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 6 PetscLogEvent DMPLEX_CreateFromFile, DMPLEX_BuildFromCellList, DMPLEX_BuildCoordinatesFromCellList; 7 8 /* External function declarations here */ 9 static PetscErrorCode DMInitialize_Plex(DM dm); 10 11 /* Replace dm with the contents of ndm, and then destroy ndm 12 - Share the DM_Plex structure 13 - Share the coordinates 14 - Share the SF 15 */ 16 static PetscErrorCode DMPlexReplace_Static(DM dm, DM *ndm) 17 { 18 PetscSF sf; 19 DM dmNew = *ndm, coordDM, coarseDM; 20 Vec coords; 21 PetscBool isper; 22 const PetscReal *maxCell, *L; 23 const DMBoundaryType *bd; 24 PetscInt dim, cdim; 25 PetscErrorCode ierr; 26 27 PetscFunctionBegin; 28 if (dm == dmNew) { 29 ierr = DMDestroy(ndm);CHKERRQ(ierr); 30 PetscFunctionReturn(0); 31 } 32 dm->setupcalled = dmNew->setupcalled; 33 ierr = DMGetDimension(dmNew, &dim);CHKERRQ(ierr); 34 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 35 ierr = DMGetCoordinateDim(dmNew, &cdim);CHKERRQ(ierr); 36 ierr = DMSetCoordinateDim(dm, cdim);CHKERRQ(ierr); 37 ierr = DMGetPointSF(dmNew, &sf);CHKERRQ(ierr); 38 ierr = DMSetPointSF(dm, sf);CHKERRQ(ierr); 39 ierr = DMGetCoordinateDM(dmNew, &coordDM);CHKERRQ(ierr); 40 ierr = DMGetCoordinatesLocal(dmNew, &coords);CHKERRQ(ierr); 41 ierr = DMSetCoordinateDM(dm, coordDM);CHKERRQ(ierr); 42 ierr = DMSetCoordinatesLocal(dm, coords);CHKERRQ(ierr); 43 /* Do not want to create the coordinate field if it does not already exist, so do not call DMGetCoordinateField() */ 44 ierr = DMFieldDestroy(&dm->coordinateField);CHKERRQ(ierr); 45 dm->coordinateField = dmNew->coordinateField; 46 ((DM_Plex *) dmNew->data)->coordFunc = ((DM_Plex *) dm->data)->coordFunc; 47 ierr = DMGetPeriodicity(dmNew, &isper, &maxCell, &L, &bd);CHKERRQ(ierr); 48 ierr = DMSetPeriodicity(dm, isper, maxCell, L, bd);CHKERRQ(ierr); 49 ierr = DMDestroy_Plex(dm);CHKERRQ(ierr); 50 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 51 dm->data = dmNew->data; 52 ((DM_Plex *) dmNew->data)->refct++; 53 ierr = DMDestroyLabelLinkList_Internal(dm);CHKERRQ(ierr); 54 ierr = DMCopyLabels(dmNew, dm, PETSC_OWN_POINTER, PETSC_TRUE, DM_COPY_LABELS_FAIL);CHKERRQ(ierr); 55 ierr = DMGetCoarseDM(dmNew,&coarseDM);CHKERRQ(ierr); 56 ierr = DMSetCoarseDM(dm,coarseDM);CHKERRQ(ierr); 57 ierr = DMDestroy(ndm);CHKERRQ(ierr); 58 PetscFunctionReturn(0); 59 } 60 61 /* Swap dm with the contents of dmNew 62 - Swap the DM_Plex structure 63 - Swap the coordinates 64 - Swap the point PetscSF 65 */ 66 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 67 { 68 DM coordDMA, coordDMB; 69 Vec coordsA, coordsB; 70 PetscSF sfA, sfB; 71 DMField fieldTmp; 72 void *tmp; 73 DMLabelLink listTmp; 74 DMLabel depthTmp; 75 PetscInt tmpI; 76 PetscErrorCode ierr; 77 78 PetscFunctionBegin; 79 if (dmA == dmB) PetscFunctionReturn(0); 80 ierr = DMGetPointSF(dmA, &sfA);CHKERRQ(ierr); 81 ierr = DMGetPointSF(dmB, &sfB);CHKERRQ(ierr); 82 ierr = PetscObjectReference((PetscObject) sfA);CHKERRQ(ierr); 83 ierr = DMSetPointSF(dmA, sfB);CHKERRQ(ierr); 84 ierr = DMSetPointSF(dmB, sfA);CHKERRQ(ierr); 85 ierr = PetscObjectDereference((PetscObject) sfA);CHKERRQ(ierr); 86 87 ierr = DMGetCoordinateDM(dmA, &coordDMA);CHKERRQ(ierr); 88 ierr = DMGetCoordinateDM(dmB, &coordDMB);CHKERRQ(ierr); 89 ierr = PetscObjectReference((PetscObject) coordDMA);CHKERRQ(ierr); 90 ierr = DMSetCoordinateDM(dmA, coordDMB);CHKERRQ(ierr); 91 ierr = DMSetCoordinateDM(dmB, coordDMA);CHKERRQ(ierr); 92 ierr = PetscObjectDereference((PetscObject) coordDMA);CHKERRQ(ierr); 93 94 ierr = DMGetCoordinatesLocal(dmA, &coordsA);CHKERRQ(ierr); 95 ierr = DMGetCoordinatesLocal(dmB, &coordsB);CHKERRQ(ierr); 96 ierr = PetscObjectReference((PetscObject) coordsA);CHKERRQ(ierr); 97 ierr = DMSetCoordinatesLocal(dmA, coordsB);CHKERRQ(ierr); 98 ierr = DMSetCoordinatesLocal(dmB, coordsA);CHKERRQ(ierr); 99 ierr = PetscObjectDereference((PetscObject) coordsA);CHKERRQ(ierr); 100 101 fieldTmp = dmA->coordinateField; 102 dmA->coordinateField = dmB->coordinateField; 103 dmB->coordinateField = fieldTmp; 104 tmp = dmA->data; 105 dmA->data = dmB->data; 106 dmB->data = tmp; 107 listTmp = dmA->labels; 108 dmA->labels = dmB->labels; 109 dmB->labels = listTmp; 110 depthTmp = dmA->depthLabel; 111 dmA->depthLabel = dmB->depthLabel; 112 dmB->depthLabel = depthTmp; 113 depthTmp = dmA->celltypeLabel; 114 dmA->celltypeLabel = dmB->celltypeLabel; 115 dmB->celltypeLabel = depthTmp; 116 tmpI = dmA->levelup; 117 dmA->levelup = dmB->levelup; 118 dmB->levelup = tmpI; 119 PetscFunctionReturn(0); 120 } 121 122 static PetscErrorCode DMPlexInterpolateInPlace_Internal(DM dm) 123 { 124 DM idm; 125 PetscErrorCode ierr; 126 127 PetscFunctionBegin; 128 ierr = DMPlexInterpolate(dm, &idm);CHKERRQ(ierr); 129 ierr = DMPlexCopyCoordinates(dm, idm);CHKERRQ(ierr); 130 ierr = DMPlexReplace_Static(dm, &idm);CHKERRQ(ierr); 131 PetscFunctionReturn(0); 132 } 133 134 /*@C 135 DMPlexCreateCoordinateSpace - Creates a finite element space for the coordinates 136 137 Collective 138 139 Input Parameters: 140 + DM - The DM 141 . degree - The degree of the finite element 142 - coordFunc - An optional function to map new points from refinement to the surface 143 144 Level: advanced 145 146 .seealso: PetscFECreateLagrange(), DMGetCoordinateDM() 147 @*/ 148 PetscErrorCode DMPlexCreateCoordinateSpace(DM dm, PetscInt degree, PetscPointFunc coordFunc) 149 { 150 DM_Plex *mesh = (DM_Plex *) dm->data; 151 DM cdm; 152 PetscDS cds; 153 PetscFE fe; 154 PetscClassId id; 155 PetscErrorCode ierr; 156 157 PetscFunctionBegin; 158 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 159 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 160 ierr = PetscDSGetDiscretization(cds, 0, (PetscObject *) &fe);CHKERRQ(ierr); 161 ierr = PetscObjectGetClassId((PetscObject) fe, &id);CHKERRQ(ierr); 162 if (id != PETSCFE_CLASSID) { 163 PetscBool simplex; 164 PetscInt dim, dE, qorder; 165 166 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 167 ierr = DMGetCoordinateDim(dm, &dE);CHKERRQ(ierr); 168 ierr = DMPlexIsSimplex(dm, &simplex);CHKERRQ(ierr); 169 qorder = degree; 170 ierr = PetscObjectOptionsBegin((PetscObject) cdm);CHKERRQ(ierr); 171 ierr = PetscOptionsBoundedInt("-coord_dm_default_quadrature_order", "Quadrature order is one less than quadrature points per edge", "DMPlexCreateCoordinateSpace", qorder, &qorder, NULL, 0);CHKERRQ(ierr); 172 ierr = PetscOptionsEnd();CHKERRQ(ierr); 173 ierr = PetscFECreateLagrange(PETSC_COMM_SELF, dim, dE, simplex, degree, qorder, &fe);CHKERRQ(ierr); 174 ierr = DMSetField(cdm, 0, NULL, (PetscObject) fe);CHKERRQ(ierr); 175 ierr = DMCreateDS(cdm);CHKERRQ(ierr); 176 ierr = DMProjectCoordinates(dm, fe);CHKERRQ(ierr); 177 ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); 178 } 179 mesh->coordFunc = coordFunc; 180 PetscFunctionReturn(0); 181 } 182 183 /*@ 184 DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement. 185 186 Collective 187 188 Input Parameters: 189 + comm - The communicator for the DM object 190 . dim - The spatial dimension 191 . simplex - Flag for simplicial cells, otherwise they are tensor product cells 192 . interpolate - Flag to create intermediate mesh pieces (edges, faces) 193 - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell 194 195 Output Parameter: 196 . dm - The DM object 197 198 Level: beginner 199 200 .seealso: DMSetType(), DMCreate() 201 @*/ 202 PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscReal refinementLimit, DM *newdm) 203 { 204 DM dm; 205 PetscMPIInt rank; 206 PetscErrorCode ierr; 207 208 PetscFunctionBegin; 209 ierr = DMCreate(comm, &dm);CHKERRQ(ierr); 210 ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr); 211 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 212 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 213 switch (dim) { 214 case 2: 215 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "triangular");CHKERRQ(ierr);} 216 else {ierr = PetscObjectSetName((PetscObject) dm, "quadrilateral");CHKERRQ(ierr);} 217 break; 218 case 3: 219 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "tetrahedral");CHKERRQ(ierr);} 220 else {ierr = PetscObjectSetName((PetscObject) dm, "hexahedral");CHKERRQ(ierr);} 221 break; 222 default: 223 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %D", dim); 224 } 225 if (rank) { 226 PetscInt numPoints[2] = {0, 0}; 227 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 228 } else { 229 switch (dim) { 230 case 2: 231 if (simplex) { 232 PetscInt numPoints[2] = {4, 2}; 233 PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; 234 PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; 235 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 236 PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5}; 237 238 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 239 } else { 240 PetscInt numPoints[2] = {6, 2}; 241 PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; 242 PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4}; 243 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 244 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}; 245 246 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 247 } 248 break; 249 case 3: 250 if (simplex) { 251 PetscInt numPoints[2] = {5, 2}; 252 PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; 253 PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; 254 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 255 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}; 256 257 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 258 } else { 259 PetscInt numPoints[2] = {12, 2}; 260 PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 261 PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8}; 262 PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 263 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, 264 -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5, 265 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5}; 266 267 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 268 } 269 break; 270 default: 271 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %D", dim); 272 } 273 } 274 *newdm = dm; 275 if (refinementLimit > 0.0) { 276 DM rdm; 277 const char *name; 278 279 ierr = DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);CHKERRQ(ierr); 280 ierr = DMPlexSetRefinementLimit(*newdm, refinementLimit);CHKERRQ(ierr); 281 ierr = DMRefine(*newdm, comm, &rdm);CHKERRQ(ierr); 282 ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); 283 ierr = PetscObjectSetName((PetscObject) rdm, name);CHKERRQ(ierr); 284 ierr = DMDestroy(newdm);CHKERRQ(ierr); 285 *newdm = rdm; 286 } 287 if (interpolate) { 288 DM idm; 289 290 ierr = DMPlexInterpolate(*newdm, &idm);CHKERRQ(ierr); 291 ierr = DMDestroy(newdm);CHKERRQ(ierr); 292 *newdm = idm; 293 } 294 PetscFunctionReturn(0); 295 } 296 297 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 298 { 299 const PetscInt numVertices = 2; 300 PetscInt markerRight = 1; 301 PetscInt markerLeft = 1; 302 PetscBool markerSeparate = PETSC_FALSE; 303 Vec coordinates; 304 PetscSection coordSection; 305 PetscScalar *coords; 306 PetscInt coordSize; 307 PetscMPIInt rank; 308 PetscInt cdim = 1, v; 309 PetscErrorCode ierr; 310 311 PetscFunctionBegin; 312 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 313 if (markerSeparate) { 314 markerRight = 2; 315 markerLeft = 1; 316 } 317 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRMPI(ierr); 318 if (!rank) { 319 ierr = DMPlexSetChart(dm, 0, numVertices);CHKERRQ(ierr); 320 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 321 ierr = DMSetLabelValue(dm, "marker", 0, markerLeft);CHKERRQ(ierr); 322 ierr = DMSetLabelValue(dm, "marker", 1, markerRight);CHKERRQ(ierr); 323 } 324 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 325 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 326 /* Build coordinates */ 327 ierr = DMSetCoordinateDim(dm, cdim);CHKERRQ(ierr); 328 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 329 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 330 ierr = PetscSectionSetChart(coordSection, 0, numVertices);CHKERRQ(ierr); 331 ierr = PetscSectionSetFieldComponents(coordSection, 0, cdim);CHKERRQ(ierr); 332 for (v = 0; v < numVertices; ++v) { 333 ierr = PetscSectionSetDof(coordSection, v, cdim);CHKERRQ(ierr); 334 ierr = PetscSectionSetFieldDof(coordSection, v, 0, cdim);CHKERRQ(ierr); 335 } 336 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 337 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 338 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 339 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 340 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 341 ierr = VecSetBlockSize(coordinates, cdim);CHKERRQ(ierr); 342 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 343 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 344 coords[0] = lower[0]; 345 coords[1] = upper[0]; 346 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 347 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 348 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 349 PetscFunctionReturn(0); 350 } 351 352 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 353 { 354 const PetscInt numVertices = (edges[0]+1)*(edges[1]+1); 355 const PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1]; 356 PetscInt markerTop = 1; 357 PetscInt markerBottom = 1; 358 PetscInt markerRight = 1; 359 PetscInt markerLeft = 1; 360 PetscBool markerSeparate = PETSC_FALSE; 361 Vec coordinates; 362 PetscSection coordSection; 363 PetscScalar *coords; 364 PetscInt coordSize; 365 PetscMPIInt rank; 366 PetscInt v, vx, vy; 367 PetscErrorCode ierr; 368 369 PetscFunctionBegin; 370 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 371 if (markerSeparate) { 372 markerTop = 3; 373 markerBottom = 1; 374 markerRight = 2; 375 markerLeft = 4; 376 } 377 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRMPI(ierr); 378 if (rank == 0) { 379 PetscInt e, ex, ey; 380 381 ierr = DMPlexSetChart(dm, 0, numEdges+numVertices);CHKERRQ(ierr); 382 for (e = 0; e < numEdges; ++e) { 383 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 384 } 385 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 386 for (vx = 0; vx <= edges[0]; vx++) { 387 for (ey = 0; ey < edges[1]; ey++) { 388 PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1); 389 PetscInt vertex = ey*(edges[0]+1) + vx + numEdges; 390 PetscInt cone[2]; 391 392 cone[0] = vertex; cone[1] = vertex+edges[0]+1; 393 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 394 if (vx == edges[0]) { 395 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 396 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 397 if (ey == edges[1]-1) { 398 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 399 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerRight);CHKERRQ(ierr); 400 } 401 } else if (vx == 0) { 402 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 403 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 404 if (ey == edges[1]-1) { 405 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 406 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft);CHKERRQ(ierr); 407 } 408 } 409 } 410 } 411 for (vy = 0; vy <= edges[1]; vy++) { 412 for (ex = 0; ex < edges[0]; ex++) { 413 PetscInt edge = vy*edges[0] + ex; 414 PetscInt vertex = vy*(edges[0]+1) + ex + numEdges; 415 PetscInt cone[2]; 416 417 cone[0] = vertex; cone[1] = vertex+1; 418 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 419 if (vy == edges[1]) { 420 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 421 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 422 if (ex == edges[0]-1) { 423 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 424 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerTop);CHKERRQ(ierr); 425 } 426 } else if (vy == 0) { 427 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 428 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 429 if (ex == edges[0]-1) { 430 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 431 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom);CHKERRQ(ierr); 432 } 433 } 434 } 435 } 436 } 437 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 438 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 439 /* Build coordinates */ 440 ierr = DMSetCoordinateDim(dm, 2);CHKERRQ(ierr); 441 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 442 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 443 ierr = PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);CHKERRQ(ierr); 444 ierr = PetscSectionSetFieldComponents(coordSection, 0, 2);CHKERRQ(ierr); 445 for (v = numEdges; v < numEdges+numVertices; ++v) { 446 ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr); 447 ierr = PetscSectionSetFieldDof(coordSection, v, 0, 2);CHKERRQ(ierr); 448 } 449 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 450 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 451 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 452 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 453 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 454 ierr = VecSetBlockSize(coordinates, 2);CHKERRQ(ierr); 455 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 456 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 457 for (vy = 0; vy <= edges[1]; ++vy) { 458 for (vx = 0; vx <= edges[0]; ++vx) { 459 coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx; 460 coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy; 461 } 462 } 463 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 464 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 465 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 466 PetscFunctionReturn(0); 467 } 468 469 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) 470 { 471 PetscInt vertices[3], numVertices; 472 PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2]; 473 Vec coordinates; 474 PetscSection coordSection; 475 PetscScalar *coords; 476 PetscInt coordSize; 477 PetscMPIInt rank; 478 PetscInt v, vx, vy, vz; 479 PetscInt voffset, iface=0, cone[4]; 480 PetscErrorCode ierr; 481 482 PetscFunctionBegin; 483 if ((faces[0] < 1) || (faces[1] < 1) || (faces[2] < 1)) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Must have at least 1 face per side"); 484 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRMPI(ierr); 485 vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1; 486 numVertices = vertices[0]*vertices[1]*vertices[2]; 487 if (rank == 0) { 488 PetscInt f; 489 490 ierr = DMPlexSetChart(dm, 0, numFaces+numVertices);CHKERRQ(ierr); 491 for (f = 0; f < numFaces; ++f) { 492 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 493 } 494 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 495 496 /* Side 0 (Top) */ 497 for (vy = 0; vy < faces[1]; vy++) { 498 for (vx = 0; vx < faces[0]; vx++) { 499 voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx; 500 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0]; 501 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 502 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 503 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 504 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 505 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 506 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);CHKERRQ(ierr); 507 iface++; 508 } 509 } 510 511 /* Side 1 (Bottom) */ 512 for (vy = 0; vy < faces[1]; vy++) { 513 for (vx = 0; vx < faces[0]; vx++) { 514 voffset = numFaces + vy*(faces[0]+1) + vx; 515 cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1; 516 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 517 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 518 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 519 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 520 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 521 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);CHKERRQ(ierr); 522 iface++; 523 } 524 } 525 526 /* Side 2 (Front) */ 527 for (vz = 0; vz < faces[2]; vz++) { 528 for (vx = 0; vx < faces[0]; vx++) { 529 voffset = numFaces + vz*vertices[0]*vertices[1] + vx; 530 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1]; 531 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 532 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 533 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 534 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 535 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 536 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);CHKERRQ(ierr); 537 iface++; 538 } 539 } 540 541 /* Side 3 (Back) */ 542 for (vz = 0; vz < faces[2]; vz++) { 543 for (vx = 0; vx < faces[0]; vx++) { 544 voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx; 545 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1; 546 cone[2] = voffset+1; cone[3] = voffset; 547 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 548 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 549 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 550 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 551 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 552 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);CHKERRQ(ierr); 553 iface++; 554 } 555 } 556 557 /* Side 4 (Left) */ 558 for (vz = 0; vz < faces[2]; vz++) { 559 for (vy = 0; vy < faces[1]; vy++) { 560 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0]; 561 cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1]; 562 cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0]; 563 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 564 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 565 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 566 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 567 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[1]+0, 1);CHKERRQ(ierr); 568 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);CHKERRQ(ierr); 569 iface++; 570 } 571 } 572 573 /* Side 5 (Right) */ 574 for (vz = 0; vz < faces[2]; vz++) { 575 for (vy = 0; vy < faces[1]; vy++) { 576 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + faces[0]; 577 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset; 578 cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0]; 579 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 580 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 581 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 582 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 583 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 584 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);CHKERRQ(ierr); 585 iface++; 586 } 587 } 588 } 589 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 590 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 591 /* Build coordinates */ 592 ierr = DMSetCoordinateDim(dm, 3);CHKERRQ(ierr); 593 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 594 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 595 ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr); 596 ierr = PetscSectionSetFieldComponents(coordSection, 0, 3);CHKERRQ(ierr); 597 for (v = numFaces; v < numFaces+numVertices; ++v) { 598 ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr); 599 ierr = PetscSectionSetFieldDof(coordSection, v, 0, 3);CHKERRQ(ierr); 600 } 601 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 602 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 603 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 604 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 605 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 606 ierr = VecSetBlockSize(coordinates, 3);CHKERRQ(ierr); 607 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 608 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 609 for (vz = 0; vz <= faces[2]; ++vz) { 610 for (vy = 0; vy <= faces[1]; ++vy) { 611 for (vx = 0; vx <= faces[0]; ++vx) { 612 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx; 613 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy; 614 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz; 615 } 616 } 617 } 618 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 619 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 620 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 621 PetscFunctionReturn(0); 622 } 623 624 static PetscErrorCode DMPlexCreateBoxSurfaceMesh_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate) 625 { 626 PetscErrorCode ierr; 627 628 PetscFunctionBegin; 629 PetscValidLogicalCollectiveInt(dm, dim, 2); 630 ierr = DMSetDimension(dm, dim-1);CHKERRQ(ierr); 631 ierr = DMSetCoordinateDim(dm, dim);CHKERRQ(ierr); 632 switch (dim) { 633 case 1: ierr = DMPlexCreateBoxSurfaceMesh_Tensor_1D_Internal(dm, lower, upper, faces);CHKERRQ(ierr);break; 634 case 2: ierr = DMPlexCreateBoxSurfaceMesh_Tensor_2D_Internal(dm, lower, upper, faces);CHKERRQ(ierr);break; 635 case 3: ierr = DMPlexCreateBoxSurfaceMesh_Tensor_3D_Internal(dm, lower, upper, faces);CHKERRQ(ierr);break; 636 default: SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Dimension not supported: %D", dim); 637 } 638 if (interpolate) {ierr = DMPlexInterpolateInPlace_Internal(dm);CHKERRQ(ierr);} 639 PetscFunctionReturn(0); 640 } 641 642 /*@C 643 DMPlexCreateBoxSurfaceMesh - Creates a mesh on the surface of the tensor product of unit intervals (box) using tensor cells (hexahedra). 644 645 Collective 646 647 Input Parameters: 648 + comm - The communicator for the DM object 649 . dim - The spatial dimension of the box, so the resulting mesh is has dimension dim-1 650 . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 651 . lower - The lower left corner, or NULL for (0, 0, 0) 652 . upper - The upper right corner, or NULL for (1, 1, 1) 653 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 654 655 Output Parameter: 656 . dm - The DM object 657 658 Level: beginner 659 660 .seealso: DMSetFromOptions(), DMPlexCreateBoxMesh(), DMPlexCreateFromFile(), DMSetType(), DMCreate() 661 @*/ 662 PetscErrorCode DMPlexCreateBoxSurfaceMesh(MPI_Comm comm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], PetscBool interpolate, DM *dm) 663 { 664 PetscInt fac[3] = {1, 1, 1}; 665 PetscReal low[3] = {0, 0, 0}; 666 PetscReal upp[3] = {1, 1, 1}; 667 PetscErrorCode ierr; 668 669 PetscFunctionBegin; 670 ierr = DMCreate(comm,dm);CHKERRQ(ierr); 671 ierr = DMSetType(*dm,DMPLEX);CHKERRQ(ierr); 672 ierr = DMPlexCreateBoxSurfaceMesh_Internal(*dm, dim, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, interpolate);CHKERRQ(ierr); 673 PetscFunctionReturn(0); 674 } 675 676 static PetscErrorCode DMPlexCreateLineMesh_Internal(DM dm,PetscInt segments,PetscReal lower,PetscReal upper,DMBoundaryType bd) 677 { 678 PetscInt i,fStart,fEnd,numCells = 0,numVerts = 0; 679 PetscInt numPoints[2],*coneSize,*cones,*coneOrientations; 680 PetscScalar *vertexCoords; 681 PetscReal L,maxCell; 682 PetscBool markerSeparate = PETSC_FALSE; 683 PetscInt markerLeft = 1, faceMarkerLeft = 1; 684 PetscInt markerRight = 1, faceMarkerRight = 2; 685 PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE; 686 PetscMPIInt rank; 687 PetscErrorCode ierr; 688 689 PetscFunctionBegin; 690 PetscValidPointer(dm,1); 691 692 ierr = DMSetDimension(dm,1);CHKERRQ(ierr); 693 ierr = DMCreateLabel(dm,"marker");CHKERRQ(ierr); 694 ierr = DMCreateLabel(dm,"Face Sets");CHKERRQ(ierr); 695 696 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm),&rank);CHKERRMPI(ierr); 697 if (rank == 0) numCells = segments; 698 if (rank == 0) numVerts = segments + (wrap ? 0 : 1); 699 700 numPoints[0] = numVerts ; numPoints[1] = numCells; 701 ierr = PetscMalloc4(numCells+numVerts,&coneSize,numCells*2,&cones,numCells+numVerts,&coneOrientations,numVerts,&vertexCoords);CHKERRQ(ierr); 702 ierr = PetscArrayzero(coneOrientations,numCells+numVerts);CHKERRQ(ierr); 703 for (i = 0; i < numCells; ++i) { coneSize[i] = 2; } 704 for (i = 0; i < numVerts; ++i) { coneSize[numCells+i] = 0; } 705 for (i = 0; i < numCells; ++i) { cones[2*i] = numCells + i%numVerts; cones[2*i+1] = numCells + (i+1)%numVerts; } 706 for (i = 0; i < numVerts; ++i) { vertexCoords[i] = lower + (upper-lower)*((PetscReal)i/(PetscReal)numCells); } 707 ierr = DMPlexCreateFromDAG(dm,1,numPoints,coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 708 ierr = PetscFree4(coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 709 710 ierr = PetscOptionsGetBool(((PetscObject)dm)->options,((PetscObject)dm)->prefix,"-dm_plex_separate_marker",&markerSeparate,NULL);CHKERRQ(ierr); 711 if (markerSeparate) { markerLeft = faceMarkerLeft; markerRight = faceMarkerRight;} 712 if (!wrap && rank == 0) { 713 ierr = DMPlexGetHeightStratum(dm,1,&fStart,&fEnd);CHKERRQ(ierr); 714 ierr = DMSetLabelValue(dm,"marker",fStart,markerLeft);CHKERRQ(ierr); 715 ierr = DMSetLabelValue(dm,"marker",fEnd-1,markerRight);CHKERRQ(ierr); 716 ierr = DMSetLabelValue(dm,"Face Sets",fStart,faceMarkerLeft);CHKERRQ(ierr); 717 ierr = DMSetLabelValue(dm,"Face Sets",fEnd-1,faceMarkerRight);CHKERRQ(ierr); 718 } 719 if (wrap) { 720 L = upper - lower; 721 maxCell = (PetscReal)1.1*(L/(PetscReal)PetscMax(1,segments)); 722 ierr = DMSetPeriodicity(dm,PETSC_TRUE,&maxCell,&L,&bd);CHKERRQ(ierr); 723 } 724 ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr); 725 PetscFunctionReturn(0); 726 } 727 728 static PetscErrorCode DMPlexCreateBoxMesh_Simplex_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate) 729 { 730 DM boundary, vol; 731 PetscInt i; 732 PetscErrorCode ierr; 733 734 PetscFunctionBegin; 735 PetscValidPointer(dm, 1); 736 for (i = 0; i < dim; ++i) if (periodicity[i] != DM_BOUNDARY_NONE) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Periodicity is not supported for simplex meshes"); 737 ierr = DMCreate(PetscObjectComm((PetscObject) dm), &boundary);CHKERRQ(ierr); 738 ierr = DMSetType(boundary, DMPLEX);CHKERRQ(ierr); 739 ierr = DMPlexCreateBoxSurfaceMesh_Internal(boundary, dim, faces, lower, upper, PETSC_FALSE);CHKERRQ(ierr); 740 ierr = DMPlexGenerate(boundary, NULL, interpolate, &vol);CHKERRQ(ierr); 741 ierr = DMPlexReplace_Static(dm, &vol);CHKERRQ(ierr); 742 ierr = DMDestroy(&boundary);CHKERRQ(ierr); 743 PetscFunctionReturn(0); 744 } 745 746 static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ) 747 { 748 DMLabel cutLabel = NULL; 749 PetscInt markerTop = 1, faceMarkerTop = 1; 750 PetscInt markerBottom = 1, faceMarkerBottom = 1; 751 PetscInt markerFront = 1, faceMarkerFront = 1; 752 PetscInt markerBack = 1, faceMarkerBack = 1; 753 PetscInt markerRight = 1, faceMarkerRight = 1; 754 PetscInt markerLeft = 1, faceMarkerLeft = 1; 755 PetscInt dim; 756 PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE; 757 PetscMPIInt rank; 758 PetscErrorCode ierr; 759 760 PetscFunctionBegin; 761 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 762 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRMPI(ierr); 763 ierr = DMCreateLabel(dm,"marker");CHKERRQ(ierr); 764 ierr = DMCreateLabel(dm,"Face Sets");CHKERRQ(ierr); 765 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL);CHKERRQ(ierr); 766 if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST || 767 bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST || 768 bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) { 769 770 if (cutMarker) {ierr = DMCreateLabel(dm, "periodic_cut");CHKERRQ(ierr); ierr = DMGetLabel(dm, "periodic_cut", &cutLabel);CHKERRQ(ierr);} 771 } 772 switch (dim) { 773 case 2: 774 faceMarkerTop = 3; 775 faceMarkerBottom = 1; 776 faceMarkerRight = 2; 777 faceMarkerLeft = 4; 778 break; 779 case 3: 780 faceMarkerBottom = 1; 781 faceMarkerTop = 2; 782 faceMarkerFront = 3; 783 faceMarkerBack = 4; 784 faceMarkerRight = 5; 785 faceMarkerLeft = 6; 786 break; 787 default: 788 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %D not supported",dim); 789 } 790 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 791 if (markerSeparate) { 792 markerBottom = faceMarkerBottom; 793 markerTop = faceMarkerTop; 794 markerFront = faceMarkerFront; 795 markerBack = faceMarkerBack; 796 markerRight = faceMarkerRight; 797 markerLeft = faceMarkerLeft; 798 } 799 { 800 const PetscInt numXEdges = rank == 0 ? edges[0] : 0; 801 const PetscInt numYEdges = rank == 0 ? edges[1] : 0; 802 const PetscInt numZEdges = rank == 0 ? edges[2] : 0; 803 const PetscInt numXVertices = rank == 0 ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; 804 const PetscInt numYVertices = rank == 0 ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; 805 const PetscInt numZVertices = rank == 0 ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0; 806 const PetscInt numCells = numXEdges*numYEdges*numZEdges; 807 const PetscInt numXFaces = numYEdges*numZEdges; 808 const PetscInt numYFaces = numXEdges*numZEdges; 809 const PetscInt numZFaces = numXEdges*numYEdges; 810 const PetscInt numTotXFaces = numXVertices*numXFaces; 811 const PetscInt numTotYFaces = numYVertices*numYFaces; 812 const PetscInt numTotZFaces = numZVertices*numZFaces; 813 const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces; 814 const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices; 815 const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices; 816 const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices; 817 const PetscInt numVertices = numXVertices*numYVertices*numZVertices; 818 const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges; 819 const PetscInt firstVertex = (dim == 2) ? numFaces : numCells; 820 const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices; 821 const PetscInt firstYFace = firstXFace + numTotXFaces; 822 const PetscInt firstZFace = firstYFace + numTotYFaces; 823 const PetscInt firstXEdge = numCells + numFaces + numVertices; 824 const PetscInt firstYEdge = firstXEdge + numTotXEdges; 825 const PetscInt firstZEdge = firstYEdge + numTotYEdges; 826 Vec coordinates; 827 PetscSection coordSection; 828 PetscScalar *coords; 829 PetscInt coordSize; 830 PetscInt v, vx, vy, vz; 831 PetscInt c, f, fx, fy, fz, e, ex, ey, ez; 832 833 ierr = DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);CHKERRQ(ierr); 834 for (c = 0; c < numCells; c++) { 835 ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr); 836 } 837 for (f = firstXFace; f < firstXFace+numFaces; ++f) { 838 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 839 } 840 for (e = firstXEdge; e < firstXEdge+numEdges; ++e) { 841 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 842 } 843 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 844 /* Build cells */ 845 for (fz = 0; fz < numZEdges; ++fz) { 846 for (fy = 0; fy < numYEdges; ++fy) { 847 for (fx = 0; fx < numXEdges; ++fx) { 848 PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx; 849 PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 850 PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices); 851 PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 852 PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices); 853 PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 854 PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices); 855 /* B, T, F, K, R, L */ 856 PetscInt ornt[6] = {-2, 0, 0, -3, 0, -2}; /* ??? */ 857 PetscInt cone[6]; 858 859 /* no boundary twisting in 3D */ 860 cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL; 861 ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr); 862 ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr); 863 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 864 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 865 if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 866 } 867 } 868 } 869 /* Build x faces */ 870 for (fz = 0; fz < numZEdges; ++fz) { 871 for (fy = 0; fy < numYEdges; ++fy) { 872 for (fx = 0; fx < numXVertices; ++fx) { 873 PetscInt face = firstXFace + (fz*numYEdges+fy) *numXVertices+fx; 874 PetscInt edgeL = firstZEdge + (fy *numXVertices+fx)*numZEdges + fz; 875 PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz; 876 PetscInt edgeB = firstYEdge + (fz *numXVertices+fx)*numYEdges + fy; 877 PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy; 878 PetscInt ornt[4] = {0, 0, -1, -1}; 879 PetscInt cone[4]; 880 881 if (dim == 3) { 882 /* markers */ 883 if (bdX != DM_BOUNDARY_PERIODIC) { 884 if (fx == numXVertices-1) { 885 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);CHKERRQ(ierr); 886 ierr = DMSetLabelValue(dm, "marker", face, markerRight);CHKERRQ(ierr); 887 } 888 else if (fx == 0) { 889 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);CHKERRQ(ierr); 890 ierr = DMSetLabelValue(dm, "marker", face, markerLeft);CHKERRQ(ierr); 891 } 892 } 893 } 894 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 895 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 896 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 897 } 898 } 899 } 900 /* Build y faces */ 901 for (fz = 0; fz < numZEdges; ++fz) { 902 for (fx = 0; fx < numXEdges; ++fx) { 903 for (fy = 0; fy < numYVertices; ++fy) { 904 PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 905 PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx)*numZEdges + fz; 906 PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz; 907 PetscInt edgeB = firstXEdge + (fz *numYVertices+fy)*numXEdges + fx; 908 PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx; 909 PetscInt ornt[4] = {0, 0, -1, -1}; 910 PetscInt cone[4]; 911 912 if (dim == 3) { 913 /* markers */ 914 if (bdY != DM_BOUNDARY_PERIODIC) { 915 if (fy == numYVertices-1) { 916 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);CHKERRQ(ierr); 917 ierr = DMSetLabelValue(dm, "marker", face, markerBack);CHKERRQ(ierr); 918 } 919 else if (fy == 0) { 920 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);CHKERRQ(ierr); 921 ierr = DMSetLabelValue(dm, "marker", face, markerFront);CHKERRQ(ierr); 922 } 923 } 924 } 925 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 926 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 927 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 928 } 929 } 930 } 931 /* Build z faces */ 932 for (fy = 0; fy < numYEdges; ++fy) { 933 for (fx = 0; fx < numXEdges; ++fx) { 934 for (fz = 0; fz < numZVertices; fz++) { 935 PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 936 PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx)*numYEdges + fy; 937 PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy; 938 PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy)*numXEdges + fx; 939 PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx; 940 PetscInt ornt[4] = {0, 0, -1, -1}; 941 PetscInt cone[4]; 942 943 if (dim == 2) { 944 if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -1;} 945 if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;} 946 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 947 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 948 } else { 949 /* markers */ 950 if (bdZ != DM_BOUNDARY_PERIODIC) { 951 if (fz == numZVertices-1) { 952 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);CHKERRQ(ierr); 953 ierr = DMSetLabelValue(dm, "marker", face, markerTop);CHKERRQ(ierr); 954 } 955 else if (fz == 0) { 956 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);CHKERRQ(ierr); 957 ierr = DMSetLabelValue(dm, "marker", face, markerBottom);CHKERRQ(ierr); 958 } 959 } 960 } 961 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 962 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 963 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 964 } 965 } 966 } 967 /* Build Z edges*/ 968 for (vy = 0; vy < numYVertices; vy++) { 969 for (vx = 0; vx < numXVertices; vx++) { 970 for (ez = 0; ez < numZEdges; ez++) { 971 const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez; 972 const PetscInt vertexB = firstVertex + (ez *numYVertices+vy)*numXVertices + vx; 973 const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx; 974 PetscInt cone[2]; 975 976 if (dim == 3) { 977 if (bdX != DM_BOUNDARY_PERIODIC) { 978 if (vx == numXVertices-1) { 979 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 980 } 981 else if (vx == 0) { 982 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 983 } 984 } 985 if (bdY != DM_BOUNDARY_PERIODIC) { 986 if (vy == numYVertices-1) { 987 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 988 } 989 else if (vy == 0) { 990 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 991 } 992 } 993 } 994 cone[0] = vertexB; cone[1] = vertexT; 995 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 996 } 997 } 998 } 999 /* Build Y edges*/ 1000 for (vz = 0; vz < numZVertices; vz++) { 1001 for (vx = 0; vx < numXVertices; vx++) { 1002 for (ey = 0; ey < numYEdges; ey++) { 1003 const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx; 1004 const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey; 1005 const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx; 1006 const PetscInt vertexK = firstVertex + nextv; 1007 PetscInt cone[2]; 1008 1009 cone[0] = vertexF; cone[1] = vertexK; 1010 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 1011 if (dim == 2) { 1012 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 1013 if (vx == numXVertices-1) { 1014 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);CHKERRQ(ierr); 1015 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 1016 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 1017 if (ey == numYEdges-1) { 1018 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 1019 } 1020 } else if (vx == 0) { 1021 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);CHKERRQ(ierr); 1022 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 1023 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 1024 if (ey == numYEdges-1) { 1025 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 1026 } 1027 } 1028 } else { 1029 if (vx == 0 && cutLabel) { 1030 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 1031 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 1032 if (ey == numYEdges-1) { 1033 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 1034 } 1035 } 1036 } 1037 } else { 1038 if (bdX != DM_BOUNDARY_PERIODIC) { 1039 if (vx == numXVertices-1) { 1040 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 1041 } else if (vx == 0) { 1042 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 1043 } 1044 } 1045 if (bdZ != DM_BOUNDARY_PERIODIC) { 1046 if (vz == numZVertices-1) { 1047 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 1048 } else if (vz == 0) { 1049 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 1050 } 1051 } 1052 } 1053 } 1054 } 1055 } 1056 /* Build X edges*/ 1057 for (vz = 0; vz < numZVertices; vz++) { 1058 for (vy = 0; vy < numYVertices; vy++) { 1059 for (ex = 0; ex < numXEdges; ex++) { 1060 const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices; 1061 const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex; 1062 const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex; 1063 const PetscInt vertexR = firstVertex + nextv; 1064 PetscInt cone[2]; 1065 1066 cone[0] = vertexL; cone[1] = vertexR; 1067 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 1068 if (dim == 2) { 1069 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 1070 if (vy == numYVertices-1) { 1071 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);CHKERRQ(ierr); 1072 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 1073 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 1074 if (ex == numXEdges-1) { 1075 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 1076 } 1077 } else if (vy == 0) { 1078 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);CHKERRQ(ierr); 1079 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 1080 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 1081 if (ex == numXEdges-1) { 1082 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 1083 } 1084 } 1085 } else { 1086 if (vy == 0 && cutLabel) { 1087 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 1088 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 1089 if (ex == numXEdges-1) { 1090 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 1091 } 1092 } 1093 } 1094 } else { 1095 if (bdY != DM_BOUNDARY_PERIODIC) { 1096 if (vy == numYVertices-1) { 1097 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 1098 } 1099 else if (vy == 0) { 1100 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 1101 } 1102 } 1103 if (bdZ != DM_BOUNDARY_PERIODIC) { 1104 if (vz == numZVertices-1) { 1105 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 1106 } 1107 else if (vz == 0) { 1108 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 1109 } 1110 } 1111 } 1112 } 1113 } 1114 } 1115 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1116 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1117 /* Build coordinates */ 1118 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1119 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1120 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1121 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr); 1122 for (v = firstVertex; v < firstVertex+numVertices; ++v) { 1123 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1124 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1125 } 1126 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1127 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1128 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1129 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1130 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1131 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1132 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1133 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1134 for (vz = 0; vz < numZVertices; ++vz) { 1135 for (vy = 0; vy < numYVertices; ++vy) { 1136 for (vx = 0; vx < numXVertices; ++vx) { 1137 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx; 1138 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy; 1139 if (dim == 3) { 1140 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz; 1141 } 1142 } 1143 } 1144 } 1145 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1146 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1147 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1148 } 1149 PetscFunctionReturn(0); 1150 } 1151 1152 static PetscErrorCode DMPlexCreateBoxMesh_Tensor_Internal(DM dm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[]) 1153 { 1154 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1155 PetscInt fac[3] = {0, 0, 0}, d; 1156 PetscErrorCode ierr; 1157 1158 PetscFunctionBegin; 1159 PetscValidPointer(dm, 1); 1160 PetscValidLogicalCollectiveInt(dm, dim, 2); 1161 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 1162 for (d = 0; d < dim; ++d) {fac[d] = faces[d]; bdt[d] = periodicity[d];} 1163 ierr = DMPlexCreateCubeMesh_Internal(dm, lower, upper, fac, bdt[0], bdt[1], bdt[2]);CHKERRQ(ierr); 1164 if (periodicity[0] == DM_BOUNDARY_PERIODIC || periodicity[0] == DM_BOUNDARY_TWIST || 1165 periodicity[1] == DM_BOUNDARY_PERIODIC || periodicity[1] == DM_BOUNDARY_TWIST || 1166 (dim > 2 && (periodicity[2] == DM_BOUNDARY_PERIODIC || periodicity[2] == DM_BOUNDARY_TWIST))) { 1167 PetscReal L[3]; 1168 PetscReal maxCell[3]; 1169 1170 for (d = 0; d < dim; ++d) { 1171 L[d] = upper[d] - lower[d]; 1172 maxCell[d] = 1.1 * (L[d] / PetscMax(1, faces[d])); 1173 } 1174 ierr = DMSetPeriodicity(dm, PETSC_TRUE, maxCell, L, periodicity);CHKERRQ(ierr); 1175 } 1176 ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr); 1177 PetscFunctionReturn(0); 1178 } 1179 1180 static PetscErrorCode DMPlexCreateBoxMesh_Internal(DM dm, PetscInt dim, PetscBool simplex, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate) 1181 { 1182 PetscErrorCode ierr; 1183 1184 PetscFunctionBegin; 1185 if (dim == 1) {ierr = DMPlexCreateLineMesh_Internal(dm, faces[0], lower[0], upper[0], periodicity[0]);CHKERRQ(ierr);} 1186 else if (simplex) {ierr = DMPlexCreateBoxMesh_Simplex_Internal(dm, dim, faces, lower, upper, periodicity, interpolate);CHKERRQ(ierr);} 1187 else {ierr = DMPlexCreateBoxMesh_Tensor_Internal(dm, dim, faces, lower, upper, periodicity);CHKERRQ(ierr);} 1188 if (!interpolate && dim > 1 && !simplex) { 1189 DM udm; 1190 1191 ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr); 1192 ierr = DMPlexCopyCoordinates(dm, udm);CHKERRQ(ierr); 1193 ierr = DMPlexReplace_Static(dm, &udm);CHKERRQ(ierr); 1194 } 1195 PetscFunctionReturn(0); 1196 } 1197 1198 /*@C 1199 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra). 1200 1201 Collective 1202 1203 Input Parameters: 1204 + comm - The communicator for the DM object 1205 . dim - The spatial dimension 1206 . simplex - PETSC_TRUE for simplices, PETSC_FALSE for tensor cells 1207 . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 1208 . lower - The lower left corner, or NULL for (0, 0, 0) 1209 . upper - The upper right corner, or NULL for (1, 1, 1) 1210 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 1211 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1212 1213 Output Parameter: 1214 . dm - The DM object 1215 1216 Note: If you want to customize this mesh using options, you just need to 1217 $ DMCreate(comm, &dm); 1218 $ DMSetType(dm, DMPLEX); 1219 $ DMSetFromOptions(dm); 1220 and use the options on the DMSetFromOptions() page. 1221 1222 Here is the numbering returned for 2 faces in each direction for tensor cells: 1223 $ 10---17---11---18----12 1224 $ | | | 1225 $ | | | 1226 $ 20 2 22 3 24 1227 $ | | | 1228 $ | | | 1229 $ 7---15----8---16----9 1230 $ | | | 1231 $ | | | 1232 $ 19 0 21 1 23 1233 $ | | | 1234 $ | | | 1235 $ 4---13----5---14----6 1236 1237 and for simplicial cells 1238 1239 $ 14----8---15----9----16 1240 $ |\ 5 |\ 7 | 1241 $ | \ | \ | 1242 $ 13 2 14 3 15 1243 $ | 4 \ | 6 \ | 1244 $ | \ | \ | 1245 $ 11----6---12----7----13 1246 $ |\ |\ | 1247 $ | \ 1 | \ 3 | 1248 $ 10 0 11 1 12 1249 $ | 0 \ | 2 \ | 1250 $ | \ | \ | 1251 $ 8----4----9----5----10 1252 1253 Level: beginner 1254 1255 .seealso: DMSetFromOptions(), DMPlexCreateFromFile(), DMPlexCreateHexCylinderMesh(), DMSetType(), DMCreate() 1256 @*/ 1257 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) 1258 { 1259 PetscInt fac[3] = {1, 1, 1}; 1260 PetscReal low[3] = {0, 0, 0}; 1261 PetscReal upp[3] = {1, 1, 1}; 1262 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1263 PetscErrorCode ierr; 1264 1265 PetscFunctionBegin; 1266 ierr = DMCreate(comm,dm);CHKERRQ(ierr); 1267 ierr = DMSetType(*dm,DMPLEX);CHKERRQ(ierr); 1268 ierr = DMPlexCreateBoxMesh_Internal(*dm, dim, simplex, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt, interpolate);CHKERRQ(ierr); 1269 PetscFunctionReturn(0); 1270 } 1271 1272 static PetscErrorCode DMPlexCreateWedgeBoxMesh_Internal(DM dm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[]) 1273 { 1274 DM bdm, vol; 1275 PetscInt i; 1276 PetscErrorCode ierr; 1277 1278 PetscFunctionBegin; 1279 for (i = 0; i < 3; ++i) if (periodicity[i] != DM_BOUNDARY_NONE) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Periodicity not yet supported"); 1280 ierr = DMCreate(PetscObjectComm((PetscObject) dm), &bdm);CHKERRQ(ierr); 1281 ierr = DMSetType(bdm, DMPLEX);CHKERRQ(ierr); 1282 ierr = DMSetDimension(bdm, 2);CHKERRQ(ierr); 1283 ierr = DMPlexCreateBoxMesh_Simplex_Internal(bdm, 2, faces, lower, upper, periodicity, PETSC_TRUE);CHKERRQ(ierr); 1284 ierr = DMPlexExtrude(bdm, faces[2], upper[2] - lower[2], PETSC_TRUE, PETSC_FALSE, NULL, NULL, &vol);CHKERRQ(ierr); 1285 ierr = DMDestroy(&bdm);CHKERRQ(ierr); 1286 ierr = DMPlexReplace_Static(dm, &vol);CHKERRQ(ierr); 1287 if (lower[2] != 0.0) { 1288 Vec v; 1289 PetscScalar *x; 1290 PetscInt cDim, n; 1291 1292 ierr = DMGetCoordinatesLocal(dm, &v);CHKERRQ(ierr); 1293 ierr = VecGetBlockSize(v, &cDim);CHKERRQ(ierr); 1294 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 1295 ierr = VecGetArray(v, &x);CHKERRQ(ierr); 1296 x += cDim; 1297 for (i = 0; i < n; i += cDim) x[i] += lower[2]; 1298 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 1299 ierr = DMSetCoordinatesLocal(dm, v);CHKERRQ(ierr); 1300 } 1301 PetscFunctionReturn(0); 1302 } 1303 1304 /*@ 1305 DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells. 1306 1307 Collective 1308 1309 Input Parameters: 1310 + comm - The communicator for the DM object 1311 . faces - Number of faces per dimension, or NULL for (1, 1, 1) 1312 . lower - The lower left corner, or NULL for (0, 0, 0) 1313 . upper - The upper right corner, or NULL for (1, 1, 1) 1314 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 1315 . orderHeight - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1316 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1317 1318 Output Parameter: 1319 . dm - The DM object 1320 1321 Level: beginner 1322 1323 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateWedgeCylinderMesh(), DMExtrude(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1324 @*/ 1325 PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool orderHeight, PetscBool interpolate, DM *dm) 1326 { 1327 PetscInt fac[3] = {1, 1, 1}; 1328 PetscReal low[3] = {0, 0, 0}; 1329 PetscReal upp[3] = {1, 1, 1}; 1330 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1331 PetscErrorCode ierr; 1332 1333 PetscFunctionBegin; 1334 ierr = DMCreate(comm,dm);CHKERRQ(ierr); 1335 ierr = DMSetType(*dm,DMPLEX);CHKERRQ(ierr); 1336 ierr = DMPlexCreateWedgeBoxMesh_Internal(*dm, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt);CHKERRQ(ierr); 1337 if (!interpolate) { 1338 DM udm; 1339 1340 ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr); 1341 ierr = DMPlexReplace_Static(*dm, &udm);CHKERRQ(ierr); 1342 } 1343 PetscFunctionReturn(0); 1344 } 1345 1346 /*@C 1347 DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database. 1348 1349 Logically Collective on dm 1350 1351 Input Parameters: 1352 + dm - the DM context 1353 - prefix - the prefix to prepend to all option names 1354 1355 Notes: 1356 A hyphen (-) must NOT be given at the beginning of the prefix name. 1357 The first character of all runtime options is AUTOMATICALLY the hyphen. 1358 1359 Level: advanced 1360 1361 .seealso: SNESSetFromOptions() 1362 @*/ 1363 PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) 1364 { 1365 DM_Plex *mesh = (DM_Plex *) dm->data; 1366 PetscErrorCode ierr; 1367 1368 PetscFunctionBegin; 1369 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1370 ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);CHKERRQ(ierr); 1371 ierr = PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);CHKERRQ(ierr); 1372 PetscFunctionReturn(0); 1373 } 1374 1375 /* Remap geometry to cylinder 1376 TODO: This only works for a single refinement, then it is broken 1377 1378 Interior square: Linear interpolation is correct 1379 The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing 1380 such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance 1381 1382 phi = arctan(y/x) 1383 d_close = sqrt(1/8 + 1/4 sin^2(phi)) 1384 d_far = sqrt(1/2 + sin^2(phi)) 1385 1386 so we remap them using 1387 1388 x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) 1389 y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) 1390 1391 If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. 1392 */ 1393 static void snapToCylinder(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1394 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1395 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1396 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 1397 { 1398 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1399 const PetscReal ds2 = 0.5*dis; 1400 1401 if ((PetscAbsScalar(u[0]) <= ds2) && (PetscAbsScalar(u[1]) <= ds2)) { 1402 f0[0] = u[0]; 1403 f0[1] = u[1]; 1404 } else { 1405 PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; 1406 1407 x = PetscRealPart(u[0]); 1408 y = PetscRealPart(u[1]); 1409 phi = PetscAtan2Real(y, x); 1410 sinp = PetscSinReal(phi); 1411 cosp = PetscCosReal(phi); 1412 if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) { 1413 dc = PetscAbsReal(ds2/sinp); 1414 df = PetscAbsReal(dis/sinp); 1415 xc = ds2*x/PetscAbsReal(y); 1416 yc = ds2*PetscSignReal(y); 1417 } else { 1418 dc = PetscAbsReal(ds2/cosp); 1419 df = PetscAbsReal(dis/cosp); 1420 xc = ds2*PetscSignReal(x); 1421 yc = ds2*y/PetscAbsReal(x); 1422 } 1423 f0[0] = xc + (u[0] - xc)*(1.0 - dc)/(df - dc); 1424 f0[1] = yc + (u[1] - yc)*(1.0 - dc)/(df - dc); 1425 } 1426 f0[2] = u[2]; 1427 } 1428 1429 static PetscErrorCode DMPlexCreateHexCylinderMesh_Internal(DM dm, DMBoundaryType periodicZ) 1430 { 1431 const PetscInt dim = 3; 1432 PetscInt numCells, numVertices; 1433 PetscMPIInt rank; 1434 PetscErrorCode ierr; 1435 1436 PetscFunctionBegin; 1437 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 1438 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 1439 /* Create topology */ 1440 { 1441 PetscInt cone[8], c; 1442 1443 numCells = rank == 0 ? 5 : 0; 1444 numVertices = rank == 0 ? 16 : 0; 1445 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1446 numCells *= 3; 1447 numVertices = rank == 0 ? 24 : 0; 1448 } 1449 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 1450 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(dm, c, 8);CHKERRQ(ierr);} 1451 ierr = DMSetUp(dm);CHKERRQ(ierr); 1452 if (rank == 0) { 1453 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1454 cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16; 1455 cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34; 1456 ierr = DMPlexSetCone(dm, 0, cone);CHKERRQ(ierr); 1457 cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23; 1458 cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */ 1459 ierr = DMPlexSetCone(dm, 1, cone);CHKERRQ(ierr); 1460 cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17; 1461 cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38; 1462 ierr = DMPlexSetCone(dm, 2, cone);CHKERRQ(ierr); 1463 cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15; 1464 cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38; 1465 ierr = DMPlexSetCone(dm, 3, cone);CHKERRQ(ierr); 1466 cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23; 1467 cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31; 1468 ierr = DMPlexSetCone(dm, 4, cone);CHKERRQ(ierr); 1469 1470 cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32; 1471 cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20; 1472 ierr = DMPlexSetCone(dm, 5, cone);CHKERRQ(ierr); 1473 cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36; 1474 cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21; 1475 ierr = DMPlexSetCone(dm, 6, cone);CHKERRQ(ierr); 1476 cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33; 1477 cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28; 1478 ierr = DMPlexSetCone(dm, 7, cone);CHKERRQ(ierr); 1479 cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31; 1480 cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28; 1481 ierr = DMPlexSetCone(dm, 8, cone);CHKERRQ(ierr); 1482 cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36; 1483 cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19; 1484 ierr = DMPlexSetCone(dm, 9, cone);CHKERRQ(ierr); 1485 1486 cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22; 1487 cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18; 1488 ierr = DMPlexSetCone(dm, 10, cone);CHKERRQ(ierr); 1489 cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25; 1490 cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17; 1491 ierr = DMPlexSetCone(dm, 11, cone);CHKERRQ(ierr); 1492 cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21; 1493 cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27; 1494 ierr = DMPlexSetCone(dm, 12, cone);CHKERRQ(ierr); 1495 cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19; 1496 cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27; 1497 ierr = DMPlexSetCone(dm, 13, cone);CHKERRQ(ierr); 1498 cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25; 1499 cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15; 1500 ierr = DMPlexSetCone(dm, 14, cone);CHKERRQ(ierr); 1501 } else { 1502 cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6; 1503 cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10; 1504 ierr = DMPlexSetCone(dm, 0, cone);CHKERRQ(ierr); 1505 cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13; 1506 cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11; 1507 ierr = DMPlexSetCone(dm, 1, cone);CHKERRQ(ierr); 1508 cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7; 1509 cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18; 1510 ierr = DMPlexSetCone(dm, 2, cone);CHKERRQ(ierr); 1511 cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5; 1512 cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18; 1513 ierr = DMPlexSetCone(dm, 3, cone);CHKERRQ(ierr); 1514 cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13; 1515 cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9; 1516 ierr = DMPlexSetCone(dm, 4, cone);CHKERRQ(ierr); 1517 } 1518 } 1519 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1520 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1521 } 1522 /* Create cube geometry */ 1523 { 1524 Vec coordinates; 1525 PetscSection coordSection; 1526 PetscScalar *coords; 1527 PetscInt coordSize, v; 1528 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1529 const PetscReal ds2 = dis/2.0; 1530 1531 /* Build coordinates */ 1532 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1533 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1534 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1535 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1536 for (v = numCells; v < numCells+numVertices; ++v) { 1537 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1538 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1539 } 1540 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1541 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1542 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1543 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1544 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1545 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1546 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1547 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1548 if (rank == 0) { 1549 coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0; 1550 coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0; 1551 coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0; 1552 coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0; 1553 coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0; 1554 coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0; 1555 coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0; 1556 coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0; 1557 coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0; 1558 coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0; 1559 coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0; 1560 coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0; 1561 coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0; 1562 coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0; 1563 coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0; 1564 coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0; 1565 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1566 /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5; 1567 /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5; 1568 /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5; 1569 /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5; 1570 /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5; 1571 /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5; 1572 /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5; 1573 /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5; 1574 } 1575 } 1576 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1577 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1578 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1579 } 1580 /* Create periodicity */ 1581 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1582 PetscReal L[3]; 1583 PetscReal maxCell[3]; 1584 DMBoundaryType bdType[3]; 1585 PetscReal lower[3] = {0.0, 0.0, 0.0}; 1586 PetscReal upper[3] = {1.0, 1.0, 1.5}; 1587 PetscInt i, numZCells = 3; 1588 1589 bdType[0] = DM_BOUNDARY_NONE; 1590 bdType[1] = DM_BOUNDARY_NONE; 1591 bdType[2] = periodicZ; 1592 for (i = 0; i < dim; i++) { 1593 L[i] = upper[i] - lower[i]; 1594 maxCell[i] = 1.1 * (L[i] / numZCells); 1595 } 1596 ierr = DMSetPeriodicity(dm, PETSC_TRUE, maxCell, L, bdType);CHKERRQ(ierr); 1597 } 1598 { 1599 DM cdm; 1600 PetscDS cds; 1601 PetscScalar c[2] = {1.0, 1.0}; 1602 1603 ierr = DMPlexCreateCoordinateSpace(dm, 1, snapToCylinder);CHKERRQ(ierr); 1604 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 1605 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 1606 ierr = PetscDSSetConstants(cds, 2, c);CHKERRQ(ierr); 1607 } 1608 /* Wait for coordinate creation before doing in-place modification */ 1609 ierr = DMPlexInterpolateInPlace_Internal(dm);CHKERRQ(ierr); 1610 PetscFunctionReturn(0); 1611 } 1612 1613 /*@ 1614 DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. 1615 1616 Collective 1617 1618 Input Parameters: 1619 + comm - The communicator for the DM object 1620 - periodicZ - The boundary type for the Z direction 1621 1622 Output Parameter: 1623 . dm - The DM object 1624 1625 Note: 1626 Here is the output numbering looking from the bottom of the cylinder: 1627 $ 17-----14 1628 $ | | 1629 $ | 2 | 1630 $ | | 1631 $ 17-----8-----7-----14 1632 $ | | | | 1633 $ | 3 | 0 | 1 | 1634 $ | | | | 1635 $ 19-----5-----6-----13 1636 $ | | 1637 $ | 4 | 1638 $ | | 1639 $ 19-----13 1640 $ 1641 $ and up through the top 1642 $ 1643 $ 18-----16 1644 $ | | 1645 $ | 2 | 1646 $ | | 1647 $ 18----10----11-----16 1648 $ | | | | 1649 $ | 3 | 0 | 1 | 1650 $ | | | | 1651 $ 20-----9----12-----15 1652 $ | | 1653 $ | 4 | 1654 $ | | 1655 $ 20-----15 1656 1657 Level: beginner 1658 1659 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1660 @*/ 1661 PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, DMBoundaryType periodicZ, DM *dm) 1662 { 1663 PetscErrorCode ierr; 1664 1665 PetscFunctionBegin; 1666 PetscValidPointer(dm, 3); 1667 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1668 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1669 ierr = DMPlexCreateHexCylinderMesh_Internal(*dm, periodicZ);CHKERRQ(ierr); 1670 PetscFunctionReturn(0); 1671 } 1672 1673 static PetscErrorCode DMPlexCreateWedgeCylinderMesh_Internal(DM dm, PetscInt n, PetscBool interpolate) 1674 { 1675 const PetscInt dim = 3; 1676 PetscInt numCells, numVertices, v; 1677 PetscMPIInt rank; 1678 PetscErrorCode ierr; 1679 1680 PetscFunctionBegin; 1681 if (n < 0) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n); 1682 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 1683 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 1684 /* Must create the celltype label here so that we do not automatically try to compute the types */ 1685 ierr = DMCreateLabel(dm, "celltype");CHKERRQ(ierr); 1686 /* Create topology */ 1687 { 1688 PetscInt cone[6], c; 1689 1690 numCells = rank == 0 ? n : 0; 1691 numVertices = rank == 0 ? 2*(n+1) : 0; 1692 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 1693 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr);} 1694 ierr = DMSetUp(dm);CHKERRQ(ierr); 1695 for (c = 0; c < numCells; c++) { 1696 cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n; 1697 cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n; 1698 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 1699 ierr = DMPlexSetCellType(dm, c, DM_POLYTOPE_TRI_PRISM_TENSOR);CHKERRQ(ierr); 1700 } 1701 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1702 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1703 } 1704 for (v = numCells; v < numCells+numVertices; ++v) { 1705 ierr = DMPlexSetCellType(dm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr); 1706 } 1707 /* Create cylinder geometry */ 1708 { 1709 Vec coordinates; 1710 PetscSection coordSection; 1711 PetscScalar *coords; 1712 PetscInt coordSize, c; 1713 1714 /* Build coordinates */ 1715 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1716 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1717 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1718 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1719 for (v = numCells; v < numCells+numVertices; ++v) { 1720 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1721 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1722 } 1723 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1724 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1725 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1726 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1727 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1728 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1729 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1730 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1731 for (c = 0; c < numCells; c++) { 1732 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; 1733 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; 1734 } 1735 if (rank == 0) { 1736 coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0; 1737 coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0; 1738 } 1739 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1740 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1741 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1742 } 1743 /* Interpolate */ 1744 if (interpolate) {ierr = DMPlexInterpolateInPlace_Internal(dm);CHKERRQ(ierr);} 1745 PetscFunctionReturn(0); 1746 } 1747 1748 /*@ 1749 DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges. 1750 1751 Collective 1752 1753 Input Parameters: 1754 + comm - The communicator for the DM object 1755 . n - The number of wedges around the origin 1756 - interpolate - Create edges and faces 1757 1758 Output Parameter: 1759 . dm - The DM object 1760 1761 Level: beginner 1762 1763 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1764 @*/ 1765 PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm) 1766 { 1767 PetscErrorCode ierr; 1768 1769 PetscFunctionBegin; 1770 PetscValidPointer(dm, 4); 1771 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1772 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1773 ierr = DMPlexCreateWedgeCylinderMesh_Internal(*dm, n, interpolate);CHKERRQ(ierr); 1774 PetscFunctionReturn(0); 1775 } 1776 1777 PETSC_STATIC_INLINE PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1778 { 1779 PetscReal prod = 0.0; 1780 PetscInt i; 1781 for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]); 1782 return PetscSqrtReal(prod); 1783 } 1784 PETSC_STATIC_INLINE PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1785 { 1786 PetscReal prod = 0.0; 1787 PetscInt i; 1788 for (i = 0; i < dim; ++i) prod += x[i]*y[i]; 1789 return prod; 1790 } 1791 1792 /* The first constant is the sphere radius */ 1793 static void snapToSphere(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1794 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1795 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1796 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 1797 { 1798 PetscReal r = PetscRealPart(constants[0]); 1799 PetscReal norm2 = 0.0, fac; 1800 PetscInt n = uOff[1] - uOff[0], d; 1801 1802 for (d = 0; d < n; ++d) norm2 += PetscSqr(PetscRealPart(u[d])); 1803 fac = r/PetscSqrtReal(norm2); 1804 for (d = 0; d < n; ++d) f0[d] = u[d]*fac; 1805 } 1806 1807 static PetscErrorCode DMPlexCreateSphereMesh_Internal(DM dm, PetscInt dim, PetscBool simplex, PetscReal R) 1808 { 1809 const PetscInt embedDim = dim+1; 1810 PetscSection coordSection; 1811 Vec coordinates; 1812 PetscScalar *coords; 1813 PetscReal *coordsIn; 1814 PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e; 1815 PetscMPIInt rank; 1816 PetscErrorCode ierr; 1817 1818 PetscFunctionBegin; 1819 PetscValidLogicalCollectiveBool(dm, simplex, 3); 1820 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 1821 ierr = DMSetCoordinateDim(dm, dim+1);CHKERRQ(ierr); 1822 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 1823 switch (dim) { 1824 case 2: 1825 if (simplex) { 1826 const PetscReal radius = PetscSqrtReal(1 + PETSC_PHI*PETSC_PHI)/(1.0 + PETSC_PHI); 1827 const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI) * (R/radius); 1828 const PetscInt degree = 5; 1829 PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)}; 1830 PetscInt s[3] = {1, 1, 1}; 1831 PetscInt cone[3]; 1832 PetscInt *graph, p, i, j, k; 1833 1834 vertex[0] *= R/radius; vertex[1] *= R/radius; vertex[2] *= R/radius; 1835 numCells = rank == 0 ? 20 : 0; 1836 numVerts = rank == 0 ? 12 : 0; 1837 firstVertex = numCells; 1838 /* Use icosahedron, which for a R-sphere has coordinates which are all cyclic permutations of 1839 1840 (0, \pm 1/\phi+1, \pm \phi/\phi+1) 1841 1842 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 1843 length is then given by 2/(1+\phi) = 2 * 0.38197 = 0.76393. 1844 */ 1845 /* Construct vertices */ 1846 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 1847 if (rank == 0) { 1848 for (p = 0, i = 0; p < embedDim; ++p) { 1849 for (s[1] = -1; s[1] < 2; s[1] += 2) { 1850 for (s[2] = -1; s[2] < 2; s[2] += 2) { 1851 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim]; 1852 ++i; 1853 } 1854 } 1855 } 1856 } 1857 /* Construct graph */ 1858 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 1859 for (i = 0; i < numVerts; ++i) { 1860 for (j = 0, k = 0; j < numVerts; ++j) { 1861 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 1862 } 1863 if (k != degree) SETERRQ3(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree); 1864 } 1865 /* Build Topology */ 1866 ierr = DMPlexSetChart(dm, 0, numCells+numVerts);CHKERRQ(ierr); 1867 for (c = 0; c < numCells; c++) { 1868 ierr = DMPlexSetConeSize(dm, c, embedDim);CHKERRQ(ierr); 1869 } 1870 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 1871 /* Cells */ 1872 for (i = 0, c = 0; i < numVerts; ++i) { 1873 for (j = 0; j < i; ++j) { 1874 for (k = 0; k < j; ++k) { 1875 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) { 1876 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; 1877 /* Check orientation */ 1878 { 1879 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}}}; 1880 PetscReal normal[3]; 1881 PetscInt e, f; 1882 1883 for (d = 0; d < embedDim; ++d) { 1884 normal[d] = 0.0; 1885 for (e = 0; e < embedDim; ++e) { 1886 for (f = 0; f < embedDim; ++f) { 1887 normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]); 1888 } 1889 } 1890 } 1891 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 1892 } 1893 ierr = DMPlexSetCone(dm, c++, cone);CHKERRQ(ierr); 1894 } 1895 } 1896 } 1897 } 1898 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1899 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1900 ierr = PetscFree(graph);CHKERRQ(ierr); 1901 } else { 1902 /* 1903 12-21--13 1904 | | 1905 25 4 24 1906 | | 1907 12-25--9-16--8-24--13 1908 | | | | 1909 23 5 17 0 15 3 22 1910 | | | | 1911 10-20--6-14--7-19--11 1912 | | 1913 20 1 19 1914 | | 1915 10-18--11 1916 | | 1917 23 2 22 1918 | | 1919 12-21--13 1920 */ 1921 PetscInt cone[4], ornt[4]; 1922 1923 numCells = rank == 0 ? 6 : 0; 1924 numEdges = rank == 0 ? 12 : 0; 1925 numVerts = rank == 0 ? 8 : 0; 1926 firstVertex = numCells; 1927 firstEdge = numCells + numVerts; 1928 /* Build Topology */ 1929 ierr = DMPlexSetChart(dm, 0, numCells+numEdges+numVerts);CHKERRQ(ierr); 1930 for (c = 0; c < numCells; c++) { 1931 ierr = DMPlexSetConeSize(dm, c, 4);CHKERRQ(ierr); 1932 } 1933 for (e = firstEdge; e < firstEdge+numEdges; ++e) { 1934 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 1935 } 1936 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 1937 if (rank == 0) { 1938 /* Cell 0 */ 1939 cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17; 1940 ierr = DMPlexSetCone(dm, 0, cone);CHKERRQ(ierr); 1941 ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0; 1942 ierr = DMPlexSetConeOrientation(dm, 0, ornt);CHKERRQ(ierr); 1943 /* Cell 1 */ 1944 cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20; 1945 ierr = DMPlexSetCone(dm, 1, cone);CHKERRQ(ierr); 1946 ornt[0] = 0; ornt[1] = 0; ornt[2] = -1; ornt[3] = 0; 1947 ierr = DMPlexSetConeOrientation(dm, 1, ornt);CHKERRQ(ierr); 1948 /* Cell 2 */ 1949 cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23; 1950 ierr = DMPlexSetCone(dm, 2, cone);CHKERRQ(ierr); 1951 ornt[0] = 0; ornt[1] = 0; ornt[2] = -1; ornt[3] = 0; 1952 ierr = DMPlexSetConeOrientation(dm, 2, ornt);CHKERRQ(ierr); 1953 /* Cell 3 */ 1954 cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15; 1955 ierr = DMPlexSetCone(dm, 3, cone);CHKERRQ(ierr); 1956 ornt[0] = -1; ornt[1] = -1; ornt[2] = 0; ornt[3] = -1; 1957 ierr = DMPlexSetConeOrientation(dm, 3, ornt);CHKERRQ(ierr); 1958 /* Cell 4 */ 1959 cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25; 1960 ierr = DMPlexSetCone(dm, 4, cone);CHKERRQ(ierr); 1961 ornt[0] = -1; ornt[1] = -1; ornt[2] = -1; ornt[3] = 0; 1962 ierr = DMPlexSetConeOrientation(dm, 4, ornt);CHKERRQ(ierr); 1963 /* Cell 5 */ 1964 cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23; 1965 ierr = DMPlexSetCone(dm, 5, cone);CHKERRQ(ierr); 1966 ornt[0] = -1; ornt[1] = -1; ornt[2] = -1; ornt[3] = -1; 1967 ierr = DMPlexSetConeOrientation(dm, 5, ornt);CHKERRQ(ierr); 1968 /* Edges */ 1969 cone[0] = 6; cone[1] = 7; 1970 ierr = DMPlexSetCone(dm, 14, cone);CHKERRQ(ierr); 1971 cone[0] = 7; cone[1] = 8; 1972 ierr = DMPlexSetCone(dm, 15, cone);CHKERRQ(ierr); 1973 cone[0] = 8; cone[1] = 9; 1974 ierr = DMPlexSetCone(dm, 16, cone);CHKERRQ(ierr); 1975 cone[0] = 9; cone[1] = 6; 1976 ierr = DMPlexSetCone(dm, 17, cone);CHKERRQ(ierr); 1977 cone[0] = 10; cone[1] = 11; 1978 ierr = DMPlexSetCone(dm, 18, cone);CHKERRQ(ierr); 1979 cone[0] = 11; cone[1] = 7; 1980 ierr = DMPlexSetCone(dm, 19, cone);CHKERRQ(ierr); 1981 cone[0] = 6; cone[1] = 10; 1982 ierr = DMPlexSetCone(dm, 20, cone);CHKERRQ(ierr); 1983 cone[0] = 12; cone[1] = 13; 1984 ierr = DMPlexSetCone(dm, 21, cone);CHKERRQ(ierr); 1985 cone[0] = 13; cone[1] = 11; 1986 ierr = DMPlexSetCone(dm, 22, cone);CHKERRQ(ierr); 1987 cone[0] = 10; cone[1] = 12; 1988 ierr = DMPlexSetCone(dm, 23, cone);CHKERRQ(ierr); 1989 cone[0] = 13; cone[1] = 8; 1990 ierr = DMPlexSetCone(dm, 24, cone);CHKERRQ(ierr); 1991 cone[0] = 12; cone[1] = 9; 1992 ierr = DMPlexSetCone(dm, 25, cone);CHKERRQ(ierr); 1993 } 1994 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1995 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1996 /* Build coordinates */ 1997 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 1998 if (rank == 0) { 1999 coordsIn[0*embedDim+0] = -R; coordsIn[0*embedDim+1] = R; coordsIn[0*embedDim+2] = -R; 2000 coordsIn[1*embedDim+0] = R; coordsIn[1*embedDim+1] = R; coordsIn[1*embedDim+2] = -R; 2001 coordsIn[2*embedDim+0] = R; coordsIn[2*embedDim+1] = -R; coordsIn[2*embedDim+2] = -R; 2002 coordsIn[3*embedDim+0] = -R; coordsIn[3*embedDim+1] = -R; coordsIn[3*embedDim+2] = -R; 2003 coordsIn[4*embedDim+0] = -R; coordsIn[4*embedDim+1] = R; coordsIn[4*embedDim+2] = R; 2004 coordsIn[5*embedDim+0] = R; coordsIn[5*embedDim+1] = R; coordsIn[5*embedDim+2] = R; 2005 coordsIn[6*embedDim+0] = -R; coordsIn[6*embedDim+1] = -R; coordsIn[6*embedDim+2] = R; 2006 coordsIn[7*embedDim+0] = R; coordsIn[7*embedDim+1] = -R; coordsIn[7*embedDim+2] = R; 2007 } 2008 } 2009 break; 2010 case 3: 2011 if (simplex) { 2012 const PetscReal edgeLen = 1.0/PETSC_PHI; 2013 PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5}; 2014 PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0}; 2015 PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0}; 2016 const PetscInt degree = 12; 2017 PetscInt s[4] = {1, 1, 1}; 2018 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}, 2019 {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}}; 2020 PetscInt cone[4]; 2021 PetscInt *graph, p, i, j, k, l; 2022 2023 vertexA[0] *= R; vertexA[1] *= R; vertexA[2] *= R; vertexA[3] *= R; 2024 vertexB[0] *= R; vertexB[1] *= R; vertexB[2] *= R; vertexB[3] *= R; 2025 vertexC[0] *= R; vertexC[1] *= R; vertexC[2] *= R; vertexC[3] *= R; 2026 numCells = rank == 0 ? 600 : 0; 2027 numVerts = rank == 0 ? 120 : 0; 2028 firstVertex = numCells; 2029 /* Use the 600-cell, which for a unit sphere has coordinates which are 2030 2031 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16 2032 (\pm 1, 0, 0, 0) all cyclic permutations 8 2033 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96 2034 2035 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 2036 length is then given by 1/\phi = 0.61803. 2037 2038 http://buzzard.pugetsound.edu/sage-practice/ch03s03.html 2039 http://mathworld.wolfram.com/600-Cell.html 2040 */ 2041 /* Construct vertices */ 2042 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 2043 i = 0; 2044 if (rank == 0) { 2045 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2046 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2047 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2048 for (s[3] = -1; s[3] < 2; s[3] += 2) { 2049 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d]; 2050 ++i; 2051 } 2052 } 2053 } 2054 } 2055 for (p = 0; p < embedDim; ++p) { 2056 s[1] = s[2] = s[3] = 1; 2057 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2058 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim]; 2059 ++i; 2060 } 2061 } 2062 for (p = 0; p < 12; ++p) { 2063 s[3] = 1; 2064 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2065 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2066 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2067 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]]; 2068 ++i; 2069 } 2070 } 2071 } 2072 } 2073 } 2074 if (i != numVerts) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts); 2075 /* Construct graph */ 2076 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 2077 for (i = 0; i < numVerts; ++i) { 2078 for (j = 0, k = 0; j < numVerts; ++j) { 2079 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 2080 } 2081 if (k != degree) SETERRQ3(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree); 2082 } 2083 /* Build Topology */ 2084 ierr = DMPlexSetChart(dm, 0, numCells+numVerts);CHKERRQ(ierr); 2085 for (c = 0; c < numCells; c++) { 2086 ierr = DMPlexSetConeSize(dm, c, embedDim);CHKERRQ(ierr); 2087 } 2088 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 2089 /* Cells */ 2090 if (rank == 0) { 2091 for (i = 0, c = 0; i < numVerts; ++i) { 2092 for (j = 0; j < i; ++j) { 2093 for (k = 0; k < j; ++k) { 2094 for (l = 0; l < k; ++l) { 2095 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] && 2096 graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) { 2097 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l; 2098 /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */ 2099 { 2100 const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2101 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}}, 2102 {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}}, 2103 {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}}, 2104 2105 {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}}, 2106 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2107 {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}}, 2108 {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}}, 2109 2110 {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}}, 2111 {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}}, 2112 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2113 {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}, 2114 2115 {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}}, 2116 {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}}, 2117 {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2118 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}}; 2119 PetscReal normal[4]; 2120 PetscInt e, f, g; 2121 2122 for (d = 0; d < embedDim; ++d) { 2123 normal[d] = 0.0; 2124 for (e = 0; e < embedDim; ++e) { 2125 for (f = 0; f < embedDim; ++f) { 2126 for (g = 0; g < embedDim; ++g) { 2127 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]); 2128 } 2129 } 2130 } 2131 } 2132 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 2133 } 2134 ierr = DMPlexSetCone(dm, c++, cone);CHKERRQ(ierr); 2135 } 2136 } 2137 } 2138 } 2139 } 2140 } 2141 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2142 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2143 ierr = PetscFree(graph);CHKERRQ(ierr); 2144 break; 2145 } 2146 default: SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim); 2147 } 2148 /* Create coordinates */ 2149 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2150 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2151 ierr = PetscSectionSetFieldComponents(coordSection, 0, embedDim);CHKERRQ(ierr); 2152 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);CHKERRQ(ierr); 2153 for (v = firstVertex; v < firstVertex+numVerts; ++v) { 2154 ierr = PetscSectionSetDof(coordSection, v, embedDim);CHKERRQ(ierr); 2155 ierr = PetscSectionSetFieldDof(coordSection, v, 0, embedDim);CHKERRQ(ierr); 2156 } 2157 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2158 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2159 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 2160 ierr = VecSetBlockSize(coordinates, embedDim);CHKERRQ(ierr); 2161 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2162 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2163 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2164 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2165 for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];} 2166 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2167 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2168 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2169 ierr = PetscFree(coordsIn);CHKERRQ(ierr); 2170 { 2171 DM cdm; 2172 PetscDS cds; 2173 PetscScalar c = R; 2174 2175 ierr = DMPlexCreateCoordinateSpace(dm, 1, snapToSphere);CHKERRQ(ierr); 2176 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 2177 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 2178 ierr = PetscDSSetConstants(cds, 1, &c);CHKERRQ(ierr); 2179 } 2180 /* Wait for coordinate creation before doing in-place modification */ 2181 if (simplex) {ierr = DMPlexInterpolateInPlace_Internal(dm);CHKERRQ(ierr);} 2182 PetscFunctionReturn(0); 2183 } 2184 2185 /*@ 2186 DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d. 2187 2188 Collective 2189 2190 Input Parameters: 2191 + comm - The communicator for the DM object 2192 . dim - The dimension 2193 . simplex - Use simplices, or tensor product cells 2194 - R - The radius 2195 2196 Output Parameter: 2197 . dm - The DM object 2198 2199 Level: beginner 2200 2201 .seealso: DMPlexCreateBallMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 2202 @*/ 2203 PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscReal R, DM *dm) 2204 { 2205 PetscErrorCode ierr; 2206 2207 PetscFunctionBegin; 2208 PetscValidPointer(dm, 5); 2209 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2210 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2211 ierr = DMPlexCreateSphereMesh_Internal(*dm, dim, simplex, R);CHKERRQ(ierr); 2212 PetscFunctionReturn(0); 2213 } 2214 2215 static PetscErrorCode DMPlexCreateBallMesh_Internal(DM dm, PetscInt dim, PetscReal R) 2216 { 2217 DM sdm, vol; 2218 DMLabel bdlabel; 2219 PetscErrorCode ierr; 2220 2221 PetscFunctionBegin; 2222 ierr = DMCreate(PetscObjectComm((PetscObject) dm), &sdm);CHKERRQ(ierr); 2223 ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr); 2224 ierr = PetscObjectSetOptionsPrefix((PetscObject) sdm, "bd_");CHKERRQ(ierr); 2225 ierr = DMPlexCreateSphereMesh_Internal(sdm, dim-1, PETSC_TRUE, R);CHKERRQ(ierr); 2226 ierr = DMSetFromOptions(sdm);CHKERRQ(ierr); 2227 ierr = DMViewFromOptions(sdm, NULL, "-dm_view");CHKERRQ(ierr); 2228 ierr = DMPlexGenerate(sdm, NULL, PETSC_TRUE, &vol);CHKERRQ(ierr); 2229 ierr = DMDestroy(&sdm);CHKERRQ(ierr); 2230 ierr = DMPlexReplace_Static(dm, &vol);CHKERRQ(ierr); 2231 ierr = DMCreateLabel(dm, "marker");CHKERRQ(ierr); 2232 ierr = DMGetLabel(dm, "marker", &bdlabel);CHKERRQ(ierr); 2233 ierr = DMPlexMarkBoundaryFaces(dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 2234 ierr = DMPlexLabelComplete(dm, bdlabel);CHKERRQ(ierr); 2235 PetscFunctionReturn(0); 2236 } 2237 2238 /*@ 2239 DMPlexCreateBallMesh - Creates a simplex mesh on the d-dimensional ball, B^d. 2240 2241 Collective 2242 2243 Input Parameters: 2244 + comm - The communicator for the DM object 2245 . dim - The dimension 2246 - R - The radius 2247 2248 Output Parameter: 2249 . dm - The DM object 2250 2251 Options Database Keys: 2252 - bd_dm_refine - This will refine the surface mesh preserving the sphere geometry 2253 2254 Level: beginner 2255 2256 .seealso: DMPlexCreateSphereMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 2257 @*/ 2258 PetscErrorCode DMPlexCreateBallMesh(MPI_Comm comm, PetscInt dim, PetscReal R, DM *dm) 2259 { 2260 PetscErrorCode ierr; 2261 2262 PetscFunctionBegin; 2263 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2264 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2265 ierr = DMPlexCreateBallMesh_Internal(*dm, dim, R);CHKERRQ(ierr); 2266 PetscFunctionReturn(0); 2267 } 2268 2269 static PetscErrorCode DMPlexCreateReferenceCell_Internal(DM rdm, DMPolytopeType ct) 2270 { 2271 PetscErrorCode ierr; 2272 2273 PetscFunctionBegin; 2274 switch (ct) { 2275 case DM_POLYTOPE_POINT: 2276 { 2277 PetscInt numPoints[1] = {1}; 2278 PetscInt coneSize[1] = {0}; 2279 PetscInt cones[1] = {0}; 2280 PetscInt coneOrientations[1] = {0}; 2281 PetscScalar vertexCoords[1] = {0.0}; 2282 2283 ierr = DMSetDimension(rdm, 0);CHKERRQ(ierr); 2284 ierr = DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2285 } 2286 break; 2287 case DM_POLYTOPE_SEGMENT: 2288 { 2289 PetscInt numPoints[2] = {2, 1}; 2290 PetscInt coneSize[3] = {2, 0, 0}; 2291 PetscInt cones[2] = {1, 2}; 2292 PetscInt coneOrientations[2] = {0, 0}; 2293 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 2294 2295 ierr = DMSetDimension(rdm, 1);CHKERRQ(ierr); 2296 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2297 } 2298 break; 2299 case DM_POLYTOPE_POINT_PRISM_TENSOR: 2300 { 2301 PetscInt numPoints[2] = {2, 1}; 2302 PetscInt coneSize[3] = {2, 0, 0}; 2303 PetscInt cones[2] = {1, 2}; 2304 PetscInt coneOrientations[2] = {0, 0}; 2305 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 2306 2307 ierr = DMSetDimension(rdm, 1);CHKERRQ(ierr); 2308 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2309 } 2310 break; 2311 case DM_POLYTOPE_TRIANGLE: 2312 { 2313 PetscInt numPoints[2] = {3, 1}; 2314 PetscInt coneSize[4] = {3, 0, 0, 0}; 2315 PetscInt cones[3] = {1, 2, 3}; 2316 PetscInt coneOrientations[3] = {0, 0, 0}; 2317 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 2318 2319 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 2320 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2321 } 2322 break; 2323 case DM_POLYTOPE_QUADRILATERAL: 2324 { 2325 PetscInt numPoints[2] = {4, 1}; 2326 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 2327 PetscInt cones[4] = {1, 2, 3, 4}; 2328 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 2329 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 2330 2331 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 2332 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2333 } 2334 break; 2335 case DM_POLYTOPE_SEG_PRISM_TENSOR: 2336 { 2337 PetscInt numPoints[2] = {4, 1}; 2338 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 2339 PetscInt cones[4] = {1, 2, 3, 4}; 2340 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 2341 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, 1.0}; 2342 2343 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 2344 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2345 } 2346 break; 2347 case DM_POLYTOPE_TETRAHEDRON: 2348 { 2349 PetscInt numPoints[2] = {4, 1}; 2350 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 2351 PetscInt cones[4] = {1, 2, 3, 4}; 2352 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 2353 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}; 2354 2355 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 2356 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2357 } 2358 break; 2359 case DM_POLYTOPE_HEXAHEDRON: 2360 { 2361 PetscInt numPoints[2] = {8, 1}; 2362 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 2363 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 2364 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 2365 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, 2366 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 2367 2368 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 2369 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2370 } 2371 break; 2372 case DM_POLYTOPE_TRI_PRISM: 2373 { 2374 PetscInt numPoints[2] = {6, 1}; 2375 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 2376 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 2377 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 2378 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, -1.0, -1.0, 2379 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 2380 2381 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 2382 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2383 } 2384 break; 2385 case DM_POLYTOPE_TRI_PRISM_TENSOR: 2386 { 2387 PetscInt numPoints[2] = {6, 1}; 2388 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 2389 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 2390 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 2391 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 2392 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 2393 2394 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 2395 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2396 } 2397 break; 2398 case DM_POLYTOPE_QUAD_PRISM_TENSOR: 2399 { 2400 PetscInt numPoints[2] = {8, 1}; 2401 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 2402 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 2403 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 2404 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, 2405 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 2406 2407 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 2408 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2409 } 2410 break; 2411 case DM_POLYTOPE_PYRAMID: 2412 { 2413 PetscInt numPoints[2] = {5, 1}; 2414 PetscInt coneSize[6] = {5, 0, 0, 0, 0, 0}; 2415 PetscInt cones[5] = {1, 2, 3, 4, 5}; 2416 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 2417 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, 2418 0.0, 0.0, 1.0}; 2419 2420 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 2421 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2422 } 2423 break; 2424 default: SETERRQ1(PetscObjectComm((PetscObject) rdm), PETSC_ERR_ARG_WRONG, "Cannot create reference cell for cell type %s", DMPolytopeTypes[ct]); 2425 } 2426 { 2427 PetscInt Nv, v; 2428 2429 /* Must create the celltype label here so that we do not automatically try to compute the types */ 2430 ierr = DMCreateLabel(rdm, "celltype");CHKERRQ(ierr); 2431 ierr = DMPlexSetCellType(rdm, 0, ct);CHKERRQ(ierr); 2432 ierr = DMPlexGetChart(rdm, NULL, &Nv);CHKERRQ(ierr); 2433 for (v = 1; v < Nv; ++v) {ierr = DMPlexSetCellType(rdm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr);} 2434 } 2435 ierr = DMPlexInterpolateInPlace_Internal(rdm);CHKERRQ(ierr); 2436 ierr = PetscObjectSetName((PetscObject) rdm, DMPolytopeTypes[ct]);CHKERRQ(ierr); 2437 PetscFunctionReturn(0); 2438 } 2439 2440 /*@ 2441 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 2442 2443 Collective 2444 2445 Input Parameters: 2446 + comm - The communicator 2447 - ct - The cell type of the reference cell 2448 2449 Output Parameter: 2450 . refdm - The reference cell 2451 2452 Level: intermediate 2453 2454 .seealso: DMPlexCreateReferenceCell(), DMPlexCreateBoxMesh() 2455 @*/ 2456 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, DMPolytopeType ct, DM *refdm) 2457 { 2458 PetscErrorCode ierr; 2459 2460 PetscFunctionBegin; 2461 ierr = DMCreate(comm, refdm);CHKERRQ(ierr); 2462 ierr = DMSetType(*refdm, DMPLEX);CHKERRQ(ierr); 2463 ierr = DMPlexCreateReferenceCell_Internal(*refdm, ct);CHKERRQ(ierr); 2464 PetscFunctionReturn(0); 2465 } 2466 2467 static PetscErrorCode DMPlexCreateBoundaryLabel_Private(DM dm, const char name[]) 2468 { 2469 DM plex; 2470 DMLabel label; 2471 PetscBool hasLabel; 2472 PetscErrorCode ierr; 2473 2474 PetscFunctionBeginUser; 2475 ierr = DMHasLabel(dm, name, &hasLabel);CHKERRQ(ierr); 2476 if (hasLabel) PetscFunctionReturn(0); 2477 ierr = DMCreateLabel(dm, name);CHKERRQ(ierr); 2478 ierr = DMGetLabel(dm, name, &label);CHKERRQ(ierr); 2479 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 2480 ierr = DMPlexMarkBoundaryFaces(plex, 1, label);CHKERRQ(ierr); 2481 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2482 PetscFunctionReturn(0); 2483 } 2484 2485 const char * const DMPlexShapes[] = {"box", "box_surface", "ball", "sphere", "cylinder", "unknown", "DMPlexShape", "DM_SHAPE_", NULL}; 2486 2487 static PetscErrorCode DMPlexCreateFromOptions_Internal(PetscOptionItems *PetscOptionsObject, PetscBool *useCoordSpace, DM dm) 2488 { 2489 DMPlexShape shape = DM_SHAPE_BOX; 2490 DMPolytopeType cell = DM_POLYTOPE_TRIANGLE; 2491 PetscInt dim = 2; 2492 PetscBool simplex = PETSC_TRUE, interpolate = PETSC_TRUE, adjCone = PETSC_FALSE, adjClosure = PETSC_TRUE, refDomain = PETSC_FALSE; 2493 PetscBool flg, flg2, fflg, bdfflg; 2494 MPI_Comm comm; 2495 char filename[PETSC_MAX_PATH_LEN], bdFilename[PETSC_MAX_PATH_LEN]; 2496 PetscErrorCode ierr; 2497 2498 PetscFunctionBegin; 2499 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 2500 /* TODO Turn this into a registration interface */ 2501 ierr = PetscOptionsString("-dm_plex_filename", "File containing a mesh", "DMPlexCreateFromFile", filename, filename, sizeof(filename), &fflg);CHKERRQ(ierr); 2502 ierr = PetscOptionsString("-dm_plex_boundary_filename", "File containing a mesh boundary", "DMPlexCreateFromFile", bdFilename, bdFilename, sizeof(bdFilename), &bdfflg);CHKERRQ(ierr); 2503 ierr = PetscOptionsEnum("-dm_plex_cell", "Cell shape", "", DMPolytopeTypes, (PetscEnum) cell, (PetscEnum *) &cell, NULL);CHKERRQ(ierr); 2504 ierr = PetscOptionsBool("-dm_plex_reference_cell_domain", "Use a reference cell domain", "", refDomain, &refDomain, NULL);CHKERRQ(ierr); 2505 ierr = PetscOptionsEnum("-dm_plex_shape", "Shape for built-in mesh", "", DMPlexShapes, (PetscEnum) shape, (PetscEnum *) &shape, &flg);CHKERRQ(ierr); 2506 ierr = PetscOptionsBoundedInt("-dm_plex_dim", "Topological dimension of the mesh", "DMGetDimension", dim, &dim, &flg, 0);CHKERRQ(ierr); 2507 if ((dim < 0) || (dim > 3)) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Dimension %D should be in [1, 3]", dim); 2508 ierr = PetscOptionsBool("-dm_plex_simplex", "Mesh cell shape", "", simplex, &simplex, &flg);CHKERRQ(ierr); 2509 ierr = PetscOptionsBool("-dm_plex_interpolate", "Flag to create edges and faces automatically", "", interpolate, &interpolate, &flg);CHKERRQ(ierr); 2510 ierr = PetscOptionsBool("-dm_plex_adj_cone", "Set adjacency direction", "DMSetBasicAdjacency", adjCone, &adjCone, &flg);CHKERRQ(ierr); 2511 ierr = PetscOptionsBool("-dm_plex_adj_closure", "Set adjacency size", "DMSetBasicAdjacency", adjClosure, &adjClosure, &flg2);CHKERRQ(ierr); 2512 if (flg || flg2) {ierr = DMSetBasicAdjacency(dm, adjCone, adjClosure);CHKERRQ(ierr);} 2513 2514 switch (cell) { 2515 case DM_POLYTOPE_POINT: 2516 case DM_POLYTOPE_SEGMENT: 2517 case DM_POLYTOPE_POINT_PRISM_TENSOR: 2518 case DM_POLYTOPE_TRIANGLE: 2519 case DM_POLYTOPE_QUADRILATERAL: 2520 case DM_POLYTOPE_TETRAHEDRON: 2521 case DM_POLYTOPE_HEXAHEDRON: 2522 *useCoordSpace = PETSC_TRUE;break; 2523 default: *useCoordSpace = PETSC_FALSE;break; 2524 } 2525 2526 if (fflg) { 2527 DM dmnew; 2528 2529 ierr = DMPlexCreateFromFile(PetscObjectComm((PetscObject) dm), filename, interpolate, &dmnew);CHKERRQ(ierr); 2530 ierr = DMPlexReplace_Static(dm, &dmnew);CHKERRQ(ierr); 2531 } else if (refDomain) { 2532 ierr = DMPlexCreateReferenceCell_Internal(dm, cell);CHKERRQ(ierr); 2533 } else if (bdfflg) { 2534 DM bdm, dmnew; 2535 2536 ierr = DMPlexCreateFromFile(PetscObjectComm((PetscObject) dm), bdFilename, interpolate, &bdm);CHKERRQ(ierr); 2537 ierr = PetscObjectSetOptionsPrefix((PetscObject) bdm, "bd_");CHKERRQ(ierr); 2538 ierr = DMSetFromOptions(bdm);CHKERRQ(ierr); 2539 ierr = DMPlexGenerate(bdm, NULL, interpolate, &dmnew);CHKERRQ(ierr); 2540 ierr = DMDestroy(&bdm);CHKERRQ(ierr); 2541 ierr = DMPlexReplace_Static(dm, &dmnew);CHKERRQ(ierr); 2542 } else { 2543 ierr = PetscObjectSetName((PetscObject) dm, DMPlexShapes[shape]);CHKERRQ(ierr); 2544 switch (shape) { 2545 case DM_SHAPE_BOX: 2546 { 2547 PetscInt faces[3] = {0, 0, 0}; 2548 PetscReal lower[3] = {0, 0, 0}; 2549 PetscReal upper[3] = {1, 1, 1}; 2550 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 2551 PetscInt i, n; 2552 2553 n = dim; 2554 for (i = 0; i < dim; ++i) faces[i] = (dim == 1 ? 1 : 4-dim); 2555 ierr = PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg);CHKERRQ(ierr); 2556 n = 3; 2557 ierr = PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg);CHKERRQ(ierr); 2558 if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim); 2559 n = 3; 2560 ierr = PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg);CHKERRQ(ierr); 2561 if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim); 2562 n = 3; 2563 ierr = PetscOptionsEnumArray("-dm_plex_box_bd", "Boundary type for each dimension", "", DMBoundaryTypes, (PetscEnum *) bdt, &n, &flg);CHKERRQ(ierr); 2564 if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Box boundary types had %D values, should have been %D", n, dim); 2565 switch (cell) { 2566 case DM_POLYTOPE_TRI_PRISM_TENSOR: 2567 ierr = DMPlexCreateWedgeBoxMesh_Internal(dm, faces, lower, upper, bdt);CHKERRQ(ierr); 2568 if (!interpolate) { 2569 DM udm; 2570 2571 ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr); 2572 ierr = DMPlexReplace_Static(dm, &udm);CHKERRQ(ierr); 2573 } 2574 break; 2575 default: 2576 ierr = DMPlexCreateBoxMesh_Internal(dm, dim, simplex, faces, lower, upper, bdt, interpolate);CHKERRQ(ierr); 2577 break; 2578 } 2579 } 2580 break; 2581 case DM_SHAPE_BOX_SURFACE: 2582 { 2583 PetscInt faces[3] = {0, 0, 0}; 2584 PetscReal lower[3] = {0, 0, 0}; 2585 PetscReal upper[3] = {1, 1, 1}; 2586 PetscInt i, n; 2587 2588 n = dim+1; 2589 for (i = 0; i < dim+1; ++i) faces[i] = (dim+1 == 1 ? 1 : 4-(dim+1)); 2590 ierr = PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg);CHKERRQ(ierr); 2591 n = 3; 2592 ierr = PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg);CHKERRQ(ierr); 2593 if (flg && (n != dim+1)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim+1); 2594 n = 3; 2595 ierr = PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg);CHKERRQ(ierr); 2596 if (flg && (n != dim+1)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim+1); 2597 ierr = DMPlexCreateBoxSurfaceMesh_Internal(dm, dim+1, faces, lower, upper, interpolate);CHKERRQ(ierr); 2598 } 2599 break; 2600 case DM_SHAPE_SPHERE: 2601 { 2602 PetscReal R = 1.0; 2603 2604 ierr = PetscOptionsReal("-dm_plex_sphere_radius", "Radius of the sphere", "", R, &R, &flg);CHKERRQ(ierr); 2605 ierr = DMPlexCreateSphereMesh_Internal(dm, dim, simplex, R);CHKERRQ(ierr); 2606 } 2607 break; 2608 case DM_SHAPE_BALL: 2609 { 2610 PetscReal R = 1.0; 2611 2612 ierr = PetscOptionsReal("-dm_plex_ball_radius", "Radius of the ball", "", R, &R, &flg);CHKERRQ(ierr); 2613 ierr = DMPlexCreateBallMesh_Internal(dm, dim, R);CHKERRQ(ierr); 2614 } 2615 break; 2616 case DM_SHAPE_CYLINDER: 2617 { 2618 DMBoundaryType bdt = DM_BOUNDARY_NONE; 2619 PetscInt Nw = 6; 2620 2621 ierr = PetscOptionsEnum("-dm_plex_cylinder_bd", "Boundary type in the z direction", "", DMBoundaryTypes, (PetscEnum) bdt, (PetscEnum *) &bdt, NULL);CHKERRQ(ierr); 2622 ierr = PetscOptionsInt("-dm_plex_cylinder_num_wedges", "Number of wedges around the cylinder", "", Nw, &Nw, NULL);CHKERRQ(ierr); 2623 switch (cell) { 2624 case DM_POLYTOPE_TRI_PRISM_TENSOR: 2625 ierr = DMPlexCreateWedgeCylinderMesh_Internal(dm, Nw, interpolate);CHKERRQ(ierr); 2626 break; 2627 default: 2628 ierr = DMPlexCreateHexCylinderMesh_Internal(dm, bdt);CHKERRQ(ierr); 2629 break; 2630 } 2631 } 2632 break; 2633 default: SETERRQ1(comm, PETSC_ERR_SUP, "Domain shape %s is unsupported", DMPlexShapes[shape]); 2634 } 2635 } 2636 ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr); 2637 PetscFunctionReturn(0); 2638 } 2639 2640 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject, DM dm) 2641 { 2642 DM_Plex *mesh = (DM_Plex*) dm->data; 2643 PetscBool flg; 2644 char bdLabel[PETSC_MAX_PATH_LEN]; 2645 PetscErrorCode ierr; 2646 2647 PetscFunctionBegin; 2648 /* Handle viewing */ 2649 ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); 2650 ierr = PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL,0);CHKERRQ(ierr); 2651 ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL);CHKERRQ(ierr); 2652 ierr = PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL,0);CHKERRQ(ierr); 2653 ierr = DMMonitorSetFromOptions(dm, "-dm_plex_monitor_throughput", "Monitor the simulation throughput", "DMPlexMonitorThroughput", DMPlexMonitorThroughput, NULL, &flg);CHKERRQ(ierr); 2654 if (flg) {ierr = PetscLogDefaultBegin();CHKERRQ(ierr);} 2655 /* Labeling */ 2656 ierr = PetscOptionsString("-dm_plex_boundary_label", "Label to mark the mesh boundary", "", bdLabel, bdLabel, sizeof(bdLabel), &flg);CHKERRQ(ierr); 2657 if (flg) {ierr = DMPlexCreateBoundaryLabel_Private(dm, bdLabel);CHKERRQ(ierr);} 2658 /* Point Location */ 2659 ierr = PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL);CHKERRQ(ierr); 2660 /* Partitioning and distribution */ 2661 ierr = PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL);CHKERRQ(ierr); 2662 /* Generation and remeshing */ 2663 ierr = PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL);CHKERRQ(ierr); 2664 /* Projection behavior */ 2665 ierr = PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL,0);CHKERRQ(ierr); 2666 ierr = PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);CHKERRQ(ierr); 2667 /* Checking structure */ 2668 { 2669 PetscBool flg = PETSC_FALSE, flg2 = PETSC_FALSE, all = PETSC_FALSE; 2670 2671 ierr = PetscOptionsBool("-dm_plex_check_all", "Perform all checks", NULL, PETSC_FALSE, &all, &flg2);CHKERRQ(ierr); 2672 ierr = PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2673 if (all || (flg && flg2)) {ierr = DMPlexCheckSymmetry(dm);CHKERRQ(ierr);} 2674 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); 2675 if (all || (flg && flg2)) {ierr = DMPlexCheckSkeleton(dm, 0);CHKERRQ(ierr);} 2676 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); 2677 if (all || (flg && flg2)) {ierr = DMPlexCheckFaces(dm, 0);CHKERRQ(ierr);} 2678 ierr = PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2679 if (all || (flg && flg2)) {ierr = DMPlexCheckGeometry(dm);CHKERRQ(ierr);} 2680 ierr = PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2681 if (all || (flg && flg2)) {ierr = DMPlexCheckPointSF(dm);CHKERRQ(ierr);} 2682 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); 2683 if (all || (flg && flg2)) {ierr = DMPlexCheckInterfaceCones(dm);CHKERRQ(ierr);} 2684 ierr = PetscOptionsBool("-dm_plex_check_cell_shape", "Check cell shape", "DMPlexCheckCellShape", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2685 if (flg && flg2) {ierr = DMPlexCheckCellShape(dm, PETSC_TRUE, PETSC_DETERMINE);CHKERRQ(ierr);} 2686 } 2687 { 2688 PetscReal scale = 1.0; 2689 2690 ierr = PetscOptionsReal("-dm_plex_scale", "Scale factor for mesh coordinates", "DMPlexScale", scale, &scale, &flg);CHKERRQ(ierr); 2691 if (flg) { 2692 Vec coordinates, coordinatesLocal; 2693 2694 ierr = DMGetCoordinates(dm, &coordinates);CHKERRQ(ierr); 2695 ierr = DMGetCoordinatesLocal(dm, &coordinatesLocal);CHKERRQ(ierr); 2696 ierr = VecScale(coordinates, scale);CHKERRQ(ierr); 2697 ierr = VecScale(coordinatesLocal, scale);CHKERRQ(ierr); 2698 } 2699 } 2700 ierr = PetscPartitionerSetFromOptions(mesh->partitioner);CHKERRQ(ierr); 2701 PetscFunctionReturn(0); 2702 } 2703 2704 static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 2705 { 2706 PetscReal volume = -1.0; 2707 PetscInt prerefine = 0, refine = 0, r, coarsen = 0, overlap = 0, extLayers = 0, dim; 2708 PetscBool uniformOrig, created = PETSC_FALSE, uniform = PETSC_TRUE, distribute = PETSC_FALSE, interpolate = PETSC_TRUE, coordSpace = PETSC_TRUE, remap = PETSC_TRUE, ghostCells = PETSC_FALSE, isHierarchy, ignoreModel = PETSC_FALSE, flg; 2709 PetscErrorCode ierr; 2710 2711 PetscFunctionBegin; 2712 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 2713 ierr = PetscOptionsHead(PetscOptionsObject,"DMPlex Options");CHKERRQ(ierr); 2714 /* Handle automatic creation */ 2715 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2716 if (dim < 0) {ierr = DMPlexCreateFromOptions_Internal(PetscOptionsObject, &coordSpace, dm);CHKERRQ(ierr);created = PETSC_TRUE;} 2717 /* Handle interpolation before distribution */ 2718 ierr = PetscOptionsBool("-dm_plex_interpolate_pre", "Flag to interpolate mesh before distribution", "", interpolate, &interpolate, &flg);CHKERRQ(ierr); 2719 if (flg) { 2720 DMPlexInterpolatedFlag interpolated; 2721 2722 ierr = DMPlexIsInterpolated(dm, &interpolated);CHKERRQ(ierr); 2723 if (interpolated == DMPLEX_INTERPOLATED_FULL && !interpolate) { 2724 DM udm; 2725 2726 ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr); 2727 ierr = DMPlexReplace_Static(dm, &udm);CHKERRQ(ierr); 2728 } else if (interpolated != DMPLEX_INTERPOLATED_FULL && interpolate) { 2729 DM idm; 2730 2731 ierr = DMPlexInterpolate(dm, &idm);CHKERRQ(ierr); 2732 ierr = DMPlexReplace_Static(dm, &idm);CHKERRQ(ierr); 2733 } 2734 } 2735 /* Handle DMPlex refinement before distribution */ 2736 ierr = PetscOptionsBool("-dm_refine_ignore_model", "Flag to ignore the geometry model when refining", "DMCreate", ignoreModel, &ignoreModel, &flg);CHKERRQ(ierr); 2737 if (flg) {((DM_Plex *) dm->data)->ignoreModel = ignoreModel;} 2738 ierr = DMPlexGetRefinementUniform(dm, &uniformOrig);CHKERRQ(ierr); 2739 ierr = PetscOptionsBoundedInt("-dm_refine_pre", "The number of refinements before distribution", "DMCreate", prerefine, &prerefine, NULL,0);CHKERRQ(ierr); 2740 ierr = PetscOptionsBool("-dm_refine_remap_pre", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL);CHKERRQ(ierr); 2741 ierr = PetscOptionsBool("-dm_refine_uniform_pre", "Flag for uniform refinement before distribution", "DMCreate", uniform, &uniform, &flg);CHKERRQ(ierr); 2742 if (flg) {ierr = DMPlexSetRefinementUniform(dm, uniform);CHKERRQ(ierr);} 2743 ierr = PetscOptionsReal("-dm_refine_volume_limit_pre", "The maximum cell volume after refinement before distribution", "DMCreate", volume, &volume, &flg);CHKERRQ(ierr); 2744 if (flg) { 2745 ierr = DMPlexSetRefinementUniform(dm, PETSC_FALSE);CHKERRQ(ierr); 2746 ierr = DMPlexSetRefinementLimit(dm, volume);CHKERRQ(ierr); 2747 prerefine = PetscMax(prerefine, 1); 2748 } 2749 for (r = 0; r < prerefine; ++r) { 2750 DM rdm; 2751 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 2752 2753 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2754 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &rdm);CHKERRQ(ierr); 2755 ierr = DMPlexReplace_Static(dm, &rdm);CHKERRQ(ierr); 2756 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2757 if (coordFunc && remap) { 2758 ierr = DMPlexRemapGeometry(dm, 0.0, coordFunc);CHKERRQ(ierr); 2759 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 2760 } 2761 } 2762 ierr = DMPlexSetRefinementUniform(dm, uniformOrig);CHKERRQ(ierr); 2763 /* Handle DMPlex extrusion before distribution */ 2764 ierr = PetscOptionsBoundedInt("-dm_extrude", "The number of layers to extrude", "", extLayers, &extLayers, NULL, 0);CHKERRQ(ierr); 2765 if (extLayers) { 2766 DM edm; 2767 2768 ierr = DMExtrude(dm, extLayers, &edm);CHKERRQ(ierr); 2769 ierr = DMPlexReplace_Static(dm, &edm);CHKERRQ(ierr); 2770 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2771 extLayers = 0; 2772 } 2773 /* TODO Old-style extrusion which can be removed */ 2774 ierr = PetscOptionsBool("-dm_plex_interpolate", "Flag to create edges and faces automatically", "", interpolate, &interpolate, NULL);CHKERRQ(ierr); 2775 /* Handle DMPlex distribution */ 2776 ierr = PetscOptionsBool("-dm_distribute", "Flag to redistribute a mesh among processes", "DMCreate", distribute, &distribute, NULL);CHKERRQ(ierr); 2777 ierr = PetscOptionsBoundedInt("-dm_distribute_overlap", "The size of the overlap halo", "DMCreate", overlap, &overlap, NULL, 0);CHKERRQ(ierr); 2778 if (distribute) { 2779 DM pdm = NULL; 2780 PetscPartitioner part; 2781 2782 ierr = DMPlexGetPartitioner(dm, &part);CHKERRQ(ierr); 2783 ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr); 2784 ierr = DMPlexDistribute(dm, overlap, NULL, &pdm);CHKERRQ(ierr); 2785 if (pdm) { 2786 ierr = DMPlexReplace_Static(dm, &pdm);CHKERRQ(ierr); 2787 } 2788 } 2789 /* Create coordinate space */ 2790 if (created) { 2791 DM_Plex *mesh = (DM_Plex *) dm->data; 2792 PetscInt degree = 1; 2793 PetscBool periodic, flg; 2794 2795 ierr = PetscOptionsBool("-dm_coord_space", "Use an FEM space for coordinates", "", coordSpace, &coordSpace, &flg);CHKERRQ(ierr); 2796 ierr = PetscOptionsInt("-dm_coord_petscspace_degree", "FEM degree for coordinate space", "", degree, °ree, NULL);CHKERRQ(ierr); 2797 if (coordSpace) {ierr = DMPlexCreateCoordinateSpace(dm, degree, mesh->coordFunc);CHKERRQ(ierr);} 2798 if (flg && !coordSpace) { 2799 DM cdm; 2800 PetscDS cds; 2801 PetscObject obj; 2802 PetscClassId id; 2803 2804 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 2805 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 2806 ierr = PetscDSGetDiscretization(cds, 0, &obj);CHKERRQ(ierr); 2807 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 2808 if (id == PETSCFE_CLASSID) { 2809 PetscContainer dummy; 2810 2811 ierr = PetscContainerCreate(PETSC_COMM_SELF, &dummy);CHKERRQ(ierr); 2812 ierr = PetscObjectSetName((PetscObject) dummy, "coordinates");CHKERRQ(ierr); 2813 ierr = DMSetField(cdm, 0, NULL, (PetscObject) dummy);CHKERRQ(ierr); 2814 ierr = PetscContainerDestroy(&dummy);CHKERRQ(ierr); 2815 ierr = DMClearDS(cdm);CHKERRQ(ierr); 2816 } 2817 mesh->coordFunc = NULL; 2818 } 2819 ierr = DMLocalizeCoordinates(dm);CHKERRQ(ierr); 2820 ierr = DMGetPeriodicity(dm, &periodic, NULL, NULL, NULL);CHKERRQ(ierr); 2821 if (periodic) {ierr = DMSetPeriodicity(dm, PETSC_TRUE, NULL, NULL, NULL);CHKERRQ(ierr);} 2822 } 2823 /* Handle DMPlex refinement */ 2824 remap = PETSC_TRUE; 2825 ierr = PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL,0);CHKERRQ(ierr); 2826 ierr = PetscOptionsBool("-dm_refine_remap", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL);CHKERRQ(ierr); 2827 ierr = PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy,0);CHKERRQ(ierr); 2828 if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 2829 if (refine && isHierarchy) { 2830 DM *dms, coarseDM; 2831 2832 ierr = DMGetCoarseDM(dm, &coarseDM);CHKERRQ(ierr); 2833 ierr = PetscObjectReference((PetscObject)coarseDM);CHKERRQ(ierr); 2834 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 2835 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 2836 /* Total hack since we do not pass in a pointer */ 2837 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 2838 if (refine == 1) { 2839 ierr = DMSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 2840 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2841 } else { 2842 ierr = DMSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 2843 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2844 ierr = DMSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 2845 ierr = DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);CHKERRQ(ierr); 2846 } 2847 ierr = DMSetCoarseDM(dms[refine-1], coarseDM);CHKERRQ(ierr); 2848 ierr = PetscObjectDereference((PetscObject)coarseDM);CHKERRQ(ierr); 2849 /* Free DMs */ 2850 for (r = 0; r < refine; ++r) { 2851 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2852 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2853 } 2854 ierr = PetscFree(dms);CHKERRQ(ierr); 2855 } else { 2856 for (r = 0; r < refine; ++r) { 2857 DM rdm; 2858 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 2859 2860 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2861 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &rdm);CHKERRQ(ierr); 2862 /* Total hack since we do not pass in a pointer */ 2863 ierr = DMPlexReplace_Static(dm, &rdm);CHKERRQ(ierr); 2864 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2865 if (coordFunc && remap) { 2866 ierr = DMPlexRemapGeometry(dm, 0.0, coordFunc);CHKERRQ(ierr); 2867 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 2868 } 2869 } 2870 } 2871 /* Handle DMPlex coarsening */ 2872 ierr = PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL,0);CHKERRQ(ierr); 2873 ierr = PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy,0);CHKERRQ(ierr); 2874 if (coarsen && isHierarchy) { 2875 DM *dms; 2876 2877 ierr = PetscMalloc1(coarsen, &dms);CHKERRQ(ierr); 2878 ierr = DMCoarsenHierarchy(dm, coarsen, dms);CHKERRQ(ierr); 2879 /* Free DMs */ 2880 for (r = 0; r < coarsen; ++r) { 2881 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2882 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2883 } 2884 ierr = PetscFree(dms);CHKERRQ(ierr); 2885 } else { 2886 for (r = 0; r < coarsen; ++r) { 2887 DM cdm; 2888 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 2889 2890 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2891 ierr = DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &cdm);CHKERRQ(ierr); 2892 /* Total hack since we do not pass in a pointer */ 2893 ierr = DMPlexReplace_Static(dm, &cdm);CHKERRQ(ierr); 2894 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2895 if (coordFunc) { 2896 ierr = DMPlexRemapGeometry(dm, 0.0, coordFunc);CHKERRQ(ierr); 2897 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 2898 } 2899 } 2900 } 2901 /* Handle ghost cells */ 2902 ierr = PetscOptionsBool("-dm_plex_create_fv_ghost_cells", "Flag to create finite volume ghost cells on the boundary", "DMCreate", ghostCells, &ghostCells, NULL);CHKERRQ(ierr); 2903 if (ghostCells) { 2904 DM gdm; 2905 char lname[PETSC_MAX_PATH_LEN]; 2906 2907 lname[0] = '\0'; 2908 ierr = PetscOptionsString("-dm_plex_fv_ghost_cells_label", "Label name for ghost cells boundary", "DMCreate", lname, lname, sizeof(lname), &flg);CHKERRQ(ierr); 2909 ierr = DMPlexConstructGhostCells(dm, flg ? lname : NULL, NULL, &gdm);CHKERRQ(ierr); 2910 ierr = DMPlexReplace_Static(dm, &gdm);CHKERRQ(ierr); 2911 } 2912 /* Handle */ 2913 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2914 ierr = PetscOptionsTail();CHKERRQ(ierr); 2915 PetscFunctionReturn(0); 2916 } 2917 2918 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 2919 { 2920 PetscErrorCode ierr; 2921 2922 PetscFunctionBegin; 2923 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2924 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 2925 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 2926 ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); 2927 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 2928 ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); 2929 PetscFunctionReturn(0); 2930 } 2931 2932 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 2933 { 2934 PetscErrorCode ierr; 2935 2936 PetscFunctionBegin; 2937 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2938 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 2939 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 2940 PetscFunctionReturn(0); 2941 } 2942 2943 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 2944 { 2945 PetscInt depth, d; 2946 PetscErrorCode ierr; 2947 2948 PetscFunctionBegin; 2949 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2950 if (depth == 1) { 2951 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 2952 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 2953 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 2954 else {*pStart = 0; *pEnd = 0;} 2955 } else { 2956 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 2957 } 2958 PetscFunctionReturn(0); 2959 } 2960 2961 static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 2962 { 2963 PetscSF sf; 2964 PetscInt niranks, njranks, n; 2965 const PetscMPIInt *iranks, *jranks; 2966 DM_Plex *data = (DM_Plex*) dm->data; 2967 PetscErrorCode ierr; 2968 2969 PetscFunctionBegin; 2970 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 2971 if (!data->neighbors) { 2972 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 2973 ierr = PetscSFGetRootRanks(sf, &njranks, &jranks, NULL, NULL, NULL);CHKERRQ(ierr); 2974 ierr = PetscSFGetLeafRanks(sf, &niranks, &iranks, NULL, NULL);CHKERRQ(ierr); 2975 ierr = PetscMalloc1(njranks + niranks + 1, &data->neighbors);CHKERRQ(ierr); 2976 ierr = PetscArraycpy(data->neighbors + 1, jranks, njranks);CHKERRQ(ierr); 2977 ierr = PetscArraycpy(data->neighbors + njranks + 1, iranks, niranks);CHKERRQ(ierr); 2978 n = njranks + niranks; 2979 ierr = PetscSortRemoveDupsMPIInt(&n, data->neighbors + 1);CHKERRQ(ierr); 2980 /* The following cast should never fail: can't have more neighbors than PETSC_MPI_INT_MAX */ 2981 ierr = PetscMPIIntCast(n, data->neighbors);CHKERRQ(ierr); 2982 } 2983 if (nranks) *nranks = data->neighbors[0]; 2984 if (ranks) { 2985 if (data->neighbors[0]) *ranks = data->neighbors + 1; 2986 else *ranks = NULL; 2987 } 2988 PetscFunctionReturn(0); 2989 } 2990 2991 PETSC_INTERN PetscErrorCode DMInterpolateSolution_Plex(DM, DM, Mat, Vec, Vec); 2992 2993 static PetscErrorCode DMInitialize_Plex(DM dm) 2994 { 2995 PetscErrorCode ierr; 2996 2997 PetscFunctionBegin; 2998 dm->ops->view = DMView_Plex; 2999 dm->ops->load = DMLoad_Plex; 3000 dm->ops->setfromoptions = DMSetFromOptions_Plex; 3001 dm->ops->clone = DMClone_Plex; 3002 dm->ops->setup = DMSetUp_Plex; 3003 dm->ops->createlocalsection = DMCreateLocalSection_Plex; 3004 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 3005 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 3006 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 3007 dm->ops->getlocaltoglobalmapping = NULL; 3008 dm->ops->createfieldis = NULL; 3009 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 3010 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 3011 dm->ops->getcoloring = NULL; 3012 dm->ops->creatematrix = DMCreateMatrix_Plex; 3013 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 3014 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 3015 dm->ops->createinjection = DMCreateInjection_Plex; 3016 dm->ops->refine = DMRefine_Plex; 3017 dm->ops->coarsen = DMCoarsen_Plex; 3018 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 3019 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 3020 dm->ops->adaptlabel = DMAdaptLabel_Plex; 3021 dm->ops->adaptmetric = DMAdaptMetric_Plex; 3022 dm->ops->extrude = DMExtrude_Plex; 3023 dm->ops->globaltolocalbegin = NULL; 3024 dm->ops->globaltolocalend = NULL; 3025 dm->ops->localtoglobalbegin = NULL; 3026 dm->ops->localtoglobalend = NULL; 3027 dm->ops->destroy = DMDestroy_Plex; 3028 dm->ops->createsubdm = DMCreateSubDM_Plex; 3029 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 3030 dm->ops->getdimpoints = DMGetDimPoints_Plex; 3031 dm->ops->locatepoints = DMLocatePoints_Plex; 3032 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 3033 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 3034 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 3035 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 3036 dm->ops->projectbdfieldlabellocal = DMProjectBdFieldLabelLocal_Plex; 3037 dm->ops->computel2diff = DMComputeL2Diff_Plex; 3038 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 3039 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 3040 dm->ops->getneighbors = DMGetNeighbors_Plex; 3041 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);CHKERRQ(ierr); 3042 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertTimeDerviativeBoundaryValues_C",DMPlexInsertTimeDerivativeBoundaryValues_Plex);CHKERRQ(ierr); 3043 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);CHKERRQ(ierr); 3044 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C",DMCreateNeumannOverlap_Plex);CHKERRQ(ierr); 3045 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex);CHKERRQ(ierr); 3046 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMInterpolateSolution_C",DMInterpolateSolution_Plex);CHKERRQ(ierr); 3047 PetscFunctionReturn(0); 3048 } 3049 3050 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 3051 { 3052 DM_Plex *mesh = (DM_Plex *) dm->data; 3053 PetscErrorCode ierr; 3054 3055 PetscFunctionBegin; 3056 mesh->refct++; 3057 (*newdm)->data = mesh; 3058 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 3059 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 3060 PetscFunctionReturn(0); 3061 } 3062 3063 /*MC 3064 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 3065 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 3066 specified by a PetscSection object. Ownership in the global representation is determined by 3067 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 3068 3069 Options Database Keys: 3070 + -dm_refine_pre - Refine mesh before distribution 3071 + -dm_refine_uniform_pre - Choose uniform or generator-based refinement 3072 + -dm_refine_volume_limit_pre - Cell volume limit after pre-refinement using generator 3073 . -dm_distribute - Distribute mesh across processes 3074 . -dm_distribute_overlap - Number of cells to overlap for distribution 3075 . -dm_refine - Refine mesh after distribution 3076 . -dm_plex_hash_location - Use grid hashing for point location 3077 . -dm_plex_hash_box_faces <n,m,p> - The number of divisions in each direction of the grid hash 3078 . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes 3079 . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing 3080 . -dm_plex_max_projection_height - Maxmimum mesh point height used to project locally 3081 . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement 3082 . -dm_plex_check_all - Perform all shecks below 3083 . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric 3084 . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices 3085 . -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 3086 . -dm_plex_check_geometry - Check that cells have positive volume 3087 . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ 3088 . -dm_plex_view_scale <num> - Scale the TikZ 3089 - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices 3090 3091 Level: intermediate 3092 3093 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 3094 M*/ 3095 3096 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 3097 { 3098 DM_Plex *mesh; 3099 PetscInt unit; 3100 PetscErrorCode ierr; 3101 3102 PetscFunctionBegin; 3103 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3104 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 3105 dm->data = mesh; 3106 3107 mesh->refct = 1; 3108 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 3109 mesh->maxConeSize = 0; 3110 mesh->cones = NULL; 3111 mesh->coneOrientations = NULL; 3112 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 3113 mesh->maxSupportSize = 0; 3114 mesh->supports = NULL; 3115 mesh->refinementUniform = PETSC_TRUE; 3116 mesh->refinementLimit = -1.0; 3117 mesh->interpolated = DMPLEX_INTERPOLATED_INVALID; 3118 mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID; 3119 3120 mesh->facesTmp = NULL; 3121 3122 mesh->tetgenOpts = NULL; 3123 mesh->triangleOpts = NULL; 3124 ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); 3125 mesh->remeshBd = PETSC_FALSE; 3126 3127 mesh->subpointMap = NULL; 3128 3129 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 3130 3131 mesh->regularRefinement = PETSC_FALSE; 3132 mesh->depthState = -1; 3133 mesh->celltypeState = -1; 3134 mesh->globalVertexNumbers = NULL; 3135 mesh->globalCellNumbers = NULL; 3136 mesh->anchorSection = NULL; 3137 mesh->anchorIS = NULL; 3138 mesh->createanchors = NULL; 3139 mesh->computeanchormatrix = NULL; 3140 mesh->parentSection = NULL; 3141 mesh->parents = NULL; 3142 mesh->childIDs = NULL; 3143 mesh->childSection = NULL; 3144 mesh->children = NULL; 3145 mesh->referenceTree = NULL; 3146 mesh->getchildsymmetry = NULL; 3147 mesh->vtkCellHeight = 0; 3148 mesh->useAnchors = PETSC_FALSE; 3149 3150 mesh->maxProjectionHeight = 0; 3151 3152 mesh->neighbors = NULL; 3153 3154 mesh->printSetValues = PETSC_FALSE; 3155 mesh->printFEM = 0; 3156 mesh->printTol = 1.0e-10; 3157 3158 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 3159 PetscFunctionReturn(0); 3160 } 3161 3162 /*@ 3163 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 3164 3165 Collective 3166 3167 Input Parameter: 3168 . comm - The communicator for the DMPlex object 3169 3170 Output Parameter: 3171 . mesh - The DMPlex object 3172 3173 Level: beginner 3174 3175 @*/ 3176 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 3177 { 3178 PetscErrorCode ierr; 3179 3180 PetscFunctionBegin; 3181 PetscValidPointer(mesh,2); 3182 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 3183 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 3184 PetscFunctionReturn(0); 3185 } 3186 3187 /*@C 3188 DMPlexBuildFromCellListParallel - Build distributed DMPLEX topology from a list of vertices for each cell (common mesh generator output) 3189 3190 Input Parameters: 3191 + dm - The DM 3192 . numCells - The number of cells owned by this process 3193 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 3194 . NVertices - The global number of vertices, or PETSC_DECIDE 3195 . numCorners - The number of vertices for each cell 3196 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 3197 3198 Output Parameter: 3199 . vertexSF - (Optional) SF describing complete vertex ownership 3200 3201 Notes: 3202 Two triangles sharing a face 3203 $ 3204 $ 2 3205 $ / | \ 3206 $ / | \ 3207 $ / | \ 3208 $ 0 0 | 1 3 3209 $ \ | / 3210 $ \ | / 3211 $ \ | / 3212 $ 1 3213 would have input 3214 $ numCells = 2, numVertices = 4 3215 $ cells = [0 1 2 1 3 2] 3216 $ 3217 which would result in the DMPlex 3218 $ 3219 $ 4 3220 $ / | \ 3221 $ / | \ 3222 $ / | \ 3223 $ 2 0 | 1 5 3224 $ \ | / 3225 $ \ | / 3226 $ \ | / 3227 $ 3 3228 3229 Vertices are implicitly numbered consecutively 0,...,NVertices. 3230 Each rank owns a chunk of numVertices consecutive vertices. 3231 If numVertices is PETSC_DECIDE, PETSc will distribute them as evenly as possible using PetscLayout. 3232 If both NVertices and numVertices are PETSC_DECIDE, NVertices is computed by PETSc as the maximum vertex index in cells + 1. 3233 If only NVertices is PETSC_DECIDE, it is computed as the sum of numVertices over all ranks. 3234 3235 The cell distribution is arbitrary non-overlapping, independent of the vertex distribution. 3236 3237 Not currently supported in Fortran. 3238 3239 Level: advanced 3240 3241 .seealso: DMPlexBuildFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildCoordinatesFromCellListParallel() 3242 @*/ 3243 PetscErrorCode DMPlexBuildFromCellListParallel(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, const PetscInt cells[], PetscSF *vertexSF) 3244 { 3245 PetscSF sfPoint; 3246 PetscLayout layout; 3247 PetscInt numVerticesAdj, *verticesAdj, *cones, c, p, dim; 3248 PetscMPIInt rank, size; 3249 PetscErrorCode ierr; 3250 3251 PetscFunctionBegin; 3252 PetscValidLogicalCollectiveInt(dm,NVertices,4); 3253 ierr = PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3254 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 3255 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRMPI(ierr); 3256 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3257 /* Get/check global number of vertices */ 3258 { 3259 PetscInt NVerticesInCells, i; 3260 const PetscInt len = numCells * numCorners; 3261 3262 /* NVerticesInCells = max(cells) + 1 */ 3263 NVerticesInCells = PETSC_MIN_INT; 3264 for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 3265 ++NVerticesInCells; 3266 ierr = MPI_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject) dm));CHKERRMPI(ierr); 3267 3268 if (numVertices == PETSC_DECIDE && NVertices == PETSC_DECIDE) NVertices = NVerticesInCells; 3269 else if (NVertices != PETSC_DECIDE && NVertices < NVerticesInCells) SETERRQ2(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); 3270 } 3271 /* Count locally unique vertices */ 3272 { 3273 PetscHSetI vhash; 3274 PetscInt off = 0; 3275 3276 ierr = PetscHSetICreate(&vhash);CHKERRQ(ierr); 3277 for (c = 0; c < numCells; ++c) { 3278 for (p = 0; p < numCorners; ++p) { 3279 ierr = PetscHSetIAdd(vhash, cells[c*numCorners+p]);CHKERRQ(ierr); 3280 } 3281 } 3282 ierr = PetscHSetIGetSize(vhash, &numVerticesAdj);CHKERRQ(ierr); 3283 ierr = PetscMalloc1(numVerticesAdj, &verticesAdj);CHKERRQ(ierr); 3284 ierr = PetscHSetIGetElems(vhash, &off, verticesAdj);CHKERRQ(ierr); 3285 ierr = PetscHSetIDestroy(&vhash);CHKERRQ(ierr); 3286 if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj); 3287 } 3288 ierr = PetscSortInt(numVerticesAdj, verticesAdj);CHKERRQ(ierr); 3289 /* Create cones */ 3290 ierr = DMPlexSetChart(dm, 0, numCells+numVerticesAdj);CHKERRQ(ierr); 3291 for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);} 3292 ierr = DMSetUp(dm);CHKERRQ(ierr); 3293 ierr = DMPlexGetCones(dm,&cones);CHKERRQ(ierr); 3294 for (c = 0; c < numCells; ++c) { 3295 for (p = 0; p < numCorners; ++p) { 3296 const PetscInt gv = cells[c*numCorners+p]; 3297 PetscInt lv; 3298 3299 /* Positions within verticesAdj form 0-based local vertex numbering; 3300 we need to shift it by numCells to get correct DAG points (cells go first) */ 3301 ierr = PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);CHKERRQ(ierr); 3302 if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv); 3303 cones[c*numCorners+p] = lv+numCells; 3304 } 3305 } 3306 /* Build point sf */ 3307 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &layout);CHKERRQ(ierr); 3308 ierr = PetscLayoutSetSize(layout, NVertices);CHKERRQ(ierr); 3309 ierr = PetscLayoutSetLocalSize(layout, numVertices);CHKERRQ(ierr); 3310 ierr = PetscLayoutSetBlockSize(layout, 1);CHKERRQ(ierr); 3311 ierr = PetscSFCreateByMatchingIndices(layout, numVerticesAdj, verticesAdj, NULL, numCells, numVerticesAdj, verticesAdj, NULL, numCells, vertexSF, &sfPoint);CHKERRQ(ierr); 3312 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 3313 ierr = PetscFree(verticesAdj);CHKERRQ(ierr); 3314 ierr = PetscObjectSetName((PetscObject) sfPoint, "point SF");CHKERRQ(ierr); 3315 if (dm->sf) { 3316 const char *prefix; 3317 3318 ierr = PetscObjectGetOptionsPrefix((PetscObject)dm->sf, &prefix);CHKERRQ(ierr); 3319 ierr = PetscObjectSetOptionsPrefix((PetscObject)sfPoint, prefix);CHKERRQ(ierr); 3320 } 3321 ierr = DMSetPointSF(dm, sfPoint);CHKERRQ(ierr); 3322 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 3323 if (vertexSF) {ierr = PetscObjectSetName((PetscObject)(*vertexSF), "Vertex Ownership SF");CHKERRQ(ierr);} 3324 /* Fill in the rest of the topology structure */ 3325 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3326 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3327 ierr = PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3328 PetscFunctionReturn(0); 3329 } 3330 3331 /*@C 3332 DMPlexBuildCoordinatesFromCellListParallel - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output) 3333 3334 Input Parameters: 3335 + dm - The DM 3336 . spaceDim - The spatial dimension used for coordinates 3337 . sfVert - SF describing complete vertex ownership 3338 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3339 3340 Level: advanced 3341 3342 Notes: 3343 Not currently supported in Fortran. 3344 3345 .seealso: DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellListParallel() 3346 @*/ 3347 PetscErrorCode DMPlexBuildCoordinatesFromCellListParallel(DM dm, PetscInt spaceDim, PetscSF sfVert, const PetscReal vertexCoords[]) 3348 { 3349 PetscSection coordSection; 3350 Vec coordinates; 3351 PetscScalar *coords; 3352 PetscInt numVertices, numVerticesAdj, coordSize, v, vStart, vEnd; 3353 PetscErrorCode ierr; 3354 3355 PetscFunctionBegin; 3356 ierr = PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3357 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 3358 if (vStart < 0 || vEnd < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 3359 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 3360 ierr = PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);CHKERRQ(ierr); 3361 if (vEnd - vStart != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Supplied sfVert has wrong number of leaves = %D != %D = vEnd - vStart",numVerticesAdj,vEnd - vStart); 3362 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3363 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3364 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 3365 ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr); 3366 for (v = vStart; v < vEnd; ++v) { 3367 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 3368 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 3369 } 3370 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3371 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3372 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 3373 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 3374 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3375 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3376 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 3377 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3378 { 3379 MPI_Datatype coordtype; 3380 3381 /* Need a temp buffer for coords if we have complex/single */ 3382 ierr = MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);CHKERRMPI(ierr); 3383 ierr = MPI_Type_commit(&coordtype);CHKERRMPI(ierr); 3384 #if defined(PETSC_USE_COMPLEX) 3385 { 3386 PetscScalar *svertexCoords; 3387 PetscInt i; 3388 ierr = PetscMalloc1(numVertices*spaceDim,&svertexCoords);CHKERRQ(ierr); 3389 for (i=0; i<numVertices*spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 3390 ierr = PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 3391 ierr = PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 3392 ierr = PetscFree(svertexCoords);CHKERRQ(ierr); 3393 } 3394 #else 3395 ierr = PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 3396 ierr = PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 3397 #endif 3398 ierr = MPI_Type_free(&coordtype);CHKERRMPI(ierr); 3399 } 3400 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3401 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3402 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3403 ierr = PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3404 PetscFunctionReturn(0); 3405 } 3406 3407 /*@ 3408 DMPlexCreateFromCellListParallelPetsc - Create distributed DMPLEX from a list of vertices for each cell (common mesh generator output) 3409 3410 Input Parameters: 3411 + comm - The communicator 3412 . dim - The topological dimension of the mesh 3413 . numCells - The number of cells owned by this process 3414 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 3415 . NVertices - The global number of vertices, or PETSC_DECIDE 3416 . numCorners - The number of vertices for each cell 3417 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 3418 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 3419 . spaceDim - The spatial dimension used for coordinates 3420 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3421 3422 Output Parameters: 3423 + dm - The DM 3424 - vertexSF - (Optional) SF describing complete vertex ownership 3425 3426 Notes: 3427 This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), 3428 DMPlexBuildFromCellListParallel(), DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellListParallel() 3429 3430 See DMPlexBuildFromCellListParallel() for an example and details about the topology-related parameters. 3431 See DMPlexBuildCoordinatesFromCellListParallel() for details about the geometry-related parameters. 3432 3433 Level: intermediate 3434 3435 .seealso: DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromDAG(), DMPlexCreate() 3436 @*/ 3437 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, DM *dm) 3438 { 3439 PetscSF sfVert; 3440 PetscErrorCode ierr; 3441 3442 PetscFunctionBegin; 3443 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3444 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3445 PetscValidLogicalCollectiveInt(*dm, dim, 2); 3446 PetscValidLogicalCollectiveInt(*dm, spaceDim, 9); 3447 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3448 ierr = DMPlexBuildFromCellListParallel(*dm, numCells, numVertices, NVertices, numCorners, cells, &sfVert);CHKERRQ(ierr); 3449 if (interpolate) { 3450 DM idm; 3451 3452 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3453 ierr = DMDestroy(dm);CHKERRQ(ierr); 3454 *dm = idm; 3455 } 3456 ierr = DMPlexBuildCoordinatesFromCellListParallel(*dm, spaceDim, sfVert, vertexCoords);CHKERRQ(ierr); 3457 if (vertexSF) *vertexSF = sfVert; 3458 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 3459 PetscFunctionReturn(0); 3460 } 3461 3462 /*@ 3463 DMPlexCreateFromCellListParallel - Deprecated, use DMPlexCreateFromCellListParallelPetsc() 3464 3465 Level: deprecated 3466 3467 .seealso: DMPlexCreateFromCellListParallelPetsc() 3468 @*/ 3469 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) 3470 { 3471 PetscErrorCode ierr; 3472 PetscInt i; 3473 PetscInt *pintCells; 3474 3475 PetscFunctionBegin; 3476 if (sizeof(int) > sizeof(PetscInt)) SETERRQ2(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)); 3477 if (sizeof(int) == sizeof(PetscInt)) { 3478 pintCells = (PetscInt *) cells; 3479 } else { 3480 ierr = PetscMalloc1(numCells*numCorners, &pintCells);CHKERRQ(ierr); 3481 for (i = 0; i < numCells*numCorners; i++) { 3482 pintCells[i] = (PetscInt) cells[i]; 3483 } 3484 } 3485 ierr = DMPlexCreateFromCellListParallelPetsc(comm, dim, numCells, numVertices, PETSC_DECIDE, numCorners, interpolate, pintCells, spaceDim, vertexCoords, vertexSF, dm);CHKERRQ(ierr); 3486 if (sizeof(int) != sizeof(PetscInt)) { 3487 ierr = PetscFree(pintCells);CHKERRQ(ierr); 3488 } 3489 PetscFunctionReturn(0); 3490 } 3491 3492 /*@C 3493 DMPlexBuildFromCellList - Build DMPLEX topology from a list of vertices for each cell (common mesh generator output) 3494 3495 Input Parameters: 3496 + dm - The DM 3497 . numCells - The number of cells owned by this process 3498 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 3499 . numCorners - The number of vertices for each cell 3500 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 3501 3502 Level: advanced 3503 3504 Notes: 3505 Two triangles sharing a face 3506 $ 3507 $ 2 3508 $ / | \ 3509 $ / | \ 3510 $ / | \ 3511 $ 0 0 | 1 3 3512 $ \ | / 3513 $ \ | / 3514 $ \ | / 3515 $ 1 3516 would have input 3517 $ numCells = 2, numVertices = 4 3518 $ cells = [0 1 2 1 3 2] 3519 $ 3520 which would result in the DMPlex 3521 $ 3522 $ 4 3523 $ / | \ 3524 $ / | \ 3525 $ / | \ 3526 $ 2 0 | 1 5 3527 $ \ | / 3528 $ \ | / 3529 $ \ | / 3530 $ 3 3531 3532 If numVertices is PETSC_DECIDE, it is computed by PETSc as the maximum vertex index in cells + 1. 3533 3534 Not currently supported in Fortran. 3535 3536 .seealso: DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListPetsc() 3537 @*/ 3538 PetscErrorCode DMPlexBuildFromCellList(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[]) 3539 { 3540 PetscInt *cones, c, p, dim; 3541 PetscErrorCode ierr; 3542 3543 PetscFunctionBegin; 3544 ierr = PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3545 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3546 /* Get/check global number of vertices */ 3547 { 3548 PetscInt NVerticesInCells, i; 3549 const PetscInt len = numCells * numCorners; 3550 3551 /* NVerticesInCells = max(cells) + 1 */ 3552 NVerticesInCells = PETSC_MIN_INT; 3553 for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 3554 ++NVerticesInCells; 3555 3556 if (numVertices == PETSC_DECIDE) numVertices = NVerticesInCells; 3557 else if (numVertices < NVerticesInCells) SETERRQ2(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); 3558 } 3559 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 3560 for (c = 0; c < numCells; ++c) { 3561 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 3562 } 3563 ierr = DMSetUp(dm);CHKERRQ(ierr); 3564 ierr = DMPlexGetCones(dm,&cones);CHKERRQ(ierr); 3565 for (c = 0; c < numCells; ++c) { 3566 for (p = 0; p < numCorners; ++p) { 3567 cones[c*numCorners+p] = cells[c*numCorners+p]+numCells; 3568 } 3569 } 3570 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3571 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3572 ierr = PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3573 PetscFunctionReturn(0); 3574 } 3575 3576 /*@C 3577 DMPlexBuildCoordinatesFromCellList - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output) 3578 3579 Input Parameters: 3580 + dm - The DM 3581 . spaceDim - The spatial dimension used for coordinates 3582 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3583 3584 Level: advanced 3585 3586 Notes: 3587 Not currently supported in Fortran. 3588 3589 .seealso: DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellList() 3590 @*/ 3591 PetscErrorCode DMPlexBuildCoordinatesFromCellList(DM dm, PetscInt spaceDim, const PetscReal vertexCoords[]) 3592 { 3593 PetscSection coordSection; 3594 Vec coordinates; 3595 DM cdm; 3596 PetscScalar *coords; 3597 PetscInt v, vStart, vEnd, d; 3598 PetscErrorCode ierr; 3599 3600 PetscFunctionBegin; 3601 ierr = PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3602 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 3603 if (vStart < 0 || vEnd < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 3604 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 3605 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3606 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3607 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 3608 ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr); 3609 for (v = vStart; v < vEnd; ++v) { 3610 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 3611 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 3612 } 3613 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3614 3615 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 3616 ierr = DMCreateLocalVector(cdm, &coordinates);CHKERRQ(ierr); 3617 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 3618 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3619 ierr = VecGetArrayWrite(coordinates, &coords);CHKERRQ(ierr); 3620 for (v = 0; v < vEnd-vStart; ++v) { 3621 for (d = 0; d < spaceDim; ++d) { 3622 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 3623 } 3624 } 3625 ierr = VecRestoreArrayWrite(coordinates, &coords);CHKERRQ(ierr); 3626 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3627 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3628 ierr = PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3629 PetscFunctionReturn(0); 3630 } 3631 3632 /*@ 3633 DMPlexCreateFromCellListPetsc - Create DMPLEX from a list of vertices for each cell (common mesh generator output), but only process 0 takes in the input 3634 3635 Collective on comm 3636 3637 Input Parameters: 3638 + comm - The communicator 3639 . dim - The topological dimension of the mesh 3640 . numCells - The number of cells, only on process 0 3641 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE, only on process 0 3642 . numCorners - The number of vertices for each cell, only on process 0 3643 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 3644 . cells - An array of numCells*numCorners numbers, the vertices for each cell, only on process 0 3645 . spaceDim - The spatial dimension used for coordinates 3646 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex, only on process 0 3647 3648 Output Parameter: 3649 . dm - The DM, which only has points on process 0 3650 3651 Notes: 3652 This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), DMPlexBuildFromCellList(), 3653 DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellList() 3654 3655 See DMPlexBuildFromCellList() for an example and details about the topology-related parameters. 3656 See DMPlexBuildCoordinatesFromCellList() for details about the geometry-related parameters. 3657 See DMPlexCreateFromCellListParallelPetsc() for parallel input 3658 3659 Level: intermediate 3660 3661 .seealso: DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellList(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate() 3662 @*/ 3663 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) 3664 { 3665 PetscMPIInt rank; 3666 PetscErrorCode ierr; 3667 3668 PetscFunctionBegin; 3669 if (!dim) SETERRQ(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."); 3670 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 3671 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3672 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3673 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3674 if (!rank) {ierr = DMPlexBuildFromCellList(*dm, numCells, numVertices, numCorners, cells);CHKERRQ(ierr);} 3675 else {ierr = DMPlexBuildFromCellList(*dm, 0, 0, 0, NULL);CHKERRQ(ierr);} 3676 if (interpolate) { 3677 DM idm; 3678 3679 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3680 ierr = DMDestroy(dm);CHKERRQ(ierr); 3681 *dm = idm; 3682 } 3683 if (!rank) {ierr = DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, vertexCoords);CHKERRQ(ierr);} 3684 else {ierr = DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, NULL);CHKERRQ(ierr);} 3685 PetscFunctionReturn(0); 3686 } 3687 3688 /*@ 3689 DMPlexCreateFromCellList - Deprecated, use DMPlexCreateFromCellListPetsc() 3690 3691 Level: deprecated 3692 3693 .seealso: DMPlexCreateFromCellListPetsc() 3694 @*/ 3695 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) 3696 { 3697 PetscErrorCode ierr; 3698 PetscInt i; 3699 PetscInt *pintCells; 3700 PetscReal *prealVC; 3701 3702 PetscFunctionBegin; 3703 if (sizeof(int) > sizeof(PetscInt)) SETERRQ2(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)); 3704 if (sizeof(int) == sizeof(PetscInt)) { 3705 pintCells = (PetscInt *) cells; 3706 } else { 3707 ierr = PetscMalloc1(numCells*numCorners, &pintCells);CHKERRQ(ierr); 3708 for (i = 0; i < numCells*numCorners; i++) { 3709 pintCells[i] = (PetscInt) cells[i]; 3710 } 3711 } 3712 if (sizeof(double) > sizeof(PetscReal)) SETERRQ2(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)); 3713 if (sizeof(double) == sizeof(PetscReal)) { 3714 prealVC = (PetscReal *) vertexCoords; 3715 } else { 3716 ierr = PetscMalloc1(numVertices*spaceDim, &prealVC);CHKERRQ(ierr); 3717 for (i = 0; i < numVertices*spaceDim; i++) { 3718 prealVC[i] = (PetscReal) vertexCoords[i]; 3719 } 3720 } 3721 ierr = DMPlexCreateFromCellListPetsc(comm, dim, numCells, numVertices, numCorners, interpolate, pintCells, spaceDim, prealVC, dm);CHKERRQ(ierr); 3722 if (sizeof(int) != sizeof(PetscInt)) { 3723 ierr = PetscFree(pintCells);CHKERRQ(ierr); 3724 } 3725 if (sizeof(double) != sizeof(PetscReal)) { 3726 ierr = PetscFree(prealVC);CHKERRQ(ierr); 3727 } 3728 PetscFunctionReturn(0); 3729 } 3730 3731 /*@ 3732 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 3733 3734 Input Parameters: 3735 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 3736 . depth - The depth of the DAG 3737 . numPoints - Array of size depth + 1 containing the number of points at each depth 3738 . coneSize - The cone size of each point 3739 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 3740 . coneOrientations - The orientation of each cone point 3741 - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim() 3742 3743 Output Parameter: 3744 . dm - The DM 3745 3746 Note: Two triangles sharing a face would have input 3747 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 3748 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 3749 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 3750 $ 3751 which would result in the DMPlex 3752 $ 3753 $ 4 3754 $ / | \ 3755 $ / | \ 3756 $ / | \ 3757 $ 2 0 | 1 5 3758 $ \ | / 3759 $ \ | / 3760 $ \ | / 3761 $ 3 3762 $ 3763 $ Notice that all points are numbered consecutively, unlike DMPlexCreateFromCellListPetsc() 3764 3765 Level: advanced 3766 3767 .seealso: DMPlexCreateFromCellListPetsc(), DMPlexCreate() 3768 @*/ 3769 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 3770 { 3771 Vec coordinates; 3772 PetscSection coordSection; 3773 PetscScalar *coords; 3774 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 3775 PetscErrorCode ierr; 3776 3777 PetscFunctionBegin; 3778 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3779 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 3780 if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %D cannot be less than intrinsic dimension %d",dimEmbed,dim); 3781 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 3782 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 3783 for (p = pStart; p < pEnd; ++p) { 3784 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 3785 if (firstVertex < 0 && !coneSize[p - pStart]) { 3786 firstVertex = p - pStart; 3787 } 3788 } 3789 if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %D vertices but could not find any", numPoints[0]); 3790 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 3791 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 3792 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 3793 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 3794 } 3795 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3796 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3797 /* Build coordinates */ 3798 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3799 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3800 ierr = PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);CHKERRQ(ierr); 3801 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 3802 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 3803 ierr = PetscSectionSetDof(coordSection, v, dimEmbed);CHKERRQ(ierr); 3804 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);CHKERRQ(ierr); 3805 } 3806 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3807 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3808 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3809 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3810 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3811 ierr = VecSetBlockSize(coordinates, dimEmbed);CHKERRQ(ierr); 3812 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 3813 if (vertexCoords) { 3814 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3815 for (v = 0; v < numPoints[0]; ++v) { 3816 PetscInt off; 3817 3818 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 3819 for (d = 0; d < dimEmbed; ++d) { 3820 coords[off+d] = vertexCoords[v*dimEmbed+d]; 3821 } 3822 } 3823 } 3824 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3825 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3826 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3827 PetscFunctionReturn(0); 3828 } 3829 3830 /*@C 3831 DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file. 3832 3833 + comm - The MPI communicator 3834 . filename - Name of the .dat file 3835 - interpolate - Create faces and edges in the mesh 3836 3837 Output Parameter: 3838 . dm - The DM object representing the mesh 3839 3840 Note: The format is the simplest possible: 3841 $ Ne 3842 $ v0 v1 ... vk 3843 $ Nv 3844 $ x y z marker 3845 3846 Level: beginner 3847 3848 .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate() 3849 @*/ 3850 PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3851 { 3852 DMLabel marker; 3853 PetscViewer viewer; 3854 Vec coordinates; 3855 PetscSection coordSection; 3856 PetscScalar *coords; 3857 char line[PETSC_MAX_PATH_LEN]; 3858 PetscInt dim = 3, cdim = 3, coordSize, v, c, d; 3859 PetscMPIInt rank; 3860 int snum, Nv, Nc; 3861 PetscErrorCode ierr; 3862 3863 PetscFunctionBegin; 3864 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 3865 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 3866 ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr); 3867 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 3868 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 3869 if (rank == 0) { 3870 ierr = PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);CHKERRQ(ierr); 3871 snum = sscanf(line, "%d %d", &Nc, &Nv); 3872 if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3873 } else { 3874 Nc = Nv = 0; 3875 } 3876 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3877 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3878 ierr = DMPlexSetChart(*dm, 0, Nc+Nv);CHKERRQ(ierr); 3879 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3880 ierr = DMSetCoordinateDim(*dm, cdim);CHKERRQ(ierr); 3881 /* Read topology */ 3882 if (rank == 0) { 3883 PetscInt cone[8], corners = 8; 3884 int vbuf[8], v; 3885 3886 for (c = 0; c < Nc; ++c) {ierr = DMPlexSetConeSize(*dm, c, corners);CHKERRQ(ierr);} 3887 ierr = DMSetUp(*dm);CHKERRQ(ierr); 3888 for (c = 0; c < Nc; ++c) { 3889 ierr = PetscViewerRead(viewer, line, corners, NULL, PETSC_STRING);CHKERRQ(ierr); 3890 snum = sscanf(line, "%d %d %d %d %d %d %d %d", &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5], &vbuf[6], &vbuf[7]); 3891 if (snum != corners) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3892 for (v = 0; v < corners; ++v) cone[v] = vbuf[v] + Nc; 3893 /* Hexahedra are inverted */ 3894 { 3895 PetscInt tmp = cone[1]; 3896 cone[1] = cone[3]; 3897 cone[3] = tmp; 3898 } 3899 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 3900 } 3901 } 3902 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 3903 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 3904 /* Read coordinates */ 3905 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 3906 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3907 ierr = PetscSectionSetFieldComponents(coordSection, 0, cdim);CHKERRQ(ierr); 3908 ierr = PetscSectionSetChart(coordSection, Nc, Nc + Nv);CHKERRQ(ierr); 3909 for (v = Nc; v < Nc+Nv; ++v) { 3910 ierr = PetscSectionSetDof(coordSection, v, cdim);CHKERRQ(ierr); 3911 ierr = PetscSectionSetFieldDof(coordSection, v, 0, cdim);CHKERRQ(ierr); 3912 } 3913 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3914 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3915 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3916 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3917 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3918 ierr = VecSetBlockSize(coordinates, cdim);CHKERRQ(ierr); 3919 ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr); 3920 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3921 if (rank == 0) { 3922 double x[3]; 3923 int val; 3924 3925 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 3926 ierr = DMGetLabel(*dm, "marker", &marker);CHKERRQ(ierr); 3927 for (v = 0; v < Nv; ++v) { 3928 ierr = PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);CHKERRQ(ierr); 3929 snum = sscanf(line, "%lg %lg %lg %d", &x[0], &x[1], &x[2], &val); 3930 if (snum != 4) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3931 for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d]; 3932 if (val) {ierr = DMLabelSetValue(marker, v+Nc, val);CHKERRQ(ierr);} 3933 } 3934 } 3935 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3936 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 3937 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3938 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 3939 if (interpolate) { 3940 DM idm; 3941 DMLabel bdlabel; 3942 3943 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3944 ierr = DMDestroy(dm);CHKERRQ(ierr); 3945 *dm = idm; 3946 3947 ierr = DMGetLabel(*dm, "marker", &bdlabel);CHKERRQ(ierr); 3948 ierr = DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 3949 ierr = DMPlexLabelComplete(*dm, bdlabel);CHKERRQ(ierr); 3950 } 3951 PetscFunctionReturn(0); 3952 } 3953 3954 /*@C 3955 DMPlexCreateFromFile - This takes a filename and produces a DM 3956 3957 Input Parameters: 3958 + comm - The communicator 3959 . filename - A file name 3960 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 3961 3962 Output Parameter: 3963 . dm - The DM 3964 3965 Options Database Keys: 3966 . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5 3967 3968 Use -dm_plex_create_ prefix to pass options to the internal PetscViewer, e.g. 3969 $ -dm_plex_create_viewer_hdf5_collective 3970 3971 Level: beginner 3972 3973 .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellListPetsc(), DMPlexCreate() 3974 @*/ 3975 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3976 { 3977 const char *extGmsh = ".msh"; 3978 const char *extGmsh2 = ".msh2"; 3979 const char *extGmsh4 = ".msh4"; 3980 const char *extCGNS = ".cgns"; 3981 const char *extExodus = ".exo"; 3982 const char *extGenesis = ".gen"; 3983 const char *extFluent = ".cas"; 3984 const char *extHDF5 = ".h5"; 3985 const char *extMed = ".med"; 3986 const char *extPLY = ".ply"; 3987 const char *extEGADSLite = ".egadslite"; 3988 const char *extEGADS = ".egads"; 3989 const char *extIGES = ".igs"; 3990 const char *extSTEP = ".stp"; 3991 const char *extCV = ".dat"; 3992 size_t len; 3993 PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isEGADSLite, isEGADS, isIGES, isSTEP, isCV; 3994 PetscMPIInt rank; 3995 PetscErrorCode ierr; 3996 3997 PetscFunctionBegin; 3998 PetscValidCharPointer(filename, 2); 3999 PetscValidPointer(dm, 4); 4000 ierr = DMInitializePackage();CHKERRQ(ierr); 4001 ierr = PetscLogEventBegin(DMPLEX_CreateFromFile,0,0,0,0);CHKERRQ(ierr); 4002 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 4003 ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); 4004 if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 4005 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);CHKERRQ(ierr); 4006 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh2, 5, &isGmsh2);CHKERRQ(ierr); 4007 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh4, 5, &isGmsh4);CHKERRQ(ierr); 4008 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);CHKERRQ(ierr); 4009 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);CHKERRQ(ierr); 4010 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);CHKERRQ(ierr); 4011 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);CHKERRQ(ierr); 4012 ierr = PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);CHKERRQ(ierr); 4013 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);CHKERRQ(ierr); 4014 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);CHKERRQ(ierr); 4015 ierr = PetscStrncmp(&filename[PetscMax(0,len-10)], extEGADSLite, 10, &isEGADSLite);CHKERRQ(ierr); 4016 ierr = PetscStrncmp(&filename[PetscMax(0,len-6)], extEGADS, 6, &isEGADS);CHKERRQ(ierr); 4017 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extIGES, 4, &isIGES);CHKERRQ(ierr); 4018 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extSTEP, 4, &isSTEP);CHKERRQ(ierr); 4019 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);CHKERRQ(ierr); 4020 if (isGmsh || isGmsh2 || isGmsh4) { 4021 ierr = DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4022 } else if (isCGNS) { 4023 ierr = DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4024 } else if (isExodus || isGenesis) { 4025 ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4026 } else if (isFluent) { 4027 ierr = DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4028 } else if (isHDF5) { 4029 PetscBool load_hdf5_xdmf = PETSC_FALSE; 4030 PetscViewer viewer; 4031 4032 /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */ 4033 ierr = PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf", 5, &load_hdf5_xdmf);CHKERRQ(ierr); 4034 ierr = PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);CHKERRQ(ierr); 4035 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 4036 ierr = PetscViewerSetType(viewer, PETSCVIEWERHDF5);CHKERRQ(ierr); 4037 ierr = PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_");CHKERRQ(ierr); 4038 ierr = PetscViewerSetFromOptions(viewer);CHKERRQ(ierr); 4039 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 4040 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 4041 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 4042 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 4043 if (load_hdf5_xdmf) {ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);CHKERRQ(ierr);} 4044 ierr = DMLoad(*dm, viewer);CHKERRQ(ierr); 4045 if (load_hdf5_xdmf) {ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);} 4046 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 4047 4048 if (interpolate) { 4049 DM idm; 4050 4051 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 4052 ierr = DMDestroy(dm);CHKERRQ(ierr); 4053 *dm = idm; 4054 } 4055 } else if (isMed) { 4056 ierr = DMPlexCreateMedFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4057 } else if (isPLY) { 4058 ierr = DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4059 } else if (isEGADSLite || isEGADS || isIGES || isSTEP) { 4060 if (isEGADSLite) {ierr = DMPlexCreateEGADSLiteFromFile(comm, filename, dm);CHKERRQ(ierr);} 4061 else {ierr = DMPlexCreateEGADSFromFile(comm, filename, dm);CHKERRQ(ierr);} 4062 if (!interpolate) { 4063 DM udm; 4064 4065 ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr); 4066 ierr = DMDestroy(dm);CHKERRQ(ierr); 4067 *dm = udm; 4068 } 4069 } else if (isCV) { 4070 ierr = DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4071 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 4072 ierr = PetscLogEventEnd(DMPLEX_CreateFromFile,0,0,0,0);CHKERRQ(ierr); 4073 PetscFunctionReturn(0); 4074 } 4075