Actual source code: plexreorder.c

petsc-master 2020-05-29
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  1:  #include <petsc/private/dmpleximpl.h>
  2:  #include <petsc/private/matorderimpl.h>

  4: static PetscErrorCode DMPlexCreateOrderingClosure_Static(DM dm, PetscInt numPoints, const PetscInt pperm[], PetscInt **clperm, PetscInt **invclperm)
  5: {
  6:   PetscInt      *perm, *iperm;
  7:   PetscInt       depth, d, pStart, pEnd, fStart, fMax, fEnd, p;

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

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

 35:         if (newc < 0) {
 36:           perm[fMax]  = oldc;
 37:           iperm[oldc] = fMax++;
 38:         }
 39:       }
 40:     }
 41:     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);
 42:   }
 43:   *clperm    = perm;
 44:   *invclperm = iperm;
 45:   return(0);
 46: }

 48: /*@
 49:   DMPlexGetOrdering - Calculate a reordering of the mesh

 51:   Collective on dm

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


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

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

 70:   Level: intermediate

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

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

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

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

141: /*@
142:   DMPlexPermute - Reorder the mesh according to the input permutation

144:   Collective on dm

146:   Input Parameter:
147: + dm - The DMPlex object
148: - perm - The point permutation, perm[old point number] = new point number

150:   Output Parameter:
151: . pdm - The permuted DM

153:   Level: intermediate

155: .seealso: MatPermute()
156: @*/
157: PetscErrorCode DMPlexPermute(DM dm, IS perm, DM *pdm)
158: {
159:   DM_Plex       *plex = (DM_Plex *) dm->data, *plexNew;
160:   PetscSection   section, sectionNew;
161:   PetscInt       dim;

168:   DMCreate(PetscObjectComm((PetscObject) dm), pdm);
169:   DMSetType(*pdm, DMPLEX);
170:   DMGetDimension(dm, &dim);
171:   DMSetDimension(*pdm, dim);
172:   DMCopyDisc(dm, *pdm);
173:   DMGetLocalSection(dm, &section);
174:   if (section) {
175:     PetscSectionPermute(section, perm, &sectionNew);
176:     DMSetLocalSection(*pdm, sectionNew);
177:     PetscSectionDestroy(&sectionNew);
178:   }
179:   plexNew = (DM_Plex *) (*pdm)->data;
180:   /* Ignore ltogmap, ltogmapb */
181:   /* Ignore sf, sectionSF */
182:   /* Ignore globalVertexNumbers, globalCellNumbers */
183:   /* Reorder labels */
184:   {
185:     PetscInt numLabels, l;
186:     DMLabel  label, labelNew;

188:     DMGetNumLabels(dm, &numLabels);
189:     for (l = 0; l < numLabels; ++l) {
190:       DMGetLabelByNum(dm, l, &label);
191:       DMLabelPermute(label, perm, &labelNew);
192:       DMAddLabel(*pdm, labelNew);
193:       DMLabelDestroy(&labelNew);
194:     }
195:     DMGetLabel(*pdm, "depth", &(*pdm)->depthLabel);
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:   /* Remap coordinates */
242:   {
243:     DM              cdm, cdmNew;
244:     PetscSection    csection, csectionNew;
245:     Vec             coordinates, coordinatesNew;
246:     PetscScalar    *coords, *coordsNew;
247:     const PetscInt *pperm;
248:     PetscInt        pStart, pEnd, p;
249:     const char     *name;

251:     DMGetCoordinateDM(dm, &cdm);
252:     DMGetLocalSection(cdm, &csection);
253:     PetscSectionPermute(csection, perm, &csectionNew);
254:     DMGetCoordinatesLocal(dm, &coordinates);
255:     VecDuplicate(coordinates, &coordinatesNew);
256:     PetscObjectGetName((PetscObject)coordinates,&name);
257:     PetscObjectSetName((PetscObject)coordinatesNew,name);
258:     VecGetArray(coordinates, &coords);
259:     VecGetArray(coordinatesNew, &coordsNew);
260:     PetscSectionGetChart(csectionNew, &pStart, &pEnd);
261:     ISGetIndices(perm, &pperm);
262:     for (p = pStart; p < pEnd; ++p) {
263:       PetscInt dof, off, offNew, d;

265:       PetscSectionGetDof(csectionNew, p, &dof);
266:       PetscSectionGetOffset(csection, p, &off);
267:       PetscSectionGetOffset(csectionNew, pperm[p], &offNew);
268:       for (d = 0; d < dof; ++d) coordsNew[offNew+d] = coords[off+d];
269:     }
270:     ISRestoreIndices(perm, &pperm);
271:     VecRestoreArray(coordinates, &coords);
272:     VecRestoreArray(coordinatesNew, &coordsNew);
273:     DMGetCoordinateDM(*pdm, &cdmNew);
274:     DMSetLocalSection(cdmNew, csectionNew);
275:     DMSetCoordinatesLocal(*pdm, coordinatesNew);
276:     PetscSectionDestroy(&csectionNew);
277:     VecDestroy(&coordinatesNew);
278:   }
279:   (*pdm)->setupcalled = PETSC_TRUE;
280:   return(0);
281: }