Date: 2021-03-03T22:26:49+00:00

Actual source code: plexadapt.c
petsc-3.14.5 2021-03-03
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      1: #include <petsc/private/dmpleximpl.h>
      2: #if defined(PETSC_HAVE_PRAGMATIC)
      3: #include <pragmatic/cpragmatic.h>
      4: #endif

      6: static PetscErrorCode DMPlexLabelToVolumeConstraint(DM dm, DMLabel adaptLabel, PetscInt cStart, PetscInt cEnd, PetscReal refRatio, PetscReal maxVolumes[])
      7: {
      8:   PetscInt       dim, c;

     12:   DMGetDimension(dm, &dim);
     13:   refRatio = refRatio == PETSC_DEFAULT ? (PetscReal) ((PetscInt) 1 << dim) : refRatio;
     14:   for (c = cStart; c < cEnd; c++) {
     15:     PetscReal vol;
     16:     PetscInt  closureSize = 0, cl;
     17:     PetscInt *closure     = NULL;
     18:     PetscBool anyRefine   = PETSC_FALSE;
     19:     PetscBool anyCoarsen  = PETSC_FALSE;
     20:     PetscBool anyKeep     = PETSC_FALSE;

     22:     DMPlexComputeCellGeometryFVM(dm, c, &vol, NULL, NULL);
     23:     maxVolumes[c - cStart] = vol;
     24:     DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
     25:     for (cl = 0; cl < closureSize*2; cl += 2) {
     26:       const PetscInt point = closure[cl];
     27:       PetscInt       refFlag;

     29:       DMLabelGetValue(adaptLabel, point, &refFlag);
     30:       switch (refFlag) {
     31:       case DM_ADAPT_REFINE:
     32:         anyRefine  = PETSC_TRUE;break;
     33:       case DM_ADAPT_COARSEN:
     34:         anyCoarsen = PETSC_TRUE;break;
     35:       case DM_ADAPT_KEEP:
     36:         anyKeep    = PETSC_TRUE;break;
     37:       case DM_ADAPT_DETERMINE:
     38:         break;
     39:       default:
     40:         SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP, "DMPlex does not support refinement flag %D\n", refFlag);
     41:       }
     42:       if (anyRefine) break;
     43:     }
     44:     DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);
     45:     if (anyRefine) {
     46:       maxVolumes[c - cStart] = vol / refRatio;
     47:     } else if (anyKeep) {
     48:       maxVolumes[c - cStart] = vol;
     49:     } else if (anyCoarsen) {
     50:       maxVolumes[c - cStart] = vol * refRatio;
     51:     }
     52:   }
     53:   return(0);
     54: }

     56: static PetscErrorCode DMPlexLabelToMetricConstraint(DM dm, DMLabel adaptLabel, PetscInt cStart, PetscInt cEnd, PetscInt vStart, PetscInt vEnd, PetscReal refRatio, Vec *metricVec)
     57: {
     58:   DM              udm, coordDM;
     59:   PetscSection    coordSection;
     60:   Vec             coordinates, mb, mx;
     61:   Mat             A;
     62:   PetscScalar    *metric, *eqns;
     63:   const PetscReal coarseRatio = refRatio == PETSC_DEFAULT ? PetscSqr(0.5) : 1/refRatio;
     64:   PetscInt        dim, Nv, Neq, c, v;
     65:   PetscErrorCode  ierr;

     68:   DMPlexUninterpolate(dm, &udm);
     69:   DMGetDimension(dm, &dim);
     70:   DMGetCoordinateDM(dm, &coordDM);
     71:   DMGetLocalSection(coordDM, &coordSection);
     72:   DMGetCoordinatesLocal(dm, &coordinates);
     73:   Nv   = vEnd - vStart;
     74:   VecCreateSeq(PETSC_COMM_SELF, Nv*PetscSqr(dim), metricVec);
     75:   VecGetArray(*metricVec, &metric);
     76:   Neq  = (dim*(dim+1))/2;
     77:   PetscMalloc1(PetscSqr(Neq), &eqns);
     78:   MatCreateSeqDense(PETSC_COMM_SELF, Neq, Neq, eqns, &A);
     79:   MatCreateVecs(A, &mx, &mb);
     80:   VecSet(mb, 1.0);
     81:   for (c = cStart; c < cEnd; ++c) {
     82:     const PetscScalar *sol;
     83:     PetscScalar       *cellCoords = NULL;
     84:     PetscReal          e[3], vol;
     85:     const PetscInt    *cone;
     86:     PetscInt           coneSize, cl, i, j, d, r;

     88:     DMPlexVecGetClosure(dm, coordSection, coordinates, c, NULL, &cellCoords);
     89:     /* Only works for simplices */
     90:     for (i = 0, r = 0; i < dim+1; ++i) {
     91:       for (j = 0; j < i; ++j, ++r) {
     92:         for (d = 0; d < dim; ++d) e[d] = PetscRealPart(cellCoords[i*dim+d] - cellCoords[j*dim+d]);
     93:         /* FORTRAN ORDERING */
     94:         switch (dim) {
     95:         case 2:
     96:           eqns[0*Neq+r] = PetscSqr(e[0]);
     97:           eqns[1*Neq+r] = 2.0*e[0]*e[1];
     98:           eqns[2*Neq+r] = PetscSqr(e[1]);
     99:           break;
    100:         case 3:
    101:           eqns[0*Neq+r] = PetscSqr(e[0]);
    102:           eqns[1*Neq+r] = 2.0*e[0]*e[1];
    103:           eqns[2*Neq+r] = 2.0*e[0]*e[2];
    104:           eqns[3*Neq+r] = PetscSqr(e[1]);
    105:           eqns[4*Neq+r] = 2.0*e[1]*e[2];
    106:           eqns[5*Neq+r] = PetscSqr(e[2]);
    107:           break;
    108:         }
    109:       }
    110:     }
    111:     MatSetUnfactored(A);
    112:     DMPlexVecRestoreClosure(dm, coordSection, coordinates, c, NULL, &cellCoords);
    113:     MatLUFactor(A, NULL, NULL, NULL);
    114:     MatSolve(A, mb, mx);
    115:     VecGetArrayRead(mx, &sol);
    116:     DMPlexComputeCellGeometryFVM(dm, c, &vol, NULL, NULL);
    117:     DMPlexGetCone(udm, c, &cone);
    118:     DMPlexGetConeSize(udm, c, &coneSize);
    119:     for (cl = 0; cl < coneSize; ++cl) {
    120:       const PetscInt v = cone[cl] - vStart;

    122:       if (dim == 2) {
    123:         metric[v*4+0] += vol*coarseRatio*sol[0];
    124:         metric[v*4+1] += vol*coarseRatio*sol[1];
    125:         metric[v*4+2] += vol*coarseRatio*sol[1];
    126:         metric[v*4+3] += vol*coarseRatio*sol[2];
    127:       } else {
    128:         metric[v*9+0] += vol*coarseRatio*sol[0];
    129:         metric[v*9+1] += vol*coarseRatio*sol[1];
    130:         metric[v*9+3] += vol*coarseRatio*sol[1];
    131:         metric[v*9+2] += vol*coarseRatio*sol[2];
    132:         metric[v*9+6] += vol*coarseRatio*sol[2];
    133:         metric[v*9+4] += vol*coarseRatio*sol[3];
    134:         metric[v*9+5] += vol*coarseRatio*sol[4];
    135:         metric[v*9+7] += vol*coarseRatio*sol[4];
    136:         metric[v*9+8] += vol*coarseRatio*sol[5];
    137:       }
    138:     }
    139:     VecRestoreArrayRead(mx, &sol);
    140:   }
    141:   for (v = 0; v < Nv; ++v) {
    142:     const PetscInt *support;
    143:     PetscInt        supportSize, s;
    144:     PetscReal       vol, totVol = 0.0;

    146:     DMPlexGetSupport(udm, v+vStart, &support);
    147:     DMPlexGetSupportSize(udm, v+vStart, &supportSize);
    148:     for (s = 0; s < supportSize; ++s) {DMPlexComputeCellGeometryFVM(dm, support[s], &vol, NULL, NULL); totVol += vol;}
    149:     for (s = 0; s < PetscSqr(dim); ++s) metric[v*PetscSqr(dim)+s] /= totVol;
    150:   }
    151:   PetscFree(eqns);
    152:   VecRestoreArray(*metricVec, &metric);
    153:   VecDestroy(&mx);
    154:   VecDestroy(&mb);
    155:   MatDestroy(&A);
    156:   DMDestroy(&udm);
    157:   return(0);
    158: }

    160: /*
    161:    Contains the list of registered DMPlexGenerators routines
    162: */
    163: extern PetscFunctionList DMPlexGenerateList;

    165: struct _n_PetscFunctionList {
    166:   PetscErrorCode    (*generate)(DM, PetscBool, DM*);
    167:   PetscErrorCode    (*refine)(DM,PetscReal*, DM*);
    168:   char              *name;               /* string to identify routine */
    169:   PetscInt          dim;
    170:   PetscFunctionList next;                /* next pointer */
    171: };

    173: PetscErrorCode DMPlexRefine_Internal(DM dm, DMLabel adaptLabel, DM *dmRefined)
    174: {
    175:   PetscErrorCode    (*refinementFunc)(const PetscReal [], PetscReal *);
    176:   PetscReal         refinementLimit;
    177:   PetscInt          dim, cStart, cEnd;
    178:   char              genname[1024], *name = NULL;
    179:   PetscBool         flg, localized;
    180:   PetscErrorCode    ierr;
    181:   PetscErrorCode    (*refine)(DM,PetscReal*,DM*);
    182:   PetscFunctionList fl;
    183:   PetscReal         *maxVolumes;
    184:   PetscInt          c;

    187:   DMGetCoordinatesLocalized(dm, &localized);
    188:   DMPlexGetRefinementLimit(dm, &refinementLimit);
    189:   DMPlexGetRefinementFunction(dm, &refinementFunc);
    190:   if (refinementLimit == 0.0 && !refinementFunc && !adaptLabel) return(0);
    191:   DMGetDimension(dm, &dim);
    192:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
    193:   PetscOptionsGetString(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_generator", genname, sizeof(genname), &flg);
    194:   if (flg) name = genname;

    196:   fl = DMPlexGenerateList;
    197:   if (name) {
    198:     while (fl) {
    199:       PetscStrcmp(fl->name,name,&flg);
    200:       if (flg) {
    201:         refine = fl->refine;
    202:         goto gotit;
    203:       }
    204:       fl = fl->next;
    205:     }
    206:     SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Grid refiner %s not registered",name);
    207:   } else {
    208:     while (fl) {
    209:       if (dim-1 == fl->dim) {
    210:         refine = fl->refine;
    211:         goto gotit;
    212:       }
    213:       fl = fl->next;
    214:     }
    215:     SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"No grid refiner of dimension %D registered",dim);
    216:   }

    218:   gotit: switch (dim) {
    219:   case 2:
    220:       PetscMalloc1(cEnd - cStart, &maxVolumes);
    221:       if (adaptLabel) {
    222:         DMPlexLabelToVolumeConstraint(dm, adaptLabel, cStart, cEnd, PETSC_DEFAULT, maxVolumes);
    223:       } else if (refinementFunc) {
    224:         for (c = cStart; c < cEnd; ++c) {
    225:           PetscReal vol, centroid[3];
    226:           PetscReal maxVol;

    228:           DMPlexComputeCellGeometryFVM(dm, c, &vol, centroid, NULL);
    229:           (*refinementFunc)(centroid, &maxVol);
    230:           maxVolumes[c - cStart] = (double) maxVol;
    231:         }
    232:       } else {
    233:         for (c = 0; c < cEnd-cStart; ++c) maxVolumes[c] = refinementLimit;
    234:       }
    235:       (*refine)(dm, maxVolumes, dmRefined);
    236:       PetscFree(maxVolumes);
    237:     break;
    238:   case 3:
    239:       PetscMalloc1(cEnd - cStart, &maxVolumes);
    240:       if (adaptLabel) {
    241:         DMPlexLabelToVolumeConstraint(dm, adaptLabel, cStart, cEnd, PETSC_DEFAULT, maxVolumes);
    242:       } else if (refinementFunc) {
    243:         for (c = cStart; c < cEnd; ++c) {
    244:           PetscReal vol, centroid[3];

    246:           DMPlexComputeCellGeometryFVM(dm, c, &vol, centroid, NULL);
    247:           (*refinementFunc)(centroid, &maxVolumes[c-cStart]);
    248:         }
    249:       } else {
    250:         for (c = 0; c < cEnd-cStart; ++c) maxVolumes[c] = refinementLimit;
    251:       }
    252:       (*refine)(dm, maxVolumes, dmRefined);
    253:       PetscFree(maxVolumes);
    254:     break;
    255:   default:
    256:     SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Mesh refinement in dimension %D is not supported.", dim);
    257:   }
    258:   DMCopyBoundary(dm, *dmRefined);
    259:   if (localized) {DMLocalizeCoordinates(*dmRefined);}
    260:   return(0);
    261: }

    263: PetscErrorCode DMPlexCoarsen_Internal(DM dm, DMLabel adaptLabel, DM *dmCoarsened)
    264: {
    265:   Vec            metricVec;
    266:   PetscInt       cStart, cEnd, vStart, vEnd;
    267:   DMLabel        bdLabel = NULL;
    268:   char           bdLabelName[PETSC_MAX_PATH_LEN];
    269:   PetscBool      localized, flg;

    273:   DMGetCoordinatesLocalized(dm, &localized);
    274:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
    275:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
    276:   DMPlexLabelToMetricConstraint(dm, adaptLabel, cStart, cEnd, vStart, vEnd, PETSC_DEFAULT, &metricVec);
    277:   PetscOptionsGetString(NULL, dm->hdr.prefix, "-dm_plex_coarsen_bd_label", bdLabelName, sizeof(bdLabelName), &flg);
    278:   if (flg) {DMGetLabel(dm, bdLabelName, &bdLabel);}
    279:   DMAdaptMetric_Plex(dm, metricVec, bdLabel, dmCoarsened);
    280:   VecDestroy(&metricVec);
    281:   if (localized) {DMLocalizeCoordinates(*dmCoarsened);}
    282:   return(0);
    283: }

    285: PetscErrorCode DMAdaptLabel_Plex(DM dm, DMLabel adaptLabel, DM *dmAdapted)
    286: {
    287:   IS              flagIS;
    288:   const PetscInt *flags;
    289:   PetscInt        defFlag, minFlag, maxFlag, numFlags, f;
    290:   PetscErrorCode  ierr;

    293:   DMLabelGetDefaultValue(adaptLabel, &defFlag);
    294:   minFlag = defFlag;
    295:   maxFlag = defFlag;
    296:   DMLabelGetValueIS(adaptLabel, &flagIS);
    297:   ISGetLocalSize(flagIS, &numFlags);
    298:   ISGetIndices(flagIS, &flags);
    299:   for (f = 0; f < numFlags; ++f) {
    300:     const PetscInt flag = flags[f];

    302:     minFlag = PetscMin(minFlag, flag);
    303:     maxFlag = PetscMax(maxFlag, flag);
    304:   }
    305:   ISRestoreIndices(flagIS, &flags);
    306:   ISDestroy(&flagIS);
    307:   {
    308:     PetscInt minMaxFlag[2], minMaxFlagGlobal[2];

    310:     minMaxFlag[0] =  minFlag;
    311:     minMaxFlag[1] = -maxFlag;
    312:     MPI_Allreduce(minMaxFlag, minMaxFlagGlobal, 2, MPIU_INT, MPI_MIN, PetscObjectComm((PetscObject)dm));
    313:     minFlag =  minMaxFlagGlobal[0];
    314:     maxFlag = -minMaxFlagGlobal[1];
    315:   }
    316:   if (minFlag == maxFlag) {
    317:     switch (minFlag) {
    318:     case DM_ADAPT_DETERMINE:
    319:       *dmAdapted = NULL;break;
    320:     case DM_ADAPT_REFINE:
    321:       DMPlexSetRefinementUniform(dm, PETSC_TRUE);
    322:       DMRefine(dm, MPI_COMM_NULL, dmAdapted);break;
    323:     case DM_ADAPT_COARSEN:
    324:       DMCoarsen(dm, MPI_COMM_NULL, dmAdapted);break;
    325:     default:
    326:       SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_SUP,"DMPlex does not support refinement flag %D\n", minFlag);
    327:     }
    328:   } else {
    329:     DMPlexSetRefinementUniform(dm, PETSC_FALSE);
    330:     DMPlexRefine_Internal(dm, adaptLabel, dmAdapted);
    331:   }
    332:   return(0);
    333: }

    335: /*
    336:   DMAdaptMetric_Plex - Generates a new mesh conforming to a metric field.

    338:   Input Parameters:
    339: + dm - The DM object
    340: . vertexMetric - The metric to which the mesh is adapted, defined vertex-wise in a LOCAL vector
    341: - bdLabel - Label for boundary tags which are preserved in dmNew, or NULL. Should not be named "_boundary_".

    343:   Output Parameter:
    344: . dmNew  - the new DM

    346:   Level: advanced

    348: .seealso: DMCoarsen(), DMRefine()
    349: */
    350: PetscErrorCode DMAdaptMetric_Plex(DM dm, Vec vertexMetric, DMLabel bdLabel, DM *dmNew)
    351: {
    352: #if defined(PETSC_HAVE_PRAGMATIC)
    353:   MPI_Comm           comm;
    354:   const char        *bdName = "_boundary_";
    355: #if 0
    356:   DM                 odm = dm;
    357: #endif
    358:   DM                 udm, cdm;
    359:   DMLabel            bdLabelFull;
    360:   const char        *bdLabelName;
    361:   IS                 bdIS, globalVertexNum;
    362:   PetscSection       coordSection;
    363:   Vec                coordinates;
    364:   const PetscScalar *coords, *met;
    365:   const PetscInt    *bdFacesFull, *gV;
    366:   PetscInt          *bdFaces, *bdFaceIds, *l2gv;
    367:   PetscReal         *x, *y, *z, *metric;
    368:   PetscInt          *cells;
    369:   PetscInt           dim, cStart, cEnd, numCells, c, coff, vStart, vEnd, numVertices, numLocVertices, v;
    370:   PetscInt           off, maxConeSize, numBdFaces, f, bdSize;
    371:   PetscBool          flg;
    372:   DMLabel            bdLabelNew;
    373:   PetscReal         *coordsNew;
    374:   PetscInt          *bdTags;
    375:   PetscReal         *xNew[3] = {NULL, NULL, NULL};
    376:   PetscInt          *cellsNew;
    377:   PetscInt           d, numCellsNew, numVerticesNew;
    378:   PetscInt           numCornersNew, fStart, fEnd;
    379:   PetscMPIInt        numProcs;
    380:   PetscErrorCode     ierr;

    383:   /* Check for FEM adjacency flags */
    384:   PetscObjectGetComm((PetscObject) dm, &comm);
    385:   MPI_Comm_size(comm, &numProcs);
    386:   if (bdLabel) {
    387:     PetscObjectGetName((PetscObject) bdLabel, &bdLabelName);
    388:     PetscStrcmp(bdLabelName, bdName, &flg);
    389:     if (flg) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "\"%s\" cannot be used as label for boundary facets", bdLabelName);
    390:   }
    391:   /* Add overlap for Pragmatic */
    392: #if 0
    393:   /* Check for overlap by looking for cell in the SF */
    394:   if (!overlapped) {
    395:     DMPlexDistributeOverlap(odm, 1, NULL, &dm);
    396:     if (!dm) {dm = odm; PetscObjectReference((PetscObject) dm);}
    397:   }
    398: #endif
    399:   /* Get mesh information */
    400:   DMGetDimension(dm, &dim);
    401:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
    402:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
    403:   DMPlexUninterpolate(dm, &udm);
    404:   DMPlexGetMaxSizes(udm, &maxConeSize, NULL);
    405:   numCells    = cEnd - cStart;
    406:   numVertices = vEnd - vStart;
    407:   PetscCalloc5(numVertices, &x, numVertices, &y, numVertices, &z, numVertices*PetscSqr(dim), &metric, numCells*maxConeSize, &cells);
    408:   for (c = 0, coff = 0; c < numCells; ++c) {
    409:     const PetscInt *cone;
    410:     PetscInt        coneSize, cl;

    412:     DMPlexGetConeSize(udm, c, &coneSize);
    413:     DMPlexGetCone(udm, c, &cone);
    414:     for (cl = 0; cl < coneSize; ++cl) cells[coff++] = cone[cl] - vStart;
    415:   }
    416:   PetscCalloc1(numVertices, &l2gv);
    417:   DMPlexGetVertexNumbering(udm, &globalVertexNum);
    418:   ISGetIndices(globalVertexNum, &gV);
    419:   for (v = 0, numLocVertices = 0; v < numVertices; ++v) {
    420:     if (gV[v] >= 0) ++numLocVertices;
    421:     l2gv[v] = gV[v] < 0 ? -(gV[v]+1) : gV[v];
    422:   }
    423:   ISRestoreIndices(globalVertexNum, &gV);
    424:   DMDestroy(&udm);
    425:   DMGetCoordinateDM(dm, &cdm);
    426:   DMGetLocalSection(cdm, &coordSection);
    427:   DMGetCoordinatesLocal(dm, &coordinates);
    428:   VecGetArrayRead(coordinates, &coords);
    429:   for (v = vStart; v < vEnd; ++v) {
    430:     PetscSectionGetOffset(coordSection, v, &off);
    431:     x[v-vStart] = PetscRealPart(coords[off+0]);
    432:     if (dim > 1) y[v-vStart] = PetscRealPart(coords[off+1]);
    433:     if (dim > 2) z[v-vStart] = PetscRealPart(coords[off+2]);
    434:   }
    435:   VecRestoreArrayRead(coordinates, &coords);
    436:   /* Get boundary mesh */
    437:   DMLabelCreate(PETSC_COMM_SELF, bdName, &bdLabelFull);
    438:   DMPlexMarkBoundaryFaces(dm, 1, bdLabelFull);
    439:   DMLabelGetStratumIS(bdLabelFull, 1, &bdIS);
    440:   DMLabelGetStratumSize(bdLabelFull, 1, &numBdFaces);
    441:   ISGetIndices(bdIS, &bdFacesFull);
    442:   for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
    443:     PetscInt *closure = NULL;
    444:     PetscInt  closureSize, cl;

    446:     DMPlexGetTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure);
    447:     for (cl = 0; cl < closureSize*2; cl += 2) {
    448:       if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) ++bdSize;
    449:     }
    450:     DMPlexRestoreTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure);
    451:   }
    452:   PetscMalloc2(bdSize, &bdFaces, numBdFaces, &bdFaceIds);
    453:   for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
    454:     PetscInt *closure = NULL;
    455:     PetscInt  closureSize, cl;

    457:     DMPlexGetTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure);
    458:     for (cl = 0; cl < closureSize*2; cl += 2) {
    459:       if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) bdFaces[bdSize++] = closure[cl] - vStart;
    460:     }
    461:     DMPlexRestoreTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure);
    462:     if (bdLabel) {DMLabelGetValue(bdLabel, bdFacesFull[f], &bdFaceIds[f]);}
    463:     else         {bdFaceIds[f] = 1;}
    464:   }
    465:   ISDestroy(&bdIS);
    466:   DMLabelDestroy(&bdLabelFull);
    467:   /* Get metric */
    468:   VecViewFromOptions(vertexMetric, NULL, "-adapt_metric_view");
    469:   VecGetArrayRead(vertexMetric, &met);
    470:   for (v = 0; v < (vEnd-vStart)*PetscSqr(dim); ++v) metric[v] = PetscRealPart(met[v]);
    471:   VecRestoreArrayRead(vertexMetric, &met);
    472: #if 0
    473:   /* Destroy overlap mesh */
    474:   DMDestroy(&dm);
    475: #endif
    476:   /* Create new mesh */
    477:   switch (dim) {
    478:   case 2:
    479:     pragmatic_2d_mpi_init(&numVertices, &numCells, cells, x, y, l2gv, numLocVertices, comm);break;
    480:   case 3:
    481:     pragmatic_3d_mpi_init(&numVertices, &numCells, cells, x, y, z, l2gv, numLocVertices, comm);break;
    482:   default: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic adaptation defined for dimension %D", dim);
    483:   }
    484:   pragmatic_set_boundary(&numBdFaces, bdFaces, bdFaceIds);
    485:   pragmatic_set_metric(metric);
    486:   pragmatic_adapt(((DM_Plex *) dm->data)->remeshBd ? 1 : 0);
    487:   PetscFree(l2gv);
    488:   /* Read out mesh */
    489:   pragmatic_get_info_mpi(&numVerticesNew, &numCellsNew);
    490:   PetscMalloc1(numVerticesNew*dim, &coordsNew);
    491:   switch (dim) {
    492:   case 2:
    493:     numCornersNew = 3;
    494:     PetscMalloc2(numVerticesNew, &xNew[0], numVerticesNew, &xNew[1]);
    495:     pragmatic_get_coords_2d_mpi(xNew[0], xNew[1]);
    496:     break;
    497:   case 3:
    498:     numCornersNew = 4;
    499:     PetscMalloc3(numVerticesNew, &xNew[0], numVerticesNew, &xNew[1], numVerticesNew, &xNew[2]);
    500:     pragmatic_get_coords_3d_mpi(xNew[0], xNew[1], xNew[2]);
    501:     break;
    502:   default:
    503:     SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic adaptation defined for dimension %D", dim);
    504:   }
    505:   for (v = 0; v < numVerticesNew; ++v) {for (d = 0; d < dim; ++d) coordsNew[v*dim+d] = xNew[d][v];}
    506:   PetscMalloc1(numCellsNew*(dim+1), &cellsNew);
    507:   pragmatic_get_elements(cellsNew);
    508:   DMPlexCreateFromCellListParallelPetsc(comm, dim, numCellsNew, numVerticesNew, PETSC_DECIDE, numCornersNew, PETSC_TRUE, cellsNew, dim, coordsNew, NULL, dmNew);
    509:   /* Read out boundary label */
    510:   pragmatic_get_boundaryTags(&bdTags);
    511:   DMCreateLabel(*dmNew, bdLabel ? bdLabelName : bdName);
    512:   DMGetLabel(*dmNew, bdLabel ? bdLabelName : bdName, &bdLabelNew);
    513:   DMPlexGetHeightStratum(*dmNew, 0, &cStart, &cEnd);
    514:   DMPlexGetHeightStratum(*dmNew, 1, &fStart, &fEnd);
    515:   DMPlexGetDepthStratum(*dmNew, 0, &vStart, &vEnd);
    516:   for (c = cStart; c < cEnd; ++c) {
    517:     /* Only for simplicial meshes */
    518:     coff = (c-cStart)*(dim+1);
    519:     /* d is the local cell number of the vertex opposite to the face we are marking */
    520:     for (d = 0; d < dim+1; ++d) {
    521:       if (bdTags[coff+d]) {
    522:         const PetscInt  perm[4][4] = {{-1, -1, -1, -1}, {-1, -1, -1, -1}, {1, 2, 0, -1}, {3, 2, 1, 0}}; /* perm[d] = face opposite */
    523:         const PetscInt *cone;

    525:         /* Mark face opposite to this vertex: This pattern is specified in DMPlexGetRawFaces_Internal() */
    526:         DMPlexGetCone(*dmNew, c, &cone);
    527:         DMLabelSetValue(bdLabelNew, cone[perm[dim][d]], bdTags[coff+d]);
    528:       }
    529:     }
    530:   }
    531:   /* Cleanup */
    532:   switch (dim) {
    533:   case 2: PetscFree2(xNew[0], xNew[1]);break;
    534:   case 3: PetscFree3(xNew[0], xNew[1], xNew[2]);break;
    535:   }
    536:   PetscFree(cellsNew);
    537:   PetscFree5(x, y, z, metric, cells);
    538:   PetscFree2(bdFaces, bdFaceIds);
    539:   PetscFree(coordsNew);
    540:   pragmatic_finalize();
    541:   return(0);
    542: #else
    544:   SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Remeshing needs external package support.\nPlease reconfigure with --download-pragmatic.");
    545: #endif
    546: }