1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petsc/private/dmlabelimpl.h> 3 #include <petsc/private/isimpl.h> 4 #include <petsc/private/vecimpl.h> 5 #include <petsc/private/glvisvecimpl.h> 6 #include <petscsf.h> 7 #include <petscds.h> 8 #include <petscdraw.h> 9 #include <petscdmfield.h> 10 #include <petscdmplextransform.h> 11 12 /* Logging support */ 13 PetscLogEvent DMPLEX_Interpolate, DMPLEX_Partition, DMPLEX_Distribute, DMPLEX_DistributeCones, DMPLEX_DistributeLabels, DMPLEX_DistributeSF, DMPLEX_DistributeOverlap, DMPLEX_DistributeField, DMPLEX_DistributeData, DMPLEX_Migrate, DMPLEX_InterpolateSF, DMPLEX_GlobalToNaturalBegin, DMPLEX_GlobalToNaturalEnd, DMPLEX_NaturalToGlobalBegin, DMPLEX_NaturalToGlobalEnd, DMPLEX_Stratify, DMPLEX_Symmetrize, DMPLEX_Preallocate, DMPLEX_ResidualFEM, DMPLEX_JacobianFEM, DMPLEX_InterpolatorFEM, DMPLEX_InjectorFEM, DMPLEX_IntegralFEM, DMPLEX_CreateGmsh, DMPLEX_RebalanceSharedPoints, DMPLEX_PartSelf, DMPLEX_PartLabelInvert, DMPLEX_PartLabelCreateSF, DMPLEX_PartStratSF, DMPLEX_CreatePointSF, DMPLEX_LocatePoints, DMPLEX_TopologyView, DMPLEX_LabelsView, DMPLEX_CoordinatesView, DMPLEX_SectionView, DMPLEX_GlobalVectorView, DMPLEX_LocalVectorView, DMPLEX_TopologyLoad, DMPLEX_LabelsLoad, DMPLEX_CoordinatesLoad, DMPLEX_SectionLoad, DMPLEX_GlobalVectorLoad, DMPLEX_LocalVectorLoad; 14 PetscLogEvent DMPLEX_RebalBuildGraph, DMPLEX_RebalRewriteSF, DMPLEX_RebalGatherGraph, DMPLEX_RebalPartition, DMPLEX_RebalScatterPart, DMPLEX_Generate, DMPLEX_Transform, DMPLEX_GetLocalOffsets, DMPLEX_Uninterpolate; 15 16 PetscBool Plexcite = PETSC_FALSE; 17 const char PlexCitation[] = "@article{LangeMitchellKnepleyGorman2015,\n" 18 "title = {Efficient mesh management in {Firedrake} using {PETSc-DMPlex}},\n" 19 "author = {Michael Lange and Lawrence Mitchell and Matthew G. Knepley and Gerard J. Gorman},\n" 20 "journal = {SIAM Journal on Scientific Computing},\n" 21 "volume = {38},\n" 22 "number = {5},\n" 23 "pages = {S143--S155},\n" 24 "eprint = {http://arxiv.org/abs/1506.07749},\n" 25 "doi = {10.1137/15M1026092},\n" 26 "year = {2016},\n" 27 "petsc_uses={DMPlex},\n}\n"; 28 29 PETSC_EXTERN PetscErrorCode VecView_MPI(Vec, PetscViewer); 30 31 /*@ 32 DMPlexIsSimplex - Is the first cell in this mesh a simplex? 33 34 Input Parameter: 35 . dm - The `DMPLEX` object 36 37 Output Parameter: 38 . simplex - Flag checking for a simplex 39 40 Level: intermediate 41 42 Note: 43 This just gives the first range of cells found. If the mesh has several cell types, it will only give the first. 44 If the mesh has no cells, this returns `PETSC_FALSE`. 45 46 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetSimplexOrBoxCells()`, `DMPlexGetCellType()`, `DMPlexGetHeightStratum()`, `DMPolytopeTypeGetNumVertices()` 47 @*/ 48 PetscErrorCode DMPlexIsSimplex(DM dm, PetscBool *simplex) 49 { 50 DMPolytopeType ct; 51 PetscInt cStart, cEnd; 52 53 PetscFunctionBegin; 54 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 55 if (cEnd <= cStart) { 56 *simplex = PETSC_FALSE; 57 PetscFunctionReturn(PETSC_SUCCESS); 58 } 59 PetscCall(DMPlexGetCellType(dm, cStart, &ct)); 60 *simplex = DMPolytopeTypeGetNumVertices(ct) == DMPolytopeTypeGetDim(ct) + 1 ? PETSC_TRUE : PETSC_FALSE; 61 PetscFunctionReturn(PETSC_SUCCESS); 62 } 63 64 /*@ 65 DMPlexGetSimplexOrBoxCells - Get the range of cells which are neither prisms nor ghost FV cells 66 67 Input Parameters: 68 + dm - The `DMPLEX` object 69 - height - The cell height in the Plex, 0 is the default 70 71 Output Parameters: 72 + cStart - The first "normal" cell 73 - cEnd - The upper bound on "normal" cells 74 75 Level: developer 76 77 Note: 78 This function requires that tensor cells are ordered last. 79 80 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexConstructGhostCells()`, `DMPlexGetCellTypeStratum()` 81 @*/ 82 PetscErrorCode DMPlexGetSimplexOrBoxCells(DM dm, PetscInt height, PetscInt *cStart, PetscInt *cEnd) 83 { 84 DMLabel ctLabel; 85 IS valueIS; 86 const PetscInt *ctypes; 87 PetscInt Nct, cS = PETSC_MAX_INT, cE = 0; 88 89 PetscFunctionBegin; 90 PetscCall(DMPlexGetCellTypeLabel(dm, &ctLabel)); 91 PetscCall(DMLabelGetValueIS(ctLabel, &valueIS)); 92 PetscCall(ISGetLocalSize(valueIS, &Nct)); 93 PetscCall(ISGetIndices(valueIS, &ctypes)); 94 if (!Nct) cS = cE = 0; 95 for (PetscInt t = 0; t < Nct; ++t) { 96 const DMPolytopeType ct = (DMPolytopeType)ctypes[t]; 97 PetscInt ctS, ctE, ht; 98 99 if (ct == DM_POLYTOPE_UNKNOWN) { 100 // If any cells are not typed, just use all cells 101 PetscCall(DMPlexGetHeightStratum(dm, PetscMax(height, 0), cStart, cEnd)); 102 break; 103 } 104 if (DMPolytopeTypeIsHybrid(ct) || ct == DM_POLYTOPE_FV_GHOST) continue; 105 PetscCall(DMLabelGetStratumBounds(ctLabel, ct, &ctS, &ctE)); 106 if (ctS >= ctE) continue; 107 // Check that a point has the right height 108 PetscCall(DMPlexGetPointHeight(dm, ctS, &ht)); 109 if (ht != height) continue; 110 cS = PetscMin(cS, ctS); 111 cE = PetscMax(cE, ctE); 112 } 113 PetscCall(ISDestroy(&valueIS)); 114 // Reset label for fast lookup 115 PetscCall(DMLabelMakeAllInvalid_Internal(ctLabel)); 116 if (cStart) *cStart = cS; 117 if (cEnd) *cEnd = cE; 118 PetscFunctionReturn(PETSC_SUCCESS); 119 } 120 121 PetscErrorCode DMPlexGetFieldTypes_Internal(DM dm, PetscSection section, PetscInt field, PetscInt *types, PetscInt **ssStart, PetscInt **ssEnd, PetscViewerVTKFieldType **sft) 122 { 123 PetscInt cdim, pStart, pEnd, vStart, vEnd, cStart, cEnd, c, depth, cellHeight, t; 124 PetscInt *sStart, *sEnd; 125 PetscViewerVTKFieldType *ft; 126 PetscInt vcdof[DM_NUM_POLYTOPES + 1], globalvcdof[DM_NUM_POLYTOPES + 1]; 127 DMLabel depthLabel, ctLabel; 128 129 PetscFunctionBegin; 130 /* the vcdof and globalvcdof are sized to allow every polytope type and simple vertex at DM_NUM_POLYTOPES */ 131 PetscCall(PetscArrayzero(vcdof, DM_NUM_POLYTOPES + 1)); 132 PetscCall(DMGetCoordinateDim(dm, &cdim)); 133 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 134 PetscCall(PetscSectionGetChart(section, &pStart, &pEnd)); 135 if (field >= 0) { 136 if ((vStart >= pStart) && (vStart < pEnd)) PetscCall(PetscSectionGetFieldDof(section, vStart, field, &vcdof[DM_NUM_POLYTOPES])); 137 } else { 138 if ((vStart >= pStart) && (vStart < pEnd)) PetscCall(PetscSectionGetDof(section, vStart, &vcdof[DM_NUM_POLYTOPES])); 139 } 140 141 PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight)); 142 PetscCall(DMPlexGetDepth(dm, &depth)); 143 PetscCall(DMPlexGetDepthLabel(dm, &depthLabel)); 144 PetscCall(DMPlexGetCellTypeLabel(dm, &ctLabel)); 145 for (c = 0; c < DM_NUM_POLYTOPES; ++c) { 146 const DMPolytopeType ict = (DMPolytopeType)c; 147 PetscInt dep; 148 149 if (ict == DM_POLYTOPE_FV_GHOST) continue; 150 PetscCall(DMLabelGetStratumBounds(ctLabel, ict, &cStart, &cEnd)); 151 if (pStart >= 0) { 152 PetscCall(DMLabelGetValue(depthLabel, cStart, &dep)); 153 if (dep != depth - cellHeight) continue; 154 } 155 if (field >= 0) { 156 if ((cStart >= pStart) && (cStart < pEnd)) PetscCall(PetscSectionGetFieldDof(section, cStart, field, &vcdof[c])); 157 } else { 158 if ((cStart >= pStart) && (cStart < pEnd)) PetscCall(PetscSectionGetDof(section, cStart, &vcdof[c])); 159 } 160 } 161 162 PetscCall(MPIU_Allreduce(vcdof, globalvcdof, DM_NUM_POLYTOPES + 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm))); 163 *types = 0; 164 165 for (c = 0; c < DM_NUM_POLYTOPES + 1; ++c) { 166 if (globalvcdof[c]) ++(*types); 167 } 168 169 PetscCall(PetscMalloc3(*types, &sStart, *types, &sEnd, *types, &ft)); 170 t = 0; 171 if (globalvcdof[DM_NUM_POLYTOPES]) { 172 sStart[t] = vStart; 173 sEnd[t] = vEnd; 174 ft[t] = (globalvcdof[t] == cdim) ? PETSC_VTK_POINT_VECTOR_FIELD : PETSC_VTK_POINT_FIELD; 175 ++t; 176 } 177 178 for (c = 0; c < DM_NUM_POLYTOPES; ++c) { 179 if (globalvcdof[c]) { 180 const DMPolytopeType ict = (DMPolytopeType)c; 181 182 PetscCall(DMLabelGetStratumBounds(ctLabel, ict, &cStart, &cEnd)); 183 sStart[t] = cStart; 184 sEnd[t] = cEnd; 185 ft[t] = (globalvcdof[c] == cdim) ? PETSC_VTK_CELL_VECTOR_FIELD : PETSC_VTK_CELL_FIELD; 186 ++t; 187 } 188 } 189 190 if (!*types) { 191 if (field >= 0) { 192 const char *fieldname; 193 194 PetscCall(PetscSectionGetFieldName(section, field, &fieldname)); 195 PetscCall(PetscInfo((PetscObject)dm, "Could not classify VTK output type of section field %" PetscInt_FMT " \"%s\"\n", field, fieldname)); 196 } else { 197 PetscCall(PetscInfo((PetscObject)dm, "Could not classify VTK output type of section\n")); 198 } 199 } 200 201 *ssStart = sStart; 202 *ssEnd = sEnd; 203 *sft = ft; 204 PetscFunctionReturn(PETSC_SUCCESS); 205 } 206 207 PetscErrorCode DMPlexRestoreFieldTypes_Internal(DM dm, PetscSection section, PetscInt field, PetscInt *types, PetscInt **sStart, PetscInt **sEnd, PetscViewerVTKFieldType **ft) 208 { 209 PetscFunctionBegin; 210 PetscCall(PetscFree3(*sStart, *sEnd, *ft)); 211 PetscFunctionReturn(PETSC_SUCCESS); 212 } 213 214 PetscErrorCode DMPlexGetFieldType_Internal(DM dm, PetscSection section, PetscInt field, PetscInt *sStart, PetscInt *sEnd, PetscViewerVTKFieldType *ft) 215 { 216 PetscInt cdim, pStart, pEnd, vStart, vEnd, cStart, cEnd; 217 PetscInt vcdof[2] = {0, 0}, globalvcdof[2]; 218 219 PetscFunctionBegin; 220 *ft = PETSC_VTK_INVALID; 221 PetscCall(DMGetCoordinateDim(dm, &cdim)); 222 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 223 PetscCall(DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd)); 224 PetscCall(PetscSectionGetChart(section, &pStart, &pEnd)); 225 if (field >= 0) { 226 if ((vStart >= pStart) && (vStart < pEnd)) PetscCall(PetscSectionGetFieldDof(section, vStart, field, &vcdof[0])); 227 if ((cStart >= pStart) && (cStart < pEnd)) PetscCall(PetscSectionGetFieldDof(section, cStart, field, &vcdof[1])); 228 } else { 229 if ((vStart >= pStart) && (vStart < pEnd)) PetscCall(PetscSectionGetDof(section, vStart, &vcdof[0])); 230 if ((cStart >= pStart) && (cStart < pEnd)) PetscCall(PetscSectionGetDof(section, cStart, &vcdof[1])); 231 } 232 PetscCall(MPIU_Allreduce(vcdof, globalvcdof, 2, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm))); 233 if (globalvcdof[0]) { 234 *sStart = vStart; 235 *sEnd = vEnd; 236 if (globalvcdof[0] == cdim) *ft = PETSC_VTK_POINT_VECTOR_FIELD; 237 else *ft = PETSC_VTK_POINT_FIELD; 238 } else if (globalvcdof[1]) { 239 *sStart = cStart; 240 *sEnd = cEnd; 241 if (globalvcdof[1] == cdim) *ft = PETSC_VTK_CELL_VECTOR_FIELD; 242 else *ft = PETSC_VTK_CELL_FIELD; 243 } else { 244 if (field >= 0) { 245 const char *fieldname; 246 247 PetscCall(PetscSectionGetFieldName(section, field, &fieldname)); 248 PetscCall(PetscInfo((PetscObject)dm, "Could not classify VTK output type of section field %" PetscInt_FMT " \"%s\"\n", field, fieldname)); 249 } else { 250 PetscCall(PetscInfo((PetscObject)dm, "Could not classify VTK output type of section\n")); 251 } 252 } 253 PetscFunctionReturn(PETSC_SUCCESS); 254 } 255 256 /*@ 257 DMPlexVecView1D - Plot many 1D solutions on the same line graph 258 259 Collective 260 261 Input Parameters: 262 + dm - The `DMPLEX` object 263 . n - The number of vectors 264 . u - The array of local vectors 265 - viewer - The `PetscViewer` 266 267 Level: advanced 268 269 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `VecViewFromOptions()`, `VecView()` 270 @*/ 271 PetscErrorCode DMPlexVecView1D(DM dm, PetscInt n, Vec u[], PetscViewer viewer) 272 { 273 PetscDS ds; 274 PetscDraw draw = NULL; 275 PetscDrawLG lg; 276 Vec coordinates; 277 const PetscScalar *coords, **sol; 278 PetscReal *vals; 279 PetscInt *Nc; 280 PetscInt Nf, f, c, Nl, l, i, vStart, vEnd, v; 281 char **names; 282 283 PetscFunctionBegin; 284 PetscCall(DMGetDS(dm, &ds)); 285 PetscCall(PetscDSGetNumFields(ds, &Nf)); 286 PetscCall(PetscDSGetTotalComponents(ds, &Nl)); 287 PetscCall(PetscDSGetComponents(ds, &Nc)); 288 289 PetscCall(PetscViewerDrawGetDraw(viewer, 0, &draw)); 290 if (!draw) PetscFunctionReturn(PETSC_SUCCESS); 291 PetscCall(PetscDrawLGCreate(draw, n * Nl, &lg)); 292 293 PetscCall(PetscMalloc3(n, &sol, n * Nl, &names, n * Nl, &vals)); 294 for (i = 0, l = 0; i < n; ++i) { 295 const char *vname; 296 297 PetscCall(PetscObjectGetName((PetscObject)u[i], &vname)); 298 for (f = 0; f < Nf; ++f) { 299 PetscObject disc; 300 const char *fname; 301 char tmpname[PETSC_MAX_PATH_LEN]; 302 303 PetscCall(PetscDSGetDiscretization(ds, f, &disc)); 304 /* TODO Create names for components */ 305 for (c = 0; c < Nc[f]; ++c, ++l) { 306 PetscCall(PetscObjectGetName(disc, &fname)); 307 PetscCall(PetscStrncpy(tmpname, vname, sizeof(tmpname))); 308 PetscCall(PetscStrlcat(tmpname, ":", sizeof(tmpname))); 309 PetscCall(PetscStrlcat(tmpname, fname, sizeof(tmpname))); 310 PetscCall(PetscStrallocpy(tmpname, &names[l])); 311 } 312 } 313 } 314 PetscCall(PetscDrawLGSetLegend(lg, (const char *const *)names)); 315 /* Just add P_1 support for now */ 316 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 317 PetscCall(DMGetCoordinatesLocal(dm, &coordinates)); 318 PetscCall(VecGetArrayRead(coordinates, &coords)); 319 for (i = 0; i < n; ++i) PetscCall(VecGetArrayRead(u[i], &sol[i])); 320 for (v = vStart; v < vEnd; ++v) { 321 PetscScalar *x, *svals; 322 323 PetscCall(DMPlexPointLocalRead(dm, v, coords, &x)); 324 for (i = 0; i < n; ++i) { 325 PetscCall(DMPlexPointLocalRead(dm, v, sol[i], &svals)); 326 for (l = 0; l < Nl; ++l) vals[i * Nl + l] = PetscRealPart(svals[l]); 327 } 328 PetscCall(PetscDrawLGAddCommonPoint(lg, PetscRealPart(x[0]), vals)); 329 } 330 PetscCall(VecRestoreArrayRead(coordinates, &coords)); 331 for (i = 0; i < n; ++i) PetscCall(VecRestoreArrayRead(u[i], &sol[i])); 332 for (l = 0; l < n * Nl; ++l) PetscCall(PetscFree(names[l])); 333 PetscCall(PetscFree3(sol, names, vals)); 334 335 PetscCall(PetscDrawLGDraw(lg)); 336 PetscCall(PetscDrawLGDestroy(&lg)); 337 PetscFunctionReturn(PETSC_SUCCESS); 338 } 339 340 static PetscErrorCode VecView_Plex_Local_Draw_1D(Vec u, PetscViewer viewer) 341 { 342 DM dm; 343 344 PetscFunctionBegin; 345 PetscCall(VecGetDM(u, &dm)); 346 PetscCall(DMPlexVecView1D(dm, 1, &u, viewer)); 347 PetscFunctionReturn(PETSC_SUCCESS); 348 } 349 350 static PetscErrorCode VecView_Plex_Local_Draw_2D(Vec v, PetscViewer viewer) 351 { 352 DM dm; 353 PetscSection s; 354 PetscDraw draw, popup; 355 DM cdm; 356 PetscSection coordSection; 357 Vec coordinates; 358 const PetscScalar *array; 359 PetscReal lbound[3], ubound[3]; 360 PetscReal vbound[2], time; 361 PetscBool flg; 362 PetscInt dim, Nf, f, Nc, comp, vStart, vEnd, cStart, cEnd, c, N, level, step, w = 0; 363 const char *name; 364 char title[PETSC_MAX_PATH_LEN]; 365 366 PetscFunctionBegin; 367 PetscCall(PetscViewerDrawGetDraw(viewer, 0, &draw)); 368 PetscCall(VecGetDM(v, &dm)); 369 PetscCall(DMGetCoordinateDim(dm, &dim)); 370 PetscCall(DMGetLocalSection(dm, &s)); 371 PetscCall(PetscSectionGetNumFields(s, &Nf)); 372 PetscCall(DMGetCoarsenLevel(dm, &level)); 373 PetscCall(DMGetCoordinateDM(dm, &cdm)); 374 PetscCall(DMGetLocalSection(cdm, &coordSection)); 375 PetscCall(DMGetCoordinatesLocal(dm, &coordinates)); 376 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 377 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 378 379 PetscCall(PetscObjectGetName((PetscObject)v, &name)); 380 PetscCall(DMGetOutputSequenceNumber(dm, &step, &time)); 381 382 PetscCall(VecGetLocalSize(coordinates, &N)); 383 PetscCall(DMGetBoundingBox(dm, lbound, ubound)); 384 PetscCall(PetscDrawClear(draw)); 385 386 /* Could implement something like DMDASelectFields() */ 387 for (f = 0; f < Nf; ++f) { 388 DM fdm = dm; 389 Vec fv = v; 390 IS fis; 391 char prefix[PETSC_MAX_PATH_LEN]; 392 const char *fname; 393 394 PetscCall(PetscSectionGetFieldComponents(s, f, &Nc)); 395 PetscCall(PetscSectionGetFieldName(s, f, &fname)); 396 397 if (v->hdr.prefix) PetscCall(PetscStrncpy(prefix, v->hdr.prefix, sizeof(prefix))); 398 else prefix[0] = '\0'; 399 if (Nf > 1) { 400 PetscCall(DMCreateSubDM(dm, 1, &f, &fis, &fdm)); 401 PetscCall(VecGetSubVector(v, fis, &fv)); 402 PetscCall(PetscStrlcat(prefix, fname, sizeof(prefix))); 403 PetscCall(PetscStrlcat(prefix, "_", sizeof(prefix))); 404 } 405 for (comp = 0; comp < Nc; ++comp, ++w) { 406 PetscInt nmax = 2; 407 408 PetscCall(PetscViewerDrawGetDraw(viewer, w, &draw)); 409 if (Nc > 1) PetscCall(PetscSNPrintf(title, sizeof(title), "%s:%s_%" PetscInt_FMT " Step: %" PetscInt_FMT " Time: %.4g", name, fname, comp, step, (double)time)); 410 else PetscCall(PetscSNPrintf(title, sizeof(title), "%s:%s Step: %" PetscInt_FMT " Time: %.4g", name, fname, step, (double)time)); 411 PetscCall(PetscDrawSetTitle(draw, title)); 412 413 /* TODO Get max and min only for this component */ 414 PetscCall(PetscOptionsGetRealArray(NULL, prefix, "-vec_view_bounds", vbound, &nmax, &flg)); 415 if (!flg) { 416 PetscCall(VecMin(fv, NULL, &vbound[0])); 417 PetscCall(VecMax(fv, NULL, &vbound[1])); 418 if (vbound[1] <= vbound[0]) vbound[1] = vbound[0] + 1.0; 419 } 420 421 PetscCall(PetscDrawGetPopup(draw, &popup)); 422 PetscCall(PetscDrawScalePopup(popup, vbound[0], vbound[1])); 423 PetscCall(PetscDrawSetCoordinates(draw, lbound[0], lbound[1], ubound[0], ubound[1])); 424 PetscCall(VecGetArrayRead(fv, &array)); 425 for (c = cStart; c < cEnd; ++c) { 426 PetscScalar *coords = NULL, *a = NULL; 427 const PetscScalar *coords_arr; 428 PetscBool isDG; 429 PetscInt numCoords, color[4] = {-1, -1, -1, -1}; 430 431 PetscCall(DMPlexPointLocalRead(fdm, c, array, &a)); 432 if (a) { 433 color[0] = PetscDrawRealToColor(PetscRealPart(a[comp]), vbound[0], vbound[1]); 434 color[1] = color[2] = color[3] = color[0]; 435 } else { 436 PetscScalar *vals = NULL; 437 PetscInt numVals, va; 438 439 PetscCall(DMPlexVecGetClosure(fdm, NULL, fv, c, &numVals, &vals)); 440 PetscCheck(numVals % Nc == 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of components %" PetscInt_FMT " does not divide the number of values in the closure %" PetscInt_FMT, Nc, numVals); 441 switch (numVals / Nc) { 442 case 3: /* P1 Triangle */ 443 case 4: /* P1 Quadrangle */ 444 for (va = 0; va < numVals / Nc; ++va) color[va] = PetscDrawRealToColor(PetscRealPart(vals[va * Nc + comp]), vbound[0], vbound[1]); 445 break; 446 case 6: /* P2 Triangle */ 447 case 8: /* P2 Quadrangle */ 448 for (va = 0; va < numVals / (Nc * 2); ++va) color[va] = PetscDrawRealToColor(PetscRealPart(vals[va * Nc + comp + numVals / (Nc * 2)]), vbound[0], vbound[1]); 449 break; 450 default: 451 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of values for cell closure %" PetscInt_FMT " cannot be handled", numVals / Nc); 452 } 453 PetscCall(DMPlexVecRestoreClosure(fdm, NULL, fv, c, &numVals, &vals)); 454 } 455 PetscCall(DMPlexGetCellCoordinates(dm, c, &isDG, &numCoords, &coords_arr, &coords)); 456 switch (numCoords) { 457 case 6: 458 case 12: /* Localized triangle */ 459 PetscCall(PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), color[0], color[1], color[2])); 460 break; 461 case 8: 462 case 16: /* Localized quadrilateral */ 463 PetscCall(PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), color[0], color[1], color[2])); 464 PetscCall(PetscDrawTriangle(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[6]), PetscRealPart(coords[7]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), color[2], color[3], color[0])); 465 break; 466 default: 467 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells with %" PetscInt_FMT " coordinates", numCoords); 468 } 469 PetscCall(DMPlexRestoreCellCoordinates(dm, c, &isDG, &numCoords, &coords_arr, &coords)); 470 } 471 PetscCall(VecRestoreArrayRead(fv, &array)); 472 PetscCall(PetscDrawFlush(draw)); 473 PetscCall(PetscDrawPause(draw)); 474 PetscCall(PetscDrawSave(draw)); 475 } 476 if (Nf > 1) { 477 PetscCall(VecRestoreSubVector(v, fis, &fv)); 478 PetscCall(ISDestroy(&fis)); 479 PetscCall(DMDestroy(&fdm)); 480 } 481 } 482 PetscFunctionReturn(PETSC_SUCCESS); 483 } 484 485 static PetscErrorCode VecView_Plex_Local_Draw(Vec v, PetscViewer viewer) 486 { 487 DM dm; 488 PetscDraw draw; 489 PetscInt dim; 490 PetscBool isnull; 491 492 PetscFunctionBegin; 493 PetscCall(PetscViewerDrawGetDraw(viewer, 0, &draw)); 494 PetscCall(PetscDrawIsNull(draw, &isnull)); 495 if (isnull) PetscFunctionReturn(PETSC_SUCCESS); 496 497 PetscCall(VecGetDM(v, &dm)); 498 PetscCall(DMGetCoordinateDim(dm, &dim)); 499 switch (dim) { 500 case 1: 501 PetscCall(VecView_Plex_Local_Draw_1D(v, viewer)); 502 break; 503 case 2: 504 PetscCall(VecView_Plex_Local_Draw_2D(v, viewer)); 505 break; 506 default: 507 SETERRQ(PetscObjectComm((PetscObject)v), PETSC_ERR_SUP, "Cannot draw meshes of dimension %" PetscInt_FMT ". Try PETSCVIEWERGLVIS", dim); 508 } 509 PetscFunctionReturn(PETSC_SUCCESS); 510 } 511 512 static PetscErrorCode VecView_Plex_Local_VTK(Vec v, PetscViewer viewer) 513 { 514 DM dm; 515 Vec locv; 516 const char *name; 517 PetscSection section; 518 PetscInt pStart, pEnd; 519 PetscInt numFields; 520 PetscViewerVTKFieldType ft; 521 522 PetscFunctionBegin; 523 PetscCall(VecGetDM(v, &dm)); 524 PetscCall(DMCreateLocalVector(dm, &locv)); /* VTK viewer requires exclusive ownership of the vector */ 525 PetscCall(PetscObjectGetName((PetscObject)v, &name)); 526 PetscCall(PetscObjectSetName((PetscObject)locv, name)); 527 PetscCall(VecCopy(v, locv)); 528 PetscCall(DMGetLocalSection(dm, §ion)); 529 PetscCall(PetscSectionGetNumFields(section, &numFields)); 530 if (!numFields) { 531 PetscCall(DMPlexGetFieldType_Internal(dm, section, PETSC_DETERMINE, &pStart, &pEnd, &ft)); 532 PetscCall(PetscViewerVTKAddField(viewer, (PetscObject)dm, DMPlexVTKWriteAll, PETSC_DEFAULT, ft, PETSC_TRUE, (PetscObject)locv)); 533 } else { 534 PetscInt f; 535 536 for (f = 0; f < numFields; f++) { 537 PetscCall(DMPlexGetFieldType_Internal(dm, section, f, &pStart, &pEnd, &ft)); 538 if (ft == PETSC_VTK_INVALID) continue; 539 PetscCall(PetscObjectReference((PetscObject)locv)); 540 PetscCall(PetscViewerVTKAddField(viewer, (PetscObject)dm, DMPlexVTKWriteAll, f, ft, PETSC_TRUE, (PetscObject)locv)); 541 } 542 PetscCall(VecDestroy(&locv)); 543 } 544 PetscFunctionReturn(PETSC_SUCCESS); 545 } 546 547 PetscErrorCode VecView_Plex_Local(Vec v, PetscViewer viewer) 548 { 549 DM dm; 550 PetscBool isvtk, ishdf5, isdraw, isglvis, iscgns; 551 552 PetscFunctionBegin; 553 PetscCall(VecGetDM(v, &dm)); 554 PetscCheck(dm, PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 555 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERVTK, &isvtk)); 556 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 557 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERDRAW, &isdraw)); 558 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERGLVIS, &isglvis)); 559 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERCGNS, &iscgns)); 560 if (isvtk || ishdf5 || isdraw || isglvis || iscgns) { 561 PetscInt i, numFields; 562 PetscObject fe; 563 PetscBool fem = PETSC_FALSE; 564 Vec locv = v; 565 const char *name; 566 PetscInt step; 567 PetscReal time; 568 569 PetscCall(DMGetNumFields(dm, &numFields)); 570 for (i = 0; i < numFields; i++) { 571 PetscCall(DMGetField(dm, i, NULL, &fe)); 572 if (fe->classid == PETSCFE_CLASSID) { 573 fem = PETSC_TRUE; 574 break; 575 } 576 } 577 if (fem) { 578 PetscObject isZero; 579 580 PetscCall(DMGetLocalVector(dm, &locv)); 581 PetscCall(PetscObjectGetName((PetscObject)v, &name)); 582 PetscCall(PetscObjectSetName((PetscObject)locv, name)); 583 PetscCall(PetscObjectQuery((PetscObject)v, "__Vec_bc_zero__", &isZero)); 584 PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", isZero)); 585 PetscCall(VecCopy(v, locv)); 586 PetscCall(DMGetOutputSequenceNumber(dm, NULL, &time)); 587 PetscCall(DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locv, time, NULL, NULL, NULL)); 588 } 589 if (isvtk) { 590 PetscCall(VecView_Plex_Local_VTK(locv, viewer)); 591 } else if (ishdf5) { 592 #if defined(PETSC_HAVE_HDF5) 593 PetscCall(VecView_Plex_Local_HDF5_Internal(locv, viewer)); 594 #else 595 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 596 #endif 597 } else if (isdraw) { 598 PetscCall(VecView_Plex_Local_Draw(locv, viewer)); 599 } else if (isglvis) { 600 PetscCall(DMGetOutputSequenceNumber(dm, &step, NULL)); 601 PetscCall(PetscViewerGLVisSetSnapId(viewer, step)); 602 PetscCall(VecView_GLVis(locv, viewer)); 603 } else if (iscgns) { 604 #if defined(PETSC_HAVE_CGNS) 605 PetscCall(VecView_Plex_Local_CGNS(locv, viewer)); 606 #else 607 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "CGNS not supported in this build.\nPlease reconfigure using --download-cgns"); 608 #endif 609 } 610 if (fem) { 611 PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", NULL)); 612 PetscCall(DMRestoreLocalVector(dm, &locv)); 613 } 614 } else { 615 PetscBool isseq; 616 617 PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq)); 618 if (isseq) PetscCall(VecView_Seq(v, viewer)); 619 else PetscCall(VecView_MPI(v, viewer)); 620 } 621 PetscFunctionReturn(PETSC_SUCCESS); 622 } 623 624 PetscErrorCode VecView_Plex(Vec v, PetscViewer viewer) 625 { 626 DM dm; 627 PetscBool isvtk, ishdf5, isdraw, isglvis, isexodusii, iscgns; 628 629 PetscFunctionBegin; 630 PetscCall(VecGetDM(v, &dm)); 631 PetscCheck(dm, PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 632 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERVTK, &isvtk)); 633 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 634 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERDRAW, &isdraw)); 635 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERGLVIS, &isglvis)); 636 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERCGNS, &iscgns)); 637 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWEREXODUSII, &isexodusii)); 638 if (isvtk || isdraw || isglvis || iscgns) { 639 Vec locv; 640 PetscObject isZero; 641 const char *name; 642 643 PetscCall(DMGetLocalVector(dm, &locv)); 644 PetscCall(PetscObjectGetName((PetscObject)v, &name)); 645 PetscCall(PetscObjectSetName((PetscObject)locv, name)); 646 PetscCall(DMGlobalToLocalBegin(dm, v, INSERT_VALUES, locv)); 647 PetscCall(DMGlobalToLocalEnd(dm, v, INSERT_VALUES, locv)); 648 PetscCall(PetscObjectQuery((PetscObject)v, "__Vec_bc_zero__", &isZero)); 649 PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", isZero)); 650 PetscCall(VecView_Plex_Local(locv, viewer)); 651 PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", NULL)); 652 PetscCall(DMRestoreLocalVector(dm, &locv)); 653 } else if (ishdf5) { 654 #if defined(PETSC_HAVE_HDF5) 655 PetscCall(VecView_Plex_HDF5_Internal(v, viewer)); 656 #else 657 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 658 #endif 659 } else if (isexodusii) { 660 #if defined(PETSC_HAVE_EXODUSII) 661 PetscCall(VecView_PlexExodusII_Internal(v, viewer)); 662 #else 663 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "ExodusII not supported in this build.\nPlease reconfigure using --download-exodusii"); 664 #endif 665 } else { 666 PetscBool isseq; 667 668 PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq)); 669 if (isseq) PetscCall(VecView_Seq(v, viewer)); 670 else PetscCall(VecView_MPI(v, viewer)); 671 } 672 PetscFunctionReturn(PETSC_SUCCESS); 673 } 674 675 PetscErrorCode VecView_Plex_Native(Vec originalv, PetscViewer viewer) 676 { 677 DM dm; 678 MPI_Comm comm; 679 PetscViewerFormat format; 680 Vec v; 681 PetscBool isvtk, ishdf5; 682 683 PetscFunctionBegin; 684 PetscCall(VecGetDM(originalv, &dm)); 685 PetscCall(PetscObjectGetComm((PetscObject)originalv, &comm)); 686 PetscCheck(dm, comm, PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 687 PetscCall(PetscViewerGetFormat(viewer, &format)); 688 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 689 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERVTK, &isvtk)); 690 if (format == PETSC_VIEWER_NATIVE) { 691 /* Natural ordering is the common case for DMDA, NATIVE means plain vector, for PLEX is the opposite */ 692 /* this need a better fix */ 693 if (dm->useNatural) { 694 if (dm->sfNatural) { 695 const char *vecname; 696 PetscInt n, nroots; 697 698 PetscCall(VecGetLocalSize(originalv, &n)); 699 PetscCall(PetscSFGetGraph(dm->sfNatural, &nroots, NULL, NULL, NULL)); 700 if (n == nroots) { 701 PetscCall(DMPlexCreateNaturalVector(dm, &v)); 702 PetscCall(DMPlexGlobalToNaturalBegin(dm, originalv, v)); 703 PetscCall(DMPlexGlobalToNaturalEnd(dm, originalv, v)); 704 PetscCall(PetscObjectGetName((PetscObject)originalv, &vecname)); 705 PetscCall(PetscObjectSetName((PetscObject)v, vecname)); 706 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "DM global to natural SF only handles global vectors"); 707 } else SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "DM global to natural SF was not created"); 708 } else v = originalv; 709 } else v = originalv; 710 711 if (ishdf5) { 712 #if defined(PETSC_HAVE_HDF5) 713 PetscCall(VecView_Plex_HDF5_Native_Internal(v, viewer)); 714 #else 715 SETERRQ(comm, PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 716 #endif 717 } else if (isvtk) { 718 SETERRQ(comm, PETSC_ERR_SUP, "VTK format does not support viewing in natural order. Please switch to HDF5."); 719 } else { 720 PetscBool isseq; 721 722 PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq)); 723 if (isseq) PetscCall(VecView_Seq(v, viewer)); 724 else PetscCall(VecView_MPI(v, viewer)); 725 } 726 if (v != originalv) PetscCall(VecDestroy(&v)); 727 PetscFunctionReturn(PETSC_SUCCESS); 728 } 729 730 PetscErrorCode VecLoad_Plex_Local(Vec v, PetscViewer viewer) 731 { 732 DM dm; 733 PetscBool ishdf5; 734 735 PetscFunctionBegin; 736 PetscCall(VecGetDM(v, &dm)); 737 PetscCheck(dm, PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 738 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 739 if (ishdf5) { 740 DM dmBC; 741 Vec gv; 742 const char *name; 743 744 PetscCall(DMGetOutputDM(dm, &dmBC)); 745 PetscCall(DMGetGlobalVector(dmBC, &gv)); 746 PetscCall(PetscObjectGetName((PetscObject)v, &name)); 747 PetscCall(PetscObjectSetName((PetscObject)gv, name)); 748 PetscCall(VecLoad_Default(gv, viewer)); 749 PetscCall(DMGlobalToLocalBegin(dmBC, gv, INSERT_VALUES, v)); 750 PetscCall(DMGlobalToLocalEnd(dmBC, gv, INSERT_VALUES, v)); 751 PetscCall(DMRestoreGlobalVector(dmBC, &gv)); 752 } else PetscCall(VecLoad_Default(v, viewer)); 753 PetscFunctionReturn(PETSC_SUCCESS); 754 } 755 756 PetscErrorCode VecLoad_Plex(Vec v, PetscViewer viewer) 757 { 758 DM dm; 759 PetscBool ishdf5, isexodusii; 760 761 PetscFunctionBegin; 762 PetscCall(VecGetDM(v, &dm)); 763 PetscCheck(dm, PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 764 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 765 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWEREXODUSII, &isexodusii)); 766 if (ishdf5) { 767 #if defined(PETSC_HAVE_HDF5) 768 PetscCall(VecLoad_Plex_HDF5_Internal(v, viewer)); 769 #else 770 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 771 #endif 772 } else if (isexodusii) { 773 #if defined(PETSC_HAVE_EXODUSII) 774 PetscCall(VecLoad_PlexExodusII_Internal(v, viewer)); 775 #else 776 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "ExodusII not supported in this build.\nPlease reconfigure using --download-exodusii"); 777 #endif 778 } else PetscCall(VecLoad_Default(v, viewer)); 779 PetscFunctionReturn(PETSC_SUCCESS); 780 } 781 782 PetscErrorCode VecLoad_Plex_Native(Vec originalv, PetscViewer viewer) 783 { 784 DM dm; 785 PetscViewerFormat format; 786 PetscBool ishdf5; 787 788 PetscFunctionBegin; 789 PetscCall(VecGetDM(originalv, &dm)); 790 PetscCheck(dm, PetscObjectComm((PetscObject)originalv), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 791 PetscCall(PetscViewerGetFormat(viewer, &format)); 792 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 793 if (format == PETSC_VIEWER_NATIVE) { 794 if (dm->useNatural) { 795 if (dm->sfNatural) { 796 if (ishdf5) { 797 #if defined(PETSC_HAVE_HDF5) 798 Vec v; 799 const char *vecname; 800 801 PetscCall(DMPlexCreateNaturalVector(dm, &v)); 802 PetscCall(PetscObjectGetName((PetscObject)originalv, &vecname)); 803 PetscCall(PetscObjectSetName((PetscObject)v, vecname)); 804 PetscCall(VecLoad_Plex_HDF5_Native_Internal(v, viewer)); 805 PetscCall(DMPlexNaturalToGlobalBegin(dm, v, originalv)); 806 PetscCall(DMPlexNaturalToGlobalEnd(dm, v, originalv)); 807 PetscCall(VecDestroy(&v)); 808 #else 809 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 810 #endif 811 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Reading in natural order is not supported for anything but HDF5."); 812 } 813 } else PetscCall(VecLoad_Default(originalv, viewer)); 814 } 815 PetscFunctionReturn(PETSC_SUCCESS); 816 } 817 818 PETSC_UNUSED static PetscErrorCode DMPlexView_Ascii_Geometry(DM dm, PetscViewer viewer) 819 { 820 PetscSection coordSection; 821 Vec coordinates; 822 DMLabel depthLabel, celltypeLabel; 823 const char *name[4]; 824 const PetscScalar *a; 825 PetscInt dim, pStart, pEnd, cStart, cEnd, c; 826 827 PetscFunctionBegin; 828 PetscCall(DMGetDimension(dm, &dim)); 829 PetscCall(DMGetCoordinatesLocal(dm, &coordinates)); 830 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 831 PetscCall(DMPlexGetDepthLabel(dm, &depthLabel)); 832 PetscCall(DMPlexGetCellTypeLabel(dm, &celltypeLabel)); 833 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 834 PetscCall(PetscSectionGetChart(coordSection, &pStart, &pEnd)); 835 PetscCall(VecGetArrayRead(coordinates, &a)); 836 name[0] = "vertex"; 837 name[1] = "edge"; 838 name[dim - 1] = "face"; 839 name[dim] = "cell"; 840 for (c = cStart; c < cEnd; ++c) { 841 PetscInt *closure = NULL; 842 PetscInt closureSize, cl, ct; 843 844 PetscCall(DMLabelGetValue(celltypeLabel, c, &ct)); 845 PetscCall(PetscViewerASCIIPrintf(viewer, "Geometry for cell %" PetscInt_FMT " polytope type %s:\n", c, DMPolytopeTypes[ct])); 846 PetscCall(DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 847 PetscCall(PetscViewerASCIIPushTab(viewer)); 848 for (cl = 0; cl < closureSize * 2; cl += 2) { 849 PetscInt point = closure[cl], depth, dof, off, d, p; 850 851 if ((point < pStart) || (point >= pEnd)) continue; 852 PetscCall(PetscSectionGetDof(coordSection, point, &dof)); 853 if (!dof) continue; 854 PetscCall(DMLabelGetValue(depthLabel, point, &depth)); 855 PetscCall(PetscSectionGetOffset(coordSection, point, &off)); 856 PetscCall(PetscViewerASCIIPrintf(viewer, "%s %" PetscInt_FMT " coords:", name[depth], point)); 857 for (p = 0; p < dof / dim; ++p) { 858 PetscCall(PetscViewerASCIIPrintf(viewer, " (")); 859 for (d = 0; d < dim; ++d) { 860 if (d > 0) PetscCall(PetscViewerASCIIPrintf(viewer, ", ")); 861 PetscCall(PetscViewerASCIIPrintf(viewer, "%g", (double)PetscRealPart(a[off + p * dim + d]))); 862 } 863 PetscCall(PetscViewerASCIIPrintf(viewer, ")")); 864 } 865 PetscCall(PetscViewerASCIIPrintf(viewer, "\n")); 866 } 867 PetscCall(DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 868 PetscCall(PetscViewerASCIIPopTab(viewer)); 869 } 870 PetscCall(VecRestoreArrayRead(coordinates, &a)); 871 PetscFunctionReturn(PETSC_SUCCESS); 872 } 873 874 typedef enum { 875 CS_CARTESIAN, 876 CS_POLAR, 877 CS_CYLINDRICAL, 878 CS_SPHERICAL 879 } CoordSystem; 880 const char *CoordSystems[] = {"cartesian", "polar", "cylindrical", "spherical", "CoordSystem", "CS_", NULL}; 881 882 static PetscErrorCode DMPlexView_Ascii_Coordinates(PetscViewer viewer, CoordSystem cs, PetscInt dim, const PetscScalar x[]) 883 { 884 PetscInt i; 885 886 PetscFunctionBegin; 887 if (dim > 3) { 888 for (i = 0; i < dim; ++i) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %g", (double)PetscRealPart(x[i]))); 889 } else { 890 PetscReal coords[3], trcoords[3] = {0., 0., 0.}; 891 892 for (i = 0; i < dim; ++i) coords[i] = PetscRealPart(x[i]); 893 switch (cs) { 894 case CS_CARTESIAN: 895 for (i = 0; i < dim; ++i) trcoords[i] = coords[i]; 896 break; 897 case CS_POLAR: 898 PetscCheck(dim == 2, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Polar coordinates are for 2 dimension, not %" PetscInt_FMT, dim); 899 trcoords[0] = PetscSqrtReal(PetscSqr(coords[0]) + PetscSqr(coords[1])); 900 trcoords[1] = PetscAtan2Real(coords[1], coords[0]); 901 break; 902 case CS_CYLINDRICAL: 903 PetscCheck(dim == 3, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cylindrical coordinates are for 3 dimension, not %" PetscInt_FMT, dim); 904 trcoords[0] = PetscSqrtReal(PetscSqr(coords[0]) + PetscSqr(coords[1])); 905 trcoords[1] = PetscAtan2Real(coords[1], coords[0]); 906 trcoords[2] = coords[2]; 907 break; 908 case CS_SPHERICAL: 909 PetscCheck(dim == 3, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Spherical coordinates are for 3 dimension, not %" PetscInt_FMT, dim); 910 trcoords[0] = PetscSqrtReal(PetscSqr(coords[0]) + PetscSqr(coords[1]) + PetscSqr(coords[2])); 911 trcoords[1] = PetscAtan2Real(PetscSqrtReal(PetscSqr(coords[0]) + PetscSqr(coords[1])), coords[2]); 912 trcoords[2] = PetscAtan2Real(coords[1], coords[0]); 913 break; 914 } 915 for (i = 0; i < dim; ++i) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %g", (double)trcoords[i])); 916 } 917 PetscFunctionReturn(PETSC_SUCCESS); 918 } 919 920 static PetscErrorCode DMPlexView_Ascii(DM dm, PetscViewer viewer) 921 { 922 DM_Plex *mesh = (DM_Plex *)dm->data; 923 DM cdm, cdmCell; 924 PetscSection coordSection, coordSectionCell; 925 Vec coordinates, coordinatesCell; 926 PetscViewerFormat format; 927 928 PetscFunctionBegin; 929 PetscCall(PetscViewerGetFormat(viewer, &format)); 930 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 931 const char *name; 932 PetscInt dim, cellHeight, maxConeSize, maxSupportSize; 933 PetscInt pStart, pEnd, p, numLabels, l; 934 PetscMPIInt rank, size; 935 936 PetscCall(DMGetCoordinateDM(dm, &cdm)); 937 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 938 PetscCall(DMGetCoordinatesLocal(dm, &coordinates)); 939 PetscCall(DMGetCellCoordinateDM(dm, &cdmCell)); 940 PetscCall(DMGetCellCoordinateSection(dm, &coordSectionCell)); 941 PetscCall(DMGetCellCoordinatesLocal(dm, &coordinatesCell)); 942 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 943 PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size)); 944 PetscCall(PetscObjectGetName((PetscObject)dm, &name)); 945 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 946 PetscCall(DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize)); 947 PetscCall(DMGetDimension(dm, &dim)); 948 PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight)); 949 if (name) PetscCall(PetscViewerASCIIPrintf(viewer, "%s in %" PetscInt_FMT " dimension%s:\n", name, dim, dim == 1 ? "" : "s")); 950 else PetscCall(PetscViewerASCIIPrintf(viewer, "Mesh in %" PetscInt_FMT " dimension%s:\n", dim, dim == 1 ? "" : "s")); 951 if (cellHeight) PetscCall(PetscViewerASCIIPrintf(viewer, " Cells are at height %" PetscInt_FMT "\n", cellHeight)); 952 PetscCall(PetscViewerASCIIPrintf(viewer, "Supports:\n")); 953 PetscCall(PetscViewerASCIIPushSynchronized(viewer)); 954 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "[%d] Max support size: %" PetscInt_FMT "\n", rank, maxSupportSize)); 955 for (p = pStart; p < pEnd; ++p) { 956 PetscInt dof, off, s; 957 958 PetscCall(PetscSectionGetDof(mesh->supportSection, p, &dof)); 959 PetscCall(PetscSectionGetOffset(mesh->supportSection, p, &off)); 960 for (s = off; s < off + dof; ++s) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "[%d]: %" PetscInt_FMT " ----> %" PetscInt_FMT "\n", rank, p, mesh->supports[s])); 961 } 962 PetscCall(PetscViewerFlush(viewer)); 963 PetscCall(PetscViewerASCIIPrintf(viewer, "Cones:\n")); 964 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "[%d] Max cone size: %" PetscInt_FMT "\n", rank, maxConeSize)); 965 for (p = pStart; p < pEnd; ++p) { 966 PetscInt dof, off, c; 967 968 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 969 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 970 for (c = off; c < off + dof; ++c) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "[%d]: %" PetscInt_FMT " <---- %" PetscInt_FMT " (%" PetscInt_FMT ")\n", rank, p, mesh->cones[c], mesh->coneOrientations[c])); 971 } 972 PetscCall(PetscViewerFlush(viewer)); 973 PetscCall(PetscViewerASCIIPopSynchronized(viewer)); 974 if (coordSection && coordinates) { 975 CoordSystem cs = CS_CARTESIAN; 976 const PetscScalar *array, *arrayCell = NULL; 977 PetscInt Nf, Nc, pvStart, pvEnd, pcStart = PETSC_MAX_INT, pcEnd = PETSC_MIN_INT, pStart, pEnd, p; 978 PetscMPIInt rank; 979 const char *name; 980 981 PetscCall(PetscOptionsGetEnum(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_coord_system", CoordSystems, (PetscEnum *)&cs, NULL)); 982 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank)); 983 PetscCall(PetscSectionGetNumFields(coordSection, &Nf)); 984 PetscCheck(Nf == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Coordinate section should have 1 field, not %" PetscInt_FMT, Nf); 985 PetscCall(PetscSectionGetFieldComponents(coordSection, 0, &Nc)); 986 PetscCall(PetscSectionGetChart(coordSection, &pvStart, &pvEnd)); 987 if (coordSectionCell) PetscCall(PetscSectionGetChart(coordSectionCell, &pcStart, &pcEnd)); 988 pStart = PetscMin(pvStart, pcStart); 989 pEnd = PetscMax(pvEnd, pcEnd); 990 PetscCall(PetscObjectGetName((PetscObject)coordinates, &name)); 991 PetscCall(PetscViewerASCIIPrintf(viewer, "%s with %" PetscInt_FMT " fields\n", name, Nf)); 992 PetscCall(PetscViewerASCIIPrintf(viewer, " field 0 with %" PetscInt_FMT " components\n", Nc)); 993 if (cs != CS_CARTESIAN) PetscCall(PetscViewerASCIIPrintf(viewer, " output coordinate system: %s\n", CoordSystems[cs])); 994 995 PetscCall(VecGetArrayRead(coordinates, &array)); 996 if (coordinatesCell) PetscCall(VecGetArrayRead(coordinatesCell, &arrayCell)); 997 PetscCall(PetscViewerASCIIPushSynchronized(viewer)); 998 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "Process %d:\n", rank)); 999 for (p = pStart; p < pEnd; ++p) { 1000 PetscInt dof, off; 1001 1002 if (p >= pvStart && p < pvEnd) { 1003 PetscCall(PetscSectionGetDof(coordSection, p, &dof)); 1004 PetscCall(PetscSectionGetOffset(coordSection, p, &off)); 1005 if (dof) { 1006 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " (%4" PetscInt_FMT ") dim %2" PetscInt_FMT " offset %3" PetscInt_FMT, p, dof, off)); 1007 PetscCall(DMPlexView_Ascii_Coordinates(viewer, cs, dof, &array[off])); 1008 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\n")); 1009 } 1010 } 1011 if (cdmCell && p >= pcStart && p < pcEnd) { 1012 PetscCall(PetscSectionGetDof(coordSectionCell, p, &dof)); 1013 PetscCall(PetscSectionGetOffset(coordSectionCell, p, &off)); 1014 if (dof) { 1015 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " (%4" PetscInt_FMT ") dim %2" PetscInt_FMT " offset %3" PetscInt_FMT, p, dof, off)); 1016 PetscCall(DMPlexView_Ascii_Coordinates(viewer, cs, dof, &arrayCell[off])); 1017 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\n")); 1018 } 1019 } 1020 } 1021 PetscCall(PetscViewerFlush(viewer)); 1022 PetscCall(PetscViewerASCIIPopSynchronized(viewer)); 1023 PetscCall(VecRestoreArrayRead(coordinates, &array)); 1024 if (coordinatesCell) PetscCall(VecRestoreArrayRead(coordinatesCell, &arrayCell)); 1025 } 1026 PetscCall(DMGetNumLabels(dm, &numLabels)); 1027 if (numLabels) PetscCall(PetscViewerASCIIPrintf(viewer, "Labels:\n")); 1028 for (l = 0; l < numLabels; ++l) { 1029 DMLabel label; 1030 PetscBool isdepth; 1031 const char *name; 1032 1033 PetscCall(DMGetLabelName(dm, l, &name)); 1034 PetscCall(PetscStrcmp(name, "depth", &isdepth)); 1035 if (isdepth) continue; 1036 PetscCall(DMGetLabel(dm, name, &label)); 1037 PetscCall(DMLabelView(label, viewer)); 1038 } 1039 if (size > 1) { 1040 PetscSF sf; 1041 1042 PetscCall(DMGetPointSF(dm, &sf)); 1043 PetscCall(PetscSFView(sf, viewer)); 1044 } 1045 if (mesh->periodic.face_sf) PetscCall(PetscSFView(mesh->periodic.face_sf, viewer)); 1046 PetscCall(PetscViewerFlush(viewer)); 1047 } else if (format == PETSC_VIEWER_ASCII_LATEX) { 1048 const char *name, *color; 1049 const char *defcolors[3] = {"gray", "orange", "green"}; 1050 const char *deflcolors[4] = {"blue", "cyan", "red", "magenta"}; 1051 char lname[PETSC_MAX_PATH_LEN]; 1052 PetscReal scale = 2.0; 1053 PetscReal tikzscale = 1.0; 1054 PetscBool useNumbers = PETSC_TRUE, drawNumbers[4], drawColors[4], useLabels, useColors, plotEdges, drawHasse = PETSC_FALSE; 1055 double tcoords[3]; 1056 PetscScalar *coords; 1057 PetscInt numLabels, l, numColors, numLColors, dim, d, depth, cStart, cEnd, c, vStart, vEnd, v, eStart = 0, eEnd = 0, e, p, n; 1058 PetscMPIInt rank, size; 1059 char **names, **colors, **lcolors; 1060 PetscBool flg, lflg; 1061 PetscBT wp = NULL; 1062 PetscInt pEnd, pStart; 1063 1064 PetscCall(DMGetCoordinateDM(dm, &cdm)); 1065 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 1066 PetscCall(DMGetCoordinatesLocal(dm, &coordinates)); 1067 PetscCall(DMGetCellCoordinateDM(dm, &cdmCell)); 1068 PetscCall(DMGetCellCoordinateSection(dm, &coordSectionCell)); 1069 PetscCall(DMGetCellCoordinatesLocal(dm, &coordinatesCell)); 1070 PetscCall(DMGetDimension(dm, &dim)); 1071 PetscCall(DMPlexGetDepth(dm, &depth)); 1072 PetscCall(DMGetNumLabels(dm, &numLabels)); 1073 numLabels = PetscMax(numLabels, 10); 1074 numColors = 10; 1075 numLColors = 10; 1076 PetscCall(PetscCalloc3(numLabels, &names, numColors, &colors, numLColors, &lcolors)); 1077 PetscCall(PetscOptionsGetReal(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_scale", &scale, NULL)); 1078 PetscCall(PetscOptionsGetReal(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_tikzscale", &tikzscale, NULL)); 1079 PetscCall(PetscOptionsGetBool(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_numbers", &useNumbers, NULL)); 1080 for (d = 0; d < 4; ++d) drawNumbers[d] = useNumbers; 1081 for (d = 0; d < 4; ++d) drawColors[d] = PETSC_TRUE; 1082 n = 4; 1083 PetscCall(PetscOptionsGetBoolArray(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_numbers_depth", drawNumbers, &n, &flg)); 1084 PetscCheck(!flg || n == dim + 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_SIZ, "Number of flags %" PetscInt_FMT " != %" PetscInt_FMT " dim+1", n, dim + 1); 1085 n = 4; 1086 PetscCall(PetscOptionsGetBoolArray(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_colors_depth", drawColors, &n, &flg)); 1087 PetscCheck(!flg || n == dim + 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_SIZ, "Number of flags %" PetscInt_FMT " != %" PetscInt_FMT " dim+1", n, dim + 1); 1088 PetscCall(PetscOptionsGetStringArray(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_labels", names, &numLabels, &useLabels)); 1089 if (!useLabels) numLabels = 0; 1090 PetscCall(PetscOptionsGetStringArray(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_colors", colors, &numColors, &useColors)); 1091 if (!useColors) { 1092 numColors = 3; 1093 for (c = 0; c < numColors; ++c) PetscCall(PetscStrallocpy(defcolors[c], &colors[c])); 1094 } 1095 PetscCall(PetscOptionsGetStringArray(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_lcolors", lcolors, &numLColors, &useColors)); 1096 if (!useColors) { 1097 numLColors = 4; 1098 for (c = 0; c < numLColors; ++c) PetscCall(PetscStrallocpy(deflcolors[c], &lcolors[c])); 1099 } 1100 PetscCall(PetscOptionsGetString(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_label_filter", lname, sizeof(lname), &lflg)); 1101 plotEdges = (PetscBool)(depth > 1 && drawNumbers[1] && dim < 3); 1102 PetscCall(PetscOptionsGetBool(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_edges", &plotEdges, &flg)); 1103 PetscCheck(!flg || !plotEdges || depth >= dim, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Mesh must be interpolated"); 1104 if (depth < dim) plotEdges = PETSC_FALSE; 1105 PetscCall(PetscOptionsGetBool(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_hasse", &drawHasse, NULL)); 1106 1107 /* filter points with labelvalue != labeldefaultvalue */ 1108 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 1109 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 1110 PetscCall(DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd)); 1111 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 1112 if (lflg) { 1113 DMLabel lbl; 1114 1115 PetscCall(DMGetLabel(dm, lname, &lbl)); 1116 if (lbl) { 1117 PetscInt val, defval; 1118 1119 PetscCall(DMLabelGetDefaultValue(lbl, &defval)); 1120 PetscCall(PetscBTCreate(pEnd - pStart, &wp)); 1121 for (c = pStart; c < pEnd; c++) { 1122 PetscInt *closure = NULL; 1123 PetscInt closureSize; 1124 1125 PetscCall(DMLabelGetValue(lbl, c, &val)); 1126 if (val == defval) continue; 1127 1128 PetscCall(DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 1129 for (p = 0; p < closureSize * 2; p += 2) PetscCall(PetscBTSet(wp, closure[p] - pStart)); 1130 PetscCall(DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 1131 } 1132 } 1133 } 1134 1135 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 1136 PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size)); 1137 PetscCall(PetscObjectGetName((PetscObject)dm, &name)); 1138 PetscCall(PetscViewerASCIIPrintf(viewer, "\ 1139 \\documentclass[tikz]{standalone}\n\n\ 1140 \\usepackage{pgflibraryshapes}\n\ 1141 \\usetikzlibrary{backgrounds}\n\ 1142 \\usetikzlibrary{arrows}\n\ 1143 \\begin{document}\n")); 1144 if (size > 1) { 1145 PetscCall(PetscViewerASCIIPrintf(viewer, "%s for process ", name)); 1146 for (p = 0; p < size; ++p) { 1147 if (p) PetscCall(PetscViewerASCIIPrintf(viewer, (p == size - 1) ? ", and " : ", ")); 1148 PetscCall(PetscViewerASCIIPrintf(viewer, "{\\textcolor{%s}%" PetscInt_FMT "}", colors[p % numColors], p)); 1149 } 1150 PetscCall(PetscViewerASCIIPrintf(viewer, ".\n\n\n")); 1151 } 1152 if (drawHasse) { 1153 PetscInt maxStratum = PetscMax(vEnd - vStart, PetscMax(eEnd - eStart, cEnd - cStart)); 1154 1155 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\vStart}{%" PetscInt_FMT "}\n", vStart)); 1156 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\vEnd}{%" PetscInt_FMT "}\n", vEnd - 1)); 1157 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\numVertices}{%" PetscInt_FMT "}\n", vEnd - vStart)); 1158 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\vShift}{%.2f}\n", 3 + (maxStratum - (vEnd - vStart)) / 2.)); 1159 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\eStart}{%" PetscInt_FMT "}\n", eStart)); 1160 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\eEnd}{%" PetscInt_FMT "}\n", eEnd - 1)); 1161 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\eShift}{%.2f}\n", 3 + (maxStratum - (eEnd - eStart)) / 2.)); 1162 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\numEdges}{%" PetscInt_FMT "}\n", eEnd - eStart)); 1163 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\cStart}{%" PetscInt_FMT "}\n", cStart)); 1164 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\cEnd}{%" PetscInt_FMT "}\n", cEnd - 1)); 1165 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\numCells}{%" PetscInt_FMT "}\n", cEnd - cStart)); 1166 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\cShift}{%.2f}\n", 3 + (maxStratum - (cEnd - cStart)) / 2.)); 1167 } 1168 PetscCall(PetscViewerASCIIPrintf(viewer, "\\begin{tikzpicture}[scale = %g,font=\\fontsize{8}{8}\\selectfont]\n", (double)tikzscale)); 1169 1170 /* Plot vertices */ 1171 PetscCall(VecGetArray(coordinates, &coords)); 1172 PetscCall(PetscViewerASCIIPushSynchronized(viewer)); 1173 for (v = vStart; v < vEnd; ++v) { 1174 PetscInt off, dof, d; 1175 PetscBool isLabeled = PETSC_FALSE; 1176 1177 if (wp && !PetscBTLookup(wp, v - pStart)) continue; 1178 PetscCall(PetscSectionGetDof(coordSection, v, &dof)); 1179 PetscCall(PetscSectionGetOffset(coordSection, v, &off)); 1180 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\\path (")); 1181 PetscCheck(dof <= 3, PETSC_COMM_SELF, PETSC_ERR_PLIB, "coordSection vertex %" PetscInt_FMT " has dof %" PetscInt_FMT " > 3", v, dof); 1182 for (d = 0; d < dof; ++d) { 1183 tcoords[d] = (double)(scale * PetscRealPart(coords[off + d])); 1184 tcoords[d] = PetscAbs(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d]; 1185 } 1186 /* Rotate coordinates since PGF makes z point out of the page instead of up */ 1187 if (dim == 3) { 1188 PetscReal tmp = tcoords[1]; 1189 tcoords[1] = tcoords[2]; 1190 tcoords[2] = -tmp; 1191 } 1192 for (d = 0; d < dof; ++d) { 1193 if (d > 0) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ",")); 1194 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "%g", (double)tcoords[d])); 1195 } 1196 if (drawHasse) color = colors[0 % numColors]; 1197 else color = colors[rank % numColors]; 1198 for (l = 0; l < numLabels; ++l) { 1199 PetscInt val; 1200 PetscCall(DMGetLabelValue(dm, names[l], v, &val)); 1201 if (val >= 0) { 1202 color = lcolors[l % numLColors]; 1203 isLabeled = PETSC_TRUE; 1204 break; 1205 } 1206 } 1207 if (drawNumbers[0]) { 1208 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ") node(%" PetscInt_FMT "_%d) [draw,shape=circle,color=%s] {%" PetscInt_FMT "};\n", v, rank, color, v)); 1209 } else if (drawColors[0]) { 1210 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ") node(%" PetscInt_FMT "_%d) [fill,inner sep=%dpt,shape=circle,color=%s] {};\n", v, rank, !isLabeled ? 1 : 2, color)); 1211 } else PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ") node(%" PetscInt_FMT "_%d) [] {};\n", v, rank)); 1212 } 1213 PetscCall(VecRestoreArray(coordinates, &coords)); 1214 PetscCall(PetscViewerFlush(viewer)); 1215 /* Plot edges */ 1216 if (plotEdges) { 1217 PetscCall(VecGetArray(coordinates, &coords)); 1218 PetscCall(PetscViewerASCIIPrintf(viewer, "\\path\n")); 1219 for (e = eStart; e < eEnd; ++e) { 1220 const PetscInt *cone; 1221 PetscInt coneSize, offA, offB, dof, d; 1222 1223 if (wp && !PetscBTLookup(wp, e - pStart)) continue; 1224 PetscCall(DMPlexGetConeSize(dm, e, &coneSize)); 1225 PetscCheck(coneSize == 2, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Edge %" PetscInt_FMT " cone should have two vertices, not %" PetscInt_FMT, e, coneSize); 1226 PetscCall(DMPlexGetCone(dm, e, &cone)); 1227 PetscCall(PetscSectionGetDof(coordSection, cone[0], &dof)); 1228 PetscCall(PetscSectionGetOffset(coordSection, cone[0], &offA)); 1229 PetscCall(PetscSectionGetOffset(coordSection, cone[1], &offB)); 1230 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "(")); 1231 for (d = 0; d < dof; ++d) { 1232 tcoords[d] = (double)(0.5 * scale * PetscRealPart(coords[offA + d] + coords[offB + d])); 1233 tcoords[d] = PetscAbs(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d]; 1234 } 1235 /* Rotate coordinates since PGF makes z point out of the page instead of up */ 1236 if (dim == 3) { 1237 PetscReal tmp = tcoords[1]; 1238 tcoords[1] = tcoords[2]; 1239 tcoords[2] = -tmp; 1240 } 1241 for (d = 0; d < dof; ++d) { 1242 if (d > 0) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ",")); 1243 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "%g", (double)tcoords[d])); 1244 } 1245 if (drawHasse) color = colors[1 % numColors]; 1246 else color = colors[rank % numColors]; 1247 for (l = 0; l < numLabels; ++l) { 1248 PetscInt val; 1249 PetscCall(DMGetLabelValue(dm, names[l], e, &val)); 1250 if (val >= 0) { 1251 color = lcolors[l % numLColors]; 1252 break; 1253 } 1254 } 1255 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ") node(%" PetscInt_FMT "_%d) [draw,shape=circle,color=%s] {%" PetscInt_FMT "} --\n", e, rank, color, e)); 1256 } 1257 PetscCall(VecRestoreArray(coordinates, &coords)); 1258 PetscCall(PetscViewerFlush(viewer)); 1259 PetscCall(PetscViewerASCIIPrintf(viewer, "(0,0);\n")); 1260 } 1261 /* Plot cells */ 1262 if (dim == 3 || !drawNumbers[1]) { 1263 for (e = eStart; e < eEnd; ++e) { 1264 const PetscInt *cone; 1265 1266 if (wp && !PetscBTLookup(wp, e - pStart)) continue; 1267 color = colors[rank % numColors]; 1268 for (l = 0; l < numLabels; ++l) { 1269 PetscInt val; 1270 PetscCall(DMGetLabelValue(dm, names[l], e, &val)); 1271 if (val >= 0) { 1272 color = lcolors[l % numLColors]; 1273 break; 1274 } 1275 } 1276 PetscCall(DMPlexGetCone(dm, e, &cone)); 1277 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\\draw[color=%s] (%" PetscInt_FMT "_%d) -- (%" PetscInt_FMT "_%d);\n", color, cone[0], rank, cone[1], rank)); 1278 } 1279 } else { 1280 DMPolytopeType ct; 1281 1282 /* Drawing a 2D polygon */ 1283 for (c = cStart; c < cEnd; ++c) { 1284 if (wp && !PetscBTLookup(wp, c - pStart)) continue; 1285 PetscCall(DMPlexGetCellType(dm, c, &ct)); 1286 if (DMPolytopeTypeIsHybrid(ct)) { 1287 const PetscInt *cone; 1288 PetscInt coneSize, e; 1289 1290 PetscCall(DMPlexGetCone(dm, c, &cone)); 1291 PetscCall(DMPlexGetConeSize(dm, c, &coneSize)); 1292 for (e = 0; e < coneSize; ++e) { 1293 const PetscInt *econe; 1294 1295 PetscCall(DMPlexGetCone(dm, cone[e], &econe)); 1296 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\\draw[color=%s] (%" PetscInt_FMT "_%d) -- (%" PetscInt_FMT "_%d) -- (%" PetscInt_FMT "_%d);\n", colors[rank % numColors], econe[0], rank, cone[e], rank, econe[1], rank)); 1297 } 1298 } else { 1299 PetscInt *closure = NULL; 1300 PetscInt closureSize, Nv = 0, v; 1301 1302 PetscCall(DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 1303 for (p = 0; p < closureSize * 2; p += 2) { 1304 const PetscInt point = closure[p]; 1305 1306 if ((point >= vStart) && (point < vEnd)) closure[Nv++] = point; 1307 } 1308 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\\draw[color=%s] ", colors[rank % numColors])); 1309 for (v = 0; v <= Nv; ++v) { 1310 const PetscInt vertex = closure[v % Nv]; 1311 1312 if (v > 0) { 1313 if (plotEdges) { 1314 const PetscInt *edge; 1315 PetscInt endpoints[2], ne; 1316 1317 endpoints[0] = closure[v - 1]; 1318 endpoints[1] = vertex; 1319 PetscCall(DMPlexGetJoin(dm, 2, endpoints, &ne, &edge)); 1320 PetscCheck(ne == 1, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find edge for vertices %" PetscInt_FMT ", %" PetscInt_FMT, endpoints[0], endpoints[1]); 1321 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " -- (%" PetscInt_FMT "_%d) -- ", edge[0], rank)); 1322 PetscCall(DMPlexRestoreJoin(dm, 2, endpoints, &ne, &edge)); 1323 } else PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " -- ")); 1324 } 1325 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "(%" PetscInt_FMT "_%d)", vertex, rank)); 1326 } 1327 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ";\n")); 1328 PetscCall(DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 1329 } 1330 } 1331 } 1332 for (c = cStart; c < cEnd; ++c) { 1333 double ccoords[3] = {0.0, 0.0, 0.0}; 1334 PetscBool isLabeled = PETSC_FALSE; 1335 PetscScalar *cellCoords = NULL; 1336 const PetscScalar *array; 1337 PetscInt numCoords, cdim, d; 1338 PetscBool isDG; 1339 1340 if (wp && !PetscBTLookup(wp, c - pStart)) continue; 1341 PetscCall(DMGetCoordinateDim(dm, &cdim)); 1342 PetscCall(DMPlexGetCellCoordinates(dm, c, &isDG, &numCoords, &array, &cellCoords)); 1343 PetscCheck(!(numCoords % cdim), PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "coordinate dim %" PetscInt_FMT " does not divide numCoords %" PetscInt_FMT, cdim, numCoords); 1344 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\\path (")); 1345 for (p = 0; p < numCoords / cdim; ++p) { 1346 for (d = 0; d < cdim; ++d) { 1347 tcoords[d] = (double)(scale * PetscRealPart(cellCoords[p * cdim + d])); 1348 tcoords[d] = PetscAbs(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d]; 1349 } 1350 /* Rotate coordinates since PGF makes z point out of the page instead of up */ 1351 if (cdim == 3) { 1352 PetscReal tmp = tcoords[1]; 1353 tcoords[1] = tcoords[2]; 1354 tcoords[2] = -tmp; 1355 } 1356 for (d = 0; d < dim; ++d) ccoords[d] += tcoords[d]; 1357 } 1358 for (d = 0; d < cdim; ++d) ccoords[d] /= (numCoords / cdim); 1359 PetscCall(DMPlexRestoreCellCoordinates(dm, c, &isDG, &numCoords, &array, &cellCoords)); 1360 for (d = 0; d < cdim; ++d) { 1361 if (d > 0) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ",")); 1362 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "%g", (double)ccoords[d])); 1363 } 1364 if (drawHasse) color = colors[depth % numColors]; 1365 else color = colors[rank % numColors]; 1366 for (l = 0; l < numLabels; ++l) { 1367 PetscInt val; 1368 PetscCall(DMGetLabelValue(dm, names[l], c, &val)); 1369 if (val >= 0) { 1370 color = lcolors[l % numLColors]; 1371 isLabeled = PETSC_TRUE; 1372 break; 1373 } 1374 } 1375 if (drawNumbers[dim]) { 1376 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ") node(%" PetscInt_FMT "_%d) [draw,shape=circle,color=%s] {%" PetscInt_FMT "};\n", c, rank, color, c)); 1377 } else if (drawColors[dim]) { 1378 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ") node(%" PetscInt_FMT "_%d) [fill,inner sep=%dpt,shape=circle,color=%s] {};\n", c, rank, !isLabeled ? 1 : 2, color)); 1379 } else PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ") node(%" PetscInt_FMT "_%d) [] {};\n", c, rank)); 1380 } 1381 if (drawHasse) { 1382 color = colors[depth % numColors]; 1383 PetscCall(PetscViewerASCIIPrintf(viewer, "%% Cells\n")); 1384 PetscCall(PetscViewerASCIIPrintf(viewer, "\\foreach \\c in {\\cStart,...,\\cEnd}\n")); 1385 PetscCall(PetscViewerASCIIPrintf(viewer, "{\n")); 1386 PetscCall(PetscViewerASCIIPrintf(viewer, " \\node(\\c_%d) [draw,shape=circle,color=%s,minimum size = 6mm] at (\\cShift+\\c-\\cStart,0) {\\c};\n", rank, color)); 1387 PetscCall(PetscViewerASCIIPrintf(viewer, "}\n")); 1388 1389 color = colors[1 % numColors]; 1390 PetscCall(PetscViewerASCIIPrintf(viewer, "%% Edges\n")); 1391 PetscCall(PetscViewerASCIIPrintf(viewer, "\\foreach \\e in {\\eStart,...,\\eEnd}\n")); 1392 PetscCall(PetscViewerASCIIPrintf(viewer, "{\n")); 1393 PetscCall(PetscViewerASCIIPrintf(viewer, " \\node(\\e_%d) [draw,shape=circle,color=%s,minimum size = 6mm] at (\\eShift+\\e-\\eStart,1) {\\e};\n", rank, color)); 1394 PetscCall(PetscViewerASCIIPrintf(viewer, "}\n")); 1395 1396 color = colors[0 % numColors]; 1397 PetscCall(PetscViewerASCIIPrintf(viewer, "%% Vertices\n")); 1398 PetscCall(PetscViewerASCIIPrintf(viewer, "\\foreach \\v in {\\vStart,...,\\vEnd}\n")); 1399 PetscCall(PetscViewerASCIIPrintf(viewer, "{\n")); 1400 PetscCall(PetscViewerASCIIPrintf(viewer, " \\node(\\v_%d) [draw,shape=circle,color=%s,minimum size = 6mm] at (\\vShift+\\v-\\vStart,2) {\\v};\n", rank, color)); 1401 PetscCall(PetscViewerASCIIPrintf(viewer, "}\n")); 1402 1403 for (p = pStart; p < pEnd; ++p) { 1404 const PetscInt *cone; 1405 PetscInt coneSize, cp; 1406 1407 PetscCall(DMPlexGetCone(dm, p, &cone)); 1408 PetscCall(DMPlexGetConeSize(dm, p, &coneSize)); 1409 for (cp = 0; cp < coneSize; ++cp) PetscCall(PetscViewerASCIIPrintf(viewer, "\\draw[->, shorten >=1pt] (%" PetscInt_FMT "_%d) -- (%" PetscInt_FMT "_%d);\n", cone[cp], rank, p, rank)); 1410 } 1411 } 1412 PetscCall(PetscViewerFlush(viewer)); 1413 PetscCall(PetscViewerASCIIPopSynchronized(viewer)); 1414 PetscCall(PetscViewerASCIIPrintf(viewer, "\\end{tikzpicture}\n")); 1415 PetscCall(PetscViewerASCIIPrintf(viewer, "\\end{document}\n")); 1416 for (l = 0; l < numLabels; ++l) PetscCall(PetscFree(names[l])); 1417 for (c = 0; c < numColors; ++c) PetscCall(PetscFree(colors[c])); 1418 for (c = 0; c < numLColors; ++c) PetscCall(PetscFree(lcolors[c])); 1419 PetscCall(PetscFree3(names, colors, lcolors)); 1420 PetscCall(PetscBTDestroy(&wp)); 1421 } else if (format == PETSC_VIEWER_LOAD_BALANCE) { 1422 Vec cown, acown; 1423 VecScatter sct; 1424 ISLocalToGlobalMapping g2l; 1425 IS gid, acis; 1426 MPI_Comm comm, ncomm = MPI_COMM_NULL; 1427 MPI_Group ggroup, ngroup; 1428 PetscScalar *array, nid; 1429 const PetscInt *idxs; 1430 PetscInt *idxs2, *start, *adjacency, *work; 1431 PetscInt64 lm[3], gm[3]; 1432 PetscInt i, c, cStart, cEnd, cum, numVertices, ect, ectn, cellHeight; 1433 PetscMPIInt d1, d2, rank; 1434 1435 PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); 1436 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 1437 #if defined(PETSC_HAVE_MPI_PROCESS_SHARED_MEMORY) 1438 PetscCallMPI(MPI_Comm_split_type(comm, MPI_COMM_TYPE_SHARED, rank, MPI_INFO_NULL, &ncomm)); 1439 #endif 1440 if (ncomm != MPI_COMM_NULL) { 1441 PetscCallMPI(MPI_Comm_group(comm, &ggroup)); 1442 PetscCallMPI(MPI_Comm_group(ncomm, &ngroup)); 1443 d1 = 0; 1444 PetscCallMPI(MPI_Group_translate_ranks(ngroup, 1, &d1, ggroup, &d2)); 1445 nid = d2; 1446 PetscCallMPI(MPI_Group_free(&ggroup)); 1447 PetscCallMPI(MPI_Group_free(&ngroup)); 1448 PetscCallMPI(MPI_Comm_free(&ncomm)); 1449 } else nid = 0.0; 1450 1451 /* Get connectivity */ 1452 PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight)); 1453 PetscCall(DMPlexCreatePartitionerGraph(dm, cellHeight, &numVertices, &start, &adjacency, &gid)); 1454 1455 /* filter overlapped local cells */ 1456 PetscCall(DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd)); 1457 PetscCall(ISGetIndices(gid, &idxs)); 1458 PetscCall(ISGetLocalSize(gid, &cum)); 1459 PetscCall(PetscMalloc1(cum, &idxs2)); 1460 for (c = cStart, cum = 0; c < cEnd; c++) { 1461 if (idxs[c - cStart] < 0) continue; 1462 idxs2[cum++] = idxs[c - cStart]; 1463 } 1464 PetscCall(ISRestoreIndices(gid, &idxs)); 1465 PetscCheck(numVertices == cum, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unexpected %" PetscInt_FMT " != %" PetscInt_FMT, numVertices, cum); 1466 PetscCall(ISDestroy(&gid)); 1467 PetscCall(ISCreateGeneral(comm, numVertices, idxs2, PETSC_OWN_POINTER, &gid)); 1468 1469 /* support for node-aware cell locality */ 1470 PetscCall(ISCreateGeneral(comm, start[numVertices], adjacency, PETSC_USE_POINTER, &acis)); 1471 PetscCall(VecCreateSeq(PETSC_COMM_SELF, start[numVertices], &acown)); 1472 PetscCall(VecCreateMPI(comm, numVertices, PETSC_DECIDE, &cown)); 1473 PetscCall(VecGetArray(cown, &array)); 1474 for (c = 0; c < numVertices; c++) array[c] = nid; 1475 PetscCall(VecRestoreArray(cown, &array)); 1476 PetscCall(VecScatterCreate(cown, acis, acown, NULL, &sct)); 1477 PetscCall(VecScatterBegin(sct, cown, acown, INSERT_VALUES, SCATTER_FORWARD)); 1478 PetscCall(VecScatterEnd(sct, cown, acown, INSERT_VALUES, SCATTER_FORWARD)); 1479 PetscCall(ISDestroy(&acis)); 1480 PetscCall(VecScatterDestroy(&sct)); 1481 PetscCall(VecDestroy(&cown)); 1482 1483 /* compute edgeCut */ 1484 for (c = 0, cum = 0; c < numVertices; c++) cum = PetscMax(cum, start[c + 1] - start[c]); 1485 PetscCall(PetscMalloc1(cum, &work)); 1486 PetscCall(ISLocalToGlobalMappingCreateIS(gid, &g2l)); 1487 PetscCall(ISLocalToGlobalMappingSetType(g2l, ISLOCALTOGLOBALMAPPINGHASH)); 1488 PetscCall(ISDestroy(&gid)); 1489 PetscCall(VecGetArray(acown, &array)); 1490 for (c = 0, ect = 0, ectn = 0; c < numVertices; c++) { 1491 PetscInt totl; 1492 1493 totl = start[c + 1] - start[c]; 1494 PetscCall(ISGlobalToLocalMappingApply(g2l, IS_GTOLM_MASK, totl, adjacency + start[c], NULL, work)); 1495 for (i = 0; i < totl; i++) { 1496 if (work[i] < 0) { 1497 ect += 1; 1498 ectn += (array[i + start[c]] != nid) ? 0 : 1; 1499 } 1500 } 1501 } 1502 PetscCall(PetscFree(work)); 1503 PetscCall(VecRestoreArray(acown, &array)); 1504 lm[0] = numVertices > 0 ? numVertices : PETSC_MAX_INT; 1505 lm[1] = -numVertices; 1506 PetscCall(MPIU_Allreduce(lm, gm, 2, MPIU_INT64, MPI_MIN, comm)); 1507 PetscCall(PetscViewerASCIIPrintf(viewer, " Cell balance: %.2f (max %" PetscInt_FMT ", min %" PetscInt_FMT, -((double)gm[1]) / ((double)gm[0]), -(PetscInt)gm[1], (PetscInt)gm[0])); 1508 lm[0] = ect; /* edgeCut */ 1509 lm[1] = ectn; /* node-aware edgeCut */ 1510 lm[2] = numVertices > 0 ? 0 : 1; /* empty processes */ 1511 PetscCall(MPIU_Allreduce(lm, gm, 3, MPIU_INT64, MPI_SUM, comm)); 1512 PetscCall(PetscViewerASCIIPrintf(viewer, ", empty %" PetscInt_FMT ")\n", (PetscInt)gm[2])); 1513 #if defined(PETSC_HAVE_MPI_PROCESS_SHARED_MEMORY) 1514 PetscCall(PetscViewerASCIIPrintf(viewer, " Edge Cut: %" PetscInt_FMT " (on node %.3f)\n", (PetscInt)(gm[0] / 2), gm[0] ? ((double)gm[1]) / ((double)gm[0]) : 1.)); 1515 #else 1516 PetscCall(PetscViewerASCIIPrintf(viewer, " Edge Cut: %" PetscInt_FMT " (on node %.3f)\n", (PetscInt)(gm[0] / 2), 0.0)); 1517 #endif 1518 PetscCall(ISLocalToGlobalMappingDestroy(&g2l)); 1519 PetscCall(PetscFree(start)); 1520 PetscCall(PetscFree(adjacency)); 1521 PetscCall(VecDestroy(&acown)); 1522 } else { 1523 const char *name; 1524 PetscInt *sizes, *hybsizes, *ghostsizes; 1525 PetscInt locDepth, depth, cellHeight, dim, d; 1526 PetscInt pStart, pEnd, p, gcStart, gcEnd, gcNum; 1527 PetscInt numLabels, l, maxSize = 17; 1528 DMPolytopeType ct0 = DM_POLYTOPE_UNKNOWN; 1529 MPI_Comm comm; 1530 PetscMPIInt size, rank; 1531 1532 PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); 1533 PetscCallMPI(MPI_Comm_size(comm, &size)); 1534 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 1535 PetscCall(DMGetDimension(dm, &dim)); 1536 PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight)); 1537 PetscCall(PetscObjectGetName((PetscObject)dm, &name)); 1538 if (name) PetscCall(PetscViewerASCIIPrintf(viewer, "%s in %" PetscInt_FMT " dimension%s:\n", name, dim, dim == 1 ? "" : "s")); 1539 else PetscCall(PetscViewerASCIIPrintf(viewer, "Mesh in %" PetscInt_FMT " dimension%s:\n", dim, dim == 1 ? "" : "s")); 1540 if (cellHeight) PetscCall(PetscViewerASCIIPrintf(viewer, " Cells are at height %" PetscInt_FMT "\n", cellHeight)); 1541 PetscCall(DMPlexGetDepth(dm, &locDepth)); 1542 PetscCall(MPIU_Allreduce(&locDepth, &depth, 1, MPIU_INT, MPI_MAX, comm)); 1543 PetscCall(DMPlexGetCellTypeStratum(dm, DM_POLYTOPE_FV_GHOST, &gcStart, &gcEnd)); 1544 gcNum = gcEnd - gcStart; 1545 if (size < maxSize) PetscCall(PetscCalloc3(size, &sizes, size, &hybsizes, size, &ghostsizes)); 1546 else PetscCall(PetscCalloc3(3, &sizes, 3, &hybsizes, 3, &ghostsizes)); 1547 for (d = 0; d <= depth; d++) { 1548 PetscInt Nc[2] = {0, 0}, ict; 1549 1550 PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd)); 1551 if (pStart < pEnd) PetscCall(DMPlexGetCellType(dm, pStart, &ct0)); 1552 ict = ct0; 1553 PetscCallMPI(MPI_Bcast(&ict, 1, MPIU_INT, 0, comm)); 1554 ct0 = (DMPolytopeType)ict; 1555 for (p = pStart; p < pEnd; ++p) { 1556 DMPolytopeType ct; 1557 1558 PetscCall(DMPlexGetCellType(dm, p, &ct)); 1559 if (ct == ct0) ++Nc[0]; 1560 else ++Nc[1]; 1561 } 1562 if (size < maxSize) { 1563 PetscCallMPI(MPI_Gather(&Nc[0], 1, MPIU_INT, sizes, 1, MPIU_INT, 0, comm)); 1564 PetscCallMPI(MPI_Gather(&Nc[1], 1, MPIU_INT, hybsizes, 1, MPIU_INT, 0, comm)); 1565 if (d == depth) PetscCallMPI(MPI_Gather(&gcNum, 1, MPIU_INT, ghostsizes, 1, MPIU_INT, 0, comm)); 1566 PetscCall(PetscViewerASCIIPrintf(viewer, " Number of %" PetscInt_FMT "-cells per rank:", (depth == 1) && d ? dim : d)); 1567 for (p = 0; p < size; ++p) { 1568 if (rank == 0) { 1569 PetscCall(PetscViewerASCIIPrintf(viewer, " %" PetscInt_FMT, sizes[p] + hybsizes[p])); 1570 if (hybsizes[p] > 0) PetscCall(PetscViewerASCIIPrintf(viewer, " (%" PetscInt_FMT ")", hybsizes[p])); 1571 if (ghostsizes[p] > 0) PetscCall(PetscViewerASCIIPrintf(viewer, " [%" PetscInt_FMT "]", ghostsizes[p])); 1572 } 1573 } 1574 } else { 1575 PetscInt locMinMax[2]; 1576 1577 locMinMax[0] = Nc[0] + Nc[1]; 1578 locMinMax[1] = Nc[0] + Nc[1]; 1579 PetscCall(PetscGlobalMinMaxInt(comm, locMinMax, sizes)); 1580 locMinMax[0] = Nc[1]; 1581 locMinMax[1] = Nc[1]; 1582 PetscCall(PetscGlobalMinMaxInt(comm, locMinMax, hybsizes)); 1583 if (d == depth) { 1584 locMinMax[0] = gcNum; 1585 locMinMax[1] = gcNum; 1586 PetscCall(PetscGlobalMinMaxInt(comm, locMinMax, ghostsizes)); 1587 } 1588 PetscCall(PetscViewerASCIIPrintf(viewer, " Min/Max of %" PetscInt_FMT "-cells per rank:", (depth == 1) && d ? dim : d)); 1589 PetscCall(PetscViewerASCIIPrintf(viewer, " %" PetscInt_FMT "/%" PetscInt_FMT, sizes[0], sizes[1])); 1590 if (hybsizes[0] > 0) PetscCall(PetscViewerASCIIPrintf(viewer, " (%" PetscInt_FMT "/%" PetscInt_FMT ")", hybsizes[0], hybsizes[1])); 1591 if (ghostsizes[0] > 0) PetscCall(PetscViewerASCIIPrintf(viewer, " [%" PetscInt_FMT "/%" PetscInt_FMT "]", ghostsizes[0], ghostsizes[1])); 1592 } 1593 PetscCall(PetscViewerASCIIPrintf(viewer, "\n")); 1594 } 1595 PetscCall(PetscFree3(sizes, hybsizes, ghostsizes)); 1596 { 1597 const PetscReal *maxCell; 1598 const PetscReal *L; 1599 PetscBool localized; 1600 1601 PetscCall(DMGetPeriodicity(dm, &maxCell, NULL, &L)); 1602 PetscCall(DMGetCoordinatesLocalized(dm, &localized)); 1603 if (L || localized) { 1604 PetscCall(PetscViewerASCIIPrintf(viewer, "Periodic mesh")); 1605 PetscCall(PetscViewerASCIIUseTabs(viewer, PETSC_FALSE)); 1606 if (L) { 1607 PetscCall(PetscViewerASCIIPrintf(viewer, " (")); 1608 for (d = 0; d < dim; ++d) { 1609 if (d > 0) PetscCall(PetscViewerASCIIPrintf(viewer, ", ")); 1610 PetscCall(PetscViewerASCIIPrintf(viewer, "%s", L[d] > 0.0 ? "PERIODIC" : "NONE")); 1611 } 1612 PetscCall(PetscViewerASCIIPrintf(viewer, ")")); 1613 } 1614 PetscCall(PetscViewerASCIIPrintf(viewer, " coordinates %s\n", localized ? "localized" : "not localized")); 1615 PetscCall(PetscViewerASCIIUseTabs(viewer, PETSC_TRUE)); 1616 } 1617 } 1618 PetscCall(DMGetNumLabels(dm, &numLabels)); 1619 if (numLabels) PetscCall(PetscViewerASCIIPrintf(viewer, "Labels:\n")); 1620 for (l = 0; l < numLabels; ++l) { 1621 DMLabel label; 1622 const char *name; 1623 IS valueIS; 1624 const PetscInt *values; 1625 PetscInt numValues, v; 1626 1627 PetscCall(DMGetLabelName(dm, l, &name)); 1628 PetscCall(DMGetLabel(dm, name, &label)); 1629 PetscCall(DMLabelGetNumValues(label, &numValues)); 1630 PetscCall(PetscViewerASCIIPrintf(viewer, " %s: %" PetscInt_FMT " strata with value/size (", name, numValues)); 1631 PetscCall(DMLabelGetValueIS(label, &valueIS)); 1632 PetscCall(ISGetIndices(valueIS, &values)); 1633 PetscCall(PetscViewerASCIIUseTabs(viewer, PETSC_FALSE)); 1634 for (v = 0; v < numValues; ++v) { 1635 PetscInt size; 1636 1637 PetscCall(DMLabelGetStratumSize(label, values[v], &size)); 1638 if (v > 0) PetscCall(PetscViewerASCIIPrintf(viewer, ", ")); 1639 PetscCall(PetscViewerASCIIPrintf(viewer, "%" PetscInt_FMT " (%" PetscInt_FMT ")", values[v], size)); 1640 } 1641 PetscCall(PetscViewerASCIIPrintf(viewer, ")\n")); 1642 PetscCall(PetscViewerASCIIUseTabs(viewer, PETSC_TRUE)); 1643 PetscCall(ISRestoreIndices(valueIS, &values)); 1644 PetscCall(ISDestroy(&valueIS)); 1645 } 1646 { 1647 char **labelNames; 1648 PetscInt Nl = numLabels; 1649 PetscBool flg; 1650 1651 PetscCall(PetscMalloc1(Nl, &labelNames)); 1652 PetscCall(PetscOptionsGetStringArray(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_view_labels", labelNames, &Nl, &flg)); 1653 for (l = 0; l < Nl; ++l) { 1654 DMLabel label; 1655 1656 PetscCall(DMHasLabel(dm, labelNames[l], &flg)); 1657 if (flg) { 1658 PetscCall(DMGetLabel(dm, labelNames[l], &label)); 1659 PetscCall(DMLabelView(label, viewer)); 1660 } 1661 PetscCall(PetscFree(labelNames[l])); 1662 } 1663 PetscCall(PetscFree(labelNames)); 1664 } 1665 /* If no fields are specified, people do not want to see adjacency */ 1666 if (dm->Nf) { 1667 PetscInt f; 1668 1669 for (f = 0; f < dm->Nf; ++f) { 1670 const char *name; 1671 1672 PetscCall(PetscObjectGetName(dm->fields[f].disc, &name)); 1673 if (numLabels) PetscCall(PetscViewerASCIIPrintf(viewer, "Field %s:\n", name)); 1674 PetscCall(PetscViewerASCIIPushTab(viewer)); 1675 if (dm->fields[f].label) PetscCall(DMLabelView(dm->fields[f].label, viewer)); 1676 if (dm->fields[f].adjacency[0]) { 1677 if (dm->fields[f].adjacency[1]) PetscCall(PetscViewerASCIIPrintf(viewer, "adjacency FVM++\n")); 1678 else PetscCall(PetscViewerASCIIPrintf(viewer, "adjacency FVM\n")); 1679 } else { 1680 if (dm->fields[f].adjacency[1]) PetscCall(PetscViewerASCIIPrintf(viewer, "adjacency FEM\n")); 1681 else PetscCall(PetscViewerASCIIPrintf(viewer, "adjacency FUNKY\n")); 1682 } 1683 PetscCall(PetscViewerASCIIPopTab(viewer)); 1684 } 1685 } 1686 PetscCall(DMGetCoarseDM(dm, &cdm)); 1687 if (cdm) { 1688 PetscCall(PetscViewerASCIIPushTab(viewer)); 1689 PetscCall(PetscViewerASCIIPrintf(viewer, "Defined by transform from:\n")); 1690 PetscCall(DMPlexView_Ascii(cdm, viewer)); 1691 PetscCall(PetscViewerASCIIPopTab(viewer)); 1692 } 1693 } 1694 PetscFunctionReturn(PETSC_SUCCESS); 1695 } 1696 1697 static PetscErrorCode DMPlexDrawCell(DM dm, PetscDraw draw, PetscInt cell, const PetscScalar coords[]) 1698 { 1699 DMPolytopeType ct; 1700 PetscMPIInt rank; 1701 PetscInt cdim; 1702 1703 PetscFunctionBegin; 1704 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 1705 PetscCall(DMPlexGetCellType(dm, cell, &ct)); 1706 PetscCall(DMGetCoordinateDim(dm, &cdim)); 1707 switch (ct) { 1708 case DM_POLYTOPE_SEGMENT: 1709 case DM_POLYTOPE_POINT_PRISM_TENSOR: 1710 switch (cdim) { 1711 case 1: { 1712 const PetscReal y = 0.5; /* TODO Put it in the middle of the viewport */ 1713 const PetscReal dy = 0.05; /* TODO Make it a fraction of the total length */ 1714 1715 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[0]), y, PetscRealPart(coords[1]), y, PETSC_DRAW_BLACK)); 1716 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[0]), y + dy, PetscRealPart(coords[0]), y - dy, PETSC_DRAW_BLACK)); 1717 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[1]), y + dy, PetscRealPart(coords[1]), y - dy, PETSC_DRAW_BLACK)); 1718 } break; 1719 case 2: { 1720 const PetscReal dx = (PetscRealPart(coords[3]) - PetscRealPart(coords[1])); 1721 const PetscReal dy = (PetscRealPart(coords[2]) - PetscRealPart(coords[0])); 1722 const PetscReal l = 0.1 / PetscSqrtReal(dx * dx + dy * dy); 1723 1724 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK)); 1725 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[0]) + l * dx, PetscRealPart(coords[1]) + l * dy, PetscRealPart(coords[0]) - l * dx, PetscRealPart(coords[1]) - l * dy, PETSC_DRAW_BLACK)); 1726 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[2]) + l * dx, PetscRealPart(coords[3]) + l * dy, PetscRealPart(coords[2]) - l * dx, PetscRealPart(coords[3]) - l * dy, PETSC_DRAW_BLACK)); 1727 } break; 1728 default: 1729 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells of dimension %" PetscInt_FMT, cdim); 1730 } 1731 break; 1732 case DM_POLYTOPE_TRIANGLE: 1733 PetscCall(PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2, PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2, PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2)); 1734 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK)); 1735 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_BLACK)); 1736 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), PETSC_DRAW_BLACK)); 1737 break; 1738 case DM_POLYTOPE_QUADRILATERAL: 1739 PetscCall(PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2, PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2, PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2)); 1740 PetscCall(PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[6]), PetscRealPart(coords[7]), PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2, PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2, PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2)); 1741 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK)); 1742 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_BLACK)); 1743 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[6]), PetscRealPart(coords[7]), PETSC_DRAW_BLACK)); 1744 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[6]), PetscRealPart(coords[7]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), PETSC_DRAW_BLACK)); 1745 break; 1746 case DM_POLYTOPE_SEG_PRISM_TENSOR: 1747 PetscCall(PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2, PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2, PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2)); 1748 PetscCall(PetscDrawTriangle(draw, PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[6]), PetscRealPart(coords[7]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2, PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2, PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2)); 1749 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK)); 1750 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[6]), PetscRealPart(coords[7]), PETSC_DRAW_BLACK)); 1751 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[6]), PetscRealPart(coords[7]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_BLACK)); 1752 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), PETSC_DRAW_BLACK)); 1753 break; 1754 case DM_POLYTOPE_FV_GHOST: 1755 break; 1756 default: 1757 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells of type %s", DMPolytopeTypes[ct]); 1758 } 1759 PetscFunctionReturn(PETSC_SUCCESS); 1760 } 1761 1762 static PetscErrorCode DrawPolygon_Private(DM dm, PetscDraw draw, PetscInt cell, PetscInt Nv, const PetscReal refVertices[], const PetscScalar coords[], PetscInt edgeDiv, PetscReal refCoords[], PetscReal edgeCoords[]) 1763 { 1764 PetscReal centroid[2] = {0., 0.}; 1765 PetscMPIInt rank; 1766 PetscInt fillColor; 1767 1768 PetscFunctionBegin; 1769 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 1770 fillColor = PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2; 1771 for (PetscInt v = 0; v < Nv; ++v) { 1772 centroid[0] += PetscRealPart(coords[v * 2 + 0]) / Nv; 1773 centroid[1] += PetscRealPart(coords[v * 2 + 1]) / Nv; 1774 } 1775 for (PetscInt e = 0; e < Nv; ++e) { 1776 refCoords[0] = refVertices[e * 2 + 0]; 1777 refCoords[1] = refVertices[e * 2 + 1]; 1778 for (PetscInt d = 1; d <= edgeDiv; ++d) { 1779 refCoords[d * 2 + 0] = refCoords[0] + (refVertices[(e + 1) % Nv * 2 + 0] - refCoords[0]) * d / edgeDiv; 1780 refCoords[d * 2 + 1] = refCoords[1] + (refVertices[(e + 1) % Nv * 2 + 1] - refCoords[1]) * d / edgeDiv; 1781 } 1782 PetscCall(DMPlexReferenceToCoordinates(dm, cell, edgeDiv + 1, refCoords, edgeCoords)); 1783 for (PetscInt d = 0; d < edgeDiv; ++d) { 1784 PetscCall(PetscDrawTriangle(draw, centroid[0], centroid[1], edgeCoords[d * 2 + 0], edgeCoords[d * 2 + 1], edgeCoords[(d + 1) * 2 + 0], edgeCoords[(d + 1) * 2 + 1], fillColor, fillColor, fillColor)); 1785 PetscCall(PetscDrawLine(draw, edgeCoords[d * 2 + 0], edgeCoords[d * 2 + 1], edgeCoords[(d + 1) * 2 + 0], edgeCoords[(d + 1) * 2 + 1], PETSC_DRAW_BLACK)); 1786 } 1787 } 1788 PetscFunctionReturn(PETSC_SUCCESS); 1789 } 1790 1791 static PetscErrorCode DMPlexDrawCellHighOrder(DM dm, PetscDraw draw, PetscInt cell, const PetscScalar coords[], PetscInt edgeDiv, PetscReal refCoords[], PetscReal edgeCoords[]) 1792 { 1793 DMPolytopeType ct; 1794 1795 PetscFunctionBegin; 1796 PetscCall(DMPlexGetCellType(dm, cell, &ct)); 1797 switch (ct) { 1798 case DM_POLYTOPE_TRIANGLE: { 1799 PetscReal refVertices[6] = {-1., -1., 1., -1., -1., 1.}; 1800 1801 PetscCall(DrawPolygon_Private(dm, draw, cell, 3, refVertices, coords, edgeDiv, refCoords, edgeCoords)); 1802 } break; 1803 case DM_POLYTOPE_QUADRILATERAL: { 1804 PetscReal refVertices[8] = {-1., -1., 1., -1., 1., 1., -1., 1.}; 1805 1806 PetscCall(DrawPolygon_Private(dm, draw, cell, 4, refVertices, coords, edgeDiv, refCoords, edgeCoords)); 1807 } break; 1808 default: 1809 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells of type %s", DMPolytopeTypes[ct]); 1810 } 1811 PetscFunctionReturn(PETSC_SUCCESS); 1812 } 1813 1814 static PetscErrorCode DMPlexView_Draw(DM dm, PetscViewer viewer) 1815 { 1816 PetscDraw draw; 1817 DM cdm; 1818 PetscSection coordSection; 1819 Vec coordinates; 1820 PetscReal xyl[3], xyr[3]; 1821 PetscReal *refCoords, *edgeCoords; 1822 PetscBool isnull, drawAffine; 1823 PetscInt dim, vStart, vEnd, cStart, cEnd, c, cDegree, edgeDiv; 1824 1825 PetscFunctionBegin; 1826 PetscCall(DMGetCoordinateDim(dm, &dim)); 1827 PetscCheck(dim <= 2, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Cannot draw meshes of dimension %" PetscInt_FMT, dim); 1828 PetscCall(DMGetCoordinateDegree_Internal(dm, &cDegree)); 1829 drawAffine = cDegree > 1 ? PETSC_FALSE : PETSC_TRUE; 1830 edgeDiv = cDegree + 1; 1831 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_view_draw_affine", &drawAffine, NULL)); 1832 if (!drawAffine) PetscCall(PetscMalloc2((edgeDiv + 1) * dim, &refCoords, (edgeDiv + 1) * dim, &edgeCoords)); 1833 PetscCall(DMGetCoordinateDM(dm, &cdm)); 1834 PetscCall(DMGetLocalSection(cdm, &coordSection)); 1835 PetscCall(DMGetCoordinatesLocal(dm, &coordinates)); 1836 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 1837 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 1838 1839 PetscCall(PetscViewerDrawGetDraw(viewer, 0, &draw)); 1840 PetscCall(PetscDrawIsNull(draw, &isnull)); 1841 if (isnull) PetscFunctionReturn(PETSC_SUCCESS); 1842 PetscCall(PetscDrawSetTitle(draw, "Mesh")); 1843 1844 PetscCall(DMGetBoundingBox(dm, xyl, xyr)); 1845 PetscCall(PetscDrawSetCoordinates(draw, xyl[0], xyl[1], xyr[0], xyr[1])); 1846 PetscCall(PetscDrawClear(draw)); 1847 1848 for (c = cStart; c < cEnd; ++c) { 1849 PetscScalar *coords = NULL; 1850 const PetscScalar *coords_arr; 1851 PetscInt numCoords; 1852 PetscBool isDG; 1853 1854 PetscCall(DMPlexGetCellCoordinates(dm, c, &isDG, &numCoords, &coords_arr, &coords)); 1855 if (drawAffine) PetscCall(DMPlexDrawCell(dm, draw, c, coords)); 1856 else PetscCall(DMPlexDrawCellHighOrder(dm, draw, c, coords, edgeDiv, refCoords, edgeCoords)); 1857 PetscCall(DMPlexRestoreCellCoordinates(dm, c, &isDG, &numCoords, &coords_arr, &coords)); 1858 } 1859 if (!drawAffine) PetscCall(PetscFree2(refCoords, edgeCoords)); 1860 PetscCall(PetscDrawFlush(draw)); 1861 PetscCall(PetscDrawPause(draw)); 1862 PetscCall(PetscDrawSave(draw)); 1863 PetscFunctionReturn(PETSC_SUCCESS); 1864 } 1865 1866 static PetscErrorCode DMPlexCreateHighOrderSurrogate_Internal(DM dm, DM *hdm) 1867 { 1868 DM odm = dm, rdm = dm, cdm; 1869 PetscFE fe; 1870 PetscSpace sp; 1871 PetscClassId id; 1872 PetscInt degree; 1873 PetscBool hoView = PETSC_TRUE; 1874 1875 PetscFunctionBegin; 1876 PetscObjectOptionsBegin((PetscObject)dm); 1877 PetscCall(PetscOptionsBool("-dm_plex_high_order_view", "Subsample to view meshes with high order coordinates", "DMPlexCreateHighOrderSurrogate_Internal", hoView, &hoView, NULL)); 1878 PetscOptionsEnd(); 1879 PetscCall(PetscObjectReference((PetscObject)dm)); 1880 *hdm = dm; 1881 if (!hoView) PetscFunctionReturn(PETSC_SUCCESS); 1882 PetscCall(DMGetCoordinateDM(dm, &cdm)); 1883 PetscCall(DMGetField(cdm, 0, NULL, (PetscObject *)&fe)); 1884 PetscCall(PetscObjectGetClassId((PetscObject)fe, &id)); 1885 if (id != PETSCFE_CLASSID) PetscFunctionReturn(PETSC_SUCCESS); 1886 PetscCall(PetscFEGetBasisSpace(fe, &sp)); 1887 PetscCall(PetscSpaceGetDegree(sp, °ree, NULL)); 1888 for (PetscInt r = 0, rd = PetscCeilReal(((PetscReal)degree) / 2.); r < (PetscInt)PetscCeilReal(PetscLog2Real(degree)); ++r, rd = PetscCeilReal(((PetscReal)rd) / 2.)) { 1889 DM cdm, rcdm; 1890 Mat In; 1891 Vec cl, rcl; 1892 1893 PetscCall(DMRefine(odm, PetscObjectComm((PetscObject)odm), &rdm)); 1894 PetscCall(DMPlexCreateCoordinateSpace(rdm, rd, PETSC_FALSE, NULL)); 1895 PetscCall(PetscObjectSetName((PetscObject)rdm, "Refined Mesh with Linear Coordinates")); 1896 PetscCall(DMGetCoordinateDM(odm, &cdm)); 1897 PetscCall(DMGetCoordinateDM(rdm, &rcdm)); 1898 PetscCall(DMGetCoordinatesLocal(odm, &cl)); 1899 PetscCall(DMGetCoordinatesLocal(rdm, &rcl)); 1900 PetscCall(DMSetCoarseDM(rcdm, cdm)); 1901 PetscCall(DMCreateInterpolation(cdm, rcdm, &In, NULL)); 1902 PetscCall(MatMult(In, cl, rcl)); 1903 PetscCall(MatDestroy(&In)); 1904 PetscCall(DMSetCoordinatesLocal(rdm, rcl)); 1905 PetscCall(DMDestroy(&odm)); 1906 odm = rdm; 1907 } 1908 *hdm = rdm; 1909 PetscFunctionReturn(PETSC_SUCCESS); 1910 } 1911 1912 #if defined(PETSC_HAVE_EXODUSII) 1913 #include <exodusII.h> 1914 #include <petscviewerexodusii.h> 1915 #endif 1916 1917 PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer) 1918 { 1919 PetscBool iascii, ishdf5, isvtk, isdraw, flg, isglvis, isexodus, iscgns; 1920 char name[PETSC_MAX_PATH_LEN]; 1921 1922 PetscFunctionBegin; 1923 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1924 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 1925 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &iascii)); 1926 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERVTK, &isvtk)); 1927 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 1928 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERDRAW, &isdraw)); 1929 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERGLVIS, &isglvis)); 1930 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWEREXODUSII, &isexodus)); 1931 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERCGNS, &iscgns)); 1932 if (iascii) { 1933 PetscViewerFormat format; 1934 PetscCall(PetscViewerGetFormat(viewer, &format)); 1935 if (format == PETSC_VIEWER_ASCII_GLVIS) PetscCall(DMPlexView_GLVis(dm, viewer)); 1936 else PetscCall(DMPlexView_Ascii(dm, viewer)); 1937 } else if (ishdf5) { 1938 #if defined(PETSC_HAVE_HDF5) 1939 PetscCall(DMPlexView_HDF5_Internal(dm, viewer)); 1940 #else 1941 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 1942 #endif 1943 } else if (isvtk) { 1944 PetscCall(DMPlexVTKWriteAll((PetscObject)dm, viewer)); 1945 } else if (isdraw) { 1946 DM hdm; 1947 1948 PetscCall(DMPlexCreateHighOrderSurrogate_Internal(dm, &hdm)); 1949 PetscCall(DMPlexView_Draw(hdm, viewer)); 1950 PetscCall(DMDestroy(&hdm)); 1951 } else if (isglvis) { 1952 PetscCall(DMPlexView_GLVis(dm, viewer)); 1953 #if defined(PETSC_HAVE_EXODUSII) 1954 } else if (isexodus) { 1955 /* 1956 exodusII requires that all sets be part of exactly one cell set. 1957 If the dm does not have a "Cell Sets" label defined, we create one 1958 with ID 1, containing all cells. 1959 Note that if the Cell Sets label is defined but does not cover all cells, 1960 we may still have a problem. This should probably be checked here or in the viewer; 1961 */ 1962 PetscInt numCS; 1963 PetscCall(DMGetLabelSize(dm, "Cell Sets", &numCS)); 1964 if (!numCS) { 1965 PetscInt cStart, cEnd, c; 1966 PetscCall(DMCreateLabel(dm, "Cell Sets")); 1967 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 1968 for (c = cStart; c < cEnd; ++c) PetscCall(DMSetLabelValue(dm, "Cell Sets", c, 1)); 1969 } 1970 PetscCall(DMView_PlexExodusII(dm, viewer)); 1971 #endif 1972 #if defined(PETSC_HAVE_CGNS) 1973 } else if (iscgns) { 1974 PetscCall(DMView_PlexCGNS(dm, viewer)); 1975 #endif 1976 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Viewer type %s not yet supported for DMPlex writing", ((PetscObject)viewer)->type_name); 1977 /* Optionally view the partition */ 1978 PetscCall(PetscOptionsHasName(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_partition_view", &flg)); 1979 if (flg) { 1980 Vec ranks; 1981 PetscCall(DMPlexCreateRankField(dm, &ranks)); 1982 PetscCall(VecView(ranks, viewer)); 1983 PetscCall(VecDestroy(&ranks)); 1984 } 1985 /* Optionally view a label */ 1986 PetscCall(PetscOptionsGetString(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_label_view", name, sizeof(name), &flg)); 1987 if (flg) { 1988 DMLabel label; 1989 Vec val; 1990 1991 PetscCall(DMGetLabel(dm, name, &label)); 1992 PetscCheck(label, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Label %s provided to -dm_label_view does not exist in this DM", name); 1993 PetscCall(DMPlexCreateLabelField(dm, label, &val)); 1994 PetscCall(VecView(val, viewer)); 1995 PetscCall(VecDestroy(&val)); 1996 } 1997 PetscFunctionReturn(PETSC_SUCCESS); 1998 } 1999 2000 /*@ 2001 DMPlexTopologyView - Saves a `DMPLEX` topology into a file 2002 2003 Collective 2004 2005 Input Parameters: 2006 + dm - The `DM` whose topology is to be saved 2007 - viewer - The `PetscViewer` to save it in 2008 2009 Level: advanced 2010 2011 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMView()`, `DMPlexCoordinatesView()`, `DMPlexLabelsView()`, `DMPlexTopologyLoad()`, `PetscViewer` 2012 @*/ 2013 PetscErrorCode DMPlexTopologyView(DM dm, PetscViewer viewer) 2014 { 2015 PetscBool ishdf5; 2016 2017 PetscFunctionBegin; 2018 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2019 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2020 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2021 PetscCall(PetscLogEventBegin(DMPLEX_TopologyView, viewer, 0, 0, 0)); 2022 if (ishdf5) { 2023 #if defined(PETSC_HAVE_HDF5) 2024 PetscViewerFormat format; 2025 PetscCall(PetscViewerGetFormat(viewer, &format)); 2026 if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) { 2027 IS globalPointNumbering; 2028 2029 PetscCall(DMPlexCreatePointNumbering(dm, &globalPointNumbering)); 2030 PetscCall(DMPlexTopologyView_HDF5_Internal(dm, globalPointNumbering, viewer)); 2031 PetscCall(ISDestroy(&globalPointNumbering)); 2032 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 output.", PetscViewerFormats[format]); 2033 #else 2034 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2035 #endif 2036 } 2037 PetscCall(PetscLogEventEnd(DMPLEX_TopologyView, viewer, 0, 0, 0)); 2038 PetscFunctionReturn(PETSC_SUCCESS); 2039 } 2040 2041 /*@ 2042 DMPlexCoordinatesView - Saves `DMPLEX` coordinates into a file 2043 2044 Collective 2045 2046 Input Parameters: 2047 + dm - The `DM` whose coordinates are to be saved 2048 - viewer - The `PetscViewer` for saving 2049 2050 Level: advanced 2051 2052 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMView()`, `DMPlexTopologyView()`, `DMPlexLabelsView()`, `DMPlexCoordinatesLoad()`, `PetscViewer` 2053 @*/ 2054 PetscErrorCode DMPlexCoordinatesView(DM dm, PetscViewer viewer) 2055 { 2056 PetscBool ishdf5; 2057 2058 PetscFunctionBegin; 2059 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2060 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2061 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2062 PetscCall(PetscLogEventBegin(DMPLEX_CoordinatesView, viewer, 0, 0, 0)); 2063 if (ishdf5) { 2064 #if defined(PETSC_HAVE_HDF5) 2065 PetscViewerFormat format; 2066 PetscCall(PetscViewerGetFormat(viewer, &format)); 2067 if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) { 2068 PetscCall(DMPlexCoordinatesView_HDF5_Internal(dm, viewer)); 2069 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 output.", PetscViewerFormats[format]); 2070 #else 2071 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2072 #endif 2073 } 2074 PetscCall(PetscLogEventEnd(DMPLEX_CoordinatesView, viewer, 0, 0, 0)); 2075 PetscFunctionReturn(PETSC_SUCCESS); 2076 } 2077 2078 /*@ 2079 DMPlexLabelsView - Saves `DMPLEX` labels into a file 2080 2081 Collective 2082 2083 Input Parameters: 2084 + dm - The `DM` whose labels are to be saved 2085 - viewer - The `PetscViewer` for saving 2086 2087 Level: advanced 2088 2089 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMView()`, `DMPlexTopologyView()`, `DMPlexCoordinatesView()`, `DMPlexLabelsLoad()`, `PetscViewer` 2090 @*/ 2091 PetscErrorCode DMPlexLabelsView(DM dm, PetscViewer viewer) 2092 { 2093 PetscBool ishdf5; 2094 2095 PetscFunctionBegin; 2096 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2097 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2098 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2099 PetscCall(PetscLogEventBegin(DMPLEX_LabelsView, viewer, 0, 0, 0)); 2100 if (ishdf5) { 2101 #if defined(PETSC_HAVE_HDF5) 2102 IS globalPointNumbering; 2103 PetscViewerFormat format; 2104 2105 PetscCall(PetscViewerGetFormat(viewer, &format)); 2106 if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) { 2107 PetscCall(DMPlexCreatePointNumbering(dm, &globalPointNumbering)); 2108 PetscCall(DMPlexLabelsView_HDF5_Internal(dm, globalPointNumbering, viewer)); 2109 PetscCall(ISDestroy(&globalPointNumbering)); 2110 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]); 2111 #else 2112 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2113 #endif 2114 } 2115 PetscCall(PetscLogEventEnd(DMPLEX_LabelsView, viewer, 0, 0, 0)); 2116 PetscFunctionReturn(PETSC_SUCCESS); 2117 } 2118 2119 /*@ 2120 DMPlexSectionView - Saves a section associated with a `DMPLEX` 2121 2122 Collective 2123 2124 Input Parameters: 2125 + dm - The `DM` that contains the topology on which the section to be saved is defined 2126 . viewer - The `PetscViewer` for saving 2127 - sectiondm - The `DM` that contains the section to be saved, can be `NULL` 2128 2129 Level: advanced 2130 2131 Notes: 2132 This function is a wrapper around `PetscSectionView()`; in addition to the raw section, it saves information that associates the section points to the topology (`dm`) points. When the topology (`dm`) and the section are later loaded with `DMPlexTopologyLoad()` and `DMPlexSectionLoad()`, respectively, this information is used to match section points with topology points. 2133 2134 In general `dm` and `sectiondm` are two different objects, the former carrying the topology and the latter carrying the section, and have been given a topology name and a section name, respectively, with `PetscObjectSetName()`. In practice, however, they can be the same object (or in case `sectiondm` is `NULL`) if it carries both topology and section; in that case the name of the object is used as both the topology name and the section name. 2135 2136 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMView()`, `DMPlexTopologyView()`, `DMPlexCoordinatesView()`, `DMPlexLabelsView()`, `DMPlexGlobalVectorView()`, `DMPlexLocalVectorView()`, `PetscSectionView()`, `DMPlexSectionLoad()`, `PetscViewer` 2137 @*/ 2138 PetscErrorCode DMPlexSectionView(DM dm, PetscViewer viewer, DM sectiondm) 2139 { 2140 PetscBool ishdf5; 2141 2142 PetscFunctionBegin; 2143 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2144 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2145 if (!sectiondm) sectiondm = dm; 2146 PetscValidHeaderSpecific(sectiondm, DM_CLASSID, 3); 2147 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2148 PetscCall(PetscLogEventBegin(DMPLEX_SectionView, viewer, 0, 0, 0)); 2149 if (ishdf5) { 2150 #if defined(PETSC_HAVE_HDF5) 2151 PetscCall(DMPlexSectionView_HDF5_Internal(dm, viewer, sectiondm)); 2152 #else 2153 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2154 #endif 2155 } 2156 PetscCall(PetscLogEventEnd(DMPLEX_SectionView, viewer, 0, 0, 0)); 2157 PetscFunctionReturn(PETSC_SUCCESS); 2158 } 2159 2160 /*@ 2161 DMPlexGlobalVectorView - Saves a global vector 2162 2163 Collective 2164 2165 Input Parameters: 2166 + dm - The `DM` that represents the topology 2167 . viewer - The `PetscViewer` to save data with 2168 . sectiondm - The `DM` that contains the global section on which vec is defined, can be `NULL` 2169 - vec - The global vector to be saved 2170 2171 Level: advanced 2172 2173 Notes: 2174 In general `dm` and `sectiondm` are two different objects, the former carrying the topology and the latter carrying the section, and have been given a topology name and a section name, respectively, with `PetscObjectSetName()`. In practice, however, they can be the same object (or in case `sectiondm` is `NULL`) if it carries both topology and section; in that case the name of the object is used as both the topology name and the section name. 2175 2176 Calling sequence: 2177 .vb 2178 DMCreate(PETSC_COMM_WORLD, &dm); 2179 DMSetType(dm, DMPLEX); 2180 PetscObjectSetName((PetscObject)dm, "topologydm_name"); 2181 DMClone(dm, §iondm); 2182 PetscObjectSetName((PetscObject)sectiondm, "sectiondm_name"); 2183 PetscSectionCreate(PETSC_COMM_WORLD, §ion); 2184 DMPlexGetChart(sectiondm, &pStart, &pEnd); 2185 PetscSectionSetChart(section, pStart, pEnd); 2186 PetscSectionSetUp(section); 2187 DMSetLocalSection(sectiondm, section); 2188 PetscSectionDestroy(§ion); 2189 DMGetGlobalVector(sectiondm, &vec); 2190 PetscObjectSetName((PetscObject)vec, "vec_name"); 2191 DMPlexTopologyView(dm, viewer); 2192 DMPlexSectionView(dm, viewer, sectiondm); 2193 DMPlexGlobalVectorView(dm, viewer, sectiondm, vec); 2194 DMRestoreGlobalVector(sectiondm, &vec); 2195 DMDestroy(§iondm); 2196 DMDestroy(&dm); 2197 .ve 2198 2199 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexTopologyView()`, `DMPlexSectionView()`, `DMPlexLocalVectorView()`, `DMPlexGlobalVectorLoad()`, `DMPlexLocalVectorLoad()` 2200 @*/ 2201 PetscErrorCode DMPlexGlobalVectorView(DM dm, PetscViewer viewer, DM sectiondm, Vec vec) 2202 { 2203 PetscBool ishdf5; 2204 2205 PetscFunctionBegin; 2206 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2207 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2208 if (!sectiondm) sectiondm = dm; 2209 PetscValidHeaderSpecific(sectiondm, DM_CLASSID, 3); 2210 PetscValidHeaderSpecific(vec, VEC_CLASSID, 4); 2211 /* Check consistency */ 2212 { 2213 PetscSection section; 2214 PetscBool includesConstraints; 2215 PetscInt m, m1; 2216 2217 PetscCall(VecGetLocalSize(vec, &m1)); 2218 PetscCall(DMGetGlobalSection(sectiondm, §ion)); 2219 PetscCall(PetscSectionGetIncludesConstraints(section, &includesConstraints)); 2220 if (includesConstraints) PetscCall(PetscSectionGetStorageSize(section, &m)); 2221 else PetscCall(PetscSectionGetConstrainedStorageSize(section, &m)); 2222 PetscCheck(m1 == m, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Global vector size (%" PetscInt_FMT ") != global section storage size (%" PetscInt_FMT ")", m1, m); 2223 } 2224 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2225 PetscCall(PetscLogEventBegin(DMPLEX_GlobalVectorView, viewer, 0, 0, 0)); 2226 if (ishdf5) { 2227 #if defined(PETSC_HAVE_HDF5) 2228 PetscCall(DMPlexGlobalVectorView_HDF5_Internal(dm, viewer, sectiondm, vec)); 2229 #else 2230 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2231 #endif 2232 } 2233 PetscCall(PetscLogEventEnd(DMPLEX_GlobalVectorView, viewer, 0, 0, 0)); 2234 PetscFunctionReturn(PETSC_SUCCESS); 2235 } 2236 2237 /*@ 2238 DMPlexLocalVectorView - Saves a local vector 2239 2240 Collective 2241 2242 Input Parameters: 2243 + dm - The `DM` that represents the topology 2244 . viewer - The `PetscViewer` to save data with 2245 . sectiondm - The `DM` that contains the local section on which `vec` is defined, can be `NULL` 2246 - vec - The local vector to be saved 2247 2248 Level: advanced 2249 2250 Note: 2251 In general `dm` and `sectiondm` are two different objects, the former carrying the topology and the latter carrying the section, and have been given a topology name and a section name, respectively, with `PetscObjectSetName()`. In practice, however, they can be the same object (or in case `sectiondm` is `NULL`) if it carries both topology and section; in that case the name of the object is used as both the topology name and the section name. 2252 2253 Calling sequence: 2254 .vb 2255 DMCreate(PETSC_COMM_WORLD, &dm); 2256 DMSetType(dm, DMPLEX); 2257 PetscObjectSetName((PetscObject)dm, "topologydm_name"); 2258 DMClone(dm, §iondm); 2259 PetscObjectSetName((PetscObject)sectiondm, "sectiondm_name"); 2260 PetscSectionCreate(PETSC_COMM_WORLD, §ion); 2261 DMPlexGetChart(sectiondm, &pStart, &pEnd); 2262 PetscSectionSetChart(section, pStart, pEnd); 2263 PetscSectionSetUp(section); 2264 DMSetLocalSection(sectiondm, section); 2265 DMGetLocalVector(sectiondm, &vec); 2266 PetscObjectSetName((PetscObject)vec, "vec_name"); 2267 DMPlexTopologyView(dm, viewer); 2268 DMPlexSectionView(dm, viewer, sectiondm); 2269 DMPlexLocalVectorView(dm, viewer, sectiondm, vec); 2270 DMRestoreLocalVector(sectiondm, &vec); 2271 DMDestroy(§iondm); 2272 DMDestroy(&dm); 2273 .ve 2274 2275 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexTopologyView()`, `DMPlexSectionView()`, `DMPlexGlobalVectorView()`, `DMPlexGlobalVectorLoad()`, `DMPlexLocalVectorLoad()` 2276 @*/ 2277 PetscErrorCode DMPlexLocalVectorView(DM dm, PetscViewer viewer, DM sectiondm, Vec vec) 2278 { 2279 PetscBool ishdf5; 2280 2281 PetscFunctionBegin; 2282 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2283 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2284 if (!sectiondm) sectiondm = dm; 2285 PetscValidHeaderSpecific(sectiondm, DM_CLASSID, 3); 2286 PetscValidHeaderSpecific(vec, VEC_CLASSID, 4); 2287 /* Check consistency */ 2288 { 2289 PetscSection section; 2290 PetscBool includesConstraints; 2291 PetscInt m, m1; 2292 2293 PetscCall(VecGetLocalSize(vec, &m1)); 2294 PetscCall(DMGetLocalSection(sectiondm, §ion)); 2295 PetscCall(PetscSectionGetIncludesConstraints(section, &includesConstraints)); 2296 if (includesConstraints) PetscCall(PetscSectionGetStorageSize(section, &m)); 2297 else PetscCall(PetscSectionGetConstrainedStorageSize(section, &m)); 2298 PetscCheck(m1 == m, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Local vector size (%" PetscInt_FMT ") != local section storage size (%" PetscInt_FMT ")", m1, m); 2299 } 2300 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2301 PetscCall(PetscLogEventBegin(DMPLEX_LocalVectorView, viewer, 0, 0, 0)); 2302 if (ishdf5) { 2303 #if defined(PETSC_HAVE_HDF5) 2304 PetscCall(DMPlexLocalVectorView_HDF5_Internal(dm, viewer, sectiondm, vec)); 2305 #else 2306 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2307 #endif 2308 } 2309 PetscCall(PetscLogEventEnd(DMPLEX_LocalVectorView, viewer, 0, 0, 0)); 2310 PetscFunctionReturn(PETSC_SUCCESS); 2311 } 2312 2313 PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer) 2314 { 2315 PetscBool ishdf5; 2316 2317 PetscFunctionBegin; 2318 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2319 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2320 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2321 if (ishdf5) { 2322 #if defined(PETSC_HAVE_HDF5) 2323 PetscViewerFormat format; 2324 PetscCall(PetscViewerGetFormat(viewer, &format)); 2325 if (format == PETSC_VIEWER_HDF5_XDMF || format == PETSC_VIEWER_HDF5_VIZ) { 2326 PetscCall(DMPlexLoad_HDF5_Xdmf_Internal(dm, viewer)); 2327 } else if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) { 2328 PetscCall(DMPlexLoad_HDF5_Internal(dm, viewer)); 2329 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]); 2330 PetscFunctionReturn(PETSC_SUCCESS); 2331 #else 2332 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2333 #endif 2334 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Viewer type %s not yet supported for DMPlex loading", ((PetscObject)viewer)->type_name); 2335 } 2336 2337 /*@ 2338 DMPlexTopologyLoad - Loads a topology into a `DMPLEX` 2339 2340 Collective 2341 2342 Input Parameters: 2343 + dm - The `DM` into which the topology is loaded 2344 - viewer - The `PetscViewer` for the saved topology 2345 2346 Output Parameter: 2347 . globalToLocalPointSF - The `PetscSF` that pushes points in [0, N) to the associated points in the loaded `DMPLEX`, where N is the global number of points; `NULL` if unneeded 2348 2349 Level: advanced 2350 2351 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMLoad()`, `DMPlexCoordinatesLoad()`, `DMPlexLabelsLoad()`, `DMView()`, `PetscViewerHDF5Open()`, `PetscViewerPushFormat()`, 2352 `PetscViewer`, `PetscSF` 2353 @*/ 2354 PetscErrorCode DMPlexTopologyLoad(DM dm, PetscViewer viewer, PetscSF *globalToLocalPointSF) 2355 { 2356 PetscBool ishdf5; 2357 2358 PetscFunctionBegin; 2359 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2360 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2361 if (globalToLocalPointSF) PetscAssertPointer(globalToLocalPointSF, 3); 2362 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2363 PetscCall(PetscLogEventBegin(DMPLEX_TopologyLoad, viewer, 0, 0, 0)); 2364 if (ishdf5) { 2365 #if defined(PETSC_HAVE_HDF5) 2366 PetscViewerFormat format; 2367 PetscCall(PetscViewerGetFormat(viewer, &format)); 2368 if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) { 2369 PetscCall(DMPlexTopologyLoad_HDF5_Internal(dm, viewer, globalToLocalPointSF)); 2370 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]); 2371 #else 2372 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2373 #endif 2374 } 2375 PetscCall(PetscLogEventEnd(DMPLEX_TopologyLoad, viewer, 0, 0, 0)); 2376 PetscFunctionReturn(PETSC_SUCCESS); 2377 } 2378 2379 /*@ 2380 DMPlexCoordinatesLoad - Loads coordinates into a `DMPLEX` 2381 2382 Collective 2383 2384 Input Parameters: 2385 + dm - The `DM` into which the coordinates are loaded 2386 . viewer - The `PetscViewer` for the saved coordinates 2387 - globalToLocalPointSF - The `PetscSF` returned by `DMPlexTopologyLoad()` when loading dm from viewer 2388 2389 Level: advanced 2390 2391 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMLoad()`, `DMPlexTopologyLoad()`, `DMPlexLabelsLoad()`, `DMView()`, `PetscViewerHDF5Open()`, `PetscViewerPushFormat()`, 2392 `PetscSF`, `PetscViewer` 2393 @*/ 2394 PetscErrorCode DMPlexCoordinatesLoad(DM dm, PetscViewer viewer, PetscSF globalToLocalPointSF) 2395 { 2396 PetscBool ishdf5; 2397 2398 PetscFunctionBegin; 2399 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2400 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2401 PetscValidHeaderSpecific(globalToLocalPointSF, PETSCSF_CLASSID, 3); 2402 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2403 PetscCall(PetscLogEventBegin(DMPLEX_CoordinatesLoad, viewer, 0, 0, 0)); 2404 if (ishdf5) { 2405 #if defined(PETSC_HAVE_HDF5) 2406 PetscViewerFormat format; 2407 PetscCall(PetscViewerGetFormat(viewer, &format)); 2408 if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) { 2409 PetscCall(DMPlexCoordinatesLoad_HDF5_Internal(dm, viewer, globalToLocalPointSF)); 2410 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]); 2411 #else 2412 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2413 #endif 2414 } 2415 PetscCall(PetscLogEventEnd(DMPLEX_CoordinatesLoad, viewer, 0, 0, 0)); 2416 PetscFunctionReturn(PETSC_SUCCESS); 2417 } 2418 2419 /*@ 2420 DMPlexLabelsLoad - Loads labels into a `DMPLEX` 2421 2422 Collective 2423 2424 Input Parameters: 2425 + dm - The `DM` into which the labels are loaded 2426 . viewer - The `PetscViewer` for the saved labels 2427 - globalToLocalPointSF - The `PetscSF` returned by `DMPlexTopologyLoad()` when loading `dm` from viewer 2428 2429 Level: advanced 2430 2431 Note: 2432 The `PetscSF` argument must not be NULL if the `DM` is distributed, otherwise an error occurs. 2433 2434 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMLoad()`, `DMPlexTopologyLoad()`, `DMPlexCoordinatesLoad()`, `DMView()`, `PetscViewerHDF5Open()`, `PetscViewerPushFormat()`, 2435 `PetscSF`, `PetscViewer` 2436 @*/ 2437 PetscErrorCode DMPlexLabelsLoad(DM dm, PetscViewer viewer, PetscSF globalToLocalPointSF) 2438 { 2439 PetscBool ishdf5; 2440 2441 PetscFunctionBegin; 2442 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2443 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2444 if (globalToLocalPointSF) PetscValidHeaderSpecific(globalToLocalPointSF, PETSCSF_CLASSID, 3); 2445 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2446 PetscCall(PetscLogEventBegin(DMPLEX_LabelsLoad, viewer, 0, 0, 0)); 2447 if (ishdf5) { 2448 #if defined(PETSC_HAVE_HDF5) 2449 PetscViewerFormat format; 2450 2451 PetscCall(PetscViewerGetFormat(viewer, &format)); 2452 if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) { 2453 PetscCall(DMPlexLabelsLoad_HDF5_Internal(dm, viewer, globalToLocalPointSF)); 2454 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]); 2455 #else 2456 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2457 #endif 2458 } 2459 PetscCall(PetscLogEventEnd(DMPLEX_LabelsLoad, viewer, 0, 0, 0)); 2460 PetscFunctionReturn(PETSC_SUCCESS); 2461 } 2462 2463 /*@ 2464 DMPlexSectionLoad - Loads section into a `DMPLEX` 2465 2466 Collective 2467 2468 Input Parameters: 2469 + dm - The `DM` that represents the topology 2470 . viewer - The `PetscViewer` that represents the on-disk section (sectionA) 2471 . sectiondm - The `DM` into which the on-disk section (sectionA) is migrated, can be `NULL` 2472 - globalToLocalPointSF - The `PetscSF` returned by `DMPlexTopologyLoad(`) when loading dm from viewer 2473 2474 Output Parameters: 2475 + globalDofSF - The `PetscSF` that migrates any on-disk `Vec` data associated with sectionA into a global `Vec` associated with the `sectiondm`'s global section (`NULL` if not needed) 2476 - localDofSF - The `PetscSF` that migrates any on-disk `Vec` data associated with sectionA into a local `Vec` associated with the `sectiondm`'s local section (`NULL` if not needed) 2477 2478 Level: advanced 2479 2480 Notes: 2481 This function is a wrapper around `PetscSectionLoad()`; it loads, in addition to the raw section, a list of global point numbers that associates each on-disk section point with a global point number in [0, NX), where NX is the number of topology points in `dm`. Noting that globalToLocalPointSF associates each topology point in dm with a global number in [0, NX), one can readily establish an association of the on-disk section points with the topology points. 2482 2483 In general `dm` and `sectiondm` are two different objects, the former carrying the topology and the latter carrying the section, and have been given a topology name and a section name, respectively, with `PetscObjectSetName()`. In practice, however, they can be the same object (or in case `sectiondm` is `NULL`) if it carries both topology and section; in that case the name of the object is used as both the topology name and the section name. 2484 2485 The output parameter, `globalDofSF` (`localDofSF`), can later be used with `DMPlexGlobalVectorLoad()` (`DMPlexLocalVectorLoad()`) to load on-disk vectors into global (local) vectors associated with sectiondm's global (local) section. 2486 2487 Example using 2 processes: 2488 .vb 2489 NX (number of points on dm): 4 2490 sectionA : the on-disk section 2491 vecA : a vector associated with sectionA 2492 sectionB : sectiondm's local section constructed in this function 2493 vecB (local) : a vector associated with sectiondm's local section 2494 vecB (global) : a vector associated with sectiondm's global section 2495 2496 rank 0 rank 1 2497 vecA (global) : [.0 .4 .1 | .2 .3] <- to be loaded in DMPlexGlobalVectorLoad() or DMPlexLocalVectorLoad() 2498 sectionA->atlasOff : 0 2 | 1 <- loaded in PetscSectionLoad() 2499 sectionA->atlasDof : 1 3 | 1 <- loaded in PetscSectionLoad() 2500 sectionA's global point numbers: 0 2 | 3 <- loaded in DMPlexSectionLoad() 2501 [0, NX) : 0 1 | 2 3 <- conceptual partition used in globalToLocalPointSF 2502 sectionB's global point numbers: 0 1 3 | 3 2 <- associated with [0, NX) by globalToLocalPointSF 2503 sectionB->atlasDof : 1 0 1 | 1 3 2504 sectionB->atlasOff (no perm) : 0 1 1 | 0 1 2505 vecB (local) : [.0 .4] | [.4 .1 .2 .3] <- to be constructed by calling DMPlexLocalVectorLoad() with localDofSF 2506 vecB (global) : [.0 .4 | .1 .2 .3] <- to be constructed by calling DMPlexGlobalVectorLoad() with globalDofSF 2507 .ve 2508 where "|" represents a partition of loaded data, and global point 3 is assumed to be owned by rank 0. 2509 2510 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMLoad()`, `DMPlexTopologyLoad()`, `DMPlexCoordinatesLoad()`, `DMPlexLabelsLoad()`, `DMPlexGlobalVectorLoad()`, `DMPlexLocalVectorLoad()`, `PetscSectionLoad()`, `DMPlexSectionView()`, `PetscSF`, `PetscViewer` 2511 @*/ 2512 PetscErrorCode DMPlexSectionLoad(DM dm, PetscViewer viewer, DM sectiondm, PetscSF globalToLocalPointSF, PetscSF *globalDofSF, PetscSF *localDofSF) 2513 { 2514 PetscBool ishdf5; 2515 2516 PetscFunctionBegin; 2517 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2518 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2519 if (!sectiondm) sectiondm = dm; 2520 PetscValidHeaderSpecific(sectiondm, DM_CLASSID, 3); 2521 PetscValidHeaderSpecific(globalToLocalPointSF, PETSCSF_CLASSID, 4); 2522 if (globalDofSF) PetscAssertPointer(globalDofSF, 5); 2523 if (localDofSF) PetscAssertPointer(localDofSF, 6); 2524 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2525 PetscCall(PetscLogEventBegin(DMPLEX_SectionLoad, viewer, 0, 0, 0)); 2526 if (ishdf5) { 2527 #if defined(PETSC_HAVE_HDF5) 2528 PetscCall(DMPlexSectionLoad_HDF5_Internal(dm, viewer, sectiondm, globalToLocalPointSF, globalDofSF, localDofSF)); 2529 #else 2530 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2531 #endif 2532 } 2533 PetscCall(PetscLogEventEnd(DMPLEX_SectionLoad, viewer, 0, 0, 0)); 2534 PetscFunctionReturn(PETSC_SUCCESS); 2535 } 2536 2537 /*@ 2538 DMPlexGlobalVectorLoad - Loads on-disk vector data into a global vector 2539 2540 Collective 2541 2542 Input Parameters: 2543 + dm - The `DM` that represents the topology 2544 . viewer - The `PetscViewer` that represents the on-disk vector data 2545 . sectiondm - The `DM` that contains the global section on which vec is defined, can be `NULL` 2546 . sf - The `PetscSF` that migrates the on-disk vector data into vec 2547 - vec - The global vector to set values of 2548 2549 Level: advanced 2550 2551 Notes: 2552 In general dm and sectiondm are two different objects, the former carrying the topology and the latter carrying the section, and have been given a topology name and a section name, respectively, with `PetscObjectSetName()`. In practice, however, they can be the same object (or in case `sectiondm` is `NULL`) if it carries both topology and section; in that case the name of the object is used as both the topology name and the section name. 2553 2554 Calling sequence: 2555 .vb 2556 DMCreate(PETSC_COMM_WORLD, &dm); 2557 DMSetType(dm, DMPLEX); 2558 PetscObjectSetName((PetscObject)dm, "topologydm_name"); 2559 DMPlexTopologyLoad(dm, viewer, &sfX); 2560 DMClone(dm, §iondm); 2561 PetscObjectSetName((PetscObject)sectiondm, "sectiondm_name"); 2562 DMPlexSectionLoad(dm, viewer, sectiondm, sfX, &gsf, NULL); 2563 DMGetGlobalVector(sectiondm, &vec); 2564 PetscObjectSetName((PetscObject)vec, "vec_name"); 2565 DMPlexGlobalVectorLoad(dm, viewer, sectiondm, gsf, vec); 2566 DMRestoreGlobalVector(sectiondm, &vec); 2567 PetscSFDestroy(&gsf); 2568 PetscSFDestroy(&sfX); 2569 DMDestroy(§iondm); 2570 DMDestroy(&dm); 2571 .ve 2572 2573 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexTopologyLoad()`, `DMPlexSectionLoad()`, `DMPlexLocalVectorLoad()`, `DMPlexGlobalVectorView()`, `DMPlexLocalVectorView()`, 2574 `PetscSF`, `PetscViewer` 2575 @*/ 2576 PetscErrorCode DMPlexGlobalVectorLoad(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sf, Vec vec) 2577 { 2578 PetscBool ishdf5; 2579 2580 PetscFunctionBegin; 2581 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2582 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2583 if (!sectiondm) sectiondm = dm; 2584 PetscValidHeaderSpecific(sectiondm, DM_CLASSID, 3); 2585 PetscValidHeaderSpecific(sf, PETSCSF_CLASSID, 4); 2586 PetscValidHeaderSpecific(vec, VEC_CLASSID, 5); 2587 /* Check consistency */ 2588 { 2589 PetscSection section; 2590 PetscBool includesConstraints; 2591 PetscInt m, m1; 2592 2593 PetscCall(VecGetLocalSize(vec, &m1)); 2594 PetscCall(DMGetGlobalSection(sectiondm, §ion)); 2595 PetscCall(PetscSectionGetIncludesConstraints(section, &includesConstraints)); 2596 if (includesConstraints) PetscCall(PetscSectionGetStorageSize(section, &m)); 2597 else PetscCall(PetscSectionGetConstrainedStorageSize(section, &m)); 2598 PetscCheck(m1 == m, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Global vector size (%" PetscInt_FMT ") != global section storage size (%" PetscInt_FMT ")", m1, m); 2599 } 2600 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2601 PetscCall(PetscLogEventBegin(DMPLEX_GlobalVectorLoad, viewer, 0, 0, 0)); 2602 if (ishdf5) { 2603 #if defined(PETSC_HAVE_HDF5) 2604 PetscCall(DMPlexVecLoad_HDF5_Internal(dm, viewer, sectiondm, sf, vec)); 2605 #else 2606 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2607 #endif 2608 } 2609 PetscCall(PetscLogEventEnd(DMPLEX_GlobalVectorLoad, viewer, 0, 0, 0)); 2610 PetscFunctionReturn(PETSC_SUCCESS); 2611 } 2612 2613 /*@ 2614 DMPlexLocalVectorLoad - Loads on-disk vector data into a local vector 2615 2616 Collective 2617 2618 Input Parameters: 2619 + dm - The `DM` that represents the topology 2620 . viewer - The `PetscViewer` that represents the on-disk vector data 2621 . sectiondm - The `DM` that contains the local section on which vec is defined, can be `NULL` 2622 . sf - The `PetscSF` that migrates the on-disk vector data into vec 2623 - vec - The local vector to set values of 2624 2625 Level: advanced 2626 2627 Notes: 2628 In general `dm` and `sectiondm` are two different objects, the former carrying the topology and the latter carrying the section, and have been given a topology name and a section name, respectively, with `PetscObjectSetName()`. In practice, however, they can be the same object (or in case `sectiondm` is `NULL`) if it carries both topology and section; in that case the name of the object is used as both the topology name and the section name. 2629 2630 Calling sequence: 2631 .vb 2632 DMCreate(PETSC_COMM_WORLD, &dm); 2633 DMSetType(dm, DMPLEX); 2634 PetscObjectSetName((PetscObject)dm, "topologydm_name"); 2635 DMPlexTopologyLoad(dm, viewer, &sfX); 2636 DMClone(dm, §iondm); 2637 PetscObjectSetName((PetscObject)sectiondm, "sectiondm_name"); 2638 DMPlexSectionLoad(dm, viewer, sectiondm, sfX, NULL, &lsf); 2639 DMGetLocalVector(sectiondm, &vec); 2640 PetscObjectSetName((PetscObject)vec, "vec_name"); 2641 DMPlexLocalVectorLoad(dm, viewer, sectiondm, lsf, vec); 2642 DMRestoreLocalVector(sectiondm, &vec); 2643 PetscSFDestroy(&lsf); 2644 PetscSFDestroy(&sfX); 2645 DMDestroy(§iondm); 2646 DMDestroy(&dm); 2647 .ve 2648 2649 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexTopologyLoad()`, `DMPlexSectionLoad()`, `DMPlexGlobalVectorLoad()`, `DMPlexGlobalVectorView()`, `DMPlexLocalVectorView()`, 2650 `PetscSF`, `PetscViewer` 2651 @*/ 2652 PetscErrorCode DMPlexLocalVectorLoad(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sf, Vec vec) 2653 { 2654 PetscBool ishdf5; 2655 2656 PetscFunctionBegin; 2657 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2658 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2659 if (!sectiondm) sectiondm = dm; 2660 PetscValidHeaderSpecific(sectiondm, DM_CLASSID, 3); 2661 PetscValidHeaderSpecific(sf, PETSCSF_CLASSID, 4); 2662 PetscValidHeaderSpecific(vec, VEC_CLASSID, 5); 2663 /* Check consistency */ 2664 { 2665 PetscSection section; 2666 PetscBool includesConstraints; 2667 PetscInt m, m1; 2668 2669 PetscCall(VecGetLocalSize(vec, &m1)); 2670 PetscCall(DMGetLocalSection(sectiondm, §ion)); 2671 PetscCall(PetscSectionGetIncludesConstraints(section, &includesConstraints)); 2672 if (includesConstraints) PetscCall(PetscSectionGetStorageSize(section, &m)); 2673 else PetscCall(PetscSectionGetConstrainedStorageSize(section, &m)); 2674 PetscCheck(m1 == m, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Local vector size (%" PetscInt_FMT ") != local section storage size (%" PetscInt_FMT ")", m1, m); 2675 } 2676 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2677 PetscCall(PetscLogEventBegin(DMPLEX_LocalVectorLoad, viewer, 0, 0, 0)); 2678 if (ishdf5) { 2679 #if defined(PETSC_HAVE_HDF5) 2680 PetscCall(DMPlexVecLoad_HDF5_Internal(dm, viewer, sectiondm, sf, vec)); 2681 #else 2682 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2683 #endif 2684 } 2685 PetscCall(PetscLogEventEnd(DMPLEX_LocalVectorLoad, viewer, 0, 0, 0)); 2686 PetscFunctionReturn(PETSC_SUCCESS); 2687 } 2688 2689 PetscErrorCode DMDestroy_Plex(DM dm) 2690 { 2691 DM_Plex *mesh = (DM_Plex *)dm->data; 2692 2693 PetscFunctionBegin; 2694 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMSetUpGLVisViewer_C", NULL)); 2695 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexInsertBoundaryValues_C", NULL)); 2696 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMCreateNeumannOverlap_C", NULL)); 2697 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMInterpolateSolution_C", NULL)); 2698 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexInsertTimeDerivativeBoundaryValues_C", NULL)); 2699 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexGetOverlap_C", NULL)); 2700 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexDistributeGetDefault_C", NULL)); 2701 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexDistributeSetDefault_C", NULL)); 2702 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "MatComputeNeumannOverlap_C", NULL)); 2703 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexReorderGetDefault_C", NULL)); 2704 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexReorderSetDefault_C", NULL)); 2705 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMReorderSectionGetDefault_C", NULL)); 2706 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMReorderSectionSetDefault_C", NULL)); 2707 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMReorderSectionGetType_C", NULL)); 2708 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMReorderSectionSetType_C", NULL)); 2709 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexGetOverlap_C", NULL)); 2710 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexSetOverlap_C", NULL)); 2711 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexGetUseCeed_C", NULL)); 2712 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexSetUseCeed_C", NULL)); 2713 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMGetIsoperiodicPointSF_C", NULL)); 2714 if (--mesh->refct > 0) PetscFunctionReturn(PETSC_SUCCESS); 2715 PetscCall(PetscSectionDestroy(&mesh->coneSection)); 2716 PetscCall(PetscFree(mesh->cones)); 2717 PetscCall(PetscFree(mesh->coneOrientations)); 2718 PetscCall(PetscSectionDestroy(&mesh->supportSection)); 2719 PetscCall(PetscSectionDestroy(&mesh->subdomainSection)); 2720 PetscCall(PetscFree(mesh->supports)); 2721 PetscCall(PetscFree(mesh->cellTypes)); 2722 PetscCall(DMPlexTransformDestroy(&mesh->tr)); 2723 PetscCall(PetscFree(mesh->tetgenOpts)); 2724 PetscCall(PetscFree(mesh->triangleOpts)); 2725 PetscCall(PetscFree(mesh->transformType)); 2726 PetscCall(PetscFree(mesh->distributionName)); 2727 PetscCall(PetscPartitionerDestroy(&mesh->partitioner)); 2728 PetscCall(DMLabelDestroy(&mesh->subpointMap)); 2729 PetscCall(ISDestroy(&mesh->subpointIS)); 2730 PetscCall(ISDestroy(&mesh->globalVertexNumbers)); 2731 PetscCall(ISDestroy(&mesh->globalCellNumbers)); 2732 PetscCall(PetscSFDestroy(&mesh->periodic.face_sf)); 2733 PetscCall(PetscSFDestroy(&mesh->periodic.composed_sf)); 2734 PetscCall(ISDestroy(&mesh->periodic.periodic_points)); 2735 PetscCall(PetscSectionDestroy(&mesh->anchorSection)); 2736 PetscCall(ISDestroy(&mesh->anchorIS)); 2737 PetscCall(PetscSectionDestroy(&mesh->parentSection)); 2738 PetscCall(PetscFree(mesh->parents)); 2739 PetscCall(PetscFree(mesh->childIDs)); 2740 PetscCall(PetscSectionDestroy(&mesh->childSection)); 2741 PetscCall(PetscFree(mesh->children)); 2742 PetscCall(DMDestroy(&mesh->referenceTree)); 2743 PetscCall(PetscGridHashDestroy(&mesh->lbox)); 2744 PetscCall(PetscFree(mesh->neighbors)); 2745 if (mesh->metricCtx) PetscCall(PetscFree(mesh->metricCtx)); 2746 /* This was originally freed in DMDestroy(), but that prevents reference counting of backend objects */ 2747 PetscCall(PetscFree(mesh)); 2748 PetscFunctionReturn(PETSC_SUCCESS); 2749 } 2750 2751 PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J) 2752 { 2753 PetscSection sectionGlobal, sectionLocal; 2754 PetscInt bs = -1, mbs; 2755 PetscInt localSize, localStart = 0; 2756 PetscBool isShell, isBlock, isSeqBlock, isMPIBlock, isSymBlock, isSymSeqBlock, isSymMPIBlock, isMatIS; 2757 MatType mtype; 2758 ISLocalToGlobalMapping ltog; 2759 2760 PetscFunctionBegin; 2761 PetscCall(MatInitializePackage()); 2762 mtype = dm->mattype; 2763 PetscCall(DMGetLocalSection(dm, §ionLocal)); 2764 PetscCall(DMGetGlobalSection(dm, §ionGlobal)); 2765 /* PetscCall(PetscSectionGetStorageSize(sectionGlobal, &localSize)); */ 2766 PetscCall(PetscSectionGetConstrainedStorageSize(sectionGlobal, &localSize)); 2767 PetscCallMPI(MPI_Exscan(&localSize, &localStart, 1, MPIU_INT, MPI_SUM, PetscObjectComm((PetscObject)dm))); 2768 PetscCall(MatCreate(PetscObjectComm((PetscObject)dm), J)); 2769 PetscCall(MatSetSizes(*J, localSize, localSize, PETSC_DETERMINE, PETSC_DETERMINE)); 2770 PetscCall(MatSetType(*J, mtype)); 2771 PetscCall(MatSetFromOptions(*J)); 2772 PetscCall(MatGetBlockSize(*J, &mbs)); 2773 if (mbs > 1) bs = mbs; 2774 PetscCall(PetscStrcmp(mtype, MATSHELL, &isShell)); 2775 PetscCall(PetscStrcmp(mtype, MATBAIJ, &isBlock)); 2776 PetscCall(PetscStrcmp(mtype, MATSEQBAIJ, &isSeqBlock)); 2777 PetscCall(PetscStrcmp(mtype, MATMPIBAIJ, &isMPIBlock)); 2778 PetscCall(PetscStrcmp(mtype, MATSBAIJ, &isSymBlock)); 2779 PetscCall(PetscStrcmp(mtype, MATSEQSBAIJ, &isSymSeqBlock)); 2780 PetscCall(PetscStrcmp(mtype, MATMPISBAIJ, &isSymMPIBlock)); 2781 PetscCall(PetscStrcmp(mtype, MATIS, &isMatIS)); 2782 if (!isShell) { 2783 PetscBool fillMatrix = (PetscBool)(!dm->prealloc_only && !isMatIS); 2784 PetscInt *dnz, *onz, *dnzu, *onzu, bsLocal[2], bsMinMax[2], *pblocks; 2785 PetscInt pStart, pEnd, p, dof, cdof, num_fields; 2786 2787 PetscCall(DMGetLocalToGlobalMapping(dm, <og)); 2788 2789 PetscCall(PetscCalloc1(localSize, &pblocks)); 2790 PetscCall(PetscSectionGetChart(sectionGlobal, &pStart, &pEnd)); 2791 PetscCall(PetscSectionGetNumFields(sectionGlobal, &num_fields)); 2792 for (p = pStart; p < pEnd; ++p) { 2793 switch (dm->blocking_type) { 2794 case DM_BLOCKING_TOPOLOGICAL_POINT: { // One block per topological point 2795 PetscInt bdof, offset; 2796 2797 PetscCall(PetscSectionGetDof(sectionGlobal, p, &dof)); 2798 PetscCall(PetscSectionGetOffset(sectionGlobal, p, &offset)); 2799 PetscCall(PetscSectionGetConstraintDof(sectionGlobal, p, &cdof)); 2800 for (PetscInt i = 0; i < dof - cdof; ++i) pblocks[offset - localStart + i] = dof - cdof; 2801 // Signal block concatenation 2802 if (dof - cdof && sectionLocal->blockStarts && !PetscBTLookup(sectionLocal->blockStarts, p)) pblocks[offset - localStart] = -(dof - cdof); 2803 dof = dof < 0 ? -(dof + 1) : dof; 2804 bdof = cdof && (dof - cdof) ? 1 : dof; 2805 if (dof) { 2806 if (bs < 0) { 2807 bs = bdof; 2808 } else if (bs != bdof) { 2809 bs = 1; 2810 } 2811 } 2812 } break; 2813 case DM_BLOCKING_FIELD_NODE: { 2814 for (PetscInt field = 0; field < num_fields; field++) { 2815 PetscInt num_comp, bdof, offset; 2816 PetscCall(PetscSectionGetFieldComponents(sectionGlobal, field, &num_comp)); 2817 PetscCall(PetscSectionGetFieldDof(sectionGlobal, p, field, &dof)); 2818 if (dof < 0) continue; 2819 PetscCall(PetscSectionGetFieldOffset(sectionGlobal, p, field, &offset)); 2820 PetscCall(PetscSectionGetFieldConstraintDof(sectionGlobal, p, field, &cdof)); 2821 PetscAssert(dof % num_comp == 0, PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Point %" PetscInt_FMT " field %" PetscInt_FMT " has %" PetscInt_FMT " dof, not divisible by %" PetscInt_FMT " component ", p, field, dof, num_comp); 2822 PetscInt num_nodes = dof / num_comp; 2823 for (PetscInt i = 0; i < dof - cdof; i++) pblocks[offset - localStart + i] = (dof - cdof) / num_nodes; 2824 // Handle possibly constant block size (unlikely) 2825 bdof = cdof && (dof - cdof) ? 1 : dof; 2826 if (dof) { 2827 if (bs < 0) { 2828 bs = bdof; 2829 } else if (bs != bdof) { 2830 bs = 1; 2831 } 2832 } 2833 } 2834 } break; 2835 } 2836 } 2837 /* Must have same blocksize on all procs (some might have no points) */ 2838 bsLocal[0] = bs < 0 ? PETSC_MAX_INT : bs; 2839 bsLocal[1] = bs; 2840 PetscCall(PetscGlobalMinMaxInt(PetscObjectComm((PetscObject)dm), bsLocal, bsMinMax)); 2841 if (bsMinMax[0] != bsMinMax[1]) bs = 1; 2842 else bs = bsMinMax[0]; 2843 bs = PetscMax(1, bs); 2844 PetscCall(MatSetLocalToGlobalMapping(*J, ltog, ltog)); 2845 if (dm->prealloc_skip) { // User will likely use MatSetPreallocationCOO(), but still set structural parameters 2846 PetscCall(MatSetBlockSize(*J, bs)); 2847 PetscCall(MatSetUp(*J)); 2848 } else { 2849 PetscCall(PetscCalloc4(localSize / bs, &dnz, localSize / bs, &onz, localSize / bs, &dnzu, localSize / bs, &onzu)); 2850 PetscCall(DMPlexPreallocateOperator(dm, bs, dnz, onz, dnzu, onzu, *J, fillMatrix)); 2851 PetscCall(PetscFree4(dnz, onz, dnzu, onzu)); 2852 } 2853 { // Consolidate blocks 2854 PetscInt nblocks = 0; 2855 for (PetscInt i = 0; i < localSize; i += PetscMax(1, pblocks[i])) { 2856 if (pblocks[i] == 0) continue; 2857 // Negative block size indicates the blocks should be concatenated 2858 if (pblocks[i] < 0) { 2859 pblocks[i] = -pblocks[i]; 2860 pblocks[nblocks - 1] += pblocks[i]; 2861 } else { 2862 pblocks[nblocks++] = pblocks[i]; // nblocks always <= i 2863 } 2864 for (PetscInt j = 1; j < pblocks[i]; j++) PetscCheck(pblocks[i + j] == pblocks[i], PETSC_COMM_SELF, PETSC_ERR_PLIB, "Block of size %" PetscInt_FMT " mismatches entry %" PetscInt_FMT, pblocks[i], pblocks[i + j]); 2865 } 2866 PetscCall(MatSetVariableBlockSizes(*J, nblocks, pblocks)); 2867 } 2868 PetscCall(PetscFree(pblocks)); 2869 } 2870 PetscCall(MatSetDM(*J, dm)); 2871 PetscFunctionReturn(PETSC_SUCCESS); 2872 } 2873 2874 /*@ 2875 DMPlexGetSubdomainSection - Returns the section associated with the subdomain 2876 2877 Not Collective 2878 2879 Input Parameter: 2880 . dm - The `DMPLEX` 2881 2882 Output Parameter: 2883 . subsection - The subdomain section 2884 2885 Level: developer 2886 2887 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `PetscSection` 2888 @*/ 2889 PetscErrorCode DMPlexGetSubdomainSection(DM dm, PetscSection *subsection) 2890 { 2891 DM_Plex *mesh = (DM_Plex *)dm->data; 2892 2893 PetscFunctionBegin; 2894 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2895 if (!mesh->subdomainSection) { 2896 PetscSection section; 2897 PetscSF sf; 2898 2899 PetscCall(PetscSFCreate(PETSC_COMM_SELF, &sf)); 2900 PetscCall(DMGetLocalSection(dm, §ion)); 2901 PetscCall(PetscSectionCreateGlobalSection(section, sf, PETSC_TRUE, PETSC_FALSE, PETSC_TRUE, &mesh->subdomainSection)); 2902 PetscCall(PetscSFDestroy(&sf)); 2903 } 2904 *subsection = mesh->subdomainSection; 2905 PetscFunctionReturn(PETSC_SUCCESS); 2906 } 2907 2908 /*@ 2909 DMPlexGetChart - Return the interval for all mesh points [`pStart`, `pEnd`) 2910 2911 Not Collective 2912 2913 Input Parameter: 2914 . dm - The `DMPLEX` 2915 2916 Output Parameters: 2917 + pStart - The first mesh point 2918 - pEnd - The upper bound for mesh points 2919 2920 Level: beginner 2921 2922 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexSetChart()` 2923 @*/ 2924 PetscErrorCode DMPlexGetChart(DM dm, PetscInt *pStart, PetscInt *pEnd) 2925 { 2926 DM_Plex *mesh = (DM_Plex *)dm->data; 2927 2928 PetscFunctionBegin; 2929 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2930 if (mesh->tr) PetscCall(DMPlexTransformGetChart(mesh->tr, pStart, pEnd)); 2931 else PetscCall(PetscSectionGetChart(mesh->coneSection, pStart, pEnd)); 2932 PetscFunctionReturn(PETSC_SUCCESS); 2933 } 2934 2935 /*@ 2936 DMPlexSetChart - Set the interval for all mesh points [`pStart`, `pEnd`) 2937 2938 Not Collective 2939 2940 Input Parameters: 2941 + dm - The `DMPLEX` 2942 . pStart - The first mesh point 2943 - pEnd - The upper bound for mesh points 2944 2945 Level: beginner 2946 2947 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetChart()` 2948 @*/ 2949 PetscErrorCode DMPlexSetChart(DM dm, PetscInt pStart, PetscInt pEnd) 2950 { 2951 DM_Plex *mesh = (DM_Plex *)dm->data; 2952 2953 PetscFunctionBegin; 2954 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2955 PetscCall(PetscSectionSetChart(mesh->coneSection, pStart, pEnd)); 2956 PetscCall(PetscSectionSetChart(mesh->supportSection, pStart, pEnd)); 2957 PetscCall(PetscFree(mesh->cellTypes)); 2958 PetscFunctionReturn(PETSC_SUCCESS); 2959 } 2960 2961 /*@ 2962 DMPlexGetConeSize - Return the number of in-edges for this point in the DAG 2963 2964 Not Collective 2965 2966 Input Parameters: 2967 + dm - The `DMPLEX` 2968 - p - The point, which must lie in the chart set with `DMPlexSetChart()` 2969 2970 Output Parameter: 2971 . size - The cone size for point `p` 2972 2973 Level: beginner 2974 2975 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexSetConeSize()`, `DMPlexSetChart()` 2976 @*/ 2977 PetscErrorCode DMPlexGetConeSize(DM dm, PetscInt p, PetscInt *size) 2978 { 2979 DM_Plex *mesh = (DM_Plex *)dm->data; 2980 2981 PetscFunctionBegin; 2982 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2983 PetscAssertPointer(size, 3); 2984 if (mesh->tr) PetscCall(DMPlexTransformGetConeSize(mesh->tr, p, size)); 2985 else PetscCall(PetscSectionGetDof(mesh->coneSection, p, size)); 2986 PetscFunctionReturn(PETSC_SUCCESS); 2987 } 2988 2989 /*@ 2990 DMPlexSetConeSize - Set the number of in-edges for this point in the DAG 2991 2992 Not Collective 2993 2994 Input Parameters: 2995 + dm - The `DMPLEX` 2996 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 2997 - size - The cone size for point `p` 2998 2999 Level: beginner 3000 3001 Note: 3002 This should be called after `DMPlexSetChart()`. 3003 3004 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetConeSize()`, `DMPlexSetChart()` 3005 @*/ 3006 PetscErrorCode DMPlexSetConeSize(DM dm, PetscInt p, PetscInt size) 3007 { 3008 DM_Plex *mesh = (DM_Plex *)dm->data; 3009 3010 PetscFunctionBegin; 3011 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3012 PetscCheck(!mesh->tr, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Cannot call DMPlexSetConeSize() on a mesh with a transform defined."); 3013 PetscCall(PetscSectionSetDof(mesh->coneSection, p, size)); 3014 PetscFunctionReturn(PETSC_SUCCESS); 3015 } 3016 3017 /*@C 3018 DMPlexGetCone - Return the points on the in-edges for this point in the DAG 3019 3020 Not Collective 3021 3022 Input Parameters: 3023 + dm - The `DMPLEX` 3024 - p - The point, which must lie in the chart set with `DMPlexSetChart()` 3025 3026 Output Parameter: 3027 . cone - An array of points which are on the in-edges for point `p` 3028 3029 Level: beginner 3030 3031 Fortran Notes: 3032 You must also call `DMPlexRestoreCone()` after you finish using the returned array. 3033 `DMPlexRestoreCone()` is not needed/available in C. 3034 3035 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetConeSize()`, `DMPlexSetCone()`, `DMPlexGetConeTuple()`, `DMPlexSetChart()`, `DMPlexRestoreCone()` 3036 @*/ 3037 PetscErrorCode DMPlexGetCone(DM dm, PetscInt p, const PetscInt *cone[]) 3038 { 3039 DM_Plex *mesh = (DM_Plex *)dm->data; 3040 PetscInt off; 3041 3042 PetscFunctionBegin; 3043 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3044 PetscAssertPointer(cone, 3); 3045 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 3046 *cone = PetscSafePointerPlusOffset(mesh->cones, off); 3047 PetscFunctionReturn(PETSC_SUCCESS); 3048 } 3049 3050 /*@C 3051 DMPlexGetConeTuple - Return the points on the in-edges of several points in the DAG 3052 3053 Not Collective 3054 3055 Input Parameters: 3056 + dm - The `DMPLEX` 3057 - p - The `IS` of points, which must lie in the chart set with `DMPlexSetChart()` 3058 3059 Output Parameters: 3060 + pConesSection - `PetscSection` describing the layout of `pCones` 3061 - pCones - An array of points which are on the in-edges for the point set `p` 3062 3063 Level: intermediate 3064 3065 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexGetConeRecursive()`, `DMPlexSetChart()`, `PetscSection`, `IS` 3066 @*/ 3067 PetscErrorCode DMPlexGetConeTuple(DM dm, IS p, PetscSection *pConesSection, IS *pCones) 3068 { 3069 PetscSection cs, newcs; 3070 PetscInt *cones; 3071 PetscInt *newarr = NULL; 3072 PetscInt n; 3073 3074 PetscFunctionBegin; 3075 PetscCall(DMPlexGetCones(dm, &cones)); 3076 PetscCall(DMPlexGetConeSection(dm, &cs)); 3077 PetscCall(PetscSectionExtractDofsFromArray(cs, MPIU_INT, cones, p, &newcs, pCones ? ((void **)&newarr) : NULL)); 3078 if (pConesSection) *pConesSection = newcs; 3079 if (pCones) { 3080 PetscCall(PetscSectionGetStorageSize(newcs, &n)); 3081 PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)p), n, newarr, PETSC_OWN_POINTER, pCones)); 3082 } 3083 PetscFunctionReturn(PETSC_SUCCESS); 3084 } 3085 3086 /*@ 3087 DMPlexGetConeRecursiveVertices - Expand each given point into its cone points and do that recursively until we end up just with vertices. 3088 3089 Not Collective 3090 3091 Input Parameters: 3092 + dm - The `DMPLEX` 3093 - points - The `IS` of points, which must lie in the chart set with `DMPlexSetChart()` 3094 3095 Output Parameter: 3096 . expandedPoints - An array of vertices recursively expanded from input points 3097 3098 Level: advanced 3099 3100 Notes: 3101 Like `DMPlexGetConeRecursive()` but returns only the 0-depth `IS` (i.e. vertices only) and no sections. 3102 3103 There is no corresponding Restore function, just call `ISDestroy()` on the returned `IS` to deallocate. 3104 3105 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexGetConeTuple()`, `DMPlexGetConeRecursive()`, `DMPlexRestoreConeRecursive()`, 3106 `DMPlexGetDepth()`, `IS` 3107 @*/ 3108 PetscErrorCode DMPlexGetConeRecursiveVertices(DM dm, IS points, IS *expandedPoints) 3109 { 3110 IS *expandedPointsAll; 3111 PetscInt depth; 3112 3113 PetscFunctionBegin; 3114 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3115 PetscValidHeaderSpecific(points, IS_CLASSID, 2); 3116 PetscAssertPointer(expandedPoints, 3); 3117 PetscCall(DMPlexGetConeRecursive(dm, points, &depth, &expandedPointsAll, NULL)); 3118 *expandedPoints = expandedPointsAll[0]; 3119 PetscCall(PetscObjectReference((PetscObject)expandedPointsAll[0])); 3120 PetscCall(DMPlexRestoreConeRecursive(dm, points, &depth, &expandedPointsAll, NULL)); 3121 PetscFunctionReturn(PETSC_SUCCESS); 3122 } 3123 3124 /*@ 3125 DMPlexGetConeRecursive - Expand each given point into its cone points and do that recursively until we end up just with vertices (DAG points of depth 0, i.e. without cones). 3126 3127 Not Collective 3128 3129 Input Parameters: 3130 + dm - The `DMPLEX` 3131 - points - The `IS` of points, which must lie in the chart set with `DMPlexSetChart()` 3132 3133 Output Parameters: 3134 + depth - (optional) Size of the output arrays, equal to `DMPLEX` depth, returned by `DMPlexGetDepth()` 3135 . expandedPoints - (optional) An array of index sets with recursively expanded cones 3136 - sections - (optional) An array of sections which describe mappings from points to their cone points 3137 3138 Level: advanced 3139 3140 Notes: 3141 Like `DMPlexGetConeTuple()` but recursive. 3142 3143 Array `expandedPoints` has size equal to `depth`. Each `expandedPoints`[d] contains DAG points with maximum depth d, recursively cone-wise expanded from the input points. 3144 For example, for d=0 it contains only vertices, for d=1 it can contain vertices and edges, etc. 3145 3146 Array section has size equal to `depth`. Each `PetscSection` `sections`[d] realizes mapping from `expandedPoints`[d+1] (section points) to `expandedPoints`[d] (section dofs) as follows\: 3147 (1) DAG points in `expandedPoints`[d+1] with `depth` d+1 to their cone points in `expandedPoints`[d]; 3148 (2) DAG points in `expandedPoints`[d+1] with `depth` in [0,d] to the same points in `expandedPoints`[d]. 3149 3150 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexGetConeTuple()`, `DMPlexRestoreConeRecursive()`, `DMPlexGetConeRecursiveVertices()`, 3151 `DMPlexGetDepth()`, `PetscSection`, `IS` 3152 @*/ 3153 PetscErrorCode DMPlexGetConeRecursive(DM dm, IS points, PetscInt *depth, IS *expandedPoints[], PetscSection *sections[]) 3154 { 3155 const PetscInt *arr0 = NULL, *cone = NULL; 3156 PetscInt *arr = NULL, *newarr = NULL; 3157 PetscInt d, depth_, i, n, newn, cn, co, start, end; 3158 IS *expandedPoints_; 3159 PetscSection *sections_; 3160 3161 PetscFunctionBegin; 3162 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3163 PetscValidHeaderSpecific(points, IS_CLASSID, 2); 3164 if (depth) PetscAssertPointer(depth, 3); 3165 if (expandedPoints) PetscAssertPointer(expandedPoints, 4); 3166 if (sections) PetscAssertPointer(sections, 5); 3167 PetscCall(ISGetLocalSize(points, &n)); 3168 PetscCall(ISGetIndices(points, &arr0)); 3169 PetscCall(DMPlexGetDepth(dm, &depth_)); 3170 PetscCall(PetscCalloc1(depth_, &expandedPoints_)); 3171 PetscCall(PetscCalloc1(depth_, §ions_)); 3172 arr = (PetscInt *)arr0; /* this is ok because first generation of arr is not modified */ 3173 for (d = depth_ - 1; d >= 0; d--) { 3174 PetscCall(PetscSectionCreate(PETSC_COMM_SELF, §ions_[d])); 3175 PetscCall(PetscSectionSetChart(sections_[d], 0, n)); 3176 for (i = 0; i < n; i++) { 3177 PetscCall(DMPlexGetDepthStratum(dm, d + 1, &start, &end)); 3178 if (arr[i] >= start && arr[i] < end) { 3179 PetscCall(DMPlexGetConeSize(dm, arr[i], &cn)); 3180 PetscCall(PetscSectionSetDof(sections_[d], i, cn)); 3181 } else { 3182 PetscCall(PetscSectionSetDof(sections_[d], i, 1)); 3183 } 3184 } 3185 PetscCall(PetscSectionSetUp(sections_[d])); 3186 PetscCall(PetscSectionGetStorageSize(sections_[d], &newn)); 3187 PetscCall(PetscMalloc1(newn, &newarr)); 3188 for (i = 0; i < n; i++) { 3189 PetscCall(PetscSectionGetDof(sections_[d], i, &cn)); 3190 PetscCall(PetscSectionGetOffset(sections_[d], i, &co)); 3191 if (cn > 1) { 3192 PetscCall(DMPlexGetCone(dm, arr[i], &cone)); 3193 PetscCall(PetscMemcpy(&newarr[co], cone, cn * sizeof(PetscInt))); 3194 } else { 3195 newarr[co] = arr[i]; 3196 } 3197 } 3198 PetscCall(ISCreateGeneral(PETSC_COMM_SELF, newn, newarr, PETSC_OWN_POINTER, &expandedPoints_[d])); 3199 arr = newarr; 3200 n = newn; 3201 } 3202 PetscCall(ISRestoreIndices(points, &arr0)); 3203 *depth = depth_; 3204 if (expandedPoints) *expandedPoints = expandedPoints_; 3205 else { 3206 for (d = 0; d < depth_; d++) PetscCall(ISDestroy(&expandedPoints_[d])); 3207 PetscCall(PetscFree(expandedPoints_)); 3208 } 3209 if (sections) *sections = sections_; 3210 else { 3211 for (d = 0; d < depth_; d++) PetscCall(PetscSectionDestroy(§ions_[d])); 3212 PetscCall(PetscFree(sections_)); 3213 } 3214 PetscFunctionReturn(PETSC_SUCCESS); 3215 } 3216 3217 /*@ 3218 DMPlexRestoreConeRecursive - Deallocates arrays created by `DMPlexGetConeRecursive()` 3219 3220 Not Collective 3221 3222 Input Parameters: 3223 + dm - The `DMPLEX` 3224 - points - The `IS` of points, which must lie in the chart set with `DMPlexSetChart()` 3225 3226 Output Parameters: 3227 + depth - (optional) Size of the output arrays, equal to `DMPLEX` depth, returned by `DMPlexGetDepth()` 3228 . expandedPoints - (optional) An array of recursively expanded cones 3229 - sections - (optional) An array of sections which describe mappings from points to their cone points 3230 3231 Level: advanced 3232 3233 Note: 3234 See `DMPlexGetConeRecursive()` 3235 3236 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexGetConeTuple()`, `DMPlexGetConeRecursive()`, `DMPlexGetConeRecursiveVertices()`, 3237 `DMPlexGetDepth()`, `IS`, `PetscSection` 3238 @*/ 3239 PetscErrorCode DMPlexRestoreConeRecursive(DM dm, IS points, PetscInt *depth, IS *expandedPoints[], PetscSection *sections[]) 3240 { 3241 PetscInt d, depth_; 3242 3243 PetscFunctionBegin; 3244 PetscCall(DMPlexGetDepth(dm, &depth_)); 3245 PetscCheck(!depth || *depth == depth_, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "depth changed since last call to DMPlexGetConeRecursive"); 3246 if (depth) *depth = 0; 3247 if (expandedPoints) { 3248 for (d = 0; d < depth_; d++) PetscCall(ISDestroy(&((*expandedPoints)[d]))); 3249 PetscCall(PetscFree(*expandedPoints)); 3250 } 3251 if (sections) { 3252 for (d = 0; d < depth_; d++) PetscCall(PetscSectionDestroy(&((*sections)[d]))); 3253 PetscCall(PetscFree(*sections)); 3254 } 3255 PetscFunctionReturn(PETSC_SUCCESS); 3256 } 3257 3258 /*@ 3259 DMPlexSetCone - Set the points on the in-edges for this point in the DAG; that is these are the points that cover the specific point 3260 3261 Not Collective 3262 3263 Input Parameters: 3264 + dm - The `DMPLEX` 3265 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 3266 - cone - An array of points which are on the in-edges for point `p` 3267 3268 Level: beginner 3269 3270 Note: 3271 This should be called after all calls to `DMPlexSetConeSize()` and `DMSetUp()`. 3272 3273 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexSetChart()`, `DMPlexSetConeSize()`, `DMSetUp()`, `DMPlexSetSupport()`, `DMPlexSetSupportSize()` 3274 @*/ 3275 PetscErrorCode DMPlexSetCone(DM dm, PetscInt p, const PetscInt cone[]) 3276 { 3277 DM_Plex *mesh = (DM_Plex *)dm->data; 3278 PetscInt dof, off, c; 3279 3280 PetscFunctionBegin; 3281 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3282 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 3283 if (dof) PetscAssertPointer(cone, 3); 3284 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 3285 if (PetscDefined(USE_DEBUG)) { 3286 PetscInt pStart, pEnd; 3287 PetscCall(PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd)); 3288 PetscCheck(!(p < pStart) && !(p >= pEnd), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %" PetscInt_FMT " is not in the valid range [%" PetscInt_FMT ", %" PetscInt_FMT ")", p, pStart, pEnd); 3289 for (c = 0; c < dof; ++c) { 3290 PetscCheck(!(cone[c] < pStart) && !(cone[c] >= pEnd), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cone point %" PetscInt_FMT " is not in the valid range [%" PetscInt_FMT ", %" PetscInt_FMT ")", cone[c], pStart, pEnd); 3291 mesh->cones[off + c] = cone[c]; 3292 } 3293 } else { 3294 for (c = 0; c < dof; ++c) mesh->cones[off + c] = cone[c]; 3295 } 3296 PetscFunctionReturn(PETSC_SUCCESS); 3297 } 3298 3299 /*@C 3300 DMPlexGetConeOrientation - Return the orientations on the in-edges for this point in the DAG 3301 3302 Not Collective 3303 3304 Input Parameters: 3305 + dm - The `DMPLEX` 3306 - p - The point, which must lie in the chart set with `DMPlexSetChart()` 3307 3308 Output Parameter: 3309 . coneOrientation - An array of orientations which are on the in-edges for point `p`. An orientation is an 3310 integer giving the prescription for cone traversal. 3311 3312 Level: beginner 3313 3314 Note: 3315 The number indexes the symmetry transformations for the cell type (see manual). Orientation 0 is always 3316 the identity transformation. Negative orientation indicates reflection so that -(o+1) is the reflection 3317 of o, however it is not necessarily the inverse. To get the inverse, use `DMPolytopeTypeComposeOrientationInv()` 3318 with the identity. 3319 3320 Fortran Notes: 3321 You must also call `DMPlexRestoreConeOrientation()` after you finish using the returned array. 3322 `DMPlexRestoreConeOrientation()` is not needed/available in C. 3323 3324 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPolytopeTypeComposeOrientation()`, `DMPolytopeTypeComposeOrientationInv()`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexSetCone()`, `DMPlexSetChart()` 3325 @*/ 3326 PetscErrorCode DMPlexGetConeOrientation(DM dm, PetscInt p, const PetscInt *coneOrientation[]) 3327 { 3328 DM_Plex *mesh = (DM_Plex *)dm->data; 3329 PetscInt off; 3330 3331 PetscFunctionBegin; 3332 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3333 if (PetscDefined(USE_DEBUG)) { 3334 PetscInt dof; 3335 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 3336 if (dof) PetscAssertPointer(coneOrientation, 3); 3337 } 3338 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 3339 3340 *coneOrientation = &mesh->coneOrientations[off]; 3341 PetscFunctionReturn(PETSC_SUCCESS); 3342 } 3343 3344 /*@ 3345 DMPlexSetConeOrientation - Set the orientations on the in-edges for this point in the DAG 3346 3347 Not Collective 3348 3349 Input Parameters: 3350 + dm - The `DMPLEX` 3351 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 3352 - coneOrientation - An array of orientations 3353 3354 Level: beginner 3355 3356 Notes: 3357 This should be called after all calls to `DMPlexSetConeSize()` and `DMSetUp()`. 3358 3359 The meaning of coneOrientation is detailed in `DMPlexGetConeOrientation()`. 3360 3361 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetConeOrientation()`, `DMPlexSetCone()`, `DMPlexSetChart()`, `DMPlexSetConeSize()`, `DMSetUp()` 3362 @*/ 3363 PetscErrorCode DMPlexSetConeOrientation(DM dm, PetscInt p, const PetscInt coneOrientation[]) 3364 { 3365 DM_Plex *mesh = (DM_Plex *)dm->data; 3366 PetscInt pStart, pEnd; 3367 PetscInt dof, off, c; 3368 3369 PetscFunctionBegin; 3370 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3371 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 3372 if (dof) PetscAssertPointer(coneOrientation, 3); 3373 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 3374 if (PetscDefined(USE_DEBUG)) { 3375 PetscCall(PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd)); 3376 PetscCheck(!(p < pStart) && !(p >= pEnd), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %" PetscInt_FMT " is not in the valid range [%" PetscInt_FMT ", %" PetscInt_FMT ")", p, pStart, pEnd); 3377 for (c = 0; c < dof; ++c) { 3378 PetscInt cdof, o = coneOrientation[c]; 3379 3380 PetscCall(PetscSectionGetDof(mesh->coneSection, mesh->cones[off + c], &cdof)); 3381 PetscCheck(!o || (o >= -(cdof + 1) && o < cdof), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cone orientation %" PetscInt_FMT " is not in the valid range [%" PetscInt_FMT ". %" PetscInt_FMT ")", o, -(cdof + 1), cdof); 3382 mesh->coneOrientations[off + c] = o; 3383 } 3384 } else { 3385 for (c = 0; c < dof; ++c) mesh->coneOrientations[off + c] = coneOrientation[c]; 3386 } 3387 PetscFunctionReturn(PETSC_SUCCESS); 3388 } 3389 3390 /*@ 3391 DMPlexInsertCone - Insert a point into the in-edges for the point p in the DAG 3392 3393 Not Collective 3394 3395 Input Parameters: 3396 + dm - The `DMPLEX` 3397 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 3398 . conePos - The local index in the cone where the point should be put 3399 - conePoint - The mesh point to insert 3400 3401 Level: beginner 3402 3403 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexSetChart()`, `DMPlexSetConeSize()`, `DMSetUp()` 3404 @*/ 3405 PetscErrorCode DMPlexInsertCone(DM dm, PetscInt p, PetscInt conePos, PetscInt conePoint) 3406 { 3407 DM_Plex *mesh = (DM_Plex *)dm->data; 3408 PetscInt pStart, pEnd; 3409 PetscInt dof, off; 3410 3411 PetscFunctionBegin; 3412 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3413 if (PetscDefined(USE_DEBUG)) { 3414 PetscCall(PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd)); 3415 PetscCheck(!(p < pStart) && !(p >= pEnd), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %" PetscInt_FMT " is not in the valid range [%" PetscInt_FMT ", %" PetscInt_FMT ")", p, pStart, pEnd); 3416 PetscCheck(!(conePoint < pStart) && !(conePoint >= pEnd), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cone point %" PetscInt_FMT " is not in the valid range [%" PetscInt_FMT ", %" PetscInt_FMT ")", conePoint, pStart, pEnd); 3417 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 3418 PetscCheck(!(conePos < 0) && !(conePos >= dof), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cone position %" PetscInt_FMT " of point %" PetscInt_FMT " is not in the valid range [0, %" PetscInt_FMT ")", conePos, p, dof); 3419 } 3420 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 3421 mesh->cones[off + conePos] = conePoint; 3422 PetscFunctionReturn(PETSC_SUCCESS); 3423 } 3424 3425 /*@ 3426 DMPlexInsertConeOrientation - Insert a point orientation for the in-edge for the point p in the DAG 3427 3428 Not Collective 3429 3430 Input Parameters: 3431 + dm - The `DMPLEX` 3432 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 3433 . conePos - The local index in the cone where the point should be put 3434 - coneOrientation - The point orientation to insert 3435 3436 Level: beginner 3437 3438 Note: 3439 The meaning of coneOrientation values is detailed in `DMPlexGetConeOrientation()`. 3440 3441 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexSetChart()`, `DMPlexSetConeSize()`, `DMSetUp()` 3442 @*/ 3443 PetscErrorCode DMPlexInsertConeOrientation(DM dm, PetscInt p, PetscInt conePos, PetscInt coneOrientation) 3444 { 3445 DM_Plex *mesh = (DM_Plex *)dm->data; 3446 PetscInt pStart, pEnd; 3447 PetscInt dof, off; 3448 3449 PetscFunctionBegin; 3450 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3451 if (PetscDefined(USE_DEBUG)) { 3452 PetscCall(PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd)); 3453 PetscCheck(!(p < pStart) && !(p >= pEnd), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %" PetscInt_FMT " is not in the valid range [%" PetscInt_FMT ", %" PetscInt_FMT ")", p, pStart, pEnd); 3454 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 3455 PetscCheck(!(conePos < 0) && !(conePos >= dof), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cone position %" PetscInt_FMT " of point %" PetscInt_FMT " is not in the valid range [0, %" PetscInt_FMT ")", conePos, p, dof); 3456 } 3457 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 3458 mesh->coneOrientations[off + conePos] = coneOrientation; 3459 PetscFunctionReturn(PETSC_SUCCESS); 3460 } 3461 3462 /*@C 3463 DMPlexGetOrientedCone - Return the points and orientations on the in-edges for this point in the DAG 3464 3465 Not collective 3466 3467 Input Parameters: 3468 + dm - The DMPlex 3469 - p - The point, which must lie in the chart set with DMPlexSetChart() 3470 3471 Output Parameters: 3472 + cone - An array of points which are on the in-edges for point `p` 3473 - ornt - An array of orientations which are on the in-edges for point `p`. An orientation is an 3474 integer giving the prescription for cone traversal. 3475 3476 Level: beginner 3477 3478 Notes: 3479 The number indexes the symmetry transformations for the cell type (see manual). Orientation 0 is always 3480 the identity transformation. Negative orientation indicates reflection so that -(o+1) is the reflection 3481 of o, however it is not necessarily the inverse. To get the inverse, use `DMPolytopeTypeComposeOrientationInv()` 3482 with the identity. 3483 3484 Fortran Notes: 3485 You must also call `DMPlexRestoreCone()` after you finish using the returned array. 3486 `DMPlexRestoreCone()` is not needed/available in C. 3487 3488 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexRestoreOrientedCone()`, `DMPlexGetConeSize()`, `DMPlexGetCone()`, `DMPlexGetChart()` 3489 @*/ 3490 PetscErrorCode DMPlexGetOrientedCone(DM dm, PetscInt p, const PetscInt *cone[], const PetscInt *ornt[]) 3491 { 3492 DM_Plex *mesh = (DM_Plex *)dm->data; 3493 3494 PetscFunctionBegin; 3495 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3496 if (mesh->tr) { 3497 PetscCall(DMPlexTransformGetCone(mesh->tr, p, cone, ornt)); 3498 } else { 3499 PetscInt off; 3500 if (PetscDefined(USE_DEBUG)) { 3501 PetscInt dof; 3502 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 3503 if (dof) { 3504 if (cone) PetscAssertPointer(cone, 3); 3505 if (ornt) PetscAssertPointer(ornt, 4); 3506 } 3507 } 3508 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 3509 if (cone) *cone = PetscSafePointerPlusOffset(mesh->cones, off); 3510 if (ornt) *ornt = PetscSafePointerPlusOffset(mesh->coneOrientations, off); 3511 } 3512 PetscFunctionReturn(PETSC_SUCCESS); 3513 } 3514 3515 /*@C 3516 DMPlexRestoreOrientedCone - Restore the points and orientations on the in-edges for this point in the DAG 3517 3518 Not Collective 3519 3520 Input Parameters: 3521 + dm - The DMPlex 3522 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 3523 . cone - An array of points which are on the in-edges for point p 3524 - ornt - An array of orientations which are on the in-edges for point `p`. An orientation is an 3525 integer giving the prescription for cone traversal. 3526 3527 Level: beginner 3528 3529 Notes: 3530 The number indexes the symmetry transformations for the cell type (see manual). Orientation 0 is always 3531 the identity transformation. Negative orientation indicates reflection so that -(o+1) is the reflection 3532 of o, however it is not necessarily the inverse. To get the inverse, use `DMPolytopeTypeComposeOrientationInv()` 3533 with the identity. 3534 3535 Fortran Notes: 3536 You must also call `DMPlexRestoreCone()` after you finish using the returned array. 3537 `DMPlexRestoreCone()` is not needed/available in C. 3538 3539 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetOrientedCone()`, `DMPlexGetConeSize()`, `DMPlexGetCone()`, `DMPlexGetChart()` 3540 @*/ 3541 PetscErrorCode DMPlexRestoreOrientedCone(DM dm, PetscInt p, const PetscInt *cone[], const PetscInt *ornt[]) 3542 { 3543 DM_Plex *mesh = (DM_Plex *)dm->data; 3544 3545 PetscFunctionBegin; 3546 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3547 if (mesh->tr) PetscCall(DMPlexTransformRestoreCone(mesh->tr, p, cone, ornt)); 3548 PetscFunctionReturn(PETSC_SUCCESS); 3549 } 3550 3551 /*@ 3552 DMPlexGetSupportSize - Return the number of out-edges for this point in the DAG 3553 3554 Not Collective 3555 3556 Input Parameters: 3557 + dm - The `DMPLEX` 3558 - p - The point, which must lie in the chart set with `DMPlexSetChart()` 3559 3560 Output Parameter: 3561 . size - The support size for point `p` 3562 3563 Level: beginner 3564 3565 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexSetConeSize()`, `DMPlexSetChart()`, `DMPlexGetConeSize()` 3566 @*/ 3567 PetscErrorCode DMPlexGetSupportSize(DM dm, PetscInt p, PetscInt *size) 3568 { 3569 DM_Plex *mesh = (DM_Plex *)dm->data; 3570 3571 PetscFunctionBegin; 3572 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3573 PetscAssertPointer(size, 3); 3574 PetscCall(PetscSectionGetDof(mesh->supportSection, p, size)); 3575 PetscFunctionReturn(PETSC_SUCCESS); 3576 } 3577 3578 /*@ 3579 DMPlexSetSupportSize - Set the number of out-edges for this point in the DAG 3580 3581 Not Collective 3582 3583 Input Parameters: 3584 + dm - The `DMPLEX` 3585 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 3586 - size - The support size for point `p` 3587 3588 Level: beginner 3589 3590 Note: 3591 This should be called after `DMPlexSetChart()`. 3592 3593 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetSupportSize()`, `DMPlexSetChart()` 3594 @*/ 3595 PetscErrorCode DMPlexSetSupportSize(DM dm, PetscInt p, PetscInt size) 3596 { 3597 DM_Plex *mesh = (DM_Plex *)dm->data; 3598 3599 PetscFunctionBegin; 3600 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3601 PetscCall(PetscSectionSetDof(mesh->supportSection, p, size)); 3602 PetscFunctionReturn(PETSC_SUCCESS); 3603 } 3604 3605 /*@C 3606 DMPlexGetSupport - Return the points on the out-edges for this point in the DAG 3607 3608 Not Collective 3609 3610 Input Parameters: 3611 + dm - The `DMPLEX` 3612 - p - The point, which must lie in the chart set with `DMPlexSetChart()` 3613 3614 Output Parameter: 3615 . support - An array of points which are on the out-edges for point `p` 3616 3617 Level: beginner 3618 3619 Fortran Notes: 3620 You must also call `DMPlexRestoreSupport()` after you finish using the returned array. 3621 `DMPlexRestoreSupport()` is not needed/available in C. 3622 3623 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetSupportSize()`, `DMPlexSetSupport()`, `DMPlexGetCone()`, `DMPlexSetChart()` 3624 @*/ 3625 PetscErrorCode DMPlexGetSupport(DM dm, PetscInt p, const PetscInt *support[]) 3626 { 3627 DM_Plex *mesh = (DM_Plex *)dm->data; 3628 PetscInt off; 3629 3630 PetscFunctionBegin; 3631 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3632 PetscAssertPointer(support, 3); 3633 PetscCall(PetscSectionGetOffset(mesh->supportSection, p, &off)); 3634 *support = PetscSafePointerPlusOffset(mesh->supports, off); 3635 PetscFunctionReturn(PETSC_SUCCESS); 3636 } 3637 3638 /*@ 3639 DMPlexSetSupport - Set the points on the out-edges for this point in the DAG, that is the list of points that this point covers 3640 3641 Not Collective 3642 3643 Input Parameters: 3644 + dm - The `DMPLEX` 3645 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 3646 - support - An array of points which are on the out-edges for point `p` 3647 3648 Level: beginner 3649 3650 Note: 3651 This should be called after all calls to `DMPlexSetSupportSize()` and `DMSetUp()`. 3652 3653 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexSetCone()`, `DMPlexSetConeSize()`, `DMPlexCreate()`, `DMPlexGetSupport()`, `DMPlexSetChart()`, `DMPlexSetSupportSize()`, `DMSetUp()` 3654 @*/ 3655 PetscErrorCode DMPlexSetSupport(DM dm, PetscInt p, const PetscInt support[]) 3656 { 3657 DM_Plex *mesh = (DM_Plex *)dm->data; 3658 PetscInt pStart, pEnd; 3659 PetscInt dof, off, c; 3660 3661 PetscFunctionBegin; 3662 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3663 PetscCall(PetscSectionGetChart(mesh->supportSection, &pStart, &pEnd)); 3664 PetscCall(PetscSectionGetDof(mesh->supportSection, p, &dof)); 3665 if (dof) PetscAssertPointer(support, 3); 3666 PetscCall(PetscSectionGetOffset(mesh->supportSection, p, &off)); 3667 PetscCheck(!(p < pStart) && !(p >= pEnd), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %" PetscInt_FMT " is not in the valid range [%" PetscInt_FMT ", %" PetscInt_FMT ")", p, pStart, pEnd); 3668 for (c = 0; c < dof; ++c) { 3669 PetscCheck(!(support[c] < pStart) && !(support[c] >= pEnd), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Support point %" PetscInt_FMT " is not in the valid range [%" PetscInt_FMT ", %" PetscInt_FMT ")", support[c], pStart, pEnd); 3670 mesh->supports[off + c] = support[c]; 3671 } 3672 PetscFunctionReturn(PETSC_SUCCESS); 3673 } 3674 3675 /*@ 3676 DMPlexInsertSupport - Insert a point into the out-edges for the point p in the DAG 3677 3678 Not Collective 3679 3680 Input Parameters: 3681 + dm - The `DMPLEX` 3682 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 3683 . supportPos - The local index in the cone where the point should be put 3684 - supportPoint - The mesh point to insert 3685 3686 Level: beginner 3687 3688 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexSetChart()`, `DMPlexSetConeSize()`, `DMSetUp()` 3689 @*/ 3690 PetscErrorCode DMPlexInsertSupport(DM dm, PetscInt p, PetscInt supportPos, PetscInt supportPoint) 3691 { 3692 DM_Plex *mesh = (DM_Plex *)dm->data; 3693 PetscInt pStart, pEnd; 3694 PetscInt dof, off; 3695 3696 PetscFunctionBegin; 3697 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3698 PetscCall(PetscSectionGetChart(mesh->supportSection, &pStart, &pEnd)); 3699 PetscCall(PetscSectionGetDof(mesh->supportSection, p, &dof)); 3700 PetscCall(PetscSectionGetOffset(mesh->supportSection, p, &off)); 3701 PetscCheck(!(p < pStart) && !(p >= pEnd), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %" PetscInt_FMT " is not in the valid range [%" PetscInt_FMT ", %" PetscInt_FMT ")", p, pStart, pEnd); 3702 PetscCheck(!(supportPoint < pStart) && !(supportPoint >= pEnd), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Support point %" PetscInt_FMT " is not in the valid range [%" PetscInt_FMT ", %" PetscInt_FMT ")", supportPoint, pStart, pEnd); 3703 PetscCheck(supportPos < dof, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Support position %" PetscInt_FMT " of point %" PetscInt_FMT " is not in the valid range [0, %" PetscInt_FMT ")", supportPos, p, dof); 3704 mesh->supports[off + supportPos] = supportPoint; 3705 PetscFunctionReturn(PETSC_SUCCESS); 3706 } 3707 3708 /* Converts an orientation o in the current numbering to the previous scheme used in Plex */ 3709 PetscInt DMPolytopeConvertNewOrientation_Internal(DMPolytopeType ct, PetscInt o) 3710 { 3711 switch (ct) { 3712 case DM_POLYTOPE_SEGMENT: 3713 if (o == -1) return -2; 3714 break; 3715 case DM_POLYTOPE_TRIANGLE: 3716 if (o == -3) return -1; 3717 if (o == -2) return -3; 3718 if (o == -1) return -2; 3719 break; 3720 case DM_POLYTOPE_QUADRILATERAL: 3721 if (o == -4) return -2; 3722 if (o == -3) return -1; 3723 if (o == -2) return -4; 3724 if (o == -1) return -3; 3725 break; 3726 default: 3727 return o; 3728 } 3729 return o; 3730 } 3731 3732 /* Converts an orientation o in the previous scheme used in Plex to the current numbering */ 3733 PetscInt DMPolytopeConvertOldOrientation_Internal(DMPolytopeType ct, PetscInt o) 3734 { 3735 switch (ct) { 3736 case DM_POLYTOPE_SEGMENT: 3737 if ((o == -2) || (o == 1)) return -1; 3738 if (o == -1) return 0; 3739 break; 3740 case DM_POLYTOPE_TRIANGLE: 3741 if (o == -3) return -2; 3742 if (o == -2) return -1; 3743 if (o == -1) return -3; 3744 break; 3745 case DM_POLYTOPE_QUADRILATERAL: 3746 if (o == -4) return -2; 3747 if (o == -3) return -1; 3748 if (o == -2) return -4; 3749 if (o == -1) return -3; 3750 break; 3751 default: 3752 return o; 3753 } 3754 return o; 3755 } 3756 3757 /* Takes in a mesh whose orientations are in the previous scheme and converts them all to the current numbering */ 3758 PetscErrorCode DMPlexConvertOldOrientations_Internal(DM dm) 3759 { 3760 PetscInt pStart, pEnd, p; 3761 3762 PetscFunctionBegin; 3763 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 3764 for (p = pStart; p < pEnd; ++p) { 3765 const PetscInt *cone, *ornt; 3766 PetscInt coneSize, c; 3767 3768 PetscCall(DMPlexGetConeSize(dm, p, &coneSize)); 3769 PetscCall(DMPlexGetCone(dm, p, &cone)); 3770 PetscCall(DMPlexGetConeOrientation(dm, p, &ornt)); 3771 for (c = 0; c < coneSize; ++c) { 3772 DMPolytopeType ct; 3773 const PetscInt o = ornt[c]; 3774 3775 PetscCall(DMPlexGetCellType(dm, cone[c], &ct)); 3776 switch (ct) { 3777 case DM_POLYTOPE_SEGMENT: 3778 if ((o == -2) || (o == 1)) PetscCall(DMPlexInsertConeOrientation(dm, p, c, -1)); 3779 if (o == -1) PetscCall(DMPlexInsertConeOrientation(dm, p, c, 0)); 3780 break; 3781 case DM_POLYTOPE_TRIANGLE: 3782 if (o == -3) PetscCall(DMPlexInsertConeOrientation(dm, p, c, -2)); 3783 if (o == -2) PetscCall(DMPlexInsertConeOrientation(dm, p, c, -1)); 3784 if (o == -1) PetscCall(DMPlexInsertConeOrientation(dm, p, c, -3)); 3785 break; 3786 case DM_POLYTOPE_QUADRILATERAL: 3787 if (o == -4) PetscCall(DMPlexInsertConeOrientation(dm, p, c, -2)); 3788 if (o == -3) PetscCall(DMPlexInsertConeOrientation(dm, p, c, -1)); 3789 if (o == -2) PetscCall(DMPlexInsertConeOrientation(dm, p, c, -4)); 3790 if (o == -1) PetscCall(DMPlexInsertConeOrientation(dm, p, c, -3)); 3791 break; 3792 default: 3793 break; 3794 } 3795 } 3796 } 3797 PetscFunctionReturn(PETSC_SUCCESS); 3798 } 3799 3800 static inline PetscErrorCode DMPlexGetTransitiveClosure_Hot_Private(DM dm, PetscInt p, PetscBool useCone, PetscInt *size, const PetscInt *arr[], const PetscInt *ornt[]) 3801 { 3802 DM_Plex *mesh = (DM_Plex *)dm->data; 3803 3804 PetscFunctionBeginHot; 3805 if (PetscDefined(USE_DEBUG) || mesh->tr) { 3806 if (useCone) { 3807 PetscCall(DMPlexGetConeSize(dm, p, size)); 3808 PetscCall(DMPlexGetOrientedCone(dm, p, arr, ornt)); 3809 } else { 3810 PetscCall(DMPlexGetSupportSize(dm, p, size)); 3811 PetscCall(DMPlexGetSupport(dm, p, arr)); 3812 } 3813 } else { 3814 if (useCone) { 3815 const PetscSection s = mesh->coneSection; 3816 const PetscInt ps = p - s->pStart; 3817 const PetscInt off = s->atlasOff[ps]; 3818 3819 *size = s->atlasDof[ps]; 3820 *arr = mesh->cones + off; 3821 *ornt = mesh->coneOrientations + off; 3822 } else { 3823 const PetscSection s = mesh->supportSection; 3824 const PetscInt ps = p - s->pStart; 3825 const PetscInt off = s->atlasOff[ps]; 3826 3827 *size = s->atlasDof[ps]; 3828 *arr = mesh->supports + off; 3829 } 3830 } 3831 PetscFunctionReturn(PETSC_SUCCESS); 3832 } 3833 3834 static inline PetscErrorCode DMPlexRestoreTransitiveClosure_Hot_Private(DM dm, PetscInt p, PetscBool useCone, PetscInt *size, const PetscInt *arr[], const PetscInt *ornt[]) 3835 { 3836 DM_Plex *mesh = (DM_Plex *)dm->data; 3837 3838 PetscFunctionBeginHot; 3839 if (PetscDefined(USE_DEBUG) || mesh->tr) { 3840 if (useCone) PetscCall(DMPlexRestoreOrientedCone(dm, p, arr, ornt)); 3841 } 3842 PetscFunctionReturn(PETSC_SUCCESS); 3843 } 3844 3845 static PetscErrorCode DMPlexGetTransitiveClosure_Depth1_Private(DM dm, PetscInt p, PetscInt ornt, PetscBool useCone, PetscInt *numPoints, PetscInt *points[]) 3846 { 3847 DMPolytopeType ct = DM_POLYTOPE_UNKNOWN; 3848 PetscInt *closure; 3849 const PetscInt *tmp = NULL, *tmpO = NULL; 3850 PetscInt off = 0, tmpSize, t; 3851 3852 PetscFunctionBeginHot; 3853 if (ornt) { 3854 PetscCall(DMPlexGetCellType(dm, p, &ct)); 3855 if (ct == DM_POLYTOPE_FV_GHOST || ct == DM_POLYTOPE_INTERIOR_GHOST || ct == DM_POLYTOPE_UNKNOWN || ct == DM_POLYTOPE_UNKNOWN_CELL || ct == DM_POLYTOPE_UNKNOWN_FACE) ct = DM_POLYTOPE_UNKNOWN; 3856 } 3857 if (*points) { 3858 closure = *points; 3859 } else { 3860 PetscInt maxConeSize, maxSupportSize; 3861 PetscCall(DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize)); 3862 PetscCall(DMGetWorkArray(dm, 2 * (PetscMax(maxConeSize, maxSupportSize) + 1), MPIU_INT, &closure)); 3863 } 3864 PetscCall(DMPlexGetTransitiveClosure_Hot_Private(dm, p, useCone, &tmpSize, &tmp, &tmpO)); 3865 if (ct == DM_POLYTOPE_UNKNOWN) { 3866 closure[off++] = p; 3867 closure[off++] = 0; 3868 for (t = 0; t < tmpSize; ++t) { 3869 closure[off++] = tmp[t]; 3870 closure[off++] = tmpO ? tmpO[t] : 0; 3871 } 3872 } else { 3873 const PetscInt *arr = DMPolytopeTypeGetArrangement(ct, ornt); 3874 3875 /* We assume that cells with a valid type have faces with a valid type */ 3876 closure[off++] = p; 3877 closure[off++] = ornt; 3878 for (t = 0; t < tmpSize; ++t) { 3879 DMPolytopeType ft; 3880 3881 PetscCall(DMPlexGetCellType(dm, tmp[t], &ft)); 3882 closure[off++] = tmp[arr[t]]; 3883 closure[off++] = tmpO ? DMPolytopeTypeComposeOrientation(ft, ornt, tmpO[t]) : 0; 3884 } 3885 } 3886 PetscCall(DMPlexRestoreTransitiveClosure_Hot_Private(dm, p, useCone, &tmpSize, &tmp, &tmpO)); 3887 if (numPoints) *numPoints = tmpSize + 1; 3888 if (points) *points = closure; 3889 PetscFunctionReturn(PETSC_SUCCESS); 3890 } 3891 3892 /* We need a special tensor version because we want to allow duplicate points in the endcaps for hybrid cells */ 3893 static PetscErrorCode DMPlexTransitiveClosure_Tensor_Internal(DM dm, PetscInt point, DMPolytopeType ct, PetscInt o, PetscBool useCone, PetscInt *numPoints, PetscInt **points) 3894 { 3895 const PetscInt *arr = DMPolytopeTypeGetArrangement(ct, o); 3896 const PetscInt *cone, *ornt; 3897 PetscInt *pts, *closure = NULL; 3898 DMPolytopeType ft; 3899 PetscInt maxConeSize, maxSupportSize, coneSeries, supportSeries, maxSize; 3900 PetscInt dim, coneSize, c, d, clSize, cl; 3901 3902 PetscFunctionBeginHot; 3903 PetscCall(DMGetDimension(dm, &dim)); 3904 PetscCall(DMPlexGetTransitiveClosure_Hot_Private(dm, point, PETSC_TRUE, &coneSize, &cone, &ornt)); 3905 PetscCall(DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize)); 3906 coneSeries = (maxConeSize > 1) ? ((PetscPowInt(maxConeSize, dim + 1) - 1) / (maxConeSize - 1)) : dim + 1; 3907 supportSeries = (maxSupportSize > 1) ? ((PetscPowInt(maxSupportSize, dim + 1) - 1) / (maxSupportSize - 1)) : dim + 1; 3908 maxSize = PetscMax(coneSeries, supportSeries); 3909 if (*points) { 3910 pts = *points; 3911 } else PetscCall(DMGetWorkArray(dm, 2 * maxSize, MPIU_INT, &pts)); 3912 c = 0; 3913 pts[c++] = point; 3914 pts[c++] = o; 3915 PetscCall(DMPlexGetCellType(dm, cone[arr[0 * 2 + 0]], &ft)); 3916 PetscCall(DMPlexGetTransitiveClosure_Internal(dm, cone[arr[0 * 2 + 0]], DMPolytopeTypeComposeOrientation(ft, arr[0 * 2 + 1], ornt[0]), useCone, &clSize, &closure)); 3917 for (cl = 0; cl < clSize * 2; cl += 2) { 3918 pts[c++] = closure[cl]; 3919 pts[c++] = closure[cl + 1]; 3920 } 3921 PetscCall(DMPlexGetTransitiveClosure_Internal(dm, cone[arr[1 * 2 + 0]], DMPolytopeTypeComposeOrientation(ft, arr[1 * 2 + 1], ornt[1]), useCone, &clSize, &closure)); 3922 for (cl = 0; cl < clSize * 2; cl += 2) { 3923 pts[c++] = closure[cl]; 3924 pts[c++] = closure[cl + 1]; 3925 } 3926 PetscCall(DMPlexRestoreTransitiveClosure(dm, cone[0], useCone, &clSize, &closure)); 3927 for (d = 2; d < coneSize; ++d) { 3928 PetscCall(DMPlexGetCellType(dm, cone[arr[d * 2 + 0]], &ft)); 3929 pts[c++] = cone[arr[d * 2 + 0]]; 3930 pts[c++] = DMPolytopeTypeComposeOrientation(ft, arr[d * 2 + 1], ornt[d]); 3931 } 3932 PetscCall(DMPlexRestoreTransitiveClosure_Hot_Private(dm, point, PETSC_TRUE, &coneSize, &cone, &ornt)); 3933 if (dim >= 3) { 3934 for (d = 2; d < coneSize; ++d) { 3935 const PetscInt fpoint = cone[arr[d * 2 + 0]]; 3936 const PetscInt *fcone, *fornt; 3937 PetscInt fconeSize, fc, i; 3938 3939 PetscCall(DMPlexGetCellType(dm, fpoint, &ft)); 3940 const PetscInt *farr = DMPolytopeTypeGetArrangement(ft, DMPolytopeTypeComposeOrientation(ft, arr[d * 2 + 1], ornt[d])); 3941 PetscCall(DMPlexGetTransitiveClosure_Hot_Private(dm, fpoint, PETSC_TRUE, &fconeSize, &fcone, &fornt)); 3942 for (fc = 0; fc < fconeSize; ++fc) { 3943 const PetscInt cp = fcone[farr[fc * 2 + 0]]; 3944 const PetscInt co = farr[fc * 2 + 1]; 3945 3946 for (i = 0; i < c; i += 2) 3947 if (pts[i] == cp) break; 3948 if (i == c) { 3949 PetscCall(DMPlexGetCellType(dm, cp, &ft)); 3950 pts[c++] = cp; 3951 pts[c++] = DMPolytopeTypeComposeOrientation(ft, co, fornt[farr[fc * 2 + 0]]); 3952 } 3953 } 3954 PetscCall(DMPlexRestoreTransitiveClosure_Hot_Private(dm, fpoint, PETSC_TRUE, &fconeSize, &fcone, &fornt)); 3955 } 3956 } 3957 *numPoints = c / 2; 3958 *points = pts; 3959 PetscFunctionReturn(PETSC_SUCCESS); 3960 } 3961 3962 PetscErrorCode DMPlexGetTransitiveClosure_Internal(DM dm, PetscInt p, PetscInt ornt, PetscBool useCone, PetscInt *numPoints, PetscInt *points[]) 3963 { 3964 DMPolytopeType ct; 3965 PetscInt *closure, *fifo; 3966 PetscInt closureSize = 0, fifoStart = 0, fifoSize = 0; 3967 PetscInt maxConeSize, maxSupportSize, coneSeries, supportSeries; 3968 PetscInt depth, maxSize; 3969 3970 PetscFunctionBeginHot; 3971 PetscCall(DMPlexGetDepth(dm, &depth)); 3972 if (depth == 1) { 3973 PetscCall(DMPlexGetTransitiveClosure_Depth1_Private(dm, p, ornt, useCone, numPoints, points)); 3974 PetscFunctionReturn(PETSC_SUCCESS); 3975 } 3976 PetscCall(DMPlexGetCellType(dm, p, &ct)); 3977 if (ct == DM_POLYTOPE_FV_GHOST || ct == DM_POLYTOPE_INTERIOR_GHOST || ct == DM_POLYTOPE_UNKNOWN || ct == DM_POLYTOPE_UNKNOWN_CELL || ct == DM_POLYTOPE_UNKNOWN_FACE) ct = DM_POLYTOPE_UNKNOWN; 3978 if (DMPolytopeTypeIsHybrid(ct) && ct != DM_POLYTOPE_POINT_PRISM_TENSOR) { 3979 PetscCall(DMPlexTransitiveClosure_Tensor_Internal(dm, p, ct, ornt, useCone, numPoints, points)); 3980 PetscFunctionReturn(PETSC_SUCCESS); 3981 } 3982 PetscCall(DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize)); 3983 coneSeries = (maxConeSize > 1) ? ((PetscPowInt(maxConeSize, depth + 1) - 1) / (maxConeSize - 1)) : depth + 1; 3984 supportSeries = (maxSupportSize > 1) ? ((PetscPowInt(maxSupportSize, depth + 1) - 1) / (maxSupportSize - 1)) : depth + 1; 3985 maxSize = PetscMax(coneSeries, supportSeries); 3986 PetscCall(DMGetWorkArray(dm, 3 * maxSize, MPIU_INT, &fifo)); 3987 if (*points) { 3988 closure = *points; 3989 } else PetscCall(DMGetWorkArray(dm, 2 * maxSize, MPIU_INT, &closure)); 3990 closure[closureSize++] = p; 3991 closure[closureSize++] = ornt; 3992 fifo[fifoSize++] = p; 3993 fifo[fifoSize++] = ornt; 3994 fifo[fifoSize++] = ct; 3995 /* Should kick out early when depth is reached, rather than checking all vertices for empty cones */ 3996 while (fifoSize - fifoStart) { 3997 const PetscInt q = fifo[fifoStart++]; 3998 const PetscInt o = fifo[fifoStart++]; 3999 const DMPolytopeType qt = (DMPolytopeType)fifo[fifoStart++]; 4000 const PetscInt *qarr = DMPolytopeTypeGetArrangement(qt, o); 4001 const PetscInt *tmp, *tmpO = NULL; 4002 PetscInt tmpSize, t; 4003 4004 if (PetscDefined(USE_DEBUG)) { 4005 PetscInt nO = DMPolytopeTypeGetNumArrangements(qt) / 2; 4006 PetscCheck(!o || !(o >= nO || o < -nO), PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid orientation %" PetscInt_FMT " not in [%" PetscInt_FMT ",%" PetscInt_FMT ") for %s %" PetscInt_FMT, o, -nO, nO, DMPolytopeTypes[qt], q); 4007 } 4008 PetscCall(DMPlexGetTransitiveClosure_Hot_Private(dm, q, useCone, &tmpSize, &tmp, &tmpO)); 4009 for (t = 0; t < tmpSize; ++t) { 4010 const PetscInt ip = useCone && qarr ? qarr[t * 2] : t; 4011 const PetscInt io = useCone && qarr ? qarr[t * 2 + 1] : 0; 4012 const PetscInt cp = tmp[ip]; 4013 PetscCall(DMPlexGetCellType(dm, cp, &ct)); 4014 const PetscInt co = tmpO ? DMPolytopeTypeComposeOrientation(ct, io, tmpO[ip]) : 0; 4015 PetscInt c; 4016 4017 /* Check for duplicate */ 4018 for (c = 0; c < closureSize; c += 2) { 4019 if (closure[c] == cp) break; 4020 } 4021 if (c == closureSize) { 4022 closure[closureSize++] = cp; 4023 closure[closureSize++] = co; 4024 fifo[fifoSize++] = cp; 4025 fifo[fifoSize++] = co; 4026 fifo[fifoSize++] = ct; 4027 } 4028 } 4029 PetscCall(DMPlexRestoreTransitiveClosure_Hot_Private(dm, q, useCone, &tmpSize, &tmp, &tmpO)); 4030 } 4031 PetscCall(DMRestoreWorkArray(dm, 3 * maxSize, MPIU_INT, &fifo)); 4032 if (numPoints) *numPoints = closureSize / 2; 4033 if (points) *points = closure; 4034 PetscFunctionReturn(PETSC_SUCCESS); 4035 } 4036 4037 /*@C 4038 DMPlexGetTransitiveClosure - Return the points on the transitive closure of the in-edges or out-edges for this point in the DAG 4039 4040 Not Collective 4041 4042 Input Parameters: 4043 + dm - The `DMPLEX` 4044 . p - The mesh point 4045 - useCone - `PETSC_TRUE` for the closure, otherwise return the star 4046 4047 Input/Output Parameter: 4048 . points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...]; 4049 if `NULL` on input, internal storage will be returned, otherwise the provided array is used 4050 4051 Output Parameter: 4052 . numPoints - The number of points in the closure, so points[] is of size 2*`numPoints` 4053 4054 Level: beginner 4055 4056 Note: 4057 If using internal storage (points is `NULL` on input), each call overwrites the last output. 4058 4059 Fortran Notes: 4060 The `numPoints` argument is not present in the Fortran binding since it is internal to the array. 4061 4062 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexRestoreTransitiveClosure()`, `DMPlexCreate()`, `DMPlexSetCone()`, `DMPlexSetChart()`, `DMPlexGetCone()` 4063 @*/ 4064 PetscErrorCode DMPlexGetTransitiveClosure(DM dm, PetscInt p, PetscBool useCone, PetscInt *numPoints, PetscInt *points[]) 4065 { 4066 PetscFunctionBeginHot; 4067 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4068 if (numPoints) PetscAssertPointer(numPoints, 4); 4069 if (points) PetscAssertPointer(points, 5); 4070 PetscCall(DMPlexGetTransitiveClosure_Internal(dm, p, 0, useCone, numPoints, points)); 4071 PetscFunctionReturn(PETSC_SUCCESS); 4072 } 4073 4074 /*@C 4075 DMPlexRestoreTransitiveClosure - Restore the array of points on the transitive closure of the in-edges or out-edges for this point in the DAG 4076 4077 Not Collective 4078 4079 Input Parameters: 4080 + dm - The `DMPLEX` 4081 . p - The mesh point 4082 . useCone - `PETSC_TRUE` for the closure, otherwise return the star 4083 . numPoints - The number of points in the closure, so points[] is of size 2*`numPoints` 4084 - points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...] 4085 4086 Level: beginner 4087 4088 Note: 4089 If not using internal storage (points is not `NULL` on input), this call is unnecessary 4090 4091 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetTransitiveClosure()`, `DMPlexCreate()`, `DMPlexSetCone()`, `DMPlexSetChart()`, `DMPlexGetCone()` 4092 @*/ 4093 PetscErrorCode DMPlexRestoreTransitiveClosure(DM dm, PetscInt p, PetscBool useCone, PetscInt *numPoints, PetscInt *points[]) 4094 { 4095 PetscFunctionBeginHot; 4096 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4097 if (numPoints) *numPoints = 0; 4098 PetscCall(DMRestoreWorkArray(dm, 0, MPIU_INT, points)); 4099 PetscFunctionReturn(PETSC_SUCCESS); 4100 } 4101 4102 /*@ 4103 DMPlexGetMaxSizes - Return the maximum number of in-edges (cone) and out-edges (support) for any point in the DAG 4104 4105 Not Collective 4106 4107 Input Parameter: 4108 . dm - The `DMPLEX` 4109 4110 Output Parameters: 4111 + maxConeSize - The maximum number of in-edges 4112 - maxSupportSize - The maximum number of out-edges 4113 4114 Level: beginner 4115 4116 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexSetConeSize()`, `DMPlexSetChart()` 4117 @*/ 4118 PetscErrorCode DMPlexGetMaxSizes(DM dm, PetscInt *maxConeSize, PetscInt *maxSupportSize) 4119 { 4120 DM_Plex *mesh = (DM_Plex *)dm->data; 4121 4122 PetscFunctionBegin; 4123 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4124 if (maxConeSize) PetscCall(PetscSectionGetMaxDof(mesh->coneSection, maxConeSize)); 4125 if (maxSupportSize) PetscCall(PetscSectionGetMaxDof(mesh->supportSection, maxSupportSize)); 4126 PetscFunctionReturn(PETSC_SUCCESS); 4127 } 4128 4129 PetscErrorCode DMSetUp_Plex(DM dm) 4130 { 4131 DM_Plex *mesh = (DM_Plex *)dm->data; 4132 PetscInt size, maxSupportSize; 4133 4134 PetscFunctionBegin; 4135 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4136 PetscCall(PetscSectionSetUp(mesh->coneSection)); 4137 PetscCall(PetscSectionGetStorageSize(mesh->coneSection, &size)); 4138 PetscCall(PetscMalloc1(size, &mesh->cones)); 4139 PetscCall(PetscCalloc1(size, &mesh->coneOrientations)); 4140 PetscCall(PetscSectionGetMaxDof(mesh->supportSection, &maxSupportSize)); 4141 if (maxSupportSize) { 4142 PetscCall(PetscSectionSetUp(mesh->supportSection)); 4143 PetscCall(PetscSectionGetStorageSize(mesh->supportSection, &size)); 4144 PetscCall(PetscMalloc1(size, &mesh->supports)); 4145 } 4146 PetscFunctionReturn(PETSC_SUCCESS); 4147 } 4148 4149 PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm) 4150 { 4151 PetscFunctionBegin; 4152 if (subdm) PetscCall(DMClone(dm, subdm)); 4153 PetscCall(DMCreateSectionSubDM(dm, numFields, fields, NULL, NULL, is, subdm)); 4154 if (subdm) (*subdm)->useNatural = dm->useNatural; 4155 if (dm->useNatural && dm->sfMigration) { 4156 PetscSF sfNatural; 4157 4158 (*subdm)->sfMigration = dm->sfMigration; 4159 PetscCall(PetscObjectReference((PetscObject)dm->sfMigration)); 4160 PetscCall(DMPlexCreateGlobalToNaturalSF(*subdm, NULL, (*subdm)->sfMigration, &sfNatural)); 4161 (*subdm)->sfNatural = sfNatural; 4162 } 4163 PetscFunctionReturn(PETSC_SUCCESS); 4164 } 4165 4166 PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm) 4167 { 4168 PetscInt i = 0; 4169 4170 PetscFunctionBegin; 4171 PetscCall(DMClone(dms[0], superdm)); 4172 PetscCall(DMCreateSectionSuperDM(dms, len, is, superdm)); 4173 (*superdm)->useNatural = PETSC_FALSE; 4174 for (i = 0; i < len; i++) { 4175 if (dms[i]->useNatural && dms[i]->sfMigration) { 4176 PetscSF sfNatural; 4177 4178 (*superdm)->sfMigration = dms[i]->sfMigration; 4179 PetscCall(PetscObjectReference((PetscObject)dms[i]->sfMigration)); 4180 (*superdm)->useNatural = PETSC_TRUE; 4181 PetscCall(DMPlexCreateGlobalToNaturalSF(*superdm, NULL, (*superdm)->sfMigration, &sfNatural)); 4182 (*superdm)->sfNatural = sfNatural; 4183 break; 4184 } 4185 } 4186 PetscFunctionReturn(PETSC_SUCCESS); 4187 } 4188 4189 /*@ 4190 DMPlexSymmetrize - Create support (out-edge) information from cone (in-edge) information 4191 4192 Not Collective 4193 4194 Input Parameter: 4195 . dm - The `DMPLEX` 4196 4197 Level: beginner 4198 4199 Note: 4200 This should be called after all calls to `DMPlexSetCone()` 4201 4202 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexSetChart()`, `DMPlexSetConeSize()`, `DMPlexSetCone()` 4203 @*/ 4204 PetscErrorCode DMPlexSymmetrize(DM dm) 4205 { 4206 DM_Plex *mesh = (DM_Plex *)dm->data; 4207 PetscInt *offsets; 4208 PetscInt supportSize; 4209 PetscInt pStart, pEnd, p; 4210 4211 PetscFunctionBegin; 4212 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4213 PetscCheck(!mesh->supports, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE, "Supports were already setup in this DMPlex"); 4214 PetscCall(PetscLogEventBegin(DMPLEX_Symmetrize, dm, 0, 0, 0)); 4215 /* Calculate support sizes */ 4216 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 4217 for (p = pStart; p < pEnd; ++p) { 4218 PetscInt dof, off, c; 4219 4220 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 4221 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 4222 for (c = off; c < off + dof; ++c) PetscCall(PetscSectionAddDof(mesh->supportSection, mesh->cones[c], 1)); 4223 } 4224 PetscCall(PetscSectionSetUp(mesh->supportSection)); 4225 /* Calculate supports */ 4226 PetscCall(PetscSectionGetStorageSize(mesh->supportSection, &supportSize)); 4227 PetscCall(PetscMalloc1(supportSize, &mesh->supports)); 4228 PetscCall(PetscCalloc1(pEnd - pStart, &offsets)); 4229 for (p = pStart; p < pEnd; ++p) { 4230 PetscInt dof, off, c; 4231 4232 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 4233 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 4234 for (c = off; c < off + dof; ++c) { 4235 const PetscInt q = mesh->cones[c]; 4236 PetscInt offS; 4237 4238 PetscCall(PetscSectionGetOffset(mesh->supportSection, q, &offS)); 4239 4240 mesh->supports[offS + offsets[q]] = p; 4241 ++offsets[q]; 4242 } 4243 } 4244 PetscCall(PetscFree(offsets)); 4245 PetscCall(PetscLogEventEnd(DMPLEX_Symmetrize, dm, 0, 0, 0)); 4246 PetscFunctionReturn(PETSC_SUCCESS); 4247 } 4248 4249 static PetscErrorCode DMPlexCreateDepthStratum(DM dm, DMLabel label, PetscInt depth, PetscInt pStart, PetscInt pEnd) 4250 { 4251 IS stratumIS; 4252 4253 PetscFunctionBegin; 4254 if (pStart >= pEnd) PetscFunctionReturn(PETSC_SUCCESS); 4255 if (PetscDefined(USE_DEBUG)) { 4256 PetscInt qStart, qEnd, numLevels, level; 4257 PetscBool overlap = PETSC_FALSE; 4258 PetscCall(DMLabelGetNumValues(label, &numLevels)); 4259 for (level = 0; level < numLevels; level++) { 4260 PetscCall(DMLabelGetStratumBounds(label, level, &qStart, &qEnd)); 4261 if ((pStart >= qStart && pStart < qEnd) || (pEnd > qStart && pEnd <= qEnd)) { 4262 overlap = PETSC_TRUE; 4263 break; 4264 } 4265 } 4266 PetscCheck(!overlap, PETSC_COMM_SELF, PETSC_ERR_PLIB, "New depth %" PetscInt_FMT " range [%" PetscInt_FMT ",%" PetscInt_FMT ") overlaps with depth %" PetscInt_FMT " range [%" PetscInt_FMT ",%" PetscInt_FMT ")", depth, pStart, pEnd, level, qStart, qEnd); 4267 } 4268 PetscCall(ISCreateStride(PETSC_COMM_SELF, pEnd - pStart, pStart, 1, &stratumIS)); 4269 PetscCall(DMLabelSetStratumIS(label, depth, stratumIS)); 4270 PetscCall(ISDestroy(&stratumIS)); 4271 PetscFunctionReturn(PETSC_SUCCESS); 4272 } 4273 4274 static PetscErrorCode DMPlexStratify_CellType_Private(DM dm, DMLabel label) 4275 { 4276 PetscInt *pMin, *pMax; 4277 PetscInt pStart, pEnd; 4278 PetscInt dmin = PETSC_MAX_INT, dmax = PETSC_MIN_INT; 4279 4280 PetscFunctionBegin; 4281 { 4282 DMLabel label2; 4283 4284 PetscCall(DMPlexGetCellTypeLabel(dm, &label2)); 4285 PetscCall(PetscObjectViewFromOptions((PetscObject)label2, NULL, "-ct_view")); 4286 } 4287 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 4288 for (PetscInt p = pStart; p < pEnd; ++p) { 4289 DMPolytopeType ct; 4290 4291 PetscCall(DMPlexGetCellType(dm, p, &ct)); 4292 dmin = PetscMin(DMPolytopeTypeGetDim(ct), dmin); 4293 dmax = PetscMax(DMPolytopeTypeGetDim(ct), dmax); 4294 } 4295 PetscCall(PetscMalloc2(dmax + 1, &pMin, dmax + 1, &pMax)); 4296 for (PetscInt d = dmin; d <= dmax; ++d) { 4297 pMin[d] = PETSC_MAX_INT; 4298 pMax[d] = PETSC_MIN_INT; 4299 } 4300 for (PetscInt p = pStart; p < pEnd; ++p) { 4301 DMPolytopeType ct; 4302 PetscInt d; 4303 4304 PetscCall(DMPlexGetCellType(dm, p, &ct)); 4305 d = DMPolytopeTypeGetDim(ct); 4306 pMin[d] = PetscMin(p, pMin[d]); 4307 pMax[d] = PetscMax(p, pMax[d]); 4308 } 4309 for (PetscInt d = dmin; d <= dmax; ++d) { 4310 if (pMin[d] > pMax[d]) continue; 4311 PetscCall(DMPlexCreateDepthStratum(dm, label, d, pMin[d], pMax[d] + 1)); 4312 } 4313 PetscCall(PetscFree2(pMin, pMax)); 4314 PetscFunctionReturn(PETSC_SUCCESS); 4315 } 4316 4317 static PetscErrorCode DMPlexStratify_Topological_Private(DM dm, DMLabel label) 4318 { 4319 PetscInt pStart, pEnd; 4320 PetscInt numRoots = 0, numLeaves = 0; 4321 4322 PetscFunctionBegin; 4323 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 4324 { 4325 /* Initialize roots and count leaves */ 4326 PetscInt sMin = PETSC_MAX_INT; 4327 PetscInt sMax = PETSC_MIN_INT; 4328 PetscInt coneSize, supportSize; 4329 4330 for (PetscInt p = pStart; p < pEnd; ++p) { 4331 PetscCall(DMPlexGetConeSize(dm, p, &coneSize)); 4332 PetscCall(DMPlexGetSupportSize(dm, p, &supportSize)); 4333 if (!coneSize && supportSize) { 4334 sMin = PetscMin(p, sMin); 4335 sMax = PetscMax(p, sMax); 4336 ++numRoots; 4337 } else if (!supportSize && coneSize) { 4338 ++numLeaves; 4339 } else if (!supportSize && !coneSize) { 4340 /* Isolated points */ 4341 sMin = PetscMin(p, sMin); 4342 sMax = PetscMax(p, sMax); 4343 } 4344 } 4345 PetscCall(DMPlexCreateDepthStratum(dm, label, 0, sMin, sMax + 1)); 4346 } 4347 4348 if (numRoots + numLeaves == (pEnd - pStart)) { 4349 PetscInt sMin = PETSC_MAX_INT; 4350 PetscInt sMax = PETSC_MIN_INT; 4351 PetscInt coneSize, supportSize; 4352 4353 for (PetscInt p = pStart; p < pEnd; ++p) { 4354 PetscCall(DMPlexGetConeSize(dm, p, &coneSize)); 4355 PetscCall(DMPlexGetSupportSize(dm, p, &supportSize)); 4356 if (!supportSize && coneSize) { 4357 sMin = PetscMin(p, sMin); 4358 sMax = PetscMax(p, sMax); 4359 } 4360 } 4361 PetscCall(DMPlexCreateDepthStratum(dm, label, 1, sMin, sMax + 1)); 4362 } else { 4363 PetscInt level = 0; 4364 PetscInt qStart, qEnd; 4365 4366 PetscCall(DMLabelGetStratumBounds(label, level, &qStart, &qEnd)); 4367 while (qEnd > qStart) { 4368 PetscInt sMin = PETSC_MAX_INT; 4369 PetscInt sMax = PETSC_MIN_INT; 4370 4371 for (PetscInt q = qStart; q < qEnd; ++q) { 4372 const PetscInt *support; 4373 PetscInt supportSize; 4374 4375 PetscCall(DMPlexGetSupportSize(dm, q, &supportSize)); 4376 PetscCall(DMPlexGetSupport(dm, q, &support)); 4377 for (PetscInt s = 0; s < supportSize; ++s) { 4378 sMin = PetscMin(support[s], sMin); 4379 sMax = PetscMax(support[s], sMax); 4380 } 4381 } 4382 PetscCall(DMLabelGetNumValues(label, &level)); 4383 PetscCall(DMPlexCreateDepthStratum(dm, label, level, sMin, sMax + 1)); 4384 PetscCall(DMLabelGetStratumBounds(label, level, &qStart, &qEnd)); 4385 } 4386 } 4387 PetscFunctionReturn(PETSC_SUCCESS); 4388 } 4389 4390 /*@ 4391 DMPlexStratify - Computes the strata for all points in the `DMPLEX` 4392 4393 Collective 4394 4395 Input Parameter: 4396 . dm - The `DMPLEX` 4397 4398 Level: beginner 4399 4400 Notes: 4401 The strata group all points of the same grade, and this function calculates the strata. This 4402 grade can be seen as the height (or depth) of the point in the DAG. 4403 4404 The DAG for most topologies is a graded poset (https://en.wikipedia.org/wiki/Graded_poset), and 4405 can be illustrated by a Hasse Diagram (https://en.wikipedia.org/wiki/Hasse_diagram). 4406 Concretely, `DMPlexStratify()` creates a new label named "depth" containing the depth in the DAG of each point. For cell-vertex 4407 meshes, vertices are depth 0 and cells are depth 1. For fully interpolated meshes, depth 0 for vertices, 1 for edges, and so on 4408 until cells have depth equal to the dimension of the mesh. The depth label can be accessed through `DMPlexGetDepthLabel()` or `DMPlexGetDepthStratum()`, or 4409 manually via `DMGetLabel()`. The height is defined implicitly by height = maxDimension - depth, and can be accessed 4410 via `DMPlexGetHeightStratum()`. For example, cells have height 0 and faces have height 1. 4411 4412 The depth of a point is calculated by executing a breadth-first search (BFS) on the DAG. This could produce surprising results 4413 if run on a partially interpolated mesh, meaning one that had some edges and faces, but not others. For example, suppose that 4414 we had a mesh consisting of one triangle (c0) and three vertices (v0, v1, v2), and only one edge is on the boundary so we choose 4415 to interpolate only that one (e0), so that 4416 .vb 4417 cone(c0) = {e0, v2} 4418 cone(e0) = {v0, v1} 4419 .ve 4420 If `DMPlexStratify()` is run on this mesh, it will give depths 4421 .vb 4422 depth 0 = {v0, v1, v2} 4423 depth 1 = {e0, c0} 4424 .ve 4425 where the triangle has been given depth 1, instead of 2, because it is reachable from vertex v2. 4426 4427 `DMPlexStratify()` should be called after all calls to `DMPlexSymmetrize()` 4428 4429 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexSymmetrize()`, `DMPlexComputeCellTypes()` 4430 @*/ 4431 PetscErrorCode DMPlexStratify(DM dm) 4432 { 4433 DM_Plex *mesh = (DM_Plex *)dm->data; 4434 DMLabel label; 4435 PetscBool flg = PETSC_FALSE; 4436 4437 PetscFunctionBegin; 4438 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4439 PetscCall(PetscLogEventBegin(DMPLEX_Stratify, dm, 0, 0, 0)); 4440 4441 // Create depth label 4442 PetscCall(DMCreateLabel(dm, "depth")); 4443 PetscCall(DMPlexGetDepthLabel(dm, &label)); 4444 4445 PetscCall(PetscOptionsGetBool(NULL, dm->hdr.prefix, "-dm_plex_stratify_celltype", &flg, NULL)); 4446 if (flg) PetscCall(DMPlexStratify_CellType_Private(dm, label)); 4447 else PetscCall(DMPlexStratify_Topological_Private(dm, label)); 4448 4449 { /* just in case there is an empty process */ 4450 PetscInt numValues, maxValues = 0, v; 4451 4452 PetscCall(DMLabelGetNumValues(label, &numValues)); 4453 PetscCall(MPIU_Allreduce(&numValues, &maxValues, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm))); 4454 for (v = numValues; v < maxValues; v++) PetscCall(DMLabelAddStratum(label, v)); 4455 } 4456 PetscCall(PetscObjectStateGet((PetscObject)label, &mesh->depthState)); 4457 PetscCall(PetscLogEventEnd(DMPLEX_Stratify, dm, 0, 0, 0)); 4458 PetscFunctionReturn(PETSC_SUCCESS); 4459 } 4460 4461 PetscErrorCode DMPlexComputeCellType_Internal(DM dm, PetscInt p, PetscInt pdepth, DMPolytopeType *pt) 4462 { 4463 DMPolytopeType ct = DM_POLYTOPE_UNKNOWN; 4464 PetscInt dim, depth, pheight, coneSize; 4465 4466 PetscFunctionBeginHot; 4467 PetscCall(DMGetDimension(dm, &dim)); 4468 PetscCall(DMPlexGetDepth(dm, &depth)); 4469 PetscCall(DMPlexGetConeSize(dm, p, &coneSize)); 4470 pheight = depth - pdepth; 4471 if (depth <= 1) { 4472 switch (pdepth) { 4473 case 0: 4474 ct = DM_POLYTOPE_POINT; 4475 break; 4476 case 1: 4477 switch (coneSize) { 4478 case 2: 4479 ct = DM_POLYTOPE_SEGMENT; 4480 break; 4481 case 3: 4482 ct = DM_POLYTOPE_TRIANGLE; 4483 break; 4484 case 4: 4485 switch (dim) { 4486 case 2: 4487 ct = DM_POLYTOPE_QUADRILATERAL; 4488 break; 4489 case 3: 4490 ct = DM_POLYTOPE_TETRAHEDRON; 4491 break; 4492 default: 4493 break; 4494 } 4495 break; 4496 case 5: 4497 ct = DM_POLYTOPE_PYRAMID; 4498 break; 4499 case 6: 4500 ct = DM_POLYTOPE_TRI_PRISM_TENSOR; 4501 break; 4502 case 8: 4503 ct = DM_POLYTOPE_HEXAHEDRON; 4504 break; 4505 default: 4506 break; 4507 } 4508 } 4509 } else { 4510 if (pdepth == 0) { 4511 ct = DM_POLYTOPE_POINT; 4512 } else if (pheight == 0) { 4513 switch (dim) { 4514 case 1: 4515 switch (coneSize) { 4516 case 2: 4517 ct = DM_POLYTOPE_SEGMENT; 4518 break; 4519 default: 4520 break; 4521 } 4522 break; 4523 case 2: 4524 switch (coneSize) { 4525 case 3: 4526 ct = DM_POLYTOPE_TRIANGLE; 4527 break; 4528 case 4: 4529 ct = DM_POLYTOPE_QUADRILATERAL; 4530 break; 4531 default: 4532 break; 4533 } 4534 break; 4535 case 3: 4536 switch (coneSize) { 4537 case 4: 4538 ct = DM_POLYTOPE_TETRAHEDRON; 4539 break; 4540 case 5: { 4541 const PetscInt *cone; 4542 PetscInt faceConeSize; 4543 4544 PetscCall(DMPlexGetCone(dm, p, &cone)); 4545 PetscCall(DMPlexGetConeSize(dm, cone[0], &faceConeSize)); 4546 switch (faceConeSize) { 4547 case 3: 4548 ct = DM_POLYTOPE_TRI_PRISM_TENSOR; 4549 break; 4550 case 4: 4551 ct = DM_POLYTOPE_PYRAMID; 4552 break; 4553 } 4554 } break; 4555 case 6: 4556 ct = DM_POLYTOPE_HEXAHEDRON; 4557 break; 4558 default: 4559 break; 4560 } 4561 break; 4562 default: 4563 break; 4564 } 4565 } else if (pheight > 0) { 4566 switch (coneSize) { 4567 case 2: 4568 ct = DM_POLYTOPE_SEGMENT; 4569 break; 4570 case 3: 4571 ct = DM_POLYTOPE_TRIANGLE; 4572 break; 4573 case 4: 4574 ct = DM_POLYTOPE_QUADRILATERAL; 4575 break; 4576 default: 4577 break; 4578 } 4579 } 4580 } 4581 *pt = ct; 4582 PetscFunctionReturn(PETSC_SUCCESS); 4583 } 4584 4585 /*@ 4586 DMPlexComputeCellTypes - Infer the polytope type of every cell using its dimension and cone size. 4587 4588 Collective 4589 4590 Input Parameter: 4591 . dm - The `DMPLEX` 4592 4593 Level: developer 4594 4595 Note: 4596 This function is normally called automatically when a cell type is requested. It creates an 4597 internal `DMLabel` named "celltype" which can be directly accessed using `DMGetLabel()`. A user may disable 4598 automatic creation by creating the label manually, using `DMCreateLabel`(dm, "celltype"). 4599 4600 `DMPlexComputeCellTypes()` should be called after all calls to `DMPlexSymmetrize()` and `DMPlexStratify()` 4601 4602 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexSymmetrize()`, `DMPlexStratify()`, `DMGetLabel()`, `DMCreateLabel()` 4603 @*/ 4604 PetscErrorCode DMPlexComputeCellTypes(DM dm) 4605 { 4606 DM_Plex *mesh; 4607 DMLabel ctLabel; 4608 PetscInt pStart, pEnd, p; 4609 4610 PetscFunctionBegin; 4611 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4612 mesh = (DM_Plex *)dm->data; 4613 PetscCall(DMCreateLabel(dm, "celltype")); 4614 PetscCall(DMPlexGetCellTypeLabel(dm, &ctLabel)); 4615 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 4616 PetscCall(PetscFree(mesh->cellTypes)); 4617 PetscCall(PetscMalloc1(pEnd - pStart, &mesh->cellTypes)); 4618 for (p = pStart; p < pEnd; ++p) { 4619 DMPolytopeType ct = DM_POLYTOPE_UNKNOWN; 4620 PetscInt pdepth; 4621 4622 PetscCall(DMPlexGetPointDepth(dm, p, &pdepth)); 4623 PetscCall(DMPlexComputeCellType_Internal(dm, p, pdepth, &ct)); 4624 PetscCheck(ct != DM_POLYTOPE_UNKNOWN && ct != DM_POLYTOPE_UNKNOWN_CELL && ct != DM_POLYTOPE_UNKNOWN_FACE, PETSC_COMM_SELF, PETSC_ERR_SUP, "Point %" PetscInt_FMT " is screwed up", p); 4625 PetscCall(DMLabelSetValue(ctLabel, p, ct)); 4626 mesh->cellTypes[p - pStart].value_as_uint8 = ct; 4627 } 4628 PetscCall(PetscObjectStateGet((PetscObject)ctLabel, &mesh->celltypeState)); 4629 PetscCall(PetscObjectViewFromOptions((PetscObject)ctLabel, NULL, "-dm_plex_celltypes_view")); 4630 PetscFunctionReturn(PETSC_SUCCESS); 4631 } 4632 4633 /*@C 4634 DMPlexGetJoin - Get an array for the join of the set of points 4635 4636 Not Collective 4637 4638 Input Parameters: 4639 + dm - The `DMPLEX` object 4640 . numPoints - The number of input points for the join 4641 - points - The input points 4642 4643 Output Parameters: 4644 + numCoveredPoints - The number of points in the join 4645 - coveredPoints - The points in the join 4646 4647 Level: intermediate 4648 4649 Note: 4650 Currently, this is restricted to a single level join 4651 4652 Fortran Notes: 4653 The `numCoveredPoints` argument is not present in the Fortran binding since it is internal to the array. 4654 4655 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexRestoreJoin()`, `DMPlexGetMeet()` 4656 @*/ 4657 PetscErrorCode DMPlexGetJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 4658 { 4659 DM_Plex *mesh = (DM_Plex *)dm->data; 4660 PetscInt *join[2]; 4661 PetscInt joinSize, i = 0; 4662 PetscInt dof, off, p, c, m; 4663 PetscInt maxSupportSize; 4664 4665 PetscFunctionBegin; 4666 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4667 PetscAssertPointer(points, 3); 4668 PetscAssertPointer(numCoveredPoints, 4); 4669 PetscAssertPointer(coveredPoints, 5); 4670 PetscCall(PetscSectionGetMaxDof(mesh->supportSection, &maxSupportSize)); 4671 PetscCall(DMGetWorkArray(dm, maxSupportSize, MPIU_INT, &join[0])); 4672 PetscCall(DMGetWorkArray(dm, maxSupportSize, MPIU_INT, &join[1])); 4673 /* Copy in support of first point */ 4674 PetscCall(PetscSectionGetDof(mesh->supportSection, points[0], &dof)); 4675 PetscCall(PetscSectionGetOffset(mesh->supportSection, points[0], &off)); 4676 for (joinSize = 0; joinSize < dof; ++joinSize) join[i][joinSize] = mesh->supports[off + joinSize]; 4677 /* Check each successive support */ 4678 for (p = 1; p < numPoints; ++p) { 4679 PetscInt newJoinSize = 0; 4680 4681 PetscCall(PetscSectionGetDof(mesh->supportSection, points[p], &dof)); 4682 PetscCall(PetscSectionGetOffset(mesh->supportSection, points[p], &off)); 4683 for (c = 0; c < dof; ++c) { 4684 const PetscInt point = mesh->supports[off + c]; 4685 4686 for (m = 0; m < joinSize; ++m) { 4687 if (point == join[i][m]) { 4688 join[1 - i][newJoinSize++] = point; 4689 break; 4690 } 4691 } 4692 } 4693 joinSize = newJoinSize; 4694 i = 1 - i; 4695 } 4696 *numCoveredPoints = joinSize; 4697 *coveredPoints = join[i]; 4698 PetscCall(DMRestoreWorkArray(dm, maxSupportSize, MPIU_INT, &join[1 - i])); 4699 PetscFunctionReturn(PETSC_SUCCESS); 4700 } 4701 4702 /*@C 4703 DMPlexRestoreJoin - Restore an array for the join of the set of points 4704 4705 Not Collective 4706 4707 Input Parameters: 4708 + dm - The `DMPLEX` object 4709 . numPoints - The number of input points for the join 4710 - points - The input points 4711 4712 Output Parameters: 4713 + numCoveredPoints - The number of points in the join 4714 - coveredPoints - The points in the join 4715 4716 Level: intermediate 4717 4718 Fortran Notes: 4719 The `numCoveredPoints` argument is not present in the Fortran binding since it is internal to the array. 4720 4721 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetJoin()`, `DMPlexGetFullJoin()`, `DMPlexGetMeet()` 4722 @*/ 4723 PetscErrorCode DMPlexRestoreJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 4724 { 4725 PetscFunctionBegin; 4726 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4727 if (points) PetscAssertPointer(points, 3); 4728 if (numCoveredPoints) PetscAssertPointer(numCoveredPoints, 4); 4729 PetscAssertPointer(coveredPoints, 5); 4730 PetscCall(DMRestoreWorkArray(dm, 0, MPIU_INT, (void *)coveredPoints)); 4731 if (numCoveredPoints) *numCoveredPoints = 0; 4732 PetscFunctionReturn(PETSC_SUCCESS); 4733 } 4734 4735 /*@C 4736 DMPlexGetFullJoin - Get an array for the join of the set of points 4737 4738 Not Collective 4739 4740 Input Parameters: 4741 + dm - The `DMPLEX` object 4742 . numPoints - The number of input points for the join 4743 - points - The input points 4744 4745 Output Parameters: 4746 + numCoveredPoints - The number of points in the join 4747 - coveredPoints - The points in the join 4748 4749 Level: intermediate 4750 4751 Fortran Notes: 4752 The `numCoveredPoints` argument is not present in the Fortran binding since it is internal to the array. 4753 4754 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetJoin()`, `DMPlexRestoreJoin()`, `DMPlexGetMeet()` 4755 @*/ 4756 PetscErrorCode DMPlexGetFullJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 4757 { 4758 PetscInt *offsets, **closures; 4759 PetscInt *join[2]; 4760 PetscInt depth = 0, maxSize, joinSize = 0, i = 0; 4761 PetscInt p, d, c, m, ms; 4762 4763 PetscFunctionBegin; 4764 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4765 PetscAssertPointer(points, 3); 4766 PetscAssertPointer(numCoveredPoints, 4); 4767 PetscAssertPointer(coveredPoints, 5); 4768 4769 PetscCall(DMPlexGetDepth(dm, &depth)); 4770 PetscCall(PetscCalloc1(numPoints, &closures)); 4771 PetscCall(DMGetWorkArray(dm, numPoints * (depth + 2), MPIU_INT, &offsets)); 4772 PetscCall(DMPlexGetMaxSizes(dm, NULL, &ms)); 4773 maxSize = (ms > 1) ? ((PetscPowInt(ms, depth + 1) - 1) / (ms - 1)) : depth + 1; 4774 PetscCall(DMGetWorkArray(dm, maxSize, MPIU_INT, &join[0])); 4775 PetscCall(DMGetWorkArray(dm, maxSize, MPIU_INT, &join[1])); 4776 4777 for (p = 0; p < numPoints; ++p) { 4778 PetscInt closureSize; 4779 4780 PetscCall(DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &closureSize, &closures[p])); 4781 4782 offsets[p * (depth + 2) + 0] = 0; 4783 for (d = 0; d < depth + 1; ++d) { 4784 PetscInt pStart, pEnd, i; 4785 4786 PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd)); 4787 for (i = offsets[p * (depth + 2) + d]; i < closureSize; ++i) { 4788 if ((pStart > closures[p][i * 2]) || (pEnd <= closures[p][i * 2])) { 4789 offsets[p * (depth + 2) + d + 1] = i; 4790 break; 4791 } 4792 } 4793 if (i == closureSize) offsets[p * (depth + 2) + d + 1] = i; 4794 } 4795 PetscCheck(offsets[p * (depth + 2) + depth + 1] == closureSize, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Total size of closure %" PetscInt_FMT " should be %" PetscInt_FMT, offsets[p * (depth + 2) + depth + 1], closureSize); 4796 } 4797 for (d = 0; d < depth + 1; ++d) { 4798 PetscInt dof; 4799 4800 /* Copy in support of first point */ 4801 dof = offsets[d + 1] - offsets[d]; 4802 for (joinSize = 0; joinSize < dof; ++joinSize) join[i][joinSize] = closures[0][(offsets[d] + joinSize) * 2]; 4803 /* Check each successive cone */ 4804 for (p = 1; p < numPoints && joinSize; ++p) { 4805 PetscInt newJoinSize = 0; 4806 4807 dof = offsets[p * (depth + 2) + d + 1] - offsets[p * (depth + 2) + d]; 4808 for (c = 0; c < dof; ++c) { 4809 const PetscInt point = closures[p][(offsets[p * (depth + 2) + d] + c) * 2]; 4810 4811 for (m = 0; m < joinSize; ++m) { 4812 if (point == join[i][m]) { 4813 join[1 - i][newJoinSize++] = point; 4814 break; 4815 } 4816 } 4817 } 4818 joinSize = newJoinSize; 4819 i = 1 - i; 4820 } 4821 if (joinSize) break; 4822 } 4823 *numCoveredPoints = joinSize; 4824 *coveredPoints = join[i]; 4825 for (p = 0; p < numPoints; ++p) PetscCall(DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, NULL, &closures[p])); 4826 PetscCall(PetscFree(closures)); 4827 PetscCall(DMRestoreWorkArray(dm, numPoints * (depth + 2), MPIU_INT, &offsets)); 4828 PetscCall(DMRestoreWorkArray(dm, ms, MPIU_INT, &join[1 - i])); 4829 PetscFunctionReturn(PETSC_SUCCESS); 4830 } 4831 4832 /*@C 4833 DMPlexGetMeet - Get an array for the meet of the set of points 4834 4835 Not Collective 4836 4837 Input Parameters: 4838 + dm - The `DMPLEX` object 4839 . numPoints - The number of input points for the meet 4840 - points - The input points 4841 4842 Output Parameters: 4843 + numCoveringPoints - The number of points in the meet 4844 - coveringPoints - The points in the meet 4845 4846 Level: intermediate 4847 4848 Note: 4849 Currently, this is restricted to a single level meet 4850 4851 Fortran Notes: 4852 The `numCoveredPoints` argument is not present in the Fortran binding since it is internal to the array. 4853 4854 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexRestoreMeet()`, `DMPlexGetJoin()` 4855 @*/ 4856 PetscErrorCode DMPlexGetMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveringPoints, const PetscInt **coveringPoints) 4857 { 4858 DM_Plex *mesh = (DM_Plex *)dm->data; 4859 PetscInt *meet[2]; 4860 PetscInt meetSize, i = 0; 4861 PetscInt dof, off, p, c, m; 4862 PetscInt maxConeSize; 4863 4864 PetscFunctionBegin; 4865 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4866 PetscAssertPointer(points, 3); 4867 PetscAssertPointer(numCoveringPoints, 4); 4868 PetscAssertPointer(coveringPoints, 5); 4869 PetscCall(PetscSectionGetMaxDof(mesh->coneSection, &maxConeSize)); 4870 PetscCall(DMGetWorkArray(dm, maxConeSize, MPIU_INT, &meet[0])); 4871 PetscCall(DMGetWorkArray(dm, maxConeSize, MPIU_INT, &meet[1])); 4872 /* Copy in cone of first point */ 4873 PetscCall(PetscSectionGetDof(mesh->coneSection, points[0], &dof)); 4874 PetscCall(PetscSectionGetOffset(mesh->coneSection, points[0], &off)); 4875 for (meetSize = 0; meetSize < dof; ++meetSize) meet[i][meetSize] = mesh->cones[off + meetSize]; 4876 /* Check each successive cone */ 4877 for (p = 1; p < numPoints; ++p) { 4878 PetscInt newMeetSize = 0; 4879 4880 PetscCall(PetscSectionGetDof(mesh->coneSection, points[p], &dof)); 4881 PetscCall(PetscSectionGetOffset(mesh->coneSection, points[p], &off)); 4882 for (c = 0; c < dof; ++c) { 4883 const PetscInt point = mesh->cones[off + c]; 4884 4885 for (m = 0; m < meetSize; ++m) { 4886 if (point == meet[i][m]) { 4887 meet[1 - i][newMeetSize++] = point; 4888 break; 4889 } 4890 } 4891 } 4892 meetSize = newMeetSize; 4893 i = 1 - i; 4894 } 4895 *numCoveringPoints = meetSize; 4896 *coveringPoints = meet[i]; 4897 PetscCall(DMRestoreWorkArray(dm, maxConeSize, MPIU_INT, &meet[1 - i])); 4898 PetscFunctionReturn(PETSC_SUCCESS); 4899 } 4900 4901 /*@C 4902 DMPlexRestoreMeet - Restore an array for the meet of the set of points 4903 4904 Not Collective 4905 4906 Input Parameters: 4907 + dm - The `DMPLEX` object 4908 . numPoints - The number of input points for the meet 4909 - points - The input points 4910 4911 Output Parameters: 4912 + numCoveredPoints - The number of points in the meet 4913 - coveredPoints - The points in the meet 4914 4915 Level: intermediate 4916 4917 Fortran Notes: 4918 The `numCoveredPoints` argument is not present in the Fortran binding since it is internal to the array. 4919 4920 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetMeet()`, `DMPlexGetFullMeet()`, `DMPlexGetJoin()` 4921 @*/ 4922 PetscErrorCode DMPlexRestoreMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 4923 { 4924 PetscFunctionBegin; 4925 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4926 if (points) PetscAssertPointer(points, 3); 4927 if (numCoveredPoints) PetscAssertPointer(numCoveredPoints, 4); 4928 PetscAssertPointer(coveredPoints, 5); 4929 PetscCall(DMRestoreWorkArray(dm, 0, MPIU_INT, (void *)coveredPoints)); 4930 if (numCoveredPoints) *numCoveredPoints = 0; 4931 PetscFunctionReturn(PETSC_SUCCESS); 4932 } 4933 4934 /*@C 4935 DMPlexGetFullMeet - Get an array for the meet of the set of points 4936 4937 Not Collective 4938 4939 Input Parameters: 4940 + dm - The `DMPLEX` object 4941 . numPoints - The number of input points for the meet 4942 - points - The input points 4943 4944 Output Parameters: 4945 + numCoveredPoints - The number of points in the meet 4946 - coveredPoints - The points in the meet 4947 4948 Level: intermediate 4949 4950 Fortran Notes: 4951 The `numCoveredPoints` argument is not present in the Fortran binding since it is internal to the array. 4952 4953 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetMeet()`, `DMPlexRestoreMeet()`, `DMPlexGetJoin()` 4954 @*/ 4955 PetscErrorCode DMPlexGetFullMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 4956 { 4957 PetscInt *offsets, **closures; 4958 PetscInt *meet[2]; 4959 PetscInt height = 0, maxSize, meetSize = 0, i = 0; 4960 PetscInt p, h, c, m, mc; 4961 4962 PetscFunctionBegin; 4963 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4964 PetscAssertPointer(points, 3); 4965 PetscAssertPointer(numCoveredPoints, 4); 4966 PetscAssertPointer(coveredPoints, 5); 4967 4968 PetscCall(DMPlexGetDepth(dm, &height)); 4969 PetscCall(PetscMalloc1(numPoints, &closures)); 4970 PetscCall(DMGetWorkArray(dm, numPoints * (height + 2), MPIU_INT, &offsets)); 4971 PetscCall(DMPlexGetMaxSizes(dm, &mc, NULL)); 4972 maxSize = (mc > 1) ? ((PetscPowInt(mc, height + 1) - 1) / (mc - 1)) : height + 1; 4973 PetscCall(DMGetWorkArray(dm, maxSize, MPIU_INT, &meet[0])); 4974 PetscCall(DMGetWorkArray(dm, maxSize, MPIU_INT, &meet[1])); 4975 4976 for (p = 0; p < numPoints; ++p) { 4977 PetscInt closureSize; 4978 4979 PetscCall(DMPlexGetTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closures[p])); 4980 4981 offsets[p * (height + 2) + 0] = 0; 4982 for (h = 0; h < height + 1; ++h) { 4983 PetscInt pStart, pEnd, i; 4984 4985 PetscCall(DMPlexGetHeightStratum(dm, h, &pStart, &pEnd)); 4986 for (i = offsets[p * (height + 2) + h]; i < closureSize; ++i) { 4987 if ((pStart > closures[p][i * 2]) || (pEnd <= closures[p][i * 2])) { 4988 offsets[p * (height + 2) + h + 1] = i; 4989 break; 4990 } 4991 } 4992 if (i == closureSize) offsets[p * (height + 2) + h + 1] = i; 4993 } 4994 PetscCheck(offsets[p * (height + 2) + height + 1] == closureSize, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Total size of closure %" PetscInt_FMT " should be %" PetscInt_FMT, offsets[p * (height + 2) + height + 1], closureSize); 4995 } 4996 for (h = 0; h < height + 1; ++h) { 4997 PetscInt dof; 4998 4999 /* Copy in cone of first point */ 5000 dof = offsets[h + 1] - offsets[h]; 5001 for (meetSize = 0; meetSize < dof; ++meetSize) meet[i][meetSize] = closures[0][(offsets[h] + meetSize) * 2]; 5002 /* Check each successive cone */ 5003 for (p = 1; p < numPoints && meetSize; ++p) { 5004 PetscInt newMeetSize = 0; 5005 5006 dof = offsets[p * (height + 2) + h + 1] - offsets[p * (height + 2) + h]; 5007 for (c = 0; c < dof; ++c) { 5008 const PetscInt point = closures[p][(offsets[p * (height + 2) + h] + c) * 2]; 5009 5010 for (m = 0; m < meetSize; ++m) { 5011 if (point == meet[i][m]) { 5012 meet[1 - i][newMeetSize++] = point; 5013 break; 5014 } 5015 } 5016 } 5017 meetSize = newMeetSize; 5018 i = 1 - i; 5019 } 5020 if (meetSize) break; 5021 } 5022 *numCoveredPoints = meetSize; 5023 *coveredPoints = meet[i]; 5024 for (p = 0; p < numPoints; ++p) PetscCall(DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_TRUE, NULL, &closures[p])); 5025 PetscCall(PetscFree(closures)); 5026 PetscCall(DMRestoreWorkArray(dm, numPoints * (height + 2), MPIU_INT, &offsets)); 5027 PetscCall(DMRestoreWorkArray(dm, mc, MPIU_INT, &meet[1 - i])); 5028 PetscFunctionReturn(PETSC_SUCCESS); 5029 } 5030 5031 /*@C 5032 DMPlexEqual - Determine if two `DM` have the same topology 5033 5034 Not Collective 5035 5036 Input Parameters: 5037 + dmA - A `DMPLEX` object 5038 - dmB - A `DMPLEX` object 5039 5040 Output Parameter: 5041 . equal - `PETSC_TRUE` if the topologies are identical 5042 5043 Level: intermediate 5044 5045 Note: 5046 We are not solving graph isomorphism, so we do not permute. 5047 5048 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetCone()` 5049 @*/ 5050 PetscErrorCode DMPlexEqual(DM dmA, DM dmB, PetscBool *equal) 5051 { 5052 PetscInt depth, depthB, pStart, pEnd, pStartB, pEndB, p; 5053 5054 PetscFunctionBegin; 5055 PetscValidHeaderSpecific(dmA, DM_CLASSID, 1); 5056 PetscValidHeaderSpecific(dmB, DM_CLASSID, 2); 5057 PetscAssertPointer(equal, 3); 5058 5059 *equal = PETSC_FALSE; 5060 PetscCall(DMPlexGetDepth(dmA, &depth)); 5061 PetscCall(DMPlexGetDepth(dmB, &depthB)); 5062 if (depth != depthB) PetscFunctionReturn(PETSC_SUCCESS); 5063 PetscCall(DMPlexGetChart(dmA, &pStart, &pEnd)); 5064 PetscCall(DMPlexGetChart(dmB, &pStartB, &pEndB)); 5065 if ((pStart != pStartB) || (pEnd != pEndB)) PetscFunctionReturn(PETSC_SUCCESS); 5066 for (p = pStart; p < pEnd; ++p) { 5067 const PetscInt *cone, *coneB, *ornt, *orntB, *support, *supportB; 5068 PetscInt coneSize, coneSizeB, c, supportSize, supportSizeB, s; 5069 5070 PetscCall(DMPlexGetConeSize(dmA, p, &coneSize)); 5071 PetscCall(DMPlexGetCone(dmA, p, &cone)); 5072 PetscCall(DMPlexGetConeOrientation(dmA, p, &ornt)); 5073 PetscCall(DMPlexGetConeSize(dmB, p, &coneSizeB)); 5074 PetscCall(DMPlexGetCone(dmB, p, &coneB)); 5075 PetscCall(DMPlexGetConeOrientation(dmB, p, &orntB)); 5076 if (coneSize != coneSizeB) PetscFunctionReturn(PETSC_SUCCESS); 5077 for (c = 0; c < coneSize; ++c) { 5078 if (cone[c] != coneB[c]) PetscFunctionReturn(PETSC_SUCCESS); 5079 if (ornt[c] != orntB[c]) PetscFunctionReturn(PETSC_SUCCESS); 5080 } 5081 PetscCall(DMPlexGetSupportSize(dmA, p, &supportSize)); 5082 PetscCall(DMPlexGetSupport(dmA, p, &support)); 5083 PetscCall(DMPlexGetSupportSize(dmB, p, &supportSizeB)); 5084 PetscCall(DMPlexGetSupport(dmB, p, &supportB)); 5085 if (supportSize != supportSizeB) PetscFunctionReturn(PETSC_SUCCESS); 5086 for (s = 0; s < supportSize; ++s) { 5087 if (support[s] != supportB[s]) PetscFunctionReturn(PETSC_SUCCESS); 5088 } 5089 } 5090 *equal = PETSC_TRUE; 5091 PetscFunctionReturn(PETSC_SUCCESS); 5092 } 5093 5094 /*@C 5095 DMPlexGetNumFaceVertices - Returns the number of vertices on a face 5096 5097 Not Collective 5098 5099 Input Parameters: 5100 + dm - The `DMPLEX` 5101 . cellDim - The cell dimension 5102 - numCorners - The number of vertices on a cell 5103 5104 Output Parameter: 5105 . numFaceVertices - The number of vertices on a face 5106 5107 Level: developer 5108 5109 Note: 5110 Of course this can only work for a restricted set of symmetric shapes 5111 5112 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetCone()` 5113 @*/ 5114 PetscErrorCode DMPlexGetNumFaceVertices(DM dm, PetscInt cellDim, PetscInt numCorners, PetscInt *numFaceVertices) 5115 { 5116 MPI_Comm comm; 5117 5118 PetscFunctionBegin; 5119 PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); 5120 PetscAssertPointer(numFaceVertices, 4); 5121 switch (cellDim) { 5122 case 0: 5123 *numFaceVertices = 0; 5124 break; 5125 case 1: 5126 *numFaceVertices = 1; 5127 break; 5128 case 2: 5129 switch (numCorners) { 5130 case 3: /* triangle */ 5131 *numFaceVertices = 2; /* Edge has 2 vertices */ 5132 break; 5133 case 4: /* quadrilateral */ 5134 *numFaceVertices = 2; /* Edge has 2 vertices */ 5135 break; 5136 case 6: /* quadratic triangle, tri and quad cohesive Lagrange cells */ 5137 *numFaceVertices = 3; /* Edge has 3 vertices */ 5138 break; 5139 case 9: /* quadratic quadrilateral, quadratic quad cohesive Lagrange cells */ 5140 *numFaceVertices = 3; /* Edge has 3 vertices */ 5141 break; 5142 default: 5143 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of face corners %" PetscInt_FMT " for dimension %" PetscInt_FMT, numCorners, cellDim); 5144 } 5145 break; 5146 case 3: 5147 switch (numCorners) { 5148 case 4: /* tetradehdron */ 5149 *numFaceVertices = 3; /* Face has 3 vertices */ 5150 break; 5151 case 6: /* tet cohesive cells */ 5152 *numFaceVertices = 4; /* Face has 4 vertices */ 5153 break; 5154 case 8: /* hexahedron */ 5155 *numFaceVertices = 4; /* Face has 4 vertices */ 5156 break; 5157 case 9: /* tet cohesive Lagrange cells */ 5158 *numFaceVertices = 6; /* Face has 6 vertices */ 5159 break; 5160 case 10: /* quadratic tetrahedron */ 5161 *numFaceVertices = 6; /* Face has 6 vertices */ 5162 break; 5163 case 12: /* hex cohesive Lagrange cells */ 5164 *numFaceVertices = 6; /* Face has 6 vertices */ 5165 break; 5166 case 18: /* quadratic tet cohesive Lagrange cells */ 5167 *numFaceVertices = 6; /* Face has 6 vertices */ 5168 break; 5169 case 27: /* quadratic hexahedron, quadratic hex cohesive Lagrange cells */ 5170 *numFaceVertices = 9; /* Face has 9 vertices */ 5171 break; 5172 default: 5173 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of face corners %" PetscInt_FMT " for dimension %" PetscInt_FMT, numCorners, cellDim); 5174 } 5175 break; 5176 default: 5177 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid cell dimension %" PetscInt_FMT, cellDim); 5178 } 5179 PetscFunctionReturn(PETSC_SUCCESS); 5180 } 5181 5182 /*@ 5183 DMPlexGetDepthLabel - Get the `DMLabel` recording the depth of each point 5184 5185 Not Collective 5186 5187 Input Parameter: 5188 . dm - The `DMPLEX` object 5189 5190 Output Parameter: 5191 . depthLabel - The `DMLabel` recording point depth 5192 5193 Level: developer 5194 5195 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetDepth()`, `DMPlexGetHeightStratum()`, `DMPlexGetDepthStratum()`, `DMPlexGetPointDepth()`, 5196 @*/ 5197 PetscErrorCode DMPlexGetDepthLabel(DM dm, DMLabel *depthLabel) 5198 { 5199 PetscFunctionBegin; 5200 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5201 PetscAssertPointer(depthLabel, 2); 5202 *depthLabel = dm->depthLabel; 5203 PetscFunctionReturn(PETSC_SUCCESS); 5204 } 5205 5206 /*@ 5207 DMPlexGetDepth - Get the depth of the DAG representing this mesh 5208 5209 Not Collective 5210 5211 Input Parameter: 5212 . dm - The `DMPLEX` object 5213 5214 Output Parameter: 5215 . depth - The number of strata (breadth first levels) in the DAG 5216 5217 Level: developer 5218 5219 Notes: 5220 This returns maximum of point depths over all points, i.e. maximum value of the label returned by `DMPlexGetDepthLabel()`. 5221 5222 The point depth is described more in detail in `DMPlexGetDepthStratum()`. 5223 5224 An empty mesh gives -1. 5225 5226 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetDepthLabel()`, `DMPlexGetDepthStratum()`, `DMPlexGetPointDepth()`, `DMPlexSymmetrize()` 5227 @*/ 5228 PetscErrorCode DMPlexGetDepth(DM dm, PetscInt *depth) 5229 { 5230 DM_Plex *mesh = (DM_Plex *)dm->data; 5231 DMLabel label; 5232 PetscInt d = 0; 5233 5234 PetscFunctionBegin; 5235 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5236 PetscAssertPointer(depth, 2); 5237 if (mesh->tr) { 5238 PetscCall(DMPlexTransformGetDepth(mesh->tr, depth)); 5239 } else { 5240 PetscCall(DMPlexGetDepthLabel(dm, &label)); 5241 if (label) PetscCall(DMLabelGetNumValues(label, &d)); 5242 *depth = d - 1; 5243 } 5244 PetscFunctionReturn(PETSC_SUCCESS); 5245 } 5246 5247 /*@ 5248 DMPlexGetDepthStratum - Get the bounds [`start`, `end`) for all points at a certain depth. 5249 5250 Not Collective 5251 5252 Input Parameters: 5253 + dm - The `DMPLEX` object 5254 - depth - The requested depth 5255 5256 Output Parameters: 5257 + start - The first point at this `depth` 5258 - end - One beyond the last point at this `depth` 5259 5260 Level: developer 5261 5262 Notes: 5263 Depth indexing is related to topological dimension. Depth stratum 0 contains the lowest topological dimension points, 5264 often "vertices". If the mesh is "interpolated" (see `DMPlexInterpolate()`), then depth stratum 1 contains the next 5265 higher dimension, e.g., "edges". 5266 5267 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetHeightStratum()`, `DMPlexGetCellTypeStratum()`, `DMPlexGetDepth()`, `DMPlexGetDepthLabel()`, `DMPlexGetPointDepth()`, `DMPlexSymmetrize()`, `DMPlexInterpolate()` 5268 @*/ 5269 PetscErrorCode DMPlexGetDepthStratum(DM dm, PetscInt depth, PetscInt *start, PetscInt *end) 5270 { 5271 DM_Plex *mesh = (DM_Plex *)dm->data; 5272 DMLabel label; 5273 PetscInt pStart, pEnd; 5274 5275 PetscFunctionBegin; 5276 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5277 if (start) { 5278 PetscAssertPointer(start, 3); 5279 *start = 0; 5280 } 5281 if (end) { 5282 PetscAssertPointer(end, 4); 5283 *end = 0; 5284 } 5285 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 5286 if (pStart == pEnd) PetscFunctionReturn(PETSC_SUCCESS); 5287 if (depth < 0) { 5288 if (start) *start = pStart; 5289 if (end) *end = pEnd; 5290 PetscFunctionReturn(PETSC_SUCCESS); 5291 } 5292 if (mesh->tr) { 5293 PetscCall(DMPlexTransformGetDepthStratum(mesh->tr, depth, start, end)); 5294 } else { 5295 PetscCall(DMPlexGetDepthLabel(dm, &label)); 5296 PetscCheck(label, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "No label named depth was found"); 5297 PetscCall(DMLabelGetStratumBounds(label, depth, start, end)); 5298 } 5299 PetscFunctionReturn(PETSC_SUCCESS); 5300 } 5301 5302 /*@ 5303 DMPlexGetHeightStratum - Get the bounds [`start`, `end`) for all points at a certain height. 5304 5305 Not Collective 5306 5307 Input Parameters: 5308 + dm - The `DMPLEX` object 5309 - height - The requested height 5310 5311 Output Parameters: 5312 + start - The first point at this `height` 5313 - end - One beyond the last point at this `height` 5314 5315 Level: developer 5316 5317 Notes: 5318 Height indexing is related to topological codimension. Height stratum 0 contains the highest topological dimension 5319 points, often called "cells" or "elements". If the mesh is "interpolated" (see `DMPlexInterpolate()`), then height 5320 stratum 1 contains the boundary of these "cells", often called "faces" or "facets". 5321 5322 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetDepthStratum()`, `DMPlexGetCellTypeStratum()`, `DMPlexGetDepth()`, `DMPlexGetPointHeight()` 5323 @*/ 5324 PetscErrorCode DMPlexGetHeightStratum(DM dm, PetscInt height, PetscInt *start, PetscInt *end) 5325 { 5326 DMLabel label; 5327 PetscInt depth, pStart, pEnd; 5328 5329 PetscFunctionBegin; 5330 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5331 if (start) { 5332 PetscAssertPointer(start, 3); 5333 *start = 0; 5334 } 5335 if (end) { 5336 PetscAssertPointer(end, 4); 5337 *end = 0; 5338 } 5339 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 5340 if (pStart == pEnd) PetscFunctionReturn(PETSC_SUCCESS); 5341 if (height < 0) { 5342 if (start) *start = pStart; 5343 if (end) *end = pEnd; 5344 PetscFunctionReturn(PETSC_SUCCESS); 5345 } 5346 PetscCall(DMPlexGetDepthLabel(dm, &label)); 5347 if (label) PetscCall(DMLabelGetNumValues(label, &depth)); 5348 else PetscCall(DMGetDimension(dm, &depth)); 5349 PetscCheck(depth >= 0, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Depth not yet computed"); 5350 PetscCall(DMPlexGetDepthStratum(dm, depth - 1 - height, start, end)); 5351 PetscFunctionReturn(PETSC_SUCCESS); 5352 } 5353 5354 /*@ 5355 DMPlexGetPointDepth - Get the `depth` of a given point 5356 5357 Not Collective 5358 5359 Input Parameters: 5360 + dm - The `DMPLEX` object 5361 - point - The point 5362 5363 Output Parameter: 5364 . depth - The depth of the `point` 5365 5366 Level: intermediate 5367 5368 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetCellType()`, `DMPlexGetDepthLabel()`, `DMPlexGetDepth()`, `DMPlexGetPointHeight()` 5369 @*/ 5370 PetscErrorCode DMPlexGetPointDepth(DM dm, PetscInt point, PetscInt *depth) 5371 { 5372 PetscFunctionBegin; 5373 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5374 PetscAssertPointer(depth, 3); 5375 PetscCall(DMLabelGetValue(dm->depthLabel, point, depth)); 5376 PetscFunctionReturn(PETSC_SUCCESS); 5377 } 5378 5379 /*@ 5380 DMPlexGetPointHeight - Get the `height` of a given point 5381 5382 Not Collective 5383 5384 Input Parameters: 5385 + dm - The `DMPLEX` object 5386 - point - The point 5387 5388 Output Parameter: 5389 . height - The height of the `point` 5390 5391 Level: intermediate 5392 5393 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetCellType()`, `DMPlexGetDepthLabel()`, `DMPlexGetDepth()`, `DMPlexGetPointDepth()` 5394 @*/ 5395 PetscErrorCode DMPlexGetPointHeight(DM dm, PetscInt point, PetscInt *height) 5396 { 5397 PetscInt n, pDepth; 5398 5399 PetscFunctionBegin; 5400 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5401 PetscAssertPointer(height, 3); 5402 PetscCall(DMLabelGetNumValues(dm->depthLabel, &n)); 5403 PetscCall(DMLabelGetValue(dm->depthLabel, point, &pDepth)); 5404 *height = n - 1 - pDepth; /* DAG depth is n-1 */ 5405 PetscFunctionReturn(PETSC_SUCCESS); 5406 } 5407 5408 /*@ 5409 DMPlexGetCellTypeLabel - Get the `DMLabel` recording the polytope type of each cell 5410 5411 Not Collective 5412 5413 Input Parameter: 5414 . dm - The `DMPLEX` object 5415 5416 Output Parameter: 5417 . celltypeLabel - The `DMLabel` recording cell polytope type 5418 5419 Level: developer 5420 5421 Note: 5422 This function will trigger automatica computation of cell types. This can be disabled by calling 5423 `DMCreateLabel`(dm, "celltype") beforehand. 5424 5425 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetCellType()`, `DMPlexGetDepthLabel()`, `DMCreateLabel()` 5426 @*/ 5427 PetscErrorCode DMPlexGetCellTypeLabel(DM dm, DMLabel *celltypeLabel) 5428 { 5429 PetscFunctionBegin; 5430 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5431 PetscAssertPointer(celltypeLabel, 2); 5432 if (!dm->celltypeLabel) PetscCall(DMPlexComputeCellTypes(dm)); 5433 *celltypeLabel = dm->celltypeLabel; 5434 PetscFunctionReturn(PETSC_SUCCESS); 5435 } 5436 5437 /*@ 5438 DMPlexGetCellType - Get the polytope type of a given cell 5439 5440 Not Collective 5441 5442 Input Parameters: 5443 + dm - The `DMPLEX` object 5444 - cell - The cell 5445 5446 Output Parameter: 5447 . celltype - The polytope type of the cell 5448 5449 Level: intermediate 5450 5451 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPolytopeType`, `DMPlexGetCellTypeLabel()`, `DMPlexGetDepthLabel()`, `DMPlexGetDepth()` 5452 @*/ 5453 PetscErrorCode DMPlexGetCellType(DM dm, PetscInt cell, DMPolytopeType *celltype) 5454 { 5455 DM_Plex *mesh = (DM_Plex *)dm->data; 5456 DMLabel label; 5457 PetscInt ct; 5458 5459 PetscFunctionBegin; 5460 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5461 PetscAssertPointer(celltype, 3); 5462 if (mesh->tr) { 5463 PetscCall(DMPlexTransformGetCellType(mesh->tr, cell, celltype)); 5464 } else { 5465 PetscInt pStart, pEnd; 5466 5467 PetscCall(PetscSectionGetChart(mesh->coneSection, &pStart, NULL)); 5468 if (!mesh->cellTypes) { /* XXX remove? optimize? */ 5469 PetscCall(PetscSectionGetChart(mesh->coneSection, NULL, &pEnd)); 5470 PetscCall(PetscMalloc1(pEnd - pStart, &mesh->cellTypes)); 5471 PetscCall(DMPlexGetCellTypeLabel(dm, &label)); 5472 for (PetscInt p = pStart; p < pEnd; p++) { 5473 PetscCall(DMLabelGetValue(label, p, &ct)); 5474 mesh->cellTypes[p - pStart].value_as_uint8 = (DMPolytopeType)ct; 5475 } 5476 } 5477 *celltype = (DMPolytopeType)mesh->cellTypes[cell - pStart].value_as_uint8; 5478 if (PetscDefined(USE_DEBUG)) { 5479 PetscCall(DMPlexGetCellTypeLabel(dm, &label)); 5480 PetscCall(DMLabelGetValue(label, cell, &ct)); 5481 PetscCheck(ct >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Cell %" PetscInt_FMT " has not been assigned a cell type", cell); 5482 PetscCheck(ct == (PetscInt)*celltype, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid cellType for %" PetscInt_FMT ": %d != %" PetscInt_FMT, cell, (int)*celltype, ct); 5483 } 5484 } 5485 PetscFunctionReturn(PETSC_SUCCESS); 5486 } 5487 5488 /*@ 5489 DMPlexSetCellType - Set the polytope type of a given cell 5490 5491 Not Collective 5492 5493 Input Parameters: 5494 + dm - The `DMPLEX` object 5495 . cell - The cell 5496 - celltype - The polytope type of the cell 5497 5498 Level: advanced 5499 5500 Note: 5501 By default, cell types will be automatically computed using `DMPlexComputeCellTypes()` before this function 5502 is executed. This function will override the computed type. However, if automatic classification will not succeed 5503 and a user wants to manually specify all types, the classification must be disabled by calling 5504 DMCreateLabel(dm, "celltype") before getting or setting any cell types. 5505 5506 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetCellTypeLabel()`, `DMPlexGetDepthLabel()`, `DMPlexGetDepth()`, `DMPlexComputeCellTypes()`, `DMCreateLabel()` 5507 @*/ 5508 PetscErrorCode DMPlexSetCellType(DM dm, PetscInt cell, DMPolytopeType celltype) 5509 { 5510 DM_Plex *mesh = (DM_Plex *)dm->data; 5511 DMLabel label; 5512 PetscInt pStart, pEnd; 5513 5514 PetscFunctionBegin; 5515 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5516 PetscCall(PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd)); 5517 PetscCall(DMPlexGetCellTypeLabel(dm, &label)); 5518 PetscCall(DMLabelSetValue(label, cell, celltype)); 5519 if (!mesh->cellTypes) PetscCall(PetscMalloc1(pEnd - pStart, &mesh->cellTypes)); 5520 mesh->cellTypes[cell - pStart].value_as_uint8 = celltype; 5521 PetscFunctionReturn(PETSC_SUCCESS); 5522 } 5523 5524 PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm) 5525 { 5526 PetscSection section, s; 5527 Mat m; 5528 PetscInt maxHeight; 5529 const char *prefix; 5530 5531 PetscFunctionBegin; 5532 PetscCall(DMClone(dm, cdm)); 5533 PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm, &prefix)); 5534 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)*cdm, prefix)); 5535 PetscCall(PetscObjectAppendOptionsPrefix((PetscObject)*cdm, "cdm_")); 5536 PetscCall(DMPlexGetMaxProjectionHeight(dm, &maxHeight)); 5537 PetscCall(DMPlexSetMaxProjectionHeight(*cdm, maxHeight)); 5538 PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)dm), §ion)); 5539 PetscCall(DMSetLocalSection(*cdm, section)); 5540 PetscCall(PetscSectionDestroy(§ion)); 5541 PetscCall(PetscSectionCreate(PETSC_COMM_SELF, &s)); 5542 PetscCall(MatCreate(PETSC_COMM_SELF, &m)); 5543 PetscCall(DMSetDefaultConstraints(*cdm, s, m, NULL)); 5544 PetscCall(PetscSectionDestroy(&s)); 5545 PetscCall(MatDestroy(&m)); 5546 5547 PetscCall(DMSetNumFields(*cdm, 1)); 5548 PetscCall(DMCreateDS(*cdm)); 5549 (*cdm)->cloneOpts = PETSC_TRUE; 5550 if (dm->setfromoptionscalled) PetscCall(DMSetFromOptions(*cdm)); 5551 PetscFunctionReturn(PETSC_SUCCESS); 5552 } 5553 5554 PetscErrorCode DMCreateCoordinateField_Plex(DM dm, DMField *field) 5555 { 5556 Vec coordsLocal, cellCoordsLocal; 5557 DM coordsDM, cellCoordsDM; 5558 5559 PetscFunctionBegin; 5560 *field = NULL; 5561 PetscCall(DMGetCoordinatesLocal(dm, &coordsLocal)); 5562 PetscCall(DMGetCoordinateDM(dm, &coordsDM)); 5563 PetscCall(DMGetCellCoordinatesLocal(dm, &cellCoordsLocal)); 5564 PetscCall(DMGetCellCoordinateDM(dm, &cellCoordsDM)); 5565 if (coordsLocal && coordsDM) { 5566 if (cellCoordsLocal && cellCoordsDM) PetscCall(DMFieldCreateDSWithDG(coordsDM, cellCoordsDM, 0, coordsLocal, cellCoordsLocal, field)); 5567 else PetscCall(DMFieldCreateDS(coordsDM, 0, coordsLocal, field)); 5568 } 5569 PetscFunctionReturn(PETSC_SUCCESS); 5570 } 5571 5572 /*@C 5573 DMPlexGetConeSection - Return a section which describes the layout of cone data 5574 5575 Not Collective 5576 5577 Input Parameter: 5578 . dm - The `DMPLEX` object 5579 5580 Output Parameter: 5581 . section - The `PetscSection` object 5582 5583 Level: developer 5584 5585 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetSupportSection()`, `DMPlexGetCones()`, `DMPlexGetConeOrientations()`, `PetscSection` 5586 @*/ 5587 PetscErrorCode DMPlexGetConeSection(DM dm, PetscSection *section) 5588 { 5589 DM_Plex *mesh = (DM_Plex *)dm->data; 5590 5591 PetscFunctionBegin; 5592 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5593 if (section) *section = mesh->coneSection; 5594 PetscFunctionReturn(PETSC_SUCCESS); 5595 } 5596 5597 /*@C 5598 DMPlexGetSupportSection - Return a section which describes the layout of support data 5599 5600 Not Collective 5601 5602 Input Parameter: 5603 . dm - The `DMPLEX` object 5604 5605 Output Parameter: 5606 . section - The `PetscSection` object 5607 5608 Level: developer 5609 5610 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetConeSection()`, `PetscSection` 5611 @*/ 5612 PetscErrorCode DMPlexGetSupportSection(DM dm, PetscSection *section) 5613 { 5614 DM_Plex *mesh = (DM_Plex *)dm->data; 5615 5616 PetscFunctionBegin; 5617 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5618 if (section) *section = mesh->supportSection; 5619 PetscFunctionReturn(PETSC_SUCCESS); 5620 } 5621 5622 /*@C 5623 DMPlexGetCones - Return cone data 5624 5625 Not Collective 5626 5627 Input Parameter: 5628 . dm - The `DMPLEX` object 5629 5630 Output Parameter: 5631 . cones - The cone for each point 5632 5633 Level: developer 5634 5635 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetConeSection()` 5636 @*/ 5637 PetscErrorCode DMPlexGetCones(DM dm, PetscInt *cones[]) 5638 { 5639 DM_Plex *mesh = (DM_Plex *)dm->data; 5640 5641 PetscFunctionBegin; 5642 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5643 if (cones) *cones = mesh->cones; 5644 PetscFunctionReturn(PETSC_SUCCESS); 5645 } 5646 5647 /*@C 5648 DMPlexGetConeOrientations - Return cone orientation data 5649 5650 Not Collective 5651 5652 Input Parameter: 5653 . dm - The `DMPLEX` object 5654 5655 Output Parameter: 5656 . coneOrientations - The array of cone orientations for all points 5657 5658 Level: developer 5659 5660 Notes: 5661 The `PetscSection` returned by `DMPlexGetConeSection()` partitions coneOrientations into cone orientations of particular points as returned by `DMPlexGetConeOrientation()`. 5662 5663 The meaning of coneOrientations values is detailed in `DMPlexGetConeOrientation()`. 5664 5665 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetConeSection()`, `DMPlexGetConeOrientation()`, `PetscSection` 5666 @*/ 5667 PetscErrorCode DMPlexGetConeOrientations(DM dm, PetscInt *coneOrientations[]) 5668 { 5669 DM_Plex *mesh = (DM_Plex *)dm->data; 5670 5671 PetscFunctionBegin; 5672 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5673 if (coneOrientations) *coneOrientations = mesh->coneOrientations; 5674 PetscFunctionReturn(PETSC_SUCCESS); 5675 } 5676 5677 /******************************** FEM Support **********************************/ 5678 5679 PetscErrorCode DMPlexGetAllCells_Internal(DM plex, IS *cellIS) 5680 { 5681 PetscInt depth; 5682 5683 PetscFunctionBegin; 5684 PetscCall(DMPlexGetDepth(plex, &depth)); 5685 PetscCall(DMGetStratumIS(plex, "dim", depth, cellIS)); 5686 if (!*cellIS) PetscCall(DMGetStratumIS(plex, "depth", depth, cellIS)); 5687 PetscFunctionReturn(PETSC_SUCCESS); 5688 } 5689 5690 PetscErrorCode DMPlexGetAllFaces_Internal(DM plex, IS *faceIS) 5691 { 5692 PetscInt depth; 5693 5694 PetscFunctionBegin; 5695 PetscCall(DMPlexGetDepth(plex, &depth)); 5696 PetscCall(DMGetStratumIS(plex, "dim", depth - 1, faceIS)); 5697 if (!*faceIS) PetscCall(DMGetStratumIS(plex, "depth", depth - 1, faceIS)); 5698 PetscFunctionReturn(PETSC_SUCCESS); 5699 } 5700 5701 /* 5702 Returns number of components and tensor degree for the field. For interpolated meshes, line should be a point 5703 representing a line in the section. 5704 */ 5705 static PetscErrorCode PetscSectionFieldGetTensorDegree_Private(DM dm, PetscSection section, PetscInt field, PetscInt line, PetscInt *Nc, PetscInt *k, PetscBool *continuous, PetscBool *tensor) 5706 { 5707 PetscObject obj; 5708 PetscClassId id; 5709 PetscFE fe = NULL; 5710 5711 PetscFunctionBeginHot; 5712 PetscCall(PetscSectionGetFieldComponents(section, field, Nc)); 5713 PetscCall(DMGetField(dm, field, NULL, &obj)); 5714 PetscCall(PetscObjectGetClassId(obj, &id)); 5715 if (id == PETSCFE_CLASSID) fe = (PetscFE)obj; 5716 5717 if (!fe) { 5718 /* Assume the full interpolated mesh is in the chart; lines in particular */ 5719 /* An order k SEM disc has k-1 dofs on an edge */ 5720 PetscCall(PetscSectionGetFieldDof(section, line, field, k)); 5721 *k = *k / *Nc + 1; 5722 } else { 5723 PetscInt dual_space_size, dim; 5724 PetscDualSpace dsp; 5725 5726 PetscCall(DMGetDimension(dm, &dim)); 5727 PetscCall(PetscFEGetDualSpace(fe, &dsp)); 5728 PetscCall(PetscDualSpaceGetDimension(dsp, &dual_space_size)); 5729 *k = (PetscInt)PetscCeilReal(PetscPowReal(dual_space_size / *Nc, 1.0 / dim)) - 1; 5730 PetscCall(PetscDualSpaceLagrangeGetContinuity(dsp, continuous)); 5731 PetscCall(PetscDualSpaceLagrangeGetTensor(dsp, tensor)); 5732 } 5733 PetscFunctionReturn(PETSC_SUCCESS); 5734 } 5735 5736 static PetscErrorCode GetFieldSize_Private(PetscInt dim, PetscInt k, PetscBool tensor, PetscInt *dof) 5737 { 5738 PetscFunctionBeginHot; 5739 if (tensor) { 5740 *dof = PetscPowInt(k + 1, dim); 5741 } else { 5742 switch (dim) { 5743 case 1: 5744 *dof = k + 1; 5745 break; 5746 case 2: 5747 *dof = ((k + 1) * (k + 2)) / 2; 5748 break; 5749 case 3: 5750 *dof = ((k + 1) * (k + 2) * (k + 3)) / 6; 5751 break; 5752 default: 5753 *dof = 0; 5754 } 5755 } 5756 PetscFunctionReturn(PETSC_SUCCESS); 5757 } 5758 5759 /*@ 5760 5761 DMPlexSetClosurePermutationTensor - Create a permutation from the default (BFS) point ordering in the closure, to a 5762 lexicographic ordering over the tensor product cell (i.e., line, quad, hex, etc.), and set this permutation in the 5763 section provided (or the section of the `DM`). 5764 5765 Input Parameters: 5766 + dm - The `DM` 5767 . point - Either a cell (highest dim point) or an edge (dim 1 point), or `PETSC_DETERMINE` 5768 - section - The `PetscSection` to reorder, or `NULL` for the default section 5769 5770 Example: 5771 A typical interpolated single-quad mesh might order points as 5772 .vb 5773 [c0, v1, v2, v3, v4, e5, e6, e7, e8] 5774 5775 v4 -- e6 -- v3 5776 | | 5777 e7 c0 e8 5778 | | 5779 v1 -- e5 -- v2 5780 .ve 5781 5782 (There is no significance to the ordering described here.) The default section for a Q3 quad might typically assign 5783 dofs in the order of points, e.g., 5784 .vb 5785 c0 -> [0,1,2,3] 5786 v1 -> [4] 5787 ... 5788 e5 -> [8, 9] 5789 .ve 5790 5791 which corresponds to the dofs 5792 .vb 5793 6 10 11 7 5794 13 2 3 15 5795 12 0 1 14 5796 4 8 9 5 5797 .ve 5798 5799 The closure in BFS ordering works through height strata (cells, edges, vertices) to produce the ordering 5800 .vb 5801 0 1 2 3 8 9 14 15 11 10 13 12 4 5 7 6 5802 .ve 5803 5804 After calling DMPlexSetClosurePermutationTensor(), the closure will be ordered lexicographically, 5805 .vb 5806 4 8 9 5 12 0 1 14 13 2 3 15 6 10 11 7 5807 .ve 5808 5809 Level: developer 5810 5811 Notes: 5812 The point is used to determine the number of dofs/field on an edge. For SEM, this is related to the polynomial 5813 degree of the basis. 5814 5815 This is required to run with libCEED. 5816 5817 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMGetLocalSection()`, `PetscSectionSetClosurePermutation()`, `DMSetGlobalSection()` 5818 @*/ 5819 PetscErrorCode DMPlexSetClosurePermutationTensor(DM dm, PetscInt point, PetscSection section) 5820 { 5821 DMLabel label; 5822 PetscInt dim, depth = -1, eStart = -1, Nf; 5823 PetscBool continuous = PETSC_TRUE, tensor = PETSC_TRUE; 5824 5825 PetscFunctionBegin; 5826 PetscCall(DMGetDimension(dm, &dim)); 5827 if (dim < 1) PetscFunctionReturn(PETSC_SUCCESS); 5828 if (point < 0) { 5829 PetscInt sStart, sEnd; 5830 5831 PetscCall(DMPlexGetDepthStratum(dm, 1, &sStart, &sEnd)); 5832 point = sEnd - sStart ? sStart : point; 5833 } 5834 PetscCall(DMPlexGetDepthLabel(dm, &label)); 5835 if (point >= 0) PetscCall(DMLabelGetValue(label, point, &depth)); 5836 if (!section) PetscCall(DMGetLocalSection(dm, §ion)); 5837 if (depth == 1) { 5838 eStart = point; 5839 } else if (depth == dim) { 5840 const PetscInt *cone; 5841 5842 PetscCall(DMPlexGetCone(dm, point, &cone)); 5843 if (dim == 2) eStart = cone[0]; 5844 else if (dim == 3) { 5845 const PetscInt *cone2; 5846 PetscCall(DMPlexGetCone(dm, cone[0], &cone2)); 5847 eStart = cone2[0]; 5848 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Point %" PetscInt_FMT " of depth %" PetscInt_FMT " cannot be used to bootstrap spectral ordering for dim %" PetscInt_FMT, point, depth, dim); 5849 } else PetscCheck(depth < 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Point %" PetscInt_FMT " of depth %" PetscInt_FMT " cannot be used to bootstrap spectral ordering for dim %" PetscInt_FMT, point, depth, dim); 5850 5851 PetscCall(PetscSectionGetNumFields(section, &Nf)); 5852 for (PetscInt d = 1; d <= dim; d++) { 5853 PetscInt k, f, Nc, c, i, j, size = 0, offset = 0, foffset = 0; 5854 PetscInt *perm; 5855 5856 for (f = 0; f < Nf; ++f) { 5857 PetscInt dof; 5858 5859 PetscCall(PetscSectionFieldGetTensorDegree_Private(dm, section, f, eStart, &Nc, &k, &continuous, &tensor)); 5860 PetscCheck(dim == 1 || tensor || !continuous, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Continuous field %" PetscInt_FMT " must have a tensor product discretization", f); 5861 if (!continuous && d < dim) continue; 5862 PetscCall(GetFieldSize_Private(d, k, tensor, &dof)); 5863 size += dof * Nc; 5864 } 5865 PetscCall(PetscMalloc1(size, &perm)); 5866 for (f = 0; f < Nf; ++f) { 5867 switch (d) { 5868 case 1: 5869 PetscCall(PetscSectionFieldGetTensorDegree_Private(dm, section, f, eStart, &Nc, &k, &continuous, &tensor)); 5870 if (!continuous && d < dim) continue; 5871 /* 5872 Original ordering is [ edge of length k-1; vtx0; vtx1 ] 5873 We want [ vtx0; edge of length k-1; vtx1 ] 5874 */ 5875 if (continuous) { 5876 for (c = 0; c < Nc; c++, offset++) perm[offset] = (k - 1) * Nc + c + foffset; 5877 for (i = 0; i < k - 1; i++) 5878 for (c = 0; c < Nc; c++, offset++) perm[offset] = i * Nc + c + foffset; 5879 for (c = 0; c < Nc; c++, offset++) perm[offset] = k * Nc + c + foffset; 5880 foffset = offset; 5881 } else { 5882 PetscInt dof; 5883 5884 PetscCall(GetFieldSize_Private(d, k, tensor, &dof)); 5885 for (i = 0; i < dof * Nc; ++i, ++offset) perm[offset] = i + foffset; 5886 foffset = offset; 5887 } 5888 break; 5889 case 2: 5890 /* The original quad closure is oriented clockwise, {f, e_b, e_r, e_t, e_l, v_lb, v_rb, v_tr, v_tl} */ 5891 PetscCall(PetscSectionFieldGetTensorDegree_Private(dm, section, f, eStart, &Nc, &k, &continuous, &tensor)); 5892 if (!continuous && d < dim) continue; 5893 /* The SEM order is 5894 5895 v_lb, {e_b}, v_rb, 5896 e^{(k-1)-i}_l, {f^{i*(k-1)}}, e^i_r, 5897 v_lt, reverse {e_t}, v_rt 5898 */ 5899 if (continuous) { 5900 const PetscInt of = 0; 5901 const PetscInt oeb = of + PetscSqr(k - 1); 5902 const PetscInt oer = oeb + (k - 1); 5903 const PetscInt oet = oer + (k - 1); 5904 const PetscInt oel = oet + (k - 1); 5905 const PetscInt ovlb = oel + (k - 1); 5906 const PetscInt ovrb = ovlb + 1; 5907 const PetscInt ovrt = ovrb + 1; 5908 const PetscInt ovlt = ovrt + 1; 5909 PetscInt o; 5910 5911 /* bottom */ 5912 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovlb * Nc + c + foffset; 5913 for (o = oeb; o < oer; ++o) 5914 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 5915 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovrb * Nc + c + foffset; 5916 /* middle */ 5917 for (i = 0; i < k - 1; ++i) { 5918 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oel + (k - 2) - i) * Nc + c + foffset; 5919 for (o = of + (k - 1) * i; o < of + (k - 1) * (i + 1); ++o) 5920 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 5921 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oer + i) * Nc + c + foffset; 5922 } 5923 /* top */ 5924 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovlt * Nc + c + foffset; 5925 for (o = oel - 1; o >= oet; --o) 5926 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 5927 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovrt * Nc + c + foffset; 5928 foffset = offset; 5929 } else { 5930 PetscInt dof; 5931 5932 PetscCall(GetFieldSize_Private(d, k, tensor, &dof)); 5933 for (i = 0; i < dof * Nc; ++i, ++offset) perm[offset] = i + foffset; 5934 foffset = offset; 5935 } 5936 break; 5937 case 3: 5938 /* The original hex closure is 5939 5940 {c, 5941 f_b, f_t, f_f, f_b, f_r, f_l, 5942 e_bl, e_bb, e_br, e_bf, e_tf, e_tr, e_tb, e_tl, e_rf, e_lf, e_lb, e_rb, 5943 v_blf, v_blb, v_brb, v_brf, v_tlf, v_trf, v_trb, v_tlb} 5944 */ 5945 PetscCall(PetscSectionFieldGetTensorDegree_Private(dm, section, f, eStart, &Nc, &k, &continuous, &tensor)); 5946 if (!continuous && d < dim) continue; 5947 /* The SEM order is 5948 Bottom Slice 5949 v_blf, {e^{(k-1)-n}_bf}, v_brf, 5950 e^{i}_bl, f^{n*(k-1)+(k-1)-i}_b, e^{(k-1)-i}_br, 5951 v_blb, {e_bb}, v_brb, 5952 5953 Middle Slice (j) 5954 {e^{(k-1)-j}_lf}, {f^{j*(k-1)+n}_f}, e^j_rf, 5955 f^{i*(k-1)+j}_l, {c^{(j*(k-1) + i)*(k-1)+n}_t}, f^{j*(k-1)+i}_r, 5956 e^j_lb, {f^{j*(k-1)+(k-1)-n}_b}, e^{(k-1)-j}_rb, 5957 5958 Top Slice 5959 v_tlf, {e_tf}, v_trf, 5960 e^{(k-1)-i}_tl, {f^{i*(k-1)}_t}, e^{i}_tr, 5961 v_tlb, {e^{(k-1)-n}_tb}, v_trb, 5962 */ 5963 if (continuous) { 5964 const PetscInt oc = 0; 5965 const PetscInt ofb = oc + PetscSqr(k - 1) * (k - 1); 5966 const PetscInt oft = ofb + PetscSqr(k - 1); 5967 const PetscInt off = oft + PetscSqr(k - 1); 5968 const PetscInt ofk = off + PetscSqr(k - 1); 5969 const PetscInt ofr = ofk + PetscSqr(k - 1); 5970 const PetscInt ofl = ofr + PetscSqr(k - 1); 5971 const PetscInt oebl = ofl + PetscSqr(k - 1); 5972 const PetscInt oebb = oebl + (k - 1); 5973 const PetscInt oebr = oebb + (k - 1); 5974 const PetscInt oebf = oebr + (k - 1); 5975 const PetscInt oetf = oebf + (k - 1); 5976 const PetscInt oetr = oetf + (k - 1); 5977 const PetscInt oetb = oetr + (k - 1); 5978 const PetscInt oetl = oetb + (k - 1); 5979 const PetscInt oerf = oetl + (k - 1); 5980 const PetscInt oelf = oerf + (k - 1); 5981 const PetscInt oelb = oelf + (k - 1); 5982 const PetscInt oerb = oelb + (k - 1); 5983 const PetscInt ovblf = oerb + (k - 1); 5984 const PetscInt ovblb = ovblf + 1; 5985 const PetscInt ovbrb = ovblb + 1; 5986 const PetscInt ovbrf = ovbrb + 1; 5987 const PetscInt ovtlf = ovbrf + 1; 5988 const PetscInt ovtrf = ovtlf + 1; 5989 const PetscInt ovtrb = ovtrf + 1; 5990 const PetscInt ovtlb = ovtrb + 1; 5991 PetscInt o, n; 5992 5993 /* Bottom Slice */ 5994 /* bottom */ 5995 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovblf * Nc + c + foffset; 5996 for (o = oetf - 1; o >= oebf; --o) 5997 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 5998 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovbrf * Nc + c + foffset; 5999 /* middle */ 6000 for (i = 0; i < k - 1; ++i) { 6001 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oebl + i) * Nc + c + foffset; 6002 for (n = 0; n < k - 1; ++n) { 6003 o = ofb + n * (k - 1) + i; 6004 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 6005 } 6006 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oebr + (k - 2) - i) * Nc + c + foffset; 6007 } 6008 /* top */ 6009 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovblb * Nc + c + foffset; 6010 for (o = oebb; o < oebr; ++o) 6011 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 6012 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovbrb * Nc + c + foffset; 6013 6014 /* Middle Slice */ 6015 for (j = 0; j < k - 1; ++j) { 6016 /* bottom */ 6017 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oelf + (k - 2) - j) * Nc + c + foffset; 6018 for (o = off + j * (k - 1); o < off + (j + 1) * (k - 1); ++o) 6019 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 6020 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oerf + j) * Nc + c + foffset; 6021 /* middle */ 6022 for (i = 0; i < k - 1; ++i) { 6023 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (ofl + i * (k - 1) + j) * Nc + c + foffset; 6024 for (n = 0; n < k - 1; ++n) 6025 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oc + (j * (k - 1) + i) * (k - 1) + n) * Nc + c + foffset; 6026 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (ofr + j * (k - 1) + i) * Nc + c + foffset; 6027 } 6028 /* top */ 6029 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oelb + j) * Nc + c + foffset; 6030 for (o = ofk + j * (k - 1) + (k - 2); o >= ofk + j * (k - 1); --o) 6031 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 6032 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oerb + (k - 2) - j) * Nc + c + foffset; 6033 } 6034 6035 /* Top Slice */ 6036 /* bottom */ 6037 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtlf * Nc + c + foffset; 6038 for (o = oetf; o < oetr; ++o) 6039 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 6040 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtrf * Nc + c + foffset; 6041 /* middle */ 6042 for (i = 0; i < k - 1; ++i) { 6043 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oetl + (k - 2) - i) * Nc + c + foffset; 6044 for (n = 0; n < k - 1; ++n) 6045 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oft + i * (k - 1) + n) * Nc + c + foffset; 6046 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oetr + i) * Nc + c + foffset; 6047 } 6048 /* top */ 6049 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtlb * Nc + c + foffset; 6050 for (o = oetl - 1; o >= oetb; --o) 6051 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 6052 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtrb * Nc + c + foffset; 6053 6054 foffset = offset; 6055 } else { 6056 PetscInt dof; 6057 6058 PetscCall(GetFieldSize_Private(d, k, tensor, &dof)); 6059 for (i = 0; i < dof * Nc; ++i, ++offset) perm[offset] = i + foffset; 6060 foffset = offset; 6061 } 6062 break; 6063 default: 6064 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "No spectral ordering for dimension %" PetscInt_FMT, d); 6065 } 6066 } 6067 PetscCheck(offset == size, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Number of permutation entries %" PetscInt_FMT " != %" PetscInt_FMT, offset, size); 6068 /* Check permutation */ 6069 { 6070 PetscInt *check; 6071 6072 PetscCall(PetscMalloc1(size, &check)); 6073 for (i = 0; i < size; ++i) { 6074 check[i] = -1; 6075 PetscCheck(perm[i] >= 0 && perm[i] < size, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid permutation index p[%" PetscInt_FMT "] = %" PetscInt_FMT, i, perm[i]); 6076 } 6077 for (i = 0; i < size; ++i) check[perm[i]] = i; 6078 for (i = 0; i < size; ++i) PetscCheck(check[i] >= 0, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Missing permutation index %" PetscInt_FMT, i); 6079 PetscCall(PetscFree(check)); 6080 } 6081 PetscCall(PetscSectionSetClosurePermutation_Internal(section, (PetscObject)dm, d, size, PETSC_OWN_POINTER, perm)); 6082 if (d == dim) { // Add permutation for localized (in case this is a coordinate DM) 6083 PetscInt *loc_perm; 6084 PetscCall(PetscMalloc1(size * 2, &loc_perm)); 6085 for (PetscInt i = 0; i < size; i++) { 6086 loc_perm[i] = perm[i]; 6087 loc_perm[size + i] = size + perm[i]; 6088 } 6089 PetscCall(PetscSectionSetClosurePermutation_Internal(section, (PetscObject)dm, d, size * 2, PETSC_OWN_POINTER, loc_perm)); 6090 } 6091 } 6092 PetscFunctionReturn(PETSC_SUCCESS); 6093 } 6094 6095 PetscErrorCode DMPlexGetPointDualSpaceFEM(DM dm, PetscInt point, PetscInt field, PetscDualSpace *dspace) 6096 { 6097 PetscDS prob; 6098 PetscInt depth, Nf, h; 6099 DMLabel label; 6100 6101 PetscFunctionBeginHot; 6102 PetscCall(DMGetDS(dm, &prob)); 6103 Nf = prob->Nf; 6104 label = dm->depthLabel; 6105 *dspace = NULL; 6106 if (field < Nf) { 6107 PetscObject disc = prob->disc[field]; 6108 6109 if (disc->classid == PETSCFE_CLASSID) { 6110 PetscDualSpace dsp; 6111 6112 PetscCall(PetscFEGetDualSpace((PetscFE)disc, &dsp)); 6113 PetscCall(DMLabelGetNumValues(label, &depth)); 6114 PetscCall(DMLabelGetValue(label, point, &h)); 6115 h = depth - 1 - h; 6116 if (h) { 6117 PetscCall(PetscDualSpaceGetHeightSubspace(dsp, h, dspace)); 6118 } else { 6119 *dspace = dsp; 6120 } 6121 } 6122 } 6123 PetscFunctionReturn(PETSC_SUCCESS); 6124 } 6125 6126 static inline PetscErrorCode DMPlexVecGetClosure_Depth1_Static(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[]) 6127 { 6128 PetscScalar *array; 6129 const PetscScalar *vArray; 6130 const PetscInt *cone, *coneO; 6131 PetscInt pStart, pEnd, p, numPoints, size = 0, offset = 0; 6132 6133 PetscFunctionBeginHot; 6134 PetscCall(PetscSectionGetChart(section, &pStart, &pEnd)); 6135 PetscCall(DMPlexGetConeSize(dm, point, &numPoints)); 6136 PetscCall(DMPlexGetCone(dm, point, &cone)); 6137 PetscCall(DMPlexGetConeOrientation(dm, point, &coneO)); 6138 if (!values || !*values) { 6139 if ((point >= pStart) && (point < pEnd)) { 6140 PetscInt dof; 6141 6142 PetscCall(PetscSectionGetDof(section, point, &dof)); 6143 size += dof; 6144 } 6145 for (p = 0; p < numPoints; ++p) { 6146 const PetscInt cp = cone[p]; 6147 PetscInt dof; 6148 6149 if ((cp < pStart) || (cp >= pEnd)) continue; 6150 PetscCall(PetscSectionGetDof(section, cp, &dof)); 6151 size += dof; 6152 } 6153 if (!values) { 6154 if (csize) *csize = size; 6155 PetscFunctionReturn(PETSC_SUCCESS); 6156 } 6157 PetscCall(DMGetWorkArray(dm, size, MPIU_SCALAR, &array)); 6158 } else { 6159 array = *values; 6160 } 6161 size = 0; 6162 PetscCall(VecGetArrayRead(v, &vArray)); 6163 if ((point >= pStart) && (point < pEnd)) { 6164 PetscInt dof, off, d; 6165 const PetscScalar *varr; 6166 6167 PetscCall(PetscSectionGetDof(section, point, &dof)); 6168 PetscCall(PetscSectionGetOffset(section, point, &off)); 6169 varr = PetscSafePointerPlusOffset(vArray, off); 6170 for (d = 0; d < dof; ++d, ++offset) array[offset] = varr[d]; 6171 size += dof; 6172 } 6173 for (p = 0; p < numPoints; ++p) { 6174 const PetscInt cp = cone[p]; 6175 PetscInt o = coneO[p]; 6176 PetscInt dof, off, d; 6177 const PetscScalar *varr; 6178 6179 if ((cp < pStart) || (cp >= pEnd)) continue; 6180 PetscCall(PetscSectionGetDof(section, cp, &dof)); 6181 PetscCall(PetscSectionGetOffset(section, cp, &off)); 6182 varr = PetscSafePointerPlusOffset(vArray, off); 6183 if (o >= 0) { 6184 for (d = 0; d < dof; ++d, ++offset) array[offset] = varr[d]; 6185 } else { 6186 for (d = dof - 1; d >= 0; --d, ++offset) array[offset] = varr[d]; 6187 } 6188 size += dof; 6189 } 6190 PetscCall(VecRestoreArrayRead(v, &vArray)); 6191 if (!*values) { 6192 if (csize) *csize = size; 6193 *values = array; 6194 } else { 6195 PetscCheck(size <= *csize, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Size of input array %" PetscInt_FMT " < actual size %" PetscInt_FMT, *csize, size); 6196 *csize = size; 6197 } 6198 PetscFunctionReturn(PETSC_SUCCESS); 6199 } 6200 6201 /* Compress out points not in the section */ 6202 static inline PetscErrorCode CompressPoints_Private(PetscSection section, PetscInt *numPoints, PetscInt points[]) 6203 { 6204 const PetscInt np = *numPoints; 6205 PetscInt pStart, pEnd, p, q; 6206 6207 PetscCall(PetscSectionGetChart(section, &pStart, &pEnd)); 6208 for (p = 0, q = 0; p < np; ++p) { 6209 const PetscInt r = points[p * 2]; 6210 if ((r >= pStart) && (r < pEnd)) { 6211 points[q * 2] = r; 6212 points[q * 2 + 1] = points[p * 2 + 1]; 6213 ++q; 6214 } 6215 } 6216 *numPoints = q; 6217 return PETSC_SUCCESS; 6218 } 6219 6220 /* Compressed closure does not apply closure permutation */ 6221 PetscErrorCode DMPlexGetCompressedClosure(DM dm, PetscSection section, PetscInt point, PetscInt ornt, PetscInt *numPoints, PetscInt **points, PetscSection *clSec, IS *clPoints, const PetscInt **clp) 6222 { 6223 const PetscInt *cla = NULL; 6224 PetscInt np, *pts = NULL; 6225 6226 PetscFunctionBeginHot; 6227 PetscCall(PetscSectionGetClosureIndex(section, (PetscObject)dm, clSec, clPoints)); 6228 if (!ornt && *clPoints) { 6229 PetscInt dof, off; 6230 6231 PetscCall(PetscSectionGetDof(*clSec, point, &dof)); 6232 PetscCall(PetscSectionGetOffset(*clSec, point, &off)); 6233 PetscCall(ISGetIndices(*clPoints, &cla)); 6234 np = dof / 2; 6235 pts = PetscSafePointerPlusOffset((PetscInt *)cla, off); 6236 } else { 6237 PetscCall(DMPlexGetTransitiveClosure_Internal(dm, point, ornt, PETSC_TRUE, &np, &pts)); 6238 PetscCall(CompressPoints_Private(section, &np, pts)); 6239 } 6240 *numPoints = np; 6241 *points = pts; 6242 *clp = cla; 6243 PetscFunctionReturn(PETSC_SUCCESS); 6244 } 6245 6246 PetscErrorCode DMPlexRestoreCompressedClosure(DM dm, PetscSection section, PetscInt point, PetscInt *numPoints, PetscInt **points, PetscSection *clSec, IS *clPoints, const PetscInt **clp) 6247 { 6248 PetscFunctionBeginHot; 6249 if (!*clPoints) { 6250 PetscCall(DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, numPoints, points)); 6251 } else { 6252 PetscCall(ISRestoreIndices(*clPoints, clp)); 6253 } 6254 *numPoints = 0; 6255 *points = NULL; 6256 *clSec = NULL; 6257 *clPoints = NULL; 6258 *clp = NULL; 6259 PetscFunctionReturn(PETSC_SUCCESS); 6260 } 6261 6262 static inline PetscErrorCode DMPlexVecGetClosure_Static(DM dm, PetscSection section, PetscInt numPoints, const PetscInt points[], const PetscInt clperm[], const PetscScalar vArray[], PetscInt *size, PetscScalar array[]) 6263 { 6264 PetscInt offset = 0, p; 6265 const PetscInt **perms = NULL; 6266 const PetscScalar **flips = NULL; 6267 6268 PetscFunctionBeginHot; 6269 *size = 0; 6270 PetscCall(PetscSectionGetPointSyms(section, numPoints, points, &perms, &flips)); 6271 for (p = 0; p < numPoints; p++) { 6272 const PetscInt point = points[2 * p]; 6273 const PetscInt *perm = perms ? perms[p] : NULL; 6274 const PetscScalar *flip = flips ? flips[p] : NULL; 6275 PetscInt dof, off, d; 6276 const PetscScalar *varr; 6277 6278 PetscCall(PetscSectionGetDof(section, point, &dof)); 6279 PetscCall(PetscSectionGetOffset(section, point, &off)); 6280 varr = PetscSafePointerPlusOffset(vArray, off); 6281 if (clperm) { 6282 if (perm) { 6283 for (d = 0; d < dof; d++) array[clperm[offset + perm[d]]] = varr[d]; 6284 } else { 6285 for (d = 0; d < dof; d++) array[clperm[offset + d]] = varr[d]; 6286 } 6287 if (flip) { 6288 for (d = 0; d < dof; d++) array[clperm[offset + d]] *= flip[d]; 6289 } 6290 } else { 6291 if (perm) { 6292 for (d = 0; d < dof; d++) array[offset + perm[d]] = varr[d]; 6293 } else { 6294 for (d = 0; d < dof; d++) array[offset + d] = varr[d]; 6295 } 6296 if (flip) { 6297 for (d = 0; d < dof; d++) array[offset + d] *= flip[d]; 6298 } 6299 } 6300 offset += dof; 6301 } 6302 PetscCall(PetscSectionRestorePointSyms(section, numPoints, points, &perms, &flips)); 6303 *size = offset; 6304 PetscFunctionReturn(PETSC_SUCCESS); 6305 } 6306 6307 static inline PetscErrorCode DMPlexVecGetClosure_Fields_Static(DM dm, PetscSection section, PetscInt numPoints, const PetscInt points[], PetscInt numFields, const PetscInt clperm[], const PetscScalar vArray[], PetscInt *size, PetscScalar array[]) 6308 { 6309 PetscInt offset = 0, f; 6310 6311 PetscFunctionBeginHot; 6312 *size = 0; 6313 for (f = 0; f < numFields; ++f) { 6314 PetscInt p; 6315 const PetscInt **perms = NULL; 6316 const PetscScalar **flips = NULL; 6317 6318 PetscCall(PetscSectionGetFieldPointSyms(section, f, numPoints, points, &perms, &flips)); 6319 for (p = 0; p < numPoints; p++) { 6320 const PetscInt point = points[2 * p]; 6321 PetscInt fdof, foff, b; 6322 const PetscScalar *varr; 6323 const PetscInt *perm = perms ? perms[p] : NULL; 6324 const PetscScalar *flip = flips ? flips[p] : NULL; 6325 6326 PetscCall(PetscSectionGetFieldDof(section, point, f, &fdof)); 6327 PetscCall(PetscSectionGetFieldOffset(section, point, f, &foff)); 6328 varr = &vArray[foff]; 6329 if (clperm) { 6330 if (perm) { 6331 for (b = 0; b < fdof; b++) array[clperm[offset + perm[b]]] = varr[b]; 6332 } else { 6333 for (b = 0; b < fdof; b++) array[clperm[offset + b]] = varr[b]; 6334 } 6335 if (flip) { 6336 for (b = 0; b < fdof; b++) array[clperm[offset + b]] *= flip[b]; 6337 } 6338 } else { 6339 if (perm) { 6340 for (b = 0; b < fdof; b++) array[offset + perm[b]] = varr[b]; 6341 } else { 6342 for (b = 0; b < fdof; b++) array[offset + b] = varr[b]; 6343 } 6344 if (flip) { 6345 for (b = 0; b < fdof; b++) array[offset + b] *= flip[b]; 6346 } 6347 } 6348 offset += fdof; 6349 } 6350 PetscCall(PetscSectionRestoreFieldPointSyms(section, f, numPoints, points, &perms, &flips)); 6351 } 6352 *size = offset; 6353 PetscFunctionReturn(PETSC_SUCCESS); 6354 } 6355 6356 PetscErrorCode DMPlexVecGetOrientedClosure_Internal(DM dm, PetscSection section, PetscBool useClPerm, Vec v, PetscInt point, PetscInt ornt, PetscInt *csize, PetscScalar *values[]) 6357 { 6358 PetscSection clSection; 6359 IS clPoints; 6360 PetscInt *points = NULL; 6361 const PetscInt *clp, *perm = NULL; 6362 PetscInt depth, numFields, numPoints, asize; 6363 6364 PetscFunctionBeginHot; 6365 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6366 if (!section) PetscCall(DMGetLocalSection(dm, §ion)); 6367 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 6368 PetscValidHeaderSpecific(v, VEC_CLASSID, 4); 6369 PetscCall(DMPlexGetDepth(dm, &depth)); 6370 PetscCall(PetscSectionGetNumFields(section, &numFields)); 6371 if (depth == 1 && numFields < 2) { 6372 PetscCall(DMPlexVecGetClosure_Depth1_Static(dm, section, v, point, csize, values)); 6373 PetscFunctionReturn(PETSC_SUCCESS); 6374 } 6375 /* Get points */ 6376 PetscCall(DMPlexGetCompressedClosure(dm, section, point, ornt, &numPoints, &points, &clSection, &clPoints, &clp)); 6377 /* Get sizes */ 6378 asize = 0; 6379 for (PetscInt p = 0; p < numPoints * 2; p += 2) { 6380 PetscInt dof; 6381 PetscCall(PetscSectionGetDof(section, points[p], &dof)); 6382 asize += dof; 6383 } 6384 if (values) { 6385 const PetscScalar *vArray; 6386 PetscInt size; 6387 6388 if (*values) { 6389 PetscCheck(*csize >= asize, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Provided array size %" PetscInt_FMT " not sufficient to hold closure size %" PetscInt_FMT, *csize, asize); 6390 } else PetscCall(DMGetWorkArray(dm, asize, MPIU_SCALAR, values)); 6391 if (useClPerm) PetscCall(PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject)dm, depth, asize, &perm)); 6392 PetscCall(VecGetArrayRead(v, &vArray)); 6393 /* Get values */ 6394 if (numFields > 0) PetscCall(DMPlexVecGetClosure_Fields_Static(dm, section, numPoints, points, numFields, perm, vArray, &size, *values)); 6395 else PetscCall(DMPlexVecGetClosure_Static(dm, section, numPoints, points, perm, vArray, &size, *values)); 6396 PetscCheck(asize == size, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Section size %" PetscInt_FMT " does not match Vec closure size %" PetscInt_FMT, asize, size); 6397 /* Cleanup array */ 6398 PetscCall(VecRestoreArrayRead(v, &vArray)); 6399 } 6400 if (csize) *csize = asize; 6401 /* Cleanup points */ 6402 PetscCall(DMPlexRestoreCompressedClosure(dm, section, point, &numPoints, &points, &clSection, &clPoints, &clp)); 6403 PetscFunctionReturn(PETSC_SUCCESS); 6404 } 6405 6406 /*@C 6407 DMPlexVecGetClosure - Get an array of the values on the closure of 'point' 6408 6409 Not collective 6410 6411 Input Parameters: 6412 + dm - The `DM` 6413 . section - The section describing the layout in `v`, or `NULL` to use the default section 6414 . v - The local vector 6415 - point - The point in the `DM` 6416 6417 Input/Output Parameters: 6418 + csize - The size of the input values array, or `NULL`; on output the number of values in the closure 6419 - values - An array to use for the values, or `NULL` to have it allocated automatically; 6420 if the user provided `NULL`, it is a borrowed array and should not be freed 6421 6422 Level: intermediate 6423 6424 Notes: 6425 `DMPlexVecGetClosure()`/`DMPlexVecRestoreClosure()` only allocates the values array if it set to `NULL` in the 6426 calling function. This is because `DMPlexVecGetClosure()` is typically called in the inner loop of a `Vec` or `Mat` 6427 assembly function, and a user may already have allocated storage for this operation. 6428 6429 A typical use could be 6430 .vb 6431 values = NULL; 6432 PetscCall(DMPlexVecGetClosure(dm, NULL, v, p, &clSize, &values)); 6433 for (cl = 0; cl < clSize; ++cl) { 6434 <Compute on closure> 6435 } 6436 PetscCall(DMPlexVecRestoreClosure(dm, NULL, v, p, &clSize, &values)); 6437 .ve 6438 or 6439 .vb 6440 PetscMalloc1(clMaxSize, &values); 6441 for (p = pStart; p < pEnd; ++p) { 6442 clSize = clMaxSize; 6443 PetscCall(DMPlexVecGetClosure(dm, NULL, v, p, &clSize, &values)); 6444 for (cl = 0; cl < clSize; ++cl) { 6445 <Compute on closure> 6446 } 6447 } 6448 PetscFree(values); 6449 .ve 6450 6451 Fortran Notes: 6452 The `csize` argument is not present in the Fortran binding since it is internal to the array. 6453 6454 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexVecRestoreClosure()`, `DMPlexVecSetClosure()`, `DMPlexMatSetClosure()` 6455 @*/ 6456 PetscErrorCode DMPlexVecGetClosure(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[]) 6457 { 6458 PetscFunctionBeginHot; 6459 PetscCall(DMPlexVecGetOrientedClosure_Internal(dm, section, PETSC_TRUE, v, point, 0, csize, values)); 6460 PetscFunctionReturn(PETSC_SUCCESS); 6461 } 6462 6463 PetscErrorCode DMPlexVecGetClosureAtDepth_Internal(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt depth, PetscInt *csize, PetscScalar *values[]) 6464 { 6465 DMLabel depthLabel; 6466 PetscSection clSection; 6467 IS clPoints; 6468 PetscScalar *array; 6469 const PetscScalar *vArray; 6470 PetscInt *points = NULL; 6471 const PetscInt *clp, *perm = NULL; 6472 PetscInt mdepth, numFields, numPoints, Np = 0, p, clsize, size; 6473 6474 PetscFunctionBeginHot; 6475 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6476 if (!section) PetscCall(DMGetLocalSection(dm, §ion)); 6477 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 6478 PetscValidHeaderSpecific(v, VEC_CLASSID, 3); 6479 PetscCall(DMPlexGetDepth(dm, &mdepth)); 6480 PetscCall(DMPlexGetDepthLabel(dm, &depthLabel)); 6481 PetscCall(PetscSectionGetNumFields(section, &numFields)); 6482 if (mdepth == 1 && numFields < 2) { 6483 PetscCall(DMPlexVecGetClosure_Depth1_Static(dm, section, v, point, csize, values)); 6484 PetscFunctionReturn(PETSC_SUCCESS); 6485 } 6486 /* Get points */ 6487 PetscCall(DMPlexGetCompressedClosure(dm, section, point, 0, &numPoints, &points, &clSection, &clPoints, &clp)); 6488 for (clsize = 0, p = 0; p < Np; p++) { 6489 PetscInt dof; 6490 PetscCall(PetscSectionGetDof(section, points[2 * p], &dof)); 6491 clsize += dof; 6492 } 6493 PetscCall(PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject)dm, depth, clsize, &perm)); 6494 /* Filter points */ 6495 for (p = 0; p < numPoints * 2; p += 2) { 6496 PetscInt dep; 6497 6498 PetscCall(DMLabelGetValue(depthLabel, points[p], &dep)); 6499 if (dep != depth) continue; 6500 points[Np * 2 + 0] = points[p]; 6501 points[Np * 2 + 1] = points[p + 1]; 6502 ++Np; 6503 } 6504 /* Get array */ 6505 if (!values || !*values) { 6506 PetscInt asize = 0, dof; 6507 6508 for (p = 0; p < Np * 2; p += 2) { 6509 PetscCall(PetscSectionGetDof(section, points[p], &dof)); 6510 asize += dof; 6511 } 6512 if (!values) { 6513 PetscCall(DMPlexRestoreCompressedClosure(dm, section, point, &numPoints, &points, &clSection, &clPoints, &clp)); 6514 if (csize) *csize = asize; 6515 PetscFunctionReturn(PETSC_SUCCESS); 6516 } 6517 PetscCall(DMGetWorkArray(dm, asize, MPIU_SCALAR, &array)); 6518 } else { 6519 array = *values; 6520 } 6521 PetscCall(VecGetArrayRead(v, &vArray)); 6522 /* Get values */ 6523 if (numFields > 0) PetscCall(DMPlexVecGetClosure_Fields_Static(dm, section, Np, points, numFields, perm, vArray, &size, array)); 6524 else PetscCall(DMPlexVecGetClosure_Static(dm, section, Np, points, perm, vArray, &size, array)); 6525 /* Cleanup points */ 6526 PetscCall(DMPlexRestoreCompressedClosure(dm, section, point, &numPoints, &points, &clSection, &clPoints, &clp)); 6527 /* Cleanup array */ 6528 PetscCall(VecRestoreArrayRead(v, &vArray)); 6529 if (!*values) { 6530 if (csize) *csize = size; 6531 *values = array; 6532 } else { 6533 PetscCheck(size <= *csize, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Size of input array %" PetscInt_FMT " < actual size %" PetscInt_FMT, *csize, size); 6534 *csize = size; 6535 } 6536 PetscFunctionReturn(PETSC_SUCCESS); 6537 } 6538 6539 /*@C 6540 DMPlexVecRestoreClosure - Restore the array of the values on the closure of 'point' 6541 6542 Not collective 6543 6544 Input Parameters: 6545 + dm - The `DM` 6546 . section - The section describing the layout in `v`, or `NULL` to use the default section 6547 . v - The local vector 6548 . point - The point in the `DM` 6549 . csize - The number of values in the closure, or `NULL` 6550 - values - The array of values, which is a borrowed array and should not be freed 6551 6552 Level: intermediate 6553 6554 Note: 6555 The array values are discarded and not copied back into `v`. In order to copy values back to `v`, use `DMPlexVecSetClosure()` 6556 6557 Fortran Notes: 6558 The `csize` argument is not present in the Fortran binding since it is internal to the array. 6559 6560 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexVecGetClosure()`, `DMPlexVecSetClosure()`, `DMPlexMatSetClosure()` 6561 @*/ 6562 PetscErrorCode DMPlexVecRestoreClosure(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[]) 6563 { 6564 PetscInt size = 0; 6565 6566 PetscFunctionBegin; 6567 /* Should work without recalculating size */ 6568 PetscCall(DMRestoreWorkArray(dm, size, MPIU_SCALAR, (void *)values)); 6569 *values = NULL; 6570 PetscFunctionReturn(PETSC_SUCCESS); 6571 } 6572 6573 static inline void add(PetscScalar *x, PetscScalar y) 6574 { 6575 *x += y; 6576 } 6577 static inline void insert(PetscScalar *x, PetscScalar y) 6578 { 6579 *x = y; 6580 } 6581 6582 static inline PetscErrorCode updatePoint_private(PetscSection section, PetscInt point, PetscInt dof, void (*fuse)(PetscScalar *, PetscScalar), PetscBool setBC, const PetscInt perm[], const PetscScalar flip[], const PetscInt clperm[], const PetscScalar values[], PetscInt offset, PetscScalar array[]) 6583 { 6584 PetscInt cdof; /* The number of constraints on this point */ 6585 const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ 6586 PetscScalar *a; 6587 PetscInt off, cind = 0, k; 6588 6589 PetscFunctionBegin; 6590 PetscCall(PetscSectionGetConstraintDof(section, point, &cdof)); 6591 PetscCall(PetscSectionGetOffset(section, point, &off)); 6592 a = &array[off]; 6593 if (!cdof || setBC) { 6594 if (clperm) { 6595 if (perm) { 6596 for (k = 0; k < dof; ++k) fuse(&a[k], values[clperm[offset + perm[k]]] * (flip ? flip[perm[k]] : 1.)); 6597 } else { 6598 for (k = 0; k < dof; ++k) fuse(&a[k], values[clperm[offset + k]] * (flip ? flip[k] : 1.)); 6599 } 6600 } else { 6601 if (perm) { 6602 for (k = 0; k < dof; ++k) fuse(&a[k], values[offset + perm[k]] * (flip ? flip[perm[k]] : 1.)); 6603 } else { 6604 for (k = 0; k < dof; ++k) fuse(&a[k], values[offset + k] * (flip ? flip[k] : 1.)); 6605 } 6606 } 6607 } else { 6608 PetscCall(PetscSectionGetConstraintIndices(section, point, &cdofs)); 6609 if (clperm) { 6610 if (perm) { 6611 for (k = 0; k < dof; ++k) { 6612 if ((cind < cdof) && (k == cdofs[cind])) { 6613 ++cind; 6614 continue; 6615 } 6616 fuse(&a[k], values[clperm[offset + perm[k]]] * (flip ? flip[perm[k]] : 1.)); 6617 } 6618 } else { 6619 for (k = 0; k < dof; ++k) { 6620 if ((cind < cdof) && (k == cdofs[cind])) { 6621 ++cind; 6622 continue; 6623 } 6624 fuse(&a[k], values[clperm[offset + k]] * (flip ? flip[k] : 1.)); 6625 } 6626 } 6627 } else { 6628 if (perm) { 6629 for (k = 0; k < dof; ++k) { 6630 if ((cind < cdof) && (k == cdofs[cind])) { 6631 ++cind; 6632 continue; 6633 } 6634 fuse(&a[k], values[offset + perm[k]] * (flip ? flip[perm[k]] : 1.)); 6635 } 6636 } else { 6637 for (k = 0; k < dof; ++k) { 6638 if ((cind < cdof) && (k == cdofs[cind])) { 6639 ++cind; 6640 continue; 6641 } 6642 fuse(&a[k], values[offset + k] * (flip ? flip[k] : 1.)); 6643 } 6644 } 6645 } 6646 } 6647 PetscFunctionReturn(PETSC_SUCCESS); 6648 } 6649 6650 static inline PetscErrorCode updatePointBC_private(PetscSection section, PetscInt point, PetscInt dof, void (*fuse)(PetscScalar *, PetscScalar), const PetscInt perm[], const PetscScalar flip[], const PetscInt clperm[], const PetscScalar values[], PetscInt offset, PetscScalar array[]) 6651 { 6652 PetscInt cdof; /* The number of constraints on this point */ 6653 const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ 6654 PetscScalar *a; 6655 PetscInt off, cind = 0, k; 6656 6657 PetscFunctionBegin; 6658 PetscCall(PetscSectionGetConstraintDof(section, point, &cdof)); 6659 PetscCall(PetscSectionGetOffset(section, point, &off)); 6660 a = &array[off]; 6661 if (cdof) { 6662 PetscCall(PetscSectionGetConstraintIndices(section, point, &cdofs)); 6663 if (clperm) { 6664 if (perm) { 6665 for (k = 0; k < dof; ++k) { 6666 if ((cind < cdof) && (k == cdofs[cind])) { 6667 fuse(&a[k], values[clperm[offset + perm[k]]] * (flip ? flip[perm[k]] : 1.)); 6668 cind++; 6669 } 6670 } 6671 } else { 6672 for (k = 0; k < dof; ++k) { 6673 if ((cind < cdof) && (k == cdofs[cind])) { 6674 fuse(&a[k], values[clperm[offset + k]] * (flip ? flip[k] : 1.)); 6675 cind++; 6676 } 6677 } 6678 } 6679 } else { 6680 if (perm) { 6681 for (k = 0; k < dof; ++k) { 6682 if ((cind < cdof) && (k == cdofs[cind])) { 6683 fuse(&a[k], values[offset + perm[k]] * (flip ? flip[perm[k]] : 1.)); 6684 cind++; 6685 } 6686 } 6687 } else { 6688 for (k = 0; k < dof; ++k) { 6689 if ((cind < cdof) && (k == cdofs[cind])) { 6690 fuse(&a[k], values[offset + k] * (flip ? flip[k] : 1.)); 6691 cind++; 6692 } 6693 } 6694 } 6695 } 6696 } 6697 PetscFunctionReturn(PETSC_SUCCESS); 6698 } 6699 6700 static inline PetscErrorCode updatePointFields_private(PetscSection section, PetscInt point, const PetscInt *perm, const PetscScalar *flip, PetscInt f, void (*fuse)(PetscScalar *, PetscScalar), PetscBool setBC, const PetscInt clperm[], const PetscScalar values[], PetscInt *offset, PetscScalar array[]) 6701 { 6702 PetscScalar *a; 6703 PetscInt fdof, foff, fcdof, foffset = *offset; 6704 const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ 6705 PetscInt cind = 0, b; 6706 6707 PetscFunctionBegin; 6708 PetscCall(PetscSectionGetFieldDof(section, point, f, &fdof)); 6709 PetscCall(PetscSectionGetFieldConstraintDof(section, point, f, &fcdof)); 6710 PetscCall(PetscSectionGetFieldOffset(section, point, f, &foff)); 6711 a = &array[foff]; 6712 if (!fcdof || setBC) { 6713 if (clperm) { 6714 if (perm) { 6715 for (b = 0; b < fdof; b++) fuse(&a[b], values[clperm[foffset + perm[b]]] * (flip ? flip[perm[b]] : 1.)); 6716 } else { 6717 for (b = 0; b < fdof; b++) fuse(&a[b], values[clperm[foffset + b]] * (flip ? flip[b] : 1.)); 6718 } 6719 } else { 6720 if (perm) { 6721 for (b = 0; b < fdof; b++) fuse(&a[b], values[foffset + perm[b]] * (flip ? flip[perm[b]] : 1.)); 6722 } else { 6723 for (b = 0; b < fdof; b++) fuse(&a[b], values[foffset + b] * (flip ? flip[b] : 1.)); 6724 } 6725 } 6726 } else { 6727 PetscCall(PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs)); 6728 if (clperm) { 6729 if (perm) { 6730 for (b = 0; b < fdof; b++) { 6731 if ((cind < fcdof) && (b == fcdofs[cind])) { 6732 ++cind; 6733 continue; 6734 } 6735 fuse(&a[b], values[clperm[foffset + perm[b]]] * (flip ? flip[perm[b]] : 1.)); 6736 } 6737 } else { 6738 for (b = 0; b < fdof; b++) { 6739 if ((cind < fcdof) && (b == fcdofs[cind])) { 6740 ++cind; 6741 continue; 6742 } 6743 fuse(&a[b], values[clperm[foffset + b]] * (flip ? flip[b] : 1.)); 6744 } 6745 } 6746 } else { 6747 if (perm) { 6748 for (b = 0; b < fdof; b++) { 6749 if ((cind < fcdof) && (b == fcdofs[cind])) { 6750 ++cind; 6751 continue; 6752 } 6753 fuse(&a[b], values[foffset + perm[b]] * (flip ? flip[perm[b]] : 1.)); 6754 } 6755 } else { 6756 for (b = 0; b < fdof; b++) { 6757 if ((cind < fcdof) && (b == fcdofs[cind])) { 6758 ++cind; 6759 continue; 6760 } 6761 fuse(&a[b], values[foffset + b] * (flip ? flip[b] : 1.)); 6762 } 6763 } 6764 } 6765 } 6766 *offset += fdof; 6767 PetscFunctionReturn(PETSC_SUCCESS); 6768 } 6769 6770 static inline PetscErrorCode updatePointFieldsBC_private(PetscSection section, PetscInt point, const PetscInt perm[], const PetscScalar flip[], PetscInt f, PetscInt Ncc, const PetscInt comps[], void (*fuse)(PetscScalar *, PetscScalar), const PetscInt clperm[], const PetscScalar values[], PetscInt *offset, PetscScalar array[]) 6771 { 6772 PetscScalar *a; 6773 PetscInt fdof, foff, fcdof, foffset = *offset; 6774 const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ 6775 PetscInt Nc, cind = 0, ncind = 0, b; 6776 PetscBool ncSet, fcSet; 6777 6778 PetscFunctionBegin; 6779 PetscCall(PetscSectionGetFieldComponents(section, f, &Nc)); 6780 PetscCall(PetscSectionGetFieldDof(section, point, f, &fdof)); 6781 PetscCall(PetscSectionGetFieldConstraintDof(section, point, f, &fcdof)); 6782 PetscCall(PetscSectionGetFieldOffset(section, point, f, &foff)); 6783 a = &array[foff]; 6784 if (fcdof) { 6785 /* We just override fcdof and fcdofs with Ncc and comps */ 6786 PetscCall(PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs)); 6787 if (clperm) { 6788 if (perm) { 6789 if (comps) { 6790 for (b = 0; b < fdof; b++) { 6791 ncSet = fcSet = PETSC_FALSE; 6792 if (b % Nc == comps[ncind]) { 6793 ncind = (ncind + 1) % Ncc; 6794 ncSet = PETSC_TRUE; 6795 } 6796 if ((cind < fcdof) && (b == fcdofs[cind])) { 6797 ++cind; 6798 fcSet = PETSC_TRUE; 6799 } 6800 if (ncSet && fcSet) fuse(&a[b], values[clperm[foffset + perm[b]]] * (flip ? flip[perm[b]] : 1.)); 6801 } 6802 } else { 6803 for (b = 0; b < fdof; b++) { 6804 if ((cind < fcdof) && (b == fcdofs[cind])) { 6805 fuse(&a[b], values[clperm[foffset + perm[b]]] * (flip ? flip[perm[b]] : 1.)); 6806 ++cind; 6807 } 6808 } 6809 } 6810 } else { 6811 if (comps) { 6812 for (b = 0; b < fdof; b++) { 6813 ncSet = fcSet = PETSC_FALSE; 6814 if (b % Nc == comps[ncind]) { 6815 ncind = (ncind + 1) % Ncc; 6816 ncSet = PETSC_TRUE; 6817 } 6818 if ((cind < fcdof) && (b == fcdofs[cind])) { 6819 ++cind; 6820 fcSet = PETSC_TRUE; 6821 } 6822 if (ncSet && fcSet) fuse(&a[b], values[clperm[foffset + b]] * (flip ? flip[b] : 1.)); 6823 } 6824 } else { 6825 for (b = 0; b < fdof; b++) { 6826 if ((cind < fcdof) && (b == fcdofs[cind])) { 6827 fuse(&a[b], values[clperm[foffset + b]] * (flip ? flip[b] : 1.)); 6828 ++cind; 6829 } 6830 } 6831 } 6832 } 6833 } else { 6834 if (perm) { 6835 if (comps) { 6836 for (b = 0; b < fdof; b++) { 6837 ncSet = fcSet = PETSC_FALSE; 6838 if (b % Nc == comps[ncind]) { 6839 ncind = (ncind + 1) % Ncc; 6840 ncSet = PETSC_TRUE; 6841 } 6842 if ((cind < fcdof) && (b == fcdofs[cind])) { 6843 ++cind; 6844 fcSet = PETSC_TRUE; 6845 } 6846 if (ncSet && fcSet) fuse(&a[b], values[foffset + perm[b]] * (flip ? flip[perm[b]] : 1.)); 6847 } 6848 } else { 6849 for (b = 0; b < fdof; b++) { 6850 if ((cind < fcdof) && (b == fcdofs[cind])) { 6851 fuse(&a[b], values[foffset + perm[b]] * (flip ? flip[perm[b]] : 1.)); 6852 ++cind; 6853 } 6854 } 6855 } 6856 } else { 6857 if (comps) { 6858 for (b = 0; b < fdof; b++) { 6859 ncSet = fcSet = PETSC_FALSE; 6860 if (b % Nc == comps[ncind]) { 6861 ncind = (ncind + 1) % Ncc; 6862 ncSet = PETSC_TRUE; 6863 } 6864 if ((cind < fcdof) && (b == fcdofs[cind])) { 6865 ++cind; 6866 fcSet = PETSC_TRUE; 6867 } 6868 if (ncSet && fcSet) fuse(&a[b], values[foffset + b] * (flip ? flip[b] : 1.)); 6869 } 6870 } else { 6871 for (b = 0; b < fdof; b++) { 6872 if ((cind < fcdof) && (b == fcdofs[cind])) { 6873 fuse(&a[b], values[foffset + b] * (flip ? flip[b] : 1.)); 6874 ++cind; 6875 } 6876 } 6877 } 6878 } 6879 } 6880 } 6881 *offset += fdof; 6882 PetscFunctionReturn(PETSC_SUCCESS); 6883 } 6884 6885 static inline PetscErrorCode DMPlexVecSetClosure_Depth1_Static(DM dm, PetscSection section, Vec v, PetscInt point, const PetscScalar values[], InsertMode mode) 6886 { 6887 PetscScalar *array; 6888 const PetscInt *cone, *coneO; 6889 PetscInt pStart, pEnd, p, numPoints, off, dof; 6890 6891 PetscFunctionBeginHot; 6892 PetscCall(PetscSectionGetChart(section, &pStart, &pEnd)); 6893 PetscCall(DMPlexGetConeSize(dm, point, &numPoints)); 6894 PetscCall(DMPlexGetCone(dm, point, &cone)); 6895 PetscCall(DMPlexGetConeOrientation(dm, point, &coneO)); 6896 PetscCall(VecGetArray(v, &array)); 6897 for (p = 0, off = 0; p <= numPoints; ++p, off += dof) { 6898 const PetscInt cp = !p ? point : cone[p - 1]; 6899 const PetscInt o = !p ? 0 : coneO[p - 1]; 6900 6901 if ((cp < pStart) || (cp >= pEnd)) { 6902 dof = 0; 6903 continue; 6904 } 6905 PetscCall(PetscSectionGetDof(section, cp, &dof)); 6906 /* ADD_VALUES */ 6907 { 6908 const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ 6909 PetscScalar *a; 6910 PetscInt cdof, coff, cind = 0, k; 6911 6912 PetscCall(PetscSectionGetConstraintDof(section, cp, &cdof)); 6913 PetscCall(PetscSectionGetOffset(section, cp, &coff)); 6914 a = &array[coff]; 6915 if (!cdof) { 6916 if (o >= 0) { 6917 for (k = 0; k < dof; ++k) a[k] += values[off + k]; 6918 } else { 6919 for (k = 0; k < dof; ++k) a[k] += values[off + dof - k - 1]; 6920 } 6921 } else { 6922 PetscCall(PetscSectionGetConstraintIndices(section, cp, &cdofs)); 6923 if (o >= 0) { 6924 for (k = 0; k < dof; ++k) { 6925 if ((cind < cdof) && (k == cdofs[cind])) { 6926 ++cind; 6927 continue; 6928 } 6929 a[k] += values[off + k]; 6930 } 6931 } else { 6932 for (k = 0; k < dof; ++k) { 6933 if ((cind < cdof) && (k == cdofs[cind])) { 6934 ++cind; 6935 continue; 6936 } 6937 a[k] += values[off + dof - k - 1]; 6938 } 6939 } 6940 } 6941 } 6942 } 6943 PetscCall(VecRestoreArray(v, &array)); 6944 PetscFunctionReturn(PETSC_SUCCESS); 6945 } 6946 6947 /*@C 6948 DMPlexVecSetClosure - Set an array of the values on the closure of `point` 6949 6950 Not collective 6951 6952 Input Parameters: 6953 + dm - The `DM` 6954 . section - The section describing the layout in `v`, or `NULL` to use the default section 6955 . v - The local vector 6956 . point - The point in the `DM` 6957 . values - The array of values 6958 - mode - The insert mode. One of `INSERT_ALL_VALUES`, `ADD_ALL_VALUES`, `INSERT_VALUES`, `ADD_VALUES`, `INSERT_BC_VALUES`, and `ADD_BC_VALUES`, 6959 where `INSERT_ALL_VALUES` and `ADD_ALL_VALUES` also overwrite boundary conditions. 6960 6961 Level: intermediate 6962 6963 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexVecGetClosure()`, `DMPlexMatSetClosure()` 6964 @*/ 6965 PetscErrorCode DMPlexVecSetClosure(DM dm, PetscSection section, Vec v, PetscInt point, const PetscScalar values[], InsertMode mode) 6966 { 6967 PetscSection clSection; 6968 IS clPoints; 6969 PetscScalar *array; 6970 PetscInt *points = NULL; 6971 const PetscInt *clp, *clperm = NULL; 6972 PetscInt depth, numFields, numPoints, p, clsize; 6973 6974 PetscFunctionBeginHot; 6975 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6976 if (!section) PetscCall(DMGetLocalSection(dm, §ion)); 6977 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 6978 PetscValidHeaderSpecific(v, VEC_CLASSID, 3); 6979 PetscCall(DMPlexGetDepth(dm, &depth)); 6980 PetscCall(PetscSectionGetNumFields(section, &numFields)); 6981 if (depth == 1 && numFields < 2 && mode == ADD_VALUES) { 6982 PetscCall(DMPlexVecSetClosure_Depth1_Static(dm, section, v, point, values, mode)); 6983 PetscFunctionReturn(PETSC_SUCCESS); 6984 } 6985 /* Get points */ 6986 PetscCall(DMPlexGetCompressedClosure(dm, section, point, 0, &numPoints, &points, &clSection, &clPoints, &clp)); 6987 for (clsize = 0, p = 0; p < numPoints; p++) { 6988 PetscInt dof; 6989 PetscCall(PetscSectionGetDof(section, points[2 * p], &dof)); 6990 clsize += dof; 6991 } 6992 PetscCall(PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject)dm, depth, clsize, &clperm)); 6993 /* Get array */ 6994 PetscCall(VecGetArray(v, &array)); 6995 /* Get values */ 6996 if (numFields > 0) { 6997 PetscInt offset = 0, f; 6998 for (f = 0; f < numFields; ++f) { 6999 const PetscInt **perms = NULL; 7000 const PetscScalar **flips = NULL; 7001 7002 PetscCall(PetscSectionGetFieldPointSyms(section, f, numPoints, points, &perms, &flips)); 7003 switch (mode) { 7004 case INSERT_VALUES: 7005 for (p = 0; p < numPoints; p++) { 7006 const PetscInt point = points[2 * p]; 7007 const PetscInt *perm = perms ? perms[p] : NULL; 7008 const PetscScalar *flip = flips ? flips[p] : NULL; 7009 PetscCall(updatePointFields_private(section, point, perm, flip, f, insert, PETSC_FALSE, clperm, values, &offset, array)); 7010 } 7011 break; 7012 case INSERT_ALL_VALUES: 7013 for (p = 0; p < numPoints; p++) { 7014 const PetscInt point = points[2 * p]; 7015 const PetscInt *perm = perms ? perms[p] : NULL; 7016 const PetscScalar *flip = flips ? flips[p] : NULL; 7017 PetscCall(updatePointFields_private(section, point, perm, flip, f, insert, PETSC_TRUE, clperm, values, &offset, array)); 7018 } 7019 break; 7020 case INSERT_BC_VALUES: 7021 for (p = 0; p < numPoints; p++) { 7022 const PetscInt point = points[2 * p]; 7023 const PetscInt *perm = perms ? perms[p] : NULL; 7024 const PetscScalar *flip = flips ? flips[p] : NULL; 7025 PetscCall(updatePointFieldsBC_private(section, point, perm, flip, f, -1, NULL, insert, clperm, values, &offset, array)); 7026 } 7027 break; 7028 case ADD_VALUES: 7029 for (p = 0; p < numPoints; p++) { 7030 const PetscInt point = points[2 * p]; 7031 const PetscInt *perm = perms ? perms[p] : NULL; 7032 const PetscScalar *flip = flips ? flips[p] : NULL; 7033 PetscCall(updatePointFields_private(section, point, perm, flip, f, add, PETSC_FALSE, clperm, values, &offset, array)); 7034 } 7035 break; 7036 case ADD_ALL_VALUES: 7037 for (p = 0; p < numPoints; p++) { 7038 const PetscInt point = points[2 * p]; 7039 const PetscInt *perm = perms ? perms[p] : NULL; 7040 const PetscScalar *flip = flips ? flips[p] : NULL; 7041 PetscCall(updatePointFields_private(section, point, perm, flip, f, add, PETSC_TRUE, clperm, values, &offset, array)); 7042 } 7043 break; 7044 case ADD_BC_VALUES: 7045 for (p = 0; p < numPoints; p++) { 7046 const PetscInt point = points[2 * p]; 7047 const PetscInt *perm = perms ? perms[p] : NULL; 7048 const PetscScalar *flip = flips ? flips[p] : NULL; 7049 PetscCall(updatePointFieldsBC_private(section, point, perm, flip, f, -1, NULL, add, clperm, values, &offset, array)); 7050 } 7051 break; 7052 default: 7053 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode); 7054 } 7055 PetscCall(PetscSectionRestoreFieldPointSyms(section, f, numPoints, points, &perms, &flips)); 7056 } 7057 } else { 7058 PetscInt dof, off; 7059 const PetscInt **perms = NULL; 7060 const PetscScalar **flips = NULL; 7061 7062 PetscCall(PetscSectionGetPointSyms(section, numPoints, points, &perms, &flips)); 7063 switch (mode) { 7064 case INSERT_VALUES: 7065 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 7066 const PetscInt point = points[2 * p]; 7067 const PetscInt *perm = perms ? perms[p] : NULL; 7068 const PetscScalar *flip = flips ? flips[p] : NULL; 7069 PetscCall(PetscSectionGetDof(section, point, &dof)); 7070 PetscCall(updatePoint_private(section, point, dof, insert, PETSC_FALSE, perm, flip, clperm, values, off, array)); 7071 } 7072 break; 7073 case INSERT_ALL_VALUES: 7074 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 7075 const PetscInt point = points[2 * p]; 7076 const PetscInt *perm = perms ? perms[p] : NULL; 7077 const PetscScalar *flip = flips ? flips[p] : NULL; 7078 PetscCall(PetscSectionGetDof(section, point, &dof)); 7079 PetscCall(updatePoint_private(section, point, dof, insert, PETSC_TRUE, perm, flip, clperm, values, off, array)); 7080 } 7081 break; 7082 case INSERT_BC_VALUES: 7083 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 7084 const PetscInt point = points[2 * p]; 7085 const PetscInt *perm = perms ? perms[p] : NULL; 7086 const PetscScalar *flip = flips ? flips[p] : NULL; 7087 PetscCall(PetscSectionGetDof(section, point, &dof)); 7088 PetscCall(updatePointBC_private(section, point, dof, insert, perm, flip, clperm, values, off, array)); 7089 } 7090 break; 7091 case ADD_VALUES: 7092 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 7093 const PetscInt point = points[2 * p]; 7094 const PetscInt *perm = perms ? perms[p] : NULL; 7095 const PetscScalar *flip = flips ? flips[p] : NULL; 7096 PetscCall(PetscSectionGetDof(section, point, &dof)); 7097 PetscCall(updatePoint_private(section, point, dof, add, PETSC_FALSE, perm, flip, clperm, values, off, array)); 7098 } 7099 break; 7100 case ADD_ALL_VALUES: 7101 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 7102 const PetscInt point = points[2 * p]; 7103 const PetscInt *perm = perms ? perms[p] : NULL; 7104 const PetscScalar *flip = flips ? flips[p] : NULL; 7105 PetscCall(PetscSectionGetDof(section, point, &dof)); 7106 PetscCall(updatePoint_private(section, point, dof, add, PETSC_TRUE, perm, flip, clperm, values, off, array)); 7107 } 7108 break; 7109 case ADD_BC_VALUES: 7110 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 7111 const PetscInt point = points[2 * p]; 7112 const PetscInt *perm = perms ? perms[p] : NULL; 7113 const PetscScalar *flip = flips ? flips[p] : NULL; 7114 PetscCall(PetscSectionGetDof(section, point, &dof)); 7115 PetscCall(updatePointBC_private(section, point, dof, add, perm, flip, clperm, values, off, array)); 7116 } 7117 break; 7118 default: 7119 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode); 7120 } 7121 PetscCall(PetscSectionRestorePointSyms(section, numPoints, points, &perms, &flips)); 7122 } 7123 /* Cleanup points */ 7124 PetscCall(DMPlexRestoreCompressedClosure(dm, section, point, &numPoints, &points, &clSection, &clPoints, &clp)); 7125 /* Cleanup array */ 7126 PetscCall(VecRestoreArray(v, &array)); 7127 PetscFunctionReturn(PETSC_SUCCESS); 7128 } 7129 7130 /* Check whether the given point is in the label. If not, update the offset to skip this point */ 7131 static inline PetscErrorCode CheckPoint_Private(DMLabel label, PetscInt labelId, PetscSection section, PetscInt point, PetscInt f, PetscInt *offset, PetscBool *contains) 7132 { 7133 PetscFunctionBegin; 7134 *contains = PETSC_TRUE; 7135 if (label) { 7136 PetscInt fdof; 7137 7138 PetscCall(DMLabelStratumHasPoint(label, labelId, point, contains)); 7139 if (!*contains) { 7140 PetscCall(PetscSectionGetFieldDof(section, point, f, &fdof)); 7141 *offset += fdof; 7142 PetscFunctionReturn(PETSC_SUCCESS); 7143 } 7144 } 7145 PetscFunctionReturn(PETSC_SUCCESS); 7146 } 7147 7148 /* Unlike DMPlexVecSetClosure(), this uses plex-native closure permutation, not a user-specified permutation such as DMPlexSetClosurePermutationTensor(). */ 7149 PetscErrorCode DMPlexVecSetFieldClosure_Internal(DM dm, PetscSection section, Vec v, PetscBool fieldActive[], PetscInt point, PetscInt Ncc, const PetscInt comps[], DMLabel label, PetscInt labelId, const PetscScalar values[], InsertMode mode) 7150 { 7151 PetscSection clSection; 7152 IS clPoints; 7153 PetscScalar *array; 7154 PetscInt *points = NULL; 7155 const PetscInt *clp; 7156 PetscInt numFields, numPoints, p; 7157 PetscInt offset = 0, f; 7158 7159 PetscFunctionBeginHot; 7160 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 7161 if (!section) PetscCall(DMGetLocalSection(dm, §ion)); 7162 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 7163 PetscValidHeaderSpecific(v, VEC_CLASSID, 3); 7164 PetscCall(PetscSectionGetNumFields(section, &numFields)); 7165 /* Get points */ 7166 PetscCall(DMPlexGetCompressedClosure(dm, section, point, 0, &numPoints, &points, &clSection, &clPoints, &clp)); 7167 /* Get array */ 7168 PetscCall(VecGetArray(v, &array)); 7169 /* Get values */ 7170 for (f = 0; f < numFields; ++f) { 7171 const PetscInt **perms = NULL; 7172 const PetscScalar **flips = NULL; 7173 PetscBool contains; 7174 7175 if (!fieldActive[f]) { 7176 for (p = 0; p < numPoints * 2; p += 2) { 7177 PetscInt fdof; 7178 PetscCall(PetscSectionGetFieldDof(section, points[p], f, &fdof)); 7179 offset += fdof; 7180 } 7181 continue; 7182 } 7183 PetscCall(PetscSectionGetFieldPointSyms(section, f, numPoints, points, &perms, &flips)); 7184 switch (mode) { 7185 case INSERT_VALUES: 7186 for (p = 0; p < numPoints; p++) { 7187 const PetscInt point = points[2 * p]; 7188 const PetscInt *perm = perms ? perms[p] : NULL; 7189 const PetscScalar *flip = flips ? flips[p] : NULL; 7190 PetscCall(CheckPoint_Private(label, labelId, section, point, f, &offset, &contains)); 7191 if (!contains) continue; 7192 PetscCall(updatePointFields_private(section, point, perm, flip, f, insert, PETSC_FALSE, NULL, values, &offset, array)); 7193 } 7194 break; 7195 case INSERT_ALL_VALUES: 7196 for (p = 0; p < numPoints; p++) { 7197 const PetscInt point = points[2 * p]; 7198 const PetscInt *perm = perms ? perms[p] : NULL; 7199 const PetscScalar *flip = flips ? flips[p] : NULL; 7200 PetscCall(CheckPoint_Private(label, labelId, section, point, f, &offset, &contains)); 7201 if (!contains) continue; 7202 PetscCall(updatePointFields_private(section, point, perm, flip, f, insert, PETSC_TRUE, NULL, values, &offset, array)); 7203 } 7204 break; 7205 case INSERT_BC_VALUES: 7206 for (p = 0; p < numPoints; p++) { 7207 const PetscInt point = points[2 * p]; 7208 const PetscInt *perm = perms ? perms[p] : NULL; 7209 const PetscScalar *flip = flips ? flips[p] : NULL; 7210 PetscCall(CheckPoint_Private(label, labelId, section, point, f, &offset, &contains)); 7211 if (!contains) continue; 7212 PetscCall(updatePointFieldsBC_private(section, point, perm, flip, f, Ncc, comps, insert, NULL, values, &offset, array)); 7213 } 7214 break; 7215 case ADD_VALUES: 7216 for (p = 0; p < numPoints; p++) { 7217 const PetscInt point = points[2 * p]; 7218 const PetscInt *perm = perms ? perms[p] : NULL; 7219 const PetscScalar *flip = flips ? flips[p] : NULL; 7220 PetscCall(CheckPoint_Private(label, labelId, section, point, f, &offset, &contains)); 7221 if (!contains) continue; 7222 PetscCall(updatePointFields_private(section, point, perm, flip, f, add, PETSC_FALSE, NULL, values, &offset, array)); 7223 } 7224 break; 7225 case ADD_ALL_VALUES: 7226 for (p = 0; p < numPoints; p++) { 7227 const PetscInt point = points[2 * p]; 7228 const PetscInt *perm = perms ? perms[p] : NULL; 7229 const PetscScalar *flip = flips ? flips[p] : NULL; 7230 PetscCall(CheckPoint_Private(label, labelId, section, point, f, &offset, &contains)); 7231 if (!contains) continue; 7232 PetscCall(updatePointFields_private(section, point, perm, flip, f, add, PETSC_TRUE, NULL, values, &offset, array)); 7233 } 7234 break; 7235 default: 7236 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode); 7237 } 7238 PetscCall(PetscSectionRestoreFieldPointSyms(section, f, numPoints, points, &perms, &flips)); 7239 } 7240 /* Cleanup points */ 7241 PetscCall(DMPlexRestoreCompressedClosure(dm, section, point, &numPoints, &points, &clSection, &clPoints, &clp)); 7242 /* Cleanup array */ 7243 PetscCall(VecRestoreArray(v, &array)); 7244 PetscFunctionReturn(PETSC_SUCCESS); 7245 } 7246 7247 static PetscErrorCode DMPlexPrintMatSetValues(PetscViewer viewer, Mat A, PetscInt point, PetscInt numRIndices, const PetscInt rindices[], PetscInt numCIndices, const PetscInt cindices[], const PetscScalar values[]) 7248 { 7249 PetscMPIInt rank; 7250 PetscInt i, j; 7251 7252 PetscFunctionBegin; 7253 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank)); 7254 PetscCall(PetscViewerASCIIPrintf(viewer, "[%d]mat for point %" PetscInt_FMT "\n", rank, point)); 7255 for (i = 0; i < numRIndices; i++) PetscCall(PetscViewerASCIIPrintf(viewer, "[%d]mat row indices[%" PetscInt_FMT "] = %" PetscInt_FMT "\n", rank, i, rindices[i])); 7256 for (i = 0; i < numCIndices; i++) PetscCall(PetscViewerASCIIPrintf(viewer, "[%d]mat col indices[%" PetscInt_FMT "] = %" PetscInt_FMT "\n", rank, i, cindices[i])); 7257 numCIndices = numCIndices ? numCIndices : numRIndices; 7258 if (!values) PetscFunctionReturn(PETSC_SUCCESS); 7259 for (i = 0; i < numRIndices; i++) { 7260 PetscCall(PetscViewerASCIIPrintf(viewer, "[%d]", rank)); 7261 for (j = 0; j < numCIndices; j++) { 7262 #if defined(PETSC_USE_COMPLEX) 7263 PetscCall(PetscViewerASCIIPrintf(viewer, " (%g,%g)", (double)PetscRealPart(values[i * numCIndices + j]), (double)PetscImaginaryPart(values[i * numCIndices + j]))); 7264 #else 7265 PetscCall(PetscViewerASCIIPrintf(viewer, " %g", (double)values[i * numCIndices + j])); 7266 #endif 7267 } 7268 PetscCall(PetscViewerASCIIPrintf(viewer, "\n")); 7269 } 7270 PetscFunctionReturn(PETSC_SUCCESS); 7271 } 7272 7273 /* 7274 DMPlexGetIndicesPoint_Internal - Add the indices for dofs on a point to an index array 7275 7276 Input Parameters: 7277 + section - The section for this data layout 7278 . islocal - Is the section (and thus indices being requested) local or global? 7279 . point - The point contributing dofs with these indices 7280 . off - The global offset of this point 7281 . loff - The local offset of each field 7282 . setBC - The flag determining whether to include indices of boundary values 7283 . perm - A permutation of the dofs on this point, or NULL 7284 - indperm - A permutation of the entire indices array, or NULL 7285 7286 Output Parameter: 7287 . indices - Indices for dofs on this point 7288 7289 Level: developer 7290 7291 Note: The indices could be local or global, depending on the value of 'off'. 7292 */ 7293 PetscErrorCode DMPlexGetIndicesPoint_Internal(PetscSection section, PetscBool islocal, PetscInt point, PetscInt off, PetscInt *loff, PetscBool setBC, const PetscInt perm[], const PetscInt indperm[], PetscInt indices[]) 7294 { 7295 PetscInt dof; /* The number of unknowns on this point */ 7296 PetscInt cdof; /* The number of constraints on this point */ 7297 const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ 7298 PetscInt cind = 0, k; 7299 7300 PetscFunctionBegin; 7301 PetscCheck(islocal || !setBC, PetscObjectComm((PetscObject)section), PETSC_ERR_ARG_INCOMP, "setBC incompatible with global indices; use a local section or disable setBC"); 7302 PetscCall(PetscSectionGetDof(section, point, &dof)); 7303 PetscCall(PetscSectionGetConstraintDof(section, point, &cdof)); 7304 if (!cdof || setBC) { 7305 for (k = 0; k < dof; ++k) { 7306 const PetscInt preind = perm ? *loff + perm[k] : *loff + k; 7307 const PetscInt ind = indperm ? indperm[preind] : preind; 7308 7309 indices[ind] = off + k; 7310 } 7311 } else { 7312 PetscCall(PetscSectionGetConstraintIndices(section, point, &cdofs)); 7313 for (k = 0; k < dof; ++k) { 7314 const PetscInt preind = perm ? *loff + perm[k] : *loff + k; 7315 const PetscInt ind = indperm ? indperm[preind] : preind; 7316 7317 if ((cind < cdof) && (k == cdofs[cind])) { 7318 /* Insert check for returning constrained indices */ 7319 indices[ind] = -(off + k + 1); 7320 ++cind; 7321 } else { 7322 indices[ind] = off + k - (islocal ? 0 : cind); 7323 } 7324 } 7325 } 7326 *loff += dof; 7327 PetscFunctionReturn(PETSC_SUCCESS); 7328 } 7329 7330 /* 7331 DMPlexGetIndicesPointFields_Internal - gets section indices for a point in its canonical ordering. 7332 7333 Input Parameters: 7334 + section - a section (global or local) 7335 - islocal - `PETSC_TRUE` if requesting local indices (i.e., section is local); `PETSC_FALSE` for global 7336 . point - point within section 7337 . off - The offset of this point in the (local or global) indexed space - should match islocal and (usually) the section 7338 . foffs - array of length numFields containing the offset in canonical point ordering (the location in indices) of each field 7339 . setBC - identify constrained (boundary condition) points via involution. 7340 . perms - perms[f][permsoff][:] is a permutation of dofs within each field 7341 . permsoff - offset 7342 - indperm - index permutation 7343 7344 Output Parameter: 7345 . foffs - each entry is incremented by the number of (unconstrained if setBC=FALSE) dofs in that field 7346 . indices - array to hold indices (as defined by section) of each dof associated with point 7347 7348 Notes: 7349 If section is local and setBC=true, there is no distinction between constrained and unconstrained dofs. 7350 If section is local and setBC=false, the indices for constrained points are the involution -(i+1) of their position 7351 in the local vector. 7352 7353 If section is global and setBC=false, the indices for constrained points are negative (and their value is not 7354 significant). It is invalid to call with a global section and setBC=true. 7355 7356 Developer Note: 7357 The section is only used for field layout, so islocal is technically a statement about the offset (off). At some point 7358 in the future, global sections may have fields set, in which case we could pass the global section and obtain the 7359 offset could be obtained from the section instead of passing it explicitly as we do now. 7360 7361 Example: 7362 Suppose a point contains one field with three components, and for which the unconstrained indices are {10, 11, 12}. 7363 When the middle component is constrained, we get the array {10, -12, 12} for (islocal=TRUE, setBC=FALSE). 7364 Note that -12 is the involution of 11, so the user can involute negative indices to recover local indices. 7365 The global vector does not store constrained dofs, so when this function returns global indices, say {110, -112, 111}, the value of -112 is an arbitrary flag that should not be interpreted beyond its sign. 7366 7367 Level: developer 7368 */ 7369 PetscErrorCode DMPlexGetIndicesPointFields_Internal(PetscSection section, PetscBool islocal, PetscInt point, PetscInt off, PetscInt foffs[], PetscBool setBC, const PetscInt ***perms, PetscInt permsoff, const PetscInt indperm[], PetscInt indices[]) 7370 { 7371 PetscInt numFields, foff, f; 7372 7373 PetscFunctionBegin; 7374 PetscCheck(islocal || !setBC, PetscObjectComm((PetscObject)section), PETSC_ERR_ARG_INCOMP, "setBC incompatible with global indices; use a local section or disable setBC"); 7375 PetscCall(PetscSectionGetNumFields(section, &numFields)); 7376 for (f = 0, foff = 0; f < numFields; ++f) { 7377 PetscInt fdof, cfdof; 7378 const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ 7379 PetscInt cind = 0, b; 7380 const PetscInt *perm = (perms && perms[f]) ? perms[f][permsoff] : NULL; 7381 7382 PetscCall(PetscSectionGetFieldDof(section, point, f, &fdof)); 7383 PetscCall(PetscSectionGetFieldConstraintDof(section, point, f, &cfdof)); 7384 if (!cfdof || setBC) { 7385 for (b = 0; b < fdof; ++b) { 7386 const PetscInt preind = perm ? foffs[f] + perm[b] : foffs[f] + b; 7387 const PetscInt ind = indperm ? indperm[preind] : preind; 7388 7389 indices[ind] = off + foff + b; 7390 } 7391 } else { 7392 PetscCall(PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs)); 7393 for (b = 0; b < fdof; ++b) { 7394 const PetscInt preind = perm ? foffs[f] + perm[b] : foffs[f] + b; 7395 const PetscInt ind = indperm ? indperm[preind] : preind; 7396 7397 if ((cind < cfdof) && (b == fcdofs[cind])) { 7398 indices[ind] = -(off + foff + b + 1); 7399 ++cind; 7400 } else { 7401 indices[ind] = off + foff + b - (islocal ? 0 : cind); 7402 } 7403 } 7404 } 7405 foff += (setBC || islocal ? fdof : (fdof - cfdof)); 7406 foffs[f] += fdof; 7407 } 7408 PetscFunctionReturn(PETSC_SUCCESS); 7409 } 7410 7411 /* 7412 This version believes the globalSection offsets for each field, rather than just the point offset 7413 7414 . foffs - The offset into 'indices' for each field, since it is segregated by field 7415 7416 Notes: 7417 The semantics of this function relate to that of setBC=FALSE in DMPlexGetIndicesPointFields_Internal. 7418 Since this function uses global indices, setBC=TRUE would be invalid, so no such argument exists. 7419 */ 7420 static PetscErrorCode DMPlexGetIndicesPointFieldsSplit_Internal(PetscSection section, PetscSection globalSection, PetscInt point, PetscInt foffs[], const PetscInt ***perms, PetscInt permsoff, const PetscInt indperm[], PetscInt indices[]) 7421 { 7422 PetscInt numFields, foff, f; 7423 7424 PetscFunctionBegin; 7425 PetscCall(PetscSectionGetNumFields(section, &numFields)); 7426 for (f = 0; f < numFields; ++f) { 7427 PetscInt fdof, cfdof; 7428 const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ 7429 PetscInt cind = 0, b; 7430 const PetscInt *perm = (perms && perms[f]) ? perms[f][permsoff] : NULL; 7431 7432 PetscCall(PetscSectionGetFieldDof(section, point, f, &fdof)); 7433 PetscCall(PetscSectionGetFieldConstraintDof(section, point, f, &cfdof)); 7434 PetscCall(PetscSectionGetFieldOffset(globalSection, point, f, &foff)); 7435 if (!cfdof) { 7436 for (b = 0; b < fdof; ++b) { 7437 const PetscInt preind = perm ? foffs[f] + perm[b] : foffs[f] + b; 7438 const PetscInt ind = indperm ? indperm[preind] : preind; 7439 7440 indices[ind] = foff + b; 7441 } 7442 } else { 7443 PetscCall(PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs)); 7444 for (b = 0; b < fdof; ++b) { 7445 const PetscInt preind = perm ? foffs[f] + perm[b] : foffs[f] + b; 7446 const PetscInt ind = indperm ? indperm[preind] : preind; 7447 7448 if ((cind < cfdof) && (b == fcdofs[cind])) { 7449 indices[ind] = -(foff + b + 1); 7450 ++cind; 7451 } else { 7452 indices[ind] = foff + b - cind; 7453 } 7454 } 7455 } 7456 foffs[f] += fdof; 7457 } 7458 PetscFunctionReturn(PETSC_SUCCESS); 7459 } 7460 7461 PetscErrorCode DMPlexAnchorsModifyMat(DM dm, PetscSection section, PetscInt numPoints, PetscInt numIndices, const PetscInt points[], const PetscInt ***perms, const PetscScalar values[], PetscInt *outNumPoints, PetscInt *outNumIndices, PetscInt *outPoints[], PetscScalar *outValues[], PetscInt offsets[], PetscBool multiplyLeft) 7462 { 7463 Mat cMat; 7464 PetscSection aSec, cSec; 7465 IS aIS; 7466 PetscInt aStart = -1, aEnd = -1; 7467 const PetscInt *anchors; 7468 PetscInt numFields, f, p, q, newP = 0; 7469 PetscInt newNumPoints = 0, newNumIndices = 0; 7470 PetscInt *newPoints, *indices, *newIndices; 7471 PetscInt maxAnchor, maxDof; 7472 PetscInt newOffsets[32]; 7473 PetscInt *pointMatOffsets[32]; 7474 PetscInt *newPointOffsets[32]; 7475 PetscScalar *pointMat[32]; 7476 PetscScalar *newValues = NULL, *tmpValues; 7477 PetscBool anyConstrained = PETSC_FALSE; 7478 7479 PetscFunctionBegin; 7480 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 7481 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 7482 PetscCall(PetscSectionGetNumFields(section, &numFields)); 7483 7484 PetscCall(DMPlexGetAnchors(dm, &aSec, &aIS)); 7485 /* if there are point-to-point constraints */ 7486 if (aSec) { 7487 PetscCall(PetscArrayzero(newOffsets, 32)); 7488 PetscCall(ISGetIndices(aIS, &anchors)); 7489 PetscCall(PetscSectionGetChart(aSec, &aStart, &aEnd)); 7490 /* figure out how many points are going to be in the new element matrix 7491 * (we allow double counting, because it's all just going to be summed 7492 * into the global matrix anyway) */ 7493 for (p = 0; p < 2 * numPoints; p += 2) { 7494 PetscInt b = points[p]; 7495 PetscInt bDof = 0, bSecDof; 7496 7497 PetscCall(PetscSectionGetDof(section, b, &bSecDof)); 7498 if (!bSecDof) continue; 7499 if (b >= aStart && b < aEnd) PetscCall(PetscSectionGetDof(aSec, b, &bDof)); 7500 if (bDof) { 7501 /* this point is constrained */ 7502 /* it is going to be replaced by its anchors */ 7503 PetscInt bOff, q; 7504 7505 anyConstrained = PETSC_TRUE; 7506 newNumPoints += bDof; 7507 PetscCall(PetscSectionGetOffset(aSec, b, &bOff)); 7508 for (q = 0; q < bDof; q++) { 7509 PetscInt a = anchors[bOff + q]; 7510 PetscInt aDof; 7511 7512 PetscCall(PetscSectionGetDof(section, a, &aDof)); 7513 newNumIndices += aDof; 7514 for (f = 0; f < numFields; ++f) { 7515 PetscInt fDof; 7516 7517 PetscCall(PetscSectionGetFieldDof(section, a, f, &fDof)); 7518 newOffsets[f + 1] += fDof; 7519 } 7520 } 7521 } else { 7522 /* this point is not constrained */ 7523 newNumPoints++; 7524 newNumIndices += bSecDof; 7525 for (f = 0; f < numFields; ++f) { 7526 PetscInt fDof; 7527 7528 PetscCall(PetscSectionGetFieldDof(section, b, f, &fDof)); 7529 newOffsets[f + 1] += fDof; 7530 } 7531 } 7532 } 7533 } 7534 if (!anyConstrained) { 7535 if (outNumPoints) *outNumPoints = 0; 7536 if (outNumIndices) *outNumIndices = 0; 7537 if (outPoints) *outPoints = NULL; 7538 if (outValues) *outValues = NULL; 7539 if (aSec) PetscCall(ISRestoreIndices(aIS, &anchors)); 7540 PetscFunctionReturn(PETSC_SUCCESS); 7541 } 7542 7543 if (outNumPoints) *outNumPoints = newNumPoints; 7544 if (outNumIndices) *outNumIndices = newNumIndices; 7545 7546 for (f = 0; f < numFields; ++f) newOffsets[f + 1] += newOffsets[f]; 7547 7548 if (!outPoints && !outValues) { 7549 if (offsets) { 7550 for (f = 0; f <= numFields; f++) offsets[f] = newOffsets[f]; 7551 } 7552 if (aSec) PetscCall(ISRestoreIndices(aIS, &anchors)); 7553 PetscFunctionReturn(PETSC_SUCCESS); 7554 } 7555 7556 PetscCheck(!numFields || newOffsets[numFields] == newNumIndices, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid size for closure %" PetscInt_FMT " should be %" PetscInt_FMT, newOffsets[numFields], newNumIndices); 7557 7558 PetscCall(DMGetDefaultConstraints(dm, &cSec, &cMat, NULL)); 7559 7560 /* workspaces */ 7561 if (numFields) { 7562 for (f = 0; f < numFields; f++) { 7563 PetscCall(DMGetWorkArray(dm, numPoints + 1, MPIU_INT, &pointMatOffsets[f])); 7564 PetscCall(DMGetWorkArray(dm, numPoints + 1, MPIU_INT, &newPointOffsets[f])); 7565 } 7566 } else { 7567 PetscCall(DMGetWorkArray(dm, numPoints + 1, MPIU_INT, &pointMatOffsets[0])); 7568 PetscCall(DMGetWorkArray(dm, numPoints, MPIU_INT, &newPointOffsets[0])); 7569 } 7570 7571 /* get workspaces for the point-to-point matrices */ 7572 if (numFields) { 7573 PetscInt totalOffset, totalMatOffset; 7574 7575 for (p = 0; p < numPoints; p++) { 7576 PetscInt b = points[2 * p]; 7577 PetscInt bDof = 0, bSecDof; 7578 7579 PetscCall(PetscSectionGetDof(section, b, &bSecDof)); 7580 if (!bSecDof) { 7581 for (f = 0; f < numFields; f++) { 7582 newPointOffsets[f][p + 1] = 0; 7583 pointMatOffsets[f][p + 1] = 0; 7584 } 7585 continue; 7586 } 7587 if (b >= aStart && b < aEnd) PetscCall(PetscSectionGetDof(aSec, b, &bDof)); 7588 if (bDof) { 7589 for (f = 0; f < numFields; f++) { 7590 PetscInt fDof, q, bOff, allFDof = 0; 7591 7592 PetscCall(PetscSectionGetFieldDof(section, b, f, &fDof)); 7593 PetscCall(PetscSectionGetOffset(aSec, b, &bOff)); 7594 for (q = 0; q < bDof; q++) { 7595 PetscInt a = anchors[bOff + q]; 7596 PetscInt aFDof; 7597 7598 PetscCall(PetscSectionGetFieldDof(section, a, f, &aFDof)); 7599 allFDof += aFDof; 7600 } 7601 newPointOffsets[f][p + 1] = allFDof; 7602 pointMatOffsets[f][p + 1] = fDof * allFDof; 7603 } 7604 } else { 7605 for (f = 0; f < numFields; f++) { 7606 PetscInt fDof; 7607 7608 PetscCall(PetscSectionGetFieldDof(section, b, f, &fDof)); 7609 newPointOffsets[f][p + 1] = fDof; 7610 pointMatOffsets[f][p + 1] = 0; 7611 } 7612 } 7613 } 7614 for (f = 0, totalOffset = 0, totalMatOffset = 0; f < numFields; f++) { 7615 newPointOffsets[f][0] = totalOffset; 7616 pointMatOffsets[f][0] = totalMatOffset; 7617 for (p = 0; p < numPoints; p++) { 7618 newPointOffsets[f][p + 1] += newPointOffsets[f][p]; 7619 pointMatOffsets[f][p + 1] += pointMatOffsets[f][p]; 7620 } 7621 totalOffset = newPointOffsets[f][numPoints]; 7622 totalMatOffset = pointMatOffsets[f][numPoints]; 7623 PetscCall(DMGetWorkArray(dm, pointMatOffsets[f][numPoints], MPIU_SCALAR, &pointMat[f])); 7624 } 7625 } else { 7626 for (p = 0; p < numPoints; p++) { 7627 PetscInt b = points[2 * p]; 7628 PetscInt bDof = 0, bSecDof; 7629 7630 PetscCall(PetscSectionGetDof(section, b, &bSecDof)); 7631 if (!bSecDof) { 7632 newPointOffsets[0][p + 1] = 0; 7633 pointMatOffsets[0][p + 1] = 0; 7634 continue; 7635 } 7636 if (b >= aStart && b < aEnd) PetscCall(PetscSectionGetDof(aSec, b, &bDof)); 7637 if (bDof) { 7638 PetscInt bOff, q, allDof = 0; 7639 7640 PetscCall(PetscSectionGetOffset(aSec, b, &bOff)); 7641 for (q = 0; q < bDof; q++) { 7642 PetscInt a = anchors[bOff + q], aDof; 7643 7644 PetscCall(PetscSectionGetDof(section, a, &aDof)); 7645 allDof += aDof; 7646 } 7647 newPointOffsets[0][p + 1] = allDof; 7648 pointMatOffsets[0][p + 1] = bSecDof * allDof; 7649 } else { 7650 newPointOffsets[0][p + 1] = bSecDof; 7651 pointMatOffsets[0][p + 1] = 0; 7652 } 7653 } 7654 newPointOffsets[0][0] = 0; 7655 pointMatOffsets[0][0] = 0; 7656 for (p = 0; p < numPoints; p++) { 7657 newPointOffsets[0][p + 1] += newPointOffsets[0][p]; 7658 pointMatOffsets[0][p + 1] += pointMatOffsets[0][p]; 7659 } 7660 PetscCall(DMGetWorkArray(dm, pointMatOffsets[0][numPoints], MPIU_SCALAR, &pointMat[0])); 7661 } 7662 7663 /* output arrays */ 7664 PetscCall(DMGetWorkArray(dm, 2 * newNumPoints, MPIU_INT, &newPoints)); 7665 7666 /* get the point-to-point matrices; construct newPoints */ 7667 PetscCall(PetscSectionGetMaxDof(aSec, &maxAnchor)); 7668 PetscCall(PetscSectionGetMaxDof(section, &maxDof)); 7669 PetscCall(DMGetWorkArray(dm, maxDof, MPIU_INT, &indices)); 7670 PetscCall(DMGetWorkArray(dm, maxAnchor * maxDof, MPIU_INT, &newIndices)); 7671 if (numFields) { 7672 for (p = 0, newP = 0; p < numPoints; p++) { 7673 PetscInt b = points[2 * p]; 7674 PetscInt o = points[2 * p + 1]; 7675 PetscInt bDof = 0, bSecDof; 7676 7677 PetscCall(PetscSectionGetDof(section, b, &bSecDof)); 7678 if (!bSecDof) continue; 7679 if (b >= aStart && b < aEnd) PetscCall(PetscSectionGetDof(aSec, b, &bDof)); 7680 if (bDof) { 7681 PetscInt fStart[32], fEnd[32], fAnchorStart[32], fAnchorEnd[32], bOff, q; 7682 7683 fStart[0] = 0; 7684 fEnd[0] = 0; 7685 for (f = 0; f < numFields; f++) { 7686 PetscInt fDof; 7687 7688 PetscCall(PetscSectionGetFieldDof(cSec, b, f, &fDof)); 7689 fStart[f + 1] = fStart[f] + fDof; 7690 fEnd[f + 1] = fStart[f + 1]; 7691 } 7692 PetscCall(PetscSectionGetOffset(cSec, b, &bOff)); 7693 PetscCall(DMPlexGetIndicesPointFields_Internal(cSec, PETSC_TRUE, b, bOff, fEnd, PETSC_TRUE, perms, p, NULL, indices)); 7694 7695 fAnchorStart[0] = 0; 7696 fAnchorEnd[0] = 0; 7697 for (f = 0; f < numFields; f++) { 7698 PetscInt fDof = newPointOffsets[f][p + 1] - newPointOffsets[f][p]; 7699 7700 fAnchorStart[f + 1] = fAnchorStart[f] + fDof; 7701 fAnchorEnd[f + 1] = fAnchorStart[f + 1]; 7702 } 7703 PetscCall(PetscSectionGetOffset(aSec, b, &bOff)); 7704 for (q = 0; q < bDof; q++) { 7705 PetscInt a = anchors[bOff + q], aOff; 7706 7707 /* we take the orientation of ap into account in the order that we constructed the indices above: the newly added points have no orientation */ 7708 newPoints[2 * (newP + q)] = a; 7709 newPoints[2 * (newP + q) + 1] = 0; 7710 PetscCall(PetscSectionGetOffset(section, a, &aOff)); 7711 PetscCall(DMPlexGetIndicesPointFields_Internal(section, PETSC_TRUE, a, aOff, fAnchorEnd, PETSC_TRUE, NULL, -1, NULL, newIndices)); 7712 } 7713 newP += bDof; 7714 7715 if (outValues) { 7716 /* get the point-to-point submatrix */ 7717 for (f = 0; f < numFields; f++) PetscCall(MatGetValues(cMat, fEnd[f] - fStart[f], indices + fStart[f], fAnchorEnd[f] - fAnchorStart[f], newIndices + fAnchorStart[f], pointMat[f] + pointMatOffsets[f][p])); 7718 } 7719 } else { 7720 newPoints[2 * newP] = b; 7721 newPoints[2 * newP + 1] = o; 7722 newP++; 7723 } 7724 } 7725 } else { 7726 for (p = 0; p < numPoints; p++) { 7727 PetscInt b = points[2 * p]; 7728 PetscInt o = points[2 * p + 1]; 7729 PetscInt bDof = 0, bSecDof; 7730 7731 PetscCall(PetscSectionGetDof(section, b, &bSecDof)); 7732 if (!bSecDof) continue; 7733 if (b >= aStart && b < aEnd) PetscCall(PetscSectionGetDof(aSec, b, &bDof)); 7734 if (bDof) { 7735 PetscInt bEnd = 0, bAnchorEnd = 0, bOff; 7736 7737 PetscCall(PetscSectionGetOffset(cSec, b, &bOff)); 7738 PetscCall(DMPlexGetIndicesPoint_Internal(cSec, PETSC_TRUE, b, bOff, &bEnd, PETSC_TRUE, (perms && perms[0]) ? perms[0][p] : NULL, NULL, indices)); 7739 7740 PetscCall(PetscSectionGetOffset(aSec, b, &bOff)); 7741 for (q = 0; q < bDof; q++) { 7742 PetscInt a = anchors[bOff + q], aOff; 7743 7744 /* we take the orientation of ap into account in the order that we constructed the indices above: the newly added points have no orientation */ 7745 7746 newPoints[2 * (newP + q)] = a; 7747 newPoints[2 * (newP + q) + 1] = 0; 7748 PetscCall(PetscSectionGetOffset(section, a, &aOff)); 7749 PetscCall(DMPlexGetIndicesPoint_Internal(section, PETSC_TRUE, a, aOff, &bAnchorEnd, PETSC_TRUE, NULL, NULL, newIndices)); 7750 } 7751 newP += bDof; 7752 7753 /* get the point-to-point submatrix */ 7754 if (outValues) PetscCall(MatGetValues(cMat, bEnd, indices, bAnchorEnd, newIndices, pointMat[0] + pointMatOffsets[0][p])); 7755 } else { 7756 newPoints[2 * newP] = b; 7757 newPoints[2 * newP + 1] = o; 7758 newP++; 7759 } 7760 } 7761 } 7762 7763 if (outValues) { 7764 PetscCall(DMGetWorkArray(dm, newNumIndices * numIndices, MPIU_SCALAR, &tmpValues)); 7765 PetscCall(PetscArrayzero(tmpValues, newNumIndices * numIndices)); 7766 /* multiply constraints on the right */ 7767 if (numFields) { 7768 for (f = 0; f < numFields; f++) { 7769 PetscInt oldOff = offsets[f]; 7770 7771 for (p = 0; p < numPoints; p++) { 7772 PetscInt cStart = newPointOffsets[f][p]; 7773 PetscInt b = points[2 * p]; 7774 PetscInt c, r, k; 7775 PetscInt dof; 7776 7777 PetscCall(PetscSectionGetFieldDof(section, b, f, &dof)); 7778 if (!dof) continue; 7779 if (pointMatOffsets[f][p] < pointMatOffsets[f][p + 1]) { 7780 PetscInt nCols = newPointOffsets[f][p + 1] - cStart; 7781 const PetscScalar *mat = pointMat[f] + pointMatOffsets[f][p]; 7782 7783 for (r = 0; r < numIndices; r++) { 7784 for (c = 0; c < nCols; c++) { 7785 for (k = 0; k < dof; k++) tmpValues[r * newNumIndices + cStart + c] += values[r * numIndices + oldOff + k] * mat[k * nCols + c]; 7786 } 7787 } 7788 } else { 7789 /* copy this column as is */ 7790 for (r = 0; r < numIndices; r++) { 7791 for (c = 0; c < dof; c++) tmpValues[r * newNumIndices + cStart + c] = values[r * numIndices + oldOff + c]; 7792 } 7793 } 7794 oldOff += dof; 7795 } 7796 } 7797 } else { 7798 PetscInt oldOff = 0; 7799 for (p = 0; p < numPoints; p++) { 7800 PetscInt cStart = newPointOffsets[0][p]; 7801 PetscInt b = points[2 * p]; 7802 PetscInt c, r, k; 7803 PetscInt dof; 7804 7805 PetscCall(PetscSectionGetDof(section, b, &dof)); 7806 if (!dof) continue; 7807 if (pointMatOffsets[0][p] < pointMatOffsets[0][p + 1]) { 7808 PetscInt nCols = newPointOffsets[0][p + 1] - cStart; 7809 const PetscScalar *mat = pointMat[0] + pointMatOffsets[0][p]; 7810 7811 for (r = 0; r < numIndices; r++) { 7812 for (c = 0; c < nCols; c++) { 7813 for (k = 0; k < dof; k++) tmpValues[r * newNumIndices + cStart + c] += mat[k * nCols + c] * values[r * numIndices + oldOff + k]; 7814 } 7815 } 7816 } else { 7817 /* copy this column as is */ 7818 for (r = 0; r < numIndices; r++) { 7819 for (c = 0; c < dof; c++) tmpValues[r * newNumIndices + cStart + c] = values[r * numIndices + oldOff + c]; 7820 } 7821 } 7822 oldOff += dof; 7823 } 7824 } 7825 7826 if (multiplyLeft) { 7827 PetscCall(DMGetWorkArray(dm, newNumIndices * newNumIndices, MPIU_SCALAR, &newValues)); 7828 PetscCall(PetscArrayzero(newValues, newNumIndices * newNumIndices)); 7829 /* multiply constraints transpose on the left */ 7830 if (numFields) { 7831 for (f = 0; f < numFields; f++) { 7832 PetscInt oldOff = offsets[f]; 7833 7834 for (p = 0; p < numPoints; p++) { 7835 PetscInt rStart = newPointOffsets[f][p]; 7836 PetscInt b = points[2 * p]; 7837 PetscInt c, r, k; 7838 PetscInt dof; 7839 7840 PetscCall(PetscSectionGetFieldDof(section, b, f, &dof)); 7841 if (pointMatOffsets[f][p] < pointMatOffsets[f][p + 1]) { 7842 PetscInt nRows = newPointOffsets[f][p + 1] - rStart; 7843 const PetscScalar *PETSC_RESTRICT mat = pointMat[f] + pointMatOffsets[f][p]; 7844 7845 for (r = 0; r < nRows; r++) { 7846 for (c = 0; c < newNumIndices; c++) { 7847 for (k = 0; k < dof; k++) newValues[(rStart + r) * newNumIndices + c] += mat[k * nRows + r] * tmpValues[(oldOff + k) * newNumIndices + c]; 7848 } 7849 } 7850 } else { 7851 /* copy this row as is */ 7852 for (r = 0; r < dof; r++) { 7853 for (c = 0; c < newNumIndices; c++) newValues[(rStart + r) * newNumIndices + c] = tmpValues[(oldOff + r) * newNumIndices + c]; 7854 } 7855 } 7856 oldOff += dof; 7857 } 7858 } 7859 } else { 7860 PetscInt oldOff = 0; 7861 7862 for (p = 0; p < numPoints; p++) { 7863 PetscInt rStart = newPointOffsets[0][p]; 7864 PetscInt b = points[2 * p]; 7865 PetscInt c, r, k; 7866 PetscInt dof; 7867 7868 PetscCall(PetscSectionGetDof(section, b, &dof)); 7869 if (pointMatOffsets[0][p] < pointMatOffsets[0][p + 1]) { 7870 PetscInt nRows = newPointOffsets[0][p + 1] - rStart; 7871 const PetscScalar *PETSC_RESTRICT mat = pointMat[0] + pointMatOffsets[0][p]; 7872 7873 for (r = 0; r < nRows; r++) { 7874 for (c = 0; c < newNumIndices; c++) { 7875 for (k = 0; k < dof; k++) newValues[(rStart + r) * newNumIndices + c] += mat[k * nRows + r] * tmpValues[(oldOff + k) * newNumIndices + c]; 7876 } 7877 } 7878 } else { 7879 /* copy this row as is */ 7880 for (r = 0; r < dof; r++) { 7881 for (c = 0; c < newNumIndices; c++) newValues[(rStart + r) * newNumIndices + c] = tmpValues[(oldOff + r) * newNumIndices + c]; 7882 } 7883 } 7884 oldOff += dof; 7885 } 7886 } 7887 7888 PetscCall(DMRestoreWorkArray(dm, newNumIndices * numIndices, MPIU_SCALAR, &tmpValues)); 7889 } else { 7890 newValues = tmpValues; 7891 } 7892 } 7893 7894 /* clean up */ 7895 PetscCall(DMRestoreWorkArray(dm, maxDof, MPIU_INT, &indices)); 7896 PetscCall(DMRestoreWorkArray(dm, maxAnchor * maxDof, MPIU_INT, &newIndices)); 7897 7898 if (numFields) { 7899 for (f = 0; f < numFields; f++) { 7900 PetscCall(DMRestoreWorkArray(dm, pointMatOffsets[f][numPoints], MPIU_SCALAR, &pointMat[f])); 7901 PetscCall(DMRestoreWorkArray(dm, numPoints + 1, MPIU_INT, &pointMatOffsets[f])); 7902 PetscCall(DMRestoreWorkArray(dm, numPoints + 1, MPIU_INT, &newPointOffsets[f])); 7903 } 7904 } else { 7905 PetscCall(DMRestoreWorkArray(dm, pointMatOffsets[0][numPoints], MPIU_SCALAR, &pointMat[0])); 7906 PetscCall(DMRestoreWorkArray(dm, numPoints + 1, MPIU_INT, &pointMatOffsets[0])); 7907 PetscCall(DMRestoreWorkArray(dm, numPoints + 1, MPIU_INT, &newPointOffsets[0])); 7908 } 7909 PetscCall(ISRestoreIndices(aIS, &anchors)); 7910 7911 /* output */ 7912 if (outPoints) { 7913 *outPoints = newPoints; 7914 } else { 7915 PetscCall(DMRestoreWorkArray(dm, 2 * newNumPoints, MPIU_INT, &newPoints)); 7916 } 7917 if (outValues) *outValues = newValues; 7918 for (f = 0; f <= numFields; f++) offsets[f] = newOffsets[f]; 7919 PetscFunctionReturn(PETSC_SUCCESS); 7920 } 7921 7922 /*@C 7923 DMPlexGetClosureIndices - Gets the global dof indices associated with the closure of the given point within the provided sections. 7924 7925 Not collective 7926 7927 Input Parameters: 7928 + dm - The `DM` 7929 . section - The `PetscSection` describing the points (a local section) 7930 . idxSection - The `PetscSection` from which to obtain indices (may be local or global) 7931 . point - The point defining the closure 7932 - useClPerm - Use the closure point permutation if available 7933 7934 Output Parameters: 7935 + numIndices - The number of dof indices in the closure of point with the input sections 7936 . indices - The dof indices 7937 . outOffsets - Array to write the field offsets into, or `NULL` 7938 - values - The input values, which may be modified if sign flips are induced by the point symmetries, or `NULL` 7939 7940 Level: advanced 7941 7942 Notes: 7943 Must call `DMPlexRestoreClosureIndices()` to free allocated memory 7944 7945 If `idxSection` is global, any constrained dofs (see `DMAddBoundary()`, for example) will get negative indices. The value 7946 of those indices is not significant. If `idxSection` is local, the constrained dofs will yield the involution -(idx+1) 7947 of their index in a local vector. A caller who does not wish to distinguish those points may recover the nonnegative 7948 indices via involution, -(-(idx+1)+1)==idx. Local indices are provided when `idxSection` == section, otherwise global 7949 indices (with the above semantics) are implied. 7950 7951 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexRestoreClosureIndices()`, `DMPlexVecGetClosure()`, `DMPlexMatSetClosure()`, `DMGetLocalSection()`, 7952 `PetscSection`, `DMGetGlobalSection()` 7953 @*/ 7954 PetscErrorCode DMPlexGetClosureIndices(DM dm, PetscSection section, PetscSection idxSection, PetscInt point, PetscBool useClPerm, PetscInt *numIndices, PetscInt *indices[], PetscInt outOffsets[], PetscScalar *values[]) 7955 { 7956 /* Closure ordering */ 7957 PetscSection clSection; 7958 IS clPoints; 7959 const PetscInt *clp; 7960 PetscInt *points; 7961 const PetscInt *clperm = NULL; 7962 /* Dof permutation and sign flips */ 7963 const PetscInt **perms[32] = {NULL}; 7964 const PetscScalar **flips[32] = {NULL}; 7965 PetscScalar *valCopy = NULL; 7966 /* Hanging node constraints */ 7967 PetscInt *pointsC = NULL; 7968 PetscScalar *valuesC = NULL; 7969 PetscInt NclC, NiC; 7970 7971 PetscInt *idx; 7972 PetscInt Nf, Ncl, Ni = 0, offsets[32], p, f; 7973 PetscBool isLocal = (section == idxSection) ? PETSC_TRUE : PETSC_FALSE; 7974 7975 PetscFunctionBeginHot; 7976 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 7977 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 7978 PetscValidHeaderSpecific(idxSection, PETSC_SECTION_CLASSID, 3); 7979 if (numIndices) PetscAssertPointer(numIndices, 6); 7980 if (indices) PetscAssertPointer(indices, 7); 7981 if (outOffsets) PetscAssertPointer(outOffsets, 8); 7982 if (values) PetscAssertPointer(values, 9); 7983 PetscCall(PetscSectionGetNumFields(section, &Nf)); 7984 PetscCheck(Nf <= 31, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %" PetscInt_FMT " limited to 31", Nf); 7985 PetscCall(PetscArrayzero(offsets, 32)); 7986 /* 1) Get points in closure */ 7987 PetscCall(DMPlexGetCompressedClosure(dm, section, point, 0, &Ncl, &points, &clSection, &clPoints, &clp)); 7988 if (useClPerm) { 7989 PetscInt depth, clsize; 7990 PetscCall(DMPlexGetPointDepth(dm, point, &depth)); 7991 for (clsize = 0, p = 0; p < Ncl; p++) { 7992 PetscInt dof; 7993 PetscCall(PetscSectionGetDof(section, points[2 * p], &dof)); 7994 clsize += dof; 7995 } 7996 PetscCall(PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject)dm, depth, clsize, &clperm)); 7997 } 7998 /* 2) Get number of indices on these points and field offsets from section */ 7999 for (p = 0; p < Ncl * 2; p += 2) { 8000 PetscInt dof, fdof; 8001 8002 PetscCall(PetscSectionGetDof(section, points[p], &dof)); 8003 for (f = 0; f < Nf; ++f) { 8004 PetscCall(PetscSectionGetFieldDof(section, points[p], f, &fdof)); 8005 offsets[f + 1] += fdof; 8006 } 8007 Ni += dof; 8008 } 8009 for (f = 1; f < Nf; ++f) offsets[f + 1] += offsets[f]; 8010 PetscCheck(!Nf || offsets[Nf] == Ni, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid size for closure %" PetscInt_FMT " should be %" PetscInt_FMT, offsets[Nf], Ni); 8011 /* 3) Get symmetries and sign flips. Apply sign flips to values if passed in (only works for square values matrix) */ 8012 for (f = 0; f < PetscMax(1, Nf); ++f) { 8013 if (Nf) PetscCall(PetscSectionGetFieldPointSyms(section, f, Ncl, points, &perms[f], &flips[f])); 8014 else PetscCall(PetscSectionGetPointSyms(section, Ncl, points, &perms[f], &flips[f])); 8015 /* may need to apply sign changes to the element matrix */ 8016 if (values && flips[f]) { 8017 PetscInt foffset = offsets[f]; 8018 8019 for (p = 0; p < Ncl; ++p) { 8020 PetscInt pnt = points[2 * p], fdof; 8021 const PetscScalar *flip = flips[f] ? flips[f][p] : NULL; 8022 8023 if (!Nf) PetscCall(PetscSectionGetDof(section, pnt, &fdof)); 8024 else PetscCall(PetscSectionGetFieldDof(section, pnt, f, &fdof)); 8025 if (flip) { 8026 PetscInt i, j, k; 8027 8028 if (!valCopy) { 8029 PetscCall(DMGetWorkArray(dm, Ni * Ni, MPIU_SCALAR, &valCopy)); 8030 for (j = 0; j < Ni * Ni; ++j) valCopy[j] = (*values)[j]; 8031 *values = valCopy; 8032 } 8033 for (i = 0; i < fdof; ++i) { 8034 PetscScalar fval = flip[i]; 8035 8036 for (k = 0; k < Ni; ++k) { 8037 valCopy[Ni * (foffset + i) + k] *= fval; 8038 valCopy[Ni * k + (foffset + i)] *= fval; 8039 } 8040 } 8041 } 8042 foffset += fdof; 8043 } 8044 } 8045 } 8046 /* 4) Apply hanging node constraints. Get new symmetries and replace all storage with constrained storage */ 8047 PetscCall(DMPlexAnchorsModifyMat(dm, section, Ncl, Ni, points, perms, values ? *values : NULL, &NclC, &NiC, &pointsC, values ? &valuesC : NULL, offsets, PETSC_TRUE)); 8048 if (NclC) { 8049 if (valCopy) PetscCall(DMRestoreWorkArray(dm, Ni * Ni, MPIU_SCALAR, &valCopy)); 8050 for (f = 0; f < PetscMax(1, Nf); ++f) { 8051 if (Nf) PetscCall(PetscSectionRestoreFieldPointSyms(section, f, Ncl, points, &perms[f], &flips[f])); 8052 else PetscCall(PetscSectionRestorePointSyms(section, Ncl, points, &perms[f], &flips[f])); 8053 } 8054 for (f = 0; f < PetscMax(1, Nf); ++f) { 8055 if (Nf) PetscCall(PetscSectionGetFieldPointSyms(section, f, NclC, pointsC, &perms[f], &flips[f])); 8056 else PetscCall(PetscSectionGetPointSyms(section, NclC, pointsC, &perms[f], &flips[f])); 8057 } 8058 PetscCall(DMPlexRestoreCompressedClosure(dm, section, point, &Ncl, &points, &clSection, &clPoints, &clp)); 8059 Ncl = NclC; 8060 Ni = NiC; 8061 points = pointsC; 8062 if (values) *values = valuesC; 8063 } 8064 /* 5) Calculate indices */ 8065 PetscCall(DMGetWorkArray(dm, Ni, MPIU_INT, &idx)); 8066 if (Nf) { 8067 PetscInt idxOff; 8068 PetscBool useFieldOffsets; 8069 8070 if (outOffsets) { 8071 for (f = 0; f <= Nf; f++) outOffsets[f] = offsets[f]; 8072 } 8073 PetscCall(PetscSectionGetUseFieldOffsets(idxSection, &useFieldOffsets)); 8074 if (useFieldOffsets) { 8075 for (p = 0; p < Ncl; ++p) { 8076 const PetscInt pnt = points[p * 2]; 8077 8078 PetscCall(DMPlexGetIndicesPointFieldsSplit_Internal(section, idxSection, pnt, offsets, perms, p, clperm, idx)); 8079 } 8080 } else { 8081 for (p = 0; p < Ncl; ++p) { 8082 const PetscInt pnt = points[p * 2]; 8083 8084 PetscCall(PetscSectionGetOffset(idxSection, pnt, &idxOff)); 8085 /* Note that we pass a local section even though we're using global offsets. This is because global sections do 8086 * not (at the time of this writing) have fields set. They probably should, in which case we would pass the 8087 * global section. */ 8088 PetscCall(DMPlexGetIndicesPointFields_Internal(section, isLocal, pnt, idxOff < 0 ? -(idxOff + 1) : idxOff, offsets, PETSC_FALSE, perms, p, clperm, idx)); 8089 } 8090 } 8091 } else { 8092 PetscInt off = 0, idxOff; 8093 8094 for (p = 0; p < Ncl; ++p) { 8095 const PetscInt pnt = points[p * 2]; 8096 const PetscInt *perm = perms[0] ? perms[0][p] : NULL; 8097 8098 PetscCall(PetscSectionGetOffset(idxSection, pnt, &idxOff)); 8099 /* Note that we pass a local section even though we're using global offsets. This is because global sections do 8100 * not (at the time of this writing) have fields set. They probably should, in which case we would pass the global section. */ 8101 PetscCall(DMPlexGetIndicesPoint_Internal(section, isLocal, pnt, idxOff < 0 ? -(idxOff + 1) : idxOff, &off, PETSC_FALSE, perm, clperm, idx)); 8102 } 8103 } 8104 /* 6) Cleanup */ 8105 for (f = 0; f < PetscMax(1, Nf); ++f) { 8106 if (Nf) PetscCall(PetscSectionRestoreFieldPointSyms(section, f, Ncl, points, &perms[f], &flips[f])); 8107 else PetscCall(PetscSectionRestorePointSyms(section, Ncl, points, &perms[f], &flips[f])); 8108 } 8109 if (NclC) { 8110 PetscCall(DMRestoreWorkArray(dm, NclC * 2, MPIU_INT, &pointsC)); 8111 } else { 8112 PetscCall(DMPlexRestoreCompressedClosure(dm, section, point, &Ncl, &points, &clSection, &clPoints, &clp)); 8113 } 8114 8115 if (numIndices) *numIndices = Ni; 8116 if (indices) *indices = idx; 8117 PetscFunctionReturn(PETSC_SUCCESS); 8118 } 8119 8120 /*@C 8121 DMPlexRestoreClosureIndices - Restores the global dof indices associated with the closure of the given point within the provided sections. 8122 8123 Not collective 8124 8125 Input Parameters: 8126 + dm - The `DM` 8127 . section - The `PetscSection` describing the points (a local section) 8128 . idxSection - The `PetscSection` from which to obtain indices (may be local or global) 8129 . point - The point defining the closure 8130 - useClPerm - Use the closure point permutation if available 8131 8132 Output Parameters: 8133 + numIndices - The number of dof indices in the closure of point with the input sections 8134 . indices - The dof indices 8135 . outOffsets - Array to write the field offsets into, or `NULL` 8136 - values - The input values, which may be modified if sign flips are induced by the point symmetries, or `NULL` 8137 8138 Level: advanced 8139 8140 Notes: 8141 If values were modified, the user is responsible for calling `DMRestoreWorkArray`(dm, 0, `MPIU_SCALAR`, &values). 8142 8143 If idxSection is global, any constrained dofs (see `DMAddBoundary()`, for example) will get negative indices. The value 8144 of those indices is not significant. If idxSection is local, the constrained dofs will yield the involution -(idx+1) 8145 of their index in a local vector. A caller who does not wish to distinguish those points may recover the nonnegative 8146 indices via involution, -(-(idx+1)+1)==idx. Local indices are provided when idxSection == section, otherwise global 8147 indices (with the above semantics) are implied. 8148 8149 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetClosureIndices()`, `DMPlexVecGetClosure()`, `DMPlexMatSetClosure()`, `DMGetLocalSection()`, `DMGetGlobalSection()` 8150 @*/ 8151 PetscErrorCode DMPlexRestoreClosureIndices(DM dm, PetscSection section, PetscSection idxSection, PetscInt point, PetscBool useClPerm, PetscInt *numIndices, PetscInt *indices[], PetscInt outOffsets[], PetscScalar *values[]) 8152 { 8153 PetscFunctionBegin; 8154 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8155 PetscAssertPointer(indices, 7); 8156 PetscCall(DMRestoreWorkArray(dm, 0, MPIU_INT, indices)); 8157 PetscFunctionReturn(PETSC_SUCCESS); 8158 } 8159 8160 PetscErrorCode DMPlexMatSetClosure_Internal(DM dm, PetscSection section, PetscSection globalSection, PetscBool useClPerm, Mat A, PetscInt point, const PetscScalar values[], InsertMode mode) 8161 { 8162 DM_Plex *mesh = (DM_Plex *)dm->data; 8163 PetscInt *indices; 8164 PetscInt numIndices; 8165 const PetscScalar *valuesOrig = values; 8166 PetscErrorCode ierr; 8167 8168 PetscFunctionBegin; 8169 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8170 if (!section) PetscCall(DMGetLocalSection(dm, §ion)); 8171 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 8172 if (!globalSection) PetscCall(DMGetGlobalSection(dm, &globalSection)); 8173 PetscValidHeaderSpecific(globalSection, PETSC_SECTION_CLASSID, 3); 8174 PetscValidHeaderSpecific(A, MAT_CLASSID, 5); 8175 8176 PetscCall(DMPlexGetClosureIndices(dm, section, globalSection, point, useClPerm, &numIndices, &indices, NULL, (PetscScalar **)&values)); 8177 8178 if (mesh->printSetValues) PetscCall(DMPlexPrintMatSetValues(PETSC_VIEWER_STDOUT_SELF, A, point, numIndices, indices, 0, NULL, values)); 8179 /* TODO: fix this code to not use error codes as handle-able exceptions! */ 8180 ierr = MatSetValues(A, numIndices, indices, numIndices, indices, values, mode); 8181 if (ierr) { 8182 PetscMPIInt rank; 8183 8184 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank)); 8185 PetscCall((*PetscErrorPrintf)("[%d]ERROR in DMPlexMatSetClosure\n", rank)); 8186 PetscCall(DMPlexPrintMatSetValues(PETSC_VIEWER_STDERR_SELF, A, point, numIndices, indices, 0, NULL, values)); 8187 PetscCall(DMPlexRestoreClosureIndices(dm, section, globalSection, point, PETSC_TRUE, &numIndices, &indices, NULL, (PetscScalar **)&values)); 8188 if (values != valuesOrig) PetscCall(DMRestoreWorkArray(dm, 0, MPIU_SCALAR, &values)); 8189 SETERRQ(PetscObjectComm((PetscObject)dm), ierr, "Not possible to set matrix values"); 8190 } 8191 if (mesh->printFEM > 1) { 8192 PetscInt i; 8193 PetscCall(PetscPrintf(PETSC_COMM_SELF, " Indices:")); 8194 for (i = 0; i < numIndices; ++i) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, indices[i])); 8195 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 8196 } 8197 8198 PetscCall(DMPlexRestoreClosureIndices(dm, section, globalSection, point, PETSC_TRUE, &numIndices, &indices, NULL, (PetscScalar **)&values)); 8199 if (values != valuesOrig) PetscCall(DMRestoreWorkArray(dm, 0, MPIU_SCALAR, &values)); 8200 PetscFunctionReturn(PETSC_SUCCESS); 8201 } 8202 8203 /*@C 8204 DMPlexMatSetClosure - Set an array of the values on the closure of 'point' 8205 8206 Not collective 8207 8208 Input Parameters: 8209 + dm - The `DM` 8210 . section - The section describing the layout in `v`, or `NULL` to use the default section 8211 . globalSection - The section describing the layout in `v`, or `NULL` to use the default global section 8212 . A - The matrix 8213 . point - The point in the `DM` 8214 . values - The array of values 8215 - mode - The insert mode, where `INSERT_ALL_VALUES` and `ADD_ALL_VALUES` also overwrite boundary conditions 8216 8217 Level: intermediate 8218 8219 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexMatSetClosureGeneral()`, `DMPlexVecGetClosure()`, `DMPlexVecSetClosure()` 8220 @*/ 8221 PetscErrorCode DMPlexMatSetClosure(DM dm, PetscSection section, PetscSection globalSection, Mat A, PetscInt point, const PetscScalar values[], InsertMode mode) 8222 { 8223 PetscFunctionBegin; 8224 PetscCall(DMPlexMatSetClosure_Internal(dm, section, globalSection, PETSC_TRUE, A, point, values, mode)); 8225 PetscFunctionReturn(PETSC_SUCCESS); 8226 } 8227 8228 /*@C 8229 DMPlexMatSetClosureGeneral - Set an array of the values on the closure of 'point' using a different row and column section 8230 8231 Not collective 8232 8233 Input Parameters: 8234 + dmRow - The `DM` for the row fields 8235 . sectionRow - The section describing the layout, or `NULL` to use the default section in `dmRow` 8236 . useRowPerm - The flag to use the closure permutation of the `dmRow` if available 8237 . globalSectionRow - The section describing the layout, or `NULL` to use the default global section in `dmRow` 8238 . dmCol - The `DM` for the column fields 8239 . sectionCol - The section describing the layout, or `NULL` to use the default section in `dmCol` 8240 . useColPerm - The flag to use the closure permutation of the `dmCol` if available 8241 . globalSectionCol - The section describing the layout, or `NULL` to use the default global section in `dmCol` 8242 . A - The matrix 8243 . point - The point in the `DM` 8244 . values - The array of values 8245 - mode - The insert mode, where `INSERT_ALL_VALUES` and `ADD_ALL_VALUES` also overwrite boundary conditions 8246 8247 Level: intermediate 8248 8249 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexMatSetClosure()`, `DMPlexVecGetClosure()`, `DMPlexVecSetClosure()` 8250 @*/ 8251 PetscErrorCode DMPlexMatSetClosureGeneral(DM dmRow, PetscSection sectionRow, PetscSection globalSectionRow, PetscBool useRowPerm, DM dmCol, PetscSection sectionCol, PetscSection globalSectionCol, PetscBool useColPerm, Mat A, PetscInt point, const PetscScalar values[], InsertMode mode) 8252 { 8253 DM_Plex *mesh = (DM_Plex *)dmRow->data; 8254 PetscInt *indicesRow, *indicesCol; 8255 PetscInt numIndicesRow, numIndicesCol; 8256 const PetscScalar *valuesOrig = values; 8257 PetscErrorCode ierr; 8258 8259 PetscFunctionBegin; 8260 PetscValidHeaderSpecific(dmRow, DM_CLASSID, 1); 8261 if (!sectionRow) PetscCall(DMGetLocalSection(dmRow, §ionRow)); 8262 PetscValidHeaderSpecific(sectionRow, PETSC_SECTION_CLASSID, 2); 8263 if (!globalSectionRow) PetscCall(DMGetGlobalSection(dmRow, &globalSectionRow)); 8264 PetscValidHeaderSpecific(globalSectionRow, PETSC_SECTION_CLASSID, 3); 8265 PetscValidHeaderSpecific(dmCol, DM_CLASSID, 5); 8266 if (!sectionCol) PetscCall(DMGetLocalSection(dmCol, §ionCol)); 8267 PetscValidHeaderSpecific(sectionCol, PETSC_SECTION_CLASSID, 6); 8268 if (!globalSectionCol) PetscCall(DMGetGlobalSection(dmCol, &globalSectionCol)); 8269 PetscValidHeaderSpecific(globalSectionCol, PETSC_SECTION_CLASSID, 7); 8270 PetscValidHeaderSpecific(A, MAT_CLASSID, 9); 8271 8272 PetscCall(DMPlexGetClosureIndices(dmRow, sectionRow, globalSectionRow, point, useRowPerm, &numIndicesRow, &indicesRow, NULL, (PetscScalar **)&values)); 8273 PetscCall(DMPlexGetClosureIndices(dmCol, sectionCol, globalSectionCol, point, useColPerm, &numIndicesCol, &indicesCol, NULL, (PetscScalar **)&values)); 8274 8275 if (mesh->printSetValues) PetscCall(DMPlexPrintMatSetValues(PETSC_VIEWER_STDOUT_SELF, A, point, numIndicesRow, indicesRow, numIndicesCol, indicesCol, values)); 8276 /* TODO: fix this code to not use error codes as handle-able exceptions! */ 8277 ierr = MatSetValues(A, numIndicesRow, indicesRow, numIndicesCol, indicesCol, values, mode); 8278 if (ierr) { 8279 PetscMPIInt rank; 8280 8281 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank)); 8282 PetscCall((*PetscErrorPrintf)("[%d]ERROR in DMPlexMatSetClosure\n", rank)); 8283 PetscCall(DMPlexPrintMatSetValues(PETSC_VIEWER_STDERR_SELF, A, point, numIndicesRow, indicesRow, numIndicesCol, indicesCol, values)); 8284 PetscCall(DMPlexRestoreClosureIndices(dmRow, sectionRow, globalSectionRow, point, PETSC_TRUE, &numIndicesRow, &indicesRow, NULL, (PetscScalar **)&values)); 8285 PetscCall(DMPlexRestoreClosureIndices(dmCol, sectionCol, globalSectionCol, point, PETSC_TRUE, &numIndicesCol, &indicesRow, NULL, (PetscScalar **)&values)); 8286 if (values != valuesOrig) PetscCall(DMRestoreWorkArray(dmRow, 0, MPIU_SCALAR, &values)); 8287 } 8288 8289 PetscCall(DMPlexRestoreClosureIndices(dmRow, sectionRow, globalSectionRow, point, useRowPerm, &numIndicesRow, &indicesRow, NULL, (PetscScalar **)&values)); 8290 PetscCall(DMPlexRestoreClosureIndices(dmCol, sectionCol, globalSectionCol, point, useColPerm, &numIndicesCol, &indicesCol, NULL, (PetscScalar **)&values)); 8291 if (values != valuesOrig) PetscCall(DMRestoreWorkArray(dmRow, 0, MPIU_SCALAR, &values)); 8292 PetscFunctionReturn(PETSC_SUCCESS); 8293 } 8294 8295 PetscErrorCode DMPlexMatSetClosureRefined(DM dmf, PetscSection fsection, PetscSection globalFSection, DM dmc, PetscSection csection, PetscSection globalCSection, Mat A, PetscInt point, const PetscScalar values[], InsertMode mode) 8296 { 8297 DM_Plex *mesh = (DM_Plex *)dmf->data; 8298 PetscInt *fpoints = NULL, *ftotpoints = NULL; 8299 PetscInt *cpoints = NULL; 8300 PetscInt *findices, *cindices; 8301 const PetscInt *fclperm = NULL, *cclperm = NULL; /* Closure permutations cannot work here */ 8302 PetscInt foffsets[32], coffsets[32]; 8303 DMPolytopeType ct; 8304 PetscInt numFields, numSubcells, maxFPoints, numFPoints, numCPoints, numFIndices, numCIndices, dof, off, globalOff, pStart, pEnd, p, q, r, s, f; 8305 PetscErrorCode ierr; 8306 8307 PetscFunctionBegin; 8308 PetscValidHeaderSpecific(dmf, DM_CLASSID, 1); 8309 PetscValidHeaderSpecific(dmc, DM_CLASSID, 4); 8310 if (!fsection) PetscCall(DMGetLocalSection(dmf, &fsection)); 8311 PetscValidHeaderSpecific(fsection, PETSC_SECTION_CLASSID, 2); 8312 if (!csection) PetscCall(DMGetLocalSection(dmc, &csection)); 8313 PetscValidHeaderSpecific(csection, PETSC_SECTION_CLASSID, 5); 8314 if (!globalFSection) PetscCall(DMGetGlobalSection(dmf, &globalFSection)); 8315 PetscValidHeaderSpecific(globalFSection, PETSC_SECTION_CLASSID, 3); 8316 if (!globalCSection) PetscCall(DMGetGlobalSection(dmc, &globalCSection)); 8317 PetscValidHeaderSpecific(globalCSection, PETSC_SECTION_CLASSID, 6); 8318 PetscValidHeaderSpecific(A, MAT_CLASSID, 7); 8319 PetscCall(PetscSectionGetNumFields(fsection, &numFields)); 8320 PetscCheck(numFields <= 31, PetscObjectComm((PetscObject)dmf), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %" PetscInt_FMT " limited to 31", numFields); 8321 PetscCall(PetscArrayzero(foffsets, 32)); 8322 PetscCall(PetscArrayzero(coffsets, 32)); 8323 /* Column indices */ 8324 PetscCall(DMPlexGetTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints)); 8325 maxFPoints = numCPoints; 8326 /* Compress out points not in the section */ 8327 /* TODO: Squeeze out points with 0 dof as well */ 8328 PetscCall(PetscSectionGetChart(csection, &pStart, &pEnd)); 8329 for (p = 0, q = 0; p < numCPoints * 2; p += 2) { 8330 if ((cpoints[p] >= pStart) && (cpoints[p] < pEnd)) { 8331 cpoints[q * 2] = cpoints[p]; 8332 cpoints[q * 2 + 1] = cpoints[p + 1]; 8333 ++q; 8334 } 8335 } 8336 numCPoints = q; 8337 for (p = 0, numCIndices = 0; p < numCPoints * 2; p += 2) { 8338 PetscInt fdof; 8339 8340 PetscCall(PetscSectionGetDof(csection, cpoints[p], &dof)); 8341 if (!dof) continue; 8342 for (f = 0; f < numFields; ++f) { 8343 PetscCall(PetscSectionGetFieldDof(csection, cpoints[p], f, &fdof)); 8344 coffsets[f + 1] += fdof; 8345 } 8346 numCIndices += dof; 8347 } 8348 for (f = 1; f < numFields; ++f) coffsets[f + 1] += coffsets[f]; 8349 /* Row indices */ 8350 PetscCall(DMPlexGetCellType(dmc, point, &ct)); 8351 { 8352 DMPlexTransform tr; 8353 DMPolytopeType *rct; 8354 PetscInt *rsize, *rcone, *rornt, Nt; 8355 8356 PetscCall(DMPlexTransformCreate(PETSC_COMM_SELF, &tr)); 8357 PetscCall(DMPlexTransformSetType(tr, DMPLEXREFINEREGULAR)); 8358 PetscCall(DMPlexTransformCellTransform(tr, ct, point, NULL, &Nt, &rct, &rsize, &rcone, &rornt)); 8359 numSubcells = rsize[Nt - 1]; 8360 PetscCall(DMPlexTransformDestroy(&tr)); 8361 } 8362 PetscCall(DMGetWorkArray(dmf, maxFPoints * 2 * numSubcells, MPIU_INT, &ftotpoints)); 8363 for (r = 0, q = 0; r < numSubcells; ++r) { 8364 /* TODO Map from coarse to fine cells */ 8365 PetscCall(DMPlexGetTransitiveClosure(dmf, point * numSubcells + r, PETSC_TRUE, &numFPoints, &fpoints)); 8366 /* Compress out points not in the section */ 8367 PetscCall(PetscSectionGetChart(fsection, &pStart, &pEnd)); 8368 for (p = 0; p < numFPoints * 2; p += 2) { 8369 if ((fpoints[p] >= pStart) && (fpoints[p] < pEnd)) { 8370 PetscCall(PetscSectionGetDof(fsection, fpoints[p], &dof)); 8371 if (!dof) continue; 8372 for (s = 0; s < q; ++s) 8373 if (fpoints[p] == ftotpoints[s * 2]) break; 8374 if (s < q) continue; 8375 ftotpoints[q * 2] = fpoints[p]; 8376 ftotpoints[q * 2 + 1] = fpoints[p + 1]; 8377 ++q; 8378 } 8379 } 8380 PetscCall(DMPlexRestoreTransitiveClosure(dmf, point, PETSC_TRUE, &numFPoints, &fpoints)); 8381 } 8382 numFPoints = q; 8383 for (p = 0, numFIndices = 0; p < numFPoints * 2; p += 2) { 8384 PetscInt fdof; 8385 8386 PetscCall(PetscSectionGetDof(fsection, ftotpoints[p], &dof)); 8387 if (!dof) continue; 8388 for (f = 0; f < numFields; ++f) { 8389 PetscCall(PetscSectionGetFieldDof(fsection, ftotpoints[p], f, &fdof)); 8390 foffsets[f + 1] += fdof; 8391 } 8392 numFIndices += dof; 8393 } 8394 for (f = 1; f < numFields; ++f) foffsets[f + 1] += foffsets[f]; 8395 8396 PetscCheck(!numFields || foffsets[numFields] == numFIndices, PetscObjectComm((PetscObject)dmf), PETSC_ERR_PLIB, "Invalid size for closure %" PetscInt_FMT " should be %" PetscInt_FMT, foffsets[numFields], numFIndices); 8397 PetscCheck(!numFields || coffsets[numFields] == numCIndices, PetscObjectComm((PetscObject)dmc), PETSC_ERR_PLIB, "Invalid size for closure %" PetscInt_FMT " should be %" PetscInt_FMT, coffsets[numFields], numCIndices); 8398 PetscCall(DMGetWorkArray(dmf, numFIndices, MPIU_INT, &findices)); 8399 PetscCall(DMGetWorkArray(dmc, numCIndices, MPIU_INT, &cindices)); 8400 if (numFields) { 8401 const PetscInt **permsF[32] = {NULL}; 8402 const PetscInt **permsC[32] = {NULL}; 8403 8404 for (f = 0; f < numFields; f++) { 8405 PetscCall(PetscSectionGetFieldPointSyms(fsection, f, numFPoints, ftotpoints, &permsF[f], NULL)); 8406 PetscCall(PetscSectionGetFieldPointSyms(csection, f, numCPoints, cpoints, &permsC[f], NULL)); 8407 } 8408 for (p = 0; p < numFPoints; p++) { 8409 PetscCall(PetscSectionGetOffset(globalFSection, ftotpoints[2 * p], &globalOff)); 8410 PetscCall(DMPlexGetIndicesPointFields_Internal(fsection, PETSC_FALSE, ftotpoints[2 * p], globalOff < 0 ? -(globalOff + 1) : globalOff, foffsets, PETSC_FALSE, permsF, p, fclperm, findices)); 8411 } 8412 for (p = 0; p < numCPoints; p++) { 8413 PetscCall(PetscSectionGetOffset(globalCSection, cpoints[2 * p], &globalOff)); 8414 PetscCall(DMPlexGetIndicesPointFields_Internal(csection, PETSC_FALSE, cpoints[2 * p], globalOff < 0 ? -(globalOff + 1) : globalOff, coffsets, PETSC_FALSE, permsC, p, cclperm, cindices)); 8415 } 8416 for (f = 0; f < numFields; f++) { 8417 PetscCall(PetscSectionRestoreFieldPointSyms(fsection, f, numFPoints, ftotpoints, &permsF[f], NULL)); 8418 PetscCall(PetscSectionRestoreFieldPointSyms(csection, f, numCPoints, cpoints, &permsC[f], NULL)); 8419 } 8420 } else { 8421 const PetscInt **permsF = NULL; 8422 const PetscInt **permsC = NULL; 8423 8424 PetscCall(PetscSectionGetPointSyms(fsection, numFPoints, ftotpoints, &permsF, NULL)); 8425 PetscCall(PetscSectionGetPointSyms(csection, numCPoints, cpoints, &permsC, NULL)); 8426 for (p = 0, off = 0; p < numFPoints; p++) { 8427 const PetscInt *perm = permsF ? permsF[p] : NULL; 8428 8429 PetscCall(PetscSectionGetOffset(globalFSection, ftotpoints[2 * p], &globalOff)); 8430 PetscCall(DMPlexGetIndicesPoint_Internal(fsection, PETSC_FALSE, ftotpoints[2 * p], globalOff < 0 ? -(globalOff + 1) : globalOff, &off, PETSC_FALSE, perm, fclperm, findices)); 8431 } 8432 for (p = 0, off = 0; p < numCPoints; p++) { 8433 const PetscInt *perm = permsC ? permsC[p] : NULL; 8434 8435 PetscCall(PetscSectionGetOffset(globalCSection, cpoints[2 * p], &globalOff)); 8436 PetscCall(DMPlexGetIndicesPoint_Internal(csection, PETSC_FALSE, cpoints[2 * p], globalOff < 0 ? -(globalOff + 1) : globalOff, &off, PETSC_FALSE, perm, cclperm, cindices)); 8437 } 8438 PetscCall(PetscSectionRestorePointSyms(fsection, numFPoints, ftotpoints, &permsF, NULL)); 8439 PetscCall(PetscSectionRestorePointSyms(csection, numCPoints, cpoints, &permsC, NULL)); 8440 } 8441 if (mesh->printSetValues) PetscCall(DMPlexPrintMatSetValues(PETSC_VIEWER_STDOUT_SELF, A, point, numFIndices, findices, numCIndices, cindices, values)); 8442 /* TODO: flips */ 8443 /* TODO: fix this code to not use error codes as handle-able exceptions! */ 8444 ierr = MatSetValues(A, numFIndices, findices, numCIndices, cindices, values, mode); 8445 if (ierr) { 8446 PetscMPIInt rank; 8447 8448 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank)); 8449 PetscCall((*PetscErrorPrintf)("[%d]ERROR in DMPlexMatSetClosure\n", rank)); 8450 PetscCall(DMPlexPrintMatSetValues(PETSC_VIEWER_STDERR_SELF, A, point, numFIndices, findices, numCIndices, cindices, values)); 8451 PetscCall(DMRestoreWorkArray(dmf, numFIndices, MPIU_INT, &findices)); 8452 PetscCall(DMRestoreWorkArray(dmc, numCIndices, MPIU_INT, &cindices)); 8453 } 8454 PetscCall(DMRestoreWorkArray(dmf, numCPoints * 2 * 4, MPIU_INT, &ftotpoints)); 8455 PetscCall(DMPlexRestoreTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints)); 8456 PetscCall(DMRestoreWorkArray(dmf, numFIndices, MPIU_INT, &findices)); 8457 PetscCall(DMRestoreWorkArray(dmc, numCIndices, MPIU_INT, &cindices)); 8458 PetscFunctionReturn(PETSC_SUCCESS); 8459 } 8460 8461 PetscErrorCode DMPlexMatGetClosureIndicesRefined(DM dmf, PetscSection fsection, PetscSection globalFSection, DM dmc, PetscSection csection, PetscSection globalCSection, PetscInt point, PetscInt cindices[], PetscInt findices[]) 8462 { 8463 PetscInt *fpoints = NULL, *ftotpoints = NULL; 8464 PetscInt *cpoints = NULL; 8465 PetscInt foffsets[32] = {0}, coffsets[32] = {0}; 8466 const PetscInt *fclperm = NULL, *cclperm = NULL; /* Closure permutations cannot work here */ 8467 DMPolytopeType ct; 8468 PetscInt numFields, numSubcells, maxFPoints, numFPoints, numCPoints, numFIndices, numCIndices, dof, off, globalOff, pStart, pEnd, p, q, r, s, f; 8469 8470 PetscFunctionBegin; 8471 PetscValidHeaderSpecific(dmf, DM_CLASSID, 1); 8472 PetscValidHeaderSpecific(dmc, DM_CLASSID, 4); 8473 if (!fsection) PetscCall(DMGetLocalSection(dmf, &fsection)); 8474 PetscValidHeaderSpecific(fsection, PETSC_SECTION_CLASSID, 2); 8475 if (!csection) PetscCall(DMGetLocalSection(dmc, &csection)); 8476 PetscValidHeaderSpecific(csection, PETSC_SECTION_CLASSID, 5); 8477 if (!globalFSection) PetscCall(DMGetGlobalSection(dmf, &globalFSection)); 8478 PetscValidHeaderSpecific(globalFSection, PETSC_SECTION_CLASSID, 3); 8479 if (!globalCSection) PetscCall(DMGetGlobalSection(dmc, &globalCSection)); 8480 PetscValidHeaderSpecific(globalCSection, PETSC_SECTION_CLASSID, 6); 8481 PetscCall(PetscSectionGetNumFields(fsection, &numFields)); 8482 PetscCheck(numFields <= 31, PetscObjectComm((PetscObject)dmf), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %" PetscInt_FMT " limited to 31", numFields); 8483 /* Column indices */ 8484 PetscCall(DMPlexGetTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints)); 8485 maxFPoints = numCPoints; 8486 /* Compress out points not in the section */ 8487 /* TODO: Squeeze out points with 0 dof as well */ 8488 PetscCall(PetscSectionGetChart(csection, &pStart, &pEnd)); 8489 for (p = 0, q = 0; p < numCPoints * 2; p += 2) { 8490 if ((cpoints[p] >= pStart) && (cpoints[p] < pEnd)) { 8491 cpoints[q * 2] = cpoints[p]; 8492 cpoints[q * 2 + 1] = cpoints[p + 1]; 8493 ++q; 8494 } 8495 } 8496 numCPoints = q; 8497 for (p = 0, numCIndices = 0; p < numCPoints * 2; p += 2) { 8498 PetscInt fdof; 8499 8500 PetscCall(PetscSectionGetDof(csection, cpoints[p], &dof)); 8501 if (!dof) continue; 8502 for (f = 0; f < numFields; ++f) { 8503 PetscCall(PetscSectionGetFieldDof(csection, cpoints[p], f, &fdof)); 8504 coffsets[f + 1] += fdof; 8505 } 8506 numCIndices += dof; 8507 } 8508 for (f = 1; f < numFields; ++f) coffsets[f + 1] += coffsets[f]; 8509 /* Row indices */ 8510 PetscCall(DMPlexGetCellType(dmc, point, &ct)); 8511 { 8512 DMPlexTransform tr; 8513 DMPolytopeType *rct; 8514 PetscInt *rsize, *rcone, *rornt, Nt; 8515 8516 PetscCall(DMPlexTransformCreate(PETSC_COMM_SELF, &tr)); 8517 PetscCall(DMPlexTransformSetType(tr, DMPLEXREFINEREGULAR)); 8518 PetscCall(DMPlexTransformCellTransform(tr, ct, point, NULL, &Nt, &rct, &rsize, &rcone, &rornt)); 8519 numSubcells = rsize[Nt - 1]; 8520 PetscCall(DMPlexTransformDestroy(&tr)); 8521 } 8522 PetscCall(DMGetWorkArray(dmf, maxFPoints * 2 * numSubcells, MPIU_INT, &ftotpoints)); 8523 for (r = 0, q = 0; r < numSubcells; ++r) { 8524 /* TODO Map from coarse to fine cells */ 8525 PetscCall(DMPlexGetTransitiveClosure(dmf, point * numSubcells + r, PETSC_TRUE, &numFPoints, &fpoints)); 8526 /* Compress out points not in the section */ 8527 PetscCall(PetscSectionGetChart(fsection, &pStart, &pEnd)); 8528 for (p = 0; p < numFPoints * 2; p += 2) { 8529 if ((fpoints[p] >= pStart) && (fpoints[p] < pEnd)) { 8530 PetscCall(PetscSectionGetDof(fsection, fpoints[p], &dof)); 8531 if (!dof) continue; 8532 for (s = 0; s < q; ++s) 8533 if (fpoints[p] == ftotpoints[s * 2]) break; 8534 if (s < q) continue; 8535 ftotpoints[q * 2] = fpoints[p]; 8536 ftotpoints[q * 2 + 1] = fpoints[p + 1]; 8537 ++q; 8538 } 8539 } 8540 PetscCall(DMPlexRestoreTransitiveClosure(dmf, point, PETSC_TRUE, &numFPoints, &fpoints)); 8541 } 8542 numFPoints = q; 8543 for (p = 0, numFIndices = 0; p < numFPoints * 2; p += 2) { 8544 PetscInt fdof; 8545 8546 PetscCall(PetscSectionGetDof(fsection, ftotpoints[p], &dof)); 8547 if (!dof) continue; 8548 for (f = 0; f < numFields; ++f) { 8549 PetscCall(PetscSectionGetFieldDof(fsection, ftotpoints[p], f, &fdof)); 8550 foffsets[f + 1] += fdof; 8551 } 8552 numFIndices += dof; 8553 } 8554 for (f = 1; f < numFields; ++f) foffsets[f + 1] += foffsets[f]; 8555 8556 PetscCheck(!numFields || foffsets[numFields] == numFIndices, PetscObjectComm((PetscObject)dmf), PETSC_ERR_PLIB, "Invalid size for closure %" PetscInt_FMT " should be %" PetscInt_FMT, foffsets[numFields], numFIndices); 8557 PetscCheck(!numFields || coffsets[numFields] == numCIndices, PetscObjectComm((PetscObject)dmc), PETSC_ERR_PLIB, "Invalid size for closure %" PetscInt_FMT " should be %" PetscInt_FMT, coffsets[numFields], numCIndices); 8558 if (numFields) { 8559 const PetscInt **permsF[32] = {NULL}; 8560 const PetscInt **permsC[32] = {NULL}; 8561 8562 for (f = 0; f < numFields; f++) { 8563 PetscCall(PetscSectionGetFieldPointSyms(fsection, f, numFPoints, ftotpoints, &permsF[f], NULL)); 8564 PetscCall(PetscSectionGetFieldPointSyms(csection, f, numCPoints, cpoints, &permsC[f], NULL)); 8565 } 8566 for (p = 0; p < numFPoints; p++) { 8567 PetscCall(PetscSectionGetOffset(globalFSection, ftotpoints[2 * p], &globalOff)); 8568 PetscCall(DMPlexGetIndicesPointFields_Internal(fsection, PETSC_FALSE, ftotpoints[2 * p], globalOff < 0 ? -(globalOff + 1) : globalOff, foffsets, PETSC_FALSE, permsF, p, fclperm, findices)); 8569 } 8570 for (p = 0; p < numCPoints; p++) { 8571 PetscCall(PetscSectionGetOffset(globalCSection, cpoints[2 * p], &globalOff)); 8572 PetscCall(DMPlexGetIndicesPointFields_Internal(csection, PETSC_FALSE, cpoints[2 * p], globalOff < 0 ? -(globalOff + 1) : globalOff, coffsets, PETSC_FALSE, permsC, p, cclperm, cindices)); 8573 } 8574 for (f = 0; f < numFields; f++) { 8575 PetscCall(PetscSectionRestoreFieldPointSyms(fsection, f, numFPoints, ftotpoints, &permsF[f], NULL)); 8576 PetscCall(PetscSectionRestoreFieldPointSyms(csection, f, numCPoints, cpoints, &permsC[f], NULL)); 8577 } 8578 } else { 8579 const PetscInt **permsF = NULL; 8580 const PetscInt **permsC = NULL; 8581 8582 PetscCall(PetscSectionGetPointSyms(fsection, numFPoints, ftotpoints, &permsF, NULL)); 8583 PetscCall(PetscSectionGetPointSyms(csection, numCPoints, cpoints, &permsC, NULL)); 8584 for (p = 0, off = 0; p < numFPoints; p++) { 8585 const PetscInt *perm = permsF ? permsF[p] : NULL; 8586 8587 PetscCall(PetscSectionGetOffset(globalFSection, ftotpoints[2 * p], &globalOff)); 8588 PetscCall(DMPlexGetIndicesPoint_Internal(fsection, PETSC_FALSE, ftotpoints[2 * p], globalOff < 0 ? -(globalOff + 1) : globalOff, &off, PETSC_FALSE, perm, fclperm, findices)); 8589 } 8590 for (p = 0, off = 0; p < numCPoints; p++) { 8591 const PetscInt *perm = permsC ? permsC[p] : NULL; 8592 8593 PetscCall(PetscSectionGetOffset(globalCSection, cpoints[2 * p], &globalOff)); 8594 PetscCall(DMPlexGetIndicesPoint_Internal(csection, PETSC_FALSE, cpoints[2 * p], globalOff < 0 ? -(globalOff + 1) : globalOff, &off, PETSC_FALSE, perm, cclperm, cindices)); 8595 } 8596 PetscCall(PetscSectionRestorePointSyms(fsection, numFPoints, ftotpoints, &permsF, NULL)); 8597 PetscCall(PetscSectionRestorePointSyms(csection, numCPoints, cpoints, &permsC, NULL)); 8598 } 8599 PetscCall(DMRestoreWorkArray(dmf, numCPoints * 2 * 4, MPIU_INT, &ftotpoints)); 8600 PetscCall(DMPlexRestoreTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints)); 8601 PetscFunctionReturn(PETSC_SUCCESS); 8602 } 8603 8604 /*@C 8605 DMPlexGetVTKCellHeight - Returns the height in the DAG used to determine which points are cells (normally 0) 8606 8607 Input Parameter: 8608 . dm - The `DMPLEX` object 8609 8610 Output Parameter: 8611 . cellHeight - The height of a cell 8612 8613 Level: developer 8614 8615 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexSetVTKCellHeight()` 8616 @*/ 8617 PetscErrorCode DMPlexGetVTKCellHeight(DM dm, PetscInt *cellHeight) 8618 { 8619 DM_Plex *mesh = (DM_Plex *)dm->data; 8620 8621 PetscFunctionBegin; 8622 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8623 PetscAssertPointer(cellHeight, 2); 8624 *cellHeight = mesh->vtkCellHeight; 8625 PetscFunctionReturn(PETSC_SUCCESS); 8626 } 8627 8628 /*@C 8629 DMPlexSetVTKCellHeight - Sets the height in the DAG used to determine which points are cells (normally 0) 8630 8631 Input Parameters: 8632 + dm - The `DMPLEX` object 8633 - cellHeight - The height of a cell 8634 8635 Level: developer 8636 8637 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetVTKCellHeight()` 8638 @*/ 8639 PetscErrorCode DMPlexSetVTKCellHeight(DM dm, PetscInt cellHeight) 8640 { 8641 DM_Plex *mesh = (DM_Plex *)dm->data; 8642 8643 PetscFunctionBegin; 8644 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8645 mesh->vtkCellHeight = cellHeight; 8646 PetscFunctionReturn(PETSC_SUCCESS); 8647 } 8648 8649 /*@ 8650 DMPlexGetCellTypeStratum - Get the range of cells of a given celltype 8651 8652 Input Parameters: 8653 + dm - The `DMPLEX` object 8654 - ct - The `DMPolytopeType` of the cell 8655 8656 Output Parameters: 8657 + start - The first cell of this type, or `NULL` 8658 - end - The upper bound on this celltype, or `NULL` 8659 8660 Level: advanced 8661 8662 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexConstructGhostCells()`, `DMPlexGetDepthStratum()`, `DMPlexGetHeightStratum()` 8663 @*/ 8664 PetscErrorCode DMPlexGetCellTypeStratum(DM dm, DMPolytopeType ct, PetscInt *start, PetscInt *end) 8665 { 8666 DM_Plex *mesh = (DM_Plex *)dm->data; 8667 DMLabel label; 8668 PetscInt pStart, pEnd; 8669 8670 PetscFunctionBegin; 8671 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8672 if (start) { 8673 PetscAssertPointer(start, 3); 8674 *start = 0; 8675 } 8676 if (end) { 8677 PetscAssertPointer(end, 4); 8678 *end = 0; 8679 } 8680 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 8681 if (pStart == pEnd) PetscFunctionReturn(PETSC_SUCCESS); 8682 if (mesh->tr) { 8683 PetscCall(DMPlexTransformGetCellTypeStratum(mesh->tr, ct, start, end)); 8684 } else { 8685 PetscCall(DMPlexGetCellTypeLabel(dm, &label)); 8686 PetscCheck(label, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "No label named celltype was found"); 8687 PetscCall(DMLabelGetStratumBounds(label, ct, start, end)); 8688 } 8689 PetscFunctionReturn(PETSC_SUCCESS); 8690 } 8691 8692 PetscErrorCode DMPlexCreateNumbering_Plex(DM dm, PetscInt pStart, PetscInt pEnd, PetscInt shift, PetscInt *globalSize, PetscSF sf, IS *numbering) 8693 { 8694 PetscSection section, globalSection; 8695 PetscInt *numbers, p; 8696 8697 PetscFunctionBegin; 8698 if (PetscDefined(USE_DEBUG)) PetscCall(DMPlexCheckPointSF(dm, sf, PETSC_TRUE)); 8699 PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)dm), §ion)); 8700 PetscCall(PetscSectionSetChart(section, pStart, pEnd)); 8701 for (p = pStart; p < pEnd; ++p) PetscCall(PetscSectionSetDof(section, p, 1)); 8702 PetscCall(PetscSectionSetUp(section)); 8703 PetscCall(PetscSectionCreateGlobalSection(section, sf, PETSC_TRUE, PETSC_FALSE, PETSC_FALSE, &globalSection)); 8704 PetscCall(PetscMalloc1(pEnd - pStart, &numbers)); 8705 for (p = pStart; p < pEnd; ++p) { 8706 PetscCall(PetscSectionGetOffset(globalSection, p, &numbers[p - pStart])); 8707 if (numbers[p - pStart] < 0) numbers[p - pStart] -= shift; 8708 else numbers[p - pStart] += shift; 8709 } 8710 PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), pEnd - pStart, numbers, PETSC_OWN_POINTER, numbering)); 8711 if (globalSize) { 8712 PetscLayout layout; 8713 PetscCall(PetscSectionGetPointLayout(PetscObjectComm((PetscObject)dm), globalSection, &layout)); 8714 PetscCall(PetscLayoutGetSize(layout, globalSize)); 8715 PetscCall(PetscLayoutDestroy(&layout)); 8716 } 8717 PetscCall(PetscSectionDestroy(§ion)); 8718 PetscCall(PetscSectionDestroy(&globalSection)); 8719 PetscFunctionReturn(PETSC_SUCCESS); 8720 } 8721 8722 PetscErrorCode DMPlexCreateCellNumbering_Internal(DM dm, PetscBool includeHybrid, IS *globalCellNumbers) 8723 { 8724 PetscInt cellHeight, cStart, cEnd; 8725 8726 PetscFunctionBegin; 8727 PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight)); 8728 if (includeHybrid) PetscCall(DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd)); 8729 else PetscCall(DMPlexGetSimplexOrBoxCells(dm, cellHeight, &cStart, &cEnd)); 8730 PetscCall(DMPlexCreateNumbering_Plex(dm, cStart, cEnd, 0, NULL, dm->sf, globalCellNumbers)); 8731 PetscFunctionReturn(PETSC_SUCCESS); 8732 } 8733 8734 /*@ 8735 DMPlexGetCellNumbering - Get a global cell numbering for all cells on this process 8736 8737 Input Parameter: 8738 . dm - The `DMPLEX` object 8739 8740 Output Parameter: 8741 . globalCellNumbers - Global cell numbers for all cells on this process 8742 8743 Level: developer 8744 8745 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetVertexNumbering()` 8746 @*/ 8747 PetscErrorCode DMPlexGetCellNumbering(DM dm, IS *globalCellNumbers) 8748 { 8749 DM_Plex *mesh = (DM_Plex *)dm->data; 8750 8751 PetscFunctionBegin; 8752 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8753 if (!mesh->globalCellNumbers) PetscCall(DMPlexCreateCellNumbering_Internal(dm, PETSC_FALSE, &mesh->globalCellNumbers)); 8754 *globalCellNumbers = mesh->globalCellNumbers; 8755 PetscFunctionReturn(PETSC_SUCCESS); 8756 } 8757 8758 PetscErrorCode DMPlexCreateVertexNumbering_Internal(DM dm, PetscBool includeHybrid, IS *globalVertexNumbers) 8759 { 8760 PetscInt vStart, vEnd; 8761 8762 PetscFunctionBegin; 8763 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8764 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 8765 PetscCall(DMPlexCreateNumbering_Plex(dm, vStart, vEnd, 0, NULL, dm->sf, globalVertexNumbers)); 8766 PetscFunctionReturn(PETSC_SUCCESS); 8767 } 8768 8769 /*@ 8770 DMPlexGetVertexNumbering - Get a global vertex numbering for all vertices on this process 8771 8772 Input Parameter: 8773 . dm - The `DMPLEX` object 8774 8775 Output Parameter: 8776 . globalVertexNumbers - Global vertex numbers for all vertices on this process 8777 8778 Level: developer 8779 8780 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetCellNumbering()` 8781 @*/ 8782 PetscErrorCode DMPlexGetVertexNumbering(DM dm, IS *globalVertexNumbers) 8783 { 8784 DM_Plex *mesh = (DM_Plex *)dm->data; 8785 8786 PetscFunctionBegin; 8787 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8788 if (!mesh->globalVertexNumbers) PetscCall(DMPlexCreateVertexNumbering_Internal(dm, PETSC_FALSE, &mesh->globalVertexNumbers)); 8789 *globalVertexNumbers = mesh->globalVertexNumbers; 8790 PetscFunctionReturn(PETSC_SUCCESS); 8791 } 8792 8793 /*@ 8794 DMPlexCreatePointNumbering - Create a global numbering for all points. 8795 8796 Collective 8797 8798 Input Parameter: 8799 . dm - The `DMPLEX` object 8800 8801 Output Parameter: 8802 . globalPointNumbers - Global numbers for all points on this process 8803 8804 Level: developer 8805 8806 Notes: 8807 The point numbering `IS` is parallel, with local portion indexed by local points (see `DMGetLocalSection()`). The global 8808 points are taken as stratified, with each MPI rank owning a contiguous subset of each stratum. In the IS, owned points 8809 will have their non-negative value while points owned by different ranks will be involuted -(idx+1). As an example, 8810 consider a parallel mesh in which the first two elements and first two vertices are owned by rank 0. 8811 8812 The partitioned mesh is 8813 ``` 8814 (2)--0--(3)--1--(4) (1)--0--(2) 8815 ``` 8816 and its global numbering is 8817 ``` 8818 (3)--0--(4)--1--(5)--2--(6) 8819 ``` 8820 Then the global numbering is provided as 8821 ``` 8822 [0] Number of indices in set 5 8823 [0] 0 0 8824 [0] 1 1 8825 [0] 2 3 8826 [0] 3 4 8827 [0] 4 -6 8828 [1] Number of indices in set 3 8829 [1] 0 2 8830 [1] 1 5 8831 [1] 2 6 8832 ``` 8833 8834 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetCellNumbering()` 8835 @*/ 8836 PetscErrorCode DMPlexCreatePointNumbering(DM dm, IS *globalPointNumbers) 8837 { 8838 IS nums[4]; 8839 PetscInt depths[4], gdepths[4], starts[4]; 8840 PetscInt depth, d, shift = 0; 8841 PetscBool empty = PETSC_FALSE; 8842 8843 PetscFunctionBegin; 8844 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8845 PetscCall(DMPlexGetDepth(dm, &depth)); 8846 // For unstratified meshes use dim instead of depth 8847 if (depth < 0) PetscCall(DMGetDimension(dm, &depth)); 8848 // If any stratum is empty, we must mark all empty 8849 for (d = 0; d <= depth; ++d) { 8850 PetscInt end; 8851 8852 depths[d] = depth - d; 8853 PetscCall(DMPlexGetDepthStratum(dm, depths[d], &starts[d], &end)); 8854 if (!(starts[d] - end)) empty = PETSC_TRUE; 8855 } 8856 if (empty) 8857 for (d = 0; d <= depth; ++d) { 8858 depths[d] = -1; 8859 starts[d] = -1; 8860 } 8861 else PetscCall(PetscSortIntWithArray(depth + 1, starts, depths)); 8862 PetscCall(MPIU_Allreduce(depths, gdepths, depth + 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm))); 8863 for (d = 0; d <= depth; ++d) PetscCheck(starts[d] < 0 || depths[d] == gdepths[d], PETSC_COMM_SELF, PETSC_ERR_PLIB, "Expected depth %" PetscInt_FMT ", found %" PetscInt_FMT, depths[d], gdepths[d]); 8864 // Note here that 'shift' is collective, so that the numbering is stratified by depth 8865 for (d = 0; d <= depth; ++d) { 8866 PetscInt pStart, pEnd, gsize; 8867 8868 PetscCall(DMPlexGetDepthStratum(dm, gdepths[d], &pStart, &pEnd)); 8869 PetscCall(DMPlexCreateNumbering_Plex(dm, pStart, pEnd, shift, &gsize, dm->sf, &nums[d])); 8870 shift += gsize; 8871 } 8872 PetscCall(ISConcatenate(PETSC_COMM_SELF, depth + 1, nums, globalPointNumbers)); 8873 for (d = 0; d <= depth; ++d) PetscCall(ISDestroy(&nums[d])); 8874 PetscFunctionReturn(PETSC_SUCCESS); 8875 } 8876 8877 /*@ 8878 DMPlexCreateRankField - Create a cell field whose value is the rank of the owner 8879 8880 Input Parameter: 8881 . dm - The `DMPLEX` object 8882 8883 Output Parameter: 8884 . ranks - The rank field 8885 8886 Options Database Key: 8887 . -dm_partition_view - Adds the rank field into the `DM` output from `-dm_view` using the same viewer 8888 8889 Level: intermediate 8890 8891 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMView()` 8892 @*/ 8893 PetscErrorCode DMPlexCreateRankField(DM dm, Vec *ranks) 8894 { 8895 DM rdm; 8896 PetscFE fe; 8897 PetscScalar *r; 8898 PetscMPIInt rank; 8899 DMPolytopeType ct; 8900 PetscInt dim, cStart, cEnd, c; 8901 PetscBool simplex; 8902 8903 PetscFunctionBeginUser; 8904 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8905 PetscAssertPointer(ranks, 2); 8906 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 8907 PetscCall(DMClone(dm, &rdm)); 8908 PetscCall(DMGetDimension(rdm, &dim)); 8909 PetscCall(DMPlexGetHeightStratum(rdm, 0, &cStart, &cEnd)); 8910 PetscCall(DMPlexGetCellType(dm, cStart, &ct)); 8911 simplex = DMPolytopeTypeGetNumVertices(ct) == DMPolytopeTypeGetDim(ct) + 1 ? PETSC_TRUE : PETSC_FALSE; 8912 PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, simplex, "PETSc___rank_", -1, &fe)); 8913 PetscCall(PetscObjectSetName((PetscObject)fe, "rank")); 8914 PetscCall(DMSetField(rdm, 0, NULL, (PetscObject)fe)); 8915 PetscCall(PetscFEDestroy(&fe)); 8916 PetscCall(DMCreateDS(rdm)); 8917 PetscCall(DMCreateGlobalVector(rdm, ranks)); 8918 PetscCall(PetscObjectSetName((PetscObject)*ranks, "partition")); 8919 PetscCall(VecGetArray(*ranks, &r)); 8920 for (c = cStart; c < cEnd; ++c) { 8921 PetscScalar *lr; 8922 8923 PetscCall(DMPlexPointGlobalRef(rdm, c, r, &lr)); 8924 if (lr) *lr = rank; 8925 } 8926 PetscCall(VecRestoreArray(*ranks, &r)); 8927 PetscCall(DMDestroy(&rdm)); 8928 PetscFunctionReturn(PETSC_SUCCESS); 8929 } 8930 8931 /*@ 8932 DMPlexCreateLabelField - Create a field whose value is the label value for that point 8933 8934 Input Parameters: 8935 + dm - The `DMPLEX` 8936 - label - The `DMLabel` 8937 8938 Output Parameter: 8939 . val - The label value field 8940 8941 Options Database Key: 8942 . -dm_label_view - Adds the label value field into the `DM` output from `-dm_view` using the same viewer 8943 8944 Level: intermediate 8945 8946 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMView()` 8947 @*/ 8948 PetscErrorCode DMPlexCreateLabelField(DM dm, DMLabel label, Vec *val) 8949 { 8950 DM rdm, plex; 8951 Vec lval; 8952 PetscSection section; 8953 PetscFE fe; 8954 PetscScalar *v; 8955 PetscInt dim, pStart, pEnd, p, cStart; 8956 DMPolytopeType ct; 8957 char name[PETSC_MAX_PATH_LEN]; 8958 const char *lname, *prefix; 8959 8960 PetscFunctionBeginUser; 8961 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8962 PetscAssertPointer(label, 2); 8963 PetscAssertPointer(val, 3); 8964 PetscCall(DMClone(dm, &rdm)); 8965 PetscCall(DMConvert(rdm, DMPLEX, &plex)); 8966 PetscCall(DMPlexGetHeightStratum(plex, 0, &cStart, NULL)); 8967 PetscCall(DMPlexGetCellType(plex, cStart, &ct)); 8968 PetscCall(DMDestroy(&plex)); 8969 PetscCall(DMGetDimension(rdm, &dim)); 8970 PetscCall(DMGetOptionsPrefix(dm, &prefix)); 8971 PetscCall(PetscObjectGetName((PetscObject)label, &lname)); 8972 PetscCall(PetscSNPrintf(name, sizeof(name), "%s%s_", prefix ? prefix : "", lname)); 8973 PetscCall(PetscFECreateByCell(PETSC_COMM_SELF, dim, 1, ct, name, -1, &fe)); 8974 PetscCall(PetscObjectSetName((PetscObject)fe, "")); 8975 PetscCall(DMSetField(rdm, 0, NULL, (PetscObject)fe)); 8976 PetscCall(PetscFEDestroy(&fe)); 8977 PetscCall(DMCreateDS(rdm)); 8978 PetscCall(DMCreateGlobalVector(rdm, val)); 8979 PetscCall(DMCreateLocalVector(rdm, &lval)); 8980 PetscCall(PetscObjectSetName((PetscObject)*val, lname)); 8981 PetscCall(DMGetLocalSection(rdm, §ion)); 8982 PetscCall(PetscSectionGetChart(section, &pStart, &pEnd)); 8983 PetscCall(VecGetArray(lval, &v)); 8984 for (p = pStart; p < pEnd; ++p) { 8985 PetscInt cval, dof, off; 8986 8987 PetscCall(PetscSectionGetDof(section, p, &dof)); 8988 if (!dof) continue; 8989 PetscCall(DMLabelGetValue(label, p, &cval)); 8990 PetscCall(PetscSectionGetOffset(section, p, &off)); 8991 for (PetscInt d = 0; d < dof; d++) v[off + d] = cval; 8992 } 8993 PetscCall(VecRestoreArray(lval, &v)); 8994 PetscCall(DMLocalToGlobal(rdm, lval, INSERT_VALUES, *val)); 8995 PetscCall(VecDestroy(&lval)); 8996 PetscCall(DMDestroy(&rdm)); 8997 PetscFunctionReturn(PETSC_SUCCESS); 8998 } 8999 9000 /*@ 9001 DMPlexCheckSymmetry - Check that the adjacency information in the mesh is symmetric. 9002 9003 Input Parameter: 9004 . dm - The `DMPLEX` object 9005 9006 Level: developer 9007 9008 Notes: 9009 This is a useful diagnostic when creating meshes programmatically. 9010 9011 For the complete list of DMPlexCheck* functions, see `DMSetFromOptions()`. 9012 9013 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMCreate()`, `DMSetFromOptions()` 9014 @*/ 9015 PetscErrorCode DMPlexCheckSymmetry(DM dm) 9016 { 9017 PetscSection coneSection, supportSection; 9018 const PetscInt *cone, *support; 9019 PetscInt coneSize, c, supportSize, s; 9020 PetscInt pStart, pEnd, p, pp, csize, ssize; 9021 PetscBool storagecheck = PETSC_TRUE; 9022 9023 PetscFunctionBegin; 9024 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 9025 PetscCall(DMViewFromOptions(dm, NULL, "-sym_dm_view")); 9026 PetscCall(DMPlexGetConeSection(dm, &coneSection)); 9027 PetscCall(DMPlexGetSupportSection(dm, &supportSection)); 9028 /* Check that point p is found in the support of its cone points, and vice versa */ 9029 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 9030 for (p = pStart; p < pEnd; ++p) { 9031 PetscCall(DMPlexGetConeSize(dm, p, &coneSize)); 9032 PetscCall(DMPlexGetCone(dm, p, &cone)); 9033 for (c = 0; c < coneSize; ++c) { 9034 PetscBool dup = PETSC_FALSE; 9035 PetscInt d; 9036 for (d = c - 1; d >= 0; --d) { 9037 if (cone[c] == cone[d]) { 9038 dup = PETSC_TRUE; 9039 break; 9040 } 9041 } 9042 PetscCall(DMPlexGetSupportSize(dm, cone[c], &supportSize)); 9043 PetscCall(DMPlexGetSupport(dm, cone[c], &support)); 9044 for (s = 0; s < supportSize; ++s) { 9045 if (support[s] == p) break; 9046 } 9047 if ((s >= supportSize) || (dup && (support[s + 1] != p))) { 9048 PetscCall(PetscPrintf(PETSC_COMM_SELF, "p: %" PetscInt_FMT " cone: ", p)); 9049 for (s = 0; s < coneSize; ++s) PetscCall(PetscPrintf(PETSC_COMM_SELF, "%" PetscInt_FMT ", ", cone[s])); 9050 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 9051 PetscCall(PetscPrintf(PETSC_COMM_SELF, "p: %" PetscInt_FMT " support: ", cone[c])); 9052 for (s = 0; s < supportSize; ++s) PetscCall(PetscPrintf(PETSC_COMM_SELF, "%" PetscInt_FMT ", ", support[s])); 9053 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 9054 PetscCheck(!dup, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %" PetscInt_FMT " not repeatedly found in support of repeated cone point %" PetscInt_FMT, p, cone[c]); 9055 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %" PetscInt_FMT " not found in support of cone point %" PetscInt_FMT, p, cone[c]); 9056 } 9057 } 9058 PetscCall(DMPlexGetTreeParent(dm, p, &pp, NULL)); 9059 if (p != pp) { 9060 storagecheck = PETSC_FALSE; 9061 continue; 9062 } 9063 PetscCall(DMPlexGetSupportSize(dm, p, &supportSize)); 9064 PetscCall(DMPlexGetSupport(dm, p, &support)); 9065 for (s = 0; s < supportSize; ++s) { 9066 PetscCall(DMPlexGetConeSize(dm, support[s], &coneSize)); 9067 PetscCall(DMPlexGetCone(dm, support[s], &cone)); 9068 for (c = 0; c < coneSize; ++c) { 9069 PetscCall(DMPlexGetTreeParent(dm, cone[c], &pp, NULL)); 9070 if (cone[c] != pp) { 9071 c = 0; 9072 break; 9073 } 9074 if (cone[c] == p) break; 9075 } 9076 if (c >= coneSize) { 9077 PetscCall(PetscPrintf(PETSC_COMM_SELF, "p: %" PetscInt_FMT " support: ", p)); 9078 for (c = 0; c < supportSize; ++c) PetscCall(PetscPrintf(PETSC_COMM_SELF, "%" PetscInt_FMT ", ", support[c])); 9079 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 9080 PetscCall(PetscPrintf(PETSC_COMM_SELF, "p: %" PetscInt_FMT " cone: ", support[s])); 9081 for (c = 0; c < coneSize; ++c) PetscCall(PetscPrintf(PETSC_COMM_SELF, "%" PetscInt_FMT ", ", cone[c])); 9082 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 9083 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %" PetscInt_FMT " not found in cone of support point %" PetscInt_FMT, p, support[s]); 9084 } 9085 } 9086 } 9087 if (storagecheck) { 9088 PetscCall(PetscSectionGetStorageSize(coneSection, &csize)); 9089 PetscCall(PetscSectionGetStorageSize(supportSection, &ssize)); 9090 PetscCheck(csize == ssize, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Total cone size %" PetscInt_FMT " != Total support size %" PetscInt_FMT, csize, ssize); 9091 } 9092 PetscFunctionReturn(PETSC_SUCCESS); 9093 } 9094 9095 /* 9096 For submeshes with cohesive cells (see DMPlexConstructCohesiveCells()), we allow a special case where some of the boundary of a face (edges and vertices) are not duplicated. We call these special boundary points "unsplit", since the same edge or vertex appears in both copies of the face. These unsplit points throw off our counting, so we have to explicitly account for them here. 9097 */ 9098 static PetscErrorCode DMPlexCellUnsplitVertices_Private(DM dm, PetscInt c, DMPolytopeType ct, PetscInt *unsplit) 9099 { 9100 DMPolytopeType cct; 9101 PetscInt ptpoints[4]; 9102 const PetscInt *cone, *ccone, *ptcone; 9103 PetscInt coneSize, cp, cconeSize, ccp, npt = 0, pt; 9104 9105 PetscFunctionBegin; 9106 *unsplit = 0; 9107 switch (ct) { 9108 case DM_POLYTOPE_POINT_PRISM_TENSOR: 9109 ptpoints[npt++] = c; 9110 break; 9111 case DM_POLYTOPE_SEG_PRISM_TENSOR: 9112 PetscCall(DMPlexGetCone(dm, c, &cone)); 9113 PetscCall(DMPlexGetConeSize(dm, c, &coneSize)); 9114 for (cp = 0; cp < coneSize; ++cp) { 9115 PetscCall(DMPlexGetCellType(dm, cone[cp], &cct)); 9116 if (cct == DM_POLYTOPE_POINT_PRISM_TENSOR) ptpoints[npt++] = cone[cp]; 9117 } 9118 break; 9119 case DM_POLYTOPE_TRI_PRISM_TENSOR: 9120 case DM_POLYTOPE_QUAD_PRISM_TENSOR: 9121 PetscCall(DMPlexGetCone(dm, c, &cone)); 9122 PetscCall(DMPlexGetConeSize(dm, c, &coneSize)); 9123 for (cp = 0; cp < coneSize; ++cp) { 9124 PetscCall(DMPlexGetCone(dm, cone[cp], &ccone)); 9125 PetscCall(DMPlexGetConeSize(dm, cone[cp], &cconeSize)); 9126 for (ccp = 0; ccp < cconeSize; ++ccp) { 9127 PetscCall(DMPlexGetCellType(dm, ccone[ccp], &cct)); 9128 if (cct == DM_POLYTOPE_POINT_PRISM_TENSOR) { 9129 PetscInt p; 9130 for (p = 0; p < npt; ++p) 9131 if (ptpoints[p] == ccone[ccp]) break; 9132 if (p == npt) ptpoints[npt++] = ccone[ccp]; 9133 } 9134 } 9135 } 9136 break; 9137 default: 9138 break; 9139 } 9140 for (pt = 0; pt < npt; ++pt) { 9141 PetscCall(DMPlexGetCone(dm, ptpoints[pt], &ptcone)); 9142 if (ptcone[0] == ptcone[1]) ++(*unsplit); 9143 } 9144 PetscFunctionReturn(PETSC_SUCCESS); 9145 } 9146 9147 /*@ 9148 DMPlexCheckSkeleton - Check that each cell has the correct number of vertices 9149 9150 Input Parameters: 9151 + dm - The `DMPLEX` object 9152 - cellHeight - Normally 0 9153 9154 Level: developer 9155 9156 Notes: 9157 This is a useful diagnostic when creating meshes programmatically. 9158 Currently applicable only to homogeneous simplex or tensor meshes. 9159 9160 For the complete list of DMPlexCheck* functions, see `DMSetFromOptions()`. 9161 9162 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMCreate()`, `DMSetFromOptions()` 9163 @*/ 9164 PetscErrorCode DMPlexCheckSkeleton(DM dm, PetscInt cellHeight) 9165 { 9166 DMPlexInterpolatedFlag interp; 9167 DMPolytopeType ct; 9168 PetscInt vStart, vEnd, cStart, cEnd, c; 9169 9170 PetscFunctionBegin; 9171 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 9172 PetscCall(DMPlexIsInterpolated(dm, &interp)); 9173 PetscCall(DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd)); 9174 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 9175 for (c = cStart; c < cEnd; ++c) { 9176 PetscInt *closure = NULL; 9177 PetscInt coneSize, closureSize, cl, Nv = 0; 9178 9179 PetscCall(DMPlexGetCellType(dm, c, &ct)); 9180 PetscCheck((PetscInt)ct >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %" PetscInt_FMT " has no cell type", c); 9181 if (ct == DM_POLYTOPE_UNKNOWN) continue; 9182 if (interp == DMPLEX_INTERPOLATED_FULL) { 9183 PetscCall(DMPlexGetConeSize(dm, c, &coneSize)); 9184 PetscCheck(coneSize == DMPolytopeTypeGetConeSize(ct), PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %" PetscInt_FMT " of type %s has cone size %" PetscInt_FMT " != %" PetscInt_FMT, c, DMPolytopeTypes[ct], coneSize, DMPolytopeTypeGetConeSize(ct)); 9185 } 9186 PetscCall(DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 9187 for (cl = 0; cl < closureSize * 2; cl += 2) { 9188 const PetscInt p = closure[cl]; 9189 if ((p >= vStart) && (p < vEnd)) ++Nv; 9190 } 9191 PetscCall(DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 9192 /* Special Case: Tensor faces with identified vertices */ 9193 if (Nv < DMPolytopeTypeGetNumVertices(ct)) { 9194 PetscInt unsplit; 9195 9196 PetscCall(DMPlexCellUnsplitVertices_Private(dm, c, ct, &unsplit)); 9197 if (Nv + unsplit == DMPolytopeTypeGetNumVertices(ct)) continue; 9198 } 9199 PetscCheck(Nv == DMPolytopeTypeGetNumVertices(ct), PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %" PetscInt_FMT " of type %s has %" PetscInt_FMT " vertices != %" PetscInt_FMT, c, DMPolytopeTypes[ct], Nv, DMPolytopeTypeGetNumVertices(ct)); 9200 } 9201 PetscFunctionReturn(PETSC_SUCCESS); 9202 } 9203 9204 /*@ 9205 DMPlexCheckFaces - Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type 9206 9207 Collective 9208 9209 Input Parameters: 9210 + dm - The `DMPLEX` object 9211 - cellHeight - Normally 0 9212 9213 Level: developer 9214 9215 Notes: 9216 This is a useful diagnostic when creating meshes programmatically. 9217 This routine is only relevant for meshes that are fully interpolated across all ranks. 9218 It will error out if a partially interpolated mesh is given on some rank. 9219 It will do nothing for locally uninterpolated mesh (as there is nothing to check). 9220 9221 For the complete list of DMPlexCheck* functions, see `DMSetFromOptions()`. 9222 9223 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMCreate()`, `DMPlexGetVTKCellHeight()`, `DMSetFromOptions()` 9224 @*/ 9225 PetscErrorCode DMPlexCheckFaces(DM dm, PetscInt cellHeight) 9226 { 9227 PetscInt dim, depth, vStart, vEnd, cStart, cEnd, c, h; 9228 DMPlexInterpolatedFlag interpEnum; 9229 9230 PetscFunctionBegin; 9231 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 9232 PetscCall(DMPlexIsInterpolatedCollective(dm, &interpEnum)); 9233 if (interpEnum == DMPLEX_INTERPOLATED_NONE) PetscFunctionReturn(PETSC_SUCCESS); 9234 if (interpEnum != DMPLEX_INTERPOLATED_FULL) { 9235 PetscCall(PetscPrintf(PetscObjectComm((PetscObject)dm), "DMPlexCheckFaces() warning: Mesh is only partially interpolated, this is currently not supported")); 9236 PetscFunctionReturn(PETSC_SUCCESS); 9237 } 9238 9239 PetscCall(DMGetDimension(dm, &dim)); 9240 PetscCall(DMPlexGetDepth(dm, &depth)); 9241 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 9242 for (h = cellHeight; h < PetscMin(depth, dim); ++h) { 9243 PetscCall(DMPlexGetHeightStratum(dm, h, &cStart, &cEnd)); 9244 for (c = cStart; c < cEnd; ++c) { 9245 const PetscInt *cone, *ornt, *faceSizes, *faces; 9246 const DMPolytopeType *faceTypes; 9247 DMPolytopeType ct; 9248 PetscInt numFaces, coneSize, f; 9249 PetscInt *closure = NULL, closureSize, cl, numCorners = 0, fOff = 0, unsplit; 9250 9251 PetscCall(DMPlexGetCellType(dm, c, &ct)); 9252 PetscCall(DMPlexCellUnsplitVertices_Private(dm, c, ct, &unsplit)); 9253 if (unsplit) continue; 9254 PetscCall(DMPlexGetConeSize(dm, c, &coneSize)); 9255 PetscCall(DMPlexGetCone(dm, c, &cone)); 9256 PetscCall(DMPlexGetConeOrientation(dm, c, &ornt)); 9257 PetscCall(DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 9258 for (cl = 0; cl < closureSize * 2; cl += 2) { 9259 const PetscInt p = closure[cl]; 9260 if ((p >= vStart) && (p < vEnd)) closure[numCorners++] = p; 9261 } 9262 PetscCall(DMPlexGetRawFaces_Internal(dm, ct, closure, &numFaces, &faceTypes, &faceSizes, &faces)); 9263 PetscCheck(coneSize == numFaces, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %" PetscInt_FMT " of type %s has %" PetscInt_FMT " faces but should have %" PetscInt_FMT, c, DMPolytopeTypes[ct], coneSize, numFaces); 9264 for (f = 0; f < numFaces; ++f) { 9265 DMPolytopeType fct; 9266 PetscInt *fclosure = NULL, fclosureSize, cl, fnumCorners = 0, v; 9267 9268 PetscCall(DMPlexGetCellType(dm, cone[f], &fct)); 9269 PetscCall(DMPlexGetTransitiveClosure_Internal(dm, cone[f], ornt[f], PETSC_TRUE, &fclosureSize, &fclosure)); 9270 for (cl = 0; cl < fclosureSize * 2; cl += 2) { 9271 const PetscInt p = fclosure[cl]; 9272 if ((p >= vStart) && (p < vEnd)) fclosure[fnumCorners++] = p; 9273 } 9274 PetscCheck(fnumCorners == faceSizes[f], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %" PetscInt_FMT " of type %s (cone idx %" PetscInt_FMT ") of cell %" PetscInt_FMT " of type %s has %" PetscInt_FMT " vertices but should have %" PetscInt_FMT, cone[f], DMPolytopeTypes[fct], f, c, DMPolytopeTypes[ct], fnumCorners, faceSizes[f]); 9275 for (v = 0; v < fnumCorners; ++v) { 9276 if (fclosure[v] != faces[fOff + v]) { 9277 PetscInt v1; 9278 9279 PetscCall(PetscPrintf(PETSC_COMM_SELF, "face closure:")); 9280 for (v1 = 0; v1 < fnumCorners; ++v1) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, fclosure[v1])); 9281 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\ncell face:")); 9282 for (v1 = 0; v1 < fnumCorners; ++v1) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, faces[fOff + v1])); 9283 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 9284 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %" PetscInt_FMT " of type %s (cone idx %" PetscInt_FMT ", ornt %" PetscInt_FMT ") of cell %" PetscInt_FMT " of type %s vertex %" PetscInt_FMT ", %" PetscInt_FMT " != %" PetscInt_FMT, cone[f], DMPolytopeTypes[fct], f, ornt[f], c, DMPolytopeTypes[ct], v, fclosure[v], faces[fOff + v]); 9285 } 9286 } 9287 PetscCall(DMPlexRestoreTransitiveClosure(dm, cone[f], PETSC_TRUE, &fclosureSize, &fclosure)); 9288 fOff += faceSizes[f]; 9289 } 9290 PetscCall(DMPlexRestoreRawFaces_Internal(dm, ct, closure, &numFaces, &faceTypes, &faceSizes, &faces)); 9291 PetscCall(DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 9292 } 9293 } 9294 PetscFunctionReturn(PETSC_SUCCESS); 9295 } 9296 9297 /*@ 9298 DMPlexCheckGeometry - Check the geometry of mesh cells 9299 9300 Input Parameter: 9301 . dm - The `DMPLEX` object 9302 9303 Level: developer 9304 9305 Notes: 9306 This is a useful diagnostic when creating meshes programmatically. 9307 9308 For the complete list of DMPlexCheck* functions, see `DMSetFromOptions()`. 9309 9310 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMCreate()`, `DMSetFromOptions()` 9311 @*/ 9312 PetscErrorCode DMPlexCheckGeometry(DM dm) 9313 { 9314 Vec coordinates; 9315 PetscReal detJ, J[9], refVol = 1.0; 9316 PetscReal vol; 9317 PetscInt dim, depth, dE, d, cStart, cEnd, c; 9318 9319 PetscFunctionBegin; 9320 PetscCall(DMGetDimension(dm, &dim)); 9321 PetscCall(DMGetCoordinateDim(dm, &dE)); 9322 if (dim != dE) PetscFunctionReturn(PETSC_SUCCESS); 9323 PetscCall(DMPlexGetDepth(dm, &depth)); 9324 for (d = 0; d < dim; ++d) refVol *= 2.0; 9325 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 9326 /* Make sure local coordinates are created, because that step is collective */ 9327 PetscCall(DMGetCoordinatesLocal(dm, &coordinates)); 9328 if (!coordinates) PetscFunctionReturn(PETSC_SUCCESS); 9329 for (c = cStart; c < cEnd; ++c) { 9330 DMPolytopeType ct; 9331 PetscInt unsplit; 9332 PetscBool ignoreZeroVol = PETSC_FALSE; 9333 9334 PetscCall(DMPlexGetCellType(dm, c, &ct)); 9335 switch (ct) { 9336 case DM_POLYTOPE_SEG_PRISM_TENSOR: 9337 case DM_POLYTOPE_TRI_PRISM_TENSOR: 9338 case DM_POLYTOPE_QUAD_PRISM_TENSOR: 9339 ignoreZeroVol = PETSC_TRUE; 9340 break; 9341 default: 9342 break; 9343 } 9344 switch (ct) { 9345 case DM_POLYTOPE_TRI_PRISM: 9346 case DM_POLYTOPE_TRI_PRISM_TENSOR: 9347 case DM_POLYTOPE_QUAD_PRISM_TENSOR: 9348 case DM_POLYTOPE_PYRAMID: 9349 continue; 9350 default: 9351 break; 9352 } 9353 PetscCall(DMPlexCellUnsplitVertices_Private(dm, c, ct, &unsplit)); 9354 if (unsplit) continue; 9355 PetscCall(DMPlexComputeCellGeometryFEM(dm, c, NULL, NULL, J, NULL, &detJ)); 9356 PetscCheck(detJ >= -PETSC_SMALL && (detJ > 0.0 || ignoreZeroVol), PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh cell %" PetscInt_FMT " of type %s is inverted, |J| = %g", c, DMPolytopeTypes[ct], (double)detJ); 9357 PetscCall(PetscInfo(dm, "Cell %" PetscInt_FMT " FEM Volume %g\n", c, (double)(detJ * refVol))); 9358 /* This should work with periodicity since DG coordinates should be used */ 9359 if (depth > 1) { 9360 PetscCall(DMPlexComputeCellGeometryFVM(dm, c, &vol, NULL, NULL)); 9361 PetscCheck(vol >= -PETSC_SMALL && (vol > 0.0 || ignoreZeroVol), PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh cell %" PetscInt_FMT " of type %s is inverted, vol = %g", c, DMPolytopeTypes[ct], (double)vol); 9362 PetscCall(PetscInfo(dm, "Cell %" PetscInt_FMT " FVM Volume %g\n", c, (double)vol)); 9363 } 9364 } 9365 PetscFunctionReturn(PETSC_SUCCESS); 9366 } 9367 9368 /*@ 9369 DMPlexCheckPointSF - Check that several necessary conditions are met for the point `PetscSF` of this plex. 9370 9371 Collective 9372 9373 Input Parameters: 9374 + dm - The `DMPLEX` object 9375 . pointSF - The `PetscSF`, or `NULL` for `PointSF` attached to `DM` 9376 - allowExtraRoots - Flag to allow extra points not present in the `DM` 9377 9378 Level: developer 9379 9380 Notes: 9381 This is mainly intended for debugging/testing purposes. 9382 9383 For the complete list of DMPlexCheck* functions, see `DMSetFromOptions()`. 9384 9385 Extra roots can come from periodic cuts, where additional points appear on the boundary 9386 9387 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMGetPointSF()`, `DMSetFromOptions()` 9388 @*/ 9389 PetscErrorCode DMPlexCheckPointSF(DM dm, PetscSF pointSF, PetscBool allowExtraRoots) 9390 { 9391 PetscInt l, nleaves, nroots, overlap; 9392 const PetscInt *locals; 9393 const PetscSFNode *remotes; 9394 PetscBool distributed; 9395 MPI_Comm comm; 9396 PetscMPIInt rank; 9397 9398 PetscFunctionBegin; 9399 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 9400 if (pointSF) PetscValidHeaderSpecific(pointSF, PETSCSF_CLASSID, 2); 9401 else pointSF = dm->sf; 9402 PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); 9403 PetscCheck(pointSF, comm, PETSC_ERR_ARG_WRONGSTATE, "DMPlex must have Point SF attached"); 9404 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 9405 { 9406 PetscMPIInt mpiFlag; 9407 9408 PetscCallMPI(MPI_Comm_compare(comm, PetscObjectComm((PetscObject)pointSF), &mpiFlag)); 9409 PetscCheck(mpiFlag == MPI_CONGRUENT || mpiFlag == MPI_IDENT, PETSC_COMM_SELF, PETSC_ERR_ARG_NOTSAMECOMM, "DM and Point SF have different communicators (flag %d)", mpiFlag); 9410 } 9411 PetscCall(PetscSFGetGraph(pointSF, &nroots, &nleaves, &locals, &remotes)); 9412 PetscCall(DMPlexIsDistributed(dm, &distributed)); 9413 if (!distributed) { 9414 PetscCheck(nroots < 0 || nleaves == 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Undistributed DMPlex cannot have non-empty PointSF (has %" PetscInt_FMT " roots, %" PetscInt_FMT " leaves)", nroots, nleaves); 9415 PetscFunctionReturn(PETSC_SUCCESS); 9416 } 9417 PetscCheck(nroots >= 0, comm, PETSC_ERR_ARG_WRONGSTATE, "This DMPlex is distributed but its PointSF has no graph set (has %" PetscInt_FMT " roots, %" PetscInt_FMT " leaves)", nroots, nleaves); 9418 PetscCall(DMPlexGetOverlap(dm, &overlap)); 9419 9420 /* Check SF graph is compatible with DMPlex chart */ 9421 { 9422 PetscInt pStart, pEnd, maxLeaf; 9423 9424 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 9425 PetscCall(PetscSFGetLeafRange(pointSF, NULL, &maxLeaf)); 9426 PetscCheck(allowExtraRoots || pEnd - pStart == nroots, PETSC_COMM_SELF, PETSC_ERR_PLIB, "pEnd - pStart = %" PetscInt_FMT " != nroots = %" PetscInt_FMT, pEnd - pStart, nroots); 9427 PetscCheck(maxLeaf < pEnd, PETSC_COMM_SELF, PETSC_ERR_PLIB, "maxLeaf = %" PetscInt_FMT " >= pEnd = %" PetscInt_FMT, maxLeaf, pEnd); 9428 } 9429 9430 /* Check Point SF has no local points referenced */ 9431 for (l = 0; l < nleaves; l++) { 9432 PetscAssert(remotes[l].rank != (PetscInt)rank, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point SF contains local point %" PetscInt_FMT " <- (%" PetscInt_FMT ",%" PetscInt_FMT ")", locals ? locals[l] : l, remotes[l].rank, remotes[l].index); 9433 } 9434 9435 /* Check there are no cells in interface */ 9436 if (!overlap) { 9437 PetscInt cellHeight, cStart, cEnd; 9438 9439 PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight)); 9440 PetscCall(DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd)); 9441 for (l = 0; l < nleaves; ++l) { 9442 const PetscInt point = locals ? locals[l] : l; 9443 9444 PetscCheck(point < cStart || point >= cEnd, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point SF contains %" PetscInt_FMT " which is a cell", point); 9445 } 9446 } 9447 9448 /* If some point is in interface, then all its cone points must be also in interface (either as leaves or roots) */ 9449 { 9450 const PetscInt *rootdegree; 9451 9452 PetscCall(PetscSFComputeDegreeBegin(pointSF, &rootdegree)); 9453 PetscCall(PetscSFComputeDegreeEnd(pointSF, &rootdegree)); 9454 for (l = 0; l < nleaves; ++l) { 9455 const PetscInt point = locals ? locals[l] : l; 9456 const PetscInt *cone; 9457 PetscInt coneSize, c, idx; 9458 9459 PetscCall(DMPlexGetConeSize(dm, point, &coneSize)); 9460 PetscCall(DMPlexGetCone(dm, point, &cone)); 9461 for (c = 0; c < coneSize; ++c) { 9462 if (!rootdegree[cone[c]]) { 9463 if (locals) { 9464 PetscCall(PetscFindInt(cone[c], nleaves, locals, &idx)); 9465 } else { 9466 idx = (cone[c] < nleaves) ? cone[c] : -1; 9467 } 9468 PetscCheck(idx >= 0, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point SF contains %" PetscInt_FMT " but not %" PetscInt_FMT " from its cone", point, cone[c]); 9469 } 9470 } 9471 } 9472 } 9473 PetscFunctionReturn(PETSC_SUCCESS); 9474 } 9475 9476 /*@ 9477 DMPlexCheck - Perform various checks of `DMPLEX` sanity 9478 9479 Input Parameter: 9480 . dm - The `DMPLEX` object 9481 9482 Level: developer 9483 9484 Notes: 9485 This is a useful diagnostic when creating meshes programmatically. 9486 9487 For the complete list of DMPlexCheck* functions, see `DMSetFromOptions()`. 9488 9489 Currently does not include `DMPlexCheckCellShape()`. 9490 9491 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMCreate()`, `DMSetFromOptions()` 9492 @*/ 9493 PetscErrorCode DMPlexCheck(DM dm) 9494 { 9495 PetscInt cellHeight; 9496 9497 PetscFunctionBegin; 9498 PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight)); 9499 PetscCall(DMPlexCheckSymmetry(dm)); 9500 PetscCall(DMPlexCheckSkeleton(dm, cellHeight)); 9501 PetscCall(DMPlexCheckFaces(dm, cellHeight)); 9502 PetscCall(DMPlexCheckGeometry(dm)); 9503 PetscCall(DMPlexCheckPointSF(dm, NULL, PETSC_FALSE)); 9504 PetscCall(DMPlexCheckInterfaceCones(dm)); 9505 PetscFunctionReturn(PETSC_SUCCESS); 9506 } 9507 9508 typedef struct cell_stats { 9509 PetscReal min, max, sum, squaresum; 9510 PetscInt count; 9511 } cell_stats_t; 9512 9513 static void MPIAPI cell_stats_reduce(void *a, void *b, int *len, MPI_Datatype *datatype) 9514 { 9515 PetscInt i, N = *len; 9516 9517 for (i = 0; i < N; i++) { 9518 cell_stats_t *A = (cell_stats_t *)a; 9519 cell_stats_t *B = (cell_stats_t *)b; 9520 9521 B->min = PetscMin(A->min, B->min); 9522 B->max = PetscMax(A->max, B->max); 9523 B->sum += A->sum; 9524 B->squaresum += A->squaresum; 9525 B->count += A->count; 9526 } 9527 } 9528 9529 /*@ 9530 DMPlexCheckCellShape - Checks the Jacobian of the mapping from reference to real cells and computes some minimal statistics. 9531 9532 Collective 9533 9534 Input Parameters: 9535 + dm - The `DMPLEX` object 9536 . output - If true, statistics will be displayed on `stdout` 9537 - condLimit - Display all cells above this condition number, or `PETSC_DETERMINE` for no cell output 9538 9539 Level: developer 9540 9541 Notes: 9542 This is mainly intended for debugging/testing purposes. 9543 9544 For the complete list of DMPlexCheck* functions, see `DMSetFromOptions()`. 9545 9546 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMSetFromOptions()`, `DMPlexComputeOrthogonalQuality()` 9547 @*/ 9548 PetscErrorCode DMPlexCheckCellShape(DM dm, PetscBool output, PetscReal condLimit) 9549 { 9550 DM dmCoarse; 9551 cell_stats_t stats, globalStats; 9552 MPI_Comm comm = PetscObjectComm((PetscObject)dm); 9553 PetscReal *J, *invJ, min = 0, max = 0, mean = 0, stdev = 0; 9554 PetscReal limit = condLimit > 0 ? condLimit : PETSC_MAX_REAL; 9555 PetscInt cdim, cStart, cEnd, c, eStart, eEnd, count = 0; 9556 PetscMPIInt rank, size; 9557 9558 PetscFunctionBegin; 9559 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 9560 stats.min = PETSC_MAX_REAL; 9561 stats.max = PETSC_MIN_REAL; 9562 stats.sum = stats.squaresum = 0.; 9563 stats.count = 0; 9564 9565 PetscCallMPI(MPI_Comm_size(comm, &size)); 9566 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 9567 PetscCall(DMGetCoordinateDim(dm, &cdim)); 9568 PetscCall(PetscMalloc2(PetscSqr(cdim), &J, PetscSqr(cdim), &invJ)); 9569 PetscCall(DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd)); 9570 PetscCall(DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd)); 9571 for (c = cStart; c < cEnd; c++) { 9572 PetscInt i; 9573 PetscReal frobJ = 0., frobInvJ = 0., cond2, cond, detJ; 9574 9575 PetscCall(DMPlexComputeCellGeometryAffineFEM(dm, c, NULL, J, invJ, &detJ)); 9576 PetscCheck(detJ >= 0.0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh cell %" PetscInt_FMT " is inverted", c); 9577 for (i = 0; i < PetscSqr(cdim); ++i) { 9578 frobJ += J[i] * J[i]; 9579 frobInvJ += invJ[i] * invJ[i]; 9580 } 9581 cond2 = frobJ * frobInvJ; 9582 cond = PetscSqrtReal(cond2); 9583 9584 stats.min = PetscMin(stats.min, cond); 9585 stats.max = PetscMax(stats.max, cond); 9586 stats.sum += cond; 9587 stats.squaresum += cond2; 9588 stats.count++; 9589 if (output && cond > limit) { 9590 PetscSection coordSection; 9591 Vec coordsLocal; 9592 PetscScalar *coords = NULL; 9593 PetscInt Nv, d, clSize, cl, *closure = NULL; 9594 9595 PetscCall(DMGetCoordinatesLocal(dm, &coordsLocal)); 9596 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 9597 PetscCall(DMPlexVecGetClosure(dm, coordSection, coordsLocal, c, &Nv, &coords)); 9598 PetscCall(PetscSynchronizedPrintf(comm, "[%d] Cell %" PetscInt_FMT " cond %g\n", rank, c, (double)cond)); 9599 for (i = 0; i < Nv / cdim; ++i) { 9600 PetscCall(PetscSynchronizedPrintf(comm, " Vertex %" PetscInt_FMT ": (", i)); 9601 for (d = 0; d < cdim; ++d) { 9602 if (d > 0) PetscCall(PetscSynchronizedPrintf(comm, ", ")); 9603 PetscCall(PetscSynchronizedPrintf(comm, "%g", (double)PetscRealPart(coords[i * cdim + d]))); 9604 } 9605 PetscCall(PetscSynchronizedPrintf(comm, ")\n")); 9606 } 9607 PetscCall(DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &clSize, &closure)); 9608 for (cl = 0; cl < clSize * 2; cl += 2) { 9609 const PetscInt edge = closure[cl]; 9610 9611 if ((edge >= eStart) && (edge < eEnd)) { 9612 PetscReal len; 9613 9614 PetscCall(DMPlexComputeCellGeometryFVM(dm, edge, &len, NULL, NULL)); 9615 PetscCall(PetscSynchronizedPrintf(comm, " Edge %" PetscInt_FMT ": length %g\n", edge, (double)len)); 9616 } 9617 } 9618 PetscCall(DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &clSize, &closure)); 9619 PetscCall(DMPlexVecRestoreClosure(dm, coordSection, coordsLocal, c, &Nv, &coords)); 9620 } 9621 } 9622 if (output) PetscCall(PetscSynchronizedFlush(comm, NULL)); 9623 9624 if (size > 1) { 9625 PetscMPIInt blockLengths[2] = {4, 1}; 9626 MPI_Aint blockOffsets[2] = {offsetof(cell_stats_t, min), offsetof(cell_stats_t, count)}; 9627 MPI_Datatype blockTypes[2] = {MPIU_REAL, MPIU_INT}, statType; 9628 MPI_Op statReduce; 9629 9630 PetscCallMPI(MPI_Type_create_struct(2, blockLengths, blockOffsets, blockTypes, &statType)); 9631 PetscCallMPI(MPI_Type_commit(&statType)); 9632 PetscCallMPI(MPI_Op_create(cell_stats_reduce, PETSC_TRUE, &statReduce)); 9633 PetscCallMPI(MPI_Reduce(&stats, &globalStats, 1, statType, statReduce, 0, comm)); 9634 PetscCallMPI(MPI_Op_free(&statReduce)); 9635 PetscCallMPI(MPI_Type_free(&statType)); 9636 } else { 9637 PetscCall(PetscArraycpy(&globalStats, &stats, 1)); 9638 } 9639 if (rank == 0) { 9640 count = globalStats.count; 9641 min = globalStats.min; 9642 max = globalStats.max; 9643 mean = globalStats.sum / globalStats.count; 9644 stdev = globalStats.count > 1 ? PetscSqrtReal(PetscMax((globalStats.squaresum - globalStats.count * mean * mean) / (globalStats.count - 1), 0)) : 0.0; 9645 } 9646 9647 if (output) PetscCall(PetscPrintf(comm, "Mesh with %" PetscInt_FMT " cells, shape condition numbers: min = %g, max = %g, mean = %g, stddev = %g\n", count, (double)min, (double)max, (double)mean, (double)stdev)); 9648 PetscCall(PetscFree2(J, invJ)); 9649 9650 PetscCall(DMGetCoarseDM(dm, &dmCoarse)); 9651 if (dmCoarse) { 9652 PetscBool isplex; 9653 9654 PetscCall(PetscObjectTypeCompare((PetscObject)dmCoarse, DMPLEX, &isplex)); 9655 if (isplex) PetscCall(DMPlexCheckCellShape(dmCoarse, output, condLimit)); 9656 } 9657 PetscFunctionReturn(PETSC_SUCCESS); 9658 } 9659 9660 /*@ 9661 DMPlexComputeOrthogonalQuality - Compute cell-wise orthogonal quality mesh statistic. Optionally tags all cells with 9662 orthogonal quality below given tolerance. 9663 9664 Collective 9665 9666 Input Parameters: 9667 + dm - The `DMPLEX` object 9668 . fv - Optional `PetscFV` object for pre-computed cell/face centroid information 9669 - atol - [0, 1] Absolute tolerance for tagging cells. 9670 9671 Output Parameters: 9672 + OrthQual - `Vec` containing orthogonal quality per cell 9673 - OrthQualLabel - `DMLabel` tagging cells below atol with `DM_ADAPT_REFINE` 9674 9675 Options Database Keys: 9676 + -dm_plex_orthogonal_quality_label_view - view OrthQualLabel if label is requested. Currently only `PETSCVIEWERASCII` is supported. 9677 - -dm_plex_orthogonal_quality_vec_view - view OrthQual vector. 9678 9679 Level: intermediate 9680 9681 Notes: 9682 Orthogonal quality is given by the following formula\: 9683 9684 $ \min \left[ \frac{A_i \cdot f_i}{\|A_i\| \|f_i\|} , \frac{A_i \cdot c_i}{\|A_i\| \|c_i\|} \right]$ 9685 9686 Where A_i is the i'th face-normal vector, f_i is the vector from the cell centroid to the i'th face centroid, and c_i 9687 is the vector from the current cells centroid to the centroid of its i'th neighbor (which shares a face with the 9688 current cell). This computes the vector similarity between each cell face and its corresponding neighbor centroid by 9689 calculating the cosine of the angle between these vectors. 9690 9691 Orthogonal quality ranges from 1 (best) to 0 (worst). 9692 9693 This routine is mainly useful for FVM, however is not restricted to only FVM. The `PetscFV` object is optionally used to check for 9694 pre-computed FVM cell data, but if it is not passed in then this data will be computed. 9695 9696 Cells are tagged if they have an orthogonal quality less than or equal to the absolute tolerance. 9697 9698 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCheckCellShape()`, `DMCreateLabel()`, `PetscFV`, `DMLabel`, `Vec` 9699 @*/ 9700 PetscErrorCode DMPlexComputeOrthogonalQuality(DM dm, PetscFV fv, PetscReal atol, Vec *OrthQual, DMLabel *OrthQualLabel) 9701 { 9702 PetscInt nc, cellHeight, cStart, cEnd, cell, cellIter = 0; 9703 PetscInt *idx; 9704 PetscScalar *oqVals; 9705 const PetscScalar *cellGeomArr, *faceGeomArr; 9706 PetscReal *ci, *fi, *Ai; 9707 MPI_Comm comm; 9708 Vec cellgeom, facegeom; 9709 DM dmFace, dmCell; 9710 IS glob; 9711 ISLocalToGlobalMapping ltog; 9712 PetscViewer vwr; 9713 9714 PetscFunctionBegin; 9715 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 9716 if (fv) PetscValidHeaderSpecific(fv, PETSCFV_CLASSID, 2); 9717 PetscAssertPointer(OrthQual, 4); 9718 PetscCheck(atol >= 0.0 && atol <= 1.0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Absolute tolerance %g not in [0,1]", (double)atol); 9719 PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); 9720 PetscCall(DMGetDimension(dm, &nc)); 9721 PetscCheck(nc >= 2, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "DM must have dimension >= 2 (current %" PetscInt_FMT ")", nc); 9722 { 9723 DMPlexInterpolatedFlag interpFlag; 9724 9725 PetscCall(DMPlexIsInterpolated(dm, &interpFlag)); 9726 if (interpFlag != DMPLEX_INTERPOLATED_FULL) { 9727 PetscMPIInt rank; 9728 9729 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 9730 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "DM must be fully interpolated, DM on rank %d is not fully interpolated", rank); 9731 } 9732 } 9733 if (OrthQualLabel) { 9734 PetscAssertPointer(OrthQualLabel, 5); 9735 PetscCall(DMCreateLabel(dm, "Orthogonal_Quality")); 9736 PetscCall(DMGetLabel(dm, "Orthogonal_Quality", OrthQualLabel)); 9737 } else { 9738 *OrthQualLabel = NULL; 9739 } 9740 PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight)); 9741 PetscCall(DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd)); 9742 PetscCall(DMPlexCreateCellNumbering_Internal(dm, PETSC_TRUE, &glob)); 9743 PetscCall(ISLocalToGlobalMappingCreateIS(glob, <og)); 9744 PetscCall(ISLocalToGlobalMappingSetType(ltog, ISLOCALTOGLOBALMAPPINGHASH)); 9745 PetscCall(VecCreate(comm, OrthQual)); 9746 PetscCall(VecSetType(*OrthQual, VECSTANDARD)); 9747 PetscCall(VecSetSizes(*OrthQual, cEnd - cStart, PETSC_DETERMINE)); 9748 PetscCall(VecSetLocalToGlobalMapping(*OrthQual, ltog)); 9749 PetscCall(VecSetUp(*OrthQual)); 9750 PetscCall(ISDestroy(&glob)); 9751 PetscCall(ISLocalToGlobalMappingDestroy(<og)); 9752 PetscCall(DMPlexGetDataFVM(dm, fv, &cellgeom, &facegeom, NULL)); 9753 PetscCall(VecGetArrayRead(cellgeom, &cellGeomArr)); 9754 PetscCall(VecGetArrayRead(facegeom, &faceGeomArr)); 9755 PetscCall(VecGetDM(cellgeom, &dmCell)); 9756 PetscCall(VecGetDM(facegeom, &dmFace)); 9757 PetscCall(PetscMalloc5(cEnd - cStart, &idx, cEnd - cStart, &oqVals, nc, &ci, nc, &fi, nc, &Ai)); 9758 for (cell = cStart; cell < cEnd; cellIter++, cell++) { 9759 PetscInt cellneigh, cellneighiter = 0, adjSize = PETSC_DETERMINE; 9760 PetscInt cellarr[2], *adj = NULL; 9761 PetscScalar *cArr, *fArr; 9762 PetscReal minvalc = 1.0, minvalf = 1.0; 9763 PetscFVCellGeom *cg; 9764 9765 idx[cellIter] = cell - cStart; 9766 cellarr[0] = cell; 9767 /* Make indexing into cellGeom easier */ 9768 PetscCall(DMPlexPointLocalRead(dmCell, cell, cellGeomArr, &cg)); 9769 PetscCall(DMPlexGetAdjacency_Internal(dm, cell, PETSC_TRUE, PETSC_FALSE, PETSC_FALSE, &adjSize, &adj)); 9770 /* Technically 1 too big, but easier than fiddling with empty adjacency array */ 9771 PetscCall(PetscCalloc2(adjSize, &cArr, adjSize, &fArr)); 9772 for (cellneigh = 0; cellneigh < adjSize; cellneighiter++, cellneigh++) { 9773 PetscInt i; 9774 const PetscInt neigh = adj[cellneigh]; 9775 PetscReal normci = 0, normfi = 0, normai = 0; 9776 PetscFVCellGeom *cgneigh; 9777 PetscFVFaceGeom *fg; 9778 9779 /* Don't count ourselves in the neighbor list */ 9780 if (neigh == cell) continue; 9781 PetscCall(DMPlexPointLocalRead(dmCell, neigh, cellGeomArr, &cgneigh)); 9782 cellarr[1] = neigh; 9783 { 9784 PetscInt numcovpts; 9785 const PetscInt *covpts; 9786 9787 PetscCall(DMPlexGetMeet(dm, 2, cellarr, &numcovpts, &covpts)); 9788 PetscCall(DMPlexPointLocalRead(dmFace, covpts[0], faceGeomArr, &fg)); 9789 PetscCall(DMPlexRestoreMeet(dm, 2, cellarr, &numcovpts, &covpts)); 9790 } 9791 9792 /* Compute c_i, f_i and their norms */ 9793 for (i = 0; i < nc; i++) { 9794 ci[i] = cgneigh->centroid[i] - cg->centroid[i]; 9795 fi[i] = fg->centroid[i] - cg->centroid[i]; 9796 Ai[i] = fg->normal[i]; 9797 normci += PetscPowReal(ci[i], 2); 9798 normfi += PetscPowReal(fi[i], 2); 9799 normai += PetscPowReal(Ai[i], 2); 9800 } 9801 normci = PetscSqrtReal(normci); 9802 normfi = PetscSqrtReal(normfi); 9803 normai = PetscSqrtReal(normai); 9804 9805 /* Normalize and compute for each face-cell-normal pair */ 9806 for (i = 0; i < nc; i++) { 9807 ci[i] = ci[i] / normci; 9808 fi[i] = fi[i] / normfi; 9809 Ai[i] = Ai[i] / normai; 9810 /* PetscAbs because I don't know if normals are guaranteed to point out */ 9811 cArr[cellneighiter] += PetscAbs(Ai[i] * ci[i]); 9812 fArr[cellneighiter] += PetscAbs(Ai[i] * fi[i]); 9813 } 9814 if (PetscRealPart(cArr[cellneighiter]) < minvalc) minvalc = PetscRealPart(cArr[cellneighiter]); 9815 if (PetscRealPart(fArr[cellneighiter]) < minvalf) minvalf = PetscRealPart(fArr[cellneighiter]); 9816 } 9817 PetscCall(PetscFree(adj)); 9818 PetscCall(PetscFree2(cArr, fArr)); 9819 /* Defer to cell if they're equal */ 9820 oqVals[cellIter] = PetscMin(minvalf, minvalc); 9821 if (OrthQualLabel) { 9822 if (PetscRealPart(oqVals[cellIter]) <= atol) PetscCall(DMLabelSetValue(*OrthQualLabel, cell, DM_ADAPT_REFINE)); 9823 } 9824 } 9825 PetscCall(VecSetValuesLocal(*OrthQual, cEnd - cStart, idx, oqVals, INSERT_VALUES)); 9826 PetscCall(VecAssemblyBegin(*OrthQual)); 9827 PetscCall(VecAssemblyEnd(*OrthQual)); 9828 PetscCall(VecRestoreArrayRead(cellgeom, &cellGeomArr)); 9829 PetscCall(VecRestoreArrayRead(facegeom, &faceGeomArr)); 9830 PetscCall(PetscOptionsGetViewer(comm, NULL, NULL, "-dm_plex_orthogonal_quality_label_view", &vwr, NULL, NULL)); 9831 if (OrthQualLabel) { 9832 if (vwr) PetscCall(DMLabelView(*OrthQualLabel, vwr)); 9833 } 9834 PetscCall(PetscFree5(idx, oqVals, ci, fi, Ai)); 9835 PetscCall(PetscOptionsRestoreViewer(&vwr)); 9836 PetscCall(VecViewFromOptions(*OrthQual, NULL, "-dm_plex_orthogonal_quality_vec_view")); 9837 PetscFunctionReturn(PETSC_SUCCESS); 9838 } 9839 9840 /* this is here instead of DMGetOutputDM because output DM still has constraints in the local indices that affect 9841 * interpolator construction */ 9842 static PetscErrorCode DMGetFullDM(DM dm, DM *odm) 9843 { 9844 PetscSection section, newSection, gsection; 9845 PetscSF sf; 9846 PetscBool hasConstraints, ghasConstraints; 9847 9848 PetscFunctionBegin; 9849 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 9850 PetscAssertPointer(odm, 2); 9851 PetscCall(DMGetLocalSection(dm, §ion)); 9852 PetscCall(PetscSectionHasConstraints(section, &hasConstraints)); 9853 PetscCall(MPIU_Allreduce(&hasConstraints, &ghasConstraints, 1, MPIU_BOOL, MPI_LOR, PetscObjectComm((PetscObject)dm))); 9854 if (!ghasConstraints) { 9855 PetscCall(PetscObjectReference((PetscObject)dm)); 9856 *odm = dm; 9857 PetscFunctionReturn(PETSC_SUCCESS); 9858 } 9859 PetscCall(DMClone(dm, odm)); 9860 PetscCall(DMCopyFields(dm, *odm)); 9861 PetscCall(DMGetLocalSection(*odm, &newSection)); 9862 PetscCall(DMGetPointSF(*odm, &sf)); 9863 PetscCall(PetscSectionCreateGlobalSection(newSection, sf, PETSC_TRUE, PETSC_TRUE, PETSC_FALSE, &gsection)); 9864 PetscCall(DMSetGlobalSection(*odm, gsection)); 9865 PetscCall(PetscSectionDestroy(&gsection)); 9866 PetscFunctionReturn(PETSC_SUCCESS); 9867 } 9868 9869 static PetscErrorCode DMCreateAffineInterpolationCorrection_Plex(DM dmc, DM dmf, Vec *shift) 9870 { 9871 DM dmco, dmfo; 9872 Mat interpo; 9873 Vec rscale; 9874 Vec cglobalo, clocal; 9875 Vec fglobal, fglobalo, flocal; 9876 PetscBool regular; 9877 9878 PetscFunctionBegin; 9879 PetscCall(DMGetFullDM(dmc, &dmco)); 9880 PetscCall(DMGetFullDM(dmf, &dmfo)); 9881 PetscCall(DMSetCoarseDM(dmfo, dmco)); 9882 PetscCall(DMPlexGetRegularRefinement(dmf, ®ular)); 9883 PetscCall(DMPlexSetRegularRefinement(dmfo, regular)); 9884 PetscCall(DMCreateInterpolation(dmco, dmfo, &interpo, &rscale)); 9885 PetscCall(DMCreateGlobalVector(dmco, &cglobalo)); 9886 PetscCall(DMCreateLocalVector(dmc, &clocal)); 9887 PetscCall(VecSet(cglobalo, 0.)); 9888 PetscCall(VecSet(clocal, 0.)); 9889 PetscCall(DMCreateGlobalVector(dmf, &fglobal)); 9890 PetscCall(DMCreateGlobalVector(dmfo, &fglobalo)); 9891 PetscCall(DMCreateLocalVector(dmf, &flocal)); 9892 PetscCall(VecSet(fglobal, 0.)); 9893 PetscCall(VecSet(fglobalo, 0.)); 9894 PetscCall(VecSet(flocal, 0.)); 9895 PetscCall(DMPlexInsertBoundaryValues(dmc, PETSC_TRUE, clocal, 0., NULL, NULL, NULL)); 9896 PetscCall(DMLocalToGlobalBegin(dmco, clocal, INSERT_VALUES, cglobalo)); 9897 PetscCall(DMLocalToGlobalEnd(dmco, clocal, INSERT_VALUES, cglobalo)); 9898 PetscCall(MatMult(interpo, cglobalo, fglobalo)); 9899 PetscCall(DMGlobalToLocalBegin(dmfo, fglobalo, INSERT_VALUES, flocal)); 9900 PetscCall(DMGlobalToLocalEnd(dmfo, fglobalo, INSERT_VALUES, flocal)); 9901 PetscCall(DMLocalToGlobalBegin(dmf, flocal, INSERT_VALUES, fglobal)); 9902 PetscCall(DMLocalToGlobalEnd(dmf, flocal, INSERT_VALUES, fglobal)); 9903 *shift = fglobal; 9904 PetscCall(VecDestroy(&flocal)); 9905 PetscCall(VecDestroy(&fglobalo)); 9906 PetscCall(VecDestroy(&clocal)); 9907 PetscCall(VecDestroy(&cglobalo)); 9908 PetscCall(VecDestroy(&rscale)); 9909 PetscCall(MatDestroy(&interpo)); 9910 PetscCall(DMDestroy(&dmfo)); 9911 PetscCall(DMDestroy(&dmco)); 9912 PetscFunctionReturn(PETSC_SUCCESS); 9913 } 9914 9915 PETSC_INTERN PetscErrorCode DMInterpolateSolution_Plex(DM coarse, DM fine, Mat interp, Vec coarseSol, Vec fineSol) 9916 { 9917 PetscObject shifto; 9918 Vec shift; 9919 9920 PetscFunctionBegin; 9921 if (!interp) { 9922 Vec rscale; 9923 9924 PetscCall(DMCreateInterpolation(coarse, fine, &interp, &rscale)); 9925 PetscCall(VecDestroy(&rscale)); 9926 } else { 9927 PetscCall(PetscObjectReference((PetscObject)interp)); 9928 } 9929 PetscCall(PetscObjectQuery((PetscObject)interp, "_DMInterpolateSolution_Plex_Vec", &shifto)); 9930 if (!shifto) { 9931 PetscCall(DMCreateAffineInterpolationCorrection_Plex(coarse, fine, &shift)); 9932 PetscCall(PetscObjectCompose((PetscObject)interp, "_DMInterpolateSolution_Plex_Vec", (PetscObject)shift)); 9933 shifto = (PetscObject)shift; 9934 PetscCall(VecDestroy(&shift)); 9935 } 9936 shift = (Vec)shifto; 9937 PetscCall(MatInterpolate(interp, coarseSol, fineSol)); 9938 PetscCall(VecAXPY(fineSol, 1.0, shift)); 9939 PetscCall(MatDestroy(&interp)); 9940 PetscFunctionReturn(PETSC_SUCCESS); 9941 } 9942 9943 /* Pointwise interpolation 9944 Just code FEM for now 9945 u^f = I u^c 9946 sum_k u^f_k phi^f_k = I sum_j u^c_j phi^c_j 9947 u^f_i = sum_j psi^f_i I phi^c_j u^c_j 9948 I_{ij} = psi^f_i phi^c_j 9949 */ 9950 PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling) 9951 { 9952 PetscSection gsc, gsf; 9953 PetscInt m, n; 9954 void *ctx; 9955 DM cdm; 9956 PetscBool regular, ismatis, isRefined = dmCoarse->data == dmFine->data ? PETSC_FALSE : PETSC_TRUE; 9957 9958 PetscFunctionBegin; 9959 PetscCall(DMGetGlobalSection(dmFine, &gsf)); 9960 PetscCall(PetscSectionGetConstrainedStorageSize(gsf, &m)); 9961 PetscCall(DMGetGlobalSection(dmCoarse, &gsc)); 9962 PetscCall(PetscSectionGetConstrainedStorageSize(gsc, &n)); 9963 9964 PetscCall(PetscStrcmp(dmCoarse->mattype, MATIS, &ismatis)); 9965 PetscCall(MatCreate(PetscObjectComm((PetscObject)dmCoarse), interpolation)); 9966 PetscCall(MatSetSizes(*interpolation, m, n, PETSC_DETERMINE, PETSC_DETERMINE)); 9967 PetscCall(MatSetType(*interpolation, ismatis ? MATAIJ : dmCoarse->mattype)); 9968 PetscCall(DMGetApplicationContext(dmFine, &ctx)); 9969 9970 PetscCall(DMGetCoarseDM(dmFine, &cdm)); 9971 PetscCall(DMPlexGetRegularRefinement(dmFine, ®ular)); 9972 if (!isRefined || (regular && cdm == dmCoarse)) PetscCall(DMPlexComputeInterpolatorNested(dmCoarse, dmFine, isRefined, *interpolation, ctx)); 9973 else PetscCall(DMPlexComputeInterpolatorGeneral(dmCoarse, dmFine, *interpolation, ctx)); 9974 PetscCall(MatViewFromOptions(*interpolation, NULL, "-interp_mat_view")); 9975 if (scaling) { 9976 /* Use naive scaling */ 9977 PetscCall(DMCreateInterpolationScale(dmCoarse, dmFine, *interpolation, scaling)); 9978 } 9979 PetscFunctionReturn(PETSC_SUCCESS); 9980 } 9981 9982 PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat) 9983 { 9984 VecScatter ctx; 9985 9986 PetscFunctionBegin; 9987 PetscCall(DMPlexComputeInjectorFEM(dmCoarse, dmFine, &ctx, NULL)); 9988 PetscCall(MatCreateScatter(PetscObjectComm((PetscObject)ctx), ctx, mat)); 9989 PetscCall(VecScatterDestroy(&ctx)); 9990 PetscFunctionReturn(PETSC_SUCCESS); 9991 } 9992 9993 static void g0_identity_private(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[]) 9994 { 9995 const PetscInt Nc = uOff[1] - uOff[0]; 9996 PetscInt c; 9997 for (c = 0; c < Nc; ++c) g0[c * Nc + c] = 1.0; 9998 } 9999 10000 PetscErrorCode DMCreateMassMatrixLumped_Plex(DM dm, Vec *mass) 10001 { 10002 DM dmc; 10003 PetscDS ds; 10004 Vec ones, locmass; 10005 IS cellIS; 10006 PetscFormKey key; 10007 PetscInt depth; 10008 10009 PetscFunctionBegin; 10010 PetscCall(DMClone(dm, &dmc)); 10011 PetscCall(DMCopyDisc(dm, dmc)); 10012 PetscCall(DMGetDS(dmc, &ds)); 10013 PetscCall(PetscDSSetJacobian(ds, 0, 0, g0_identity_private, NULL, NULL, NULL)); 10014 PetscCall(DMCreateGlobalVector(dmc, mass)); 10015 PetscCall(DMGetLocalVector(dmc, &ones)); 10016 PetscCall(DMGetLocalVector(dmc, &locmass)); 10017 PetscCall(DMPlexGetDepth(dmc, &depth)); 10018 PetscCall(DMGetStratumIS(dmc, "depth", depth, &cellIS)); 10019 PetscCall(VecSet(locmass, 0.0)); 10020 PetscCall(VecSet(ones, 1.0)); 10021 key.label = NULL; 10022 key.value = 0; 10023 key.field = 0; 10024 key.part = 0; 10025 PetscCall(DMPlexComputeJacobian_Action_Internal(dmc, key, cellIS, 0.0, 0.0, ones, NULL, ones, locmass, NULL)); 10026 PetscCall(ISDestroy(&cellIS)); 10027 PetscCall(VecSet(*mass, 0.0)); 10028 PetscCall(DMLocalToGlobalBegin(dmc, locmass, ADD_VALUES, *mass)); 10029 PetscCall(DMLocalToGlobalEnd(dmc, locmass, ADD_VALUES, *mass)); 10030 PetscCall(DMRestoreLocalVector(dmc, &ones)); 10031 PetscCall(DMRestoreLocalVector(dmc, &locmass)); 10032 PetscCall(DMDestroy(&dmc)); 10033 PetscFunctionReturn(PETSC_SUCCESS); 10034 } 10035 10036 PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mass) 10037 { 10038 PetscSection gsc, gsf; 10039 PetscInt m, n; 10040 void *ctx; 10041 DM cdm; 10042 PetscBool regular; 10043 10044 PetscFunctionBegin; 10045 if (dmFine == dmCoarse) { 10046 DM dmc; 10047 PetscDS ds; 10048 PetscWeakForm wf; 10049 Vec u; 10050 IS cellIS; 10051 PetscFormKey key; 10052 PetscInt depth; 10053 10054 PetscCall(DMClone(dmFine, &dmc)); 10055 PetscCall(DMCopyDisc(dmFine, dmc)); 10056 PetscCall(DMGetDS(dmc, &ds)); 10057 PetscCall(PetscDSGetWeakForm(ds, &wf)); 10058 PetscCall(PetscWeakFormClear(wf)); 10059 PetscCall(PetscDSSetJacobian(ds, 0, 0, g0_identity_private, NULL, NULL, NULL)); 10060 PetscCall(DMCreateMatrix(dmc, mass)); 10061 PetscCall(DMGetLocalVector(dmc, &u)); 10062 PetscCall(DMPlexGetDepth(dmc, &depth)); 10063 PetscCall(DMGetStratumIS(dmc, "depth", depth, &cellIS)); 10064 PetscCall(MatZeroEntries(*mass)); 10065 key.label = NULL; 10066 key.value = 0; 10067 key.field = 0; 10068 key.part = 0; 10069 PetscCall(DMPlexComputeJacobian_Internal(dmc, key, cellIS, 0.0, 0.0, u, NULL, *mass, *mass, NULL)); 10070 PetscCall(ISDestroy(&cellIS)); 10071 PetscCall(DMRestoreLocalVector(dmc, &u)); 10072 PetscCall(DMDestroy(&dmc)); 10073 } else { 10074 PetscCall(DMGetGlobalSection(dmFine, &gsf)); 10075 PetscCall(PetscSectionGetConstrainedStorageSize(gsf, &m)); 10076 PetscCall(DMGetGlobalSection(dmCoarse, &gsc)); 10077 PetscCall(PetscSectionGetConstrainedStorageSize(gsc, &n)); 10078 10079 PetscCall(MatCreate(PetscObjectComm((PetscObject)dmCoarse), mass)); 10080 PetscCall(MatSetSizes(*mass, m, n, PETSC_DETERMINE, PETSC_DETERMINE)); 10081 PetscCall(MatSetType(*mass, dmCoarse->mattype)); 10082 PetscCall(DMGetApplicationContext(dmFine, &ctx)); 10083 10084 PetscCall(DMGetCoarseDM(dmFine, &cdm)); 10085 PetscCall(DMPlexGetRegularRefinement(dmFine, ®ular)); 10086 if (regular && cdm == dmCoarse) PetscCall(DMPlexComputeMassMatrixNested(dmCoarse, dmFine, *mass, ctx)); 10087 else PetscCall(DMPlexComputeMassMatrixGeneral(dmCoarse, dmFine, *mass, ctx)); 10088 } 10089 PetscCall(MatViewFromOptions(*mass, NULL, "-mass_mat_view")); 10090 PetscFunctionReturn(PETSC_SUCCESS); 10091 } 10092 10093 /*@ 10094 DMPlexGetRegularRefinement - Get the flag indicating that this mesh was obtained by regular refinement from its coarse mesh 10095 10096 Input Parameter: 10097 . dm - The `DMPLEX` object 10098 10099 Output Parameter: 10100 . regular - The flag 10101 10102 Level: intermediate 10103 10104 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexSetRegularRefinement()` 10105 @*/ 10106 PetscErrorCode DMPlexGetRegularRefinement(DM dm, PetscBool *regular) 10107 { 10108 PetscFunctionBegin; 10109 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 10110 PetscAssertPointer(regular, 2); 10111 *regular = ((DM_Plex *)dm->data)->regularRefinement; 10112 PetscFunctionReturn(PETSC_SUCCESS); 10113 } 10114 10115 /*@ 10116 DMPlexSetRegularRefinement - Set the flag indicating that this mesh was obtained by regular refinement from its coarse mesh 10117 10118 Input Parameters: 10119 + dm - The `DMPLEX` object 10120 - regular - The flag 10121 10122 Level: intermediate 10123 10124 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetRegularRefinement()` 10125 @*/ 10126 PetscErrorCode DMPlexSetRegularRefinement(DM dm, PetscBool regular) 10127 { 10128 PetscFunctionBegin; 10129 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 10130 ((DM_Plex *)dm->data)->regularRefinement = regular; 10131 PetscFunctionReturn(PETSC_SUCCESS); 10132 } 10133 10134 /*@ 10135 DMPlexGetAnchors - Get the layout of the anchor (point-to-point) constraints. Typically, the user will not have to 10136 call DMPlexGetAnchors() directly: if there are anchors, then `DMPlexGetAnchors()` is called during `DMGetDefaultConstraints()`. 10137 10138 Not Collective 10139 10140 Input Parameter: 10141 . dm - The `DMPLEX` object 10142 10143 Output Parameters: 10144 + anchorSection - If not `NULL`, set to the section describing which points anchor the constrained points. 10145 - anchorIS - If not `NULL`, set to the list of anchors indexed by `anchorSection` 10146 10147 Level: intermediate 10148 10149 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexSetAnchors()`, `DMGetDefaultConstraints()`, `DMSetDefaultConstraints()`, `IS`, `PetscSection` 10150 @*/ 10151 PetscErrorCode DMPlexGetAnchors(DM dm, PetscSection *anchorSection, IS *anchorIS) 10152 { 10153 DM_Plex *plex = (DM_Plex *)dm->data; 10154 10155 PetscFunctionBegin; 10156 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 10157 if (!plex->anchorSection && !plex->anchorIS && plex->createanchors) PetscCall((*plex->createanchors)(dm)); 10158 if (anchorSection) *anchorSection = plex->anchorSection; 10159 if (anchorIS) *anchorIS = plex->anchorIS; 10160 PetscFunctionReturn(PETSC_SUCCESS); 10161 } 10162 10163 /*@ 10164 DMPlexSetAnchors - Set the layout of the local anchor (point-to-point) constraints. 10165 10166 Collective 10167 10168 Input Parameters: 10169 + dm - The `DMPLEX` object 10170 . anchorSection - The section that describes the mapping from constrained points to the anchor points listed in anchorIS. 10171 Must have a local communicator (`PETSC_COMM_SELF` or derivative). 10172 - anchorIS - The list of all anchor points. Must have a local communicator (`PETSC_COMM_SELF` or derivative). 10173 10174 Level: intermediate 10175 10176 Notes: 10177 Unlike boundary conditions, when a point's degrees of freedom in a section are constrained to 10178 an outside value, the anchor constraints set a point's degrees of freedom to be a linear 10179 combination of other points' degrees of freedom. 10180 10181 After specifying the layout of constraints with `DMPlexSetAnchors()`, one specifies the constraints by calling 10182 `DMGetDefaultConstraints()` and filling in the entries in the constraint matrix. 10183 10184 The reference counts of `anchorSection` and `anchorIS` are incremented. 10185 10186 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetAnchors()`, `DMGetDefaultConstraints()`, `DMSetDefaultConstraints()` 10187 @*/ 10188 PetscErrorCode DMPlexSetAnchors(DM dm, PetscSection anchorSection, IS anchorIS) 10189 { 10190 DM_Plex *plex = (DM_Plex *)dm->data; 10191 PetscMPIInt result; 10192 10193 PetscFunctionBegin; 10194 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 10195 if (anchorSection) { 10196 PetscValidHeaderSpecific(anchorSection, PETSC_SECTION_CLASSID, 2); 10197 PetscCallMPI(MPI_Comm_compare(PETSC_COMM_SELF, PetscObjectComm((PetscObject)anchorSection), &result)); 10198 PetscCheck(result == MPI_CONGRUENT || result == MPI_IDENT, PETSC_COMM_SELF, PETSC_ERR_ARG_NOTSAMECOMM, "anchor section must have local communicator"); 10199 } 10200 if (anchorIS) { 10201 PetscValidHeaderSpecific(anchorIS, IS_CLASSID, 3); 10202 PetscCallMPI(MPI_Comm_compare(PETSC_COMM_SELF, PetscObjectComm((PetscObject)anchorIS), &result)); 10203 PetscCheck(result == MPI_CONGRUENT || result == MPI_IDENT, PETSC_COMM_SELF, PETSC_ERR_ARG_NOTSAMECOMM, "anchor IS must have local communicator"); 10204 } 10205 10206 PetscCall(PetscObjectReference((PetscObject)anchorSection)); 10207 PetscCall(PetscSectionDestroy(&plex->anchorSection)); 10208 plex->anchorSection = anchorSection; 10209 10210 PetscCall(PetscObjectReference((PetscObject)anchorIS)); 10211 PetscCall(ISDestroy(&plex->anchorIS)); 10212 plex->anchorIS = anchorIS; 10213 10214 if (PetscUnlikelyDebug(anchorIS && anchorSection)) { 10215 PetscInt size, a, pStart, pEnd; 10216 const PetscInt *anchors; 10217 10218 PetscCall(PetscSectionGetChart(anchorSection, &pStart, &pEnd)); 10219 PetscCall(ISGetLocalSize(anchorIS, &size)); 10220 PetscCall(ISGetIndices(anchorIS, &anchors)); 10221 for (a = 0; a < size; a++) { 10222 PetscInt p; 10223 10224 p = anchors[a]; 10225 if (p >= pStart && p < pEnd) { 10226 PetscInt dof; 10227 10228 PetscCall(PetscSectionGetDof(anchorSection, p, &dof)); 10229 if (dof) { 10230 PetscCall(ISRestoreIndices(anchorIS, &anchors)); 10231 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Point %" PetscInt_FMT " cannot be constrained and an anchor", p); 10232 } 10233 } 10234 } 10235 PetscCall(ISRestoreIndices(anchorIS, &anchors)); 10236 } 10237 /* reset the generic constraints */ 10238 PetscCall(DMSetDefaultConstraints(dm, NULL, NULL, NULL)); 10239 PetscFunctionReturn(PETSC_SUCCESS); 10240 } 10241 10242 static PetscErrorCode DMPlexCreateConstraintSection_Anchors(DM dm, PetscSection section, PetscSection *cSec) 10243 { 10244 PetscSection anchorSection; 10245 PetscInt pStart, pEnd, sStart, sEnd, p, dof, numFields, f; 10246 10247 PetscFunctionBegin; 10248 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 10249 PetscCall(DMPlexGetAnchors(dm, &anchorSection, NULL)); 10250 PetscCall(PetscSectionCreate(PETSC_COMM_SELF, cSec)); 10251 PetscCall(PetscSectionGetNumFields(section, &numFields)); 10252 if (numFields) { 10253 PetscInt f; 10254 PetscCall(PetscSectionSetNumFields(*cSec, numFields)); 10255 10256 for (f = 0; f < numFields; f++) { 10257 PetscInt numComp; 10258 10259 PetscCall(PetscSectionGetFieldComponents(section, f, &numComp)); 10260 PetscCall(PetscSectionSetFieldComponents(*cSec, f, numComp)); 10261 } 10262 } 10263 PetscCall(PetscSectionGetChart(anchorSection, &pStart, &pEnd)); 10264 PetscCall(PetscSectionGetChart(section, &sStart, &sEnd)); 10265 pStart = PetscMax(pStart, sStart); 10266 pEnd = PetscMin(pEnd, sEnd); 10267 pEnd = PetscMax(pStart, pEnd); 10268 PetscCall(PetscSectionSetChart(*cSec, pStart, pEnd)); 10269 for (p = pStart; p < pEnd; p++) { 10270 PetscCall(PetscSectionGetDof(anchorSection, p, &dof)); 10271 if (dof) { 10272 PetscCall(PetscSectionGetDof(section, p, &dof)); 10273 PetscCall(PetscSectionSetDof(*cSec, p, dof)); 10274 for (f = 0; f < numFields; f++) { 10275 PetscCall(PetscSectionGetFieldDof(section, p, f, &dof)); 10276 PetscCall(PetscSectionSetFieldDof(*cSec, p, f, dof)); 10277 } 10278 } 10279 } 10280 PetscCall(PetscSectionSetUp(*cSec)); 10281 PetscCall(PetscObjectSetName((PetscObject)*cSec, "Constraint Section")); 10282 PetscFunctionReturn(PETSC_SUCCESS); 10283 } 10284 10285 static PetscErrorCode DMPlexCreateConstraintMatrix_Anchors(DM dm, PetscSection section, PetscSection cSec, Mat *cMat) 10286 { 10287 PetscSection aSec; 10288 PetscInt pStart, pEnd, p, sStart, sEnd, dof, aDof, aOff, off, nnz, annz, m, n, q, a, offset, *i, *j; 10289 const PetscInt *anchors; 10290 PetscInt numFields, f; 10291 IS aIS; 10292 MatType mtype; 10293 PetscBool iscuda, iskokkos; 10294 10295 PetscFunctionBegin; 10296 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 10297 PetscCall(PetscSectionGetStorageSize(cSec, &m)); 10298 PetscCall(PetscSectionGetStorageSize(section, &n)); 10299 PetscCall(MatCreate(PETSC_COMM_SELF, cMat)); 10300 PetscCall(MatSetSizes(*cMat, m, n, m, n)); 10301 PetscCall(PetscStrcmp(dm->mattype, MATSEQAIJCUSPARSE, &iscuda)); 10302 if (!iscuda) PetscCall(PetscStrcmp(dm->mattype, MATMPIAIJCUSPARSE, &iscuda)); 10303 PetscCall(PetscStrcmp(dm->mattype, MATSEQAIJKOKKOS, &iskokkos)); 10304 if (!iskokkos) PetscCall(PetscStrcmp(dm->mattype, MATMPIAIJKOKKOS, &iskokkos)); 10305 if (iscuda) mtype = MATSEQAIJCUSPARSE; 10306 else if (iskokkos) mtype = MATSEQAIJKOKKOS; 10307 else mtype = MATSEQAIJ; 10308 PetscCall(MatSetType(*cMat, mtype)); 10309 PetscCall(DMPlexGetAnchors(dm, &aSec, &aIS)); 10310 PetscCall(ISGetIndices(aIS, &anchors)); 10311 /* cSec will be a subset of aSec and section */ 10312 PetscCall(PetscSectionGetChart(cSec, &pStart, &pEnd)); 10313 PetscCall(PetscSectionGetChart(section, &sStart, &sEnd)); 10314 PetscCall(PetscMalloc1(m + 1, &i)); 10315 i[0] = 0; 10316 PetscCall(PetscSectionGetNumFields(section, &numFields)); 10317 for (p = pStart; p < pEnd; p++) { 10318 PetscInt rDof, rOff, r; 10319 10320 PetscCall(PetscSectionGetDof(aSec, p, &rDof)); 10321 if (!rDof) continue; 10322 PetscCall(PetscSectionGetOffset(aSec, p, &rOff)); 10323 if (numFields) { 10324 for (f = 0; f < numFields; f++) { 10325 annz = 0; 10326 for (r = 0; r < rDof; r++) { 10327 a = anchors[rOff + r]; 10328 if (a < sStart || a >= sEnd) continue; 10329 PetscCall(PetscSectionGetFieldDof(section, a, f, &aDof)); 10330 annz += aDof; 10331 } 10332 PetscCall(PetscSectionGetFieldDof(cSec, p, f, &dof)); 10333 PetscCall(PetscSectionGetFieldOffset(cSec, p, f, &off)); 10334 for (q = 0; q < dof; q++) i[off + q + 1] = i[off + q] + annz; 10335 } 10336 } else { 10337 annz = 0; 10338 PetscCall(PetscSectionGetDof(cSec, p, &dof)); 10339 for (q = 0; q < dof; q++) { 10340 a = anchors[rOff + q]; 10341 if (a < sStart || a >= sEnd) continue; 10342 PetscCall(PetscSectionGetDof(section, a, &aDof)); 10343 annz += aDof; 10344 } 10345 PetscCall(PetscSectionGetDof(cSec, p, &dof)); 10346 PetscCall(PetscSectionGetOffset(cSec, p, &off)); 10347 for (q = 0; q < dof; q++) i[off + q + 1] = i[off + q] + annz; 10348 } 10349 } 10350 nnz = i[m]; 10351 PetscCall(PetscMalloc1(nnz, &j)); 10352 offset = 0; 10353 for (p = pStart; p < pEnd; p++) { 10354 if (numFields) { 10355 for (f = 0; f < numFields; f++) { 10356 PetscCall(PetscSectionGetFieldDof(cSec, p, f, &dof)); 10357 for (q = 0; q < dof; q++) { 10358 PetscInt rDof, rOff, r; 10359 PetscCall(PetscSectionGetDof(aSec, p, &rDof)); 10360 PetscCall(PetscSectionGetOffset(aSec, p, &rOff)); 10361 for (r = 0; r < rDof; r++) { 10362 PetscInt s; 10363 10364 a = anchors[rOff + r]; 10365 if (a < sStart || a >= sEnd) continue; 10366 PetscCall(PetscSectionGetFieldDof(section, a, f, &aDof)); 10367 PetscCall(PetscSectionGetFieldOffset(section, a, f, &aOff)); 10368 for (s = 0; s < aDof; s++) j[offset++] = aOff + s; 10369 } 10370 } 10371 } 10372 } else { 10373 PetscCall(PetscSectionGetDof(cSec, p, &dof)); 10374 for (q = 0; q < dof; q++) { 10375 PetscInt rDof, rOff, r; 10376 PetscCall(PetscSectionGetDof(aSec, p, &rDof)); 10377 PetscCall(PetscSectionGetOffset(aSec, p, &rOff)); 10378 for (r = 0; r < rDof; r++) { 10379 PetscInt s; 10380 10381 a = anchors[rOff + r]; 10382 if (a < sStart || a >= sEnd) continue; 10383 PetscCall(PetscSectionGetDof(section, a, &aDof)); 10384 PetscCall(PetscSectionGetOffset(section, a, &aOff)); 10385 for (s = 0; s < aDof; s++) j[offset++] = aOff + s; 10386 } 10387 } 10388 } 10389 } 10390 PetscCall(MatSeqAIJSetPreallocationCSR(*cMat, i, j, NULL)); 10391 PetscCall(PetscFree(i)); 10392 PetscCall(PetscFree(j)); 10393 PetscCall(ISRestoreIndices(aIS, &anchors)); 10394 PetscFunctionReturn(PETSC_SUCCESS); 10395 } 10396 10397 PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm) 10398 { 10399 DM_Plex *plex = (DM_Plex *)dm->data; 10400 PetscSection anchorSection, section, cSec; 10401 Mat cMat; 10402 10403 PetscFunctionBegin; 10404 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 10405 PetscCall(DMPlexGetAnchors(dm, &anchorSection, NULL)); 10406 if (anchorSection) { 10407 PetscInt Nf; 10408 10409 PetscCall(DMGetLocalSection(dm, §ion)); 10410 PetscCall(DMPlexCreateConstraintSection_Anchors(dm, section, &cSec)); 10411 PetscCall(DMPlexCreateConstraintMatrix_Anchors(dm, section, cSec, &cMat)); 10412 PetscCall(DMGetNumFields(dm, &Nf)); 10413 if (Nf && plex->computeanchormatrix) PetscCall((*plex->computeanchormatrix)(dm, section, cSec, cMat)); 10414 PetscCall(DMSetDefaultConstraints(dm, cSec, cMat, NULL)); 10415 PetscCall(PetscSectionDestroy(&cSec)); 10416 PetscCall(MatDestroy(&cMat)); 10417 } 10418 PetscFunctionReturn(PETSC_SUCCESS); 10419 } 10420 10421 PetscErrorCode DMCreateSubDomainDM_Plex(DM dm, DMLabel label, PetscInt value, IS *is, DM *subdm) 10422 { 10423 IS subis; 10424 PetscSection section, subsection; 10425 10426 PetscFunctionBegin; 10427 PetscCall(DMGetLocalSection(dm, §ion)); 10428 PetscCheck(section, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Must set default section for DM before splitting subdomain"); 10429 PetscCheck(subdm, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Must set output subDM for splitting subdomain"); 10430 /* Create subdomain */ 10431 PetscCall(DMPlexFilter(dm, label, value, subdm)); 10432 /* Create submodel */ 10433 PetscCall(DMPlexGetSubpointIS(*subdm, &subis)); 10434 PetscCall(PetscSectionCreateSubmeshSection(section, subis, &subsection)); 10435 PetscCall(DMSetLocalSection(*subdm, subsection)); 10436 PetscCall(PetscSectionDestroy(&subsection)); 10437 PetscCall(DMCopyDisc(dm, *subdm)); 10438 /* Create map from submodel to global model */ 10439 if (is) { 10440 PetscSection sectionGlobal, subsectionGlobal; 10441 IS spIS; 10442 const PetscInt *spmap; 10443 PetscInt *subIndices; 10444 PetscInt subSize = 0, subOff = 0, pStart, pEnd, p; 10445 PetscInt Nf, f, bs = -1, bsLocal[2], bsMinMax[2]; 10446 10447 PetscCall(DMPlexGetSubpointIS(*subdm, &spIS)); 10448 PetscCall(ISGetIndices(spIS, &spmap)); 10449 PetscCall(PetscSectionGetNumFields(section, &Nf)); 10450 PetscCall(DMGetGlobalSection(dm, §ionGlobal)); 10451 PetscCall(DMGetGlobalSection(*subdm, &subsectionGlobal)); 10452 PetscCall(PetscSectionGetChart(subsection, &pStart, &pEnd)); 10453 for (p = pStart; p < pEnd; ++p) { 10454 PetscInt gdof, pSubSize = 0; 10455 10456 PetscCall(PetscSectionGetDof(sectionGlobal, p, &gdof)); 10457 if (gdof > 0) { 10458 for (f = 0; f < Nf; ++f) { 10459 PetscInt fdof, fcdof; 10460 10461 PetscCall(PetscSectionGetFieldDof(subsection, p, f, &fdof)); 10462 PetscCall(PetscSectionGetFieldConstraintDof(subsection, p, f, &fcdof)); 10463 pSubSize += fdof - fcdof; 10464 } 10465 subSize += pSubSize; 10466 if (pSubSize) { 10467 if (bs < 0) { 10468 bs = pSubSize; 10469 } else if (bs != pSubSize) { 10470 /* Layout does not admit a pointwise block size */ 10471 bs = 1; 10472 } 10473 } 10474 } 10475 } 10476 /* Must have same blocksize on all procs (some might have no points) */ 10477 bsLocal[0] = bs < 0 ? PETSC_MAX_INT : bs; 10478 bsLocal[1] = bs; 10479 PetscCall(PetscGlobalMinMaxInt(PetscObjectComm((PetscObject)dm), bsLocal, bsMinMax)); 10480 if (bsMinMax[0] != bsMinMax[1]) { 10481 bs = 1; 10482 } else { 10483 bs = bsMinMax[0]; 10484 } 10485 PetscCall(PetscMalloc1(subSize, &subIndices)); 10486 for (p = pStart; p < pEnd; ++p) { 10487 PetscInt gdof, goff; 10488 10489 PetscCall(PetscSectionGetDof(subsectionGlobal, p, &gdof)); 10490 if (gdof > 0) { 10491 const PetscInt point = spmap[p]; 10492 10493 PetscCall(PetscSectionGetOffset(sectionGlobal, point, &goff)); 10494 for (f = 0; f < Nf; ++f) { 10495 PetscInt fdof, fcdof, fc, f2, poff = 0; 10496 10497 /* Can get rid of this loop by storing field information in the global section */ 10498 for (f2 = 0; f2 < f; ++f2) { 10499 PetscCall(PetscSectionGetFieldDof(section, p, f2, &fdof)); 10500 PetscCall(PetscSectionGetFieldConstraintDof(section, p, f2, &fcdof)); 10501 poff += fdof - fcdof; 10502 } 10503 PetscCall(PetscSectionGetFieldDof(section, p, f, &fdof)); 10504 PetscCall(PetscSectionGetFieldConstraintDof(section, p, f, &fcdof)); 10505 for (fc = 0; fc < fdof - fcdof; ++fc, ++subOff) subIndices[subOff] = goff + poff + fc; 10506 } 10507 } 10508 } 10509 PetscCall(ISRestoreIndices(spIS, &spmap)); 10510 PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), subSize, subIndices, PETSC_OWN_POINTER, is)); 10511 if (bs > 1) { 10512 /* We need to check that the block size does not come from non-contiguous fields */ 10513 PetscInt i, j, set = 1; 10514 for (i = 0; i < subSize; i += bs) { 10515 for (j = 0; j < bs; ++j) { 10516 if (subIndices[i + j] != subIndices[i] + j) { 10517 set = 0; 10518 break; 10519 } 10520 } 10521 } 10522 if (set) PetscCall(ISSetBlockSize(*is, bs)); 10523 } 10524 /* Attach nullspace */ 10525 for (f = 0; f < Nf; ++f) { 10526 (*subdm)->nullspaceConstructors[f] = dm->nullspaceConstructors[f]; 10527 if ((*subdm)->nullspaceConstructors[f]) break; 10528 } 10529 if (f < Nf) { 10530 MatNullSpace nullSpace; 10531 PetscCall((*(*subdm)->nullspaceConstructors[f])(*subdm, f, f, &nullSpace)); 10532 10533 PetscCall(PetscObjectCompose((PetscObject)*is, "nullspace", (PetscObject)nullSpace)); 10534 PetscCall(MatNullSpaceDestroy(&nullSpace)); 10535 } 10536 } 10537 PetscFunctionReturn(PETSC_SUCCESS); 10538 } 10539 10540 /*@ 10541 DMPlexMonitorThroughput - Report the cell throughput of FE integration 10542 10543 Input Parameters: 10544 + dm - The `DM` 10545 - dummy - unused argument 10546 10547 Options Database Key: 10548 . -dm_plex_monitor_throughput - Activate the monitor 10549 10550 Level: developer 10551 10552 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMSetFromOptions()`, `DMPlexCreate()` 10553 @*/ 10554 PetscErrorCode DMPlexMonitorThroughput(DM dm, void *dummy) 10555 { 10556 PetscLogHandler default_handler; 10557 10558 PetscFunctionBegin; 10559 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 10560 PetscCall(PetscLogGetDefaultHandler(&default_handler)); 10561 if (default_handler) { 10562 PetscLogEvent event; 10563 PetscEventPerfInfo eventInfo; 10564 PetscReal cellRate, flopRate; 10565 PetscInt cStart, cEnd, Nf, N; 10566 const char *name; 10567 10568 PetscCall(PetscObjectGetName((PetscObject)dm, &name)); 10569 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 10570 PetscCall(DMGetNumFields(dm, &Nf)); 10571 PetscCall(PetscLogEventGetId("DMPlexResidualFE", &event)); 10572 PetscCall(PetscLogEventGetPerfInfo(PETSC_DEFAULT, event, &eventInfo)); 10573 N = (cEnd - cStart) * Nf * eventInfo.count; 10574 flopRate = eventInfo.flops / eventInfo.time; 10575 cellRate = N / eventInfo.time; 10576 PetscCall(PetscPrintf(PetscObjectComm((PetscObject)dm), "DM (%s) FE Residual Integration: %" PetscInt_FMT " integrals %d reps\n Cell rate: %.2g/s flop rate: %.2g MF/s\n", name ? name : "unknown", N, eventInfo.count, (double)cellRate, (double)(flopRate / 1.e6))); 10577 } else { 10578 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Plex Throughput Monitor is not supported if logging is turned off or the default log handler is not running. Reconfigure using --with-log and run with -log_view."); 10579 } 10580 PetscFunctionReturn(PETSC_SUCCESS); 10581 } 10582