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 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 ierr = PetscFECreateLagrange(PETSC_COMM_SELF, dim, dE, simplex, degree, qorder, &fe);CHKERRQ(ierr); 195 ierr = DMSetField(cdm, 0, NULL, (PetscObject) fe);CHKERRQ(ierr); 196 ierr = DMCreateDS(cdm);CHKERRQ(ierr); 197 ierr = DMProjectCoordinates(dm, fe);CHKERRQ(ierr); 198 ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); 199 } 200 mesh->coordFunc = coordFunc; 201 PetscFunctionReturn(0); 202 } 203 204 /*@ 205 DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement. 206 207 Collective 208 209 Input Parameters: 210 + comm - The communicator for the DM object 211 . dim - The spatial dimension 212 . simplex - Flag for simplicial cells, otherwise they are tensor product cells 213 . interpolate - Flag to create intermediate mesh pieces (edges, faces) 214 - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell 215 216 Output Parameter: 217 . dm - The DM object 218 219 Level: beginner 220 221 .seealso: DMSetType(), DMCreate() 222 @*/ 223 PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscReal refinementLimit, DM *newdm) 224 { 225 DM dm; 226 PetscMPIInt rank; 227 PetscErrorCode ierr; 228 229 PetscFunctionBegin; 230 ierr = DMCreate(comm, &dm);CHKERRQ(ierr); 231 ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr); 232 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 233 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 234 switch (dim) { 235 case 2: 236 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "triangular");CHKERRQ(ierr);} 237 else {ierr = PetscObjectSetName((PetscObject) dm, "quadrilateral");CHKERRQ(ierr);} 238 break; 239 case 3: 240 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "tetrahedral");CHKERRQ(ierr);} 241 else {ierr = PetscObjectSetName((PetscObject) dm, "hexahedral");CHKERRQ(ierr);} 242 break; 243 default: 244 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %D", dim); 245 } 246 if (rank) { 247 PetscInt numPoints[2] = {0, 0}; 248 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 249 } else { 250 switch (dim) { 251 case 2: 252 if (simplex) { 253 PetscInt numPoints[2] = {4, 2}; 254 PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; 255 PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; 256 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 257 PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5}; 258 259 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 260 } else { 261 PetscInt numPoints[2] = {6, 2}; 262 PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; 263 PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4}; 264 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 265 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}; 266 267 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 268 } 269 break; 270 case 3: 271 if (simplex) { 272 PetscInt numPoints[2] = {5, 2}; 273 PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; 274 PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; 275 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 276 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}; 277 278 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 279 } else { 280 PetscInt numPoints[2] = {12, 2}; 281 PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 282 PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8}; 283 PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 284 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, 285 -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5, 286 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5}; 287 288 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 289 } 290 break; 291 default: 292 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %D", dim); 293 } 294 } 295 *newdm = dm; 296 if (refinementLimit > 0.0) { 297 DM rdm; 298 const char *name; 299 300 ierr = DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);CHKERRQ(ierr); 301 ierr = DMPlexSetRefinementLimit(*newdm, refinementLimit);CHKERRQ(ierr); 302 ierr = DMRefine(*newdm, comm, &rdm);CHKERRQ(ierr); 303 ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); 304 ierr = PetscObjectSetName((PetscObject) rdm, name);CHKERRQ(ierr); 305 ierr = DMDestroy(newdm);CHKERRQ(ierr); 306 *newdm = rdm; 307 } 308 if (interpolate) { 309 DM idm; 310 311 ierr = DMPlexInterpolate(*newdm, &idm);CHKERRQ(ierr); 312 ierr = DMDestroy(newdm);CHKERRQ(ierr); 313 *newdm = idm; 314 } 315 PetscFunctionReturn(0); 316 } 317 318 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 319 { 320 const PetscInt numVertices = 2; 321 PetscInt markerRight = 1; 322 PetscInt markerLeft = 1; 323 PetscBool markerSeparate = PETSC_FALSE; 324 Vec coordinates; 325 PetscSection coordSection; 326 PetscScalar *coords; 327 PetscInt coordSize; 328 PetscMPIInt rank; 329 PetscInt cdim = 1, v; 330 PetscErrorCode ierr; 331 332 PetscFunctionBegin; 333 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 334 if (markerSeparate) { 335 markerRight = 2; 336 markerLeft = 1; 337 } 338 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRMPI(ierr); 339 if (!rank) { 340 ierr = DMPlexSetChart(dm, 0, numVertices);CHKERRQ(ierr); 341 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 342 ierr = DMSetLabelValue(dm, "marker", 0, markerLeft);CHKERRQ(ierr); 343 ierr = DMSetLabelValue(dm, "marker", 1, markerRight);CHKERRQ(ierr); 344 } 345 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 346 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 347 /* Build coordinates */ 348 ierr = DMSetCoordinateDim(dm, cdim);CHKERRQ(ierr); 349 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 350 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 351 ierr = PetscSectionSetChart(coordSection, 0, numVertices);CHKERRQ(ierr); 352 ierr = PetscSectionSetFieldComponents(coordSection, 0, cdim);CHKERRQ(ierr); 353 for (v = 0; v < numVertices; ++v) { 354 ierr = PetscSectionSetDof(coordSection, v, cdim);CHKERRQ(ierr); 355 ierr = PetscSectionSetFieldDof(coordSection, v, 0, cdim);CHKERRQ(ierr); 356 } 357 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 358 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 359 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 360 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 361 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 362 ierr = VecSetBlockSize(coordinates, cdim);CHKERRQ(ierr); 363 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 364 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 365 coords[0] = lower[0]; 366 coords[1] = upper[0]; 367 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 368 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 369 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 370 PetscFunctionReturn(0); 371 } 372 373 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 374 { 375 const PetscInt numVertices = (edges[0]+1)*(edges[1]+1); 376 const PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1]; 377 PetscInt markerTop = 1; 378 PetscInt markerBottom = 1; 379 PetscInt markerRight = 1; 380 PetscInt markerLeft = 1; 381 PetscBool markerSeparate = PETSC_FALSE; 382 Vec coordinates; 383 PetscSection coordSection; 384 PetscScalar *coords; 385 PetscInt coordSize; 386 PetscMPIInt rank; 387 PetscInt v, vx, vy; 388 PetscErrorCode ierr; 389 390 PetscFunctionBegin; 391 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 392 if (markerSeparate) { 393 markerTop = 3; 394 markerBottom = 1; 395 markerRight = 2; 396 markerLeft = 4; 397 } 398 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRMPI(ierr); 399 if (rank == 0) { 400 PetscInt e, ex, ey; 401 402 ierr = DMPlexSetChart(dm, 0, numEdges+numVertices);CHKERRQ(ierr); 403 for (e = 0; e < numEdges; ++e) { 404 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 405 } 406 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 407 for (vx = 0; vx <= edges[0]; vx++) { 408 for (ey = 0; ey < edges[1]; ey++) { 409 PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1); 410 PetscInt vertex = ey*(edges[0]+1) + vx + numEdges; 411 PetscInt cone[2]; 412 413 cone[0] = vertex; cone[1] = vertex+edges[0]+1; 414 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 415 if (vx == edges[0]) { 416 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 417 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 418 if (ey == edges[1]-1) { 419 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 420 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerRight);CHKERRQ(ierr); 421 } 422 } else if (vx == 0) { 423 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 424 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 425 if (ey == edges[1]-1) { 426 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 427 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft);CHKERRQ(ierr); 428 } 429 } 430 } 431 } 432 for (vy = 0; vy <= edges[1]; vy++) { 433 for (ex = 0; ex < edges[0]; ex++) { 434 PetscInt edge = vy*edges[0] + ex; 435 PetscInt vertex = vy*(edges[0]+1) + ex + numEdges; 436 PetscInt cone[2]; 437 438 cone[0] = vertex; cone[1] = vertex+1; 439 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 440 if (vy == edges[1]) { 441 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 442 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 443 if (ex == edges[0]-1) { 444 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 445 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerTop);CHKERRQ(ierr); 446 } 447 } else if (vy == 0) { 448 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 449 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 450 if (ex == edges[0]-1) { 451 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 452 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom);CHKERRQ(ierr); 453 } 454 } 455 } 456 } 457 } 458 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 459 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 460 /* Build coordinates */ 461 ierr = DMSetCoordinateDim(dm, 2);CHKERRQ(ierr); 462 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 463 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 464 ierr = PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);CHKERRQ(ierr); 465 ierr = PetscSectionSetFieldComponents(coordSection, 0, 2);CHKERRQ(ierr); 466 for (v = numEdges; v < numEdges+numVertices; ++v) { 467 ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr); 468 ierr = PetscSectionSetFieldDof(coordSection, v, 0, 2);CHKERRQ(ierr); 469 } 470 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 471 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 472 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 473 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 474 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 475 ierr = VecSetBlockSize(coordinates, 2);CHKERRQ(ierr); 476 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 477 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 478 for (vy = 0; vy <= edges[1]; ++vy) { 479 for (vx = 0; vx <= edges[0]; ++vx) { 480 coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx; 481 coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy; 482 } 483 } 484 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 485 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 486 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 487 PetscFunctionReturn(0); 488 } 489 490 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) 491 { 492 PetscInt vertices[3], numVertices; 493 PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2]; 494 Vec coordinates; 495 PetscSection coordSection; 496 PetscScalar *coords; 497 PetscInt coordSize; 498 PetscMPIInt rank; 499 PetscInt v, vx, vy, vz; 500 PetscInt voffset, iface=0, cone[4]; 501 PetscErrorCode ierr; 502 503 PetscFunctionBegin; 504 PetscCheckFalse((faces[0] < 1) || (faces[1] < 1) || (faces[2] < 1),PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Must have at least 1 face per side"); 505 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRMPI(ierr); 506 vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1; 507 numVertices = vertices[0]*vertices[1]*vertices[2]; 508 if (rank == 0) { 509 PetscInt f; 510 511 ierr = DMPlexSetChart(dm, 0, numFaces+numVertices);CHKERRQ(ierr); 512 for (f = 0; f < numFaces; ++f) { 513 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 514 } 515 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 516 517 /* Side 0 (Top) */ 518 for (vy = 0; vy < faces[1]; vy++) { 519 for (vx = 0; vx < faces[0]; vx++) { 520 voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx; 521 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0]; 522 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 523 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 524 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 525 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 526 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 527 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);CHKERRQ(ierr); 528 iface++; 529 } 530 } 531 532 /* Side 1 (Bottom) */ 533 for (vy = 0; vy < faces[1]; vy++) { 534 for (vx = 0; vx < faces[0]; vx++) { 535 voffset = numFaces + vy*(faces[0]+1) + vx; 536 cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1; 537 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 538 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 539 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 540 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 541 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 542 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);CHKERRQ(ierr); 543 iface++; 544 } 545 } 546 547 /* Side 2 (Front) */ 548 for (vz = 0; vz < faces[2]; vz++) { 549 for (vx = 0; vx < faces[0]; vx++) { 550 voffset = numFaces + vz*vertices[0]*vertices[1] + vx; 551 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1]; 552 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 553 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 554 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 555 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 556 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 557 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);CHKERRQ(ierr); 558 iface++; 559 } 560 } 561 562 /* Side 3 (Back) */ 563 for (vz = 0; vz < faces[2]; vz++) { 564 for (vx = 0; vx < faces[0]; vx++) { 565 voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx; 566 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1; 567 cone[2] = voffset+1; cone[3] = voffset; 568 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 569 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 570 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 571 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 572 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 573 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);CHKERRQ(ierr); 574 iface++; 575 } 576 } 577 578 /* Side 4 (Left) */ 579 for (vz = 0; vz < faces[2]; vz++) { 580 for (vy = 0; vy < faces[1]; vy++) { 581 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0]; 582 cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1]; 583 cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0]; 584 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 585 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 586 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 587 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 588 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[1]+0, 1);CHKERRQ(ierr); 589 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);CHKERRQ(ierr); 590 iface++; 591 } 592 } 593 594 /* Side 5 (Right) */ 595 for (vz = 0; vz < faces[2]; vz++) { 596 for (vy = 0; vy < faces[1]; vy++) { 597 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + faces[0]; 598 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset; 599 cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0]; 600 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 601 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 602 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 603 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 604 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 605 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);CHKERRQ(ierr); 606 iface++; 607 } 608 } 609 } 610 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 611 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 612 /* Build coordinates */ 613 ierr = DMSetCoordinateDim(dm, 3);CHKERRQ(ierr); 614 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 615 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 616 ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr); 617 ierr = PetscSectionSetFieldComponents(coordSection, 0, 3);CHKERRQ(ierr); 618 for (v = numFaces; v < numFaces+numVertices; ++v) { 619 ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr); 620 ierr = PetscSectionSetFieldDof(coordSection, v, 0, 3);CHKERRQ(ierr); 621 } 622 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 623 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 624 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 625 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 626 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 627 ierr = VecSetBlockSize(coordinates, 3);CHKERRQ(ierr); 628 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 629 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 630 for (vz = 0; vz <= faces[2]; ++vz) { 631 for (vy = 0; vy <= faces[1]; ++vy) { 632 for (vx = 0; vx <= faces[0]; ++vx) { 633 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx; 634 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy; 635 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz; 636 } 637 } 638 } 639 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 640 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 641 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 642 PetscFunctionReturn(0); 643 } 644 645 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate) 646 { 647 PetscErrorCode ierr; 648 649 PetscFunctionBegin; 650 PetscValidLogicalCollectiveInt(dm, dim, 2); 651 ierr = DMSetDimension(dm, dim-1);CHKERRQ(ierr); 652 ierr = DMSetCoordinateDim(dm, dim);CHKERRQ(ierr); 653 switch (dim) { 654 case 1: ierr = DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(dm, lower, upper, faces);CHKERRQ(ierr);break; 655 case 2: ierr = DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(dm, lower, upper, faces);CHKERRQ(ierr);break; 656 case 3: ierr = DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(dm, lower, upper, faces);CHKERRQ(ierr);break; 657 default: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Dimension not supported: %D", dim); 658 } 659 if (interpolate) {ierr = DMPlexInterpolateInPlace_Internal(dm);CHKERRQ(ierr);} 660 PetscFunctionReturn(0); 661 } 662 663 /*@C 664 DMPlexCreateBoxSurfaceMesh - Creates a mesh on the surface of the tensor product of unit intervals (box) using tensor cells (hexahedra). 665 666 Collective 667 668 Input Parameters: 669 + comm - The communicator for the DM object 670 . dim - The spatial dimension of the box, so the resulting mesh is has dimension dim-1 671 . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 672 . lower - The lower left corner, or NULL for (0, 0, 0) 673 . upper - The upper right corner, or NULL for (1, 1, 1) 674 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 675 676 Output Parameter: 677 . dm - The DM object 678 679 Level: beginner 680 681 .seealso: DMSetFromOptions(), DMPlexCreateBoxMesh(), DMPlexCreateFromFile(), DMSetType(), DMCreate() 682 @*/ 683 PetscErrorCode DMPlexCreateBoxSurfaceMesh(MPI_Comm comm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate, DM *dm) 684 { 685 PetscInt fac[3] = {1, 1, 1}; 686 PetscReal low[3] = {0, 0, 0}; 687 PetscReal upp[3] = {1, 1, 1}; 688 PetscErrorCode ierr; 689 690 PetscFunctionBegin; 691 ierr = DMCreate(comm,dm);CHKERRQ(ierr); 692 ierr = DMSetType(*dm,DMPLEX);CHKERRQ(ierr); 693 ierr = DMPlexCreateBoxSurfaceMesh_Internal(*dm, dim, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, interpolate);CHKERRQ(ierr); 694 PetscFunctionReturn(0); 695 } 696 697 static PetscErrorCode DMPlexCreateLineMesh_Internal(DM dm,PetscInt segments,PetscReal lower,PetscReal upper,DMBoundaryType bd) 698 { 699 PetscInt i,fStart,fEnd,numCells = 0,numVerts = 0; 700 PetscInt numPoints[2],*coneSize,*cones,*coneOrientations; 701 PetscScalar *vertexCoords; 702 PetscReal L,maxCell; 703 PetscBool markerSeparate = PETSC_FALSE; 704 PetscInt markerLeft = 1, faceMarkerLeft = 1; 705 PetscInt markerRight = 1, faceMarkerRight = 2; 706 PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE; 707 PetscMPIInt rank; 708 PetscErrorCode ierr; 709 710 PetscFunctionBegin; 711 PetscValidPointer(dm,1); 712 713 ierr = DMSetDimension(dm,1);CHKERRQ(ierr); 714 ierr = DMCreateLabel(dm,"marker");CHKERRQ(ierr); 715 ierr = DMCreateLabel(dm,"Face Sets");CHKERRQ(ierr); 716 717 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm),&rank);CHKERRMPI(ierr); 718 if (rank == 0) numCells = segments; 719 if (rank == 0) numVerts = segments + (wrap ? 0 : 1); 720 721 numPoints[0] = numVerts ; numPoints[1] = numCells; 722 ierr = PetscMalloc4(numCells+numVerts,&coneSize,numCells*2,&cones,numCells+numVerts,&coneOrientations,numVerts,&vertexCoords);CHKERRQ(ierr); 723 ierr = PetscArrayzero(coneOrientations,numCells+numVerts);CHKERRQ(ierr); 724 for (i = 0; i < numCells; ++i) { coneSize[i] = 2; } 725 for (i = 0; i < numVerts; ++i) { coneSize[numCells+i] = 0; } 726 for (i = 0; i < numCells; ++i) { cones[2*i] = numCells + i%numVerts; cones[2*i+1] = numCells + (i+1)%numVerts; } 727 for (i = 0; i < numVerts; ++i) { vertexCoords[i] = lower + (upper-lower)*((PetscReal)i/(PetscReal)numCells); } 728 ierr = DMPlexCreateFromDAG(dm,1,numPoints,coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 729 ierr = PetscFree4(coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 730 731 ierr = PetscOptionsGetBool(((PetscObject)dm)->options,((PetscObject)dm)->prefix,"-dm_plex_separate_marker",&markerSeparate,NULL);CHKERRQ(ierr); 732 if (markerSeparate) { markerLeft = faceMarkerLeft; markerRight = faceMarkerRight;} 733 if (!wrap && rank == 0) { 734 ierr = DMPlexGetHeightStratum(dm,1,&fStart,&fEnd);CHKERRQ(ierr); 735 ierr = DMSetLabelValue(dm,"marker",fStart,markerLeft);CHKERRQ(ierr); 736 ierr = DMSetLabelValue(dm,"marker",fEnd-1,markerRight);CHKERRQ(ierr); 737 ierr = DMSetLabelValue(dm,"Face Sets",fStart,faceMarkerLeft);CHKERRQ(ierr); 738 ierr = DMSetLabelValue(dm,"Face Sets",fEnd-1,faceMarkerRight);CHKERRQ(ierr); 739 } 740 if (wrap) { 741 L = upper - lower; 742 maxCell = (PetscReal)1.1*(L/(PetscReal)PetscMax(1,segments)); 743 ierr = DMSetPeriodicity(dm,PETSC_TRUE,&maxCell,&L,&bd);CHKERRQ(ierr); 744 } 745 ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr); 746 PetscFunctionReturn(0); 747 } 748 749 static PetscErrorCode DMPlexCreateBoxMesh_Simplex_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate) 750 { 751 DM boundary, vol; 752 PetscInt i; 753 PetscErrorCode ierr; 754 755 PetscFunctionBegin; 756 PetscValidPointer(dm, 1); 757 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"); 758 ierr = DMCreate(PetscObjectComm((PetscObject) dm), &boundary);CHKERRQ(ierr); 759 ierr = DMSetType(boundary, DMPLEX);CHKERRQ(ierr); 760 ierr = DMPlexCreateBoxSurfaceMesh_Internal(boundary, dim, faces, lower, upper, PETSC_FALSE);CHKERRQ(ierr); 761 ierr = DMPlexGenerate(boundary, NULL, interpolate, &vol);CHKERRQ(ierr); 762 ierr = DMPlexCopy_Internal(dm, PETSC_TRUE, vol);CHKERRQ(ierr); 763 ierr = DMPlexReplace_Static(dm, &vol);CHKERRQ(ierr); 764 ierr = DMDestroy(&boundary);CHKERRQ(ierr); 765 PetscFunctionReturn(0); 766 } 767 768 static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ) 769 { 770 DMLabel cutLabel = NULL; 771 PetscInt markerTop = 1, faceMarkerTop = 1; 772 PetscInt markerBottom = 1, faceMarkerBottom = 1; 773 PetscInt markerFront = 1, faceMarkerFront = 1; 774 PetscInt markerBack = 1, faceMarkerBack = 1; 775 PetscInt markerRight = 1, faceMarkerRight = 1; 776 PetscInt markerLeft = 1, faceMarkerLeft = 1; 777 PetscInt dim; 778 PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE; 779 PetscMPIInt rank; 780 PetscErrorCode ierr; 781 782 PetscFunctionBegin; 783 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 784 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRMPI(ierr); 785 ierr = DMCreateLabel(dm,"marker");CHKERRQ(ierr); 786 ierr = DMCreateLabel(dm,"Face Sets");CHKERRQ(ierr); 787 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL);CHKERRQ(ierr); 788 if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST || 789 bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST || 790 bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) { 791 792 if (cutMarker) {ierr = DMCreateLabel(dm, "periodic_cut");CHKERRQ(ierr); ierr = DMGetLabel(dm, "periodic_cut", &cutLabel);CHKERRQ(ierr);} 793 } 794 switch (dim) { 795 case 2: 796 faceMarkerTop = 3; 797 faceMarkerBottom = 1; 798 faceMarkerRight = 2; 799 faceMarkerLeft = 4; 800 break; 801 case 3: 802 faceMarkerBottom = 1; 803 faceMarkerTop = 2; 804 faceMarkerFront = 3; 805 faceMarkerBack = 4; 806 faceMarkerRight = 5; 807 faceMarkerLeft = 6; 808 break; 809 default: 810 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %D not supported",dim); 811 } 812 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 813 if (markerSeparate) { 814 markerBottom = faceMarkerBottom; 815 markerTop = faceMarkerTop; 816 markerFront = faceMarkerFront; 817 markerBack = faceMarkerBack; 818 markerRight = faceMarkerRight; 819 markerLeft = faceMarkerLeft; 820 } 821 { 822 const PetscInt numXEdges = rank == 0 ? edges[0] : 0; 823 const PetscInt numYEdges = rank == 0 ? edges[1] : 0; 824 const PetscInt numZEdges = rank == 0 ? edges[2] : 0; 825 const PetscInt numXVertices = rank == 0 ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; 826 const PetscInt numYVertices = rank == 0 ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; 827 const PetscInt numZVertices = rank == 0 ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0; 828 const PetscInt numCells = numXEdges*numYEdges*numZEdges; 829 const PetscInt numXFaces = numYEdges*numZEdges; 830 const PetscInt numYFaces = numXEdges*numZEdges; 831 const PetscInt numZFaces = numXEdges*numYEdges; 832 const PetscInt numTotXFaces = numXVertices*numXFaces; 833 const PetscInt numTotYFaces = numYVertices*numYFaces; 834 const PetscInt numTotZFaces = numZVertices*numZFaces; 835 const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces; 836 const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices; 837 const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices; 838 const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices; 839 const PetscInt numVertices = numXVertices*numYVertices*numZVertices; 840 const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges; 841 const PetscInt firstVertex = (dim == 2) ? numFaces : numCells; 842 const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices; 843 const PetscInt firstYFace = firstXFace + numTotXFaces; 844 const PetscInt firstZFace = firstYFace + numTotYFaces; 845 const PetscInt firstXEdge = numCells + numFaces + numVertices; 846 const PetscInt firstYEdge = firstXEdge + numTotXEdges; 847 const PetscInt firstZEdge = firstYEdge + numTotYEdges; 848 Vec coordinates; 849 PetscSection coordSection; 850 PetscScalar *coords; 851 PetscInt coordSize; 852 PetscInt v, vx, vy, vz; 853 PetscInt c, f, fx, fy, fz, e, ex, ey, ez; 854 855 ierr = DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);CHKERRQ(ierr); 856 for (c = 0; c < numCells; c++) { 857 ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr); 858 } 859 for (f = firstXFace; f < firstXFace+numFaces; ++f) { 860 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 861 } 862 for (e = firstXEdge; e < firstXEdge+numEdges; ++e) { 863 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 864 } 865 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 866 /* Build cells */ 867 for (fz = 0; fz < numZEdges; ++fz) { 868 for (fy = 0; fy < numYEdges; ++fy) { 869 for (fx = 0; fx < numXEdges; ++fx) { 870 PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx; 871 PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 872 PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices); 873 PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 874 PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices); 875 PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 876 PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices); 877 /* B, T, F, K, R, L */ 878 PetscInt ornt[6] = {-2, 0, 0, -3, 0, -2}; /* ??? */ 879 PetscInt cone[6]; 880 881 /* no boundary twisting in 3D */ 882 cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL; 883 ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr); 884 ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr); 885 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 886 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 887 if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 888 } 889 } 890 } 891 /* Build x faces */ 892 for (fz = 0; fz < numZEdges; ++fz) { 893 for (fy = 0; fy < numYEdges; ++fy) { 894 for (fx = 0; fx < numXVertices; ++fx) { 895 PetscInt face = firstXFace + (fz*numYEdges+fy) *numXVertices+fx; 896 PetscInt edgeL = firstZEdge + (fy *numXVertices+fx)*numZEdges + fz; 897 PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz; 898 PetscInt edgeB = firstYEdge + (fz *numXVertices+fx)*numYEdges + fy; 899 PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy; 900 PetscInt ornt[4] = {0, 0, -1, -1}; 901 PetscInt cone[4]; 902 903 if (dim == 3) { 904 /* markers */ 905 if (bdX != DM_BOUNDARY_PERIODIC) { 906 if (fx == numXVertices-1) { 907 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);CHKERRQ(ierr); 908 ierr = DMSetLabelValue(dm, "marker", face, markerRight);CHKERRQ(ierr); 909 } 910 else if (fx == 0) { 911 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);CHKERRQ(ierr); 912 ierr = DMSetLabelValue(dm, "marker", face, markerLeft);CHKERRQ(ierr); 913 } 914 } 915 } 916 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 917 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 918 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 919 } 920 } 921 } 922 /* Build y faces */ 923 for (fz = 0; fz < numZEdges; ++fz) { 924 for (fx = 0; fx < numXEdges; ++fx) { 925 for (fy = 0; fy < numYVertices; ++fy) { 926 PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 927 PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx)*numZEdges + fz; 928 PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz; 929 PetscInt edgeB = firstXEdge + (fz *numYVertices+fy)*numXEdges + fx; 930 PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx; 931 PetscInt ornt[4] = {0, 0, -1, -1}; 932 PetscInt cone[4]; 933 934 if (dim == 3) { 935 /* markers */ 936 if (bdY != DM_BOUNDARY_PERIODIC) { 937 if (fy == numYVertices-1) { 938 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);CHKERRQ(ierr); 939 ierr = DMSetLabelValue(dm, "marker", face, markerBack);CHKERRQ(ierr); 940 } 941 else if (fy == 0) { 942 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);CHKERRQ(ierr); 943 ierr = DMSetLabelValue(dm, "marker", face, markerFront);CHKERRQ(ierr); 944 } 945 } 946 } 947 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 948 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 949 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 950 } 951 } 952 } 953 /* Build z faces */ 954 for (fy = 0; fy < numYEdges; ++fy) { 955 for (fx = 0; fx < numXEdges; ++fx) { 956 for (fz = 0; fz < numZVertices; fz++) { 957 PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 958 PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx)*numYEdges + fy; 959 PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy; 960 PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy)*numXEdges + fx; 961 PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx; 962 PetscInt ornt[4] = {0, 0, -1, -1}; 963 PetscInt cone[4]; 964 965 if (dim == 2) { 966 if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -1;} 967 if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;} 968 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 969 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 970 } else { 971 /* markers */ 972 if (bdZ != DM_BOUNDARY_PERIODIC) { 973 if (fz == numZVertices-1) { 974 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);CHKERRQ(ierr); 975 ierr = DMSetLabelValue(dm, "marker", face, markerTop);CHKERRQ(ierr); 976 } 977 else if (fz == 0) { 978 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);CHKERRQ(ierr); 979 ierr = DMSetLabelValue(dm, "marker", face, markerBottom);CHKERRQ(ierr); 980 } 981 } 982 } 983 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 984 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 985 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 986 } 987 } 988 } 989 /* Build Z edges*/ 990 for (vy = 0; vy < numYVertices; vy++) { 991 for (vx = 0; vx < numXVertices; vx++) { 992 for (ez = 0; ez < numZEdges; ez++) { 993 const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez; 994 const PetscInt vertexB = firstVertex + (ez *numYVertices+vy)*numXVertices + vx; 995 const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx; 996 PetscInt cone[2]; 997 998 if (dim == 3) { 999 if (bdX != DM_BOUNDARY_PERIODIC) { 1000 if (vx == numXVertices-1) { 1001 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 1002 } 1003 else if (vx == 0) { 1004 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 1005 } 1006 } 1007 if (bdY != DM_BOUNDARY_PERIODIC) { 1008 if (vy == numYVertices-1) { 1009 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 1010 } 1011 else if (vy == 0) { 1012 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 1013 } 1014 } 1015 } 1016 cone[0] = vertexB; cone[1] = vertexT; 1017 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 1018 } 1019 } 1020 } 1021 /* Build Y edges*/ 1022 for (vz = 0; vz < numZVertices; vz++) { 1023 for (vx = 0; vx < numXVertices; vx++) { 1024 for (ey = 0; ey < numYEdges; ey++) { 1025 const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx; 1026 const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey; 1027 const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx; 1028 const PetscInt vertexK = firstVertex + nextv; 1029 PetscInt cone[2]; 1030 1031 cone[0] = vertexF; cone[1] = vertexK; 1032 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 1033 if (dim == 2) { 1034 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 1035 if (vx == numXVertices-1) { 1036 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);CHKERRQ(ierr); 1037 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 1038 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 1039 if (ey == numYEdges-1) { 1040 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 1041 } 1042 } else if (vx == 0) { 1043 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);CHKERRQ(ierr); 1044 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 1045 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 1046 if (ey == numYEdges-1) { 1047 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 1048 } 1049 } 1050 } else { 1051 if (vx == 0 && cutLabel) { 1052 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 1053 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 1054 if (ey == numYEdges-1) { 1055 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 1056 } 1057 } 1058 } 1059 } else { 1060 if (bdX != DM_BOUNDARY_PERIODIC) { 1061 if (vx == numXVertices-1) { 1062 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 1063 } else if (vx == 0) { 1064 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 1065 } 1066 } 1067 if (bdZ != DM_BOUNDARY_PERIODIC) { 1068 if (vz == numZVertices-1) { 1069 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 1070 } else if (vz == 0) { 1071 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 1072 } 1073 } 1074 } 1075 } 1076 } 1077 } 1078 /* Build X edges*/ 1079 for (vz = 0; vz < numZVertices; vz++) { 1080 for (vy = 0; vy < numYVertices; vy++) { 1081 for (ex = 0; ex < numXEdges; ex++) { 1082 const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices; 1083 const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex; 1084 const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex; 1085 const PetscInt vertexR = firstVertex + nextv; 1086 PetscInt cone[2]; 1087 1088 cone[0] = vertexL; cone[1] = vertexR; 1089 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 1090 if (dim == 2) { 1091 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 1092 if (vy == numYVertices-1) { 1093 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);CHKERRQ(ierr); 1094 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 1095 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 1096 if (ex == numXEdges-1) { 1097 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 1098 } 1099 } else if (vy == 0) { 1100 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);CHKERRQ(ierr); 1101 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 1102 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 1103 if (ex == numXEdges-1) { 1104 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 1105 } 1106 } 1107 } else { 1108 if (vy == 0 && cutLabel) { 1109 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 1110 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 1111 if (ex == numXEdges-1) { 1112 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 1113 } 1114 } 1115 } 1116 } else { 1117 if (bdY != DM_BOUNDARY_PERIODIC) { 1118 if (vy == numYVertices-1) { 1119 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 1120 } 1121 else if (vy == 0) { 1122 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 1123 } 1124 } 1125 if (bdZ != DM_BOUNDARY_PERIODIC) { 1126 if (vz == numZVertices-1) { 1127 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 1128 } 1129 else if (vz == 0) { 1130 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 1131 } 1132 } 1133 } 1134 } 1135 } 1136 } 1137 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1138 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1139 /* Build coordinates */ 1140 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1141 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1142 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1143 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr); 1144 for (v = firstVertex; v < firstVertex+numVertices; ++v) { 1145 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1146 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1147 } 1148 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1149 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1150 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1151 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1152 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1153 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1154 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1155 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1156 for (vz = 0; vz < numZVertices; ++vz) { 1157 for (vy = 0; vy < numYVertices; ++vy) { 1158 for (vx = 0; vx < numXVertices; ++vx) { 1159 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx; 1160 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy; 1161 if (dim == 3) { 1162 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz; 1163 } 1164 } 1165 } 1166 } 1167 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1168 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1169 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1170 } 1171 PetscFunctionReturn(0); 1172 } 1173 1174 static PetscErrorCode DMPlexCreateBoxMesh_Tensor_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[]) 1175 { 1176 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1177 PetscInt fac[3] = {0, 0, 0}, d; 1178 PetscErrorCode ierr; 1179 1180 PetscFunctionBegin; 1181 PetscValidPointer(dm, 1); 1182 PetscValidLogicalCollectiveInt(dm, dim, 2); 1183 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 1184 for (d = 0; d < dim; ++d) {fac[d] = faces[d]; bdt[d] = periodicity[d];} 1185 ierr = DMPlexCreateCubeMesh_Internal(dm, lower, upper, fac, bdt[0], bdt[1], bdt[2]);CHKERRQ(ierr); 1186 if (periodicity[0] == DM_BOUNDARY_PERIODIC || periodicity[0] == DM_BOUNDARY_TWIST || 1187 periodicity[1] == DM_BOUNDARY_PERIODIC || periodicity[1] == DM_BOUNDARY_TWIST || 1188 (dim > 2 && (periodicity[2] == DM_BOUNDARY_PERIODIC || periodicity[2] == DM_BOUNDARY_TWIST))) { 1189 PetscReal L[3]; 1190 PetscReal maxCell[3]; 1191 1192 for (d = 0; d < dim; ++d) { 1193 L[d] = upper[d] - lower[d]; 1194 maxCell[d] = 1.1 * (L[d] / PetscMax(1, faces[d])); 1195 } 1196 ierr = DMSetPeriodicity(dm, PETSC_TRUE, maxCell, L, periodicity);CHKERRQ(ierr); 1197 } 1198 ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr); 1199 PetscFunctionReturn(0); 1200 } 1201 1202 static PetscErrorCode DMPlexCreateBoxMesh_Internal(DM dm, PetscInt dim, PetscBool simplex, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate) 1203 { 1204 PetscErrorCode ierr; 1205 1206 PetscFunctionBegin; 1207 if (dim == 1) {ierr = DMPlexCreateLineMesh_Internal(dm, faces[0], lower[0], upper[0], periodicity[0]);CHKERRQ(ierr);} 1208 else if (simplex) {ierr = DMPlexCreateBoxMesh_Simplex_Internal(dm, dim, faces, lower, upper, periodicity, interpolate);CHKERRQ(ierr);} 1209 else {ierr = DMPlexCreateBoxMesh_Tensor_Internal(dm, dim, faces, lower, upper, periodicity);CHKERRQ(ierr);} 1210 if (!interpolate && dim > 1 && !simplex) { 1211 DM udm; 1212 1213 ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr); 1214 ierr = DMPlexCopyCoordinates(dm, udm);CHKERRQ(ierr); 1215 ierr = DMPlexReplace_Static(dm, &udm);CHKERRQ(ierr); 1216 } 1217 PetscFunctionReturn(0); 1218 } 1219 1220 /*@C 1221 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra). 1222 1223 Collective 1224 1225 Input Parameters: 1226 + comm - The communicator for the DM object 1227 . dim - The spatial dimension 1228 . simplex - PETSC_TRUE for simplices, PETSC_FALSE for tensor cells 1229 . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 1230 . lower - The lower left corner, or NULL for (0, 0, 0) 1231 . upper - The upper right corner, or NULL for (1, 1, 1) 1232 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 1233 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1234 1235 Output Parameter: 1236 . dm - The DM object 1237 1238 Note: If you want to customize this mesh using options, you just need to 1239 $ DMCreate(comm, &dm); 1240 $ DMSetType(dm, DMPLEX); 1241 $ DMSetFromOptions(dm); 1242 and use the options on the DMSetFromOptions() page. 1243 1244 Here is the numbering returned for 2 faces in each direction for tensor cells: 1245 $ 10---17---11---18----12 1246 $ | | | 1247 $ | | | 1248 $ 20 2 22 3 24 1249 $ | | | 1250 $ | | | 1251 $ 7---15----8---16----9 1252 $ | | | 1253 $ | | | 1254 $ 19 0 21 1 23 1255 $ | | | 1256 $ | | | 1257 $ 4---13----5---14----6 1258 1259 and for simplicial cells 1260 1261 $ 14----8---15----9----16 1262 $ |\ 5 |\ 7 | 1263 $ | \ | \ | 1264 $ 13 2 14 3 15 1265 $ | 4 \ | 6 \ | 1266 $ | \ | \ | 1267 $ 11----6---12----7----13 1268 $ |\ |\ | 1269 $ | \ 1 | \ 3 | 1270 $ 10 0 11 1 12 1271 $ | 0 \ | 2 \ | 1272 $ | \ | \ | 1273 $ 8----4----9----5----10 1274 1275 Level: beginner 1276 1277 .seealso: DMSetFromOptions(), DMPlexCreateFromFile(), DMPlexCreateHexCylinderMesh(), DMSetType(), DMCreate() 1278 @*/ 1279 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) 1280 { 1281 PetscInt fac[3] = {1, 1, 1}; 1282 PetscReal low[3] = {0, 0, 0}; 1283 PetscReal upp[3] = {1, 1, 1}; 1284 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1285 PetscErrorCode ierr; 1286 1287 PetscFunctionBegin; 1288 ierr = DMCreate(comm,dm);CHKERRQ(ierr); 1289 ierr = DMSetType(*dm,DMPLEX);CHKERRQ(ierr); 1290 ierr = DMPlexCreateBoxMesh_Internal(*dm, dim, simplex, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt, interpolate);CHKERRQ(ierr); 1291 PetscFunctionReturn(0); 1292 } 1293 1294 static PetscErrorCode DMPlexCreateWedgeBoxMesh_Internal(DM dm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[]) 1295 { 1296 DM bdm, vol; 1297 PetscInt i; 1298 PetscErrorCode ierr; 1299 1300 PetscFunctionBegin; 1301 for (i = 0; i < 3; ++i) PetscCheckFalse(periodicity[i] != DM_BOUNDARY_NONE,PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Periodicity not yet supported"); 1302 ierr = DMCreate(PetscObjectComm((PetscObject) dm), &bdm);CHKERRQ(ierr); 1303 ierr = DMSetType(bdm, DMPLEX);CHKERRQ(ierr); 1304 ierr = DMSetDimension(bdm, 2);CHKERRQ(ierr); 1305 ierr = DMPlexCreateBoxMesh_Simplex_Internal(bdm, 2, faces, lower, upper, periodicity, PETSC_TRUE);CHKERRQ(ierr); 1306 ierr = DMPlexExtrude(bdm, faces[2], upper[2] - lower[2], PETSC_TRUE, PETSC_FALSE, NULL, NULL, &vol);CHKERRQ(ierr); 1307 ierr = DMDestroy(&bdm);CHKERRQ(ierr); 1308 ierr = DMPlexReplace_Static(dm, &vol);CHKERRQ(ierr); 1309 if (lower[2] != 0.0) { 1310 Vec v; 1311 PetscScalar *x; 1312 PetscInt cDim, n; 1313 1314 ierr = DMGetCoordinatesLocal(dm, &v);CHKERRQ(ierr); 1315 ierr = VecGetBlockSize(v, &cDim);CHKERRQ(ierr); 1316 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 1317 ierr = VecGetArray(v, &x);CHKERRQ(ierr); 1318 x += cDim; 1319 for (i = 0; i < n; i += cDim) x[i] += lower[2]; 1320 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 1321 ierr = DMSetCoordinatesLocal(dm, v);CHKERRQ(ierr); 1322 } 1323 PetscFunctionReturn(0); 1324 } 1325 1326 /*@ 1327 DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells. 1328 1329 Collective 1330 1331 Input Parameters: 1332 + comm - The communicator for the DM object 1333 . faces - Number of faces per dimension, or NULL for (1, 1, 1) 1334 . lower - The lower left corner, or NULL for (0, 0, 0) 1335 . upper - The upper right corner, or NULL for (1, 1, 1) 1336 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 1337 . orderHeight - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1338 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1339 1340 Output Parameter: 1341 . dm - The DM object 1342 1343 Level: beginner 1344 1345 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateWedgeCylinderMesh(), DMExtrude(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1346 @*/ 1347 PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool orderHeight, PetscBool interpolate, DM *dm) 1348 { 1349 PetscInt fac[3] = {1, 1, 1}; 1350 PetscReal low[3] = {0, 0, 0}; 1351 PetscReal upp[3] = {1, 1, 1}; 1352 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1353 PetscErrorCode ierr; 1354 1355 PetscFunctionBegin; 1356 ierr = DMCreate(comm,dm);CHKERRQ(ierr); 1357 ierr = DMSetType(*dm,DMPLEX);CHKERRQ(ierr); 1358 ierr = DMPlexCreateWedgeBoxMesh_Internal(*dm, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt);CHKERRQ(ierr); 1359 if (!interpolate) { 1360 DM udm; 1361 1362 ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr); 1363 ierr = DMPlexReplace_Static(*dm, &udm);CHKERRQ(ierr); 1364 } 1365 PetscFunctionReturn(0); 1366 } 1367 1368 /*@C 1369 DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database. 1370 1371 Logically Collective on dm 1372 1373 Input Parameters: 1374 + dm - the DM context 1375 - prefix - the prefix to prepend to all option names 1376 1377 Notes: 1378 A hyphen (-) must NOT be given at the beginning of the prefix name. 1379 The first character of all runtime options is AUTOMATICALLY the hyphen. 1380 1381 Level: advanced 1382 1383 .seealso: SNESSetFromOptions() 1384 @*/ 1385 PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) 1386 { 1387 DM_Plex *mesh = (DM_Plex *) dm->data; 1388 PetscErrorCode ierr; 1389 1390 PetscFunctionBegin; 1391 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1392 ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);CHKERRQ(ierr); 1393 ierr = PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);CHKERRQ(ierr); 1394 PetscFunctionReturn(0); 1395 } 1396 1397 /* Remap geometry to cylinder 1398 TODO: This only works for a single refinement, then it is broken 1399 1400 Interior square: Linear interpolation is correct 1401 The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing 1402 such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance 1403 1404 phi = arctan(y/x) 1405 d_close = sqrt(1/8 + 1/4 sin^2(phi)) 1406 d_far = sqrt(1/2 + sin^2(phi)) 1407 1408 so we remap them using 1409 1410 x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) 1411 y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) 1412 1413 If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. 1414 */ 1415 static void snapToCylinder(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1416 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1417 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1418 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 1419 { 1420 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1421 const PetscReal ds2 = 0.5*dis; 1422 1423 if ((PetscAbsScalar(u[0]) <= ds2) && (PetscAbsScalar(u[1]) <= ds2)) { 1424 f0[0] = u[0]; 1425 f0[1] = u[1]; 1426 } else { 1427 PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; 1428 1429 x = PetscRealPart(u[0]); 1430 y = PetscRealPart(u[1]); 1431 phi = PetscAtan2Real(y, x); 1432 sinp = PetscSinReal(phi); 1433 cosp = PetscCosReal(phi); 1434 if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) { 1435 dc = PetscAbsReal(ds2/sinp); 1436 df = PetscAbsReal(dis/sinp); 1437 xc = ds2*x/PetscAbsReal(y); 1438 yc = ds2*PetscSignReal(y); 1439 } else { 1440 dc = PetscAbsReal(ds2/cosp); 1441 df = PetscAbsReal(dis/cosp); 1442 xc = ds2*PetscSignReal(x); 1443 yc = ds2*y/PetscAbsReal(x); 1444 } 1445 f0[0] = xc + (u[0] - xc)*(1.0 - dc)/(df - dc); 1446 f0[1] = yc + (u[1] - yc)*(1.0 - dc)/(df - dc); 1447 } 1448 f0[2] = u[2]; 1449 } 1450 1451 static PetscErrorCode DMPlexCreateHexCylinderMesh_Internal(DM dm, DMBoundaryType periodicZ) 1452 { 1453 const PetscInt dim = 3; 1454 PetscInt numCells, numVertices; 1455 PetscMPIInt rank; 1456 PetscErrorCode ierr; 1457 1458 PetscFunctionBegin; 1459 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 1460 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 1461 /* Create topology */ 1462 { 1463 PetscInt cone[8], c; 1464 1465 numCells = rank == 0 ? 5 : 0; 1466 numVertices = rank == 0 ? 16 : 0; 1467 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1468 numCells *= 3; 1469 numVertices = rank == 0 ? 24 : 0; 1470 } 1471 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 1472 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(dm, c, 8);CHKERRQ(ierr);} 1473 ierr = DMSetUp(dm);CHKERRQ(ierr); 1474 if (rank == 0) { 1475 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1476 cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16; 1477 cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34; 1478 ierr = DMPlexSetCone(dm, 0, cone);CHKERRQ(ierr); 1479 cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23; 1480 cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */ 1481 ierr = DMPlexSetCone(dm, 1, cone);CHKERRQ(ierr); 1482 cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17; 1483 cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38; 1484 ierr = DMPlexSetCone(dm, 2, cone);CHKERRQ(ierr); 1485 cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15; 1486 cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38; 1487 ierr = DMPlexSetCone(dm, 3, cone);CHKERRQ(ierr); 1488 cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23; 1489 cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31; 1490 ierr = DMPlexSetCone(dm, 4, cone);CHKERRQ(ierr); 1491 1492 cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32; 1493 cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20; 1494 ierr = DMPlexSetCone(dm, 5, cone);CHKERRQ(ierr); 1495 cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36; 1496 cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21; 1497 ierr = DMPlexSetCone(dm, 6, cone);CHKERRQ(ierr); 1498 cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33; 1499 cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28; 1500 ierr = DMPlexSetCone(dm, 7, cone);CHKERRQ(ierr); 1501 cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31; 1502 cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28; 1503 ierr = DMPlexSetCone(dm, 8, cone);CHKERRQ(ierr); 1504 cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36; 1505 cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19; 1506 ierr = DMPlexSetCone(dm, 9, cone);CHKERRQ(ierr); 1507 1508 cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22; 1509 cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18; 1510 ierr = DMPlexSetCone(dm, 10, cone);CHKERRQ(ierr); 1511 cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25; 1512 cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17; 1513 ierr = DMPlexSetCone(dm, 11, cone);CHKERRQ(ierr); 1514 cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21; 1515 cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27; 1516 ierr = DMPlexSetCone(dm, 12, cone);CHKERRQ(ierr); 1517 cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19; 1518 cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27; 1519 ierr = DMPlexSetCone(dm, 13, cone);CHKERRQ(ierr); 1520 cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25; 1521 cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15; 1522 ierr = DMPlexSetCone(dm, 14, cone);CHKERRQ(ierr); 1523 } else { 1524 cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6; 1525 cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10; 1526 ierr = DMPlexSetCone(dm, 0, cone);CHKERRQ(ierr); 1527 cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13; 1528 cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11; 1529 ierr = DMPlexSetCone(dm, 1, cone);CHKERRQ(ierr); 1530 cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7; 1531 cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18; 1532 ierr = DMPlexSetCone(dm, 2, cone);CHKERRQ(ierr); 1533 cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5; 1534 cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18; 1535 ierr = DMPlexSetCone(dm, 3, cone);CHKERRQ(ierr); 1536 cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13; 1537 cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9; 1538 ierr = DMPlexSetCone(dm, 4, cone);CHKERRQ(ierr); 1539 } 1540 } 1541 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1542 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1543 } 1544 /* Create cube geometry */ 1545 { 1546 Vec coordinates; 1547 PetscSection coordSection; 1548 PetscScalar *coords; 1549 PetscInt coordSize, v; 1550 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1551 const PetscReal ds2 = dis/2.0; 1552 1553 /* Build coordinates */ 1554 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1555 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1556 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1557 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1558 for (v = numCells; v < numCells+numVertices; ++v) { 1559 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1560 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1561 } 1562 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1563 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1564 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1565 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1566 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1567 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1568 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1569 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1570 if (rank == 0) { 1571 coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0; 1572 coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0; 1573 coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0; 1574 coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0; 1575 coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0; 1576 coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0; 1577 coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0; 1578 coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0; 1579 coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0; 1580 coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0; 1581 coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0; 1582 coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0; 1583 coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0; 1584 coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0; 1585 coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0; 1586 coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0; 1587 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1588 /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5; 1589 /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5; 1590 /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5; 1591 /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5; 1592 /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5; 1593 /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5; 1594 /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5; 1595 /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5; 1596 } 1597 } 1598 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1599 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1600 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1601 } 1602 /* Create periodicity */ 1603 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1604 PetscReal L[3]; 1605 PetscReal maxCell[3]; 1606 DMBoundaryType bdType[3]; 1607 PetscReal lower[3] = {0.0, 0.0, 0.0}; 1608 PetscReal upper[3] = {1.0, 1.0, 1.5}; 1609 PetscInt i, numZCells = 3; 1610 1611 bdType[0] = DM_BOUNDARY_NONE; 1612 bdType[1] = DM_BOUNDARY_NONE; 1613 bdType[2] = periodicZ; 1614 for (i = 0; i < dim; i++) { 1615 L[i] = upper[i] - lower[i]; 1616 maxCell[i] = 1.1 * (L[i] / numZCells); 1617 } 1618 ierr = DMSetPeriodicity(dm, PETSC_TRUE, maxCell, L, bdType);CHKERRQ(ierr); 1619 } 1620 { 1621 DM cdm; 1622 PetscDS cds; 1623 PetscScalar c[2] = {1.0, 1.0}; 1624 1625 ierr = DMPlexCreateCoordinateSpace(dm, 1, snapToCylinder);CHKERRQ(ierr); 1626 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 1627 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 1628 ierr = PetscDSSetConstants(cds, 2, c);CHKERRQ(ierr); 1629 } 1630 /* Wait for coordinate creation before doing in-place modification */ 1631 ierr = DMPlexInterpolateInPlace_Internal(dm);CHKERRQ(ierr); 1632 PetscFunctionReturn(0); 1633 } 1634 1635 /*@ 1636 DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. 1637 1638 Collective 1639 1640 Input Parameters: 1641 + comm - The communicator for the DM object 1642 - periodicZ - The boundary type for the Z direction 1643 1644 Output Parameter: 1645 . dm - The DM object 1646 1647 Note: 1648 Here is the output numbering looking from the bottom of the cylinder: 1649 $ 17-----14 1650 $ | | 1651 $ | 2 | 1652 $ | | 1653 $ 17-----8-----7-----14 1654 $ | | | | 1655 $ | 3 | 0 | 1 | 1656 $ | | | | 1657 $ 19-----5-----6-----13 1658 $ | | 1659 $ | 4 | 1660 $ | | 1661 $ 19-----13 1662 $ 1663 $ and up through the top 1664 $ 1665 $ 18-----16 1666 $ | | 1667 $ | 2 | 1668 $ | | 1669 $ 18----10----11-----16 1670 $ | | | | 1671 $ | 3 | 0 | 1 | 1672 $ | | | | 1673 $ 20-----9----12-----15 1674 $ | | 1675 $ | 4 | 1676 $ | | 1677 $ 20-----15 1678 1679 Level: beginner 1680 1681 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1682 @*/ 1683 PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, DMBoundaryType periodicZ, DM *dm) 1684 { 1685 PetscErrorCode ierr; 1686 1687 PetscFunctionBegin; 1688 PetscValidPointer(dm, 3); 1689 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1690 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1691 ierr = DMPlexCreateHexCylinderMesh_Internal(*dm, periodicZ);CHKERRQ(ierr); 1692 PetscFunctionReturn(0); 1693 } 1694 1695 static PetscErrorCode DMPlexCreateWedgeCylinderMesh_Internal(DM dm, PetscInt n, PetscBool interpolate) 1696 { 1697 const PetscInt dim = 3; 1698 PetscInt numCells, numVertices, v; 1699 PetscMPIInt rank; 1700 PetscErrorCode ierr; 1701 1702 PetscFunctionBegin; 1703 PetscCheckFalse(n < 0,PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n); 1704 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 1705 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 1706 /* Must create the celltype label here so that we do not automatically try to compute the types */ 1707 ierr = DMCreateLabel(dm, "celltype");CHKERRQ(ierr); 1708 /* Create topology */ 1709 { 1710 PetscInt cone[6], c; 1711 1712 numCells = rank == 0 ? n : 0; 1713 numVertices = rank == 0 ? 2*(n+1) : 0; 1714 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 1715 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr);} 1716 ierr = DMSetUp(dm);CHKERRQ(ierr); 1717 for (c = 0; c < numCells; c++) { 1718 cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n; 1719 cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n; 1720 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 1721 ierr = DMPlexSetCellType(dm, c, DM_POLYTOPE_TRI_PRISM_TENSOR);CHKERRQ(ierr); 1722 } 1723 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1724 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1725 } 1726 for (v = numCells; v < numCells+numVertices; ++v) { 1727 ierr = DMPlexSetCellType(dm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr); 1728 } 1729 /* Create cylinder geometry */ 1730 { 1731 Vec coordinates; 1732 PetscSection coordSection; 1733 PetscScalar *coords; 1734 PetscInt coordSize, c; 1735 1736 /* Build coordinates */ 1737 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1738 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1739 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1740 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1741 for (v = numCells; v < numCells+numVertices; ++v) { 1742 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1743 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1744 } 1745 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1746 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1747 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1748 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1749 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1750 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1751 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1752 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1753 for (c = 0; c < numCells; c++) { 1754 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; 1755 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; 1756 } 1757 if (rank == 0) { 1758 coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0; 1759 coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0; 1760 } 1761 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1762 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1763 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1764 } 1765 /* Interpolate */ 1766 if (interpolate) {ierr = DMPlexInterpolateInPlace_Internal(dm);CHKERRQ(ierr);} 1767 PetscFunctionReturn(0); 1768 } 1769 1770 /*@ 1771 DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges. 1772 1773 Collective 1774 1775 Input Parameters: 1776 + comm - The communicator for the DM object 1777 . n - The number of wedges around the origin 1778 - interpolate - Create edges and faces 1779 1780 Output Parameter: 1781 . dm - The DM object 1782 1783 Level: beginner 1784 1785 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1786 @*/ 1787 PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm) 1788 { 1789 PetscErrorCode ierr; 1790 1791 PetscFunctionBegin; 1792 PetscValidPointer(dm, 4); 1793 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1794 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1795 ierr = DMPlexCreateWedgeCylinderMesh_Internal(*dm, n, interpolate);CHKERRQ(ierr); 1796 PetscFunctionReturn(0); 1797 } 1798 1799 static inline PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1800 { 1801 PetscReal prod = 0.0; 1802 PetscInt i; 1803 for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]); 1804 return PetscSqrtReal(prod); 1805 } 1806 static inline PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1807 { 1808 PetscReal prod = 0.0; 1809 PetscInt i; 1810 for (i = 0; i < dim; ++i) prod += x[i]*y[i]; 1811 return prod; 1812 } 1813 1814 /* The first constant is the sphere radius */ 1815 static void snapToSphere(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1816 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1817 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1818 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 1819 { 1820 PetscReal r = PetscRealPart(constants[0]); 1821 PetscReal norm2 = 0.0, fac; 1822 PetscInt n = uOff[1] - uOff[0], d; 1823 1824 for (d = 0; d < n; ++d) norm2 += PetscSqr(PetscRealPart(u[d])); 1825 fac = r/PetscSqrtReal(norm2); 1826 for (d = 0; d < n; ++d) f0[d] = u[d]*fac; 1827 } 1828 1829 static PetscErrorCode DMPlexCreateSphereMesh_Internal(DM dm, PetscInt dim, PetscBool simplex, PetscReal R) 1830 { 1831 const PetscInt embedDim = dim+1; 1832 PetscSection coordSection; 1833 Vec coordinates; 1834 PetscScalar *coords; 1835 PetscReal *coordsIn; 1836 PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e; 1837 PetscMPIInt rank; 1838 PetscErrorCode ierr; 1839 1840 PetscFunctionBegin; 1841 PetscValidLogicalCollectiveBool(dm, simplex, 3); 1842 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 1843 ierr = DMSetCoordinateDim(dm, dim+1);CHKERRQ(ierr); 1844 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 1845 switch (dim) { 1846 case 2: 1847 if (simplex) { 1848 const PetscReal radius = PetscSqrtReal(1 + PETSC_PHI*PETSC_PHI)/(1.0 + PETSC_PHI); 1849 const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI) * (R/radius); 1850 const PetscInt degree = 5; 1851 PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)}; 1852 PetscInt s[3] = {1, 1, 1}; 1853 PetscInt cone[3]; 1854 PetscInt *graph, p, i, j, k; 1855 1856 vertex[0] *= R/radius; vertex[1] *= R/radius; vertex[2] *= R/radius; 1857 numCells = rank == 0 ? 20 : 0; 1858 numVerts = rank == 0 ? 12 : 0; 1859 firstVertex = numCells; 1860 /* Use icosahedron, which for a R-sphere has coordinates which are all cyclic permutations of 1861 1862 (0, \pm 1/\phi+1, \pm \phi/\phi+1) 1863 1864 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 1865 length is then given by 2/(1+\phi) = 2 * 0.38197 = 0.76393. 1866 */ 1867 /* Construct vertices */ 1868 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 1869 if (rank == 0) { 1870 for (p = 0, i = 0; p < embedDim; ++p) { 1871 for (s[1] = -1; s[1] < 2; s[1] += 2) { 1872 for (s[2] = -1; s[2] < 2; s[2] += 2) { 1873 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim]; 1874 ++i; 1875 } 1876 } 1877 } 1878 } 1879 /* Construct graph */ 1880 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 1881 for (i = 0; i < numVerts; ++i) { 1882 for (j = 0, k = 0; j < numVerts; ++j) { 1883 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 1884 } 1885 PetscCheckFalse(k != degree,PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree); 1886 } 1887 /* Build Topology */ 1888 ierr = DMPlexSetChart(dm, 0, numCells+numVerts);CHKERRQ(ierr); 1889 for (c = 0; c < numCells; c++) { 1890 ierr = DMPlexSetConeSize(dm, c, embedDim);CHKERRQ(ierr); 1891 } 1892 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 1893 /* Cells */ 1894 for (i = 0, c = 0; i < numVerts; ++i) { 1895 for (j = 0; j < i; ++j) { 1896 for (k = 0; k < j; ++k) { 1897 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) { 1898 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; 1899 /* Check orientation */ 1900 { 1901 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}}}; 1902 PetscReal normal[3]; 1903 PetscInt e, f; 1904 1905 for (d = 0; d < embedDim; ++d) { 1906 normal[d] = 0.0; 1907 for (e = 0; e < embedDim; ++e) { 1908 for (f = 0; f < embedDim; ++f) { 1909 normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]); 1910 } 1911 } 1912 } 1913 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 1914 } 1915 ierr = DMPlexSetCone(dm, c++, cone);CHKERRQ(ierr); 1916 } 1917 } 1918 } 1919 } 1920 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1921 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1922 ierr = PetscFree(graph);CHKERRQ(ierr); 1923 } else { 1924 /* 1925 12-21--13 1926 | | 1927 25 4 24 1928 | | 1929 12-25--9-16--8-24--13 1930 | | | | 1931 23 5 17 0 15 3 22 1932 | | | | 1933 10-20--6-14--7-19--11 1934 | | 1935 20 1 19 1936 | | 1937 10-18--11 1938 | | 1939 23 2 22 1940 | | 1941 12-21--13 1942 */ 1943 PetscInt cone[4], ornt[4]; 1944 1945 numCells = rank == 0 ? 6 : 0; 1946 numEdges = rank == 0 ? 12 : 0; 1947 numVerts = rank == 0 ? 8 : 0; 1948 firstVertex = numCells; 1949 firstEdge = numCells + numVerts; 1950 /* Build Topology */ 1951 ierr = DMPlexSetChart(dm, 0, numCells+numEdges+numVerts);CHKERRQ(ierr); 1952 for (c = 0; c < numCells; c++) { 1953 ierr = DMPlexSetConeSize(dm, c, 4);CHKERRQ(ierr); 1954 } 1955 for (e = firstEdge; e < firstEdge+numEdges; ++e) { 1956 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 1957 } 1958 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 1959 if (rank == 0) { 1960 /* Cell 0 */ 1961 cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17; 1962 ierr = DMPlexSetCone(dm, 0, cone);CHKERRQ(ierr); 1963 ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0; 1964 ierr = DMPlexSetConeOrientation(dm, 0, ornt);CHKERRQ(ierr); 1965 /* Cell 1 */ 1966 cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20; 1967 ierr = DMPlexSetCone(dm, 1, cone);CHKERRQ(ierr); 1968 ornt[0] = 0; ornt[1] = 0; ornt[2] = -1; ornt[3] = 0; 1969 ierr = DMPlexSetConeOrientation(dm, 1, ornt);CHKERRQ(ierr); 1970 /* Cell 2 */ 1971 cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23; 1972 ierr = DMPlexSetCone(dm, 2, cone);CHKERRQ(ierr); 1973 ornt[0] = 0; ornt[1] = 0; ornt[2] = -1; ornt[3] = 0; 1974 ierr = DMPlexSetConeOrientation(dm, 2, ornt);CHKERRQ(ierr); 1975 /* Cell 3 */ 1976 cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15; 1977 ierr = DMPlexSetCone(dm, 3, cone);CHKERRQ(ierr); 1978 ornt[0] = -1; ornt[1] = -1; ornt[2] = 0; ornt[3] = -1; 1979 ierr = DMPlexSetConeOrientation(dm, 3, ornt);CHKERRQ(ierr); 1980 /* Cell 4 */ 1981 cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25; 1982 ierr = DMPlexSetCone(dm, 4, cone);CHKERRQ(ierr); 1983 ornt[0] = -1; ornt[1] = -1; ornt[2] = -1; ornt[3] = 0; 1984 ierr = DMPlexSetConeOrientation(dm, 4, ornt);CHKERRQ(ierr); 1985 /* Cell 5 */ 1986 cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23; 1987 ierr = DMPlexSetCone(dm, 5, cone);CHKERRQ(ierr); 1988 ornt[0] = -1; ornt[1] = -1; ornt[2] = -1; ornt[3] = -1; 1989 ierr = DMPlexSetConeOrientation(dm, 5, ornt);CHKERRQ(ierr); 1990 /* Edges */ 1991 cone[0] = 6; cone[1] = 7; 1992 ierr = DMPlexSetCone(dm, 14, cone);CHKERRQ(ierr); 1993 cone[0] = 7; cone[1] = 8; 1994 ierr = DMPlexSetCone(dm, 15, cone);CHKERRQ(ierr); 1995 cone[0] = 8; cone[1] = 9; 1996 ierr = DMPlexSetCone(dm, 16, cone);CHKERRQ(ierr); 1997 cone[0] = 9; cone[1] = 6; 1998 ierr = DMPlexSetCone(dm, 17, cone);CHKERRQ(ierr); 1999 cone[0] = 10; cone[1] = 11; 2000 ierr = DMPlexSetCone(dm, 18, cone);CHKERRQ(ierr); 2001 cone[0] = 11; cone[1] = 7; 2002 ierr = DMPlexSetCone(dm, 19, cone);CHKERRQ(ierr); 2003 cone[0] = 6; cone[1] = 10; 2004 ierr = DMPlexSetCone(dm, 20, cone);CHKERRQ(ierr); 2005 cone[0] = 12; cone[1] = 13; 2006 ierr = DMPlexSetCone(dm, 21, cone);CHKERRQ(ierr); 2007 cone[0] = 13; cone[1] = 11; 2008 ierr = DMPlexSetCone(dm, 22, cone);CHKERRQ(ierr); 2009 cone[0] = 10; cone[1] = 12; 2010 ierr = DMPlexSetCone(dm, 23, cone);CHKERRQ(ierr); 2011 cone[0] = 13; cone[1] = 8; 2012 ierr = DMPlexSetCone(dm, 24, cone);CHKERRQ(ierr); 2013 cone[0] = 12; cone[1] = 9; 2014 ierr = DMPlexSetCone(dm, 25, cone);CHKERRQ(ierr); 2015 } 2016 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2017 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2018 /* Build coordinates */ 2019 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 2020 if (rank == 0) { 2021 coordsIn[0*embedDim+0] = -R; coordsIn[0*embedDim+1] = R; coordsIn[0*embedDim+2] = -R; 2022 coordsIn[1*embedDim+0] = R; coordsIn[1*embedDim+1] = R; coordsIn[1*embedDim+2] = -R; 2023 coordsIn[2*embedDim+0] = R; coordsIn[2*embedDim+1] = -R; coordsIn[2*embedDim+2] = -R; 2024 coordsIn[3*embedDim+0] = -R; coordsIn[3*embedDim+1] = -R; coordsIn[3*embedDim+2] = -R; 2025 coordsIn[4*embedDim+0] = -R; coordsIn[4*embedDim+1] = R; coordsIn[4*embedDim+2] = R; 2026 coordsIn[5*embedDim+0] = R; coordsIn[5*embedDim+1] = R; coordsIn[5*embedDim+2] = R; 2027 coordsIn[6*embedDim+0] = -R; coordsIn[6*embedDim+1] = -R; coordsIn[6*embedDim+2] = R; 2028 coordsIn[7*embedDim+0] = R; coordsIn[7*embedDim+1] = -R; coordsIn[7*embedDim+2] = R; 2029 } 2030 } 2031 break; 2032 case 3: 2033 if (simplex) { 2034 const PetscReal edgeLen = 1.0/PETSC_PHI; 2035 PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5}; 2036 PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0}; 2037 PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0}; 2038 const PetscInt degree = 12; 2039 PetscInt s[4] = {1, 1, 1}; 2040 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}, 2041 {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}}; 2042 PetscInt cone[4]; 2043 PetscInt *graph, p, i, j, k, l; 2044 2045 vertexA[0] *= R; vertexA[1] *= R; vertexA[2] *= R; vertexA[3] *= R; 2046 vertexB[0] *= R; vertexB[1] *= R; vertexB[2] *= R; vertexB[3] *= R; 2047 vertexC[0] *= R; vertexC[1] *= R; vertexC[2] *= R; vertexC[3] *= R; 2048 numCells = rank == 0 ? 600 : 0; 2049 numVerts = rank == 0 ? 120 : 0; 2050 firstVertex = numCells; 2051 /* Use the 600-cell, which for a unit sphere has coordinates which are 2052 2053 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16 2054 (\pm 1, 0, 0, 0) all cyclic permutations 8 2055 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96 2056 2057 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 2058 length is then given by 1/\phi = 0.61803. 2059 2060 http://buzzard.pugetsound.edu/sage-practice/ch03s03.html 2061 http://mathworld.wolfram.com/600-Cell.html 2062 */ 2063 /* Construct vertices */ 2064 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 2065 i = 0; 2066 if (rank == 0) { 2067 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2068 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2069 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2070 for (s[3] = -1; s[3] < 2; s[3] += 2) { 2071 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d]; 2072 ++i; 2073 } 2074 } 2075 } 2076 } 2077 for (p = 0; p < embedDim; ++p) { 2078 s[1] = s[2] = s[3] = 1; 2079 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2080 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim]; 2081 ++i; 2082 } 2083 } 2084 for (p = 0; p < 12; ++p) { 2085 s[3] = 1; 2086 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2087 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2088 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2089 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]]; 2090 ++i; 2091 } 2092 } 2093 } 2094 } 2095 } 2096 PetscCheckFalse(i != numVerts,PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts); 2097 /* Construct graph */ 2098 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 2099 for (i = 0; i < numVerts; ++i) { 2100 for (j = 0, k = 0; j < numVerts; ++j) { 2101 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 2102 } 2103 PetscCheckFalse(k != degree,PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree); 2104 } 2105 /* Build Topology */ 2106 ierr = DMPlexSetChart(dm, 0, numCells+numVerts);CHKERRQ(ierr); 2107 for (c = 0; c < numCells; c++) { 2108 ierr = DMPlexSetConeSize(dm, c, embedDim);CHKERRQ(ierr); 2109 } 2110 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 2111 /* Cells */ 2112 if (rank == 0) { 2113 for (i = 0, c = 0; i < numVerts; ++i) { 2114 for (j = 0; j < i; ++j) { 2115 for (k = 0; k < j; ++k) { 2116 for (l = 0; l < k; ++l) { 2117 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] && 2118 graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) { 2119 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l; 2120 /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */ 2121 { 2122 const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2123 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}}, 2124 {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}}, 2125 {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}}, 2126 2127 {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}}, 2128 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2129 {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}}, 2130 {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}}, 2131 2132 {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}}, 2133 {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}}, 2134 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2135 {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}, 2136 2137 {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}}, 2138 {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}}, 2139 {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2140 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}}; 2141 PetscReal normal[4]; 2142 PetscInt e, f, g; 2143 2144 for (d = 0; d < embedDim; ++d) { 2145 normal[d] = 0.0; 2146 for (e = 0; e < embedDim; ++e) { 2147 for (f = 0; f < embedDim; ++f) { 2148 for (g = 0; g < embedDim; ++g) { 2149 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]); 2150 } 2151 } 2152 } 2153 } 2154 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 2155 } 2156 ierr = DMPlexSetCone(dm, c++, cone);CHKERRQ(ierr); 2157 } 2158 } 2159 } 2160 } 2161 } 2162 } 2163 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2164 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2165 ierr = PetscFree(graph);CHKERRQ(ierr); 2166 break; 2167 } 2168 default: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim); 2169 } 2170 /* Create coordinates */ 2171 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2172 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2173 ierr = PetscSectionSetFieldComponents(coordSection, 0, embedDim);CHKERRQ(ierr); 2174 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);CHKERRQ(ierr); 2175 for (v = firstVertex; v < firstVertex+numVerts; ++v) { 2176 ierr = PetscSectionSetDof(coordSection, v, embedDim);CHKERRQ(ierr); 2177 ierr = PetscSectionSetFieldDof(coordSection, v, 0, embedDim);CHKERRQ(ierr); 2178 } 2179 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2180 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2181 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 2182 ierr = VecSetBlockSize(coordinates, embedDim);CHKERRQ(ierr); 2183 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2184 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2185 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2186 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2187 for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];} 2188 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2189 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2190 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2191 ierr = PetscFree(coordsIn);CHKERRQ(ierr); 2192 { 2193 DM cdm; 2194 PetscDS cds; 2195 PetscScalar c = R; 2196 2197 ierr = DMPlexCreateCoordinateSpace(dm, 1, snapToSphere);CHKERRQ(ierr); 2198 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 2199 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 2200 ierr = PetscDSSetConstants(cds, 1, &c);CHKERRQ(ierr); 2201 } 2202 /* Wait for coordinate creation before doing in-place modification */ 2203 if (simplex) {ierr = DMPlexInterpolateInPlace_Internal(dm);CHKERRQ(ierr);} 2204 PetscFunctionReturn(0); 2205 } 2206 2207 typedef void (*TPSEvaluateFunc)(const PetscReal[], PetscReal*, PetscReal[], PetscReal(*)[3]); 2208 2209 /* 2210 The Schwarz P implicit surface is 2211 2212 f(x) = cos(x0) + cos(x1) + cos(x2) = 0 2213 */ 2214 static void TPSEvaluate_SchwarzP(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3]) 2215 { 2216 PetscReal c[3] = {PetscCosReal(y[0] * PETSC_PI), PetscCosReal(y[1] * PETSC_PI), PetscCosReal(y[2] * PETSC_PI)}; 2217 PetscReal g[3] = {-PetscSinReal(y[0] * PETSC_PI), -PetscSinReal(y[1] * PETSC_PI), -PetscSinReal(y[2] * PETSC_PI)}; 2218 f[0] = c[0] + c[1] + c[2]; 2219 for (PetscInt i=0; i<3; i++) { 2220 grad[i] = PETSC_PI * g[i]; 2221 for (PetscInt j=0; j<3; j++) { 2222 hess[i][j] = (i == j) ? -PetscSqr(PETSC_PI) * c[i] : 0.; 2223 } 2224 } 2225 } 2226 2227 /* 2228 The Gyroid implicit surface is 2229 2230 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) 2231 2232 */ 2233 static void TPSEvaluate_Gyroid(const PetscReal y[3], PetscReal *f, PetscReal grad[], PetscReal (*hess)[3]) 2234 { 2235 PetscReal s[3] = {PetscSinReal(PETSC_PI * y[0]), PetscSinReal(PETSC_PI * (y[1] + .5)), PetscSinReal(PETSC_PI * (y[2] + .25))}; 2236 PetscReal c[3] = {PetscCosReal(PETSC_PI * y[0]), PetscCosReal(PETSC_PI * (y[1] + .5)), PetscCosReal(PETSC_PI * (y[2] + .25))}; 2237 f[0] = s[0] * c[1] + s[1] * c[2] + s[2] * c[0]; 2238 grad[0] = PETSC_PI * (c[0] * c[1] - s[2] * s[0]); 2239 grad[1] = PETSC_PI * (c[1] * c[2] - s[0] * s[1]); 2240 grad[2] = PETSC_PI * (c[2] * c[0] - s[1] * s[2]); 2241 hess[0][0] = -PetscSqr(PETSC_PI) * (s[0] * c[1] + s[2] * c[0]); 2242 hess[0][1] = -PetscSqr(PETSC_PI) * (c[0] * s[1]); 2243 hess[0][2] = -PetscSqr(PETSC_PI) * (c[2] * s[0]); 2244 hess[1][0] = -PetscSqr(PETSC_PI) * (s[1] * c[2] + s[0] * c[1]); 2245 hess[1][1] = -PetscSqr(PETSC_PI) * (c[1] * s[2]); 2246 hess[2][2] = -PetscSqr(PETSC_PI) * (c[0] * s[1]); 2247 hess[2][0] = -PetscSqr(PETSC_PI) * (s[2] * c[0] + s[1] * c[2]); 2248 hess[2][1] = -PetscSqr(PETSC_PI) * (c[2] * s[0]); 2249 hess[2][2] = -PetscSqr(PETSC_PI) * (c[1] * s[2]); 2250 } 2251 2252 /* 2253 We wish to solve 2254 2255 min_y || y - x ||^2 subject to f(y) = 0 2256 2257 Let g(y) = grad(f). The minimization problem is equivalent to asking to satisfy 2258 f(y) = 0 and (y-x) is parallel to g(y). We do this by using Householder QR to obtain a basis for the 2259 tangent space and ask for both components in the tangent space to be zero. 2260 2261 Take g to be a column vector and compute the "full QR" factorization Q R = g, 2262 where Q = I - 2 n n^T is a symmetric orthogonal matrix. 2263 The first column of Q is parallel to g so the remaining two columns span the null space. 2264 Let Qn = Q[:,1:] be those remaining columns. Then Qn Qn^T is an orthogonal projector into the tangent space. 2265 Since Q is symmetric, this is equivalent to multipyling by Q and taking the last two entries. 2266 In total, we have a system of 3 equations in 3 unknowns: 2267 2268 f(y) = 0 1 equation 2269 Qn^T (y - x) = 0 2 equations 2270 2271 Here, we compute the residual and Jacobian of this system. 2272 */ 2273 static void TPSNearestPointResJac(TPSEvaluateFunc feval, const PetscScalar x[], const PetscScalar y[], PetscScalar res[], PetscScalar J[]) 2274 { 2275 PetscReal yreal[3] = {PetscRealPart(y[0]), PetscRealPart(y[1]), PetscRealPart(y[2])}; 2276 PetscReal d[3] = {PetscRealPart(y[0] - x[0]), PetscRealPart(y[1] - x[1]), PetscRealPart(y[2] - x[2])}; 2277 PetscReal f, grad[3], n[3], n_y[3][3], norm, norm_y[3], nd, nd_y[3], sign; 2278 2279 feval(yreal, &f, grad, n_y); 2280 2281 for (PetscInt i=0; i<3; i++) n[i] = grad[i]; 2282 norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2])); 2283 for (PetscInt i=0; i<3; i++) { 2284 norm_y[i] = 1. / norm * n[i] * n_y[i][i]; 2285 } 2286 2287 // Define the Householder reflector 2288 sign = n[0] >= 0 ? 1. : -1.; 2289 n[0] += norm * sign; 2290 for (PetscInt i=0; i<3; i++) n_y[0][i] += norm_y[i] * sign; 2291 2292 norm = PetscSqrtReal(PetscSqr(n[0]) + PetscSqr(n[1]) + PetscSqr(n[2])); 2293 norm_y[0] = 1. / norm * (n[0] * n_y[0][0]); 2294 norm_y[1] = 1. / norm * (n[0] * n_y[0][1] + n[1] * n_y[1][1]); 2295 norm_y[2] = 1. / norm * (n[0] * n_y[0][2] + n[2] * n_y[2][2]); 2296 2297 for (PetscInt i=0; i<3; i++) { 2298 n[i] /= norm; 2299 for (PetscInt j=0; j<3; j++) { 2300 // note that n[i] is n_old[i]/norm when executing the code below 2301 n_y[i][j] = n_y[i][j] / norm - n[i] / norm * norm_y[j]; 2302 } 2303 } 2304 2305 nd = n[0] * d[0] + n[1] * d[1] + n[2] * d[2]; 2306 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]; 2307 2308 res[0] = f; 2309 res[1] = d[1] - 2 * n[1] * nd; 2310 res[2] = d[2] - 2 * n[2] * nd; 2311 // J[j][i] is J_{ij} (column major) 2312 for (PetscInt j=0; j<3; j++) { 2313 J[0 + j*3] = grad[j]; 2314 J[1 + j*3] = (j == 1)*1. - 2 * (n_y[1][j] * nd + n[1] * nd_y[j]); 2315 J[2 + j*3] = (j == 2)*1. - 2 * (n_y[2][j] * nd + n[2] * nd_y[j]); 2316 } 2317 } 2318 2319 /* 2320 Project x to the nearest point on the implicit surface using Newton's method. 2321 */ 2322 static PetscErrorCode TPSNearestPoint(TPSEvaluateFunc feval, PetscScalar x[]) 2323 { 2324 PetscScalar y[3] = {x[0], x[1], x[2]}; // Initial guess 2325 PetscErrorCode ierr; 2326 2327 PetscFunctionBegin; 2328 for (PetscInt iter=0; iter<10; iter++) { 2329 PetscScalar res[3], J[9]; 2330 PetscReal resnorm; 2331 TPSNearestPointResJac(feval, x, y, res, J); 2332 resnorm = PetscSqrtReal(PetscSqr(PetscRealPart(res[0])) + PetscSqr(PetscRealPart(res[1])) + PetscSqr(PetscRealPart(res[2]))); 2333 if (0) { // Turn on this monitor if you need to confirm quadratic convergence 2334 ierr = PetscPrintf(PETSC_COMM_SELF, "[%D] res [%g %g %g]\n", iter, PetscRealPart(res[0]), PetscRealPart(res[1]), PetscRealPart(res[2]));CHKERRQ(ierr); 2335 } 2336 if (resnorm < PETSC_SMALL) break; 2337 2338 // Take the Newton step 2339 ierr = PetscKernel_A_gets_inverse_A_3(J, 0., PETSC_FALSE, NULL);CHKERRQ(ierr); 2340 PetscKernel_v_gets_v_minus_A_times_w_3(y, J, res); 2341 } 2342 for (PetscInt i=0; i<3; i++) x[i] = y[i]; 2343 PetscFunctionReturn(0); 2344 } 2345 2346 const char *const DMPlexTPSTypes[] = {"SCHWARZ_P", "GYROID", "DMPlexTPSType", "DMPLEX_TPS_", NULL}; 2347 2348 static PetscErrorCode DMPlexCreateTPSMesh_Internal(DM dm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscInt refinements, PetscInt layers, PetscReal thickness) 2349 { 2350 PetscErrorCode ierr; 2351 PetscMPIInt rank; 2352 PetscInt topoDim = 2, spaceDim = 3, numFaces = 0, numVertices = 0, numEdges = 0; 2353 PetscInt (*edges)[2] = NULL, *edgeSets = NULL; 2354 PetscInt *cells_flat = NULL; 2355 PetscReal *vtxCoords = NULL; 2356 TPSEvaluateFunc evalFunc = NULL; 2357 DMLabel label; 2358 2359 PetscFunctionBegin; 2360 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRMPI(ierr); 2361 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); 2362 switch (tpstype) { 2363 case DMPLEX_TPS_SCHWARZ_P: 2364 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"); 2365 if (!rank) { 2366 PetscInt (*cells)[6][4][4] = NULL; // [junction, junction-face, cell, conn] 2367 PetscInt Njunctions = 0, Ncuts = 0, Npipes[3], vcount; 2368 PetscReal L = 1; 2369 2370 Npipes[0] = (extent[0] + 1) * extent[1] * extent[2]; 2371 Npipes[1] = extent[0] * (extent[1] + 1) * extent[2]; 2372 Npipes[2] = extent[0] * extent[1] * (extent[2] + 1); 2373 Njunctions = extent[0] * extent[1] * extent[2]; 2374 Ncuts = 2 * (extent[0] * extent[1] + extent[1] * extent[2] + extent[2] * extent[0]); 2375 numVertices = 4 * (Npipes[0] + Npipes[1] + Npipes[2]) + 8 * Njunctions; 2376 ierr = PetscMalloc1(3*numVertices, &vtxCoords);CHKERRQ(ierr); 2377 ierr = PetscMalloc1(Njunctions, &cells);CHKERRQ(ierr); 2378 ierr = PetscMalloc1(Ncuts*4, &edges);CHKERRQ(ierr); 2379 ierr = PetscMalloc1(Ncuts*4, &edgeSets);CHKERRQ(ierr); 2380 // x-normal pipes 2381 vcount = 0; 2382 for (PetscInt i=0; i<extent[0]+1; i++) { 2383 for (PetscInt j=0; j<extent[1]; j++) { 2384 for (PetscInt k=0; k<extent[2]; k++) { 2385 for (PetscInt l=0; l<4; l++) { 2386 vtxCoords[vcount++] = (2*i - 1) * L; 2387 vtxCoords[vcount++] = 2 * j * L + PetscCosReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2388 vtxCoords[vcount++] = 2 * k * L + PetscSinReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2389 } 2390 } 2391 } 2392 } 2393 // y-normal pipes 2394 for (PetscInt i=0; i<extent[0]; i++) { 2395 for (PetscInt j=0; j<extent[1]+1; j++) { 2396 for (PetscInt k=0; k<extent[2]; k++) { 2397 for (PetscInt l=0; l<4; l++) { 2398 vtxCoords[vcount++] = 2 * i * L + PetscSinReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2399 vtxCoords[vcount++] = (2*j - 1) * L; 2400 vtxCoords[vcount++] = 2 * k * L + PetscCosReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2401 } 2402 } 2403 } 2404 } 2405 // z-normal pipes 2406 for (PetscInt i=0; i<extent[0]; i++) { 2407 for (PetscInt j=0; j<extent[1]; j++) { 2408 for (PetscInt k=0; k<extent[2]+1; k++) { 2409 for (PetscInt l=0; l<4; l++) { 2410 vtxCoords[vcount++] = 2 * i * L + PetscCosReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2411 vtxCoords[vcount++] = 2 * j * L + PetscSinReal((2*l + 1) * PETSC_PI / 4) * L / 2; 2412 vtxCoords[vcount++] = (2*k - 1) * L; 2413 } 2414 } 2415 } 2416 } 2417 // junctions 2418 for (PetscInt i=0; i<extent[0]; i++) { 2419 for (PetscInt j=0; j<extent[1]; j++) { 2420 for (PetscInt k=0; k<extent[2]; k++) { 2421 const PetscInt J = (i*extent[1] + j)*extent[2] + k, Jvoff = (Npipes[0] + Npipes[1] + Npipes[2])*4 + J*8; 2422 PetscCheck(vcount / 3 == Jvoff, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unexpected vertex count"); 2423 for (PetscInt ii=0; ii<2; ii++) { 2424 for (PetscInt jj=0; jj<2; jj++) { 2425 for (PetscInt kk=0; kk<2; kk++) { 2426 double Ls = (1 - sqrt(2) / 4) * L; 2427 vtxCoords[vcount++] = 2*i*L + (2*ii-1) * Ls; 2428 vtxCoords[vcount++] = 2*j*L + (2*jj-1) * Ls; 2429 vtxCoords[vcount++] = 2*k*L + (2*kk-1) * Ls; 2430 } 2431 } 2432 } 2433 const PetscInt jfaces[3][2][4] = { 2434 {{3,1,0,2}, {7,5,4,6}}, // x-aligned 2435 {{5,4,0,1}, {7,6,2,3}}, // y-aligned 2436 {{6,2,0,4}, {7,3,1,5}} // z-aligned 2437 }; 2438 const PetscInt pipe_lo[3] = { // vertex numbers of pipes 2439 ((i * extent[1] + j) * extent[2] + k)*4, 2440 ((i * (extent[1] + 1) + j) * extent[2] + k + Npipes[0])*4, 2441 ((i * extent[1] + j) * (extent[2]+1) + k + Npipes[0] + Npipes[1])*4 2442 }; 2443 const PetscInt pipe_hi[3] = { // vertex numbers of pipes 2444 (((i + 1) * extent[1] + j) * extent[2] + k)*4, 2445 ((i * (extent[1] + 1) + j + 1) * extent[2] + k + Npipes[0])*4, 2446 ((i * extent[1] + j) * (extent[2]+1) + k + 1 + Npipes[0] + Npipes[1])*4 2447 }; 2448 for (PetscInt dir=0; dir<3; dir++) { // x,y,z 2449 const PetscInt ijk[3] = {i, j, k}; 2450 for (PetscInt l=0; l<4; l++) { // rotations 2451 cells[J][dir*2+0][l][0] = pipe_lo[dir] + l; 2452 cells[J][dir*2+0][l][1] = Jvoff + jfaces[dir][0][l]; 2453 cells[J][dir*2+0][l][2] = Jvoff + jfaces[dir][0][(l-1+4)%4]; 2454 cells[J][dir*2+0][l][3] = pipe_lo[dir] + (l-1+4)%4; 2455 cells[J][dir*2+1][l][0] = Jvoff + jfaces[dir][1][l]; 2456 cells[J][dir*2+1][l][1] = pipe_hi[dir] + l; 2457 cells[J][dir*2+1][l][2] = pipe_hi[dir] + (l-1+4)%4; 2458 cells[J][dir*2+1][l][3] = Jvoff + jfaces[dir][1][(l-1+4)%4]; 2459 if (ijk[dir] == 0) { 2460 edges[numEdges][0] = pipe_lo[dir] + l; 2461 edges[numEdges][1] = pipe_lo[dir] + (l+1) % 4; 2462 edgeSets[numEdges] = dir*2 + 1; 2463 numEdges++; 2464 } 2465 if (ijk[dir] + 1 == extent[dir]) { 2466 edges[numEdges][0] = pipe_hi[dir] + l; 2467 edges[numEdges][1] = pipe_hi[dir] + (l+1) % 4; 2468 edgeSets[numEdges] = dir*2 + 2; 2469 numEdges++; 2470 } 2471 } 2472 } 2473 } 2474 } 2475 } 2476 PetscCheck(numEdges == Ncuts * 4, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Edge count %D incompatible with number of cuts %D", numEdges, Ncuts); 2477 numFaces = 24 * Njunctions; 2478 cells_flat = cells[0][0][0]; 2479 } 2480 evalFunc = TPSEvaluate_SchwarzP; 2481 break; 2482 case DMPLEX_TPS_GYROID: 2483 if (!rank) { 2484 // This is a coarse mesh approximation of the gyroid shifted to being the zero of the level set 2485 // 2486 // 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) 2487 // 2488 // on the cell [0,2]^3. 2489 // 2490 // Think about dividing that cell into four columns, and focus on the column [0,1]x[0,1]x[0,2]. 2491 // If you looked at the gyroid in that column at different slices of z you would see that it kind of spins 2492 // like a boomerang: 2493 // 2494 // z = 0 z = 1/4 z = 1/2 z = 3/4 // 2495 // ----- ------- ------- ------- // 2496 // // 2497 // + + + + + + + \ + // 2498 // \ / \ // 2499 // \ `-_ _-' / } // 2500 // *-_ `-' _-' / // 2501 // + `-+ + + +-' + + / + // 2502 // // 2503 // // 2504 // z = 1 z = 5/4 z = 3/2 z = 7/4 // 2505 // ----- ------- ------- ------- // 2506 // // 2507 // +-_ + + + + _-+ + / + // 2508 // `-_ _-_ _-` / // 2509 // \ _-' `-_ / { // 2510 // \ / \ // 2511 // + + + + + + + \ + // 2512 // 2513 // 2514 // This course mesh approximates each of these slices by two line segments, 2515 // and then connects the segments in consecutive layers with quadrilateral faces. 2516 // All of the end points of the segments are multiples of 1/4 except for the 2517 // point * in the picture for z = 0 above and the similar points in other layers. 2518 // That point is at (gamma, gamma, 0), where gamma is calculated below. 2519 // 2520 // The column [1,2]x[1,2]x[0,2] looks the same as this column; 2521 // The columns [1,2]x[0,1]x[0,2] and [0,1]x[1,2]x[0,2] are mirror images. 2522 // 2523 // As for how this method turned into the names given to the vertices: 2524 // that was not systematic, it was just the way it worked out in my handwritten notes. 2525 2526 PetscInt facesPerBlock = 64; 2527 PetscInt vertsPerBlock = 56; 2528 PetscInt extentPlus[3]; 2529 PetscInt numBlocks, numBlocksPlus; 2530 const PetscInt A = 0, B = 1, C = 2, D = 3, E = 4, F = 5, G = 6, H = 7, 2531 II = 8, J = 9, K = 10, L = 11, M = 12, N = 13, O = 14, P = 15, 2532 Q = 16, R = 17, S = 18, T = 19, U = 20, V = 21, W = 22, X = 23, 2533 Y = 24, Z = 25, Ap = 26, Bp = 27, Cp = 28, Dp = 29, Ep = 30, Fp = 31, 2534 Gp = 32, Hp = 33, Ip = 34, Jp = 35, Kp = 36, Lp = 37, Mp = 38, Np = 39, 2535 Op = 40, Pp = 41, Qp = 42, Rp = 43, Sp = 44, Tp = 45, Up = 46, Vp = 47, 2536 Wp = 48, Xp = 49, Yp = 50, Zp = 51, Aq = 52, Bq = 53, Cq = 54, Dq = 55; 2537 const PetscInt pattern[64][4] = 2538 { /* face to vertex within the coarse discretization of a single gyroid block */ 2539 /* layer 0 */ 2540 {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}, 2541 /* layer 1 */ 2542 {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}, 2543 /* layer 2 */ 2544 {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}, 2545 /* layer 3 */ 2546 {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}, 2547 /* layer 4 */ 2548 {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}, 2549 /* layer 5 */ 2550 {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}, 2551 /* layer 6 */ 2552 {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}, 2553 /* layer 7 (the top is the periodic image of the bottom of layer 0) */ 2554 {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} 2555 }; 2556 const PetscReal gamma = PetscAcosReal((PetscSqrtReal(3.)-1.) / PetscSqrtReal(2.)) / PETSC_PI; 2557 const PetscReal patternCoords[56][3] = 2558 { 2559 /* A */ {1.,0.,0.}, 2560 /* B */ {0.,1.,0.}, 2561 /* C */ {gamma,gamma,0.}, 2562 /* D */ {1+gamma,1-gamma,0.}, 2563 /* E */ {2-gamma,2-gamma,0.}, 2564 /* F */ {1-gamma,1+gamma,0.}, 2565 2566 /* G */ {.5,0,.25}, 2567 /* H */ {1.5,0.,.25}, 2568 /* II */ {.5,1.,.25}, 2569 /* J */ {1.5,1.,.25}, 2570 /* K */ {.25,.5,.25}, 2571 /* L */ {1.25,.5,.25}, 2572 /* M */ {.75,1.5,.25}, 2573 /* N */ {1.75,1.5,.25}, 2574 2575 /* O */ {0.,0.,.5}, 2576 /* P */ {1.,1.,.5}, 2577 /* Q */ {gamma,1-gamma,.5}, 2578 /* R */ {1+gamma,gamma,.5}, 2579 /* S */ {2-gamma,1+gamma,.5}, 2580 /* T */ {1-gamma,2-gamma,.5}, 2581 2582 /* U */ {0.,.5,.75}, 2583 /* V */ {0.,1.5,.75}, 2584 /* W */ {1.,.5,.75}, 2585 /* X */ {1.,1.5,.75}, 2586 /* Y */ {.5,.75,.75}, 2587 /* Z */ {.5,1.75,.75}, 2588 /* Ap */ {1.5,.25,.75}, 2589 /* Bp */ {1.5,1.25,.75}, 2590 2591 /* Cp */ {1.,0.,1.}, 2592 /* Dp */ {0.,1.,1.}, 2593 /* Ep */ {1-gamma,1-gamma,1.}, 2594 /* Fp */ {1+gamma,1+gamma,1.}, 2595 /* Gp */ {2-gamma,gamma,1.}, 2596 /* Hp */ {gamma,2-gamma,1.}, 2597 2598 /* Ip */ {.5,0.,1.25}, 2599 /* Jp */ {1.5,0.,1.25}, 2600 /* Kp */ {.5,1.,1.25}, 2601 /* Lp */ {1.5,1.,1.25}, 2602 /* Mp */ {.75,.5,1.25}, 2603 /* Np */ {1.75,.5,1.25}, 2604 /* Op */ {.25,1.5,1.25}, 2605 /* Pp */ {1.25,1.5,1.25}, 2606 2607 /* Qp */ {0.,0.,1.5}, 2608 /* Rp */ {1.,1.,1.5}, 2609 /* Sp */ {1-gamma,gamma,1.5}, 2610 /* Tp */ {2-gamma,1-gamma,1.5}, 2611 /* Up */ {1+gamma,2-gamma,1.5}, 2612 /* Vp */ {gamma,1+gamma,1.5}, 2613 2614 /* Wp */ {0.,.5,1.75}, 2615 /* Xp */ {0.,1.5,1.75}, 2616 /* Yp */ {1.,.5,1.75}, 2617 /* Zp */ {1.,1.5,1.75}, 2618 /* Aq */ {.5,.25,1.75}, 2619 /* Bq */ {.5,1.25,1.75}, 2620 /* Cq */ {1.5,.75,1.75}, 2621 /* Dq */ {1.5,1.75,1.75}, 2622 }; 2623 PetscInt (*cells)[64][4] = NULL; 2624 PetscBool *seen; 2625 PetscInt *vertToTrueVert; 2626 PetscInt count; 2627 2628 for (PetscInt i = 0; i < 3; i++) extentPlus[i] = extent[i] + 1; 2629 numBlocks = 1; 2630 for (PetscInt i = 0; i < 3; i++) numBlocks *= extent[i]; 2631 numBlocksPlus = 1; 2632 for (PetscInt i = 0; i < 3; i++) numBlocksPlus *= extentPlus[i]; 2633 numFaces = numBlocks * facesPerBlock; 2634 ierr = PetscMalloc1(numBlocks, &cells);CHKERRQ(ierr); 2635 ierr = PetscCalloc1(numBlocksPlus * vertsPerBlock,&seen);CHKERRQ(ierr); 2636 for (PetscInt k = 0; k < extent[2]; k++) { 2637 for (PetscInt j = 0; j < extent[1]; j++) { 2638 for (PetscInt i = 0; i < extent[0]; i++) { 2639 for (PetscInt f = 0; f < facesPerBlock; f++) { 2640 for (PetscInt v = 0; v < 4; v++) { 2641 PetscInt vertRaw = pattern[f][v]; 2642 PetscInt blockidx = vertRaw / 56; 2643 PetscInt patternvert = vertRaw % 56; 2644 PetscInt xplus = (blockidx & 1); 2645 PetscInt yplus = (blockidx & 2) >> 1; 2646 PetscInt zplus = (blockidx & 4) >> 2; 2647 PetscInt zcoord = (periodic && periodic[2] == DM_BOUNDARY_PERIODIC) ? ((k + zplus) % extent[2]) : (k + zplus); 2648 PetscInt ycoord = (periodic && periodic[1] == DM_BOUNDARY_PERIODIC) ? ((j + yplus) % extent[1]) : (j + yplus); 2649 PetscInt xcoord = (periodic && periodic[0] == DM_BOUNDARY_PERIODIC) ? ((i + xplus) % extent[0]) : (i + xplus); 2650 PetscInt vert = ((zcoord * extentPlus[1] + ycoord) * extentPlus[0] + xcoord) * 56 + patternvert; 2651 2652 cells[(k * extent[1] + j) * extent[0] + i][f][v] = vert; 2653 seen[vert] = PETSC_TRUE; 2654 } 2655 } 2656 } 2657 } 2658 } 2659 for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++) if (seen[i]) numVertices++; 2660 count = 0; 2661 ierr = PetscMalloc1(numBlocksPlus * vertsPerBlock, &vertToTrueVert);CHKERRQ(ierr); 2662 ierr = PetscMalloc1(numVertices * 3, &vtxCoords);CHKERRQ(ierr); 2663 for (PetscInt i = 0; i < numBlocksPlus * vertsPerBlock; i++) vertToTrueVert[i] = -1; 2664 for (PetscInt k = 0; k < extentPlus[2]; k++) { 2665 for (PetscInt j = 0; j < extentPlus[1]; j++) { 2666 for (PetscInt i = 0; i < extentPlus[0]; i++) { 2667 for (PetscInt v = 0; v < vertsPerBlock; v++) { 2668 PetscInt vIdx = ((k * extentPlus[1] + j) * extentPlus[0] + i) * vertsPerBlock + v; 2669 2670 if (seen[vIdx]) { 2671 PetscInt thisVert; 2672 2673 vertToTrueVert[vIdx] = thisVert = count++; 2674 2675 for (PetscInt d = 0; d < 3; d++) vtxCoords[3 * thisVert + d] = patternCoords[v][d]; 2676 vtxCoords[3 * thisVert + 0] += i * 2; 2677 vtxCoords[3 * thisVert + 1] += j * 2; 2678 vtxCoords[3 * thisVert + 2] += k * 2; 2679 } 2680 } 2681 } 2682 } 2683 } 2684 for (PetscInt i = 0; i < numBlocks; i++) { 2685 for (PetscInt f = 0; f < facesPerBlock; f++) { 2686 for (PetscInt v = 0; v < 4; v++) { 2687 cells[i][f][v] = vertToTrueVert[cells[i][f][v]]; 2688 } 2689 } 2690 } 2691 ierr = PetscFree(vertToTrueVert);CHKERRQ(ierr); 2692 ierr = PetscFree(seen);CHKERRQ(ierr); 2693 cells_flat = cells[0][0]; 2694 numEdges = 0; 2695 for (PetscInt i = 0; i < numFaces; i++) { 2696 for (PetscInt e = 0; e < 4; e++) { 2697 PetscInt ev[] = {cells_flat[i*4 + e], cells_flat[i*4 + ((e+1)%4)]}; 2698 const PetscReal *evCoords[] = {&vtxCoords[3*ev[0]], &vtxCoords[3*ev[1]]}; 2699 2700 for (PetscInt d = 0; d < 3; d++) { 2701 if (!periodic || periodic[0] != DM_BOUNDARY_PERIODIC) { 2702 if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) numEdges++; 2703 if (evCoords[0][d] == 2.*extent[d] && evCoords[1][d] == 2.*extent[d]) numEdges++; 2704 } 2705 } 2706 } 2707 } 2708 ierr = PetscMalloc1(numEdges, &edges);CHKERRQ(ierr); 2709 ierr = PetscMalloc1(numEdges, &edgeSets);CHKERRQ(ierr); 2710 for (PetscInt edge = 0, i = 0; i < numFaces; i++) { 2711 for (PetscInt e = 0; e < 4; e++) { 2712 PetscInt ev[] = {cells_flat[i*4 + e], cells_flat[i*4 + ((e+1)%4)]}; 2713 const PetscReal *evCoords[] = {&vtxCoords[3*ev[0]], &vtxCoords[3*ev[1]]}; 2714 2715 for (PetscInt d = 0; d < 3; d++) { 2716 if (!periodic || periodic[d] != DM_BOUNDARY_PERIODIC) { 2717 if (evCoords[0][d] == 0. && evCoords[1][d] == 0.) { 2718 edges[edge][0] = ev[0]; 2719 edges[edge][1] = ev[1]; 2720 edgeSets[edge++] = 2 * d; 2721 } 2722 if (evCoords[0][d] == 2.*extent[d] && evCoords[1][d] == 2.*extent[d]) { 2723 edges[edge][0] = ev[0]; 2724 edges[edge][1] = ev[1]; 2725 edgeSets[edge++] = 2 * d + 1; 2726 } 2727 } 2728 } 2729 } 2730 } 2731 } 2732 evalFunc = TPSEvaluate_Gyroid; 2733 break; 2734 } 2735 2736 ierr = DMSetDimension(dm, topoDim);CHKERRQ(ierr); 2737 if (!rank) {ierr = DMPlexBuildFromCellList(dm, numFaces, numVertices, 4, cells_flat);CHKERRQ(ierr);} 2738 else {ierr = DMPlexBuildFromCellList(dm, 0, 0, 0, NULL);CHKERRQ(ierr);} 2739 ierr = PetscFree(cells_flat);CHKERRQ(ierr); 2740 { 2741 DM idm; 2742 ierr = DMPlexInterpolate(dm, &idm);CHKERRQ(ierr); 2743 ierr = DMPlexReplace_Static(dm, &idm);CHKERRQ(ierr); 2744 } 2745 if (!rank) {ierr = DMPlexBuildCoordinatesFromCellList(dm, spaceDim, vtxCoords);CHKERRQ(ierr);} 2746 else {ierr = DMPlexBuildCoordinatesFromCellList(dm, spaceDim, NULL);CHKERRQ(ierr);} 2747 ierr = PetscFree(vtxCoords);CHKERRQ(ierr); 2748 2749 ierr = DMCreateLabel(dm, "Face Sets");CHKERRQ(ierr); 2750 ierr = DMGetLabel(dm, "Face Sets", &label);CHKERRQ(ierr); 2751 for (PetscInt e=0; e<numEdges; e++) { 2752 PetscInt njoin; 2753 const PetscInt *join, verts[] = {numFaces + edges[e][0], numFaces + edges[e][1]}; 2754 ierr = DMPlexGetJoin(dm, 2, verts, &njoin, &join);CHKERRQ(ierr); 2755 PetscCheck(njoin == 1, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Expected unique join of vertices %D and %D", edges[e][0], edges[e][1]); 2756 ierr = DMLabelSetValue(label, join[0], edgeSets[e]);CHKERRQ(ierr); 2757 ierr = DMPlexRestoreJoin(dm, 2, verts, &njoin, &join);CHKERRQ(ierr); 2758 } 2759 ierr = PetscFree(edges);CHKERRQ(ierr); 2760 ierr = PetscFree(edgeSets);CHKERRQ(ierr); 2761 2762 ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr); 2763 for (PetscInt refine=0; refine<refinements; refine++) { 2764 PetscInt m; 2765 DM dmf; 2766 Vec X; 2767 PetscScalar *x; 2768 ierr = DMRefine(dm, MPI_COMM_NULL, &dmf);CHKERRQ(ierr); 2769 ierr = DMPlexReplace_Static(dm, &dmf);CHKERRQ(ierr); 2770 2771 ierr = DMGetCoordinatesLocal(dm, &X);CHKERRQ(ierr); 2772 ierr = VecGetLocalSize(X, &m);CHKERRQ(ierr); 2773 ierr = VecGetArray(X, &x);CHKERRQ(ierr); 2774 for (PetscInt i=0; i<m; i+=3) { 2775 ierr = TPSNearestPoint(evalFunc, &x[i]);CHKERRQ(ierr); 2776 } 2777 ierr = VecRestoreArray(X, &x);CHKERRQ(ierr); 2778 } 2779 2780 // Face Sets has already been propagated to new vertices during refinement; this propagates to the initial vertices. 2781 ierr = DMGetLabel(dm, "Face Sets", &label);CHKERRQ(ierr); 2782 ierr = DMPlexLabelComplete(dm, label);CHKERRQ(ierr); 2783 2784 if (thickness > 0) { 2785 DM dm3; 2786 ierr = DMPlexExtrude(dm, layers, thickness, PETSC_FALSE, PETSC_TRUE, NULL, NULL, &dm3);CHKERRQ(ierr); 2787 ierr = DMPlexReplace_Static(dm, &dm3);CHKERRQ(ierr); 2788 } 2789 PetscFunctionReturn(0); 2790 } 2791 2792 /*@ 2793 DMPlexCreateTPSMesh - Create a distributed, interpolated mesh of a triply-periodic surface 2794 2795 Collective 2796 2797 Input Parameters: 2798 + comm - The communicator for the DM object 2799 . tpstype - Type of triply-periodic surface 2800 . extent - Array of length 3 containing number of periods in each direction 2801 . periodic - array of length 3 with periodicity, or NULL for non-periodic 2802 . thickness - Thickness in normal direction 2803 - refinements - Number of factor-of-2 refinements 2804 2805 Output Parameter: 2806 . dm - The DM object 2807 2808 Notes: 2809 This meshes the surface of the Schwarz P or Gyroid surfaces. Schwarz P is is the simplest member of the triply-periodic minimal surfaces. 2810 https://en.wikipedia.org/wiki/Schwarz_minimal_surface#Schwarz_P_(%22Primitive%22) and can be cut with "clean" boundaries. 2811 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. 2812 Our implementation creates a very coarse mesh of the surface and refines (by 4-way splitting) as many times as requested. 2813 On each refinement, all vertices are projected to their nearest point on the surface. 2814 This projection could readily be extended to related surfaces. 2815 2816 The face (edge) sets for the Schwarz P surface are numbered 1(-x), 2(+x), 3(-y), 4(+y), 5(-z), 6(+z). 2817 When the mesh is refined, "Face Sets" contain the new vertices (created during refinement). Use DMPlexLabelComplete() to propagate to coarse-level vertices. 2818 2819 References: 2820 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 2821 2822 Developer Notes: 2823 The Gyroid mesh does not currently mark boundary sets. 2824 2825 Level: beginner 2826 2827 .seealso: DMPlexCreateSphereMesh(), DMSetType(), DMCreate() 2828 @*/ 2829 PetscErrorCode DMPlexCreateTPSMesh(MPI_Comm comm, DMPlexTPSType tpstype, const PetscInt extent[], const DMBoundaryType periodic[], PetscInt refinements, PetscInt layers, PetscReal thickness, DM *dm) 2830 { 2831 PetscErrorCode ierr; 2832 2833 PetscFunctionBegin; 2834 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2835 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2836 ierr = DMPlexCreateTPSMesh_Internal(*dm, tpstype, extent, periodic, refinements, layers, thickness);CHKERRQ(ierr); 2837 PetscFunctionReturn(0); 2838 } 2839 2840 /*@ 2841 DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d. 2842 2843 Collective 2844 2845 Input Parameters: 2846 + comm - The communicator for the DM object 2847 . dim - The dimension 2848 . simplex - Use simplices, or tensor product cells 2849 - R - The radius 2850 2851 Output Parameter: 2852 . dm - The DM object 2853 2854 Level: beginner 2855 2856 .seealso: DMPlexCreateBallMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 2857 @*/ 2858 PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscReal R, DM *dm) 2859 { 2860 PetscErrorCode ierr; 2861 2862 PetscFunctionBegin; 2863 PetscValidPointer(dm, 5); 2864 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2865 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2866 ierr = DMPlexCreateSphereMesh_Internal(*dm, dim, simplex, R);CHKERRQ(ierr); 2867 PetscFunctionReturn(0); 2868 } 2869 2870 static PetscErrorCode DMPlexCreateBallMesh_Internal(DM dm, PetscInt dim, PetscReal R) 2871 { 2872 DM sdm, vol; 2873 DMLabel bdlabel; 2874 PetscErrorCode ierr; 2875 2876 PetscFunctionBegin; 2877 ierr = DMCreate(PetscObjectComm((PetscObject) dm), &sdm);CHKERRQ(ierr); 2878 ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr); 2879 ierr = PetscObjectSetOptionsPrefix((PetscObject) sdm, "bd_");CHKERRQ(ierr); 2880 ierr = DMPlexCreateSphereMesh_Internal(sdm, dim-1, PETSC_TRUE, R);CHKERRQ(ierr); 2881 ierr = DMSetFromOptions(sdm);CHKERRQ(ierr); 2882 ierr = DMViewFromOptions(sdm, NULL, "-dm_view");CHKERRQ(ierr); 2883 ierr = DMPlexGenerate(sdm, NULL, PETSC_TRUE, &vol);CHKERRQ(ierr); 2884 ierr = DMDestroy(&sdm);CHKERRQ(ierr); 2885 ierr = DMPlexReplace_Static(dm, &vol);CHKERRQ(ierr); 2886 ierr = DMCreateLabel(dm, "marker");CHKERRQ(ierr); 2887 ierr = DMGetLabel(dm, "marker", &bdlabel);CHKERRQ(ierr); 2888 ierr = DMPlexMarkBoundaryFaces(dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 2889 ierr = DMPlexLabelComplete(dm, bdlabel);CHKERRQ(ierr); 2890 PetscFunctionReturn(0); 2891 } 2892 2893 /*@ 2894 DMPlexCreateBallMesh - Creates a simplex mesh on the d-dimensional ball, B^d. 2895 2896 Collective 2897 2898 Input Parameters: 2899 + comm - The communicator for the DM object 2900 . dim - The dimension 2901 - R - The radius 2902 2903 Output Parameter: 2904 . dm - The DM object 2905 2906 Options Database Keys: 2907 - bd_dm_refine - This will refine the surface mesh preserving the sphere geometry 2908 2909 Level: beginner 2910 2911 .seealso: DMPlexCreateSphereMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 2912 @*/ 2913 PetscErrorCode DMPlexCreateBallMesh(MPI_Comm comm, PetscInt dim, PetscReal R, DM *dm) 2914 { 2915 PetscErrorCode ierr; 2916 2917 PetscFunctionBegin; 2918 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2919 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2920 ierr = DMPlexCreateBallMesh_Internal(*dm, dim, R);CHKERRQ(ierr); 2921 PetscFunctionReturn(0); 2922 } 2923 2924 static PetscErrorCode DMPlexCreateReferenceCell_Internal(DM rdm, DMPolytopeType ct) 2925 { 2926 PetscErrorCode ierr; 2927 2928 PetscFunctionBegin; 2929 switch (ct) { 2930 case DM_POLYTOPE_POINT: 2931 { 2932 PetscInt numPoints[1] = {1}; 2933 PetscInt coneSize[1] = {0}; 2934 PetscInt cones[1] = {0}; 2935 PetscInt coneOrientations[1] = {0}; 2936 PetscScalar vertexCoords[1] = {0.0}; 2937 2938 ierr = DMSetDimension(rdm, 0);CHKERRQ(ierr); 2939 ierr = DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2940 } 2941 break; 2942 case DM_POLYTOPE_SEGMENT: 2943 { 2944 PetscInt numPoints[2] = {2, 1}; 2945 PetscInt coneSize[3] = {2, 0, 0}; 2946 PetscInt cones[2] = {1, 2}; 2947 PetscInt coneOrientations[2] = {0, 0}; 2948 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 2949 2950 ierr = DMSetDimension(rdm, 1);CHKERRQ(ierr); 2951 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2952 } 2953 break; 2954 case DM_POLYTOPE_POINT_PRISM_TENSOR: 2955 { 2956 PetscInt numPoints[2] = {2, 1}; 2957 PetscInt coneSize[3] = {2, 0, 0}; 2958 PetscInt cones[2] = {1, 2}; 2959 PetscInt coneOrientations[2] = {0, 0}; 2960 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 2961 2962 ierr = DMSetDimension(rdm, 1);CHKERRQ(ierr); 2963 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2964 } 2965 break; 2966 case DM_POLYTOPE_TRIANGLE: 2967 { 2968 PetscInt numPoints[2] = {3, 1}; 2969 PetscInt coneSize[4] = {3, 0, 0, 0}; 2970 PetscInt cones[3] = {1, 2, 3}; 2971 PetscInt coneOrientations[3] = {0, 0, 0}; 2972 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 2973 2974 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 2975 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2976 } 2977 break; 2978 case DM_POLYTOPE_QUADRILATERAL: 2979 { 2980 PetscInt numPoints[2] = {4, 1}; 2981 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 2982 PetscInt cones[4] = {1, 2, 3, 4}; 2983 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 2984 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 2985 2986 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 2987 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2988 } 2989 break; 2990 case DM_POLYTOPE_SEG_PRISM_TENSOR: 2991 { 2992 PetscInt numPoints[2] = {4, 1}; 2993 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 2994 PetscInt cones[4] = {1, 2, 3, 4}; 2995 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 2996 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, 1.0}; 2997 2998 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 2999 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3000 } 3001 break; 3002 case DM_POLYTOPE_TETRAHEDRON: 3003 { 3004 PetscInt numPoints[2] = {4, 1}; 3005 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3006 PetscInt cones[4] = {1, 2, 3, 4}; 3007 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3008 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}; 3009 3010 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3011 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3012 } 3013 break; 3014 case DM_POLYTOPE_HEXAHEDRON: 3015 { 3016 PetscInt numPoints[2] = {8, 1}; 3017 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3018 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 3019 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3020 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, 3021 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3022 3023 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3024 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3025 } 3026 break; 3027 case DM_POLYTOPE_TRI_PRISM: 3028 { 3029 PetscInt numPoints[2] = {6, 1}; 3030 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3031 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 3032 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3033 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, -1.0, -1.0, 3034 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 3035 3036 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3037 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3038 } 3039 break; 3040 case DM_POLYTOPE_TRI_PRISM_TENSOR: 3041 { 3042 PetscInt numPoints[2] = {6, 1}; 3043 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3044 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 3045 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3046 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 3047 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 3048 3049 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3050 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3051 } 3052 break; 3053 case DM_POLYTOPE_QUAD_PRISM_TENSOR: 3054 { 3055 PetscInt numPoints[2] = {8, 1}; 3056 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3057 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 3058 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3059 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, 3060 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3061 3062 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3063 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3064 } 3065 break; 3066 case DM_POLYTOPE_PYRAMID: 3067 { 3068 PetscInt numPoints[2] = {5, 1}; 3069 PetscInt coneSize[6] = {5, 0, 0, 0, 0, 0}; 3070 PetscInt cones[5] = {1, 2, 3, 4, 5}; 3071 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3072 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, 3073 0.0, 0.0, 1.0}; 3074 3075 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3076 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3077 } 3078 break; 3079 default: SETERRQ(PetscObjectComm((PetscObject) rdm), PETSC_ERR_ARG_WRONG, "Cannot create reference cell for cell type %s", DMPolytopeTypes[ct]); 3080 } 3081 { 3082 PetscInt Nv, v; 3083 3084 /* Must create the celltype label here so that we do not automatically try to compute the types */ 3085 ierr = DMCreateLabel(rdm, "celltype");CHKERRQ(ierr); 3086 ierr = DMPlexSetCellType(rdm, 0, ct);CHKERRQ(ierr); 3087 ierr = DMPlexGetChart(rdm, NULL, &Nv);CHKERRQ(ierr); 3088 for (v = 1; v < Nv; ++v) {ierr = DMPlexSetCellType(rdm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr);} 3089 } 3090 ierr = DMPlexInterpolateInPlace_Internal(rdm);CHKERRQ(ierr); 3091 ierr = PetscObjectSetName((PetscObject) rdm, DMPolytopeTypes[ct]);CHKERRQ(ierr); 3092 PetscFunctionReturn(0); 3093 } 3094 3095 /*@ 3096 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 3097 3098 Collective 3099 3100 Input Parameters: 3101 + comm - The communicator 3102 - ct - The cell type of the reference cell 3103 3104 Output Parameter: 3105 . refdm - The reference cell 3106 3107 Level: intermediate 3108 3109 .seealso: DMPlexCreateReferenceCell(), DMPlexCreateBoxMesh() 3110 @*/ 3111 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, DMPolytopeType ct, DM *refdm) 3112 { 3113 PetscErrorCode ierr; 3114 3115 PetscFunctionBegin; 3116 ierr = DMCreate(comm, refdm);CHKERRQ(ierr); 3117 ierr = DMSetType(*refdm, DMPLEX);CHKERRQ(ierr); 3118 ierr = DMPlexCreateReferenceCell_Internal(*refdm, ct);CHKERRQ(ierr); 3119 PetscFunctionReturn(0); 3120 } 3121 3122 static PetscErrorCode DMPlexCreateBoundaryLabel_Private(DM dm, const char name[]) 3123 { 3124 DM plex; 3125 DMLabel label; 3126 PetscBool hasLabel; 3127 PetscErrorCode ierr; 3128 3129 PetscFunctionBeginUser; 3130 ierr = DMHasLabel(dm, name, &hasLabel);CHKERRQ(ierr); 3131 if (hasLabel) PetscFunctionReturn(0); 3132 ierr = DMCreateLabel(dm, name);CHKERRQ(ierr); 3133 ierr = DMGetLabel(dm, name, &label);CHKERRQ(ierr); 3134 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 3135 ierr = DMPlexMarkBoundaryFaces(plex, 1, label);CHKERRQ(ierr); 3136 ierr = DMDestroy(&plex);CHKERRQ(ierr); 3137 PetscFunctionReturn(0); 3138 } 3139 3140 const char * const DMPlexShapes[] = {"box", "box_surface", "ball", "sphere", "cylinder", "schwarz_p", "gyroid", "unknown", "DMPlexShape", "DM_SHAPE_", NULL}; 3141 3142 static PetscErrorCode DMPlexCreateFromOptions_Internal(PetscOptionItems *PetscOptionsObject, PetscBool *useCoordSpace, DM dm) 3143 { 3144 DMPlexShape shape = DM_SHAPE_BOX; 3145 DMPolytopeType cell = DM_POLYTOPE_TRIANGLE; 3146 PetscInt dim = 2; 3147 PetscBool simplex = PETSC_TRUE, interpolate = PETSC_TRUE, adjCone = PETSC_FALSE, adjClosure = PETSC_TRUE, refDomain = PETSC_FALSE; 3148 PetscBool flg, flg2, fflg, bdfflg, nameflg; 3149 MPI_Comm comm; 3150 char filename[PETSC_MAX_PATH_LEN] = "<unspecified>"; 3151 char bdFilename[PETSC_MAX_PATH_LEN] = "<unspecified>"; 3152 char plexname[PETSC_MAX_PATH_LEN] = ""; 3153 PetscErrorCode ierr; 3154 3155 PetscFunctionBegin; 3156 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 3157 /* TODO Turn this into a registration interface */ 3158 ierr = PetscOptionsString("-dm_plex_filename", "File containing a mesh", "DMPlexCreateFromFile", filename, filename, sizeof(filename), &fflg);CHKERRQ(ierr); 3159 ierr = PetscOptionsString("-dm_plex_boundary_filename", "File containing a mesh boundary", "DMPlexCreateFromFile", bdFilename, bdFilename, sizeof(bdFilename), &bdfflg);CHKERRQ(ierr); 3160 ierr = PetscOptionsString("-dm_plex_name", "Name of the mesh in the file", "DMPlexCreateFromFile", plexname, plexname, sizeof(plexname), &nameflg);CHKERRQ(ierr); 3161 ierr = PetscOptionsEnum("-dm_plex_cell", "Cell shape", "", DMPolytopeTypes, (PetscEnum) cell, (PetscEnum *) &cell, NULL);CHKERRQ(ierr); 3162 ierr = PetscOptionsBool("-dm_plex_reference_cell_domain", "Use a reference cell domain", "", refDomain, &refDomain, NULL);CHKERRQ(ierr); 3163 ierr = PetscOptionsEnum("-dm_plex_shape", "Shape for built-in mesh", "", DMPlexShapes, (PetscEnum) shape, (PetscEnum *) &shape, &flg);CHKERRQ(ierr); 3164 ierr = PetscOptionsBoundedInt("-dm_plex_dim", "Topological dimension of the mesh", "DMGetDimension", dim, &dim, &flg, 0);CHKERRQ(ierr); 3165 PetscCheckFalse((dim < 0) || (dim > 3),comm, PETSC_ERR_ARG_OUTOFRANGE, "Dimension %D should be in [1, 3]", dim); 3166 ierr = PetscOptionsBool("-dm_plex_simplex", "Mesh cell shape", "", simplex, &simplex, &flg);CHKERRQ(ierr); 3167 ierr = PetscOptionsBool("-dm_plex_interpolate", "Flag to create edges and faces automatically", "", interpolate, &interpolate, &flg);CHKERRQ(ierr); 3168 ierr = PetscOptionsBool("-dm_plex_adj_cone", "Set adjacency direction", "DMSetBasicAdjacency", adjCone, &adjCone, &flg);CHKERRQ(ierr); 3169 ierr = PetscOptionsBool("-dm_plex_adj_closure", "Set adjacency size", "DMSetBasicAdjacency", adjClosure, &adjClosure, &flg2);CHKERRQ(ierr); 3170 if (flg || flg2) {ierr = DMSetBasicAdjacency(dm, adjCone, adjClosure);CHKERRQ(ierr);} 3171 3172 switch (cell) { 3173 case DM_POLYTOPE_POINT: 3174 case DM_POLYTOPE_SEGMENT: 3175 case DM_POLYTOPE_POINT_PRISM_TENSOR: 3176 case DM_POLYTOPE_TRIANGLE: 3177 case DM_POLYTOPE_QUADRILATERAL: 3178 case DM_POLYTOPE_TETRAHEDRON: 3179 case DM_POLYTOPE_HEXAHEDRON: 3180 *useCoordSpace = PETSC_TRUE;break; 3181 default: *useCoordSpace = PETSC_FALSE;break; 3182 } 3183 3184 if (fflg) { 3185 DM dmnew; 3186 3187 ierr = DMPlexCreateFromFile(PetscObjectComm((PetscObject) dm), filename, plexname, interpolate, &dmnew);CHKERRQ(ierr); 3188 ierr = DMPlexCopy_Internal(dm, PETSC_FALSE, dmnew);CHKERRQ(ierr); 3189 ierr = DMPlexReplace_Static(dm, &dmnew);CHKERRQ(ierr); 3190 } else if (refDomain) { 3191 ierr = DMPlexCreateReferenceCell_Internal(dm, cell);CHKERRQ(ierr); 3192 } else if (bdfflg) { 3193 DM bdm, dmnew; 3194 3195 ierr = DMPlexCreateFromFile(PetscObjectComm((PetscObject) dm), bdFilename, plexname, interpolate, &bdm);CHKERRQ(ierr); 3196 ierr = PetscObjectSetOptionsPrefix((PetscObject) bdm, "bd_");CHKERRQ(ierr); 3197 ierr = DMSetFromOptions(bdm);CHKERRQ(ierr); 3198 ierr = DMPlexGenerate(bdm, NULL, interpolate, &dmnew);CHKERRQ(ierr); 3199 ierr = DMDestroy(&bdm);CHKERRQ(ierr); 3200 ierr = DMPlexCopy_Internal(dm, PETSC_FALSE, dmnew);CHKERRQ(ierr); 3201 ierr = DMPlexReplace_Static(dm, &dmnew);CHKERRQ(ierr); 3202 } else { 3203 ierr = PetscObjectSetName((PetscObject) dm, DMPlexShapes[shape]);CHKERRQ(ierr); 3204 switch (shape) { 3205 case DM_SHAPE_BOX: 3206 { 3207 PetscInt faces[3] = {0, 0, 0}; 3208 PetscReal lower[3] = {0, 0, 0}; 3209 PetscReal upper[3] = {1, 1, 1}; 3210 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 3211 PetscInt i, n; 3212 3213 n = dim; 3214 for (i = 0; i < dim; ++i) faces[i] = (dim == 1 ? 1 : 4-dim); 3215 ierr = PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg);CHKERRQ(ierr); 3216 n = 3; 3217 ierr = PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg);CHKERRQ(ierr); 3218 PetscCheckFalse(flg && (n != dim),comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim); 3219 n = 3; 3220 ierr = PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg);CHKERRQ(ierr); 3221 PetscCheckFalse(flg && (n != dim),comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim); 3222 n = 3; 3223 ierr = PetscOptionsEnumArray("-dm_plex_box_bd", "Boundary type for each dimension", "", DMBoundaryTypes, (PetscEnum *) bdt, &n, &flg);CHKERRQ(ierr); 3224 PetscCheckFalse(flg && (n != dim),comm, PETSC_ERR_ARG_SIZ, "Box boundary types had %D values, should have been %D", n, dim); 3225 switch (cell) { 3226 case DM_POLYTOPE_TRI_PRISM_TENSOR: 3227 ierr = DMPlexCreateWedgeBoxMesh_Internal(dm, faces, lower, upper, bdt);CHKERRQ(ierr); 3228 if (!interpolate) { 3229 DM udm; 3230 3231 ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr); 3232 ierr = DMPlexReplace_Static(dm, &udm);CHKERRQ(ierr); 3233 } 3234 break; 3235 default: 3236 ierr = DMPlexCreateBoxMesh_Internal(dm, dim, simplex, faces, lower, upper, bdt, interpolate);CHKERRQ(ierr); 3237 break; 3238 } 3239 } 3240 break; 3241 case DM_SHAPE_BOX_SURFACE: 3242 { 3243 PetscInt faces[3] = {0, 0, 0}; 3244 PetscReal lower[3] = {0, 0, 0}; 3245 PetscReal upper[3] = {1, 1, 1}; 3246 PetscInt i, n; 3247 3248 n = dim+1; 3249 for (i = 0; i < dim+1; ++i) faces[i] = (dim+1 == 1 ? 1 : 4-(dim+1)); 3250 ierr = PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg);CHKERRQ(ierr); 3251 n = 3; 3252 ierr = PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg);CHKERRQ(ierr); 3253 PetscCheckFalse(flg && (n != dim+1),comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim+1); 3254 n = 3; 3255 ierr = PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg);CHKERRQ(ierr); 3256 PetscCheckFalse(flg && (n != dim+1),comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim+1); 3257 ierr = DMPlexCreateBoxSurfaceMesh_Internal(dm, dim+1, faces, lower, upper, interpolate);CHKERRQ(ierr); 3258 } 3259 break; 3260 case DM_SHAPE_SPHERE: 3261 { 3262 PetscReal R = 1.0; 3263 3264 ierr = PetscOptionsReal("-dm_plex_sphere_radius", "Radius of the sphere", "", R, &R, &flg);CHKERRQ(ierr); 3265 ierr = DMPlexCreateSphereMesh_Internal(dm, dim, simplex, R);CHKERRQ(ierr); 3266 } 3267 break; 3268 case DM_SHAPE_BALL: 3269 { 3270 PetscReal R = 1.0; 3271 3272 ierr = PetscOptionsReal("-dm_plex_ball_radius", "Radius of the ball", "", R, &R, &flg);CHKERRQ(ierr); 3273 ierr = DMPlexCreateBallMesh_Internal(dm, dim, R);CHKERRQ(ierr); 3274 } 3275 break; 3276 case DM_SHAPE_CYLINDER: 3277 { 3278 DMBoundaryType bdt = DM_BOUNDARY_NONE; 3279 PetscInt Nw = 6; 3280 3281 ierr = PetscOptionsEnum("-dm_plex_cylinder_bd", "Boundary type in the z direction", "", DMBoundaryTypes, (PetscEnum) bdt, (PetscEnum *) &bdt, NULL);CHKERRQ(ierr); 3282 ierr = PetscOptionsInt("-dm_plex_cylinder_num_wedges", "Number of wedges around the cylinder", "", Nw, &Nw, NULL);CHKERRQ(ierr); 3283 switch (cell) { 3284 case DM_POLYTOPE_TRI_PRISM_TENSOR: 3285 ierr = DMPlexCreateWedgeCylinderMesh_Internal(dm, Nw, interpolate);CHKERRQ(ierr); 3286 break; 3287 default: 3288 ierr = DMPlexCreateHexCylinderMesh_Internal(dm, bdt);CHKERRQ(ierr); 3289 break; 3290 } 3291 } 3292 break; 3293 case DM_SHAPE_SCHWARZ_P: // fallthrough 3294 case DM_SHAPE_GYROID: 3295 { 3296 PetscInt extent[3] = {1,1,1}, refine = 0, layers = 0, three; 3297 PetscReal thickness = 0.; 3298 DMBoundaryType periodic[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 3299 DMPlexTPSType tps_type = shape == DM_SHAPE_SCHWARZ_P ? DMPLEX_TPS_SCHWARZ_P : DMPLEX_TPS_GYROID; 3300 ierr = PetscOptionsIntArray("-dm_plex_tps_extent", "Number of replicas for each of three dimensions", NULL, extent, (three=3, &three), NULL);CHKERRQ(ierr); 3301 ierr = PetscOptionsInt("-dm_plex_tps_refine", "Number of refinements", NULL, refine, &refine, NULL);CHKERRQ(ierr); 3302 ierr = PetscOptionsEnumArray("-dm_plex_tps_periodic", "Periodicity in each of three dimensions", NULL, DMBoundaryTypes, (PetscEnum*)periodic, (three=3, &three), NULL);CHKERRQ(ierr); 3303 ierr = PetscOptionsInt("-dm_plex_tps_layers", "Number of layers in volumetric extrusion (or zero to not extrude)", NULL, layers, &layers, NULL);CHKERRQ(ierr); 3304 ierr = PetscOptionsReal("-dm_plex_tps_thickness", "Thickness of volumetric extrusion", NULL, thickness, &thickness, NULL);CHKERRQ(ierr); 3305 3306 ierr = DMPlexCreateTPSMesh_Internal(dm, tps_type, extent, periodic, refine, layers, thickness);CHKERRQ(ierr); 3307 } 3308 break; 3309 default: SETERRQ(comm, PETSC_ERR_SUP, "Domain shape %s is unsupported", DMPlexShapes[shape]); 3310 } 3311 } 3312 ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr); 3313 if (!((PetscObject)dm)->name && nameflg) { 3314 ierr = PetscObjectSetName((PetscObject)dm, plexname);CHKERRQ(ierr); 3315 } 3316 PetscFunctionReturn(0); 3317 } 3318 3319 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject, DM dm) 3320 { 3321 DM_Plex *mesh = (DM_Plex*) dm->data; 3322 PetscBool flg; 3323 char bdLabel[PETSC_MAX_PATH_LEN]; 3324 PetscErrorCode ierr; 3325 3326 PetscFunctionBegin; 3327 /* Handle viewing */ 3328 ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); 3329 ierr = PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL,0);CHKERRQ(ierr); 3330 ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL);CHKERRQ(ierr); 3331 ierr = PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL,0);CHKERRQ(ierr); 3332 ierr = DMMonitorSetFromOptions(dm, "-dm_plex_monitor_throughput", "Monitor the simulation throughput", "DMPlexMonitorThroughput", DMPlexMonitorThroughput, NULL, &flg);CHKERRQ(ierr); 3333 if (flg) {ierr = PetscLogDefaultBegin();CHKERRQ(ierr);} 3334 /* Labeling */ 3335 ierr = PetscOptionsString("-dm_plex_boundary_label", "Label to mark the mesh boundary", "", bdLabel, bdLabel, sizeof(bdLabel), &flg);CHKERRQ(ierr); 3336 if (flg) {ierr = DMPlexCreateBoundaryLabel_Private(dm, bdLabel);CHKERRQ(ierr);} 3337 /* Point Location */ 3338 ierr = PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL);CHKERRQ(ierr); 3339 /* Partitioning and distribution */ 3340 ierr = PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL);CHKERRQ(ierr); 3341 /* Generation and remeshing */ 3342 ierr = PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL);CHKERRQ(ierr); 3343 /* Projection behavior */ 3344 ierr = PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL,0);CHKERRQ(ierr); 3345 ierr = PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);CHKERRQ(ierr); 3346 /* Checking structure */ 3347 { 3348 PetscBool flg = PETSC_FALSE, flg2 = PETSC_FALSE, all = PETSC_FALSE; 3349 3350 ierr = PetscOptionsBool("-dm_plex_check_all", "Perform all checks", NULL, PETSC_FALSE, &all, &flg2);CHKERRQ(ierr); 3351 ierr = PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 3352 if (all || (flg && flg2)) {ierr = DMPlexCheckSymmetry(dm);CHKERRQ(ierr);} 3353 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); 3354 if (all || (flg && flg2)) {ierr = DMPlexCheckSkeleton(dm, 0);CHKERRQ(ierr);} 3355 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); 3356 if (all || (flg && flg2)) {ierr = DMPlexCheckFaces(dm, 0);CHKERRQ(ierr);} 3357 ierr = PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 3358 if (all || (flg && flg2)) {ierr = DMPlexCheckGeometry(dm);CHKERRQ(ierr);} 3359 ierr = PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 3360 if (all || (flg && flg2)) {ierr = DMPlexCheckPointSF(dm);CHKERRQ(ierr);} 3361 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); 3362 if (all || (flg && flg2)) {ierr = DMPlexCheckInterfaceCones(dm);CHKERRQ(ierr);} 3363 ierr = PetscOptionsBool("-dm_plex_check_cell_shape", "Check cell shape", "DMPlexCheckCellShape", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 3364 if (flg && flg2) {ierr = DMPlexCheckCellShape(dm, PETSC_TRUE, PETSC_DETERMINE);CHKERRQ(ierr);} 3365 } 3366 { 3367 PetscReal scale = 1.0; 3368 3369 ierr = PetscOptionsReal("-dm_plex_scale", "Scale factor for mesh coordinates", "DMPlexScale", scale, &scale, &flg);CHKERRQ(ierr); 3370 if (flg) { 3371 Vec coordinates, coordinatesLocal; 3372 3373 ierr = DMGetCoordinates(dm, &coordinates);CHKERRQ(ierr); 3374 ierr = DMGetCoordinatesLocal(dm, &coordinatesLocal);CHKERRQ(ierr); 3375 ierr = VecScale(coordinates, scale);CHKERRQ(ierr); 3376 ierr = VecScale(coordinatesLocal, scale);CHKERRQ(ierr); 3377 } 3378 } 3379 ierr = PetscPartitionerSetFromOptions(mesh->partitioner);CHKERRQ(ierr); 3380 PetscFunctionReturn(0); 3381 } 3382 3383 static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 3384 { 3385 PetscFunctionList ordlist; 3386 char oname[256]; 3387 PetscReal volume = -1.0; 3388 PetscInt prerefine = 0, refine = 0, r, coarsen = 0, overlap = 0, extLayers = 0, dim; 3389 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; 3390 PetscErrorCode ierr; 3391 3392 PetscFunctionBegin; 3393 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 3394 ierr = PetscOptionsHead(PetscOptionsObject,"DMPlex Options");CHKERRQ(ierr); 3395 /* Handle automatic creation */ 3396 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3397 if (dim < 0) {ierr = DMPlexCreateFromOptions_Internal(PetscOptionsObject, &coordSpace, dm);CHKERRQ(ierr);created = PETSC_TRUE;} 3398 /* Handle interpolation before distribution */ 3399 ierr = PetscOptionsBool("-dm_plex_interpolate_pre", "Flag to interpolate mesh before distribution", "", interpolate, &interpolate, &flg);CHKERRQ(ierr); 3400 if (flg) { 3401 DMPlexInterpolatedFlag interpolated; 3402 3403 ierr = DMPlexIsInterpolated(dm, &interpolated);CHKERRQ(ierr); 3404 if (interpolated == DMPLEX_INTERPOLATED_FULL && !interpolate) { 3405 DM udm; 3406 3407 ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr); 3408 ierr = DMPlexReplace_Static(dm, &udm);CHKERRQ(ierr); 3409 } else if (interpolated != DMPLEX_INTERPOLATED_FULL && interpolate) { 3410 DM idm; 3411 3412 ierr = DMPlexInterpolate(dm, &idm);CHKERRQ(ierr); 3413 ierr = DMPlexReplace_Static(dm, &idm);CHKERRQ(ierr); 3414 } 3415 } 3416 /* Handle DMPlex refinement before distribution */ 3417 ierr = PetscOptionsBool("-dm_refine_ignore_model", "Flag to ignore the geometry model when refining", "DMCreate", ignoreModel, &ignoreModel, &flg);CHKERRQ(ierr); 3418 if (flg) {((DM_Plex *) dm->data)->ignoreModel = ignoreModel;} 3419 ierr = DMPlexGetRefinementUniform(dm, &uniformOrig);CHKERRQ(ierr); 3420 ierr = PetscOptionsBoundedInt("-dm_refine_pre", "The number of refinements before distribution", "DMCreate", prerefine, &prerefine, NULL,0);CHKERRQ(ierr); 3421 ierr = PetscOptionsBool("-dm_refine_remap_pre", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL);CHKERRQ(ierr); 3422 ierr = PetscOptionsBool("-dm_refine_uniform_pre", "Flag for uniform refinement before distribution", "DMCreate", uniform, &uniform, &flg);CHKERRQ(ierr); 3423 if (flg) {ierr = DMPlexSetRefinementUniform(dm, uniform);CHKERRQ(ierr);} 3424 ierr = PetscOptionsReal("-dm_refine_volume_limit_pre", "The maximum cell volume after refinement before distribution", "DMCreate", volume, &volume, &flg);CHKERRQ(ierr); 3425 if (flg) { 3426 ierr = DMPlexSetRefinementUniform(dm, PETSC_FALSE);CHKERRQ(ierr); 3427 ierr = DMPlexSetRefinementLimit(dm, volume);CHKERRQ(ierr); 3428 prerefine = PetscMax(prerefine, 1); 3429 } 3430 for (r = 0; r < prerefine; ++r) { 3431 DM rdm; 3432 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 3433 3434 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3435 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &rdm);CHKERRQ(ierr); 3436 ierr = DMPlexReplace_Static(dm, &rdm);CHKERRQ(ierr); 3437 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3438 if (coordFunc && remap) { 3439 ierr = DMPlexRemapGeometry(dm, 0.0, coordFunc);CHKERRQ(ierr); 3440 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 3441 } 3442 } 3443 ierr = DMPlexSetRefinementUniform(dm, uniformOrig);CHKERRQ(ierr); 3444 /* Handle DMPlex extrusion before distribution */ 3445 ierr = PetscOptionsBoundedInt("-dm_extrude", "The number of layers to extrude", "", extLayers, &extLayers, NULL, 0);CHKERRQ(ierr); 3446 if (extLayers) { 3447 DM edm; 3448 3449 ierr = DMExtrude(dm, extLayers, &edm);CHKERRQ(ierr); 3450 ierr = DMPlexReplace_Static(dm, &edm);CHKERRQ(ierr); 3451 ((DM_Plex *) dm->data)->coordFunc = NULL; 3452 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3453 extLayers = 0; 3454 } 3455 /* Handle DMPlex reordering before distribution */ 3456 ierr = MatGetOrderingList(&ordlist);CHKERRQ(ierr); 3457 ierr = PetscOptionsFList("-dm_plex_reorder", "Set mesh reordering type", "DMPlexGetOrdering", ordlist, MATORDERINGNATURAL, oname, sizeof(oname), &flg);CHKERRQ(ierr); 3458 if (flg) { 3459 DM pdm; 3460 IS perm; 3461 3462 ierr = DMPlexGetOrdering(dm, oname, NULL, &perm);CHKERRQ(ierr); 3463 ierr = DMPlexPermute(dm, perm, &pdm);CHKERRQ(ierr); 3464 ierr = ISDestroy(&perm);CHKERRQ(ierr); 3465 ierr = DMPlexReplace_Static(dm, &pdm);CHKERRQ(ierr); 3466 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3467 } 3468 /* Handle DMPlex distribution */ 3469 ierr = DMPlexDistributeGetDefault(dm, &distribute);CHKERRQ(ierr); 3470 ierr = PetscOptionsBool("-dm_distribute", "Flag to redistribute a mesh among processes", "DMCreate", distribute, &distribute, NULL);CHKERRQ(ierr); 3471 ierr = PetscOptionsBoundedInt("-dm_distribute_overlap", "The size of the overlap halo", "DMCreate", overlap, &overlap, NULL, 0);CHKERRQ(ierr); 3472 if (distribute) { 3473 DM pdm = NULL; 3474 PetscPartitioner part; 3475 3476 ierr = DMPlexGetPartitioner(dm, &part);CHKERRQ(ierr); 3477 ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr); 3478 ierr = DMPlexDistribute(dm, overlap, NULL, &pdm);CHKERRQ(ierr); 3479 if (pdm) { 3480 ierr = DMPlexReplace_Static(dm, &pdm);CHKERRQ(ierr); 3481 } 3482 } 3483 /* Create coordinate space */ 3484 if (created) { 3485 DM_Plex *mesh = (DM_Plex *) dm->data; 3486 PetscInt degree = 1; 3487 PetscBool periodic, flg; 3488 3489 ierr = PetscOptionsBool("-dm_coord_space", "Use an FEM space for coordinates", "", coordSpace, &coordSpace, &flg);CHKERRQ(ierr); 3490 ierr = PetscOptionsInt("-dm_coord_petscspace_degree", "FEM degree for coordinate space", "", degree, °ree, NULL);CHKERRQ(ierr); 3491 if (coordSpace) {ierr = DMPlexCreateCoordinateSpace(dm, degree, mesh->coordFunc);CHKERRQ(ierr);} 3492 if (flg && !coordSpace) { 3493 DM cdm; 3494 PetscDS cds; 3495 PetscObject obj; 3496 PetscClassId id; 3497 3498 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 3499 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 3500 ierr = PetscDSGetDiscretization(cds, 0, &obj);CHKERRQ(ierr); 3501 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 3502 if (id == PETSCFE_CLASSID) { 3503 PetscContainer dummy; 3504 3505 ierr = PetscContainerCreate(PETSC_COMM_SELF, &dummy);CHKERRQ(ierr); 3506 ierr = PetscObjectSetName((PetscObject) dummy, "coordinates");CHKERRQ(ierr); 3507 ierr = DMSetField(cdm, 0, NULL, (PetscObject) dummy);CHKERRQ(ierr); 3508 ierr = PetscContainerDestroy(&dummy);CHKERRQ(ierr); 3509 ierr = DMClearDS(cdm);CHKERRQ(ierr); 3510 } 3511 mesh->coordFunc = NULL; 3512 } 3513 ierr = DMLocalizeCoordinates(dm);CHKERRQ(ierr); 3514 ierr = DMGetPeriodicity(dm, &periodic, NULL, NULL, NULL);CHKERRQ(ierr); 3515 if (periodic) {ierr = DMSetPeriodicity(dm, PETSC_TRUE, NULL, NULL, NULL);CHKERRQ(ierr);} 3516 } 3517 /* Handle DMPlex refinement */ 3518 remap = PETSC_TRUE; 3519 ierr = PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL,0);CHKERRQ(ierr); 3520 ierr = PetscOptionsBool("-dm_refine_remap", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL);CHKERRQ(ierr); 3521 ierr = PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy,0);CHKERRQ(ierr); 3522 if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 3523 if (refine && isHierarchy) { 3524 DM *dms, coarseDM; 3525 3526 ierr = DMGetCoarseDM(dm, &coarseDM);CHKERRQ(ierr); 3527 ierr = PetscObjectReference((PetscObject)coarseDM);CHKERRQ(ierr); 3528 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 3529 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 3530 /* Total hack since we do not pass in a pointer */ 3531 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 3532 if (refine == 1) { 3533 ierr = DMSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 3534 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 3535 } else { 3536 ierr = DMSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 3537 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 3538 ierr = DMSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 3539 ierr = DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);CHKERRQ(ierr); 3540 } 3541 ierr = DMSetCoarseDM(dms[refine-1], coarseDM);CHKERRQ(ierr); 3542 ierr = PetscObjectDereference((PetscObject)coarseDM);CHKERRQ(ierr); 3543 /* Free DMs */ 3544 for (r = 0; r < refine; ++r) { 3545 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 3546 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 3547 } 3548 ierr = PetscFree(dms);CHKERRQ(ierr); 3549 } else { 3550 for (r = 0; r < refine; ++r) { 3551 DM rdm; 3552 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 3553 3554 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3555 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &rdm);CHKERRQ(ierr); 3556 /* Total hack since we do not pass in a pointer */ 3557 ierr = DMPlexReplace_Static(dm, &rdm);CHKERRQ(ierr); 3558 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3559 if (coordFunc && remap) { 3560 ierr = DMPlexRemapGeometry(dm, 0.0, coordFunc);CHKERRQ(ierr); 3561 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 3562 } 3563 } 3564 } 3565 /* Handle DMPlex coarsening */ 3566 ierr = PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL,0);CHKERRQ(ierr); 3567 ierr = PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy,0);CHKERRQ(ierr); 3568 if (coarsen && isHierarchy) { 3569 DM *dms; 3570 3571 ierr = PetscMalloc1(coarsen, &dms);CHKERRQ(ierr); 3572 ierr = DMCoarsenHierarchy(dm, coarsen, dms);CHKERRQ(ierr); 3573 /* Free DMs */ 3574 for (r = 0; r < coarsen; ++r) { 3575 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 3576 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 3577 } 3578 ierr = PetscFree(dms);CHKERRQ(ierr); 3579 } else { 3580 for (r = 0; r < coarsen; ++r) { 3581 DM cdm; 3582 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 3583 3584 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3585 ierr = DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &cdm);CHKERRQ(ierr); 3586 /* Total hack since we do not pass in a pointer */ 3587 ierr = DMPlexReplace_Static(dm, &cdm);CHKERRQ(ierr); 3588 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3589 if (coordFunc) { 3590 ierr = DMPlexRemapGeometry(dm, 0.0, coordFunc);CHKERRQ(ierr); 3591 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 3592 } 3593 } 3594 } 3595 /* Handle ghost cells */ 3596 ierr = PetscOptionsBool("-dm_plex_create_fv_ghost_cells", "Flag to create finite volume ghost cells on the boundary", "DMCreate", ghostCells, &ghostCells, NULL);CHKERRQ(ierr); 3597 if (ghostCells) { 3598 DM gdm; 3599 char lname[PETSC_MAX_PATH_LEN]; 3600 3601 lname[0] = '\0'; 3602 ierr = PetscOptionsString("-dm_plex_fv_ghost_cells_label", "Label name for ghost cells boundary", "DMCreate", lname, lname, sizeof(lname), &flg);CHKERRQ(ierr); 3603 ierr = DMPlexConstructGhostCells(dm, flg ? lname : NULL, NULL, &gdm);CHKERRQ(ierr); 3604 ierr = DMPlexReplace_Static(dm, &gdm);CHKERRQ(ierr); 3605 } 3606 /* Handle */ 3607 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3608 ierr = PetscOptionsTail();CHKERRQ(ierr); 3609 PetscFunctionReturn(0); 3610 } 3611 3612 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 3613 { 3614 PetscErrorCode ierr; 3615 3616 PetscFunctionBegin; 3617 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 3618 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 3619 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 3620 ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); 3621 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 3622 ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); 3623 PetscFunctionReturn(0); 3624 } 3625 3626 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 3627 { 3628 PetscErrorCode ierr; 3629 3630 PetscFunctionBegin; 3631 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 3632 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 3633 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 3634 PetscFunctionReturn(0); 3635 } 3636 3637 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 3638 { 3639 PetscInt depth, d; 3640 PetscErrorCode ierr; 3641 3642 PetscFunctionBegin; 3643 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 3644 if (depth == 1) { 3645 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 3646 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 3647 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 3648 else {*pStart = 0; *pEnd = 0;} 3649 } else { 3650 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 3651 } 3652 PetscFunctionReturn(0); 3653 } 3654 3655 static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 3656 { 3657 PetscSF sf; 3658 PetscInt niranks, njranks, n; 3659 const PetscMPIInt *iranks, *jranks; 3660 DM_Plex *data = (DM_Plex*) dm->data; 3661 PetscErrorCode ierr; 3662 3663 PetscFunctionBegin; 3664 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 3665 if (!data->neighbors) { 3666 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 3667 ierr = PetscSFGetRootRanks(sf, &njranks, &jranks, NULL, NULL, NULL);CHKERRQ(ierr); 3668 ierr = PetscSFGetLeafRanks(sf, &niranks, &iranks, NULL, NULL);CHKERRQ(ierr); 3669 ierr = PetscMalloc1(njranks + niranks + 1, &data->neighbors);CHKERRQ(ierr); 3670 ierr = PetscArraycpy(data->neighbors + 1, jranks, njranks);CHKERRQ(ierr); 3671 ierr = PetscArraycpy(data->neighbors + njranks + 1, iranks, niranks);CHKERRQ(ierr); 3672 n = njranks + niranks; 3673 ierr = PetscSortRemoveDupsMPIInt(&n, data->neighbors + 1);CHKERRQ(ierr); 3674 /* The following cast should never fail: can't have more neighbors than PETSC_MPI_INT_MAX */ 3675 ierr = PetscMPIIntCast(n, data->neighbors);CHKERRQ(ierr); 3676 } 3677 if (nranks) *nranks = data->neighbors[0]; 3678 if (ranks) { 3679 if (data->neighbors[0]) *ranks = data->neighbors + 1; 3680 else *ranks = NULL; 3681 } 3682 PetscFunctionReturn(0); 3683 } 3684 3685 PETSC_INTERN PetscErrorCode DMInterpolateSolution_Plex(DM, DM, Mat, Vec, Vec); 3686 3687 static PetscErrorCode DMInitialize_Plex(DM dm) 3688 { 3689 PetscErrorCode ierr; 3690 3691 PetscFunctionBegin; 3692 dm->ops->view = DMView_Plex; 3693 dm->ops->load = DMLoad_Plex; 3694 dm->ops->setfromoptions = DMSetFromOptions_Plex; 3695 dm->ops->clone = DMClone_Plex; 3696 dm->ops->setup = DMSetUp_Plex; 3697 dm->ops->createlocalsection = DMCreateLocalSection_Plex; 3698 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 3699 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 3700 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 3701 dm->ops->getlocaltoglobalmapping = NULL; 3702 dm->ops->createfieldis = NULL; 3703 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 3704 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 3705 dm->ops->getcoloring = NULL; 3706 dm->ops->creatematrix = DMCreateMatrix_Plex; 3707 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 3708 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 3709 dm->ops->createmassmatrixlumped = DMCreateMassMatrixLumped_Plex; 3710 dm->ops->createinjection = DMCreateInjection_Plex; 3711 dm->ops->refine = DMRefine_Plex; 3712 dm->ops->coarsen = DMCoarsen_Plex; 3713 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 3714 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 3715 dm->ops->extrude = DMExtrude_Plex; 3716 dm->ops->globaltolocalbegin = NULL; 3717 dm->ops->globaltolocalend = NULL; 3718 dm->ops->localtoglobalbegin = NULL; 3719 dm->ops->localtoglobalend = NULL; 3720 dm->ops->destroy = DMDestroy_Plex; 3721 dm->ops->createsubdm = DMCreateSubDM_Plex; 3722 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 3723 dm->ops->getdimpoints = DMGetDimPoints_Plex; 3724 dm->ops->locatepoints = DMLocatePoints_Plex; 3725 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 3726 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 3727 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 3728 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 3729 dm->ops->projectbdfieldlabellocal = DMProjectBdFieldLabelLocal_Plex; 3730 dm->ops->computel2diff = DMComputeL2Diff_Plex; 3731 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 3732 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 3733 dm->ops->getneighbors = DMGetNeighbors_Plex; 3734 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);CHKERRQ(ierr); 3735 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertTimeDerviativeBoundaryValues_C",DMPlexInsertTimeDerivativeBoundaryValues_Plex);CHKERRQ(ierr); 3736 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);CHKERRQ(ierr); 3737 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C",DMCreateNeumannOverlap_Plex);CHKERRQ(ierr); 3738 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex);CHKERRQ(ierr); 3739 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexDistributeGetDefault_C",DMPlexDistributeGetDefault_Plex);CHKERRQ(ierr); 3740 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexDistributeSetDefault_C",DMPlexDistributeSetDefault_Plex);CHKERRQ(ierr); 3741 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMInterpolateSolution_C",DMInterpolateSolution_Plex);CHKERRQ(ierr); 3742 PetscFunctionReturn(0); 3743 } 3744 3745 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 3746 { 3747 DM_Plex *mesh = (DM_Plex *) dm->data; 3748 PetscErrorCode ierr; 3749 3750 PetscFunctionBegin; 3751 mesh->refct++; 3752 (*newdm)->data = mesh; 3753 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 3754 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 3755 PetscFunctionReturn(0); 3756 } 3757 3758 /*MC 3759 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 3760 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 3761 specified by a PetscSection object. Ownership in the global representation is determined by 3762 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 3763 3764 Options Database Keys: 3765 + -dm_refine_pre - Refine mesh before distribution 3766 + -dm_refine_uniform_pre - Choose uniform or generator-based refinement 3767 + -dm_refine_volume_limit_pre - Cell volume limit after pre-refinement using generator 3768 . -dm_distribute - Distribute mesh across processes 3769 . -dm_distribute_overlap - Number of cells to overlap for distribution 3770 . -dm_refine - Refine mesh after distribution 3771 . -dm_plex_hash_location - Use grid hashing for point location 3772 . -dm_plex_hash_box_faces <n,m,p> - The number of divisions in each direction of the grid hash 3773 . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes 3774 . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing 3775 . -dm_plex_max_projection_height - Maxmimum mesh point height used to project locally 3776 . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement 3777 . -dm_plex_check_all - Perform all shecks below 3778 . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric 3779 . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices 3780 . -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 3781 . -dm_plex_check_geometry - Check that cells have positive volume 3782 . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ 3783 . -dm_plex_view_scale <num> - Scale the TikZ 3784 - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices 3785 3786 Level: intermediate 3787 3788 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 3789 M*/ 3790 3791 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 3792 { 3793 DM_Plex *mesh; 3794 PetscInt unit; 3795 PetscErrorCode ierr; 3796 3797 PetscFunctionBegin; 3798 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3799 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 3800 dm->data = mesh; 3801 3802 mesh->refct = 1; 3803 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 3804 mesh->maxConeSize = 0; 3805 mesh->cones = NULL; 3806 mesh->coneOrientations = NULL; 3807 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 3808 mesh->maxSupportSize = 0; 3809 mesh->supports = NULL; 3810 mesh->refinementUniform = PETSC_TRUE; 3811 mesh->refinementLimit = -1.0; 3812 mesh->distDefault = PETSC_TRUE; 3813 mesh->interpolated = DMPLEX_INTERPOLATED_INVALID; 3814 mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID; 3815 3816 mesh->facesTmp = NULL; 3817 3818 mesh->tetgenOpts = NULL; 3819 mesh->triangleOpts = NULL; 3820 ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); 3821 mesh->remeshBd = PETSC_FALSE; 3822 3823 mesh->subpointMap = NULL; 3824 3825 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 3826 3827 mesh->regularRefinement = PETSC_FALSE; 3828 mesh->depthState = -1; 3829 mesh->celltypeState = -1; 3830 mesh->globalVertexNumbers = NULL; 3831 mesh->globalCellNumbers = NULL; 3832 mesh->anchorSection = NULL; 3833 mesh->anchorIS = NULL; 3834 mesh->createanchors = NULL; 3835 mesh->computeanchormatrix = NULL; 3836 mesh->parentSection = NULL; 3837 mesh->parents = NULL; 3838 mesh->childIDs = NULL; 3839 mesh->childSection = NULL; 3840 mesh->children = NULL; 3841 mesh->referenceTree = NULL; 3842 mesh->getchildsymmetry = NULL; 3843 mesh->vtkCellHeight = 0; 3844 mesh->useAnchors = PETSC_FALSE; 3845 3846 mesh->maxProjectionHeight = 0; 3847 3848 mesh->neighbors = NULL; 3849 3850 mesh->printSetValues = PETSC_FALSE; 3851 mesh->printFEM = 0; 3852 mesh->printTol = 1.0e-10; 3853 3854 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 3855 PetscFunctionReturn(0); 3856 } 3857 3858 /*@ 3859 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 3860 3861 Collective 3862 3863 Input Parameter: 3864 . comm - The communicator for the DMPlex object 3865 3866 Output Parameter: 3867 . mesh - The DMPlex object 3868 3869 Level: beginner 3870 3871 @*/ 3872 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 3873 { 3874 PetscErrorCode ierr; 3875 3876 PetscFunctionBegin; 3877 PetscValidPointer(mesh,2); 3878 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 3879 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 3880 PetscFunctionReturn(0); 3881 } 3882 3883 /*@C 3884 DMPlexBuildFromCellListParallel - Build distributed DMPLEX topology from a list of vertices for each cell (common mesh generator output) 3885 3886 Input Parameters: 3887 + dm - The DM 3888 . numCells - The number of cells owned by this process 3889 . numVertices - The number of vertices to be owned by this process, or PETSC_DECIDE 3890 . NVertices - The global number of vertices, or PETSC_DETERMINE 3891 . numCorners - The number of vertices for each cell 3892 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 3893 3894 Output Parameters: 3895 + vertexSF - (Optional) SF describing complete vertex ownership 3896 - verticesAdjSaved - (Optional) vertex adjacency array 3897 3898 Notes: 3899 Two triangles sharing a face 3900 $ 3901 $ 2 3902 $ / | \ 3903 $ / | \ 3904 $ / | \ 3905 $ 0 0 | 1 3 3906 $ \ | / 3907 $ \ | / 3908 $ \ | / 3909 $ 1 3910 would have input 3911 $ numCells = 2, numVertices = 4 3912 $ cells = [0 1 2 1 3 2] 3913 $ 3914 which would result in the DMPlex 3915 $ 3916 $ 4 3917 $ / | \ 3918 $ / | \ 3919 $ / | \ 3920 $ 2 0 | 1 5 3921 $ \ | / 3922 $ \ | / 3923 $ \ | / 3924 $ 3 3925 3926 Vertices are implicitly numbered consecutively 0,...,NVertices. 3927 Each rank owns a chunk of numVertices consecutive vertices. 3928 If numVertices is PETSC_DECIDE, PETSc will distribute them as evenly as possible using PetscLayout. 3929 If NVertices is PETSC_DETERMINE and numVertices is PETSC_DECIDE, NVertices is computed by PETSc as the maximum vertex index in cells + 1. 3930 If only NVertices is PETSC_DETERMINE, it is computed as the sum of numVertices over all ranks. 3931 3932 The cell distribution is arbitrary non-overlapping, independent of the vertex distribution. 3933 3934 Not currently supported in Fortran. 3935 3936 Level: advanced 3937 3938 .seealso: DMPlexBuildFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildCoordinatesFromCellListParallel() 3939 @*/ 3940 PetscErrorCode DMPlexBuildFromCellListParallel(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, const PetscInt cells[], PetscSF *vertexSF, PetscInt **verticesAdjSaved) 3941 { 3942 PetscSF sfPoint; 3943 PetscLayout layout; 3944 PetscInt numVerticesAdj, *verticesAdj, *cones, c, p, dim; 3945 PetscMPIInt rank, size; 3946 PetscErrorCode ierr; 3947 3948 PetscFunctionBegin; 3949 PetscValidLogicalCollectiveInt(dm,NVertices,4); 3950 ierr = PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3951 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 3952 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRMPI(ierr); 3953 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3954 /* Get/check global number of vertices */ 3955 { 3956 PetscInt NVerticesInCells, i; 3957 const PetscInt len = numCells * numCorners; 3958 3959 /* NVerticesInCells = max(cells) + 1 */ 3960 NVerticesInCells = PETSC_MIN_INT; 3961 for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 3962 ++NVerticesInCells; 3963 ierr = MPI_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject) dm));CHKERRMPI(ierr); 3964 3965 if (numVertices == PETSC_DECIDE && NVertices == PETSC_DECIDE) NVertices = NVerticesInCells; 3966 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); 3967 } 3968 /* Count locally unique vertices */ 3969 { 3970 PetscHSetI vhash; 3971 PetscInt off = 0; 3972 3973 ierr = PetscHSetICreate(&vhash);CHKERRQ(ierr); 3974 for (c = 0; c < numCells; ++c) { 3975 for (p = 0; p < numCorners; ++p) { 3976 ierr = PetscHSetIAdd(vhash, cells[c*numCorners+p]);CHKERRQ(ierr); 3977 } 3978 } 3979 ierr = PetscHSetIGetSize(vhash, &numVerticesAdj);CHKERRQ(ierr); 3980 if (!verticesAdjSaved) { ierr = PetscMalloc1(numVerticesAdj, &verticesAdj);CHKERRQ(ierr); } 3981 else { verticesAdj = *verticesAdjSaved; } 3982 ierr = PetscHSetIGetElems(vhash, &off, verticesAdj);CHKERRQ(ierr); 3983 ierr = PetscHSetIDestroy(&vhash);CHKERRQ(ierr); 3984 PetscCheckFalse(off != numVerticesAdj,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj); 3985 } 3986 ierr = PetscSortInt(numVerticesAdj, verticesAdj);CHKERRQ(ierr); 3987 /* Create cones */ 3988 ierr = DMPlexSetChart(dm, 0, numCells+numVerticesAdj);CHKERRQ(ierr); 3989 for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);} 3990 ierr = DMSetUp(dm);CHKERRQ(ierr); 3991 ierr = DMPlexGetCones(dm,&cones);CHKERRQ(ierr); 3992 for (c = 0; c < numCells; ++c) { 3993 for (p = 0; p < numCorners; ++p) { 3994 const PetscInt gv = cells[c*numCorners+p]; 3995 PetscInt lv; 3996 3997 /* Positions within verticesAdj form 0-based local vertex numbering; 3998 we need to shift it by numCells to get correct DAG points (cells go first) */ 3999 ierr = PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);CHKERRQ(ierr); 4000 PetscCheckFalse(lv < 0,PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv); 4001 cones[c*numCorners+p] = lv+numCells; 4002 } 4003 } 4004 /* Build point sf */ 4005 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &layout);CHKERRQ(ierr); 4006 ierr = PetscLayoutSetSize(layout, NVertices);CHKERRQ(ierr); 4007 ierr = PetscLayoutSetLocalSize(layout, numVertices);CHKERRQ(ierr); 4008 ierr = PetscLayoutSetBlockSize(layout, 1);CHKERRQ(ierr); 4009 ierr = PetscSFCreateByMatchingIndices(layout, numVerticesAdj, verticesAdj, NULL, numCells, numVerticesAdj, verticesAdj, NULL, numCells, vertexSF, &sfPoint);CHKERRQ(ierr); 4010 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 4011 if (!verticesAdjSaved) { ierr = PetscFree(verticesAdj);CHKERRQ(ierr); } 4012 ierr = PetscObjectSetName((PetscObject) sfPoint, "point SF");CHKERRQ(ierr); 4013 if (dm->sf) { 4014 const char *prefix; 4015 4016 ierr = PetscObjectGetOptionsPrefix((PetscObject)dm->sf, &prefix);CHKERRQ(ierr); 4017 ierr = PetscObjectSetOptionsPrefix((PetscObject)sfPoint, prefix);CHKERRQ(ierr); 4018 } 4019 ierr = DMSetPointSF(dm, sfPoint);CHKERRQ(ierr); 4020 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 4021 if (vertexSF) {ierr = PetscObjectSetName((PetscObject)(*vertexSF), "Vertex Ownership SF");CHKERRQ(ierr);} 4022 /* Fill in the rest of the topology structure */ 4023 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 4024 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 4025 ierr = PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 4026 PetscFunctionReturn(0); 4027 } 4028 4029 /*@C 4030 DMPlexBuildCoordinatesFromCellListParallel - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output) 4031 4032 Input Parameters: 4033 + dm - The DM 4034 . spaceDim - The spatial dimension used for coordinates 4035 . sfVert - SF describing complete vertex ownership 4036 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 4037 4038 Level: advanced 4039 4040 Notes: 4041 Not currently supported in Fortran. 4042 4043 .seealso: DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellListParallel() 4044 @*/ 4045 PetscErrorCode DMPlexBuildCoordinatesFromCellListParallel(DM dm, PetscInt spaceDim, PetscSF sfVert, const PetscReal vertexCoords[]) 4046 { 4047 PetscSection coordSection; 4048 Vec coordinates; 4049 PetscScalar *coords; 4050 PetscInt numVertices, numVerticesAdj, coordSize, v, vStart, vEnd; 4051 PetscErrorCode ierr; 4052 4053 PetscFunctionBegin; 4054 ierr = PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 4055 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 4056 PetscCheckFalse(vStart < 0 || vEnd < 0,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 4057 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 4058 ierr = PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);CHKERRQ(ierr); 4059 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); 4060 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 4061 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 4062 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 4063 ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr); 4064 for (v = vStart; v < vEnd; ++v) { 4065 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 4066 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 4067 } 4068 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 4069 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 4070 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 4071 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 4072 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 4073 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 4074 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 4075 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 4076 { 4077 MPI_Datatype coordtype; 4078 4079 /* Need a temp buffer for coords if we have complex/single */ 4080 ierr = MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);CHKERRMPI(ierr); 4081 ierr = MPI_Type_commit(&coordtype);CHKERRMPI(ierr); 4082 #if defined(PETSC_USE_COMPLEX) 4083 { 4084 PetscScalar *svertexCoords; 4085 PetscInt i; 4086 ierr = PetscMalloc1(numVertices*spaceDim,&svertexCoords);CHKERRQ(ierr); 4087 for (i=0; i<numVertices*spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 4088 ierr = PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 4089 ierr = PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 4090 ierr = PetscFree(svertexCoords);CHKERRQ(ierr); 4091 } 4092 #else 4093 ierr = PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 4094 ierr = PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 4095 #endif 4096 ierr = MPI_Type_free(&coordtype);CHKERRMPI(ierr); 4097 } 4098 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 4099 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 4100 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 4101 ierr = PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 4102 PetscFunctionReturn(0); 4103 } 4104 4105 /*@ 4106 DMPlexCreateFromCellListParallelPetsc - Create distributed DMPLEX from a list of vertices for each cell (common mesh generator output) 4107 4108 Input Parameters: 4109 + comm - The communicator 4110 . dim - The topological dimension of the mesh 4111 . numCells - The number of cells owned by this process 4112 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 4113 . NVertices - The global number of vertices, or PETSC_DECIDE 4114 . numCorners - The number of vertices for each cell 4115 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 4116 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 4117 . spaceDim - The spatial dimension used for coordinates 4118 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 4119 4120 Output Parameters: 4121 + dm - The DM 4122 . vertexSF - (Optional) SF describing complete vertex ownership 4123 - verticesAdjSaved - (Optional) vertex adjacency array 4124 4125 Notes: 4126 This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), 4127 DMPlexBuildFromCellListParallel(), DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellListParallel() 4128 4129 See DMPlexBuildFromCellListParallel() for an example and details about the topology-related parameters. 4130 See DMPlexBuildCoordinatesFromCellListParallel() for details about the geometry-related parameters. 4131 4132 Level: intermediate 4133 4134 .seealso: DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromDAG(), DMPlexCreate() 4135 @*/ 4136 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) 4137 { 4138 PetscSF sfVert; 4139 PetscErrorCode ierr; 4140 4141 PetscFunctionBegin; 4142 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 4143 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 4144 PetscValidLogicalCollectiveInt(*dm, dim, 2); 4145 PetscValidLogicalCollectiveInt(*dm, spaceDim, 9); 4146 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 4147 ierr = DMPlexBuildFromCellListParallel(*dm, numCells, numVertices, NVertices, numCorners, cells, &sfVert, verticesAdj);CHKERRQ(ierr); 4148 if (interpolate) { 4149 DM idm; 4150 4151 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 4152 ierr = DMDestroy(dm);CHKERRQ(ierr); 4153 *dm = idm; 4154 } 4155 ierr = DMPlexBuildCoordinatesFromCellListParallel(*dm, spaceDim, sfVert, vertexCoords);CHKERRQ(ierr); 4156 if (vertexSF) *vertexSF = sfVert; 4157 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 4158 PetscFunctionReturn(0); 4159 } 4160 4161 /*@ 4162 DMPlexCreateFromCellListParallel - Deprecated, use DMPlexCreateFromCellListParallelPetsc() 4163 4164 Level: deprecated 4165 4166 .seealso: DMPlexCreateFromCellListParallelPetsc() 4167 @*/ 4168 PetscErrorCode DMPlexCreateFromCellListParallel(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, PetscBool interpolate, const int cells[], PetscInt spaceDim, const PetscReal vertexCoords[], PetscSF *vertexSF, DM *dm) 4169 { 4170 PetscErrorCode ierr; 4171 PetscInt i; 4172 PetscInt *pintCells; 4173 4174 PetscFunctionBegin; 4175 PetscCheckFalse(sizeof(int) > sizeof(PetscInt),comm, PETSC_ERR_ARG_SIZ, "Size of int %zd greater than size of PetscInt %zd. Reconfigure PETSc --with-64-bit-indices=1", sizeof(int), sizeof(PetscInt)); 4176 if (sizeof(int) == sizeof(PetscInt)) { 4177 pintCells = (PetscInt *) cells; 4178 } else { 4179 ierr = PetscMalloc1(numCells*numCorners, &pintCells);CHKERRQ(ierr); 4180 for (i = 0; i < numCells*numCorners; i++) { 4181 pintCells[i] = (PetscInt) cells[i]; 4182 } 4183 } 4184 ierr = DMPlexCreateFromCellListParallelPetsc(comm, dim, numCells, numVertices, PETSC_DECIDE, numCorners, interpolate, pintCells, spaceDim, vertexCoords, vertexSF, NULL, dm);CHKERRQ(ierr); 4185 if (sizeof(int) != sizeof(PetscInt)) { 4186 ierr = PetscFree(pintCells);CHKERRQ(ierr); 4187 } 4188 PetscFunctionReturn(0); 4189 } 4190 4191 /*@C 4192 DMPlexBuildFromCellList - Build DMPLEX topology from a list of vertices for each cell (common mesh generator output) 4193 4194 Input Parameters: 4195 + dm - The DM 4196 . numCells - The number of cells owned by this process 4197 . numVertices - The number of vertices owned by this process, or PETSC_DETERMINE 4198 . numCorners - The number of vertices for each cell 4199 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 4200 4201 Level: advanced 4202 4203 Notes: 4204 Two triangles sharing a face 4205 $ 4206 $ 2 4207 $ / | \ 4208 $ / | \ 4209 $ / | \ 4210 $ 0 0 | 1 3 4211 $ \ | / 4212 $ \ | / 4213 $ \ | / 4214 $ 1 4215 would have input 4216 $ numCells = 2, numVertices = 4 4217 $ cells = [0 1 2 1 3 2] 4218 $ 4219 which would result in the DMPlex 4220 $ 4221 $ 4 4222 $ / | \ 4223 $ / | \ 4224 $ / | \ 4225 $ 2 0 | 1 5 4226 $ \ | / 4227 $ \ | / 4228 $ \ | / 4229 $ 3 4230 4231 If numVertices is PETSC_DETERMINE, it is computed by PETSc as the maximum vertex index in cells + 1. 4232 4233 Not currently supported in Fortran. 4234 4235 .seealso: DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListPetsc() 4236 @*/ 4237 PetscErrorCode DMPlexBuildFromCellList(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[]) 4238 { 4239 PetscInt *cones, c, p, dim; 4240 PetscErrorCode ierr; 4241 4242 PetscFunctionBegin; 4243 ierr = PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 4244 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 4245 /* Get/check global number of vertices */ 4246 { 4247 PetscInt NVerticesInCells, i; 4248 const PetscInt len = numCells * numCorners; 4249 4250 /* NVerticesInCells = max(cells) + 1 */ 4251 NVerticesInCells = PETSC_MIN_INT; 4252 for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 4253 ++NVerticesInCells; 4254 4255 if (numVertices == PETSC_DECIDE) numVertices = NVerticesInCells; 4256 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); 4257 } 4258 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 4259 for (c = 0; c < numCells; ++c) { 4260 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 4261 } 4262 ierr = DMSetUp(dm);CHKERRQ(ierr); 4263 ierr = DMPlexGetCones(dm,&cones);CHKERRQ(ierr); 4264 for (c = 0; c < numCells; ++c) { 4265 for (p = 0; p < numCorners; ++p) { 4266 cones[c*numCorners+p] = cells[c*numCorners+p]+numCells; 4267 } 4268 } 4269 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 4270 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 4271 ierr = PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 4272 PetscFunctionReturn(0); 4273 } 4274 4275 /*@C 4276 DMPlexBuildCoordinatesFromCellList - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output) 4277 4278 Input Parameters: 4279 + dm - The DM 4280 . spaceDim - The spatial dimension used for coordinates 4281 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 4282 4283 Level: advanced 4284 4285 Notes: 4286 Not currently supported in Fortran. 4287 4288 .seealso: DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellList() 4289 @*/ 4290 PetscErrorCode DMPlexBuildCoordinatesFromCellList(DM dm, PetscInt spaceDim, const PetscReal vertexCoords[]) 4291 { 4292 PetscSection coordSection; 4293 Vec coordinates; 4294 DM cdm; 4295 PetscScalar *coords; 4296 PetscInt v, vStart, vEnd, d; 4297 PetscErrorCode ierr; 4298 4299 PetscFunctionBegin; 4300 ierr = PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 4301 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 4302 PetscCheckFalse(vStart < 0 || vEnd < 0,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 4303 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 4304 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 4305 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 4306 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 4307 ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr); 4308 for (v = vStart; v < vEnd; ++v) { 4309 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 4310 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 4311 } 4312 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 4313 4314 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 4315 ierr = DMCreateLocalVector(cdm, &coordinates);CHKERRQ(ierr); 4316 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 4317 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 4318 ierr = VecGetArrayWrite(coordinates, &coords);CHKERRQ(ierr); 4319 for (v = 0; v < vEnd-vStart; ++v) { 4320 for (d = 0; d < spaceDim; ++d) { 4321 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 4322 } 4323 } 4324 ierr = VecRestoreArrayWrite(coordinates, &coords);CHKERRQ(ierr); 4325 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 4326 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 4327 ierr = PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 4328 PetscFunctionReturn(0); 4329 } 4330 4331 /*@ 4332 DMPlexCreateFromCellListPetsc - Create DMPLEX from a list of vertices for each cell (common mesh generator output), but only process 0 takes in the input 4333 4334 Collective on comm 4335 4336 Input Parameters: 4337 + comm - The communicator 4338 . dim - The topological dimension of the mesh 4339 . numCells - The number of cells, only on process 0 4340 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE, only on process 0 4341 . numCorners - The number of vertices for each cell, only on process 0 4342 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 4343 . cells - An array of numCells*numCorners numbers, the vertices for each cell, only on process 0 4344 . spaceDim - The spatial dimension used for coordinates 4345 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex, only on process 0 4346 4347 Output Parameter: 4348 . dm - The DM, which only has points on process 0 4349 4350 Notes: 4351 This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), DMPlexBuildFromCellList(), 4352 DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellList() 4353 4354 See DMPlexBuildFromCellList() for an example and details about the topology-related parameters. 4355 See DMPlexBuildCoordinatesFromCellList() for details about the geometry-related parameters. 4356 See DMPlexCreateFromCellListParallelPetsc() for parallel input 4357 4358 Level: intermediate 4359 4360 .seealso: DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellList(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate() 4361 @*/ 4362 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) 4363 { 4364 PetscMPIInt rank; 4365 PetscErrorCode ierr; 4366 4367 PetscFunctionBegin; 4368 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."); 4369 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 4370 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 4371 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 4372 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 4373 if (!rank) {ierr = DMPlexBuildFromCellList(*dm, numCells, numVertices, numCorners, cells);CHKERRQ(ierr);} 4374 else {ierr = DMPlexBuildFromCellList(*dm, 0, 0, 0, NULL);CHKERRQ(ierr);} 4375 if (interpolate) { 4376 DM idm; 4377 4378 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 4379 ierr = DMDestroy(dm);CHKERRQ(ierr); 4380 *dm = idm; 4381 } 4382 if (!rank) {ierr = DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, vertexCoords);CHKERRQ(ierr);} 4383 else {ierr = DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, NULL);CHKERRQ(ierr);} 4384 PetscFunctionReturn(0); 4385 } 4386 4387 /*@ 4388 DMPlexCreateFromCellList - Deprecated, use DMPlexCreateFromCellListPetsc() 4389 4390 Level: deprecated 4391 4392 .seealso: DMPlexCreateFromCellListPetsc() 4393 @*/ 4394 PetscErrorCode DMPlexCreateFromCellList(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, PetscBool interpolate, const int cells[], PetscInt spaceDim, const double vertexCoords[], DM *dm) 4395 { 4396 PetscErrorCode ierr; 4397 PetscInt i; 4398 PetscInt *pintCells; 4399 PetscReal *prealVC; 4400 4401 PetscFunctionBegin; 4402 PetscCheckFalse(sizeof(int) > sizeof(PetscInt),comm, PETSC_ERR_ARG_SIZ, "Size of int %zd greater than size of PetscInt %zd. Reconfigure PETSc --with-64-bit-indices=1", sizeof(int), sizeof(PetscInt)); 4403 if (sizeof(int) == sizeof(PetscInt)) { 4404 pintCells = (PetscInt *) cells; 4405 } else { 4406 ierr = PetscMalloc1(numCells*numCorners, &pintCells);CHKERRQ(ierr); 4407 for (i = 0; i < numCells*numCorners; i++) { 4408 pintCells[i] = (PetscInt) cells[i]; 4409 } 4410 } 4411 PetscCheckFalse(sizeof(double) > sizeof(PetscReal),comm, PETSC_ERR_ARG_SIZ, "Size of double %zd greater than size of PetscReal %zd. Reconfigure PETSc --with-precision=<higher precision>.", sizeof(double), sizeof(PetscReal)); 4412 if (sizeof(double) == sizeof(PetscReal)) { 4413 prealVC = (PetscReal *) vertexCoords; 4414 } else { 4415 ierr = PetscMalloc1(numVertices*spaceDim, &prealVC);CHKERRQ(ierr); 4416 for (i = 0; i < numVertices*spaceDim; i++) { 4417 prealVC[i] = (PetscReal) vertexCoords[i]; 4418 } 4419 } 4420 ierr = DMPlexCreateFromCellListPetsc(comm, dim, numCells, numVertices, numCorners, interpolate, pintCells, spaceDim, prealVC, dm);CHKERRQ(ierr); 4421 if (sizeof(int) != sizeof(PetscInt)) { 4422 ierr = PetscFree(pintCells);CHKERRQ(ierr); 4423 } 4424 if (sizeof(double) != sizeof(PetscReal)) { 4425 ierr = PetscFree(prealVC);CHKERRQ(ierr); 4426 } 4427 PetscFunctionReturn(0); 4428 } 4429 4430 /*@ 4431 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 4432 4433 Input Parameters: 4434 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 4435 . depth - The depth of the DAG 4436 . numPoints - Array of size depth + 1 containing the number of points at each depth 4437 . coneSize - The cone size of each point 4438 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 4439 . coneOrientations - The orientation of each cone point 4440 - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim() 4441 4442 Output Parameter: 4443 . dm - The DM 4444 4445 Note: Two triangles sharing a face would have input 4446 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 4447 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 4448 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 4449 $ 4450 which would result in the DMPlex 4451 $ 4452 $ 4 4453 $ / | \ 4454 $ / | \ 4455 $ / | \ 4456 $ 2 0 | 1 5 4457 $ \ | / 4458 $ \ | / 4459 $ \ | / 4460 $ 3 4461 $ 4462 $ Notice that all points are numbered consecutively, unlike DMPlexCreateFromCellListPetsc() 4463 4464 Level: advanced 4465 4466 .seealso: DMPlexCreateFromCellListPetsc(), DMPlexCreate() 4467 @*/ 4468 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 4469 { 4470 Vec coordinates; 4471 PetscSection coordSection; 4472 PetscScalar *coords; 4473 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 4474 PetscErrorCode ierr; 4475 4476 PetscFunctionBegin; 4477 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 4478 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 4479 PetscCheckFalse(dimEmbed < dim,PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %D cannot be less than intrinsic dimension %d",dimEmbed,dim); 4480 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 4481 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 4482 for (p = pStart; p < pEnd; ++p) { 4483 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 4484 if (firstVertex < 0 && !coneSize[p - pStart]) { 4485 firstVertex = p - pStart; 4486 } 4487 } 4488 PetscCheckFalse(firstVertex < 0 && numPoints[0],PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %D vertices but could not find any", numPoints[0]); 4489 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 4490 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 4491 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 4492 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 4493 } 4494 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 4495 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 4496 /* Build coordinates */ 4497 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 4498 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 4499 ierr = PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);CHKERRQ(ierr); 4500 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 4501 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 4502 ierr = PetscSectionSetDof(coordSection, v, dimEmbed);CHKERRQ(ierr); 4503 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);CHKERRQ(ierr); 4504 } 4505 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 4506 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 4507 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 4508 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 4509 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 4510 ierr = VecSetBlockSize(coordinates, dimEmbed);CHKERRQ(ierr); 4511 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 4512 if (vertexCoords) { 4513 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 4514 for (v = 0; v < numPoints[0]; ++v) { 4515 PetscInt off; 4516 4517 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 4518 for (d = 0; d < dimEmbed; ++d) { 4519 coords[off+d] = vertexCoords[v*dimEmbed+d]; 4520 } 4521 } 4522 } 4523 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 4524 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 4525 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 4526 PetscFunctionReturn(0); 4527 } 4528 4529 /*@C 4530 DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file. 4531 4532 + comm - The MPI communicator 4533 . filename - Name of the .dat file 4534 - interpolate - Create faces and edges in the mesh 4535 4536 Output Parameter: 4537 . dm - The DM object representing the mesh 4538 4539 Note: The format is the simplest possible: 4540 $ Ne 4541 $ v0 v1 ... vk 4542 $ Nv 4543 $ x y z marker 4544 4545 Level: beginner 4546 4547 .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate() 4548 @*/ 4549 PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 4550 { 4551 DMLabel marker; 4552 PetscViewer viewer; 4553 Vec coordinates; 4554 PetscSection coordSection; 4555 PetscScalar *coords; 4556 char line[PETSC_MAX_PATH_LEN]; 4557 PetscInt dim = 3, cdim = 3, coordSize, v, c, d; 4558 PetscMPIInt rank; 4559 int snum, Nv, Nc, Ncn, Nl; 4560 PetscErrorCode ierr; 4561 4562 PetscFunctionBegin; 4563 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 4564 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 4565 ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr); 4566 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 4567 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 4568 if (rank == 0) { 4569 ierr = PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);CHKERRQ(ierr); 4570 snum = sscanf(line, "%d %d %d %d", &Nc, &Nv, &Ncn, &Nl); 4571 PetscCheckFalse(snum != 4,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4572 } else { 4573 Nc = Nv = Ncn = Nl = 0; 4574 } 4575 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 4576 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 4577 ierr = DMPlexSetChart(*dm, 0, Nc+Nv);CHKERRQ(ierr); 4578 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 4579 ierr = DMSetCoordinateDim(*dm, cdim);CHKERRQ(ierr); 4580 /* Read topology */ 4581 if (rank == 0) { 4582 char format[PETSC_MAX_PATH_LEN]; 4583 PetscInt cone[8]; 4584 int vbuf[8], v; 4585 4586 for (c = 0; c < Ncn; ++c) {format[c*3+0] = '%'; format[c*3+1] = 'd'; format[c*3+2] = ' ';} 4587 format[Ncn*3-1] = '\0'; 4588 for (c = 0; c < Nc; ++c) {ierr = DMPlexSetConeSize(*dm, c, Ncn);CHKERRQ(ierr);} 4589 ierr = DMSetUp(*dm);CHKERRQ(ierr); 4590 for (c = 0; c < Nc; ++c) { 4591 ierr = PetscViewerRead(viewer, line, Ncn, NULL, PETSC_STRING);CHKERRQ(ierr); 4592 switch (Ncn) { 4593 case 2: snum = sscanf(line, format, &vbuf[0], &vbuf[1]);break; 4594 case 3: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2]);break; 4595 case 4: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3]);break; 4596 case 6: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5]);break; 4597 case 8: snum = sscanf(line, format, &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5], &vbuf[6], &vbuf[7]);break; 4598 default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "No cell shape with %D vertices", Ncn); 4599 } 4600 PetscCheckFalse(snum != Ncn,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4601 for (v = 0; v < Ncn; ++v) cone[v] = vbuf[v] + Nc; 4602 /* Hexahedra are inverted */ 4603 if (Ncn == 8) { 4604 PetscInt tmp = cone[1]; 4605 cone[1] = cone[3]; 4606 cone[3] = tmp; 4607 } 4608 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 4609 } 4610 } 4611 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 4612 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 4613 /* Read coordinates */ 4614 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 4615 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 4616 ierr = PetscSectionSetFieldComponents(coordSection, 0, cdim);CHKERRQ(ierr); 4617 ierr = PetscSectionSetChart(coordSection, Nc, Nc + Nv);CHKERRQ(ierr); 4618 for (v = Nc; v < Nc+Nv; ++v) { 4619 ierr = PetscSectionSetDof(coordSection, v, cdim);CHKERRQ(ierr); 4620 ierr = PetscSectionSetFieldDof(coordSection, v, 0, cdim);CHKERRQ(ierr); 4621 } 4622 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 4623 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 4624 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 4625 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 4626 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 4627 ierr = VecSetBlockSize(coordinates, cdim);CHKERRQ(ierr); 4628 ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr); 4629 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 4630 if (rank == 0) { 4631 char format[PETSC_MAX_PATH_LEN]; 4632 double x[3]; 4633 int l, val[3]; 4634 4635 if (Nl) { 4636 for (l = 0; l < Nl; ++l) {format[l*3+0] = '%'; format[l*3+1] = 'd'; format[l*3+2] = ' ';} 4637 format[Nl*3-1] = '\0'; 4638 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 4639 ierr = DMGetLabel(*dm, "marker", &marker);CHKERRQ(ierr); 4640 } 4641 for (v = 0; v < Nv; ++v) { 4642 ierr = PetscViewerRead(viewer, line, 3+Nl, NULL, PETSC_STRING);CHKERRQ(ierr); 4643 snum = sscanf(line, "%lg %lg %lg", &x[0], &x[1], &x[2]); 4644 PetscCheckFalse(snum != 3,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4645 switch (Nl) { 4646 case 0: snum = 0;break; 4647 case 1: snum = sscanf(line, format, &val[0]);break; 4648 case 2: snum = sscanf(line, format, &val[0], &val[1]);break; 4649 case 3: snum = sscanf(line, format, &val[0], &val[1], &val[2]);break; 4650 default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Request support for %D labels", Nl); 4651 } 4652 PetscCheckFalse(snum != Nl,PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4653 for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d]; 4654 for (l = 0; l < Nl; ++l) {ierr = DMLabelSetValue(marker, v+Nc, val[l]);CHKERRQ(ierr);} 4655 } 4656 } 4657 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 4658 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 4659 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 4660 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 4661 if (interpolate) { 4662 DM idm; 4663 DMLabel bdlabel; 4664 4665 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 4666 ierr = DMDestroy(dm);CHKERRQ(ierr); 4667 *dm = idm; 4668 4669 if (!Nl) { 4670 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 4671 ierr = DMGetLabel(*dm, "marker", &bdlabel);CHKERRQ(ierr); 4672 ierr = DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 4673 ierr = DMPlexLabelComplete(*dm, bdlabel);CHKERRQ(ierr); 4674 } 4675 } 4676 PetscFunctionReturn(0); 4677 } 4678 4679 /*@C 4680 DMPlexCreateFromFile - This takes a filename and produces a DM 4681 4682 Input Parameters: 4683 + comm - The communicator 4684 . filename - A file name 4685 . plexname - The object name of the resulting DM, also used for intra-datafile lookup by some formats 4686 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 4687 4688 Output Parameter: 4689 . dm - The DM 4690 4691 Options Database Keys: 4692 . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5 4693 4694 Use -dm_plex_create_ prefix to pass options to the internal PetscViewer, e.g. 4695 $ -dm_plex_create_viewer_hdf5_collective 4696 4697 Notes: 4698 Using PETSCVIEWERHDF5 type with PETSC_VIEWER_HDF5_PETSC format, one can save multiple DMPlex 4699 meshes in a single HDF5 file. This in turn requires one to name the DMPlex object with PetscObjectSetName() 4700 before saving it with DMView() and before loading it with DMLoad() for identification of the mesh object. 4701 The input parameter name is thus used to name the DMPlex object when DMPlexCreateFromFile() internally 4702 calls DMLoad(). Currently, name is ignored for other viewer types and/or formats. 4703 4704 Level: beginner 4705 4706 .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellListPetsc(), DMPlexCreate(), PetscObjectSetName(), DMView(), DMLoad() 4707 @*/ 4708 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], const char plexname[], PetscBool interpolate, DM *dm) 4709 { 4710 const char *extGmsh = ".msh"; 4711 const char *extGmsh2 = ".msh2"; 4712 const char *extGmsh4 = ".msh4"; 4713 const char *extCGNS = ".cgns"; 4714 const char *extExodus = ".exo"; 4715 const char *extExodus_e = ".e"; 4716 const char *extGenesis = ".gen"; 4717 const char *extFluent = ".cas"; 4718 const char *extHDF5 = ".h5"; 4719 const char *extMed = ".med"; 4720 const char *extPLY = ".ply"; 4721 const char *extEGADSLite = ".egadslite"; 4722 const char *extEGADS = ".egads"; 4723 const char *extIGES = ".igs"; 4724 const char *extSTEP = ".stp"; 4725 const char *extCV = ".dat"; 4726 size_t len; 4727 PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isEGADSLite, isEGADS, isIGES, isSTEP, isCV; 4728 PetscMPIInt rank; 4729 PetscErrorCode ierr; 4730 4731 PetscFunctionBegin; 4732 PetscValidCharPointer(filename, 2); 4733 if (plexname) PetscValidCharPointer(plexname, 3); 4734 PetscValidPointer(dm, 5); 4735 ierr = DMInitializePackage();CHKERRQ(ierr); 4736 ierr = PetscLogEventBegin(DMPLEX_CreateFromFile,0,0,0,0);CHKERRQ(ierr); 4737 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 4738 ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); 4739 PetscCheckFalse(!len,comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 4740 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);CHKERRQ(ierr); 4741 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh2, 5, &isGmsh2);CHKERRQ(ierr); 4742 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh4, 5, &isGmsh4);CHKERRQ(ierr); 4743 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);CHKERRQ(ierr); 4744 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);CHKERRQ(ierr); 4745 if (!isExodus) { 4746 ierr = PetscStrncmp(&filename[PetscMax(0,len-2)], extExodus_e, 2, &isExodus);CHKERRQ(ierr); 4747 } 4748 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);CHKERRQ(ierr); 4749 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);CHKERRQ(ierr); 4750 ierr = PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);CHKERRQ(ierr); 4751 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);CHKERRQ(ierr); 4752 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);CHKERRQ(ierr); 4753 ierr = PetscStrncmp(&filename[PetscMax(0,len-10)], extEGADSLite, 10, &isEGADSLite);CHKERRQ(ierr); 4754 ierr = PetscStrncmp(&filename[PetscMax(0,len-6)], extEGADS, 6, &isEGADS);CHKERRQ(ierr); 4755 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extIGES, 4, &isIGES);CHKERRQ(ierr); 4756 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extSTEP, 4, &isSTEP);CHKERRQ(ierr); 4757 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);CHKERRQ(ierr); 4758 if (isGmsh || isGmsh2 || isGmsh4) { 4759 ierr = DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4760 } else if (isCGNS) { 4761 ierr = DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4762 } else if (isExodus || isGenesis) { 4763 ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4764 } else if (isFluent) { 4765 ierr = DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4766 } else if (isHDF5) { 4767 PetscBool load_hdf5_xdmf = PETSC_FALSE; 4768 PetscViewer viewer; 4769 4770 /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */ 4771 ierr = PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf", 5, &load_hdf5_xdmf);CHKERRQ(ierr); 4772 ierr = PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);CHKERRQ(ierr); 4773 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 4774 ierr = PetscViewerSetType(viewer, PETSCVIEWERHDF5);CHKERRQ(ierr); 4775 ierr = PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_");CHKERRQ(ierr); 4776 ierr = PetscViewerSetFromOptions(viewer);CHKERRQ(ierr); 4777 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 4778 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 4779 4780 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 4781 ierr = PetscObjectSetName((PetscObject)(*dm), plexname);CHKERRQ(ierr); 4782 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 4783 if (load_hdf5_xdmf) {ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);CHKERRQ(ierr);} 4784 ierr = DMLoad(*dm, viewer);CHKERRQ(ierr); 4785 if (load_hdf5_xdmf) {ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);} 4786 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 4787 4788 if (interpolate) { 4789 DM idm; 4790 4791 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 4792 ierr = DMDestroy(dm);CHKERRQ(ierr); 4793 *dm = idm; 4794 } 4795 } else if (isMed) { 4796 ierr = DMPlexCreateMedFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4797 } else if (isPLY) { 4798 ierr = DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4799 } else if (isEGADSLite || isEGADS || isIGES || isSTEP) { 4800 if (isEGADSLite) {ierr = DMPlexCreateEGADSLiteFromFile(comm, filename, dm);CHKERRQ(ierr);} 4801 else {ierr = DMPlexCreateEGADSFromFile(comm, filename, dm);CHKERRQ(ierr);} 4802 if (!interpolate) { 4803 DM udm; 4804 4805 ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr); 4806 ierr = DMDestroy(dm);CHKERRQ(ierr); 4807 *dm = udm; 4808 } 4809 } else if (isCV) { 4810 ierr = DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4811 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 4812 ierr = PetscStrlen(plexname, &len);CHKERRQ(ierr); 4813 if (len) {ierr = PetscObjectSetName((PetscObject)(*dm), plexname);CHKERRQ(ierr);} 4814 ierr = PetscLogEventEnd(DMPLEX_CreateFromFile,0,0,0,0);CHKERRQ(ierr); 4815 PetscFunctionReturn(0); 4816 } 4817