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 <petscdmlabelephemeral.h> 7 #include <petsc/private/kernels/blockmatmult.h> 8 #include <petsc/private/kernels/blockinvert.h> 9 10 PetscLogEvent DMPLEX_CreateFromFile, DMPLEX_CreateFromOptions, DMPLEX_BuildFromCellList, DMPLEX_BuildCoordinatesFromCellList; 11 12 /* External function declarations here */ 13 static PetscErrorCode DMInitialize_Plex(DM dm); 14 15 /* This copies internal things in the Plex structure that we generally want when making a new, related Plex */ 16 PetscErrorCode DMPlexCopy_Internal(DM dmin, PetscBool copyPeriodicity, PetscBool copyOverlap, DM dmout) 17 { 18 const PetscReal *maxCell, *Lstart, *L; 19 PetscBool dist; 20 DMPlexReorderDefaultFlag reorder; 21 22 PetscFunctionBegin; 23 if (copyPeriodicity) { 24 PetscCall(DMGetPeriodicity(dmin, &maxCell, &Lstart, &L)); 25 PetscCall(DMSetPeriodicity(dmout, maxCell, Lstart, L)); 26 } 27 PetscCall(DMPlexDistributeGetDefault(dmin, &dist)); 28 PetscCall(DMPlexDistributeSetDefault(dmout, dist)); 29 PetscCall(DMPlexReorderGetDefault(dmin, &reorder)); 30 PetscCall(DMPlexReorderSetDefault(dmout, reorder)); 31 ((DM_Plex *)dmout->data)->useHashLocation = ((DM_Plex *)dmin->data)->useHashLocation; 32 if (copyOverlap) PetscCall(DMPlexSetOverlap_Plex(dmout, dmin, 0)); 33 PetscFunctionReturn(PETSC_SUCCESS); 34 } 35 36 /* Replace dm with the contents of ndm, and then destroy ndm 37 - Share the DM_Plex structure 38 - Share the coordinates 39 - Share the SF 40 */ 41 PetscErrorCode DMPlexReplace_Internal(DM dm, DM *ndm) 42 { 43 PetscSF sf; 44 DM dmNew = *ndm, coordDM, coarseDM; 45 Vec coords; 46 const PetscReal *maxCell, *Lstart, *L; 47 PetscInt dim, cdim; 48 49 PetscFunctionBegin; 50 if (dm == dmNew) { 51 PetscCall(DMDestroy(ndm)); 52 PetscFunctionReturn(PETSC_SUCCESS); 53 } 54 dm->setupcalled = dmNew->setupcalled; 55 PetscCall(DMGetDimension(dmNew, &dim)); 56 PetscCall(DMSetDimension(dm, dim)); 57 PetscCall(DMGetCoordinateDim(dmNew, &cdim)); 58 PetscCall(DMSetCoordinateDim(dm, cdim)); 59 PetscCall(DMGetPointSF(dmNew, &sf)); 60 PetscCall(DMSetPointSF(dm, sf)); 61 PetscCall(DMGetCoordinateDM(dmNew, &coordDM)); 62 PetscCall(DMGetCoordinatesLocal(dmNew, &coords)); 63 PetscCall(DMSetCoordinateDM(dm, coordDM)); 64 PetscCall(DMSetCoordinatesLocal(dm, coords)); 65 PetscCall(DMGetCellCoordinateDM(dmNew, &coordDM)); 66 PetscCall(DMGetCellCoordinatesLocal(dmNew, &coords)); 67 PetscCall(DMSetCellCoordinateDM(dm, coordDM)); 68 PetscCall(DMSetCellCoordinatesLocal(dm, coords)); 69 /* Do not want to create the coordinate field if it does not already exist, so do not call DMGetCoordinateField() */ 70 PetscCall(DMFieldDestroy(&dm->coordinates[0].field)); 71 dm->coordinates[0].field = dmNew->coordinates[0].field; 72 ((DM_Plex *)dmNew->data)->coordFunc = ((DM_Plex *)dm->data)->coordFunc; 73 PetscCall(DMGetPeriodicity(dmNew, &maxCell, &Lstart, &L)); 74 PetscCall(DMSetPeriodicity(dm, maxCell, Lstart, L)); 75 PetscCall(DMDestroy_Plex(dm)); 76 PetscCall(DMInitialize_Plex(dm)); 77 dm->data = dmNew->data; 78 ((DM_Plex *)dmNew->data)->refct++; 79 PetscCall(DMPlexGetIsoperiodicFaceSF(dm, &sf)); 80 PetscCall(DMPlexSetIsoperiodicFaceSF(dm, sf)); // for the compose function effect on dm 81 PetscCall(DMDestroyLabelLinkList_Internal(dm)); 82 PetscCall(DMCopyLabels(dmNew, dm, PETSC_OWN_POINTER, PETSC_TRUE, DM_COPY_LABELS_FAIL)); 83 PetscCall(DMGetCoarseDM(dmNew, &coarseDM)); 84 PetscCall(DMSetCoarseDM(dm, coarseDM)); 85 PetscCall(DMDestroy(ndm)); 86 PetscFunctionReturn(PETSC_SUCCESS); 87 } 88 89 /* Swap dm with the contents of dmNew 90 - Swap the DM_Plex structure 91 - Swap the coordinates 92 - Swap the point PetscSF 93 */ 94 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 95 { 96 DM coordDMA, coordDMB; 97 Vec coordsA, coordsB; 98 PetscSF sfA, sfB; 99 DMField fieldTmp; 100 void *tmp; 101 DMLabelLink listTmp; 102 DMLabel depthTmp; 103 PetscInt tmpI; 104 105 PetscFunctionBegin; 106 if (dmA == dmB) PetscFunctionReturn(PETSC_SUCCESS); 107 PetscCall(DMGetPointSF(dmA, &sfA)); 108 PetscCall(DMGetPointSF(dmB, &sfB)); 109 PetscCall(PetscObjectReference((PetscObject)sfA)); 110 PetscCall(DMSetPointSF(dmA, sfB)); 111 PetscCall(DMSetPointSF(dmB, sfA)); 112 PetscCall(PetscObjectDereference((PetscObject)sfA)); 113 114 PetscCall(DMGetCoordinateDM(dmA, &coordDMA)); 115 PetscCall(DMGetCoordinateDM(dmB, &coordDMB)); 116 PetscCall(PetscObjectReference((PetscObject)coordDMA)); 117 PetscCall(DMSetCoordinateDM(dmA, coordDMB)); 118 PetscCall(DMSetCoordinateDM(dmB, coordDMA)); 119 PetscCall(PetscObjectDereference((PetscObject)coordDMA)); 120 121 PetscCall(DMGetCoordinatesLocal(dmA, &coordsA)); 122 PetscCall(DMGetCoordinatesLocal(dmB, &coordsB)); 123 PetscCall(PetscObjectReference((PetscObject)coordsA)); 124 PetscCall(DMSetCoordinatesLocal(dmA, coordsB)); 125 PetscCall(DMSetCoordinatesLocal(dmB, coordsA)); 126 PetscCall(PetscObjectDereference((PetscObject)coordsA)); 127 128 PetscCall(DMGetCellCoordinateDM(dmA, &coordDMA)); 129 PetscCall(DMGetCellCoordinateDM(dmB, &coordDMB)); 130 PetscCall(PetscObjectReference((PetscObject)coordDMA)); 131 PetscCall(DMSetCellCoordinateDM(dmA, coordDMB)); 132 PetscCall(DMSetCellCoordinateDM(dmB, coordDMA)); 133 PetscCall(PetscObjectDereference((PetscObject)coordDMA)); 134 135 PetscCall(DMGetCellCoordinatesLocal(dmA, &coordsA)); 136 PetscCall(DMGetCellCoordinatesLocal(dmB, &coordsB)); 137 PetscCall(PetscObjectReference((PetscObject)coordsA)); 138 PetscCall(DMSetCellCoordinatesLocal(dmA, coordsB)); 139 PetscCall(DMSetCellCoordinatesLocal(dmB, coordsA)); 140 PetscCall(PetscObjectDereference((PetscObject)coordsA)); 141 142 fieldTmp = dmA->coordinates[0].field; 143 dmA->coordinates[0].field = dmB->coordinates[0].field; 144 dmB->coordinates[0].field = fieldTmp; 145 fieldTmp = dmA->coordinates[1].field; 146 dmA->coordinates[1].field = dmB->coordinates[1].field; 147 dmB->coordinates[1].field = fieldTmp; 148 tmp = dmA->data; 149 dmA->data = dmB->data; 150 dmB->data = tmp; 151 listTmp = dmA->labels; 152 dmA->labels = dmB->labels; 153 dmB->labels = listTmp; 154 depthTmp = dmA->depthLabel; 155 dmA->depthLabel = dmB->depthLabel; 156 dmB->depthLabel = depthTmp; 157 depthTmp = dmA->celltypeLabel; 158 dmA->celltypeLabel = dmB->celltypeLabel; 159 dmB->celltypeLabel = depthTmp; 160 tmpI = dmA->levelup; 161 dmA->levelup = dmB->levelup; 162 dmB->levelup = tmpI; 163 PetscFunctionReturn(PETSC_SUCCESS); 164 } 165 166 PetscErrorCode DMPlexInterpolateInPlace_Internal(DM dm) 167 { 168 DM idm; 169 170 PetscFunctionBegin; 171 PetscCall(DMPlexInterpolate(dm, &idm)); 172 PetscCall(DMPlexCopyCoordinates(dm, idm)); 173 PetscCall(DMPlexReplace_Internal(dm, &idm)); 174 PetscFunctionReturn(PETSC_SUCCESS); 175 } 176 177 /*@C 178 DMPlexCreateCoordinateSpace - Creates a finite element space for the coordinates 179 180 Collective 181 182 Input Parameters: 183 + dm - The `DMPLEX` 184 . degree - The degree of the finite element or `PETSC_DECIDE` 185 - coordFunc - An optional function to map new points from refinement to the surface 186 187 Level: advanced 188 189 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `PetscPointFunc`, `PetscFECreateLagrange()`, `DMGetCoordinateDM()` 190 @*/ 191 PetscErrorCode DMPlexCreateCoordinateSpace(DM dm, PetscInt degree, PetscPointFunc coordFunc) 192 { 193 DM_Plex *mesh = (DM_Plex *)dm->data; 194 DM cdm; 195 PetscDS cds; 196 PetscFE fe; 197 PetscClassId id; 198 199 PetscFunctionBegin; 200 PetscCall(DMGetCoordinateDM(dm, &cdm)); 201 PetscCall(DMGetDS(cdm, &cds)); 202 PetscCall(PetscDSGetDiscretization(cds, 0, (PetscObject *)&fe)); 203 PetscCall(PetscObjectGetClassId((PetscObject)fe, &id)); 204 if (id != PETSCFE_CLASSID) { 205 PetscInt dim, dE, qorder; 206 207 PetscCall(DMGetDimension(dm, &dim)); 208 PetscCall(DMGetCoordinateDim(dm, &dE)); 209 qorder = degree; 210 PetscObjectOptionsBegin((PetscObject)cdm); 211 PetscCall(PetscOptionsBoundedInt("-default_quadrature_order", "Quadrature order is one less than quadrature points per edge", "DMPlexCreateCoordinateSpace", qorder, &qorder, NULL, 0)); 212 PetscOptionsEnd(); 213 if (degree == PETSC_DECIDE) fe = NULL; 214 else { 215 DMPolytopeType ct; 216 PetscInt cStart, cEnd, ctTmp; 217 218 PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 219 // Want to match cell types 220 if (cEnd > cStart) PetscCall(DMPlexGetCellType(dm, cStart, &ct)); 221 else ct = DM_POLYTOPE_UNKNOWN; 222 ctTmp = (PetscInt)ct; 223 PetscCall(MPIU_Allreduce(MPI_IN_PLACE, &ctTmp, 1, MPIU_INT, MPI_MIN, PetscObjectComm((PetscObject)dm))); 224 ct = (DMPolytopeType)ctTmp; 225 // Work around current bug 226 if (ct == DM_POLYTOPE_SEG_PRISM_TENSOR || ct == DM_POLYTOPE_TRI_PRISM_TENSOR || ct == DM_POLYTOPE_QUAD_PRISM_TENSOR) fe = NULL; 227 else PetscCall(PetscFECreateLagrangeByCell(PETSC_COMM_SELF, dim, dE, ct, degree, qorder, &fe)); 228 } 229 if (fe) PetscCall(DMProjectCoordinates(dm, fe)); 230 PetscCall(PetscFEDestroy(&fe)); 231 } 232 mesh->coordFunc = coordFunc; 233 PetscFunctionReturn(PETSC_SUCCESS); 234 } 235 236 /*@ 237 DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement. 238 239 Collective 240 241 Input Parameters: 242 + comm - The communicator for the `DM` object 243 . dim - The spatial dimension 244 . simplex - Flag for simplicial cells, otherwise they are tensor product cells 245 . interpolate - Flag to create intermediate mesh pieces (edges, faces) 246 - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell 247 248 Output Parameter: 249 . newdm - The `DM` object 250 251 Level: beginner 252 253 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMSetType()`, `DMCreate()` 254 @*/ 255 PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscReal refinementLimit, DM *newdm) 256 { 257 DM dm; 258 PetscMPIInt rank; 259 260 PetscFunctionBegin; 261 PetscCall(DMCreate(comm, &dm)); 262 PetscCall(DMSetType(dm, DMPLEX)); 263 PetscCall(DMSetDimension(dm, dim)); 264 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 265 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 266 switch (dim) { 267 case 2: 268 if (simplex) PetscCall(PetscObjectSetName((PetscObject)dm, "triangular")); 269 else PetscCall(PetscObjectSetName((PetscObject)dm, "quadrilateral")); 270 break; 271 case 3: 272 if (simplex) PetscCall(PetscObjectSetName((PetscObject)dm, "tetrahedral")); 273 else PetscCall(PetscObjectSetName((PetscObject)dm, "hexahedral")); 274 break; 275 default: 276 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %" PetscInt_FMT, dim); 277 } 278 if (rank) { 279 PetscInt numPoints[2] = {0, 0}; 280 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL)); 281 } else { 282 switch (dim) { 283 case 2: 284 if (simplex) { 285 PetscInt numPoints[2] = {4, 2}; 286 PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; 287 PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; 288 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 289 PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5}; 290 291 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 292 } else { 293 PetscInt numPoints[2] = {6, 2}; 294 PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; 295 PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4}; 296 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 297 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}; 298 299 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 300 } 301 break; 302 case 3: 303 if (simplex) { 304 PetscInt numPoints[2] = {5, 2}; 305 PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; 306 PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; 307 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 308 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}; 309 310 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 311 } else { 312 PetscInt numPoints[2] = {12, 2}; 313 PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 314 PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8}; 315 PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 316 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, -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5, 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5}; 317 318 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 319 } 320 break; 321 default: 322 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %" PetscInt_FMT, dim); 323 } 324 } 325 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 326 *newdm = dm; 327 if (refinementLimit > 0.0) { 328 DM rdm; 329 const char *name; 330 331 PetscCall(DMPlexSetRefinementUniform(*newdm, PETSC_FALSE)); 332 PetscCall(DMPlexSetRefinementLimit(*newdm, refinementLimit)); 333 PetscCall(DMRefine(*newdm, comm, &rdm)); 334 PetscCall(PetscObjectGetName((PetscObject)*newdm, &name)); 335 PetscCall(PetscObjectSetName((PetscObject)rdm, name)); 336 PetscCall(DMDestroy(newdm)); 337 *newdm = rdm; 338 } 339 if (interpolate) { 340 DM idm; 341 342 PetscCall(DMPlexInterpolate(*newdm, &idm)); 343 PetscCall(DMDestroy(newdm)); 344 *newdm = idm; 345 } 346 PetscFunctionReturn(PETSC_SUCCESS); 347 } 348 349 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 350 { 351 const PetscInt numVertices = 2; 352 PetscInt markerRight = 1; 353 PetscInt markerLeft = 1; 354 PetscBool markerSeparate = PETSC_FALSE; 355 Vec coordinates; 356 PetscSection coordSection; 357 PetscScalar *coords; 358 PetscInt coordSize; 359 PetscMPIInt rank; 360 PetscInt cdim = 1, v; 361 362 PetscFunctionBegin; 363 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL)); 364 if (markerSeparate) { 365 markerRight = 2; 366 markerLeft = 1; 367 } 368 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 369 if (rank == 0) { 370 PetscCall(DMPlexSetChart(dm, 0, numVertices)); 371 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 372 PetscCall(DMSetLabelValue(dm, "marker", 0, markerLeft)); 373 PetscCall(DMSetLabelValue(dm, "marker", 1, markerRight)); 374 } 375 PetscCall(DMPlexSymmetrize(dm)); 376 PetscCall(DMPlexStratify(dm)); 377 /* Build coordinates */ 378 PetscCall(DMSetCoordinateDim(dm, cdim)); 379 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 380 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 381 PetscCall(PetscSectionSetChart(coordSection, 0, numVertices)); 382 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, cdim)); 383 for (v = 0; v < numVertices; ++v) { 384 PetscCall(PetscSectionSetDof(coordSection, v, cdim)); 385 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, cdim)); 386 } 387 PetscCall(PetscSectionSetUp(coordSection)); 388 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 389 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 390 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 391 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 392 PetscCall(VecSetBlockSize(coordinates, cdim)); 393 PetscCall(VecSetType(coordinates, VECSTANDARD)); 394 PetscCall(VecGetArray(coordinates, &coords)); 395 coords[0] = lower[0]; 396 coords[1] = upper[0]; 397 PetscCall(VecRestoreArray(coordinates, &coords)); 398 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 399 PetscCall(VecDestroy(&coordinates)); 400 PetscFunctionReturn(PETSC_SUCCESS); 401 } 402 403 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 404 { 405 const PetscInt numVertices = (edges[0] + 1) * (edges[1] + 1); 406 const PetscInt numEdges = edges[0] * (edges[1] + 1) + (edges[0] + 1) * edges[1]; 407 PetscInt markerTop = 1; 408 PetscInt markerBottom = 1; 409 PetscInt markerRight = 1; 410 PetscInt markerLeft = 1; 411 PetscBool markerSeparate = PETSC_FALSE; 412 Vec coordinates; 413 PetscSection coordSection; 414 PetscScalar *coords; 415 PetscInt coordSize; 416 PetscMPIInt rank; 417 PetscInt v, vx, vy; 418 419 PetscFunctionBegin; 420 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL)); 421 if (markerSeparate) { 422 markerTop = 3; 423 markerBottom = 1; 424 markerRight = 2; 425 markerLeft = 4; 426 } 427 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 428 if (rank == 0) { 429 PetscInt e, ex, ey; 430 431 PetscCall(DMPlexSetChart(dm, 0, numEdges + numVertices)); 432 for (e = 0; e < numEdges; ++e) PetscCall(DMPlexSetConeSize(dm, e, 2)); 433 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 434 for (vx = 0; vx <= edges[0]; vx++) { 435 for (ey = 0; ey < edges[1]; ey++) { 436 PetscInt edge = vx * edges[1] + ey + edges[0] * (edges[1] + 1); 437 PetscInt vertex = ey * (edges[0] + 1) + vx + numEdges; 438 PetscInt cone[2]; 439 440 cone[0] = vertex; 441 cone[1] = vertex + edges[0] + 1; 442 PetscCall(DMPlexSetCone(dm, edge, cone)); 443 if (vx == edges[0]) { 444 PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight)); 445 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight)); 446 if (ey == edges[1] - 1) { 447 PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight)); 448 PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerRight)); 449 } 450 } else if (vx == 0) { 451 PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft)); 452 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft)); 453 if (ey == edges[1] - 1) { 454 PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft)); 455 PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft)); 456 } 457 } 458 } 459 } 460 for (vy = 0; vy <= edges[1]; vy++) { 461 for (ex = 0; ex < edges[0]; ex++) { 462 PetscInt edge = vy * edges[0] + ex; 463 PetscInt vertex = vy * (edges[0] + 1) + ex + numEdges; 464 PetscInt cone[2]; 465 466 cone[0] = vertex; 467 cone[1] = vertex + 1; 468 PetscCall(DMPlexSetCone(dm, edge, cone)); 469 if (vy == edges[1]) { 470 PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop)); 471 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop)); 472 if (ex == edges[0] - 1) { 473 PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop)); 474 PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerTop)); 475 } 476 } else if (vy == 0) { 477 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom)); 478 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom)); 479 if (ex == edges[0] - 1) { 480 PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom)); 481 PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom)); 482 } 483 } 484 } 485 } 486 } 487 PetscCall(DMPlexSymmetrize(dm)); 488 PetscCall(DMPlexStratify(dm)); 489 /* Build coordinates */ 490 PetscCall(DMSetCoordinateDim(dm, 2)); 491 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 492 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 493 PetscCall(PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices)); 494 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, 2)); 495 for (v = numEdges; v < numEdges + numVertices; ++v) { 496 PetscCall(PetscSectionSetDof(coordSection, v, 2)); 497 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, 2)); 498 } 499 PetscCall(PetscSectionSetUp(coordSection)); 500 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 501 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 502 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 503 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 504 PetscCall(VecSetBlockSize(coordinates, 2)); 505 PetscCall(VecSetType(coordinates, VECSTANDARD)); 506 PetscCall(VecGetArray(coordinates, &coords)); 507 for (vy = 0; vy <= edges[1]; ++vy) { 508 for (vx = 0; vx <= edges[0]; ++vx) { 509 coords[(vy * (edges[0] + 1) + vx) * 2 + 0] = lower[0] + ((upper[0] - lower[0]) / edges[0]) * vx; 510 coords[(vy * (edges[0] + 1) + vx) * 2 + 1] = lower[1] + ((upper[1] - lower[1]) / edges[1]) * vy; 511 } 512 } 513 PetscCall(VecRestoreArray(coordinates, &coords)); 514 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 515 PetscCall(VecDestroy(&coordinates)); 516 PetscFunctionReturn(PETSC_SUCCESS); 517 } 518 519 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) 520 { 521 PetscInt vertices[3], numVertices; 522 PetscInt numFaces = 2 * faces[0] * faces[1] + 2 * faces[1] * faces[2] + 2 * faces[0] * faces[2]; 523 PetscInt markerTop = 1; 524 PetscInt markerBottom = 1; 525 PetscInt markerFront = 1; 526 PetscInt markerBack = 1; 527 PetscInt markerRight = 1; 528 PetscInt markerLeft = 1; 529 PetscBool markerSeparate = PETSC_FALSE; 530 Vec coordinates; 531 PetscSection coordSection; 532 PetscScalar *coords; 533 PetscInt coordSize; 534 PetscMPIInt rank; 535 PetscInt v, vx, vy, vz; 536 PetscInt voffset, iface = 0, cone[4]; 537 538 PetscFunctionBegin; 539 PetscCheck(faces[0] >= 1 && faces[1] >= 1 && faces[2] >= 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Must have at least 1 face per side"); 540 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 541 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL)); 542 if (markerSeparate) { 543 markerBottom = 1; 544 markerTop = 2; 545 markerFront = 3; 546 markerBack = 4; 547 markerRight = 5; 548 markerLeft = 6; 549 } 550 vertices[0] = faces[0] + 1; 551 vertices[1] = faces[1] + 1; 552 vertices[2] = faces[2] + 1; 553 numVertices = vertices[0] * vertices[1] * vertices[2]; 554 if (rank == 0) { 555 PetscInt f; 556 557 PetscCall(DMPlexSetChart(dm, 0, numFaces + numVertices)); 558 for (f = 0; f < numFaces; ++f) PetscCall(DMPlexSetConeSize(dm, f, 4)); 559 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 560 561 /* Side 0 (Top) */ 562 for (vy = 0; vy < faces[1]; vy++) { 563 for (vx = 0; vx < faces[0]; vx++) { 564 voffset = numFaces + vertices[0] * vertices[1] * (vertices[2] - 1) + vy * vertices[0] + vx; 565 cone[0] = voffset; 566 cone[1] = voffset + 1; 567 cone[2] = voffset + vertices[0] + 1; 568 cone[3] = voffset + vertices[0]; 569 PetscCall(DMPlexSetCone(dm, iface, cone)); 570 PetscCall(DMSetLabelValue(dm, "marker", iface, markerTop)); 571 PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerTop)); 572 PetscCall(DMSetLabelValue(dm, "marker", voffset + 1, markerTop)); 573 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 0, markerTop)); 574 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 1, markerTop)); 575 iface++; 576 } 577 } 578 579 /* Side 1 (Bottom) */ 580 for (vy = 0; vy < faces[1]; vy++) { 581 for (vx = 0; vx < faces[0]; vx++) { 582 voffset = numFaces + vy * (faces[0] + 1) + vx; 583 cone[0] = voffset + 1; 584 cone[1] = voffset; 585 cone[2] = voffset + vertices[0]; 586 cone[3] = voffset + vertices[0] + 1; 587 PetscCall(DMPlexSetCone(dm, iface, cone)); 588 PetscCall(DMSetLabelValue(dm, "marker", iface, markerBottom)); 589 PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerBottom)); 590 PetscCall(DMSetLabelValue(dm, "marker", voffset + 1, markerBottom)); 591 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 0, markerBottom)); 592 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 1, markerBottom)); 593 iface++; 594 } 595 } 596 597 /* Side 2 (Front) */ 598 for (vz = 0; vz < faces[2]; vz++) { 599 for (vx = 0; vx < faces[0]; vx++) { 600 voffset = numFaces + vz * vertices[0] * vertices[1] + vx; 601 cone[0] = voffset; 602 cone[1] = voffset + 1; 603 cone[2] = voffset + vertices[0] * vertices[1] + 1; 604 cone[3] = voffset + vertices[0] * vertices[1]; 605 PetscCall(DMPlexSetCone(dm, iface, cone)); 606 PetscCall(DMSetLabelValue(dm, "marker", iface, markerFront)); 607 PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerFront)); 608 PetscCall(DMSetLabelValue(dm, "marker", voffset + 1, markerFront)); 609 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 0, markerFront)); 610 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 1, markerFront)); 611 iface++; 612 } 613 } 614 615 /* Side 3 (Back) */ 616 for (vz = 0; vz < faces[2]; vz++) { 617 for (vx = 0; vx < faces[0]; vx++) { 618 voffset = numFaces + vz * vertices[0] * vertices[1] + vertices[0] * (vertices[1] - 1) + vx; 619 cone[0] = voffset + vertices[0] * vertices[1]; 620 cone[1] = voffset + vertices[0] * vertices[1] + 1; 621 cone[2] = voffset + 1; 622 cone[3] = voffset; 623 PetscCall(DMPlexSetCone(dm, iface, cone)); 624 PetscCall(DMSetLabelValue(dm, "marker", iface, markerBack)); 625 PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerBack)); 626 PetscCall(DMSetLabelValue(dm, "marker", voffset + 1, markerBack)); 627 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 0, markerBack)); 628 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 1, markerBack)); 629 iface++; 630 } 631 } 632 633 /* Side 4 (Left) */ 634 for (vz = 0; vz < faces[2]; vz++) { 635 for (vy = 0; vy < faces[1]; vy++) { 636 voffset = numFaces + vz * vertices[0] * vertices[1] + vy * vertices[0]; 637 cone[0] = voffset; 638 cone[1] = voffset + vertices[0] * vertices[1]; 639 cone[2] = voffset + vertices[0] * vertices[1] + vertices[0]; 640 cone[3] = voffset + vertices[0]; 641 PetscCall(DMPlexSetCone(dm, iface, cone)); 642 PetscCall(DMSetLabelValue(dm, "marker", iface, markerLeft)); 643 PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerLeft)); 644 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 0, markerLeft)); 645 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[1] + 0, markerLeft)); 646 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + vertices[0], markerLeft)); 647 iface++; 648 } 649 } 650 651 /* Side 5 (Right) */ 652 for (vz = 0; vz < faces[2]; vz++) { 653 for (vy = 0; vy < faces[1]; vy++) { 654 voffset = numFaces + vz * vertices[0] * vertices[1] + vy * vertices[0] + faces[0]; 655 cone[0] = voffset + vertices[0] * vertices[1]; 656 cone[1] = voffset; 657 cone[2] = voffset + vertices[0]; 658 cone[3] = voffset + vertices[0] * vertices[1] + vertices[0]; 659 PetscCall(DMPlexSetCone(dm, iface, cone)); 660 PetscCall(DMSetLabelValue(dm, "marker", iface, markerRight)); 661 PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerRight)); 662 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 0, markerRight)); 663 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 0, markerRight)); 664 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + vertices[0], markerRight)); 665 iface++; 666 } 667 } 668 } 669 PetscCall(DMPlexSymmetrize(dm)); 670 PetscCall(DMPlexStratify(dm)); 671 /* Build coordinates */ 672 PetscCall(DMSetCoordinateDim(dm, 3)); 673 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 674 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 675 PetscCall(PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices)); 676 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, 3)); 677 for (v = numFaces; v < numFaces + numVertices; ++v) { 678 PetscCall(PetscSectionSetDof(coordSection, v, 3)); 679 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, 3)); 680 } 681 PetscCall(PetscSectionSetUp(coordSection)); 682 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 683 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 684 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 685 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 686 PetscCall(VecSetBlockSize(coordinates, 3)); 687 PetscCall(VecSetType(coordinates, VECSTANDARD)); 688 PetscCall(VecGetArray(coordinates, &coords)); 689 for (vz = 0; vz <= faces[2]; ++vz) { 690 for (vy = 0; vy <= faces[1]; ++vy) { 691 for (vx = 0; vx <= faces[0]; ++vx) { 692 coords[((vz * (faces[1] + 1) + vy) * (faces[0] + 1) + vx) * 3 + 0] = lower[0] + ((upper[0] - lower[0]) / faces[0]) * vx; 693 coords[((vz * (faces[1] + 1) + vy) * (faces[0] + 1) + vx) * 3 + 1] = lower[1] + ((upper[1] - lower[1]) / faces[1]) * vy; 694 coords[((vz * (faces[1] + 1) + vy) * (faces[0] + 1) + vx) * 3 + 2] = lower[2] + ((upper[2] - lower[2]) / faces[2]) * vz; 695 } 696 } 697 } 698 PetscCall(VecRestoreArray(coordinates, &coords)); 699 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 700 PetscCall(VecDestroy(&coordinates)); 701 PetscFunctionReturn(PETSC_SUCCESS); 702 } 703 704 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate) 705 { 706 PetscFunctionBegin; 707 PetscValidLogicalCollectiveInt(dm, dim, 2); 708 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 709 PetscCall(DMSetDimension(dm, dim - 1)); 710 PetscCall(DMSetCoordinateDim(dm, dim)); 711 switch (dim) { 712 case 1: 713 PetscCall(DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(dm, lower, upper, faces)); 714 break; 715 case 2: 716 PetscCall(DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(dm, lower, upper, faces)); 717 break; 718 case 3: 719 PetscCall(DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(dm, lower, upper, faces)); 720 break; 721 default: 722 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Dimension not supported: %" PetscInt_FMT, dim); 723 } 724 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 725 if (interpolate) PetscCall(DMPlexInterpolateInPlace_Internal(dm)); 726 PetscFunctionReturn(PETSC_SUCCESS); 727 } 728 729 /*@C 730 DMPlexCreateBoxSurfaceMesh - Creates a mesh on the surface of the tensor product of unit intervals (box) using tensor cells (hexahedra). 731 732 Collective 733 734 Input Parameters: 735 + comm - The communicator for the `DM` object 736 . dim - The spatial dimension of the box, so the resulting mesh is has dimension `dim`-1 737 . faces - Number of faces per dimension, or `NULL` for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 738 . lower - The lower left corner, or `NULL` for (0, 0, 0) 739 . upper - The upper right corner, or `NULL` for (1, 1, 1) 740 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 741 742 Output Parameter: 743 . dm - The `DM` object 744 745 Level: beginner 746 747 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMSetFromOptions()`, `DMPlexCreateBoxMesh()`, `DMPlexCreateFromFile()`, `DMSetType()`, `DMCreate()` 748 @*/ 749 PetscErrorCode DMPlexCreateBoxSurfaceMesh(MPI_Comm comm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate, DM *dm) 750 { 751 PetscInt fac[3] = {1, 1, 1}; 752 PetscReal low[3] = {0, 0, 0}; 753 PetscReal upp[3] = {1, 1, 1}; 754 755 PetscFunctionBegin; 756 PetscCall(DMCreate(comm, dm)); 757 PetscCall(DMSetType(*dm, DMPLEX)); 758 PetscCall(DMPlexCreateBoxSurfaceMesh_Internal(*dm, dim, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, interpolate)); 759 PetscFunctionReturn(PETSC_SUCCESS); 760 } 761 762 static PetscErrorCode DMPlexCreateLineMesh_Internal(DM dm, PetscInt segments, PetscReal lower, PetscReal upper, DMBoundaryType bd) 763 { 764 PetscInt i, fStart, fEnd, numCells = 0, numVerts = 0; 765 PetscInt numPoints[2], *coneSize, *cones, *coneOrientations; 766 PetscScalar *vertexCoords; 767 PetscReal L, maxCell; 768 PetscBool markerSeparate = PETSC_FALSE; 769 PetscInt markerLeft = 1, faceMarkerLeft = 1; 770 PetscInt markerRight = 1, faceMarkerRight = 2; 771 PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE; 772 PetscMPIInt rank; 773 774 PetscFunctionBegin; 775 PetscAssertPointer(dm, 1); 776 777 PetscCall(DMSetDimension(dm, 1)); 778 PetscCall(DMCreateLabel(dm, "marker")); 779 PetscCall(DMCreateLabel(dm, "Face Sets")); 780 781 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 782 if (rank == 0) numCells = segments; 783 if (rank == 0) numVerts = segments + (wrap ? 0 : 1); 784 785 numPoints[0] = numVerts; 786 numPoints[1] = numCells; 787 PetscCall(PetscMalloc4(numCells + numVerts, &coneSize, numCells * 2, &cones, numCells + numVerts, &coneOrientations, numVerts, &vertexCoords)); 788 PetscCall(PetscArrayzero(coneOrientations, numCells + numVerts)); 789 for (i = 0; i < numCells; ++i) coneSize[i] = 2; 790 for (i = 0; i < numVerts; ++i) coneSize[numCells + i] = 0; 791 for (i = 0; i < numCells; ++i) { 792 cones[2 * i] = numCells + i % numVerts; 793 cones[2 * i + 1] = numCells + (i + 1) % numVerts; 794 } 795 for (i = 0; i < numVerts; ++i) vertexCoords[i] = lower + (upper - lower) * ((PetscReal)i / (PetscReal)numCells); 796 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 797 PetscCall(PetscFree4(coneSize, cones, coneOrientations, vertexCoords)); 798 799 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL)); 800 if (markerSeparate) { 801 markerLeft = faceMarkerLeft; 802 markerRight = faceMarkerRight; 803 } 804 if (!wrap && rank == 0) { 805 PetscCall(DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd)); 806 PetscCall(DMSetLabelValue(dm, "marker", fStart, markerLeft)); 807 PetscCall(DMSetLabelValue(dm, "marker", fEnd - 1, markerRight)); 808 PetscCall(DMSetLabelValue(dm, "Face Sets", fStart, faceMarkerLeft)); 809 PetscCall(DMSetLabelValue(dm, "Face Sets", fEnd - 1, faceMarkerRight)); 810 } 811 if (wrap) { 812 L = upper - lower; 813 maxCell = (PetscReal)1.1 * (L / (PetscReal)PetscMax(1, segments)); 814 PetscCall(DMSetPeriodicity(dm, &maxCell, &lower, &L)); 815 } 816 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 817 PetscFunctionReturn(PETSC_SUCCESS); 818 } 819 820 static PetscErrorCode DMPlexCreateBoxMesh_Simplex_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate) 821 { 822 DM boundary, vol; 823 DMLabel bdlabel; 824 825 PetscFunctionBegin; 826 PetscAssertPointer(dm, 1); 827 for (PetscInt i = 0; i < dim; ++i) PetscCheck(periodicity[i] == DM_BOUNDARY_NONE, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Periodicity is not supported for simplex meshes"); 828 PetscCall(DMCreate(PetscObjectComm((PetscObject)dm), &boundary)); 829 PetscCall(DMSetType(boundary, DMPLEX)); 830 PetscCall(DMPlexCreateBoxSurfaceMesh_Internal(boundary, dim, faces, lower, upper, PETSC_FALSE)); 831 PetscCall(DMPlexGenerate(boundary, NULL, interpolate, &vol)); 832 PetscCall(DMGetLabel(vol, "marker", &bdlabel)); 833 if (bdlabel) PetscCall(DMPlexLabelComplete(vol, bdlabel)); 834 PetscCall(DMPlexCopy_Internal(dm, PETSC_TRUE, PETSC_FALSE, vol)); 835 PetscCall(DMPlexReplace_Internal(dm, &vol)); 836 PetscCall(DMDestroy(&boundary)); 837 PetscFunctionReturn(PETSC_SUCCESS); 838 } 839 840 static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ) 841 { 842 DMLabel cutLabel = NULL; 843 PetscInt markerTop = 1, faceMarkerTop = 1; 844 PetscInt markerBottom = 1, faceMarkerBottom = 1; 845 PetscInt markerFront = 1, faceMarkerFront = 1; 846 PetscInt markerBack = 1, faceMarkerBack = 1; 847 PetscInt markerRight = 1, faceMarkerRight = 1; 848 PetscInt markerLeft = 1, faceMarkerLeft = 1; 849 PetscInt dim; 850 PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE; 851 PetscMPIInt rank; 852 853 PetscFunctionBegin; 854 PetscCall(DMGetDimension(dm, &dim)); 855 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 856 PetscCall(DMCreateLabel(dm, "marker")); 857 PetscCall(DMCreateLabel(dm, "Face Sets")); 858 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL)); 859 if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST || bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST || bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) { 860 if (cutMarker) { 861 PetscCall(DMCreateLabel(dm, "periodic_cut")); 862 PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel)); 863 } 864 } 865 switch (dim) { 866 case 2: 867 faceMarkerTop = 3; 868 faceMarkerBottom = 1; 869 faceMarkerRight = 2; 870 faceMarkerLeft = 4; 871 break; 872 case 3: 873 faceMarkerBottom = 1; 874 faceMarkerTop = 2; 875 faceMarkerFront = 3; 876 faceMarkerBack = 4; 877 faceMarkerRight = 5; 878 faceMarkerLeft = 6; 879 break; 880 default: 881 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Dimension %" PetscInt_FMT " not supported", dim); 882 } 883 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL)); 884 if (markerSeparate) { 885 markerBottom = faceMarkerBottom; 886 markerTop = faceMarkerTop; 887 markerFront = faceMarkerFront; 888 markerBack = faceMarkerBack; 889 markerRight = faceMarkerRight; 890 markerLeft = faceMarkerLeft; 891 } 892 { 893 const PetscInt numXEdges = rank == 0 ? edges[0] : 0; 894 const PetscInt numYEdges = rank == 0 ? edges[1] : 0; 895 const PetscInt numZEdges = rank == 0 ? edges[2] : 0; 896 const PetscInt numXVertices = rank == 0 ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0] + 1) : 0; 897 const PetscInt numYVertices = rank == 0 ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1] + 1) : 0; 898 const PetscInt numZVertices = rank == 0 ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2] + 1) : 0; 899 const PetscInt numCells = numXEdges * numYEdges * numZEdges; 900 const PetscInt numXFaces = numYEdges * numZEdges; 901 const PetscInt numYFaces = numXEdges * numZEdges; 902 const PetscInt numZFaces = numXEdges * numYEdges; 903 const PetscInt numTotXFaces = numXVertices * numXFaces; 904 const PetscInt numTotYFaces = numYVertices * numYFaces; 905 const PetscInt numTotZFaces = numZVertices * numZFaces; 906 const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces; 907 const PetscInt numTotXEdges = numXEdges * numYVertices * numZVertices; 908 const PetscInt numTotYEdges = numYEdges * numXVertices * numZVertices; 909 const PetscInt numTotZEdges = numZEdges * numXVertices * numYVertices; 910 const PetscInt numVertices = numXVertices * numYVertices * numZVertices; 911 const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges; 912 const PetscInt firstVertex = (dim == 2) ? numFaces : numCells; 913 const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices; 914 const PetscInt firstYFace = firstXFace + numTotXFaces; 915 const PetscInt firstZFace = firstYFace + numTotYFaces; 916 const PetscInt firstXEdge = numCells + numFaces + numVertices; 917 const PetscInt firstYEdge = firstXEdge + numTotXEdges; 918 const PetscInt firstZEdge = firstYEdge + numTotYEdges; 919 Vec coordinates; 920 PetscSection coordSection; 921 PetscScalar *coords; 922 PetscInt coordSize; 923 PetscInt v, vx, vy, vz; 924 PetscInt c, f, fx, fy, fz, e, ex, ey, ez; 925 926 PetscCall(DMPlexSetChart(dm, 0, numCells + numFaces + numEdges + numVertices)); 927 for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 6)); 928 for (f = firstXFace; f < firstXFace + numFaces; ++f) PetscCall(DMPlexSetConeSize(dm, f, 4)); 929 for (e = firstXEdge; e < firstXEdge + numEdges; ++e) PetscCall(DMPlexSetConeSize(dm, e, 2)); 930 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 931 /* Build cells */ 932 for (fz = 0; fz < numZEdges; ++fz) { 933 for (fy = 0; fy < numYEdges; ++fy) { 934 for (fx = 0; fx < numXEdges; ++fx) { 935 PetscInt cell = (fz * numYEdges + fy) * numXEdges + fx; 936 PetscInt faceB = firstZFace + (fy * numXEdges + fx) * numZVertices + fz; 937 PetscInt faceT = firstZFace + (fy * numXEdges + fx) * numZVertices + ((fz + 1) % numZVertices); 938 PetscInt faceF = firstYFace + (fz * numXEdges + fx) * numYVertices + fy; 939 PetscInt faceK = firstYFace + (fz * numXEdges + fx) * numYVertices + ((fy + 1) % numYVertices); 940 PetscInt faceL = firstXFace + (fz * numYEdges + fy) * numXVertices + fx; 941 PetscInt faceR = firstXFace + (fz * numYEdges + fy) * numXVertices + ((fx + 1) % numXVertices); 942 /* B, T, F, K, R, L */ 943 PetscInt ornt[6] = {-2, 0, 0, -3, 0, -2}; /* ??? */ 944 PetscInt cone[6]; 945 946 /* no boundary twisting in 3D */ 947 cone[0] = faceB; 948 cone[1] = faceT; 949 cone[2] = faceF; 950 cone[3] = faceK; 951 cone[4] = faceR; 952 cone[5] = faceL; 953 PetscCall(DMPlexSetCone(dm, cell, cone)); 954 PetscCall(DMPlexSetConeOrientation(dm, cell, ornt)); 955 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, cell, 2)); 956 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, cell, 2)); 957 if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, cell, 2)); 958 } 959 } 960 } 961 /* Build x faces */ 962 for (fz = 0; fz < numZEdges; ++fz) { 963 for (fy = 0; fy < numYEdges; ++fy) { 964 for (fx = 0; fx < numXVertices; ++fx) { 965 PetscInt face = firstXFace + (fz * numYEdges + fy) * numXVertices + fx; 966 PetscInt edgeL = firstZEdge + (fy * numXVertices + fx) * numZEdges + fz; 967 PetscInt edgeR = firstZEdge + (((fy + 1) % numYVertices) * numXVertices + fx) * numZEdges + fz; 968 PetscInt edgeB = firstYEdge + (fz * numXVertices + fx) * numYEdges + fy; 969 PetscInt edgeT = firstYEdge + (((fz + 1) % numZVertices) * numXVertices + fx) * numYEdges + fy; 970 PetscInt ornt[4] = {0, 0, -1, -1}; 971 PetscInt cone[4]; 972 973 if (dim == 3) { 974 /* markers */ 975 if (bdX != DM_BOUNDARY_PERIODIC) { 976 if (fx == numXVertices - 1) { 977 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight)); 978 PetscCall(DMSetLabelValue(dm, "marker", face, markerRight)); 979 } else if (fx == 0) { 980 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft)); 981 PetscCall(DMSetLabelValue(dm, "marker", face, markerLeft)); 982 } 983 } 984 } 985 cone[0] = edgeB; 986 cone[1] = edgeR; 987 cone[2] = edgeT; 988 cone[3] = edgeL; 989 PetscCall(DMPlexSetCone(dm, face, cone)); 990 PetscCall(DMPlexSetConeOrientation(dm, face, ornt)); 991 } 992 } 993 } 994 /* Build y faces */ 995 for (fz = 0; fz < numZEdges; ++fz) { 996 for (fx = 0; fx < numXEdges; ++fx) { 997 for (fy = 0; fy < numYVertices; ++fy) { 998 PetscInt face = firstYFace + (fz * numXEdges + fx) * numYVertices + fy; 999 PetscInt edgeL = firstZEdge + (fy * numXVertices + fx) * numZEdges + fz; 1000 PetscInt edgeR = firstZEdge + (fy * numXVertices + ((fx + 1) % numXVertices)) * numZEdges + fz; 1001 PetscInt edgeB = firstXEdge + (fz * numYVertices + fy) * numXEdges + fx; 1002 PetscInt edgeT = firstXEdge + (((fz + 1) % numZVertices) * numYVertices + fy) * numXEdges + fx; 1003 PetscInt ornt[4] = {0, 0, -1, -1}; 1004 PetscInt cone[4]; 1005 1006 if (dim == 3) { 1007 /* markers */ 1008 if (bdY != DM_BOUNDARY_PERIODIC) { 1009 if (fy == numYVertices - 1) { 1010 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack)); 1011 PetscCall(DMSetLabelValue(dm, "marker", face, markerBack)); 1012 } else if (fy == 0) { 1013 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront)); 1014 PetscCall(DMSetLabelValue(dm, "marker", face, markerFront)); 1015 } 1016 } 1017 } 1018 cone[0] = edgeB; 1019 cone[1] = edgeR; 1020 cone[2] = edgeT; 1021 cone[3] = edgeL; 1022 PetscCall(DMPlexSetCone(dm, face, cone)); 1023 PetscCall(DMPlexSetConeOrientation(dm, face, ornt)); 1024 } 1025 } 1026 } 1027 /* Build z faces */ 1028 for (fy = 0; fy < numYEdges; ++fy) { 1029 for (fx = 0; fx < numXEdges; ++fx) { 1030 for (fz = 0; fz < numZVertices; fz++) { 1031 PetscInt face = firstZFace + (fy * numXEdges + fx) * numZVertices + fz; 1032 PetscInt edgeL = firstYEdge + (fz * numXVertices + fx) * numYEdges + fy; 1033 PetscInt edgeR = firstYEdge + (fz * numXVertices + ((fx + 1) % numXVertices)) * numYEdges + fy; 1034 PetscInt edgeB = firstXEdge + (fz * numYVertices + fy) * numXEdges + fx; 1035 PetscInt edgeT = firstXEdge + (fz * numYVertices + ((fy + 1) % numYVertices)) * numXEdges + fx; 1036 PetscInt ornt[4] = {0, 0, -1, -1}; 1037 PetscInt cone[4]; 1038 1039 if (dim == 2) { 1040 if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges - 1) { 1041 edgeR += numYEdges - 1 - 2 * fy; 1042 ornt[1] = -1; 1043 } 1044 if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges - 1) { 1045 edgeT += numXEdges - 1 - 2 * fx; 1046 ornt[2] = 0; 1047 } 1048 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, face, 2)); 1049 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, face, 2)); 1050 } else { 1051 /* markers */ 1052 if (bdZ != DM_BOUNDARY_PERIODIC) { 1053 if (fz == numZVertices - 1) { 1054 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop)); 1055 PetscCall(DMSetLabelValue(dm, "marker", face, markerTop)); 1056 } else if (fz == 0) { 1057 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom)); 1058 PetscCall(DMSetLabelValue(dm, "marker", face, markerBottom)); 1059 } 1060 } 1061 } 1062 cone[0] = edgeB; 1063 cone[1] = edgeR; 1064 cone[2] = edgeT; 1065 cone[3] = edgeL; 1066 PetscCall(DMPlexSetCone(dm, face, cone)); 1067 PetscCall(DMPlexSetConeOrientation(dm, face, ornt)); 1068 } 1069 } 1070 } 1071 /* Build Z edges*/ 1072 for (vy = 0; vy < numYVertices; vy++) { 1073 for (vx = 0; vx < numXVertices; vx++) { 1074 for (ez = 0; ez < numZEdges; ez++) { 1075 const PetscInt edge = firstZEdge + (vy * numXVertices + vx) * numZEdges + ez; 1076 const PetscInt vertexB = firstVertex + (ez * numYVertices + vy) * numXVertices + vx; 1077 const PetscInt vertexT = firstVertex + (((ez + 1) % numZVertices) * numYVertices + vy) * numXVertices + vx; 1078 PetscInt cone[2]; 1079 1080 cone[0] = vertexB; 1081 cone[1] = vertexT; 1082 PetscCall(DMPlexSetCone(dm, edge, cone)); 1083 if (dim == 3) { 1084 if (bdX != DM_BOUNDARY_PERIODIC) { 1085 if (vx == numXVertices - 1) { 1086 PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight)); 1087 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight)); 1088 if (ez == numZEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight)); 1089 } else if (vx == 0) { 1090 PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft)); 1091 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft)); 1092 if (ez == numZEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft)); 1093 } 1094 } 1095 if (bdY != DM_BOUNDARY_PERIODIC) { 1096 if (vy == numYVertices - 1) { 1097 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBack)); 1098 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBack)); 1099 if (ez == numZEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBack)); 1100 } else if (vy == 0) { 1101 PetscCall(DMSetLabelValue(dm, "marker", edge, markerFront)); 1102 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerFront)); 1103 if (ez == numZEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerFront)); 1104 } 1105 } 1106 } 1107 } 1108 } 1109 } 1110 /* Build Y edges*/ 1111 for (vz = 0; vz < numZVertices; vz++) { 1112 for (vx = 0; vx < numXVertices; vx++) { 1113 for (ey = 0; ey < numYEdges; ey++) { 1114 const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges - 1) ? (numXVertices - vx - 1) : (vz * numYVertices + ((ey + 1) % numYVertices)) * numXVertices + vx; 1115 const PetscInt edge = firstYEdge + (vz * numXVertices + vx) * numYEdges + ey; 1116 const PetscInt vertexF = firstVertex + (vz * numYVertices + ey) * numXVertices + vx; 1117 const PetscInt vertexK = firstVertex + nextv; 1118 PetscInt cone[2]; 1119 1120 cone[0] = vertexF; 1121 cone[1] = vertexK; 1122 PetscCall(DMPlexSetCone(dm, edge, cone)); 1123 if (dim == 2) { 1124 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 1125 if (vx == numXVertices - 1) { 1126 PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight)); 1127 PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight)); 1128 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight)); 1129 if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight)); 1130 } else if (vx == 0) { 1131 PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft)); 1132 PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft)); 1133 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft)); 1134 if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft)); 1135 } 1136 } else { 1137 if (vx == 0 && cutLabel) { 1138 PetscCall(DMLabelSetValue(cutLabel, edge, 1)); 1139 PetscCall(DMLabelSetValue(cutLabel, cone[0], 1)); 1140 if (ey == numYEdges - 1) PetscCall(DMLabelSetValue(cutLabel, cone[1], 1)); 1141 } 1142 } 1143 } else { 1144 if (bdX != DM_BOUNDARY_PERIODIC) { 1145 if (vx == numXVertices - 1) { 1146 PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight)); 1147 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight)); 1148 if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight)); 1149 } else if (vx == 0) { 1150 PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft)); 1151 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft)); 1152 if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft)); 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 (ey == numYEdges - 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 (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom)); 1164 } 1165 } 1166 } 1167 } 1168 } 1169 } 1170 /* Build X edges*/ 1171 for (vz = 0; vz < numZVertices; vz++) { 1172 for (vy = 0; vy < numYVertices; vy++) { 1173 for (ex = 0; ex < numXEdges; ex++) { 1174 const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges - 1) ? (numYVertices - vy - 1) * numXVertices : (vz * numYVertices + vy) * numXVertices + (ex + 1) % numXVertices; 1175 const PetscInt edge = firstXEdge + (vz * numYVertices + vy) * numXEdges + ex; 1176 const PetscInt vertexL = firstVertex + (vz * numYVertices + vy) * numXVertices + ex; 1177 const PetscInt vertexR = firstVertex + nextv; 1178 PetscInt cone[2]; 1179 1180 cone[0] = vertexL; 1181 cone[1] = vertexR; 1182 PetscCall(DMPlexSetCone(dm, edge, cone)); 1183 if (dim == 2) { 1184 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 1185 if (vy == numYVertices - 1) { 1186 PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop)); 1187 PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop)); 1188 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop)); 1189 if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop)); 1190 } else if (vy == 0) { 1191 PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom)); 1192 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom)); 1193 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom)); 1194 if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom)); 1195 } 1196 } else { 1197 if (vy == 0 && cutLabel) { 1198 PetscCall(DMLabelSetValue(cutLabel, edge, 1)); 1199 PetscCall(DMLabelSetValue(cutLabel, cone[0], 1)); 1200 if (ex == numXEdges - 1) PetscCall(DMLabelSetValue(cutLabel, cone[1], 1)); 1201 } 1202 } 1203 } else { 1204 if (bdY != DM_BOUNDARY_PERIODIC) { 1205 if (vy == numYVertices - 1) { 1206 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBack)); 1207 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBack)); 1208 if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBack)); 1209 } else if (vy == 0) { 1210 PetscCall(DMSetLabelValue(dm, "marker", edge, markerFront)); 1211 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerFront)); 1212 if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerFront)); 1213 } 1214 } 1215 if (bdZ != DM_BOUNDARY_PERIODIC) { 1216 if (vz == numZVertices - 1) { 1217 PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop)); 1218 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop)); 1219 if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop)); 1220 } else if (vz == 0) { 1221 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom)); 1222 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom)); 1223 if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom)); 1224 } 1225 } 1226 } 1227 } 1228 } 1229 } 1230 PetscCall(DMPlexSymmetrize(dm)); 1231 PetscCall(DMPlexStratify(dm)); 1232 /* Build coordinates */ 1233 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 1234 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 1235 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim)); 1236 PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex + numVertices)); 1237 for (v = firstVertex; v < firstVertex + numVertices; ++v) { 1238 PetscCall(PetscSectionSetDof(coordSection, v, dim)); 1239 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim)); 1240 } 1241 PetscCall(PetscSectionSetUp(coordSection)); 1242 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 1243 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 1244 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 1245 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 1246 PetscCall(VecSetBlockSize(coordinates, dim)); 1247 PetscCall(VecSetType(coordinates, VECSTANDARD)); 1248 PetscCall(VecGetArray(coordinates, &coords)); 1249 for (vz = 0; vz < numZVertices; ++vz) { 1250 for (vy = 0; vy < numYVertices; ++vy) { 1251 for (vx = 0; vx < numXVertices; ++vx) { 1252 coords[((vz * numYVertices + vy) * numXVertices + vx) * dim + 0] = lower[0] + ((upper[0] - lower[0]) / numXEdges) * vx; 1253 coords[((vz * numYVertices + vy) * numXVertices + vx) * dim + 1] = lower[1] + ((upper[1] - lower[1]) / numYEdges) * vy; 1254 if (dim == 3) coords[((vz * numYVertices + vy) * numXVertices + vx) * dim + 2] = lower[2] + ((upper[2] - lower[2]) / numZEdges) * vz; 1255 } 1256 } 1257 } 1258 PetscCall(VecRestoreArray(coordinates, &coords)); 1259 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 1260 PetscCall(VecDestroy(&coordinates)); 1261 } 1262 PetscFunctionReturn(PETSC_SUCCESS); 1263 } 1264 1265 static PetscErrorCode DMPlexCreateBoxMesh_Tensor_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[]) 1266 { 1267 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1268 PetscInt fac[3] = {0, 0, 0}, d; 1269 1270 PetscFunctionBegin; 1271 PetscAssertPointer(dm, 1); 1272 PetscValidLogicalCollectiveInt(dm, dim, 2); 1273 PetscCall(DMSetDimension(dm, dim)); 1274 for (d = 0; d < dim; ++d) { 1275 fac[d] = faces[d]; 1276 bdt[d] = periodicity[d]; 1277 } 1278 PetscCall(DMPlexCreateCubeMesh_Internal(dm, lower, upper, fac, bdt[0], bdt[1], bdt[2])); 1279 if (periodicity[0] == DM_BOUNDARY_PERIODIC || periodicity[0] == DM_BOUNDARY_TWIST || periodicity[1] == DM_BOUNDARY_PERIODIC || periodicity[1] == DM_BOUNDARY_TWIST || (dim > 2 && (periodicity[2] == DM_BOUNDARY_PERIODIC || periodicity[2] == DM_BOUNDARY_TWIST))) { 1280 PetscReal L[3] = {-1., -1., 0.}; 1281 PetscReal maxCell[3] = {-1., -1., 0.}; 1282 1283 for (d = 0; d < dim; ++d) { 1284 if (periodicity[d] != DM_BOUNDARY_NONE) { 1285 L[d] = upper[d] - lower[d]; 1286 maxCell[d] = 1.1 * (L[d] / PetscMax(1, faces[d])); 1287 } 1288 } 1289 PetscCall(DMSetPeriodicity(dm, maxCell, lower, L)); 1290 } 1291 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 1292 PetscFunctionReturn(PETSC_SUCCESS); 1293 } 1294 1295 static PetscErrorCode DMPlexCreateBoxMesh_Internal(DM dm, DMPlexShape shape, PetscInt dim, PetscBool simplex, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate) 1296 { 1297 PetscFunctionBegin; 1298 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 1299 if (shape == DM_SHAPE_ZBOX) PetscCall(DMPlexCreateBoxMesh_Tensor_SFC_Internal(dm, dim, faces, lower, upper, periodicity, interpolate)); 1300 else if (dim == 1) PetscCall(DMPlexCreateLineMesh_Internal(dm, faces[0], lower[0], upper[0], periodicity[0])); 1301 else if (simplex) PetscCall(DMPlexCreateBoxMesh_Simplex_Internal(dm, dim, faces, lower, upper, periodicity, interpolate)); 1302 else PetscCall(DMPlexCreateBoxMesh_Tensor_Internal(dm, dim, faces, lower, upper, periodicity)); 1303 if (!interpolate && dim > 1 && !simplex) { 1304 DM udm; 1305 1306 PetscCall(DMPlexUninterpolate(dm, &udm)); 1307 PetscCall(DMPlexCopyCoordinates(dm, udm)); 1308 PetscCall(DMPlexReplace_Internal(dm, &udm)); 1309 } 1310 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 1311 PetscFunctionReturn(PETSC_SUCCESS); 1312 } 1313 1314 /*@C 1315 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra). 1316 1317 Collective 1318 1319 Input Parameters: 1320 + comm - The communicator for the `DM` object 1321 . dim - The spatial dimension 1322 . simplex - `PETSC_TRUE` for simplices, `PETSC_FALSE` for tensor cells 1323 . faces - Number of faces per dimension, or `NULL` for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 1324 . lower - The lower left corner, or `NULL` for (0, 0, 0) 1325 . upper - The upper right corner, or `NULL` for (1, 1, 1) 1326 . periodicity - The boundary type for the X,Y,Z direction, or `NULL` for `DM_BOUNDARY_NONE` 1327 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1328 1329 Output Parameter: 1330 . dm - The `DM` object 1331 1332 Level: beginner 1333 1334 Note: 1335 To customize this mesh using options, use 1336 .vb 1337 DMCreate(comm, &dm); 1338 DMSetType(dm, DMPLEX); 1339 DMSetFromOptions(dm); 1340 .ve 1341 and use the options in `DMSetFromOptions()`. 1342 1343 Here is the numbering returned for 2 faces in each direction for tensor cells: 1344 .vb 1345 10---17---11---18----12 1346 | | | 1347 | | | 1348 20 2 22 3 24 1349 | | | 1350 | | | 1351 7---15----8---16----9 1352 | | | 1353 | | | 1354 19 0 21 1 23 1355 | | | 1356 | | | 1357 4---13----5---14----6 1358 .ve 1359 and for simplicial cells 1360 .vb 1361 14----8---15----9----16 1362 |\ 5 |\ 7 | 1363 | \ | \ | 1364 13 2 14 3 15 1365 | 4 \ | 6 \ | 1366 | \ | \ | 1367 11----6---12----7----13 1368 |\ |\ | 1369 | \ 1 | \ 3 | 1370 10 0 11 1 12 1371 | 0 \ | 2 \ | 1372 | \ | \ | 1373 8----4----9----5----10 1374 .ve 1375 1376 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMSetFromOptions()`, `DMPlexCreateFromFile()`, `DMPlexCreateHexCylinderMesh()`, `DMSetType()`, `DMCreate()` 1377 @*/ 1378 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) 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(DMPlexCreateBoxMesh_Internal(*dm, DM_SHAPE_BOX, dim, simplex, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt, interpolate)); 1389 if (periodicity) PetscCall(DMLocalizeCoordinates(*dm)); 1390 PetscFunctionReturn(PETSC_SUCCESS); 1391 } 1392 1393 static PetscErrorCode DMPlexCreateWedgeBoxMesh_Internal(DM dm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[]) 1394 { 1395 DM bdm, vol; 1396 PetscInt i; 1397 1398 PetscFunctionBegin; 1399 // TODO Now we can support periodicity 1400 for (i = 0; i < 3; ++i) PetscCheck(periodicity[i] == DM_BOUNDARY_NONE, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Periodicity not yet supported"); 1401 PetscCall(DMCreate(PetscObjectComm((PetscObject)dm), &bdm)); 1402 PetscCall(DMSetType(bdm, DMPLEX)); 1403 PetscCall(DMSetDimension(bdm, 2)); 1404 PetscCall(PetscLogEventBegin(DMPLEX_Generate, bdm, 0, 0, 0)); 1405 PetscCall(DMPlexCreateBoxMesh_Simplex_Internal(bdm, 2, faces, lower, upper, periodicity, PETSC_TRUE)); 1406 PetscCall(DMPlexExtrude(bdm, faces[2], upper[2] - lower[2], PETSC_TRUE, PETSC_FALSE, PETSC_FALSE, NULL, NULL, &vol)); 1407 PetscCall(PetscLogEventEnd(DMPLEX_Generate, bdm, 0, 0, 0)); 1408 PetscCall(DMDestroy(&bdm)); 1409 PetscCall(DMPlexReplace_Internal(dm, &vol)); 1410 if (lower[2] != 0.0) { 1411 Vec v; 1412 PetscScalar *x; 1413 PetscInt cDim, n; 1414 1415 PetscCall(DMGetCoordinatesLocal(dm, &v)); 1416 PetscCall(VecGetBlockSize(v, &cDim)); 1417 PetscCall(VecGetLocalSize(v, &n)); 1418 PetscCall(VecGetArray(v, &x)); 1419 x += cDim; 1420 for (i = 0; i < n; i += cDim) x[i] += lower[2]; 1421 PetscCall(VecRestoreArray(v, &x)); 1422 PetscCall(DMSetCoordinatesLocal(dm, v)); 1423 } 1424 PetscFunctionReturn(PETSC_SUCCESS); 1425 } 1426 1427 /*@ 1428 DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells. 1429 1430 Collective 1431 1432 Input Parameters: 1433 + comm - The communicator for the `DM` object 1434 . faces - Number of faces per dimension, or `NULL` for (1, 1, 1) 1435 . lower - The lower left corner, or `NULL` for (0, 0, 0) 1436 . upper - The upper right corner, or `NULL` for (1, 1, 1) 1437 . periodicity - The boundary type for the X,Y,Z direction, or `NULL` for `DM_BOUNDARY_NONE` 1438 . orderHeight - If `PETSC_TRUE`, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1439 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1440 1441 Output Parameter: 1442 . dm - The `DM` object 1443 1444 Level: beginner 1445 1446 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateHexCylinderMesh()`, `DMPlexCreateWedgeCylinderMesh()`, `DMExtrude()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 1447 @*/ 1448 PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool orderHeight, PetscBool interpolate, DM *dm) 1449 { 1450 PetscInt fac[3] = {1, 1, 1}; 1451 PetscReal low[3] = {0, 0, 0}; 1452 PetscReal upp[3] = {1, 1, 1}; 1453 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1454 1455 PetscFunctionBegin; 1456 PetscCall(DMCreate(comm, dm)); 1457 PetscCall(DMSetType(*dm, DMPLEX)); 1458 PetscCall(DMPlexCreateWedgeBoxMesh_Internal(*dm, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt)); 1459 if (!interpolate) { 1460 DM udm; 1461 1462 PetscCall(DMPlexUninterpolate(*dm, &udm)); 1463 PetscCall(DMPlexReplace_Internal(*dm, &udm)); 1464 } 1465 if (periodicity) PetscCall(DMLocalizeCoordinates(*dm)); 1466 PetscFunctionReturn(PETSC_SUCCESS); 1467 } 1468 1469 /* 1470 DMPlexTensorPointLexicographic_Private - Returns all tuples of size 'len' with nonnegative integers that are all less than or equal to 'max' for that dimension. 1471 1472 Input Parameters: 1473 + len - The length of the tuple 1474 . max - The maximum for each dimension, so values are in [0, max) 1475 - tup - A tuple of length len+1: tup[len] > 0 indicates a stopping condition 1476 1477 Output Parameter: 1478 . tup - A tuple of `len` integers whose entries are at most `max` 1479 1480 Level: developer 1481 1482 Note: 1483 Ordering is lexicographic with lowest index as least significant in ordering. 1484 e.g. for len == 2 and max == 2, this will return, in order, {0,0}, {1,0}, {2,0}, {0,1}, {1,1}, {2,1}, {0,2}, {1,2}, {2,2}. 1485 1486 .seealso: PetscDualSpaceTensorPointLexicographic_Internal(), PetscDualSpaceLatticePointLexicographic_Internal() 1487 */ 1488 static PetscErrorCode DMPlexTensorPointLexicographic_Private(PetscInt len, const PetscInt max[], PetscInt tup[]) 1489 { 1490 PetscInt i; 1491 1492 PetscFunctionBegin; 1493 for (i = 0; i < len; ++i) { 1494 if (tup[i] < max[i] - 1) { 1495 break; 1496 } else { 1497 tup[i] = 0; 1498 } 1499 } 1500 if (i == len) tup[i - 1] = max[i - 1]; 1501 else ++tup[i]; 1502 PetscFunctionReturn(PETSC_SUCCESS); 1503 } 1504 1505 static PetscInt TupleToIndex_Private(PetscInt len, const PetscInt max[], const PetscInt tup[]) 1506 { 1507 PetscInt i, idx = tup[len - 1]; 1508 1509 for (i = len - 2; i >= 0; --i) { 1510 idx *= max[i]; 1511 idx += tup[i]; 1512 } 1513 return idx; 1514 } 1515 1516 static PetscErrorCode DestroyExtent_Private(void *extent) 1517 { 1518 return PetscFree(extent); 1519 } 1520 1521 static PetscErrorCode DMPlexCreateHypercubicMesh_Internal(DM dm, PetscInt dim, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], const DMBoundaryType bd[]) 1522 { 1523 Vec coordinates; 1524 PetscSection coordSection; 1525 DMLabel cutLabel = NULL; 1526 PetscBool cutMarker = PETSC_FALSE; 1527 PetscBool periodic = PETSC_FALSE; 1528 PetscInt numCells = 1, c; 1529 PetscInt numVertices = 1, v; 1530 PetscScalar *coords; 1531 PetscInt *vertices, *vert, *vtmp, *supp, cone[2]; 1532 PetscInt d, e, cell = 0, coordSize; 1533 PetscMPIInt rank; 1534 1535 PetscFunctionBegin; 1536 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 1537 PetscCall(DMSetDimension(dm, dim)); 1538 PetscCall(PetscCalloc4(dim, &vertices, dim, &vert, dim, &vtmp, 2 * dim, &supp)); 1539 PetscCall(DMCreateLabel(dm, "marker")); 1540 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL)); 1541 for (d = 0; d < dim; ++d) periodic = (periodic || bd[d] == DM_BOUNDARY_PERIODIC) ? PETSC_TRUE : PETSC_FALSE; 1542 if (periodic && cutMarker) { 1543 PetscCall(DMCreateLabel(dm, "periodic_cut")); 1544 PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel)); 1545 } 1546 for (d = 0; d < dim; ++d) PetscCheck(bd[d] == DM_BOUNDARY_PERIODIC, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Hypercubic mesh must be periodic now"); 1547 for (d = 0; d < dim; ++d) { 1548 vertices[d] = edges[d]; 1549 numVertices *= vertices[d]; 1550 } 1551 numCells = numVertices * dim; 1552 PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices)); 1553 for (c = 0; c < numCells; ++c) PetscCall(DMPlexSetConeSize(dm, c, 2)); 1554 for (v = numCells; v < numCells + numVertices; ++v) PetscCall(DMPlexSetSupportSize(dm, v, 2 * dim)); 1555 /* TODO Loop over boundary and reset support sizes */ 1556 PetscCall(DMSetUp(dm)); /* Allocate space for cones and supports */ 1557 /* Build cell cones and vertex supports */ 1558 PetscCall(DMCreateLabel(dm, "celltype")); 1559 while (vert[dim - 1] < vertices[dim - 1]) { 1560 const PetscInt vertex = TupleToIndex_Private(dim, vertices, vert) + numCells; 1561 PetscInt s = 0; 1562 1563 PetscCall(PetscPrintf(PETSC_COMM_SELF, "Vertex %" PetscInt_FMT ":", vertex)); 1564 for (d = 0; d < dim; ++d) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, vert[d])); 1565 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 1566 PetscCall(DMPlexSetCellType(dm, vertex, DM_POLYTOPE_POINT)); 1567 for (d = 0; d < dim; ++d) { 1568 for (e = 0; e < dim; ++e) vtmp[e] = vert[e]; 1569 vtmp[d] = (vert[d] + 1) % vertices[d]; 1570 cone[0] = vertex; 1571 cone[1] = TupleToIndex_Private(dim, vertices, vtmp) + numCells; 1572 PetscCall(PetscPrintf(PETSC_COMM_SELF, " Vertex %" PetscInt_FMT ":", cone[1])); 1573 for (e = 0; e < dim; ++e) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, vtmp[e])); 1574 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 1575 PetscCall(DMPlexSetCone(dm, cell, cone)); 1576 PetscCall(DMPlexSetCellType(dm, cell, DM_POLYTOPE_SEGMENT)); 1577 PetscCall(PetscPrintf(PETSC_COMM_SELF, " Edge %" PetscInt_FMT " (%" PetscInt_FMT " %" PetscInt_FMT ")\n", cell, cone[0], cone[1])); 1578 ++cell; 1579 } 1580 for (d = 0; d < dim; ++d) { 1581 for (e = 0; e < dim; ++e) vtmp[e] = vert[e]; 1582 vtmp[d] = (vert[d] + vertices[d] - 1) % vertices[d]; 1583 supp[s++] = TupleToIndex_Private(dim, vertices, vtmp) * dim + d; 1584 supp[s++] = (vertex - numCells) * dim + d; 1585 PetscCall(DMPlexSetSupport(dm, vertex, supp)); 1586 } 1587 PetscCall(DMPlexTensorPointLexicographic_Private(dim, vertices, vert)); 1588 } 1589 PetscCall(DMPlexStratify(dm)); 1590 /* Build coordinates */ 1591 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 1592 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 1593 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim)); 1594 PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices)); 1595 for (v = numCells; v < numCells + numVertices; ++v) { 1596 PetscCall(PetscSectionSetDof(coordSection, v, dim)); 1597 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim)); 1598 } 1599 PetscCall(PetscSectionSetUp(coordSection)); 1600 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 1601 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 1602 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 1603 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 1604 PetscCall(VecSetBlockSize(coordinates, dim)); 1605 PetscCall(VecSetType(coordinates, VECSTANDARD)); 1606 PetscCall(VecGetArray(coordinates, &coords)); 1607 for (d = 0; d < dim; ++d) vert[d] = 0; 1608 while (vert[dim - 1] < vertices[dim - 1]) { 1609 const PetscInt vertex = TupleToIndex_Private(dim, vertices, vert); 1610 1611 for (d = 0; d < dim; ++d) coords[vertex * dim + d] = lower[d] + ((upper[d] - lower[d]) / vertices[d]) * vert[d]; 1612 PetscCall(PetscPrintf(PETSC_COMM_SELF, "Vertex %" PetscInt_FMT ":", vertex)); 1613 for (d = 0; d < dim; ++d) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, vert[d])); 1614 for (d = 0; d < dim; ++d) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %g", (double)PetscRealPart(coords[vertex * dim + d]))); 1615 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 1616 PetscCall(DMPlexTensorPointLexicographic_Private(dim, vertices, vert)); 1617 } 1618 PetscCall(VecRestoreArray(coordinates, &coords)); 1619 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 1620 PetscCall(VecDestroy(&coordinates)); 1621 PetscCall(PetscFree4(vertices, vert, vtmp, supp)); 1622 //PetscCall(DMSetPeriodicity(dm, NULL, lower, upper)); 1623 // Attach the extent 1624 { 1625 PetscContainer c; 1626 PetscInt *extent; 1627 1628 PetscCall(PetscMalloc1(dim, &extent)); 1629 for (PetscInt d = 0; d < dim; ++d) extent[d] = edges[d]; 1630 PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &c)); 1631 PetscCall(PetscContainerSetUserDestroy(c, DestroyExtent_Private)); 1632 PetscCall(PetscContainerSetPointer(c, extent)); 1633 PetscCall(PetscObjectCompose((PetscObject)dm, "_extent", (PetscObject)c)); 1634 PetscCall(PetscContainerDestroy(&c)); 1635 } 1636 PetscFunctionReturn(PETSC_SUCCESS); 1637 } 1638 1639 /*@C 1640 DMPlexCreateHypercubicMesh - Creates a periodic mesh on the tensor product of unit intervals using only vertices and edges. 1641 1642 Collective 1643 1644 Input Parameters: 1645 + comm - The communicator for the DM object 1646 . dim - The spatial dimension 1647 . edges - Number of edges per dimension, or `NULL` for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 1648 . lower - The lower left corner, or `NULL` for (0, 0, 0) 1649 - upper - The upper right corner, or `NULL` for (1, 1, 1) 1650 1651 Output Parameter: 1652 . dm - The DM object 1653 1654 Level: beginner 1655 1656 Note: 1657 If you want to customize this mesh using options, you just need to 1658 .vb 1659 DMCreate(comm, &dm); 1660 DMSetType(dm, DMPLEX); 1661 DMSetFromOptions(dm); 1662 .ve 1663 and use the options on the `DMSetFromOptions()` page. 1664 1665 The vertices are numbered is lexicographic order, and the dim edges exiting a vertex in the positive orthant are number consecutively, 1666 .vb 1667 18--0-19--2-20--4-18 1668 | | | | 1669 13 15 17 13 1670 | | | | 1671 24-12-25-14-26-16-24 1672 | | | | 1673 7 9 11 7 1674 | | | | 1675 21--6-22--8-23-10-21 1676 | | | | 1677 1 3 5 1 1678 | | | | 1679 18--0-19--2-20--4-18 1680 .ve 1681 1682 .seealso: `DMSetFromOptions()`, `DMPlexCreateFromFile()`, `DMPlexCreateHexCylinderMesh()`, `DMSetType()`, `DMCreate()` 1683 @*/ 1684 PetscErrorCode DMPlexCreateHypercubicMesh(MPI_Comm comm, PetscInt dim, const PetscInt edges[], const PetscReal lower[], const PetscReal upper[], DM *dm) 1685 { 1686 PetscInt *edg; 1687 PetscReal *low, *upp; 1688 DMBoundaryType *bdt; 1689 PetscInt d; 1690 1691 PetscFunctionBegin; 1692 PetscCall(DMCreate(comm, dm)); 1693 PetscCall(DMSetType(*dm, DMPLEX)); 1694 PetscCall(PetscMalloc4(dim, &edg, dim, &low, dim, &upp, dim, &bdt)); 1695 for (d = 0; d < dim; ++d) { 1696 edg[d] = edges ? edges[d] : 1; 1697 low[d] = lower ? lower[d] : 0.; 1698 upp[d] = upper ? upper[d] : 1.; 1699 bdt[d] = DM_BOUNDARY_PERIODIC; 1700 } 1701 PetscCall(DMPlexCreateHypercubicMesh_Internal(*dm, dim, low, upp, edg, bdt)); 1702 PetscCall(PetscFree4(edg, low, upp, bdt)); 1703 PetscFunctionReturn(PETSC_SUCCESS); 1704 } 1705 1706 /*@C 1707 DMPlexSetOptionsPrefix - Sets the prefix used for searching for all `DM` options in the database. 1708 1709 Logically Collective 1710 1711 Input Parameters: 1712 + dm - the `DM` context 1713 - prefix - the prefix to prepend to all option names 1714 1715 Level: advanced 1716 1717 Note: 1718 A hyphen (-) must NOT be given at the beginning of the prefix name. 1719 The first character of all runtime options is AUTOMATICALLY the hyphen. 1720 1721 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `SNESSetFromOptions()` 1722 @*/ 1723 PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) 1724 { 1725 DM_Plex *mesh = (DM_Plex *)dm->data; 1726 1727 PetscFunctionBegin; 1728 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1729 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dm, prefix)); 1730 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)mesh->partitioner, prefix)); 1731 PetscFunctionReturn(PETSC_SUCCESS); 1732 } 1733 1734 /* Remap geometry to cylinder 1735 TODO: This only works for a single refinement, then it is broken 1736 1737 Interior square: Linear interpolation is correct 1738 The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing 1739 such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance 1740 1741 phi = arctan(y/x) 1742 d_close = sqrt(1/8 + 1/4 sin^2(phi)) 1743 d_far = sqrt(1/2 + sin^2(phi)) 1744 1745 so we remap them using 1746 1747 x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) 1748 y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) 1749 1750 If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. 1751 */ 1752 static void snapToCylinder(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 1753 { 1754 const PetscReal dis = 1.0 / PetscSqrtReal(2.0); 1755 const PetscReal ds2 = 0.5 * dis; 1756 1757 if ((PetscAbsScalar(u[0]) <= ds2) && (PetscAbsScalar(u[1]) <= ds2)) { 1758 f0[0] = u[0]; 1759 f0[1] = u[1]; 1760 } else { 1761 PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; 1762 1763 x = PetscRealPart(u[0]); 1764 y = PetscRealPart(u[1]); 1765 phi = PetscAtan2Real(y, x); 1766 sinp = PetscSinReal(phi); 1767 cosp = PetscCosReal(phi); 1768 if ((PetscAbsReal(phi) > PETSC_PI / 4.0) && (PetscAbsReal(phi) < 3.0 * PETSC_PI / 4.0)) { 1769 dc = PetscAbsReal(ds2 / sinp); 1770 df = PetscAbsReal(dis / sinp); 1771 xc = ds2 * x / PetscAbsReal(y); 1772 yc = ds2 * PetscSignReal(y); 1773 } else { 1774 dc = PetscAbsReal(ds2 / cosp); 1775 df = PetscAbsReal(dis / cosp); 1776 xc = ds2 * PetscSignReal(x); 1777 yc = ds2 * y / PetscAbsReal(x); 1778 } 1779 f0[0] = xc + (u[0] - xc) * (1.0 - dc) / (df - dc); 1780 f0[1] = yc + (u[1] - yc) * (1.0 - dc) / (df - dc); 1781 } 1782 f0[2] = u[2]; 1783 } 1784 1785 static PetscErrorCode DMPlexCreateHexCylinderMesh_Internal(DM dm, DMBoundaryType periodicZ) 1786 { 1787 const PetscInt dim = 3; 1788 PetscInt numCells, numVertices; 1789 PetscMPIInt rank; 1790 1791 PetscFunctionBegin; 1792 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 1793 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 1794 PetscCall(DMSetDimension(dm, dim)); 1795 /* Create topology */ 1796 { 1797 PetscInt cone[8], c; 1798 1799 numCells = rank == 0 ? 5 : 0; 1800 numVertices = rank == 0 ? 16 : 0; 1801 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1802 numCells *= 3; 1803 numVertices = rank == 0 ? 24 : 0; 1804 } 1805 PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices)); 1806 for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 8)); 1807 PetscCall(DMSetUp(dm)); 1808 if (rank == 0) { 1809 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1810 cone[0] = 15; 1811 cone[1] = 18; 1812 cone[2] = 17; 1813 cone[3] = 16; 1814 cone[4] = 31; 1815 cone[5] = 32; 1816 cone[6] = 33; 1817 cone[7] = 34; 1818 PetscCall(DMPlexSetCone(dm, 0, cone)); 1819 cone[0] = 16; 1820 cone[1] = 17; 1821 cone[2] = 24; 1822 cone[3] = 23; 1823 cone[4] = 32; 1824 cone[5] = 36; 1825 cone[6] = 37; 1826 cone[7] = 33; /* 22 25 26 21 */ 1827 PetscCall(DMPlexSetCone(dm, 1, cone)); 1828 cone[0] = 18; 1829 cone[1] = 27; 1830 cone[2] = 24; 1831 cone[3] = 17; 1832 cone[4] = 34; 1833 cone[5] = 33; 1834 cone[6] = 37; 1835 cone[7] = 38; 1836 PetscCall(DMPlexSetCone(dm, 2, cone)); 1837 cone[0] = 29; 1838 cone[1] = 27; 1839 cone[2] = 18; 1840 cone[3] = 15; 1841 cone[4] = 35; 1842 cone[5] = 31; 1843 cone[6] = 34; 1844 cone[7] = 38; 1845 PetscCall(DMPlexSetCone(dm, 3, cone)); 1846 cone[0] = 29; 1847 cone[1] = 15; 1848 cone[2] = 16; 1849 cone[3] = 23; 1850 cone[4] = 35; 1851 cone[5] = 36; 1852 cone[6] = 32; 1853 cone[7] = 31; 1854 PetscCall(DMPlexSetCone(dm, 4, cone)); 1855 1856 cone[0] = 31; 1857 cone[1] = 34; 1858 cone[2] = 33; 1859 cone[3] = 32; 1860 cone[4] = 19; 1861 cone[5] = 22; 1862 cone[6] = 21; 1863 cone[7] = 20; 1864 PetscCall(DMPlexSetCone(dm, 5, cone)); 1865 cone[0] = 32; 1866 cone[1] = 33; 1867 cone[2] = 37; 1868 cone[3] = 36; 1869 cone[4] = 22; 1870 cone[5] = 25; 1871 cone[6] = 26; 1872 cone[7] = 21; 1873 PetscCall(DMPlexSetCone(dm, 6, cone)); 1874 cone[0] = 34; 1875 cone[1] = 38; 1876 cone[2] = 37; 1877 cone[3] = 33; 1878 cone[4] = 20; 1879 cone[5] = 21; 1880 cone[6] = 26; 1881 cone[7] = 28; 1882 PetscCall(DMPlexSetCone(dm, 7, cone)); 1883 cone[0] = 35; 1884 cone[1] = 38; 1885 cone[2] = 34; 1886 cone[3] = 31; 1887 cone[4] = 30; 1888 cone[5] = 19; 1889 cone[6] = 20; 1890 cone[7] = 28; 1891 PetscCall(DMPlexSetCone(dm, 8, cone)); 1892 cone[0] = 35; 1893 cone[1] = 31; 1894 cone[2] = 32; 1895 cone[3] = 36; 1896 cone[4] = 30; 1897 cone[5] = 25; 1898 cone[6] = 22; 1899 cone[7] = 19; 1900 PetscCall(DMPlexSetCone(dm, 9, cone)); 1901 1902 cone[0] = 19; 1903 cone[1] = 20; 1904 cone[2] = 21; 1905 cone[3] = 22; 1906 cone[4] = 15; 1907 cone[5] = 16; 1908 cone[6] = 17; 1909 cone[7] = 18; 1910 PetscCall(DMPlexSetCone(dm, 10, cone)); 1911 cone[0] = 22; 1912 cone[1] = 21; 1913 cone[2] = 26; 1914 cone[3] = 25; 1915 cone[4] = 16; 1916 cone[5] = 23; 1917 cone[6] = 24; 1918 cone[7] = 17; 1919 PetscCall(DMPlexSetCone(dm, 11, cone)); 1920 cone[0] = 20; 1921 cone[1] = 28; 1922 cone[2] = 26; 1923 cone[3] = 21; 1924 cone[4] = 18; 1925 cone[5] = 17; 1926 cone[6] = 24; 1927 cone[7] = 27; 1928 PetscCall(DMPlexSetCone(dm, 12, cone)); 1929 cone[0] = 30; 1930 cone[1] = 28; 1931 cone[2] = 20; 1932 cone[3] = 19; 1933 cone[4] = 29; 1934 cone[5] = 15; 1935 cone[6] = 18; 1936 cone[7] = 27; 1937 PetscCall(DMPlexSetCone(dm, 13, cone)); 1938 cone[0] = 30; 1939 cone[1] = 19; 1940 cone[2] = 22; 1941 cone[3] = 25; 1942 cone[4] = 29; 1943 cone[5] = 23; 1944 cone[6] = 16; 1945 cone[7] = 15; 1946 PetscCall(DMPlexSetCone(dm, 14, cone)); 1947 } else { 1948 cone[0] = 5; 1949 cone[1] = 8; 1950 cone[2] = 7; 1951 cone[3] = 6; 1952 cone[4] = 9; 1953 cone[5] = 12; 1954 cone[6] = 11; 1955 cone[7] = 10; 1956 PetscCall(DMPlexSetCone(dm, 0, cone)); 1957 cone[0] = 6; 1958 cone[1] = 7; 1959 cone[2] = 14; 1960 cone[3] = 13; 1961 cone[4] = 12; 1962 cone[5] = 15; 1963 cone[6] = 16; 1964 cone[7] = 11; 1965 PetscCall(DMPlexSetCone(dm, 1, cone)); 1966 cone[0] = 8; 1967 cone[1] = 17; 1968 cone[2] = 14; 1969 cone[3] = 7; 1970 cone[4] = 10; 1971 cone[5] = 11; 1972 cone[6] = 16; 1973 cone[7] = 18; 1974 PetscCall(DMPlexSetCone(dm, 2, cone)); 1975 cone[0] = 19; 1976 cone[1] = 17; 1977 cone[2] = 8; 1978 cone[3] = 5; 1979 cone[4] = 20; 1980 cone[5] = 9; 1981 cone[6] = 10; 1982 cone[7] = 18; 1983 PetscCall(DMPlexSetCone(dm, 3, cone)); 1984 cone[0] = 19; 1985 cone[1] = 5; 1986 cone[2] = 6; 1987 cone[3] = 13; 1988 cone[4] = 20; 1989 cone[5] = 15; 1990 cone[6] = 12; 1991 cone[7] = 9; 1992 PetscCall(DMPlexSetCone(dm, 4, cone)); 1993 } 1994 } 1995 PetscCall(DMPlexSymmetrize(dm)); 1996 PetscCall(DMPlexStratify(dm)); 1997 } 1998 /* Create cube geometry */ 1999 { 2000 Vec coordinates; 2001 PetscSection coordSection; 2002 PetscScalar *coords; 2003 PetscInt coordSize, v; 2004 const PetscReal dis = 1.0 / PetscSqrtReal(2.0); 2005 const PetscReal ds2 = dis / 2.0; 2006 2007 /* Build coordinates */ 2008 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 2009 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 2010 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim)); 2011 PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices)); 2012 for (v = numCells; v < numCells + numVertices; ++v) { 2013 PetscCall(PetscSectionSetDof(coordSection, v, dim)); 2014 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim)); 2015 } 2016 PetscCall(PetscSectionSetUp(coordSection)); 2017 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 2018 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 2019 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 2020 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 2021 PetscCall(VecSetBlockSize(coordinates, dim)); 2022 PetscCall(VecSetType(coordinates, VECSTANDARD)); 2023 PetscCall(VecGetArray(coordinates, &coords)); 2024 if (rank == 0) { 2025 coords[0 * dim + 0] = -ds2; 2026 coords[0 * dim + 1] = -ds2; 2027 coords[0 * dim + 2] = 0.0; 2028 coords[1 * dim + 0] = ds2; 2029 coords[1 * dim + 1] = -ds2; 2030 coords[1 * dim + 2] = 0.0; 2031 coords[2 * dim + 0] = ds2; 2032 coords[2 * dim + 1] = ds2; 2033 coords[2 * dim + 2] = 0.0; 2034 coords[3 * dim + 0] = -ds2; 2035 coords[3 * dim + 1] = ds2; 2036 coords[3 * dim + 2] = 0.0; 2037 coords[4 * dim + 0] = -ds2; 2038 coords[4 * dim + 1] = -ds2; 2039 coords[4 * dim + 2] = 1.0; 2040 coords[5 * dim + 0] = -ds2; 2041 coords[5 * dim + 1] = ds2; 2042 coords[5 * dim + 2] = 1.0; 2043 coords[6 * dim + 0] = ds2; 2044 coords[6 * dim + 1] = ds2; 2045 coords[6 * dim + 2] = 1.0; 2046 coords[7 * dim + 0] = ds2; 2047 coords[7 * dim + 1] = -ds2; 2048 coords[7 * dim + 2] = 1.0; 2049 coords[8 * dim + 0] = dis; 2050 coords[8 * dim + 1] = -dis; 2051 coords[8 * dim + 2] = 0.0; 2052 coords[9 * dim + 0] = dis; 2053 coords[9 * dim + 1] = dis; 2054 coords[9 * dim + 2] = 0.0; 2055 coords[10 * dim + 0] = dis; 2056 coords[10 * dim + 1] = -dis; 2057 coords[10 * dim + 2] = 1.0; 2058 coords[11 * dim + 0] = dis; 2059 coords[11 * dim + 1] = dis; 2060 coords[11 * dim + 2] = 1.0; 2061 coords[12 * dim + 0] = -dis; 2062 coords[12 * dim + 1] = dis; 2063 coords[12 * dim + 2] = 0.0; 2064 coords[13 * dim + 0] = -dis; 2065 coords[13 * dim + 1] = dis; 2066 coords[13 * dim + 2] = 1.0; 2067 coords[14 * dim + 0] = -dis; 2068 coords[14 * dim + 1] = -dis; 2069 coords[14 * dim + 2] = 0.0; 2070 coords[15 * dim + 0] = -dis; 2071 coords[15 * dim + 1] = -dis; 2072 coords[15 * dim + 2] = 1.0; 2073 if (periodicZ == DM_BOUNDARY_PERIODIC) { 2074 /* 15 31 19 */ coords[16 * dim + 0] = -ds2; 2075 coords[16 * dim + 1] = -ds2; 2076 coords[16 * dim + 2] = 0.5; 2077 /* 16 32 22 */ coords[17 * dim + 0] = ds2; 2078 coords[17 * dim + 1] = -ds2; 2079 coords[17 * dim + 2] = 0.5; 2080 /* 17 33 21 */ coords[18 * dim + 0] = ds2; 2081 coords[18 * dim + 1] = ds2; 2082 coords[18 * dim + 2] = 0.5; 2083 /* 18 34 20 */ coords[19 * dim + 0] = -ds2; 2084 coords[19 * dim + 1] = ds2; 2085 coords[19 * dim + 2] = 0.5; 2086 /* 29 35 30 */ coords[20 * dim + 0] = -dis; 2087 coords[20 * dim + 1] = -dis; 2088 coords[20 * dim + 2] = 0.5; 2089 /* 23 36 25 */ coords[21 * dim + 0] = dis; 2090 coords[21 * dim + 1] = -dis; 2091 coords[21 * dim + 2] = 0.5; 2092 /* 24 37 26 */ coords[22 * dim + 0] = dis; 2093 coords[22 * dim + 1] = dis; 2094 coords[22 * dim + 2] = 0.5; 2095 /* 27 38 28 */ coords[23 * dim + 0] = -dis; 2096 coords[23 * dim + 1] = dis; 2097 coords[23 * dim + 2] = 0.5; 2098 } 2099 } 2100 PetscCall(VecRestoreArray(coordinates, &coords)); 2101 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 2102 PetscCall(VecDestroy(&coordinates)); 2103 } 2104 /* Create periodicity */ 2105 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 2106 PetscReal L[3] = {-1., -1., 0.}; 2107 PetscReal maxCell[3] = {-1., -1., 0.}; 2108 PetscReal lower[3] = {0.0, 0.0, 0.0}; 2109 PetscReal upper[3] = {1.0, 1.0, 1.5}; 2110 PetscInt numZCells = 3; 2111 2112 L[2] = upper[2] - lower[2]; 2113 maxCell[2] = 1.1 * (L[2] / numZCells); 2114 PetscCall(DMSetPeriodicity(dm, maxCell, lower, L)); 2115 } 2116 { 2117 DM cdm; 2118 PetscDS cds; 2119 PetscScalar c[2] = {1.0, 1.0}; 2120 2121 PetscCall(DMPlexCreateCoordinateSpace(dm, 1, snapToCylinder)); 2122 PetscCall(DMGetCoordinateDM(dm, &cdm)); 2123 PetscCall(DMGetDS(cdm, &cds)); 2124 PetscCall(PetscDSSetConstants(cds, 2, c)); 2125 } 2126 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 2127 2128 /* Wait for coordinate creation before doing in-place modification */ 2129 PetscCall(DMPlexInterpolateInPlace_Internal(dm)); 2130 PetscFunctionReturn(PETSC_SUCCESS); 2131 } 2132 2133 /*@ 2134 DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. 2135 2136 Collective 2137 2138 Input Parameters: 2139 + comm - The communicator for the `DM` object 2140 - periodicZ - The boundary type for the Z direction 2141 2142 Output Parameter: 2143 . dm - The `DM` object 2144 2145 Level: beginner 2146 2147 Note: 2148 2149 Here is the output numbering looking from the bottom of the cylinder: 2150 .vb 2151 17-----14 2152 | | 2153 | 2 | 2154 | | 2155 17-----8-----7-----14 2156 | | | | 2157 | 3 | 0 | 1 | 2158 | | | | 2159 19-----5-----6-----13 2160 | | 2161 | 4 | 2162 | | 2163 19-----13 2164 2165 and up through the top 2166 2167 18-----16 2168 | | 2169 | 2 | 2170 | | 2171 18----10----11-----16 2172 | | | | 2173 | 3 | 0 | 1 | 2174 | | | | 2175 20-----9----12-----15 2176 | | 2177 | 4 | 2178 | | 2179 20-----15 2180 .ve 2181 2182 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 2183 @*/ 2184 PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, DMBoundaryType periodicZ, DM *dm) 2185 { 2186 PetscFunctionBegin; 2187 PetscAssertPointer(dm, 3); 2188 PetscCall(DMCreate(comm, dm)); 2189 PetscCall(DMSetType(*dm, DMPLEX)); 2190 PetscCall(DMPlexCreateHexCylinderMesh_Internal(*dm, periodicZ)); 2191 PetscFunctionReturn(PETSC_SUCCESS); 2192 } 2193 2194 static PetscErrorCode DMPlexCreateWedgeCylinderMesh_Internal(DM dm, PetscInt n, PetscBool interpolate) 2195 { 2196 const PetscInt dim = 3; 2197 PetscInt numCells, numVertices, v; 2198 PetscMPIInt rank; 2199 2200 PetscFunctionBegin; 2201 PetscCheck(n >= 0, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %" PetscInt_FMT " cannot be negative", n); 2202 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 2203 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 2204 PetscCall(DMSetDimension(dm, dim)); 2205 /* Must create the celltype label here so that we do not automatically try to compute the types */ 2206 PetscCall(DMCreateLabel(dm, "celltype")); 2207 /* Create topology */ 2208 { 2209 PetscInt cone[6], c; 2210 2211 numCells = rank == 0 ? n : 0; 2212 numVertices = rank == 0 ? 2 * (n + 1) : 0; 2213 PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices)); 2214 for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 6)); 2215 PetscCall(DMSetUp(dm)); 2216 for (c = 0; c < numCells; c++) { 2217 cone[0] = c + n * 1; 2218 cone[1] = (c + 1) % n + n * 1; 2219 cone[2] = 0 + 3 * n; 2220 cone[3] = c + n * 2; 2221 cone[4] = (c + 1) % n + n * 2; 2222 cone[5] = 1 + 3 * n; 2223 PetscCall(DMPlexSetCone(dm, c, cone)); 2224 PetscCall(DMPlexSetCellType(dm, c, DM_POLYTOPE_TRI_PRISM_TENSOR)); 2225 } 2226 PetscCall(DMPlexSymmetrize(dm)); 2227 PetscCall(DMPlexStratify(dm)); 2228 } 2229 for (v = numCells; v < numCells + numVertices; ++v) PetscCall(DMPlexSetCellType(dm, v, DM_POLYTOPE_POINT)); 2230 /* Create cylinder geometry */ 2231 { 2232 Vec coordinates; 2233 PetscSection coordSection; 2234 PetscScalar *coords; 2235 PetscInt coordSize, c; 2236 2237 /* Build coordinates */ 2238 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 2239 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 2240 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim)); 2241 PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices)); 2242 for (v = numCells; v < numCells + numVertices; ++v) { 2243 PetscCall(PetscSectionSetDof(coordSection, v, dim)); 2244 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim)); 2245 } 2246 PetscCall(PetscSectionSetUp(coordSection)); 2247 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 2248 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 2249 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 2250 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 2251 PetscCall(VecSetBlockSize(coordinates, dim)); 2252 PetscCall(VecSetType(coordinates, VECSTANDARD)); 2253 PetscCall(VecGetArray(coordinates, &coords)); 2254 for (c = 0; c < numCells; c++) { 2255 coords[(c + 0 * n) * dim + 0] = PetscCosReal(2.0 * c * PETSC_PI / n); 2256 coords[(c + 0 * n) * dim + 1] = PetscSinReal(2.0 * c * PETSC_PI / n); 2257 coords[(c + 0 * n) * dim + 2] = 1.0; 2258 coords[(c + 1 * n) * dim + 0] = PetscCosReal(2.0 * c * PETSC_PI / n); 2259 coords[(c + 1 * n) * dim + 1] = PetscSinReal(2.0 * c * PETSC_PI / n); 2260 coords[(c + 1 * n) * dim + 2] = 0.0; 2261 } 2262 if (rank == 0) { 2263 coords[(2 * n + 0) * dim + 0] = 0.0; 2264 coords[(2 * n + 0) * dim + 1] = 0.0; 2265 coords[(2 * n + 0) * dim + 2] = 1.0; 2266 coords[(2 * n + 1) * dim + 0] = 0.0; 2267 coords[(2 * n + 1) * dim + 1] = 0.0; 2268 coords[(2 * n + 1) * dim + 2] = 0.0; 2269 } 2270 PetscCall(VecRestoreArray(coordinates, &coords)); 2271 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 2272 PetscCall(VecDestroy(&coordinates)); 2273 } 2274 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 2275 /* Interpolate */ 2276 if (interpolate) PetscCall(DMPlexInterpolateInPlace_Internal(dm)); 2277 PetscFunctionReturn(PETSC_SUCCESS); 2278 } 2279 2280 /*@ 2281 DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges. 2282 2283 Collective 2284 2285 Input Parameters: 2286 + comm - The communicator for the `DM` object 2287 . n - The number of wedges around the origin 2288 - interpolate - Create edges and faces 2289 2290 Output Parameter: 2291 . dm - The `DM` object 2292 2293 Level: beginner 2294 2295 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateHexCylinderMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 2296 @*/ 2297 PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm) 2298 { 2299 PetscFunctionBegin; 2300 PetscAssertPointer(dm, 4); 2301 PetscCall(DMCreate(comm, dm)); 2302 PetscCall(DMSetType(*dm, DMPLEX)); 2303 PetscCall(DMPlexCreateWedgeCylinderMesh_Internal(*dm, n, interpolate)); 2304 PetscFunctionReturn(PETSC_SUCCESS); 2305 } 2306 2307 static inline PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 2308 { 2309 PetscReal prod = 0.0; 2310 PetscInt i; 2311 for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]); 2312 return PetscSqrtReal(prod); 2313 } 2314 static inline PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 2315 { 2316 PetscReal prod = 0.0; 2317 PetscInt i; 2318 for (i = 0; i < dim; ++i) prod += x[i] * y[i]; 2319 return prod; 2320 } 2321 2322 /* The first constant is the sphere radius */ 2323 static void snapToSphere(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 2324 { 2325 PetscReal r = PetscRealPart(constants[0]); 2326 PetscReal norm2 = 0.0, fac; 2327 PetscInt n = uOff[1] - uOff[0], d; 2328 2329 for (d = 0; d < n; ++d) norm2 += PetscSqr(PetscRealPart(u[d])); 2330 fac = r / PetscSqrtReal(norm2); 2331 for (d = 0; d < n; ++d) f0[d] = u[d] * fac; 2332 } 2333 2334 static PetscErrorCode DMPlexCreateSphereMesh_Internal(DM dm, PetscInt dim, PetscBool simplex, PetscReal R) 2335 { 2336 const PetscInt embedDim = dim + 1; 2337 PetscSection coordSection; 2338 Vec coordinates; 2339 PetscScalar *coords; 2340 PetscReal *coordsIn; 2341 PetscInt numCells, numEdges, numVerts = 0, firstVertex = 0, v, firstEdge, coordSize, d, c, e; 2342 PetscMPIInt rank; 2343 2344 PetscFunctionBegin; 2345 PetscValidLogicalCollectiveBool(dm, simplex, 3); 2346 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 2347 PetscCall(DMSetDimension(dm, dim)); 2348 PetscCall(DMSetCoordinateDim(dm, dim + 1)); 2349 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 2350 switch (dim) { 2351 case 2: 2352 if (simplex) { 2353 const PetscReal radius = PetscSqrtReal(1 + PETSC_PHI * PETSC_PHI) / (1.0 + PETSC_PHI); 2354 const PetscReal edgeLen = 2.0 / (1.0 + PETSC_PHI) * (R / radius); 2355 const PetscInt degree = 5; 2356 PetscReal vertex[3] = {0.0, 1.0 / (1.0 + PETSC_PHI), PETSC_PHI / (1.0 + PETSC_PHI)}; 2357 PetscInt s[3] = {1, 1, 1}; 2358 PetscInt cone[3]; 2359 PetscInt *graph, p, i, j, k; 2360 2361 vertex[0] *= R / radius; 2362 vertex[1] *= R / radius; 2363 vertex[2] *= R / radius; 2364 numCells = rank == 0 ? 20 : 0; 2365 numVerts = rank == 0 ? 12 : 0; 2366 firstVertex = numCells; 2367 /* Use icosahedron, which for a R-sphere has coordinates which are all cyclic permutations of 2368 2369 (0, \pm 1/\phi+1, \pm \phi/\phi+1) 2370 2371 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 2372 length is then given by 2/(1+\phi) = 2 * 0.38197 = 0.76393. 2373 */ 2374 /* Construct vertices */ 2375 PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn)); 2376 if (rank == 0) { 2377 for (p = 0, i = 0; p < embedDim; ++p) { 2378 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2379 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2380 for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[(d + p) % embedDim] * vertex[(d + p) % embedDim]; 2381 ++i; 2382 } 2383 } 2384 } 2385 } 2386 /* Construct graph */ 2387 PetscCall(PetscCalloc1(numVerts * numVerts, &graph)); 2388 for (i = 0; i < numVerts; ++i) { 2389 for (j = 0, k = 0; j < numVerts; ++j) { 2390 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i * embedDim], &coordsIn[j * embedDim]) - edgeLen) < PETSC_SMALL) { 2391 graph[i * numVerts + j] = 1; 2392 ++k; 2393 } 2394 } 2395 PetscCheck(k == degree, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid icosahedron, vertex %" PetscInt_FMT " degree %" PetscInt_FMT " != %" PetscInt_FMT, i, k, degree); 2396 } 2397 /* Build Topology */ 2398 PetscCall(DMPlexSetChart(dm, 0, numCells + numVerts)); 2399 for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, embedDim)); 2400 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 2401 /* Cells */ 2402 for (i = 0, c = 0; i < numVerts; ++i) { 2403 for (j = 0; j < i; ++j) { 2404 for (k = 0; k < j; ++k) { 2405 if (graph[i * numVerts + j] && graph[j * numVerts + k] && graph[k * numVerts + i]) { 2406 cone[0] = firstVertex + i; 2407 cone[1] = firstVertex + j; 2408 cone[2] = firstVertex + k; 2409 /* Check orientation */ 2410 { 2411 const PetscInt epsilon[3][3][3] = { 2412 {{0, 0, 0}, {0, 0, 1}, {0, -1, 0}}, 2413 {{0, 0, -1}, {0, 0, 0}, {1, 0, 0} }, 2414 {{0, 1, 0}, {-1, 0, 0}, {0, 0, 0} } 2415 }; 2416 PetscReal normal[3]; 2417 PetscInt e, f; 2418 2419 for (d = 0; d < embedDim; ++d) { 2420 normal[d] = 0.0; 2421 for (e = 0; e < embedDim; ++e) { 2422 for (f = 0; f < embedDim; ++f) normal[d] += epsilon[d][e][f] * (coordsIn[j * embedDim + e] - coordsIn[i * embedDim + e]) * (coordsIn[k * embedDim + f] - coordsIn[i * embedDim + f]); 2423 } 2424 } 2425 if (DotReal(embedDim, normal, &coordsIn[i * embedDim]) < 0) { 2426 PetscInt tmp = cone[1]; 2427 cone[1] = cone[2]; 2428 cone[2] = tmp; 2429 } 2430 } 2431 PetscCall(DMPlexSetCone(dm, c++, cone)); 2432 } 2433 } 2434 } 2435 } 2436 PetscCall(DMPlexSymmetrize(dm)); 2437 PetscCall(DMPlexStratify(dm)); 2438 PetscCall(PetscFree(graph)); 2439 } else { 2440 /* 2441 12-21--13 2442 | | 2443 25 4 24 2444 | | 2445 12-25--9-16--8-24--13 2446 | | | | 2447 23 5 17 0 15 3 22 2448 | | | | 2449 10-20--6-14--7-19--11 2450 | | 2451 20 1 19 2452 | | 2453 10-18--11 2454 | | 2455 23 2 22 2456 | | 2457 12-21--13 2458 */ 2459 PetscInt cone[4], ornt[4]; 2460 2461 numCells = rank == 0 ? 6 : 0; 2462 numEdges = rank == 0 ? 12 : 0; 2463 numVerts = rank == 0 ? 8 : 0; 2464 firstVertex = numCells; 2465 firstEdge = numCells + numVerts; 2466 /* Build Topology */ 2467 PetscCall(DMPlexSetChart(dm, 0, numCells + numEdges + numVerts)); 2468 for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 4)); 2469 for (e = firstEdge; e < firstEdge + numEdges; ++e) PetscCall(DMPlexSetConeSize(dm, e, 2)); 2470 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 2471 if (rank == 0) { 2472 /* Cell 0 */ 2473 cone[0] = 14; 2474 cone[1] = 15; 2475 cone[2] = 16; 2476 cone[3] = 17; 2477 PetscCall(DMPlexSetCone(dm, 0, cone)); 2478 ornt[0] = 0; 2479 ornt[1] = 0; 2480 ornt[2] = 0; 2481 ornt[3] = 0; 2482 PetscCall(DMPlexSetConeOrientation(dm, 0, ornt)); 2483 /* Cell 1 */ 2484 cone[0] = 18; 2485 cone[1] = 19; 2486 cone[2] = 14; 2487 cone[3] = 20; 2488 PetscCall(DMPlexSetCone(dm, 1, cone)); 2489 ornt[0] = 0; 2490 ornt[1] = 0; 2491 ornt[2] = -1; 2492 ornt[3] = 0; 2493 PetscCall(DMPlexSetConeOrientation(dm, 1, ornt)); 2494 /* Cell 2 */ 2495 cone[0] = 21; 2496 cone[1] = 22; 2497 cone[2] = 18; 2498 cone[3] = 23; 2499 PetscCall(DMPlexSetCone(dm, 2, cone)); 2500 ornt[0] = 0; 2501 ornt[1] = 0; 2502 ornt[2] = -1; 2503 ornt[3] = 0; 2504 PetscCall(DMPlexSetConeOrientation(dm, 2, ornt)); 2505 /* Cell 3 */ 2506 cone[0] = 19; 2507 cone[1] = 22; 2508 cone[2] = 24; 2509 cone[3] = 15; 2510 PetscCall(DMPlexSetCone(dm, 3, cone)); 2511 ornt[0] = -1; 2512 ornt[1] = -1; 2513 ornt[2] = 0; 2514 ornt[3] = -1; 2515 PetscCall(DMPlexSetConeOrientation(dm, 3, ornt)); 2516 /* Cell 4 */ 2517 cone[0] = 16; 2518 cone[1] = 24; 2519 cone[2] = 21; 2520 cone[3] = 25; 2521 PetscCall(DMPlexSetCone(dm, 4, cone)); 2522 ornt[0] = -1; 2523 ornt[1] = -1; 2524 ornt[2] = -1; 2525 ornt[3] = 0; 2526 PetscCall(DMPlexSetConeOrientation(dm, 4, ornt)); 2527 /* Cell 5 */ 2528 cone[0] = 20; 2529 cone[1] = 17; 2530 cone[2] = 25; 2531 cone[3] = 23; 2532 PetscCall(DMPlexSetCone(dm, 5, cone)); 2533 ornt[0] = -1; 2534 ornt[1] = -1; 2535 ornt[2] = -1; 2536 ornt[3] = -1; 2537 PetscCall(DMPlexSetConeOrientation(dm, 5, ornt)); 2538 /* Edges */ 2539 cone[0] = 6; 2540 cone[1] = 7; 2541 PetscCall(DMPlexSetCone(dm, 14, cone)); 2542 cone[0] = 7; 2543 cone[1] = 8; 2544 PetscCall(DMPlexSetCone(dm, 15, cone)); 2545 cone[0] = 8; 2546 cone[1] = 9; 2547 PetscCall(DMPlexSetCone(dm, 16, cone)); 2548 cone[0] = 9; 2549 cone[1] = 6; 2550 PetscCall(DMPlexSetCone(dm, 17, cone)); 2551 cone[0] = 10; 2552 cone[1] = 11; 2553 PetscCall(DMPlexSetCone(dm, 18, cone)); 2554 cone[0] = 11; 2555 cone[1] = 7; 2556 PetscCall(DMPlexSetCone(dm, 19, cone)); 2557 cone[0] = 6; 2558 cone[1] = 10; 2559 PetscCall(DMPlexSetCone(dm, 20, cone)); 2560 cone[0] = 12; 2561 cone[1] = 13; 2562 PetscCall(DMPlexSetCone(dm, 21, cone)); 2563 cone[0] = 13; 2564 cone[1] = 11; 2565 PetscCall(DMPlexSetCone(dm, 22, cone)); 2566 cone[0] = 10; 2567 cone[1] = 12; 2568 PetscCall(DMPlexSetCone(dm, 23, cone)); 2569 cone[0] = 13; 2570 cone[1] = 8; 2571 PetscCall(DMPlexSetCone(dm, 24, cone)); 2572 cone[0] = 12; 2573 cone[1] = 9; 2574 PetscCall(DMPlexSetCone(dm, 25, cone)); 2575 } 2576 PetscCall(DMPlexSymmetrize(dm)); 2577 PetscCall(DMPlexStratify(dm)); 2578 /* Build coordinates */ 2579 PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn)); 2580 if (rank == 0) { 2581 coordsIn[0 * embedDim + 0] = -R; 2582 coordsIn[0 * embedDim + 1] = R; 2583 coordsIn[0 * embedDim + 2] = -R; 2584 coordsIn[1 * embedDim + 0] = R; 2585 coordsIn[1 * embedDim + 1] = R; 2586 coordsIn[1 * embedDim + 2] = -R; 2587 coordsIn[2 * embedDim + 0] = R; 2588 coordsIn[2 * embedDim + 1] = -R; 2589 coordsIn[2 * embedDim + 2] = -R; 2590 coordsIn[3 * embedDim + 0] = -R; 2591 coordsIn[3 * embedDim + 1] = -R; 2592 coordsIn[3 * embedDim + 2] = -R; 2593 coordsIn[4 * embedDim + 0] = -R; 2594 coordsIn[4 * embedDim + 1] = R; 2595 coordsIn[4 * embedDim + 2] = R; 2596 coordsIn[5 * embedDim + 0] = R; 2597 coordsIn[5 * embedDim + 1] = R; 2598 coordsIn[5 * embedDim + 2] = R; 2599 coordsIn[6 * embedDim + 0] = -R; 2600 coordsIn[6 * embedDim + 1] = -R; 2601 coordsIn[6 * embedDim + 2] = R; 2602 coordsIn[7 * embedDim + 0] = R; 2603 coordsIn[7 * embedDim + 1] = -R; 2604 coordsIn[7 * embedDim + 2] = R; 2605 } 2606 } 2607 break; 2608 case 3: 2609 if (simplex) { 2610 const PetscReal edgeLen = 1.0 / PETSC_PHI; 2611 PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5}; 2612 PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0}; 2613 PetscReal vertexC[4] = {0.5, 0.5 * PETSC_PHI, 0.5 / PETSC_PHI, 0.0}; 2614 const PetscInt degree = 12; 2615 PetscInt s[4] = {1, 1, 1}; 2616 PetscInt evenPerm[12][4] = { 2617 {0, 1, 2, 3}, 2618 {0, 2, 3, 1}, 2619 {0, 3, 1, 2}, 2620 {1, 0, 3, 2}, 2621 {1, 2, 0, 3}, 2622 {1, 3, 2, 0}, 2623 {2, 0, 1, 3}, 2624 {2, 1, 3, 0}, 2625 {2, 3, 0, 1}, 2626 {3, 0, 2, 1}, 2627 {3, 1, 0, 2}, 2628 {3, 2, 1, 0} 2629 }; 2630 PetscInt cone[4]; 2631 PetscInt *graph, p, i, j, k, l; 2632 2633 vertexA[0] *= R; 2634 vertexA[1] *= R; 2635 vertexA[2] *= R; 2636 vertexA[3] *= R; 2637 vertexB[0] *= R; 2638 vertexB[1] *= R; 2639 vertexB[2] *= R; 2640 vertexB[3] *= R; 2641 vertexC[0] *= R; 2642 vertexC[1] *= R; 2643 vertexC[2] *= R; 2644 vertexC[3] *= R; 2645 numCells = rank == 0 ? 600 : 0; 2646 numVerts = rank == 0 ? 120 : 0; 2647 firstVertex = numCells; 2648 /* Use the 600-cell, which for a unit sphere has coordinates which are 2649 2650 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16 2651 (\pm 1, 0, 0, 0) all cyclic permutations 8 2652 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96 2653 2654 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 2655 length is then given by 1/\phi = 0.61803. 2656 2657 http://buzzard.pugetsound.edu/sage-practice/ch03s03.html 2658 http://mathworld.wolfram.com/600-Cell.html 2659 */ 2660 /* Construct vertices */ 2661 PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn)); 2662 i = 0; 2663 if (rank == 0) { 2664 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2665 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2666 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2667 for (s[3] = -1; s[3] < 2; s[3] += 2) { 2668 for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[d] * vertexA[d]; 2669 ++i; 2670 } 2671 } 2672 } 2673 } 2674 for (p = 0; p < embedDim; ++p) { 2675 s[1] = s[2] = s[3] = 1; 2676 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2677 for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[(d + p) % embedDim] * vertexB[(d + p) % embedDim]; 2678 ++i; 2679 } 2680 } 2681 for (p = 0; p < 12; ++p) { 2682 s[3] = 1; 2683 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2684 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2685 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2686 for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[evenPerm[p][d]] * vertexC[evenPerm[p][d]]; 2687 ++i; 2688 } 2689 } 2690 } 2691 } 2692 } 2693 PetscCheck(i == numVerts, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertices %" PetscInt_FMT " != %" PetscInt_FMT, i, numVerts); 2694 /* Construct graph */ 2695 PetscCall(PetscCalloc1(numVerts * numVerts, &graph)); 2696 for (i = 0; i < numVerts; ++i) { 2697 for (j = 0, k = 0; j < numVerts; ++j) { 2698 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i * embedDim], &coordsIn[j * embedDim]) - edgeLen) < PETSC_SMALL) { 2699 graph[i * numVerts + j] = 1; 2700 ++k; 2701 } 2702 } 2703 PetscCheck(k == degree, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertex %" PetscInt_FMT " degree %" PetscInt_FMT " != %" PetscInt_FMT, i, k, degree); 2704 } 2705 /* Build Topology */ 2706 PetscCall(DMPlexSetChart(dm, 0, numCells + numVerts)); 2707 for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, embedDim)); 2708 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 2709 /* Cells */ 2710 if (rank == 0) { 2711 for (i = 0, c = 0; i < numVerts; ++i) { 2712 for (j = 0; j < i; ++j) { 2713 for (k = 0; k < j; ++k) { 2714 for (l = 0; l < k; ++l) { 2715 if (graph[i * numVerts + j] && graph[j * numVerts + k] && graph[k * numVerts + i] && graph[l * numVerts + i] && graph[l * numVerts + j] && graph[l * numVerts + k]) { 2716 cone[0] = firstVertex + i; 2717 cone[1] = firstVertex + j; 2718 cone[2] = firstVertex + k; 2719 cone[3] = firstVertex + l; 2720 /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */ 2721 { 2722 const PetscInt epsilon[4][4][4][4] = { 2723 {{{0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0}}, {{0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 1}, {0, 0, -1, 0}}, {{0, 0, 0, 0}, {0, 0, 0, -1}, {0, 0, 0, 0}, {0, 1, 0, 0}}, {{0, 0, 0, 0}, {0, 0, 1, 0}, {0, -1, 0, 0}, {0, 0, 0, 0}}}, 2724 2725 {{{0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, -1}, {0, 0, 1, 0}}, {{0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0}}, {{0, 0, 0, 1}, {0, 0, 0, 0}, {0, 0, 0, 0}, {-1, 0, 0, 0}}, {{0, 0, -1, 0}, {0, 0, 0, 0}, {1, 0, 0, 0}, {0, 0, 0, 0}}}, 2726 2727 {{{0, 0, 0, 0}, {0, 0, 0, 1}, {0, 0, 0, 0}, {0, -1, 0, 0}}, {{0, 0, 0, -1}, {0, 0, 0, 0}, {0, 0, 0, 0}, {1, 0, 0, 0}}, {{0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0}}, {{0, 1, 0, 0}, {-1, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0}}}, 2728 2729 {{{0, 0, 0, 0}, {0, 0, -1, 0}, {0, 1, 0, 0}, {0, 0, 0, 0}}, {{0, 0, 1, 0}, {0, 0, 0, 0}, {-1, 0, 0, 0}, {0, 0, 0, 0}}, {{0, -1, 0, 0}, {1, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0}}, {{0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0}} } 2730 }; 2731 PetscReal normal[4]; 2732 PetscInt e, f, g; 2733 2734 for (d = 0; d < embedDim; ++d) { 2735 normal[d] = 0.0; 2736 for (e = 0; e < embedDim; ++e) { 2737 for (f = 0; f < embedDim; ++f) { 2738 for (g = 0; g < embedDim; ++g) { 2739 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]); 2740 } 2741 } 2742 } 2743 } 2744 if (DotReal(embedDim, normal, &coordsIn[i * embedDim]) < 0) { 2745 PetscInt tmp = cone[1]; 2746 cone[1] = cone[2]; 2747 cone[2] = tmp; 2748 } 2749 } 2750 PetscCall(DMPlexSetCone(dm, c++, cone)); 2751 } 2752 } 2753 } 2754 } 2755 } 2756 } 2757 PetscCall(DMPlexSymmetrize(dm)); 2758 PetscCall(DMPlexStratify(dm)); 2759 PetscCall(PetscFree(graph)); 2760 } 2761 break; 2762 default: 2763 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported dimension for sphere: %" PetscInt_FMT, dim); 2764 } 2765 /* Create coordinates */ 2766 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 2767 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 2768 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, embedDim)); 2769 PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex + numVerts)); 2770 for (v = firstVertex; v < firstVertex + numVerts; ++v) { 2771 PetscCall(PetscSectionSetDof(coordSection, v, embedDim)); 2772 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, embedDim)); 2773 } 2774 PetscCall(PetscSectionSetUp(coordSection)); 2775 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 2776 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 2777 PetscCall(VecSetBlockSize(coordinates, embedDim)); 2778 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 2779 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 2780 PetscCall(VecSetType(coordinates, VECSTANDARD)); 2781 PetscCall(VecGetArray(coordinates, &coords)); 2782 for (v = 0; v < numVerts; ++v) 2783 for (d = 0; d < embedDim; ++d) coords[v * embedDim + d] = coordsIn[v * embedDim + d]; 2784 PetscCall(VecRestoreArray(coordinates, &coords)); 2785 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 2786 PetscCall(VecDestroy(&coordinates)); 2787 PetscCall(PetscFree(coordsIn)); 2788 { 2789 DM cdm; 2790 PetscDS cds; 2791 PetscScalar c = R; 2792 2793 PetscCall(DMPlexCreateCoordinateSpace(dm, 1, snapToSphere)); 2794 PetscCall(DMGetCoordinateDM(dm, &cdm)); 2795 PetscCall(DMGetDS(cdm, &cds)); 2796 PetscCall(PetscDSSetConstants(cds, 1, &c)); 2797 } 2798 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 2799 /* Wait for coordinate creation before doing in-place modification */ 2800 if (simplex) PetscCall(DMPlexInterpolateInPlace_Internal(dm)); 2801 PetscFunctionReturn(PETSC_SUCCESS); 2802 } 2803 2804 typedef void (*TPSEvaluateFunc)(const PetscReal[], PetscReal *, PetscReal[], PetscReal (*)[3]); 2805 2806 /* 2807 The Schwarz P implicit surface is 2808 2809 f(x) = cos(x0) + cos(x1) + cos(x2) = 0 2810 */ 2811 static void TPSEvaluate_SchwarzP(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3]) 2812 { 2813 PetscReal c[3] = {PetscCosReal(y[0] * PETSC_PI), PetscCosReal(y[1] * PETSC_PI), PetscCosReal(y[2] * PETSC_PI)}; 2814 PetscReal g[3] = {-PetscSinReal(y[0] * PETSC_PI), -PetscSinReal(y[1] * PETSC_PI), -PetscSinReal(y[2] * PETSC_PI)}; 2815 f[0] = c[0] + c[1] + c[2]; 2816 for (PetscInt i = 0; i < 3; i++) { 2817 grad[i] = PETSC_PI * g[i]; 2818 for (PetscInt j = 0; j < 3; j++) hess[i][j] = (i == j) ? -PetscSqr(PETSC_PI) * c[i] : 0.; 2819 } 2820 } 2821 2822 // u[] is a tentative normal on input. Replace with the implicit function gradient in the same direction 2823 static PetscErrorCode TPSExtrudeNormalFunc_SchwarzP(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt r, PetscScalar u[], void *ctx) 2824 { 2825 for (PetscInt i = 0; i < 3; i++) u[i] = -PETSC_PI * PetscSinReal(x[i] * PETSC_PI); 2826 return PETSC_SUCCESS; 2827 } 2828 2829 /* 2830 The Gyroid implicit surface is 2831 2832 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) 2833 2834 */ 2835 static void TPSEvaluate_Gyroid(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3]) 2836 { 2837 PetscReal s[3] = {PetscSinReal(PETSC_PI * y[0]), PetscSinReal(PETSC_PI * (y[1] + .5)), PetscSinReal(PETSC_PI * (y[2] + .25))}; 2838 PetscReal c[3] = {PetscCosReal(PETSC_PI * y[0]), PetscCosReal(PETSC_PI * (y[1] + .5)), PetscCosReal(PETSC_PI * (y[2] + .25))}; 2839 f[0] = s[0] * c[1] + s[1] * c[2] + s[2] * c[0]; 2840 grad[0] = PETSC_PI * (c[0] * c[1] - s[2] * s[0]); 2841 grad[1] = PETSC_PI * (c[1] * c[2] - s[0] * s[1]); 2842 grad[2] = PETSC_PI * (c[2] * c[0] - s[1] * s[2]); 2843 hess[0][0] = -PetscSqr(PETSC_PI) * (s[0] * c[1] + s[2] * c[0]); 2844 hess[0][1] = -PetscSqr(PETSC_PI) * (c[0] * s[1]); 2845 hess[0][2] = -PetscSqr(PETSC_PI) * (c[2] * s[0]); 2846 hess[1][0] = -PetscSqr(PETSC_PI) * (s[1] * c[2] + s[0] * c[1]); 2847 hess[1][1] = -PetscSqr(PETSC_PI) * (c[1] * s[2]); 2848 hess[2][2] = -PetscSqr(PETSC_PI) * (c[0] * s[1]); 2849 hess[2][0] = -PetscSqr(PETSC_PI) * (s[2] * c[0] + s[1] * c[2]); 2850 hess[2][1] = -PetscSqr(PETSC_PI) * (c[2] * s[0]); 2851 hess[2][2] = -PetscSqr(PETSC_PI) * (c[1] * s[2]); 2852 } 2853 2854 // u[] is a tentative normal on input. Replace with the implicit function gradient in the same direction 2855 static PetscErrorCode TPSExtrudeNormalFunc_Gyroid(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt r, PetscScalar u[], void *ctx) 2856 { 2857 PetscReal s[3] = {PetscSinReal(PETSC_PI * x[0]), PetscSinReal(PETSC_PI * (x[1] + .5)), PetscSinReal(PETSC_PI * (x[2] + .25))}; 2858 PetscReal c[3] = {PetscCosReal(PETSC_PI * x[0]), PetscCosReal(PETSC_PI * (x[1] + .5)), PetscCosReal(PETSC_PI * (x[2] + .25))}; 2859 u[0] = PETSC_PI * (c[0] * c[1] - s[2] * s[0]); 2860 u[1] = PETSC_PI * (c[1] * c[2] - s[0] * s[1]); 2861 u[2] = PETSC_PI * (c[2] * c[0] - s[1] * s[2]); 2862 return PETSC_SUCCESS; 2863 } 2864 2865 /* 2866 We wish to solve 2867 2868 min_y || y - x ||^2 subject to f(y) = 0 2869 2870 Let g(y) = grad(f). The minimization problem is equivalent to asking to satisfy 2871 f(y) = 0 and (y-x) is parallel to g(y). We do this by using Householder QR to obtain a basis for the 2872 tangent space and ask for both components in the tangent space to be zero. 2873 2874 Take g to be a column vector and compute the "full QR" factorization Q R = g, 2875 where Q = I - 2 n n^T is a symmetric orthogonal matrix. 2876 The first column of Q is parallel to g so the remaining two columns span the null space. 2877 Let Qn = Q[:,1:] be those remaining columns. Then Qn Qn^T is an orthogonal projector into the tangent space. 2878 Since Q is symmetric, this is equivalent to multiplying by Q and taking the last two entries. 2879 In total, we have a system of 3 equations in 3 unknowns: 2880 2881 f(y) = 0 1 equation 2882 Qn^T (y - x) = 0 2 equations 2883 2884 Here, we compute the residual and Jacobian of this system. 2885 */ 2886 static void TPSNearestPointResJac(TPSEvaluateFunc feval, const PetscScalar x[], const PetscScalar y[], PetscScalar res[], PetscScalar J[]) 2887 { 2888 PetscReal yreal[3] = {PetscRealPart(y[0]), PetscRealPart(y[1]), PetscRealPart(y[2])}; 2889 PetscReal d[3] = {PetscRealPart(y[0] - x[0]), PetscRealPart(y[1] - x[1]), PetscRealPart(y[2] - x[2])}; 2890 PetscReal f, grad[3], n[3], norm, norm_y[3], nd, nd_y[3], sign; 2891 PetscReal n_y[3][3] = { 2892 {0, 0, 0}, 2893 {0, 0, 0}, 2894 {0, 0, 0} 2895 }; 2896 2897 feval(yreal, &f, grad, n_y); 2898 2899 for (PetscInt i = 0; i < 3; i++) n[i] = grad[i]; 2900 norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2])); 2901 for (PetscInt i = 0; i < 3; i++) norm_y[i] = 1. / norm * n[i] * n_y[i][i]; 2902 2903 // Define the Householder reflector 2904 sign = n[0] >= 0 ? 1. : -1.; 2905 n[0] += norm * sign; 2906 for (PetscInt i = 0; i < 3; i++) n_y[0][i] += norm_y[i] * sign; 2907 2908 norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2])); 2909 norm_y[0] = 1. / norm * (n[0] * n_y[0][0]); 2910 norm_y[1] = 1. / norm * (n[0] * n_y[0][1] + n[1] * n_y[1][1]); 2911 norm_y[2] = 1. / norm * (n[0] * n_y[0][2] + n[2] * n_y[2][2]); 2912 2913 for (PetscInt i = 0; i < 3; i++) { 2914 n[i] /= norm; 2915 for (PetscInt j = 0; j < 3; j++) { 2916 // note that n[i] is n_old[i]/norm when executing the code below 2917 n_y[i][j] = n_y[i][j] / norm - n[i] / norm * norm_y[j]; 2918 } 2919 } 2920 2921 nd = n[0] * d[0] + n[1] * d[1] + n[2] * d[2]; 2922 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]; 2923 2924 res[0] = f; 2925 res[1] = d[1] - 2 * n[1] * nd; 2926 res[2] = d[2] - 2 * n[2] * nd; 2927 // J[j][i] is J_{ij} (column major) 2928 for (PetscInt j = 0; j < 3; j++) { 2929 J[0 + j * 3] = grad[j]; 2930 J[1 + j * 3] = (j == 1) * 1. - 2 * (n_y[1][j] * nd + n[1] * nd_y[j]); 2931 J[2 + j * 3] = (j == 2) * 1. - 2 * (n_y[2][j] * nd + n[2] * nd_y[j]); 2932 } 2933 } 2934 2935 /* 2936 Project x to the nearest point on the implicit surface using Newton's method. 2937 */ 2938 static PetscErrorCode TPSNearestPoint(TPSEvaluateFunc feval, PetscScalar x[]) 2939 { 2940 PetscScalar y[3] = {x[0], x[1], x[2]}; // Initial guess 2941 2942 PetscFunctionBegin; 2943 for (PetscInt iter = 0; iter < 10; iter++) { 2944 PetscScalar res[3], J[9]; 2945 PetscReal resnorm; 2946 TPSNearestPointResJac(feval, x, y, res, J); 2947 resnorm = PetscSqrtReal(PetscSqr(PetscRealPart(res[0])) + PetscSqr(PetscRealPart(res[1])) + PetscSqr(PetscRealPart(res[2]))); 2948 if (0) { // Turn on this monitor if you need to confirm quadratic convergence 2949 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]))); 2950 } 2951 if (resnorm < PETSC_SMALL) break; 2952 2953 // Take the Newton step 2954 PetscCall(PetscKernel_A_gets_inverse_A_3(J, 0., PETSC_FALSE, NULL)); 2955 PetscKernel_v_gets_v_minus_A_times_w_3(y, J, res); 2956 } 2957 for (PetscInt i = 0; i < 3; i++) x[i] = y[i]; 2958 PetscFunctionReturn(PETSC_SUCCESS); 2959 } 2960 2961 const char *const DMPlexTPSTypes[] = {"SCHWARZ_P", "GYROID", "DMPlexTPSType", "DMPLEX_TPS_", NULL}; 2962 2963 static PetscErrorCode DMPlexCreateTPSMesh_Internal(DM dm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscBool tps_distribute, PetscInt refinements, PetscInt layers, PetscReal thickness) 2964 { 2965 PetscMPIInt rank; 2966 PetscInt topoDim = 2, spaceDim = 3, numFaces = 0, numVertices = 0, numEdges = 0; 2967 PetscInt(*edges)[2] = NULL, *edgeSets = NULL; 2968 PetscInt *cells_flat = NULL; 2969 PetscReal *vtxCoords = NULL; 2970 TPSEvaluateFunc evalFunc = NULL; 2971 PetscSimplePointFunc normalFunc = NULL; 2972 DMLabel label; 2973 2974 PetscFunctionBegin; 2975 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 2976 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 2977 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); 2978 switch (tpstype) { 2979 case DMPLEX_TPS_SCHWARZ_P: 2980 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"); 2981 if (rank == 0) { 2982 PetscInt(*cells)[6][4][4] = NULL; // [junction, junction-face, cell, conn] 2983 PetscInt Njunctions = 0, Ncuts = 0, Npipes[3], vcount; 2984 PetscReal L = 1; 2985 2986 Npipes[0] = (extent[0] + 1) * extent[1] * extent[2]; 2987 Npipes[1] = extent[0] * (extent[1] + 1) * extent[2]; 2988 Npipes[2] = extent[0] * extent[1] * (extent[2] + 1); 2989 Njunctions = extent[0] * extent[1] * extent[2]; 2990 Ncuts = 2 * (extent[0] * extent[1] + extent[1] * extent[2] + extent[2] * extent[0]); 2991 numVertices = 4 * (Npipes[0] + Npipes[1] + Npipes[2]) + 8 * Njunctions; 2992 PetscCall(PetscMalloc1(3 * numVertices, &vtxCoords)); 2993 PetscCall(PetscMalloc1(Njunctions, &cells)); 2994 PetscCall(PetscMalloc1(Ncuts * 4, &edges)); 2995 PetscCall(PetscMalloc1(Ncuts * 4, &edgeSets)); 2996 // x-normal pipes 2997 vcount = 0; 2998 for (PetscInt i = 0; i < extent[0] + 1; i++) { 2999 for (PetscInt j = 0; j < extent[1]; j++) { 3000 for (PetscInt k = 0; k < extent[2]; k++) { 3001 for (PetscInt l = 0; l < 4; l++) { 3002 vtxCoords[vcount++] = (2 * i - 1) * L; 3003 vtxCoords[vcount++] = 2 * j * L + PetscCosReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3004 vtxCoords[vcount++] = 2 * k * L + PetscSinReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3005 } 3006 } 3007 } 3008 } 3009 // y-normal pipes 3010 for (PetscInt i = 0; i < extent[0]; i++) { 3011 for (PetscInt j = 0; j < extent[1] + 1; j++) { 3012 for (PetscInt k = 0; k < extent[2]; k++) { 3013 for (PetscInt l = 0; l < 4; l++) { 3014 vtxCoords[vcount++] = 2 * i * L + PetscSinReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3015 vtxCoords[vcount++] = (2 * j - 1) * L; 3016 vtxCoords[vcount++] = 2 * k * L + PetscCosReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3017 } 3018 } 3019 } 3020 } 3021 // z-normal pipes 3022 for (PetscInt i = 0; i < extent[0]; i++) { 3023 for (PetscInt j = 0; j < extent[1]; j++) { 3024 for (PetscInt k = 0; k < extent[2] + 1; k++) { 3025 for (PetscInt l = 0; l < 4; l++) { 3026 vtxCoords[vcount++] = 2 * i * L + PetscCosReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3027 vtxCoords[vcount++] = 2 * j * L + PetscSinReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3028 vtxCoords[vcount++] = (2 * k - 1) * L; 3029 } 3030 } 3031 } 3032 } 3033 // junctions 3034 for (PetscInt i = 0; i < extent[0]; i++) { 3035 for (PetscInt j = 0; j < extent[1]; j++) { 3036 for (PetscInt k = 0; k < extent[2]; k++) { 3037 const PetscInt J = (i * extent[1] + j) * extent[2] + k, Jvoff = (Npipes[0] + Npipes[1] + Npipes[2]) * 4 + J * 8; 3038 PetscCheck(vcount / 3 == Jvoff, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unexpected vertex count"); 3039 for (PetscInt ii = 0; ii < 2; ii++) { 3040 for (PetscInt jj = 0; jj < 2; jj++) { 3041 for (PetscInt kk = 0; kk < 2; kk++) { 3042 double Ls = (1 - sqrt(2) / 4) * L; 3043 vtxCoords[vcount++] = 2 * i * L + (2 * ii - 1) * Ls; 3044 vtxCoords[vcount++] = 2 * j * L + (2 * jj - 1) * Ls; 3045 vtxCoords[vcount++] = 2 * k * L + (2 * kk - 1) * Ls; 3046 } 3047 } 3048 } 3049 const PetscInt jfaces[3][2][4] = { 3050 {{3, 1, 0, 2}, {7, 5, 4, 6}}, // x-aligned 3051 {{5, 4, 0, 1}, {7, 6, 2, 3}}, // y-aligned 3052 {{6, 2, 0, 4}, {7, 3, 1, 5}} // z-aligned 3053 }; 3054 const PetscInt pipe_lo[3] = {// vertex numbers of pipes 3055 ((i * extent[1] + j) * extent[2] + k) * 4, ((i * (extent[1] + 1) + j) * extent[2] + k + Npipes[0]) * 4, ((i * extent[1] + j) * (extent[2] + 1) + k + Npipes[0] + Npipes[1]) * 4}; 3056 const PetscInt pipe_hi[3] = {// vertex numbers of pipes 3057 (((i + 1) * extent[1] + j) * extent[2] + k) * 4, ((i * (extent[1] + 1) + j + 1) * extent[2] + k + Npipes[0]) * 4, ((i * extent[1] + j) * (extent[2] + 1) + k + 1 + Npipes[0] + Npipes[1]) * 4}; 3058 for (PetscInt dir = 0; dir < 3; dir++) { // x,y,z 3059 const PetscInt ijk[3] = {i, j, k}; 3060 for (PetscInt l = 0; l < 4; l++) { // rotations 3061 cells[J][dir * 2 + 0][l][0] = pipe_lo[dir] + l; 3062 cells[J][dir * 2 + 0][l][1] = Jvoff + jfaces[dir][0][l]; 3063 cells[J][dir * 2 + 0][l][2] = Jvoff + jfaces[dir][0][(l - 1 + 4) % 4]; 3064 cells[J][dir * 2 + 0][l][3] = pipe_lo[dir] + (l - 1 + 4) % 4; 3065 cells[J][dir * 2 + 1][l][0] = Jvoff + jfaces[dir][1][l]; 3066 cells[J][dir * 2 + 1][l][1] = pipe_hi[dir] + l; 3067 cells[J][dir * 2 + 1][l][2] = pipe_hi[dir] + (l - 1 + 4) % 4; 3068 cells[J][dir * 2 + 1][l][3] = Jvoff + jfaces[dir][1][(l - 1 + 4) % 4]; 3069 if (ijk[dir] == 0) { 3070 edges[numEdges][0] = pipe_lo[dir] + l; 3071 edges[numEdges][1] = pipe_lo[dir] + (l + 1) % 4; 3072 edgeSets[numEdges] = dir * 2 + 1; 3073 numEdges++; 3074 } 3075 if (ijk[dir] + 1 == extent[dir]) { 3076 edges[numEdges][0] = pipe_hi[dir] + l; 3077 edges[numEdges][1] = pipe_hi[dir] + (l + 1) % 4; 3078 edgeSets[numEdges] = dir * 2 + 2; 3079 numEdges++; 3080 } 3081 } 3082 } 3083 } 3084 } 3085 } 3086 PetscCheck(numEdges == Ncuts * 4, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Edge count %" PetscInt_FMT " incompatible with number of cuts %" PetscInt_FMT, numEdges, Ncuts); 3087 numFaces = 24 * Njunctions; 3088 cells_flat = cells[0][0][0]; 3089 } 3090 evalFunc = TPSEvaluate_SchwarzP; 3091 normalFunc = TPSExtrudeNormalFunc_SchwarzP; 3092 break; 3093 case DMPLEX_TPS_GYROID: 3094 if (rank == 0) { 3095 // This is a coarse mesh approximation of the gyroid shifted to being the zero of the level set 3096 // 3097 // 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) 3098 // 3099 // on the cell [0,2]^3. 3100 // 3101 // Think about dividing that cell into four columns, and focus on the column [0,1]x[0,1]x[0,2]. 3102 // If you looked at the gyroid in that column at different slices of z you would see that it kind of spins 3103 // like a boomerang: 3104 // 3105 // z = 0 z = 1/4 z = 1/2 z = 3/4 // 3106 // ----- ------- ------- ------- // 3107 // // 3108 // + + + + + + + \ + // 3109 // \ / \ // 3110 // \ `-_ _-' / } // 3111 // *-_ `-' _-' / // 3112 // + `-+ + + +-' + + / + // 3113 // // 3114 // // 3115 // z = 1 z = 5/4 z = 3/2 z = 7/4 // 3116 // ----- ------- ------- ------- // 3117 // // 3118 // +-_ + + + + _-+ + / + // 3119 // `-_ _-_ _-` / // 3120 // \ _-' `-_ / { // 3121 // \ / \ // 3122 // + + + + + + + \ + // 3123 // 3124 // 3125 // This course mesh approximates each of these slices by two line segments, 3126 // and then connects the segments in consecutive layers with quadrilateral faces. 3127 // All of the end points of the segments are multiples of 1/4 except for the 3128 // point * in the picture for z = 0 above and the similar points in other layers. 3129 // That point is at (gamma, gamma, 0), where gamma is calculated below. 3130 // 3131 // The column [1,2]x[1,2]x[0,2] looks the same as this column; 3132 // The columns [1,2]x[0,1]x[0,2] and [0,1]x[1,2]x[0,2] are mirror images. 3133 // 3134 // As for how this method turned into the names given to the vertices: 3135 // that was not systematic, it was just the way it worked out in my handwritten notes. 3136 3137 PetscInt facesPerBlock = 64; 3138 PetscInt vertsPerBlock = 56; 3139 PetscInt extentPlus[3]; 3140 PetscInt numBlocks, numBlocksPlus; 3141 const PetscInt A = 0, B = 1, C = 2, D = 3, E = 4, F = 5, G = 6, H = 7, II = 8, J = 9, K = 10, L = 11, M = 12, N = 13, O = 14, P = 15, Q = 16, R = 17, S = 18, T = 19, U = 20, V = 21, W = 22, X = 23, Y = 24, Z = 25, Ap = 26, Bp = 27, Cp = 28, Dp = 29, Ep = 30, Fp = 31, Gp = 32, Hp = 33, Ip = 34, Jp = 35, Kp = 36, Lp = 37, Mp = 38, Np = 39, Op = 40, Pp = 41, Qp = 42, Rp = 43, Sp = 44, Tp = 45, Up = 46, Vp = 47, Wp = 48, Xp = 49, Yp = 50, Zp = 51, Aq = 52, Bq = 53, Cq = 54, Dq = 55; 3142 const PetscInt pattern[64][4] = { 3143 /* face to vertex within the coarse discretization of a single gyroid block */ 3144 /* layer 0 */ 3145 {A, C, K, G }, 3146 {C, B, II, K }, 3147 {D, A, H, L }, 3148 {B + 56 * 1, D, L, J }, 3149 {E, B + 56 * 1, J, N }, 3150 {A + 56 * 2, E, N, H + 56 * 2 }, 3151 {F, A + 56 * 2, G + 56 * 2, M }, 3152 {B, F, M, II }, 3153 /* layer 1 */ 3154 {G, K, Q, O }, 3155 {K, II, P, Q }, 3156 {L, H, O + 56 * 1, R }, 3157 {J, L, R, P }, 3158 {N, J, P, S }, 3159 {H + 56 * 2, N, S, O + 56 * 3 }, 3160 {M, G + 56 * 2, O + 56 * 2, T }, 3161 {II, M, T, P }, 3162 /* layer 2 */ 3163 {O, Q, Y, U }, 3164 {Q, P, W, Y }, 3165 {R, O + 56 * 1, U + 56 * 1, Ap }, 3166 {P, R, Ap, W }, 3167 {S, P, X, Bp }, 3168 {O + 56 * 3, S, Bp, V + 56 * 1 }, 3169 {T, O + 56 * 2, V, Z }, 3170 {P, T, Z, X }, 3171 /* layer 3 */ 3172 {U, Y, Ep, Dp }, 3173 {Y, W, Cp, Ep }, 3174 {Ap, U + 56 * 1, Dp + 56 * 1, Gp }, 3175 {W, Ap, Gp, Cp }, 3176 {Bp, X, Cp + 56 * 2, Fp }, 3177 {V + 56 * 1, Bp, Fp, Dp + 56 * 1}, 3178 {Z, V, Dp, Hp }, 3179 {X, Z, Hp, Cp + 56 * 2}, 3180 /* layer 4 */ 3181 {Dp, Ep, Mp, Kp }, 3182 {Ep, Cp, Ip, Mp }, 3183 {Gp, Dp + 56 * 1, Lp, Np }, 3184 {Cp, Gp, Np, Jp }, 3185 {Fp, Cp + 56 * 2, Jp + 56 * 2, Pp }, 3186 {Dp + 56 * 1, Fp, Pp, Lp }, 3187 {Hp, Dp, Kp, Op }, 3188 {Cp + 56 * 2, Hp, Op, Ip + 56 * 2}, 3189 /* layer 5 */ 3190 {Kp, Mp, Sp, Rp }, 3191 {Mp, Ip, Qp, Sp }, 3192 {Np, Lp, Rp, Tp }, 3193 {Jp, Np, Tp, Qp + 56 * 1}, 3194 {Pp, Jp + 56 * 2, Qp + 56 * 3, Up }, 3195 {Lp, Pp, Up, Rp }, 3196 {Op, Kp, Rp, Vp }, 3197 {Ip + 56 * 2, Op, Vp, Qp + 56 * 2}, 3198 /* layer 6 */ 3199 {Rp, Sp, Aq, Yp }, 3200 {Sp, Qp, Wp, Aq }, 3201 {Tp, Rp, Yp, Cq }, 3202 {Qp + 56 * 1, Tp, Cq, Wp + 56 * 1}, 3203 {Up, Qp + 56 * 3, Xp + 56 * 1, Dq }, 3204 {Rp, Up, Dq, Zp }, 3205 {Vp, Rp, Zp, Bq }, 3206 {Qp + 56 * 2, Vp, Bq, Xp }, 3207 /* layer 7 (the top is the periodic image of the bottom of layer 0) */ 3208 {Yp, Aq, C + 56 * 4, A + 56 * 4 }, 3209 {Aq, Wp, B + 56 * 4, C + 56 * 4 }, 3210 {Cq, Yp, A + 56 * 4, D + 56 * 4 }, 3211 {Wp + 56 * 1, Cq, D + 56 * 4, B + 56 * 5 }, 3212 {Dq, Xp + 56 * 1, B + 56 * 5, E + 56 * 4 }, 3213 {Zp, Dq, E + 56 * 4, A + 56 * 6 }, 3214 {Bq, Zp, A + 56 * 6, F + 56 * 4 }, 3215 {Xp, Bq, F + 56 * 4, B + 56 * 4 } 3216 }; 3217 const PetscReal gamma = PetscAcosReal((PetscSqrtReal(3.) - 1.) / PetscSqrtReal(2.)) / PETSC_PI; 3218 const PetscReal patternCoords[56][3] = { 3219 {1., 0., 0. }, /* A */ 3220 {0., 1., 0. }, /* B */ 3221 {gamma, gamma, 0. }, /* C */ 3222 {1 + gamma, 1 - gamma, 0. }, /* D */ 3223 {2 - gamma, 2 - gamma, 0. }, /* E */ 3224 {1 - gamma, 1 + gamma, 0. }, /* F */ 3225 3226 {.5, 0, .25 }, /* G */ 3227 {1.5, 0., .25 }, /* H */ 3228 {.5, 1., .25 }, /* II */ 3229 {1.5, 1., .25 }, /* J */ 3230 {.25, .5, .25 }, /* K */ 3231 {1.25, .5, .25 }, /* L */ 3232 {.75, 1.5, .25 }, /* M */ 3233 {1.75, 1.5, .25 }, /* N */ 3234 3235 {0., 0., .5 }, /* O */ 3236 {1., 1., .5 }, /* P */ 3237 {gamma, 1 - gamma, .5 }, /* Q */ 3238 {1 + gamma, gamma, .5 }, /* R */ 3239 {2 - gamma, 1 + gamma, .5 }, /* S */ 3240 {1 - gamma, 2 - gamma, .5 }, /* T */ 3241 3242 {0., .5, .75 }, /* U */ 3243 {0., 1.5, .75 }, /* V */ 3244 {1., .5, .75 }, /* W */ 3245 {1., 1.5, .75 }, /* X */ 3246 {.5, .75, .75 }, /* Y */ 3247 {.5, 1.75, .75 }, /* Z */ 3248 {1.5, .25, .75 }, /* Ap */ 3249 {1.5, 1.25, .75 }, /* Bp */ 3250 3251 {1., 0., 1. }, /* Cp */ 3252 {0., 1., 1. }, /* Dp */ 3253 {1 - gamma, 1 - gamma, 1. }, /* Ep */ 3254 {1 + gamma, 1 + gamma, 1. }, /* Fp */ 3255 {2 - gamma, gamma, 1. }, /* Gp */ 3256 {gamma, 2 - gamma, 1. }, /* Hp */ 3257 3258 {.5, 0., 1.25}, /* Ip */ 3259 {1.5, 0., 1.25}, /* Jp */ 3260 {.5, 1., 1.25}, /* Kp */ 3261 {1.5, 1., 1.25}, /* Lp */ 3262 {.75, .5, 1.25}, /* Mp */ 3263 {1.75, .5, 1.25}, /* Np */ 3264 {.25, 1.5, 1.25}, /* Op */ 3265 {1.25, 1.5, 1.25}, /* Pp */ 3266 3267 {0., 0., 1.5 }, /* Qp */ 3268 {1., 1., 1.5 }, /* Rp */ 3269 {1 - gamma, gamma, 1.5 }, /* Sp */ 3270 {2 - gamma, 1 - gamma, 1.5 }, /* Tp */ 3271 {1 + gamma, 2 - gamma, 1.5 }, /* Up */ 3272 {gamma, 1 + gamma, 1.5 }, /* Vp */ 3273 3274 {0., .5, 1.75}, /* Wp */ 3275 {0., 1.5, 1.75}, /* Xp */ 3276 {1., .5, 1.75}, /* Yp */ 3277 {1., 1.5, 1.75}, /* Zp */ 3278 {.5, .25, 1.75}, /* Aq */ 3279 {.5, 1.25, 1.75}, /* Bq */ 3280 {1.5, .75, 1.75}, /* Cq */ 3281 {1.5, 1.75, 1.75}, /* Dq */ 3282 }; 3283 PetscInt(*cells)[64][4] = NULL; 3284 PetscBool *seen; 3285 PetscInt *vertToTrueVert; 3286 PetscInt count; 3287 3288 for (PetscInt i = 0; i < 3; i++) extentPlus[i] = extent[i] + 1; 3289 numBlocks = 1; 3290 for (PetscInt i = 0; i < 3; i++) numBlocks *= extent[i]; 3291 numBlocksPlus = 1; 3292 for (PetscInt i = 0; i < 3; i++) numBlocksPlus *= extentPlus[i]; 3293 numFaces = numBlocks * facesPerBlock; 3294 PetscCall(PetscMalloc1(numBlocks, &cells)); 3295 PetscCall(PetscCalloc1(numBlocksPlus * vertsPerBlock, &seen)); 3296 for (PetscInt k = 0; k < extent[2]; k++) { 3297 for (PetscInt j = 0; j < extent[1]; j++) { 3298 for (PetscInt i = 0; i < extent[0]; i++) { 3299 for (PetscInt f = 0; f < facesPerBlock; f++) { 3300 for (PetscInt v = 0; v < 4; v++) { 3301 PetscInt vertRaw = pattern[f][v]; 3302 PetscInt blockidx = vertRaw / 56; 3303 PetscInt patternvert = vertRaw % 56; 3304 PetscInt xplus = (blockidx & 1); 3305 PetscInt yplus = (blockidx & 2) >> 1; 3306 PetscInt zplus = (blockidx & 4) >> 2; 3307 PetscInt zcoord = (periodic && periodic[2] == DM_BOUNDARY_PERIODIC) ? ((k + zplus) % extent[2]) : (k + zplus); 3308 PetscInt ycoord = (periodic && periodic[1] == DM_BOUNDARY_PERIODIC) ? ((j + yplus) % extent[1]) : (j + yplus); 3309 PetscInt xcoord = (periodic && periodic[0] == DM_BOUNDARY_PERIODIC) ? ((i + xplus) % extent[0]) : (i + xplus); 3310 PetscInt vert = ((zcoord * extentPlus[1] + ycoord) * extentPlus[0] + xcoord) * 56 + patternvert; 3311 3312 cells[(k * extent[1] + j) * extent[0] + i][f][v] = vert; 3313 seen[vert] = PETSC_TRUE; 3314 } 3315 } 3316 } 3317 } 3318 } 3319 for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++) 3320 if (seen[i]) numVertices++; 3321 count = 0; 3322 PetscCall(PetscMalloc1(numBlocksPlus * vertsPerBlock, &vertToTrueVert)); 3323 PetscCall(PetscMalloc1(numVertices * 3, &vtxCoords)); 3324 for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++) vertToTrueVert[i] = -1; 3325 for (PetscInt k = 0; k < extentPlus[2]; k++) { 3326 for (PetscInt j = 0; j < extentPlus[1]; j++) { 3327 for (PetscInt i = 0; i < extentPlus[0]; i++) { 3328 for (PetscInt v = 0; v < vertsPerBlock; v++) { 3329 PetscInt vIdx = ((k * extentPlus[1] + j) * extentPlus[0] + i) * vertsPerBlock + v; 3330 3331 if (seen[vIdx]) { 3332 PetscInt thisVert; 3333 3334 vertToTrueVert[vIdx] = thisVert = count++; 3335 3336 for (PetscInt d = 0; d < 3; d++) vtxCoords[3 * thisVert + d] = patternCoords[v][d]; 3337 vtxCoords[3 * thisVert + 0] += i * 2; 3338 vtxCoords[3 * thisVert + 1] += j * 2; 3339 vtxCoords[3 * thisVert + 2] += k * 2; 3340 } 3341 } 3342 } 3343 } 3344 } 3345 for (PetscInt i = 0; i < numBlocks; i++) { 3346 for (PetscInt f = 0; f < facesPerBlock; f++) { 3347 for (PetscInt v = 0; v < 4; v++) cells[i][f][v] = vertToTrueVert[cells[i][f][v]]; 3348 } 3349 } 3350 PetscCall(PetscFree(vertToTrueVert)); 3351 PetscCall(PetscFree(seen)); 3352 cells_flat = cells[0][0]; 3353 numEdges = 0; 3354 for (PetscInt i = 0; i < numFaces; i++) { 3355 for (PetscInt e = 0; e < 4; e++) { 3356 PetscInt ev[] = {cells_flat[i * 4 + e], cells_flat[i * 4 + ((e + 1) % 4)]}; 3357 const PetscReal *evCoords[] = {&vtxCoords[3 * ev[0]], &vtxCoords[3 * ev[1]]}; 3358 3359 for (PetscInt d = 0; d < 3; d++) { 3360 if (!periodic || periodic[0] != DM_BOUNDARY_PERIODIC) { 3361 if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) numEdges++; 3362 if (evCoords[0][d] == 2. * extent[d] && evCoords[1][d] == 2. * extent[d]) numEdges++; 3363 } 3364 } 3365 } 3366 } 3367 PetscCall(PetscMalloc1(numEdges, &edges)); 3368 PetscCall(PetscMalloc1(numEdges, &edgeSets)); 3369 for (PetscInt edge = 0, i = 0; i < numFaces; i++) { 3370 for (PetscInt e = 0; e < 4; e++) { 3371 PetscInt ev[] = {cells_flat[i * 4 + e], cells_flat[i * 4 + ((e + 1) % 4)]}; 3372 const PetscReal *evCoords[] = {&vtxCoords[3 * ev[0]], &vtxCoords[3 * ev[1]]}; 3373 3374 for (PetscInt d = 0; d < 3; d++) { 3375 if (!periodic || periodic[d] != DM_BOUNDARY_PERIODIC) { 3376 if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) { 3377 edges[edge][0] = ev[0]; 3378 edges[edge][1] = ev[1]; 3379 edgeSets[edge++] = 2 * d; 3380 } 3381 if (evCoords[0][d] == 2. * extent[d] && evCoords[1][d] == 2. * extent[d]) { 3382 edges[edge][0] = ev[0]; 3383 edges[edge][1] = ev[1]; 3384 edgeSets[edge++] = 2 * d + 1; 3385 } 3386 } 3387 } 3388 } 3389 } 3390 } 3391 evalFunc = TPSEvaluate_Gyroid; 3392 normalFunc = TPSExtrudeNormalFunc_Gyroid; 3393 break; 3394 } 3395 3396 PetscCall(DMSetDimension(dm, topoDim)); 3397 if (rank == 0) PetscCall(DMPlexBuildFromCellList(dm, numFaces, numVertices, 4, cells_flat)); 3398 else PetscCall(DMPlexBuildFromCellList(dm, 0, 0, 0, NULL)); 3399 PetscCall(PetscFree(cells_flat)); 3400 { 3401 DM idm; 3402 PetscCall(DMPlexInterpolate(dm, &idm)); 3403 PetscCall(DMPlexReplace_Internal(dm, &idm)); 3404 } 3405 if (rank == 0) PetscCall(DMPlexBuildCoordinatesFromCellList(dm, spaceDim, vtxCoords)); 3406 else PetscCall(DMPlexBuildCoordinatesFromCellList(dm, spaceDim, NULL)); 3407 PetscCall(PetscFree(vtxCoords)); 3408 3409 PetscCall(DMCreateLabel(dm, "Face Sets")); 3410 PetscCall(DMGetLabel(dm, "Face Sets", &label)); 3411 for (PetscInt e = 0; e < numEdges; e++) { 3412 PetscInt njoin; 3413 const PetscInt *join, verts[] = {numFaces + edges[e][0], numFaces + edges[e][1]}; 3414 PetscCall(DMPlexGetJoin(dm, 2, verts, &njoin, &join)); 3415 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]); 3416 PetscCall(DMLabelSetValue(label, join[0], edgeSets[e])); 3417 PetscCall(DMPlexRestoreJoin(dm, 2, verts, &njoin, &join)); 3418 } 3419 PetscCall(PetscFree(edges)); 3420 PetscCall(PetscFree(edgeSets)); 3421 if (tps_distribute) { 3422 DM pdm = NULL; 3423 PetscPartitioner part; 3424 3425 PetscCall(DMPlexGetPartitioner(dm, &part)); 3426 PetscCall(PetscPartitionerSetFromOptions(part)); 3427 PetscCall(DMPlexDistribute(dm, 0, NULL, &pdm)); 3428 if (pdm) PetscCall(DMPlexReplace_Internal(dm, &pdm)); 3429 // Do not auto-distribute again 3430 PetscCall(DMPlexDistributeSetDefault(dm, PETSC_FALSE)); 3431 } 3432 3433 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 3434 for (PetscInt refine = 0; refine < refinements; refine++) { 3435 PetscInt m; 3436 DM dmf; 3437 Vec X; 3438 PetscScalar *x; 3439 PetscCall(DMRefine(dm, MPI_COMM_NULL, &dmf)); 3440 PetscCall(DMPlexReplace_Internal(dm, &dmf)); 3441 3442 PetscCall(DMGetCoordinatesLocal(dm, &X)); 3443 PetscCall(VecGetLocalSize(X, &m)); 3444 PetscCall(VecGetArray(X, &x)); 3445 for (PetscInt i = 0; i < m; i += 3) PetscCall(TPSNearestPoint(evalFunc, &x[i])); 3446 PetscCall(VecRestoreArray(X, &x)); 3447 } 3448 3449 // Face Sets has already been propagated to new vertices during refinement; this propagates to the initial vertices. 3450 PetscCall(DMGetLabel(dm, "Face Sets", &label)); 3451 PetscCall(DMPlexLabelComplete(dm, label)); 3452 3453 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 3454 3455 if (thickness > 0) { 3456 DM edm, cdm, ecdm; 3457 DMPlexTransform tr; 3458 const char *prefix; 3459 PetscOptions options; 3460 // Code from DMPlexExtrude 3461 PetscCall(DMPlexTransformCreate(PetscObjectComm((PetscObject)dm), &tr)); 3462 PetscCall(DMPlexTransformSetDM(tr, dm)); 3463 PetscCall(DMPlexTransformSetType(tr, DMPLEXEXTRUDE)); 3464 PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm, &prefix)); 3465 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)tr, prefix)); 3466 PetscCall(PetscObjectGetOptions((PetscObject)dm, &options)); 3467 PetscCall(PetscObjectSetOptions((PetscObject)tr, options)); 3468 PetscCall(DMPlexTransformExtrudeSetLayers(tr, layers)); 3469 PetscCall(DMPlexTransformExtrudeSetThickness(tr, thickness)); 3470 PetscCall(DMPlexTransformExtrudeSetTensor(tr, PETSC_FALSE)); 3471 PetscCall(DMPlexTransformExtrudeSetSymmetric(tr, PETSC_TRUE)); 3472 PetscCall(DMPlexTransformExtrudeSetNormalFunction(tr, normalFunc)); 3473 PetscCall(DMPlexTransformSetFromOptions(tr)); 3474 PetscCall(PetscObjectSetOptions((PetscObject)tr, NULL)); 3475 PetscCall(DMPlexTransformSetUp(tr)); 3476 PetscCall(PetscObjectViewFromOptions((PetscObject)tr, NULL, "-dm_plex_tps_transform_view")); 3477 PetscCall(DMPlexTransformApply(tr, dm, &edm)); 3478 PetscCall(DMCopyDisc(dm, edm)); 3479 PetscCall(DMGetCoordinateDM(dm, &cdm)); 3480 PetscCall(DMGetCoordinateDM(edm, &ecdm)); 3481 PetscCall(DMCopyDisc(cdm, ecdm)); 3482 PetscCall(DMPlexTransformCreateDiscLabels(tr, edm)); 3483 PetscCall(DMPlexTransformDestroy(&tr)); 3484 if (edm) { 3485 ((DM_Plex *)edm->data)->printFEM = ((DM_Plex *)dm->data)->printFEM; 3486 ((DM_Plex *)edm->data)->printL2 = ((DM_Plex *)dm->data)->printL2; 3487 ((DM_Plex *)edm->data)->printLocate = ((DM_Plex *)dm->data)->printLocate; 3488 } 3489 PetscCall(DMPlexReplace_Internal(dm, &edm)); 3490 } 3491 PetscFunctionReturn(PETSC_SUCCESS); 3492 } 3493 3494 /*@ 3495 DMPlexCreateTPSMesh - Create a distributed, interpolated mesh of a triply-periodic surface 3496 3497 Collective 3498 3499 Input Parameters: 3500 + comm - The communicator for the `DM` object 3501 . tpstype - Type of triply-periodic surface 3502 . extent - Array of length 3 containing number of periods in each direction 3503 . periodic - array of length 3 with periodicity, or `NULL` for non-periodic 3504 . tps_distribute - Distribute 2D manifold mesh prior to refinement and extrusion (more scalable) 3505 . refinements - Number of factor-of-2 refinements of 2D manifold mesh 3506 . layers - Number of cell layers extruded in normal direction 3507 - thickness - Thickness in normal direction 3508 3509 Output Parameter: 3510 . dm - The `DM` object 3511 3512 Level: beginner 3513 3514 Notes: 3515 This meshes the surface of the Schwarz P or Gyroid surfaces. Schwarz P is is the simplest member of the triply-periodic minimal surfaces. 3516 https://en.wikipedia.org/wiki/Schwarz_minimal_surface#Schwarz_P_(%22Primitive%22) and can be cut with "clean" boundaries. 3517 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. 3518 Our implementation creates a very coarse mesh of the surface and refines (by 4-way splitting) as many times as requested. 3519 On each refinement, all vertices are projected to their nearest point on the surface. 3520 This projection could readily be extended to related surfaces. 3521 3522 The face (edge) sets for the Schwarz P surface are numbered 1(-x), 2(+x), 3(-y), 4(+y), 5(-z), 6(+z). 3523 When the mesh is refined, "Face Sets" contain the new vertices (created during refinement). Use `DMPlexLabelComplete()` to propagate to coarse-level vertices. 3524 3525 Developer Notes: 3526 The Gyroid mesh does not currently mark boundary sets. 3527 3528 References: 3529 . * - Maskery et al, Insights into the mechanical properties of several triply periodic minimal surface lattice structures made by polymer additive manufacturing, 2017. 3530 https://doi.org/10.1016/j.polymer.2017.11.049 3531 3532 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateSphereMesh()`, `DMSetType()`, `DMCreate()` 3533 @*/ 3534 PetscErrorCode DMPlexCreateTPSMesh(MPI_Comm comm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscBool tps_distribute, PetscInt refinements, PetscInt layers, PetscReal thickness, DM *dm) 3535 { 3536 PetscFunctionBegin; 3537 PetscCall(DMCreate(comm, dm)); 3538 PetscCall(DMSetType(*dm, DMPLEX)); 3539 PetscCall(DMPlexCreateTPSMesh_Internal(*dm, tpstype, extent, periodic, tps_distribute, refinements, layers, thickness)); 3540 PetscFunctionReturn(PETSC_SUCCESS); 3541 } 3542 3543 /*@ 3544 DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d. 3545 3546 Collective 3547 3548 Input Parameters: 3549 + comm - The communicator for the `DM` object 3550 . dim - The dimension 3551 . simplex - Use simplices, or tensor product cells 3552 - R - The radius 3553 3554 Output Parameter: 3555 . dm - The `DM` object 3556 3557 Level: beginner 3558 3559 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateBallMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 3560 @*/ 3561 PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscReal R, DM *dm) 3562 { 3563 PetscFunctionBegin; 3564 PetscAssertPointer(dm, 5); 3565 PetscCall(DMCreate(comm, dm)); 3566 PetscCall(DMSetType(*dm, DMPLEX)); 3567 PetscCall(DMPlexCreateSphereMesh_Internal(*dm, dim, simplex, R)); 3568 PetscFunctionReturn(PETSC_SUCCESS); 3569 } 3570 3571 static PetscErrorCode DMPlexCreateBallMesh_Internal(DM dm, PetscInt dim, PetscReal R) 3572 { 3573 DM sdm, vol; 3574 DMLabel bdlabel; 3575 3576 PetscFunctionBegin; 3577 PetscCall(DMCreate(PetscObjectComm((PetscObject)dm), &sdm)); 3578 PetscCall(DMSetType(sdm, DMPLEX)); 3579 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)sdm, "bd_")); 3580 PetscCall(DMPlexCreateSphereMesh_Internal(sdm, dim - 1, PETSC_TRUE, R)); 3581 PetscCall(DMSetFromOptions(sdm)); 3582 PetscCall(DMViewFromOptions(sdm, NULL, "-dm_view")); 3583 PetscCall(DMPlexGenerate(sdm, NULL, PETSC_TRUE, &vol)); 3584 PetscCall(DMDestroy(&sdm)); 3585 PetscCall(DMPlexReplace_Internal(dm, &vol)); 3586 PetscCall(DMCreateLabel(dm, "marker")); 3587 PetscCall(DMGetLabel(dm, "marker", &bdlabel)); 3588 PetscCall(DMPlexMarkBoundaryFaces(dm, PETSC_DETERMINE, bdlabel)); 3589 PetscCall(DMPlexLabelComplete(dm, bdlabel)); 3590 PetscFunctionReturn(PETSC_SUCCESS); 3591 } 3592 3593 /*@ 3594 DMPlexCreateBallMesh - Creates a simplex mesh on the d-dimensional ball, B^d. 3595 3596 Collective 3597 3598 Input Parameters: 3599 + comm - The communicator for the `DM` object 3600 . dim - The dimension 3601 - R - The radius 3602 3603 Output Parameter: 3604 . dm - The `DM` object 3605 3606 Options Database Key: 3607 . bd_dm_refine - This will refine the surface mesh preserving the sphere geometry 3608 3609 Level: beginner 3610 3611 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateSphereMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 3612 @*/ 3613 PetscErrorCode DMPlexCreateBallMesh(MPI_Comm comm, PetscInt dim, PetscReal R, DM *dm) 3614 { 3615 PetscFunctionBegin; 3616 PetscCall(DMCreate(comm, dm)); 3617 PetscCall(DMSetType(*dm, DMPLEX)); 3618 PetscCall(DMPlexCreateBallMesh_Internal(*dm, dim, R)); 3619 PetscFunctionReturn(PETSC_SUCCESS); 3620 } 3621 3622 static PetscErrorCode DMPlexCreateReferenceCell_Internal(DM rdm, DMPolytopeType ct) 3623 { 3624 PetscFunctionBegin; 3625 switch (ct) { 3626 case DM_POLYTOPE_POINT: { 3627 PetscInt numPoints[1] = {1}; 3628 PetscInt coneSize[1] = {0}; 3629 PetscInt cones[1] = {0}; 3630 PetscInt coneOrientations[1] = {0}; 3631 PetscScalar vertexCoords[1] = {0.0}; 3632 3633 PetscCall(DMSetDimension(rdm, 0)); 3634 PetscCall(DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3635 } break; 3636 case DM_POLYTOPE_SEGMENT: { 3637 PetscInt numPoints[2] = {2, 1}; 3638 PetscInt coneSize[3] = {2, 0, 0}; 3639 PetscInt cones[2] = {1, 2}; 3640 PetscInt coneOrientations[2] = {0, 0}; 3641 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 3642 3643 PetscCall(DMSetDimension(rdm, 1)); 3644 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3645 } break; 3646 case DM_POLYTOPE_POINT_PRISM_TENSOR: { 3647 PetscInt numPoints[2] = {2, 1}; 3648 PetscInt coneSize[3] = {2, 0, 0}; 3649 PetscInt cones[2] = {1, 2}; 3650 PetscInt coneOrientations[2] = {0, 0}; 3651 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 3652 3653 PetscCall(DMSetDimension(rdm, 1)); 3654 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3655 } break; 3656 case DM_POLYTOPE_TRIANGLE: { 3657 PetscInt numPoints[2] = {3, 1}; 3658 PetscInt coneSize[4] = {3, 0, 0, 0}; 3659 PetscInt cones[3] = {1, 2, 3}; 3660 PetscInt coneOrientations[3] = {0, 0, 0}; 3661 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 3662 3663 PetscCall(DMSetDimension(rdm, 2)); 3664 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3665 } break; 3666 case DM_POLYTOPE_QUADRILATERAL: { 3667 PetscInt numPoints[2] = {4, 1}; 3668 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3669 PetscInt cones[4] = {1, 2, 3, 4}; 3670 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3671 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 3672 3673 PetscCall(DMSetDimension(rdm, 2)); 3674 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3675 } break; 3676 case DM_POLYTOPE_SEG_PRISM_TENSOR: { 3677 PetscInt numPoints[2] = {4, 1}; 3678 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3679 PetscInt cones[4] = {1, 2, 3, 4}; 3680 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3681 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, 1.0}; 3682 3683 PetscCall(DMSetDimension(rdm, 2)); 3684 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3685 } break; 3686 case DM_POLYTOPE_TETRAHEDRON: { 3687 PetscInt numPoints[2] = {4, 1}; 3688 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3689 PetscInt cones[4] = {1, 2, 3, 4}; 3690 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3691 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}; 3692 3693 PetscCall(DMSetDimension(rdm, 3)); 3694 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3695 } break; 3696 case DM_POLYTOPE_HEXAHEDRON: { 3697 PetscInt numPoints[2] = {8, 1}; 3698 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3699 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 3700 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3701 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, -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3702 3703 PetscCall(DMSetDimension(rdm, 3)); 3704 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3705 } break; 3706 case DM_POLYTOPE_TRI_PRISM: { 3707 PetscInt numPoints[2] = {6, 1}; 3708 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3709 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 3710 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3711 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, -1.0, -1.0, -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 3712 3713 PetscCall(DMSetDimension(rdm, 3)); 3714 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3715 } break; 3716 case DM_POLYTOPE_TRI_PRISM_TENSOR: { 3717 PetscInt numPoints[2] = {6, 1}; 3718 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3719 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 3720 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3721 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 3722 3723 PetscCall(DMSetDimension(rdm, 3)); 3724 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3725 } break; 3726 case DM_POLYTOPE_QUAD_PRISM_TENSOR: { 3727 PetscInt numPoints[2] = {8, 1}; 3728 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3729 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 3730 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3731 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, -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3732 3733 PetscCall(DMSetDimension(rdm, 3)); 3734 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3735 } break; 3736 case DM_POLYTOPE_PYRAMID: { 3737 PetscInt numPoints[2] = {5, 1}; 3738 PetscInt coneSize[6] = {5, 0, 0, 0, 0, 0}; 3739 PetscInt cones[5] = {1, 2, 3, 4, 5}; 3740 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3741 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, 0.0, 0.0, 1.0}; 3742 3743 PetscCall(DMSetDimension(rdm, 3)); 3744 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3745 } break; 3746 default: 3747 SETERRQ(PetscObjectComm((PetscObject)rdm), PETSC_ERR_ARG_WRONG, "Cannot create reference cell for cell type %s", DMPolytopeTypes[ct]); 3748 } 3749 { 3750 PetscInt Nv, v; 3751 3752 /* Must create the celltype label here so that we do not automatically try to compute the types */ 3753 PetscCall(DMCreateLabel(rdm, "celltype")); 3754 PetscCall(DMPlexSetCellType(rdm, 0, ct)); 3755 PetscCall(DMPlexGetChart(rdm, NULL, &Nv)); 3756 for (v = 1; v < Nv; ++v) PetscCall(DMPlexSetCellType(rdm, v, DM_POLYTOPE_POINT)); 3757 } 3758 PetscCall(DMPlexInterpolateInPlace_Internal(rdm)); 3759 PetscCall(PetscObjectSetName((PetscObject)rdm, DMPolytopeTypes[ct])); 3760 PetscFunctionReturn(PETSC_SUCCESS); 3761 } 3762 3763 /*@ 3764 DMPlexCreateReferenceCell - Create a `DMPLEX` with the appropriate FEM reference cell 3765 3766 Collective 3767 3768 Input Parameters: 3769 + comm - The communicator 3770 - ct - The cell type of the reference cell 3771 3772 Output Parameter: 3773 . refdm - The reference cell 3774 3775 Level: intermediate 3776 3777 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateBoxMesh()` 3778 @*/ 3779 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, DMPolytopeType ct, DM *refdm) 3780 { 3781 PetscFunctionBegin; 3782 PetscCall(DMCreate(comm, refdm)); 3783 PetscCall(DMSetType(*refdm, DMPLEX)); 3784 PetscCall(DMPlexCreateReferenceCell_Internal(*refdm, ct)); 3785 PetscFunctionReturn(PETSC_SUCCESS); 3786 } 3787 3788 static PetscErrorCode DMPlexCreateBoundaryLabel_Private(DM dm, const char name[]) 3789 { 3790 DM plex; 3791 DMLabel label; 3792 PetscBool hasLabel; 3793 3794 PetscFunctionBegin; 3795 PetscCall(DMHasLabel(dm, name, &hasLabel)); 3796 if (hasLabel) PetscFunctionReturn(PETSC_SUCCESS); 3797 PetscCall(DMCreateLabel(dm, name)); 3798 PetscCall(DMGetLabel(dm, name, &label)); 3799 PetscCall(DMConvert(dm, DMPLEX, &plex)); 3800 PetscCall(DMPlexMarkBoundaryFaces(plex, 1, label)); 3801 PetscCall(DMPlexLabelComplete(plex, label)); 3802 PetscCall(DMDestroy(&plex)); 3803 PetscFunctionReturn(PETSC_SUCCESS); 3804 } 3805 3806 /* 3807 We use the last coordinate as the radius, the inner radius is lower[dim-1] and the outer radius is upper[dim-1]. Then we map the first coordinate around the circle. 3808 3809 (x, y) -> (r, theta) = (x[1], (x[0] - lower[0]) * 2\pi/(upper[0] - lower[0])) 3810 */ 3811 static void boxToAnnulus(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 3812 { 3813 const PetscReal low = PetscRealPart(constants[0]); 3814 const PetscReal upp = PetscRealPart(constants[1]); 3815 const PetscReal r = PetscRealPart(u[1]); 3816 const PetscReal th = 2. * PETSC_PI * (PetscRealPart(u[0]) - low) / (upp - low); 3817 3818 f0[0] = r * PetscCosReal(th); 3819 f0[1] = r * PetscSinReal(th); 3820 } 3821 3822 const char *const DMPlexShapes[] = {"box", "box_surface", "ball", "sphere", "cylinder", "schwarz_p", "gyroid", "doublet", "annulus", "hypercubic", "zbox", "unknown", "DMPlexShape", "DM_SHAPE_", NULL}; 3823 3824 static PetscErrorCode DMPlexCreateFromOptions_Internal(PetscOptionItems *PetscOptionsObject, PetscBool *useCoordSpace, DM dm) 3825 { 3826 DMPlexShape shape = DM_SHAPE_BOX; 3827 DMPolytopeType cell = DM_POLYTOPE_TRIANGLE; 3828 PetscInt dim = 2; 3829 PetscBool simplex = PETSC_TRUE, interpolate = PETSC_TRUE, adjCone = PETSC_FALSE, adjClosure = PETSC_TRUE, refDomain = PETSC_FALSE; 3830 PetscBool flg, flg2, fflg, bdfflg, nameflg; 3831 MPI_Comm comm; 3832 char filename[PETSC_MAX_PATH_LEN] = "<unspecified>"; 3833 char bdFilename[PETSC_MAX_PATH_LEN] = "<unspecified>"; 3834 char plexname[PETSC_MAX_PATH_LEN] = ""; 3835 3836 PetscFunctionBegin; 3837 PetscCall(PetscLogEventBegin(DMPLEX_CreateFromOptions, dm, 0, 0, 0)); 3838 PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); 3839 /* TODO Turn this into a registration interface */ 3840 PetscCall(PetscOptionsString("-dm_plex_filename", "File containing a mesh", "DMPlexCreateFromFile", filename, filename, sizeof(filename), &fflg)); 3841 PetscCall(PetscOptionsString("-dm_plex_boundary_filename", "File containing a mesh boundary", "DMPlexCreateFromFile", bdFilename, bdFilename, sizeof(bdFilename), &bdfflg)); 3842 PetscCall(PetscOptionsString("-dm_plex_name", "Name of the mesh in the file", "DMPlexCreateFromFile", plexname, plexname, sizeof(plexname), &nameflg)); 3843 PetscCall(PetscOptionsEnum("-dm_plex_cell", "Cell shape", "", DMPolytopeTypes, (PetscEnum)cell, (PetscEnum *)&cell, NULL)); 3844 PetscCall(PetscOptionsBool("-dm_plex_reference_cell_domain", "Use a reference cell domain", "", refDomain, &refDomain, NULL)); 3845 PetscCall(PetscOptionsEnum("-dm_plex_shape", "Shape for built-in mesh", "", DMPlexShapes, (PetscEnum)shape, (PetscEnum *)&shape, &flg)); 3846 PetscCall(PetscOptionsBoundedInt("-dm_plex_dim", "Topological dimension of the mesh", "DMGetDimension", dim, &dim, &flg, 0)); 3847 PetscCheck(dim >= 0, comm, PETSC_ERR_ARG_OUTOFRANGE, "Dimension %" PetscInt_FMT " should be in [0, infinity)", dim); 3848 PetscCall(PetscOptionsBool("-dm_plex_simplex", "Mesh cell shape", "", simplex, &simplex, &flg)); 3849 PetscCall(PetscOptionsBool("-dm_plex_interpolate", "Flag to create edges and faces automatically", "", interpolate, &interpolate, &flg)); 3850 PetscCall(PetscOptionsBool("-dm_plex_adj_cone", "Set adjacency direction", "DMSetBasicAdjacency", adjCone, &adjCone, &flg)); 3851 PetscCall(PetscOptionsBool("-dm_plex_adj_closure", "Set adjacency size", "DMSetBasicAdjacency", adjClosure, &adjClosure, &flg2)); 3852 if (flg || flg2) PetscCall(DMSetBasicAdjacency(dm, adjCone, adjClosure)); 3853 3854 switch (cell) { 3855 case DM_POLYTOPE_POINT: 3856 case DM_POLYTOPE_SEGMENT: 3857 case DM_POLYTOPE_POINT_PRISM_TENSOR: 3858 case DM_POLYTOPE_TRIANGLE: 3859 case DM_POLYTOPE_QUADRILATERAL: 3860 case DM_POLYTOPE_TETRAHEDRON: 3861 case DM_POLYTOPE_HEXAHEDRON: 3862 *useCoordSpace = PETSC_TRUE; 3863 break; 3864 default: 3865 *useCoordSpace = PETSC_FALSE; 3866 break; 3867 } 3868 3869 if (fflg) { 3870 DM dmnew; 3871 3872 PetscCall(DMPlexCreateFromFile(PetscObjectComm((PetscObject)dm), filename, plexname, interpolate, &dmnew)); 3873 PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew)); 3874 PetscCall(DMPlexReplace_Internal(dm, &dmnew)); 3875 } else if (refDomain) { 3876 PetscCall(DMPlexCreateReferenceCell_Internal(dm, cell)); 3877 } else if (bdfflg) { 3878 DM bdm, dmnew; 3879 3880 PetscCall(DMPlexCreateFromFile(PetscObjectComm((PetscObject)dm), bdFilename, plexname, interpolate, &bdm)); 3881 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)bdm, "bd_")); 3882 PetscCall(DMSetFromOptions(bdm)); 3883 PetscCall(DMPlexGenerate(bdm, NULL, interpolate, &dmnew)); 3884 PetscCall(DMDestroy(&bdm)); 3885 PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew)); 3886 PetscCall(DMPlexReplace_Internal(dm, &dmnew)); 3887 } else { 3888 PetscCall(PetscObjectSetName((PetscObject)dm, DMPlexShapes[shape])); 3889 switch (shape) { 3890 case DM_SHAPE_BOX: 3891 case DM_SHAPE_ZBOX: 3892 case DM_SHAPE_ANNULUS: { 3893 PetscInt faces[3] = {0, 0, 0}; 3894 PetscReal lower[3] = {0, 0, 0}; 3895 PetscReal upper[3] = {1, 1, 1}; 3896 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 3897 PetscBool isAnnular = shape == DM_SHAPE_ANNULUS ? PETSC_TRUE : PETSC_FALSE; 3898 PetscInt i, n; 3899 3900 n = dim; 3901 for (i = 0; i < dim; ++i) faces[i] = (dim == 1 ? 1 : 4 - dim); 3902 PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg)); 3903 n = 3; 3904 PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg)); 3905 PetscCheck(!flg || !(n != dim), comm, PETSC_ERR_ARG_SIZ, "Lower box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 3906 n = 3; 3907 PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg)); 3908 PetscCheck(!flg || !(n != dim), comm, PETSC_ERR_ARG_SIZ, "Upper box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 3909 n = 3; 3910 PetscCall(PetscOptionsEnumArray("-dm_plex_box_bd", "Boundary type for each dimension", "", DMBoundaryTypes, (PetscEnum *)bdt, &n, &flg)); 3911 PetscCheck(!flg || !(n != dim), comm, PETSC_ERR_ARG_SIZ, "Box boundary types had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 3912 3913 PetscCheck(!isAnnular || dim == 2, comm, PETSC_ERR_ARG_OUTOFRANGE, "Only two dimensional annuli have been implemented"); 3914 if (isAnnular) 3915 for (i = 0; i < dim - 1; ++i) bdt[i] = DM_BOUNDARY_PERIODIC; 3916 3917 switch (cell) { 3918 case DM_POLYTOPE_TRI_PRISM_TENSOR: 3919 PetscCall(DMPlexCreateWedgeBoxMesh_Internal(dm, faces, lower, upper, bdt)); 3920 if (!interpolate) { 3921 DM udm; 3922 3923 PetscCall(DMPlexUninterpolate(dm, &udm)); 3924 PetscCall(DMPlexReplace_Internal(dm, &udm)); 3925 } 3926 break; 3927 default: 3928 PetscCall(DMPlexCreateBoxMesh_Internal(dm, shape, dim, simplex, faces, lower, upper, bdt, interpolate)); 3929 break; 3930 } 3931 if (isAnnular) { 3932 DM cdm; 3933 PetscDS cds; 3934 PetscScalar bounds[2] = {lower[0], upper[0]}; 3935 3936 // Fix coordinates for annular region 3937 PetscCall(DMSetPeriodicity(dm, NULL, NULL, NULL)); 3938 PetscCall(DMSetCellCoordinatesLocal(dm, NULL)); 3939 PetscCall(DMSetCellCoordinates(dm, NULL)); 3940 PetscCall(DMPlexCreateCoordinateSpace(dm, 1, NULL)); 3941 PetscCall(DMGetCoordinateDM(dm, &cdm)); 3942 PetscCall(DMGetDS(cdm, &cds)); 3943 PetscCall(PetscDSSetConstants(cds, 2, bounds)); 3944 PetscCall(DMPlexRemapGeometry(dm, 0.0, boxToAnnulus)); 3945 } 3946 } break; 3947 case DM_SHAPE_BOX_SURFACE: { 3948 PetscInt faces[3] = {0, 0, 0}; 3949 PetscReal lower[3] = {0, 0, 0}; 3950 PetscReal upper[3] = {1, 1, 1}; 3951 PetscInt i, n; 3952 3953 n = dim + 1; 3954 for (i = 0; i < dim + 1; ++i) faces[i] = (dim + 1 == 1 ? 1 : 4 - (dim + 1)); 3955 PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg)); 3956 n = 3; 3957 PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg)); 3958 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); 3959 n = 3; 3960 PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg)); 3961 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); 3962 PetscCall(DMPlexCreateBoxSurfaceMesh_Internal(dm, dim + 1, faces, lower, upper, interpolate)); 3963 } break; 3964 case DM_SHAPE_SPHERE: { 3965 PetscReal R = 1.0; 3966 3967 PetscCall(PetscOptionsReal("-dm_plex_sphere_radius", "Radius of the sphere", "", R, &R, &flg)); 3968 PetscCall(DMPlexCreateSphereMesh_Internal(dm, dim, simplex, R)); 3969 } break; 3970 case DM_SHAPE_BALL: { 3971 PetscReal R = 1.0; 3972 3973 PetscCall(PetscOptionsReal("-dm_plex_ball_radius", "Radius of the ball", "", R, &R, &flg)); 3974 PetscCall(DMPlexCreateBallMesh_Internal(dm, dim, R)); 3975 } break; 3976 case DM_SHAPE_CYLINDER: { 3977 DMBoundaryType bdt = DM_BOUNDARY_NONE; 3978 PetscInt Nw = 6; 3979 3980 PetscCall(PetscOptionsEnum("-dm_plex_cylinder_bd", "Boundary type in the z direction", "", DMBoundaryTypes, (PetscEnum)bdt, (PetscEnum *)&bdt, NULL)); 3981 PetscCall(PetscOptionsInt("-dm_plex_cylinder_num_wedges", "Number of wedges around the cylinder", "", Nw, &Nw, NULL)); 3982 switch (cell) { 3983 case DM_POLYTOPE_TRI_PRISM_TENSOR: 3984 PetscCall(DMPlexCreateWedgeCylinderMesh_Internal(dm, Nw, interpolate)); 3985 break; 3986 default: 3987 PetscCall(DMPlexCreateHexCylinderMesh_Internal(dm, bdt)); 3988 break; 3989 } 3990 } break; 3991 case DM_SHAPE_SCHWARZ_P: // fallthrough 3992 case DM_SHAPE_GYROID: { 3993 PetscInt extent[3] = {1, 1, 1}, refine = 0, layers = 0, three; 3994 PetscReal thickness = 0.; 3995 DMBoundaryType periodic[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 3996 DMPlexTPSType tps_type = shape == DM_SHAPE_SCHWARZ_P ? DMPLEX_TPS_SCHWARZ_P : DMPLEX_TPS_GYROID; 3997 PetscBool tps_distribute; 3998 PetscCall(PetscOptionsIntArray("-dm_plex_tps_extent", "Number of replicas for each of three dimensions", NULL, extent, (three = 3, &three), NULL)); 3999 PetscCall(PetscOptionsInt("-dm_plex_tps_refine", "Number of refinements", NULL, refine, &refine, NULL)); 4000 PetscCall(PetscOptionsEnumArray("-dm_plex_tps_periodic", "Periodicity in each of three dimensions", NULL, DMBoundaryTypes, (PetscEnum *)periodic, (three = 3, &three), NULL)); 4001 PetscCall(PetscOptionsInt("-dm_plex_tps_layers", "Number of layers in volumetric extrusion (or zero to not extrude)", NULL, layers, &layers, NULL)); 4002 PetscCall(PetscOptionsReal("-dm_plex_tps_thickness", "Thickness of volumetric extrusion", NULL, thickness, &thickness, NULL)); 4003 PetscCall(DMPlexDistributeGetDefault(dm, &tps_distribute)); 4004 PetscCall(PetscOptionsBool("-dm_plex_tps_distribute", "Distribute the 2D mesh prior to refinement and extrusion", NULL, tps_distribute, &tps_distribute, NULL)); 4005 PetscCall(DMPlexCreateTPSMesh_Internal(dm, tps_type, extent, periodic, tps_distribute, refine, layers, thickness)); 4006 } break; 4007 case DM_SHAPE_DOUBLET: { 4008 DM dmnew; 4009 PetscReal rl = 0.0; 4010 4011 PetscCall(PetscOptionsReal("-dm_plex_doublet_refinementlimit", "Refinement limit", NULL, rl, &rl, NULL)); 4012 PetscCall(DMPlexCreateDoublet(PetscObjectComm((PetscObject)dm), dim, simplex, interpolate, rl, &dmnew)); 4013 PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew)); 4014 PetscCall(DMPlexReplace_Internal(dm, &dmnew)); 4015 } break; 4016 case DM_SHAPE_HYPERCUBIC: { 4017 PetscInt *edges; 4018 PetscReal *lower, *upper; 4019 DMBoundaryType *bdt; 4020 PetscInt n, d; 4021 4022 *useCoordSpace = PETSC_FALSE; 4023 PetscCall(PetscMalloc4(dim, &edges, dim, &lower, dim, &upper, dim, &bdt)); 4024 for (d = 0; d < dim; ++d) { 4025 edges[d] = 1; 4026 lower[d] = 0.; 4027 upper[d] = 1.; 4028 bdt[d] = DM_BOUNDARY_PERIODIC; 4029 } 4030 n = dim; 4031 PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", edges, &n, &flg)); 4032 n = dim; 4033 PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg)); 4034 PetscCheck(!flg || n == dim, comm, PETSC_ERR_ARG_SIZ, "Lower box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 4035 n = dim; 4036 PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg)); 4037 PetscCheck(!flg || n == dim, comm, PETSC_ERR_ARG_SIZ, "Upper box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 4038 n = dim; 4039 PetscCall(PetscOptionsEnumArray("-dm_plex_box_bd", "Boundary type for each dimension", "", DMBoundaryTypes, (PetscEnum *)bdt, &n, &flg)); 4040 PetscCheck(!flg || n == dim, comm, PETSC_ERR_ARG_SIZ, "Box boundary types had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 4041 PetscCall(DMPlexCreateHypercubicMesh_Internal(dm, dim, lower, upper, edges, bdt)); 4042 PetscCall(PetscFree4(edges, lower, upper, bdt)); 4043 } break; 4044 default: 4045 SETERRQ(comm, PETSC_ERR_SUP, "Domain shape %s is unsupported", DMPlexShapes[shape]); 4046 } 4047 } 4048 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 4049 if (!((PetscObject)dm)->name && nameflg) PetscCall(PetscObjectSetName((PetscObject)dm, plexname)); 4050 PetscCall(PetscLogEventEnd(DMPLEX_CreateFromOptions, dm, 0, 0, 0)); 4051 PetscFunctionReturn(PETSC_SUCCESS); 4052 } 4053 4054 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(DM dm, PetscOptionItems *PetscOptionsObject) 4055 { 4056 DM_Plex *mesh = (DM_Plex *)dm->data; 4057 PetscBool flg, flg2; 4058 char bdLabel[PETSC_MAX_PATH_LEN]; 4059 4060 PetscFunctionBegin; 4061 /* Handle viewing */ 4062 PetscCall(PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL)); 4063 PetscCall(PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL, 0)); 4064 PetscCall(PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL)); 4065 PetscCall(PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL, 0)); 4066 PetscCall(PetscOptionsBoundedInt("-dm_plex_print_locate", "Debug output level all point location computations", "DMLocatePoints", 0, &mesh->printLocate, NULL, 0)); 4067 PetscCall(DMMonitorSetFromOptions(dm, "-dm_plex_monitor_throughput", "Monitor the simulation throughput", "DMPlexMonitorThroughput", DMPlexMonitorThroughput, NULL, &flg)); 4068 if (flg) PetscCall(PetscLogDefaultBegin()); 4069 /* Labeling */ 4070 PetscCall(PetscOptionsString("-dm_plex_boundary_label", "Label to mark the mesh boundary", "", bdLabel, bdLabel, sizeof(bdLabel), &flg)); 4071 if (flg) PetscCall(DMPlexCreateBoundaryLabel_Private(dm, bdLabel)); 4072 /* Point Location */ 4073 PetscCall(PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL)); 4074 /* Partitioning and distribution */ 4075 PetscCall(PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL)); 4076 /* Generation and remeshing */ 4077 PetscCall(PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL)); 4078 /* Projection behavior */ 4079 PetscCall(PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maximum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL, 0)); 4080 PetscCall(PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL)); 4081 /* Checking structure */ 4082 { 4083 PetscBool all = PETSC_FALSE; 4084 4085 PetscCall(PetscOptionsBool("-dm_plex_check_all", "Perform all basic checks", "DMPlexCheck", PETSC_FALSE, &all, NULL)); 4086 if (all) { 4087 PetscCall(DMPlexCheck(dm)); 4088 } else { 4089 PetscCall(PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2)); 4090 if (flg && flg2) PetscCall(DMPlexCheckSymmetry(dm)); 4091 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)); 4092 if (flg && flg2) PetscCall(DMPlexCheckSkeleton(dm, 0)); 4093 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)); 4094 if (flg && flg2) PetscCall(DMPlexCheckFaces(dm, 0)); 4095 PetscCall(PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2)); 4096 if (flg && flg2) PetscCall(DMPlexCheckGeometry(dm)); 4097 PetscCall(PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2)); 4098 if (flg && flg2) PetscCall(DMPlexCheckPointSF(dm, NULL, PETSC_FALSE)); 4099 PetscCall(PetscOptionsBool("-dm_plex_check_interface_cones", "Check points on inter-partition interfaces have conforming order of cone points", "DMPlexCheckInterfaceCones", PETSC_FALSE, &flg, &flg2)); 4100 if (flg && flg2) PetscCall(DMPlexCheckInterfaceCones(dm)); 4101 } 4102 PetscCall(PetscOptionsBool("-dm_plex_check_cell_shape", "Check cell shape", "DMPlexCheckCellShape", PETSC_FALSE, &flg, &flg2)); 4103 if (flg && flg2) PetscCall(DMPlexCheckCellShape(dm, PETSC_TRUE, PETSC_DETERMINE)); 4104 } 4105 { 4106 PetscReal scale = 1.0; 4107 4108 PetscCall(PetscOptionsReal("-dm_plex_scale", "Scale factor for mesh coordinates", "DMPlexScale", scale, &scale, &flg)); 4109 if (flg) { 4110 Vec coordinates, coordinatesLocal; 4111 4112 PetscCall(DMGetCoordinates(dm, &coordinates)); 4113 PetscCall(DMGetCoordinatesLocal(dm, &coordinatesLocal)); 4114 PetscCall(VecScale(coordinates, scale)); 4115 PetscCall(VecScale(coordinatesLocal, scale)); 4116 } 4117 } 4118 PetscCall(PetscPartitionerSetFromOptions(mesh->partitioner)); 4119 PetscFunctionReturn(PETSC_SUCCESS); 4120 } 4121 4122 PetscErrorCode DMSetFromOptions_Overlap_Plex(DM dm, PetscOptionItems *PetscOptionsObject, PetscInt *overlap) 4123 { 4124 PetscInt numOvLabels = 16, numOvExLabels = 16; 4125 char *ovLabelNames[16], *ovExLabelNames[16]; 4126 PetscInt numOvValues = 16, numOvExValues = 16, l; 4127 PetscBool flg; 4128 4129 PetscFunctionBegin; 4130 PetscCall(PetscOptionsBoundedInt("-dm_distribute_overlap", "The size of the overlap halo", "DMPlexDistribute", *overlap, overlap, NULL, 0)); 4131 PetscCall(PetscOptionsStringArray("-dm_distribute_overlap_labels", "List of overlap label names", "DMPlexDistribute", ovLabelNames, &numOvLabels, &flg)); 4132 if (!flg) numOvLabels = 0; 4133 if (numOvLabels) { 4134 ((DM_Plex *)dm->data)->numOvLabels = numOvLabels; 4135 for (l = 0; l < numOvLabels; ++l) { 4136 PetscCall(DMGetLabel(dm, ovLabelNames[l], &((DM_Plex *)dm->data)->ovLabels[l])); 4137 PetscCheck(((DM_Plex *)dm->data)->ovLabels[l], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid label name %s", ovLabelNames[l]); 4138 PetscCall(PetscFree(ovLabelNames[l])); 4139 } 4140 PetscCall(PetscOptionsIntArray("-dm_distribute_overlap_values", "List of overlap label values", "DMPlexDistribute", ((DM_Plex *)dm->data)->ovValues, &numOvValues, &flg)); 4141 if (!flg) numOvValues = 0; 4142 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); 4143 4144 PetscCall(PetscOptionsStringArray("-dm_distribute_overlap_exclude_labels", "List of overlap exclude label names", "DMPlexDistribute", ovExLabelNames, &numOvExLabels, &flg)); 4145 if (!flg) numOvExLabels = 0; 4146 ((DM_Plex *)dm->data)->numOvExLabels = numOvExLabels; 4147 for (l = 0; l < numOvExLabels; ++l) { 4148 PetscCall(DMGetLabel(dm, ovExLabelNames[l], &((DM_Plex *)dm->data)->ovExLabels[l])); 4149 PetscCheck(((DM_Plex *)dm->data)->ovExLabels[l], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid label name %s", ovExLabelNames[l]); 4150 PetscCall(PetscFree(ovExLabelNames[l])); 4151 } 4152 PetscCall(PetscOptionsIntArray("-dm_distribute_overlap_exclude_values", "List of overlap exclude label values", "DMPlexDistribute", ((DM_Plex *)dm->data)->ovExValues, &numOvExValues, &flg)); 4153 if (!flg) numOvExValues = 0; 4154 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); 4155 } 4156 PetscFunctionReturn(PETSC_SUCCESS); 4157 } 4158 4159 static PetscErrorCode DMSetFromOptions_Plex(DM dm, PetscOptionItems *PetscOptionsObject) 4160 { 4161 PetscFunctionList ordlist; 4162 char oname[256]; 4163 PetscReal volume = -1.0; 4164 PetscInt prerefine = 0, refine = 0, r, coarsen = 0, overlap = 0, extLayers = 0, dim; 4165 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; 4166 DMPlexReorderDefaultFlag reorder; 4167 4168 PetscFunctionBegin; 4169 PetscOptionsHeadBegin(PetscOptionsObject, "DMPlex Options"); 4170 if (dm->cloneOpts) goto non_refine; 4171 /* Handle automatic creation */ 4172 PetscCall(DMGetDimension(dm, &dim)); 4173 if (dim < 0) { 4174 PetscCall(DMPlexCreateFromOptions_Internal(PetscOptionsObject, &coordSpace, dm)); 4175 created = PETSC_TRUE; 4176 } 4177 PetscCall(DMGetDimension(dm, &dim)); 4178 /* Handle interpolation before distribution */ 4179 PetscCall(PetscOptionsBool("-dm_plex_interpolate_pre", "Flag to interpolate mesh before distribution", "", interpolate, &interpolate, &flg)); 4180 if (flg) { 4181 DMPlexInterpolatedFlag interpolated; 4182 4183 PetscCall(DMPlexIsInterpolated(dm, &interpolated)); 4184 if (interpolated == DMPLEX_INTERPOLATED_FULL && !interpolate) { 4185 DM udm; 4186 4187 PetscCall(DMPlexUninterpolate(dm, &udm)); 4188 PetscCall(DMPlexReplace_Internal(dm, &udm)); 4189 } else if (interpolated != DMPLEX_INTERPOLATED_FULL && interpolate) { 4190 DM idm; 4191 4192 PetscCall(DMPlexInterpolate(dm, &idm)); 4193 PetscCall(DMPlexReplace_Internal(dm, &idm)); 4194 } 4195 } 4196 /* Handle DMPlex refinement before distribution */ 4197 PetscCall(PetscOptionsBool("-dm_refine_ignore_model", "Flag to ignore the geometry model when refining", "DMCreate", ignoreModel, &ignoreModel, &flg)); 4198 if (flg) ((DM_Plex *)dm->data)->ignoreModel = ignoreModel; 4199 PetscCall(DMPlexGetRefinementUniform(dm, &uniformOrig)); 4200 PetscCall(PetscOptionsBoundedInt("-dm_refine_pre", "The number of refinements before distribution", "DMCreate", prerefine, &prerefine, NULL, 0)); 4201 PetscCall(PetscOptionsBool("-dm_refine_remap_pre", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL)); 4202 PetscCall(PetscOptionsBool("-dm_refine_uniform_pre", "Flag for uniform refinement before distribution", "DMCreate", uniform, &uniform, &flg)); 4203 if (flg) PetscCall(DMPlexSetRefinementUniform(dm, uniform)); 4204 PetscCall(PetscOptionsReal("-dm_refine_volume_limit_pre", "The maximum cell volume after refinement before distribution", "DMCreate", volume, &volume, &flg)); 4205 if (flg) { 4206 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_FALSE)); 4207 PetscCall(DMPlexSetRefinementLimit(dm, volume)); 4208 prerefine = PetscMax(prerefine, 1); 4209 } 4210 for (r = 0; r < prerefine; ++r) { 4211 DM rdm; 4212 PetscPointFunc coordFunc = ((DM_Plex *)dm->data)->coordFunc; 4213 4214 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4215 PetscCall(DMRefine(dm, PetscObjectComm((PetscObject)dm), &rdm)); 4216 PetscCall(DMPlexReplace_Internal(dm, &rdm)); 4217 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4218 if (coordFunc && remap) { 4219 PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc)); 4220 ((DM_Plex *)dm->data)->coordFunc = coordFunc; 4221 } 4222 } 4223 PetscCall(DMPlexSetRefinementUniform(dm, uniformOrig)); 4224 /* Handle DMPlex extrusion before distribution */ 4225 PetscCall(PetscOptionsBoundedInt("-dm_extrude", "The number of layers to extrude", "", extLayers, &extLayers, NULL, 0)); 4226 if (extLayers) { 4227 DM edm; 4228 4229 PetscCall(DMExtrude(dm, extLayers, &edm)); 4230 PetscCall(DMPlexReplace_Internal(dm, &edm)); 4231 ((DM_Plex *)dm->data)->coordFunc = NULL; 4232 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4233 extLayers = 0; 4234 PetscCall(DMGetDimension(dm, &dim)); 4235 } 4236 /* Handle DMPlex reordering before distribution */ 4237 PetscCall(DMPlexReorderGetDefault(dm, &reorder)); 4238 PetscCall(MatGetOrderingList(&ordlist)); 4239 PetscCall(PetscStrncpy(oname, MATORDERINGNATURAL, sizeof(oname))); 4240 PetscCall(PetscOptionsFList("-dm_plex_reorder", "Set mesh reordering type", "DMPlexGetOrdering", ordlist, MATORDERINGNATURAL, oname, sizeof(oname), &flg)); 4241 if (reorder == DMPLEX_REORDER_DEFAULT_TRUE || flg) { 4242 DM pdm; 4243 IS perm; 4244 4245 PetscCall(DMPlexGetOrdering(dm, oname, NULL, &perm)); 4246 PetscCall(DMPlexPermute(dm, perm, &pdm)); 4247 PetscCall(ISDestroy(&perm)); 4248 PetscCall(DMPlexReplace_Internal(dm, &pdm)); 4249 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4250 } 4251 /* Handle DMPlex distribution */ 4252 PetscCall(DMPlexDistributeGetDefault(dm, &distribute)); 4253 PetscCall(PetscOptionsBool("-dm_distribute", "Flag to redistribute a mesh among processes", "DMPlexDistribute", distribute, &distribute, NULL)); 4254 PetscCall(DMSetFromOptions_Overlap_Plex(dm, PetscOptionsObject, &overlap)); 4255 if (distribute) { 4256 DM pdm = NULL; 4257 PetscPartitioner part; 4258 4259 PetscCall(DMPlexGetPartitioner(dm, &part)); 4260 PetscCall(PetscPartitionerSetFromOptions(part)); 4261 PetscCall(DMPlexDistribute(dm, overlap, NULL, &pdm)); 4262 if (pdm) PetscCall(DMPlexReplace_Internal(dm, &pdm)); 4263 } 4264 /* Create coordinate space */ 4265 if (created) { 4266 DM_Plex *mesh = (DM_Plex *)dm->data; 4267 PetscInt degree = 1; 4268 PetscInt height = 0; 4269 DM cdm; 4270 PetscBool flg; 4271 4272 PetscCall(PetscOptionsBool("-dm_coord_space", "Use an FEM space for coordinates", "", coordSpace, &coordSpace, &flg)); 4273 PetscCall(PetscOptionsInt("-dm_coord_petscspace_degree", "FEM degree for coordinate space", "", degree, °ree, NULL)); 4274 if (coordSpace) PetscCall(DMPlexCreateCoordinateSpace(dm, degree, mesh->coordFunc)); 4275 PetscCall(DMGetCoordinateDM(dm, &cdm)); 4276 if (flg && !coordSpace) { 4277 PetscDS cds; 4278 PetscObject obj; 4279 PetscClassId id; 4280 4281 PetscCall(DMGetDS(cdm, &cds)); 4282 PetscCall(PetscDSGetDiscretization(cds, 0, &obj)); 4283 PetscCall(PetscObjectGetClassId(obj, &id)); 4284 if (id == PETSCFE_CLASSID) { 4285 PetscContainer dummy; 4286 4287 PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &dummy)); 4288 PetscCall(PetscObjectSetName((PetscObject)dummy, "coordinates")); 4289 PetscCall(DMSetField(cdm, 0, NULL, (PetscObject)dummy)); 4290 PetscCall(PetscContainerDestroy(&dummy)); 4291 PetscCall(DMClearDS(cdm)); 4292 } 4293 mesh->coordFunc = NULL; 4294 } 4295 PetscCall(PetscOptionsBool("-dm_sparse_localize", "Localize only necessary cells", "", dm->sparseLocalize, &dm->sparseLocalize, &flg)); 4296 PetscCall(PetscOptionsInt("-dm_localize_height", "Localize edges and faces in addition to cells", "", height, &height, &flg)); 4297 if (flg) PetscCall(DMPlexSetMaxProjectionHeight(cdm, height)); 4298 PetscCall(DMLocalizeCoordinates(dm)); 4299 } 4300 /* Handle DMPlex refinement */ 4301 remap = PETSC_TRUE; 4302 PetscCall(PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL, 0)); 4303 PetscCall(PetscOptionsBool("-dm_refine_remap", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL)); 4304 PetscCall(PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy, 0)); 4305 if (refine) PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 4306 if (refine && isHierarchy) { 4307 DM *dms, coarseDM; 4308 4309 PetscCall(DMGetCoarseDM(dm, &coarseDM)); 4310 PetscCall(PetscObjectReference((PetscObject)coarseDM)); 4311 PetscCall(PetscMalloc1(refine, &dms)); 4312 PetscCall(DMRefineHierarchy(dm, refine, dms)); 4313 /* Total hack since we do not pass in a pointer */ 4314 PetscCall(DMPlexSwap_Static(dm, dms[refine - 1])); 4315 if (refine == 1) { 4316 PetscCall(DMSetCoarseDM(dm, dms[0])); 4317 PetscCall(DMPlexSetRegularRefinement(dm, PETSC_TRUE)); 4318 } else { 4319 PetscCall(DMSetCoarseDM(dm, dms[refine - 2])); 4320 PetscCall(DMPlexSetRegularRefinement(dm, PETSC_TRUE)); 4321 PetscCall(DMSetCoarseDM(dms[0], dms[refine - 1])); 4322 PetscCall(DMPlexSetRegularRefinement(dms[0], PETSC_TRUE)); 4323 } 4324 PetscCall(DMSetCoarseDM(dms[refine - 1], coarseDM)); 4325 PetscCall(PetscObjectDereference((PetscObject)coarseDM)); 4326 /* Free DMs */ 4327 for (r = 0; r < refine; ++r) { 4328 PetscCall(DMSetFromOptions_NonRefinement_Plex(dms[r], PetscOptionsObject)); 4329 PetscCall(DMDestroy(&dms[r])); 4330 } 4331 PetscCall(PetscFree(dms)); 4332 } else { 4333 for (r = 0; r < refine; ++r) { 4334 DM rdm; 4335 PetscPointFunc coordFunc = ((DM_Plex *)dm->data)->coordFunc; 4336 4337 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4338 PetscCall(DMRefine(dm, PetscObjectComm((PetscObject)dm), &rdm)); 4339 /* Total hack since we do not pass in a pointer */ 4340 PetscCall(DMPlexReplace_Internal(dm, &rdm)); 4341 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4342 if (coordFunc && remap) { 4343 PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc)); 4344 ((DM_Plex *)dm->data)->coordFunc = coordFunc; 4345 } 4346 } 4347 } 4348 /* Handle DMPlex coarsening */ 4349 PetscCall(PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL, 0)); 4350 PetscCall(PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy, 0)); 4351 if (coarsen && isHierarchy) { 4352 DM *dms; 4353 4354 PetscCall(PetscMalloc1(coarsen, &dms)); 4355 PetscCall(DMCoarsenHierarchy(dm, coarsen, dms)); 4356 /* Free DMs */ 4357 for (r = 0; r < coarsen; ++r) { 4358 PetscCall(DMSetFromOptions_NonRefinement_Plex(dms[r], PetscOptionsObject)); 4359 PetscCall(DMDestroy(&dms[r])); 4360 } 4361 PetscCall(PetscFree(dms)); 4362 } else { 4363 for (r = 0; r < coarsen; ++r) { 4364 DM cdm; 4365 PetscPointFunc coordFunc = ((DM_Plex *)dm->data)->coordFunc; 4366 4367 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4368 PetscCall(DMCoarsen(dm, PetscObjectComm((PetscObject)dm), &cdm)); 4369 /* Total hack since we do not pass in a pointer */ 4370 PetscCall(DMPlexReplace_Internal(dm, &cdm)); 4371 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4372 if (coordFunc) { 4373 PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc)); 4374 ((DM_Plex *)dm->data)->coordFunc = coordFunc; 4375 } 4376 } 4377 } 4378 /* Handle ghost cells */ 4379 PetscCall(PetscOptionsBool("-dm_plex_create_fv_ghost_cells", "Flag to create finite volume ghost cells on the boundary", "DMCreate", ghostCells, &ghostCells, NULL)); 4380 if (ghostCells) { 4381 DM gdm; 4382 char lname[PETSC_MAX_PATH_LEN]; 4383 4384 lname[0] = '\0'; 4385 PetscCall(PetscOptionsString("-dm_plex_fv_ghost_cells_label", "Label name for ghost cells boundary", "DMCreate", lname, lname, sizeof(lname), &flg)); 4386 PetscCall(DMPlexConstructGhostCells(dm, flg ? lname : NULL, NULL, &gdm)); 4387 PetscCall(DMPlexReplace_Internal(dm, &gdm)); 4388 } 4389 /* Handle 1D order */ 4390 if (reorder != DMPLEX_REORDER_DEFAULT_FALSE && dim == 1) { 4391 DM cdm, rdm; 4392 PetscDS cds; 4393 PetscObject obj; 4394 PetscClassId id = PETSC_OBJECT_CLASSID; 4395 IS perm; 4396 PetscInt Nf; 4397 PetscBool distributed; 4398 4399 PetscCall(DMPlexIsDistributed(dm, &distributed)); 4400 PetscCall(DMGetCoordinateDM(dm, &cdm)); 4401 PetscCall(DMGetDS(cdm, &cds)); 4402 PetscCall(PetscDSGetNumFields(cds, &Nf)); 4403 if (Nf) { 4404 PetscCall(PetscDSGetDiscretization(cds, 0, &obj)); 4405 PetscCall(PetscObjectGetClassId(obj, &id)); 4406 } 4407 if (!distributed && id != PETSCFE_CLASSID) { 4408 PetscCall(DMPlexGetOrdering1D(dm, &perm)); 4409 PetscCall(DMPlexPermute(dm, perm, &rdm)); 4410 PetscCall(DMPlexReplace_Internal(dm, &rdm)); 4411 PetscCall(ISDestroy(&perm)); 4412 } 4413 } 4414 /* Handle */ 4415 non_refine: 4416 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4417 PetscOptionsHeadEnd(); 4418 PetscFunctionReturn(PETSC_SUCCESS); 4419 } 4420 4421 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm, Vec *vec) 4422 { 4423 PetscFunctionBegin; 4424 PetscCall(DMCreateGlobalVector_Section_Private(dm, vec)); 4425 /* PetscCall(VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM)); */ 4426 PetscCall(VecSetOperation(*vec, VECOP_VIEW, (void (*)(void))VecView_Plex)); 4427 PetscCall(VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void))VecView_Plex_Native)); 4428 PetscCall(VecSetOperation(*vec, VECOP_LOAD, (void (*)(void))VecLoad_Plex)); 4429 PetscCall(VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void))VecLoad_Plex_Native)); 4430 PetscFunctionReturn(PETSC_SUCCESS); 4431 } 4432 4433 static PetscErrorCode DMCreateLocalVector_Plex(DM dm, Vec *vec) 4434 { 4435 PetscFunctionBegin; 4436 PetscCall(DMCreateLocalVector_Section_Private(dm, vec)); 4437 PetscCall(VecSetOperation(*vec, VECOP_VIEW, (void (*)(void))VecView_Plex_Local)); 4438 PetscCall(VecSetOperation(*vec, VECOP_LOAD, (void (*)(void))VecLoad_Plex_Local)); 4439 PetscFunctionReturn(PETSC_SUCCESS); 4440 } 4441 4442 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 4443 { 4444 PetscInt depth, d; 4445 4446 PetscFunctionBegin; 4447 PetscCall(DMPlexGetDepth(dm, &depth)); 4448 if (depth == 1) { 4449 PetscCall(DMGetDimension(dm, &d)); 4450 if (dim == 0) PetscCall(DMPlexGetDepthStratum(dm, dim, pStart, pEnd)); 4451 else if (dim == d) PetscCall(DMPlexGetDepthStratum(dm, 1, pStart, pEnd)); 4452 else { 4453 *pStart = 0; 4454 *pEnd = 0; 4455 } 4456 } else { 4457 PetscCall(DMPlexGetDepthStratum(dm, dim, pStart, pEnd)); 4458 } 4459 PetscFunctionReturn(PETSC_SUCCESS); 4460 } 4461 4462 static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 4463 { 4464 PetscSF sf; 4465 PetscInt niranks, njranks, n; 4466 const PetscMPIInt *iranks, *jranks; 4467 DM_Plex *data = (DM_Plex *)dm->data; 4468 4469 PetscFunctionBegin; 4470 PetscCall(DMGetPointSF(dm, &sf)); 4471 if (!data->neighbors) { 4472 PetscCall(PetscSFSetUp(sf)); 4473 PetscCall(PetscSFGetRootRanks(sf, &njranks, &jranks, NULL, NULL, NULL)); 4474 PetscCall(PetscSFGetLeafRanks(sf, &niranks, &iranks, NULL, NULL)); 4475 PetscCall(PetscMalloc1(njranks + niranks + 1, &data->neighbors)); 4476 PetscCall(PetscArraycpy(data->neighbors + 1, jranks, njranks)); 4477 PetscCall(PetscArraycpy(data->neighbors + njranks + 1, iranks, niranks)); 4478 n = njranks + niranks; 4479 PetscCall(PetscSortRemoveDupsMPIInt(&n, data->neighbors + 1)); 4480 /* The following cast should never fail: can't have more neighbors than PETSC_MPI_INT_MAX */ 4481 PetscCall(PetscMPIIntCast(n, data->neighbors)); 4482 } 4483 if (nranks) *nranks = data->neighbors[0]; 4484 if (ranks) { 4485 if (data->neighbors[0]) *ranks = data->neighbors + 1; 4486 else *ranks = NULL; 4487 } 4488 PetscFunctionReturn(PETSC_SUCCESS); 4489 } 4490 4491 PETSC_INTERN PetscErrorCode DMInterpolateSolution_Plex(DM, DM, Mat, Vec, Vec); 4492 4493 static PetscErrorCode DMInitialize_Plex(DM dm) 4494 { 4495 PetscFunctionBegin; 4496 dm->ops->view = DMView_Plex; 4497 dm->ops->load = DMLoad_Plex; 4498 dm->ops->setfromoptions = DMSetFromOptions_Plex; 4499 dm->ops->clone = DMClone_Plex; 4500 dm->ops->setup = DMSetUp_Plex; 4501 dm->ops->createlocalsection = DMCreateLocalSection_Plex; 4502 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 4503 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 4504 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 4505 dm->ops->getlocaltoglobalmapping = NULL; 4506 dm->ops->createfieldis = NULL; 4507 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 4508 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 4509 dm->ops->getcoloring = NULL; 4510 dm->ops->creatematrix = DMCreateMatrix_Plex; 4511 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 4512 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 4513 dm->ops->createmassmatrixlumped = DMCreateMassMatrixLumped_Plex; 4514 dm->ops->createinjection = DMCreateInjection_Plex; 4515 dm->ops->refine = DMRefine_Plex; 4516 dm->ops->coarsen = DMCoarsen_Plex; 4517 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 4518 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 4519 dm->ops->extrude = DMExtrude_Plex; 4520 dm->ops->globaltolocalbegin = NULL; 4521 dm->ops->globaltolocalend = NULL; 4522 dm->ops->localtoglobalbegin = NULL; 4523 dm->ops->localtoglobalend = NULL; 4524 dm->ops->destroy = DMDestroy_Plex; 4525 dm->ops->createsubdm = DMCreateSubDM_Plex; 4526 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 4527 dm->ops->getdimpoints = DMGetDimPoints_Plex; 4528 dm->ops->locatepoints = DMLocatePoints_Plex; 4529 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 4530 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 4531 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 4532 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 4533 dm->ops->projectbdfieldlabellocal = DMProjectBdFieldLabelLocal_Plex; 4534 dm->ops->computel2diff = DMComputeL2Diff_Plex; 4535 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 4536 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 4537 dm->ops->getneighbors = DMGetNeighbors_Plex; 4538 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexInsertBoundaryValues_C", DMPlexInsertBoundaryValues_Plex)); 4539 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexInsertTimeDerviativeBoundaryValues_C", DMPlexInsertTimeDerivativeBoundaryValues_Plex)); 4540 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMSetUpGLVisViewer_C", DMSetUpGLVisViewer_Plex)); 4541 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMCreateNeumannOverlap_C", DMCreateNeumannOverlap_Plex)); 4542 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexGetOverlap_C", DMPlexGetOverlap_Plex)); 4543 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexDistributeGetDefault_C", DMPlexDistributeGetDefault_Plex)); 4544 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexDistributeSetDefault_C", DMPlexDistributeSetDefault_Plex)); 4545 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexReorderGetDefault_C", DMPlexReorderGetDefault_Plex)); 4546 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexReorderSetDefault_C", DMPlexReorderSetDefault_Plex)); 4547 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMInterpolateSolution_C", DMInterpolateSolution_Plex)); 4548 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexGetOverlap_C", DMPlexGetOverlap_Plex)); 4549 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexSetOverlap_C", DMPlexSetOverlap_Plex)); 4550 PetscFunctionReturn(PETSC_SUCCESS); 4551 } 4552 4553 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 4554 { 4555 DM_Plex *mesh = (DM_Plex *)dm->data; 4556 PetscSF face_sf; 4557 4558 PetscFunctionBegin; 4559 mesh->refct++; 4560 (*newdm)->data = mesh; 4561 PetscCall(DMPlexGetIsoperiodicFaceSF(dm, &face_sf)); 4562 PetscCall(DMPlexSetIsoperiodicFaceSF(*newdm, face_sf)); 4563 PetscCall(PetscObjectChangeTypeName((PetscObject)*newdm, DMPLEX)); 4564 PetscCall(DMInitialize_Plex(*newdm)); 4565 PetscFunctionReturn(PETSC_SUCCESS); 4566 } 4567 4568 /*MC 4569 DMPLEX = "plex" - A `DM` object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 4570 In the local representation, `Vec`s contain all unknowns in the interior and shared boundary. This is 4571 specified by a PetscSection object. Ownership in the global representation is determined by 4572 ownership of the underlying `DMPLEX` points. This is specified by another `PetscSection` object. 4573 4574 Options Database Keys: 4575 + -dm_refine_pre - Refine mesh before distribution 4576 + -dm_refine_uniform_pre - Choose uniform or generator-based refinement 4577 + -dm_refine_volume_limit_pre - Cell volume limit after pre-refinement using generator 4578 . -dm_distribute - Distribute mesh across processes 4579 . -dm_distribute_overlap - Number of cells to overlap for distribution 4580 . -dm_refine - Refine mesh after distribution 4581 . -dm_plex_hash_location - Use grid hashing for point location 4582 . -dm_plex_hash_box_faces <n,m,p> - The number of divisions in each direction of the grid hash 4583 . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes 4584 . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing 4585 . -dm_plex_max_projection_height - Maximum mesh point height used to project locally 4586 . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement 4587 . -dm_plex_check_all - Perform all checks below 4588 . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric 4589 . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices 4590 . -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 4591 . -dm_plex_check_geometry - Check that cells have positive volume 4592 . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ 4593 . -dm_plex_view_scale <num> - Scale the TikZ 4594 - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices 4595 4596 Level: intermediate 4597 4598 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMType`, `DMPlexCreate()`, `DMCreate()`, `DMSetType()`, `PetscSection` 4599 M*/ 4600 4601 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 4602 { 4603 DM_Plex *mesh; 4604 PetscInt unit; 4605 4606 PetscFunctionBegin; 4607 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4608 PetscCall(PetscNew(&mesh)); 4609 dm->data = mesh; 4610 4611 mesh->refct = 1; 4612 PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection)); 4613 PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection)); 4614 mesh->refinementUniform = PETSC_TRUE; 4615 mesh->refinementLimit = -1.0; 4616 mesh->distDefault = PETSC_TRUE; 4617 mesh->reorderDefault = DMPLEX_REORDER_DEFAULT_NOTSET; 4618 mesh->distributionName = NULL; 4619 mesh->interpolated = DMPLEX_INTERPOLATED_INVALID; 4620 mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID; 4621 4622 PetscCall(PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner)); 4623 mesh->remeshBd = PETSC_FALSE; 4624 4625 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 4626 4627 mesh->depthState = -1; 4628 mesh->celltypeState = -1; 4629 mesh->printTol = 1.0e-10; 4630 4631 PetscCall(DMInitialize_Plex(dm)); 4632 PetscFunctionReturn(PETSC_SUCCESS); 4633 } 4634 4635 /*@ 4636 DMPlexCreate - Creates a `DMPLEX` object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 4637 4638 Collective 4639 4640 Input Parameter: 4641 . comm - The communicator for the `DMPLEX` object 4642 4643 Output Parameter: 4644 . mesh - The `DMPLEX` object 4645 4646 Level: beginner 4647 4648 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMType`, `DMCreate()`, `DMSetType()` 4649 @*/ 4650 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 4651 { 4652 PetscFunctionBegin; 4653 PetscAssertPointer(mesh, 2); 4654 PetscCall(DMCreate(comm, mesh)); 4655 PetscCall(DMSetType(*mesh, DMPLEX)); 4656 PetscFunctionReturn(PETSC_SUCCESS); 4657 } 4658 4659 /*@C 4660 DMPlexBuildFromCellListParallel - Build distributed `DMPLEX` topology from a list of vertices for each cell (common mesh generator output) 4661 4662 Collective; No Fortran Support 4663 4664 Input Parameters: 4665 + dm - The `DM` 4666 . numCells - The number of cells owned by this process 4667 . numVertices - The number of vertices to be owned by this process, or `PETSC_DECIDE` 4668 . NVertices - The global number of vertices, or `PETSC_DETERMINE` 4669 . numCorners - The number of vertices for each cell 4670 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 4671 4672 Output Parameters: 4673 + vertexSF - (Optional) `PetscSF` describing complete vertex ownership 4674 - verticesAdjSaved - (Optional) vertex adjacency array 4675 4676 Level: advanced 4677 4678 Notes: 4679 Two triangles sharing a face 4680 .vb 4681 4682 2 4683 / | \ 4684 / | \ 4685 / | \ 4686 0 0 | 1 3 4687 \ | / 4688 \ | / 4689 \ | / 4690 1 4691 .ve 4692 would have input 4693 .vb 4694 numCells = 2, numVertices = 4 4695 cells = [0 1 2 1 3 2] 4696 .ve 4697 which would result in the `DMPLEX` 4698 .vb 4699 4700 4 4701 / | \ 4702 / | \ 4703 / | \ 4704 2 0 | 1 5 4705 \ | / 4706 \ | / 4707 \ | / 4708 3 4709 .ve 4710 4711 Vertices are implicitly numbered consecutively 0,...,NVertices. 4712 Each rank owns a chunk of numVertices consecutive vertices. 4713 If numVertices is `PETSC_DECIDE`, PETSc will distribute them as evenly as possible using PetscLayout. 4714 If NVertices is `PETSC_DETERMINE` and numVertices is PETSC_DECIDE, NVertices is computed by PETSc as the maximum vertex index in cells + 1. 4715 If only NVertices is `PETSC_DETERMINE`, it is computed as the sum of numVertices over all ranks. 4716 4717 The cell distribution is arbitrary non-overlapping, independent of the vertex distribution. 4718 4719 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildFromCellList()`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildCoordinatesFromCellListParallel()`, 4720 `PetscSF` 4721 @*/ 4722 PetscErrorCode DMPlexBuildFromCellListParallel(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, const PetscInt cells[], PetscSF *vertexSF, PetscInt **verticesAdjSaved) 4723 { 4724 PetscSF sfPoint; 4725 PetscLayout layout; 4726 PetscInt numVerticesAdj, *verticesAdj, *cones, c, p; 4727 4728 PetscFunctionBegin; 4729 PetscValidLogicalCollectiveInt(dm, NVertices, 4); 4730 PetscCall(PetscLogEventBegin(DMPLEX_BuildFromCellList, dm, 0, 0, 0)); 4731 /* Get/check global number of vertices */ 4732 { 4733 PetscInt NVerticesInCells, i; 4734 const PetscInt len = numCells * numCorners; 4735 4736 /* NVerticesInCells = max(cells) + 1 */ 4737 NVerticesInCells = PETSC_MIN_INT; 4738 for (i = 0; i < len; i++) 4739 if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 4740 ++NVerticesInCells; 4741 PetscCall(MPIU_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm))); 4742 4743 if (numVertices == PETSC_DECIDE && NVertices == PETSC_DECIDE) NVertices = NVerticesInCells; 4744 else 4745 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); 4746 } 4747 /* Count locally unique vertices */ 4748 { 4749 PetscHSetI vhash; 4750 PetscInt off = 0; 4751 4752 PetscCall(PetscHSetICreate(&vhash)); 4753 for (c = 0; c < numCells; ++c) { 4754 for (p = 0; p < numCorners; ++p) PetscCall(PetscHSetIAdd(vhash, cells[c * numCorners + p])); 4755 } 4756 PetscCall(PetscHSetIGetSize(vhash, &numVerticesAdj)); 4757 if (!verticesAdjSaved) PetscCall(PetscMalloc1(numVerticesAdj, &verticesAdj)); 4758 else verticesAdj = *verticesAdjSaved; 4759 PetscCall(PetscHSetIGetElems(vhash, &off, verticesAdj)); 4760 PetscCall(PetscHSetIDestroy(&vhash)); 4761 PetscCheck(off == numVerticesAdj, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %" PetscInt_FMT " should be %" PetscInt_FMT, off, numVerticesAdj); 4762 } 4763 PetscCall(PetscSortInt(numVerticesAdj, verticesAdj)); 4764 /* Create cones */ 4765 PetscCall(DMPlexSetChart(dm, 0, numCells + numVerticesAdj)); 4766 for (c = 0; c < numCells; ++c) PetscCall(DMPlexSetConeSize(dm, c, numCorners)); 4767 PetscCall(DMSetUp(dm)); 4768 PetscCall(DMPlexGetCones(dm, &cones)); 4769 for (c = 0; c < numCells; ++c) { 4770 for (p = 0; p < numCorners; ++p) { 4771 const PetscInt gv = cells[c * numCorners + p]; 4772 PetscInt lv; 4773 4774 /* Positions within verticesAdj form 0-based local vertex numbering; 4775 we need to shift it by numCells to get correct DAG points (cells go first) */ 4776 PetscCall(PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv)); 4777 PetscCheck(lv >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %" PetscInt_FMT " in local connectivity", gv); 4778 cones[c * numCorners + p] = lv + numCells; 4779 } 4780 } 4781 /* Build point sf */ 4782 PetscCall(PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &layout)); 4783 PetscCall(PetscLayoutSetSize(layout, NVertices)); 4784 PetscCall(PetscLayoutSetLocalSize(layout, numVertices)); 4785 PetscCall(PetscLayoutSetBlockSize(layout, 1)); 4786 PetscCall(PetscSFCreateByMatchingIndices(layout, numVerticesAdj, verticesAdj, NULL, numCells, numVerticesAdj, verticesAdj, NULL, numCells, vertexSF, &sfPoint)); 4787 PetscCall(PetscLayoutDestroy(&layout)); 4788 if (!verticesAdjSaved) PetscCall(PetscFree(verticesAdj)); 4789 PetscCall(PetscObjectSetName((PetscObject)sfPoint, "point SF")); 4790 if (dm->sf) { 4791 const char *prefix; 4792 4793 PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm->sf, &prefix)); 4794 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)sfPoint, prefix)); 4795 } 4796 PetscCall(DMSetPointSF(dm, sfPoint)); 4797 PetscCall(PetscSFDestroy(&sfPoint)); 4798 if (vertexSF) PetscCall(PetscObjectSetName((PetscObject)(*vertexSF), "Vertex Ownership SF")); 4799 /* Fill in the rest of the topology structure */ 4800 PetscCall(DMPlexSymmetrize(dm)); 4801 PetscCall(DMPlexStratify(dm)); 4802 PetscCall(PetscLogEventEnd(DMPLEX_BuildFromCellList, dm, 0, 0, 0)); 4803 PetscFunctionReturn(PETSC_SUCCESS); 4804 } 4805 4806 /*@C 4807 DMPlexBuildCoordinatesFromCellListParallel - Build `DM` coordinates from a list of coordinates for each owned vertex (common mesh generator output) 4808 4809 Collective; No Fortran Support 4810 4811 Input Parameters: 4812 + dm - The `DM` 4813 . spaceDim - The spatial dimension used for coordinates 4814 . sfVert - `PetscSF` describing complete vertex ownership 4815 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 4816 4817 Level: advanced 4818 4819 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildFromCellListParallel()` 4820 @*/ 4821 PetscErrorCode DMPlexBuildCoordinatesFromCellListParallel(DM dm, PetscInt spaceDim, PetscSF sfVert, const PetscReal vertexCoords[]) 4822 { 4823 PetscSection coordSection; 4824 Vec coordinates; 4825 PetscScalar *coords; 4826 PetscInt numVertices, numVerticesAdj, coordSize, v, vStart, vEnd; 4827 4828 PetscFunctionBegin; 4829 PetscCall(PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0)); 4830 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 4831 PetscCheck(vStart >= 0 && vEnd >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 4832 PetscCall(DMSetCoordinateDim(dm, spaceDim)); 4833 PetscCall(PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL)); 4834 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); 4835 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 4836 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 4837 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spaceDim)); 4838 PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd)); 4839 for (v = vStart; v < vEnd; ++v) { 4840 PetscCall(PetscSectionSetDof(coordSection, v, spaceDim)); 4841 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spaceDim)); 4842 } 4843 PetscCall(PetscSectionSetUp(coordSection)); 4844 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 4845 PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &coordinates)); 4846 PetscCall(VecSetBlockSize(coordinates, spaceDim)); 4847 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 4848 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 4849 PetscCall(VecSetType(coordinates, VECSTANDARD)); 4850 PetscCall(VecGetArray(coordinates, &coords)); 4851 { 4852 MPI_Datatype coordtype; 4853 4854 /* Need a temp buffer for coords if we have complex/single */ 4855 PetscCallMPI(MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype)); 4856 PetscCallMPI(MPI_Type_commit(&coordtype)); 4857 #if defined(PETSC_USE_COMPLEX) 4858 { 4859 PetscScalar *svertexCoords; 4860 PetscInt i; 4861 PetscCall(PetscMalloc1(numVertices * spaceDim, &svertexCoords)); 4862 for (i = 0; i < numVertices * spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 4863 PetscCall(PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords, MPI_REPLACE)); 4864 PetscCall(PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords, MPI_REPLACE)); 4865 PetscCall(PetscFree(svertexCoords)); 4866 } 4867 #else 4868 PetscCall(PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords, MPI_REPLACE)); 4869 PetscCall(PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords, MPI_REPLACE)); 4870 #endif 4871 PetscCallMPI(MPI_Type_free(&coordtype)); 4872 } 4873 PetscCall(VecRestoreArray(coordinates, &coords)); 4874 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 4875 PetscCall(VecDestroy(&coordinates)); 4876 PetscCall(PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0)); 4877 PetscFunctionReturn(PETSC_SUCCESS); 4878 } 4879 4880 /*@ 4881 DMPlexCreateFromCellListParallelPetsc - Create distributed `DMPLEX` from a list of vertices for each cell (common mesh generator output) 4882 4883 Collective 4884 4885 Input Parameters: 4886 + comm - The communicator 4887 . dim - The topological dimension of the mesh 4888 . numCells - The number of cells owned by this process 4889 . numVertices - The number of vertices owned by this process, or `PETSC_DECIDE` 4890 . NVertices - The global number of vertices, or `PETSC_DECIDE` 4891 . numCorners - The number of vertices for each cell 4892 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 4893 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 4894 . spaceDim - The spatial dimension used for coordinates 4895 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 4896 4897 Output Parameters: 4898 + dm - The `DM` 4899 . vertexSF - (Optional) `PetscSF` describing complete vertex ownership 4900 - verticesAdj - (Optional) vertex adjacency array 4901 4902 Level: intermediate 4903 4904 Notes: 4905 This function is just a convenient sequence of `DMCreate()`, `DMSetType()`, `DMSetDimension()`, 4906 `DMPlexBuildFromCellListParallel()`, `DMPlexInterpolate()`, `DMPlexBuildCoordinatesFromCellListParallel()` 4907 4908 See `DMPlexBuildFromCellListParallel()` for an example and details about the topology-related parameters. 4909 4910 See `DMPlexBuildCoordinatesFromCellListParallel()` for details about the geometry-related parameters. 4911 4912 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromCellListPetsc()`, `DMPlexBuildFromCellListParallel()`, `DMPlexBuildCoordinatesFromCellListParallel()`, `DMPlexCreateFromDAG()`, `DMPlexCreate()` 4913 @*/ 4914 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) 4915 { 4916 PetscSF sfVert; 4917 4918 PetscFunctionBegin; 4919 PetscCall(DMCreate(comm, dm)); 4920 PetscCall(DMSetType(*dm, DMPLEX)); 4921 PetscValidLogicalCollectiveInt(*dm, dim, 2); 4922 PetscValidLogicalCollectiveInt(*dm, spaceDim, 9); 4923 PetscCall(DMSetDimension(*dm, dim)); 4924 PetscCall(DMPlexBuildFromCellListParallel(*dm, numCells, numVertices, NVertices, numCorners, cells, &sfVert, verticesAdj)); 4925 if (interpolate) { 4926 DM idm; 4927 4928 PetscCall(DMPlexInterpolate(*dm, &idm)); 4929 PetscCall(DMDestroy(dm)); 4930 *dm = idm; 4931 } 4932 PetscCall(DMPlexBuildCoordinatesFromCellListParallel(*dm, spaceDim, sfVert, vertexCoords)); 4933 if (vertexSF) *vertexSF = sfVert; 4934 else PetscCall(PetscSFDestroy(&sfVert)); 4935 PetscFunctionReturn(PETSC_SUCCESS); 4936 } 4937 4938 /*@C 4939 DMPlexBuildFromCellList - Build `DMPLEX` topology from a list of vertices for each cell (common mesh generator output) 4940 4941 Collective; No Fortran Support 4942 4943 Input Parameters: 4944 + dm - The `DM` 4945 . numCells - The number of cells owned by this process 4946 . numVertices - The number of vertices owned by this process, or `PETSC_DETERMINE` 4947 . numCorners - The number of vertices for each cell 4948 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 4949 4950 Level: advanced 4951 4952 Notes: 4953 Two triangles sharing a face 4954 .vb 4955 4956 2 4957 / | \ 4958 / | \ 4959 / | \ 4960 0 0 | 1 3 4961 \ | / 4962 \ | / 4963 \ | / 4964 1 4965 .ve 4966 would have input 4967 .vb 4968 numCells = 2, numVertices = 4 4969 cells = [0 1 2 1 3 2] 4970 .ve 4971 which would result in the `DMPLEX` 4972 .vb 4973 4974 4 4975 / | \ 4976 / | \ 4977 / | \ 4978 2 0 | 1 5 4979 \ | / 4980 \ | / 4981 \ | / 4982 3 4983 .ve 4984 4985 If numVertices is `PETSC_DETERMINE`, it is computed by PETSc as the maximum vertex index in cells + 1. 4986 4987 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildFromCellListParallel()`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromCellListPetsc()` 4988 @*/ 4989 PetscErrorCode DMPlexBuildFromCellList(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[]) 4990 { 4991 PetscInt *cones, c, p, dim; 4992 4993 PetscFunctionBegin; 4994 PetscCall(PetscLogEventBegin(DMPLEX_BuildFromCellList, dm, 0, 0, 0)); 4995 PetscCall(DMGetDimension(dm, &dim)); 4996 /* Get/check global number of vertices */ 4997 { 4998 PetscInt NVerticesInCells, i; 4999 const PetscInt len = numCells * numCorners; 5000 5001 /* NVerticesInCells = max(cells) + 1 */ 5002 NVerticesInCells = PETSC_MIN_INT; 5003 for (i = 0; i < len; i++) 5004 if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 5005 ++NVerticesInCells; 5006 5007 if (numVertices == PETSC_DECIDE) numVertices = NVerticesInCells; 5008 else 5009 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); 5010 } 5011 PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices)); 5012 for (c = 0; c < numCells; ++c) PetscCall(DMPlexSetConeSize(dm, c, numCorners)); 5013 PetscCall(DMSetUp(dm)); 5014 PetscCall(DMPlexGetCones(dm, &cones)); 5015 for (c = 0; c < numCells; ++c) { 5016 for (p = 0; p < numCorners; ++p) cones[c * numCorners + p] = cells[c * numCorners + p] + numCells; 5017 } 5018 PetscCall(DMPlexSymmetrize(dm)); 5019 PetscCall(DMPlexStratify(dm)); 5020 PetscCall(PetscLogEventEnd(DMPLEX_BuildFromCellList, dm, 0, 0, 0)); 5021 PetscFunctionReturn(PETSC_SUCCESS); 5022 } 5023 5024 /*@C 5025 DMPlexBuildCoordinatesFromCellList - Build `DM` coordinates from a list of coordinates for each owned vertex (common mesh generator output) 5026 5027 Collective; No Fortran Support 5028 5029 Input Parameters: 5030 + dm - The `DM` 5031 . spaceDim - The spatial dimension used for coordinates 5032 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 5033 5034 Level: advanced 5035 5036 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildCoordinatesFromCellListParallel()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexBuildFromCellList()` 5037 @*/ 5038 PetscErrorCode DMPlexBuildCoordinatesFromCellList(DM dm, PetscInt spaceDim, const PetscReal vertexCoords[]) 5039 { 5040 PetscSection coordSection; 5041 Vec coordinates; 5042 DM cdm; 5043 PetscScalar *coords; 5044 PetscInt v, vStart, vEnd, d; 5045 5046 PetscFunctionBegin; 5047 PetscCall(PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0)); 5048 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 5049 PetscCheck(vStart >= 0 && vEnd >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 5050 PetscCall(DMSetCoordinateDim(dm, spaceDim)); 5051 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 5052 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 5053 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spaceDim)); 5054 PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd)); 5055 for (v = vStart; v < vEnd; ++v) { 5056 PetscCall(PetscSectionSetDof(coordSection, v, spaceDim)); 5057 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spaceDim)); 5058 } 5059 PetscCall(PetscSectionSetUp(coordSection)); 5060 5061 PetscCall(DMGetCoordinateDM(dm, &cdm)); 5062 PetscCall(DMCreateLocalVector(cdm, &coordinates)); 5063 PetscCall(VecSetBlockSize(coordinates, spaceDim)); 5064 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 5065 PetscCall(VecGetArrayWrite(coordinates, &coords)); 5066 for (v = 0; v < vEnd - vStart; ++v) { 5067 for (d = 0; d < spaceDim; ++d) coords[v * spaceDim + d] = vertexCoords[v * spaceDim + d]; 5068 } 5069 PetscCall(VecRestoreArrayWrite(coordinates, &coords)); 5070 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 5071 PetscCall(VecDestroy(&coordinates)); 5072 PetscCall(PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0)); 5073 PetscFunctionReturn(PETSC_SUCCESS); 5074 } 5075 5076 /*@ 5077 DMPlexCreateFromCellListPetsc - Create `DMPLEX` from a list of vertices for each cell (common mesh generator output), but only process 0 takes in the input 5078 5079 Collective 5080 5081 Input Parameters: 5082 + comm - The communicator 5083 . dim - The topological dimension of the mesh 5084 . numCells - The number of cells, only on process 0 5085 . numVertices - The number of vertices owned by this process, or `PETSC_DECIDE`, only on process 0 5086 . numCorners - The number of vertices for each cell, only on process 0 5087 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 5088 . cells - An array of numCells*numCorners numbers, the vertices for each cell, only on process 0 5089 . spaceDim - The spatial dimension used for coordinates 5090 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex, only on process 0 5091 5092 Output Parameter: 5093 . dm - The `DM`, which only has points on process 0 5094 5095 Level: intermediate 5096 5097 Notes: 5098 This function is just a convenient sequence of `DMCreate()`, `DMSetType()`, `DMSetDimension()`, `DMPlexBuildFromCellList()`, 5099 `DMPlexInterpolate()`, `DMPlexBuildCoordinatesFromCellList()` 5100 5101 See `DMPlexBuildFromCellList()` for an example and details about the topology-related parameters. 5102 See `DMPlexBuildCoordinatesFromCellList()` for details about the geometry-related parameters. 5103 See `DMPlexCreateFromCellListParallelPetsc()` for parallel input 5104 5105 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildFromCellList()`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromDAG()`, `DMPlexCreate()` 5106 @*/ 5107 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) 5108 { 5109 PetscMPIInt rank; 5110 5111 PetscFunctionBegin; 5112 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."); 5113 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 5114 PetscCall(DMCreate(comm, dm)); 5115 PetscCall(DMSetType(*dm, DMPLEX)); 5116 PetscCall(DMSetDimension(*dm, dim)); 5117 if (rank == 0) PetscCall(DMPlexBuildFromCellList(*dm, numCells, numVertices, numCorners, cells)); 5118 else PetscCall(DMPlexBuildFromCellList(*dm, 0, 0, 0, NULL)); 5119 if (interpolate) { 5120 DM idm; 5121 5122 PetscCall(DMPlexInterpolate(*dm, &idm)); 5123 PetscCall(DMDestroy(dm)); 5124 *dm = idm; 5125 } 5126 if (rank == 0) PetscCall(DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, vertexCoords)); 5127 else PetscCall(DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, NULL)); 5128 PetscFunctionReturn(PETSC_SUCCESS); 5129 } 5130 5131 /*@ 5132 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a `DM` 5133 5134 Input Parameters: 5135 + dm - The empty `DM` object, usually from `DMCreate()` and `DMSetDimension()` 5136 . depth - The depth of the DAG 5137 . numPoints - Array of size depth + 1 containing the number of points at each `depth` 5138 . coneSize - The cone size of each point 5139 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 5140 . coneOrientations - The orientation of each cone point 5141 - vertexCoords - An array of `numPoints`[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via `DMSetCoordinateDim()` 5142 5143 Output Parameter: 5144 . dm - The `DM` 5145 5146 Level: advanced 5147 5148 Note: 5149 Two triangles sharing a face would have input 5150 .vb 5151 depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 5152 cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 5153 vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 5154 .ve 5155 which would result in the DMPlex 5156 .vb 5157 4 5158 / | \ 5159 / | \ 5160 / | \ 5161 2 0 | 1 5 5162 \ | / 5163 \ | / 5164 \ | / 5165 3 5166 .ve 5167 Notice that all points are numbered consecutively, unlike `DMPlexCreateFromCellListPetsc()` 5168 5169 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()` 5170 @*/ 5171 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 5172 { 5173 Vec coordinates; 5174 PetscSection coordSection; 5175 PetscScalar *coords; 5176 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 5177 5178 PetscFunctionBegin; 5179 PetscCall(DMGetDimension(dm, &dim)); 5180 PetscCall(DMGetCoordinateDim(dm, &dimEmbed)); 5181 PetscCheck(dimEmbed >= dim, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Embedding dimension %" PetscInt_FMT " cannot be less than intrinsic dimension %" PetscInt_FMT, dimEmbed, dim); 5182 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 5183 PetscCall(DMPlexSetChart(dm, pStart, pEnd)); 5184 for (p = pStart; p < pEnd; ++p) { 5185 PetscCall(DMPlexSetConeSize(dm, p, coneSize[p - pStart])); 5186 if (firstVertex < 0 && !coneSize[p - pStart]) firstVertex = p - pStart; 5187 } 5188 PetscCheck(firstVertex >= 0 || !numPoints[0], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Expected %" PetscInt_FMT " vertices but could not find any", numPoints[0]); 5189 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 5190 for (p = pStart, off = 0; p < pEnd; off += coneSize[p - pStart], ++p) { 5191 PetscCall(DMPlexSetCone(dm, p, &cones[off])); 5192 PetscCall(DMPlexSetConeOrientation(dm, p, &coneOrientations[off])); 5193 } 5194 PetscCall(DMPlexSymmetrize(dm)); 5195 PetscCall(DMPlexStratify(dm)); 5196 /* Build coordinates */ 5197 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 5198 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 5199 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dimEmbed)); 5200 PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex + numPoints[0])); 5201 for (v = firstVertex; v < firstVertex + numPoints[0]; ++v) { 5202 PetscCall(PetscSectionSetDof(coordSection, v, dimEmbed)); 5203 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed)); 5204 } 5205 PetscCall(PetscSectionSetUp(coordSection)); 5206 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 5207 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 5208 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 5209 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 5210 PetscCall(VecSetBlockSize(coordinates, dimEmbed)); 5211 PetscCall(VecSetType(coordinates, VECSTANDARD)); 5212 if (vertexCoords) { 5213 PetscCall(VecGetArray(coordinates, &coords)); 5214 for (v = 0; v < numPoints[0]; ++v) { 5215 PetscInt off; 5216 5217 PetscCall(PetscSectionGetOffset(coordSection, v + firstVertex, &off)); 5218 for (d = 0; d < dimEmbed; ++d) coords[off + d] = vertexCoords[v * dimEmbed + d]; 5219 } 5220 } 5221 PetscCall(VecRestoreArray(coordinates, &coords)); 5222 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 5223 PetscCall(VecDestroy(&coordinates)); 5224 PetscFunctionReturn(PETSC_SUCCESS); 5225 } 5226 5227 /*@C 5228 DMPlexCreateCellVertexFromFile - Create a `DMPLEX` mesh from a simple cell-vertex file. 5229 5230 Collective 5231 5232 + comm - The MPI communicator 5233 . filename - Name of the .dat file 5234 - interpolate - Create faces and edges in the mesh 5235 5236 Output Parameter: 5237 . dm - The `DM` object representing the mesh 5238 5239 Level: beginner 5240 5241 Note: 5242 The format is the simplest possible: 5243 .vb 5244 Ne 5245 v0 v1 ... vk 5246 Nv 5247 x y z marker 5248 .ve 5249 5250 Developer Note: 5251 Should use a `PetscViewer` not a filename 5252 5253 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromFile()`, `DMPlexCreateMedFromFile()`, `DMPlexCreateGmsh()`, `DMPlexCreate()` 5254 @*/ 5255 static PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 5256 { 5257 DMLabel marker; 5258 PetscViewer viewer; 5259 Vec coordinates; 5260 PetscSection coordSection; 5261 PetscScalar *coords; 5262 char line[PETSC_MAX_PATH_LEN]; 5263 PetscInt dim = 3, cdim = 3, coordSize, v, c, d; 5264 PetscMPIInt rank; 5265 int snum, Nv, Nc, Ncn, Nl; 5266 5267 PetscFunctionBegin; 5268 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 5269 PetscCall(PetscViewerCreate(comm, &viewer)); 5270 PetscCall(PetscViewerSetType(viewer, PETSCVIEWERASCII)); 5271 PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ)); 5272 PetscCall(PetscViewerFileSetName(viewer, filename)); 5273 if (rank == 0) { 5274 PetscCall(PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING)); 5275 snum = sscanf(line, "%d %d %d %d", &Nc, &Nv, &Ncn, &Nl); 5276 PetscCheck(snum == 4, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 5277 } else { 5278 Nc = Nv = Ncn = Nl = 0; 5279 } 5280 PetscCall(DMCreate(comm, dm)); 5281 PetscCall(DMSetType(*dm, DMPLEX)); 5282 PetscCall(DMPlexSetChart(*dm, 0, Nc + Nv)); 5283 PetscCall(DMSetDimension(*dm, dim)); 5284 PetscCall(DMSetCoordinateDim(*dm, cdim)); 5285 /* Read topology */ 5286 if (rank == 0) { 5287 char format[PETSC_MAX_PATH_LEN]; 5288 PetscInt cone[8]; 5289 int vbuf[8], v; 5290 5291 for (c = 0; c < Ncn; ++c) { 5292 format[c * 3 + 0] = '%'; 5293 format[c * 3 + 1] = 'd'; 5294 format[c * 3 + 2] = ' '; 5295 } 5296 format[Ncn * 3 - 1] = '\0'; 5297 for (c = 0; c < Nc; ++c) PetscCall(DMPlexSetConeSize(*dm, c, Ncn)); 5298 PetscCall(DMSetUp(*dm)); 5299 for (c = 0; c < Nc; ++c) { 5300 PetscCall(PetscViewerRead(viewer, line, Ncn, NULL, PETSC_STRING)); 5301 switch (Ncn) { 5302 case 2: 5303 snum = sscanf(line, format, &vbuf[0], &vbuf[1]); 5304 break; 5305 case 3: 5306 snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2]); 5307 break; 5308 case 4: 5309 snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3]); 5310 break; 5311 case 6: 5312 snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5]); 5313 break; 5314 case 8: 5315 snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5], &vbuf[6], &vbuf[7]); 5316 break; 5317 default: 5318 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "No cell shape with %d vertices", Ncn); 5319 } 5320 PetscCheck(snum == Ncn, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 5321 for (v = 0; v < Ncn; ++v) cone[v] = vbuf[v] + Nc; 5322 /* Hexahedra are inverted */ 5323 if (Ncn == 8) { 5324 PetscInt tmp = cone[1]; 5325 cone[1] = cone[3]; 5326 cone[3] = tmp; 5327 } 5328 PetscCall(DMPlexSetCone(*dm, c, cone)); 5329 } 5330 } 5331 PetscCall(DMPlexSymmetrize(*dm)); 5332 PetscCall(DMPlexStratify(*dm)); 5333 /* Read coordinates */ 5334 PetscCall(DMGetCoordinateSection(*dm, &coordSection)); 5335 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 5336 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, cdim)); 5337 PetscCall(PetscSectionSetChart(coordSection, Nc, Nc + Nv)); 5338 for (v = Nc; v < Nc + Nv; ++v) { 5339 PetscCall(PetscSectionSetDof(coordSection, v, cdim)); 5340 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, cdim)); 5341 } 5342 PetscCall(PetscSectionSetUp(coordSection)); 5343 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 5344 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 5345 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 5346 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 5347 PetscCall(VecSetBlockSize(coordinates, cdim)); 5348 PetscCall(VecSetType(coordinates, VECSTANDARD)); 5349 PetscCall(VecGetArray(coordinates, &coords)); 5350 if (rank == 0) { 5351 char format[PETSC_MAX_PATH_LEN]; 5352 double x[3]; 5353 int l, val[3]; 5354 5355 if (Nl) { 5356 for (l = 0; l < Nl; ++l) { 5357 format[l * 3 + 0] = '%'; 5358 format[l * 3 + 1] = 'd'; 5359 format[l * 3 + 2] = ' '; 5360 } 5361 format[Nl * 3 - 1] = '\0'; 5362 PetscCall(DMCreateLabel(*dm, "marker")); 5363 PetscCall(DMGetLabel(*dm, "marker", &marker)); 5364 } 5365 for (v = 0; v < Nv; ++v) { 5366 PetscCall(PetscViewerRead(viewer, line, 3 + Nl, NULL, PETSC_STRING)); 5367 snum = sscanf(line, "%lg %lg %lg", &x[0], &x[1], &x[2]); 5368 PetscCheck(snum == 3, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 5369 switch (Nl) { 5370 case 0: 5371 snum = 0; 5372 break; 5373 case 1: 5374 snum = sscanf(line, format, &val[0]); 5375 break; 5376 case 2: 5377 snum = sscanf(line, format, &val[0], &val[1]); 5378 break; 5379 case 3: 5380 snum = sscanf(line, format, &val[0], &val[1], &val[2]); 5381 break; 5382 default: 5383 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Request support for %d labels", Nl); 5384 } 5385 PetscCheck(snum == Nl, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 5386 for (d = 0; d < cdim; ++d) coords[v * cdim + d] = x[d]; 5387 for (l = 0; l < Nl; ++l) PetscCall(DMLabelSetValue(marker, v + Nc, val[l])); 5388 } 5389 } 5390 PetscCall(VecRestoreArray(coordinates, &coords)); 5391 PetscCall(DMSetCoordinatesLocal(*dm, coordinates)); 5392 PetscCall(VecDestroy(&coordinates)); 5393 PetscCall(PetscViewerDestroy(&viewer)); 5394 if (interpolate) { 5395 DM idm; 5396 DMLabel bdlabel; 5397 5398 PetscCall(DMPlexInterpolate(*dm, &idm)); 5399 PetscCall(DMDestroy(dm)); 5400 *dm = idm; 5401 5402 if (!Nl) { 5403 PetscCall(DMCreateLabel(*dm, "marker")); 5404 PetscCall(DMGetLabel(*dm, "marker", &bdlabel)); 5405 PetscCall(DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel)); 5406 PetscCall(DMPlexLabelComplete(*dm, bdlabel)); 5407 } 5408 } 5409 PetscFunctionReturn(PETSC_SUCCESS); 5410 } 5411 5412 /*@C 5413 DMPlexCreateFromFile - This takes a filename and produces a `DM` 5414 5415 Collective 5416 5417 Input Parameters: 5418 + comm - The communicator 5419 . filename - A file name 5420 . plexname - The object name of the resulting `DM`, also used for intra-datafile lookup by some formats 5421 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 5422 5423 Output Parameter: 5424 . dm - The `DM` 5425 5426 Options Database Key: 5427 . -dm_plex_create_from_hdf5_xdmf - use the `PETSC_VIEWER_HDF5_XDMF` format for reading HDF5 5428 5429 Use `-dm_plex_create_ prefix` to pass options to the internal `PetscViewer`, e.g. 5430 $ -dm_plex_create_viewer_hdf5_collective 5431 5432 Level: beginner 5433 5434 Notes: 5435 Using `PETSCVIEWERHDF5` type with `PETSC_VIEWER_HDF5_PETSC` format, one can save multiple `DMPLEX` 5436 meshes in a single HDF5 file. This in turn requires one to name the `DMPLEX` object with `PetscObjectSetName()` 5437 before saving it with `DMView()` and before loading it with `DMLoad()` for identification of the mesh object. 5438 The input parameter name is thus used to name the `DMPLEX` object when `DMPlexCreateFromFile()` internally 5439 calls `DMLoad()`. Currently, name is ignored for other viewer types and/or formats. 5440 5441 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromDAG()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()`, `PetscObjectSetName()`, `DMView()`, `DMLoad()` 5442 @*/ 5443 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], const char plexname[], PetscBool interpolate, DM *dm) 5444 { 5445 const char extGmsh[] = ".msh"; 5446 const char extGmsh2[] = ".msh2"; 5447 const char extGmsh4[] = ".msh4"; 5448 const char extCGNS[] = ".cgns"; 5449 const char extExodus[] = ".exo"; 5450 const char extExodus_e[] = ".e"; 5451 const char extGenesis[] = ".gen"; 5452 const char extFluent[] = ".cas"; 5453 const char extHDF5[] = ".h5"; 5454 const char extXDMFHDF5[] = ".xdmf.h5"; 5455 const char extMed[] = ".med"; 5456 const char extPLY[] = ".ply"; 5457 const char extEGADSLite[] = ".egadslite"; 5458 const char extEGADS[] = ".egads"; 5459 const char extIGES[] = ".igs"; 5460 const char extSTEP[] = ".stp"; 5461 const char extCV[] = ".dat"; 5462 size_t len; 5463 PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isEGADSLite, isEGADS, isIGES, isSTEP, isCV, isXDMFHDF5; 5464 PetscMPIInt rank; 5465 5466 PetscFunctionBegin; 5467 PetscAssertPointer(filename, 2); 5468 if (plexname) PetscAssertPointer(plexname, 3); 5469 PetscAssertPointer(dm, 5); 5470 PetscCall(DMInitializePackage()); 5471 PetscCall(PetscLogEventBegin(DMPLEX_CreateFromFile, 0, 0, 0, 0)); 5472 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 5473 PetscCall(PetscStrlen(filename, &len)); 5474 PetscCheck(len, comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 5475 5476 #define CheckExtension(extension__, is_extension__) \ 5477 do { \ 5478 PetscAssert(sizeof(extension__), comm, PETSC_ERR_PLIB, "Zero-size extension: %s", extension__); \ 5479 /* don't count the null-terminator at the end */ \ 5480 const size_t ext_len = sizeof(extension__) - 1; \ 5481 if (len < ext_len) { \ 5482 is_extension__ = PETSC_FALSE; \ 5483 } else { \ 5484 PetscCall(PetscStrncmp(filename + len - ext_len, extension__, ext_len, &is_extension__)); \ 5485 } \ 5486 } while (0) 5487 5488 CheckExtension(extGmsh, isGmsh); 5489 CheckExtension(extGmsh2, isGmsh2); 5490 CheckExtension(extGmsh4, isGmsh4); 5491 CheckExtension(extCGNS, isCGNS); 5492 CheckExtension(extExodus, isExodus); 5493 if (!isExodus) CheckExtension(extExodus_e, isExodus); 5494 CheckExtension(extGenesis, isGenesis); 5495 CheckExtension(extFluent, isFluent); 5496 CheckExtension(extHDF5, isHDF5); 5497 CheckExtension(extMed, isMed); 5498 CheckExtension(extPLY, isPLY); 5499 CheckExtension(extEGADSLite, isEGADSLite); 5500 CheckExtension(extEGADS, isEGADS); 5501 CheckExtension(extIGES, isIGES); 5502 CheckExtension(extSTEP, isSTEP); 5503 CheckExtension(extCV, isCV); 5504 CheckExtension(extXDMFHDF5, isXDMFHDF5); 5505 5506 #undef CheckExtension 5507 5508 if (isGmsh || isGmsh2 || isGmsh4) { 5509 PetscCall(DMPlexCreateGmshFromFile(comm, filename, interpolate, dm)); 5510 } else if (isCGNS) { 5511 PetscCall(DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm)); 5512 } else if (isExodus || isGenesis) { 5513 PetscCall(DMPlexCreateExodusFromFile(comm, filename, interpolate, dm)); 5514 } else if (isFluent) { 5515 PetscCall(DMPlexCreateFluentFromFile(comm, filename, interpolate, dm)); 5516 } else if (isHDF5) { 5517 PetscViewer viewer; 5518 5519 /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */ 5520 PetscCall(PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &isXDMFHDF5, NULL)); 5521 PetscCall(PetscViewerCreate(comm, &viewer)); 5522 PetscCall(PetscViewerSetType(viewer, PETSCVIEWERHDF5)); 5523 PetscCall(PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_")); 5524 PetscCall(PetscViewerSetFromOptions(viewer)); 5525 PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ)); 5526 PetscCall(PetscViewerFileSetName(viewer, filename)); 5527 5528 PetscCall(DMCreate(comm, dm)); 5529 PetscCall(PetscObjectSetName((PetscObject)(*dm), plexname)); 5530 PetscCall(DMSetType(*dm, DMPLEX)); 5531 if (isXDMFHDF5) PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF)); 5532 PetscCall(DMLoad(*dm, viewer)); 5533 if (isXDMFHDF5) PetscCall(PetscViewerPopFormat(viewer)); 5534 PetscCall(PetscViewerDestroy(&viewer)); 5535 5536 if (interpolate) { 5537 DM idm; 5538 5539 PetscCall(DMPlexInterpolate(*dm, &idm)); 5540 PetscCall(DMDestroy(dm)); 5541 *dm = idm; 5542 } 5543 } else if (isMed) { 5544 PetscCall(DMPlexCreateMedFromFile(comm, filename, interpolate, dm)); 5545 } else if (isPLY) { 5546 PetscCall(DMPlexCreatePLYFromFile(comm, filename, interpolate, dm)); 5547 } else if (isEGADSLite || isEGADS || isIGES || isSTEP) { 5548 if (isEGADSLite) PetscCall(DMPlexCreateEGADSLiteFromFile(comm, filename, dm)); 5549 else PetscCall(DMPlexCreateEGADSFromFile(comm, filename, dm)); 5550 if (!interpolate) { 5551 DM udm; 5552 5553 PetscCall(DMPlexUninterpolate(*dm, &udm)); 5554 PetscCall(DMDestroy(dm)); 5555 *dm = udm; 5556 } 5557 } else if (isCV) { 5558 PetscCall(DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm)); 5559 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 5560 PetscCall(PetscStrlen(plexname, &len)); 5561 if (len) PetscCall(PetscObjectSetName((PetscObject)(*dm), plexname)); 5562 PetscCall(PetscLogEventEnd(DMPLEX_CreateFromFile, 0, 0, 0, 0)); 5563 PetscFunctionReturn(PETSC_SUCCESS); 5564 } 5565 5566 /*@C 5567 DMPlexCreateEphemeral - This takes a `DMPlexTransform` and a base `DMPlex` and produces an ephemeral `DM`, meaning one that is created on the fly in response to queries. 5568 5569 Input Parameters: 5570 + tr - The `DMPlexTransform` 5571 - prefix - An options prefix, or NULL 5572 5573 Output Parameter: 5574 . dm - The `DM` 5575 5576 Level: beginner 5577 5578 Notes: 5579 An emphemeral mesh is one that is not stored concretely, as in the default `DMPLEX` implementation, but rather is produced on the fly in response to queries, using information from the transform and the base mesh. 5580 5581 .seealso: `DMPlexCreateFromFile`, `DMPlexCreateFromDAG()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()` 5582 @*/ 5583 PetscErrorCode DMPlexCreateEphemeral(DMPlexTransform tr, const char prefix[], DM *dm) 5584 { 5585 DM bdm, bcdm, cdm; 5586 Vec coordinates, coordinatesNew; 5587 PetscSection cs; 5588 PetscInt dim, cdim, Nl; 5589 5590 PetscFunctionBegin; 5591 PetscCall(DMCreate(PetscObjectComm((PetscObject)tr), dm)); 5592 PetscCall(DMSetType(*dm, DMPLEX)); 5593 ((DM_Plex *)(*dm)->data)->interpolated = DMPLEX_INTERPOLATED_FULL; 5594 // Handle coordinates 5595 PetscCall(DMPlexTransformGetDM(tr, &bdm)); 5596 PetscCall(DMGetCoordinateDim(bdm, &cdim)); 5597 PetscCall(DMSetCoordinateDim(*dm, cdim)); 5598 PetscCall(DMGetDimension(bdm, &dim)); 5599 PetscCall(DMSetDimension(*dm, dim)); 5600 PetscCall(DMGetCoordinateDM(bdm, &bcdm)); 5601 PetscCall(DMGetCoordinateDM(*dm, &cdm)); 5602 PetscCall(DMCopyDisc(bcdm, cdm)); 5603 PetscCall(DMGetLocalSection(cdm, &cs)); 5604 PetscCall(PetscSectionSetNumFields(cs, 1)); 5605 PetscCall(PetscSectionSetFieldComponents(cs, 0, cdim)); 5606 PetscCall(DMGetCoordinatesLocal(bdm, &coordinates)); 5607 PetscCall(VecDuplicate(coordinates, &coordinatesNew)); 5608 PetscCall(VecCopy(coordinates, coordinatesNew)); 5609 PetscCall(DMSetCoordinatesLocal(*dm, coordinatesNew)); 5610 PetscCall(VecDestroy(&coordinatesNew)); 5611 5612 PetscCall(PetscObjectReference((PetscObject)tr)); 5613 PetscCall(DMPlexTransformDestroy(&((DM_Plex *)(*dm)->data)->tr)); 5614 ((DM_Plex *)(*dm)->data)->tr = tr; 5615 PetscCall(DMPlexDistributeSetDefault(*dm, PETSC_FALSE)); 5616 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)*dm, prefix)); 5617 PetscCall(DMSetFromOptions(*dm)); 5618 5619 PetscCall(DMGetNumLabels(bdm, &Nl)); 5620 for (PetscInt l = 0; l < Nl; ++l) { 5621 DMLabel label, labelNew; 5622 const char *lname; 5623 PetscBool isDepth, isCellType; 5624 5625 PetscCall(DMGetLabelName(bdm, l, &lname)); 5626 PetscCall(PetscStrcmp(lname, "depth", &isDepth)); 5627 if (isDepth) continue; 5628 PetscCall(PetscStrcmp(lname, "celltype", &isCellType)); 5629 if (isCellType) continue; 5630 PetscCall(DMCreateLabel(*dm, lname)); 5631 PetscCall(DMGetLabel(bdm, lname, &label)); 5632 PetscCall(DMGetLabel(*dm, lname, &labelNew)); 5633 PetscCall(DMLabelSetType(labelNew, DMLABELEPHEMERAL)); 5634 PetscCall(DMLabelEphemeralSetLabel(labelNew, label)); 5635 PetscCall(DMLabelEphemeralSetTransform(labelNew, tr)); 5636 PetscCall(DMLabelSetUp(labelNew)); 5637 } 5638 PetscFunctionReturn(PETSC_SUCCESS); 5639 } 5640