1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petsc/private/matorderimpl.h> /*I "petscmat.h" I*/ 3 #include <petsc/private/dmlabelimpl.h> 4 5 static PetscErrorCode DMPlexCreateOrderingClosure_Static(DM dm, PetscInt numPoints, const PetscInt pperm[], PetscInt **clperm, PetscInt **invclperm) { 6 PetscInt *perm, *iperm; 7 PetscInt depth, d, pStart, pEnd, fStart, fMax, fEnd, p; 8 9 PetscFunctionBegin; 10 PetscCall(DMPlexGetDepth(dm, &depth)); 11 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 12 PetscCall(PetscMalloc1(pEnd - pStart, &perm)); 13 PetscCall(PetscMalloc1(pEnd - pStart, &iperm)); 14 for (p = pStart; p < pEnd; ++p) iperm[p] = -1; 15 for (d = depth; d > 0; --d) { 16 PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd)); 17 PetscCall(DMPlexGetDepthStratum(dm, d - 1, &fStart, &fEnd)); 18 fMax = fStart; 19 for (p = pStart; p < pEnd; ++p) { 20 const PetscInt *cone; 21 PetscInt point, coneSize, c; 22 23 if (d == depth) { 24 perm[p] = pperm[p]; 25 iperm[pperm[p]] = p; 26 } 27 point = perm[p]; 28 PetscCall(DMPlexGetConeSize(dm, point, &coneSize)); 29 PetscCall(DMPlexGetCone(dm, point, &cone)); 30 for (c = 0; c < coneSize; ++c) { 31 const PetscInt oldc = cone[c]; 32 const PetscInt newc = iperm[oldc]; 33 34 if (newc < 0) { 35 perm[fMax] = oldc; 36 iperm[oldc] = fMax++; 37 } 38 } 39 } 40 PetscCheck(fMax == fEnd, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of depth %" PetscInt_FMT " faces %" PetscInt_FMT " does not match permuted number %" PetscInt_FMT, d, fEnd - fStart, fMax - fStart); 41 } 42 *clperm = perm; 43 *invclperm = iperm; 44 PetscFunctionReturn(0); 45 } 46 47 /*@ 48 DMPlexGetOrdering - Calculate a reordering of the mesh 49 50 Collective on dm 51 52 Input Parameters: 53 + dm - The DMPlex object 54 . otype - type of reordering, one of the following: 55 $ MATORDERINGNATURAL - Natural 56 $ MATORDERINGND - Nested Dissection 57 $ MATORDERING1WD - One-way Dissection 58 $ MATORDERINGRCM - Reverse Cuthill-McKee 59 $ MATORDERINGQMD - Quotient Minimum Degree 60 - label - [Optional] Label used to segregate ordering into sets, or NULL 61 62 Output Parameter: 63 . perm - The point permutation as an IS, perm[old point number] = new point number 64 65 Note: The label is used to group sets of points together by label value. This makes it easy to reorder a mesh which 66 has different types of cells, and then loop over each set of reordered cells for assembly. 67 68 Level: intermediate 69 70 .seealso: `DMPlexPermute()`, `MatGetOrdering()` 71 @*/ 72 PetscErrorCode DMPlexGetOrdering(DM dm, MatOrderingType otype, DMLabel label, IS *perm) { 73 PetscInt numCells = 0; 74 PetscInt *start = NULL, *adjacency = NULL, *cperm, *clperm = NULL, *invclperm = NULL, *mask, *xls, pStart, pEnd, c, i; 75 76 PetscFunctionBegin; 77 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 78 PetscValidPointer(perm, 4); 79 PetscCall(DMPlexCreateNeighborCSR(dm, 0, &numCells, &start, &adjacency)); 80 PetscCall(PetscMalloc3(numCells, &cperm, numCells, &mask, numCells * 2, &xls)); 81 if (numCells) { 82 /* Shift for Fortran numbering */ 83 for (i = 0; i < start[numCells]; ++i) ++adjacency[i]; 84 for (i = 0; i <= numCells; ++i) ++start[i]; 85 PetscCall(SPARSEPACKgenrcm(&numCells, start, adjacency, cperm, mask, xls)); 86 } 87 PetscCall(PetscFree(start)); 88 PetscCall(PetscFree(adjacency)); 89 /* Shift for Fortran numbering */ 90 for (c = 0; c < numCells; ++c) --cperm[c]; 91 /* Segregate */ 92 if (label) { 93 IS valueIS; 94 const PetscInt *valuesTmp; 95 PetscInt *values; 96 PetscInt numValues, numPoints = 0; 97 PetscInt *sperm, *vsize, *voff, v; 98 99 // Can't directly sort the valueIS, since it is a view into the DMLabel 100 PetscCall(DMLabelGetValueIS(label, &valueIS)); 101 PetscCall(ISGetLocalSize(valueIS, &numValues)); 102 PetscCall(ISGetIndices(valueIS, &valuesTmp)); 103 PetscCall(PetscCalloc4(numCells, &sperm, numValues, &values, numValues, &vsize, numValues + 1, &voff)); 104 PetscCall(PetscArraycpy(values, valuesTmp, numValues)); 105 PetscCall(PetscSortInt(numValues, values)); 106 PetscCall(ISRestoreIndices(valueIS, &valuesTmp)); 107 PetscCall(ISDestroy(&valueIS)); 108 for (v = 0; v < numValues; ++v) { 109 PetscCall(DMLabelGetStratumSize(label, values[v], &vsize[v])); 110 if (v < numValues - 1) voff[v + 2] += vsize[v] + voff[v + 1]; 111 numPoints += vsize[v]; 112 } 113 PetscCheck(numPoints == numCells, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Label only covers %" PetscInt_FMT " cells != %" PetscInt_FMT " total cells", numPoints, numCells); 114 for (c = 0; c < numCells; ++c) { 115 const PetscInt oldc = cperm[c]; 116 PetscInt val, vloc; 117 118 PetscCall(DMLabelGetValue(label, oldc, &val)); 119 PetscCheck(val != -1, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Cell %" PetscInt_FMT " not present in label", oldc); 120 PetscCall(PetscFindInt(val, numValues, values, &vloc)); 121 PetscCheck(vloc >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Value %" PetscInt_FMT " not present label", val); 122 sperm[voff[vloc + 1]++] = oldc; 123 } 124 for (v = 0; v < numValues; ++v) PetscCheck(voff[v + 1] - voff[v] == vsize[v], PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of %" PetscInt_FMT " values found is %" PetscInt_FMT " != %" PetscInt_FMT, values[v], voff[v + 1] - voff[v], vsize[v]); 125 PetscCall(PetscArraycpy(cperm, sperm, numCells)); 126 PetscCall(PetscFree4(sperm, values, vsize, voff)); 127 } 128 /* Construct closure */ 129 PetscCall(DMPlexCreateOrderingClosure_Static(dm, numCells, cperm, &clperm, &invclperm)); 130 PetscCall(PetscFree3(cperm, mask, xls)); 131 PetscCall(PetscFree(clperm)); 132 /* Invert permutation */ 133 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 134 PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), pEnd - pStart, invclperm, PETSC_OWN_POINTER, perm)); 135 PetscFunctionReturn(0); 136 } 137 138 /*@ 139 DMPlexGetOrdering1D - Reorder the vertices so that the mesh is in a line 140 141 Collective on dm 142 143 Input Parameter: 144 . dm - The DMPlex object 145 146 Output Parameter: 147 . perm - The point permutation as an IS, perm[old point number] = new point number 148 149 Level: intermediate 150 151 .seealso: `DMPlexGetOrdering()`, `DMPlexPermute()`, `MatGetOrdering()` 152 @*/ 153 PetscErrorCode DMPlexGetOrdering1D(DM dm, IS *perm) { 154 PetscInt *points; 155 const PetscInt *support, *cone; 156 PetscInt dim, pStart, pEnd, cStart, cEnd, c, vStart, vEnd, v, suppSize, lastCell = 0; 157 158 PetscFunctionBegin; 159 PetscCall(DMGetDimension(dm, &dim)); 160 PetscCheck(dim == 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Input mesh must be one dimensional, not %" PetscInt_FMT, dim); 161 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 162 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 163 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 164 PetscCall(PetscMalloc1(pEnd - pStart, &points)); 165 for (c = cStart; c < cEnd; ++c) points[c] = c; 166 for (v = vStart; v < vEnd; ++v) points[v] = v; 167 for (v = vStart; v < vEnd; ++v) { 168 PetscCall(DMPlexGetSupportSize(dm, v, &suppSize)); 169 PetscCall(DMPlexGetSupport(dm, v, &support)); 170 if (suppSize == 1) { 171 lastCell = support[0]; 172 break; 173 } 174 } 175 if (v < vEnd) { 176 PetscInt pos = cEnd; 177 178 points[v] = pos++; 179 while (lastCell >= cStart) { 180 PetscCall(DMPlexGetCone(dm, lastCell, &cone)); 181 if (cone[0] == v) v = cone[1]; 182 else v = cone[0]; 183 PetscCall(DMPlexGetSupport(dm, v, &support)); 184 PetscCall(DMPlexGetSupportSize(dm, v, &suppSize)); 185 if (suppSize == 1) { 186 lastCell = -1; 187 } else { 188 if (support[0] == lastCell) lastCell = support[1]; 189 else lastCell = support[0]; 190 } 191 points[v] = pos++; 192 } 193 PetscCheck(pos == pEnd, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Last vertex was %" PetscInt_FMT ", not %" PetscInt_FMT, pos, pEnd); 194 } 195 PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), pEnd - pStart, points, PETSC_OWN_POINTER, perm)); 196 PetscFunctionReturn(0); 197 } 198 199 static PetscErrorCode DMPlexRemapCoordinates_Private(IS perm, PetscSection cs, Vec coordinates, PetscSection *csNew, Vec *coordinatesNew) { 200 PetscScalar *coords, *coordsNew; 201 const PetscInt *pperm; 202 PetscInt pStart, pEnd, p; 203 const char *name; 204 205 PetscFunctionBegin; 206 PetscCall(PetscSectionPermute(cs, perm, csNew)); 207 PetscCall(VecDuplicate(coordinates, coordinatesNew)); 208 PetscCall(PetscObjectGetName((PetscObject)coordinates, &name)); 209 PetscCall(PetscObjectSetName((PetscObject)*coordinatesNew, name)); 210 PetscCall(VecGetArray(coordinates, &coords)); 211 PetscCall(VecGetArray(*coordinatesNew, &coordsNew)); 212 PetscCall(PetscSectionGetChart(*csNew, &pStart, &pEnd)); 213 PetscCall(ISGetIndices(perm, &pperm)); 214 for (p = pStart; p < pEnd; ++p) { 215 PetscInt dof, off, offNew, d; 216 217 PetscCall(PetscSectionGetDof(*csNew, p, &dof)); 218 PetscCall(PetscSectionGetOffset(cs, p, &off)); 219 PetscCall(PetscSectionGetOffset(*csNew, pperm[p], &offNew)); 220 for (d = 0; d < dof; ++d) coordsNew[offNew + d] = coords[off + d]; 221 } 222 PetscCall(ISRestoreIndices(perm, &pperm)); 223 PetscCall(VecRestoreArray(coordinates, &coords)); 224 PetscCall(VecRestoreArray(*coordinatesNew, &coordsNew)); 225 PetscFunctionReturn(0); 226 } 227 228 /*@ 229 DMPlexPermute - Reorder the mesh according to the input permutation 230 231 Collective on dm 232 233 Input Parameters: 234 + dm - The DMPlex object 235 - perm - The point permutation, perm[old point number] = new point number 236 237 Output Parameter: 238 . pdm - The permuted DM 239 240 Level: intermediate 241 242 .seealso: `MatPermute()` 243 @*/ 244 PetscErrorCode DMPlexPermute(DM dm, IS perm, DM *pdm) { 245 DM_Plex *plex = (DM_Plex *)dm->data, *plexNew; 246 PetscInt dim, cdim; 247 const char *name; 248 249 PetscFunctionBegin; 250 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 251 PetscValidHeaderSpecific(perm, IS_CLASSID, 2); 252 PetscValidPointer(pdm, 3); 253 PetscCall(DMCreate(PetscObjectComm((PetscObject)dm), pdm)); 254 PetscCall(DMSetType(*pdm, DMPLEX)); 255 PetscCall(PetscObjectGetName((PetscObject)dm, &name)); 256 PetscCall(PetscObjectSetName((PetscObject)*pdm, name)); 257 PetscCall(DMGetDimension(dm, &dim)); 258 PetscCall(DMSetDimension(*pdm, dim)); 259 PetscCall(DMGetCoordinateDim(dm, &cdim)); 260 PetscCall(DMSetCoordinateDim(*pdm, cdim)); 261 PetscCall(DMCopyDisc(dm, *pdm)); 262 if (dm->localSection) { 263 PetscSection section, sectionNew; 264 265 PetscCall(DMGetLocalSection(dm, §ion)); 266 PetscCall(PetscSectionPermute(section, perm, §ionNew)); 267 PetscCall(DMSetLocalSection(*pdm, sectionNew)); 268 PetscCall(PetscSectionDestroy(§ionNew)); 269 } 270 plexNew = (DM_Plex *)(*pdm)->data; 271 /* Ignore ltogmap, ltogmapb */ 272 /* Ignore sf, sectionSF */ 273 /* Ignore globalVertexNumbers, globalCellNumbers */ 274 /* Reorder labels */ 275 { 276 PetscInt numLabels, l; 277 DMLabel label, labelNew; 278 279 PetscCall(DMGetNumLabels(dm, &numLabels)); 280 for (l = 0; l < numLabels; ++l) { 281 PetscCall(DMGetLabelByNum(dm, l, &label)); 282 PetscCall(DMLabelPermute(label, perm, &labelNew)); 283 PetscCall(DMAddLabel(*pdm, labelNew)); 284 PetscCall(DMLabelDestroy(&labelNew)); 285 } 286 PetscCall(DMGetLabel(*pdm, "depth", &(*pdm)->depthLabel)); 287 if (plex->subpointMap) PetscCall(DMLabelPermute(plex->subpointMap, perm, &plexNew->subpointMap)); 288 } 289 if ((*pdm)->celltypeLabel) { 290 DMLabel ctLabel; 291 292 // Reset label for fast lookup 293 PetscCall(DMPlexGetCellTypeLabel(*pdm, &ctLabel)); 294 PetscCall(DMLabelMakeAllInvalid_Internal(ctLabel)); 295 } 296 /* Reorder topology */ 297 { 298 const PetscInt *pperm; 299 PetscInt n, pStart, pEnd, p; 300 301 PetscCall(PetscSectionDestroy(&plexNew->coneSection)); 302 PetscCall(PetscSectionPermute(plex->coneSection, perm, &plexNew->coneSection)); 303 PetscCall(PetscSectionGetStorageSize(plexNew->coneSection, &n)); 304 PetscCall(PetscMalloc1(n, &plexNew->cones)); 305 PetscCall(PetscMalloc1(n, &plexNew->coneOrientations)); 306 PetscCall(ISGetIndices(perm, &pperm)); 307 PetscCall(PetscSectionGetChart(plex->coneSection, &pStart, &pEnd)); 308 for (p = pStart; p < pEnd; ++p) { 309 PetscInt dof, off, offNew, d; 310 311 PetscCall(PetscSectionGetDof(plexNew->coneSection, pperm[p], &dof)); 312 PetscCall(PetscSectionGetOffset(plex->coneSection, p, &off)); 313 PetscCall(PetscSectionGetOffset(plexNew->coneSection, pperm[p], &offNew)); 314 for (d = 0; d < dof; ++d) { 315 plexNew->cones[offNew + d] = pperm[plex->cones[off + d]]; 316 plexNew->coneOrientations[offNew + d] = plex->coneOrientations[off + d]; 317 } 318 } 319 PetscCall(PetscSectionDestroy(&plexNew->supportSection)); 320 PetscCall(PetscSectionPermute(plex->supportSection, perm, &plexNew->supportSection)); 321 PetscCall(PetscSectionGetStorageSize(plexNew->supportSection, &n)); 322 PetscCall(PetscMalloc1(n, &plexNew->supports)); 323 PetscCall(PetscSectionGetChart(plex->supportSection, &pStart, &pEnd)); 324 for (p = pStart; p < pEnd; ++p) { 325 PetscInt dof, off, offNew, d; 326 327 PetscCall(PetscSectionGetDof(plexNew->supportSection, pperm[p], &dof)); 328 PetscCall(PetscSectionGetOffset(plex->supportSection, p, &off)); 329 PetscCall(PetscSectionGetOffset(plexNew->supportSection, pperm[p], &offNew)); 330 for (d = 0; d < dof; ++d) plexNew->supports[offNew + d] = pperm[plex->supports[off + d]]; 331 } 332 PetscCall(ISRestoreIndices(perm, &pperm)); 333 } 334 /* Remap coordinates */ 335 { 336 DM cdm, cdmNew; 337 PetscSection cs, csNew; 338 Vec coordinates, coordinatesNew; 339 340 PetscCall(DMGetCoordinateSection(dm, &cs)); 341 PetscCall(DMGetCoordinatesLocal(dm, &coordinates)); 342 PetscCall(DMPlexRemapCoordinates_Private(perm, cs, coordinates, &csNew, &coordinatesNew)); 343 PetscCall(DMSetCoordinateSection(*pdm, PETSC_DETERMINE, csNew)); 344 PetscCall(DMSetCoordinatesLocal(*pdm, coordinatesNew)); 345 PetscCall(PetscSectionDestroy(&csNew)); 346 PetscCall(VecDestroy(&coordinatesNew)); 347 348 PetscCall(DMGetCellCoordinateDM(dm, &cdm)); 349 if (cdm) { 350 PetscCall(DMGetCoordinateDM(*pdm, &cdm)); 351 PetscCall(DMClone(cdm, &cdmNew)); 352 PetscCall(DMSetCellCoordinateDM(*pdm, cdmNew)); 353 PetscCall(DMDestroy(&cdmNew)); 354 PetscCall(DMGetCellCoordinateSection(dm, &cs)); 355 PetscCall(DMGetCellCoordinatesLocal(dm, &coordinates)); 356 PetscCall(DMPlexRemapCoordinates_Private(perm, cs, coordinates, &csNew, &coordinatesNew)); 357 PetscCall(DMSetCellCoordinateSection(*pdm, PETSC_DETERMINE, csNew)); 358 PetscCall(DMSetCellCoordinatesLocal(*pdm, coordinatesNew)); 359 PetscCall(PetscSectionDestroy(&csNew)); 360 PetscCall(VecDestroy(&coordinatesNew)); 361 } 362 } 363 PetscCall(DMPlexCopy_Internal(dm, PETSC_TRUE, PETSC_TRUE, *pdm)); 364 (*pdm)->setupcalled = PETSC_TRUE; 365 PetscFunctionReturn(0); 366 } 367 368 PetscErrorCode DMPlexReorderSetDefault_Plex(DM dm, DMPlexReorderDefaultFlag reorder) { 369 DM_Plex *mesh = (DM_Plex *)dm->data; 370 371 PetscFunctionBegin; 372 mesh->reorderDefault = reorder; 373 PetscFunctionReturn(0); 374 } 375 376 /*@ 377 DMPlexReorderSetDefault - Set flag indicating whether the DM should be reordered by default 378 379 Logically collective 380 381 Input Parameters: 382 + dm - The DM 383 - reorder - Flag for reordering 384 385 Level: intermediate 386 387 .seealso: `DMPlexReorderGetDefault()` 388 @*/ 389 PetscErrorCode DMPlexReorderSetDefault(DM dm, DMPlexReorderDefaultFlag reorder) { 390 PetscFunctionBegin; 391 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 392 PetscTryMethod(dm, "DMPlexReorderSetDefault_C", (DM, DMPlexReorderDefaultFlag), (dm, reorder)); 393 PetscFunctionReturn(0); 394 } 395 396 PetscErrorCode DMPlexReorderGetDefault_Plex(DM dm, DMPlexReorderDefaultFlag *reorder) { 397 DM_Plex *mesh = (DM_Plex *)dm->data; 398 399 PetscFunctionBegin; 400 *reorder = mesh->reorderDefault; 401 PetscFunctionReturn(0); 402 } 403 404 /*@ 405 DMPlexReorderGetDefault - Get flag indicating whether the DM should be reordered by default 406 407 Not collective 408 409 Input Parameter: 410 . dm - The DM 411 412 Output Parameter: 413 . reorder - Flag for reordering 414 415 Level: intermediate 416 417 .seealso: `DMPlexReorderSetDefault()` 418 @*/ 419 PetscErrorCode DMPlexReorderGetDefault(DM dm, DMPlexReorderDefaultFlag *reorder) { 420 PetscFunctionBegin; 421 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 422 PetscValidPointer(reorder, 2); 423 PetscUseMethod(dm, "DMPlexReorderGetDefault_C", (DM, DMPlexReorderDefaultFlag *), (dm, reorder)); 424 PetscFunctionReturn(0); 425 } 426