1 #define PETSCDM_DLL 2 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 #include <petsc/private/hashseti.h> /*I "petscdmplex.h" I*/ 4 #include <petscsf.h> 5 #include <petsc/private/kernels/blockmatmult.h> 6 #include <petsc/private/kernels/blockinvert.h> 7 8 PetscLogEvent DMPLEX_CreateFromFile, DMPLEX_BuildFromCellList, DMPLEX_BuildCoordinatesFromCellList; 9 10 /* External function declarations here */ 11 static PetscErrorCode DMInitialize_Plex(DM dm); 12 13 /* This copies internal things in the Plex structure that we generally want when making a new, related Plex */ 14 PetscErrorCode DMPlexCopy_Internal(DM dmin, PetscBool copyPeriodicity, DM dmout) 15 { 16 const DMBoundaryType *bd; 17 const PetscReal *maxCell, *L; 18 PetscBool isper, dist; 19 PetscErrorCode ierr; 20 21 PetscFunctionBegin; 22 if (copyPeriodicity) { 23 ierr = DMGetPeriodicity(dmin, &isper, &maxCell, &L, &bd);CHKERRQ(ierr); 24 ierr = DMSetPeriodicity(dmout, isper, maxCell, L, bd);CHKERRQ(ierr); 25 } 26 ierr = DMPlexDistributeGetDefault(dmin, &dist);CHKERRQ(ierr); 27 ierr = DMPlexDistributeSetDefault(dmout, dist);CHKERRQ(ierr); 28 ((DM_Plex *) dmout->data)->useHashLocation = ((DM_Plex *) dmin->data)->useHashLocation; 29 PetscFunctionReturn(0); 30 } 31 32 /* Replace dm with the contents of ndm, and then destroy ndm 33 - Share the DM_Plex structure 34 - Share the coordinates 35 - Share the SF 36 */ 37 static PetscErrorCode DMPlexReplace_Static(DM dm, DM *ndm) 38 { 39 PetscSF sf; 40 DM dmNew = *ndm, coordDM, coarseDM; 41 Vec coords; 42 PetscBool isper; 43 const PetscReal *maxCell, *L; 44 const DMBoundaryType *bd; 45 PetscInt dim, cdim; 46 PetscErrorCode ierr; 47 48 PetscFunctionBegin; 49 if (dm == dmNew) { 50 ierr = DMDestroy(ndm);CHKERRQ(ierr); 51 PetscFunctionReturn(0); 52 } 53 dm->setupcalled = dmNew->setupcalled; 54 ierr = DMGetDimension(dmNew, &dim);CHKERRQ(ierr); 55 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 56 ierr = DMGetCoordinateDim(dmNew, &cdim);CHKERRQ(ierr); 57 ierr = DMSetCoordinateDim(dm, cdim);CHKERRQ(ierr); 58 ierr = DMGetPointSF(dmNew, &sf);CHKERRQ(ierr); 59 ierr = DMSetPointSF(dm, sf);CHKERRQ(ierr); 60 ierr = DMGetCoordinateDM(dmNew, &coordDM);CHKERRQ(ierr); 61 ierr = DMGetCoordinatesLocal(dmNew, &coords);CHKERRQ(ierr); 62 ierr = DMSetCoordinateDM(dm, coordDM);CHKERRQ(ierr); 63 ierr = DMSetCoordinatesLocal(dm, coords);CHKERRQ(ierr); 64 /* Do not want to create the coordinate field if it does not already exist, so do not call DMGetCoordinateField() */ 65 ierr = DMFieldDestroy(&dm->coordinateField);CHKERRQ(ierr); 66 dm->coordinateField = dmNew->coordinateField; 67 ((DM_Plex *) dmNew->data)->coordFunc = ((DM_Plex *) dm->data)->coordFunc; 68 ierr = DMGetPeriodicity(dmNew, &isper, &maxCell, &L, &bd);CHKERRQ(ierr); 69 ierr = DMSetPeriodicity(dm, isper, maxCell, L, bd);CHKERRQ(ierr); 70 ierr = DMDestroy_Plex(dm);CHKERRQ(ierr); 71 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 72 dm->data = dmNew->data; 73 ((DM_Plex *) dmNew->data)->refct++; 74 ierr = DMDestroyLabelLinkList_Internal(dm);CHKERRQ(ierr); 75 ierr = DMCopyLabels(dmNew, dm, PETSC_OWN_POINTER, PETSC_TRUE, DM_COPY_LABELS_FAIL);CHKERRQ(ierr); 76 ierr = DMGetCoarseDM(dmNew,&coarseDM);CHKERRQ(ierr); 77 ierr = DMSetCoarseDM(dm,coarseDM);CHKERRQ(ierr); 78 ierr = DMDestroy(ndm);CHKERRQ(ierr); 79 PetscFunctionReturn(0); 80 } 81 82 /* Swap dm with the contents of dmNew 83 - Swap the DM_Plex structure 84 - Swap the coordinates 85 - Swap the point PetscSF 86 */ 87 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 88 { 89 DM coordDMA, coordDMB; 90 Vec coordsA, coordsB; 91 PetscSF sfA, sfB; 92 DMField fieldTmp; 93 void *tmp; 94 DMLabelLink listTmp; 95 DMLabel depthTmp; 96 PetscInt tmpI; 97 PetscErrorCode ierr; 98 99 PetscFunctionBegin; 100 if (dmA == dmB) PetscFunctionReturn(0); 101 ierr = DMGetPointSF(dmA, &sfA);CHKERRQ(ierr); 102 ierr = DMGetPointSF(dmB, &sfB);CHKERRQ(ierr); 103 ierr = PetscObjectReference((PetscObject) sfA);CHKERRQ(ierr); 104 ierr = DMSetPointSF(dmA, sfB);CHKERRQ(ierr); 105 ierr = DMSetPointSF(dmB, sfA);CHKERRQ(ierr); 106 ierr = PetscObjectDereference((PetscObject) sfA);CHKERRQ(ierr); 107 108 ierr = DMGetCoordinateDM(dmA, &coordDMA);CHKERRQ(ierr); 109 ierr = DMGetCoordinateDM(dmB, &coordDMB);CHKERRQ(ierr); 110 ierr = PetscObjectReference((PetscObject) coordDMA);CHKERRQ(ierr); 111 ierr = DMSetCoordinateDM(dmA, coordDMB);CHKERRQ(ierr); 112 ierr = DMSetCoordinateDM(dmB, coordDMA);CHKERRQ(ierr); 113 ierr = PetscObjectDereference((PetscObject) coordDMA);CHKERRQ(ierr); 114 115 ierr = DMGetCoordinatesLocal(dmA, &coordsA);CHKERRQ(ierr); 116 ierr = DMGetCoordinatesLocal(dmB, &coordsB);CHKERRQ(ierr); 117 ierr = PetscObjectReference((PetscObject) coordsA);CHKERRQ(ierr); 118 ierr = DMSetCoordinatesLocal(dmA, coordsB);CHKERRQ(ierr); 119 ierr = DMSetCoordinatesLocal(dmB, coordsA);CHKERRQ(ierr); 120 ierr = PetscObjectDereference((PetscObject) coordsA);CHKERRQ(ierr); 121 122 fieldTmp = dmA->coordinateField; 123 dmA->coordinateField = dmB->coordinateField; 124 dmB->coordinateField = fieldTmp; 125 tmp = dmA->data; 126 dmA->data = dmB->data; 127 dmB->data = tmp; 128 listTmp = dmA->labels; 129 dmA->labels = dmB->labels; 130 dmB->labels = listTmp; 131 depthTmp = dmA->depthLabel; 132 dmA->depthLabel = dmB->depthLabel; 133 dmB->depthLabel = depthTmp; 134 depthTmp = dmA->celltypeLabel; 135 dmA->celltypeLabel = dmB->celltypeLabel; 136 dmB->celltypeLabel = depthTmp; 137 tmpI = dmA->levelup; 138 dmA->levelup = dmB->levelup; 139 dmB->levelup = tmpI; 140 PetscFunctionReturn(0); 141 } 142 143 static PetscErrorCode DMPlexInterpolateInPlace_Internal(DM dm) 144 { 145 DM idm; 146 PetscErrorCode ierr; 147 148 PetscFunctionBegin; 149 ierr = DMPlexInterpolate(dm, &idm);CHKERRQ(ierr); 150 ierr = DMPlexCopyCoordinates(dm, idm);CHKERRQ(ierr); 151 ierr = DMPlexReplace_Static(dm, &idm);CHKERRQ(ierr); 152 PetscFunctionReturn(0); 153 } 154 155 /*@C 156 DMPlexCreateCoordinateSpace - Creates a finite element space for the coordinates 157 158 Collective 159 160 Input Parameters: 161 + DM - The DM 162 . degree - The degree of the finite element or PETSC_DECIDE 163 - coordFunc - An optional function to map new points from refinement to the surface 164 165 Level: advanced 166 167 .seealso: PetscFECreateLagrange(), DMGetCoordinateDM() 168 @*/ 169 PetscErrorCode DMPlexCreateCoordinateSpace(DM dm, PetscInt degree, PetscPointFunc coordFunc) 170 { 171 DM_Plex *mesh = (DM_Plex *) dm->data; 172 DM cdm; 173 PetscDS cds; 174 PetscFE fe; 175 PetscClassId id; 176 PetscErrorCode ierr; 177 178 PetscFunctionBegin; 179 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 180 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 181 ierr = PetscDSGetDiscretization(cds, 0, (PetscObject *) &fe);CHKERRQ(ierr); 182 ierr = PetscObjectGetClassId((PetscObject) fe, &id);CHKERRQ(ierr); 183 if (id != PETSCFE_CLASSID) { 184 PetscBool simplex; 185 PetscInt dim, dE, qorder; 186 187 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 188 ierr = DMGetCoordinateDim(dm, &dE);CHKERRQ(ierr); 189 ierr = DMPlexIsSimplex(dm, &simplex);CHKERRQ(ierr); 190 qorder = degree; 191 ierr = PetscObjectOptionsBegin((PetscObject) cdm);CHKERRQ(ierr); 192 ierr = PetscOptionsBoundedInt("-coord_dm_default_quadrature_order", "Quadrature order is one less than quadrature points per edge", "DMPlexCreateCoordinateSpace", qorder, &qorder, NULL, 0);CHKERRQ(ierr); 193 ierr = PetscOptionsEnd();CHKERRQ(ierr); 194 if (degree == PETSC_DECIDE) fe = NULL; 195 else { 196 ierr = PetscFECreateLagrange(PETSC_COMM_SELF, dim, dE, simplex, degree, qorder, &fe);CHKERRQ(ierr); 197 ierr = DMSetField(cdm, 0, NULL, (PetscObject) fe);CHKERRQ(ierr); 198 ierr = DMCreateDS(cdm);CHKERRQ(ierr); 199 } 200 ierr = DMProjectCoordinates(dm, fe);CHKERRQ(ierr); 201 ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); 202 } 203 mesh->coordFunc = coordFunc; 204 PetscFunctionReturn(0); 205 } 206 207 /*@ 208 DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement. 209 210 Collective 211 212 Input Parameters: 213 + comm - The communicator for the DM object 214 . dim - The spatial dimension 215 . simplex - Flag for simplicial cells, otherwise they are tensor product cells 216 . interpolate - Flag to create intermediate mesh pieces (edges, faces) 217 - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell 218 219 Output Parameter: 220 . dm - The DM object 221 222 Level: beginner 223 224 .seealso: DMSetType(), DMCreate() 225 @*/ 226 PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscReal refinementLimit, DM *newdm) 227 { 228 DM dm; 229 PetscMPIInt rank; 230 PetscErrorCode ierr; 231 232 PetscFunctionBegin; 233 ierr = DMCreate(comm, &dm);CHKERRQ(ierr); 234 ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr); 235 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 236 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 237 switch (dim) { 238 case 2: 239 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "triangular");CHKERRQ(ierr);} 240 else {ierr = PetscObjectSetName((PetscObject) dm, "quadrilateral");CHKERRQ(ierr);} 241 break; 242 case 3: 243 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "tetrahedral");CHKERRQ(ierr);} 244 else {ierr = PetscObjectSetName((PetscObject) dm, "hexahedral");CHKERRQ(ierr);} 245 break; 246 default: 247 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %D", dim); 248 } 249 if (rank) { 250 PetscInt numPoints[2] = {0, 0}; 251 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 252 } else { 253 switch (dim) { 254 case 2: 255 if (simplex) { 256 PetscInt numPoints[2] = {4, 2}; 257 PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; 258 PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; 259 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 260 PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5}; 261 262 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 263 } else { 264 PetscInt numPoints[2] = {6, 2}; 265 PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; 266 PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4}; 267 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 268 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}; 269 270 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 271 } 272 break; 273 case 3: 274 if (simplex) { 275 PetscInt numPoints[2] = {5, 2}; 276 PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; 277 PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; 278 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 279 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}; 280 281 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 282 } else { 283 PetscInt numPoints[2] = {12, 2}; 284 PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 285 PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8}; 286 PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 287 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, 288 -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5, 289 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5}; 290 291 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 292 } 293 break; 294 default: 295 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %D", dim); 296 } 297 } 298 *newdm = dm; 299 if (refinementLimit > 0.0) { 300 DM rdm; 301 const char *name; 302 303 ierr = DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);CHKERRQ(ierr); 304 ierr = DMPlexSetRefinementLimit(*newdm, refinementLimit);CHKERRQ(ierr); 305 ierr = DMRefine(*newdm, comm, &rdm);CHKERRQ(ierr); 306 ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); 307 ierr = PetscObjectSetName((PetscObject) rdm, name);CHKERRQ(ierr); 308 ierr = DMDestroy(newdm);CHKERRQ(ierr); 309 *newdm = rdm; 310 } 311 if (interpolate) { 312 DM idm; 313 314 ierr = DMPlexInterpolate(*newdm, &idm);CHKERRQ(ierr); 315 ierr = DMDestroy(newdm);CHKERRQ(ierr); 316 *newdm = idm; 317 } 318 PetscFunctionReturn(0); 319 } 320 321 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 322 { 323 const PetscInt numVertices = 2; 324 PetscInt markerRight = 1; 325 PetscInt markerLeft = 1; 326 PetscBool markerSeparate = PETSC_FALSE; 327 Vec coordinates; 328 PetscSection coordSection; 329 PetscScalar *coords; 330 PetscInt coordSize; 331 PetscMPIInt rank; 332 PetscInt cdim = 1, v; 333 PetscErrorCode ierr; 334 335 PetscFunctionBegin; 336 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 337 if (markerSeparate) { 338 markerRight = 2; 339 markerLeft = 1; 340 } 341 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRMPI(ierr); 342 if (!rank) { 343 ierr = DMPlexSetChart(dm, 0, numVertices);CHKERRQ(ierr); 344 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 345 ierr = DMSetLabelValue(dm, "marker", 0, markerLeft);CHKERRQ(ierr); 346 ierr = DMSetLabelValue(dm, "marker", 1, markerRight);CHKERRQ(ierr); 347 } 348 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 349 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 350 /* Build coordinates */ 351 ierr = DMSetCoordinateDim(dm, cdim);CHKERRQ(ierr); 352 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 353 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 354 ierr = PetscSectionSetChart(coordSection, 0, numVertices);CHKERRQ(ierr); 355 ierr = PetscSectionSetFieldComponents(coordSection, 0, cdim);CHKERRQ(ierr); 356 for (v = 0; v < numVertices; ++v) { 357 ierr = PetscSectionSetDof(coordSection, v, cdim);CHKERRQ(ierr); 358 ierr = PetscSectionSetFieldDof(coordSection, v, 0, cdim);CHKERRQ(ierr); 359 } 360 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 361 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 362 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 363 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 364 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 365 ierr = VecSetBlockSize(coordinates, cdim);CHKERRQ(ierr); 366 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 367 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 368 coords[0] = lower[0]; 369 coords[1] = upper[0]; 370 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 371 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 372 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 373 PetscFunctionReturn(0); 374 } 375 376 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 377 { 378 const PetscInt numVertices = (edges[0]+1)*(edges[1]+1); 379 const PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1]; 380 PetscInt markerTop = 1; 381 PetscInt markerBottom = 1; 382 PetscInt markerRight = 1; 383 PetscInt markerLeft = 1; 384 PetscBool markerSeparate = PETSC_FALSE; 385 Vec coordinates; 386 PetscSection coordSection; 387 PetscScalar *coords; 388 PetscInt coordSize; 389 PetscMPIInt rank; 390 PetscInt v, vx, vy; 391 PetscErrorCode ierr; 392 393 PetscFunctionBegin; 394 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 395 if (markerSeparate) { 396 markerTop = 3; 397 markerBottom = 1; 398 markerRight = 2; 399 markerLeft = 4; 400 } 401 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRMPI(ierr); 402 if (rank == 0) { 403 PetscInt e, ex, ey; 404 405 ierr = DMPlexSetChart(dm, 0, numEdges+numVertices);CHKERRQ(ierr); 406 for (e = 0; e < numEdges; ++e) { 407 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 408 } 409 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 410 for (vx = 0; vx <= edges[0]; vx++) { 411 for (ey = 0; ey < edges[1]; ey++) { 412 PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1); 413 PetscInt vertex = ey*(edges[0]+1) + vx + numEdges; 414 PetscInt cone[2]; 415 416 cone[0] = vertex; cone[1] = vertex+edges[0]+1; 417 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 418 if (vx == edges[0]) { 419 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 420 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 421 if (ey == edges[1]-1) { 422 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 423 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerRight);CHKERRQ(ierr); 424 } 425 } else if (vx == 0) { 426 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 427 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 428 if (ey == edges[1]-1) { 429 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 430 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft);CHKERRQ(ierr); 431 } 432 } 433 } 434 } 435 for (vy = 0; vy <= edges[1]; vy++) { 436 for (ex = 0; ex < edges[0]; ex++) { 437 PetscInt edge = vy*edges[0] + ex; 438 PetscInt vertex = vy*(edges[0]+1) + ex + numEdges; 439 PetscInt cone[2]; 440 441 cone[0] = vertex; cone[1] = vertex+1; 442 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 443 if (vy == edges[1]) { 444 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 445 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 446 if (ex == edges[0]-1) { 447 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 448 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerTop);CHKERRQ(ierr); 449 } 450 } else if (vy == 0) { 451 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 452 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 453 if (ex == edges[0]-1) { 454 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 455 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom);CHKERRQ(ierr); 456 } 457 } 458 } 459 } 460 } 461 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 462 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 463 /* Build coordinates */ 464 ierr = DMSetCoordinateDim(dm, 2);CHKERRQ(ierr); 465 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 466 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 467 ierr = PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);CHKERRQ(ierr); 468 ierr = PetscSectionSetFieldComponents(coordSection, 0, 2);CHKERRQ(ierr); 469 for (v = numEdges; v < numEdges+numVertices; ++v) { 470 ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr); 471 ierr = PetscSectionSetFieldDof(coordSection, v, 0, 2);CHKERRQ(ierr); 472 } 473 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 474 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 475 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 476 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 477 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 478 ierr = VecSetBlockSize(coordinates, 2);CHKERRQ(ierr); 479 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 480 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 481 for (vy = 0; vy <= edges[1]; ++vy) { 482 for (vx = 0; vx <= edges[0]; ++vx) { 483 coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx; 484 coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy; 485 } 486 } 487 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 488 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 489 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 490 PetscFunctionReturn(0); 491 } 492 493 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) 494 { 495 PetscInt vertices[3], numVertices; 496 PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2]; 497 Vec coordinates; 498 PetscSection coordSection; 499 PetscScalar *coords; 500 PetscInt coordSize; 501 PetscMPIInt rank; 502 PetscInt v, vx, vy, vz; 503 PetscInt voffset, iface=0, cone[4]; 504 PetscErrorCode ierr; 505 506 PetscFunctionBegin; 507 PetscCheckFalse((faces[0] < 1) || (faces[1] < 1) || (faces[2] < 1),PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Must have at least 1 face per side"); 508 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRMPI(ierr); 509 vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1; 510 numVertices = vertices[0]*vertices[1]*vertices[2]; 511 if (rank == 0) { 512 PetscInt f; 513 514 ierr = DMPlexSetChart(dm, 0, numFaces+numVertices);CHKERRQ(ierr); 515 for (f = 0; f < numFaces; ++f) { 516 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 517 } 518 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 519 520 /* Side 0 (Top) */ 521 for (vy = 0; vy < faces[1]; vy++) { 522 for (vx = 0; vx < faces[0]; vx++) { 523 voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx; 524 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0]; 525 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 526 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 527 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 528 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 529 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 530 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);CHKERRQ(ierr); 531 iface++; 532 } 533 } 534 535 /* Side 1 (Bottom) */ 536 for (vy = 0; vy < faces[1]; vy++) { 537 for (vx = 0; vx < faces[0]; vx++) { 538 voffset = numFaces + vy*(faces[0]+1) + vx; 539 cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1; 540 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 541 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 542 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 543 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 544 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 545 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);CHKERRQ(ierr); 546 iface++; 547 } 548 } 549 550 /* Side 2 (Front) */ 551 for (vz = 0; vz < faces[2]; vz++) { 552 for (vx = 0; vx < faces[0]; vx++) { 553 voffset = numFaces + vz*vertices[0]*vertices[1] + vx; 554 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1]; 555 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 556 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 557 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 558 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 559 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 560 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);CHKERRQ(ierr); 561 iface++; 562 } 563 } 564 565 /* Side 3 (Back) */ 566 for (vz = 0; vz < faces[2]; vz++) { 567 for (vx = 0; vx < faces[0]; vx++) { 568 voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx; 569 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1; 570 cone[2] = voffset+1; cone[3] = voffset; 571 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 572 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 573 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 574 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 575 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 576 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);CHKERRQ(ierr); 577 iface++; 578 } 579 } 580 581 /* Side 4 (Left) */ 582 for (vz = 0; vz < faces[2]; vz++) { 583 for (vy = 0; vy < faces[1]; vy++) { 584 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0]; 585 cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1]; 586 cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0]; 587 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 588 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 589 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 590 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 591 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[1]+0, 1);CHKERRQ(ierr); 592 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);CHKERRQ(ierr); 593 iface++; 594 } 595 } 596 597 /* Side 5 (Right) */ 598 for (vz = 0; vz < faces[2]; vz++) { 599 for (vy = 0; vy < faces[1]; vy++) { 600 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + faces[0]; 601 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset; 602 cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0]; 603 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 604 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 605 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 606 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 607 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 608 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);CHKERRQ(ierr); 609 iface++; 610 } 611 } 612 } 613 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 614 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 615 /* Build coordinates */ 616 ierr = DMSetCoordinateDim(dm, 3);CHKERRQ(ierr); 617 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 618 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 619 ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr); 620 ierr = PetscSectionSetFieldComponents(coordSection, 0, 3);CHKERRQ(ierr); 621 for (v = numFaces; v < numFaces+numVertices; ++v) { 622 ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr); 623 ierr = PetscSectionSetFieldDof(coordSection, v, 0, 3);CHKERRQ(ierr); 624 } 625 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 626 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 627 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 628 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 629 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 630 ierr = VecSetBlockSize(coordinates, 3);CHKERRQ(ierr); 631 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 632 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 633 for (vz = 0; vz <= faces[2]; ++vz) { 634 for (vy = 0; vy <= faces[1]; ++vy) { 635 for (vx = 0; vx <= faces[0]; ++vx) { 636 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx; 637 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy; 638 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz; 639 } 640 } 641 } 642 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 643 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 644 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 645 PetscFunctionReturn(0); 646 } 647 648 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate) 649 { 650 PetscErrorCode ierr; 651 652 PetscFunctionBegin; 653 PetscValidLogicalCollectiveInt(dm, dim, 2); 654 ierr = DMSetDimension(dm, dim-1);CHKERRQ(ierr); 655 ierr = DMSetCoordinateDim(dm, dim);CHKERRQ(ierr); 656 switch (dim) { 657 case 1: ierr = DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(dm, lower, upper, faces);CHKERRQ(ierr);break; 658 case 2: ierr = DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(dm, lower, upper, faces);CHKERRQ(ierr);break; 659 case 3: ierr = DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(dm, lower, upper, faces);CHKERRQ(ierr);break; 660 default: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Dimension not supported: %D", dim); 661 } 662 if (interpolate) {ierr = DMPlexInterpolateInPlace_Internal(dm);CHKERRQ(ierr);} 663 PetscFunctionReturn(0); 664 } 665 666 /*@C 667 DMPlexCreateBoxSurfaceMesh - Creates a mesh on the surface of the tensor product of unit intervals (box) using tensor cells (hexahedra). 668 669 Collective 670 671 Input Parameters: 672 + comm - The communicator for the DM object 673 . dim - The spatial dimension of the box, so the resulting mesh is has dimension dim-1 674 . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 675 . lower - The lower left corner, or NULL for (0, 0, 0) 676 . upper - The upper right corner, or NULL for (1, 1, 1) 677 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 678 679 Output Parameter: 680 . dm - The DM object 681 682 Level: beginner 683 684 .seealso: DMSetFromOptions(), DMPlexCreateBoxMesh(), DMPlexCreateFromFile(), DMSetType(), DMCreate() 685 @*/ 686 PetscErrorCode DMPlexCreateBoxSurfaceMesh(MPI_Comm comm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate, DM *dm) 687 { 688 PetscInt fac[3] = {1, 1, 1}; 689 PetscReal low[3] = {0, 0, 0}; 690 PetscReal upp[3] = {1, 1, 1}; 691 PetscErrorCode ierr; 692 693 PetscFunctionBegin; 694 ierr = DMCreate(comm,dm);CHKERRQ(ierr); 695 ierr = DMSetType(*dm,DMPLEX);CHKERRQ(ierr); 696 ierr = DMPlexCreateBoxSurfaceMesh_Internal(*dm, dim, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, interpolate);CHKERRQ(ierr); 697 PetscFunctionReturn(0); 698 } 699 700 static PetscErrorCode DMPlexCreateLineMesh_Internal(DM dm,PetscInt segments,PetscReal lower,PetscReal upper,DMBoundaryType bd) 701 { 702 PetscInt i,fStart,fEnd,numCells = 0,numVerts = 0; 703 PetscInt numPoints[2],*coneSize,*cones,*coneOrientations; 704 PetscScalar *vertexCoords; 705 PetscReal L,maxCell; 706 PetscBool markerSeparate = PETSC_FALSE; 707 PetscInt markerLeft = 1, faceMarkerLeft = 1; 708 PetscInt markerRight = 1, faceMarkerRight = 2; 709 PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE; 710 PetscMPIInt rank; 711 PetscErrorCode ierr; 712 713 PetscFunctionBegin; 714 PetscValidPointer(dm,1); 715 716 ierr = DMSetDimension(dm,1);CHKERRQ(ierr); 717 ierr = DMCreateLabel(dm,"marker");CHKERRQ(ierr); 718 ierr = DMCreateLabel(dm,"Face Sets");CHKERRQ(ierr); 719 720 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm),&rank);CHKERRMPI(ierr); 721 if (rank == 0) numCells = segments; 722 if (rank == 0) numVerts = segments + (wrap ? 0 : 1); 723 724 numPoints[0] = numVerts ; numPoints[1] = numCells; 725 ierr = PetscMalloc4(numCells+numVerts,&coneSize,numCells*2,&cones,numCells+numVerts,&coneOrientations,numVerts,&vertexCoords);CHKERRQ(ierr); 726 ierr = PetscArrayzero(coneOrientations,numCells+numVerts);CHKERRQ(ierr); 727 for (i = 0; i < numCells; ++i) { coneSize[i] = 2; } 728 for (i = 0; i < numVerts; ++i) { coneSize[numCells+i] = 0; } 729 for (i = 0; i < numCells; ++i) { cones[2*i] = numCells + i%numVerts; cones[2*i+1] = numCells + (i+1)%numVerts; } 730 for (i = 0; i < numVerts; ++i) { vertexCoords[i] = lower + (upper-lower)*((PetscReal)i/(PetscReal)numCells); } 731 ierr = DMPlexCreateFromDAG(dm,1,numPoints,coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 732 ierr = PetscFree4(coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 733 734 ierr = PetscOptionsGetBool(((PetscObject)dm)->options,((PetscObject)dm)->prefix,"-dm_plex_separate_marker",&markerSeparate,NULL);CHKERRQ(ierr); 735 if (markerSeparate) { markerLeft = faceMarkerLeft; markerRight = faceMarkerRight;} 736 if (!wrap && rank == 0) { 737 ierr = DMPlexGetHeightStratum(dm,1,&fStart,&fEnd);CHKERRQ(ierr); 738 ierr = DMSetLabelValue(dm,"marker",fStart,markerLeft);CHKERRQ(ierr); 739 ierr = DMSetLabelValue(dm,"marker",fEnd-1,markerRight);CHKERRQ(ierr); 740 ierr = DMSetLabelValue(dm,"Face Sets",fStart,faceMarkerLeft);CHKERRQ(ierr); 741 ierr = DMSetLabelValue(dm,"Face Sets",fEnd-1,faceMarkerRight);CHKERRQ(ierr); 742 } 743 if (wrap) { 744 L = upper - lower; 745 maxCell = (PetscReal)1.1*(L/(PetscReal)PetscMax(1,segments)); 746 ierr = DMSetPeriodicity(dm,PETSC_TRUE,&maxCell,&L,&bd);CHKERRQ(ierr); 747 } 748 ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr); 749 PetscFunctionReturn(0); 750 } 751 752 static PetscErrorCode DMPlexCreateBoxMesh_Simplex_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate) 753 { 754 DM boundary, vol; 755 PetscInt i; 756 PetscErrorCode ierr; 757 758 PetscFunctionBegin; 759 PetscValidPointer(dm, 1); 760 for (i = 0; i < dim; ++i) PetscCheckFalse(periodicity[i] != DM_BOUNDARY_NONE,PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Periodicity is not supported for simplex meshes"); 761 ierr = DMCreate(PetscObjectComm((PetscObject) dm), &boundary);CHKERRQ(ierr); 762 ierr = DMSetType(boundary, DMPLEX);CHKERRQ(ierr); 763 ierr = DMPlexCreateBoxSurfaceMesh_Internal(boundary, dim, faces, lower, upper, PETSC_FALSE);CHKERRQ(ierr); 764 ierr = DMPlexGenerate(boundary, NULL, interpolate, &vol);CHKERRQ(ierr); 765 ierr = DMPlexCopy_Internal(dm, PETSC_TRUE, vol);CHKERRQ(ierr); 766 ierr = DMPlexReplace_Static(dm, &vol);CHKERRQ(ierr); 767 ierr = DMDestroy(&boundary);CHKERRQ(ierr); 768 PetscFunctionReturn(0); 769 } 770 771 static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ) 772 { 773 DMLabel cutLabel = NULL; 774 PetscInt markerTop = 1, faceMarkerTop = 1; 775 PetscInt markerBottom = 1, faceMarkerBottom = 1; 776 PetscInt markerFront = 1, faceMarkerFront = 1; 777 PetscInt markerBack = 1, faceMarkerBack = 1; 778 PetscInt markerRight = 1, faceMarkerRight = 1; 779 PetscInt markerLeft = 1, faceMarkerLeft = 1; 780 PetscInt dim; 781 PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE; 782 PetscMPIInt rank; 783 PetscErrorCode ierr; 784 785 PetscFunctionBegin; 786 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 787 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRMPI(ierr); 788 ierr = DMCreateLabel(dm,"marker");CHKERRQ(ierr); 789 ierr = DMCreateLabel(dm,"Face Sets");CHKERRQ(ierr); 790 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL);CHKERRQ(ierr); 791 if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST || 792 bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST || 793 bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) { 794 795 if (cutMarker) {ierr = DMCreateLabel(dm, "periodic_cut");CHKERRQ(ierr); ierr = DMGetLabel(dm, "periodic_cut", &cutLabel);CHKERRQ(ierr);} 796 } 797 switch (dim) { 798 case 2: 799 faceMarkerTop = 3; 800 faceMarkerBottom = 1; 801 faceMarkerRight = 2; 802 faceMarkerLeft = 4; 803 break; 804 case 3: 805 faceMarkerBottom = 1; 806 faceMarkerTop = 2; 807 faceMarkerFront = 3; 808 faceMarkerBack = 4; 809 faceMarkerRight = 5; 810 faceMarkerLeft = 6; 811 break; 812 default: 813 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %D not supported",dim); 814 } 815 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 816 if (markerSeparate) { 817 markerBottom = faceMarkerBottom; 818 markerTop = faceMarkerTop; 819 markerFront = faceMarkerFront; 820 markerBack = faceMarkerBack; 821 markerRight = faceMarkerRight; 822 markerLeft = faceMarkerLeft; 823 } 824 { 825 const PetscInt numXEdges = rank == 0 ? edges[0] : 0; 826 const PetscInt numYEdges = rank == 0 ? edges[1] : 0; 827 const PetscInt numZEdges = rank == 0 ? edges[2] : 0; 828 const PetscInt numXVertices = rank == 0 ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; 829 const PetscInt numYVertices = rank == 0 ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; 830 const PetscInt numZVertices = rank == 0 ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0; 831 const PetscInt numCells = numXEdges*numYEdges*numZEdges; 832 const PetscInt numXFaces = numYEdges*numZEdges; 833 const PetscInt numYFaces = numXEdges*numZEdges; 834 const PetscInt numZFaces = numXEdges*numYEdges; 835 const PetscInt numTotXFaces = numXVertices*numXFaces; 836 const PetscInt numTotYFaces = numYVertices*numYFaces; 837 const PetscInt numTotZFaces = numZVertices*numZFaces; 838 const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces; 839 const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices; 840 const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices; 841 const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices; 842 const PetscInt numVertices = numXVertices*numYVertices*numZVertices; 843 const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges; 844 const PetscInt firstVertex = (dim == 2) ? numFaces : numCells; 845 const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices; 846 const PetscInt firstYFace = firstXFace + numTotXFaces; 847 const PetscInt firstZFace = firstYFace + numTotYFaces; 848 const PetscInt firstXEdge = numCells + numFaces + numVertices; 849 const PetscInt firstYEdge = firstXEdge + numTotXEdges; 850 const PetscInt firstZEdge = firstYEdge + numTotYEdges; 851 Vec coordinates; 852 PetscSection coordSection; 853 PetscScalar *coords; 854 PetscInt coordSize; 855 PetscInt v, vx, vy, vz; 856 PetscInt c, f, fx, fy, fz, e, ex, ey, ez; 857 858 ierr = DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);CHKERRQ(ierr); 859 for (c = 0; c < numCells; c++) { 860 ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr); 861 } 862 for (f = firstXFace; f < firstXFace+numFaces; ++f) { 863 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 864 } 865 for (e = firstXEdge; e < firstXEdge+numEdges; ++e) { 866 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 867 } 868 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 869 /* Build cells */ 870 for (fz = 0; fz < numZEdges; ++fz) { 871 for (fy = 0; fy < numYEdges; ++fy) { 872 for (fx = 0; fx < numXEdges; ++fx) { 873 PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx; 874 PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 875 PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices); 876 PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 877 PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices); 878 PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 879 PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices); 880 /* B, T, F, K, R, L */ 881 PetscInt ornt[6] = {-2, 0, 0, -3, 0, -2}; /* ??? */ 882 PetscInt cone[6]; 883 884 /* no boundary twisting in 3D */ 885 cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL; 886 ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr); 887 ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr); 888 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 889 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 890 if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 891 } 892 } 893 } 894 /* Build x faces */ 895 for (fz = 0; fz < numZEdges; ++fz) { 896 for (fy = 0; fy < numYEdges; ++fy) { 897 for (fx = 0; fx < numXVertices; ++fx) { 898 PetscInt face = firstXFace + (fz*numYEdges+fy) *numXVertices+fx; 899 PetscInt edgeL = firstZEdge + (fy *numXVertices+fx)*numZEdges + fz; 900 PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz; 901 PetscInt edgeB = firstYEdge + (fz *numXVertices+fx)*numYEdges + fy; 902 PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy; 903 PetscInt ornt[4] = {0, 0, -1, -1}; 904 PetscInt cone[4]; 905 906 if (dim == 3) { 907 /* markers */ 908 if (bdX != DM_BOUNDARY_PERIODIC) { 909 if (fx == numXVertices-1) { 910 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);CHKERRQ(ierr); 911 ierr = DMSetLabelValue(dm, "marker", face, markerRight);CHKERRQ(ierr); 912 } 913 else if (fx == 0) { 914 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);CHKERRQ(ierr); 915 ierr = DMSetLabelValue(dm, "marker", face, markerLeft);CHKERRQ(ierr); 916 } 917 } 918 } 919 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 920 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 921 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 922 } 923 } 924 } 925 /* Build y faces */ 926 for (fz = 0; fz < numZEdges; ++fz) { 927 for (fx = 0; fx < numXEdges; ++fx) { 928 for (fy = 0; fy < numYVertices; ++fy) { 929 PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 930 PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx)*numZEdges + fz; 931 PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz; 932 PetscInt edgeB = firstXEdge + (fz *numYVertices+fy)*numXEdges + fx; 933 PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx; 934 PetscInt ornt[4] = {0, 0, -1, -1}; 935 PetscInt cone[4]; 936 937 if (dim == 3) { 938 /* markers */ 939 if (bdY != DM_BOUNDARY_PERIODIC) { 940 if (fy == numYVertices-1) { 941 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);CHKERRQ(ierr); 942 ierr = DMSetLabelValue(dm, "marker", face, markerBack);CHKERRQ(ierr); 943 } 944 else if (fy == 0) { 945 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);CHKERRQ(ierr); 946 ierr = DMSetLabelValue(dm, "marker", face, markerFront);CHKERRQ(ierr); 947 } 948 } 949 } 950 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 951 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 952 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 953 } 954 } 955 } 956 /* Build z faces */ 957 for (fy = 0; fy < numYEdges; ++fy) { 958 for (fx = 0; fx < numXEdges; ++fx) { 959 for (fz = 0; fz < numZVertices; fz++) { 960 PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 961 PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx)*numYEdges + fy; 962 PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy; 963 PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy)*numXEdges + fx; 964 PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx; 965 PetscInt ornt[4] = {0, 0, -1, -1}; 966 PetscInt cone[4]; 967 968 if (dim == 2) { 969 if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -1;} 970 if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;} 971 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 972 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 973 } else { 974 /* markers */ 975 if (bdZ != DM_BOUNDARY_PERIODIC) { 976 if (fz == numZVertices-1) { 977 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);CHKERRQ(ierr); 978 ierr = DMSetLabelValue(dm, "marker", face, markerTop);CHKERRQ(ierr); 979 } 980 else if (fz == 0) { 981 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);CHKERRQ(ierr); 982 ierr = DMSetLabelValue(dm, "marker", face, markerBottom);CHKERRQ(ierr); 983 } 984 } 985 } 986 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 987 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 988 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 989 } 990 } 991 } 992 /* Build Z edges*/ 993 for (vy = 0; vy < numYVertices; vy++) { 994 for (vx = 0; vx < numXVertices; vx++) { 995 for (ez = 0; ez < numZEdges; ez++) { 996 const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez; 997 const PetscInt vertexB = firstVertex + (ez *numYVertices+vy)*numXVertices + vx; 998 const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx; 999 PetscInt cone[2]; 1000 1001 if (dim == 3) { 1002 if (bdX != DM_BOUNDARY_PERIODIC) { 1003 if (vx == numXVertices-1) { 1004 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 1005 } 1006 else if (vx == 0) { 1007 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 1008 } 1009 } 1010 if (bdY != DM_BOUNDARY_PERIODIC) { 1011 if (vy == numYVertices-1) { 1012 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 1013 } 1014 else if (vy == 0) { 1015 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 1016 } 1017 } 1018 } 1019 cone[0] = vertexB; cone[1] = vertexT; 1020 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 1021 } 1022 } 1023 } 1024 /* Build Y edges*/ 1025 for (vz = 0; vz < numZVertices; vz++) { 1026 for (vx = 0; vx < numXVertices; vx++) { 1027 for (ey = 0; ey < numYEdges; ey++) { 1028 const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx; 1029 const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey; 1030 const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx; 1031 const PetscInt vertexK = firstVertex + nextv; 1032 PetscInt cone[2]; 1033 1034 cone[0] = vertexF; cone[1] = vertexK; 1035 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 1036 if (dim == 2) { 1037 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 1038 if (vx == numXVertices-1) { 1039 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);CHKERRQ(ierr); 1040 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 1041 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 1042 if (ey == numYEdges-1) { 1043 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 1044 } 1045 } else if (vx == 0) { 1046 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);CHKERRQ(ierr); 1047 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 1048 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 1049 if (ey == numYEdges-1) { 1050 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 1051 } 1052 } 1053 } else { 1054 if (vx == 0 && cutLabel) { 1055 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 1056 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 1057 if (ey == numYEdges-1) { 1058 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 1059 } 1060 } 1061 } 1062 } else { 1063 if (bdX != DM_BOUNDARY_PERIODIC) { 1064 if (vx == numXVertices-1) { 1065 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 1066 } else if (vx == 0) { 1067 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 1068 } 1069 } 1070 if (bdZ != DM_BOUNDARY_PERIODIC) { 1071 if (vz == numZVertices-1) { 1072 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 1073 } else if (vz == 0) { 1074 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 1075 } 1076 } 1077 } 1078 } 1079 } 1080 } 1081 /* Build X edges*/ 1082 for (vz = 0; vz < numZVertices; vz++) { 1083 for (vy = 0; vy < numYVertices; vy++) { 1084 for (ex = 0; ex < numXEdges; ex++) { 1085 const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices; 1086 const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex; 1087 const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex; 1088 const PetscInt vertexR = firstVertex + nextv; 1089 PetscInt cone[2]; 1090 1091 cone[0] = vertexL; cone[1] = vertexR; 1092 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 1093 if (dim == 2) { 1094 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 1095 if (vy == numYVertices-1) { 1096 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);CHKERRQ(ierr); 1097 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 1098 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 1099 if (ex == numXEdges-1) { 1100 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 1101 } 1102 } else if (vy == 0) { 1103 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);CHKERRQ(ierr); 1104 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 1105 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 1106 if (ex == numXEdges-1) { 1107 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 1108 } 1109 } 1110 } else { 1111 if (vy == 0 && cutLabel) { 1112 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 1113 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 1114 if (ex == numXEdges-1) { 1115 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 1116 } 1117 } 1118 } 1119 } else { 1120 if (bdY != DM_BOUNDARY_PERIODIC) { 1121 if (vy == numYVertices-1) { 1122 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 1123 } 1124 else if (vy == 0) { 1125 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 1126 } 1127 } 1128 if (bdZ != DM_BOUNDARY_PERIODIC) { 1129 if (vz == numZVertices-1) { 1130 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 1131 } 1132 else if (vz == 0) { 1133 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 1134 } 1135 } 1136 } 1137 } 1138 } 1139 } 1140 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1141 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1142 /* Build coordinates */ 1143 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1144 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1145 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1146 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr); 1147 for (v = firstVertex; v < firstVertex+numVertices; ++v) { 1148 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1149 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1150 } 1151 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1152 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1153 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1154 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1155 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1156 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1157 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1158 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1159 for (vz = 0; vz < numZVertices; ++vz) { 1160 for (vy = 0; vy < numYVertices; ++vy) { 1161 for (vx = 0; vx < numXVertices; ++vx) { 1162 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx; 1163 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy; 1164 if (dim == 3) { 1165 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz; 1166 } 1167 } 1168 } 1169 } 1170 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1171 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1172 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1173 } 1174 PetscFunctionReturn(0); 1175 } 1176 1177 static PetscErrorCode DMPlexCreateBoxMesh_Tensor_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[]) 1178 { 1179 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1180 PetscInt fac[3] = {0, 0, 0}, d; 1181 PetscErrorCode ierr; 1182 1183 PetscFunctionBegin; 1184 PetscValidPointer(dm, 1); 1185 PetscValidLogicalCollectiveInt(dm, dim, 2); 1186 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 1187 for (d = 0; d < dim; ++d) {fac[d] = faces[d]; bdt[d] = periodicity[d];} 1188 ierr = DMPlexCreateCubeMesh_Internal(dm, lower, upper, fac, bdt[0], bdt[1], bdt[2]);CHKERRQ(ierr); 1189 if (periodicity[0] == DM_BOUNDARY_PERIODIC || periodicity[0] == DM_BOUNDARY_TWIST || 1190 periodicity[1] == DM_BOUNDARY_PERIODIC || periodicity[1] == DM_BOUNDARY_TWIST || 1191 (dim > 2 && (periodicity[2] == DM_BOUNDARY_PERIODIC || periodicity[2] == DM_BOUNDARY_TWIST))) { 1192 PetscReal L[3]; 1193 PetscReal maxCell[3]; 1194 1195 for (d = 0; d < dim; ++d) { 1196 L[d] = upper[d] - lower[d]; 1197 maxCell[d] = 1.1 * (L[d] / PetscMax(1, faces[d])); 1198 } 1199 ierr = DMSetPeriodicity(dm, PETSC_TRUE, maxCell, L, periodicity);CHKERRQ(ierr); 1200 } 1201 ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr); 1202 PetscFunctionReturn(0); 1203 } 1204 1205 static PetscErrorCode DMPlexCreateBoxMesh_Internal(DM dm, PetscInt dim, PetscBool simplex, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate) 1206 { 1207 PetscErrorCode ierr; 1208 1209 PetscFunctionBegin; 1210 if (dim == 1) {ierr = DMPlexCreateLineMesh_Internal(dm, faces[0], lower[0], upper[0], periodicity[0]);CHKERRQ(ierr);} 1211 else if (simplex) {ierr = DMPlexCreateBoxMesh_Simplex_Internal(dm, dim, faces, lower, upper, periodicity, interpolate);CHKERRQ(ierr);} 1212 else {ierr = DMPlexCreateBoxMesh_Tensor_Internal(dm, dim, faces, lower, upper, periodicity);CHKERRQ(ierr);} 1213 if (!interpolate && dim > 1 && !simplex) { 1214 DM udm; 1215 1216 ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr); 1217 ierr = DMPlexCopyCoordinates(dm, udm);CHKERRQ(ierr); 1218 ierr = DMPlexReplace_Static(dm, &udm);CHKERRQ(ierr); 1219 } 1220 PetscFunctionReturn(0); 1221 } 1222 1223 /*@C 1224 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra). 1225 1226 Collective 1227 1228 Input Parameters: 1229 + comm - The communicator for the DM object 1230 . dim - The spatial dimension 1231 . simplex - PETSC_TRUE for simplices, PETSC_FALSE for tensor cells 1232 . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 1233 . lower - The lower left corner, or NULL for (0, 0, 0) 1234 . upper - The upper right corner, or NULL for (1, 1, 1) 1235 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 1236 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1237 1238 Output Parameter: 1239 . dm - The DM object 1240 1241 Note: If you want to customize this mesh using options, you just need to 1242 $ DMCreate(comm, &dm); 1243 $ DMSetType(dm, DMPLEX); 1244 $ DMSetFromOptions(dm); 1245 and use the options on the DMSetFromOptions() page. 1246 1247 Here is the numbering returned for 2 faces in each direction for tensor cells: 1248 $ 10---17---11---18----12 1249 $ | | | 1250 $ | | | 1251 $ 20 2 22 3 24 1252 $ | | | 1253 $ | | | 1254 $ 7---15----8---16----9 1255 $ | | | 1256 $ | | | 1257 $ 19 0 21 1 23 1258 $ | | | 1259 $ | | | 1260 $ 4---13----5---14----6 1261 1262 and for simplicial cells 1263 1264 $ 14----8---15----9----16 1265 $ |\ 5 |\ 7 | 1266 $ | \ | \ | 1267 $ 13 2 14 3 15 1268 $ | 4 \ | 6 \ | 1269 $ | \ | \ | 1270 $ 11----6---12----7----13 1271 $ |\ |\ | 1272 $ | \ 1 | \ 3 | 1273 $ 10 0 11 1 12 1274 $ | 0 \ | 2 \ | 1275 $ | \ | \ | 1276 $ 8----4----9----5----10 1277 1278 Level: beginner 1279 1280 .seealso: DMSetFromOptions(), DMPlexCreateFromFile(), DMPlexCreateHexCylinderMesh(), DMSetType(), DMCreate() 1281 @*/ 1282 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) 1283 { 1284 PetscInt fac[3] = {1, 1, 1}; 1285 PetscReal low[3] = {0, 0, 0}; 1286 PetscReal upp[3] = {1, 1, 1}; 1287 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1288 PetscErrorCode ierr; 1289 1290 PetscFunctionBegin; 1291 ierr = DMCreate(comm,dm);CHKERRQ(ierr); 1292 ierr = DMSetType(*dm,DMPLEX);CHKERRQ(ierr); 1293 ierr = DMPlexCreateBoxMesh_Internal(*dm, dim, simplex, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt, interpolate);CHKERRQ(ierr); 1294 PetscFunctionReturn(0); 1295 } 1296 1297 static PetscErrorCode DMPlexCreateWedgeBoxMesh_Internal(DM dm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[]) 1298 { 1299 DM bdm, vol; 1300 PetscInt i; 1301 PetscErrorCode ierr; 1302 1303 PetscFunctionBegin; 1304 for (i = 0; i < 3; ++i) PetscCheckFalse(periodicity[i] != DM_BOUNDARY_NONE,PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Periodicity not yet supported"); 1305 ierr = DMCreate(PetscObjectComm((PetscObject) dm), &bdm);CHKERRQ(ierr); 1306 ierr = DMSetType(bdm, DMPLEX);CHKERRQ(ierr); 1307 ierr = DMSetDimension(bdm, 2);CHKERRQ(ierr); 1308 ierr = DMPlexCreateBoxMesh_Simplex_Internal(bdm, 2, faces, lower, upper, periodicity, PETSC_TRUE);CHKERRQ(ierr); 1309 ierr = DMPlexExtrude(bdm, faces[2], upper[2] - lower[2], PETSC_TRUE, PETSC_FALSE, NULL, NULL, &vol);CHKERRQ(ierr); 1310 ierr = DMDestroy(&bdm);CHKERRQ(ierr); 1311 ierr = DMPlexReplace_Static(dm, &vol);CHKERRQ(ierr); 1312 if (lower[2] != 0.0) { 1313 Vec v; 1314 PetscScalar *x; 1315 PetscInt cDim, n; 1316 1317 ierr = DMGetCoordinatesLocal(dm, &v);CHKERRQ(ierr); 1318 ierr = VecGetBlockSize(v, &cDim);CHKERRQ(ierr); 1319 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 1320 ierr = VecGetArray(v, &x);CHKERRQ(ierr); 1321 x += cDim; 1322 for (i = 0; i < n; i += cDim) x[i] += lower[2]; 1323 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 1324 ierr = DMSetCoordinatesLocal(dm, v);CHKERRQ(ierr); 1325 } 1326 PetscFunctionReturn(0); 1327 } 1328 1329 /*@ 1330 DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells. 1331 1332 Collective 1333 1334 Input Parameters: 1335 + comm - The communicator for the DM object 1336 . faces - Number of faces per dimension, or NULL for (1, 1, 1) 1337 . lower - The lower left corner, or NULL for (0, 0, 0) 1338 . upper - The upper right corner, or NULL for (1, 1, 1) 1339 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 1340 . orderHeight - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1341 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1342 1343 Output Parameter: 1344 . dm - The DM object 1345 1346 Level: beginner 1347 1348 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateWedgeCylinderMesh(), DMExtrude(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1349 @*/ 1350 PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool orderHeight, PetscBool interpolate, DM *dm) 1351 { 1352 PetscInt fac[3] = {1, 1, 1}; 1353 PetscReal low[3] = {0, 0, 0}; 1354 PetscReal upp[3] = {1, 1, 1}; 1355 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1356 PetscErrorCode ierr; 1357 1358 PetscFunctionBegin; 1359 ierr = DMCreate(comm,dm);CHKERRQ(ierr); 1360 ierr = DMSetType(*dm,DMPLEX);CHKERRQ(ierr); 1361 ierr = DMPlexCreateWedgeBoxMesh_Internal(*dm, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt);CHKERRQ(ierr); 1362 if (!interpolate) { 1363 DM udm; 1364 1365 ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr); 1366 ierr = DMPlexReplace_Static(*dm, &udm);CHKERRQ(ierr); 1367 } 1368 PetscFunctionReturn(0); 1369 } 1370 1371 /*@C 1372 DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database. 1373 1374 Logically Collective on dm 1375 1376 Input Parameters: 1377 + dm - the DM context 1378 - prefix - the prefix to prepend to all option names 1379 1380 Notes: 1381 A hyphen (-) must NOT be given at the beginning of the prefix name. 1382 The first character of all runtime options is AUTOMATICALLY the hyphen. 1383 1384 Level: advanced 1385 1386 .seealso: SNESSetFromOptions() 1387 @*/ 1388 PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) 1389 { 1390 DM_Plex *mesh = (DM_Plex *) dm->data; 1391 PetscErrorCode ierr; 1392 1393 PetscFunctionBegin; 1394 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1395 ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);CHKERRQ(ierr); 1396 ierr = PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);CHKERRQ(ierr); 1397 PetscFunctionReturn(0); 1398 } 1399 1400 /* Remap geometry to cylinder 1401 TODO: This only works for a single refinement, then it is broken 1402 1403 Interior square: Linear interpolation is correct 1404 The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing 1405 such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance 1406 1407 phi = arctan(y/x) 1408 d_close = sqrt(1/8 + 1/4 sin^2(phi)) 1409 d_far = sqrt(1/2 + sin^2(phi)) 1410 1411 so we remap them using 1412 1413 x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) 1414 y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) 1415 1416 If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. 1417 */ 1418 static void snapToCylinder(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1419 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1420 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1421 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 1422 { 1423 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1424 const PetscReal ds2 = 0.5*dis; 1425 1426 if ((PetscAbsScalar(u[0]) <= ds2) && (PetscAbsScalar(u[1]) <= ds2)) { 1427 f0[0] = u[0]; 1428 f0[1] = u[1]; 1429 } else { 1430 PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; 1431 1432 x = PetscRealPart(u[0]); 1433 y = PetscRealPart(u[1]); 1434 phi = PetscAtan2Real(y, x); 1435 sinp = PetscSinReal(phi); 1436 cosp = PetscCosReal(phi); 1437 if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) { 1438 dc = PetscAbsReal(ds2/sinp); 1439 df = PetscAbsReal(dis/sinp); 1440 xc = ds2*x/PetscAbsReal(y); 1441 yc = ds2*PetscSignReal(y); 1442 } else { 1443 dc = PetscAbsReal(ds2/cosp); 1444 df = PetscAbsReal(dis/cosp); 1445 xc = ds2*PetscSignReal(x); 1446 yc = ds2*y/PetscAbsReal(x); 1447 } 1448 f0[0] = xc + (u[0] - xc)*(1.0 - dc)/(df - dc); 1449 f0[1] = yc + (u[1] - yc)*(1.0 - dc)/(df - dc); 1450 } 1451 f0[2] = u[2]; 1452 } 1453 1454 static PetscErrorCode DMPlexCreateHexCylinderMesh_Internal(DM dm, DMBoundaryType periodicZ) 1455 { 1456 const PetscInt dim = 3; 1457 PetscInt numCells, numVertices; 1458 PetscMPIInt rank; 1459 PetscErrorCode ierr; 1460 1461 PetscFunctionBegin; 1462 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 1463 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 1464 /* Create topology */ 1465 { 1466 PetscInt cone[8], c; 1467 1468 numCells = rank == 0 ? 5 : 0; 1469 numVertices = rank == 0 ? 16 : 0; 1470 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1471 numCells *= 3; 1472 numVertices = rank == 0 ? 24 : 0; 1473 } 1474 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 1475 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(dm, c, 8);CHKERRQ(ierr);} 1476 ierr = DMSetUp(dm);CHKERRQ(ierr); 1477 if (rank == 0) { 1478 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1479 cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16; 1480 cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34; 1481 ierr = DMPlexSetCone(dm, 0, cone);CHKERRQ(ierr); 1482 cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23; 1483 cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */ 1484 ierr = DMPlexSetCone(dm, 1, cone);CHKERRQ(ierr); 1485 cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17; 1486 cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38; 1487 ierr = DMPlexSetCone(dm, 2, cone);CHKERRQ(ierr); 1488 cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15; 1489 cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38; 1490 ierr = DMPlexSetCone(dm, 3, cone);CHKERRQ(ierr); 1491 cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23; 1492 cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31; 1493 ierr = DMPlexSetCone(dm, 4, cone);CHKERRQ(ierr); 1494 1495 cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32; 1496 cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20; 1497 ierr = DMPlexSetCone(dm, 5, cone);CHKERRQ(ierr); 1498 cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36; 1499 cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21; 1500 ierr = DMPlexSetCone(dm, 6, cone);CHKERRQ(ierr); 1501 cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33; 1502 cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28; 1503 ierr = DMPlexSetCone(dm, 7, cone);CHKERRQ(ierr); 1504 cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31; 1505 cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28; 1506 ierr = DMPlexSetCone(dm, 8, cone);CHKERRQ(ierr); 1507 cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36; 1508 cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19; 1509 ierr = DMPlexSetCone(dm, 9, cone);CHKERRQ(ierr); 1510 1511 cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22; 1512 cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18; 1513 ierr = DMPlexSetCone(dm, 10, cone);CHKERRQ(ierr); 1514 cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25; 1515 cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17; 1516 ierr = DMPlexSetCone(dm, 11, cone);CHKERRQ(ierr); 1517 cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21; 1518 cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27; 1519 ierr = DMPlexSetCone(dm, 12, cone);CHKERRQ(ierr); 1520 cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19; 1521 cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27; 1522 ierr = DMPlexSetCone(dm, 13, cone);CHKERRQ(ierr); 1523 cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25; 1524 cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15; 1525 ierr = DMPlexSetCone(dm, 14, cone);CHKERRQ(ierr); 1526 } else { 1527 cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6; 1528 cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10; 1529 ierr = DMPlexSetCone(dm, 0, cone);CHKERRQ(ierr); 1530 cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13; 1531 cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11; 1532 ierr = DMPlexSetCone(dm, 1, cone);CHKERRQ(ierr); 1533 cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7; 1534 cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18; 1535 ierr = DMPlexSetCone(dm, 2, cone);CHKERRQ(ierr); 1536 cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5; 1537 cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18; 1538 ierr = DMPlexSetCone(dm, 3, cone);CHKERRQ(ierr); 1539 cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13; 1540 cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9; 1541 ierr = DMPlexSetCone(dm, 4, cone);CHKERRQ(ierr); 1542 } 1543 } 1544 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1545 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1546 } 1547 /* Create cube geometry */ 1548 { 1549 Vec coordinates; 1550 PetscSection coordSection; 1551 PetscScalar *coords; 1552 PetscInt coordSize, v; 1553 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1554 const PetscReal ds2 = dis/2.0; 1555 1556 /* Build coordinates */ 1557 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1558 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1559 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1560 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1561 for (v = numCells; v < numCells+numVertices; ++v) { 1562 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1563 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1564 } 1565 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1566 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1567 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1568 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1569 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1570 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1571 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1572 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1573 if (rank == 0) { 1574 coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0; 1575 coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0; 1576 coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0; 1577 coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0; 1578 coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0; 1579 coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0; 1580 coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0; 1581 coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0; 1582 coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0; 1583 coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0; 1584 coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0; 1585 coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0; 1586 coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0; 1587 coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0; 1588 coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0; 1589 coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0; 1590 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1591 /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5; 1592 /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5; 1593 /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5; 1594 /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5; 1595 /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5; 1596 /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5; 1597 /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5; 1598 /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5; 1599 } 1600 } 1601 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1602 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1603 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1604 } 1605 /* Create periodicity */ 1606 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1607 PetscReal L[3]; 1608 PetscReal maxCell[3]; 1609 DMBoundaryType bdType[3]; 1610 PetscReal lower[3] = {0.0, 0.0, 0.0}; 1611 PetscReal upper[3] = {1.0, 1.0, 1.5}; 1612 PetscInt i, numZCells = 3; 1613 1614 bdType[0] = DM_BOUNDARY_NONE; 1615 bdType[1] = DM_BOUNDARY_NONE; 1616 bdType[2] = periodicZ; 1617 for (i = 0; i < dim; i++) { 1618 L[i] = upper[i] - lower[i]; 1619 maxCell[i] = 1.1 * (L[i] / numZCells); 1620 } 1621 ierr = DMSetPeriodicity(dm, PETSC_TRUE, maxCell, L, bdType);CHKERRQ(ierr); 1622 } 1623 { 1624 DM cdm; 1625 PetscDS cds; 1626 PetscScalar c[2] = {1.0, 1.0}; 1627 1628 ierr = DMPlexCreateCoordinateSpace(dm, 1, snapToCylinder);CHKERRQ(ierr); 1629 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 1630 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 1631 ierr = PetscDSSetConstants(cds, 2, c);CHKERRQ(ierr); 1632 } 1633 /* Wait for coordinate creation before doing in-place modification */ 1634 ierr = DMPlexInterpolateInPlace_Internal(dm);CHKERRQ(ierr); 1635 PetscFunctionReturn(0); 1636 } 1637 1638 /*@ 1639 DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. 1640 1641 Collective 1642 1643 Input Parameters: 1644 + comm - The communicator for the DM object 1645 - periodicZ - The boundary type for the Z direction 1646 1647 Output Parameter: 1648 . dm - The DM object 1649 1650 Note: 1651 Here is the output numbering looking from the bottom of the cylinder: 1652 $ 17-----14 1653 $ | | 1654 $ | 2 | 1655 $ | | 1656 $ 17-----8-----7-----14 1657 $ | | | | 1658 $ | 3 | 0 | 1 | 1659 $ | | | | 1660 $ 19-----5-----6-----13 1661 $ | | 1662 $ | 4 | 1663 $ | | 1664 $ 19-----13 1665 $ 1666 $ and up through the top 1667 $ 1668 $ 18-----16 1669 $ | | 1670 $ | 2 | 1671 $ | | 1672 $ 18----10----11-----16 1673 $ | | | | 1674 $ | 3 | 0 | 1 | 1675 $ | | | | 1676 $ 20-----9----12-----15 1677 $ | | 1678 $ | 4 | 1679 $ | | 1680 $ 20-----15 1681 1682 Level: beginner 1683 1684 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1685 @*/ 1686 PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, DMBoundaryType periodicZ, DM *dm) 1687 { 1688 PetscErrorCode ierr; 1689 1690 PetscFunctionBegin; 1691 PetscValidPointer(dm, 3); 1692 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1693 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1694 ierr = DMPlexCreateHexCylinderMesh_Internal(*dm, periodicZ);CHKERRQ(ierr); 1695 PetscFunctionReturn(0); 1696 } 1697 1698 static PetscErrorCode DMPlexCreateWedgeCylinderMesh_Internal(DM dm, PetscInt n, PetscBool interpolate) 1699 { 1700 const PetscInt dim = 3; 1701 PetscInt numCells, numVertices, v; 1702 PetscMPIInt rank; 1703 PetscErrorCode ierr; 1704 1705 PetscFunctionBegin; 1706 PetscCheckFalse(n < 0,PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n); 1707 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 1708 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 1709 /* Must create the celltype label here so that we do not automatically try to compute the types */ 1710 ierr = DMCreateLabel(dm, "celltype");CHKERRQ(ierr); 1711 /* Create topology */ 1712 { 1713 PetscInt cone[6], c; 1714 1715 numCells = rank == 0 ? n : 0; 1716 numVertices = rank == 0 ? 2*(n+1) : 0; 1717 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 1718 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr);} 1719 ierr = DMSetUp(dm);CHKERRQ(ierr); 1720 for (c = 0; c < numCells; c++) { 1721 cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n; 1722 cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n; 1723 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 1724 ierr = DMPlexSetCellType(dm, c, DM_POLYTOPE_TRI_PRISM_TENSOR);CHKERRQ(ierr); 1725 } 1726 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1727 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1728 } 1729 for (v = numCells; v < numCells+numVertices; ++v) { 1730 ierr = DMPlexSetCellType(dm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr); 1731 } 1732 /* Create cylinder geometry */ 1733 { 1734 Vec coordinates; 1735 PetscSection coordSection; 1736 PetscScalar *coords; 1737 PetscInt coordSize, c; 1738 1739 /* Build coordinates */ 1740 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1741 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1742 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1743 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1744 for (v = numCells; v < numCells+numVertices; ++v) { 1745 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1746 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1747 } 1748 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1749 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1750 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1751 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1752 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1753 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1754 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1755 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1756 for (c = 0; c < numCells; c++) { 1757 coords[(c+0*n)*dim+0] = PetscCosReal(2.0*c*PETSC_PI/n); coords[(c+0*n)*dim+1] = PetscSinReal(2.0*c*PETSC_PI/n); coords[(c+0*n)*dim+2] = 1.0; 1758 coords[(c+1*n)*dim+0] = PetscCosReal(2.0*c*PETSC_PI/n); coords[(c+1*n)*dim+1] = PetscSinReal(2.0*c*PETSC_PI/n); coords[(c+1*n)*dim+2] = 0.0; 1759 } 1760 if (rank == 0) { 1761 coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0; 1762 coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0; 1763 } 1764 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1765 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1766 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1767 } 1768 /* Interpolate */ 1769 if (interpolate) {ierr = DMPlexInterpolateInPlace_Internal(dm);CHKERRQ(ierr);} 1770 PetscFunctionReturn(0); 1771 } 1772 1773 /*@ 1774 DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges. 1775 1776 Collective 1777 1778 Input Parameters: 1779 + comm - The communicator for the DM object 1780 . n - The number of wedges around the origin 1781 - interpolate - Create edges and faces 1782 1783 Output Parameter: 1784 . dm - The DM object 1785 1786 Level: beginner 1787 1788 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1789 @*/ 1790 PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm) 1791 { 1792 PetscErrorCode ierr; 1793 1794 PetscFunctionBegin; 1795 PetscValidPointer(dm, 4); 1796 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1797 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1798 ierr = DMPlexCreateWedgeCylinderMesh_Internal(*dm, n, interpolate);CHKERRQ(ierr); 1799 PetscFunctionReturn(0); 1800 } 1801 1802 static inline PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1803 { 1804 PetscReal prod = 0.0; 1805 PetscInt i; 1806 for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]); 1807 return PetscSqrtReal(prod); 1808 } 1809 static inline PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1810 { 1811 PetscReal prod = 0.0; 1812 PetscInt i; 1813 for (i = 0; i < dim; ++i) prod += x[i]*y[i]; 1814 return prod; 1815 } 1816 1817 /* The first constant is the sphere radius */ 1818 static void snapToSphere(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1819 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1820 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1821 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 1822 { 1823 PetscReal r = PetscRealPart(constants[0]); 1824 PetscReal norm2 = 0.0, fac; 1825 PetscInt n = uOff[1] - uOff[0], d; 1826 1827 for (d = 0; d < n; ++d) norm2 += PetscSqr(PetscRealPart(u[d])); 1828 fac = r/PetscSqrtReal(norm2); 1829 for (d = 0; d < n; ++d) f0[d] = u[d]*fac; 1830 } 1831 1832 static PetscErrorCode DMPlexCreateSphereMesh_Internal(DM dm, PetscInt dim, PetscBool simplex, PetscReal R) 1833 { 1834 const PetscInt embedDim = dim+1; 1835 PetscSection coordSection; 1836 Vec coordinates; 1837 PetscScalar *coords; 1838 PetscReal *coordsIn; 1839 PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e; 1840 PetscMPIInt rank; 1841 PetscErrorCode ierr; 1842 1843 PetscFunctionBegin; 1844 PetscValidLogicalCollectiveBool(dm, simplex, 3); 1845 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 1846 ierr = DMSetCoordinateDim(dm, dim+1);CHKERRQ(ierr); 1847 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 1848 switch (dim) { 1849 case 2: 1850 if (simplex) { 1851 const PetscReal radius = PetscSqrtReal(1 + PETSC_PHI*PETSC_PHI)/(1.0 + PETSC_PHI); 1852 const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI) * (R/radius); 1853 const PetscInt degree = 5; 1854 PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)}; 1855 PetscInt s[3] = {1, 1, 1}; 1856 PetscInt cone[3]; 1857 PetscInt *graph, p, i, j, k; 1858 1859 vertex[0] *= R/radius; vertex[1] *= R/radius; vertex[2] *= R/radius; 1860 numCells = rank == 0 ? 20 : 0; 1861 numVerts = rank == 0 ? 12 : 0; 1862 firstVertex = numCells; 1863 /* Use icosahedron, which for a R-sphere has coordinates which are all cyclic permutations of 1864 1865 (0, \pm 1/\phi+1, \pm \phi/\phi+1) 1866 1867 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 1868 length is then given by 2/(1+\phi) = 2 * 0.38197 = 0.76393. 1869 */ 1870 /* Construct vertices */ 1871 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 1872 if (rank == 0) { 1873 for (p = 0, i = 0; p < embedDim; ++p) { 1874 for (s[1] = -1; s[1] < 2; s[1] += 2) { 1875 for (s[2] = -1; s[2] < 2; s[2] += 2) { 1876 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim]; 1877 ++i; 1878 } 1879 } 1880 } 1881 } 1882 /* Construct graph */ 1883 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 1884 for (i = 0; i < numVerts; ++i) { 1885 for (j = 0, k = 0; j < numVerts; ++j) { 1886 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 1887 } 1888 PetscCheckFalse(k != degree,PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree); 1889 } 1890 /* Build Topology */ 1891 ierr = DMPlexSetChart(dm, 0, numCells+numVerts);CHKERRQ(ierr); 1892 for (c = 0; c < numCells; c++) { 1893 ierr = DMPlexSetConeSize(dm, c, embedDim);CHKERRQ(ierr); 1894 } 1895 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 1896 /* Cells */ 1897 for (i = 0, c = 0; i < numVerts; ++i) { 1898 for (j = 0; j < i; ++j) { 1899 for (k = 0; k < j; ++k) { 1900 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) { 1901 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; 1902 /* Check orientation */ 1903 { 1904 const PetscInt epsilon[3][3][3] = {{{0, 0, 0}, {0, 0, 1}, {0, -1, 0}}, {{0, 0, -1}, {0, 0, 0}, {1, 0, 0}}, {{0, 1, 0}, {-1, 0, 0}, {0, 0, 0}}}; 1905 PetscReal normal[3]; 1906 PetscInt e, f; 1907 1908 for (d = 0; d < embedDim; ++d) { 1909 normal[d] = 0.0; 1910 for (e = 0; e < embedDim; ++e) { 1911 for (f = 0; f < embedDim; ++f) { 1912 normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]); 1913 } 1914 } 1915 } 1916 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 1917 } 1918 ierr = DMPlexSetCone(dm, c++, cone);CHKERRQ(ierr); 1919 } 1920 } 1921 } 1922 } 1923 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1924 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1925 ierr = PetscFree(graph);CHKERRQ(ierr); 1926 } else { 1927 /* 1928 12-21--13 1929 | | 1930 25 4 24 1931 | | 1932 12-25--9-16--8-24--13 1933 | | | | 1934 23 5 17 0 15 3 22 1935 | | | | 1936 10-20--6-14--7-19--11 1937 | | 1938 20 1 19 1939 | | 1940 10-18--11 1941 | | 1942 23 2 22 1943 | | 1944 12-21--13 1945 */ 1946 PetscInt cone[4], ornt[4]; 1947 1948 numCells = rank == 0 ? 6 : 0; 1949 numEdges = rank == 0 ? 12 : 0; 1950 numVerts = rank == 0 ? 8 : 0; 1951 firstVertex = numCells; 1952 firstEdge = numCells + numVerts; 1953 /* Build Topology */ 1954 ierr = DMPlexSetChart(dm, 0, numCells+numEdges+numVerts);CHKERRQ(ierr); 1955 for (c = 0; c < numCells; c++) { 1956 ierr = DMPlexSetConeSize(dm, c, 4);CHKERRQ(ierr); 1957 } 1958 for (e = firstEdge; e < firstEdge+numEdges; ++e) { 1959 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 1960 } 1961 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 1962 if (rank == 0) { 1963 /* Cell 0 */ 1964 cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17; 1965 ierr = DMPlexSetCone(dm, 0, cone);CHKERRQ(ierr); 1966 ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0; 1967 ierr = DMPlexSetConeOrientation(dm, 0, ornt);CHKERRQ(ierr); 1968 /* Cell 1 */ 1969 cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20; 1970 ierr = DMPlexSetCone(dm, 1, cone);CHKERRQ(ierr); 1971 ornt[0] = 0; ornt[1] = 0; ornt[2] = -1; ornt[3] = 0; 1972 ierr = DMPlexSetConeOrientation(dm, 1, ornt);CHKERRQ(ierr); 1973 /* Cell 2 */ 1974 cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23; 1975 ierr = DMPlexSetCone(dm, 2, cone);CHKERRQ(ierr); 1976 ornt[0] = 0; ornt[1] = 0; ornt[2] = -1; ornt[3] = 0; 1977 ierr = DMPlexSetConeOrientation(dm, 2, ornt);CHKERRQ(ierr); 1978 /* Cell 3 */ 1979 cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15; 1980 ierr = DMPlexSetCone(dm, 3, cone);CHKERRQ(ierr); 1981 ornt[0] = -1; ornt[1] = -1; ornt[2] = 0; ornt[3] = -1; 1982 ierr = DMPlexSetConeOrientation(dm, 3, ornt);CHKERRQ(ierr); 1983 /* Cell 4 */ 1984 cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25; 1985 ierr = DMPlexSetCone(dm, 4, cone);CHKERRQ(ierr); 1986 ornt[0] = -1; ornt[1] = -1; ornt[2] = -1; ornt[3] = 0; 1987 ierr = DMPlexSetConeOrientation(dm, 4, ornt);CHKERRQ(ierr); 1988 /* Cell 5 */ 1989 cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23; 1990 ierr = DMPlexSetCone(dm, 5, cone);CHKERRQ(ierr); 1991 ornt[0] = -1; ornt[1] = -1; ornt[2] = -1; ornt[3] = -1; 1992 ierr = DMPlexSetConeOrientation(dm, 5, ornt);CHKERRQ(ierr); 1993 /* Edges */ 1994 cone[0] = 6; cone[1] = 7; 1995 ierr = DMPlexSetCone(dm, 14, cone);CHKERRQ(ierr); 1996 cone[0] = 7; cone[1] = 8; 1997 ierr = DMPlexSetCone(dm, 15, cone);CHKERRQ(ierr); 1998 cone[0] = 8; cone[1] = 9; 1999 ierr = DMPlexSetCone(dm, 16, cone);CHKERRQ(ierr); 2000 cone[0] = 9; cone[1] = 6; 2001 ierr = DMPlexSetCone(dm, 17, cone);CHKERRQ(ierr); 2002 cone[0] = 10; cone[1] = 11; 2003 ierr = DMPlexSetCone(dm, 18, cone);CHKERRQ(ierr); 2004 cone[0] = 11; cone[1] = 7; 2005 ierr = DMPlexSetCone(dm, 19, cone);CHKERRQ(ierr); 2006 cone[0] = 6; cone[1] = 10; 2007 ierr = DMPlexSetCone(dm, 20, cone);CHKERRQ(ierr); 2008 cone[0] = 12; cone[1] = 13; 2009 ierr = DMPlexSetCone(dm, 21, cone);CHKERRQ(ierr); 2010 cone[0] = 13; cone[1] = 11; 2011 ierr = DMPlexSetCone(dm, 22, cone);CHKERRQ(ierr); 2012 cone[0] = 10; cone[1] = 12; 2013 ierr = DMPlexSetCone(dm, 23, cone);CHKERRQ(ierr); 2014 cone[0] = 13; cone[1] = 8; 2015 ierr = DMPlexSetCone(dm, 24, cone);CHKERRQ(ierr); 2016 cone[0] = 12; cone[1] = 9; 2017 ierr = DMPlexSetCone(dm, 25, cone);CHKERRQ(ierr); 2018 } 2019 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2020 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2021 /* Build coordinates */ 2022 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 2023 if (rank == 0) { 2024 coordsIn[0*embedDim+0] = -R; coordsIn[0*embedDim+1] = R; coordsIn[0*embedDim+2] = -R; 2025 coordsIn[1*embedDim+0] = R; coordsIn[1*embedDim+1] = R; coordsIn[1*embedDim+2] = -R; 2026 coordsIn[2*embedDim+0] = R; coordsIn[2*embedDim+1] = -R; coordsIn[2*embedDim+2] = -R; 2027 coordsIn[3*embedDim+0] = -R; coordsIn[3*embedDim+1] = -R; coordsIn[3*embedDim+2] = -R; 2028 coordsIn[4*embedDim+0] = -R; coordsIn[4*embedDim+1] = R; coordsIn[4*embedDim+2] = R; 2029 coordsIn[5*embedDim+0] = R; coordsIn[5*embedDim+1] = R; coordsIn[5*embedDim+2] = R; 2030 coordsIn[6*embedDim+0] = -R; coordsIn[6*embedDim+1] = -R; coordsIn[6*embedDim+2] = R; 2031 coordsIn[7*embedDim+0] = R; coordsIn[7*embedDim+1] = -R; coordsIn[7*embedDim+2] = R; 2032 } 2033 } 2034 break; 2035 case 3: 2036 if (simplex) { 2037 const PetscReal edgeLen = 1.0/PETSC_PHI; 2038 PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5}; 2039 PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0}; 2040 PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0}; 2041 const PetscInt degree = 12; 2042 PetscInt s[4] = {1, 1, 1}; 2043 PetscInt evenPerm[12][4] = {{0, 1, 2, 3}, {0, 2, 3, 1}, {0, 3, 1, 2}, {1, 0, 3, 2}, {1, 2, 0, 3}, {1, 3, 2, 0}, 2044 {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}}; 2045 PetscInt cone[4]; 2046 PetscInt *graph, p, i, j, k, l; 2047 2048 vertexA[0] *= R; vertexA[1] *= R; vertexA[2] *= R; vertexA[3] *= R; 2049 vertexB[0] *= R; vertexB[1] *= R; vertexB[2] *= R; vertexB[3] *= R; 2050 vertexC[0] *= R; vertexC[1] *= R; vertexC[2] *= R; vertexC[3] *= R; 2051 numCells = rank == 0 ? 600 : 0; 2052 numVerts = rank == 0 ? 120 : 0; 2053 firstVertex = numCells; 2054 /* Use the 600-cell, which for a unit sphere has coordinates which are 2055 2056 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16 2057 (\pm 1, 0, 0, 0) all cyclic permutations 8 2058 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96 2059 2060 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 2061 length is then given by 1/\phi = 0.61803. 2062 2063 http://buzzard.pugetsound.edu/sage-practice/ch03s03.html 2064 http://mathworld.wolfram.com/600-Cell.html 2065 */ 2066 /* Construct vertices */ 2067 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 2068 i = 0; 2069 if (rank == 0) { 2070 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2071 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2072 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2073 for (s[3] = -1; s[3] < 2; s[3] += 2) { 2074 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d]; 2075 ++i; 2076 } 2077 } 2078 } 2079 } 2080 for (p = 0; p < embedDim; ++p) { 2081 s[1] = s[2] = s[3] = 1; 2082 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2083 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim]; 2084 ++i; 2085 } 2086 } 2087 for (p = 0; p < 12; ++p) { 2088 s[3] = 1; 2089 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2090 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2091 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2092 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]]; 2093 ++i; 2094 } 2095 } 2096 } 2097 } 2098 } 2099 PetscCheckFalse(i != numVerts,PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts); 2100 /* Construct graph */ 2101 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 2102 for (i = 0; i < numVerts; ++i) { 2103 for (j = 0, k = 0; j < numVerts; ++j) { 2104 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 2105 } 2106 PetscCheckFalse(k != degree,PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree); 2107 } 2108 /* Build Topology */ 2109 ierr = DMPlexSetChart(dm, 0, numCells+numVerts);CHKERRQ(ierr); 2110 for (c = 0; c < numCells; c++) { 2111 ierr = DMPlexSetConeSize(dm, c, embedDim);CHKERRQ(ierr); 2112 } 2113 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 2114 /* Cells */ 2115 if (rank == 0) { 2116 for (i = 0, c = 0; i < numVerts; ++i) { 2117 for (j = 0; j < i; ++j) { 2118 for (k = 0; k < j; ++k) { 2119 for (l = 0; l < k; ++l) { 2120 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] && 2121 graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) { 2122 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l; 2123 /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */ 2124 { 2125 const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2126 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}}, 2127 {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}}, 2128 {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}}, 2129 2130 {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}}, 2131 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2132 {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}}, 2133 {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}}, 2134 2135 {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}}, 2136 {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}}, 2137 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2138 {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}, 2139 2140 {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}}, 2141 {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}}, 2142 {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2143 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}}; 2144 PetscReal normal[4]; 2145 PetscInt e, f, g; 2146 2147 for (d = 0; d < embedDim; ++d) { 2148 normal[d] = 0.0; 2149 for (e = 0; e < embedDim; ++e) { 2150 for (f = 0; f < embedDim; ++f) { 2151 for (g = 0; g < embedDim; ++g) { 2152 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]); 2153 } 2154 } 2155 } 2156 } 2157 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 2158 } 2159 ierr = DMPlexSetCone(dm, c++, cone);CHKERRQ(ierr); 2160 } 2161 } 2162 } 2163 } 2164 } 2165 } 2166 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2167 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2168 ierr = PetscFree(graph);CHKERRQ(ierr); 2169 break; 2170 } 2171 default: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim); 2172 } 2173 /* Create coordinates */ 2174 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2175 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2176 ierr = PetscSectionSetFieldComponents(coordSection, 0, embedDim);CHKERRQ(ierr); 2177 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);CHKERRQ(ierr); 2178 for (v = firstVertex; v < firstVertex+numVerts; ++v) { 2179 ierr = PetscSectionSetDof(coordSection, v, embedDim);CHKERRQ(ierr); 2180 ierr = PetscSectionSetFieldDof(coordSection, v, 0, embedDim);CHKERRQ(ierr); 2181 } 2182 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2183 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2184 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 2185 ierr = VecSetBlockSize(coordinates, embedDim);CHKERRQ(ierr); 2186 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2187 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2188 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2189 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2190 for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];} 2191 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2192 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2193 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2194 ierr = PetscFree(coordsIn);CHKERRQ(ierr); 2195 { 2196 DM cdm; 2197 PetscDS cds; 2198 PetscScalar c = R; 2199 2200 ierr = DMPlexCreateCoordinateSpace(dm, 1, snapToSphere);CHKERRQ(ierr); 2201 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 2202 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 2203 ierr = PetscDSSetConstants(cds, 1, &c);CHKERRQ(ierr); 2204 } 2205 /* Wait for coordinate creation before doing in-place modification */ 2206 if (simplex) {ierr = DMPlexInterpolateInPlace_Internal(dm);CHKERRQ(ierr);} 2207 PetscFunctionReturn(0); 2208 } 2209 2210 typedef void (*TPSEvaluateFunc)(const PetscReal[], PetscReal*, PetscReal[], PetscReal(*)[3]); 2211 2212 /* 2213 The Schwarz P implicit surface is 2214 2215 f(x) = cos(x0) + cos(x1) + cos(x2) = 0 2216 */ 2217 static void TPSEvaluate_SchwarzP(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3]) 2218 { 2219 PetscReal c[3] = {PetscCosReal(y[0] * PETSC_PI), PetscCosReal(y[1] * PETSC_PI), PetscCosReal(y[2] * PETSC_PI)}; 2220 PetscReal g[3] = {-PetscSinReal(y[0] * PETSC_PI), -PetscSinReal(y[1] * PETSC_PI), -PetscSinReal(y[2] * PETSC_PI)}; 2221 f[0] = c[0] + c[1] + c[2]; 2222 for (PetscInt i=0; i<3; i++) { 2223 grad[i] = PETSC_PI * g[i]; 2224 for (PetscInt j=0; j<3; j++) { 2225 hess[i][j] = (i == j) ? -PetscSqr(PETSC_PI) * c[i] : 0.; 2226 } 2227 } 2228 } 2229 2230 /* 2231 The Gyroid implicit surface is 2232 2233 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) 2234 2235 */ 2236 static void TPSEvaluate_Gyroid(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3]) 2237 { 2238 PetscReal s[3] = {PetscSinReal(PETSC_PI * y[0]), PetscSinReal(PETSC_PI * (y[1] + .5)), PetscSinReal(PETSC_PI * (y[2] + .25))}; 2239 PetscReal c[3] = {PetscCosReal(PETSC_PI * y[0]), PetscCosReal(PETSC_PI * (y[1] + .5)), PetscCosReal(PETSC_PI * (y[2] + .25))}; 2240 f[0] = s[0] * c[1] + s[1] * c[2] + s[2] * c[0]; 2241 grad[0] = PETSC_PI * (c[0] * c[1] - s[2] * s[0]); 2242 grad[1] = PETSC_PI * (c[1] * c[2] - s[0] * s[1]); 2243 grad[2] = PETSC_PI * (c[2] * c[0] - s[1] * s[2]); 2244 hess[0][0] = -PetscSqr(PETSC_PI) * (s[0] * c[1] + s[2] * c[0]); 2245 hess[0][1] = -PetscSqr(PETSC_PI) * (c[0] * s[1]); 2246 hess[0][2] = -PetscSqr(PETSC_PI) * (c[2] * s[0]); 2247 hess[1][0] = -PetscSqr(PETSC_PI) * (s[1] * c[2] + s[0] * c[1]); 2248 hess[1][1] = -PetscSqr(PETSC_PI) * (c[1] * s[2]); 2249 hess[2][2] = -PetscSqr(PETSC_PI) * (c[0] * s[1]); 2250 hess[2][0] = -PetscSqr(PETSC_PI) * (s[2] * c[0] + s[1] * c[2]); 2251 hess[2][1] = -PetscSqr(PETSC_PI) * (c[2] * s[0]); 2252 hess[2][2] = -PetscSqr(PETSC_PI) * (c[1] * s[2]); 2253 } 2254 2255 /* 2256 We wish to solve 2257 2258 min_y || y - x ||^2 subject to f(y) = 0 2259 2260 Let g(y) = grad(f). The minimization problem is equivalent to asking to satisfy 2261 f(y) = 0 and (y-x) is parallel to g(y). We do this by using Householder QR to obtain a basis for the 2262 tangent space and ask for both components in the tangent space to be zero. 2263 2264 Take g to be a column vector and compute the "full QR" factorization Q R = g, 2265 where Q = I - 2 n n^T is a symmetric orthogonal matrix. 2266 The first column of Q is parallel to g so the remaining two columns span the null space. 2267 Let Qn = Q[:,1:] be those remaining columns. Then Qn Qn^T is an orthogonal projector into the tangent space. 2268 Since Q is symmetric, this is equivalent to multipyling by Q and taking the last two entries. 2269 In total, we have a system of 3 equations in 3 unknowns: 2270 2271 f(y) = 0 1 equation 2272 Qn^T (y - x) = 0 2 equations 2273 2274 Here, we compute the residual and Jacobian of this system. 2275 */ 2276 static void TPSNearestPointResJac(TPSEvaluateFunc feval, const PetscScalar x[], const PetscScalar y[], PetscScalar res[], PetscScalar J[]) 2277 { 2278 PetscReal yreal[3] = {PetscRealPart(y[0]), PetscRealPart(y[1]), PetscRealPart(y[2])}; 2279 PetscReal d[3] = {PetscRealPart(y[0] - x[0]), PetscRealPart(y[1] - x[1]), PetscRealPart(y[2] - x[2])}; 2280 PetscReal f, grad[3], n[3], n_y[3][3], norm, norm_y[3], nd, nd_y[3], sign; 2281 2282 feval(yreal, &f, grad, n_y); 2283 2284 for (PetscInt i=0; i<3; i++) n[i] = grad[i]; 2285 norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2])); 2286 for (PetscInt i=0; i<3; i++) { 2287 norm_y[i] = 1. / norm * n[i] * n_y[i][i]; 2288 } 2289 2290 // Define the Householder reflector 2291 sign = n[0] >= 0 ? 1. : -1.; 2292 n[0] += norm * sign; 2293 for (PetscInt i=0; i<3; i++) n_y[0][i] += norm_y[i] * sign; 2294 2295 norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2])); 2296 norm_y[0] = 1. / norm * (n[0] * n_y[0][0]); 2297 norm_y[1] = 1. / norm * (n[0] * n_y[0][1] + n[1] * n_y[1][1]); 2298 norm_y[2] = 1. / norm * (n[0] * n_y[0][2] + n[2] * n_y[2][2]); 2299 2300 for (PetscInt i=0; i<3; i++) { 2301 n[i] /= norm; 2302 for (PetscInt j=0; j<3; j++) { 2303 // note that n[i] is n_old[i]/norm when executing the code below 2304 n_y[i][j] = n_y[i][j] / norm - n[i] / norm * norm_y[j]; 2305 } 2306 } 2307 2308 nd = n[0] * d[0] + n[1] * d[1] + n[2] * d[2]; 2309 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]; 2310 2311 res[0] = f; 2312 res[1] = d[1] - 2 * n[1] * nd; 2313 res[2] = d[2] - 2 * n[2] * nd; 2314 // J[j][i] is J_{ij} (column major) 2315 for (PetscInt j=0; j<3; j++) { 2316 J[0 + j*3] = grad[j]; 2317 J[1 + j*3] = (j == 1)*1. - 2 * (n_y[1][j] * nd + n[1] * nd_y[j]); 2318 J[2 + j*3] = (j == 2)*1. - 2 * (n_y[2][j] * nd + n[2] * nd_y[j]); 2319 } 2320 } 2321 2322 /* 2323 Project x to the nearest point on the implicit surface using Newton's method. 2324 */ 2325 static PetscErrorCode TPSNearestPoint(TPSEvaluateFunc feval, PetscScalar x[]) 2326 { 2327 PetscScalar y[3] = {x[0], x[1], x[2]}; // Initial guess 2328 PetscErrorCode ierr; 2329 2330 PetscFunctionBegin; 2331 for (PetscInt iter=0; iter<10; iter++) { 2332 PetscScalar res[3], J[9]; 2333 PetscReal resnorm; 2334 TPSNearestPointResJac(feval, x, y, res, J); 2335 resnorm = PetscSqrtReal(PetscSqr(PetscRealPart(res[0])) + PetscSqr(PetscRealPart(res[1])) + PetscSqr(PetscRealPart(res[2]))); 2336 if (0) { // Turn on this monitor if you need to confirm quadratic convergence 2337 ierr = PetscPrintf(PETSC_COMM_SELF, "[%D] res [%g %g %g]\n", iter, PetscRealPart(res[0]), PetscRealPart(res[1]), PetscRealPart(res[2]));CHKERRQ(ierr); 2338 } 2339 if (resnorm < PETSC_SMALL) break; 2340 2341 // Take the Newton step 2342 ierr = PetscKernel_A_gets_inverse_A_3(J, 0., PETSC_FALSE, NULL);CHKERRQ(ierr); 2343 PetscKernel_v_gets_v_minus_A_times_w_3(y, J, res); 2344 } 2345 for (PetscInt i=0; i<3; i++) x[i] = y[i]; 2346 PetscFunctionReturn(0); 2347 } 2348 2349 const char *const DMPlexTPSTypes[] = {"SCHWARZ_P", "GYROID", "DMPlexTPSType", "DMPLEX_TPS_", NULL}; 2350 2351 static PetscErrorCode DMPlexCreateTPSMesh_Internal(DM dm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscBool tps_distribute, PetscInt refinements, PetscInt layers, PetscReal thickness) 2352 { 2353 PetscErrorCode ierr; 2354 PetscMPIInt rank; 2355 PetscInt topoDim = 2, spaceDim = 3, numFaces = 0, numVertices = 0, numEdges = 0; 2356 PetscInt (*edges)[2] = NULL, *edgeSets = NULL; 2357 PetscInt *cells_flat = NULL; 2358 PetscReal *vtxCoords = NULL; 2359 TPSEvaluateFunc evalFunc = NULL; 2360 DMLabel label; 2361 2362 PetscFunctionBegin; 2363 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRMPI(ierr); 2364 PetscCheck((layers != 0) ^ (thickness == 0.), PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_INCOMP, "Layers %D must be nonzero iff thickness %g is nonzero", layers, (double)thickness); 2365 switch (tpstype) { 2366 case DMPLEX_TPS_SCHWARZ_P: 2367 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"); 2368 if (!rank) { 2369 PetscInt (*cells)[6][4][4] = NULL; // [junction, junction-face, cell, conn] 2370 PetscInt Njunctions = 0, Ncuts = 0, Npipes[3], vcount; 2371 PetscReal L = 1; 2372 2373 Npipes[0] = (extent[0] + 1) * extent[1] * extent[2]; 2374 Npipes[1] = extent[0] * (extent[1] + 1) * extent[2]; 2375 Npipes[2] = extent[0] * extent[1] * (extent[2] + 1); 2376 Njunctions = extent[0] * extent[1] * extent[2]; 2377 Ncuts = 2 * (extent[0] * extent[1] + extent[1] * extent[2] + extent[2] * extent[0]); 2378 numVertices = 4 * (Npipes[0] + Npipes[1] + Npipes[2]) + 8 * Njunctions; 2379 ierr = PetscMalloc1(3*numVertices, &vtxCoords);CHKERRQ(ierr); 2380 ierr = PetscMalloc1(Njunctions, &cells);CHKERRQ(ierr); 2381 ierr = PetscMalloc1(Ncuts*4, &edges);CHKERRQ(ierr); 2382 ierr = PetscMalloc1(Ncuts*4, &edgeSets);CHKERRQ(ierr); 2383 // x-normal pipes 2384 vcount = 0; 2385 for (PetscInt i=0; i<extent[0]+1; i++) { 2386 for (PetscInt j=0; j<extent[1]; j++) { 2387 for (PetscInt k=0; k<extent[2]; k++) { 2388 for (PetscInt l=0; l<4; l++) { 2389 vtxCoords[vcount++] = (2*i - 1) * L; 2390 vtxCoords[vcount++] = 2 * j * L + PetscCosReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2391 vtxCoords[vcount++] = 2 * k * L + PetscSinReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2392 } 2393 } 2394 } 2395 } 2396 // y-normal pipes 2397 for (PetscInt i=0; i<extent[0]; i++) { 2398 for (PetscInt j=0; j<extent[1]+1; j++) { 2399 for (PetscInt k=0; k<extent[2]; k++) { 2400 for (PetscInt l=0; l<4; l++) { 2401 vtxCoords[vcount++] = 2 * i * L + PetscSinReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2402 vtxCoords[vcount++] = (2*j - 1) * L; 2403 vtxCoords[vcount++] = 2 * k * L + PetscCosReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2404 } 2405 } 2406 } 2407 } 2408 // z-normal pipes 2409 for (PetscInt i=0; i<extent[0]; i++) { 2410 for (PetscInt j=0; j<extent[1]; j++) { 2411 for (PetscInt k=0; k<extent[2]+1; k++) { 2412 for (PetscInt l=0; l<4; l++) { 2413 vtxCoords[vcount++] = 2 * i * L + PetscCosReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2414 vtxCoords[vcount++] = 2 * j * L + PetscSinReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2415 vtxCoords[vcount++] = (2*k - 1) * L; 2416 } 2417 } 2418 } 2419 } 2420 // junctions 2421 for (PetscInt i=0; i<extent[0]; i++) { 2422 for (PetscInt j=0; j<extent[1]; j++) { 2423 for (PetscInt k=0; k<extent[2]; k++) { 2424 const PetscInt J = (i*extent[1] + j)*extent[2] + k, Jvoff = (Npipes[0] + Npipes[1] + Npipes[2])*4 + J*8; 2425 PetscCheck(vcount / 3 == Jvoff, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unexpected vertex count"); 2426 for (PetscInt ii=0; ii<2; ii++) { 2427 for (PetscInt jj=0; jj<2; jj++) { 2428 for (PetscInt kk=0; kk<2; kk++) { 2429 double Ls = (1 - sqrt(2) / 4) * L; 2430 vtxCoords[vcount++] = 2*i*L + (2*ii-1) * Ls; 2431 vtxCoords[vcount++] = 2*j*L + (2*jj-1) * Ls; 2432 vtxCoords[vcount++] = 2*k*L + (2*kk-1) * Ls; 2433 } 2434 } 2435 } 2436 const PetscInt jfaces[3][2][4] = { 2437 {{3,1,0,2}, {7,5,4,6}}, // x-aligned 2438 {{5,4,0,1}, {7,6,2,3}}, // y-aligned 2439 {{6,2,0,4}, {7,3,1,5}} // z-aligned 2440 }; 2441 const PetscInt pipe_lo[3] = { // vertex numbers of pipes 2442 ((i * extent[1] + j) * extent[2] + k)*4, 2443 ((i * (extent[1] + 1) + j) * extent[2] + k + Npipes[0])*4, 2444 ((i * extent[1] + j) * (extent[2]+1) + k + Npipes[0] + Npipes[1])*4 2445 }; 2446 const PetscInt pipe_hi[3] = { // vertex numbers of pipes 2447 (((i + 1) * extent[1] + j) * extent[2] + k)*4, 2448 ((i * (extent[1] + 1) + j + 1) * extent[2] + k + Npipes[0])*4, 2449 ((i * extent[1] + j) * (extent[2]+1) + k + 1 + Npipes[0] + Npipes[1])*4 2450 }; 2451 for (PetscInt dir=0; dir<3; dir++) { // x,y,z 2452 const PetscInt ijk[3] = {i, j, k}; 2453 for (PetscInt l=0; l<4; l++) { // rotations 2454 cells[J][dir*2+0][l][0] = pipe_lo[dir] + l; 2455 cells[J][dir*2+0][l][1] = Jvoff + jfaces[dir][0][l]; 2456 cells[J][dir*2+0][l][2] = Jvoff + jfaces[dir][0][(l-1+4)%4]; 2457 cells[J][dir*2+0][l][3] = pipe_lo[dir] + (l-1+4)%4; 2458 cells[J][dir*2+1][l][0] = Jvoff + jfaces[dir][1][l]; 2459 cells[J][dir*2+1][l][1] = pipe_hi[dir] + l; 2460 cells[J][dir*2+1][l][2] = pipe_hi[dir] + (l-1+4)%4; 2461 cells[J][dir*2+1][l][3] = Jvoff + jfaces[dir][1][(l-1+4)%4]; 2462 if (ijk[dir] == 0) { 2463 edges[numEdges][0] = pipe_lo[dir] + l; 2464 edges[numEdges][1] = pipe_lo[dir] + (l+1) % 4; 2465 edgeSets[numEdges] = dir*2 + 1; 2466 numEdges++; 2467 } 2468 if (ijk[dir] + 1 == extent[dir]) { 2469 edges[numEdges][0] = pipe_hi[dir] + l; 2470 edges[numEdges][1] = pipe_hi[dir] + (l+1) % 4; 2471 edgeSets[numEdges] = dir*2 + 2; 2472 numEdges++; 2473 } 2474 } 2475 } 2476 } 2477 } 2478 } 2479 PetscCheck(numEdges == Ncuts * 4, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Edge count %D incompatible with number of cuts %D", numEdges, Ncuts); 2480 numFaces = 24 * Njunctions; 2481 cells_flat = cells[0][0][0]; 2482 } 2483 evalFunc = TPSEvaluate_SchwarzP; 2484 break; 2485 case DMPLEX_TPS_GYROID: 2486 if (!rank) { 2487 // This is a coarse mesh approximation of the gyroid shifted to being the zero of the level set 2488 // 2489 // 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) 2490 // 2491 // on the cell [0,2]^3. 2492 // 2493 // Think about dividing that cell into four columns, and focus on the column [0,1]x[0,1]x[0,2]. 2494 // If you looked at the gyroid in that column at different slices of z you would see that it kind of spins 2495 // like a boomerang: 2496 // 2497 // z = 0 z = 1/4 z = 1/2 z = 3/4 // 2498 // ----- ------- ------- ------- // 2499 // // 2500 // + + + + + + + \ + // 2501 // \ / \ // 2502 // \ `-_ _-' / } // 2503 // *-_ `-' _-' / // 2504 // + `-+ + + +-' + + / + // 2505 // // 2506 // // 2507 // z = 1 z = 5/4 z = 3/2 z = 7/4 // 2508 // ----- ------- ------- ------- // 2509 // // 2510 // +-_ + + + + _-+ + / + // 2511 // `-_ _-_ _-` / // 2512 // \ _-' `-_ / { // 2513 // \ / \ // 2514 // + + + + + + + \ + // 2515 // 2516 // 2517 // This course mesh approximates each of these slices by two line segments, 2518 // and then connects the segments in consecutive layers with quadrilateral faces. 2519 // All of the end points of the segments are multiples of 1/4 except for the 2520 // point * in the picture for z = 0 above and the similar points in other layers. 2521 // That point is at (gamma, gamma, 0), where gamma is calculated below. 2522 // 2523 // The column [1,2]x[1,2]x[0,2] looks the same as this column; 2524 // The columns [1,2]x[0,1]x[0,2] and [0,1]x[1,2]x[0,2] are mirror images. 2525 // 2526 // As for how this method turned into the names given to the vertices: 2527 // that was not systematic, it was just the way it worked out in my handwritten notes. 2528 2529 PetscInt facesPerBlock = 64; 2530 PetscInt vertsPerBlock = 56; 2531 PetscInt extentPlus[3]; 2532 PetscInt numBlocks, numBlocksPlus; 2533 const PetscInt A = 0, B = 1, C = 2, D = 3, E = 4, F = 5, G = 6, H = 7, 2534 II = 8, J = 9, K = 10, L = 11, M = 12, N = 13, O = 14, P = 15, 2535 Q = 16, R = 17, S = 18, T = 19, U = 20, V = 21, W = 22, X = 23, 2536 Y = 24, Z = 25, Ap = 26, Bp = 27, Cp = 28, Dp = 29, Ep = 30, Fp = 31, 2537 Gp = 32, Hp = 33, Ip = 34, Jp = 35, Kp = 36, Lp = 37, Mp = 38, Np = 39, 2538 Op = 40, Pp = 41, Qp = 42, Rp = 43, Sp = 44, Tp = 45, Up = 46, Vp = 47, 2539 Wp = 48, Xp = 49, Yp = 50, Zp = 51, Aq = 52, Bq = 53, Cq = 54, Dq = 55; 2540 const PetscInt pattern[64][4] = 2541 { /* face to vertex within the coarse discretization of a single gyroid block */ 2542 /* layer 0 */ 2543 {A,C,K,G},{C,B,II,K},{D,A,H,L},{B+56*1,D,L,J},{E,B+56*1,J,N},{A+56*2,E,N,H+56*2},{F,A+56*2,G+56*2,M},{B,F,M,II}, 2544 /* layer 1 */ 2545 {G,K,Q,O},{K,II,P,Q},{L,H,O+56*1,R},{J,L,R,P},{N,J,P,S},{H+56*2,N,S,O+56*3},{M,G+56*2,O+56*2,T},{II,M,T,P}, 2546 /* layer 2 */ 2547 {O,Q,Y,U},{Q,P,W,Y},{R,O+56*1,U+56*1,Ap},{P,R,Ap,W},{S,P,X,Bp},{O+56*3,S,Bp,V+56*1},{T,O+56*2,V,Z},{P,T,Z,X}, 2548 /* layer 3 */ 2549 {U,Y,Ep,Dp},{Y,W,Cp,Ep},{Ap,U+56*1,Dp+56*1,Gp},{W,Ap,Gp,Cp},{Bp,X,Cp+56*2,Fp},{V+56*1,Bp,Fp,Dp+56*1},{Z,V,Dp,Hp},{X,Z,Hp,Cp+56*2}, 2550 /* layer 4 */ 2551 {Dp,Ep,Mp,Kp},{Ep,Cp,Ip,Mp},{Gp,Dp+56*1,Lp,Np},{Cp,Gp,Np,Jp},{Fp,Cp+56*2,Jp+56*2,Pp},{Dp+56*1,Fp,Pp,Lp},{Hp,Dp,Kp,Op},{Cp+56*2,Hp,Op,Ip+56*2}, 2552 /* layer 5 */ 2553 {Kp,Mp,Sp,Rp},{Mp,Ip,Qp,Sp},{Np,Lp,Rp,Tp},{Jp,Np,Tp,Qp+56*1},{Pp,Jp+56*2,Qp+56*3,Up},{Lp,Pp,Up,Rp},{Op,Kp,Rp,Vp},{Ip+56*2,Op,Vp,Qp+56*2}, 2554 /* layer 6 */ 2555 {Rp,Sp,Aq,Yp},{Sp,Qp,Wp,Aq},{Tp,Rp,Yp,Cq},{Qp+56*1,Tp,Cq,Wp+56*1},{Up,Qp+56*3,Xp+56*1,Dq},{Rp,Up,Dq,Zp},{Vp,Rp,Zp,Bq},{Qp+56*2,Vp,Bq,Xp}, 2556 /* layer 7 (the top is the periodic image of the bottom of layer 0) */ 2557 {Yp,Aq,C+56*4,A+56*4},{Aq,Wp,B+56*4,C+56*4},{Cq,Yp,A+56*4,D+56*4},{Wp+56*1,Cq,D+56*4,B+56*5},{Dq,Xp+56*1,B+56*5,E+56*4},{Zp,Dq,E+56*4,A+56*6},{Bq,Zp,A+56*6,F+56*4},{Xp,Bq,F+56*4,B+56*4} 2558 }; 2559 const PetscReal gamma = PetscAcosReal((PetscSqrtReal(3.)-1.) / PetscSqrtReal(2.)) / PETSC_PI; 2560 const PetscReal patternCoords[56][3] = 2561 { 2562 /* A */ {1.,0.,0.}, 2563 /* B */ {0.,1.,0.}, 2564 /* C */ {gamma,gamma,0.}, 2565 /* D */ {1+gamma,1-gamma,0.}, 2566 /* E */ {2-gamma,2-gamma,0.}, 2567 /* F */ {1-gamma,1+gamma,0.}, 2568 2569 /* G */ {.5,0,.25}, 2570 /* H */ {1.5,0.,.25}, 2571 /* II */ {.5,1.,.25}, 2572 /* J */ {1.5,1.,.25}, 2573 /* K */ {.25,.5,.25}, 2574 /* L */ {1.25,.5,.25}, 2575 /* M */ {.75,1.5,.25}, 2576 /* N */ {1.75,1.5,.25}, 2577 2578 /* O */ {0.,0.,.5}, 2579 /* P */ {1.,1.,.5}, 2580 /* Q */ {gamma,1-gamma,.5}, 2581 /* R */ {1+gamma,gamma,.5}, 2582 /* S */ {2-gamma,1+gamma,.5}, 2583 /* T */ {1-gamma,2-gamma,.5}, 2584 2585 /* U */ {0.,.5,.75}, 2586 /* V */ {0.,1.5,.75}, 2587 /* W */ {1.,.5,.75}, 2588 /* X */ {1.,1.5,.75}, 2589 /* Y */ {.5,.75,.75}, 2590 /* Z */ {.5,1.75,.75}, 2591 /* Ap */ {1.5,.25,.75}, 2592 /* Bp */ {1.5,1.25,.75}, 2593 2594 /* Cp */ {1.,0.,1.}, 2595 /* Dp */ {0.,1.,1.}, 2596 /* Ep */ {1-gamma,1-gamma,1.}, 2597 /* Fp */ {1+gamma,1+gamma,1.}, 2598 /* Gp */ {2-gamma,gamma,1.}, 2599 /* Hp */ {gamma,2-gamma,1.}, 2600 2601 /* Ip */ {.5,0.,1.25}, 2602 /* Jp */ {1.5,0.,1.25}, 2603 /* Kp */ {.5,1.,1.25}, 2604 /* Lp */ {1.5,1.,1.25}, 2605 /* Mp */ {.75,.5,1.25}, 2606 /* Np */ {1.75,.5,1.25}, 2607 /* Op */ {.25,1.5,1.25}, 2608 /* Pp */ {1.25,1.5,1.25}, 2609 2610 /* Qp */ {0.,0.,1.5}, 2611 /* Rp */ {1.,1.,1.5}, 2612 /* Sp */ {1-gamma,gamma,1.5}, 2613 /* Tp */ {2-gamma,1-gamma,1.5}, 2614 /* Up */ {1+gamma,2-gamma,1.5}, 2615 /* Vp */ {gamma,1+gamma,1.5}, 2616 2617 /* Wp */ {0.,.5,1.75}, 2618 /* Xp */ {0.,1.5,1.75}, 2619 /* Yp */ {1.,.5,1.75}, 2620 /* Zp */ {1.,1.5,1.75}, 2621 /* Aq */ {.5,.25,1.75}, 2622 /* Bq */ {.5,1.25,1.75}, 2623 /* Cq */ {1.5,.75,1.75}, 2624 /* Dq */ {1.5,1.75,1.75}, 2625 }; 2626 PetscInt (*cells)[64][4] = NULL; 2627 PetscBool *seen; 2628 PetscInt *vertToTrueVert; 2629 PetscInt count; 2630 2631 for (PetscInt i = 0; i < 3; i++) extentPlus[i] = extent[i] + 1; 2632 numBlocks = 1; 2633 for (PetscInt i = 0; i < 3; i++) numBlocks *= extent[i]; 2634 numBlocksPlus = 1; 2635 for (PetscInt i = 0; i < 3; i++) numBlocksPlus *= extentPlus[i]; 2636 numFaces = numBlocks * facesPerBlock; 2637 ierr = PetscMalloc1(numBlocks, &cells);CHKERRQ(ierr); 2638 ierr = PetscCalloc1(numBlocksPlus * vertsPerBlock,&seen);CHKERRQ(ierr); 2639 for (PetscInt k = 0; k < extent[2]; k++) { 2640 for (PetscInt j = 0; j < extent[1]; j++) { 2641 for (PetscInt i = 0; i < extent[0]; i++) { 2642 for (PetscInt f = 0; f < facesPerBlock; f++) { 2643 for (PetscInt v = 0; v < 4; v++) { 2644 PetscInt vertRaw = pattern[f][v]; 2645 PetscInt blockidx = vertRaw / 56; 2646 PetscInt patternvert = vertRaw % 56; 2647 PetscInt xplus = (blockidx & 1); 2648 PetscInt yplus = (blockidx & 2) >> 1; 2649 PetscInt zplus = (blockidx & 4) >> 2; 2650 PetscInt zcoord = (periodic && periodic[2] == DM_BOUNDARY_PERIODIC) ? ((k + zplus) % extent[2]) : (k + zplus); 2651 PetscInt ycoord = (periodic && periodic[1] == DM_BOUNDARY_PERIODIC) ? ((j + yplus) % extent[1]) : (j + yplus); 2652 PetscInt xcoord = (periodic && periodic[0] == DM_BOUNDARY_PERIODIC) ? ((i + xplus) % extent[0]) : (i + xplus); 2653 PetscInt vert = ((zcoord * extentPlus[1] + ycoord) * extentPlus[0] + xcoord) * 56 + patternvert; 2654 2655 cells[(k * extent[1] + j) * extent[0] + i][f][v] = vert; 2656 seen[vert] = PETSC_TRUE; 2657 } 2658 } 2659 } 2660 } 2661 } 2662 for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++) if (seen[i]) numVertices++; 2663 count = 0; 2664 ierr = PetscMalloc1(numBlocksPlus * vertsPerBlock, &vertToTrueVert);CHKERRQ(ierr); 2665 ierr = PetscMalloc1(numVertices * 3, &vtxCoords);CHKERRQ(ierr); 2666 for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++) vertToTrueVert[i] = -1; 2667 for (PetscInt k = 0; k < extentPlus[2]; k++) { 2668 for (PetscInt j = 0; j < extentPlus[1]; j++) { 2669 for (PetscInt i = 0; i < extentPlus[0]; i++) { 2670 for (PetscInt v = 0; v < vertsPerBlock; v++) { 2671 PetscInt vIdx = ((k * extentPlus[1] + j) * extentPlus[0] + i) * vertsPerBlock + v; 2672 2673 if (seen[vIdx]) { 2674 PetscInt thisVert; 2675 2676 vertToTrueVert[vIdx] = thisVert = count++; 2677 2678 for (PetscInt d = 0; d < 3; d++) vtxCoords[3 * thisVert + d] = patternCoords[v][d]; 2679 vtxCoords[3 * thisVert + 0] += i * 2; 2680 vtxCoords[3 * thisVert + 1] += j * 2; 2681 vtxCoords[3 * thisVert + 2] += k * 2; 2682 } 2683 } 2684 } 2685 } 2686 } 2687 for (PetscInt i = 0; i < numBlocks; i++) { 2688 for (PetscInt f = 0; f < facesPerBlock; f++) { 2689 for (PetscInt v = 0; v < 4; v++) { 2690 cells[i][f][v] = vertToTrueVert[cells[i][f][v]]; 2691 } 2692 } 2693 } 2694 ierr = PetscFree(vertToTrueVert);CHKERRQ(ierr); 2695 ierr = PetscFree(seen);CHKERRQ(ierr); 2696 cells_flat = cells[0][0]; 2697 numEdges = 0; 2698 for (PetscInt i = 0; i < numFaces; i++) { 2699 for (PetscInt e = 0; e < 4; e++) { 2700 PetscInt ev[] = {cells_flat[i*4 + e], cells_flat[i*4 + ((e+1)%4)]}; 2701 const PetscReal *evCoords[] = {&vtxCoords[3*ev[0]], &vtxCoords[3*ev[1]]}; 2702 2703 for (PetscInt d = 0; d < 3; d++) { 2704 if (!periodic || periodic[0] != DM_BOUNDARY_PERIODIC) { 2705 if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) numEdges++; 2706 if (evCoords[0][d] == 2.*extent[d] && evCoords[1][d] == 2.*extent[d]) numEdges++; 2707 } 2708 } 2709 } 2710 } 2711 ierr = PetscMalloc1(numEdges, &edges);CHKERRQ(ierr); 2712 ierr = PetscMalloc1(numEdges, &edgeSets);CHKERRQ(ierr); 2713 for (PetscInt edge = 0, i = 0; i < numFaces; i++) { 2714 for (PetscInt e = 0; e < 4; e++) { 2715 PetscInt ev[] = {cells_flat[i*4 + e], cells_flat[i*4 + ((e+1)%4)]}; 2716 const PetscReal *evCoords[] = {&vtxCoords[3*ev[0]], &vtxCoords[3*ev[1]]}; 2717 2718 for (PetscInt d = 0; d < 3; d++) { 2719 if (!periodic || periodic[d] != DM_BOUNDARY_PERIODIC) { 2720 if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) { 2721 edges[edge][0] = ev[0]; 2722 edges[edge][1] = ev[1]; 2723 edgeSets[edge++] = 2 * d; 2724 } 2725 if (evCoords[0][d] == 2.*extent[d] && evCoords[1][d] == 2.*extent[d]) { 2726 edges[edge][0] = ev[0]; 2727 edges[edge][1] = ev[1]; 2728 edgeSets[edge++] = 2 * d + 1; 2729 } 2730 } 2731 } 2732 } 2733 } 2734 } 2735 evalFunc = TPSEvaluate_Gyroid; 2736 break; 2737 } 2738 2739 ierr = DMSetDimension(dm, topoDim);CHKERRQ(ierr); 2740 if (!rank) {ierr = DMPlexBuildFromCellList(dm, numFaces, numVertices, 4, cells_flat);CHKERRQ(ierr);} 2741 else {ierr = DMPlexBuildFromCellList(dm, 0, 0, 0, NULL);CHKERRQ(ierr);} 2742 ierr = PetscFree(cells_flat);CHKERRQ(ierr); 2743 { 2744 DM idm; 2745 ierr = DMPlexInterpolate(dm, &idm);CHKERRQ(ierr); 2746 ierr = DMPlexReplace_Static(dm, &idm);CHKERRQ(ierr); 2747 } 2748 if (!rank) {ierr = DMPlexBuildCoordinatesFromCellList(dm, spaceDim, vtxCoords);CHKERRQ(ierr);} 2749 else {ierr = DMPlexBuildCoordinatesFromCellList(dm, spaceDim, NULL);CHKERRQ(ierr);} 2750 ierr = PetscFree(vtxCoords);CHKERRQ(ierr); 2751 2752 ierr = DMCreateLabel(dm, "Face Sets");CHKERRQ(ierr); 2753 ierr = DMGetLabel(dm, "Face Sets", &label);CHKERRQ(ierr); 2754 for (PetscInt e=0; e<numEdges; e++) { 2755 PetscInt njoin; 2756 const PetscInt *join, verts[] = {numFaces + edges[e][0], numFaces + edges[e][1]}; 2757 ierr = DMPlexGetJoin(dm, 2, verts, &njoin, &join);CHKERRQ(ierr); 2758 PetscCheck(njoin == 1, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Expected unique join of vertices %D and %D", edges[e][0], edges[e][1]); 2759 ierr = DMLabelSetValue(label, join[0], edgeSets[e]);CHKERRQ(ierr); 2760 ierr = DMPlexRestoreJoin(dm, 2, verts, &njoin, &join);CHKERRQ(ierr); 2761 } 2762 ierr = PetscFree(edges);CHKERRQ(ierr); 2763 ierr = PetscFree(edgeSets);CHKERRQ(ierr); 2764 if (tps_distribute) { 2765 DM pdm = NULL; 2766 PetscPartitioner part; 2767 2768 ierr = DMPlexGetPartitioner(dm, &part);CHKERRQ(ierr); 2769 ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr); 2770 ierr = DMPlexDistribute(dm, 0, NULL, &pdm);CHKERRQ(ierr); 2771 if (pdm) { 2772 ierr = DMPlexReplace_Static(dm, &pdm);CHKERRQ(ierr); 2773 } 2774 // Do not auto-distribute again 2775 ierr = DMPlexDistributeSetDefault(dm, PETSC_FALSE);CHKERRQ(ierr); 2776 } 2777 2778 ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr); 2779 for (PetscInt refine=0; refine<refinements; refine++) { 2780 PetscInt m; 2781 DM dmf; 2782 Vec X; 2783 PetscScalar *x; 2784 ierr = DMRefine(dm, MPI_COMM_NULL, &dmf);CHKERRQ(ierr); 2785 ierr = DMPlexReplace_Static(dm, &dmf);CHKERRQ(ierr); 2786 2787 ierr = DMGetCoordinatesLocal(dm, &X);CHKERRQ(ierr); 2788 ierr = VecGetLocalSize(X, &m);CHKERRQ(ierr); 2789 ierr = VecGetArray(X, &x);CHKERRQ(ierr); 2790 for (PetscInt i=0; i<m; i+=3) { 2791 ierr = TPSNearestPoint(evalFunc, &x[i]);CHKERRQ(ierr); 2792 } 2793 ierr = VecRestoreArray(X, &x);CHKERRQ(ierr); 2794 } 2795 2796 // Face Sets has already been propagated to new vertices during refinement; this propagates to the initial vertices. 2797 ierr = DMGetLabel(dm, "Face Sets", &label);CHKERRQ(ierr); 2798 ierr = DMPlexLabelComplete(dm, label);CHKERRQ(ierr); 2799 2800 if (thickness > 0) { 2801 DM dm3; 2802 ierr = DMPlexExtrude(dm, layers, thickness, PETSC_FALSE, PETSC_TRUE, NULL, NULL, &dm3);CHKERRQ(ierr); 2803 ierr = DMPlexReplace_Static(dm, &dm3);CHKERRQ(ierr); 2804 } 2805 PetscFunctionReturn(0); 2806 } 2807 2808 /*@ 2809 DMPlexCreateTPSMesh - Create a distributed, interpolated mesh of a triply-periodic surface 2810 2811 Collective 2812 2813 Input Parameters: 2814 + comm - The communicator for the DM object 2815 . tpstype - Type of triply-periodic surface 2816 . extent - Array of length 3 containing number of periods in each direction 2817 . periodic - array of length 3 with periodicity, or NULL for non-periodic 2818 . tps_distribute - Distribute 2D manifold mesh prior to refinement and extrusion (more scalable) 2819 . refinements - Number of factor-of-2 refinements of 2D manifold mesh 2820 . layers - Number of cell layers extruded in normal direction 2821 - thickness - Thickness in normal direction 2822 2823 Output Parameter: 2824 . dm - The DM object 2825 2826 Notes: 2827 This meshes the surface of the Schwarz P or Gyroid surfaces. Schwarz P is is the simplest member of the triply-periodic minimal surfaces. 2828 https://en.wikipedia.org/wiki/Schwarz_minimal_surface#Schwarz_P_(%22Primitive%22) and can be cut with "clean" boundaries. 2829 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. 2830 Our implementation creates a very coarse mesh of the surface and refines (by 4-way splitting) as many times as requested. 2831 On each refinement, all vertices are projected to their nearest point on the surface. 2832 This projection could readily be extended to related surfaces. 2833 2834 The face (edge) sets for the Schwarz P surface are numbered 1(-x), 2(+x), 3(-y), 4(+y), 5(-z), 6(+z). 2835 When the mesh is refined, "Face Sets" contain the new vertices (created during refinement). Use DMPlexLabelComplete() to propagate to coarse-level vertices. 2836 2837 References: 2838 . * - Maskery et al, Insights into the mechanical properties of several triply periodic minimal surface lattice structures made by polymer additive manufacturing, 2017. https://doi.org/10.1016/j.polymer.2017.11.049 2839 2840 Developer Notes: 2841 The Gyroid mesh does not currently mark boundary sets. 2842 2843 Level: beginner 2844 2845 .seealso: DMPlexCreateSphereMesh(), DMSetType(), DMCreate() 2846 @*/ 2847 PetscErrorCode DMPlexCreateTPSMesh(MPI_Comm comm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscBool tps_distribute, PetscInt refinements, PetscInt layers, PetscReal thickness, DM *dm) 2848 { 2849 PetscErrorCode ierr; 2850 2851 PetscFunctionBegin; 2852 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2853 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2854 ierr = DMPlexCreateTPSMesh_Internal(*dm, tpstype, extent, periodic, tps_distribute, refinements, layers, thickness);CHKERRQ(ierr); 2855 PetscFunctionReturn(0); 2856 } 2857 2858 /*@ 2859 DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d. 2860 2861 Collective 2862 2863 Input Parameters: 2864 + comm - The communicator for the DM object 2865 . dim - The dimension 2866 . simplex - Use simplices, or tensor product cells 2867 - R - The radius 2868 2869 Output Parameter: 2870 . dm - The DM object 2871 2872 Level: beginner 2873 2874 .seealso: DMPlexCreateBallMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 2875 @*/ 2876 PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscReal R, DM *dm) 2877 { 2878 PetscErrorCode ierr; 2879 2880 PetscFunctionBegin; 2881 PetscValidPointer(dm, 5); 2882 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2883 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2884 ierr = DMPlexCreateSphereMesh_Internal(*dm, dim, simplex, R);CHKERRQ(ierr); 2885 PetscFunctionReturn(0); 2886 } 2887 2888 static PetscErrorCode DMPlexCreateBallMesh_Internal(DM dm, PetscInt dim, PetscReal R) 2889 { 2890 DM sdm, vol; 2891 DMLabel bdlabel; 2892 PetscErrorCode ierr; 2893 2894 PetscFunctionBegin; 2895 ierr = DMCreate(PetscObjectComm((PetscObject) dm), &sdm);CHKERRQ(ierr); 2896 ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr); 2897 ierr = PetscObjectSetOptionsPrefix((PetscObject) sdm, "bd_");CHKERRQ(ierr); 2898 ierr = DMPlexCreateSphereMesh_Internal(sdm, dim-1, PETSC_TRUE, R);CHKERRQ(ierr); 2899 ierr = DMSetFromOptions(sdm);CHKERRQ(ierr); 2900 ierr = DMViewFromOptions(sdm, NULL, "-dm_view");CHKERRQ(ierr); 2901 ierr = DMPlexGenerate(sdm, NULL, PETSC_TRUE, &vol);CHKERRQ(ierr); 2902 ierr = DMDestroy(&sdm);CHKERRQ(ierr); 2903 ierr = DMPlexReplace_Static(dm, &vol);CHKERRQ(ierr); 2904 ierr = DMCreateLabel(dm, "marker");CHKERRQ(ierr); 2905 ierr = DMGetLabel(dm, "marker", &bdlabel);CHKERRQ(ierr); 2906 ierr = DMPlexMarkBoundaryFaces(dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 2907 ierr = DMPlexLabelComplete(dm, bdlabel);CHKERRQ(ierr); 2908 PetscFunctionReturn(0); 2909 } 2910 2911 /*@ 2912 DMPlexCreateBallMesh - Creates a simplex mesh on the d-dimensional ball, B^d. 2913 2914 Collective 2915 2916 Input Parameters: 2917 + comm - The communicator for the DM object 2918 . dim - The dimension 2919 - R - The radius 2920 2921 Output Parameter: 2922 . dm - The DM object 2923 2924 Options Database Keys: 2925 - bd_dm_refine - This will refine the surface mesh preserving the sphere geometry 2926 2927 Level: beginner 2928 2929 .seealso: DMPlexCreateSphereMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 2930 @*/ 2931 PetscErrorCode DMPlexCreateBallMesh(MPI_Comm comm, PetscInt dim, PetscReal R, DM *dm) 2932 { 2933 PetscErrorCode ierr; 2934 2935 PetscFunctionBegin; 2936 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2937 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2938 ierr = DMPlexCreateBallMesh_Internal(*dm, dim, R);CHKERRQ(ierr); 2939 PetscFunctionReturn(0); 2940 } 2941 2942 static PetscErrorCode DMPlexCreateReferenceCell_Internal(DM rdm, DMPolytopeType ct) 2943 { 2944 PetscErrorCode ierr; 2945 2946 PetscFunctionBegin; 2947 switch (ct) { 2948 case DM_POLYTOPE_POINT: 2949 { 2950 PetscInt numPoints[1] = {1}; 2951 PetscInt coneSize[1] = {0}; 2952 PetscInt cones[1] = {0}; 2953 PetscInt coneOrientations[1] = {0}; 2954 PetscScalar vertexCoords[1] = {0.0}; 2955 2956 ierr = DMSetDimension(rdm, 0);CHKERRQ(ierr); 2957 ierr = DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2958 } 2959 break; 2960 case DM_POLYTOPE_SEGMENT: 2961 { 2962 PetscInt numPoints[2] = {2, 1}; 2963 PetscInt coneSize[3] = {2, 0, 0}; 2964 PetscInt cones[2] = {1, 2}; 2965 PetscInt coneOrientations[2] = {0, 0}; 2966 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 2967 2968 ierr = DMSetDimension(rdm, 1);CHKERRQ(ierr); 2969 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2970 } 2971 break; 2972 case DM_POLYTOPE_POINT_PRISM_TENSOR: 2973 { 2974 PetscInt numPoints[2] = {2, 1}; 2975 PetscInt coneSize[3] = {2, 0, 0}; 2976 PetscInt cones[2] = {1, 2}; 2977 PetscInt coneOrientations[2] = {0, 0}; 2978 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 2979 2980 ierr = DMSetDimension(rdm, 1);CHKERRQ(ierr); 2981 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2982 } 2983 break; 2984 case DM_POLYTOPE_TRIANGLE: 2985 { 2986 PetscInt numPoints[2] = {3, 1}; 2987 PetscInt coneSize[4] = {3, 0, 0, 0}; 2988 PetscInt cones[3] = {1, 2, 3}; 2989 PetscInt coneOrientations[3] = {0, 0, 0}; 2990 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 2991 2992 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 2993 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2994 } 2995 break; 2996 case DM_POLYTOPE_QUADRILATERAL: 2997 { 2998 PetscInt numPoints[2] = {4, 1}; 2999 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3000 PetscInt cones[4] = {1, 2, 3, 4}; 3001 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3002 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 3003 3004 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 3005 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3006 } 3007 break; 3008 case DM_POLYTOPE_SEG_PRISM_TENSOR: 3009 { 3010 PetscInt numPoints[2] = {4, 1}; 3011 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3012 PetscInt cones[4] = {1, 2, 3, 4}; 3013 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3014 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, 1.0}; 3015 3016 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 3017 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3018 } 3019 break; 3020 case DM_POLYTOPE_TETRAHEDRON: 3021 { 3022 PetscInt numPoints[2] = {4, 1}; 3023 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3024 PetscInt cones[4] = {1, 2, 3, 4}; 3025 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3026 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}; 3027 3028 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3029 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3030 } 3031 break; 3032 case DM_POLYTOPE_HEXAHEDRON: 3033 { 3034 PetscInt numPoints[2] = {8, 1}; 3035 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3036 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 3037 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3038 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, 3039 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3040 3041 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3042 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3043 } 3044 break; 3045 case DM_POLYTOPE_TRI_PRISM: 3046 { 3047 PetscInt numPoints[2] = {6, 1}; 3048 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3049 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 3050 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3051 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, -1.0, -1.0, 3052 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 3053 3054 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3055 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3056 } 3057 break; 3058 case DM_POLYTOPE_TRI_PRISM_TENSOR: 3059 { 3060 PetscInt numPoints[2] = {6, 1}; 3061 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3062 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 3063 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3064 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 3065 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 3066 3067 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3068 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3069 } 3070 break; 3071 case DM_POLYTOPE_QUAD_PRISM_TENSOR: 3072 { 3073 PetscInt numPoints[2] = {8, 1}; 3074 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3075 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 3076 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3077 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, 3078 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3079 3080 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3081 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3082 } 3083 break; 3084 case DM_POLYTOPE_PYRAMID: 3085 { 3086 PetscInt numPoints[2] = {5, 1}; 3087 PetscInt coneSize[6] = {5, 0, 0, 0, 0, 0}; 3088 PetscInt cones[5] = {1, 2, 3, 4, 5}; 3089 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3090 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, 3091 0.0, 0.0, 1.0}; 3092 3093 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3094 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3095 } 3096 break; 3097 default: SETERRQ(PetscObjectComm((PetscObject) rdm), PETSC_ERR_ARG_WRONG, "Cannot create reference cell for cell type %s", DMPolytopeTypes[ct]); 3098 } 3099 { 3100 PetscInt Nv, v; 3101 3102 /* Must create the celltype label here so that we do not automatically try to compute the types */ 3103 ierr = DMCreateLabel(rdm, "celltype");CHKERRQ(ierr); 3104 ierr = DMPlexSetCellType(rdm, 0, ct);CHKERRQ(ierr); 3105 ierr = DMPlexGetChart(rdm, NULL, &Nv);CHKERRQ(ierr); 3106 for (v = 1; v < Nv; ++v) {ierr = DMPlexSetCellType(rdm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr);} 3107 } 3108 ierr = DMPlexInterpolateInPlace_Internal(rdm);CHKERRQ(ierr); 3109 ierr = PetscObjectSetName((PetscObject) rdm, DMPolytopeTypes[ct]);CHKERRQ(ierr); 3110 PetscFunctionReturn(0); 3111 } 3112 3113 /*@ 3114 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 3115 3116 Collective 3117 3118 Input Parameters: 3119 + comm - The communicator 3120 - ct - The cell type of the reference cell 3121 3122 Output Parameter: 3123 . refdm - The reference cell 3124 3125 Level: intermediate 3126 3127 .seealso: DMPlexCreateReferenceCell(), DMPlexCreateBoxMesh() 3128 @*/ 3129 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, DMPolytopeType ct, DM *refdm) 3130 { 3131 PetscErrorCode ierr; 3132 3133 PetscFunctionBegin; 3134 ierr = DMCreate(comm, refdm);CHKERRQ(ierr); 3135 ierr = DMSetType(*refdm, DMPLEX);CHKERRQ(ierr); 3136 ierr = DMPlexCreateReferenceCell_Internal(*refdm, ct);CHKERRQ(ierr); 3137 PetscFunctionReturn(0); 3138 } 3139 3140 static PetscErrorCode DMPlexCreateBoundaryLabel_Private(DM dm, const char name[]) 3141 { 3142 DM plex; 3143 DMLabel label; 3144 PetscBool hasLabel; 3145 PetscErrorCode ierr; 3146 3147 PetscFunctionBeginUser; 3148 ierr = DMHasLabel(dm, name, &hasLabel);CHKERRQ(ierr); 3149 if (hasLabel) PetscFunctionReturn(0); 3150 ierr = DMCreateLabel(dm, name);CHKERRQ(ierr); 3151 ierr = DMGetLabel(dm, name, &label);CHKERRQ(ierr); 3152 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 3153 ierr = DMPlexMarkBoundaryFaces(plex, 1, label);CHKERRQ(ierr); 3154 ierr = DMDestroy(&plex);CHKERRQ(ierr); 3155 PetscFunctionReturn(0); 3156 } 3157 3158 const char * const DMPlexShapes[] = {"box", "box_surface", "ball", "sphere", "cylinder", "schwarz_p", "gyroid", "unknown", "DMPlexShape", "DM_SHAPE_", NULL}; 3159 3160 static PetscErrorCode DMPlexCreateFromOptions_Internal(PetscOptionItems *PetscOptionsObject, PetscBool *useCoordSpace, DM dm) 3161 { 3162 DMPlexShape shape = DM_SHAPE_BOX; 3163 DMPolytopeType cell = DM_POLYTOPE_TRIANGLE; 3164 PetscInt dim = 2; 3165 PetscBool simplex = PETSC_TRUE, interpolate = PETSC_TRUE, adjCone = PETSC_FALSE, adjClosure = PETSC_TRUE, refDomain = PETSC_FALSE; 3166 PetscBool flg, flg2, fflg, bdfflg, nameflg; 3167 MPI_Comm comm; 3168 char filename[PETSC_MAX_PATH_LEN] = "<unspecified>"; 3169 char bdFilename[PETSC_MAX_PATH_LEN] = "<unspecified>"; 3170 char plexname[PETSC_MAX_PATH_LEN] = ""; 3171 PetscErrorCode ierr; 3172 3173 PetscFunctionBegin; 3174 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 3175 /* TODO Turn this into a registration interface */ 3176 ierr = PetscOptionsString("-dm_plex_filename", "File containing a mesh", "DMPlexCreateFromFile", filename, filename, sizeof(filename), &fflg);CHKERRQ(ierr); 3177 ierr = PetscOptionsString("-dm_plex_boundary_filename", "File containing a mesh boundary", "DMPlexCreateFromFile", bdFilename, bdFilename, sizeof(bdFilename), &bdfflg);CHKERRQ(ierr); 3178 ierr = PetscOptionsString("-dm_plex_name", "Name of the mesh in the file", "DMPlexCreateFromFile", plexname, plexname, sizeof(plexname), &nameflg);CHKERRQ(ierr); 3179 ierr = PetscOptionsEnum("-dm_plex_cell", "Cell shape", "", DMPolytopeTypes, (PetscEnum) cell, (PetscEnum *) &cell, NULL);CHKERRQ(ierr); 3180 ierr = PetscOptionsBool("-dm_plex_reference_cell_domain", "Use a reference cell domain", "", refDomain, &refDomain, NULL);CHKERRQ(ierr); 3181 ierr = PetscOptionsEnum("-dm_plex_shape", "Shape for built-in mesh", "", DMPlexShapes, (PetscEnum) shape, (PetscEnum *) &shape, &flg);CHKERRQ(ierr); 3182 ierr = PetscOptionsBoundedInt("-dm_plex_dim", "Topological dimension of the mesh", "DMGetDimension", dim, &dim, &flg, 0);CHKERRQ(ierr); 3183 PetscCheckFalse((dim < 0) || (dim > 3),comm, PETSC_ERR_ARG_OUTOFRANGE, "Dimension %D should be in [1, 3]", dim); 3184 ierr = PetscOptionsBool("-dm_plex_simplex", "Mesh cell shape", "", simplex, &simplex, &flg);CHKERRQ(ierr); 3185 ierr = PetscOptionsBool("-dm_plex_interpolate", "Flag to create edges and faces automatically", "", interpolate, &interpolate, &flg);CHKERRQ(ierr); 3186 ierr = PetscOptionsBool("-dm_plex_adj_cone", "Set adjacency direction", "DMSetBasicAdjacency", adjCone, &adjCone, &flg);CHKERRQ(ierr); 3187 ierr = PetscOptionsBool("-dm_plex_adj_closure", "Set adjacency size", "DMSetBasicAdjacency", adjClosure, &adjClosure, &flg2);CHKERRQ(ierr); 3188 if (flg || flg2) {ierr = DMSetBasicAdjacency(dm, adjCone, adjClosure);CHKERRQ(ierr);} 3189 3190 switch (cell) { 3191 case DM_POLYTOPE_POINT: 3192 case DM_POLYTOPE_SEGMENT: 3193 case DM_POLYTOPE_POINT_PRISM_TENSOR: 3194 case DM_POLYTOPE_TRIANGLE: 3195 case DM_POLYTOPE_QUADRILATERAL: 3196 case DM_POLYTOPE_TETRAHEDRON: 3197 case DM_POLYTOPE_HEXAHEDRON: 3198 *useCoordSpace = PETSC_TRUE;break; 3199 default: *useCoordSpace = PETSC_FALSE;break; 3200 } 3201 3202 if (fflg) { 3203 DM dmnew; 3204 3205 ierr = DMPlexCreateFromFile(PetscObjectComm((PetscObject) dm), filename, plexname, interpolate, &dmnew);CHKERRQ(ierr); 3206 ierr = DMPlexCopy_Internal(dm, PETSC_FALSE, dmnew);CHKERRQ(ierr); 3207 ierr = DMPlexReplace_Static(dm, &dmnew);CHKERRQ(ierr); 3208 } else if (refDomain) { 3209 ierr = DMPlexCreateReferenceCell_Internal(dm, cell);CHKERRQ(ierr); 3210 } else if (bdfflg) { 3211 DM bdm, dmnew; 3212 3213 ierr = DMPlexCreateFromFile(PetscObjectComm((PetscObject) dm), bdFilename, plexname, interpolate, &bdm);CHKERRQ(ierr); 3214 ierr = PetscObjectSetOptionsPrefix((PetscObject) bdm, "bd_");CHKERRQ(ierr); 3215 ierr = DMSetFromOptions(bdm);CHKERRQ(ierr); 3216 ierr = DMPlexGenerate(bdm, NULL, interpolate, &dmnew);CHKERRQ(ierr); 3217 ierr = DMDestroy(&bdm);CHKERRQ(ierr); 3218 ierr = DMPlexCopy_Internal(dm, PETSC_FALSE, dmnew);CHKERRQ(ierr); 3219 ierr = DMPlexReplace_Static(dm, &dmnew);CHKERRQ(ierr); 3220 } else { 3221 ierr = PetscObjectSetName((PetscObject) dm, DMPlexShapes[shape]);CHKERRQ(ierr); 3222 switch (shape) { 3223 case DM_SHAPE_BOX: 3224 { 3225 PetscInt faces[3] = {0, 0, 0}; 3226 PetscReal lower[3] = {0, 0, 0}; 3227 PetscReal upper[3] = {1, 1, 1}; 3228 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 3229 PetscInt i, n; 3230 3231 n = dim; 3232 for (i = 0; i < dim; ++i) faces[i] = (dim == 1 ? 1 : 4-dim); 3233 ierr = PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg);CHKERRQ(ierr); 3234 n = 3; 3235 ierr = PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg);CHKERRQ(ierr); 3236 PetscCheckFalse(flg && (n != dim),comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim); 3237 n = 3; 3238 ierr = PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg);CHKERRQ(ierr); 3239 PetscCheckFalse(flg && (n != dim),comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim); 3240 n = 3; 3241 ierr = PetscOptionsEnumArray("-dm_plex_box_bd", "Boundary type for each dimension", "", DMBoundaryTypes, (PetscEnum *) bdt, &n, &flg);CHKERRQ(ierr); 3242 PetscCheckFalse(flg && (n != dim),comm, PETSC_ERR_ARG_SIZ, "Box boundary types had %D values, should have been %D", n, dim); 3243 switch (cell) { 3244 case DM_POLYTOPE_TRI_PRISM_TENSOR: 3245 ierr = DMPlexCreateWedgeBoxMesh_Internal(dm, faces, lower, upper, bdt);CHKERRQ(ierr); 3246 if (!interpolate) { 3247 DM udm; 3248 3249 ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr); 3250 ierr = DMPlexReplace_Static(dm, &udm);CHKERRQ(ierr); 3251 } 3252 break; 3253 default: 3254 ierr = DMPlexCreateBoxMesh_Internal(dm, dim, simplex, faces, lower, upper, bdt, interpolate);CHKERRQ(ierr); 3255 break; 3256 } 3257 } 3258 break; 3259 case DM_SHAPE_BOX_SURFACE: 3260 { 3261 PetscInt faces[3] = {0, 0, 0}; 3262 PetscReal lower[3] = {0, 0, 0}; 3263 PetscReal upper[3] = {1, 1, 1}; 3264 PetscInt i, n; 3265 3266 n = dim+1; 3267 for (i = 0; i < dim+1; ++i) faces[i] = (dim+1 == 1 ? 1 : 4-(dim+1)); 3268 ierr = PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg);CHKERRQ(ierr); 3269 n = 3; 3270 ierr = PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg);CHKERRQ(ierr); 3271 PetscCheckFalse(flg && (n != dim+1),comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim+1); 3272 n = 3; 3273 ierr = PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg);CHKERRQ(ierr); 3274 PetscCheckFalse(flg && (n != dim+1),comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim+1); 3275 ierr = DMPlexCreateBoxSurfaceMesh_Internal(dm, dim+1, faces, lower, upper, interpolate);CHKERRQ(ierr); 3276 } 3277 break; 3278 case DM_SHAPE_SPHERE: 3279 { 3280 PetscReal R = 1.0; 3281 3282 ierr = PetscOptionsReal("-dm_plex_sphere_radius", "Radius of the sphere", "", R, &R, &flg);CHKERRQ(ierr); 3283 ierr = DMPlexCreateSphereMesh_Internal(dm, dim, simplex, R);CHKERRQ(ierr); 3284 } 3285 break; 3286 case DM_SHAPE_BALL: 3287 { 3288 PetscReal R = 1.0; 3289 3290 ierr = PetscOptionsReal("-dm_plex_ball_radius", "Radius of the ball", "", R, &R, &flg);CHKERRQ(ierr); 3291 ierr = DMPlexCreateBallMesh_Internal(dm, dim, R);CHKERRQ(ierr); 3292 } 3293 break; 3294 case DM_SHAPE_CYLINDER: 3295 { 3296 DMBoundaryType bdt = DM_BOUNDARY_NONE; 3297 PetscInt Nw = 6; 3298 3299 ierr = PetscOptionsEnum("-dm_plex_cylinder_bd", "Boundary type in the z direction", "", DMBoundaryTypes, (PetscEnum) bdt, (PetscEnum *) &bdt, NULL);CHKERRQ(ierr); 3300 ierr = PetscOptionsInt("-dm_plex_cylinder_num_wedges", "Number of wedges around the cylinder", "", Nw, &Nw, NULL);CHKERRQ(ierr); 3301 switch (cell) { 3302 case DM_POLYTOPE_TRI_PRISM_TENSOR: 3303 ierr = DMPlexCreateWedgeCylinderMesh_Internal(dm, Nw, interpolate);CHKERRQ(ierr); 3304 break; 3305 default: 3306 ierr = DMPlexCreateHexCylinderMesh_Internal(dm, bdt);CHKERRQ(ierr); 3307 break; 3308 } 3309 } 3310 break; 3311 case DM_SHAPE_SCHWARZ_P: // fallthrough 3312 case DM_SHAPE_GYROID: 3313 { 3314 PetscInt extent[3] = {1,1,1}, refine = 0, layers = 0, three; 3315 PetscReal thickness = 0.; 3316 DMBoundaryType periodic[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 3317 DMPlexTPSType tps_type = shape == DM_SHAPE_SCHWARZ_P ? DMPLEX_TPS_SCHWARZ_P : DMPLEX_TPS_GYROID; 3318 PetscBool tps_distribute; 3319 ierr = PetscOptionsIntArray("-dm_plex_tps_extent", "Number of replicas for each of three dimensions", NULL, extent, (three=3, &three), NULL);CHKERRQ(ierr); 3320 ierr = PetscOptionsInt("-dm_plex_tps_refine", "Number of refinements", NULL, refine, &refine, NULL);CHKERRQ(ierr); 3321 ierr = PetscOptionsEnumArray("-dm_plex_tps_periodic", "Periodicity in each of three dimensions", NULL, DMBoundaryTypes, (PetscEnum*)periodic, (three=3, &three), NULL);CHKERRQ(ierr); 3322 ierr = PetscOptionsInt("-dm_plex_tps_layers", "Number of layers in volumetric extrusion (or zero to not extrude)", NULL, layers, &layers, NULL);CHKERRQ(ierr); 3323 ierr = PetscOptionsReal("-dm_plex_tps_thickness", "Thickness of volumetric extrusion", NULL, thickness, &thickness, NULL);CHKERRQ(ierr); 3324 ierr = DMPlexDistributeGetDefault(dm, &tps_distribute);CHKERRQ(ierr); 3325 ierr = PetscOptionsBool("-dm_plex_tps_distribute", "Distribute the 2D mesh prior to refinement and extrusion", NULL, tps_distribute, &tps_distribute, NULL);CHKERRQ(ierr); 3326 ierr = DMPlexCreateTPSMesh_Internal(dm, tps_type, extent, periodic, tps_distribute, refine, layers, thickness);CHKERRQ(ierr); 3327 } 3328 break; 3329 default: SETERRQ(comm, PETSC_ERR_SUP, "Domain shape %s is unsupported", DMPlexShapes[shape]); 3330 } 3331 } 3332 ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr); 3333 if (!((PetscObject)dm)->name && nameflg) { 3334 ierr = PetscObjectSetName((PetscObject)dm, plexname);CHKERRQ(ierr); 3335 } 3336 PetscFunctionReturn(0); 3337 } 3338 3339 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject, DM dm) 3340 { 3341 DM_Plex *mesh = (DM_Plex*) dm->data; 3342 PetscBool flg; 3343 char bdLabel[PETSC_MAX_PATH_LEN]; 3344 PetscErrorCode ierr; 3345 3346 PetscFunctionBegin; 3347 /* Handle viewing */ 3348 ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); 3349 ierr = PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL,0);CHKERRQ(ierr); 3350 ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL);CHKERRQ(ierr); 3351 ierr = PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL,0);CHKERRQ(ierr); 3352 ierr = DMMonitorSetFromOptions(dm, "-dm_plex_monitor_throughput", "Monitor the simulation throughput", "DMPlexMonitorThroughput", DMPlexMonitorThroughput, NULL, &flg);CHKERRQ(ierr); 3353 if (flg) {ierr = PetscLogDefaultBegin();CHKERRQ(ierr);} 3354 /* Labeling */ 3355 ierr = PetscOptionsString("-dm_plex_boundary_label", "Label to mark the mesh boundary", "", bdLabel, bdLabel, sizeof(bdLabel), &flg);CHKERRQ(ierr); 3356 if (flg) {ierr = DMPlexCreateBoundaryLabel_Private(dm, bdLabel);CHKERRQ(ierr);} 3357 /* Point Location */ 3358 ierr = PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL);CHKERRQ(ierr); 3359 /* Partitioning and distribution */ 3360 ierr = PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL);CHKERRQ(ierr); 3361 /* Generation and remeshing */ 3362 ierr = PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL);CHKERRQ(ierr); 3363 /* Projection behavior */ 3364 ierr = PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL,0);CHKERRQ(ierr); 3365 ierr = PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);CHKERRQ(ierr); 3366 /* Checking structure */ 3367 { 3368 PetscBool flg = PETSC_FALSE, flg2 = PETSC_FALSE, all = PETSC_FALSE; 3369 3370 ierr = PetscOptionsBool("-dm_plex_check_all", "Perform all checks", NULL, PETSC_FALSE, &all, &flg2);CHKERRQ(ierr); 3371 ierr = PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 3372 if (all || (flg && flg2)) {ierr = DMPlexCheckSymmetry(dm);CHKERRQ(ierr);} 3373 ierr = 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);CHKERRQ(ierr); 3374 if (all || (flg && flg2)) {ierr = DMPlexCheckSkeleton(dm, 0);CHKERRQ(ierr);} 3375 ierr = 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);CHKERRQ(ierr); 3376 if (all || (flg && flg2)) {ierr = DMPlexCheckFaces(dm, 0);CHKERRQ(ierr);} 3377 ierr = PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 3378 if (all || (flg && flg2)) {ierr = DMPlexCheckGeometry(dm);CHKERRQ(ierr);} 3379 ierr = PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 3380 if (all || (flg && flg2)) {ierr = DMPlexCheckPointSF(dm);CHKERRQ(ierr);} 3381 ierr = PetscOptionsBool("-dm_plex_check_interface_cones", "Check points on inter-partition interfaces have conforming order of cone points", "DMPlexCheckInterfaceCones", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 3382 if (all || (flg && flg2)) {ierr = DMPlexCheckInterfaceCones(dm);CHKERRQ(ierr);} 3383 ierr = PetscOptionsBool("-dm_plex_check_cell_shape", "Check cell shape", "DMPlexCheckCellShape", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 3384 if (flg && flg2) {ierr = DMPlexCheckCellShape(dm, PETSC_TRUE, PETSC_DETERMINE);CHKERRQ(ierr);} 3385 } 3386 { 3387 PetscReal scale = 1.0; 3388 3389 ierr = PetscOptionsReal("-dm_plex_scale", "Scale factor for mesh coordinates", "DMPlexScale", scale, &scale, &flg);CHKERRQ(ierr); 3390 if (flg) { 3391 Vec coordinates, coordinatesLocal; 3392 3393 ierr = DMGetCoordinates(dm, &coordinates);CHKERRQ(ierr); 3394 ierr = DMGetCoordinatesLocal(dm, &coordinatesLocal);CHKERRQ(ierr); 3395 ierr = VecScale(coordinates, scale);CHKERRQ(ierr); 3396 ierr = VecScale(coordinatesLocal, scale);CHKERRQ(ierr); 3397 } 3398 } 3399 ierr = PetscPartitionerSetFromOptions(mesh->partitioner);CHKERRQ(ierr); 3400 PetscFunctionReturn(0); 3401 } 3402 3403 static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 3404 { 3405 PetscFunctionList ordlist; 3406 char oname[256]; 3407 PetscReal volume = -1.0; 3408 PetscInt prerefine = 0, refine = 0, r, coarsen = 0, overlap = 0, extLayers = 0, dim; 3409 PetscBool uniformOrig, created = PETSC_FALSE, uniform = PETSC_TRUE, distribute, interpolate = PETSC_TRUE, coordSpace = PETSC_TRUE, remap = PETSC_TRUE, ghostCells = PETSC_FALSE, isHierarchy, ignoreModel = PETSC_FALSE, flg; 3410 PetscErrorCode ierr; 3411 3412 PetscFunctionBegin; 3413 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 3414 ierr = PetscOptionsHead(PetscOptionsObject,"DMPlex Options");CHKERRQ(ierr); 3415 /* Handle automatic creation */ 3416 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3417 if (dim < 0) {ierr = DMPlexCreateFromOptions_Internal(PetscOptionsObject, &coordSpace, dm);CHKERRQ(ierr);created = PETSC_TRUE;} 3418 /* Handle interpolation before distribution */ 3419 ierr = PetscOptionsBool("-dm_plex_interpolate_pre", "Flag to interpolate mesh before distribution", "", interpolate, &interpolate, &flg);CHKERRQ(ierr); 3420 if (flg) { 3421 DMPlexInterpolatedFlag interpolated; 3422 3423 ierr = DMPlexIsInterpolated(dm, &interpolated);CHKERRQ(ierr); 3424 if (interpolated == DMPLEX_INTERPOLATED_FULL && !interpolate) { 3425 DM udm; 3426 3427 ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr); 3428 ierr = DMPlexReplace_Static(dm, &udm);CHKERRQ(ierr); 3429 } else if (interpolated != DMPLEX_INTERPOLATED_FULL && interpolate) { 3430 DM idm; 3431 3432 ierr = DMPlexInterpolate(dm, &idm);CHKERRQ(ierr); 3433 ierr = DMPlexReplace_Static(dm, &idm);CHKERRQ(ierr); 3434 } 3435 } 3436 /* Handle DMPlex refinement before distribution */ 3437 ierr = PetscOptionsBool("-dm_refine_ignore_model", "Flag to ignore the geometry model when refining", "DMCreate", ignoreModel, &ignoreModel, &flg);CHKERRQ(ierr); 3438 if (flg) {((DM_Plex *) dm->data)->ignoreModel = ignoreModel;} 3439 ierr = DMPlexGetRefinementUniform(dm, &uniformOrig);CHKERRQ(ierr); 3440 ierr = PetscOptionsBoundedInt("-dm_refine_pre", "The number of refinements before distribution", "DMCreate", prerefine, &prerefine, NULL,0);CHKERRQ(ierr); 3441 ierr = PetscOptionsBool("-dm_refine_remap_pre", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL);CHKERRQ(ierr); 3442 ierr = PetscOptionsBool("-dm_refine_uniform_pre", "Flag for uniform refinement before distribution", "DMCreate", uniform, &uniform, &flg);CHKERRQ(ierr); 3443 if (flg) {ierr = DMPlexSetRefinementUniform(dm, uniform);CHKERRQ(ierr);} 3444 ierr = PetscOptionsReal("-dm_refine_volume_limit_pre", "The maximum cell volume after refinement before distribution", "DMCreate", volume, &volume, &flg);CHKERRQ(ierr); 3445 if (flg) { 3446 ierr = DMPlexSetRefinementUniform(dm, PETSC_FALSE);CHKERRQ(ierr); 3447 ierr = DMPlexSetRefinementLimit(dm, volume);CHKERRQ(ierr); 3448 prerefine = PetscMax(prerefine, 1); 3449 } 3450 for (r = 0; r < prerefine; ++r) { 3451 DM rdm; 3452 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 3453 3454 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3455 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &rdm);CHKERRQ(ierr); 3456 ierr = DMPlexReplace_Static(dm, &rdm);CHKERRQ(ierr); 3457 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3458 if (coordFunc && remap) { 3459 ierr = DMPlexRemapGeometry(dm, 0.0, coordFunc);CHKERRQ(ierr); 3460 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 3461 } 3462 } 3463 ierr = DMPlexSetRefinementUniform(dm, uniformOrig);CHKERRQ(ierr); 3464 /* Handle DMPlex extrusion before distribution */ 3465 ierr = PetscOptionsBoundedInt("-dm_extrude", "The number of layers to extrude", "", extLayers, &extLayers, NULL, 0);CHKERRQ(ierr); 3466 if (extLayers) { 3467 DM edm; 3468 3469 ierr = DMExtrude(dm, extLayers, &edm);CHKERRQ(ierr); 3470 ierr = DMPlexReplace_Static(dm, &edm);CHKERRQ(ierr); 3471 ((DM_Plex *) dm->data)->coordFunc = NULL; 3472 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3473 extLayers = 0; 3474 } 3475 /* Handle DMPlex reordering before distribution */ 3476 ierr = MatGetOrderingList(&ordlist);CHKERRQ(ierr); 3477 ierr = PetscOptionsFList("-dm_plex_reorder", "Set mesh reordering type", "DMPlexGetOrdering", ordlist, MATORDERINGNATURAL, oname, sizeof(oname), &flg);CHKERRQ(ierr); 3478 if (flg) { 3479 DM pdm; 3480 IS perm; 3481 3482 ierr = DMPlexGetOrdering(dm, oname, NULL, &perm);CHKERRQ(ierr); 3483 ierr = DMPlexPermute(dm, perm, &pdm);CHKERRQ(ierr); 3484 ierr = ISDestroy(&perm);CHKERRQ(ierr); 3485 ierr = DMPlexReplace_Static(dm, &pdm);CHKERRQ(ierr); 3486 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3487 } 3488 /* Handle DMPlex distribution */ 3489 ierr = DMPlexDistributeGetDefault(dm, &distribute);CHKERRQ(ierr); 3490 ierr = PetscOptionsBool("-dm_distribute", "Flag to redistribute a mesh among processes", "DMCreate", distribute, &distribute, NULL);CHKERRQ(ierr); 3491 ierr = PetscOptionsBoundedInt("-dm_distribute_overlap", "The size of the overlap halo", "DMCreate", overlap, &overlap, NULL, 0);CHKERRQ(ierr); 3492 if (distribute) { 3493 DM pdm = NULL; 3494 PetscPartitioner part; 3495 3496 ierr = DMPlexGetPartitioner(dm, &part);CHKERRQ(ierr); 3497 ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr); 3498 ierr = DMPlexDistribute(dm, overlap, NULL, &pdm);CHKERRQ(ierr); 3499 if (pdm) { 3500 ierr = DMPlexReplace_Static(dm, &pdm);CHKERRQ(ierr); 3501 } 3502 } 3503 /* Create coordinate space */ 3504 if (created) { 3505 DM_Plex *mesh = (DM_Plex *) dm->data; 3506 PetscInt degree = 1; 3507 PetscBool periodic, flg; 3508 3509 ierr = PetscOptionsBool("-dm_coord_space", "Use an FEM space for coordinates", "", coordSpace, &coordSpace, &flg);CHKERRQ(ierr); 3510 ierr = PetscOptionsInt("-dm_coord_petscspace_degree", "FEM degree for coordinate space", "", degree, °ree, NULL);CHKERRQ(ierr); 3511 if (coordSpace) {ierr = DMPlexCreateCoordinateSpace(dm, degree, mesh->coordFunc);CHKERRQ(ierr);} 3512 if (flg && !coordSpace) { 3513 DM cdm; 3514 PetscDS cds; 3515 PetscObject obj; 3516 PetscClassId id; 3517 3518 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 3519 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 3520 ierr = PetscDSGetDiscretization(cds, 0, &obj);CHKERRQ(ierr); 3521 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 3522 if (id == PETSCFE_CLASSID) { 3523 PetscContainer dummy; 3524 3525 ierr = PetscContainerCreate(PETSC_COMM_SELF, &dummy);CHKERRQ(ierr); 3526 ierr = PetscObjectSetName((PetscObject) dummy, "coordinates");CHKERRQ(ierr); 3527 ierr = DMSetField(cdm, 0, NULL, (PetscObject) dummy);CHKERRQ(ierr); 3528 ierr = PetscContainerDestroy(&dummy);CHKERRQ(ierr); 3529 ierr = DMClearDS(cdm);CHKERRQ(ierr); 3530 } 3531 mesh->coordFunc = NULL; 3532 } 3533 ierr = DMLocalizeCoordinates(dm);CHKERRQ(ierr); 3534 ierr = DMGetPeriodicity(dm, &periodic, NULL, NULL, NULL);CHKERRQ(ierr); 3535 if (periodic) {ierr = DMSetPeriodicity(dm, PETSC_TRUE, NULL, NULL, NULL);CHKERRQ(ierr);} 3536 } 3537 /* Handle DMPlex refinement */ 3538 remap = PETSC_TRUE; 3539 ierr = PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL,0);CHKERRQ(ierr); 3540 ierr = PetscOptionsBool("-dm_refine_remap", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL);CHKERRQ(ierr); 3541 ierr = PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy,0);CHKERRQ(ierr); 3542 if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 3543 if (refine && isHierarchy) { 3544 DM *dms, coarseDM; 3545 3546 ierr = DMGetCoarseDM(dm, &coarseDM);CHKERRQ(ierr); 3547 ierr = PetscObjectReference((PetscObject)coarseDM);CHKERRQ(ierr); 3548 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 3549 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 3550 /* Total hack since we do not pass in a pointer */ 3551 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 3552 if (refine == 1) { 3553 ierr = DMSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 3554 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 3555 } else { 3556 ierr = DMSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 3557 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 3558 ierr = DMSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 3559 ierr = DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);CHKERRQ(ierr); 3560 } 3561 ierr = DMSetCoarseDM(dms[refine-1], coarseDM);CHKERRQ(ierr); 3562 ierr = PetscObjectDereference((PetscObject)coarseDM);CHKERRQ(ierr); 3563 /* Free DMs */ 3564 for (r = 0; r < refine; ++r) { 3565 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 3566 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 3567 } 3568 ierr = PetscFree(dms);CHKERRQ(ierr); 3569 } else { 3570 for (r = 0; r < refine; ++r) { 3571 DM rdm; 3572 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 3573 3574 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3575 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &rdm);CHKERRQ(ierr); 3576 /* Total hack since we do not pass in a pointer */ 3577 ierr = DMPlexReplace_Static(dm, &rdm);CHKERRQ(ierr); 3578 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3579 if (coordFunc && remap) { 3580 ierr = DMPlexRemapGeometry(dm, 0.0, coordFunc);CHKERRQ(ierr); 3581 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 3582 } 3583 } 3584 } 3585 /* Handle DMPlex coarsening */ 3586 ierr = PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL,0);CHKERRQ(ierr); 3587 ierr = PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy,0);CHKERRQ(ierr); 3588 if (coarsen && isHierarchy) { 3589 DM *dms; 3590 3591 ierr = PetscMalloc1(coarsen, &dms);CHKERRQ(ierr); 3592 ierr = DMCoarsenHierarchy(dm, coarsen, dms);CHKERRQ(ierr); 3593 /* Free DMs */ 3594 for (r = 0; r < coarsen; ++r) { 3595 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 3596 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 3597 } 3598 ierr = PetscFree(dms);CHKERRQ(ierr); 3599 } else { 3600 for (r = 0; r < coarsen; ++r) { 3601 DM cdm; 3602 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 3603 3604 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3605 ierr = DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &cdm);CHKERRQ(ierr); 3606 /* Total hack since we do not pass in a pointer */ 3607 ierr = DMPlexReplace_Static(dm, &cdm);CHKERRQ(ierr); 3608 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3609 if (coordFunc) { 3610 ierr = DMPlexRemapGeometry(dm, 0.0, coordFunc);CHKERRQ(ierr); 3611 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 3612 } 3613 } 3614 } 3615 /* Handle ghost cells */ 3616 ierr = PetscOptionsBool("-dm_plex_create_fv_ghost_cells", "Flag to create finite volume ghost cells on the boundary", "DMCreate", ghostCells, &ghostCells, NULL);CHKERRQ(ierr); 3617 if (ghostCells) { 3618 DM gdm; 3619 char lname[PETSC_MAX_PATH_LEN]; 3620 3621 lname[0] = '\0'; 3622 ierr = PetscOptionsString("-dm_plex_fv_ghost_cells_label", "Label name for ghost cells boundary", "DMCreate", lname, lname, sizeof(lname), &flg);CHKERRQ(ierr); 3623 ierr = DMPlexConstructGhostCells(dm, flg ? lname : NULL, NULL, &gdm);CHKERRQ(ierr); 3624 ierr = DMPlexReplace_Static(dm, &gdm);CHKERRQ(ierr); 3625 } 3626 /* Handle 1D order */ 3627 { 3628 DM cdm, rdm; 3629 PetscDS cds; 3630 PetscObject obj; 3631 PetscClassId id = PETSC_OBJECT_CLASSID; 3632 IS perm; 3633 PetscInt dim, Nf; 3634 PetscBool distributed; 3635 3636 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3637 ierr = DMPlexIsDistributed(dm, &distributed);CHKERRQ(ierr); 3638 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 3639 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 3640 ierr = PetscDSGetNumFields(cds, &Nf);CHKERRQ(ierr); 3641 if (Nf) { 3642 ierr = PetscDSGetDiscretization(cds, 0, &obj);CHKERRQ(ierr); 3643 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 3644 } 3645 if (dim == 1 && !distributed && id != PETSCFE_CLASSID) { 3646 ierr = DMPlexGetOrdering1D(dm, &perm);CHKERRQ(ierr); 3647 ierr = DMPlexPermute(dm, perm, &rdm);CHKERRQ(ierr); 3648 ierr = DMPlexReplace_Static(dm, &rdm);CHKERRQ(ierr); 3649 ierr = ISDestroy(&perm);CHKERRQ(ierr); 3650 } 3651 } 3652 /* Handle */ 3653 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3654 ierr = PetscOptionsTail();CHKERRQ(ierr); 3655 PetscFunctionReturn(0); 3656 } 3657 3658 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 3659 { 3660 PetscErrorCode ierr; 3661 3662 PetscFunctionBegin; 3663 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 3664 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 3665 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 3666 ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); 3667 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 3668 ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); 3669 PetscFunctionReturn(0); 3670 } 3671 3672 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 3673 { 3674 PetscErrorCode ierr; 3675 3676 PetscFunctionBegin; 3677 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 3678 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 3679 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 3680 PetscFunctionReturn(0); 3681 } 3682 3683 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 3684 { 3685 PetscInt depth, d; 3686 PetscErrorCode ierr; 3687 3688 PetscFunctionBegin; 3689 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 3690 if (depth == 1) { 3691 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 3692 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 3693 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 3694 else {*pStart = 0; *pEnd = 0;} 3695 } else { 3696 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 3697 } 3698 PetscFunctionReturn(0); 3699 } 3700 3701 static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 3702 { 3703 PetscSF sf; 3704 PetscInt niranks, njranks, n; 3705 const PetscMPIInt *iranks, *jranks; 3706 DM_Plex *data = (DM_Plex*) dm->data; 3707 PetscErrorCode ierr; 3708 3709 PetscFunctionBegin; 3710 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 3711 if (!data->neighbors) { 3712 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 3713 ierr = PetscSFGetRootRanks(sf, &njranks, &jranks, NULL, NULL, NULL);CHKERRQ(ierr); 3714 ierr = PetscSFGetLeafRanks(sf, &niranks, &iranks, NULL, NULL);CHKERRQ(ierr); 3715 ierr = PetscMalloc1(njranks + niranks + 1, &data->neighbors);CHKERRQ(ierr); 3716 ierr = PetscArraycpy(data->neighbors + 1, jranks, njranks);CHKERRQ(ierr); 3717 ierr = PetscArraycpy(data->neighbors + njranks + 1, iranks, niranks);CHKERRQ(ierr); 3718 n = njranks + niranks; 3719 ierr = PetscSortRemoveDupsMPIInt(&n, data->neighbors + 1);CHKERRQ(ierr); 3720 /* The following cast should never fail: can't have more neighbors than PETSC_MPI_INT_MAX */ 3721 ierr = PetscMPIIntCast(n, data->neighbors);CHKERRQ(ierr); 3722 } 3723 if (nranks) *nranks = data->neighbors[0]; 3724 if (ranks) { 3725 if (data->neighbors[0]) *ranks = data->neighbors + 1; 3726 else *ranks = NULL; 3727 } 3728 PetscFunctionReturn(0); 3729 } 3730 3731 PETSC_INTERN PetscErrorCode DMInterpolateSolution_Plex(DM, DM, Mat, Vec, Vec); 3732 3733 static PetscErrorCode DMInitialize_Plex(DM dm) 3734 { 3735 PetscErrorCode ierr; 3736 3737 PetscFunctionBegin; 3738 dm->ops->view = DMView_Plex; 3739 dm->ops->load = DMLoad_Plex; 3740 dm->ops->setfromoptions = DMSetFromOptions_Plex; 3741 dm->ops->clone = DMClone_Plex; 3742 dm->ops->setup = DMSetUp_Plex; 3743 dm->ops->createlocalsection = DMCreateLocalSection_Plex; 3744 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 3745 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 3746 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 3747 dm->ops->getlocaltoglobalmapping = NULL; 3748 dm->ops->createfieldis = NULL; 3749 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 3750 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 3751 dm->ops->getcoloring = NULL; 3752 dm->ops->creatematrix = DMCreateMatrix_Plex; 3753 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 3754 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 3755 dm->ops->createmassmatrixlumped = DMCreateMassMatrixLumped_Plex; 3756 dm->ops->createinjection = DMCreateInjection_Plex; 3757 dm->ops->refine = DMRefine_Plex; 3758 dm->ops->coarsen = DMCoarsen_Plex; 3759 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 3760 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 3761 dm->ops->extrude = DMExtrude_Plex; 3762 dm->ops->globaltolocalbegin = NULL; 3763 dm->ops->globaltolocalend = NULL; 3764 dm->ops->localtoglobalbegin = NULL; 3765 dm->ops->localtoglobalend = NULL; 3766 dm->ops->destroy = DMDestroy_Plex; 3767 dm->ops->createsubdm = DMCreateSubDM_Plex; 3768 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 3769 dm->ops->getdimpoints = DMGetDimPoints_Plex; 3770 dm->ops->locatepoints = DMLocatePoints_Plex; 3771 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 3772 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 3773 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 3774 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 3775 dm->ops->projectbdfieldlabellocal = DMProjectBdFieldLabelLocal_Plex; 3776 dm->ops->computel2diff = DMComputeL2Diff_Plex; 3777 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 3778 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 3779 dm->ops->getneighbors = DMGetNeighbors_Plex; 3780 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);CHKERRQ(ierr); 3781 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertTimeDerviativeBoundaryValues_C",DMPlexInsertTimeDerivativeBoundaryValues_Plex);CHKERRQ(ierr); 3782 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);CHKERRQ(ierr); 3783 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C",DMCreateNeumannOverlap_Plex);CHKERRQ(ierr); 3784 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex);CHKERRQ(ierr); 3785 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexDistributeGetDefault_C",DMPlexDistributeGetDefault_Plex);CHKERRQ(ierr); 3786 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexDistributeSetDefault_C",DMPlexDistributeSetDefault_Plex);CHKERRQ(ierr); 3787 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMInterpolateSolution_C",DMInterpolateSolution_Plex);CHKERRQ(ierr); 3788 PetscFunctionReturn(0); 3789 } 3790 3791 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 3792 { 3793 DM_Plex *mesh = (DM_Plex *) dm->data; 3794 PetscErrorCode ierr; 3795 3796 PetscFunctionBegin; 3797 mesh->refct++; 3798 (*newdm)->data = mesh; 3799 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 3800 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 3801 PetscFunctionReturn(0); 3802 } 3803 3804 /*MC 3805 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 3806 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 3807 specified by a PetscSection object. Ownership in the global representation is determined by 3808 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 3809 3810 Options Database Keys: 3811 + -dm_refine_pre - Refine mesh before distribution 3812 + -dm_refine_uniform_pre - Choose uniform or generator-based refinement 3813 + -dm_refine_volume_limit_pre - Cell volume limit after pre-refinement using generator 3814 . -dm_distribute - Distribute mesh across processes 3815 . -dm_distribute_overlap - Number of cells to overlap for distribution 3816 . -dm_refine - Refine mesh after distribution 3817 . -dm_plex_hash_location - Use grid hashing for point location 3818 . -dm_plex_hash_box_faces <n,m,p> - The number of divisions in each direction of the grid hash 3819 . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes 3820 . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing 3821 . -dm_plex_max_projection_height - Maxmimum mesh point height used to project locally 3822 . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement 3823 . -dm_plex_check_all - Perform all shecks below 3824 . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric 3825 . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices 3826 . -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 3827 . -dm_plex_check_geometry - Check that cells have positive volume 3828 . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ 3829 . -dm_plex_view_scale <num> - Scale the TikZ 3830 - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices 3831 3832 Level: intermediate 3833 3834 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 3835 M*/ 3836 3837 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 3838 { 3839 DM_Plex *mesh; 3840 PetscInt unit; 3841 PetscErrorCode ierr; 3842 3843 PetscFunctionBegin; 3844 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3845 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 3846 dm->data = mesh; 3847 3848 mesh->refct = 1; 3849 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 3850 mesh->maxConeSize = 0; 3851 mesh->cones = NULL; 3852 mesh->coneOrientations = NULL; 3853 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 3854 mesh->maxSupportSize = 0; 3855 mesh->supports = NULL; 3856 mesh->refinementUniform = PETSC_TRUE; 3857 mesh->refinementLimit = -1.0; 3858 mesh->distDefault = PETSC_TRUE; 3859 mesh->interpolated = DMPLEX_INTERPOLATED_INVALID; 3860 mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID; 3861 3862 mesh->facesTmp = NULL; 3863 3864 mesh->tetgenOpts = NULL; 3865 mesh->triangleOpts = NULL; 3866 ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); 3867 mesh->remeshBd = PETSC_FALSE; 3868 3869 mesh->subpointMap = NULL; 3870 3871 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 3872 3873 mesh->regularRefinement = PETSC_FALSE; 3874 mesh->depthState = -1; 3875 mesh->celltypeState = -1; 3876 mesh->globalVertexNumbers = NULL; 3877 mesh->globalCellNumbers = NULL; 3878 mesh->anchorSection = NULL; 3879 mesh->anchorIS = NULL; 3880 mesh->createanchors = NULL; 3881 mesh->computeanchormatrix = NULL; 3882 mesh->parentSection = NULL; 3883 mesh->parents = NULL; 3884 mesh->childIDs = NULL; 3885 mesh->childSection = NULL; 3886 mesh->children = NULL; 3887 mesh->referenceTree = NULL; 3888 mesh->getchildsymmetry = NULL; 3889 mesh->vtkCellHeight = 0; 3890 mesh->useAnchors = PETSC_FALSE; 3891 3892 mesh->maxProjectionHeight = 0; 3893 3894 mesh->neighbors = NULL; 3895 3896 mesh->printSetValues = PETSC_FALSE; 3897 mesh->printFEM = 0; 3898 mesh->printTol = 1.0e-10; 3899 3900 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 3901 PetscFunctionReturn(0); 3902 } 3903 3904 /*@ 3905 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 3906 3907 Collective 3908 3909 Input Parameter: 3910 . comm - The communicator for the DMPlex object 3911 3912 Output Parameter: 3913 . mesh - The DMPlex object 3914 3915 Level: beginner 3916 3917 @*/ 3918 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 3919 { 3920 PetscErrorCode ierr; 3921 3922 PetscFunctionBegin; 3923 PetscValidPointer(mesh,2); 3924 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 3925 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 3926 PetscFunctionReturn(0); 3927 } 3928 3929 /*@C 3930 DMPlexBuildFromCellListParallel - Build distributed DMPLEX topology from a list of vertices for each cell (common mesh generator output) 3931 3932 Input Parameters: 3933 + dm - The DM 3934 . numCells - The number of cells owned by this process 3935 . numVertices - The number of vertices to be owned by this process, or PETSC_DECIDE 3936 . NVertices - The global number of vertices, or PETSC_DETERMINE 3937 . numCorners - The number of vertices for each cell 3938 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 3939 3940 Output Parameters: 3941 + vertexSF - (Optional) SF describing complete vertex ownership 3942 - verticesAdjSaved - (Optional) vertex adjacency array 3943 3944 Notes: 3945 Two triangles sharing a face 3946 $ 3947 $ 2 3948 $ / | \ 3949 $ / | \ 3950 $ / | \ 3951 $ 0 0 | 1 3 3952 $ \ | / 3953 $ \ | / 3954 $ \ | / 3955 $ 1 3956 would have input 3957 $ numCells = 2, numVertices = 4 3958 $ cells = [0 1 2 1 3 2] 3959 $ 3960 which would result in the DMPlex 3961 $ 3962 $ 4 3963 $ / | \ 3964 $ / | \ 3965 $ / | \ 3966 $ 2 0 | 1 5 3967 $ \ | / 3968 $ \ | / 3969 $ \ | / 3970 $ 3 3971 3972 Vertices are implicitly numbered consecutively 0,...,NVertices. 3973 Each rank owns a chunk of numVertices consecutive vertices. 3974 If numVertices is PETSC_DECIDE, PETSc will distribute them as evenly as possible using PetscLayout. 3975 If NVertices is PETSC_DETERMINE and numVertices is PETSC_DECIDE, NVertices is computed by PETSc as the maximum vertex index in cells + 1. 3976 If only NVertices is PETSC_DETERMINE, it is computed as the sum of numVertices over all ranks. 3977 3978 The cell distribution is arbitrary non-overlapping, independent of the vertex distribution. 3979 3980 Not currently supported in Fortran. 3981 3982 Level: advanced 3983 3984 .seealso: DMPlexBuildFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildCoordinatesFromCellListParallel() 3985 @*/ 3986 PetscErrorCode DMPlexBuildFromCellListParallel(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, const PetscInt cells[], PetscSF *vertexSF, PetscInt **verticesAdjSaved) 3987 { 3988 PetscSF sfPoint; 3989 PetscLayout layout; 3990 PetscInt numVerticesAdj, *verticesAdj, *cones, c, p; 3991 PetscErrorCode ierr; 3992 3993 PetscFunctionBegin; 3994 PetscValidLogicalCollectiveInt(dm,NVertices,4); 3995 ierr = PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3996 /* Get/check global number of vertices */ 3997 { 3998 PetscInt NVerticesInCells, i; 3999 const PetscInt len = numCells * numCorners; 4000 4001 /* NVerticesInCells = max(cells) + 1 */ 4002 NVerticesInCells = PETSC_MIN_INT; 4003 for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 4004 ++NVerticesInCells; 4005 ierr = MPI_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject) dm));CHKERRMPI(ierr); 4006 4007 if (numVertices == PETSC_DECIDE && NVertices == PETSC_DECIDE) NVertices = NVerticesInCells; 4008 else PetscCheckFalse(NVertices != PETSC_DECIDE && NVertices < NVerticesInCells,PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Specified global number of vertices %D must be greater than or equal to the number of vertices in cells %D",NVertices,NVerticesInCells); 4009 } 4010 /* Count locally unique vertices */ 4011 { 4012 PetscHSetI vhash; 4013 PetscInt off = 0; 4014 4015 ierr = PetscHSetICreate(&vhash);CHKERRQ(ierr); 4016 for (c = 0; c < numCells; ++c) { 4017 for (p = 0; p < numCorners; ++p) { 4018 ierr = PetscHSetIAdd(vhash, cells[c*numCorners+p]);CHKERRQ(ierr); 4019 } 4020 } 4021 ierr = PetscHSetIGetSize(vhash, &numVerticesAdj);CHKERRQ(ierr); 4022 if (!verticesAdjSaved) { ierr = PetscMalloc1(numVerticesAdj, &verticesAdj);CHKERRQ(ierr); } 4023 else { verticesAdj = *verticesAdjSaved; } 4024 ierr = PetscHSetIGetElems(vhash, &off, verticesAdj);CHKERRQ(ierr); 4025 ierr = PetscHSetIDestroy(&vhash);CHKERRQ(ierr); 4026 PetscCheckFalse(off != numVerticesAdj,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj); 4027 } 4028 ierr = PetscSortInt(numVerticesAdj, verticesAdj);CHKERRQ(ierr); 4029 /* Create cones */ 4030 ierr = DMPlexSetChart(dm, 0, numCells+numVerticesAdj);CHKERRQ(ierr); 4031 for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);} 4032 ierr = DMSetUp(dm);CHKERRQ(ierr); 4033 ierr = DMPlexGetCones(dm,&cones);CHKERRQ(ierr); 4034 for (c = 0; c < numCells; ++c) { 4035 for (p = 0; p < numCorners; ++p) { 4036 const PetscInt gv = cells[c*numCorners+p]; 4037 PetscInt lv; 4038 4039 /* Positions within verticesAdj form 0-based local vertex numbering; 4040 we need to shift it by numCells to get correct DAG points (cells go first) */ 4041 ierr = PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);CHKERRQ(ierr); 4042 PetscCheckFalse(lv < 0,PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv); 4043 cones[c*numCorners+p] = lv+numCells; 4044 } 4045 } 4046 /* Build point sf */ 4047 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &layout);CHKERRQ(ierr); 4048 ierr = PetscLayoutSetSize(layout, NVertices);CHKERRQ(ierr); 4049 ierr = PetscLayoutSetLocalSize(layout, numVertices);CHKERRQ(ierr); 4050 ierr = PetscLayoutSetBlockSize(layout, 1);CHKERRQ(ierr); 4051 ierr = PetscSFCreateByMatchingIndices(layout, numVerticesAdj, verticesAdj, NULL, numCells, numVerticesAdj, verticesAdj, NULL, numCells, vertexSF, &sfPoint);CHKERRQ(ierr); 4052 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 4053 if (!verticesAdjSaved) { ierr = PetscFree(verticesAdj);CHKERRQ(ierr); } 4054 ierr = PetscObjectSetName((PetscObject) sfPoint, "point SF");CHKERRQ(ierr); 4055 if (dm->sf) { 4056 const char *prefix; 4057 4058 ierr = PetscObjectGetOptionsPrefix((PetscObject)dm->sf, &prefix);CHKERRQ(ierr); 4059 ierr = PetscObjectSetOptionsPrefix((PetscObject)sfPoint, prefix);CHKERRQ(ierr); 4060 } 4061 ierr = DMSetPointSF(dm, sfPoint);CHKERRQ(ierr); 4062 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 4063 if (vertexSF) {ierr = PetscObjectSetName((PetscObject)(*vertexSF), "Vertex Ownership SF");CHKERRQ(ierr);} 4064 /* Fill in the rest of the topology structure */ 4065 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 4066 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 4067 ierr = PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 4068 PetscFunctionReturn(0); 4069 } 4070 4071 /*@C 4072 DMPlexBuildCoordinatesFromCellListParallel - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output) 4073 4074 Input Parameters: 4075 + dm - The DM 4076 . spaceDim - The spatial dimension used for coordinates 4077 . sfVert - SF describing complete vertex ownership 4078 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 4079 4080 Level: advanced 4081 4082 Notes: 4083 Not currently supported in Fortran. 4084 4085 .seealso: DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellListParallel() 4086 @*/ 4087 PetscErrorCode DMPlexBuildCoordinatesFromCellListParallel(DM dm, PetscInt spaceDim, PetscSF sfVert, const PetscReal vertexCoords[]) 4088 { 4089 PetscSection coordSection; 4090 Vec coordinates; 4091 PetscScalar *coords; 4092 PetscInt numVertices, numVerticesAdj, coordSize, v, vStart, vEnd; 4093 PetscErrorCode ierr; 4094 4095 PetscFunctionBegin; 4096 ierr = PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 4097 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 4098 PetscCheckFalse(vStart < 0 || vEnd < 0,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 4099 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 4100 ierr = PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);CHKERRQ(ierr); 4101 PetscCheckFalse(vEnd - vStart != numVerticesAdj,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Supplied sfVert has wrong number of leaves = %D != %D = vEnd - vStart",numVerticesAdj,vEnd - vStart); 4102 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 4103 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 4104 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 4105 ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr); 4106 for (v = vStart; v < vEnd; ++v) { 4107 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 4108 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 4109 } 4110 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 4111 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 4112 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 4113 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 4114 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 4115 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 4116 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 4117 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 4118 { 4119 MPI_Datatype coordtype; 4120 4121 /* Need a temp buffer for coords if we have complex/single */ 4122 ierr = MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);CHKERRMPI(ierr); 4123 ierr = MPI_Type_commit(&coordtype);CHKERRMPI(ierr); 4124 #if defined(PETSC_USE_COMPLEX) 4125 { 4126 PetscScalar *svertexCoords; 4127 PetscInt i; 4128 ierr = PetscMalloc1(numVertices*spaceDim,&svertexCoords);CHKERRQ(ierr); 4129 for (i=0; i<numVertices*spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 4130 ierr = PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 4131 ierr = PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 4132 ierr = PetscFree(svertexCoords);CHKERRQ(ierr); 4133 } 4134 #else 4135 ierr = PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 4136 ierr = PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 4137 #endif 4138 ierr = MPI_Type_free(&coordtype);CHKERRMPI(ierr); 4139 } 4140 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 4141 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 4142 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 4143 ierr = PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 4144 PetscFunctionReturn(0); 4145 } 4146 4147 /*@ 4148 DMPlexCreateFromCellListParallelPetsc - Create distributed DMPLEX from a list of vertices for each cell (common mesh generator output) 4149 4150 Input Parameters: 4151 + comm - The communicator 4152 . dim - The topological dimension of the mesh 4153 . numCells - The number of cells owned by this process 4154 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 4155 . NVertices - The global number of vertices, or PETSC_DECIDE 4156 . numCorners - The number of vertices for each cell 4157 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 4158 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 4159 . spaceDim - The spatial dimension used for coordinates 4160 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 4161 4162 Output Parameters: 4163 + dm - The DM 4164 . vertexSF - (Optional) SF describing complete vertex ownership 4165 - verticesAdjSaved - (Optional) vertex adjacency array 4166 4167 Notes: 4168 This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), 4169 DMPlexBuildFromCellListParallel(), DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellListParallel() 4170 4171 See DMPlexBuildFromCellListParallel() for an example and details about the topology-related parameters. 4172 See DMPlexBuildCoordinatesFromCellListParallel() for details about the geometry-related parameters. 4173 4174 Level: intermediate 4175 4176 .seealso: DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromDAG(), DMPlexCreate() 4177 @*/ 4178 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) 4179 { 4180 PetscSF sfVert; 4181 PetscErrorCode ierr; 4182 4183 PetscFunctionBegin; 4184 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 4185 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 4186 PetscValidLogicalCollectiveInt(*dm, dim, 2); 4187 PetscValidLogicalCollectiveInt(*dm, spaceDim, 9); 4188 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 4189 ierr = DMPlexBuildFromCellListParallel(*dm, numCells, numVertices, NVertices, numCorners, cells, &sfVert, verticesAdj);CHKERRQ(ierr); 4190 if (interpolate) { 4191 DM idm; 4192 4193 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 4194 ierr = DMDestroy(dm);CHKERRQ(ierr); 4195 *dm = idm; 4196 } 4197 ierr = DMPlexBuildCoordinatesFromCellListParallel(*dm, spaceDim, sfVert, vertexCoords);CHKERRQ(ierr); 4198 if (vertexSF) *vertexSF = sfVert; 4199 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 4200 PetscFunctionReturn(0); 4201 } 4202 4203 /*@C 4204 DMPlexBuildFromCellList - Build DMPLEX topology from a list of vertices for each cell (common mesh generator output) 4205 4206 Input Parameters: 4207 + dm - The DM 4208 . numCells - The number of cells owned by this process 4209 . numVertices - The number of vertices owned by this process, or PETSC_DETERMINE 4210 . numCorners - The number of vertices for each cell 4211 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 4212 4213 Level: advanced 4214 4215 Notes: 4216 Two triangles sharing a face 4217 $ 4218 $ 2 4219 $ / | \ 4220 $ / | \ 4221 $ / | \ 4222 $ 0 0 | 1 3 4223 $ \ | / 4224 $ \ | / 4225 $ \ | / 4226 $ 1 4227 would have input 4228 $ numCells = 2, numVertices = 4 4229 $ cells = [0 1 2 1 3 2] 4230 $ 4231 which would result in the DMPlex 4232 $ 4233 $ 4 4234 $ / | \ 4235 $ / | \ 4236 $ / | \ 4237 $ 2 0 | 1 5 4238 $ \ | / 4239 $ \ | / 4240 $ \ | / 4241 $ 3 4242 4243 If numVertices is PETSC_DETERMINE, it is computed by PETSc as the maximum vertex index in cells + 1. 4244 4245 Not currently supported in Fortran. 4246 4247 .seealso: DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListPetsc() 4248 @*/ 4249 PetscErrorCode DMPlexBuildFromCellList(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[]) 4250 { 4251 PetscInt *cones, c, p, dim; 4252 PetscErrorCode ierr; 4253 4254 PetscFunctionBegin; 4255 ierr = PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 4256 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 4257 /* Get/check global number of vertices */ 4258 { 4259 PetscInt NVerticesInCells, i; 4260 const PetscInt len = numCells * numCorners; 4261 4262 /* NVerticesInCells = max(cells) + 1 */ 4263 NVerticesInCells = PETSC_MIN_INT; 4264 for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 4265 ++NVerticesInCells; 4266 4267 if (numVertices == PETSC_DECIDE) numVertices = NVerticesInCells; 4268 else PetscCheckFalse(numVertices < NVerticesInCells,PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Specified number of vertices %D must be greater than or equal to the number of vertices in cells %D",numVertices,NVerticesInCells); 4269 } 4270 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 4271 for (c = 0; c < numCells; ++c) { 4272 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 4273 } 4274 ierr = DMSetUp(dm);CHKERRQ(ierr); 4275 ierr = DMPlexGetCones(dm,&cones);CHKERRQ(ierr); 4276 for (c = 0; c < numCells; ++c) { 4277 for (p = 0; p < numCorners; ++p) { 4278 cones[c*numCorners+p] = cells[c*numCorners+p]+numCells; 4279 } 4280 } 4281 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 4282 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 4283 ierr = PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 4284 PetscFunctionReturn(0); 4285 } 4286 4287 /*@C 4288 DMPlexBuildCoordinatesFromCellList - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output) 4289 4290 Input Parameters: 4291 + dm - The DM 4292 . spaceDim - The spatial dimension used for coordinates 4293 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 4294 4295 Level: advanced 4296 4297 Notes: 4298 Not currently supported in Fortran. 4299 4300 .seealso: DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellList() 4301 @*/ 4302 PetscErrorCode DMPlexBuildCoordinatesFromCellList(DM dm, PetscInt spaceDim, const PetscReal vertexCoords[]) 4303 { 4304 PetscSection coordSection; 4305 Vec coordinates; 4306 DM cdm; 4307 PetscScalar *coords; 4308 PetscInt v, vStart, vEnd, d; 4309 PetscErrorCode ierr; 4310 4311 PetscFunctionBegin; 4312 ierr = PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 4313 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 4314 PetscCheckFalse(vStart < 0 || vEnd < 0,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 4315 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 4316 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 4317 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 4318 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 4319 ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr); 4320 for (v = vStart; v < vEnd; ++v) { 4321 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 4322 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 4323 } 4324 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 4325 4326 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 4327 ierr = DMCreateLocalVector(cdm, &coordinates);CHKERRQ(ierr); 4328 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 4329 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 4330 ierr = VecGetArrayWrite(coordinates, &coords);CHKERRQ(ierr); 4331 for (v = 0; v < vEnd-vStart; ++v) { 4332 for (d = 0; d < spaceDim; ++d) { 4333 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 4334 } 4335 } 4336 ierr = VecRestoreArrayWrite(coordinates, &coords);CHKERRQ(ierr); 4337 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 4338 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 4339 ierr = PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 4340 PetscFunctionReturn(0); 4341 } 4342 4343 /*@ 4344 DMPlexCreateFromCellListPetsc - Create DMPLEX from a list of vertices for each cell (common mesh generator output), but only process 0 takes in the input 4345 4346 Collective on comm 4347 4348 Input Parameters: 4349 + comm - The communicator 4350 . dim - The topological dimension of the mesh 4351 . numCells - The number of cells, only on process 0 4352 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE, only on process 0 4353 . numCorners - The number of vertices for each cell, only on process 0 4354 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 4355 . cells - An array of numCells*numCorners numbers, the vertices for each cell, only on process 0 4356 . spaceDim - The spatial dimension used for coordinates 4357 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex, only on process 0 4358 4359 Output Parameter: 4360 . dm - The DM, which only has points on process 0 4361 4362 Notes: 4363 This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), DMPlexBuildFromCellList(), 4364 DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellList() 4365 4366 See DMPlexBuildFromCellList() for an example and details about the topology-related parameters. 4367 See DMPlexBuildCoordinatesFromCellList() for details about the geometry-related parameters. 4368 See DMPlexCreateFromCellListParallelPetsc() for parallel input 4369 4370 Level: intermediate 4371 4372 .seealso: DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellList(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate() 4373 @*/ 4374 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) 4375 { 4376 PetscMPIInt rank; 4377 PetscErrorCode ierr; 4378 4379 PetscFunctionBegin; 4380 PetscCheckFalse(!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."); 4381 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 4382 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 4383 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 4384 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 4385 if (!rank) {ierr = DMPlexBuildFromCellList(*dm, numCells, numVertices, numCorners, cells);CHKERRQ(ierr);} 4386 else {ierr = DMPlexBuildFromCellList(*dm, 0, 0, 0, NULL);CHKERRQ(ierr);} 4387 if (interpolate) { 4388 DM idm; 4389 4390 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 4391 ierr = DMDestroy(dm);CHKERRQ(ierr); 4392 *dm = idm; 4393 } 4394 if (!rank) {ierr = DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, vertexCoords);CHKERRQ(ierr);} 4395 else {ierr = DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, NULL);CHKERRQ(ierr);} 4396 PetscFunctionReturn(0); 4397 } 4398 4399 /*@ 4400 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 4401 4402 Input Parameters: 4403 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 4404 . depth - The depth of the DAG 4405 . numPoints - Array of size depth + 1 containing the number of points at each depth 4406 . coneSize - The cone size of each point 4407 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 4408 . coneOrientations - The orientation of each cone point 4409 - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim() 4410 4411 Output Parameter: 4412 . dm - The DM 4413 4414 Note: Two triangles sharing a face would have input 4415 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 4416 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 4417 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 4418 $ 4419 which would result in the DMPlex 4420 $ 4421 $ 4 4422 $ / | \ 4423 $ / | \ 4424 $ / | \ 4425 $ 2 0 | 1 5 4426 $ \ | / 4427 $ \ | / 4428 $ \ | / 4429 $ 3 4430 $ 4431 $ Notice that all points are numbered consecutively, unlike DMPlexCreateFromCellListPetsc() 4432 4433 Level: advanced 4434 4435 .seealso: DMPlexCreateFromCellListPetsc(), DMPlexCreate() 4436 @*/ 4437 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 4438 { 4439 Vec coordinates; 4440 PetscSection coordSection; 4441 PetscScalar *coords; 4442 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 4443 PetscErrorCode ierr; 4444 4445 PetscFunctionBegin; 4446 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 4447 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 4448 PetscCheckFalse(dimEmbed < dim,PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %D cannot be less than intrinsic dimension %d",dimEmbed,dim); 4449 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 4450 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 4451 for (p = pStart; p < pEnd; ++p) { 4452 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 4453 if (firstVertex < 0 && !coneSize[p - pStart]) { 4454 firstVertex = p - pStart; 4455 } 4456 } 4457 PetscCheckFalse(firstVertex < 0 && numPoints[0],PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %D vertices but could not find any", numPoints[0]); 4458 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 4459 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 4460 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 4461 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 4462 } 4463 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 4464 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 4465 /* Build coordinates */ 4466 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 4467 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 4468 ierr = PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);CHKERRQ(ierr); 4469 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 4470 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 4471 ierr = PetscSectionSetDof(coordSection, v, dimEmbed);CHKERRQ(ierr); 4472 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);CHKERRQ(ierr); 4473 } 4474 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 4475 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 4476 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 4477 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 4478 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 4479 ierr = VecSetBlockSize(coordinates, dimEmbed);CHKERRQ(ierr); 4480 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 4481 if (vertexCoords) { 4482 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 4483 for (v = 0; v < numPoints[0]; ++v) { 4484 PetscInt off; 4485 4486 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 4487 for (d = 0; d < dimEmbed; ++d) { 4488 coords[off+d] = vertexCoords[v*dimEmbed+d]; 4489 } 4490 } 4491 } 4492 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 4493 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 4494 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 4495 PetscFunctionReturn(0); 4496 } 4497 4498 /*@C 4499 DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file. 4500 4501 + comm - The MPI communicator 4502 . filename - Name of the .dat file 4503 - interpolate - Create faces and edges in the mesh 4504 4505 Output Parameter: 4506 . dm - The DM object representing the mesh 4507 4508 Note: The format is the simplest possible: 4509 $ Ne 4510 $ v0 v1 ... vk 4511 $ Nv 4512 $ x y z marker 4513 4514 Level: beginner 4515 4516 .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate() 4517 @*/ 4518 PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 4519 { 4520 DMLabel marker; 4521 PetscViewer viewer; 4522 Vec coordinates; 4523 PetscSection coordSection; 4524 PetscScalar *coords; 4525 char line[PETSC_MAX_PATH_LEN]; 4526 PetscInt dim = 3, cdim = 3, coordSize, v, c, d; 4527 PetscMPIInt rank; 4528 int snum, Nv, Nc, Ncn, Nl; 4529 PetscErrorCode ierr; 4530 4531 PetscFunctionBegin; 4532 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 4533 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 4534 ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr); 4535 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 4536 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 4537 if (rank == 0) { 4538 ierr = PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);CHKERRQ(ierr); 4539 snum = sscanf(line, "%d %d %d %d", &Nc, &Nv, &Ncn, &Nl); 4540 PetscCheckFalse(snum != 4,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4541 } else { 4542 Nc = Nv = Ncn = Nl = 0; 4543 } 4544 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 4545 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 4546 ierr = DMPlexSetChart(*dm, 0, Nc+Nv);CHKERRQ(ierr); 4547 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 4548 ierr = DMSetCoordinateDim(*dm, cdim);CHKERRQ(ierr); 4549 /* Read topology */ 4550 if (rank == 0) { 4551 char format[PETSC_MAX_PATH_LEN]; 4552 PetscInt cone[8]; 4553 int vbuf[8], v; 4554 4555 for (c = 0; c < Ncn; ++c) {format[c*3+0] = '%'; format[c*3+1] = 'd'; format[c*3+2] = ' ';} 4556 format[Ncn*3-1] = '\0'; 4557 for (c = 0; c < Nc; ++c) {ierr = DMPlexSetConeSize(*dm, c, Ncn);CHKERRQ(ierr);} 4558 ierr = DMSetUp(*dm);CHKERRQ(ierr); 4559 for (c = 0; c < Nc; ++c) { 4560 ierr = PetscViewerRead(viewer, line, Ncn, NULL, PETSC_STRING);CHKERRQ(ierr); 4561 switch (Ncn) { 4562 case 2: snum = sscanf(line, format, &vbuf[0], &vbuf[1]);break; 4563 case 3: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2]);break; 4564 case 4: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3]);break; 4565 case 6: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5]);break; 4566 case 8: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5], &vbuf[6], &vbuf[7]);break; 4567 default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "No cell shape with %D vertices", Ncn); 4568 } 4569 PetscCheckFalse(snum != Ncn,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4570 for (v = 0; v < Ncn; ++v) cone[v] = vbuf[v] + Nc; 4571 /* Hexahedra are inverted */ 4572 if (Ncn == 8) { 4573 PetscInt tmp = cone[1]; 4574 cone[1] = cone[3]; 4575 cone[3] = tmp; 4576 } 4577 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 4578 } 4579 } 4580 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 4581 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 4582 /* Read coordinates */ 4583 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 4584 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 4585 ierr = PetscSectionSetFieldComponents(coordSection, 0, cdim);CHKERRQ(ierr); 4586 ierr = PetscSectionSetChart(coordSection, Nc, Nc + Nv);CHKERRQ(ierr); 4587 for (v = Nc; v < Nc+Nv; ++v) { 4588 ierr = PetscSectionSetDof(coordSection, v, cdim);CHKERRQ(ierr); 4589 ierr = PetscSectionSetFieldDof(coordSection, v, 0, cdim);CHKERRQ(ierr); 4590 } 4591 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 4592 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 4593 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 4594 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 4595 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 4596 ierr = VecSetBlockSize(coordinates, cdim);CHKERRQ(ierr); 4597 ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr); 4598 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 4599 if (rank == 0) { 4600 char format[PETSC_MAX_PATH_LEN]; 4601 double x[3]; 4602 int l, val[3]; 4603 4604 if (Nl) { 4605 for (l = 0; l < Nl; ++l) {format[l*3+0] = '%'; format[l*3+1] = 'd'; format[l*3+2] = ' ';} 4606 format[Nl*3-1] = '\0'; 4607 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 4608 ierr = DMGetLabel(*dm, "marker", &marker);CHKERRQ(ierr); 4609 } 4610 for (v = 0; v < Nv; ++v) { 4611 ierr = PetscViewerRead(viewer, line, 3+Nl, NULL, PETSC_STRING);CHKERRQ(ierr); 4612 snum = sscanf(line, "%lg %lg %lg", &x[0], &x[1], &x[2]); 4613 PetscCheckFalse(snum != 3,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4614 switch (Nl) { 4615 case 0: snum = 0;break; 4616 case 1: snum = sscanf(line, format, &val[0]);break; 4617 case 2: snum = sscanf(line, format, &val[0], &val[1]);break; 4618 case 3: snum = sscanf(line, format, &val[0], &val[1], &val[2]);break; 4619 default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Request support for %D labels", Nl); 4620 } 4621 PetscCheckFalse(snum != Nl,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4622 for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d]; 4623 for (l = 0; l < Nl; ++l) {ierr = DMLabelSetValue(marker, v+Nc, val[l]);CHKERRQ(ierr);} 4624 } 4625 } 4626 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 4627 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 4628 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 4629 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 4630 if (interpolate) { 4631 DM idm; 4632 DMLabel bdlabel; 4633 4634 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 4635 ierr = DMDestroy(dm);CHKERRQ(ierr); 4636 *dm = idm; 4637 4638 if (!Nl) { 4639 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 4640 ierr = DMGetLabel(*dm, "marker", &bdlabel);CHKERRQ(ierr); 4641 ierr = DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 4642 ierr = DMPlexLabelComplete(*dm, bdlabel);CHKERRQ(ierr); 4643 } 4644 } 4645 PetscFunctionReturn(0); 4646 } 4647 4648 /*@C 4649 DMPlexCreateFromFile - This takes a filename and produces a DM 4650 4651 Input Parameters: 4652 + comm - The communicator 4653 . filename - A file name 4654 . plexname - The object name of the resulting DM, also used for intra-datafile lookup by some formats 4655 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 4656 4657 Output Parameter: 4658 . dm - The DM 4659 4660 Options Database Keys: 4661 . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5 4662 4663 Use -dm_plex_create_ prefix to pass options to the internal PetscViewer, e.g. 4664 $ -dm_plex_create_viewer_hdf5_collective 4665 4666 Notes: 4667 Using PETSCVIEWERHDF5 type with PETSC_VIEWER_HDF5_PETSC format, one can save multiple DMPlex 4668 meshes in a single HDF5 file. This in turn requires one to name the DMPlex object with PetscObjectSetName() 4669 before saving it with DMView() and before loading it with DMLoad() for identification of the mesh object. 4670 The input parameter name is thus used to name the DMPlex object when DMPlexCreateFromFile() internally 4671 calls DMLoad(). Currently, name is ignored for other viewer types and/or formats. 4672 4673 Level: beginner 4674 4675 .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellListPetsc(), DMPlexCreate(), PetscObjectSetName(), DMView(), DMLoad() 4676 @*/ 4677 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], const char plexname[], PetscBool interpolate, DM *dm) 4678 { 4679 const char *extGmsh = ".msh"; 4680 const char *extGmsh2 = ".msh2"; 4681 const char *extGmsh4 = ".msh4"; 4682 const char *extCGNS = ".cgns"; 4683 const char *extExodus = ".exo"; 4684 const char *extExodus_e = ".e"; 4685 const char *extGenesis = ".gen"; 4686 const char *extFluent = ".cas"; 4687 const char *extHDF5 = ".h5"; 4688 const char *extMed = ".med"; 4689 const char *extPLY = ".ply"; 4690 const char *extEGADSLite = ".egadslite"; 4691 const char *extEGADS = ".egads"; 4692 const char *extIGES = ".igs"; 4693 const char *extSTEP = ".stp"; 4694 const char *extCV = ".dat"; 4695 size_t len; 4696 PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isEGADSLite, isEGADS, isIGES, isSTEP, isCV; 4697 PetscMPIInt rank; 4698 PetscErrorCode ierr; 4699 4700 PetscFunctionBegin; 4701 PetscValidCharPointer(filename, 2); 4702 if (plexname) PetscValidCharPointer(plexname, 3); 4703 PetscValidPointer(dm, 5); 4704 ierr = DMInitializePackage();CHKERRQ(ierr); 4705 ierr = PetscLogEventBegin(DMPLEX_CreateFromFile,0,0,0,0);CHKERRQ(ierr); 4706 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 4707 ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); 4708 PetscCheckFalse(!len,comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 4709 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);CHKERRQ(ierr); 4710 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh2, 5, &isGmsh2);CHKERRQ(ierr); 4711 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh4, 5, &isGmsh4);CHKERRQ(ierr); 4712 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);CHKERRQ(ierr); 4713 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);CHKERRQ(ierr); 4714 if (!isExodus) { 4715 ierr = PetscStrncmp(&filename[PetscMax(0,len-2)], extExodus_e, 2, &isExodus);CHKERRQ(ierr); 4716 } 4717 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);CHKERRQ(ierr); 4718 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);CHKERRQ(ierr); 4719 ierr = PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);CHKERRQ(ierr); 4720 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);CHKERRQ(ierr); 4721 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);CHKERRQ(ierr); 4722 ierr = PetscStrncmp(&filename[PetscMax(0,len-10)], extEGADSLite, 10, &isEGADSLite);CHKERRQ(ierr); 4723 ierr = PetscStrncmp(&filename[PetscMax(0,len-6)], extEGADS, 6, &isEGADS);CHKERRQ(ierr); 4724 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extIGES, 4, &isIGES);CHKERRQ(ierr); 4725 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extSTEP, 4, &isSTEP);CHKERRQ(ierr); 4726 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);CHKERRQ(ierr); 4727 if (isGmsh || isGmsh2 || isGmsh4) { 4728 ierr = DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4729 } else if (isCGNS) { 4730 ierr = DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4731 } else if (isExodus || isGenesis) { 4732 ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4733 } else if (isFluent) { 4734 ierr = DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4735 } else if (isHDF5) { 4736 PetscBool load_hdf5_xdmf = PETSC_FALSE; 4737 PetscViewer viewer; 4738 4739 /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */ 4740 ierr = PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf", 5, &load_hdf5_xdmf);CHKERRQ(ierr); 4741 ierr = PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);CHKERRQ(ierr); 4742 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 4743 ierr = PetscViewerSetType(viewer, PETSCVIEWERHDF5);CHKERRQ(ierr); 4744 ierr = PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_");CHKERRQ(ierr); 4745 ierr = PetscViewerSetFromOptions(viewer);CHKERRQ(ierr); 4746 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 4747 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 4748 4749 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 4750 ierr = PetscObjectSetName((PetscObject)(*dm), plexname);CHKERRQ(ierr); 4751 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 4752 if (load_hdf5_xdmf) {ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);CHKERRQ(ierr);} 4753 ierr = DMLoad(*dm, viewer);CHKERRQ(ierr); 4754 if (load_hdf5_xdmf) {ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);} 4755 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 4756 4757 if (interpolate) { 4758 DM idm; 4759 4760 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 4761 ierr = DMDestroy(dm);CHKERRQ(ierr); 4762 *dm = idm; 4763 } 4764 } else if (isMed) { 4765 ierr = DMPlexCreateMedFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4766 } else if (isPLY) { 4767 ierr = DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4768 } else if (isEGADSLite || isEGADS || isIGES || isSTEP) { 4769 if (isEGADSLite) {ierr = DMPlexCreateEGADSLiteFromFile(comm, filename, dm);CHKERRQ(ierr);} 4770 else {ierr = DMPlexCreateEGADSFromFile(comm, filename, dm);CHKERRQ(ierr);} 4771 if (!interpolate) { 4772 DM udm; 4773 4774 ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr); 4775 ierr = DMDestroy(dm);CHKERRQ(ierr); 4776 *dm = udm; 4777 } 4778 } else if (isCV) { 4779 ierr = DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4780 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 4781 ierr = PetscStrlen(plexname, &len);CHKERRQ(ierr); 4782 if (len) {ierr = PetscObjectSetName((PetscObject)(*dm), plexname);CHKERRQ(ierr);} 4783 ierr = PetscLogEventEnd(DMPLEX_CreateFromFile,0,0,0,0);CHKERRQ(ierr); 4784 PetscFunctionReturn(0); 4785 } 4786