Actual source code: plexreorder.c

petsc-3.7.3 2016-08-01
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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: }