1 #define PETSCDM_DLL 2 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 #include <petscdmda.h> 4 #include <petscsf.h> 5 6 /*@ 7 DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement. 8 9 Collective on MPI_Comm 10 11 Input Parameters: 12 + comm - The communicator for the DM object 13 . dim - The spatial dimension 14 . simplex - Flag for simplicial cells, otherwise they are tensor product cells 15 . interpolate - Flag to create intermediate mesh pieces (edges, faces) 16 . refinementUniform - Flag for uniform parallel refinement 17 - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell 18 19 Output Parameter: 20 . dm - The DM object 21 22 Level: beginner 23 24 .keywords: DM, create 25 .seealso: DMSetType(), DMCreate() 26 @*/ 27 PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscBool refinementUniform, PetscReal refinementLimit, DM *newdm) 28 { 29 DM dm; 30 PetscInt p; 31 PetscMPIInt rank; 32 PetscErrorCode ierr; 33 34 PetscFunctionBegin; 35 ierr = DMCreate(comm, &dm);CHKERRQ(ierr); 36 ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr); 37 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 38 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 39 switch (dim) { 40 case 2: 41 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "triangular");CHKERRQ(ierr);} 42 else {ierr = PetscObjectSetName((PetscObject) dm, "quadrilateral");CHKERRQ(ierr);} 43 break; 44 case 3: 45 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "tetrahedral");CHKERRQ(ierr);} 46 else {ierr = PetscObjectSetName((PetscObject) dm, "hexahedral");CHKERRQ(ierr);} 47 break; 48 default: 49 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); 50 } 51 if (rank) { 52 PetscInt numPoints[2] = {0, 0}; 53 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 54 } else { 55 switch (dim) { 56 case 2: 57 if (simplex) { 58 PetscInt numPoints[2] = {4, 2}; 59 PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; 60 PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; 61 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 62 PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5}; 63 PetscInt markerPoints[8] = {2, 1, 3, 1, 4, 1, 5, 1}; 64 65 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 66 for (p = 0; p < 4; ++p) {ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 67 } else { 68 PetscInt numPoints[2] = {6, 2}; 69 PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; 70 PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4}; 71 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 72 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}; 73 74 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 75 } 76 break; 77 case 3: 78 if (simplex) { 79 PetscInt numPoints[2] = {5, 2}; 80 PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; 81 PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; 82 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 83 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}; 84 PetscInt markerPoints[10] = {2, 1, 3, 1, 4, 1, 5, 1, 6, 1}; 85 86 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 87 for (p = 0; p < 5; ++p) {ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 88 } else { 89 PetscInt numPoints[2] = {12, 2}; 90 PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 91 PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8}; 92 PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 93 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, 94 -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5, 95 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5}; 96 97 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 98 } 99 break; 100 default: 101 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); 102 } 103 } 104 *newdm = dm; 105 if (refinementLimit > 0.0) { 106 DM rdm; 107 const char *name; 108 109 ierr = DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);CHKERRQ(ierr); 110 ierr = DMPlexSetRefinementLimit(*newdm, refinementLimit);CHKERRQ(ierr); 111 ierr = DMRefine(*newdm, comm, &rdm);CHKERRQ(ierr); 112 ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); 113 ierr = PetscObjectSetName((PetscObject) rdm, name);CHKERRQ(ierr); 114 ierr = DMDestroy(newdm);CHKERRQ(ierr); 115 *newdm = rdm; 116 } 117 if (interpolate) { 118 DM idm = NULL; 119 const char *name; 120 121 ierr = DMPlexInterpolate(*newdm, &idm);CHKERRQ(ierr); 122 ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); 123 ierr = PetscObjectSetName((PetscObject) idm, name);CHKERRQ(ierr); 124 ierr = DMPlexCopyCoordinates(*newdm, idm);CHKERRQ(ierr); 125 ierr = DMCopyLabels(*newdm, idm);CHKERRQ(ierr); 126 ierr = DMDestroy(newdm);CHKERRQ(ierr); 127 *newdm = idm; 128 } 129 { 130 DM refinedMesh = NULL; 131 DM distributedMesh = NULL; 132 133 /* Distribute mesh over processes */ 134 ierr = DMPlexDistribute(*newdm, 0, NULL, &distributedMesh);CHKERRQ(ierr); 135 if (distributedMesh) { 136 ierr = DMDestroy(newdm);CHKERRQ(ierr); 137 *newdm = distributedMesh; 138 } 139 if (refinementUniform) { 140 ierr = DMPlexSetRefinementUniform(*newdm, refinementUniform);CHKERRQ(ierr); 141 ierr = DMRefine(*newdm, comm, &refinedMesh);CHKERRQ(ierr); 142 if (refinedMesh) { 143 ierr = DMDestroy(newdm);CHKERRQ(ierr); 144 *newdm = refinedMesh; 145 } 146 } 147 } 148 PetscFunctionReturn(0); 149 } 150 151 /*@ 152 DMPlexCreateSquareBoundary - Creates a 1D mesh the is the boundary of a square lattice. 153 154 Collective on MPI_Comm 155 156 Input Parameters: 157 + comm - The communicator for the DM object 158 . lower - The lower left corner coordinates 159 . upper - The upper right corner coordinates 160 - edges - The number of cells in each direction 161 162 Output Parameter: 163 . dm - The DM object 164 165 Note: Here is the numbering returned for 2 cells in each direction: 166 $ 18--5-17--4--16 167 $ | | | 168 $ 6 10 3 169 $ | | | 170 $ 19-11-20--9--15 171 $ | | | 172 $ 7 8 2 173 $ | | | 174 $ 12--0-13--1--14 175 176 Level: beginner 177 178 .keywords: DM, create 179 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate() 180 @*/ 181 PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 182 { 183 const PetscInt numVertices = (edges[0]+1)*(edges[1]+1); 184 const PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1]; 185 PetscInt markerTop = 1; 186 PetscInt markerBottom = 1; 187 PetscInt markerRight = 1; 188 PetscInt markerLeft = 1; 189 PetscBool markerSeparate = PETSC_FALSE; 190 Vec coordinates; 191 PetscSection coordSection; 192 PetscScalar *coords; 193 PetscInt coordSize; 194 PetscMPIInt rank; 195 PetscInt v, vx, vy; 196 PetscErrorCode ierr; 197 198 PetscFunctionBegin; 199 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 200 if (markerSeparate) { 201 markerTop = 3; 202 markerBottom = 1; 203 markerRight = 2; 204 markerLeft = 4; 205 } 206 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 207 if (!rank) { 208 PetscInt e, ex, ey; 209 210 ierr = DMPlexSetChart(dm, 0, numEdges+numVertices);CHKERRQ(ierr); 211 for (e = 0; e < numEdges; ++e) { 212 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 213 } 214 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 215 for (vx = 0; vx <= edges[0]; vx++) { 216 for (ey = 0; ey < edges[1]; ey++) { 217 PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1); 218 PetscInt vertex = ey*(edges[0]+1) + vx + numEdges; 219 PetscInt cone[2]; 220 221 cone[0] = vertex; cone[1] = vertex+edges[0]+1; 222 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 223 if (vx == edges[0]) { 224 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 225 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 226 if (ey == edges[1]-1) { 227 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 228 } 229 } else if (vx == 0) { 230 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 231 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 232 if (ey == edges[1]-1) { 233 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 234 } 235 } 236 } 237 } 238 for (vy = 0; vy <= edges[1]; vy++) { 239 for (ex = 0; ex < edges[0]; ex++) { 240 PetscInt edge = vy*edges[0] + ex; 241 PetscInt vertex = vy*(edges[0]+1) + ex + numEdges; 242 PetscInt cone[2]; 243 244 cone[0] = vertex; cone[1] = vertex+1; 245 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 246 if (vy == edges[1]) { 247 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 248 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 249 if (ex == edges[0]-1) { 250 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 251 } 252 } else if (vy == 0) { 253 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 254 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 255 if (ex == edges[0]-1) { 256 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 257 } 258 } 259 } 260 } 261 } 262 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 263 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 264 /* Build coordinates */ 265 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 266 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 267 ierr = PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);CHKERRQ(ierr); 268 ierr = PetscSectionSetFieldComponents(coordSection, 0, 2);CHKERRQ(ierr); 269 for (v = numEdges; v < numEdges+numVertices; ++v) { 270 ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr); 271 ierr = PetscSectionSetFieldDof(coordSection, v, 0, 2);CHKERRQ(ierr); 272 } 273 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 274 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 275 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 276 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 277 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 278 ierr = VecSetBlockSize(coordinates, 2);CHKERRQ(ierr); 279 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 280 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 281 for (vy = 0; vy <= edges[1]; ++vy) { 282 for (vx = 0; vx <= edges[0]; ++vx) { 283 coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx; 284 coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy; 285 } 286 } 287 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 288 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 289 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 290 PetscFunctionReturn(0); 291 } 292 293 /*@ 294 DMPlexCreateCubeBoundary - Creates a 2D mesh the is the boundary of a cubic lattice. 295 296 Collective on MPI_Comm 297 298 Input Parameters: 299 + comm - The communicator for the DM object 300 . lower - The lower left front corner coordinates 301 . upper - The upper right back corner coordinates 302 - edges - The number of cells in each direction 303 304 Output Parameter: 305 . dm - The DM object 306 307 Level: beginner 308 309 .keywords: DM, create 310 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMSetType(), DMCreate() 311 @*/ 312 PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) 313 { 314 PetscInt vertices[3], numVertices; 315 PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2]; 316 Vec coordinates; 317 PetscSection coordSection; 318 PetscScalar *coords; 319 PetscInt coordSize; 320 PetscMPIInt rank; 321 PetscInt v, vx, vy, vz; 322 PetscInt voffset, iface=0, cone[4]; 323 PetscErrorCode ierr; 324 325 PetscFunctionBegin; 326 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"); 327 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 328 vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1; 329 numVertices = vertices[0]*vertices[1]*vertices[2]; 330 if (!rank) { 331 PetscInt f; 332 333 ierr = DMPlexSetChart(dm, 0, numFaces+numVertices);CHKERRQ(ierr); 334 for (f = 0; f < numFaces; ++f) { 335 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 336 } 337 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 338 for (v = 0; v < numFaces+numVertices; ++v) { 339 ierr = DMSetLabelValue(dm, "marker", v, 1);CHKERRQ(ierr); 340 } 341 342 /* Side 0 (Top) */ 343 for (vy = 0; vy < faces[1]; vy++) { 344 for (vx = 0; vx < faces[0]; vx++) { 345 voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx; 346 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0]; 347 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 348 iface++; 349 } 350 } 351 352 /* Side 1 (Bottom) */ 353 for (vy = 0; vy < faces[1]; vy++) { 354 for (vx = 0; vx < faces[0]; vx++) { 355 voffset = numFaces + vy*(faces[0]+1) + vx; 356 cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1; 357 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 358 iface++; 359 } 360 } 361 362 /* Side 2 (Front) */ 363 for (vz = 0; vz < faces[2]; vz++) { 364 for (vx = 0; vx < faces[0]; vx++) { 365 voffset = numFaces + vz*vertices[0]*vertices[1] + vx; 366 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1]; 367 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 368 iface++; 369 } 370 } 371 372 /* Side 3 (Back) */ 373 for (vz = 0; vz < faces[2]; vz++) { 374 for (vx = 0; vx < faces[0]; vx++) { 375 voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx; 376 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1; 377 cone[2] = voffset+1; cone[3] = voffset; 378 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 379 iface++; 380 } 381 } 382 383 /* Side 4 (Left) */ 384 for (vz = 0; vz < faces[2]; vz++) { 385 for (vy = 0; vy < faces[1]; vy++) { 386 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0]; 387 cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1]; 388 cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0]; 389 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 390 iface++; 391 } 392 } 393 394 /* Side 5 (Right) */ 395 for (vz = 0; vz < faces[2]; vz++) { 396 for (vy = 0; vy < faces[1]; vy++) { 397 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + vx; 398 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset; 399 cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0]; 400 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 401 iface++; 402 } 403 } 404 } 405 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 406 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 407 /* Build coordinates */ 408 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 409 ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr); 410 for (v = numFaces; v < numFaces+numVertices; ++v) { 411 ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr); 412 } 413 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 414 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 415 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 416 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 417 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 418 ierr = VecSetBlockSize(coordinates, 3);CHKERRQ(ierr); 419 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 420 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 421 for (vz = 0; vz <= faces[2]; ++vz) { 422 for (vy = 0; vy <= faces[1]; ++vy) { 423 for (vx = 0; vx <= faces[0]; ++vx) { 424 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx; 425 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy; 426 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz; 427 } 428 } 429 } 430 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 431 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 432 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 433 PetscFunctionReturn(0); 434 } 435 436 /*@ 437 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices. 438 439 Collective on MPI_Comm 440 441 Input Parameters: 442 + comm - The communicator for the DM object 443 . dim - The spatial dimension 444 . numFaces - Number of faces per dimension 445 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 446 447 Output Parameter: 448 . dm - The DM object 449 450 Level: beginner 451 452 .keywords: DM, create 453 .seealso: DMPlexCreateHexBoxMesh(), DMSetType(), DMCreate() 454 @*/ 455 PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscInt numFaces, PetscBool interpolate, DM *dm) 456 { 457 DM boundary; 458 PetscErrorCode ierr; 459 460 PetscFunctionBegin; 461 PetscValidPointer(dm, 4); 462 ierr = DMCreate(comm, &boundary);CHKERRQ(ierr); 463 PetscValidLogicalCollectiveInt(boundary,dim,2); 464 ierr = DMSetType(boundary, DMPLEX);CHKERRQ(ierr); 465 ierr = DMSetDimension(boundary, dim-1);CHKERRQ(ierr); 466 ierr = DMSetCoordinateDim(boundary, dim);CHKERRQ(ierr); 467 switch (dim) { 468 case 2: 469 { 470 PetscReal lower[2] = {0.0, 0.0}; 471 PetscReal upper[2] = {1.0, 1.0}; 472 PetscInt edges[2]; 473 474 edges[0] = numFaces; edges[1] = numFaces; 475 ierr = DMPlexCreateSquareBoundary(boundary, lower, upper, edges);CHKERRQ(ierr); 476 break; 477 } 478 case 3: 479 { 480 PetscReal lower[3] = {0.0, 0.0, 0.0}; 481 PetscReal upper[3] = {1.0, 1.0, 1.0}; 482 PetscInt faces[3]; 483 484 faces[0] = numFaces; faces[1] = numFaces; faces[2] = numFaces; 485 ierr = DMPlexCreateCubeBoundary(boundary, lower, upper, faces);CHKERRQ(ierr); 486 break; 487 } 488 default: 489 SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 490 } 491 ierr = DMPlexGenerate(boundary, NULL, interpolate, dm);CHKERRQ(ierr); 492 ierr = DMDestroy(&boundary);CHKERRQ(ierr); 493 PetscFunctionReturn(0); 494 } 495 496 static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ) 497 { 498 DMLabel cutLabel = NULL; 499 PetscInt markerTop = 1, faceMarkerTop = 1; 500 PetscInt markerBottom = 1, faceMarkerBottom = 1; 501 PetscInt markerFront = 1, faceMarkerFront = 1; 502 PetscInt markerBack = 1, faceMarkerBack = 1; 503 PetscInt markerRight = 1, faceMarkerRight = 1; 504 PetscInt markerLeft = 1, faceMarkerLeft = 1; 505 PetscInt dim; 506 PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE; 507 PetscMPIInt rank; 508 PetscErrorCode ierr; 509 510 PetscFunctionBegin; 511 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 512 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 513 ierr = DMCreateLabel(dm,"marker");CHKERRQ(ierr); 514 ierr = DMCreateLabel(dm,"Face Sets");CHKERRQ(ierr); 515 if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST || 516 bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST || 517 bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) { 518 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL);CHKERRQ(ierr); 519 if (cutMarker) {ierr = DMCreateLabel(dm, "periodic_cut");CHKERRQ(ierr); ierr = DMGetLabel(dm, "periodic_cut", &cutLabel);CHKERRQ(ierr);} 520 } 521 switch (dim) { 522 case 2: 523 faceMarkerTop = 3; 524 faceMarkerBottom = 1; 525 faceMarkerRight = 2; 526 faceMarkerLeft = 4; 527 break; 528 case 3: 529 faceMarkerBottom = 1; 530 faceMarkerTop = 2; 531 faceMarkerFront = 3; 532 faceMarkerBack = 4; 533 faceMarkerRight = 5; 534 faceMarkerLeft = 6; 535 break; 536 default: 537 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %d not supported",dim); 538 break; 539 } 540 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 541 if (markerSeparate) { 542 markerBottom = faceMarkerBottom; 543 markerTop = faceMarkerTop; 544 markerFront = faceMarkerFront; 545 markerBack = faceMarkerBack; 546 markerRight = faceMarkerRight; 547 markerLeft = faceMarkerLeft; 548 } 549 { 550 const PetscInt numXEdges = !rank ? edges[0] : 0; 551 const PetscInt numYEdges = !rank ? edges[1] : 0; 552 const PetscInt numZEdges = !rank ? edges[2] : 0; 553 const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; 554 const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; 555 const PetscInt numZVertices = !rank ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0; 556 const PetscInt numCells = numXEdges*numYEdges*numZEdges; 557 const PetscInt numXFaces = numYEdges*numZEdges; 558 const PetscInt numYFaces = numXEdges*numZEdges; 559 const PetscInt numZFaces = numXEdges*numYEdges; 560 const PetscInt numTotXFaces = numXVertices*numXFaces; 561 const PetscInt numTotYFaces = numYVertices*numYFaces; 562 const PetscInt numTotZFaces = numZVertices*numZFaces; 563 const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces; 564 const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices; 565 const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices; 566 const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices; 567 const PetscInt numVertices = numXVertices*numYVertices*numZVertices; 568 const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges; 569 const PetscInt firstVertex = (dim == 2) ? numFaces : numCells; 570 const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices; 571 const PetscInt firstYFace = firstXFace + numTotXFaces; 572 const PetscInt firstZFace = firstYFace + numTotYFaces; 573 const PetscInt firstXEdge = numCells + numFaces + numVertices; 574 const PetscInt firstYEdge = firstXEdge + numTotXEdges; 575 const PetscInt firstZEdge = firstYEdge + numTotYEdges; 576 Vec coordinates; 577 PetscSection coordSection; 578 PetscScalar *coords; 579 PetscInt coordSize; 580 PetscInt v, vx, vy, vz; 581 PetscInt c, f, fx, fy, fz, e, ex, ey, ez; 582 583 ierr = DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);CHKERRQ(ierr); 584 for (c = 0; c < numCells; c++) { 585 ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr); 586 } 587 for (f = firstXFace; f < firstXFace+numFaces; ++f) { 588 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 589 } 590 for (e = firstXEdge; e < firstXEdge+numEdges; ++e) { 591 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 592 } 593 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 594 /* Build cells */ 595 for (fz = 0; fz < numZEdges; ++fz) { 596 for (fy = 0; fy < numYEdges; ++fy) { 597 for (fx = 0; fx < numXEdges; ++fx) { 598 PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx; 599 PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 600 PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices); 601 PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 602 PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices); 603 PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 604 PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices); 605 /* B, T, F, K, R, L */ 606 PetscInt ornt[6] = {-4, 0, 0, -1, 0, -4}; /* ??? */ 607 PetscInt cone[6]; 608 609 /* no boundary twisting in 3D */ 610 cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL; 611 ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr); 612 ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr); 613 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 614 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 615 if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 616 } 617 } 618 } 619 /* Build x faces */ 620 for (fz = 0; fz < numZEdges; ++fz) { 621 for (fy = 0; fy < numYEdges; ++fy) { 622 for (fx = 0; fx < numXVertices; ++fx) { 623 PetscInt face = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 624 PetscInt edgeL = firstZEdge + ( fy* numXVertices+fx)*numZEdges + fz; 625 PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz; 626 PetscInt edgeB = firstYEdge + ( fz* numXVertices+fx)*numYEdges + fy; 627 PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy; 628 PetscInt ornt[4] = {0, 0, -2, -2}; 629 PetscInt cone[4]; 630 631 if (dim == 3) { 632 /* markers */ 633 if (bdX != DM_BOUNDARY_PERIODIC) { 634 if (fx == numXVertices-1) { 635 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);CHKERRQ(ierr); 636 ierr = DMSetLabelValue(dm, "marker", face, markerRight);CHKERRQ(ierr); 637 } 638 else if (fx == 0) { 639 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);CHKERRQ(ierr); 640 ierr = DMSetLabelValue(dm, "marker", face, markerLeft);CHKERRQ(ierr); 641 } 642 } 643 } 644 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 645 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 646 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 647 } 648 } 649 } 650 /* Build y faces */ 651 for (fz = 0; fz < numZEdges; ++fz) { 652 for (fx = 0; fx < numXEdges; ++fx) { 653 for (fy = 0; fy < numYVertices; ++fy) { 654 PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 655 PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx )*numZEdges + fz; 656 PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz; 657 PetscInt edgeB = firstXEdge + ( fz *numYVertices+fy)*numXEdges + fx; 658 PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx; 659 PetscInt ornt[4] = {0, 0, -2, -2}; 660 PetscInt cone[4]; 661 662 if (dim == 3) { 663 /* markers */ 664 if (bdY != DM_BOUNDARY_PERIODIC) { 665 if (fy == numYVertices-1) { 666 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);CHKERRQ(ierr); 667 ierr = DMSetLabelValue(dm, "marker", face, markerBack);CHKERRQ(ierr); 668 } 669 else if (fy == 0) { 670 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);CHKERRQ(ierr); 671 ierr = DMSetLabelValue(dm, "marker", face, markerFront);CHKERRQ(ierr); 672 } 673 } 674 } 675 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 676 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 677 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 678 } 679 } 680 } 681 /* Build z faces */ 682 for (fy = 0; fy < numYEdges; ++fy) { 683 for (fx = 0; fx < numXEdges; ++fx) { 684 for (fz = 0; fz < numZVertices; fz++) { 685 PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 686 PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx )*numYEdges + fy; 687 PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy; 688 PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy )*numXEdges + fx; 689 PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx; 690 PetscInt ornt[4] = {0, 0, -2, -2}; 691 PetscInt cone[4]; 692 693 if (dim == 2) { 694 if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -2;} 695 if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;} 696 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 697 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 698 } else { 699 /* markers */ 700 if (bdZ != DM_BOUNDARY_PERIODIC) { 701 if (fz == numZVertices-1) { 702 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);CHKERRQ(ierr); 703 ierr = DMSetLabelValue(dm, "marker", face, markerTop);CHKERRQ(ierr); 704 } 705 else if (fz == 0) { 706 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);CHKERRQ(ierr); 707 ierr = DMSetLabelValue(dm, "marker", face, markerBottom);CHKERRQ(ierr); 708 } 709 } 710 } 711 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 712 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 713 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 714 } 715 } 716 } 717 /* Build Z edges*/ 718 for (vy = 0; vy < numYVertices; vy++) { 719 for (vx = 0; vx < numXVertices; vx++) { 720 for (ez = 0; ez < numZEdges; ez++) { 721 const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez; 722 const PetscInt vertexB = firstVertex + ( ez *numYVertices+vy)*numXVertices + vx; 723 const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx; 724 PetscInt cone[2]; 725 726 if (dim == 3) { 727 if (bdX != DM_BOUNDARY_PERIODIC) { 728 if (vx == numXVertices-1) { 729 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 730 } 731 else if (vx == 0) { 732 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 733 } 734 } 735 if (bdY != DM_BOUNDARY_PERIODIC) { 736 if (vy == numYVertices-1) { 737 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 738 } 739 else if (vy == 0) { 740 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 741 } 742 } 743 } 744 cone[0] = vertexB; cone[1] = vertexT; 745 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 746 } 747 } 748 } 749 /* Build Y edges*/ 750 for (vz = 0; vz < numZVertices; vz++) { 751 for (vx = 0; vx < numXVertices; vx++) { 752 for (ey = 0; ey < numYEdges; ey++) { 753 const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx; 754 const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey; 755 const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx; 756 const PetscInt vertexK = firstVertex + nextv; 757 PetscInt cone[2]; 758 759 cone[0] = vertexF; cone[1] = vertexK; 760 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 761 if (dim == 2) { 762 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 763 if (vx == numXVertices-1) { 764 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);CHKERRQ(ierr); 765 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 766 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 767 if (ey == numYEdges-1) { 768 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 769 } 770 } else if (vx == 0) { 771 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);CHKERRQ(ierr); 772 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 773 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 774 if (ey == numYEdges-1) { 775 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 776 } 777 } 778 } else { 779 if (vx == 0 && cutMarker) { 780 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 781 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 782 if (ey == numYEdges-1) { 783 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 784 } 785 } 786 } 787 } else { 788 if (bdX != DM_BOUNDARY_PERIODIC) { 789 if (vx == numXVertices-1) { 790 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 791 } else if (vx == 0) { 792 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 793 } 794 } 795 if (bdZ != DM_BOUNDARY_PERIODIC) { 796 if (vz == numZVertices-1) { 797 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 798 } else if (vz == 0) { 799 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 800 } 801 } 802 } 803 } 804 } 805 } 806 /* Build X edges*/ 807 for (vz = 0; vz < numZVertices; vz++) { 808 for (vy = 0; vy < numYVertices; vy++) { 809 for (ex = 0; ex < numXEdges; ex++) { 810 const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices; 811 const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex; 812 const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex; 813 const PetscInt vertexR = firstVertex + nextv; 814 PetscInt cone[2]; 815 816 cone[0] = vertexL; cone[1] = vertexR; 817 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 818 if (dim == 2) { 819 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 820 if (vy == numYVertices-1) { 821 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);CHKERRQ(ierr); 822 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 823 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 824 if (ex == numXEdges-1) { 825 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 826 } 827 } else if (vy == 0) { 828 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);CHKERRQ(ierr); 829 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 830 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 831 if (ex == numXEdges-1) { 832 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 833 } 834 } 835 } else { 836 if (vy == 0 && cutMarker) { 837 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 838 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 839 if (ex == numXEdges-1) { 840 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 841 } 842 } 843 } 844 } else { 845 if (bdY != DM_BOUNDARY_PERIODIC) { 846 if (vy == numYVertices-1) { 847 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 848 } 849 else if (vy == 0) { 850 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 851 } 852 } 853 if (bdZ != DM_BOUNDARY_PERIODIC) { 854 if (vz == numZVertices-1) { 855 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 856 } 857 else if (vz == 0) { 858 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 859 } 860 } 861 } 862 } 863 } 864 } 865 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 866 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 867 /* Build coordinates */ 868 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 869 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 870 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 871 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr); 872 for (v = firstVertex; v < firstVertex+numVertices; ++v) { 873 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 874 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 875 } 876 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 877 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 878 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 879 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 880 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 881 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 882 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 883 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 884 for (vz = 0; vz < numZVertices; ++vz) { 885 for (vy = 0; vy < numYVertices; ++vy) { 886 for (vx = 0; vx < numXVertices; ++vx) { 887 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx; 888 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy; 889 if (dim == 3) { 890 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz; 891 } 892 } 893 } 894 } 895 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 896 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 897 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 898 } 899 PetscFunctionReturn(0); 900 } 901 902 /*@ 903 DMPlexCreateHexBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using hexahedra. 904 905 Collective on MPI_Comm 906 907 Input Parameters: 908 + comm - The communicator for the DM object 909 . dim - The spatial dimension 910 . periodicX - The boundary type for the X direction 911 . periodicY - The boundary type for the Y direction 912 . periodicZ - The boundary type for the Z direction 913 - cells - The number of cells in each direction 914 915 Output Parameter: 916 . dm - The DM object 917 918 Note: Here is the numbering returned for 2 cells in each direction: 919 $ 22--8-23--9--24 920 $ | | | 921 $ 13 2 14 3 15 922 $ | | | 923 $ 19--6-20--7--21 924 $ | | | 925 $ 10 0 11 1 12 926 $ | | | 927 $ 16--4-17--5--18 928 929 Level: beginner 930 931 .keywords: DM, create 932 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 933 @*/ 934 PetscErrorCode DMPlexCreateHexBoxMesh(MPI_Comm comm, PetscInt dim, const PetscInt cells[], DMBoundaryType periodicX, DMBoundaryType periodicY, DMBoundaryType periodicZ, DM *dm) 935 { 936 PetscInt i; 937 PetscErrorCode ierr; 938 939 PetscFunctionBegin; 940 PetscValidPointer(dm, 7); 941 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 942 PetscValidLogicalCollectiveInt(*dm,dim,2); 943 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 944 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 945 switch (dim) { 946 case 2: 947 { 948 PetscReal lower[3] = {0.0, 0.0, 0.0}; 949 PetscReal upper[3] = {1.0, 1.0, 0.0}; 950 PetscInt edges[3]; 951 952 edges[0] = cells[0]; 953 edges[1] = cells[1]; 954 edges[2] = 0; 955 956 ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, edges, periodicX, periodicY, DM_BOUNDARY_NONE);CHKERRQ(ierr); 957 if (periodicX == DM_BOUNDARY_PERIODIC || periodicX == DM_BOUNDARY_TWIST || 958 periodicY == DM_BOUNDARY_PERIODIC || periodicY == DM_BOUNDARY_TWIST) { 959 PetscReal L[2]; 960 PetscReal maxCell[2]; 961 DMBoundaryType bdType[2]; 962 963 bdType[0] = periodicX; 964 bdType[1] = periodicY; 965 for (i = 0; i < dim; i++) { 966 L[i] = upper[i] - lower[i]; 967 maxCell[i] = 1.1 * (L[i] / PetscMax(1,cells[i])); 968 } 969 970 ierr = DMSetPeriodicity(*dm,maxCell,L,bdType);CHKERRQ(ierr); 971 } 972 break; 973 } 974 case 3: 975 { 976 PetscReal lower[3] = {0.0, 0.0, 0.0}; 977 PetscReal upper[3] = {1.0, 1.0, 1.0}; 978 979 ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, cells, periodicX, periodicY, periodicZ);CHKERRQ(ierr); 980 if (periodicX == DM_BOUNDARY_PERIODIC || periodicX == DM_BOUNDARY_TWIST || 981 periodicY == DM_BOUNDARY_PERIODIC || periodicY == DM_BOUNDARY_TWIST || 982 periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 983 PetscReal L[3]; 984 PetscReal maxCell[3]; 985 DMBoundaryType bdType[3]; 986 987 bdType[0] = periodicX; 988 bdType[1] = periodicY; 989 bdType[2] = periodicZ; 990 for (i = 0; i < dim; i++) { 991 L[i] = upper[i] - lower[i]; 992 maxCell[i] = 1.1 * (L[i] / cells[i]); 993 } 994 995 ierr = DMSetPeriodicity(*dm,maxCell,L,bdType);CHKERRQ(ierr); 996 } 997 break; 998 } 999 default: 1000 SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 1001 } 1002 PetscFunctionReturn(0); 1003 } 1004 1005 /*@C 1006 DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database. 1007 1008 Logically Collective on DM 1009 1010 Input Parameters: 1011 + dm - the DM context 1012 - prefix - the prefix to prepend to all option names 1013 1014 Notes: 1015 A hyphen (-) must NOT be given at the beginning of the prefix name. 1016 The first character of all runtime options is AUTOMATICALLY the hyphen. 1017 1018 Level: advanced 1019 1020 .seealso: SNESSetFromOptions() 1021 @*/ 1022 PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) 1023 { 1024 DM_Plex *mesh = (DM_Plex *) dm->data; 1025 PetscErrorCode ierr; 1026 1027 PetscFunctionBegin; 1028 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1029 ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);CHKERRQ(ierr); 1030 ierr = PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);CHKERRQ(ierr); 1031 PetscFunctionReturn(0); 1032 } 1033 1034 /*@ 1035 DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. 1036 1037 Collective on MPI_Comm 1038 1039 Input Parameters: 1040 + comm - The communicator for the DM object 1041 . numRefine - The number of regular refinements to the basic 5 cell structure 1042 - periodicZ - The boundary type for the Z direction 1043 1044 Output Parameter: 1045 . dm - The DM object 1046 1047 Note: Here is the output numbering looking from the bottom of the cylinder: 1048 $ 17-----14 1049 $ | | 1050 $ | 2 | 1051 $ | | 1052 $ 17-----8-----7-----14 1053 $ | | | | 1054 $ | 3 | 0 | 1 | 1055 $ | | | | 1056 $ 19-----5-----6-----13 1057 $ | | 1058 $ | 4 | 1059 $ | | 1060 $ 19-----13 1061 $ 1062 $ and up through the top 1063 $ 1064 $ 18-----16 1065 $ | | 1066 $ | 2 | 1067 $ | | 1068 $ 18----10----11-----16 1069 $ | | | | 1070 $ | 3 | 0 | 1 | 1071 $ | | | | 1072 $ 20-----9----12-----15 1073 $ | | 1074 $ | 4 | 1075 $ | | 1076 $ 20-----15 1077 1078 Level: beginner 1079 1080 .keywords: DM, create 1081 .seealso: DMPlexCreateHexBoxMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1082 @*/ 1083 PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, PetscInt numRefine, DMBoundaryType periodicZ, DM *dm) 1084 { 1085 const PetscInt dim = 3; 1086 PetscInt numCells, numVertices, r; 1087 PetscErrorCode ierr; 1088 1089 PetscFunctionBegin; 1090 PetscValidPointer(dm, 4); 1091 if (numRefine < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of refinements %D cannot be negative", numRefine); 1092 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1093 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1094 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1095 /* Create topology */ 1096 { 1097 PetscInt cone[8], c; 1098 1099 numCells = 5; 1100 numVertices = 16; 1101 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1102 numCells *= 3; 1103 numVertices = 24; 1104 } 1105 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1106 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 8);CHKERRQ(ierr);} 1107 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1108 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1109 cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16; 1110 cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34; 1111 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1112 cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23; 1113 cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */ 1114 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1115 cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17; 1116 cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38; 1117 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1118 cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15; 1119 cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38; 1120 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1121 cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23; 1122 cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31; 1123 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1124 1125 cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32; 1126 cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20; 1127 ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); 1128 cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36; 1129 cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21; 1130 ierr = DMPlexSetCone(*dm, 6, cone);CHKERRQ(ierr); 1131 cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33; 1132 cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28; 1133 ierr = DMPlexSetCone(*dm, 7, cone);CHKERRQ(ierr); 1134 cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31; 1135 cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28; 1136 ierr = DMPlexSetCone(*dm, 8, cone);CHKERRQ(ierr); 1137 cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36; 1138 cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19; 1139 ierr = DMPlexSetCone(*dm, 9, cone);CHKERRQ(ierr); 1140 1141 cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22; 1142 cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18; 1143 ierr = DMPlexSetCone(*dm, 10, cone);CHKERRQ(ierr); 1144 cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25; 1145 cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17; 1146 ierr = DMPlexSetCone(*dm, 11, cone);CHKERRQ(ierr); 1147 cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21; 1148 cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27; 1149 ierr = DMPlexSetCone(*dm, 12, cone);CHKERRQ(ierr); 1150 cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19; 1151 cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27; 1152 ierr = DMPlexSetCone(*dm, 13, cone);CHKERRQ(ierr); 1153 cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25; 1154 cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15; 1155 ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); 1156 } else { 1157 cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6; 1158 cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10; 1159 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1160 cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13; 1161 cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11; 1162 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1163 cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7; 1164 cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18; 1165 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1166 cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5; 1167 cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18; 1168 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1169 cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13; 1170 cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9; 1171 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1172 } 1173 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1174 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1175 } 1176 /* Interpolate */ 1177 { 1178 DM idm = NULL; 1179 1180 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1181 ierr = DMDestroy(dm);CHKERRQ(ierr); 1182 *dm = idm; 1183 } 1184 /* Create cube geometry */ 1185 { 1186 Vec coordinates; 1187 PetscSection coordSection; 1188 PetscScalar *coords; 1189 PetscInt coordSize, v; 1190 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1191 const PetscReal ds2 = dis/2.0; 1192 1193 /* Build coordinates */ 1194 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1195 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1196 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1197 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1198 for (v = numCells; v < numCells+numVertices; ++v) { 1199 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1200 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1201 } 1202 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1203 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1204 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1205 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1206 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1207 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1208 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1209 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1210 coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0; 1211 coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0; 1212 coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0; 1213 coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0; 1214 coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0; 1215 coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0; 1216 coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0; 1217 coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0; 1218 coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0; 1219 coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0; 1220 coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0; 1221 coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0; 1222 coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0; 1223 coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0; 1224 coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0; 1225 coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0; 1226 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1227 /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5; 1228 /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5; 1229 /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5; 1230 /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5; 1231 /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5; 1232 /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5; 1233 /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5; 1234 /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5; 1235 } 1236 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1237 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 1238 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1239 } 1240 /* Create periodicity */ 1241 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1242 PetscReal L[3]; 1243 PetscReal maxCell[3]; 1244 DMBoundaryType bdType[3]; 1245 PetscReal lower[3] = {0.0, 0.0, 0.0}; 1246 PetscReal upper[3] = {1.0, 1.0, 1.5}; 1247 PetscInt i, numZCells = 3; 1248 1249 bdType[0] = DM_BOUNDARY_NONE; 1250 bdType[1] = DM_BOUNDARY_NONE; 1251 bdType[2] = periodicZ; 1252 for (i = 0; i < dim; i++) { 1253 L[i] = upper[i] - lower[i]; 1254 maxCell[i] = 1.1 * (L[i] / numZCells); 1255 } 1256 ierr = DMSetPeriodicity(*dm, maxCell, L, bdType);CHKERRQ(ierr); 1257 } 1258 /* Refine topology */ 1259 for (r = 0; r < numRefine; ++r) { 1260 DM rdm = NULL; 1261 1262 ierr = DMRefine(*dm, comm, &rdm);CHKERRQ(ierr); 1263 ierr = DMDestroy(dm);CHKERRQ(ierr); 1264 *dm = rdm; 1265 } 1266 /* Remap geometry to cylinder 1267 Interior square: Linear interpolation is correct 1268 The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing 1269 such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance 1270 1271 phi = arctan(y/x) 1272 d_close = sqrt(1/8 + 1/4 sin^2(phi)) 1273 d_far = sqrt(1/2 + sin^2(phi)) 1274 1275 so we remap them using 1276 1277 x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) 1278 y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) 1279 1280 If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. 1281 */ 1282 { 1283 Vec coordinates; 1284 PetscSection coordSection; 1285 PetscScalar *coords; 1286 PetscInt vStart, vEnd, v; 1287 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1288 const PetscReal ds2 = 0.5*dis; 1289 1290 ierr = DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1291 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1292 ierr = DMGetCoordinatesLocal(*dm, &coordinates);CHKERRQ(ierr); 1293 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1294 for (v = vStart; v < vEnd; ++v) { 1295 PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; 1296 PetscInt off; 1297 1298 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 1299 if ((PetscAbsScalar(coords[off+0]) <= ds2) && (PetscAbsScalar(coords[off+1]) <= ds2)) continue; 1300 x = PetscRealPart(coords[off]); 1301 y = PetscRealPart(coords[off+1]); 1302 phi = PetscAtan2Real(y, x); 1303 sinp = PetscSinReal(phi); 1304 cosp = PetscCosReal(phi); 1305 if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) { 1306 dc = PetscAbsReal(ds2/sinp); 1307 df = PetscAbsReal(dis/sinp); 1308 xc = ds2*x/PetscAbsScalar(y); 1309 yc = ds2*PetscSignReal(y); 1310 } else { 1311 dc = PetscAbsReal(ds2/cosp); 1312 df = PetscAbsReal(dis/cosp); 1313 xc = ds2*PetscSignReal(x); 1314 yc = ds2*y/PetscAbsScalar(x); 1315 } 1316 coords[off+0] = xc + (coords[off+0] - xc)*(1.0 - dc)/(df - dc); 1317 coords[off+1] = yc + (coords[off+1] - yc)*(1.0 - dc)/(df - dc); 1318 } 1319 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1320 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1321 ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); 1322 } 1323 } 1324 PetscFunctionReturn(0); 1325 } 1326 1327 /*@ 1328 DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges. 1329 1330 Collective on MPI_Comm 1331 1332 Input Parameters: 1333 + comm - The communicator for the DM object 1334 . n - The number of wedges around the origin 1335 - interpolate - Create edges and faces 1336 1337 Output Parameter: 1338 . dm - The DM object 1339 1340 Level: beginner 1341 1342 .keywords: DM, create 1343 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateHexBoxMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1344 @*/ 1345 PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm) 1346 { 1347 const PetscInt dim = 3; 1348 PetscInt numCells, numVertices; 1349 PetscErrorCode ierr; 1350 1351 PetscFunctionBegin; 1352 PetscValidPointer(dm, 3); 1353 if (n < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n); 1354 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1355 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1356 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1357 /* Create topology */ 1358 { 1359 PetscInt cone[6], c; 1360 1361 numCells = n; 1362 numVertices = 2*(n+1); 1363 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1364 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 6);CHKERRQ(ierr);} 1365 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1366 for (c = 0; c < numCells; c++) { 1367 cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n; 1368 cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n; 1369 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 1370 } 1371 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1372 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1373 } 1374 /* Interpolate */ 1375 if (interpolate) { 1376 DM idm = NULL; 1377 1378 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1379 ierr = DMDestroy(dm);CHKERRQ(ierr); 1380 *dm = idm; 1381 } 1382 /* Create cylinder geometry */ 1383 { 1384 Vec coordinates; 1385 PetscSection coordSection; 1386 PetscScalar *coords; 1387 PetscInt coordSize, v, c; 1388 1389 /* Build coordinates */ 1390 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1391 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1392 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1393 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1394 for (v = numCells; v < numCells+numVertices; ++v) { 1395 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1396 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1397 } 1398 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1399 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1400 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1401 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1402 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1403 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1404 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1405 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1406 for (c = 0; c < numCells; c++) { 1407 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; 1408 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; 1409 } 1410 coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0; 1411 coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0; 1412 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1413 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 1414 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1415 } 1416 PetscFunctionReturn(0); 1417 } 1418 1419 /* External function declarations here */ 1420 extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling); 1421 extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat); 1422 extern PetscErrorCode DMCreateDefaultSection_Plex(DM dm); 1423 extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm); 1424 extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J); 1425 extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm); 1426 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm); 1427 extern PetscErrorCode DMSetUp_Plex(DM dm); 1428 extern PetscErrorCode DMDestroy_Plex(DM dm); 1429 extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer); 1430 extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer); 1431 extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm); 1432 1433 /* Replace dm with the contents of dmNew 1434 - Share the DM_Plex structure 1435 - Share the coordinates 1436 - Share the SF 1437 */ 1438 static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew) 1439 { 1440 PetscSF sf; 1441 DM coordDM, coarseDM; 1442 Vec coords; 1443 const PetscReal *maxCell, *L; 1444 const DMBoundaryType *bd; 1445 PetscErrorCode ierr; 1446 1447 PetscFunctionBegin; 1448 ierr = DMGetPointSF(dmNew, &sf);CHKERRQ(ierr); 1449 ierr = DMSetPointSF(dm, sf);CHKERRQ(ierr); 1450 ierr = DMGetCoordinateDM(dmNew, &coordDM);CHKERRQ(ierr); 1451 ierr = DMGetCoordinatesLocal(dmNew, &coords);CHKERRQ(ierr); 1452 ierr = DMSetCoordinateDM(dm, coordDM);CHKERRQ(ierr); 1453 ierr = DMSetCoordinatesLocal(dm, coords);CHKERRQ(ierr); 1454 ierr = DMGetPeriodicity(dm, &maxCell, &L, &bd);CHKERRQ(ierr); 1455 if (L) {ierr = DMSetPeriodicity(dmNew, maxCell, L, bd);CHKERRQ(ierr);} 1456 ierr = DMDestroy_Plex(dm);CHKERRQ(ierr); 1457 dm->data = dmNew->data; 1458 ((DM_Plex *) dmNew->data)->refct++; 1459 dmNew->labels->refct++; 1460 if (!--(dm->labels->refct)) { 1461 DMLabelLink next = dm->labels->next; 1462 1463 /* destroy the labels */ 1464 while (next) { 1465 DMLabelLink tmp = next->next; 1466 1467 ierr = DMLabelDestroy(&next->label);CHKERRQ(ierr); 1468 ierr = PetscFree(next);CHKERRQ(ierr); 1469 next = tmp; 1470 } 1471 ierr = PetscFree(dm->labels);CHKERRQ(ierr); 1472 } 1473 dm->labels = dmNew->labels; 1474 dm->depthLabel = dmNew->depthLabel; 1475 ierr = DMGetCoarseDM(dmNew,&coarseDM);CHKERRQ(ierr); 1476 ierr = DMSetCoarseDM(dm,coarseDM);CHKERRQ(ierr); 1477 PetscFunctionReturn(0); 1478 } 1479 1480 /* Swap dm with the contents of dmNew 1481 - Swap the DM_Plex structure 1482 - Swap the coordinates 1483 - Swap the point PetscSF 1484 */ 1485 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 1486 { 1487 DM coordDMA, coordDMB; 1488 Vec coordsA, coordsB; 1489 PetscSF sfA, sfB; 1490 void *tmp; 1491 DMLabelLinkList listTmp; 1492 DMLabel depthTmp; 1493 PetscErrorCode ierr; 1494 1495 PetscFunctionBegin; 1496 ierr = DMGetPointSF(dmA, &sfA);CHKERRQ(ierr); 1497 ierr = DMGetPointSF(dmB, &sfB);CHKERRQ(ierr); 1498 ierr = PetscObjectReference((PetscObject) sfA);CHKERRQ(ierr); 1499 ierr = DMSetPointSF(dmA, sfB);CHKERRQ(ierr); 1500 ierr = DMSetPointSF(dmB, sfA);CHKERRQ(ierr); 1501 ierr = PetscObjectDereference((PetscObject) sfA);CHKERRQ(ierr); 1502 1503 ierr = DMGetCoordinateDM(dmA, &coordDMA);CHKERRQ(ierr); 1504 ierr = DMGetCoordinateDM(dmB, &coordDMB);CHKERRQ(ierr); 1505 ierr = PetscObjectReference((PetscObject) coordDMA);CHKERRQ(ierr); 1506 ierr = DMSetCoordinateDM(dmA, coordDMB);CHKERRQ(ierr); 1507 ierr = DMSetCoordinateDM(dmB, coordDMA);CHKERRQ(ierr); 1508 ierr = PetscObjectDereference((PetscObject) coordDMA);CHKERRQ(ierr); 1509 1510 ierr = DMGetCoordinatesLocal(dmA, &coordsA);CHKERRQ(ierr); 1511 ierr = DMGetCoordinatesLocal(dmB, &coordsB);CHKERRQ(ierr); 1512 ierr = PetscObjectReference((PetscObject) coordsA);CHKERRQ(ierr); 1513 ierr = DMSetCoordinatesLocal(dmA, coordsB);CHKERRQ(ierr); 1514 ierr = DMSetCoordinatesLocal(dmB, coordsA);CHKERRQ(ierr); 1515 ierr = PetscObjectDereference((PetscObject) coordsA);CHKERRQ(ierr); 1516 1517 tmp = dmA->data; 1518 dmA->data = dmB->data; 1519 dmB->data = tmp; 1520 listTmp = dmA->labels; 1521 dmA->labels = dmB->labels; 1522 dmB->labels = listTmp; 1523 depthTmp = dmA->depthLabel; 1524 dmA->depthLabel = dmB->depthLabel; 1525 dmB->depthLabel = depthTmp; 1526 PetscFunctionReturn(0); 1527 } 1528 1529 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 1530 { 1531 DM_Plex *mesh = (DM_Plex*) dm->data; 1532 PetscErrorCode ierr; 1533 1534 PetscFunctionBegin; 1535 /* Handle viewing */ 1536 ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMView", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); 1537 ierr = PetscOptionsInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMView", 0, &mesh->printFEM, NULL);CHKERRQ(ierr); 1538 ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMView", mesh->printTol, &mesh->printTol, NULL);CHKERRQ(ierr); 1539 /* Point Location */ 1540 ierr = PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMView", PETSC_FALSE, &mesh->useHashLocation, NULL);CHKERRQ(ierr); 1541 /* Generation and remeshing */ 1542 ierr = PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMView", PETSC_FALSE, &mesh->remeshBd, NULL);CHKERRQ(ierr); 1543 /* Projection behavior */ 1544 ierr = PetscOptionsInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL);CHKERRQ(ierr); 1545 ierr = PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);CHKERRQ(ierr); 1546 1547 ierr = PetscPartitionerSetFromOptions(mesh->partitioner);CHKERRQ(ierr); 1548 PetscFunctionReturn(0); 1549 } 1550 1551 static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 1552 { 1553 PetscInt refine = 0, coarsen = 0, r; 1554 PetscBool isHierarchy; 1555 PetscErrorCode ierr; 1556 1557 PetscFunctionBegin; 1558 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1559 ierr = PetscOptionsHead(PetscOptionsObject,"DMPlex Options");CHKERRQ(ierr); 1560 /* Handle DMPlex refinement */ 1561 ierr = PetscOptionsInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL);CHKERRQ(ierr); 1562 ierr = PetscOptionsInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy);CHKERRQ(ierr); 1563 if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 1564 if (refine && isHierarchy) { 1565 DM *dms, coarseDM; 1566 1567 ierr = DMGetCoarseDM(dm, &coarseDM);CHKERRQ(ierr); 1568 ierr = PetscObjectReference((PetscObject)coarseDM);CHKERRQ(ierr); 1569 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 1570 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 1571 /* Total hack since we do not pass in a pointer */ 1572 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 1573 if (refine == 1) { 1574 ierr = DMSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 1575 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 1576 } else { 1577 ierr = DMSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 1578 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 1579 ierr = DMSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 1580 ierr = DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);CHKERRQ(ierr); 1581 } 1582 ierr = DMSetCoarseDM(dms[refine-1], coarseDM);CHKERRQ(ierr); 1583 ierr = PetscObjectDereference((PetscObject)coarseDM);CHKERRQ(ierr); 1584 /* Free DMs */ 1585 for (r = 0; r < refine; ++r) { 1586 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 1587 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 1588 } 1589 ierr = PetscFree(dms);CHKERRQ(ierr); 1590 } else { 1591 for (r = 0; r < refine; ++r) { 1592 DM refinedMesh; 1593 1594 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 1595 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);CHKERRQ(ierr); 1596 /* Total hack since we do not pass in a pointer */ 1597 ierr = DMPlexReplace_Static(dm, refinedMesh);CHKERRQ(ierr); 1598 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 1599 ierr = DMDestroy(&refinedMesh);CHKERRQ(ierr); 1600 } 1601 } 1602 /* Handle DMPlex coarsening */ 1603 ierr = PetscOptionsInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL);CHKERRQ(ierr); 1604 ierr = PetscOptionsInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy);CHKERRQ(ierr); 1605 if (coarsen && isHierarchy) { 1606 DM *dms; 1607 1608 ierr = PetscMalloc1(coarsen, &dms);CHKERRQ(ierr); 1609 ierr = DMCoarsenHierarchy(dm, coarsen, dms);CHKERRQ(ierr); 1610 /* Free DMs */ 1611 for (r = 0; r < coarsen; ++r) { 1612 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 1613 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 1614 } 1615 ierr = PetscFree(dms);CHKERRQ(ierr); 1616 } else { 1617 for (r = 0; r < coarsen; ++r) { 1618 DM coarseMesh; 1619 1620 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 1621 ierr = DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);CHKERRQ(ierr); 1622 /* Total hack since we do not pass in a pointer */ 1623 ierr = DMPlexReplace_Static(dm, coarseMesh);CHKERRQ(ierr); 1624 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 1625 ierr = DMDestroy(&coarseMesh);CHKERRQ(ierr); 1626 } 1627 } 1628 /* Handle */ 1629 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 1630 ierr = PetscOptionsTail();CHKERRQ(ierr); 1631 PetscFunctionReturn(0); 1632 } 1633 1634 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 1635 { 1636 PetscErrorCode ierr; 1637 1638 PetscFunctionBegin; 1639 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 1640 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 1641 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 1642 ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); 1643 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 1644 ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); 1645 PetscFunctionReturn(0); 1646 } 1647 1648 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 1649 { 1650 PetscErrorCode ierr; 1651 1652 PetscFunctionBegin; 1653 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 1654 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 1655 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 1656 PetscFunctionReturn(0); 1657 } 1658 1659 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 1660 { 1661 PetscInt depth, d; 1662 PetscErrorCode ierr; 1663 1664 PetscFunctionBegin; 1665 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1666 if (depth == 1) { 1667 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 1668 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 1669 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 1670 else {*pStart = 0; *pEnd = 0;} 1671 } else { 1672 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 1673 } 1674 PetscFunctionReturn(0); 1675 } 1676 1677 static PetscErrorCode DMGetNeighors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 1678 { 1679 PetscSF sf; 1680 PetscErrorCode ierr; 1681 1682 PetscFunctionBegin; 1683 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 1684 ierr = PetscSFGetRanks(sf, nranks, ranks, NULL, NULL, NULL);CHKERRQ(ierr); 1685 PetscFunctionReturn(0); 1686 } 1687 1688 static PetscErrorCode DMInitialize_Plex(DM dm) 1689 { 1690 PetscErrorCode ierr; 1691 1692 PetscFunctionBegin; 1693 dm->ops->view = DMView_Plex; 1694 dm->ops->load = DMLoad_Plex; 1695 dm->ops->setfromoptions = DMSetFromOptions_Plex; 1696 dm->ops->clone = DMClone_Plex; 1697 dm->ops->setup = DMSetUp_Plex; 1698 dm->ops->createdefaultsection = DMCreateDefaultSection_Plex; 1699 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 1700 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 1701 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 1702 dm->ops->getlocaltoglobalmapping = NULL; 1703 dm->ops->createfieldis = NULL; 1704 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 1705 dm->ops->getcoloring = NULL; 1706 dm->ops->creatematrix = DMCreateMatrix_Plex; 1707 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 1708 dm->ops->getaggregates = NULL; 1709 dm->ops->getinjection = DMCreateInjection_Plex; 1710 dm->ops->refine = DMRefine_Plex; 1711 dm->ops->coarsen = DMCoarsen_Plex; 1712 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 1713 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 1714 dm->ops->globaltolocalbegin = NULL; 1715 dm->ops->globaltolocalend = NULL; 1716 dm->ops->localtoglobalbegin = NULL; 1717 dm->ops->localtoglobalend = NULL; 1718 dm->ops->destroy = DMDestroy_Plex; 1719 dm->ops->createsubdm = DMCreateSubDM_Plex; 1720 dm->ops->getdimpoints = DMGetDimPoints_Plex; 1721 dm->ops->locatepoints = DMLocatePoints_Plex; 1722 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 1723 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 1724 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 1725 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 1726 dm->ops->computel2diff = DMComputeL2Diff_Plex; 1727 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 1728 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 1729 dm->ops->getneighbors = DMGetNeighors_Plex; 1730 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMAdaptLabel_C",DMAdaptLabel_Plex);CHKERRQ(ierr); 1731 PetscFunctionReturn(0); 1732 } 1733 1734 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 1735 { 1736 DM_Plex *mesh = (DM_Plex *) dm->data; 1737 PetscErrorCode ierr; 1738 1739 PetscFunctionBegin; 1740 mesh->refct++; 1741 (*newdm)->data = mesh; 1742 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 1743 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 1744 PetscFunctionReturn(0); 1745 } 1746 1747 /*MC 1748 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 1749 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 1750 specified by a PetscSection object. Ownership in the global representation is determined by 1751 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 1752 1753 Level: intermediate 1754 1755 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 1756 M*/ 1757 1758 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 1759 { 1760 DM_Plex *mesh; 1761 PetscInt unit, d; 1762 PetscErrorCode ierr; 1763 1764 PetscFunctionBegin; 1765 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1766 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 1767 dm->dim = 0; 1768 dm->data = mesh; 1769 1770 mesh->refct = 1; 1771 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 1772 mesh->maxConeSize = 0; 1773 mesh->cones = NULL; 1774 mesh->coneOrientations = NULL; 1775 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 1776 mesh->maxSupportSize = 0; 1777 mesh->supports = NULL; 1778 mesh->refinementUniform = PETSC_TRUE; 1779 mesh->refinementLimit = -1.0; 1780 1781 mesh->facesTmp = NULL; 1782 1783 mesh->tetgenOpts = NULL; 1784 mesh->triangleOpts = NULL; 1785 ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); 1786 mesh->remeshBd = PETSC_FALSE; 1787 1788 mesh->subpointMap = NULL; 1789 1790 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 1791 1792 mesh->regularRefinement = PETSC_FALSE; 1793 mesh->depthState = -1; 1794 mesh->globalVertexNumbers = NULL; 1795 mesh->globalCellNumbers = NULL; 1796 mesh->anchorSection = NULL; 1797 mesh->anchorIS = NULL; 1798 mesh->createanchors = NULL; 1799 mesh->computeanchormatrix = NULL; 1800 mesh->parentSection = NULL; 1801 mesh->parents = NULL; 1802 mesh->childIDs = NULL; 1803 mesh->childSection = NULL; 1804 mesh->children = NULL; 1805 mesh->referenceTree = NULL; 1806 mesh->getchildsymmetry = NULL; 1807 for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE; 1808 mesh->vtkCellHeight = 0; 1809 mesh->useCone = PETSC_FALSE; 1810 mesh->useClosure = PETSC_TRUE; 1811 mesh->useAnchors = PETSC_FALSE; 1812 1813 mesh->maxProjectionHeight = 0; 1814 1815 mesh->printSetValues = PETSC_FALSE; 1816 mesh->printFEM = 0; 1817 mesh->printTol = 1.0e-10; 1818 1819 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 1820 PetscFunctionReturn(0); 1821 } 1822 1823 /*@ 1824 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 1825 1826 Collective on MPI_Comm 1827 1828 Input Parameter: 1829 . comm - The communicator for the DMPlex object 1830 1831 Output Parameter: 1832 . mesh - The DMPlex object 1833 1834 Level: beginner 1835 1836 .keywords: DMPlex, create 1837 @*/ 1838 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 1839 { 1840 PetscErrorCode ierr; 1841 1842 PetscFunctionBegin; 1843 PetscValidPointer(mesh,2); 1844 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 1845 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 1846 PetscFunctionReturn(0); 1847 } 1848 1849 /* 1850 This takes as input the common mesh generator output, a list of the vertices for each cell, but vertex numbers are global and an SF is built for them 1851 */ 1852 static PetscErrorCode DMPlexBuildFromCellList_Parallel_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscSF *sfVert) 1853 { 1854 PetscSF sfPoint; 1855 PetscLayout vLayout; 1856 PetscHashI vhash; 1857 PetscSFNode *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex; 1858 const PetscInt *vrange; 1859 PetscInt numVerticesAdj, off, *verticesAdj, numVerticesGhost = 0, *localVertex, *cone, c, p, v, g; 1860 PETSC_UNUSED PetscHashIIter ret, iter; 1861 PetscMPIInt rank, size; 1862 PetscErrorCode ierr; 1863 1864 PetscFunctionBegin; 1865 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 1866 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); 1867 /* Partition vertices */ 1868 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);CHKERRQ(ierr); 1869 ierr = PetscLayoutSetLocalSize(vLayout, numVertices);CHKERRQ(ierr); 1870 ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr); 1871 ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr); 1872 ierr = PetscLayoutGetRanges(vLayout, &vrange);CHKERRQ(ierr); 1873 /* Count vertices and map them to procs */ 1874 PetscHashICreate(vhash); 1875 for (c = 0; c < numCells; ++c) { 1876 for (p = 0; p < numCorners; ++p) { 1877 PetscHashIPut(vhash, cells[c*numCorners+p], ret, iter); 1878 } 1879 } 1880 PetscHashISize(vhash, numVerticesAdj); 1881 ierr = PetscMalloc1(numVerticesAdj, &verticesAdj);CHKERRQ(ierr); 1882 off = 0; ierr = PetscHashIGetKeys(vhash, &off, verticesAdj);CHKERRQ(ierr); 1883 if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj); 1884 ierr = PetscSortInt(numVerticesAdj, verticesAdj);CHKERRQ(ierr); 1885 ierr = PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);CHKERRQ(ierr); 1886 for (v = 0; v < numVerticesAdj; ++v) { 1887 const PetscInt gv = verticesAdj[v]; 1888 PetscInt vrank; 1889 1890 ierr = PetscFindInt(gv, size+1, vrange, &vrank);CHKERRQ(ierr); 1891 vrank = vrank < 0 ? -(vrank+2) : vrank; 1892 remoteVerticesAdj[v].index = gv - vrange[vrank]; 1893 remoteVerticesAdj[v].rank = vrank; 1894 } 1895 /* Create cones */ 1896 ierr = DMPlexSetChart(dm, 0, numCells+numVerticesAdj);CHKERRQ(ierr); 1897 for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);} 1898 ierr = DMSetUp(dm);CHKERRQ(ierr); 1899 ierr = DMGetWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); 1900 for (c = 0; c < numCells; ++c) { 1901 for (p = 0; p < numCorners; ++p) { 1902 const PetscInt gv = cells[c*numCorners+p]; 1903 PetscInt lv; 1904 1905 ierr = PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);CHKERRQ(ierr); 1906 if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv); 1907 cone[p] = lv+numCells; 1908 } 1909 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 1910 } 1911 ierr = DMRestoreWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); 1912 /* Create SF for vertices */ 1913 ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfVert);CHKERRQ(ierr); 1914 ierr = PetscObjectSetName((PetscObject) *sfVert, "Vertex Ownership SF");CHKERRQ(ierr); 1915 ierr = PetscSFSetFromOptions(*sfVert);CHKERRQ(ierr); 1916 ierr = PetscSFSetGraph(*sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);CHKERRQ(ierr); 1917 ierr = PetscFree(verticesAdj);CHKERRQ(ierr); 1918 /* Build pointSF */ 1919 ierr = PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);CHKERRQ(ierr); 1920 for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;} 1921 for (v = 0; v < numVertices; ++v) {vertexOwner[v].index = -1; vertexOwner[v].rank = -1;} 1922 ierr = PetscSFReduceBegin(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 1923 ierr = PetscSFReduceEnd(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 1924 for (v = 0; v < numVertices; ++v) if (vertexOwner[v].rank < 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Global vertex %d on rank %d was unclaimed", v + vrange[rank], rank); 1925 ierr = PetscSFBcastBegin(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 1926 ierr = PetscSFBcastEnd(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 1927 for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost; 1928 ierr = PetscMalloc1(numVerticesGhost, &localVertex);CHKERRQ(ierr); 1929 ierr = PetscMalloc1(numVerticesGhost, &remoteVertex);CHKERRQ(ierr); 1930 for (v = 0, g = 0; v < numVerticesAdj; ++v) { 1931 if (vertexLocal[v].rank != rank) { 1932 localVertex[g] = v+numCells; 1933 remoteVertex[g].index = vertexLocal[v].index; 1934 remoteVertex[g].rank = vertexLocal[v].rank; 1935 ++g; 1936 } 1937 } 1938 ierr = PetscFree2(vertexLocal, vertexOwner);CHKERRQ(ierr); 1939 if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost); 1940 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 1941 ierr = PetscObjectSetName((PetscObject) sfPoint, "point SF");CHKERRQ(ierr); 1942 ierr = PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);CHKERRQ(ierr); 1943 ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr); 1944 PetscHashIDestroy(vhash); 1945 /* Fill in the rest of the topology structure */ 1946 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1947 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1948 PetscFunctionReturn(0); 1949 } 1950 1951 /* 1952 This takes as input the coordinates for each owned vertex 1953 */ 1954 static PetscErrorCode DMPlexBuildCoordinates_Parallel_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numV, PetscSF sfVert, const PetscReal vertexCoords[]) 1955 { 1956 PetscSection coordSection; 1957 Vec coordinates; 1958 PetscScalar *coords; 1959 PetscInt numVertices, numVerticesAdj, coordSize, v; 1960 PetscErrorCode ierr; 1961 1962 PetscFunctionBegin; 1963 ierr = PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);CHKERRQ(ierr); 1964 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1965 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1966 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 1967 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVerticesAdj);CHKERRQ(ierr); 1968 for (v = numCells; v < numCells+numVerticesAdj; ++v) { 1969 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 1970 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 1971 } 1972 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1973 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1974 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 1975 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 1976 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1977 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1978 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1979 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1980 { 1981 MPI_Datatype coordtype; 1982 1983 /* Need a temp buffer for coords if we have complex/single */ 1984 ierr = MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);CHKERRQ(ierr); 1985 ierr = MPI_Type_commit(&coordtype);CHKERRQ(ierr); 1986 #if defined(PETSC_USE_COMPLEX) 1987 { 1988 PetscScalar *svertexCoords; 1989 PetscInt i; 1990 ierr = PetscMalloc1(numV*spaceDim,&svertexCoords);CHKERRQ(ierr); 1991 for (i=0; i<numV*spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 1992 ierr = PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 1993 ierr = PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 1994 ierr = PetscFree(svertexCoords);CHKERRQ(ierr); 1995 } 1996 #else 1997 ierr = PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 1998 ierr = PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 1999 #endif 2000 ierr = MPI_Type_free(&coordtype);CHKERRQ(ierr); 2001 } 2002 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2003 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2004 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2005 PetscFunctionReturn(0); 2006 } 2007 2008 /*@C 2009 DMPlexCreateFromCellListParallel - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 2010 2011 Input Parameters: 2012 + comm - The communicator 2013 . dim - The topological dimension of the mesh 2014 . numCells - The number of cells owned by this process 2015 . numVertices - The number of vertices owned by this process 2016 . numCorners - The number of vertices for each cell 2017 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 2018 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 2019 . spaceDim - The spatial dimension used for coordinates 2020 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2021 2022 Output Parameter: 2023 + dm - The DM 2024 - vertexSF - Optional, SF describing complete vertex ownership 2025 2026 Note: Two triangles sharing a face 2027 $ 2028 $ 2 2029 $ / | \ 2030 $ / | \ 2031 $ / | \ 2032 $ 0 0 | 1 3 2033 $ \ | / 2034 $ \ | / 2035 $ \ | / 2036 $ 1 2037 would have input 2038 $ numCells = 2, numVertices = 4 2039 $ cells = [0 1 2 1 3 2] 2040 $ 2041 which would result in the DMPlex 2042 $ 2043 $ 4 2044 $ / | \ 2045 $ / | \ 2046 $ / | \ 2047 $ 2 0 | 1 5 2048 $ \ | / 2049 $ \ | / 2050 $ \ | / 2051 $ 3 2052 2053 Level: beginner 2054 2055 .seealso: DMPlexCreateFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate() 2056 @*/ 2057 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) 2058 { 2059 PetscSF sfVert; 2060 PetscErrorCode ierr; 2061 2062 PetscFunctionBegin; 2063 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2064 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2065 PetscValidLogicalCollectiveInt(*dm, dim, 2); 2066 PetscValidLogicalCollectiveInt(*dm, spaceDim, 8); 2067 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 2068 ierr = DMPlexBuildFromCellList_Parallel_Private(*dm, numCells, numVertices, numCorners, cells, &sfVert);CHKERRQ(ierr); 2069 if (interpolate) { 2070 DM idm = NULL; 2071 2072 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2073 ierr = DMDestroy(dm);CHKERRQ(ierr); 2074 *dm = idm; 2075 } 2076 ierr = DMPlexBuildCoordinates_Parallel_Private(*dm, spaceDim, numCells, numVertices,sfVert, vertexCoords);CHKERRQ(ierr); 2077 if (vertexSF) *vertexSF = sfVert; 2078 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 2079 PetscFunctionReturn(0); 2080 } 2081 2082 /* 2083 This takes as input the common mesh generator output, a list of the vertices for each cell 2084 */ 2085 static PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]) 2086 { 2087 PetscInt *cone, c, p; 2088 PetscErrorCode ierr; 2089 2090 PetscFunctionBegin; 2091 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 2092 for (c = 0; c < numCells; ++c) { 2093 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 2094 } 2095 ierr = DMSetUp(dm);CHKERRQ(ierr); 2096 ierr = DMGetWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); 2097 for (c = 0; c < numCells; ++c) { 2098 for (p = 0; p < numCorners; ++p) { 2099 cone[p] = cells[c*numCorners+p]+numCells; 2100 } 2101 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 2102 } 2103 ierr = DMRestoreWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); 2104 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2105 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2106 PetscFunctionReturn(0); 2107 } 2108 2109 /* 2110 This takes as input the coordinates for each vertex 2111 */ 2112 static PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]) 2113 { 2114 PetscSection coordSection; 2115 Vec coordinates; 2116 DM cdm; 2117 PetscScalar *coords; 2118 PetscInt v, d; 2119 PetscErrorCode ierr; 2120 2121 PetscFunctionBegin; 2122 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2123 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2124 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 2125 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); 2126 for (v = numCells; v < numCells+numVertices; ++v) { 2127 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 2128 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 2129 } 2130 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2131 2132 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 2133 ierr = DMCreateLocalVector(cdm, &coordinates);CHKERRQ(ierr); 2134 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 2135 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2136 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2137 for (v = 0; v < numVertices; ++v) { 2138 for (d = 0; d < spaceDim; ++d) { 2139 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 2140 } 2141 } 2142 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2143 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2144 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2145 PetscFunctionReturn(0); 2146 } 2147 2148 /*@C 2149 DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 2150 2151 Input Parameters: 2152 + comm - The communicator 2153 . dim - The topological dimension of the mesh 2154 . numCells - The number of cells 2155 . numVertices - The number of vertices 2156 . numCorners - The number of vertices for each cell 2157 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 2158 . cells - An array of numCells*numCorners numbers, the vertices for each cell 2159 . spaceDim - The spatial dimension used for coordinates 2160 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2161 2162 Output Parameter: 2163 . dm - The DM 2164 2165 Note: Two triangles sharing a face 2166 $ 2167 $ 2 2168 $ / | \ 2169 $ / | \ 2170 $ / | \ 2171 $ 0 0 | 1 3 2172 $ \ | / 2173 $ \ | / 2174 $ \ | / 2175 $ 1 2176 would have input 2177 $ numCells = 2, numVertices = 4 2178 $ cells = [0 1 2 1 3 2] 2179 $ 2180 which would result in the DMPlex 2181 $ 2182 $ 4 2183 $ / | \ 2184 $ / | \ 2185 $ / | \ 2186 $ 2 0 | 1 5 2187 $ \ | / 2188 $ \ | / 2189 $ \ | / 2190 $ 3 2191 2192 Level: beginner 2193 2194 .seealso: DMPlexCreateFromDAG(), DMPlexCreate() 2195 @*/ 2196 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) 2197 { 2198 PetscErrorCode ierr; 2199 2200 PetscFunctionBegin; 2201 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2202 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2203 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 2204 ierr = DMPlexBuildFromCellList_Private(*dm, numCells, numVertices, numCorners, cells);CHKERRQ(ierr); 2205 if (interpolate) { 2206 DM idm = NULL; 2207 2208 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2209 ierr = DMDestroy(dm);CHKERRQ(ierr); 2210 *dm = idm; 2211 } 2212 ierr = DMPlexBuildCoordinates_Private(*dm, spaceDim, numCells, numVertices, vertexCoords);CHKERRQ(ierr); 2213 PetscFunctionReturn(0); 2214 } 2215 2216 /*@ 2217 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 2218 2219 Input Parameters: 2220 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 2221 . depth - The depth of the DAG 2222 . numPoints - The number of points at each depth 2223 . coneSize - The cone size of each point 2224 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 2225 . coneOrientations - The orientation of each cone point 2226 - vertexCoords - An array of numVertices*dim numbers, the coordinates of each vertex 2227 2228 Output Parameter: 2229 . dm - The DM 2230 2231 Note: Two triangles sharing a face would have input 2232 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 2233 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 2234 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 2235 $ 2236 which would result in the DMPlex 2237 $ 2238 $ 4 2239 $ / | \ 2240 $ / | \ 2241 $ / | \ 2242 $ 2 0 | 1 5 2243 $ \ | / 2244 $ \ | / 2245 $ \ | / 2246 $ 3 2247 $ 2248 $ Notice that all points are numbered consecutively, unlikely DMPlexCreateFromCellList() 2249 2250 Level: advanced 2251 2252 .seealso: DMPlexCreateFromCellList(), DMPlexCreate() 2253 @*/ 2254 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 2255 { 2256 Vec coordinates; 2257 PetscSection coordSection; 2258 PetscScalar *coords; 2259 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 2260 PetscErrorCode ierr; 2261 2262 PetscFunctionBegin; 2263 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2264 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 2265 if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %d cannot be less than intrinsic dimension %d",dimEmbed,dim); 2266 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 2267 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 2268 for (p = pStart; p < pEnd; ++p) { 2269 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 2270 if (firstVertex < 0 && !coneSize[p - pStart]) { 2271 firstVertex = p - pStart; 2272 } 2273 } 2274 if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %d vertices but could not find any", numPoints[0]); 2275 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 2276 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 2277 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 2278 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 2279 } 2280 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2281 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2282 /* Build coordinates */ 2283 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2284 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2285 ierr = PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);CHKERRQ(ierr); 2286 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 2287 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 2288 ierr = PetscSectionSetDof(coordSection, v, dimEmbed);CHKERRQ(ierr); 2289 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);CHKERRQ(ierr); 2290 } 2291 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2292 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2293 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 2294 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2295 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2296 ierr = VecSetBlockSize(coordinates, dimEmbed);CHKERRQ(ierr); 2297 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2298 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2299 for (v = 0; v < numPoints[0]; ++v) { 2300 PetscInt off; 2301 2302 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 2303 for (d = 0; d < dimEmbed; ++d) { 2304 coords[off+d] = vertexCoords[v*dimEmbed+d]; 2305 } 2306 } 2307 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2308 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2309 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2310 PetscFunctionReturn(0); 2311 } 2312 2313 /*@C 2314 DMPlexCreateFromFile - This takes a filename and produces a DM 2315 2316 Input Parameters: 2317 + comm - The communicator 2318 . filename - A file name 2319 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 2320 2321 Output Parameter: 2322 . dm - The DM 2323 2324 Level: beginner 2325 2326 .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellList(), DMPlexCreate() 2327 @*/ 2328 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 2329 { 2330 const char *extGmsh = ".msh"; 2331 const char *extCGNS = ".cgns"; 2332 const char *extExodus = ".exo"; 2333 const char *extFluent = ".cas"; 2334 const char *extHDF5 = ".h5"; 2335 const char *extMed = ".med"; 2336 const char *extPLY = ".ply"; 2337 size_t len; 2338 PetscBool isGmsh, isCGNS, isExodus, isFluent, isHDF5, isMed, isPLY; 2339 PetscMPIInt rank; 2340 PetscErrorCode ierr; 2341 2342 PetscFunctionBegin; 2343 PetscValidPointer(filename, 2); 2344 PetscValidPointer(dm, 4); 2345 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 2346 ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); 2347 if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 2348 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);CHKERRQ(ierr); 2349 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);CHKERRQ(ierr); 2350 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);CHKERRQ(ierr); 2351 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);CHKERRQ(ierr); 2352 ierr = PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);CHKERRQ(ierr); 2353 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);CHKERRQ(ierr); 2354 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);CHKERRQ(ierr); 2355 if (isGmsh) { 2356 ierr = DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2357 } else if (isCGNS) { 2358 ierr = DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2359 } else if (isExodus) { 2360 ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2361 } else if (isFluent) { 2362 ierr = DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2363 } else if (isHDF5) { 2364 PetscViewer viewer; 2365 2366 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 2367 ierr = PetscViewerSetType(viewer, PETSCVIEWERHDF5);CHKERRQ(ierr); 2368 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 2369 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 2370 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2371 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2372 ierr = DMLoad(*dm, viewer);CHKERRQ(ierr); 2373 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 2374 } else if (isMed) { 2375 ierr = DMPlexCreateMedFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2376 } else if (isPLY) { 2377 ierr = DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2378 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 2379 PetscFunctionReturn(0); 2380 } 2381 2382 /*@ 2383 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 2384 2385 Collective on comm 2386 2387 Input Parameters: 2388 + comm - The communicator 2389 . dim - The spatial dimension 2390 - simplex - Flag for simplex, otherwise use a tensor-product cell 2391 2392 Output Parameter: 2393 . refdm - The reference cell 2394 2395 Level: intermediate 2396 2397 .keywords: reference cell 2398 .seealso: 2399 @*/ 2400 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm) 2401 { 2402 DM rdm; 2403 Vec coords; 2404 PetscErrorCode ierr; 2405 2406 PetscFunctionBeginUser; 2407 ierr = DMCreate(comm, &rdm);CHKERRQ(ierr); 2408 ierr = DMSetType(rdm, DMPLEX);CHKERRQ(ierr); 2409 ierr = DMSetDimension(rdm, dim);CHKERRQ(ierr); 2410 switch (dim) { 2411 case 0: 2412 { 2413 PetscInt numPoints[1] = {1}; 2414 PetscInt coneSize[1] = {0}; 2415 PetscInt cones[1] = {0}; 2416 PetscInt coneOrientations[1] = {0}; 2417 PetscScalar vertexCoords[1] = {0.0}; 2418 2419 ierr = DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2420 } 2421 break; 2422 case 1: 2423 { 2424 PetscInt numPoints[2] = {2, 1}; 2425 PetscInt coneSize[3] = {2, 0, 0}; 2426 PetscInt cones[2] = {1, 2}; 2427 PetscInt coneOrientations[2] = {0, 0}; 2428 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 2429 2430 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2431 } 2432 break; 2433 case 2: 2434 if (simplex) { 2435 PetscInt numPoints[2] = {3, 1}; 2436 PetscInt coneSize[4] = {3, 0, 0, 0}; 2437 PetscInt cones[3] = {1, 2, 3}; 2438 PetscInt coneOrientations[3] = {0, 0, 0}; 2439 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 2440 2441 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2442 } else { 2443 PetscInt numPoints[2] = {4, 1}; 2444 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 2445 PetscInt cones[4] = {1, 2, 3, 4}; 2446 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 2447 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 2448 2449 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2450 } 2451 break; 2452 case 3: 2453 if (simplex) { 2454 PetscInt numPoints[2] = {4, 1}; 2455 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 2456 PetscInt cones[4] = {1, 3, 2, 4}; 2457 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 2458 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}; 2459 2460 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2461 } else { 2462 PetscInt numPoints[2] = {8, 1}; 2463 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 2464 PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8}; 2465 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 2466 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, 2467 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 2468 2469 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2470 } 2471 break; 2472 default: 2473 SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %d", dim); 2474 } 2475 *refdm = NULL; 2476 ierr = DMPlexInterpolate(rdm, refdm);CHKERRQ(ierr); 2477 if (rdm->coordinateDM) { 2478 DM ncdm; 2479 PetscSection cs; 2480 PetscInt pEnd = -1; 2481 2482 ierr = DMGetDefaultSection(rdm->coordinateDM, &cs);CHKERRQ(ierr); 2483 if (cs) {ierr = PetscSectionGetChart(cs, NULL, &pEnd);CHKERRQ(ierr);} 2484 if (pEnd >= 0) { 2485 ierr = DMClone(rdm->coordinateDM, &ncdm);CHKERRQ(ierr); 2486 ierr = DMSetDefaultSection(ncdm, cs);CHKERRQ(ierr); 2487 ierr = DMSetCoordinateDM(*refdm, ncdm);CHKERRQ(ierr); 2488 ierr = DMDestroy(&ncdm);CHKERRQ(ierr); 2489 } 2490 } 2491 ierr = DMGetCoordinatesLocal(rdm, &coords);CHKERRQ(ierr); 2492 if (coords) { 2493 ierr = DMSetCoordinatesLocal(*refdm, coords);CHKERRQ(ierr); 2494 } else { 2495 ierr = DMGetCoordinates(rdm, &coords);CHKERRQ(ierr); 2496 if (coords) {ierr = DMSetCoordinates(*refdm, coords);CHKERRQ(ierr);} 2497 } 2498 ierr = DMDestroy(&rdm);CHKERRQ(ierr); 2499 PetscFunctionReturn(0); 2500 } 2501