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 just gives the first range of cells found. If the mesh has several cell types, it will only give the first. 79 80 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexConstructGhostCells()`, `DMPlexGetCellTypeStratum()` 81 @*/ 82 PetscErrorCode DMPlexGetSimplexOrBoxCells(DM dm, PetscInt height, PetscInt *cStart, PetscInt *cEnd) 83 { 84 DMPolytopeType ct = DM_POLYTOPE_UNKNOWN; 85 PetscInt cS, cE, c; 86 87 PetscFunctionBegin; 88 PetscCall(DMPlexGetHeightStratum(dm, PetscMax(height, 0), &cS, &cE)); 89 for (c = cS; c < cE; ++c) { 90 DMPolytopeType cct; 91 92 PetscCall(DMPlexGetCellType(dm, c, &cct)); 93 if ((PetscInt)cct < 0) break; 94 switch (cct) { 95 case DM_POLYTOPE_POINT: 96 case DM_POLYTOPE_SEGMENT: 97 case DM_POLYTOPE_TRIANGLE: 98 case DM_POLYTOPE_QUADRILATERAL: 99 case DM_POLYTOPE_TETRAHEDRON: 100 case DM_POLYTOPE_HEXAHEDRON: 101 ct = cct; 102 break; 103 default: 104 break; 105 } 106 if (ct != DM_POLYTOPE_UNKNOWN) break; 107 } 108 if (ct != DM_POLYTOPE_UNKNOWN) { 109 DMLabel ctLabel; 110 111 PetscCall(DMPlexGetCellTypeLabel(dm, &ctLabel)); 112 PetscCall(DMLabelGetStratumBounds(ctLabel, ct, &cS, &cE)); 113 // Reset label for fast lookup 114 PetscCall(DMLabelMakeAllInvalid_Internal(ctLabel)); 115 } 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; 130 131 /* the vcdof and globalvcdof are sized to allow every polytope type and simple vertex at DM_NUM_POLYTOPES */ 132 PetscCall(PetscArrayzero(vcdof, DM_NUM_POLYTOPES + 1)); 133 PetscCall(DMGetCoordinateDim(dm, &cdim)); 134 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 135 PetscCall(PetscSectionGetChart(section, &pStart, &pEnd)); 136 if (field >= 0) { 137 if ((vStart >= pStart) && (vStart < pEnd)) PetscCall(PetscSectionGetFieldDof(section, vStart, field, &vcdof[DM_NUM_POLYTOPES])); 138 } else { 139 if ((vStart >= pStart) && (vStart < pEnd)) PetscCall(PetscSectionGetDof(section, vStart, &vcdof[DM_NUM_POLYTOPES])); 140 } 141 142 PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight)); 143 PetscCall(DMPlexGetDepth(dm, &depth)); 144 PetscCall(DMPlexGetDepthLabel(dm, &depthLabel)); 145 PetscCall(DMPlexGetCellTypeLabel(dm, &ctLabel)); 146 for (c = 0; c < DM_NUM_POLYTOPES; ++c) { 147 const DMPolytopeType ict = (DMPolytopeType)c; 148 PetscInt dep; 149 150 if (ict == DM_POLYTOPE_FV_GHOST) continue; 151 PetscCall(DMLabelGetStratumBounds(ctLabel, ict, &cStart, &cEnd)); 152 if (pStart >= 0) { 153 PetscCall(DMLabelGetValue(depthLabel, cStart, &dep)); 154 if (dep != depth - cellHeight) continue; 155 } 156 if (field >= 0) { 157 if ((cStart >= pStart) && (cStart < pEnd)) PetscCall(PetscSectionGetFieldDof(section, cStart, field, &vcdof[c])); 158 } else { 159 if ((cStart >= pStart) && (cStart < pEnd)) PetscCall(PetscSectionGetDof(section, cStart, &vcdof[c])); 160 } 161 PetscCall(MPIU_Allreduce(vcdof, globalvcdof, 2, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm))); 162 } 163 164 PetscCall(MPIU_Allreduce(vcdof, globalvcdof, DM_NUM_POLYTOPES + 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm))); 165 *types = 0; 166 167 for (c = 0; c < DM_NUM_POLYTOPES + 1; ++c) { 168 if (globalvcdof[c]) ++(*types); 169 } 170 171 PetscCall(PetscMalloc3(*types, &sStart, *types, &sEnd, *types, &ft)); 172 t = 0; 173 if (globalvcdof[DM_NUM_POLYTOPES]) { 174 sStart[t] = vStart; 175 sEnd[t] = vEnd; 176 ft[t] = (globalvcdof[t] == cdim) ? PETSC_VTK_POINT_VECTOR_FIELD : PETSC_VTK_POINT_FIELD; 177 ++t; 178 } 179 180 for (c = 0; c < DM_NUM_POLYTOPES; ++c) { 181 if (globalvcdof[c]) { 182 const DMPolytopeType ict = (DMPolytopeType)c; 183 184 PetscCall(DMLabelGetStratumBounds(ctLabel, ict, &cStart, &cEnd)); 185 sStart[t] = cStart; 186 sEnd[t] = cEnd; 187 ft[t] = (globalvcdof[c] == cdim) ? PETSC_VTK_CELL_VECTOR_FIELD : PETSC_VTK_CELL_FIELD; 188 ++t; 189 } 190 } 191 192 if (!(*types)) { 193 if (field >= 0) { 194 const char *fieldname; 195 196 PetscCall(PetscSectionGetFieldName(section, field, &fieldname)); 197 PetscCall(PetscInfo((PetscObject)dm, "Could not classify VTK output type of section field %" PetscInt_FMT " \"%s\"\n", field, fieldname)); 198 } else { 199 PetscCall(PetscInfo((PetscObject)dm, "Could not classify VTK output type of section\n")); 200 } 201 } 202 203 *ssStart = sStart; 204 *ssEnd = sEnd; 205 *sft = ft; 206 PetscFunctionReturn(PETSC_SUCCESS); 207 } 208 209 PetscErrorCode DMPlexRestoreFieldTypes_Internal(DM dm, PetscSection section, PetscInt field, PetscInt *types, PetscInt **sStart, PetscInt **sEnd, PetscViewerVTKFieldType **ft) 210 { 211 PetscFunctionBegin; 212 PetscCall(PetscFree3(*sStart, *sEnd, *ft)); 213 PetscFunctionReturn(PETSC_SUCCESS); 214 } 215 216 PetscErrorCode DMPlexGetFieldType_Internal(DM dm, PetscSection section, PetscInt field, PetscInt *sStart, PetscInt *sEnd, PetscViewerVTKFieldType *ft) 217 { 218 PetscInt cdim, pStart, pEnd, vStart, vEnd, cStart, cEnd; 219 PetscInt vcdof[2] = {0, 0}, globalvcdof[2]; 220 221 PetscFunctionBegin; 222 *ft = PETSC_VTK_INVALID; 223 PetscCall(DMGetCoordinateDim(dm, &cdim)); 224 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 225 PetscCall(DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd)); 226 PetscCall(PetscSectionGetChart(section, &pStart, &pEnd)); 227 if (field >= 0) { 228 if ((vStart >= pStart) && (vStart < pEnd)) PetscCall(PetscSectionGetFieldDof(section, vStart, field, &vcdof[0])); 229 if ((cStart >= pStart) && (cStart < pEnd)) PetscCall(PetscSectionGetFieldDof(section, cStart, field, &vcdof[1])); 230 } else { 231 if ((vStart >= pStart) && (vStart < pEnd)) PetscCall(PetscSectionGetDof(section, vStart, &vcdof[0])); 232 if ((cStart >= pStart) && (cStart < pEnd)) PetscCall(PetscSectionGetDof(section, cStart, &vcdof[1])); 233 } 234 PetscCall(MPIU_Allreduce(vcdof, globalvcdof, 2, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm))); 235 if (globalvcdof[0]) { 236 *sStart = vStart; 237 *sEnd = vEnd; 238 if (globalvcdof[0] == cdim) *ft = PETSC_VTK_POINT_VECTOR_FIELD; 239 else *ft = PETSC_VTK_POINT_FIELD; 240 } else if (globalvcdof[1]) { 241 *sStart = cStart; 242 *sEnd = cEnd; 243 if (globalvcdof[1] == cdim) *ft = PETSC_VTK_CELL_VECTOR_FIELD; 244 else *ft = PETSC_VTK_CELL_FIELD; 245 } else { 246 if (field >= 0) { 247 const char *fieldname; 248 249 PetscCall(PetscSectionGetFieldName(section, field, &fieldname)); 250 PetscCall(PetscInfo((PetscObject)dm, "Could not classify VTK output type of section field %" PetscInt_FMT " \"%s\"\n", field, fieldname)); 251 } else { 252 PetscCall(PetscInfo((PetscObject)dm, "Could not classify VTK output type of section\n")); 253 } 254 } 255 PetscFunctionReturn(PETSC_SUCCESS); 256 } 257 258 /*@ 259 DMPlexVecView1D - Plot many 1D solutions on the same line graph 260 261 Collective 262 263 Input Parameters: 264 + dm - The `DMPLEX` object 265 . n - The number of vectors 266 . u - The array of local vectors 267 - viewer - The `PetscViewer` 268 269 Level: advanced 270 271 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `VecViewFromOptions()`, `VecView()` 272 @*/ 273 PetscErrorCode DMPlexVecView1D(DM dm, PetscInt n, Vec u[], PetscViewer viewer) 274 { 275 PetscDS ds; 276 PetscDraw draw = NULL; 277 PetscDrawLG lg; 278 Vec coordinates; 279 const PetscScalar *coords, **sol; 280 PetscReal *vals; 281 PetscInt *Nc; 282 PetscInt Nf, f, c, Nl, l, i, vStart, vEnd, v; 283 char **names; 284 285 PetscFunctionBegin; 286 PetscCall(DMGetDS(dm, &ds)); 287 PetscCall(PetscDSGetNumFields(ds, &Nf)); 288 PetscCall(PetscDSGetTotalComponents(ds, &Nl)); 289 PetscCall(PetscDSGetComponents(ds, &Nc)); 290 291 PetscCall(PetscViewerDrawGetDraw(viewer, 0, &draw)); 292 if (!draw) PetscFunctionReturn(PETSC_SUCCESS); 293 PetscCall(PetscDrawLGCreate(draw, n * Nl, &lg)); 294 295 PetscCall(PetscMalloc3(n, &sol, n * Nl, &names, n * Nl, &vals)); 296 for (i = 0, l = 0; i < n; ++i) { 297 const char *vname; 298 299 PetscCall(PetscObjectGetName((PetscObject)u[i], &vname)); 300 for (f = 0; f < Nf; ++f) { 301 PetscObject disc; 302 const char *fname; 303 char tmpname[PETSC_MAX_PATH_LEN]; 304 305 PetscCall(PetscDSGetDiscretization(ds, f, &disc)); 306 /* TODO Create names for components */ 307 for (c = 0; c < Nc[f]; ++c, ++l) { 308 PetscCall(PetscObjectGetName(disc, &fname)); 309 PetscCall(PetscStrncpy(tmpname, vname, sizeof(tmpname))); 310 PetscCall(PetscStrlcat(tmpname, ":", sizeof(tmpname))); 311 PetscCall(PetscStrlcat(tmpname, fname, sizeof(tmpname))); 312 PetscCall(PetscStrallocpy(tmpname, &names[l])); 313 } 314 } 315 } 316 PetscCall(PetscDrawLGSetLegend(lg, (const char *const *)names)); 317 /* Just add P_1 support for now */ 318 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 319 PetscCall(DMGetCoordinatesLocal(dm, &coordinates)); 320 PetscCall(VecGetArrayRead(coordinates, &coords)); 321 for (i = 0; i < n; ++i) PetscCall(VecGetArrayRead(u[i], &sol[i])); 322 for (v = vStart; v < vEnd; ++v) { 323 PetscScalar *x, *svals; 324 325 PetscCall(DMPlexPointLocalRead(dm, v, coords, &x)); 326 for (i = 0; i < n; ++i) { 327 PetscCall(DMPlexPointLocalRead(dm, v, sol[i], &svals)); 328 for (l = 0; l < Nl; ++l) vals[i * Nl + l] = PetscRealPart(svals[l]); 329 } 330 PetscCall(PetscDrawLGAddCommonPoint(lg, PetscRealPart(x[0]), vals)); 331 } 332 PetscCall(VecRestoreArrayRead(coordinates, &coords)); 333 for (i = 0; i < n; ++i) PetscCall(VecRestoreArrayRead(u[i], &sol[i])); 334 for (l = 0; l < n * Nl; ++l) PetscCall(PetscFree(names[l])); 335 PetscCall(PetscFree3(sol, names, vals)); 336 337 PetscCall(PetscDrawLGDraw(lg)); 338 PetscCall(PetscDrawLGDestroy(&lg)); 339 PetscFunctionReturn(PETSC_SUCCESS); 340 } 341 342 static PetscErrorCode VecView_Plex_Local_Draw_1D(Vec u, PetscViewer viewer) 343 { 344 DM dm; 345 346 PetscFunctionBegin; 347 PetscCall(VecGetDM(u, &dm)); 348 PetscCall(DMPlexVecView1D(dm, 1, &u, viewer)); 349 PetscFunctionReturn(PETSC_SUCCESS); 350 } 351 352 static PetscErrorCode VecView_Plex_Local_Draw_2D(Vec v, PetscViewer viewer) 353 { 354 DM dm; 355 PetscSection s; 356 PetscDraw draw, popup; 357 DM cdm; 358 PetscSection coordSection; 359 Vec coordinates; 360 const PetscScalar *array; 361 PetscReal lbound[3], ubound[3]; 362 PetscReal vbound[2], time; 363 PetscBool flg; 364 PetscInt dim, Nf, f, Nc, comp, vStart, vEnd, cStart, cEnd, c, N, level, step, w = 0; 365 const char *name; 366 char title[PETSC_MAX_PATH_LEN]; 367 368 PetscFunctionBegin; 369 PetscCall(PetscViewerDrawGetDraw(viewer, 0, &draw)); 370 PetscCall(VecGetDM(v, &dm)); 371 PetscCall(DMGetCoordinateDim(dm, &dim)); 372 PetscCall(DMGetLocalSection(dm, &s)); 373 PetscCall(PetscSectionGetNumFields(s, &Nf)); 374 PetscCall(DMGetCoarsenLevel(dm, &level)); 375 PetscCall(DMGetCoordinateDM(dm, &cdm)); 376 PetscCall(DMGetLocalSection(cdm, &coordSection)); 377 PetscCall(DMGetCoordinatesLocal(dm, &coordinates)); 378 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 379 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 380 381 PetscCall(PetscObjectGetName((PetscObject)v, &name)); 382 PetscCall(DMGetOutputSequenceNumber(dm, &step, &time)); 383 384 PetscCall(VecGetLocalSize(coordinates, &N)); 385 PetscCall(DMGetBoundingBox(dm, lbound, ubound)); 386 PetscCall(PetscDrawClear(draw)); 387 388 /* Could implement something like DMDASelectFields() */ 389 for (f = 0; f < Nf; ++f) { 390 DM fdm = dm; 391 Vec fv = v; 392 IS fis; 393 char prefix[PETSC_MAX_PATH_LEN]; 394 const char *fname; 395 396 PetscCall(PetscSectionGetFieldComponents(s, f, &Nc)); 397 PetscCall(PetscSectionGetFieldName(s, f, &fname)); 398 399 if (v->hdr.prefix) PetscCall(PetscStrncpy(prefix, v->hdr.prefix, sizeof(prefix))); 400 else prefix[0] = '\0'; 401 if (Nf > 1) { 402 PetscCall(DMCreateSubDM(dm, 1, &f, &fis, &fdm)); 403 PetscCall(VecGetSubVector(v, fis, &fv)); 404 PetscCall(PetscStrlcat(prefix, fname, sizeof(prefix))); 405 PetscCall(PetscStrlcat(prefix, "_", sizeof(prefix))); 406 } 407 for (comp = 0; comp < Nc; ++comp, ++w) { 408 PetscInt nmax = 2; 409 410 PetscCall(PetscViewerDrawGetDraw(viewer, w, &draw)); 411 if (Nc > 1) PetscCall(PetscSNPrintf(title, sizeof(title), "%s:%s_%" PetscInt_FMT " Step: %" PetscInt_FMT " Time: %.4g", name, fname, comp, step, (double)time)); 412 else PetscCall(PetscSNPrintf(title, sizeof(title), "%s:%s Step: %" PetscInt_FMT " Time: %.4g", name, fname, step, (double)time)); 413 PetscCall(PetscDrawSetTitle(draw, title)); 414 415 /* TODO Get max and min only for this component */ 416 PetscCall(PetscOptionsGetRealArray(NULL, prefix, "-vec_view_bounds", vbound, &nmax, &flg)); 417 if (!flg) { 418 PetscCall(VecMin(fv, NULL, &vbound[0])); 419 PetscCall(VecMax(fv, NULL, &vbound[1])); 420 if (vbound[1] <= vbound[0]) vbound[1] = vbound[0] + 1.0; 421 } 422 423 PetscCall(PetscDrawGetPopup(draw, &popup)); 424 PetscCall(PetscDrawScalePopup(popup, vbound[0], vbound[1])); 425 PetscCall(PetscDrawSetCoordinates(draw, lbound[0], lbound[1], ubound[0], ubound[1])); 426 PetscCall(VecGetArrayRead(fv, &array)); 427 for (c = cStart; c < cEnd; ++c) { 428 PetscScalar *coords = NULL, *a = NULL; 429 const PetscScalar *coords_arr; 430 PetscBool isDG; 431 PetscInt numCoords, color[4] = {-1, -1, -1, -1}; 432 433 PetscCall(DMPlexPointLocalRead(fdm, c, array, &a)); 434 if (a) { 435 color[0] = PetscDrawRealToColor(PetscRealPart(a[comp]), vbound[0], vbound[1]); 436 color[1] = color[2] = color[3] = color[0]; 437 } else { 438 PetscScalar *vals = NULL; 439 PetscInt numVals, va; 440 441 PetscCall(DMPlexVecGetClosure(fdm, NULL, fv, c, &numVals, &vals)); 442 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); 443 switch (numVals / Nc) { 444 case 3: /* P1 Triangle */ 445 case 4: /* P1 Quadrangle */ 446 for (va = 0; va < numVals / Nc; ++va) color[va] = PetscDrawRealToColor(PetscRealPart(vals[va * Nc + comp]), vbound[0], vbound[1]); 447 break; 448 case 6: /* P2 Triangle */ 449 case 8: /* P2 Quadrangle */ 450 for (va = 0; va < numVals / (Nc * 2); ++va) color[va] = PetscDrawRealToColor(PetscRealPart(vals[va * Nc + comp + numVals / (Nc * 2)]), vbound[0], vbound[1]); 451 break; 452 default: 453 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of values for cell closure %" PetscInt_FMT " cannot be handled", numVals / Nc); 454 } 455 PetscCall(DMPlexVecRestoreClosure(fdm, NULL, fv, c, &numVals, &vals)); 456 } 457 PetscCall(DMPlexGetCellCoordinates(dm, c, &isDG, &numCoords, &coords_arr, &coords)); 458 switch (numCoords) { 459 case 6: 460 case 12: /* Localized triangle */ 461 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])); 462 break; 463 case 8: 464 case 16: /* Localized quadrilateral */ 465 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])); 466 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])); 467 break; 468 default: 469 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells with %" PetscInt_FMT " coordinates", numCoords); 470 } 471 PetscCall(DMPlexRestoreCellCoordinates(dm, c, &isDG, &numCoords, &coords_arr, &coords)); 472 } 473 PetscCall(VecRestoreArrayRead(fv, &array)); 474 PetscCall(PetscDrawFlush(draw)); 475 PetscCall(PetscDrawPause(draw)); 476 PetscCall(PetscDrawSave(draw)); 477 } 478 if (Nf > 1) { 479 PetscCall(VecRestoreSubVector(v, fis, &fv)); 480 PetscCall(ISDestroy(&fis)); 481 PetscCall(DMDestroy(&fdm)); 482 } 483 } 484 PetscFunctionReturn(PETSC_SUCCESS); 485 } 486 487 static PetscErrorCode VecView_Plex_Local_Draw(Vec v, PetscViewer viewer) 488 { 489 DM dm; 490 PetscDraw draw; 491 PetscInt dim; 492 PetscBool isnull; 493 494 PetscFunctionBegin; 495 PetscCall(PetscViewerDrawGetDraw(viewer, 0, &draw)); 496 PetscCall(PetscDrawIsNull(draw, &isnull)); 497 if (isnull) PetscFunctionReturn(PETSC_SUCCESS); 498 499 PetscCall(VecGetDM(v, &dm)); 500 PetscCall(DMGetCoordinateDim(dm, &dim)); 501 switch (dim) { 502 case 1: 503 PetscCall(VecView_Plex_Local_Draw_1D(v, viewer)); 504 break; 505 case 2: 506 PetscCall(VecView_Plex_Local_Draw_2D(v, viewer)); 507 break; 508 default: 509 SETERRQ(PetscObjectComm((PetscObject)v), PETSC_ERR_SUP, "Cannot draw meshes of dimension %" PetscInt_FMT ". Try PETSCVIEWERGLVIS", dim); 510 } 511 PetscFunctionReturn(PETSC_SUCCESS); 512 } 513 514 static PetscErrorCode VecView_Plex_Local_VTK(Vec v, PetscViewer viewer) 515 { 516 DM dm; 517 Vec locv; 518 const char *name; 519 PetscSection section; 520 PetscInt pStart, pEnd; 521 PetscInt numFields; 522 PetscViewerVTKFieldType ft; 523 524 PetscFunctionBegin; 525 PetscCall(VecGetDM(v, &dm)); 526 PetscCall(DMCreateLocalVector(dm, &locv)); /* VTK viewer requires exclusive ownership of the vector */ 527 PetscCall(PetscObjectGetName((PetscObject)v, &name)); 528 PetscCall(PetscObjectSetName((PetscObject)locv, name)); 529 PetscCall(VecCopy(v, locv)); 530 PetscCall(DMGetLocalSection(dm, §ion)); 531 PetscCall(PetscSectionGetNumFields(section, &numFields)); 532 if (!numFields) { 533 PetscCall(DMPlexGetFieldType_Internal(dm, section, PETSC_DETERMINE, &pStart, &pEnd, &ft)); 534 PetscCall(PetscViewerVTKAddField(viewer, (PetscObject)dm, DMPlexVTKWriteAll, PETSC_DEFAULT, ft, PETSC_TRUE, (PetscObject)locv)); 535 } else { 536 PetscInt f; 537 538 for (f = 0; f < numFields; f++) { 539 PetscCall(DMPlexGetFieldType_Internal(dm, section, f, &pStart, &pEnd, &ft)); 540 if (ft == PETSC_VTK_INVALID) continue; 541 PetscCall(PetscObjectReference((PetscObject)locv)); 542 PetscCall(PetscViewerVTKAddField(viewer, (PetscObject)dm, DMPlexVTKWriteAll, f, ft, PETSC_TRUE, (PetscObject)locv)); 543 } 544 PetscCall(VecDestroy(&locv)); 545 } 546 PetscFunctionReturn(PETSC_SUCCESS); 547 } 548 549 PetscErrorCode VecView_Plex_Local(Vec v, PetscViewer viewer) 550 { 551 DM dm; 552 PetscBool isvtk, ishdf5, isdraw, isglvis, iscgns; 553 554 PetscFunctionBegin; 555 PetscCall(VecGetDM(v, &dm)); 556 PetscCheck(dm, PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 557 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERVTK, &isvtk)); 558 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 559 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERDRAW, &isdraw)); 560 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERGLVIS, &isglvis)); 561 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERCGNS, &iscgns)); 562 if (isvtk || ishdf5 || isdraw || isglvis || iscgns) { 563 PetscInt i, numFields; 564 PetscObject fe; 565 PetscBool fem = PETSC_FALSE; 566 Vec locv = v; 567 const char *name; 568 PetscInt step; 569 PetscReal time; 570 571 PetscCall(DMGetNumFields(dm, &numFields)); 572 for (i = 0; i < numFields; i++) { 573 PetscCall(DMGetField(dm, i, NULL, &fe)); 574 if (fe->classid == PETSCFE_CLASSID) { 575 fem = PETSC_TRUE; 576 break; 577 } 578 } 579 if (fem) { 580 PetscObject isZero; 581 582 PetscCall(DMGetLocalVector(dm, &locv)); 583 PetscCall(PetscObjectGetName((PetscObject)v, &name)); 584 PetscCall(PetscObjectSetName((PetscObject)locv, name)); 585 PetscCall(PetscObjectQuery((PetscObject)v, "__Vec_bc_zero__", &isZero)); 586 PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", isZero)); 587 PetscCall(VecCopy(v, locv)); 588 PetscCall(DMGetOutputSequenceNumber(dm, NULL, &time)); 589 PetscCall(DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locv, time, NULL, NULL, NULL)); 590 } 591 if (isvtk) { 592 PetscCall(VecView_Plex_Local_VTK(locv, viewer)); 593 } else if (ishdf5) { 594 #if defined(PETSC_HAVE_HDF5) 595 PetscCall(VecView_Plex_Local_HDF5_Internal(locv, viewer)); 596 #else 597 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 598 #endif 599 } else if (isdraw) { 600 PetscCall(VecView_Plex_Local_Draw(locv, viewer)); 601 } else if (isglvis) { 602 PetscCall(DMGetOutputSequenceNumber(dm, &step, NULL)); 603 PetscCall(PetscViewerGLVisSetSnapId(viewer, step)); 604 PetscCall(VecView_GLVis(locv, viewer)); 605 } else if (iscgns) { 606 #if defined(PETSC_HAVE_CGNS) 607 PetscCall(VecView_Plex_Local_CGNS(locv, viewer)); 608 #else 609 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "CGNS not supported in this build.\nPlease reconfigure using --download-cgns"); 610 #endif 611 } 612 if (fem) { 613 PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", NULL)); 614 PetscCall(DMRestoreLocalVector(dm, &locv)); 615 } 616 } else { 617 PetscBool isseq; 618 619 PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq)); 620 if (isseq) PetscCall(VecView_Seq(v, viewer)); 621 else PetscCall(VecView_MPI(v, viewer)); 622 } 623 PetscFunctionReturn(PETSC_SUCCESS); 624 } 625 626 PetscErrorCode VecView_Plex(Vec v, PetscViewer viewer) 627 { 628 DM dm; 629 PetscBool isvtk, ishdf5, isdraw, isglvis, isexodusii, iscgns; 630 631 PetscFunctionBegin; 632 PetscCall(VecGetDM(v, &dm)); 633 PetscCheck(dm, PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 634 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERVTK, &isvtk)); 635 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 636 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERDRAW, &isdraw)); 637 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERGLVIS, &isglvis)); 638 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERCGNS, &iscgns)); 639 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWEREXODUSII, &isexodusii)); 640 if (isvtk || isdraw || isglvis || iscgns) { 641 Vec locv; 642 PetscObject isZero; 643 const char *name; 644 645 PetscCall(DMGetLocalVector(dm, &locv)); 646 PetscCall(PetscObjectGetName((PetscObject)v, &name)); 647 PetscCall(PetscObjectSetName((PetscObject)locv, name)); 648 PetscCall(DMGlobalToLocalBegin(dm, v, INSERT_VALUES, locv)); 649 PetscCall(DMGlobalToLocalEnd(dm, v, INSERT_VALUES, locv)); 650 PetscCall(PetscObjectQuery((PetscObject)v, "__Vec_bc_zero__", &isZero)); 651 PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", isZero)); 652 PetscCall(VecView_Plex_Local(locv, viewer)); 653 PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", NULL)); 654 PetscCall(DMRestoreLocalVector(dm, &locv)); 655 } else if (ishdf5) { 656 #if defined(PETSC_HAVE_HDF5) 657 PetscCall(VecView_Plex_HDF5_Internal(v, viewer)); 658 #else 659 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 660 #endif 661 } else if (isexodusii) { 662 #if defined(PETSC_HAVE_EXODUSII) 663 PetscCall(VecView_PlexExodusII_Internal(v, viewer)); 664 #else 665 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "ExodusII not supported in this build.\nPlease reconfigure using --download-exodusii"); 666 #endif 667 } else { 668 PetscBool isseq; 669 670 PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq)); 671 if (isseq) PetscCall(VecView_Seq(v, viewer)); 672 else PetscCall(VecView_MPI(v, viewer)); 673 } 674 PetscFunctionReturn(PETSC_SUCCESS); 675 } 676 677 PetscErrorCode VecView_Plex_Native(Vec originalv, PetscViewer viewer) 678 { 679 DM dm; 680 MPI_Comm comm; 681 PetscViewerFormat format; 682 Vec v; 683 PetscBool isvtk, ishdf5; 684 685 PetscFunctionBegin; 686 PetscCall(VecGetDM(originalv, &dm)); 687 PetscCall(PetscObjectGetComm((PetscObject)originalv, &comm)); 688 PetscCheck(dm, comm, PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 689 PetscCall(PetscViewerGetFormat(viewer, &format)); 690 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 691 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERVTK, &isvtk)); 692 if (format == PETSC_VIEWER_NATIVE) { 693 /* Natural ordering is the common case for DMDA, NATIVE means plain vector, for PLEX is the opposite */ 694 /* this need a better fix */ 695 if (dm->useNatural) { 696 if (dm->sfNatural) { 697 const char *vecname; 698 PetscInt n, nroots; 699 700 PetscCall(VecGetLocalSize(originalv, &n)); 701 PetscCall(PetscSFGetGraph(dm->sfNatural, &nroots, NULL, NULL, NULL)); 702 if (n == nroots) { 703 PetscCall(DMPlexCreateNaturalVector(dm, &v)); 704 PetscCall(DMPlexGlobalToNaturalBegin(dm, originalv, v)); 705 PetscCall(DMPlexGlobalToNaturalEnd(dm, originalv, v)); 706 PetscCall(PetscObjectGetName((PetscObject)originalv, &vecname)); 707 PetscCall(PetscObjectSetName((PetscObject)v, vecname)); 708 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "DM global to natural SF only handles global vectors"); 709 } else SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "DM global to natural SF was not created"); 710 } else v = originalv; 711 } else v = originalv; 712 713 if (ishdf5) { 714 #if defined(PETSC_HAVE_HDF5) 715 PetscCall(VecView_Plex_HDF5_Native_Internal(v, viewer)); 716 #else 717 SETERRQ(comm, PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 718 #endif 719 } else if (isvtk) { 720 SETERRQ(comm, PETSC_ERR_SUP, "VTK format does not support viewing in natural order. Please switch to HDF5."); 721 } else { 722 PetscBool isseq; 723 724 PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq)); 725 if (isseq) PetscCall(VecView_Seq(v, viewer)); 726 else PetscCall(VecView_MPI(v, viewer)); 727 } 728 if (v != originalv) PetscCall(VecDestroy(&v)); 729 PetscFunctionReturn(PETSC_SUCCESS); 730 } 731 732 PetscErrorCode VecLoad_Plex_Local(Vec v, PetscViewer viewer) 733 { 734 DM dm; 735 PetscBool ishdf5; 736 737 PetscFunctionBegin; 738 PetscCall(VecGetDM(v, &dm)); 739 PetscCheck(dm, PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 740 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 741 if (ishdf5) { 742 DM dmBC; 743 Vec gv; 744 const char *name; 745 746 PetscCall(DMGetOutputDM(dm, &dmBC)); 747 PetscCall(DMGetGlobalVector(dmBC, &gv)); 748 PetscCall(PetscObjectGetName((PetscObject)v, &name)); 749 PetscCall(PetscObjectSetName((PetscObject)gv, name)); 750 PetscCall(VecLoad_Default(gv, viewer)); 751 PetscCall(DMGlobalToLocalBegin(dmBC, gv, INSERT_VALUES, v)); 752 PetscCall(DMGlobalToLocalEnd(dmBC, gv, INSERT_VALUES, v)); 753 PetscCall(DMRestoreGlobalVector(dmBC, &gv)); 754 } else PetscCall(VecLoad_Default(v, viewer)); 755 PetscFunctionReturn(PETSC_SUCCESS); 756 } 757 758 PetscErrorCode VecLoad_Plex(Vec v, PetscViewer viewer) 759 { 760 DM dm; 761 PetscBool ishdf5, isexodusii; 762 763 PetscFunctionBegin; 764 PetscCall(VecGetDM(v, &dm)); 765 PetscCheck(dm, PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 766 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 767 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWEREXODUSII, &isexodusii)); 768 if (ishdf5) { 769 #if defined(PETSC_HAVE_HDF5) 770 PetscCall(VecLoad_Plex_HDF5_Internal(v, viewer)); 771 #else 772 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 773 #endif 774 } else if (isexodusii) { 775 #if defined(PETSC_HAVE_EXODUSII) 776 PetscCall(VecLoad_PlexExodusII_Internal(v, viewer)); 777 #else 778 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "ExodusII not supported in this build.\nPlease reconfigure using --download-exodusii"); 779 #endif 780 } else PetscCall(VecLoad_Default(v, viewer)); 781 PetscFunctionReturn(PETSC_SUCCESS); 782 } 783 784 PetscErrorCode VecLoad_Plex_Native(Vec originalv, PetscViewer viewer) 785 { 786 DM dm; 787 PetscViewerFormat format; 788 PetscBool ishdf5; 789 790 PetscFunctionBegin; 791 PetscCall(VecGetDM(originalv, &dm)); 792 PetscCheck(dm, PetscObjectComm((PetscObject)originalv), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 793 PetscCall(PetscViewerGetFormat(viewer, &format)); 794 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 795 if (format == PETSC_VIEWER_NATIVE) { 796 if (dm->useNatural) { 797 if (dm->sfNatural) { 798 if (ishdf5) { 799 #if defined(PETSC_HAVE_HDF5) 800 Vec v; 801 const char *vecname; 802 803 PetscCall(DMPlexCreateNaturalVector(dm, &v)); 804 PetscCall(PetscObjectGetName((PetscObject)originalv, &vecname)); 805 PetscCall(PetscObjectSetName((PetscObject)v, vecname)); 806 PetscCall(VecLoad_Plex_HDF5_Native_Internal(v, viewer)); 807 PetscCall(DMPlexNaturalToGlobalBegin(dm, v, originalv)); 808 PetscCall(DMPlexNaturalToGlobalEnd(dm, v, originalv)); 809 PetscCall(VecDestroy(&v)); 810 #else 811 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 812 #endif 813 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Reading in natural order is not supported for anything but HDF5."); 814 } 815 } else PetscCall(VecLoad_Default(originalv, viewer)); 816 } 817 PetscFunctionReturn(PETSC_SUCCESS); 818 } 819 820 PETSC_UNUSED static PetscErrorCode DMPlexView_Ascii_Geometry(DM dm, PetscViewer viewer) 821 { 822 PetscSection coordSection; 823 Vec coordinates; 824 DMLabel depthLabel, celltypeLabel; 825 const char *name[4]; 826 const PetscScalar *a; 827 PetscInt dim, pStart, pEnd, cStart, cEnd, c; 828 829 PetscFunctionBegin; 830 PetscCall(DMGetDimension(dm, &dim)); 831 PetscCall(DMGetCoordinatesLocal(dm, &coordinates)); 832 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 833 PetscCall(DMPlexGetDepthLabel(dm, &depthLabel)); 834 PetscCall(DMPlexGetCellTypeLabel(dm, &celltypeLabel)); 835 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 836 PetscCall(PetscSectionGetChart(coordSection, &pStart, &pEnd)); 837 PetscCall(VecGetArrayRead(coordinates, &a)); 838 name[0] = "vertex"; 839 name[1] = "edge"; 840 name[dim - 1] = "face"; 841 name[dim] = "cell"; 842 for (c = cStart; c < cEnd; ++c) { 843 PetscInt *closure = NULL; 844 PetscInt closureSize, cl, ct; 845 846 PetscCall(DMLabelGetValue(celltypeLabel, c, &ct)); 847 PetscCall(PetscViewerASCIIPrintf(viewer, "Geometry for cell %" PetscInt_FMT " polytope type %s:\n", c, DMPolytopeTypes[ct])); 848 PetscCall(DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 849 PetscCall(PetscViewerASCIIPushTab(viewer)); 850 for (cl = 0; cl < closureSize * 2; cl += 2) { 851 PetscInt point = closure[cl], depth, dof, off, d, p; 852 853 if ((point < pStart) || (point >= pEnd)) continue; 854 PetscCall(PetscSectionGetDof(coordSection, point, &dof)); 855 if (!dof) continue; 856 PetscCall(DMLabelGetValue(depthLabel, point, &depth)); 857 PetscCall(PetscSectionGetOffset(coordSection, point, &off)); 858 PetscCall(PetscViewerASCIIPrintf(viewer, "%s %" PetscInt_FMT " coords:", name[depth], point)); 859 for (p = 0; p < dof / dim; ++p) { 860 PetscCall(PetscViewerASCIIPrintf(viewer, " (")); 861 for (d = 0; d < dim; ++d) { 862 if (d > 0) PetscCall(PetscViewerASCIIPrintf(viewer, ", ")); 863 PetscCall(PetscViewerASCIIPrintf(viewer, "%g", (double)PetscRealPart(a[off + p * dim + d]))); 864 } 865 PetscCall(PetscViewerASCIIPrintf(viewer, ")")); 866 } 867 PetscCall(PetscViewerASCIIPrintf(viewer, "\n")); 868 } 869 PetscCall(DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 870 PetscCall(PetscViewerASCIIPopTab(viewer)); 871 } 872 PetscCall(VecRestoreArrayRead(coordinates, &a)); 873 PetscFunctionReturn(PETSC_SUCCESS); 874 } 875 876 typedef enum { 877 CS_CARTESIAN, 878 CS_POLAR, 879 CS_CYLINDRICAL, 880 CS_SPHERICAL 881 } CoordSystem; 882 const char *CoordSystems[] = {"cartesian", "polar", "cylindrical", "spherical", "CoordSystem", "CS_", NULL}; 883 884 static PetscErrorCode DMPlexView_Ascii_Coordinates(PetscViewer viewer, CoordSystem cs, PetscInt dim, const PetscScalar x[]) 885 { 886 PetscInt i; 887 888 PetscFunctionBegin; 889 if (dim > 3) { 890 for (i = 0; i < dim; ++i) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %g", (double)PetscRealPart(x[i]))); 891 } else { 892 PetscReal coords[3], trcoords[3] = {0., 0., 0.}; 893 894 for (i = 0; i < dim; ++i) coords[i] = PetscRealPart(x[i]); 895 switch (cs) { 896 case CS_CARTESIAN: 897 for (i = 0; i < dim; ++i) trcoords[i] = coords[i]; 898 break; 899 case CS_POLAR: 900 PetscCheck(dim == 2, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Polar coordinates are for 2 dimension, not %" PetscInt_FMT, dim); 901 trcoords[0] = PetscSqrtReal(PetscSqr(coords[0]) + PetscSqr(coords[1])); 902 trcoords[1] = PetscAtan2Real(coords[1], coords[0]); 903 break; 904 case CS_CYLINDRICAL: 905 PetscCheck(dim == 3, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cylindrical coordinates are for 3 dimension, not %" PetscInt_FMT, dim); 906 trcoords[0] = PetscSqrtReal(PetscSqr(coords[0]) + PetscSqr(coords[1])); 907 trcoords[1] = PetscAtan2Real(coords[1], coords[0]); 908 trcoords[2] = coords[2]; 909 break; 910 case CS_SPHERICAL: 911 PetscCheck(dim == 3, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Spherical coordinates are for 3 dimension, not %" PetscInt_FMT, dim); 912 trcoords[0] = PetscSqrtReal(PetscSqr(coords[0]) + PetscSqr(coords[1]) + PetscSqr(coords[2])); 913 trcoords[1] = PetscAtan2Real(PetscSqrtReal(PetscSqr(coords[0]) + PetscSqr(coords[1])), coords[2]); 914 trcoords[2] = PetscAtan2Real(coords[1], coords[0]); 915 break; 916 } 917 for (i = 0; i < dim; ++i) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %g", (double)trcoords[i])); 918 } 919 PetscFunctionReturn(PETSC_SUCCESS); 920 } 921 922 static PetscErrorCode DMPlexView_Ascii(DM dm, PetscViewer viewer) 923 { 924 DM_Plex *mesh = (DM_Plex *)dm->data; 925 DM cdm, cdmCell; 926 PetscSection coordSection, coordSectionCell; 927 Vec coordinates, coordinatesCell; 928 PetscViewerFormat format; 929 930 PetscFunctionBegin; 931 PetscCall(PetscViewerGetFormat(viewer, &format)); 932 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 933 const char *name; 934 PetscInt dim, cellHeight, maxConeSize, maxSupportSize; 935 PetscInt pStart, pEnd, p, numLabels, l; 936 PetscMPIInt rank, size; 937 938 PetscCall(DMGetCoordinateDM(dm, &cdm)); 939 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 940 PetscCall(DMGetCoordinatesLocal(dm, &coordinates)); 941 PetscCall(DMGetCellCoordinateDM(dm, &cdmCell)); 942 PetscCall(DMGetCellCoordinateSection(dm, &coordSectionCell)); 943 PetscCall(DMGetCellCoordinatesLocal(dm, &coordinatesCell)); 944 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 945 PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size)); 946 PetscCall(PetscObjectGetName((PetscObject)dm, &name)); 947 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 948 PetscCall(DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize)); 949 PetscCall(DMGetDimension(dm, &dim)); 950 PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight)); 951 if (name) PetscCall(PetscViewerASCIIPrintf(viewer, "%s in %" PetscInt_FMT " dimension%s:\n", name, dim, dim == 1 ? "" : "s")); 952 else PetscCall(PetscViewerASCIIPrintf(viewer, "Mesh in %" PetscInt_FMT " dimension%s:\n", dim, dim == 1 ? "" : "s")); 953 if (cellHeight) PetscCall(PetscViewerASCIIPrintf(viewer, " Cells are at height %" PetscInt_FMT "\n", cellHeight)); 954 PetscCall(PetscViewerASCIIPrintf(viewer, "Supports:\n")); 955 PetscCall(PetscViewerASCIIPushSynchronized(viewer)); 956 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "[%d] Max support size: %" PetscInt_FMT "\n", rank, maxSupportSize)); 957 for (p = pStart; p < pEnd; ++p) { 958 PetscInt dof, off, s; 959 960 PetscCall(PetscSectionGetDof(mesh->supportSection, p, &dof)); 961 PetscCall(PetscSectionGetOffset(mesh->supportSection, p, &off)); 962 for (s = off; s < off + dof; ++s) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "[%d]: %" PetscInt_FMT " ----> %" PetscInt_FMT "\n", rank, p, mesh->supports[s])); 963 } 964 PetscCall(PetscViewerFlush(viewer)); 965 PetscCall(PetscViewerASCIIPrintf(viewer, "Cones:\n")); 966 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "[%d] Max cone size: %" PetscInt_FMT "\n", rank, maxConeSize)); 967 for (p = pStart; p < pEnd; ++p) { 968 PetscInt dof, off, c; 969 970 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 971 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 972 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])); 973 } 974 PetscCall(PetscViewerFlush(viewer)); 975 PetscCall(PetscViewerASCIIPopSynchronized(viewer)); 976 if (coordSection && coordinates) { 977 CoordSystem cs = CS_CARTESIAN; 978 const PetscScalar *array, *arrayCell = NULL; 979 PetscInt Nf, Nc, pvStart, pvEnd, pcStart = PETSC_MAX_INT, pcEnd = PETSC_MIN_INT, pStart, pEnd, p; 980 PetscMPIInt rank; 981 const char *name; 982 983 PetscCall(PetscOptionsGetEnum(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_coord_system", CoordSystems, (PetscEnum *)&cs, NULL)); 984 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank)); 985 PetscCall(PetscSectionGetNumFields(coordSection, &Nf)); 986 PetscCheck(Nf == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Coordinate section should have 1 field, not %" PetscInt_FMT, Nf); 987 PetscCall(PetscSectionGetFieldComponents(coordSection, 0, &Nc)); 988 PetscCall(PetscSectionGetChart(coordSection, &pvStart, &pvEnd)); 989 if (coordSectionCell) PetscCall(PetscSectionGetChart(coordSectionCell, &pcStart, &pcEnd)); 990 pStart = PetscMin(pvStart, pcStart); 991 pEnd = PetscMax(pvEnd, pcEnd); 992 PetscCall(PetscObjectGetName((PetscObject)coordinates, &name)); 993 PetscCall(PetscViewerASCIIPrintf(viewer, "%s with %" PetscInt_FMT " fields\n", name, Nf)); 994 PetscCall(PetscViewerASCIIPrintf(viewer, " field 0 with %" PetscInt_FMT " components\n", Nc)); 995 if (cs != CS_CARTESIAN) PetscCall(PetscViewerASCIIPrintf(viewer, " output coordinate system: %s\n", CoordSystems[cs])); 996 997 PetscCall(VecGetArrayRead(coordinates, &array)); 998 if (coordinatesCell) PetscCall(VecGetArrayRead(coordinatesCell, &arrayCell)); 999 PetscCall(PetscViewerASCIIPushSynchronized(viewer)); 1000 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "Process %d:\n", rank)); 1001 for (p = pStart; p < pEnd; ++p) { 1002 PetscInt dof, off; 1003 1004 if (p >= pvStart && p < pvEnd) { 1005 PetscCall(PetscSectionGetDof(coordSection, p, &dof)); 1006 PetscCall(PetscSectionGetOffset(coordSection, p, &off)); 1007 if (dof) { 1008 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " (%4" PetscInt_FMT ") dim %2" PetscInt_FMT " offset %3" PetscInt_FMT, p, dof, off)); 1009 PetscCall(DMPlexView_Ascii_Coordinates(viewer, cs, dof, &array[off])); 1010 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\n")); 1011 } 1012 } 1013 if (cdmCell && p >= pcStart && p < pcEnd) { 1014 PetscCall(PetscSectionGetDof(coordSectionCell, p, &dof)); 1015 PetscCall(PetscSectionGetOffset(coordSectionCell, p, &off)); 1016 if (dof) { 1017 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " (%4" PetscInt_FMT ") dim %2" PetscInt_FMT " offset %3" PetscInt_FMT, p, dof, off)); 1018 PetscCall(DMPlexView_Ascii_Coordinates(viewer, cs, dof, &arrayCell[off])); 1019 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\n")); 1020 } 1021 } 1022 } 1023 PetscCall(PetscViewerFlush(viewer)); 1024 PetscCall(PetscViewerASCIIPopSynchronized(viewer)); 1025 PetscCall(VecRestoreArrayRead(coordinates, &array)); 1026 if (coordinatesCell) PetscCall(VecRestoreArrayRead(coordinatesCell, &arrayCell)); 1027 } 1028 PetscCall(DMGetNumLabels(dm, &numLabels)); 1029 if (numLabels) PetscCall(PetscViewerASCIIPrintf(viewer, "Labels:\n")); 1030 for (l = 0; l < numLabels; ++l) { 1031 DMLabel label; 1032 PetscBool isdepth; 1033 const char *name; 1034 1035 PetscCall(DMGetLabelName(dm, l, &name)); 1036 PetscCall(PetscStrcmp(name, "depth", &isdepth)); 1037 if (isdepth) continue; 1038 PetscCall(DMGetLabel(dm, name, &label)); 1039 PetscCall(DMLabelView(label, viewer)); 1040 } 1041 if (size > 1) { 1042 PetscSF sf; 1043 1044 PetscCall(DMGetPointSF(dm, &sf)); 1045 PetscCall(PetscSFView(sf, viewer)); 1046 } 1047 if (mesh->periodic.face_sf) PetscCall(PetscSFView(mesh->periodic.face_sf, viewer)); 1048 PetscCall(PetscViewerFlush(viewer)); 1049 } else if (format == PETSC_VIEWER_ASCII_LATEX) { 1050 const char *name, *color; 1051 const char *defcolors[3] = {"gray", "orange", "green"}; 1052 const char *deflcolors[4] = {"blue", "cyan", "red", "magenta"}; 1053 char lname[PETSC_MAX_PATH_LEN]; 1054 PetscReal scale = 2.0; 1055 PetscReal tikzscale = 1.0; 1056 PetscBool useNumbers = PETSC_TRUE, drawNumbers[4], drawColors[4], useLabels, useColors, plotEdges, drawHasse = PETSC_FALSE; 1057 double tcoords[3]; 1058 PetscScalar *coords; 1059 PetscInt numLabels, l, numColors, numLColors, dim, d, depth, cStart, cEnd, c, vStart, vEnd, v, eStart = 0, eEnd = 0, e, p, n; 1060 PetscMPIInt rank, size; 1061 char **names, **colors, **lcolors; 1062 PetscBool flg, lflg; 1063 PetscBT wp = NULL; 1064 PetscInt pEnd, pStart; 1065 1066 PetscCall(DMGetCoordinateDM(dm, &cdm)); 1067 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 1068 PetscCall(DMGetCoordinatesLocal(dm, &coordinates)); 1069 PetscCall(DMGetCellCoordinateDM(dm, &cdmCell)); 1070 PetscCall(DMGetCellCoordinateSection(dm, &coordSectionCell)); 1071 PetscCall(DMGetCellCoordinatesLocal(dm, &coordinatesCell)); 1072 PetscCall(DMGetDimension(dm, &dim)); 1073 PetscCall(DMPlexGetDepth(dm, &depth)); 1074 PetscCall(DMGetNumLabels(dm, &numLabels)); 1075 numLabels = PetscMax(numLabels, 10); 1076 numColors = 10; 1077 numLColors = 10; 1078 PetscCall(PetscCalloc3(numLabels, &names, numColors, &colors, numLColors, &lcolors)); 1079 PetscCall(PetscOptionsGetReal(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_scale", &scale, NULL)); 1080 PetscCall(PetscOptionsGetReal(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_tikzscale", &tikzscale, NULL)); 1081 PetscCall(PetscOptionsGetBool(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_numbers", &useNumbers, NULL)); 1082 for (d = 0; d < 4; ++d) drawNumbers[d] = useNumbers; 1083 for (d = 0; d < 4; ++d) drawColors[d] = PETSC_TRUE; 1084 n = 4; 1085 PetscCall(PetscOptionsGetBoolArray(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_numbers_depth", drawNumbers, &n, &flg)); 1086 PetscCheck(!flg || n == dim + 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_SIZ, "Number of flags %" PetscInt_FMT " != %" PetscInt_FMT " dim+1", n, dim + 1); 1087 PetscCall(PetscOptionsGetBoolArray(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_colors_depth", drawColors, &n, &flg)); 1088 PetscCheck(!flg || n == dim + 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_SIZ, "Number of flags %" PetscInt_FMT " != %" PetscInt_FMT " dim+1", n, dim + 1); 1089 PetscCall(PetscOptionsGetStringArray(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_labels", names, &numLabels, &useLabels)); 1090 if (!useLabels) numLabels = 0; 1091 PetscCall(PetscOptionsGetStringArray(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_colors", colors, &numColors, &useColors)); 1092 if (!useColors) { 1093 numColors = 3; 1094 for (c = 0; c < numColors; ++c) PetscCall(PetscStrallocpy(defcolors[c], &colors[c])); 1095 } 1096 PetscCall(PetscOptionsGetStringArray(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_lcolors", lcolors, &numLColors, &useColors)); 1097 if (!useColors) { 1098 numLColors = 4; 1099 for (c = 0; c < numLColors; ++c) PetscCall(PetscStrallocpy(deflcolors[c], &lcolors[c])); 1100 } 1101 PetscCall(PetscOptionsGetString(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_label_filter", lname, sizeof(lname), &lflg)); 1102 plotEdges = (PetscBool)(depth > 1 && drawNumbers[1] && dim < 3); 1103 PetscCall(PetscOptionsGetBool(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_edges", &plotEdges, &flg)); 1104 PetscCheck(!flg || !plotEdges || depth >= dim, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Mesh must be interpolated"); 1105 if (depth < dim) plotEdges = PETSC_FALSE; 1106 PetscCall(PetscOptionsGetBool(((PetscObject)viewer)->options, ((PetscObject)viewer)->prefix, "-dm_plex_view_hasse", &drawHasse, NULL)); 1107 1108 /* filter points with labelvalue != labeldefaultvalue */ 1109 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 1110 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 1111 PetscCall(DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd)); 1112 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 1113 if (lflg) { 1114 DMLabel lbl; 1115 1116 PetscCall(DMGetLabel(dm, lname, &lbl)); 1117 if (lbl) { 1118 PetscInt val, defval; 1119 1120 PetscCall(DMLabelGetDefaultValue(lbl, &defval)); 1121 PetscCall(PetscBTCreate(pEnd - pStart, &wp)); 1122 for (c = pStart; c < pEnd; c++) { 1123 PetscInt *closure = NULL; 1124 PetscInt closureSize; 1125 1126 PetscCall(DMLabelGetValue(lbl, c, &val)); 1127 if (val == defval) continue; 1128 1129 PetscCall(DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 1130 for (p = 0; p < closureSize * 2; p += 2) PetscCall(PetscBTSet(wp, closure[p] - pStart)); 1131 PetscCall(DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 1132 } 1133 } 1134 } 1135 1136 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 1137 PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size)); 1138 PetscCall(PetscObjectGetName((PetscObject)dm, &name)); 1139 PetscCall(PetscViewerASCIIPrintf(viewer, "\ 1140 \\documentclass[tikz]{standalone}\n\n\ 1141 \\usepackage{pgflibraryshapes}\n\ 1142 \\usetikzlibrary{backgrounds}\n\ 1143 \\usetikzlibrary{arrows}\n\ 1144 \\begin{document}\n")); 1145 if (size > 1) { 1146 PetscCall(PetscViewerASCIIPrintf(viewer, "%s for process ", name)); 1147 for (p = 0; p < size; ++p) { 1148 if (p) PetscCall(PetscViewerASCIIPrintf(viewer, (p == size - 1) ? ", and " : ", ")); 1149 PetscCall(PetscViewerASCIIPrintf(viewer, "{\\textcolor{%s}%" PetscInt_FMT "}", colors[p % numColors], p)); 1150 } 1151 PetscCall(PetscViewerASCIIPrintf(viewer, ".\n\n\n")); 1152 } 1153 if (drawHasse) { 1154 PetscInt maxStratum = PetscMax(vEnd - vStart, PetscMax(eEnd - eStart, cEnd - cStart)); 1155 1156 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\vStart}{%" PetscInt_FMT "}\n", vStart)); 1157 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\vEnd}{%" PetscInt_FMT "}\n", vEnd - 1)); 1158 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\numVertices}{%" PetscInt_FMT "}\n", vEnd - vStart)); 1159 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\vShift}{%.2f}\n", 3 + (maxStratum - (vEnd - vStart)) / 2.)); 1160 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\eStart}{%" PetscInt_FMT "}\n", eStart)); 1161 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\eEnd}{%" PetscInt_FMT "}\n", eEnd - 1)); 1162 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\eShift}{%.2f}\n", 3 + (maxStratum - (eEnd - eStart)) / 2.)); 1163 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\numEdges}{%" PetscInt_FMT "}\n", eEnd - eStart)); 1164 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\cStart}{%" PetscInt_FMT "}\n", cStart)); 1165 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\cEnd}{%" PetscInt_FMT "}\n", cEnd - 1)); 1166 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\numCells}{%" PetscInt_FMT "}\n", cEnd - cStart)); 1167 PetscCall(PetscViewerASCIIPrintf(viewer, "\\newcommand{\\cShift}{%.2f}\n", 3 + (maxStratum - (cEnd - cStart)) / 2.)); 1168 } 1169 PetscCall(PetscViewerASCIIPrintf(viewer, "\\begin{tikzpicture}[scale = %g,font=\\fontsize{8}{8}\\selectfont]\n", (double)tikzscale)); 1170 1171 /* Plot vertices */ 1172 PetscCall(VecGetArray(coordinates, &coords)); 1173 PetscCall(PetscViewerASCIIPushSynchronized(viewer)); 1174 for (v = vStart; v < vEnd; ++v) { 1175 PetscInt off, dof, d; 1176 PetscBool isLabeled = PETSC_FALSE; 1177 1178 if (wp && !PetscBTLookup(wp, v - pStart)) continue; 1179 PetscCall(PetscSectionGetDof(coordSection, v, &dof)); 1180 PetscCall(PetscSectionGetOffset(coordSection, v, &off)); 1181 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\\path (")); 1182 PetscCheck(dof <= 3, PETSC_COMM_SELF, PETSC_ERR_PLIB, "coordSection vertex %" PetscInt_FMT " has dof %" PetscInt_FMT " > 3", v, dof); 1183 for (d = 0; d < dof; ++d) { 1184 tcoords[d] = (double)(scale * PetscRealPart(coords[off + d])); 1185 tcoords[d] = PetscAbs(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d]; 1186 } 1187 /* Rotate coordinates since PGF makes z point out of the page instead of up */ 1188 if (dim == 3) { 1189 PetscReal tmp = tcoords[1]; 1190 tcoords[1] = tcoords[2]; 1191 tcoords[2] = -tmp; 1192 } 1193 for (d = 0; d < dof; ++d) { 1194 if (d > 0) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ",")); 1195 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "%g", (double)tcoords[d])); 1196 } 1197 if (drawHasse) color = colors[0 % numColors]; 1198 else color = colors[rank % numColors]; 1199 for (l = 0; l < numLabels; ++l) { 1200 PetscInt val; 1201 PetscCall(DMGetLabelValue(dm, names[l], v, &val)); 1202 if (val >= 0) { 1203 color = lcolors[l % numLColors]; 1204 isLabeled = PETSC_TRUE; 1205 break; 1206 } 1207 } 1208 if (drawNumbers[0]) { 1209 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ") node(%" PetscInt_FMT "_%d) [draw,shape=circle,color=%s] {%" PetscInt_FMT "};\n", v, rank, color, v)); 1210 } else if (drawColors[0]) { 1211 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ") node(%" PetscInt_FMT "_%d) [fill,inner sep=%dpt,shape=circle,color=%s] {};\n", v, rank, !isLabeled ? 1 : 2, color)); 1212 } else PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ") node(%" PetscInt_FMT "_%d) [] {};\n", v, rank)); 1213 } 1214 PetscCall(VecRestoreArray(coordinates, &coords)); 1215 PetscCall(PetscViewerFlush(viewer)); 1216 /* Plot edges */ 1217 if (plotEdges) { 1218 PetscCall(VecGetArray(coordinates, &coords)); 1219 PetscCall(PetscViewerASCIIPrintf(viewer, "\\path\n")); 1220 for (e = eStart; e < eEnd; ++e) { 1221 const PetscInt *cone; 1222 PetscInt coneSize, offA, offB, dof, d; 1223 1224 if (wp && !PetscBTLookup(wp, e - pStart)) continue; 1225 PetscCall(DMPlexGetConeSize(dm, e, &coneSize)); 1226 PetscCheck(coneSize == 2, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Edge %" PetscInt_FMT " cone should have two vertices, not %" PetscInt_FMT, e, coneSize); 1227 PetscCall(DMPlexGetCone(dm, e, &cone)); 1228 PetscCall(PetscSectionGetDof(coordSection, cone[0], &dof)); 1229 PetscCall(PetscSectionGetOffset(coordSection, cone[0], &offA)); 1230 PetscCall(PetscSectionGetOffset(coordSection, cone[1], &offB)); 1231 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "(")); 1232 for (d = 0; d < dof; ++d) { 1233 tcoords[d] = (double)(0.5 * scale * PetscRealPart(coords[offA + d] + coords[offB + d])); 1234 tcoords[d] = PetscAbs(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d]; 1235 } 1236 /* Rotate coordinates since PGF makes z point out of the page instead of up */ 1237 if (dim == 3) { 1238 PetscReal tmp = tcoords[1]; 1239 tcoords[1] = tcoords[2]; 1240 tcoords[2] = -tmp; 1241 } 1242 for (d = 0; d < dof; ++d) { 1243 if (d > 0) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ",")); 1244 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "%g", (double)tcoords[d])); 1245 } 1246 if (drawHasse) color = colors[1 % numColors]; 1247 else color = colors[rank % numColors]; 1248 for (l = 0; l < numLabels; ++l) { 1249 PetscInt val; 1250 PetscCall(DMGetLabelValue(dm, names[l], v, &val)); 1251 if (val >= 0) { 1252 color = lcolors[l % numLColors]; 1253 break; 1254 } 1255 } 1256 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ") node(%" PetscInt_FMT "_%d) [draw,shape=circle,color=%s] {%" PetscInt_FMT "} --\n", e, rank, color, e)); 1257 } 1258 PetscCall(VecRestoreArray(coordinates, &coords)); 1259 PetscCall(PetscViewerFlush(viewer)); 1260 PetscCall(PetscViewerASCIIPrintf(viewer, "(0,0);\n")); 1261 } 1262 /* Plot cells */ 1263 if (dim == 3 || !drawNumbers[1]) { 1264 for (e = eStart; e < eEnd; ++e) { 1265 const PetscInt *cone; 1266 1267 if (wp && !PetscBTLookup(wp, e - pStart)) continue; 1268 color = colors[rank % numColors]; 1269 for (l = 0; l < numLabels; ++l) { 1270 PetscInt val; 1271 PetscCall(DMGetLabelValue(dm, names[l], e, &val)); 1272 if (val >= 0) { 1273 color = lcolors[l % numLColors]; 1274 break; 1275 } 1276 } 1277 PetscCall(DMPlexGetCone(dm, e, &cone)); 1278 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\\draw[color=%s] (%" PetscInt_FMT "_%d) -- (%" PetscInt_FMT "_%d);\n", color, cone[0], rank, cone[1], rank)); 1279 } 1280 } else { 1281 DMPolytopeType ct; 1282 1283 /* Drawing a 2D polygon */ 1284 for (c = cStart; c < cEnd; ++c) { 1285 if (wp && !PetscBTLookup(wp, c - pStart)) continue; 1286 PetscCall(DMPlexGetCellType(dm, c, &ct)); 1287 if (ct == DM_POLYTOPE_SEG_PRISM_TENSOR || ct == DM_POLYTOPE_TRI_PRISM_TENSOR || ct == DM_POLYTOPE_QUAD_PRISM_TENSOR) { 1288 const PetscInt *cone; 1289 PetscInt coneSize, e; 1290 1291 PetscCall(DMPlexGetCone(dm, c, &cone)); 1292 PetscCall(DMPlexGetConeSize(dm, c, &coneSize)); 1293 for (e = 0; e < coneSize; ++e) { 1294 const PetscInt *econe; 1295 1296 PetscCall(DMPlexGetCone(dm, cone[e], &econe)); 1297 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)); 1298 } 1299 } else { 1300 PetscInt *closure = NULL; 1301 PetscInt closureSize, Nv = 0, v; 1302 1303 PetscCall(DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 1304 for (p = 0; p < closureSize * 2; p += 2) { 1305 const PetscInt point = closure[p]; 1306 1307 if ((point >= vStart) && (point < vEnd)) closure[Nv++] = point; 1308 } 1309 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\\draw[color=%s] ", colors[rank % numColors])); 1310 for (v = 0; v <= Nv; ++v) { 1311 const PetscInt vertex = closure[v % Nv]; 1312 1313 if (v > 0) { 1314 if (plotEdges) { 1315 const PetscInt *edge; 1316 PetscInt endpoints[2], ne; 1317 1318 endpoints[0] = closure[v - 1]; 1319 endpoints[1] = vertex; 1320 PetscCall(DMPlexGetJoin(dm, 2, endpoints, &ne, &edge)); 1321 PetscCheck(ne == 1, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find edge for vertices %" PetscInt_FMT ", %" PetscInt_FMT, endpoints[0], endpoints[1]); 1322 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " -- (%" PetscInt_FMT "_%d) -- ", edge[0], rank)); 1323 PetscCall(DMPlexRestoreJoin(dm, 2, endpoints, &ne, &edge)); 1324 } else PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " -- ")); 1325 } 1326 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "(%" PetscInt_FMT "_%d)", vertex, rank)); 1327 } 1328 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ";\n")); 1329 PetscCall(DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 1330 } 1331 } 1332 } 1333 for (c = cStart; c < cEnd; ++c) { 1334 double ccoords[3] = {0.0, 0.0, 0.0}; 1335 PetscBool isLabeled = PETSC_FALSE; 1336 PetscScalar *cellCoords = NULL; 1337 const PetscScalar *array; 1338 PetscInt numCoords, cdim, d; 1339 PetscBool isDG; 1340 1341 if (wp && !PetscBTLookup(wp, c - pStart)) continue; 1342 PetscCall(DMGetCoordinateDim(dm, &cdim)); 1343 PetscCall(DMPlexGetCellCoordinates(dm, c, &isDG, &numCoords, &array, &cellCoords)); 1344 PetscCheck(!(numCoords % cdim), PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "coordinate dim %" PetscInt_FMT " does not divide numCoords %" PetscInt_FMT, cdim, numCoords); 1345 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\\path (")); 1346 for (p = 0; p < numCoords / cdim; ++p) { 1347 for (d = 0; d < cdim; ++d) { 1348 tcoords[d] = (double)(scale * PetscRealPart(cellCoords[p * cdim + d])); 1349 tcoords[d] = PetscAbs(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d]; 1350 } 1351 /* Rotate coordinates since PGF makes z point out of the page instead of up */ 1352 if (cdim == 3) { 1353 PetscReal tmp = tcoords[1]; 1354 tcoords[1] = tcoords[2]; 1355 tcoords[2] = -tmp; 1356 } 1357 for (d = 0; d < dim; ++d) ccoords[d] += tcoords[d]; 1358 } 1359 for (d = 0; d < cdim; ++d) ccoords[d] /= (numCoords / cdim); 1360 PetscCall(DMPlexRestoreCellCoordinates(dm, c, &isDG, &numCoords, &array, &cellCoords)); 1361 for (d = 0; d < cdim; ++d) { 1362 if (d > 0) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ",")); 1363 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "%g", (double)ccoords[d])); 1364 } 1365 if (drawHasse) color = colors[depth % numColors]; 1366 else color = colors[rank % numColors]; 1367 for (l = 0; l < numLabels; ++l) { 1368 PetscInt val; 1369 PetscCall(DMGetLabelValue(dm, names[l], c, &val)); 1370 if (val >= 0) { 1371 color = lcolors[l % numLColors]; 1372 isLabeled = PETSC_TRUE; 1373 break; 1374 } 1375 } 1376 if (drawNumbers[dim]) { 1377 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ") node(%" PetscInt_FMT "_%d) [draw,shape=circle,color=%s] {%" PetscInt_FMT "};\n", c, rank, color, c)); 1378 } else if (drawColors[dim]) { 1379 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ") node(%" PetscInt_FMT "_%d) [fill,inner sep=%dpt,shape=circle,color=%s] {};\n", c, rank, !isLabeled ? 1 : 2, color)); 1380 } else PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ") node(%" PetscInt_FMT "_%d) [] {};\n", c, rank)); 1381 } 1382 if (drawHasse) { 1383 color = colors[depth % numColors]; 1384 PetscCall(PetscViewerASCIIPrintf(viewer, "%% Cells\n")); 1385 PetscCall(PetscViewerASCIIPrintf(viewer, "\\foreach \\c in {\\cStart,...,\\cEnd}\n")); 1386 PetscCall(PetscViewerASCIIPrintf(viewer, "{\n")); 1387 PetscCall(PetscViewerASCIIPrintf(viewer, " \\node(\\c_%d) [draw,shape=circle,color=%s,minimum size = 6mm] at (\\cShift+\\c-\\cStart,0) {\\c};\n", rank, color)); 1388 PetscCall(PetscViewerASCIIPrintf(viewer, "}\n")); 1389 1390 color = colors[1 % numColors]; 1391 PetscCall(PetscViewerASCIIPrintf(viewer, "%% Edges\n")); 1392 PetscCall(PetscViewerASCIIPrintf(viewer, "\\foreach \\e in {\\eStart,...,\\eEnd}\n")); 1393 PetscCall(PetscViewerASCIIPrintf(viewer, "{\n")); 1394 PetscCall(PetscViewerASCIIPrintf(viewer, " \\node(\\e_%d) [draw,shape=circle,color=%s,minimum size = 6mm] at (\\eShift+\\e-\\eStart,1) {\\e};\n", rank, color)); 1395 PetscCall(PetscViewerASCIIPrintf(viewer, "}\n")); 1396 1397 color = colors[0 % numColors]; 1398 PetscCall(PetscViewerASCIIPrintf(viewer, "%% Vertices\n")); 1399 PetscCall(PetscViewerASCIIPrintf(viewer, "\\foreach \\v in {\\vStart,...,\\vEnd}\n")); 1400 PetscCall(PetscViewerASCIIPrintf(viewer, "{\n")); 1401 PetscCall(PetscViewerASCIIPrintf(viewer, " \\node(\\v_%d) [draw,shape=circle,color=%s,minimum size = 6mm] at (\\vShift+\\v-\\vStart,2) {\\v};\n", rank, color)); 1402 PetscCall(PetscViewerASCIIPrintf(viewer, "}\n")); 1403 1404 for (p = pStart; p < pEnd; ++p) { 1405 const PetscInt *cone; 1406 PetscInt coneSize, cp; 1407 1408 PetscCall(DMPlexGetCone(dm, p, &cone)); 1409 PetscCall(DMPlexGetConeSize(dm, p, &coneSize)); 1410 for (cp = 0; cp < coneSize; ++cp) PetscCall(PetscViewerASCIIPrintf(viewer, "\\draw[->, shorten >=1pt] (%" PetscInt_FMT "_%d) -- (%" PetscInt_FMT "_%d);\n", cone[cp], rank, p, rank)); 1411 } 1412 } 1413 PetscCall(PetscViewerFlush(viewer)); 1414 PetscCall(PetscViewerASCIIPopSynchronized(viewer)); 1415 PetscCall(PetscViewerASCIIPrintf(viewer, "\\end{tikzpicture}\n")); 1416 PetscCall(PetscViewerASCIIPrintf(viewer, "\\end{document}\n")); 1417 for (l = 0; l < numLabels; ++l) PetscCall(PetscFree(names[l])); 1418 for (c = 0; c < numColors; ++c) PetscCall(PetscFree(colors[c])); 1419 for (c = 0; c < numLColors; ++c) PetscCall(PetscFree(lcolors[c])); 1420 PetscCall(PetscFree3(names, colors, lcolors)); 1421 PetscCall(PetscBTDestroy(&wp)); 1422 } else if (format == PETSC_VIEWER_LOAD_BALANCE) { 1423 Vec cown, acown; 1424 VecScatter sct; 1425 ISLocalToGlobalMapping g2l; 1426 IS gid, acis; 1427 MPI_Comm comm, ncomm = MPI_COMM_NULL; 1428 MPI_Group ggroup, ngroup; 1429 PetscScalar *array, nid; 1430 const PetscInt *idxs; 1431 PetscInt *idxs2, *start, *adjacency, *work; 1432 PetscInt64 lm[3], gm[3]; 1433 PetscInt i, c, cStart, cEnd, cum, numVertices, ect, ectn, cellHeight; 1434 PetscMPIInt d1, d2, rank; 1435 1436 PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); 1437 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 1438 #if defined(PETSC_HAVE_MPI_PROCESS_SHARED_MEMORY) 1439 PetscCallMPI(MPI_Comm_split_type(comm, MPI_COMM_TYPE_SHARED, rank, MPI_INFO_NULL, &ncomm)); 1440 #endif 1441 if (ncomm != MPI_COMM_NULL) { 1442 PetscCallMPI(MPI_Comm_group(comm, &ggroup)); 1443 PetscCallMPI(MPI_Comm_group(ncomm, &ngroup)); 1444 d1 = 0; 1445 PetscCallMPI(MPI_Group_translate_ranks(ngroup, 1, &d1, ggroup, &d2)); 1446 nid = d2; 1447 PetscCallMPI(MPI_Group_free(&ggroup)); 1448 PetscCallMPI(MPI_Group_free(&ngroup)); 1449 PetscCallMPI(MPI_Comm_free(&ncomm)); 1450 } else nid = 0.0; 1451 1452 /* Get connectivity */ 1453 PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight)); 1454 PetscCall(DMPlexCreatePartitionerGraph(dm, cellHeight, &numVertices, &start, &adjacency, &gid)); 1455 1456 /* filter overlapped local cells */ 1457 PetscCall(DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd)); 1458 PetscCall(ISGetIndices(gid, &idxs)); 1459 PetscCall(ISGetLocalSize(gid, &cum)); 1460 PetscCall(PetscMalloc1(cum, &idxs2)); 1461 for (c = cStart, cum = 0; c < cEnd; c++) { 1462 if (idxs[c - cStart] < 0) continue; 1463 idxs2[cum++] = idxs[c - cStart]; 1464 } 1465 PetscCall(ISRestoreIndices(gid, &idxs)); 1466 PetscCheck(numVertices == cum, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unexpected %" PetscInt_FMT " != %" PetscInt_FMT, numVertices, cum); 1467 PetscCall(ISDestroy(&gid)); 1468 PetscCall(ISCreateGeneral(comm, numVertices, idxs2, PETSC_OWN_POINTER, &gid)); 1469 1470 /* support for node-aware cell locality */ 1471 PetscCall(ISCreateGeneral(comm, start[numVertices], adjacency, PETSC_USE_POINTER, &acis)); 1472 PetscCall(VecCreateSeq(PETSC_COMM_SELF, start[numVertices], &acown)); 1473 PetscCall(VecCreateMPI(comm, numVertices, PETSC_DECIDE, &cown)); 1474 PetscCall(VecGetArray(cown, &array)); 1475 for (c = 0; c < numVertices; c++) array[c] = nid; 1476 PetscCall(VecRestoreArray(cown, &array)); 1477 PetscCall(VecScatterCreate(cown, acis, acown, NULL, &sct)); 1478 PetscCall(VecScatterBegin(sct, cown, acown, INSERT_VALUES, SCATTER_FORWARD)); 1479 PetscCall(VecScatterEnd(sct, cown, acown, INSERT_VALUES, SCATTER_FORWARD)); 1480 PetscCall(ISDestroy(&acis)); 1481 PetscCall(VecScatterDestroy(&sct)); 1482 PetscCall(VecDestroy(&cown)); 1483 1484 /* compute edgeCut */ 1485 for (c = 0, cum = 0; c < numVertices; c++) cum = PetscMax(cum, start[c + 1] - start[c]); 1486 PetscCall(PetscMalloc1(cum, &work)); 1487 PetscCall(ISLocalToGlobalMappingCreateIS(gid, &g2l)); 1488 PetscCall(ISLocalToGlobalMappingSetType(g2l, ISLOCALTOGLOBALMAPPINGHASH)); 1489 PetscCall(ISDestroy(&gid)); 1490 PetscCall(VecGetArray(acown, &array)); 1491 for (c = 0, ect = 0, ectn = 0; c < numVertices; c++) { 1492 PetscInt totl; 1493 1494 totl = start[c + 1] - start[c]; 1495 PetscCall(ISGlobalToLocalMappingApply(g2l, IS_GTOLM_MASK, totl, adjacency + start[c], NULL, work)); 1496 for (i = 0; i < totl; i++) { 1497 if (work[i] < 0) { 1498 ect += 1; 1499 ectn += (array[i + start[c]] != nid) ? 0 : 1; 1500 } 1501 } 1502 } 1503 PetscCall(PetscFree(work)); 1504 PetscCall(VecRestoreArray(acown, &array)); 1505 lm[0] = numVertices > 0 ? numVertices : PETSC_MAX_INT; 1506 lm[1] = -numVertices; 1507 PetscCall(MPIU_Allreduce(lm, gm, 2, MPIU_INT64, MPI_MIN, comm)); 1508 PetscCall(PetscViewerASCIIPrintf(viewer, " Cell balance: %.2f (max %" PetscInt_FMT ", min %" PetscInt_FMT, -((double)gm[1]) / ((double)gm[0]), -(PetscInt)gm[1], (PetscInt)gm[0])); 1509 lm[0] = ect; /* edgeCut */ 1510 lm[1] = ectn; /* node-aware edgeCut */ 1511 lm[2] = numVertices > 0 ? 0 : 1; /* empty processes */ 1512 PetscCall(MPIU_Allreduce(lm, gm, 3, MPIU_INT64, MPI_SUM, comm)); 1513 PetscCall(PetscViewerASCIIPrintf(viewer, ", empty %" PetscInt_FMT ")\n", (PetscInt)gm[2])); 1514 #if defined(PETSC_HAVE_MPI_PROCESS_SHARED_MEMORY) 1515 PetscCall(PetscViewerASCIIPrintf(viewer, " Edge Cut: %" PetscInt_FMT " (on node %.3f)\n", (PetscInt)(gm[0] / 2), gm[0] ? ((double)(gm[1])) / ((double)gm[0]) : 1.)); 1516 #else 1517 PetscCall(PetscViewerASCIIPrintf(viewer, " Edge Cut: %" PetscInt_FMT " (on node %.3f)\n", (PetscInt)(gm[0] / 2), 0.0)); 1518 #endif 1519 PetscCall(ISLocalToGlobalMappingDestroy(&g2l)); 1520 PetscCall(PetscFree(start)); 1521 PetscCall(PetscFree(adjacency)); 1522 PetscCall(VecDestroy(&acown)); 1523 } else { 1524 const char *name; 1525 PetscInt *sizes, *hybsizes, *ghostsizes; 1526 PetscInt locDepth, depth, cellHeight, dim, d; 1527 PetscInt pStart, pEnd, p, gcStart, gcEnd, gcNum; 1528 PetscInt numLabels, l, maxSize = 17; 1529 DMPolytopeType ct0 = DM_POLYTOPE_UNKNOWN; 1530 MPI_Comm comm; 1531 PetscMPIInt size, rank; 1532 1533 PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); 1534 PetscCallMPI(MPI_Comm_size(comm, &size)); 1535 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 1536 PetscCall(DMGetDimension(dm, &dim)); 1537 PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight)); 1538 PetscCall(PetscObjectGetName((PetscObject)dm, &name)); 1539 if (name) PetscCall(PetscViewerASCIIPrintf(viewer, "%s in %" PetscInt_FMT " dimension%s:\n", name, dim, dim == 1 ? "" : "s")); 1540 else PetscCall(PetscViewerASCIIPrintf(viewer, "Mesh in %" PetscInt_FMT " dimension%s:\n", dim, dim == 1 ? "" : "s")); 1541 if (cellHeight) PetscCall(PetscViewerASCIIPrintf(viewer, " Cells are at height %" PetscInt_FMT "\n", cellHeight)); 1542 PetscCall(DMPlexGetDepth(dm, &locDepth)); 1543 PetscCall(MPIU_Allreduce(&locDepth, &depth, 1, MPIU_INT, MPI_MAX, comm)); 1544 PetscCall(DMPlexGetCellTypeStratum(dm, DM_POLYTOPE_FV_GHOST, &gcStart, &gcEnd)); 1545 gcNum = gcEnd - gcStart; 1546 if (size < maxSize) PetscCall(PetscCalloc3(size, &sizes, size, &hybsizes, size, &ghostsizes)); 1547 else PetscCall(PetscCalloc3(3, &sizes, 3, &hybsizes, 3, &ghostsizes)); 1548 for (d = 0; d <= depth; d++) { 1549 PetscInt Nc[2] = {0, 0}, ict; 1550 1551 PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd)); 1552 if (pStart < pEnd) PetscCall(DMPlexGetCellType(dm, pStart, &ct0)); 1553 ict = ct0; 1554 PetscCallMPI(MPI_Bcast(&ict, 1, MPIU_INT, 0, comm)); 1555 ct0 = (DMPolytopeType)ict; 1556 for (p = pStart; p < pEnd; ++p) { 1557 DMPolytopeType ct; 1558 1559 PetscCall(DMPlexGetCellType(dm, p, &ct)); 1560 if (ct == ct0) ++Nc[0]; 1561 else ++Nc[1]; 1562 } 1563 if (size < maxSize) { 1564 PetscCallMPI(MPI_Gather(&Nc[0], 1, MPIU_INT, sizes, 1, MPIU_INT, 0, comm)); 1565 PetscCallMPI(MPI_Gather(&Nc[1], 1, MPIU_INT, hybsizes, 1, MPIU_INT, 0, comm)); 1566 if (d == depth) PetscCallMPI(MPI_Gather(&gcNum, 1, MPIU_INT, ghostsizes, 1, MPIU_INT, 0, comm)); 1567 PetscCall(PetscViewerASCIIPrintf(viewer, " Number of %" PetscInt_FMT "-cells per rank:", (depth == 1) && d ? dim : d)); 1568 for (p = 0; p < size; ++p) { 1569 if (rank == 0) { 1570 PetscCall(PetscViewerASCIIPrintf(viewer, " %" PetscInt_FMT, sizes[p] + hybsizes[p])); 1571 if (hybsizes[p] > 0) PetscCall(PetscViewerASCIIPrintf(viewer, " (%" PetscInt_FMT ")", hybsizes[p])); 1572 if (ghostsizes[p] > 0) PetscCall(PetscViewerASCIIPrintf(viewer, " [%" PetscInt_FMT "]", ghostsizes[p])); 1573 } 1574 } 1575 } else { 1576 PetscInt locMinMax[2]; 1577 1578 locMinMax[0] = Nc[0] + Nc[1]; 1579 locMinMax[1] = Nc[0] + Nc[1]; 1580 PetscCall(PetscGlobalMinMaxInt(comm, locMinMax, sizes)); 1581 locMinMax[0] = Nc[1]; 1582 locMinMax[1] = Nc[1]; 1583 PetscCall(PetscGlobalMinMaxInt(comm, locMinMax, hybsizes)); 1584 if (d == depth) { 1585 locMinMax[0] = gcNum; 1586 locMinMax[1] = gcNum; 1587 PetscCall(PetscGlobalMinMaxInt(comm, locMinMax, ghostsizes)); 1588 } 1589 PetscCall(PetscViewerASCIIPrintf(viewer, " Min/Max of %" PetscInt_FMT "-cells per rank:", (depth == 1) && d ? dim : d)); 1590 PetscCall(PetscViewerASCIIPrintf(viewer, " %" PetscInt_FMT "/%" PetscInt_FMT, sizes[0], sizes[1])); 1591 if (hybsizes[0] > 0) PetscCall(PetscViewerASCIIPrintf(viewer, " (%" PetscInt_FMT "/%" PetscInt_FMT ")", hybsizes[0], hybsizes[1])); 1592 if (ghostsizes[0] > 0) PetscCall(PetscViewerASCIIPrintf(viewer, " [%" PetscInt_FMT "/%" PetscInt_FMT "]", ghostsizes[0], ghostsizes[1])); 1593 } 1594 PetscCall(PetscViewerASCIIPrintf(viewer, "\n")); 1595 } 1596 PetscCall(PetscFree3(sizes, hybsizes, ghostsizes)); 1597 { 1598 const PetscReal *maxCell; 1599 const PetscReal *L; 1600 PetscBool localized; 1601 1602 PetscCall(DMGetPeriodicity(dm, &maxCell, NULL, &L)); 1603 PetscCall(DMGetCoordinatesLocalized(dm, &localized)); 1604 if (L || localized) { 1605 PetscCall(PetscViewerASCIIPrintf(viewer, "Periodic mesh")); 1606 PetscCall(PetscViewerASCIIUseTabs(viewer, PETSC_FALSE)); 1607 if (L) { 1608 PetscCall(PetscViewerASCIIPrintf(viewer, " (")); 1609 for (d = 0; d < dim; ++d) { 1610 if (d > 0) PetscCall(PetscViewerASCIIPrintf(viewer, ", ")); 1611 PetscCall(PetscViewerASCIIPrintf(viewer, "%s", L[d] > 0.0 ? "PERIODIC" : "NONE")); 1612 } 1613 PetscCall(PetscViewerASCIIPrintf(viewer, ")")); 1614 } 1615 PetscCall(PetscViewerASCIIPrintf(viewer, " coordinates %s\n", localized ? "localized" : "not localized")); 1616 PetscCall(PetscViewerASCIIUseTabs(viewer, PETSC_TRUE)); 1617 } 1618 } 1619 PetscCall(DMGetNumLabels(dm, &numLabels)); 1620 if (numLabels) PetscCall(PetscViewerASCIIPrintf(viewer, "Labels:\n")); 1621 for (l = 0; l < numLabels; ++l) { 1622 DMLabel label; 1623 const char *name; 1624 IS valueIS; 1625 const PetscInt *values; 1626 PetscInt numValues, v; 1627 1628 PetscCall(DMGetLabelName(dm, l, &name)); 1629 PetscCall(DMGetLabel(dm, name, &label)); 1630 PetscCall(DMLabelGetNumValues(label, &numValues)); 1631 PetscCall(PetscViewerASCIIPrintf(viewer, " %s: %" PetscInt_FMT " strata with value/size (", name, numValues)); 1632 PetscCall(DMLabelGetValueIS(label, &valueIS)); 1633 PetscCall(ISGetIndices(valueIS, &values)); 1634 PetscCall(PetscViewerASCIIUseTabs(viewer, PETSC_FALSE)); 1635 for (v = 0; v < numValues; ++v) { 1636 PetscInt size; 1637 1638 PetscCall(DMLabelGetStratumSize(label, values[v], &size)); 1639 if (v > 0) PetscCall(PetscViewerASCIIPrintf(viewer, ", ")); 1640 PetscCall(PetscViewerASCIIPrintf(viewer, "%" PetscInt_FMT " (%" PetscInt_FMT ")", values[v], size)); 1641 } 1642 PetscCall(PetscViewerASCIIPrintf(viewer, ")\n")); 1643 PetscCall(PetscViewerASCIIUseTabs(viewer, PETSC_TRUE)); 1644 PetscCall(ISRestoreIndices(valueIS, &values)); 1645 PetscCall(ISDestroy(&valueIS)); 1646 } 1647 { 1648 char **labelNames; 1649 PetscInt Nl = numLabels; 1650 PetscBool flg; 1651 1652 PetscCall(PetscMalloc1(Nl, &labelNames)); 1653 PetscCall(PetscOptionsGetStringArray(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_view_labels", labelNames, &Nl, &flg)); 1654 for (l = 0; l < Nl; ++l) { 1655 DMLabel label; 1656 1657 PetscCall(DMHasLabel(dm, labelNames[l], &flg)); 1658 if (flg) { 1659 PetscCall(DMGetLabel(dm, labelNames[l], &label)); 1660 PetscCall(DMLabelView(label, viewer)); 1661 } 1662 PetscCall(PetscFree(labelNames[l])); 1663 } 1664 PetscCall(PetscFree(labelNames)); 1665 } 1666 /* If no fields are specified, people do not want to see adjacency */ 1667 if (dm->Nf) { 1668 PetscInt f; 1669 1670 for (f = 0; f < dm->Nf; ++f) { 1671 const char *name; 1672 1673 PetscCall(PetscObjectGetName(dm->fields[f].disc, &name)); 1674 if (numLabels) PetscCall(PetscViewerASCIIPrintf(viewer, "Field %s:\n", name)); 1675 PetscCall(PetscViewerASCIIPushTab(viewer)); 1676 if (dm->fields[f].label) PetscCall(DMLabelView(dm->fields[f].label, viewer)); 1677 if (dm->fields[f].adjacency[0]) { 1678 if (dm->fields[f].adjacency[1]) PetscCall(PetscViewerASCIIPrintf(viewer, "adjacency FVM++\n")); 1679 else PetscCall(PetscViewerASCIIPrintf(viewer, "adjacency FVM\n")); 1680 } else { 1681 if (dm->fields[f].adjacency[1]) PetscCall(PetscViewerASCIIPrintf(viewer, "adjacency FEM\n")); 1682 else PetscCall(PetscViewerASCIIPrintf(viewer, "adjacency FUNKY\n")); 1683 } 1684 PetscCall(PetscViewerASCIIPopTab(viewer)); 1685 } 1686 } 1687 PetscCall(DMGetCoarseDM(dm, &cdm)); 1688 if (cdm) { 1689 PetscCall(PetscViewerASCIIPushTab(viewer)); 1690 PetscCall(PetscViewerASCIIPrintf(viewer, "Defined by transform from:\n")); 1691 PetscCall(DMPlexView_Ascii(cdm, viewer)); 1692 PetscCall(PetscViewerASCIIPopTab(viewer)); 1693 } 1694 } 1695 PetscFunctionReturn(PETSC_SUCCESS); 1696 } 1697 1698 static PetscErrorCode DMPlexDrawCell(DM dm, PetscDraw draw, PetscInt cell, const PetscScalar coords[]) 1699 { 1700 DMPolytopeType ct; 1701 PetscMPIInt rank; 1702 PetscInt cdim; 1703 1704 PetscFunctionBegin; 1705 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 1706 PetscCall(DMPlexGetCellType(dm, cell, &ct)); 1707 PetscCall(DMGetCoordinateDim(dm, &cdim)); 1708 switch (ct) { 1709 case DM_POLYTOPE_SEGMENT: 1710 case DM_POLYTOPE_POINT_PRISM_TENSOR: 1711 switch (cdim) { 1712 case 1: { 1713 const PetscReal y = 0.5; /* TODO Put it in the middle of the viewport */ 1714 const PetscReal dy = 0.05; /* TODO Make it a fraction of the total length */ 1715 1716 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[0]), y, PetscRealPart(coords[1]), y, PETSC_DRAW_BLACK)); 1717 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[0]), y + dy, PetscRealPart(coords[0]), y - dy, PETSC_DRAW_BLACK)); 1718 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[1]), y + dy, PetscRealPart(coords[1]), y - dy, PETSC_DRAW_BLACK)); 1719 } break; 1720 case 2: { 1721 const PetscReal dx = (PetscRealPart(coords[3]) - PetscRealPart(coords[1])); 1722 const PetscReal dy = (PetscRealPart(coords[2]) - PetscRealPart(coords[0])); 1723 const PetscReal l = 0.1 / PetscSqrtReal(dx * dx + dy * dy); 1724 1725 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK)); 1726 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)); 1727 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)); 1728 } break; 1729 default: 1730 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells of dimension %" PetscInt_FMT, cdim); 1731 } 1732 break; 1733 case DM_POLYTOPE_TRIANGLE: 1734 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)); 1735 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK)); 1736 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_BLACK)); 1737 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), PETSC_DRAW_BLACK)); 1738 break; 1739 case DM_POLYTOPE_QUADRILATERAL: 1740 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)); 1741 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)); 1742 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK)); 1743 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_BLACK)); 1744 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[6]), PetscRealPart(coords[7]), PETSC_DRAW_BLACK)); 1745 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[6]), PetscRealPart(coords[7]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), PETSC_DRAW_BLACK)); 1746 break; 1747 case DM_POLYTOPE_SEG_PRISM_TENSOR: 1748 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)); 1749 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)); 1750 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK)); 1751 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[6]), PetscRealPart(coords[7]), PETSC_DRAW_BLACK)); 1752 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[6]), PetscRealPart(coords[7]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_BLACK)); 1753 PetscCall(PetscDrawLine(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), PETSC_DRAW_BLACK)); 1754 break; 1755 case DM_POLYTOPE_FV_GHOST: 1756 break; 1757 default: 1758 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells of type %s", DMPolytopeTypes[ct]); 1759 } 1760 PetscFunctionReturn(PETSC_SUCCESS); 1761 } 1762 1763 static PetscErrorCode DMPlexDrawCellHighOrder(DM dm, PetscDraw draw, PetscInt cell, const PetscScalar coords[], PetscInt edgeDiv, PetscReal refCoords[], PetscReal edgeCoords[]) 1764 { 1765 DMPolytopeType ct; 1766 PetscReal centroid[2] = {0., 0.}; 1767 PetscMPIInt rank; 1768 PetscInt fillColor, v, e, d; 1769 1770 PetscFunctionBegin; 1771 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 1772 PetscCall(DMPlexGetCellType(dm, cell, &ct)); 1773 fillColor = PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS - 2) + 2; 1774 switch (ct) { 1775 case DM_POLYTOPE_TRIANGLE: { 1776 PetscReal refVertices[6] = {-1., -1., 1., -1., -1., 1.}; 1777 1778 for (v = 0; v < 3; ++v) { 1779 centroid[0] += PetscRealPart(coords[v * 2 + 0]) / 3.; 1780 centroid[1] += PetscRealPart(coords[v * 2 + 1]) / 3.; 1781 } 1782 for (e = 0; e < 3; ++e) { 1783 refCoords[0] = refVertices[e * 2 + 0]; 1784 refCoords[1] = refVertices[e * 2 + 1]; 1785 for (d = 1; d <= edgeDiv; ++d) { 1786 refCoords[d * 2 + 0] = refCoords[0] + (refVertices[(e + 1) % 3 * 2 + 0] - refCoords[0]) * d / edgeDiv; 1787 refCoords[d * 2 + 1] = refCoords[1] + (refVertices[(e + 1) % 3 * 2 + 1] - refCoords[1]) * d / edgeDiv; 1788 } 1789 PetscCall(DMPlexReferenceToCoordinates(dm, cell, edgeDiv + 1, refCoords, edgeCoords)); 1790 for (d = 0; d < edgeDiv; ++d) { 1791 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)); 1792 PetscCall(PetscDrawLine(draw, edgeCoords[d * 2 + 0], edgeCoords[d * 2 + 1], edgeCoords[(d + 1) * 2 + 0], edgeCoords[(d + 1) * 2 + 1], PETSC_DRAW_BLACK)); 1793 } 1794 } 1795 } break; 1796 default: 1797 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells of type %s", DMPolytopeTypes[ct]); 1798 } 1799 PetscFunctionReturn(PETSC_SUCCESS); 1800 } 1801 1802 static PetscErrorCode DMPlexView_Draw(DM dm, PetscViewer viewer) 1803 { 1804 PetscDraw draw; 1805 DM cdm; 1806 PetscSection coordSection; 1807 Vec coordinates; 1808 PetscReal xyl[3], xyr[3]; 1809 PetscReal *refCoords, *edgeCoords; 1810 PetscBool isnull, drawAffine = PETSC_TRUE; 1811 PetscInt dim, vStart, vEnd, cStart, cEnd, c, edgeDiv = 4; 1812 1813 PetscFunctionBegin; 1814 PetscCall(DMGetCoordinateDim(dm, &dim)); 1815 PetscCheck(dim <= 2, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Cannot draw meshes of dimension %" PetscInt_FMT, dim); 1816 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_view_draw_affine", &drawAffine, NULL)); 1817 if (!drawAffine) PetscCall(PetscMalloc2((edgeDiv + 1) * dim, &refCoords, (edgeDiv + 1) * dim, &edgeCoords)); 1818 PetscCall(DMGetCoordinateDM(dm, &cdm)); 1819 PetscCall(DMGetLocalSection(cdm, &coordSection)); 1820 PetscCall(DMGetCoordinatesLocal(dm, &coordinates)); 1821 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 1822 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 1823 1824 PetscCall(PetscViewerDrawGetDraw(viewer, 0, &draw)); 1825 PetscCall(PetscDrawIsNull(draw, &isnull)); 1826 if (isnull) PetscFunctionReturn(PETSC_SUCCESS); 1827 PetscCall(PetscDrawSetTitle(draw, "Mesh")); 1828 1829 PetscCall(DMGetBoundingBox(dm, xyl, xyr)); 1830 PetscCall(PetscDrawSetCoordinates(draw, xyl[0], xyl[1], xyr[0], xyr[1])); 1831 PetscCall(PetscDrawClear(draw)); 1832 1833 for (c = cStart; c < cEnd; ++c) { 1834 PetscScalar *coords = NULL; 1835 const PetscScalar *coords_arr; 1836 PetscInt numCoords; 1837 PetscBool isDG; 1838 1839 PetscCall(DMPlexGetCellCoordinates(dm, c, &isDG, &numCoords, &coords_arr, &coords)); 1840 if (drawAffine) PetscCall(DMPlexDrawCell(dm, draw, c, coords)); 1841 else PetscCall(DMPlexDrawCellHighOrder(dm, draw, c, coords, edgeDiv, refCoords, edgeCoords)); 1842 PetscCall(DMPlexRestoreCellCoordinates(dm, c, &isDG, &numCoords, &coords_arr, &coords)); 1843 } 1844 if (!drawAffine) PetscCall(PetscFree2(refCoords, edgeCoords)); 1845 PetscCall(PetscDrawFlush(draw)); 1846 PetscCall(PetscDrawPause(draw)); 1847 PetscCall(PetscDrawSave(draw)); 1848 PetscFunctionReturn(PETSC_SUCCESS); 1849 } 1850 1851 static PetscErrorCode DMPlexCreateHighOrderSurrogate_Internal(DM dm, DM *hdm) 1852 { 1853 DM odm = dm, rdm = dm, cdm; 1854 PetscFE fe; 1855 PetscSpace sp; 1856 PetscClassId id; 1857 PetscInt degree; 1858 PetscBool hoView = PETSC_TRUE; 1859 1860 PetscFunctionBegin; 1861 PetscObjectOptionsBegin((PetscObject)dm); 1862 PetscCall(PetscOptionsBool("-dm_plex_high_order_view", "Subsample to view meshes with high order coordinates", "DMPlexCreateHighOrderSurrogate_Internal", hoView, &hoView, NULL)); 1863 PetscOptionsEnd(); 1864 PetscCall(PetscObjectReference((PetscObject)dm)); 1865 *hdm = dm; 1866 if (!hoView) PetscFunctionReturn(PETSC_SUCCESS); 1867 PetscCall(DMGetCoordinateDM(dm, &cdm)); 1868 PetscCall(DMGetField(cdm, 0, NULL, (PetscObject *)&fe)); 1869 PetscCall(PetscObjectGetClassId((PetscObject)fe, &id)); 1870 if (id != PETSCFE_CLASSID) PetscFunctionReturn(PETSC_SUCCESS); 1871 PetscCall(PetscFEGetBasisSpace(fe, &sp)); 1872 PetscCall(PetscSpaceGetDegree(sp, °ree, NULL)); 1873 for (PetscInt r = 0, rd = PetscCeilReal(((PetscReal)degree) / 2.); r < (PetscInt)PetscCeilReal(PetscLog2Real(degree)); ++r, rd = PetscCeilReal(((PetscReal)rd) / 2.)) { 1874 DM cdm, rcdm; 1875 Mat In; 1876 Vec cl, rcl; 1877 1878 PetscCall(DMRefine(odm, PetscObjectComm((PetscObject)odm), &rdm)); 1879 if (rd > 1) PetscCall(DMPlexCreateCoordinateSpace(rdm, rd, PETSC_FALSE, NULL)); 1880 PetscCall(PetscObjectSetName((PetscObject)rdm, "Refined Mesh with Linear Coordinates")); 1881 PetscCall(DMGetCoordinateDM(odm, &cdm)); 1882 PetscCall(DMGetCoordinateDM(rdm, &rcdm)); 1883 PetscCall(DMGetCoordinatesLocal(odm, &cl)); 1884 PetscCall(DMGetCoordinatesLocal(rdm, &rcl)); 1885 PetscCall(DMSetCoarseDM(rcdm, cdm)); 1886 PetscCall(DMCreateInterpolation(cdm, rcdm, &In, NULL)); 1887 PetscCall(MatMult(In, cl, rcl)); 1888 PetscCall(MatDestroy(&In)); 1889 PetscCall(DMSetCoordinatesLocal(rdm, rcl)); 1890 PetscCall(DMDestroy(&odm)); 1891 odm = rdm; 1892 } 1893 *hdm = rdm; 1894 PetscFunctionReturn(PETSC_SUCCESS); 1895 } 1896 1897 #if defined(PETSC_HAVE_EXODUSII) 1898 #include <exodusII.h> 1899 #include <petscviewerexodusii.h> 1900 #endif 1901 1902 PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer) 1903 { 1904 PetscBool iascii, ishdf5, isvtk, isdraw, flg, isglvis, isexodus, iscgns; 1905 char name[PETSC_MAX_PATH_LEN]; 1906 1907 PetscFunctionBegin; 1908 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1909 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 1910 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &iascii)); 1911 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERVTK, &isvtk)); 1912 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 1913 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERDRAW, &isdraw)); 1914 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERGLVIS, &isglvis)); 1915 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWEREXODUSII, &isexodus)); 1916 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERCGNS, &iscgns)); 1917 if (iascii) { 1918 PetscViewerFormat format; 1919 PetscCall(PetscViewerGetFormat(viewer, &format)); 1920 if (format == PETSC_VIEWER_ASCII_GLVIS) PetscCall(DMPlexView_GLVis(dm, viewer)); 1921 else PetscCall(DMPlexView_Ascii(dm, viewer)); 1922 } else if (ishdf5) { 1923 #if defined(PETSC_HAVE_HDF5) 1924 PetscCall(DMPlexView_HDF5_Internal(dm, viewer)); 1925 #else 1926 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 1927 #endif 1928 } else if (isvtk) { 1929 PetscCall(DMPlexVTKWriteAll((PetscObject)dm, viewer)); 1930 } else if (isdraw) { 1931 DM hdm; 1932 1933 PetscCall(DMPlexCreateHighOrderSurrogate_Internal(dm, &hdm)); 1934 PetscCall(DMPlexView_Draw(hdm, viewer)); 1935 PetscCall(DMDestroy(&hdm)); 1936 } else if (isglvis) { 1937 PetscCall(DMPlexView_GLVis(dm, viewer)); 1938 #if defined(PETSC_HAVE_EXODUSII) 1939 } else if (isexodus) { 1940 /* 1941 exodusII requires that all sets be part of exactly one cell set. 1942 If the dm does not have a "Cell Sets" label defined, we create one 1943 with ID 1, containing all cells. 1944 Note that if the Cell Sets label is defined but does not cover all cells, 1945 we may still have a problem. This should probably be checked here or in the viewer; 1946 */ 1947 PetscInt numCS; 1948 PetscCall(DMGetLabelSize(dm, "Cell Sets", &numCS)); 1949 if (!numCS) { 1950 PetscInt cStart, cEnd, c; 1951 PetscCall(DMCreateLabel(dm, "Cell Sets")); 1952 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 1953 for (c = cStart; c < cEnd; ++c) PetscCall(DMSetLabelValue(dm, "Cell Sets", c, 1)); 1954 } 1955 PetscCall(DMView_PlexExodusII(dm, viewer)); 1956 #endif 1957 #if defined(PETSC_HAVE_CGNS) 1958 } else if (iscgns) { 1959 PetscCall(DMView_PlexCGNS(dm, viewer)); 1960 #endif 1961 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Viewer type %s not yet supported for DMPlex writing", ((PetscObject)viewer)->type_name); 1962 /* Optionally view the partition */ 1963 PetscCall(PetscOptionsHasName(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_partition_view", &flg)); 1964 if (flg) { 1965 Vec ranks; 1966 PetscCall(DMPlexCreateRankField(dm, &ranks)); 1967 PetscCall(VecView(ranks, viewer)); 1968 PetscCall(VecDestroy(&ranks)); 1969 } 1970 /* Optionally view a label */ 1971 PetscCall(PetscOptionsGetString(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_label_view", name, sizeof(name), &flg)); 1972 if (flg) { 1973 DMLabel label; 1974 Vec val; 1975 1976 PetscCall(DMGetLabel(dm, name, &label)); 1977 PetscCheck(label, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Label %s provided to -dm_label_view does not exist in this DM", name); 1978 PetscCall(DMPlexCreateLabelField(dm, label, &val)); 1979 PetscCall(VecView(val, viewer)); 1980 PetscCall(VecDestroy(&val)); 1981 } 1982 PetscFunctionReturn(PETSC_SUCCESS); 1983 } 1984 1985 /*@ 1986 DMPlexTopologyView - Saves a `DMPLEX` topology into a file 1987 1988 Collective 1989 1990 Input Parameters: 1991 + dm - The `DM` whose topology is to be saved 1992 - viewer - The `PetscViewer` to save it in 1993 1994 Level: advanced 1995 1996 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMView()`, `DMPlexCoordinatesView()`, `DMPlexLabelsView()`, `DMPlexTopologyLoad()`, `PetscViewer` 1997 @*/ 1998 PetscErrorCode DMPlexTopologyView(DM dm, PetscViewer viewer) 1999 { 2000 PetscBool ishdf5; 2001 2002 PetscFunctionBegin; 2003 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2004 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2005 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2006 PetscCall(PetscLogEventBegin(DMPLEX_TopologyView, viewer, 0, 0, 0)); 2007 if (ishdf5) { 2008 #if defined(PETSC_HAVE_HDF5) 2009 PetscViewerFormat format; 2010 PetscCall(PetscViewerGetFormat(viewer, &format)); 2011 if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) { 2012 IS globalPointNumbering; 2013 2014 PetscCall(DMPlexCreatePointNumbering(dm, &globalPointNumbering)); 2015 PetscCall(DMPlexTopologyView_HDF5_Internal(dm, globalPointNumbering, viewer)); 2016 PetscCall(ISDestroy(&globalPointNumbering)); 2017 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 output.", PetscViewerFormats[format]); 2018 #else 2019 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2020 #endif 2021 } 2022 PetscCall(PetscLogEventEnd(DMPLEX_TopologyView, viewer, 0, 0, 0)); 2023 PetscFunctionReturn(PETSC_SUCCESS); 2024 } 2025 2026 /*@ 2027 DMPlexCoordinatesView - Saves `DMPLEX` coordinates into a file 2028 2029 Collective 2030 2031 Input Parameters: 2032 + dm - The `DM` whose coordinates are to be saved 2033 - viewer - The `PetscViewer` for saving 2034 2035 Level: advanced 2036 2037 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMView()`, `DMPlexTopologyView()`, `DMPlexLabelsView()`, `DMPlexCoordinatesLoad()`, `PetscViewer` 2038 @*/ 2039 PetscErrorCode DMPlexCoordinatesView(DM dm, PetscViewer viewer) 2040 { 2041 PetscBool ishdf5; 2042 2043 PetscFunctionBegin; 2044 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2045 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2046 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2047 PetscCall(PetscLogEventBegin(DMPLEX_CoordinatesView, viewer, 0, 0, 0)); 2048 if (ishdf5) { 2049 #if defined(PETSC_HAVE_HDF5) 2050 PetscViewerFormat format; 2051 PetscCall(PetscViewerGetFormat(viewer, &format)); 2052 if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) { 2053 PetscCall(DMPlexCoordinatesView_HDF5_Internal(dm, viewer)); 2054 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 output.", PetscViewerFormats[format]); 2055 #else 2056 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2057 #endif 2058 } 2059 PetscCall(PetscLogEventEnd(DMPLEX_CoordinatesView, viewer, 0, 0, 0)); 2060 PetscFunctionReturn(PETSC_SUCCESS); 2061 } 2062 2063 /*@ 2064 DMPlexLabelsView - Saves `DMPLEX` labels into a file 2065 2066 Collective 2067 2068 Input Parameters: 2069 + dm - The `DM` whose labels are to be saved 2070 - viewer - The `PetscViewer` for saving 2071 2072 Level: advanced 2073 2074 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMView()`, `DMPlexTopologyView()`, `DMPlexCoordinatesView()`, `DMPlexLabelsLoad()`, `PetscViewer` 2075 @*/ 2076 PetscErrorCode DMPlexLabelsView(DM dm, PetscViewer viewer) 2077 { 2078 PetscBool ishdf5; 2079 2080 PetscFunctionBegin; 2081 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2082 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2083 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2084 PetscCall(PetscLogEventBegin(DMPLEX_LabelsView, viewer, 0, 0, 0)); 2085 if (ishdf5) { 2086 #if defined(PETSC_HAVE_HDF5) 2087 IS globalPointNumbering; 2088 PetscViewerFormat format; 2089 2090 PetscCall(PetscViewerGetFormat(viewer, &format)); 2091 if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) { 2092 PetscCall(DMPlexCreatePointNumbering(dm, &globalPointNumbering)); 2093 PetscCall(DMPlexLabelsView_HDF5_Internal(dm, globalPointNumbering, viewer)); 2094 PetscCall(ISDestroy(&globalPointNumbering)); 2095 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]); 2096 #else 2097 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2098 #endif 2099 } 2100 PetscCall(PetscLogEventEnd(DMPLEX_LabelsView, viewer, 0, 0, 0)); 2101 PetscFunctionReturn(PETSC_SUCCESS); 2102 } 2103 2104 /*@ 2105 DMPlexSectionView - Saves a section associated with a `DMPLEX` 2106 2107 Collective 2108 2109 Input Parameters: 2110 + dm - The `DM` that contains the topology on which the section to be saved is defined 2111 . viewer - The `PetscViewer` for saving 2112 - sectiondm - The `DM` that contains the section to be saved 2113 2114 Level: advanced 2115 2116 Notes: 2117 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. 2118 2119 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 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. 2120 2121 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMView()`, `DMPlexTopologyView()`, `DMPlexCoordinatesView()`, `DMPlexLabelsView()`, `DMPlexGlobalVectorView()`, `DMPlexLocalVectorView()`, `PetscSectionView()`, `DMPlexSectionLoad()`, `PetscViewer` 2122 @*/ 2123 PetscErrorCode DMPlexSectionView(DM dm, PetscViewer viewer, DM sectiondm) 2124 { 2125 PetscBool ishdf5; 2126 2127 PetscFunctionBegin; 2128 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2129 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2130 PetscValidHeaderSpecific(sectiondm, DM_CLASSID, 3); 2131 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2132 PetscCall(PetscLogEventBegin(DMPLEX_SectionView, viewer, 0, 0, 0)); 2133 if (ishdf5) { 2134 #if defined(PETSC_HAVE_HDF5) 2135 PetscCall(DMPlexSectionView_HDF5_Internal(dm, viewer, sectiondm)); 2136 #else 2137 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2138 #endif 2139 } 2140 PetscCall(PetscLogEventEnd(DMPLEX_SectionView, viewer, 0, 0, 0)); 2141 PetscFunctionReturn(PETSC_SUCCESS); 2142 } 2143 2144 /*@ 2145 DMPlexGlobalVectorView - Saves a global vector 2146 2147 Collective 2148 2149 Input Parameters: 2150 + dm - The `DM` that represents the topology 2151 . viewer - The `PetscViewer` to save data with 2152 . sectiondm - The `DM` that contains the global section on which vec is defined 2153 - vec - The global vector to be saved 2154 2155 Level: advanced 2156 2157 Notes: 2158 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 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. 2159 2160 Calling sequence: 2161 .vb 2162 DMCreate(PETSC_COMM_WORLD, &dm); 2163 DMSetType(dm, DMPLEX); 2164 PetscObjectSetName((PetscObject)dm, "topologydm_name"); 2165 DMClone(dm, §iondm); 2166 PetscObjectSetName((PetscObject)sectiondm, "sectiondm_name"); 2167 PetscSectionCreate(PETSC_COMM_WORLD, §ion); 2168 DMPlexGetChart(sectiondm, &pStart, &pEnd); 2169 PetscSectionSetChart(section, pStart, pEnd); 2170 PetscSectionSetUp(section); 2171 DMSetLocalSection(sectiondm, section); 2172 PetscSectionDestroy(§ion); 2173 DMGetGlobalVector(sectiondm, &vec); 2174 PetscObjectSetName((PetscObject)vec, "vec_name"); 2175 DMPlexTopologyView(dm, viewer); 2176 DMPlexSectionView(dm, viewer, sectiondm); 2177 DMPlexGlobalVectorView(dm, viewer, sectiondm, vec); 2178 DMRestoreGlobalVector(sectiondm, &vec); 2179 DMDestroy(§iondm); 2180 DMDestroy(&dm); 2181 .ve 2182 2183 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexTopologyView()`, `DMPlexSectionView()`, `DMPlexLocalVectorView()`, `DMPlexGlobalVectorLoad()`, `DMPlexLocalVectorLoad()` 2184 @*/ 2185 PetscErrorCode DMPlexGlobalVectorView(DM dm, PetscViewer viewer, DM sectiondm, Vec vec) 2186 { 2187 PetscBool ishdf5; 2188 2189 PetscFunctionBegin; 2190 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2191 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2192 PetscValidHeaderSpecific(sectiondm, DM_CLASSID, 3); 2193 PetscValidHeaderSpecific(vec, VEC_CLASSID, 4); 2194 /* Check consistency */ 2195 { 2196 PetscSection section; 2197 PetscBool includesConstraints; 2198 PetscInt m, m1; 2199 2200 PetscCall(VecGetLocalSize(vec, &m1)); 2201 PetscCall(DMGetGlobalSection(sectiondm, §ion)); 2202 PetscCall(PetscSectionGetIncludesConstraints(section, &includesConstraints)); 2203 if (includesConstraints) PetscCall(PetscSectionGetStorageSize(section, &m)); 2204 else PetscCall(PetscSectionGetConstrainedStorageSize(section, &m)); 2205 PetscCheck(m1 == m, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Global vector size (%" PetscInt_FMT ") != global section storage size (%" PetscInt_FMT ")", m1, m); 2206 } 2207 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2208 PetscCall(PetscLogEventBegin(DMPLEX_GlobalVectorView, viewer, 0, 0, 0)); 2209 if (ishdf5) { 2210 #if defined(PETSC_HAVE_HDF5) 2211 PetscCall(DMPlexGlobalVectorView_HDF5_Internal(dm, viewer, sectiondm, vec)); 2212 #else 2213 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2214 #endif 2215 } 2216 PetscCall(PetscLogEventEnd(DMPLEX_GlobalVectorView, viewer, 0, 0, 0)); 2217 PetscFunctionReturn(PETSC_SUCCESS); 2218 } 2219 2220 /*@ 2221 DMPlexLocalVectorView - Saves a local vector 2222 2223 Collective 2224 2225 Input Parameters: 2226 + dm - The `DM` that represents the topology 2227 . viewer - The `PetscViewer` to save data with 2228 . sectiondm - The `DM` that contains the local section on which `vec` is defined; may be the same as `dm` 2229 - vec - The local vector to be saved 2230 2231 Level: advanced 2232 2233 Note: 2234 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 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. 2235 2236 Calling sequence: 2237 .vb 2238 DMCreate(PETSC_COMM_WORLD, &dm); 2239 DMSetType(dm, DMPLEX); 2240 PetscObjectSetName((PetscObject)dm, "topologydm_name"); 2241 DMClone(dm, §iondm); 2242 PetscObjectSetName((PetscObject)sectiondm, "sectiondm_name"); 2243 PetscSectionCreate(PETSC_COMM_WORLD, §ion); 2244 DMPlexGetChart(sectiondm, &pStart, &pEnd); 2245 PetscSectionSetChart(section, pStart, pEnd); 2246 PetscSectionSetUp(section); 2247 DMSetLocalSection(sectiondm, section); 2248 DMGetLocalVector(sectiondm, &vec); 2249 PetscObjectSetName((PetscObject)vec, "vec_name"); 2250 DMPlexTopologyView(dm, viewer); 2251 DMPlexSectionView(dm, viewer, sectiondm); 2252 DMPlexLocalVectorView(dm, viewer, sectiondm, vec); 2253 DMRestoreLocalVector(sectiondm, &vec); 2254 DMDestroy(§iondm); 2255 DMDestroy(&dm); 2256 .ve 2257 2258 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexTopologyView()`, `DMPlexSectionView()`, `DMPlexGlobalVectorView()`, `DMPlexGlobalVectorLoad()`, `DMPlexLocalVectorLoad()` 2259 @*/ 2260 PetscErrorCode DMPlexLocalVectorView(DM dm, PetscViewer viewer, DM sectiondm, Vec vec) 2261 { 2262 PetscBool ishdf5; 2263 2264 PetscFunctionBegin; 2265 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2266 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2267 PetscValidHeaderSpecific(sectiondm, DM_CLASSID, 3); 2268 PetscValidHeaderSpecific(vec, VEC_CLASSID, 4); 2269 /* Check consistency */ 2270 { 2271 PetscSection section; 2272 PetscBool includesConstraints; 2273 PetscInt m, m1; 2274 2275 PetscCall(VecGetLocalSize(vec, &m1)); 2276 PetscCall(DMGetLocalSection(sectiondm, §ion)); 2277 PetscCall(PetscSectionGetIncludesConstraints(section, &includesConstraints)); 2278 if (includesConstraints) PetscCall(PetscSectionGetStorageSize(section, &m)); 2279 else PetscCall(PetscSectionGetConstrainedStorageSize(section, &m)); 2280 PetscCheck(m1 == m, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Local vector size (%" PetscInt_FMT ") != local section storage size (%" PetscInt_FMT ")", m1, m); 2281 } 2282 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2283 PetscCall(PetscLogEventBegin(DMPLEX_LocalVectorView, viewer, 0, 0, 0)); 2284 if (ishdf5) { 2285 #if defined(PETSC_HAVE_HDF5) 2286 PetscCall(DMPlexLocalVectorView_HDF5_Internal(dm, viewer, sectiondm, vec)); 2287 #else 2288 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2289 #endif 2290 } 2291 PetscCall(PetscLogEventEnd(DMPLEX_LocalVectorView, viewer, 0, 0, 0)); 2292 PetscFunctionReturn(PETSC_SUCCESS); 2293 } 2294 2295 PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer) 2296 { 2297 PetscBool ishdf5; 2298 2299 PetscFunctionBegin; 2300 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2301 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2302 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2303 if (ishdf5) { 2304 #if defined(PETSC_HAVE_HDF5) 2305 PetscViewerFormat format; 2306 PetscCall(PetscViewerGetFormat(viewer, &format)); 2307 if (format == PETSC_VIEWER_HDF5_XDMF || format == PETSC_VIEWER_HDF5_VIZ) { 2308 PetscCall(DMPlexLoad_HDF5_Xdmf_Internal(dm, viewer)); 2309 } else if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) { 2310 PetscCall(DMPlexLoad_HDF5_Internal(dm, viewer)); 2311 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]); 2312 PetscFunctionReturn(PETSC_SUCCESS); 2313 #else 2314 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2315 #endif 2316 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Viewer type %s not yet supported for DMPlex loading", ((PetscObject)viewer)->type_name); 2317 } 2318 2319 /*@ 2320 DMPlexTopologyLoad - Loads a topology into a `DMPLEX` 2321 2322 Collective 2323 2324 Input Parameters: 2325 + dm - The `DM` into which the topology is loaded 2326 - viewer - The `PetscViewer` for the saved topology 2327 2328 Output Parameter: 2329 . 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 2330 2331 Level: advanced 2332 2333 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMLoad()`, `DMPlexCoordinatesLoad()`, `DMPlexLabelsLoad()`, `DMView()`, `PetscViewerHDF5Open()`, `PetscViewerPushFormat()`, 2334 `PetscViewer`, `PetscSF` 2335 @*/ 2336 PetscErrorCode DMPlexTopologyLoad(DM dm, PetscViewer viewer, PetscSF *globalToLocalPointSF) 2337 { 2338 PetscBool ishdf5; 2339 2340 PetscFunctionBegin; 2341 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2342 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2343 if (globalToLocalPointSF) PetscAssertPointer(globalToLocalPointSF, 3); 2344 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2345 PetscCall(PetscLogEventBegin(DMPLEX_TopologyLoad, viewer, 0, 0, 0)); 2346 if (ishdf5) { 2347 #if defined(PETSC_HAVE_HDF5) 2348 PetscViewerFormat format; 2349 PetscCall(PetscViewerGetFormat(viewer, &format)); 2350 if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) { 2351 PetscCall(DMPlexTopologyLoad_HDF5_Internal(dm, viewer, globalToLocalPointSF)); 2352 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]); 2353 #else 2354 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2355 #endif 2356 } 2357 PetscCall(PetscLogEventEnd(DMPLEX_TopologyLoad, viewer, 0, 0, 0)); 2358 PetscFunctionReturn(PETSC_SUCCESS); 2359 } 2360 2361 /*@ 2362 DMPlexCoordinatesLoad - Loads coordinates into a `DMPLEX` 2363 2364 Collective 2365 2366 Input Parameters: 2367 + dm - The `DM` into which the coordinates are loaded 2368 . viewer - The `PetscViewer` for the saved coordinates 2369 - globalToLocalPointSF - The `PetscSF` returned by `DMPlexTopologyLoad()` when loading dm from viewer 2370 2371 Level: advanced 2372 2373 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMLoad()`, `DMPlexTopologyLoad()`, `DMPlexLabelsLoad()`, `DMView()`, `PetscViewerHDF5Open()`, `PetscViewerPushFormat()`, 2374 `PetscSF`, `PetscViewer` 2375 @*/ 2376 PetscErrorCode DMPlexCoordinatesLoad(DM dm, PetscViewer viewer, PetscSF globalToLocalPointSF) 2377 { 2378 PetscBool ishdf5; 2379 2380 PetscFunctionBegin; 2381 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2382 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2383 PetscValidHeaderSpecific(globalToLocalPointSF, PETSCSF_CLASSID, 3); 2384 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2385 PetscCall(PetscLogEventBegin(DMPLEX_CoordinatesLoad, viewer, 0, 0, 0)); 2386 if (ishdf5) { 2387 #if defined(PETSC_HAVE_HDF5) 2388 PetscViewerFormat format; 2389 PetscCall(PetscViewerGetFormat(viewer, &format)); 2390 if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) { 2391 PetscCall(DMPlexCoordinatesLoad_HDF5_Internal(dm, viewer, globalToLocalPointSF)); 2392 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]); 2393 #else 2394 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2395 #endif 2396 } 2397 PetscCall(PetscLogEventEnd(DMPLEX_CoordinatesLoad, viewer, 0, 0, 0)); 2398 PetscFunctionReturn(PETSC_SUCCESS); 2399 } 2400 2401 /*@ 2402 DMPlexLabelsLoad - Loads labels into a `DMPLEX` 2403 2404 Collective 2405 2406 Input Parameters: 2407 + dm - The `DM` into which the labels are loaded 2408 . viewer - The `PetscViewer` for the saved labels 2409 - globalToLocalPointSF - The `PetscSF` returned by `DMPlexTopologyLoad()` when loading `dm` from viewer 2410 2411 Level: advanced 2412 2413 Note: 2414 The `PetscSF` argument must not be NULL if the `DM` is distributed, otherwise an error occurs. 2415 2416 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMLoad()`, `DMPlexTopologyLoad()`, `DMPlexCoordinatesLoad()`, `DMView()`, `PetscViewerHDF5Open()`, `PetscViewerPushFormat()`, 2417 `PetscSF`, `PetscViewer` 2418 @*/ 2419 PetscErrorCode DMPlexLabelsLoad(DM dm, PetscViewer viewer, PetscSF globalToLocalPointSF) 2420 { 2421 PetscBool ishdf5; 2422 2423 PetscFunctionBegin; 2424 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2425 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2426 if (globalToLocalPointSF) PetscValidHeaderSpecific(globalToLocalPointSF, PETSCSF_CLASSID, 3); 2427 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2428 PetscCall(PetscLogEventBegin(DMPLEX_LabelsLoad, viewer, 0, 0, 0)); 2429 if (ishdf5) { 2430 #if defined(PETSC_HAVE_HDF5) 2431 PetscViewerFormat format; 2432 2433 PetscCall(PetscViewerGetFormat(viewer, &format)); 2434 if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) { 2435 PetscCall(DMPlexLabelsLoad_HDF5_Internal(dm, viewer, globalToLocalPointSF)); 2436 } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]); 2437 #else 2438 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2439 #endif 2440 } 2441 PetscCall(PetscLogEventEnd(DMPLEX_LabelsLoad, viewer, 0, 0, 0)); 2442 PetscFunctionReturn(PETSC_SUCCESS); 2443 } 2444 2445 /*@ 2446 DMPlexSectionLoad - Loads section into a `DMPLEX` 2447 2448 Collective 2449 2450 Input Parameters: 2451 + dm - The `DM` that represents the topology 2452 . viewer - The `PetscViewer` that represents the on-disk section (sectionA) 2453 . sectiondm - The `DM` into which the on-disk section (sectionA) is migrated 2454 - globalToLocalPointSF - The `PetscSF` returned by `DMPlexTopologyLoad(`) when loading dm from viewer 2455 2456 Output Parameters: 2457 + 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) 2458 - 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) 2459 2460 Level: advanced 2461 2462 Notes: 2463 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. 2464 2465 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 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. 2466 2467 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. 2468 2469 Example using 2 processes: 2470 .vb 2471 NX (number of points on dm): 4 2472 sectionA : the on-disk section 2473 vecA : a vector associated with sectionA 2474 sectionB : sectiondm's local section constructed in this function 2475 vecB (local) : a vector associated with sectiondm's local section 2476 vecB (global) : a vector associated with sectiondm's global section 2477 2478 rank 0 rank 1 2479 vecA (global) : [.0 .4 .1 | .2 .3] <- to be loaded in DMPlexGlobalVectorLoad() or DMPlexLocalVectorLoad() 2480 sectionA->atlasOff : 0 2 | 1 <- loaded in PetscSectionLoad() 2481 sectionA->atlasDof : 1 3 | 1 <- loaded in PetscSectionLoad() 2482 sectionA's global point numbers: 0 2 | 3 <- loaded in DMPlexSectionLoad() 2483 [0, NX) : 0 1 | 2 3 <- conceptual partition used in globalToLocalPointSF 2484 sectionB's global point numbers: 0 1 3 | 3 2 <- associated with [0, NX) by globalToLocalPointSF 2485 sectionB->atlasDof : 1 0 1 | 1 3 2486 sectionB->atlasOff (no perm) : 0 1 1 | 0 1 2487 vecB (local) : [.0 .4] | [.4 .1 .2 .3] <- to be constructed by calling DMPlexLocalVectorLoad() with localDofSF 2488 vecB (global) : [.0 .4 | .1 .2 .3] <- to be constructed by calling DMPlexGlobalVectorLoad() with globalDofSF 2489 .ve 2490 where "|" represents a partition of loaded data, and global point 3 is assumed to be owned by rank 0. 2491 2492 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMLoad()`, `DMPlexTopologyLoad()`, `DMPlexCoordinatesLoad()`, `DMPlexLabelsLoad()`, `DMPlexGlobalVectorLoad()`, `DMPlexLocalVectorLoad()`, `PetscSectionLoad()`, `DMPlexSectionView()`, `PetscSF`, `PetscViewer` 2493 @*/ 2494 PetscErrorCode DMPlexSectionLoad(DM dm, PetscViewer viewer, DM sectiondm, PetscSF globalToLocalPointSF, PetscSF *globalDofSF, PetscSF *localDofSF) 2495 { 2496 PetscBool ishdf5; 2497 2498 PetscFunctionBegin; 2499 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2500 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2501 PetscValidHeaderSpecific(sectiondm, DM_CLASSID, 3); 2502 PetscValidHeaderSpecific(globalToLocalPointSF, PETSCSF_CLASSID, 4); 2503 if (globalDofSF) PetscAssertPointer(globalDofSF, 5); 2504 if (localDofSF) PetscAssertPointer(localDofSF, 6); 2505 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2506 PetscCall(PetscLogEventBegin(DMPLEX_SectionLoad, viewer, 0, 0, 0)); 2507 if (ishdf5) { 2508 #if defined(PETSC_HAVE_HDF5) 2509 PetscCall(DMPlexSectionLoad_HDF5_Internal(dm, viewer, sectiondm, globalToLocalPointSF, globalDofSF, localDofSF)); 2510 #else 2511 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2512 #endif 2513 } 2514 PetscCall(PetscLogEventEnd(DMPLEX_SectionLoad, viewer, 0, 0, 0)); 2515 PetscFunctionReturn(PETSC_SUCCESS); 2516 } 2517 2518 /*@ 2519 DMPlexGlobalVectorLoad - Loads on-disk vector data into a global vector 2520 2521 Collective 2522 2523 Input Parameters: 2524 + dm - The `DM` that represents the topology 2525 . viewer - The `PetscViewer` that represents the on-disk vector data 2526 . sectiondm - The `DM` that contains the global section on which vec is defined 2527 . sf - The `PetscSF` that migrates the on-disk vector data into vec 2528 - vec - The global vector to set values of 2529 2530 Level: advanced 2531 2532 Notes: 2533 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 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. 2534 2535 Calling sequence: 2536 .vb 2537 DMCreate(PETSC_COMM_WORLD, &dm); 2538 DMSetType(dm, DMPLEX); 2539 PetscObjectSetName((PetscObject)dm, "topologydm_name"); 2540 DMPlexTopologyLoad(dm, viewer, &sfX); 2541 DMClone(dm, §iondm); 2542 PetscObjectSetName((PetscObject)sectiondm, "sectiondm_name"); 2543 DMPlexSectionLoad(dm, viewer, sectiondm, sfX, &gsf, NULL); 2544 DMGetGlobalVector(sectiondm, &vec); 2545 PetscObjectSetName((PetscObject)vec, "vec_name"); 2546 DMPlexGlobalVectorLoad(dm, viewer, sectiondm, gsf, vec); 2547 DMRestoreGlobalVector(sectiondm, &vec); 2548 PetscSFDestroy(&gsf); 2549 PetscSFDestroy(&sfX); 2550 DMDestroy(§iondm); 2551 DMDestroy(&dm); 2552 .ve 2553 2554 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexTopologyLoad()`, `DMPlexSectionLoad()`, `DMPlexLocalVectorLoad()`, `DMPlexGlobalVectorView()`, `DMPlexLocalVectorView()`, 2555 `PetscSF`, `PetscViewer` 2556 @*/ 2557 PetscErrorCode DMPlexGlobalVectorLoad(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sf, Vec vec) 2558 { 2559 PetscBool ishdf5; 2560 2561 PetscFunctionBegin; 2562 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2563 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2564 PetscValidHeaderSpecific(sectiondm, DM_CLASSID, 3); 2565 PetscValidHeaderSpecific(sf, PETSCSF_CLASSID, 4); 2566 PetscValidHeaderSpecific(vec, VEC_CLASSID, 5); 2567 /* Check consistency */ 2568 { 2569 PetscSection section; 2570 PetscBool includesConstraints; 2571 PetscInt m, m1; 2572 2573 PetscCall(VecGetLocalSize(vec, &m1)); 2574 PetscCall(DMGetGlobalSection(sectiondm, §ion)); 2575 PetscCall(PetscSectionGetIncludesConstraints(section, &includesConstraints)); 2576 if (includesConstraints) PetscCall(PetscSectionGetStorageSize(section, &m)); 2577 else PetscCall(PetscSectionGetConstrainedStorageSize(section, &m)); 2578 PetscCheck(m1 == m, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Global vector size (%" PetscInt_FMT ") != global section storage size (%" PetscInt_FMT ")", m1, m); 2579 } 2580 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2581 PetscCall(PetscLogEventBegin(DMPLEX_GlobalVectorLoad, viewer, 0, 0, 0)); 2582 if (ishdf5) { 2583 #if defined(PETSC_HAVE_HDF5) 2584 PetscCall(DMPlexVecLoad_HDF5_Internal(dm, viewer, sectiondm, sf, vec)); 2585 #else 2586 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2587 #endif 2588 } 2589 PetscCall(PetscLogEventEnd(DMPLEX_GlobalVectorLoad, viewer, 0, 0, 0)); 2590 PetscFunctionReturn(PETSC_SUCCESS); 2591 } 2592 2593 /*@ 2594 DMPlexLocalVectorLoad - Loads on-disk vector data into a local vector 2595 2596 Collective 2597 2598 Input Parameters: 2599 + dm - The `DM` that represents the topology 2600 . viewer - The `PetscViewer` that represents the on-disk vector data 2601 . sectiondm - The `DM` that contains the local section on which vec is defined 2602 . sf - The `PetscSF` that migrates the on-disk vector data into vec 2603 - vec - The local vector to set values of 2604 2605 Level: advanced 2606 2607 Notes: 2608 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 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. 2609 2610 Calling sequence: 2611 .vb 2612 DMCreate(PETSC_COMM_WORLD, &dm); 2613 DMSetType(dm, DMPLEX); 2614 PetscObjectSetName((PetscObject)dm, "topologydm_name"); 2615 DMPlexTopologyLoad(dm, viewer, &sfX); 2616 DMClone(dm, §iondm); 2617 PetscObjectSetName((PetscObject)sectiondm, "sectiondm_name"); 2618 DMPlexSectionLoad(dm, viewer, sectiondm, sfX, NULL, &lsf); 2619 DMGetLocalVector(sectiondm, &vec); 2620 PetscObjectSetName((PetscObject)vec, "vec_name"); 2621 DMPlexLocalVectorLoad(dm, viewer, sectiondm, lsf, vec); 2622 DMRestoreLocalVector(sectiondm, &vec); 2623 PetscSFDestroy(&lsf); 2624 PetscSFDestroy(&sfX); 2625 DMDestroy(§iondm); 2626 DMDestroy(&dm); 2627 .ve 2628 2629 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexTopologyLoad()`, `DMPlexSectionLoad()`, `DMPlexGlobalVectorLoad()`, `DMPlexGlobalVectorView()`, `DMPlexLocalVectorView()`, 2630 `PetscSF`, `PetscViewer` 2631 @*/ 2632 PetscErrorCode DMPlexLocalVectorLoad(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sf, Vec vec) 2633 { 2634 PetscBool ishdf5; 2635 2636 PetscFunctionBegin; 2637 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2638 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 2639 PetscValidHeaderSpecific(sectiondm, DM_CLASSID, 3); 2640 PetscValidHeaderSpecific(sf, PETSCSF_CLASSID, 4); 2641 PetscValidHeaderSpecific(vec, VEC_CLASSID, 5); 2642 /* Check consistency */ 2643 { 2644 PetscSection section; 2645 PetscBool includesConstraints; 2646 PetscInt m, m1; 2647 2648 PetscCall(VecGetLocalSize(vec, &m1)); 2649 PetscCall(DMGetLocalSection(sectiondm, §ion)); 2650 PetscCall(PetscSectionGetIncludesConstraints(section, &includesConstraints)); 2651 if (includesConstraints) PetscCall(PetscSectionGetStorageSize(section, &m)); 2652 else PetscCall(PetscSectionGetConstrainedStorageSize(section, &m)); 2653 PetscCheck(m1 == m, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Local vector size (%" PetscInt_FMT ") != local section storage size (%" PetscInt_FMT ")", m1, m); 2654 } 2655 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 2656 PetscCall(PetscLogEventBegin(DMPLEX_LocalVectorLoad, viewer, 0, 0, 0)); 2657 if (ishdf5) { 2658 #if defined(PETSC_HAVE_HDF5) 2659 PetscCall(DMPlexVecLoad_HDF5_Internal(dm, viewer, sectiondm, sf, vec)); 2660 #else 2661 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 2662 #endif 2663 } 2664 PetscCall(PetscLogEventEnd(DMPLEX_LocalVectorLoad, viewer, 0, 0, 0)); 2665 PetscFunctionReturn(PETSC_SUCCESS); 2666 } 2667 2668 PetscErrorCode DMDestroy_Plex(DM dm) 2669 { 2670 DM_Plex *mesh = (DM_Plex *)dm->data; 2671 2672 PetscFunctionBegin; 2673 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMSetUpGLVisViewer_C", NULL)); 2674 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexInsertBoundaryValues_C", NULL)); 2675 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMCreateNeumannOverlap_C", NULL)); 2676 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMInterpolateSolution_C", NULL)); 2677 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexInsertTimeDerviativeBoundaryValues_C", NULL)); 2678 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexGetOverlap_C", NULL)); 2679 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexDistributeGetDefault_C", NULL)); 2680 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexDistributeSetDefault_C", NULL)); 2681 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "MatComputeNeumannOverlap_C", NULL)); 2682 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexReorderGetDefault_C", NULL)); 2683 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexReorderSetDefault_C", NULL)); 2684 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexGetOverlap_C", NULL)); 2685 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexSetOverlap_C", NULL)); 2686 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexGetUseCeed_C", NULL)); 2687 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexSetUseCeed_C", NULL)); 2688 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMGetIsoperiodicPointSF_C", NULL)); 2689 if (--mesh->refct > 0) PetscFunctionReturn(PETSC_SUCCESS); 2690 PetscCall(PetscSectionDestroy(&mesh->coneSection)); 2691 PetscCall(PetscFree(mesh->cones)); 2692 PetscCall(PetscFree(mesh->coneOrientations)); 2693 PetscCall(PetscSectionDestroy(&mesh->supportSection)); 2694 PetscCall(PetscSectionDestroy(&mesh->subdomainSection)); 2695 PetscCall(PetscFree(mesh->supports)); 2696 PetscCall(PetscFree(mesh->cellTypes)); 2697 PetscCall(DMPlexTransformDestroy(&mesh->tr)); 2698 PetscCall(PetscFree(mesh->tetgenOpts)); 2699 PetscCall(PetscFree(mesh->triangleOpts)); 2700 PetscCall(PetscFree(mesh->transformType)); 2701 PetscCall(PetscFree(mesh->distributionName)); 2702 PetscCall(PetscPartitionerDestroy(&mesh->partitioner)); 2703 PetscCall(DMLabelDestroy(&mesh->subpointMap)); 2704 PetscCall(ISDestroy(&mesh->subpointIS)); 2705 PetscCall(ISDestroy(&mesh->globalVertexNumbers)); 2706 PetscCall(ISDestroy(&mesh->globalCellNumbers)); 2707 PetscCall(PetscSFDestroy(&mesh->periodic.face_sf)); 2708 PetscCall(PetscSFDestroy(&mesh->periodic.composed_sf)); 2709 PetscCall(ISDestroy(&mesh->periodic.periodic_points)); 2710 PetscCall(PetscSectionDestroy(&mesh->anchorSection)); 2711 PetscCall(ISDestroy(&mesh->anchorIS)); 2712 PetscCall(PetscSectionDestroy(&mesh->parentSection)); 2713 PetscCall(PetscFree(mesh->parents)); 2714 PetscCall(PetscFree(mesh->childIDs)); 2715 PetscCall(PetscSectionDestroy(&mesh->childSection)); 2716 PetscCall(PetscFree(mesh->children)); 2717 PetscCall(DMDestroy(&mesh->referenceTree)); 2718 PetscCall(PetscGridHashDestroy(&mesh->lbox)); 2719 PetscCall(PetscFree(mesh->neighbors)); 2720 if (mesh->metricCtx) PetscCall(PetscFree(mesh->metricCtx)); 2721 /* This was originally freed in DMDestroy(), but that prevents reference counting of backend objects */ 2722 PetscCall(PetscFree(mesh)); 2723 PetscFunctionReturn(PETSC_SUCCESS); 2724 } 2725 2726 PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J) 2727 { 2728 PetscSection sectionGlobal; 2729 PetscInt bs = -1, mbs; 2730 PetscInt localSize, localStart = 0; 2731 PetscBool isShell, isBlock, isSeqBlock, isMPIBlock, isSymBlock, isSymSeqBlock, isSymMPIBlock, isMatIS; 2732 MatType mtype; 2733 ISLocalToGlobalMapping ltog; 2734 2735 PetscFunctionBegin; 2736 PetscCall(MatInitializePackage()); 2737 mtype = dm->mattype; 2738 PetscCall(DMGetGlobalSection(dm, §ionGlobal)); 2739 /* PetscCall(PetscSectionGetStorageSize(sectionGlobal, &localSize)); */ 2740 PetscCall(PetscSectionGetConstrainedStorageSize(sectionGlobal, &localSize)); 2741 PetscCallMPI(MPI_Exscan(&localSize, &localStart, 1, MPIU_INT, MPI_SUM, PetscObjectComm((PetscObject)dm))); 2742 PetscCall(MatCreate(PetscObjectComm((PetscObject)dm), J)); 2743 PetscCall(MatSetSizes(*J, localSize, localSize, PETSC_DETERMINE, PETSC_DETERMINE)); 2744 PetscCall(MatSetType(*J, mtype)); 2745 PetscCall(MatSetFromOptions(*J)); 2746 PetscCall(MatGetBlockSize(*J, &mbs)); 2747 if (mbs > 1) bs = mbs; 2748 PetscCall(PetscStrcmp(mtype, MATSHELL, &isShell)); 2749 PetscCall(PetscStrcmp(mtype, MATBAIJ, &isBlock)); 2750 PetscCall(PetscStrcmp(mtype, MATSEQBAIJ, &isSeqBlock)); 2751 PetscCall(PetscStrcmp(mtype, MATMPIBAIJ, &isMPIBlock)); 2752 PetscCall(PetscStrcmp(mtype, MATSBAIJ, &isSymBlock)); 2753 PetscCall(PetscStrcmp(mtype, MATSEQSBAIJ, &isSymSeqBlock)); 2754 PetscCall(PetscStrcmp(mtype, MATMPISBAIJ, &isSymMPIBlock)); 2755 PetscCall(PetscStrcmp(mtype, MATIS, &isMatIS)); 2756 if (!isShell) { 2757 PetscBool fillMatrix = (PetscBool)(!dm->prealloc_only && !isMatIS); 2758 PetscInt *dnz, *onz, *dnzu, *onzu, bsLocal[2], bsMinMax[2], *pblocks; 2759 PetscInt pStart, pEnd, p, dof, cdof, num_fields; 2760 2761 PetscCall(DMGetLocalToGlobalMapping(dm, <og)); 2762 2763 PetscCall(PetscCalloc1(localSize, &pblocks)); 2764 PetscCall(PetscSectionGetChart(sectionGlobal, &pStart, &pEnd)); 2765 PetscCall(PetscSectionGetNumFields(sectionGlobal, &num_fields)); 2766 for (p = pStart; p < pEnd; ++p) { 2767 switch (dm->blocking_type) { 2768 case DM_BLOCKING_TOPOLOGICAL_POINT: { // One block per topological point 2769 PetscInt bdof, offset; 2770 2771 PetscCall(PetscSectionGetDof(sectionGlobal, p, &dof)); 2772 PetscCall(PetscSectionGetOffset(sectionGlobal, p, &offset)); 2773 PetscCall(PetscSectionGetConstraintDof(sectionGlobal, p, &cdof)); 2774 for (PetscInt i = 0; i < dof - cdof; i++) pblocks[offset - localStart + i] = dof - cdof; 2775 dof = dof < 0 ? -(dof + 1) : dof; 2776 bdof = cdof && (dof - cdof) ? 1 : dof; 2777 if (dof) { 2778 if (bs < 0) { 2779 bs = bdof; 2780 } else if (bs != bdof) { 2781 bs = 1; 2782 } 2783 } 2784 } break; 2785 case DM_BLOCKING_FIELD_NODE: { 2786 for (PetscInt field = 0; field < num_fields; field++) { 2787 PetscInt num_comp, bdof, offset; 2788 PetscCall(PetscSectionGetFieldComponents(sectionGlobal, field, &num_comp)); 2789 PetscCall(PetscSectionGetFieldDof(sectionGlobal, p, field, &dof)); 2790 if (dof < 0) continue; 2791 PetscCall(PetscSectionGetFieldOffset(sectionGlobal, p, field, &offset)); 2792 PetscCall(PetscSectionGetFieldConstraintDof(sectionGlobal, p, field, &cdof)); 2793 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); 2794 PetscInt num_nodes = dof / num_comp; 2795 for (PetscInt i = 0; i < dof - cdof; i++) pblocks[offset - localStart + i] = (dof - cdof) / num_nodes; 2796 // Handle possibly constant block size (unlikely) 2797 bdof = cdof && (dof - cdof) ? 1 : dof; 2798 if (dof) { 2799 if (bs < 0) { 2800 bs = bdof; 2801 } else if (bs != bdof) { 2802 bs = 1; 2803 } 2804 } 2805 } 2806 } break; 2807 } 2808 } 2809 /* Must have same blocksize on all procs (some might have no points) */ 2810 bsLocal[0] = bs < 0 ? PETSC_MAX_INT : bs; 2811 bsLocal[1] = bs; 2812 PetscCall(PetscGlobalMinMaxInt(PetscObjectComm((PetscObject)dm), bsLocal, bsMinMax)); 2813 if (bsMinMax[0] != bsMinMax[1]) bs = 1; 2814 else bs = bsMinMax[0]; 2815 bs = PetscMax(1, bs); 2816 PetscCall(MatSetLocalToGlobalMapping(*J, ltog, ltog)); 2817 if (dm->prealloc_skip) { // User will likely use MatSetPreallocationCOO(), but still set structural parameters 2818 PetscCall(MatSetBlockSize(*J, bs)); 2819 PetscCall(MatSetUp(*J)); 2820 } else { 2821 PetscCall(PetscCalloc4(localSize / bs, &dnz, localSize / bs, &onz, localSize / bs, &dnzu, localSize / bs, &onzu)); 2822 PetscCall(DMPlexPreallocateOperator(dm, bs, dnz, onz, dnzu, onzu, *J, fillMatrix)); 2823 PetscCall(PetscFree4(dnz, onz, dnzu, onzu)); 2824 } 2825 { // Consolidate blocks 2826 PetscInt nblocks = 0; 2827 for (PetscInt i = 0; i < localSize; i += PetscMax(1, pblocks[i])) { 2828 if (pblocks[i] == 0) continue; 2829 pblocks[nblocks++] = pblocks[i]; // nblocks always <= i 2830 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]); 2831 } 2832 PetscCall(MatSetVariableBlockSizes(*J, nblocks, pblocks)); 2833 } 2834 PetscCall(PetscFree(pblocks)); 2835 } 2836 PetscCall(MatSetDM(*J, dm)); 2837 PetscFunctionReturn(PETSC_SUCCESS); 2838 } 2839 2840 /*@ 2841 DMPlexGetSubdomainSection - Returns the section associated with the subdomain 2842 2843 Not Collective 2844 2845 Input Parameter: 2846 . dm - The `DMPLEX` 2847 2848 Output Parameter: 2849 . subsection - The subdomain section 2850 2851 Level: developer 2852 2853 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `PetscSection` 2854 @*/ 2855 PetscErrorCode DMPlexGetSubdomainSection(DM dm, PetscSection *subsection) 2856 { 2857 DM_Plex *mesh = (DM_Plex *)dm->data; 2858 2859 PetscFunctionBegin; 2860 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2861 if (!mesh->subdomainSection) { 2862 PetscSection section; 2863 PetscSF sf; 2864 2865 PetscCall(PetscSFCreate(PETSC_COMM_SELF, &sf)); 2866 PetscCall(DMGetLocalSection(dm, §ion)); 2867 PetscCall(PetscSectionCreateGlobalSection(section, sf, PETSC_FALSE, PETSC_TRUE, &mesh->subdomainSection)); 2868 PetscCall(PetscSFDestroy(&sf)); 2869 } 2870 *subsection = mesh->subdomainSection; 2871 PetscFunctionReturn(PETSC_SUCCESS); 2872 } 2873 2874 /*@ 2875 DMPlexGetChart - Return the interval for all mesh points [`pStart`, `pEnd`) 2876 2877 Not Collective 2878 2879 Input Parameter: 2880 . dm - The `DMPLEX` 2881 2882 Output Parameters: 2883 + pStart - The first mesh point 2884 - pEnd - The upper bound for mesh points 2885 2886 Level: beginner 2887 2888 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexSetChart()` 2889 @*/ 2890 PetscErrorCode DMPlexGetChart(DM dm, PetscInt *pStart, PetscInt *pEnd) 2891 { 2892 DM_Plex *mesh = (DM_Plex *)dm->data; 2893 2894 PetscFunctionBegin; 2895 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2896 if (mesh->tr) PetscCall(DMPlexTransformGetChart(mesh->tr, pStart, pEnd)); 2897 else PetscCall(PetscSectionGetChart(mesh->coneSection, pStart, pEnd)); 2898 PetscFunctionReturn(PETSC_SUCCESS); 2899 } 2900 2901 /*@ 2902 DMPlexSetChart - Set the interval for all mesh points [`pStart`, `pEnd`) 2903 2904 Not Collective 2905 2906 Input Parameters: 2907 + dm - The `DMPLEX` 2908 . pStart - The first mesh point 2909 - pEnd - The upper bound for mesh points 2910 2911 Level: beginner 2912 2913 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetChart()` 2914 @*/ 2915 PetscErrorCode DMPlexSetChart(DM dm, PetscInt pStart, PetscInt pEnd) 2916 { 2917 DM_Plex *mesh = (DM_Plex *)dm->data; 2918 2919 PetscFunctionBegin; 2920 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2921 PetscCall(PetscSectionSetChart(mesh->coneSection, pStart, pEnd)); 2922 PetscCall(PetscSectionSetChart(mesh->supportSection, pStart, pEnd)); 2923 PetscCall(PetscFree(mesh->cellTypes)); 2924 PetscFunctionReturn(PETSC_SUCCESS); 2925 } 2926 2927 /*@ 2928 DMPlexGetConeSize - Return the number of in-edges for this point in the DAG 2929 2930 Not Collective 2931 2932 Input Parameters: 2933 + dm - The `DMPLEX` 2934 - p - The point, which must lie in the chart set with `DMPlexSetChart()` 2935 2936 Output Parameter: 2937 . size - The cone size for point `p` 2938 2939 Level: beginner 2940 2941 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexSetConeSize()`, `DMPlexSetChart()` 2942 @*/ 2943 PetscErrorCode DMPlexGetConeSize(DM dm, PetscInt p, PetscInt *size) 2944 { 2945 DM_Plex *mesh = (DM_Plex *)dm->data; 2946 2947 PetscFunctionBegin; 2948 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2949 PetscAssertPointer(size, 3); 2950 if (mesh->tr) PetscCall(DMPlexTransformGetConeSize(mesh->tr, p, size)); 2951 else PetscCall(PetscSectionGetDof(mesh->coneSection, p, size)); 2952 PetscFunctionReturn(PETSC_SUCCESS); 2953 } 2954 2955 /*@ 2956 DMPlexSetConeSize - Set the number of in-edges for this point in the DAG 2957 2958 Not Collective 2959 2960 Input Parameters: 2961 + dm - The `DMPLEX` 2962 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 2963 - size - The cone size for point `p` 2964 2965 Level: beginner 2966 2967 Note: 2968 This should be called after `DMPlexSetChart()`. 2969 2970 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetConeSize()`, `DMPlexSetChart()` 2971 @*/ 2972 PetscErrorCode DMPlexSetConeSize(DM dm, PetscInt p, PetscInt size) 2973 { 2974 DM_Plex *mesh = (DM_Plex *)dm->data; 2975 2976 PetscFunctionBegin; 2977 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2978 PetscCheck(!mesh->tr, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Cannot call DMPlexSetConeSize() on a mesh with a transform defined."); 2979 PetscCall(PetscSectionSetDof(mesh->coneSection, p, size)); 2980 PetscFunctionReturn(PETSC_SUCCESS); 2981 } 2982 2983 /*@C 2984 DMPlexGetCone - Return the points on the in-edges for this point in the DAG 2985 2986 Not Collective 2987 2988 Input Parameters: 2989 + dm - The `DMPLEX` 2990 - p - The point, which must lie in the chart set with `DMPlexSetChart()` 2991 2992 Output Parameter: 2993 . cone - An array of points which are on the in-edges for point `p` 2994 2995 Level: beginner 2996 2997 Fortran Notes: 2998 You must also call `DMPlexRestoreCone()` after you finish using the returned array. 2999 `DMPlexRestoreCone()` is not needed/available in C. 3000 3001 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetConeSize()`, `DMPlexSetCone()`, `DMPlexGetConeTuple()`, `DMPlexSetChart()`, `DMPlexRestoreCone()` 3002 @*/ 3003 PetscErrorCode DMPlexGetCone(DM dm, PetscInt p, const PetscInt *cone[]) 3004 { 3005 DM_Plex *mesh = (DM_Plex *)dm->data; 3006 PetscInt off; 3007 3008 PetscFunctionBegin; 3009 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3010 PetscAssertPointer(cone, 3); 3011 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 3012 *cone = &mesh->cones[off]; 3013 PetscFunctionReturn(PETSC_SUCCESS); 3014 } 3015 3016 /*@C 3017 DMPlexGetConeTuple - Return the points on the in-edges of several points in the DAG 3018 3019 Not Collective 3020 3021 Input Parameters: 3022 + dm - The `DMPLEX` 3023 - p - The `IS` of points, which must lie in the chart set with `DMPlexSetChart()` 3024 3025 Output Parameters: 3026 + pConesSection - `PetscSection` describing the layout of `pCones` 3027 - pCones - An array of points which are on the in-edges for the point set `p` 3028 3029 Level: intermediate 3030 3031 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexGetConeRecursive()`, `DMPlexSetChart()`, `PetscSection`, `IS` 3032 @*/ 3033 PetscErrorCode DMPlexGetConeTuple(DM dm, IS p, PetscSection *pConesSection, IS *pCones) 3034 { 3035 PetscSection cs, newcs; 3036 PetscInt *cones; 3037 PetscInt *newarr = NULL; 3038 PetscInt n; 3039 3040 PetscFunctionBegin; 3041 PetscCall(DMPlexGetCones(dm, &cones)); 3042 PetscCall(DMPlexGetConeSection(dm, &cs)); 3043 PetscCall(PetscSectionExtractDofsFromArray(cs, MPIU_INT, cones, p, &newcs, pCones ? ((void **)&newarr) : NULL)); 3044 if (pConesSection) *pConesSection = newcs; 3045 if (pCones) { 3046 PetscCall(PetscSectionGetStorageSize(newcs, &n)); 3047 PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)p), n, newarr, PETSC_OWN_POINTER, pCones)); 3048 } 3049 PetscFunctionReturn(PETSC_SUCCESS); 3050 } 3051 3052 /*@ 3053 DMPlexGetConeRecursiveVertices - Expand each given point into its cone points and do that recursively until we end up just with vertices. 3054 3055 Not Collective 3056 3057 Input Parameters: 3058 + dm - The `DMPLEX` 3059 - points - The `IS` of points, which must lie in the chart set with `DMPlexSetChart()` 3060 3061 Output Parameter: 3062 . expandedPoints - An array of vertices recursively expanded from input points 3063 3064 Level: advanced 3065 3066 Notes: 3067 Like `DMPlexGetConeRecursive()` but returns only the 0-depth `IS` (i.e. vertices only) and no sections. 3068 3069 There is no corresponding Restore function, just call `ISDestroy()` on the returned `IS` to deallocate. 3070 3071 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexGetConeTuple()`, `DMPlexGetConeRecursive()`, `DMPlexRestoreConeRecursive()`, 3072 `DMPlexGetDepth()`, `IS` 3073 @*/ 3074 PetscErrorCode DMPlexGetConeRecursiveVertices(DM dm, IS points, IS *expandedPoints) 3075 { 3076 IS *expandedPointsAll; 3077 PetscInt depth; 3078 3079 PetscFunctionBegin; 3080 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3081 PetscValidHeaderSpecific(points, IS_CLASSID, 2); 3082 PetscAssertPointer(expandedPoints, 3); 3083 PetscCall(DMPlexGetConeRecursive(dm, points, &depth, &expandedPointsAll, NULL)); 3084 *expandedPoints = expandedPointsAll[0]; 3085 PetscCall(PetscObjectReference((PetscObject)expandedPointsAll[0])); 3086 PetscCall(DMPlexRestoreConeRecursive(dm, points, &depth, &expandedPointsAll, NULL)); 3087 PetscFunctionReturn(PETSC_SUCCESS); 3088 } 3089 3090 /*@ 3091 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). 3092 3093 Not Collective 3094 3095 Input Parameters: 3096 + dm - The `DMPLEX` 3097 - points - The `IS` of points, which must lie in the chart set with `DMPlexSetChart()` 3098 3099 Output Parameters: 3100 + depth - (optional) Size of the output arrays, equal to `DMPLEX` depth, returned by `DMPlexGetDepth()` 3101 . expandedPoints - (optional) An array of index sets with recursively expanded cones 3102 - sections - (optional) An array of sections which describe mappings from points to their cone points 3103 3104 Level: advanced 3105 3106 Notes: 3107 Like `DMPlexGetConeTuple()` but recursive. 3108 3109 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. 3110 For example, for d=0 it contains only vertices, for d=1 it can contain vertices and edges, etc. 3111 3112 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\: 3113 (1) DAG points in `expandedPoints`[d+1] with `depth` d+1 to their cone points in `expandedPoints`[d]; 3114 (2) DAG points in `expandedPoints`[d+1] with `depth` in [0,d] to the same points in `expandedPoints`[d]. 3115 3116 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexGetConeTuple()`, `DMPlexRestoreConeRecursive()`, `DMPlexGetConeRecursiveVertices()`, 3117 `DMPlexGetDepth()`, `PetscSection`, `IS` 3118 @*/ 3119 PetscErrorCode DMPlexGetConeRecursive(DM dm, IS points, PetscInt *depth, IS *expandedPoints[], PetscSection *sections[]) 3120 { 3121 const PetscInt *arr0 = NULL, *cone = NULL; 3122 PetscInt *arr = NULL, *newarr = NULL; 3123 PetscInt d, depth_, i, n, newn, cn, co, start, end; 3124 IS *expandedPoints_; 3125 PetscSection *sections_; 3126 3127 PetscFunctionBegin; 3128 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3129 PetscValidHeaderSpecific(points, IS_CLASSID, 2); 3130 if (depth) PetscAssertPointer(depth, 3); 3131 if (expandedPoints) PetscAssertPointer(expandedPoints, 4); 3132 if (sections) PetscAssertPointer(sections, 5); 3133 PetscCall(ISGetLocalSize(points, &n)); 3134 PetscCall(ISGetIndices(points, &arr0)); 3135 PetscCall(DMPlexGetDepth(dm, &depth_)); 3136 PetscCall(PetscCalloc1(depth_, &expandedPoints_)); 3137 PetscCall(PetscCalloc1(depth_, §ions_)); 3138 arr = (PetscInt *)arr0; /* this is ok because first generation of arr is not modified */ 3139 for (d = depth_ - 1; d >= 0; d--) { 3140 PetscCall(PetscSectionCreate(PETSC_COMM_SELF, §ions_[d])); 3141 PetscCall(PetscSectionSetChart(sections_[d], 0, n)); 3142 for (i = 0; i < n; i++) { 3143 PetscCall(DMPlexGetDepthStratum(dm, d + 1, &start, &end)); 3144 if (arr[i] >= start && arr[i] < end) { 3145 PetscCall(DMPlexGetConeSize(dm, arr[i], &cn)); 3146 PetscCall(PetscSectionSetDof(sections_[d], i, cn)); 3147 } else { 3148 PetscCall(PetscSectionSetDof(sections_[d], i, 1)); 3149 } 3150 } 3151 PetscCall(PetscSectionSetUp(sections_[d])); 3152 PetscCall(PetscSectionGetStorageSize(sections_[d], &newn)); 3153 PetscCall(PetscMalloc1(newn, &newarr)); 3154 for (i = 0; i < n; i++) { 3155 PetscCall(PetscSectionGetDof(sections_[d], i, &cn)); 3156 PetscCall(PetscSectionGetOffset(sections_[d], i, &co)); 3157 if (cn > 1) { 3158 PetscCall(DMPlexGetCone(dm, arr[i], &cone)); 3159 PetscCall(PetscMemcpy(&newarr[co], cone, cn * sizeof(PetscInt))); 3160 } else { 3161 newarr[co] = arr[i]; 3162 } 3163 } 3164 PetscCall(ISCreateGeneral(PETSC_COMM_SELF, newn, newarr, PETSC_OWN_POINTER, &expandedPoints_[d])); 3165 arr = newarr; 3166 n = newn; 3167 } 3168 PetscCall(ISRestoreIndices(points, &arr0)); 3169 *depth = depth_; 3170 if (expandedPoints) *expandedPoints = expandedPoints_; 3171 else { 3172 for (d = 0; d < depth_; d++) PetscCall(ISDestroy(&expandedPoints_[d])); 3173 PetscCall(PetscFree(expandedPoints_)); 3174 } 3175 if (sections) *sections = sections_; 3176 else { 3177 for (d = 0; d < depth_; d++) PetscCall(PetscSectionDestroy(§ions_[d])); 3178 PetscCall(PetscFree(sections_)); 3179 } 3180 PetscFunctionReturn(PETSC_SUCCESS); 3181 } 3182 3183 /*@ 3184 DMPlexRestoreConeRecursive - Deallocates arrays created by `DMPlexGetConeRecursive()` 3185 3186 Not Collective 3187 3188 Input Parameters: 3189 + dm - The `DMPLEX` 3190 - points - The `IS` of points, which must lie in the chart set with `DMPlexSetChart()` 3191 3192 Output Parameters: 3193 + depth - (optional) Size of the output arrays, equal to `DMPLEX` depth, returned by `DMPlexGetDepth()` 3194 . expandedPoints - (optional) An array of recursively expanded cones 3195 - sections - (optional) An array of sections which describe mappings from points to their cone points 3196 3197 Level: advanced 3198 3199 Note: 3200 See `DMPlexGetConeRecursive()` 3201 3202 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexGetConeTuple()`, `DMPlexGetConeRecursive()`, `DMPlexGetConeRecursiveVertices()`, 3203 `DMPlexGetDepth()`, `IS`, `PetscSection` 3204 @*/ 3205 PetscErrorCode DMPlexRestoreConeRecursive(DM dm, IS points, PetscInt *depth, IS *expandedPoints[], PetscSection *sections[]) 3206 { 3207 PetscInt d, depth_; 3208 3209 PetscFunctionBegin; 3210 PetscCall(DMPlexGetDepth(dm, &depth_)); 3211 PetscCheck(!depth || *depth == depth_, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "depth changed since last call to DMPlexGetConeRecursive"); 3212 if (depth) *depth = 0; 3213 if (expandedPoints) { 3214 for (d = 0; d < depth_; d++) PetscCall(ISDestroy(&((*expandedPoints)[d]))); 3215 PetscCall(PetscFree(*expandedPoints)); 3216 } 3217 if (sections) { 3218 for (d = 0; d < depth_; d++) PetscCall(PetscSectionDestroy(&((*sections)[d]))); 3219 PetscCall(PetscFree(*sections)); 3220 } 3221 PetscFunctionReturn(PETSC_SUCCESS); 3222 } 3223 3224 /*@ 3225 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 3226 3227 Not Collective 3228 3229 Input Parameters: 3230 + dm - The `DMPLEX` 3231 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 3232 - cone - An array of points which are on the in-edges for point `p` 3233 3234 Level: beginner 3235 3236 Note: 3237 This should be called after all calls to `DMPlexSetConeSize()` and `DMSetUp()`. 3238 3239 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexSetChart()`, `DMPlexSetConeSize()`, `DMSetUp()`, `DMPlexSetSupport()`, `DMPlexSetSupportSize()` 3240 @*/ 3241 PetscErrorCode DMPlexSetCone(DM dm, PetscInt p, const PetscInt cone[]) 3242 { 3243 DM_Plex *mesh = (DM_Plex *)dm->data; 3244 PetscInt dof, off, c; 3245 3246 PetscFunctionBegin; 3247 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3248 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 3249 if (dof) PetscAssertPointer(cone, 3); 3250 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 3251 if (PetscDefined(USE_DEBUG)) { 3252 PetscInt pStart, pEnd; 3253 PetscCall(PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd)); 3254 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); 3255 for (c = 0; c < dof; ++c) { 3256 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); 3257 mesh->cones[off + c] = cone[c]; 3258 } 3259 } else { 3260 for (c = 0; c < dof; ++c) mesh->cones[off + c] = cone[c]; 3261 } 3262 PetscFunctionReturn(PETSC_SUCCESS); 3263 } 3264 3265 /*@C 3266 DMPlexGetConeOrientation - Return the orientations on the in-edges for this point in the DAG 3267 3268 Not Collective 3269 3270 Input Parameters: 3271 + dm - The `DMPLEX` 3272 - p - The point, which must lie in the chart set with `DMPlexSetChart()` 3273 3274 Output Parameter: 3275 . coneOrientation - An array of orientations which are on the in-edges for point `p`. An orientation is an 3276 integer giving the prescription for cone traversal. 3277 3278 Level: beginner 3279 3280 Note: 3281 The number indexes the symmetry transformations for the cell type (see manual). Orientation 0 is always 3282 the identity transformation. Negative orientation indicates reflection so that -(o+1) is the reflection 3283 of o, however it is not necessarily the inverse. To get the inverse, use `DMPolytopeTypeComposeOrientationInv()` 3284 with the identity. 3285 3286 Fortran Notes: 3287 You must also call `DMPlexRestoreConeOrientation()` after you finish using the returned array. 3288 `DMPlexRestoreConeOrientation()` is not needed/available in C. 3289 3290 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPolytopeTypeComposeOrientation()`, `DMPolytopeTypeComposeOrientationInv()`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexSetCone()`, `DMPlexSetChart()` 3291 @*/ 3292 PetscErrorCode DMPlexGetConeOrientation(DM dm, PetscInt p, const PetscInt *coneOrientation[]) 3293 { 3294 DM_Plex *mesh = (DM_Plex *)dm->data; 3295 PetscInt off; 3296 3297 PetscFunctionBegin; 3298 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3299 if (PetscDefined(USE_DEBUG)) { 3300 PetscInt dof; 3301 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 3302 if (dof) PetscAssertPointer(coneOrientation, 3); 3303 } 3304 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 3305 3306 *coneOrientation = &mesh->coneOrientations[off]; 3307 PetscFunctionReturn(PETSC_SUCCESS); 3308 } 3309 3310 /*@ 3311 DMPlexSetConeOrientation - Set the orientations on the in-edges for this point in the DAG 3312 3313 Not Collective 3314 3315 Input Parameters: 3316 + dm - The `DMPLEX` 3317 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 3318 - coneOrientation - An array of orientations 3319 3320 Level: beginner 3321 3322 Notes: 3323 This should be called after all calls to `DMPlexSetConeSize()` and `DMSetUp()`. 3324 3325 The meaning of coneOrientation is detailed in `DMPlexGetConeOrientation()`. 3326 3327 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetConeOrientation()`, `DMPlexSetCone()`, `DMPlexSetChart()`, `DMPlexSetConeSize()`, `DMSetUp()` 3328 @*/ 3329 PetscErrorCode DMPlexSetConeOrientation(DM dm, PetscInt p, const PetscInt coneOrientation[]) 3330 { 3331 DM_Plex *mesh = (DM_Plex *)dm->data; 3332 PetscInt pStart, pEnd; 3333 PetscInt dof, off, c; 3334 3335 PetscFunctionBegin; 3336 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3337 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 3338 if (dof) PetscAssertPointer(coneOrientation, 3); 3339 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 3340 if (PetscDefined(USE_DEBUG)) { 3341 PetscCall(PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd)); 3342 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); 3343 for (c = 0; c < dof; ++c) { 3344 PetscInt cdof, o = coneOrientation[c]; 3345 3346 PetscCall(PetscSectionGetDof(mesh->coneSection, mesh->cones[off + c], &cdof)); 3347 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); 3348 mesh->coneOrientations[off + c] = o; 3349 } 3350 } else { 3351 for (c = 0; c < dof; ++c) mesh->coneOrientations[off + c] = coneOrientation[c]; 3352 } 3353 PetscFunctionReturn(PETSC_SUCCESS); 3354 } 3355 3356 /*@ 3357 DMPlexInsertCone - Insert a point into the in-edges for the point p in the DAG 3358 3359 Not Collective 3360 3361 Input Parameters: 3362 + dm - The `DMPLEX` 3363 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 3364 . conePos - The local index in the cone where the point should be put 3365 - conePoint - The mesh point to insert 3366 3367 Level: beginner 3368 3369 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexSetChart()`, `DMPlexSetConeSize()`, `DMSetUp()` 3370 @*/ 3371 PetscErrorCode DMPlexInsertCone(DM dm, PetscInt p, PetscInt conePos, PetscInt conePoint) 3372 { 3373 DM_Plex *mesh = (DM_Plex *)dm->data; 3374 PetscInt pStart, pEnd; 3375 PetscInt dof, off; 3376 3377 PetscFunctionBegin; 3378 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3379 if (PetscDefined(USE_DEBUG)) { 3380 PetscCall(PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd)); 3381 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); 3382 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); 3383 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 3384 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); 3385 } 3386 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 3387 mesh->cones[off + conePos] = conePoint; 3388 PetscFunctionReturn(PETSC_SUCCESS); 3389 } 3390 3391 /*@ 3392 DMPlexInsertConeOrientation - Insert a point orientation for the in-edge for the point p in the DAG 3393 3394 Not Collective 3395 3396 Input Parameters: 3397 + dm - The `DMPLEX` 3398 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 3399 . conePos - The local index in the cone where the point should be put 3400 - coneOrientation - The point orientation to insert 3401 3402 Level: beginner 3403 3404 Note: 3405 The meaning of coneOrientation values is detailed in `DMPlexGetConeOrientation()`. 3406 3407 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexSetChart()`, `DMPlexSetConeSize()`, `DMSetUp()` 3408 @*/ 3409 PetscErrorCode DMPlexInsertConeOrientation(DM dm, PetscInt p, PetscInt conePos, PetscInt coneOrientation) 3410 { 3411 DM_Plex *mesh = (DM_Plex *)dm->data; 3412 PetscInt pStart, pEnd; 3413 PetscInt dof, off; 3414 3415 PetscFunctionBegin; 3416 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3417 if (PetscDefined(USE_DEBUG)) { 3418 PetscCall(PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd)); 3419 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); 3420 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 3421 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); 3422 } 3423 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 3424 mesh->coneOrientations[off + conePos] = coneOrientation; 3425 PetscFunctionReturn(PETSC_SUCCESS); 3426 } 3427 3428 /*@C 3429 DMPlexGetOrientedCone - Return the points and orientations on the in-edges for this point in the DAG 3430 3431 Not collective 3432 3433 Input Parameters: 3434 + dm - The DMPlex 3435 - p - The point, which must lie in the chart set with DMPlexSetChart() 3436 3437 Output Parameters: 3438 + cone - An array of points which are on the in-edges for point `p` 3439 - ornt - An array of orientations which are on the in-edges for point `p`. An orientation is an 3440 integer giving the prescription for cone traversal. 3441 3442 Level: beginner 3443 3444 Notes: 3445 The number indexes the symmetry transformations for the cell type (see manual). Orientation 0 is always 3446 the identity transformation. Negative orientation indicates reflection so that -(o+1) is the reflection 3447 of o, however it is not necessarily the inverse. To get the inverse, use `DMPolytopeTypeComposeOrientationInv()` 3448 with the identity. 3449 3450 Fortran Notes: 3451 You must also call `DMPlexRestoreCone()` after you finish using the returned array. 3452 `DMPlexRestoreCone()` is not needed/available in C. 3453 3454 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexRestoreOrientedCone()`, `DMPlexGetConeSize()`, `DMPlexGetCone()`, `DMPlexGetChart()` 3455 @*/ 3456 PetscErrorCode DMPlexGetOrientedCone(DM dm, PetscInt p, const PetscInt *cone[], const PetscInt *ornt[]) 3457 { 3458 DM_Plex *mesh = (DM_Plex *)dm->data; 3459 3460 PetscFunctionBegin; 3461 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3462 if (mesh->tr) { 3463 PetscCall(DMPlexTransformGetCone(mesh->tr, p, cone, ornt)); 3464 } else { 3465 PetscInt off; 3466 if (PetscDefined(USE_DEBUG)) { 3467 PetscInt dof; 3468 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 3469 if (dof) { 3470 if (cone) PetscAssertPointer(cone, 3); 3471 if (ornt) PetscAssertPointer(ornt, 4); 3472 } 3473 } 3474 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 3475 if (cone) *cone = mesh->cones ? mesh->cones + off : NULL; // NULL + 0 is UB 3476 if (ornt) *ornt = mesh->coneOrientations ? mesh->coneOrientations + off : NULL; 3477 } 3478 PetscFunctionReturn(PETSC_SUCCESS); 3479 } 3480 3481 /*@C 3482 DMPlexRestoreOrientedCone - Restore the points and orientations on the in-edges for this point in the DAG 3483 3484 Not Collective 3485 3486 Input Parameters: 3487 + dm - The DMPlex 3488 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 3489 . cone - An array of points which are on the in-edges for point p 3490 - ornt - An array of orientations which are on the in-edges for point `p`. An orientation is an 3491 integer giving the prescription for cone traversal. 3492 3493 Level: beginner 3494 3495 Notes: 3496 The number indexes the symmetry transformations for the cell type (see manual). Orientation 0 is always 3497 the identity transformation. Negative orientation indicates reflection so that -(o+1) is the reflection 3498 of o, however it is not necessarily the inverse. To get the inverse, use `DMPolytopeTypeComposeOrientationInv()` 3499 with the identity. 3500 3501 Fortran Notes: 3502 You must also call `DMPlexRestoreCone()` after you finish using the returned array. 3503 `DMPlexRestoreCone()` is not needed/available in C. 3504 3505 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetOrientedCone()`, `DMPlexGetConeSize()`, `DMPlexGetCone()`, `DMPlexGetChart()` 3506 @*/ 3507 PetscErrorCode DMPlexRestoreOrientedCone(DM dm, PetscInt p, const PetscInt *cone[], const PetscInt *ornt[]) 3508 { 3509 DM_Plex *mesh = (DM_Plex *)dm->data; 3510 3511 PetscFunctionBegin; 3512 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3513 if (mesh->tr) PetscCall(DMPlexTransformRestoreCone(mesh->tr, p, cone, ornt)); 3514 PetscFunctionReturn(PETSC_SUCCESS); 3515 } 3516 3517 /*@ 3518 DMPlexGetSupportSize - Return the number of out-edges for this point in the DAG 3519 3520 Not Collective 3521 3522 Input Parameters: 3523 + dm - The `DMPLEX` 3524 - p - The point, which must lie in the chart set with `DMPlexSetChart()` 3525 3526 Output Parameter: 3527 . size - The support size for point `p` 3528 3529 Level: beginner 3530 3531 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexSetConeSize()`, `DMPlexSetChart()`, `DMPlexGetConeSize()` 3532 @*/ 3533 PetscErrorCode DMPlexGetSupportSize(DM dm, PetscInt p, PetscInt *size) 3534 { 3535 DM_Plex *mesh = (DM_Plex *)dm->data; 3536 3537 PetscFunctionBegin; 3538 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3539 PetscAssertPointer(size, 3); 3540 PetscCall(PetscSectionGetDof(mesh->supportSection, p, size)); 3541 PetscFunctionReturn(PETSC_SUCCESS); 3542 } 3543 3544 /*@ 3545 DMPlexSetSupportSize - Set the number of out-edges for this point in the DAG 3546 3547 Not Collective 3548 3549 Input Parameters: 3550 + dm - The `DMPLEX` 3551 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 3552 - size - The support size for point `p` 3553 3554 Level: beginner 3555 3556 Note: 3557 This should be called after `DMPlexSetChart()`. 3558 3559 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetSupportSize()`, `DMPlexSetChart()` 3560 @*/ 3561 PetscErrorCode DMPlexSetSupportSize(DM dm, PetscInt p, PetscInt size) 3562 { 3563 DM_Plex *mesh = (DM_Plex *)dm->data; 3564 3565 PetscFunctionBegin; 3566 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3567 PetscCall(PetscSectionSetDof(mesh->supportSection, p, size)); 3568 PetscFunctionReturn(PETSC_SUCCESS); 3569 } 3570 3571 /*@C 3572 DMPlexGetSupport - Return the points on the out-edges for this point in the DAG 3573 3574 Not Collective 3575 3576 Input Parameters: 3577 + dm - The `DMPLEX` 3578 - p - The point, which must lie in the chart set with `DMPlexSetChart()` 3579 3580 Output Parameter: 3581 . support - An array of points which are on the out-edges for point `p` 3582 3583 Level: beginner 3584 3585 Fortran Notes: 3586 You must also call `DMPlexRestoreSupport()` after you finish using the returned array. 3587 `DMPlexRestoreSupport()` is not needed/available in C. 3588 3589 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetSupportSize()`, `DMPlexSetSupport()`, `DMPlexGetCone()`, `DMPlexSetChart()` 3590 @*/ 3591 PetscErrorCode DMPlexGetSupport(DM dm, PetscInt p, const PetscInt *support[]) 3592 { 3593 DM_Plex *mesh = (DM_Plex *)dm->data; 3594 PetscInt off; 3595 3596 PetscFunctionBegin; 3597 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3598 PetscAssertPointer(support, 3); 3599 PetscCall(PetscSectionGetOffset(mesh->supportSection, p, &off)); 3600 *support = mesh->supports ? mesh->supports + off : NULL; //NULL + 0 is UB 3601 PetscFunctionReturn(PETSC_SUCCESS); 3602 } 3603 3604 /*@ 3605 DMPlexSetSupport - Set the points on the out-edges for this point in the DAG, that is the list of points that this point covers 3606 3607 Not Collective 3608 3609 Input Parameters: 3610 + dm - The `DMPLEX` 3611 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 3612 - support - An array of points which are on the out-edges for point `p` 3613 3614 Level: beginner 3615 3616 Note: 3617 This should be called after all calls to `DMPlexSetSupportSize()` and `DMSetUp()`. 3618 3619 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexSetCone()`, `DMPlexSetConeSize()`, `DMPlexCreate()`, `DMPlexGetSupport()`, `DMPlexSetChart()`, `DMPlexSetSupportSize()`, `DMSetUp()` 3620 @*/ 3621 PetscErrorCode DMPlexSetSupport(DM dm, PetscInt p, const PetscInt support[]) 3622 { 3623 DM_Plex *mesh = (DM_Plex *)dm->data; 3624 PetscInt pStart, pEnd; 3625 PetscInt dof, off, c; 3626 3627 PetscFunctionBegin; 3628 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3629 PetscCall(PetscSectionGetChart(mesh->supportSection, &pStart, &pEnd)); 3630 PetscCall(PetscSectionGetDof(mesh->supportSection, p, &dof)); 3631 if (dof) PetscAssertPointer(support, 3); 3632 PetscCall(PetscSectionGetOffset(mesh->supportSection, p, &off)); 3633 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); 3634 for (c = 0; c < dof; ++c) { 3635 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); 3636 mesh->supports[off + c] = support[c]; 3637 } 3638 PetscFunctionReturn(PETSC_SUCCESS); 3639 } 3640 3641 /*@ 3642 DMPlexInsertSupport - Insert a point into the out-edges for the point p in the DAG 3643 3644 Not Collective 3645 3646 Input Parameters: 3647 + dm - The `DMPLEX` 3648 . p - The point, which must lie in the chart set with `DMPlexSetChart()` 3649 . supportPos - The local index in the cone where the point should be put 3650 - supportPoint - The mesh point to insert 3651 3652 Level: beginner 3653 3654 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexGetCone()`, `DMPlexSetChart()`, `DMPlexSetConeSize()`, `DMSetUp()` 3655 @*/ 3656 PetscErrorCode DMPlexInsertSupport(DM dm, PetscInt p, PetscInt supportPos, PetscInt supportPoint) 3657 { 3658 DM_Plex *mesh = (DM_Plex *)dm->data; 3659 PetscInt pStart, pEnd; 3660 PetscInt dof, off; 3661 3662 PetscFunctionBegin; 3663 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3664 PetscCall(PetscSectionGetChart(mesh->supportSection, &pStart, &pEnd)); 3665 PetscCall(PetscSectionGetDof(mesh->supportSection, p, &dof)); 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 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); 3669 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); 3670 mesh->supports[off + supportPos] = supportPoint; 3671 PetscFunctionReturn(PETSC_SUCCESS); 3672 } 3673 3674 /* Converts an orientation o in the current numbering to the previous scheme used in Plex */ 3675 PetscInt DMPolytopeConvertNewOrientation_Internal(DMPolytopeType ct, PetscInt o) 3676 { 3677 switch (ct) { 3678 case DM_POLYTOPE_SEGMENT: 3679 if (o == -1) return -2; 3680 break; 3681 case DM_POLYTOPE_TRIANGLE: 3682 if (o == -3) return -1; 3683 if (o == -2) return -3; 3684 if (o == -1) return -2; 3685 break; 3686 case DM_POLYTOPE_QUADRILATERAL: 3687 if (o == -4) return -2; 3688 if (o == -3) return -1; 3689 if (o == -2) return -4; 3690 if (o == -1) return -3; 3691 break; 3692 default: 3693 return o; 3694 } 3695 return o; 3696 } 3697 3698 /* Converts an orientation o in the previous scheme used in Plex to the current numbering */ 3699 PetscInt DMPolytopeConvertOldOrientation_Internal(DMPolytopeType ct, PetscInt o) 3700 { 3701 switch (ct) { 3702 case DM_POLYTOPE_SEGMENT: 3703 if ((o == -2) || (o == 1)) return -1; 3704 if (o == -1) return 0; 3705 break; 3706 case DM_POLYTOPE_TRIANGLE: 3707 if (o == -3) return -2; 3708 if (o == -2) return -1; 3709 if (o == -1) return -3; 3710 break; 3711 case DM_POLYTOPE_QUADRILATERAL: 3712 if (o == -4) return -2; 3713 if (o == -3) return -1; 3714 if (o == -2) return -4; 3715 if (o == -1) return -3; 3716 break; 3717 default: 3718 return o; 3719 } 3720 return o; 3721 } 3722 3723 /* Takes in a mesh whose orientations are in the previous scheme and converts them all to the current numbering */ 3724 PetscErrorCode DMPlexConvertOldOrientations_Internal(DM dm) 3725 { 3726 PetscInt pStart, pEnd, p; 3727 3728 PetscFunctionBegin; 3729 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 3730 for (p = pStart; p < pEnd; ++p) { 3731 const PetscInt *cone, *ornt; 3732 PetscInt coneSize, c; 3733 3734 PetscCall(DMPlexGetConeSize(dm, p, &coneSize)); 3735 PetscCall(DMPlexGetCone(dm, p, &cone)); 3736 PetscCall(DMPlexGetConeOrientation(dm, p, &ornt)); 3737 for (c = 0; c < coneSize; ++c) { 3738 DMPolytopeType ct; 3739 const PetscInt o = ornt[c]; 3740 3741 PetscCall(DMPlexGetCellType(dm, cone[c], &ct)); 3742 switch (ct) { 3743 case DM_POLYTOPE_SEGMENT: 3744 if ((o == -2) || (o == 1)) PetscCall(DMPlexInsertConeOrientation(dm, p, c, -1)); 3745 if (o == -1) PetscCall(DMPlexInsertConeOrientation(dm, p, c, 0)); 3746 break; 3747 case DM_POLYTOPE_TRIANGLE: 3748 if (o == -3) PetscCall(DMPlexInsertConeOrientation(dm, p, c, -2)); 3749 if (o == -2) PetscCall(DMPlexInsertConeOrientation(dm, p, c, -1)); 3750 if (o == -1) PetscCall(DMPlexInsertConeOrientation(dm, p, c, -3)); 3751 break; 3752 case DM_POLYTOPE_QUADRILATERAL: 3753 if (o == -4) PetscCall(DMPlexInsertConeOrientation(dm, p, c, -2)); 3754 if (o == -3) PetscCall(DMPlexInsertConeOrientation(dm, p, c, -1)); 3755 if (o == -2) PetscCall(DMPlexInsertConeOrientation(dm, p, c, -4)); 3756 if (o == -1) PetscCall(DMPlexInsertConeOrientation(dm, p, c, -3)); 3757 break; 3758 default: 3759 break; 3760 } 3761 } 3762 } 3763 PetscFunctionReturn(PETSC_SUCCESS); 3764 } 3765 3766 static inline PetscErrorCode DMPlexGetTransitiveClosure_Hot_Private(DM dm, PetscInt p, PetscBool useCone, PetscInt *size, const PetscInt *arr[], const PetscInt *ornt[]) 3767 { 3768 DM_Plex *mesh = (DM_Plex *)dm->data; 3769 3770 PetscFunctionBeginHot; 3771 if (PetscDefined(USE_DEBUG) || mesh->tr) { 3772 if (useCone) { 3773 PetscCall(DMPlexGetConeSize(dm, p, size)); 3774 PetscCall(DMPlexGetOrientedCone(dm, p, arr, ornt)); 3775 } else { 3776 PetscCall(DMPlexGetSupportSize(dm, p, size)); 3777 PetscCall(DMPlexGetSupport(dm, p, arr)); 3778 } 3779 } else { 3780 if (useCone) { 3781 const PetscSection s = mesh->coneSection; 3782 const PetscInt ps = p - s->pStart; 3783 const PetscInt off = s->atlasOff[ps]; 3784 3785 *size = s->atlasDof[ps]; 3786 *arr = mesh->cones + off; 3787 *ornt = mesh->coneOrientations + off; 3788 } else { 3789 const PetscSection s = mesh->supportSection; 3790 const PetscInt ps = p - s->pStart; 3791 const PetscInt off = s->atlasOff[ps]; 3792 3793 *size = s->atlasDof[ps]; 3794 *arr = mesh->supports + off; 3795 } 3796 } 3797 PetscFunctionReturn(PETSC_SUCCESS); 3798 } 3799 3800 static inline PetscErrorCode DMPlexRestoreTransitiveClosure_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) PetscCall(DMPlexRestoreOrientedCone(dm, p, arr, ornt)); 3807 } 3808 PetscFunctionReturn(PETSC_SUCCESS); 3809 } 3810 3811 static PetscErrorCode DMPlexGetTransitiveClosure_Depth1_Private(DM dm, PetscInt p, PetscInt ornt, PetscBool useCone, PetscInt *numPoints, PetscInt *points[]) 3812 { 3813 DMPolytopeType ct = DM_POLYTOPE_UNKNOWN; 3814 PetscInt *closure; 3815 const PetscInt *tmp = NULL, *tmpO = NULL; 3816 PetscInt off = 0, tmpSize, t; 3817 3818 PetscFunctionBeginHot; 3819 if (ornt) { 3820 PetscCall(DMPlexGetCellType(dm, p, &ct)); 3821 if (ct == DM_POLYTOPE_FV_GHOST || ct == DM_POLYTOPE_INTERIOR_GHOST || ct == DM_POLYTOPE_UNKNOWN) ct = DM_POLYTOPE_UNKNOWN; 3822 } 3823 if (*points) { 3824 closure = *points; 3825 } else { 3826 PetscInt maxConeSize, maxSupportSize; 3827 PetscCall(DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize)); 3828 PetscCall(DMGetWorkArray(dm, 2 * (PetscMax(maxConeSize, maxSupportSize) + 1), MPIU_INT, &closure)); 3829 } 3830 PetscCall(DMPlexGetTransitiveClosure_Hot_Private(dm, p, useCone, &tmpSize, &tmp, &tmpO)); 3831 if (ct == DM_POLYTOPE_UNKNOWN) { 3832 closure[off++] = p; 3833 closure[off++] = 0; 3834 for (t = 0; t < tmpSize; ++t) { 3835 closure[off++] = tmp[t]; 3836 closure[off++] = tmpO ? tmpO[t] : 0; 3837 } 3838 } else { 3839 const PetscInt *arr = DMPolytopeTypeGetArrangment(ct, ornt); 3840 3841 /* We assume that cells with a valid type have faces with a valid type */ 3842 closure[off++] = p; 3843 closure[off++] = ornt; 3844 for (t = 0; t < tmpSize; ++t) { 3845 DMPolytopeType ft; 3846 3847 PetscCall(DMPlexGetCellType(dm, tmp[t], &ft)); 3848 closure[off++] = tmp[arr[t]]; 3849 closure[off++] = tmpO ? DMPolytopeTypeComposeOrientation(ft, ornt, tmpO[t]) : 0; 3850 } 3851 } 3852 PetscCall(DMPlexRestoreTransitiveClosure_Hot_Private(dm, p, useCone, &tmpSize, &tmp, &tmpO)); 3853 if (numPoints) *numPoints = tmpSize + 1; 3854 if (points) *points = closure; 3855 PetscFunctionReturn(PETSC_SUCCESS); 3856 } 3857 3858 /* We need a special tensor version because we want to allow duplicate points in the endcaps for hybrid cells */ 3859 static PetscErrorCode DMPlexTransitiveClosure_Tensor_Internal(DM dm, PetscInt point, DMPolytopeType ct, PetscInt o, PetscBool useCone, PetscInt *numPoints, PetscInt **points) 3860 { 3861 const PetscInt *arr = DMPolytopeTypeGetArrangment(ct, o); 3862 const PetscInt *cone, *ornt; 3863 PetscInt *pts, *closure = NULL; 3864 DMPolytopeType ft; 3865 PetscInt maxConeSize, maxSupportSize, coneSeries, supportSeries, maxSize; 3866 PetscInt dim, coneSize, c, d, clSize, cl; 3867 3868 PetscFunctionBeginHot; 3869 PetscCall(DMGetDimension(dm, &dim)); 3870 PetscCall(DMPlexGetTransitiveClosure_Hot_Private(dm, point, PETSC_TRUE, &coneSize, &cone, &ornt)); 3871 PetscCall(DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize)); 3872 coneSeries = (maxConeSize > 1) ? ((PetscPowInt(maxConeSize, dim + 1) - 1) / (maxConeSize - 1)) : dim + 1; 3873 supportSeries = (maxSupportSize > 1) ? ((PetscPowInt(maxSupportSize, dim + 1) - 1) / (maxSupportSize - 1)) : dim + 1; 3874 maxSize = PetscMax(coneSeries, supportSeries); 3875 if (*points) { 3876 pts = *points; 3877 } else PetscCall(DMGetWorkArray(dm, 2 * maxSize, MPIU_INT, &pts)); 3878 c = 0; 3879 pts[c++] = point; 3880 pts[c++] = o; 3881 PetscCall(DMPlexGetCellType(dm, cone[arr[0 * 2 + 0]], &ft)); 3882 PetscCall(DMPlexGetTransitiveClosure_Internal(dm, cone[arr[0 * 2 + 0]], DMPolytopeTypeComposeOrientation(ft, arr[0 * 2 + 1], ornt[0]), useCone, &clSize, &closure)); 3883 for (cl = 0; cl < clSize * 2; cl += 2) { 3884 pts[c++] = closure[cl]; 3885 pts[c++] = closure[cl + 1]; 3886 } 3887 PetscCall(DMPlexGetTransitiveClosure_Internal(dm, cone[arr[1 * 2 + 0]], DMPolytopeTypeComposeOrientation(ft, arr[1 * 2 + 1], ornt[1]), useCone, &clSize, &closure)); 3888 for (cl = 0; cl < clSize * 2; cl += 2) { 3889 pts[c++] = closure[cl]; 3890 pts[c++] = closure[cl + 1]; 3891 } 3892 PetscCall(DMPlexRestoreTransitiveClosure(dm, cone[0], useCone, &clSize, &closure)); 3893 for (d = 2; d < coneSize; ++d) { 3894 PetscCall(DMPlexGetCellType(dm, cone[arr[d * 2 + 0]], &ft)); 3895 pts[c++] = cone[arr[d * 2 + 0]]; 3896 pts[c++] = DMPolytopeTypeComposeOrientation(ft, arr[d * 2 + 1], ornt[d]); 3897 } 3898 PetscCall(DMPlexRestoreTransitiveClosure_Hot_Private(dm, point, PETSC_TRUE, &coneSize, &cone, &ornt)); 3899 if (dim >= 3) { 3900 for (d = 2; d < coneSize; ++d) { 3901 const PetscInt fpoint = cone[arr[d * 2 + 0]]; 3902 const PetscInt *fcone, *fornt; 3903 PetscInt fconeSize, fc, i; 3904 3905 PetscCall(DMPlexGetCellType(dm, fpoint, &ft)); 3906 const PetscInt *farr = DMPolytopeTypeGetArrangment(ft, DMPolytopeTypeComposeOrientation(ft, arr[d * 2 + 1], ornt[d])); 3907 PetscCall(DMPlexGetTransitiveClosure_Hot_Private(dm, fpoint, PETSC_TRUE, &fconeSize, &fcone, &fornt)); 3908 for (fc = 0; fc < fconeSize; ++fc) { 3909 const PetscInt cp = fcone[farr[fc * 2 + 0]]; 3910 const PetscInt co = farr[fc * 2 + 1]; 3911 3912 for (i = 0; i < c; i += 2) 3913 if (pts[i] == cp) break; 3914 if (i == c) { 3915 PetscCall(DMPlexGetCellType(dm, cp, &ft)); 3916 pts[c++] = cp; 3917 pts[c++] = DMPolytopeTypeComposeOrientation(ft, co, fornt[farr[fc * 2 + 0]]); 3918 } 3919 } 3920 PetscCall(DMPlexRestoreTransitiveClosure_Hot_Private(dm, fpoint, PETSC_TRUE, &fconeSize, &fcone, &fornt)); 3921 } 3922 } 3923 *numPoints = c / 2; 3924 *points = pts; 3925 PetscFunctionReturn(PETSC_SUCCESS); 3926 } 3927 3928 PetscErrorCode DMPlexGetTransitiveClosure_Internal(DM dm, PetscInt p, PetscInt ornt, PetscBool useCone, PetscInt *numPoints, PetscInt *points[]) 3929 { 3930 DMPolytopeType ct; 3931 PetscInt *closure, *fifo; 3932 PetscInt closureSize = 0, fifoStart = 0, fifoSize = 0; 3933 PetscInt maxConeSize, maxSupportSize, coneSeries, supportSeries; 3934 PetscInt depth, maxSize; 3935 3936 PetscFunctionBeginHot; 3937 PetscCall(DMPlexGetDepth(dm, &depth)); 3938 if (depth == 1) { 3939 PetscCall(DMPlexGetTransitiveClosure_Depth1_Private(dm, p, ornt, useCone, numPoints, points)); 3940 PetscFunctionReturn(PETSC_SUCCESS); 3941 } 3942 PetscCall(DMPlexGetCellType(dm, p, &ct)); 3943 if (ct == DM_POLYTOPE_FV_GHOST || ct == DM_POLYTOPE_INTERIOR_GHOST || ct == DM_POLYTOPE_UNKNOWN) ct = DM_POLYTOPE_UNKNOWN; 3944 if (ct == DM_POLYTOPE_SEG_PRISM_TENSOR || ct == DM_POLYTOPE_TRI_PRISM_TENSOR || ct == DM_POLYTOPE_QUAD_PRISM_TENSOR) { 3945 PetscCall(DMPlexTransitiveClosure_Tensor_Internal(dm, p, ct, ornt, useCone, numPoints, points)); 3946 PetscFunctionReturn(PETSC_SUCCESS); 3947 } 3948 PetscCall(DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize)); 3949 coneSeries = (maxConeSize > 1) ? ((PetscPowInt(maxConeSize, depth + 1) - 1) / (maxConeSize - 1)) : depth + 1; 3950 supportSeries = (maxSupportSize > 1) ? ((PetscPowInt(maxSupportSize, depth + 1) - 1) / (maxSupportSize - 1)) : depth + 1; 3951 maxSize = PetscMax(coneSeries, supportSeries); 3952 PetscCall(DMGetWorkArray(dm, 3 * maxSize, MPIU_INT, &fifo)); 3953 if (*points) { 3954 closure = *points; 3955 } else PetscCall(DMGetWorkArray(dm, 2 * maxSize, MPIU_INT, &closure)); 3956 closure[closureSize++] = p; 3957 closure[closureSize++] = ornt; 3958 fifo[fifoSize++] = p; 3959 fifo[fifoSize++] = ornt; 3960 fifo[fifoSize++] = ct; 3961 /* Should kick out early when depth is reached, rather than checking all vertices for empty cones */ 3962 while (fifoSize - fifoStart) { 3963 const PetscInt q = fifo[fifoStart++]; 3964 const PetscInt o = fifo[fifoStart++]; 3965 const DMPolytopeType qt = (DMPolytopeType)fifo[fifoStart++]; 3966 const PetscInt *qarr = DMPolytopeTypeGetArrangment(qt, o); 3967 const PetscInt *tmp, *tmpO = NULL; 3968 PetscInt tmpSize, t; 3969 3970 if (PetscDefined(USE_DEBUG)) { 3971 PetscInt nO = DMPolytopeTypeGetNumArrangments(qt) / 2; 3972 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); 3973 } 3974 PetscCall(DMPlexGetTransitiveClosure_Hot_Private(dm, q, useCone, &tmpSize, &tmp, &tmpO)); 3975 for (t = 0; t < tmpSize; ++t) { 3976 const PetscInt ip = useCone && qarr ? qarr[t * 2] : t; 3977 const PetscInt io = useCone && qarr ? qarr[t * 2 + 1] : 0; 3978 const PetscInt cp = tmp[ip]; 3979 PetscCall(DMPlexGetCellType(dm, cp, &ct)); 3980 const PetscInt co = tmpO ? DMPolytopeTypeComposeOrientation(ct, io, tmpO[ip]) : 0; 3981 PetscInt c; 3982 3983 /* Check for duplicate */ 3984 for (c = 0; c < closureSize; c += 2) { 3985 if (closure[c] == cp) break; 3986 } 3987 if (c == closureSize) { 3988 closure[closureSize++] = cp; 3989 closure[closureSize++] = co; 3990 fifo[fifoSize++] = cp; 3991 fifo[fifoSize++] = co; 3992 fifo[fifoSize++] = ct; 3993 } 3994 } 3995 PetscCall(DMPlexRestoreTransitiveClosure_Hot_Private(dm, q, useCone, &tmpSize, &tmp, &tmpO)); 3996 } 3997 PetscCall(DMRestoreWorkArray(dm, 3 * maxSize, MPIU_INT, &fifo)); 3998 if (numPoints) *numPoints = closureSize / 2; 3999 if (points) *points = closure; 4000 PetscFunctionReturn(PETSC_SUCCESS); 4001 } 4002 4003 /*@C 4004 DMPlexGetTransitiveClosure - Return the points on the transitive closure of the in-edges or out-edges for this point in the DAG 4005 4006 Not Collective 4007 4008 Input Parameters: 4009 + dm - The `DMPLEX` 4010 . p - The mesh point 4011 - useCone - `PETSC_TRUE` for the closure, otherwise return the star 4012 4013 Input/Output Parameter: 4014 . points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...]; 4015 if `NULL` on input, internal storage will be returned, otherwise the provided array is used 4016 4017 Output Parameter: 4018 . numPoints - The number of points in the closure, so points[] is of size 2*`numPoints` 4019 4020 Level: beginner 4021 4022 Note: 4023 If using internal storage (points is `NULL` on input), each call overwrites the last output. 4024 4025 Fortran Notes: 4026 The `numPoints` argument is not present in the Fortran binding since it is internal to the array. 4027 4028 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexRestoreTransitiveClosure()`, `DMPlexCreate()`, `DMPlexSetCone()`, `DMPlexSetChart()`, `DMPlexGetCone()` 4029 @*/ 4030 PetscErrorCode DMPlexGetTransitiveClosure(DM dm, PetscInt p, PetscBool useCone, PetscInt *numPoints, PetscInt *points[]) 4031 { 4032 PetscFunctionBeginHot; 4033 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4034 if (numPoints) PetscAssertPointer(numPoints, 4); 4035 if (points) PetscAssertPointer(points, 5); 4036 PetscCall(DMPlexGetTransitiveClosure_Internal(dm, p, 0, useCone, numPoints, points)); 4037 PetscFunctionReturn(PETSC_SUCCESS); 4038 } 4039 4040 /*@C 4041 DMPlexRestoreTransitiveClosure - Restore the array of points on the transitive closure of the in-edges or out-edges for this point in the DAG 4042 4043 Not Collective 4044 4045 Input Parameters: 4046 + dm - The `DMPLEX` 4047 . p - The mesh point 4048 . useCone - `PETSC_TRUE` for the closure, otherwise return the star 4049 . numPoints - The number of points in the closure, so points[] is of size 2*`numPoints` 4050 - points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...] 4051 4052 Level: beginner 4053 4054 Note: 4055 If not using internal storage (points is not `NULL` on input), this call is unnecessary 4056 4057 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetTransitiveClosure()`, `DMPlexCreate()`, `DMPlexSetCone()`, `DMPlexSetChart()`, `DMPlexGetCone()` 4058 @*/ 4059 PetscErrorCode DMPlexRestoreTransitiveClosure(DM dm, PetscInt p, PetscBool useCone, PetscInt *numPoints, PetscInt *points[]) 4060 { 4061 PetscFunctionBeginHot; 4062 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4063 if (numPoints) *numPoints = 0; 4064 PetscCall(DMRestoreWorkArray(dm, 0, MPIU_INT, points)); 4065 PetscFunctionReturn(PETSC_SUCCESS); 4066 } 4067 4068 /*@ 4069 DMPlexGetMaxSizes - Return the maximum number of in-edges (cone) and out-edges (support) for any point in the DAG 4070 4071 Not Collective 4072 4073 Input Parameter: 4074 . dm - The `DMPLEX` 4075 4076 Output Parameters: 4077 + maxConeSize - The maximum number of in-edges 4078 - maxSupportSize - The maximum number of out-edges 4079 4080 Level: beginner 4081 4082 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexSetConeSize()`, `DMPlexSetChart()` 4083 @*/ 4084 PetscErrorCode DMPlexGetMaxSizes(DM dm, PetscInt *maxConeSize, PetscInt *maxSupportSize) 4085 { 4086 DM_Plex *mesh = (DM_Plex *)dm->data; 4087 4088 PetscFunctionBegin; 4089 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4090 if (maxConeSize) PetscCall(PetscSectionGetMaxDof(mesh->coneSection, maxConeSize)); 4091 if (maxSupportSize) PetscCall(PetscSectionGetMaxDof(mesh->supportSection, maxSupportSize)); 4092 PetscFunctionReturn(PETSC_SUCCESS); 4093 } 4094 4095 PetscErrorCode DMSetUp_Plex(DM dm) 4096 { 4097 DM_Plex *mesh = (DM_Plex *)dm->data; 4098 PetscInt size, maxSupportSize; 4099 4100 PetscFunctionBegin; 4101 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4102 PetscCall(PetscSectionSetUp(mesh->coneSection)); 4103 PetscCall(PetscSectionGetStorageSize(mesh->coneSection, &size)); 4104 PetscCall(PetscMalloc1(size, &mesh->cones)); 4105 PetscCall(PetscCalloc1(size, &mesh->coneOrientations)); 4106 PetscCall(PetscSectionGetMaxDof(mesh->supportSection, &maxSupportSize)); 4107 if (maxSupportSize) { 4108 PetscCall(PetscSectionSetUp(mesh->supportSection)); 4109 PetscCall(PetscSectionGetStorageSize(mesh->supportSection, &size)); 4110 PetscCall(PetscMalloc1(size, &mesh->supports)); 4111 } 4112 PetscFunctionReturn(PETSC_SUCCESS); 4113 } 4114 4115 PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm) 4116 { 4117 PetscFunctionBegin; 4118 if (subdm) PetscCall(DMClone(dm, subdm)); 4119 PetscCall(DMCreateSectionSubDM(dm, numFields, fields, is, subdm)); 4120 if (subdm) (*subdm)->useNatural = dm->useNatural; 4121 if (dm->useNatural && dm->sfMigration) { 4122 PetscSF sfNatural; 4123 4124 (*subdm)->sfMigration = dm->sfMigration; 4125 PetscCall(PetscObjectReference((PetscObject)dm->sfMigration)); 4126 PetscCall(DMPlexCreateGlobalToNaturalSF(*subdm, NULL, (*subdm)->sfMigration, &sfNatural)); 4127 (*subdm)->sfNatural = sfNatural; 4128 } 4129 PetscFunctionReturn(PETSC_SUCCESS); 4130 } 4131 4132 PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm) 4133 { 4134 PetscInt i = 0; 4135 4136 PetscFunctionBegin; 4137 PetscCall(DMClone(dms[0], superdm)); 4138 PetscCall(DMCreateSectionSuperDM(dms, len, is, superdm)); 4139 (*superdm)->useNatural = PETSC_FALSE; 4140 for (i = 0; i < len; i++) { 4141 if (dms[i]->useNatural && dms[i]->sfMigration) { 4142 PetscSF sfNatural; 4143 4144 (*superdm)->sfMigration = dms[i]->sfMigration; 4145 PetscCall(PetscObjectReference((PetscObject)dms[i]->sfMigration)); 4146 (*superdm)->useNatural = PETSC_TRUE; 4147 PetscCall(DMPlexCreateGlobalToNaturalSF(*superdm, NULL, (*superdm)->sfMigration, &sfNatural)); 4148 (*superdm)->sfNatural = sfNatural; 4149 break; 4150 } 4151 } 4152 PetscFunctionReturn(PETSC_SUCCESS); 4153 } 4154 4155 /*@ 4156 DMPlexSymmetrize - Create support (out-edge) information from cone (in-edge) information 4157 4158 Not Collective 4159 4160 Input Parameter: 4161 . dm - The `DMPLEX` 4162 4163 Level: beginner 4164 4165 Note: 4166 This should be called after all calls to `DMPlexSetCone()` 4167 4168 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexSetChart()`, `DMPlexSetConeSize()`, `DMPlexSetCone()` 4169 @*/ 4170 PetscErrorCode DMPlexSymmetrize(DM dm) 4171 { 4172 DM_Plex *mesh = (DM_Plex *)dm->data; 4173 PetscInt *offsets; 4174 PetscInt supportSize; 4175 PetscInt pStart, pEnd, p; 4176 4177 PetscFunctionBegin; 4178 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4179 PetscCheck(!mesh->supports, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE, "Supports were already setup in this DMPlex"); 4180 PetscCall(PetscLogEventBegin(DMPLEX_Symmetrize, dm, 0, 0, 0)); 4181 /* Calculate support sizes */ 4182 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 4183 for (p = pStart; p < pEnd; ++p) { 4184 PetscInt dof, off, c; 4185 4186 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 4187 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 4188 for (c = off; c < off + dof; ++c) PetscCall(PetscSectionAddDof(mesh->supportSection, mesh->cones[c], 1)); 4189 } 4190 PetscCall(PetscSectionSetUp(mesh->supportSection)); 4191 /* Calculate supports */ 4192 PetscCall(PetscSectionGetStorageSize(mesh->supportSection, &supportSize)); 4193 PetscCall(PetscMalloc1(supportSize, &mesh->supports)); 4194 PetscCall(PetscCalloc1(pEnd - pStart, &offsets)); 4195 for (p = pStart; p < pEnd; ++p) { 4196 PetscInt dof, off, c; 4197 4198 PetscCall(PetscSectionGetDof(mesh->coneSection, p, &dof)); 4199 PetscCall(PetscSectionGetOffset(mesh->coneSection, p, &off)); 4200 for (c = off; c < off + dof; ++c) { 4201 const PetscInt q = mesh->cones[c]; 4202 PetscInt offS; 4203 4204 PetscCall(PetscSectionGetOffset(mesh->supportSection, q, &offS)); 4205 4206 mesh->supports[offS + offsets[q]] = p; 4207 ++offsets[q]; 4208 } 4209 } 4210 PetscCall(PetscFree(offsets)); 4211 PetscCall(PetscLogEventEnd(DMPLEX_Symmetrize, dm, 0, 0, 0)); 4212 PetscFunctionReturn(PETSC_SUCCESS); 4213 } 4214 4215 static PetscErrorCode DMPlexCreateDepthStratum(DM dm, DMLabel label, PetscInt depth, PetscInt pStart, PetscInt pEnd) 4216 { 4217 IS stratumIS; 4218 4219 PetscFunctionBegin; 4220 if (pStart >= pEnd) PetscFunctionReturn(PETSC_SUCCESS); 4221 if (PetscDefined(USE_DEBUG)) { 4222 PetscInt qStart, qEnd, numLevels, level; 4223 PetscBool overlap = PETSC_FALSE; 4224 PetscCall(DMLabelGetNumValues(label, &numLevels)); 4225 for (level = 0; level < numLevels; level++) { 4226 PetscCall(DMLabelGetStratumBounds(label, level, &qStart, &qEnd)); 4227 if ((pStart >= qStart && pStart < qEnd) || (pEnd > qStart && pEnd <= qEnd)) { 4228 overlap = PETSC_TRUE; 4229 break; 4230 } 4231 } 4232 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); 4233 } 4234 PetscCall(ISCreateStride(PETSC_COMM_SELF, pEnd - pStart, pStart, 1, &stratumIS)); 4235 PetscCall(DMLabelSetStratumIS(label, depth, stratumIS)); 4236 PetscCall(ISDestroy(&stratumIS)); 4237 PetscFunctionReturn(PETSC_SUCCESS); 4238 } 4239 4240 /*@ 4241 DMPlexStratify - Computes the strata for all points in the `DMPLEX` 4242 4243 Collective 4244 4245 Input Parameter: 4246 . dm - The `DMPLEX` 4247 4248 Level: beginner 4249 4250 Notes: 4251 The strata group all points of the same grade, and this function calculates the strata. This 4252 grade can be seen as the height (or depth) of the point in the DAG. 4253 4254 The DAG for most topologies is a graded poset (https://en.wikipedia.org/wiki/Graded_poset), and 4255 can be illustrated by a Hasse Diagram (https://en.wikipedia.org/wiki/Hasse_diagram). 4256 Concretely, `DMPlexStratify()` creates a new label named "depth" containing the depth in the DAG of each point. For cell-vertex 4257 meshes, vertices are depth 0 and cells are depth 1. For fully interpolated meshes, depth 0 for vertices, 1 for edges, and so on 4258 until cells have depth equal to the dimension of the mesh. The depth label can be accessed through `DMPlexGetDepthLabel()` or `DMPlexGetDepthStratum()`, or 4259 manually via `DMGetLabel()`. The height is defined implicitly by height = maxDimension - depth, and can be accessed 4260 via `DMPlexGetHeightStratum()`. For example, cells have height 0 and faces have height 1. 4261 4262 The depth of a point is calculated by executing a breadth-first search (BFS) on the DAG. This could produce surprising results 4263 if run on a partially interpolated mesh, meaning one that had some edges and faces, but not others. For example, suppose that 4264 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 4265 to interpolate only that one (e0), so that 4266 .vb 4267 cone(c0) = {e0, v2} 4268 cone(e0) = {v0, v1} 4269 .ve 4270 If `DMPlexStratify()` is run on this mesh, it will give depths 4271 .vb 4272 depth 0 = {v0, v1, v2} 4273 depth 1 = {e0, c0} 4274 .ve 4275 where the triangle has been given depth 1, instead of 2, because it is reachable from vertex v2. 4276 4277 `DMPlexStratify()` should be called after all calls to `DMPlexSymmetrize()` 4278 4279 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexSymmetrize()`, `DMPlexComputeCellTypes()` 4280 @*/ 4281 PetscErrorCode DMPlexStratify(DM dm) 4282 { 4283 DM_Plex *mesh = (DM_Plex *)dm->data; 4284 DMLabel label; 4285 PetscInt pStart, pEnd, p; 4286 PetscInt numRoots = 0, numLeaves = 0; 4287 4288 PetscFunctionBegin; 4289 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4290 PetscCall(PetscLogEventBegin(DMPLEX_Stratify, dm, 0, 0, 0)); 4291 4292 /* Create depth label */ 4293 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 4294 PetscCall(DMCreateLabel(dm, "depth")); 4295 PetscCall(DMPlexGetDepthLabel(dm, &label)); 4296 4297 { 4298 /* Initialize roots and count leaves */ 4299 PetscInt sMin = PETSC_MAX_INT; 4300 PetscInt sMax = PETSC_MIN_INT; 4301 PetscInt coneSize, supportSize; 4302 4303 for (p = pStart; p < pEnd; ++p) { 4304 PetscCall(DMPlexGetConeSize(dm, p, &coneSize)); 4305 PetscCall(DMPlexGetSupportSize(dm, p, &supportSize)); 4306 if (!coneSize && supportSize) { 4307 sMin = PetscMin(p, sMin); 4308 sMax = PetscMax(p, sMax); 4309 ++numRoots; 4310 } else if (!supportSize && coneSize) { 4311 ++numLeaves; 4312 } else if (!supportSize && !coneSize) { 4313 /* Isolated points */ 4314 sMin = PetscMin(p, sMin); 4315 sMax = PetscMax(p, sMax); 4316 } 4317 } 4318 PetscCall(DMPlexCreateDepthStratum(dm, label, 0, sMin, sMax + 1)); 4319 } 4320 4321 if (numRoots + numLeaves == (pEnd - pStart)) { 4322 PetscInt sMin = PETSC_MAX_INT; 4323 PetscInt sMax = PETSC_MIN_INT; 4324 PetscInt coneSize, supportSize; 4325 4326 for (p = pStart; p < pEnd; ++p) { 4327 PetscCall(DMPlexGetConeSize(dm, p, &coneSize)); 4328 PetscCall(DMPlexGetSupportSize(dm, p, &supportSize)); 4329 if (!supportSize && coneSize) { 4330 sMin = PetscMin(p, sMin); 4331 sMax = PetscMax(p, sMax); 4332 } 4333 } 4334 PetscCall(DMPlexCreateDepthStratum(dm, label, 1, sMin, sMax + 1)); 4335 } else { 4336 PetscInt level = 0; 4337 PetscInt qStart, qEnd, q; 4338 4339 PetscCall(DMLabelGetStratumBounds(label, level, &qStart, &qEnd)); 4340 while (qEnd > qStart) { 4341 PetscInt sMin = PETSC_MAX_INT; 4342 PetscInt sMax = PETSC_MIN_INT; 4343 4344 for (q = qStart; q < qEnd; ++q) { 4345 const PetscInt *support; 4346 PetscInt supportSize, s; 4347 4348 PetscCall(DMPlexGetSupportSize(dm, q, &supportSize)); 4349 PetscCall(DMPlexGetSupport(dm, q, &support)); 4350 for (s = 0; s < supportSize; ++s) { 4351 sMin = PetscMin(support[s], sMin); 4352 sMax = PetscMax(support[s], sMax); 4353 } 4354 } 4355 PetscCall(DMLabelGetNumValues(label, &level)); 4356 PetscCall(DMPlexCreateDepthStratum(dm, label, level, sMin, sMax + 1)); 4357 PetscCall(DMLabelGetStratumBounds(label, level, &qStart, &qEnd)); 4358 } 4359 } 4360 { /* just in case there is an empty process */ 4361 PetscInt numValues, maxValues = 0, v; 4362 4363 PetscCall(DMLabelGetNumValues(label, &numValues)); 4364 PetscCall(MPIU_Allreduce(&numValues, &maxValues, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm))); 4365 for (v = numValues; v < maxValues; v++) PetscCall(DMLabelAddStratum(label, v)); 4366 } 4367 PetscCall(PetscObjectStateGet((PetscObject)label, &mesh->depthState)); 4368 PetscCall(PetscLogEventEnd(DMPLEX_Stratify, dm, 0, 0, 0)); 4369 PetscFunctionReturn(PETSC_SUCCESS); 4370 } 4371 4372 PetscErrorCode DMPlexComputeCellType_Internal(DM dm, PetscInt p, PetscInt pdepth, DMPolytopeType *pt) 4373 { 4374 DMPolytopeType ct = DM_POLYTOPE_UNKNOWN; 4375 PetscInt dim, depth, pheight, coneSize; 4376 4377 PetscFunctionBeginHot; 4378 PetscCall(DMGetDimension(dm, &dim)); 4379 PetscCall(DMPlexGetDepth(dm, &depth)); 4380 PetscCall(DMPlexGetConeSize(dm, p, &coneSize)); 4381 pheight = depth - pdepth; 4382 if (depth <= 1) { 4383 switch (pdepth) { 4384 case 0: 4385 ct = DM_POLYTOPE_POINT; 4386 break; 4387 case 1: 4388 switch (coneSize) { 4389 case 2: 4390 ct = DM_POLYTOPE_SEGMENT; 4391 break; 4392 case 3: 4393 ct = DM_POLYTOPE_TRIANGLE; 4394 break; 4395 case 4: 4396 switch (dim) { 4397 case 2: 4398 ct = DM_POLYTOPE_QUADRILATERAL; 4399 break; 4400 case 3: 4401 ct = DM_POLYTOPE_TETRAHEDRON; 4402 break; 4403 default: 4404 break; 4405 } 4406 break; 4407 case 5: 4408 ct = DM_POLYTOPE_PYRAMID; 4409 break; 4410 case 6: 4411 ct = DM_POLYTOPE_TRI_PRISM_TENSOR; 4412 break; 4413 case 8: 4414 ct = DM_POLYTOPE_HEXAHEDRON; 4415 break; 4416 default: 4417 break; 4418 } 4419 } 4420 } else { 4421 if (pdepth == 0) { 4422 ct = DM_POLYTOPE_POINT; 4423 } else if (pheight == 0) { 4424 switch (dim) { 4425 case 1: 4426 switch (coneSize) { 4427 case 2: 4428 ct = DM_POLYTOPE_SEGMENT; 4429 break; 4430 default: 4431 break; 4432 } 4433 break; 4434 case 2: 4435 switch (coneSize) { 4436 case 3: 4437 ct = DM_POLYTOPE_TRIANGLE; 4438 break; 4439 case 4: 4440 ct = DM_POLYTOPE_QUADRILATERAL; 4441 break; 4442 default: 4443 break; 4444 } 4445 break; 4446 case 3: 4447 switch (coneSize) { 4448 case 4: 4449 ct = DM_POLYTOPE_TETRAHEDRON; 4450 break; 4451 case 5: { 4452 const PetscInt *cone; 4453 PetscInt faceConeSize; 4454 4455 PetscCall(DMPlexGetCone(dm, p, &cone)); 4456 PetscCall(DMPlexGetConeSize(dm, cone[0], &faceConeSize)); 4457 switch (faceConeSize) { 4458 case 3: 4459 ct = DM_POLYTOPE_TRI_PRISM_TENSOR; 4460 break; 4461 case 4: 4462 ct = DM_POLYTOPE_PYRAMID; 4463 break; 4464 } 4465 } break; 4466 case 6: 4467 ct = DM_POLYTOPE_HEXAHEDRON; 4468 break; 4469 default: 4470 break; 4471 } 4472 break; 4473 default: 4474 break; 4475 } 4476 } else if (pheight > 0) { 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 ct = DM_POLYTOPE_QUADRILATERAL; 4486 break; 4487 default: 4488 break; 4489 } 4490 } 4491 } 4492 *pt = ct; 4493 PetscFunctionReturn(PETSC_SUCCESS); 4494 } 4495 4496 /*@ 4497 DMPlexComputeCellTypes - Infer the polytope type of every cell using its dimension and cone size. 4498 4499 Collective 4500 4501 Input Parameter: 4502 . dm - The `DMPLEX` 4503 4504 Level: developer 4505 4506 Note: 4507 This function is normally called automatically when a cell type is requested. It creates an 4508 internal `DMLabel` named "celltype" which can be directly accessed using `DMGetLabel()`. A user may disable 4509 automatic creation by creating the label manually, using `DMCreateLabel`(dm, "celltype"). 4510 4511 `DMPlexComputeCellTypes()` should be called after all calls to `DMPlexSymmetrize()` and `DMPlexStratify()` 4512 4513 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreate()`, `DMPlexSymmetrize()`, `DMPlexStratify()`, `DMGetLabel()`, `DMCreateLabel()` 4514 @*/ 4515 PetscErrorCode DMPlexComputeCellTypes(DM dm) 4516 { 4517 DM_Plex *mesh; 4518 DMLabel ctLabel; 4519 PetscInt pStart, pEnd, p; 4520 4521 PetscFunctionBegin; 4522 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4523 mesh = (DM_Plex *)dm->data; 4524 PetscCall(DMCreateLabel(dm, "celltype")); 4525 PetscCall(DMPlexGetCellTypeLabel(dm, &ctLabel)); 4526 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 4527 PetscCall(PetscFree(mesh->cellTypes)); 4528 PetscCall(PetscMalloc1(pEnd - pStart, &mesh->cellTypes)); 4529 for (p = pStart; p < pEnd; ++p) { 4530 DMPolytopeType ct = DM_POLYTOPE_UNKNOWN; 4531 PetscInt pdepth; 4532 4533 PetscCall(DMPlexGetPointDepth(dm, p, &pdepth)); 4534 PetscCall(DMPlexComputeCellType_Internal(dm, p, pdepth, &ct)); 4535 PetscCheck(ct != DM_POLYTOPE_UNKNOWN, PETSC_COMM_SELF, PETSC_ERR_SUP, "Point %" PetscInt_FMT " is screwed up", p); 4536 PetscCall(DMLabelSetValue(ctLabel, p, ct)); 4537 mesh->cellTypes[p - pStart].value_as_uint8 = ct; 4538 } 4539 PetscCall(PetscObjectStateGet((PetscObject)ctLabel, &mesh->celltypeState)); 4540 PetscCall(PetscObjectViewFromOptions((PetscObject)ctLabel, NULL, "-dm_plex_celltypes_view")); 4541 PetscFunctionReturn(PETSC_SUCCESS); 4542 } 4543 4544 /*@C 4545 DMPlexGetJoin - Get an array for the join of the set of points 4546 4547 Not Collective 4548 4549 Input Parameters: 4550 + dm - The `DMPLEX` object 4551 . numPoints - The number of input points for the join 4552 - points - The input points 4553 4554 Output Parameters: 4555 + numCoveredPoints - The number of points in the join 4556 - coveredPoints - The points in the join 4557 4558 Level: intermediate 4559 4560 Note: 4561 Currently, this is restricted to a single level join 4562 4563 Fortran Notes: 4564 The `numCoveredPoints` argument is not present in the Fortran binding since it is internal to the array. 4565 4566 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexRestoreJoin()`, `DMPlexGetMeet()` 4567 @*/ 4568 PetscErrorCode DMPlexGetJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 4569 { 4570 DM_Plex *mesh = (DM_Plex *)dm->data; 4571 PetscInt *join[2]; 4572 PetscInt joinSize, i = 0; 4573 PetscInt dof, off, p, c, m; 4574 PetscInt maxSupportSize; 4575 4576 PetscFunctionBegin; 4577 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4578 PetscAssertPointer(points, 3); 4579 PetscAssertPointer(numCoveredPoints, 4); 4580 PetscAssertPointer(coveredPoints, 5); 4581 PetscCall(PetscSectionGetMaxDof(mesh->supportSection, &maxSupportSize)); 4582 PetscCall(DMGetWorkArray(dm, maxSupportSize, MPIU_INT, &join[0])); 4583 PetscCall(DMGetWorkArray(dm, maxSupportSize, MPIU_INT, &join[1])); 4584 /* Copy in support of first point */ 4585 PetscCall(PetscSectionGetDof(mesh->supportSection, points[0], &dof)); 4586 PetscCall(PetscSectionGetOffset(mesh->supportSection, points[0], &off)); 4587 for (joinSize = 0; joinSize < dof; ++joinSize) join[i][joinSize] = mesh->supports[off + joinSize]; 4588 /* Check each successive support */ 4589 for (p = 1; p < numPoints; ++p) { 4590 PetscInt newJoinSize = 0; 4591 4592 PetscCall(PetscSectionGetDof(mesh->supportSection, points[p], &dof)); 4593 PetscCall(PetscSectionGetOffset(mesh->supportSection, points[p], &off)); 4594 for (c = 0; c < dof; ++c) { 4595 const PetscInt point = mesh->supports[off + c]; 4596 4597 for (m = 0; m < joinSize; ++m) { 4598 if (point == join[i][m]) { 4599 join[1 - i][newJoinSize++] = point; 4600 break; 4601 } 4602 } 4603 } 4604 joinSize = newJoinSize; 4605 i = 1 - i; 4606 } 4607 *numCoveredPoints = joinSize; 4608 *coveredPoints = join[i]; 4609 PetscCall(DMRestoreWorkArray(dm, maxSupportSize, MPIU_INT, &join[1 - i])); 4610 PetscFunctionReturn(PETSC_SUCCESS); 4611 } 4612 4613 /*@C 4614 DMPlexRestoreJoin - Restore an array for the join of the set of points 4615 4616 Not Collective 4617 4618 Input Parameters: 4619 + dm - The `DMPLEX` object 4620 . numPoints - The number of input points for the join 4621 - points - The input points 4622 4623 Output Parameters: 4624 + numCoveredPoints - The number of points in the join 4625 - coveredPoints - The points in the join 4626 4627 Level: intermediate 4628 4629 Fortran Notes: 4630 The `numCoveredPoints` argument is not present in the Fortran binding since it is internal to the array. 4631 4632 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetJoin()`, `DMPlexGetFullJoin()`, `DMPlexGetMeet()` 4633 @*/ 4634 PetscErrorCode DMPlexRestoreJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 4635 { 4636 PetscFunctionBegin; 4637 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4638 if (points) PetscAssertPointer(points, 3); 4639 if (numCoveredPoints) PetscAssertPointer(numCoveredPoints, 4); 4640 PetscAssertPointer(coveredPoints, 5); 4641 PetscCall(DMRestoreWorkArray(dm, 0, MPIU_INT, (void *)coveredPoints)); 4642 if (numCoveredPoints) *numCoveredPoints = 0; 4643 PetscFunctionReturn(PETSC_SUCCESS); 4644 } 4645 4646 /*@C 4647 DMPlexGetFullJoin - Get an array for the join of the set of points 4648 4649 Not Collective 4650 4651 Input Parameters: 4652 + dm - The `DMPLEX` object 4653 . numPoints - The number of input points for the join 4654 - points - The input points 4655 4656 Output Parameters: 4657 + numCoveredPoints - The number of points in the join 4658 - coveredPoints - The points in the join 4659 4660 Level: intermediate 4661 4662 Fortran Notes: 4663 The `numCoveredPoints` argument is not present in the Fortran binding since it is internal to the array. 4664 4665 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetJoin()`, `DMPlexRestoreJoin()`, `DMPlexGetMeet()` 4666 @*/ 4667 PetscErrorCode DMPlexGetFullJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 4668 { 4669 PetscInt *offsets, **closures; 4670 PetscInt *join[2]; 4671 PetscInt depth = 0, maxSize, joinSize = 0, i = 0; 4672 PetscInt p, d, c, m, ms; 4673 4674 PetscFunctionBegin; 4675 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4676 PetscAssertPointer(points, 3); 4677 PetscAssertPointer(numCoveredPoints, 4); 4678 PetscAssertPointer(coveredPoints, 5); 4679 4680 PetscCall(DMPlexGetDepth(dm, &depth)); 4681 PetscCall(PetscCalloc1(numPoints, &closures)); 4682 PetscCall(DMGetWorkArray(dm, numPoints * (depth + 2), MPIU_INT, &offsets)); 4683 PetscCall(DMPlexGetMaxSizes(dm, NULL, &ms)); 4684 maxSize = (ms > 1) ? ((PetscPowInt(ms, depth + 1) - 1) / (ms - 1)) : depth + 1; 4685 PetscCall(DMGetWorkArray(dm, maxSize, MPIU_INT, &join[0])); 4686 PetscCall(DMGetWorkArray(dm, maxSize, MPIU_INT, &join[1])); 4687 4688 for (p = 0; p < numPoints; ++p) { 4689 PetscInt closureSize; 4690 4691 PetscCall(DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &closureSize, &closures[p])); 4692 4693 offsets[p * (depth + 2) + 0] = 0; 4694 for (d = 0; d < depth + 1; ++d) { 4695 PetscInt pStart, pEnd, i; 4696 4697 PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd)); 4698 for (i = offsets[p * (depth + 2) + d]; i < closureSize; ++i) { 4699 if ((pStart > closures[p][i * 2]) || (pEnd <= closures[p][i * 2])) { 4700 offsets[p * (depth + 2) + d + 1] = i; 4701 break; 4702 } 4703 } 4704 if (i == closureSize) offsets[p * (depth + 2) + d + 1] = i; 4705 } 4706 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); 4707 } 4708 for (d = 0; d < depth + 1; ++d) { 4709 PetscInt dof; 4710 4711 /* Copy in support of first point */ 4712 dof = offsets[d + 1] - offsets[d]; 4713 for (joinSize = 0; joinSize < dof; ++joinSize) join[i][joinSize] = closures[0][(offsets[d] + joinSize) * 2]; 4714 /* Check each successive cone */ 4715 for (p = 1; p < numPoints && joinSize; ++p) { 4716 PetscInt newJoinSize = 0; 4717 4718 dof = offsets[p * (depth + 2) + d + 1] - offsets[p * (depth + 2) + d]; 4719 for (c = 0; c < dof; ++c) { 4720 const PetscInt point = closures[p][(offsets[p * (depth + 2) + d] + c) * 2]; 4721 4722 for (m = 0; m < joinSize; ++m) { 4723 if (point == join[i][m]) { 4724 join[1 - i][newJoinSize++] = point; 4725 break; 4726 } 4727 } 4728 } 4729 joinSize = newJoinSize; 4730 i = 1 - i; 4731 } 4732 if (joinSize) break; 4733 } 4734 *numCoveredPoints = joinSize; 4735 *coveredPoints = join[i]; 4736 for (p = 0; p < numPoints; ++p) PetscCall(DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, NULL, &closures[p])); 4737 PetscCall(PetscFree(closures)); 4738 PetscCall(DMRestoreWorkArray(dm, numPoints * (depth + 2), MPIU_INT, &offsets)); 4739 PetscCall(DMRestoreWorkArray(dm, ms, MPIU_INT, &join[1 - i])); 4740 PetscFunctionReturn(PETSC_SUCCESS); 4741 } 4742 4743 /*@C 4744 DMPlexGetMeet - Get an array for the meet of the set of points 4745 4746 Not Collective 4747 4748 Input Parameters: 4749 + dm - The `DMPLEX` object 4750 . numPoints - The number of input points for the meet 4751 - points - The input points 4752 4753 Output Parameters: 4754 + numCoveringPoints - The number of points in the meet 4755 - coveringPoints - The points in the meet 4756 4757 Level: intermediate 4758 4759 Note: 4760 Currently, this is restricted to a single level meet 4761 4762 Fortran Notes: 4763 The `numCoveredPoints` argument is not present in the Fortran binding since it is internal to the array. 4764 4765 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexRestoreMeet()`, `DMPlexGetJoin()` 4766 @*/ 4767 PetscErrorCode DMPlexGetMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveringPoints, const PetscInt **coveringPoints) 4768 { 4769 DM_Plex *mesh = (DM_Plex *)dm->data; 4770 PetscInt *meet[2]; 4771 PetscInt meetSize, i = 0; 4772 PetscInt dof, off, p, c, m; 4773 PetscInt maxConeSize; 4774 4775 PetscFunctionBegin; 4776 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4777 PetscAssertPointer(points, 3); 4778 PetscAssertPointer(numCoveringPoints, 4); 4779 PetscAssertPointer(coveringPoints, 5); 4780 PetscCall(PetscSectionGetMaxDof(mesh->coneSection, &maxConeSize)); 4781 PetscCall(DMGetWorkArray(dm, maxConeSize, MPIU_INT, &meet[0])); 4782 PetscCall(DMGetWorkArray(dm, maxConeSize, MPIU_INT, &meet[1])); 4783 /* Copy in cone of first point */ 4784 PetscCall(PetscSectionGetDof(mesh->coneSection, points[0], &dof)); 4785 PetscCall(PetscSectionGetOffset(mesh->coneSection, points[0], &off)); 4786 for (meetSize = 0; meetSize < dof; ++meetSize) meet[i][meetSize] = mesh->cones[off + meetSize]; 4787 /* Check each successive cone */ 4788 for (p = 1; p < numPoints; ++p) { 4789 PetscInt newMeetSize = 0; 4790 4791 PetscCall(PetscSectionGetDof(mesh->coneSection, points[p], &dof)); 4792 PetscCall(PetscSectionGetOffset(mesh->coneSection, points[p], &off)); 4793 for (c = 0; c < dof; ++c) { 4794 const PetscInt point = mesh->cones[off + c]; 4795 4796 for (m = 0; m < meetSize; ++m) { 4797 if (point == meet[i][m]) { 4798 meet[1 - i][newMeetSize++] = point; 4799 break; 4800 } 4801 } 4802 } 4803 meetSize = newMeetSize; 4804 i = 1 - i; 4805 } 4806 *numCoveringPoints = meetSize; 4807 *coveringPoints = meet[i]; 4808 PetscCall(DMRestoreWorkArray(dm, maxConeSize, MPIU_INT, &meet[1 - i])); 4809 PetscFunctionReturn(PETSC_SUCCESS); 4810 } 4811 4812 /*@C 4813 DMPlexRestoreMeet - Restore an array for the meet of the set of points 4814 4815 Not Collective 4816 4817 Input Parameters: 4818 + dm - The `DMPLEX` object 4819 . numPoints - The number of input points for the meet 4820 - points - The input points 4821 4822 Output Parameters: 4823 + numCoveredPoints - The number of points in the meet 4824 - coveredPoints - The points in the meet 4825 4826 Level: intermediate 4827 4828 Fortran Notes: 4829 The `numCoveredPoints` argument is not present in the Fortran binding since it is internal to the array. 4830 4831 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetMeet()`, `DMPlexGetFullMeet()`, `DMPlexGetJoin()` 4832 @*/ 4833 PetscErrorCode DMPlexRestoreMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 4834 { 4835 PetscFunctionBegin; 4836 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4837 if (points) PetscAssertPointer(points, 3); 4838 if (numCoveredPoints) PetscAssertPointer(numCoveredPoints, 4); 4839 PetscAssertPointer(coveredPoints, 5); 4840 PetscCall(DMRestoreWorkArray(dm, 0, MPIU_INT, (void *)coveredPoints)); 4841 if (numCoveredPoints) *numCoveredPoints = 0; 4842 PetscFunctionReturn(PETSC_SUCCESS); 4843 } 4844 4845 /*@C 4846 DMPlexGetFullMeet - Get an array for the meet of the set of points 4847 4848 Not Collective 4849 4850 Input Parameters: 4851 + dm - The `DMPLEX` object 4852 . numPoints - The number of input points for the meet 4853 - points - The input points 4854 4855 Output Parameters: 4856 + numCoveredPoints - The number of points in the meet 4857 - coveredPoints - The points in the meet 4858 4859 Level: intermediate 4860 4861 Fortran Notes: 4862 The `numCoveredPoints` argument is not present in the Fortran binding since it is internal to the array. 4863 4864 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetMeet()`, `DMPlexRestoreMeet()`, `DMPlexGetJoin()` 4865 @*/ 4866 PetscErrorCode DMPlexGetFullMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 4867 { 4868 PetscInt *offsets, **closures; 4869 PetscInt *meet[2]; 4870 PetscInt height = 0, maxSize, meetSize = 0, i = 0; 4871 PetscInt p, h, c, m, mc; 4872 4873 PetscFunctionBegin; 4874 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4875 PetscAssertPointer(points, 3); 4876 PetscAssertPointer(numCoveredPoints, 4); 4877 PetscAssertPointer(coveredPoints, 5); 4878 4879 PetscCall(DMPlexGetDepth(dm, &height)); 4880 PetscCall(PetscMalloc1(numPoints, &closures)); 4881 PetscCall(DMGetWorkArray(dm, numPoints * (height + 2), MPIU_INT, &offsets)); 4882 PetscCall(DMPlexGetMaxSizes(dm, &mc, NULL)); 4883 maxSize = (mc > 1) ? ((PetscPowInt(mc, height + 1) - 1) / (mc - 1)) : height + 1; 4884 PetscCall(DMGetWorkArray(dm, maxSize, MPIU_INT, &meet[0])); 4885 PetscCall(DMGetWorkArray(dm, maxSize, MPIU_INT, &meet[1])); 4886 4887 for (p = 0; p < numPoints; ++p) { 4888 PetscInt closureSize; 4889 4890 PetscCall(DMPlexGetTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closures[p])); 4891 4892 offsets[p * (height + 2) + 0] = 0; 4893 for (h = 0; h < height + 1; ++h) { 4894 PetscInt pStart, pEnd, i; 4895 4896 PetscCall(DMPlexGetHeightStratum(dm, h, &pStart, &pEnd)); 4897 for (i = offsets[p * (height + 2) + h]; i < closureSize; ++i) { 4898 if ((pStart > closures[p][i * 2]) || (pEnd <= closures[p][i * 2])) { 4899 offsets[p * (height + 2) + h + 1] = i; 4900 break; 4901 } 4902 } 4903 if (i == closureSize) offsets[p * (height + 2) + h + 1] = i; 4904 } 4905 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); 4906 } 4907 for (h = 0; h < height + 1; ++h) { 4908 PetscInt dof; 4909 4910 /* Copy in cone of first point */ 4911 dof = offsets[h + 1] - offsets[h]; 4912 for (meetSize = 0; meetSize < dof; ++meetSize) meet[i][meetSize] = closures[0][(offsets[h] + meetSize) * 2]; 4913 /* Check each successive cone */ 4914 for (p = 1; p < numPoints && meetSize; ++p) { 4915 PetscInt newMeetSize = 0; 4916 4917 dof = offsets[p * (height + 2) + h + 1] - offsets[p * (height + 2) + h]; 4918 for (c = 0; c < dof; ++c) { 4919 const PetscInt point = closures[p][(offsets[p * (height + 2) + h] + c) * 2]; 4920 4921 for (m = 0; m < meetSize; ++m) { 4922 if (point == meet[i][m]) { 4923 meet[1 - i][newMeetSize++] = point; 4924 break; 4925 } 4926 } 4927 } 4928 meetSize = newMeetSize; 4929 i = 1 - i; 4930 } 4931 if (meetSize) break; 4932 } 4933 *numCoveredPoints = meetSize; 4934 *coveredPoints = meet[i]; 4935 for (p = 0; p < numPoints; ++p) PetscCall(DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_TRUE, NULL, &closures[p])); 4936 PetscCall(PetscFree(closures)); 4937 PetscCall(DMRestoreWorkArray(dm, numPoints * (height + 2), MPIU_INT, &offsets)); 4938 PetscCall(DMRestoreWorkArray(dm, mc, MPIU_INT, &meet[1 - i])); 4939 PetscFunctionReturn(PETSC_SUCCESS); 4940 } 4941 4942 /*@C 4943 DMPlexEqual - Determine if two `DM` have the same topology 4944 4945 Not Collective 4946 4947 Input Parameters: 4948 + dmA - A `DMPLEX` object 4949 - dmB - A `DMPLEX` object 4950 4951 Output Parameter: 4952 . equal - `PETSC_TRUE` if the topologies are identical 4953 4954 Level: intermediate 4955 4956 Note: 4957 We are not solving graph isomorphism, so we do not permute. 4958 4959 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetCone()` 4960 @*/ 4961 PetscErrorCode DMPlexEqual(DM dmA, DM dmB, PetscBool *equal) 4962 { 4963 PetscInt depth, depthB, pStart, pEnd, pStartB, pEndB, p; 4964 4965 PetscFunctionBegin; 4966 PetscValidHeaderSpecific(dmA, DM_CLASSID, 1); 4967 PetscValidHeaderSpecific(dmB, DM_CLASSID, 2); 4968 PetscAssertPointer(equal, 3); 4969 4970 *equal = PETSC_FALSE; 4971 PetscCall(DMPlexGetDepth(dmA, &depth)); 4972 PetscCall(DMPlexGetDepth(dmB, &depthB)); 4973 if (depth != depthB) PetscFunctionReturn(PETSC_SUCCESS); 4974 PetscCall(DMPlexGetChart(dmA, &pStart, &pEnd)); 4975 PetscCall(DMPlexGetChart(dmB, &pStartB, &pEndB)); 4976 if ((pStart != pStartB) || (pEnd != pEndB)) PetscFunctionReturn(PETSC_SUCCESS); 4977 for (p = pStart; p < pEnd; ++p) { 4978 const PetscInt *cone, *coneB, *ornt, *orntB, *support, *supportB; 4979 PetscInt coneSize, coneSizeB, c, supportSize, supportSizeB, s; 4980 4981 PetscCall(DMPlexGetConeSize(dmA, p, &coneSize)); 4982 PetscCall(DMPlexGetCone(dmA, p, &cone)); 4983 PetscCall(DMPlexGetConeOrientation(dmA, p, &ornt)); 4984 PetscCall(DMPlexGetConeSize(dmB, p, &coneSizeB)); 4985 PetscCall(DMPlexGetCone(dmB, p, &coneB)); 4986 PetscCall(DMPlexGetConeOrientation(dmB, p, &orntB)); 4987 if (coneSize != coneSizeB) PetscFunctionReturn(PETSC_SUCCESS); 4988 for (c = 0; c < coneSize; ++c) { 4989 if (cone[c] != coneB[c]) PetscFunctionReturn(PETSC_SUCCESS); 4990 if (ornt[c] != orntB[c]) PetscFunctionReturn(PETSC_SUCCESS); 4991 } 4992 PetscCall(DMPlexGetSupportSize(dmA, p, &supportSize)); 4993 PetscCall(DMPlexGetSupport(dmA, p, &support)); 4994 PetscCall(DMPlexGetSupportSize(dmB, p, &supportSizeB)); 4995 PetscCall(DMPlexGetSupport(dmB, p, &supportB)); 4996 if (supportSize != supportSizeB) PetscFunctionReturn(PETSC_SUCCESS); 4997 for (s = 0; s < supportSize; ++s) { 4998 if (support[s] != supportB[s]) PetscFunctionReturn(PETSC_SUCCESS); 4999 } 5000 } 5001 *equal = PETSC_TRUE; 5002 PetscFunctionReturn(PETSC_SUCCESS); 5003 } 5004 5005 /*@C 5006 DMPlexGetNumFaceVertices - Returns the number of vertices on a face 5007 5008 Not Collective 5009 5010 Input Parameters: 5011 + dm - The `DMPLEX` 5012 . cellDim - The cell dimension 5013 - numCorners - The number of vertices on a cell 5014 5015 Output Parameter: 5016 . numFaceVertices - The number of vertices on a face 5017 5018 Level: developer 5019 5020 Note: 5021 Of course this can only work for a restricted set of symmetric shapes 5022 5023 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetCone()` 5024 @*/ 5025 PetscErrorCode DMPlexGetNumFaceVertices(DM dm, PetscInt cellDim, PetscInt numCorners, PetscInt *numFaceVertices) 5026 { 5027 MPI_Comm comm; 5028 5029 PetscFunctionBegin; 5030 PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); 5031 PetscAssertPointer(numFaceVertices, 4); 5032 switch (cellDim) { 5033 case 0: 5034 *numFaceVertices = 0; 5035 break; 5036 case 1: 5037 *numFaceVertices = 1; 5038 break; 5039 case 2: 5040 switch (numCorners) { 5041 case 3: /* triangle */ 5042 *numFaceVertices = 2; /* Edge has 2 vertices */ 5043 break; 5044 case 4: /* quadrilateral */ 5045 *numFaceVertices = 2; /* Edge has 2 vertices */ 5046 break; 5047 case 6: /* quadratic triangle, tri and quad cohesive Lagrange cells */ 5048 *numFaceVertices = 3; /* Edge has 3 vertices */ 5049 break; 5050 case 9: /* quadratic quadrilateral, quadratic quad cohesive Lagrange cells */ 5051 *numFaceVertices = 3; /* Edge has 3 vertices */ 5052 break; 5053 default: 5054 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of face corners %" PetscInt_FMT " for dimension %" PetscInt_FMT, numCorners, cellDim); 5055 } 5056 break; 5057 case 3: 5058 switch (numCorners) { 5059 case 4: /* tetradehdron */ 5060 *numFaceVertices = 3; /* Face has 3 vertices */ 5061 break; 5062 case 6: /* tet cohesive cells */ 5063 *numFaceVertices = 4; /* Face has 4 vertices */ 5064 break; 5065 case 8: /* hexahedron */ 5066 *numFaceVertices = 4; /* Face has 4 vertices */ 5067 break; 5068 case 9: /* tet cohesive Lagrange cells */ 5069 *numFaceVertices = 6; /* Face has 6 vertices */ 5070 break; 5071 case 10: /* quadratic tetrahedron */ 5072 *numFaceVertices = 6; /* Face has 6 vertices */ 5073 break; 5074 case 12: /* hex cohesive Lagrange cells */ 5075 *numFaceVertices = 6; /* Face has 6 vertices */ 5076 break; 5077 case 18: /* quadratic tet cohesive Lagrange cells */ 5078 *numFaceVertices = 6; /* Face has 6 vertices */ 5079 break; 5080 case 27: /* quadratic hexahedron, quadratic hex cohesive Lagrange cells */ 5081 *numFaceVertices = 9; /* Face has 9 vertices */ 5082 break; 5083 default: 5084 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of face corners %" PetscInt_FMT " for dimension %" PetscInt_FMT, numCorners, cellDim); 5085 } 5086 break; 5087 default: 5088 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid cell dimension %" PetscInt_FMT, cellDim); 5089 } 5090 PetscFunctionReturn(PETSC_SUCCESS); 5091 } 5092 5093 /*@ 5094 DMPlexGetDepthLabel - Get the `DMLabel` recording the depth of each point 5095 5096 Not Collective 5097 5098 Input Parameter: 5099 . dm - The `DMPLEX` object 5100 5101 Output Parameter: 5102 . depthLabel - The `DMLabel` recording point depth 5103 5104 Level: developer 5105 5106 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetDepth()`, `DMPlexGetHeightStratum()`, `DMPlexGetDepthStratum()`, `DMPlexGetPointDepth()`, 5107 @*/ 5108 PetscErrorCode DMPlexGetDepthLabel(DM dm, DMLabel *depthLabel) 5109 { 5110 PetscFunctionBegin; 5111 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5112 PetscAssertPointer(depthLabel, 2); 5113 *depthLabel = dm->depthLabel; 5114 PetscFunctionReturn(PETSC_SUCCESS); 5115 } 5116 5117 /*@ 5118 DMPlexGetDepth - Get the depth of the DAG representing this mesh 5119 5120 Not Collective 5121 5122 Input Parameter: 5123 . dm - The `DMPLEX` object 5124 5125 Output Parameter: 5126 . depth - The number of strata (breadth first levels) in the DAG 5127 5128 Level: developer 5129 5130 Notes: 5131 This returns maximum of point depths over all points, i.e. maximum value of the label returned by `DMPlexGetDepthLabel()`. 5132 5133 The point depth is described more in detail in `DMPlexGetDepthStratum()`. 5134 5135 An empty mesh gives -1. 5136 5137 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetDepthLabel()`, `DMPlexGetDepthStratum()`, `DMPlexGetPointDepth()`, `DMPlexSymmetrize()` 5138 @*/ 5139 PetscErrorCode DMPlexGetDepth(DM dm, PetscInt *depth) 5140 { 5141 DM_Plex *mesh = (DM_Plex *)dm->data; 5142 DMLabel label; 5143 PetscInt d = 0; 5144 5145 PetscFunctionBegin; 5146 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5147 PetscAssertPointer(depth, 2); 5148 if (mesh->tr) { 5149 PetscCall(DMPlexTransformGetDepth(mesh->tr, depth)); 5150 } else { 5151 PetscCall(DMPlexGetDepthLabel(dm, &label)); 5152 if (label) PetscCall(DMLabelGetNumValues(label, &d)); 5153 *depth = d - 1; 5154 } 5155 PetscFunctionReturn(PETSC_SUCCESS); 5156 } 5157 5158 /*@ 5159 DMPlexGetDepthStratum - Get the bounds [`start`, `end`) for all points at a certain depth. 5160 5161 Not Collective 5162 5163 Input Parameters: 5164 + dm - The `DMPLEX` object 5165 - depth - The requested depth 5166 5167 Output Parameters: 5168 + start - The first point at this `depth` 5169 - end - One beyond the last point at this `depth` 5170 5171 Level: developer 5172 5173 Notes: 5174 Depth indexing is related to topological dimension. Depth stratum 0 contains the lowest topological dimension points, 5175 often "vertices". If the mesh is "interpolated" (see `DMPlexInterpolate()`), then depth stratum 1 contains the next 5176 higher dimension, e.g., "edges". 5177 5178 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetHeightStratum()`, `DMPlexGetCellTypeStratum()`, `DMPlexGetDepth()`, `DMPlexGetDepthLabel()`, `DMPlexGetPointDepth()`, `DMPlexSymmetrize()`, `DMPlexInterpolate()` 5179 @*/ 5180 PetscErrorCode DMPlexGetDepthStratum(DM dm, PetscInt depth, PetscInt *start, PetscInt *end) 5181 { 5182 DM_Plex *mesh = (DM_Plex *)dm->data; 5183 DMLabel label; 5184 PetscInt pStart, pEnd; 5185 5186 PetscFunctionBegin; 5187 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5188 if (start) { 5189 PetscAssertPointer(start, 3); 5190 *start = 0; 5191 } 5192 if (end) { 5193 PetscAssertPointer(end, 4); 5194 *end = 0; 5195 } 5196 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 5197 if (pStart == pEnd) PetscFunctionReturn(PETSC_SUCCESS); 5198 if (depth < 0) { 5199 if (start) *start = pStart; 5200 if (end) *end = pEnd; 5201 PetscFunctionReturn(PETSC_SUCCESS); 5202 } 5203 if (mesh->tr) { 5204 PetscCall(DMPlexTransformGetDepthStratum(mesh->tr, depth, start, end)); 5205 } else { 5206 PetscCall(DMPlexGetDepthLabel(dm, &label)); 5207 PetscCheck(label, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "No label named depth was found"); 5208 PetscCall(DMLabelGetStratumBounds(label, depth, start, end)); 5209 } 5210 PetscFunctionReturn(PETSC_SUCCESS); 5211 } 5212 5213 /*@ 5214 DMPlexGetHeightStratum - Get the bounds [`start`, `end`) for all points at a certain height. 5215 5216 Not Collective 5217 5218 Input Parameters: 5219 + dm - The `DMPLEX` object 5220 - height - The requested height 5221 5222 Output Parameters: 5223 + start - The first point at this `height` 5224 - end - One beyond the last point at this `height` 5225 5226 Level: developer 5227 5228 Notes: 5229 Height indexing is related to topological codimension. Height stratum 0 contains the highest topological dimension 5230 points, often called "cells" or "elements". If the mesh is "interpolated" (see `DMPlexInterpolate()`), then height 5231 stratum 1 contains the boundary of these "cells", often called "faces" or "facets". 5232 5233 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetDepthStratum()`, `DMPlexGetCellTypeStratum()`, `DMPlexGetDepth()`, `DMPlexGetPointHeight()` 5234 @*/ 5235 PetscErrorCode DMPlexGetHeightStratum(DM dm, PetscInt height, PetscInt *start, PetscInt *end) 5236 { 5237 DMLabel label; 5238 PetscInt depth, pStart, pEnd; 5239 5240 PetscFunctionBegin; 5241 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5242 if (start) { 5243 PetscAssertPointer(start, 3); 5244 *start = 0; 5245 } 5246 if (end) { 5247 PetscAssertPointer(end, 4); 5248 *end = 0; 5249 } 5250 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 5251 if (pStart == pEnd) PetscFunctionReturn(PETSC_SUCCESS); 5252 if (height < 0) { 5253 if (start) *start = pStart; 5254 if (end) *end = pEnd; 5255 PetscFunctionReturn(PETSC_SUCCESS); 5256 } 5257 PetscCall(DMPlexGetDepthLabel(dm, &label)); 5258 if (label) PetscCall(DMLabelGetNumValues(label, &depth)); 5259 else PetscCall(DMGetDimension(dm, &depth)); 5260 PetscCheck(depth >= 0, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Depth not yet computed"); 5261 PetscCall(DMPlexGetDepthStratum(dm, depth - 1 - height, start, end)); 5262 PetscFunctionReturn(PETSC_SUCCESS); 5263 } 5264 5265 /*@ 5266 DMPlexGetPointDepth - Get the `depth` of a given point 5267 5268 Not Collective 5269 5270 Input Parameters: 5271 + dm - The `DMPLEX` object 5272 - point - The point 5273 5274 Output Parameter: 5275 . depth - The depth of the `point` 5276 5277 Level: intermediate 5278 5279 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetCellType()`, `DMPlexGetDepthLabel()`, `DMPlexGetDepth()`, `DMPlexGetPointHeight()` 5280 @*/ 5281 PetscErrorCode DMPlexGetPointDepth(DM dm, PetscInt point, PetscInt *depth) 5282 { 5283 PetscFunctionBegin; 5284 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5285 PetscAssertPointer(depth, 3); 5286 PetscCall(DMLabelGetValue(dm->depthLabel, point, depth)); 5287 PetscFunctionReturn(PETSC_SUCCESS); 5288 } 5289 5290 /*@ 5291 DMPlexGetPointHeight - Get the `height` of a given point 5292 5293 Not Collective 5294 5295 Input Parameters: 5296 + dm - The `DMPLEX` object 5297 - point - The point 5298 5299 Output Parameter: 5300 . height - The height of the `point` 5301 5302 Level: intermediate 5303 5304 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetCellType()`, `DMPlexGetDepthLabel()`, `DMPlexGetDepth()`, `DMPlexGetPointDepth()` 5305 @*/ 5306 PetscErrorCode DMPlexGetPointHeight(DM dm, PetscInt point, PetscInt *height) 5307 { 5308 PetscInt n, pDepth; 5309 5310 PetscFunctionBegin; 5311 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5312 PetscAssertPointer(height, 3); 5313 PetscCall(DMLabelGetNumValues(dm->depthLabel, &n)); 5314 PetscCall(DMLabelGetValue(dm->depthLabel, point, &pDepth)); 5315 *height = n - 1 - pDepth; /* DAG depth is n-1 */ 5316 PetscFunctionReturn(PETSC_SUCCESS); 5317 } 5318 5319 /*@ 5320 DMPlexGetCellTypeLabel - Get the `DMLabel` recording the polytope type of each cell 5321 5322 Not Collective 5323 5324 Input Parameter: 5325 . dm - The `DMPLEX` object 5326 5327 Output Parameter: 5328 . celltypeLabel - The `DMLabel` recording cell polytope type 5329 5330 Level: developer 5331 5332 Note: 5333 This function will trigger automatica computation of cell types. This can be disabled by calling 5334 `DMCreateLabel`(dm, "celltype") beforehand. 5335 5336 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetCellType()`, `DMPlexGetDepthLabel()`, `DMCreateLabel()` 5337 @*/ 5338 PetscErrorCode DMPlexGetCellTypeLabel(DM dm, DMLabel *celltypeLabel) 5339 { 5340 PetscFunctionBegin; 5341 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5342 PetscAssertPointer(celltypeLabel, 2); 5343 if (!dm->celltypeLabel) PetscCall(DMPlexComputeCellTypes(dm)); 5344 *celltypeLabel = dm->celltypeLabel; 5345 PetscFunctionReturn(PETSC_SUCCESS); 5346 } 5347 5348 /*@ 5349 DMPlexGetCellType - Get the polytope type of a given cell 5350 5351 Not Collective 5352 5353 Input Parameters: 5354 + dm - The `DMPLEX` object 5355 - cell - The cell 5356 5357 Output Parameter: 5358 . celltype - The polytope type of the cell 5359 5360 Level: intermediate 5361 5362 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPolytopeType`, `DMPlexGetCellTypeLabel()`, `DMPlexGetDepthLabel()`, `DMPlexGetDepth()` 5363 @*/ 5364 PetscErrorCode DMPlexGetCellType(DM dm, PetscInt cell, DMPolytopeType *celltype) 5365 { 5366 DM_Plex *mesh = (DM_Plex *)dm->data; 5367 DMLabel label; 5368 PetscInt ct; 5369 5370 PetscFunctionBegin; 5371 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5372 PetscAssertPointer(celltype, 3); 5373 if (mesh->tr) { 5374 PetscCall(DMPlexTransformGetCellType(mesh->tr, cell, celltype)); 5375 } else { 5376 PetscInt pStart, pEnd; 5377 5378 PetscCall(PetscSectionGetChart(mesh->coneSection, &pStart, NULL)); 5379 if (!mesh->cellTypes) { /* XXX remove? optimize? */ 5380 PetscCall(PetscSectionGetChart(mesh->coneSection, NULL, &pEnd)); 5381 PetscCall(PetscMalloc1(pEnd - pStart, &mesh->cellTypes)); 5382 PetscCall(DMPlexGetCellTypeLabel(dm, &label)); 5383 for (PetscInt p = pStart; p < pEnd; p++) { 5384 PetscCall(DMLabelGetValue(label, p, &ct)); 5385 mesh->cellTypes[p - pStart].value_as_uint8 = (DMPolytopeType)ct; 5386 } 5387 } 5388 *celltype = (DMPolytopeType)mesh->cellTypes[cell - pStart].value_as_uint8; 5389 if (PetscDefined(USE_DEBUG)) { 5390 PetscCall(DMPlexGetCellTypeLabel(dm, &label)); 5391 PetscCall(DMLabelGetValue(label, cell, &ct)); 5392 PetscCheck(ct >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Cell %" PetscInt_FMT " has not been assigned a cell type", cell); 5393 PetscCheck(ct == (PetscInt)*celltype, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid cellType for %" PetscInt_FMT ": %d != %" PetscInt_FMT, cell, (int)*celltype, ct); 5394 } 5395 } 5396 PetscFunctionReturn(PETSC_SUCCESS); 5397 } 5398 5399 /*@ 5400 DMPlexSetCellType - Set the polytope type of a given cell 5401 5402 Not Collective 5403 5404 Input Parameters: 5405 + dm - The `DMPLEX` object 5406 . cell - The cell 5407 - celltype - The polytope type of the cell 5408 5409 Level: advanced 5410 5411 Note: 5412 By default, cell types will be automatically computed using `DMPlexComputeCellTypes()` before this function 5413 is executed. This function will override the computed type. However, if automatic classification will not succeed 5414 and a user wants to manually specify all types, the classification must be disabled by calling 5415 DMCreateLabel(dm, "celltype") before getting or setting any cell types. 5416 5417 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetCellTypeLabel()`, `DMPlexGetDepthLabel()`, `DMPlexGetDepth()`, `DMPlexComputeCellTypes()`, `DMCreateLabel()` 5418 @*/ 5419 PetscErrorCode DMPlexSetCellType(DM dm, PetscInt cell, DMPolytopeType celltype) 5420 { 5421 DM_Plex *mesh = (DM_Plex *)dm->data; 5422 DMLabel label; 5423 PetscInt pStart, pEnd; 5424 5425 PetscFunctionBegin; 5426 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5427 PetscCall(PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd)); 5428 PetscCall(DMPlexGetCellTypeLabel(dm, &label)); 5429 PetscCall(DMLabelSetValue(label, cell, celltype)); 5430 if (!mesh->cellTypes) PetscCall(PetscMalloc1(pEnd - pStart, &mesh->cellTypes)); 5431 mesh->cellTypes[cell - pStart].value_as_uint8 = celltype; 5432 PetscFunctionReturn(PETSC_SUCCESS); 5433 } 5434 5435 PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm) 5436 { 5437 PetscSection section, s; 5438 Mat m; 5439 PetscInt maxHeight; 5440 const char *prefix; 5441 5442 PetscFunctionBegin; 5443 PetscCall(DMClone(dm, cdm)); 5444 PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm, &prefix)); 5445 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)*cdm, prefix)); 5446 PetscCall(PetscObjectAppendOptionsPrefix((PetscObject)*cdm, "cdm_")); 5447 PetscCall(DMPlexGetMaxProjectionHeight(dm, &maxHeight)); 5448 PetscCall(DMPlexSetMaxProjectionHeight(*cdm, maxHeight)); 5449 PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)dm), §ion)); 5450 PetscCall(DMSetLocalSection(*cdm, section)); 5451 PetscCall(PetscSectionDestroy(§ion)); 5452 PetscCall(PetscSectionCreate(PETSC_COMM_SELF, &s)); 5453 PetscCall(MatCreate(PETSC_COMM_SELF, &m)); 5454 PetscCall(DMSetDefaultConstraints(*cdm, s, m, NULL)); 5455 PetscCall(PetscSectionDestroy(&s)); 5456 PetscCall(MatDestroy(&m)); 5457 5458 PetscCall(DMSetNumFields(*cdm, 1)); 5459 PetscCall(DMCreateDS(*cdm)); 5460 (*cdm)->cloneOpts = PETSC_TRUE; 5461 if (dm->setfromoptionscalled) PetscCall(DMSetFromOptions(*cdm)); 5462 PetscFunctionReturn(PETSC_SUCCESS); 5463 } 5464 5465 PetscErrorCode DMCreateCoordinateField_Plex(DM dm, DMField *field) 5466 { 5467 Vec coordsLocal, cellCoordsLocal; 5468 DM coordsDM, cellCoordsDM; 5469 5470 PetscFunctionBegin; 5471 *field = NULL; 5472 PetscCall(DMGetCoordinatesLocal(dm, &coordsLocal)); 5473 PetscCall(DMGetCoordinateDM(dm, &coordsDM)); 5474 PetscCall(DMGetCellCoordinatesLocal(dm, &cellCoordsLocal)); 5475 PetscCall(DMGetCellCoordinateDM(dm, &cellCoordsDM)); 5476 if (coordsLocal && coordsDM) { 5477 if (cellCoordsLocal && cellCoordsDM) PetscCall(DMFieldCreateDSWithDG(coordsDM, cellCoordsDM, 0, coordsLocal, cellCoordsLocal, field)); 5478 else PetscCall(DMFieldCreateDS(coordsDM, 0, coordsLocal, field)); 5479 } 5480 PetscFunctionReturn(PETSC_SUCCESS); 5481 } 5482 5483 /*@C 5484 DMPlexGetConeSection - Return a section which describes the layout of cone data 5485 5486 Not Collective 5487 5488 Input Parameter: 5489 . dm - The `DMPLEX` object 5490 5491 Output Parameter: 5492 . section - The `PetscSection` object 5493 5494 Level: developer 5495 5496 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetSupportSection()`, `DMPlexGetCones()`, `DMPlexGetConeOrientations()`, `PetscSection` 5497 @*/ 5498 PetscErrorCode DMPlexGetConeSection(DM dm, PetscSection *section) 5499 { 5500 DM_Plex *mesh = (DM_Plex *)dm->data; 5501 5502 PetscFunctionBegin; 5503 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5504 if (section) *section = mesh->coneSection; 5505 PetscFunctionReturn(PETSC_SUCCESS); 5506 } 5507 5508 /*@C 5509 DMPlexGetSupportSection - Return a section which describes the layout of support data 5510 5511 Not Collective 5512 5513 Input Parameter: 5514 . dm - The `DMPLEX` object 5515 5516 Output Parameter: 5517 . section - The `PetscSection` object 5518 5519 Level: developer 5520 5521 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetConeSection()`, `PetscSection` 5522 @*/ 5523 PetscErrorCode DMPlexGetSupportSection(DM dm, PetscSection *section) 5524 { 5525 DM_Plex *mesh = (DM_Plex *)dm->data; 5526 5527 PetscFunctionBegin; 5528 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5529 if (section) *section = mesh->supportSection; 5530 PetscFunctionReturn(PETSC_SUCCESS); 5531 } 5532 5533 /*@C 5534 DMPlexGetCones - Return cone data 5535 5536 Not Collective 5537 5538 Input Parameter: 5539 . dm - The `DMPLEX` object 5540 5541 Output Parameter: 5542 . cones - The cone for each point 5543 5544 Level: developer 5545 5546 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetConeSection()` 5547 @*/ 5548 PetscErrorCode DMPlexGetCones(DM dm, PetscInt *cones[]) 5549 { 5550 DM_Plex *mesh = (DM_Plex *)dm->data; 5551 5552 PetscFunctionBegin; 5553 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5554 if (cones) *cones = mesh->cones; 5555 PetscFunctionReturn(PETSC_SUCCESS); 5556 } 5557 5558 /*@C 5559 DMPlexGetConeOrientations - Return cone orientation data 5560 5561 Not Collective 5562 5563 Input Parameter: 5564 . dm - The `DMPLEX` object 5565 5566 Output Parameter: 5567 . coneOrientations - The array of cone orientations for all points 5568 5569 Level: developer 5570 5571 Notes: 5572 The `PetscSection` returned by `DMPlexGetConeSection()` partitions coneOrientations into cone orientations of particular points as returned by `DMPlexGetConeOrientation()`. 5573 5574 The meaning of coneOrientations values is detailed in `DMPlexGetConeOrientation()`. 5575 5576 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetConeSection()`, `DMPlexGetConeOrientation()`, `PetscSection` 5577 @*/ 5578 PetscErrorCode DMPlexGetConeOrientations(DM dm, PetscInt *coneOrientations[]) 5579 { 5580 DM_Plex *mesh = (DM_Plex *)dm->data; 5581 5582 PetscFunctionBegin; 5583 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5584 if (coneOrientations) *coneOrientations = mesh->coneOrientations; 5585 PetscFunctionReturn(PETSC_SUCCESS); 5586 } 5587 5588 /******************************** FEM Support **********************************/ 5589 5590 PetscErrorCode DMPlexGetAllCells_Internal(DM plex, IS *cellIS) 5591 { 5592 PetscInt depth; 5593 5594 PetscFunctionBegin; 5595 PetscCall(DMPlexGetDepth(plex, &depth)); 5596 PetscCall(DMGetStratumIS(plex, "dim", depth, cellIS)); 5597 if (!*cellIS) PetscCall(DMGetStratumIS(plex, "depth", depth, cellIS)); 5598 PetscFunctionReturn(PETSC_SUCCESS); 5599 } 5600 5601 /* 5602 Returns number of components and tensor degree for the field. For interpolated meshes, line should be a point 5603 representing a line in the section. 5604 */ 5605 static PetscErrorCode PetscSectionFieldGetTensorDegree_Private(PetscSection section, PetscInt field, PetscInt line, PetscBool vertexchart, PetscInt *Nc, PetscInt *k) 5606 { 5607 PetscFunctionBeginHot; 5608 PetscCall(PetscSectionGetFieldComponents(section, field, Nc)); 5609 if (line < 0) { 5610 *k = 0; 5611 *Nc = 0; 5612 } else if (vertexchart) { /* If we only have a vertex chart, we must have degree k=1 */ 5613 *k = 1; 5614 } else { /* Assume the full interpolated mesh is in the chart; lines in particular */ 5615 /* An order k SEM disc has k-1 dofs on an edge */ 5616 PetscCall(PetscSectionGetFieldDof(section, line, field, k)); 5617 *k = *k / *Nc + 1; 5618 } 5619 PetscFunctionReturn(PETSC_SUCCESS); 5620 } 5621 5622 /*@ 5623 5624 DMPlexSetClosurePermutationTensor - Create a permutation from the default (BFS) point ordering in the closure, to a 5625 lexicographic ordering over the tensor product cell (i.e., line, quad, hex, etc.), and set this permutation in the 5626 section provided (or the section of the `DM`). 5627 5628 Input Parameters: 5629 + dm - The `DM` 5630 . point - Either a cell (highest dim point) or an edge (dim 1 point), or `PETSC_DETERMINE` 5631 - section - The `PetscSection` to reorder, or `NULL` for the default section 5632 5633 Example: 5634 A typical interpolated single-quad mesh might order points as 5635 .vb 5636 [c0, v1, v2, v3, v4, e5, e6, e7, e8] 5637 5638 v4 -- e6 -- v3 5639 | | 5640 e7 c0 e8 5641 | | 5642 v1 -- e5 -- v2 5643 .ve 5644 5645 (There is no significance to the ordering described here.) The default section for a Q3 quad might typically assign 5646 dofs in the order of points, e.g., 5647 .vb 5648 c0 -> [0,1,2,3] 5649 v1 -> [4] 5650 ... 5651 e5 -> [8, 9] 5652 .ve 5653 5654 which corresponds to the dofs 5655 .vb 5656 6 10 11 7 5657 13 2 3 15 5658 12 0 1 14 5659 4 8 9 5 5660 .ve 5661 5662 The closure in BFS ordering works through height strata (cells, edges, vertices) to produce the ordering 5663 .vb 5664 0 1 2 3 8 9 14 15 11 10 13 12 4 5 7 6 5665 .ve 5666 5667 After calling DMPlexSetClosurePermutationTensor(), the closure will be ordered lexicographically, 5668 .vb 5669 4 8 9 5 12 0 1 14 13 2 3 15 6 10 11 7 5670 .ve 5671 5672 Level: developer 5673 5674 Notes: 5675 The point is used to determine the number of dofs/field on an edge. For SEM, this is related to the polynomial 5676 degree of the basis. 5677 5678 This is required to run with libCEED. 5679 5680 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMGetLocalSection()`, `PetscSectionSetClosurePermutation()`, `DMSetGlobalSection()` 5681 @*/ 5682 PetscErrorCode DMPlexSetClosurePermutationTensor(DM dm, PetscInt point, PetscSection section) 5683 { 5684 DMLabel label; 5685 PetscInt dim, depth = -1, eStart = -1, Nf; 5686 PetscBool vertexchart; 5687 5688 PetscFunctionBegin; 5689 PetscCall(DMGetDimension(dm, &dim)); 5690 if (dim < 1) PetscFunctionReturn(PETSC_SUCCESS); 5691 if (point < 0) { 5692 PetscInt sStart, sEnd; 5693 5694 PetscCall(DMPlexGetDepthStratum(dm, 1, &sStart, &sEnd)); 5695 point = sEnd - sStart ? sStart : point; 5696 } 5697 PetscCall(DMPlexGetDepthLabel(dm, &label)); 5698 if (point >= 0) PetscCall(DMLabelGetValue(label, point, &depth)); 5699 if (!section) PetscCall(DMGetLocalSection(dm, §ion)); 5700 if (depth == 1) { 5701 eStart = point; 5702 } else if (depth == dim) { 5703 const PetscInt *cone; 5704 5705 PetscCall(DMPlexGetCone(dm, point, &cone)); 5706 if (dim == 2) eStart = cone[0]; 5707 else if (dim == 3) { 5708 const PetscInt *cone2; 5709 PetscCall(DMPlexGetCone(dm, cone[0], &cone2)); 5710 eStart = cone2[0]; 5711 } 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); 5712 } 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); 5713 { /* Determine whether the chart covers all points or just vertices. */ 5714 PetscInt pStart, pEnd, cStart, cEnd; 5715 PetscCall(DMPlexGetDepthStratum(dm, 0, &pStart, &pEnd)); 5716 PetscCall(PetscSectionGetChart(section, &cStart, &cEnd)); 5717 if (pStart == cStart && pEnd == cEnd) vertexchart = PETSC_TRUE; /* Only vertices are in the chart */ 5718 else if (cStart <= point && point < cEnd) vertexchart = PETSC_FALSE; /* Some interpolated points exist in the chart */ 5719 else vertexchart = PETSC_TRUE; /* Some interpolated points are not in chart; assume dofs only at cells and vertices */ 5720 } 5721 PetscCall(PetscSectionGetNumFields(section, &Nf)); 5722 for (PetscInt d = 1; d <= dim; d++) { 5723 PetscInt k, f, Nc, c, i, j, size = 0, offset = 0, foffset = 0; 5724 PetscInt *perm; 5725 5726 for (f = 0; f < Nf; ++f) { 5727 PetscCall(PetscSectionFieldGetTensorDegree_Private(section, f, eStart, vertexchart, &Nc, &k)); 5728 size += PetscPowInt(k + 1, d) * Nc; 5729 } 5730 PetscCall(PetscMalloc1(size, &perm)); 5731 for (f = 0; f < Nf; ++f) { 5732 switch (d) { 5733 case 1: 5734 PetscCall(PetscSectionFieldGetTensorDegree_Private(section, f, eStart, vertexchart, &Nc, &k)); 5735 /* 5736 Original ordering is [ edge of length k-1; vtx0; vtx1 ] 5737 We want [ vtx0; edge of length k-1; vtx1 ] 5738 */ 5739 for (c = 0; c < Nc; c++, offset++) perm[offset] = (k - 1) * Nc + c + foffset; 5740 for (i = 0; i < k - 1; i++) 5741 for (c = 0; c < Nc; c++, offset++) perm[offset] = i * Nc + c + foffset; 5742 for (c = 0; c < Nc; c++, offset++) perm[offset] = k * Nc + c + foffset; 5743 foffset = offset; 5744 break; 5745 case 2: 5746 /* The original quad closure is oriented clockwise, {f, e_b, e_r, e_t, e_l, v_lb, v_rb, v_tr, v_tl} */ 5747 PetscCall(PetscSectionFieldGetTensorDegree_Private(section, f, eStart, vertexchart, &Nc, &k)); 5748 /* The SEM order is 5749 5750 v_lb, {e_b}, v_rb, 5751 e^{(k-1)-i}_l, {f^{i*(k-1)}}, e^i_r, 5752 v_lt, reverse {e_t}, v_rt 5753 */ 5754 { 5755 const PetscInt of = 0; 5756 const PetscInt oeb = of + PetscSqr(k - 1); 5757 const PetscInt oer = oeb + (k - 1); 5758 const PetscInt oet = oer + (k - 1); 5759 const PetscInt oel = oet + (k - 1); 5760 const PetscInt ovlb = oel + (k - 1); 5761 const PetscInt ovrb = ovlb + 1; 5762 const PetscInt ovrt = ovrb + 1; 5763 const PetscInt ovlt = ovrt + 1; 5764 PetscInt o; 5765 5766 /* bottom */ 5767 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovlb * Nc + c + foffset; 5768 for (o = oeb; o < oer; ++o) 5769 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 5770 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovrb * Nc + c + foffset; 5771 /* middle */ 5772 for (i = 0; i < k - 1; ++i) { 5773 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oel + (k - 2) - i) * Nc + c + foffset; 5774 for (o = of + (k - 1) * i; o < of + (k - 1) * (i + 1); ++o) 5775 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 5776 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oer + i) * Nc + c + foffset; 5777 } 5778 /* top */ 5779 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovlt * Nc + c + foffset; 5780 for (o = oel - 1; o >= oet; --o) 5781 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 5782 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovrt * Nc + c + foffset; 5783 foffset = offset; 5784 } 5785 break; 5786 case 3: 5787 /* The original hex closure is 5788 5789 {c, 5790 f_b, f_t, f_f, f_b, f_r, f_l, 5791 e_bl, e_bb, e_br, e_bf, e_tf, e_tr, e_tb, e_tl, e_rf, e_lf, e_lb, e_rb, 5792 v_blf, v_blb, v_brb, v_brf, v_tlf, v_trf, v_trb, v_tlb} 5793 */ 5794 PetscCall(PetscSectionFieldGetTensorDegree_Private(section, f, eStart, vertexchart, &Nc, &k)); 5795 /* The SEM order is 5796 Bottom Slice 5797 v_blf, {e^{(k-1)-n}_bf}, v_brf, 5798 e^{i}_bl, f^{n*(k-1)+(k-1)-i}_b, e^{(k-1)-i}_br, 5799 v_blb, {e_bb}, v_brb, 5800 5801 Middle Slice (j) 5802 {e^{(k-1)-j}_lf}, {f^{j*(k-1)+n}_f}, e^j_rf, 5803 f^{i*(k-1)+j}_l, {c^{(j*(k-1) + i)*(k-1)+n}_t}, f^{j*(k-1)+i}_r, 5804 e^j_lb, {f^{j*(k-1)+(k-1)-n}_b}, e^{(k-1)-j}_rb, 5805 5806 Top Slice 5807 v_tlf, {e_tf}, v_trf, 5808 e^{(k-1)-i}_tl, {f^{i*(k-1)}_t}, e^{i}_tr, 5809 v_tlb, {e^{(k-1)-n}_tb}, v_trb, 5810 */ 5811 { 5812 const PetscInt oc = 0; 5813 const PetscInt ofb = oc + PetscSqr(k - 1) * (k - 1); 5814 const PetscInt oft = ofb + PetscSqr(k - 1); 5815 const PetscInt off = oft + PetscSqr(k - 1); 5816 const PetscInt ofk = off + PetscSqr(k - 1); 5817 const PetscInt ofr = ofk + PetscSqr(k - 1); 5818 const PetscInt ofl = ofr + PetscSqr(k - 1); 5819 const PetscInt oebl = ofl + PetscSqr(k - 1); 5820 const PetscInt oebb = oebl + (k - 1); 5821 const PetscInt oebr = oebb + (k - 1); 5822 const PetscInt oebf = oebr + (k - 1); 5823 const PetscInt oetf = oebf + (k - 1); 5824 const PetscInt oetr = oetf + (k - 1); 5825 const PetscInt oetb = oetr + (k - 1); 5826 const PetscInt oetl = oetb + (k - 1); 5827 const PetscInt oerf = oetl + (k - 1); 5828 const PetscInt oelf = oerf + (k - 1); 5829 const PetscInt oelb = oelf + (k - 1); 5830 const PetscInt oerb = oelb + (k - 1); 5831 const PetscInt ovblf = oerb + (k - 1); 5832 const PetscInt ovblb = ovblf + 1; 5833 const PetscInt ovbrb = ovblb + 1; 5834 const PetscInt ovbrf = ovbrb + 1; 5835 const PetscInt ovtlf = ovbrf + 1; 5836 const PetscInt ovtrf = ovtlf + 1; 5837 const PetscInt ovtrb = ovtrf + 1; 5838 const PetscInt ovtlb = ovtrb + 1; 5839 PetscInt o, n; 5840 5841 /* Bottom Slice */ 5842 /* bottom */ 5843 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovblf * Nc + c + foffset; 5844 for (o = oetf - 1; o >= oebf; --o) 5845 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 5846 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovbrf * Nc + c + foffset; 5847 /* middle */ 5848 for (i = 0; i < k - 1; ++i) { 5849 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oebl + i) * Nc + c + foffset; 5850 for (n = 0; n < k - 1; ++n) { 5851 o = ofb + n * (k - 1) + i; 5852 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 5853 } 5854 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oebr + (k - 2) - i) * Nc + c + foffset; 5855 } 5856 /* top */ 5857 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovblb * Nc + c + foffset; 5858 for (o = oebb; o < oebr; ++o) 5859 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 5860 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovbrb * Nc + c + foffset; 5861 5862 /* Middle Slice */ 5863 for (j = 0; j < k - 1; ++j) { 5864 /* bottom */ 5865 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oelf + (k - 2) - j) * Nc + c + foffset; 5866 for (o = off + j * (k - 1); o < off + (j + 1) * (k - 1); ++o) 5867 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 5868 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oerf + j) * Nc + c + foffset; 5869 /* middle */ 5870 for (i = 0; i < k - 1; ++i) { 5871 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (ofl + i * (k - 1) + j) * Nc + c + foffset; 5872 for (n = 0; n < k - 1; ++n) 5873 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oc + (j * (k - 1) + i) * (k - 1) + n) * Nc + c + foffset; 5874 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (ofr + j * (k - 1) + i) * Nc + c + foffset; 5875 } 5876 /* top */ 5877 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oelb + j) * Nc + c + foffset; 5878 for (o = ofk + j * (k - 1) + (k - 2); o >= ofk + j * (k - 1); --o) 5879 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 5880 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oerb + (k - 2) - j) * Nc + c + foffset; 5881 } 5882 5883 /* Top Slice */ 5884 /* bottom */ 5885 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtlf * Nc + c + foffset; 5886 for (o = oetf; o < oetr; ++o) 5887 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 5888 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtrf * Nc + c + foffset; 5889 /* middle */ 5890 for (i = 0; i < k - 1; ++i) { 5891 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oetl + (k - 2) - i) * Nc + c + foffset; 5892 for (n = 0; n < k - 1; ++n) 5893 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oft + i * (k - 1) + n) * Nc + c + foffset; 5894 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oetr + i) * Nc + c + foffset; 5895 } 5896 /* top */ 5897 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtlb * Nc + c + foffset; 5898 for (o = oetl - 1; o >= oetb; --o) 5899 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o * Nc + c + foffset; 5900 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtrb * Nc + c + foffset; 5901 5902 foffset = offset; 5903 } 5904 break; 5905 default: 5906 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "No spectral ordering for dimension %" PetscInt_FMT, d); 5907 } 5908 } 5909 PetscCheck(offset == size, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Number of permutation entries %" PetscInt_FMT " != %" PetscInt_FMT, offset, size); 5910 /* Check permutation */ 5911 { 5912 PetscInt *check; 5913 5914 PetscCall(PetscMalloc1(size, &check)); 5915 for (i = 0; i < size; ++i) { 5916 check[i] = -1; 5917 PetscCheck(perm[i] >= 0 && perm[i] < size, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid permutation index p[%" PetscInt_FMT "] = %" PetscInt_FMT, i, perm[i]); 5918 } 5919 for (i = 0; i < size; ++i) check[perm[i]] = i; 5920 for (i = 0; i < size; ++i) PetscCheck(check[i] >= 0, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Missing permutation index %" PetscInt_FMT, i); 5921 PetscCall(PetscFree(check)); 5922 } 5923 PetscCall(PetscSectionSetClosurePermutation_Internal(section, (PetscObject)dm, d, size, PETSC_OWN_POINTER, perm)); 5924 if (d == dim) { // Add permutation for localized (in case this is a coordinate DM) 5925 PetscInt *loc_perm; 5926 PetscCall(PetscMalloc1(size * 2, &loc_perm)); 5927 for (PetscInt i = 0; i < size; i++) { 5928 loc_perm[i] = perm[i]; 5929 loc_perm[size + i] = size + perm[i]; 5930 } 5931 PetscCall(PetscSectionSetClosurePermutation_Internal(section, (PetscObject)dm, d, size * 2, PETSC_OWN_POINTER, loc_perm)); 5932 } 5933 } 5934 PetscFunctionReturn(PETSC_SUCCESS); 5935 } 5936 5937 PetscErrorCode DMPlexGetPointDualSpaceFEM(DM dm, PetscInt point, PetscInt field, PetscDualSpace *dspace) 5938 { 5939 PetscDS prob; 5940 PetscInt depth, Nf, h; 5941 DMLabel label; 5942 5943 PetscFunctionBeginHot; 5944 PetscCall(DMGetDS(dm, &prob)); 5945 Nf = prob->Nf; 5946 label = dm->depthLabel; 5947 *dspace = NULL; 5948 if (field < Nf) { 5949 PetscObject disc = prob->disc[field]; 5950 5951 if (disc->classid == PETSCFE_CLASSID) { 5952 PetscDualSpace dsp; 5953 5954 PetscCall(PetscFEGetDualSpace((PetscFE)disc, &dsp)); 5955 PetscCall(DMLabelGetNumValues(label, &depth)); 5956 PetscCall(DMLabelGetValue(label, point, &h)); 5957 h = depth - 1 - h; 5958 if (h) { 5959 PetscCall(PetscDualSpaceGetHeightSubspace(dsp, h, dspace)); 5960 } else { 5961 *dspace = dsp; 5962 } 5963 } 5964 } 5965 PetscFunctionReturn(PETSC_SUCCESS); 5966 } 5967 5968 static inline PetscErrorCode DMPlexVecGetClosure_Depth1_Static(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[]) 5969 { 5970 PetscScalar *array; 5971 const PetscScalar *vArray; 5972 const PetscInt *cone, *coneO; 5973 PetscInt pStart, pEnd, p, numPoints, size = 0, offset = 0; 5974 5975 PetscFunctionBeginHot; 5976 PetscCall(PetscSectionGetChart(section, &pStart, &pEnd)); 5977 PetscCall(DMPlexGetConeSize(dm, point, &numPoints)); 5978 PetscCall(DMPlexGetCone(dm, point, &cone)); 5979 PetscCall(DMPlexGetConeOrientation(dm, point, &coneO)); 5980 if (!values || !*values) { 5981 if ((point >= pStart) && (point < pEnd)) { 5982 PetscInt dof; 5983 5984 PetscCall(PetscSectionGetDof(section, point, &dof)); 5985 size += dof; 5986 } 5987 for (p = 0; p < numPoints; ++p) { 5988 const PetscInt cp = cone[p]; 5989 PetscInt dof; 5990 5991 if ((cp < pStart) || (cp >= pEnd)) continue; 5992 PetscCall(PetscSectionGetDof(section, cp, &dof)); 5993 size += dof; 5994 } 5995 if (!values) { 5996 if (csize) *csize = size; 5997 PetscFunctionReturn(PETSC_SUCCESS); 5998 } 5999 PetscCall(DMGetWorkArray(dm, size, MPIU_SCALAR, &array)); 6000 } else { 6001 array = *values; 6002 } 6003 size = 0; 6004 PetscCall(VecGetArrayRead(v, &vArray)); 6005 if ((point >= pStart) && (point < pEnd)) { 6006 PetscInt dof, off, d; 6007 const PetscScalar *varr; 6008 6009 PetscCall(PetscSectionGetDof(section, point, &dof)); 6010 PetscCall(PetscSectionGetOffset(section, point, &off)); 6011 varr = &vArray[off]; 6012 for (d = 0; d < dof; ++d, ++offset) array[offset] = varr[d]; 6013 size += dof; 6014 } 6015 for (p = 0; p < numPoints; ++p) { 6016 const PetscInt cp = cone[p]; 6017 PetscInt o = coneO[p]; 6018 PetscInt dof, off, d; 6019 const PetscScalar *varr; 6020 6021 if ((cp < pStart) || (cp >= pEnd)) continue; 6022 PetscCall(PetscSectionGetDof(section, cp, &dof)); 6023 PetscCall(PetscSectionGetOffset(section, cp, &off)); 6024 varr = &vArray[off]; 6025 if (o >= 0) { 6026 for (d = 0; d < dof; ++d, ++offset) array[offset] = varr[d]; 6027 } else { 6028 for (d = dof - 1; d >= 0; --d, ++offset) array[offset] = varr[d]; 6029 } 6030 size += dof; 6031 } 6032 PetscCall(VecRestoreArrayRead(v, &vArray)); 6033 if (!*values) { 6034 if (csize) *csize = size; 6035 *values = array; 6036 } else { 6037 PetscCheck(size <= *csize, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Size of input array %" PetscInt_FMT " < actual size %" PetscInt_FMT, *csize, size); 6038 *csize = size; 6039 } 6040 PetscFunctionReturn(PETSC_SUCCESS); 6041 } 6042 6043 /* Compress out points not in the section */ 6044 static inline PetscErrorCode CompressPoints_Private(PetscSection section, PetscInt *numPoints, PetscInt points[]) 6045 { 6046 const PetscInt np = *numPoints; 6047 PetscInt pStart, pEnd, p, q; 6048 6049 PetscCall(PetscSectionGetChart(section, &pStart, &pEnd)); 6050 for (p = 0, q = 0; p < np; ++p) { 6051 const PetscInt r = points[p * 2]; 6052 if ((r >= pStart) && (r < pEnd)) { 6053 points[q * 2] = r; 6054 points[q * 2 + 1] = points[p * 2 + 1]; 6055 ++q; 6056 } 6057 } 6058 *numPoints = q; 6059 return PETSC_SUCCESS; 6060 } 6061 6062 /* Compressed closure does not apply closure permutation */ 6063 PetscErrorCode DMPlexGetCompressedClosure(DM dm, PetscSection section, PetscInt point, PetscInt ornt, PetscInt *numPoints, PetscInt **points, PetscSection *clSec, IS *clPoints, const PetscInt **clp) 6064 { 6065 const PetscInt *cla = NULL; 6066 PetscInt np, *pts = NULL; 6067 6068 PetscFunctionBeginHot; 6069 PetscCall(PetscSectionGetClosureIndex(section, (PetscObject)dm, clSec, clPoints)); 6070 if (!ornt && *clPoints) { 6071 PetscInt dof, off; 6072 6073 PetscCall(PetscSectionGetDof(*clSec, point, &dof)); 6074 PetscCall(PetscSectionGetOffset(*clSec, point, &off)); 6075 PetscCall(ISGetIndices(*clPoints, &cla)); 6076 np = dof / 2; 6077 pts = (PetscInt *)&cla[off]; 6078 } else { 6079 PetscCall(DMPlexGetTransitiveClosure_Internal(dm, point, ornt, PETSC_TRUE, &np, &pts)); 6080 PetscCall(CompressPoints_Private(section, &np, pts)); 6081 } 6082 *numPoints = np; 6083 *points = pts; 6084 *clp = cla; 6085 PetscFunctionReturn(PETSC_SUCCESS); 6086 } 6087 6088 PetscErrorCode DMPlexRestoreCompressedClosure(DM dm, PetscSection section, PetscInt point, PetscInt *numPoints, PetscInt **points, PetscSection *clSec, IS *clPoints, const PetscInt **clp) 6089 { 6090 PetscFunctionBeginHot; 6091 if (!*clPoints) { 6092 PetscCall(DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, numPoints, points)); 6093 } else { 6094 PetscCall(ISRestoreIndices(*clPoints, clp)); 6095 } 6096 *numPoints = 0; 6097 *points = NULL; 6098 *clSec = NULL; 6099 *clPoints = NULL; 6100 *clp = NULL; 6101 PetscFunctionReturn(PETSC_SUCCESS); 6102 } 6103 6104 static inline PetscErrorCode DMPlexVecGetClosure_Static(DM dm, PetscSection section, PetscInt numPoints, const PetscInt points[], const PetscInt clperm[], const PetscScalar vArray[], PetscInt *size, PetscScalar array[]) 6105 { 6106 PetscInt offset = 0, p; 6107 const PetscInt **perms = NULL; 6108 const PetscScalar **flips = NULL; 6109 6110 PetscFunctionBeginHot; 6111 *size = 0; 6112 PetscCall(PetscSectionGetPointSyms(section, numPoints, points, &perms, &flips)); 6113 for (p = 0; p < numPoints; p++) { 6114 const PetscInt point = points[2 * p]; 6115 const PetscInt *perm = perms ? perms[p] : NULL; 6116 const PetscScalar *flip = flips ? flips[p] : NULL; 6117 PetscInt dof, off, d; 6118 const PetscScalar *varr; 6119 6120 PetscCall(PetscSectionGetDof(section, point, &dof)); 6121 PetscCall(PetscSectionGetOffset(section, point, &off)); 6122 varr = &vArray[off]; 6123 if (clperm) { 6124 if (perm) { 6125 for (d = 0; d < dof; d++) array[clperm[offset + perm[d]]] = varr[d]; 6126 } else { 6127 for (d = 0; d < dof; d++) array[clperm[offset + d]] = varr[d]; 6128 } 6129 if (flip) { 6130 for (d = 0; d < dof; d++) array[clperm[offset + d]] *= flip[d]; 6131 } 6132 } else { 6133 if (perm) { 6134 for (d = 0; d < dof; d++) array[offset + perm[d]] = varr[d]; 6135 } else { 6136 for (d = 0; d < dof; d++) array[offset + d] = varr[d]; 6137 } 6138 if (flip) { 6139 for (d = 0; d < dof; d++) array[offset + d] *= flip[d]; 6140 } 6141 } 6142 offset += dof; 6143 } 6144 PetscCall(PetscSectionRestorePointSyms(section, numPoints, points, &perms, &flips)); 6145 *size = offset; 6146 PetscFunctionReturn(PETSC_SUCCESS); 6147 } 6148 6149 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[]) 6150 { 6151 PetscInt offset = 0, f; 6152 6153 PetscFunctionBeginHot; 6154 *size = 0; 6155 for (f = 0; f < numFields; ++f) { 6156 PetscInt p; 6157 const PetscInt **perms = NULL; 6158 const PetscScalar **flips = NULL; 6159 6160 PetscCall(PetscSectionGetFieldPointSyms(section, f, numPoints, points, &perms, &flips)); 6161 for (p = 0; p < numPoints; p++) { 6162 const PetscInt point = points[2 * p]; 6163 PetscInt fdof, foff, b; 6164 const PetscScalar *varr; 6165 const PetscInt *perm = perms ? perms[p] : NULL; 6166 const PetscScalar *flip = flips ? flips[p] : NULL; 6167 6168 PetscCall(PetscSectionGetFieldDof(section, point, f, &fdof)); 6169 PetscCall(PetscSectionGetFieldOffset(section, point, f, &foff)); 6170 varr = &vArray[foff]; 6171 if (clperm) { 6172 if (perm) { 6173 for (b = 0; b < fdof; b++) array[clperm[offset + perm[b]]] = varr[b]; 6174 } else { 6175 for (b = 0; b < fdof; b++) array[clperm[offset + b]] = varr[b]; 6176 } 6177 if (flip) { 6178 for (b = 0; b < fdof; b++) array[clperm[offset + b]] *= flip[b]; 6179 } 6180 } else { 6181 if (perm) { 6182 for (b = 0; b < fdof; b++) array[offset + perm[b]] = varr[b]; 6183 } else { 6184 for (b = 0; b < fdof; b++) array[offset + b] = varr[b]; 6185 } 6186 if (flip) { 6187 for (b = 0; b < fdof; b++) array[offset + b] *= flip[b]; 6188 } 6189 } 6190 offset += fdof; 6191 } 6192 PetscCall(PetscSectionRestoreFieldPointSyms(section, f, numPoints, points, &perms, &flips)); 6193 } 6194 *size = offset; 6195 PetscFunctionReturn(PETSC_SUCCESS); 6196 } 6197 6198 PetscErrorCode DMPlexVecGetOrientedClosure_Internal(DM dm, PetscSection section, PetscBool useClPerm, Vec v, PetscInt point, PetscInt ornt, PetscInt *csize, PetscScalar *values[]) 6199 { 6200 PetscSection clSection; 6201 IS clPoints; 6202 PetscInt *points = NULL; 6203 const PetscInt *clp, *perm = NULL; 6204 PetscInt depth, numFields, numPoints, asize; 6205 6206 PetscFunctionBeginHot; 6207 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6208 if (!section) PetscCall(DMGetLocalSection(dm, §ion)); 6209 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 6210 PetscValidHeaderSpecific(v, VEC_CLASSID, 4); 6211 PetscCall(DMPlexGetDepth(dm, &depth)); 6212 PetscCall(PetscSectionGetNumFields(section, &numFields)); 6213 if (depth == 1 && numFields < 2) { 6214 PetscCall(DMPlexVecGetClosure_Depth1_Static(dm, section, v, point, csize, values)); 6215 PetscFunctionReturn(PETSC_SUCCESS); 6216 } 6217 /* Get points */ 6218 PetscCall(DMPlexGetCompressedClosure(dm, section, point, ornt, &numPoints, &points, &clSection, &clPoints, &clp)); 6219 /* Get sizes */ 6220 asize = 0; 6221 for (PetscInt p = 0; p < numPoints * 2; p += 2) { 6222 PetscInt dof; 6223 PetscCall(PetscSectionGetDof(section, points[p], &dof)); 6224 asize += dof; 6225 } 6226 if (values) { 6227 const PetscScalar *vArray; 6228 PetscInt size; 6229 6230 if (*values) { 6231 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); 6232 } else PetscCall(DMGetWorkArray(dm, asize, MPIU_SCALAR, values)); 6233 if (useClPerm) PetscCall(PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject)dm, depth, asize, &perm)); 6234 PetscCall(VecGetArrayRead(v, &vArray)); 6235 /* Get values */ 6236 if (numFields > 0) PetscCall(DMPlexVecGetClosure_Fields_Static(dm, section, numPoints, points, numFields, perm, vArray, &size, *values)); 6237 else PetscCall(DMPlexVecGetClosure_Static(dm, section, numPoints, points, perm, vArray, &size, *values)); 6238 PetscCheck(asize == size, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Section size %" PetscInt_FMT " does not match Vec closure size %" PetscInt_FMT, asize, size); 6239 /* Cleanup array */ 6240 PetscCall(VecRestoreArrayRead(v, &vArray)); 6241 } 6242 if (csize) *csize = asize; 6243 /* Cleanup points */ 6244 PetscCall(DMPlexRestoreCompressedClosure(dm, section, point, &numPoints, &points, &clSection, &clPoints, &clp)); 6245 PetscFunctionReturn(PETSC_SUCCESS); 6246 } 6247 6248 /*@C 6249 DMPlexVecGetClosure - Get an array of the values on the closure of 'point' 6250 6251 Not collective 6252 6253 Input Parameters: 6254 + dm - The `DM` 6255 . section - The section describing the layout in `v`, or `NULL` to use the default section 6256 . v - The local vector 6257 - point - The point in the `DM` 6258 6259 Input/Output Parameters: 6260 + csize - The size of the input values array, or `NULL`; on output the number of values in the closure 6261 - values - An array to use for the values, or `NULL` to have it allocated automatically; 6262 if the user provided `NULL`, it is a borrowed array and should not be freed 6263 6264 Level: intermediate 6265 6266 Notes: 6267 `DMPlexVecGetClosure()`/`DMPlexVecRestoreClosure()` only allocates the values array if it set to `NULL` in the 6268 calling function. This is because `DMPlexVecGetClosure()` is typically called in the inner loop of a `Vec` or `Mat` 6269 assembly function, and a user may already have allocated storage for this operation. 6270 6271 A typical use could be 6272 .vb 6273 values = NULL; 6274 PetscCall(DMPlexVecGetClosure(dm, NULL, v, p, &clSize, &values)); 6275 for (cl = 0; cl < clSize; ++cl) { 6276 <Compute on closure> 6277 } 6278 PetscCall(DMPlexVecRestoreClosure(dm, NULL, v, p, &clSize, &values)); 6279 .ve 6280 or 6281 .vb 6282 PetscMalloc1(clMaxSize, &values); 6283 for (p = pStart; p < pEnd; ++p) { 6284 clSize = clMaxSize; 6285 PetscCall(DMPlexVecGetClosure(dm, NULL, v, p, &clSize, &values)); 6286 for (cl = 0; cl < clSize; ++cl) { 6287 <Compute on closure> 6288 } 6289 } 6290 PetscFree(values); 6291 .ve 6292 6293 Fortran Notes: 6294 The `csize` argument is not present in the Fortran binding since it is internal to the array. 6295 6296 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexVecRestoreClosure()`, `DMPlexVecSetClosure()`, `DMPlexMatSetClosure()` 6297 @*/ 6298 PetscErrorCode DMPlexVecGetClosure(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[]) 6299 { 6300 PetscFunctionBeginHot; 6301 PetscCall(DMPlexVecGetOrientedClosure_Internal(dm, section, PETSC_TRUE, v, point, 0, csize, values)); 6302 PetscFunctionReturn(PETSC_SUCCESS); 6303 } 6304 6305 PetscErrorCode DMPlexVecGetClosureAtDepth_Internal(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt depth, PetscInt *csize, PetscScalar *values[]) 6306 { 6307 DMLabel depthLabel; 6308 PetscSection clSection; 6309 IS clPoints; 6310 PetscScalar *array; 6311 const PetscScalar *vArray; 6312 PetscInt *points = NULL; 6313 const PetscInt *clp, *perm = NULL; 6314 PetscInt mdepth, numFields, numPoints, Np = 0, p, clsize, size; 6315 6316 PetscFunctionBeginHot; 6317 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6318 if (!section) PetscCall(DMGetLocalSection(dm, §ion)); 6319 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 6320 PetscValidHeaderSpecific(v, VEC_CLASSID, 3); 6321 PetscCall(DMPlexGetDepth(dm, &mdepth)); 6322 PetscCall(DMPlexGetDepthLabel(dm, &depthLabel)); 6323 PetscCall(PetscSectionGetNumFields(section, &numFields)); 6324 if (mdepth == 1 && numFields < 2) { 6325 PetscCall(DMPlexVecGetClosure_Depth1_Static(dm, section, v, point, csize, values)); 6326 PetscFunctionReturn(PETSC_SUCCESS); 6327 } 6328 /* Get points */ 6329 PetscCall(DMPlexGetCompressedClosure(dm, section, point, 0, &numPoints, &points, &clSection, &clPoints, &clp)); 6330 for (clsize = 0, p = 0; p < Np; p++) { 6331 PetscInt dof; 6332 PetscCall(PetscSectionGetDof(section, points[2 * p], &dof)); 6333 clsize += dof; 6334 } 6335 PetscCall(PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject)dm, depth, clsize, &perm)); 6336 /* Filter points */ 6337 for (p = 0; p < numPoints * 2; p += 2) { 6338 PetscInt dep; 6339 6340 PetscCall(DMLabelGetValue(depthLabel, points[p], &dep)); 6341 if (dep != depth) continue; 6342 points[Np * 2 + 0] = points[p]; 6343 points[Np * 2 + 1] = points[p + 1]; 6344 ++Np; 6345 } 6346 /* Get array */ 6347 if (!values || !*values) { 6348 PetscInt asize = 0, dof; 6349 6350 for (p = 0; p < Np * 2; p += 2) { 6351 PetscCall(PetscSectionGetDof(section, points[p], &dof)); 6352 asize += dof; 6353 } 6354 if (!values) { 6355 PetscCall(DMPlexRestoreCompressedClosure(dm, section, point, &numPoints, &points, &clSection, &clPoints, &clp)); 6356 if (csize) *csize = asize; 6357 PetscFunctionReturn(PETSC_SUCCESS); 6358 } 6359 PetscCall(DMGetWorkArray(dm, asize, MPIU_SCALAR, &array)); 6360 } else { 6361 array = *values; 6362 } 6363 PetscCall(VecGetArrayRead(v, &vArray)); 6364 /* Get values */ 6365 if (numFields > 0) PetscCall(DMPlexVecGetClosure_Fields_Static(dm, section, Np, points, numFields, perm, vArray, &size, array)); 6366 else PetscCall(DMPlexVecGetClosure_Static(dm, section, Np, points, perm, vArray, &size, array)); 6367 /* Cleanup points */ 6368 PetscCall(DMPlexRestoreCompressedClosure(dm, section, point, &numPoints, &points, &clSection, &clPoints, &clp)); 6369 /* Cleanup array */ 6370 PetscCall(VecRestoreArrayRead(v, &vArray)); 6371 if (!*values) { 6372 if (csize) *csize = size; 6373 *values = array; 6374 } else { 6375 PetscCheck(size <= *csize, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Size of input array %" PetscInt_FMT " < actual size %" PetscInt_FMT, *csize, size); 6376 *csize = size; 6377 } 6378 PetscFunctionReturn(PETSC_SUCCESS); 6379 } 6380 6381 /*@C 6382 DMPlexVecRestoreClosure - Restore the array of the values on the closure of 'point' 6383 6384 Not collective 6385 6386 Input Parameters: 6387 + dm - The `DM` 6388 . section - The section describing the layout in `v`, or `NULL` to use the default section 6389 . v - The local vector 6390 . point - The point in the `DM` 6391 . csize - The number of values in the closure, or `NULL` 6392 - values - The array of values, which is a borrowed array and should not be freed 6393 6394 Level: intermediate 6395 6396 Note: 6397 The array values are discarded and not copied back into `v`. In order to copy values back to `v`, use `DMPlexVecSetClosure()` 6398 6399 Fortran Notes: 6400 The `csize` argument is not present in the Fortran binding since it is internal to the array. 6401 6402 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexVecGetClosure()`, `DMPlexVecSetClosure()`, `DMPlexMatSetClosure()` 6403 @*/ 6404 PetscErrorCode DMPlexVecRestoreClosure(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[]) 6405 { 6406 PetscInt size = 0; 6407 6408 PetscFunctionBegin; 6409 /* Should work without recalculating size */ 6410 PetscCall(DMRestoreWorkArray(dm, size, MPIU_SCALAR, (void *)values)); 6411 *values = NULL; 6412 PetscFunctionReturn(PETSC_SUCCESS); 6413 } 6414 6415 static inline void add(PetscScalar *x, PetscScalar y) 6416 { 6417 *x += y; 6418 } 6419 static inline void insert(PetscScalar *x, PetscScalar y) 6420 { 6421 *x = y; 6422 } 6423 6424 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[]) 6425 { 6426 PetscInt cdof; /* The number of constraints on this point */ 6427 const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ 6428 PetscScalar *a; 6429 PetscInt off, cind = 0, k; 6430 6431 PetscFunctionBegin; 6432 PetscCall(PetscSectionGetConstraintDof(section, point, &cdof)); 6433 PetscCall(PetscSectionGetOffset(section, point, &off)); 6434 a = &array[off]; 6435 if (!cdof || setBC) { 6436 if (clperm) { 6437 if (perm) { 6438 for (k = 0; k < dof; ++k) fuse(&a[k], values[clperm[offset + perm[k]]] * (flip ? flip[perm[k]] : 1.)); 6439 } else { 6440 for (k = 0; k < dof; ++k) fuse(&a[k], values[clperm[offset + k]] * (flip ? flip[k] : 1.)); 6441 } 6442 } else { 6443 if (perm) { 6444 for (k = 0; k < dof; ++k) fuse(&a[k], values[offset + perm[k]] * (flip ? flip[perm[k]] : 1.)); 6445 } else { 6446 for (k = 0; k < dof; ++k) fuse(&a[k], values[offset + k] * (flip ? flip[k] : 1.)); 6447 } 6448 } 6449 } else { 6450 PetscCall(PetscSectionGetConstraintIndices(section, point, &cdofs)); 6451 if (clperm) { 6452 if (perm) { 6453 for (k = 0; k < dof; ++k) { 6454 if ((cind < cdof) && (k == cdofs[cind])) { 6455 ++cind; 6456 continue; 6457 } 6458 fuse(&a[k], values[clperm[offset + perm[k]]] * (flip ? flip[perm[k]] : 1.)); 6459 } 6460 } else { 6461 for (k = 0; k < dof; ++k) { 6462 if ((cind < cdof) && (k == cdofs[cind])) { 6463 ++cind; 6464 continue; 6465 } 6466 fuse(&a[k], values[clperm[offset + k]] * (flip ? flip[k] : 1.)); 6467 } 6468 } 6469 } else { 6470 if (perm) { 6471 for (k = 0; k < dof; ++k) { 6472 if ((cind < cdof) && (k == cdofs[cind])) { 6473 ++cind; 6474 continue; 6475 } 6476 fuse(&a[k], values[offset + perm[k]] * (flip ? flip[perm[k]] : 1.)); 6477 } 6478 } else { 6479 for (k = 0; k < dof; ++k) { 6480 if ((cind < cdof) && (k == cdofs[cind])) { 6481 ++cind; 6482 continue; 6483 } 6484 fuse(&a[k], values[offset + k] * (flip ? flip[k] : 1.)); 6485 } 6486 } 6487 } 6488 } 6489 PetscFunctionReturn(PETSC_SUCCESS); 6490 } 6491 6492 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[]) 6493 { 6494 PetscInt cdof; /* The number of constraints on this point */ 6495 const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ 6496 PetscScalar *a; 6497 PetscInt off, cind = 0, k; 6498 6499 PetscFunctionBegin; 6500 PetscCall(PetscSectionGetConstraintDof(section, point, &cdof)); 6501 PetscCall(PetscSectionGetOffset(section, point, &off)); 6502 a = &array[off]; 6503 if (cdof) { 6504 PetscCall(PetscSectionGetConstraintIndices(section, point, &cdofs)); 6505 if (clperm) { 6506 if (perm) { 6507 for (k = 0; k < dof; ++k) { 6508 if ((cind < cdof) && (k == cdofs[cind])) { 6509 fuse(&a[k], values[clperm[offset + perm[k]]] * (flip ? flip[perm[k]] : 1.)); 6510 cind++; 6511 } 6512 } 6513 } else { 6514 for (k = 0; k < dof; ++k) { 6515 if ((cind < cdof) && (k == cdofs[cind])) { 6516 fuse(&a[k], values[clperm[offset + k]] * (flip ? flip[k] : 1.)); 6517 cind++; 6518 } 6519 } 6520 } 6521 } else { 6522 if (perm) { 6523 for (k = 0; k < dof; ++k) { 6524 if ((cind < cdof) && (k == cdofs[cind])) { 6525 fuse(&a[k], values[offset + perm[k]] * (flip ? flip[perm[k]] : 1.)); 6526 cind++; 6527 } 6528 } 6529 } else { 6530 for (k = 0; k < dof; ++k) { 6531 if ((cind < cdof) && (k == cdofs[cind])) { 6532 fuse(&a[k], values[offset + k] * (flip ? flip[k] : 1.)); 6533 cind++; 6534 } 6535 } 6536 } 6537 } 6538 } 6539 PetscFunctionReturn(PETSC_SUCCESS); 6540 } 6541 6542 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[]) 6543 { 6544 PetscScalar *a; 6545 PetscInt fdof, foff, fcdof, foffset = *offset; 6546 const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ 6547 PetscInt cind = 0, b; 6548 6549 PetscFunctionBegin; 6550 PetscCall(PetscSectionGetFieldDof(section, point, f, &fdof)); 6551 PetscCall(PetscSectionGetFieldConstraintDof(section, point, f, &fcdof)); 6552 PetscCall(PetscSectionGetFieldOffset(section, point, f, &foff)); 6553 a = &array[foff]; 6554 if (!fcdof || setBC) { 6555 if (clperm) { 6556 if (perm) { 6557 for (b = 0; b < fdof; b++) fuse(&a[b], values[clperm[foffset + perm[b]]] * (flip ? flip[perm[b]] : 1.)); 6558 } else { 6559 for (b = 0; b < fdof; b++) fuse(&a[b], values[clperm[foffset + b]] * (flip ? flip[b] : 1.)); 6560 } 6561 } else { 6562 if (perm) { 6563 for (b = 0; b < fdof; b++) fuse(&a[b], values[foffset + perm[b]] * (flip ? flip[perm[b]] : 1.)); 6564 } else { 6565 for (b = 0; b < fdof; b++) fuse(&a[b], values[foffset + b] * (flip ? flip[b] : 1.)); 6566 } 6567 } 6568 } else { 6569 PetscCall(PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs)); 6570 if (clperm) { 6571 if (perm) { 6572 for (b = 0; b < fdof; b++) { 6573 if ((cind < fcdof) && (b == fcdofs[cind])) { 6574 ++cind; 6575 continue; 6576 } 6577 fuse(&a[b], values[clperm[foffset + perm[b]]] * (flip ? flip[perm[b]] : 1.)); 6578 } 6579 } else { 6580 for (b = 0; b < fdof; b++) { 6581 if ((cind < fcdof) && (b == fcdofs[cind])) { 6582 ++cind; 6583 continue; 6584 } 6585 fuse(&a[b], values[clperm[foffset + b]] * (flip ? flip[b] : 1.)); 6586 } 6587 } 6588 } else { 6589 if (perm) { 6590 for (b = 0; b < fdof; b++) { 6591 if ((cind < fcdof) && (b == fcdofs[cind])) { 6592 ++cind; 6593 continue; 6594 } 6595 fuse(&a[b], values[foffset + perm[b]] * (flip ? flip[perm[b]] : 1.)); 6596 } 6597 } else { 6598 for (b = 0; b < fdof; b++) { 6599 if ((cind < fcdof) && (b == fcdofs[cind])) { 6600 ++cind; 6601 continue; 6602 } 6603 fuse(&a[b], values[foffset + b] * (flip ? flip[b] : 1.)); 6604 } 6605 } 6606 } 6607 } 6608 *offset += fdof; 6609 PetscFunctionReturn(PETSC_SUCCESS); 6610 } 6611 6612 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[]) 6613 { 6614 PetscScalar *a; 6615 PetscInt fdof, foff, fcdof, foffset = *offset; 6616 const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ 6617 PetscInt Nc, cind = 0, ncind = 0, b; 6618 PetscBool ncSet, fcSet; 6619 6620 PetscFunctionBegin; 6621 PetscCall(PetscSectionGetFieldComponents(section, f, &Nc)); 6622 PetscCall(PetscSectionGetFieldDof(section, point, f, &fdof)); 6623 PetscCall(PetscSectionGetFieldConstraintDof(section, point, f, &fcdof)); 6624 PetscCall(PetscSectionGetFieldOffset(section, point, f, &foff)); 6625 a = &array[foff]; 6626 if (fcdof) { 6627 /* We just override fcdof and fcdofs with Ncc and comps */ 6628 PetscCall(PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs)); 6629 if (clperm) { 6630 if (perm) { 6631 if (comps) { 6632 for (b = 0; b < fdof; b++) { 6633 ncSet = fcSet = PETSC_FALSE; 6634 if (b % Nc == comps[ncind]) { 6635 ncind = (ncind + 1) % Ncc; 6636 ncSet = PETSC_TRUE; 6637 } 6638 if ((cind < fcdof) && (b == fcdofs[cind])) { 6639 ++cind; 6640 fcSet = PETSC_TRUE; 6641 } 6642 if (ncSet && fcSet) fuse(&a[b], values[clperm[foffset + perm[b]]] * (flip ? flip[perm[b]] : 1.)); 6643 } 6644 } else { 6645 for (b = 0; b < fdof; b++) { 6646 if ((cind < fcdof) && (b == fcdofs[cind])) { 6647 fuse(&a[b], values[clperm[foffset + perm[b]]] * (flip ? flip[perm[b]] : 1.)); 6648 ++cind; 6649 } 6650 } 6651 } 6652 } else { 6653 if (comps) { 6654 for (b = 0; b < fdof; b++) { 6655 ncSet = fcSet = PETSC_FALSE; 6656 if (b % Nc == comps[ncind]) { 6657 ncind = (ncind + 1) % Ncc; 6658 ncSet = PETSC_TRUE; 6659 } 6660 if ((cind < fcdof) && (b == fcdofs[cind])) { 6661 ++cind; 6662 fcSet = PETSC_TRUE; 6663 } 6664 if (ncSet && fcSet) fuse(&a[b], values[clperm[foffset + b]] * (flip ? flip[b] : 1.)); 6665 } 6666 } else { 6667 for (b = 0; b < fdof; b++) { 6668 if ((cind < fcdof) && (b == fcdofs[cind])) { 6669 fuse(&a[b], values[clperm[foffset + b]] * (flip ? flip[b] : 1.)); 6670 ++cind; 6671 } 6672 } 6673 } 6674 } 6675 } else { 6676 if (perm) { 6677 if (comps) { 6678 for (b = 0; b < fdof; b++) { 6679 ncSet = fcSet = PETSC_FALSE; 6680 if (b % Nc == comps[ncind]) { 6681 ncind = (ncind + 1) % Ncc; 6682 ncSet = PETSC_TRUE; 6683 } 6684 if ((cind < fcdof) && (b == fcdofs[cind])) { 6685 ++cind; 6686 fcSet = PETSC_TRUE; 6687 } 6688 if (ncSet && fcSet) fuse(&a[b], values[foffset + perm[b]] * (flip ? flip[perm[b]] : 1.)); 6689 } 6690 } else { 6691 for (b = 0; b < fdof; b++) { 6692 if ((cind < fcdof) && (b == fcdofs[cind])) { 6693 fuse(&a[b], values[foffset + perm[b]] * (flip ? flip[perm[b]] : 1.)); 6694 ++cind; 6695 } 6696 } 6697 } 6698 } else { 6699 if (comps) { 6700 for (b = 0; b < fdof; b++) { 6701 ncSet = fcSet = PETSC_FALSE; 6702 if (b % Nc == comps[ncind]) { 6703 ncind = (ncind + 1) % Ncc; 6704 ncSet = PETSC_TRUE; 6705 } 6706 if ((cind < fcdof) && (b == fcdofs[cind])) { 6707 ++cind; 6708 fcSet = PETSC_TRUE; 6709 } 6710 if (ncSet && fcSet) fuse(&a[b], values[foffset + b] * (flip ? flip[b] : 1.)); 6711 } 6712 } else { 6713 for (b = 0; b < fdof; b++) { 6714 if ((cind < fcdof) && (b == fcdofs[cind])) { 6715 fuse(&a[b], values[foffset + b] * (flip ? flip[b] : 1.)); 6716 ++cind; 6717 } 6718 } 6719 } 6720 } 6721 } 6722 } 6723 *offset += fdof; 6724 PetscFunctionReturn(PETSC_SUCCESS); 6725 } 6726 6727 static inline PetscErrorCode DMPlexVecSetClosure_Depth1_Static(DM dm, PetscSection section, Vec v, PetscInt point, const PetscScalar values[], InsertMode mode) 6728 { 6729 PetscScalar *array; 6730 const PetscInt *cone, *coneO; 6731 PetscInt pStart, pEnd, p, numPoints, off, dof; 6732 6733 PetscFunctionBeginHot; 6734 PetscCall(PetscSectionGetChart(section, &pStart, &pEnd)); 6735 PetscCall(DMPlexGetConeSize(dm, point, &numPoints)); 6736 PetscCall(DMPlexGetCone(dm, point, &cone)); 6737 PetscCall(DMPlexGetConeOrientation(dm, point, &coneO)); 6738 PetscCall(VecGetArray(v, &array)); 6739 for (p = 0, off = 0; p <= numPoints; ++p, off += dof) { 6740 const PetscInt cp = !p ? point : cone[p - 1]; 6741 const PetscInt o = !p ? 0 : coneO[p - 1]; 6742 6743 if ((cp < pStart) || (cp >= pEnd)) { 6744 dof = 0; 6745 continue; 6746 } 6747 PetscCall(PetscSectionGetDof(section, cp, &dof)); 6748 /* ADD_VALUES */ 6749 { 6750 const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ 6751 PetscScalar *a; 6752 PetscInt cdof, coff, cind = 0, k; 6753 6754 PetscCall(PetscSectionGetConstraintDof(section, cp, &cdof)); 6755 PetscCall(PetscSectionGetOffset(section, cp, &coff)); 6756 a = &array[coff]; 6757 if (!cdof) { 6758 if (o >= 0) { 6759 for (k = 0; k < dof; ++k) a[k] += values[off + k]; 6760 } else { 6761 for (k = 0; k < dof; ++k) a[k] += values[off + dof - k - 1]; 6762 } 6763 } else { 6764 PetscCall(PetscSectionGetConstraintIndices(section, cp, &cdofs)); 6765 if (o >= 0) { 6766 for (k = 0; k < dof; ++k) { 6767 if ((cind < cdof) && (k == cdofs[cind])) { 6768 ++cind; 6769 continue; 6770 } 6771 a[k] += values[off + k]; 6772 } 6773 } else { 6774 for (k = 0; k < dof; ++k) { 6775 if ((cind < cdof) && (k == cdofs[cind])) { 6776 ++cind; 6777 continue; 6778 } 6779 a[k] += values[off + dof - k - 1]; 6780 } 6781 } 6782 } 6783 } 6784 } 6785 PetscCall(VecRestoreArray(v, &array)); 6786 PetscFunctionReturn(PETSC_SUCCESS); 6787 } 6788 6789 /*@C 6790 DMPlexVecSetClosure - Set an array of the values on the closure of `point` 6791 6792 Not collective 6793 6794 Input Parameters: 6795 + dm - The `DM` 6796 . section - The section describing the layout in `v`, or `NULL` to use the default section 6797 . v - The local vector 6798 . point - The point in the `DM` 6799 . values - The array of values 6800 - mode - The insert mode. One of `INSERT_ALL_VALUES`, `ADD_ALL_VALUES`, `INSERT_VALUES`, `ADD_VALUES`, `INSERT_BC_VALUES`, and `ADD_BC_VALUES`, 6801 where `INSERT_ALL_VALUES` and `ADD_ALL_VALUES` also overwrite boundary conditions. 6802 6803 Level: intermediate 6804 6805 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexVecGetClosure()`, `DMPlexMatSetClosure()` 6806 @*/ 6807 PetscErrorCode DMPlexVecSetClosure(DM dm, PetscSection section, Vec v, PetscInt point, const PetscScalar values[], InsertMode mode) 6808 { 6809 PetscSection clSection; 6810 IS clPoints; 6811 PetscScalar *array; 6812 PetscInt *points = NULL; 6813 const PetscInt *clp, *clperm = NULL; 6814 PetscInt depth, numFields, numPoints, p, clsize; 6815 6816 PetscFunctionBeginHot; 6817 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6818 if (!section) PetscCall(DMGetLocalSection(dm, §ion)); 6819 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 6820 PetscValidHeaderSpecific(v, VEC_CLASSID, 3); 6821 PetscCall(DMPlexGetDepth(dm, &depth)); 6822 PetscCall(PetscSectionGetNumFields(section, &numFields)); 6823 if (depth == 1 && numFields < 2 && mode == ADD_VALUES) { 6824 PetscCall(DMPlexVecSetClosure_Depth1_Static(dm, section, v, point, values, mode)); 6825 PetscFunctionReturn(PETSC_SUCCESS); 6826 } 6827 /* Get points */ 6828 PetscCall(DMPlexGetCompressedClosure(dm, section, point, 0, &numPoints, &points, &clSection, &clPoints, &clp)); 6829 for (clsize = 0, p = 0; p < numPoints; p++) { 6830 PetscInt dof; 6831 PetscCall(PetscSectionGetDof(section, points[2 * p], &dof)); 6832 clsize += dof; 6833 } 6834 PetscCall(PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject)dm, depth, clsize, &clperm)); 6835 /* Get array */ 6836 PetscCall(VecGetArray(v, &array)); 6837 /* Get values */ 6838 if (numFields > 0) { 6839 PetscInt offset = 0, f; 6840 for (f = 0; f < numFields; ++f) { 6841 const PetscInt **perms = NULL; 6842 const PetscScalar **flips = NULL; 6843 6844 PetscCall(PetscSectionGetFieldPointSyms(section, f, numPoints, points, &perms, &flips)); 6845 switch (mode) { 6846 case INSERT_VALUES: 6847 for (p = 0; p < numPoints; p++) { 6848 const PetscInt point = points[2 * p]; 6849 const PetscInt *perm = perms ? perms[p] : NULL; 6850 const PetscScalar *flip = flips ? flips[p] : NULL; 6851 PetscCall(updatePointFields_private(section, point, perm, flip, f, insert, PETSC_FALSE, clperm, values, &offset, array)); 6852 } 6853 break; 6854 case INSERT_ALL_VALUES: 6855 for (p = 0; p < numPoints; p++) { 6856 const PetscInt point = points[2 * p]; 6857 const PetscInt *perm = perms ? perms[p] : NULL; 6858 const PetscScalar *flip = flips ? flips[p] : NULL; 6859 PetscCall(updatePointFields_private(section, point, perm, flip, f, insert, PETSC_TRUE, clperm, values, &offset, array)); 6860 } 6861 break; 6862 case INSERT_BC_VALUES: 6863 for (p = 0; p < numPoints; p++) { 6864 const PetscInt point = points[2 * p]; 6865 const PetscInt *perm = perms ? perms[p] : NULL; 6866 const PetscScalar *flip = flips ? flips[p] : NULL; 6867 PetscCall(updatePointFieldsBC_private(section, point, perm, flip, f, -1, NULL, insert, clperm, values, &offset, array)); 6868 } 6869 break; 6870 case ADD_VALUES: 6871 for (p = 0; p < numPoints; p++) { 6872 const PetscInt point = points[2 * p]; 6873 const PetscInt *perm = perms ? perms[p] : NULL; 6874 const PetscScalar *flip = flips ? flips[p] : NULL; 6875 PetscCall(updatePointFields_private(section, point, perm, flip, f, add, PETSC_FALSE, clperm, values, &offset, array)); 6876 } 6877 break; 6878 case ADD_ALL_VALUES: 6879 for (p = 0; p < numPoints; p++) { 6880 const PetscInt point = points[2 * p]; 6881 const PetscInt *perm = perms ? perms[p] : NULL; 6882 const PetscScalar *flip = flips ? flips[p] : NULL; 6883 PetscCall(updatePointFields_private(section, point, perm, flip, f, add, PETSC_TRUE, clperm, values, &offset, array)); 6884 } 6885 break; 6886 case ADD_BC_VALUES: 6887 for (p = 0; p < numPoints; p++) { 6888 const PetscInt point = points[2 * p]; 6889 const PetscInt *perm = perms ? perms[p] : NULL; 6890 const PetscScalar *flip = flips ? flips[p] : NULL; 6891 PetscCall(updatePointFieldsBC_private(section, point, perm, flip, f, -1, NULL, add, clperm, values, &offset, array)); 6892 } 6893 break; 6894 default: 6895 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode); 6896 } 6897 PetscCall(PetscSectionRestoreFieldPointSyms(section, f, numPoints, points, &perms, &flips)); 6898 } 6899 } else { 6900 PetscInt dof, off; 6901 const PetscInt **perms = NULL; 6902 const PetscScalar **flips = NULL; 6903 6904 PetscCall(PetscSectionGetPointSyms(section, numPoints, points, &perms, &flips)); 6905 switch (mode) { 6906 case INSERT_VALUES: 6907 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 6908 const PetscInt point = points[2 * p]; 6909 const PetscInt *perm = perms ? perms[p] : NULL; 6910 const PetscScalar *flip = flips ? flips[p] : NULL; 6911 PetscCall(PetscSectionGetDof(section, point, &dof)); 6912 PetscCall(updatePoint_private(section, point, dof, insert, PETSC_FALSE, perm, flip, clperm, values, off, array)); 6913 } 6914 break; 6915 case INSERT_ALL_VALUES: 6916 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 6917 const PetscInt point = points[2 * p]; 6918 const PetscInt *perm = perms ? perms[p] : NULL; 6919 const PetscScalar *flip = flips ? flips[p] : NULL; 6920 PetscCall(PetscSectionGetDof(section, point, &dof)); 6921 PetscCall(updatePoint_private(section, point, dof, insert, PETSC_TRUE, perm, flip, clperm, values, off, array)); 6922 } 6923 break; 6924 case INSERT_BC_VALUES: 6925 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 6926 const PetscInt point = points[2 * p]; 6927 const PetscInt *perm = perms ? perms[p] : NULL; 6928 const PetscScalar *flip = flips ? flips[p] : NULL; 6929 PetscCall(PetscSectionGetDof(section, point, &dof)); 6930 PetscCall(updatePointBC_private(section, point, dof, insert, perm, flip, clperm, values, off, array)); 6931 } 6932 break; 6933 case ADD_VALUES: 6934 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 6935 const PetscInt point = points[2 * p]; 6936 const PetscInt *perm = perms ? perms[p] : NULL; 6937 const PetscScalar *flip = flips ? flips[p] : NULL; 6938 PetscCall(PetscSectionGetDof(section, point, &dof)); 6939 PetscCall(updatePoint_private(section, point, dof, add, PETSC_FALSE, perm, flip, clperm, values, off, array)); 6940 } 6941 break; 6942 case ADD_ALL_VALUES: 6943 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 6944 const PetscInt point = points[2 * p]; 6945 const PetscInt *perm = perms ? perms[p] : NULL; 6946 const PetscScalar *flip = flips ? flips[p] : NULL; 6947 PetscCall(PetscSectionGetDof(section, point, &dof)); 6948 PetscCall(updatePoint_private(section, point, dof, add, PETSC_TRUE, perm, flip, clperm, values, off, array)); 6949 } 6950 break; 6951 case ADD_BC_VALUES: 6952 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 6953 const PetscInt point = points[2 * p]; 6954 const PetscInt *perm = perms ? perms[p] : NULL; 6955 const PetscScalar *flip = flips ? flips[p] : NULL; 6956 PetscCall(PetscSectionGetDof(section, point, &dof)); 6957 PetscCall(updatePointBC_private(section, point, dof, add, perm, flip, clperm, values, off, array)); 6958 } 6959 break; 6960 default: 6961 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode); 6962 } 6963 PetscCall(PetscSectionRestorePointSyms(section, numPoints, points, &perms, &flips)); 6964 } 6965 /* Cleanup points */ 6966 PetscCall(DMPlexRestoreCompressedClosure(dm, section, point, &numPoints, &points, &clSection, &clPoints, &clp)); 6967 /* Cleanup array */ 6968 PetscCall(VecRestoreArray(v, &array)); 6969 PetscFunctionReturn(PETSC_SUCCESS); 6970 } 6971 6972 /* Check whether the given point is in the label. If not, update the offset to skip this point */ 6973 static inline PetscErrorCode CheckPoint_Private(DMLabel label, PetscInt labelId, PetscSection section, PetscInt point, PetscInt f, PetscInt *offset, PetscBool *contains) 6974 { 6975 PetscFunctionBegin; 6976 *contains = PETSC_TRUE; 6977 if (label) { 6978 PetscInt fdof; 6979 6980 PetscCall(DMLabelStratumHasPoint(label, labelId, point, contains)); 6981 if (!*contains) { 6982 PetscCall(PetscSectionGetFieldDof(section, point, f, &fdof)); 6983 *offset += fdof; 6984 PetscFunctionReturn(PETSC_SUCCESS); 6985 } 6986 } 6987 PetscFunctionReturn(PETSC_SUCCESS); 6988 } 6989 6990 /* Unlike DMPlexVecSetClosure(), this uses plex-native closure permutation, not a user-specified permutation such as DMPlexSetClosurePermutationTensor(). */ 6991 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) 6992 { 6993 PetscSection clSection; 6994 IS clPoints; 6995 PetscScalar *array; 6996 PetscInt *points = NULL; 6997 const PetscInt *clp; 6998 PetscInt numFields, numPoints, p; 6999 PetscInt offset = 0, f; 7000 7001 PetscFunctionBeginHot; 7002 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 7003 if (!section) PetscCall(DMGetLocalSection(dm, §ion)); 7004 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 7005 PetscValidHeaderSpecific(v, VEC_CLASSID, 3); 7006 PetscCall(PetscSectionGetNumFields(section, &numFields)); 7007 /* Get points */ 7008 PetscCall(DMPlexGetCompressedClosure(dm, section, point, 0, &numPoints, &points, &clSection, &clPoints, &clp)); 7009 /* Get array */ 7010 PetscCall(VecGetArray(v, &array)); 7011 /* Get values */ 7012 for (f = 0; f < numFields; ++f) { 7013 const PetscInt **perms = NULL; 7014 const PetscScalar **flips = NULL; 7015 PetscBool contains; 7016 7017 if (!fieldActive[f]) { 7018 for (p = 0; p < numPoints * 2; p += 2) { 7019 PetscInt fdof; 7020 PetscCall(PetscSectionGetFieldDof(section, points[p], f, &fdof)); 7021 offset += fdof; 7022 } 7023 continue; 7024 } 7025 PetscCall(PetscSectionGetFieldPointSyms(section, f, numPoints, points, &perms, &flips)); 7026 switch (mode) { 7027 case INSERT_VALUES: 7028 for (p = 0; p < numPoints; p++) { 7029 const PetscInt point = points[2 * p]; 7030 const PetscInt *perm = perms ? perms[p] : NULL; 7031 const PetscScalar *flip = flips ? flips[p] : NULL; 7032 PetscCall(CheckPoint_Private(label, labelId, section, point, f, &offset, &contains)); 7033 if (!contains) continue; 7034 PetscCall(updatePointFields_private(section, point, perm, flip, f, insert, PETSC_FALSE, NULL, values, &offset, array)); 7035 } 7036 break; 7037 case INSERT_ALL_VALUES: 7038 for (p = 0; p < numPoints; p++) { 7039 const PetscInt point = points[2 * p]; 7040 const PetscInt *perm = perms ? perms[p] : NULL; 7041 const PetscScalar *flip = flips ? flips[p] : NULL; 7042 PetscCall(CheckPoint_Private(label, labelId, section, point, f, &offset, &contains)); 7043 if (!contains) continue; 7044 PetscCall(updatePointFields_private(section, point, perm, flip, f, insert, PETSC_TRUE, NULL, values, &offset, array)); 7045 } 7046 break; 7047 case INSERT_BC_VALUES: 7048 for (p = 0; p < numPoints; p++) { 7049 const PetscInt point = points[2 * p]; 7050 const PetscInt *perm = perms ? perms[p] : NULL; 7051 const PetscScalar *flip = flips ? flips[p] : NULL; 7052 PetscCall(CheckPoint_Private(label, labelId, section, point, f, &offset, &contains)); 7053 if (!contains) continue; 7054 PetscCall(updatePointFieldsBC_private(section, point, perm, flip, f, Ncc, comps, insert, NULL, values, &offset, array)); 7055 } 7056 break; 7057 case ADD_VALUES: 7058 for (p = 0; p < numPoints; p++) { 7059 const PetscInt point = points[2 * p]; 7060 const PetscInt *perm = perms ? perms[p] : NULL; 7061 const PetscScalar *flip = flips ? flips[p] : NULL; 7062 PetscCall(CheckPoint_Private(label, labelId, section, point, f, &offset, &contains)); 7063 if (!contains) continue; 7064 PetscCall(updatePointFields_private(section, point, perm, flip, f, add, PETSC_FALSE, NULL, values, &offset, array)); 7065 } 7066 break; 7067 case ADD_ALL_VALUES: 7068 for (p = 0; p < numPoints; p++) { 7069 const PetscInt point = points[2 * p]; 7070 const PetscInt *perm = perms ? perms[p] : NULL; 7071 const PetscScalar *flip = flips ? flips[p] : NULL; 7072 PetscCall(CheckPoint_Private(label, labelId, section, point, f, &offset, &contains)); 7073 if (!contains) continue; 7074 PetscCall(updatePointFields_private(section, point, perm, flip, f, add, PETSC_TRUE, NULL, values, &offset, array)); 7075 } 7076 break; 7077 default: 7078 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode); 7079 } 7080 PetscCall(PetscSectionRestoreFieldPointSyms(section, f, numPoints, points, &perms, &flips)); 7081 } 7082 /* Cleanup points */ 7083 PetscCall(DMPlexRestoreCompressedClosure(dm, section, point, &numPoints, &points, &clSection, &clPoints, &clp)); 7084 /* Cleanup array */ 7085 PetscCall(VecRestoreArray(v, &array)); 7086 PetscFunctionReturn(PETSC_SUCCESS); 7087 } 7088 7089 static PetscErrorCode DMPlexPrintMatSetValues(PetscViewer viewer, Mat A, PetscInt point, PetscInt numRIndices, const PetscInt rindices[], PetscInt numCIndices, const PetscInt cindices[], const PetscScalar values[]) 7090 { 7091 PetscMPIInt rank; 7092 PetscInt i, j; 7093 7094 PetscFunctionBegin; 7095 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank)); 7096 PetscCall(PetscViewerASCIIPrintf(viewer, "[%d]mat for point %" PetscInt_FMT "\n", rank, point)); 7097 for (i = 0; i < numRIndices; i++) PetscCall(PetscViewerASCIIPrintf(viewer, "[%d]mat row indices[%" PetscInt_FMT "] = %" PetscInt_FMT "\n", rank, i, rindices[i])); 7098 for (i = 0; i < numCIndices; i++) PetscCall(PetscViewerASCIIPrintf(viewer, "[%d]mat col indices[%" PetscInt_FMT "] = %" PetscInt_FMT "\n", rank, i, cindices[i])); 7099 numCIndices = numCIndices ? numCIndices : numRIndices; 7100 if (!values) PetscFunctionReturn(PETSC_SUCCESS); 7101 for (i = 0; i < numRIndices; i++) { 7102 PetscCall(PetscViewerASCIIPrintf(viewer, "[%d]", rank)); 7103 for (j = 0; j < numCIndices; j++) { 7104 #if defined(PETSC_USE_COMPLEX) 7105 PetscCall(PetscViewerASCIIPrintf(viewer, " (%g,%g)", (double)PetscRealPart(values[i * numCIndices + j]), (double)PetscImaginaryPart(values[i * numCIndices + j]))); 7106 #else 7107 PetscCall(PetscViewerASCIIPrintf(viewer, " %g", (double)values[i * numCIndices + j])); 7108 #endif 7109 } 7110 PetscCall(PetscViewerASCIIPrintf(viewer, "\n")); 7111 } 7112 PetscFunctionReturn(PETSC_SUCCESS); 7113 } 7114 7115 /* 7116 DMPlexGetIndicesPoint_Internal - Add the indices for dofs on a point to an index array 7117 7118 Input Parameters: 7119 + section - The section for this data layout 7120 . islocal - Is the section (and thus indices being requested) local or global? 7121 . point - The point contributing dofs with these indices 7122 . off - The global offset of this point 7123 . loff - The local offset of each field 7124 . setBC - The flag determining whether to include indices of boundary values 7125 . perm - A permutation of the dofs on this point, or NULL 7126 - indperm - A permutation of the entire indices array, or NULL 7127 7128 Output Parameter: 7129 . indices - Indices for dofs on this point 7130 7131 Level: developer 7132 7133 Note: The indices could be local or global, depending on the value of 'off'. 7134 */ 7135 PetscErrorCode DMPlexGetIndicesPoint_Internal(PetscSection section, PetscBool islocal, PetscInt point, PetscInt off, PetscInt *loff, PetscBool setBC, const PetscInt perm[], const PetscInt indperm[], PetscInt indices[]) 7136 { 7137 PetscInt dof; /* The number of unknowns on this point */ 7138 PetscInt cdof; /* The number of constraints on this point */ 7139 const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ 7140 PetscInt cind = 0, k; 7141 7142 PetscFunctionBegin; 7143 PetscCheck(islocal || !setBC, PetscObjectComm((PetscObject)section), PETSC_ERR_ARG_INCOMP, "setBC incompatible with global indices; use a local section or disable setBC"); 7144 PetscCall(PetscSectionGetDof(section, point, &dof)); 7145 PetscCall(PetscSectionGetConstraintDof(section, point, &cdof)); 7146 if (!cdof || setBC) { 7147 for (k = 0; k < dof; ++k) { 7148 const PetscInt preind = perm ? *loff + perm[k] : *loff + k; 7149 const PetscInt ind = indperm ? indperm[preind] : preind; 7150 7151 indices[ind] = off + k; 7152 } 7153 } else { 7154 PetscCall(PetscSectionGetConstraintIndices(section, point, &cdofs)); 7155 for (k = 0; k < dof; ++k) { 7156 const PetscInt preind = perm ? *loff + perm[k] : *loff + k; 7157 const PetscInt ind = indperm ? indperm[preind] : preind; 7158 7159 if ((cind < cdof) && (k == cdofs[cind])) { 7160 /* Insert check for returning constrained indices */ 7161 indices[ind] = -(off + k + 1); 7162 ++cind; 7163 } else { 7164 indices[ind] = off + k - (islocal ? 0 : cind); 7165 } 7166 } 7167 } 7168 *loff += dof; 7169 PetscFunctionReturn(PETSC_SUCCESS); 7170 } 7171 7172 /* 7173 DMPlexGetIndicesPointFields_Internal - gets section indices for a point in its canonical ordering. 7174 7175 Input Parameters: 7176 + section - a section (global or local) 7177 - islocal - `PETSC_TRUE` if requesting local indices (i.e., section is local); `PETSC_FALSE` for global 7178 . point - point within section 7179 . off - The offset of this point in the (local or global) indexed space - should match islocal and (usually) the section 7180 . foffs - array of length numFields containing the offset in canonical point ordering (the location in indices) of each field 7181 . setBC - identify constrained (boundary condition) points via involution. 7182 . perms - perms[f][permsoff][:] is a permutation of dofs within each field 7183 . permsoff - offset 7184 - indperm - index permutation 7185 7186 Output Parameter: 7187 . foffs - each entry is incremented by the number of (unconstrained if setBC=FALSE) dofs in that field 7188 . indices - array to hold indices (as defined by section) of each dof associated with point 7189 7190 Notes: 7191 If section is local and setBC=true, there is no distinction between constrained and unconstrained dofs. 7192 If section is local and setBC=false, the indices for constrained points are the involution -(i+1) of their position 7193 in the local vector. 7194 7195 If section is global and setBC=false, the indices for constrained points are negative (and their value is not 7196 significant). It is invalid to call with a global section and setBC=true. 7197 7198 Developer Note: 7199 The section is only used for field layout, so islocal is technically a statement about the offset (off). At some point 7200 in the future, global sections may have fields set, in which case we could pass the global section and obtain the 7201 offset could be obtained from the section instead of passing it explicitly as we do now. 7202 7203 Example: 7204 Suppose a point contains one field with three components, and for which the unconstrained indices are {10, 11, 12}. 7205 When the middle component is constrained, we get the array {10, -12, 12} for (islocal=TRUE, setBC=FALSE). 7206 Note that -12 is the involution of 11, so the user can involute negative indices to recover local indices. 7207 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. 7208 7209 Level: developer 7210 */ 7211 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[]) 7212 { 7213 PetscInt numFields, foff, f; 7214 7215 PetscFunctionBegin; 7216 PetscCheck(islocal || !setBC, PetscObjectComm((PetscObject)section), PETSC_ERR_ARG_INCOMP, "setBC incompatible with global indices; use a local section or disable setBC"); 7217 PetscCall(PetscSectionGetNumFields(section, &numFields)); 7218 for (f = 0, foff = 0; f < numFields; ++f) { 7219 PetscInt fdof, cfdof; 7220 const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ 7221 PetscInt cind = 0, b; 7222 const PetscInt *perm = (perms && perms[f]) ? perms[f][permsoff] : NULL; 7223 7224 PetscCall(PetscSectionGetFieldDof(section, point, f, &fdof)); 7225 PetscCall(PetscSectionGetFieldConstraintDof(section, point, f, &cfdof)); 7226 if (!cfdof || setBC) { 7227 for (b = 0; b < fdof; ++b) { 7228 const PetscInt preind = perm ? foffs[f] + perm[b] : foffs[f] + b; 7229 const PetscInt ind = indperm ? indperm[preind] : preind; 7230 7231 indices[ind] = off + foff + b; 7232 } 7233 } else { 7234 PetscCall(PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs)); 7235 for (b = 0; b < fdof; ++b) { 7236 const PetscInt preind = perm ? foffs[f] + perm[b] : foffs[f] + b; 7237 const PetscInt ind = indperm ? indperm[preind] : preind; 7238 7239 if ((cind < cfdof) && (b == fcdofs[cind])) { 7240 indices[ind] = -(off + foff + b + 1); 7241 ++cind; 7242 } else { 7243 indices[ind] = off + foff + b - (islocal ? 0 : cind); 7244 } 7245 } 7246 } 7247 foff += (setBC || islocal ? fdof : (fdof - cfdof)); 7248 foffs[f] += fdof; 7249 } 7250 PetscFunctionReturn(PETSC_SUCCESS); 7251 } 7252 7253 /* 7254 This version believes the globalSection offsets for each field, rather than just the point offset 7255 7256 . foffs - The offset into 'indices' for each field, since it is segregated by field 7257 7258 Notes: 7259 The semantics of this function relate to that of setBC=FALSE in DMPlexGetIndicesPointFields_Internal. 7260 Since this function uses global indices, setBC=TRUE would be invalid, so no such argument exists. 7261 */ 7262 static PetscErrorCode DMPlexGetIndicesPointFieldsSplit_Internal(PetscSection section, PetscSection globalSection, PetscInt point, PetscInt foffs[], const PetscInt ***perms, PetscInt permsoff, const PetscInt indperm[], PetscInt indices[]) 7263 { 7264 PetscInt numFields, foff, f; 7265 7266 PetscFunctionBegin; 7267 PetscCall(PetscSectionGetNumFields(section, &numFields)); 7268 for (f = 0; f < numFields; ++f) { 7269 PetscInt fdof, cfdof; 7270 const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ 7271 PetscInt cind = 0, b; 7272 const PetscInt *perm = (perms && perms[f]) ? perms[f][permsoff] : NULL; 7273 7274 PetscCall(PetscSectionGetFieldDof(section, point, f, &fdof)); 7275 PetscCall(PetscSectionGetFieldConstraintDof(section, point, f, &cfdof)); 7276 PetscCall(PetscSectionGetFieldOffset(globalSection, point, f, &foff)); 7277 if (!cfdof) { 7278 for (b = 0; b < fdof; ++b) { 7279 const PetscInt preind = perm ? foffs[f] + perm[b] : foffs[f] + b; 7280 const PetscInt ind = indperm ? indperm[preind] : preind; 7281 7282 indices[ind] = foff + b; 7283 } 7284 } else { 7285 PetscCall(PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs)); 7286 for (b = 0; b < fdof; ++b) { 7287 const PetscInt preind = perm ? foffs[f] + perm[b] : foffs[f] + b; 7288 const PetscInt ind = indperm ? indperm[preind] : preind; 7289 7290 if ((cind < cfdof) && (b == fcdofs[cind])) { 7291 indices[ind] = -(foff + b + 1); 7292 ++cind; 7293 } else { 7294 indices[ind] = foff + b - cind; 7295 } 7296 } 7297 } 7298 foffs[f] += fdof; 7299 } 7300 PetscFunctionReturn(PETSC_SUCCESS); 7301 } 7302 7303 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) 7304 { 7305 Mat cMat; 7306 PetscSection aSec, cSec; 7307 IS aIS; 7308 PetscInt aStart = -1, aEnd = -1; 7309 const PetscInt *anchors; 7310 PetscInt numFields, f, p, q, newP = 0; 7311 PetscInt newNumPoints = 0, newNumIndices = 0; 7312 PetscInt *newPoints, *indices, *newIndices; 7313 PetscInt maxAnchor, maxDof; 7314 PetscInt newOffsets[32]; 7315 PetscInt *pointMatOffsets[32]; 7316 PetscInt *newPointOffsets[32]; 7317 PetscScalar *pointMat[32]; 7318 PetscScalar *newValues = NULL, *tmpValues; 7319 PetscBool anyConstrained = PETSC_FALSE; 7320 7321 PetscFunctionBegin; 7322 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 7323 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 7324 PetscCall(PetscSectionGetNumFields(section, &numFields)); 7325 7326 PetscCall(DMPlexGetAnchors(dm, &aSec, &aIS)); 7327 /* if there are point-to-point constraints */ 7328 if (aSec) { 7329 PetscCall(PetscArrayzero(newOffsets, 32)); 7330 PetscCall(ISGetIndices(aIS, &anchors)); 7331 PetscCall(PetscSectionGetChart(aSec, &aStart, &aEnd)); 7332 /* figure out how many points are going to be in the new element matrix 7333 * (we allow double counting, because it's all just going to be summed 7334 * into the global matrix anyway) */ 7335 for (p = 0; p < 2 * numPoints; p += 2) { 7336 PetscInt b = points[p]; 7337 PetscInt bDof = 0, bSecDof; 7338 7339 PetscCall(PetscSectionGetDof(section, b, &bSecDof)); 7340 if (!bSecDof) continue; 7341 if (b >= aStart && b < aEnd) PetscCall(PetscSectionGetDof(aSec, b, &bDof)); 7342 if (bDof) { 7343 /* this point is constrained */ 7344 /* it is going to be replaced by its anchors */ 7345 PetscInt bOff, q; 7346 7347 anyConstrained = PETSC_TRUE; 7348 newNumPoints += bDof; 7349 PetscCall(PetscSectionGetOffset(aSec, b, &bOff)); 7350 for (q = 0; q < bDof; q++) { 7351 PetscInt a = anchors[bOff + q]; 7352 PetscInt aDof; 7353 7354 PetscCall(PetscSectionGetDof(section, a, &aDof)); 7355 newNumIndices += aDof; 7356 for (f = 0; f < numFields; ++f) { 7357 PetscInt fDof; 7358 7359 PetscCall(PetscSectionGetFieldDof(section, a, f, &fDof)); 7360 newOffsets[f + 1] += fDof; 7361 } 7362 } 7363 } else { 7364 /* this point is not constrained */ 7365 newNumPoints++; 7366 newNumIndices += bSecDof; 7367 for (f = 0; f < numFields; ++f) { 7368 PetscInt fDof; 7369 7370 PetscCall(PetscSectionGetFieldDof(section, b, f, &fDof)); 7371 newOffsets[f + 1] += fDof; 7372 } 7373 } 7374 } 7375 } 7376 if (!anyConstrained) { 7377 if (outNumPoints) *outNumPoints = 0; 7378 if (outNumIndices) *outNumIndices = 0; 7379 if (outPoints) *outPoints = NULL; 7380 if (outValues) *outValues = NULL; 7381 if (aSec) PetscCall(ISRestoreIndices(aIS, &anchors)); 7382 PetscFunctionReturn(PETSC_SUCCESS); 7383 } 7384 7385 if (outNumPoints) *outNumPoints = newNumPoints; 7386 if (outNumIndices) *outNumIndices = newNumIndices; 7387 7388 for (f = 0; f < numFields; ++f) newOffsets[f + 1] += newOffsets[f]; 7389 7390 if (!outPoints && !outValues) { 7391 if (offsets) { 7392 for (f = 0; f <= numFields; f++) offsets[f] = newOffsets[f]; 7393 } 7394 if (aSec) PetscCall(ISRestoreIndices(aIS, &anchors)); 7395 PetscFunctionReturn(PETSC_SUCCESS); 7396 } 7397 7398 PetscCheck(!numFields || newOffsets[numFields] == newNumIndices, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid size for closure %" PetscInt_FMT " should be %" PetscInt_FMT, newOffsets[numFields], newNumIndices); 7399 7400 PetscCall(DMGetDefaultConstraints(dm, &cSec, &cMat, NULL)); 7401 7402 /* workspaces */ 7403 if (numFields) { 7404 for (f = 0; f < numFields; f++) { 7405 PetscCall(DMGetWorkArray(dm, numPoints + 1, MPIU_INT, &pointMatOffsets[f])); 7406 PetscCall(DMGetWorkArray(dm, numPoints + 1, MPIU_INT, &newPointOffsets[f])); 7407 } 7408 } else { 7409 PetscCall(DMGetWorkArray(dm, numPoints + 1, MPIU_INT, &pointMatOffsets[0])); 7410 PetscCall(DMGetWorkArray(dm, numPoints, MPIU_INT, &newPointOffsets[0])); 7411 } 7412 7413 /* get workspaces for the point-to-point matrices */ 7414 if (numFields) { 7415 PetscInt totalOffset, totalMatOffset; 7416 7417 for (p = 0; p < numPoints; p++) { 7418 PetscInt b = points[2 * p]; 7419 PetscInt bDof = 0, bSecDof; 7420 7421 PetscCall(PetscSectionGetDof(section, b, &bSecDof)); 7422 if (!bSecDof) { 7423 for (f = 0; f < numFields; f++) { 7424 newPointOffsets[f][p + 1] = 0; 7425 pointMatOffsets[f][p + 1] = 0; 7426 } 7427 continue; 7428 } 7429 if (b >= aStart && b < aEnd) PetscCall(PetscSectionGetDof(aSec, b, &bDof)); 7430 if (bDof) { 7431 for (f = 0; f < numFields; f++) { 7432 PetscInt fDof, q, bOff, allFDof = 0; 7433 7434 PetscCall(PetscSectionGetFieldDof(section, b, f, &fDof)); 7435 PetscCall(PetscSectionGetOffset(aSec, b, &bOff)); 7436 for (q = 0; q < bDof; q++) { 7437 PetscInt a = anchors[bOff + q]; 7438 PetscInt aFDof; 7439 7440 PetscCall(PetscSectionGetFieldDof(section, a, f, &aFDof)); 7441 allFDof += aFDof; 7442 } 7443 newPointOffsets[f][p + 1] = allFDof; 7444 pointMatOffsets[f][p + 1] = fDof * allFDof; 7445 } 7446 } else { 7447 for (f = 0; f < numFields; f++) { 7448 PetscInt fDof; 7449 7450 PetscCall(PetscSectionGetFieldDof(section, b, f, &fDof)); 7451 newPointOffsets[f][p + 1] = fDof; 7452 pointMatOffsets[f][p + 1] = 0; 7453 } 7454 } 7455 } 7456 for (f = 0, totalOffset = 0, totalMatOffset = 0; f < numFields; f++) { 7457 newPointOffsets[f][0] = totalOffset; 7458 pointMatOffsets[f][0] = totalMatOffset; 7459 for (p = 0; p < numPoints; p++) { 7460 newPointOffsets[f][p + 1] += newPointOffsets[f][p]; 7461 pointMatOffsets[f][p + 1] += pointMatOffsets[f][p]; 7462 } 7463 totalOffset = newPointOffsets[f][numPoints]; 7464 totalMatOffset = pointMatOffsets[f][numPoints]; 7465 PetscCall(DMGetWorkArray(dm, pointMatOffsets[f][numPoints], MPIU_SCALAR, &pointMat[f])); 7466 } 7467 } else { 7468 for (p = 0; p < numPoints; p++) { 7469 PetscInt b = points[2 * p]; 7470 PetscInt bDof = 0, bSecDof; 7471 7472 PetscCall(PetscSectionGetDof(section, b, &bSecDof)); 7473 if (!bSecDof) { 7474 newPointOffsets[0][p + 1] = 0; 7475 pointMatOffsets[0][p + 1] = 0; 7476 continue; 7477 } 7478 if (b >= aStart && b < aEnd) PetscCall(PetscSectionGetDof(aSec, b, &bDof)); 7479 if (bDof) { 7480 PetscInt bOff, q, allDof = 0; 7481 7482 PetscCall(PetscSectionGetOffset(aSec, b, &bOff)); 7483 for (q = 0; q < bDof; q++) { 7484 PetscInt a = anchors[bOff + q], aDof; 7485 7486 PetscCall(PetscSectionGetDof(section, a, &aDof)); 7487 allDof += aDof; 7488 } 7489 newPointOffsets[0][p + 1] = allDof; 7490 pointMatOffsets[0][p + 1] = bSecDof * allDof; 7491 } else { 7492 newPointOffsets[0][p + 1] = bSecDof; 7493 pointMatOffsets[0][p + 1] = 0; 7494 } 7495 } 7496 newPointOffsets[0][0] = 0; 7497 pointMatOffsets[0][0] = 0; 7498 for (p = 0; p < numPoints; p++) { 7499 newPointOffsets[0][p + 1] += newPointOffsets[0][p]; 7500 pointMatOffsets[0][p + 1] += pointMatOffsets[0][p]; 7501 } 7502 PetscCall(DMGetWorkArray(dm, pointMatOffsets[0][numPoints], MPIU_SCALAR, &pointMat[0])); 7503 } 7504 7505 /* output arrays */ 7506 PetscCall(DMGetWorkArray(dm, 2 * newNumPoints, MPIU_INT, &newPoints)); 7507 7508 /* get the point-to-point matrices; construct newPoints */ 7509 PetscCall(PetscSectionGetMaxDof(aSec, &maxAnchor)); 7510 PetscCall(PetscSectionGetMaxDof(section, &maxDof)); 7511 PetscCall(DMGetWorkArray(dm, maxDof, MPIU_INT, &indices)); 7512 PetscCall(DMGetWorkArray(dm, maxAnchor * maxDof, MPIU_INT, &newIndices)); 7513 if (numFields) { 7514 for (p = 0, newP = 0; p < numPoints; p++) { 7515 PetscInt b = points[2 * p]; 7516 PetscInt o = points[2 * p + 1]; 7517 PetscInt bDof = 0, bSecDof; 7518 7519 PetscCall(PetscSectionGetDof(section, b, &bSecDof)); 7520 if (!bSecDof) continue; 7521 if (b >= aStart && b < aEnd) PetscCall(PetscSectionGetDof(aSec, b, &bDof)); 7522 if (bDof) { 7523 PetscInt fStart[32], fEnd[32], fAnchorStart[32], fAnchorEnd[32], bOff, q; 7524 7525 fStart[0] = 0; 7526 fEnd[0] = 0; 7527 for (f = 0; f < numFields; f++) { 7528 PetscInt fDof; 7529 7530 PetscCall(PetscSectionGetFieldDof(cSec, b, f, &fDof)); 7531 fStart[f + 1] = fStart[f] + fDof; 7532 fEnd[f + 1] = fStart[f + 1]; 7533 } 7534 PetscCall(PetscSectionGetOffset(cSec, b, &bOff)); 7535 PetscCall(DMPlexGetIndicesPointFields_Internal(cSec, PETSC_TRUE, b, bOff, fEnd, PETSC_TRUE, perms, p, NULL, indices)); 7536 7537 fAnchorStart[0] = 0; 7538 fAnchorEnd[0] = 0; 7539 for (f = 0; f < numFields; f++) { 7540 PetscInt fDof = newPointOffsets[f][p + 1] - newPointOffsets[f][p]; 7541 7542 fAnchorStart[f + 1] = fAnchorStart[f] + fDof; 7543 fAnchorEnd[f + 1] = fAnchorStart[f + 1]; 7544 } 7545 PetscCall(PetscSectionGetOffset(aSec, b, &bOff)); 7546 for (q = 0; q < bDof; q++) { 7547 PetscInt a = anchors[bOff + q], aOff; 7548 7549 /* we take the orientation of ap into account in the order that we constructed the indices above: the newly added points have no orientation */ 7550 newPoints[2 * (newP + q)] = a; 7551 newPoints[2 * (newP + q) + 1] = 0; 7552 PetscCall(PetscSectionGetOffset(section, a, &aOff)); 7553 PetscCall(DMPlexGetIndicesPointFields_Internal(section, PETSC_TRUE, a, aOff, fAnchorEnd, PETSC_TRUE, NULL, -1, NULL, newIndices)); 7554 } 7555 newP += bDof; 7556 7557 if (outValues) { 7558 /* get the point-to-point submatrix */ 7559 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])); 7560 } 7561 } else { 7562 newPoints[2 * newP] = b; 7563 newPoints[2 * newP + 1] = o; 7564 newP++; 7565 } 7566 } 7567 } else { 7568 for (p = 0; p < numPoints; p++) { 7569 PetscInt b = points[2 * p]; 7570 PetscInt o = points[2 * p + 1]; 7571 PetscInt bDof = 0, bSecDof; 7572 7573 PetscCall(PetscSectionGetDof(section, b, &bSecDof)); 7574 if (!bSecDof) continue; 7575 if (b >= aStart && b < aEnd) PetscCall(PetscSectionGetDof(aSec, b, &bDof)); 7576 if (bDof) { 7577 PetscInt bEnd = 0, bAnchorEnd = 0, bOff; 7578 7579 PetscCall(PetscSectionGetOffset(cSec, b, &bOff)); 7580 PetscCall(DMPlexGetIndicesPoint_Internal(cSec, PETSC_TRUE, b, bOff, &bEnd, PETSC_TRUE, (perms && perms[0]) ? perms[0][p] : NULL, NULL, indices)); 7581 7582 PetscCall(PetscSectionGetOffset(aSec, b, &bOff)); 7583 for (q = 0; q < bDof; q++) { 7584 PetscInt a = anchors[bOff + q], aOff; 7585 7586 /* we take the orientation of ap into account in the order that we constructed the indices above: the newly added points have no orientation */ 7587 7588 newPoints[2 * (newP + q)] = a; 7589 newPoints[2 * (newP + q) + 1] = 0; 7590 PetscCall(PetscSectionGetOffset(section, a, &aOff)); 7591 PetscCall(DMPlexGetIndicesPoint_Internal(section, PETSC_TRUE, a, aOff, &bAnchorEnd, PETSC_TRUE, NULL, NULL, newIndices)); 7592 } 7593 newP += bDof; 7594 7595 /* get the point-to-point submatrix */ 7596 if (outValues) PetscCall(MatGetValues(cMat, bEnd, indices, bAnchorEnd, newIndices, pointMat[0] + pointMatOffsets[0][p])); 7597 } else { 7598 newPoints[2 * newP] = b; 7599 newPoints[2 * newP + 1] = o; 7600 newP++; 7601 } 7602 } 7603 } 7604 7605 if (outValues) { 7606 PetscCall(DMGetWorkArray(dm, newNumIndices * numIndices, MPIU_SCALAR, &tmpValues)); 7607 PetscCall(PetscArrayzero(tmpValues, newNumIndices * numIndices)); 7608 /* multiply constraints on the right */ 7609 if (numFields) { 7610 for (f = 0; f < numFields; f++) { 7611 PetscInt oldOff = offsets[f]; 7612 7613 for (p = 0; p < numPoints; p++) { 7614 PetscInt cStart = newPointOffsets[f][p]; 7615 PetscInt b = points[2 * p]; 7616 PetscInt c, r, k; 7617 PetscInt dof; 7618 7619 PetscCall(PetscSectionGetFieldDof(section, b, f, &dof)); 7620 if (!dof) continue; 7621 if (pointMatOffsets[f][p] < pointMatOffsets[f][p + 1]) { 7622 PetscInt nCols = newPointOffsets[f][p + 1] - cStart; 7623 const PetscScalar *mat = pointMat[f] + pointMatOffsets[f][p]; 7624 7625 for (r = 0; r < numIndices; r++) { 7626 for (c = 0; c < nCols; c++) { 7627 for (k = 0; k < dof; k++) tmpValues[r * newNumIndices + cStart + c] += values[r * numIndices + oldOff + k] * mat[k * nCols + c]; 7628 } 7629 } 7630 } else { 7631 /* copy this column as is */ 7632 for (r = 0; r < numIndices; r++) { 7633 for (c = 0; c < dof; c++) tmpValues[r * newNumIndices + cStart + c] = values[r * numIndices + oldOff + c]; 7634 } 7635 } 7636 oldOff += dof; 7637 } 7638 } 7639 } else { 7640 PetscInt oldOff = 0; 7641 for (p = 0; p < numPoints; p++) { 7642 PetscInt cStart = newPointOffsets[0][p]; 7643 PetscInt b = points[2 * p]; 7644 PetscInt c, r, k; 7645 PetscInt dof; 7646 7647 PetscCall(PetscSectionGetDof(section, b, &dof)); 7648 if (!dof) continue; 7649 if (pointMatOffsets[0][p] < pointMatOffsets[0][p + 1]) { 7650 PetscInt nCols = newPointOffsets[0][p + 1] - cStart; 7651 const PetscScalar *mat = pointMat[0] + pointMatOffsets[0][p]; 7652 7653 for (r = 0; r < numIndices; r++) { 7654 for (c = 0; c < nCols; c++) { 7655 for (k = 0; k < dof; k++) tmpValues[r * newNumIndices + cStart + c] += mat[k * nCols + c] * values[r * numIndices + oldOff + k]; 7656 } 7657 } 7658 } else { 7659 /* copy this column as is */ 7660 for (r = 0; r < numIndices; r++) { 7661 for (c = 0; c < dof; c++) tmpValues[r * newNumIndices + cStart + c] = values[r * numIndices + oldOff + c]; 7662 } 7663 } 7664 oldOff += dof; 7665 } 7666 } 7667 7668 if (multiplyLeft) { 7669 PetscCall(DMGetWorkArray(dm, newNumIndices * newNumIndices, MPIU_SCALAR, &newValues)); 7670 PetscCall(PetscArrayzero(newValues, newNumIndices * newNumIndices)); 7671 /* multiply constraints transpose on the left */ 7672 if (numFields) { 7673 for (f = 0; f < numFields; f++) { 7674 PetscInt oldOff = offsets[f]; 7675 7676 for (p = 0; p < numPoints; p++) { 7677 PetscInt rStart = newPointOffsets[f][p]; 7678 PetscInt b = points[2 * p]; 7679 PetscInt c, r, k; 7680 PetscInt dof; 7681 7682 PetscCall(PetscSectionGetFieldDof(section, b, f, &dof)); 7683 if (pointMatOffsets[f][p] < pointMatOffsets[f][p + 1]) { 7684 PetscInt nRows = newPointOffsets[f][p + 1] - rStart; 7685 const PetscScalar *PETSC_RESTRICT mat = pointMat[f] + pointMatOffsets[f][p]; 7686 7687 for (r = 0; r < nRows; r++) { 7688 for (c = 0; c < newNumIndices; c++) { 7689 for (k = 0; k < dof; k++) newValues[(rStart + r) * newNumIndices + c] += mat[k * nRows + r] * tmpValues[(oldOff + k) * newNumIndices + c]; 7690 } 7691 } 7692 } else { 7693 /* copy this row as is */ 7694 for (r = 0; r < dof; r++) { 7695 for (c = 0; c < newNumIndices; c++) newValues[(rStart + r) * newNumIndices + c] = tmpValues[(oldOff + r) * newNumIndices + c]; 7696 } 7697 } 7698 oldOff += dof; 7699 } 7700 } 7701 } else { 7702 PetscInt oldOff = 0; 7703 7704 for (p = 0; p < numPoints; p++) { 7705 PetscInt rStart = newPointOffsets[0][p]; 7706 PetscInt b = points[2 * p]; 7707 PetscInt c, r, k; 7708 PetscInt dof; 7709 7710 PetscCall(PetscSectionGetDof(section, b, &dof)); 7711 if (pointMatOffsets[0][p] < pointMatOffsets[0][p + 1]) { 7712 PetscInt nRows = newPointOffsets[0][p + 1] - rStart; 7713 const PetscScalar *PETSC_RESTRICT mat = pointMat[0] + pointMatOffsets[0][p]; 7714 7715 for (r = 0; r < nRows; r++) { 7716 for (c = 0; c < newNumIndices; c++) { 7717 for (k = 0; k < dof; k++) newValues[(rStart + r) * newNumIndices + c] += mat[k * nRows + r] * tmpValues[(oldOff + k) * newNumIndices + c]; 7718 } 7719 } 7720 } else { 7721 /* copy this row as is */ 7722 for (r = 0; r < dof; r++) { 7723 for (c = 0; c < newNumIndices; c++) newValues[(rStart + r) * newNumIndices + c] = tmpValues[(oldOff + r) * newNumIndices + c]; 7724 } 7725 } 7726 oldOff += dof; 7727 } 7728 } 7729 7730 PetscCall(DMRestoreWorkArray(dm, newNumIndices * numIndices, MPIU_SCALAR, &tmpValues)); 7731 } else { 7732 newValues = tmpValues; 7733 } 7734 } 7735 7736 /* clean up */ 7737 PetscCall(DMRestoreWorkArray(dm, maxDof, MPIU_INT, &indices)); 7738 PetscCall(DMRestoreWorkArray(dm, maxAnchor * maxDof, MPIU_INT, &newIndices)); 7739 7740 if (numFields) { 7741 for (f = 0; f < numFields; f++) { 7742 PetscCall(DMRestoreWorkArray(dm, pointMatOffsets[f][numPoints], MPIU_SCALAR, &pointMat[f])); 7743 PetscCall(DMRestoreWorkArray(dm, numPoints + 1, MPIU_INT, &pointMatOffsets[f])); 7744 PetscCall(DMRestoreWorkArray(dm, numPoints + 1, MPIU_INT, &newPointOffsets[f])); 7745 } 7746 } else { 7747 PetscCall(DMRestoreWorkArray(dm, pointMatOffsets[0][numPoints], MPIU_SCALAR, &pointMat[0])); 7748 PetscCall(DMRestoreWorkArray(dm, numPoints + 1, MPIU_INT, &pointMatOffsets[0])); 7749 PetscCall(DMRestoreWorkArray(dm, numPoints + 1, MPIU_INT, &newPointOffsets[0])); 7750 } 7751 PetscCall(ISRestoreIndices(aIS, &anchors)); 7752 7753 /* output */ 7754 if (outPoints) { 7755 *outPoints = newPoints; 7756 } else { 7757 PetscCall(DMRestoreWorkArray(dm, 2 * newNumPoints, MPIU_INT, &newPoints)); 7758 } 7759 if (outValues) *outValues = newValues; 7760 for (f = 0; f <= numFields; f++) offsets[f] = newOffsets[f]; 7761 PetscFunctionReturn(PETSC_SUCCESS); 7762 } 7763 7764 /*@C 7765 DMPlexGetClosureIndices - Gets the global dof indices associated with the closure of the given point within the provided sections. 7766 7767 Not collective 7768 7769 Input Parameters: 7770 + dm - The `DM` 7771 . section - The `PetscSection` describing the points (a local section) 7772 . idxSection - The `PetscSection` from which to obtain indices (may be local or global) 7773 . point - The point defining the closure 7774 - useClPerm - Use the closure point permutation if available 7775 7776 Output Parameters: 7777 + numIndices - The number of dof indices in the closure of point with the input sections 7778 . indices - The dof indices 7779 . outOffsets - Array to write the field offsets into, or `NULL` 7780 - values - The input values, which may be modified if sign flips are induced by the point symmetries, or `NULL` 7781 7782 Level: advanced 7783 7784 Notes: 7785 Must call `DMPlexRestoreClosureIndices()` to free allocated memory 7786 7787 If `idxSection` is global, any constrained dofs (see `DMAddBoundary()`, for example) will get negative indices. The value 7788 of those indices is not significant. If `idxSection` is local, the constrained dofs will yield the involution -(idx+1) 7789 of their index in a local vector. A caller who does not wish to distinguish those points may recover the nonnegative 7790 indices via involution, -(-(idx+1)+1)==idx. Local indices are provided when `idxSection` == section, otherwise global 7791 indices (with the above semantics) are implied. 7792 7793 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexRestoreClosureIndices()`, `DMPlexVecGetClosure()`, `DMPlexMatSetClosure()`, `DMGetLocalSection()`, 7794 `PetscSection`, `DMGetGlobalSection()` 7795 @*/ 7796 PetscErrorCode DMPlexGetClosureIndices(DM dm, PetscSection section, PetscSection idxSection, PetscInt point, PetscBool useClPerm, PetscInt *numIndices, PetscInt *indices[], PetscInt outOffsets[], PetscScalar *values[]) 7797 { 7798 /* Closure ordering */ 7799 PetscSection clSection; 7800 IS clPoints; 7801 const PetscInt *clp; 7802 PetscInt *points; 7803 const PetscInt *clperm = NULL; 7804 /* Dof permutation and sign flips */ 7805 const PetscInt **perms[32] = {NULL}; 7806 const PetscScalar **flips[32] = {NULL}; 7807 PetscScalar *valCopy = NULL; 7808 /* Hanging node constraints */ 7809 PetscInt *pointsC = NULL; 7810 PetscScalar *valuesC = NULL; 7811 PetscInt NclC, NiC; 7812 7813 PetscInt *idx; 7814 PetscInt Nf, Ncl, Ni = 0, offsets[32], p, f; 7815 PetscBool isLocal = (section == idxSection) ? PETSC_TRUE : PETSC_FALSE; 7816 7817 PetscFunctionBeginHot; 7818 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 7819 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 7820 PetscValidHeaderSpecific(idxSection, PETSC_SECTION_CLASSID, 3); 7821 if (numIndices) PetscAssertPointer(numIndices, 6); 7822 if (indices) PetscAssertPointer(indices, 7); 7823 if (outOffsets) PetscAssertPointer(outOffsets, 8); 7824 if (values) PetscAssertPointer(values, 9); 7825 PetscCall(PetscSectionGetNumFields(section, &Nf)); 7826 PetscCheck(Nf <= 31, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %" PetscInt_FMT " limited to 31", Nf); 7827 PetscCall(PetscArrayzero(offsets, 32)); 7828 /* 1) Get points in closure */ 7829 PetscCall(DMPlexGetCompressedClosure(dm, section, point, 0, &Ncl, &points, &clSection, &clPoints, &clp)); 7830 if (useClPerm) { 7831 PetscInt depth, clsize; 7832 PetscCall(DMPlexGetPointDepth(dm, point, &depth)); 7833 for (clsize = 0, p = 0; p < Ncl; p++) { 7834 PetscInt dof; 7835 PetscCall(PetscSectionGetDof(section, points[2 * p], &dof)); 7836 clsize += dof; 7837 } 7838 PetscCall(PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject)dm, depth, clsize, &clperm)); 7839 } 7840 /* 2) Get number of indices on these points and field offsets from section */ 7841 for (p = 0; p < Ncl * 2; p += 2) { 7842 PetscInt dof, fdof; 7843 7844 PetscCall(PetscSectionGetDof(section, points[p], &dof)); 7845 for (f = 0; f < Nf; ++f) { 7846 PetscCall(PetscSectionGetFieldDof(section, points[p], f, &fdof)); 7847 offsets[f + 1] += fdof; 7848 } 7849 Ni += dof; 7850 } 7851 for (f = 1; f < Nf; ++f) offsets[f + 1] += offsets[f]; 7852 PetscCheck(!Nf || offsets[Nf] == Ni, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid size for closure %" PetscInt_FMT " should be %" PetscInt_FMT, offsets[Nf], Ni); 7853 /* 3) Get symmetries and sign flips. Apply sign flips to values if passed in (only works for square values matrix) */ 7854 for (f = 0; f < PetscMax(1, Nf); ++f) { 7855 if (Nf) PetscCall(PetscSectionGetFieldPointSyms(section, f, Ncl, points, &perms[f], &flips[f])); 7856 else PetscCall(PetscSectionGetPointSyms(section, Ncl, points, &perms[f], &flips[f])); 7857 /* may need to apply sign changes to the element matrix */ 7858 if (values && flips[f]) { 7859 PetscInt foffset = offsets[f]; 7860 7861 for (p = 0; p < Ncl; ++p) { 7862 PetscInt pnt = points[2 * p], fdof; 7863 const PetscScalar *flip = flips[f] ? flips[f][p] : NULL; 7864 7865 if (!Nf) PetscCall(PetscSectionGetDof(section, pnt, &fdof)); 7866 else PetscCall(PetscSectionGetFieldDof(section, pnt, f, &fdof)); 7867 if (flip) { 7868 PetscInt i, j, k; 7869 7870 if (!valCopy) { 7871 PetscCall(DMGetWorkArray(dm, Ni * Ni, MPIU_SCALAR, &valCopy)); 7872 for (j = 0; j < Ni * Ni; ++j) valCopy[j] = (*values)[j]; 7873 *values = valCopy; 7874 } 7875 for (i = 0; i < fdof; ++i) { 7876 PetscScalar fval = flip[i]; 7877 7878 for (k = 0; k < Ni; ++k) { 7879 valCopy[Ni * (foffset + i) + k] *= fval; 7880 valCopy[Ni * k + (foffset + i)] *= fval; 7881 } 7882 } 7883 } 7884 foffset += fdof; 7885 } 7886 } 7887 } 7888 /* 4) Apply hanging node constraints. Get new symmetries and replace all storage with constrained storage */ 7889 PetscCall(DMPlexAnchorsModifyMat(dm, section, Ncl, Ni, points, perms, values ? *values : NULL, &NclC, &NiC, &pointsC, values ? &valuesC : NULL, offsets, PETSC_TRUE)); 7890 if (NclC) { 7891 if (valCopy) PetscCall(DMRestoreWorkArray(dm, Ni * Ni, MPIU_SCALAR, &valCopy)); 7892 for (f = 0; f < PetscMax(1, Nf); ++f) { 7893 if (Nf) PetscCall(PetscSectionRestoreFieldPointSyms(section, f, Ncl, points, &perms[f], &flips[f])); 7894 else PetscCall(PetscSectionRestorePointSyms(section, Ncl, points, &perms[f], &flips[f])); 7895 } 7896 for (f = 0; f < PetscMax(1, Nf); ++f) { 7897 if (Nf) PetscCall(PetscSectionGetFieldPointSyms(section, f, NclC, pointsC, &perms[f], &flips[f])); 7898 else PetscCall(PetscSectionGetPointSyms(section, NclC, pointsC, &perms[f], &flips[f])); 7899 } 7900 PetscCall(DMPlexRestoreCompressedClosure(dm, section, point, &Ncl, &points, &clSection, &clPoints, &clp)); 7901 Ncl = NclC; 7902 Ni = NiC; 7903 points = pointsC; 7904 if (values) *values = valuesC; 7905 } 7906 /* 5) Calculate indices */ 7907 PetscCall(DMGetWorkArray(dm, Ni, MPIU_INT, &idx)); 7908 if (Nf) { 7909 PetscInt idxOff; 7910 PetscBool useFieldOffsets; 7911 7912 if (outOffsets) { 7913 for (f = 0; f <= Nf; f++) outOffsets[f] = offsets[f]; 7914 } 7915 PetscCall(PetscSectionGetUseFieldOffsets(idxSection, &useFieldOffsets)); 7916 if (useFieldOffsets) { 7917 for (p = 0; p < Ncl; ++p) { 7918 const PetscInt pnt = points[p * 2]; 7919 7920 PetscCall(DMPlexGetIndicesPointFieldsSplit_Internal(section, idxSection, pnt, offsets, perms, p, clperm, idx)); 7921 } 7922 } else { 7923 for (p = 0; p < Ncl; ++p) { 7924 const PetscInt pnt = points[p * 2]; 7925 7926 PetscCall(PetscSectionGetOffset(idxSection, pnt, &idxOff)); 7927 /* Note that we pass a local section even though we're using global offsets. This is because global sections do 7928 * not (at the time of this writing) have fields set. They probably should, in which case we would pass the 7929 * global section. */ 7930 PetscCall(DMPlexGetIndicesPointFields_Internal(section, isLocal, pnt, idxOff < 0 ? -(idxOff + 1) : idxOff, offsets, PETSC_FALSE, perms, p, clperm, idx)); 7931 } 7932 } 7933 } else { 7934 PetscInt off = 0, idxOff; 7935 7936 for (p = 0; p < Ncl; ++p) { 7937 const PetscInt pnt = points[p * 2]; 7938 const PetscInt *perm = perms[0] ? perms[0][p] : NULL; 7939 7940 PetscCall(PetscSectionGetOffset(idxSection, pnt, &idxOff)); 7941 /* Note that we pass a local section even though we're using global offsets. This is because global sections do 7942 * not (at the time of this writing) have fields set. They probably should, in which case we would pass the global section. */ 7943 PetscCall(DMPlexGetIndicesPoint_Internal(section, isLocal, pnt, idxOff < 0 ? -(idxOff + 1) : idxOff, &off, PETSC_FALSE, perm, clperm, idx)); 7944 } 7945 } 7946 /* 6) Cleanup */ 7947 for (f = 0; f < PetscMax(1, Nf); ++f) { 7948 if (Nf) PetscCall(PetscSectionRestoreFieldPointSyms(section, f, Ncl, points, &perms[f], &flips[f])); 7949 else PetscCall(PetscSectionRestorePointSyms(section, Ncl, points, &perms[f], &flips[f])); 7950 } 7951 if (NclC) { 7952 PetscCall(DMRestoreWorkArray(dm, NclC * 2, MPIU_INT, &pointsC)); 7953 } else { 7954 PetscCall(DMPlexRestoreCompressedClosure(dm, section, point, &Ncl, &points, &clSection, &clPoints, &clp)); 7955 } 7956 7957 if (numIndices) *numIndices = Ni; 7958 if (indices) *indices = idx; 7959 PetscFunctionReturn(PETSC_SUCCESS); 7960 } 7961 7962 /*@C 7963 DMPlexRestoreClosureIndices - Restores the global dof indices associated with the closure of the given point within the provided sections. 7964 7965 Not collective 7966 7967 Input Parameters: 7968 + dm - The `DM` 7969 . section - The `PetscSection` describing the points (a local section) 7970 . idxSection - The `PetscSection` from which to obtain indices (may be local or global) 7971 . point - The point defining the closure 7972 - useClPerm - Use the closure point permutation if available 7973 7974 Output Parameters: 7975 + numIndices - The number of dof indices in the closure of point with the input sections 7976 . indices - The dof indices 7977 . outOffsets - Array to write the field offsets into, or `NULL` 7978 - values - The input values, which may be modified if sign flips are induced by the point symmetries, or `NULL` 7979 7980 Level: advanced 7981 7982 Notes: 7983 If values were modified, the user is responsible for calling `DMRestoreWorkArray`(dm, 0, `MPIU_SCALAR`, &values). 7984 7985 If idxSection is global, any constrained dofs (see `DMAddBoundary()`, for example) will get negative indices. The value 7986 of those indices is not significant. If idxSection is local, the constrained dofs will yield the involution -(idx+1) 7987 of their index in a local vector. A caller who does not wish to distinguish those points may recover the nonnegative 7988 indices via involution, -(-(idx+1)+1)==idx. Local indices are provided when idxSection == section, otherwise global 7989 indices (with the above semantics) are implied. 7990 7991 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetClosureIndices()`, `DMPlexVecGetClosure()`, `DMPlexMatSetClosure()`, `DMGetLocalSection()`, `DMGetGlobalSection()` 7992 @*/ 7993 PetscErrorCode DMPlexRestoreClosureIndices(DM dm, PetscSection section, PetscSection idxSection, PetscInt point, PetscBool useClPerm, PetscInt *numIndices, PetscInt *indices[], PetscInt outOffsets[], PetscScalar *values[]) 7994 { 7995 PetscFunctionBegin; 7996 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 7997 PetscAssertPointer(indices, 7); 7998 PetscCall(DMRestoreWorkArray(dm, 0, MPIU_INT, indices)); 7999 PetscFunctionReturn(PETSC_SUCCESS); 8000 } 8001 8002 PetscErrorCode DMPlexMatSetClosure_Internal(DM dm, PetscSection section, PetscSection globalSection, PetscBool useClPerm, Mat A, PetscInt point, const PetscScalar values[], InsertMode mode) 8003 { 8004 DM_Plex *mesh = (DM_Plex *)dm->data; 8005 PetscInt *indices; 8006 PetscInt numIndices; 8007 const PetscScalar *valuesOrig = values; 8008 PetscErrorCode ierr; 8009 8010 PetscFunctionBegin; 8011 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8012 if (!section) PetscCall(DMGetLocalSection(dm, §ion)); 8013 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 8014 if (!globalSection) PetscCall(DMGetGlobalSection(dm, &globalSection)); 8015 PetscValidHeaderSpecific(globalSection, PETSC_SECTION_CLASSID, 3); 8016 PetscValidHeaderSpecific(A, MAT_CLASSID, 5); 8017 8018 PetscCall(DMPlexGetClosureIndices(dm, section, globalSection, point, useClPerm, &numIndices, &indices, NULL, (PetscScalar **)&values)); 8019 8020 if (mesh->printSetValues) PetscCall(DMPlexPrintMatSetValues(PETSC_VIEWER_STDOUT_SELF, A, point, numIndices, indices, 0, NULL, values)); 8021 /* TODO: fix this code to not use error codes as handle-able exceptions! */ 8022 ierr = MatSetValues(A, numIndices, indices, numIndices, indices, values, mode); 8023 if (ierr) { 8024 PetscMPIInt rank; 8025 8026 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank)); 8027 PetscCall((*PetscErrorPrintf)("[%d]ERROR in DMPlexMatSetClosure\n", rank)); 8028 PetscCall(DMPlexPrintMatSetValues(PETSC_VIEWER_STDERR_SELF, A, point, numIndices, indices, 0, NULL, values)); 8029 PetscCall(DMPlexRestoreClosureIndices(dm, section, globalSection, point, PETSC_TRUE, &numIndices, &indices, NULL, (PetscScalar **)&values)); 8030 if (values != valuesOrig) PetscCall(DMRestoreWorkArray(dm, 0, MPIU_SCALAR, &values)); 8031 SETERRQ(PetscObjectComm((PetscObject)dm), ierr, "Not possible to set matrix values"); 8032 } 8033 if (mesh->printFEM > 1) { 8034 PetscInt i; 8035 PetscCall(PetscPrintf(PETSC_COMM_SELF, " Indices:")); 8036 for (i = 0; i < numIndices; ++i) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, indices[i])); 8037 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 8038 } 8039 8040 PetscCall(DMPlexRestoreClosureIndices(dm, section, globalSection, point, PETSC_TRUE, &numIndices, &indices, NULL, (PetscScalar **)&values)); 8041 if (values != valuesOrig) PetscCall(DMRestoreWorkArray(dm, 0, MPIU_SCALAR, &values)); 8042 PetscFunctionReturn(PETSC_SUCCESS); 8043 } 8044 8045 /*@C 8046 DMPlexMatSetClosure - Set an array of the values on the closure of 'point' 8047 8048 Not collective 8049 8050 Input Parameters: 8051 + dm - The `DM` 8052 . section - The section describing the layout in `v`, or `NULL` to use the default section 8053 . globalSection - The section describing the layout in `v`, or `NULL` to use the default global section 8054 . A - The matrix 8055 . point - The point in the `DM` 8056 . values - The array of values 8057 - mode - The insert mode, where `INSERT_ALL_VALUES` and `ADD_ALL_VALUES` also overwrite boundary conditions 8058 8059 Level: intermediate 8060 8061 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexMatSetClosureGeneral()`, `DMPlexVecGetClosure()`, `DMPlexVecSetClosure()` 8062 @*/ 8063 PetscErrorCode DMPlexMatSetClosure(DM dm, PetscSection section, PetscSection globalSection, Mat A, PetscInt point, const PetscScalar values[], InsertMode mode) 8064 { 8065 PetscFunctionBegin; 8066 PetscCall(DMPlexMatSetClosure_Internal(dm, section, globalSection, PETSC_TRUE, A, point, values, mode)); 8067 PetscFunctionReturn(PETSC_SUCCESS); 8068 } 8069 8070 /*@C 8071 DMPlexMatSetClosureGeneral - Set an array of the values on the closure of 'point' using a different row and column section 8072 8073 Not collective 8074 8075 Input Parameters: 8076 + dmRow - The `DM` for the row fields 8077 . sectionRow - The section describing the layout, or `NULL` to use the default section in `dmRow` 8078 . useRowPerm - The flag to use the closure permutation of the `dmRow` if available 8079 . globalSectionRow - The section describing the layout, or `NULL` to use the default global section in `dmRow` 8080 . dmCol - The `DM` for the column fields 8081 . sectionCol - The section describing the layout, or `NULL` to use the default section in `dmCol` 8082 . useColPerm - The flag to use the closure permutation of the `dmCol` if available 8083 . globalSectionCol - The section describing the layout, or `NULL` to use the default global section in `dmCol` 8084 . A - The matrix 8085 . point - The point in the `DM` 8086 . values - The array of values 8087 - mode - The insert mode, where `INSERT_ALL_VALUES` and `ADD_ALL_VALUES` also overwrite boundary conditions 8088 8089 Level: intermediate 8090 8091 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexMatSetClosure()`, `DMPlexVecGetClosure()`, `DMPlexVecSetClosure()` 8092 @*/ 8093 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) 8094 { 8095 DM_Plex *mesh = (DM_Plex *)dmRow->data; 8096 PetscInt *indicesRow, *indicesCol; 8097 PetscInt numIndicesRow, numIndicesCol; 8098 const PetscScalar *valuesOrig = values; 8099 PetscErrorCode ierr; 8100 8101 PetscFunctionBegin; 8102 PetscValidHeaderSpecific(dmRow, DM_CLASSID, 1); 8103 if (!sectionRow) PetscCall(DMGetLocalSection(dmRow, §ionRow)); 8104 PetscValidHeaderSpecific(sectionRow, PETSC_SECTION_CLASSID, 2); 8105 if (!globalSectionRow) PetscCall(DMGetGlobalSection(dmRow, &globalSectionRow)); 8106 PetscValidHeaderSpecific(globalSectionRow, PETSC_SECTION_CLASSID, 3); 8107 PetscValidHeaderSpecific(dmCol, DM_CLASSID, 5); 8108 if (!sectionCol) PetscCall(DMGetLocalSection(dmCol, §ionCol)); 8109 PetscValidHeaderSpecific(sectionCol, PETSC_SECTION_CLASSID, 6); 8110 if (!globalSectionCol) PetscCall(DMGetGlobalSection(dmCol, &globalSectionCol)); 8111 PetscValidHeaderSpecific(globalSectionCol, PETSC_SECTION_CLASSID, 7); 8112 PetscValidHeaderSpecific(A, MAT_CLASSID, 9); 8113 8114 PetscCall(DMPlexGetClosureIndices(dmRow, sectionRow, globalSectionRow, point, useRowPerm, &numIndicesRow, &indicesRow, NULL, (PetscScalar **)&values)); 8115 PetscCall(DMPlexGetClosureIndices(dmCol, sectionCol, globalSectionCol, point, useColPerm, &numIndicesCol, &indicesCol, NULL, (PetscScalar **)&values)); 8116 8117 if (mesh->printSetValues) PetscCall(DMPlexPrintMatSetValues(PETSC_VIEWER_STDOUT_SELF, A, point, numIndicesRow, indicesRow, numIndicesCol, indicesCol, values)); 8118 /* TODO: fix this code to not use error codes as handle-able exceptions! */ 8119 ierr = MatSetValues(A, numIndicesRow, indicesRow, numIndicesCol, indicesCol, values, mode); 8120 if (ierr) { 8121 PetscMPIInt rank; 8122 8123 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank)); 8124 PetscCall((*PetscErrorPrintf)("[%d]ERROR in DMPlexMatSetClosure\n", rank)); 8125 PetscCall(DMPlexPrintMatSetValues(PETSC_VIEWER_STDERR_SELF, A, point, numIndicesRow, indicesRow, numIndicesCol, indicesCol, values)); 8126 PetscCall(DMPlexRestoreClosureIndices(dmRow, sectionRow, globalSectionRow, point, PETSC_TRUE, &numIndicesRow, &indicesRow, NULL, (PetscScalar **)&values)); 8127 PetscCall(DMPlexRestoreClosureIndices(dmCol, sectionCol, globalSectionCol, point, PETSC_TRUE, &numIndicesCol, &indicesRow, NULL, (PetscScalar **)&values)); 8128 if (values != valuesOrig) PetscCall(DMRestoreWorkArray(dmRow, 0, MPIU_SCALAR, &values)); 8129 } 8130 8131 PetscCall(DMPlexRestoreClosureIndices(dmRow, sectionRow, globalSectionRow, point, useRowPerm, &numIndicesRow, &indicesRow, NULL, (PetscScalar **)&values)); 8132 PetscCall(DMPlexRestoreClosureIndices(dmCol, sectionCol, globalSectionCol, point, useColPerm, &numIndicesCol, &indicesCol, NULL, (PetscScalar **)&values)); 8133 if (values != valuesOrig) PetscCall(DMRestoreWorkArray(dmRow, 0, MPIU_SCALAR, &values)); 8134 PetscFunctionReturn(PETSC_SUCCESS); 8135 } 8136 8137 PetscErrorCode DMPlexMatSetClosureRefined(DM dmf, PetscSection fsection, PetscSection globalFSection, DM dmc, PetscSection csection, PetscSection globalCSection, Mat A, PetscInt point, const PetscScalar values[], InsertMode mode) 8138 { 8139 DM_Plex *mesh = (DM_Plex *)dmf->data; 8140 PetscInt *fpoints = NULL, *ftotpoints = NULL; 8141 PetscInt *cpoints = NULL; 8142 PetscInt *findices, *cindices; 8143 const PetscInt *fclperm = NULL, *cclperm = NULL; /* Closure permutations cannot work here */ 8144 PetscInt foffsets[32], coffsets[32]; 8145 DMPolytopeType ct; 8146 PetscInt numFields, numSubcells, maxFPoints, numFPoints, numCPoints, numFIndices, numCIndices, dof, off, globalOff, pStart, pEnd, p, q, r, s, f; 8147 PetscErrorCode ierr; 8148 8149 PetscFunctionBegin; 8150 PetscValidHeaderSpecific(dmf, DM_CLASSID, 1); 8151 PetscValidHeaderSpecific(dmc, DM_CLASSID, 4); 8152 if (!fsection) PetscCall(DMGetLocalSection(dmf, &fsection)); 8153 PetscValidHeaderSpecific(fsection, PETSC_SECTION_CLASSID, 2); 8154 if (!csection) PetscCall(DMGetLocalSection(dmc, &csection)); 8155 PetscValidHeaderSpecific(csection, PETSC_SECTION_CLASSID, 5); 8156 if (!globalFSection) PetscCall(DMGetGlobalSection(dmf, &globalFSection)); 8157 PetscValidHeaderSpecific(globalFSection, PETSC_SECTION_CLASSID, 3); 8158 if (!globalCSection) PetscCall(DMGetGlobalSection(dmc, &globalCSection)); 8159 PetscValidHeaderSpecific(globalCSection, PETSC_SECTION_CLASSID, 6); 8160 PetscValidHeaderSpecific(A, MAT_CLASSID, 7); 8161 PetscCall(PetscSectionGetNumFields(fsection, &numFields)); 8162 PetscCheck(numFields <= 31, PetscObjectComm((PetscObject)dmf), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %" PetscInt_FMT " limited to 31", numFields); 8163 PetscCall(PetscArrayzero(foffsets, 32)); 8164 PetscCall(PetscArrayzero(coffsets, 32)); 8165 /* Column indices */ 8166 PetscCall(DMPlexGetTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints)); 8167 maxFPoints = numCPoints; 8168 /* Compress out points not in the section */ 8169 /* TODO: Squeeze out points with 0 dof as well */ 8170 PetscCall(PetscSectionGetChart(csection, &pStart, &pEnd)); 8171 for (p = 0, q = 0; p < numCPoints * 2; p += 2) { 8172 if ((cpoints[p] >= pStart) && (cpoints[p] < pEnd)) { 8173 cpoints[q * 2] = cpoints[p]; 8174 cpoints[q * 2 + 1] = cpoints[p + 1]; 8175 ++q; 8176 } 8177 } 8178 numCPoints = q; 8179 for (p = 0, numCIndices = 0; p < numCPoints * 2; p += 2) { 8180 PetscInt fdof; 8181 8182 PetscCall(PetscSectionGetDof(csection, cpoints[p], &dof)); 8183 if (!dof) continue; 8184 for (f = 0; f < numFields; ++f) { 8185 PetscCall(PetscSectionGetFieldDof(csection, cpoints[p], f, &fdof)); 8186 coffsets[f + 1] += fdof; 8187 } 8188 numCIndices += dof; 8189 } 8190 for (f = 1; f < numFields; ++f) coffsets[f + 1] += coffsets[f]; 8191 /* Row indices */ 8192 PetscCall(DMPlexGetCellType(dmc, point, &ct)); 8193 { 8194 DMPlexTransform tr; 8195 DMPolytopeType *rct; 8196 PetscInt *rsize, *rcone, *rornt, Nt; 8197 8198 PetscCall(DMPlexTransformCreate(PETSC_COMM_SELF, &tr)); 8199 PetscCall(DMPlexTransformSetType(tr, DMPLEXREFINEREGULAR)); 8200 PetscCall(DMPlexTransformCellTransform(tr, ct, point, NULL, &Nt, &rct, &rsize, &rcone, &rornt)); 8201 numSubcells = rsize[Nt - 1]; 8202 PetscCall(DMPlexTransformDestroy(&tr)); 8203 } 8204 PetscCall(DMGetWorkArray(dmf, maxFPoints * 2 * numSubcells, MPIU_INT, &ftotpoints)); 8205 for (r = 0, q = 0; r < numSubcells; ++r) { 8206 /* TODO Map from coarse to fine cells */ 8207 PetscCall(DMPlexGetTransitiveClosure(dmf, point * numSubcells + r, PETSC_TRUE, &numFPoints, &fpoints)); 8208 /* Compress out points not in the section */ 8209 PetscCall(PetscSectionGetChart(fsection, &pStart, &pEnd)); 8210 for (p = 0; p < numFPoints * 2; p += 2) { 8211 if ((fpoints[p] >= pStart) && (fpoints[p] < pEnd)) { 8212 PetscCall(PetscSectionGetDof(fsection, fpoints[p], &dof)); 8213 if (!dof) continue; 8214 for (s = 0; s < q; ++s) 8215 if (fpoints[p] == ftotpoints[s * 2]) break; 8216 if (s < q) continue; 8217 ftotpoints[q * 2] = fpoints[p]; 8218 ftotpoints[q * 2 + 1] = fpoints[p + 1]; 8219 ++q; 8220 } 8221 } 8222 PetscCall(DMPlexRestoreTransitiveClosure(dmf, point, PETSC_TRUE, &numFPoints, &fpoints)); 8223 } 8224 numFPoints = q; 8225 for (p = 0, numFIndices = 0; p < numFPoints * 2; p += 2) { 8226 PetscInt fdof; 8227 8228 PetscCall(PetscSectionGetDof(fsection, ftotpoints[p], &dof)); 8229 if (!dof) continue; 8230 for (f = 0; f < numFields; ++f) { 8231 PetscCall(PetscSectionGetFieldDof(fsection, ftotpoints[p], f, &fdof)); 8232 foffsets[f + 1] += fdof; 8233 } 8234 numFIndices += dof; 8235 } 8236 for (f = 1; f < numFields; ++f) foffsets[f + 1] += foffsets[f]; 8237 8238 PetscCheck(!numFields || foffsets[numFields] == numFIndices, PetscObjectComm((PetscObject)dmf), PETSC_ERR_PLIB, "Invalid size for closure %" PetscInt_FMT " should be %" PetscInt_FMT, foffsets[numFields], numFIndices); 8239 PetscCheck(!numFields || coffsets[numFields] == numCIndices, PetscObjectComm((PetscObject)dmc), PETSC_ERR_PLIB, "Invalid size for closure %" PetscInt_FMT " should be %" PetscInt_FMT, coffsets[numFields], numCIndices); 8240 PetscCall(DMGetWorkArray(dmf, numFIndices, MPIU_INT, &findices)); 8241 PetscCall(DMGetWorkArray(dmc, numCIndices, MPIU_INT, &cindices)); 8242 if (numFields) { 8243 const PetscInt **permsF[32] = {NULL}; 8244 const PetscInt **permsC[32] = {NULL}; 8245 8246 for (f = 0; f < numFields; f++) { 8247 PetscCall(PetscSectionGetFieldPointSyms(fsection, f, numFPoints, ftotpoints, &permsF[f], NULL)); 8248 PetscCall(PetscSectionGetFieldPointSyms(csection, f, numCPoints, cpoints, &permsC[f], NULL)); 8249 } 8250 for (p = 0; p < numFPoints; p++) { 8251 PetscCall(PetscSectionGetOffset(globalFSection, ftotpoints[2 * p], &globalOff)); 8252 PetscCall(DMPlexGetIndicesPointFields_Internal(fsection, PETSC_FALSE, ftotpoints[2 * p], globalOff < 0 ? -(globalOff + 1) : globalOff, foffsets, PETSC_FALSE, permsF, p, fclperm, findices)); 8253 } 8254 for (p = 0; p < numCPoints; p++) { 8255 PetscCall(PetscSectionGetOffset(globalCSection, cpoints[2 * p], &globalOff)); 8256 PetscCall(DMPlexGetIndicesPointFields_Internal(csection, PETSC_FALSE, cpoints[2 * p], globalOff < 0 ? -(globalOff + 1) : globalOff, coffsets, PETSC_FALSE, permsC, p, cclperm, cindices)); 8257 } 8258 for (f = 0; f < numFields; f++) { 8259 PetscCall(PetscSectionRestoreFieldPointSyms(fsection, f, numFPoints, ftotpoints, &permsF[f], NULL)); 8260 PetscCall(PetscSectionRestoreFieldPointSyms(csection, f, numCPoints, cpoints, &permsC[f], NULL)); 8261 } 8262 } else { 8263 const PetscInt **permsF = NULL; 8264 const PetscInt **permsC = NULL; 8265 8266 PetscCall(PetscSectionGetPointSyms(fsection, numFPoints, ftotpoints, &permsF, NULL)); 8267 PetscCall(PetscSectionGetPointSyms(csection, numCPoints, cpoints, &permsC, NULL)); 8268 for (p = 0, off = 0; p < numFPoints; p++) { 8269 const PetscInt *perm = permsF ? permsF[p] : NULL; 8270 8271 PetscCall(PetscSectionGetOffset(globalFSection, ftotpoints[2 * p], &globalOff)); 8272 PetscCall(DMPlexGetIndicesPoint_Internal(fsection, PETSC_FALSE, ftotpoints[2 * p], globalOff < 0 ? -(globalOff + 1) : globalOff, &off, PETSC_FALSE, perm, fclperm, findices)); 8273 } 8274 for (p = 0, off = 0; p < numCPoints; p++) { 8275 const PetscInt *perm = permsC ? permsC[p] : NULL; 8276 8277 PetscCall(PetscSectionGetOffset(globalCSection, cpoints[2 * p], &globalOff)); 8278 PetscCall(DMPlexGetIndicesPoint_Internal(csection, PETSC_FALSE, cpoints[2 * p], globalOff < 0 ? -(globalOff + 1) : globalOff, &off, PETSC_FALSE, perm, cclperm, cindices)); 8279 } 8280 PetscCall(PetscSectionRestorePointSyms(fsection, numFPoints, ftotpoints, &permsF, NULL)); 8281 PetscCall(PetscSectionRestorePointSyms(csection, numCPoints, cpoints, &permsC, NULL)); 8282 } 8283 if (mesh->printSetValues) PetscCall(DMPlexPrintMatSetValues(PETSC_VIEWER_STDOUT_SELF, A, point, numFIndices, findices, numCIndices, cindices, values)); 8284 /* TODO: flips */ 8285 /* TODO: fix this code to not use error codes as handle-able exceptions! */ 8286 ierr = MatSetValues(A, numFIndices, findices, numCIndices, cindices, values, mode); 8287 if (ierr) { 8288 PetscMPIInt rank; 8289 8290 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank)); 8291 PetscCall((*PetscErrorPrintf)("[%d]ERROR in DMPlexMatSetClosure\n", rank)); 8292 PetscCall(DMPlexPrintMatSetValues(PETSC_VIEWER_STDERR_SELF, A, point, numFIndices, findices, numCIndices, cindices, values)); 8293 PetscCall(DMRestoreWorkArray(dmf, numFIndices, MPIU_INT, &findices)); 8294 PetscCall(DMRestoreWorkArray(dmc, numCIndices, MPIU_INT, &cindices)); 8295 } 8296 PetscCall(DMRestoreWorkArray(dmf, numCPoints * 2 * 4, MPIU_INT, &ftotpoints)); 8297 PetscCall(DMPlexRestoreTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints)); 8298 PetscCall(DMRestoreWorkArray(dmf, numFIndices, MPIU_INT, &findices)); 8299 PetscCall(DMRestoreWorkArray(dmc, numCIndices, MPIU_INT, &cindices)); 8300 PetscFunctionReturn(PETSC_SUCCESS); 8301 } 8302 8303 PetscErrorCode DMPlexMatGetClosureIndicesRefined(DM dmf, PetscSection fsection, PetscSection globalFSection, DM dmc, PetscSection csection, PetscSection globalCSection, PetscInt point, PetscInt cindices[], PetscInt findices[]) 8304 { 8305 PetscInt *fpoints = NULL, *ftotpoints = NULL; 8306 PetscInt *cpoints = NULL; 8307 PetscInt foffsets[32], coffsets[32]; 8308 const PetscInt *fclperm = NULL, *cclperm = NULL; /* Closure permutations cannot work here */ 8309 DMPolytopeType ct; 8310 PetscInt numFields, numSubcells, maxFPoints, numFPoints, numCPoints, numFIndices, numCIndices, dof, off, globalOff, pStart, pEnd, p, q, r, s, f; 8311 8312 PetscFunctionBegin; 8313 PetscValidHeaderSpecific(dmf, DM_CLASSID, 1); 8314 PetscValidHeaderSpecific(dmc, DM_CLASSID, 4); 8315 if (!fsection) PetscCall(DMGetLocalSection(dmf, &fsection)); 8316 PetscValidHeaderSpecific(fsection, PETSC_SECTION_CLASSID, 2); 8317 if (!csection) PetscCall(DMGetLocalSection(dmc, &csection)); 8318 PetscValidHeaderSpecific(csection, PETSC_SECTION_CLASSID, 5); 8319 if (!globalFSection) PetscCall(DMGetGlobalSection(dmf, &globalFSection)); 8320 PetscValidHeaderSpecific(globalFSection, PETSC_SECTION_CLASSID, 3); 8321 if (!globalCSection) PetscCall(DMGetGlobalSection(dmc, &globalCSection)); 8322 PetscValidHeaderSpecific(globalCSection, PETSC_SECTION_CLASSID, 6); 8323 PetscCall(PetscSectionGetNumFields(fsection, &numFields)); 8324 PetscCheck(numFields <= 31, PetscObjectComm((PetscObject)dmf), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %" PetscInt_FMT " limited to 31", numFields); 8325 PetscCall(PetscArrayzero(foffsets, 32)); 8326 PetscCall(PetscArrayzero(coffsets, 32)); 8327 /* Column indices */ 8328 PetscCall(DMPlexGetTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints)); 8329 maxFPoints = numCPoints; 8330 /* Compress out points not in the section */ 8331 /* TODO: Squeeze out points with 0 dof as well */ 8332 PetscCall(PetscSectionGetChart(csection, &pStart, &pEnd)); 8333 for (p = 0, q = 0; p < numCPoints * 2; p += 2) { 8334 if ((cpoints[p] >= pStart) && (cpoints[p] < pEnd)) { 8335 cpoints[q * 2] = cpoints[p]; 8336 cpoints[q * 2 + 1] = cpoints[p + 1]; 8337 ++q; 8338 } 8339 } 8340 numCPoints = q; 8341 for (p = 0, numCIndices = 0; p < numCPoints * 2; p += 2) { 8342 PetscInt fdof; 8343 8344 PetscCall(PetscSectionGetDof(csection, cpoints[p], &dof)); 8345 if (!dof) continue; 8346 for (f = 0; f < numFields; ++f) { 8347 PetscCall(PetscSectionGetFieldDof(csection, cpoints[p], f, &fdof)); 8348 coffsets[f + 1] += fdof; 8349 } 8350 numCIndices += dof; 8351 } 8352 for (f = 1; f < numFields; ++f) coffsets[f + 1] += coffsets[f]; 8353 /* Row indices */ 8354 PetscCall(DMPlexGetCellType(dmc, point, &ct)); 8355 { 8356 DMPlexTransform tr; 8357 DMPolytopeType *rct; 8358 PetscInt *rsize, *rcone, *rornt, Nt; 8359 8360 PetscCall(DMPlexTransformCreate(PETSC_COMM_SELF, &tr)); 8361 PetscCall(DMPlexTransformSetType(tr, DMPLEXREFINEREGULAR)); 8362 PetscCall(DMPlexTransformCellTransform(tr, ct, point, NULL, &Nt, &rct, &rsize, &rcone, &rornt)); 8363 numSubcells = rsize[Nt - 1]; 8364 PetscCall(DMPlexTransformDestroy(&tr)); 8365 } 8366 PetscCall(DMGetWorkArray(dmf, maxFPoints * 2 * numSubcells, MPIU_INT, &ftotpoints)); 8367 for (r = 0, q = 0; r < numSubcells; ++r) { 8368 /* TODO Map from coarse to fine cells */ 8369 PetscCall(DMPlexGetTransitiveClosure(dmf, point * numSubcells + r, PETSC_TRUE, &numFPoints, &fpoints)); 8370 /* Compress out points not in the section */ 8371 PetscCall(PetscSectionGetChart(fsection, &pStart, &pEnd)); 8372 for (p = 0; p < numFPoints * 2; p += 2) { 8373 if ((fpoints[p] >= pStart) && (fpoints[p] < pEnd)) { 8374 PetscCall(PetscSectionGetDof(fsection, fpoints[p], &dof)); 8375 if (!dof) continue; 8376 for (s = 0; s < q; ++s) 8377 if (fpoints[p] == ftotpoints[s * 2]) break; 8378 if (s < q) continue; 8379 ftotpoints[q * 2] = fpoints[p]; 8380 ftotpoints[q * 2 + 1] = fpoints[p + 1]; 8381 ++q; 8382 } 8383 } 8384 PetscCall(DMPlexRestoreTransitiveClosure(dmf, point, PETSC_TRUE, &numFPoints, &fpoints)); 8385 } 8386 numFPoints = q; 8387 for (p = 0, numFIndices = 0; p < numFPoints * 2; p += 2) { 8388 PetscInt fdof; 8389 8390 PetscCall(PetscSectionGetDof(fsection, ftotpoints[p], &dof)); 8391 if (!dof) continue; 8392 for (f = 0; f < numFields; ++f) { 8393 PetscCall(PetscSectionGetFieldDof(fsection, ftotpoints[p], f, &fdof)); 8394 foffsets[f + 1] += fdof; 8395 } 8396 numFIndices += dof; 8397 } 8398 for (f = 1; f < numFields; ++f) foffsets[f + 1] += foffsets[f]; 8399 8400 PetscCheck(!numFields || foffsets[numFields] == numFIndices, PetscObjectComm((PetscObject)dmf), PETSC_ERR_PLIB, "Invalid size for closure %" PetscInt_FMT " should be %" PetscInt_FMT, foffsets[numFields], numFIndices); 8401 PetscCheck(!numFields || coffsets[numFields] == numCIndices, PetscObjectComm((PetscObject)dmc), PETSC_ERR_PLIB, "Invalid size for closure %" PetscInt_FMT " should be %" PetscInt_FMT, coffsets[numFields], numCIndices); 8402 if (numFields) { 8403 const PetscInt **permsF[32] = {NULL}; 8404 const PetscInt **permsC[32] = {NULL}; 8405 8406 for (f = 0; f < numFields; f++) { 8407 PetscCall(PetscSectionGetFieldPointSyms(fsection, f, numFPoints, ftotpoints, &permsF[f], NULL)); 8408 PetscCall(PetscSectionGetFieldPointSyms(csection, f, numCPoints, cpoints, &permsC[f], NULL)); 8409 } 8410 for (p = 0; p < numFPoints; p++) { 8411 PetscCall(PetscSectionGetOffset(globalFSection, ftotpoints[2 * p], &globalOff)); 8412 PetscCall(DMPlexGetIndicesPointFields_Internal(fsection, PETSC_FALSE, ftotpoints[2 * p], globalOff < 0 ? -(globalOff + 1) : globalOff, foffsets, PETSC_FALSE, permsF, p, fclperm, findices)); 8413 } 8414 for (p = 0; p < numCPoints; p++) { 8415 PetscCall(PetscSectionGetOffset(globalCSection, cpoints[2 * p], &globalOff)); 8416 PetscCall(DMPlexGetIndicesPointFields_Internal(csection, PETSC_FALSE, cpoints[2 * p], globalOff < 0 ? -(globalOff + 1) : globalOff, coffsets, PETSC_FALSE, permsC, p, cclperm, cindices)); 8417 } 8418 for (f = 0; f < numFields; f++) { 8419 PetscCall(PetscSectionRestoreFieldPointSyms(fsection, f, numFPoints, ftotpoints, &permsF[f], NULL)); 8420 PetscCall(PetscSectionRestoreFieldPointSyms(csection, f, numCPoints, cpoints, &permsC[f], NULL)); 8421 } 8422 } else { 8423 const PetscInt **permsF = NULL; 8424 const PetscInt **permsC = NULL; 8425 8426 PetscCall(PetscSectionGetPointSyms(fsection, numFPoints, ftotpoints, &permsF, NULL)); 8427 PetscCall(PetscSectionGetPointSyms(csection, numCPoints, cpoints, &permsC, NULL)); 8428 for (p = 0, off = 0; p < numFPoints; p++) { 8429 const PetscInt *perm = permsF ? permsF[p] : NULL; 8430 8431 PetscCall(PetscSectionGetOffset(globalFSection, ftotpoints[2 * p], &globalOff)); 8432 PetscCall(DMPlexGetIndicesPoint_Internal(fsection, PETSC_FALSE, ftotpoints[2 * p], globalOff < 0 ? -(globalOff + 1) : globalOff, &off, PETSC_FALSE, perm, fclperm, findices)); 8433 } 8434 for (p = 0, off = 0; p < numCPoints; p++) { 8435 const PetscInt *perm = permsC ? permsC[p] : NULL; 8436 8437 PetscCall(PetscSectionGetOffset(globalCSection, cpoints[2 * p], &globalOff)); 8438 PetscCall(DMPlexGetIndicesPoint_Internal(csection, PETSC_FALSE, cpoints[2 * p], globalOff < 0 ? -(globalOff + 1) : globalOff, &off, PETSC_FALSE, perm, cclperm, cindices)); 8439 } 8440 PetscCall(PetscSectionRestorePointSyms(fsection, numFPoints, ftotpoints, &permsF, NULL)); 8441 PetscCall(PetscSectionRestorePointSyms(csection, numCPoints, cpoints, &permsC, NULL)); 8442 } 8443 PetscCall(DMRestoreWorkArray(dmf, numCPoints * 2 * 4, MPIU_INT, &ftotpoints)); 8444 PetscCall(DMPlexRestoreTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints)); 8445 PetscFunctionReturn(PETSC_SUCCESS); 8446 } 8447 8448 /*@C 8449 DMPlexGetVTKCellHeight - Returns the height in the DAG used to determine which points are cells (normally 0) 8450 8451 Input Parameter: 8452 . dm - The `DMPLEX` object 8453 8454 Output Parameter: 8455 . cellHeight - The height of a cell 8456 8457 Level: developer 8458 8459 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexSetVTKCellHeight()` 8460 @*/ 8461 PetscErrorCode DMPlexGetVTKCellHeight(DM dm, PetscInt *cellHeight) 8462 { 8463 DM_Plex *mesh = (DM_Plex *)dm->data; 8464 8465 PetscFunctionBegin; 8466 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8467 PetscAssertPointer(cellHeight, 2); 8468 *cellHeight = mesh->vtkCellHeight; 8469 PetscFunctionReturn(PETSC_SUCCESS); 8470 } 8471 8472 /*@C 8473 DMPlexSetVTKCellHeight - Sets the height in the DAG used to determine which points are cells (normally 0) 8474 8475 Input Parameters: 8476 + dm - The `DMPLEX` object 8477 - cellHeight - The height of a cell 8478 8479 Level: developer 8480 8481 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetVTKCellHeight()` 8482 @*/ 8483 PetscErrorCode DMPlexSetVTKCellHeight(DM dm, PetscInt cellHeight) 8484 { 8485 DM_Plex *mesh = (DM_Plex *)dm->data; 8486 8487 PetscFunctionBegin; 8488 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8489 mesh->vtkCellHeight = cellHeight; 8490 PetscFunctionReturn(PETSC_SUCCESS); 8491 } 8492 8493 /*@ 8494 DMPlexGetCellTypeStratum - Get the range of cells of a given celltype 8495 8496 Input Parameters: 8497 + dm - The `DMPLEX` object 8498 - ct - The `DMPolytopeType` of the cell 8499 8500 Output Parameters: 8501 + start - The first cell of this type, or `NULL` 8502 - end - The upper bound on this celltype, or `NULL` 8503 8504 Level: advanced 8505 8506 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexConstructGhostCells()`, `DMPlexGetDepthStratum()`, `DMPlexGetHeightStratum()` 8507 @*/ 8508 PetscErrorCode DMPlexGetCellTypeStratum(DM dm, DMPolytopeType ct, PetscInt *start, PetscInt *end) 8509 { 8510 DM_Plex *mesh = (DM_Plex *)dm->data; 8511 DMLabel label; 8512 PetscInt pStart, pEnd; 8513 8514 PetscFunctionBegin; 8515 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8516 if (start) { 8517 PetscAssertPointer(start, 3); 8518 *start = 0; 8519 } 8520 if (end) { 8521 PetscAssertPointer(end, 4); 8522 *end = 0; 8523 } 8524 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 8525 if (pStart == pEnd) PetscFunctionReturn(PETSC_SUCCESS); 8526 if (mesh->tr) { 8527 PetscCall(DMPlexTransformGetCellTypeStratum(mesh->tr, ct, start, end)); 8528 } else { 8529 PetscCall(DMPlexGetCellTypeLabel(dm, &label)); 8530 PetscCheck(label, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "No label named celltype was found"); 8531 PetscCall(DMLabelGetStratumBounds(label, ct, start, end)); 8532 } 8533 PetscFunctionReturn(PETSC_SUCCESS); 8534 } 8535 8536 PetscErrorCode DMPlexCreateNumbering_Plex(DM dm, PetscInt pStart, PetscInt pEnd, PetscInt shift, PetscInt *globalSize, PetscSF sf, IS *numbering) 8537 { 8538 PetscSection section, globalSection; 8539 PetscInt *numbers, p; 8540 8541 PetscFunctionBegin; 8542 if (PetscDefined(USE_DEBUG)) PetscCall(DMPlexCheckPointSF(dm, sf, PETSC_TRUE)); 8543 PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)dm), §ion)); 8544 PetscCall(PetscSectionSetChart(section, pStart, pEnd)); 8545 for (p = pStart; p < pEnd; ++p) PetscCall(PetscSectionSetDof(section, p, 1)); 8546 PetscCall(PetscSectionSetUp(section)); 8547 PetscCall(PetscSectionCreateGlobalSection(section, sf, PETSC_FALSE, PETSC_FALSE, &globalSection)); 8548 PetscCall(PetscMalloc1(pEnd - pStart, &numbers)); 8549 for (p = pStart; p < pEnd; ++p) { 8550 PetscCall(PetscSectionGetOffset(globalSection, p, &numbers[p - pStart])); 8551 if (numbers[p - pStart] < 0) numbers[p - pStart] -= shift; 8552 else numbers[p - pStart] += shift; 8553 } 8554 PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), pEnd - pStart, numbers, PETSC_OWN_POINTER, numbering)); 8555 if (globalSize) { 8556 PetscLayout layout; 8557 PetscCall(PetscSectionGetPointLayout(PetscObjectComm((PetscObject)dm), globalSection, &layout)); 8558 PetscCall(PetscLayoutGetSize(layout, globalSize)); 8559 PetscCall(PetscLayoutDestroy(&layout)); 8560 } 8561 PetscCall(PetscSectionDestroy(§ion)); 8562 PetscCall(PetscSectionDestroy(&globalSection)); 8563 PetscFunctionReturn(PETSC_SUCCESS); 8564 } 8565 8566 PetscErrorCode DMPlexCreateCellNumbering_Internal(DM dm, PetscBool includeHybrid, IS *globalCellNumbers) 8567 { 8568 PetscInt cellHeight, cStart, cEnd; 8569 8570 PetscFunctionBegin; 8571 PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight)); 8572 if (includeHybrid) PetscCall(DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd)); 8573 else PetscCall(DMPlexGetSimplexOrBoxCells(dm, cellHeight, &cStart, &cEnd)); 8574 PetscCall(DMPlexCreateNumbering_Plex(dm, cStart, cEnd, 0, NULL, dm->sf, globalCellNumbers)); 8575 PetscFunctionReturn(PETSC_SUCCESS); 8576 } 8577 8578 /*@ 8579 DMPlexGetCellNumbering - Get a global cell numbering for all cells on this process 8580 8581 Input Parameter: 8582 . dm - The `DMPLEX` object 8583 8584 Output Parameter: 8585 . globalCellNumbers - Global cell numbers for all cells on this process 8586 8587 Level: developer 8588 8589 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetVertexNumbering()` 8590 @*/ 8591 PetscErrorCode DMPlexGetCellNumbering(DM dm, IS *globalCellNumbers) 8592 { 8593 DM_Plex *mesh = (DM_Plex *)dm->data; 8594 8595 PetscFunctionBegin; 8596 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8597 if (!mesh->globalCellNumbers) PetscCall(DMPlexCreateCellNumbering_Internal(dm, PETSC_FALSE, &mesh->globalCellNumbers)); 8598 *globalCellNumbers = mesh->globalCellNumbers; 8599 PetscFunctionReturn(PETSC_SUCCESS); 8600 } 8601 8602 PetscErrorCode DMPlexCreateVertexNumbering_Internal(DM dm, PetscBool includeHybrid, IS *globalVertexNumbers) 8603 { 8604 PetscInt vStart, vEnd; 8605 8606 PetscFunctionBegin; 8607 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8608 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 8609 PetscCall(DMPlexCreateNumbering_Plex(dm, vStart, vEnd, 0, NULL, dm->sf, globalVertexNumbers)); 8610 PetscFunctionReturn(PETSC_SUCCESS); 8611 } 8612 8613 /*@ 8614 DMPlexGetVertexNumbering - Get a global vertex numbering for all vertices on this process 8615 8616 Input Parameter: 8617 . dm - The `DMPLEX` object 8618 8619 Output Parameter: 8620 . globalVertexNumbers - Global vertex numbers for all vertices on this process 8621 8622 Level: developer 8623 8624 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetCellNumbering()` 8625 @*/ 8626 PetscErrorCode DMPlexGetVertexNumbering(DM dm, IS *globalVertexNumbers) 8627 { 8628 DM_Plex *mesh = (DM_Plex *)dm->data; 8629 8630 PetscFunctionBegin; 8631 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8632 if (!mesh->globalVertexNumbers) PetscCall(DMPlexCreateVertexNumbering_Internal(dm, PETSC_FALSE, &mesh->globalVertexNumbers)); 8633 *globalVertexNumbers = mesh->globalVertexNumbers; 8634 PetscFunctionReturn(PETSC_SUCCESS); 8635 } 8636 8637 /*@ 8638 DMPlexCreatePointNumbering - Create a global numbering for all points. 8639 8640 Collective 8641 8642 Input Parameter: 8643 . dm - The `DMPLEX` object 8644 8645 Output Parameter: 8646 . globalPointNumbers - Global numbers for all points on this process 8647 8648 Level: developer 8649 8650 Notes: 8651 The point numbering `IS` is parallel, with local portion indexed by local points (see `DMGetLocalSection()`). The global 8652 points are taken as stratified, with each MPI rank owning a contiguous subset of each stratum. In the IS, owned points 8653 will have their non-negative value while points owned by different ranks will be involuted -(idx+1). As an example, 8654 consider a parallel mesh in which the first two elements and first two vertices are owned by rank 0. 8655 8656 The partitioned mesh is 8657 ``` 8658 (2)--0--(3)--1--(4) (1)--0--(2) 8659 ``` 8660 and its global numbering is 8661 ``` 8662 (3)--0--(4)--1--(5)--2--(6) 8663 ``` 8664 Then the global numbering is provided as 8665 ``` 8666 [0] Number of indices in set 5 8667 [0] 0 0 8668 [0] 1 1 8669 [0] 2 3 8670 [0] 3 4 8671 [0] 4 -6 8672 [1] Number of indices in set 3 8673 [1] 0 2 8674 [1] 1 5 8675 [1] 2 6 8676 ``` 8677 8678 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetCellNumbering()` 8679 @*/ 8680 PetscErrorCode DMPlexCreatePointNumbering(DM dm, IS *globalPointNumbers) 8681 { 8682 IS nums[4]; 8683 PetscInt depths[4], gdepths[4], starts[4]; 8684 PetscInt depth, d, shift = 0; 8685 PetscBool empty = PETSC_FALSE; 8686 8687 PetscFunctionBegin; 8688 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8689 PetscCall(DMPlexGetDepth(dm, &depth)); 8690 // For unstratified meshes use dim instead of depth 8691 if (depth < 0) PetscCall(DMGetDimension(dm, &depth)); 8692 // If any stratum is empty, we must mark all empty 8693 for (d = 0; d <= depth; ++d) { 8694 PetscInt end; 8695 8696 depths[d] = depth - d; 8697 PetscCall(DMPlexGetDepthStratum(dm, depths[d], &starts[d], &end)); 8698 if (!(starts[d] - end)) empty = PETSC_TRUE; 8699 } 8700 if (empty) 8701 for (d = 0; d <= depth; ++d) { 8702 depths[d] = -1; 8703 starts[d] = -1; 8704 } 8705 else PetscCall(PetscSortIntWithArray(depth + 1, starts, depths)); 8706 PetscCall(MPIU_Allreduce(depths, gdepths, depth + 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm))); 8707 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]); 8708 // Note here that 'shift' is collective, so that the numbering is stratified by depth 8709 for (d = 0; d <= depth; ++d) { 8710 PetscInt pStart, pEnd, gsize; 8711 8712 PetscCall(DMPlexGetDepthStratum(dm, gdepths[d], &pStart, &pEnd)); 8713 PetscCall(DMPlexCreateNumbering_Plex(dm, pStart, pEnd, shift, &gsize, dm->sf, &nums[d])); 8714 shift += gsize; 8715 } 8716 PetscCall(ISConcatenate(PETSC_COMM_SELF, depth + 1, nums, globalPointNumbers)); 8717 for (d = 0; d <= depth; ++d) PetscCall(ISDestroy(&nums[d])); 8718 PetscFunctionReturn(PETSC_SUCCESS); 8719 } 8720 8721 /*@ 8722 DMPlexCreateRankField - Create a cell field whose value is the rank of the owner 8723 8724 Input Parameter: 8725 . dm - The `DMPLEX` object 8726 8727 Output Parameter: 8728 . ranks - The rank field 8729 8730 Options Database Key: 8731 . -dm_partition_view - Adds the rank field into the `DM` output from `-dm_view` using the same viewer 8732 8733 Level: intermediate 8734 8735 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMView()` 8736 @*/ 8737 PetscErrorCode DMPlexCreateRankField(DM dm, Vec *ranks) 8738 { 8739 DM rdm; 8740 PetscFE fe; 8741 PetscScalar *r; 8742 PetscMPIInt rank; 8743 DMPolytopeType ct; 8744 PetscInt dim, cStart, cEnd, c; 8745 PetscBool simplex; 8746 8747 PetscFunctionBeginUser; 8748 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8749 PetscAssertPointer(ranks, 2); 8750 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 8751 PetscCall(DMClone(dm, &rdm)); 8752 PetscCall(DMGetDimension(rdm, &dim)); 8753 PetscCall(DMPlexGetHeightStratum(rdm, 0, &cStart, &cEnd)); 8754 PetscCall(DMPlexGetCellType(dm, cStart, &ct)); 8755 simplex = DMPolytopeTypeGetNumVertices(ct) == DMPolytopeTypeGetDim(ct) + 1 ? PETSC_TRUE : PETSC_FALSE; 8756 PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, simplex, "PETSc___rank_", -1, &fe)); 8757 PetscCall(PetscObjectSetName((PetscObject)fe, "rank")); 8758 PetscCall(DMSetField(rdm, 0, NULL, (PetscObject)fe)); 8759 PetscCall(PetscFEDestroy(&fe)); 8760 PetscCall(DMCreateDS(rdm)); 8761 PetscCall(DMCreateGlobalVector(rdm, ranks)); 8762 PetscCall(PetscObjectSetName((PetscObject)*ranks, "partition")); 8763 PetscCall(VecGetArray(*ranks, &r)); 8764 for (c = cStart; c < cEnd; ++c) { 8765 PetscScalar *lr; 8766 8767 PetscCall(DMPlexPointGlobalRef(rdm, c, r, &lr)); 8768 if (lr) *lr = rank; 8769 } 8770 PetscCall(VecRestoreArray(*ranks, &r)); 8771 PetscCall(DMDestroy(&rdm)); 8772 PetscFunctionReturn(PETSC_SUCCESS); 8773 } 8774 8775 /*@ 8776 DMPlexCreateLabelField - Create a cell field whose value is the label value for that cell 8777 8778 Input Parameters: 8779 + dm - The `DMPLEX` 8780 - label - The `DMLabel` 8781 8782 Output Parameter: 8783 . val - The label value field 8784 8785 Options Database Key: 8786 . -dm_label_view - Adds the label value field into the `DM` output from `-dm_view` using the same viewer 8787 8788 Level: intermediate 8789 8790 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMView()` 8791 @*/ 8792 PetscErrorCode DMPlexCreateLabelField(DM dm, DMLabel label, Vec *val) 8793 { 8794 DM rdm; 8795 PetscFE fe; 8796 PetscScalar *v; 8797 PetscInt dim, cStart, cEnd, c; 8798 8799 PetscFunctionBeginUser; 8800 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8801 PetscAssertPointer(label, 2); 8802 PetscAssertPointer(val, 3); 8803 PetscCall(DMClone(dm, &rdm)); 8804 PetscCall(DMGetDimension(rdm, &dim)); 8805 PetscCall(PetscFECreateDefault(PetscObjectComm((PetscObject)rdm), dim, 1, PETSC_TRUE, "PETSc___label_value_", -1, &fe)); 8806 PetscCall(PetscObjectSetName((PetscObject)fe, "label_value")); 8807 PetscCall(DMSetField(rdm, 0, NULL, (PetscObject)fe)); 8808 PetscCall(PetscFEDestroy(&fe)); 8809 PetscCall(DMCreateDS(rdm)); 8810 PetscCall(DMPlexGetHeightStratum(rdm, 0, &cStart, &cEnd)); 8811 PetscCall(DMCreateGlobalVector(rdm, val)); 8812 PetscCall(PetscObjectSetName((PetscObject)*val, "label_value")); 8813 PetscCall(VecGetArray(*val, &v)); 8814 for (c = cStart; c < cEnd; ++c) { 8815 PetscScalar *lv; 8816 PetscInt cval; 8817 8818 PetscCall(DMPlexPointGlobalRef(rdm, c, v, &lv)); 8819 PetscCall(DMLabelGetValue(label, c, &cval)); 8820 *lv = cval; 8821 } 8822 PetscCall(VecRestoreArray(*val, &v)); 8823 PetscCall(DMDestroy(&rdm)); 8824 PetscFunctionReturn(PETSC_SUCCESS); 8825 } 8826 8827 /*@ 8828 DMPlexCheckSymmetry - Check that the adjacency information in the mesh is symmetric. 8829 8830 Input Parameter: 8831 . dm - The `DMPLEX` object 8832 8833 Level: developer 8834 8835 Notes: 8836 This is a useful diagnostic when creating meshes programmatically. 8837 8838 For the complete list of DMPlexCheck* functions, see `DMSetFromOptions()`. 8839 8840 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMCreate()`, `DMSetFromOptions()` 8841 @*/ 8842 PetscErrorCode DMPlexCheckSymmetry(DM dm) 8843 { 8844 PetscSection coneSection, supportSection; 8845 const PetscInt *cone, *support; 8846 PetscInt coneSize, c, supportSize, s; 8847 PetscInt pStart, pEnd, p, pp, csize, ssize; 8848 PetscBool storagecheck = PETSC_TRUE; 8849 8850 PetscFunctionBegin; 8851 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8852 PetscCall(DMViewFromOptions(dm, NULL, "-sym_dm_view")); 8853 PetscCall(DMPlexGetConeSection(dm, &coneSection)); 8854 PetscCall(DMPlexGetSupportSection(dm, &supportSection)); 8855 /* Check that point p is found in the support of its cone points, and vice versa */ 8856 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 8857 for (p = pStart; p < pEnd; ++p) { 8858 PetscCall(DMPlexGetConeSize(dm, p, &coneSize)); 8859 PetscCall(DMPlexGetCone(dm, p, &cone)); 8860 for (c = 0; c < coneSize; ++c) { 8861 PetscBool dup = PETSC_FALSE; 8862 PetscInt d; 8863 for (d = c - 1; d >= 0; --d) { 8864 if (cone[c] == cone[d]) { 8865 dup = PETSC_TRUE; 8866 break; 8867 } 8868 } 8869 PetscCall(DMPlexGetSupportSize(dm, cone[c], &supportSize)); 8870 PetscCall(DMPlexGetSupport(dm, cone[c], &support)); 8871 for (s = 0; s < supportSize; ++s) { 8872 if (support[s] == p) break; 8873 } 8874 if ((s >= supportSize) || (dup && (support[s + 1] != p))) { 8875 PetscCall(PetscPrintf(PETSC_COMM_SELF, "p: %" PetscInt_FMT " cone: ", p)); 8876 for (s = 0; s < coneSize; ++s) PetscCall(PetscPrintf(PETSC_COMM_SELF, "%" PetscInt_FMT ", ", cone[s])); 8877 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 8878 PetscCall(PetscPrintf(PETSC_COMM_SELF, "p: %" PetscInt_FMT " support: ", cone[c])); 8879 for (s = 0; s < supportSize; ++s) PetscCall(PetscPrintf(PETSC_COMM_SELF, "%" PetscInt_FMT ", ", support[s])); 8880 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 8881 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]); 8882 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %" PetscInt_FMT " not found in support of cone point %" PetscInt_FMT, p, cone[c]); 8883 } 8884 } 8885 PetscCall(DMPlexGetTreeParent(dm, p, &pp, NULL)); 8886 if (p != pp) { 8887 storagecheck = PETSC_FALSE; 8888 continue; 8889 } 8890 PetscCall(DMPlexGetSupportSize(dm, p, &supportSize)); 8891 PetscCall(DMPlexGetSupport(dm, p, &support)); 8892 for (s = 0; s < supportSize; ++s) { 8893 PetscCall(DMPlexGetConeSize(dm, support[s], &coneSize)); 8894 PetscCall(DMPlexGetCone(dm, support[s], &cone)); 8895 for (c = 0; c < coneSize; ++c) { 8896 PetscCall(DMPlexGetTreeParent(dm, cone[c], &pp, NULL)); 8897 if (cone[c] != pp) { 8898 c = 0; 8899 break; 8900 } 8901 if (cone[c] == p) break; 8902 } 8903 if (c >= coneSize) { 8904 PetscCall(PetscPrintf(PETSC_COMM_SELF, "p: %" PetscInt_FMT " support: ", p)); 8905 for (c = 0; c < supportSize; ++c) PetscCall(PetscPrintf(PETSC_COMM_SELF, "%" PetscInt_FMT ", ", support[c])); 8906 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 8907 PetscCall(PetscPrintf(PETSC_COMM_SELF, "p: %" PetscInt_FMT " cone: ", support[s])); 8908 for (c = 0; c < coneSize; ++c) PetscCall(PetscPrintf(PETSC_COMM_SELF, "%" PetscInt_FMT ", ", cone[c])); 8909 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 8910 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %" PetscInt_FMT " not found in cone of support point %" PetscInt_FMT, p, support[s]); 8911 } 8912 } 8913 } 8914 if (storagecheck) { 8915 PetscCall(PetscSectionGetStorageSize(coneSection, &csize)); 8916 PetscCall(PetscSectionGetStorageSize(supportSection, &ssize)); 8917 PetscCheck(csize == ssize, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Total cone size %" PetscInt_FMT " != Total support size %" PetscInt_FMT, csize, ssize); 8918 } 8919 PetscFunctionReturn(PETSC_SUCCESS); 8920 } 8921 8922 /* 8923 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. 8924 */ 8925 static PetscErrorCode DMPlexCellUnsplitVertices_Private(DM dm, PetscInt c, DMPolytopeType ct, PetscInt *unsplit) 8926 { 8927 DMPolytopeType cct; 8928 PetscInt ptpoints[4]; 8929 const PetscInt *cone, *ccone, *ptcone; 8930 PetscInt coneSize, cp, cconeSize, ccp, npt = 0, pt; 8931 8932 PetscFunctionBegin; 8933 *unsplit = 0; 8934 switch (ct) { 8935 case DM_POLYTOPE_POINT_PRISM_TENSOR: 8936 ptpoints[npt++] = c; 8937 break; 8938 case DM_POLYTOPE_SEG_PRISM_TENSOR: 8939 PetscCall(DMPlexGetCone(dm, c, &cone)); 8940 PetscCall(DMPlexGetConeSize(dm, c, &coneSize)); 8941 for (cp = 0; cp < coneSize; ++cp) { 8942 PetscCall(DMPlexGetCellType(dm, cone[cp], &cct)); 8943 if (cct == DM_POLYTOPE_POINT_PRISM_TENSOR) ptpoints[npt++] = cone[cp]; 8944 } 8945 break; 8946 case DM_POLYTOPE_TRI_PRISM_TENSOR: 8947 case DM_POLYTOPE_QUAD_PRISM_TENSOR: 8948 PetscCall(DMPlexGetCone(dm, c, &cone)); 8949 PetscCall(DMPlexGetConeSize(dm, c, &coneSize)); 8950 for (cp = 0; cp < coneSize; ++cp) { 8951 PetscCall(DMPlexGetCone(dm, cone[cp], &ccone)); 8952 PetscCall(DMPlexGetConeSize(dm, cone[cp], &cconeSize)); 8953 for (ccp = 0; ccp < cconeSize; ++ccp) { 8954 PetscCall(DMPlexGetCellType(dm, ccone[ccp], &cct)); 8955 if (cct == DM_POLYTOPE_POINT_PRISM_TENSOR) { 8956 PetscInt p; 8957 for (p = 0; p < npt; ++p) 8958 if (ptpoints[p] == ccone[ccp]) break; 8959 if (p == npt) ptpoints[npt++] = ccone[ccp]; 8960 } 8961 } 8962 } 8963 break; 8964 default: 8965 break; 8966 } 8967 for (pt = 0; pt < npt; ++pt) { 8968 PetscCall(DMPlexGetCone(dm, ptpoints[pt], &ptcone)); 8969 if (ptcone[0] == ptcone[1]) ++(*unsplit); 8970 } 8971 PetscFunctionReturn(PETSC_SUCCESS); 8972 } 8973 8974 /*@ 8975 DMPlexCheckSkeleton - Check that each cell has the correct number of vertices 8976 8977 Input Parameters: 8978 + dm - The `DMPLEX` object 8979 - cellHeight - Normally 0 8980 8981 Level: developer 8982 8983 Notes: 8984 This is a useful diagnostic when creating meshes programmatically. 8985 Currently applicable only to homogeneous simplex or tensor meshes. 8986 8987 For the complete list of DMPlexCheck* functions, see `DMSetFromOptions()`. 8988 8989 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMCreate()`, `DMSetFromOptions()` 8990 @*/ 8991 PetscErrorCode DMPlexCheckSkeleton(DM dm, PetscInt cellHeight) 8992 { 8993 DMPlexInterpolatedFlag interp; 8994 DMPolytopeType ct; 8995 PetscInt vStart, vEnd, cStart, cEnd, c; 8996 8997 PetscFunctionBegin; 8998 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 8999 PetscCall(DMPlexIsInterpolated(dm, &interp)); 9000 PetscCall(DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd)); 9001 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 9002 for (c = cStart; c < cEnd; ++c) { 9003 PetscInt *closure = NULL; 9004 PetscInt coneSize, closureSize, cl, Nv = 0; 9005 9006 PetscCall(DMPlexGetCellType(dm, c, &ct)); 9007 PetscCheck((PetscInt)ct >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %" PetscInt_FMT " has no cell type", c); 9008 if (ct == DM_POLYTOPE_UNKNOWN) continue; 9009 if (interp == DMPLEX_INTERPOLATED_FULL) { 9010 PetscCall(DMPlexGetConeSize(dm, c, &coneSize)); 9011 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)); 9012 } 9013 PetscCall(DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 9014 for (cl = 0; cl < closureSize * 2; cl += 2) { 9015 const PetscInt p = closure[cl]; 9016 if ((p >= vStart) && (p < vEnd)) ++Nv; 9017 } 9018 PetscCall(DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 9019 /* Special Case: Tensor faces with identified vertices */ 9020 if (Nv < DMPolytopeTypeGetNumVertices(ct)) { 9021 PetscInt unsplit; 9022 9023 PetscCall(DMPlexCellUnsplitVertices_Private(dm, c, ct, &unsplit)); 9024 if (Nv + unsplit == DMPolytopeTypeGetNumVertices(ct)) continue; 9025 } 9026 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)); 9027 } 9028 PetscFunctionReturn(PETSC_SUCCESS); 9029 } 9030 9031 /*@ 9032 DMPlexCheckFaces - Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type 9033 9034 Collective 9035 9036 Input Parameters: 9037 + dm - The `DMPLEX` object 9038 - cellHeight - Normally 0 9039 9040 Level: developer 9041 9042 Notes: 9043 This is a useful diagnostic when creating meshes programmatically. 9044 This routine is only relevant for meshes that are fully interpolated across all ranks. 9045 It will error out if a partially interpolated mesh is given on some rank. 9046 It will do nothing for locally uninterpolated mesh (as there is nothing to check). 9047 9048 For the complete list of DMPlexCheck* functions, see `DMSetFromOptions()`. 9049 9050 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMCreate()`, `DMPlexGetVTKCellHeight()`, `DMSetFromOptions()` 9051 @*/ 9052 PetscErrorCode DMPlexCheckFaces(DM dm, PetscInt cellHeight) 9053 { 9054 PetscInt dim, depth, vStart, vEnd, cStart, cEnd, c, h; 9055 DMPlexInterpolatedFlag interpEnum; 9056 9057 PetscFunctionBegin; 9058 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 9059 PetscCall(DMPlexIsInterpolatedCollective(dm, &interpEnum)); 9060 if (interpEnum == DMPLEX_INTERPOLATED_NONE) PetscFunctionReturn(PETSC_SUCCESS); 9061 if (interpEnum != DMPLEX_INTERPOLATED_FULL) { 9062 PetscCall(PetscPrintf(PetscObjectComm((PetscObject)dm), "DMPlexCheckFaces() warning: Mesh is only partially interpolated, this is currently not supported")); 9063 PetscFunctionReturn(PETSC_SUCCESS); 9064 } 9065 9066 PetscCall(DMGetDimension(dm, &dim)); 9067 PetscCall(DMPlexGetDepth(dm, &depth)); 9068 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 9069 for (h = cellHeight; h < PetscMin(depth, dim); ++h) { 9070 PetscCall(DMPlexGetHeightStratum(dm, h, &cStart, &cEnd)); 9071 for (c = cStart; c < cEnd; ++c) { 9072 const PetscInt *cone, *ornt, *faceSizes, *faces; 9073 const DMPolytopeType *faceTypes; 9074 DMPolytopeType ct; 9075 PetscInt numFaces, coneSize, f; 9076 PetscInt *closure = NULL, closureSize, cl, numCorners = 0, fOff = 0, unsplit; 9077 9078 PetscCall(DMPlexGetCellType(dm, c, &ct)); 9079 PetscCall(DMPlexCellUnsplitVertices_Private(dm, c, ct, &unsplit)); 9080 if (unsplit) continue; 9081 PetscCall(DMPlexGetConeSize(dm, c, &coneSize)); 9082 PetscCall(DMPlexGetCone(dm, c, &cone)); 9083 PetscCall(DMPlexGetConeOrientation(dm, c, &ornt)); 9084 PetscCall(DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 9085 for (cl = 0; cl < closureSize * 2; cl += 2) { 9086 const PetscInt p = closure[cl]; 9087 if ((p >= vStart) && (p < vEnd)) closure[numCorners++] = p; 9088 } 9089 PetscCall(DMPlexGetRawFaces_Internal(dm, ct, closure, &numFaces, &faceTypes, &faceSizes, &faces)); 9090 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); 9091 for (f = 0; f < numFaces; ++f) { 9092 DMPolytopeType fct; 9093 PetscInt *fclosure = NULL, fclosureSize, cl, fnumCorners = 0, v; 9094 9095 PetscCall(DMPlexGetCellType(dm, cone[f], &fct)); 9096 PetscCall(DMPlexGetTransitiveClosure_Internal(dm, cone[f], ornt[f], PETSC_TRUE, &fclosureSize, &fclosure)); 9097 for (cl = 0; cl < fclosureSize * 2; cl += 2) { 9098 const PetscInt p = fclosure[cl]; 9099 if ((p >= vStart) && (p < vEnd)) fclosure[fnumCorners++] = p; 9100 } 9101 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]); 9102 for (v = 0; v < fnumCorners; ++v) { 9103 if (fclosure[v] != faces[fOff + v]) { 9104 PetscInt v1; 9105 9106 PetscCall(PetscPrintf(PETSC_COMM_SELF, "face closure:")); 9107 for (v1 = 0; v1 < fnumCorners; ++v1) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, fclosure[v1])); 9108 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\ncell face:")); 9109 for (v1 = 0; v1 < fnumCorners; ++v1) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, faces[fOff + v1])); 9110 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 9111 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]); 9112 } 9113 } 9114 PetscCall(DMPlexRestoreTransitiveClosure(dm, cone[f], PETSC_TRUE, &fclosureSize, &fclosure)); 9115 fOff += faceSizes[f]; 9116 } 9117 PetscCall(DMPlexRestoreRawFaces_Internal(dm, ct, closure, &numFaces, &faceTypes, &faceSizes, &faces)); 9118 PetscCall(DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure)); 9119 } 9120 } 9121 PetscFunctionReturn(PETSC_SUCCESS); 9122 } 9123 9124 /*@ 9125 DMPlexCheckGeometry - Check the geometry of mesh cells 9126 9127 Input Parameter: 9128 . dm - The `DMPLEX` object 9129 9130 Level: developer 9131 9132 Notes: 9133 This is a useful diagnostic when creating meshes programmatically. 9134 9135 For the complete list of DMPlexCheck* functions, see `DMSetFromOptions()`. 9136 9137 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMCreate()`, `DMSetFromOptions()` 9138 @*/ 9139 PetscErrorCode DMPlexCheckGeometry(DM dm) 9140 { 9141 Vec coordinates; 9142 PetscReal detJ, J[9], refVol = 1.0; 9143 PetscReal vol; 9144 PetscInt dim, depth, dE, d, cStart, cEnd, c; 9145 9146 PetscFunctionBegin; 9147 PetscCall(DMGetDimension(dm, &dim)); 9148 PetscCall(DMGetCoordinateDim(dm, &dE)); 9149 if (dim != dE) PetscFunctionReturn(PETSC_SUCCESS); 9150 PetscCall(DMPlexGetDepth(dm, &depth)); 9151 for (d = 0; d < dim; ++d) refVol *= 2.0; 9152 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 9153 /* Make sure local coordinates are created, because that step is collective */ 9154 PetscCall(DMGetCoordinatesLocal(dm, &coordinates)); 9155 if (!coordinates) PetscFunctionReturn(PETSC_SUCCESS); 9156 for (c = cStart; c < cEnd; ++c) { 9157 DMPolytopeType ct; 9158 PetscInt unsplit; 9159 PetscBool ignoreZeroVol = PETSC_FALSE; 9160 9161 PetscCall(DMPlexGetCellType(dm, c, &ct)); 9162 switch (ct) { 9163 case DM_POLYTOPE_SEG_PRISM_TENSOR: 9164 case DM_POLYTOPE_TRI_PRISM_TENSOR: 9165 case DM_POLYTOPE_QUAD_PRISM_TENSOR: 9166 ignoreZeroVol = PETSC_TRUE; 9167 break; 9168 default: 9169 break; 9170 } 9171 switch (ct) { 9172 case DM_POLYTOPE_TRI_PRISM: 9173 case DM_POLYTOPE_TRI_PRISM_TENSOR: 9174 case DM_POLYTOPE_QUAD_PRISM_TENSOR: 9175 case DM_POLYTOPE_PYRAMID: 9176 continue; 9177 default: 9178 break; 9179 } 9180 PetscCall(DMPlexCellUnsplitVertices_Private(dm, c, ct, &unsplit)); 9181 if (unsplit) continue; 9182 PetscCall(DMPlexComputeCellGeometryFEM(dm, c, NULL, NULL, J, NULL, &detJ)); 9183 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); 9184 PetscCall(PetscInfo(dm, "Cell %" PetscInt_FMT " FEM Volume %g\n", c, (double)(detJ * refVol))); 9185 /* This should work with periodicity since DG coordinates should be used */ 9186 if (depth > 1) { 9187 PetscCall(DMPlexComputeCellGeometryFVM(dm, c, &vol, NULL, NULL)); 9188 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); 9189 PetscCall(PetscInfo(dm, "Cell %" PetscInt_FMT " FVM Volume %g\n", c, (double)vol)); 9190 } 9191 } 9192 PetscFunctionReturn(PETSC_SUCCESS); 9193 } 9194 9195 /*@ 9196 DMPlexCheckPointSF - Check that several necessary conditions are met for the point `PetscSF` of this plex. 9197 9198 Collective 9199 9200 Input Parameters: 9201 + dm - The `DMPLEX` object 9202 . pointSF - The `PetscSF`, or `NULL` for `PointSF` attached to `DM` 9203 - allowExtraRoots - Flag to allow extra points not present in the `DM` 9204 9205 Level: developer 9206 9207 Notes: 9208 This is mainly intended for debugging/testing purposes. 9209 9210 For the complete list of DMPlexCheck* functions, see `DMSetFromOptions()`. 9211 9212 Extra roots can come from periodic cuts, where additional points appear on the boundary 9213 9214 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMGetPointSF()`, `DMSetFromOptions()` 9215 @*/ 9216 PetscErrorCode DMPlexCheckPointSF(DM dm, PetscSF pointSF, PetscBool allowExtraRoots) 9217 { 9218 PetscInt l, nleaves, nroots, overlap; 9219 const PetscInt *locals; 9220 const PetscSFNode *remotes; 9221 PetscBool distributed; 9222 MPI_Comm comm; 9223 PetscMPIInt rank; 9224 9225 PetscFunctionBegin; 9226 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 9227 if (pointSF) PetscValidHeaderSpecific(pointSF, PETSCSF_CLASSID, 2); 9228 else pointSF = dm->sf; 9229 PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); 9230 PetscCheck(pointSF, comm, PETSC_ERR_ARG_WRONGSTATE, "DMPlex must have Point SF attached"); 9231 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 9232 { 9233 PetscMPIInt mpiFlag; 9234 9235 PetscCallMPI(MPI_Comm_compare(comm, PetscObjectComm((PetscObject)pointSF), &mpiFlag)); 9236 PetscCheck(mpiFlag == MPI_CONGRUENT || mpiFlag == MPI_IDENT, PETSC_COMM_SELF, PETSC_ERR_ARG_NOTSAMECOMM, "DM and Point SF have different communicators (flag %d)", mpiFlag); 9237 } 9238 PetscCall(PetscSFGetGraph(pointSF, &nroots, &nleaves, &locals, &remotes)); 9239 PetscCall(DMPlexIsDistributed(dm, &distributed)); 9240 if (!distributed) { 9241 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); 9242 PetscFunctionReturn(PETSC_SUCCESS); 9243 } 9244 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); 9245 PetscCall(DMPlexGetOverlap(dm, &overlap)); 9246 9247 /* Check SF graph is compatible with DMPlex chart */ 9248 { 9249 PetscInt pStart, pEnd, maxLeaf; 9250 9251 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 9252 PetscCall(PetscSFGetLeafRange(pointSF, NULL, &maxLeaf)); 9253 PetscCheck(allowExtraRoots || pEnd - pStart == nroots, PETSC_COMM_SELF, PETSC_ERR_PLIB, "pEnd - pStart = %" PetscInt_FMT " != nroots = %" PetscInt_FMT, pEnd - pStart, nroots); 9254 PetscCheck(maxLeaf < pEnd, PETSC_COMM_SELF, PETSC_ERR_PLIB, "maxLeaf = %" PetscInt_FMT " >= pEnd = %" PetscInt_FMT, maxLeaf, pEnd); 9255 } 9256 9257 /* Check Point SF has no local points referenced */ 9258 for (l = 0; l < nleaves; l++) { 9259 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); 9260 } 9261 9262 /* Check there are no cells in interface */ 9263 if (!overlap) { 9264 PetscInt cellHeight, cStart, cEnd; 9265 9266 PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight)); 9267 PetscCall(DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd)); 9268 for (l = 0; l < nleaves; ++l) { 9269 const PetscInt point = locals ? locals[l] : l; 9270 9271 PetscCheck(point < cStart || point >= cEnd, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point SF contains %" PetscInt_FMT " which is a cell", point); 9272 } 9273 } 9274 9275 /* If some point is in interface, then all its cone points must be also in interface (either as leaves or roots) */ 9276 { 9277 const PetscInt *rootdegree; 9278 9279 PetscCall(PetscSFComputeDegreeBegin(pointSF, &rootdegree)); 9280 PetscCall(PetscSFComputeDegreeEnd(pointSF, &rootdegree)); 9281 for (l = 0; l < nleaves; ++l) { 9282 const PetscInt point = locals ? locals[l] : l; 9283 const PetscInt *cone; 9284 PetscInt coneSize, c, idx; 9285 9286 PetscCall(DMPlexGetConeSize(dm, point, &coneSize)); 9287 PetscCall(DMPlexGetCone(dm, point, &cone)); 9288 for (c = 0; c < coneSize; ++c) { 9289 if (!rootdegree[cone[c]]) { 9290 if (locals) { 9291 PetscCall(PetscFindInt(cone[c], nleaves, locals, &idx)); 9292 } else { 9293 idx = (cone[c] < nleaves) ? cone[c] : -1; 9294 } 9295 PetscCheck(idx >= 0, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point SF contains %" PetscInt_FMT " but not %" PetscInt_FMT " from its cone", point, cone[c]); 9296 } 9297 } 9298 } 9299 } 9300 PetscFunctionReturn(PETSC_SUCCESS); 9301 } 9302 9303 /*@ 9304 DMPlexCheck - Perform various checks of `DMPLEX` sanity 9305 9306 Input Parameter: 9307 . dm - The `DMPLEX` object 9308 9309 Level: developer 9310 9311 Notes: 9312 This is a useful diagnostic when creating meshes programmatically. 9313 9314 For the complete list of DMPlexCheck* functions, see `DMSetFromOptions()`. 9315 9316 Currently does not include `DMPlexCheckCellShape()`. 9317 9318 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMCreate()`, `DMSetFromOptions()` 9319 @*/ 9320 PetscErrorCode DMPlexCheck(DM dm) 9321 { 9322 PetscInt cellHeight; 9323 9324 PetscFunctionBegin; 9325 PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight)); 9326 PetscCall(DMPlexCheckSymmetry(dm)); 9327 PetscCall(DMPlexCheckSkeleton(dm, cellHeight)); 9328 PetscCall(DMPlexCheckFaces(dm, cellHeight)); 9329 PetscCall(DMPlexCheckGeometry(dm)); 9330 PetscCall(DMPlexCheckPointSF(dm, NULL, PETSC_FALSE)); 9331 PetscCall(DMPlexCheckInterfaceCones(dm)); 9332 PetscFunctionReturn(PETSC_SUCCESS); 9333 } 9334 9335 typedef struct cell_stats { 9336 PetscReal min, max, sum, squaresum; 9337 PetscInt count; 9338 } cell_stats_t; 9339 9340 static void MPIAPI cell_stats_reduce(void *a, void *b, int *len, MPI_Datatype *datatype) 9341 { 9342 PetscInt i, N = *len; 9343 9344 for (i = 0; i < N; i++) { 9345 cell_stats_t *A = (cell_stats_t *)a; 9346 cell_stats_t *B = (cell_stats_t *)b; 9347 9348 B->min = PetscMin(A->min, B->min); 9349 B->max = PetscMax(A->max, B->max); 9350 B->sum += A->sum; 9351 B->squaresum += A->squaresum; 9352 B->count += A->count; 9353 } 9354 } 9355 9356 /*@ 9357 DMPlexCheckCellShape - Checks the Jacobian of the mapping from reference to real cells and computes some minimal statistics. 9358 9359 Collective 9360 9361 Input Parameters: 9362 + dm - The `DMPLEX` object 9363 . output - If true, statistics will be displayed on `stdout` 9364 - condLimit - Display all cells above this condition number, or `PETSC_DETERMINE` for no cell output 9365 9366 Level: developer 9367 9368 Notes: 9369 This is mainly intended for debugging/testing purposes. 9370 9371 For the complete list of DMPlexCheck* functions, see `DMSetFromOptions()`. 9372 9373 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMSetFromOptions()`, `DMPlexComputeOrthogonalQuality()` 9374 @*/ 9375 PetscErrorCode DMPlexCheckCellShape(DM dm, PetscBool output, PetscReal condLimit) 9376 { 9377 DM dmCoarse; 9378 cell_stats_t stats, globalStats; 9379 MPI_Comm comm = PetscObjectComm((PetscObject)dm); 9380 PetscReal *J, *invJ, min = 0, max = 0, mean = 0, stdev = 0; 9381 PetscReal limit = condLimit > 0 ? condLimit : PETSC_MAX_REAL; 9382 PetscInt cdim, cStart, cEnd, c, eStart, eEnd, count = 0; 9383 PetscMPIInt rank, size; 9384 9385 PetscFunctionBegin; 9386 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 9387 stats.min = PETSC_MAX_REAL; 9388 stats.max = PETSC_MIN_REAL; 9389 stats.sum = stats.squaresum = 0.; 9390 stats.count = 0; 9391 9392 PetscCallMPI(MPI_Comm_size(comm, &size)); 9393 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 9394 PetscCall(DMGetCoordinateDim(dm, &cdim)); 9395 PetscCall(PetscMalloc2(PetscSqr(cdim), &J, PetscSqr(cdim), &invJ)); 9396 PetscCall(DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd)); 9397 PetscCall(DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd)); 9398 for (c = cStart; c < cEnd; c++) { 9399 PetscInt i; 9400 PetscReal frobJ = 0., frobInvJ = 0., cond2, cond, detJ; 9401 9402 PetscCall(DMPlexComputeCellGeometryAffineFEM(dm, c, NULL, J, invJ, &detJ)); 9403 PetscCheck(detJ >= 0.0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh cell %" PetscInt_FMT " is inverted", c); 9404 for (i = 0; i < PetscSqr(cdim); ++i) { 9405 frobJ += J[i] * J[i]; 9406 frobInvJ += invJ[i] * invJ[i]; 9407 } 9408 cond2 = frobJ * frobInvJ; 9409 cond = PetscSqrtReal(cond2); 9410 9411 stats.min = PetscMin(stats.min, cond); 9412 stats.max = PetscMax(stats.max, cond); 9413 stats.sum += cond; 9414 stats.squaresum += cond2; 9415 stats.count++; 9416 if (output && cond > limit) { 9417 PetscSection coordSection; 9418 Vec coordsLocal; 9419 PetscScalar *coords = NULL; 9420 PetscInt Nv, d, clSize, cl, *closure = NULL; 9421 9422 PetscCall(DMGetCoordinatesLocal(dm, &coordsLocal)); 9423 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 9424 PetscCall(DMPlexVecGetClosure(dm, coordSection, coordsLocal, c, &Nv, &coords)); 9425 PetscCall(PetscSynchronizedPrintf(comm, "[%d] Cell %" PetscInt_FMT " cond %g\n", rank, c, (double)cond)); 9426 for (i = 0; i < Nv / cdim; ++i) { 9427 PetscCall(PetscSynchronizedPrintf(comm, " Vertex %" PetscInt_FMT ": (", i)); 9428 for (d = 0; d < cdim; ++d) { 9429 if (d > 0) PetscCall(PetscSynchronizedPrintf(comm, ", ")); 9430 PetscCall(PetscSynchronizedPrintf(comm, "%g", (double)PetscRealPart(coords[i * cdim + d]))); 9431 } 9432 PetscCall(PetscSynchronizedPrintf(comm, ")\n")); 9433 } 9434 PetscCall(DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &clSize, &closure)); 9435 for (cl = 0; cl < clSize * 2; cl += 2) { 9436 const PetscInt edge = closure[cl]; 9437 9438 if ((edge >= eStart) && (edge < eEnd)) { 9439 PetscReal len; 9440 9441 PetscCall(DMPlexComputeCellGeometryFVM(dm, edge, &len, NULL, NULL)); 9442 PetscCall(PetscSynchronizedPrintf(comm, " Edge %" PetscInt_FMT ": length %g\n", edge, (double)len)); 9443 } 9444 } 9445 PetscCall(DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &clSize, &closure)); 9446 PetscCall(DMPlexVecRestoreClosure(dm, coordSection, coordsLocal, c, &Nv, &coords)); 9447 } 9448 } 9449 if (output) PetscCall(PetscSynchronizedFlush(comm, NULL)); 9450 9451 if (size > 1) { 9452 PetscMPIInt blockLengths[2] = {4, 1}; 9453 MPI_Aint blockOffsets[2] = {offsetof(cell_stats_t, min), offsetof(cell_stats_t, count)}; 9454 MPI_Datatype blockTypes[2] = {MPIU_REAL, MPIU_INT}, statType; 9455 MPI_Op statReduce; 9456 9457 PetscCallMPI(MPI_Type_create_struct(2, blockLengths, blockOffsets, blockTypes, &statType)); 9458 PetscCallMPI(MPI_Type_commit(&statType)); 9459 PetscCallMPI(MPI_Op_create(cell_stats_reduce, PETSC_TRUE, &statReduce)); 9460 PetscCallMPI(MPI_Reduce(&stats, &globalStats, 1, statType, statReduce, 0, comm)); 9461 PetscCallMPI(MPI_Op_free(&statReduce)); 9462 PetscCallMPI(MPI_Type_free(&statType)); 9463 } else { 9464 PetscCall(PetscArraycpy(&globalStats, &stats, 1)); 9465 } 9466 if (rank == 0) { 9467 count = globalStats.count; 9468 min = globalStats.min; 9469 max = globalStats.max; 9470 mean = globalStats.sum / globalStats.count; 9471 stdev = globalStats.count > 1 ? PetscSqrtReal(PetscMax((globalStats.squaresum - globalStats.count * mean * mean) / (globalStats.count - 1), 0)) : 0.0; 9472 } 9473 9474 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)); 9475 PetscCall(PetscFree2(J, invJ)); 9476 9477 PetscCall(DMGetCoarseDM(dm, &dmCoarse)); 9478 if (dmCoarse) { 9479 PetscBool isplex; 9480 9481 PetscCall(PetscObjectTypeCompare((PetscObject)dmCoarse, DMPLEX, &isplex)); 9482 if (isplex) PetscCall(DMPlexCheckCellShape(dmCoarse, output, condLimit)); 9483 } 9484 PetscFunctionReturn(PETSC_SUCCESS); 9485 } 9486 9487 /*@ 9488 DMPlexComputeOrthogonalQuality - Compute cell-wise orthogonal quality mesh statistic. Optionally tags all cells with 9489 orthogonal quality below given tolerance. 9490 9491 Collective 9492 9493 Input Parameters: 9494 + dm - The `DMPLEX` object 9495 . fv - Optional `PetscFV` object for pre-computed cell/face centroid information 9496 - atol - [0, 1] Absolute tolerance for tagging cells. 9497 9498 Output Parameters: 9499 + OrthQual - `Vec` containing orthogonal quality per cell 9500 - OrthQualLabel - `DMLabel` tagging cells below atol with `DM_ADAPT_REFINE` 9501 9502 Options Database Keys: 9503 + -dm_plex_orthogonal_quality_label_view - view OrthQualLabel if label is requested. Currently only `PETSCVIEWERASCII` is supported. 9504 - -dm_plex_orthogonal_quality_vec_view - view OrthQual vector. 9505 9506 Level: intermediate 9507 9508 Notes: 9509 Orthogonal quality is given by the following formula\: 9510 9511 $ \min \left[ \frac{A_i \cdot f_i}{\|A_i\| \|f_i\|} , \frac{A_i \cdot c_i}{\|A_i\| \|c_i\|} \right]$ 9512 9513 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 9514 is the vector from the current cells centroid to the centroid of its i'th neighbor (which shares a face with the 9515 current cell). This computes the vector similarity between each cell face and its corresponding neighbor centroid by 9516 calculating the cosine of the angle between these vectors. 9517 9518 Orthogonal quality ranges from 1 (best) to 0 (worst). 9519 9520 This routine is mainly useful for FVM, however is not restricted to only FVM. The `PetscFV` object is optionally used to check for 9521 pre-computed FVM cell data, but if it is not passed in then this data will be computed. 9522 9523 Cells are tagged if they have an orthogonal quality less than or equal to the absolute tolerance. 9524 9525 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCheckCellShape()`, `DMCreateLabel()`, `PetscFV`, `DMLabel`, `Vec` 9526 @*/ 9527 PetscErrorCode DMPlexComputeOrthogonalQuality(DM dm, PetscFV fv, PetscReal atol, Vec *OrthQual, DMLabel *OrthQualLabel) 9528 { 9529 PetscInt nc, cellHeight, cStart, cEnd, cell, cellIter = 0; 9530 PetscInt *idx; 9531 PetscScalar *oqVals; 9532 const PetscScalar *cellGeomArr, *faceGeomArr; 9533 PetscReal *ci, *fi, *Ai; 9534 MPI_Comm comm; 9535 Vec cellgeom, facegeom; 9536 DM dmFace, dmCell; 9537 IS glob; 9538 ISLocalToGlobalMapping ltog; 9539 PetscViewer vwr; 9540 9541 PetscFunctionBegin; 9542 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 9543 if (fv) PetscValidHeaderSpecific(fv, PETSCFV_CLASSID, 2); 9544 PetscAssertPointer(OrthQual, 4); 9545 PetscCheck(atol >= 0.0 && atol <= 1.0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Absolute tolerance %g not in [0,1]", (double)atol); 9546 PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); 9547 PetscCall(DMGetDimension(dm, &nc)); 9548 PetscCheck(nc >= 2, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "DM must have dimension >= 2 (current %" PetscInt_FMT ")", nc); 9549 { 9550 DMPlexInterpolatedFlag interpFlag; 9551 9552 PetscCall(DMPlexIsInterpolated(dm, &interpFlag)); 9553 if (interpFlag != DMPLEX_INTERPOLATED_FULL) { 9554 PetscMPIInt rank; 9555 9556 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 9557 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "DM must be fully interpolated, DM on rank %d is not fully interpolated", rank); 9558 } 9559 } 9560 if (OrthQualLabel) { 9561 PetscAssertPointer(OrthQualLabel, 5); 9562 PetscCall(DMCreateLabel(dm, "Orthogonal_Quality")); 9563 PetscCall(DMGetLabel(dm, "Orthogonal_Quality", OrthQualLabel)); 9564 } else { 9565 *OrthQualLabel = NULL; 9566 } 9567 PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight)); 9568 PetscCall(DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd)); 9569 PetscCall(DMPlexCreateCellNumbering_Internal(dm, PETSC_TRUE, &glob)); 9570 PetscCall(ISLocalToGlobalMappingCreateIS(glob, <og)); 9571 PetscCall(ISLocalToGlobalMappingSetType(ltog, ISLOCALTOGLOBALMAPPINGHASH)); 9572 PetscCall(VecCreate(comm, OrthQual)); 9573 PetscCall(VecSetType(*OrthQual, VECSTANDARD)); 9574 PetscCall(VecSetSizes(*OrthQual, cEnd - cStart, PETSC_DETERMINE)); 9575 PetscCall(VecSetLocalToGlobalMapping(*OrthQual, ltog)); 9576 PetscCall(VecSetUp(*OrthQual)); 9577 PetscCall(ISDestroy(&glob)); 9578 PetscCall(ISLocalToGlobalMappingDestroy(<og)); 9579 PetscCall(DMPlexGetDataFVM(dm, fv, &cellgeom, &facegeom, NULL)); 9580 PetscCall(VecGetArrayRead(cellgeom, &cellGeomArr)); 9581 PetscCall(VecGetArrayRead(facegeom, &faceGeomArr)); 9582 PetscCall(VecGetDM(cellgeom, &dmCell)); 9583 PetscCall(VecGetDM(facegeom, &dmFace)); 9584 PetscCall(PetscMalloc5(cEnd - cStart, &idx, cEnd - cStart, &oqVals, nc, &ci, nc, &fi, nc, &Ai)); 9585 for (cell = cStart; cell < cEnd; cellIter++, cell++) { 9586 PetscInt cellneigh, cellneighiter = 0, adjSize = PETSC_DETERMINE; 9587 PetscInt cellarr[2], *adj = NULL; 9588 PetscScalar *cArr, *fArr; 9589 PetscReal minvalc = 1.0, minvalf = 1.0; 9590 PetscFVCellGeom *cg; 9591 9592 idx[cellIter] = cell - cStart; 9593 cellarr[0] = cell; 9594 /* Make indexing into cellGeom easier */ 9595 PetscCall(DMPlexPointLocalRead(dmCell, cell, cellGeomArr, &cg)); 9596 PetscCall(DMPlexGetAdjacency_Internal(dm, cell, PETSC_TRUE, PETSC_FALSE, PETSC_FALSE, &adjSize, &adj)); 9597 /* Technically 1 too big, but easier than fiddling with empty adjacency array */ 9598 PetscCall(PetscCalloc2(adjSize, &cArr, adjSize, &fArr)); 9599 for (cellneigh = 0; cellneigh < adjSize; cellneighiter++, cellneigh++) { 9600 PetscInt i; 9601 const PetscInt neigh = adj[cellneigh]; 9602 PetscReal normci = 0, normfi = 0, normai = 0; 9603 PetscFVCellGeom *cgneigh; 9604 PetscFVFaceGeom *fg; 9605 9606 /* Don't count ourselves in the neighbor list */ 9607 if (neigh == cell) continue; 9608 PetscCall(DMPlexPointLocalRead(dmCell, neigh, cellGeomArr, &cgneigh)); 9609 cellarr[1] = neigh; 9610 { 9611 PetscInt numcovpts; 9612 const PetscInt *covpts; 9613 9614 PetscCall(DMPlexGetMeet(dm, 2, cellarr, &numcovpts, &covpts)); 9615 PetscCall(DMPlexPointLocalRead(dmFace, covpts[0], faceGeomArr, &fg)); 9616 PetscCall(DMPlexRestoreMeet(dm, 2, cellarr, &numcovpts, &covpts)); 9617 } 9618 9619 /* Compute c_i, f_i and their norms */ 9620 for (i = 0; i < nc; i++) { 9621 ci[i] = cgneigh->centroid[i] - cg->centroid[i]; 9622 fi[i] = fg->centroid[i] - cg->centroid[i]; 9623 Ai[i] = fg->normal[i]; 9624 normci += PetscPowReal(ci[i], 2); 9625 normfi += PetscPowReal(fi[i], 2); 9626 normai += PetscPowReal(Ai[i], 2); 9627 } 9628 normci = PetscSqrtReal(normci); 9629 normfi = PetscSqrtReal(normfi); 9630 normai = PetscSqrtReal(normai); 9631 9632 /* Normalize and compute for each face-cell-normal pair */ 9633 for (i = 0; i < nc; i++) { 9634 ci[i] = ci[i] / normci; 9635 fi[i] = fi[i] / normfi; 9636 Ai[i] = Ai[i] / normai; 9637 /* PetscAbs because I don't know if normals are guaranteed to point out */ 9638 cArr[cellneighiter] += PetscAbs(Ai[i] * ci[i]); 9639 fArr[cellneighiter] += PetscAbs(Ai[i] * fi[i]); 9640 } 9641 if (PetscRealPart(cArr[cellneighiter]) < minvalc) minvalc = PetscRealPart(cArr[cellneighiter]); 9642 if (PetscRealPart(fArr[cellneighiter]) < minvalf) minvalf = PetscRealPart(fArr[cellneighiter]); 9643 } 9644 PetscCall(PetscFree(adj)); 9645 PetscCall(PetscFree2(cArr, fArr)); 9646 /* Defer to cell if they're equal */ 9647 oqVals[cellIter] = PetscMin(minvalf, minvalc); 9648 if (OrthQualLabel) { 9649 if (PetscRealPart(oqVals[cellIter]) <= atol) PetscCall(DMLabelSetValue(*OrthQualLabel, cell, DM_ADAPT_REFINE)); 9650 } 9651 } 9652 PetscCall(VecSetValuesLocal(*OrthQual, cEnd - cStart, idx, oqVals, INSERT_VALUES)); 9653 PetscCall(VecAssemblyBegin(*OrthQual)); 9654 PetscCall(VecAssemblyEnd(*OrthQual)); 9655 PetscCall(VecRestoreArrayRead(cellgeom, &cellGeomArr)); 9656 PetscCall(VecRestoreArrayRead(facegeom, &faceGeomArr)); 9657 PetscCall(PetscOptionsGetViewer(comm, NULL, NULL, "-dm_plex_orthogonal_quality_label_view", &vwr, NULL, NULL)); 9658 if (OrthQualLabel) { 9659 if (vwr) PetscCall(DMLabelView(*OrthQualLabel, vwr)); 9660 } 9661 PetscCall(PetscFree5(idx, oqVals, ci, fi, Ai)); 9662 PetscCall(PetscViewerDestroy(&vwr)); 9663 PetscCall(VecViewFromOptions(*OrthQual, NULL, "-dm_plex_orthogonal_quality_vec_view")); 9664 PetscFunctionReturn(PETSC_SUCCESS); 9665 } 9666 9667 /* this is here instead of DMGetOutputDM because output DM still has constraints in the local indices that affect 9668 * interpolator construction */ 9669 static PetscErrorCode DMGetFullDM(DM dm, DM *odm) 9670 { 9671 PetscSection section, newSection, gsection; 9672 PetscSF sf; 9673 PetscBool hasConstraints, ghasConstraints; 9674 9675 PetscFunctionBegin; 9676 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 9677 PetscAssertPointer(odm, 2); 9678 PetscCall(DMGetLocalSection(dm, §ion)); 9679 PetscCall(PetscSectionHasConstraints(section, &hasConstraints)); 9680 PetscCall(MPIU_Allreduce(&hasConstraints, &ghasConstraints, 1, MPIU_BOOL, MPI_LOR, PetscObjectComm((PetscObject)dm))); 9681 if (!ghasConstraints) { 9682 PetscCall(PetscObjectReference((PetscObject)dm)); 9683 *odm = dm; 9684 PetscFunctionReturn(PETSC_SUCCESS); 9685 } 9686 PetscCall(DMClone(dm, odm)); 9687 PetscCall(DMCopyFields(dm, *odm)); 9688 PetscCall(DMGetLocalSection(*odm, &newSection)); 9689 PetscCall(DMGetPointSF(*odm, &sf)); 9690 PetscCall(PetscSectionCreateGlobalSection(newSection, sf, PETSC_TRUE, PETSC_FALSE, &gsection)); 9691 PetscCall(DMSetGlobalSection(*odm, gsection)); 9692 PetscCall(PetscSectionDestroy(&gsection)); 9693 PetscFunctionReturn(PETSC_SUCCESS); 9694 } 9695 9696 static PetscErrorCode DMCreateAffineInterpolationCorrection_Plex(DM dmc, DM dmf, Vec *shift) 9697 { 9698 DM dmco, dmfo; 9699 Mat interpo; 9700 Vec rscale; 9701 Vec cglobalo, clocal; 9702 Vec fglobal, fglobalo, flocal; 9703 PetscBool regular; 9704 9705 PetscFunctionBegin; 9706 PetscCall(DMGetFullDM(dmc, &dmco)); 9707 PetscCall(DMGetFullDM(dmf, &dmfo)); 9708 PetscCall(DMSetCoarseDM(dmfo, dmco)); 9709 PetscCall(DMPlexGetRegularRefinement(dmf, ®ular)); 9710 PetscCall(DMPlexSetRegularRefinement(dmfo, regular)); 9711 PetscCall(DMCreateInterpolation(dmco, dmfo, &interpo, &rscale)); 9712 PetscCall(DMCreateGlobalVector(dmco, &cglobalo)); 9713 PetscCall(DMCreateLocalVector(dmc, &clocal)); 9714 PetscCall(VecSet(cglobalo, 0.)); 9715 PetscCall(VecSet(clocal, 0.)); 9716 PetscCall(DMCreateGlobalVector(dmf, &fglobal)); 9717 PetscCall(DMCreateGlobalVector(dmfo, &fglobalo)); 9718 PetscCall(DMCreateLocalVector(dmf, &flocal)); 9719 PetscCall(VecSet(fglobal, 0.)); 9720 PetscCall(VecSet(fglobalo, 0.)); 9721 PetscCall(VecSet(flocal, 0.)); 9722 PetscCall(DMPlexInsertBoundaryValues(dmc, PETSC_TRUE, clocal, 0., NULL, NULL, NULL)); 9723 PetscCall(DMLocalToGlobalBegin(dmco, clocal, INSERT_VALUES, cglobalo)); 9724 PetscCall(DMLocalToGlobalEnd(dmco, clocal, INSERT_VALUES, cglobalo)); 9725 PetscCall(MatMult(interpo, cglobalo, fglobalo)); 9726 PetscCall(DMGlobalToLocalBegin(dmfo, fglobalo, INSERT_VALUES, flocal)); 9727 PetscCall(DMGlobalToLocalEnd(dmfo, fglobalo, INSERT_VALUES, flocal)); 9728 PetscCall(DMLocalToGlobalBegin(dmf, flocal, INSERT_VALUES, fglobal)); 9729 PetscCall(DMLocalToGlobalEnd(dmf, flocal, INSERT_VALUES, fglobal)); 9730 *shift = fglobal; 9731 PetscCall(VecDestroy(&flocal)); 9732 PetscCall(VecDestroy(&fglobalo)); 9733 PetscCall(VecDestroy(&clocal)); 9734 PetscCall(VecDestroy(&cglobalo)); 9735 PetscCall(VecDestroy(&rscale)); 9736 PetscCall(MatDestroy(&interpo)); 9737 PetscCall(DMDestroy(&dmfo)); 9738 PetscCall(DMDestroy(&dmco)); 9739 PetscFunctionReturn(PETSC_SUCCESS); 9740 } 9741 9742 PETSC_INTERN PetscErrorCode DMInterpolateSolution_Plex(DM coarse, DM fine, Mat interp, Vec coarseSol, Vec fineSol) 9743 { 9744 PetscObject shifto; 9745 Vec shift; 9746 9747 PetscFunctionBegin; 9748 if (!interp) { 9749 Vec rscale; 9750 9751 PetscCall(DMCreateInterpolation(coarse, fine, &interp, &rscale)); 9752 PetscCall(VecDestroy(&rscale)); 9753 } else { 9754 PetscCall(PetscObjectReference((PetscObject)interp)); 9755 } 9756 PetscCall(PetscObjectQuery((PetscObject)interp, "_DMInterpolateSolution_Plex_Vec", &shifto)); 9757 if (!shifto) { 9758 PetscCall(DMCreateAffineInterpolationCorrection_Plex(coarse, fine, &shift)); 9759 PetscCall(PetscObjectCompose((PetscObject)interp, "_DMInterpolateSolution_Plex_Vec", (PetscObject)shift)); 9760 shifto = (PetscObject)shift; 9761 PetscCall(VecDestroy(&shift)); 9762 } 9763 shift = (Vec)shifto; 9764 PetscCall(MatInterpolate(interp, coarseSol, fineSol)); 9765 PetscCall(VecAXPY(fineSol, 1.0, shift)); 9766 PetscCall(MatDestroy(&interp)); 9767 PetscFunctionReturn(PETSC_SUCCESS); 9768 } 9769 9770 /* Pointwise interpolation 9771 Just code FEM for now 9772 u^f = I u^c 9773 sum_k u^f_k phi^f_k = I sum_j u^c_j phi^c_j 9774 u^f_i = sum_j psi^f_i I phi^c_j u^c_j 9775 I_{ij} = psi^f_i phi^c_j 9776 */ 9777 PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling) 9778 { 9779 PetscSection gsc, gsf; 9780 PetscInt m, n; 9781 void *ctx; 9782 DM cdm; 9783 PetscBool regular, ismatis, isRefined = dmCoarse->data == dmFine->data ? PETSC_FALSE : PETSC_TRUE; 9784 9785 PetscFunctionBegin; 9786 PetscCall(DMGetGlobalSection(dmFine, &gsf)); 9787 PetscCall(PetscSectionGetConstrainedStorageSize(gsf, &m)); 9788 PetscCall(DMGetGlobalSection(dmCoarse, &gsc)); 9789 PetscCall(PetscSectionGetConstrainedStorageSize(gsc, &n)); 9790 9791 PetscCall(PetscStrcmp(dmCoarse->mattype, MATIS, &ismatis)); 9792 PetscCall(MatCreate(PetscObjectComm((PetscObject)dmCoarse), interpolation)); 9793 PetscCall(MatSetSizes(*interpolation, m, n, PETSC_DETERMINE, PETSC_DETERMINE)); 9794 PetscCall(MatSetType(*interpolation, ismatis ? MATAIJ : dmCoarse->mattype)); 9795 PetscCall(DMGetApplicationContext(dmFine, &ctx)); 9796 9797 PetscCall(DMGetCoarseDM(dmFine, &cdm)); 9798 PetscCall(DMPlexGetRegularRefinement(dmFine, ®ular)); 9799 if (!isRefined || (regular && cdm == dmCoarse)) PetscCall(DMPlexComputeInterpolatorNested(dmCoarse, dmFine, isRefined, *interpolation, ctx)); 9800 else PetscCall(DMPlexComputeInterpolatorGeneral(dmCoarse, dmFine, *interpolation, ctx)); 9801 PetscCall(MatViewFromOptions(*interpolation, NULL, "-interp_mat_view")); 9802 if (scaling) { 9803 /* Use naive scaling */ 9804 PetscCall(DMCreateInterpolationScale(dmCoarse, dmFine, *interpolation, scaling)); 9805 } 9806 PetscFunctionReturn(PETSC_SUCCESS); 9807 } 9808 9809 PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat) 9810 { 9811 VecScatter ctx; 9812 9813 PetscFunctionBegin; 9814 PetscCall(DMPlexComputeInjectorFEM(dmCoarse, dmFine, &ctx, NULL)); 9815 PetscCall(MatCreateScatter(PetscObjectComm((PetscObject)ctx), ctx, mat)); 9816 PetscCall(VecScatterDestroy(&ctx)); 9817 PetscFunctionReturn(PETSC_SUCCESS); 9818 } 9819 9820 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[]) 9821 { 9822 const PetscInt Nc = uOff[1] - uOff[0]; 9823 PetscInt c; 9824 for (c = 0; c < Nc; ++c) g0[c * Nc + c] = 1.0; 9825 } 9826 9827 PetscErrorCode DMCreateMassMatrixLumped_Plex(DM dm, Vec *mass) 9828 { 9829 DM dmc; 9830 PetscDS ds; 9831 Vec ones, locmass; 9832 IS cellIS; 9833 PetscFormKey key; 9834 PetscInt depth; 9835 9836 PetscFunctionBegin; 9837 PetscCall(DMClone(dm, &dmc)); 9838 PetscCall(DMCopyDisc(dm, dmc)); 9839 PetscCall(DMGetDS(dmc, &ds)); 9840 PetscCall(PetscDSSetJacobian(ds, 0, 0, g0_identity_private, NULL, NULL, NULL)); 9841 PetscCall(DMCreateGlobalVector(dmc, mass)); 9842 PetscCall(DMGetLocalVector(dmc, &ones)); 9843 PetscCall(DMGetLocalVector(dmc, &locmass)); 9844 PetscCall(DMPlexGetDepth(dmc, &depth)); 9845 PetscCall(DMGetStratumIS(dmc, "depth", depth, &cellIS)); 9846 PetscCall(VecSet(locmass, 0.0)); 9847 PetscCall(VecSet(ones, 1.0)); 9848 key.label = NULL; 9849 key.value = 0; 9850 key.field = 0; 9851 key.part = 0; 9852 PetscCall(DMPlexComputeJacobian_Action_Internal(dmc, key, cellIS, 0.0, 0.0, ones, NULL, ones, locmass, NULL)); 9853 PetscCall(ISDestroy(&cellIS)); 9854 PetscCall(VecSet(*mass, 0.0)); 9855 PetscCall(DMLocalToGlobalBegin(dmc, locmass, ADD_VALUES, *mass)); 9856 PetscCall(DMLocalToGlobalEnd(dmc, locmass, ADD_VALUES, *mass)); 9857 PetscCall(DMRestoreLocalVector(dmc, &ones)); 9858 PetscCall(DMRestoreLocalVector(dmc, &locmass)); 9859 PetscCall(DMDestroy(&dmc)); 9860 PetscFunctionReturn(PETSC_SUCCESS); 9861 } 9862 9863 PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mass) 9864 { 9865 PetscSection gsc, gsf; 9866 PetscInt m, n; 9867 void *ctx; 9868 DM cdm; 9869 PetscBool regular; 9870 9871 PetscFunctionBegin; 9872 if (dmFine == dmCoarse) { 9873 DM dmc; 9874 PetscDS ds; 9875 PetscWeakForm wf; 9876 Vec u; 9877 IS cellIS; 9878 PetscFormKey key; 9879 PetscInt depth; 9880 9881 PetscCall(DMClone(dmFine, &dmc)); 9882 PetscCall(DMCopyDisc(dmFine, dmc)); 9883 PetscCall(DMGetDS(dmc, &ds)); 9884 PetscCall(PetscDSGetWeakForm(ds, &wf)); 9885 PetscCall(PetscWeakFormClear(wf)); 9886 PetscCall(PetscDSSetJacobian(ds, 0, 0, g0_identity_private, NULL, NULL, NULL)); 9887 PetscCall(DMCreateMatrix(dmc, mass)); 9888 PetscCall(DMGetLocalVector(dmc, &u)); 9889 PetscCall(DMPlexGetDepth(dmc, &depth)); 9890 PetscCall(DMGetStratumIS(dmc, "depth", depth, &cellIS)); 9891 PetscCall(MatZeroEntries(*mass)); 9892 key.label = NULL; 9893 key.value = 0; 9894 key.field = 0; 9895 key.part = 0; 9896 PetscCall(DMPlexComputeJacobian_Internal(dmc, key, cellIS, 0.0, 0.0, u, NULL, *mass, *mass, NULL)); 9897 PetscCall(ISDestroy(&cellIS)); 9898 PetscCall(DMRestoreLocalVector(dmc, &u)); 9899 PetscCall(DMDestroy(&dmc)); 9900 } else { 9901 PetscCall(DMGetGlobalSection(dmFine, &gsf)); 9902 PetscCall(PetscSectionGetConstrainedStorageSize(gsf, &m)); 9903 PetscCall(DMGetGlobalSection(dmCoarse, &gsc)); 9904 PetscCall(PetscSectionGetConstrainedStorageSize(gsc, &n)); 9905 9906 PetscCall(MatCreate(PetscObjectComm((PetscObject)dmCoarse), mass)); 9907 PetscCall(MatSetSizes(*mass, m, n, PETSC_DETERMINE, PETSC_DETERMINE)); 9908 PetscCall(MatSetType(*mass, dmCoarse->mattype)); 9909 PetscCall(DMGetApplicationContext(dmFine, &ctx)); 9910 9911 PetscCall(DMGetCoarseDM(dmFine, &cdm)); 9912 PetscCall(DMPlexGetRegularRefinement(dmFine, ®ular)); 9913 if (regular && cdm == dmCoarse) PetscCall(DMPlexComputeMassMatrixNested(dmCoarse, dmFine, *mass, ctx)); 9914 else PetscCall(DMPlexComputeMassMatrixGeneral(dmCoarse, dmFine, *mass, ctx)); 9915 } 9916 PetscCall(MatViewFromOptions(*mass, NULL, "-mass_mat_view")); 9917 PetscFunctionReturn(PETSC_SUCCESS); 9918 } 9919 9920 /*@ 9921 DMPlexGetRegularRefinement - Get the flag indicating that this mesh was obtained by regular refinement from its coarse mesh 9922 9923 Input Parameter: 9924 . dm - The `DMPLEX` object 9925 9926 Output Parameter: 9927 . regular - The flag 9928 9929 Level: intermediate 9930 9931 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexSetRegularRefinement()` 9932 @*/ 9933 PetscErrorCode DMPlexGetRegularRefinement(DM dm, PetscBool *regular) 9934 { 9935 PetscFunctionBegin; 9936 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 9937 PetscAssertPointer(regular, 2); 9938 *regular = ((DM_Plex *)dm->data)->regularRefinement; 9939 PetscFunctionReturn(PETSC_SUCCESS); 9940 } 9941 9942 /*@ 9943 DMPlexSetRegularRefinement - Set the flag indicating that this mesh was obtained by regular refinement from its coarse mesh 9944 9945 Input Parameters: 9946 + dm - The `DMPLEX` object 9947 - regular - The flag 9948 9949 Level: intermediate 9950 9951 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetRegularRefinement()` 9952 @*/ 9953 PetscErrorCode DMPlexSetRegularRefinement(DM dm, PetscBool regular) 9954 { 9955 PetscFunctionBegin; 9956 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 9957 ((DM_Plex *)dm->data)->regularRefinement = regular; 9958 PetscFunctionReturn(PETSC_SUCCESS); 9959 } 9960 9961 /*@ 9962 DMPlexGetAnchors - Get the layout of the anchor (point-to-point) constraints. Typically, the user will not have to 9963 call DMPlexGetAnchors() directly: if there are anchors, then `DMPlexGetAnchors()` is called during `DMGetDefaultConstraints()`. 9964 9965 Not Collective 9966 9967 Input Parameter: 9968 . dm - The `DMPLEX` object 9969 9970 Output Parameters: 9971 + anchorSection - If not `NULL`, set to the section describing which points anchor the constrained points. 9972 - anchorIS - If not `NULL`, set to the list of anchors indexed by `anchorSection` 9973 9974 Level: intermediate 9975 9976 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexSetAnchors()`, `DMGetDefaultConstraints()`, `DMSetDefaultConstraints()`, `IS`, `PetscSection` 9977 @*/ 9978 PetscErrorCode DMPlexGetAnchors(DM dm, PetscSection *anchorSection, IS *anchorIS) 9979 { 9980 DM_Plex *plex = (DM_Plex *)dm->data; 9981 9982 PetscFunctionBegin; 9983 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 9984 if (!plex->anchorSection && !plex->anchorIS && plex->createanchors) PetscCall((*plex->createanchors)(dm)); 9985 if (anchorSection) *anchorSection = plex->anchorSection; 9986 if (anchorIS) *anchorIS = plex->anchorIS; 9987 PetscFunctionReturn(PETSC_SUCCESS); 9988 } 9989 9990 /*@ 9991 DMPlexSetAnchors - Set the layout of the local anchor (point-to-point) constraints. 9992 9993 Collective 9994 9995 Input Parameters: 9996 + dm - The `DMPLEX` object 9997 . anchorSection - The section that describes the mapping from constrained points to the anchor points listed in anchorIS. 9998 Must have a local communicator (`PETSC_COMM_SELF` or derivative). 9999 - anchorIS - The list of all anchor points. Must have a local communicator (`PETSC_COMM_SELF` or derivative). 10000 10001 Level: intermediate 10002 10003 Notes: 10004 Unlike boundary conditions, when a point's degrees of freedom in a section are constrained to 10005 an outside value, the anchor constraints set a point's degrees of freedom to be a linear 10006 combination of other points' degrees of freedom. 10007 10008 After specifying the layout of constraints with `DMPlexSetAnchors()`, one specifies the constraints by calling 10009 `DMGetDefaultConstraints()` and filling in the entries in the constraint matrix. 10010 10011 The reference counts of `anchorSection` and `anchorIS` are incremented. 10012 10013 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexGetAnchors()`, `DMGetDefaultConstraints()`, `DMSetDefaultConstraints()` 10014 @*/ 10015 PetscErrorCode DMPlexSetAnchors(DM dm, PetscSection anchorSection, IS anchorIS) 10016 { 10017 DM_Plex *plex = (DM_Plex *)dm->data; 10018 PetscMPIInt result; 10019 10020 PetscFunctionBegin; 10021 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 10022 if (anchorSection) { 10023 PetscValidHeaderSpecific(anchorSection, PETSC_SECTION_CLASSID, 2); 10024 PetscCallMPI(MPI_Comm_compare(PETSC_COMM_SELF, PetscObjectComm((PetscObject)anchorSection), &result)); 10025 PetscCheck(result == MPI_CONGRUENT || result == MPI_IDENT, PETSC_COMM_SELF, PETSC_ERR_ARG_NOTSAMECOMM, "anchor section must have local communicator"); 10026 } 10027 if (anchorIS) { 10028 PetscValidHeaderSpecific(anchorIS, IS_CLASSID, 3); 10029 PetscCallMPI(MPI_Comm_compare(PETSC_COMM_SELF, PetscObjectComm((PetscObject)anchorIS), &result)); 10030 PetscCheck(result == MPI_CONGRUENT || result == MPI_IDENT, PETSC_COMM_SELF, PETSC_ERR_ARG_NOTSAMECOMM, "anchor IS must have local communicator"); 10031 } 10032 10033 PetscCall(PetscObjectReference((PetscObject)anchorSection)); 10034 PetscCall(PetscSectionDestroy(&plex->anchorSection)); 10035 plex->anchorSection = anchorSection; 10036 10037 PetscCall(PetscObjectReference((PetscObject)anchorIS)); 10038 PetscCall(ISDestroy(&plex->anchorIS)); 10039 plex->anchorIS = anchorIS; 10040 10041 if (PetscUnlikelyDebug(anchorIS && anchorSection)) { 10042 PetscInt size, a, pStart, pEnd; 10043 const PetscInt *anchors; 10044 10045 PetscCall(PetscSectionGetChart(anchorSection, &pStart, &pEnd)); 10046 PetscCall(ISGetLocalSize(anchorIS, &size)); 10047 PetscCall(ISGetIndices(anchorIS, &anchors)); 10048 for (a = 0; a < size; a++) { 10049 PetscInt p; 10050 10051 p = anchors[a]; 10052 if (p >= pStart && p < pEnd) { 10053 PetscInt dof; 10054 10055 PetscCall(PetscSectionGetDof(anchorSection, p, &dof)); 10056 if (dof) { 10057 PetscCall(ISRestoreIndices(anchorIS, &anchors)); 10058 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Point %" PetscInt_FMT " cannot be constrained and an anchor", p); 10059 } 10060 } 10061 } 10062 PetscCall(ISRestoreIndices(anchorIS, &anchors)); 10063 } 10064 /* reset the generic constraints */ 10065 PetscCall(DMSetDefaultConstraints(dm, NULL, NULL, NULL)); 10066 PetscFunctionReturn(PETSC_SUCCESS); 10067 } 10068 10069 static PetscErrorCode DMPlexCreateConstraintSection_Anchors(DM dm, PetscSection section, PetscSection *cSec) 10070 { 10071 PetscSection anchorSection; 10072 PetscInt pStart, pEnd, sStart, sEnd, p, dof, numFields, f; 10073 10074 PetscFunctionBegin; 10075 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 10076 PetscCall(DMPlexGetAnchors(dm, &anchorSection, NULL)); 10077 PetscCall(PetscSectionCreate(PETSC_COMM_SELF, cSec)); 10078 PetscCall(PetscSectionGetNumFields(section, &numFields)); 10079 if (numFields) { 10080 PetscInt f; 10081 PetscCall(PetscSectionSetNumFields(*cSec, numFields)); 10082 10083 for (f = 0; f < numFields; f++) { 10084 PetscInt numComp; 10085 10086 PetscCall(PetscSectionGetFieldComponents(section, f, &numComp)); 10087 PetscCall(PetscSectionSetFieldComponents(*cSec, f, numComp)); 10088 } 10089 } 10090 PetscCall(PetscSectionGetChart(anchorSection, &pStart, &pEnd)); 10091 PetscCall(PetscSectionGetChart(section, &sStart, &sEnd)); 10092 pStart = PetscMax(pStart, sStart); 10093 pEnd = PetscMin(pEnd, sEnd); 10094 pEnd = PetscMax(pStart, pEnd); 10095 PetscCall(PetscSectionSetChart(*cSec, pStart, pEnd)); 10096 for (p = pStart; p < pEnd; p++) { 10097 PetscCall(PetscSectionGetDof(anchorSection, p, &dof)); 10098 if (dof) { 10099 PetscCall(PetscSectionGetDof(section, p, &dof)); 10100 PetscCall(PetscSectionSetDof(*cSec, p, dof)); 10101 for (f = 0; f < numFields; f++) { 10102 PetscCall(PetscSectionGetFieldDof(section, p, f, &dof)); 10103 PetscCall(PetscSectionSetFieldDof(*cSec, p, f, dof)); 10104 } 10105 } 10106 } 10107 PetscCall(PetscSectionSetUp(*cSec)); 10108 PetscCall(PetscObjectSetName((PetscObject)*cSec, "Constraint Section")); 10109 PetscFunctionReturn(PETSC_SUCCESS); 10110 } 10111 10112 static PetscErrorCode DMPlexCreateConstraintMatrix_Anchors(DM dm, PetscSection section, PetscSection cSec, Mat *cMat) 10113 { 10114 PetscSection aSec; 10115 PetscInt pStart, pEnd, p, sStart, sEnd, dof, aDof, aOff, off, nnz, annz, m, n, q, a, offset, *i, *j; 10116 const PetscInt *anchors; 10117 PetscInt numFields, f; 10118 IS aIS; 10119 MatType mtype; 10120 PetscBool iscuda, iskokkos; 10121 10122 PetscFunctionBegin; 10123 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 10124 PetscCall(PetscSectionGetStorageSize(cSec, &m)); 10125 PetscCall(PetscSectionGetStorageSize(section, &n)); 10126 PetscCall(MatCreate(PETSC_COMM_SELF, cMat)); 10127 PetscCall(MatSetSizes(*cMat, m, n, m, n)); 10128 PetscCall(PetscStrcmp(dm->mattype, MATSEQAIJCUSPARSE, &iscuda)); 10129 if (!iscuda) PetscCall(PetscStrcmp(dm->mattype, MATMPIAIJCUSPARSE, &iscuda)); 10130 PetscCall(PetscStrcmp(dm->mattype, MATSEQAIJKOKKOS, &iskokkos)); 10131 if (!iskokkos) PetscCall(PetscStrcmp(dm->mattype, MATMPIAIJKOKKOS, &iskokkos)); 10132 if (iscuda) mtype = MATSEQAIJCUSPARSE; 10133 else if (iskokkos) mtype = MATSEQAIJKOKKOS; 10134 else mtype = MATSEQAIJ; 10135 PetscCall(MatSetType(*cMat, mtype)); 10136 PetscCall(DMPlexGetAnchors(dm, &aSec, &aIS)); 10137 PetscCall(ISGetIndices(aIS, &anchors)); 10138 /* cSec will be a subset of aSec and section */ 10139 PetscCall(PetscSectionGetChart(cSec, &pStart, &pEnd)); 10140 PetscCall(PetscSectionGetChart(section, &sStart, &sEnd)); 10141 PetscCall(PetscMalloc1(m + 1, &i)); 10142 i[0] = 0; 10143 PetscCall(PetscSectionGetNumFields(section, &numFields)); 10144 for (p = pStart; p < pEnd; p++) { 10145 PetscInt rDof, rOff, r; 10146 10147 PetscCall(PetscSectionGetDof(aSec, p, &rDof)); 10148 if (!rDof) continue; 10149 PetscCall(PetscSectionGetOffset(aSec, p, &rOff)); 10150 if (numFields) { 10151 for (f = 0; f < numFields; f++) { 10152 annz = 0; 10153 for (r = 0; r < rDof; r++) { 10154 a = anchors[rOff + r]; 10155 if (a < sStart || a >= sEnd) continue; 10156 PetscCall(PetscSectionGetFieldDof(section, a, f, &aDof)); 10157 annz += aDof; 10158 } 10159 PetscCall(PetscSectionGetFieldDof(cSec, p, f, &dof)); 10160 PetscCall(PetscSectionGetFieldOffset(cSec, p, f, &off)); 10161 for (q = 0; q < dof; q++) i[off + q + 1] = i[off + q] + annz; 10162 } 10163 } else { 10164 annz = 0; 10165 PetscCall(PetscSectionGetDof(cSec, p, &dof)); 10166 for (q = 0; q < dof; q++) { 10167 a = anchors[rOff + q]; 10168 if (a < sStart || a >= sEnd) continue; 10169 PetscCall(PetscSectionGetDof(section, a, &aDof)); 10170 annz += aDof; 10171 } 10172 PetscCall(PetscSectionGetDof(cSec, p, &dof)); 10173 PetscCall(PetscSectionGetOffset(cSec, p, &off)); 10174 for (q = 0; q < dof; q++) i[off + q + 1] = i[off + q] + annz; 10175 } 10176 } 10177 nnz = i[m]; 10178 PetscCall(PetscMalloc1(nnz, &j)); 10179 offset = 0; 10180 for (p = pStart; p < pEnd; p++) { 10181 if (numFields) { 10182 for (f = 0; f < numFields; f++) { 10183 PetscCall(PetscSectionGetFieldDof(cSec, p, f, &dof)); 10184 for (q = 0; q < dof; q++) { 10185 PetscInt rDof, rOff, r; 10186 PetscCall(PetscSectionGetDof(aSec, p, &rDof)); 10187 PetscCall(PetscSectionGetOffset(aSec, p, &rOff)); 10188 for (r = 0; r < rDof; r++) { 10189 PetscInt s; 10190 10191 a = anchors[rOff + r]; 10192 if (a < sStart || a >= sEnd) continue; 10193 PetscCall(PetscSectionGetFieldDof(section, a, f, &aDof)); 10194 PetscCall(PetscSectionGetFieldOffset(section, a, f, &aOff)); 10195 for (s = 0; s < aDof; s++) j[offset++] = aOff + s; 10196 } 10197 } 10198 } 10199 } else { 10200 PetscCall(PetscSectionGetDof(cSec, p, &dof)); 10201 for (q = 0; q < dof; q++) { 10202 PetscInt rDof, rOff, r; 10203 PetscCall(PetscSectionGetDof(aSec, p, &rDof)); 10204 PetscCall(PetscSectionGetOffset(aSec, p, &rOff)); 10205 for (r = 0; r < rDof; r++) { 10206 PetscInt s; 10207 10208 a = anchors[rOff + r]; 10209 if (a < sStart || a >= sEnd) continue; 10210 PetscCall(PetscSectionGetDof(section, a, &aDof)); 10211 PetscCall(PetscSectionGetOffset(section, a, &aOff)); 10212 for (s = 0; s < aDof; s++) j[offset++] = aOff + s; 10213 } 10214 } 10215 } 10216 } 10217 PetscCall(MatSeqAIJSetPreallocationCSR(*cMat, i, j, NULL)); 10218 PetscCall(PetscFree(i)); 10219 PetscCall(PetscFree(j)); 10220 PetscCall(ISRestoreIndices(aIS, &anchors)); 10221 PetscFunctionReturn(PETSC_SUCCESS); 10222 } 10223 10224 PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm) 10225 { 10226 DM_Plex *plex = (DM_Plex *)dm->data; 10227 PetscSection anchorSection, section, cSec; 10228 Mat cMat; 10229 10230 PetscFunctionBegin; 10231 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 10232 PetscCall(DMPlexGetAnchors(dm, &anchorSection, NULL)); 10233 if (anchorSection) { 10234 PetscInt Nf; 10235 10236 PetscCall(DMGetLocalSection(dm, §ion)); 10237 PetscCall(DMPlexCreateConstraintSection_Anchors(dm, section, &cSec)); 10238 PetscCall(DMPlexCreateConstraintMatrix_Anchors(dm, section, cSec, &cMat)); 10239 PetscCall(DMGetNumFields(dm, &Nf)); 10240 if (Nf && plex->computeanchormatrix) PetscCall((*plex->computeanchormatrix)(dm, section, cSec, cMat)); 10241 PetscCall(DMSetDefaultConstraints(dm, cSec, cMat, NULL)); 10242 PetscCall(PetscSectionDestroy(&cSec)); 10243 PetscCall(MatDestroy(&cMat)); 10244 } 10245 PetscFunctionReturn(PETSC_SUCCESS); 10246 } 10247 10248 PetscErrorCode DMCreateSubDomainDM_Plex(DM dm, DMLabel label, PetscInt value, IS *is, DM *subdm) 10249 { 10250 IS subis; 10251 PetscSection section, subsection; 10252 10253 PetscFunctionBegin; 10254 PetscCall(DMGetLocalSection(dm, §ion)); 10255 PetscCheck(section, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Must set default section for DM before splitting subdomain"); 10256 PetscCheck(subdm, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Must set output subDM for splitting subdomain"); 10257 /* Create subdomain */ 10258 PetscCall(DMPlexFilter(dm, label, value, subdm)); 10259 /* Create submodel */ 10260 PetscCall(DMPlexGetSubpointIS(*subdm, &subis)); 10261 PetscCall(PetscSectionCreateSubmeshSection(section, subis, &subsection)); 10262 PetscCall(DMSetLocalSection(*subdm, subsection)); 10263 PetscCall(PetscSectionDestroy(&subsection)); 10264 PetscCall(DMCopyDisc(dm, *subdm)); 10265 /* Create map from submodel to global model */ 10266 if (is) { 10267 PetscSection sectionGlobal, subsectionGlobal; 10268 IS spIS; 10269 const PetscInt *spmap; 10270 PetscInt *subIndices; 10271 PetscInt subSize = 0, subOff = 0, pStart, pEnd, p; 10272 PetscInt Nf, f, bs = -1, bsLocal[2], bsMinMax[2]; 10273 10274 PetscCall(DMPlexGetSubpointIS(*subdm, &spIS)); 10275 PetscCall(ISGetIndices(spIS, &spmap)); 10276 PetscCall(PetscSectionGetNumFields(section, &Nf)); 10277 PetscCall(DMGetGlobalSection(dm, §ionGlobal)); 10278 PetscCall(DMGetGlobalSection(*subdm, &subsectionGlobal)); 10279 PetscCall(PetscSectionGetChart(subsection, &pStart, &pEnd)); 10280 for (p = pStart; p < pEnd; ++p) { 10281 PetscInt gdof, pSubSize = 0; 10282 10283 PetscCall(PetscSectionGetDof(sectionGlobal, p, &gdof)); 10284 if (gdof > 0) { 10285 for (f = 0; f < Nf; ++f) { 10286 PetscInt fdof, fcdof; 10287 10288 PetscCall(PetscSectionGetFieldDof(subsection, p, f, &fdof)); 10289 PetscCall(PetscSectionGetFieldConstraintDof(subsection, p, f, &fcdof)); 10290 pSubSize += fdof - fcdof; 10291 } 10292 subSize += pSubSize; 10293 if (pSubSize) { 10294 if (bs < 0) { 10295 bs = pSubSize; 10296 } else if (bs != pSubSize) { 10297 /* Layout does not admit a pointwise block size */ 10298 bs = 1; 10299 } 10300 } 10301 } 10302 } 10303 /* Must have same blocksize on all procs (some might have no points) */ 10304 bsLocal[0] = bs < 0 ? PETSC_MAX_INT : bs; 10305 bsLocal[1] = bs; 10306 PetscCall(PetscGlobalMinMaxInt(PetscObjectComm((PetscObject)dm), bsLocal, bsMinMax)); 10307 if (bsMinMax[0] != bsMinMax[1]) { 10308 bs = 1; 10309 } else { 10310 bs = bsMinMax[0]; 10311 } 10312 PetscCall(PetscMalloc1(subSize, &subIndices)); 10313 for (p = pStart; p < pEnd; ++p) { 10314 PetscInt gdof, goff; 10315 10316 PetscCall(PetscSectionGetDof(subsectionGlobal, p, &gdof)); 10317 if (gdof > 0) { 10318 const PetscInt point = spmap[p]; 10319 10320 PetscCall(PetscSectionGetOffset(sectionGlobal, point, &goff)); 10321 for (f = 0; f < Nf; ++f) { 10322 PetscInt fdof, fcdof, fc, f2, poff = 0; 10323 10324 /* Can get rid of this loop by storing field information in the global section */ 10325 for (f2 = 0; f2 < f; ++f2) { 10326 PetscCall(PetscSectionGetFieldDof(section, p, f2, &fdof)); 10327 PetscCall(PetscSectionGetFieldConstraintDof(section, p, f2, &fcdof)); 10328 poff += fdof - fcdof; 10329 } 10330 PetscCall(PetscSectionGetFieldDof(section, p, f, &fdof)); 10331 PetscCall(PetscSectionGetFieldConstraintDof(section, p, f, &fcdof)); 10332 for (fc = 0; fc < fdof - fcdof; ++fc, ++subOff) subIndices[subOff] = goff + poff + fc; 10333 } 10334 } 10335 } 10336 PetscCall(ISRestoreIndices(spIS, &spmap)); 10337 PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), subSize, subIndices, PETSC_OWN_POINTER, is)); 10338 if (bs > 1) { 10339 /* We need to check that the block size does not come from non-contiguous fields */ 10340 PetscInt i, j, set = 1; 10341 for (i = 0; i < subSize; i += bs) { 10342 for (j = 0; j < bs; ++j) { 10343 if (subIndices[i + j] != subIndices[i] + j) { 10344 set = 0; 10345 break; 10346 } 10347 } 10348 } 10349 if (set) PetscCall(ISSetBlockSize(*is, bs)); 10350 } 10351 /* Attach nullspace */ 10352 for (f = 0; f < Nf; ++f) { 10353 (*subdm)->nullspaceConstructors[f] = dm->nullspaceConstructors[f]; 10354 if ((*subdm)->nullspaceConstructors[f]) break; 10355 } 10356 if (f < Nf) { 10357 MatNullSpace nullSpace; 10358 PetscCall((*(*subdm)->nullspaceConstructors[f])(*subdm, f, f, &nullSpace)); 10359 10360 PetscCall(PetscObjectCompose((PetscObject)*is, "nullspace", (PetscObject)nullSpace)); 10361 PetscCall(MatNullSpaceDestroy(&nullSpace)); 10362 } 10363 } 10364 PetscFunctionReturn(PETSC_SUCCESS); 10365 } 10366 10367 /*@ 10368 DMPlexMonitorThroughput - Report the cell throughput of FE integration 10369 10370 Input Parameters: 10371 + dm - The `DM` 10372 - dummy - unused argument 10373 10374 Options Database Key: 10375 . -dm_plex_monitor_throughput - Activate the monitor 10376 10377 Level: developer 10378 10379 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMSetFromOptions()`, `DMPlexCreate()` 10380 @*/ 10381 PetscErrorCode DMPlexMonitorThroughput(DM dm, void *dummy) 10382 { 10383 PetscLogHandler default_handler; 10384 10385 PetscFunctionBegin; 10386 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 10387 PetscCall(PetscLogGetDefaultHandler(&default_handler)); 10388 if (default_handler) { 10389 PetscLogEvent event; 10390 PetscEventPerfInfo eventInfo; 10391 PetscReal cellRate, flopRate; 10392 PetscInt cStart, cEnd, Nf, N; 10393 const char *name; 10394 10395 PetscCall(PetscObjectGetName((PetscObject)dm, &name)); 10396 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 10397 PetscCall(DMGetNumFields(dm, &Nf)); 10398 PetscCall(PetscLogEventGetId("DMPlexResidualFE", &event)); 10399 PetscCall(PetscLogEventGetPerfInfo(PETSC_DEFAULT, event, &eventInfo)); 10400 N = (cEnd - cStart) * Nf * eventInfo.count; 10401 flopRate = eventInfo.flops / eventInfo.time; 10402 cellRate = N / eventInfo.time; 10403 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))); 10404 } else { 10405 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."); 10406 } 10407 PetscFunctionReturn(PETSC_SUCCESS); 10408 } 10409