1 #define PETSCDM_DLL 2 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 #include <petsc/private/hashseti.h> /*I "petscdmplex.h" I*/ 4 #include <petscsf.h> 5 #include <petscdmplextransform.h> 6 #include <petsc/private/kernels/blockmatmult.h> 7 #include <petsc/private/kernels/blockinvert.h> 8 9 PetscLogEvent DMPLEX_CreateFromFile, DMPLEX_BuildFromCellList, DMPLEX_BuildCoordinatesFromCellList; 10 11 /* External function declarations here */ 12 static PetscErrorCode DMInitialize_Plex(DM dm); 13 14 /* This copies internal things in the Plex structure that we generally want when making a new, related Plex */ 15 PetscErrorCode DMPlexCopy_Internal(DM dmin, PetscBool copyPeriodicity, PetscBool copyOverlap, DM dmout) 16 { 17 const PetscReal *maxCell, *Lstart, *L; 18 PetscBool dist; 19 DMPlexReorderDefaultFlag reorder; 20 21 PetscFunctionBegin; 22 if (copyPeriodicity) { 23 PetscCall(DMGetPeriodicity(dmin, &maxCell, &Lstart, &L)); 24 PetscCall(DMSetPeriodicity(dmout, maxCell, Lstart, L)); 25 } 26 PetscCall(DMPlexDistributeGetDefault(dmin, &dist)); 27 PetscCall(DMPlexDistributeSetDefault(dmout, dist)); 28 PetscCall(DMPlexReorderGetDefault(dmin, &reorder)); 29 PetscCall(DMPlexReorderSetDefault(dmout, reorder)); 30 ((DM_Plex *) dmout->data)->useHashLocation = ((DM_Plex *) dmin->data)->useHashLocation; 31 if (copyOverlap) PetscCall(DMPlexSetOverlap_Plex(dmout, dmin, 0)); 32 PetscFunctionReturn(0); 33 } 34 35 /* Replace dm with the contents of ndm, and then destroy ndm 36 - Share the DM_Plex structure 37 - Share the coordinates 38 - Share the SF 39 */ 40 static PetscErrorCode DMPlexReplace_Static(DM dm, DM *ndm) 41 { 42 PetscSF sf; 43 DM dmNew = *ndm, coordDM, coarseDM; 44 Vec coords; 45 const PetscReal *maxCell, *Lstart, *L; 46 PetscInt dim, cdim; 47 48 PetscFunctionBegin; 49 if (dm == dmNew) { 50 PetscCall(DMDestroy(ndm)); 51 PetscFunctionReturn(0); 52 } 53 dm->setupcalled = dmNew->setupcalled; 54 PetscCall(DMGetDimension(dmNew, &dim)); 55 PetscCall(DMSetDimension(dm, dim)); 56 PetscCall(DMGetCoordinateDim(dmNew, &cdim)); 57 PetscCall(DMSetCoordinateDim(dm, cdim)); 58 PetscCall(DMGetPointSF(dmNew, &sf)); 59 PetscCall(DMSetPointSF(dm, sf)); 60 PetscCall(DMGetCoordinateDM(dmNew, &coordDM)); 61 PetscCall(DMGetCoordinatesLocal(dmNew, &coords)); 62 PetscCall(DMSetCoordinateDM(dm, coordDM)); 63 PetscCall(DMSetCoordinatesLocal(dm, coords)); 64 PetscCall(DMGetCellCoordinateDM(dmNew, &coordDM)); 65 PetscCall(DMGetCellCoordinatesLocal(dmNew, &coords)); 66 PetscCall(DMSetCellCoordinateDM(dm, coordDM)); 67 PetscCall(DMSetCellCoordinatesLocal(dm, coords)); 68 /* Do not want to create the coordinate field if it does not already exist, so do not call DMGetCoordinateField() */ 69 PetscCall(DMFieldDestroy(&dm->coordinates[0].field)); 70 dm->coordinates[0].field = dmNew->coordinates[0].field; 71 ((DM_Plex *) dmNew->data)->coordFunc = ((DM_Plex *) dm->data)->coordFunc; 72 PetscCall(DMGetPeriodicity(dmNew, &maxCell, &Lstart, &L)); 73 PetscCall(DMSetPeriodicity(dm, maxCell, Lstart, L)); 74 PetscCall(DMDestroy_Plex(dm)); 75 PetscCall(DMInitialize_Plex(dm)); 76 dm->data = dmNew->data; 77 ((DM_Plex *) dmNew->data)->refct++; 78 PetscCall(DMDestroyLabelLinkList_Internal(dm)); 79 PetscCall(DMCopyLabels(dmNew, dm, PETSC_OWN_POINTER, PETSC_TRUE, DM_COPY_LABELS_FAIL)); 80 PetscCall(DMGetCoarseDM(dmNew,&coarseDM)); 81 PetscCall(DMSetCoarseDM(dm,coarseDM)); 82 PetscCall(DMDestroy(ndm)); 83 PetscFunctionReturn(0); 84 } 85 86 /* Swap dm with the contents of dmNew 87 - Swap the DM_Plex structure 88 - Swap the coordinates 89 - Swap the point PetscSF 90 */ 91 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 92 { 93 DM coordDMA, coordDMB; 94 Vec coordsA, coordsB; 95 PetscSF sfA, sfB; 96 DMField fieldTmp; 97 void *tmp; 98 DMLabelLink listTmp; 99 DMLabel depthTmp; 100 PetscInt tmpI; 101 102 PetscFunctionBegin; 103 if (dmA == dmB) PetscFunctionReturn(0); 104 PetscCall(DMGetPointSF(dmA, &sfA)); 105 PetscCall(DMGetPointSF(dmB, &sfB)); 106 PetscCall(PetscObjectReference((PetscObject) sfA)); 107 PetscCall(DMSetPointSF(dmA, sfB)); 108 PetscCall(DMSetPointSF(dmB, sfA)); 109 PetscCall(PetscObjectDereference((PetscObject) sfA)); 110 111 PetscCall(DMGetCoordinateDM(dmA, &coordDMA)); 112 PetscCall(DMGetCoordinateDM(dmB, &coordDMB)); 113 PetscCall(PetscObjectReference((PetscObject) coordDMA)); 114 PetscCall(DMSetCoordinateDM(dmA, coordDMB)); 115 PetscCall(DMSetCoordinateDM(dmB, coordDMA)); 116 PetscCall(PetscObjectDereference((PetscObject) coordDMA)); 117 118 PetscCall(DMGetCoordinatesLocal(dmA, &coordsA)); 119 PetscCall(DMGetCoordinatesLocal(dmB, &coordsB)); 120 PetscCall(PetscObjectReference((PetscObject) coordsA)); 121 PetscCall(DMSetCoordinatesLocal(dmA, coordsB)); 122 PetscCall(DMSetCoordinatesLocal(dmB, coordsA)); 123 PetscCall(PetscObjectDereference((PetscObject) coordsA)); 124 125 PetscCall(DMGetCellCoordinateDM(dmA, &coordDMA)); 126 PetscCall(DMGetCellCoordinateDM(dmB, &coordDMB)); 127 PetscCall(PetscObjectReference((PetscObject) coordDMA)); 128 PetscCall(DMSetCellCoordinateDM(dmA, coordDMB)); 129 PetscCall(DMSetCellCoordinateDM(dmB, coordDMA)); 130 PetscCall(PetscObjectDereference((PetscObject) coordDMA)); 131 132 PetscCall(DMGetCellCoordinatesLocal(dmA, &coordsA)); 133 PetscCall(DMGetCellCoordinatesLocal(dmB, &coordsB)); 134 PetscCall(PetscObjectReference((PetscObject) coordsA)); 135 PetscCall(DMSetCellCoordinatesLocal(dmA, coordsB)); 136 PetscCall(DMSetCellCoordinatesLocal(dmB, coordsA)); 137 PetscCall(PetscObjectDereference((PetscObject) coordsA)); 138 139 fieldTmp = dmA->coordinates[0].field; 140 dmA->coordinates[0].field = dmB->coordinates[0].field; 141 dmB->coordinates[0].field = fieldTmp; 142 fieldTmp = dmA->coordinates[1].field; 143 dmA->coordinates[1].field = dmB->coordinates[1].field; 144 dmB->coordinates[1].field = fieldTmp; 145 tmp = dmA->data; 146 dmA->data = dmB->data; 147 dmB->data = tmp; 148 listTmp = dmA->labels; 149 dmA->labels = dmB->labels; 150 dmB->labels = listTmp; 151 depthTmp = dmA->depthLabel; 152 dmA->depthLabel = dmB->depthLabel; 153 dmB->depthLabel = depthTmp; 154 depthTmp = dmA->celltypeLabel; 155 dmA->celltypeLabel = dmB->celltypeLabel; 156 dmB->celltypeLabel = depthTmp; 157 tmpI = dmA->levelup; 158 dmA->levelup = dmB->levelup; 159 dmB->levelup = tmpI; 160 PetscFunctionReturn(0); 161 } 162 163 static PetscErrorCode DMPlexInterpolateInPlace_Internal(DM dm) 164 { 165 DM idm; 166 167 PetscFunctionBegin; 168 PetscCall(DMPlexInterpolate(dm, &idm)); 169 PetscCall(DMPlexCopyCoordinates(dm, idm)); 170 PetscCall(DMPlexReplace_Static(dm, &idm)); 171 PetscFunctionReturn(0); 172 } 173 174 /*@C 175 DMPlexCreateCoordinateSpace - Creates a finite element space for the coordinates 176 177 Collective 178 179 Input Parameters: 180 + DM - The DM 181 . degree - The degree of the finite element or PETSC_DECIDE 182 - coordFunc - An optional function to map new points from refinement to the surface 183 184 Level: advanced 185 186 .seealso: `PetscFECreateLagrange()`, `DMGetCoordinateDM()` 187 @*/ 188 PetscErrorCode DMPlexCreateCoordinateSpace(DM dm, PetscInt degree, PetscPointFunc coordFunc) 189 { 190 DM_Plex *mesh = (DM_Plex *) dm->data; 191 DM cdm; 192 PetscDS cds; 193 PetscFE fe; 194 PetscClassId id; 195 196 PetscFunctionBegin; 197 PetscCall(DMGetCoordinateDM(dm, &cdm)); 198 PetscCall(DMGetDS(cdm, &cds)); 199 PetscCall(PetscDSGetDiscretization(cds, 0, (PetscObject *) &fe)); 200 PetscCall(PetscObjectGetClassId((PetscObject) fe, &id)); 201 if (id != PETSCFE_CLASSID) { 202 PetscBool simplex; 203 PetscInt dim, dE, qorder; 204 205 PetscCall(DMGetDimension(dm, &dim)); 206 PetscCall(DMGetCoordinateDim(dm, &dE)); 207 qorder = degree; 208 PetscObjectOptionsBegin((PetscObject) cdm); 209 PetscCall(PetscOptionsBoundedInt("-coord_dm_default_quadrature_order", "Quadrature order is one less than quadrature points per edge", "DMPlexCreateCoordinateSpace", qorder, &qorder, NULL, 0)); 210 PetscOptionsEnd(); 211 if (degree == PETSC_DECIDE) fe = NULL; 212 else { 213 PetscCall(DMPlexIsSimplex(dm, &simplex)); 214 PetscCall(PetscFECreateLagrange(PETSC_COMM_SELF, dim, dE, simplex, degree, qorder, &fe)); 215 } 216 PetscCall(DMProjectCoordinates(dm, fe)); 217 PetscCall(PetscFEDestroy(&fe)); 218 } 219 mesh->coordFunc = coordFunc; 220 PetscFunctionReturn(0); 221 } 222 223 /*@ 224 DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement. 225 226 Collective 227 228 Input Parameters: 229 + comm - The communicator for the DM object 230 . dim - The spatial dimension 231 . simplex - Flag for simplicial cells, otherwise they are tensor product cells 232 . interpolate - Flag to create intermediate mesh pieces (edges, faces) 233 - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell 234 235 Output Parameter: 236 . dm - The DM object 237 238 Level: beginner 239 240 .seealso: `DMSetType()`, `DMCreate()` 241 @*/ 242 PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscReal refinementLimit, DM *newdm) 243 { 244 DM dm; 245 PetscMPIInt rank; 246 247 PetscFunctionBegin; 248 PetscCall(DMCreate(comm, &dm)); 249 PetscCall(DMSetType(dm, DMPLEX)); 250 PetscCall(DMSetDimension(dm, dim)); 251 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 252 switch (dim) { 253 case 2: 254 if (simplex) PetscCall(PetscObjectSetName((PetscObject) dm, "triangular")); 255 else PetscCall(PetscObjectSetName((PetscObject) dm, "quadrilateral")); 256 break; 257 case 3: 258 if (simplex) PetscCall(PetscObjectSetName((PetscObject) dm, "tetrahedral")); 259 else PetscCall(PetscObjectSetName((PetscObject) dm, "hexahedral")); 260 break; 261 default: 262 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %" PetscInt_FMT, dim); 263 } 264 if (rank) { 265 PetscInt numPoints[2] = {0, 0}; 266 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL)); 267 } else { 268 switch (dim) { 269 case 2: 270 if (simplex) { 271 PetscInt numPoints[2] = {4, 2}; 272 PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; 273 PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; 274 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 275 PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5}; 276 277 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 278 } else { 279 PetscInt numPoints[2] = {6, 2}; 280 PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; 281 PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4}; 282 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 283 PetscScalar vertexCoords[12] = {-1.0, -0.5, 0.0, -0.5, 0.0, 0.5, -1.0, 0.5, 1.0, -0.5, 1.0, 0.5}; 284 285 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 286 } 287 break; 288 case 3: 289 if (simplex) { 290 PetscInt numPoints[2] = {5, 2}; 291 PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; 292 PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; 293 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 294 PetscScalar vertexCoords[15] = {-1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0}; 295 296 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 297 } else { 298 PetscInt numPoints[2] = {12, 2}; 299 PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 300 PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8}; 301 PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 302 PetscScalar vertexCoords[36] = {-1.0, -0.5, -0.5, -1.0, 0.5, -0.5, 0.0, 0.5, -0.5, 0.0, -0.5, -0.5, 303 -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5, 304 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5}; 305 306 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 307 } 308 break; 309 default: 310 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %" PetscInt_FMT, dim); 311 } 312 } 313 *newdm = dm; 314 if (refinementLimit > 0.0) { 315 DM rdm; 316 const char *name; 317 318 PetscCall(DMPlexSetRefinementUniform(*newdm, PETSC_FALSE)); 319 PetscCall(DMPlexSetRefinementLimit(*newdm, refinementLimit)); 320 PetscCall(DMRefine(*newdm, comm, &rdm)); 321 PetscCall(PetscObjectGetName((PetscObject) *newdm, &name)); 322 PetscCall(PetscObjectSetName((PetscObject) rdm, name)); 323 PetscCall(DMDestroy(newdm)); 324 *newdm = rdm; 325 } 326 if (interpolate) { 327 DM idm; 328 329 PetscCall(DMPlexInterpolate(*newdm, &idm)); 330 PetscCall(DMDestroy(newdm)); 331 *newdm = idm; 332 } 333 PetscFunctionReturn(0); 334 } 335 336 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 337 { 338 const PetscInt numVertices = 2; 339 PetscInt markerRight = 1; 340 PetscInt markerLeft = 1; 341 PetscBool markerSeparate = PETSC_FALSE; 342 Vec coordinates; 343 PetscSection coordSection; 344 PetscScalar *coords; 345 PetscInt coordSize; 346 PetscMPIInt rank; 347 PetscInt cdim = 1, v; 348 349 PetscFunctionBegin; 350 PetscCall(PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL)); 351 if (markerSeparate) { 352 markerRight = 2; 353 markerLeft = 1; 354 } 355 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 356 if (rank == 0) { 357 PetscCall(DMPlexSetChart(dm, 0, numVertices)); 358 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 359 PetscCall(DMSetLabelValue(dm, "marker", 0, markerLeft)); 360 PetscCall(DMSetLabelValue(dm, "marker", 1, markerRight)); 361 } 362 PetscCall(DMPlexSymmetrize(dm)); 363 PetscCall(DMPlexStratify(dm)); 364 /* Build coordinates */ 365 PetscCall(DMSetCoordinateDim(dm, cdim)); 366 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 367 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 368 PetscCall(PetscSectionSetChart(coordSection, 0, numVertices)); 369 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, cdim)); 370 for (v = 0; v < numVertices; ++v) { 371 PetscCall(PetscSectionSetDof(coordSection, v, cdim)); 372 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, cdim)); 373 } 374 PetscCall(PetscSectionSetUp(coordSection)); 375 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 376 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 377 PetscCall(PetscObjectSetName((PetscObject) coordinates, "coordinates")); 378 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 379 PetscCall(VecSetBlockSize(coordinates, cdim)); 380 PetscCall(VecSetType(coordinates,VECSTANDARD)); 381 PetscCall(VecGetArray(coordinates, &coords)); 382 coords[0] = lower[0]; 383 coords[1] = upper[0]; 384 PetscCall(VecRestoreArray(coordinates, &coords)); 385 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 386 PetscCall(VecDestroy(&coordinates)); 387 PetscFunctionReturn(0); 388 } 389 390 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 391 { 392 const PetscInt numVertices = (edges[0]+1)*(edges[1]+1); 393 const PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1]; 394 PetscInt markerTop = 1; 395 PetscInt markerBottom = 1; 396 PetscInt markerRight = 1; 397 PetscInt markerLeft = 1; 398 PetscBool markerSeparate = PETSC_FALSE; 399 Vec coordinates; 400 PetscSection coordSection; 401 PetscScalar *coords; 402 PetscInt coordSize; 403 PetscMPIInt rank; 404 PetscInt v, vx, vy; 405 406 PetscFunctionBegin; 407 PetscCall(PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL)); 408 if (markerSeparate) { 409 markerTop = 3; 410 markerBottom = 1; 411 markerRight = 2; 412 markerLeft = 4; 413 } 414 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 415 if (rank == 0) { 416 PetscInt e, ex, ey; 417 418 PetscCall(DMPlexSetChart(dm, 0, numEdges+numVertices)); 419 for (e = 0; e < numEdges; ++e) { 420 PetscCall(DMPlexSetConeSize(dm, e, 2)); 421 } 422 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 423 for (vx = 0; vx <= edges[0]; vx++) { 424 for (ey = 0; ey < edges[1]; ey++) { 425 PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1); 426 PetscInt vertex = ey*(edges[0]+1) + vx + numEdges; 427 PetscInt cone[2]; 428 429 cone[0] = vertex; cone[1] = vertex+edges[0]+1; 430 PetscCall(DMPlexSetCone(dm, edge, cone)); 431 if (vx == edges[0]) { 432 PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight)); 433 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight)); 434 if (ey == edges[1]-1) { 435 PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight)); 436 PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerRight)); 437 } 438 } else if (vx == 0) { 439 PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft)); 440 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft)); 441 if (ey == edges[1]-1) { 442 PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft)); 443 PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft)); 444 } 445 } 446 } 447 } 448 for (vy = 0; vy <= edges[1]; vy++) { 449 for (ex = 0; ex < edges[0]; ex++) { 450 PetscInt edge = vy*edges[0] + ex; 451 PetscInt vertex = vy*(edges[0]+1) + ex + numEdges; 452 PetscInt cone[2]; 453 454 cone[0] = vertex; cone[1] = vertex+1; 455 PetscCall(DMPlexSetCone(dm, edge, cone)); 456 if (vy == edges[1]) { 457 PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop)); 458 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop)); 459 if (ex == edges[0]-1) { 460 PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop)); 461 PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerTop)); 462 } 463 } else if (vy == 0) { 464 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom)); 465 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom)); 466 if (ex == edges[0]-1) { 467 PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom)); 468 PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom)); 469 } 470 } 471 } 472 } 473 } 474 PetscCall(DMPlexSymmetrize(dm)); 475 PetscCall(DMPlexStratify(dm)); 476 /* Build coordinates */ 477 PetscCall(DMSetCoordinateDim(dm, 2)); 478 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 479 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 480 PetscCall(PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices)); 481 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, 2)); 482 for (v = numEdges; v < numEdges+numVertices; ++v) { 483 PetscCall(PetscSectionSetDof(coordSection, v, 2)); 484 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, 2)); 485 } 486 PetscCall(PetscSectionSetUp(coordSection)); 487 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 488 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 489 PetscCall(PetscObjectSetName((PetscObject) coordinates, "coordinates")); 490 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 491 PetscCall(VecSetBlockSize(coordinates, 2)); 492 PetscCall(VecSetType(coordinates,VECSTANDARD)); 493 PetscCall(VecGetArray(coordinates, &coords)); 494 for (vy = 0; vy <= edges[1]; ++vy) { 495 for (vx = 0; vx <= edges[0]; ++vx) { 496 coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx; 497 coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy; 498 } 499 } 500 PetscCall(VecRestoreArray(coordinates, &coords)); 501 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 502 PetscCall(VecDestroy(&coordinates)); 503 PetscFunctionReturn(0); 504 } 505 506 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) 507 { 508 PetscInt vertices[3], numVertices; 509 PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2]; 510 PetscInt markerTop = 1; 511 PetscInt markerBottom = 1; 512 PetscInt markerFront = 1; 513 PetscInt markerBack = 1; 514 PetscInt markerRight = 1; 515 PetscInt markerLeft = 1; 516 PetscBool markerSeparate = PETSC_FALSE; 517 Vec coordinates; 518 PetscSection coordSection; 519 PetscScalar *coords; 520 PetscInt coordSize; 521 PetscMPIInt rank; 522 PetscInt v, vx, vy, vz; 523 PetscInt voffset, iface=0, cone[4]; 524 525 PetscFunctionBegin; 526 PetscCheck(faces[0] >= 1 && faces[1] >= 1 && faces[2] >= 1,PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Must have at least 1 face per side"); 527 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 528 PetscCall(PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL)); 529 if (markerSeparate) { 530 markerBottom = 1; 531 markerTop = 2; 532 markerFront = 3; 533 markerBack = 4; 534 markerRight = 5; 535 markerLeft = 6; 536 } 537 vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1; 538 numVertices = vertices[0]*vertices[1]*vertices[2]; 539 if (rank == 0) { 540 PetscInt f; 541 542 PetscCall(DMPlexSetChart(dm, 0, numFaces+numVertices)); 543 for (f = 0; f < numFaces; ++f) { 544 PetscCall(DMPlexSetConeSize(dm, f, 4)); 545 } 546 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 547 548 /* Side 0 (Top) */ 549 for (vy = 0; vy < faces[1]; vy++) { 550 for (vx = 0; vx < faces[0]; vx++) { 551 voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx; 552 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0]; 553 PetscCall(DMPlexSetCone(dm, iface, cone)); 554 PetscCall(DMSetLabelValue(dm, "marker", iface, markerTop)); 555 PetscCall(DMSetLabelValue(dm, "marker", voffset+0, markerTop)); 556 PetscCall(DMSetLabelValue(dm, "marker", voffset+1, markerTop)); 557 PetscCall(DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, markerTop)); 558 PetscCall(DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, markerTop)); 559 iface++; 560 } 561 } 562 563 /* Side 1 (Bottom) */ 564 for (vy = 0; vy < faces[1]; vy++) { 565 for (vx = 0; vx < faces[0]; vx++) { 566 voffset = numFaces + vy*(faces[0]+1) + vx; 567 cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1; 568 PetscCall(DMPlexSetCone(dm, iface, cone)); 569 PetscCall(DMSetLabelValue(dm, "marker", iface, markerBottom)); 570 PetscCall(DMSetLabelValue(dm, "marker", voffset+0, markerBottom)); 571 PetscCall(DMSetLabelValue(dm, "marker", voffset+1, markerBottom)); 572 PetscCall(DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, markerBottom)); 573 PetscCall(DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, markerBottom)); 574 iface++; 575 } 576 } 577 578 /* Side 2 (Front) */ 579 for (vz = 0; vz < faces[2]; vz++) { 580 for (vx = 0; vx < faces[0]; vx++) { 581 voffset = numFaces + vz*vertices[0]*vertices[1] + vx; 582 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1]; 583 PetscCall(DMPlexSetCone(dm, iface, cone)); 584 PetscCall(DMSetLabelValue(dm, "marker", iface, markerFront)); 585 PetscCall(DMSetLabelValue(dm, "marker", voffset+0, markerFront)); 586 PetscCall(DMSetLabelValue(dm, "marker", voffset+1, markerFront)); 587 PetscCall(DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, markerFront)); 588 PetscCall(DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, markerFront)); 589 iface++; 590 } 591 } 592 593 /* Side 3 (Back) */ 594 for (vz = 0; vz < faces[2]; vz++) { 595 for (vx = 0; vx < faces[0]; vx++) { 596 voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx; 597 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1; 598 cone[2] = voffset+1; cone[3] = voffset; 599 PetscCall(DMPlexSetCone(dm, iface, cone)); 600 PetscCall(DMSetLabelValue(dm, "marker", iface, markerBack)); 601 PetscCall(DMSetLabelValue(dm, "marker", voffset+0, markerBack)); 602 PetscCall(DMSetLabelValue(dm, "marker", voffset+1, markerBack)); 603 PetscCall(DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, markerBack)); 604 PetscCall(DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, markerBack)); 605 iface++; 606 } 607 } 608 609 /* Side 4 (Left) */ 610 for (vz = 0; vz < faces[2]; vz++) { 611 for (vy = 0; vy < faces[1]; vy++) { 612 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0]; 613 cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1]; 614 cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0]; 615 PetscCall(DMPlexSetCone(dm, iface, cone)); 616 PetscCall(DMSetLabelValue(dm, "marker", iface, markerLeft)); 617 PetscCall(DMSetLabelValue(dm, "marker", voffset+0, markerLeft)); 618 PetscCall(DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, markerLeft)); 619 PetscCall(DMSetLabelValue(dm, "marker", voffset+vertices[1]+0, markerLeft)); 620 PetscCall(DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], markerLeft)); 621 iface++; 622 } 623 } 624 625 /* Side 5 (Right) */ 626 for (vz = 0; vz < faces[2]; vz++) { 627 for (vy = 0; vy < faces[1]; vy++) { 628 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + faces[0]; 629 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset; 630 cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0]; 631 PetscCall(DMPlexSetCone(dm, iface, cone)); 632 PetscCall(DMSetLabelValue(dm, "marker", iface, markerRight)); 633 PetscCall(DMSetLabelValue(dm, "marker", voffset+0, markerRight)); 634 PetscCall(DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, markerRight)); 635 PetscCall(DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, markerRight)); 636 PetscCall(DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], markerRight)); 637 iface++; 638 } 639 } 640 } 641 PetscCall(DMPlexSymmetrize(dm)); 642 PetscCall(DMPlexStratify(dm)); 643 /* Build coordinates */ 644 PetscCall(DMSetCoordinateDim(dm, 3)); 645 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 646 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 647 PetscCall(PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices)); 648 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, 3)); 649 for (v = numFaces; v < numFaces+numVertices; ++v) { 650 PetscCall(PetscSectionSetDof(coordSection, v, 3)); 651 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, 3)); 652 } 653 PetscCall(PetscSectionSetUp(coordSection)); 654 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 655 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 656 PetscCall(PetscObjectSetName((PetscObject) coordinates, "coordinates")); 657 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 658 PetscCall(VecSetBlockSize(coordinates, 3)); 659 PetscCall(VecSetType(coordinates,VECSTANDARD)); 660 PetscCall(VecGetArray(coordinates, &coords)); 661 for (vz = 0; vz <= faces[2]; ++vz) { 662 for (vy = 0; vy <= faces[1]; ++vy) { 663 for (vx = 0; vx <= faces[0]; ++vx) { 664 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx; 665 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy; 666 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz; 667 } 668 } 669 } 670 PetscCall(VecRestoreArray(coordinates, &coords)); 671 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 672 PetscCall(VecDestroy(&coordinates)); 673 PetscFunctionReturn(0); 674 } 675 676 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate) 677 { 678 PetscFunctionBegin; 679 PetscValidLogicalCollectiveInt(dm, dim, 2); 680 PetscCall(DMSetDimension(dm, dim-1)); 681 PetscCall(DMSetCoordinateDim(dm, dim)); 682 switch (dim) { 683 case 1: PetscCall(DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(dm, lower, upper, faces));break; 684 case 2: PetscCall(DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(dm, lower, upper, faces));break; 685 case 3: PetscCall(DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(dm, lower, upper, faces));break; 686 default: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Dimension not supported: %" PetscInt_FMT, dim); 687 } 688 if (interpolate) PetscCall(DMPlexInterpolateInPlace_Internal(dm)); 689 PetscFunctionReturn(0); 690 } 691 692 /*@C 693 DMPlexCreateBoxSurfaceMesh - Creates a mesh on the surface of the tensor product of unit intervals (box) using tensor cells (hexahedra). 694 695 Collective 696 697 Input Parameters: 698 + comm - The communicator for the DM object 699 . dim - The spatial dimension of the box, so the resulting mesh is has dimension dim-1 700 . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 701 . lower - The lower left corner, or NULL for (0, 0, 0) 702 . upper - The upper right corner, or NULL for (1, 1, 1) 703 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 704 705 Output Parameter: 706 . dm - The DM object 707 708 Level: beginner 709 710 .seealso: `DMSetFromOptions()`, `DMPlexCreateBoxMesh()`, `DMPlexCreateFromFile()`, `DMSetType()`, `DMCreate()` 711 @*/ 712 PetscErrorCode DMPlexCreateBoxSurfaceMesh(MPI_Comm comm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate, DM *dm) 713 { 714 PetscInt fac[3] = {1, 1, 1}; 715 PetscReal low[3] = {0, 0, 0}; 716 PetscReal upp[3] = {1, 1, 1}; 717 718 PetscFunctionBegin; 719 PetscCall(DMCreate(comm,dm)); 720 PetscCall(DMSetType(*dm,DMPLEX)); 721 PetscCall(DMPlexCreateBoxSurfaceMesh_Internal(*dm, dim, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, interpolate)); 722 PetscFunctionReturn(0); 723 } 724 725 static PetscErrorCode DMPlexCreateLineMesh_Internal(DM dm,PetscInt segments,PetscReal lower,PetscReal upper,DMBoundaryType bd) 726 { 727 PetscInt i,fStart,fEnd,numCells = 0,numVerts = 0; 728 PetscInt numPoints[2],*coneSize,*cones,*coneOrientations; 729 PetscScalar *vertexCoords; 730 PetscReal L,maxCell; 731 PetscBool markerSeparate = PETSC_FALSE; 732 PetscInt markerLeft = 1, faceMarkerLeft = 1; 733 PetscInt markerRight = 1, faceMarkerRight = 2; 734 PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE; 735 PetscMPIInt rank; 736 737 PetscFunctionBegin; 738 PetscValidPointer(dm,1); 739 740 PetscCall(DMSetDimension(dm,1)); 741 PetscCall(DMCreateLabel(dm,"marker")); 742 PetscCall(DMCreateLabel(dm,"Face Sets")); 743 744 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject) dm),&rank)); 745 if (rank == 0) numCells = segments; 746 if (rank == 0) numVerts = segments + (wrap ? 0 : 1); 747 748 numPoints[0] = numVerts ; numPoints[1] = numCells; 749 PetscCall(PetscMalloc4(numCells+numVerts,&coneSize,numCells*2,&cones,numCells+numVerts,&coneOrientations,numVerts,&vertexCoords)); 750 PetscCall(PetscArrayzero(coneOrientations,numCells+numVerts)); 751 for (i = 0; i < numCells; ++i) { coneSize[i] = 2; } 752 for (i = 0; i < numVerts; ++i) { coneSize[numCells+i] = 0; } 753 for (i = 0; i < numCells; ++i) { cones[2*i] = numCells + i%numVerts; cones[2*i+1] = numCells + (i+1)%numVerts; } 754 for (i = 0; i < numVerts; ++i) { vertexCoords[i] = lower + (upper-lower)*((PetscReal)i/(PetscReal)numCells); } 755 PetscCall(DMPlexCreateFromDAG(dm,1,numPoints,coneSize,cones,coneOrientations,vertexCoords)); 756 PetscCall(PetscFree4(coneSize,cones,coneOrientations,vertexCoords)); 757 758 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options,((PetscObject)dm)->prefix,"-dm_plex_separate_marker",&markerSeparate,NULL)); 759 if (markerSeparate) { markerLeft = faceMarkerLeft; markerRight = faceMarkerRight;} 760 if (!wrap && rank == 0) { 761 PetscCall(DMPlexGetHeightStratum(dm,1,&fStart,&fEnd)); 762 PetscCall(DMSetLabelValue(dm,"marker",fStart,markerLeft)); 763 PetscCall(DMSetLabelValue(dm,"marker",fEnd-1,markerRight)); 764 PetscCall(DMSetLabelValue(dm,"Face Sets",fStart,faceMarkerLeft)); 765 PetscCall(DMSetLabelValue(dm,"Face Sets",fEnd-1,faceMarkerRight)); 766 } 767 if (wrap) { 768 L = upper - lower; 769 maxCell = (PetscReal)1.1*(L/(PetscReal)PetscMax(1,segments)); 770 PetscCall(DMSetPeriodicity(dm, &maxCell, &lower, &L)); 771 } 772 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 773 PetscFunctionReturn(0); 774 } 775 776 static PetscErrorCode DMPlexCreateBoxMesh_Simplex_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate) 777 { 778 DM boundary, vol; 779 PetscInt i; 780 781 PetscFunctionBegin; 782 PetscValidPointer(dm, 1); 783 for (i = 0; i < dim; ++i) PetscCheck(periodicity[i] == DM_BOUNDARY_NONE,PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Periodicity is not supported for simplex meshes"); 784 PetscCall(DMCreate(PetscObjectComm((PetscObject) dm), &boundary)); 785 PetscCall(DMSetType(boundary, DMPLEX)); 786 PetscCall(DMPlexCreateBoxSurfaceMesh_Internal(boundary, dim, faces, lower, upper, PETSC_FALSE)); 787 PetscCall(DMPlexGenerate(boundary, NULL, interpolate, &vol)); 788 PetscCall(DMPlexCopy_Internal(dm, PETSC_TRUE, PETSC_FALSE, vol)); 789 PetscCall(DMPlexReplace_Static(dm, &vol)); 790 PetscCall(DMDestroy(&boundary)); 791 PetscFunctionReturn(0); 792 } 793 794 static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ) 795 { 796 DMLabel cutLabel = NULL; 797 PetscInt markerTop = 1, faceMarkerTop = 1; 798 PetscInt markerBottom = 1, faceMarkerBottom = 1; 799 PetscInt markerFront = 1, faceMarkerFront = 1; 800 PetscInt markerBack = 1, faceMarkerBack = 1; 801 PetscInt markerRight = 1, faceMarkerRight = 1; 802 PetscInt markerLeft = 1, faceMarkerLeft = 1; 803 PetscInt dim; 804 PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE; 805 PetscMPIInt rank; 806 807 PetscFunctionBegin; 808 PetscCall(DMGetDimension(dm,&dim)); 809 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 810 PetscCall(DMCreateLabel(dm,"marker")); 811 PetscCall(DMCreateLabel(dm,"Face Sets")); 812 PetscCall(PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL)); 813 if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST || 814 bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST || 815 bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) { 816 817 if (cutMarker) {PetscCall(DMCreateLabel(dm, "periodic_cut")); PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));} 818 } 819 switch (dim) { 820 case 2: 821 faceMarkerTop = 3; 822 faceMarkerBottom = 1; 823 faceMarkerRight = 2; 824 faceMarkerLeft = 4; 825 break; 826 case 3: 827 faceMarkerBottom = 1; 828 faceMarkerTop = 2; 829 faceMarkerFront = 3; 830 faceMarkerBack = 4; 831 faceMarkerRight = 5; 832 faceMarkerLeft = 6; 833 break; 834 default: 835 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %" PetscInt_FMT " not supported",dim); 836 } 837 PetscCall(PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL)); 838 if (markerSeparate) { 839 markerBottom = faceMarkerBottom; 840 markerTop = faceMarkerTop; 841 markerFront = faceMarkerFront; 842 markerBack = faceMarkerBack; 843 markerRight = faceMarkerRight; 844 markerLeft = faceMarkerLeft; 845 } 846 { 847 const PetscInt numXEdges = rank == 0 ? edges[0] : 0; 848 const PetscInt numYEdges = rank == 0 ? edges[1] : 0; 849 const PetscInt numZEdges = rank == 0 ? edges[2] : 0; 850 const PetscInt numXVertices = rank == 0 ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; 851 const PetscInt numYVertices = rank == 0 ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; 852 const PetscInt numZVertices = rank == 0 ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0; 853 const PetscInt numCells = numXEdges*numYEdges*numZEdges; 854 const PetscInt numXFaces = numYEdges*numZEdges; 855 const PetscInt numYFaces = numXEdges*numZEdges; 856 const PetscInt numZFaces = numXEdges*numYEdges; 857 const PetscInt numTotXFaces = numXVertices*numXFaces; 858 const PetscInt numTotYFaces = numYVertices*numYFaces; 859 const PetscInt numTotZFaces = numZVertices*numZFaces; 860 const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces; 861 const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices; 862 const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices; 863 const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices; 864 const PetscInt numVertices = numXVertices*numYVertices*numZVertices; 865 const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges; 866 const PetscInt firstVertex = (dim == 2) ? numFaces : numCells; 867 const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices; 868 const PetscInt firstYFace = firstXFace + numTotXFaces; 869 const PetscInt firstZFace = firstYFace + numTotYFaces; 870 const PetscInt firstXEdge = numCells + numFaces + numVertices; 871 const PetscInt firstYEdge = firstXEdge + numTotXEdges; 872 const PetscInt firstZEdge = firstYEdge + numTotYEdges; 873 Vec coordinates; 874 PetscSection coordSection; 875 PetscScalar *coords; 876 PetscInt coordSize; 877 PetscInt v, vx, vy, vz; 878 PetscInt c, f, fx, fy, fz, e, ex, ey, ez; 879 880 PetscCall(DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices)); 881 for (c = 0; c < numCells; c++) { 882 PetscCall(DMPlexSetConeSize(dm, c, 6)); 883 } 884 for (f = firstXFace; f < firstXFace+numFaces; ++f) { 885 PetscCall(DMPlexSetConeSize(dm, f, 4)); 886 } 887 for (e = firstXEdge; e < firstXEdge+numEdges; ++e) { 888 PetscCall(DMPlexSetConeSize(dm, e, 2)); 889 } 890 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 891 /* Build cells */ 892 for (fz = 0; fz < numZEdges; ++fz) { 893 for (fy = 0; fy < numYEdges; ++fy) { 894 for (fx = 0; fx < numXEdges; ++fx) { 895 PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx; 896 PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 897 PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices); 898 PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 899 PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices); 900 PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 901 PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices); 902 /* B, T, F, K, R, L */ 903 PetscInt ornt[6] = {-2, 0, 0, -3, 0, -2}; /* ??? */ 904 PetscInt cone[6]; 905 906 /* no boundary twisting in 3D */ 907 cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL; 908 PetscCall(DMPlexSetCone(dm, cell, cone)); 909 PetscCall(DMPlexSetConeOrientation(dm, cell, ornt)); 910 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, cell, 2)); 911 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, cell, 2)); 912 if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, cell, 2)); 913 } 914 } 915 } 916 /* Build x faces */ 917 for (fz = 0; fz < numZEdges; ++fz) { 918 for (fy = 0; fy < numYEdges; ++fy) { 919 for (fx = 0; fx < numXVertices; ++fx) { 920 PetscInt face = firstXFace + (fz*numYEdges+fy) *numXVertices+fx; 921 PetscInt edgeL = firstZEdge + (fy *numXVertices+fx)*numZEdges + fz; 922 PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz; 923 PetscInt edgeB = firstYEdge + (fz *numXVertices+fx)*numYEdges + fy; 924 PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy; 925 PetscInt ornt[4] = {0, 0, -1, -1}; 926 PetscInt cone[4]; 927 928 if (dim == 3) { 929 /* markers */ 930 if (bdX != DM_BOUNDARY_PERIODIC) { 931 if (fx == numXVertices-1) { 932 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight)); 933 PetscCall(DMSetLabelValue(dm, "marker", face, markerRight)); 934 } 935 else if (fx == 0) { 936 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft)); 937 PetscCall(DMSetLabelValue(dm, "marker", face, markerLeft)); 938 } 939 } 940 } 941 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 942 PetscCall(DMPlexSetCone(dm, face, cone)); 943 PetscCall(DMPlexSetConeOrientation(dm, face, ornt)); 944 } 945 } 946 } 947 /* Build y faces */ 948 for (fz = 0; fz < numZEdges; ++fz) { 949 for (fx = 0; fx < numXEdges; ++fx) { 950 for (fy = 0; fy < numYVertices; ++fy) { 951 PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 952 PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx)*numZEdges + fz; 953 PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz; 954 PetscInt edgeB = firstXEdge + (fz *numYVertices+fy)*numXEdges + fx; 955 PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx; 956 PetscInt ornt[4] = {0, 0, -1, -1}; 957 PetscInt cone[4]; 958 959 if (dim == 3) { 960 /* markers */ 961 if (bdY != DM_BOUNDARY_PERIODIC) { 962 if (fy == numYVertices-1) { 963 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack)); 964 PetscCall(DMSetLabelValue(dm, "marker", face, markerBack)); 965 } 966 else if (fy == 0) { 967 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront)); 968 PetscCall(DMSetLabelValue(dm, "marker", face, markerFront)); 969 } 970 } 971 } 972 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 973 PetscCall(DMPlexSetCone(dm, face, cone)); 974 PetscCall(DMPlexSetConeOrientation(dm, face, ornt)); 975 } 976 } 977 } 978 /* Build z faces */ 979 for (fy = 0; fy < numYEdges; ++fy) { 980 for (fx = 0; fx < numXEdges; ++fx) { 981 for (fz = 0; fz < numZVertices; fz++) { 982 PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 983 PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx)*numYEdges + fy; 984 PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy; 985 PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy)*numXEdges + fx; 986 PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx; 987 PetscInt ornt[4] = {0, 0, -1, -1}; 988 PetscInt cone[4]; 989 990 if (dim == 2) { 991 if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -1;} 992 if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;} 993 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, face, 2)); 994 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, face, 2)); 995 } else { 996 /* markers */ 997 if (bdZ != DM_BOUNDARY_PERIODIC) { 998 if (fz == numZVertices-1) { 999 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop)); 1000 PetscCall(DMSetLabelValue(dm, "marker", face, markerTop)); 1001 } 1002 else if (fz == 0) { 1003 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom)); 1004 PetscCall(DMSetLabelValue(dm, "marker", face, markerBottom)); 1005 } 1006 } 1007 } 1008 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 1009 PetscCall(DMPlexSetCone(dm, face, cone)); 1010 PetscCall(DMPlexSetConeOrientation(dm, face, ornt)); 1011 } 1012 } 1013 } 1014 /* Build Z edges*/ 1015 for (vy = 0; vy < numYVertices; vy++) { 1016 for (vx = 0; vx < numXVertices; vx++) { 1017 for (ez = 0; ez < numZEdges; ez++) { 1018 const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez; 1019 const PetscInt vertexB = firstVertex + (ez *numYVertices+vy)*numXVertices + vx; 1020 const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx; 1021 PetscInt cone[2]; 1022 1023 cone[0] = vertexB; cone[1] = vertexT; 1024 PetscCall(DMPlexSetCone(dm, edge, cone)); 1025 if (dim == 3) { 1026 if (bdX != DM_BOUNDARY_PERIODIC) { 1027 if (vx == numXVertices-1) { 1028 PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight)); 1029 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight)); 1030 if (ez == numZEdges-1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight)); 1031 } else if (vx == 0) { 1032 PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft)); 1033 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft)); 1034 if (ez == numZEdges-1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft)); 1035 } 1036 } 1037 if (bdY != DM_BOUNDARY_PERIODIC) { 1038 if (vy == numYVertices-1) { 1039 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBack)); 1040 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBack)); 1041 if (ez == numZEdges-1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBack)); 1042 } else if (vy == 0) { 1043 PetscCall(DMSetLabelValue(dm, "marker", edge, markerFront)); 1044 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerFront)); 1045 if (ez == numZEdges-1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerFront)); 1046 } 1047 } 1048 } 1049 } 1050 } 1051 } 1052 /* Build Y edges*/ 1053 for (vz = 0; vz < numZVertices; vz++) { 1054 for (vx = 0; vx < numXVertices; vx++) { 1055 for (ey = 0; ey < numYEdges; ey++) { 1056 const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx; 1057 const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey; 1058 const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx; 1059 const PetscInt vertexK = firstVertex + nextv; 1060 PetscInt cone[2]; 1061 1062 cone[0] = vertexF; cone[1] = vertexK; 1063 PetscCall(DMPlexSetCone(dm, edge, cone)); 1064 if (dim == 2) { 1065 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 1066 if (vx == numXVertices-1) { 1067 PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight)); 1068 PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight)); 1069 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight)); 1070 if (ey == numYEdges-1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight)); 1071 } else if (vx == 0) { 1072 PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft)); 1073 PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft)); 1074 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft)); 1075 if (ey == numYEdges-1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft)); 1076 } 1077 } else { 1078 if (vx == 0 && cutLabel) { 1079 PetscCall(DMLabelSetValue(cutLabel, edge, 1)); 1080 PetscCall(DMLabelSetValue(cutLabel, cone[0], 1)); 1081 if (ey == numYEdges-1) PetscCall(DMLabelSetValue(cutLabel, cone[1], 1)); 1082 } 1083 } 1084 } else { 1085 if (bdX != DM_BOUNDARY_PERIODIC) { 1086 if (vx == numXVertices-1) { 1087 PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight)); 1088 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight)); 1089 if (ey == numYEdges-1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight)); 1090 } else if (vx == 0) { 1091 PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft)); 1092 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft)); 1093 if (ey == numYEdges-1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft)); 1094 } 1095 } 1096 if (bdZ != DM_BOUNDARY_PERIODIC) { 1097 if (vz == numZVertices-1) { 1098 PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop)); 1099 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop)); 1100 if (ey == numYEdges-1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop)); 1101 } else if (vz == 0) { 1102 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom)); 1103 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom)); 1104 if (ey == numYEdges-1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom)); 1105 } 1106 } 1107 } 1108 } 1109 } 1110 } 1111 /* Build X edges*/ 1112 for (vz = 0; vz < numZVertices; vz++) { 1113 for (vy = 0; vy < numYVertices; vy++) { 1114 for (ex = 0; ex < numXEdges; ex++) { 1115 const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices; 1116 const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex; 1117 const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex; 1118 const PetscInt vertexR = firstVertex + nextv; 1119 PetscInt cone[2]; 1120 1121 cone[0] = vertexL; cone[1] = vertexR; 1122 PetscCall(DMPlexSetCone(dm, edge, cone)); 1123 if (dim == 2) { 1124 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 1125 if (vy == numYVertices-1) { 1126 PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop)); 1127 PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop)); 1128 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop)); 1129 if (ex == numXEdges-1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop)); 1130 } else if (vy == 0) { 1131 PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom)); 1132 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom)); 1133 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom)); 1134 if (ex == numXEdges-1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom)); 1135 } 1136 } else { 1137 if (vy == 0 && cutLabel) { 1138 PetscCall(DMLabelSetValue(cutLabel, edge, 1)); 1139 PetscCall(DMLabelSetValue(cutLabel, cone[0], 1)); 1140 if (ex == numXEdges-1) PetscCall(DMLabelSetValue(cutLabel, cone[1], 1)); 1141 } 1142 } 1143 } else { 1144 if (bdY != DM_BOUNDARY_PERIODIC) { 1145 if (vy == numYVertices-1) { 1146 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBack)); 1147 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBack)); 1148 if (ex == numXEdges-1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBack)); 1149 } else if (vy == 0) { 1150 PetscCall(DMSetLabelValue(dm, "marker", edge, markerFront)); 1151 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerFront)); 1152 if (ex == numXEdges-1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerFront)); 1153 } 1154 } 1155 if (bdZ != DM_BOUNDARY_PERIODIC) { 1156 if (vz == numZVertices-1) { 1157 PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop)); 1158 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop)); 1159 if (ex == numXEdges-1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop)); 1160 } else if (vz == 0) { 1161 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom)); 1162 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom)); 1163 if (ex == numXEdges-1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom)); 1164 } 1165 } 1166 } 1167 } 1168 } 1169 } 1170 PetscCall(DMPlexSymmetrize(dm)); 1171 PetscCall(DMPlexStratify(dm)); 1172 /* Build coordinates */ 1173 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 1174 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 1175 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim)); 1176 PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices)); 1177 for (v = firstVertex; v < firstVertex+numVertices; ++v) { 1178 PetscCall(PetscSectionSetDof(coordSection, v, dim)); 1179 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim)); 1180 } 1181 PetscCall(PetscSectionSetUp(coordSection)); 1182 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 1183 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 1184 PetscCall(PetscObjectSetName((PetscObject) coordinates, "coordinates")); 1185 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 1186 PetscCall(VecSetBlockSize(coordinates, dim)); 1187 PetscCall(VecSetType(coordinates,VECSTANDARD)); 1188 PetscCall(VecGetArray(coordinates, &coords)); 1189 for (vz = 0; vz < numZVertices; ++vz) { 1190 for (vy = 0; vy < numYVertices; ++vy) { 1191 for (vx = 0; vx < numXVertices; ++vx) { 1192 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx; 1193 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy; 1194 if (dim == 3) { 1195 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz; 1196 } 1197 } 1198 } 1199 } 1200 PetscCall(VecRestoreArray(coordinates, &coords)); 1201 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 1202 PetscCall(VecDestroy(&coordinates)); 1203 } 1204 PetscFunctionReturn(0); 1205 } 1206 1207 static PetscErrorCode DMPlexCreateBoxMesh_Tensor_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[]) 1208 { 1209 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1210 PetscInt fac[3] = {0, 0, 0}, d; 1211 1212 PetscFunctionBegin; 1213 PetscValidPointer(dm, 1); 1214 PetscValidLogicalCollectiveInt(dm, dim, 2); 1215 PetscCall(DMSetDimension(dm, dim)); 1216 for (d = 0; d < dim; ++d) {fac[d] = faces[d]; bdt[d] = periodicity[d];} 1217 PetscCall(DMPlexCreateCubeMesh_Internal(dm, lower, upper, fac, bdt[0], bdt[1], bdt[2])); 1218 if (periodicity[0] == DM_BOUNDARY_PERIODIC || periodicity[0] == DM_BOUNDARY_TWIST || 1219 periodicity[1] == DM_BOUNDARY_PERIODIC || periodicity[1] == DM_BOUNDARY_TWIST || 1220 (dim > 2 && (periodicity[2] == DM_BOUNDARY_PERIODIC || periodicity[2] == DM_BOUNDARY_TWIST))) { 1221 PetscReal L[3] = {-1., -1., 0.}; 1222 PetscReal maxCell[3] = {-1., -1., 0.}; 1223 1224 for (d = 0; d < dim; ++d) { 1225 if (periodicity[d] != DM_BOUNDARY_NONE) { 1226 L[d] = upper[d] - lower[d]; 1227 maxCell[d] = 1.1 * (L[d] / PetscMax(1, faces[d])); 1228 } 1229 } 1230 PetscCall(DMSetPeriodicity(dm, maxCell, lower, L)); 1231 } 1232 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 1233 PetscFunctionReturn(0); 1234 } 1235 1236 static PetscErrorCode DMPlexCreateBoxMesh_Internal(DM dm, PetscInt dim, PetscBool simplex, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate) 1237 { 1238 PetscFunctionBegin; 1239 if (dim == 1) PetscCall(DMPlexCreateLineMesh_Internal(dm, faces[0], lower[0], upper[0], periodicity[0])); 1240 else if (simplex) PetscCall(DMPlexCreateBoxMesh_Simplex_Internal(dm, dim, faces, lower, upper, periodicity, interpolate)); 1241 else PetscCall(DMPlexCreateBoxMesh_Tensor_Internal(dm, dim, faces, lower, upper, periodicity)); 1242 if (!interpolate && dim > 1 && !simplex) { 1243 DM udm; 1244 1245 PetscCall(DMPlexUninterpolate(dm, &udm)); 1246 PetscCall(DMPlexCopyCoordinates(dm, udm)); 1247 PetscCall(DMPlexReplace_Static(dm, &udm)); 1248 } 1249 PetscFunctionReturn(0); 1250 } 1251 1252 /*@C 1253 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra). 1254 1255 Collective 1256 1257 Input Parameters: 1258 + comm - The communicator for the DM object 1259 . dim - The spatial dimension 1260 . simplex - PETSC_TRUE for simplices, PETSC_FALSE for tensor cells 1261 . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 1262 . lower - The lower left corner, or NULL for (0, 0, 0) 1263 . upper - The upper right corner, or NULL for (1, 1, 1) 1264 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 1265 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1266 1267 Output Parameter: 1268 . dm - The DM object 1269 1270 Note: If you want to customize this mesh using options, you just need to 1271 $ DMCreate(comm, &dm); 1272 $ DMSetType(dm, DMPLEX); 1273 $ DMSetFromOptions(dm); 1274 and use the options on the DMSetFromOptions() page. 1275 1276 Here is the numbering returned for 2 faces in each direction for tensor cells: 1277 $ 10---17---11---18----12 1278 $ | | | 1279 $ | | | 1280 $ 20 2 22 3 24 1281 $ | | | 1282 $ | | | 1283 $ 7---15----8---16----9 1284 $ | | | 1285 $ | | | 1286 $ 19 0 21 1 23 1287 $ | | | 1288 $ | | | 1289 $ 4---13----5---14----6 1290 1291 and for simplicial cells 1292 1293 $ 14----8---15----9----16 1294 $ |\ 5 |\ 7 | 1295 $ | \ | \ | 1296 $ 13 2 14 3 15 1297 $ | 4 \ | 6 \ | 1298 $ | \ | \ | 1299 $ 11----6---12----7----13 1300 $ |\ |\ | 1301 $ | \ 1 | \ 3 | 1302 $ 10 0 11 1 12 1303 $ | 0 \ | 2 \ | 1304 $ | \ | \ | 1305 $ 8----4----9----5----10 1306 1307 Level: beginner 1308 1309 .seealso: `DMSetFromOptions()`, `DMPlexCreateFromFile()`, `DMPlexCreateHexCylinderMesh()`, `DMSetType()`, `DMCreate()` 1310 @*/ 1311 PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate, DM *dm) 1312 { 1313 PetscInt fac[3] = {1, 1, 1}; 1314 PetscReal low[3] = {0, 0, 0}; 1315 PetscReal upp[3] = {1, 1, 1}; 1316 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1317 1318 PetscFunctionBegin; 1319 PetscCall(DMCreate(comm,dm)); 1320 PetscCall(DMSetType(*dm,DMPLEX)); 1321 PetscCall(DMPlexCreateBoxMesh_Internal(*dm, dim, simplex, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt, interpolate)); 1322 if (periodicity) PetscCall(DMLocalizeCoordinates(*dm)); 1323 PetscFunctionReturn(0); 1324 } 1325 1326 static PetscErrorCode DMPlexCreateWedgeBoxMesh_Internal(DM dm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[]) 1327 { 1328 DM bdm, vol; 1329 PetscInt i; 1330 1331 PetscFunctionBegin; 1332 for (i = 0; i < 3; ++i) PetscCheck(periodicity[i] == DM_BOUNDARY_NONE,PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Periodicity not yet supported"); 1333 PetscCall(DMCreate(PetscObjectComm((PetscObject) dm), &bdm)); 1334 PetscCall(DMSetType(bdm, DMPLEX)); 1335 PetscCall(DMSetDimension(bdm, 2)); 1336 PetscCall(DMPlexCreateBoxMesh_Simplex_Internal(bdm, 2, faces, lower, upper, periodicity, PETSC_TRUE)); 1337 PetscCall(DMPlexExtrude(bdm, faces[2], upper[2] - lower[2], PETSC_TRUE, PETSC_FALSE, NULL, NULL, &vol)); 1338 PetscCall(DMDestroy(&bdm)); 1339 PetscCall(DMPlexReplace_Static(dm, &vol)); 1340 if (lower[2] != 0.0) { 1341 Vec v; 1342 PetscScalar *x; 1343 PetscInt cDim, n; 1344 1345 PetscCall(DMGetCoordinatesLocal(dm, &v)); 1346 PetscCall(VecGetBlockSize(v, &cDim)); 1347 PetscCall(VecGetLocalSize(v, &n)); 1348 PetscCall(VecGetArray(v, &x)); 1349 x += cDim; 1350 for (i = 0; i < n; i += cDim) x[i] += lower[2]; 1351 PetscCall(VecRestoreArray(v,&x)); 1352 PetscCall(DMSetCoordinatesLocal(dm, v)); 1353 } 1354 PetscFunctionReturn(0); 1355 } 1356 1357 /*@ 1358 DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells. 1359 1360 Collective 1361 1362 Input Parameters: 1363 + comm - The communicator for the DM object 1364 . faces - Number of faces per dimension, or NULL for (1, 1, 1) 1365 . lower - The lower left corner, or NULL for (0, 0, 0) 1366 . upper - The upper right corner, or NULL for (1, 1, 1) 1367 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 1368 . orderHeight - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1369 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1370 1371 Output Parameter: 1372 . dm - The DM object 1373 1374 Level: beginner 1375 1376 .seealso: `DMPlexCreateHexCylinderMesh()`, `DMPlexCreateWedgeCylinderMesh()`, `DMExtrude()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 1377 @*/ 1378 PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool orderHeight, PetscBool interpolate, DM *dm) 1379 { 1380 PetscInt fac[3] = {1, 1, 1}; 1381 PetscReal low[3] = {0, 0, 0}; 1382 PetscReal upp[3] = {1, 1, 1}; 1383 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1384 1385 PetscFunctionBegin; 1386 PetscCall(DMCreate(comm,dm)); 1387 PetscCall(DMSetType(*dm,DMPLEX)); 1388 PetscCall(DMPlexCreateWedgeBoxMesh_Internal(*dm, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt)); 1389 if (!interpolate) { 1390 DM udm; 1391 1392 PetscCall(DMPlexUninterpolate(*dm, &udm)); 1393 PetscCall(DMPlexReplace_Static(*dm, &udm)); 1394 } 1395 if (periodicity) PetscCall(DMLocalizeCoordinates(*dm)); 1396 PetscFunctionReturn(0); 1397 } 1398 1399 /*@C 1400 DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database. 1401 1402 Logically Collective on dm 1403 1404 Input Parameters: 1405 + dm - the DM context 1406 - prefix - the prefix to prepend to all option names 1407 1408 Notes: 1409 A hyphen (-) must NOT be given at the beginning of the prefix name. 1410 The first character of all runtime options is AUTOMATICALLY the hyphen. 1411 1412 Level: advanced 1413 1414 .seealso: `SNESSetFromOptions()` 1415 @*/ 1416 PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) 1417 { 1418 DM_Plex *mesh = (DM_Plex *) dm->data; 1419 1420 PetscFunctionBegin; 1421 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1422 PetscCall(PetscObjectSetOptionsPrefix((PetscObject) dm, prefix)); 1423 PetscCall(PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix)); 1424 PetscFunctionReturn(0); 1425 } 1426 1427 /* Remap geometry to cylinder 1428 TODO: This only works for a single refinement, then it is broken 1429 1430 Interior square: Linear interpolation is correct 1431 The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing 1432 such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance 1433 1434 phi = arctan(y/x) 1435 d_close = sqrt(1/8 + 1/4 sin^2(phi)) 1436 d_far = sqrt(1/2 + sin^2(phi)) 1437 1438 so we remap them using 1439 1440 x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) 1441 y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) 1442 1443 If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. 1444 */ 1445 static void snapToCylinder(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1446 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1447 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1448 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 1449 { 1450 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1451 const PetscReal ds2 = 0.5*dis; 1452 1453 if ((PetscAbsScalar(u[0]) <= ds2) && (PetscAbsScalar(u[1]) <= ds2)) { 1454 f0[0] = u[0]; 1455 f0[1] = u[1]; 1456 } else { 1457 PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; 1458 1459 x = PetscRealPart(u[0]); 1460 y = PetscRealPart(u[1]); 1461 phi = PetscAtan2Real(y, x); 1462 sinp = PetscSinReal(phi); 1463 cosp = PetscCosReal(phi); 1464 if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) { 1465 dc = PetscAbsReal(ds2/sinp); 1466 df = PetscAbsReal(dis/sinp); 1467 xc = ds2*x/PetscAbsReal(y); 1468 yc = ds2*PetscSignReal(y); 1469 } else { 1470 dc = PetscAbsReal(ds2/cosp); 1471 df = PetscAbsReal(dis/cosp); 1472 xc = ds2*PetscSignReal(x); 1473 yc = ds2*y/PetscAbsReal(x); 1474 } 1475 f0[0] = xc + (u[0] - xc)*(1.0 - dc)/(df - dc); 1476 f0[1] = yc + (u[1] - yc)*(1.0 - dc)/(df - dc); 1477 } 1478 f0[2] = u[2]; 1479 } 1480 1481 static PetscErrorCode DMPlexCreateHexCylinderMesh_Internal(DM dm, DMBoundaryType periodicZ) 1482 { 1483 const PetscInt dim = 3; 1484 PetscInt numCells, numVertices; 1485 PetscMPIInt rank; 1486 1487 PetscFunctionBegin; 1488 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank)); 1489 PetscCall(DMSetDimension(dm, dim)); 1490 /* Create topology */ 1491 { 1492 PetscInt cone[8], c; 1493 1494 numCells = rank == 0 ? 5 : 0; 1495 numVertices = rank == 0 ? 16 : 0; 1496 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1497 numCells *= 3; 1498 numVertices = rank == 0 ? 24 : 0; 1499 } 1500 PetscCall(DMPlexSetChart(dm, 0, numCells+numVertices)); 1501 for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 8)); 1502 PetscCall(DMSetUp(dm)); 1503 if (rank == 0) { 1504 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1505 cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16; 1506 cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34; 1507 PetscCall(DMPlexSetCone(dm, 0, cone)); 1508 cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23; 1509 cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */ 1510 PetscCall(DMPlexSetCone(dm, 1, cone)); 1511 cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17; 1512 cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38; 1513 PetscCall(DMPlexSetCone(dm, 2, cone)); 1514 cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15; 1515 cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38; 1516 PetscCall(DMPlexSetCone(dm, 3, cone)); 1517 cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23; 1518 cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31; 1519 PetscCall(DMPlexSetCone(dm, 4, cone)); 1520 1521 cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32; 1522 cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20; 1523 PetscCall(DMPlexSetCone(dm, 5, cone)); 1524 cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36; 1525 cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21; 1526 PetscCall(DMPlexSetCone(dm, 6, cone)); 1527 cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33; 1528 cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28; 1529 PetscCall(DMPlexSetCone(dm, 7, cone)); 1530 cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31; 1531 cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28; 1532 PetscCall(DMPlexSetCone(dm, 8, cone)); 1533 cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36; 1534 cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19; 1535 PetscCall(DMPlexSetCone(dm, 9, cone)); 1536 1537 cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22; 1538 cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18; 1539 PetscCall(DMPlexSetCone(dm, 10, cone)); 1540 cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25; 1541 cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17; 1542 PetscCall(DMPlexSetCone(dm, 11, cone)); 1543 cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21; 1544 cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27; 1545 PetscCall(DMPlexSetCone(dm, 12, cone)); 1546 cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19; 1547 cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27; 1548 PetscCall(DMPlexSetCone(dm, 13, cone)); 1549 cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25; 1550 cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15; 1551 PetscCall(DMPlexSetCone(dm, 14, cone)); 1552 } else { 1553 cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6; 1554 cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10; 1555 PetscCall(DMPlexSetCone(dm, 0, cone)); 1556 cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13; 1557 cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11; 1558 PetscCall(DMPlexSetCone(dm, 1, cone)); 1559 cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7; 1560 cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18; 1561 PetscCall(DMPlexSetCone(dm, 2, cone)); 1562 cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5; 1563 cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18; 1564 PetscCall(DMPlexSetCone(dm, 3, cone)); 1565 cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13; 1566 cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9; 1567 PetscCall(DMPlexSetCone(dm, 4, cone)); 1568 } 1569 } 1570 PetscCall(DMPlexSymmetrize(dm)); 1571 PetscCall(DMPlexStratify(dm)); 1572 } 1573 /* Create cube geometry */ 1574 { 1575 Vec coordinates; 1576 PetscSection coordSection; 1577 PetscScalar *coords; 1578 PetscInt coordSize, v; 1579 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1580 const PetscReal ds2 = dis/2.0; 1581 1582 /* Build coordinates */ 1583 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 1584 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 1585 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim)); 1586 PetscCall(PetscSectionSetChart(coordSection, numCells, numCells+numVertices)); 1587 for (v = numCells; v < numCells+numVertices; ++v) { 1588 PetscCall(PetscSectionSetDof(coordSection, v, dim)); 1589 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim)); 1590 } 1591 PetscCall(PetscSectionSetUp(coordSection)); 1592 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 1593 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 1594 PetscCall(PetscObjectSetName((PetscObject) coordinates, "coordinates")); 1595 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 1596 PetscCall(VecSetBlockSize(coordinates, dim)); 1597 PetscCall(VecSetType(coordinates,VECSTANDARD)); 1598 PetscCall(VecGetArray(coordinates, &coords)); 1599 if (rank == 0) { 1600 coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0; 1601 coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0; 1602 coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0; 1603 coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0; 1604 coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0; 1605 coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0; 1606 coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0; 1607 coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0; 1608 coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0; 1609 coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0; 1610 coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0; 1611 coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0; 1612 coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0; 1613 coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0; 1614 coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0; 1615 coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0; 1616 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1617 /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5; 1618 /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5; 1619 /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5; 1620 /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5; 1621 /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5; 1622 /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5; 1623 /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5; 1624 /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5; 1625 } 1626 } 1627 PetscCall(VecRestoreArray(coordinates, &coords)); 1628 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 1629 PetscCall(VecDestroy(&coordinates)); 1630 } 1631 /* Create periodicity */ 1632 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1633 PetscReal L[3] = {-1., -1., 0.}; 1634 PetscReal maxCell[3] = {-1., -1., 0.}; 1635 PetscReal lower[3] = {0.0, 0.0, 0.0}; 1636 PetscReal upper[3] = {1.0, 1.0, 1.5}; 1637 PetscInt numZCells = 3; 1638 1639 L[2] = upper[2] - lower[2]; 1640 maxCell[2] = 1.1 * (L[2] / numZCells); 1641 PetscCall(DMSetPeriodicity(dm, maxCell, lower, L)); 1642 } 1643 { 1644 DM cdm; 1645 PetscDS cds; 1646 PetscScalar c[2] = {1.0, 1.0}; 1647 1648 PetscCall(DMPlexCreateCoordinateSpace(dm, 1, snapToCylinder)); 1649 PetscCall(DMGetCoordinateDM(dm, &cdm)); 1650 PetscCall(DMGetDS(cdm, &cds)); 1651 PetscCall(PetscDSSetConstants(cds, 2, c)); 1652 } 1653 /* Wait for coordinate creation before doing in-place modification */ 1654 PetscCall(DMPlexInterpolateInPlace_Internal(dm)); 1655 PetscFunctionReturn(0); 1656 } 1657 1658 /*@ 1659 DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. 1660 1661 Collective 1662 1663 Input Parameters: 1664 + comm - The communicator for the DM object 1665 - periodicZ - The boundary type for the Z direction 1666 1667 Output Parameter: 1668 . dm - The DM object 1669 1670 Note: 1671 Here is the output numbering looking from the bottom of the cylinder: 1672 $ 17-----14 1673 $ | | 1674 $ | 2 | 1675 $ | | 1676 $ 17-----8-----7-----14 1677 $ | | | | 1678 $ | 3 | 0 | 1 | 1679 $ | | | | 1680 $ 19-----5-----6-----13 1681 $ | | 1682 $ | 4 | 1683 $ | | 1684 $ 19-----13 1685 $ 1686 $ and up through the top 1687 $ 1688 $ 18-----16 1689 $ | | 1690 $ | 2 | 1691 $ | | 1692 $ 18----10----11-----16 1693 $ | | | | 1694 $ | 3 | 0 | 1 | 1695 $ | | | | 1696 $ 20-----9----12-----15 1697 $ | | 1698 $ | 4 | 1699 $ | | 1700 $ 20-----15 1701 1702 Level: beginner 1703 1704 .seealso: `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 1705 @*/ 1706 PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, DMBoundaryType periodicZ, DM *dm) 1707 { 1708 PetscFunctionBegin; 1709 PetscValidPointer(dm, 3); 1710 PetscCall(DMCreate(comm, dm)); 1711 PetscCall(DMSetType(*dm, DMPLEX)); 1712 PetscCall(DMPlexCreateHexCylinderMesh_Internal(*dm, periodicZ)); 1713 PetscFunctionReturn(0); 1714 } 1715 1716 static PetscErrorCode DMPlexCreateWedgeCylinderMesh_Internal(DM dm, PetscInt n, PetscBool interpolate) 1717 { 1718 const PetscInt dim = 3; 1719 PetscInt numCells, numVertices, v; 1720 PetscMPIInt rank; 1721 1722 PetscFunctionBegin; 1723 PetscCheck(n >= 0,PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %" PetscInt_FMT " cannot be negative", n); 1724 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank)); 1725 PetscCall(DMSetDimension(dm, dim)); 1726 /* Must create the celltype label here so that we do not automatically try to compute the types */ 1727 PetscCall(DMCreateLabel(dm, "celltype")); 1728 /* Create topology */ 1729 { 1730 PetscInt cone[6], c; 1731 1732 numCells = rank == 0 ? n : 0; 1733 numVertices = rank == 0 ? 2*(n+1) : 0; 1734 PetscCall(DMPlexSetChart(dm, 0, numCells+numVertices)); 1735 for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 6)); 1736 PetscCall(DMSetUp(dm)); 1737 for (c = 0; c < numCells; c++) { 1738 cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n; 1739 cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n; 1740 PetscCall(DMPlexSetCone(dm, c, cone)); 1741 PetscCall(DMPlexSetCellType(dm, c, DM_POLYTOPE_TRI_PRISM_TENSOR)); 1742 } 1743 PetscCall(DMPlexSymmetrize(dm)); 1744 PetscCall(DMPlexStratify(dm)); 1745 } 1746 for (v = numCells; v < numCells+numVertices; ++v) { 1747 PetscCall(DMPlexSetCellType(dm, v, DM_POLYTOPE_POINT)); 1748 } 1749 /* Create cylinder geometry */ 1750 { 1751 Vec coordinates; 1752 PetscSection coordSection; 1753 PetscScalar *coords; 1754 PetscInt coordSize, c; 1755 1756 /* Build coordinates */ 1757 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 1758 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 1759 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim)); 1760 PetscCall(PetscSectionSetChart(coordSection, numCells, numCells+numVertices)); 1761 for (v = numCells; v < numCells+numVertices; ++v) { 1762 PetscCall(PetscSectionSetDof(coordSection, v, dim)); 1763 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim)); 1764 } 1765 PetscCall(PetscSectionSetUp(coordSection)); 1766 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 1767 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 1768 PetscCall(PetscObjectSetName((PetscObject) coordinates, "coordinates")); 1769 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 1770 PetscCall(VecSetBlockSize(coordinates, dim)); 1771 PetscCall(VecSetType(coordinates,VECSTANDARD)); 1772 PetscCall(VecGetArray(coordinates, &coords)); 1773 for (c = 0; c < numCells; c++) { 1774 coords[(c+0*n)*dim+0] = PetscCosReal(2.0*c*PETSC_PI/n); coords[(c+0*n)*dim+1] = PetscSinReal(2.0*c*PETSC_PI/n); coords[(c+0*n)*dim+2] = 1.0; 1775 coords[(c+1*n)*dim+0] = PetscCosReal(2.0*c*PETSC_PI/n); coords[(c+1*n)*dim+1] = PetscSinReal(2.0*c*PETSC_PI/n); coords[(c+1*n)*dim+2] = 0.0; 1776 } 1777 if (rank == 0) { 1778 coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0; 1779 coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0; 1780 } 1781 PetscCall(VecRestoreArray(coordinates, &coords)); 1782 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 1783 PetscCall(VecDestroy(&coordinates)); 1784 } 1785 /* Interpolate */ 1786 if (interpolate) PetscCall(DMPlexInterpolateInPlace_Internal(dm)); 1787 PetscFunctionReturn(0); 1788 } 1789 1790 /*@ 1791 DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges. 1792 1793 Collective 1794 1795 Input Parameters: 1796 + comm - The communicator for the DM object 1797 . n - The number of wedges around the origin 1798 - interpolate - Create edges and faces 1799 1800 Output Parameter: 1801 . dm - The DM object 1802 1803 Level: beginner 1804 1805 .seealso: `DMPlexCreateHexCylinderMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 1806 @*/ 1807 PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm) 1808 { 1809 PetscFunctionBegin; 1810 PetscValidPointer(dm, 4); 1811 PetscCall(DMCreate(comm, dm)); 1812 PetscCall(DMSetType(*dm, DMPLEX)); 1813 PetscCall(DMPlexCreateWedgeCylinderMesh_Internal(*dm, n, interpolate)); 1814 PetscFunctionReturn(0); 1815 } 1816 1817 static inline PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1818 { 1819 PetscReal prod = 0.0; 1820 PetscInt i; 1821 for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]); 1822 return PetscSqrtReal(prod); 1823 } 1824 static inline PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1825 { 1826 PetscReal prod = 0.0; 1827 PetscInt i; 1828 for (i = 0; i < dim; ++i) prod += x[i]*y[i]; 1829 return prod; 1830 } 1831 1832 /* The first constant is the sphere radius */ 1833 static void snapToSphere(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1834 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1835 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1836 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 1837 { 1838 PetscReal r = PetscRealPart(constants[0]); 1839 PetscReal norm2 = 0.0, fac; 1840 PetscInt n = uOff[1] - uOff[0], d; 1841 1842 for (d = 0; d < n; ++d) norm2 += PetscSqr(PetscRealPart(u[d])); 1843 fac = r/PetscSqrtReal(norm2); 1844 for (d = 0; d < n; ++d) f0[d] = u[d]*fac; 1845 } 1846 1847 static PetscErrorCode DMPlexCreateSphereMesh_Internal(DM dm, PetscInt dim, PetscBool simplex, PetscReal R) 1848 { 1849 const PetscInt embedDim = dim+1; 1850 PetscSection coordSection; 1851 Vec coordinates; 1852 PetscScalar *coords; 1853 PetscReal *coordsIn; 1854 PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e; 1855 PetscMPIInt rank; 1856 1857 PetscFunctionBegin; 1858 PetscValidLogicalCollectiveBool(dm, simplex, 3); 1859 PetscCall(DMSetDimension(dm, dim)); 1860 PetscCall(DMSetCoordinateDim(dm, dim+1)); 1861 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank)); 1862 switch (dim) { 1863 case 2: 1864 if (simplex) { 1865 const PetscReal radius = PetscSqrtReal(1 + PETSC_PHI*PETSC_PHI)/(1.0 + PETSC_PHI); 1866 const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI) * (R/radius); 1867 const PetscInt degree = 5; 1868 PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)}; 1869 PetscInt s[3] = {1, 1, 1}; 1870 PetscInt cone[3]; 1871 PetscInt *graph, p, i, j, k; 1872 1873 vertex[0] *= R/radius; vertex[1] *= R/radius; vertex[2] *= R/radius; 1874 numCells = rank == 0 ? 20 : 0; 1875 numVerts = rank == 0 ? 12 : 0; 1876 firstVertex = numCells; 1877 /* Use icosahedron, which for a R-sphere has coordinates which are all cyclic permutations of 1878 1879 (0, \pm 1/\phi+1, \pm \phi/\phi+1) 1880 1881 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 1882 length is then given by 2/(1+\phi) = 2 * 0.38197 = 0.76393. 1883 */ 1884 /* Construct vertices */ 1885 PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn)); 1886 if (rank == 0) { 1887 for (p = 0, i = 0; p < embedDim; ++p) { 1888 for (s[1] = -1; s[1] < 2; s[1] += 2) { 1889 for (s[2] = -1; s[2] < 2; s[2] += 2) { 1890 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim]; 1891 ++i; 1892 } 1893 } 1894 } 1895 } 1896 /* Construct graph */ 1897 PetscCall(PetscCalloc1(numVerts * numVerts, &graph)); 1898 for (i = 0; i < numVerts; ++i) { 1899 for (j = 0, k = 0; j < numVerts; ++j) { 1900 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 1901 } 1902 PetscCheck(k == degree,PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid icosahedron, vertex %" PetscInt_FMT " degree %" PetscInt_FMT " != %" PetscInt_FMT, i, k, degree); 1903 } 1904 /* Build Topology */ 1905 PetscCall(DMPlexSetChart(dm, 0, numCells+numVerts)); 1906 for (c = 0; c < numCells; c++) { 1907 PetscCall(DMPlexSetConeSize(dm, c, embedDim)); 1908 } 1909 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 1910 /* Cells */ 1911 for (i = 0, c = 0; i < numVerts; ++i) { 1912 for (j = 0; j < i; ++j) { 1913 for (k = 0; k < j; ++k) { 1914 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) { 1915 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; 1916 /* Check orientation */ 1917 { 1918 const PetscInt epsilon[3][3][3] = {{{0, 0, 0}, {0, 0, 1}, {0, -1, 0}}, {{0, 0, -1}, {0, 0, 0}, {1, 0, 0}}, {{0, 1, 0}, {-1, 0, 0}, {0, 0, 0}}}; 1919 PetscReal normal[3]; 1920 PetscInt e, f; 1921 1922 for (d = 0; d < embedDim; ++d) { 1923 normal[d] = 0.0; 1924 for (e = 0; e < embedDim; ++e) { 1925 for (f = 0; f < embedDim; ++f) { 1926 normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]); 1927 } 1928 } 1929 } 1930 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 1931 } 1932 PetscCall(DMPlexSetCone(dm, c++, cone)); 1933 } 1934 } 1935 } 1936 } 1937 PetscCall(DMPlexSymmetrize(dm)); 1938 PetscCall(DMPlexStratify(dm)); 1939 PetscCall(PetscFree(graph)); 1940 } else { 1941 /* 1942 12-21--13 1943 | | 1944 25 4 24 1945 | | 1946 12-25--9-16--8-24--13 1947 | | | | 1948 23 5 17 0 15 3 22 1949 | | | | 1950 10-20--6-14--7-19--11 1951 | | 1952 20 1 19 1953 | | 1954 10-18--11 1955 | | 1956 23 2 22 1957 | | 1958 12-21--13 1959 */ 1960 PetscInt cone[4], ornt[4]; 1961 1962 numCells = rank == 0 ? 6 : 0; 1963 numEdges = rank == 0 ? 12 : 0; 1964 numVerts = rank == 0 ? 8 : 0; 1965 firstVertex = numCells; 1966 firstEdge = numCells + numVerts; 1967 /* Build Topology */ 1968 PetscCall(DMPlexSetChart(dm, 0, numCells+numEdges+numVerts)); 1969 for (c = 0; c < numCells; c++) { 1970 PetscCall(DMPlexSetConeSize(dm, c, 4)); 1971 } 1972 for (e = firstEdge; e < firstEdge+numEdges; ++e) { 1973 PetscCall(DMPlexSetConeSize(dm, e, 2)); 1974 } 1975 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 1976 if (rank == 0) { 1977 /* Cell 0 */ 1978 cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17; 1979 PetscCall(DMPlexSetCone(dm, 0, cone)); 1980 ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0; 1981 PetscCall(DMPlexSetConeOrientation(dm, 0, ornt)); 1982 /* Cell 1 */ 1983 cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20; 1984 PetscCall(DMPlexSetCone(dm, 1, cone)); 1985 ornt[0] = 0; ornt[1] = 0; ornt[2] = -1; ornt[3] = 0; 1986 PetscCall(DMPlexSetConeOrientation(dm, 1, ornt)); 1987 /* Cell 2 */ 1988 cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23; 1989 PetscCall(DMPlexSetCone(dm, 2, cone)); 1990 ornt[0] = 0; ornt[1] = 0; ornt[2] = -1; ornt[3] = 0; 1991 PetscCall(DMPlexSetConeOrientation(dm, 2, ornt)); 1992 /* Cell 3 */ 1993 cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15; 1994 PetscCall(DMPlexSetCone(dm, 3, cone)); 1995 ornt[0] = -1; ornt[1] = -1; ornt[2] = 0; ornt[3] = -1; 1996 PetscCall(DMPlexSetConeOrientation(dm, 3, ornt)); 1997 /* Cell 4 */ 1998 cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25; 1999 PetscCall(DMPlexSetCone(dm, 4, cone)); 2000 ornt[0] = -1; ornt[1] = -1; ornt[2] = -1; ornt[3] = 0; 2001 PetscCall(DMPlexSetConeOrientation(dm, 4, ornt)); 2002 /* Cell 5 */ 2003 cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23; 2004 PetscCall(DMPlexSetCone(dm, 5, cone)); 2005 ornt[0] = -1; ornt[1] = -1; ornt[2] = -1; ornt[3] = -1; 2006 PetscCall(DMPlexSetConeOrientation(dm, 5, ornt)); 2007 /* Edges */ 2008 cone[0] = 6; cone[1] = 7; 2009 PetscCall(DMPlexSetCone(dm, 14, cone)); 2010 cone[0] = 7; cone[1] = 8; 2011 PetscCall(DMPlexSetCone(dm, 15, cone)); 2012 cone[0] = 8; cone[1] = 9; 2013 PetscCall(DMPlexSetCone(dm, 16, cone)); 2014 cone[0] = 9; cone[1] = 6; 2015 PetscCall(DMPlexSetCone(dm, 17, cone)); 2016 cone[0] = 10; cone[1] = 11; 2017 PetscCall(DMPlexSetCone(dm, 18, cone)); 2018 cone[0] = 11; cone[1] = 7; 2019 PetscCall(DMPlexSetCone(dm, 19, cone)); 2020 cone[0] = 6; cone[1] = 10; 2021 PetscCall(DMPlexSetCone(dm, 20, cone)); 2022 cone[0] = 12; cone[1] = 13; 2023 PetscCall(DMPlexSetCone(dm, 21, cone)); 2024 cone[0] = 13; cone[1] = 11; 2025 PetscCall(DMPlexSetCone(dm, 22, cone)); 2026 cone[0] = 10; cone[1] = 12; 2027 PetscCall(DMPlexSetCone(dm, 23, cone)); 2028 cone[0] = 13; cone[1] = 8; 2029 PetscCall(DMPlexSetCone(dm, 24, cone)); 2030 cone[0] = 12; cone[1] = 9; 2031 PetscCall(DMPlexSetCone(dm, 25, cone)); 2032 } 2033 PetscCall(DMPlexSymmetrize(dm)); 2034 PetscCall(DMPlexStratify(dm)); 2035 /* Build coordinates */ 2036 PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn)); 2037 if (rank == 0) { 2038 coordsIn[0*embedDim+0] = -R; coordsIn[0*embedDim+1] = R; coordsIn[0*embedDim+2] = -R; 2039 coordsIn[1*embedDim+0] = R; coordsIn[1*embedDim+1] = R; coordsIn[1*embedDim+2] = -R; 2040 coordsIn[2*embedDim+0] = R; coordsIn[2*embedDim+1] = -R; coordsIn[2*embedDim+2] = -R; 2041 coordsIn[3*embedDim+0] = -R; coordsIn[3*embedDim+1] = -R; coordsIn[3*embedDim+2] = -R; 2042 coordsIn[4*embedDim+0] = -R; coordsIn[4*embedDim+1] = R; coordsIn[4*embedDim+2] = R; 2043 coordsIn[5*embedDim+0] = R; coordsIn[5*embedDim+1] = R; coordsIn[5*embedDim+2] = R; 2044 coordsIn[6*embedDim+0] = -R; coordsIn[6*embedDim+1] = -R; coordsIn[6*embedDim+2] = R; 2045 coordsIn[7*embedDim+0] = R; coordsIn[7*embedDim+1] = -R; coordsIn[7*embedDim+2] = R; 2046 } 2047 } 2048 break; 2049 case 3: 2050 if (simplex) { 2051 const PetscReal edgeLen = 1.0/PETSC_PHI; 2052 PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5}; 2053 PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0}; 2054 PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0}; 2055 const PetscInt degree = 12; 2056 PetscInt s[4] = {1, 1, 1}; 2057 PetscInt evenPerm[12][4] = {{0, 1, 2, 3}, {0, 2, 3, 1}, {0, 3, 1, 2}, {1, 0, 3, 2}, {1, 2, 0, 3}, {1, 3, 2, 0}, 2058 {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}}; 2059 PetscInt cone[4]; 2060 PetscInt *graph, p, i, j, k, l; 2061 2062 vertexA[0] *= R; vertexA[1] *= R; vertexA[2] *= R; vertexA[3] *= R; 2063 vertexB[0] *= R; vertexB[1] *= R; vertexB[2] *= R; vertexB[3] *= R; 2064 vertexC[0] *= R; vertexC[1] *= R; vertexC[2] *= R; vertexC[3] *= R; 2065 numCells = rank == 0 ? 600 : 0; 2066 numVerts = rank == 0 ? 120 : 0; 2067 firstVertex = numCells; 2068 /* Use the 600-cell, which for a unit sphere has coordinates which are 2069 2070 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16 2071 (\pm 1, 0, 0, 0) all cyclic permutations 8 2072 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96 2073 2074 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 2075 length is then given by 1/\phi = 0.61803. 2076 2077 http://buzzard.pugetsound.edu/sage-practice/ch03s03.html 2078 http://mathworld.wolfram.com/600-Cell.html 2079 */ 2080 /* Construct vertices */ 2081 PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn)); 2082 i = 0; 2083 if (rank == 0) { 2084 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2085 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2086 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2087 for (s[3] = -1; s[3] < 2; s[3] += 2) { 2088 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d]; 2089 ++i; 2090 } 2091 } 2092 } 2093 } 2094 for (p = 0; p < embedDim; ++p) { 2095 s[1] = s[2] = s[3] = 1; 2096 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2097 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim]; 2098 ++i; 2099 } 2100 } 2101 for (p = 0; p < 12; ++p) { 2102 s[3] = 1; 2103 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2104 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2105 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2106 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]]; 2107 ++i; 2108 } 2109 } 2110 } 2111 } 2112 } 2113 PetscCheck(i == numVerts,PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertices %" PetscInt_FMT " != %" PetscInt_FMT, i, numVerts); 2114 /* Construct graph */ 2115 PetscCall(PetscCalloc1(numVerts * numVerts, &graph)); 2116 for (i = 0; i < numVerts; ++i) { 2117 for (j = 0, k = 0; j < numVerts; ++j) { 2118 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 2119 } 2120 PetscCheck(k == degree,PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertex %" PetscInt_FMT " degree %" PetscInt_FMT " != %" PetscInt_FMT, i, k, degree); 2121 } 2122 /* Build Topology */ 2123 PetscCall(DMPlexSetChart(dm, 0, numCells+numVerts)); 2124 for (c = 0; c < numCells; c++) { 2125 PetscCall(DMPlexSetConeSize(dm, c, embedDim)); 2126 } 2127 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 2128 /* Cells */ 2129 if (rank == 0) { 2130 for (i = 0, c = 0; i < numVerts; ++i) { 2131 for (j = 0; j < i; ++j) { 2132 for (k = 0; k < j; ++k) { 2133 for (l = 0; l < k; ++l) { 2134 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] && 2135 graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) { 2136 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l; 2137 /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */ 2138 { 2139 const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2140 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}}, 2141 {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}}, 2142 {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}}, 2143 2144 {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}}, 2145 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2146 {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}}, 2147 {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}}, 2148 2149 {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}}, 2150 {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}}, 2151 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2152 {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}, 2153 2154 {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}}, 2155 {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}}, 2156 {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2157 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}}; 2158 PetscReal normal[4]; 2159 PetscInt e, f, g; 2160 2161 for (d = 0; d < embedDim; ++d) { 2162 normal[d] = 0.0; 2163 for (e = 0; e < embedDim; ++e) { 2164 for (f = 0; f < embedDim; ++f) { 2165 for (g = 0; g < embedDim; ++g) { 2166 normal[d] += epsilon[d][e][f][g]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f])*(coordsIn[l*embedDim+f] - coordsIn[i*embedDim+f]); 2167 } 2168 } 2169 } 2170 } 2171 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 2172 } 2173 PetscCall(DMPlexSetCone(dm, c++, cone)); 2174 } 2175 } 2176 } 2177 } 2178 } 2179 } 2180 PetscCall(DMPlexSymmetrize(dm)); 2181 PetscCall(DMPlexStratify(dm)); 2182 PetscCall(PetscFree(graph)); 2183 break; 2184 } 2185 default: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Unsupported dimension for sphere: %" PetscInt_FMT, dim); 2186 } 2187 /* Create coordinates */ 2188 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 2189 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 2190 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, embedDim)); 2191 PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts)); 2192 for (v = firstVertex; v < firstVertex+numVerts; ++v) { 2193 PetscCall(PetscSectionSetDof(coordSection, v, embedDim)); 2194 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, embedDim)); 2195 } 2196 PetscCall(PetscSectionSetUp(coordSection)); 2197 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 2198 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 2199 PetscCall(VecSetBlockSize(coordinates, embedDim)); 2200 PetscCall(PetscObjectSetName((PetscObject) coordinates, "coordinates")); 2201 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 2202 PetscCall(VecSetType(coordinates,VECSTANDARD)); 2203 PetscCall(VecGetArray(coordinates, &coords)); 2204 for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];} 2205 PetscCall(VecRestoreArray(coordinates, &coords)); 2206 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 2207 PetscCall(VecDestroy(&coordinates)); 2208 PetscCall(PetscFree(coordsIn)); 2209 { 2210 DM cdm; 2211 PetscDS cds; 2212 PetscScalar c = R; 2213 2214 PetscCall(DMPlexCreateCoordinateSpace(dm, 1, snapToSphere)); 2215 PetscCall(DMGetCoordinateDM(dm, &cdm)); 2216 PetscCall(DMGetDS(cdm, &cds)); 2217 PetscCall(PetscDSSetConstants(cds, 1, &c)); 2218 } 2219 /* Wait for coordinate creation before doing in-place modification */ 2220 if (simplex) PetscCall(DMPlexInterpolateInPlace_Internal(dm)); 2221 PetscFunctionReturn(0); 2222 } 2223 2224 typedef void (*TPSEvaluateFunc)(const PetscReal[], PetscReal*, PetscReal[], PetscReal(*)[3]); 2225 2226 /* 2227 The Schwarz P implicit surface is 2228 2229 f(x) = cos(x0) + cos(x1) + cos(x2) = 0 2230 */ 2231 static void TPSEvaluate_SchwarzP(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3]) 2232 { 2233 PetscReal c[3] = {PetscCosReal(y[0] * PETSC_PI), PetscCosReal(y[1] * PETSC_PI), PetscCosReal(y[2] * PETSC_PI)}; 2234 PetscReal g[3] = {-PetscSinReal(y[0] * PETSC_PI), -PetscSinReal(y[1] * PETSC_PI), -PetscSinReal(y[2] * PETSC_PI)}; 2235 f[0] = c[0] + c[1] + c[2]; 2236 for (PetscInt i=0; i<3; i++) { 2237 grad[i] = PETSC_PI * g[i]; 2238 for (PetscInt j=0; j<3; j++) { 2239 hess[i][j] = (i == j) ? -PetscSqr(PETSC_PI) * c[i] : 0.; 2240 } 2241 } 2242 } 2243 2244 // u[] is a tentative normal on input. Replace with the implicit function gradient in the same direction 2245 static PetscErrorCode TPSExtrudeNormalFunc_SchwarzP(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt r, PetscScalar u[], void *ctx) { 2246 for (PetscInt i=0; i<3; i++) { 2247 u[i] = -PETSC_PI * PetscSinReal(x[i] * PETSC_PI); 2248 } 2249 return 0; 2250 } 2251 2252 /* 2253 The Gyroid implicit surface is 2254 2255 f(x,y,z) = sin(pi * x) * cos (pi * (y + 1/2)) + sin(pi * (y + 1/2)) * cos(pi * (z + 1/4)) + sin(pi * (z + 1/4)) * cos(pi * x) 2256 2257 */ 2258 static void TPSEvaluate_Gyroid(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3]) 2259 { 2260 PetscReal s[3] = {PetscSinReal(PETSC_PI * y[0]), PetscSinReal(PETSC_PI * (y[1] + .5)), PetscSinReal(PETSC_PI * (y[2] + .25))}; 2261 PetscReal c[3] = {PetscCosReal(PETSC_PI * y[0]), PetscCosReal(PETSC_PI * (y[1] + .5)), PetscCosReal(PETSC_PI * (y[2] + .25))}; 2262 f[0] = s[0] * c[1] + s[1] * c[2] + s[2] * c[0]; 2263 grad[0] = PETSC_PI * (c[0] * c[1] - s[2] * s[0]); 2264 grad[1] = PETSC_PI * (c[1] * c[2] - s[0] * s[1]); 2265 grad[2] = PETSC_PI * (c[2] * c[0] - s[1] * s[2]); 2266 hess[0][0] = -PetscSqr(PETSC_PI) * (s[0] * c[1] + s[2] * c[0]); 2267 hess[0][1] = -PetscSqr(PETSC_PI) * (c[0] * s[1]); 2268 hess[0][2] = -PetscSqr(PETSC_PI) * (c[2] * s[0]); 2269 hess[1][0] = -PetscSqr(PETSC_PI) * (s[1] * c[2] + s[0] * c[1]); 2270 hess[1][1] = -PetscSqr(PETSC_PI) * (c[1] * s[2]); 2271 hess[2][2] = -PetscSqr(PETSC_PI) * (c[0] * s[1]); 2272 hess[2][0] = -PetscSqr(PETSC_PI) * (s[2] * c[0] + s[1] * c[2]); 2273 hess[2][1] = -PetscSqr(PETSC_PI) * (c[2] * s[0]); 2274 hess[2][2] = -PetscSqr(PETSC_PI) * (c[1] * s[2]); 2275 } 2276 2277 // u[] is a tentative normal on input. Replace with the implicit function gradient in the same direction 2278 static PetscErrorCode TPSExtrudeNormalFunc_Gyroid(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt r, PetscScalar u[], void *ctx) { 2279 PetscReal s[3] = {PetscSinReal(PETSC_PI * x[0]), PetscSinReal(PETSC_PI * (x[1] + .5)), PetscSinReal(PETSC_PI * (x[2] + .25))}; 2280 PetscReal c[3] = {PetscCosReal(PETSC_PI * x[0]), PetscCosReal(PETSC_PI * (x[1] + .5)), PetscCosReal(PETSC_PI * (x[2] + .25))}; 2281 u[0] = PETSC_PI * (c[0] * c[1] - s[2] * s[0]); 2282 u[1] = PETSC_PI * (c[1] * c[2] - s[0] * s[1]); 2283 u[2] = PETSC_PI * (c[2] * c[0] - s[1] * s[2]); 2284 return 0; 2285 } 2286 2287 /* 2288 We wish to solve 2289 2290 min_y || y - x ||^2 subject to f(y) = 0 2291 2292 Let g(y) = grad(f). The minimization problem is equivalent to asking to satisfy 2293 f(y) = 0 and (y-x) is parallel to g(y). We do this by using Householder QR to obtain a basis for the 2294 tangent space and ask for both components in the tangent space to be zero. 2295 2296 Take g to be a column vector and compute the "full QR" factorization Q R = g, 2297 where Q = I - 2 n n^T is a symmetric orthogonal matrix. 2298 The first column of Q is parallel to g so the remaining two columns span the null space. 2299 Let Qn = Q[:,1:] be those remaining columns. Then Qn Qn^T is an orthogonal projector into the tangent space. 2300 Since Q is symmetric, this is equivalent to multipyling by Q and taking the last two entries. 2301 In total, we have a system of 3 equations in 3 unknowns: 2302 2303 f(y) = 0 1 equation 2304 Qn^T (y - x) = 0 2 equations 2305 2306 Here, we compute the residual and Jacobian of this system. 2307 */ 2308 static void TPSNearestPointResJac(TPSEvaluateFunc feval, const PetscScalar x[], const PetscScalar y[], PetscScalar res[], PetscScalar J[]) 2309 { 2310 PetscReal yreal[3] = {PetscRealPart(y[0]), PetscRealPart(y[1]), PetscRealPart(y[2])}; 2311 PetscReal d[3] = {PetscRealPart(y[0] - x[0]), PetscRealPart(y[1] - x[1]), PetscRealPart(y[2] - x[2])}; 2312 PetscReal f, grad[3], n[3], norm, norm_y[3], nd, nd_y[3], sign; 2313 PetscReal n_y[3][3] = {{0,0,0},{0,0,0},{0,0,0}}; 2314 2315 feval(yreal, &f, grad, n_y); 2316 2317 for (PetscInt i=0; i<3; i++) n[i] = grad[i]; 2318 norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2])); 2319 for (PetscInt i=0; i<3; i++) { 2320 norm_y[i] = 1. / norm * n[i] * n_y[i][i]; 2321 } 2322 2323 // Define the Householder reflector 2324 sign = n[0] >= 0 ? 1. : -1.; 2325 n[0] += norm * sign; 2326 for (PetscInt i=0; i<3; i++) n_y[0][i] += norm_y[i] * sign; 2327 2328 norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2])); 2329 norm_y[0] = 1. / norm * (n[0] * n_y[0][0]); 2330 norm_y[1] = 1. / norm * (n[0] * n_y[0][1] + n[1] * n_y[1][1]); 2331 norm_y[2] = 1. / norm * (n[0] * n_y[0][2] + n[2] * n_y[2][2]); 2332 2333 for (PetscInt i=0; i<3; i++) { 2334 n[i] /= norm; 2335 for (PetscInt j=0; j<3; j++) { 2336 // note that n[i] is n_old[i]/norm when executing the code below 2337 n_y[i][j] = n_y[i][j] / norm - n[i] / norm * norm_y[j]; 2338 } 2339 } 2340 2341 nd = n[0] * d[0] + n[1] * d[1] + n[2] * d[2]; 2342 for (PetscInt i=0; i<3; i++) nd_y[i] = n[i] + n_y[0][i] * d[0] + n_y[1][i] * d[1] + n_y[2][i] * d[2]; 2343 2344 res[0] = f; 2345 res[1] = d[1] - 2 * n[1] * nd; 2346 res[2] = d[2] - 2 * n[2] * nd; 2347 // J[j][i] is J_{ij} (column major) 2348 for (PetscInt j=0; j<3; j++) { 2349 J[0 + j*3] = grad[j]; 2350 J[1 + j*3] = (j == 1)*1. - 2 * (n_y[1][j] * nd + n[1] * nd_y[j]); 2351 J[2 + j*3] = (j == 2)*1. - 2 * (n_y[2][j] * nd + n[2] * nd_y[j]); 2352 } 2353 } 2354 2355 /* 2356 Project x to the nearest point on the implicit surface using Newton's method. 2357 */ 2358 static PetscErrorCode TPSNearestPoint(TPSEvaluateFunc feval, PetscScalar x[]) 2359 { 2360 PetscScalar y[3] = {x[0], x[1], x[2]}; // Initial guess 2361 2362 PetscFunctionBegin; 2363 for (PetscInt iter=0; iter<10; iter++) { 2364 PetscScalar res[3], J[9]; 2365 PetscReal resnorm; 2366 TPSNearestPointResJac(feval, x, y, res, J); 2367 resnorm = PetscSqrtReal(PetscSqr(PetscRealPart(res[0])) + PetscSqr(PetscRealPart(res[1])) + PetscSqr(PetscRealPart(res[2]))); 2368 if (0) { // Turn on this monitor if you need to confirm quadratic convergence 2369 PetscCall(PetscPrintf(PETSC_COMM_SELF, "[%" PetscInt_FMT "] res [%g %g %g]\n", iter, (double)PetscRealPart(res[0]), (double)PetscRealPart(res[1]), (double)PetscRealPart(res[2]))); 2370 } 2371 if (resnorm < PETSC_SMALL) break; 2372 2373 // Take the Newton step 2374 PetscCall(PetscKernel_A_gets_inverse_A_3(J, 0., PETSC_FALSE, NULL)); 2375 PetscKernel_v_gets_v_minus_A_times_w_3(y, J, res); 2376 } 2377 for (PetscInt i=0; i<3; i++) x[i] = y[i]; 2378 PetscFunctionReturn(0); 2379 } 2380 2381 const char *const DMPlexTPSTypes[] = {"SCHWARZ_P", "GYROID", "DMPlexTPSType", "DMPLEX_TPS_", NULL}; 2382 2383 static PetscErrorCode DMPlexCreateTPSMesh_Internal(DM dm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscBool tps_distribute, PetscInt refinements, PetscInt layers, PetscReal thickness) 2384 { 2385 PetscMPIInt rank; 2386 PetscInt topoDim = 2, spaceDim = 3, numFaces = 0, numVertices = 0, numEdges = 0; 2387 PetscInt (*edges)[2] = NULL, *edgeSets = NULL; 2388 PetscInt *cells_flat = NULL; 2389 PetscReal *vtxCoords = NULL; 2390 TPSEvaluateFunc evalFunc = NULL; 2391 PetscSimplePointFunc normalFunc = NULL; 2392 DMLabel label; 2393 2394 PetscFunctionBegin; 2395 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 2396 PetscCheck((layers != 0) ^ (thickness == 0.), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_INCOMP, "Layers %" PetscInt_FMT " must be nonzero iff thickness %g is nonzero", layers, (double)thickness); 2397 switch (tpstype) { 2398 case DMPLEX_TPS_SCHWARZ_P: 2399 PetscCheck(!periodic || (periodic[0] == DM_BOUNDARY_NONE && periodic[1] == DM_BOUNDARY_NONE && periodic[2] == DM_BOUNDARY_NONE), PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Schwarz P does not support periodic meshes"); 2400 if (rank == 0) { 2401 PetscInt (*cells)[6][4][4] = NULL; // [junction, junction-face, cell, conn] 2402 PetscInt Njunctions = 0, Ncuts = 0, Npipes[3], vcount; 2403 PetscReal L = 1; 2404 2405 Npipes[0] = (extent[0] + 1) * extent[1] * extent[2]; 2406 Npipes[1] = extent[0] * (extent[1] + 1) * extent[2]; 2407 Npipes[2] = extent[0] * extent[1] * (extent[2] + 1); 2408 Njunctions = extent[0] * extent[1] * extent[2]; 2409 Ncuts = 2 * (extent[0] * extent[1] + extent[1] * extent[2] + extent[2] * extent[0]); 2410 numVertices = 4 * (Npipes[0] + Npipes[1] + Npipes[2]) + 8 * Njunctions; 2411 PetscCall(PetscMalloc1(3*numVertices, &vtxCoords)); 2412 PetscCall(PetscMalloc1(Njunctions, &cells)); 2413 PetscCall(PetscMalloc1(Ncuts*4, &edges)); 2414 PetscCall(PetscMalloc1(Ncuts*4, &edgeSets)); 2415 // x-normal pipes 2416 vcount = 0; 2417 for (PetscInt i=0; i<extent[0]+1; i++) { 2418 for (PetscInt j=0; j<extent[1]; j++) { 2419 for (PetscInt k=0; k<extent[2]; k++) { 2420 for (PetscInt l=0; l<4; l++) { 2421 vtxCoords[vcount++] = (2*i - 1) * L; 2422 vtxCoords[vcount++] = 2 * j * L + PetscCosReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2423 vtxCoords[vcount++] = 2 * k * L + PetscSinReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2424 } 2425 } 2426 } 2427 } 2428 // y-normal pipes 2429 for (PetscInt i=0; i<extent[0]; i++) { 2430 for (PetscInt j=0; j<extent[1]+1; j++) { 2431 for (PetscInt k=0; k<extent[2]; k++) { 2432 for (PetscInt l=0; l<4; l++) { 2433 vtxCoords[vcount++] = 2 * i * L + PetscSinReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2434 vtxCoords[vcount++] = (2*j - 1) * L; 2435 vtxCoords[vcount++] = 2 * k * L + PetscCosReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2436 } 2437 } 2438 } 2439 } 2440 // z-normal pipes 2441 for (PetscInt i=0; i<extent[0]; i++) { 2442 for (PetscInt j=0; j<extent[1]; j++) { 2443 for (PetscInt k=0; k<extent[2]+1; k++) { 2444 for (PetscInt l=0; l<4; l++) { 2445 vtxCoords[vcount++] = 2 * i * L + PetscCosReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2446 vtxCoords[vcount++] = 2 * j * L + PetscSinReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2447 vtxCoords[vcount++] = (2*k - 1) * L; 2448 } 2449 } 2450 } 2451 } 2452 // junctions 2453 for (PetscInt i=0; i<extent[0]; i++) { 2454 for (PetscInt j=0; j<extent[1]; j++) { 2455 for (PetscInt k=0; k<extent[2]; k++) { 2456 const PetscInt J = (i*extent[1] + j)*extent[2] + k, Jvoff = (Npipes[0] + Npipes[1] + Npipes[2])*4 + J*8; 2457 PetscCheck(vcount / 3 == Jvoff, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unexpected vertex count"); 2458 for (PetscInt ii=0; ii<2; ii++) { 2459 for (PetscInt jj=0; jj<2; jj++) { 2460 for (PetscInt kk=0; kk<2; kk++) { 2461 double Ls = (1 - sqrt(2) / 4) * L; 2462 vtxCoords[vcount++] = 2*i*L + (2*ii-1) * Ls; 2463 vtxCoords[vcount++] = 2*j*L + (2*jj-1) * Ls; 2464 vtxCoords[vcount++] = 2*k*L + (2*kk-1) * Ls; 2465 } 2466 } 2467 } 2468 const PetscInt jfaces[3][2][4] = { 2469 {{3,1,0,2}, {7,5,4,6}}, // x-aligned 2470 {{5,4,0,1}, {7,6,2,3}}, // y-aligned 2471 {{6,2,0,4}, {7,3,1,5}} // z-aligned 2472 }; 2473 const PetscInt pipe_lo[3] = { // vertex numbers of pipes 2474 ((i * extent[1] + j) * extent[2] + k)*4, 2475 ((i * (extent[1] + 1) + j) * extent[2] + k + Npipes[0])*4, 2476 ((i * extent[1] + j) * (extent[2]+1) + k + Npipes[0] + Npipes[1])*4 2477 }; 2478 const PetscInt pipe_hi[3] = { // vertex numbers of pipes 2479 (((i + 1) * extent[1] + j) * extent[2] + k)*4, 2480 ((i * (extent[1] + 1) + j + 1) * extent[2] + k + Npipes[0])*4, 2481 ((i * extent[1] + j) * (extent[2]+1) + k + 1 + Npipes[0] + Npipes[1])*4 2482 }; 2483 for (PetscInt dir=0; dir<3; dir++) { // x,y,z 2484 const PetscInt ijk[3] = {i, j, k}; 2485 for (PetscInt l=0; l<4; l++) { // rotations 2486 cells[J][dir*2+0][l][0] = pipe_lo[dir] + l; 2487 cells[J][dir*2+0][l][1] = Jvoff + jfaces[dir][0][l]; 2488 cells[J][dir*2+0][l][2] = Jvoff + jfaces[dir][0][(l-1+4)%4]; 2489 cells[J][dir*2+0][l][3] = pipe_lo[dir] + (l-1+4)%4; 2490 cells[J][dir*2+1][l][0] = Jvoff + jfaces[dir][1][l]; 2491 cells[J][dir*2+1][l][1] = pipe_hi[dir] + l; 2492 cells[J][dir*2+1][l][2] = pipe_hi[dir] + (l-1+4)%4; 2493 cells[J][dir*2+1][l][3] = Jvoff + jfaces[dir][1][(l-1+4)%4]; 2494 if (ijk[dir] == 0) { 2495 edges[numEdges][0] = pipe_lo[dir] + l; 2496 edges[numEdges][1] = pipe_lo[dir] + (l+1) % 4; 2497 edgeSets[numEdges] = dir*2 + 1; 2498 numEdges++; 2499 } 2500 if (ijk[dir] + 1 == extent[dir]) { 2501 edges[numEdges][0] = pipe_hi[dir] + l; 2502 edges[numEdges][1] = pipe_hi[dir] + (l+1) % 4; 2503 edgeSets[numEdges] = dir*2 + 2; 2504 numEdges++; 2505 } 2506 } 2507 } 2508 } 2509 } 2510 } 2511 PetscCheck(numEdges == Ncuts * 4, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Edge count %" PetscInt_FMT " incompatible with number of cuts %" PetscInt_FMT, numEdges, Ncuts); 2512 numFaces = 24 * Njunctions; 2513 cells_flat = cells[0][0][0]; 2514 } 2515 evalFunc = TPSEvaluate_SchwarzP; 2516 normalFunc = TPSExtrudeNormalFunc_SchwarzP; 2517 break; 2518 case DMPLEX_TPS_GYROID: 2519 if (rank == 0) { 2520 // This is a coarse mesh approximation of the gyroid shifted to being the zero of the level set 2521 // 2522 // sin(pi*x)*cos(pi*(y+1/2)) + sin(pi*(y+1/2))*cos(pi*(z+1/4)) + sin(pi*(z+1/4))*cos(x) 2523 // 2524 // on the cell [0,2]^3. 2525 // 2526 // Think about dividing that cell into four columns, and focus on the column [0,1]x[0,1]x[0,2]. 2527 // If you looked at the gyroid in that column at different slices of z you would see that it kind of spins 2528 // like a boomerang: 2529 // 2530 // z = 0 z = 1/4 z = 1/2 z = 3/4 // 2531 // ----- ------- ------- ------- // 2532 // // 2533 // + + + + + + + \ + // 2534 // \ / \ // 2535 // \ `-_ _-' / } // 2536 // *-_ `-' _-' / // 2537 // + `-+ + + +-' + + / + // 2538 // // 2539 // // 2540 // z = 1 z = 5/4 z = 3/2 z = 7/4 // 2541 // ----- ------- ------- ------- // 2542 // // 2543 // +-_ + + + + _-+ + / + // 2544 // `-_ _-_ _-` / // 2545 // \ _-' `-_ / { // 2546 // \ / \ // 2547 // + + + + + + + \ + // 2548 // 2549 // 2550 // This course mesh approximates each of these slices by two line segments, 2551 // and then connects the segments in consecutive layers with quadrilateral faces. 2552 // All of the end points of the segments are multiples of 1/4 except for the 2553 // point * in the picture for z = 0 above and the similar points in other layers. 2554 // That point is at (gamma, gamma, 0), where gamma is calculated below. 2555 // 2556 // The column [1,2]x[1,2]x[0,2] looks the same as this column; 2557 // The columns [1,2]x[0,1]x[0,2] and [0,1]x[1,2]x[0,2] are mirror images. 2558 // 2559 // As for how this method turned into the names given to the vertices: 2560 // that was not systematic, it was just the way it worked out in my handwritten notes. 2561 2562 PetscInt facesPerBlock = 64; 2563 PetscInt vertsPerBlock = 56; 2564 PetscInt extentPlus[3]; 2565 PetscInt numBlocks, numBlocksPlus; 2566 const PetscInt A = 0, B = 1, C = 2, D = 3, E = 4, F = 5, G = 6, H = 7, 2567 II = 8, J = 9, K = 10, L = 11, M = 12, N = 13, O = 14, P = 15, 2568 Q = 16, R = 17, S = 18, T = 19, U = 20, V = 21, W = 22, X = 23, 2569 Y = 24, Z = 25, Ap = 26, Bp = 27, Cp = 28, Dp = 29, Ep = 30, Fp = 31, 2570 Gp = 32, Hp = 33, Ip = 34, Jp = 35, Kp = 36, Lp = 37, Mp = 38, Np = 39, 2571 Op = 40, Pp = 41, Qp = 42, Rp = 43, Sp = 44, Tp = 45, Up = 46, Vp = 47, 2572 Wp = 48, Xp = 49, Yp = 50, Zp = 51, Aq = 52, Bq = 53, Cq = 54, Dq = 55; 2573 const PetscInt pattern[64][4] = 2574 { /* face to vertex within the coarse discretization of a single gyroid block */ 2575 /* layer 0 */ 2576 {A,C,K,G},{C,B,II,K},{D,A,H,L},{B+56*1,D,L,J},{E,B+56*1,J,N},{A+56*2,E,N,H+56*2},{F,A+56*2,G+56*2,M},{B,F,M,II}, 2577 /* layer 1 */ 2578 {G,K,Q,O},{K,II,P,Q},{L,H,O+56*1,R},{J,L,R,P},{N,J,P,S},{H+56*2,N,S,O+56*3},{M,G+56*2,O+56*2,T},{II,M,T,P}, 2579 /* layer 2 */ 2580 {O,Q,Y,U},{Q,P,W,Y},{R,O+56*1,U+56*1,Ap},{P,R,Ap,W},{S,P,X,Bp},{O+56*3,S,Bp,V+56*1},{T,O+56*2,V,Z},{P,T,Z,X}, 2581 /* layer 3 */ 2582 {U,Y,Ep,Dp},{Y,W,Cp,Ep},{Ap,U+56*1,Dp+56*1,Gp},{W,Ap,Gp,Cp},{Bp,X,Cp+56*2,Fp},{V+56*1,Bp,Fp,Dp+56*1},{Z,V,Dp,Hp},{X,Z,Hp,Cp+56*2}, 2583 /* layer 4 */ 2584 {Dp,Ep,Mp,Kp},{Ep,Cp,Ip,Mp},{Gp,Dp+56*1,Lp,Np},{Cp,Gp,Np,Jp},{Fp,Cp+56*2,Jp+56*2,Pp},{Dp+56*1,Fp,Pp,Lp},{Hp,Dp,Kp,Op},{Cp+56*2,Hp,Op,Ip+56*2}, 2585 /* layer 5 */ 2586 {Kp,Mp,Sp,Rp},{Mp,Ip,Qp,Sp},{Np,Lp,Rp,Tp},{Jp,Np,Tp,Qp+56*1},{Pp,Jp+56*2,Qp+56*3,Up},{Lp,Pp,Up,Rp},{Op,Kp,Rp,Vp},{Ip+56*2,Op,Vp,Qp+56*2}, 2587 /* layer 6 */ 2588 {Rp,Sp,Aq,Yp},{Sp,Qp,Wp,Aq},{Tp,Rp,Yp,Cq},{Qp+56*1,Tp,Cq,Wp+56*1},{Up,Qp+56*3,Xp+56*1,Dq},{Rp,Up,Dq,Zp},{Vp,Rp,Zp,Bq},{Qp+56*2,Vp,Bq,Xp}, 2589 /* layer 7 (the top is the periodic image of the bottom of layer 0) */ 2590 {Yp,Aq,C+56*4,A+56*4},{Aq,Wp,B+56*4,C+56*4},{Cq,Yp,A+56*4,D+56*4},{Wp+56*1,Cq,D+56*4,B+56*5},{Dq,Xp+56*1,B+56*5,E+56*4},{Zp,Dq,E+56*4,A+56*6},{Bq,Zp,A+56*6,F+56*4},{Xp,Bq,F+56*4,B+56*4} 2591 }; 2592 const PetscReal gamma = PetscAcosReal((PetscSqrtReal(3.)-1.) / PetscSqrtReal(2.)) / PETSC_PI; 2593 const PetscReal patternCoords[56][3] = 2594 { 2595 /* A */ {1.,0.,0.}, 2596 /* B */ {0.,1.,0.}, 2597 /* C */ {gamma,gamma,0.}, 2598 /* D */ {1+gamma,1-gamma,0.}, 2599 /* E */ {2-gamma,2-gamma,0.}, 2600 /* F */ {1-gamma,1+gamma,0.}, 2601 2602 /* G */ {.5,0,.25}, 2603 /* H */ {1.5,0.,.25}, 2604 /* II */ {.5,1.,.25}, 2605 /* J */ {1.5,1.,.25}, 2606 /* K */ {.25,.5,.25}, 2607 /* L */ {1.25,.5,.25}, 2608 /* M */ {.75,1.5,.25}, 2609 /* N */ {1.75,1.5,.25}, 2610 2611 /* O */ {0.,0.,.5}, 2612 /* P */ {1.,1.,.5}, 2613 /* Q */ {gamma,1-gamma,.5}, 2614 /* R */ {1+gamma,gamma,.5}, 2615 /* S */ {2-gamma,1+gamma,.5}, 2616 /* T */ {1-gamma,2-gamma,.5}, 2617 2618 /* U */ {0.,.5,.75}, 2619 /* V */ {0.,1.5,.75}, 2620 /* W */ {1.,.5,.75}, 2621 /* X */ {1.,1.5,.75}, 2622 /* Y */ {.5,.75,.75}, 2623 /* Z */ {.5,1.75,.75}, 2624 /* Ap */ {1.5,.25,.75}, 2625 /* Bp */ {1.5,1.25,.75}, 2626 2627 /* Cp */ {1.,0.,1.}, 2628 /* Dp */ {0.,1.,1.}, 2629 /* Ep */ {1-gamma,1-gamma,1.}, 2630 /* Fp */ {1+gamma,1+gamma,1.}, 2631 /* Gp */ {2-gamma,gamma,1.}, 2632 /* Hp */ {gamma,2-gamma,1.}, 2633 2634 /* Ip */ {.5,0.,1.25}, 2635 /* Jp */ {1.5,0.,1.25}, 2636 /* Kp */ {.5,1.,1.25}, 2637 /* Lp */ {1.5,1.,1.25}, 2638 /* Mp */ {.75,.5,1.25}, 2639 /* Np */ {1.75,.5,1.25}, 2640 /* Op */ {.25,1.5,1.25}, 2641 /* Pp */ {1.25,1.5,1.25}, 2642 2643 /* Qp */ {0.,0.,1.5}, 2644 /* Rp */ {1.,1.,1.5}, 2645 /* Sp */ {1-gamma,gamma,1.5}, 2646 /* Tp */ {2-gamma,1-gamma,1.5}, 2647 /* Up */ {1+gamma,2-gamma,1.5}, 2648 /* Vp */ {gamma,1+gamma,1.5}, 2649 2650 /* Wp */ {0.,.5,1.75}, 2651 /* Xp */ {0.,1.5,1.75}, 2652 /* Yp */ {1.,.5,1.75}, 2653 /* Zp */ {1.,1.5,1.75}, 2654 /* Aq */ {.5,.25,1.75}, 2655 /* Bq */ {.5,1.25,1.75}, 2656 /* Cq */ {1.5,.75,1.75}, 2657 /* Dq */ {1.5,1.75,1.75}, 2658 }; 2659 PetscInt (*cells)[64][4] = NULL; 2660 PetscBool *seen; 2661 PetscInt *vertToTrueVert; 2662 PetscInt count; 2663 2664 for (PetscInt i = 0; i < 3; i++) extentPlus[i] = extent[i] + 1; 2665 numBlocks = 1; 2666 for (PetscInt i = 0; i < 3; i++) numBlocks *= extent[i]; 2667 numBlocksPlus = 1; 2668 for (PetscInt i = 0; i < 3; i++) numBlocksPlus *= extentPlus[i]; 2669 numFaces = numBlocks * facesPerBlock; 2670 PetscCall(PetscMalloc1(numBlocks, &cells)); 2671 PetscCall(PetscCalloc1(numBlocksPlus * vertsPerBlock,&seen)); 2672 for (PetscInt k = 0; k < extent[2]; k++) { 2673 for (PetscInt j = 0; j < extent[1]; j++) { 2674 for (PetscInt i = 0; i < extent[0]; i++) { 2675 for (PetscInt f = 0; f < facesPerBlock; f++) { 2676 for (PetscInt v = 0; v < 4; v++) { 2677 PetscInt vertRaw = pattern[f][v]; 2678 PetscInt blockidx = vertRaw / 56; 2679 PetscInt patternvert = vertRaw % 56; 2680 PetscInt xplus = (blockidx & 1); 2681 PetscInt yplus = (blockidx & 2) >> 1; 2682 PetscInt zplus = (blockidx & 4) >> 2; 2683 PetscInt zcoord = (periodic && periodic[2] == DM_BOUNDARY_PERIODIC) ? ((k + zplus) % extent[2]) : (k + zplus); 2684 PetscInt ycoord = (periodic && periodic[1] == DM_BOUNDARY_PERIODIC) ? ((j + yplus) % extent[1]) : (j + yplus); 2685 PetscInt xcoord = (periodic && periodic[0] == DM_BOUNDARY_PERIODIC) ? ((i + xplus) % extent[0]) : (i + xplus); 2686 PetscInt vert = ((zcoord * extentPlus[1] + ycoord) * extentPlus[0] + xcoord) * 56 + patternvert; 2687 2688 cells[(k * extent[1] + j) * extent[0] + i][f][v] = vert; 2689 seen[vert] = PETSC_TRUE; 2690 } 2691 } 2692 } 2693 } 2694 } 2695 for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++) if (seen[i]) numVertices++; 2696 count = 0; 2697 PetscCall(PetscMalloc1(numBlocksPlus * vertsPerBlock, &vertToTrueVert)); 2698 PetscCall(PetscMalloc1(numVertices * 3, &vtxCoords)); 2699 for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++) vertToTrueVert[i] = -1; 2700 for (PetscInt k = 0; k < extentPlus[2]; k++) { 2701 for (PetscInt j = 0; j < extentPlus[1]; j++) { 2702 for (PetscInt i = 0; i < extentPlus[0]; i++) { 2703 for (PetscInt v = 0; v < vertsPerBlock; v++) { 2704 PetscInt vIdx = ((k * extentPlus[1] + j) * extentPlus[0] + i) * vertsPerBlock + v; 2705 2706 if (seen[vIdx]) { 2707 PetscInt thisVert; 2708 2709 vertToTrueVert[vIdx] = thisVert = count++; 2710 2711 for (PetscInt d = 0; d < 3; d++) vtxCoords[3 * thisVert + d] = patternCoords[v][d]; 2712 vtxCoords[3 * thisVert + 0] += i * 2; 2713 vtxCoords[3 * thisVert + 1] += j * 2; 2714 vtxCoords[3 * thisVert + 2] += k * 2; 2715 } 2716 } 2717 } 2718 } 2719 } 2720 for (PetscInt i = 0; i < numBlocks; i++) { 2721 for (PetscInt f = 0; f < facesPerBlock; f++) { 2722 for (PetscInt v = 0; v < 4; v++) { 2723 cells[i][f][v] = vertToTrueVert[cells[i][f][v]]; 2724 } 2725 } 2726 } 2727 PetscCall(PetscFree(vertToTrueVert)); 2728 PetscCall(PetscFree(seen)); 2729 cells_flat = cells[0][0]; 2730 numEdges = 0; 2731 for (PetscInt i = 0; i < numFaces; i++) { 2732 for (PetscInt e = 0; e < 4; e++) { 2733 PetscInt ev[] = {cells_flat[i*4 + e], cells_flat[i*4 + ((e+1)%4)]}; 2734 const PetscReal *evCoords[] = {&vtxCoords[3*ev[0]], &vtxCoords[3*ev[1]]}; 2735 2736 for (PetscInt d = 0; d < 3; d++) { 2737 if (!periodic || periodic[0] != DM_BOUNDARY_PERIODIC) { 2738 if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) numEdges++; 2739 if (evCoords[0][d] == 2.*extent[d] && evCoords[1][d] == 2.*extent[d]) numEdges++; 2740 } 2741 } 2742 } 2743 } 2744 PetscCall(PetscMalloc1(numEdges, &edges)); 2745 PetscCall(PetscMalloc1(numEdges, &edgeSets)); 2746 for (PetscInt edge = 0, i = 0; i < numFaces; i++) { 2747 for (PetscInt e = 0; e < 4; e++) { 2748 PetscInt ev[] = {cells_flat[i*4 + e], cells_flat[i*4 + ((e+1)%4)]}; 2749 const PetscReal *evCoords[] = {&vtxCoords[3*ev[0]], &vtxCoords[3*ev[1]]}; 2750 2751 for (PetscInt d = 0; d < 3; d++) { 2752 if (!periodic || periodic[d] != DM_BOUNDARY_PERIODIC) { 2753 if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) { 2754 edges[edge][0] = ev[0]; 2755 edges[edge][1] = ev[1]; 2756 edgeSets[edge++] = 2 * d; 2757 } 2758 if (evCoords[0][d] == 2.*extent[d] && evCoords[1][d] == 2.*extent[d]) { 2759 edges[edge][0] = ev[0]; 2760 edges[edge][1] = ev[1]; 2761 edgeSets[edge++] = 2 * d + 1; 2762 } 2763 } 2764 } 2765 } 2766 } 2767 } 2768 evalFunc = TPSEvaluate_Gyroid; 2769 normalFunc = TPSExtrudeNormalFunc_Gyroid; 2770 break; 2771 } 2772 2773 PetscCall(DMSetDimension(dm, topoDim)); 2774 if (rank == 0) PetscCall(DMPlexBuildFromCellList(dm, numFaces, numVertices, 4, cells_flat)); 2775 else PetscCall(DMPlexBuildFromCellList(dm, 0, 0, 0, NULL)); 2776 PetscCall(PetscFree(cells_flat)); 2777 { 2778 DM idm; 2779 PetscCall(DMPlexInterpolate(dm, &idm)); 2780 PetscCall(DMPlexReplace_Static(dm, &idm)); 2781 } 2782 if (rank == 0) PetscCall(DMPlexBuildCoordinatesFromCellList(dm, spaceDim, vtxCoords)); 2783 else PetscCall(DMPlexBuildCoordinatesFromCellList(dm, spaceDim, NULL)); 2784 PetscCall(PetscFree(vtxCoords)); 2785 2786 PetscCall(DMCreateLabel(dm, "Face Sets")); 2787 PetscCall(DMGetLabel(dm, "Face Sets", &label)); 2788 for (PetscInt e=0; e<numEdges; e++) { 2789 PetscInt njoin; 2790 const PetscInt *join, verts[] = {numFaces + edges[e][0], numFaces + edges[e][1]}; 2791 PetscCall(DMPlexGetJoin(dm, 2, verts, &njoin, &join)); 2792 PetscCheck(njoin == 1, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Expected unique join of vertices %" PetscInt_FMT " and %" PetscInt_FMT, edges[e][0], edges[e][1]); 2793 PetscCall(DMLabelSetValue(label, join[0], edgeSets[e])); 2794 PetscCall(DMPlexRestoreJoin(dm, 2, verts, &njoin, &join)); 2795 } 2796 PetscCall(PetscFree(edges)); 2797 PetscCall(PetscFree(edgeSets)); 2798 if (tps_distribute) { 2799 DM pdm = NULL; 2800 PetscPartitioner part; 2801 2802 PetscCall(DMPlexGetPartitioner(dm, &part)); 2803 PetscCall(PetscPartitionerSetFromOptions(part)); 2804 PetscCall(DMPlexDistribute(dm, 0, NULL, &pdm)); 2805 if (pdm) { 2806 PetscCall(DMPlexReplace_Static(dm, &pdm)); 2807 } 2808 // Do not auto-distribute again 2809 PetscCall(DMPlexDistributeSetDefault(dm, PETSC_FALSE)); 2810 } 2811 2812 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 2813 for (PetscInt refine=0; refine<refinements; refine++) { 2814 PetscInt m; 2815 DM dmf; 2816 Vec X; 2817 PetscScalar *x; 2818 PetscCall(DMRefine(dm, MPI_COMM_NULL, &dmf)); 2819 PetscCall(DMPlexReplace_Static(dm, &dmf)); 2820 2821 PetscCall(DMGetCoordinatesLocal(dm, &X)); 2822 PetscCall(VecGetLocalSize(X, &m)); 2823 PetscCall(VecGetArray(X, &x)); 2824 for (PetscInt i=0; i<m; i+=3) { 2825 PetscCall(TPSNearestPoint(evalFunc, &x[i])); 2826 } 2827 PetscCall(VecRestoreArray(X, &x)); 2828 } 2829 2830 // Face Sets has already been propagated to new vertices during refinement; this propagates to the initial vertices. 2831 PetscCall(DMGetLabel(dm, "Face Sets", &label)); 2832 PetscCall(DMPlexLabelComplete(dm, label)); 2833 2834 if (thickness > 0) { 2835 DM edm,cdm,ecdm; 2836 DMPlexTransform tr; 2837 const char *prefix; 2838 PetscOptions options; 2839 // Code from DMPlexExtrude 2840 PetscCall(DMPlexTransformCreate(PetscObjectComm((PetscObject)dm), &tr)); 2841 PetscCall(DMPlexTransformSetDM(tr, dm)); 2842 PetscCall(DMPlexTransformSetType(tr, DMPLEXEXTRUDE)); 2843 PetscCall(PetscObjectGetOptionsPrefix((PetscObject) dm, &prefix)); 2844 PetscCall(PetscObjectSetOptionsPrefix((PetscObject) tr, prefix)); 2845 PetscCall(PetscObjectGetOptions((PetscObject) dm, &options)); 2846 PetscCall(PetscObjectSetOptions((PetscObject) tr, options)); 2847 PetscCall(DMPlexTransformExtrudeSetLayers(tr, layers)); 2848 PetscCall(DMPlexTransformExtrudeSetThickness(tr, thickness)); 2849 PetscCall(DMPlexTransformExtrudeSetTensor(tr, PETSC_FALSE)); 2850 PetscCall(DMPlexTransformExtrudeSetSymmetric(tr, PETSC_TRUE)); 2851 PetscCall(DMPlexTransformExtrudeSetNormalFunction(tr, normalFunc)); 2852 PetscCall(DMPlexTransformSetFromOptions(tr)); 2853 PetscCall(PetscObjectSetOptions((PetscObject) tr, NULL)); 2854 PetscCall(DMPlexTransformSetUp(tr)); 2855 PetscCall(PetscObjectViewFromOptions((PetscObject) tr, NULL, "-dm_plex_tps_transform_view")); 2856 PetscCall(DMPlexTransformApply(tr, dm, &edm)); 2857 PetscCall(DMCopyDisc(dm, edm)); 2858 PetscCall(DMGetCoordinateDM(dm, &cdm)); 2859 PetscCall(DMGetCoordinateDM(edm, &ecdm)); 2860 PetscCall(DMCopyDisc(cdm, ecdm)); 2861 PetscCall(DMPlexTransformCreateDiscLabels(tr, edm)); 2862 PetscCall(DMPlexTransformDestroy(&tr)); 2863 if (edm) { 2864 ((DM_Plex *)edm->data)->printFEM = ((DM_Plex *)dm->data)->printFEM; 2865 ((DM_Plex *)edm->data)->printL2 = ((DM_Plex *)dm->data)->printL2; 2866 ((DM_Plex *)edm->data)->printLocate = ((DM_Plex *)dm->data)->printLocate; 2867 } 2868 PetscCall(DMPlexReplace_Static(dm, &edm)); 2869 } 2870 PetscFunctionReturn(0); 2871 } 2872 2873 /*@ 2874 DMPlexCreateTPSMesh - Create a distributed, interpolated mesh of a triply-periodic surface 2875 2876 Collective 2877 2878 Input Parameters: 2879 + comm - The communicator for the DM object 2880 . tpstype - Type of triply-periodic surface 2881 . extent - Array of length 3 containing number of periods in each direction 2882 . periodic - array of length 3 with periodicity, or NULL for non-periodic 2883 . tps_distribute - Distribute 2D manifold mesh prior to refinement and extrusion (more scalable) 2884 . refinements - Number of factor-of-2 refinements of 2D manifold mesh 2885 . layers - Number of cell layers extruded in normal direction 2886 - thickness - Thickness in normal direction 2887 2888 Output Parameter: 2889 . dm - The DM object 2890 2891 Notes: 2892 This meshes the surface of the Schwarz P or Gyroid surfaces. Schwarz P is is the simplest member of the triply-periodic minimal surfaces. 2893 https://en.wikipedia.org/wiki/Schwarz_minimal_surface#Schwarz_P_(%22Primitive%22) and can be cut with "clean" boundaries. 2894 The Gyroid (https://en.wikipedia.org/wiki/Gyroid) is another triply-periodic minimal surface with applications in additive manufacturing; it is much more difficult to "cut" since there are no planes of symmetry. 2895 Our implementation creates a very coarse mesh of the surface and refines (by 4-way splitting) as many times as requested. 2896 On each refinement, all vertices are projected to their nearest point on the surface. 2897 This projection could readily be extended to related surfaces. 2898 2899 The face (edge) sets for the Schwarz P surface are numbered 1(-x), 2(+x), 3(-y), 4(+y), 5(-z), 6(+z). 2900 When the mesh is refined, "Face Sets" contain the new vertices (created during refinement). Use DMPlexLabelComplete() to propagate to coarse-level vertices. 2901 2902 References: 2903 . * - Maskery et al, Insights into the mechanical properties of several triply periodic minimal surface lattice structures made by polymer additive manufacturing, 2017. https://doi.org/10.1016/j.polymer.2017.11.049 2904 2905 Developer Notes: 2906 The Gyroid mesh does not currently mark boundary sets. 2907 2908 Level: beginner 2909 2910 .seealso: `DMPlexCreateSphereMesh()`, `DMSetType()`, `DMCreate()` 2911 @*/ 2912 PetscErrorCode DMPlexCreateTPSMesh(MPI_Comm comm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscBool tps_distribute, PetscInt refinements, PetscInt layers, PetscReal thickness, DM *dm) 2913 { 2914 PetscFunctionBegin; 2915 PetscCall(DMCreate(comm, dm)); 2916 PetscCall(DMSetType(*dm, DMPLEX)); 2917 PetscCall(DMPlexCreateTPSMesh_Internal(*dm, tpstype, extent, periodic, tps_distribute, refinements, layers, thickness)); 2918 PetscFunctionReturn(0); 2919 } 2920 2921 /*@ 2922 DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d. 2923 2924 Collective 2925 2926 Input Parameters: 2927 + comm - The communicator for the DM object 2928 . dim - The dimension 2929 . simplex - Use simplices, or tensor product cells 2930 - R - The radius 2931 2932 Output Parameter: 2933 . dm - The DM object 2934 2935 Level: beginner 2936 2937 .seealso: `DMPlexCreateBallMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 2938 @*/ 2939 PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscReal R, DM *dm) 2940 { 2941 PetscFunctionBegin; 2942 PetscValidPointer(dm, 5); 2943 PetscCall(DMCreate(comm, dm)); 2944 PetscCall(DMSetType(*dm, DMPLEX)); 2945 PetscCall(DMPlexCreateSphereMesh_Internal(*dm, dim, simplex, R)); 2946 PetscFunctionReturn(0); 2947 } 2948 2949 static PetscErrorCode DMPlexCreateBallMesh_Internal(DM dm, PetscInt dim, PetscReal R) 2950 { 2951 DM sdm, vol; 2952 DMLabel bdlabel; 2953 2954 PetscFunctionBegin; 2955 PetscCall(DMCreate(PetscObjectComm((PetscObject) dm), &sdm)); 2956 PetscCall(DMSetType(sdm, DMPLEX)); 2957 PetscCall(PetscObjectSetOptionsPrefix((PetscObject) sdm, "bd_")); 2958 PetscCall(DMPlexCreateSphereMesh_Internal(sdm, dim-1, PETSC_TRUE, R)); 2959 PetscCall(DMSetFromOptions(sdm)); 2960 PetscCall(DMViewFromOptions(sdm, NULL, "-dm_view")); 2961 PetscCall(DMPlexGenerate(sdm, NULL, PETSC_TRUE, &vol)); 2962 PetscCall(DMDestroy(&sdm)); 2963 PetscCall(DMPlexReplace_Static(dm, &vol)); 2964 PetscCall(DMCreateLabel(dm, "marker")); 2965 PetscCall(DMGetLabel(dm, "marker", &bdlabel)); 2966 PetscCall(DMPlexMarkBoundaryFaces(dm, PETSC_DETERMINE, bdlabel)); 2967 PetscCall(DMPlexLabelComplete(dm, bdlabel)); 2968 PetscFunctionReturn(0); 2969 } 2970 2971 /*@ 2972 DMPlexCreateBallMesh - Creates a simplex mesh on the d-dimensional ball, B^d. 2973 2974 Collective 2975 2976 Input Parameters: 2977 + comm - The communicator for the DM object 2978 . dim - The dimension 2979 - R - The radius 2980 2981 Output Parameter: 2982 . dm - The DM object 2983 2984 Options Database Keys: 2985 - bd_dm_refine - This will refine the surface mesh preserving the sphere geometry 2986 2987 Level: beginner 2988 2989 .seealso: `DMPlexCreateSphereMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 2990 @*/ 2991 PetscErrorCode DMPlexCreateBallMesh(MPI_Comm comm, PetscInt dim, PetscReal R, DM *dm) 2992 { 2993 PetscFunctionBegin; 2994 PetscCall(DMCreate(comm, dm)); 2995 PetscCall(DMSetType(*dm, DMPLEX)); 2996 PetscCall(DMPlexCreateBallMesh_Internal(*dm, dim, R)); 2997 PetscFunctionReturn(0); 2998 } 2999 3000 static PetscErrorCode DMPlexCreateReferenceCell_Internal(DM rdm, DMPolytopeType ct) 3001 { 3002 PetscFunctionBegin; 3003 switch (ct) { 3004 case DM_POLYTOPE_POINT: 3005 { 3006 PetscInt numPoints[1] = {1}; 3007 PetscInt coneSize[1] = {0}; 3008 PetscInt cones[1] = {0}; 3009 PetscInt coneOrientations[1] = {0}; 3010 PetscScalar vertexCoords[1] = {0.0}; 3011 3012 PetscCall(DMSetDimension(rdm, 0)); 3013 PetscCall(DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3014 } 3015 break; 3016 case DM_POLYTOPE_SEGMENT: 3017 { 3018 PetscInt numPoints[2] = {2, 1}; 3019 PetscInt coneSize[3] = {2, 0, 0}; 3020 PetscInt cones[2] = {1, 2}; 3021 PetscInt coneOrientations[2] = {0, 0}; 3022 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 3023 3024 PetscCall(DMSetDimension(rdm, 1)); 3025 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3026 } 3027 break; 3028 case DM_POLYTOPE_POINT_PRISM_TENSOR: 3029 { 3030 PetscInt numPoints[2] = {2, 1}; 3031 PetscInt coneSize[3] = {2, 0, 0}; 3032 PetscInt cones[2] = {1, 2}; 3033 PetscInt coneOrientations[2] = {0, 0}; 3034 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 3035 3036 PetscCall(DMSetDimension(rdm, 1)); 3037 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3038 } 3039 break; 3040 case DM_POLYTOPE_TRIANGLE: 3041 { 3042 PetscInt numPoints[2] = {3, 1}; 3043 PetscInt coneSize[4] = {3, 0, 0, 0}; 3044 PetscInt cones[3] = {1, 2, 3}; 3045 PetscInt coneOrientations[3] = {0, 0, 0}; 3046 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 3047 3048 PetscCall(DMSetDimension(rdm, 2)); 3049 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3050 } 3051 break; 3052 case DM_POLYTOPE_QUADRILATERAL: 3053 { 3054 PetscInt numPoints[2] = {4, 1}; 3055 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3056 PetscInt cones[4] = {1, 2, 3, 4}; 3057 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3058 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 3059 3060 PetscCall(DMSetDimension(rdm, 2)); 3061 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3062 } 3063 break; 3064 case DM_POLYTOPE_SEG_PRISM_TENSOR: 3065 { 3066 PetscInt numPoints[2] = {4, 1}; 3067 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3068 PetscInt cones[4] = {1, 2, 3, 4}; 3069 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3070 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, 1.0}; 3071 3072 PetscCall(DMSetDimension(rdm, 2)); 3073 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3074 } 3075 break; 3076 case DM_POLYTOPE_TETRAHEDRON: 3077 { 3078 PetscInt numPoints[2] = {4, 1}; 3079 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3080 PetscInt cones[4] = {1, 2, 3, 4}; 3081 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3082 PetscScalar vertexCoords[12] = {-1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, -1.0, -1.0, -1.0, -1.0, 1.0}; 3083 3084 PetscCall(DMSetDimension(rdm, 3)); 3085 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3086 } 3087 break; 3088 case DM_POLYTOPE_HEXAHEDRON: 3089 { 3090 PetscInt numPoints[2] = {8, 1}; 3091 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3092 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 3093 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3094 PetscScalar vertexCoords[24] = {-1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, -1.0, 3095 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3096 3097 PetscCall(DMSetDimension(rdm, 3)); 3098 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3099 } 3100 break; 3101 case DM_POLYTOPE_TRI_PRISM: 3102 { 3103 PetscInt numPoints[2] = {6, 1}; 3104 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3105 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 3106 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3107 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, -1.0, -1.0, 3108 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 3109 3110 PetscCall(DMSetDimension(rdm, 3)); 3111 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3112 } 3113 break; 3114 case DM_POLYTOPE_TRI_PRISM_TENSOR: 3115 { 3116 PetscInt numPoints[2] = {6, 1}; 3117 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3118 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 3119 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3120 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 3121 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 3122 3123 PetscCall(DMSetDimension(rdm, 3)); 3124 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3125 } 3126 break; 3127 case DM_POLYTOPE_QUAD_PRISM_TENSOR: 3128 { 3129 PetscInt numPoints[2] = {8, 1}; 3130 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3131 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 3132 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3133 PetscScalar vertexCoords[24] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, -1.0, -1.0, 1.0, -1.0, 3134 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3135 3136 PetscCall(DMSetDimension(rdm, 3)); 3137 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3138 } 3139 break; 3140 case DM_POLYTOPE_PYRAMID: 3141 { 3142 PetscInt numPoints[2] = {5, 1}; 3143 PetscInt coneSize[6] = {5, 0, 0, 0, 0, 0}; 3144 PetscInt cones[5] = {1, 2, 3, 4, 5}; 3145 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3146 PetscScalar vertexCoords[24] = {-1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, -1.0, 3147 0.0, 0.0, 1.0}; 3148 3149 PetscCall(DMSetDimension(rdm, 3)); 3150 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3151 } 3152 break; 3153 default: SETERRQ(PetscObjectComm((PetscObject) rdm), PETSC_ERR_ARG_WRONG, "Cannot create reference cell for cell type %s", DMPolytopeTypes[ct]); 3154 } 3155 { 3156 PetscInt Nv, v; 3157 3158 /* Must create the celltype label here so that we do not automatically try to compute the types */ 3159 PetscCall(DMCreateLabel(rdm, "celltype")); 3160 PetscCall(DMPlexSetCellType(rdm, 0, ct)); 3161 PetscCall(DMPlexGetChart(rdm, NULL, &Nv)); 3162 for (v = 1; v < Nv; ++v) PetscCall(DMPlexSetCellType(rdm, v, DM_POLYTOPE_POINT)); 3163 } 3164 PetscCall(DMPlexInterpolateInPlace_Internal(rdm)); 3165 PetscCall(PetscObjectSetName((PetscObject) rdm, DMPolytopeTypes[ct])); 3166 PetscFunctionReturn(0); 3167 } 3168 3169 /*@ 3170 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 3171 3172 Collective 3173 3174 Input Parameters: 3175 + comm - The communicator 3176 - ct - The cell type of the reference cell 3177 3178 Output Parameter: 3179 . refdm - The reference cell 3180 3181 Level: intermediate 3182 3183 .seealso: `DMPlexCreateReferenceCell()`, `DMPlexCreateBoxMesh()` 3184 @*/ 3185 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, DMPolytopeType ct, DM *refdm) 3186 { 3187 PetscFunctionBegin; 3188 PetscCall(DMCreate(comm, refdm)); 3189 PetscCall(DMSetType(*refdm, DMPLEX)); 3190 PetscCall(DMPlexCreateReferenceCell_Internal(*refdm, ct)); 3191 PetscFunctionReturn(0); 3192 } 3193 3194 static PetscErrorCode DMPlexCreateBoundaryLabel_Private(DM dm, const char name[]) 3195 { 3196 DM plex; 3197 DMLabel label; 3198 PetscBool hasLabel; 3199 3200 PetscFunctionBeginUser; 3201 PetscCall(DMHasLabel(dm, name, &hasLabel)); 3202 if (hasLabel) PetscFunctionReturn(0); 3203 PetscCall(DMCreateLabel(dm, name)); 3204 PetscCall(DMGetLabel(dm, name, &label)); 3205 PetscCall(DMConvert(dm, DMPLEX, &plex)); 3206 PetscCall(DMPlexMarkBoundaryFaces(plex, 1, label)); 3207 PetscCall(DMPlexLabelComplete(plex, label)); 3208 PetscCall(DMDestroy(&plex)); 3209 PetscFunctionReturn(0); 3210 } 3211 3212 const char * const DMPlexShapes[] = {"box", "box_surface", "ball", "sphere", "cylinder", "schwarz_p", "gyroid", "doublet", "unknown", "DMPlexShape", "DM_SHAPE_", NULL}; 3213 3214 static PetscErrorCode DMPlexCreateFromOptions_Internal(PetscOptionItems *PetscOptionsObject, PetscBool *useCoordSpace, DM dm) 3215 { 3216 DMPlexShape shape = DM_SHAPE_BOX; 3217 DMPolytopeType cell = DM_POLYTOPE_TRIANGLE; 3218 PetscInt dim = 2; 3219 PetscBool simplex = PETSC_TRUE, interpolate = PETSC_TRUE, adjCone = PETSC_FALSE, adjClosure = PETSC_TRUE, refDomain = PETSC_FALSE; 3220 PetscBool flg, flg2, fflg, bdfflg, nameflg; 3221 MPI_Comm comm; 3222 char filename[PETSC_MAX_PATH_LEN] = "<unspecified>"; 3223 char bdFilename[PETSC_MAX_PATH_LEN] = "<unspecified>"; 3224 char plexname[PETSC_MAX_PATH_LEN] = ""; 3225 3226 PetscFunctionBegin; 3227 PetscCall(PetscObjectGetComm((PetscObject) dm, &comm)); 3228 /* TODO Turn this into a registration interface */ 3229 PetscCall(PetscOptionsString("-dm_plex_filename", "File containing a mesh", "DMPlexCreateFromFile", filename, filename, sizeof(filename), &fflg)); 3230 PetscCall(PetscOptionsString("-dm_plex_boundary_filename", "File containing a mesh boundary", "DMPlexCreateFromFile", bdFilename, bdFilename, sizeof(bdFilename), &bdfflg)); 3231 PetscCall(PetscOptionsString("-dm_plex_name", "Name of the mesh in the file", "DMPlexCreateFromFile", plexname, plexname, sizeof(plexname), &nameflg)); 3232 PetscCall(PetscOptionsEnum("-dm_plex_cell", "Cell shape", "", DMPolytopeTypes, (PetscEnum) cell, (PetscEnum *) &cell, NULL)); 3233 PetscCall(PetscOptionsBool("-dm_plex_reference_cell_domain", "Use a reference cell domain", "", refDomain, &refDomain, NULL)); 3234 PetscCall(PetscOptionsEnum("-dm_plex_shape", "Shape for built-in mesh", "", DMPlexShapes, (PetscEnum) shape, (PetscEnum *) &shape, &flg)); 3235 PetscCall(PetscOptionsBoundedInt("-dm_plex_dim", "Topological dimension of the mesh", "DMGetDimension", dim, &dim, &flg, 0)); 3236 PetscCheck(!(dim < 0) && !(dim > 3),comm, PETSC_ERR_ARG_OUTOFRANGE, "Dimension %" PetscInt_FMT " should be in [1, 3]", dim); 3237 PetscCall(PetscOptionsBool("-dm_plex_simplex", "Mesh cell shape", "", simplex, &simplex, &flg)); 3238 PetscCall(PetscOptionsBool("-dm_plex_interpolate", "Flag to create edges and faces automatically", "", interpolate, &interpolate, &flg)); 3239 PetscCall(PetscOptionsBool("-dm_plex_adj_cone", "Set adjacency direction", "DMSetBasicAdjacency", adjCone, &adjCone, &flg)); 3240 PetscCall(PetscOptionsBool("-dm_plex_adj_closure", "Set adjacency size", "DMSetBasicAdjacency", adjClosure, &adjClosure, &flg2)); 3241 if (flg || flg2) PetscCall(DMSetBasicAdjacency(dm, adjCone, adjClosure)); 3242 3243 switch (cell) { 3244 case DM_POLYTOPE_POINT: 3245 case DM_POLYTOPE_SEGMENT: 3246 case DM_POLYTOPE_POINT_PRISM_TENSOR: 3247 case DM_POLYTOPE_TRIANGLE: 3248 case DM_POLYTOPE_QUADRILATERAL: 3249 case DM_POLYTOPE_TETRAHEDRON: 3250 case DM_POLYTOPE_HEXAHEDRON: 3251 *useCoordSpace = PETSC_TRUE;break; 3252 default: *useCoordSpace = PETSC_FALSE;break; 3253 } 3254 3255 if (fflg) { 3256 DM dmnew; 3257 3258 PetscCall(DMPlexCreateFromFile(PetscObjectComm((PetscObject) dm), filename, plexname, interpolate, &dmnew)); 3259 PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew)); 3260 PetscCall(DMPlexReplace_Static(dm, &dmnew)); 3261 } else if (refDomain) { 3262 PetscCall(DMPlexCreateReferenceCell_Internal(dm, cell)); 3263 } else if (bdfflg) { 3264 DM bdm, dmnew; 3265 3266 PetscCall(DMPlexCreateFromFile(PetscObjectComm((PetscObject) dm), bdFilename, plexname, interpolate, &bdm)); 3267 PetscCall(PetscObjectSetOptionsPrefix((PetscObject) bdm, "bd_")); 3268 PetscCall(DMSetFromOptions(bdm)); 3269 PetscCall(DMPlexGenerate(bdm, NULL, interpolate, &dmnew)); 3270 PetscCall(DMDestroy(&bdm)); 3271 PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew)); 3272 PetscCall(DMPlexReplace_Static(dm, &dmnew)); 3273 } else { 3274 PetscCall(PetscObjectSetName((PetscObject) dm, DMPlexShapes[shape])); 3275 switch (shape) { 3276 case DM_SHAPE_BOX: 3277 { 3278 PetscInt faces[3] = {0, 0, 0}; 3279 PetscReal lower[3] = {0, 0, 0}; 3280 PetscReal upper[3] = {1, 1, 1}; 3281 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 3282 PetscInt i, n; 3283 3284 n = dim; 3285 for (i = 0; i < dim; ++i) faces[i] = (dim == 1 ? 1 : 4-dim); 3286 PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg)); 3287 n = 3; 3288 PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg)); 3289 PetscCheck(!flg || !(n != dim),comm, PETSC_ERR_ARG_SIZ, "Lower box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 3290 n = 3; 3291 PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg)); 3292 PetscCheck(!flg || !(n != dim),comm, PETSC_ERR_ARG_SIZ, "Upper box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 3293 n = 3; 3294 PetscCall(PetscOptionsEnumArray("-dm_plex_box_bd", "Boundary type for each dimension", "", DMBoundaryTypes, (PetscEnum *) bdt, &n, &flg)); 3295 PetscCheck(!flg || !(n != dim),comm, PETSC_ERR_ARG_SIZ, "Box boundary types had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 3296 switch (cell) { 3297 case DM_POLYTOPE_TRI_PRISM_TENSOR: 3298 PetscCall(DMPlexCreateWedgeBoxMesh_Internal(dm, faces, lower, upper, bdt)); 3299 if (!interpolate) { 3300 DM udm; 3301 3302 PetscCall(DMPlexUninterpolate(dm, &udm)); 3303 PetscCall(DMPlexReplace_Static(dm, &udm)); 3304 } 3305 break; 3306 default: 3307 PetscCall(DMPlexCreateBoxMesh_Internal(dm, dim, simplex, faces, lower, upper, bdt, interpolate)); 3308 break; 3309 } 3310 } 3311 break; 3312 case DM_SHAPE_BOX_SURFACE: 3313 { 3314 PetscInt faces[3] = {0, 0, 0}; 3315 PetscReal lower[3] = {0, 0, 0}; 3316 PetscReal upper[3] = {1, 1, 1}; 3317 PetscInt i, n; 3318 3319 n = dim+1; 3320 for (i = 0; i < dim+1; ++i) faces[i] = (dim+1 == 1 ? 1 : 4-(dim+1)); 3321 PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg)); 3322 n = 3; 3323 PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg)); 3324 PetscCheck(!flg || !(n != dim+1),comm, PETSC_ERR_ARG_SIZ, "Lower box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim+1); 3325 n = 3; 3326 PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg)); 3327 PetscCheck(!flg || !(n != dim+1),comm, PETSC_ERR_ARG_SIZ, "Upper box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim+1); 3328 PetscCall(DMPlexCreateBoxSurfaceMesh_Internal(dm, dim+1, faces, lower, upper, interpolate)); 3329 } 3330 break; 3331 case DM_SHAPE_SPHERE: 3332 { 3333 PetscReal R = 1.0; 3334 3335 PetscCall(PetscOptionsReal("-dm_plex_sphere_radius", "Radius of the sphere", "", R, &R, &flg)); 3336 PetscCall(DMPlexCreateSphereMesh_Internal(dm, dim, simplex, R)); 3337 } 3338 break; 3339 case DM_SHAPE_BALL: 3340 { 3341 PetscReal R = 1.0; 3342 3343 PetscCall(PetscOptionsReal("-dm_plex_ball_radius", "Radius of the ball", "", R, &R, &flg)); 3344 PetscCall(DMPlexCreateBallMesh_Internal(dm, dim, R)); 3345 } 3346 break; 3347 case DM_SHAPE_CYLINDER: 3348 { 3349 DMBoundaryType bdt = DM_BOUNDARY_NONE; 3350 PetscInt Nw = 6; 3351 3352 PetscCall(PetscOptionsEnum("-dm_plex_cylinder_bd", "Boundary type in the z direction", "", DMBoundaryTypes, (PetscEnum) bdt, (PetscEnum *) &bdt, NULL)); 3353 PetscCall(PetscOptionsInt("-dm_plex_cylinder_num_wedges", "Number of wedges around the cylinder", "", Nw, &Nw, NULL)); 3354 switch (cell) { 3355 case DM_POLYTOPE_TRI_PRISM_TENSOR: 3356 PetscCall(DMPlexCreateWedgeCylinderMesh_Internal(dm, Nw, interpolate)); 3357 break; 3358 default: 3359 PetscCall(DMPlexCreateHexCylinderMesh_Internal(dm, bdt)); 3360 break; 3361 } 3362 } 3363 break; 3364 case DM_SHAPE_SCHWARZ_P: // fallthrough 3365 case DM_SHAPE_GYROID: 3366 { 3367 PetscInt extent[3] = {1,1,1}, refine = 0, layers = 0, three; 3368 PetscReal thickness = 0.; 3369 DMBoundaryType periodic[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 3370 DMPlexTPSType tps_type = shape == DM_SHAPE_SCHWARZ_P ? DMPLEX_TPS_SCHWARZ_P : DMPLEX_TPS_GYROID; 3371 PetscBool tps_distribute; 3372 PetscCall(PetscOptionsIntArray("-dm_plex_tps_extent", "Number of replicas for each of three dimensions", NULL, extent, (three=3, &three), NULL)); 3373 PetscCall(PetscOptionsInt("-dm_plex_tps_refine", "Number of refinements", NULL, refine, &refine, NULL)); 3374 PetscCall(PetscOptionsEnumArray("-dm_plex_tps_periodic", "Periodicity in each of three dimensions", NULL, DMBoundaryTypes, (PetscEnum*)periodic, (three=3, &three), NULL)); 3375 PetscCall(PetscOptionsInt("-dm_plex_tps_layers", "Number of layers in volumetric extrusion (or zero to not extrude)", NULL, layers, &layers, NULL)); 3376 PetscCall(PetscOptionsReal("-dm_plex_tps_thickness", "Thickness of volumetric extrusion", NULL, thickness, &thickness, NULL)); 3377 PetscCall(DMPlexDistributeGetDefault(dm, &tps_distribute)); 3378 PetscCall(PetscOptionsBool("-dm_plex_tps_distribute", "Distribute the 2D mesh prior to refinement and extrusion", NULL, tps_distribute, &tps_distribute, NULL)); 3379 PetscCall(DMPlexCreateTPSMesh_Internal(dm, tps_type, extent, periodic, tps_distribute, refine, layers, thickness)); 3380 } 3381 break; 3382 case DM_SHAPE_DOUBLET: 3383 { 3384 DM dmnew; 3385 PetscReal rl = 0.0; 3386 3387 PetscCall(PetscOptionsReal("-dm_plex_doublet_refinementlimit", "Refinement limit", NULL, rl, &rl, NULL)); 3388 PetscCall(DMPlexCreateDoublet(PetscObjectComm((PetscObject)dm), dim, simplex, interpolate, rl, &dmnew)); 3389 PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew)); 3390 PetscCall(DMPlexReplace_Static(dm, &dmnew)); 3391 } 3392 break; 3393 default: SETERRQ(comm, PETSC_ERR_SUP, "Domain shape %s is unsupported", DMPlexShapes[shape]); 3394 } 3395 } 3396 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 3397 if (!((PetscObject)dm)->name && nameflg) { 3398 PetscCall(PetscObjectSetName((PetscObject)dm, plexname)); 3399 } 3400 PetscFunctionReturn(0); 3401 } 3402 3403 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject, DM dm) 3404 { 3405 DM_Plex *mesh = (DM_Plex*) dm->data; 3406 PetscBool flg, flg2; 3407 char bdLabel[PETSC_MAX_PATH_LEN]; 3408 3409 PetscFunctionBegin; 3410 /* Handle viewing */ 3411 PetscCall(PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL)); 3412 PetscCall(PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL,0)); 3413 PetscCall(PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL)); 3414 PetscCall(PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL,0)); 3415 PetscCall(PetscOptionsBoundedInt("-dm_plex_print_locate", "Debug output level all point location computations", "DMLocatePoints", 0, &mesh->printLocate, NULL,0)); 3416 PetscCall(DMMonitorSetFromOptions(dm, "-dm_plex_monitor_throughput", "Monitor the simulation throughput", "DMPlexMonitorThroughput", DMPlexMonitorThroughput, NULL, &flg)); 3417 if (flg) PetscCall(PetscLogDefaultBegin()); 3418 /* Labeling */ 3419 PetscCall(PetscOptionsString("-dm_plex_boundary_label", "Label to mark the mesh boundary", "", bdLabel, bdLabel, sizeof(bdLabel), &flg)); 3420 if (flg) PetscCall(DMPlexCreateBoundaryLabel_Private(dm, bdLabel)); 3421 /* Point Location */ 3422 PetscCall(PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL)); 3423 /* Partitioning and distribution */ 3424 PetscCall(PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL)); 3425 /* Generation and remeshing */ 3426 PetscCall(PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL)); 3427 /* Projection behavior */ 3428 PetscCall(PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL,0)); 3429 PetscCall(PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL)); 3430 /* Checking structure */ 3431 { 3432 PetscBool all = PETSC_FALSE; 3433 3434 PetscCall(PetscOptionsBool("-dm_plex_check_all", "Perform all basic checks", "DMPlexCheck", PETSC_FALSE, &all, NULL)); 3435 if (all) { 3436 PetscCall(DMPlexCheck(dm)); 3437 } else { 3438 PetscCall(PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2)); 3439 if (flg && flg2) PetscCall(DMPlexCheckSymmetry(dm)); 3440 PetscCall(PetscOptionsBool("-dm_plex_check_skeleton", "Check that each cell has the correct number of vertices (only for homogeneous simplex or tensor meshes)", "DMPlexCheckSkeleton", PETSC_FALSE, &flg, &flg2)); 3441 if (flg && flg2) PetscCall(DMPlexCheckSkeleton(dm, 0)); 3442 PetscCall(PetscOptionsBool("-dm_plex_check_faces", "Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type", "DMPlexCheckFaces", PETSC_FALSE, &flg, &flg2)); 3443 if (flg && flg2) PetscCall(DMPlexCheckFaces(dm, 0)); 3444 PetscCall(PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2)); 3445 if (flg && flg2) PetscCall(DMPlexCheckGeometry(dm)); 3446 PetscCall(PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2)); 3447 if (flg && flg2) PetscCall(DMPlexCheckPointSF(dm, NULL)); 3448 PetscCall(PetscOptionsBool("-dm_plex_check_interface_cones", "Check points on inter-partition interfaces have conforming order of cone points", "DMPlexCheckInterfaceCones", PETSC_FALSE, &flg, &flg2)); 3449 if (flg && flg2) PetscCall(DMPlexCheckInterfaceCones(dm)); 3450 } 3451 PetscCall(PetscOptionsBool("-dm_plex_check_cell_shape", "Check cell shape", "DMPlexCheckCellShape", PETSC_FALSE, &flg, &flg2)); 3452 if (flg && flg2) PetscCall(DMPlexCheckCellShape(dm, PETSC_TRUE, PETSC_DETERMINE)); 3453 } 3454 { 3455 PetscReal scale = 1.0; 3456 3457 PetscCall(PetscOptionsReal("-dm_plex_scale", "Scale factor for mesh coordinates", "DMPlexScale", scale, &scale, &flg)); 3458 if (flg) { 3459 Vec coordinates, coordinatesLocal; 3460 3461 PetscCall(DMGetCoordinates(dm, &coordinates)); 3462 PetscCall(DMGetCoordinatesLocal(dm, &coordinatesLocal)); 3463 PetscCall(VecScale(coordinates, scale)); 3464 PetscCall(VecScale(coordinatesLocal, scale)); 3465 } 3466 } 3467 PetscCall(PetscPartitionerSetFromOptions(mesh->partitioner)); 3468 PetscFunctionReturn(0); 3469 } 3470 3471 PetscErrorCode DMSetFromOptions_Overlap_Plex(PetscOptionItems *PetscOptionsObject, DM dm, PetscInt *overlap) 3472 { 3473 PetscInt numOvLabels = 16, numOvExLabels = 16; 3474 char *ovLabelNames[16], *ovExLabelNames[16]; 3475 PetscInt numOvValues = 16, numOvExValues = 16, l; 3476 PetscBool flg; 3477 3478 PetscFunctionBegin; 3479 PetscCall(PetscOptionsBoundedInt("-dm_distribute_overlap", "The size of the overlap halo", "DMPlexDistribute", *overlap, overlap, NULL, 0)); 3480 PetscCall(PetscOptionsStringArray("-dm_distribute_overlap_labels", "List of overlap label names", "DMPlexDistribute", ovLabelNames, &numOvLabels, &flg)); 3481 if (!flg) numOvLabels = 0; 3482 if (numOvLabels) { 3483 ((DM_Plex*) dm->data)->numOvLabels = numOvLabels; 3484 for (l = 0; l < numOvLabels; ++l) { 3485 PetscCall(DMGetLabel(dm, ovLabelNames[l], &((DM_Plex*) dm->data)->ovLabels[l])); 3486 PetscCheck(((DM_Plex*) dm->data)->ovLabels[l], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid label name %s", ovLabelNames[l]); 3487 PetscCall(PetscFree(ovLabelNames[l])); 3488 } 3489 PetscCall(PetscOptionsIntArray("-dm_distribute_overlap_values", "List of overlap label values", "DMPlexDistribute", ((DM_Plex*) dm->data)->ovValues, &numOvValues, &flg)); 3490 if (!flg) numOvValues = 0; 3491 PetscCheck(numOvLabels == numOvValues, PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "The number of labels %" PetscInt_FMT " must match the number of values %" PetscInt_FMT, numOvLabels, numOvValues); 3492 3493 PetscCall(PetscOptionsStringArray("-dm_distribute_overlap_exclude_labels", "List of overlap exclude label names", "DMPlexDistribute", ovExLabelNames, &numOvExLabels, &flg)); 3494 if (!flg) numOvExLabels = 0; 3495 ((DM_Plex*) dm->data)->numOvExLabels = numOvExLabels; 3496 for (l = 0; l < numOvExLabels; ++l) { 3497 PetscCall(DMGetLabel(dm, ovExLabelNames[l], &((DM_Plex*) dm->data)->ovExLabels[l])); 3498 PetscCheck(((DM_Plex*) dm->data)->ovExLabels[l], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid label name %s", ovExLabelNames[l]); 3499 PetscCall(PetscFree(ovExLabelNames[l])); 3500 } 3501 PetscCall(PetscOptionsIntArray("-dm_distribute_overlap_exclude_values", "List of overlap exclude label values", "DMPlexDistribute", ((DM_Plex*) dm->data)->ovExValues, &numOvExValues, &flg)); 3502 if (!flg) numOvExValues = 0; 3503 PetscCheck(numOvExLabels == numOvExValues, PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "The number of exclude labels %" PetscInt_FMT " must match the number of values %" PetscInt_FMT, numOvExLabels, numOvExValues); 3504 } 3505 PetscFunctionReturn(0); 3506 } 3507 3508 static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 3509 { 3510 PetscFunctionList ordlist; 3511 char oname[256]; 3512 PetscReal volume = -1.0; 3513 PetscInt prerefine = 0, refine = 0, r, coarsen = 0, overlap = 0, extLayers = 0, dim; 3514 PetscBool uniformOrig, created = PETSC_FALSE, uniform = PETSC_TRUE, distribute, interpolate = PETSC_TRUE, coordSpace = PETSC_TRUE, remap = PETSC_TRUE, ghostCells = PETSC_FALSE, isHierarchy, ignoreModel = PETSC_FALSE, flg; 3515 DMPlexReorderDefaultFlag reorder; 3516 3517 PetscFunctionBegin; 3518 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 3519 PetscOptionsHeadBegin(PetscOptionsObject,"DMPlex Options"); 3520 /* Handle automatic creation */ 3521 PetscCall(DMGetDimension(dm, &dim)); 3522 if (dim < 0) { 3523 PetscCall(DMPlexCreateFromOptions_Internal(PetscOptionsObject, &coordSpace, dm)); 3524 created = PETSC_TRUE; 3525 } 3526 PetscCall(DMGetDimension(dm, &dim)); 3527 /* Handle interpolation before distribution */ 3528 PetscCall(PetscOptionsBool("-dm_plex_interpolate_pre", "Flag to interpolate mesh before distribution", "", interpolate, &interpolate, &flg)); 3529 if (flg) { 3530 DMPlexInterpolatedFlag interpolated; 3531 3532 PetscCall(DMPlexIsInterpolated(dm, &interpolated)); 3533 if (interpolated == DMPLEX_INTERPOLATED_FULL && !interpolate) { 3534 DM udm; 3535 3536 PetscCall(DMPlexUninterpolate(dm, &udm)); 3537 PetscCall(DMPlexReplace_Static(dm, &udm)); 3538 } else if (interpolated != DMPLEX_INTERPOLATED_FULL && interpolate) { 3539 DM idm; 3540 3541 PetscCall(DMPlexInterpolate(dm, &idm)); 3542 PetscCall(DMPlexReplace_Static(dm, &idm)); 3543 } 3544 } 3545 /* Handle DMPlex refinement before distribution */ 3546 PetscCall(PetscOptionsBool("-dm_refine_ignore_model", "Flag to ignore the geometry model when refining", "DMCreate", ignoreModel, &ignoreModel, &flg)); 3547 if (flg) {((DM_Plex *) dm->data)->ignoreModel = ignoreModel;} 3548 PetscCall(DMPlexGetRefinementUniform(dm, &uniformOrig)); 3549 PetscCall(PetscOptionsBoundedInt("-dm_refine_pre", "The number of refinements before distribution", "DMCreate", prerefine, &prerefine, NULL,0)); 3550 PetscCall(PetscOptionsBool("-dm_refine_remap_pre", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL)); 3551 PetscCall(PetscOptionsBool("-dm_refine_uniform_pre", "Flag for uniform refinement before distribution", "DMCreate", uniform, &uniform, &flg)); 3552 if (flg) PetscCall(DMPlexSetRefinementUniform(dm, uniform)); 3553 PetscCall(PetscOptionsReal("-dm_refine_volume_limit_pre", "The maximum cell volume after refinement before distribution", "DMCreate", volume, &volume, &flg)); 3554 if (flg) { 3555 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_FALSE)); 3556 PetscCall(DMPlexSetRefinementLimit(dm, volume)); 3557 prerefine = PetscMax(prerefine, 1); 3558 } 3559 for (r = 0; r < prerefine; ++r) { 3560 DM rdm; 3561 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 3562 3563 PetscCall(DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm)); 3564 PetscCall(DMRefine(dm, PetscObjectComm((PetscObject) dm), &rdm)); 3565 PetscCall(DMPlexReplace_Static(dm, &rdm)); 3566 PetscCall(DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm)); 3567 if (coordFunc && remap) { 3568 PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc)); 3569 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 3570 } 3571 } 3572 PetscCall(DMPlexSetRefinementUniform(dm, uniformOrig)); 3573 /* Handle DMPlex extrusion before distribution */ 3574 PetscCall(PetscOptionsBoundedInt("-dm_extrude", "The number of layers to extrude", "", extLayers, &extLayers, NULL, 0)); 3575 if (extLayers) { 3576 DM edm; 3577 3578 PetscCall(DMExtrude(dm, extLayers, &edm)); 3579 PetscCall(DMPlexReplace_Static(dm, &edm)); 3580 ((DM_Plex *) dm->data)->coordFunc = NULL; 3581 PetscCall(DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm)); 3582 extLayers = 0; 3583 } 3584 /* Handle DMPlex reordering before distribution */ 3585 PetscCall(DMPlexReorderGetDefault(dm, &reorder)); 3586 PetscCall(MatGetOrderingList(&ordlist)); 3587 PetscCall(PetscStrncpy(oname, MATORDERINGNATURAL, sizeof(oname))); 3588 PetscCall(PetscOptionsFList("-dm_plex_reorder", "Set mesh reordering type", "DMPlexGetOrdering", ordlist, MATORDERINGNATURAL, oname, sizeof(oname), &flg)); 3589 if (reorder == DMPLEX_REORDER_DEFAULT_TRUE || flg) { 3590 DM pdm; 3591 IS perm; 3592 3593 PetscCall(DMPlexGetOrdering(dm, oname, NULL, &perm)); 3594 PetscCall(DMPlexPermute(dm, perm, &pdm)); 3595 PetscCall(ISDestroy(&perm)); 3596 PetscCall(DMPlexReplace_Static(dm, &pdm)); 3597 PetscCall(DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm)); 3598 } 3599 /* Handle DMPlex distribution */ 3600 PetscCall(DMPlexDistributeGetDefault(dm, &distribute)); 3601 PetscCall(PetscOptionsBool("-dm_distribute", "Flag to redistribute a mesh among processes", "DMPlexDistribute", distribute, &distribute, NULL)); 3602 PetscCall(DMSetFromOptions_Overlap_Plex(PetscOptionsObject, dm, &overlap)); 3603 if (distribute) { 3604 DM pdm = NULL; 3605 PetscPartitioner part; 3606 3607 PetscCall(DMPlexGetPartitioner(dm, &part)); 3608 PetscCall(PetscPartitionerSetFromOptions(part)); 3609 PetscCall(DMPlexDistribute(dm, overlap, NULL, &pdm)); 3610 if (pdm) { 3611 PetscCall(DMPlexReplace_Static(dm, &pdm)); 3612 } 3613 } 3614 /* Create coordinate space */ 3615 if (created) { 3616 DM_Plex *mesh = (DM_Plex *) dm->data; 3617 PetscInt degree = 1; 3618 PetscBool flg; 3619 3620 PetscCall(PetscOptionsBool("-dm_coord_space", "Use an FEM space for coordinates", "", coordSpace, &coordSpace, &flg)); 3621 PetscCall(PetscOptionsInt("-dm_coord_petscspace_degree", "FEM degree for coordinate space", "", degree, °ree, NULL)); 3622 if (coordSpace) PetscCall(DMPlexCreateCoordinateSpace(dm, degree, mesh->coordFunc)); 3623 if (flg && !coordSpace) { 3624 DM cdm; 3625 PetscDS cds; 3626 PetscObject obj; 3627 PetscClassId id; 3628 3629 PetscCall(DMGetCoordinateDM(dm, &cdm)); 3630 PetscCall(DMGetDS(cdm, &cds)); 3631 PetscCall(PetscDSGetDiscretization(cds, 0, &obj)); 3632 PetscCall(PetscObjectGetClassId(obj, &id)); 3633 if (id == PETSCFE_CLASSID) { 3634 PetscContainer dummy; 3635 3636 PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &dummy)); 3637 PetscCall(PetscObjectSetName((PetscObject) dummy, "coordinates")); 3638 PetscCall(DMSetField(cdm, 0, NULL, (PetscObject) dummy)); 3639 PetscCall(PetscContainerDestroy(&dummy)); 3640 PetscCall(DMClearDS(cdm)); 3641 } 3642 mesh->coordFunc = NULL; 3643 } 3644 PetscCall(PetscOptionsBool("-dm_sparse_localize", "Localize only necessary cells", "", dm->sparseLocalize, &dm->sparseLocalize, &flg)); 3645 PetscCall(DMLocalizeCoordinates(dm)); 3646 } 3647 /* Handle DMPlex refinement */ 3648 remap = PETSC_TRUE; 3649 PetscCall(PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL,0)); 3650 PetscCall(PetscOptionsBool("-dm_refine_remap", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL)); 3651 PetscCall(PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy,0)); 3652 if (refine) PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 3653 if (refine && isHierarchy) { 3654 DM *dms, coarseDM; 3655 3656 PetscCall(DMGetCoarseDM(dm, &coarseDM)); 3657 PetscCall(PetscObjectReference((PetscObject)coarseDM)); 3658 PetscCall(PetscMalloc1(refine,&dms)); 3659 PetscCall(DMRefineHierarchy(dm, refine, dms)); 3660 /* Total hack since we do not pass in a pointer */ 3661 PetscCall(DMPlexSwap_Static(dm, dms[refine-1])); 3662 if (refine == 1) { 3663 PetscCall(DMSetCoarseDM(dm, dms[0])); 3664 PetscCall(DMPlexSetRegularRefinement(dm, PETSC_TRUE)); 3665 } else { 3666 PetscCall(DMSetCoarseDM(dm, dms[refine-2])); 3667 PetscCall(DMPlexSetRegularRefinement(dm, PETSC_TRUE)); 3668 PetscCall(DMSetCoarseDM(dms[0], dms[refine-1])); 3669 PetscCall(DMPlexSetRegularRefinement(dms[0], PETSC_TRUE)); 3670 } 3671 PetscCall(DMSetCoarseDM(dms[refine-1], coarseDM)); 3672 PetscCall(PetscObjectDereference((PetscObject)coarseDM)); 3673 /* Free DMs */ 3674 for (r = 0; r < refine; ++r) { 3675 PetscCall(DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r])); 3676 PetscCall(DMDestroy(&dms[r])); 3677 } 3678 PetscCall(PetscFree(dms)); 3679 } else { 3680 for (r = 0; r < refine; ++r) { 3681 DM rdm; 3682 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 3683 3684 PetscCall(DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm)); 3685 PetscCall(DMRefine(dm, PetscObjectComm((PetscObject) dm), &rdm)); 3686 /* Total hack since we do not pass in a pointer */ 3687 PetscCall(DMPlexReplace_Static(dm, &rdm)); 3688 PetscCall(DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm)); 3689 if (coordFunc && remap) { 3690 PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc)); 3691 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 3692 } 3693 } 3694 } 3695 /* Handle DMPlex coarsening */ 3696 PetscCall(PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL,0)); 3697 PetscCall(PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy,0)); 3698 if (coarsen && isHierarchy) { 3699 DM *dms; 3700 3701 PetscCall(PetscMalloc1(coarsen, &dms)); 3702 PetscCall(DMCoarsenHierarchy(dm, coarsen, dms)); 3703 /* Free DMs */ 3704 for (r = 0; r < coarsen; ++r) { 3705 PetscCall(DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r])); 3706 PetscCall(DMDestroy(&dms[r])); 3707 } 3708 PetscCall(PetscFree(dms)); 3709 } else { 3710 for (r = 0; r < coarsen; ++r) { 3711 DM cdm; 3712 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 3713 3714 PetscCall(DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm)); 3715 PetscCall(DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &cdm)); 3716 /* Total hack since we do not pass in a pointer */ 3717 PetscCall(DMPlexReplace_Static(dm, &cdm)); 3718 PetscCall(DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm)); 3719 if (coordFunc) { 3720 PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc)); 3721 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 3722 } 3723 } 3724 } 3725 /* Handle ghost cells */ 3726 PetscCall(PetscOptionsBool("-dm_plex_create_fv_ghost_cells", "Flag to create finite volume ghost cells on the boundary", "DMCreate", ghostCells, &ghostCells, NULL)); 3727 if (ghostCells) { 3728 DM gdm; 3729 char lname[PETSC_MAX_PATH_LEN]; 3730 3731 lname[0] = '\0'; 3732 PetscCall(PetscOptionsString("-dm_plex_fv_ghost_cells_label", "Label name for ghost cells boundary", "DMCreate", lname, lname, sizeof(lname), &flg)); 3733 PetscCall(DMPlexConstructGhostCells(dm, flg ? lname : NULL, NULL, &gdm)); 3734 PetscCall(DMPlexReplace_Static(dm, &gdm)); 3735 } 3736 /* Handle 1D order */ 3737 if (reorder != DMPLEX_REORDER_DEFAULT_FALSE && dim == 1) { 3738 DM cdm, rdm; 3739 PetscDS cds; 3740 PetscObject obj; 3741 PetscClassId id = PETSC_OBJECT_CLASSID; 3742 IS perm; 3743 PetscInt Nf; 3744 PetscBool distributed; 3745 3746 PetscCall(DMPlexIsDistributed(dm, &distributed)); 3747 PetscCall(DMGetCoordinateDM(dm, &cdm)); 3748 PetscCall(DMGetDS(cdm, &cds)); 3749 PetscCall(PetscDSGetNumFields(cds, &Nf)); 3750 if (Nf) { 3751 PetscCall(PetscDSGetDiscretization(cds, 0, &obj)); 3752 PetscCall(PetscObjectGetClassId(obj, &id)); 3753 } 3754 if (!distributed && id != PETSCFE_CLASSID) { 3755 PetscCall(DMPlexGetOrdering1D(dm, &perm)); 3756 PetscCall(DMPlexPermute(dm, perm, &rdm)); 3757 PetscCall(DMPlexReplace_Static(dm, &rdm)); 3758 PetscCall(ISDestroy(&perm)); 3759 } 3760 } 3761 /* Handle */ 3762 PetscCall(DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm)); 3763 PetscOptionsHeadEnd(); 3764 PetscFunctionReturn(0); 3765 } 3766 3767 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 3768 { 3769 PetscFunctionBegin; 3770 PetscCall(DMCreateGlobalVector_Section_Private(dm,vec)); 3771 /* PetscCall(VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM)); */ 3772 PetscCall(VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex)); 3773 PetscCall(VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native)); 3774 PetscCall(VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex)); 3775 PetscCall(VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native)); 3776 PetscFunctionReturn(0); 3777 } 3778 3779 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 3780 { 3781 PetscFunctionBegin; 3782 PetscCall(DMCreateLocalVector_Section_Private(dm,vec)); 3783 PetscCall(VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local)); 3784 PetscCall(VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local)); 3785 PetscFunctionReturn(0); 3786 } 3787 3788 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 3789 { 3790 PetscInt depth, d; 3791 3792 PetscFunctionBegin; 3793 PetscCall(DMPlexGetDepth(dm, &depth)); 3794 if (depth == 1) { 3795 PetscCall(DMGetDimension(dm, &d)); 3796 if (dim == 0) PetscCall(DMPlexGetDepthStratum(dm, dim, pStart, pEnd)); 3797 else if (dim == d) PetscCall(DMPlexGetDepthStratum(dm, 1, pStart, pEnd)); 3798 else {*pStart = 0; *pEnd = 0;} 3799 } else { 3800 PetscCall(DMPlexGetDepthStratum(dm, dim, pStart, pEnd)); 3801 } 3802 PetscFunctionReturn(0); 3803 } 3804 3805 static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 3806 { 3807 PetscSF sf; 3808 PetscInt niranks, njranks, n; 3809 const PetscMPIInt *iranks, *jranks; 3810 DM_Plex *data = (DM_Plex*) dm->data; 3811 3812 PetscFunctionBegin; 3813 PetscCall(DMGetPointSF(dm, &sf)); 3814 if (!data->neighbors) { 3815 PetscCall(PetscSFSetUp(sf)); 3816 PetscCall(PetscSFGetRootRanks(sf, &njranks, &jranks, NULL, NULL, NULL)); 3817 PetscCall(PetscSFGetLeafRanks(sf, &niranks, &iranks, NULL, NULL)); 3818 PetscCall(PetscMalloc1(njranks + niranks + 1, &data->neighbors)); 3819 PetscCall(PetscArraycpy(data->neighbors + 1, jranks, njranks)); 3820 PetscCall(PetscArraycpy(data->neighbors + njranks + 1, iranks, niranks)); 3821 n = njranks + niranks; 3822 PetscCall(PetscSortRemoveDupsMPIInt(&n, data->neighbors + 1)); 3823 /* The following cast should never fail: can't have more neighbors than PETSC_MPI_INT_MAX */ 3824 PetscCall(PetscMPIIntCast(n, data->neighbors)); 3825 } 3826 if (nranks) *nranks = data->neighbors[0]; 3827 if (ranks) { 3828 if (data->neighbors[0]) *ranks = data->neighbors + 1; 3829 else *ranks = NULL; 3830 } 3831 PetscFunctionReturn(0); 3832 } 3833 3834 PETSC_INTERN PetscErrorCode DMInterpolateSolution_Plex(DM, DM, Mat, Vec, Vec); 3835 3836 static PetscErrorCode DMInitialize_Plex(DM dm) 3837 { 3838 PetscFunctionBegin; 3839 dm->ops->view = DMView_Plex; 3840 dm->ops->load = DMLoad_Plex; 3841 dm->ops->setfromoptions = DMSetFromOptions_Plex; 3842 dm->ops->clone = DMClone_Plex; 3843 dm->ops->setup = DMSetUp_Plex; 3844 dm->ops->createlocalsection = DMCreateLocalSection_Plex; 3845 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 3846 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 3847 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 3848 dm->ops->getlocaltoglobalmapping = NULL; 3849 dm->ops->createfieldis = NULL; 3850 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 3851 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 3852 dm->ops->getcoloring = NULL; 3853 dm->ops->creatematrix = DMCreateMatrix_Plex; 3854 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 3855 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 3856 dm->ops->createmassmatrixlumped = DMCreateMassMatrixLumped_Plex; 3857 dm->ops->createinjection = DMCreateInjection_Plex; 3858 dm->ops->refine = DMRefine_Plex; 3859 dm->ops->coarsen = DMCoarsen_Plex; 3860 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 3861 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 3862 dm->ops->extrude = DMExtrude_Plex; 3863 dm->ops->globaltolocalbegin = NULL; 3864 dm->ops->globaltolocalend = NULL; 3865 dm->ops->localtoglobalbegin = NULL; 3866 dm->ops->localtoglobalend = NULL; 3867 dm->ops->destroy = DMDestroy_Plex; 3868 dm->ops->createsubdm = DMCreateSubDM_Plex; 3869 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 3870 dm->ops->getdimpoints = DMGetDimPoints_Plex; 3871 dm->ops->locatepoints = DMLocatePoints_Plex; 3872 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 3873 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 3874 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 3875 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 3876 dm->ops->projectbdfieldlabellocal = DMProjectBdFieldLabelLocal_Plex; 3877 dm->ops->computel2diff = DMComputeL2Diff_Plex; 3878 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 3879 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 3880 dm->ops->getneighbors = DMGetNeighbors_Plex; 3881 PetscCall(PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex)); 3882 PetscCall(PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertTimeDerviativeBoundaryValues_C",DMPlexInsertTimeDerivativeBoundaryValues_Plex)); 3883 PetscCall(PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex)); 3884 PetscCall(PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C",DMCreateNeumannOverlap_Plex)); 3885 PetscCall(PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex)); 3886 PetscCall(PetscObjectComposeFunction((PetscObject)dm,"DMPlexDistributeGetDefault_C",DMPlexDistributeGetDefault_Plex)); 3887 PetscCall(PetscObjectComposeFunction((PetscObject)dm,"DMPlexDistributeSetDefault_C",DMPlexDistributeSetDefault_Plex)); 3888 PetscCall(PetscObjectComposeFunction((PetscObject)dm,"DMPlexReorderGetDefault_C",DMPlexReorderGetDefault_Plex)); 3889 PetscCall(PetscObjectComposeFunction((PetscObject)dm,"DMPlexReorderSetDefault_C",DMPlexReorderSetDefault_Plex)); 3890 PetscCall(PetscObjectComposeFunction((PetscObject)dm,"DMInterpolateSolution_C",DMInterpolateSolution_Plex)); 3891 PetscCall(PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex)); 3892 PetscCall(PetscObjectComposeFunction((PetscObject)dm,"DMPlexSetOverlap_C",DMPlexSetOverlap_Plex)); 3893 PetscFunctionReturn(0); 3894 } 3895 3896 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 3897 { 3898 DM_Plex *mesh = (DM_Plex *) dm->data; 3899 3900 PetscFunctionBegin; 3901 mesh->refct++; 3902 (*newdm)->data = mesh; 3903 PetscCall(PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX)); 3904 PetscCall(DMInitialize_Plex(*newdm)); 3905 PetscFunctionReturn(0); 3906 } 3907 3908 /*MC 3909 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 3910 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 3911 specified by a PetscSection object. Ownership in the global representation is determined by 3912 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 3913 3914 Options Database Keys: 3915 + -dm_refine_pre - Refine mesh before distribution 3916 + -dm_refine_uniform_pre - Choose uniform or generator-based refinement 3917 + -dm_refine_volume_limit_pre - Cell volume limit after pre-refinement using generator 3918 . -dm_distribute - Distribute mesh across processes 3919 . -dm_distribute_overlap - Number of cells to overlap for distribution 3920 . -dm_refine - Refine mesh after distribution 3921 . -dm_plex_hash_location - Use grid hashing for point location 3922 . -dm_plex_hash_box_faces <n,m,p> - The number of divisions in each direction of the grid hash 3923 . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes 3924 . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing 3925 . -dm_plex_max_projection_height - Maxmimum mesh point height used to project locally 3926 . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement 3927 . -dm_plex_check_all - Perform all shecks below 3928 . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric 3929 . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices 3930 . -dm_plex_check_faces <celltype> - Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type 3931 . -dm_plex_check_geometry - Check that cells have positive volume 3932 . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ 3933 . -dm_plex_view_scale <num> - Scale the TikZ 3934 - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices 3935 3936 Level: intermediate 3937 3938 .seealso: `DMType`, `DMPlexCreate()`, `DMCreate()`, `DMSetType()` 3939 M*/ 3940 3941 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 3942 { 3943 DM_Plex *mesh; 3944 PetscInt unit; 3945 3946 PetscFunctionBegin; 3947 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3948 PetscCall(PetscNewLog(dm,&mesh)); 3949 dm->data = mesh; 3950 3951 mesh->refct = 1; 3952 PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection)); 3953 PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection)); 3954 mesh->refinementUniform = PETSC_TRUE; 3955 mesh->refinementLimit = -1.0; 3956 mesh->distDefault = PETSC_TRUE; 3957 mesh->reorderDefault = DMPLEX_REORDER_DEFAULT_NOTSET; 3958 mesh->interpolated = DMPLEX_INTERPOLATED_INVALID; 3959 mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID; 3960 3961 PetscCall(PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner)); 3962 mesh->remeshBd = PETSC_FALSE; 3963 3964 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 3965 3966 mesh->depthState = -1; 3967 mesh->celltypeState = -1; 3968 mesh->printTol = 1.0e-10; 3969 3970 PetscCall(DMInitialize_Plex(dm)); 3971 PetscFunctionReturn(0); 3972 } 3973 3974 /*@ 3975 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 3976 3977 Collective 3978 3979 Input Parameter: 3980 . comm - The communicator for the DMPlex object 3981 3982 Output Parameter: 3983 . mesh - The DMPlex object 3984 3985 Level: beginner 3986 3987 @*/ 3988 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 3989 { 3990 PetscFunctionBegin; 3991 PetscValidPointer(mesh,2); 3992 PetscCall(DMCreate(comm, mesh)); 3993 PetscCall(DMSetType(*mesh, DMPLEX)); 3994 PetscFunctionReturn(0); 3995 } 3996 3997 /*@C 3998 DMPlexBuildFromCellListParallel - Build distributed DMPLEX topology from a list of vertices for each cell (common mesh generator output) 3999 4000 Input Parameters: 4001 + dm - The DM 4002 . numCells - The number of cells owned by this process 4003 . numVertices - The number of vertices to be owned by this process, or PETSC_DECIDE 4004 . NVertices - The global number of vertices, or PETSC_DETERMINE 4005 . numCorners - The number of vertices for each cell 4006 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 4007 4008 Output Parameters: 4009 + vertexSF - (Optional) SF describing complete vertex ownership 4010 - verticesAdjSaved - (Optional) vertex adjacency array 4011 4012 Notes: 4013 Two triangles sharing a face 4014 $ 4015 $ 2 4016 $ / | \ 4017 $ / | \ 4018 $ / | \ 4019 $ 0 0 | 1 3 4020 $ \ | / 4021 $ \ | / 4022 $ \ | / 4023 $ 1 4024 would have input 4025 $ numCells = 2, numVertices = 4 4026 $ cells = [0 1 2 1 3 2] 4027 $ 4028 which would result in the DMPlex 4029 $ 4030 $ 4 4031 $ / | \ 4032 $ / | \ 4033 $ / | \ 4034 $ 2 0 | 1 5 4035 $ \ | / 4036 $ \ | / 4037 $ \ | / 4038 $ 3 4039 4040 Vertices are implicitly numbered consecutively 0,...,NVertices. 4041 Each rank owns a chunk of numVertices consecutive vertices. 4042 If numVertices is PETSC_DECIDE, PETSc will distribute them as evenly as possible using PetscLayout. 4043 If NVertices is PETSC_DETERMINE and numVertices is PETSC_DECIDE, NVertices is computed by PETSc as the maximum vertex index in cells + 1. 4044 If only NVertices is PETSC_DETERMINE, it is computed as the sum of numVertices over all ranks. 4045 4046 The cell distribution is arbitrary non-overlapping, independent of the vertex distribution. 4047 4048 Not currently supported in Fortran. 4049 4050 Level: advanced 4051 4052 .seealso: `DMPlexBuildFromCellList()`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildCoordinatesFromCellListParallel()` 4053 @*/ 4054 PetscErrorCode DMPlexBuildFromCellListParallel(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, const PetscInt cells[], PetscSF *vertexSF, PetscInt **verticesAdjSaved) 4055 { 4056 PetscSF sfPoint; 4057 PetscLayout layout; 4058 PetscInt numVerticesAdj, *verticesAdj, *cones, c, p; 4059 4060 PetscFunctionBegin; 4061 PetscValidLogicalCollectiveInt(dm,NVertices,4); 4062 PetscCall(PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0)); 4063 /* Get/check global number of vertices */ 4064 { 4065 PetscInt NVerticesInCells, i; 4066 const PetscInt len = numCells * numCorners; 4067 4068 /* NVerticesInCells = max(cells) + 1 */ 4069 NVerticesInCells = PETSC_MIN_INT; 4070 for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 4071 ++NVerticesInCells; 4072 PetscCallMPI(MPI_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject) dm))); 4073 4074 if (numVertices == PETSC_DECIDE && NVertices == PETSC_DECIDE) NVertices = NVerticesInCells; 4075 else PetscCheck(NVertices == PETSC_DECIDE || NVertices >= NVerticesInCells,PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Specified global number of vertices %" PetscInt_FMT " must be greater than or equal to the number of vertices in cells %" PetscInt_FMT,NVertices,NVerticesInCells); 4076 } 4077 /* Count locally unique vertices */ 4078 { 4079 PetscHSetI vhash; 4080 PetscInt off = 0; 4081 4082 PetscCall(PetscHSetICreate(&vhash)); 4083 for (c = 0; c < numCells; ++c) { 4084 for (p = 0; p < numCorners; ++p) { 4085 PetscCall(PetscHSetIAdd(vhash, cells[c*numCorners+p])); 4086 } 4087 } 4088 PetscCall(PetscHSetIGetSize(vhash, &numVerticesAdj)); 4089 if (!verticesAdjSaved) PetscCall(PetscMalloc1(numVerticesAdj, &verticesAdj)); 4090 else { verticesAdj = *verticesAdjSaved; } 4091 PetscCall(PetscHSetIGetElems(vhash, &off, verticesAdj)); 4092 PetscCall(PetscHSetIDestroy(&vhash)); 4093 PetscCheck(off == numVerticesAdj,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %" PetscInt_FMT " should be %" PetscInt_FMT, off, numVerticesAdj); 4094 } 4095 PetscCall(PetscSortInt(numVerticesAdj, verticesAdj)); 4096 /* Create cones */ 4097 PetscCall(DMPlexSetChart(dm, 0, numCells+numVerticesAdj)); 4098 for (c = 0; c < numCells; ++c) PetscCall(DMPlexSetConeSize(dm, c, numCorners)); 4099 PetscCall(DMSetUp(dm)); 4100 PetscCall(DMPlexGetCones(dm,&cones)); 4101 for (c = 0; c < numCells; ++c) { 4102 for (p = 0; p < numCorners; ++p) { 4103 const PetscInt gv = cells[c*numCorners+p]; 4104 PetscInt lv; 4105 4106 /* Positions within verticesAdj form 0-based local vertex numbering; 4107 we need to shift it by numCells to get correct DAG points (cells go first) */ 4108 PetscCall(PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv)); 4109 PetscCheck(lv >= 0,PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %" PetscInt_FMT " in local connectivity", gv); 4110 cones[c*numCorners+p] = lv+numCells; 4111 } 4112 } 4113 /* Build point sf */ 4114 PetscCall(PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &layout)); 4115 PetscCall(PetscLayoutSetSize(layout, NVertices)); 4116 PetscCall(PetscLayoutSetLocalSize(layout, numVertices)); 4117 PetscCall(PetscLayoutSetBlockSize(layout, 1)); 4118 PetscCall(PetscSFCreateByMatchingIndices(layout, numVerticesAdj, verticesAdj, NULL, numCells, numVerticesAdj, verticesAdj, NULL, numCells, vertexSF, &sfPoint)); 4119 PetscCall(PetscLayoutDestroy(&layout)); 4120 if (!verticesAdjSaved) PetscCall(PetscFree(verticesAdj)); 4121 PetscCall(PetscObjectSetName((PetscObject) sfPoint, "point SF")); 4122 if (dm->sf) { 4123 const char *prefix; 4124 4125 PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm->sf, &prefix)); 4126 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)sfPoint, prefix)); 4127 } 4128 PetscCall(DMSetPointSF(dm, sfPoint)); 4129 PetscCall(PetscSFDestroy(&sfPoint)); 4130 if (vertexSF) PetscCall(PetscObjectSetName((PetscObject)(*vertexSF), "Vertex Ownership SF")); 4131 /* Fill in the rest of the topology structure */ 4132 PetscCall(DMPlexSymmetrize(dm)); 4133 PetscCall(DMPlexStratify(dm)); 4134 PetscCall(PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0)); 4135 PetscFunctionReturn(0); 4136 } 4137 4138 /*@C 4139 DMPlexBuildCoordinatesFromCellListParallel - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output) 4140 4141 Input Parameters: 4142 + dm - The DM 4143 . spaceDim - The spatial dimension used for coordinates 4144 . sfVert - SF describing complete vertex ownership 4145 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 4146 4147 Level: advanced 4148 4149 Notes: 4150 Not currently supported in Fortran. 4151 4152 .seealso: `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildFromCellListParallel()` 4153 @*/ 4154 PetscErrorCode DMPlexBuildCoordinatesFromCellListParallel(DM dm, PetscInt spaceDim, PetscSF sfVert, const PetscReal vertexCoords[]) 4155 { 4156 PetscSection coordSection; 4157 Vec coordinates; 4158 PetscScalar *coords; 4159 PetscInt numVertices, numVerticesAdj, coordSize, v, vStart, vEnd; 4160 4161 PetscFunctionBegin; 4162 PetscCall(PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0)); 4163 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 4164 PetscCheck(vStart >= 0 && vEnd >= 0,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 4165 PetscCall(DMSetCoordinateDim(dm, spaceDim)); 4166 PetscCall(PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL)); 4167 PetscCheck(vEnd - vStart == numVerticesAdj,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Supplied sfVert has wrong number of leaves = %" PetscInt_FMT " != %" PetscInt_FMT " = vEnd - vStart",numVerticesAdj,vEnd - vStart); 4168 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 4169 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 4170 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spaceDim)); 4171 PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd)); 4172 for (v = vStart; v < vEnd; ++v) { 4173 PetscCall(PetscSectionSetDof(coordSection, v, spaceDim)); 4174 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spaceDim)); 4175 } 4176 PetscCall(PetscSectionSetUp(coordSection)); 4177 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 4178 PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &coordinates)); 4179 PetscCall(VecSetBlockSize(coordinates, spaceDim)); 4180 PetscCall(PetscObjectSetName((PetscObject) coordinates, "coordinates")); 4181 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 4182 PetscCall(VecSetType(coordinates,VECSTANDARD)); 4183 PetscCall(VecGetArray(coordinates, &coords)); 4184 { 4185 MPI_Datatype coordtype; 4186 4187 /* Need a temp buffer for coords if we have complex/single */ 4188 PetscCallMPI(MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype)); 4189 PetscCallMPI(MPI_Type_commit(&coordtype)); 4190 #if defined(PETSC_USE_COMPLEX) 4191 { 4192 PetscScalar *svertexCoords; 4193 PetscInt i; 4194 PetscCall(PetscMalloc1(numVertices*spaceDim,&svertexCoords)); 4195 for (i=0; i<numVertices*spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 4196 PetscCall(PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords,MPI_REPLACE)); 4197 PetscCall(PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords,MPI_REPLACE)); 4198 PetscCall(PetscFree(svertexCoords)); 4199 } 4200 #else 4201 PetscCall(PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords,MPI_REPLACE)); 4202 PetscCall(PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords,MPI_REPLACE)); 4203 #endif 4204 PetscCallMPI(MPI_Type_free(&coordtype)); 4205 } 4206 PetscCall(VecRestoreArray(coordinates, &coords)); 4207 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 4208 PetscCall(VecDestroy(&coordinates)); 4209 PetscCall(PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0)); 4210 PetscFunctionReturn(0); 4211 } 4212 4213 /*@ 4214 DMPlexCreateFromCellListParallelPetsc - Create distributed DMPLEX from a list of vertices for each cell (common mesh generator output) 4215 4216 Input Parameters: 4217 + comm - The communicator 4218 . dim - The topological dimension of the mesh 4219 . numCells - The number of cells owned by this process 4220 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 4221 . NVertices - The global number of vertices, or PETSC_DECIDE 4222 . numCorners - The number of vertices for each cell 4223 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 4224 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 4225 . spaceDim - The spatial dimension used for coordinates 4226 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 4227 4228 Output Parameters: 4229 + dm - The DM 4230 . vertexSF - (Optional) SF describing complete vertex ownership 4231 - verticesAdjSaved - (Optional) vertex adjacency array 4232 4233 Notes: 4234 This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), 4235 DMPlexBuildFromCellListParallel(), DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellListParallel() 4236 4237 See DMPlexBuildFromCellListParallel() for an example and details about the topology-related parameters. 4238 See DMPlexBuildCoordinatesFromCellListParallel() for details about the geometry-related parameters. 4239 4240 Level: intermediate 4241 4242 .seealso: `DMPlexCreateFromCellListPetsc()`, `DMPlexBuildFromCellListParallel()`, `DMPlexBuildCoordinatesFromCellListParallel()`, `DMPlexCreateFromDAG()`, `DMPlexCreate()` 4243 @*/ 4244 PetscErrorCode DMPlexCreateFromCellListParallelPetsc(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, PetscBool interpolate, const PetscInt cells[], PetscInt spaceDim, const PetscReal vertexCoords[], PetscSF *vertexSF, PetscInt **verticesAdj, DM *dm) 4245 { 4246 PetscSF sfVert; 4247 4248 PetscFunctionBegin; 4249 PetscCall(DMCreate(comm, dm)); 4250 PetscCall(DMSetType(*dm, DMPLEX)); 4251 PetscValidLogicalCollectiveInt(*dm, dim, 2); 4252 PetscValidLogicalCollectiveInt(*dm, spaceDim, 9); 4253 PetscCall(DMSetDimension(*dm, dim)); 4254 PetscCall(DMPlexBuildFromCellListParallel(*dm, numCells, numVertices, NVertices, numCorners, cells, &sfVert, verticesAdj)); 4255 if (interpolate) { 4256 DM idm; 4257 4258 PetscCall(DMPlexInterpolate(*dm, &idm)); 4259 PetscCall(DMDestroy(dm)); 4260 *dm = idm; 4261 } 4262 PetscCall(DMPlexBuildCoordinatesFromCellListParallel(*dm, spaceDim, sfVert, vertexCoords)); 4263 if (vertexSF) *vertexSF = sfVert; 4264 else PetscCall(PetscSFDestroy(&sfVert)); 4265 PetscFunctionReturn(0); 4266 } 4267 4268 /*@C 4269 DMPlexBuildFromCellList - Build DMPLEX topology from a list of vertices for each cell (common mesh generator output) 4270 4271 Input Parameters: 4272 + dm - The DM 4273 . numCells - The number of cells owned by this process 4274 . numVertices - The number of vertices owned by this process, or PETSC_DETERMINE 4275 . numCorners - The number of vertices for each cell 4276 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 4277 4278 Level: advanced 4279 4280 Notes: 4281 Two triangles sharing a face 4282 $ 4283 $ 2 4284 $ / | \ 4285 $ / | \ 4286 $ / | \ 4287 $ 0 0 | 1 3 4288 $ \ | / 4289 $ \ | / 4290 $ \ | / 4291 $ 1 4292 would have input 4293 $ numCells = 2, numVertices = 4 4294 $ cells = [0 1 2 1 3 2] 4295 $ 4296 which would result in the DMPlex 4297 $ 4298 $ 4 4299 $ / | \ 4300 $ / | \ 4301 $ / | \ 4302 $ 2 0 | 1 5 4303 $ \ | / 4304 $ \ | / 4305 $ \ | / 4306 $ 3 4307 4308 If numVertices is PETSC_DETERMINE, it is computed by PETSc as the maximum vertex index in cells + 1. 4309 4310 Not currently supported in Fortran. 4311 4312 .seealso: `DMPlexBuildFromCellListParallel()`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromCellListPetsc()` 4313 @*/ 4314 PetscErrorCode DMPlexBuildFromCellList(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[]) 4315 { 4316 PetscInt *cones, c, p, dim; 4317 4318 PetscFunctionBegin; 4319 PetscCall(PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0)); 4320 PetscCall(DMGetDimension(dm, &dim)); 4321 /* Get/check global number of vertices */ 4322 { 4323 PetscInt NVerticesInCells, i; 4324 const PetscInt len = numCells * numCorners; 4325 4326 /* NVerticesInCells = max(cells) + 1 */ 4327 NVerticesInCells = PETSC_MIN_INT; 4328 for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 4329 ++NVerticesInCells; 4330 4331 if (numVertices == PETSC_DECIDE) numVertices = NVerticesInCells; 4332 else PetscCheck(numVertices >= NVerticesInCells,PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Specified number of vertices %" PetscInt_FMT " must be greater than or equal to the number of vertices in cells %" PetscInt_FMT,numVertices,NVerticesInCells); 4333 } 4334 PetscCall(DMPlexSetChart(dm, 0, numCells+numVertices)); 4335 for (c = 0; c < numCells; ++c) { 4336 PetscCall(DMPlexSetConeSize(dm, c, numCorners)); 4337 } 4338 PetscCall(DMSetUp(dm)); 4339 PetscCall(DMPlexGetCones(dm,&cones)); 4340 for (c = 0; c < numCells; ++c) { 4341 for (p = 0; p < numCorners; ++p) { 4342 cones[c*numCorners+p] = cells[c*numCorners+p]+numCells; 4343 } 4344 } 4345 PetscCall(DMPlexSymmetrize(dm)); 4346 PetscCall(DMPlexStratify(dm)); 4347 PetscCall(PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0)); 4348 PetscFunctionReturn(0); 4349 } 4350 4351 /*@C 4352 DMPlexBuildCoordinatesFromCellList - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output) 4353 4354 Input Parameters: 4355 + dm - The DM 4356 . spaceDim - The spatial dimension used for coordinates 4357 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 4358 4359 Level: advanced 4360 4361 Notes: 4362 Not currently supported in Fortran. 4363 4364 .seealso: `DMPlexBuildCoordinatesFromCellListParallel()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexBuildFromCellList()` 4365 @*/ 4366 PetscErrorCode DMPlexBuildCoordinatesFromCellList(DM dm, PetscInt spaceDim, const PetscReal vertexCoords[]) 4367 { 4368 PetscSection coordSection; 4369 Vec coordinates; 4370 DM cdm; 4371 PetscScalar *coords; 4372 PetscInt v, vStart, vEnd, d; 4373 4374 PetscFunctionBegin; 4375 PetscCall(PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0)); 4376 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 4377 PetscCheck(vStart >= 0 && vEnd >= 0,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 4378 PetscCall(DMSetCoordinateDim(dm, spaceDim)); 4379 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 4380 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 4381 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spaceDim)); 4382 PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd)); 4383 for (v = vStart; v < vEnd; ++v) { 4384 PetscCall(PetscSectionSetDof(coordSection, v, spaceDim)); 4385 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spaceDim)); 4386 } 4387 PetscCall(PetscSectionSetUp(coordSection)); 4388 4389 PetscCall(DMGetCoordinateDM(dm, &cdm)); 4390 PetscCall(DMCreateLocalVector(cdm, &coordinates)); 4391 PetscCall(VecSetBlockSize(coordinates, spaceDim)); 4392 PetscCall(PetscObjectSetName((PetscObject) coordinates, "coordinates")); 4393 PetscCall(VecGetArrayWrite(coordinates, &coords)); 4394 for (v = 0; v < vEnd-vStart; ++v) { 4395 for (d = 0; d < spaceDim; ++d) { 4396 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 4397 } 4398 } 4399 PetscCall(VecRestoreArrayWrite(coordinates, &coords)); 4400 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 4401 PetscCall(VecDestroy(&coordinates)); 4402 PetscCall(PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0)); 4403 PetscFunctionReturn(0); 4404 } 4405 4406 /*@ 4407 DMPlexCreateFromCellListPetsc - Create DMPLEX from a list of vertices for each cell (common mesh generator output), but only process 0 takes in the input 4408 4409 Collective on comm 4410 4411 Input Parameters: 4412 + comm - The communicator 4413 . dim - The topological dimension of the mesh 4414 . numCells - The number of cells, only on process 0 4415 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE, only on process 0 4416 . numCorners - The number of vertices for each cell, only on process 0 4417 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 4418 . cells - An array of numCells*numCorners numbers, the vertices for each cell, only on process 0 4419 . spaceDim - The spatial dimension used for coordinates 4420 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex, only on process 0 4421 4422 Output Parameter: 4423 . dm - The DM, which only has points on process 0 4424 4425 Notes: 4426 This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), DMPlexBuildFromCellList(), 4427 DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellList() 4428 4429 See DMPlexBuildFromCellList() for an example and details about the topology-related parameters. 4430 See DMPlexBuildCoordinatesFromCellList() for details about the geometry-related parameters. 4431 See DMPlexCreateFromCellListParallelPetsc() for parallel input 4432 4433 Level: intermediate 4434 4435 .seealso: `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildFromCellList()`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromDAG()`, `DMPlexCreate()` 4436 @*/ 4437 PetscErrorCode DMPlexCreateFromCellListPetsc(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, PetscBool interpolate, const PetscInt cells[], PetscInt spaceDim, const PetscReal vertexCoords[], DM *dm) 4438 { 4439 PetscMPIInt rank; 4440 4441 PetscFunctionBegin; 4442 PetscCheck(dim,comm, PETSC_ERR_ARG_OUTOFRANGE, "This is not appropriate for 0-dimensional meshes. Consider either creating the DM using DMPlexCreateFromDAG(), by hand, or using DMSwarm."); 4443 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 4444 PetscCall(DMCreate(comm, dm)); 4445 PetscCall(DMSetType(*dm, DMPLEX)); 4446 PetscCall(DMSetDimension(*dm, dim)); 4447 if (rank == 0) PetscCall(DMPlexBuildFromCellList(*dm, numCells, numVertices, numCorners, cells)); 4448 else PetscCall(DMPlexBuildFromCellList(*dm, 0, 0, 0, NULL)); 4449 if (interpolate) { 4450 DM idm; 4451 4452 PetscCall(DMPlexInterpolate(*dm, &idm)); 4453 PetscCall(DMDestroy(dm)); 4454 *dm = idm; 4455 } 4456 if (rank == 0) PetscCall(DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, vertexCoords)); 4457 else PetscCall(DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, NULL)); 4458 PetscFunctionReturn(0); 4459 } 4460 4461 /*@ 4462 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 4463 4464 Input Parameters: 4465 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 4466 . depth - The depth of the DAG 4467 . numPoints - Array of size depth + 1 containing the number of points at each depth 4468 . coneSize - The cone size of each point 4469 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 4470 . coneOrientations - The orientation of each cone point 4471 - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim() 4472 4473 Output Parameter: 4474 . dm - The DM 4475 4476 Note: Two triangles sharing a face would have input 4477 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 4478 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 4479 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 4480 $ 4481 which would result in the DMPlex 4482 $ 4483 $ 4 4484 $ / | \ 4485 $ / | \ 4486 $ / | \ 4487 $ 2 0 | 1 5 4488 $ \ | / 4489 $ \ | / 4490 $ \ | / 4491 $ 3 4492 $ 4493 $ Notice that all points are numbered consecutively, unlike DMPlexCreateFromCellListPetsc() 4494 4495 Level: advanced 4496 4497 .seealso: `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()` 4498 @*/ 4499 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 4500 { 4501 Vec coordinates; 4502 PetscSection coordSection; 4503 PetscScalar *coords; 4504 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 4505 4506 PetscFunctionBegin; 4507 PetscCall(DMGetDimension(dm, &dim)); 4508 PetscCall(DMGetCoordinateDim(dm, &dimEmbed)); 4509 PetscCheck(dimEmbed >= dim,PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %" PetscInt_FMT " cannot be less than intrinsic dimension %" PetscInt_FMT,dimEmbed,dim); 4510 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 4511 PetscCall(DMPlexSetChart(dm, pStart, pEnd)); 4512 for (p = pStart; p < pEnd; ++p) { 4513 PetscCall(DMPlexSetConeSize(dm, p, coneSize[p-pStart])); 4514 if (firstVertex < 0 && !coneSize[p - pStart]) { 4515 firstVertex = p - pStart; 4516 } 4517 } 4518 PetscCheck(firstVertex >= 0 || !numPoints[0],PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %" PetscInt_FMT " vertices but could not find any", numPoints[0]); 4519 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 4520 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 4521 PetscCall(DMPlexSetCone(dm, p, &cones[off])); 4522 PetscCall(DMPlexSetConeOrientation(dm, p, &coneOrientations[off])); 4523 } 4524 PetscCall(DMPlexSymmetrize(dm)); 4525 PetscCall(DMPlexStratify(dm)); 4526 /* Build coordinates */ 4527 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 4528 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 4529 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dimEmbed)); 4530 PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0])); 4531 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 4532 PetscCall(PetscSectionSetDof(coordSection, v, dimEmbed)); 4533 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed)); 4534 } 4535 PetscCall(PetscSectionSetUp(coordSection)); 4536 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 4537 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 4538 PetscCall(PetscObjectSetName((PetscObject) coordinates, "coordinates")); 4539 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 4540 PetscCall(VecSetBlockSize(coordinates, dimEmbed)); 4541 PetscCall(VecSetType(coordinates,VECSTANDARD)); 4542 if (vertexCoords) { 4543 PetscCall(VecGetArray(coordinates, &coords)); 4544 for (v = 0; v < numPoints[0]; ++v) { 4545 PetscInt off; 4546 4547 PetscCall(PetscSectionGetOffset(coordSection, v+firstVertex, &off)); 4548 for (d = 0; d < dimEmbed; ++d) { 4549 coords[off+d] = vertexCoords[v*dimEmbed+d]; 4550 } 4551 } 4552 } 4553 PetscCall(VecRestoreArray(coordinates, &coords)); 4554 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 4555 PetscCall(VecDestroy(&coordinates)); 4556 PetscFunctionReturn(0); 4557 } 4558 4559 /*@C 4560 DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file. 4561 4562 + comm - The MPI communicator 4563 . filename - Name of the .dat file 4564 - interpolate - Create faces and edges in the mesh 4565 4566 Output Parameter: 4567 . dm - The DM object representing the mesh 4568 4569 Note: The format is the simplest possible: 4570 $ Ne 4571 $ v0 v1 ... vk 4572 $ Nv 4573 $ x y z marker 4574 4575 Level: beginner 4576 4577 .seealso: `DMPlexCreateFromFile()`, `DMPlexCreateMedFromFile()`, `DMPlexCreateGmsh()`, `DMPlexCreate()` 4578 @*/ 4579 PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 4580 { 4581 DMLabel marker; 4582 PetscViewer viewer; 4583 Vec coordinates; 4584 PetscSection coordSection; 4585 PetscScalar *coords; 4586 char line[PETSC_MAX_PATH_LEN]; 4587 PetscInt dim = 3, cdim = 3, coordSize, v, c, d; 4588 PetscMPIInt rank; 4589 int snum, Nv, Nc, Ncn, Nl; 4590 4591 PetscFunctionBegin; 4592 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 4593 PetscCall(PetscViewerCreate(comm, &viewer)); 4594 PetscCall(PetscViewerSetType(viewer, PETSCVIEWERASCII)); 4595 PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ)); 4596 PetscCall(PetscViewerFileSetName(viewer, filename)); 4597 if (rank == 0) { 4598 PetscCall(PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING)); 4599 snum = sscanf(line, "%d %d %d %d", &Nc, &Nv, &Ncn, &Nl); 4600 PetscCheck(snum == 4,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4601 } else { 4602 Nc = Nv = Ncn = Nl = 0; 4603 } 4604 PetscCall(DMCreate(comm, dm)); 4605 PetscCall(DMSetType(*dm, DMPLEX)); 4606 PetscCall(DMPlexSetChart(*dm, 0, Nc+Nv)); 4607 PetscCall(DMSetDimension(*dm, dim)); 4608 PetscCall(DMSetCoordinateDim(*dm, cdim)); 4609 /* Read topology */ 4610 if (rank == 0) { 4611 char format[PETSC_MAX_PATH_LEN]; 4612 PetscInt cone[8]; 4613 int vbuf[8], v; 4614 4615 for (c = 0; c < Ncn; ++c) {format[c*3+0] = '%'; format[c*3+1] = 'd'; format[c*3+2] = ' ';} 4616 format[Ncn*3-1] = '\0'; 4617 for (c = 0; c < Nc; ++c) PetscCall(DMPlexSetConeSize(*dm, c, Ncn)); 4618 PetscCall(DMSetUp(*dm)); 4619 for (c = 0; c < Nc; ++c) { 4620 PetscCall(PetscViewerRead(viewer, line, Ncn, NULL, PETSC_STRING)); 4621 switch (Ncn) { 4622 case 2: snum = sscanf(line, format, &vbuf[0], &vbuf[1]);break; 4623 case 3: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2]);break; 4624 case 4: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3]);break; 4625 case 6: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5]);break; 4626 case 8: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5], &vbuf[6], &vbuf[7]);break; 4627 default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "No cell shape with %d vertices", Ncn); 4628 } 4629 PetscCheck(snum == Ncn,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4630 for (v = 0; v < Ncn; ++v) cone[v] = vbuf[v] + Nc; 4631 /* Hexahedra are inverted */ 4632 if (Ncn == 8) { 4633 PetscInt tmp = cone[1]; 4634 cone[1] = cone[3]; 4635 cone[3] = tmp; 4636 } 4637 PetscCall(DMPlexSetCone(*dm, c, cone)); 4638 } 4639 } 4640 PetscCall(DMPlexSymmetrize(*dm)); 4641 PetscCall(DMPlexStratify(*dm)); 4642 /* Read coordinates */ 4643 PetscCall(DMGetCoordinateSection(*dm, &coordSection)); 4644 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 4645 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, cdim)); 4646 PetscCall(PetscSectionSetChart(coordSection, Nc, Nc + Nv)); 4647 for (v = Nc; v < Nc+Nv; ++v) { 4648 PetscCall(PetscSectionSetDof(coordSection, v, cdim)); 4649 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, cdim)); 4650 } 4651 PetscCall(PetscSectionSetUp(coordSection)); 4652 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 4653 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 4654 PetscCall(PetscObjectSetName((PetscObject) coordinates, "coordinates")); 4655 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 4656 PetscCall(VecSetBlockSize(coordinates, cdim)); 4657 PetscCall(VecSetType(coordinates, VECSTANDARD)); 4658 PetscCall(VecGetArray(coordinates, &coords)); 4659 if (rank == 0) { 4660 char format[PETSC_MAX_PATH_LEN]; 4661 double x[3]; 4662 int l, val[3]; 4663 4664 if (Nl) { 4665 for (l = 0; l < Nl; ++l) {format[l*3+0] = '%'; format[l*3+1] = 'd'; format[l*3+2] = ' ';} 4666 format[Nl*3-1] = '\0'; 4667 PetscCall(DMCreateLabel(*dm, "marker")); 4668 PetscCall(DMGetLabel(*dm, "marker", &marker)); 4669 } 4670 for (v = 0; v < Nv; ++v) { 4671 PetscCall(PetscViewerRead(viewer, line, 3+Nl, NULL, PETSC_STRING)); 4672 snum = sscanf(line, "%lg %lg %lg", &x[0], &x[1], &x[2]); 4673 PetscCheck(snum == 3,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4674 switch (Nl) { 4675 case 0: snum = 0;break; 4676 case 1: snum = sscanf(line, format, &val[0]);break; 4677 case 2: snum = sscanf(line, format, &val[0], &val[1]);break; 4678 case 3: snum = sscanf(line, format, &val[0], &val[1], &val[2]);break; 4679 default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Request support for %d labels", Nl); 4680 } 4681 PetscCheck(snum == Nl,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4682 for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d]; 4683 for (l = 0; l < Nl; ++l) PetscCall(DMLabelSetValue(marker, v+Nc, val[l])); 4684 } 4685 } 4686 PetscCall(VecRestoreArray(coordinates, &coords)); 4687 PetscCall(DMSetCoordinatesLocal(*dm, coordinates)); 4688 PetscCall(VecDestroy(&coordinates)); 4689 PetscCall(PetscViewerDestroy(&viewer)); 4690 if (interpolate) { 4691 DM idm; 4692 DMLabel bdlabel; 4693 4694 PetscCall(DMPlexInterpolate(*dm, &idm)); 4695 PetscCall(DMDestroy(dm)); 4696 *dm = idm; 4697 4698 if (!Nl) { 4699 PetscCall(DMCreateLabel(*dm, "marker")); 4700 PetscCall(DMGetLabel(*dm, "marker", &bdlabel)); 4701 PetscCall(DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel)); 4702 PetscCall(DMPlexLabelComplete(*dm, bdlabel)); 4703 } 4704 } 4705 PetscFunctionReturn(0); 4706 } 4707 4708 /*@C 4709 DMPlexCreateFromFile - This takes a filename and produces a DM 4710 4711 Input Parameters: 4712 + comm - The communicator 4713 . filename - A file name 4714 . plexname - The object name of the resulting DM, also used for intra-datafile lookup by some formats 4715 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 4716 4717 Output Parameter: 4718 . dm - The DM 4719 4720 Options Database Keys: 4721 . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5 4722 4723 Use -dm_plex_create_ prefix to pass options to the internal PetscViewer, e.g. 4724 $ -dm_plex_create_viewer_hdf5_collective 4725 4726 Notes: 4727 Using PETSCVIEWERHDF5 type with PETSC_VIEWER_HDF5_PETSC format, one can save multiple DMPlex 4728 meshes in a single HDF5 file. This in turn requires one to name the DMPlex object with PetscObjectSetName() 4729 before saving it with DMView() and before loading it with DMLoad() for identification of the mesh object. 4730 The input parameter name is thus used to name the DMPlex object when DMPlexCreateFromFile() internally 4731 calls DMLoad(). Currently, name is ignored for other viewer types and/or formats. 4732 4733 Level: beginner 4734 4735 .seealso: `DMPlexCreateFromDAG()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()`, `PetscObjectSetName()`, `DMView()`, `DMLoad()` 4736 @*/ 4737 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], const char plexname[], PetscBool interpolate, DM *dm) 4738 { 4739 const char extGmsh[] = ".msh"; 4740 const char extGmsh2[] = ".msh2"; 4741 const char extGmsh4[] = ".msh4"; 4742 const char extCGNS[] = ".cgns"; 4743 const char extExodus[] = ".exo"; 4744 const char extExodus_e[] = ".e"; 4745 const char extGenesis[] = ".gen"; 4746 const char extFluent[] = ".cas"; 4747 const char extHDF5[] = ".h5"; 4748 const char extMed[] = ".med"; 4749 const char extPLY[] = ".ply"; 4750 const char extEGADSLite[] = ".egadslite"; 4751 const char extEGADS[] = ".egads"; 4752 const char extIGES[] = ".igs"; 4753 const char extSTEP[] = ".stp"; 4754 const char extCV[] = ".dat"; 4755 size_t len; 4756 PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isEGADSLite, isEGADS, isIGES, isSTEP, isCV; 4757 PetscMPIInt rank; 4758 4759 PetscFunctionBegin; 4760 PetscValidCharPointer(filename, 2); 4761 if (plexname) PetscValidCharPointer(plexname, 3); 4762 PetscValidPointer(dm, 5); 4763 PetscCall(DMInitializePackage()); 4764 PetscCall(PetscLogEventBegin(DMPLEX_CreateFromFile,0,0,0,0)); 4765 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 4766 PetscCall(PetscStrlen(filename, &len)); 4767 PetscCheck(len,comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 4768 4769 #define CheckExtension(extension__,is_extension__) do { \ 4770 PetscAssert(sizeof(extension__), comm, PETSC_ERR_PLIB, "Zero-size extension: %s", extension__); \ 4771 /* don't count the null-terminator at the end */ \ 4772 const size_t ext_len = sizeof(extension__)-1; \ 4773 if (len < ext_len) { \ 4774 is_extension__ = PETSC_FALSE; \ 4775 } else { \ 4776 PetscCall(PetscStrncmp(filename+len-ext_len, extension__, ext_len, &is_extension__)); \ 4777 } \ 4778 } while (0) 4779 4780 CheckExtension(extGmsh, isGmsh); 4781 CheckExtension(extGmsh2, isGmsh2); 4782 CheckExtension(extGmsh4, isGmsh4); 4783 CheckExtension(extCGNS, isCGNS); 4784 CheckExtension(extExodus, isExodus); 4785 if (!isExodus) CheckExtension(extExodus_e, isExodus); 4786 CheckExtension(extGenesis, isGenesis); 4787 CheckExtension(extFluent, isFluent); 4788 CheckExtension(extHDF5, isHDF5); 4789 CheckExtension(extMed, isMed); 4790 CheckExtension(extPLY, isPLY); 4791 CheckExtension(extEGADSLite, isEGADSLite); 4792 CheckExtension(extEGADS, isEGADS); 4793 CheckExtension(extIGES, isIGES); 4794 CheckExtension(extSTEP, isSTEP); 4795 CheckExtension(extCV, isCV); 4796 4797 #undef CheckExtension 4798 4799 if (isGmsh || isGmsh2 || isGmsh4) { 4800 PetscCall(DMPlexCreateGmshFromFile(comm, filename, interpolate, dm)); 4801 } else if (isCGNS) { 4802 PetscCall(DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm)); 4803 } else if (isExodus || isGenesis) { 4804 PetscCall(DMPlexCreateExodusFromFile(comm, filename, interpolate, dm)); 4805 } else if (isFluent) { 4806 PetscCall(DMPlexCreateFluentFromFile(comm, filename, interpolate, dm)); 4807 } else if (isHDF5) { 4808 PetscBool load_hdf5_xdmf = PETSC_FALSE; 4809 PetscViewer viewer; 4810 4811 /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */ 4812 PetscCall(PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf", 5, &load_hdf5_xdmf)); 4813 PetscCall(PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL)); 4814 PetscCall(PetscViewerCreate(comm, &viewer)); 4815 PetscCall(PetscViewerSetType(viewer, PETSCVIEWERHDF5)); 4816 PetscCall(PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_")); 4817 PetscCall(PetscViewerSetFromOptions(viewer)); 4818 PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ)); 4819 PetscCall(PetscViewerFileSetName(viewer, filename)); 4820 4821 PetscCall(DMCreate(comm, dm)); 4822 PetscCall(PetscObjectSetName((PetscObject)(*dm), plexname)); 4823 PetscCall(DMSetType(*dm, DMPLEX)); 4824 if (load_hdf5_xdmf) PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF)); 4825 PetscCall(DMLoad(*dm, viewer)); 4826 if (load_hdf5_xdmf) PetscCall(PetscViewerPopFormat(viewer)); 4827 PetscCall(PetscViewerDestroy(&viewer)); 4828 4829 if (interpolate) { 4830 DM idm; 4831 4832 PetscCall(DMPlexInterpolate(*dm, &idm)); 4833 PetscCall(DMDestroy(dm)); 4834 *dm = idm; 4835 } 4836 } else if (isMed) { 4837 PetscCall(DMPlexCreateMedFromFile(comm, filename, interpolate, dm)); 4838 } else if (isPLY) { 4839 PetscCall(DMPlexCreatePLYFromFile(comm, filename, interpolate, dm)); 4840 } else if (isEGADSLite || isEGADS || isIGES || isSTEP) { 4841 if (isEGADSLite) PetscCall(DMPlexCreateEGADSLiteFromFile(comm, filename, dm)); 4842 else PetscCall(DMPlexCreateEGADSFromFile(comm, filename, dm)); 4843 if (!interpolate) { 4844 DM udm; 4845 4846 PetscCall(DMPlexUninterpolate(*dm, &udm)); 4847 PetscCall(DMDestroy(dm)); 4848 *dm = udm; 4849 } 4850 } else if (isCV) { 4851 PetscCall(DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm)); 4852 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 4853 PetscCall(PetscStrlen(plexname, &len)); 4854 if (len) PetscCall(PetscObjectSetName((PetscObject)(*dm), plexname)); 4855 PetscCall(PetscLogEventEnd(DMPLEX_CreateFromFile,0,0,0,0)); 4856 PetscFunctionReturn(0); 4857 } 4858