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, 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 */ 3068 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 3069 ierr = PetscOptionsTail();CHKERRQ(ierr); 3070 PetscFunctionReturn(0); 3071 } 3072 3073 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 3074 { 3075 PetscErrorCode ierr; 3076 3077 PetscFunctionBegin; 3078 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 3079 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 3080 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 3081 ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); 3082 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 3083 ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); 3084 PetscFunctionReturn(0); 3085 } 3086 3087 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 3088 { 3089 PetscErrorCode ierr; 3090 3091 PetscFunctionBegin; 3092 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 3093 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 3094 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 3095 PetscFunctionReturn(0); 3096 } 3097 3098 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 3099 { 3100 PetscInt depth, d; 3101 PetscErrorCode ierr; 3102 3103 PetscFunctionBegin; 3104 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 3105 if (depth == 1) { 3106 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 3107 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 3108 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 3109 else {*pStart = 0; *pEnd = 0;} 3110 } else { 3111 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 3112 } 3113 PetscFunctionReturn(0); 3114 } 3115 3116 static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 3117 { 3118 PetscSF sf; 3119 PetscInt niranks, njranks, n; 3120 const PetscMPIInt *iranks, *jranks; 3121 DM_Plex *data = (DM_Plex*) dm->data; 3122 PetscErrorCode ierr; 3123 3124 PetscFunctionBegin; 3125 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 3126 if (!data->neighbors) { 3127 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 3128 ierr = PetscSFGetRootRanks(sf, &njranks, &jranks, NULL, NULL, NULL);CHKERRQ(ierr); 3129 ierr = PetscSFGetLeafRanks(sf, &niranks, &iranks, NULL, NULL);CHKERRQ(ierr); 3130 ierr = PetscMalloc1(njranks + niranks + 1, &data->neighbors);CHKERRQ(ierr); 3131 ierr = PetscArraycpy(data->neighbors + 1, jranks, njranks);CHKERRQ(ierr); 3132 ierr = PetscArraycpy(data->neighbors + njranks + 1, iranks, niranks);CHKERRQ(ierr); 3133 n = njranks + niranks; 3134 ierr = PetscSortRemoveDupsMPIInt(&n, data->neighbors + 1);CHKERRQ(ierr); 3135 /* The following cast should never fail: can't have more neighbors than PETSC_MPI_INT_MAX */ 3136 ierr = PetscMPIIntCast(n, data->neighbors);CHKERRQ(ierr); 3137 } 3138 if (nranks) *nranks = data->neighbors[0]; 3139 if (ranks) { 3140 if (data->neighbors[0]) *ranks = data->neighbors + 1; 3141 else *ranks = NULL; 3142 } 3143 PetscFunctionReturn(0); 3144 } 3145 3146 PETSC_INTERN PetscErrorCode DMInterpolateSolution_Plex(DM, DM, Mat, Vec, Vec); 3147 3148 static PetscErrorCode DMInitialize_Plex(DM dm) 3149 { 3150 PetscErrorCode ierr; 3151 3152 PetscFunctionBegin; 3153 dm->ops->view = DMView_Plex; 3154 dm->ops->load = DMLoad_Plex; 3155 dm->ops->setfromoptions = DMSetFromOptions_Plex; 3156 dm->ops->clone = DMClone_Plex; 3157 dm->ops->setup = DMSetUp_Plex; 3158 dm->ops->createlocalsection = DMCreateLocalSection_Plex; 3159 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 3160 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 3161 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 3162 dm->ops->getlocaltoglobalmapping = NULL; 3163 dm->ops->createfieldis = NULL; 3164 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 3165 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 3166 dm->ops->getcoloring = NULL; 3167 dm->ops->creatematrix = DMCreateMatrix_Plex; 3168 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 3169 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 3170 dm->ops->createinjection = DMCreateInjection_Plex; 3171 dm->ops->refine = DMRefine_Plex; 3172 dm->ops->coarsen = DMCoarsen_Plex; 3173 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 3174 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 3175 dm->ops->adaptlabel = DMAdaptLabel_Plex; 3176 dm->ops->adaptmetric = DMAdaptMetric_Plex; 3177 dm->ops->globaltolocalbegin = NULL; 3178 dm->ops->globaltolocalend = NULL; 3179 dm->ops->localtoglobalbegin = NULL; 3180 dm->ops->localtoglobalend = NULL; 3181 dm->ops->destroy = DMDestroy_Plex; 3182 dm->ops->createsubdm = DMCreateSubDM_Plex; 3183 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 3184 dm->ops->getdimpoints = DMGetDimPoints_Plex; 3185 dm->ops->locatepoints = DMLocatePoints_Plex; 3186 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 3187 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 3188 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 3189 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 3190 dm->ops->projectbdfieldlabellocal = DMProjectBdFieldLabelLocal_Plex; 3191 dm->ops->computel2diff = DMComputeL2Diff_Plex; 3192 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 3193 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 3194 dm->ops->getneighbors = DMGetNeighbors_Plex; 3195 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);CHKERRQ(ierr); 3196 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertTimeDerviativeBoundaryValues_C",DMPlexInsertTimeDerivativeBoundaryValues_Plex);CHKERRQ(ierr); 3197 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);CHKERRQ(ierr); 3198 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C",DMCreateNeumannOverlap_Plex);CHKERRQ(ierr); 3199 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex);CHKERRQ(ierr); 3200 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMInterpolateSolution_C",DMInterpolateSolution_Plex);CHKERRQ(ierr); 3201 PetscFunctionReturn(0); 3202 } 3203 3204 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 3205 { 3206 DM_Plex *mesh = (DM_Plex *) dm->data; 3207 PetscErrorCode ierr; 3208 3209 PetscFunctionBegin; 3210 mesh->refct++; 3211 (*newdm)->data = mesh; 3212 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 3213 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 3214 PetscFunctionReturn(0); 3215 } 3216 3217 /*MC 3218 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 3219 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 3220 specified by a PetscSection object. Ownership in the global representation is determined by 3221 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 3222 3223 Options Database Keys: 3224 + -dm_refine_pre - Refine mesh before distribution 3225 + -dm_refine_uniform_pre - Choose uniform or generator-based refinement 3226 + -dm_refine_volume_limit_pre - Cell volume limit after pre-refinement using generator 3227 . -dm_distribute - Distribute mesh across processes 3228 . -dm_distribute_overlap - Number of cells to overlap for distribution 3229 . -dm_refine - Refine mesh after distribution 3230 . -dm_plex_hash_location - Use grid hashing for point location 3231 . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes 3232 . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing 3233 . -dm_plex_max_projection_height - Maxmimum mesh point height used to project locally 3234 . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement 3235 . -dm_plex_check_all - Perform all shecks below 3236 . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric 3237 . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices 3238 . -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 3239 . -dm_plex_check_geometry - Check that cells have positive volume 3240 . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ 3241 . -dm_plex_view_scale <num> - Scale the TikZ 3242 - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices 3243 3244 3245 Level: intermediate 3246 3247 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 3248 M*/ 3249 3250 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 3251 { 3252 DM_Plex *mesh; 3253 PetscInt unit; 3254 PetscErrorCode ierr; 3255 3256 PetscFunctionBegin; 3257 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3258 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 3259 dm->data = mesh; 3260 3261 mesh->refct = 1; 3262 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 3263 mesh->maxConeSize = 0; 3264 mesh->cones = NULL; 3265 mesh->coneOrientations = NULL; 3266 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 3267 mesh->maxSupportSize = 0; 3268 mesh->supports = NULL; 3269 mesh->refinementUniform = PETSC_TRUE; 3270 mesh->refinementLimit = -1.0; 3271 mesh->interpolated = DMPLEX_INTERPOLATED_INVALID; 3272 mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID; 3273 3274 mesh->facesTmp = NULL; 3275 3276 mesh->tetgenOpts = NULL; 3277 mesh->triangleOpts = NULL; 3278 ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); 3279 mesh->remeshBd = PETSC_FALSE; 3280 3281 mesh->subpointMap = NULL; 3282 3283 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 3284 3285 mesh->regularRefinement = PETSC_FALSE; 3286 mesh->depthState = -1; 3287 mesh->celltypeState = -1; 3288 mesh->globalVertexNumbers = NULL; 3289 mesh->globalCellNumbers = NULL; 3290 mesh->anchorSection = NULL; 3291 mesh->anchorIS = NULL; 3292 mesh->createanchors = NULL; 3293 mesh->computeanchormatrix = NULL; 3294 mesh->parentSection = NULL; 3295 mesh->parents = NULL; 3296 mesh->childIDs = NULL; 3297 mesh->childSection = NULL; 3298 mesh->children = NULL; 3299 mesh->referenceTree = NULL; 3300 mesh->getchildsymmetry = NULL; 3301 mesh->vtkCellHeight = 0; 3302 mesh->useAnchors = PETSC_FALSE; 3303 3304 mesh->maxProjectionHeight = 0; 3305 3306 mesh->neighbors = NULL; 3307 3308 mesh->printSetValues = PETSC_FALSE; 3309 mesh->printFEM = 0; 3310 mesh->printTol = 1.0e-10; 3311 3312 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 3313 PetscFunctionReturn(0); 3314 } 3315 3316 /*@ 3317 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 3318 3319 Collective 3320 3321 Input Parameter: 3322 . comm - The communicator for the DMPlex object 3323 3324 Output Parameter: 3325 . mesh - The DMPlex object 3326 3327 Level: beginner 3328 3329 @*/ 3330 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 3331 { 3332 PetscErrorCode ierr; 3333 3334 PetscFunctionBegin; 3335 PetscValidPointer(mesh,2); 3336 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 3337 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 3338 PetscFunctionReturn(0); 3339 } 3340 3341 /*@C 3342 DMPlexBuildFromCellListParallel - Build distributed DMPLEX topology from a list of vertices for each cell (common mesh generator output) 3343 3344 Input Parameters: 3345 + dm - The DM 3346 . numCells - The number of cells owned by this process 3347 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 3348 . NVertices - The global number of vertices, or PETSC_DECIDE 3349 . numCorners - The number of vertices for each cell 3350 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 3351 3352 Output Parameter: 3353 . vertexSF - (Optional) SF describing complete vertex ownership 3354 3355 Notes: 3356 Two triangles sharing a face 3357 $ 3358 $ 2 3359 $ / | \ 3360 $ / | \ 3361 $ / | \ 3362 $ 0 0 | 1 3 3363 $ \ | / 3364 $ \ | / 3365 $ \ | / 3366 $ 1 3367 would have input 3368 $ numCells = 2, numVertices = 4 3369 $ cells = [0 1 2 1 3 2] 3370 $ 3371 which would result in the DMPlex 3372 $ 3373 $ 4 3374 $ / | \ 3375 $ / | \ 3376 $ / | \ 3377 $ 2 0 | 1 5 3378 $ \ | / 3379 $ \ | / 3380 $ \ | / 3381 $ 3 3382 3383 Vertices are implicitly numbered consecutively 0,...,NVertices. 3384 Each rank owns a chunk of numVertices consecutive vertices. 3385 If numVertices is PETSC_DECIDE, PETSc will distribute them as evenly as possible using PetscLayout. 3386 If both NVertices and numVertices are PETSC_DECIDE, NVertices is computed by PETSc as the maximum vertex index in cells + 1. 3387 If only NVertices is PETSC_DECIDE, it is computed as the sum of numVertices over all ranks. 3388 3389 The cell distribution is arbitrary non-overlapping, independent of the vertex distribution. 3390 3391 Not currently supported in Fortran. 3392 3393 Level: advanced 3394 3395 .seealso: DMPlexBuildFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildCoordinatesFromCellListParallel() 3396 @*/ 3397 PetscErrorCode DMPlexBuildFromCellListParallel(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, const PetscInt cells[], PetscSF *vertexSF) 3398 { 3399 PetscSF sfPoint; 3400 PetscLayout layout; 3401 PetscInt numVerticesAdj, *verticesAdj, *cones, c, p, dim; 3402 PetscMPIInt rank, size; 3403 PetscErrorCode ierr; 3404 3405 PetscFunctionBegin; 3406 PetscValidLogicalCollectiveInt(dm,NVertices,4); 3407 ierr = PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3408 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 3409 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRMPI(ierr); 3410 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3411 /* Get/check global number of vertices */ 3412 { 3413 PetscInt NVerticesInCells, i; 3414 const PetscInt len = numCells * numCorners; 3415 3416 /* NVerticesInCells = max(cells) + 1 */ 3417 NVerticesInCells = PETSC_MIN_INT; 3418 for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 3419 ++NVerticesInCells; 3420 ierr = MPI_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject) dm));CHKERRMPI(ierr); 3421 3422 if (numVertices == PETSC_DECIDE && NVertices == PETSC_DECIDE) NVertices = NVerticesInCells; 3423 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); 3424 } 3425 /* Count locally unique vertices */ 3426 { 3427 PetscHSetI vhash; 3428 PetscInt off = 0; 3429 3430 ierr = PetscHSetICreate(&vhash);CHKERRQ(ierr); 3431 for (c = 0; c < numCells; ++c) { 3432 for (p = 0; p < numCorners; ++p) { 3433 ierr = PetscHSetIAdd(vhash, cells[c*numCorners+p]);CHKERRQ(ierr); 3434 } 3435 } 3436 ierr = PetscHSetIGetSize(vhash, &numVerticesAdj);CHKERRQ(ierr); 3437 ierr = PetscMalloc1(numVerticesAdj, &verticesAdj);CHKERRQ(ierr); 3438 ierr = PetscHSetIGetElems(vhash, &off, verticesAdj);CHKERRQ(ierr); 3439 ierr = PetscHSetIDestroy(&vhash);CHKERRQ(ierr); 3440 if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj); 3441 } 3442 ierr = PetscSortInt(numVerticesAdj, verticesAdj);CHKERRQ(ierr); 3443 /* Create cones */ 3444 ierr = DMPlexSetChart(dm, 0, numCells+numVerticesAdj);CHKERRQ(ierr); 3445 for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);} 3446 ierr = DMSetUp(dm);CHKERRQ(ierr); 3447 ierr = DMPlexGetCones(dm,&cones);CHKERRQ(ierr); 3448 for (c = 0; c < numCells; ++c) { 3449 for (p = 0; p < numCorners; ++p) { 3450 const PetscInt gv = cells[c*numCorners+p]; 3451 PetscInt lv; 3452 3453 /* Positions within verticesAdj form 0-based local vertex numbering; 3454 we need to shift it by numCells to get correct DAG points (cells go first) */ 3455 ierr = PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);CHKERRQ(ierr); 3456 if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv); 3457 cones[c*numCorners+p] = lv+numCells; 3458 } 3459 } 3460 /* Build point sf */ 3461 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &layout);CHKERRQ(ierr); 3462 ierr = PetscLayoutSetSize(layout, NVertices);CHKERRQ(ierr); 3463 ierr = PetscLayoutSetLocalSize(layout, numVertices);CHKERRQ(ierr); 3464 ierr = PetscLayoutSetBlockSize(layout, 1);CHKERRQ(ierr); 3465 ierr = PetscSFCreateByMatchingIndices(layout, numVerticesAdj, verticesAdj, NULL, numCells, numVerticesAdj, verticesAdj, NULL, numCells, vertexSF, &sfPoint);CHKERRQ(ierr); 3466 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 3467 ierr = PetscFree(verticesAdj);CHKERRQ(ierr); 3468 ierr = PetscObjectSetName((PetscObject) sfPoint, "point SF");CHKERRQ(ierr); 3469 if (dm->sf) { 3470 const char *prefix; 3471 3472 ierr = PetscObjectGetOptionsPrefix((PetscObject)dm->sf, &prefix);CHKERRQ(ierr); 3473 ierr = PetscObjectSetOptionsPrefix((PetscObject)sfPoint, prefix);CHKERRQ(ierr); 3474 } 3475 ierr = DMSetPointSF(dm, sfPoint);CHKERRQ(ierr); 3476 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 3477 if (vertexSF) {ierr = PetscObjectSetName((PetscObject)(*vertexSF), "Vertex Ownership SF");CHKERRQ(ierr);} 3478 /* Fill in the rest of the topology structure */ 3479 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3480 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3481 ierr = PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3482 PetscFunctionReturn(0); 3483 } 3484 3485 /*@C 3486 DMPlexBuildCoordinatesFromCellListParallel - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output) 3487 3488 Input Parameters: 3489 + dm - The DM 3490 . spaceDim - The spatial dimension used for coordinates 3491 . sfVert - SF describing complete vertex ownership 3492 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3493 3494 Level: advanced 3495 3496 Notes: 3497 Not currently supported in Fortran. 3498 3499 .seealso: DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellListParallel() 3500 @*/ 3501 PetscErrorCode DMPlexBuildCoordinatesFromCellListParallel(DM dm, PetscInt spaceDim, PetscSF sfVert, const PetscReal vertexCoords[]) 3502 { 3503 PetscSection coordSection; 3504 Vec coordinates; 3505 PetscScalar *coords; 3506 PetscInt numVertices, numVerticesAdj, coordSize, v, vStart, vEnd; 3507 PetscErrorCode ierr; 3508 3509 PetscFunctionBegin; 3510 ierr = PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3511 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 3512 if (vStart < 0 || vEnd < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 3513 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 3514 ierr = PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);CHKERRQ(ierr); 3515 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); 3516 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3517 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3518 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 3519 ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr); 3520 for (v = vStart; v < vEnd; ++v) { 3521 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 3522 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 3523 } 3524 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3525 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3526 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 3527 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 3528 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3529 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3530 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 3531 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3532 { 3533 MPI_Datatype coordtype; 3534 3535 /* Need a temp buffer for coords if we have complex/single */ 3536 ierr = MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);CHKERRMPI(ierr); 3537 ierr = MPI_Type_commit(&coordtype);CHKERRMPI(ierr); 3538 #if defined(PETSC_USE_COMPLEX) 3539 { 3540 PetscScalar *svertexCoords; 3541 PetscInt i; 3542 ierr = PetscMalloc1(numVertices*spaceDim,&svertexCoords);CHKERRQ(ierr); 3543 for (i=0; i<numVertices*spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 3544 ierr = PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 3545 ierr = PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 3546 ierr = PetscFree(svertexCoords);CHKERRQ(ierr); 3547 } 3548 #else 3549 ierr = PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 3550 ierr = PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords,MPI_REPLACE);CHKERRQ(ierr); 3551 #endif 3552 ierr = MPI_Type_free(&coordtype);CHKERRMPI(ierr); 3553 } 3554 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3555 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3556 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3557 ierr = PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3558 PetscFunctionReturn(0); 3559 } 3560 3561 /*@ 3562 DMPlexCreateFromCellListParallelPetsc - Create distributed DMPLEX from a list of vertices for each cell (common mesh generator output) 3563 3564 Input Parameters: 3565 + comm - The communicator 3566 . dim - The topological dimension of the mesh 3567 . numCells - The number of cells owned by this process 3568 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 3569 . NVertices - The global number of vertices, or PETSC_DECIDE 3570 . numCorners - The number of vertices for each cell 3571 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 3572 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 3573 . spaceDim - The spatial dimension used for coordinates 3574 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3575 3576 Output Parameter: 3577 + dm - The DM 3578 - vertexSF - (Optional) SF describing complete vertex ownership 3579 3580 Notes: 3581 This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), 3582 DMPlexBuildFromCellListParallel(), DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellListParallel() 3583 3584 See DMPlexBuildFromCellListParallel() for an example and details about the topology-related parameters. 3585 See DMPlexBuildCoordinatesFromCellListParallel() for details about the geometry-related parameters. 3586 3587 Level: intermediate 3588 3589 .seealso: DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromDAG(), DMPlexCreate() 3590 @*/ 3591 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) 3592 { 3593 PetscSF sfVert; 3594 PetscErrorCode ierr; 3595 3596 PetscFunctionBegin; 3597 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3598 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3599 PetscValidLogicalCollectiveInt(*dm, dim, 2); 3600 PetscValidLogicalCollectiveInt(*dm, spaceDim, 9); 3601 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3602 ierr = DMPlexBuildFromCellListParallel(*dm, numCells, numVertices, NVertices, numCorners, cells, &sfVert);CHKERRQ(ierr); 3603 if (interpolate) { 3604 DM idm; 3605 3606 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3607 ierr = DMDestroy(dm);CHKERRQ(ierr); 3608 *dm = idm; 3609 } 3610 ierr = DMPlexBuildCoordinatesFromCellListParallel(*dm, spaceDim, sfVert, vertexCoords);CHKERRQ(ierr); 3611 if (vertexSF) *vertexSF = sfVert; 3612 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 3613 PetscFunctionReturn(0); 3614 } 3615 3616 3617 /*@ 3618 DMPlexCreateFromCellListParallel - Deprecated, use DMPlexCreateFromCellListParallelPetsc() 3619 3620 Level: deprecated 3621 3622 .seealso: DMPlexCreateFromCellListParallelPetsc() 3623 @*/ 3624 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) 3625 { 3626 PetscErrorCode ierr; 3627 PetscInt i; 3628 PetscInt *pintCells; 3629 3630 PetscFunctionBegin; 3631 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)); 3632 if (sizeof(int) == sizeof(PetscInt)) { 3633 pintCells = (PetscInt *) cells; 3634 } else { 3635 ierr = PetscMalloc1(numCells*numCorners, &pintCells);CHKERRQ(ierr); 3636 for (i = 0; i < numCells*numCorners; i++) { 3637 pintCells[i] = (PetscInt) cells[i]; 3638 } 3639 } 3640 ierr = DMPlexCreateFromCellListParallelPetsc(comm, dim, numCells, numVertices, PETSC_DECIDE, numCorners, interpolate, pintCells, spaceDim, vertexCoords, vertexSF, dm);CHKERRQ(ierr); 3641 if (sizeof(int) != sizeof(PetscInt)) { 3642 ierr = PetscFree(pintCells);CHKERRQ(ierr); 3643 } 3644 PetscFunctionReturn(0); 3645 } 3646 3647 /*@C 3648 DMPlexBuildFromCellList - Build DMPLEX topology from a list of vertices for each cell (common mesh generator output) 3649 3650 Input Parameters: 3651 + dm - The DM 3652 . numCells - The number of cells owned by this process 3653 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 3654 . numCorners - The number of vertices for each cell 3655 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 3656 3657 Level: advanced 3658 3659 Notes: 3660 Two triangles sharing a face 3661 $ 3662 $ 2 3663 $ / | \ 3664 $ / | \ 3665 $ / | \ 3666 $ 0 0 | 1 3 3667 $ \ | / 3668 $ \ | / 3669 $ \ | / 3670 $ 1 3671 would have input 3672 $ numCells = 2, numVertices = 4 3673 $ cells = [0 1 2 1 3 2] 3674 $ 3675 which would result in the DMPlex 3676 $ 3677 $ 4 3678 $ / | \ 3679 $ / | \ 3680 $ / | \ 3681 $ 2 0 | 1 5 3682 $ \ | / 3683 $ \ | / 3684 $ \ | / 3685 $ 3 3686 3687 If numVertices is PETSC_DECIDE, it is computed by PETSc as the maximum vertex index in cells + 1. 3688 3689 Not currently supported in Fortran. 3690 3691 .seealso: DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListPetsc() 3692 @*/ 3693 PetscErrorCode DMPlexBuildFromCellList(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[]) 3694 { 3695 PetscInt *cones, c, p, dim; 3696 PetscErrorCode ierr; 3697 3698 PetscFunctionBegin; 3699 ierr = PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3700 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3701 /* Get/check global number of vertices */ 3702 { 3703 PetscInt NVerticesInCells, i; 3704 const PetscInt len = numCells * numCorners; 3705 3706 /* NVerticesInCells = max(cells) + 1 */ 3707 NVerticesInCells = PETSC_MIN_INT; 3708 for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 3709 ++NVerticesInCells; 3710 3711 if (numVertices == PETSC_DECIDE) numVertices = NVerticesInCells; 3712 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); 3713 } 3714 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 3715 for (c = 0; c < numCells; ++c) { 3716 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 3717 } 3718 ierr = DMSetUp(dm);CHKERRQ(ierr); 3719 ierr = DMPlexGetCones(dm,&cones);CHKERRQ(ierr); 3720 for (c = 0; c < numCells; ++c) { 3721 for (p = 0; p < numCorners; ++p) { 3722 cones[c*numCorners+p] = cells[c*numCorners+p]+numCells; 3723 } 3724 } 3725 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3726 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3727 ierr = PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3728 PetscFunctionReturn(0); 3729 } 3730 3731 /*@C 3732 DMPlexBuildCoordinatesFromCellList - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output) 3733 3734 Input Parameters: 3735 + dm - The DM 3736 . spaceDim - The spatial dimension used for coordinates 3737 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3738 3739 Level: advanced 3740 3741 Notes: 3742 Not currently supported in Fortran. 3743 3744 .seealso: DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellList() 3745 @*/ 3746 PetscErrorCode DMPlexBuildCoordinatesFromCellList(DM dm, PetscInt spaceDim, const PetscReal vertexCoords[]) 3747 { 3748 PetscSection coordSection; 3749 Vec coordinates; 3750 DM cdm; 3751 PetscScalar *coords; 3752 PetscInt v, vStart, vEnd, d; 3753 PetscErrorCode ierr; 3754 3755 PetscFunctionBegin; 3756 ierr = PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3757 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 3758 if (vStart < 0 || vEnd < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 3759 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 3760 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3761 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3762 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 3763 ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr); 3764 for (v = vStart; v < vEnd; ++v) { 3765 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 3766 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 3767 } 3768 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3769 3770 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 3771 ierr = DMCreateLocalVector(cdm, &coordinates);CHKERRQ(ierr); 3772 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 3773 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3774 ierr = VecGetArrayWrite(coordinates, &coords);CHKERRQ(ierr); 3775 for (v = 0; v < vEnd-vStart; ++v) { 3776 for (d = 0; d < spaceDim; ++d) { 3777 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 3778 } 3779 } 3780 ierr = VecRestoreArrayWrite(coordinates, &coords);CHKERRQ(ierr); 3781 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3782 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3783 ierr = PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3784 PetscFunctionReturn(0); 3785 } 3786 3787 /*@ 3788 DMPlexCreateFromCellListPetsc - Create DMPLEX from a list of vertices for each cell (common mesh generator output) 3789 3790 Input Parameters: 3791 + comm - The communicator 3792 . dim - The topological dimension of the mesh 3793 . numCells - The number of cells 3794 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 3795 . numCorners - The number of vertices for each cell 3796 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 3797 . cells - An array of numCells*numCorners numbers, the vertices for each cell 3798 . spaceDim - The spatial dimension used for coordinates 3799 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3800 3801 Output Parameter: 3802 . dm - The DM 3803 3804 Notes: 3805 This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), DMPlexBuildFromCellList(), 3806 DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellList() 3807 3808 See DMPlexBuildFromCellList() for an example and details about the topology-related parameters. 3809 See DMPlexBuildCoordinatesFromCellList() for details about the geometry-related parameters. 3810 3811 Level: intermediate 3812 3813 .seealso: DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellList(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate() 3814 @*/ 3815 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) 3816 { 3817 PetscErrorCode ierr; 3818 3819 PetscFunctionBegin; 3820 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."); 3821 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3822 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3823 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3824 ierr = DMPlexBuildFromCellList(*dm, numCells, numVertices, numCorners, cells);CHKERRQ(ierr); 3825 if (interpolate) { 3826 DM idm; 3827 3828 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3829 ierr = DMDestroy(dm);CHKERRQ(ierr); 3830 *dm = idm; 3831 } 3832 ierr = DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, vertexCoords);CHKERRQ(ierr); 3833 PetscFunctionReturn(0); 3834 } 3835 3836 /*@ 3837 DMPlexCreateFromCellList - Deprecated, use DMPlexCreateFromCellListPetsc() 3838 3839 Level: deprecated 3840 3841 .seealso: DMPlexCreateFromCellListPetsc() 3842 @*/ 3843 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) 3844 { 3845 PetscErrorCode ierr; 3846 PetscInt i; 3847 PetscInt *pintCells; 3848 PetscReal *prealVC; 3849 3850 PetscFunctionBegin; 3851 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)); 3852 if (sizeof(int) == sizeof(PetscInt)) { 3853 pintCells = (PetscInt *) cells; 3854 } else { 3855 ierr = PetscMalloc1(numCells*numCorners, &pintCells);CHKERRQ(ierr); 3856 for (i = 0; i < numCells*numCorners; i++) { 3857 pintCells[i] = (PetscInt) cells[i]; 3858 } 3859 } 3860 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)); 3861 if (sizeof(double) == sizeof(PetscReal)) { 3862 prealVC = (PetscReal *) vertexCoords; 3863 } else { 3864 ierr = PetscMalloc1(numVertices*spaceDim, &prealVC);CHKERRQ(ierr); 3865 for (i = 0; i < numVertices*spaceDim; i++) { 3866 prealVC[i] = (PetscReal) vertexCoords[i]; 3867 } 3868 } 3869 ierr = DMPlexCreateFromCellListPetsc(comm, dim, numCells, numVertices, numCorners, interpolate, pintCells, spaceDim, prealVC, dm);CHKERRQ(ierr); 3870 if (sizeof(int) != sizeof(PetscInt)) { 3871 ierr = PetscFree(pintCells);CHKERRQ(ierr); 3872 } 3873 if (sizeof(double) != sizeof(PetscReal)) { 3874 ierr = PetscFree(prealVC);CHKERRQ(ierr); 3875 } 3876 PetscFunctionReturn(0); 3877 } 3878 3879 /*@ 3880 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 3881 3882 Input Parameters: 3883 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 3884 . depth - The depth of the DAG 3885 . numPoints - Array of size depth + 1 containing the number of points at each depth 3886 . coneSize - The cone size of each point 3887 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 3888 . coneOrientations - The orientation of each cone point 3889 - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim() 3890 3891 Output Parameter: 3892 . dm - The DM 3893 3894 Note: Two triangles sharing a face would have input 3895 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 3896 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 3897 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 3898 $ 3899 which would result in the DMPlex 3900 $ 3901 $ 4 3902 $ / | \ 3903 $ / | \ 3904 $ / | \ 3905 $ 2 0 | 1 5 3906 $ \ | / 3907 $ \ | / 3908 $ \ | / 3909 $ 3 3910 $ 3911 $ Notice that all points are numbered consecutively, unlike DMPlexCreateFromCellListPetsc() 3912 3913 Level: advanced 3914 3915 .seealso: DMPlexCreateFromCellListPetsc(), DMPlexCreate() 3916 @*/ 3917 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 3918 { 3919 Vec coordinates; 3920 PetscSection coordSection; 3921 PetscScalar *coords; 3922 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 3923 PetscErrorCode ierr; 3924 3925 PetscFunctionBegin; 3926 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3927 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 3928 if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %D cannot be less than intrinsic dimension %d",dimEmbed,dim); 3929 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 3930 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 3931 for (p = pStart; p < pEnd; ++p) { 3932 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 3933 if (firstVertex < 0 && !coneSize[p - pStart]) { 3934 firstVertex = p - pStart; 3935 } 3936 } 3937 if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %D vertices but could not find any", numPoints[0]); 3938 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 3939 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 3940 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 3941 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 3942 } 3943 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3944 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3945 /* Build coordinates */ 3946 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3947 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3948 ierr = PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);CHKERRQ(ierr); 3949 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 3950 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 3951 ierr = PetscSectionSetDof(coordSection, v, dimEmbed);CHKERRQ(ierr); 3952 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);CHKERRQ(ierr); 3953 } 3954 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3955 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3956 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3957 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3958 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3959 ierr = VecSetBlockSize(coordinates, dimEmbed);CHKERRQ(ierr); 3960 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 3961 if (vertexCoords) { 3962 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3963 for (v = 0; v < numPoints[0]; ++v) { 3964 PetscInt off; 3965 3966 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 3967 for (d = 0; d < dimEmbed; ++d) { 3968 coords[off+d] = vertexCoords[v*dimEmbed+d]; 3969 } 3970 } 3971 } 3972 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3973 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3974 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3975 PetscFunctionReturn(0); 3976 } 3977 3978 /*@C 3979 DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file. 3980 3981 + comm - The MPI communicator 3982 . filename - Name of the .dat file 3983 - interpolate - Create faces and edges in the mesh 3984 3985 Output Parameter: 3986 . dm - The DM object representing the mesh 3987 3988 Note: The format is the simplest possible: 3989 $ Ne 3990 $ v0 v1 ... vk 3991 $ Nv 3992 $ x y z marker 3993 3994 Level: beginner 3995 3996 .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate() 3997 @*/ 3998 PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3999 { 4000 DMLabel marker; 4001 PetscViewer viewer; 4002 Vec coordinates; 4003 PetscSection coordSection; 4004 PetscScalar *coords; 4005 char line[PETSC_MAX_PATH_LEN]; 4006 PetscInt dim = 3, cdim = 3, coordSize, v, c, d; 4007 PetscMPIInt rank; 4008 int snum, Nv, Nc; 4009 PetscErrorCode ierr; 4010 4011 PetscFunctionBegin; 4012 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 4013 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 4014 ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr); 4015 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 4016 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 4017 if (!rank) { 4018 ierr = PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);CHKERRQ(ierr); 4019 snum = sscanf(line, "%d %d", &Nc, &Nv); 4020 if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4021 } else { 4022 Nc = Nv = 0; 4023 } 4024 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 4025 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 4026 ierr = DMPlexSetChart(*dm, 0, Nc+Nv);CHKERRQ(ierr); 4027 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 4028 ierr = DMSetCoordinateDim(*dm, cdim);CHKERRQ(ierr); 4029 /* Read topology */ 4030 if (!rank) { 4031 PetscInt cone[8], corners = 8; 4032 int vbuf[8], v; 4033 4034 for (c = 0; c < Nc; ++c) {ierr = DMPlexSetConeSize(*dm, c, corners);CHKERRQ(ierr);} 4035 ierr = DMSetUp(*dm);CHKERRQ(ierr); 4036 for (c = 0; c < Nc; ++c) { 4037 ierr = PetscViewerRead(viewer, line, corners, NULL, PETSC_STRING);CHKERRQ(ierr); 4038 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]); 4039 if (snum != corners) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4040 for (v = 0; v < corners; ++v) cone[v] = vbuf[v] + Nc; 4041 /* Hexahedra are inverted */ 4042 { 4043 PetscInt tmp = cone[1]; 4044 cone[1] = cone[3]; 4045 cone[3] = tmp; 4046 } 4047 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 4048 } 4049 } 4050 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 4051 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 4052 /* Read coordinates */ 4053 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 4054 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 4055 ierr = PetscSectionSetFieldComponents(coordSection, 0, cdim);CHKERRQ(ierr); 4056 ierr = PetscSectionSetChart(coordSection, Nc, Nc + Nv);CHKERRQ(ierr); 4057 for (v = Nc; v < Nc+Nv; ++v) { 4058 ierr = PetscSectionSetDof(coordSection, v, cdim);CHKERRQ(ierr); 4059 ierr = PetscSectionSetFieldDof(coordSection, v, 0, cdim);CHKERRQ(ierr); 4060 } 4061 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 4062 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 4063 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 4064 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 4065 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 4066 ierr = VecSetBlockSize(coordinates, cdim);CHKERRQ(ierr); 4067 ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr); 4068 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 4069 if (!rank) { 4070 double x[3]; 4071 int val; 4072 4073 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 4074 ierr = DMGetLabel(*dm, "marker", &marker);CHKERRQ(ierr); 4075 for (v = 0; v < Nv; ++v) { 4076 ierr = PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);CHKERRQ(ierr); 4077 snum = sscanf(line, "%lg %lg %lg %d", &x[0], &x[1], &x[2], &val); 4078 if (snum != 4) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 4079 for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d]; 4080 if (val) {ierr = DMLabelSetValue(marker, v+Nc, val);CHKERRQ(ierr);} 4081 } 4082 } 4083 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 4084 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 4085 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 4086 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 4087 if (interpolate) { 4088 DM idm; 4089 DMLabel bdlabel; 4090 4091 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 4092 ierr = DMDestroy(dm);CHKERRQ(ierr); 4093 *dm = idm; 4094 4095 ierr = DMGetLabel(*dm, "marker", &bdlabel);CHKERRQ(ierr); 4096 ierr = DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 4097 ierr = DMPlexLabelComplete(*dm, bdlabel);CHKERRQ(ierr); 4098 } 4099 PetscFunctionReturn(0); 4100 } 4101 4102 /*@C 4103 DMPlexCreateFromFile - This takes a filename and produces a DM 4104 4105 Input Parameters: 4106 + comm - The communicator 4107 . filename - A file name 4108 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 4109 4110 Output Parameter: 4111 . dm - The DM 4112 4113 Options Database Keys: 4114 . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5 4115 4116 Use -dm_plex_create_ prefix to pass options to the internal PetscViewer, e.g. 4117 $ -dm_plex_create_viewer_hdf5_collective 4118 4119 Level: beginner 4120 4121 .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellListPetsc(), DMPlexCreate() 4122 @*/ 4123 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 4124 { 4125 const char *extGmsh = ".msh"; 4126 const char *extGmsh2 = ".msh2"; 4127 const char *extGmsh4 = ".msh4"; 4128 const char *extCGNS = ".cgns"; 4129 const char *extExodus = ".exo"; 4130 const char *extGenesis = ".gen"; 4131 const char *extFluent = ".cas"; 4132 const char *extHDF5 = ".h5"; 4133 const char *extMed = ".med"; 4134 const char *extPLY = ".ply"; 4135 const char *extEGADS = ".egadslite"; 4136 const char *extCV = ".dat"; 4137 size_t len; 4138 PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isEGADS, isCV; 4139 PetscMPIInt rank; 4140 PetscErrorCode ierr; 4141 4142 PetscFunctionBegin; 4143 PetscValidCharPointer(filename, 2); 4144 PetscValidPointer(dm, 4); 4145 ierr = DMInitializePackage();CHKERRQ(ierr); 4146 ierr = PetscLogEventBegin(DMPLEX_CreateFromFile,0,0,0,0);CHKERRQ(ierr); 4147 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 4148 ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); 4149 if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 4150 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);CHKERRQ(ierr); 4151 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh2, 5, &isGmsh2);CHKERRQ(ierr); 4152 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh4, 5, &isGmsh4);CHKERRQ(ierr); 4153 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);CHKERRQ(ierr); 4154 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);CHKERRQ(ierr); 4155 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);CHKERRQ(ierr); 4156 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);CHKERRQ(ierr); 4157 ierr = PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);CHKERRQ(ierr); 4158 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);CHKERRQ(ierr); 4159 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);CHKERRQ(ierr); 4160 ierr = PetscStrncmp(&filename[PetscMax(0,len-10)], extEGADS, 9, &isEGADS);CHKERRQ(ierr); 4161 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);CHKERRQ(ierr); 4162 if (isGmsh || isGmsh2 || isGmsh4) { 4163 ierr = DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4164 } else if (isCGNS) { 4165 ierr = DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4166 } else if (isExodus || isGenesis) { 4167 ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4168 } else if (isFluent) { 4169 ierr = DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4170 } else if (isHDF5) { 4171 PetscBool load_hdf5_xdmf = PETSC_FALSE; 4172 PetscViewer viewer; 4173 4174 /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */ 4175 ierr = PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf", 5, &load_hdf5_xdmf);CHKERRQ(ierr); 4176 ierr = PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);CHKERRQ(ierr); 4177 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 4178 ierr = PetscViewerSetType(viewer, PETSCVIEWERHDF5);CHKERRQ(ierr); 4179 ierr = PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_");CHKERRQ(ierr); 4180 ierr = PetscViewerSetFromOptions(viewer);CHKERRQ(ierr); 4181 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 4182 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 4183 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 4184 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 4185 if (load_hdf5_xdmf) {ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);CHKERRQ(ierr);} 4186 ierr = DMLoad(*dm, viewer);CHKERRQ(ierr); 4187 if (load_hdf5_xdmf) {ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);} 4188 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 4189 4190 if (interpolate) { 4191 DM idm; 4192 4193 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 4194 ierr = DMDestroy(dm);CHKERRQ(ierr); 4195 *dm = idm; 4196 } 4197 } else if (isMed) { 4198 ierr = DMPlexCreateMedFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4199 } else if (isPLY) { 4200 ierr = DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4201 } else if (isEGADS) { 4202 ierr = DMPlexCreateEGADSFromFile(comm, filename, dm);CHKERRQ(ierr); 4203 if (!interpolate) { 4204 DM udm; 4205 4206 ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr); 4207 ierr = DMDestroy(dm);CHKERRQ(ierr); 4208 *dm = udm; 4209 } 4210 } else if (isCV) { 4211 ierr = DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 4212 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 4213 ierr = PetscLogEventEnd(DMPLEX_CreateFromFile,0,0,0,0);CHKERRQ(ierr); 4214 PetscFunctionReturn(0); 4215 } 4216