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);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) { 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) { 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) numCells = segments; 698 if (!rank) 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) { 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 ? edges[0] : 0; 801 const PetscInt numYEdges = !rank ? edges[1] : 0; 802 const PetscInt numZEdges = !rank ? edges[2] : 0; 803 const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; 804 const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; 805 const PetscInt numZVertices = !rank ? (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] = {-4, 0, 0, -1, 0, -4}; /* ??? */ 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, -2, -2}; 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, -2, -2}; 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, -2, -2}; 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] = -2;} 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[], PetscBool orderHeight, PetscBool interpolate) 1273 { 1274 DM bdm, vol; 1275 PetscReal normal[3] = {0., 0., 1.}; 1276 PetscInt i; 1277 PetscErrorCode ierr; 1278 1279 PetscFunctionBegin; 1280 for (i = 0; i < 3; ++i) if (periodicity[i] != DM_BOUNDARY_NONE) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Periodicity not yet supported"); 1281 ierr = DMCreate(PetscObjectComm((PetscObject) dm), &bdm);CHKERRQ(ierr); 1282 ierr = DMSetType(bdm, DMPLEX);CHKERRQ(ierr); 1283 ierr = DMSetDimension(bdm, 2);CHKERRQ(ierr); 1284 ierr = DMPlexCreateBoxMesh_Simplex_Internal(bdm, 2, faces, lower, upper, periodicity, interpolate);CHKERRQ(ierr); 1285 ierr = DMPlexExtrude(bdm, faces[2], upper[2] - lower[2], orderHeight, normal, interpolate, &vol);CHKERRQ(ierr); 1286 ierr = DMDestroy(&bdm);CHKERRQ(ierr); 1287 ierr = DMPlexReplace_Static(dm, &vol);CHKERRQ(ierr); 1288 if (lower[2] != 0.0) { 1289 Vec v; 1290 PetscScalar *x; 1291 PetscInt cDim, n; 1292 1293 ierr = DMGetCoordinatesLocal(dm, &v);CHKERRQ(ierr); 1294 ierr = VecGetBlockSize(v, &cDim);CHKERRQ(ierr); 1295 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 1296 ierr = VecGetArray(v, &x);CHKERRQ(ierr); 1297 x += cDim; 1298 for (i = 0; i < n; i += cDim) x[i] += lower[2]; 1299 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 1300 ierr = DMSetCoordinatesLocal(dm, v);CHKERRQ(ierr); 1301 } 1302 PetscFunctionReturn(0); 1303 } 1304 1305 /*@ 1306 DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells. 1307 1308 Collective 1309 1310 Input Parameters: 1311 + comm - The communicator for the DM object 1312 . faces - Number of faces per dimension, or NULL for (1, 1, 1) 1313 . lower - The lower left corner, or NULL for (0, 0, 0) 1314 . upper - The upper right corner, or NULL for (1, 1, 1) 1315 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 1316 . orderHeight - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1317 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1318 1319 Output Parameter: 1320 . dm - The DM object 1321 1322 Level: beginner 1323 1324 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateWedgeCylinderMesh(), DMPlexExtrude(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1325 @*/ 1326 PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool orderHeight, PetscBool interpolate, DM *dm) 1327 { 1328 PetscInt fac[3] = {1, 1, 1}; 1329 PetscReal low[3] = {0, 0, 0}; 1330 PetscReal upp[3] = {1, 1, 1}; 1331 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1332 PetscErrorCode ierr; 1333 1334 PetscFunctionBegin; 1335 ierr = DMCreate(comm,dm);CHKERRQ(ierr); 1336 ierr = DMSetType(*dm,DMPLEX);CHKERRQ(ierr); 1337 ierr = DMPlexCreateWedgeBoxMesh_Internal(*dm, faces ? faces : fac, lower ? lower : low, upper ? upper : upp, periodicity ? periodicity : bdt, orderHeight, interpolate);CHKERRQ(ierr); 1338 PetscFunctionReturn(0); 1339 } 1340 1341 /*@C 1342 DMPlexExtrude - Creates a (d+1)-D mesh by extruding a d-D mesh in the normal direction using prismatic cells. 1343 1344 Collective on idm 1345 1346 Input Parameters: 1347 + idm - The mesh to be extruded 1348 . layers - The number of layers, or PETSC_DETERMINE to use the default 1349 . height - The total height of the extrusion, or PETSC_DETERMINE to use the default 1350 . orderHeight - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1351 . extNormal - The normal direction in which the mesh should be extruded, or NULL to extrude using the surface normal 1352 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1353 1354 Output Parameter: 1355 . dm - The DM object 1356 1357 Notes: 1358 The mesh created has prismatic cells, and the vertex ordering in the cone of the cell is that of the tensor prismatic cells. Not currently supported in Fortran. 1359 1360 Options Database Keys: 1361 + -dm_plex_extrude_layers <k> - Sets the number of layers k 1362 . -dm_plex_extrude_height <h> - Sets the total height of the extrusion 1363 . -dm_plex_extrude_heights <h0,h1,...> - Sets the height of each layer 1364 . -dm_plex_extrude_order_height - If true, order cells by height first 1365 - -dm_plex_extrude_normal <n0,...,nd> - Sets the normal vector along which to extrude 1366 1367 Level: advanced 1368 1369 .seealso: DMPlexCreateWedgeCylinderMesh(), DMPlexCreateWedgeBoxMesh(), DMSetType(), DMCreate() 1370 @*/ 1371 PetscErrorCode DMPlexExtrude(DM idm, PetscInt layers, PetscReal height, PetscBool orderHeight, const PetscReal extNormal[], PetscBool interpolate, DM* dm) 1372 { 1373 PetscScalar *coordsB; 1374 const PetscScalar *coordsA; 1375 PetscReal *normals = NULL, *heights = NULL; 1376 PetscReal clNormal[3]; 1377 Vec coordinatesA, coordinatesB; 1378 PetscSection coordSectionA, coordSectionB; 1379 PetscInt dim, cDim, cDimB, c, l, v, coordSize, *newCone, nl; 1380 PetscInt cStart, cEnd, vStart, vEnd, cellV, numCells, numVertices; 1381 const char *prefix; 1382 PetscBool haveCLNormal, flg; 1383 PetscErrorCode ierr; 1384 1385 PetscFunctionBegin; 1386 PetscValidHeaderSpecific(idm, DM_CLASSID, 1); 1387 PetscValidLogicalCollectiveInt(idm, layers, 2); 1388 PetscValidLogicalCollectiveReal(idm, height, 3); 1389 PetscValidLogicalCollectiveBool(idm, interpolate, 6); 1390 ierr = DMGetDimension(idm, &dim);CHKERRQ(ierr); 1391 ierr = DMGetCoordinateDim(idm, &cDim);CHKERRQ(ierr); 1392 cDimB = cDim == dim ? cDim+1 : cDim; 1393 if (dim < 1 || dim > 3) SETERRQ1(PetscObjectComm((PetscObject)idm), PETSC_ERR_SUP, "Support for dimension %D not coded", dim); 1394 1395 ierr = PetscObjectGetOptionsPrefix((PetscObject) idm, &prefix);CHKERRQ(ierr); 1396 if (layers < 0) layers = 1; 1397 ierr = PetscOptionsGetInt(NULL, prefix, "-dm_plex_extrude_layers", &layers, NULL);CHKERRQ(ierr); 1398 if (layers <= 0) SETERRQ1(PetscObjectComm((PetscObject) idm), PETSC_ERR_ARG_OUTOFRANGE, "Number of layers %D must be positive", layers); 1399 if (height < 0.) height = 1.; 1400 ierr = PetscOptionsGetReal(NULL, prefix, "-dm_plex_extrude_height", &height, NULL);CHKERRQ(ierr); 1401 if (height <= 0.) SETERRQ1(PetscObjectComm((PetscObject) idm), PETSC_ERR_ARG_OUTOFRANGE, "Height of layers %g must be positive", (double) height); 1402 ierr = PetscMalloc1(layers, &heights);CHKERRQ(ierr); 1403 nl = layers; 1404 ierr = PetscOptionsGetRealArray(NULL, prefix, "-dm_plex_extrude_heights", heights, &nl, &flg);CHKERRQ(ierr); 1405 if (flg) { 1406 if (!nl) SETERRQ(PetscObjectComm((PetscObject) idm), PETSC_ERR_ARG_OUTOFRANGE, "Must give at least one height for -dm_plex_extrude_heights"); 1407 for (l = nl; l < layers; ++l) heights[l] = heights[l-1]; 1408 for (l = 0; l < layers; ++l) if (heights[l] <= 0.) SETERRQ2(PetscObjectComm((PetscObject) idm), PETSC_ERR_ARG_OUTOFRANGE, "Height %g of layers %D must be positive", (double) heights[l], l); 1409 } else { 1410 for (l = 0; l < layers; ++l) heights[l] = height/layers; 1411 } 1412 ierr = PetscOptionsGetBool(NULL, prefix, "-dm_plex_extrude_order_height", &orderHeight, NULL);CHKERRQ(ierr); 1413 c = 3; 1414 ierr = PetscOptionsGetRealArray(NULL, prefix, "-dm_plex_extrude_normal", clNormal, &c, &haveCLNormal);CHKERRQ(ierr); 1415 if (haveCLNormal && c != cDimB) SETERRQ2(PetscObjectComm((PetscObject)idm), PETSC_ERR_ARG_SIZ, "Input normal has size %D != %D extruded coordinate dimension", c, cDimB); 1416 1417 ierr = DMPlexGetHeightStratum(idm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1418 ierr = DMPlexGetDepthStratum(idm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1419 numCells = (cEnd - cStart)*layers; 1420 numVertices = (vEnd - vStart)*(layers+1); 1421 ierr = DMCreate(PetscObjectComm((PetscObject)idm), dm);CHKERRQ(ierr); 1422 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1423 ierr = DMSetDimension(*dm, dim+1);CHKERRQ(ierr); 1424 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1425 /* Must create the celltype label here so that we do not automatically try to compute the types */ 1426 ierr = DMCreateLabel(*dm, "celltype");CHKERRQ(ierr); 1427 for (c = cStart, cellV = 0; c < cEnd; ++c) { 1428 DMPolytopeType ct, nct; 1429 PetscInt *closure = NULL; 1430 PetscInt closureSize, numCorners = 0; 1431 1432 ierr = DMPlexGetCellType(idm, c, &ct);CHKERRQ(ierr); 1433 switch (ct) { 1434 case DM_POLYTOPE_SEGMENT: nct = DM_POLYTOPE_SEG_PRISM_TENSOR;break; 1435 case DM_POLYTOPE_TRIANGLE: nct = DM_POLYTOPE_TRI_PRISM_TENSOR;break; 1436 case DM_POLYTOPE_QUADRILATERAL: nct = DM_POLYTOPE_QUAD_PRISM_TENSOR;break; 1437 default: nct = DM_POLYTOPE_UNKNOWN; 1438 } 1439 ierr = DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1440 for (v = 0; v < closureSize*2; v += 2) if ((closure[v] >= vStart) && (closure[v] < vEnd)) numCorners++; 1441 ierr = DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1442 for (l = 0; l < layers; ++l) { 1443 const PetscInt cell = orderHeight ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart; 1444 1445 ierr = DMPlexSetConeSize(*dm, cell, 2*numCorners);CHKERRQ(ierr); 1446 ierr = DMPlexSetCellType(*dm, cell, nct);CHKERRQ(ierr); 1447 } 1448 cellV = PetscMax(numCorners,cellV); 1449 } 1450 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1451 1452 if (dim != cDim && !(extNormal || haveCLNormal)) {ierr = PetscCalloc1(cDim*(vEnd - vStart), &normals);CHKERRQ(ierr);} 1453 ierr = PetscMalloc1(3*cellV,&newCone);CHKERRQ(ierr); 1454 for (c = cStart; c < cEnd; ++c) { 1455 PetscInt *closure = NULL; 1456 PetscInt closureSize, numCorners = 0, l; 1457 PetscReal normal[3] = {0, 0, 0}; 1458 1459 if (normals) {ierr = DMPlexComputeCellGeometryFVM(idm, c, NULL, NULL, normal);CHKERRQ(ierr);} 1460 ierr = DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1461 for (v = 0; v < closureSize*2; v += 2) { 1462 if ((closure[v] >= vStart) && (closure[v] < vEnd)) { 1463 PetscInt d; 1464 1465 newCone[numCorners++] = closure[v] - vStart; 1466 if (normals) {for (d = 0; d < cDim; ++d) normals[cDim*(closure[v]-vStart)+d] += normal[d];} 1467 } 1468 } 1469 ierr = DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1470 for (l = 0; l < layers; ++l) { 1471 PetscInt i; 1472 1473 for (i = 0; i < numCorners; ++i) { 1474 newCone[ numCorners + i] = orderHeight ? (layers+1)*newCone[i] + l + numCells : l*(vEnd - vStart) + newCone[i] + numCells; 1475 newCone[2*numCorners + i] = orderHeight ? (layers+1)*newCone[i] + l + 1 + numCells : (l+1)*(vEnd - vStart) + newCone[i] + numCells; 1476 } 1477 ierr = DMPlexSetCone(*dm, orderHeight ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart, newCone + numCorners);CHKERRQ(ierr); 1478 } 1479 } 1480 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1481 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1482 ierr = PetscFree(newCone);CHKERRQ(ierr); 1483 1484 ierr = DMGetCoordinateSection(*dm, &coordSectionB);CHKERRQ(ierr); 1485 ierr = PetscSectionSetNumFields(coordSectionB, 1);CHKERRQ(ierr); 1486 ierr = PetscSectionSetFieldComponents(coordSectionB, 0, cDimB);CHKERRQ(ierr); 1487 ierr = PetscSectionSetChart(coordSectionB, numCells, numCells+numVertices);CHKERRQ(ierr); 1488 for (v = numCells; v < numCells+numVertices; ++v) { 1489 ierr = PetscSectionSetDof(coordSectionB, v, cDimB);CHKERRQ(ierr); 1490 ierr = PetscSectionSetFieldDof(coordSectionB, v, 0, cDimB);CHKERRQ(ierr); 1491 ierr = DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr); 1492 } 1493 ierr = PetscSectionSetUp(coordSectionB);CHKERRQ(ierr); 1494 ierr = PetscSectionGetStorageSize(coordSectionB, &coordSize);CHKERRQ(ierr); 1495 ierr = VecCreate(PETSC_COMM_SELF, &coordinatesB);CHKERRQ(ierr); 1496 ierr = PetscObjectSetName((PetscObject) coordinatesB, "coordinates");CHKERRQ(ierr); 1497 ierr = VecSetSizes(coordinatesB, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1498 ierr = VecSetBlockSize(coordinatesB, cDimB);CHKERRQ(ierr); 1499 ierr = VecSetType(coordinatesB,VECSTANDARD);CHKERRQ(ierr); 1500 1501 ierr = DMGetCoordinateSection(idm, &coordSectionA);CHKERRQ(ierr); 1502 ierr = DMGetCoordinatesLocal(idm, &coordinatesA);CHKERRQ(ierr); 1503 ierr = VecGetArray(coordinatesB, &coordsB);CHKERRQ(ierr); 1504 ierr = VecGetArrayRead(coordinatesA, &coordsA);CHKERRQ(ierr); 1505 for (v = vStart; v < vEnd; ++v) { 1506 const PetscScalar *cptr; 1507 PetscReal ones2[2] = { 0., 1.}, ones3[3] = { 0., 0., 1.}; 1508 PetscReal normal[3]; 1509 PetscReal norm; 1510 PetscInt offA, d, cDimA = cDim; 1511 1512 if (normals) {for (d = 0; d < cDimB; ++d) normal[d] = normals[cDimB*(v - vStart)+d];} 1513 else if (haveCLNormal) {for (d = 0; d < cDimB; ++d) normal[d] = clNormal[d];} 1514 else if (extNormal) {for (d = 0; d < cDimB; ++d) normal[d] = extNormal[d];} 1515 else if (cDimB == 2) {for (d = 0; d < cDimB; ++d) normal[d] = ones2[d];} 1516 else if (cDimB == 3) {for (d = 0; d < cDimB; ++d) normal[d] = ones3[d];} 1517 else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unable to determine normal for extrusion"); 1518 for (d = 0, norm = 0.0; d < cDimB; ++d) norm += normal[d]*normal[d]; 1519 for (d = 0; d < cDimB; ++d) normal[d] *= 1./PetscSqrtReal(norm); 1520 1521 ierr = PetscSectionGetOffset(coordSectionA, v, &offA);CHKERRQ(ierr); 1522 cptr = coordsA + offA; 1523 for (l = 0; l <= layers; ++l) { 1524 PetscInt offB, d, newV; 1525 1526 newV = orderHeight ? (layers+1)*(v -vStart) + l + numCells : (vEnd -vStart)*l + (v -vStart) + numCells; 1527 ierr = PetscSectionGetOffset(coordSectionB, newV, &offB);CHKERRQ(ierr); 1528 for (d = 0; d < cDimA; ++d) { coordsB[offB+d] = cptr[d]; } 1529 for (d = 0; d < cDimB; ++d) { coordsB[offB+d] += l ? normal[d]*heights[l-1] : 0.0; } 1530 cptr = coordsB + offB; 1531 cDimA = cDimB; 1532 } 1533 } 1534 ierr = VecRestoreArrayRead(coordinatesA, &coordsA);CHKERRQ(ierr); 1535 ierr = VecRestoreArray(coordinatesB, &coordsB);CHKERRQ(ierr); 1536 ierr = DMSetCoordinatesLocal(*dm, coordinatesB);CHKERRQ(ierr); 1537 ierr = VecDestroy(&coordinatesB);CHKERRQ(ierr); 1538 ierr = PetscFree(normals);CHKERRQ(ierr); 1539 ierr = PetscFree(heights);CHKERRQ(ierr); 1540 if (interpolate) { 1541 DM idm; 1542 1543 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1544 ierr = DMPlexCopyCoordinates(*dm, idm);CHKERRQ(ierr); 1545 ierr = DMDestroy(dm);CHKERRQ(ierr); 1546 *dm = idm; 1547 } 1548 PetscFunctionReturn(0); 1549 } 1550 1551 /*@C 1552 DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database. 1553 1554 Logically Collective on dm 1555 1556 Input Parameters: 1557 + dm - the DM context 1558 - prefix - the prefix to prepend to all option names 1559 1560 Notes: 1561 A hyphen (-) must NOT be given at the beginning of the prefix name. 1562 The first character of all runtime options is AUTOMATICALLY the hyphen. 1563 1564 Level: advanced 1565 1566 .seealso: SNESSetFromOptions() 1567 @*/ 1568 PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) 1569 { 1570 DM_Plex *mesh = (DM_Plex *) dm->data; 1571 PetscErrorCode ierr; 1572 1573 PetscFunctionBegin; 1574 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1575 ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);CHKERRQ(ierr); 1576 ierr = PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);CHKERRQ(ierr); 1577 PetscFunctionReturn(0); 1578 } 1579 1580 /* Remap geometry to cylinder 1581 TODO: This only works for a single refinement, then it is broken 1582 1583 Interior square: Linear interpolation is correct 1584 The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing 1585 such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance 1586 1587 phi = arctan(y/x) 1588 d_close = sqrt(1/8 + 1/4 sin^2(phi)) 1589 d_far = sqrt(1/2 + sin^2(phi)) 1590 1591 so we remap them using 1592 1593 x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) 1594 y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) 1595 1596 If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. 1597 */ 1598 static void snapToCylinder(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1599 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1600 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1601 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 1602 { 1603 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1604 const PetscReal ds2 = 0.5*dis; 1605 1606 if ((PetscAbsScalar(u[0]) <= ds2) && (PetscAbsScalar(u[1]) <= ds2)) { 1607 f0[0] = u[0]; 1608 f0[1] = u[1]; 1609 } else { 1610 PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; 1611 1612 x = PetscRealPart(u[0]); 1613 y = PetscRealPart(u[1]); 1614 phi = PetscAtan2Real(y, x); 1615 sinp = PetscSinReal(phi); 1616 cosp = PetscCosReal(phi); 1617 if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) { 1618 dc = PetscAbsReal(ds2/sinp); 1619 df = PetscAbsReal(dis/sinp); 1620 xc = ds2*x/PetscAbsReal(y); 1621 yc = ds2*PetscSignReal(y); 1622 } else { 1623 dc = PetscAbsReal(ds2/cosp); 1624 df = PetscAbsReal(dis/cosp); 1625 xc = ds2*PetscSignReal(x); 1626 yc = ds2*y/PetscAbsReal(x); 1627 } 1628 f0[0] = xc + (u[0] - xc)*(1.0 - dc)/(df - dc); 1629 f0[1] = yc + (u[1] - yc)*(1.0 - dc)/(df - dc); 1630 } 1631 f0[2] = u[2]; 1632 } 1633 1634 static PetscErrorCode DMPlexCreateHexCylinderMesh_Internal(DM dm, DMBoundaryType periodicZ) 1635 { 1636 const PetscInt dim = 3; 1637 PetscInt numCells, numVertices; 1638 PetscMPIInt rank; 1639 PetscErrorCode ierr; 1640 1641 PetscFunctionBegin; 1642 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 1643 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 1644 /* Create topology */ 1645 { 1646 PetscInt cone[8], c; 1647 1648 numCells = !rank ? 5 : 0; 1649 numVertices = !rank ? 16 : 0; 1650 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1651 numCells *= 3; 1652 numVertices = !rank ? 24 : 0; 1653 } 1654 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 1655 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(dm, c, 8);CHKERRQ(ierr);} 1656 ierr = DMSetUp(dm);CHKERRQ(ierr); 1657 if (!rank) { 1658 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1659 cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16; 1660 cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34; 1661 ierr = DMPlexSetCone(dm, 0, cone);CHKERRQ(ierr); 1662 cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23; 1663 cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */ 1664 ierr = DMPlexSetCone(dm, 1, cone);CHKERRQ(ierr); 1665 cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17; 1666 cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38; 1667 ierr = DMPlexSetCone(dm, 2, cone);CHKERRQ(ierr); 1668 cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15; 1669 cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38; 1670 ierr = DMPlexSetCone(dm, 3, cone);CHKERRQ(ierr); 1671 cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23; 1672 cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31; 1673 ierr = DMPlexSetCone(dm, 4, cone);CHKERRQ(ierr); 1674 1675 cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32; 1676 cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20; 1677 ierr = DMPlexSetCone(dm, 5, cone);CHKERRQ(ierr); 1678 cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36; 1679 cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21; 1680 ierr = DMPlexSetCone(dm, 6, cone);CHKERRQ(ierr); 1681 cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33; 1682 cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28; 1683 ierr = DMPlexSetCone(dm, 7, cone);CHKERRQ(ierr); 1684 cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31; 1685 cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28; 1686 ierr = DMPlexSetCone(dm, 8, cone);CHKERRQ(ierr); 1687 cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36; 1688 cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19; 1689 ierr = DMPlexSetCone(dm, 9, cone);CHKERRQ(ierr); 1690 1691 cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22; 1692 cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18; 1693 ierr = DMPlexSetCone(dm, 10, cone);CHKERRQ(ierr); 1694 cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25; 1695 cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17; 1696 ierr = DMPlexSetCone(dm, 11, cone);CHKERRQ(ierr); 1697 cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21; 1698 cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27; 1699 ierr = DMPlexSetCone(dm, 12, cone);CHKERRQ(ierr); 1700 cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19; 1701 cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27; 1702 ierr = DMPlexSetCone(dm, 13, cone);CHKERRQ(ierr); 1703 cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25; 1704 cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15; 1705 ierr = DMPlexSetCone(dm, 14, cone);CHKERRQ(ierr); 1706 } else { 1707 cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6; 1708 cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10; 1709 ierr = DMPlexSetCone(dm, 0, cone);CHKERRQ(ierr); 1710 cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13; 1711 cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11; 1712 ierr = DMPlexSetCone(dm, 1, cone);CHKERRQ(ierr); 1713 cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7; 1714 cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18; 1715 ierr = DMPlexSetCone(dm, 2, cone);CHKERRQ(ierr); 1716 cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5; 1717 cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18; 1718 ierr = DMPlexSetCone(dm, 3, cone);CHKERRQ(ierr); 1719 cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13; 1720 cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9; 1721 ierr = DMPlexSetCone(dm, 4, cone);CHKERRQ(ierr); 1722 } 1723 } 1724 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1725 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1726 } 1727 /* Create cube geometry */ 1728 { 1729 Vec coordinates; 1730 PetscSection coordSection; 1731 PetscScalar *coords; 1732 PetscInt coordSize, v; 1733 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1734 const PetscReal ds2 = dis/2.0; 1735 1736 /* Build coordinates */ 1737 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1738 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1739 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1740 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1741 for (v = numCells; v < numCells+numVertices; ++v) { 1742 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1743 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1744 } 1745 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1746 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1747 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1748 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1749 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1750 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1751 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1752 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1753 if (!rank) { 1754 coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0; 1755 coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0; 1756 coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0; 1757 coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0; 1758 coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0; 1759 coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0; 1760 coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0; 1761 coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0; 1762 coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0; 1763 coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0; 1764 coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0; 1765 coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0; 1766 coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0; 1767 coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0; 1768 coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0; 1769 coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0; 1770 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1771 /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5; 1772 /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5; 1773 /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5; 1774 /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5; 1775 /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5; 1776 /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5; 1777 /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5; 1778 /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5; 1779 } 1780 } 1781 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1782 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1783 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1784 } 1785 /* Create periodicity */ 1786 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1787 PetscReal L[3]; 1788 PetscReal maxCell[3]; 1789 DMBoundaryType bdType[3]; 1790 PetscReal lower[3] = {0.0, 0.0, 0.0}; 1791 PetscReal upper[3] = {1.0, 1.0, 1.5}; 1792 PetscInt i, numZCells = 3; 1793 1794 bdType[0] = DM_BOUNDARY_NONE; 1795 bdType[1] = DM_BOUNDARY_NONE; 1796 bdType[2] = periodicZ; 1797 for (i = 0; i < dim; i++) { 1798 L[i] = upper[i] - lower[i]; 1799 maxCell[i] = 1.1 * (L[i] / numZCells); 1800 } 1801 ierr = DMSetPeriodicity(dm, PETSC_TRUE, maxCell, L, bdType);CHKERRQ(ierr); 1802 } 1803 { 1804 DM cdm; 1805 PetscDS cds; 1806 PetscScalar c[2] = {1.0, 1.0}; 1807 1808 ierr = DMPlexCreateCoordinateSpace(dm, 1, snapToCylinder);CHKERRQ(ierr); 1809 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 1810 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 1811 ierr = PetscDSSetConstants(cds, 2, c);CHKERRQ(ierr); 1812 } 1813 /* Wait for coordinate creation before doing in-place modification */ 1814 ierr = DMPlexInterpolateInPlace_Internal(dm);CHKERRQ(ierr); 1815 PetscFunctionReturn(0); 1816 } 1817 1818 /*@ 1819 DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. 1820 1821 Collective 1822 1823 Input Parameters: 1824 + comm - The communicator for the DM object 1825 - periodicZ - The boundary type for the Z direction 1826 1827 Output Parameter: 1828 . dm - The DM object 1829 1830 Note: 1831 Here is the output numbering looking from the bottom of the cylinder: 1832 $ 17-----14 1833 $ | | 1834 $ | 2 | 1835 $ | | 1836 $ 17-----8-----7-----14 1837 $ | | | | 1838 $ | 3 | 0 | 1 | 1839 $ | | | | 1840 $ 19-----5-----6-----13 1841 $ | | 1842 $ | 4 | 1843 $ | | 1844 $ 19-----13 1845 $ 1846 $ and up through the top 1847 $ 1848 $ 18-----16 1849 $ | | 1850 $ | 2 | 1851 $ | | 1852 $ 18----10----11-----16 1853 $ | | | | 1854 $ | 3 | 0 | 1 | 1855 $ | | | | 1856 $ 20-----9----12-----15 1857 $ | | 1858 $ | 4 | 1859 $ | | 1860 $ 20-----15 1861 1862 Level: beginner 1863 1864 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1865 @*/ 1866 PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, DMBoundaryType periodicZ, DM *dm) 1867 { 1868 PetscErrorCode ierr; 1869 1870 PetscFunctionBegin; 1871 PetscValidPointer(dm, 3); 1872 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1873 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1874 ierr = DMPlexCreateHexCylinderMesh_Internal(*dm, periodicZ);CHKERRQ(ierr); 1875 PetscFunctionReturn(0); 1876 } 1877 1878 static PetscErrorCode DMPlexCreateWedgeCylinderMesh_Internal(DM dm, PetscInt n, PetscBool interpolate) 1879 { 1880 const PetscInt dim = 3; 1881 PetscInt numCells, numVertices, v; 1882 PetscMPIInt rank; 1883 PetscErrorCode ierr; 1884 1885 PetscFunctionBegin; 1886 if (n < 0) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n); 1887 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 1888 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 1889 /* Must create the celltype label here so that we do not automatically try to compute the types */ 1890 ierr = DMCreateLabel(dm, "celltype");CHKERRQ(ierr); 1891 /* Create topology */ 1892 { 1893 PetscInt cone[6], c; 1894 1895 numCells = !rank ? n : 0; 1896 numVertices = !rank ? 2*(n+1) : 0; 1897 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 1898 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr);} 1899 ierr = DMSetUp(dm);CHKERRQ(ierr); 1900 for (c = 0; c < numCells; c++) { 1901 cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n; 1902 cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n; 1903 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 1904 ierr = DMPlexSetCellType(dm, c, DM_POLYTOPE_TRI_PRISM_TENSOR);CHKERRQ(ierr); 1905 } 1906 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1907 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1908 } 1909 for (v = numCells; v < numCells+numVertices; ++v) { 1910 ierr = DMPlexSetCellType(dm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr); 1911 } 1912 /* Create cylinder geometry */ 1913 { 1914 Vec coordinates; 1915 PetscSection coordSection; 1916 PetscScalar *coords; 1917 PetscInt coordSize, c; 1918 1919 /* Build coordinates */ 1920 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1921 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1922 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1923 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1924 for (v = numCells; v < numCells+numVertices; ++v) { 1925 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1926 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1927 } 1928 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1929 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1930 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1931 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1932 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1933 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1934 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1935 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1936 for (c = 0; c < numCells; c++) { 1937 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; 1938 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; 1939 } 1940 if (!rank) { 1941 coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0; 1942 coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0; 1943 } 1944 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1945 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1946 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1947 } 1948 /* Interpolate */ 1949 if (interpolate) {ierr = DMPlexInterpolateInPlace_Internal(dm);CHKERRQ(ierr);} 1950 PetscFunctionReturn(0); 1951 } 1952 1953 /*@ 1954 DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges. 1955 1956 Collective 1957 1958 Input Parameters: 1959 + comm - The communicator for the DM object 1960 . n - The number of wedges around the origin 1961 - interpolate - Create edges and faces 1962 1963 Output Parameter: 1964 . dm - The DM object 1965 1966 Level: beginner 1967 1968 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1969 @*/ 1970 PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm) 1971 { 1972 PetscErrorCode ierr; 1973 1974 PetscFunctionBegin; 1975 PetscValidPointer(dm, 4); 1976 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1977 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1978 ierr = DMPlexCreateWedgeCylinderMesh_Internal(*dm, n, interpolate);CHKERRQ(ierr); 1979 PetscFunctionReturn(0); 1980 } 1981 1982 PETSC_STATIC_INLINE PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1983 { 1984 PetscReal prod = 0.0; 1985 PetscInt i; 1986 for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]); 1987 return PetscSqrtReal(prod); 1988 } 1989 PETSC_STATIC_INLINE PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1990 { 1991 PetscReal prod = 0.0; 1992 PetscInt i; 1993 for (i = 0; i < dim; ++i) prod += x[i]*y[i]; 1994 return prod; 1995 } 1996 1997 /* The first constant is the sphere radius */ 1998 static void snapToSphere(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1999 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 2000 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 2001 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 2002 { 2003 PetscReal r = PetscRealPart(constants[0]); 2004 PetscReal norm2 = 0.0, fac; 2005 PetscInt n = uOff[1] - uOff[0], d; 2006 2007 for (d = 0; d < n; ++d) norm2 += PetscSqr(PetscRealPart(u[d])); 2008 fac = r/PetscSqrtReal(norm2); 2009 for (d = 0; d < n; ++d) f0[d] = u[d]*fac; 2010 } 2011 2012 static PetscErrorCode DMPlexCreateSphereMesh_Internal(DM dm, PetscInt dim, PetscBool simplex, PetscReal R) 2013 { 2014 const PetscInt embedDim = dim+1; 2015 PetscSection coordSection; 2016 Vec coordinates; 2017 PetscScalar *coords; 2018 PetscReal *coordsIn; 2019 PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e; 2020 PetscMPIInt rank; 2021 PetscErrorCode ierr; 2022 2023 PetscFunctionBegin; 2024 PetscValidLogicalCollectiveBool(dm, simplex, 3); 2025 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 2026 ierr = DMSetCoordinateDim(dm, dim+1);CHKERRQ(ierr); 2027 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 2028 switch (dim) { 2029 case 2: 2030 if (simplex) { 2031 const PetscReal radius = PetscSqrtReal(1 + PETSC_PHI*PETSC_PHI)/(1.0 + PETSC_PHI); 2032 const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI) * (R/radius); 2033 const PetscInt degree = 5; 2034 PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)}; 2035 PetscInt s[3] = {1, 1, 1}; 2036 PetscInt cone[3]; 2037 PetscInt *graph, p, i, j, k; 2038 2039 vertex[0] *= R/radius; vertex[1] *= R/radius; vertex[2] *= R/radius; 2040 numCells = !rank ? 20 : 0; 2041 numVerts = !rank ? 12 : 0; 2042 firstVertex = numCells; 2043 /* Use icosahedron, which for a R-sphere has coordinates which are all cyclic permutations of 2044 2045 (0, \pm 1/\phi+1, \pm \phi/\phi+1) 2046 2047 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 2048 length is then given by 2/(1+\phi) = 2 * 0.38197 = 0.76393. 2049 */ 2050 /* Construct vertices */ 2051 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 2052 if (!rank) { 2053 for (p = 0, i = 0; p < embedDim; ++p) { 2054 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2055 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2056 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim]; 2057 ++i; 2058 } 2059 } 2060 } 2061 } 2062 /* Construct graph */ 2063 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 2064 for (i = 0; i < numVerts; ++i) { 2065 for (j = 0, k = 0; j < numVerts; ++j) { 2066 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 2067 } 2068 if (k != degree) SETERRQ3(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree); 2069 } 2070 /* Build Topology */ 2071 ierr = DMPlexSetChart(dm, 0, numCells+numVerts);CHKERRQ(ierr); 2072 for (c = 0; c < numCells; c++) { 2073 ierr = DMPlexSetConeSize(dm, c, embedDim);CHKERRQ(ierr); 2074 } 2075 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 2076 /* Cells */ 2077 for (i = 0, c = 0; i < numVerts; ++i) { 2078 for (j = 0; j < i; ++j) { 2079 for (k = 0; k < j; ++k) { 2080 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) { 2081 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; 2082 /* Check orientation */ 2083 { 2084 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}}}; 2085 PetscReal normal[3]; 2086 PetscInt e, f; 2087 2088 for (d = 0; d < embedDim; ++d) { 2089 normal[d] = 0.0; 2090 for (e = 0; e < embedDim; ++e) { 2091 for (f = 0; f < embedDim; ++f) { 2092 normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]); 2093 } 2094 } 2095 } 2096 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 2097 } 2098 ierr = DMPlexSetCone(dm, c++, cone);CHKERRQ(ierr); 2099 } 2100 } 2101 } 2102 } 2103 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2104 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2105 ierr = PetscFree(graph);CHKERRQ(ierr); 2106 } else { 2107 /* 2108 12-21--13 2109 | | 2110 25 4 24 2111 | | 2112 12-25--9-16--8-24--13 2113 | | | | 2114 23 5 17 0 15 3 22 2115 | | | | 2116 10-20--6-14--7-19--11 2117 | | 2118 20 1 19 2119 | | 2120 10-18--11 2121 | | 2122 23 2 22 2123 | | 2124 12-21--13 2125 */ 2126 PetscInt cone[4], ornt[4]; 2127 2128 numCells = !rank ? 6 : 0; 2129 numEdges = !rank ? 12 : 0; 2130 numVerts = !rank ? 8 : 0; 2131 firstVertex = numCells; 2132 firstEdge = numCells + numVerts; 2133 /* Build Topology */ 2134 ierr = DMPlexSetChart(dm, 0, numCells+numEdges+numVerts);CHKERRQ(ierr); 2135 for (c = 0; c < numCells; c++) { 2136 ierr = DMPlexSetConeSize(dm, c, 4);CHKERRQ(ierr); 2137 } 2138 for (e = firstEdge; e < firstEdge+numEdges; ++e) { 2139 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 2140 } 2141 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 2142 if (!rank) { 2143 /* Cell 0 */ 2144 cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17; 2145 ierr = DMPlexSetCone(dm, 0, cone);CHKERRQ(ierr); 2146 ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0; 2147 ierr = DMPlexSetConeOrientation(dm, 0, ornt);CHKERRQ(ierr); 2148 /* Cell 1 */ 2149 cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20; 2150 ierr = DMPlexSetCone(dm, 1, cone);CHKERRQ(ierr); 2151 ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; 2152 ierr = DMPlexSetConeOrientation(dm, 1, ornt);CHKERRQ(ierr); 2153 /* Cell 2 */ 2154 cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23; 2155 ierr = DMPlexSetCone(dm, 2, cone);CHKERRQ(ierr); 2156 ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; 2157 ierr = DMPlexSetConeOrientation(dm, 2, ornt);CHKERRQ(ierr); 2158 /* Cell 3 */ 2159 cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15; 2160 ierr = DMPlexSetCone(dm, 3, cone);CHKERRQ(ierr); 2161 ornt[0] = -2; ornt[1] = -2; ornt[2] = 0; ornt[3] = -2; 2162 ierr = DMPlexSetConeOrientation(dm, 3, ornt);CHKERRQ(ierr); 2163 /* Cell 4 */ 2164 cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25; 2165 ierr = DMPlexSetCone(dm, 4, cone);CHKERRQ(ierr); 2166 ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = 0; 2167 ierr = DMPlexSetConeOrientation(dm, 4, ornt);CHKERRQ(ierr); 2168 /* Cell 5 */ 2169 cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23; 2170 ierr = DMPlexSetCone(dm, 5, cone);CHKERRQ(ierr); 2171 ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = -2; 2172 ierr = DMPlexSetConeOrientation(dm, 5, ornt);CHKERRQ(ierr); 2173 /* Edges */ 2174 cone[0] = 6; cone[1] = 7; 2175 ierr = DMPlexSetCone(dm, 14, cone);CHKERRQ(ierr); 2176 cone[0] = 7; cone[1] = 8; 2177 ierr = DMPlexSetCone(dm, 15, cone);CHKERRQ(ierr); 2178 cone[0] = 8; cone[1] = 9; 2179 ierr = DMPlexSetCone(dm, 16, cone);CHKERRQ(ierr); 2180 cone[0] = 9; cone[1] = 6; 2181 ierr = DMPlexSetCone(dm, 17, cone);CHKERRQ(ierr); 2182 cone[0] = 10; cone[1] = 11; 2183 ierr = DMPlexSetCone(dm, 18, cone);CHKERRQ(ierr); 2184 cone[0] = 11; cone[1] = 7; 2185 ierr = DMPlexSetCone(dm, 19, cone);CHKERRQ(ierr); 2186 cone[0] = 6; cone[1] = 10; 2187 ierr = DMPlexSetCone(dm, 20, cone);CHKERRQ(ierr); 2188 cone[0] = 12; cone[1] = 13; 2189 ierr = DMPlexSetCone(dm, 21, cone);CHKERRQ(ierr); 2190 cone[0] = 13; cone[1] = 11; 2191 ierr = DMPlexSetCone(dm, 22, cone);CHKERRQ(ierr); 2192 cone[0] = 10; cone[1] = 12; 2193 ierr = DMPlexSetCone(dm, 23, cone);CHKERRQ(ierr); 2194 cone[0] = 13; cone[1] = 8; 2195 ierr = DMPlexSetCone(dm, 24, cone);CHKERRQ(ierr); 2196 cone[0] = 12; cone[1] = 9; 2197 ierr = DMPlexSetCone(dm, 25, cone);CHKERRQ(ierr); 2198 } 2199 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2200 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2201 /* Build coordinates */ 2202 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 2203 if (!rank) { 2204 coordsIn[0*embedDim+0] = -R; coordsIn[0*embedDim+1] = R; coordsIn[0*embedDim+2] = -R; 2205 coordsIn[1*embedDim+0] = R; coordsIn[1*embedDim+1] = R; coordsIn[1*embedDim+2] = -R; 2206 coordsIn[2*embedDim+0] = R; coordsIn[2*embedDim+1] = -R; coordsIn[2*embedDim+2] = -R; 2207 coordsIn[3*embedDim+0] = -R; coordsIn[3*embedDim+1] = -R; coordsIn[3*embedDim+2] = -R; 2208 coordsIn[4*embedDim+0] = -R; coordsIn[4*embedDim+1] = R; coordsIn[4*embedDim+2] = R; 2209 coordsIn[5*embedDim+0] = R; coordsIn[5*embedDim+1] = R; coordsIn[5*embedDim+2] = R; 2210 coordsIn[6*embedDim+0] = -R; coordsIn[6*embedDim+1] = -R; coordsIn[6*embedDim+2] = R; 2211 coordsIn[7*embedDim+0] = R; coordsIn[7*embedDim+1] = -R; coordsIn[7*embedDim+2] = R; 2212 } 2213 } 2214 break; 2215 case 3: 2216 if (simplex) { 2217 const PetscReal edgeLen = 1.0/PETSC_PHI; 2218 PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5}; 2219 PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0}; 2220 PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0}; 2221 const PetscInt degree = 12; 2222 PetscInt s[4] = {1, 1, 1}; 2223 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}, 2224 {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}}; 2225 PetscInt cone[4]; 2226 PetscInt *graph, p, i, j, k, l; 2227 2228 vertexA[0] *= R; vertexA[1] *= R; vertexA[2] *= R; vertexA[3] *= R; 2229 vertexB[0] *= R; vertexB[1] *= R; vertexB[2] *= R; vertexB[3] *= R; 2230 vertexC[0] *= R; vertexC[1] *= R; vertexC[2] *= R; vertexC[3] *= R; 2231 numCells = !rank ? 600 : 0; 2232 numVerts = !rank ? 120 : 0; 2233 firstVertex = numCells; 2234 /* Use the 600-cell, which for a unit sphere has coordinates which are 2235 2236 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16 2237 (\pm 1, 0, 0, 0) all cyclic permutations 8 2238 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96 2239 2240 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 2241 length is then given by 1/\phi = 0.61803. 2242 2243 http://buzzard.pugetsound.edu/sage-practice/ch03s03.html 2244 http://mathworld.wolfram.com/600-Cell.html 2245 */ 2246 /* Construct vertices */ 2247 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 2248 i = 0; 2249 if (!rank) { 2250 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2251 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2252 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2253 for (s[3] = -1; s[3] < 2; s[3] += 2) { 2254 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d]; 2255 ++i; 2256 } 2257 } 2258 } 2259 } 2260 for (p = 0; p < embedDim; ++p) { 2261 s[1] = s[2] = s[3] = 1; 2262 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2263 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim]; 2264 ++i; 2265 } 2266 } 2267 for (p = 0; p < 12; ++p) { 2268 s[3] = 1; 2269 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2270 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2271 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2272 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]]; 2273 ++i; 2274 } 2275 } 2276 } 2277 } 2278 } 2279 if (i != numVerts) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts); 2280 /* Construct graph */ 2281 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 2282 for (i = 0; i < numVerts; ++i) { 2283 for (j = 0, k = 0; j < numVerts; ++j) { 2284 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 2285 } 2286 if (k != degree) SETERRQ3(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree); 2287 } 2288 /* Build Topology */ 2289 ierr = DMPlexSetChart(dm, 0, numCells+numVerts);CHKERRQ(ierr); 2290 for (c = 0; c < numCells; c++) { 2291 ierr = DMPlexSetConeSize(dm, c, embedDim);CHKERRQ(ierr); 2292 } 2293 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 2294 /* Cells */ 2295 if (!rank) { 2296 for (i = 0, c = 0; i < numVerts; ++i) { 2297 for (j = 0; j < i; ++j) { 2298 for (k = 0; k < j; ++k) { 2299 for (l = 0; l < k; ++l) { 2300 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] && 2301 graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) { 2302 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l; 2303 /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */ 2304 { 2305 const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2306 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}}, 2307 {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}}, 2308 {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}}, 2309 2310 {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}}, 2311 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2312 {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}}, 2313 {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}}, 2314 2315 {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}}, 2316 {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}}, 2317 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2318 {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}, 2319 2320 {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}}, 2321 {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}}, 2322 {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2323 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}}; 2324 PetscReal normal[4]; 2325 PetscInt e, f, g; 2326 2327 for (d = 0; d < embedDim; ++d) { 2328 normal[d] = 0.0; 2329 for (e = 0; e < embedDim; ++e) { 2330 for (f = 0; f < embedDim; ++f) { 2331 for (g = 0; g < embedDim; ++g) { 2332 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]); 2333 } 2334 } 2335 } 2336 } 2337 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 2338 } 2339 ierr = DMPlexSetCone(dm, c++, cone);CHKERRQ(ierr); 2340 } 2341 } 2342 } 2343 } 2344 } 2345 } 2346 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2347 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2348 ierr = PetscFree(graph);CHKERRQ(ierr); 2349 break; 2350 } 2351 default: SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim); 2352 } 2353 /* Create coordinates */ 2354 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2355 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2356 ierr = PetscSectionSetFieldComponents(coordSection, 0, embedDim);CHKERRQ(ierr); 2357 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);CHKERRQ(ierr); 2358 for (v = firstVertex; v < firstVertex+numVerts; ++v) { 2359 ierr = PetscSectionSetDof(coordSection, v, embedDim);CHKERRQ(ierr); 2360 ierr = PetscSectionSetFieldDof(coordSection, v, 0, embedDim);CHKERRQ(ierr); 2361 } 2362 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2363 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2364 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 2365 ierr = VecSetBlockSize(coordinates, embedDim);CHKERRQ(ierr); 2366 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2367 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2368 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2369 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2370 for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];} 2371 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2372 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2373 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2374 ierr = PetscFree(coordsIn);CHKERRQ(ierr); 2375 { 2376 DM cdm; 2377 PetscDS cds; 2378 PetscScalar c = R; 2379 2380 ierr = DMPlexCreateCoordinateSpace(dm, 1, snapToSphere);CHKERRQ(ierr); 2381 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 2382 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 2383 ierr = PetscDSSetConstants(cds, 1, &c);CHKERRQ(ierr); 2384 } 2385 /* Wait for coordinate creation before doing in-place modification */ 2386 if (simplex) {ierr = DMPlexInterpolateInPlace_Internal(dm);CHKERRQ(ierr);} 2387 PetscFunctionReturn(0); 2388 } 2389 2390 /*@ 2391 DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d. 2392 2393 Collective 2394 2395 Input Parameters: 2396 + comm - The communicator for the DM object 2397 . dim - The dimension 2398 . simplex - Use simplices, or tensor product cells 2399 - R - The radius 2400 2401 Output Parameter: 2402 . dm - The DM object 2403 2404 Level: beginner 2405 2406 .seealso: DMPlexCreateBallMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 2407 @*/ 2408 PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscReal R, DM *dm) 2409 { 2410 PetscErrorCode ierr; 2411 2412 PetscFunctionBegin; 2413 PetscValidPointer(dm, 5); 2414 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2415 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2416 ierr = DMPlexCreateSphereMesh_Internal(*dm, dim, simplex, R);CHKERRQ(ierr); 2417 PetscFunctionReturn(0); 2418 } 2419 2420 static PetscErrorCode DMPlexCreateBallMesh_Internal(DM dm, PetscInt dim, PetscReal R) 2421 { 2422 DM sdm, vol; 2423 DMLabel bdlabel; 2424 PetscErrorCode ierr; 2425 2426 PetscFunctionBegin; 2427 ierr = DMCreate(PetscObjectComm((PetscObject) dm), &sdm);CHKERRQ(ierr); 2428 ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr); 2429 ierr = PetscObjectSetOptionsPrefix((PetscObject) sdm, "bd_");CHKERRQ(ierr); 2430 ierr = DMPlexCreateSphereMesh_Internal(sdm, dim-1, PETSC_TRUE, R);CHKERRQ(ierr); 2431 ierr = DMSetFromOptions(sdm);CHKERRQ(ierr); 2432 ierr = DMViewFromOptions(sdm, NULL, "-dm_view");CHKERRQ(ierr); 2433 ierr = DMPlexGenerate(sdm, NULL, PETSC_TRUE, &vol);CHKERRQ(ierr); 2434 ierr = DMDestroy(&sdm);CHKERRQ(ierr); 2435 ierr = DMPlexReplace_Static(dm, &vol);CHKERRQ(ierr); 2436 ierr = DMCreateLabel(dm, "marker");CHKERRQ(ierr); 2437 ierr = DMGetLabel(dm, "marker", &bdlabel);CHKERRQ(ierr); 2438 ierr = DMPlexMarkBoundaryFaces(dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 2439 ierr = DMPlexLabelComplete(dm, bdlabel);CHKERRQ(ierr); 2440 PetscFunctionReturn(0); 2441 } 2442 2443 /*@ 2444 DMPlexCreateBallMesh - Creates a simplex mesh on the d-dimensional ball, B^d. 2445 2446 Collective 2447 2448 Input Parameters: 2449 + comm - The communicator for the DM object 2450 . dim - The dimension 2451 - R - The radius 2452 2453 Output Parameter: 2454 . dm - The DM object 2455 2456 Options Database Keys: 2457 - bd_dm_refine - This will refine the surface mesh preserving the sphere geometry 2458 2459 Level: beginner 2460 2461 .seealso: DMPlexCreateSphereMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 2462 @*/ 2463 PetscErrorCode DMPlexCreateBallMesh(MPI_Comm comm, PetscInt dim, PetscReal R, DM *dm) 2464 { 2465 PetscErrorCode ierr; 2466 2467 PetscFunctionBegin; 2468 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2469 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2470 ierr = DMPlexCreateBallMesh_Internal(*dm, dim, R);CHKERRQ(ierr); 2471 PetscFunctionReturn(0); 2472 } 2473 2474 static PetscErrorCode DMPlexCreateReferenceCell_Internal(DM rdm, DMPolytopeType ct) 2475 { 2476 PetscErrorCode ierr; 2477 2478 PetscFunctionBegin; 2479 switch (ct) { 2480 case DM_POLYTOPE_POINT: 2481 { 2482 PetscInt numPoints[1] = {1}; 2483 PetscInt coneSize[1] = {0}; 2484 PetscInt cones[1] = {0}; 2485 PetscInt coneOrientations[1] = {0}; 2486 PetscScalar vertexCoords[1] = {0.0}; 2487 2488 ierr = DMSetDimension(rdm, 0);CHKERRQ(ierr); 2489 ierr = DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2490 } 2491 break; 2492 case DM_POLYTOPE_SEGMENT: 2493 { 2494 PetscInt numPoints[2] = {2, 1}; 2495 PetscInt coneSize[3] = {2, 0, 0}; 2496 PetscInt cones[2] = {1, 2}; 2497 PetscInt coneOrientations[2] = {0, 0}; 2498 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 2499 2500 ierr = DMSetDimension(rdm, 1);CHKERRQ(ierr); 2501 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2502 } 2503 break; 2504 case DM_POLYTOPE_TRIANGLE: 2505 { 2506 PetscInt numPoints[2] = {3, 1}; 2507 PetscInt coneSize[4] = {3, 0, 0, 0}; 2508 PetscInt cones[3] = {1, 2, 3}; 2509 PetscInt coneOrientations[3] = {0, 0, 0}; 2510 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 2511 2512 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 2513 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2514 } 2515 break; 2516 case DM_POLYTOPE_QUADRILATERAL: 2517 { 2518 PetscInt numPoints[2] = {4, 1}; 2519 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 2520 PetscInt cones[4] = {1, 2, 3, 4}; 2521 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 2522 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 2523 2524 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 2525 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2526 } 2527 break; 2528 case DM_POLYTOPE_SEG_PRISM_TENSOR: 2529 { 2530 PetscInt numPoints[2] = {4, 1}; 2531 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 2532 PetscInt cones[4] = {1, 2, 3, 4}; 2533 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 2534 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, 1.0}; 2535 2536 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 2537 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2538 } 2539 break; 2540 case DM_POLYTOPE_TETRAHEDRON: 2541 { 2542 PetscInt numPoints[2] = {4, 1}; 2543 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 2544 PetscInt cones[4] = {1, 3, 2, 4}; 2545 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 2546 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}; 2547 2548 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 2549 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2550 } 2551 break; 2552 case DM_POLYTOPE_HEXAHEDRON: 2553 { 2554 PetscInt numPoints[2] = {8, 1}; 2555 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 2556 PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8}; 2557 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 2558 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, 2559 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 2560 2561 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 2562 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2563 } 2564 break; 2565 case DM_POLYTOPE_TRI_PRISM: 2566 { 2567 PetscInt numPoints[2] = {6, 1}; 2568 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 2569 PetscInt cones[6] = {1, 3, 2, 4, 5, 6}; 2570 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 2571 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 2572 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 2573 2574 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 2575 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2576 } 2577 break; 2578 case DM_POLYTOPE_TRI_PRISM_TENSOR: 2579 { 2580 PetscInt numPoints[2] = {6, 1}; 2581 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 2582 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 2583 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 2584 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 2585 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 2586 2587 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 2588 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2589 } 2590 break; 2591 case DM_POLYTOPE_QUAD_PRISM_TENSOR: 2592 { 2593 PetscInt numPoints[2] = {8, 1}; 2594 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 2595 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 2596 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 2597 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, 2598 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 2599 2600 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 2601 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2602 } 2603 break; 2604 case DM_POLYTOPE_PYRAMID: 2605 { 2606 PetscInt numPoints[2] = {5, 1}; 2607 PetscInt coneSize[6] = {5, 0, 0, 0, 0, 0}; 2608 PetscInt cones[5] = {1, 4, 3, 2, 5}; 2609 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 2610 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, 2611 0.0, 0.0, 1.0}; 2612 2613 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 2614 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2615 } 2616 break; 2617 default: SETERRQ1(PetscObjectComm((PetscObject) rdm), PETSC_ERR_ARG_WRONG, "Cannot create reference cell for cell type %s", DMPolytopeTypes[ct]); 2618 } 2619 { 2620 PetscInt Nv, v; 2621 2622 /* Must create the celltype label here so that we do not automatically try to compute the types */ 2623 ierr = DMCreateLabel(rdm, "celltype");CHKERRQ(ierr); 2624 ierr = DMPlexSetCellType(rdm, 0, ct);CHKERRQ(ierr); 2625 ierr = DMPlexGetChart(rdm, NULL, &Nv);CHKERRQ(ierr); 2626 for (v = 1; v < Nv; ++v) {ierr = DMPlexSetCellType(rdm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr);} 2627 } 2628 ierr = DMPlexInterpolateInPlace_Internal(rdm);CHKERRQ(ierr); 2629 PetscFunctionReturn(0); 2630 } 2631 2632 /*@ 2633 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 2634 2635 Collective 2636 2637 Input Parameters: 2638 + comm - The communicator 2639 - ct - The cell type of the reference cell 2640 2641 Output Parameter: 2642 . refdm - The reference cell 2643 2644 Level: intermediate 2645 2646 .seealso: DMPlexCreateReferenceCell(), DMPlexCreateBoxMesh() 2647 @*/ 2648 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, DMPolytopeType ct, DM *refdm) 2649 { 2650 PetscErrorCode ierr; 2651 2652 PetscFunctionBegin; 2653 ierr = DMCreate(comm, refdm);CHKERRQ(ierr); 2654 ierr = DMSetType(*refdm, DMPLEX);CHKERRQ(ierr); 2655 ierr = DMPlexCreateReferenceCell_Internal(*refdm, ct);CHKERRQ(ierr); 2656 PetscFunctionReturn(0); 2657 } 2658 2659 static PetscErrorCode DMPlexCreateBoundaryLabel_Private(DM dm, const char name[]) 2660 { 2661 DM plex; 2662 DMLabel label; 2663 PetscBool hasLabel; 2664 PetscErrorCode ierr; 2665 2666 PetscFunctionBeginUser; 2667 ierr = DMHasLabel(dm, name, &hasLabel);CHKERRQ(ierr); 2668 if (hasLabel) PetscFunctionReturn(0); 2669 ierr = DMCreateLabel(dm, name);CHKERRQ(ierr); 2670 ierr = DMGetLabel(dm, name, &label);CHKERRQ(ierr); 2671 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 2672 ierr = DMPlexMarkBoundaryFaces(plex, 1, label);CHKERRQ(ierr); 2673 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2674 PetscFunctionReturn(0); 2675 } 2676 2677 const char * const DMPlexShapes[] = {"box", "box_surface", "ball", "sphere", "cylinder", "unknown", "DMPlexShape", "DM_SHAPE_", NULL}; 2678 2679 static PetscErrorCode DMPlexCreateFromOptions_Internal(PetscOptionItems *PetscOptionsObject, PetscBool *useCoordSpace, DM dm) 2680 { 2681 DMPlexShape shape = DM_SHAPE_BOX; 2682 DMPolytopeType cell = DM_POLYTOPE_TRIANGLE; 2683 PetscInt dim = 2; 2684 PetscBool simplex = PETSC_TRUE, interpolate = PETSC_TRUE, adjCone = PETSC_FALSE, adjClosure = PETSC_TRUE, refDomain = PETSC_FALSE; 2685 PetscBool flg, flg2, fflg, bdfflg; 2686 MPI_Comm comm; 2687 char filename[PETSC_MAX_PATH_LEN], bdFilename[PETSC_MAX_PATH_LEN]; 2688 PetscErrorCode ierr; 2689 2690 PetscFunctionBegin; 2691 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 2692 /* TODO Turn this into a registration interface */ 2693 ierr = PetscOptionsString("-dm_plex_filename", "File containing a mesh", "DMPlexCreateFromFile", filename, filename, sizeof(filename), &fflg);CHKERRQ(ierr); 2694 ierr = PetscOptionsString("-dm_plex_boundary_filename", "File containing a mesh boundary", "DMPlexCreateFromFile", bdFilename, bdFilename, sizeof(bdFilename), &bdfflg);CHKERRQ(ierr); 2695 ierr = PetscOptionsEnum("-dm_plex_cell", "Cell shape", "", DMPolytopeTypes, (PetscEnum) cell, (PetscEnum *) &cell, NULL);CHKERRQ(ierr); 2696 ierr = PetscOptionsBool("-dm_plex_reference_cell_domain", "Use a reference cell domain", "", refDomain, &refDomain, NULL);CHKERRQ(ierr); 2697 ierr = PetscOptionsEnum("-dm_plex_shape", "Shape for built-in mesh", "", DMPlexShapes, (PetscEnum) shape, (PetscEnum *) &shape, &flg);CHKERRQ(ierr); 2698 ierr = PetscOptionsBoundedInt("-dm_plex_dim", "Topological dimension of the mesh", "DMGetDimension", dim, &dim, &flg, 0);CHKERRQ(ierr); 2699 if ((dim < 0) || (dim > 3)) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Dimension %D should be in [1, 3]", dim); 2700 ierr = PetscOptionsBool("-dm_plex_simplex", "Mesh cell shape", "", simplex, &simplex, &flg);CHKERRQ(ierr); 2701 ierr = PetscOptionsBool("-dm_plex_interpolate", "Flag to create edges and faces automatically", "", interpolate, &interpolate, &flg);CHKERRQ(ierr); 2702 ierr = PetscOptionsBool("-dm_plex_adj_cone", "Set adjacency direction", "DMSetBasicAdjacency", adjCone, &adjCone, &flg);CHKERRQ(ierr); 2703 ierr = PetscOptionsBool("-dm_plex_adj_closure", "Set adjacency size", "DMSetBasicAdjacency", adjClosure, &adjClosure, &flg2);CHKERRQ(ierr); 2704 if (flg || flg2) {ierr = DMSetBasicAdjacency(dm, adjCone, adjClosure);CHKERRQ(ierr);} 2705 2706 switch (cell) { 2707 case DM_POLYTOPE_POINT: 2708 case DM_POLYTOPE_SEGMENT: 2709 case DM_POLYTOPE_POINT_PRISM_TENSOR: 2710 case DM_POLYTOPE_TRIANGLE: 2711 case DM_POLYTOPE_QUADRILATERAL: 2712 case DM_POLYTOPE_TETRAHEDRON: 2713 case DM_POLYTOPE_HEXAHEDRON: 2714 *useCoordSpace = PETSC_TRUE;break; 2715 default: *useCoordSpace = PETSC_FALSE;break; 2716 } 2717 2718 if (fflg) { 2719 DM dmnew; 2720 2721 ierr = DMPlexCreateFromFile(PetscObjectComm((PetscObject) dm), filename, interpolate, &dmnew);CHKERRQ(ierr); 2722 ierr = DMPlexReplace_Static(dm, &dmnew);CHKERRQ(ierr); 2723 } else if (refDomain) { 2724 ierr = DMPlexCreateReferenceCell_Internal(dm, cell);CHKERRQ(ierr); 2725 } else if (bdfflg) { 2726 DM bdm, dmnew; 2727 2728 ierr = DMPlexCreateFromFile(PetscObjectComm((PetscObject) dm), bdFilename, interpolate, &bdm);CHKERRQ(ierr); 2729 ierr = PetscObjectSetOptionsPrefix((PetscObject) bdm, "bd_");CHKERRQ(ierr); 2730 ierr = DMSetFromOptions(bdm);CHKERRQ(ierr); 2731 ierr = DMPlexGenerate(bdm, NULL, interpolate, &dmnew);CHKERRQ(ierr); 2732 ierr = DMDestroy(&bdm);CHKERRQ(ierr); 2733 ierr = DMPlexReplace_Static(dm, &dmnew);CHKERRQ(ierr); 2734 } else { 2735 ierr = PetscObjectSetName((PetscObject) dm, DMPlexShapes[shape]);CHKERRQ(ierr); 2736 switch (shape) { 2737 case DM_SHAPE_BOX: 2738 { 2739 PetscInt faces[3] = {0, 0, 0}; 2740 PetscReal lower[3] = {0, 0, 0}; 2741 PetscReal upper[3] = {1, 1, 1}; 2742 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 2743 PetscInt i, n; 2744 2745 n = dim; 2746 for (i = 0; i < dim; ++i) faces[i] = (dim == 1 ? 1 : 4-dim); 2747 ierr = PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg);CHKERRQ(ierr); 2748 n = 3; 2749 ierr = PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg);CHKERRQ(ierr); 2750 if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim); 2751 n = 3; 2752 ierr = PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg);CHKERRQ(ierr); 2753 if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim); 2754 n = 3; 2755 ierr = PetscOptionsEnumArray("-dm_plex_box_bd", "Boundary type for each dimension", "", DMBoundaryTypes, (PetscEnum *) bdt, &n, &flg);CHKERRQ(ierr); 2756 if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Box boundary types had %D values, should have been %D", n, dim); 2757 switch (cell) { 2758 case DM_POLYTOPE_TRI_PRISM_TENSOR: 2759 ierr = DMPlexCreateWedgeBoxMesh_Internal(dm, faces, lower, upper, bdt, PETSC_FALSE, interpolate);CHKERRQ(ierr); 2760 break; 2761 default: 2762 ierr = DMPlexCreateBoxMesh_Internal(dm, dim, simplex, faces, lower, upper, bdt, interpolate);CHKERRQ(ierr); 2763 break; 2764 } 2765 } 2766 break; 2767 case DM_SHAPE_BOX_SURFACE: 2768 { 2769 PetscInt faces[3] = {0, 0, 0}; 2770 PetscReal lower[3] = {0, 0, 0}; 2771 PetscReal upper[3] = {1, 1, 1}; 2772 PetscInt i, n; 2773 2774 n = dim+1; 2775 for (i = 0; i < dim+1; ++i) faces[i] = (dim+1 == 1 ? 1 : 4-(dim+1)); 2776 ierr = PetscOptionsIntArray("-dm_plex_box_faces", "Number of faces along each dimension", "", faces, &n, &flg);CHKERRQ(ierr); 2777 n = 3; 2778 ierr = PetscOptionsRealArray("-dm_plex_box_lower", "Lower left corner of box", "", lower, &n, &flg);CHKERRQ(ierr); 2779 if (flg && (n != dim+1)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim+1); 2780 n = 3; 2781 ierr = PetscOptionsRealArray("-dm_plex_box_upper", "Upper right corner of box", "", upper, &n, &flg);CHKERRQ(ierr); 2782 if (flg && (n != dim+1)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim+1); 2783 ierr = DMPlexCreateBoxSurfaceMesh_Internal(dm, dim+1, faces, lower, upper, interpolate);CHKERRQ(ierr); 2784 } 2785 break; 2786 case DM_SHAPE_SPHERE: 2787 { 2788 PetscReal R = 1.0; 2789 2790 ierr = PetscOptionsReal("-dm_plex_sphere_radius", "Radius of the sphere", "", R, &R, &flg);CHKERRQ(ierr); 2791 ierr = DMPlexCreateSphereMesh_Internal(dm, dim, simplex, R);CHKERRQ(ierr); 2792 } 2793 break; 2794 case DM_SHAPE_BALL: 2795 { 2796 PetscReal R = 1.0; 2797 2798 ierr = PetscOptionsReal("-dm_plex_ball_radius", "Radius of the ball", "", R, &R, &flg);CHKERRQ(ierr); 2799 ierr = DMPlexCreateBallMesh_Internal(dm, dim, R);CHKERRQ(ierr); 2800 } 2801 break; 2802 case DM_SHAPE_CYLINDER: 2803 { 2804 DMBoundaryType bdt = DM_BOUNDARY_NONE; 2805 PetscInt Nw = 6; 2806 2807 ierr = PetscOptionsEnum("-dm_plex_cylinder_bd", "Boundary type in the z direction", "", DMBoundaryTypes, (PetscEnum) bdt, (PetscEnum *) &bdt, NULL);CHKERRQ(ierr); 2808 ierr = PetscOptionsInt("-dm_plex_cylinder_num_wedges", "Number of wedges around the cylinder", "", Nw, &Nw, NULL);CHKERRQ(ierr); 2809 switch (cell) { 2810 case DM_POLYTOPE_TRI_PRISM_TENSOR: 2811 ierr = DMPlexCreateWedgeCylinderMesh_Internal(dm, Nw, interpolate);CHKERRQ(ierr); 2812 break; 2813 default: 2814 ierr = DMPlexCreateHexCylinderMesh_Internal(dm, bdt);CHKERRQ(ierr); 2815 break; 2816 } 2817 } 2818 break; 2819 default: SETERRQ1(comm, PETSC_ERR_SUP, "Domain shape %s is unsupported", DMPlexShapes[shape]); 2820 } 2821 } 2822 ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr); 2823 PetscFunctionReturn(0); 2824 } 2825 2826 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject, DM dm) 2827 { 2828 DM_Plex *mesh = (DM_Plex*) dm->data; 2829 PetscBool flg; 2830 char bdLabel[PETSC_MAX_PATH_LEN]; 2831 PetscErrorCode ierr; 2832 2833 PetscFunctionBegin; 2834 /* Handle viewing */ 2835 ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); 2836 ierr = PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL,0);CHKERRQ(ierr); 2837 ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL);CHKERRQ(ierr); 2838 ierr = PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL,0);CHKERRQ(ierr); 2839 ierr = DMMonitorSetFromOptions(dm, "-dm_plex_monitor_throughput", "Monitor the simulation throughput", "DMPlexMonitorThroughput", DMPlexMonitorThroughput, NULL, &flg);CHKERRQ(ierr); 2840 if (flg) {ierr = PetscLogDefaultBegin();CHKERRQ(ierr);} 2841 /* Labeling */ 2842 ierr = PetscOptionsString("-dm_plex_boundary_label", "Label to mark the mesh boundary", "", bdLabel, bdLabel, sizeof(bdLabel), &flg);CHKERRQ(ierr); 2843 if (flg) {ierr = DMPlexCreateBoundaryLabel_Private(dm, bdLabel);CHKERRQ(ierr);} 2844 /* Point Location */ 2845 ierr = PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL);CHKERRQ(ierr); 2846 /* Partitioning and distribution */ 2847 ierr = PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL);CHKERRQ(ierr); 2848 /* Generation and remeshing */ 2849 ierr = PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL);CHKERRQ(ierr); 2850 /* Projection behavior */ 2851 ierr = PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL,0);CHKERRQ(ierr); 2852 ierr = PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);CHKERRQ(ierr); 2853 ierr = PetscOptionsEnum("-dm_plex_cell_refiner", "Strategy for cell refinment", "", DMPlexCellRefinerTypes, (PetscEnum) mesh->cellRefiner, (PetscEnum *) &mesh->cellRefiner, NULL);CHKERRQ(ierr); 2854 /* Checking structure */ 2855 { 2856 PetscBool flg = PETSC_FALSE, flg2 = PETSC_FALSE, all = PETSC_FALSE; 2857 2858 ierr = PetscOptionsBool("-dm_plex_check_all", "Perform all checks", NULL, PETSC_FALSE, &all, &flg2);CHKERRQ(ierr); 2859 ierr = PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2860 if (all || (flg && flg2)) {ierr = DMPlexCheckSymmetry(dm);CHKERRQ(ierr);} 2861 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); 2862 if (all || (flg && flg2)) {ierr = DMPlexCheckSkeleton(dm, 0);CHKERRQ(ierr);} 2863 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); 2864 if (all || (flg && flg2)) {ierr = DMPlexCheckFaces(dm, 0);CHKERRQ(ierr);} 2865 ierr = PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2866 if (all || (flg && flg2)) {ierr = DMPlexCheckGeometry(dm);CHKERRQ(ierr);} 2867 ierr = PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2868 if (all || (flg && flg2)) {ierr = DMPlexCheckPointSF(dm);CHKERRQ(ierr);} 2869 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); 2870 if (all || (flg && flg2)) {ierr = DMPlexCheckInterfaceCones(dm);CHKERRQ(ierr);} 2871 ierr = PetscOptionsBool("-dm_plex_check_cell_shape", "Check cell shape", "DMPlexCheckCellShape", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2872 if (flg && flg2) {ierr = DMPlexCheckCellShape(dm, PETSC_TRUE, PETSC_DETERMINE);CHKERRQ(ierr);} 2873 } 2874 { 2875 PetscReal scale = 1.0; 2876 2877 ierr = PetscOptionsReal("-dm_plex_scale", "Scale factor for mesh coordinates", "DMPlexScale", scale, &scale, &flg);CHKERRQ(ierr); 2878 if (flg) { 2879 Vec coordinates, coordinatesLocal; 2880 2881 ierr = DMGetCoordinates(dm, &coordinates);CHKERRQ(ierr); 2882 ierr = DMGetCoordinatesLocal(dm, &coordinatesLocal);CHKERRQ(ierr); 2883 ierr = VecScale(coordinates, scale);CHKERRQ(ierr); 2884 ierr = VecScale(coordinatesLocal, scale);CHKERRQ(ierr); 2885 } 2886 } 2887 ierr = PetscPartitionerSetFromOptions(mesh->partitioner);CHKERRQ(ierr); 2888 PetscFunctionReturn(0); 2889 } 2890 2891 static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 2892 { 2893 PetscReal volume = -1.0, extThickness = 1.0; 2894 PetscInt prerefine = 0, refine = 0, r, coarsen = 0, overlap = 0, extLayers = 0, dim; 2895 PetscBool uniformOrig, created = PETSC_FALSE, uniform = PETSC_TRUE, distribute = PETSC_FALSE, interpolate = PETSC_TRUE, extColOrder = PETSC_TRUE, coordSpace = PETSC_TRUE, remap = PETSC_TRUE, ghostCells = PETSC_FALSE, isHierarchy, flg; 2896 PetscErrorCode ierr; 2897 2898 PetscFunctionBegin; 2899 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 2900 ierr = PetscOptionsHead(PetscOptionsObject,"DMPlex Options");CHKERRQ(ierr); 2901 /* Handle automatic creation */ 2902 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2903 if (dim < 0) {ierr = DMPlexCreateFromOptions_Internal(PetscOptionsObject, &coordSpace, dm);CHKERRQ(ierr);created = PETSC_TRUE;} 2904 /* Handle DMPlex refinement before distribution */ 2905 ierr = DMPlexGetRefinementUniform(dm, &uniformOrig);CHKERRQ(ierr); 2906 ierr = PetscOptionsBoundedInt("-dm_refine_pre", "The number of refinements before distribution", "DMCreate", prerefine, &prerefine, NULL,0);CHKERRQ(ierr); 2907 ierr = PetscOptionsBool("-dm_refine_remap_pre", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL);CHKERRQ(ierr); 2908 ierr = PetscOptionsBool("-dm_refine_uniform_pre", "Flag for uniform refinement before distribution", "DMCreate", uniform, &uniform, &flg);CHKERRQ(ierr); 2909 if (flg) {ierr = DMPlexSetRefinementUniform(dm, uniform);CHKERRQ(ierr);} 2910 ierr = PetscOptionsReal("-dm_refine_volume_limit_pre", "The maximum cell volume after refinement before distribution", "DMCreate", volume, &volume, &flg);CHKERRQ(ierr); 2911 if (flg) { 2912 ierr = DMPlexSetRefinementUniform(dm, PETSC_FALSE);CHKERRQ(ierr); 2913 ierr = DMPlexSetRefinementLimit(dm, volume);CHKERRQ(ierr); 2914 prerefine = PetscMax(prerefine, 1); 2915 } 2916 for (r = 0; r < prerefine; ++r) { 2917 DM rdm; 2918 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 2919 2920 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2921 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &rdm);CHKERRQ(ierr); 2922 ierr = DMPlexReplace_Static(dm, &rdm);CHKERRQ(ierr); 2923 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2924 if (coordFunc && remap) { 2925 ierr = DMPlexRemapGeometry(dm, 0.0, coordFunc);CHKERRQ(ierr); 2926 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 2927 } 2928 } 2929 ierr = DMPlexSetRefinementUniform(dm, uniformOrig);CHKERRQ(ierr); 2930 /* Handle DMPlex extrusion before distribution */ 2931 ierr = PetscOptionsBool("-dm_plex_interpolate", "Flag to create edges and faces automatically", "", interpolate, &interpolate, NULL);CHKERRQ(ierr); 2932 ierr = PetscOptionsBoundedInt("-dm_extrude_layers", "The number of layers to extrude", "", extLayers, &extLayers, NULL, 0);CHKERRQ(ierr); 2933 ierr = PetscOptionsReal("-dm_extrude_thickness", "The thickness of the layer to be extruded", "", extThickness, &extThickness, NULL);CHKERRQ(ierr); 2934 ierr = PetscOptionsBool("-dm_extrude_column_first", "Order the cells in a vertical column first", "", extColOrder, &extColOrder, NULL);CHKERRQ(ierr); 2935 if (extLayers) { 2936 DM edm; 2937 2938 ierr = DMPlexExtrude(dm, extLayers, extThickness, extColOrder, NULL, interpolate, &edm);CHKERRQ(ierr); 2939 ierr = DMPlexReplace_Static(dm, &edm);CHKERRQ(ierr); 2940 } 2941 /* Handle DMPlex distribution */ 2942 ierr = PetscOptionsBool("-dm_distribute", "Flag to redistribute a mesh among processes", "DMCreate", distribute, &distribute, NULL);CHKERRQ(ierr); 2943 ierr = PetscOptionsBoundedInt("-dm_distribute_overlap", "The size of the overlap halo", "DMCreate", overlap, &overlap, NULL, 0);CHKERRQ(ierr); 2944 if (distribute) { 2945 DM pdm = NULL; 2946 PetscPartitioner part; 2947 2948 ierr = DMPlexGetPartitioner(dm, &part);CHKERRQ(ierr); 2949 ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr); 2950 ierr = DMPlexDistribute(dm, overlap, NULL, &pdm);CHKERRQ(ierr); 2951 if (pdm) { 2952 ierr = DMPlexReplace_Static(dm, &pdm);CHKERRQ(ierr); 2953 } 2954 } 2955 /* Create coordinate space */ 2956 if (created) { 2957 DM_Plex *mesh = (DM_Plex *) dm->data; 2958 PetscInt degree = 1; 2959 PetscBool periodic, flg; 2960 2961 ierr = PetscOptionsBool("-dm_coord_space", "Use an FEM space for coordinates", "", coordSpace, &coordSpace, &flg);CHKERRQ(ierr); 2962 ierr = PetscOptionsInt("-dm_coord_petscspace_degree", "FEM degree for coordinate space", "", degree, °ree, NULL);CHKERRQ(ierr); 2963 if (coordSpace) {ierr = DMPlexCreateCoordinateSpace(dm, degree, mesh->coordFunc);CHKERRQ(ierr);} 2964 if (flg && !coordSpace) { 2965 DM cdm; 2966 PetscDS cds; 2967 PetscObject obj; 2968 PetscClassId id; 2969 2970 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 2971 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 2972 ierr = PetscDSGetDiscretization(cds, 0, &obj);CHKERRQ(ierr); 2973 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 2974 if (id == PETSCFE_CLASSID) { 2975 PetscContainer dummy; 2976 2977 ierr = PetscContainerCreate(PETSC_COMM_SELF, &dummy);CHKERRQ(ierr); 2978 ierr = PetscObjectSetName((PetscObject) dummy, "coordinates");CHKERRQ(ierr); 2979 ierr = DMSetField(cdm, 0, NULL, (PetscObject) dummy);CHKERRQ(ierr); 2980 ierr = PetscContainerDestroy(&dummy);CHKERRQ(ierr); 2981 ierr = DMClearDS(cdm);CHKERRQ(ierr); 2982 } 2983 mesh->coordFunc = NULL; 2984 } 2985 ierr = DMLocalizeCoordinates(dm);CHKERRQ(ierr); 2986 ierr = DMGetPeriodicity(dm, &periodic, NULL, NULL, NULL);CHKERRQ(ierr); 2987 if (periodic) {ierr = DMSetPeriodicity(dm, PETSC_TRUE, NULL, NULL, NULL);CHKERRQ(ierr);} 2988 } 2989 /* Handle DMPlex refinement */ 2990 remap = PETSC_TRUE; 2991 ierr = PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL,0);CHKERRQ(ierr); 2992 ierr = PetscOptionsBool("-dm_refine_remap", "Flag to control coordinate remapping", "DMCreate", remap, &remap, NULL);CHKERRQ(ierr); 2993 ierr = PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy,0);CHKERRQ(ierr); 2994 if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 2995 if (refine && isHierarchy) { 2996 DM *dms, coarseDM; 2997 2998 ierr = DMGetCoarseDM(dm, &coarseDM);CHKERRQ(ierr); 2999 ierr = PetscObjectReference((PetscObject)coarseDM);CHKERRQ(ierr); 3000 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 3001 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 3002 /* Total hack since we do not pass in a pointer */ 3003 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 3004 if (refine == 1) { 3005 ierr = DMSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 3006 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 3007 } else { 3008 ierr = DMSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 3009 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 3010 ierr = DMSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 3011 ierr = DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);CHKERRQ(ierr); 3012 } 3013 ierr = DMSetCoarseDM(dms[refine-1], coarseDM);CHKERRQ(ierr); 3014 ierr = PetscObjectDereference((PetscObject)coarseDM);CHKERRQ(ierr); 3015 /* Free DMs */ 3016 for (r = 0; r < refine; ++r) { 3017 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 3018 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 3019 } 3020 ierr = PetscFree(dms);CHKERRQ(ierr); 3021 } else { 3022 for (r = 0; r < refine; ++r) { 3023 DM rdm; 3024 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 3025 3026 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3027 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &rdm);CHKERRQ(ierr); 3028 /* Total hack since we do not pass in a pointer */ 3029 ierr = DMPlexReplace_Static(dm, &rdm);CHKERRQ(ierr); 3030 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3031 if (coordFunc && remap) { 3032 ierr = DMPlexRemapGeometry(dm, 0.0, coordFunc);CHKERRQ(ierr); 3033 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 3034 } 3035 } 3036 } 3037 /* Handle DMPlex coarsening */ 3038 ierr = PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL,0);CHKERRQ(ierr); 3039 ierr = PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy,0);CHKERRQ(ierr); 3040 if (coarsen && isHierarchy) { 3041 DM *dms; 3042 3043 ierr = PetscMalloc1(coarsen, &dms);CHKERRQ(ierr); 3044 ierr = DMCoarsenHierarchy(dm, coarsen, dms);CHKERRQ(ierr); 3045 /* Free DMs */ 3046 for (r = 0; r < coarsen; ++r) { 3047 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 3048 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 3049 } 3050 ierr = PetscFree(dms);CHKERRQ(ierr); 3051 } else { 3052 for (r = 0; r < coarsen; ++r) { 3053 DM cdm; 3054 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 3055 3056 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3057 ierr = DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &cdm);CHKERRQ(ierr); 3058 /* Total hack since we do not pass in a pointer */ 3059 ierr = DMPlexReplace_Static(dm, &cdm);CHKERRQ(ierr); 3060 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3061 if (coordFunc) { 3062 ierr = DMPlexRemapGeometry(dm, 0.0, coordFunc);CHKERRQ(ierr); 3063 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 3064 } 3065 } 3066 } 3067 /* Handle ghost cells */ 3068 ierr = PetscOptionsBool("-dm_plex_create_fv_ghost_cells", "Flag to create finite volume ghost cells on the boundary", "DMCreate", ghostCells, &ghostCells, NULL);CHKERRQ(ierr); 3069 if (ghostCells) { 3070 DM gdm; 3071 char lname[PETSC_MAX_PATH_LEN]; 3072 3073 lname[0] = '\0'; 3074 ierr = PetscOptionsString("-dm_plex_fv_ghost_cells_label", "Label name for ghost cells boundary", "DMCreate", lname, lname, sizeof(lname), &flg);CHKERRQ(ierr); 3075 ierr = DMPlexConstructGhostCells(dm, flg ? lname : NULL, NULL, &gdm);CHKERRQ(ierr); 3076 ierr = DMPlexReplace_Static(dm, &gdm);CHKERRQ(ierr); 3077 } 3078 /* Handle */ 3079 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3080 ierr = PetscOptionsTail();CHKERRQ(ierr); 3081 PetscFunctionReturn(0); 3082 } 3083 3084 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 3085 { 3086 PetscErrorCode ierr; 3087 3088 PetscFunctionBegin; 3089 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 3090 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 3091 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 3092 ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); 3093 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 3094 ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); 3095 PetscFunctionReturn(0); 3096 } 3097 3098 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 3099 { 3100 PetscErrorCode ierr; 3101 3102 PetscFunctionBegin; 3103 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 3104 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 3105 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 3106 PetscFunctionReturn(0); 3107 } 3108 3109 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 3110 { 3111 PetscInt depth, d; 3112 PetscErrorCode ierr; 3113 3114 PetscFunctionBegin; 3115 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 3116 if (depth == 1) { 3117 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 3118 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 3119 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 3120 else {*pStart = 0; *pEnd = 0;} 3121 } else { 3122 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 3123 } 3124 PetscFunctionReturn(0); 3125 } 3126 3127 static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 3128 { 3129 PetscSF sf; 3130 PetscInt niranks, njranks, n; 3131 const PetscMPIInt *iranks, *jranks; 3132 DM_Plex *data = (DM_Plex*) dm->data; 3133 PetscErrorCode ierr; 3134 3135 PetscFunctionBegin; 3136 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 3137 if (!data->neighbors) { 3138 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 3139 ierr = PetscSFGetRootRanks(sf, &njranks, &jranks, NULL, NULL, NULL);CHKERRQ(ierr); 3140 ierr = PetscSFGetLeafRanks(sf, &niranks, &iranks, NULL, NULL);CHKERRQ(ierr); 3141 ierr = PetscMalloc1(njranks + niranks + 1, &data->neighbors);CHKERRQ(ierr); 3142 ierr = PetscArraycpy(data->neighbors + 1, jranks, njranks);CHKERRQ(ierr); 3143 ierr = PetscArraycpy(data->neighbors + njranks + 1, iranks, niranks);CHKERRQ(ierr); 3144 n = njranks + niranks; 3145 ierr = PetscSortRemoveDupsMPIInt(&n, data->neighbors + 1);CHKERRQ(ierr); 3146 /* The following cast should never fail: can't have more neighbors than PETSC_MPI_INT_MAX */ 3147 ierr = PetscMPIIntCast(n, data->neighbors);CHKERRQ(ierr); 3148 } 3149 if (nranks) *nranks = data->neighbors[0]; 3150 if (ranks) { 3151 if (data->neighbors[0]) *ranks = data->neighbors + 1; 3152 else *ranks = NULL; 3153 } 3154 PetscFunctionReturn(0); 3155 } 3156 3157 PETSC_INTERN PetscErrorCode DMInterpolateSolution_Plex(DM, DM, Mat, Vec, Vec); 3158 3159 static PetscErrorCode DMInitialize_Plex(DM dm) 3160 { 3161 PetscErrorCode ierr; 3162 3163 PetscFunctionBegin; 3164 dm->ops->view = DMView_Plex; 3165 dm->ops->load = DMLoad_Plex; 3166 dm->ops->setfromoptions = DMSetFromOptions_Plex; 3167 dm->ops->clone = DMClone_Plex; 3168 dm->ops->setup = DMSetUp_Plex; 3169 dm->ops->createlocalsection = DMCreateLocalSection_Plex; 3170 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 3171 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 3172 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 3173 dm->ops->getlocaltoglobalmapping = NULL; 3174 dm->ops->createfieldis = NULL; 3175 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 3176 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 3177 dm->ops->getcoloring = NULL; 3178 dm->ops->creatematrix = DMCreateMatrix_Plex; 3179 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 3180 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 3181 dm->ops->createinjection = DMCreateInjection_Plex; 3182 dm->ops->refine = DMRefine_Plex; 3183 dm->ops->coarsen = DMCoarsen_Plex; 3184 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 3185 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 3186 dm->ops->adaptlabel = DMAdaptLabel_Plex; 3187 dm->ops->adaptmetric = DMAdaptMetric_Plex; 3188 dm->ops->globaltolocalbegin = NULL; 3189 dm->ops->globaltolocalend = NULL; 3190 dm->ops->localtoglobalbegin = NULL; 3191 dm->ops->localtoglobalend = NULL; 3192 dm->ops->destroy = DMDestroy_Plex; 3193 dm->ops->createsubdm = DMCreateSubDM_Plex; 3194 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 3195 dm->ops->getdimpoints = DMGetDimPoints_Plex; 3196 dm->ops->locatepoints = DMLocatePoints_Plex; 3197 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 3198 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 3199 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 3200 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 3201 dm->ops->projectbdfieldlabellocal = DMProjectBdFieldLabelLocal_Plex; 3202 dm->ops->computel2diff = DMComputeL2Diff_Plex; 3203 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 3204 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 3205 dm->ops->getneighbors = DMGetNeighbors_Plex; 3206 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);CHKERRQ(ierr); 3207 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertTimeDerviativeBoundaryValues_C",DMPlexInsertTimeDerivativeBoundaryValues_Plex);CHKERRQ(ierr); 3208 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);CHKERRQ(ierr); 3209 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C",DMCreateNeumannOverlap_Plex);CHKERRQ(ierr); 3210 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex);CHKERRQ(ierr); 3211 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMInterpolateSolution_C",DMInterpolateSolution_Plex);CHKERRQ(ierr); 3212 PetscFunctionReturn(0); 3213 } 3214 3215 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 3216 { 3217 DM_Plex *mesh = (DM_Plex *) dm->data; 3218 PetscErrorCode ierr; 3219 3220 PetscFunctionBegin; 3221 mesh->refct++; 3222 (*newdm)->data = mesh; 3223 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 3224 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 3225 PetscFunctionReturn(0); 3226 } 3227 3228 /*MC 3229 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 3230 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 3231 specified by a PetscSection object. Ownership in the global representation is determined by 3232 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 3233 3234 Options Database Keys: 3235 + -dm_refine_pre - Refine mesh before distribution 3236 + -dm_refine_uniform_pre - Choose uniform or generator-based refinement 3237 + -dm_refine_volume_limit_pre - Cell volume limit after pre-refinement using generator 3238 . -dm_distribute - Distribute mesh across processes 3239 . -dm_distribute_overlap - Number of cells to overlap for distribution 3240 . -dm_refine - Refine mesh after distribution 3241 . -dm_plex_hash_location - Use grid hashing for point location 3242 . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes 3243 . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing 3244 . -dm_plex_max_projection_height - Maxmimum mesh point height used to project locally 3245 . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement 3246 . -dm_plex_check_all - Perform all shecks below 3247 . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric 3248 . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices 3249 . -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 3250 . -dm_plex_check_geometry - Check that cells have positive volume 3251 . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ 3252 . -dm_plex_view_scale <num> - Scale the TikZ 3253 - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices 3254 3255 Level: intermediate 3256 3257 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 3258 M*/ 3259 3260 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 3261 { 3262 DM_Plex *mesh; 3263 PetscInt unit; 3264 PetscErrorCode ierr; 3265 3266 PetscFunctionBegin; 3267 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3268 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 3269 dm->data = mesh; 3270 3271 mesh->refct = 1; 3272 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 3273 mesh->maxConeSize = 0; 3274 mesh->cones = NULL; 3275 mesh->coneOrientations = NULL; 3276 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 3277 mesh->maxSupportSize = 0; 3278 mesh->supports = NULL; 3279 mesh->refinementUniform = PETSC_TRUE; 3280 mesh->refinementLimit = -1.0; 3281 mesh->interpolated = DMPLEX_INTERPOLATED_INVALID; 3282 mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID; 3283 3284 mesh->facesTmp = NULL; 3285 3286 mesh->tetgenOpts = NULL; 3287 mesh->triangleOpts = NULL; 3288 ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); 3289 mesh->remeshBd = PETSC_FALSE; 3290 3291 mesh->subpointMap = NULL; 3292 3293 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 3294 3295 mesh->regularRefinement = PETSC_FALSE; 3296 mesh->depthState = -1; 3297 mesh->celltypeState = -1; 3298 mesh->globalVertexNumbers = NULL; 3299 mesh->globalCellNumbers = NULL; 3300 mesh->anchorSection = NULL; 3301 mesh->anchorIS = NULL; 3302 mesh->createanchors = NULL; 3303 mesh->computeanchormatrix = NULL; 3304 mesh->parentSection = NULL; 3305 mesh->parents = NULL; 3306 mesh->childIDs = NULL; 3307 mesh->childSection = NULL; 3308 mesh->children = NULL; 3309 mesh->referenceTree = NULL; 3310 mesh->getchildsymmetry = NULL; 3311 mesh->vtkCellHeight = 0; 3312 mesh->useAnchors = PETSC_FALSE; 3313 3314 mesh->maxProjectionHeight = 0; 3315 3316 mesh->neighbors = NULL; 3317 3318 mesh->printSetValues = PETSC_FALSE; 3319 mesh->printFEM = 0; 3320 mesh->printTol = 1.0e-10; 3321 3322 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 3323 PetscFunctionReturn(0); 3324 } 3325 3326 /*@ 3327 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 3328 3329 Collective 3330 3331 Input Parameter: 3332 . comm - The communicator for the DMPlex object 3333 3334 Output Parameter: 3335 . mesh - The DMPlex object 3336 3337 Level: beginner 3338 3339 @*/ 3340 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 3341 { 3342 PetscErrorCode ierr; 3343 3344 PetscFunctionBegin; 3345 PetscValidPointer(mesh,2); 3346 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 3347 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 3348 PetscFunctionReturn(0); 3349 } 3350 3351 /*@C 3352 DMPlexBuildFromCellListParallel - Build distributed DMPLEX topology from a list of vertices for each cell (common mesh generator output) 3353 3354 Input Parameters: 3355 + dm - The DM 3356 . numCells - The number of cells owned by this process 3357 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 3358 . NVertices - The global number of vertices, or PETSC_DECIDE 3359 . numCorners - The number of vertices for each cell 3360 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 3361 3362 Output Parameter: 3363 . vertexSF - (Optional) SF describing complete vertex ownership 3364 3365 Notes: 3366 Two triangles sharing a face 3367 $ 3368 $ 2 3369 $ / | \ 3370 $ / | \ 3371 $ / | \ 3372 $ 0 0 | 1 3 3373 $ \ | / 3374 $ \ | / 3375 $ \ | / 3376 $ 1 3377 would have input 3378 $ numCells = 2, numVertices = 4 3379 $ cells = [0 1 2 1 3 2] 3380 $ 3381 which would result in the DMPlex 3382 $ 3383 $ 4 3384 $ / | \ 3385 $ / | \ 3386 $ / | \ 3387 $ 2 0 | 1 5 3388 $ \ | / 3389 $ \ | / 3390 $ \ | / 3391 $ 3 3392 3393 Vertices are implicitly numbered consecutively 0,...,NVertices. 3394 Each rank owns a chunk of numVertices consecutive vertices. 3395 If numVertices is PETSC_DECIDE, PETSc will distribute them as evenly as possible using PetscLayout. 3396 If both NVertices and numVertices are PETSC_DECIDE, NVertices is computed by PETSc as the maximum vertex index in cells + 1. 3397 If only NVertices is PETSC_DECIDE, it is computed as the sum of numVertices over all ranks. 3398 3399 The cell distribution is arbitrary non-overlapping, independent of the vertex distribution. 3400 3401 Not currently supported in Fortran. 3402 3403 Level: advanced 3404 3405 .seealso: DMPlexBuildFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildCoordinatesFromCellListParallel() 3406 @*/ 3407 PetscErrorCode DMPlexBuildFromCellListParallel(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, const PetscInt cells[], PetscSF *vertexSF) 3408 { 3409 PetscSF sfPoint; 3410 PetscLayout layout; 3411 PetscInt numVerticesAdj, *verticesAdj, *cones, c, p, dim; 3412 PetscMPIInt rank, size; 3413 PetscErrorCode ierr; 3414 3415 PetscFunctionBegin; 3416 PetscValidLogicalCollectiveInt(dm,NVertices,4); 3417 ierr = PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3418 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 3419 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRMPI(ierr); 3420 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3421 /* Get/check global number of vertices */ 3422 { 3423 PetscInt NVerticesInCells, i; 3424 const PetscInt len = numCells * numCorners; 3425 3426 /* NVerticesInCells = max(cells) + 1 */ 3427 NVerticesInCells = PETSC_MIN_INT; 3428 for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 3429 ++NVerticesInCells; 3430 ierr = MPI_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject) dm));CHKERRMPI(ierr); 3431 3432 if (numVertices == PETSC_DECIDE && NVertices == PETSC_DECIDE) NVertices = NVerticesInCells; 3433 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); 3434 } 3435 /* Count locally unique vertices */ 3436 { 3437 PetscHSetI vhash; 3438 PetscInt off = 0; 3439 3440 ierr = PetscHSetICreate(&vhash);CHKERRQ(ierr); 3441 for (c = 0; c < numCells; ++c) { 3442 for (p = 0; p < numCorners; ++p) { 3443 ierr = PetscHSetIAdd(vhash, cells[c*numCorners+p]);CHKERRQ(ierr); 3444 } 3445 } 3446 ierr = PetscHSetIGetSize(vhash, &numVerticesAdj);CHKERRQ(ierr); 3447 ierr = PetscMalloc1(numVerticesAdj, &verticesAdj);CHKERRQ(ierr); 3448 ierr = PetscHSetIGetElems(vhash, &off, verticesAdj);CHKERRQ(ierr); 3449 ierr = PetscHSetIDestroy(&vhash);CHKERRQ(ierr); 3450 if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj); 3451 } 3452 ierr = PetscSortInt(numVerticesAdj, verticesAdj);CHKERRQ(ierr); 3453 /* Create cones */ 3454 ierr = DMPlexSetChart(dm, 0, numCells+numVerticesAdj);CHKERRQ(ierr); 3455 for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);} 3456 ierr = DMSetUp(dm);CHKERRQ(ierr); 3457 ierr = DMPlexGetCones(dm,&cones);CHKERRQ(ierr); 3458 for (c = 0; c < numCells; ++c) { 3459 for (p = 0; p < numCorners; ++p) { 3460 const PetscInt gv = cells[c*numCorners+p]; 3461 PetscInt lv; 3462 3463 /* Positions within verticesAdj form 0-based local vertex numbering; 3464 we need to shift it by numCells to get correct DAG points (cells go first) */ 3465 ierr = PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);CHKERRQ(ierr); 3466 if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv); 3467 cones[c*numCorners+p] = lv+numCells; 3468 } 3469 } 3470 /* Build point sf */ 3471 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &layout);CHKERRQ(ierr); 3472 ierr = PetscLayoutSetSize(layout, NVertices);CHKERRQ(ierr); 3473 ierr = PetscLayoutSetLocalSize(layout, numVertices);CHKERRQ(ierr); 3474 ierr = PetscLayoutSetBlockSize(layout, 1);CHKERRQ(ierr); 3475 ierr = PetscSFCreateByMatchingIndices(layout, numVerticesAdj, verticesAdj, NULL, numCells, numVerticesAdj, verticesAdj, NULL, numCells, vertexSF, &sfPoint);CHKERRQ(ierr); 3476 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 3477 ierr = PetscFree(verticesAdj);CHKERRQ(ierr); 3478 ierr = PetscObjectSetName((PetscObject) sfPoint, "point SF");CHKERRQ(ierr); 3479 if (dm->sf) { 3480 const char *prefix; 3481 3482 ierr = PetscObjectGetOptionsPrefix((PetscObject)dm->sf, &prefix);CHKERRQ(ierr); 3483 ierr = PetscObjectSetOptionsPrefix((PetscObject)sfPoint, prefix);CHKERRQ(ierr); 3484 } 3485 ierr = DMSetPointSF(dm, sfPoint);CHKERRQ(ierr); 3486 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 3487 if (vertexSF) {ierr = PetscObjectSetName((PetscObject)(*vertexSF), "Vertex Ownership SF");CHKERRQ(ierr);} 3488 /* Fill in the rest of the topology structure */ 3489 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3490 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3491 ierr = PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3492 PetscFunctionReturn(0); 3493 } 3494 3495 /*@C 3496 DMPlexBuildCoordinatesFromCellListParallel - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output) 3497 3498 Input Parameters: 3499 + dm - The DM 3500 . spaceDim - The spatial dimension used for coordinates 3501 . sfVert - SF describing complete vertex ownership 3502 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3503 3504 Level: advanced 3505 3506 Notes: 3507 Not currently supported in Fortran. 3508 3509 .seealso: DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellListParallel() 3510 @*/ 3511 PetscErrorCode DMPlexBuildCoordinatesFromCellListParallel(DM dm, PetscInt spaceDim, PetscSF sfVert, const PetscReal vertexCoords[]) 3512 { 3513 PetscSection coordSection; 3514 Vec coordinates; 3515 PetscScalar *coords; 3516 PetscInt numVertices, numVerticesAdj, coordSize, v, vStart, vEnd; 3517 PetscErrorCode ierr; 3518 3519 PetscFunctionBegin; 3520 ierr = PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3521 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 3522 if (vStart < 0 || vEnd < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 3523 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 3524 ierr = PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);CHKERRQ(ierr); 3525 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); 3526 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3527 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3528 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 3529 ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr); 3530 for (v = vStart; v < vEnd; ++v) { 3531 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 3532 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 3533 } 3534 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3535 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3536 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 3537 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 3538 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3539 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3540 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 3541 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3542 { 3543 MPI_Datatype coordtype; 3544 3545 /* Need a temp buffer for coords if we have complex/single */ 3546 ierr = MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);CHKERRMPI(ierr); 3547 ierr = MPI_Type_commit(&coordtype);CHKERRMPI(ierr); 3548 #if defined(PETSC_USE_COMPLEX) 3549 { 3550 PetscScalar *svertexCoords; 3551 PetscInt i; 3552 ierr = PetscMalloc1(numVertices*spaceDim,&svertexCoords);CHKERRQ(ierr); 3553 for (i=0; i<numVertices*spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 3554 ierr = PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 3555 ierr = PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 3556 ierr = PetscFree(svertexCoords);CHKERRQ(ierr); 3557 } 3558 #else 3559 ierr = PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 3560 ierr = PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 3561 #endif 3562 ierr = MPI_Type_free(&coordtype);CHKERRMPI(ierr); 3563 } 3564 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3565 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3566 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3567 ierr = PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3568 PetscFunctionReturn(0); 3569 } 3570 3571 /*@ 3572 DMPlexCreateFromCellListParallelPetsc - Create distributed DMPLEX from a list of vertices for each cell (common mesh generator output) 3573 3574 Input Parameters: 3575 + comm - The communicator 3576 . dim - The topological dimension of the mesh 3577 . numCells - The number of cells owned by this process 3578 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 3579 . NVertices - The global number of vertices, or PETSC_DECIDE 3580 . numCorners - The number of vertices for each cell 3581 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 3582 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 3583 . spaceDim - The spatial dimension used for coordinates 3584 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3585 3586 Output Parameter: 3587 + dm - The DM 3588 - vertexSF - (Optional) SF describing complete vertex ownership 3589 3590 Notes: 3591 This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), 3592 DMPlexBuildFromCellListParallel(), DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellListParallel() 3593 3594 See DMPlexBuildFromCellListParallel() for an example and details about the topology-related parameters. 3595 See DMPlexBuildCoordinatesFromCellListParallel() for details about the geometry-related parameters. 3596 3597 Level: intermediate 3598 3599 .seealso: DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromDAG(), DMPlexCreate() 3600 @*/ 3601 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) 3602 { 3603 PetscSF sfVert; 3604 PetscErrorCode ierr; 3605 3606 PetscFunctionBegin; 3607 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3608 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3609 PetscValidLogicalCollectiveInt(*dm, dim, 2); 3610 PetscValidLogicalCollectiveInt(*dm, spaceDim, 9); 3611 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3612 ierr = DMPlexBuildFromCellListParallel(*dm, numCells, numVertices, NVertices, numCorners, cells, &sfVert);CHKERRQ(ierr); 3613 if (interpolate) { 3614 DM idm; 3615 3616 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3617 ierr = DMDestroy(dm);CHKERRQ(ierr); 3618 *dm = idm; 3619 } 3620 ierr = DMPlexBuildCoordinatesFromCellListParallel(*dm, spaceDim, sfVert, vertexCoords);CHKERRQ(ierr); 3621 if (vertexSF) *vertexSF = sfVert; 3622 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 3623 PetscFunctionReturn(0); 3624 } 3625 3626 /*@ 3627 DMPlexCreateFromCellListParallel - Deprecated, use DMPlexCreateFromCellListParallelPetsc() 3628 3629 Level: deprecated 3630 3631 .seealso: DMPlexCreateFromCellListParallelPetsc() 3632 @*/ 3633 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) 3634 { 3635 PetscErrorCode ierr; 3636 PetscInt i; 3637 PetscInt *pintCells; 3638 3639 PetscFunctionBegin; 3640 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)); 3641 if (sizeof(int) == sizeof(PetscInt)) { 3642 pintCells = (PetscInt *) cells; 3643 } else { 3644 ierr = PetscMalloc1(numCells*numCorners, &pintCells);CHKERRQ(ierr); 3645 for (i = 0; i < numCells*numCorners; i++) { 3646 pintCells[i] = (PetscInt) cells[i]; 3647 } 3648 } 3649 ierr = DMPlexCreateFromCellListParallelPetsc(comm, dim, numCells, numVertices, PETSC_DECIDE, numCorners, interpolate, pintCells, spaceDim, vertexCoords, vertexSF, dm);CHKERRQ(ierr); 3650 if (sizeof(int) != sizeof(PetscInt)) { 3651 ierr = PetscFree(pintCells);CHKERRQ(ierr); 3652 } 3653 PetscFunctionReturn(0); 3654 } 3655 3656 /*@C 3657 DMPlexBuildFromCellList - Build DMPLEX topology from a list of vertices for each cell (common mesh generator output) 3658 3659 Input Parameters: 3660 + dm - The DM 3661 . numCells - The number of cells owned by this process 3662 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 3663 . numCorners - The number of vertices for each cell 3664 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 3665 3666 Level: advanced 3667 3668 Notes: 3669 Two triangles sharing a face 3670 $ 3671 $ 2 3672 $ / | \ 3673 $ / | \ 3674 $ / | \ 3675 $ 0 0 | 1 3 3676 $ \ | / 3677 $ \ | / 3678 $ \ | / 3679 $ 1 3680 would have input 3681 $ numCells = 2, numVertices = 4 3682 $ cells = [0 1 2 1 3 2] 3683 $ 3684 which would result in the DMPlex 3685 $ 3686 $ 4 3687 $ / | \ 3688 $ / | \ 3689 $ / | \ 3690 $ 2 0 | 1 5 3691 $ \ | / 3692 $ \ | / 3693 $ \ | / 3694 $ 3 3695 3696 If numVertices is PETSC_DECIDE, it is computed by PETSc as the maximum vertex index in cells + 1. 3697 3698 Not currently supported in Fortran. 3699 3700 .seealso: DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListPetsc() 3701 @*/ 3702 PetscErrorCode DMPlexBuildFromCellList(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[]) 3703 { 3704 PetscInt *cones, c, p, dim; 3705 PetscErrorCode ierr; 3706 3707 PetscFunctionBegin; 3708 ierr = PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3709 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3710 /* Get/check global number of vertices */ 3711 { 3712 PetscInt NVerticesInCells, i; 3713 const PetscInt len = numCells * numCorners; 3714 3715 /* NVerticesInCells = max(cells) + 1 */ 3716 NVerticesInCells = PETSC_MIN_INT; 3717 for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 3718 ++NVerticesInCells; 3719 3720 if (numVertices == PETSC_DECIDE) numVertices = NVerticesInCells; 3721 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); 3722 } 3723 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 3724 for (c = 0; c < numCells; ++c) { 3725 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 3726 } 3727 ierr = DMSetUp(dm);CHKERRQ(ierr); 3728 ierr = DMPlexGetCones(dm,&cones);CHKERRQ(ierr); 3729 for (c = 0; c < numCells; ++c) { 3730 for (p = 0; p < numCorners; ++p) { 3731 cones[c*numCorners+p] = cells[c*numCorners+p]+numCells; 3732 } 3733 } 3734 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3735 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3736 ierr = PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3737 PetscFunctionReturn(0); 3738 } 3739 3740 /*@C 3741 DMPlexBuildCoordinatesFromCellList - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output) 3742 3743 Input Parameters: 3744 + dm - The DM 3745 . spaceDim - The spatial dimension used for coordinates 3746 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3747 3748 Level: advanced 3749 3750 Notes: 3751 Not currently supported in Fortran. 3752 3753 .seealso: DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellList() 3754 @*/ 3755 PetscErrorCode DMPlexBuildCoordinatesFromCellList(DM dm, PetscInt spaceDim, const PetscReal vertexCoords[]) 3756 { 3757 PetscSection coordSection; 3758 Vec coordinates; 3759 DM cdm; 3760 PetscScalar *coords; 3761 PetscInt v, vStart, vEnd, d; 3762 PetscErrorCode ierr; 3763 3764 PetscFunctionBegin; 3765 ierr = PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3766 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 3767 if (vStart < 0 || vEnd < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 3768 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 3769 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3770 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3771 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 3772 ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr); 3773 for (v = vStart; v < vEnd; ++v) { 3774 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 3775 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 3776 } 3777 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3778 3779 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 3780 ierr = DMCreateLocalVector(cdm, &coordinates);CHKERRQ(ierr); 3781 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 3782 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3783 ierr = VecGetArrayWrite(coordinates, &coords);CHKERRQ(ierr); 3784 for (v = 0; v < vEnd-vStart; ++v) { 3785 for (d = 0; d < spaceDim; ++d) { 3786 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 3787 } 3788 } 3789 ierr = VecRestoreArrayWrite(coordinates, &coords);CHKERRQ(ierr); 3790 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3791 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3792 ierr = PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3793 PetscFunctionReturn(0); 3794 } 3795 3796 /*@ 3797 DMPlexCreateFromCellListPetsc - Create DMPLEX from a list of vertices for each cell (common mesh generator output) 3798 3799 Input Parameters: 3800 + comm - The communicator 3801 . dim - The topological dimension of the mesh 3802 . numCells - The number of cells 3803 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 3804 . numCorners - The number of vertices for each cell 3805 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 3806 . cells - An array of numCells*numCorners numbers, the vertices for each cell 3807 . spaceDim - The spatial dimension used for coordinates 3808 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3809 3810 Output Parameter: 3811 . dm - The DM 3812 3813 Notes: 3814 This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), DMPlexBuildFromCellList(), 3815 DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellList() 3816 3817 See DMPlexBuildFromCellList() for an example and details about the topology-related parameters. 3818 See DMPlexBuildCoordinatesFromCellList() for details about the geometry-related parameters. 3819 3820 Level: intermediate 3821 3822 .seealso: DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellList(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate() 3823 @*/ 3824 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) 3825 { 3826 PetscErrorCode ierr; 3827 3828 PetscFunctionBegin; 3829 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."); 3830 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3831 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3832 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3833 ierr = DMPlexBuildFromCellList(*dm, numCells, numVertices, numCorners, cells);CHKERRQ(ierr); 3834 if (interpolate) { 3835 DM idm; 3836 3837 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3838 ierr = DMDestroy(dm);CHKERRQ(ierr); 3839 *dm = idm; 3840 } 3841 ierr = DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, vertexCoords);CHKERRQ(ierr); 3842 PetscFunctionReturn(0); 3843 } 3844 3845 /*@ 3846 DMPlexCreateFromCellList - Deprecated, use DMPlexCreateFromCellListPetsc() 3847 3848 Level: deprecated 3849 3850 .seealso: DMPlexCreateFromCellListPetsc() 3851 @*/ 3852 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) 3853 { 3854 PetscErrorCode ierr; 3855 PetscInt i; 3856 PetscInt *pintCells; 3857 PetscReal *prealVC; 3858 3859 PetscFunctionBegin; 3860 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)); 3861 if (sizeof(int) == sizeof(PetscInt)) { 3862 pintCells = (PetscInt *) cells; 3863 } else { 3864 ierr = PetscMalloc1(numCells*numCorners, &pintCells);CHKERRQ(ierr); 3865 for (i = 0; i < numCells*numCorners; i++) { 3866 pintCells[i] = (PetscInt) cells[i]; 3867 } 3868 } 3869 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)); 3870 if (sizeof(double) == sizeof(PetscReal)) { 3871 prealVC = (PetscReal *) vertexCoords; 3872 } else { 3873 ierr = PetscMalloc1(numVertices*spaceDim, &prealVC);CHKERRQ(ierr); 3874 for (i = 0; i < numVertices*spaceDim; i++) { 3875 prealVC[i] = (PetscReal) vertexCoords[i]; 3876 } 3877 } 3878 ierr = DMPlexCreateFromCellListPetsc(comm, dim, numCells, numVertices, numCorners, interpolate, pintCells, spaceDim, prealVC, dm);CHKERRQ(ierr); 3879 if (sizeof(int) != sizeof(PetscInt)) { 3880 ierr = PetscFree(pintCells);CHKERRQ(ierr); 3881 } 3882 if (sizeof(double) != sizeof(PetscReal)) { 3883 ierr = PetscFree(prealVC);CHKERRQ(ierr); 3884 } 3885 PetscFunctionReturn(0); 3886 } 3887 3888 /*@ 3889 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 3890 3891 Input Parameters: 3892 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 3893 . depth - The depth of the DAG 3894 . numPoints - Array of size depth + 1 containing the number of points at each depth 3895 . coneSize - The cone size of each point 3896 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 3897 . coneOrientations - The orientation of each cone point 3898 - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim() 3899 3900 Output Parameter: 3901 . dm - The DM 3902 3903 Note: Two triangles sharing a face would have input 3904 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 3905 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 3906 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 3907 $ 3908 which would result in the DMPlex 3909 $ 3910 $ 4 3911 $ / | \ 3912 $ / | \ 3913 $ / | \ 3914 $ 2 0 | 1 5 3915 $ \ | / 3916 $ \ | / 3917 $ \ | / 3918 $ 3 3919 $ 3920 $ Notice that all points are numbered consecutively, unlike DMPlexCreateFromCellListPetsc() 3921 3922 Level: advanced 3923 3924 .seealso: DMPlexCreateFromCellListPetsc(), DMPlexCreate() 3925 @*/ 3926 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 3927 { 3928 Vec coordinates; 3929 PetscSection coordSection; 3930 PetscScalar *coords; 3931 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 3932 PetscErrorCode ierr; 3933 3934 PetscFunctionBegin; 3935 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3936 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 3937 if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %D cannot be less than intrinsic dimension %d",dimEmbed,dim); 3938 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 3939 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 3940 for (p = pStart; p < pEnd; ++p) { 3941 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 3942 if (firstVertex < 0 && !coneSize[p - pStart]) { 3943 firstVertex = p - pStart; 3944 } 3945 } 3946 if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %D vertices but could not find any", numPoints[0]); 3947 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 3948 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 3949 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 3950 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 3951 } 3952 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3953 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3954 /* Build coordinates */ 3955 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3956 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3957 ierr = PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);CHKERRQ(ierr); 3958 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 3959 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 3960 ierr = PetscSectionSetDof(coordSection, v, dimEmbed);CHKERRQ(ierr); 3961 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);CHKERRQ(ierr); 3962 } 3963 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3964 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3965 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3966 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3967 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3968 ierr = VecSetBlockSize(coordinates, dimEmbed);CHKERRQ(ierr); 3969 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 3970 if (vertexCoords) { 3971 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3972 for (v = 0; v < numPoints[0]; ++v) { 3973 PetscInt off; 3974 3975 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 3976 for (d = 0; d < dimEmbed; ++d) { 3977 coords[off+d] = vertexCoords[v*dimEmbed+d]; 3978 } 3979 } 3980 } 3981 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3982 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3983 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3984 PetscFunctionReturn(0); 3985 } 3986 3987 /*@C 3988 DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file. 3989 3990 + comm - The MPI communicator 3991 . filename - Name of the .dat file 3992 - interpolate - Create faces and edges in the mesh 3993 3994 Output Parameter: 3995 . dm - The DM object representing the mesh 3996 3997 Note: The format is the simplest possible: 3998 $ Ne 3999 $ v0 v1 ... vk 4000 $ Nv 4001 $ x y z marker 4002 4003 Level: beginner 4004 4005 .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate() 4006 @*/ 4007 PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 4008 { 4009 DMLabel marker; 4010 PetscViewer viewer; 4011 Vec coordinates; 4012 PetscSection coordSection; 4013 PetscScalar *coords; 4014 char line[PETSC_MAX_PATH_LEN]; 4015 PetscInt dim = 3, cdim = 3, coordSize, v, c, d; 4016 PetscMPIInt rank; 4017 int snum, Nv, Nc; 4018 PetscErrorCode ierr; 4019 4020 PetscFunctionBegin; 4021 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 4022 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 4023 ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr); 4024 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 4025 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 4026 if (!rank) { 4027 ierr = PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);CHKERRQ(ierr); 4028 snum = sscanf(line, "%d %d", &Nc, &Nv); 4029 if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4030 } else { 4031 Nc = Nv = 0; 4032 } 4033 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 4034 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 4035 ierr = DMPlexSetChart(*dm, 0, Nc+Nv);CHKERRQ(ierr); 4036 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 4037 ierr = DMSetCoordinateDim(*dm, cdim);CHKERRQ(ierr); 4038 /* Read topology */ 4039 if (!rank) { 4040 PetscInt cone[8], corners = 8; 4041 int vbuf[8], v; 4042 4043 for (c = 0; c < Nc; ++c) {ierr = DMPlexSetConeSize(*dm, c, corners);CHKERRQ(ierr);} 4044 ierr = DMSetUp(*dm);CHKERRQ(ierr); 4045 for (c = 0; c < Nc; ++c) { 4046 ierr = PetscViewerRead(viewer, line, corners, NULL, PETSC_STRING);CHKERRQ(ierr); 4047 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]); 4048 if (snum != corners) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4049 for (v = 0; v < corners; ++v) cone[v] = vbuf[v] + Nc; 4050 /* Hexahedra are inverted */ 4051 { 4052 PetscInt tmp = cone[1]; 4053 cone[1] = cone[3]; 4054 cone[3] = tmp; 4055 } 4056 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 4057 } 4058 } 4059 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 4060 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 4061 /* Read coordinates */ 4062 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 4063 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 4064 ierr = PetscSectionSetFieldComponents(coordSection, 0, cdim);CHKERRQ(ierr); 4065 ierr = PetscSectionSetChart(coordSection, Nc, Nc + Nv);CHKERRQ(ierr); 4066 for (v = Nc; v < Nc+Nv; ++v) { 4067 ierr = PetscSectionSetDof(coordSection, v, cdim);CHKERRQ(ierr); 4068 ierr = PetscSectionSetFieldDof(coordSection, v, 0, cdim);CHKERRQ(ierr); 4069 } 4070 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 4071 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 4072 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 4073 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 4074 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 4075 ierr = VecSetBlockSize(coordinates, cdim);CHKERRQ(ierr); 4076 ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr); 4077 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 4078 if (!rank) { 4079 double x[3]; 4080 int val; 4081 4082 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 4083 ierr = DMGetLabel(*dm, "marker", &marker);CHKERRQ(ierr); 4084 for (v = 0; v < Nv; ++v) { 4085 ierr = PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);CHKERRQ(ierr); 4086 snum = sscanf(line, "%lg %lg %lg %d", &x[0], &x[1], &x[2], &val); 4087 if (snum != 4) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4088 for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d]; 4089 if (val) {ierr = DMLabelSetValue(marker, v+Nc, val);CHKERRQ(ierr);} 4090 } 4091 } 4092 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 4093 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 4094 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 4095 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 4096 if (interpolate) { 4097 DM idm; 4098 DMLabel bdlabel; 4099 4100 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 4101 ierr = DMDestroy(dm);CHKERRQ(ierr); 4102 *dm = idm; 4103 4104 ierr = DMGetLabel(*dm, "marker", &bdlabel);CHKERRQ(ierr); 4105 ierr = DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 4106 ierr = DMPlexLabelComplete(*dm, bdlabel);CHKERRQ(ierr); 4107 } 4108 PetscFunctionReturn(0); 4109 } 4110 4111 /*@C 4112 DMPlexCreateFromFile - This takes a filename and produces a DM 4113 4114 Input Parameters: 4115 + comm - The communicator 4116 . filename - A file name 4117 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 4118 4119 Output Parameter: 4120 . dm - The DM 4121 4122 Options Database Keys: 4123 . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5 4124 4125 Use -dm_plex_create_ prefix to pass options to the internal PetscViewer, e.g. 4126 $ -dm_plex_create_viewer_hdf5_collective 4127 4128 Level: beginner 4129 4130 .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellListPetsc(), DMPlexCreate() 4131 @*/ 4132 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 4133 { 4134 const char *extGmsh = ".msh"; 4135 const char *extGmsh2 = ".msh2"; 4136 const char *extGmsh4 = ".msh4"; 4137 const char *extCGNS = ".cgns"; 4138 const char *extExodus = ".exo"; 4139 const char *extGenesis = ".gen"; 4140 const char *extFluent = ".cas"; 4141 const char *extHDF5 = ".h5"; 4142 const char *extMed = ".med"; 4143 const char *extPLY = ".ply"; 4144 const char *extEGADS = ".egadslite"; 4145 const char *extCV = ".dat"; 4146 size_t len; 4147 PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isEGADS, isCV; 4148 PetscMPIInt rank; 4149 PetscErrorCode ierr; 4150 4151 PetscFunctionBegin; 4152 PetscValidCharPointer(filename, 2); 4153 PetscValidPointer(dm, 4); 4154 ierr = DMInitializePackage();CHKERRQ(ierr); 4155 ierr = PetscLogEventBegin(DMPLEX_CreateFromFile,0,0,0,0);CHKERRQ(ierr); 4156 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 4157 ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); 4158 if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 4159 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);CHKERRQ(ierr); 4160 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh2, 5, &isGmsh2);CHKERRQ(ierr); 4161 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh4, 5, &isGmsh4);CHKERRQ(ierr); 4162 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);CHKERRQ(ierr); 4163 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);CHKERRQ(ierr); 4164 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);CHKERRQ(ierr); 4165 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);CHKERRQ(ierr); 4166 ierr = PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);CHKERRQ(ierr); 4167 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);CHKERRQ(ierr); 4168 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);CHKERRQ(ierr); 4169 ierr = PetscStrncmp(&filename[PetscMax(0,len-10)], extEGADS, 9, &isEGADS);CHKERRQ(ierr); 4170 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);CHKERRQ(ierr); 4171 if (isGmsh || isGmsh2 || isGmsh4) { 4172 ierr = DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4173 } else if (isCGNS) { 4174 ierr = DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4175 } else if (isExodus || isGenesis) { 4176 ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4177 } else if (isFluent) { 4178 ierr = DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4179 } else if (isHDF5) { 4180 PetscBool load_hdf5_xdmf = PETSC_FALSE; 4181 PetscViewer viewer; 4182 4183 /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */ 4184 ierr = PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf", 5, &load_hdf5_xdmf);CHKERRQ(ierr); 4185 ierr = PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);CHKERRQ(ierr); 4186 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 4187 ierr = PetscViewerSetType(viewer, PETSCVIEWERHDF5);CHKERRQ(ierr); 4188 ierr = PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_");CHKERRQ(ierr); 4189 ierr = PetscViewerSetFromOptions(viewer);CHKERRQ(ierr); 4190 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 4191 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 4192 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 4193 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 4194 if (load_hdf5_xdmf) {ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);CHKERRQ(ierr);} 4195 ierr = DMLoad(*dm, viewer);CHKERRQ(ierr); 4196 if (load_hdf5_xdmf) {ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);} 4197 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 4198 4199 if (interpolate) { 4200 DM idm; 4201 4202 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 4203 ierr = DMDestroy(dm);CHKERRQ(ierr); 4204 *dm = idm; 4205 } 4206 } else if (isMed) { 4207 ierr = DMPlexCreateMedFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4208 } else if (isPLY) { 4209 ierr = DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4210 } else if (isEGADS) { 4211 ierr = DMPlexCreateEGADSFromFile(comm, filename, dm);CHKERRQ(ierr); 4212 if (!interpolate) { 4213 DM udm; 4214 4215 ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr); 4216 ierr = DMDestroy(dm);CHKERRQ(ierr); 4217 *dm = udm; 4218 } 4219 } else if (isCV) { 4220 ierr = DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4221 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 4222 ierr = PetscLogEventEnd(DMPLEX_CreateFromFile,0,0,0,0);CHKERRQ(ierr); 4223 PetscFunctionReturn(0); 4224 } 4225