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 = DMSetLabelValue(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 = DMSetLabelValue(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 = DMCopyLabels(*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, 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 const PetscInt numVertices = (edges[0]+1)*(edges[1]+1); 188 const 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)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 204 if (markerSeparate) { 205 markerTop = 3; 206 markerBottom = 1; 207 markerRight = 2; 208 markerLeft = 4; 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 = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 229 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 230 if (ey == edges[1]-1) { 231 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 232 } 233 } else if (vx == 0) { 234 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 235 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 236 if (ey == edges[1]-1) { 237 ierr = DMSetLabelValue(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 = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 252 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 253 if (ex == edges[0]-1) { 254 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 255 } 256 } else if (vy == 0) { 257 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 258 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 259 if (ex == edges[0]-1) { 260 ierr = DMSetLabelValue(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 = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 279 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 280 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 281 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 282 for (vy = 0; vy <= edges[1]; ++vy) { 283 for (vx = 0; vx <= edges[0]; ++vx) { 284 coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx; 285 coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy; 286 } 287 } 288 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 289 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 290 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 291 PetscFunctionReturn(0); 292 } 293 294 #undef __FUNCT__ 295 #define __FUNCT__ "DMPlexCreateCubeBoundary" 296 /*@ 297 DMPlexCreateCubeBoundary - Creates a 2D mesh the is the boundary of a cubic lattice. 298 299 Collective on MPI_Comm 300 301 Input Parameters: 302 + comm - The communicator for the DM object 303 . lower - The lower left front corner coordinates 304 . upper - The upper right back corner coordinates 305 - edges - The number of cells in each direction 306 307 Output Parameter: 308 . dm - The DM object 309 310 Level: beginner 311 312 .keywords: DM, create 313 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMSetType(), DMCreate() 314 @*/ 315 PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) 316 { 317 PetscInt vertices[3], numVertices; 318 PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2]; 319 Vec coordinates; 320 PetscSection coordSection; 321 PetscScalar *coords; 322 PetscInt coordSize; 323 PetscMPIInt rank; 324 PetscInt v, vx, vy, vz; 325 PetscInt voffset, iface=0, cone[4]; 326 PetscErrorCode ierr; 327 328 PetscFunctionBegin; 329 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"); 330 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 331 vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1; 332 numVertices = vertices[0]*vertices[1]*vertices[2]; 333 if (!rank) { 334 PetscInt f; 335 336 ierr = DMPlexSetChart(dm, 0, numFaces+numVertices);CHKERRQ(ierr); 337 for (f = 0; f < numFaces; ++f) { 338 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 339 } 340 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 341 for (v = 0; v < numFaces+numVertices; ++v) { 342 ierr = DMSetLabelValue(dm, "marker", v, 1);CHKERRQ(ierr); 343 } 344 345 /* Side 0 (Top) */ 346 for (vy = 0; vy < faces[1]; vy++) { 347 for (vx = 0; vx < faces[0]; vx++) { 348 voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx; 349 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0]; 350 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 351 iface++; 352 } 353 } 354 355 /* Side 1 (Bottom) */ 356 for (vy = 0; vy < faces[1]; vy++) { 357 for (vx = 0; vx < faces[0]; vx++) { 358 voffset = numFaces + vy*(faces[0]+1) + vx; 359 cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1; 360 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 361 iface++; 362 } 363 } 364 365 /* Side 2 (Front) */ 366 for (vz = 0; vz < faces[2]; vz++) { 367 for (vx = 0; vx < faces[0]; vx++) { 368 voffset = numFaces + vz*vertices[0]*vertices[1] + vx; 369 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1]; 370 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 371 iface++; 372 } 373 } 374 375 /* Side 3 (Back) */ 376 for (vz = 0; vz < faces[2]; vz++) { 377 for (vx = 0; vx < faces[0]; vx++) { 378 voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx; 379 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1; 380 cone[2] = voffset+1; cone[3] = voffset; 381 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 382 iface++; 383 } 384 } 385 386 /* Side 4 (Left) */ 387 for (vz = 0; vz < faces[2]; vz++) { 388 for (vy = 0; vy < faces[1]; vy++) { 389 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0]; 390 cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1]; 391 cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0]; 392 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 393 iface++; 394 } 395 } 396 397 /* Side 5 (Right) */ 398 for (vz = 0; vz < faces[2]; vz++) { 399 for (vy = 0; vy < faces[1]; vy++) { 400 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + vx; 401 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset; 402 cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0]; 403 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 404 iface++; 405 } 406 } 407 } 408 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 409 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 410 /* Build coordinates */ 411 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 412 ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr); 413 for (v = numFaces; v < numFaces+numVertices; ++v) { 414 ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr); 415 } 416 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 417 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 418 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 419 ierr = VecSetBlockSize(coordinates, 3);CHKERRQ(ierr); 420 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 421 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 422 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 423 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 424 for (vz = 0; vz <= faces[2]; ++vz) { 425 for (vy = 0; vy <= faces[1]; ++vy) { 426 for (vx = 0; vx <= faces[0]; ++vx) { 427 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx; 428 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy; 429 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz; 430 } 431 } 432 } 433 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 434 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 435 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 436 PetscFunctionReturn(0); 437 } 438 439 #undef __FUNCT__ 440 #define __FUNCT__ "DMPlexCreateCubeMesh_Internal" 441 static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ) 442 { 443 PetscInt markerTop = 1, faceMarkerTop = 1; 444 PetscInt markerBottom = 1, faceMarkerBottom = 1; 445 PetscInt markerFront = 1, faceMarkerFront = 1; 446 PetscInt markerBack = 1, faceMarkerBack = 1; 447 PetscInt markerRight = 1, faceMarkerRight = 1; 448 PetscInt markerLeft = 1, faceMarkerLeft = 1; 449 PetscInt dim; 450 PetscBool markerSeparate = PETSC_FALSE; 451 PetscMPIInt rank; 452 PetscErrorCode ierr; 453 454 PetscFunctionBegin; 455 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 456 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 457 ierr = DMCreateLabel(dm,"marker");CHKERRQ(ierr); 458 ierr = DMCreateLabel(dm,"Face Sets");CHKERRQ(ierr); 459 switch (dim) { 460 case 2: 461 faceMarkerTop = 3; 462 faceMarkerBottom = 1; 463 faceMarkerRight = 2; 464 faceMarkerLeft = 4; 465 break; 466 case 3: 467 faceMarkerBottom = 1; 468 faceMarkerTop = 2; 469 faceMarkerFront = 3; 470 faceMarkerBack = 4; 471 faceMarkerRight = 5; 472 faceMarkerLeft = 6; 473 break; 474 default: 475 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %d not supported",dim); 476 break; 477 } 478 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 479 if (markerSeparate) { 480 markerBottom = faceMarkerBottom; 481 markerTop = faceMarkerTop; 482 markerFront = faceMarkerFront; 483 markerBack = faceMarkerBack; 484 markerRight = faceMarkerRight; 485 markerLeft = faceMarkerLeft; 486 } 487 { 488 const PetscInt numXEdges = !rank ? edges[0] : 0; 489 const PetscInt numYEdges = !rank ? edges[1] : 0; 490 const PetscInt numZEdges = !rank ? edges[2] : 0; 491 const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; 492 const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; 493 const PetscInt numZVertices = !rank ? (bdZ == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0; 494 const PetscInt numCells = numXEdges*numYEdges*numZEdges; 495 const PetscInt numXFaces = numYEdges*numZEdges; 496 const PetscInt numYFaces = numXEdges*numZEdges; 497 const PetscInt numZFaces = numXEdges*numYEdges; 498 const PetscInt numTotXFaces = numXVertices*numXFaces; 499 const PetscInt numTotYFaces = numYVertices*numYFaces; 500 const PetscInt numTotZFaces = numZVertices*numZFaces; 501 const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces; 502 const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices; 503 const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices; 504 const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices; 505 const PetscInt numVertices = numXVertices*numYVertices*numZVertices; 506 const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges; 507 const PetscInt firstVertex = (dim == 2) ? numFaces : numCells; 508 const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices; 509 const PetscInt firstYFace = firstXFace + numTotXFaces; 510 const PetscInt firstZFace = firstYFace + numTotYFaces; 511 const PetscInt firstXEdge = numCells + numFaces + numVertices; 512 const PetscInt firstYEdge = firstXEdge + numTotXEdges; 513 const PetscInt firstZEdge = firstYEdge + numTotYEdges; 514 Vec coordinates; 515 PetscSection coordSection; 516 PetscScalar *coords; 517 PetscInt coordSize; 518 PetscInt v, vx, vy, vz; 519 PetscInt c, f, fx, fy, fz, e, ex, ey, ez; 520 521 ierr = DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);CHKERRQ(ierr); 522 for (c = 0; c < numCells; c++) { 523 ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr); 524 } 525 for (f = firstXFace; f < firstXFace+numFaces; ++f) { 526 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 527 } 528 for (e = firstXEdge; e < firstXEdge+numEdges; ++e) { 529 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 530 } 531 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 532 /* Build cells */ 533 for (fz = 0; fz < numZEdges; ++fz) { 534 for (fy = 0; fy < numYEdges; ++fy) { 535 for (fx = 0; fx < numXEdges; ++fx) { 536 PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx; 537 PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 538 PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices); 539 PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 540 PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices); 541 PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 542 PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices); 543 /* B, T, F, K, R, L */ 544 PetscInt ornt[8] = {-4, 0, 0, -1, 0, -4}; /* ??? */ 545 PetscInt cone[8]; 546 547 /* no boundary twisting in 3D */ 548 cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL; 549 ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr); 550 ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr); 551 } 552 } 553 } 554 /* Build x faces */ 555 for (fz = 0; fz < numZEdges; ++fz) { 556 for (fy = 0; fy < numYEdges; ++fy) { 557 for (fx = 0; fx < numXVertices; ++fx) { 558 PetscInt face = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 559 PetscInt edgeL = firstZEdge + ( fy* numXVertices+fx)*numZEdges + fz; 560 PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz; 561 PetscInt edgeB = firstYEdge + ( fz* numXVertices+fx)*numYEdges + fy; 562 PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy; 563 PetscInt ornt[4] = {0, 0, -2, -2}; 564 PetscInt cone[4]; 565 566 if (dim == 3) { 567 /* markers */ 568 if (bdX != DM_BOUNDARY_PERIODIC) { 569 if (fx == numXVertices-1) { 570 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);CHKERRQ(ierr); 571 ierr = DMSetLabelValue(dm, "marker", face, markerRight);CHKERRQ(ierr); 572 } 573 else if (fx == 0) { 574 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);CHKERRQ(ierr); 575 ierr = DMSetLabelValue(dm, "marker", face, markerLeft);CHKERRQ(ierr); 576 } 577 } 578 } 579 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 580 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 581 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 582 } 583 } 584 } 585 /* Build y faces */ 586 for (fz = 0; fz < numZEdges; ++fz) { 587 for (fx = 0; fx < numYEdges; ++fx) { 588 for (fy = 0; fy < numYVertices; ++fy) { 589 PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 590 PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx )*numZEdges + fz; 591 PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz; 592 PetscInt edgeB = firstXEdge + ( fz *numYVertices+fy)*numXEdges + fx; 593 PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx; 594 PetscInt ornt[4] = {0, 0, -2, -2}; 595 PetscInt cone[4]; 596 597 if (dim == 3) { 598 /* markers */ 599 if (bdY != DM_BOUNDARY_PERIODIC) { 600 if (fy == numYVertices-1) { 601 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);CHKERRQ(ierr); 602 ierr = DMSetLabelValue(dm, "marker", face, markerBack);CHKERRQ(ierr); 603 } 604 else if (fy == 0) { 605 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);CHKERRQ(ierr); 606 ierr = DMSetLabelValue(dm, "marker", face, markerFront);CHKERRQ(ierr); 607 } 608 } 609 } 610 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 611 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 612 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 613 } 614 } 615 } 616 /* Build z faces */ 617 for (fy = 0; fy < numYEdges; ++fy) { 618 for (fx = 0; fx < numXEdges; ++fx) { 619 for (fz = 0; fz < numZVertices; fz++) { 620 PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 621 PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx )*numYEdges + fy; 622 PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy; 623 PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy )*numXEdges + fx; 624 PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx; 625 PetscInt ornt[4] = {0, 0, -2, -2}; 626 PetscInt cone[4]; 627 628 if (dim == 2) { 629 if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -2;} 630 if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;} 631 } 632 else { 633 /* markers */ 634 if (bdZ != DM_BOUNDARY_PERIODIC) { 635 if (fz == numZVertices-1) { 636 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);CHKERRQ(ierr); 637 ierr = DMSetLabelValue(dm, "marker", face, markerTop);CHKERRQ(ierr); 638 } 639 else if (fz == 0) { 640 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);CHKERRQ(ierr); 641 ierr = DMSetLabelValue(dm, "marker", face, markerBottom);CHKERRQ(ierr); 642 } 643 } 644 } 645 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 646 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 647 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 648 } 649 } 650 } 651 /* Build Z edges*/ 652 for (vy = 0; vy < numYVertices; vy++) { 653 for (vx = 0; vx < numXVertices; vx++) { 654 for (ez = 0; ez < numZEdges; ez++) { 655 const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez; 656 const PetscInt vertexB = firstVertex + ( ez *numYVertices+vy)*numXVertices + vx; 657 const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx; 658 PetscInt cone[2]; 659 660 if (dim == 3) { 661 if (bdX != DM_BOUNDARY_PERIODIC) { 662 if (vx == numXVertices-1) { 663 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 664 } 665 else if (vx == 0) { 666 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 667 } 668 } 669 if (bdY != DM_BOUNDARY_PERIODIC) { 670 if (vy == numYVertices-1) { 671 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 672 } 673 else if (vy == 0) { 674 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 675 } 676 } 677 } 678 cone[0] = vertexB; cone[1] = vertexT; 679 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 680 } 681 } 682 } 683 /* Build Y edges*/ 684 for (vz = 0; vz < numZVertices; vz++) { 685 for (vx = 0; vx < numXVertices; vx++) { 686 for (ey = 0; ey < numYEdges; ey++) { 687 const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx; 688 const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey; 689 const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx; 690 const PetscInt vertexK = firstVertex + nextv; 691 PetscInt cone[2]; 692 693 cone[0] = vertexF; cone[1] = vertexK; 694 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 695 if (dim == 2) { 696 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 697 if (vx == numXVertices-1) { 698 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);CHKERRQ(ierr); 699 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 700 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 701 if (ey == numYEdges-1) { 702 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 703 } 704 } 705 else if (vx == 0) { 706 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);CHKERRQ(ierr); 707 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 708 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 709 if (ey == numYEdges-1) { 710 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 711 } 712 } 713 } 714 } 715 else { 716 if (bdX != DM_BOUNDARY_PERIODIC) { 717 if (vx == numXVertices-1) { 718 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 719 } 720 else if (vx == 0) { 721 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 722 } 723 } 724 if (bdZ != DM_BOUNDARY_PERIODIC) { 725 if (vz == numZVertices-1) { 726 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 727 } 728 else if (vz == 0) { 729 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 730 } 731 } 732 } 733 } 734 } 735 } 736 /* Build X edges*/ 737 for (vz = 0; vz < numZVertices; vz++) { 738 for (vy = 0; vy < numYVertices; vy++) { 739 for (ex = 0; ex < numXEdges; ex++) { 740 const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices; 741 const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex; 742 const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex; 743 const PetscInt vertexR = firstVertex + nextv; 744 PetscInt cone[2]; 745 746 cone[0] = vertexL; cone[1] = vertexR; 747 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 748 if (dim == 2) { 749 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 750 if (vy == numYVertices-1) { 751 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);CHKERRQ(ierr); 752 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 753 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 754 if (ex == numXEdges-1) { 755 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 756 } 757 } 758 else if (vy == 0) { 759 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);CHKERRQ(ierr); 760 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 761 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 762 if (ex == numXEdges-1) { 763 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 764 } 765 } 766 } 767 } 768 else { 769 if (bdY != DM_BOUNDARY_PERIODIC) { 770 if (vy == numYVertices-1) { 771 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 772 } 773 else if (vy == 0) { 774 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 775 } 776 } 777 if (bdZ != DM_BOUNDARY_PERIODIC) { 778 if (vz == numZVertices-1) { 779 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 780 } 781 else if (vz == 0) { 782 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 783 } 784 } 785 } 786 } 787 } 788 } 789 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 790 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 791 /* Build coordinates */ 792 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 793 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 794 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 795 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr); 796 for (v = firstVertex; v < firstVertex+numVertices; ++v) { 797 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 798 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 799 } 800 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 801 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 802 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 803 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 804 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 805 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 806 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 807 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 808 for (vz = 0; vz < numZVertices; ++vz) { 809 for (vy = 0; vy < numYVertices; ++vy) { 810 for (vx = 0; vx < numXVertices; ++vx) { 811 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx; 812 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy; 813 if (dim == 3) { 814 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz; 815 } 816 } 817 } 818 } 819 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 820 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 821 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 822 } 823 PetscFunctionReturn(0); 824 } 825 826 #undef __FUNCT__ 827 #define __FUNCT__ "DMPlexCreateSquareMesh" 828 /*@ 829 DMPlexCreateSquareMesh - Creates a 2D mesh for a square lattice. 830 831 Collective on MPI_Comm 832 833 Input Parameters: 834 + comm - The communicator for the DM object 835 . lower - The lower left corner coordinates 836 . upper - The upper right corner coordinates 837 . edges - The number of cells in each direction 838 . bdX - The boundary type for the X direction 839 - bdY - The boundary type for the Y direction 840 841 Output Parameter: 842 . dm - The DM object 843 844 Note: Here is the numbering returned for 2 cells in each direction: 845 $ 22--8-23--9--24 846 $ | | | 847 $ 13 2 14 3 15 848 $ | | | 849 $ 19--6-20--7--21 850 $ | | | 851 $ 10 0 11 1 12 852 $ | | | 853 $ 16--4-17--5--18 854 855 Level: beginner 856 857 .keywords: DM, create 858 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate() 859 @*/ 860 PetscErrorCode DMPlexCreateSquareMesh(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY) 861 { 862 PetscReal lower3[3], upper3[3]; 863 PetscInt edges3[3]; 864 PetscErrorCode ierr; 865 866 PetscFunctionBegin; 867 lower3[0] = lower[0]; lower3[1] = lower[1]; lower3[2] = 0.; 868 upper3[0] = upper[0]; upper3[1] = upper[1]; upper3[2] = 0.; 869 edges3[0] = edges[0]; edges3[1] = edges[1]; edges3[2] = 0; 870 ierr = DMPlexCreateCubeMesh_Internal(dm, lower3, upper3, edges3, bdX, bdY, DM_BOUNDARY_NONE);CHKERRQ(ierr); 871 PetscFunctionReturn(0); 872 } 873 874 #undef __FUNCT__ 875 #define __FUNCT__ "DMPlexCreateBoxMesh" 876 /*@ 877 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices. 878 879 Collective on MPI_Comm 880 881 Input Parameters: 882 + comm - The communicator for the DM object 883 . dim - The spatial dimension 884 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 885 886 Output Parameter: 887 . dm - The DM object 888 889 Level: beginner 890 891 .keywords: DM, create 892 .seealso: DMPlexCreateHexBoxMesh(), DMSetType(), DMCreate() 893 @*/ 894 PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscBool interpolate, DM *dm) 895 { 896 DM boundary; 897 PetscErrorCode ierr; 898 899 PetscFunctionBegin; 900 PetscValidPointer(dm, 4); 901 ierr = DMCreate(comm, &boundary);CHKERRQ(ierr); 902 PetscValidLogicalCollectiveInt(boundary,dim,2); 903 ierr = DMSetType(boundary, DMPLEX);CHKERRQ(ierr); 904 ierr = DMSetDimension(boundary, dim-1);CHKERRQ(ierr); 905 switch (dim) { 906 case 2: 907 { 908 PetscReal lower[2] = {0.0, 0.0}; 909 PetscReal upper[2] = {1.0, 1.0}; 910 PetscInt edges[2] = {2, 2}; 911 912 ierr = DMPlexCreateSquareBoundary(boundary, lower, upper, edges);CHKERRQ(ierr); 913 break; 914 } 915 case 3: 916 { 917 PetscReal lower[3] = {0.0, 0.0, 0.0}; 918 PetscReal upper[3] = {1.0, 1.0, 1.0}; 919 PetscInt faces[3] = {1, 1, 1}; 920 921 ierr = DMPlexCreateCubeBoundary(boundary, lower, upper, faces);CHKERRQ(ierr); 922 break; 923 } 924 default: 925 SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 926 } 927 ierr = DMPlexGenerate(boundary, NULL, interpolate, dm);CHKERRQ(ierr); 928 ierr = DMDestroy(&boundary);CHKERRQ(ierr); 929 PetscFunctionReturn(0); 930 } 931 932 #undef __FUNCT__ 933 #define __FUNCT__ "DMPlexCreateHexBoxMesh" 934 /*@ 935 DMPlexCreateHexBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using hexahedra. 936 937 Collective on MPI_Comm 938 939 Input Parameters: 940 + comm - The communicator for the DM object 941 . dim - The spatial dimension 942 . periodicX - The boundary type for the X direction 943 . periodicY - The boundary type for the Y direction 944 . periodicZ - The boundary type for the Z direction 945 - cells - The number of cells in each direction 946 947 Output Parameter: 948 . dm - The DM object 949 950 Level: beginner 951 952 .keywords: DM, create 953 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 954 @*/ 955 PetscErrorCode DMPlexCreateHexBoxMesh(MPI_Comm comm, PetscInt dim, const PetscInt cells[], DMBoundaryType periodicX, DMBoundaryType periodicY, DMBoundaryType periodicZ, DM *dm) 956 { 957 PetscErrorCode ierr; 958 959 PetscFunctionBegin; 960 PetscValidPointer(dm, 4); 961 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 962 PetscValidLogicalCollectiveInt(*dm,dim,2); 963 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 964 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 965 switch (dim) { 966 case 2: 967 { 968 PetscReal lower[2] = {0.0, 0.0}; 969 PetscReal upper[2] = {1.0, 1.0}; 970 971 ierr = DMPlexCreateSquareMesh(*dm, lower, upper, cells, periodicX, periodicY);CHKERRQ(ierr); 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 break; 981 } 982 default: 983 SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 984 } 985 PetscFunctionReturn(0); 986 } 987 988 /* External function declarations here */ 989 extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling); 990 extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat); 991 extern PetscErrorCode DMCreateDefaultSection_Plex(DM dm); 992 extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm); 993 extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J); 994 extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm); 995 extern PetscErrorCode DMRefine_Plex(DM dm, MPI_Comm comm, DM *dmRefined); 996 extern PetscErrorCode DMCoarsen_Plex(DM dm, MPI_Comm comm, DM *dmCoarsened); 997 extern PetscErrorCode DMRefineHierarchy_Plex(DM dm, PetscInt nlevels, DM dmRefined[]); 998 extern PetscErrorCode DMCoarsenHierarchy_Plex(DM dm, PetscInt nlevels, DM dmCoarsened[]); 999 extern PetscErrorCode DMClone_Plex(DM dm, DM *newdm); 1000 extern PetscErrorCode DMSetUp_Plex(DM dm); 1001 extern PetscErrorCode DMDestroy_Plex(DM dm); 1002 extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer); 1003 extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer); 1004 extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm); 1005 extern PetscErrorCode DMLocatePoints_Plex(DM dm, Vec v, PetscSF cellSF); 1006 extern PetscErrorCode DMProjectFunctionLocal_Plex(DM,PetscReal,PetscErrorCode(**)(PetscInt,PetscReal,const PetscReal[],PetscInt,PetscScalar *,void *),void **,InsertMode,Vec); 1007 extern PetscErrorCode DMProjectFunctionLabelLocal_Plex(DM,PetscReal,DMLabel,PetscInt,const PetscInt[],PetscErrorCode(**)(PetscInt,PetscReal,const PetscReal[],PetscInt,PetscScalar *,void *),void **,InsertMode,Vec); 1008 extern PetscErrorCode DMProjectFieldLocal_Plex(DM,Vec,void (**)(PetscInt,PetscInt,PetscInt,const PetscInt[],const PetscInt[],const PetscScalar[],const PetscScalar[],const PetscScalar[],const PetscInt[],const PetscInt[],const PetscScalar[],const PetscScalar[],const PetscScalar[],PetscReal,const PetscReal[],PetscScalar[]),InsertMode,Vec); 1009 extern PetscErrorCode DMComputeL2Diff_Plex(DM,PetscReal,PetscErrorCode(**)(PetscInt,PetscReal,const PetscReal[],PetscInt,PetscScalar *,void *),void **,Vec,PetscReal *); 1010 extern PetscErrorCode DMComputeL2GradientDiff_Plex(DM,PetscReal,PetscErrorCode(**)(PetscInt,PetscReal,const PetscReal[], const PetscReal[],PetscInt,PetscScalar *,void *),void **,Vec,const PetscReal [],PetscReal *); 1011 extern PetscErrorCode DMComputeL2FieldDiff_Plex(DM,PetscReal,PetscErrorCode(**)(PetscInt,PetscReal,const PetscReal[],PetscInt,PetscScalar *,void *),void **,Vec,PetscReal *); 1012 1013 #undef __FUNCT__ 1014 #define __FUNCT__ "DMPlexReplace_Static" 1015 /* Replace dm with the contents of dmNew 1016 - Share the DM_Plex structure 1017 - Share the coordinates 1018 - Share the SF 1019 */ 1020 static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew) 1021 { 1022 PetscSF sf; 1023 DM coordDM, coarseDM; 1024 Vec coords; 1025 const PetscReal *maxCell, *L; 1026 const DMBoundaryType *bd; 1027 PetscErrorCode ierr; 1028 1029 PetscFunctionBegin; 1030 ierr = DMGetPointSF(dmNew, &sf);CHKERRQ(ierr); 1031 ierr = DMSetPointSF(dm, sf);CHKERRQ(ierr); 1032 ierr = DMGetCoordinateDM(dmNew, &coordDM);CHKERRQ(ierr); 1033 ierr = DMGetCoordinatesLocal(dmNew, &coords);CHKERRQ(ierr); 1034 ierr = DMSetCoordinateDM(dm, coordDM);CHKERRQ(ierr); 1035 ierr = DMSetCoordinatesLocal(dm, coords);CHKERRQ(ierr); 1036 ierr = DMGetPeriodicity(dm, &maxCell, &L, &bd);CHKERRQ(ierr); 1037 if (L) {ierr = DMSetPeriodicity(dmNew, maxCell, L, bd);CHKERRQ(ierr);} 1038 ierr = DMDestroy_Plex(dm);CHKERRQ(ierr); 1039 dm->data = dmNew->data; 1040 ((DM_Plex *) dmNew->data)->refct++; 1041 dmNew->labels->refct++; 1042 if (!--(dm->labels->refct)) { 1043 DMLabelLink next = dm->labels->next; 1044 1045 /* destroy the labels */ 1046 while (next) { 1047 DMLabelLink tmp = next->next; 1048 1049 ierr = DMLabelDestroy(&next->label);CHKERRQ(ierr); 1050 ierr = PetscFree(next);CHKERRQ(ierr); 1051 next = tmp; 1052 } 1053 ierr = PetscFree(dm->labels);CHKERRQ(ierr); 1054 } 1055 dm->labels = dmNew->labels; 1056 dm->depthLabel = dmNew->depthLabel; 1057 ierr = DMGetCoarseDM(dmNew,&coarseDM);CHKERRQ(ierr); 1058 ierr = DMSetCoarseDM(dm,coarseDM);CHKERRQ(ierr); 1059 PetscFunctionReturn(0); 1060 } 1061 1062 #undef __FUNCT__ 1063 #define __FUNCT__ "DMPlexSwap_Static" 1064 /* Swap dm with the contents of dmNew 1065 - Swap the DM_Plex structure 1066 - Swap the coordinates 1067 - Swap the point PetscSF 1068 */ 1069 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 1070 { 1071 DM coordDMA, coordDMB; 1072 Vec coordsA, coordsB; 1073 PetscSF sfA, sfB; 1074 void *tmp; 1075 DMLabelLinkList listTmp; 1076 DMLabel depthTmp; 1077 PetscErrorCode ierr; 1078 1079 PetscFunctionBegin; 1080 ierr = DMGetPointSF(dmA, &sfA);CHKERRQ(ierr); 1081 ierr = DMGetPointSF(dmB, &sfB);CHKERRQ(ierr); 1082 ierr = PetscObjectReference((PetscObject) sfA);CHKERRQ(ierr); 1083 ierr = DMSetPointSF(dmA, sfB);CHKERRQ(ierr); 1084 ierr = DMSetPointSF(dmB, sfA);CHKERRQ(ierr); 1085 ierr = PetscObjectDereference((PetscObject) sfA);CHKERRQ(ierr); 1086 1087 ierr = DMGetCoordinateDM(dmA, &coordDMA);CHKERRQ(ierr); 1088 ierr = DMGetCoordinateDM(dmB, &coordDMB);CHKERRQ(ierr); 1089 ierr = PetscObjectReference((PetscObject) coordDMA);CHKERRQ(ierr); 1090 ierr = DMSetCoordinateDM(dmA, coordDMB);CHKERRQ(ierr); 1091 ierr = DMSetCoordinateDM(dmB, coordDMA);CHKERRQ(ierr); 1092 ierr = PetscObjectDereference((PetscObject) coordDMA);CHKERRQ(ierr); 1093 1094 ierr = DMGetCoordinatesLocal(dmA, &coordsA);CHKERRQ(ierr); 1095 ierr = DMGetCoordinatesLocal(dmB, &coordsB);CHKERRQ(ierr); 1096 ierr = PetscObjectReference((PetscObject) coordsA);CHKERRQ(ierr); 1097 ierr = DMSetCoordinatesLocal(dmA, coordsB);CHKERRQ(ierr); 1098 ierr = DMSetCoordinatesLocal(dmB, coordsA);CHKERRQ(ierr); 1099 ierr = PetscObjectDereference((PetscObject) coordsA);CHKERRQ(ierr); 1100 1101 tmp = dmA->data; 1102 dmA->data = dmB->data; 1103 dmB->data = tmp; 1104 listTmp = dmA->labels; 1105 dmA->labels = dmB->labels; 1106 dmB->labels = listTmp; 1107 depthTmp = dmA->depthLabel; 1108 dmA->depthLabel = dmB->depthLabel; 1109 dmB->depthLabel = depthTmp; 1110 PetscFunctionReturn(0); 1111 } 1112 1113 #undef __FUNCT__ 1114 #define __FUNCT__ "DMSetFromOptions_NonRefinement_Plex" 1115 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 1116 { 1117 DM_Plex *mesh = (DM_Plex*) dm->data; 1118 DMBoundary b; 1119 PetscErrorCode ierr; 1120 1121 PetscFunctionBegin; 1122 /* Handle boundary conditions */ 1123 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject) dm), NULL, "Boundary condition options", "");CHKERRQ(ierr); 1124 for (b = dm->boundary->next; b; b = b->next) { 1125 char optname[1024]; 1126 PetscInt ids[1024], len = 1024, i; 1127 PetscBool flg; 1128 1129 ierr = PetscSNPrintf(optname, sizeof(optname), "-bc_%s", b->name);CHKERRQ(ierr); 1130 ierr = PetscMemzero(ids, sizeof(ids));CHKERRQ(ierr); 1131 ierr = PetscOptionsIntArray(optname, "List of boundary IDs", "", ids, &len, &flg);CHKERRQ(ierr); 1132 if (flg) { 1133 DMLabel label; 1134 1135 ierr = DMGetLabel(dm, b->labelname, &label);CHKERRQ(ierr); 1136 for (i = 0; i < len; ++i) { 1137 PetscBool has; 1138 1139 ierr = DMLabelHasValue(label, ids[i], &has);CHKERRQ(ierr); 1140 if (!has) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Boundary id %D is not present in the label %s", ids[i], b->name); 1141 } 1142 b->numids = len; 1143 ierr = PetscFree(b->ids);CHKERRQ(ierr); 1144 ierr = PetscMalloc1(len, &b->ids);CHKERRQ(ierr); 1145 ierr = PetscMemcpy(b->ids, ids, len*sizeof(PetscInt));CHKERRQ(ierr); 1146 } 1147 ierr = PetscSNPrintf(optname, sizeof(optname), "-bc_%s_comp", b->name);CHKERRQ(ierr); 1148 ierr = PetscMemzero(ids, sizeof(ids));CHKERRQ(ierr); 1149 ierr = PetscOptionsIntArray(optname, "List of boundary field components", "", ids, &len, &flg);CHKERRQ(ierr); 1150 if (flg) { 1151 b->numcomps = len; 1152 ierr = PetscFree(b->comps);CHKERRQ(ierr); 1153 ierr = PetscMalloc1(len, &b->comps);CHKERRQ(ierr); 1154 ierr = PetscMemcpy(b->comps, ids, len*sizeof(PetscInt));CHKERRQ(ierr); 1155 } 1156 } 1157 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1158 /* Handle viewing */ 1159 ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMView", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); 1160 ierr = PetscOptionsInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMView", 0, &mesh->printFEM, NULL);CHKERRQ(ierr); 1161 ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMView", mesh->printTol, &mesh->printTol, NULL);CHKERRQ(ierr); 1162 /* Point Location */ 1163 ierr = PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMView", PETSC_FALSE, &mesh->useHashLocation, NULL);CHKERRQ(ierr); 1164 /* Projection behavior */ 1165 ierr = PetscOptionsInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL);CHKERRQ(ierr); 1166 ierr = PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);CHKERRQ(ierr); 1167 PetscFunctionReturn(0); 1168 } 1169 1170 #undef __FUNCT__ 1171 #define __FUNCT__ "DMSetFromOptions_Plex" 1172 PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 1173 { 1174 PetscInt refine = 0, coarsen = 0, r; 1175 PetscBool isHierarchy; 1176 PetscErrorCode ierr; 1177 1178 PetscFunctionBegin; 1179 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1180 ierr = PetscOptionsHead(PetscOptionsObject,"DMPlex Options");CHKERRQ(ierr); 1181 /* Handle DMPlex refinement */ 1182 ierr = PetscOptionsInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL);CHKERRQ(ierr); 1183 ierr = PetscOptionsInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy);CHKERRQ(ierr); 1184 if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 1185 if (refine && isHierarchy) { 1186 DM *dms, coarseDM; 1187 1188 ierr = DMGetCoarseDM(dm, &coarseDM);CHKERRQ(ierr); 1189 ierr = PetscObjectReference((PetscObject)coarseDM);CHKERRQ(ierr); 1190 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 1191 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 1192 /* Total hack since we do not pass in a pointer */ 1193 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 1194 if (refine == 1) { 1195 ierr = DMSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 1196 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 1197 } else { 1198 ierr = DMSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 1199 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 1200 ierr = DMSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 1201 ierr = DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);CHKERRQ(ierr); 1202 } 1203 ierr = DMSetCoarseDM(dms[refine-1], coarseDM);CHKERRQ(ierr); 1204 ierr = PetscObjectDereference((PetscObject)coarseDM);CHKERRQ(ierr); 1205 /* Free DMs */ 1206 for (r = 0; r < refine; ++r) { 1207 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 1208 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 1209 } 1210 ierr = PetscFree(dms);CHKERRQ(ierr); 1211 } else { 1212 for (r = 0; r < refine; ++r) { 1213 DM refinedMesh; 1214 1215 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 1216 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);CHKERRQ(ierr); 1217 /* Total hack since we do not pass in a pointer */ 1218 ierr = DMPlexReplace_Static(dm, refinedMesh);CHKERRQ(ierr); 1219 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 1220 ierr = DMDestroy(&refinedMesh);CHKERRQ(ierr); 1221 } 1222 } 1223 /* Handle DMPlex coarsening */ 1224 ierr = PetscOptionsInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL);CHKERRQ(ierr); 1225 ierr = PetscOptionsInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy);CHKERRQ(ierr); 1226 if (coarsen && isHierarchy) { 1227 DM *dms; 1228 1229 ierr = PetscMalloc1(coarsen, &dms);CHKERRQ(ierr); 1230 ierr = DMCoarsenHierarchy(dm, coarsen, dms);CHKERRQ(ierr); 1231 /* Free DMs */ 1232 for (r = 0; r < coarsen; ++r) { 1233 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 1234 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 1235 } 1236 ierr = PetscFree(dms);CHKERRQ(ierr); 1237 } else { 1238 for (r = 0; r < coarsen; ++r) { 1239 DM coarseMesh; 1240 1241 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 1242 ierr = DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);CHKERRQ(ierr); 1243 /* Total hack since we do not pass in a pointer */ 1244 ierr = DMPlexReplace_Static(dm, coarseMesh);CHKERRQ(ierr); 1245 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 1246 ierr = DMDestroy(&coarseMesh);CHKERRQ(ierr); 1247 } 1248 } 1249 /* Handle */ 1250 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 1251 ierr = PetscOptionsTail();CHKERRQ(ierr); 1252 PetscFunctionReturn(0); 1253 } 1254 1255 #undef __FUNCT__ 1256 #define __FUNCT__ "DMCreateGlobalVector_Plex" 1257 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 1258 { 1259 PetscErrorCode ierr; 1260 1261 PetscFunctionBegin; 1262 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 1263 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 1264 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 1265 ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); 1266 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 1267 ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); 1268 PetscFunctionReturn(0); 1269 } 1270 1271 #undef __FUNCT__ 1272 #define __FUNCT__ "DMCreateLocalVector_Plex" 1273 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 1274 { 1275 PetscErrorCode ierr; 1276 1277 PetscFunctionBegin; 1278 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 1279 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 1280 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 1281 PetscFunctionReturn(0); 1282 } 1283 1284 #undef __FUNCT__ 1285 #define __FUNCT__ "DMGetDimPoints_Plex" 1286 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 1287 { 1288 PetscInt depth, d; 1289 PetscErrorCode ierr; 1290 1291 PetscFunctionBegin; 1292 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1293 if (depth == 1) { 1294 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 1295 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 1296 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 1297 else {*pStart = 0; *pEnd = 0;} 1298 } else { 1299 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 1300 } 1301 PetscFunctionReturn(0); 1302 } 1303 1304 #undef __FUNCT__ 1305 #define __FUNCT__ "DMInitialize_Plex" 1306 PetscErrorCode DMInitialize_Plex(DM dm) 1307 { 1308 PetscFunctionBegin; 1309 dm->ops->view = DMView_Plex; 1310 dm->ops->load = DMLoad_Plex; 1311 dm->ops->setfromoptions = DMSetFromOptions_Plex; 1312 dm->ops->clone = DMClone_Plex; 1313 dm->ops->setup = DMSetUp_Plex; 1314 dm->ops->createdefaultsection = DMCreateDefaultSection_Plex; 1315 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 1316 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 1317 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 1318 dm->ops->getlocaltoglobalmapping = NULL; 1319 dm->ops->createfieldis = NULL; 1320 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 1321 dm->ops->getcoloring = NULL; 1322 dm->ops->creatematrix = DMCreateMatrix_Plex; 1323 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 1324 dm->ops->getaggregates = NULL; 1325 dm->ops->getinjection = DMCreateInjection_Plex; 1326 dm->ops->refine = DMRefine_Plex; 1327 dm->ops->coarsen = DMCoarsen_Plex; 1328 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 1329 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 1330 dm->ops->globaltolocalbegin = NULL; 1331 dm->ops->globaltolocalend = NULL; 1332 dm->ops->localtoglobalbegin = NULL; 1333 dm->ops->localtoglobalend = NULL; 1334 dm->ops->destroy = DMDestroy_Plex; 1335 dm->ops->createsubdm = DMCreateSubDM_Plex; 1336 dm->ops->getdimpoints = DMGetDimPoints_Plex; 1337 dm->ops->locatepoints = DMLocatePoints_Plex; 1338 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 1339 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 1340 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 1341 dm->ops->computel2diff = DMComputeL2Diff_Plex; 1342 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 1343 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 1344 PetscFunctionReturn(0); 1345 } 1346 1347 #undef __FUNCT__ 1348 #define __FUNCT__ "DMClone_Plex" 1349 PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 1350 { 1351 DM_Plex *mesh = (DM_Plex *) dm->data; 1352 PetscErrorCode ierr; 1353 1354 PetscFunctionBegin; 1355 mesh->refct++; 1356 (*newdm)->data = mesh; 1357 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 1358 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 1359 PetscFunctionReturn(0); 1360 } 1361 1362 /*MC 1363 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 1364 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 1365 specified by a PetscSection object. Ownership in the global representation is determined by 1366 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 1367 1368 Level: intermediate 1369 1370 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 1371 M*/ 1372 1373 #undef __FUNCT__ 1374 #define __FUNCT__ "DMCreate_Plex" 1375 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 1376 { 1377 DM_Plex *mesh; 1378 PetscInt unit, d; 1379 PetscErrorCode ierr; 1380 1381 PetscFunctionBegin; 1382 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1383 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 1384 dm->dim = 0; 1385 dm->data = mesh; 1386 1387 mesh->refct = 1; 1388 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 1389 mesh->maxConeSize = 0; 1390 mesh->cones = NULL; 1391 mesh->coneOrientations = NULL; 1392 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 1393 mesh->maxSupportSize = 0; 1394 mesh->supports = NULL; 1395 mesh->refinementUniform = PETSC_TRUE; 1396 mesh->refinementLimit = -1.0; 1397 1398 mesh->facesTmp = NULL; 1399 1400 mesh->tetgenOpts = NULL; 1401 mesh->triangleOpts = NULL; 1402 ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); 1403 ierr = PetscPartitionerSetTypeFromOptions_Internal(mesh->partitioner);CHKERRQ(ierr); 1404 1405 mesh->subpointMap = NULL; 1406 1407 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 1408 1409 mesh->regularRefinement = PETSC_FALSE; 1410 mesh->depthState = -1; 1411 mesh->globalVertexNumbers = NULL; 1412 mesh->globalCellNumbers = NULL; 1413 mesh->anchorSection = NULL; 1414 mesh->anchorIS = NULL; 1415 mesh->createanchors = NULL; 1416 mesh->computeanchormatrix = NULL; 1417 mesh->parentSection = NULL; 1418 mesh->parents = NULL; 1419 mesh->childIDs = NULL; 1420 mesh->childSection = NULL; 1421 mesh->children = NULL; 1422 mesh->referenceTree = NULL; 1423 mesh->getchildsymmetry = NULL; 1424 for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE; 1425 mesh->vtkCellHeight = 0; 1426 mesh->useCone = PETSC_FALSE; 1427 mesh->useClosure = PETSC_TRUE; 1428 mesh->useAnchors = PETSC_FALSE; 1429 1430 mesh->maxProjectionHeight = 0; 1431 1432 mesh->printSetValues = PETSC_FALSE; 1433 mesh->printFEM = 0; 1434 mesh->printTol = 1.0e-10; 1435 1436 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 1437 PetscFunctionReturn(0); 1438 } 1439 1440 #undef __FUNCT__ 1441 #define __FUNCT__ "DMPlexCreate" 1442 /*@ 1443 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 1444 1445 Collective on MPI_Comm 1446 1447 Input Parameter: 1448 . comm - The communicator for the DMPlex object 1449 1450 Output Parameter: 1451 . mesh - The DMPlex object 1452 1453 Level: beginner 1454 1455 .keywords: DMPlex, create 1456 @*/ 1457 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 1458 { 1459 PetscErrorCode ierr; 1460 1461 PetscFunctionBegin; 1462 PetscValidPointer(mesh,2); 1463 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 1464 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 1465 PetscFunctionReturn(0); 1466 } 1467 1468 #undef __FUNCT__ 1469 #define __FUNCT__ "DMPlexBuildFromCellList_Private" 1470 /* 1471 This takes as input the common mesh generator output, a list of the vertices for each cell 1472 */ 1473 PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]) 1474 { 1475 PetscInt *cone, c, p; 1476 PetscErrorCode ierr; 1477 1478 PetscFunctionBegin; 1479 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 1480 for (c = 0; c < numCells; ++c) { 1481 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 1482 } 1483 ierr = DMSetUp(dm);CHKERRQ(ierr); 1484 ierr = DMGetWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); 1485 for (c = 0; c < numCells; ++c) { 1486 for (p = 0; p < numCorners; ++p) { 1487 cone[p] = cells[c*numCorners+p]+numCells; 1488 } 1489 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 1490 } 1491 ierr = DMRestoreWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); 1492 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1493 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1494 PetscFunctionReturn(0); 1495 } 1496 1497 #undef __FUNCT__ 1498 #define __FUNCT__ "DMPlexBuildCoordinates_Private" 1499 /* 1500 This takes as input the coordinates for each vertex 1501 */ 1502 PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]) 1503 { 1504 PetscSection coordSection; 1505 Vec coordinates; 1506 PetscScalar *coords; 1507 PetscInt coordSize, v, d; 1508 PetscErrorCode ierr; 1509 1510 PetscFunctionBegin; 1511 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1512 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1513 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 1514 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); 1515 for (v = numCells; v < numCells+numVertices; ++v) { 1516 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 1517 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 1518 } 1519 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1520 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1521 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 1522 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 1523 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1524 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1525 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1526 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1527 for (v = 0; v < numVertices; ++v) { 1528 for (d = 0; d < spaceDim; ++d) { 1529 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 1530 } 1531 } 1532 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1533 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1534 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1535 PetscFunctionReturn(0); 1536 } 1537 1538 #undef __FUNCT__ 1539 #define __FUNCT__ "DMPlexCreateFromCellList" 1540 /*@C 1541 DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 1542 1543 Input Parameters: 1544 + comm - The communicator 1545 . dim - The topological dimension of the mesh 1546 . numCells - The number of cells 1547 . numVertices - The number of vertices 1548 . numCorners - The number of vertices for each cell 1549 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 1550 . cells - An array of numCells*numCorners numbers, the vertices for each cell 1551 . spaceDim - The spatial dimension used for coordinates 1552 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 1553 1554 Output Parameter: 1555 . dm - The DM 1556 1557 Note: Two triangles sharing a face 1558 $ 1559 $ 2 1560 $ / | \ 1561 $ / | \ 1562 $ / | \ 1563 $ 0 0 | 1 3 1564 $ \ | / 1565 $ \ | / 1566 $ \ | / 1567 $ 1 1568 would have input 1569 $ numCells = 2, numVertices = 4 1570 $ cells = [0 1 2 1 3 2] 1571 $ 1572 which would result in the DMPlex 1573 $ 1574 $ 4 1575 $ / | \ 1576 $ / | \ 1577 $ / | \ 1578 $ 2 0 | 1 5 1579 $ \ | / 1580 $ \ | / 1581 $ \ | / 1582 $ 3 1583 1584 Level: beginner 1585 1586 .seealso: DMPlexCreateFromDAG(), DMPlexCreate() 1587 @*/ 1588 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) 1589 { 1590 PetscErrorCode ierr; 1591 1592 PetscFunctionBegin; 1593 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1594 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1595 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1596 ierr = DMPlexBuildFromCellList_Private(*dm, numCells, numVertices, numCorners, cells);CHKERRQ(ierr); 1597 if (interpolate) { 1598 DM idm = NULL; 1599 1600 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1601 ierr = DMDestroy(dm);CHKERRQ(ierr); 1602 *dm = idm; 1603 } 1604 ierr = DMPlexBuildCoordinates_Private(*dm, spaceDim, numCells, numVertices, vertexCoords);CHKERRQ(ierr); 1605 PetscFunctionReturn(0); 1606 } 1607 1608 #undef __FUNCT__ 1609 #define __FUNCT__ "DMPlexCreateFromDAG" 1610 /*@ 1611 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 1612 1613 Input Parameters: 1614 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 1615 . depth - The depth of the DAG 1616 . numPoints - The number of points at each depth 1617 . coneSize - The cone size of each point 1618 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 1619 . coneOrientations - The orientation of each cone point 1620 - vertexCoords - An array of numVertices*dim numbers, the coordinates of each vertex 1621 1622 Output Parameter: 1623 . dm - The DM 1624 1625 Note: Two triangles sharing a face would have input 1626 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 1627 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 1628 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 1629 $ 1630 which would result in the DMPlex 1631 $ 1632 $ 4 1633 $ / | \ 1634 $ / | \ 1635 $ / | \ 1636 $ 2 0 | 1 5 1637 $ \ | / 1638 $ \ | / 1639 $ \ | / 1640 $ 3 1641 $ 1642 $ Notice that all points are numbered consecutively, unlikely DMPlexCreateFromCellList() 1643 1644 Level: advanced 1645 1646 .seealso: DMPlexCreateFromCellList(), DMPlexCreate() 1647 @*/ 1648 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 1649 { 1650 Vec coordinates; 1651 PetscSection coordSection; 1652 PetscScalar *coords; 1653 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 1654 PetscErrorCode ierr; 1655 1656 PetscFunctionBegin; 1657 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1658 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 1659 if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %d cannot be less than intrinsic dimension %d",dimEmbed,dim); 1660 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 1661 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 1662 for (p = pStart; p < pEnd; ++p) { 1663 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 1664 if (firstVertex < 0 && !coneSize[p - pStart]) { 1665 firstVertex = p - pStart; 1666 } 1667 } 1668 if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %d vertices but could not find any", numPoints[0]); 1669 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 1670 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 1671 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 1672 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 1673 } 1674 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1675 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1676 /* Build coordinates */ 1677 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1678 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1679 ierr = PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);CHKERRQ(ierr); 1680 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 1681 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 1682 ierr = PetscSectionSetDof(coordSection, v, dimEmbed);CHKERRQ(ierr); 1683 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);CHKERRQ(ierr); 1684 } 1685 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1686 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1687 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 1688 ierr = VecSetBlockSize(coordinates, dimEmbed);CHKERRQ(ierr); 1689 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1690 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1691 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1692 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1693 for (v = 0; v < numPoints[0]; ++v) { 1694 PetscInt off; 1695 1696 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 1697 for (d = 0; d < dimEmbed; ++d) { 1698 coords[off+d] = vertexCoords[v*dimEmbed+d]; 1699 } 1700 } 1701 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1702 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1703 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1704 PetscFunctionReturn(0); 1705 } 1706 1707 #undef __FUNCT__ 1708 #define __FUNCT__ "DMPlexCreateFromFile" 1709 /*@C 1710 DMPlexCreateFromFile - This takes a filename and produces a DM 1711 1712 Input Parameters: 1713 + comm - The communicator 1714 . filename - A file name 1715 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1716 1717 Output Parameter: 1718 . dm - The DM 1719 1720 Level: beginner 1721 1722 .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellList(), DMPlexCreate() 1723 @*/ 1724 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 1725 { 1726 const char *extGmsh = ".msh"; 1727 const char *extCGNS = ".cgns"; 1728 const char *extExodus = ".exo"; 1729 const char *extFluent = ".cas"; 1730 const char *extHDF5 = ".h5"; 1731 size_t len; 1732 PetscBool isGmsh, isCGNS, isExodus, isFluent, isHDF5; 1733 PetscMPIInt rank; 1734 PetscErrorCode ierr; 1735 1736 PetscFunctionBegin; 1737 PetscValidPointer(filename, 2); 1738 PetscValidPointer(dm, 4); 1739 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1740 ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); 1741 if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 1742 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);CHKERRQ(ierr); 1743 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);CHKERRQ(ierr); 1744 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);CHKERRQ(ierr); 1745 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);CHKERRQ(ierr); 1746 ierr = PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);CHKERRQ(ierr); 1747 if (isGmsh) { 1748 ierr = DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 1749 } else if (isCGNS) { 1750 ierr = DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 1751 } else if (isExodus) { 1752 ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 1753 } else if (isFluent) { 1754 ierr = DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 1755 } else if (isHDF5) { 1756 PetscViewer viewer; 1757 1758 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 1759 ierr = PetscViewerSetType(viewer, PETSCVIEWERHDF5);CHKERRQ(ierr); 1760 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 1761 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 1762 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1763 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1764 ierr = DMLoad(*dm, viewer);CHKERRQ(ierr); 1765 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1766 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 1767 PetscFunctionReturn(0); 1768 } 1769 1770 #undef __FUNCT__ 1771 #define __FUNCT__ "DMPlexCreateReferenceCell" 1772 /*@ 1773 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 1774 1775 Collective on comm 1776 1777 Input Parameters: 1778 + comm - The communicator 1779 . dim - The spatial dimension 1780 - simplex - Flag for simplex, otherwise use a tensor-product cell 1781 1782 Output Parameter: 1783 . refdm - The reference cell 1784 1785 Level: intermediate 1786 1787 .keywords: reference cell 1788 .seealso: 1789 @*/ 1790 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm) 1791 { 1792 DM rdm; 1793 Vec coords; 1794 PetscErrorCode ierr; 1795 1796 PetscFunctionBeginUser; 1797 ierr = DMCreate(comm, &rdm);CHKERRQ(ierr); 1798 ierr = DMSetType(rdm, DMPLEX);CHKERRQ(ierr); 1799 ierr = DMSetDimension(rdm, dim);CHKERRQ(ierr); 1800 switch (dim) { 1801 case 0: 1802 { 1803 PetscInt numPoints[1] = {1}; 1804 PetscInt coneSize[1] = {0}; 1805 PetscInt cones[1] = {0}; 1806 PetscInt coneOrientations[1] = {0}; 1807 PetscScalar vertexCoords[1] = {0.0}; 1808 1809 ierr = DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 1810 } 1811 break; 1812 case 1: 1813 { 1814 PetscInt numPoints[2] = {2, 1}; 1815 PetscInt coneSize[3] = {2, 0, 0}; 1816 PetscInt cones[2] = {1, 2}; 1817 PetscInt coneOrientations[2] = {0, 0}; 1818 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 1819 1820 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 1821 } 1822 break; 1823 case 2: 1824 if (simplex) { 1825 PetscInt numPoints[2] = {3, 1}; 1826 PetscInt coneSize[4] = {3, 0, 0, 0}; 1827 PetscInt cones[3] = {1, 2, 3}; 1828 PetscInt coneOrientations[3] = {0, 0, 0}; 1829 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 1830 1831 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 1832 } else { 1833 PetscInt numPoints[2] = {4, 1}; 1834 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 1835 PetscInt cones[4] = {1, 2, 3, 4}; 1836 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 1837 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 1838 1839 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 1840 } 1841 break; 1842 case 3: 1843 if (simplex) { 1844 PetscInt numPoints[2] = {4, 1}; 1845 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 1846 PetscInt cones[4] = {1, 3, 2, 4}; 1847 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 1848 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}; 1849 1850 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 1851 } else { 1852 PetscInt numPoints[2] = {8, 1}; 1853 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 1854 PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8}; 1855 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 1856 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, 1857 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 1858 1859 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 1860 } 1861 break; 1862 default: 1863 SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %d", dim); 1864 } 1865 *refdm = NULL; 1866 ierr = DMPlexInterpolate(rdm, refdm);CHKERRQ(ierr); 1867 if (rdm->coordinateDM) { 1868 DM ncdm; 1869 PetscSection cs; 1870 PetscInt pEnd = -1; 1871 1872 ierr = DMGetDefaultSection(rdm->coordinateDM, &cs);CHKERRQ(ierr); 1873 if (cs) {ierr = PetscSectionGetChart(cs, NULL, &pEnd);CHKERRQ(ierr);} 1874 if (pEnd >= 0) { 1875 ierr = DMClone(rdm->coordinateDM, &ncdm);CHKERRQ(ierr); 1876 ierr = DMSetDefaultSection(ncdm, cs);CHKERRQ(ierr); 1877 ierr = DMSetCoordinateDM(*refdm, ncdm);CHKERRQ(ierr); 1878 ierr = DMDestroy(&ncdm);CHKERRQ(ierr); 1879 } 1880 } 1881 ierr = DMGetCoordinatesLocal(rdm, &coords);CHKERRQ(ierr); 1882 if (coords) { 1883 ierr = DMSetCoordinatesLocal(*refdm, coords);CHKERRQ(ierr); 1884 } else { 1885 ierr = DMGetCoordinates(rdm, &coords);CHKERRQ(ierr); 1886 if (coords) {ierr = DMSetCoordinates(*refdm, coords);CHKERRQ(ierr);} 1887 } 1888 ierr = DMDestroy(&rdm);CHKERRQ(ierr); 1889 PetscFunctionReturn(0); 1890 } 1891