1 #define PETSCDM_DLL 2 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 #include <petsc/private/hashseti.h> 4 #include <petscsf.h> 5 #include <petscdmplextransform.h> /*I "petscdmplextransform.h" I*/ 6 #include <petscdmlabelephemeral.h> 7 #include <petsc/private/kernels/blockmatmult.h> 8 #include <petsc/private/kernels/blockinvert.h> 9 10 #ifdef PETSC_HAVE_UNISTD_H 11 #include <unistd.h> 12 #endif 13 #include <errno.h> 14 15 PetscLogEvent DMPLEX_CreateFromFile, DMPLEX_CreateFromOptions, DMPLEX_BuildFromCellList, DMPLEX_BuildCoordinatesFromCellList; 16 17 /* External function declarations here */ 18 static PetscErrorCode DMInitialize_Plex(DM dm); 19 20 /* This copies internal things in the Plex structure that we generally want when making a new, related Plex */ 21 PetscErrorCode DMPlexCopy_Internal(DM dmin, PetscBool copyPeriodicity, PetscBool copyOverlap, DM dmout) 22 { 23 const PetscReal *maxCell, *Lstart, *L; 24 VecType vecType; 25 MatType matType; 26 PetscBool dist, useCeed; 27 DMReorderDefaultFlag reorder; 28 29 PetscFunctionBegin; 30 PetscCall(DMGetVecType(dmin, &vecType)); 31 PetscCall(DMSetVecType(dmout, vecType)); 32 PetscCall(DMGetMatType(dmin, &matType)); 33 PetscCall(DMSetMatType(dmout, matType)); 34 if (copyPeriodicity) { 35 PetscCall(DMGetPeriodicity(dmin, &maxCell, &Lstart, &L)); 36 PetscCall(DMSetPeriodicity(dmout, maxCell, Lstart, L)); 37 PetscCall(DMLocalizeCoordinates(dmout)); 38 } 39 PetscCall(DMPlexDistributeGetDefault(dmin, &dist)); 40 PetscCall(DMPlexDistributeSetDefault(dmout, dist)); 41 PetscCall(DMPlexReorderGetDefault(dmin, &reorder)); 42 PetscCall(DMPlexReorderSetDefault(dmout, reorder)); 43 PetscCall(DMPlexGetUseCeed(dmin, &useCeed)); 44 PetscCall(DMPlexSetUseCeed(dmout, useCeed)); 45 ((DM_Plex *)dmout->data)->useHashLocation = ((DM_Plex *)dmin->data)->useHashLocation; 46 ((DM_Plex *)dmout->data)->printSetValues = ((DM_Plex *)dmin->data)->printSetValues; 47 ((DM_Plex *)dmout->data)->printFEM = ((DM_Plex *)dmin->data)->printFEM; 48 ((DM_Plex *)dmout->data)->printFVM = ((DM_Plex *)dmin->data)->printFVM; 49 ((DM_Plex *)dmout->data)->printL2 = ((DM_Plex *)dmin->data)->printL2; 50 ((DM_Plex *)dmout->data)->printLocate = ((DM_Plex *)dmin->data)->printLocate; 51 ((DM_Plex *)dmout->data)->printTol = ((DM_Plex *)dmin->data)->printTol; 52 if (copyOverlap) PetscCall(DMPlexSetOverlap_Plex(dmout, dmin, 0)); 53 PetscFunctionReturn(PETSC_SUCCESS); 54 } 55 56 /* Replace dm with the contents of ndm, and then destroy ndm 57 - Share the DM_Plex structure 58 - Share the coordinates 59 - Share the SF 60 */ 61 PetscErrorCode DMPlexReplace_Internal(DM dm, DM *ndm) 62 { 63 PetscSF sf; 64 DM dmNew = *ndm, coordDM, coarseDM; 65 Vec coords; 66 const PetscReal *maxCell, *Lstart, *L; 67 PetscInt dim, cdim; 68 69 PetscFunctionBegin; 70 if (dm == dmNew) { 71 PetscCall(DMDestroy(ndm)); 72 PetscFunctionReturn(PETSC_SUCCESS); 73 } 74 dm->setupcalled = dmNew->setupcalled; 75 if (!dm->hdr.name) { 76 const char *name; 77 78 PetscCall(PetscObjectGetName((PetscObject)*ndm, &name)); 79 PetscCall(PetscObjectSetName((PetscObject)dm, name)); 80 } 81 PetscCall(DMGetDimension(dmNew, &dim)); 82 PetscCall(DMSetDimension(dm, dim)); 83 PetscCall(DMGetCoordinateDim(dmNew, &cdim)); 84 PetscCall(DMSetCoordinateDim(dm, cdim)); 85 PetscCall(DMGetPointSF(dmNew, &sf)); 86 PetscCall(DMSetPointSF(dm, sf)); 87 PetscCall(DMGetCoordinateDM(dmNew, &coordDM)); 88 PetscCall(DMGetCoordinatesLocal(dmNew, &coords)); 89 PetscCall(DMSetCoordinateDM(dm, coordDM)); 90 PetscCall(DMSetCoordinatesLocal(dm, coords)); 91 PetscCall(DMGetCellCoordinateDM(dmNew, &coordDM)); 92 PetscCall(DMGetCellCoordinatesLocal(dmNew, &coords)); 93 PetscCall(DMSetCellCoordinateDM(dm, coordDM)); 94 PetscCall(DMSetCellCoordinatesLocal(dm, coords)); 95 /* Do not want to create the coordinate field if it does not already exist, so do not call DMGetCoordinateField() */ 96 PetscCall(DMFieldDestroy(&dm->coordinates[0].field)); 97 dm->coordinates[0].field = dmNew->coordinates[0].field; 98 ((DM_Plex *)dmNew->data)->coordFunc = ((DM_Plex *)dm->data)->coordFunc; 99 PetscCall(DMGetPeriodicity(dmNew, &maxCell, &Lstart, &L)); 100 PetscCall(DMSetPeriodicity(dm, maxCell, Lstart, L)); 101 PetscCall(DMPlexGetGlobalToNaturalSF(dmNew, &sf)); 102 PetscCall(DMPlexSetGlobalToNaturalSF(dm, sf)); 103 PetscCall(DMDestroy_Plex(dm)); 104 PetscCall(DMInitialize_Plex(dm)); 105 dm->data = dmNew->data; 106 ((DM_Plex *)dmNew->data)->refct++; 107 { 108 PetscInt num_face_sfs; 109 const PetscSF *sfs; 110 PetscCall(DMPlexGetIsoperiodicFaceSF(dm, &num_face_sfs, &sfs)); 111 PetscCall(DMPlexSetIsoperiodicFaceSF(dm, num_face_sfs, (PetscSF *)sfs)); // for the compose function effect on dm 112 } 113 PetscCall(DMDestroyLabelLinkList_Internal(dm)); 114 PetscCall(DMCopyLabels(dmNew, dm, PETSC_OWN_POINTER, PETSC_TRUE, DM_COPY_LABELS_FAIL)); 115 PetscCall(DMGetCoarseDM(dmNew, &coarseDM)); 116 PetscCall(DMSetCoarseDM(dm, coarseDM)); 117 PetscCall(DMDestroy(ndm)); 118 PetscFunctionReturn(PETSC_SUCCESS); 119 } 120 121 /* Swap dm with the contents of dmNew 122 - Swap the DM_Plex structure 123 - Swap the coordinates 124 - Swap the point PetscSF 125 */ 126 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 127 { 128 DM coordDMA, coordDMB; 129 Vec coordsA, coordsB; 130 PetscSF sfA, sfB; 131 DMField fieldTmp; 132 void *tmp; 133 DMLabelLink listTmp; 134 DMLabel depthTmp; 135 PetscInt tmpI; 136 137 PetscFunctionBegin; 138 if (dmA == dmB) PetscFunctionReturn(PETSC_SUCCESS); 139 PetscCall(DMGetPointSF(dmA, &sfA)); 140 PetscCall(DMGetPointSF(dmB, &sfB)); 141 PetscCall(PetscObjectReference((PetscObject)sfA)); 142 PetscCall(DMSetPointSF(dmA, sfB)); 143 PetscCall(DMSetPointSF(dmB, sfA)); 144 PetscCall(PetscObjectDereference((PetscObject)sfA)); 145 146 PetscCall(DMGetCoordinateDM(dmA, &coordDMA)); 147 PetscCall(DMGetCoordinateDM(dmB, &coordDMB)); 148 PetscCall(PetscObjectReference((PetscObject)coordDMA)); 149 PetscCall(DMSetCoordinateDM(dmA, coordDMB)); 150 PetscCall(DMSetCoordinateDM(dmB, coordDMA)); 151 PetscCall(PetscObjectDereference((PetscObject)coordDMA)); 152 153 PetscCall(DMGetCoordinatesLocal(dmA, &coordsA)); 154 PetscCall(DMGetCoordinatesLocal(dmB, &coordsB)); 155 PetscCall(PetscObjectReference((PetscObject)coordsA)); 156 PetscCall(DMSetCoordinatesLocal(dmA, coordsB)); 157 PetscCall(DMSetCoordinatesLocal(dmB, coordsA)); 158 PetscCall(PetscObjectDereference((PetscObject)coordsA)); 159 160 PetscCall(DMGetCellCoordinateDM(dmA, &coordDMA)); 161 PetscCall(DMGetCellCoordinateDM(dmB, &coordDMB)); 162 PetscCall(PetscObjectReference((PetscObject)coordDMA)); 163 PetscCall(DMSetCellCoordinateDM(dmA, coordDMB)); 164 PetscCall(DMSetCellCoordinateDM(dmB, coordDMA)); 165 PetscCall(PetscObjectDereference((PetscObject)coordDMA)); 166 167 PetscCall(DMGetCellCoordinatesLocal(dmA, &coordsA)); 168 PetscCall(DMGetCellCoordinatesLocal(dmB, &coordsB)); 169 PetscCall(PetscObjectReference((PetscObject)coordsA)); 170 PetscCall(DMSetCellCoordinatesLocal(dmA, coordsB)); 171 PetscCall(DMSetCellCoordinatesLocal(dmB, coordsA)); 172 PetscCall(PetscObjectDereference((PetscObject)coordsA)); 173 174 fieldTmp = dmA->coordinates[0].field; 175 dmA->coordinates[0].field = dmB->coordinates[0].field; 176 dmB->coordinates[0].field = fieldTmp; 177 fieldTmp = dmA->coordinates[1].field; 178 dmA->coordinates[1].field = dmB->coordinates[1].field; 179 dmB->coordinates[1].field = fieldTmp; 180 tmp = dmA->data; 181 dmA->data = dmB->data; 182 dmB->data = tmp; 183 listTmp = dmA->labels; 184 dmA->labels = dmB->labels; 185 dmB->labels = listTmp; 186 depthTmp = dmA->depthLabel; 187 dmA->depthLabel = dmB->depthLabel; 188 dmB->depthLabel = depthTmp; 189 depthTmp = dmA->celltypeLabel; 190 dmA->celltypeLabel = dmB->celltypeLabel; 191 dmB->celltypeLabel = depthTmp; 192 tmpI = dmA->levelup; 193 dmA->levelup = dmB->levelup; 194 dmB->levelup = tmpI; 195 PetscFunctionReturn(PETSC_SUCCESS); 196 } 197 198 PetscErrorCode DMPlexInterpolateInPlace_Internal(DM dm) 199 { 200 DM idm; 201 202 PetscFunctionBegin; 203 PetscCall(DMPlexInterpolate(dm, &idm)); 204 PetscCall(DMPlexCopyCoordinates(dm, idm)); 205 PetscCall(DMPlexReplace_Internal(dm, &idm)); 206 PetscFunctionReturn(PETSC_SUCCESS); 207 } 208 209 /*@C 210 DMPlexCreateCoordinateSpace - Creates a finite element space for the coordinates 211 212 Collective 213 214 Input Parameters: 215 + dm - The `DMPLEX` 216 . degree - The degree of the finite element or `PETSC_DECIDE` 217 . project - Flag to project current coordinates into the space 218 - coordFunc - An optional function to map new points from refinement to the surface 219 220 Level: advanced 221 222 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `PetscPointFunc`, `PetscFECreateLagrange()`, `DMGetCoordinateDM()` 223 @*/ 224 PetscErrorCode DMPlexCreateCoordinateSpace(DM dm, PetscInt degree, PetscBool project, PetscPointFunc coordFunc) 225 { 226 DM_Plex *mesh = (DM_Plex *)dm->data; 227 PetscFE fe = NULL; 228 DM cdm; 229 PetscInt dim, dE, qorder, height; 230 231 PetscFunctionBegin; 232 PetscCall(DMGetDimension(dm, &dim)); 233 PetscCall(DMGetCoordinateDim(dm, &dE)); 234 qorder = degree; 235 PetscCall(DMGetCoordinateDM(dm, &cdm)); 236 PetscObjectOptionsBegin((PetscObject)cdm); 237 PetscCall(PetscOptionsBoundedInt("-default_quadrature_order", "Quadrature order is one less than quadrature points per edge", "DMPlexCreateCoordinateSpace", qorder, &qorder, NULL, 0)); 238 PetscOptionsEnd(); 239 PetscCall(DMPlexGetVTKCellHeight(dm, &height)); 240 if (degree >= 0) { 241 DMPolytopeType ct = DM_POLYTOPE_UNKNOWN; 242 PetscInt cStart, cEnd, gct; 243 244 PetscCall(DMPlexGetHeightStratum(dm, height, &cStart, &cEnd)); 245 if (cEnd > cStart) PetscCall(DMPlexGetCellType(dm, cStart, &ct)); 246 gct = (PetscInt)ct; 247 PetscCall(MPIU_Allreduce(MPI_IN_PLACE, &gct, 1, MPIU_INT, MPI_MIN, PetscObjectComm((PetscObject)dm))); 248 ct = (DMPolytopeType)gct; 249 // Work around current bug in PetscDualSpaceSetUp_Lagrange() 250 // Can be seen in plex_tutorials-ex10_1 251 if (ct != DM_POLYTOPE_SEG_PRISM_TENSOR && ct != DM_POLYTOPE_TRI_PRISM_TENSOR && ct != DM_POLYTOPE_QUAD_PRISM_TENSOR) PetscCall(PetscFECreateLagrangeByCell(PETSC_COMM_SELF, dim, dE, ct, degree, qorder, &fe)); 252 } 253 PetscCall(DMSetCoordinateDisc(dm, fe, project)); 254 PetscCall(PetscFEDestroy(&fe)); 255 mesh->coordFunc = coordFunc; 256 PetscFunctionReturn(PETSC_SUCCESS); 257 } 258 259 /*@ 260 DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement. 261 262 Collective 263 264 Input Parameters: 265 + comm - The communicator for the `DM` object 266 . dim - The spatial dimension 267 . simplex - Flag for simplicial cells, otherwise they are tensor product cells 268 . interpolate - Flag to create intermediate mesh pieces (edges, faces) 269 - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell 270 271 Output Parameter: 272 . newdm - The `DM` object 273 274 Level: beginner 275 276 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMSetType()`, `DMCreate()` 277 @*/ 278 PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscReal refinementLimit, DM *newdm) 279 { 280 DM dm; 281 PetscMPIInt rank; 282 283 PetscFunctionBegin; 284 PetscCall(DMCreate(comm, &dm)); 285 PetscCall(DMSetType(dm, DMPLEX)); 286 PetscCall(DMSetDimension(dm, dim)); 287 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 288 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 289 switch (dim) { 290 case 2: 291 if (simplex) PetscCall(PetscObjectSetName((PetscObject)dm, "triangular")); 292 else PetscCall(PetscObjectSetName((PetscObject)dm, "quadrilateral")); 293 break; 294 case 3: 295 if (simplex) PetscCall(PetscObjectSetName((PetscObject)dm, "tetrahedral")); 296 else PetscCall(PetscObjectSetName((PetscObject)dm, "hexahedral")); 297 break; 298 default: 299 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %" PetscInt_FMT, dim); 300 } 301 if (rank) { 302 PetscInt numPoints[2] = {0, 0}; 303 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL)); 304 } else { 305 switch (dim) { 306 case 2: 307 if (simplex) { 308 PetscInt numPoints[2] = {4, 2}; 309 PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; 310 PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; 311 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 312 PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5}; 313 314 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 315 } else { 316 PetscInt numPoints[2] = {6, 2}; 317 PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; 318 PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4}; 319 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 320 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}; 321 322 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 323 } 324 break; 325 case 3: 326 if (simplex) { 327 PetscInt numPoints[2] = {5, 2}; 328 PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; 329 PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; 330 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 331 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}; 332 333 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 334 } else { 335 PetscInt numPoints[2] = {12, 2}; 336 PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 337 PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8}; 338 PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 339 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}; 340 341 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 342 } 343 break; 344 default: 345 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %" PetscInt_FMT, dim); 346 } 347 } 348 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 349 *newdm = dm; 350 if (refinementLimit > 0.0) { 351 DM rdm; 352 const char *name; 353 354 PetscCall(DMPlexSetRefinementUniform(*newdm, PETSC_FALSE)); 355 PetscCall(DMPlexSetRefinementLimit(*newdm, refinementLimit)); 356 PetscCall(DMRefine(*newdm, comm, &rdm)); 357 PetscCall(PetscObjectGetName((PetscObject)*newdm, &name)); 358 PetscCall(PetscObjectSetName((PetscObject)rdm, name)); 359 PetscCall(DMDestroy(newdm)); 360 *newdm = rdm; 361 } 362 if (interpolate) { 363 DM idm; 364 365 PetscCall(DMPlexInterpolate(*newdm, &idm)); 366 PetscCall(DMDestroy(newdm)); 367 *newdm = idm; 368 } 369 PetscFunctionReturn(PETSC_SUCCESS); 370 } 371 372 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 373 { 374 const PetscInt numVertices = 2; 375 PetscInt markerRight = 1; 376 PetscInt markerLeft = 1; 377 PetscBool markerSeparate = PETSC_FALSE; 378 Vec coordinates; 379 PetscSection coordSection; 380 PetscScalar *coords; 381 PetscInt coordSize; 382 PetscMPIInt rank; 383 PetscInt cdim = 1, v; 384 385 PetscFunctionBegin; 386 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL)); 387 if (markerSeparate) { 388 markerRight = 2; 389 markerLeft = 1; 390 } 391 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 392 if (rank == 0) { 393 PetscCall(DMPlexSetChart(dm, 0, numVertices)); 394 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 395 PetscCall(DMSetLabelValue(dm, "marker", 0, markerLeft)); 396 PetscCall(DMSetLabelValue(dm, "marker", 1, markerRight)); 397 } 398 PetscCall(DMPlexSymmetrize(dm)); 399 PetscCall(DMPlexStratify(dm)); 400 /* Build coordinates */ 401 PetscCall(DMSetCoordinateDim(dm, cdim)); 402 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 403 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 404 PetscCall(PetscSectionSetChart(coordSection, 0, numVertices)); 405 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, cdim)); 406 for (v = 0; v < numVertices; ++v) { 407 PetscCall(PetscSectionSetDof(coordSection, v, cdim)); 408 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, cdim)); 409 } 410 PetscCall(PetscSectionSetUp(coordSection)); 411 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 412 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 413 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 414 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 415 PetscCall(VecSetBlockSize(coordinates, cdim)); 416 PetscCall(VecSetType(coordinates, VECSTANDARD)); 417 PetscCall(VecGetArray(coordinates, &coords)); 418 coords[0] = lower[0]; 419 coords[1] = upper[0]; 420 PetscCall(VecRestoreArray(coordinates, &coords)); 421 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 422 PetscCall(VecDestroy(&coordinates)); 423 PetscFunctionReturn(PETSC_SUCCESS); 424 } 425 426 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 427 { 428 const PetscInt numVertices = (edges[0] + 1) * (edges[1] + 1); 429 const PetscInt numEdges = edges[0] * (edges[1] + 1) + (edges[0] + 1) * edges[1]; 430 PetscInt markerTop = 1; 431 PetscInt markerBottom = 1; 432 PetscInt markerRight = 1; 433 PetscInt markerLeft = 1; 434 PetscBool markerSeparate = PETSC_FALSE; 435 Vec coordinates; 436 PetscSection coordSection; 437 PetscScalar *coords; 438 PetscInt coordSize; 439 PetscMPIInt rank; 440 PetscInt v, vx, vy; 441 442 PetscFunctionBegin; 443 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL)); 444 if (markerSeparate) { 445 markerTop = 3; 446 markerBottom = 1; 447 markerRight = 2; 448 markerLeft = 4; 449 } 450 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 451 if (rank == 0) { 452 PetscInt e, ex, ey; 453 454 PetscCall(DMPlexSetChart(dm, 0, numEdges + numVertices)); 455 for (e = 0; e < numEdges; ++e) PetscCall(DMPlexSetConeSize(dm, e, 2)); 456 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 457 for (vx = 0; vx <= edges[0]; vx++) { 458 for (ey = 0; ey < edges[1]; ey++) { 459 PetscInt edge = vx * edges[1] + ey + edges[0] * (edges[1] + 1); 460 PetscInt vertex = ey * (edges[0] + 1) + vx + numEdges; 461 PetscInt cone[2]; 462 463 cone[0] = vertex; 464 cone[1] = vertex + edges[0] + 1; 465 PetscCall(DMPlexSetCone(dm, edge, cone)); 466 if (vx == edges[0]) { 467 PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight)); 468 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight)); 469 if (ey == edges[1] - 1) { 470 PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight)); 471 PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerRight)); 472 } 473 } else if (vx == 0) { 474 PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft)); 475 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft)); 476 if (ey == edges[1] - 1) { 477 PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft)); 478 PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft)); 479 } 480 } 481 } 482 } 483 for (vy = 0; vy <= edges[1]; vy++) { 484 for (ex = 0; ex < edges[0]; ex++) { 485 PetscInt edge = vy * edges[0] + ex; 486 PetscInt vertex = vy * (edges[0] + 1) + ex + numEdges; 487 PetscInt cone[2]; 488 489 cone[0] = vertex; 490 cone[1] = vertex + 1; 491 PetscCall(DMPlexSetCone(dm, edge, cone)); 492 if (vy == edges[1]) { 493 PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop)); 494 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop)); 495 if (ex == edges[0] - 1) { 496 PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop)); 497 PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerTop)); 498 } 499 } else if (vy == 0) { 500 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom)); 501 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom)); 502 if (ex == edges[0] - 1) { 503 PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom)); 504 PetscCall(DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom)); 505 } 506 } 507 } 508 } 509 } 510 PetscCall(DMPlexSymmetrize(dm)); 511 PetscCall(DMPlexStratify(dm)); 512 /* Build coordinates */ 513 PetscCall(DMSetCoordinateDim(dm, 2)); 514 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 515 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 516 PetscCall(PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices)); 517 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, 2)); 518 for (v = numEdges; v < numEdges + numVertices; ++v) { 519 PetscCall(PetscSectionSetDof(coordSection, v, 2)); 520 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, 2)); 521 } 522 PetscCall(PetscSectionSetUp(coordSection)); 523 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 524 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 525 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 526 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 527 PetscCall(VecSetBlockSize(coordinates, 2)); 528 PetscCall(VecSetType(coordinates, VECSTANDARD)); 529 PetscCall(VecGetArray(coordinates, &coords)); 530 for (vy = 0; vy <= edges[1]; ++vy) { 531 for (vx = 0; vx <= edges[0]; ++vx) { 532 coords[(vy * (edges[0] + 1) + vx) * 2 + 0] = lower[0] + ((upper[0] - lower[0]) / edges[0]) * vx; 533 coords[(vy * (edges[0] + 1) + vx) * 2 + 1] = lower[1] + ((upper[1] - lower[1]) / edges[1]) * vy; 534 } 535 } 536 PetscCall(VecRestoreArray(coordinates, &coords)); 537 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 538 PetscCall(VecDestroy(&coordinates)); 539 PetscFunctionReturn(PETSC_SUCCESS); 540 } 541 542 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) 543 { 544 PetscInt vertices[3], numVertices; 545 PetscInt numFaces = 2 * faces[0] * faces[1] + 2 * faces[1] * faces[2] + 2 * faces[0] * faces[2]; 546 PetscInt markerTop = 1; 547 PetscInt markerBottom = 1; 548 PetscInt markerFront = 1; 549 PetscInt markerBack = 1; 550 PetscInt markerRight = 1; 551 PetscInt markerLeft = 1; 552 PetscBool markerSeparate = PETSC_FALSE; 553 Vec coordinates; 554 PetscSection coordSection; 555 PetscScalar *coords; 556 PetscInt coordSize; 557 PetscMPIInt rank; 558 PetscInt v, vx, vy, vz; 559 PetscInt voffset, iface = 0, cone[4]; 560 561 PetscFunctionBegin; 562 PetscCheck(faces[0] >= 1 && faces[1] >= 1 && faces[2] >= 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Must have at least 1 face per side"); 563 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 564 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL)); 565 if (markerSeparate) { 566 markerBottom = 1; 567 markerTop = 2; 568 markerFront = 3; 569 markerBack = 4; 570 markerRight = 5; 571 markerLeft = 6; 572 } 573 vertices[0] = faces[0] + 1; 574 vertices[1] = faces[1] + 1; 575 vertices[2] = faces[2] + 1; 576 numVertices = vertices[0] * vertices[1] * vertices[2]; 577 if (rank == 0) { 578 PetscInt f; 579 580 PetscCall(DMPlexSetChart(dm, 0, numFaces + numVertices)); 581 for (f = 0; f < numFaces; ++f) PetscCall(DMPlexSetConeSize(dm, f, 4)); 582 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 583 584 /* Side 0 (Top) */ 585 for (vy = 0; vy < faces[1]; vy++) { 586 for (vx = 0; vx < faces[0]; vx++) { 587 voffset = numFaces + vertices[0] * vertices[1] * (vertices[2] - 1) + vy * vertices[0] + vx; 588 cone[0] = voffset; 589 cone[1] = voffset + 1; 590 cone[2] = voffset + vertices[0] + 1; 591 cone[3] = voffset + vertices[0]; 592 PetscCall(DMPlexSetCone(dm, iface, cone)); 593 PetscCall(DMSetLabelValue(dm, "marker", iface, markerTop)); 594 PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerTop)); 595 PetscCall(DMSetLabelValue(dm, "marker", voffset + 1, markerTop)); 596 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 0, markerTop)); 597 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 1, markerTop)); 598 iface++; 599 } 600 } 601 602 /* Side 1 (Bottom) */ 603 for (vy = 0; vy < faces[1]; vy++) { 604 for (vx = 0; vx < faces[0]; vx++) { 605 voffset = numFaces + vy * (faces[0] + 1) + vx; 606 cone[0] = voffset + 1; 607 cone[1] = voffset; 608 cone[2] = voffset + vertices[0]; 609 cone[3] = voffset + vertices[0] + 1; 610 PetscCall(DMPlexSetCone(dm, iface, cone)); 611 PetscCall(DMSetLabelValue(dm, "marker", iface, markerBottom)); 612 PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerBottom)); 613 PetscCall(DMSetLabelValue(dm, "marker", voffset + 1, markerBottom)); 614 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 0, markerBottom)); 615 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 1, markerBottom)); 616 iface++; 617 } 618 } 619 620 /* Side 2 (Front) */ 621 for (vz = 0; vz < faces[2]; vz++) { 622 for (vx = 0; vx < faces[0]; vx++) { 623 voffset = numFaces + vz * vertices[0] * vertices[1] + vx; 624 cone[0] = voffset; 625 cone[1] = voffset + 1; 626 cone[2] = voffset + vertices[0] * vertices[1] + 1; 627 cone[3] = voffset + vertices[0] * vertices[1]; 628 PetscCall(DMPlexSetCone(dm, iface, cone)); 629 PetscCall(DMSetLabelValue(dm, "marker", iface, markerFront)); 630 PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerFront)); 631 PetscCall(DMSetLabelValue(dm, "marker", voffset + 1, markerFront)); 632 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 0, markerFront)); 633 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 1, markerFront)); 634 iface++; 635 } 636 } 637 638 /* Side 3 (Back) */ 639 for (vz = 0; vz < faces[2]; vz++) { 640 for (vx = 0; vx < faces[0]; vx++) { 641 voffset = numFaces + vz * vertices[0] * vertices[1] + vertices[0] * (vertices[1] - 1) + vx; 642 cone[0] = voffset + vertices[0] * vertices[1]; 643 cone[1] = voffset + vertices[0] * vertices[1] + 1; 644 cone[2] = voffset + 1; 645 cone[3] = voffset; 646 PetscCall(DMPlexSetCone(dm, iface, cone)); 647 PetscCall(DMSetLabelValue(dm, "marker", iface, markerBack)); 648 PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerBack)); 649 PetscCall(DMSetLabelValue(dm, "marker", voffset + 1, markerBack)); 650 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 0, markerBack)); 651 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 1, markerBack)); 652 iface++; 653 } 654 } 655 656 /* Side 4 (Left) */ 657 for (vz = 0; vz < faces[2]; vz++) { 658 for (vy = 0; vy < faces[1]; vy++) { 659 voffset = numFaces + vz * vertices[0] * vertices[1] + vy * vertices[0]; 660 cone[0] = voffset; 661 cone[1] = voffset + vertices[0] * vertices[1]; 662 cone[2] = voffset + vertices[0] * vertices[1] + vertices[0]; 663 cone[3] = voffset + vertices[0]; 664 PetscCall(DMPlexSetCone(dm, iface, cone)); 665 PetscCall(DMSetLabelValue(dm, "marker", iface, markerLeft)); 666 PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerLeft)); 667 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 0, markerLeft)); 668 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[1] + 0, markerLeft)); 669 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + vertices[0], markerLeft)); 670 iface++; 671 } 672 } 673 674 /* Side 5 (Right) */ 675 for (vz = 0; vz < faces[2]; vz++) { 676 for (vy = 0; vy < faces[1]; vy++) { 677 voffset = numFaces + vz * vertices[0] * vertices[1] + vy * vertices[0] + faces[0]; 678 cone[0] = voffset + vertices[0] * vertices[1]; 679 cone[1] = voffset; 680 cone[2] = voffset + vertices[0]; 681 cone[3] = voffset + vertices[0] * vertices[1] + vertices[0]; 682 PetscCall(DMPlexSetCone(dm, iface, cone)); 683 PetscCall(DMSetLabelValue(dm, "marker", iface, markerRight)); 684 PetscCall(DMSetLabelValue(dm, "marker", voffset + 0, markerRight)); 685 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] + 0, markerRight)); 686 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + 0, markerRight)); 687 PetscCall(DMSetLabelValue(dm, "marker", voffset + vertices[0] * vertices[1] + vertices[0], markerRight)); 688 iface++; 689 } 690 } 691 } 692 PetscCall(DMPlexSymmetrize(dm)); 693 PetscCall(DMPlexStratify(dm)); 694 /* Build coordinates */ 695 PetscCall(DMSetCoordinateDim(dm, 3)); 696 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 697 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 698 PetscCall(PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices)); 699 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, 3)); 700 for (v = numFaces; v < numFaces + numVertices; ++v) { 701 PetscCall(PetscSectionSetDof(coordSection, v, 3)); 702 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, 3)); 703 } 704 PetscCall(PetscSectionSetUp(coordSection)); 705 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 706 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 707 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 708 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 709 PetscCall(VecSetBlockSize(coordinates, 3)); 710 PetscCall(VecSetType(coordinates, VECSTANDARD)); 711 PetscCall(VecGetArray(coordinates, &coords)); 712 for (vz = 0; vz <= faces[2]; ++vz) { 713 for (vy = 0; vy <= faces[1]; ++vy) { 714 for (vx = 0; vx <= faces[0]; ++vx) { 715 coords[((vz * (faces[1] + 1) + vy) * (faces[0] + 1) + vx) * 3 + 0] = lower[0] + ((upper[0] - lower[0]) / faces[0]) * vx; 716 coords[((vz * (faces[1] + 1) + vy) * (faces[0] + 1) + vx) * 3 + 1] = lower[1] + ((upper[1] - lower[1]) / faces[1]) * vy; 717 coords[((vz * (faces[1] + 1) + vy) * (faces[0] + 1) + vx) * 3 + 2] = lower[2] + ((upper[2] - lower[2]) / faces[2]) * vz; 718 } 719 } 720 } 721 PetscCall(VecRestoreArray(coordinates, &coords)); 722 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 723 PetscCall(VecDestroy(&coordinates)); 724 PetscFunctionReturn(PETSC_SUCCESS); 725 } 726 727 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate) 728 { 729 PetscFunctionBegin; 730 PetscValidLogicalCollectiveInt(dm, dim, 2); 731 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 732 PetscCall(DMSetDimension(dm, dim - 1)); 733 PetscCall(DMSetCoordinateDim(dm, dim)); 734 switch (dim) { 735 case 1: 736 PetscCall(DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(dm, lower, upper, faces)); 737 break; 738 case 2: 739 PetscCall(DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(dm, lower, upper, faces)); 740 break; 741 case 3: 742 PetscCall(DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(dm, lower, upper, faces)); 743 break; 744 default: 745 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Dimension not supported: %" PetscInt_FMT, dim); 746 } 747 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 748 if (interpolate) PetscCall(DMPlexInterpolateInPlace_Internal(dm)); 749 PetscFunctionReturn(PETSC_SUCCESS); 750 } 751 752 /*@C 753 DMPlexCreateBoxSurfaceMesh - Creates a mesh on the surface of the tensor product of unit intervals (box) using tensor cells (hexahedra). 754 755 Collective 756 757 Input Parameters: 758 + comm - The communicator for the `DM` object 759 . dim - The spatial dimension of the box, so the resulting mesh is has dimension `dim`-1 760 . faces - Number of faces per dimension, or `NULL` for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 761 . lower - The lower left corner, or `NULL` for (0, 0, 0) 762 . upper - The upper right corner, or `NULL` for (1, 1, 1) 763 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 764 765 Output Parameter: 766 . dm - The `DM` object 767 768 Level: beginner 769 770 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMSetFromOptions()`, `DMPlexCreateBoxMesh()`, `DMPlexCreateFromFile()`, `DMSetType()`, `DMCreate()` 771 @*/ 772 PetscErrorCode DMPlexCreateBoxSurfaceMesh(MPI_Comm comm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate, DM *dm) 773 { 774 PetscInt fac[3] = {1, 1, 1}; 775 PetscReal low[3] = {0, 0, 0}; 776 PetscReal upp[3] = {1, 1, 1}; 777 778 PetscFunctionBegin; 779 PetscCall(DMCreate(comm, dm)); 780 PetscCall(DMSetType(*dm, DMPLEX)); 781 PetscCall(DMPlexCreateBoxSurfaceMesh_Internal(*dm, dim, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, interpolate)); 782 PetscFunctionReturn(PETSC_SUCCESS); 783 } 784 785 static PetscErrorCode DMPlexCreateLineMesh_Internal(DM dm, PetscInt segments, PetscReal lower, PetscReal upper, DMBoundaryType bd) 786 { 787 PetscInt i, fStart, fEnd, numCells = 0, numVerts = 0; 788 PetscInt numPoints[2], *coneSize, *cones, *coneOrientations; 789 PetscScalar *vertexCoords; 790 PetscReal L, maxCell; 791 PetscBool markerSeparate = PETSC_FALSE; 792 PetscInt markerLeft = 1, faceMarkerLeft = 1; 793 PetscInt markerRight = 1, faceMarkerRight = 2; 794 PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE; 795 PetscMPIInt rank; 796 797 PetscFunctionBegin; 798 PetscAssertPointer(dm, 1); 799 800 PetscCall(DMSetDimension(dm, 1)); 801 PetscCall(DMCreateLabel(dm, "marker")); 802 PetscCall(DMCreateLabel(dm, "Face Sets")); 803 804 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 805 if (rank == 0) numCells = segments; 806 if (rank == 0) numVerts = segments + (wrap ? 0 : 1); 807 808 numPoints[0] = numVerts; 809 numPoints[1] = numCells; 810 PetscCall(PetscMalloc4(numCells + numVerts, &coneSize, numCells * 2, &cones, numCells + numVerts, &coneOrientations, numVerts, &vertexCoords)); 811 PetscCall(PetscArrayzero(coneOrientations, numCells + numVerts)); 812 for (i = 0; i < numCells; ++i) coneSize[i] = 2; 813 for (i = 0; i < numVerts; ++i) coneSize[numCells + i] = 0; 814 for (i = 0; i < numCells; ++i) { 815 cones[2 * i] = numCells + i % numVerts; 816 cones[2 * i + 1] = numCells + (i + 1) % numVerts; 817 } 818 for (i = 0; i < numVerts; ++i) vertexCoords[i] = lower + (upper - lower) * ((PetscReal)i / (PetscReal)numCells); 819 PetscCall(DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 820 PetscCall(PetscFree4(coneSize, cones, coneOrientations, vertexCoords)); 821 822 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL)); 823 if (markerSeparate) { 824 markerLeft = faceMarkerLeft; 825 markerRight = faceMarkerRight; 826 } 827 if (!wrap && rank == 0) { 828 PetscCall(DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd)); 829 PetscCall(DMSetLabelValue(dm, "marker", fStart, markerLeft)); 830 PetscCall(DMSetLabelValue(dm, "marker", fEnd - 1, markerRight)); 831 PetscCall(DMSetLabelValue(dm, "Face Sets", fStart, faceMarkerLeft)); 832 PetscCall(DMSetLabelValue(dm, "Face Sets", fEnd - 1, faceMarkerRight)); 833 } 834 if (wrap) { 835 L = upper - lower; 836 maxCell = (PetscReal)1.1 * (L / (PetscReal)PetscMax(1, segments)); 837 PetscCall(DMSetPeriodicity(dm, &maxCell, &lower, &L)); 838 } 839 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 840 PetscFunctionReturn(PETSC_SUCCESS); 841 } 842 843 static PetscErrorCode DMPlexCreateBoxMesh_Simplex_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate) 844 { 845 DM boundary, vol; 846 DMLabel bdlabel; 847 848 PetscFunctionBegin; 849 PetscAssertPointer(dm, 1); 850 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"); 851 PetscCall(DMCreate(PetscObjectComm((PetscObject)dm), &boundary)); 852 PetscCall(DMSetType(boundary, DMPLEX)); 853 PetscCall(DMPlexCreateBoxSurfaceMesh_Internal(boundary, dim, faces, lower, upper, PETSC_FALSE)); 854 PetscCall(DMPlexGenerate(boundary, NULL, interpolate, &vol)); 855 PetscCall(DMGetLabel(vol, "marker", &bdlabel)); 856 if (bdlabel) PetscCall(DMPlexLabelComplete(vol, bdlabel)); 857 PetscCall(DMPlexCopy_Internal(dm, PETSC_TRUE, PETSC_FALSE, vol)); 858 PetscCall(DMPlexReplace_Internal(dm, &vol)); 859 PetscCall(DMDestroy(&boundary)); 860 PetscFunctionReturn(PETSC_SUCCESS); 861 } 862 863 static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ) 864 { 865 DMLabel cutLabel = NULL; 866 PetscInt markerTop = 1, faceMarkerTop = 1; 867 PetscInt markerBottom = 1, faceMarkerBottom = 1; 868 PetscInt markerFront = 1, faceMarkerFront = 1; 869 PetscInt markerBack = 1, faceMarkerBack = 1; 870 PetscInt markerRight = 1, faceMarkerRight = 1; 871 PetscInt markerLeft = 1, faceMarkerLeft = 1; 872 PetscInt dim; 873 PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE; 874 PetscMPIInt rank; 875 876 PetscFunctionBegin; 877 PetscCall(DMGetDimension(dm, &dim)); 878 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 879 PetscCall(DMCreateLabel(dm, "marker")); 880 PetscCall(DMCreateLabel(dm, "Face Sets")); 881 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL)); 882 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) { 883 if (cutMarker) { 884 PetscCall(DMCreateLabel(dm, "periodic_cut")); 885 PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel)); 886 } 887 } 888 switch (dim) { 889 case 2: 890 faceMarkerTop = 3; 891 faceMarkerBottom = 1; 892 faceMarkerRight = 2; 893 faceMarkerLeft = 4; 894 break; 895 case 3: 896 faceMarkerBottom = 1; 897 faceMarkerTop = 2; 898 faceMarkerFront = 3; 899 faceMarkerBack = 4; 900 faceMarkerRight = 5; 901 faceMarkerLeft = 6; 902 break; 903 default: 904 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Dimension %" PetscInt_FMT " not supported", dim); 905 } 906 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL)); 907 if (markerSeparate) { 908 markerBottom = faceMarkerBottom; 909 markerTop = faceMarkerTop; 910 markerFront = faceMarkerFront; 911 markerBack = faceMarkerBack; 912 markerRight = faceMarkerRight; 913 markerLeft = faceMarkerLeft; 914 } 915 { 916 const PetscInt numXEdges = rank == 0 ? edges[0] : 0; 917 const PetscInt numYEdges = rank == 0 ? edges[1] : 0; 918 const PetscInt numZEdges = rank == 0 ? edges[2] : 0; 919 const PetscInt numXVertices = rank == 0 ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0] + 1) : 0; 920 const PetscInt numYVertices = rank == 0 ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1] + 1) : 0; 921 const PetscInt numZVertices = rank == 0 ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2] + 1) : 0; 922 const PetscInt numCells = numXEdges * numYEdges * numZEdges; 923 const PetscInt numXFaces = numYEdges * numZEdges; 924 const PetscInt numYFaces = numXEdges * numZEdges; 925 const PetscInt numZFaces = numXEdges * numYEdges; 926 const PetscInt numTotXFaces = numXVertices * numXFaces; 927 const PetscInt numTotYFaces = numYVertices * numYFaces; 928 const PetscInt numTotZFaces = numZVertices * numZFaces; 929 const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces; 930 const PetscInt numTotXEdges = numXEdges * numYVertices * numZVertices; 931 const PetscInt numTotYEdges = numYEdges * numXVertices * numZVertices; 932 const PetscInt numTotZEdges = numZEdges * numXVertices * numYVertices; 933 const PetscInt numVertices = numXVertices * numYVertices * numZVertices; 934 const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges; 935 const PetscInt firstVertex = (dim == 2) ? numFaces : numCells; 936 const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices; 937 const PetscInt firstYFace = firstXFace + numTotXFaces; 938 const PetscInt firstZFace = firstYFace + numTotYFaces; 939 const PetscInt firstXEdge = numCells + numFaces + numVertices; 940 const PetscInt firstYEdge = firstXEdge + numTotXEdges; 941 const PetscInt firstZEdge = firstYEdge + numTotYEdges; 942 Vec coordinates; 943 PetscSection coordSection; 944 PetscScalar *coords; 945 PetscInt coordSize; 946 PetscInt v, vx, vy, vz; 947 PetscInt c, f, fx, fy, fz, e, ex, ey, ez; 948 949 PetscCall(DMPlexSetChart(dm, 0, numCells + numFaces + numEdges + numVertices)); 950 for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 6)); 951 for (f = firstXFace; f < firstXFace + numFaces; ++f) PetscCall(DMPlexSetConeSize(dm, f, 4)); 952 for (e = firstXEdge; e < firstXEdge + numEdges; ++e) PetscCall(DMPlexSetConeSize(dm, e, 2)); 953 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 954 /* Build cells */ 955 for (fz = 0; fz < numZEdges; ++fz) { 956 for (fy = 0; fy < numYEdges; ++fy) { 957 for (fx = 0; fx < numXEdges; ++fx) { 958 PetscInt cell = (fz * numYEdges + fy) * numXEdges + fx; 959 PetscInt faceB = firstZFace + (fy * numXEdges + fx) * numZVertices + fz; 960 PetscInt faceT = firstZFace + (fy * numXEdges + fx) * numZVertices + ((fz + 1) % numZVertices); 961 PetscInt faceF = firstYFace + (fz * numXEdges + fx) * numYVertices + fy; 962 PetscInt faceK = firstYFace + (fz * numXEdges + fx) * numYVertices + ((fy + 1) % numYVertices); 963 PetscInt faceL = firstXFace + (fz * numYEdges + fy) * numXVertices + fx; 964 PetscInt faceR = firstXFace + (fz * numYEdges + fy) * numXVertices + ((fx + 1) % numXVertices); 965 /* B, T, F, K, R, L */ 966 PetscInt ornt[6] = {-2, 0, 0, -3, 0, -2}; /* ??? */ 967 PetscInt cone[6]; 968 969 /* no boundary twisting in 3D */ 970 cone[0] = faceB; 971 cone[1] = faceT; 972 cone[2] = faceF; 973 cone[3] = faceK; 974 cone[4] = faceR; 975 cone[5] = faceL; 976 PetscCall(DMPlexSetCone(dm, cell, cone)); 977 PetscCall(DMPlexSetConeOrientation(dm, cell, ornt)); 978 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, cell, 2)); 979 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, cell, 2)); 980 if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, cell, 2)); 981 } 982 } 983 } 984 /* Build x faces */ 985 for (fz = 0; fz < numZEdges; ++fz) { 986 for (fy = 0; fy < numYEdges; ++fy) { 987 for (fx = 0; fx < numXVertices; ++fx) { 988 PetscInt face = firstXFace + (fz * numYEdges + fy) * numXVertices + fx; 989 PetscInt edgeL = firstZEdge + (fy * numXVertices + fx) * numZEdges + fz; 990 PetscInt edgeR = firstZEdge + (((fy + 1) % numYVertices) * numXVertices + fx) * numZEdges + fz; 991 PetscInt edgeB = firstYEdge + (fz * numXVertices + fx) * numYEdges + fy; 992 PetscInt edgeT = firstYEdge + (((fz + 1) % numZVertices) * numXVertices + fx) * numYEdges + fy; 993 PetscInt ornt[4] = {0, 0, -1, -1}; 994 PetscInt cone[4]; 995 996 if (dim == 3) { 997 /* markers */ 998 if (bdX != DM_BOUNDARY_PERIODIC) { 999 if (fx == numXVertices - 1) { 1000 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight)); 1001 PetscCall(DMSetLabelValue(dm, "marker", face, markerRight)); 1002 } else if (fx == 0) { 1003 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft)); 1004 PetscCall(DMSetLabelValue(dm, "marker", face, markerLeft)); 1005 } 1006 } 1007 } 1008 cone[0] = edgeB; 1009 cone[1] = edgeR; 1010 cone[2] = edgeT; 1011 cone[3] = edgeL; 1012 PetscCall(DMPlexSetCone(dm, face, cone)); 1013 PetscCall(DMPlexSetConeOrientation(dm, face, ornt)); 1014 } 1015 } 1016 } 1017 /* Build y faces */ 1018 for (fz = 0; fz < numZEdges; ++fz) { 1019 for (fx = 0; fx < numXEdges; ++fx) { 1020 for (fy = 0; fy < numYVertices; ++fy) { 1021 PetscInt face = firstYFace + (fz * numXEdges + fx) * numYVertices + fy; 1022 PetscInt edgeL = firstZEdge + (fy * numXVertices + fx) * numZEdges + fz; 1023 PetscInt edgeR = firstZEdge + (fy * numXVertices + ((fx + 1) % numXVertices)) * numZEdges + fz; 1024 PetscInt edgeB = firstXEdge + (fz * numYVertices + fy) * numXEdges + fx; 1025 PetscInt edgeT = firstXEdge + (((fz + 1) % numZVertices) * numYVertices + fy) * numXEdges + fx; 1026 PetscInt ornt[4] = {0, 0, -1, -1}; 1027 PetscInt cone[4]; 1028 1029 if (dim == 3) { 1030 /* markers */ 1031 if (bdY != DM_BOUNDARY_PERIODIC) { 1032 if (fy == numYVertices - 1) { 1033 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack)); 1034 PetscCall(DMSetLabelValue(dm, "marker", face, markerBack)); 1035 } else if (fy == 0) { 1036 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront)); 1037 PetscCall(DMSetLabelValue(dm, "marker", face, markerFront)); 1038 } 1039 } 1040 } 1041 cone[0] = edgeB; 1042 cone[1] = edgeR; 1043 cone[2] = edgeT; 1044 cone[3] = edgeL; 1045 PetscCall(DMPlexSetCone(dm, face, cone)); 1046 PetscCall(DMPlexSetConeOrientation(dm, face, ornt)); 1047 } 1048 } 1049 } 1050 /* Build z faces */ 1051 for (fy = 0; fy < numYEdges; ++fy) { 1052 for (fx = 0; fx < numXEdges; ++fx) { 1053 for (fz = 0; fz < numZVertices; fz++) { 1054 PetscInt face = firstZFace + (fy * numXEdges + fx) * numZVertices + fz; 1055 PetscInt edgeL = firstYEdge + (fz * numXVertices + fx) * numYEdges + fy; 1056 PetscInt edgeR = firstYEdge + (fz * numXVertices + ((fx + 1) % numXVertices)) * numYEdges + fy; 1057 PetscInt edgeB = firstXEdge + (fz * numYVertices + fy) * numXEdges + fx; 1058 PetscInt edgeT = firstXEdge + (fz * numYVertices + ((fy + 1) % numYVertices)) * numXEdges + fx; 1059 PetscInt ornt[4] = {0, 0, -1, -1}; 1060 PetscInt cone[4]; 1061 1062 if (dim == 2) { 1063 if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges - 1) { 1064 edgeR += numYEdges - 1 - 2 * fy; 1065 ornt[1] = -1; 1066 } 1067 if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges - 1) { 1068 edgeT += numXEdges - 1 - 2 * fx; 1069 ornt[2] = 0; 1070 } 1071 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, face, 2)); 1072 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges - 1 && cutLabel) PetscCall(DMLabelSetValue(cutLabel, face, 2)); 1073 } else { 1074 /* markers */ 1075 if (bdZ != DM_BOUNDARY_PERIODIC) { 1076 if (fz == numZVertices - 1) { 1077 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop)); 1078 PetscCall(DMSetLabelValue(dm, "marker", face, markerTop)); 1079 } else if (fz == 0) { 1080 PetscCall(DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom)); 1081 PetscCall(DMSetLabelValue(dm, "marker", face, markerBottom)); 1082 } 1083 } 1084 } 1085 cone[0] = edgeB; 1086 cone[1] = edgeR; 1087 cone[2] = edgeT; 1088 cone[3] = edgeL; 1089 PetscCall(DMPlexSetCone(dm, face, cone)); 1090 PetscCall(DMPlexSetConeOrientation(dm, face, ornt)); 1091 } 1092 } 1093 } 1094 /* Build Z edges*/ 1095 for (vy = 0; vy < numYVertices; vy++) { 1096 for (vx = 0; vx < numXVertices; vx++) { 1097 for (ez = 0; ez < numZEdges; ez++) { 1098 const PetscInt edge = firstZEdge + (vy * numXVertices + vx) * numZEdges + ez; 1099 const PetscInt vertexB = firstVertex + (ez * numYVertices + vy) * numXVertices + vx; 1100 const PetscInt vertexT = firstVertex + (((ez + 1) % numZVertices) * numYVertices + vy) * numXVertices + vx; 1101 PetscInt cone[2]; 1102 1103 cone[0] = vertexB; 1104 cone[1] = vertexT; 1105 PetscCall(DMPlexSetCone(dm, edge, cone)); 1106 if (dim == 3) { 1107 if (bdX != DM_BOUNDARY_PERIODIC) { 1108 if (vx == numXVertices - 1) { 1109 PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight)); 1110 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight)); 1111 if (ez == numZEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight)); 1112 } else if (vx == 0) { 1113 PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft)); 1114 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft)); 1115 if (ez == numZEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft)); 1116 } 1117 } 1118 if (bdY != DM_BOUNDARY_PERIODIC) { 1119 if (vy == numYVertices - 1) { 1120 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBack)); 1121 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBack)); 1122 if (ez == numZEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBack)); 1123 } else if (vy == 0) { 1124 PetscCall(DMSetLabelValue(dm, "marker", edge, markerFront)); 1125 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerFront)); 1126 if (ez == numZEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerFront)); 1127 } 1128 } 1129 } 1130 } 1131 } 1132 } 1133 /* Build Y edges*/ 1134 for (vz = 0; vz < numZVertices; vz++) { 1135 for (vx = 0; vx < numXVertices; vx++) { 1136 for (ey = 0; ey < numYEdges; ey++) { 1137 const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges - 1) ? (numXVertices - vx - 1) : (vz * numYVertices + ((ey + 1) % numYVertices)) * numXVertices + vx; 1138 const PetscInt edge = firstYEdge + (vz * numXVertices + vx) * numYEdges + ey; 1139 const PetscInt vertexF = firstVertex + (vz * numYVertices + ey) * numXVertices + vx; 1140 const PetscInt vertexK = firstVertex + nextv; 1141 PetscInt cone[2]; 1142 1143 cone[0] = vertexF; 1144 cone[1] = vertexK; 1145 PetscCall(DMPlexSetCone(dm, edge, cone)); 1146 if (dim == 2) { 1147 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 1148 if (vx == numXVertices - 1) { 1149 PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight)); 1150 PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight)); 1151 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight)); 1152 if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight)); 1153 } else if (vx == 0) { 1154 PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft)); 1155 PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft)); 1156 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft)); 1157 if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft)); 1158 } 1159 } else { 1160 if (vx == 0 && cutLabel) { 1161 PetscCall(DMLabelSetValue(cutLabel, edge, 1)); 1162 PetscCall(DMLabelSetValue(cutLabel, cone[0], 1)); 1163 if (ey == numYEdges - 1) PetscCall(DMLabelSetValue(cutLabel, cone[1], 1)); 1164 } 1165 } 1166 } else { 1167 if (bdX != DM_BOUNDARY_PERIODIC) { 1168 if (vx == numXVertices - 1) { 1169 PetscCall(DMSetLabelValue(dm, "marker", edge, markerRight)); 1170 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerRight)); 1171 if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerRight)); 1172 } else if (vx == 0) { 1173 PetscCall(DMSetLabelValue(dm, "marker", edge, markerLeft)); 1174 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerLeft)); 1175 if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerLeft)); 1176 } 1177 } 1178 if (bdZ != DM_BOUNDARY_PERIODIC) { 1179 if (vz == numZVertices - 1) { 1180 PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop)); 1181 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop)); 1182 if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop)); 1183 } else if (vz == 0) { 1184 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom)); 1185 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom)); 1186 if (ey == numYEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom)); 1187 } 1188 } 1189 } 1190 } 1191 } 1192 } 1193 /* Build X edges*/ 1194 for (vz = 0; vz < numZVertices; vz++) { 1195 for (vy = 0; vy < numYVertices; vy++) { 1196 for (ex = 0; ex < numXEdges; ex++) { 1197 const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges - 1) ? (numYVertices - vy - 1) * numXVertices : (vz * numYVertices + vy) * numXVertices + (ex + 1) % numXVertices; 1198 const PetscInt edge = firstXEdge + (vz * numYVertices + vy) * numXEdges + ex; 1199 const PetscInt vertexL = firstVertex + (vz * numYVertices + vy) * numXVertices + ex; 1200 const PetscInt vertexR = firstVertex + nextv; 1201 PetscInt cone[2]; 1202 1203 cone[0] = vertexL; 1204 cone[1] = vertexR; 1205 PetscCall(DMPlexSetCone(dm, edge, cone)); 1206 if (dim == 2) { 1207 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 1208 if (vy == numYVertices - 1) { 1209 PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop)); 1210 PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop)); 1211 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop)); 1212 if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop)); 1213 } else if (vy == 0) { 1214 PetscCall(DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom)); 1215 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom)); 1216 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom)); 1217 if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom)); 1218 } 1219 } else { 1220 if (vy == 0 && cutLabel) { 1221 PetscCall(DMLabelSetValue(cutLabel, edge, 1)); 1222 PetscCall(DMLabelSetValue(cutLabel, cone[0], 1)); 1223 if (ex == numXEdges - 1) PetscCall(DMLabelSetValue(cutLabel, cone[1], 1)); 1224 } 1225 } 1226 } else { 1227 if (bdY != DM_BOUNDARY_PERIODIC) { 1228 if (vy == numYVertices - 1) { 1229 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBack)); 1230 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBack)); 1231 if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBack)); 1232 } else if (vy == 0) { 1233 PetscCall(DMSetLabelValue(dm, "marker", edge, markerFront)); 1234 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerFront)); 1235 if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerFront)); 1236 } 1237 } 1238 if (bdZ != DM_BOUNDARY_PERIODIC) { 1239 if (vz == numZVertices - 1) { 1240 PetscCall(DMSetLabelValue(dm, "marker", edge, markerTop)); 1241 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerTop)); 1242 if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerTop)); 1243 } else if (vz == 0) { 1244 PetscCall(DMSetLabelValue(dm, "marker", edge, markerBottom)); 1245 PetscCall(DMSetLabelValue(dm, "marker", cone[0], markerBottom)); 1246 if (ex == numXEdges - 1) PetscCall(DMSetLabelValue(dm, "marker", cone[1], markerBottom)); 1247 } 1248 } 1249 } 1250 } 1251 } 1252 } 1253 PetscCall(DMPlexSymmetrize(dm)); 1254 PetscCall(DMPlexStratify(dm)); 1255 /* Build coordinates */ 1256 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 1257 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 1258 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim)); 1259 PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex + numVertices)); 1260 for (v = firstVertex; v < firstVertex + numVertices; ++v) { 1261 PetscCall(PetscSectionSetDof(coordSection, v, dim)); 1262 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim)); 1263 } 1264 PetscCall(PetscSectionSetUp(coordSection)); 1265 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 1266 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 1267 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 1268 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 1269 PetscCall(VecSetBlockSize(coordinates, dim)); 1270 PetscCall(VecSetType(coordinates, VECSTANDARD)); 1271 PetscCall(VecGetArray(coordinates, &coords)); 1272 for (vz = 0; vz < numZVertices; ++vz) { 1273 for (vy = 0; vy < numYVertices; ++vy) { 1274 for (vx = 0; vx < numXVertices; ++vx) { 1275 coords[((vz * numYVertices + vy) * numXVertices + vx) * dim + 0] = lower[0] + ((upper[0] - lower[0]) / numXEdges) * vx; 1276 coords[((vz * numYVertices + vy) * numXVertices + vx) * dim + 1] = lower[1] + ((upper[1] - lower[1]) / numYEdges) * vy; 1277 if (dim == 3) coords[((vz * numYVertices + vy) * numXVertices + vx) * dim + 2] = lower[2] + ((upper[2] - lower[2]) / numZEdges) * vz; 1278 } 1279 } 1280 } 1281 PetscCall(VecRestoreArray(coordinates, &coords)); 1282 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 1283 PetscCall(VecDestroy(&coordinates)); 1284 } 1285 PetscFunctionReturn(PETSC_SUCCESS); 1286 } 1287 1288 static PetscErrorCode DMPlexCreateBoxMesh_Tensor_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[]) 1289 { 1290 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1291 PetscInt fac[3] = {0, 0, 0}, d; 1292 1293 PetscFunctionBegin; 1294 PetscAssertPointer(dm, 1); 1295 PetscValidLogicalCollectiveInt(dm, dim, 2); 1296 PetscCall(DMSetDimension(dm, dim)); 1297 for (d = 0; d < dim; ++d) { 1298 fac[d] = faces[d]; 1299 bdt[d] = periodicity[d]; 1300 } 1301 PetscCall(DMPlexCreateCubeMesh_Internal(dm, lower, upper, fac, bdt[0], bdt[1], bdt[2])); 1302 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))) { 1303 PetscReal L[3] = {-1., -1., 0.}; 1304 PetscReal maxCell[3] = {-1., -1., 0.}; 1305 1306 for (d = 0; d < dim; ++d) { 1307 if (periodicity[d] != DM_BOUNDARY_NONE) { 1308 L[d] = upper[d] - lower[d]; 1309 maxCell[d] = 1.1 * (L[d] / PetscMax(1, faces[d])); 1310 } 1311 } 1312 PetscCall(DMSetPeriodicity(dm, maxCell, lower, L)); 1313 } 1314 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 1315 PetscFunctionReturn(PETSC_SUCCESS); 1316 } 1317 1318 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) 1319 { 1320 PetscFunctionBegin; 1321 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 1322 if (shape == DM_SHAPE_ZBOX) PetscCall(DMPlexCreateBoxMesh_Tensor_SFC_Internal(dm, dim, faces, lower, upper, periodicity, interpolate)); 1323 else if (dim == 1) PetscCall(DMPlexCreateLineMesh_Internal(dm, faces[0], lower[0], upper[0], periodicity[0])); 1324 else if (simplex) PetscCall(DMPlexCreateBoxMesh_Simplex_Internal(dm, dim, faces, lower, upper, periodicity, interpolate)); 1325 else PetscCall(DMPlexCreateBoxMesh_Tensor_Internal(dm, dim, faces, lower, upper, periodicity)); 1326 if (!interpolate && dim > 1 && !simplex) { 1327 DM udm; 1328 1329 PetscCall(DMPlexUninterpolate(dm, &udm)); 1330 PetscCall(DMPlexCopyCoordinates(dm, udm)); 1331 PetscCall(DMPlexReplace_Internal(dm, &udm)); 1332 } 1333 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 1334 PetscFunctionReturn(PETSC_SUCCESS); 1335 } 1336 1337 /*@C 1338 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra). 1339 1340 Collective 1341 1342 Input Parameters: 1343 + comm - The communicator for the `DM` object 1344 . dim - The spatial dimension 1345 . simplex - `PETSC_TRUE` for simplices, `PETSC_FALSE` for tensor cells 1346 . faces - Number of faces per dimension, or `NULL` for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 1347 . lower - The lower left corner, or `NULL` for (0, 0, 0) 1348 . upper - The upper right corner, or `NULL` for (1, 1, 1) 1349 . periodicity - The boundary type for the X,Y,Z direction, or `NULL` for `DM_BOUNDARY_NONE` 1350 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1351 1352 Output Parameter: 1353 . dm - The `DM` object 1354 1355 Level: beginner 1356 1357 Note: 1358 To customize this mesh using options, use 1359 .vb 1360 DMCreate(comm, &dm); 1361 DMSetType(dm, DMPLEX); 1362 DMSetFromOptions(dm); 1363 .ve 1364 and use the options in `DMSetFromOptions()`. 1365 1366 Here is the numbering returned for 2 faces in each direction for tensor cells\: 1367 .vb 1368 10---17---11---18----12 1369 | | | 1370 | | | 1371 20 2 22 3 24 1372 | | | 1373 | | | 1374 7---15----8---16----9 1375 | | | 1376 | | | 1377 19 0 21 1 23 1378 | | | 1379 | | | 1380 4---13----5---14----6 1381 .ve 1382 and for simplicial cells 1383 .vb 1384 14----8---15----9----16 1385 |\ 5 |\ 7 | 1386 | \ | \ | 1387 13 2 14 3 15 1388 | 4 \ | 6 \ | 1389 | \ | \ | 1390 11----6---12----7----13 1391 |\ |\ | 1392 | \ 1 | \ 3 | 1393 10 0 11 1 12 1394 | 0 \ | 2 \ | 1395 | \ | \ | 1396 8----4----9----5----10 1397 .ve 1398 1399 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMSetFromOptions()`, `DMPlexCreateFromFile()`, `DMPlexCreateHexCylinderMesh()`, `DMSetType()`, `DMCreate()` 1400 @*/ 1401 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) 1402 { 1403 PetscInt fac[3] = {1, 1, 1}; 1404 PetscReal low[3] = {0, 0, 0}; 1405 PetscReal upp[3] = {1, 1, 1}; 1406 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1407 1408 PetscFunctionBegin; 1409 PetscCall(DMCreate(comm, dm)); 1410 PetscCall(DMSetType(*dm, DMPLEX)); 1411 PetscCall(DMPlexCreateBoxMesh_Internal(*dm, DM_SHAPE_BOX, dim, simplex, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt, interpolate)); 1412 if (periodicity) PetscCall(DMLocalizeCoordinates(*dm)); 1413 PetscFunctionReturn(PETSC_SUCCESS); 1414 } 1415 1416 static PetscErrorCode DMPlexCreateWedgeBoxMesh_Internal(DM dm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[]) 1417 { 1418 DM bdm, vol; 1419 PetscInt i; 1420 1421 PetscFunctionBegin; 1422 // TODO Now we can support periodicity 1423 for (i = 0; i < 3; ++i) PetscCheck(periodicity[i] == DM_BOUNDARY_NONE, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Periodicity not yet supported"); 1424 PetscCall(DMCreate(PetscObjectComm((PetscObject)dm), &bdm)); 1425 PetscCall(DMSetType(bdm, DMPLEX)); 1426 PetscCall(DMSetDimension(bdm, 2)); 1427 PetscCall(PetscLogEventBegin(DMPLEX_Generate, bdm, 0, 0, 0)); 1428 PetscCall(DMPlexCreateBoxMesh_Simplex_Internal(bdm, 2, faces, lower, upper, periodicity, PETSC_TRUE)); 1429 PetscCall(DMPlexExtrude(bdm, faces[2], upper[2] - lower[2], PETSC_TRUE, PETSC_FALSE, PETSC_FALSE, NULL, NULL, &vol)); 1430 PetscCall(PetscLogEventEnd(DMPLEX_Generate, bdm, 0, 0, 0)); 1431 PetscCall(DMDestroy(&bdm)); 1432 PetscCall(DMPlexReplace_Internal(dm, &vol)); 1433 if (lower[2] != 0.0) { 1434 Vec v; 1435 PetscScalar *x; 1436 PetscInt cDim, n; 1437 1438 PetscCall(DMGetCoordinatesLocal(dm, &v)); 1439 PetscCall(VecGetBlockSize(v, &cDim)); 1440 PetscCall(VecGetLocalSize(v, &n)); 1441 PetscCall(VecGetArray(v, &x)); 1442 x += cDim; 1443 for (i = 0; i < n; i += cDim) x[i] += lower[2]; 1444 PetscCall(VecRestoreArray(v, &x)); 1445 PetscCall(DMSetCoordinatesLocal(dm, v)); 1446 } 1447 PetscFunctionReturn(PETSC_SUCCESS); 1448 } 1449 1450 /*@ 1451 DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tessellating the (x,y) plane and extruding in the third direction using wedge cells. 1452 1453 Collective 1454 1455 Input Parameters: 1456 + comm - The communicator for the `DM` object 1457 . faces - Number of faces per dimension, or `NULL` for (1, 1, 1) 1458 . lower - The lower left corner, or `NULL` for (0, 0, 0) 1459 . upper - The upper right corner, or `NULL` for (1, 1, 1) 1460 . periodicity - The boundary type for the X,Y,Z direction, or `NULL` for `DM_BOUNDARY_NONE` 1461 . orderHeight - If `PETSC_TRUE`, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1462 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1463 1464 Output Parameter: 1465 . dm - The `DM` object 1466 1467 Level: beginner 1468 1469 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateHexCylinderMesh()`, `DMPlexCreateWedgeCylinderMesh()`, `DMExtrude()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 1470 @*/ 1471 PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool orderHeight, PetscBool interpolate, DM *dm) 1472 { 1473 PetscInt fac[3] = {1, 1, 1}; 1474 PetscReal low[3] = {0, 0, 0}; 1475 PetscReal upp[3] = {1, 1, 1}; 1476 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1477 1478 PetscFunctionBegin; 1479 PetscCall(DMCreate(comm, dm)); 1480 PetscCall(DMSetType(*dm, DMPLEX)); 1481 PetscCall(DMPlexCreateWedgeBoxMesh_Internal(*dm, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt)); 1482 if (!interpolate) { 1483 DM udm; 1484 1485 PetscCall(DMPlexUninterpolate(*dm, &udm)); 1486 PetscCall(DMPlexReplace_Internal(*dm, &udm)); 1487 } 1488 if (periodicity) PetscCall(DMLocalizeCoordinates(*dm)); 1489 PetscFunctionReturn(PETSC_SUCCESS); 1490 } 1491 1492 /* 1493 DMPlexTensorPointLexicographic_Private - Returns all tuples of size 'len' with nonnegative integers that are all less than or equal to 'max' for that dimension. 1494 1495 Input Parameters: 1496 + len - The length of the tuple 1497 . max - The maximum for each dimension, so values are in [0, max) 1498 - tup - A tuple of length len+1: tup[len] > 0 indicates a stopping condition 1499 1500 Output Parameter: 1501 . tup - A tuple of `len` integers whose entries are at most `max` 1502 1503 Level: developer 1504 1505 Note: 1506 Ordering is lexicographic with lowest index as least significant in ordering. 1507 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}. 1508 1509 .seealso: PetscDualSpaceTensorPointLexicographic_Internal(), PetscDualSpaceLatticePointLexicographic_Internal() 1510 */ 1511 static PetscErrorCode DMPlexTensorPointLexicographic_Private(PetscInt len, const PetscInt max[], PetscInt tup[]) 1512 { 1513 PetscInt i; 1514 1515 PetscFunctionBegin; 1516 for (i = 0; i < len; ++i) { 1517 if (tup[i] < max[i] - 1) { 1518 break; 1519 } else { 1520 tup[i] = 0; 1521 } 1522 } 1523 if (i == len) tup[i - 1] = max[i - 1]; 1524 else ++tup[i]; 1525 PetscFunctionReturn(PETSC_SUCCESS); 1526 } 1527 1528 static PetscInt TupleToIndex_Private(PetscInt len, const PetscInt max[], const PetscInt tup[]) 1529 { 1530 PetscInt i, idx = tup[len - 1]; 1531 1532 for (i = len - 2; i >= 0; --i) { 1533 idx *= max[i]; 1534 idx += tup[i]; 1535 } 1536 return idx; 1537 } 1538 1539 static PetscErrorCode DestroyExtent_Private(void *extent) 1540 { 1541 return PetscFree(extent); 1542 } 1543 1544 static PetscErrorCode DMPlexCreateHypercubicMesh_Internal(DM dm, PetscInt dim, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], const DMBoundaryType bd[]) 1545 { 1546 Vec coordinates; 1547 PetscSection coordSection; 1548 DMLabel cutLabel = NULL; 1549 PetscBool cutMarker = PETSC_FALSE; 1550 PetscBool periodic = PETSC_FALSE; 1551 PetscInt numCells = 1, c; 1552 PetscInt numVertices = 1, v; 1553 PetscScalar *coords; 1554 PetscInt *vertices, *vert, *vtmp, *supp, cone[2]; 1555 PetscInt d, e, cell = 0, coordSize; 1556 PetscMPIInt rank; 1557 1558 PetscFunctionBegin; 1559 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 1560 PetscCall(DMSetDimension(dm, dim)); 1561 PetscCall(PetscCalloc4(dim, &vertices, dim, &vert, dim, &vtmp, 2 * dim, &supp)); 1562 PetscCall(DMCreateLabel(dm, "marker")); 1563 PetscCall(PetscOptionsGetBool(((PetscObject)dm)->options, ((PetscObject)dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL)); 1564 for (d = 0; d < dim; ++d) periodic = (periodic || bd[d] == DM_BOUNDARY_PERIODIC) ? PETSC_TRUE : PETSC_FALSE; 1565 if (periodic && cutMarker) { 1566 PetscCall(DMCreateLabel(dm, "periodic_cut")); 1567 PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel)); 1568 } 1569 for (d = 0; d < dim; ++d) PetscCheck(bd[d] == DM_BOUNDARY_PERIODIC, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Hypercubic mesh must be periodic now"); 1570 for (d = 0; d < dim; ++d) { 1571 vertices[d] = edges[d]; 1572 numVertices *= vertices[d]; 1573 } 1574 numCells = numVertices * dim; 1575 PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices)); 1576 for (c = 0; c < numCells; ++c) PetscCall(DMPlexSetConeSize(dm, c, 2)); 1577 for (v = numCells; v < numCells + numVertices; ++v) PetscCall(DMPlexSetSupportSize(dm, v, 2 * dim)); 1578 /* TODO Loop over boundary and reset support sizes */ 1579 PetscCall(DMSetUp(dm)); /* Allocate space for cones and supports */ 1580 /* Build cell cones and vertex supports */ 1581 PetscCall(DMCreateLabel(dm, "celltype")); 1582 while (vert[dim - 1] < vertices[dim - 1]) { 1583 const PetscInt vertex = TupleToIndex_Private(dim, vertices, vert) + numCells; 1584 PetscInt s = 0; 1585 1586 PetscCall(PetscPrintf(PETSC_COMM_SELF, "Vertex %" PetscInt_FMT ":", vertex)); 1587 for (d = 0; d < dim; ++d) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, vert[d])); 1588 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 1589 PetscCall(DMPlexSetCellType(dm, vertex, DM_POLYTOPE_POINT)); 1590 for (d = 0; d < dim; ++d) { 1591 for (e = 0; e < dim; ++e) vtmp[e] = vert[e]; 1592 vtmp[d] = (vert[d] + 1) % vertices[d]; 1593 cone[0] = vertex; 1594 cone[1] = TupleToIndex_Private(dim, vertices, vtmp) + numCells; 1595 PetscCall(PetscPrintf(PETSC_COMM_SELF, " Vertex %" PetscInt_FMT ":", cone[1])); 1596 for (e = 0; e < dim; ++e) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, vtmp[e])); 1597 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 1598 PetscCall(DMPlexSetCone(dm, cell, cone)); 1599 PetscCall(DMPlexSetCellType(dm, cell, DM_POLYTOPE_SEGMENT)); 1600 PetscCall(PetscPrintf(PETSC_COMM_SELF, " Edge %" PetscInt_FMT " (%" PetscInt_FMT " %" PetscInt_FMT ")\n", cell, cone[0], cone[1])); 1601 ++cell; 1602 } 1603 for (d = 0; d < dim; ++d) { 1604 for (e = 0; e < dim; ++e) vtmp[e] = vert[e]; 1605 vtmp[d] = (vert[d] + vertices[d] - 1) % vertices[d]; 1606 supp[s++] = TupleToIndex_Private(dim, vertices, vtmp) * dim + d; 1607 supp[s++] = (vertex - numCells) * dim + d; 1608 PetscCall(DMPlexSetSupport(dm, vertex, supp)); 1609 } 1610 PetscCall(DMPlexTensorPointLexicographic_Private(dim, vertices, vert)); 1611 } 1612 PetscCall(DMPlexStratify(dm)); 1613 /* Build coordinates */ 1614 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 1615 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 1616 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim)); 1617 PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices)); 1618 for (v = numCells; v < numCells + numVertices; ++v) { 1619 PetscCall(PetscSectionSetDof(coordSection, v, dim)); 1620 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim)); 1621 } 1622 PetscCall(PetscSectionSetUp(coordSection)); 1623 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 1624 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 1625 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 1626 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 1627 PetscCall(VecSetBlockSize(coordinates, dim)); 1628 PetscCall(VecSetType(coordinates, VECSTANDARD)); 1629 PetscCall(VecGetArray(coordinates, &coords)); 1630 for (d = 0; d < dim; ++d) vert[d] = 0; 1631 while (vert[dim - 1] < vertices[dim - 1]) { 1632 const PetscInt vertex = TupleToIndex_Private(dim, vertices, vert); 1633 1634 for (d = 0; d < dim; ++d) coords[vertex * dim + d] = lower[d] + ((upper[d] - lower[d]) / vertices[d]) * vert[d]; 1635 PetscCall(PetscPrintf(PETSC_COMM_SELF, "Vertex %" PetscInt_FMT ":", vertex)); 1636 for (d = 0; d < dim; ++d) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %" PetscInt_FMT, vert[d])); 1637 for (d = 0; d < dim; ++d) PetscCall(PetscPrintf(PETSC_COMM_SELF, " %g", (double)PetscRealPart(coords[vertex * dim + d]))); 1638 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\n")); 1639 PetscCall(DMPlexTensorPointLexicographic_Private(dim, vertices, vert)); 1640 } 1641 PetscCall(VecRestoreArray(coordinates, &coords)); 1642 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 1643 PetscCall(VecDestroy(&coordinates)); 1644 PetscCall(PetscFree4(vertices, vert, vtmp, supp)); 1645 //PetscCall(DMSetPeriodicity(dm, NULL, lower, upper)); 1646 // Attach the extent 1647 { 1648 PetscContainer c; 1649 PetscInt *extent; 1650 1651 PetscCall(PetscMalloc1(dim, &extent)); 1652 for (PetscInt d = 0; d < dim; ++d) extent[d] = edges[d]; 1653 PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &c)); 1654 PetscCall(PetscContainerSetUserDestroy(c, DestroyExtent_Private)); 1655 PetscCall(PetscContainerSetPointer(c, extent)); 1656 PetscCall(PetscObjectCompose((PetscObject)dm, "_extent", (PetscObject)c)); 1657 PetscCall(PetscContainerDestroy(&c)); 1658 } 1659 PetscFunctionReturn(PETSC_SUCCESS); 1660 } 1661 1662 /*@C 1663 DMPlexCreateHypercubicMesh - Creates a periodic mesh on the tensor product of unit intervals using only vertices and edges. 1664 1665 Collective 1666 1667 Input Parameters: 1668 + comm - The communicator for the DM object 1669 . dim - The spatial dimension 1670 . edges - Number of edges per dimension, or `NULL` for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 1671 . lower - The lower left corner, or `NULL` for (0, 0, 0) 1672 - upper - The upper right corner, or `NULL` for (1, 1, 1) 1673 1674 Output Parameter: 1675 . dm - The DM object 1676 1677 Level: beginner 1678 1679 Note: 1680 If you want to customize this mesh using options, you just need to 1681 .vb 1682 DMCreate(comm, &dm); 1683 DMSetType(dm, DMPLEX); 1684 DMSetFromOptions(dm); 1685 .ve 1686 and use the options on the `DMSetFromOptions()` page. 1687 1688 The vertices are numbered is lexicographic order, and the dim edges exiting a vertex in the positive orthant are number consecutively, 1689 .vb 1690 18--0-19--2-20--4-18 1691 | | | | 1692 13 15 17 13 1693 | | | | 1694 24-12-25-14-26-16-24 1695 | | | | 1696 7 9 11 7 1697 | | | | 1698 21--6-22--8-23-10-21 1699 | | | | 1700 1 3 5 1 1701 | | | | 1702 18--0-19--2-20--4-18 1703 .ve 1704 1705 .seealso: `DMSetFromOptions()`, `DMPlexCreateFromFile()`, `DMPlexCreateHexCylinderMesh()`, `DMSetType()`, `DMCreate()` 1706 @*/ 1707 PetscErrorCode DMPlexCreateHypercubicMesh(MPI_Comm comm, PetscInt dim, const PetscInt edges[], const PetscReal lower[], const PetscReal upper[], DM *dm) 1708 { 1709 PetscInt *edg; 1710 PetscReal *low, *upp; 1711 DMBoundaryType *bdt; 1712 PetscInt d; 1713 1714 PetscFunctionBegin; 1715 PetscCall(DMCreate(comm, dm)); 1716 PetscCall(DMSetType(*dm, DMPLEX)); 1717 PetscCall(PetscMalloc4(dim, &edg, dim, &low, dim, &upp, dim, &bdt)); 1718 for (d = 0; d < dim; ++d) { 1719 edg[d] = edges ? edges[d] : 1; 1720 low[d] = lower ? lower[d] : 0.; 1721 upp[d] = upper ? upper[d] : 1.; 1722 bdt[d] = DM_BOUNDARY_PERIODIC; 1723 } 1724 PetscCall(DMPlexCreateHypercubicMesh_Internal(*dm, dim, low, upp, edg, bdt)); 1725 PetscCall(PetscFree4(edg, low, upp, bdt)); 1726 PetscFunctionReturn(PETSC_SUCCESS); 1727 } 1728 1729 /*@ 1730 DMPlexSetOptionsPrefix - Sets the prefix used for searching for all `DM` options in the database. 1731 1732 Logically Collective 1733 1734 Input Parameters: 1735 + dm - the `DM` context 1736 - prefix - the prefix to prepend to all option names 1737 1738 Level: advanced 1739 1740 Note: 1741 A hyphen (-) must NOT be given at the beginning of the prefix name. 1742 The first character of all runtime options is AUTOMATICALLY the hyphen. 1743 1744 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `SNESSetFromOptions()` 1745 @*/ 1746 PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) 1747 { 1748 DM_Plex *mesh = (DM_Plex *)dm->data; 1749 1750 PetscFunctionBegin; 1751 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1752 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dm, prefix)); 1753 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)mesh->partitioner, prefix)); 1754 PetscFunctionReturn(PETSC_SUCCESS); 1755 } 1756 1757 /* Remap geometry to cylinder 1758 TODO: This only works for a single refinement, then it is broken 1759 1760 Interior square: Linear interpolation is correct 1761 The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing 1762 such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance 1763 1764 phi = arctan(y/x) 1765 d_close = sqrt(1/8 + 1/4 sin^2(phi)) 1766 d_far = sqrt(1/2 + sin^2(phi)) 1767 1768 so we remap them using 1769 1770 x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) 1771 y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) 1772 1773 If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. 1774 */ 1775 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[]) 1776 { 1777 const PetscReal dis = 1.0 / PetscSqrtReal(2.0); 1778 const PetscReal ds2 = 0.5 * dis; 1779 1780 if ((PetscAbsScalar(u[0]) <= ds2) && (PetscAbsScalar(u[1]) <= ds2)) { 1781 f0[0] = u[0]; 1782 f0[1] = u[1]; 1783 } else { 1784 PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; 1785 1786 x = PetscRealPart(u[0]); 1787 y = PetscRealPart(u[1]); 1788 phi = PetscAtan2Real(y, x); 1789 sinp = PetscSinReal(phi); 1790 cosp = PetscCosReal(phi); 1791 if ((PetscAbsReal(phi) > PETSC_PI / 4.0) && (PetscAbsReal(phi) < 3.0 * PETSC_PI / 4.0)) { 1792 dc = PetscAbsReal(ds2 / sinp); 1793 df = PetscAbsReal(dis / sinp); 1794 xc = ds2 * x / PetscAbsReal(y); 1795 yc = ds2 * PetscSignReal(y); 1796 } else { 1797 dc = PetscAbsReal(ds2 / cosp); 1798 df = PetscAbsReal(dis / cosp); 1799 xc = ds2 * PetscSignReal(x); 1800 yc = ds2 * y / PetscAbsReal(x); 1801 } 1802 f0[0] = xc + (u[0] - xc) * (1.0 - dc) / (df - dc); 1803 f0[1] = yc + (u[1] - yc) * (1.0 - dc) / (df - dc); 1804 } 1805 f0[2] = u[2]; 1806 } 1807 1808 static PetscErrorCode DMPlexCreateHexCylinderMesh_Internal(DM dm, DMBoundaryType periodicZ, PetscInt Nr) 1809 { 1810 const PetscInt dim = 3; 1811 PetscInt numCells, numVertices; 1812 PetscMPIInt rank; 1813 1814 PetscFunctionBegin; 1815 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 1816 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 1817 PetscCall(DMSetDimension(dm, dim)); 1818 /* Create topology */ 1819 { 1820 PetscInt cone[8], c; 1821 1822 numCells = rank == 0 ? 5 : 0; 1823 numVertices = rank == 0 ? 16 : 0; 1824 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1825 numCells *= 3; 1826 numVertices = rank == 0 ? 24 : 0; 1827 } 1828 PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices)); 1829 for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 8)); 1830 PetscCall(DMSetUp(dm)); 1831 if (rank == 0) { 1832 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1833 cone[0] = 15; 1834 cone[1] = 18; 1835 cone[2] = 17; 1836 cone[3] = 16; 1837 cone[4] = 31; 1838 cone[5] = 32; 1839 cone[6] = 33; 1840 cone[7] = 34; 1841 PetscCall(DMPlexSetCone(dm, 0, cone)); 1842 cone[0] = 16; 1843 cone[1] = 17; 1844 cone[2] = 24; 1845 cone[3] = 23; 1846 cone[4] = 32; 1847 cone[5] = 36; 1848 cone[6] = 37; 1849 cone[7] = 33; /* 22 25 26 21 */ 1850 PetscCall(DMPlexSetCone(dm, 1, cone)); 1851 cone[0] = 18; 1852 cone[1] = 27; 1853 cone[2] = 24; 1854 cone[3] = 17; 1855 cone[4] = 34; 1856 cone[5] = 33; 1857 cone[6] = 37; 1858 cone[7] = 38; 1859 PetscCall(DMPlexSetCone(dm, 2, cone)); 1860 cone[0] = 29; 1861 cone[1] = 27; 1862 cone[2] = 18; 1863 cone[3] = 15; 1864 cone[4] = 35; 1865 cone[5] = 31; 1866 cone[6] = 34; 1867 cone[7] = 38; 1868 PetscCall(DMPlexSetCone(dm, 3, cone)); 1869 cone[0] = 29; 1870 cone[1] = 15; 1871 cone[2] = 16; 1872 cone[3] = 23; 1873 cone[4] = 35; 1874 cone[5] = 36; 1875 cone[6] = 32; 1876 cone[7] = 31; 1877 PetscCall(DMPlexSetCone(dm, 4, cone)); 1878 1879 cone[0] = 31; 1880 cone[1] = 34; 1881 cone[2] = 33; 1882 cone[3] = 32; 1883 cone[4] = 19; 1884 cone[5] = 22; 1885 cone[6] = 21; 1886 cone[7] = 20; 1887 PetscCall(DMPlexSetCone(dm, 5, cone)); 1888 cone[0] = 32; 1889 cone[1] = 33; 1890 cone[2] = 37; 1891 cone[3] = 36; 1892 cone[4] = 22; 1893 cone[5] = 25; 1894 cone[6] = 26; 1895 cone[7] = 21; 1896 PetscCall(DMPlexSetCone(dm, 6, cone)); 1897 cone[0] = 34; 1898 cone[1] = 38; 1899 cone[2] = 37; 1900 cone[3] = 33; 1901 cone[4] = 20; 1902 cone[5] = 21; 1903 cone[6] = 26; 1904 cone[7] = 28; 1905 PetscCall(DMPlexSetCone(dm, 7, cone)); 1906 cone[0] = 35; 1907 cone[1] = 38; 1908 cone[2] = 34; 1909 cone[3] = 31; 1910 cone[4] = 30; 1911 cone[5] = 19; 1912 cone[6] = 20; 1913 cone[7] = 28; 1914 PetscCall(DMPlexSetCone(dm, 8, cone)); 1915 cone[0] = 35; 1916 cone[1] = 31; 1917 cone[2] = 32; 1918 cone[3] = 36; 1919 cone[4] = 30; 1920 cone[5] = 25; 1921 cone[6] = 22; 1922 cone[7] = 19; 1923 PetscCall(DMPlexSetCone(dm, 9, cone)); 1924 1925 cone[0] = 19; 1926 cone[1] = 20; 1927 cone[2] = 21; 1928 cone[3] = 22; 1929 cone[4] = 15; 1930 cone[5] = 16; 1931 cone[6] = 17; 1932 cone[7] = 18; 1933 PetscCall(DMPlexSetCone(dm, 10, cone)); 1934 cone[0] = 22; 1935 cone[1] = 21; 1936 cone[2] = 26; 1937 cone[3] = 25; 1938 cone[4] = 16; 1939 cone[5] = 23; 1940 cone[6] = 24; 1941 cone[7] = 17; 1942 PetscCall(DMPlexSetCone(dm, 11, cone)); 1943 cone[0] = 20; 1944 cone[1] = 28; 1945 cone[2] = 26; 1946 cone[3] = 21; 1947 cone[4] = 18; 1948 cone[5] = 17; 1949 cone[6] = 24; 1950 cone[7] = 27; 1951 PetscCall(DMPlexSetCone(dm, 12, cone)); 1952 cone[0] = 30; 1953 cone[1] = 28; 1954 cone[2] = 20; 1955 cone[3] = 19; 1956 cone[4] = 29; 1957 cone[5] = 15; 1958 cone[6] = 18; 1959 cone[7] = 27; 1960 PetscCall(DMPlexSetCone(dm, 13, cone)); 1961 cone[0] = 30; 1962 cone[1] = 19; 1963 cone[2] = 22; 1964 cone[3] = 25; 1965 cone[4] = 29; 1966 cone[5] = 23; 1967 cone[6] = 16; 1968 cone[7] = 15; 1969 PetscCall(DMPlexSetCone(dm, 14, cone)); 1970 } else { 1971 cone[0] = 5; 1972 cone[1] = 8; 1973 cone[2] = 7; 1974 cone[3] = 6; 1975 cone[4] = 9; 1976 cone[5] = 12; 1977 cone[6] = 11; 1978 cone[7] = 10; 1979 PetscCall(DMPlexSetCone(dm, 0, cone)); 1980 cone[0] = 6; 1981 cone[1] = 7; 1982 cone[2] = 14; 1983 cone[3] = 13; 1984 cone[4] = 12; 1985 cone[5] = 15; 1986 cone[6] = 16; 1987 cone[7] = 11; 1988 PetscCall(DMPlexSetCone(dm, 1, cone)); 1989 cone[0] = 8; 1990 cone[1] = 17; 1991 cone[2] = 14; 1992 cone[3] = 7; 1993 cone[4] = 10; 1994 cone[5] = 11; 1995 cone[6] = 16; 1996 cone[7] = 18; 1997 PetscCall(DMPlexSetCone(dm, 2, cone)); 1998 cone[0] = 19; 1999 cone[1] = 17; 2000 cone[2] = 8; 2001 cone[3] = 5; 2002 cone[4] = 20; 2003 cone[5] = 9; 2004 cone[6] = 10; 2005 cone[7] = 18; 2006 PetscCall(DMPlexSetCone(dm, 3, cone)); 2007 cone[0] = 19; 2008 cone[1] = 5; 2009 cone[2] = 6; 2010 cone[3] = 13; 2011 cone[4] = 20; 2012 cone[5] = 15; 2013 cone[6] = 12; 2014 cone[7] = 9; 2015 PetscCall(DMPlexSetCone(dm, 4, cone)); 2016 } 2017 } 2018 PetscCall(DMPlexSymmetrize(dm)); 2019 PetscCall(DMPlexStratify(dm)); 2020 } 2021 /* Create cube geometry */ 2022 { 2023 Vec coordinates; 2024 PetscSection coordSection; 2025 PetscScalar *coords; 2026 PetscInt coordSize, v; 2027 const PetscReal dis = 1.0 / PetscSqrtReal(2.0); 2028 const PetscReal ds2 = dis / 2.0; 2029 2030 /* Build coordinates */ 2031 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 2032 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 2033 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim)); 2034 PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices)); 2035 for (v = numCells; v < numCells + numVertices; ++v) { 2036 PetscCall(PetscSectionSetDof(coordSection, v, dim)); 2037 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim)); 2038 } 2039 PetscCall(PetscSectionSetUp(coordSection)); 2040 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 2041 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 2042 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 2043 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 2044 PetscCall(VecSetBlockSize(coordinates, dim)); 2045 PetscCall(VecSetType(coordinates, VECSTANDARD)); 2046 PetscCall(VecGetArray(coordinates, &coords)); 2047 if (rank == 0) { 2048 coords[0 * dim + 0] = -ds2; 2049 coords[0 * dim + 1] = -ds2; 2050 coords[0 * dim + 2] = 0.0; 2051 coords[1 * dim + 0] = ds2; 2052 coords[1 * dim + 1] = -ds2; 2053 coords[1 * dim + 2] = 0.0; 2054 coords[2 * dim + 0] = ds2; 2055 coords[2 * dim + 1] = ds2; 2056 coords[2 * dim + 2] = 0.0; 2057 coords[3 * dim + 0] = -ds2; 2058 coords[3 * dim + 1] = ds2; 2059 coords[3 * dim + 2] = 0.0; 2060 coords[4 * dim + 0] = -ds2; 2061 coords[4 * dim + 1] = -ds2; 2062 coords[4 * dim + 2] = 1.0; 2063 coords[5 * dim + 0] = -ds2; 2064 coords[5 * dim + 1] = ds2; 2065 coords[5 * dim + 2] = 1.0; 2066 coords[6 * dim + 0] = ds2; 2067 coords[6 * dim + 1] = ds2; 2068 coords[6 * dim + 2] = 1.0; 2069 coords[7 * dim + 0] = ds2; 2070 coords[7 * dim + 1] = -ds2; 2071 coords[7 * dim + 2] = 1.0; 2072 coords[8 * dim + 0] = dis; 2073 coords[8 * dim + 1] = -dis; 2074 coords[8 * dim + 2] = 0.0; 2075 coords[9 * dim + 0] = dis; 2076 coords[9 * dim + 1] = dis; 2077 coords[9 * dim + 2] = 0.0; 2078 coords[10 * dim + 0] = dis; 2079 coords[10 * dim + 1] = -dis; 2080 coords[10 * dim + 2] = 1.0; 2081 coords[11 * dim + 0] = dis; 2082 coords[11 * dim + 1] = dis; 2083 coords[11 * dim + 2] = 1.0; 2084 coords[12 * dim + 0] = -dis; 2085 coords[12 * dim + 1] = dis; 2086 coords[12 * dim + 2] = 0.0; 2087 coords[13 * dim + 0] = -dis; 2088 coords[13 * dim + 1] = dis; 2089 coords[13 * dim + 2] = 1.0; 2090 coords[14 * dim + 0] = -dis; 2091 coords[14 * dim + 1] = -dis; 2092 coords[14 * dim + 2] = 0.0; 2093 coords[15 * dim + 0] = -dis; 2094 coords[15 * dim + 1] = -dis; 2095 coords[15 * dim + 2] = 1.0; 2096 if (periodicZ == DM_BOUNDARY_PERIODIC) { 2097 /* 15 31 19 */ coords[16 * dim + 0] = -ds2; 2098 coords[16 * dim + 1] = -ds2; 2099 coords[16 * dim + 2] = 0.5; 2100 /* 16 32 22 */ coords[17 * dim + 0] = ds2; 2101 coords[17 * dim + 1] = -ds2; 2102 coords[17 * dim + 2] = 0.5; 2103 /* 17 33 21 */ coords[18 * dim + 0] = ds2; 2104 coords[18 * dim + 1] = ds2; 2105 coords[18 * dim + 2] = 0.5; 2106 /* 18 34 20 */ coords[19 * dim + 0] = -ds2; 2107 coords[19 * dim + 1] = ds2; 2108 coords[19 * dim + 2] = 0.5; 2109 /* 29 35 30 */ coords[20 * dim + 0] = -dis; 2110 coords[20 * dim + 1] = -dis; 2111 coords[20 * dim + 2] = 0.5; 2112 /* 23 36 25 */ coords[21 * dim + 0] = dis; 2113 coords[21 * dim + 1] = -dis; 2114 coords[21 * dim + 2] = 0.5; 2115 /* 24 37 26 */ coords[22 * dim + 0] = dis; 2116 coords[22 * dim + 1] = dis; 2117 coords[22 * dim + 2] = 0.5; 2118 /* 27 38 28 */ coords[23 * dim + 0] = -dis; 2119 coords[23 * dim + 1] = dis; 2120 coords[23 * dim + 2] = 0.5; 2121 } 2122 } 2123 PetscCall(VecRestoreArray(coordinates, &coords)); 2124 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 2125 PetscCall(VecDestroy(&coordinates)); 2126 } 2127 /* Create periodicity */ 2128 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 2129 PetscReal L[3] = {-1., -1., 0.}; 2130 PetscReal maxCell[3] = {-1., -1., 0.}; 2131 PetscReal lower[3] = {0.0, 0.0, 0.0}; 2132 PetscReal upper[3] = {1.0, 1.0, 1.5}; 2133 PetscInt numZCells = 3; 2134 2135 L[2] = upper[2] - lower[2]; 2136 maxCell[2] = 1.1 * (L[2] / numZCells); 2137 PetscCall(DMSetPeriodicity(dm, maxCell, lower, L)); 2138 } 2139 { 2140 DM cdm; 2141 PetscDS cds; 2142 PetscScalar c[2] = {1.0, 1.0}; 2143 2144 PetscCall(DMPlexCreateCoordinateSpace(dm, 1, PETSC_TRUE, NULL)); 2145 PetscCall(DMGetCoordinateDM(dm, &cdm)); 2146 PetscCall(DMGetDS(cdm, &cds)); 2147 PetscCall(PetscDSSetConstants(cds, 2, c)); 2148 } 2149 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 2150 2151 /* Wait for coordinate creation before doing in-place modification */ 2152 PetscCall(DMPlexInterpolateInPlace_Internal(dm)); 2153 2154 char oldprefix[PETSC_MAX_PATH_LEN]; 2155 const char *prefix; 2156 2157 PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm, &prefix)); 2158 PetscCall(PetscStrncpy(oldprefix, prefix, PETSC_MAX_PATH_LEN)); 2159 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dm, "petsc_cyl_ref_")); 2160 for (PetscInt r = 0; r < PetscMax(0, Nr); ++r) { 2161 DM rdm; 2162 2163 PetscCall(DMRefine(dm, PetscObjectComm((PetscObject)dm), &rdm)); 2164 PetscCall(DMPlexReplace_Internal(dm, &rdm)); 2165 } 2166 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dm, oldprefix)); 2167 PetscCall(DMPlexRemapGeometry(dm, 0.0, snapToCylinder)); 2168 2169 DMLabel bdlabel, edgelabel; 2170 IS faceIS; 2171 const PetscInt *faces; 2172 PetscInt Nf; 2173 2174 PetscCall(DMCreateLabel(dm, "marker")); 2175 PetscCall(DMGetLabel(dm, "marker", &bdlabel)); 2176 PetscCall(DMCreateLabel(dm, "generatrix")); 2177 PetscCall(DMGetLabel(dm, "generatrix", &edgelabel)); 2178 PetscCall(DMPlexMarkBoundaryFaces(dm, PETSC_DETERMINE, bdlabel)); 2179 // Remove faces on top and bottom 2180 PetscCall(DMLabelGetStratumIS(bdlabel, 1, &faceIS)); 2181 PetscCall(ISGetLocalSize(faceIS, &Nf)); 2182 PetscCall(ISGetIndices(faceIS, &faces)); 2183 for (PetscInt f = 0; f < Nf; ++f) { 2184 PetscReal vol, normal[3]; 2185 2186 PetscCall(DMPlexComputeCellGeometryFVM(dm, faces[f], &vol, NULL, normal)); 2187 if (PetscAbsReal(normal[2]) < PETSC_SMALL) PetscCall(DMLabelSetValue(edgelabel, faces[f], 1)); 2188 } 2189 PetscCall(ISRestoreIndices(faceIS, &faces)); 2190 PetscCall(ISDestroy(&faceIS)); 2191 PetscCall(DMPlexLabelComplete(dm, bdlabel)); 2192 PetscCall(DMPlexLabelComplete(dm, edgelabel)); 2193 PetscFunctionReturn(PETSC_SUCCESS); 2194 } 2195 2196 /*@ 2197 DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. 2198 2199 Collective 2200 2201 Input Parameters: 2202 + comm - The communicator for the `DM` object 2203 . periodicZ - The boundary type for the Z direction 2204 - Nr - The number of refinements to carry out 2205 2206 Output Parameter: 2207 . dm - The `DM` object 2208 2209 Level: beginner 2210 2211 Note: 2212 Here is the output numbering looking from the bottom of the cylinder\: 2213 .vb 2214 17-----14 2215 | | 2216 | 2 | 2217 | | 2218 17-----8-----7-----14 2219 | | | | 2220 | 3 | 0 | 1 | 2221 | | | | 2222 19-----5-----6-----13 2223 | | 2224 | 4 | 2225 | | 2226 19-----13 2227 2228 and up through the top 2229 2230 18-----16 2231 | | 2232 | 2 | 2233 | | 2234 18----10----11-----16 2235 | | | | 2236 | 3 | 0 | 1 | 2237 | | | | 2238 20-----9----12-----15 2239 | | 2240 | 4 | 2241 | | 2242 20-----15 2243 .ve 2244 2245 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 2246 @*/ 2247 PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, DMBoundaryType periodicZ, PetscInt Nr, DM *dm) 2248 { 2249 PetscFunctionBegin; 2250 PetscAssertPointer(dm, 4); 2251 PetscCall(DMCreate(comm, dm)); 2252 PetscCall(DMSetType(*dm, DMPLEX)); 2253 PetscCall(DMPlexCreateHexCylinderMesh_Internal(*dm, periodicZ, Nr)); 2254 PetscFunctionReturn(PETSC_SUCCESS); 2255 } 2256 2257 static PetscErrorCode DMPlexCreateWedgeCylinderMesh_Internal(DM dm, PetscInt n, PetscBool interpolate) 2258 { 2259 const PetscInt dim = 3; 2260 PetscInt numCells, numVertices, v; 2261 PetscMPIInt rank; 2262 2263 PetscFunctionBegin; 2264 PetscCheck(n >= 0, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %" PetscInt_FMT " cannot be negative", n); 2265 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 2266 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 2267 PetscCall(DMSetDimension(dm, dim)); 2268 /* Must create the celltype label here so that we do not automatically try to compute the types */ 2269 PetscCall(DMCreateLabel(dm, "celltype")); 2270 /* Create topology */ 2271 { 2272 PetscInt cone[6], c; 2273 2274 numCells = rank == 0 ? n : 0; 2275 numVertices = rank == 0 ? 2 * (n + 1) : 0; 2276 PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices)); 2277 for (c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 6)); 2278 PetscCall(DMSetUp(dm)); 2279 for (c = 0; c < numCells; c++) { 2280 cone[0] = c + n * 1; 2281 cone[1] = (c + 1) % n + n * 1; 2282 cone[2] = 0 + 3 * n; 2283 cone[3] = c + n * 2; 2284 cone[4] = (c + 1) % n + n * 2; 2285 cone[5] = 1 + 3 * n; 2286 PetscCall(DMPlexSetCone(dm, c, cone)); 2287 PetscCall(DMPlexSetCellType(dm, c, DM_POLYTOPE_TRI_PRISM_TENSOR)); 2288 } 2289 PetscCall(DMPlexSymmetrize(dm)); 2290 PetscCall(DMPlexStratify(dm)); 2291 } 2292 for (v = numCells; v < numCells + numVertices; ++v) PetscCall(DMPlexSetCellType(dm, v, DM_POLYTOPE_POINT)); 2293 /* Create cylinder geometry */ 2294 { 2295 Vec coordinates; 2296 PetscSection coordSection; 2297 PetscScalar *coords; 2298 PetscInt coordSize, c; 2299 2300 /* Build coordinates */ 2301 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 2302 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 2303 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim)); 2304 PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices)); 2305 for (v = numCells; v < numCells + numVertices; ++v) { 2306 PetscCall(PetscSectionSetDof(coordSection, v, dim)); 2307 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim)); 2308 } 2309 PetscCall(PetscSectionSetUp(coordSection)); 2310 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 2311 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 2312 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 2313 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 2314 PetscCall(VecSetBlockSize(coordinates, dim)); 2315 PetscCall(VecSetType(coordinates, VECSTANDARD)); 2316 PetscCall(VecGetArray(coordinates, &coords)); 2317 for (c = 0; c < numCells; c++) { 2318 coords[(c + 0 * n) * dim + 0] = PetscCosReal(2.0 * c * PETSC_PI / n); 2319 coords[(c + 0 * n) * dim + 1] = PetscSinReal(2.0 * c * PETSC_PI / n); 2320 coords[(c + 0 * n) * dim + 2] = 1.0; 2321 coords[(c + 1 * n) * dim + 0] = PetscCosReal(2.0 * c * PETSC_PI / n); 2322 coords[(c + 1 * n) * dim + 1] = PetscSinReal(2.0 * c * PETSC_PI / n); 2323 coords[(c + 1 * n) * dim + 2] = 0.0; 2324 } 2325 if (rank == 0) { 2326 coords[(2 * n + 0) * dim + 0] = 0.0; 2327 coords[(2 * n + 0) * dim + 1] = 0.0; 2328 coords[(2 * n + 0) * dim + 2] = 1.0; 2329 coords[(2 * n + 1) * dim + 0] = 0.0; 2330 coords[(2 * n + 1) * dim + 1] = 0.0; 2331 coords[(2 * n + 1) * dim + 2] = 0.0; 2332 } 2333 PetscCall(VecRestoreArray(coordinates, &coords)); 2334 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 2335 PetscCall(VecDestroy(&coordinates)); 2336 } 2337 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 2338 /* Interpolate */ 2339 if (interpolate) PetscCall(DMPlexInterpolateInPlace_Internal(dm)); 2340 PetscFunctionReturn(PETSC_SUCCESS); 2341 } 2342 2343 /*@ 2344 DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges. 2345 2346 Collective 2347 2348 Input Parameters: 2349 + comm - The communicator for the `DM` object 2350 . n - The number of wedges around the origin 2351 - interpolate - Create edges and faces 2352 2353 Output Parameter: 2354 . dm - The `DM` object 2355 2356 Level: beginner 2357 2358 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateHexCylinderMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 2359 @*/ 2360 PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm) 2361 { 2362 PetscFunctionBegin; 2363 PetscAssertPointer(dm, 4); 2364 PetscCall(DMCreate(comm, dm)); 2365 PetscCall(DMSetType(*dm, DMPLEX)); 2366 PetscCall(DMPlexCreateWedgeCylinderMesh_Internal(*dm, n, interpolate)); 2367 PetscFunctionReturn(PETSC_SUCCESS); 2368 } 2369 2370 static inline PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 2371 { 2372 PetscReal prod = 0.0; 2373 PetscInt i; 2374 for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]); 2375 return PetscSqrtReal(prod); 2376 } 2377 2378 static inline PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 2379 { 2380 PetscReal prod = 0.0; 2381 PetscInt i; 2382 for (i = 0; i < dim; ++i) prod += x[i] * y[i]; 2383 return prod; 2384 } 2385 2386 /* The first constant is the sphere radius */ 2387 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[]) 2388 { 2389 PetscReal r = PetscRealPart(constants[0]); 2390 PetscReal norm2 = 0.0, fac; 2391 PetscInt n = uOff[1] - uOff[0], d; 2392 2393 for (d = 0; d < n; ++d) norm2 += PetscSqr(PetscRealPart(u[d])); 2394 fac = r / PetscSqrtReal(norm2); 2395 for (d = 0; d < n; ++d) f0[d] = u[d] * fac; 2396 } 2397 2398 static PetscErrorCode DMPlexCreateSphereMesh_Internal(DM dm, PetscInt dim, PetscBool simplex, PetscReal R) 2399 { 2400 const PetscInt embedDim = dim + 1; 2401 PetscSection coordSection; 2402 Vec coordinates; 2403 PetscScalar *coords; 2404 PetscReal *coordsIn; 2405 PetscInt numCells, numEdges, numVerts = 0, firstVertex = 0, v, firstEdge, coordSize, d, e; 2406 PetscMPIInt rank; 2407 2408 PetscFunctionBegin; 2409 PetscValidLogicalCollectiveBool(dm, simplex, 3); 2410 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 2411 PetscCall(DMSetDimension(dm, dim)); 2412 PetscCall(DMSetCoordinateDim(dm, dim + 1)); 2413 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 2414 switch (dim) { 2415 case 1: 2416 numCells = 16; 2417 numVerts = numCells; 2418 2419 // Build Topology 2420 PetscCall(DMPlexSetChart(dm, 0, numCells + numVerts)); 2421 for (PetscInt c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, embedDim)); 2422 PetscCall(DMSetUp(dm)); 2423 for (PetscInt c = 0; c < numCells; ++c) { 2424 PetscInt cone[2]; 2425 2426 cone[0] = c + numCells; 2427 cone[1] = (c + 1) % numVerts + numCells; 2428 PetscCall(DMPlexSetCone(dm, c, cone)); 2429 } 2430 PetscCall(DMPlexSymmetrize(dm)); 2431 PetscCall(DMPlexStratify(dm)); 2432 PetscCall(PetscMalloc1(numVerts * embedDim, &coordsIn)); 2433 for (PetscInt v = 0; v < numVerts; ++v) { 2434 const PetscReal rad = 2. * PETSC_PI * v / numVerts; 2435 2436 coordsIn[v * embedDim + 0] = PetscCosReal(rad); 2437 coordsIn[v * embedDim + 1] = PetscSinReal(rad); 2438 } 2439 break; 2440 case 2: 2441 if (simplex) { 2442 const PetscReal radius = PetscSqrtReal(1 + PETSC_PHI * PETSC_PHI) / (1.0 + PETSC_PHI); 2443 const PetscReal edgeLen = 2.0 / (1.0 + PETSC_PHI) * (R / radius); 2444 const PetscInt degree = 5; 2445 PetscReal vertex[3] = {0.0, 1.0 / (1.0 + PETSC_PHI), PETSC_PHI / (1.0 + PETSC_PHI)}; 2446 PetscInt s[3] = {1, 1, 1}; 2447 PetscInt cone[3]; 2448 PetscInt *graph; 2449 2450 vertex[0] *= R / radius; 2451 vertex[1] *= R / radius; 2452 vertex[2] *= R / radius; 2453 numCells = rank == 0 ? 20 : 0; 2454 numVerts = rank == 0 ? 12 : 0; 2455 firstVertex = numCells; 2456 /* Use icosahedron, which for a R-sphere has coordinates which are all cyclic permutations of 2457 2458 (0, \pm 1/\phi+1, \pm \phi/\phi+1) 2459 2460 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 2461 length is then given by 2/(1+\phi) = 2 * 0.38197 = 0.76393. 2462 */ 2463 /* Construct vertices */ 2464 PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn)); 2465 if (rank == 0) { 2466 for (PetscInt p = 0, i = 0; p < embedDim; ++p) { 2467 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2468 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2469 for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[(d + p) % embedDim] * vertex[(d + p) % embedDim]; 2470 ++i; 2471 } 2472 } 2473 } 2474 } 2475 /* Construct graph */ 2476 PetscCall(PetscCalloc1(numVerts * numVerts, &graph)); 2477 for (PetscInt i = 0; i < numVerts; ++i) { 2478 PetscInt k = 0; 2479 for (PetscInt j = 0; j < numVerts; ++j) { 2480 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i * embedDim], &coordsIn[j * embedDim]) - edgeLen) < PETSC_SMALL) { 2481 graph[i * numVerts + j] = 1; 2482 ++k; 2483 } 2484 } 2485 PetscCheck(k == degree, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid icosahedron, vertex %" PetscInt_FMT " degree %" PetscInt_FMT " != %" PetscInt_FMT, i, k, degree); 2486 } 2487 /* Build Topology */ 2488 PetscCall(DMPlexSetChart(dm, 0, numCells + numVerts)); 2489 for (PetscInt c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, embedDim)); 2490 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 2491 /* Cells */ 2492 for (PetscInt i = 0, c = 0; i < numVerts; ++i) { 2493 for (PetscInt j = 0; j < i; ++j) { 2494 for (PetscInt k = 0; k < j; ++k) { 2495 if (graph[i * numVerts + j] && graph[j * numVerts + k] && graph[k * numVerts + i]) { 2496 cone[0] = firstVertex + i; 2497 cone[1] = firstVertex + j; 2498 cone[2] = firstVertex + k; 2499 /* Check orientation */ 2500 { 2501 const PetscInt epsilon[3][3][3] = { 2502 {{0, 0, 0}, {0, 0, 1}, {0, -1, 0}}, 2503 {{0, 0, -1}, {0, 0, 0}, {1, 0, 0} }, 2504 {{0, 1, 0}, {-1, 0, 0}, {0, 0, 0} } 2505 }; 2506 PetscReal normal[3]; 2507 PetscInt e, f; 2508 2509 for (d = 0; d < embedDim; ++d) { 2510 normal[d] = 0.0; 2511 for (e = 0; e < embedDim; ++e) { 2512 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]); 2513 } 2514 } 2515 if (DotReal(embedDim, normal, &coordsIn[i * embedDim]) < 0) { 2516 PetscInt tmp = cone[1]; 2517 cone[1] = cone[2]; 2518 cone[2] = tmp; 2519 } 2520 } 2521 PetscCall(DMPlexSetCone(dm, c++, cone)); 2522 } 2523 } 2524 } 2525 } 2526 PetscCall(DMPlexSymmetrize(dm)); 2527 PetscCall(DMPlexStratify(dm)); 2528 PetscCall(PetscFree(graph)); 2529 } else { 2530 /* 2531 12-21--13 2532 | | 2533 25 4 24 2534 | | 2535 12-25--9-16--8-24--13 2536 | | | | 2537 23 5 17 0 15 3 22 2538 | | | | 2539 10-20--6-14--7-19--11 2540 | | 2541 20 1 19 2542 | | 2543 10-18--11 2544 | | 2545 23 2 22 2546 | | 2547 12-21--13 2548 */ 2549 PetscInt cone[4], ornt[4]; 2550 2551 numCells = rank == 0 ? 6 : 0; 2552 numEdges = rank == 0 ? 12 : 0; 2553 numVerts = rank == 0 ? 8 : 0; 2554 firstVertex = numCells; 2555 firstEdge = numCells + numVerts; 2556 /* Build Topology */ 2557 PetscCall(DMPlexSetChart(dm, 0, numCells + numEdges + numVerts)); 2558 for (PetscInt c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, 4)); 2559 for (e = firstEdge; e < firstEdge + numEdges; ++e) PetscCall(DMPlexSetConeSize(dm, e, 2)); 2560 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 2561 if (rank == 0) { 2562 /* Cell 0 */ 2563 cone[0] = 14; 2564 cone[1] = 15; 2565 cone[2] = 16; 2566 cone[3] = 17; 2567 PetscCall(DMPlexSetCone(dm, 0, cone)); 2568 ornt[0] = 0; 2569 ornt[1] = 0; 2570 ornt[2] = 0; 2571 ornt[3] = 0; 2572 PetscCall(DMPlexSetConeOrientation(dm, 0, ornt)); 2573 /* Cell 1 */ 2574 cone[0] = 18; 2575 cone[1] = 19; 2576 cone[2] = 14; 2577 cone[3] = 20; 2578 PetscCall(DMPlexSetCone(dm, 1, cone)); 2579 ornt[0] = 0; 2580 ornt[1] = 0; 2581 ornt[2] = -1; 2582 ornt[3] = 0; 2583 PetscCall(DMPlexSetConeOrientation(dm, 1, ornt)); 2584 /* Cell 2 */ 2585 cone[0] = 21; 2586 cone[1] = 22; 2587 cone[2] = 18; 2588 cone[3] = 23; 2589 PetscCall(DMPlexSetCone(dm, 2, cone)); 2590 ornt[0] = 0; 2591 ornt[1] = 0; 2592 ornt[2] = -1; 2593 ornt[3] = 0; 2594 PetscCall(DMPlexSetConeOrientation(dm, 2, ornt)); 2595 /* Cell 3 */ 2596 cone[0] = 19; 2597 cone[1] = 22; 2598 cone[2] = 24; 2599 cone[3] = 15; 2600 PetscCall(DMPlexSetCone(dm, 3, cone)); 2601 ornt[0] = -1; 2602 ornt[1] = -1; 2603 ornt[2] = 0; 2604 ornt[3] = -1; 2605 PetscCall(DMPlexSetConeOrientation(dm, 3, ornt)); 2606 /* Cell 4 */ 2607 cone[0] = 16; 2608 cone[1] = 24; 2609 cone[2] = 21; 2610 cone[3] = 25; 2611 PetscCall(DMPlexSetCone(dm, 4, cone)); 2612 ornt[0] = -1; 2613 ornt[1] = -1; 2614 ornt[2] = -1; 2615 ornt[3] = 0; 2616 PetscCall(DMPlexSetConeOrientation(dm, 4, ornt)); 2617 /* Cell 5 */ 2618 cone[0] = 20; 2619 cone[1] = 17; 2620 cone[2] = 25; 2621 cone[3] = 23; 2622 PetscCall(DMPlexSetCone(dm, 5, cone)); 2623 ornt[0] = -1; 2624 ornt[1] = -1; 2625 ornt[2] = -1; 2626 ornt[3] = -1; 2627 PetscCall(DMPlexSetConeOrientation(dm, 5, ornt)); 2628 /* Edges */ 2629 cone[0] = 6; 2630 cone[1] = 7; 2631 PetscCall(DMPlexSetCone(dm, 14, cone)); 2632 cone[0] = 7; 2633 cone[1] = 8; 2634 PetscCall(DMPlexSetCone(dm, 15, cone)); 2635 cone[0] = 8; 2636 cone[1] = 9; 2637 PetscCall(DMPlexSetCone(dm, 16, cone)); 2638 cone[0] = 9; 2639 cone[1] = 6; 2640 PetscCall(DMPlexSetCone(dm, 17, cone)); 2641 cone[0] = 10; 2642 cone[1] = 11; 2643 PetscCall(DMPlexSetCone(dm, 18, cone)); 2644 cone[0] = 11; 2645 cone[1] = 7; 2646 PetscCall(DMPlexSetCone(dm, 19, cone)); 2647 cone[0] = 6; 2648 cone[1] = 10; 2649 PetscCall(DMPlexSetCone(dm, 20, cone)); 2650 cone[0] = 12; 2651 cone[1] = 13; 2652 PetscCall(DMPlexSetCone(dm, 21, cone)); 2653 cone[0] = 13; 2654 cone[1] = 11; 2655 PetscCall(DMPlexSetCone(dm, 22, cone)); 2656 cone[0] = 10; 2657 cone[1] = 12; 2658 PetscCall(DMPlexSetCone(dm, 23, cone)); 2659 cone[0] = 13; 2660 cone[1] = 8; 2661 PetscCall(DMPlexSetCone(dm, 24, cone)); 2662 cone[0] = 12; 2663 cone[1] = 9; 2664 PetscCall(DMPlexSetCone(dm, 25, cone)); 2665 } 2666 PetscCall(DMPlexSymmetrize(dm)); 2667 PetscCall(DMPlexStratify(dm)); 2668 /* Build coordinates */ 2669 PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn)); 2670 if (rank == 0) { 2671 coordsIn[0 * embedDim + 0] = -R; 2672 coordsIn[0 * embedDim + 1] = R; 2673 coordsIn[0 * embedDim + 2] = -R; 2674 coordsIn[1 * embedDim + 0] = R; 2675 coordsIn[1 * embedDim + 1] = R; 2676 coordsIn[1 * embedDim + 2] = -R; 2677 coordsIn[2 * embedDim + 0] = R; 2678 coordsIn[2 * embedDim + 1] = -R; 2679 coordsIn[2 * embedDim + 2] = -R; 2680 coordsIn[3 * embedDim + 0] = -R; 2681 coordsIn[3 * embedDim + 1] = -R; 2682 coordsIn[3 * embedDim + 2] = -R; 2683 coordsIn[4 * embedDim + 0] = -R; 2684 coordsIn[4 * embedDim + 1] = R; 2685 coordsIn[4 * embedDim + 2] = R; 2686 coordsIn[5 * embedDim + 0] = R; 2687 coordsIn[5 * embedDim + 1] = R; 2688 coordsIn[5 * embedDim + 2] = R; 2689 coordsIn[6 * embedDim + 0] = -R; 2690 coordsIn[6 * embedDim + 1] = -R; 2691 coordsIn[6 * embedDim + 2] = R; 2692 coordsIn[7 * embedDim + 0] = R; 2693 coordsIn[7 * embedDim + 1] = -R; 2694 coordsIn[7 * embedDim + 2] = R; 2695 } 2696 } 2697 break; 2698 case 3: 2699 if (simplex) { 2700 const PetscReal edgeLen = 1.0 / PETSC_PHI; 2701 PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5}; 2702 PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0}; 2703 PetscReal vertexC[4] = {0.5, 0.5 * PETSC_PHI, 0.5 / PETSC_PHI, 0.0}; 2704 const PetscInt degree = 12; 2705 PetscInt s[4] = {1, 1, 1}; 2706 PetscInt evenPerm[12][4] = { 2707 {0, 1, 2, 3}, 2708 {0, 2, 3, 1}, 2709 {0, 3, 1, 2}, 2710 {1, 0, 3, 2}, 2711 {1, 2, 0, 3}, 2712 {1, 3, 2, 0}, 2713 {2, 0, 1, 3}, 2714 {2, 1, 3, 0}, 2715 {2, 3, 0, 1}, 2716 {3, 0, 2, 1}, 2717 {3, 1, 0, 2}, 2718 {3, 2, 1, 0} 2719 }; 2720 PetscInt cone[4]; 2721 PetscInt *graph, p, i, j, k, l; 2722 2723 vertexA[0] *= R; 2724 vertexA[1] *= R; 2725 vertexA[2] *= R; 2726 vertexA[3] *= R; 2727 vertexB[0] *= R; 2728 vertexB[1] *= R; 2729 vertexB[2] *= R; 2730 vertexB[3] *= R; 2731 vertexC[0] *= R; 2732 vertexC[1] *= R; 2733 vertexC[2] *= R; 2734 vertexC[3] *= R; 2735 numCells = rank == 0 ? 600 : 0; 2736 numVerts = rank == 0 ? 120 : 0; 2737 firstVertex = numCells; 2738 /* Use the 600-cell, which for a unit sphere has coordinates which are 2739 2740 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16 2741 (\pm 1, 0, 0, 0) all cyclic permutations 8 2742 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96 2743 2744 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 2745 length is then given by 1/\phi = 0.61803. 2746 2747 http://buzzard.pugetsound.edu/sage-practice/ch03s03.html 2748 http://mathworld.wolfram.com/600-Cell.html 2749 */ 2750 /* Construct vertices */ 2751 PetscCall(PetscCalloc1(numVerts * embedDim, &coordsIn)); 2752 i = 0; 2753 if (rank == 0) { 2754 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2755 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2756 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2757 for (s[3] = -1; s[3] < 2; s[3] += 2) { 2758 for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[d] * vertexA[d]; 2759 ++i; 2760 } 2761 } 2762 } 2763 } 2764 for (p = 0; p < embedDim; ++p) { 2765 s[1] = s[2] = s[3] = 1; 2766 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2767 for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[(d + p) % embedDim] * vertexB[(d + p) % embedDim]; 2768 ++i; 2769 } 2770 } 2771 for (p = 0; p < 12; ++p) { 2772 s[3] = 1; 2773 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2774 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2775 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2776 for (d = 0; d < embedDim; ++d) coordsIn[i * embedDim + d] = s[evenPerm[p][d]] * vertexC[evenPerm[p][d]]; 2777 ++i; 2778 } 2779 } 2780 } 2781 } 2782 } 2783 PetscCheck(i == numVerts, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertices %" PetscInt_FMT " != %" PetscInt_FMT, i, numVerts); 2784 /* Construct graph */ 2785 PetscCall(PetscCalloc1(numVerts * numVerts, &graph)); 2786 for (i = 0; i < numVerts; ++i) { 2787 for (j = 0, k = 0; j < numVerts; ++j) { 2788 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i * embedDim], &coordsIn[j * embedDim]) - edgeLen) < PETSC_SMALL) { 2789 graph[i * numVerts + j] = 1; 2790 ++k; 2791 } 2792 } 2793 PetscCheck(k == degree, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertex %" PetscInt_FMT " degree %" PetscInt_FMT " != %" PetscInt_FMT, i, k, degree); 2794 } 2795 /* Build Topology */ 2796 PetscCall(DMPlexSetChart(dm, 0, numCells + numVerts)); 2797 for (PetscInt c = 0; c < numCells; c++) PetscCall(DMPlexSetConeSize(dm, c, embedDim)); 2798 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 2799 /* Cells */ 2800 if (rank == 0) { 2801 for (PetscInt i = 0, c = 0; i < numVerts; ++i) { 2802 for (j = 0; j < i; ++j) { 2803 for (k = 0; k < j; ++k) { 2804 for (l = 0; l < k; ++l) { 2805 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]) { 2806 cone[0] = firstVertex + i; 2807 cone[1] = firstVertex + j; 2808 cone[2] = firstVertex + k; 2809 cone[3] = firstVertex + l; 2810 /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */ 2811 { 2812 const PetscInt epsilon[4][4][4][4] = { 2813 {{{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}}}, 2814 2815 {{{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}}}, 2816 2817 {{{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}}}, 2818 2819 {{{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}} } 2820 }; 2821 PetscReal normal[4]; 2822 PetscInt e, f, g; 2823 2824 for (d = 0; d < embedDim; ++d) { 2825 normal[d] = 0.0; 2826 for (e = 0; e < embedDim; ++e) { 2827 for (f = 0; f < embedDim; ++f) { 2828 for (g = 0; g < embedDim; ++g) { 2829 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]); 2830 } 2831 } 2832 } 2833 } 2834 if (DotReal(embedDim, normal, &coordsIn[i * embedDim]) < 0) { 2835 PetscInt tmp = cone[1]; 2836 cone[1] = cone[2]; 2837 cone[2] = tmp; 2838 } 2839 } 2840 PetscCall(DMPlexSetCone(dm, c++, cone)); 2841 } 2842 } 2843 } 2844 } 2845 } 2846 } 2847 PetscCall(DMPlexSymmetrize(dm)); 2848 PetscCall(DMPlexStratify(dm)); 2849 PetscCall(PetscFree(graph)); 2850 } 2851 break; 2852 default: 2853 SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported dimension for sphere: %" PetscInt_FMT, dim); 2854 } 2855 /* Create coordinates */ 2856 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 2857 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 2858 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, embedDim)); 2859 PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex + numVerts)); 2860 for (v = firstVertex; v < firstVertex + numVerts; ++v) { 2861 PetscCall(PetscSectionSetDof(coordSection, v, embedDim)); 2862 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, embedDim)); 2863 } 2864 PetscCall(PetscSectionSetUp(coordSection)); 2865 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 2866 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 2867 PetscCall(VecSetBlockSize(coordinates, embedDim)); 2868 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 2869 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 2870 PetscCall(VecSetType(coordinates, VECSTANDARD)); 2871 PetscCall(VecGetArray(coordinates, &coords)); 2872 for (v = 0; v < numVerts; ++v) 2873 for (d = 0; d < embedDim; ++d) coords[v * embedDim + d] = coordsIn[v * embedDim + d]; 2874 PetscCall(VecRestoreArray(coordinates, &coords)); 2875 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 2876 PetscCall(VecDestroy(&coordinates)); 2877 PetscCall(PetscFree(coordsIn)); 2878 { 2879 DM cdm; 2880 PetscDS cds; 2881 PetscScalar c = R; 2882 2883 PetscCall(DMPlexCreateCoordinateSpace(dm, 1, PETSC_TRUE, snapToSphere)); 2884 PetscCall(DMGetCoordinateDM(dm, &cdm)); 2885 PetscCall(DMGetDS(cdm, &cds)); 2886 PetscCall(PetscDSSetConstants(cds, 1, &c)); 2887 } 2888 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 2889 /* Wait for coordinate creation before doing in-place modification */ 2890 if (simplex) PetscCall(DMPlexInterpolateInPlace_Internal(dm)); 2891 PetscFunctionReturn(PETSC_SUCCESS); 2892 } 2893 2894 typedef void (*TPSEvaluateFunc)(const PetscReal[], PetscReal *, PetscReal[], PetscReal (*)[3]); 2895 2896 /* 2897 The Schwarz P implicit surface is 2898 2899 f(x) = cos(x0) + cos(x1) + cos(x2) = 0 2900 */ 2901 static void TPSEvaluate_SchwarzP(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3]) 2902 { 2903 PetscReal c[3] = {PetscCosReal(y[0] * PETSC_PI), PetscCosReal(y[1] * PETSC_PI), PetscCosReal(y[2] * PETSC_PI)}; 2904 PetscReal g[3] = {-PetscSinReal(y[0] * PETSC_PI), -PetscSinReal(y[1] * PETSC_PI), -PetscSinReal(y[2] * PETSC_PI)}; 2905 f[0] = c[0] + c[1] + c[2]; 2906 for (PetscInt i = 0; i < 3; i++) { 2907 grad[i] = PETSC_PI * g[i]; 2908 for (PetscInt j = 0; j < 3; j++) hess[i][j] = (i == j) ? -PetscSqr(PETSC_PI) * c[i] : 0.; 2909 } 2910 } 2911 2912 // u[] is a tentative normal on input. Replace with the implicit function gradient in the same direction 2913 static PetscErrorCode TPSExtrudeNormalFunc_SchwarzP(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt r, PetscScalar u[], void *ctx) 2914 { 2915 for (PetscInt i = 0; i < 3; i++) u[i] = -PETSC_PI * PetscSinReal(x[i] * PETSC_PI); 2916 return PETSC_SUCCESS; 2917 } 2918 2919 /* 2920 The Gyroid implicit surface is 2921 2922 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) 2923 2924 */ 2925 static void TPSEvaluate_Gyroid(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3]) 2926 { 2927 PetscReal s[3] = {PetscSinReal(PETSC_PI * y[0]), PetscSinReal(PETSC_PI * (y[1] + .5)), PetscSinReal(PETSC_PI * (y[2] + .25))}; 2928 PetscReal c[3] = {PetscCosReal(PETSC_PI * y[0]), PetscCosReal(PETSC_PI * (y[1] + .5)), PetscCosReal(PETSC_PI * (y[2] + .25))}; 2929 f[0] = s[0] * c[1] + s[1] * c[2] + s[2] * c[0]; 2930 grad[0] = PETSC_PI * (c[0] * c[1] - s[2] * s[0]); 2931 grad[1] = PETSC_PI * (c[1] * c[2] - s[0] * s[1]); 2932 grad[2] = PETSC_PI * (c[2] * c[0] - s[1] * s[2]); 2933 hess[0][0] = -PetscSqr(PETSC_PI) * (s[0] * c[1] + s[2] * c[0]); 2934 hess[0][1] = -PetscSqr(PETSC_PI) * (c[0] * s[1]); 2935 hess[0][2] = -PetscSqr(PETSC_PI) * (c[2] * s[0]); 2936 hess[1][0] = -PetscSqr(PETSC_PI) * (s[1] * c[2] + s[0] * c[1]); 2937 hess[1][1] = -PetscSqr(PETSC_PI) * (c[1] * s[2]); 2938 hess[2][2] = -PetscSqr(PETSC_PI) * (c[0] * s[1]); 2939 hess[2][0] = -PetscSqr(PETSC_PI) * (s[2] * c[0] + s[1] * c[2]); 2940 hess[2][1] = -PetscSqr(PETSC_PI) * (c[2] * s[0]); 2941 hess[2][2] = -PetscSqr(PETSC_PI) * (c[1] * s[2]); 2942 } 2943 2944 // u[] is a tentative normal on input. Replace with the implicit function gradient in the same direction 2945 static PetscErrorCode TPSExtrudeNormalFunc_Gyroid(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt r, PetscScalar u[], void *ctx) 2946 { 2947 PetscReal s[3] = {PetscSinReal(PETSC_PI * x[0]), PetscSinReal(PETSC_PI * (x[1] + .5)), PetscSinReal(PETSC_PI * (x[2] + .25))}; 2948 PetscReal c[3] = {PetscCosReal(PETSC_PI * x[0]), PetscCosReal(PETSC_PI * (x[1] + .5)), PetscCosReal(PETSC_PI * (x[2] + .25))}; 2949 u[0] = PETSC_PI * (c[0] * c[1] - s[2] * s[0]); 2950 u[1] = PETSC_PI * (c[1] * c[2] - s[0] * s[1]); 2951 u[2] = PETSC_PI * (c[2] * c[0] - s[1] * s[2]); 2952 return PETSC_SUCCESS; 2953 } 2954 2955 /* 2956 We wish to solve 2957 2958 min_y || y - x ||^2 subject to f(y) = 0 2959 2960 Let g(y) = grad(f). The minimization problem is equivalent to asking to satisfy 2961 f(y) = 0 and (y-x) is parallel to g(y). We do this by using Householder QR to obtain a basis for the 2962 tangent space and ask for both components in the tangent space to be zero. 2963 2964 Take g to be a column vector and compute the "full QR" factorization Q R = g, 2965 where Q = I - 2 n n^T is a symmetric orthogonal matrix. 2966 The first column of Q is parallel to g so the remaining two columns span the null space. 2967 Let Qn = Q[:,1:] be those remaining columns. Then Qn Qn^T is an orthogonal projector into the tangent space. 2968 Since Q is symmetric, this is equivalent to multiplying by Q and taking the last two entries. 2969 In total, we have a system of 3 equations in 3 unknowns: 2970 2971 f(y) = 0 1 equation 2972 Qn^T (y - x) = 0 2 equations 2973 2974 Here, we compute the residual and Jacobian of this system. 2975 */ 2976 static void TPSNearestPointResJac(TPSEvaluateFunc feval, const PetscScalar x[], const PetscScalar y[], PetscScalar res[], PetscScalar J[]) 2977 { 2978 PetscReal yreal[3] = {PetscRealPart(y[0]), PetscRealPart(y[1]), PetscRealPart(y[2])}; 2979 PetscReal d[3] = {PetscRealPart(y[0] - x[0]), PetscRealPart(y[1] - x[1]), PetscRealPart(y[2] - x[2])}; 2980 PetscReal f, grad[3], n[3], norm, norm_y[3], nd, nd_y[3], sign; 2981 PetscReal n_y[3][3] = { 2982 {0, 0, 0}, 2983 {0, 0, 0}, 2984 {0, 0, 0} 2985 }; 2986 2987 feval(yreal, &f, grad, n_y); 2988 2989 for (PetscInt i = 0; i < 3; i++) n[i] = grad[i]; 2990 norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2])); 2991 for (PetscInt i = 0; i < 3; i++) norm_y[i] = 1. / norm * n[i] * n_y[i][i]; 2992 2993 // Define the Householder reflector 2994 sign = n[0] >= 0 ? 1. : -1.; 2995 n[0] += norm * sign; 2996 for (PetscInt i = 0; i < 3; i++) n_y[0][i] += norm_y[i] * sign; 2997 2998 norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2])); 2999 norm_y[0] = 1. / norm * (n[0] * n_y[0][0]); 3000 norm_y[1] = 1. / norm * (n[0] * n_y[0][1] + n[1] * n_y[1][1]); 3001 norm_y[2] = 1. / norm * (n[0] * n_y[0][2] + n[2] * n_y[2][2]); 3002 3003 for (PetscInt i = 0; i < 3; i++) { 3004 n[i] /= norm; 3005 for (PetscInt j = 0; j < 3; j++) { 3006 // note that n[i] is n_old[i]/norm when executing the code below 3007 n_y[i][j] = n_y[i][j] / norm - n[i] / norm * norm_y[j]; 3008 } 3009 } 3010 3011 nd = n[0] * d[0] + n[1] * d[1] + n[2] * d[2]; 3012 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]; 3013 3014 res[0] = f; 3015 res[1] = d[1] - 2 * n[1] * nd; 3016 res[2] = d[2] - 2 * n[2] * nd; 3017 // J[j][i] is J_{ij} (column major) 3018 for (PetscInt j = 0; j < 3; j++) { 3019 J[0 + j * 3] = grad[j]; 3020 J[1 + j * 3] = (j == 1) * 1. - 2 * (n_y[1][j] * nd + n[1] * nd_y[j]); 3021 J[2 + j * 3] = (j == 2) * 1. - 2 * (n_y[2][j] * nd + n[2] * nd_y[j]); 3022 } 3023 } 3024 3025 /* 3026 Project x to the nearest point on the implicit surface using Newton's method. 3027 */ 3028 static PetscErrorCode TPSNearestPoint(TPSEvaluateFunc feval, PetscScalar x[]) 3029 { 3030 PetscScalar y[3] = {x[0], x[1], x[2]}; // Initial guess 3031 3032 PetscFunctionBegin; 3033 for (PetscInt iter = 0; iter < 10; iter++) { 3034 PetscScalar res[3], J[9]; 3035 PetscReal resnorm; 3036 TPSNearestPointResJac(feval, x, y, res, J); 3037 resnorm = PetscSqrtReal(PetscSqr(PetscRealPart(res[0])) + PetscSqr(PetscRealPart(res[1])) + PetscSqr(PetscRealPart(res[2]))); 3038 if (0) { // Turn on this monitor if you need to confirm quadratic convergence 3039 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]))); 3040 } 3041 if (resnorm < PETSC_SMALL) break; 3042 3043 // Take the Newton step 3044 PetscCall(PetscKernel_A_gets_inverse_A_3(J, 0., PETSC_FALSE, NULL)); 3045 PetscKernel_v_gets_v_minus_A_times_w_3(y, J, res); 3046 } 3047 for (PetscInt i = 0; i < 3; i++) x[i] = y[i]; 3048 PetscFunctionReturn(PETSC_SUCCESS); 3049 } 3050 3051 const char *const DMPlexTPSTypes[] = {"SCHWARZ_P", "GYROID", "DMPlexTPSType", "DMPLEX_TPS_", NULL}; 3052 3053 static PetscErrorCode DMPlexCreateTPSMesh_Internal(DM dm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscBool tps_distribute, PetscInt refinements, PetscInt layers, PetscReal thickness) 3054 { 3055 PetscMPIInt rank; 3056 PetscInt topoDim = 2, spaceDim = 3, numFaces = 0, numVertices = 0, numEdges = 0; 3057 PetscInt(*edges)[2] = NULL, *edgeSets = NULL; 3058 PetscInt *cells_flat = NULL; 3059 PetscReal *vtxCoords = NULL; 3060 TPSEvaluateFunc evalFunc = NULL; 3061 PetscSimplePointFn *normalFunc = NULL; 3062 DMLabel label; 3063 3064 PetscFunctionBegin; 3065 PetscCall(PetscLogEventBegin(DMPLEX_Generate, dm, 0, 0, 0)); 3066 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank)); 3067 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); 3068 switch (tpstype) { 3069 case DMPLEX_TPS_SCHWARZ_P: 3070 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"); 3071 if (rank == 0) { 3072 PetscInt(*cells)[6][4][4] = NULL; // [junction, junction-face, cell, conn] 3073 PetscInt Njunctions = 0, Ncuts = 0, Npipes[3], vcount; 3074 PetscReal L = 1; 3075 3076 Npipes[0] = (extent[0] + 1) * extent[1] * extent[2]; 3077 Npipes[1] = extent[0] * (extent[1] + 1) * extent[2]; 3078 Npipes[2] = extent[0] * extent[1] * (extent[2] + 1); 3079 Njunctions = extent[0] * extent[1] * extent[2]; 3080 Ncuts = 2 * (extent[0] * extent[1] + extent[1] * extent[2] + extent[2] * extent[0]); 3081 numVertices = 4 * (Npipes[0] + Npipes[1] + Npipes[2]) + 8 * Njunctions; 3082 PetscCall(PetscMalloc1(3 * numVertices, &vtxCoords)); 3083 PetscCall(PetscMalloc1(Njunctions, &cells)); 3084 PetscCall(PetscMalloc1(Ncuts * 4, &edges)); 3085 PetscCall(PetscMalloc1(Ncuts * 4, &edgeSets)); 3086 // x-normal pipes 3087 vcount = 0; 3088 for (PetscInt i = 0; i < extent[0] + 1; i++) { 3089 for (PetscInt j = 0; j < extent[1]; j++) { 3090 for (PetscInt k = 0; k < extent[2]; k++) { 3091 for (PetscInt l = 0; l < 4; l++) { 3092 vtxCoords[vcount++] = (2 * i - 1) * L; 3093 vtxCoords[vcount++] = 2 * j * L + PetscCosReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3094 vtxCoords[vcount++] = 2 * k * L + PetscSinReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3095 } 3096 } 3097 } 3098 } 3099 // y-normal pipes 3100 for (PetscInt i = 0; i < extent[0]; i++) { 3101 for (PetscInt j = 0; j < extent[1] + 1; j++) { 3102 for (PetscInt k = 0; k < extent[2]; k++) { 3103 for (PetscInt l = 0; l < 4; l++) { 3104 vtxCoords[vcount++] = 2 * i * L + PetscSinReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3105 vtxCoords[vcount++] = (2 * j - 1) * L; 3106 vtxCoords[vcount++] = 2 * k * L + PetscCosReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3107 } 3108 } 3109 } 3110 } 3111 // z-normal pipes 3112 for (PetscInt i = 0; i < extent[0]; i++) { 3113 for (PetscInt j = 0; j < extent[1]; j++) { 3114 for (PetscInt k = 0; k < extent[2] + 1; k++) { 3115 for (PetscInt l = 0; l < 4; l++) { 3116 vtxCoords[vcount++] = 2 * i * L + PetscCosReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3117 vtxCoords[vcount++] = 2 * j * L + PetscSinReal((2 * l + 1) * PETSC_PI / 4) * L / 2; 3118 vtxCoords[vcount++] = (2 * k - 1) * L; 3119 } 3120 } 3121 } 3122 } 3123 // junctions 3124 for (PetscInt i = 0; i < extent[0]; i++) { 3125 for (PetscInt j = 0; j < extent[1]; j++) { 3126 for (PetscInt k = 0; k < extent[2]; k++) { 3127 const PetscInt J = (i * extent[1] + j) * extent[2] + k, Jvoff = (Npipes[0] + Npipes[1] + Npipes[2]) * 4 + J * 8; 3128 PetscCheck(vcount / 3 == Jvoff, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unexpected vertex count"); 3129 for (PetscInt ii = 0; ii < 2; ii++) { 3130 for (PetscInt jj = 0; jj < 2; jj++) { 3131 for (PetscInt kk = 0; kk < 2; kk++) { 3132 double Ls = (1 - sqrt(2) / 4) * L; 3133 vtxCoords[vcount++] = 2 * i * L + (2 * ii - 1) * Ls; 3134 vtxCoords[vcount++] = 2 * j * L + (2 * jj - 1) * Ls; 3135 vtxCoords[vcount++] = 2 * k * L + (2 * kk - 1) * Ls; 3136 } 3137 } 3138 } 3139 const PetscInt jfaces[3][2][4] = { 3140 {{3, 1, 0, 2}, {7, 5, 4, 6}}, // x-aligned 3141 {{5, 4, 0, 1}, {7, 6, 2, 3}}, // y-aligned 3142 {{6, 2, 0, 4}, {7, 3, 1, 5}} // z-aligned 3143 }; 3144 const PetscInt pipe_lo[3] = {// vertex numbers of pipes 3145 ((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}; 3146 const PetscInt pipe_hi[3] = {// vertex numbers of pipes 3147 (((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}; 3148 for (PetscInt dir = 0; dir < 3; dir++) { // x,y,z 3149 const PetscInt ijk[3] = {i, j, k}; 3150 for (PetscInt l = 0; l < 4; l++) { // rotations 3151 cells[J][dir * 2 + 0][l][0] = pipe_lo[dir] + l; 3152 cells[J][dir * 2 + 0][l][1] = Jvoff + jfaces[dir][0][l]; 3153 cells[J][dir * 2 + 0][l][2] = Jvoff + jfaces[dir][0][(l - 1 + 4) % 4]; 3154 cells[J][dir * 2 + 0][l][3] = pipe_lo[dir] + (l - 1 + 4) % 4; 3155 cells[J][dir * 2 + 1][l][0] = Jvoff + jfaces[dir][1][l]; 3156 cells[J][dir * 2 + 1][l][1] = pipe_hi[dir] + l; 3157 cells[J][dir * 2 + 1][l][2] = pipe_hi[dir] + (l - 1 + 4) % 4; 3158 cells[J][dir * 2 + 1][l][3] = Jvoff + jfaces[dir][1][(l - 1 + 4) % 4]; 3159 if (ijk[dir] == 0) { 3160 edges[numEdges][0] = pipe_lo[dir] + l; 3161 edges[numEdges][1] = pipe_lo[dir] + (l + 1) % 4; 3162 edgeSets[numEdges] = dir * 2 + 1; 3163 numEdges++; 3164 } 3165 if (ijk[dir] + 1 == extent[dir]) { 3166 edges[numEdges][0] = pipe_hi[dir] + l; 3167 edges[numEdges][1] = pipe_hi[dir] + (l + 1) % 4; 3168 edgeSets[numEdges] = dir * 2 + 2; 3169 numEdges++; 3170 } 3171 } 3172 } 3173 } 3174 } 3175 } 3176 PetscCheck(numEdges == Ncuts * 4, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Edge count %" PetscInt_FMT " incompatible with number of cuts %" PetscInt_FMT, numEdges, Ncuts); 3177 numFaces = 24 * Njunctions; 3178 cells_flat = cells[0][0][0]; 3179 } 3180 evalFunc = TPSEvaluate_SchwarzP; 3181 normalFunc = TPSExtrudeNormalFunc_SchwarzP; 3182 break; 3183 case DMPLEX_TPS_GYROID: 3184 if (rank == 0) { 3185 // This is a coarse mesh approximation of the gyroid shifted to being the zero of the level set 3186 // 3187 // 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) 3188 // 3189 // on the cell [0,2]^3. 3190 // 3191 // Think about dividing that cell into four columns, and focus on the column [0,1]x[0,1]x[0,2]. 3192 // If you looked at the gyroid in that column at different slices of z you would see that it kind of spins 3193 // like a boomerang: 3194 // 3195 // z = 0 z = 1/4 z = 1/2 z = 3/4 // 3196 // ----- ------- ------- ------- // 3197 // // 3198 // + + + + + + + \ + // 3199 // \ / \ // 3200 // \ `-_ _-' / } // 3201 // *-_ `-' _-' / // 3202 // + `-+ + + +-' + + / + // 3203 // // 3204 // // 3205 // z = 1 z = 5/4 z = 3/2 z = 7/4 // 3206 // ----- ------- ------- ------- // 3207 // // 3208 // +-_ + + + + _-+ + / + // 3209 // `-_ _-_ _-` / // 3210 // \ _-' `-_ / { // 3211 // \ / \ // 3212 // + + + + + + + \ + // 3213 // 3214 // 3215 // This course mesh approximates each of these slices by two line segments, 3216 // and then connects the segments in consecutive layers with quadrilateral faces. 3217 // All of the end points of the segments are multiples of 1/4 except for the 3218 // point * in the picture for z = 0 above and the similar points in other layers. 3219 // That point is at (gamma, gamma, 0), where gamma is calculated below. 3220 // 3221 // The column [1,2]x[1,2]x[0,2] looks the same as this column; 3222 // The columns [1,2]x[0,1]x[0,2] and [0,1]x[1,2]x[0,2] are mirror images. 3223 // 3224 // As for how this method turned into the names given to the vertices: 3225 // that was not systematic, it was just the way it worked out in my handwritten notes. 3226 3227 PetscInt facesPerBlock = 64; 3228 PetscInt vertsPerBlock = 56; 3229 PetscInt extentPlus[3]; 3230 PetscInt numBlocks, numBlocksPlus; 3231 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; 3232 const PetscInt pattern[64][4] = { 3233 /* face to vertex within the coarse discretization of a single gyroid block */ 3234 /* layer 0 */ 3235 {A, C, K, G }, 3236 {C, B, II, K }, 3237 {D, A, H, L }, 3238 {B + 56 * 1, D, L, J }, 3239 {E, B + 56 * 1, J, N }, 3240 {A + 56 * 2, E, N, H + 56 * 2 }, 3241 {F, A + 56 * 2, G + 56 * 2, M }, 3242 {B, F, M, II }, 3243 /* layer 1 */ 3244 {G, K, Q, O }, 3245 {K, II, P, Q }, 3246 {L, H, O + 56 * 1, R }, 3247 {J, L, R, P }, 3248 {N, J, P, S }, 3249 {H + 56 * 2, N, S, O + 56 * 3 }, 3250 {M, G + 56 * 2, O + 56 * 2, T }, 3251 {II, M, T, P }, 3252 /* layer 2 */ 3253 {O, Q, Y, U }, 3254 {Q, P, W, Y }, 3255 {R, O + 56 * 1, U + 56 * 1, Ap }, 3256 {P, R, Ap, W }, 3257 {S, P, X, Bp }, 3258 {O + 56 * 3, S, Bp, V + 56 * 1 }, 3259 {T, O + 56 * 2, V, Z }, 3260 {P, T, Z, X }, 3261 /* layer 3 */ 3262 {U, Y, Ep, Dp }, 3263 {Y, W, Cp, Ep }, 3264 {Ap, U + 56 * 1, Dp + 56 * 1, Gp }, 3265 {W, Ap, Gp, Cp }, 3266 {Bp, X, Cp + 56 * 2, Fp }, 3267 {V + 56 * 1, Bp, Fp, Dp + 56 * 1}, 3268 {Z, V, Dp, Hp }, 3269 {X, Z, Hp, Cp + 56 * 2}, 3270 /* layer 4 */ 3271 {Dp, Ep, Mp, Kp }, 3272 {Ep, Cp, Ip, Mp }, 3273 {Gp, Dp + 56 * 1, Lp, Np }, 3274 {Cp, Gp, Np, Jp }, 3275 {Fp, Cp + 56 * 2, Jp + 56 * 2, Pp }, 3276 {Dp + 56 * 1, Fp, Pp, Lp }, 3277 {Hp, Dp, Kp, Op }, 3278 {Cp + 56 * 2, Hp, Op, Ip + 56 * 2}, 3279 /* layer 5 */ 3280 {Kp, Mp, Sp, Rp }, 3281 {Mp, Ip, Qp, Sp }, 3282 {Np, Lp, Rp, Tp }, 3283 {Jp, Np, Tp, Qp + 56 * 1}, 3284 {Pp, Jp + 56 * 2, Qp + 56 * 3, Up }, 3285 {Lp, Pp, Up, Rp }, 3286 {Op, Kp, Rp, Vp }, 3287 {Ip + 56 * 2, Op, Vp, Qp + 56 * 2}, 3288 /* layer 6 */ 3289 {Rp, Sp, Aq, Yp }, 3290 {Sp, Qp, Wp, Aq }, 3291 {Tp, Rp, Yp, Cq }, 3292 {Qp + 56 * 1, Tp, Cq, Wp + 56 * 1}, 3293 {Up, Qp + 56 * 3, Xp + 56 * 1, Dq }, 3294 {Rp, Up, Dq, Zp }, 3295 {Vp, Rp, Zp, Bq }, 3296 {Qp + 56 * 2, Vp, Bq, Xp }, 3297 /* layer 7 (the top is the periodic image of the bottom of layer 0) */ 3298 {Yp, Aq, C + 56 * 4, A + 56 * 4 }, 3299 {Aq, Wp, B + 56 * 4, C + 56 * 4 }, 3300 {Cq, Yp, A + 56 * 4, D + 56 * 4 }, 3301 {Wp + 56 * 1, Cq, D + 56 * 4, B + 56 * 5 }, 3302 {Dq, Xp + 56 * 1, B + 56 * 5, E + 56 * 4 }, 3303 {Zp, Dq, E + 56 * 4, A + 56 * 6 }, 3304 {Bq, Zp, A + 56 * 6, F + 56 * 4 }, 3305 {Xp, Bq, F + 56 * 4, B + 56 * 4 } 3306 }; 3307 const PetscReal gamma = PetscAcosReal((PetscSqrtReal(3.) - 1.) / PetscSqrtReal(2.)) / PETSC_PI; 3308 const PetscReal patternCoords[56][3] = { 3309 {1., 0., 0. }, /* A */ 3310 {0., 1., 0. }, /* B */ 3311 {gamma, gamma, 0. }, /* C */ 3312 {1 + gamma, 1 - gamma, 0. }, /* D */ 3313 {2 - gamma, 2 - gamma, 0. }, /* E */ 3314 {1 - gamma, 1 + gamma, 0. }, /* F */ 3315 3316 {.5, 0, .25 }, /* G */ 3317 {1.5, 0., .25 }, /* H */ 3318 {.5, 1., .25 }, /* II */ 3319 {1.5, 1., .25 }, /* J */ 3320 {.25, .5, .25 }, /* K */ 3321 {1.25, .5, .25 }, /* L */ 3322 {.75, 1.5, .25 }, /* M */ 3323 {1.75, 1.5, .25 }, /* N */ 3324 3325 {0., 0., .5 }, /* O */ 3326 {1., 1., .5 }, /* P */ 3327 {gamma, 1 - gamma, .5 }, /* Q */ 3328 {1 + gamma, gamma, .5 }, /* R */ 3329 {2 - gamma, 1 + gamma, .5 }, /* S */ 3330 {1 - gamma, 2 - gamma, .5 }, /* T */ 3331 3332 {0., .5, .75 }, /* U */ 3333 {0., 1.5, .75 }, /* V */ 3334 {1., .5, .75 }, /* W */ 3335 {1., 1.5, .75 }, /* X */ 3336 {.5, .75, .75 }, /* Y */ 3337 {.5, 1.75, .75 }, /* Z */ 3338 {1.5, .25, .75 }, /* Ap */ 3339 {1.5, 1.25, .75 }, /* Bp */ 3340 3341 {1., 0., 1. }, /* Cp */ 3342 {0., 1., 1. }, /* Dp */ 3343 {1 - gamma, 1 - gamma, 1. }, /* Ep */ 3344 {1 + gamma, 1 + gamma, 1. }, /* Fp */ 3345 {2 - gamma, gamma, 1. }, /* Gp */ 3346 {gamma, 2 - gamma, 1. }, /* Hp */ 3347 3348 {.5, 0., 1.25}, /* Ip */ 3349 {1.5, 0., 1.25}, /* Jp */ 3350 {.5, 1., 1.25}, /* Kp */ 3351 {1.5, 1., 1.25}, /* Lp */ 3352 {.75, .5, 1.25}, /* Mp */ 3353 {1.75, .5, 1.25}, /* Np */ 3354 {.25, 1.5, 1.25}, /* Op */ 3355 {1.25, 1.5, 1.25}, /* Pp */ 3356 3357 {0., 0., 1.5 }, /* Qp */ 3358 {1., 1., 1.5 }, /* Rp */ 3359 {1 - gamma, gamma, 1.5 }, /* Sp */ 3360 {2 - gamma, 1 - gamma, 1.5 }, /* Tp */ 3361 {1 + gamma, 2 - gamma, 1.5 }, /* Up */ 3362 {gamma, 1 + gamma, 1.5 }, /* Vp */ 3363 3364 {0., .5, 1.75}, /* Wp */ 3365 {0., 1.5, 1.75}, /* Xp */ 3366 {1., .5, 1.75}, /* Yp */ 3367 {1., 1.5, 1.75}, /* Zp */ 3368 {.5, .25, 1.75}, /* Aq */ 3369 {.5, 1.25, 1.75}, /* Bq */ 3370 {1.5, .75, 1.75}, /* Cq */ 3371 {1.5, 1.75, 1.75}, /* Dq */ 3372 }; 3373 PetscInt(*cells)[64][4] = NULL; 3374 PetscBool *seen; 3375 PetscInt *vertToTrueVert; 3376 PetscInt count; 3377 3378 for (PetscInt i = 0; i < 3; i++) extentPlus[i] = extent[i] + 1; 3379 numBlocks = 1; 3380 for (PetscInt i = 0; i < 3; i++) numBlocks *= extent[i]; 3381 numBlocksPlus = 1; 3382 for (PetscInt i = 0; i < 3; i++) numBlocksPlus *= extentPlus[i]; 3383 numFaces = numBlocks * facesPerBlock; 3384 PetscCall(PetscMalloc1(numBlocks, &cells)); 3385 PetscCall(PetscCalloc1(numBlocksPlus * vertsPerBlock, &seen)); 3386 for (PetscInt k = 0; k < extent[2]; k++) { 3387 for (PetscInt j = 0; j < extent[1]; j++) { 3388 for (PetscInt i = 0; i < extent[0]; i++) { 3389 for (PetscInt f = 0; f < facesPerBlock; f++) { 3390 for (PetscInt v = 0; v < 4; v++) { 3391 PetscInt vertRaw = pattern[f][v]; 3392 PetscInt blockidx = vertRaw / 56; 3393 PetscInt patternvert = vertRaw % 56; 3394 PetscInt xplus = (blockidx & 1); 3395 PetscInt yplus = (blockidx & 2) >> 1; 3396 PetscInt zplus = (blockidx & 4) >> 2; 3397 PetscInt zcoord = (periodic && periodic[2] == DM_BOUNDARY_PERIODIC) ? ((k + zplus) % extent[2]) : (k + zplus); 3398 PetscInt ycoord = (periodic && periodic[1] == DM_BOUNDARY_PERIODIC) ? ((j + yplus) % extent[1]) : (j + yplus); 3399 PetscInt xcoord = (periodic && periodic[0] == DM_BOUNDARY_PERIODIC) ? ((i + xplus) % extent[0]) : (i + xplus); 3400 PetscInt vert = ((zcoord * extentPlus[1] + ycoord) * extentPlus[0] + xcoord) * 56 + patternvert; 3401 3402 cells[(k * extent[1] + j) * extent[0] + i][f][v] = vert; 3403 seen[vert] = PETSC_TRUE; 3404 } 3405 } 3406 } 3407 } 3408 } 3409 for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++) 3410 if (seen[i]) numVertices++; 3411 count = 0; 3412 PetscCall(PetscMalloc1(numBlocksPlus * vertsPerBlock, &vertToTrueVert)); 3413 PetscCall(PetscMalloc1(numVertices * 3, &vtxCoords)); 3414 for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++) vertToTrueVert[i] = -1; 3415 for (PetscInt k = 0; k < extentPlus[2]; k++) { 3416 for (PetscInt j = 0; j < extentPlus[1]; j++) { 3417 for (PetscInt i = 0; i < extentPlus[0]; i++) { 3418 for (PetscInt v = 0; v < vertsPerBlock; v++) { 3419 PetscInt vIdx = ((k * extentPlus[1] + j) * extentPlus[0] + i) * vertsPerBlock + v; 3420 3421 if (seen[vIdx]) { 3422 PetscInt thisVert; 3423 3424 vertToTrueVert[vIdx] = thisVert = count++; 3425 3426 for (PetscInt d = 0; d < 3; d++) vtxCoords[3 * thisVert + d] = patternCoords[v][d]; 3427 vtxCoords[3 * thisVert + 0] += i * 2; 3428 vtxCoords[3 * thisVert + 1] += j * 2; 3429 vtxCoords[3 * thisVert + 2] += k * 2; 3430 } 3431 } 3432 } 3433 } 3434 } 3435 for (PetscInt i = 0; i < numBlocks; i++) { 3436 for (PetscInt f = 0; f < facesPerBlock; f++) { 3437 for (PetscInt v = 0; v < 4; v++) cells[i][f][v] = vertToTrueVert[cells[i][f][v]]; 3438 } 3439 } 3440 PetscCall(PetscFree(vertToTrueVert)); 3441 PetscCall(PetscFree(seen)); 3442 cells_flat = cells[0][0]; 3443 numEdges = 0; 3444 for (PetscInt i = 0; i < numFaces; i++) { 3445 for (PetscInt e = 0; e < 4; e++) { 3446 PetscInt ev[] = {cells_flat[i * 4 + e], cells_flat[i * 4 + ((e + 1) % 4)]}; 3447 const PetscReal *evCoords[] = {&vtxCoords[3 * ev[0]], &vtxCoords[3 * ev[1]]}; 3448 3449 for (PetscInt d = 0; d < 3; d++) { 3450 if (!periodic || periodic[0] != DM_BOUNDARY_PERIODIC) { 3451 if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) numEdges++; 3452 if (evCoords[0][d] == 2. * extent[d] && evCoords[1][d] == 2. * extent[d]) numEdges++; 3453 } 3454 } 3455 } 3456 } 3457 PetscCall(PetscMalloc1(numEdges, &edges)); 3458 PetscCall(PetscMalloc1(numEdges, &edgeSets)); 3459 for (PetscInt edge = 0, i = 0; i < numFaces; i++) { 3460 for (PetscInt e = 0; e < 4; e++) { 3461 PetscInt ev[] = {cells_flat[i * 4 + e], cells_flat[i * 4 + ((e + 1) % 4)]}; 3462 const PetscReal *evCoords[] = {&vtxCoords[3 * ev[0]], &vtxCoords[3 * ev[1]]}; 3463 3464 for (PetscInt d = 0; d < 3; d++) { 3465 if (!periodic || periodic[d] != DM_BOUNDARY_PERIODIC) { 3466 if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) { 3467 edges[edge][0] = ev[0]; 3468 edges[edge][1] = ev[1]; 3469 edgeSets[edge++] = 2 * d; 3470 } 3471 if (evCoords[0][d] == 2. * extent[d] && evCoords[1][d] == 2. * extent[d]) { 3472 edges[edge][0] = ev[0]; 3473 edges[edge][1] = ev[1]; 3474 edgeSets[edge++] = 2 * d + 1; 3475 } 3476 } 3477 } 3478 } 3479 } 3480 } 3481 evalFunc = TPSEvaluate_Gyroid; 3482 normalFunc = TPSExtrudeNormalFunc_Gyroid; 3483 break; 3484 } 3485 3486 PetscCall(DMSetDimension(dm, topoDim)); 3487 if (rank == 0) PetscCall(DMPlexBuildFromCellList(dm, numFaces, numVertices, 4, cells_flat)); 3488 else PetscCall(DMPlexBuildFromCellList(dm, 0, 0, 0, NULL)); 3489 PetscCall(PetscFree(cells_flat)); 3490 { 3491 DM idm; 3492 PetscCall(DMPlexInterpolate(dm, &idm)); 3493 PetscCall(DMPlexReplace_Internal(dm, &idm)); 3494 } 3495 if (rank == 0) PetscCall(DMPlexBuildCoordinatesFromCellList(dm, spaceDim, vtxCoords)); 3496 else PetscCall(DMPlexBuildCoordinatesFromCellList(dm, spaceDim, NULL)); 3497 PetscCall(PetscFree(vtxCoords)); 3498 3499 PetscCall(DMCreateLabel(dm, "Face Sets")); 3500 PetscCall(DMGetLabel(dm, "Face Sets", &label)); 3501 for (PetscInt e = 0; e < numEdges; e++) { 3502 PetscInt njoin; 3503 const PetscInt *join, verts[] = {numFaces + edges[e][0], numFaces + edges[e][1]}; 3504 PetscCall(DMPlexGetJoin(dm, 2, verts, &njoin, &join)); 3505 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]); 3506 PetscCall(DMLabelSetValue(label, join[0], edgeSets[e])); 3507 PetscCall(DMPlexRestoreJoin(dm, 2, verts, &njoin, &join)); 3508 } 3509 PetscCall(PetscFree(edges)); 3510 PetscCall(PetscFree(edgeSets)); 3511 if (tps_distribute) { 3512 DM pdm = NULL; 3513 PetscPartitioner part; 3514 3515 PetscCall(DMPlexGetPartitioner(dm, &part)); 3516 PetscCall(PetscPartitionerSetFromOptions(part)); 3517 PetscCall(DMPlexDistribute(dm, 0, NULL, &pdm)); 3518 if (pdm) PetscCall(DMPlexReplace_Internal(dm, &pdm)); 3519 // Do not auto-distribute again 3520 PetscCall(DMPlexDistributeSetDefault(dm, PETSC_FALSE)); 3521 } 3522 3523 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 3524 for (PetscInt refine = 0; refine < refinements; refine++) { 3525 PetscInt m; 3526 DM dmf; 3527 Vec X; 3528 PetscScalar *x; 3529 PetscCall(DMRefine(dm, MPI_COMM_NULL, &dmf)); 3530 PetscCall(DMPlexReplace_Internal(dm, &dmf)); 3531 3532 PetscCall(DMGetCoordinatesLocal(dm, &X)); 3533 PetscCall(VecGetLocalSize(X, &m)); 3534 PetscCall(VecGetArray(X, &x)); 3535 for (PetscInt i = 0; i < m; i += 3) PetscCall(TPSNearestPoint(evalFunc, &x[i])); 3536 PetscCall(VecRestoreArray(X, &x)); 3537 } 3538 3539 // Face Sets has already been propagated to new vertices during refinement; this propagates to the initial vertices. 3540 PetscCall(DMGetLabel(dm, "Face Sets", &label)); 3541 PetscCall(DMPlexLabelComplete(dm, label)); 3542 3543 PetscCall(PetscLogEventEnd(DMPLEX_Generate, dm, 0, 0, 0)); 3544 3545 if (thickness > 0) { 3546 DM edm, cdm, ecdm; 3547 DMPlexTransform tr; 3548 const char *prefix; 3549 PetscOptions options; 3550 // Code from DMPlexExtrude 3551 PetscCall(DMPlexTransformCreate(PetscObjectComm((PetscObject)dm), &tr)); 3552 PetscCall(DMPlexTransformSetDM(tr, dm)); 3553 PetscCall(DMPlexTransformSetType(tr, DMPLEXEXTRUDE)); 3554 PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm, &prefix)); 3555 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)tr, prefix)); 3556 PetscCall(PetscObjectGetOptions((PetscObject)dm, &options)); 3557 PetscCall(PetscObjectSetOptions((PetscObject)tr, options)); 3558 PetscCall(DMPlexTransformExtrudeSetLayers(tr, layers)); 3559 PetscCall(DMPlexTransformExtrudeSetThickness(tr, thickness)); 3560 PetscCall(DMPlexTransformExtrudeSetTensor(tr, PETSC_FALSE)); 3561 PetscCall(DMPlexTransformExtrudeSetSymmetric(tr, PETSC_TRUE)); 3562 PetscCall(DMPlexTransformExtrudeSetNormalFunction(tr, normalFunc)); 3563 PetscCall(DMPlexTransformSetFromOptions(tr)); 3564 PetscCall(PetscObjectSetOptions((PetscObject)tr, NULL)); 3565 PetscCall(DMPlexTransformSetUp(tr)); 3566 PetscCall(PetscObjectViewFromOptions((PetscObject)tr, NULL, "-dm_plex_tps_transform_view")); 3567 PetscCall(DMPlexTransformApply(tr, dm, &edm)); 3568 PetscCall(DMCopyDisc(dm, edm)); 3569 PetscCall(DMGetCoordinateDM(dm, &cdm)); 3570 PetscCall(DMGetCoordinateDM(edm, &ecdm)); 3571 PetscCall(DMCopyDisc(cdm, ecdm)); 3572 PetscCall(DMPlexTransformCreateDiscLabels(tr, edm)); 3573 PetscCall(DMPlexTransformDestroy(&tr)); 3574 if (edm) { 3575 ((DM_Plex *)edm->data)->printFEM = ((DM_Plex *)dm->data)->printFEM; 3576 ((DM_Plex *)edm->data)->printL2 = ((DM_Plex *)dm->data)->printL2; 3577 ((DM_Plex *)edm->data)->printLocate = ((DM_Plex *)dm->data)->printLocate; 3578 } 3579 PetscCall(DMPlexReplace_Internal(dm, &edm)); 3580 } 3581 PetscFunctionReturn(PETSC_SUCCESS); 3582 } 3583 3584 /*@ 3585 DMPlexCreateTPSMesh - Create a distributed, interpolated mesh of a triply-periodic surface 3586 3587 Collective 3588 3589 Input Parameters: 3590 + comm - The communicator for the `DM` object 3591 . tpstype - Type of triply-periodic surface 3592 . extent - Array of length 3 containing number of periods in each direction 3593 . periodic - array of length 3 with periodicity, or `NULL` for non-periodic 3594 . tps_distribute - Distribute 2D manifold mesh prior to refinement and extrusion (more scalable) 3595 . refinements - Number of factor-of-2 refinements of 2D manifold mesh 3596 . layers - Number of cell layers extruded in normal direction 3597 - thickness - Thickness in normal direction 3598 3599 Output Parameter: 3600 . dm - The `DM` object 3601 3602 Level: beginner 3603 3604 Notes: 3605 This meshes the surface of the Schwarz P or Gyroid surfaces. Schwarz P is the simplest member of the triply-periodic minimal surfaces. 3606 <https://en.wikipedia.org/wiki/Schwarz_minimal_surface#Schwarz_P_(%22Primitive%22)> and can be cut with "clean" boundaries. 3607 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. 3608 Our implementation creates a very coarse mesh of the surface and refines (by 4-way splitting) as many times as requested. 3609 On each refinement, all vertices are projected to their nearest point on the surface. 3610 This projection could readily be extended to related surfaces. 3611 3612 See {cite}`maskery2018insights` 3613 3614 The face (edge) sets for the Schwarz P surface are numbered $1(-x), 2(+x), 3(-y), 4(+y), 5(-z), 6(+z)$. 3615 When the mesh is refined, "Face Sets" contain the new vertices (created during refinement). 3616 Use `DMPlexLabelComplete()` to propagate to coarse-level vertices. 3617 3618 Developer Notes: 3619 The Gyroid mesh does not currently mark boundary sets. 3620 3621 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateSphereMesh()`, `DMSetType()`, `DMCreate()` 3622 @*/ 3623 PetscErrorCode DMPlexCreateTPSMesh(MPI_Comm comm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscBool tps_distribute, PetscInt refinements, PetscInt layers, PetscReal thickness, DM *dm) 3624 { 3625 PetscFunctionBegin; 3626 PetscCall(DMCreate(comm, dm)); 3627 PetscCall(DMSetType(*dm, DMPLEX)); 3628 PetscCall(DMPlexCreateTPSMesh_Internal(*dm, tpstype, extent, periodic, tps_distribute, refinements, layers, thickness)); 3629 PetscFunctionReturn(PETSC_SUCCESS); 3630 } 3631 3632 /*@ 3633 DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d. 3634 3635 Collective 3636 3637 Input Parameters: 3638 + comm - The communicator for the `DM` object 3639 . dim - The dimension 3640 . simplex - Use simplices, or tensor product cells 3641 - R - The radius 3642 3643 Output Parameter: 3644 . dm - The `DM` object 3645 3646 Level: beginner 3647 3648 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateBallMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 3649 @*/ 3650 PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscReal R, DM *dm) 3651 { 3652 PetscFunctionBegin; 3653 PetscAssertPointer(dm, 5); 3654 PetscCall(DMCreate(comm, dm)); 3655 PetscCall(DMSetType(*dm, DMPLEX)); 3656 PetscCall(DMPlexCreateSphereMesh_Internal(*dm, dim, simplex, R)); 3657 PetscFunctionReturn(PETSC_SUCCESS); 3658 } 3659 3660 static PetscErrorCode DMPlexCreateBallMesh_Internal(DM dm, PetscInt dim, PetscReal R) 3661 { 3662 DM sdm, vol; 3663 DMLabel bdlabel; 3664 const char *prefix; 3665 3666 PetscFunctionBegin; 3667 PetscCall(DMCreate(PetscObjectComm((PetscObject)dm), &sdm)); 3668 PetscCall(DMSetType(sdm, DMPLEX)); 3669 PetscCall(DMGetOptionsPrefix(dm, &prefix)); 3670 PetscCall(DMSetOptionsPrefix(sdm, prefix)); 3671 PetscCall(DMAppendOptionsPrefix(sdm, "bd_")); 3672 PetscCall(DMPlexDistributeSetDefault(sdm, PETSC_FALSE)); 3673 PetscCall(DMPlexCreateSphereMesh_Internal(sdm, dim - 1, PETSC_TRUE, R)); 3674 PetscCall(DMSetFromOptions(sdm)); 3675 PetscCall(DMViewFromOptions(sdm, NULL, "-dm_view")); 3676 PetscCall(DMPlexGenerate(sdm, NULL, PETSC_TRUE, &vol)); 3677 PetscCall(DMDestroy(&sdm)); 3678 PetscCall(DMPlexReplace_Internal(dm, &vol)); 3679 PetscCall(DMCreateLabel(dm, "marker")); 3680 PetscCall(DMGetLabel(dm, "marker", &bdlabel)); 3681 PetscCall(DMPlexMarkBoundaryFaces(dm, PETSC_DETERMINE, bdlabel)); 3682 PetscCall(DMPlexLabelComplete(dm, bdlabel)); 3683 PetscFunctionReturn(PETSC_SUCCESS); 3684 } 3685 3686 /*@ 3687 DMPlexCreateBallMesh - Creates a simplex mesh on the d-dimensional ball, B^d. 3688 3689 Collective 3690 3691 Input Parameters: 3692 + comm - The communicator for the `DM` object 3693 . dim - The dimension 3694 - R - The radius 3695 3696 Output Parameter: 3697 . dm - The `DM` object 3698 3699 Options Database Key: 3700 . bd_dm_refine - This will refine the surface mesh preserving the sphere geometry 3701 3702 Level: beginner 3703 3704 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateSphereMesh()`, `DMPlexCreateBoxMesh()`, `DMSetType()`, `DMCreate()` 3705 @*/ 3706 PetscErrorCode DMPlexCreateBallMesh(MPI_Comm comm, PetscInt dim, PetscReal R, DM *dm) 3707 { 3708 PetscFunctionBegin; 3709 PetscCall(DMCreate(comm, dm)); 3710 PetscCall(DMSetType(*dm, DMPLEX)); 3711 PetscCall(DMPlexCreateBallMesh_Internal(*dm, dim, R)); 3712 PetscFunctionReturn(PETSC_SUCCESS); 3713 } 3714 3715 static PetscErrorCode DMPlexCreateReferenceCell_Internal(DM rdm, DMPolytopeType ct) 3716 { 3717 PetscFunctionBegin; 3718 switch (ct) { 3719 case DM_POLYTOPE_POINT: { 3720 PetscInt numPoints[1] = {1}; 3721 PetscInt coneSize[1] = {0}; 3722 PetscInt cones[1] = {0}; 3723 PetscInt coneOrientations[1] = {0}; 3724 PetscScalar vertexCoords[1] = {0.0}; 3725 3726 PetscCall(DMSetDimension(rdm, 0)); 3727 PetscCall(DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3728 } break; 3729 case DM_POLYTOPE_SEGMENT: { 3730 PetscInt numPoints[2] = {2, 1}; 3731 PetscInt coneSize[3] = {2, 0, 0}; 3732 PetscInt cones[2] = {1, 2}; 3733 PetscInt coneOrientations[2] = {0, 0}; 3734 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 3735 3736 PetscCall(DMSetDimension(rdm, 1)); 3737 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3738 } break; 3739 case DM_POLYTOPE_POINT_PRISM_TENSOR: { 3740 PetscInt numPoints[2] = {2, 1}; 3741 PetscInt coneSize[3] = {2, 0, 0}; 3742 PetscInt cones[2] = {1, 2}; 3743 PetscInt coneOrientations[2] = {0, 0}; 3744 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 3745 3746 PetscCall(DMSetDimension(rdm, 1)); 3747 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3748 } break; 3749 case DM_POLYTOPE_TRIANGLE: { 3750 PetscInt numPoints[2] = {3, 1}; 3751 PetscInt coneSize[4] = {3, 0, 0, 0}; 3752 PetscInt cones[3] = {1, 2, 3}; 3753 PetscInt coneOrientations[3] = {0, 0, 0}; 3754 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 3755 3756 PetscCall(DMSetDimension(rdm, 2)); 3757 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3758 } break; 3759 case DM_POLYTOPE_QUADRILATERAL: { 3760 PetscInt numPoints[2] = {4, 1}; 3761 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3762 PetscInt cones[4] = {1, 2, 3, 4}; 3763 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3764 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 3765 3766 PetscCall(DMSetDimension(rdm, 2)); 3767 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3768 } break; 3769 case DM_POLYTOPE_SEG_PRISM_TENSOR: { 3770 PetscInt numPoints[2] = {4, 1}; 3771 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3772 PetscInt cones[4] = {1, 2, 3, 4}; 3773 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3774 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, 1.0}; 3775 3776 PetscCall(DMSetDimension(rdm, 2)); 3777 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3778 } break; 3779 case DM_POLYTOPE_TETRAHEDRON: { 3780 PetscInt numPoints[2] = {4, 1}; 3781 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3782 PetscInt cones[4] = {1, 2, 3, 4}; 3783 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3784 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}; 3785 3786 PetscCall(DMSetDimension(rdm, 3)); 3787 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3788 } break; 3789 case DM_POLYTOPE_HEXAHEDRON: { 3790 PetscInt numPoints[2] = {8, 1}; 3791 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3792 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 3793 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3794 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}; 3795 3796 PetscCall(DMSetDimension(rdm, 3)); 3797 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3798 } break; 3799 case DM_POLYTOPE_TRI_PRISM: { 3800 PetscInt numPoints[2] = {6, 1}; 3801 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3802 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 3803 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3804 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}; 3805 3806 PetscCall(DMSetDimension(rdm, 3)); 3807 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3808 } break; 3809 case DM_POLYTOPE_TRI_PRISM_TENSOR: { 3810 PetscInt numPoints[2] = {6, 1}; 3811 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3812 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 3813 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3814 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}; 3815 3816 PetscCall(DMSetDimension(rdm, 3)); 3817 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3818 } break; 3819 case DM_POLYTOPE_QUAD_PRISM_TENSOR: { 3820 PetscInt numPoints[2] = {8, 1}; 3821 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3822 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 3823 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3824 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}; 3825 3826 PetscCall(DMSetDimension(rdm, 3)); 3827 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3828 } break; 3829 case DM_POLYTOPE_PYRAMID: { 3830 PetscInt numPoints[2] = {5, 1}; 3831 PetscInt coneSize[6] = {5, 0, 0, 0, 0, 0}; 3832 PetscInt cones[5] = {1, 2, 3, 4, 5}; 3833 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3834 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}; 3835 3836 PetscCall(DMSetDimension(rdm, 3)); 3837 PetscCall(DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords)); 3838 } break; 3839 default: 3840 SETERRQ(PetscObjectComm((PetscObject)rdm), PETSC_ERR_ARG_WRONG, "Cannot create reference cell for cell type %s", DMPolytopeTypes[ct]); 3841 } 3842 { 3843 PetscInt Nv, v; 3844 3845 /* Must create the celltype label here so that we do not automatically try to compute the types */ 3846 PetscCall(DMCreateLabel(rdm, "celltype")); 3847 PetscCall(DMPlexSetCellType(rdm, 0, ct)); 3848 PetscCall(DMPlexGetChart(rdm, NULL, &Nv)); 3849 for (v = 1; v < Nv; ++v) PetscCall(DMPlexSetCellType(rdm, v, DM_POLYTOPE_POINT)); 3850 } 3851 PetscCall(DMPlexInterpolateInPlace_Internal(rdm)); 3852 PetscCall(PetscObjectSetName((PetscObject)rdm, DMPolytopeTypes[ct])); 3853 PetscFunctionReturn(PETSC_SUCCESS); 3854 } 3855 3856 /*@ 3857 DMPlexCreateReferenceCell - Create a `DMPLEX` with the appropriate FEM reference cell 3858 3859 Collective 3860 3861 Input Parameters: 3862 + comm - The communicator 3863 - ct - The cell type of the reference cell 3864 3865 Output Parameter: 3866 . refdm - The reference cell 3867 3868 Level: intermediate 3869 3870 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateBoxMesh()` 3871 @*/ 3872 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, DMPolytopeType ct, DM *refdm) 3873 { 3874 PetscFunctionBegin; 3875 PetscCall(DMCreate(comm, refdm)); 3876 PetscCall(DMSetType(*refdm, DMPLEX)); 3877 PetscCall(DMPlexCreateReferenceCell_Internal(*refdm, ct)); 3878 PetscFunctionReturn(PETSC_SUCCESS); 3879 } 3880 3881 static PetscErrorCode DMPlexCreateBoundaryLabel_Private(DM dm, const char name[]) 3882 { 3883 DM plex; 3884 DMLabel label; 3885 PetscBool hasLabel; 3886 3887 PetscFunctionBegin; 3888 PetscCall(DMHasLabel(dm, name, &hasLabel)); 3889 if (hasLabel) PetscFunctionReturn(PETSC_SUCCESS); 3890 PetscCall(DMCreateLabel(dm, name)); 3891 PetscCall(DMGetLabel(dm, name, &label)); 3892 PetscCall(DMConvert(dm, DMPLEX, &plex)); 3893 PetscCall(DMPlexMarkBoundaryFaces(plex, 1, label)); 3894 PetscCall(DMPlexLabelComplete(plex, label)); 3895 PetscCall(DMDestroy(&plex)); 3896 PetscFunctionReturn(PETSC_SUCCESS); 3897 } 3898 3899 /* 3900 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. 3901 3902 (x, y) -> (r, theta) = (x[1], (x[0] - lower[0]) * 2\pi/(upper[0] - lower[0])) 3903 */ 3904 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[]) 3905 { 3906 const PetscReal low = PetscRealPart(constants[0]); 3907 const PetscReal upp = PetscRealPart(constants[1]); 3908 const PetscReal r = PetscRealPart(u[1]); 3909 const PetscReal th = 2. * PETSC_PI * (PetscRealPart(u[0]) - low) / (upp - low); 3910 3911 f0[0] = r * PetscCosReal(th); 3912 f0[1] = r * PetscSinReal(th); 3913 } 3914 3915 // Insert vertices and their joins, marked by depth 3916 static PetscErrorCode ProcessCohesiveLabel_Vertices(DM dm, DMLabel label, DMLabel vlabel, PetscInt val, PetscInt n, const PetscInt vertices[]) 3917 { 3918 PetscFunctionBegin; 3919 PetscCall(DMPlexMarkSubmesh_Interpolated(dm, vlabel, val, PETSC_FALSE, PETSC_FALSE, label, NULL)); 3920 PetscFunctionReturn(PETSC_SUCCESS); 3921 } 3922 3923 // Insert faces and their closures, marked by depth 3924 static PetscErrorCode ProcessCohesiveLabel_Faces(DM dm, DMLabel label, PetscInt n, const PetscInt faces[]) 3925 { 3926 PetscFunctionBegin; 3927 for (PetscInt p = 0; p < n; ++p) { 3928 const PetscInt point = faces[p]; 3929 PetscInt *closure = NULL; 3930 PetscInt clSize, pdepth; 3931 3932 PetscCall(DMPlexGetPointDepth(dm, point, &pdepth)); 3933 PetscCall(DMLabelSetValue(label, point, pdepth)); 3934 PetscCall(DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &clSize, &closure)); 3935 for (PetscInt cl = 0; cl < clSize * 2; cl += 2) { 3936 PetscCall(DMPlexGetPointDepth(dm, closure[cl], &pdepth)); 3937 PetscCall(DMLabelSetValue(label, closure[cl], pdepth)); 3938 } 3939 PetscCall(DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &clSize, &closure)); 3940 } 3941 PetscFunctionReturn(PETSC_SUCCESS); 3942 } 3943 3944 PETSC_EXTERN PetscErrorCode PetscOptionsFindPairPrefix_Private(PetscOptions, const char pre[], const char name[], const char *option[], const char *value[], PetscBool *flg); 3945 3946 const char *const DMPlexShapes[] = {"box", "box_surface", "ball", "sphere", "cylinder", "schwarz_p", "gyroid", "doublet", "annulus", "hypercubic", "zbox", "unknown", "DMPlexShape", "DM_SHAPE_", NULL}; 3947 3948 static PetscErrorCode DMPlexCreateFromOptions_Internal(PetscOptionItems *PetscOptionsObject, PetscBool *useCoordSpace, DM dm) 3949 { 3950 DMPlexShape shape = DM_SHAPE_BOX; 3951 DMPolytopeType cell = DM_POLYTOPE_TRIANGLE; 3952 PetscInt dim = 2; 3953 PetscBool simplex = PETSC_TRUE, interpolate = PETSC_TRUE, adjCone = PETSC_FALSE, adjClosure = PETSC_TRUE, refDomain = PETSC_FALSE; 3954 PetscBool flg, flg2, fflg, strflg, bdfflg, nameflg; 3955 MPI_Comm comm; 3956 char filename[PETSC_MAX_PATH_LEN] = "<unspecified>"; 3957 char bdFilename[PETSC_MAX_PATH_LEN] = "<unspecified>"; 3958 char plexname[PETSC_MAX_PATH_LEN] = ""; 3959 const char *option; 3960 3961 PetscFunctionBegin; 3962 PetscCall(PetscLogEventBegin(DMPLEX_CreateFromOptions, dm, 0, 0, 0)); 3963 PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); 3964 /* TODO Turn this into a registration interface */ 3965 PetscCall(PetscOptionsString("-dm_plex_filename", "File containing a mesh", "DMPlexCreateFromFile", filename, filename, sizeof(filename), &fflg)); 3966 PetscCall(PetscOptionsString("-dm_plex_file_contents", "Contents of a file format in a string", "DMPlexCreateFromFile", filename, filename, sizeof(filename), &strflg)); 3967 PetscCall(PetscOptionsString("-dm_plex_boundary_filename", "File containing a mesh boundary", "DMPlexCreateFromFile", bdFilename, bdFilename, sizeof(bdFilename), &bdfflg)); 3968 PetscCall(PetscOptionsString("-dm_plex_name", "Name of the mesh in the file", "DMPlexCreateFromFile", plexname, plexname, sizeof(plexname), &nameflg)); 3969 PetscCall(PetscOptionsEnum("-dm_plex_cell", "Cell shape", "", DMPolytopeTypes, (PetscEnum)cell, (PetscEnum *)&cell, NULL)); 3970 PetscCall(PetscOptionsBool("-dm_plex_reference_cell_domain", "Use a reference cell domain", "", refDomain, &refDomain, NULL)); 3971 PetscCall(PetscOptionsEnum("-dm_plex_shape", "Shape for built-in mesh", "", DMPlexShapes, (PetscEnum)shape, (PetscEnum *)&shape, &flg)); 3972 PetscCall(PetscOptionsBoundedInt("-dm_plex_dim", "Topological dimension of the mesh", "DMGetDimension", dim, &dim, &flg, 0)); 3973 PetscCall(PetscOptionsBool("-dm_plex_simplex", "Mesh cell shape", "", simplex, &simplex, &flg)); 3974 PetscCall(PetscOptionsBool("-dm_plex_interpolate", "Flag to create edges and faces automatically", "", interpolate, &interpolate, &flg)); 3975 PetscCall(PetscOptionsBool("-dm_plex_adj_cone", "Set adjacency direction", "DMSetBasicAdjacency", adjCone, &adjCone, &flg)); 3976 PetscCall(PetscOptionsBool("-dm_plex_adj_closure", "Set adjacency size", "DMSetBasicAdjacency", adjClosure, &adjClosure, &flg2)); 3977 if (flg || flg2) PetscCall(DMSetBasicAdjacency(dm, adjCone, adjClosure)); 3978 3979 switch (cell) { 3980 case DM_POLYTOPE_POINT: 3981 case DM_POLYTOPE_SEGMENT: 3982 case DM_POLYTOPE_POINT_PRISM_TENSOR: 3983 case DM_POLYTOPE_TRIANGLE: 3984 case DM_POLYTOPE_QUADRILATERAL: 3985 case DM_POLYTOPE_TETRAHEDRON: 3986 case DM_POLYTOPE_HEXAHEDRON: 3987 *useCoordSpace = PETSC_TRUE; 3988 break; 3989 default: 3990 *useCoordSpace = PETSC_FALSE; 3991 break; 3992 } 3993 3994 if (fflg) { 3995 DM dmnew; 3996 const char *name; 3997 3998 PetscCall(PetscObjectGetName((PetscObject)dm, &name)); 3999 PetscCall(DMPlexCreateFromFile(PetscObjectComm((PetscObject)dm), filename, nameflg ? plexname : name, interpolate, &dmnew)); 4000 PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew)); 4001 PetscCall(DMPlexReplace_Internal(dm, &dmnew)); 4002 } else if (refDomain) { 4003 PetscCall(DMPlexCreateReferenceCell_Internal(dm, cell)); 4004 } else if (bdfflg) { 4005 DM bdm, dmnew; 4006 const char *name; 4007 4008 PetscCall(PetscObjectGetName((PetscObject)dm, &name)); 4009 PetscCall(DMPlexCreateFromFile(PetscObjectComm((PetscObject)dm), bdFilename, nameflg ? plexname : name, interpolate, &bdm)); 4010 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)bdm, "bd_")); 4011 PetscCall(DMSetFromOptions(bdm)); 4012 PetscCall(DMPlexGenerate(bdm, NULL, interpolate, &dmnew)); 4013 PetscCall(DMDestroy(&bdm)); 4014 PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew)); 4015 PetscCall(DMPlexReplace_Internal(dm, &dmnew)); 4016 } else if (strflg) { 4017 DM dmnew; 4018 PetscViewer viewer; 4019 const char *contents; 4020 char *strname; 4021 char tmpdir[PETSC_MAX_PATH_LEN]; 4022 char tmpfilename[PETSC_MAX_PATH_LEN]; 4023 char name[PETSC_MAX_PATH_LEN]; 4024 MPI_Comm comm; 4025 PetscMPIInt rank; 4026 4027 PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); 4028 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 4029 PetscCall(PetscStrchr(filename, ':', &strname)); 4030 PetscCheck(strname, comm, PETSC_ERR_ARG_WRONG, "File contents must have the form \"ext:string_name\", not %s", filename); 4031 strname[0] = '\0'; 4032 ++strname; 4033 PetscCall(PetscDLSym(NULL, strname, (void **)&contents)); 4034 PetscCheck(contents, comm, PETSC_ERR_ARG_WRONG, "Could not locate mesh string %s", strname); 4035 PetscCall(PetscGetTmp(comm, tmpdir, PETSC_MAX_PATH_LEN)); 4036 PetscCall(PetscStrlcat(tmpdir, "/meshXXXXXX", PETSC_MAX_PATH_LEN)); 4037 PetscCall(PetscMkdtemp(tmpdir)); 4038 PetscCall(PetscSNPrintf(tmpfilename, PETSC_MAX_PATH_LEN, "%s/mesh.%s", tmpdir, filename)); 4039 PetscCall(PetscViewerASCIIOpen(comm, tmpfilename, &viewer)); 4040 PetscCall(PetscViewerASCIIPrintf(viewer, "%s\n", contents)); 4041 PetscCall(PetscViewerDestroy(&viewer)); 4042 PetscCall(DMPlexCreateFromFile(PetscObjectComm((PetscObject)dm), tmpfilename, plexname, interpolate, &dmnew)); 4043 PetscCall(PetscRMTree(tmpdir)); 4044 PetscCall(PetscSNPrintf(name, PETSC_MAX_PATH_LEN, "%s Mesh", strname)); 4045 PetscCall(PetscObjectSetName((PetscObject)dm, name)); 4046 PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew)); 4047 PetscCall(DMPlexReplace_Internal(dm, &dmnew)); 4048 } else { 4049 PetscCall(PetscObjectSetName((PetscObject)dm, DMPlexShapes[shape])); 4050 switch (shape) { 4051 case DM_SHAPE_BOX: 4052 case DM_SHAPE_ZBOX: 4053 case DM_SHAPE_ANNULUS: { 4054 PetscInt faces[3] = {0, 0, 0}; 4055 PetscReal lower[3] = {0, 0, 0}; 4056 PetscReal upper[3] = {1, 1, 1}; 4057 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 4058 PetscBool isAnnular = shape == DM_SHAPE_ANNULUS ? PETSC_TRUE : PETSC_FALSE; 4059 PetscInt i, n; 4060 4061 n = dim; 4062 for (i = 0; i < dim; ++i) faces[i] = (dim == 1 ? 1 : 4 - dim); 4063 PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg)); 4064 n = 3; 4065 PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg)); 4066 PetscCheck(!flg || !(n != dim), comm, PETSC_ERR_ARG_SIZ, "Lower box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 4067 n = 3; 4068 PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg)); 4069 PetscCheck(!flg || !(n != dim), comm, PETSC_ERR_ARG_SIZ, "Upper box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 4070 n = 3; 4071 PetscCall(PetscOptionsEnumArray("-dm_plex_box_bd", "Boundary type for each dimension", "", DMBoundaryTypes, (PetscEnum *)bdt, &n, &flg)); 4072 PetscCheck(!flg || !(n != dim), comm, PETSC_ERR_ARG_SIZ, "Box boundary types had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 4073 4074 PetscCheck(!isAnnular || dim == 2, comm, PETSC_ERR_ARG_OUTOFRANGE, "Only two dimensional annuli have been implemented"); 4075 if (isAnnular) 4076 for (i = 0; i < dim - 1; ++i) bdt[i] = DM_BOUNDARY_PERIODIC; 4077 4078 switch (cell) { 4079 case DM_POLYTOPE_TRI_PRISM_TENSOR: 4080 PetscCall(DMPlexCreateWedgeBoxMesh_Internal(dm, faces, lower, upper, bdt)); 4081 if (!interpolate) { 4082 DM udm; 4083 4084 PetscCall(DMPlexUninterpolate(dm, &udm)); 4085 PetscCall(DMPlexReplace_Internal(dm, &udm)); 4086 } 4087 break; 4088 default: 4089 PetscCall(DMPlexCreateBoxMesh_Internal(dm, shape, dim, simplex, faces, lower, upper, bdt, interpolate)); 4090 break; 4091 } 4092 if (isAnnular) { 4093 DM cdm; 4094 PetscDS cds; 4095 PetscScalar bounds[2] = {lower[0], upper[0]}; 4096 4097 // Fix coordinates for annular region 4098 PetscCall(DMSetPeriodicity(dm, NULL, NULL, NULL)); 4099 PetscCall(DMSetCellCoordinatesLocal(dm, NULL)); 4100 PetscCall(DMSetCellCoordinates(dm, NULL)); 4101 PetscCall(DMPlexCreateCoordinateSpace(dm, 1, PETSC_TRUE, NULL)); 4102 PetscCall(DMGetCoordinateDM(dm, &cdm)); 4103 PetscCall(DMGetDS(cdm, &cds)); 4104 PetscCall(PetscDSSetConstants(cds, 2, bounds)); 4105 PetscCall(DMPlexRemapGeometry(dm, 0.0, boxToAnnulus)); 4106 } 4107 } break; 4108 case DM_SHAPE_BOX_SURFACE: { 4109 PetscInt faces[3] = {0, 0, 0}; 4110 PetscReal lower[3] = {0, 0, 0}; 4111 PetscReal upper[3] = {1, 1, 1}; 4112 PetscInt i, n; 4113 4114 n = dim + 1; 4115 for (i = 0; i < dim + 1; ++i) faces[i] = (dim + 1 == 1 ? 1 : 4 - (dim + 1)); 4116 PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg)); 4117 n = 3; 4118 PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg)); 4119 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); 4120 n = 3; 4121 PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg)); 4122 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); 4123 PetscCall(DMPlexCreateBoxSurfaceMesh_Internal(dm, dim + 1, faces, lower, upper, interpolate)); 4124 } break; 4125 case DM_SHAPE_SPHERE: { 4126 PetscReal R = 1.0; 4127 4128 PetscCall(PetscOptionsReal("-dm_plex_sphere_radius", "Radius of the sphere", "", R, &R, &flg)); 4129 PetscCall(DMPlexCreateSphereMesh_Internal(dm, dim, simplex, R)); 4130 } break; 4131 case DM_SHAPE_BALL: { 4132 PetscReal R = 1.0; 4133 4134 PetscCall(PetscOptionsReal("-dm_plex_ball_radius", "Radius of the ball", "", R, &R, &flg)); 4135 PetscCall(DMPlexCreateBallMesh_Internal(dm, dim, R)); 4136 } break; 4137 case DM_SHAPE_CYLINDER: { 4138 DMBoundaryType bdt = DM_BOUNDARY_NONE; 4139 PetscInt Nw = 6; 4140 PetscInt Nr = 0; 4141 4142 PetscCall(PetscOptionsEnum("-dm_plex_cylinder_bd", "Boundary type in the z direction", "", DMBoundaryTypes, (PetscEnum)bdt, (PetscEnum *)&bdt, NULL)); 4143 PetscCall(PetscOptionsInt("-dm_plex_cylinder_num_wedges", "Number of wedges around the cylinder", "", Nw, &Nw, NULL)); 4144 PetscCall(PetscOptionsInt("-dm_plex_cylinder_num_refine", "Number of refinements before projection", "", Nr, &Nr, NULL)); 4145 switch (cell) { 4146 case DM_POLYTOPE_TRI_PRISM_TENSOR: 4147 PetscCall(DMPlexCreateWedgeCylinderMesh_Internal(dm, Nw, interpolate)); 4148 break; 4149 default: 4150 PetscCall(DMPlexCreateHexCylinderMesh_Internal(dm, bdt, Nr)); 4151 break; 4152 } 4153 } break; 4154 case DM_SHAPE_SCHWARZ_P: // fallthrough 4155 case DM_SHAPE_GYROID: { 4156 PetscInt extent[3] = {1, 1, 1}, refine = 0, layers = 0, three; 4157 PetscReal thickness = 0.; 4158 DMBoundaryType periodic[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 4159 DMPlexTPSType tps_type = shape == DM_SHAPE_SCHWARZ_P ? DMPLEX_TPS_SCHWARZ_P : DMPLEX_TPS_GYROID; 4160 PetscBool tps_distribute; 4161 PetscCall(PetscOptionsIntArray("-dm_plex_tps_extent", "Number of replicas for each of three dimensions", NULL, extent, (three = 3, &three), NULL)); 4162 PetscCall(PetscOptionsInt("-dm_plex_tps_refine", "Number of refinements", NULL, refine, &refine, NULL)); 4163 PetscCall(PetscOptionsEnumArray("-dm_plex_tps_periodic", "Periodicity in each of three dimensions", NULL, DMBoundaryTypes, (PetscEnum *)periodic, (three = 3, &three), NULL)); 4164 PetscCall(PetscOptionsInt("-dm_plex_tps_layers", "Number of layers in volumetric extrusion (or zero to not extrude)", NULL, layers, &layers, NULL)); 4165 PetscCall(PetscOptionsReal("-dm_plex_tps_thickness", "Thickness of volumetric extrusion", NULL, thickness, &thickness, NULL)); 4166 PetscCall(DMPlexDistributeGetDefault(dm, &tps_distribute)); 4167 PetscCall(PetscOptionsBool("-dm_plex_tps_distribute", "Distribute the 2D mesh prior to refinement and extrusion", NULL, tps_distribute, &tps_distribute, NULL)); 4168 PetscCall(DMPlexCreateTPSMesh_Internal(dm, tps_type, extent, periodic, tps_distribute, refine, layers, thickness)); 4169 } break; 4170 case DM_SHAPE_DOUBLET: { 4171 DM dmnew; 4172 PetscReal rl = 0.0; 4173 4174 PetscCall(PetscOptionsReal("-dm_plex_doublet_refinementlimit", "Refinement limit", NULL, rl, &rl, NULL)); 4175 PetscCall(DMPlexCreateDoublet(PetscObjectComm((PetscObject)dm), dim, simplex, interpolate, rl, &dmnew)); 4176 PetscCall(DMPlexCopy_Internal(dm, PETSC_FALSE, PETSC_FALSE, dmnew)); 4177 PetscCall(DMPlexReplace_Internal(dm, &dmnew)); 4178 } break; 4179 case DM_SHAPE_HYPERCUBIC: { 4180 PetscInt *edges; 4181 PetscReal *lower, *upper; 4182 DMBoundaryType *bdt; 4183 PetscInt n, d; 4184 4185 *useCoordSpace = PETSC_FALSE; 4186 PetscCall(PetscMalloc4(dim, &edges, dim, &lower, dim, &upper, dim, &bdt)); 4187 for (d = 0; d < dim; ++d) { 4188 edges[d] = 1; 4189 lower[d] = 0.; 4190 upper[d] = 1.; 4191 bdt[d] = DM_BOUNDARY_PERIODIC; 4192 } 4193 n = dim; 4194 PetscCall(PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", edges, &n, &flg)); 4195 n = dim; 4196 PetscCall(PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg)); 4197 PetscCheck(!flg || n == dim, comm, PETSC_ERR_ARG_SIZ, "Lower box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 4198 n = dim; 4199 PetscCall(PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg)); 4200 PetscCheck(!flg || n == dim, comm, PETSC_ERR_ARG_SIZ, "Upper box point had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 4201 n = dim; 4202 PetscCall(PetscOptionsEnumArray("-dm_plex_box_bd", "Boundary type for each dimension", "", DMBoundaryTypes, (PetscEnum *)bdt, &n, &flg)); 4203 PetscCheck(!flg || n == dim, comm, PETSC_ERR_ARG_SIZ, "Box boundary types had %" PetscInt_FMT " values, should have been %" PetscInt_FMT, n, dim); 4204 PetscCall(DMPlexCreateHypercubicMesh_Internal(dm, dim, lower, upper, edges, bdt)); 4205 PetscCall(PetscFree4(edges, lower, upper, bdt)); 4206 } break; 4207 default: 4208 SETERRQ(comm, PETSC_ERR_SUP, "Domain shape %s is unsupported", DMPlexShapes[shape]); 4209 } 4210 } 4211 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 4212 if (!((PetscObject)dm)->name && nameflg) PetscCall(PetscObjectSetName((PetscObject)dm, plexname)); 4213 // Allow label creation 4214 PetscCall(PetscOptionsFindPairPrefix_Private(NULL, ((PetscObject)dm)->prefix, "-dm_plex_label_", &option, NULL, &flg)); 4215 if (flg) { 4216 DMLabel label; 4217 PetscInt points[1024], n = 1024; 4218 char fulloption[PETSC_MAX_PATH_LEN]; 4219 const char *name = &option[14]; 4220 4221 PetscCall(DMCreateLabel(dm, name)); 4222 PetscCall(DMGetLabel(dm, name, &label)); 4223 fulloption[0] = '-'; 4224 fulloption[1] = 0; 4225 PetscCall(PetscStrlcat(fulloption, option, PETSC_MAX_PATH_LEN)); 4226 PetscCall(PetscOptionsGetIntArray(NULL, ((PetscObject)dm)->prefix, fulloption, points, &n, NULL)); 4227 for (PetscInt p = 0; p < n; ++p) PetscCall(DMLabelSetValue(label, points[p], 1)); 4228 } 4229 // Allow cohesive label creation 4230 // Faces are input, completed, and all points are marked with their depth 4231 PetscCall(PetscOptionsFindPairPrefix_Private(NULL, ((PetscObject)dm)->prefix, "-dm_plex_cohesive_label_", &option, NULL, &flg)); 4232 if (flg) { 4233 DMLabel label; 4234 PetscInt points[1024], n, pStart, pEnd, Nl = 1; 4235 PetscBool noCreate = PETSC_FALSE; 4236 char fulloption[PETSC_MAX_PATH_LEN]; 4237 char name[PETSC_MAX_PATH_LEN]; 4238 size_t len; 4239 4240 PetscCall(DMPlexGetChart(dm, &pStart, &pEnd)); 4241 PetscCall(PetscStrncpy(name, &option[23], PETSC_MAX_PATH_LEN)); 4242 PetscCall(PetscStrlen(name, &len)); 4243 if (name[len - 1] == '0') Nl = 10; 4244 for (PetscInt l = 0; l < Nl; ++l) { 4245 if (l > 0) name[len - 1] = '0' + l; 4246 fulloption[0] = 0; 4247 PetscCall(PetscStrlcat(fulloption, "-dm_plex_cohesive_label_", 32)); 4248 PetscCall(PetscStrlcat(fulloption, name, PETSC_MAX_PATH_LEN - 32)); 4249 n = 1024; 4250 PetscCall(PetscOptionsGetIntArray(NULL, ((PetscObject)dm)->prefix, fulloption, points, &n, &flg)); 4251 if (!flg) break; 4252 PetscCall(DMHasLabel(dm, name, &noCreate)); 4253 if (noCreate) { 4254 DMLabel inlabel; 4255 IS pointIS; 4256 const PetscInt *lpoints; 4257 PetscInt pdep, ln, inval = points[0]; 4258 char newname[PETSC_MAX_PATH_LEN]; 4259 4260 PetscCheck(n == 1, comm, PETSC_ERR_ARG_WRONG, "Must specify a label value with this option"); 4261 PetscCall(DMGetLabel(dm, name, &inlabel)); 4262 PetscCall(DMLabelGetStratumIS(inlabel, inval, &pointIS)); 4263 PetscCall(ISGetLocalSize(pointIS, &ln)); 4264 PetscCall(ISGetIndices(pointIS, &lpoints)); 4265 PetscCall(DMPlexGetPointDepth(dm, lpoints[0], &pdep)); 4266 PetscCall(PetscSNPrintf(newname, PETSC_MAX_PATH_LEN, "%s%" PetscInt_FMT, name, points[0])); 4267 PetscCall(DMCreateLabel(dm, newname)); 4268 PetscCall(DMGetLabel(dm, newname, &label)); 4269 if (!pdep) PetscCall(ProcessCohesiveLabel_Vertices(dm, label, inlabel, inval, ln, lpoints)); 4270 else PetscCall(ProcessCohesiveLabel_Faces(dm, label, ln, lpoints)); 4271 PetscCall(ISRestoreIndices(pointIS, &lpoints)); 4272 PetscCall(ISDestroy(&pointIS)); 4273 } else { 4274 PetscCall(DMCreateLabel(dm, name)); 4275 PetscCall(DMGetLabel(dm, name, &label)); 4276 if (pStart >= pEnd) n = 0; 4277 PetscCall(ProcessCohesiveLabel_Faces(dm, label, n, points)); 4278 } 4279 PetscCall(DMPlexOrientLabel(dm, label)); 4280 PetscCall(DMPlexLabelCohesiveComplete(dm, label, NULL, 1, PETSC_FALSE, PETSC_FALSE, NULL)); 4281 } 4282 } 4283 PetscCall(DMViewFromOptions(dm, NULL, "-created_dm_view")); 4284 PetscCall(PetscLogEventEnd(DMPLEX_CreateFromOptions, dm, 0, 0, 0)); 4285 PetscFunctionReturn(PETSC_SUCCESS); 4286 } 4287 4288 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(DM dm, PetscOptionItems *PetscOptionsObject) 4289 { 4290 DM_Plex *mesh = (DM_Plex *)dm->data; 4291 PetscBool flg, flg2; 4292 char bdLabel[PETSC_MAX_PATH_LEN]; 4293 char method[PETSC_MAX_PATH_LEN]; 4294 4295 PetscFunctionBegin; 4296 /* Handle viewing */ 4297 PetscCall(PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL)); 4298 PetscCall(PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level for all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL, 0)); 4299 PetscCall(PetscOptionsBoundedInt("-dm_plex_print_fvm", "Debug output level for all fvm computations", "DMPlexSNESComputeResidualFVM", 0, &mesh->printFVM, NULL, 0)); 4300 PetscCall(PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL)); 4301 PetscCall(PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL, 0)); 4302 PetscCall(PetscOptionsBoundedInt("-dm_plex_print_locate", "Debug output level all point location computations", "DMLocatePoints", 0, &mesh->printLocate, NULL, 0)); 4303 PetscCall(DMMonitorSetFromOptions(dm, "-dm_plex_monitor_throughput", "Monitor the simulation throughput", "DMPlexMonitorThroughput", DMPlexMonitorThroughput, NULL, &flg)); 4304 if (flg) PetscCall(PetscLogDefaultBegin()); 4305 /* Labeling */ 4306 PetscCall(PetscOptionsString("-dm_plex_boundary_label", "Label to mark the mesh boundary", "", bdLabel, bdLabel, sizeof(bdLabel), &flg)); 4307 if (flg) PetscCall(DMPlexCreateBoundaryLabel_Private(dm, bdLabel)); 4308 /* Point Location */ 4309 PetscCall(PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL)); 4310 /* Partitioning and distribution */ 4311 PetscCall(PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL)); 4312 /* Reordering */ 4313 PetscCall(PetscOptionsBool("-dm_reorder_section", "Compute point permutation for local section", "DMReorderSectionSetDefault", PETSC_FALSE, &flg2, &flg)); 4314 if (flg) PetscCall(DMReorderSectionSetDefault(dm, flg2 ? DM_REORDER_DEFAULT_TRUE : DM_REORDER_DEFAULT_FALSE)); 4315 PetscCall(PetscOptionsString("-dm_reorder_section_type", "Reordering method for local section", "DMReorderSectionSetType", method, method, PETSC_MAX_PATH_LEN, &flg)); 4316 if (flg) PetscCall(DMReorderSectionSetType(dm, method)); 4317 /* Generation and remeshing */ 4318 PetscCall(PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL)); 4319 /* Projection behavior */ 4320 PetscCall(PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maximum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL, 0)); 4321 PetscCall(PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL)); 4322 /* Checking structure */ 4323 { 4324 PetscBool all = PETSC_FALSE; 4325 4326 PetscCall(PetscOptionsBool("-dm_plex_check_all", "Perform all basic checks", "DMPlexCheck", PETSC_FALSE, &all, NULL)); 4327 if (all) { 4328 PetscCall(DMPlexCheck(dm)); 4329 } else { 4330 PetscCall(PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2)); 4331 if (flg && flg2) PetscCall(DMPlexCheckSymmetry(dm)); 4332 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)); 4333 if (flg && flg2) PetscCall(DMPlexCheckSkeleton(dm, 0)); 4334 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)); 4335 if (flg && flg2) PetscCall(DMPlexCheckFaces(dm, 0)); 4336 PetscCall(PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2)); 4337 if (flg && flg2) PetscCall(DMPlexCheckGeometry(dm)); 4338 PetscCall(PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2)); 4339 if (flg && flg2) PetscCall(DMPlexCheckPointSF(dm, NULL, PETSC_FALSE)); 4340 PetscCall(PetscOptionsBool("-dm_plex_check_interface_cones", "Check points on inter-partition interfaces have conforming order of cone points", "DMPlexCheckInterfaceCones", PETSC_FALSE, &flg, &flg2)); 4341 if (flg && flg2) PetscCall(DMPlexCheckInterfaceCones(dm)); 4342 } 4343 PetscCall(PetscOptionsBool("-dm_plex_check_cell_shape", "Check cell shape", "DMPlexCheckCellShape", PETSC_FALSE, &flg, &flg2)); 4344 if (flg && flg2) PetscCall(DMPlexCheckCellShape(dm, PETSC_TRUE, PETSC_DETERMINE)); 4345 } 4346 { 4347 PetscReal scale = 1.0; 4348 4349 PetscCall(PetscOptionsReal("-dm_plex_scale", "Scale factor for mesh coordinates", "DMPlexScale", scale, &scale, &flg)); 4350 if (flg) { 4351 Vec coordinates, coordinatesLocal; 4352 4353 PetscCall(DMGetCoordinates(dm, &coordinates)); 4354 PetscCall(DMGetCoordinatesLocal(dm, &coordinatesLocal)); 4355 PetscCall(VecScale(coordinates, scale)); 4356 PetscCall(VecScale(coordinatesLocal, scale)); 4357 } 4358 } 4359 PetscCall(PetscPartitionerSetFromOptions(mesh->partitioner)); 4360 PetscFunctionReturn(PETSC_SUCCESS); 4361 } 4362 4363 PetscErrorCode DMSetFromOptions_Overlap_Plex(DM dm, PetscOptionItems *PetscOptionsObject, PetscInt *overlap) 4364 { 4365 PetscInt numOvLabels = 16, numOvExLabels = 16; 4366 char *ovLabelNames[16], *ovExLabelNames[16]; 4367 PetscInt numOvValues = 16, numOvExValues = 16, l; 4368 PetscBool flg; 4369 4370 PetscFunctionBegin; 4371 PetscCall(PetscOptionsBoundedInt("-dm_distribute_overlap", "The size of the overlap halo", "DMPlexDistribute", *overlap, overlap, NULL, 0)); 4372 PetscCall(PetscOptionsStringArray("-dm_distribute_overlap_labels", "List of overlap label names", "DMPlexDistribute", ovLabelNames, &numOvLabels, &flg)); 4373 if (!flg) numOvLabels = 0; 4374 if (numOvLabels) { 4375 ((DM_Plex *)dm->data)->numOvLabels = numOvLabels; 4376 for (l = 0; l < numOvLabels; ++l) { 4377 PetscCall(DMGetLabel(dm, ovLabelNames[l], &((DM_Plex *)dm->data)->ovLabels[l])); 4378 PetscCheck(((DM_Plex *)dm->data)->ovLabels[l], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid label name %s", ovLabelNames[l]); 4379 PetscCall(PetscFree(ovLabelNames[l])); 4380 } 4381 PetscCall(PetscOptionsIntArray("-dm_distribute_overlap_values", "List of overlap label values", "DMPlexDistribute", ((DM_Plex *)dm->data)->ovValues, &numOvValues, &flg)); 4382 if (!flg) numOvValues = 0; 4383 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); 4384 4385 PetscCall(PetscOptionsStringArray("-dm_distribute_overlap_exclude_labels", "List of overlap exclude label names", "DMPlexDistribute", ovExLabelNames, &numOvExLabels, &flg)); 4386 if (!flg) numOvExLabels = 0; 4387 ((DM_Plex *)dm->data)->numOvExLabels = numOvExLabels; 4388 for (l = 0; l < numOvExLabels; ++l) { 4389 PetscCall(DMGetLabel(dm, ovExLabelNames[l], &((DM_Plex *)dm->data)->ovExLabels[l])); 4390 PetscCheck(((DM_Plex *)dm->data)->ovExLabels[l], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid label name %s", ovExLabelNames[l]); 4391 PetscCall(PetscFree(ovExLabelNames[l])); 4392 } 4393 PetscCall(PetscOptionsIntArray("-dm_distribute_overlap_exclude_values", "List of overlap exclude label values", "DMPlexDistribute", ((DM_Plex *)dm->data)->ovExValues, &numOvExValues, &flg)); 4394 if (!flg) numOvExValues = 0; 4395 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); 4396 } 4397 PetscFunctionReturn(PETSC_SUCCESS); 4398 } 4399 4400 static PetscErrorCode DMSetFromOptions_Plex(DM dm, PetscOptionItems *PetscOptionsObject) 4401 { 4402 PetscFunctionList ordlist; 4403 char oname[256]; 4404 char sublabelname[PETSC_MAX_PATH_LEN] = ""; 4405 DMReorderDefaultFlag reorder; 4406 PetscReal volume = -1.0; 4407 PetscInt prerefine = 0, refine = 0, r, coarsen = 0, overlap = 0, extLayers = 0, dim; 4408 PetscBool uniformOrig = PETSC_FALSE, created = PETSC_FALSE, uniform = PETSC_TRUE, distribute, saveSF = PETSC_FALSE, interpolate = PETSC_TRUE, coordSpace = PETSC_TRUE, remap = PETSC_TRUE, ghostCells = PETSC_FALSE, isHierarchy, flg; 4409 4410 PetscFunctionBegin; 4411 PetscOptionsHeadBegin(PetscOptionsObject, "DMPlex Options"); 4412 if (dm->cloneOpts) goto non_refine; 4413 /* Handle automatic creation */ 4414 PetscCall(DMGetDimension(dm, &dim)); 4415 if (dim < 0) { 4416 PetscCall(DMPlexCreateFromOptions_Internal(PetscOptionsObject, &coordSpace, dm)); 4417 created = PETSC_TRUE; 4418 } 4419 PetscCall(DMGetDimension(dm, &dim)); 4420 /* Handle interpolation before distribution */ 4421 PetscCall(PetscOptionsBool("-dm_plex_interpolate_pre", "Flag to interpolate mesh before distribution", "", interpolate, &interpolate, &flg)); 4422 if (flg) { 4423 DMPlexInterpolatedFlag interpolated; 4424 4425 PetscCall(DMPlexIsInterpolated(dm, &interpolated)); 4426 if (interpolated == DMPLEX_INTERPOLATED_FULL && !interpolate) { 4427 DM udm; 4428 4429 PetscCall(DMPlexUninterpolate(dm, &udm)); 4430 PetscCall(DMPlexReplace_Internal(dm, &udm)); 4431 } else if (interpolated != DMPLEX_INTERPOLATED_FULL && interpolate) { 4432 DM idm; 4433 4434 PetscCall(DMPlexInterpolate(dm, &idm)); 4435 PetscCall(DMPlexReplace_Internal(dm, &idm)); 4436 } 4437 } 4438 // Handle submesh selection before distribution 4439 PetscCall(PetscOptionsString("-dm_plex_submesh", "Label to use for submesh selection", "", sublabelname, sublabelname, PETSC_MAX_PATH_LEN, &flg)); 4440 if (flg) { 4441 DM subdm; 4442 DMLabel label; 4443 IS valueIS, pointIS; 4444 const PetscInt *values, *points; 4445 PetscBool markedFaces = PETSC_FALSE; 4446 PetscInt Nv, value, Np; 4447 4448 PetscCall(DMGetLabel(dm, sublabelname, &label)); 4449 PetscCall(DMLabelGetNumValues(label, &Nv)); 4450 PetscCheck(Nv == 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only a single label value is currently supported for submesh selection, not %" PetscInt_FMT, Nv); 4451 PetscCall(DMLabelGetValueIS(label, &valueIS)); 4452 PetscCall(ISGetIndices(valueIS, &values)); 4453 value = values[0]; 4454 PetscCall(ISRestoreIndices(valueIS, &values)); 4455 PetscCall(ISDestroy(&valueIS)); 4456 PetscCall(DMLabelGetStratumSize(label, value, &Np)); 4457 PetscCall(DMLabelGetStratumIS(label, value, &pointIS)); 4458 PetscCall(ISGetIndices(pointIS, &points)); 4459 for (PetscInt p = 0; p < Np; ++p) { 4460 PetscInt pdepth; 4461 4462 PetscCall(DMPlexGetPointDepth(dm, points[p], &pdepth)); 4463 if (pdepth) { 4464 markedFaces = PETSC_TRUE; 4465 break; 4466 } 4467 } 4468 PetscCall(ISRestoreIndices(pointIS, &points)); 4469 PetscCall(ISDestroy(&pointIS)); 4470 PetscCall(DMPlexCreateSubmesh(dm, label, value, markedFaces, &subdm)); 4471 PetscCall(DMPlexReplace_Internal(dm, &subdm)); 4472 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4473 } 4474 /* Handle DMPlex refinement before distribution */ 4475 PetscCall(DMPlexGetRefinementUniform(dm, &uniformOrig)); 4476 PetscCall(PetscOptionsBoundedInt("-dm_refine_pre", "The number of refinements before distribution", "DMCreate", prerefine, &prerefine, NULL, 0)); 4477 PetscCall(PetscOptionsBool("-dm_refine_remap_pre", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL)); 4478 PetscCall(PetscOptionsBool("-dm_refine_uniform_pre", "Flag for uniform refinement before distribution", "DMCreate", uniform, &uniform, &flg)); 4479 if (flg) PetscCall(DMPlexSetRefinementUniform(dm, uniform)); 4480 PetscCall(PetscOptionsReal("-dm_refine_volume_limit_pre", "The maximum cell volume after refinement before distribution", "DMCreate", volume, &volume, &flg)); 4481 if (flg) { 4482 PetscCall(DMPlexSetRefinementUniform(dm, PETSC_FALSE)); 4483 PetscCall(DMPlexSetRefinementLimit(dm, volume)); 4484 prerefine = PetscMax(prerefine, 1); 4485 } 4486 if (prerefine) PetscCall(DMLocalizeCoordinates(dm)); 4487 for (r = 0; r < prerefine; ++r) { 4488 DM rdm; 4489 PetscPointFunc coordFunc = ((DM_Plex *)dm->data)->coordFunc; 4490 4491 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4492 PetscCall(DMRefine(dm, PetscObjectComm((PetscObject)dm), &rdm)); 4493 PetscCall(DMPlexReplace_Internal(dm, &rdm)); 4494 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4495 if (coordFunc && remap) { 4496 PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc)); 4497 ((DM_Plex *)dm->data)->coordFunc = coordFunc; 4498 } 4499 } 4500 PetscCall(DMPlexSetRefinementUniform(dm, uniformOrig)); 4501 /* Handle DMPlex extrusion before distribution */ 4502 PetscCall(PetscOptionsBoundedInt("-dm_extrude", "The number of layers to extrude", "", extLayers, &extLayers, NULL, 0)); 4503 if (extLayers) { 4504 DM edm; 4505 4506 PetscCall(DMExtrude(dm, extLayers, &edm)); 4507 PetscCall(DMPlexReplace_Internal(dm, &edm)); 4508 ((DM_Plex *)dm->data)->coordFunc = NULL; 4509 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4510 extLayers = 0; 4511 PetscCall(DMGetDimension(dm, &dim)); 4512 } 4513 /* Handle DMPlex reordering before distribution */ 4514 PetscCall(DMPlexReorderGetDefault(dm, &reorder)); 4515 PetscCall(MatGetOrderingList(&ordlist)); 4516 PetscCall(PetscStrncpy(oname, MATORDERINGNATURAL, sizeof(oname))); 4517 PetscCall(PetscOptionsFList("-dm_plex_reorder", "Set mesh reordering type", "DMPlexGetOrdering", ordlist, MATORDERINGNATURAL, oname, sizeof(oname), &flg)); 4518 if (reorder == DM_REORDER_DEFAULT_TRUE || flg) { 4519 DM pdm; 4520 IS perm; 4521 4522 PetscCall(DMPlexGetOrdering(dm, oname, NULL, &perm)); 4523 PetscCall(DMPlexPermute(dm, perm, &pdm)); 4524 PetscCall(ISDestroy(&perm)); 4525 PetscCall(DMPlexReplace_Internal(dm, &pdm)); 4526 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4527 } 4528 /* Handle DMPlex distribution */ 4529 PetscCall(DMPlexDistributeGetDefault(dm, &distribute)); 4530 PetscCall(PetscOptionsBool("-dm_distribute", "Flag to redistribute a mesh among processes", "DMPlexDistribute", distribute, &distribute, NULL)); 4531 PetscCall(PetscOptionsBool("-dm_distribute_save_sf", "Flag to save the migration SF", "DMPlexSetMigrationSF", saveSF, &saveSF, NULL)); 4532 PetscCall(DMSetFromOptions_Overlap_Plex(dm, PetscOptionsObject, &overlap)); 4533 if (distribute) { 4534 DM pdm = NULL; 4535 PetscPartitioner part; 4536 PetscSF sfMigration; 4537 4538 PetscCall(DMPlexGetPartitioner(dm, &part)); 4539 PetscCall(PetscPartitionerSetFromOptions(part)); 4540 PetscCall(DMPlexDistribute(dm, overlap, &sfMigration, &pdm)); 4541 if (pdm) PetscCall(DMPlexReplace_Internal(dm, &pdm)); 4542 if (saveSF) PetscCall(DMPlexSetMigrationSF(dm, sfMigration)); 4543 PetscCall(PetscSFDestroy(&sfMigration)); 4544 } 4545 /* Must check CEED options before creating function space for coordinates */ 4546 { 4547 PetscBool useCeed = PETSC_FALSE, flg; 4548 4549 PetscCall(PetscOptionsBool("-dm_plex_use_ceed", "Use LibCEED as the FEM backend", "DMPlexSetUseCeed", useCeed, &useCeed, &flg)); 4550 if (flg) PetscCall(DMPlexSetUseCeed(dm, useCeed)); 4551 } 4552 /* Create coordinate space */ 4553 if (created) { 4554 DM_Plex *mesh = (DM_Plex *)dm->data; 4555 PetscInt degree = 1, deg; 4556 PetscInt height = 0; 4557 DM cdm; 4558 PetscBool flg, localize = PETSC_TRUE, sparseLocalize = PETSC_TRUE; 4559 4560 PetscCall(PetscOptionsBool("-dm_coord_space", "Use an FEM space for coordinates", "", coordSpace, &coordSpace, &flg)); 4561 PetscCall(PetscOptionsInt("-dm_coord_petscspace_degree", "FEM degree for coordinate space", "", degree, °ree, NULL)); 4562 PetscCall(DMGetCoordinateDegree_Internal(dm, °)); 4563 if (coordSpace && deg <= 1) PetscCall(DMPlexCreateCoordinateSpace(dm, degree, PETSC_TRUE, mesh->coordFunc)); 4564 PetscCall(DMGetCoordinateDM(dm, &cdm)); 4565 if (flg && !coordSpace) { 4566 PetscDS cds; 4567 PetscObject obj; 4568 PetscClassId id; 4569 4570 PetscCall(DMGetDS(cdm, &cds)); 4571 PetscCall(PetscDSGetDiscretization(cds, 0, &obj)); 4572 PetscCall(PetscObjectGetClassId(obj, &id)); 4573 if (id == PETSCFE_CLASSID) { 4574 PetscContainer dummy; 4575 4576 PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &dummy)); 4577 PetscCall(PetscObjectSetName((PetscObject)dummy, "coordinates")); 4578 PetscCall(DMSetField(cdm, 0, NULL, (PetscObject)dummy)); 4579 PetscCall(PetscContainerDestroy(&dummy)); 4580 PetscCall(DMClearDS(cdm)); 4581 } 4582 mesh->coordFunc = NULL; 4583 } 4584 PetscCall(PetscOptionsBool("-dm_localize", "Localize mesh coordinates", "", localize, &localize, NULL)); 4585 PetscCall(PetscOptionsBool("-dm_sparse_localize", "Localize only necessary cells", "DMSetSparseLocalize", sparseLocalize, &sparseLocalize, &flg)); 4586 if (flg) PetscCall(DMSetSparseLocalize(dm, sparseLocalize)); 4587 PetscCall(PetscOptionsInt("-dm_localize_height", "Localize edges and faces in addition to cells", "", height, &height, &flg)); 4588 if (flg) PetscCall(DMPlexSetMaxProjectionHeight(cdm, height)); 4589 if (localize) PetscCall(DMLocalizeCoordinates(dm)); 4590 } 4591 /* Handle DMPlex refinement */ 4592 remap = PETSC_TRUE; 4593 PetscCall(PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL, 0)); 4594 PetscCall(PetscOptionsBool("-dm_refine_remap", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL)); 4595 PetscCall(PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy, 0)); 4596 if (refine) PetscCall(DMPlexSetRefinementUniform(dm, PETSC_TRUE)); 4597 if (refine && isHierarchy) { 4598 DM *dms, coarseDM; 4599 4600 PetscCall(DMGetCoarseDM(dm, &coarseDM)); 4601 PetscCall(PetscObjectReference((PetscObject)coarseDM)); 4602 PetscCall(PetscMalloc1(refine, &dms)); 4603 PetscCall(DMRefineHierarchy(dm, refine, dms)); 4604 /* Total hack since we do not pass in a pointer */ 4605 PetscCall(DMPlexSwap_Static(dm, dms[refine - 1])); 4606 if (refine == 1) { 4607 PetscCall(DMSetCoarseDM(dm, dms[0])); 4608 PetscCall(DMPlexSetRegularRefinement(dm, PETSC_TRUE)); 4609 } else { 4610 PetscCall(DMSetCoarseDM(dm, dms[refine - 2])); 4611 PetscCall(DMPlexSetRegularRefinement(dm, PETSC_TRUE)); 4612 PetscCall(DMSetCoarseDM(dms[0], dms[refine - 1])); 4613 PetscCall(DMPlexSetRegularRefinement(dms[0], PETSC_TRUE)); 4614 } 4615 PetscCall(DMSetCoarseDM(dms[refine - 1], coarseDM)); 4616 PetscCall(PetscObjectDereference((PetscObject)coarseDM)); 4617 /* Free DMs */ 4618 for (r = 0; r < refine; ++r) { 4619 PetscCall(DMSetFromOptions_NonRefinement_Plex(dms[r], PetscOptionsObject)); 4620 PetscCall(DMDestroy(&dms[r])); 4621 } 4622 PetscCall(PetscFree(dms)); 4623 } else { 4624 for (r = 0; r < refine; ++r) { 4625 DM rdm; 4626 PetscPointFunc coordFunc = ((DM_Plex *)dm->data)->coordFunc; 4627 4628 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4629 PetscCall(DMRefine(dm, PetscObjectComm((PetscObject)dm), &rdm)); 4630 /* Total hack since we do not pass in a pointer */ 4631 PetscCall(DMPlexReplace_Internal(dm, &rdm)); 4632 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4633 if (coordFunc && remap) { 4634 PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc)); 4635 ((DM_Plex *)dm->data)->coordFunc = coordFunc; 4636 } 4637 } 4638 } 4639 /* Handle DMPlex coarsening */ 4640 PetscCall(PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL, 0)); 4641 PetscCall(PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy, 0)); 4642 if (coarsen && isHierarchy) { 4643 DM *dms; 4644 4645 PetscCall(PetscMalloc1(coarsen, &dms)); 4646 PetscCall(DMCoarsenHierarchy(dm, coarsen, dms)); 4647 /* Free DMs */ 4648 for (r = 0; r < coarsen; ++r) { 4649 PetscCall(DMSetFromOptions_NonRefinement_Plex(dms[r], PetscOptionsObject)); 4650 PetscCall(DMDestroy(&dms[r])); 4651 } 4652 PetscCall(PetscFree(dms)); 4653 } else { 4654 for (r = 0; r < coarsen; ++r) { 4655 DM cdm; 4656 PetscPointFunc coordFunc = ((DM_Plex *)dm->data)->coordFunc; 4657 4658 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4659 PetscCall(DMCoarsen(dm, PetscObjectComm((PetscObject)dm), &cdm)); 4660 /* Total hack since we do not pass in a pointer */ 4661 PetscCall(DMPlexReplace_Internal(dm, &cdm)); 4662 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4663 if (coordFunc) { 4664 PetscCall(DMPlexRemapGeometry(dm, 0.0, coordFunc)); 4665 ((DM_Plex *)dm->data)->coordFunc = coordFunc; 4666 } 4667 } 4668 } 4669 // Handle coordinate remapping 4670 remap = PETSC_FALSE; 4671 PetscCall(PetscOptionsBool("-dm_coord_remap", "Flag to control coordinate remapping", "", remap, &remap, NULL)); 4672 if (remap) { 4673 DMPlexCoordMap map = DM_COORD_MAP_NONE; 4674 PetscPointFunc mapFunc = NULL; 4675 PetscScalar params[16]; 4676 PetscInt Np = PETSC_STATIC_ARRAY_LENGTH(params), cdim; 4677 MPI_Comm comm; 4678 4679 PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); 4680 PetscCall(DMGetCoordinateDim(dm, &cdim)); 4681 PetscCall(PetscOptionsScalarArray("-dm_coord_map_params", "Parameters for the coordinate remapping", "", params, &Np, &flg)); 4682 if (!flg) Np = 0; 4683 // TODO Allow user to pass a map function by name 4684 PetscCall(PetscOptionsEnum("-dm_coord_map", "Coordinate mapping for built-in mesh", "", DMPlexCoordMaps, (PetscEnum)map, (PetscEnum *)&map, &flg)); 4685 if (flg) { 4686 switch (map) { 4687 case DM_COORD_MAP_NONE: 4688 mapFunc = coordMap_identity; 4689 break; 4690 case DM_COORD_MAP_SHEAR: 4691 mapFunc = coordMap_shear; 4692 if (!Np) { 4693 Np = cdim + 1; 4694 params[0] = 0; 4695 for (PetscInt d = 1; d <= cdim; ++d) params[d] = 1.0; 4696 } 4697 PetscCheck(Np == cdim + 1, comm, PETSC_ERR_ARG_WRONG, "The shear coordinate map must have cdim + 1 = %" PetscInt_FMT " parameters, not %" PetscInt_FMT, cdim + 1, Np); 4698 break; 4699 case DM_COORD_MAP_FLARE: 4700 mapFunc = coordMap_flare; 4701 if (!Np) { 4702 Np = cdim + 1; 4703 params[0] = 0; 4704 for (PetscInt d = 1; d <= cdim; ++d) params[d] = 1.0; 4705 } 4706 PetscCheck(Np == cdim + 1, comm, PETSC_ERR_ARG_WRONG, "The flare coordinate map must have cdim + 1 = %" PetscInt_FMT " parameters, not %" PetscInt_FMT, cdim + 1, Np); 4707 break; 4708 case DM_COORD_MAP_ANNULUS: 4709 mapFunc = coordMap_annulus; 4710 if (!Np) { 4711 Np = 2; 4712 params[0] = 1.; 4713 params[1] = 2.; 4714 } 4715 PetscCheck(Np == 2, comm, PETSC_ERR_ARG_WRONG, "The annulus coordinate map must have 2 parameters, not %" PetscInt_FMT, Np); 4716 break; 4717 case DM_COORD_MAP_SHELL: 4718 mapFunc = coordMap_shell; 4719 if (!Np) { 4720 Np = 2; 4721 params[0] = 1.; 4722 params[1] = 2.; 4723 } 4724 PetscCheck(Np == 2, comm, PETSC_ERR_ARG_WRONG, "The spherical shell coordinate map must have 2 parameters, not %" PetscInt_FMT, Np); 4725 break; 4726 default: 4727 mapFunc = coordMap_identity; 4728 } 4729 } 4730 if (Np) { 4731 DM cdm; 4732 PetscDS cds; 4733 4734 PetscCall(DMGetCoordinateDM(dm, &cdm)); 4735 PetscCall(DMGetDS(cdm, &cds)); 4736 PetscCall(PetscDSSetConstants(cds, Np, params)); 4737 } 4738 PetscCall(DMPlexRemapGeometry(dm, 0.0, mapFunc)); 4739 } 4740 /* Handle ghost cells */ 4741 PetscCall(PetscOptionsBool("-dm_plex_create_fv_ghost_cells", "Flag to create finite volume ghost cells on the boundary", "DMCreate", ghostCells, &ghostCells, NULL)); 4742 if (ghostCells) { 4743 DM gdm; 4744 char lname[PETSC_MAX_PATH_LEN]; 4745 4746 lname[0] = '\0'; 4747 PetscCall(PetscOptionsString("-dm_plex_fv_ghost_cells_label", "Label name for ghost cells boundary", "DMCreate", lname, lname, sizeof(lname), &flg)); 4748 PetscCall(DMPlexConstructGhostCells(dm, flg ? lname : NULL, NULL, &gdm)); 4749 PetscCall(DMPlexReplace_Internal(dm, &gdm)); 4750 } 4751 /* Handle 1D order */ 4752 if (reorder != DM_REORDER_DEFAULT_FALSE && dim == 1) { 4753 DM cdm, rdm; 4754 PetscDS cds; 4755 PetscObject obj; 4756 PetscClassId id = PETSC_OBJECT_CLASSID; 4757 IS perm; 4758 PetscInt Nf; 4759 PetscBool distributed; 4760 4761 PetscCall(DMPlexIsDistributed(dm, &distributed)); 4762 PetscCall(DMGetCoordinateDM(dm, &cdm)); 4763 PetscCall(DMGetDS(cdm, &cds)); 4764 PetscCall(PetscDSGetNumFields(cds, &Nf)); 4765 if (Nf) { 4766 PetscCall(PetscDSGetDiscretization(cds, 0, &obj)); 4767 PetscCall(PetscObjectGetClassId(obj, &id)); 4768 } 4769 if (!distributed && id != PETSCFE_CLASSID) { 4770 PetscCall(DMPlexGetOrdering1D(dm, &perm)); 4771 PetscCall(DMPlexPermute(dm, perm, &rdm)); 4772 PetscCall(DMPlexReplace_Internal(dm, &rdm)); 4773 PetscCall(ISDestroy(&perm)); 4774 } 4775 } 4776 /* Handle */ 4777 non_refine: 4778 PetscCall(DMSetFromOptions_NonRefinement_Plex(dm, PetscOptionsObject)); 4779 PetscOptionsHeadEnd(); 4780 PetscFunctionReturn(PETSC_SUCCESS); 4781 } 4782 4783 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm, Vec *vec) 4784 { 4785 PetscFunctionBegin; 4786 PetscCall(DMCreateGlobalVector_Section_Private(dm, vec)); 4787 /* PetscCall(VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM)); */ 4788 PetscCall(VecSetOperation(*vec, VECOP_VIEW, (void (*)(void))VecView_Plex)); 4789 PetscCall(VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void))VecView_Plex_Native)); 4790 PetscCall(VecSetOperation(*vec, VECOP_LOAD, (void (*)(void))VecLoad_Plex)); 4791 PetscCall(VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void))VecLoad_Plex_Native)); 4792 PetscFunctionReturn(PETSC_SUCCESS); 4793 } 4794 4795 static PetscErrorCode DMCreateLocalVector_Plex(DM dm, Vec *vec) 4796 { 4797 PetscFunctionBegin; 4798 PetscCall(DMCreateLocalVector_Section_Private(dm, vec)); 4799 PetscCall(VecSetOperation(*vec, VECOP_VIEW, (void (*)(void))VecView_Plex_Local)); 4800 PetscCall(VecSetOperation(*vec, VECOP_LOAD, (void (*)(void))VecLoad_Plex_Local)); 4801 PetscFunctionReturn(PETSC_SUCCESS); 4802 } 4803 4804 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 4805 { 4806 PetscInt depth, d; 4807 4808 PetscFunctionBegin; 4809 PetscCall(DMPlexGetDepth(dm, &depth)); 4810 if (depth == 1) { 4811 PetscCall(DMGetDimension(dm, &d)); 4812 if (dim == 0) PetscCall(DMPlexGetDepthStratum(dm, dim, pStart, pEnd)); 4813 else if (dim == d) PetscCall(DMPlexGetDepthStratum(dm, 1, pStart, pEnd)); 4814 else { 4815 *pStart = 0; 4816 *pEnd = 0; 4817 } 4818 } else { 4819 PetscCall(DMPlexGetDepthStratum(dm, dim, pStart, pEnd)); 4820 } 4821 PetscFunctionReturn(PETSC_SUCCESS); 4822 } 4823 4824 static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 4825 { 4826 PetscSF sf; 4827 PetscInt niranks, njranks, n; 4828 const PetscMPIInt *iranks, *jranks; 4829 DM_Plex *data = (DM_Plex *)dm->data; 4830 4831 PetscFunctionBegin; 4832 PetscCall(DMGetPointSF(dm, &sf)); 4833 if (!data->neighbors) { 4834 PetscCall(PetscSFSetUp(sf)); 4835 PetscCall(PetscSFGetRootRanks(sf, &njranks, &jranks, NULL, NULL, NULL)); 4836 PetscCall(PetscSFGetLeafRanks(sf, &niranks, &iranks, NULL, NULL)); 4837 PetscCall(PetscMalloc1(njranks + niranks + 1, &data->neighbors)); 4838 PetscCall(PetscArraycpy(data->neighbors + 1, jranks, njranks)); 4839 PetscCall(PetscArraycpy(data->neighbors + njranks + 1, iranks, niranks)); 4840 n = njranks + niranks; 4841 PetscCall(PetscSortRemoveDupsMPIInt(&n, data->neighbors + 1)); 4842 /* The following cast should never fail: can't have more neighbors than PETSC_MPI_INT_MAX */ 4843 PetscCall(PetscMPIIntCast(n, data->neighbors)); 4844 } 4845 if (nranks) *nranks = data->neighbors[0]; 4846 if (ranks) { 4847 if (data->neighbors[0]) *ranks = data->neighbors + 1; 4848 else *ranks = NULL; 4849 } 4850 PetscFunctionReturn(PETSC_SUCCESS); 4851 } 4852 4853 PETSC_INTERN PetscErrorCode DMInterpolateSolution_Plex(DM, DM, Mat, Vec, Vec); 4854 4855 static PetscErrorCode DMInitialize_Plex(DM dm) 4856 { 4857 PetscFunctionBegin; 4858 dm->ops->view = DMView_Plex; 4859 dm->ops->load = DMLoad_Plex; 4860 dm->ops->setfromoptions = DMSetFromOptions_Plex; 4861 dm->ops->clone = DMClone_Plex; 4862 dm->ops->setup = DMSetUp_Plex; 4863 dm->ops->createlocalsection = DMCreateLocalSection_Plex; 4864 dm->ops->createsectionpermutation = DMCreateSectionPermutation_Plex; 4865 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 4866 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 4867 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 4868 dm->ops->getlocaltoglobalmapping = NULL; 4869 dm->ops->createfieldis = NULL; 4870 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 4871 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 4872 dm->ops->getcoloring = NULL; 4873 dm->ops->creatematrix = DMCreateMatrix_Plex; 4874 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 4875 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 4876 dm->ops->createmassmatrixlumped = DMCreateMassMatrixLumped_Plex; 4877 dm->ops->createinjection = DMCreateInjection_Plex; 4878 dm->ops->refine = DMRefine_Plex; 4879 dm->ops->coarsen = DMCoarsen_Plex; 4880 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 4881 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 4882 dm->ops->extrude = DMExtrude_Plex; 4883 dm->ops->globaltolocalbegin = NULL; 4884 dm->ops->globaltolocalend = NULL; 4885 dm->ops->localtoglobalbegin = NULL; 4886 dm->ops->localtoglobalend = NULL; 4887 dm->ops->destroy = DMDestroy_Plex; 4888 dm->ops->createsubdm = DMCreateSubDM_Plex; 4889 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 4890 dm->ops->getdimpoints = DMGetDimPoints_Plex; 4891 dm->ops->locatepoints = DMLocatePoints_Plex; 4892 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 4893 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 4894 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 4895 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 4896 dm->ops->projectbdfieldlabellocal = DMProjectBdFieldLabelLocal_Plex; 4897 dm->ops->computel2diff = DMComputeL2Diff_Plex; 4898 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 4899 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 4900 dm->ops->getneighbors = DMGetNeighbors_Plex; 4901 dm->ops->getlocalboundingbox = DMGetLocalBoundingBox_Coordinates; 4902 dm->ops->createdomaindecomposition = DMCreateDomainDecomposition_Plex; 4903 dm->ops->createddscatters = DMCreateDomainDecompositionScatters_Plex; 4904 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexInsertBoundaryValues_C", DMPlexInsertBoundaryValues_Plex)); 4905 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexInsertTimeDerivativeBoundaryValues_C", DMPlexInsertTimeDerivativeBoundaryValues_Plex)); 4906 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMSetUpGLVisViewer_C", DMSetUpGLVisViewer_Plex)); 4907 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMCreateNeumannOverlap_C", DMCreateNeumannOverlap_Plex)); 4908 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexDistributeGetDefault_C", DMPlexDistributeGetDefault_Plex)); 4909 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexDistributeSetDefault_C", DMPlexDistributeSetDefault_Plex)); 4910 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexReorderGetDefault_C", DMPlexReorderGetDefault_Plex)); 4911 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexReorderSetDefault_C", DMPlexReorderSetDefault_Plex)); 4912 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMReorderSectionGetDefault_C", DMReorderSectionGetDefault_Plex)); 4913 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMReorderSectionSetDefault_C", DMReorderSectionSetDefault_Plex)); 4914 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMReorderSectionGetType_C", DMReorderSectionGetType_Plex)); 4915 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMReorderSectionSetType_C", DMReorderSectionSetType_Plex)); 4916 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMInterpolateSolution_C", DMInterpolateSolution_Plex)); 4917 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexGetOverlap_C", DMPlexGetOverlap_Plex)); 4918 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexSetOverlap_C", DMPlexSetOverlap_Plex)); 4919 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexGetUseCeed_C", DMPlexGetUseCeed_Plex)); 4920 PetscCall(PetscObjectComposeFunction((PetscObject)dm, "DMPlexSetUseCeed_C", DMPlexSetUseCeed_Plex)); 4921 PetscFunctionReturn(PETSC_SUCCESS); 4922 } 4923 4924 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 4925 { 4926 DM_Plex *mesh = (DM_Plex *)dm->data; 4927 const PetscSF *face_sfs; 4928 PetscInt num_face_sfs; 4929 4930 PetscFunctionBegin; 4931 mesh->refct++; 4932 (*newdm)->data = mesh; 4933 PetscCall(DMPlexGetIsoperiodicFaceSF(dm, &num_face_sfs, &face_sfs)); 4934 PetscCall(DMPlexSetIsoperiodicFaceSF(*newdm, num_face_sfs, (PetscSF *)face_sfs)); 4935 PetscCall(PetscObjectChangeTypeName((PetscObject)*newdm, DMPLEX)); 4936 PetscCall(DMInitialize_Plex(*newdm)); 4937 PetscFunctionReturn(PETSC_SUCCESS); 4938 } 4939 4940 /*MC 4941 DMPLEX = "plex" - A `DM` object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 4942 In the local representation, `Vec`s contain all unknowns in the interior and shared boundary. This is 4943 specified by a PetscSection object. Ownership in the global representation is determined by 4944 ownership of the underlying `DMPLEX` points. This is specified by another `PetscSection` object. 4945 4946 Options Database Keys: 4947 + -dm_refine_pre - Refine mesh before distribution 4948 + -dm_refine_uniform_pre - Choose uniform or generator-based refinement 4949 + -dm_refine_volume_limit_pre - Cell volume limit after pre-refinement using generator 4950 . -dm_distribute - Distribute mesh across processes 4951 . -dm_distribute_overlap - Number of cells to overlap for distribution 4952 . -dm_refine - Refine mesh after distribution 4953 . -dm_localize <bool> - Whether to localize coordinates for periodic meshes 4954 . -dm_sparse_localize <bool> - Whether to only localize cells on the periodic boundary 4955 . -dm_plex_hash_location - Use grid hashing for point location 4956 . -dm_plex_hash_box_faces <n,m,p> - The number of divisions in each direction of the grid hash 4957 . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes 4958 . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing 4959 . -dm_plex_max_projection_height - Maximum mesh point height used to project locally 4960 . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement 4961 . -dm_plex_reorder_section - Use specialized blocking if available 4962 . -dm_plex_check_all - Perform all checks below 4963 . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric 4964 . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices 4965 . -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 4966 . -dm_plex_check_geometry - Check that cells have positive volume 4967 . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ 4968 . -dm_plex_view_scale <num> - Scale the TikZ 4969 . -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices 4970 - -dm_plex_print_fvm <num> - View FVM assembly information, such as flux updates 4971 4972 Level: intermediate 4973 4974 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMType`, `DMPlexCreate()`, `DMCreate()`, `DMSetType()`, `PetscSection` 4975 M*/ 4976 4977 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 4978 { 4979 DM_Plex *mesh; 4980 PetscInt unit; 4981 4982 PetscFunctionBegin; 4983 PetscCall(PetscCitationsRegister(PlexCitation, &Plexcite)); 4984 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4985 PetscCall(PetscNew(&mesh)); 4986 dm->reorderSection = DM_REORDER_DEFAULT_NOTSET; 4987 dm->data = mesh; 4988 4989 mesh->refct = 1; 4990 PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection)); 4991 PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection)); 4992 mesh->refinementUniform = PETSC_TRUE; 4993 mesh->refinementLimit = -1.0; 4994 mesh->distDefault = PETSC_TRUE; 4995 mesh->reorderDefault = DM_REORDER_DEFAULT_NOTSET; 4996 mesh->distributionName = NULL; 4997 mesh->interpolated = DMPLEX_INTERPOLATED_INVALID; 4998 mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID; 4999 5000 PetscCall(PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner)); 5001 mesh->remeshBd = PETSC_FALSE; 5002 5003 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 5004 5005 mesh->depthState = -1; 5006 mesh->celltypeState = -1; 5007 mesh->printTol = 1.0e-10; 5008 5009 PetscCall(DMInitialize_Plex(dm)); 5010 PetscFunctionReturn(PETSC_SUCCESS); 5011 } 5012 5013 /*@ 5014 DMPlexCreate - Creates a `DMPLEX` object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 5015 5016 Collective 5017 5018 Input Parameter: 5019 . comm - The communicator for the `DMPLEX` object 5020 5021 Output Parameter: 5022 . mesh - The `DMPLEX` object 5023 5024 Level: beginner 5025 5026 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMType`, `DMCreate()`, `DMSetType()` 5027 @*/ 5028 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 5029 { 5030 PetscFunctionBegin; 5031 PetscAssertPointer(mesh, 2); 5032 PetscCall(DMCreate(comm, mesh)); 5033 PetscCall(DMSetType(*mesh, DMPLEX)); 5034 PetscFunctionReturn(PETSC_SUCCESS); 5035 } 5036 5037 /*@C 5038 DMPlexBuildFromCellListParallel - Build distributed `DMPLEX` topology from a list of vertices for each cell (common mesh generator output) 5039 5040 Collective; No Fortran Support 5041 5042 Input Parameters: 5043 + dm - The `DM` 5044 . numCells - The number of cells owned by this process 5045 . numVertices - The number of vertices to be owned by this process, or `PETSC_DECIDE` 5046 . NVertices - The global number of vertices, or `PETSC_DETERMINE` 5047 . numCorners - The number of vertices for each cell 5048 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 5049 5050 Output Parameters: 5051 + vertexSF - (Optional) `PetscSF` describing complete vertex ownership 5052 - verticesAdjSaved - (Optional) vertex adjacency array 5053 5054 Level: advanced 5055 5056 Notes: 5057 Two triangles sharing a face 5058 .vb 5059 5060 2 5061 / | \ 5062 / | \ 5063 / | \ 5064 0 0 | 1 3 5065 \ | / 5066 \ | / 5067 \ | / 5068 1 5069 .ve 5070 would have input 5071 .vb 5072 numCells = 2, numVertices = 4 5073 cells = [0 1 2 1 3 2] 5074 .ve 5075 which would result in the `DMPLEX` 5076 .vb 5077 5078 4 5079 / | \ 5080 / | \ 5081 / | \ 5082 2 0 | 1 5 5083 \ | / 5084 \ | / 5085 \ | / 5086 3 5087 .ve 5088 5089 Vertices are implicitly numbered consecutively 0,...,NVertices. 5090 Each rank owns a chunk of numVertices consecutive vertices. 5091 If numVertices is `PETSC_DECIDE`, PETSc will distribute them as evenly as possible using PetscLayout. 5092 If NVertices is `PETSC_DETERMINE` and numVertices is PETSC_DECIDE, NVertices is computed by PETSc as the maximum vertex index in cells + 1. 5093 If only NVertices is `PETSC_DETERMINE`, it is computed as the sum of numVertices over all ranks. 5094 5095 The cell distribution is arbitrary non-overlapping, independent of the vertex distribution. 5096 5097 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildFromCellList()`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildCoordinatesFromCellListParallel()`, 5098 `PetscSF` 5099 @*/ 5100 PetscErrorCode DMPlexBuildFromCellListParallel(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, const PetscInt cells[], PetscSF *vertexSF, PetscInt **verticesAdjSaved) 5101 { 5102 PetscSF sfPoint; 5103 PetscLayout layout; 5104 PetscInt numVerticesAdj, *verticesAdj, *cones, c, p; 5105 5106 PetscFunctionBegin; 5107 PetscValidLogicalCollectiveInt(dm, NVertices, 4); 5108 PetscCall(PetscLogEventBegin(DMPLEX_BuildFromCellList, dm, 0, 0, 0)); 5109 /* Get/check global number of vertices */ 5110 { 5111 PetscInt NVerticesInCells, i; 5112 const PetscInt len = numCells * numCorners; 5113 5114 /* NVerticesInCells = max(cells) + 1 */ 5115 NVerticesInCells = PETSC_MIN_INT; 5116 for (i = 0; i < len; i++) 5117 if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 5118 ++NVerticesInCells; 5119 PetscCall(MPIU_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm))); 5120 5121 if (numVertices == PETSC_DECIDE && NVertices == PETSC_DECIDE) NVertices = NVerticesInCells; 5122 else 5123 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); 5124 } 5125 /* Count locally unique vertices */ 5126 { 5127 PetscHSetI vhash; 5128 PetscInt off = 0; 5129 5130 PetscCall(PetscHSetICreate(&vhash)); 5131 for (c = 0; c < numCells; ++c) { 5132 for (p = 0; p < numCorners; ++p) PetscCall(PetscHSetIAdd(vhash, cells[c * numCorners + p])); 5133 } 5134 PetscCall(PetscHSetIGetSize(vhash, &numVerticesAdj)); 5135 if (!verticesAdjSaved) PetscCall(PetscMalloc1(numVerticesAdj, &verticesAdj)); 5136 else verticesAdj = *verticesAdjSaved; 5137 PetscCall(PetscHSetIGetElems(vhash, &off, verticesAdj)); 5138 PetscCall(PetscHSetIDestroy(&vhash)); 5139 PetscCheck(off == numVerticesAdj, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %" PetscInt_FMT " should be %" PetscInt_FMT, off, numVerticesAdj); 5140 } 5141 PetscCall(PetscSortInt(numVerticesAdj, verticesAdj)); 5142 /* Create cones */ 5143 PetscCall(DMPlexSetChart(dm, 0, numCells + numVerticesAdj)); 5144 for (c = 0; c < numCells; ++c) PetscCall(DMPlexSetConeSize(dm, c, numCorners)); 5145 PetscCall(DMSetUp(dm)); 5146 PetscCall(DMPlexGetCones(dm, &cones)); 5147 for (c = 0; c < numCells; ++c) { 5148 for (p = 0; p < numCorners; ++p) { 5149 const PetscInt gv = cells[c * numCorners + p]; 5150 PetscInt lv; 5151 5152 /* Positions within verticesAdj form 0-based local vertex numbering; 5153 we need to shift it by numCells to get correct DAG points (cells go first) */ 5154 PetscCall(PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv)); 5155 PetscCheck(lv >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %" PetscInt_FMT " in local connectivity", gv); 5156 cones[c * numCorners + p] = lv + numCells; 5157 } 5158 } 5159 /* Build point sf */ 5160 PetscCall(PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &layout)); 5161 PetscCall(PetscLayoutSetSize(layout, NVertices)); 5162 PetscCall(PetscLayoutSetLocalSize(layout, numVertices)); 5163 PetscCall(PetscLayoutSetBlockSize(layout, 1)); 5164 PetscCall(PetscSFCreateByMatchingIndices(layout, numVerticesAdj, verticesAdj, NULL, numCells, numVerticesAdj, verticesAdj, NULL, numCells, vertexSF, &sfPoint)); 5165 PetscCall(PetscLayoutDestroy(&layout)); 5166 if (!verticesAdjSaved) PetscCall(PetscFree(verticesAdj)); 5167 PetscCall(PetscObjectSetName((PetscObject)sfPoint, "point SF")); 5168 if (dm->sf) { 5169 const char *prefix; 5170 5171 PetscCall(PetscObjectGetOptionsPrefix((PetscObject)dm->sf, &prefix)); 5172 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)sfPoint, prefix)); 5173 } 5174 PetscCall(DMSetPointSF(dm, sfPoint)); 5175 PetscCall(PetscSFDestroy(&sfPoint)); 5176 if (vertexSF) PetscCall(PetscObjectSetName((PetscObject)*vertexSF, "Vertex Ownership SF")); 5177 /* Fill in the rest of the topology structure */ 5178 PetscCall(DMPlexSymmetrize(dm)); 5179 PetscCall(DMPlexStratify(dm)); 5180 PetscCall(PetscLogEventEnd(DMPLEX_BuildFromCellList, dm, 0, 0, 0)); 5181 PetscFunctionReturn(PETSC_SUCCESS); 5182 } 5183 5184 /*@ 5185 DMPlexBuildCoordinatesFromCellListParallel - Build `DM` coordinates from a list of coordinates for each owned vertex (common mesh generator output) 5186 5187 Collective; No Fortran Support 5188 5189 Input Parameters: 5190 + dm - The `DM` 5191 . spaceDim - The spatial dimension used for coordinates 5192 . sfVert - `PetscSF` describing complete vertex ownership 5193 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 5194 5195 Level: advanced 5196 5197 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildFromCellListParallel()` 5198 @*/ 5199 PetscErrorCode DMPlexBuildCoordinatesFromCellListParallel(DM dm, PetscInt spaceDim, PetscSF sfVert, const PetscReal vertexCoords[]) 5200 { 5201 PetscSection coordSection; 5202 Vec coordinates; 5203 PetscScalar *coords; 5204 PetscInt numVertices, numVerticesAdj, coordSize, v, vStart, vEnd; 5205 5206 PetscFunctionBegin; 5207 PetscCall(PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0)); 5208 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 5209 PetscCheck(vStart >= 0 && vEnd >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 5210 PetscCall(DMSetCoordinateDim(dm, spaceDim)); 5211 PetscCall(PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL)); 5212 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); 5213 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 5214 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 5215 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spaceDim)); 5216 PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd)); 5217 for (v = vStart; v < vEnd; ++v) { 5218 PetscCall(PetscSectionSetDof(coordSection, v, spaceDim)); 5219 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spaceDim)); 5220 } 5221 PetscCall(PetscSectionSetUp(coordSection)); 5222 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 5223 PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &coordinates)); 5224 PetscCall(VecSetBlockSize(coordinates, spaceDim)); 5225 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 5226 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 5227 PetscCall(VecSetType(coordinates, VECSTANDARD)); 5228 PetscCall(VecGetArray(coordinates, &coords)); 5229 { 5230 MPI_Datatype coordtype; 5231 5232 /* Need a temp buffer for coords if we have complex/single */ 5233 PetscCallMPI(MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype)); 5234 PetscCallMPI(MPI_Type_commit(&coordtype)); 5235 #if defined(PETSC_USE_COMPLEX) 5236 { 5237 PetscScalar *svertexCoords; 5238 PetscInt i; 5239 PetscCall(PetscMalloc1(numVertices * spaceDim, &svertexCoords)); 5240 for (i = 0; i < numVertices * spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 5241 PetscCall(PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords, MPI_REPLACE)); 5242 PetscCall(PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords, MPI_REPLACE)); 5243 PetscCall(PetscFree(svertexCoords)); 5244 } 5245 #else 5246 PetscCall(PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords, MPI_REPLACE)); 5247 PetscCall(PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords, MPI_REPLACE)); 5248 #endif 5249 PetscCallMPI(MPI_Type_free(&coordtype)); 5250 } 5251 PetscCall(VecRestoreArray(coordinates, &coords)); 5252 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 5253 PetscCall(VecDestroy(&coordinates)); 5254 PetscCall(PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0)); 5255 PetscFunctionReturn(PETSC_SUCCESS); 5256 } 5257 5258 /*@ 5259 DMPlexCreateFromCellListParallelPetsc - Create distributed `DMPLEX` from a list of vertices for each cell (common mesh generator output) 5260 5261 Collective 5262 5263 Input Parameters: 5264 + comm - The communicator 5265 . dim - The topological dimension of the mesh 5266 . numCells - The number of cells owned by this process 5267 . numVertices - The number of vertices owned by this process, or `PETSC_DECIDE` 5268 . NVertices - The global number of vertices, or `PETSC_DECIDE` 5269 . numCorners - The number of vertices for each cell 5270 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 5271 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 5272 . spaceDim - The spatial dimension used for coordinates 5273 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 5274 5275 Output Parameters: 5276 + dm - The `DM` 5277 . vertexSF - (Optional) `PetscSF` describing complete vertex ownership 5278 - verticesAdj - (Optional) vertex adjacency array 5279 5280 Level: intermediate 5281 5282 Notes: 5283 This function is just a convenient sequence of `DMCreate()`, `DMSetType()`, `DMSetDimension()`, 5284 `DMPlexBuildFromCellListParallel()`, `DMPlexInterpolate()`, `DMPlexBuildCoordinatesFromCellListParallel()` 5285 5286 See `DMPlexBuildFromCellListParallel()` for an example and details about the topology-related parameters. 5287 5288 See `DMPlexBuildCoordinatesFromCellListParallel()` for details about the geometry-related parameters. 5289 5290 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromCellListPetsc()`, `DMPlexBuildFromCellListParallel()`, `DMPlexBuildCoordinatesFromCellListParallel()`, `DMPlexCreateFromDAG()`, `DMPlexCreate()` 5291 @*/ 5292 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) 5293 { 5294 PetscSF sfVert; 5295 5296 PetscFunctionBegin; 5297 PetscCall(DMCreate(comm, dm)); 5298 PetscCall(DMSetType(*dm, DMPLEX)); 5299 PetscValidLogicalCollectiveInt(*dm, dim, 2); 5300 PetscValidLogicalCollectiveInt(*dm, spaceDim, 9); 5301 PetscCall(DMSetDimension(*dm, dim)); 5302 PetscCall(DMPlexBuildFromCellListParallel(*dm, numCells, numVertices, NVertices, numCorners, cells, &sfVert, verticesAdj)); 5303 if (interpolate) { 5304 DM idm; 5305 5306 PetscCall(DMPlexInterpolate(*dm, &idm)); 5307 PetscCall(DMDestroy(dm)); 5308 *dm = idm; 5309 } 5310 PetscCall(DMPlexBuildCoordinatesFromCellListParallel(*dm, spaceDim, sfVert, vertexCoords)); 5311 if (vertexSF) *vertexSF = sfVert; 5312 else PetscCall(PetscSFDestroy(&sfVert)); 5313 PetscFunctionReturn(PETSC_SUCCESS); 5314 } 5315 5316 /*@ 5317 DMPlexBuildFromCellList - Build `DMPLEX` topology from a list of vertices for each cell (common mesh generator output) 5318 5319 Collective; No Fortran Support 5320 5321 Input Parameters: 5322 + dm - The `DM` 5323 . numCells - The number of cells owned by this process 5324 . numVertices - The number of vertices owned by this process, or `PETSC_DETERMINE` 5325 . numCorners - The number of vertices for each cell 5326 - cells - An array of `numCells` x `numCorners` numbers, the global vertex numbers for each cell 5327 5328 Level: advanced 5329 5330 Notes: 5331 Two triangles sharing a face 5332 .vb 5333 5334 2 5335 / | \ 5336 / | \ 5337 / | \ 5338 0 0 | 1 3 5339 \ | / 5340 \ | / 5341 \ | / 5342 1 5343 .ve 5344 would have input 5345 .vb 5346 numCells = 2, numVertices = 4 5347 cells = [0 1 2 1 3 2] 5348 .ve 5349 which would result in the `DMPLEX` 5350 .vb 5351 5352 4 5353 / | \ 5354 / | \ 5355 / | \ 5356 2 0 | 1 5 5357 \ | / 5358 \ | / 5359 \ | / 5360 3 5361 .ve 5362 5363 If numVertices is `PETSC_DETERMINE`, it is computed by PETSc as the maximum vertex index in cells + 1. 5364 5365 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildFromCellListParallel()`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromCellListPetsc()` 5366 @*/ 5367 PetscErrorCode DMPlexBuildFromCellList(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[]) 5368 { 5369 PetscInt *cones, c, p, dim; 5370 5371 PetscFunctionBegin; 5372 PetscCall(PetscLogEventBegin(DMPLEX_BuildFromCellList, dm, 0, 0, 0)); 5373 PetscCall(DMGetDimension(dm, &dim)); 5374 /* Get/check global number of vertices */ 5375 { 5376 PetscInt NVerticesInCells, i; 5377 const PetscInt len = numCells * numCorners; 5378 5379 /* NVerticesInCells = max(cells) + 1 */ 5380 NVerticesInCells = PETSC_MIN_INT; 5381 for (i = 0; i < len; i++) 5382 if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 5383 ++NVerticesInCells; 5384 5385 if (numVertices == PETSC_DECIDE) numVertices = NVerticesInCells; 5386 else 5387 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); 5388 } 5389 PetscCall(DMPlexSetChart(dm, 0, numCells + numVertices)); 5390 for (c = 0; c < numCells; ++c) PetscCall(DMPlexSetConeSize(dm, c, numCorners)); 5391 PetscCall(DMSetUp(dm)); 5392 PetscCall(DMPlexGetCones(dm, &cones)); 5393 for (c = 0; c < numCells; ++c) { 5394 for (p = 0; p < numCorners; ++p) cones[c * numCorners + p] = cells[c * numCorners + p] + numCells; 5395 } 5396 PetscCall(DMPlexSymmetrize(dm)); 5397 PetscCall(DMPlexStratify(dm)); 5398 PetscCall(PetscLogEventEnd(DMPLEX_BuildFromCellList, dm, 0, 0, 0)); 5399 PetscFunctionReturn(PETSC_SUCCESS); 5400 } 5401 5402 /*@ 5403 DMPlexBuildCoordinatesFromCellList - Build `DM` coordinates from a list of coordinates for each owned vertex (common mesh generator output) 5404 5405 Collective 5406 5407 Input Parameters: 5408 + dm - The `DM` 5409 . spaceDim - The spatial dimension used for coordinates 5410 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 5411 5412 Level: advanced 5413 5414 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexBuildCoordinatesFromCellListParallel()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexBuildFromCellList()` 5415 @*/ 5416 PetscErrorCode DMPlexBuildCoordinatesFromCellList(DM dm, PetscInt spaceDim, const PetscReal vertexCoords[]) 5417 { 5418 PetscSection coordSection; 5419 Vec coordinates; 5420 DM cdm; 5421 PetscScalar *coords; 5422 PetscInt v, vStart, vEnd, d; 5423 5424 PetscFunctionBegin; 5425 PetscCall(PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0)); 5426 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 5427 PetscCheck(vStart >= 0 && vEnd >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 5428 PetscCall(DMSetCoordinateDim(dm, spaceDim)); 5429 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 5430 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 5431 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spaceDim)); 5432 PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd)); 5433 for (v = vStart; v < vEnd; ++v) { 5434 PetscCall(PetscSectionSetDof(coordSection, v, spaceDim)); 5435 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spaceDim)); 5436 } 5437 PetscCall(PetscSectionSetUp(coordSection)); 5438 5439 PetscCall(DMGetCoordinateDM(dm, &cdm)); 5440 PetscCall(DMCreateLocalVector(cdm, &coordinates)); 5441 PetscCall(VecSetBlockSize(coordinates, spaceDim)); 5442 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 5443 PetscCall(VecGetArrayWrite(coordinates, &coords)); 5444 for (v = 0; v < vEnd - vStart; ++v) { 5445 for (d = 0; d < spaceDim; ++d) coords[v * spaceDim + d] = vertexCoords[v * spaceDim + d]; 5446 } 5447 PetscCall(VecRestoreArrayWrite(coordinates, &coords)); 5448 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 5449 PetscCall(VecDestroy(&coordinates)); 5450 PetscCall(PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList, dm, 0, 0, 0)); 5451 PetscFunctionReturn(PETSC_SUCCESS); 5452 } 5453 5454 /*@ 5455 DMPlexCreateFromCellListPetsc - Create `DMPLEX` from a list of vertices for each cell (common mesh generator output), but only process 0 takes in the input 5456 5457 Collective 5458 5459 Input Parameters: 5460 + comm - The communicator 5461 . dim - The topological dimension of the mesh 5462 . numCells - The number of cells, only on process 0 5463 . numVertices - The number of vertices owned by this process, or `PETSC_DECIDE`, only on process 0 5464 . numCorners - The number of vertices for each cell, only on process 0 5465 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 5466 . cells - An array of numCells*numCorners numbers, the vertices for each cell, only on process 0 5467 . spaceDim - The spatial dimension used for coordinates 5468 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex, only on process 0 5469 5470 Output Parameter: 5471 . dm - The `DM`, which only has points on process 0 5472 5473 Level: intermediate 5474 5475 Notes: 5476 This function is just a convenient sequence of `DMCreate()`, `DMSetType()`, `DMSetDimension()`, `DMPlexBuildFromCellList()`, 5477 `DMPlexInterpolate()`, `DMPlexBuildCoordinatesFromCellList()` 5478 5479 See `DMPlexBuildFromCellList()` for an example and details about the topology-related parameters. 5480 See `DMPlexBuildCoordinatesFromCellList()` for details about the geometry-related parameters. 5481 See `DMPlexCreateFromCellListParallelPetsc()` for parallel input 5482 5483 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromCellListParallelPetsc()`, `DMPlexBuildFromCellList()`, `DMPlexBuildCoordinatesFromCellList()`, `DMPlexCreateFromDAG()`, `DMPlexCreate()` 5484 @*/ 5485 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) 5486 { 5487 PetscMPIInt rank; 5488 5489 PetscFunctionBegin; 5490 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."); 5491 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 5492 PetscCall(DMCreate(comm, dm)); 5493 PetscCall(DMSetType(*dm, DMPLEX)); 5494 PetscCall(DMSetDimension(*dm, dim)); 5495 if (rank == 0) PetscCall(DMPlexBuildFromCellList(*dm, numCells, numVertices, numCorners, cells)); 5496 else PetscCall(DMPlexBuildFromCellList(*dm, 0, 0, 0, NULL)); 5497 if (interpolate) { 5498 DM idm; 5499 5500 PetscCall(DMPlexInterpolate(*dm, &idm)); 5501 PetscCall(DMDestroy(dm)); 5502 *dm = idm; 5503 } 5504 if (rank == 0) PetscCall(DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, vertexCoords)); 5505 else PetscCall(DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, NULL)); 5506 PetscFunctionReturn(PETSC_SUCCESS); 5507 } 5508 5509 /*@ 5510 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a `DM` 5511 5512 Input Parameters: 5513 + dm - The empty `DM` object, usually from `DMCreate()` and `DMSetDimension()` 5514 . depth - The depth of the DAG 5515 . numPoints - Array of size depth + 1 containing the number of points at each `depth` 5516 . coneSize - The cone size of each point 5517 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 5518 . coneOrientations - The orientation of each cone point 5519 - vertexCoords - An array of `numPoints`[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via `DMSetCoordinateDim()` 5520 5521 Output Parameter: 5522 . dm - The `DM` 5523 5524 Level: advanced 5525 5526 Note: 5527 Two triangles sharing a face would have input 5528 .vb 5529 depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 5530 cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 5531 vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 5532 .ve 5533 which would result in the DMPlex 5534 .vb 5535 4 5536 / | \ 5537 / | \ 5538 / | \ 5539 2 0 | 1 5 5540 \ | / 5541 \ | / 5542 \ | / 5543 3 5544 .ve 5545 Notice that all points are numbered consecutively, unlike `DMPlexCreateFromCellListPetsc()` 5546 5547 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()` 5548 @*/ 5549 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 5550 { 5551 Vec coordinates; 5552 PetscSection coordSection; 5553 PetscScalar *coords; 5554 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 5555 5556 PetscFunctionBegin; 5557 PetscCall(DMGetDimension(dm, &dim)); 5558 PetscCall(DMGetCoordinateDim(dm, &dimEmbed)); 5559 PetscCheck(dimEmbed >= dim, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Embedding dimension %" PetscInt_FMT " cannot be less than intrinsic dimension %" PetscInt_FMT, dimEmbed, dim); 5560 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 5561 PetscCall(DMPlexSetChart(dm, pStart, pEnd)); 5562 for (p = pStart; p < pEnd; ++p) { 5563 PetscCall(DMPlexSetConeSize(dm, p, coneSize[p - pStart])); 5564 if (firstVertex < 0 && !coneSize[p - pStart]) firstVertex = p - pStart; 5565 } 5566 PetscCheck(firstVertex >= 0 || !numPoints[0], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Expected %" PetscInt_FMT " vertices but could not find any", numPoints[0]); 5567 PetscCall(DMSetUp(dm)); /* Allocate space for cones */ 5568 for (p = pStart, off = 0; p < pEnd; off += coneSize[p - pStart], ++p) { 5569 PetscCall(DMPlexSetCone(dm, p, &cones[off])); 5570 PetscCall(DMPlexSetConeOrientation(dm, p, &coneOrientations[off])); 5571 } 5572 PetscCall(DMPlexSymmetrize(dm)); 5573 PetscCall(DMPlexStratify(dm)); 5574 /* Build coordinates */ 5575 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 5576 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 5577 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dimEmbed)); 5578 PetscCall(PetscSectionSetChart(coordSection, firstVertex, firstVertex + numPoints[0])); 5579 for (v = firstVertex; v < firstVertex + numPoints[0]; ++v) { 5580 PetscCall(PetscSectionSetDof(coordSection, v, dimEmbed)); 5581 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed)); 5582 } 5583 PetscCall(PetscSectionSetUp(coordSection)); 5584 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 5585 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 5586 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 5587 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 5588 PetscCall(VecSetBlockSize(coordinates, dimEmbed)); 5589 PetscCall(VecSetType(coordinates, VECSTANDARD)); 5590 if (vertexCoords) { 5591 PetscCall(VecGetArray(coordinates, &coords)); 5592 for (v = 0; v < numPoints[0]; ++v) { 5593 PetscInt off; 5594 5595 PetscCall(PetscSectionGetOffset(coordSection, v + firstVertex, &off)); 5596 for (d = 0; d < dimEmbed; ++d) coords[off + d] = vertexCoords[v * dimEmbed + d]; 5597 } 5598 } 5599 PetscCall(VecRestoreArray(coordinates, &coords)); 5600 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 5601 PetscCall(VecDestroy(&coordinates)); 5602 PetscFunctionReturn(PETSC_SUCCESS); 5603 } 5604 5605 /* 5606 DMPlexCreateCellVertexFromFile - Create a `DMPLEX` mesh from a simple cell-vertex file. 5607 5608 Collective 5609 5610 + comm - The MPI communicator 5611 . filename - Name of the .dat file 5612 - interpolate - Create faces and edges in the mesh 5613 5614 Output Parameter: 5615 . dm - The `DM` object representing the mesh 5616 5617 Level: beginner 5618 5619 Note: 5620 The format is the simplest possible: 5621 .vb 5622 dim Ne Nv Nc Nl 5623 v_1 v_2 ... v_Nc 5624 ... 5625 x y z marker_1 ... marker_Nl 5626 .ve 5627 5628 Developer Note: 5629 Should use a `PetscViewer` not a filename 5630 5631 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromFile()`, `DMPlexCreateGmsh()`, `DMPlexCreate()` 5632 */ 5633 static PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 5634 { 5635 DMLabel marker; 5636 PetscViewer viewer; 5637 Vec coordinates; 5638 PetscSection coordSection; 5639 PetscScalar *coords; 5640 char line[PETSC_MAX_PATH_LEN]; 5641 PetscInt cdim, coordSize, v, c, d; 5642 PetscMPIInt rank; 5643 int snum, dim, Nv, Nc, Ncn, Nl; 5644 5645 PetscFunctionBegin; 5646 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 5647 PetscCall(PetscViewerCreate(comm, &viewer)); 5648 PetscCall(PetscViewerSetType(viewer, PETSCVIEWERASCII)); 5649 PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ)); 5650 PetscCall(PetscViewerFileSetName(viewer, filename)); 5651 if (rank == 0) { 5652 PetscCall(PetscViewerRead(viewer, line, 5, NULL, PETSC_STRING)); 5653 snum = sscanf(line, "%d %d %d %d %d", &dim, &Nc, &Nv, &Ncn, &Nl); 5654 PetscCheck(snum == 5, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 5655 } else { 5656 Nc = Nv = Ncn = Nl = 0; 5657 } 5658 PetscCallMPI(MPI_Bcast(&dim, 1, MPI_INT, 0, comm)); 5659 cdim = (PetscInt)dim; 5660 PetscCall(DMCreate(comm, dm)); 5661 PetscCall(DMSetType(*dm, DMPLEX)); 5662 PetscCall(DMPlexSetChart(*dm, 0, Nc + Nv)); 5663 PetscCall(DMSetDimension(*dm, (PetscInt)dim)); 5664 PetscCall(DMSetCoordinateDim(*dm, cdim)); 5665 /* Read topology */ 5666 if (rank == 0) { 5667 char format[PETSC_MAX_PATH_LEN]; 5668 PetscInt cone[8]; 5669 int vbuf[8], v; 5670 5671 for (c = 0; c < Ncn; ++c) { 5672 format[c * 3 + 0] = '%'; 5673 format[c * 3 + 1] = 'd'; 5674 format[c * 3 + 2] = ' '; 5675 } 5676 format[Ncn * 3 - 1] = '\0'; 5677 for (c = 0; c < Nc; ++c) PetscCall(DMPlexSetConeSize(*dm, c, Ncn)); 5678 PetscCall(DMSetUp(*dm)); 5679 for (c = 0; c < Nc; ++c) { 5680 PetscCall(PetscViewerRead(viewer, line, Ncn, NULL, PETSC_STRING)); 5681 switch (Ncn) { 5682 case 2: 5683 snum = sscanf(line, format, &vbuf[0], &vbuf[1]); 5684 break; 5685 case 3: 5686 snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2]); 5687 break; 5688 case 4: 5689 snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3]); 5690 break; 5691 case 6: 5692 snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5]); 5693 break; 5694 case 8: 5695 snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5], &vbuf[6], &vbuf[7]); 5696 break; 5697 default: 5698 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "No cell shape with %d vertices", Ncn); 5699 } 5700 PetscCheck(snum == Ncn, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 5701 for (v = 0; v < Ncn; ++v) cone[v] = vbuf[v] + Nc; 5702 /* Hexahedra are inverted */ 5703 if (Ncn == 8) { 5704 PetscInt tmp = cone[1]; 5705 cone[1] = cone[3]; 5706 cone[3] = tmp; 5707 } 5708 PetscCall(DMPlexSetCone(*dm, c, cone)); 5709 } 5710 } 5711 PetscCall(DMPlexSymmetrize(*dm)); 5712 PetscCall(DMPlexStratify(*dm)); 5713 /* Read coordinates */ 5714 PetscCall(DMGetCoordinateSection(*dm, &coordSection)); 5715 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 5716 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, cdim)); 5717 PetscCall(PetscSectionSetChart(coordSection, Nc, Nc + Nv)); 5718 for (v = Nc; v < Nc + Nv; ++v) { 5719 PetscCall(PetscSectionSetDof(coordSection, v, cdim)); 5720 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, cdim)); 5721 } 5722 PetscCall(PetscSectionSetUp(coordSection)); 5723 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 5724 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 5725 PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); 5726 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 5727 PetscCall(VecSetBlockSize(coordinates, cdim)); 5728 PetscCall(VecSetType(coordinates, VECSTANDARD)); 5729 PetscCall(VecGetArray(coordinates, &coords)); 5730 if (rank == 0) { 5731 char format[PETSC_MAX_PATH_LEN]; 5732 double x[3]; 5733 int l, val[3]; 5734 5735 if (Nl) { 5736 for (l = 0; l < Nl; ++l) { 5737 format[l * 3 + 0] = '%'; 5738 format[l * 3 + 1] = 'd'; 5739 format[l * 3 + 2] = ' '; 5740 } 5741 format[Nl * 3 - 1] = '\0'; 5742 PetscCall(DMCreateLabel(*dm, "marker")); 5743 PetscCall(DMGetLabel(*dm, "marker", &marker)); 5744 } 5745 for (v = 0; v < Nv; ++v) { 5746 PetscCall(PetscViewerRead(viewer, line, 3 + Nl, NULL, PETSC_STRING)); 5747 snum = sscanf(line, "%lg %lg %lg", &x[0], &x[1], &x[2]); 5748 PetscCheck(snum == 3, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 5749 switch (Nl) { 5750 case 0: 5751 snum = 0; 5752 break; 5753 case 1: 5754 snum = sscanf(line, format, &val[0]); 5755 break; 5756 case 2: 5757 snum = sscanf(line, format, &val[0], &val[1]); 5758 break; 5759 case 3: 5760 snum = sscanf(line, format, &val[0], &val[1], &val[2]); 5761 break; 5762 default: 5763 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Request support for %d labels", Nl); 5764 } 5765 PetscCheck(snum == Nl, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 5766 for (d = 0; d < cdim; ++d) coords[v * cdim + d] = x[d]; 5767 for (l = 0; l < Nl; ++l) PetscCall(DMLabelSetValue(marker, v + Nc, val[l])); 5768 } 5769 } 5770 PetscCall(VecRestoreArray(coordinates, &coords)); 5771 PetscCall(DMSetCoordinatesLocal(*dm, coordinates)); 5772 PetscCall(VecDestroy(&coordinates)); 5773 PetscCall(PetscViewerDestroy(&viewer)); 5774 if (interpolate) { 5775 DM idm; 5776 DMLabel bdlabel; 5777 5778 PetscCall(DMPlexInterpolate(*dm, &idm)); 5779 PetscCall(DMDestroy(dm)); 5780 *dm = idm; 5781 5782 if (!Nl) { 5783 PetscCall(DMCreateLabel(*dm, "marker")); 5784 PetscCall(DMGetLabel(*dm, "marker", &bdlabel)); 5785 PetscCall(DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel)); 5786 PetscCall(DMPlexLabelComplete(*dm, bdlabel)); 5787 } 5788 } 5789 PetscFunctionReturn(PETSC_SUCCESS); 5790 } 5791 5792 /*@ 5793 DMPlexCreateFromFile - This takes a filename and produces a `DM` 5794 5795 Collective 5796 5797 Input Parameters: 5798 + comm - The communicator 5799 . filename - A file name 5800 . plexname - The object name of the resulting `DM`, also used for intra-datafile lookup by some formats 5801 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 5802 5803 Output Parameter: 5804 . dm - The `DM` 5805 5806 Options Database Key: 5807 . -dm_plex_create_from_hdf5_xdmf - use the `PETSC_VIEWER_HDF5_XDMF` format for reading HDF5 5808 5809 Use `-dm_plex_create_ prefix` to pass options to the internal `PetscViewer`, e.g. 5810 $ -dm_plex_create_viewer_hdf5_collective 5811 5812 Level: beginner 5813 5814 Notes: 5815 Using `PETSCVIEWERHDF5` type with `PETSC_VIEWER_HDF5_PETSC` format, one can save multiple `DMPLEX` 5816 meshes in a single HDF5 file. This in turn requires one to name the `DMPLEX` object with `PetscObjectSetName()` 5817 before saving it with `DMView()` and before loading it with `DMLoad()` for identification of the mesh object. 5818 The input parameter name is thus used to name the `DMPLEX` object when `DMPlexCreateFromFile()` internally 5819 calls `DMLoad()`. Currently, name is ignored for other viewer types and/or formats. 5820 5821 .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromDAG()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()`, `PetscObjectSetName()`, `DMView()`, `DMLoad()` 5822 @*/ 5823 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], const char plexname[], PetscBool interpolate, DM *dm) 5824 { 5825 const char extGmsh[] = ".msh"; 5826 const char extGmsh2[] = ".msh2"; 5827 const char extGmsh4[] = ".msh4"; 5828 const char extCGNS[] = ".cgns"; 5829 const char extExodus[] = ".exo"; 5830 const char extExodus_e[] = ".e"; 5831 const char extGenesis[] = ".gen"; 5832 const char extFluent[] = ".cas"; 5833 const char extHDF5[] = ".h5"; 5834 const char extXDMFHDF5[] = ".xdmf.h5"; 5835 const char extPLY[] = ".ply"; 5836 const char extEGADSLite[] = ".egadslite"; 5837 const char extEGADS[] = ".egads"; 5838 const char extIGES[] = ".igs"; 5839 const char extSTEP[] = ".stp"; 5840 const char extCV[] = ".dat"; 5841 size_t len; 5842 PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isPLY, isEGADSLite, isEGADS, isIGES, isSTEP, isCV, isXDMFHDF5; 5843 PetscMPIInt rank; 5844 5845 PetscFunctionBegin; 5846 PetscAssertPointer(filename, 2); 5847 if (plexname) PetscAssertPointer(plexname, 3); 5848 PetscAssertPointer(dm, 5); 5849 PetscCall(DMInitializePackage()); 5850 PetscCall(PetscLogEventBegin(DMPLEX_CreateFromFile, 0, 0, 0, 0)); 5851 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 5852 PetscCall(PetscStrlen(filename, &len)); 5853 PetscCheck(len, comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 5854 5855 #define CheckExtension(extension__, is_extension__) \ 5856 do { \ 5857 PetscAssert(sizeof(extension__), comm, PETSC_ERR_PLIB, "Zero-size extension: %s", extension__); \ 5858 /* don't count the null-terminator at the end */ \ 5859 const size_t ext_len = sizeof(extension__) - 1; \ 5860 if (len < ext_len) { \ 5861 is_extension__ = PETSC_FALSE; \ 5862 } else { \ 5863 PetscCall(PetscStrncmp(filename + len - ext_len, extension__, ext_len, &is_extension__)); \ 5864 } \ 5865 } while (0) 5866 5867 CheckExtension(extGmsh, isGmsh); 5868 CheckExtension(extGmsh2, isGmsh2); 5869 CheckExtension(extGmsh4, isGmsh4); 5870 CheckExtension(extCGNS, isCGNS); 5871 CheckExtension(extExodus, isExodus); 5872 if (!isExodus) CheckExtension(extExodus_e, isExodus); 5873 CheckExtension(extGenesis, isGenesis); 5874 CheckExtension(extFluent, isFluent); 5875 CheckExtension(extHDF5, isHDF5); 5876 CheckExtension(extPLY, isPLY); 5877 CheckExtension(extEGADSLite, isEGADSLite); 5878 CheckExtension(extEGADS, isEGADS); 5879 CheckExtension(extIGES, isIGES); 5880 CheckExtension(extSTEP, isSTEP); 5881 CheckExtension(extCV, isCV); 5882 CheckExtension(extXDMFHDF5, isXDMFHDF5); 5883 5884 #undef CheckExtension 5885 5886 if (isGmsh || isGmsh2 || isGmsh4) { 5887 PetscCall(DMPlexCreateGmshFromFile(comm, filename, interpolate, dm)); 5888 } else if (isCGNS) { 5889 PetscCall(DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm)); 5890 } else if (isExodus || isGenesis) { 5891 PetscCall(DMPlexCreateExodusFromFile(comm, filename, interpolate, dm)); 5892 } else if (isFluent) { 5893 PetscCall(DMPlexCreateFluentFromFile(comm, filename, interpolate, dm)); 5894 } else if (isHDF5) { 5895 PetscViewer viewer; 5896 5897 /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */ 5898 PetscCall(PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &isXDMFHDF5, NULL)); 5899 PetscCall(PetscViewerCreate(comm, &viewer)); 5900 PetscCall(PetscViewerSetType(viewer, PETSCVIEWERHDF5)); 5901 PetscCall(PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_")); 5902 PetscCall(PetscViewerSetFromOptions(viewer)); 5903 PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ)); 5904 PetscCall(PetscViewerFileSetName(viewer, filename)); 5905 5906 PetscCall(DMCreate(comm, dm)); 5907 PetscCall(PetscObjectSetName((PetscObject)*dm, plexname)); 5908 PetscCall(DMSetType(*dm, DMPLEX)); 5909 if (isXDMFHDF5) PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF)); 5910 PetscCall(DMLoad(*dm, viewer)); 5911 if (isXDMFHDF5) PetscCall(PetscViewerPopFormat(viewer)); 5912 PetscCall(PetscViewerDestroy(&viewer)); 5913 5914 if (interpolate) { 5915 DM idm; 5916 5917 PetscCall(DMPlexInterpolate(*dm, &idm)); 5918 PetscCall(DMDestroy(dm)); 5919 *dm = idm; 5920 } 5921 } else if (isPLY) { 5922 PetscCall(DMPlexCreatePLYFromFile(comm, filename, interpolate, dm)); 5923 } else if (isEGADSLite || isEGADS || isIGES || isSTEP) { 5924 if (isEGADSLite) PetscCall(DMPlexCreateEGADSLiteFromFile(comm, filename, dm)); 5925 else PetscCall(DMPlexCreateEGADSFromFile(comm, filename, dm)); 5926 if (!interpolate) { 5927 DM udm; 5928 5929 PetscCall(DMPlexUninterpolate(*dm, &udm)); 5930 PetscCall(DMDestroy(dm)); 5931 *dm = udm; 5932 } 5933 } else if (isCV) { 5934 PetscCall(DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm)); 5935 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 5936 PetscCall(PetscStrlen(plexname, &len)); 5937 if (len) PetscCall(PetscObjectSetName((PetscObject)*dm, plexname)); 5938 PetscCall(PetscLogEventEnd(DMPLEX_CreateFromFile, 0, 0, 0, 0)); 5939 PetscFunctionReturn(PETSC_SUCCESS); 5940 } 5941 5942 /*@ 5943 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. 5944 5945 Input Parameters: 5946 + tr - The `DMPlexTransform` 5947 - prefix - An options prefix, or NULL 5948 5949 Output Parameter: 5950 . dm - The `DM` 5951 5952 Level: beginner 5953 5954 Notes: 5955 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. 5956 5957 .seealso: `DMPlexCreateFromFile`, `DMPlexCreateFromDAG()`, `DMPlexCreateFromCellListPetsc()`, `DMPlexCreate()` 5958 @*/ 5959 PetscErrorCode DMPlexCreateEphemeral(DMPlexTransform tr, const char prefix[], DM *dm) 5960 { 5961 DM bdm, bcdm, cdm; 5962 Vec coordinates, coordinatesNew; 5963 PetscSection cs; 5964 PetscInt cdim, Nl; 5965 5966 PetscFunctionBegin; 5967 PetscCall(DMCreate(PetscObjectComm((PetscObject)tr), dm)); 5968 PetscCall(DMSetType(*dm, DMPLEX)); 5969 ((DM_Plex *)(*dm)->data)->interpolated = DMPLEX_INTERPOLATED_FULL; 5970 // Handle coordinates 5971 PetscCall(DMPlexTransformGetDM(tr, &bdm)); 5972 PetscCall(DMPlexTransformSetDimensions(tr, bdm, *dm)); 5973 PetscCall(DMGetCoordinateDim(*dm, &cdim)); 5974 PetscCall(DMGetCoordinateDM(bdm, &bcdm)); 5975 PetscCall(DMGetCoordinateDM(*dm, &cdm)); 5976 PetscCall(DMCopyDisc(bcdm, cdm)); 5977 PetscCall(DMGetLocalSection(cdm, &cs)); 5978 PetscCall(PetscSectionSetNumFields(cs, 1)); 5979 PetscCall(PetscSectionSetFieldComponents(cs, 0, cdim)); 5980 PetscCall(DMGetCoordinatesLocal(bdm, &coordinates)); 5981 PetscCall(VecDuplicate(coordinates, &coordinatesNew)); 5982 PetscCall(VecCopy(coordinates, coordinatesNew)); 5983 PetscCall(DMSetCoordinatesLocal(*dm, coordinatesNew)); 5984 PetscCall(VecDestroy(&coordinatesNew)); 5985 5986 PetscCall(PetscObjectReference((PetscObject)tr)); 5987 PetscCall(DMPlexTransformDestroy(&((DM_Plex *)(*dm)->data)->tr)); 5988 ((DM_Plex *)(*dm)->data)->tr = tr; 5989 PetscCall(DMPlexDistributeSetDefault(*dm, PETSC_FALSE)); 5990 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)*dm, prefix)); 5991 PetscCall(DMSetFromOptions(*dm)); 5992 5993 PetscCall(DMGetNumLabels(bdm, &Nl)); 5994 for (PetscInt l = 0; l < Nl; ++l) { 5995 DMLabel label, labelNew; 5996 const char *lname; 5997 PetscBool isDepth, isCellType; 5998 5999 PetscCall(DMGetLabelName(bdm, l, &lname)); 6000 PetscCall(PetscStrcmp(lname, "depth", &isDepth)); 6001 if (isDepth) continue; 6002 PetscCall(PetscStrcmp(lname, "celltype", &isCellType)); 6003 if (isCellType) continue; 6004 PetscCall(DMCreateLabel(*dm, lname)); 6005 PetscCall(DMGetLabel(bdm, lname, &label)); 6006 PetscCall(DMGetLabel(*dm, lname, &labelNew)); 6007 PetscCall(DMLabelSetType(labelNew, DMLABELEPHEMERAL)); 6008 PetscCall(DMLabelEphemeralSetLabel(labelNew, label)); 6009 PetscCall(DMLabelEphemeralSetTransform(labelNew, tr)); 6010 PetscCall(DMLabelSetUp(labelNew)); 6011 } 6012 PetscFunctionReturn(PETSC_SUCCESS); 6013 } 6014