDofs, &patchWithoutAllToWithAllArray);

    2711:         for (i=0; i<numPatchDofsWithAll; i++) {
    2712:           if (gtolArrayWithAll[i+offsetWithAll] == gtolArray[offset+dofWithoutAllCounter]) {
    2713:             patchWithoutAllToWithAllArray[dofWithoutAllCounter] = i;
    2714:             dofWithoutAllCounter++;
    2715:             if (dofWithoutAllCounter == numPatchDofs)
    2716:               break;
    2717:           }
    2718:         }
    2719:         ISCreateGeneral(PETSC_COMM_SELF, numPatchDofs, patchWithoutAllToWithAllArray, PETSC_OWN_POINTER, &patch->dofMappingWithoutToWithAll[p-pStart]);
    2720:         ISRestoreIndices(patch->gtol, &gtolArray);
    2721:         ISRestoreIndices(patch->gtolWithAll, &gtolArrayWithAll);
    2722:       }
    2723:     }
    2724:     if (patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    2725:       VecCreateSeq(PETSC_COMM_SELF, maxDofWithArtificial, &patch->patchRHSWithArtificial);
    2726:       VecSetUp(patch->patchRHSWithArtificial);
    2727:     }
    2728:     VecCreateSeq(PETSC_COMM_SELF, maxDof, &patch->patchRHS);
    2729:     VecSetUp(patch->patchRHS);
    2730:     VecCreateSeq(PETSC_COMM_SELF, maxDof, &patch->patchUpdate);
    2731:     VecSetUp(patch->patchUpdate);
    2732:     if (patch->save_operators) {
    2733:       PetscMalloc1(patch->npatch, &patch->mat);
    2734:       for (i = 0; i < patch->npatch; ++i) {
    2735:         PCPatchCreateMatrix_Private(pc, i, &patch->mat[i], PETSC_FALSE);
    2736:       }
    2737:     }
    2738:     PetscLogEventEnd(PC_Patch_CreatePatches, pc, 0, 0, 0);

    2740:     /* If desired, calculate weights for dof multiplicity */
    2741:     if (patch->partition_of_unity) {
    2742:       PetscScalar *input = NULL;
    2743:       PetscScalar *output = NULL;
    2744:       Vec global;

    2746:       VecDuplicate(patch->localRHS, &patch->dof_weights);
    2747:       if(patch->local_composition_type == PC_COMPOSITE_ADDITIVE) {
    2748:         for (i = 0; i < patch->npatch; ++i) {
    2749:           PetscInt dof;

    2751:           PetscSectionGetDof(patch->gtolCounts, i+pStart, &dof);
    2752:           if (dof <= 0) continue;
    2753:           VecSet(patch->patchRHS, 1.0);
    2754:           PCPatch_ScatterLocal_Private(pc, i+pStart, patch->patchRHS, patch->dof_weights, ADD_VALUES, SCATTER_REVERSE, SCATTER_INTERIOR);
    2755:         }
    2756:       } else {
    2757:         /* multiplicative is actually only locally multiplicative and globally additive. need the pou where the mesh decomposition overlaps */
    2758:         VecSet(patch->dof_weights, 1.0);
    2759:       }

    2761:       VecDuplicate(patch->dof_weights, &global);
    2762:       VecSet(global, 0.);

    2764:       VecGetArray(patch->dof_weights, &input);
    2765:       VecGetArray(global, &output);
    2766:       PetscSFReduceBegin(patch->sectionSF, MPIU_SCALAR, input, output, MPI_SUM);
    2767:       PetscSFReduceEnd(patch->sectionSF, MPIU_SCALAR, input, output, MPI_SUM);
    2768:       VecRestoreArray(patch->dof_weights, &input);
    2769:       VecRestoreArray(global, &output);

    2771:       VecReciprocal(global);

    2773:       VecGetArray(patch->dof_weights, &output);
    2774:       VecGetArray(global, &input);
    2775:       PetscSFBcastBegin(patch->sectionSF, MPIU_SCALAR, input, output);
    2776:       PetscSFBcastEnd(patch->sectionSF, MPIU_SCALAR, input, output);
    2777:       VecRestoreArray(patch->dof_weights, &output);
    2778:       VecRestoreArray(global, &input);
    2779:       VecDestroy(&global);
    2780:     }
    2781:     if(patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE && patch->save_operators) {
    2782:       PetscMalloc1(patch->npatch, &patch->matWithArtificial);
    2783:     }
    2784:   }
    2785:   (*patch->setupsolver)(pc);
    2786:   return(0);
    2787: }

    2789: static PetscErrorCode PCApply_PATCH_Linear(PC pc, PetscInt i, Vec x, Vec y)
    2790: {
    2791:   PC_PATCH      *patch = (PC_PATCH *) pc->data;
    2792:   KSP            ksp;
    2793:   Mat            op;
    2794:   PetscInt       m, n;

    2798:   if (patch->denseinverse) {
    2799:     (*patch->densesolve)(patch->mat[i], x, y);
    2800:     return(0);
    2801:   }
    2802:   ksp = (KSP) patch->solver[i];
    2803:   if (!patch->save_operators) {
    2804:     Mat mat;

    2806:     PCPatchCreateMatrix_Private(pc, i, &mat, PETSC_FALSE);
    2807:     /* Populate operator here. */
    2808:     PCPatchComputeOperator_Internal(pc, NULL, mat, i, PETSC_FALSE);
    2809:     KSPSetOperators(ksp, mat, mat);
    2810:     /* Drop reference so the KSPSetOperators below will blow it away. */
    2811:     MatDestroy(&mat);
    2812:   }
    2813:   PetscLogEventBegin(PC_Patch_Solve, pc, 0, 0, 0);
    2814:   if (!ksp->setfromoptionscalled) {
    2815:     KSPSetFromOptions(ksp);
    2816:   }
    2817:   /* Disgusting trick to reuse work vectors */
    2818:   KSPGetOperators(ksp, &op, NULL);
    2819:   MatGetLocalSize(op, &m, &n);
    2820:   x->map->n = m;
    2821:   y->map->n = n;
    2822:   x->map->N = m;
    2823:   y->map->N = n;
    2824:   KSPSolve(ksp, x, y);
    2825:   KSPCheckSolve(ksp, pc, y);
    2826:   PetscLogEventEnd(PC_Patch_Solve, pc, 0, 0, 0);
    2827:   if (!patch->save_operators) {
    2828:     PC pc;
    2829:     KSPSetOperators(ksp, NULL, NULL);
    2830:     KSPGetPC(ksp, &pc);
    2831:     /* Destroy PC context too, otherwise the factored matrix hangs around. */
    2832:     PCReset(pc);
    2833:   }
    2834:   return(0);
    2835: }

    2837: static PetscErrorCode PCUpdateMultiplicative_PATCH_Linear(PC pc, PetscInt i, PetscInt pStart)
    2838: {
    2839:   PC_PATCH      *patch = (PC_PATCH *) pc->data;
    2840:   Mat multMat;
    2841:   PetscInt n, m;

    2846:   if (patch->save_operators) {
    2847:     multMat = patch->matWithArtificial[i];
    2848:   } else {
    2849:     /*Very inefficient, hopefully we can just assemble the rectangular matrix in the first place.*/
    2850:     Mat matSquare;
    2851:     PetscInt dof;
    2852:     IS rowis;
    2853:     PCPatchCreateMatrix_Private(pc, i, &matSquare, PETSC_TRUE);
    2854:     PCPatchComputeOperator_Internal(pc, NULL, matSquare, i, PETSC_TRUE);
    2855:     MatGetSize(matSquare, &dof, NULL);
    2856:     ISCreateStride(PETSC_COMM_SELF, dof, 0, 1, &rowis);
    2857:     MatCreateSubMatrix(matSquare, rowis, patch->dofMappingWithoutToWithArtificial[i], MAT_INITIAL_MATRIX, &multMat);
    2858:     MatDestroy(&matSquare);
    2859:     ISDestroy(&rowis);
    2860:   }
    2861:   /* Disgusting trick to reuse work vectors */
    2862:   MatGetLocalSize(multMat, &m, &n);
    2863:   patch->patchUpdate->map->n = n;
    2864:   patch->patchRHSWithArtificial->map->n = m;
    2865:   patch->patchUpdate->map->N = n;
    2866:   patch->patchRHSWithArtificial->map->N = m;
    2867:   MatMult(multMat, patch->patchUpdate, patch->patchRHSWithArtificial);
    2868:   VecScale(patch->patchRHSWithArtificial, -1.0);
    2869:   PCPatch_ScatterLocal_Private(pc, i + pStart, patch->patchRHSWithArtificial, patch->localRHS, ADD_VALUES, SCATTER_REVERSE, SCATTER_WITHARTIFICIAL);
    2870:   if (!patch->save_operators) {
    2871:     MatDestroy(&multMat);
    2872:   }
    2873:   return(0);
    2874: }

    2876: static PetscErrorCode PCApply_PATCH(PC pc, Vec x, Vec y)
    2877: {
    2878:   PC_PATCH          *patch    = (PC_PATCH *) pc->data;
    2879:   const PetscScalar *globalRHS  = NULL;
    2880:   PetscScalar       *localRHS   = NULL;
    2881:   PetscScalar       *globalUpdate  = NULL;
    2882:   const PetscInt    *bcNodes  = NULL;
    2883:   PetscInt           nsweep   = patch->symmetrise_sweep ? 2 : 1;
    2884:   PetscInt           start[2] = {0, 0};
    2885:   PetscInt           end[2]   = {-1, -1};
    2886:   const PetscInt     inc[2]   = {1, -1};
    2887:   const PetscScalar *localUpdate;
    2888:   const PetscInt    *iterationSet;
    2889:   PetscInt           pStart, numBcs, n, sweep, bc, j;
    2890:   PetscErrorCode     ierr;

    2893:   PetscLogEventBegin(PC_Patch_Apply, pc, 0, 0, 0);
    2894:   PetscOptionsPushGetViewerOff(PETSC_TRUE);
    2895:   /* start, end, inc have 2 entries to manage a second backward sweep if we symmetrize */
    2896:   end[0]   = patch->npatch;
    2897:   start[1] = patch->npatch-1;
    2898:   if (patch->user_patches) {
    2899:     ISGetLocalSize(patch->iterationSet, &end[0]);
    2900:     start[1] = end[0] - 1;
    2901:     ISGetIndices(patch->iterationSet, &iterationSet);
    2902:   }
    2903:   /* Scatter from global space into overlapped local spaces */
    2904:   VecGetArrayRead(x, &globalRHS);
    2905:   VecGetArray(patch->localRHS, &localRHS);
    2906:   PetscSFBcastBegin(patch->sectionSF, MPIU_SCALAR, globalRHS, localRHS);
    2907:   PetscSFBcastEnd(patch->sectionSF, MPIU_SCALAR, globalRHS, localRHS);
    2908:   VecRestoreArrayRead(x, &globalRHS);
    2909:   VecRestoreArray(patch->localRHS, &localRHS);

    2911:   VecSet(patch->localUpdate, 0.0);
    2912:   PetscSectionGetChart(patch->gtolCounts, &pStart, NULL);
    2913:   PetscLogEventBegin(PC_Patch_Solve, pc, 0, 0, 0);
    2914:   for (sweep = 0; sweep < nsweep; sweep++) {
    2915:     for (j = start[sweep]; j*inc[sweep] < end[sweep]*inc[sweep]; j += inc[sweep]) {
    2916:       PetscInt i       = patch->user_patches ? iterationSet[j] : j;
    2917:       PetscInt start, len;

    2919:       PetscSectionGetDof(patch->gtolCounts, i+pStart, &len);
    2920:       PetscSectionGetOffset(patch->gtolCounts, i+pStart, &start);
    2921:       /* TODO: Squash out these guys in the setup as well. */
    2922:       if (len <= 0) continue;
    2923:       /* TODO: Do we need different scatters for X and Y? */
    2924:       PCPatch_ScatterLocal_Private(pc, i+pStart, patch->localRHS, patch->patchRHS, INSERT_VALUES, SCATTER_FORWARD, SCATTER_INTERIOR);
    2925:       (*patch->applysolver)(pc, i, patch->patchRHS, patch->patchUpdate);
    2926:       PCPatch_ScatterLocal_Private(pc, i+pStart, patch->patchUpdate, patch->localUpdate, ADD_VALUES, SCATTER_REVERSE, SCATTER_INTERIOR);
    2927:       if(patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    2928:         (*patch->updatemultiplicative)(pc, i, pStart);
    2929:       }
    2930:     }
    2931:   }
    2932:   PetscLogEventEnd(PC_Patch_Solve, pc, 0, 0, 0);
    2933:   if (patch->user_patches) {ISRestoreIndices(patch->iterationSet, &iterationSet);}
    2934:   /* XXX: should we do this on the global vector? */
    2935:   if (patch->partition_of_unity) {
    2936:     VecPointwiseMult(patch->localUpdate, patch->localUpdate, patch->dof_weights);
    2937:   }
    2938:   /* Now patch->localUpdate contains the solution of the patch solves, so we need to combine them all. */
    2939:   VecSet(y, 0.0);
    2940:   VecGetArray(y, &globalUpdate);
    2941:   VecGetArrayRead(patch->localUpdate, &localUpdate);
    2942:   PetscSFReduceBegin(patch->sectionSF, MPIU_SCALAR, localUpdate, globalUpdate, MPI_SUM);
    2943:   PetscSFReduceEnd(patch->sectionSF, MPIU_SCALAR, localUpdate, globalUpdate, MPI_SUM);
    2944:   VecRestoreArrayRead(patch->localUpdate, &localUpdate);

    2946:   /* Now we need to send the global BC values through */
    2947:   VecGetArrayRead(x, &globalRHS);
    2948:   ISGetSize(patch->globalBcNodes, &numBcs);
    2949:   ISGetIndices(patch->globalBcNodes, &bcNodes);
    2950:   VecGetLocalSize(x, &n);
    2951:   for (bc = 0; bc < numBcs; ++bc) {
    2952:     const PetscInt idx = bcNodes[bc];
    2953:     if (idx < n) globalUpdate[idx] = globalRHS[idx];
    2954:   }

    2956:   ISRestoreIndices(patch->globalBcNodes, &bcNodes);
    2957:   VecRestoreArrayRead(x, &globalRHS);
    2958:   VecRestoreArray(y, &globalUpdate);

    2960:   PetscOptionsPopGetViewerOff();
    2961:   PetscLogEventEnd(PC_Patch_Apply, pc, 0, 0, 0);
    2962:   return(0);
    2963: }

    2965: static PetscErrorCode PCReset_PATCH_Linear(PC pc)
    2966: {
    2967:   PC_PATCH      *patch = (PC_PATCH *) pc->data;
    2968:   PetscInt       i;

    2972:   if (patch->solver) {
    2973:     for (i = 0; i < patch->npatch; ++i) {KSPReset((KSP) patch->solver[i]);}
    2974:   }
    2975:   return(0);
    2976: }

    2978: static PetscErrorCode PCReset_PATCH(PC pc)
    2979: {
    2980:   PC_PATCH      *patch = (PC_PATCH *) pc->data;
    2981:   PetscInt       i;

    2986:   PetscSFDestroy(&patch->sectionSF);
    2987:   PetscSectionDestroy(&patch->cellCounts);
    2988:   PetscSectionDestroy(&patch->pointCounts);
    2989:   PetscSectionDestroy(&patch->cellNumbering);
    2990:   PetscSectionDestroy(&patch->gtolCounts);
    2991:   ISDestroy(&patch->gtol);
    2992:   ISDestroy(&patch->cells);
    2993:   ISDestroy(&patch->points);
    2994:   ISDestroy(&patch->dofs);
    2995:   ISDestroy(&patch->offs);
    2996:   PetscSectionDestroy(&patch->patchSection);
    2997:   ISDestroy(&patch->ghostBcNodes);
    2998:   ISDestroy(&patch->globalBcNodes);
    2999:   PetscSectionDestroy(&patch->gtolCountsWithArtificial);
    3000:   ISDestroy(&patch->gtolWithArtificial);
    3001:   ISDestroy(&patch->dofsWithArtificial);
    3002:   ISDestroy(&patch->offsWithArtificial);
    3003:   PetscSectionDestroy(&patch->gtolCountsWithAll);
    3004:   ISDestroy(&patch->gtolWithAll);
    3005:   ISDestroy(&patch->dofsWithAll);
    3006:   ISDestroy(&patch->offsWithAll);
    3007:   VecDestroy(&patch->cellMats);
    3008:   VecDestroy(&patch->intFacetMats);
    3009:   ISDestroy(&patch->allCells);
    3010:   ISDestroy(&patch->intFacets);
    3011:   ISDestroy(&patch->extFacets);
    3012:   ISDestroy(&patch->intFacetsToPatchCell);
    3013:   PetscSectionDestroy(&patch->intFacetCounts);
    3014:   PetscSectionDestroy(&patch->extFacetCounts);

    3016:   if (patch->dofSection) for (i = 0; i < patch->nsubspaces; i++) {PetscSectionDestroy(&patch->dofSection[i]);}
    3017:   PetscFree(patch->dofSection);
    3018:   PetscFree(patch->bs);
    3019:   PetscFree(patch->nodesPerCell);
    3020:   if (patch->cellNodeMap) for (i = 0; i < patch->nsubspaces; i++) {PetscFree(patch->cellNodeMap[i]);}
    3021:   PetscFree(patch->cellNodeMap);
    3022:   PetscFree(patch->subspaceOffsets);

    3024:   (*patch->resetsolver)(pc);

    3026:   if (patch->subspaces_to_exclude) {
    3027:     PetscHSetIDestroy(&patch->subspaces_to_exclude);
    3028:   }

    3030:   VecDestroy(&patch->localRHS);
    3031:   VecDestroy(&patch->localUpdate);
    3032:   VecDestroy(&patch->patchRHS);
    3033:   VecDestroy(&patch->patchUpdate);
    3034:   VecDestroy(&patch->dof_weights);
    3035:   if (patch->patch_dof_weights) {
    3036:     for (i = 0; i < patch->npatch; ++i) {VecDestroy(&patch->patch_dof_weights[i]);}
    3037:     PetscFree(patch->patch_dof_weights);
    3038:   }
    3039:   if (patch->mat) {
    3040:     for (i = 0; i < patch->npatch; ++i) {MatDestroy(&patch->mat[i]);}
    3041:     PetscFree(patch->mat);
    3042:   }
    3043:   if (patch->matWithArtificial) {
    3044:     for (i = 0; i < patch->npatch; ++i) {MatDestroy(&patch->matWithArtificial[i]);}
    3045:     PetscFree(patch->matWithArtificial);
    3046:   }
    3047:   VecDestroy(&patch->patchRHSWithArtificial);
    3048:   if(patch->dofMappingWithoutToWithArtificial) {
    3049:     for (i = 0; i < patch->npatch; ++i) {ISDestroy(&patch->dofMappingWithoutToWithArtificial[i]);}
    3050:     PetscFree(patch->dofMappingWithoutToWithArtificial);

    3052:   }
    3053:   if(patch->dofMappingWithoutToWithAll) {
    3054:     for (i = 0; i < patch->npatch; ++i) {ISDestroy(&patch->dofMappingWithoutToWithAll[i]);}
    3055:     PetscFree(patch->dofMappingWithoutToWithAll);

    3057:   }
    3058:   PetscFree(patch->sub_mat_type);
    3059:   if (patch->userIS) {
    3060:     for (i = 0; i < patch->npatch; ++i) {ISDestroy(&patch->userIS[i]);}
    3061:     PetscFree(patch->userIS);
    3062:   }
    3063:   PetscFree(patch->precomputedTensorLocations);
    3064:   PetscFree(patch->precomputedIntFacetTensorLocations);
    3065:
    3066:   patch->bs          = 0;
    3067:   patch->cellNodeMap = NULL;
    3068:   patch->nsubspaces  = 0;
    3069:   ISDestroy(&patch->iterationSet);

    3071:   PetscViewerDestroy(&patch->viewerSection);
    3072:   return(0);
    3073: }

    3075: static PetscErrorCode PCDestroy_PATCH_Linear(PC pc)
    3076: {
    3077:   PC_PATCH      *patch = (PC_PATCH *) pc->data;
    3078:   PetscInt       i;

    3082:   if (patch->solver) {
    3083:     for (i = 0; i < patch->npatch; ++i) {KSPDestroy((KSP *) &patch->solver[i]);}
    3084:     PetscFree(patch->solver);
    3085:   }
    3086:   return(0);
    3087: }

    3089: static PetscErrorCode PCDestroy_PATCH(PC pc)
    3090: {
    3091:   PC_PATCH      *patch = (PC_PATCH *) pc->data;

    3095:   PCReset_PATCH(pc);
    3096:   (*patch->destroysolver)(pc);
    3097:   PetscFree(pc->data);
    3098:   return(0);
    3099: }

    3101: static PetscErrorCode PCSetFromOptions_PATCH(PetscOptionItems *PetscOptionsObject, PC pc)
    3102: {
    3103:   PC_PATCH            *patch = (PC_PATCH *) pc->data;
    3104:   PCPatchConstructType patchConstructionType = PC_PATCH_STAR;
    3105:   char                 sub_mat_type[PETSC_MAX_PATH_LEN];
    3106:   char                 option[PETSC_MAX_PATH_LEN];
    3107:   const char          *prefix;
    3108:   PetscBool            flg, dimflg, codimflg;
    3109:   MPI_Comm             comm;
    3110:   PetscInt            *ifields, nfields, k;
    3111:   PetscErrorCode       ierr;
    3112:   PCCompositeType loctype = PC_COMPOSITE_ADDITIVE;

    3115:   PetscObjectGetComm((PetscObject) pc, &comm);
    3116:   PetscObjectGetOptionsPrefix((PetscObject) pc, &prefix);
    3117:   PetscOptionsHead(PetscOptionsObject, "Patch solver options");

    3119:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_save_operators", patch->classname);
    3120:   PetscOptionsBool(option,  "Store all patch operators for lifetime of object?", "PCPatchSetSaveOperators", patch->save_operators, &patch->save_operators, &flg);

    3122:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_precompute_element_tensors", patch->classname);
    3123:   PetscOptionsBool(option,  "Compute each element tensor only once?", "PCPatchSetPrecomputeElementTensors", patch->precomputeElementTensors, &patch->precomputeElementTensors, &flg);
    3124:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_partition_of_unity", patch->classname);
    3125:   PetscOptionsBool(option, "Weight contributions by dof multiplicity?", "PCPatchSetPartitionOfUnity", patch->partition_of_unity, &patch->partition_of_unity, &flg);

    3127:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_local_type", patch->classname);
    3128:   PetscOptionsEnum(option,"Type of local solver composition (additive or multiplicative)","PCPatchSetLocalComposition",PCCompositeTypes,(PetscEnum)loctype,(PetscEnum*)&loctype,&flg);
    3129:   if(flg) { PCPatchSetLocalComposition(pc, loctype);}
    3130:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_dense_inverse", patch->classname);
    3131:   PetscOptionsBool(option, "Compute inverses of patch matrices and apply directly? Ignores KSP/PC settings on patch.", "PCPatchSetDenseInverse", patch->denseinverse, &patch->denseinverse, &flg);
    3132:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_construct_dim", patch->classname);
    3133:   PetscOptionsInt(option, "What dimension of mesh point to construct patches by? (0 = vertices)", "PCPATCH", patch->dim, &patch->dim, &dimflg);
    3134:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_construct_codim", patch->classname);
    3135:   PetscOptionsInt(option, "What co-dimension of mesh point to construct patches by? (0 = cells)", "PCPATCH", patch->codim, &patch->codim, &codimflg);
    3136:   if (dimflg && codimflg) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Can only set one of dimension or co-dimension");

    3138:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_construct_type", patch->classname);
    3139:   PetscOptionsEnum(option, "How should the patches be constructed?", "PCPatchSetConstructType", PCPatchConstructTypes, (PetscEnum) patchConstructionType, (PetscEnum *) &patchConstructionType, &flg);
    3140:   if (flg) {PCPatchSetConstructType(pc, patchConstructionType, NULL, NULL);}

    3142:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_vanka_dim", patch->classname);
    3143:   PetscOptionsInt(option, "Topological dimension of entities for Vanka to ignore", "PCPATCH", patch->vankadim, &patch->vankadim, &flg);

    3145:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_ignore_dim", patch->classname);
    3146:   PetscOptionsInt(option, "Topological dimension of entities for completion to ignore", "PCPATCH", patch->ignoredim, &patch->ignoredim, &flg);

    3148:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_pardecomp_overlap", patch->classname);
    3149:   PetscOptionsInt(option, "What overlap should we use in construct type pardecomp?", "PCPATCH", patch->pardecomp_overlap, &patch->pardecomp_overlap, &flg);

    3151:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_sub_mat_type", patch->classname);
    3152:   PetscOptionsFList(option, "Matrix type for patch solves", "PCPatchSetSubMatType", MatList, NULL, sub_mat_type, PETSC_MAX_PATH_LEN, &flg);
    3153:   if (flg) {PCPatchSetSubMatType(pc, sub_mat_type);}

    3155:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_symmetrise_sweep", patch->classname);
    3156:   PetscOptionsBool(option, "Go start->end, end->start?", "PCPATCH", patch->symmetrise_sweep, &patch->symmetrise_sweep, &flg);

    3158:   /* If the user has set the number of subspaces, use that for the buffer size,
    3159:      otherwise use a large number */
    3160:   if (patch->nsubspaces <= 0) {
    3161:     nfields = 128;
    3162:   } else {
    3163:     nfields = patch->nsubspaces;
    3164:   }
    3165:   PetscMalloc1(nfields, &ifields);
    3166:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_exclude_subspaces", patch->classname);
    3167:   PetscOptionsGetIntArray(((PetscObject)pc)->options,((PetscObject)pc)->prefix,option,ifields,&nfields,&flg);
    3168:   if (flg && (patchConstructionType == PC_PATCH_USER)) SETERRQ(comm, PETSC_ERR_ARG_INCOMP, "We cannot support excluding a subspace with user patches because we do not index patches with a mesh point");
    3169:   if (flg) {
    3170:     PetscHSetIClear(patch->subspaces_to_exclude);
    3171:     for (k = 0; k < nfields; k++) {
    3172:       PetscHSetIAdd(patch->subspaces_to_exclude, ifields[k]);
    3173:     }
    3174:   }
    3175:   PetscFree(ifields);

    3177:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_patches_view", patch->classname);
    3178:   PetscOptionsBool(option, "Print out information during patch construction", "PCPATCH", patch->viewPatches, &patch->viewPatches, &flg);
    3179:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_cells_view", patch->classname);
    3180:   PetscOptionsGetViewer(comm,((PetscObject) pc)->options, prefix, option, &patch->viewerCells, &patch->formatCells, &patch->viewCells);
    3181:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_interior_facets_view", patch->classname);
    3182:   PetscOptionsGetViewer(comm,((PetscObject) pc)->options, prefix, option, &patch->viewerIntFacets, &patch->formatIntFacets, &patch->viewIntFacets);
    3183:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_exterior_facets_view", patch->classname);
    3184:   PetscOptionsGetViewer(comm,((PetscObject) pc)->options, prefix, option, &patch->viewerExtFacets, &patch->formatExtFacets, &patch->viewExtFacets);
    3185:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_points_view", patch->classname);
    3186:   PetscOptionsGetViewer(comm,((PetscObject) pc)->options, prefix, option, &patch->viewerPoints, &patch->formatPoints, &patch->viewPoints);
    3187:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_section_view", patch->classname);
    3188:   PetscOptionsGetViewer(comm,((PetscObject) pc)->options, prefix, option, &patch->viewerSection, &patch->formatSection, &patch->viewSection);
    3189:   PetscSNPrintf(option, PETSC_MAX_PATH_LEN, "-%s_patch_mat_view", patch->classname);
    3190:   PetscOptionsGetViewer(comm,((PetscObject) pc)->options, prefix, option, &patch->viewerMatrix, &patch->formatMatrix, &patch->viewMatrix);
    3191:   PetscOptionsTail();
    3192:   patch->optionsSet = PETSC_TRUE;
    3193:   return(0);
    3194: }

    3196: static PetscErrorCode PCSetUpOnBlocks_PATCH(PC pc)
    3197: {
    3198:   PC_PATCH          *patch = (PC_PATCH*) pc->data;
    3199:   KSPConvergedReason reason;
    3200:   PetscInt           i;
    3201:   PetscErrorCode     ierr;

    3204:   if (!patch->save_operators) {
    3205:     /* Can't do this here because the sub KSPs don't have an operator attached yet. */
    3206:     return(0);
    3207:   }
    3208:   if (patch->denseinverse) {
    3209:     /* No solvers */
    3210:     return(0);
    3211:   }
    3212:   for (i = 0; i < patch->npatch; ++i) {
    3213:     if (!((KSP) patch->solver[i])->setfromoptionscalled) {
    3214:       KSPSetFromOptions((KSP) patch->solver[i]);
    3215:     }
    3216:     KSPSetUp((KSP) patch->solver[i]);
    3217:     KSPGetConvergedReason((KSP) patch->solver[i], &reason);
    3218:     if (reason == KSP_DIVERGED_PC_FAILED) pc->failedreason = PC_SUBPC_ERROR;
    3219:   }
    3220:   return(0);
    3221: }

    3223: static PetscErrorCode PCView_PATCH(PC pc, PetscViewer viewer)
    3224: {
    3225:   PC_PATCH      *patch = (PC_PATCH *) pc->data;
    3226:   PetscViewer    sviewer;
    3227:   PetscBool      isascii;
    3228:   PetscMPIInt    rank;

    3232:   /* TODO Redo tabbing with set tbas in new style */
    3233:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &isascii);
    3234:   if (!isascii) return(0);
    3235:   MPI_Comm_rank(PetscObjectComm((PetscObject) pc), &rank);
    3236:   PetscViewerASCIIPushTab(viewer);
    3237:   PetscViewerASCIIPrintf(viewer, "Subspace Correction preconditioner with %d patches\n", patch->npatch);
    3238:   if(patch->local_composition_type == PC_COMPOSITE_MULTIPLICATIVE) {
    3239:     PetscViewerASCIIPrintf(viewer, "Schwarz type: multiplicative\n");
    3240:   } else {
    3241:     PetscViewerASCIIPrintf(viewer, "Schwarz type: additive\n");
    3242:   }
    3243:   if (patch->partition_of_unity) {PetscViewerASCIIPrintf(viewer, "Weighting by partition of unity\n");}
    3244:   else                           {PetscViewerASCIIPrintf(viewer, "Not weighting by partition of unity\n");}
    3245:   if (patch->symmetrise_sweep) {PetscViewerASCIIPrintf(viewer, "Symmetrising sweep (start->end, then end->start)\n");}
    3246:   else                         {PetscViewerASCIIPrintf(viewer, "Not symmetrising sweep\n");}
    3247:   if (!patch->precomputeElementTensors) {PetscViewerASCIIPrintf(viewer, "Not precomputing element tensors (overlapping cells rebuilt in every patch assembly)\n");}
    3248:   else                            {PetscViewerASCIIPrintf(viewer, "Precomputing element tensors (each cell assembled only once)\n");}
    3249:   if (!patch->save_operators) {PetscViewerASCIIPrintf(viewer, "Not saving patch operators (rebuilt every PCApply)\n");}
    3250:   else                        {PetscViewerASCIIPrintf(viewer, "Saving patch operators (rebuilt every PCSetUp)\n");}
    3251:   if (patch->patchconstructop == PCPatchConstruct_Star)       {PetscViewerASCIIPrintf(viewer, "Patch construction operator: star\n");}
    3252:   else if (patch->patchconstructop == PCPatchConstruct_Vanka) {PetscViewerASCIIPrintf(viewer, "Patch construction operator: Vanka\n");}
    3253:   else if (patch->patchconstructop == PCPatchConstruct_User)  {PetscViewerASCIIPrintf(viewer, "Patch construction operator: user-specified\n");}
    3254:   else                                                        {PetscViewerASCIIPrintf(viewer, "Patch construction operator: unknown\n");}

    3256:   if (patch->denseinverse) {
    3257:     PetscViewerASCIIPrintf(viewer, "Explicitly forming dense inverse and applying patch solver via MatMult.\n");
    3258:   } else {
    3259:     if (patch->isNonlinear) {
    3260:       PetscViewerASCIIPrintf(viewer, "SNES on patches (all same):\n");
    3261:     } else {
    3262:       PetscViewerASCIIPrintf(viewer, "KSP on patches (all same):\n");
    3263:     }
    3264:     if (patch->solver) {
    3265:       PetscViewerGetSubViewer(viewer, PETSC_COMM_SELF, &sviewer);
    3266:       if (!rank) {
    3267:         PetscViewerASCIIPushTab(sviewer);
    3268:         PetscObjectView(patch->solver[0], sviewer);
    3269:         PetscViewerASCIIPopTab(sviewer);
    3270:       }
    3271:       PetscViewerRestoreSubViewer(viewer, PETSC_COMM_SELF, &sviewer);
    3272:     } else {
    3273:       PetscViewerASCIIPushTab(viewer);
    3274:       PetscViewerASCIIPrintf(viewer, "Solver not yet set.\n");
    3275:       PetscViewerASCIIPopTab(viewer);
    3276:     }
    3277:   }
    3278:   PetscViewerASCIIPopTab(viewer);
    3279:   return(0);
    3280: }

    3282: /*MC
    3283:   PCPATCH - A PC object that encapsulates flexible definition of blocks for overlapping and non-overlapping
    3284:             small block additive preconditioners. Block definition is based on topology from
    3285:             a DM and equation numbering from a PetscSection.

    3287:   Options Database Keys:
    3288: + -pc_patch_cells_view   - Views the process local cell numbers for each patch
    3289: . -pc_patch_points_view  - Views the process local mesh point numbers for each patch
    3290: . -pc_patch_g2l_view     - Views the map between global dofs and patch local dofs for each patch
    3291: . -pc_patch_patches_view - Views the global dofs associated with each patch and its boundary
    3292: - -pc_patch_sub_mat_view - Views the matrix associated with each patch

    3294:   Level: intermediate

    3296: .seealso: PCType, PCCreate(), PCSetType()
    3297: M*/
    3298: PETSC_EXTERN PetscErrorCode PCCreate_Patch(PC pc)
    3299: {
    3300:   PC_PATCH      *patch;

    3304:   PetscNewLog(pc, &patch);

    3306:   if (patch->subspaces_to_exclude) {
    3307:     PetscHSetIDestroy(&patch->subspaces_to_exclude);
    3308:   }
    3309:   PetscHSetICreate(&patch->subspaces_to_exclude);

    3311:   patch->classname = "pc";
    3312:   patch->isNonlinear = PETSC_FALSE;

    3314:   /* Set some defaults */
    3315:   patch->combined           = PETSC_FALSE;
    3316:   patch->save_operators     = PETSC_TRUE;
    3317:   patch->local_composition_type = PC_COMPOSITE_ADDITIVE;
    3318:   patch->precomputeElementTensors = PETSC_FALSE;
    3319:   patch->partition_of_unity = PETSC_FALSE;
    3320:   patch->codim              = -1;
    3321:   patch->dim                = -1;
    3322:   patch->vankadim           = -1;
    3323:   patch->ignoredim          = -1;
    3324:   patch->pardecomp_overlap  = 0;
    3325:   patch->patchconstructop   = PCPatchConstruct_Star;
    3326:   patch->symmetrise_sweep   = PETSC_FALSE;
    3327:   patch->npatch             = 0;
    3328:   patch->userIS             = NULL;
    3329:   patch->optionsSet         = PETSC_FALSE;
    3330:   patch->iterationSet       = NULL;
    3331:   patch->user_patches       = PETSC_FALSE;
    3332:   PetscStrallocpy(MATDENSE, (char **) &patch->sub_mat_type);
    3333:   patch->viewPatches        = PETSC_FALSE;
    3334:   patch->viewCells          = PETSC_FALSE;
    3335:   patch->viewPoints         = PETSC_FALSE;
    3336:   patch->viewSection        = PETSC_FALSE;
    3337:   patch->viewMatrix         = PETSC_FALSE;
    3338:   patch->densesolve         = NULL;
    3339:   patch->setupsolver        = PCSetUp_PATCH_Linear;
    3340:   patch->applysolver        = PCApply_PATCH_Linear;
    3341:   patch->resetsolver        = PCReset_PATCH_Linear;
    3342:   patch->destroysolver      = PCDestroy_PATCH_Linear;
    3343:   patch->updatemultiplicative = PCUpdateMultiplicative_PATCH_Linear;
    3344:   patch->dofMappingWithoutToWithArtificial = NULL;
    3345:   patch->dofMappingWithoutToWithAll = NULL;

    3347:   pc->data                 = (void *) patch;
    3348:   pc->ops->apply           = PCApply_PATCH;
    3349:   pc->ops->applytranspose  = 0; /* PCApplyTranspose_PATCH; */
    3350:   pc->ops->setup           = PCSetUp_PATCH;
    3351:   pc->ops->reset           = PCReset_PATCH;
    3352:   pc->ops->destroy         = PCDestroy_PATCH;
    3353:   pc->ops->setfromoptions  = PCSetFromOptions_PATCH;
    3354:   pc->ops->setuponblocks   = PCSetUpOnBlocks_PATCH;
    3355:   pc->ops->view            = PCView_PATCH;
    3356:   pc->ops->applyrichardson = 0;

    3358:   return(0);
    3359: }