Actual source code: plexreorder.c

petsc-3.6.1 2015-08-06
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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


 67:   Output Parameter:
 68: . perm - The point permutation as an IS

 70:   Level: intermediate

 72: .keywords: mesh
 73: .seealso: MatGetOrdering()
 74: @*/
 75: PetscErrorCode DMPlexGetOrdering(DM dm, MatOrderingType otype, IS *perm)
 76: {
 77:   PetscInt       numCells = 0;
 78:   PetscInt      *start = NULL, *adjacency = NULL, *cperm, *clperm, *invclperm, *mask, *xls, pStart, pEnd, c, i;

 84:   DMPlexCreateNeighborCSR(dm, 0, &numCells, &start, &adjacency);
 85:   PetscMalloc3(numCells,&cperm,numCells,&mask,numCells*2,&xls);
 86:   if (numCells) {
 87:     /* Shift for Fortran numbering */
 88:     for (i = 0; i < start[numCells]; ++i) ++adjacency[i];
 89:     for (i = 0; i <= numCells; ++i)       ++start[i];
 90:     SPARSEPACKgenrcm(&numCells, start, adjacency, cperm, mask, xls);
 91:   }
 92:   PetscFree(start);
 93:   PetscFree(adjacency);
 94:   /* Shift for Fortran numbering */
 95:   for (c = 0; c < numCells; ++c) --cperm[c];
 96:   /* Construct closure */
 97:   DMPlexCreateOrderingClosure_Static(dm, numCells, cperm, &clperm, &invclperm);
 98:   PetscFree3(cperm,mask,xls);
 99:   PetscFree(clperm);
100:   /* Invert permutation */
101:   DMPlexGetChart(dm, &pStart, &pEnd);
102:   ISCreateGeneral(PetscObjectComm((PetscObject) dm), pEnd-pStart, invclperm, PETSC_OWN_POINTER, perm);
103:   return(0);
104: }

108: /*@
109:   DMPlexPermute - Reorder the mesh according to the input permutation

111:   Collective on DM

113:   Input Parameter:
114: + dm - The DMPlex object
115: - perm - The point permutation

117:   Output Parameter:
118: . pdm - The permuted DM

120:   Level: intermediate

122: .keywords: mesh
123: .seealso: MatPermute()
124: @*/
125: PetscErrorCode DMPlexPermute(DM dm, IS perm, DM *pdm)
126: {
127:   DM_Plex       *plex = (DM_Plex *) dm->data, *plexNew;
128:   PetscSection   section, sectionNew;
129:   PetscInt       dim;

136:   DMCreate(PetscObjectComm((PetscObject) dm), pdm);
137:   DMSetType(*pdm, DMPLEX);
138:   DMGetDimension(dm, &dim);
139:   DMSetDimension(*pdm, dim);
140:   DMGetDefaultSection(dm, &section);
141:   if (section) {
142:     PetscSectionPermute(section, perm, &sectionNew);
143:     DMSetDefaultSection(*pdm, sectionNew);
144:     PetscSectionDestroy(&sectionNew);
145:   }
146:   plexNew = (DM_Plex *) (*pdm)->data;
147:   /* Ignore ltogmap, ltogmapb */
148:   /* Ignore sf, defaultSF */
149:   /* Ignore globalVertexNumbers, globalCellNumbers */
150:   /* Remap coordinates */
151:   {
152:     DM              cdm, cdmNew;
153:     PetscSection    csection, csectionNew;
154:     Vec             coordinates, coordinatesNew;
155:     PetscScalar    *coords, *coordsNew;
156:     const PetscInt *pperm;
157:     PetscInt        pStart, pEnd, p;

159:     DMGetCoordinateDM(dm, &cdm);
160:     DMGetDefaultSection(cdm, &csection);
161:     PetscSectionPermute(csection, perm, &csectionNew);
162:     DMGetCoordinatesLocal(dm, &coordinates);
163:     VecDuplicate(coordinates, &coordinatesNew);
164:     VecGetArray(coordinates, &coords);
165:     VecGetArray(coordinatesNew, &coordsNew);
166:     PetscSectionGetChart(csectionNew, &pStart, &pEnd);
167:     ISGetIndices(perm, &pperm);
168:     for (p = pStart; p < pEnd; ++p) {
169:       PetscInt dof, off, offNew, d;

171:       PetscSectionGetDof(csectionNew, p, &dof);
172:       PetscSectionGetOffset(csection, p, &off);
173:       PetscSectionGetOffset(csectionNew, pperm[p], &offNew);
174:       for (d = 0; d < dof; ++d) coordsNew[offNew+d] = coords[off+d];
175:     }
176:     ISRestoreIndices(perm, &pperm);
177:     VecRestoreArray(coordinates, &coords);
178:     VecRestoreArray(coordinatesNew, &coordsNew);
179:     DMGetCoordinateDM(*pdm, &cdmNew);
180:     DMSetDefaultSection(cdmNew, csectionNew);
181:     DMSetCoordinatesLocal(*pdm, coordinatesNew);
182:     PetscSectionDestroy(&csectionNew);
183:     VecDestroy(&coordinatesNew);
184:   }
185:   /* Reorder labels */
186:   {
187:     PetscInt numLabels, l;
188:     DMLabel  label, labelNew;

190:     DMPlexGetNumLabels(dm, &numLabels);
191:     for (l = numLabels-1; l >= 0; --l) {
192:       DMPlexGetLabelByNum(dm, l, &label);
193:       DMLabelPermute(label, perm, &labelNew);
194:       DMPlexAddLabel(*pdm, labelNew);
195:     }
196:     if (plex->subpointMap) {DMLabelPermute(plex->subpointMap, perm, &plexNew->subpointMap);}
197:   }
198:   /* Reorder topology */
199:   {
200:     const PetscInt *pperm;
201:     PetscInt        maxConeSize, maxSupportSize, n, pStart, pEnd, p;

203:     DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);
204:     plexNew->maxConeSize    = maxConeSize;
205:     plexNew->maxSupportSize = maxSupportSize;
206:     PetscSectionDestroy(&plexNew->coneSection);
207:     PetscSectionPermute(plex->coneSection, perm, &plexNew->coneSection);
208:     PetscSectionGetStorageSize(plexNew->coneSection, &n);
209:     PetscMalloc1(n, &plexNew->cones);
210:     PetscMalloc1(n, &plexNew->coneOrientations);
211:     ISGetIndices(perm, &pperm);
212:     PetscSectionGetChart(plex->coneSection, &pStart, &pEnd);
213:     for (p = pStart; p < pEnd; ++p) {
214:       PetscInt dof, off, offNew, d;

216:       PetscSectionGetDof(plexNew->coneSection, pperm[p], &dof);
217:       PetscSectionGetOffset(plex->coneSection, p, &off);
218:       PetscSectionGetOffset(plexNew->coneSection, pperm[p], &offNew);
219:       for (d = 0; d < dof; ++d) {
220:         plexNew->cones[offNew+d]            = pperm[plex->cones[off+d]];
221:         plexNew->coneOrientations[offNew+d] = plex->coneOrientations[off+d];
222:       }
223:     }
224:     PetscSectionDestroy(&plexNew->supportSection);
225:     PetscSectionPermute(plex->supportSection, perm, &plexNew->supportSection);
226:     PetscSectionGetStorageSize(plexNew->supportSection, &n);
227:     PetscMalloc1(n, &plexNew->supports);
228:     PetscSectionGetChart(plex->supportSection, &pStart, &pEnd);
229:     for (p = pStart; p < pEnd; ++p) {
230:       PetscInt dof, off, offNew, d;

232:       PetscSectionGetDof(plexNew->supportSection, pperm[p], &dof);
233:       PetscSectionGetOffset(plex->supportSection, p, &off);
234:       PetscSectionGetOffset(plexNew->supportSection, pperm[p], &offNew);
235:       for (d = 0; d < dof; ++d) {
236:         plexNew->supports[offNew+d] = pperm[plex->supports[off+d]];
237:       }
238:     }
239:     ISRestoreIndices(perm, &pperm);
240:   }
241:   return(0);
242: }