Date: 2016-07-24T17:00:32+00:00

Actual source code: plexreorder.c
petsc-3.7.3 2016-07-24
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      1: #include <petsc/private/dmpleximpl.h>   /*I      "petscdmplex.h"   I*/
      2: #include <petsc/private/matorderimpl.h> /*I      "petscmat.h"      I*/

      6: PetscErrorCode DMPlexCreateOrderingClosure_Static(DM dm, PetscInt numPoints, const PetscInt pperm[], PetscInt **clperm, PetscInt **invclperm)
      7: {
      8:   PetscInt      *perm, *iperm;
      9:   PetscInt       depth, d, pStart, pEnd, fStart, fMax, fEnd, p;

     13:   DMPlexGetDepth(dm, &depth);
     14:   DMPlexGetChart(dm, &pStart, &pEnd);
     15:   PetscMalloc1(pEnd-pStart,&perm);
     16:   PetscMalloc1(pEnd-pStart,&iperm);
     17:   for (p = pStart; p < pEnd; ++p) iperm[p] = -1;
     18:   for (d = depth; d > 0; --d) {
     19:     DMPlexGetDepthStratum(dm, d,   &pStart, &pEnd);
     20:     DMPlexGetDepthStratum(dm, d-1, &fStart, &fEnd);
     21:     fMax = fStart;
     22:     for (p = pStart; p < pEnd; ++p) {
     23:       const PetscInt *cone;
     24:       PetscInt        point, coneSize, c;

     26:       if (d == depth) {
     27:         perm[p]         = pperm[p];
     28:         iperm[pperm[p]] = p;
     29:       }
     30:       point = perm[p];
     31:       DMPlexGetConeSize(dm, point, &coneSize);
     32:       DMPlexGetCone(dm, point, &cone);
     33:       for (c = 0; c < coneSize; ++c) {
     34:         const PetscInt oldc = cone[c];
     35:         const PetscInt newc = iperm[oldc];

     37:         if (newc < 0) {
     38:           perm[fMax]  = oldc;
     39:           iperm[oldc] = fMax++;
     40:         }
     41:       }
     42:     }
     43:     if (fMax != fEnd) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of depth %d faces %d does not match permuted nubmer %d", d, fEnd-fStart, fMax-fStart);
     44:   }
     45:   *clperm    = perm;
     46:   *invclperm = iperm;
     47:   return(0);
     48: }

     52: /*@
     53:   DMPlexGetOrdering - Calculate a reordering of the mesh

     55:   Collective on DM

     57:   Input Parameter:
     58: + dm - The DMPlex object
     59: . otype - type of reordering, one of the following:
     60: $     MATORDERINGNATURAL - Natural
     61: $     MATORDERINGND - Nested Dissection
     62: $     MATORDERING1WD - One-way Dissection
     63: $     MATORDERINGRCM - Reverse Cuthill-McKee
     64: $     MATORDERINGQMD - Quotient Minimum Degree
     65: - label - [Optional] Label used to segregate ordering into sets, or NULL

     68:   Output Parameter:
     69: . perm - The point permutation as an IS, perm[old point number] = new point number

     71:   Note: The label is used to group sets of points together by label value. This makes it easy to reorder a mesh which
     72:   has different types of cells, and then loop over each set of reordered cells for assembly.

     74:   Level: intermediate

     76: .keywords: mesh
     77: .seealso: MatGetOrdering()
     78: @*/
     79: PetscErrorCode DMPlexGetOrdering(DM dm, MatOrderingType otype, DMLabel label, IS *perm)
     80: {
     81:   PetscInt       numCells = 0;
     82:   PetscInt      *start = NULL, *adjacency = NULL, *cperm, *clperm, *invclperm, *mask, *xls, pStart, pEnd, c, i;

     88:   DMPlexCreateNeighborCSR(dm, 0, &numCells, &start, &adjacency);
     89:   PetscMalloc3(numCells,&cperm,numCells,&mask,numCells*2,&xls);
     90:   if (numCells) {
     91:     /* Shift for Fortran numbering */
     92:     for (i = 0; i < start[numCells]; ++i) ++adjacency[i];
     93:     for (i = 0; i <= numCells; ++i)       ++start[i];
     94:     SPARSEPACKgenrcm(&numCells, start, adjacency, cperm, mask, xls);
     95:   }
     96:   PetscFree(start);
     97:   PetscFree(adjacency);
     98:   /* Shift for Fortran numbering */
     99:   for (c = 0; c < numCells; ++c) --cperm[c];
    100:   /* Segregate */
    101:   if (label) {
    102:     IS              valueIS;
    103:     const PetscInt *values;
    104:     PetscInt        numValues, numPoints = 0;
    105:     PetscInt       *sperm, *vsize, *voff, v;

    107:     DMLabelGetValueIS(label, &valueIS);
    108:     ISGetLocalSize(valueIS, &numValues);
    109:     ISGetIndices(valueIS, &values);
    110:     PetscCalloc3(numCells,&sperm,numValues,&vsize,numValues+1,&voff);
    111:     for (v = 0; v < numValues; ++v) {
    112:       DMLabelGetStratumSize(label, values[v], &vsize[v]);
    113:       if (v < numValues-1) voff[v+2] += vsize[v] + voff[v+1];
    114:       numPoints += vsize[v];
    115:     }
    116:     if (numPoints != numCells) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Label only covers %D cells < %D total", numPoints, numCells);
    117:     for (c = 0; c < numCells; ++c) {
    118:       const PetscInt oldc = cperm[c];
    119:       PetscInt       val, vloc;

    121:       DMLabelGetValue(label, oldc, &val);
    122:       if (val == -1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Cell %D not present in label", oldc);
    123:       PetscFindInt(val, numValues, values, &vloc);
    124:       if (vloc < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Value %D not present label", val);
    125:       sperm[voff[vloc+1]++] = oldc;
    126:     }
    127:     for (v = 0; v < numValues; ++v) {
    128:       if (voff[v+1] - voff[v] != vsize[v]) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of %D values found is %D != %D", values[v], voff[v+1] - voff[v], vsize[v]);
    129:     }
    130:     ISRestoreIndices(valueIS, &values);
    131:     ISDestroy(&valueIS);
    132:     PetscMemcpy(cperm, sperm, numCells * sizeof(PetscInt));
    133:     PetscFree3(sperm, vsize, voff);
    134:   }
    135:   /* Construct closure */
    136:   DMPlexCreateOrderingClosure_Static(dm, numCells, cperm, &clperm, &invclperm);
    137:   PetscFree3(cperm,mask,xls);
    138:   PetscFree(clperm);
    139:   /* Invert permutation */
    140:   DMPlexGetChart(dm, &pStart, &pEnd);
    141:   ISCreateGeneral(PetscObjectComm((PetscObject) dm), pEnd-pStart, invclperm, PETSC_OWN_POINTER, perm);
    142:   return(0);
    143: }

    147: /*@
    148:   DMPlexPermute - Reorder the mesh according to the input permutation

    150:   Collective on DM

    152:   Input Parameter:
    153: + dm - The DMPlex object
    154: - perm - The point permutation, perm[old point number] = new point number

    156:   Output Parameter:
    157: . pdm - The permuted DM

    159:   Level: intermediate

    161: .keywords: mesh
    162: .seealso: MatPermute()
    163: @*/
    164: PetscErrorCode DMPlexPermute(DM dm, IS perm, DM *pdm)
    165: {
    166:   DM_Plex       *plex = (DM_Plex *) dm->data, *plexNew;
    167:   PetscSection   section, sectionNew;
    168:   PetscInt       dim;

    175:   DMCreate(PetscObjectComm((PetscObject) dm), pdm);
    176:   DMSetType(*pdm, DMPLEX);
    177:   DMGetDimension(dm, &dim);
    178:   DMSetDimension(*pdm, dim);
    179:   DMGetDefaultSection(dm, &section);
    180:   if (section) {
    181:     PetscSectionPermute(section, perm, &sectionNew);
    182:     DMSetDefaultSection(*pdm, sectionNew);
    183:     PetscSectionDestroy(&sectionNew);
    184:   }
    185:   plexNew = (DM_Plex *) (*pdm)->data;
    186:   /* Ignore ltogmap, ltogmapb */
    187:   /* Ignore sf, defaultSF */
    188:   /* Ignore globalVertexNumbers, globalCellNumbers */
    189:   /* Remap coordinates */
    190:   {
    191:     DM              cdm, cdmNew;
    192:     PetscSection    csection, csectionNew;
    193:     Vec             coordinates, coordinatesNew;
    194:     PetscScalar    *coords, *coordsNew;
    195:     const PetscInt *pperm;
    196:     PetscInt        pStart, pEnd, p;
    197:     const char     *name;

    199:     DMGetCoordinateDM(dm, &cdm);
    200:     DMGetDefaultSection(cdm, &csection);
    201:     PetscSectionPermute(csection, perm, &csectionNew);
    202:     DMGetCoordinatesLocal(dm, &coordinates);
    203:     VecDuplicate(coordinates, &coordinatesNew);
    204:     PetscObjectGetName((PetscObject)coordinates,&name);
    205:     PetscObjectSetName((PetscObject)coordinatesNew,name);
    206:     VecGetArray(coordinates, &coords);
    207:     VecGetArray(coordinatesNew, &coordsNew);
    208:     PetscSectionGetChart(csectionNew, &pStart, &pEnd);
    209:     ISGetIndices(perm, &pperm);
    210:     for (p = pStart; p < pEnd; ++p) {
    211:       PetscInt dof, off, offNew, d;

    213:       PetscSectionGetDof(csectionNew, p, &dof);
    214:       PetscSectionGetOffset(csection, p, &off);
    215:       PetscSectionGetOffset(csectionNew, pperm[p], &offNew);
    216:       for (d = 0; d < dof; ++d) coordsNew[offNew+d] = coords[off+d];
    217:     }
    218:     ISRestoreIndices(perm, &pperm);
    219:     VecRestoreArray(coordinates, &coords);
    220:     VecRestoreArray(coordinatesNew, &coordsNew);
    221:     DMGetCoordinateDM(*pdm, &cdmNew);
    222:     DMSetDefaultSection(cdmNew, csectionNew);
    223:     DMSetCoordinatesLocal(*pdm, coordinatesNew);
    224:     PetscSectionDestroy(&csectionNew);
    225:     VecDestroy(&coordinatesNew);
    226:   }
    227:   /* Reorder labels */
    228:   {
    229:     PetscInt numLabels, l;
    230:     DMLabel  label, labelNew;

    232:     DMGetNumLabels(dm, &numLabels);
    233:     for (l = numLabels-1; l >= 0; --l) {
    234:       DMGetLabelByNum(dm, l, &label);
    235:       DMLabelPermute(label, perm, &labelNew);
    236:       DMAddLabel(*pdm, labelNew);
    237:     }
    238:     if (plex->subpointMap) {DMLabelPermute(plex->subpointMap, perm, &plexNew->subpointMap);}
    239:   }
    240:   /* Reorder topology */
    241:   {
    242:     const PetscInt *pperm;
    243:     PetscInt        maxConeSize, maxSupportSize, n, pStart, pEnd, p;

    245:     DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);
    246:     plexNew->maxConeSize    = maxConeSize;
    247:     plexNew->maxSupportSize = maxSupportSize;
    248:     PetscSectionDestroy(&plexNew->coneSection);
    249:     PetscSectionPermute(plex->coneSection, perm, &plexNew->coneSection);
    250:     PetscSectionGetStorageSize(plexNew->coneSection, &n);
    251:     PetscMalloc1(n, &plexNew->cones);
    252:     PetscMalloc1(n, &plexNew->coneOrientations);
    253:     ISGetIndices(perm, &pperm);
    254:     PetscSectionGetChart(plex->coneSection, &pStart, &pEnd);
    255:     for (p = pStart; p < pEnd; ++p) {
    256:       PetscInt dof, off, offNew, d;

    258:       PetscSectionGetDof(plexNew->coneSection, pperm[p], &dof);
    259:       PetscSectionGetOffset(plex->coneSection, p, &off);
    260:       PetscSectionGetOffset(plexNew->coneSection, pperm[p], &offNew);
    261:       for (d = 0; d < dof; ++d) {
    262:         plexNew->cones[offNew+d]            = pperm[plex->cones[off+d]];
    263:         plexNew->coneOrientations[offNew+d] = plex->coneOrientations[off+d];
    264:       }
    265:     }
    266:     PetscSectionDestroy(&plexNew->supportSection);
    267:     PetscSectionPermute(plex->supportSection, perm, &plexNew->supportSection);
    268:     PetscSectionGetStorageSize(plexNew->supportSection, &n);
    269:     PetscMalloc1(n, &plexNew->supports);
    270:     PetscSectionGetChart(plex->supportSection, &pStart, &pEnd);
    271:     for (p = pStart; p < pEnd; ++p) {
    272:       PetscInt dof, off, offNew, d;

    274:       PetscSectionGetDof(plexNew->supportSection, pperm[p], &dof);
    275:       PetscSectionGetOffset(plex->supportSection, p, &off);
    276:       PetscSectionGetOffset(plexNew->supportSection, pperm[p], &offNew);
    277:       for (d = 0; d < dof; ++d) {
    278:         plexNew->supports[offNew+d] = pperm[plex->supports[off+d]];
    279:       }
    280:     }
    281:     ISRestoreIndices(perm, &pperm);
    282:   }
    283:   return(0);
    284: }