1 #define PETSCDM_DLL 2 #include <petsc-private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 #include <petscdmda.h> 4 #include <petscsf.h> 5 6 #undef __FUNCT__ 7 #define __FUNCT__ "DMPlexCreateDoublet" 8 /*@ 9 DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement. 10 11 Collective on MPI_Comm 12 13 Input Parameters: 14 + comm - The communicator for the DM object 15 . dim - The spatial dimension 16 . simplex - Flag for simplicial cells, otherwise they are tensor product cells 17 . interpolate - Flag to create intermediate mesh pieces (edges, faces) 18 . refinementUniform - Flag for uniform parallel refinement 19 - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell 20 21 Output Parameter: 22 . dm - The DM object 23 24 Level: beginner 25 26 .keywords: DM, create 27 .seealso: DMSetType(), DMCreate() 28 @*/ 29 PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscBool refinementUniform, PetscReal refinementLimit, DM *newdm) 30 { 31 DM dm; 32 PetscInt p; 33 PetscMPIInt rank; 34 PetscErrorCode ierr; 35 36 PetscFunctionBegin; 37 ierr = DMCreate(comm, &dm);CHKERRQ(ierr); 38 ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr); 39 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 40 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 41 switch (dim) { 42 case 2: 43 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "triangular");CHKERRQ(ierr);} 44 else {ierr = PetscObjectSetName((PetscObject) dm, "quadrilateral");CHKERRQ(ierr);} 45 break; 46 case 3: 47 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "tetrahedral");CHKERRQ(ierr);} 48 else {ierr = PetscObjectSetName((PetscObject) dm, "hexahedral");CHKERRQ(ierr);} 49 break; 50 default: 51 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); 52 } 53 if (rank) { 54 PetscInt numPoints[2] = {0, 0}; 55 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 56 } else { 57 switch (dim) { 58 case 2: 59 if (simplex) { 60 PetscInt numPoints[2] = {4, 2}; 61 PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; 62 PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; 63 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 64 PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5}; 65 PetscInt markerPoints[8] = {2, 1, 3, 1, 4, 1, 5, 1}; 66 67 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 68 for (p = 0; p < 4; ++p) {ierr = DMPlexSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 69 } else { 70 PetscInt numPoints[2] = {6, 2}; 71 PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; 72 PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4}; 73 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 74 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}; 75 76 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 77 } 78 break; 79 case 3: 80 if (simplex) { 81 PetscInt numPoints[2] = {5, 2}; 82 PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; 83 PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; 84 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 85 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}; 86 PetscInt markerPoints[10] = {2, 1, 3, 1, 4, 1, 5, 1, 6, 1}; 87 88 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 89 for (p = 0; p < 5; ++p) {ierr = DMPlexSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 90 } else { 91 PetscInt numPoints[2] = {12, 2}; 92 PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 93 PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8}; 94 PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 95 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, 96 -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5, 97 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5}; 98 99 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 100 } 101 break; 102 default: 103 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); 104 } 105 } 106 *newdm = dm; 107 if (refinementLimit > 0.0) { 108 DM rdm; 109 const char *name; 110 111 ierr = DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);CHKERRQ(ierr); 112 ierr = DMPlexSetRefinementLimit(*newdm, refinementLimit);CHKERRQ(ierr); 113 ierr = DMRefine(*newdm, comm, &rdm);CHKERRQ(ierr); 114 ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); 115 ierr = PetscObjectSetName((PetscObject) rdm, name);CHKERRQ(ierr); 116 ierr = DMDestroy(newdm);CHKERRQ(ierr); 117 *newdm = rdm; 118 } 119 if (interpolate) { 120 DM idm = NULL; 121 const char *name; 122 123 ierr = DMPlexInterpolate(*newdm, &idm);CHKERRQ(ierr); 124 ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); 125 ierr = PetscObjectSetName((PetscObject) idm, name);CHKERRQ(ierr); 126 ierr = DMPlexCopyCoordinates(*newdm, idm);CHKERRQ(ierr); 127 ierr = DMPlexCopyLabels(*newdm, idm);CHKERRQ(ierr); 128 ierr = DMDestroy(newdm);CHKERRQ(ierr); 129 *newdm = idm; 130 } 131 { 132 DM refinedMesh = NULL; 133 DM distributedMesh = NULL; 134 135 /* Distribute mesh over processes */ 136 ierr = DMPlexDistribute(*newdm, NULL, 0, NULL, &distributedMesh);CHKERRQ(ierr); 137 if (distributedMesh) { 138 ierr = DMDestroy(newdm);CHKERRQ(ierr); 139 *newdm = distributedMesh; 140 } 141 if (refinementUniform) { 142 ierr = DMPlexSetRefinementUniform(*newdm, refinementUniform);CHKERRQ(ierr); 143 ierr = DMRefine(*newdm, comm, &refinedMesh);CHKERRQ(ierr); 144 if (refinedMesh) { 145 ierr = DMDestroy(newdm);CHKERRQ(ierr); 146 *newdm = refinedMesh; 147 } 148 } 149 } 150 PetscFunctionReturn(0); 151 } 152 153 #undef __FUNCT__ 154 #define __FUNCT__ "DMPlexCreateSquareBoundary" 155 /*@ 156 DMPlexCreateSquareBoundary - Creates a 1D mesh the is the boundary of a square lattice. 157 158 Collective on MPI_Comm 159 160 Input Parameters: 161 + comm - The communicator for the DM object 162 . lower - The lower left corner coordinates 163 . upper - The upper right corner coordinates 164 - edges - The number of cells in each direction 165 166 Output Parameter: 167 . dm - The DM object 168 169 Note: Here is the numbering returned for 2 cells in each direction: 170 $ 18--5-17--4--16 171 $ | | | 172 $ 6 10 3 173 $ | | | 174 $ 19-11-20--9--15 175 $ | | | 176 $ 7 8 2 177 $ | | | 178 $ 12--0-13--1--14 179 180 Level: beginner 181 182 .keywords: DM, create 183 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate() 184 @*/ 185 PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 186 { 187 PetscInt numVertices = (edges[0]+1)*(edges[1]+1); 188 PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1]; 189 PetscInt markerTop = 1; 190 PetscInt markerBottom = 1; 191 PetscInt markerRight = 1; 192 PetscInt markerLeft = 1; 193 PetscBool markerSeparate = PETSC_FALSE; 194 Vec coordinates; 195 PetscSection coordSection; 196 PetscScalar *coords; 197 PetscInt coordSize; 198 PetscMPIInt rank; 199 PetscInt v, vx, vy; 200 PetscErrorCode ierr; 201 202 PetscFunctionBegin; 203 ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 204 if (markerSeparate) { 205 markerTop = 1; 206 markerBottom = 0; 207 markerRight = 0; 208 markerLeft = 0; 209 } 210 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 211 if (!rank) { 212 PetscInt e, ex, ey; 213 214 ierr = DMPlexSetChart(dm, 0, numEdges+numVertices);CHKERRQ(ierr); 215 for (e = 0; e < numEdges; ++e) { 216 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 217 } 218 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 219 for (vx = 0; vx <= edges[0]; vx++) { 220 for (ey = 0; ey < edges[1]; ey++) { 221 PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1); 222 PetscInt vertex = ey*(edges[0]+1) + vx + numEdges; 223 PetscInt cone[2]; 224 225 cone[0] = vertex; cone[1] = vertex+edges[0]+1; 226 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 227 if (vx == edges[0]) { 228 ierr = DMPlexSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 229 ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 230 if (ey == edges[1]-1) { 231 ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 232 } 233 } else if (vx == 0) { 234 ierr = DMPlexSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 235 ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 236 if (ey == edges[1]-1) { 237 ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 238 } 239 } 240 } 241 } 242 for (vy = 0; vy <= edges[1]; vy++) { 243 for (ex = 0; ex < edges[0]; ex++) { 244 PetscInt edge = vy*edges[0] + ex; 245 PetscInt vertex = vy*(edges[0]+1) + ex + numEdges; 246 PetscInt cone[2]; 247 248 cone[0] = vertex; cone[1] = vertex+1; 249 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 250 if (vy == edges[1]) { 251 ierr = DMPlexSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 252 ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 253 if (ex == edges[0]-1) { 254 ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 255 } 256 } else if (vy == 0) { 257 ierr = DMPlexSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 258 ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 259 if (ex == edges[0]-1) { 260 ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 261 } 262 } 263 } 264 } 265 } 266 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 267 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 268 /* Build coordinates */ 269 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 270 ierr = PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);CHKERRQ(ierr); 271 for (v = numEdges; v < numEdges+numVertices; ++v) { 272 ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr); 273 } 274 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 275 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 276 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 277 ierr = VecSetBlockSize(coordinates, 2);CHKERRQ(ierr); 278 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);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 #undef __FUNCT__ 294 #define __FUNCT__ "DMPlexCreateCubeBoundary" 295 /*@ 296 DMPlexCreateCubeBoundary - Creates a 2D mesh the is the boundary of a cubic lattice. 297 298 Collective on MPI_Comm 299 300 Input Parameters: 301 + comm - The communicator for the DM object 302 . lower - The lower left front corner coordinates 303 . upper - The upper right back corner coordinates 304 - edges - The number of cells in each direction 305 306 Output Parameter: 307 . dm - The DM object 308 309 Level: beginner 310 311 .keywords: DM, create 312 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMSetType(), DMCreate() 313 @*/ 314 PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) 315 { 316 PetscInt vertices[3], numVertices; 317 PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2]; 318 Vec coordinates; 319 PetscSection coordSection; 320 PetscScalar *coords; 321 PetscInt coordSize; 322 PetscMPIInt rank; 323 PetscInt v, vx, vy, vz; 324 PetscInt voffset, iface=0, cone[4]; 325 PetscErrorCode ierr; 326 327 PetscFunctionBegin; 328 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"); 329 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 330 vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1; 331 numVertices = vertices[0]*vertices[1]*vertices[2]; 332 if (!rank) { 333 PetscInt f; 334 335 ierr = DMPlexSetChart(dm, 0, numFaces+numVertices);CHKERRQ(ierr); 336 for (f = 0; f < numFaces; ++f) { 337 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 338 } 339 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 340 for (v = 0; v < numFaces+numVertices; ++v) { 341 ierr = DMPlexSetLabelValue(dm, "marker", v, 1);CHKERRQ(ierr); 342 } 343 344 /* Side 0 (Top) */ 345 for (vy = 0; vy < faces[1]; vy++) { 346 for (vx = 0; vx < faces[0]; vx++) { 347 voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx; 348 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0]; 349 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 350 iface++; 351 } 352 } 353 354 /* Side 1 (Bottom) */ 355 for (vy = 0; vy < faces[1]; vy++) { 356 for (vx = 0; vx < faces[0]; vx++) { 357 voffset = numFaces + vy*(faces[0]+1) + vx; 358 cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1; 359 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 360 iface++; 361 } 362 } 363 364 /* Side 2 (Front) */ 365 for (vz = 0; vz < faces[2]; vz++) { 366 for (vx = 0; vx < faces[0]; vx++) { 367 voffset = numFaces + vz*vertices[0]*vertices[1] + vx; 368 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1]; 369 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 370 iface++; 371 } 372 } 373 374 /* Side 3 (Back) */ 375 for (vz = 0; vz < faces[2]; vz++) { 376 for (vx = 0; vx < faces[0]; vx++) { 377 voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx; 378 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1; 379 cone[2] = voffset+1; cone[3] = voffset; 380 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 381 iface++; 382 } 383 } 384 385 /* Side 4 (Left) */ 386 for (vz = 0; vz < faces[2]; vz++) { 387 for (vy = 0; vy < faces[1]; vy++) { 388 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0]; 389 cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1]; 390 cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0]; 391 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 392 iface++; 393 } 394 } 395 396 /* Side 5 (Right) */ 397 for (vz = 0; vz < faces[2]; vz++) { 398 for (vy = 0; vy < faces[1]; vy++) { 399 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + vx; 400 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset; 401 cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0]; 402 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 403 iface++; 404 } 405 } 406 } 407 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 408 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 409 /* Build coordinates */ 410 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 411 ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr); 412 for (v = numFaces; v < numFaces+numVertices; ++v) { 413 ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr); 414 } 415 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 416 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 417 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 418 ierr = VecSetBlockSize(coordinates, 3);CHKERRQ(ierr); 419 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 420 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 421 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 422 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 423 for (vz = 0; vz <= faces[2]; ++vz) { 424 for (vy = 0; vy <= faces[1]; ++vy) { 425 for (vx = 0; vx <= faces[0]; ++vx) { 426 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx; 427 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy; 428 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz; 429 } 430 } 431 } 432 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 433 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 434 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 435 PetscFunctionReturn(0); 436 } 437 438 #undef __FUNCT__ 439 #define __FUNCT__ "DMPlexCreateSquareMesh" 440 /*@ 441 DMPlexCreateSquareMesh - Creates a 2D mesh for a square lattice. 442 443 Collective on MPI_Comm 444 445 Input Parameters: 446 + comm - The communicator for the DM object 447 . lower - The lower left corner coordinates 448 . upper - The upper right corner coordinates 449 . edges - The number of cells in each direction 450 . bdX - The boundary type for the X direction 451 - bdY - The boundary type for the Y direction 452 453 Output Parameter: 454 . dm - The DM object 455 456 Note: Here is the numbering returned for 2 cells in each direction: 457 $ 22--8-23--9--24 458 $ | | | 459 $ 13 2 14 3 15 460 $ | | | 461 $ 19--6-20--7--21 462 $ | | | 463 $ 10 0 11 1 12 464 $ | | | 465 $ 16--4-17--5--18 466 467 Level: beginner 468 469 .keywords: DM, create 470 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate() 471 @*/ 472 PetscErrorCode DMPlexCreateSquareMesh(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY) 473 { 474 PetscInt markerTop = 1; 475 PetscInt markerBottom = 1; 476 PetscInt markerRight = 1; 477 PetscInt markerLeft = 1; 478 PetscBool markerSeparate = PETSC_FALSE; 479 PetscMPIInt rank; 480 PetscErrorCode ierr; 481 482 PetscFunctionBegin; 483 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 484 ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 485 if (markerSeparate) { 486 markerTop = 3; 487 markerBottom = 1; 488 markerRight = 2; 489 markerLeft = 4; 490 } 491 { 492 const PetscInt numXEdges = !rank ? edges[0] : 0; 493 const PetscInt numYEdges = !rank ? edges[1] : 0; 494 const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; 495 const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; 496 const PetscInt numTotXEdges = numXEdges*numYVertices; 497 const PetscInt numTotYEdges = numYEdges*numXVertices; 498 const PetscInt numVertices = numXVertices*numYVertices; 499 const PetscInt numEdges = numTotXEdges + numTotYEdges; 500 const PetscInt numFaces = numXEdges*numYEdges; 501 const PetscInt firstVertex = numFaces; 502 const PetscInt firstXEdge = numFaces + numVertices; 503 const PetscInt firstYEdge = numFaces + numVertices + numTotXEdges; 504 Vec coordinates; 505 PetscSection coordSection; 506 PetscScalar *coords; 507 PetscInt coordSize; 508 PetscInt v, vx, vy; 509 PetscInt f, fx, fy, e, ex, ey; 510 511 ierr = DMPlexSetChart(dm, 0, numFaces+numEdges+numVertices);CHKERRQ(ierr); 512 for (f = 0; f < numFaces; ++f) { 513 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 514 } 515 for (e = firstXEdge; e < firstXEdge+numEdges; ++e) { 516 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 517 } 518 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 519 /* Build faces */ 520 for (fy = 0; fy < numYEdges; ++fy) { 521 for (fx = 0; fx < numXEdges; ++fx) { 522 PetscInt face = fy*numXEdges + fx; 523 PetscInt edgeL = firstYEdge + fx *numYEdges + fy; 524 PetscInt edgeR = firstYEdge + ((fx+1)%numXVertices)*numYEdges + fy; 525 PetscInt edgeB = firstXEdge + fy *numXEdges + fx; 526 PetscInt edgeT = firstXEdge + ((fy+1)%numYVertices)*numXEdges + fx; 527 PetscInt ornt[4] = {0, 0, -2, -2}; 528 PetscInt cone[4]; 529 530 if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -2;} 531 if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;} 532 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 533 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 534 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 535 } 536 } 537 /* Build Y edges*/ 538 for (vx = 0; vx < numXVertices; vx++) { 539 for (ey = 0; ey < numYEdges; ey++) { 540 const PetscInt nextv = (bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : ((ey+1)%numYVertices)*numXVertices + vx; 541 const PetscInt edge = firstYEdge + vx*numYEdges + ey; 542 const PetscInt vertexB = firstVertex + ey*numXVertices + vx; 543 const PetscInt vertexT = firstVertex + nextv; 544 PetscInt cone[2]; 545 546 cone[0] = vertexB; cone[1] = vertexT; 547 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 548 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 549 if (vx == numXVertices-1) { 550 ierr = DMPlexSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 551 ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 552 if (ey == numYEdges-1) { 553 ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 554 } 555 } else if (vx == 0) { 556 ierr = DMPlexSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 557 ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 558 if (ey == numYEdges-1) { 559 ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 560 } 561 } 562 } 563 } 564 } 565 /* Build X edges*/ 566 for (vy = 0; vy < numYVertices; vy++) { 567 for (ex = 0; ex < numXEdges; ex++) { 568 const PetscInt nextv = (bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : vy*numXVertices + (ex+1)%numXVertices; 569 const PetscInt edge = firstXEdge + vy*numXEdges + ex; 570 const PetscInt vertexL = firstVertex + vy*numXVertices + ex; 571 const PetscInt vertexR = firstVertex + nextv; 572 PetscInt cone[2]; 573 574 cone[0] = vertexL; cone[1] = vertexR; 575 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 576 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 577 if (vy == numYVertices-1) { 578 ierr = DMPlexSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 579 ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 580 if (ex == numXEdges-1) { 581 ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 582 } 583 } else if (vy == 0) { 584 ierr = DMPlexSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 585 ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 586 if (ex == numXEdges-1) { 587 ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 588 } 589 } 590 } 591 } 592 } 593 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 594 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 595 /* Build coordinates */ 596 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 597 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 598 ierr = PetscSectionSetFieldComponents(coordSection, 0, 2);CHKERRQ(ierr); 599 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr); 600 for (v = firstVertex; v < firstVertex+numVertices; ++v) { 601 ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr); 602 ierr = PetscSectionSetFieldDof(coordSection, v, 0, 2);CHKERRQ(ierr); 603 } 604 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 605 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 606 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 607 ierr = VecSetBlockSize(coordinates, 2);CHKERRQ(ierr); 608 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 609 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 610 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 611 for (vy = 0; vy < numYVertices; ++vy) { 612 for (vx = 0; vx < numXVertices; ++vx) { 613 coords[(vy*numXVertices+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx; 614 coords[(vy*numXVertices+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy; 615 } 616 } 617 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 618 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 619 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 620 } 621 PetscFunctionReturn(0); 622 } 623 624 #undef __FUNCT__ 625 #define __FUNCT__ "DMPlexCreateBoxMesh" 626 /*@ 627 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices. 628 629 Collective on MPI_Comm 630 631 Input Parameters: 632 + comm - The communicator for the DM object 633 . dim - The spatial dimension 634 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 635 636 Output Parameter: 637 . dm - The DM object 638 639 Level: beginner 640 641 .keywords: DM, create 642 .seealso: DMPlexCreateHexBoxMesh(), DMSetType(), DMCreate() 643 @*/ 644 PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscBool interpolate, DM *dm) 645 { 646 DM boundary; 647 PetscErrorCode ierr; 648 649 PetscFunctionBegin; 650 PetscValidPointer(dm, 4); 651 ierr = DMCreate(comm, &boundary);CHKERRQ(ierr); 652 PetscValidLogicalCollectiveInt(boundary,dim,2); 653 ierr = DMSetType(boundary, DMPLEX);CHKERRQ(ierr); 654 ierr = DMSetDimension(boundary, dim-1);CHKERRQ(ierr); 655 switch (dim) { 656 case 2: 657 { 658 PetscReal lower[2] = {0.0, 0.0}; 659 PetscReal upper[2] = {1.0, 1.0}; 660 PetscInt edges[2] = {2, 2}; 661 662 ierr = DMPlexCreateSquareBoundary(boundary, lower, upper, edges);CHKERRQ(ierr); 663 break; 664 } 665 case 3: 666 { 667 PetscReal lower[3] = {0.0, 0.0, 0.0}; 668 PetscReal upper[3] = {1.0, 1.0, 1.0}; 669 PetscInt faces[3] = {1, 1, 1}; 670 671 ierr = DMPlexCreateCubeBoundary(boundary, lower, upper, faces);CHKERRQ(ierr); 672 break; 673 } 674 default: 675 SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 676 } 677 ierr = DMPlexGenerate(boundary, NULL, interpolate, dm);CHKERRQ(ierr); 678 ierr = DMDestroy(&boundary);CHKERRQ(ierr); 679 PetscFunctionReturn(0); 680 } 681 682 #undef __FUNCT__ 683 #define __FUNCT__ "DMPlexCreateHexBoxMesh" 684 /*@ 685 DMPlexCreateHexBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using hexahedra. 686 687 Collective on MPI_Comm 688 689 Input Parameters: 690 + comm - The communicator for the DM object 691 . dim - The spatial dimension 692 . periodicX - The boundary type for the X direction 693 . periodicY - The boundary type for the Y direction 694 . periodicZ - The boundary type for the Z direction 695 - cells - The number of cells in each direction 696 697 Output Parameter: 698 . dm - The DM object 699 700 Level: beginner 701 702 .keywords: DM, create 703 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 704 @*/ 705 PetscErrorCode DMPlexCreateHexBoxMesh(MPI_Comm comm, PetscInt dim, const PetscInt cells[], DMBoundaryType periodicX, DMBoundaryType periodicY, DMBoundaryType periodicZ, DM *dm) 706 { 707 PetscErrorCode ierr; 708 709 PetscFunctionBegin; 710 PetscValidPointer(dm, 4); 711 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 712 PetscValidLogicalCollectiveInt(*dm,dim,2); 713 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 714 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 715 switch (dim) { 716 case 2: 717 { 718 PetscReal lower[2] = {0.0, 0.0}; 719 PetscReal upper[2] = {1.0, 1.0}; 720 721 ierr = DMPlexCreateSquareMesh(*dm, lower, upper, cells, periodicX, periodicY);CHKERRQ(ierr); 722 break; 723 } 724 #if 0 725 case 3: 726 { 727 PetscReal lower[3] = {0.0, 0.0, 0.0}; 728 PetscReal upper[3] = {1.0, 1.0, 1.0}; 729 730 ierr = DMPlexCreateCubeMesh(boundary, lower, upper, cells, periodicX, periodicY, periodicZ);CHKERRQ(ierr); 731 break; 732 } 733 #endif 734 default: 735 SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 736 } 737 PetscFunctionReturn(0); 738 } 739 740 /* External function declarations here */ 741 extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling); 742 extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, VecScatter *ctx); 743 extern PetscErrorCode DMCreateDefaultSection_Plex(DM dm); 744 extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J); 745 extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm); 746 extern PetscErrorCode DMRefine_Plex(DM dm, MPI_Comm comm, DM *dmRefined); 747 extern PetscErrorCode DMCoarsen_Plex(DM dm, MPI_Comm comm, DM *dmCoarsened); 748 extern PetscErrorCode DMRefineHierarchy_Plex(DM dm, PetscInt nlevels, DM dmRefined[]); 749 extern PetscErrorCode DMClone_Plex(DM dm, DM *newdm); 750 extern PetscErrorCode DMSetUp_Plex(DM dm); 751 extern PetscErrorCode DMDestroy_Plex(DM dm); 752 extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer); 753 extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer); 754 extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm); 755 extern PetscErrorCode DMLocatePoints_Plex(DM dm, Vec v, IS *cellIS); 756 757 #undef __FUNCT__ 758 #define __FUNCT__ "DMPlexReplace_Static" 759 /* Replace dm with the contents of dmNew 760 - Share the DM_Plex structure 761 - Share the coordinates 762 - Share the SF 763 */ 764 static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew) 765 { 766 PetscSF sf; 767 DM coordDM; 768 Vec coords; 769 const PetscReal *maxCell, *L; 770 PetscErrorCode ierr; 771 772 PetscFunctionBegin; 773 ierr = DMGetPointSF(dmNew, &sf);CHKERRQ(ierr); 774 ierr = DMSetPointSF(dm, sf);CHKERRQ(ierr); 775 ierr = DMGetCoordinateDM(dmNew, &coordDM);CHKERRQ(ierr); 776 ierr = DMGetCoordinatesLocal(dmNew, &coords);CHKERRQ(ierr); 777 ierr = DMSetCoordinateDM(dm, coordDM);CHKERRQ(ierr); 778 ierr = DMSetCoordinatesLocal(dm, coords);CHKERRQ(ierr); 779 ierr = DMGetPeriodicity(dm, &maxCell, &L);CHKERRQ(ierr); 780 if (L) {ierr = DMSetPeriodicity(dmNew, maxCell, L);CHKERRQ(ierr);} 781 ierr = DMDestroy_Plex(dm);CHKERRQ(ierr); 782 dm->data = dmNew->data; 783 ((DM_Plex *) dmNew->data)->refct++; 784 PetscFunctionReturn(0); 785 } 786 787 #undef __FUNCT__ 788 #define __FUNCT__ "DMPlexSwap_Static" 789 /* Swap dm with the contents of dmNew 790 - Swap the DM_Plex structure 791 - Swap the coordinates 792 */ 793 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 794 { 795 DM coordDMA, coordDMB; 796 Vec coordsA, coordsB; 797 void *tmp; 798 PetscErrorCode ierr; 799 800 PetscFunctionBegin; 801 ierr = DMGetCoordinateDM(dmA, &coordDMA);CHKERRQ(ierr); 802 ierr = DMGetCoordinateDM(dmB, &coordDMB);CHKERRQ(ierr); 803 ierr = PetscObjectReference((PetscObject) coordDMA);CHKERRQ(ierr); 804 ierr = DMSetCoordinateDM(dmA, coordDMB);CHKERRQ(ierr); 805 ierr = DMSetCoordinateDM(dmB, coordDMA);CHKERRQ(ierr); 806 ierr = PetscObjectDereference((PetscObject) coordDMA);CHKERRQ(ierr); 807 808 ierr = DMGetCoordinatesLocal(dmA, &coordsA);CHKERRQ(ierr); 809 ierr = DMGetCoordinatesLocal(dmB, &coordsB);CHKERRQ(ierr); 810 ierr = PetscObjectReference((PetscObject) coordsA);CHKERRQ(ierr); 811 ierr = DMSetCoordinatesLocal(dmA, coordsB);CHKERRQ(ierr); 812 ierr = DMSetCoordinatesLocal(dmB, coordsA);CHKERRQ(ierr); 813 ierr = PetscObjectDereference((PetscObject) coordsA);CHKERRQ(ierr); 814 tmp = dmA->data; 815 dmA->data = dmB->data; 816 dmB->data = tmp; 817 PetscFunctionReturn(0); 818 } 819 820 #undef __FUNCT__ 821 #define __FUNCT__ "DMSetFromOptions_NonRefinement_Plex" 822 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(DM dm) 823 { 824 DM_Plex *mesh = (DM_Plex*) dm->data; 825 DMBoundary b; 826 PetscErrorCode ierr; 827 828 PetscFunctionBegin; 829 /* Handle boundary conditions */ 830 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject) dm), NULL, "Boundary condition options", "");CHKERRQ(ierr); 831 for (b = mesh->boundary; b; b = b->next) { 832 char optname[1024]; 833 PetscInt ids[1024], len = 1024, i; 834 PetscBool flg; 835 836 ierr = PetscSNPrintf(optname, sizeof(optname), "-bc_%s", b->name);CHKERRQ(ierr); 837 ierr = PetscMemzero(ids, sizeof(ids));CHKERRQ(ierr); 838 ierr = PetscOptionsIntArray(optname, "List of boundary IDs", "", ids, &len, &flg);CHKERRQ(ierr); 839 if (flg) { 840 DMLabel label; 841 842 ierr = DMPlexGetLabel(dm, b->labelname, &label);CHKERRQ(ierr); 843 for (i = 0; i < len; ++i) { 844 PetscBool has; 845 846 ierr = DMLabelHasValue(label, ids[i], &has);CHKERRQ(ierr); 847 if (!has) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Boundary id %D is not present in the label %s", ids[i], b->name); 848 } 849 b->numids = len; 850 ierr = PetscFree(b->ids);CHKERRQ(ierr); 851 ierr = PetscMalloc1(len, &b->ids);CHKERRQ(ierr); 852 ierr = PetscMemcpy(b->ids, ids, len*sizeof(PetscInt));CHKERRQ(ierr); 853 } 854 } 855 ierr = PetscOptionsEnd();CHKERRQ(ierr); 856 /* Handle viewing */ 857 ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMView", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); 858 ierr = PetscOptionsInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMView", 0, &mesh->printFEM, NULL);CHKERRQ(ierr); 859 ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMView", PETSC_FALSE, &mesh->printTol, NULL);CHKERRQ(ierr); 860 PetscFunctionReturn(0); 861 } 862 863 #undef __FUNCT__ 864 #define __FUNCT__ "DMSetFromOptions_Plex" 865 PetscErrorCode DMSetFromOptions_Plex(DM dm) 866 { 867 PetscInt refine = 0, r; 868 PetscBool isHierarchy; 869 PetscErrorCode ierr; 870 871 PetscFunctionBegin; 872 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 873 ierr = PetscOptionsHead("DMPlex Options");CHKERRQ(ierr); 874 /* Handle DMPlex refinement */ 875 ierr = PetscOptionsInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL);CHKERRQ(ierr); 876 ierr = PetscOptionsInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy);CHKERRQ(ierr); 877 if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 878 if (refine && isHierarchy) { 879 DM *dms; 880 881 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 882 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 883 /* Total hack since we do not pass in a pointer */ 884 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 885 if (refine == 1) { 886 ierr = DMPlexSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 887 } else { 888 ierr = DMPlexSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 889 ierr = DMPlexSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 890 } 891 /* Free DMs */ 892 for (r = 0; r < refine; ++r) { 893 ierr = DMSetFromOptions_NonRefinement_Plex(dm);CHKERRQ(ierr); 894 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 895 } 896 ierr = PetscFree(dms);CHKERRQ(ierr); 897 } else { 898 for (r = 0; r < refine; ++r) { 899 DM refinedMesh; 900 901 ierr = DMSetFromOptions_NonRefinement_Plex(dm);CHKERRQ(ierr); 902 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);CHKERRQ(ierr); 903 /* Total hack since we do not pass in a pointer */ 904 ierr = DMPlexReplace_Static(dm, refinedMesh);CHKERRQ(ierr); 905 ierr = DMDestroy(&refinedMesh);CHKERRQ(ierr); 906 } 907 } 908 ierr = DMSetFromOptions_NonRefinement_Plex(dm);CHKERRQ(ierr); 909 ierr = PetscOptionsTail();CHKERRQ(ierr); 910 PetscFunctionReturn(0); 911 } 912 913 #undef __FUNCT__ 914 #define __FUNCT__ "DMCreateGlobalVector_Plex" 915 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 916 { 917 PetscErrorCode ierr; 918 919 PetscFunctionBegin; 920 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 921 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 922 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 923 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 924 PetscFunctionReturn(0); 925 } 926 927 #undef __FUNCT__ 928 #define __FUNCT__ "DMCreateLocalVector_Plex" 929 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 930 { 931 PetscErrorCode ierr; 932 933 PetscFunctionBegin; 934 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 935 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 936 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 937 PetscFunctionReturn(0); 938 } 939 940 #undef __FUNCT__ 941 #define __FUNCT__ "DMGetDimPoints_Plex" 942 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 943 { 944 PetscInt depth, d; 945 PetscErrorCode ierr; 946 947 PetscFunctionBegin; 948 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 949 if (depth == 1) { 950 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 951 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 952 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 953 else {*pStart = 0; *pEnd = 0;} 954 } else { 955 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 956 } 957 PetscFunctionReturn(0); 958 } 959 960 #undef __FUNCT__ 961 #define __FUNCT__ "DMInitialize_Plex" 962 PetscErrorCode DMInitialize_Plex(DM dm) 963 { 964 PetscFunctionBegin; 965 dm->ops->view = DMView_Plex; 966 dm->ops->load = DMLoad_Plex; 967 dm->ops->setfromoptions = DMSetFromOptions_Plex; 968 dm->ops->clone = DMClone_Plex; 969 dm->ops->setup = DMSetUp_Plex; 970 dm->ops->createdefaultsection = DMCreateDefaultSection_Plex; 971 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 972 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 973 dm->ops->getlocaltoglobalmapping = NULL; 974 dm->ops->createfieldis = NULL; 975 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 976 dm->ops->getcoloring = NULL; 977 dm->ops->creatematrix = DMCreateMatrix_Plex; 978 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 979 dm->ops->getaggregates = NULL; 980 dm->ops->getinjection = DMCreateInjection_Plex; 981 dm->ops->refine = DMRefine_Plex; 982 dm->ops->coarsen = DMCoarsen_Plex; 983 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 984 dm->ops->coarsenhierarchy = NULL; 985 dm->ops->globaltolocalbegin = NULL; 986 dm->ops->globaltolocalend = NULL; 987 dm->ops->localtoglobalbegin = NULL; 988 dm->ops->localtoglobalend = NULL; 989 dm->ops->destroy = DMDestroy_Plex; 990 dm->ops->createsubdm = DMCreateSubDM_Plex; 991 dm->ops->getdimpoints = DMGetDimPoints_Plex; 992 dm->ops->locatepoints = DMLocatePoints_Plex; 993 PetscFunctionReturn(0); 994 } 995 996 #undef __FUNCT__ 997 #define __FUNCT__ "DMClone_Plex" 998 PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 999 { 1000 DM_Plex *mesh = (DM_Plex *) dm->data; 1001 PetscErrorCode ierr; 1002 1003 PetscFunctionBegin; 1004 mesh->refct++; 1005 (*newdm)->data = mesh; 1006 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 1007 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 1008 PetscFunctionReturn(0); 1009 } 1010 1011 /*MC 1012 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 1013 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 1014 specified by a PetscSection object. Ownership in the global representation is determined by 1015 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 1016 1017 Level: intermediate 1018 1019 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 1020 M*/ 1021 1022 #undef __FUNCT__ 1023 #define __FUNCT__ "DMCreate_Plex" 1024 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 1025 { 1026 DM_Plex *mesh; 1027 PetscInt unit, d; 1028 PetscErrorCode ierr; 1029 1030 PetscFunctionBegin; 1031 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1032 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 1033 dm->dim = 0; 1034 dm->data = mesh; 1035 1036 mesh->refct = 1; 1037 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 1038 mesh->maxConeSize = 0; 1039 mesh->cones = NULL; 1040 mesh->coneOrientations = NULL; 1041 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 1042 mesh->maxSupportSize = 0; 1043 mesh->supports = NULL; 1044 mesh->refinementUniform = PETSC_TRUE; 1045 mesh->refinementLimit = -1.0; 1046 1047 mesh->facesTmp = NULL; 1048 1049 mesh->subpointMap = NULL; 1050 1051 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 1052 1053 mesh->labels = NULL; 1054 mesh->depthLabel = NULL; 1055 mesh->globalVertexNumbers = NULL; 1056 mesh->globalCellNumbers = NULL; 1057 for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE; 1058 mesh->vtkCellHeight = 0; 1059 mesh->useCone = PETSC_FALSE; 1060 mesh->useClosure = PETSC_TRUE; 1061 1062 mesh->printSetValues = PETSC_FALSE; 1063 mesh->printFEM = 0; 1064 mesh->printTol = 1.0e-10; 1065 1066 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 1067 PetscFunctionReturn(0); 1068 } 1069 1070 #undef __FUNCT__ 1071 #define __FUNCT__ "DMPlexCreate" 1072 /*@ 1073 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 1074 1075 Collective on MPI_Comm 1076 1077 Input Parameter: 1078 . comm - The communicator for the DMPlex object 1079 1080 Output Parameter: 1081 . mesh - The DMPlex object 1082 1083 Level: beginner 1084 1085 .keywords: DMPlex, create 1086 @*/ 1087 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 1088 { 1089 PetscErrorCode ierr; 1090 1091 PetscFunctionBegin; 1092 PetscValidPointer(mesh,2); 1093 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 1094 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 1095 PetscFunctionReturn(0); 1096 } 1097 1098 #undef __FUNCT__ 1099 #define __FUNCT__ "DMPlexBuildFromCellList_Private" 1100 /* 1101 This takes as input the common mesh generator output, a list of the vertices for each cell 1102 */ 1103 PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]) 1104 { 1105 PetscInt *cone, c, p; 1106 PetscErrorCode ierr; 1107 1108 PetscFunctionBegin; 1109 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 1110 for (c = 0; c < numCells; ++c) { 1111 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 1112 } 1113 ierr = DMSetUp(dm);CHKERRQ(ierr); 1114 ierr = DMGetWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); 1115 for (c = 0; c < numCells; ++c) { 1116 for (p = 0; p < numCorners; ++p) { 1117 cone[p] = cells[c*numCorners+p]+numCells; 1118 } 1119 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 1120 } 1121 ierr = DMRestoreWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); 1122 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1123 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1124 PetscFunctionReturn(0); 1125 } 1126 1127 #undef __FUNCT__ 1128 #define __FUNCT__ "DMPlexBuildCoordinates_Private" 1129 /* 1130 This takes as input the coordinates for each vertex 1131 */ 1132 PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]) 1133 { 1134 PetscSection coordSection; 1135 Vec coordinates; 1136 PetscScalar *coords; 1137 PetscInt coordSize, v, d; 1138 PetscErrorCode ierr; 1139 1140 PetscFunctionBegin; 1141 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1142 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1143 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 1144 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); 1145 for (v = numCells; v < numCells+numVertices; ++v) { 1146 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 1147 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 1148 } 1149 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1150 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1151 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 1152 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 1153 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1154 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1155 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1156 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1157 for (v = 0; v < numVertices; ++v) { 1158 for (d = 0; d < spaceDim; ++d) { 1159 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 1160 } 1161 } 1162 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1163 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1164 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1165 PetscFunctionReturn(0); 1166 } 1167 1168 #undef __FUNCT__ 1169 #define __FUNCT__ "DMPlexCreateFromCellList" 1170 /*@C 1171 DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 1172 1173 Input Parameters: 1174 + comm - The communicator 1175 . dim - The topological dimension of the mesh 1176 . numCells - The number of cells 1177 . numVertices - The number of vertices 1178 . numCorners - The number of vertices for each cell 1179 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 1180 . cells - An array of numCells*numCorners numbers, the vertices for each cell 1181 . spaceDim - The spatial dimension used for coordinates 1182 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 1183 1184 Output Parameter: 1185 . dm - The DM 1186 1187 Note: Two triangles sharing a face 1188 $ 1189 $ 2 1190 $ / | \ 1191 $ / | \ 1192 $ / | \ 1193 $ 0 0 | 1 3 1194 $ \ | / 1195 $ \ | / 1196 $ \ | / 1197 $ 1 1198 would have input 1199 $ numCells = 2, numVertices = 4 1200 $ cells = [0 1 2 1 3 2] 1201 $ 1202 which would result in the DMPlex 1203 $ 1204 $ 4 1205 $ / | \ 1206 $ / | \ 1207 $ / | \ 1208 $ 2 0 | 1 5 1209 $ \ | / 1210 $ \ | / 1211 $ \ | / 1212 $ 3 1213 1214 Level: beginner 1215 1216 .seealso: DMPlexCreateFromDAG(), DMPlexCreate() 1217 @*/ 1218 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) 1219 { 1220 PetscErrorCode ierr; 1221 1222 PetscFunctionBegin; 1223 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1224 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1225 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1226 ierr = DMPlexBuildFromCellList_Private(*dm, numCells, numVertices, numCorners, cells);CHKERRQ(ierr); 1227 if (interpolate) { 1228 DM idm = NULL; 1229 1230 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1231 ierr = DMDestroy(dm);CHKERRQ(ierr); 1232 *dm = idm; 1233 } 1234 ierr = DMPlexBuildCoordinates_Private(*dm, spaceDim, numCells, numVertices, vertexCoords);CHKERRQ(ierr); 1235 PetscFunctionReturn(0); 1236 } 1237 1238 #undef __FUNCT__ 1239 #define __FUNCT__ "DMPlexCreateFromDAG" 1240 /*@ 1241 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 1242 1243 Input Parameters: 1244 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 1245 . depth - The depth of the DAG 1246 . numPoints - The number of points at each depth 1247 . coneSize - The cone size of each point 1248 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 1249 . coneOrientations - The orientation of each cone point 1250 - vertexCoords - An array of numVertices*dim numbers, the coordinates of each vertex 1251 1252 Output Parameter: 1253 . dm - The DM 1254 1255 Note: Two triangles sharing a face would have input 1256 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 1257 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 1258 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 1259 $ 1260 which would result in the DMPlex 1261 $ 1262 $ 4 1263 $ / | \ 1264 $ / | \ 1265 $ / | \ 1266 $ 2 0 | 1 5 1267 $ \ | / 1268 $ \ | / 1269 $ \ | / 1270 $ 3 1271 $ 1272 $ Notice that all points are numbered consecutively, unlikely DMPlexCreateFromCellList() 1273 1274 Level: advanced 1275 1276 .seealso: DMPlexCreateFromCellList(), DMPlexCreate() 1277 @*/ 1278 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 1279 { 1280 Vec coordinates; 1281 PetscSection coordSection; 1282 PetscScalar *coords; 1283 PetscInt coordSize, firstVertex = numPoints[depth], pStart = 0, pEnd = 0, p, v, dim, d, off; 1284 PetscErrorCode ierr; 1285 1286 PetscFunctionBegin; 1287 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1288 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 1289 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 1290 for (p = pStart; p < pEnd; ++p) { 1291 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 1292 } 1293 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 1294 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 1295 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 1296 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 1297 } 1298 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1299 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1300 /* Build coordinates */ 1301 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1302 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1303 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1304 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 1305 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 1306 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1307 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1308 } 1309 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1310 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1311 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 1312 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1313 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1314 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1315 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1316 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1317 for (v = 0; v < numPoints[0]; ++v) { 1318 PetscInt off; 1319 1320 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 1321 for (d = 0; d < dim; ++d) { 1322 coords[off+d] = vertexCoords[v*dim+d]; 1323 } 1324 } 1325 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1326 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1327 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1328 PetscFunctionReturn(0); 1329 } 1330 1331 #undef __FUNCT__ 1332 #define __FUNCT__ "DMPlexCreateReferenceCell" 1333 /*@ 1334 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 1335 1336 Collective on comm 1337 1338 Input Parameters: 1339 + comm - The communicator 1340 . dim - The spatial dimension 1341 - simplex - Flag for simplex, otherwise use a tensor-product cell 1342 1343 Output Parameter: 1344 . refdm - The reference cell 1345 1346 Level: intermediate 1347 1348 .keywords: reference cell 1349 .seealso: 1350 @*/ 1351 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm) 1352 { 1353 DM rdm; 1354 PetscErrorCode ierr; 1355 1356 PetscFunctionBeginUser; 1357 ierr = DMCreate(comm, &rdm);CHKERRQ(ierr); 1358 ierr = DMSetType(rdm, DMPLEX);CHKERRQ(ierr); 1359 ierr = DMSetDimension(rdm, dim);CHKERRQ(ierr); 1360 switch (dim) { 1361 case 0: 1362 { 1363 PetscInt numPoints[1] = {1}; 1364 PetscInt coneSize[1] = {0}; 1365 PetscInt cones[1] = {0}; 1366 PetscInt coneOrientations[1] = {0}; 1367 PetscScalar vertexCoords[1] = {0.0}; 1368 1369 ierr = DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 1370 } 1371 break; 1372 case 1: 1373 { 1374 PetscInt numPoints[2] = {2, 1}; 1375 PetscInt coneSize[3] = {2, 0, 0}; 1376 PetscInt cones[2] = {1, 2}; 1377 PetscInt coneOrientations[2] = {0, 0}; 1378 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 1379 1380 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 1381 } 1382 break; 1383 case 2: 1384 if (simplex) { 1385 PetscInt numPoints[2] = {3, 1}; 1386 PetscInt coneSize[4] = {3, 0, 0, 0}; 1387 PetscInt cones[3] = {1, 2, 3}; 1388 PetscInt coneOrientations[3] = {0, 0, 0}; 1389 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 1390 1391 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 1392 } else { 1393 PetscInt numPoints[2] = {4, 1}; 1394 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 1395 PetscInt cones[4] = {1, 2, 3, 4}; 1396 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 1397 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 1398 1399 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 1400 } 1401 break; 1402 case 3: 1403 if (simplex) { 1404 PetscInt numPoints[2] = {4, 1}; 1405 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 1406 PetscInt cones[4] = {1, 3, 2, 4}; 1407 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 1408 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}; 1409 1410 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 1411 } else { 1412 PetscInt numPoints[2] = {8, 1}; 1413 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 1414 PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8}; 1415 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 1416 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, 1417 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 1418 1419 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 1420 } 1421 break; 1422 default: 1423 SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %d", dim); 1424 } 1425 *refdm = NULL; 1426 ierr = DMPlexInterpolate(rdm, refdm);CHKERRQ(ierr); 1427 ierr = DMPlexCopyCoordinates(rdm, *refdm);CHKERRQ(ierr); 1428 ierr = DMDestroy(&rdm);CHKERRQ(ierr); 1429 PetscFunctionReturn(0); 1430 } 1431