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 . dm - 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 PetscValidPointer(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 PetscValidPointer(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 PetscValidPointer(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 for (i = 0; i < 3; ++i) PetscCheck(periodicity[i] == DM_BOUNDARY_NONE, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Periodicity not yet supported"); 1400 PetscCall(DMCreate(PetscObjectComm((PetscObject)dm), &bdm)); 1401 PetscCall(DMSetType(bdm, DMPLEX)); 1402 PetscCall(DMSetDimension(bdm, 2)); 1403 PetscCall(PetscLogEventBegin(DMPLEX_Generate, bdm, 0, 0, 0)); 1404 PetscCall(DMPlexCreateBoxMesh_Simplex_Internal(bdm, 2, faces, lower, upper, periodicity, PETSC_TRUE)); 1405 PetscCall(DMPlexExtrude(bdm, faces[2], upper[2] - lower[2], PETSC_TRUE, PETSC_FALSE, NULL, NULL, &vol)); 1406 PetscCall(PetscLogEventEnd(DMPLEX_Generate, bdm, 0, 0, 0)); 1407 PetscCall(DMDestroy(&bdm)); 1408 PetscCall(DMPlexReplace_Internal(dm, &vol)); 1409 if (lower[2] != 0.0) { 1410 Vec v; 1411 PetscScalar *x; 1412 PetscInt cDim, n; 1413 1414 PetscCall(DMGetCoordinatesLocal(dm, &v)); 1415 PetscCall(VecGetBlockSize(v, &cDim)); 1416 PetscCall(VecGetLocalSize(v, &n)); 1417 PetscCall(VecGetArray(v, &x)); 1418 x += cDim; 1419 for (i = 0; i < n; i += cDim) x[i] += lower[2]; 1420 PetscCall(VecRestoreArray(v, &x)); 1421 PetscCall(DMSetCoordinatesLocal(dm, v)); 1422 } 1423 PetscFunctionReturn(PETSC_SUCCESS); 1424 } 1425 1426 /*@ 1427 DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells. 1428 1429 Collective 1430 1431 Input Parameters: 1432 + comm - The communicator for the `DM` object 1433 . faces - Number of faces per dimension, or `NULL` for (1, 1, 1) 1434 . lower - The lower left corner, or `NULL` for (0, 0, 0) 1435 . upper - The upper right corner, or `NULL` for (1, 1, 1) 1436 . periodicity - The boundary type for the X,Y,Z direction, or `NULL` for `DM_BOUNDARY_NONE` 1437 . orderHeight - If `PETSC_TRUE`, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1438 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1439 1440 Output Parameter: 1441 . dm - The `DM` object 1442 1443 Level: beginner 1444 1445 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateHexCylinderMesh()`, `DMPlexCreateWedgeCylinderMesh()`, `DMExtrude()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 1446 @*/ 1447 PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool orderHeight, PetscBool interpolate, DM *dm) 1448 { 1449 PetscInt fac[3] = {1, 1, 1}; 1450 PetscReal low[3] = {0, 0, 0}; 1451 PetscReal upp[3] = {1, 1, 1}; 1452 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1453 1454 PetscFunctionBegin; 1455 PetscCall(DMCreate(comm, dm)); 1456 PetscCall(DMSetType(*dm, DMPLEX)); 1457 PetscCall(DMPlexCreateWedgeBoxMesh_Internal(*dm, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt)); 1458 if (!interpolate) { 1459 DM udm; 1460 1461 PetscCall(DMPlexUninterpolate(*dm, &udm)); 1462 PetscCall(DMPlexReplace_Internal(*dm, &udm)); 1463 } 1464 if (periodicity) PetscCall(DMLocalizeCoordinates(*dm)); 1465 PetscFunctionReturn(PETSC_SUCCESS); 1466 } 1467 1468 /* 1469 DMPlexTensorPointLexicographic_Private - Returns all tuples of size 'len' with nonnegative integers that are all less than or equal to 'max' for that dimension. 1470 1471 Input Parameters: 1472 + len - The length of the tuple 1473 . max - The maximum for each dimension, so values are in [0, max) 1474 - tup - A tuple of length len+1: tup[len] > 0 indicates a stopping condition 1475 1476 Output Parameter: 1477 . tup - A tuple of `len` integers whose entries are at most `max` 1478 1479 Level: developer 1480 1481 Note: 1482 Ordering is lexicographic with lowest index as least significant in ordering. 1483 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}. 1484 1485 .seealso: PetscDualSpaceTensorPointLexicographic_Internal(), PetscDualSpaceLatticePointLexicographic_Internal() 1486 */ 1487 static PetscErrorCode DMPlexTensorPointLexicographic_Private(PetscInt len, const PetscInt max[], PetscInt tup[]) 1488 { 1489 PetscInt i; 1490 1491 PetscFunctionBegin; 1492 for (i = 0; i < len; ++i) { 1493 if (tup[i] < max[i] - 1) { 1494 break; 1495 } else { 1496 tup[i] = 0; 1497 } 1498 } 1499 if (i == len) tup[i - 1] = max[i - 1]; 1500 else ++tup[i]; 1501 PetscFunctionReturn(PETSC_SUCCESS); 1502 } 1503 1504 static PetscInt TupleToIndex_Private(PetscInt len, const PetscInt max[], const PetscInt tup[]) 1505 { 1506 PetscInt i, idx = tup[len - 1]; 1507 1508 for (i = len - 2; i >= 0; --i) { 1509 idx *= max[i]; 1510 idx += tup[i]; 1511 } 1512 return idx; 1513 } 1514 1515 static PetscErrorCode DestroyExtent_Private(void *extent) 1516 { 1517 return PetscFree(extent); 1518 } 1519 1520 static PetscErrorCode DMPlexCreateHypercubicMesh_Internal(DM dm, PetscInt dim, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], const DMBoundaryType bd[]) 1521 { 1522 Vec coordinates; 1523 PetscSection coordSection; 1524 DMLabel cutLabel = NULL; 1525 PetscBool cutMarker = PETSC_FALSE; 1526 PetscBool periodic = PETSC_FALSE; 1527 PetscInt numCells = 1, c; 1528 PetscInt numVertices = 1, v; 1529 PetscScalar *coords; 1530 PetscInt *vertices, *vert, *vtmp, *supp, cone[2]; 1531 PetscInt d, e, cell = 0, coordSize; 1532 PetscMPIInt rank; 1533 1534 PetscFunctionBegin; 1535 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 1536 PetscCall(DMSetDimension(dm, dim)); 1537 PetscCall(PetscCalloc4(dim, &vertices, dim, &vert, dim, &vtmp, 2 * dim, &supp)); 1538 PetscCall(DMCreateLabel(dm, "marker")); 1539 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL)); 1540 for (d = 0; d < dim; ++d) periodic = (periodic || bd[d] == DM_BOUNDARY_PERIODIC) ? PETSC_TRUE : PETSC_FALSE; 1541 if (periodic && cutMarker) { 1542 PetscCall(DMCreateLabel(dm, "periodic_cut")); 1543 PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel)); 1544 } 1545 for (d = 0; d < dim; ++d) PetscCheck(bd[d] == DM_BOUNDARY_PERIODIC, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Hypercubic mesh must be periodic now"); 1546 for (d = 0; d < dim; ++d) { 1547 vertices[d] = edges[d]; 1548 numVertices *= vertices[d]; 1549 } 1550 numCells = numVertices * dim; 1551 PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices)); 1552 for (c = 0; c < numCells; ++c) PetscCall(DMPlexSetConeSize(dm, c, 2)); 1553 for (v = numCells; v < numCells + numVertices; ++v) PetscCall(DMPlexSetSupportSize(dm, v, 2 * dim)); 1554 /* TODO Loop over boundary and reset support sizes */ 1555 PetscCall(DMSetUp(dm)); /* Allocate space for cones and supports */ 1556 /* Build cell cones and vertex supports */ 1557 PetscCall(DMCreateLabel(dm, "celltype")); 1558 while (vert[dim - 1] < vertices[dim - 1]) { 1559 const PetscInt vertex = TupleToIndex_Private(dim, vertices, vert) + numCells; 1560 PetscInt s = 0; 1561 1562 PetscCall(PetscPrintf(PETSC_COMM_SELF, "Vertex %" PetscInt_FMT ":", vertex)); 1563 for (d = 0; d < dim; ++d) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, vert[d])); 1564 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 1565 PetscCall(DMPlexSetCellType(dm, vertex, DM_POLYTOPE_POINT)); 1566 for (d = 0; d < dim; ++d) { 1567 for (e = 0; e < dim; ++e) vtmp[e] = vert[e]; 1568 vtmp[d] = (vert[d] + 1) % vertices[d]; 1569 cone[0] = vertex; 1570 cone[1] = TupleToIndex_Private(dim, vertices, vtmp) + numCells; 1571 PetscCall(PetscPrintf(PETSC_COMM_SELF, " Vertex %" PetscInt_FMT ":", cone[1])); 1572 for (e = 0; e < dim; ++e) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, vtmp[e])); 1573 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 1574 PetscCall(DMPlexSetCone(dm, cell, cone)); 1575 PetscCall(DMPlexSetCellType(dm, cell, DM_POLYTOPE_SEGMENT)); 1576 PetscCall(PetscPrintf(PETSC_COMM_SELF, " Edge %" PetscInt_FMT " (%" PetscInt_FMT " %" PetscInt_FMT ")\n", cell, cone[0], cone[1])); 1577 ++cell; 1578 } 1579 for (d = 0; d < dim; ++d) { 1580 for (e = 0; e < dim; ++e) vtmp[e] = vert[e]; 1581 vtmp[d] = (vert[d] + vertices[d] - 1) % vertices[d]; 1582 supp[s++] = TupleToIndex_Private(dim, vertices, vtmp) * dim + d; 1583 supp[s++] = (vertex - numCells) * dim + d; 1584 PetscCall(DMPlexSetSupport(dm, vertex, supp)); 1585 } 1586 PetscCall(DMPlexTensorPointLexicographic_Private(dim, vertices, vert)); 1587 } 1588 PetscCall(DMPlexStratify(dm)); 1589 /* Build coordinates */ 1590 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 1591 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 1592 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim)); 1593 PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices)); 1594 for (v = numCells; v < numCells + numVertices; ++v) { 1595 PetscCall(PetscSectionSetDof(coordSection, v, dim)); 1596 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim)); 1597 } 1598 PetscCall(PetscSectionSetUp(coordSection)); 1599 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 1600 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 1601 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 1602 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 1603 PetscCall(VecSetBlockSize(coordinates, dim)); 1604 PetscCall(VecSetType(coordinates, VECSTANDARD)); 1605 PetscCall(VecGetArray(coordinates, &coords)); 1606 for (d = 0; d < dim; ++d) vert[d] = 0; 1607 while (vert[dim - 1] < vertices[dim - 1]) { 1608 const PetscInt vertex = TupleToIndex_Private(dim, vertices, vert); 1609 1610 for (d = 0; d < dim; ++d) coords[vertex * dim + d] = lower[d] + ((upper[d] - lower[d]) / vertices[d]) * vert[d]; 1611 PetscCall(PetscPrintf(PETSC_COMM_SELF, "Vertex %" PetscInt_FMT ":", vertex)); 1612 for (d = 0; d < dim; ++d) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, vert[d])); 1613 for (d = 0; d < dim; ++d) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %g", (double)PetscRealPart(coords[vertex * dim + d]))); 1614 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 1615 PetscCall(DMPlexTensorPointLexicographic_Private(dim, vertices, vert)); 1616 } 1617 PetscCall(VecRestoreArray(coordinates, &coords)); 1618 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 1619 PetscCall(VecDestroy(&coordinates)); 1620 PetscCall(PetscFree4(vertices, vert, vtmp, supp)); 1621 //PetscCall(DMSetPeriodicity(dm, NULL, lower, upper)); 1622 // Attach the extent 1623 { 1624 PetscContainer c; 1625 PetscInt *extent; 1626 1627 PetscCall(PetscMalloc1(dim, &extent)); 1628 for (PetscInt d = 0; d < dim; ++d) extent[d] = edges[d]; 1629 PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &c)); 1630 PetscCall(PetscContainerSetUserDestroy(c, DestroyExtent_Private)); 1631 PetscCall(PetscContainerSetPointer(c, extent)); 1632 PetscCall(PetscObjectCompose((PetscObject)dm, "_extent", (PetscObject)c)); 1633 PetscCall(PetscContainerDestroy(&c)); 1634 } 1635 PetscFunctionReturn(PETSC_SUCCESS); 1636 } 1637 1638 /*@C 1639 DMPlexCreateHypercubicMesh - Creates a periodic mesh on the tensor product of unit intervals using only vertices and edges. 1640 1641 Collective 1642 1643 Input Parameters: 1644 + comm - The communicator for the DM object 1645 . dim - The spatial dimension 1646 . edges - Number of edges per dimension, or `NULL` for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 1647 . lower - The lower left corner, or `NULL` for (0, 0, 0) 1648 - upper - The upper right corner, or `NULL` for (1, 1, 1) 1649 1650 Output Parameter: 1651 . dm - The DM object 1652 1653 Level: beginner 1654 1655 Note: 1656 If you want to customize this mesh using options, you just need to 1657 .vb 1658 DMCreate(comm, &dm); 1659 DMSetType(dm, DMPLEX); 1660 DMSetFromOptions(dm); 1661 .ve 1662 and use the options on the `DMSetFromOptions()` page. 1663 1664 The vertices are numbered is lexicographic order, and the dim edges exiting a vertex in the positive orthant are number consecutively, 1665 .vb 1666 18--0-19--2-20--4-18 1667 | | | | 1668 13 15 17 13 1669 | | | | 1670 24-12-25-14-26-16-24 1671 | | | | 1672 7 9 11 7 1673 | | | | 1674 21--6-22--8-23-10-21 1675 | | | | 1676 1 3 5 1 1677 | | | | 1678 18--0-19--2-20--4-18 1679 .ve 1680 1681 .seealso: `DMSetFromOptions()`, `DMPlexCreateFromFile()`, `DMPlexCreateHexCylinderMesh()`, `DMSetType()`, `DMCreate()` 1682 @*/ 1683 PetscErrorCode DMPlexCreateHypercubicMesh(MPI_Comm comm, PetscInt dim, const PetscInt edges[], const PetscReal lower[], const PetscReal upper[], DM *dm) 1684 { 1685 PetscInt *edg; 1686 PetscReal *low, *upp; 1687 DMBoundaryType *bdt; 1688 PetscInt d; 1689 1690 PetscFunctionBegin; 1691 PetscCall(DMCreate(comm, dm)); 1692 PetscCall(DMSetType(*dm, DMPLEX)); 1693 PetscCall(PetscMalloc4(dim, &edg, dim, &low, dim, &upp, dim, &bdt)); 1694 for (d = 0; d < dim; ++d) { 1695 edg[d] = edges ? edges[d] : 1; 1696 low[d] = lower ? lower[d] : 0.; 1697 upp[d] = upper ? upper[d] : 1.; 1698 bdt[d] = DM_BOUNDARY_PERIODIC; 1699 } 1700 PetscCall(DMPlexCreateHypercubicMesh_Internal(*dm, dim, low, upp, edg, bdt)); 1701 PetscCall(PetscFree4(edg, low, upp, bdt)); 1702 PetscFunctionReturn(PETSC_SUCCESS); 1703 } 1704 1705 /*@C 1706 DMPlexSetOptionsPrefix - Sets the prefix used for searching for all `DM` options in the database. 1707 1708 Logically Collective 1709 1710 Input Parameters: 1711 + dm - the `DM` context 1712 - prefix - the prefix to prepend to all option names 1713 1714 Level: advanced 1715 1716 Note: 1717 A hyphen (-) must NOT be given at the beginning of the prefix name. 1718 The first character of all runtime options is AUTOMATICALLY the hyphen. 1719 1720 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `SNESSetFromOptions()` 1721 @*/ 1722 PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) 1723 { 1724 DM_Plex *mesh = (DM_Plex *)dm->data; 1725 1726 PetscFunctionBegin; 1727 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1728 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dm, prefix)); 1729 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)mesh->partitioner, prefix)); 1730 PetscFunctionReturn(PETSC_SUCCESS); 1731 } 1732 1733 /* Remap geometry to cylinder 1734 TODO: This only works for a single refinement, then it is broken 1735 1736 Interior square: Linear interpolation is correct 1737 The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing 1738 such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance 1739 1740 phi = arctan(y/x) 1741 d_close = sqrt(1/8 + 1/4 sin^2(phi)) 1742 d_far = sqrt(1/2 + sin^2(phi)) 1743 1744 so we remap them using 1745 1746 x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) 1747 y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) 1748 1749 If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. 1750 */ 1751 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[]) 1752 { 1753 const PetscReal dis = 1.0 / PetscSqrtReal(2.0); 1754 const PetscReal ds2 = 0.5 * dis; 1755 1756 if ((PetscAbsScalar(u[0]) <= ds2) && (PetscAbsScalar(u[1]) <= ds2)) { 1757 f0[0] = u[0]; 1758 f0[1] = u[1]; 1759 } else { 1760 PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; 1761 1762 x = PetscRealPart(u[0]); 1763 y = PetscRealPart(u[1]); 1764 phi = PetscAtan2Real(y, x); 1765 sinp = PetscSinReal(phi); 1766 cosp = PetscCosReal(phi); 1767 if ((PetscAbsReal(phi) > PETSC_PI / 4.0) && (PetscAbsReal(phi) < 3.0 * PETSC_PI / 4.0)) { 1768 dc = PetscAbsReal(ds2 / sinp); 1769 df = PetscAbsReal(dis / sinp); 1770 xc = ds2 * x / PetscAbsReal(y); 1771 yc = ds2 * PetscSignReal(y); 1772 } else { 1773 dc = PetscAbsReal(ds2 / cosp); 1774 df = PetscAbsReal(dis / cosp); 1775 xc = ds2 * PetscSignReal(x); 1776 yc = ds2 * y / PetscAbsReal(x); 1777 } 1778 f0[0] = xc + (u[0] - xc) * (1.0 - dc) / (df - dc); 1779 f0[1] = yc + (u[1] - yc) * (1.0 - dc) / (df - dc); 1780 } 1781 f0[2] = u[2]; 1782 } 1783 1784 static PetscErrorCode DMPlexCreateHexCylinderMesh_Internal(DM dm, DMBoundaryType periodicZ) 1785 { 1786 const PetscInt dim = 3; 1787 PetscInt numCells, numVertices; 1788 PetscMPIInt rank; 1789 1790 PetscFunctionBegin; 1791 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 1792 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 1793 PetscCall(DMSetDimension(dm, dim)); 1794 /* Create topology */ 1795 { 1796 PetscInt cone[8], c; 1797 1798 numCells = rank == 0 ? 5 : 0; 1799 numVertices = rank == 0 ? 16 : 0; 1800 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1801 numCells *= 3; 1802 numVertices = rank == 0 ? 24 : 0; 1803 } 1804 PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices)); 1805 for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 8)); 1806 PetscCall(DMSetUp(dm)); 1807 if (rank == 0) { 1808 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1809 cone[0] = 15; 1810 cone[1] = 18; 1811 cone[2] = 17; 1812 cone[3] = 16; 1813 cone[4] = 31; 1814 cone[5] = 32; 1815 cone[6] = 33; 1816 cone[7] = 34; 1817 PetscCall(DMPlexSetCone(dm, 0, cone)); 1818 cone[0] = 16; 1819 cone[1] = 17; 1820 cone[2] = 24; 1821 cone[3] = 23; 1822 cone[4] = 32; 1823 cone[5] = 36; 1824 cone[6] = 37; 1825 cone[7] = 33; /* 22 25 26 21 */ 1826 PetscCall(DMPlexSetCone(dm, 1, cone)); 1827 cone[0] = 18; 1828 cone[1] = 27; 1829 cone[2] = 24; 1830 cone[3] = 17; 1831 cone[4] = 34; 1832 cone[5] = 33; 1833 cone[6] = 37; 1834 cone[7] = 38; 1835 PetscCall(DMPlexSetCone(dm, 2, cone)); 1836 cone[0] = 29; 1837 cone[1] = 27; 1838 cone[2] = 18; 1839 cone[3] = 15; 1840 cone[4] = 35; 1841 cone[5] = 31; 1842 cone[6] = 34; 1843 cone[7] = 38; 1844 PetscCall(DMPlexSetCone(dm, 3, cone)); 1845 cone[0] = 29; 1846 cone[1] = 15; 1847 cone[2] = 16; 1848 cone[3] = 23; 1849 cone[4] = 35; 1850 cone[5] = 36; 1851 cone[6] = 32; 1852 cone[7] = 31; 1853 PetscCall(DMPlexSetCone(dm, 4, cone)); 1854 1855 cone[0] = 31; 1856 cone[1] = 34; 1857 cone[2] = 33; 1858 cone[3] = 32; 1859 cone[4] = 19; 1860 cone[5] = 22; 1861 cone[6] = 21; 1862 cone[7] = 20; 1863 PetscCall(DMPlexSetCone(dm, 5, cone)); 1864 cone[0] = 32; 1865 cone[1] = 33; 1866 cone[2] = 37; 1867 cone[3] = 36; 1868 cone[4] = 22; 1869 cone[5] = 25; 1870 cone[6] = 26; 1871 cone[7] = 21; 1872 PetscCall(DMPlexSetCone(dm, 6, cone)); 1873 cone[0] = 34; 1874 cone[1] = 38; 1875 cone[2] = 37; 1876 cone[3] = 33; 1877 cone[4] = 20; 1878 cone[5] = 21; 1879 cone[6] = 26; 1880 cone[7] = 28; 1881 PetscCall(DMPlexSetCone(dm, 7, cone)); 1882 cone[0] = 35; 1883 cone[1] = 38; 1884 cone[2] = 34; 1885 cone[3] = 31; 1886 cone[4] = 30; 1887 cone[5] = 19; 1888 cone[6] = 20; 1889 cone[7] = 28; 1890 PetscCall(DMPlexSetCone(dm, 8, cone)); 1891 cone[0] = 35; 1892 cone[1] = 31; 1893 cone[2] = 32; 1894 cone[3] = 36; 1895 cone[4] = 30; 1896 cone[5] = 25; 1897 cone[6] = 22; 1898 cone[7] = 19; 1899 PetscCall(DMPlexSetCone(dm, 9, cone)); 1900 1901 cone[0] = 19; 1902 cone[1] = 20; 1903 cone[2] = 21; 1904 cone[3] = 22; 1905 cone[4] = 15; 1906 cone[5] = 16; 1907 cone[6] = 17; 1908 cone[7] = 18; 1909 PetscCall(DMPlexSetCone(dm, 10, cone)); 1910 cone[0] = 22; 1911 cone[1] = 21; 1912 cone[2] = 26; 1913 cone[3] = 25; 1914 cone[4] = 16; 1915 cone[5] = 23; 1916 cone[6] = 24; 1917 cone[7] = 17; 1918 PetscCall(DMPlexSetCone(dm, 11, cone)); 1919 cone[0] = 20; 1920 cone[1] = 28; 1921 cone[2] = 26; 1922 cone[3] = 21; 1923 cone[4] = 18; 1924 cone[5] = 17; 1925 cone[6] = 24; 1926 cone[7] = 27; 1927 PetscCall(DMPlexSetCone(dm, 12, cone)); 1928 cone[0] = 30; 1929 cone[1] = 28; 1930 cone[2] = 20; 1931 cone[3] = 19; 1932 cone[4] = 29; 1933 cone[5] = 15; 1934 cone[6] = 18; 1935 cone[7] = 27; 1936 PetscCall(DMPlexSetCone(dm, 13, cone)); 1937 cone[0] = 30; 1938 cone[1] = 19; 1939 cone[2] = 22; 1940 cone[3] = 25; 1941 cone[4] = 29; 1942 cone[5] = 23; 1943 cone[6] = 16; 1944 cone[7] = 15; 1945 PetscCall(DMPlexSetCone(dm, 14, cone)); 1946 } else { 1947 cone[0] = 5; 1948 cone[1] = 8; 1949 cone[2] = 7; 1950 cone[3] = 6; 1951 cone[4] = 9; 1952 cone[5] = 12; 1953 cone[6] = 11; 1954 cone[7] = 10; 1955 PetscCall(DMPlexSetCone(dm, 0, cone)); 1956 cone[0] = 6; 1957 cone[1] = 7; 1958 cone[2] = 14; 1959 cone[3] = 13; 1960 cone[4] = 12; 1961 cone[5] = 15; 1962 cone[6] = 16; 1963 cone[7] = 11; 1964 PetscCall(DMPlexSetCone(dm, 1, cone)); 1965 cone[0] = 8; 1966 cone[1] = 17; 1967 cone[2] = 14; 1968 cone[3] = 7; 1969 cone[4] = 10; 1970 cone[5] = 11; 1971 cone[6] = 16; 1972 cone[7] = 18; 1973 PetscCall(DMPlexSetCone(dm, 2, cone)); 1974 cone[0] = 19; 1975 cone[1] = 17; 1976 cone[2] = 8; 1977 cone[3] = 5; 1978 cone[4] = 20; 1979 cone[5] = 9; 1980 cone[6] = 10; 1981 cone[7] = 18; 1982 PetscCall(DMPlexSetCone(dm, 3, cone)); 1983 cone[0] = 19; 1984 cone[1] = 5; 1985 cone[2] = 6; 1986 cone[3] = 13; 1987 cone[4] = 20; 1988 cone[5] = 15; 1989 cone[6] = 12; 1990 cone[7] = 9; 1991 PetscCall(DMPlexSetCone(dm, 4, cone)); 1992 } 1993 } 1994 PetscCall(DMPlexSymmetrize(dm)); 1995 PetscCall(DMPlexStratify(dm)); 1996 } 1997 /* Create cube geometry */ 1998 { 1999 Vec coordinates; 2000 PetscSection coordSection; 2001 PetscScalar *coords; 2002 PetscInt coordSize, v; 2003 const PetscReal dis = 1.0 / PetscSqrtReal(2.0); 2004 const PetscReal ds2 = dis / 2.0; 2005 2006 /* Build coordinates */ 2007 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 2008 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 2009 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim)); 2010 PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices)); 2011 for (v = numCells; v < numCells + numVertices; ++v) { 2012 PetscCall(PetscSectionSetDof(coordSection, v, dim)); 2013 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim)); 2014 } 2015 PetscCall(PetscSectionSetUp(coordSection)); 2016 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 2017 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 2018 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 2019 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 2020 PetscCall(VecSetBlockSize(coordinates, dim)); 2021 PetscCall(VecSetType(coordinates, VECSTANDARD)); 2022 PetscCall(VecGetArray(coordinates, &coords)); 2023 if (rank == 0) { 2024 coords[0 * dim + 0] = -ds2; 2025 coords[0 * dim + 1] = -ds2; 2026 coords[0 * dim + 2] = 0.0; 2027 coords[1 * dim + 0] = ds2; 2028 coords[1 * dim + 1] = -ds2; 2029 coords[1 * dim + 2] = 0.0; 2030 coords[2 * dim + 0] = ds2; 2031 coords[2 * dim + 1] = ds2; 2032 coords[2 * dim + 2] = 0.0; 2033 coords[3 * dim + 0] = -ds2; 2034 coords[3 * dim + 1] = ds2; 2035 coords[3 * dim + 2] = 0.0; 2036 coords[4 * dim + 0] = -ds2; 2037 coords[4 * dim + 1] = -ds2; 2038 coords[4 * dim + 2] = 1.0; 2039 coords[5 * dim + 0] = -ds2; 2040 coords[5 * dim + 1] = ds2; 2041 coords[5 * dim + 2] = 1.0; 2042 coords[6 * dim + 0] = ds2; 2043 coords[6 * dim + 1] = ds2; 2044 coords[6 * dim + 2] = 1.0; 2045 coords[7 * dim + 0] = ds2; 2046 coords[7 * dim + 1] = -ds2; 2047 coords[7 * dim + 2] = 1.0; 2048 coords[8 * dim + 0] = dis; 2049 coords[8 * dim + 1] = -dis; 2050 coords[8 * dim + 2] = 0.0; 2051 coords[9 * dim + 0] = dis; 2052 coords[9 * dim + 1] = dis; 2053 coords[9 * dim + 2] = 0.0; 2054 coords[10 * dim + 0] = dis; 2055 coords[10 * dim + 1] = -dis; 2056 coords[10 * dim + 2] = 1.0; 2057 coords[11 * dim + 0] = dis; 2058 coords[11 * dim + 1] = dis; 2059 coords[11 * dim + 2] = 1.0; 2060 coords[12 * dim + 0] = -dis; 2061 coords[12 * dim + 1] = dis; 2062 coords[12 * dim + 2] = 0.0; 2063 coords[13 * dim + 0] = -dis; 2064 coords[13 * dim + 1] = dis; 2065 coords[13 * dim + 2] = 1.0; 2066 coords[14 * dim + 0] = -dis; 2067 coords[14 * dim + 1] = -dis; 2068 coords[14 * dim + 2] = 0.0; 2069 coords[15 * dim + 0] = -dis; 2070 coords[15 * dim + 1] = -dis; 2071 coords[15 * dim + 2] = 1.0; 2072 if (periodicZ == DM_BOUNDARY_PERIODIC) { 2073 /* 15 31 19 */ coords[16 * dim + 0] = -ds2; 2074 coords[16 * dim + 1] = -ds2; 2075 coords[16 * dim + 2] = 0.5; 2076 /* 16 32 22 */ coords[17 * dim + 0] = ds2; 2077 coords[17 * dim + 1] = -ds2; 2078 coords[17 * dim + 2] = 0.5; 2079 /* 17 33 21 */ coords[18 * dim + 0] = ds2; 2080 coords[18 * dim + 1] = ds2; 2081 coords[18 * dim + 2] = 0.5; 2082 /* 18 34 20 */ coords[19 * dim + 0] = -ds2; 2083 coords[19 * dim + 1] = ds2; 2084 coords[19 * dim + 2] = 0.5; 2085 /* 29 35 30 */ coords[20 * dim + 0] = -dis; 2086 coords[20 * dim + 1] = -dis; 2087 coords[20 * dim + 2] = 0.5; 2088 /* 23 36 25 */ coords[21 * dim + 0] = dis; 2089 coords[21 * dim + 1] = -dis; 2090 coords[21 * dim + 2] = 0.5; 2091 /* 24 37 26 */ coords[22 * dim + 0] = dis; 2092 coords[22 * dim + 1] = dis; 2093 coords[22 * dim + 2] = 0.5; 2094 /* 27 38 28 */ coords[23 * dim + 0] = -dis; 2095 coords[23 * dim + 1] = dis; 2096 coords[23 * dim + 2] = 0.5; 2097 } 2098 } 2099 PetscCall(VecRestoreArray(coordinates, &coords)); 2100 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 2101 PetscCall(VecDestroy(&coordinates)); 2102 } 2103 /* Create periodicity */ 2104 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 2105 PetscReal L[3] = {-1., -1., 0.}; 2106 PetscReal maxCell[3] = {-1., -1., 0.}; 2107 PetscReal lower[3] = {0.0, 0.0, 0.0}; 2108 PetscReal upper[3] = {1.0, 1.0, 1.5}; 2109 PetscInt numZCells = 3; 2110 2111 L[2] = upper[2] - lower[2]; 2112 maxCell[2] = 1.1 * (L[2] / numZCells); 2113 PetscCall(DMSetPeriodicity(dm, maxCell, lower, L)); 2114 } 2115 { 2116 DM cdm; 2117 PetscDS cds; 2118 PetscScalar c[2] = {1.0, 1.0}; 2119 2120 PetscCall(DMPlexCreateCoordinateSpace(dm, 1, snapToCylinder)); 2121 PetscCall(DMGetCoordinateDM(dm, &cdm)); 2122 PetscCall(DMGetDS(cdm, &cds)); 2123 PetscCall(PetscDSSetConstants(cds, 2, c)); 2124 } 2125 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 2126 2127 /* Wait for coordinate creation before doing in-place modification */ 2128 PetscCall(DMPlexInterpolateInPlace_Internal(dm)); 2129 PetscFunctionReturn(PETSC_SUCCESS); 2130 } 2131 2132 /*@ 2133 DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. 2134 2135 Collective 2136 2137 Input Parameters: 2138 + comm - The communicator for the `DM` object 2139 - periodicZ - The boundary type for the Z direction 2140 2141 Output Parameter: 2142 . dm - The `DM` object 2143 2144 Level: beginner 2145 2146 Note: 2147 Here is the output numbering looking from the bottom of the cylinder: 2148 .vb 2149 17-----14 2150 | | 2151 | 2 | 2152 | | 2153 17-----8-----7-----14 2154 | | | | 2155 | 3 | 0 | 1 | 2156 | | | | 2157 19-----5-----6-----13 2158 | | 2159 | 4 | 2160 | | 2161 19-----13 2162 2163 and up through the top 2164 2165 18-----16 2166 | | 2167 | 2 | 2168 | | 2169 18----10----11-----16 2170 | | | | 2171 | 3 | 0 | 1 | 2172 | | | | 2173 20-----9----12-----15 2174 | | 2175 | 4 | 2176 | | 2177 20-----15 2178 .ve 2179 2180 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 2181 @*/ 2182 PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, DMBoundaryType periodicZ, DM *dm) 2183 { 2184 PetscFunctionBegin; 2185 PetscValidPointer(dm, 3); 2186 PetscCall(DMCreate(comm, dm)); 2187 PetscCall(DMSetType(*dm, DMPLEX)); 2188 PetscCall(DMPlexCreateHexCylinderMesh_Internal(*dm, periodicZ)); 2189 PetscFunctionReturn(PETSC_SUCCESS); 2190 } 2191 2192 static PetscErrorCode DMPlexCreateWedgeCylinderMesh_Internal(DM dm, PetscInt n, PetscBool interpolate) 2193 { 2194 const PetscInt dim = 3; 2195 PetscInt numCells, numVertices, v; 2196 PetscMPIInt rank; 2197 2198 PetscFunctionBegin; 2199 PetscCheck(n >= 0, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %" PetscInt_FMT " cannot be negative", n); 2200 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 2201 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 2202 PetscCall(DMSetDimension(dm, dim)); 2203 /* Must create the celltype label here so that we do not automatically try to compute the types */ 2204 PetscCall(DMCreateLabel(dm, "celltype")); 2205 /* Create topology */ 2206 { 2207 PetscInt cone[6], c; 2208 2209 numCells = rank == 0 ? n : 0; 2210 numVertices = rank == 0 ? 2 * (n + 1) : 0; 2211 PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices)); 2212 for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 6)); 2213 PetscCall(DMSetUp(dm)); 2214 for (c = 0; c < numCells; c++) { 2215 cone[0] = c + n * 1; 2216 cone[1] = (c + 1) % n + n * 1; 2217 cone[2] = 0 + 3 * n; 2218 cone[3] = c + n * 2; 2219 cone[4] = (c + 1) % n + n * 2; 2220 cone[5] = 1 + 3 * n; 2221 PetscCall(DMPlexSetCone(dm, c, cone)); 2222 PetscCall(DMPlexSetCellType(dm, c, DM_POLYTOPE_TRI_PRISM_TENSOR)); 2223 } 2224 PetscCall(DMPlexSymmetrize(dm)); 2225 PetscCall(DMPlexStratify(dm)); 2226 } 2227 for (v = numCells; v < numCells + numVertices; ++v) PetscCall(DMPlexSetCellType(dm, v, DM_POLYTOPE_POINT)); 2228 /* Create cylinder geometry */ 2229 { 2230 Vec coordinates; 2231 PetscSection coordSection; 2232 PetscScalar *coords; 2233 PetscInt coordSize, c; 2234 2235 /* Build coordinates */ 2236 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 2237 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 2238 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim)); 2239 PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices)); 2240 for (v = numCells; v < numCells + numVertices; ++v) { 2241 PetscCall(PetscSectionSetDof(coordSection, v, dim)); 2242 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim)); 2243 } 2244 PetscCall(PetscSectionSetUp(coordSection)); 2245 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 2246 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 2247 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 2248 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 2249 PetscCall(VecSetBlockSize(coordinates, dim)); 2250 PetscCall(VecSetType(coordinates, VECSTANDARD)); 2251 PetscCall(VecGetArray(coordinates, &coords)); 2252 for (c = 0; c < numCells; c++) { 2253 coords[(c + 0 * n) * dim + 0] = PetscCosReal(2.0 * c * PETSC_PI / n); 2254 coords[(c + 0 * n) * dim + 1] = PetscSinReal(2.0 * c * PETSC_PI / n); 2255 coords[(c + 0 * n) * dim + 2] = 1.0; 2256 coords[(c + 1 * n) * dim + 0] = PetscCosReal(2.0 * c * PETSC_PI / n); 2257 coords[(c + 1 * n) * dim + 1] = PetscSinReal(2.0 * c * PETSC_PI / n); 2258 coords[(c + 1 * n) * dim + 2] = 0.0; 2259 } 2260 if (rank == 0) { 2261 coords[(2 * n + 0) * dim + 0] = 0.0; 2262 coords[(2 * n + 0) * dim + 1] = 0.0; 2263 coords[(2 * n + 0) * dim + 2] = 1.0; 2264 coords[(2 * n + 1) * dim + 0] = 0.0; 2265 coords[(2 * n + 1) * dim + 1] = 0.0; 2266 coords[(2 * n + 1) * dim + 2] = 0.0; 2267 } 2268 PetscCall(VecRestoreArray(coordinates, &coords)); 2269 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 2270 PetscCall(VecDestroy(&coordinates)); 2271 } 2272 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 2273 /* Interpolate */ 2274 if (interpolate) PetscCall(DMPlexInterpolateInPlace_Internal(dm)); 2275 PetscFunctionReturn(PETSC_SUCCESS); 2276 } 2277 2278 /*@ 2279 DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges. 2280 2281 Collective 2282 2283 Input Parameters: 2284 + comm - The communicator for the `DM` object 2285 . n - The number of wedges around the origin 2286 - interpolate - Create edges and faces 2287 2288 Output Parameter: 2289 . dm - The `DM` object 2290 2291 Level: beginner 2292 2293 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateHexCylinderMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 2294 @*/ 2295 PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm) 2296 { 2297 PetscFunctionBegin; 2298 PetscValidPointer(dm, 4); 2299 PetscCall(DMCreate(comm, dm)); 2300 PetscCall(DMSetType(*dm, DMPLEX)); 2301 PetscCall(DMPlexCreateWedgeCylinderMesh_Internal(*dm, n, interpolate)); 2302 PetscFunctionReturn(PETSC_SUCCESS); 2303 } 2304 2305 static inline PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 2306 { 2307 PetscReal prod = 0.0; 2308 PetscInt i; 2309 for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]); 2310 return PetscSqrtReal(prod); 2311 } 2312 static inline PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 2313 { 2314 PetscReal prod = 0.0; 2315 PetscInt i; 2316 for (i = 0; i < dim; ++i) prod += x[i] * y[i]; 2317 return prod; 2318 } 2319 2320 /* The first constant is the sphere radius */ 2321 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[]) 2322 { 2323 PetscReal r = PetscRealPart(constants[0]); 2324 PetscReal norm2 = 0.0, fac; 2325 PetscInt n = uOff[1] - uOff[0], d; 2326 2327 for (d = 0; d < n; ++d) norm2 += PetscSqr(PetscRealPart(u[d])); 2328 fac = r / PetscSqrtReal(norm2); 2329 for (d = 0; d < n; ++d) f0[d] = u[d] * fac; 2330 } 2331 2332 static PetscErrorCode DMPlexCreateSphereMesh_Internal(DM dm, PetscInt dim, PetscBool simplex, PetscReal R) 2333 { 2334 const PetscInt embedDim = dim + 1; 2335 PetscSection coordSection; 2336 Vec coordinates; 2337 PetscScalar *coords; 2338 PetscReal *coordsIn; 2339 PetscInt numCells, numEdges, numVerts = 0, firstVertex = 0, v, firstEdge, coordSize, d, c, e; 2340 PetscMPIInt rank; 2341 2342 PetscFunctionBegin; 2343 PetscValidLogicalCollectiveBool(dm, simplex, 3); 2344 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 2345 PetscCall(DMSetDimension(dm, dim)); 2346 PetscCall(DMSetCoordinateDim(dm, dim + 1)); 2347 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 2348 switch (dim) { 2349 case 2: 2350 if (simplex) { 2351 const PetscReal radius = PetscSqrtReal(1 + PETSC_PHI * PETSC_PHI) / (1.0 + PETSC_PHI); 2352 const PetscReal edgeLen = 2.0 / (1.0 + PETSC_PHI) * (R / radius); 2353 const PetscInt degree = 5; 2354 PetscReal vertex[3] = {0.0, 1.0 / (1.0 + PETSC_PHI), PETSC_PHI / (1.0 + PETSC_PHI)}; 2355 PetscInt s[3] = {1, 1, 1}; 2356 PetscInt cone[3]; 2357 PetscInt *graph, p, i, j, k; 2358 2359 vertex[0] *= R / radius; 2360 vertex[1] *= R / radius; 2361 vertex[2] *= R / radius; 2362 numCells = rank == 0 ? 20 : 0; 2363 numVerts = rank == 0 ? 12 : 0; 2364 firstVertex = numCells; 2365 /* Use icosahedron, which for a R-sphere has coordinates which are all cyclic permutations of 2366 2367 (0, \pm 1/\phi+1, \pm \phi/\phi+1) 2368 2369 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 2370 length is then given by 2/(1+\phi) = 2 * 0.38197 = 0.76393. 2371 */ 2372 /* Construct vertices */ 2373 PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn)); 2374 if (rank == 0) { 2375 for (p = 0, i = 0; p < embedDim; ++p) { 2376 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2377 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2378 for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[(d + p) % embedDim] * vertex[(d + p) % embedDim]; 2379 ++i; 2380 } 2381 } 2382 } 2383 } 2384 /* Construct graph */ 2385 PetscCall(PetscCalloc1(numVerts * numVerts, &graph)); 2386 for (i = 0; i < numVerts; ++i) { 2387 for (j = 0, k = 0; j < numVerts; ++j) { 2388 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i * embedDim], &coordsIn[j * embedDim]) - edgeLen) < PETSC_SMALL) { 2389 graph[i * numVerts + j] = 1; 2390 ++k; 2391 } 2392 } 2393 PetscCheck(k == degree, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid icosahedron, vertex %" PetscInt_FMT " degree %" PetscInt_FMT " != %" PetscInt_FMT, i, k, degree); 2394 } 2395 /* Build Topology */ 2396 PetscCall(DMPlexSetChart(dm, 0, numCells + numVerts)); 2397 for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, embedDim)); 2398 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 2399 /* Cells */ 2400 for (i = 0, c = 0; i < numVerts; ++i) { 2401 for (j = 0; j < i; ++j) { 2402 for (k = 0; k < j; ++k) { 2403 if (graph[i * numVerts + j] && graph[j * numVerts + k] && graph[k * numVerts + i]) { 2404 cone[0] = firstVertex + i; 2405 cone[1] = firstVertex + j; 2406 cone[2] = firstVertex + k; 2407 /* Check orientation */ 2408 { 2409 const PetscInt epsilon[3][3][3] = { 2410 {{0, 0, 0}, {0, 0, 1}, {0, -1, 0}}, 2411 {{0, 0, -1}, {0, 0, 0}, {1, 0, 0} }, 2412 {{0, 1, 0}, {-1, 0, 0}, {0, 0, 0} } 2413 }; 2414 PetscReal normal[3]; 2415 PetscInt e, f; 2416 2417 for (d = 0; d < embedDim; ++d) { 2418 normal[d] = 0.0; 2419 for (e = 0; e < embedDim; ++e) { 2420 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]); 2421 } 2422 } 2423 if (DotReal(embedDim, normal, &coordsIn[i * embedDim]) < 0) { 2424 PetscInt tmp = cone[1]; 2425 cone[1] = cone[2]; 2426 cone[2] = tmp; 2427 } 2428 } 2429 PetscCall(DMPlexSetCone(dm, c++, cone)); 2430 } 2431 } 2432 } 2433 } 2434 PetscCall(DMPlexSymmetrize(dm)); 2435 PetscCall(DMPlexStratify(dm)); 2436 PetscCall(PetscFree(graph)); 2437 } else { 2438 /* 2439 12-21--13 2440 | | 2441 25 4 24 2442 | | 2443 12-25--9-16--8-24--13 2444 | | | | 2445 23 5 17 0 15 3 22 2446 | | | | 2447 10-20--6-14--7-19--11 2448 | | 2449 20 1 19 2450 | | 2451 10-18--11 2452 | | 2453 23 2 22 2454 | | 2455 12-21--13 2456 */ 2457 PetscInt cone[4], ornt[4]; 2458 2459 numCells = rank == 0 ? 6 : 0; 2460 numEdges = rank == 0 ? 12 : 0; 2461 numVerts = rank == 0 ? 8 : 0; 2462 firstVertex = numCells; 2463 firstEdge = numCells + numVerts; 2464 /* Build Topology */ 2465 PetscCall(DMPlexSetChart(dm, 0, numCells + numEdges + numVerts)); 2466 for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 4)); 2467 for (e = firstEdge; e < firstEdge + numEdges; ++e) PetscCall(DMPlexSetConeSize(dm, e, 2)); 2468 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 2469 if (rank == 0) { 2470 /* Cell 0 */ 2471 cone[0] = 14; 2472 cone[1] = 15; 2473 cone[2] = 16; 2474 cone[3] = 17; 2475 PetscCall(DMPlexSetCone(dm, 0, cone)); 2476 ornt[0] = 0; 2477 ornt[1] = 0; 2478 ornt[2] = 0; 2479 ornt[3] = 0; 2480 PetscCall(DMPlexSetConeOrientation(dm, 0, ornt)); 2481 /* Cell 1 */ 2482 cone[0] = 18; 2483 cone[1] = 19; 2484 cone[2] = 14; 2485 cone[3] = 20; 2486 PetscCall(DMPlexSetCone(dm, 1, cone)); 2487 ornt[0] = 0; 2488 ornt[1] = 0; 2489 ornt[2] = -1; 2490 ornt[3] = 0; 2491 PetscCall(DMPlexSetConeOrientation(dm, 1, ornt)); 2492 /* Cell 2 */ 2493 cone[0] = 21; 2494 cone[1] = 22; 2495 cone[2] = 18; 2496 cone[3] = 23; 2497 PetscCall(DMPlexSetCone(dm, 2, cone)); 2498 ornt[0] = 0; 2499 ornt[1] = 0; 2500 ornt[2] = -1; 2501 ornt[3] = 0; 2502 PetscCall(DMPlexSetConeOrientation(dm, 2, ornt)); 2503 /* Cell 3 */ 2504 cone[0] = 19; 2505 cone[1] = 22; 2506 cone[2] = 24; 2507 cone[3] = 15; 2508 PetscCall(DMPlexSetCone(dm, 3, cone)); 2509 ornt[0] = -1; 2510 ornt[1] = -1; 2511 ornt[2] = 0; 2512 ornt[3] = -1; 2513 PetscCall(DMPlexSetConeOrientation(dm, 3, ornt)); 2514 /* Cell 4 */ 2515 cone[0] = 16; 2516 cone[1] = 24; 2517 cone[2] = 21; 2518 cone[3] = 25; 2519 PetscCall(DMPlexSetCone(dm, 4, cone)); 2520 ornt[0] = -1; 2521 ornt[1] = -1; 2522 ornt[2] = -1; 2523 ornt[3] = 0; 2524 PetscCall(DMPlexSetConeOrientation(dm, 4, ornt)); 2525 /* Cell 5 */ 2526 cone[0] = 20; 2527 cone[1] = 17; 2528 cone[2] = 25; 2529 cone[3] = 23; 2530 PetscCall(DMPlexSetCone(dm, 5, cone)); 2531 ornt[0] = -1; 2532 ornt[1] = -1; 2533 ornt[2] = -1; 2534 ornt[3] = -1; 2535 PetscCall(DMPlexSetConeOrientation(dm, 5, ornt)); 2536 /* Edges */ 2537 cone[0] = 6; 2538 cone[1] = 7; 2539 PetscCall(DMPlexSetCone(dm, 14, cone)); 2540 cone[0] = 7; 2541 cone[1] = 8; 2542 PetscCall(DMPlexSetCone(dm, 15, cone)); 2543 cone[0] = 8; 2544 cone[1] = 9; 2545 PetscCall(DMPlexSetCone(dm, 16, cone)); 2546 cone[0] = 9; 2547 cone[1] = 6; 2548 PetscCall(DMPlexSetCone(dm, 17, cone)); 2549 cone[0] = 10; 2550 cone[1] = 11; 2551 PetscCall(DMPlexSetCone(dm, 18, cone)); 2552 cone[0] = 11; 2553 cone[1] = 7; 2554 PetscCall(DMPlexSetCone(dm, 19, cone)); 2555 cone[0] = 6; 2556 cone[1] = 10; 2557 PetscCall(DMPlexSetCone(dm, 20, cone)); 2558 cone[0] = 12; 2559 cone[1] = 13; 2560 PetscCall(DMPlexSetCone(dm, 21, cone)); 2561 cone[0] = 13; 2562 cone[1] = 11; 2563 PetscCall(DMPlexSetCone(dm, 22, cone)); 2564 cone[0] = 10; 2565 cone[1] = 12; 2566 PetscCall(DMPlexSetCone(dm, 23, cone)); 2567 cone[0] = 13; 2568 cone[1] = 8; 2569 PetscCall(DMPlexSetCone(dm, 24, cone)); 2570 cone[0] = 12; 2571 cone[1] = 9; 2572 PetscCall(DMPlexSetCone(dm, 25, cone)); 2573 } 2574 PetscCall(DMPlexSymmetrize(dm)); 2575 PetscCall(DMPlexStratify(dm)); 2576 /* Build coordinates */ 2577 PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn)); 2578 if (rank == 0) { 2579 coordsIn[0 * embedDim + 0] = -R; 2580 coordsIn[0 * embedDim + 1] = R; 2581 coordsIn[0 * embedDim + 2] = -R; 2582 coordsIn[1 * embedDim + 0] = R; 2583 coordsIn[1 * embedDim + 1] = R; 2584 coordsIn[1 * embedDim + 2] = -R; 2585 coordsIn[2 * embedDim + 0] = R; 2586 coordsIn[2 * embedDim + 1] = -R; 2587 coordsIn[2 * embedDim + 2] = -R; 2588 coordsIn[3 * embedDim + 0] = -R; 2589 coordsIn[3 * embedDim + 1] = -R; 2590 coordsIn[3 * embedDim + 2] = -R; 2591 coordsIn[4 * embedDim + 0] = -R; 2592 coordsIn[4 * embedDim + 1] = R; 2593 coordsIn[4 * embedDim + 2] = R; 2594 coordsIn[5 * embedDim + 0] = R; 2595 coordsIn[5 * embedDim + 1] = R; 2596 coordsIn[5 * embedDim + 2] = R; 2597 coordsIn[6 * embedDim + 0] = -R; 2598 coordsIn[6 * embedDim + 1] = -R; 2599 coordsIn[6 * embedDim + 2] = R; 2600 coordsIn[7 * embedDim + 0] = R; 2601 coordsIn[7 * embedDim + 1] = -R; 2602 coordsIn[7 * embedDim + 2] = R; 2603 } 2604 } 2605 break; 2606 case 3: 2607 if (simplex) { 2608 const PetscReal edgeLen = 1.0 / PETSC_PHI; 2609 PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5}; 2610 PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0}; 2611 PetscReal vertexC[4] = {0.5, 0.5 * PETSC_PHI, 0.5 / PETSC_PHI, 0.0}; 2612 const PetscInt degree = 12; 2613 PetscInt s[4] = {1, 1, 1}; 2614 PetscInt evenPerm[12][4] = { 2615 {0, 1, 2, 3}, 2616 {0, 2, 3, 1}, 2617 {0, 3, 1, 2}, 2618 {1, 0, 3, 2}, 2619 {1, 2, 0, 3}, 2620 {1, 3, 2, 0}, 2621 {2, 0, 1, 3}, 2622 {2, 1, 3, 0}, 2623 {2, 3, 0, 1}, 2624 {3, 0, 2, 1}, 2625 {3, 1, 0, 2}, 2626 {3, 2, 1, 0} 2627 }; 2628 PetscInt cone[4]; 2629 PetscInt *graph, p, i, j, k, l; 2630 2631 vertexA[0] *= R; 2632 vertexA[1] *= R; 2633 vertexA[2] *= R; 2634 vertexA[3] *= R; 2635 vertexB[0] *= R; 2636 vertexB[1] *= R; 2637 vertexB[2] *= R; 2638 vertexB[3] *= R; 2639 vertexC[0] *= R; 2640 vertexC[1] *= R; 2641 vertexC[2] *= R; 2642 vertexC[3] *= R; 2643 numCells = rank == 0 ? 600 : 0; 2644 numVerts = rank == 0 ? 120 : 0; 2645 firstVertex = numCells; 2646 /* Use the 600-cell, which for a unit sphere has coordinates which are 2647 2648 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16 2649 (\pm 1, 0, 0, 0) all cyclic permutations 8 2650 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96 2651 2652 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 2653 length is then given by 1/\phi = 0.61803. 2654 2655 http://buzzard.pugetsound.edu/sage-practice/ch03s03.html 2656 http://mathworld.wolfram.com/600-Cell.html 2657 */ 2658 /* Construct vertices */ 2659 PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn)); 2660 i = 0; 2661 if (rank == 0) { 2662 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2663 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2664 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2665 for (s[3] = -1; s[3] < 2; s[3] += 2) { 2666 for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[d] * vertexA[d]; 2667 ++i; 2668 } 2669 } 2670 } 2671 } 2672 for (p = 0; p < embedDim; ++p) { 2673 s[1] = s[2] = s[3] = 1; 2674 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2675 for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[(d + p) % embedDim] * vertexB[(d + p) % embedDim]; 2676 ++i; 2677 } 2678 } 2679 for (p = 0; p < 12; ++p) { 2680 s[3] = 1; 2681 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2682 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2683 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2684 for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[evenPerm[p][d]] * vertexC[evenPerm[p][d]]; 2685 ++i; 2686 } 2687 } 2688 } 2689 } 2690 } 2691 PetscCheck(i == numVerts, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertices %" PetscInt_FMT " != %" PetscInt_FMT, i, numVerts); 2692 /* Construct graph */ 2693 PetscCall(PetscCalloc1(numVerts * numVerts, &graph)); 2694 for (i = 0; i < numVerts; ++i) { 2695 for (j = 0, k = 0; j < numVerts; ++j) { 2696 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i * embedDim], &coordsIn[j * embedDim]) - edgeLen) < PETSC_SMALL) { 2697 graph[i * numVerts + j] = 1; 2698 ++k; 2699 } 2700 } 2701 PetscCheck(k == degree, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertex %" PetscInt_FMT " degree %" PetscInt_FMT " != %" PetscInt_FMT, i, k, degree); 2702 } 2703 /* Build Topology */ 2704 PetscCall(DMPlexSetChart(dm, 0, numCells + numVerts)); 2705 for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, embedDim)); 2706 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 2707 /* Cells */ 2708 if (rank == 0) { 2709 for (i = 0, c = 0; i < numVerts; ++i) { 2710 for (j = 0; j < i; ++j) { 2711 for (k = 0; k < j; ++k) { 2712 for (l = 0; l < k; ++l) { 2713 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]) { 2714 cone[0] = firstVertex + i; 2715 cone[1] = firstVertex + j; 2716 cone[2] = firstVertex + k; 2717 cone[3] = firstVertex + l; 2718 /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */ 2719 { 2720 const PetscInt epsilon[4][4][4][4] = { 2721 {{{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}}}, 2722 2723 {{{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}}}, 2724 2725 {{{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}}}, 2726 2727 {{{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}} } 2728 }; 2729 PetscReal normal[4]; 2730 PetscInt e, f, g; 2731 2732 for (d = 0; d < embedDim; ++d) { 2733 normal[d] = 0.0; 2734 for (e = 0; e < embedDim; ++e) { 2735 for (f = 0; f < embedDim; ++f) { 2736 for (g = 0; g < embedDim; ++g) { 2737 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]); 2738 } 2739 } 2740 } 2741 } 2742 if (DotReal(embedDim, normal, &coordsIn[i * embedDim]) < 0) { 2743 PetscInt tmp = cone[1]; 2744 cone[1] = cone[2]; 2745 cone[2] = tmp; 2746 } 2747 } 2748 PetscCall(DMPlexSetCone(dm, c++, cone)); 2749 } 2750 } 2751 } 2752 } 2753 } 2754 } 2755 PetscCall(DMPlexSymmetrize(dm)); 2756 PetscCall(DMPlexStratify(dm)); 2757 PetscCall(PetscFree(graph)); 2758 } 2759 break; 2760 default: 2761 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported dimension for sphere: %" PetscInt_FMT, dim); 2762 } 2763 /* Create coordinates */ 2764 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 2765 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 2766 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, embedDim)); 2767 PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex + numVerts)); 2768 for (v = firstVertex; v < firstVertex + numVerts; ++v) { 2769 PetscCall(PetscSectionSetDof(coordSection, v, embedDim)); 2770 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, embedDim)); 2771 } 2772 PetscCall(PetscSectionSetUp(coordSection)); 2773 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 2774 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 2775 PetscCall(VecSetBlockSize(coordinates, embedDim)); 2776 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 2777 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 2778 PetscCall(VecSetType(coordinates, VECSTANDARD)); 2779 PetscCall(VecGetArray(coordinates, &coords)); 2780 for (v = 0; v < numVerts; ++v) 2781 for (d = 0; d < embedDim; ++d) coords[v * embedDim + d] = coordsIn[v * embedDim + d]; 2782 PetscCall(VecRestoreArray(coordinates, &coords)); 2783 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 2784 PetscCall(VecDestroy(&coordinates)); 2785 PetscCall(PetscFree(coordsIn)); 2786 { 2787 DM cdm; 2788 PetscDS cds; 2789 PetscScalar c = R; 2790 2791 PetscCall(DMPlexCreateCoordinateSpace(dm, 1, snapToSphere)); 2792 PetscCall(DMGetCoordinateDM(dm, &cdm)); 2793 PetscCall(DMGetDS(cdm, &cds)); 2794 PetscCall(PetscDSSetConstants(cds, 1, &c)); 2795 } 2796 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 2797 /* Wait for coordinate creation before doing in-place modification */ 2798 if (simplex) PetscCall(DMPlexInterpolateInPlace_Internal(dm)); 2799 PetscFunctionReturn(PETSC_SUCCESS); 2800 } 2801 2802 typedef void (*TPSEvaluateFunc)(const PetscReal[], PetscReal *, PetscReal[], PetscReal (*)[3]); 2803 2804 /* 2805 The Schwarz P implicit surface is 2806 2807 f(x) = cos(x0) + cos(x1) + cos(x2) = 0 2808 */ 2809 static void TPSEvaluate_SchwarzP(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3]) 2810 { 2811 PetscReal c[3] = {PetscCosReal(y[0] * PETSC_PI), PetscCosReal(y[1] * PETSC_PI), PetscCosReal(y[2] * PETSC_PI)}; 2812 PetscReal g[3] = {-PetscSinReal(y[0] * PETSC_PI), -PetscSinReal(y[1] * PETSC_PI), -PetscSinReal(y[2] * PETSC_PI)}; 2813 f[0] = c[0] + c[1] + c[2]; 2814 for (PetscInt i = 0; i < 3; i++) { 2815 grad[i] = PETSC_PI * g[i]; 2816 for (PetscInt j = 0; j < 3; j++) hess[i][j] = (i == j) ? -PetscSqr(PETSC_PI) * c[i] : 0.; 2817 } 2818 } 2819 2820 // u[] is a tentative normal on input. Replace with the implicit function gradient in the same direction 2821 static PetscErrorCode TPSExtrudeNormalFunc_SchwarzP(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt r, PetscScalar u[], void *ctx) 2822 { 2823 for (PetscInt i = 0; i < 3; i++) u[i] = -PETSC_PI * PetscSinReal(x[i] * PETSC_PI); 2824 return PETSC_SUCCESS; 2825 } 2826 2827 /* 2828 The Gyroid implicit surface is 2829 2830 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) 2831 2832 */ 2833 static void TPSEvaluate_Gyroid(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3]) 2834 { 2835 PetscReal s[3] = {PetscSinReal(PETSC_PI * y[0]), PetscSinReal(PETSC_PI * (y[1] + .5)), PetscSinReal(PETSC_PI * (y[2] + .25))}; 2836 PetscReal c[3] = {PetscCosReal(PETSC_PI * y[0]), PetscCosReal(PETSC_PI * (y[1] + .5)), PetscCosReal(PETSC_PI * (y[2] + .25))}; 2837 f[0] = s[0] * c[1] + s[1] * c[2] + s[2] * c[0]; 2838 grad[0] = PETSC_PI * (c[0] * c[1] - s[2] * s[0]); 2839 grad[1] = PETSC_PI * (c[1] * c[2] - s[0] * s[1]); 2840 grad[2] = PETSC_PI * (c[2] * c[0] - s[1] * s[2]); 2841 hess[0][0] = -PetscSqr(PETSC_PI) * (s[0] * c[1] + s[2] * c[0]); 2842 hess[0][1] = -PetscSqr(PETSC_PI) * (c[0] * s[1]); 2843 hess[0][2] = -PetscSqr(PETSC_PI) * (c[2] * s[0]); 2844 hess[1][0] = -PetscSqr(PETSC_PI) * (s[1] * c[2] + s[0] * c[1]); 2845 hess[1][1] = -PetscSqr(PETSC_PI) * (c[1] * s[2]); 2846 hess[2][2] = -PetscSqr(PETSC_PI) * (c[0] * s[1]); 2847 hess[2][0] = -PetscSqr(PETSC_PI) * (s[2] * c[0] + s[1] * c[2]); 2848 hess[2][1] = -PetscSqr(PETSC_PI) * (c[2] * s[0]); 2849 hess[2][2] = -PetscSqr(PETSC_PI) * (c[1] * s[2]); 2850 } 2851 2852 // u[] is a tentative normal on input. Replace with the implicit function gradient in the same direction 2853 static PetscErrorCode TPSExtrudeNormalFunc_Gyroid(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt r, PetscScalar u[], void *ctx) 2854 { 2855 PetscReal s[3] = {PetscSinReal(PETSC_PI * x[0]), PetscSinReal(PETSC_PI * (x[1] + .5)), PetscSinReal(PETSC_PI * (x[2] + .25))}; 2856 PetscReal c[3] = {PetscCosReal(PETSC_PI * x[0]), PetscCosReal(PETSC_PI * (x[1] + .5)), PetscCosReal(PETSC_PI * (x[2] + .25))}; 2857 u[0] = PETSC_PI * (c[0] * c[1] - s[2] * s[0]); 2858 u[1] = PETSC_PI * (c[1] * c[2] - s[0] * s[1]); 2859 u[2] = PETSC_PI * (c[2] * c[0] - s[1] * s[2]); 2860 return PETSC_SUCCESS; 2861 } 2862 2863 /* 2864 We wish to solve 2865 2866 min_y || y - x ||^2 subject to f(y) = 0 2867 2868 Let g(y) = grad(f). The minimization problem is equivalent to asking to satisfy 2869 f(y) = 0 and (y-x) is parallel to g(y). We do this by using Householder QR to obtain a basis for the 2870 tangent space and ask for both components in the tangent space to be zero. 2871 2872 Take g to be a column vector and compute the "full QR" factorization Q R = g, 2873 where Q = I - 2 n n^T is a symmetric orthogonal matrix. 2874 The first column of Q is parallel to g so the remaining two columns span the null space. 2875 Let Qn = Q[:,1:] be those remaining columns. Then Qn Qn^T is an orthogonal projector into the tangent space. 2876 Since Q is symmetric, this is equivalent to multiplying by Q and taking the last two entries. 2877 In total, we have a system of 3 equations in 3 unknowns: 2878 2879 f(y) = 0 1 equation 2880 Qn^T (y - x) = 0 2 equations 2881 2882 Here, we compute the residual and Jacobian of this system. 2883 */ 2884 static void TPSNearestPointResJac(TPSEvaluateFunc feval, const PetscScalar x[], const PetscScalar y[], PetscScalar res[], PetscScalar J[]) 2885 { 2886 PetscReal yreal[3] = {PetscRealPart(y[0]), PetscRealPart(y[1]), PetscRealPart(y[2])}; 2887 PetscReal d[3] = {PetscRealPart(y[0] - x[0]), PetscRealPart(y[1] - x[1]), PetscRealPart(y[2] - x[2])}; 2888 PetscReal f, grad[3], n[3], norm, norm_y[3], nd, nd_y[3], sign; 2889 PetscReal n_y[3][3] = { 2890 {0, 0, 0}, 2891 {0, 0, 0}, 2892 {0, 0, 0} 2893 }; 2894 2895 feval(yreal, &f, grad, n_y); 2896 2897 for (PetscInt i = 0; i < 3; i++) n[i] = grad[i]; 2898 norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2])); 2899 for (PetscInt i = 0; i < 3; i++) norm_y[i] = 1. / norm * n[i] * n_y[i][i]; 2900 2901 // Define the Householder reflector 2902 sign = n[0] >= 0 ? 1. : -1.; 2903 n[0] += norm * sign; 2904 for (PetscInt i = 0; i < 3; i++) n_y[0][i] += norm_y[i] * sign; 2905 2906 norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2])); 2907 norm_y[0] = 1. / norm * (n[0] * n_y[0][0]); 2908 norm_y[1] = 1. / norm * (n[0] * n_y[0][1] + n[1] * n_y[1][1]); 2909 norm_y[2] = 1. / norm * (n[0] * n_y[0][2] + n[2] * n_y[2][2]); 2910 2911 for (PetscInt i = 0; i < 3; i++) { 2912 n[i] /= norm; 2913 for (PetscInt j = 0; j < 3; j++) { 2914 // note that n[i] is n_old[i]/norm when executing the code below 2915 n_y[i][j] = n_y[i][j] / norm - n[i] / norm * norm_y[j]; 2916 } 2917 } 2918 2919 nd = n[0] * d[0] + n[1] * d[1] + n[2] * d[2]; 2920 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]; 2921 2922 res[0] = f; 2923 res[1] = d[1] - 2 * n[1] * nd; 2924 res[2] = d[2] - 2 * n[2] * nd; 2925 // J[j][i] is J_{ij} (column major) 2926 for (PetscInt j = 0; j < 3; j++) { 2927 J[0 + j * 3] = grad[j]; 2928 J[1 + j * 3] = (j == 1) * 1. - 2 * (n_y[1][j] * nd + n[1] * nd_y[j]); 2929 J[2 + j * 3] = (j == 2) * 1. - 2 * (n_y[2][j] * nd + n[2] * nd_y[j]); 2930 } 2931 } 2932 2933 /* 2934 Project x to the nearest point on the implicit surface using Newton's method. 2935 */ 2936 static PetscErrorCode TPSNearestPoint(TPSEvaluateFunc feval, PetscScalar x[]) 2937 { 2938 PetscScalar y[3] = {x[0], x[1], x[2]}; // Initial guess 2939 2940 PetscFunctionBegin; 2941 for (PetscInt iter = 0; iter < 10; iter++) { 2942 PetscScalar res[3], J[9]; 2943 PetscReal resnorm; 2944 TPSNearestPointResJac(feval, x, y, res, J); 2945 resnorm = PetscSqrtReal(PetscSqr(PetscRealPart(res[0])) + PetscSqr(PetscRealPart(res[1])) + PetscSqr(PetscRealPart(res[2]))); 2946 if (0) { // Turn on this monitor if you need to confirm quadratic convergence 2947 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]))); 2948 } 2949 if (resnorm < PETSC_SMALL) break; 2950 2951 // Take the Newton step 2952 PetscCall(PetscKernel_A_gets_inverse_A_3(J, 0., PETSC_FALSE, NULL)); 2953 PetscKernel_v_gets_v_minus_A_times_w_3(y, J, res); 2954 } 2955 for (PetscInt i = 0; i < 3; i++) x[i] = y[i]; 2956 PetscFunctionReturn(PETSC_SUCCESS); 2957 } 2958 2959 const char *const DMPlexTPSTypes[] = {"SCHWARZ_P", "GYROID", "DMPlexTPSType", "DMPLEX_TPS_", NULL}; 2960 2961 static PetscErrorCode DMPlexCreateTPSMesh_Internal(DM dm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscBool tps_distribute, PetscInt refinements, PetscInt layers, PetscReal thickness) 2962 { 2963 PetscMPIInt rank; 2964 PetscInt topoDim = 2, spaceDim = 3, numFaces = 0, numVertices = 0, numEdges = 0; 2965 PetscInt(*edges)[2] = NULL, *edgeSets = NULL; 2966 PetscInt *cells_flat = NULL; 2967 PetscReal *vtxCoords = NULL; 2968 TPSEvaluateFunc evalFunc = NULL; 2969 PetscSimplePointFunc normalFunc = NULL; 2970 DMLabel label; 2971 2972 PetscFunctionBegin; 2973 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 2974 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 2975 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); 2976 switch (tpstype) { 2977 case DMPLEX_TPS_SCHWARZ_P: 2978 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"); 2979 if (rank == 0) { 2980 PetscInt(*cells)[6][4][4] = NULL; // [junction, junction-face, cell, conn] 2981 PetscInt Njunctions = 0, Ncuts = 0, Npipes[3], vcount; 2982 PetscReal L = 1; 2983 2984 Npipes[0] = (extent[0] + 1) * extent[1] * extent[2]; 2985 Npipes[1] = extent[0] * (extent[1] + 1) * extent[2]; 2986 Npipes[2] = extent[0] * extent[1] * (extent[2] + 1); 2987 Njunctions = extent[0] * extent[1] * extent[2]; 2988 Ncuts = 2 * (extent[0] * extent[1] + extent[1] * extent[2] + extent[2] * extent[0]); 2989 numVertices = 4 * (Npipes[0] + Npipes[1] + Npipes[2]) + 8 * Njunctions; 2990 PetscCall(PetscMalloc1(3 * numVertices, &vtxCoords)); 2991 PetscCall(PetscMalloc1(Njunctions, &cells)); 2992 PetscCall(PetscMalloc1(Ncuts * 4, &edges)); 2993 PetscCall(PetscMalloc1(Ncuts * 4, &edgeSets)); 2994 // x-normal pipes 2995 vcount = 0; 2996 for (PetscInt i = 0; i < extent[0] + 1; i++) { 2997 for (PetscInt j = 0; j < extent[1]; j++) { 2998 for (PetscInt k = 0; k < extent[2]; k++) { 2999 for (PetscInt l = 0; l < 4; l++) { 3000 vtxCoords[vcount++] = (2 * i - 1) * L; 3001 vtxCoords[vcount++] = 2 * j * L + PetscCosReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3002 vtxCoords[vcount++] = 2 * k * L + PetscSinReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3003 } 3004 } 3005 } 3006 } 3007 // y-normal pipes 3008 for (PetscInt i = 0; i < extent[0]; i++) { 3009 for (PetscInt j = 0; j < extent[1] + 1; j++) { 3010 for (PetscInt k = 0; k < extent[2]; k++) { 3011 for (PetscInt l = 0; l < 4; l++) { 3012 vtxCoords[vcount++] = 2 * i * L + PetscSinReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3013 vtxCoords[vcount++] = (2 * j - 1) * L; 3014 vtxCoords[vcount++] = 2 * k * L + PetscCosReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3015 } 3016 } 3017 } 3018 } 3019 // z-normal pipes 3020 for (PetscInt i = 0; i < extent[0]; i++) { 3021 for (PetscInt j = 0; j < extent[1]; j++) { 3022 for (PetscInt k = 0; k < extent[2] + 1; k++) { 3023 for (PetscInt l = 0; l < 4; l++) { 3024 vtxCoords[vcount++] = 2 * i * L + PetscCosReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3025 vtxCoords[vcount++] = 2 * j * L + PetscSinReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3026 vtxCoords[vcount++] = (2 * k - 1) * L; 3027 } 3028 } 3029 } 3030 } 3031 // junctions 3032 for (PetscInt i = 0; i < extent[0]; i++) { 3033 for (PetscInt j = 0; j < extent[1]; j++) { 3034 for (PetscInt k = 0; k < extent[2]; k++) { 3035 const PetscInt J = (i * extent[1] + j) * extent[2] + k, Jvoff = (Npipes[0] + Npipes[1] + Npipes[2]) * 4 + J * 8; 3036 PetscCheck(vcount / 3 == Jvoff, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unexpected vertex count"); 3037 for (PetscInt ii = 0; ii < 2; ii++) { 3038 for (PetscInt jj = 0; jj < 2; jj++) { 3039 for (PetscInt kk = 0; kk < 2; kk++) { 3040 double Ls = (1 - sqrt(2) / 4) * L; 3041 vtxCoords[vcount++] = 2 * i * L + (2 * ii - 1) * Ls; 3042 vtxCoords[vcount++] = 2 * j * L + (2 * jj - 1) * Ls; 3043 vtxCoords[vcount++] = 2 * k * L + (2 * kk - 1) * Ls; 3044 } 3045 } 3046 } 3047 const PetscInt jfaces[3][2][4] = { 3048 {{3, 1, 0, 2}, {7, 5, 4, 6}}, // x-aligned 3049 {{5, 4, 0, 1}, {7, 6, 2, 3}}, // y-aligned 3050 {{6, 2, 0, 4}, {7, 3, 1, 5}} // z-aligned 3051 }; 3052 const PetscInt pipe_lo[3] = {// vertex numbers of pipes 3053 ((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}; 3054 const PetscInt pipe_hi[3] = {// vertex numbers of pipes 3055 (((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}; 3056 for (PetscInt dir = 0; dir < 3; dir++) { // x,y,z 3057 const PetscInt ijk[3] = {i, j, k}; 3058 for (PetscInt l = 0; l < 4; l++) { // rotations 3059 cells[J][dir * 2 + 0][l][0] = pipe_lo[dir] + l; 3060 cells[J][dir * 2 + 0][l][1] = Jvoff + jfaces[dir][0][l]; 3061 cells[J][dir * 2 + 0][l][2] = Jvoff + jfaces[dir][0][(l - 1 + 4) % 4]; 3062 cells[J][dir * 2 + 0][l][3] = pipe_lo[dir] + (l - 1 + 4) % 4; 3063 cells[J][dir * 2 + 1][l][0] = Jvoff + jfaces[dir][1][l]; 3064 cells[J][dir * 2 + 1][l][1] = pipe_hi[dir] + l; 3065 cells[J][dir * 2 + 1][l][2] = pipe_hi[dir] + (l - 1 + 4) % 4; 3066 cells[J][dir * 2 + 1][l][3] = Jvoff + jfaces[dir][1][(l - 1 + 4) % 4]; 3067 if (ijk[dir] == 0) { 3068 edges[numEdges][0] = pipe_lo[dir] + l; 3069 edges[numEdges][1] = pipe_lo[dir] + (l + 1) % 4; 3070 edgeSets[numEdges] = dir * 2 + 1; 3071 numEdges++; 3072 } 3073 if (ijk[dir] + 1 == extent[dir]) { 3074 edges[numEdges][0] = pipe_hi[dir] + l; 3075 edges[numEdges][1] = pipe_hi[dir] + (l + 1) % 4; 3076 edgeSets[numEdges] = dir * 2 + 2; 3077 numEdges++; 3078 } 3079 } 3080 } 3081 } 3082 } 3083 } 3084 PetscCheck(numEdges == Ncuts * 4, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Edge count %" PetscInt_FMT " incompatible with number of cuts %" PetscInt_FMT, numEdges, Ncuts); 3085 numFaces = 24 * Njunctions; 3086 cells_flat = cells[0][0][0]; 3087 } 3088 evalFunc = TPSEvaluate_SchwarzP; 3089 normalFunc = TPSExtrudeNormalFunc_SchwarzP; 3090 break; 3091 case DMPLEX_TPS_GYROID: 3092 if (rank == 0) { 3093 // This is a coarse mesh approximation of the gyroid shifted to being the zero of the level set 3094 // 3095 // 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) 3096 // 3097 // on the cell [0,2]^3. 3098 // 3099 // Think about dividing that cell into four columns, and focus on the column [0,1]x[0,1]x[0,2]. 3100 // If you looked at the gyroid in that column at different slices of z you would see that it kind of spins 3101 // like a boomerang: 3102 // 3103 // z = 0 z = 1/4 z = 1/2 z = 3/4 // 3104 // ----- ------- ------- ------- // 3105 // // 3106 // + + + + + + + \ + // 3107 // \ / \ // 3108 // \ `-_ _-' / } // 3109 // *-_ `-' _-' / // 3110 // + `-+ + + +-' + + / + // 3111 // // 3112 // // 3113 // z = 1 z = 5/4 z = 3/2 z = 7/4 // 3114 // ----- ------- ------- ------- // 3115 // // 3116 // +-_ + + + + _-+ + / + // 3117 // `-_ _-_ _-` / // 3118 // \ _-' `-_ / { // 3119 // \ / \ // 3120 // + + + + + + + \ + // 3121 // 3122 // 3123 // This course mesh approximates each of these slices by two line segments, 3124 // and then connects the segments in consecutive layers with quadrilateral faces. 3125 // All of the end points of the segments are multiples of 1/4 except for the 3126 // point * in the picture for z = 0 above and the similar points in other layers. 3127 // That point is at (gamma, gamma, 0), where gamma is calculated below. 3128 // 3129 // The column [1,2]x[1,2]x[0,2] looks the same as this column; 3130 // The columns [1,2]x[0,1]x[0,2] and [0,1]x[1,2]x[0,2] are mirror images. 3131 // 3132 // As for how this method turned into the names given to the vertices: 3133 // that was not systematic, it was just the way it worked out in my handwritten notes. 3134 3135 PetscInt facesPerBlock = 64; 3136 PetscInt vertsPerBlock = 56; 3137 PetscInt extentPlus[3]; 3138 PetscInt numBlocks, numBlocksPlus; 3139 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; 3140 const PetscInt pattern[64][4] = { 3141 /* face to vertex within the coarse discretization of a single gyroid block */ 3142 /* layer 0 */ 3143 {A, C, K, G }, 3144 {C, B, II, K }, 3145 {D, A, H, L }, 3146 {B + 56 * 1, D, L, J }, 3147 {E, B + 56 * 1, J, N }, 3148 {A + 56 * 2, E, N, H + 56 * 2 }, 3149 {F, A + 56 * 2, G + 56 * 2, M }, 3150 {B, F, M, II }, 3151 /* layer 1 */ 3152 {G, K, Q, O }, 3153 {K, II, P, Q }, 3154 {L, H, O + 56 * 1, R }, 3155 {J, L, R, P }, 3156 {N, J, P, S }, 3157 {H + 56 * 2, N, S, O + 56 * 3 }, 3158 {M, G + 56 * 2, O + 56 * 2, T }, 3159 {II, M, T, P }, 3160 /* layer 2 */ 3161 {O, Q, Y, U }, 3162 {Q, P, W, Y }, 3163 {R, O + 56 * 1, U + 56 * 1, Ap }, 3164 {P, R, Ap, W }, 3165 {S, P, X, Bp }, 3166 {O + 56 * 3, S, Bp, V + 56 * 1 }, 3167 {T, O + 56 * 2, V, Z }, 3168 {P, T, Z, X }, 3169 /* layer 3 */ 3170 {U, Y, Ep, Dp }, 3171 {Y, W, Cp, Ep }, 3172 {Ap, U + 56 * 1, Dp + 56 * 1, Gp }, 3173 {W, Ap, Gp, Cp }, 3174 {Bp, X, Cp + 56 * 2, Fp }, 3175 {V + 56 * 1, Bp, Fp, Dp + 56 * 1}, 3176 {Z, V, Dp, Hp }, 3177 {X, Z, Hp, Cp + 56 * 2}, 3178 /* layer 4 */ 3179 {Dp, Ep, Mp, Kp }, 3180 {Ep, Cp, Ip, Mp }, 3181 {Gp, Dp + 56 * 1, Lp, Np }, 3182 {Cp, Gp, Np, Jp }, 3183 {Fp, Cp + 56 * 2, Jp + 56 * 2, Pp }, 3184 {Dp + 56 * 1, Fp, Pp, Lp }, 3185 {Hp, Dp, Kp, Op }, 3186 {Cp + 56 * 2, Hp, Op, Ip + 56 * 2}, 3187 /* layer 5 */ 3188 {Kp, Mp, Sp, Rp }, 3189 {Mp, Ip, Qp, Sp }, 3190 {Np, Lp, Rp, Tp }, 3191 {Jp, Np, Tp, Qp + 56 * 1}, 3192 {Pp, Jp + 56 * 2, Qp + 56 * 3, Up }, 3193 {Lp, Pp, Up, Rp }, 3194 {Op, Kp, Rp, Vp }, 3195 {Ip + 56 * 2, Op, Vp, Qp + 56 * 2}, 3196 /* layer 6 */ 3197 {Rp, Sp, Aq, Yp }, 3198 {Sp, Qp, Wp, Aq }, 3199 {Tp, Rp, Yp, Cq }, 3200 {Qp + 56 * 1, Tp, Cq, Wp + 56 * 1}, 3201 {Up, Qp + 56 * 3, Xp + 56 * 1, Dq }, 3202 {Rp, Up, Dq, Zp }, 3203 {Vp, Rp, Zp, Bq }, 3204 {Qp + 56 * 2, Vp, Bq, Xp }, 3205 /* layer 7 (the top is the periodic image of the bottom of layer 0) */ 3206 {Yp, Aq, C + 56 * 4, A + 56 * 4 }, 3207 {Aq, Wp, B + 56 * 4, C + 56 * 4 }, 3208 {Cq, Yp, A + 56 * 4, D + 56 * 4 }, 3209 {Wp + 56 * 1, Cq, D + 56 * 4, B + 56 * 5 }, 3210 {Dq, Xp + 56 * 1, B + 56 * 5, E + 56 * 4 }, 3211 {Zp, Dq, E + 56 * 4, A + 56 * 6 }, 3212 {Bq, Zp, A + 56 * 6, F + 56 * 4 }, 3213 {Xp, Bq, F + 56 * 4, B + 56 * 4 } 3214 }; 3215 const PetscReal gamma = PetscAcosReal((PetscSqrtReal(3.) - 1.) / PetscSqrtReal(2.)) / PETSC_PI; 3216 const PetscReal patternCoords[56][3] = { 3217 {1., 0., 0. }, /* A */ 3218 {0., 1., 0. }, /* B */ 3219 {gamma, gamma, 0. }, /* C */ 3220 {1 + gamma, 1 - gamma, 0. }, /* D */ 3221 {2 - gamma, 2 - gamma, 0. }, /* E */ 3222 {1 - gamma, 1 + gamma, 0. }, /* F */ 3223 3224 {.5, 0, .25 }, /* G */ 3225 {1.5, 0., .25 }, /* H */ 3226 {.5, 1., .25 }, /* II */ 3227 {1.5, 1., .25 }, /* J */ 3228 {.25, .5, .25 }, /* K */ 3229 {1.25, .5, .25 }, /* L */ 3230 {.75, 1.5, .25 }, /* M */ 3231 {1.75, 1.5, .25 }, /* N */ 3232 3233 {0., 0., .5 }, /* O */ 3234 {1., 1., .5 }, /* P */ 3235 {gamma, 1 - gamma, .5 }, /* Q */ 3236 {1 + gamma, gamma, .5 }, /* R */ 3237 {2 - gamma, 1 + gamma, .5 }, /* S */ 3238 {1 - gamma, 2 - gamma, .5 }, /* T */ 3239 3240 {0., .5, .75 }, /* U */ 3241 {0., 1.5, .75 }, /* V */ 3242 {1., .5, .75 }, /* W */ 3243 {1., 1.5, .75 }, /* X */ 3244 {.5, .75, .75 }, /* Y */ 3245 {.5, 1.75, .75 }, /* Z */ 3246 {1.5, .25, .75 }, /* Ap */ 3247 {1.5, 1.25, .75 }, /* Bp */ 3248 3249 {1., 0., 1. }, /* Cp */ 3250 {0., 1., 1. }, /* Dp */ 3251 {1 - gamma, 1 - gamma, 1. }, /* Ep */ 3252 {1 + gamma, 1 + gamma, 1. }, /* Fp */ 3253 {2 - gamma, gamma, 1. }, /* Gp */ 3254 {gamma, 2 - gamma, 1. }, /* Hp */ 3255 3256 {.5, 0., 1.25}, /* Ip */ 3257 {1.5, 0., 1.25}, /* Jp */ 3258 {.5, 1., 1.25}, /* Kp */ 3259 {1.5, 1., 1.25}, /* Lp */ 3260 {.75, .5, 1.25}, /* Mp */ 3261 {1.75, .5, 1.25}, /* Np */ 3262 {.25, 1.5, 1.25}, /* Op */ 3263 {1.25, 1.5, 1.25}, /* Pp */ 3264 3265 {0., 0., 1.5 }, /* Qp */ 3266 {1., 1., 1.5 }, /* Rp */ 3267 {1 - gamma, gamma, 1.5 }, /* Sp */ 3268 {2 - gamma, 1 - gamma, 1.5 }, /* Tp */ 3269 {1 + gamma, 2 - gamma, 1.5 }, /* Up */ 3270 {gamma, 1 + gamma, 1.5 }, /* Vp */ 3271 3272 {0., .5, 1.75}, /* Wp */ 3273 {0., 1.5, 1.75}, /* Xp */ 3274 {1., .5, 1.75}, /* Yp */ 3275 {1., 1.5, 1.75}, /* Zp */ 3276 {.5, .25, 1.75}, /* Aq */ 3277 {.5, 1.25, 1.75}, /* Bq */ 3278 {1.5, .75, 1.75}, /* Cq */ 3279 {1.5, 1.75, 1.75}, /* Dq */ 3280 }; 3281 PetscInt(*cells)[64][4] = NULL; 3282 PetscBool *seen; 3283 PetscInt *vertToTrueVert; 3284 PetscInt count; 3285 3286 for (PetscInt i = 0; i < 3; i++) extentPlus[i] = extent[i] + 1; 3287 numBlocks = 1; 3288 for (PetscInt i = 0; i < 3; i++) numBlocks *= extent[i]; 3289 numBlocksPlus = 1; 3290 for (PetscInt i = 0; i < 3; i++) numBlocksPlus *= extentPlus[i]; 3291 numFaces = numBlocks * facesPerBlock; 3292 PetscCall(PetscMalloc1(numBlocks, &cells)); 3293 PetscCall(PetscCalloc1(numBlocksPlus * vertsPerBlock, &seen)); 3294 for (PetscInt k = 0; k < extent[2]; k++) { 3295 for (PetscInt j = 0; j < extent[1]; j++) { 3296 for (PetscInt i = 0; i < extent[0]; i++) { 3297 for (PetscInt f = 0; f < facesPerBlock; f++) { 3298 for (PetscInt v = 0; v < 4; v++) { 3299 PetscInt vertRaw = pattern[f][v]; 3300 PetscInt blockidx = vertRaw / 56; 3301 PetscInt patternvert = vertRaw % 56; 3302 PetscInt xplus = (blockidx & 1); 3303 PetscInt yplus = (blockidx & 2) >> 1; 3304 PetscInt zplus = (blockidx & 4) >> 2; 3305 PetscInt zcoord = (periodic && periodic[2] == DM_BOUNDARY_PERIODIC) ? ((k + zplus) % extent[2]) : (k + zplus); 3306 PetscInt ycoord = (periodic && periodic[1] == DM_BOUNDARY_PERIODIC) ? ((j + yplus) % extent[1]) : (j + yplus); 3307 PetscInt xcoord = (periodic && periodic[0] == DM_BOUNDARY_PERIODIC) ? ((i + xplus) % extent[0]) : (i + xplus); 3308 PetscInt vert = ((zcoord * extentPlus[1] + ycoord) * extentPlus[0] + xcoord) * 56 + patternvert; 3309 3310 cells[(k * extent[1] + j) * extent[0] + i][f][v] = vert; 3311 seen[vert] = PETSC_TRUE; 3312 } 3313 } 3314 } 3315 } 3316 } 3317 for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++) 3318 if (seen[i]) numVertices++; 3319 count = 0; 3320 PetscCall(PetscMalloc1(numBlocksPlus * vertsPerBlock, &vertToTrueVert)); 3321 PetscCall(PetscMalloc1(numVertices * 3, &vtxCoords)); 3322 for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++) vertToTrueVert[i] = -1; 3323 for (PetscInt k = 0; k < extentPlus[2]; k++) { 3324 for (PetscInt j = 0; j < extentPlus[1]; j++) { 3325 for (PetscInt i = 0; i < extentPlus[0]; i++) { 3326 for (PetscInt v = 0; v < vertsPerBlock; v++) { 3327 PetscInt vIdx = ((k * extentPlus[1] + j) * extentPlus[0] + i) * vertsPerBlock + v; 3328 3329 if (seen[vIdx]) { 3330 PetscInt thisVert; 3331 3332 vertToTrueVert[vIdx] = thisVert = count++; 3333 3334 for (PetscInt d = 0; d < 3; d++) vtxCoords[3 * thisVert + d] = patternCoords[v][d]; 3335 vtxCoords[3 * thisVert + 0] += i * 2; 3336 vtxCoords[3 * thisVert + 1] += j * 2; 3337 vtxCoords[3 * thisVert + 2] += k * 2; 3338 } 3339 } 3340 } 3341 } 3342 } 3343 for (PetscInt i = 0; i < numBlocks; i++) { 3344 for (PetscInt f = 0; f < facesPerBlock; f++) { 3345 for (PetscInt v = 0; v < 4; v++) cells[i][f][v] = vertToTrueVert[cells[i][f][v]]; 3346 } 3347 } 3348 PetscCall(PetscFree(vertToTrueVert)); 3349 PetscCall(PetscFree(seen)); 3350 cells_flat = cells[0][0]; 3351 numEdges = 0; 3352 for (PetscInt i = 0; i < numFaces; i++) { 3353 for (PetscInt e = 0; e < 4; e++) { 3354 PetscInt ev[] = {cells_flat[i * 4 + e], cells_flat[i * 4 + ((e + 1) % 4)]}; 3355 const PetscReal *evCoords[] = {&vtxCoords[3 * ev[0]], &vtxCoords[3 * ev[1]]}; 3356 3357 for (PetscInt d = 0; d < 3; d++) { 3358 if (!periodic || periodic[0] != DM_BOUNDARY_PERIODIC) { 3359 if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) numEdges++; 3360 if (evCoords[0][d] == 2. * extent[d] && evCoords[1][d] == 2. * extent[d]) numEdges++; 3361 } 3362 } 3363 } 3364 } 3365 PetscCall(PetscMalloc1(numEdges, &edges)); 3366 PetscCall(PetscMalloc1(numEdges, &edgeSets)); 3367 for (PetscInt edge = 0, i = 0; i < numFaces; i++) { 3368 for (PetscInt e = 0; e < 4; e++) { 3369 PetscInt ev[] = {cells_flat[i * 4 + e], cells_flat[i * 4 + ((e + 1) % 4)]}; 3370 const PetscReal *evCoords[] = {&vtxCoords[3 * ev[0]], &vtxCoords[3 * ev[1]]}; 3371 3372 for (PetscInt d = 0; d < 3; d++) { 3373 if (!periodic || periodic[d] != DM_BOUNDARY_PERIODIC) { 3374 if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) { 3375 edges[edge][0] = ev[0]; 3376 edges[edge][1] = ev[1]; 3377 edgeSets[edge++] = 2 * d; 3378 } 3379 if (evCoords[0][d] == 2. * extent[d] && evCoords[1][d] == 2. * extent[d]) { 3380 edges[edge][0] = ev[0]; 3381 edges[edge][1] = ev[1]; 3382 edgeSets[edge++] = 2 * d + 1; 3383 } 3384 } 3385 } 3386 } 3387 } 3388 } 3389 evalFunc = TPSEvaluate_Gyroid; 3390 normalFunc = TPSExtrudeNormalFunc_Gyroid; 3391 break; 3392 } 3393 3394 PetscCall(DMSetDimension(dm, topoDim)); 3395 if (rank == 0) PetscCall(DMPlexBuildFromCellList(dm, numFaces, numVertices, 4, cells_flat)); 3396 else PetscCall(DMPlexBuildFromCellList(dm, 0, 0, 0, NULL)); 3397 PetscCall(PetscFree(cells_flat)); 3398 { 3399 DM idm; 3400 PetscCall(DMPlexInterpolate(dm, &idm)); 3401 PetscCall(DMPlexReplace_Internal(dm, &idm)); 3402 } 3403 if (rank == 0) PetscCall(DMPlexBuildCoordinatesFromCellList(dm, spaceDim, vtxCoords)); 3404 else PetscCall(DMPlexBuildCoordinatesFromCellList(dm, spaceDim, NULL)); 3405 PetscCall(PetscFree(vtxCoords)); 3406 3407 PetscCall(DMCreateLabel(dm, "Face Sets")); 3408 PetscCall(DMGetLabel(dm, "Face Sets", &label)); 3409 for (PetscInt e = 0; e < numEdges; e++) { 3410 PetscInt njoin; 3411 const PetscInt *join, verts[] = {numFaces + edges[e][0], numFaces + edges[e][1]}; 3412 PetscCall(DMPlexGetJoin(dm, 2, verts, &njoin, &join)); 3413 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]); 3414 PetscCall(DMLabelSetValue(label, join[0], edgeSets[e])); 3415 PetscCall(DMPlexRestoreJoin(dm, 2, verts, &njoin, &join)); 3416 } 3417 PetscCall(PetscFree(edges)); 3418 PetscCall(PetscFree(edgeSets)); 3419 if (tps_distribute) { 3420 DM pdm = NULL; 3421 PetscPartitioner part; 3422 3423 PetscCall(DMPlexGetPartitioner(dm, &part)); 3424 PetscCall(PetscPartitionerSetFromOptions(part)); 3425 PetscCall(DMPlexDistribute(dm, 0, NULL, &pdm)); 3426 if (pdm) PetscCall(DMPlexReplace_Internal(dm, &pdm)); 3427 // Do not auto-distribute again 3428 PetscCall(DMPlexDistributeSetDefault(dm, PETSC_FALSE)); 3429 } 3430 3431 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 3432 for (PetscInt refine = 0; refine < refinements; refine++) { 3433 PetscInt m; 3434 DM dmf; 3435 Vec X; 3436 PetscScalar *x; 3437 PetscCall(DMRefine(dm, MPI_COMM_NULL, &dmf)); 3438 PetscCall(DMPlexReplace_Internal(dm, &dmf)); 3439 3440 PetscCall(DMGetCoordinatesLocal(dm, &X)); 3441 PetscCall(VecGetLocalSize(X, &m)); 3442 PetscCall(VecGetArray(X, &x)); 3443 for (PetscInt i = 0; i < m; i += 3) PetscCall(TPSNearestPoint(evalFunc, &x[i])); 3444 PetscCall(VecRestoreArray(X, &x)); 3445 } 3446 3447 // Face Sets has already been propagated to new vertices during refinement; this propagates to the initial vertices. 3448 PetscCall(DMGetLabel(dm, "Face Sets", &label)); 3449 PetscCall(DMPlexLabelComplete(dm, label)); 3450 3451 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 3452 3453 if (thickness > 0) { 3454 DM edm, cdm, ecdm; 3455 DMPlexTransform tr; 3456 const char *prefix; 3457 PetscOptions options; 3458 // Code from DMPlexExtrude 3459 PetscCall(DMPlexTransformCreate(PetscObjectComm((PetscObject)dm), &tr)); 3460 PetscCall(DMPlexTransformSetDM(tr, dm)); 3461 PetscCall(DMPlexTransformSetType(tr, DMPLEXEXTRUDE)); 3462 PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm, &prefix)); 3463 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)tr, prefix)); 3464 PetscCall(PetscObjectGetOptions((PetscObject)dm, &options)); 3465 PetscCall(PetscObjectSetOptions((PetscObject)tr, options)); 3466 PetscCall(DMPlexTransformExtrudeSetLayers(tr, layers)); 3467 PetscCall(DMPlexTransformExtrudeSetThickness(tr, thickness)); 3468 PetscCall(DMPlexTransformExtrudeSetTensor(tr, PETSC_FALSE)); 3469 PetscCall(DMPlexTransformExtrudeSetSymmetric(tr, PETSC_TRUE)); 3470 PetscCall(DMPlexTransformExtrudeSetNormalFunction(tr, normalFunc)); 3471 PetscCall(DMPlexTransformSetFromOptions(tr)); 3472 PetscCall(PetscObjectSetOptions((PetscObject)tr, NULL)); 3473 PetscCall(DMPlexTransformSetUp(tr)); 3474 PetscCall(PetscObjectViewFromOptions((PetscObject)tr, NULL, "-dm_plex_tps_transform_view")); 3475 PetscCall(DMPlexTransformApply(tr, dm, &edm)); 3476 PetscCall(DMCopyDisc(dm, edm)); 3477 PetscCall(DMGetCoordinateDM(dm, &cdm)); 3478 PetscCall(DMGetCoordinateDM(edm, &ecdm)); 3479 PetscCall(DMCopyDisc(cdm, ecdm)); 3480 PetscCall(DMPlexTransformCreateDiscLabels(tr, edm)); 3481 PetscCall(DMPlexTransformDestroy(&tr)); 3482 if (edm) { 3483 ((DM_Plex *)edm->data)->printFEM = ((DM_Plex *)dm->data)->printFEM; 3484 ((DM_Plex *)edm->data)->printL2 = ((DM_Plex *)dm->data)->printL2; 3485 ((DM_Plex *)edm->data)->printLocate = ((DM_Plex *)dm->data)->printLocate; 3486 } 3487 PetscCall(DMPlexReplace_Internal(dm, &edm)); 3488 } 3489 PetscFunctionReturn(PETSC_SUCCESS); 3490 } 3491 3492 /*@ 3493 DMPlexCreateTPSMesh - Create a distributed, interpolated mesh of a triply-periodic surface 3494 3495 Collective 3496 3497 Input Parameters: 3498 + comm - The communicator for the `DM` object 3499 . tpstype - Type of triply-periodic surface 3500 . extent - Array of length 3 containing number of periods in each direction 3501 . periodic - array of length 3 with periodicity, or `NULL` for non-periodic 3502 . tps_distribute - Distribute 2D manifold mesh prior to refinement and extrusion (more scalable) 3503 . refinements - Number of factor-of-2 refinements of 2D manifold mesh 3504 . layers - Number of cell layers extruded in normal direction 3505 - thickness - Thickness in normal direction 3506 3507 Output Parameter: 3508 . dm - The `DM` object 3509 3510 Level: beginner 3511 3512 Notes: 3513 This meshes the surface of the Schwarz P or Gyroid surfaces. Schwarz P is is the simplest member of the triply-periodic minimal surfaces. 3514 https://en.wikipedia.org/wiki/Schwarz_minimal_surface#Schwarz_P_(%22Primitive%22) and can be cut with "clean" boundaries. 3515 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. 3516 Our implementation creates a very coarse mesh of the surface and refines (by 4-way splitting) as many times as requested. 3517 On each refinement, all vertices are projected to their nearest point on the surface. 3518 This projection could readily be extended to related surfaces. 3519 3520 The face (edge) sets for the Schwarz P surface are numbered 1(-x), 2(+x), 3(-y), 4(+y), 5(-z), 6(+z). 3521 When the mesh is refined, "Face Sets" contain the new vertices (created during refinement). Use `DMPlexLabelComplete()` to propagate to coarse-level vertices. 3522 3523 Developer Note: 3524 The Gyroid mesh does not currently mark boundary sets. 3525 3526 References: 3527 . * - Maskery et al, Insights into the mechanical properties of several triply periodic minimal surface lattice structures made by polymer additive manufacturing, 2017. 3528 https://doi.org/10.1016/j.polymer.2017.11.049 3529 3530 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateSphereMesh()`, `DMSetType()`, `DMCreate()` 3531 @*/ 3532 PetscErrorCode DMPlexCreateTPSMesh(MPI_Comm comm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscBool tps_distribute, PetscInt refinements, PetscInt layers, PetscReal thickness, DM *dm) 3533 { 3534 PetscFunctionBegin; 3535 PetscCall(DMCreate(comm, dm)); 3536 PetscCall(DMSetType(*dm, DMPLEX)); 3537 PetscCall(DMPlexCreateTPSMesh_Internal(*dm, tpstype, extent, periodic, tps_distribute, refinements, layers, thickness)); 3538 PetscFunctionReturn(PETSC_SUCCESS); 3539 } 3540 3541 /*@ 3542 DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d. 3543 3544 Collective 3545 3546 Input Parameters: 3547 + comm - The communicator for the `DM` object 3548 . dim - The dimension 3549 . simplex - Use simplices, or tensor product cells 3550 - R - The radius 3551 3552 Output Parameter: 3553 . dm - The `DM` object 3554 3555 Level: beginner 3556 3557 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateBallMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 3558 @*/ 3559 PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscReal R, DM *dm) 3560 { 3561 PetscFunctionBegin; 3562 PetscValidPointer(dm, 5); 3563 PetscCall(DMCreate(comm, dm)); 3564 PetscCall(DMSetType(*dm, DMPLEX)); 3565 PetscCall(DMPlexCreateSphereMesh_Internal(*dm, dim, simplex, R)); 3566 PetscFunctionReturn(PETSC_SUCCESS); 3567 } 3568 3569 static PetscErrorCode DMPlexCreateBallMesh_Internal(DM dm, PetscInt dim, PetscReal R) 3570 { 3571 DM sdm, vol; 3572 DMLabel bdlabel; 3573 3574 PetscFunctionBegin; 3575 PetscCall(DMCreate(PetscObjectComm((PetscObject)dm), &sdm)); 3576 PetscCall(DMSetType(sdm, DMPLEX)); 3577 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)sdm, "bd_")); 3578 PetscCall(DMPlexCreateSphereMesh_Internal(sdm, dim - 1, PETSC_TRUE, R)); 3579 PetscCall(DMSetFromOptions(sdm)); 3580 PetscCall(DMViewFromOptions(sdm, NULL, "-dm_view")); 3581 PetscCall(DMPlexGenerate(sdm, NULL, PETSC_TRUE, &vol)); 3582 PetscCall(DMDestroy(&sdm)); 3583 PetscCall(DMPlexReplace_Internal(dm, &vol)); 3584 PetscCall(DMCreateLabel(dm, "marker")); 3585 PetscCall(DMGetLabel(dm, "marker", &bdlabel)); 3586 PetscCall(DMPlexMarkBoundaryFaces(dm, PETSC_DETERMINE, bdlabel)); 3587 PetscCall(DMPlexLabelComplete(dm, bdlabel)); 3588 PetscFunctionReturn(PETSC_SUCCESS); 3589 } 3590 3591 /*@ 3592 DMPlexCreateBallMesh - Creates a simplex mesh on the d-dimensional ball, B^d. 3593 3594 Collective 3595 3596 Input Parameters: 3597 + comm - The communicator for the `DM` object 3598 . dim - The dimension 3599 - R - The radius 3600 3601 Output Parameter: 3602 . dm - The `DM` object 3603 3604 Options Database Key: 3605 - bd_dm_refine - This will refine the surface mesh preserving the sphere geometry 3606 3607 Level: beginner 3608 3609 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateSphereMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 3610 @*/ 3611 PetscErrorCode DMPlexCreateBallMesh(MPI_Comm comm, PetscInt dim, PetscReal R, DM *dm) 3612 { 3613 PetscFunctionBegin; 3614 PetscCall(DMCreate(comm, dm)); 3615 PetscCall(DMSetType(*dm, DMPLEX)); 3616 PetscCall(DMPlexCreateBallMesh_Internal(*dm, dim, R)); 3617 PetscFunctionReturn(PETSC_SUCCESS); 3618 } 3619 3620 static PetscErrorCode DMPlexCreateReferenceCell_Internal(DM rdm, DMPolytopeType ct) 3621 { 3622 PetscFunctionBegin; 3623 switch (ct) { 3624 case DM_POLYTOPE_POINT: { 3625 PetscInt numPoints[1] = {1}; 3626 PetscInt coneSize[1] = {0}; 3627 PetscInt cones[1] = {0}; 3628 PetscInt coneOrientations[1] = {0}; 3629 PetscScalar vertexCoords[1] = {0.0}; 3630 3631 PetscCall(DMSetDimension(rdm, 0)); 3632 PetscCall(DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3633 } break; 3634 case DM_POLYTOPE_SEGMENT: { 3635 PetscInt numPoints[2] = {2, 1}; 3636 PetscInt coneSize[3] = {2, 0, 0}; 3637 PetscInt cones[2] = {1, 2}; 3638 PetscInt coneOrientations[2] = {0, 0}; 3639 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 3640 3641 PetscCall(DMSetDimension(rdm, 1)); 3642 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3643 } break; 3644 case DM_POLYTOPE_POINT_PRISM_TENSOR: { 3645 PetscInt numPoints[2] = {2, 1}; 3646 PetscInt coneSize[3] = {2, 0, 0}; 3647 PetscInt cones[2] = {1, 2}; 3648 PetscInt coneOrientations[2] = {0, 0}; 3649 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 3650 3651 PetscCall(DMSetDimension(rdm, 1)); 3652 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3653 } break; 3654 case DM_POLYTOPE_TRIANGLE: { 3655 PetscInt numPoints[2] = {3, 1}; 3656 PetscInt coneSize[4] = {3, 0, 0, 0}; 3657 PetscInt cones[3] = {1, 2, 3}; 3658 PetscInt coneOrientations[3] = {0, 0, 0}; 3659 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 3660 3661 PetscCall(DMSetDimension(rdm, 2)); 3662 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3663 } break; 3664 case DM_POLYTOPE_QUADRILATERAL: { 3665 PetscInt numPoints[2] = {4, 1}; 3666 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3667 PetscInt cones[4] = {1, 2, 3, 4}; 3668 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3669 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 3670 3671 PetscCall(DMSetDimension(rdm, 2)); 3672 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3673 } break; 3674 case DM_POLYTOPE_SEG_PRISM_TENSOR: { 3675 PetscInt numPoints[2] = {4, 1}; 3676 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3677 PetscInt cones[4] = {1, 2, 3, 4}; 3678 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3679 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, 1.0}; 3680 3681 PetscCall(DMSetDimension(rdm, 2)); 3682 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3683 } break; 3684 case DM_POLYTOPE_TETRAHEDRON: { 3685 PetscInt numPoints[2] = {4, 1}; 3686 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3687 PetscInt cones[4] = {1, 2, 3, 4}; 3688 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3689 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}; 3690 3691 PetscCall(DMSetDimension(rdm, 3)); 3692 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3693 } break; 3694 case DM_POLYTOPE_HEXAHEDRON: { 3695 PetscInt numPoints[2] = {8, 1}; 3696 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3697 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 3698 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3699 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}; 3700 3701 PetscCall(DMSetDimension(rdm, 3)); 3702 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3703 } break; 3704 case DM_POLYTOPE_TRI_PRISM: { 3705 PetscInt numPoints[2] = {6, 1}; 3706 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3707 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 3708 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3709 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}; 3710 3711 PetscCall(DMSetDimension(rdm, 3)); 3712 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3713 } break; 3714 case DM_POLYTOPE_TRI_PRISM_TENSOR: { 3715 PetscInt numPoints[2] = {6, 1}; 3716 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3717 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 3718 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3719 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}; 3720 3721 PetscCall(DMSetDimension(rdm, 3)); 3722 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3723 } break; 3724 case DM_POLYTOPE_QUAD_PRISM_TENSOR: { 3725 PetscInt numPoints[2] = {8, 1}; 3726 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3727 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 3728 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3729 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}; 3730 3731 PetscCall(DMSetDimension(rdm, 3)); 3732 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3733 } break; 3734 case DM_POLYTOPE_PYRAMID: { 3735 PetscInt numPoints[2] = {5, 1}; 3736 PetscInt coneSize[6] = {5, 0, 0, 0, 0, 0}; 3737 PetscInt cones[5] = {1, 2, 3, 4, 5}; 3738 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3739 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}; 3740 3741 PetscCall(DMSetDimension(rdm, 3)); 3742 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3743 } break; 3744 default: 3745 SETERRQ(PetscObjectComm((PetscObject)rdm), PETSC_ERR_ARG_WRONG, "Cannot create reference cell for cell type %s", DMPolytopeTypes[ct]); 3746 } 3747 { 3748 PetscInt Nv, v; 3749 3750 /* Must create the celltype label here so that we do not automatically try to compute the types */ 3751 PetscCall(DMCreateLabel(rdm, "celltype")); 3752 PetscCall(DMPlexSetCellType(rdm, 0, ct)); 3753 PetscCall(DMPlexGetChart(rdm, NULL, &Nv)); 3754 for (v = 1; v < Nv; ++v) PetscCall(DMPlexSetCellType(rdm, v, DM_POLYTOPE_POINT)); 3755 } 3756 PetscCall(DMPlexInterpolateInPlace_Internal(rdm)); 3757 PetscCall(PetscObjectSetName((PetscObject)rdm, DMPolytopeTypes[ct])); 3758 PetscFunctionReturn(PETSC_SUCCESS); 3759 } 3760 3761 /*@ 3762 DMPlexCreateReferenceCell - Create a `DMPLEX` with the appropriate FEM reference cell 3763 3764 Collective 3765 3766 Input Parameters: 3767 + comm - The communicator 3768 - ct - The cell type of the reference cell 3769 3770 Output Parameter: 3771 . refdm - The reference cell 3772 3773 Level: intermediate 3774 3775 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateReferenceCell()`, `DMPlexCreateBoxMesh()` 3776 @*/ 3777 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, DMPolytopeType ct, DM *refdm) 3778 { 3779 PetscFunctionBegin; 3780 PetscCall(DMCreate(comm, refdm)); 3781 PetscCall(DMSetType(*refdm, DMPLEX)); 3782 PetscCall(DMPlexCreateReferenceCell_Internal(*refdm, ct)); 3783 PetscFunctionReturn(PETSC_SUCCESS); 3784 } 3785 3786 static PetscErrorCode DMPlexCreateBoundaryLabel_Private(DM dm, const char name[]) 3787 { 3788 DM plex; 3789 DMLabel label; 3790 PetscBool hasLabel; 3791 3792 PetscFunctionBegin; 3793 PetscCall(DMHasLabel(dm, name, &hasLabel)); 3794 if (hasLabel) PetscFunctionReturn(PETSC_SUCCESS); 3795 PetscCall(DMCreateLabel(dm, name)); 3796 PetscCall(DMGetLabel(dm, name, &label)); 3797 PetscCall(DMConvert(dm, DMPLEX, &plex)); 3798 PetscCall(DMPlexMarkBoundaryFaces(plex, 1, label)); 3799 PetscCall(DMPlexLabelComplete(plex, label)); 3800 PetscCall(DMDestroy(&plex)); 3801 PetscFunctionReturn(PETSC_SUCCESS); 3802 } 3803 3804 /* 3805 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. 3806 3807 (x, y) -> (r, theta) = (x[1], (x[0] - lower[0]) * 2\pi/(upper[0] - lower[0])) 3808 */ 3809 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[]) 3810 { 3811 const PetscReal low = PetscRealPart(constants[0]); 3812 const PetscReal upp = PetscRealPart(constants[1]); 3813 const PetscReal r = PetscRealPart(u[1]); 3814 const PetscReal th = 2. * PETSC_PI * (PetscRealPart(u[0]) - low) / (upp - low); 3815 3816 f0[0] = r * PetscCosReal(th); 3817 f0[1] = r * PetscSinReal(th); 3818 } 3819 3820 const char *const DMPlexShapes[] = {"box", "box_surface", "ball", "sphere", "cylinder", "schwarz_p", "gyroid", "doublet", "annulus", "hypercubic", "zbox", "unknown", "DMPlexShape", "DM_SHAPE_", NULL}; 3821 3822 static PetscErrorCode DMPlexCreateFromOptions_Internal(PetscOptionItems *PetscOptionsObject, PetscBool *useCoordSpace, DM dm) 3823 { 3824 DMPlexShape shape = DM_SHAPE_BOX; 3825 DMPolytopeType cell = DM_POLYTOPE_TRIANGLE; 3826 PetscInt dim = 2; 3827 PetscBool simplex = PETSC_TRUE, interpolate = PETSC_TRUE, adjCone = PETSC_FALSE, adjClosure = PETSC_TRUE, refDomain = PETSC_FALSE; 3828 PetscBool flg, flg2, fflg, bdfflg, nameflg; 3829 MPI_Comm comm; 3830 char filename[PETSC_MAX_PATH_LEN] = "<unspecified>"; 3831 char bdFilename[PETSC_MAX_PATH_LEN] = "<unspecified>"; 3832 char plexname[PETSC_MAX_PATH_LEN] = ""; 3833 3834 PetscFunctionBegin; 3835 PetscCall(PetscLogEventBegin(DMPLEX_CreateFromOptions, dm, 0, 0, 0)); 3836 PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); 3837 /* TODO Turn this into a registration interface */ 3838 PetscCall(PetscOptionsString("-dm_plex_filename", "File containing a mesh", "DMPlexCreateFromFile", filename, filename, sizeof(filename), &fflg)); 3839 PetscCall(PetscOptionsString("-dm_plex_boundary_filename", "File containing a mesh boundary", "DMPlexCreateFromFile", bdFilename, bdFilename, sizeof(bdFilename), &bdfflg)); 3840 PetscCall(PetscOptionsString("-dm_plex_name", "Name of the mesh in the file", "DMPlexCreateFromFile", plexname, plexname, sizeof(plexname), &nameflg)); 3841 PetscCall(PetscOptionsEnum("-dm_plex_cell", "Cell shape", "", DMPolytopeTypes, (PetscEnum)cell, (PetscEnum *)&cell, NULL)); 3842 PetscCall(PetscOptionsBool("-dm_plex_reference_cell_domain", "Use a reference cell domain", "", refDomain, &refDomain, NULL)); 3843 PetscCall(PetscOptionsEnum("-dm_plex_shape", "Shape for built-in mesh", "", DMPlexShapes, (PetscEnum)shape, (PetscEnum *)&shape, &flg)); 3844 PetscCall(PetscOptionsBoundedInt("-dm_plex_dim", "Topological dimension of the mesh", "DMGetDimension", dim, &dim, &flg, 0)); 3845 PetscCheck(dim >= 0, comm, PETSC_ERR_ARG_OUTOFRANGE, "Dimension %" PetscInt_FMT " should be in [0, infinity)", dim); 3846 PetscCall(PetscOptionsBool("-dm_plex_simplex", "Mesh cell shape", "", simplex, &simplex, &flg)); 3847 PetscCall(PetscOptionsBool("-dm_plex_interpolate", "Flag to create edges and faces automatically", "", interpolate, &interpolate, &flg)); 3848 PetscCall(PetscOptionsBool("-dm_plex_adj_cone", "Set adjacency direction", "DMSetBasicAdjacency", adjCone, &adjCone, &flg)); 3849 PetscCall(PetscOptionsBool("-dm_plex_adj_closure", "Set adjacency size", "DMSetBasicAdjacency", adjClosure, &adjClosure, &flg2)); 3850 if (flg || flg2) PetscCall(DMSetBasicAdjacency(dm, adjCone, adjClosure)); 3851 3852 switch (cell) { 3853 case DM_POLYTOPE_POINT: 3854 case DM_POLYTOPE_SEGMENT: 3855 case DM_POLYTOPE_POINT_PRISM_TENSOR: 3856 case DM_POLYTOPE_TRIANGLE: 3857 case DM_POLYTOPE_QUADRILATERAL: 3858 case DM_POLYTOPE_TETRAHEDRON: 3859 case DM_POLYTOPE_HEXAHEDRON: 3860 *useCoordSpace = PETSC_TRUE; 3861 break; 3862 default: 3863 *useCoordSpace = PETSC_FALSE; 3864 break; 3865 } 3866 3867 if (fflg) { 3868 DM dmnew; 3869 3870 PetscCall(DMPlexCreateFromFile(PetscObjectComm((PetscObject)dm), filename, plexname, interpolate, &dmnew)); 3871 PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew)); 3872 PetscCall(DMPlexReplace_Internal(dm, &dmnew)); 3873 } else if (refDomain) { 3874 PetscCall(DMPlexCreateReferenceCell_Internal(dm, cell)); 3875 } else if (bdfflg) { 3876 DM bdm, dmnew; 3877 3878 PetscCall(DMPlexCreateFromFile(PetscObjectComm((PetscObject)dm), bdFilename, plexname, interpolate, &bdm)); 3879 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)bdm, "bd_")); 3880 PetscCall(DMSetFromOptions(bdm)); 3881 PetscCall(DMPlexGenerate(bdm, NULL, interpolate, &dmnew)); 3882 PetscCall(DMDestroy(&bdm)); 3883 PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew)); 3884 PetscCall(DMPlexReplace_Internal(dm, &dmnew)); 3885 } else { 3886 PetscCall(PetscObjectSetName((PetscObject)dm, DMPlexShapes[shape])); 3887 switch (shape) { 3888 case DM_SHAPE_BOX: 3889 case DM_SHAPE_ZBOX: 3890 case DM_SHAPE_ANNULUS: { 3891 PetscInt faces[3] = {0, 0, 0}; 3892 PetscReal lower[3] = {0, 0, 0}; 3893 PetscReal upper[3] = {1, 1, 1}; 3894 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 3895 PetscBool isAnnular = shape == DM_SHAPE_ANNULUS ? PETSC_TRUE : PETSC_FALSE; 3896 PetscInt i, n; 3897 3898 n = dim; 3899 for (i = 0; i < dim; ++i) faces[i] = (dim == 1 ? 1 : 4 - dim); 3900 PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg)); 3901 n = 3; 3902 PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg)); 3903 PetscCheck(!flg || !(n != dim), comm, PETSC_ERR_ARG_SIZ, "Lower box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 3904 n = 3; 3905 PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg)); 3906 PetscCheck(!flg || !(n != dim), comm, PETSC_ERR_ARG_SIZ, "Upper box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 3907 n = 3; 3908 PetscCall(PetscOptionsEnumArray("-dm_plex_box_bd", "Boundary type for each dimension", "", DMBoundaryTypes, (PetscEnum *)bdt, &n, &flg)); 3909 PetscCheck(!flg || !(n != dim), comm, PETSC_ERR_ARG_SIZ, "Box boundary types had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 3910 3911 PetscCheck(!isAnnular || dim == 2, comm, PETSC_ERR_ARG_OUTOFRANGE, "Only two dimensional annuli have been implemented"); 3912 if (isAnnular) 3913 for (i = 0; i < dim - 1; ++i) bdt[i] = DM_BOUNDARY_PERIODIC; 3914 3915 switch (cell) { 3916 case DM_POLYTOPE_TRI_PRISM_TENSOR: 3917 PetscCall(DMPlexCreateWedgeBoxMesh_Internal(dm, faces, lower, upper, bdt)); 3918 if (!interpolate) { 3919 DM udm; 3920 3921 PetscCall(DMPlexUninterpolate(dm, &udm)); 3922 PetscCall(DMPlexReplace_Internal(dm, &udm)); 3923 } 3924 break; 3925 default: 3926 PetscCall(DMPlexCreateBoxMesh_Internal(dm, shape, dim, simplex, faces, lower, upper, bdt, interpolate)); 3927 break; 3928 } 3929 if (isAnnular) { 3930 DM cdm; 3931 PetscDS cds; 3932 PetscScalar bounds[2] = {lower[0], upper[0]}; 3933 3934 // Fix coordinates for annular region 3935 PetscCall(DMSetPeriodicity(dm, NULL, NULL, NULL)); 3936 PetscCall(DMSetCellCoordinatesLocal(dm, NULL)); 3937 PetscCall(DMSetCellCoordinates(dm, NULL)); 3938 PetscCall(DMPlexCreateCoordinateSpace(dm, 1, NULL)); 3939 PetscCall(DMGetCoordinateDM(dm, &cdm)); 3940 PetscCall(DMGetDS(cdm, &cds)); 3941 PetscCall(PetscDSSetConstants(cds, 2, bounds)); 3942 PetscCall(DMPlexRemapGeometry(dm, 0.0, boxToAnnulus)); 3943 } 3944 } break; 3945 case DM_SHAPE_BOX_SURFACE: { 3946 PetscInt faces[3] = {0, 0, 0}; 3947 PetscReal lower[3] = {0, 0, 0}; 3948 PetscReal upper[3] = {1, 1, 1}; 3949 PetscInt i, n; 3950 3951 n = dim + 1; 3952 for (i = 0; i < dim + 1; ++i) faces[i] = (dim + 1 == 1 ? 1 : 4 - (dim + 1)); 3953 PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg)); 3954 n = 3; 3955 PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg)); 3956 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); 3957 n = 3; 3958 PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg)); 3959 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); 3960 PetscCall(DMPlexCreateBoxSurfaceMesh_Internal(dm, dim + 1, faces, lower, upper, interpolate)); 3961 } break; 3962 case DM_SHAPE_SPHERE: { 3963 PetscReal R = 1.0; 3964 3965 PetscCall(PetscOptionsReal("-dm_plex_sphere_radius", "Radius of the sphere", "", R, &R, &flg)); 3966 PetscCall(DMPlexCreateSphereMesh_Internal(dm, dim, simplex, R)); 3967 } break; 3968 case DM_SHAPE_BALL: { 3969 PetscReal R = 1.0; 3970 3971 PetscCall(PetscOptionsReal("-dm_plex_ball_radius", "Radius of the ball", "", R, &R, &flg)); 3972 PetscCall(DMPlexCreateBallMesh_Internal(dm, dim, R)); 3973 } break; 3974 case DM_SHAPE_CYLINDER: { 3975 DMBoundaryType bdt = DM_BOUNDARY_NONE; 3976 PetscInt Nw = 6; 3977 3978 PetscCall(PetscOptionsEnum("-dm_plex_cylinder_bd", "Boundary type in the z direction", "", DMBoundaryTypes, (PetscEnum)bdt, (PetscEnum *)&bdt, NULL)); 3979 PetscCall(PetscOptionsInt("-dm_plex_cylinder_num_wedges", "Number of wedges around the cylinder", "", Nw, &Nw, NULL)); 3980 switch (cell) { 3981 case DM_POLYTOPE_TRI_PRISM_TENSOR: 3982 PetscCall(DMPlexCreateWedgeCylinderMesh_Internal(dm, Nw, interpolate)); 3983 break; 3984 default: 3985 PetscCall(DMPlexCreateHexCylinderMesh_Internal(dm, bdt)); 3986 break; 3987 } 3988 } break; 3989 case DM_SHAPE_SCHWARZ_P: // fallthrough 3990 case DM_SHAPE_GYROID: { 3991 PetscInt extent[3] = {1, 1, 1}, refine = 0, layers = 0, three; 3992 PetscReal thickness = 0.; 3993 DMBoundaryType periodic[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 3994 DMPlexTPSType tps_type = shape == DM_SHAPE_SCHWARZ_P ? DMPLEX_TPS_SCHWARZ_P : DMPLEX_TPS_GYROID; 3995 PetscBool tps_distribute; 3996 PetscCall(PetscOptionsIntArray("-dm_plex_tps_extent", "Number of replicas for each of three dimensions", NULL, extent, (three = 3, &three), NULL)); 3997 PetscCall(PetscOptionsInt("-dm_plex_tps_refine", "Number of refinements", NULL, refine, &refine, NULL)); 3998 PetscCall(PetscOptionsEnumArray("-dm_plex_tps_periodic", "Periodicity in each of three dimensions", NULL, DMBoundaryTypes, (PetscEnum *)periodic, (three = 3, &three), NULL)); 3999 PetscCall(PetscOptionsInt("-dm_plex_tps_layers", "Number of layers in volumetric extrusion (or zero to not extrude)", NULL, layers, &layers, NULL)); 4000 PetscCall(PetscOptionsReal("-dm_plex_tps_thickness", "Thickness of volumetric extrusion", NULL, thickness, &thickness, NULL)); 4001 PetscCall(DMPlexDistributeGetDefault(dm, &tps_distribute)); 4002 PetscCall(PetscOptionsBool("-dm_plex_tps_distribute", "Distribute the 2D mesh prior to refinement and extrusion", NULL, tps_distribute, &tps_distribute, NULL)); 4003 PetscCall(DMPlexCreateTPSMesh_Internal(dm, tps_type, extent, periodic, tps_distribute, refine, layers, thickness)); 4004 } break; 4005 case DM_SHAPE_DOUBLET: { 4006 DM dmnew; 4007 PetscReal rl = 0.0; 4008 4009 PetscCall(PetscOptionsReal("-dm_plex_doublet_refinementlimit", "Refinement limit", NULL, rl, &rl, NULL)); 4010 PetscCall(DMPlexCreateDoublet(PetscObjectComm((PetscObject)dm), dim, simplex, interpolate, rl, &dmnew)); 4011 PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew)); 4012 PetscCall(DMPlexReplace_Internal(dm, &dmnew)); 4013 } break; 4014 case DM_SHAPE_HYPERCUBIC: { 4015 PetscInt *edges; 4016 PetscReal *lower, *upper; 4017 DMBoundaryType *bdt; 4018 PetscInt n, d; 4019 4020 *useCoordSpace = PETSC_FALSE; 4021 PetscCall(PetscMalloc4(dim, &edges, dim, &lower, dim, &upper, dim, &bdt)); 4022 for (d = 0; d < dim; ++d) { 4023 edges[d] = 1; 4024 lower[d] = 0.; 4025 upper[d] = 1.; 4026 bdt[d] = DM_BOUNDARY_PERIODIC; 4027 } 4028 n = dim; 4029 PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", edges, &n, &flg)); 4030 n = dim; 4031 PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg)); 4032 PetscCheck(!flg || n == dim, comm, PETSC_ERR_ARG_SIZ, "Lower box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 4033 n = dim; 4034 PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg)); 4035 PetscCheck(!flg || n == dim, comm, PETSC_ERR_ARG_SIZ, "Upper box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 4036 n = dim; 4037 PetscCall(PetscOptionsEnumArray("-dm_plex_box_bd", "Boundary type for each dimension", "", DMBoundaryTypes, (PetscEnum *)bdt, &n, &flg)); 4038 PetscCheck(!flg || n == dim, comm, PETSC_ERR_ARG_SIZ, "Box boundary types had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 4039 PetscCall(DMPlexCreateHypercubicMesh_Internal(dm, dim, lower, upper, edges, bdt)); 4040 PetscCall(PetscFree4(edges, lower, upper, bdt)); 4041 } break; 4042 default: 4043 SETERRQ(comm, PETSC_ERR_SUP, "Domain shape %s is unsupported", DMPlexShapes[shape]); 4044 } 4045 } 4046 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 4047 if (!((PetscObject)dm)->name && nameflg) PetscCall(PetscObjectSetName((PetscObject)dm, plexname)); 4048 PetscCall(PetscLogEventEnd(DMPLEX_CreateFromOptions, dm, 0, 0, 0)); 4049 PetscFunctionReturn(PETSC_SUCCESS); 4050 } 4051 4052 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(DM dm, PetscOptionItems *PetscOptionsObject) 4053 { 4054 DM_Plex *mesh = (DM_Plex *)dm->data; 4055 PetscBool flg, flg2; 4056 char bdLabel[PETSC_MAX_PATH_LEN]; 4057 4058 PetscFunctionBegin; 4059 /* Handle viewing */ 4060 PetscCall(PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL)); 4061 PetscCall(PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL, 0)); 4062 PetscCall(PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL)); 4063 PetscCall(PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL, 0)); 4064 PetscCall(PetscOptionsBoundedInt("-dm_plex_print_locate", "Debug output level all point location computations", "DMLocatePoints", 0, &mesh->printLocate, NULL, 0)); 4065 PetscCall(DMMonitorSetFromOptions(dm, "-dm_plex_monitor_throughput", "Monitor the simulation throughput", "DMPlexMonitorThroughput", DMPlexMonitorThroughput, NULL, &flg)); 4066 if (flg) PetscCall(PetscLogDefaultBegin()); 4067 /* Labeling */ 4068 PetscCall(PetscOptionsString("-dm_plex_boundary_label", "Label to mark the mesh boundary", "", bdLabel, bdLabel, sizeof(bdLabel), &flg)); 4069 if (flg) PetscCall(DMPlexCreateBoundaryLabel_Private(dm, bdLabel)); 4070 /* Point Location */ 4071 PetscCall(PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL)); 4072 /* Partitioning and distribution */ 4073 PetscCall(PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL)); 4074 /* Generation and remeshing */ 4075 PetscCall(PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL)); 4076 /* Projection behavior */ 4077 PetscCall(PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maximum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL, 0)); 4078 PetscCall(PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL)); 4079 /* Checking structure */ 4080 { 4081 PetscBool all = PETSC_FALSE; 4082 4083 PetscCall(PetscOptionsBool("-dm_plex_check_all", "Perform all basic checks", "DMPlexCheck", PETSC_FALSE, &all, NULL)); 4084 if (all) { 4085 PetscCall(DMPlexCheck(dm)); 4086 } else { 4087 PetscCall(PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2)); 4088 if (flg && flg2) PetscCall(DMPlexCheckSymmetry(dm)); 4089 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)); 4090 if (flg && flg2) PetscCall(DMPlexCheckSkeleton(dm, 0)); 4091 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)); 4092 if (flg && flg2) PetscCall(DMPlexCheckFaces(dm, 0)); 4093 PetscCall(PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2)); 4094 if (flg && flg2) PetscCall(DMPlexCheckGeometry(dm)); 4095 PetscCall(PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2)); 4096 if (flg && flg2) PetscCall(DMPlexCheckPointSF(dm, NULL, PETSC_FALSE)); 4097 PetscCall(PetscOptionsBool("-dm_plex_check_interface_cones", "Check points on inter-partition interfaces have conforming order of cone points", "DMPlexCheckInterfaceCones", PETSC_FALSE, &flg, &flg2)); 4098 if (flg && flg2) PetscCall(DMPlexCheckInterfaceCones(dm)); 4099 } 4100 PetscCall(PetscOptionsBool("-dm_plex_check_cell_shape", "Check cell shape", "DMPlexCheckCellShape", PETSC_FALSE, &flg, &flg2)); 4101 if (flg && flg2) PetscCall(DMPlexCheckCellShape(dm, PETSC_TRUE, PETSC_DETERMINE)); 4102 } 4103 { 4104 PetscReal scale = 1.0; 4105 4106 PetscCall(PetscOptionsReal("-dm_plex_scale", "Scale factor for mesh coordinates", "DMPlexScale", scale, &scale, &flg)); 4107 if (flg) { 4108 Vec coordinates, coordinatesLocal; 4109 4110 PetscCall(DMGetCoordinates(dm, &coordinates)); 4111 PetscCall(DMGetCoordinatesLocal(dm, &coordinatesLocal)); 4112 PetscCall(VecScale(coordinates, scale)); 4113 PetscCall(VecScale(coordinatesLocal, scale)); 4114 } 4115 } 4116 PetscCall(PetscPartitionerSetFromOptions(mesh->partitioner)); 4117 PetscFunctionReturn(PETSC_SUCCESS); 4118 } 4119 4120 PetscErrorCode DMSetFromOptions_Overlap_Plex(DM dm, PetscOptionItems *PetscOptionsObject, PetscInt *overlap) 4121 { 4122 PetscInt numOvLabels = 16, numOvExLabels = 16; 4123 char *ovLabelNames[16], *ovExLabelNames[16]; 4124 PetscInt numOvValues = 16, numOvExValues = 16, l; 4125 PetscBool flg; 4126 4127 PetscFunctionBegin; 4128 PetscCall(PetscOptionsBoundedInt("-dm_distribute_overlap", "The size of the overlap halo", "DMPlexDistribute", *overlap, overlap, NULL, 0)); 4129 PetscCall(PetscOptionsStringArray("-dm_distribute_overlap_labels", "List of overlap label names", "DMPlexDistribute", ovLabelNames, &numOvLabels, &flg)); 4130 if (!flg) numOvLabels = 0; 4131 if (numOvLabels) { 4132 ((DM_Plex *)dm->data)->numOvLabels = numOvLabels; 4133 for (l = 0; l < numOvLabels; ++l) { 4134 PetscCall(DMGetLabel(dm, ovLabelNames[l], &((DM_Plex *)dm->data)->ovLabels[l])); 4135 PetscCheck(((DM_Plex *)dm->data)->ovLabels[l], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid label name %s", ovLabelNames[l]); 4136 PetscCall(PetscFree(ovLabelNames[l])); 4137 } 4138 PetscCall(PetscOptionsIntArray("-dm_distribute_overlap_values", "List of overlap label values", "DMPlexDistribute", ((DM_Plex *)dm->data)->ovValues, &numOvValues, &flg)); 4139 if (!flg) numOvValues = 0; 4140 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); 4141 4142 PetscCall(PetscOptionsStringArray("-dm_distribute_overlap_exclude_labels", "List of overlap exclude label names", "DMPlexDistribute", ovExLabelNames, &numOvExLabels, &flg)); 4143 if (!flg) numOvExLabels = 0; 4144 ((DM_Plex *)dm->data)->numOvExLabels = numOvExLabels; 4145 for (l = 0; l < numOvExLabels; ++l) { 4146 PetscCall(DMGetLabel(dm, ovExLabelNames[l], &((DM_Plex *)dm->data)->ovExLabels[l])); 4147 PetscCheck(((DM_Plex *)dm->data)->ovExLabels[l], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid label name %s", ovExLabelNames[l]); 4148 PetscCall(PetscFree(ovExLabelNames[l])); 4149 } 4150 PetscCall(PetscOptionsIntArray("-dm_distribute_overlap_exclude_values", "List of overlap exclude label values", "DMPlexDistribute", ((DM_Plex *)dm->data)->ovExValues, &numOvExValues, &flg)); 4151 if (!flg) numOvExValues = 0; 4152 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); 4153 } 4154 PetscFunctionReturn(PETSC_SUCCESS); 4155 } 4156 4157 static PetscErrorCode DMSetFromOptions_Plex(DM dm, PetscOptionItems *PetscOptionsObject) 4158 { 4159 PetscFunctionList ordlist; 4160 char oname[256]; 4161 PetscReal volume = -1.0; 4162 PetscInt prerefine = 0, refine = 0, r, coarsen = 0, overlap = 0, extLayers = 0, dim; 4163 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; 4164 DMPlexReorderDefaultFlag reorder; 4165 4166 PetscFunctionBegin; 4167 PetscOptionsHeadBegin(PetscOptionsObject, "DMPlex Options"); 4168 if (dm->cloneOpts) goto non_refine; 4169 /* Handle automatic creation */ 4170 PetscCall(DMGetDimension(dm, &dim)); 4171 if (dim < 0) { 4172 PetscCall(DMPlexCreateFromOptions_Internal(PetscOptionsObject, &coordSpace, dm)); 4173 created = PETSC_TRUE; 4174 } 4175 PetscCall(DMGetDimension(dm, &dim)); 4176 /* Handle interpolation before distribution */ 4177 PetscCall(PetscOptionsBool("-dm_plex_interpolate_pre", "Flag to interpolate mesh before distribution", "", interpolate, &interpolate, &flg)); 4178 if (flg) { 4179 DMPlexInterpolatedFlag interpolated; 4180 4181 PetscCall(DMPlexIsInterpolated(dm, &interpolated)); 4182 if (interpolated == DMPLEX_INTERPOLATED_FULL && !interpolate) { 4183 DM udm; 4184 4185 PetscCall(DMPlexUninterpolate(dm, &udm)); 4186 PetscCall(DMPlexReplace_Internal(dm, &udm)); 4187 } else if (interpolated != DMPLEX_INTERPOLATED_FULL && interpolate) { 4188 DM idm; 4189 4190 PetscCall(DMPlexInterpolate(dm, &idm)); 4191 PetscCall(DMPlexReplace_Internal(dm, &idm)); 4192 } 4193 } 4194 /* Handle DMPlex refinement before distribution */ 4195 PetscCall(PetscOptionsBool("-dm_refine_ignore_model", "Flag to ignore the geometry model when refining", "DMCreate", ignoreModel, &ignoreModel, &flg)); 4196 if (flg) ((DM_Plex *)dm->data)->ignoreModel = ignoreModel; 4197 PetscCall(DMPlexGetRefinementUniform(dm, &uniformOrig)); 4198 PetscCall(PetscOptionsBoundedInt("-dm_refine_pre", "The number of refinements before distribution", "DMCreate", prerefine, &prerefine, NULL, 0)); 4199 PetscCall(PetscOptionsBool("-dm_refine_remap_pre", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL)); 4200 PetscCall(PetscOptionsBool("-dm_refine_uniform_pre", "Flag for uniform refinement before distribution", "DMCreate", uniform, &uniform, &flg)); 4201 if (flg) PetscCall(DMPlexSetRefinementUniform(dm, uniform)); 4202 PetscCall(PetscOptionsReal("-dm_refine_volume_limit_pre", "The maximum cell volume after refinement before distribution", "DMCreate", volume, &volume, &flg)); 4203 if (flg) { 4204 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_FALSE)); 4205 PetscCall(DMPlexSetRefinementLimit(dm, volume)); 4206 prerefine = PetscMax(prerefine, 1); 4207 } 4208 for (r = 0; r < prerefine; ++r) { 4209 DM rdm; 4210 PetscPointFunc coordFunc = ((DM_Plex *)dm->data)->coordFunc; 4211 4212 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4213 PetscCall(DMRefine(dm, PetscObjectComm((PetscObject)dm), &rdm)); 4214 PetscCall(DMPlexReplace_Internal(dm, &rdm)); 4215 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4216 if (coordFunc && remap) { 4217 PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc)); 4218 ((DM_Plex *)dm->data)->coordFunc = coordFunc; 4219 } 4220 } 4221 PetscCall(DMPlexSetRefinementUniform(dm, uniformOrig)); 4222 /* Handle DMPlex extrusion before distribution */ 4223 PetscCall(PetscOptionsBoundedInt("-dm_extrude", "The number of layers to extrude", "", extLayers, &extLayers, NULL, 0)); 4224 if (extLayers) { 4225 DM edm; 4226 4227 PetscCall(DMExtrude(dm, extLayers, &edm)); 4228 PetscCall(DMPlexReplace_Internal(dm, &edm)); 4229 ((DM_Plex *)dm->data)->coordFunc = NULL; 4230 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4231 extLayers = 0; 4232 PetscCall(DMGetDimension(dm, &dim)); 4233 } 4234 /* Handle DMPlex reordering before distribution */ 4235 PetscCall(DMPlexReorderGetDefault(dm, &reorder)); 4236 PetscCall(MatGetOrderingList(&ordlist)); 4237 PetscCall(PetscStrncpy(oname, MATORDERINGNATURAL, sizeof(oname))); 4238 PetscCall(PetscOptionsFList("-dm_plex_reorder", "Set mesh reordering type", "DMPlexGetOrdering", ordlist, MATORDERINGNATURAL, oname, sizeof(oname), &flg)); 4239 if (reorder == DMPLEX_REORDER_DEFAULT_TRUE || flg) { 4240 DM pdm; 4241 IS perm; 4242 4243 PetscCall(DMPlexGetOrdering(dm, oname, NULL, &perm)); 4244 PetscCall(DMPlexPermute(dm, perm, &pdm)); 4245 PetscCall(ISDestroy(&perm)); 4246 PetscCall(DMPlexReplace_Internal(dm, &pdm)); 4247 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4248 } 4249 /* Handle DMPlex distribution */ 4250 PetscCall(DMPlexDistributeGetDefault(dm, &distribute)); 4251 PetscCall(PetscOptionsBool("-dm_distribute", "Flag to redistribute a mesh among processes", "DMPlexDistribute", distribute, &distribute, NULL)); 4252 PetscCall(DMSetFromOptions_Overlap_Plex(dm, PetscOptionsObject, &overlap)); 4253 if (distribute) { 4254 DM pdm = NULL; 4255 PetscPartitioner part; 4256 4257 PetscCall(DMPlexGetPartitioner(dm, &part)); 4258 PetscCall(PetscPartitionerSetFromOptions(part)); 4259 PetscCall(DMPlexDistribute(dm, overlap, NULL, &pdm)); 4260 if (pdm) PetscCall(DMPlexReplace_Internal(dm, &pdm)); 4261 } 4262 /* Create coordinate space */ 4263 if (created) { 4264 DM_Plex *mesh = (DM_Plex *)dm->data; 4265 PetscInt degree = 1; 4266 PetscInt height = 0; 4267 DM cdm; 4268 PetscBool flg; 4269 4270 PetscCall(PetscOptionsBool("-dm_coord_space", "Use an FEM space for coordinates", "", coordSpace, &coordSpace, &flg)); 4271 PetscCall(PetscOptionsInt("-dm_coord_petscspace_degree", "FEM degree for coordinate space", "", degree, °ree, NULL)); 4272 if (coordSpace) PetscCall(DMPlexCreateCoordinateSpace(dm, degree, mesh->coordFunc)); 4273 PetscCall(DMGetCoordinateDM(dm, &cdm)); 4274 if (flg && !coordSpace) { 4275 PetscDS cds; 4276 PetscObject obj; 4277 PetscClassId id; 4278 4279 PetscCall(DMGetDS(cdm, &cds)); 4280 PetscCall(PetscDSGetDiscretization(cds, 0, &obj)); 4281 PetscCall(PetscObjectGetClassId(obj, &id)); 4282 if (id == PETSCFE_CLASSID) { 4283 PetscContainer dummy; 4284 4285 PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &dummy)); 4286 PetscCall(PetscObjectSetName((PetscObject)dummy, "coordinates")); 4287 PetscCall(DMSetField(cdm, 0, NULL, (PetscObject)dummy)); 4288 PetscCall(PetscContainerDestroy(&dummy)); 4289 PetscCall(DMClearDS(cdm)); 4290 } 4291 mesh->coordFunc = NULL; 4292 } 4293 PetscCall(PetscOptionsBool("-dm_sparse_localize", "Localize only necessary cells", "", dm->sparseLocalize, &dm->sparseLocalize, &flg)); 4294 PetscCall(PetscOptionsInt("-dm_localize_height", "Localize edges and faces in addition to cells", "", height, &height, &flg)); 4295 if (flg) PetscCall(DMPlexSetMaxProjectionHeight(cdm, height)); 4296 PetscCall(DMLocalizeCoordinates(dm)); 4297 } 4298 /* Handle DMPlex refinement */ 4299 remap = PETSC_TRUE; 4300 PetscCall(PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL, 0)); 4301 PetscCall(PetscOptionsBool("-dm_refine_remap", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL)); 4302 PetscCall(PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy, 0)); 4303 if (refine) PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 4304 if (refine && isHierarchy) { 4305 DM *dms, coarseDM; 4306 4307 PetscCall(DMGetCoarseDM(dm, &coarseDM)); 4308 PetscCall(PetscObjectReference((PetscObject)coarseDM)); 4309 PetscCall(PetscMalloc1(refine, &dms)); 4310 PetscCall(DMRefineHierarchy(dm, refine, dms)); 4311 /* Total hack since we do not pass in a pointer */ 4312 PetscCall(DMPlexSwap_Static(dm, dms[refine - 1])); 4313 if (refine == 1) { 4314 PetscCall(DMSetCoarseDM(dm, dms[0])); 4315 PetscCall(DMPlexSetRegularRefinement(dm, PETSC_TRUE)); 4316 } else { 4317 PetscCall(DMSetCoarseDM(dm, dms[refine - 2])); 4318 PetscCall(DMPlexSetRegularRefinement(dm, PETSC_TRUE)); 4319 PetscCall(DMSetCoarseDM(dms[0], dms[refine - 1])); 4320 PetscCall(DMPlexSetRegularRefinement(dms[0], PETSC_TRUE)); 4321 } 4322 PetscCall(DMSetCoarseDM(dms[refine - 1], coarseDM)); 4323 PetscCall(PetscObjectDereference((PetscObject)coarseDM)); 4324 /* Free DMs */ 4325 for (r = 0; r < refine; ++r) { 4326 PetscCall(DMSetFromOptions_NonRefinement_Plex(dms[r], PetscOptionsObject)); 4327 PetscCall(DMDestroy(&dms[r])); 4328 } 4329 PetscCall(PetscFree(dms)); 4330 } else { 4331 for (r = 0; r < refine; ++r) { 4332 DM rdm; 4333 PetscPointFunc coordFunc = ((DM_Plex *)dm->data)->coordFunc; 4334 4335 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4336 PetscCall(DMRefine(dm, PetscObjectComm((PetscObject)dm), &rdm)); 4337 /* Total hack since we do not pass in a pointer */ 4338 PetscCall(DMPlexReplace_Internal(dm, &rdm)); 4339 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4340 if (coordFunc && remap) { 4341 PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc)); 4342 ((DM_Plex *)dm->data)->coordFunc = coordFunc; 4343 } 4344 } 4345 } 4346 /* Handle DMPlex coarsening */ 4347 PetscCall(PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL, 0)); 4348 PetscCall(PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy, 0)); 4349 if (coarsen && isHierarchy) { 4350 DM *dms; 4351 4352 PetscCall(PetscMalloc1(coarsen, &dms)); 4353 PetscCall(DMCoarsenHierarchy(dm, coarsen, dms)); 4354 /* Free DMs */ 4355 for (r = 0; r < coarsen; ++r) { 4356 PetscCall(DMSetFromOptions_NonRefinement_Plex(dms[r], PetscOptionsObject)); 4357 PetscCall(DMDestroy(&dms[r])); 4358 } 4359 PetscCall(PetscFree(dms)); 4360 } else { 4361 for (r = 0; r < coarsen; ++r) { 4362 DM cdm; 4363 PetscPointFunc coordFunc = ((DM_Plex *)dm->data)->coordFunc; 4364 4365 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4366 PetscCall(DMCoarsen(dm, PetscObjectComm((PetscObject)dm), &cdm)); 4367 /* Total hack since we do not pass in a pointer */ 4368 PetscCall(DMPlexReplace_Internal(dm, &cdm)); 4369 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4370 if (coordFunc) { 4371 PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc)); 4372 ((DM_Plex *)dm->data)->coordFunc = coordFunc; 4373 } 4374 } 4375 } 4376 /* Handle ghost cells */ 4377 PetscCall(PetscOptionsBool("-dm_plex_create_fv_ghost_cells", "Flag to create finite volume ghost cells on the boundary", "DMCreate", ghostCells, &ghostCells, NULL)); 4378 if (ghostCells) { 4379 DM gdm; 4380 char lname[PETSC_MAX_PATH_LEN]; 4381 4382 lname[0] = '\0'; 4383 PetscCall(PetscOptionsString("-dm_plex_fv_ghost_cells_label", "Label name for ghost cells boundary", "DMCreate", lname, lname, sizeof(lname), &flg)); 4384 PetscCall(DMPlexConstructGhostCells(dm, flg ? lname : NULL, NULL, &gdm)); 4385 PetscCall(DMPlexReplace_Internal(dm, &gdm)); 4386 } 4387 /* Handle 1D order */ 4388 if (reorder != DMPLEX_REORDER_DEFAULT_FALSE && dim == 1) { 4389 DM cdm, rdm; 4390 PetscDS cds; 4391 PetscObject obj; 4392 PetscClassId id = PETSC_OBJECT_CLASSID; 4393 IS perm; 4394 PetscInt Nf; 4395 PetscBool distributed; 4396 4397 PetscCall(DMPlexIsDistributed(dm, &distributed)); 4398 PetscCall(DMGetCoordinateDM(dm, &cdm)); 4399 PetscCall(DMGetDS(cdm, &cds)); 4400 PetscCall(PetscDSGetNumFields(cds, &Nf)); 4401 if (Nf) { 4402 PetscCall(PetscDSGetDiscretization(cds, 0, &obj)); 4403 PetscCall(PetscObjectGetClassId(obj, &id)); 4404 } 4405 if (!distributed && id != PETSCFE_CLASSID) { 4406 PetscCall(DMPlexGetOrdering1D(dm, &perm)); 4407 PetscCall(DMPlexPermute(dm, perm, &rdm)); 4408 PetscCall(DMPlexReplace_Internal(dm, &rdm)); 4409 PetscCall(ISDestroy(&perm)); 4410 } 4411 } 4412 /* Handle */ 4413 non_refine: 4414 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4415 PetscOptionsHeadEnd(); 4416 PetscFunctionReturn(PETSC_SUCCESS); 4417 } 4418 4419 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm, Vec *vec) 4420 { 4421 PetscFunctionBegin; 4422 PetscCall(DMCreateGlobalVector_Section_Private(dm, vec)); 4423 /* PetscCall(VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM)); */ 4424 PetscCall(VecSetOperation(*vec, VECOP_VIEW, (void (*)(void))VecView_Plex)); 4425 PetscCall(VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void))VecView_Plex_Native)); 4426 PetscCall(VecSetOperation(*vec, VECOP_LOAD, (void (*)(void))VecLoad_Plex)); 4427 PetscCall(VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void))VecLoad_Plex_Native)); 4428 PetscFunctionReturn(PETSC_SUCCESS); 4429 } 4430 4431 static PetscErrorCode DMCreateLocalVector_Plex(DM dm, Vec *vec) 4432 { 4433 PetscFunctionBegin; 4434 PetscCall(DMCreateLocalVector_Section_Private(dm, vec)); 4435 PetscCall(VecSetOperation(*vec, VECOP_VIEW, (void (*)(void))VecView_Plex_Local)); 4436 PetscCall(VecSetOperation(*vec, VECOP_LOAD, (void (*)(void))VecLoad_Plex_Local)); 4437 PetscFunctionReturn(PETSC_SUCCESS); 4438 } 4439 4440 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 4441 { 4442 PetscInt depth, d; 4443 4444 PetscFunctionBegin; 4445 PetscCall(DMPlexGetDepth(dm, &depth)); 4446 if (depth == 1) { 4447 PetscCall(DMGetDimension(dm, &d)); 4448 if (dim == 0) PetscCall(DMPlexGetDepthStratum(dm, dim, pStart, pEnd)); 4449 else if (dim == d) PetscCall(DMPlexGetDepthStratum(dm, 1, pStart, pEnd)); 4450 else { 4451 *pStart = 0; 4452 *pEnd = 0; 4453 } 4454 } else { 4455 PetscCall(DMPlexGetDepthStratum(dm, dim, pStart, pEnd)); 4456 } 4457 PetscFunctionReturn(PETSC_SUCCESS); 4458 } 4459 4460 static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 4461 { 4462 PetscSF sf; 4463 PetscInt niranks, njranks, n; 4464 const PetscMPIInt *iranks, *jranks; 4465 DM_Plex *data = (DM_Plex *)dm->data; 4466 4467 PetscFunctionBegin; 4468 PetscCall(DMGetPointSF(dm, &sf)); 4469 if (!data->neighbors) { 4470 PetscCall(PetscSFSetUp(sf)); 4471 PetscCall(PetscSFGetRootRanks(sf, &njranks, &jranks, NULL, NULL, NULL)); 4472 PetscCall(PetscSFGetLeafRanks(sf, &niranks, &iranks, NULL, NULL)); 4473 PetscCall(PetscMalloc1(njranks + niranks + 1, &data->neighbors)); 4474 PetscCall(PetscArraycpy(data->neighbors + 1, jranks, njranks)); 4475 PetscCall(PetscArraycpy(data->neighbors + njranks + 1, iranks, niranks)); 4476 n = njranks + niranks; 4477 PetscCall(PetscSortRemoveDupsMPIInt(&n, data->neighbors + 1)); 4478 /* The following cast should never fail: can't have more neighbors than PETSC_MPI_INT_MAX */ 4479 PetscCall(PetscMPIIntCast(n, data->neighbors)); 4480 } 4481 if (nranks) *nranks = data->neighbors[0]; 4482 if (ranks) { 4483 if (data->neighbors[0]) *ranks = data->neighbors + 1; 4484 else *ranks = NULL; 4485 } 4486 PetscFunctionReturn(PETSC_SUCCESS); 4487 } 4488 4489 PETSC_INTERN PetscErrorCode DMInterpolateSolution_Plex(DM, DM, Mat, Vec, Vec); 4490 4491 static PetscErrorCode DMInitialize_Plex(DM dm) 4492 { 4493 PetscFunctionBegin; 4494 dm->ops->view = DMView_Plex; 4495 dm->ops->load = DMLoad_Plex; 4496 dm->ops->setfromoptions = DMSetFromOptions_Plex; 4497 dm->ops->clone = DMClone_Plex; 4498 dm->ops->setup = DMSetUp_Plex; 4499 dm->ops->createlocalsection = DMCreateLocalSection_Plex; 4500 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 4501 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 4502 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 4503 dm->ops->getlocaltoglobalmapping = NULL; 4504 dm->ops->createfieldis = NULL; 4505 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 4506 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 4507 dm->ops->getcoloring = NULL; 4508 dm->ops->creatematrix = DMCreateMatrix_Plex; 4509 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 4510 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 4511 dm->ops->createmassmatrixlumped = DMCreateMassMatrixLumped_Plex; 4512 dm->ops->createinjection = DMCreateInjection_Plex; 4513 dm->ops->refine = DMRefine_Plex; 4514 dm->ops->coarsen = DMCoarsen_Plex; 4515 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 4516 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 4517 dm->ops->extrude = DMExtrude_Plex; 4518 dm->ops->globaltolocalbegin = NULL; 4519 dm->ops->globaltolocalend = NULL; 4520 dm->ops->localtoglobalbegin = NULL; 4521 dm->ops->localtoglobalend = NULL; 4522 dm->ops->destroy = DMDestroy_Plex; 4523 dm->ops->createsubdm = DMCreateSubDM_Plex; 4524 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 4525 dm->ops->getdimpoints = DMGetDimPoints_Plex; 4526 dm->ops->locatepoints = DMLocatePoints_Plex; 4527 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 4528 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 4529 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 4530 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 4531 dm->ops->projectbdfieldlabellocal = DMProjectBdFieldLabelLocal_Plex; 4532 dm->ops->computel2diff = DMComputeL2Diff_Plex; 4533 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 4534 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 4535 dm->ops->getneighbors = DMGetNeighbors_Plex; 4536 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexInsertBoundaryValues_C", DMPlexInsertBoundaryValues_Plex)); 4537 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexInsertTimeDerviativeBoundaryValues_C", DMPlexInsertTimeDerivativeBoundaryValues_Plex)); 4538 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMSetUpGLVisViewer_C", DMSetUpGLVisViewer_Plex)); 4539 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMCreateNeumannOverlap_C", DMCreateNeumannOverlap_Plex)); 4540 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexGetOverlap_C", DMPlexGetOverlap_Plex)); 4541 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexDistributeGetDefault_C", DMPlexDistributeGetDefault_Plex)); 4542 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexDistributeSetDefault_C", DMPlexDistributeSetDefault_Plex)); 4543 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexReorderGetDefault_C", DMPlexReorderGetDefault_Plex)); 4544 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexReorderSetDefault_C", DMPlexReorderSetDefault_Plex)); 4545 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMInterpolateSolution_C", DMInterpolateSolution_Plex)); 4546 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexGetOverlap_C", DMPlexGetOverlap_Plex)); 4547 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexSetOverlap_C", DMPlexSetOverlap_Plex)); 4548 PetscFunctionReturn(PETSC_SUCCESS); 4549 } 4550 4551 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 4552 { 4553 DM_Plex *mesh = (DM_Plex *)dm->data; 4554 PetscSF face_sf; 4555 4556 PetscFunctionBegin; 4557 mesh->refct++; 4558 (*newdm)->data = mesh; 4559 PetscCall(DMPlexGetIsoperiodicFaceSF(dm, &face_sf)); 4560 PetscCall(DMPlexSetIsoperiodicFaceSF(*newdm, face_sf)); 4561 PetscCall(PetscObjectChangeTypeName((PetscObject)*newdm, DMPLEX)); 4562 PetscCall(DMInitialize_Plex(*newdm)); 4563 PetscFunctionReturn(PETSC_SUCCESS); 4564 } 4565 4566 /*MC 4567 DMPLEX = "plex" - A `DM` object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 4568 In the local representation, `Vec`s contain all unknowns in the interior and shared boundary. This is 4569 specified by a PetscSection object. Ownership in the global representation is determined by 4570 ownership of the underlying `DMPLEX` points. This is specified by another `PetscSection` object. 4571 4572 Options Database Keys: 4573 + -dm_refine_pre - Refine mesh before distribution 4574 + -dm_refine_uniform_pre - Choose uniform or generator-based refinement 4575 + -dm_refine_volume_limit_pre - Cell volume limit after pre-refinement using generator 4576 . -dm_distribute - Distribute mesh across processes 4577 . -dm_distribute_overlap - Number of cells to overlap for distribution 4578 . -dm_refine - Refine mesh after distribution 4579 . -dm_plex_hash_location - Use grid hashing for point location 4580 . -dm_plex_hash_box_faces <n,m,p> - The number of divisions in each direction of the grid hash 4581 . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes 4582 . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing 4583 . -dm_plex_max_projection_height - Maximum mesh point height used to project locally 4584 . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement 4585 . -dm_plex_check_all - Perform all checks below 4586 . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric 4587 . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices 4588 . -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 4589 . -dm_plex_check_geometry - Check that cells have positive volume 4590 . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ 4591 . -dm_plex_view_scale <num> - Scale the TikZ 4592 - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices 4593 4594 Level: intermediate 4595 4596 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMType`, `DMPlexCreate()`, `DMCreate()`, `DMSetType()`, `PetscSection` 4597 M*/ 4598 4599 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 4600 { 4601 DM_Plex *mesh; 4602 PetscInt unit; 4603 4604 PetscFunctionBegin; 4605 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4606 PetscCall(PetscNew(&mesh)); 4607 dm->data = mesh; 4608 4609 mesh->refct = 1; 4610 PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection)); 4611 PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection)); 4612 mesh->refinementUniform = PETSC_TRUE; 4613 mesh->refinementLimit = -1.0; 4614 mesh->distDefault = PETSC_TRUE; 4615 mesh->reorderDefault = DMPLEX_REORDER_DEFAULT_NOTSET; 4616 mesh->distributionName = NULL; 4617 mesh->interpolated = DMPLEX_INTERPOLATED_INVALID; 4618 mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID; 4619 4620 PetscCall(PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner)); 4621 mesh->remeshBd = PETSC_FALSE; 4622 4623 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 4624 4625 mesh->depthState = -1; 4626 mesh->celltypeState = -1; 4627 mesh->printTol = 1.0e-10; 4628 4629 PetscCall(DMInitialize_Plex(dm)); 4630 PetscFunctionReturn(PETSC_SUCCESS); 4631 } 4632 4633 /*@ 4634 DMPlexCreate - Creates a `DMPLEX` object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 4635 4636 Collective 4637 4638 Input Parameter: 4639 . comm - The communicator for the `DMPLEX` object 4640 4641 Output Parameter: 4642 . mesh - The `DMPLEX` object 4643 4644 Level: beginner 4645 4646 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMType`, `DMPlexCreate()`, `DMCreate()`, `DMSetType()` 4647 @*/ 4648 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 4649 { 4650 PetscFunctionBegin; 4651 PetscValidPointer(mesh, 2); 4652 PetscCall(DMCreate(comm, mesh)); 4653 PetscCall(DMSetType(*mesh, DMPLEX)); 4654 PetscFunctionReturn(PETSC_SUCCESS); 4655 } 4656 4657 /*@C 4658 DMPlexBuildFromCellListParallel - Build distributed `DMPLEX` topology from a list of vertices for each cell (common mesh generator output) 4659 4660 Collective; No Fortran Support 4661 4662 Input Parameters: 4663 + dm - The `DM` 4664 . numCells - The number of cells owned by this process 4665 . numVertices - The number of vertices to be owned by this process, or `PETSC_DECIDE` 4666 . NVertices - The global number of vertices, or `PETSC_DETERMINE` 4667 . numCorners - The number of vertices for each cell 4668 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 4669 4670 Output Parameters: 4671 + vertexSF - (Optional) `PetscSF` describing complete vertex ownership 4672 - verticesAdjSaved - (Optional) vertex adjacency array 4673 4674 Level: advanced 4675 4676 Notes: 4677 Two triangles sharing a face 4678 .vb 4679 4680 2 4681 / | \ 4682 / | \ 4683 / | \ 4684 0 0 | 1 3 4685 \ | / 4686 \ | / 4687 \ | / 4688 1 4689 .ve 4690 would have input 4691 .vb 4692 numCells = 2, numVertices = 4 4693 cells = [0 1 2 1 3 2] 4694 .ve 4695 which would result in the `DMPLEX` 4696 .vb 4697 4698 4 4699 / | \ 4700 / | \ 4701 / | \ 4702 2 0 | 1 5 4703 \ | / 4704 \ | / 4705 \ | / 4706 3 4707 .ve 4708 4709 Vertices are implicitly numbered consecutively 0,...,NVertices. 4710 Each rank owns a chunk of numVertices consecutive vertices. 4711 If numVertices is `PETSC_DECIDE`, PETSc will distribute them as evenly as possible using PetscLayout. 4712 If NVertices is `PETSC_DETERMINE` and numVertices is PETSC_DECIDE, NVertices is computed by PETSc as the maximum vertex index in cells + 1. 4713 If only NVertices is `PETSC_DETERMINE`, it is computed as the sum of numVertices over all ranks. 4714 4715 The cell distribution is arbitrary non-overlapping, independent of the vertex distribution. 4716 4717 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildFromCellList()`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildCoordinatesFromCellListParallel()`, 4718 `PetscSF` 4719 @*/ 4720 PetscErrorCode DMPlexBuildFromCellListParallel(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, const PetscInt cells[], PetscSF *vertexSF, PetscInt **verticesAdjSaved) 4721 { 4722 PetscSF sfPoint; 4723 PetscLayout layout; 4724 PetscInt numVerticesAdj, *verticesAdj, *cones, c, p; 4725 4726 PetscFunctionBegin; 4727 PetscValidLogicalCollectiveInt(dm, NVertices, 4); 4728 PetscCall(PetscLogEventBegin(DMPLEX_BuildFromCellList, dm, 0, 0, 0)); 4729 /* Get/check global number of vertices */ 4730 { 4731 PetscInt NVerticesInCells, i; 4732 const PetscInt len = numCells * numCorners; 4733 4734 /* NVerticesInCells = max(cells) + 1 */ 4735 NVerticesInCells = PETSC_MIN_INT; 4736 for (i = 0; i < len; i++) 4737 if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 4738 ++NVerticesInCells; 4739 PetscCall(MPIU_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm))); 4740 4741 if (numVertices == PETSC_DECIDE && NVertices == PETSC_DECIDE) NVertices = NVerticesInCells; 4742 else 4743 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); 4744 } 4745 /* Count locally unique vertices */ 4746 { 4747 PetscHSetI vhash; 4748 PetscInt off = 0; 4749 4750 PetscCall(PetscHSetICreate(&vhash)); 4751 for (c = 0; c < numCells; ++c) { 4752 for (p = 0; p < numCorners; ++p) PetscCall(PetscHSetIAdd(vhash, cells[c * numCorners + p])); 4753 } 4754 PetscCall(PetscHSetIGetSize(vhash, &numVerticesAdj)); 4755 if (!verticesAdjSaved) PetscCall(PetscMalloc1(numVerticesAdj, &verticesAdj)); 4756 else verticesAdj = *verticesAdjSaved; 4757 PetscCall(PetscHSetIGetElems(vhash, &off, verticesAdj)); 4758 PetscCall(PetscHSetIDestroy(&vhash)); 4759 PetscCheck(off == numVerticesAdj, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %" PetscInt_FMT " should be %" PetscInt_FMT, off, numVerticesAdj); 4760 } 4761 PetscCall(PetscSortInt(numVerticesAdj, verticesAdj)); 4762 /* Create cones */ 4763 PetscCall(DMPlexSetChart(dm, 0, numCells + numVerticesAdj)); 4764 for (c = 0; c < numCells; ++c) PetscCall(DMPlexSetConeSize(dm, c, numCorners)); 4765 PetscCall(DMSetUp(dm)); 4766 PetscCall(DMPlexGetCones(dm, &cones)); 4767 for (c = 0; c < numCells; ++c) { 4768 for (p = 0; p < numCorners; ++p) { 4769 const PetscInt gv = cells[c * numCorners + p]; 4770 PetscInt lv; 4771 4772 /* Positions within verticesAdj form 0-based local vertex numbering; 4773 we need to shift it by numCells to get correct DAG points (cells go first) */ 4774 PetscCall(PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv)); 4775 PetscCheck(lv >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %" PetscInt_FMT " in local connectivity", gv); 4776 cones[c * numCorners + p] = lv + numCells; 4777 } 4778 } 4779 /* Build point sf */ 4780 PetscCall(PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &layout)); 4781 PetscCall(PetscLayoutSetSize(layout, NVertices)); 4782 PetscCall(PetscLayoutSetLocalSize(layout, numVertices)); 4783 PetscCall(PetscLayoutSetBlockSize(layout, 1)); 4784 PetscCall(PetscSFCreateByMatchingIndices(layout, numVerticesAdj, verticesAdj, NULL, numCells, numVerticesAdj, verticesAdj, NULL, numCells, vertexSF, &sfPoint)); 4785 PetscCall(PetscLayoutDestroy(&layout)); 4786 if (!verticesAdjSaved) PetscCall(PetscFree(verticesAdj)); 4787 PetscCall(PetscObjectSetName((PetscObject)sfPoint, "point SF")); 4788 if (dm->sf) { 4789 const char *prefix; 4790 4791 PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm->sf, &prefix)); 4792 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)sfPoint, prefix)); 4793 } 4794 PetscCall(DMSetPointSF(dm, sfPoint)); 4795 PetscCall(PetscSFDestroy(&sfPoint)); 4796 if (vertexSF) PetscCall(PetscObjectSetName((PetscObject)(*vertexSF), "Vertex Ownership SF")); 4797 /* Fill in the rest of the topology structure */ 4798 PetscCall(DMPlexSymmetrize(dm)); 4799 PetscCall(DMPlexStratify(dm)); 4800 PetscCall(PetscLogEventEnd(DMPLEX_BuildFromCellList, dm, 0, 0, 0)); 4801 PetscFunctionReturn(PETSC_SUCCESS); 4802 } 4803 4804 /*@C 4805 DMPlexBuildCoordinatesFromCellListParallel - Build `DM` coordinates from a list of coordinates for each owned vertex (common mesh generator output) 4806 4807 Collective; No Fortran Support 4808 4809 Input Parameters: 4810 + dm - The `DM` 4811 . spaceDim - The spatial dimension used for coordinates 4812 . sfVert - `PetscSF` describing complete vertex ownership 4813 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 4814 4815 Level: advanced 4816 4817 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildFromCellListParallel()` 4818 @*/ 4819 PetscErrorCode DMPlexBuildCoordinatesFromCellListParallel(DM dm, PetscInt spaceDim, PetscSF sfVert, const PetscReal vertexCoords[]) 4820 { 4821 PetscSection coordSection; 4822 Vec coordinates; 4823 PetscScalar *coords; 4824 PetscInt numVertices, numVerticesAdj, coordSize, v, vStart, vEnd; 4825 4826 PetscFunctionBegin; 4827 PetscCall(PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0)); 4828 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 4829 PetscCheck(vStart >= 0 && vEnd >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 4830 PetscCall(DMSetCoordinateDim(dm, spaceDim)); 4831 PetscCall(PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL)); 4832 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); 4833 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 4834 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 4835 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spaceDim)); 4836 PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd)); 4837 for (v = vStart; v < vEnd; ++v) { 4838 PetscCall(PetscSectionSetDof(coordSection, v, spaceDim)); 4839 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spaceDim)); 4840 } 4841 PetscCall(PetscSectionSetUp(coordSection)); 4842 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 4843 PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &coordinates)); 4844 PetscCall(VecSetBlockSize(coordinates, spaceDim)); 4845 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 4846 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 4847 PetscCall(VecSetType(coordinates, VECSTANDARD)); 4848 PetscCall(VecGetArray(coordinates, &coords)); 4849 { 4850 MPI_Datatype coordtype; 4851 4852 /* Need a temp buffer for coords if we have complex/single */ 4853 PetscCallMPI(MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype)); 4854 PetscCallMPI(MPI_Type_commit(&coordtype)); 4855 #if defined(PETSC_USE_COMPLEX) 4856 { 4857 PetscScalar *svertexCoords; 4858 PetscInt i; 4859 PetscCall(PetscMalloc1(numVertices * spaceDim, &svertexCoords)); 4860 for (i = 0; i < numVertices * spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 4861 PetscCall(PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords, MPI_REPLACE)); 4862 PetscCall(PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords, MPI_REPLACE)); 4863 PetscCall(PetscFree(svertexCoords)); 4864 } 4865 #else 4866 PetscCall(PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords, MPI_REPLACE)); 4867 PetscCall(PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords, MPI_REPLACE)); 4868 #endif 4869 PetscCallMPI(MPI_Type_free(&coordtype)); 4870 } 4871 PetscCall(VecRestoreArray(coordinates, &coords)); 4872 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 4873 PetscCall(VecDestroy(&coordinates)); 4874 PetscCall(PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0)); 4875 PetscFunctionReturn(PETSC_SUCCESS); 4876 } 4877 4878 /*@ 4879 DMPlexCreateFromCellListParallelPetsc - Create distributed `DMPLEX` from a list of vertices for each cell (common mesh generator output) 4880 4881 Collective 4882 4883 Input Parameters: 4884 + comm - The communicator 4885 . dim - The topological dimension of the mesh 4886 . numCells - The number of cells owned by this process 4887 . numVertices - The number of vertices owned by this process, or `PETSC_DECIDE` 4888 . NVertices - The global number of vertices, or `PETSC_DECIDE` 4889 . numCorners - The number of vertices for each cell 4890 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 4891 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 4892 . spaceDim - The spatial dimension used for coordinates 4893 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 4894 4895 Output Parameters: 4896 + dm - The `DM` 4897 . vertexSF - (Optional) `PetscSF` describing complete vertex ownership 4898 - verticesAdjSaved - (Optional) vertex adjacency array 4899 4900 Level: intermediate 4901 4902 Notes: 4903 This function is just a convenient sequence of `DMCreate()`, `DMSetType()`, `DMSetDimension()`, 4904 `DMPlexBuildFromCellListParallel()`, `DMPlexInterpolate()`, `DMPlexBuildCoordinatesFromCellListParallel()` 4905 4906 See `DMPlexBuildFromCellListParallel()` for an example and details about the topology-related parameters. 4907 4908 See `DMPlexBuildCoordinatesFromCellListParallel()` for details about the geometry-related parameters. 4909 4910 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromCellListPetsc()`, `DMPlexBuildFromCellListParallel()`, `DMPlexBuildCoordinatesFromCellListParallel()`, `DMPlexCreateFromDAG()`, `DMPlexCreate()` 4911 @*/ 4912 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) 4913 { 4914 PetscSF sfVert; 4915 4916 PetscFunctionBegin; 4917 PetscCall(DMCreate(comm, dm)); 4918 PetscCall(DMSetType(*dm, DMPLEX)); 4919 PetscValidLogicalCollectiveInt(*dm, dim, 2); 4920 PetscValidLogicalCollectiveInt(*dm, spaceDim, 9); 4921 PetscCall(DMSetDimension(*dm, dim)); 4922 PetscCall(DMPlexBuildFromCellListParallel(*dm, numCells, numVertices, NVertices, numCorners, cells, &sfVert, verticesAdj)); 4923 if (interpolate) { 4924 DM idm; 4925 4926 PetscCall(DMPlexInterpolate(*dm, &idm)); 4927 PetscCall(DMDestroy(dm)); 4928 *dm = idm; 4929 } 4930 PetscCall(DMPlexBuildCoordinatesFromCellListParallel(*dm, spaceDim, sfVert, vertexCoords)); 4931 if (vertexSF) *vertexSF = sfVert; 4932 else PetscCall(PetscSFDestroy(&sfVert)); 4933 PetscFunctionReturn(PETSC_SUCCESS); 4934 } 4935 4936 /*@C 4937 DMPlexBuildFromCellList - Build `DMPLEX` topology from a list of vertices for each cell (common mesh generator output) 4938 4939 Collective; No Fortran Support 4940 4941 Input Parameters: 4942 + dm - The `DM` 4943 . numCells - The number of cells owned by this process 4944 . numVertices - The number of vertices owned by this process, or `PETSC_DETERMINE` 4945 . numCorners - The number of vertices for each cell 4946 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 4947 4948 Level: advanced 4949 4950 Notes: 4951 Two triangles sharing a face 4952 .vb 4953 4954 2 4955 / | \ 4956 / | \ 4957 / | \ 4958 0 0 | 1 3 4959 \ | / 4960 \ | / 4961 \ | / 4962 1 4963 .ve 4964 would have input 4965 .vb 4966 numCells = 2, numVertices = 4 4967 cells = [0 1 2 1 3 2] 4968 .ve 4969 which would result in the `DMPLEX` 4970 .vb 4971 4972 4 4973 / | \ 4974 / | \ 4975 / | \ 4976 2 0 | 1 5 4977 \ | / 4978 \ | / 4979 \ | / 4980 3 4981 .ve 4982 4983 If numVertices is `PETSC_DETERMINE`, it is computed by PETSc as the maximum vertex index in cells + 1. 4984 4985 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildFromCellListParallel()`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromCellListPetsc()` 4986 @*/ 4987 PetscErrorCode DMPlexBuildFromCellList(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[]) 4988 { 4989 PetscInt *cones, c, p, dim; 4990 4991 PetscFunctionBegin; 4992 PetscCall(PetscLogEventBegin(DMPLEX_BuildFromCellList, dm, 0, 0, 0)); 4993 PetscCall(DMGetDimension(dm, &dim)); 4994 /* Get/check global number of vertices */ 4995 { 4996 PetscInt NVerticesInCells, i; 4997 const PetscInt len = numCells * numCorners; 4998 4999 /* NVerticesInCells = max(cells) + 1 */ 5000 NVerticesInCells = PETSC_MIN_INT; 5001 for (i = 0; i < len; i++) 5002 if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 5003 ++NVerticesInCells; 5004 5005 if (numVertices == PETSC_DECIDE) numVertices = NVerticesInCells; 5006 else 5007 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); 5008 } 5009 PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices)); 5010 for (c = 0; c < numCells; ++c) PetscCall(DMPlexSetConeSize(dm, c, numCorners)); 5011 PetscCall(DMSetUp(dm)); 5012 PetscCall(DMPlexGetCones(dm, &cones)); 5013 for (c = 0; c < numCells; ++c) { 5014 for (p = 0; p < numCorners; ++p) cones[c * numCorners + p] = cells[c * numCorners + p] + numCells; 5015 } 5016 PetscCall(DMPlexSymmetrize(dm)); 5017 PetscCall(DMPlexStratify(dm)); 5018 PetscCall(PetscLogEventEnd(DMPLEX_BuildFromCellList, dm, 0, 0, 0)); 5019 PetscFunctionReturn(PETSC_SUCCESS); 5020 } 5021 5022 /*@C 5023 DMPlexBuildCoordinatesFromCellList - Build `DM` coordinates from a list of coordinates for each owned vertex (common mesh generator output) 5024 5025 Collective; No Fortran Support 5026 5027 Input Parameters: 5028 + dm - The `DM` 5029 . spaceDim - The spatial dimension used for coordinates 5030 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 5031 5032 Level: advanced 5033 5034 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildCoordinatesFromCellListParallel()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexBuildFromCellList()` 5035 @*/ 5036 PetscErrorCode DMPlexBuildCoordinatesFromCellList(DM dm, PetscInt spaceDim, const PetscReal vertexCoords[]) 5037 { 5038 PetscSection coordSection; 5039 Vec coordinates; 5040 DM cdm; 5041 PetscScalar *coords; 5042 PetscInt v, vStart, vEnd, d; 5043 5044 PetscFunctionBegin; 5045 PetscCall(PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0)); 5046 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 5047 PetscCheck(vStart >= 0 && vEnd >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 5048 PetscCall(DMSetCoordinateDim(dm, spaceDim)); 5049 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 5050 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 5051 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spaceDim)); 5052 PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd)); 5053 for (v = vStart; v < vEnd; ++v) { 5054 PetscCall(PetscSectionSetDof(coordSection, v, spaceDim)); 5055 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spaceDim)); 5056 } 5057 PetscCall(PetscSectionSetUp(coordSection)); 5058 5059 PetscCall(DMGetCoordinateDM(dm, &cdm)); 5060 PetscCall(DMCreateLocalVector(cdm, &coordinates)); 5061 PetscCall(VecSetBlockSize(coordinates, spaceDim)); 5062 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 5063 PetscCall(VecGetArrayWrite(coordinates, &coords)); 5064 for (v = 0; v < vEnd - vStart; ++v) { 5065 for (d = 0; d < spaceDim; ++d) coords[v * spaceDim + d] = vertexCoords[v * spaceDim + d]; 5066 } 5067 PetscCall(VecRestoreArrayWrite(coordinates, &coords)); 5068 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 5069 PetscCall(VecDestroy(&coordinates)); 5070 PetscCall(PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0)); 5071 PetscFunctionReturn(PETSC_SUCCESS); 5072 } 5073 5074 /*@ 5075 DMPlexCreateFromCellListPetsc - Create `DMPLEX` from a list of vertices for each cell (common mesh generator output), but only process 0 takes in the input 5076 5077 Collective 5078 5079 Input Parameters: 5080 + comm - The communicator 5081 . dim - The topological dimension of the mesh 5082 . numCells - The number of cells, only on process 0 5083 . numVertices - The number of vertices owned by this process, or `PETSC_DECIDE`, only on process 0 5084 . numCorners - The number of vertices for each cell, only on process 0 5085 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 5086 . cells - An array of numCells*numCorners numbers, the vertices for each cell, only on process 0 5087 . spaceDim - The spatial dimension used for coordinates 5088 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex, only on process 0 5089 5090 Output Parameter: 5091 . dm - The `DM`, which only has points on process 0 5092 5093 Level: intermediate 5094 5095 Notes: 5096 This function is just a convenient sequence of `DMCreate()`, `DMSetType()`, `DMSetDimension()`, `DMPlexBuildFromCellList()`, 5097 `DMPlexInterpolate()`, `DMPlexBuildCoordinatesFromCellList()` 5098 5099 See `DMPlexBuildFromCellList()` for an example and details about the topology-related parameters. 5100 See `DMPlexBuildCoordinatesFromCellList()` for details about the geometry-related parameters. 5101 See `DMPlexCreateFromCellListParallelPetsc()` for parallel input 5102 5103 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildFromCellList()`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromDAG()`, `DMPlexCreate()` 5104 @*/ 5105 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) 5106 { 5107 PetscMPIInt rank; 5108 5109 PetscFunctionBegin; 5110 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."); 5111 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 5112 PetscCall(DMCreate(comm, dm)); 5113 PetscCall(DMSetType(*dm, DMPLEX)); 5114 PetscCall(DMSetDimension(*dm, dim)); 5115 if (rank == 0) PetscCall(DMPlexBuildFromCellList(*dm, numCells, numVertices, numCorners, cells)); 5116 else PetscCall(DMPlexBuildFromCellList(*dm, 0, 0, 0, NULL)); 5117 if (interpolate) { 5118 DM idm; 5119 5120 PetscCall(DMPlexInterpolate(*dm, &idm)); 5121 PetscCall(DMDestroy(dm)); 5122 *dm = idm; 5123 } 5124 if (rank == 0) PetscCall(DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, vertexCoords)); 5125 else PetscCall(DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, NULL)); 5126 PetscFunctionReturn(PETSC_SUCCESS); 5127 } 5128 5129 /*@ 5130 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a `DM` 5131 5132 Input Parameters: 5133 + dm - The empty `DM` object, usually from `DMCreate()` and `DMSetDimension()` 5134 . depth - The depth of the DAG 5135 . numPoints - Array of size depth + 1 containing the number of points at each `depth` 5136 . coneSize - The cone size of each point 5137 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 5138 . coneOrientations - The orientation of each cone point 5139 - vertexCoords - An array of `numPoints`[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via `DMSetCoordinateDim()` 5140 5141 Output Parameter: 5142 . dm - The `DM` 5143 5144 Level: advanced 5145 5146 Note: 5147 Two triangles sharing a face would have input 5148 .vb 5149 depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 5150 cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 5151 vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 5152 .ve 5153 which would result in the DMPlex 5154 .vb 5155 4 5156 / | \ 5157 / | \ 5158 / | \ 5159 2 0 | 1 5 5160 \ | / 5161 \ | / 5162 \ | / 5163 3 5164 .ve 5165 Notice that all points are numbered consecutively, unlike `DMPlexCreateFromCellListPetsc()` 5166 5167 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()` 5168 @*/ 5169 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 5170 { 5171 Vec coordinates; 5172 PetscSection coordSection; 5173 PetscScalar *coords; 5174 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 5175 5176 PetscFunctionBegin; 5177 PetscCall(DMGetDimension(dm, &dim)); 5178 PetscCall(DMGetCoordinateDim(dm, &dimEmbed)); 5179 PetscCheck(dimEmbed >= dim, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Embedding dimension %" PetscInt_FMT " cannot be less than intrinsic dimension %" PetscInt_FMT, dimEmbed, dim); 5180 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 5181 PetscCall(DMPlexSetChart(dm, pStart, pEnd)); 5182 for (p = pStart; p < pEnd; ++p) { 5183 PetscCall(DMPlexSetConeSize(dm, p, coneSize[p - pStart])); 5184 if (firstVertex < 0 && !coneSize[p - pStart]) firstVertex = p - pStart; 5185 } 5186 PetscCheck(firstVertex >= 0 || !numPoints[0], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Expected %" PetscInt_FMT " vertices but could not find any", numPoints[0]); 5187 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 5188 for (p = pStart, off = 0; p < pEnd; off += coneSize[p - pStart], ++p) { 5189 PetscCall(DMPlexSetCone(dm, p, &cones[off])); 5190 PetscCall(DMPlexSetConeOrientation(dm, p, &coneOrientations[off])); 5191 } 5192 PetscCall(DMPlexSymmetrize(dm)); 5193 PetscCall(DMPlexStratify(dm)); 5194 /* Build coordinates */ 5195 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 5196 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 5197 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dimEmbed)); 5198 PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex + numPoints[0])); 5199 for (v = firstVertex; v < firstVertex + numPoints[0]; ++v) { 5200 PetscCall(PetscSectionSetDof(coordSection, v, dimEmbed)); 5201 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed)); 5202 } 5203 PetscCall(PetscSectionSetUp(coordSection)); 5204 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 5205 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 5206 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 5207 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 5208 PetscCall(VecSetBlockSize(coordinates, dimEmbed)); 5209 PetscCall(VecSetType(coordinates, VECSTANDARD)); 5210 if (vertexCoords) { 5211 PetscCall(VecGetArray(coordinates, &coords)); 5212 for (v = 0; v < numPoints[0]; ++v) { 5213 PetscInt off; 5214 5215 PetscCall(PetscSectionGetOffset(coordSection, v + firstVertex, &off)); 5216 for (d = 0; d < dimEmbed; ++d) coords[off + d] = vertexCoords[v * dimEmbed + d]; 5217 } 5218 } 5219 PetscCall(VecRestoreArray(coordinates, &coords)); 5220 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 5221 PetscCall(VecDestroy(&coordinates)); 5222 PetscFunctionReturn(PETSC_SUCCESS); 5223 } 5224 5225 /*@C 5226 DMPlexCreateCellVertexFromFile - Create a `DMPLEX` mesh from a simple cell-vertex file. 5227 5228 Collective 5229 5230 + comm - The MPI communicator 5231 . filename - Name of the .dat file 5232 - interpolate - Create faces and edges in the mesh 5233 5234 Output Parameter: 5235 . dm - The `DM` object representing the mesh 5236 5237 Level: beginner 5238 5239 Note: 5240 The format is the simplest possible: 5241 .vb 5242 Ne 5243 v0 v1 ... vk 5244 Nv 5245 x y z marker 5246 .ve 5247 5248 Developer Note: 5249 Should use a `PetscViewer` not a filename 5250 5251 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromFile()`, `DMPlexCreateMedFromFile()`, `DMPlexCreateGmsh()`, `DMPlexCreate()` 5252 @*/ 5253 static PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 5254 { 5255 DMLabel marker; 5256 PetscViewer viewer; 5257 Vec coordinates; 5258 PetscSection coordSection; 5259 PetscScalar *coords; 5260 char line[PETSC_MAX_PATH_LEN]; 5261 PetscInt dim = 3, cdim = 3, coordSize, v, c, d; 5262 PetscMPIInt rank; 5263 int snum, Nv, Nc, Ncn, Nl; 5264 5265 PetscFunctionBegin; 5266 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 5267 PetscCall(PetscViewerCreate(comm, &viewer)); 5268 PetscCall(PetscViewerSetType(viewer, PETSCVIEWERASCII)); 5269 PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ)); 5270 PetscCall(PetscViewerFileSetName(viewer, filename)); 5271 if (rank == 0) { 5272 PetscCall(PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING)); 5273 snum = sscanf(line, "%d %d %d %d", &Nc, &Nv, &Ncn, &Nl); 5274 PetscCheck(snum == 4, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 5275 } else { 5276 Nc = Nv = Ncn = Nl = 0; 5277 } 5278 PetscCall(DMCreate(comm, dm)); 5279 PetscCall(DMSetType(*dm, DMPLEX)); 5280 PetscCall(DMPlexSetChart(*dm, 0, Nc + Nv)); 5281 PetscCall(DMSetDimension(*dm, dim)); 5282 PetscCall(DMSetCoordinateDim(*dm, cdim)); 5283 /* Read topology */ 5284 if (rank == 0) { 5285 char format[PETSC_MAX_PATH_LEN]; 5286 PetscInt cone[8]; 5287 int vbuf[8], v; 5288 5289 for (c = 0; c < Ncn; ++c) { 5290 format[c * 3 + 0] = '%'; 5291 format[c * 3 + 1] = 'd'; 5292 format[c * 3 + 2] = ' '; 5293 } 5294 format[Ncn * 3 - 1] = '\0'; 5295 for (c = 0; c < Nc; ++c) PetscCall(DMPlexSetConeSize(*dm, c, Ncn)); 5296 PetscCall(DMSetUp(*dm)); 5297 for (c = 0; c < Nc; ++c) { 5298 PetscCall(PetscViewerRead(viewer, line, Ncn, NULL, PETSC_STRING)); 5299 switch (Ncn) { 5300 case 2: 5301 snum = sscanf(line, format, &vbuf[0], &vbuf[1]); 5302 break; 5303 case 3: 5304 snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2]); 5305 break; 5306 case 4: 5307 snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3]); 5308 break; 5309 case 6: 5310 snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5]); 5311 break; 5312 case 8: 5313 snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5], &vbuf[6], &vbuf[7]); 5314 break; 5315 default: 5316 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "No cell shape with %d vertices", Ncn); 5317 } 5318 PetscCheck(snum == Ncn, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 5319 for (v = 0; v < Ncn; ++v) cone[v] = vbuf[v] + Nc; 5320 /* Hexahedra are inverted */ 5321 if (Ncn == 8) { 5322 PetscInt tmp = cone[1]; 5323 cone[1] = cone[3]; 5324 cone[3] = tmp; 5325 } 5326 PetscCall(DMPlexSetCone(*dm, c, cone)); 5327 } 5328 } 5329 PetscCall(DMPlexSymmetrize(*dm)); 5330 PetscCall(DMPlexStratify(*dm)); 5331 /* Read coordinates */ 5332 PetscCall(DMGetCoordinateSection(*dm, &coordSection)); 5333 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 5334 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, cdim)); 5335 PetscCall(PetscSectionSetChart(coordSection, Nc, Nc + Nv)); 5336 for (v = Nc; v < Nc + Nv; ++v) { 5337 PetscCall(PetscSectionSetDof(coordSection, v, cdim)); 5338 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, cdim)); 5339 } 5340 PetscCall(PetscSectionSetUp(coordSection)); 5341 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 5342 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 5343 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 5344 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 5345 PetscCall(VecSetBlockSize(coordinates, cdim)); 5346 PetscCall(VecSetType(coordinates, VECSTANDARD)); 5347 PetscCall(VecGetArray(coordinates, &coords)); 5348 if (rank == 0) { 5349 char format[PETSC_MAX_PATH_LEN]; 5350 double x[3]; 5351 int l, val[3]; 5352 5353 if (Nl) { 5354 for (l = 0; l < Nl; ++l) { 5355 format[l * 3 + 0] = '%'; 5356 format[l * 3 + 1] = 'd'; 5357 format[l * 3 + 2] = ' '; 5358 } 5359 format[Nl * 3 - 1] = '\0'; 5360 PetscCall(DMCreateLabel(*dm, "marker")); 5361 PetscCall(DMGetLabel(*dm, "marker", &marker)); 5362 } 5363 for (v = 0; v < Nv; ++v) { 5364 PetscCall(PetscViewerRead(viewer, line, 3 + Nl, NULL, PETSC_STRING)); 5365 snum = sscanf(line, "%lg %lg %lg", &x[0], &x[1], &x[2]); 5366 PetscCheck(snum == 3, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 5367 switch (Nl) { 5368 case 0: 5369 snum = 0; 5370 break; 5371 case 1: 5372 snum = sscanf(line, format, &val[0]); 5373 break; 5374 case 2: 5375 snum = sscanf(line, format, &val[0], &val[1]); 5376 break; 5377 case 3: 5378 snum = sscanf(line, format, &val[0], &val[1], &val[2]); 5379 break; 5380 default: 5381 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Request support for %d labels", Nl); 5382 } 5383 PetscCheck(snum == Nl, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 5384 for (d = 0; d < cdim; ++d) coords[v * cdim + d] = x[d]; 5385 for (l = 0; l < Nl; ++l) PetscCall(DMLabelSetValue(marker, v + Nc, val[l])); 5386 } 5387 } 5388 PetscCall(VecRestoreArray(coordinates, &coords)); 5389 PetscCall(DMSetCoordinatesLocal(*dm, coordinates)); 5390 PetscCall(VecDestroy(&coordinates)); 5391 PetscCall(PetscViewerDestroy(&viewer)); 5392 if (interpolate) { 5393 DM idm; 5394 DMLabel bdlabel; 5395 5396 PetscCall(DMPlexInterpolate(*dm, &idm)); 5397 PetscCall(DMDestroy(dm)); 5398 *dm = idm; 5399 5400 if (!Nl) { 5401 PetscCall(DMCreateLabel(*dm, "marker")); 5402 PetscCall(DMGetLabel(*dm, "marker", &bdlabel)); 5403 PetscCall(DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel)); 5404 PetscCall(DMPlexLabelComplete(*dm, bdlabel)); 5405 } 5406 } 5407 PetscFunctionReturn(PETSC_SUCCESS); 5408 } 5409 5410 /*@C 5411 DMPlexCreateFromFile - This takes a filename and produces a `DM` 5412 5413 Collective 5414 5415 Input Parameters: 5416 + comm - The communicator 5417 . filename - A file name 5418 . plexname - The object name of the resulting `DM`, also used for intra-datafile lookup by some formats 5419 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 5420 5421 Output Parameter: 5422 . dm - The `DM` 5423 5424 Options Database Key: 5425 . -dm_plex_create_from_hdf5_xdmf - use the `PETSC_VIEWER_HDF5_XDMF` format for reading HDF5 5426 5427 Use `-dm_plex_create_ prefix` to pass options to the internal `PetscViewer`, e.g. 5428 $ -dm_plex_create_viewer_hdf5_collective 5429 5430 Level: beginner 5431 5432 Notes: 5433 Using `PETSCVIEWERHDF5` type with `PETSC_VIEWER_HDF5_PETSC` format, one can save multiple `DMPLEX` 5434 meshes in a single HDF5 file. This in turn requires one to name the `DMPLEX` object with `PetscObjectSetName()` 5435 before saving it with `DMView()` and before loading it with `DMLoad()` for identification of the mesh object. 5436 The input parameter name is thus used to name the `DMPLEX` object when `DMPlexCreateFromFile()` internally 5437 calls `DMLoad()`. Currently, name is ignored for other viewer types and/or formats. 5438 5439 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromDAG()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()`, `PetscObjectSetName()`, `DMView()`, `DMLoad()` 5440 @*/ 5441 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], const char plexname[], PetscBool interpolate, DM *dm) 5442 { 5443 const char extGmsh[] = ".msh"; 5444 const char extGmsh2[] = ".msh2"; 5445 const char extGmsh4[] = ".msh4"; 5446 const char extCGNS[] = ".cgns"; 5447 const char extExodus[] = ".exo"; 5448 const char extExodus_e[] = ".e"; 5449 const char extGenesis[] = ".gen"; 5450 const char extFluent[] = ".cas"; 5451 const char extHDF5[] = ".h5"; 5452 const char extXDMFHDF5[] = ".xdmf.h5"; 5453 const char extMed[] = ".med"; 5454 const char extPLY[] = ".ply"; 5455 const char extEGADSLite[] = ".egadslite"; 5456 const char extEGADS[] = ".egads"; 5457 const char extIGES[] = ".igs"; 5458 const char extSTEP[] = ".stp"; 5459 const char extCV[] = ".dat"; 5460 size_t len; 5461 PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isEGADSLite, isEGADS, isIGES, isSTEP, isCV, isXDMFHDF5; 5462 PetscMPIInt rank; 5463 5464 PetscFunctionBegin; 5465 PetscValidCharPointer(filename, 2); 5466 if (plexname) PetscValidCharPointer(plexname, 3); 5467 PetscValidPointer(dm, 5); 5468 PetscCall(DMInitializePackage()); 5469 PetscCall(PetscLogEventBegin(DMPLEX_CreateFromFile, 0, 0, 0, 0)); 5470 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 5471 PetscCall(PetscStrlen(filename, &len)); 5472 PetscCheck(len, comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 5473 5474 #define CheckExtension(extension__, is_extension__) \ 5475 do { \ 5476 PetscAssert(sizeof(extension__), comm, PETSC_ERR_PLIB, "Zero-size extension: %s", extension__); \ 5477 /* don't count the null-terminator at the end */ \ 5478 const size_t ext_len = sizeof(extension__) - 1; \ 5479 if (len < ext_len) { \ 5480 is_extension__ = PETSC_FALSE; \ 5481 } else { \ 5482 PetscCall(PetscStrncmp(filename + len - ext_len, extension__, ext_len, &is_extension__)); \ 5483 } \ 5484 } while (0) 5485 5486 CheckExtension(extGmsh, isGmsh); 5487 CheckExtension(extGmsh2, isGmsh2); 5488 CheckExtension(extGmsh4, isGmsh4); 5489 CheckExtension(extCGNS, isCGNS); 5490 CheckExtension(extExodus, isExodus); 5491 if (!isExodus) CheckExtension(extExodus_e, isExodus); 5492 CheckExtension(extGenesis, isGenesis); 5493 CheckExtension(extFluent, isFluent); 5494 CheckExtension(extHDF5, isHDF5); 5495 CheckExtension(extMed, isMed); 5496 CheckExtension(extPLY, isPLY); 5497 CheckExtension(extEGADSLite, isEGADSLite); 5498 CheckExtension(extEGADS, isEGADS); 5499 CheckExtension(extIGES, isIGES); 5500 CheckExtension(extSTEP, isSTEP); 5501 CheckExtension(extCV, isCV); 5502 CheckExtension(extXDMFHDF5, isXDMFHDF5); 5503 5504 #undef CheckExtension 5505 5506 if (isGmsh || isGmsh2 || isGmsh4) { 5507 PetscCall(DMPlexCreateGmshFromFile(comm, filename, interpolate, dm)); 5508 } else if (isCGNS) { 5509 PetscCall(DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm)); 5510 } else if (isExodus || isGenesis) { 5511 PetscCall(DMPlexCreateExodusFromFile(comm, filename, interpolate, dm)); 5512 } else if (isFluent) { 5513 PetscCall(DMPlexCreateFluentFromFile(comm, filename, interpolate, dm)); 5514 } else if (isHDF5) { 5515 PetscViewer viewer; 5516 5517 /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */ 5518 PetscCall(PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &isXDMFHDF5, NULL)); 5519 PetscCall(PetscViewerCreate(comm, &viewer)); 5520 PetscCall(PetscViewerSetType(viewer, PETSCVIEWERHDF5)); 5521 PetscCall(PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_")); 5522 PetscCall(PetscViewerSetFromOptions(viewer)); 5523 PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ)); 5524 PetscCall(PetscViewerFileSetName(viewer, filename)); 5525 5526 PetscCall(DMCreate(comm, dm)); 5527 PetscCall(PetscObjectSetName((PetscObject)(*dm), plexname)); 5528 PetscCall(DMSetType(*dm, DMPLEX)); 5529 if (isXDMFHDF5) PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF)); 5530 PetscCall(DMLoad(*dm, viewer)); 5531 if (isXDMFHDF5) PetscCall(PetscViewerPopFormat(viewer)); 5532 PetscCall(PetscViewerDestroy(&viewer)); 5533 5534 if (interpolate) { 5535 DM idm; 5536 5537 PetscCall(DMPlexInterpolate(*dm, &idm)); 5538 PetscCall(DMDestroy(dm)); 5539 *dm = idm; 5540 } 5541 } else if (isMed) { 5542 PetscCall(DMPlexCreateMedFromFile(comm, filename, interpolate, dm)); 5543 } else if (isPLY) { 5544 PetscCall(DMPlexCreatePLYFromFile(comm, filename, interpolate, dm)); 5545 } else if (isEGADSLite || isEGADS || isIGES || isSTEP) { 5546 if (isEGADSLite) PetscCall(DMPlexCreateEGADSLiteFromFile(comm, filename, dm)); 5547 else PetscCall(DMPlexCreateEGADSFromFile(comm, filename, dm)); 5548 if (!interpolate) { 5549 DM udm; 5550 5551 PetscCall(DMPlexUninterpolate(*dm, &udm)); 5552 PetscCall(DMDestroy(dm)); 5553 *dm = udm; 5554 } 5555 } else if (isCV) { 5556 PetscCall(DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm)); 5557 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 5558 PetscCall(PetscStrlen(plexname, &len)); 5559 if (len) PetscCall(PetscObjectSetName((PetscObject)(*dm), plexname)); 5560 PetscCall(PetscLogEventEnd(DMPLEX_CreateFromFile, 0, 0, 0, 0)); 5561 PetscFunctionReturn(PETSC_SUCCESS); 5562 } 5563 /*@C 5564 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. 5565 5566 Input Parameter: 5567 . tr - The `DMPlexTransform` 5568 5569 Output Parameter: 5570 . dm - The `DM` 5571 5572 Level: beginner 5573 5574 Notes: 5575 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. 5576 5577 .seealso: `DMPlexCreateFromFile`, `DMPlexCreateFromDAG()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()` 5578 @*/ 5579 PetscErrorCode DMPlexCreateEphemeral(DMPlexTransform tr, DM *dm) 5580 { 5581 DM bdm; 5582 PetscInt Nl; 5583 5584 PetscFunctionBegin; 5585 PetscCall(DMCreate(PetscObjectComm((PetscObject)tr), dm)); 5586 PetscCall(DMSetType(*dm, DMPLEX)); 5587 PetscCall(DMSetFromOptions(*dm)); 5588 5589 PetscCall(PetscObjectReference((PetscObject)tr)); 5590 PetscCall(DMPlexTransformDestroy(&((DM_Plex *)(*dm)->data)->tr)); 5591 ((DM_Plex *)(*dm)->data)->tr = tr; 5592 5593 PetscCall(DMPlexTransformGetDM(tr, &bdm)); 5594 PetscCall(DMGetNumLabels(bdm, &Nl)); 5595 for (PetscInt l = 0; l < Nl; ++l) { 5596 DMLabel label, labelNew; 5597 const char *lname; 5598 PetscBool isDepth, isCellType; 5599 5600 PetscCall(DMGetLabelName(bdm, l, &lname)); 5601 PetscCall(PetscStrcmp(lname, "depth", &isDepth)); 5602 if (isDepth) continue; 5603 PetscCall(PetscStrcmp(lname, "celltype", &isCellType)); 5604 if (isCellType) continue; 5605 PetscCall(DMCreateLabel(*dm, lname)); 5606 PetscCall(DMGetLabel(bdm, lname, &label)); 5607 PetscCall(DMGetLabel(*dm, lname, &labelNew)); 5608 PetscCall(DMLabelSetType(labelNew, DMLABELEPHEMERAL)); 5609 PetscCall(DMLabelEphemeralSetLabel(labelNew, label)); 5610 PetscCall(DMLabelEphemeralSetTransform(labelNew, tr)); 5611 PetscCall(DMLabelSetUp(labelNew)); 5612 } 5613 PetscFunctionReturn(PETSC_SUCCESS); 5614 } 5615