1 #define PETSCDM_DLL 2 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 #include <petsc/private/hashseti.h> /*I "petscdmplex.h" I*/ 4 #include <petscsf.h> 5 6 PetscLogEvent DMPLEX_CreateFromFile, DMPLEX_CreateFromCellList, DMPLEX_CreateFromCellList_Coordinates; 7 8 /*@ 9 DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement. 10 11 Collective 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 .seealso: DMSetType(), DMCreate() 27 @*/ 28 PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscBool refinementUniform, PetscReal refinementLimit, DM *newdm) 29 { 30 DM dm; 31 PetscInt p; 32 PetscMPIInt rank; 33 PetscErrorCode ierr; 34 35 PetscFunctionBegin; 36 ierr = DMCreate(comm, &dm);CHKERRQ(ierr); 37 ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr); 38 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 39 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 40 switch (dim) { 41 case 2: 42 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "triangular");CHKERRQ(ierr);} 43 else {ierr = PetscObjectSetName((PetscObject) dm, "quadrilateral");CHKERRQ(ierr);} 44 break; 45 case 3: 46 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "tetrahedral");CHKERRQ(ierr);} 47 else {ierr = PetscObjectSetName((PetscObject) dm, "hexahedral");CHKERRQ(ierr);} 48 break; 49 default: 50 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); 51 } 52 if (rank) { 53 PetscInt numPoints[2] = {0, 0}; 54 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 55 } else { 56 switch (dim) { 57 case 2: 58 if (simplex) { 59 PetscInt numPoints[2] = {4, 2}; 60 PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; 61 PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; 62 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 63 PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5}; 64 PetscInt markerPoints[8] = {2, 1, 3, 1, 4, 1, 5, 1}; 65 66 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 67 for (p = 0; p < 4; ++p) {ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 68 } else { 69 PetscInt numPoints[2] = {6, 2}; 70 PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; 71 PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4}; 72 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 73 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}; 74 75 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 76 } 77 break; 78 case 3: 79 if (simplex) { 80 PetscInt numPoints[2] = {5, 2}; 81 PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; 82 PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; 83 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 84 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}; 85 PetscInt markerPoints[10] = {2, 1, 3, 1, 4, 1, 5, 1, 6, 1}; 86 87 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 88 for (p = 0; p < 5; ++p) {ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 89 } else { 90 PetscInt numPoints[2] = {12, 2}; 91 PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 92 PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8}; 93 PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 94 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, 95 -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5, 96 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5}; 97 98 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 99 } 100 break; 101 default: 102 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); 103 } 104 } 105 *newdm = dm; 106 if (refinementLimit > 0.0) { 107 DM rdm; 108 const char *name; 109 110 ierr = DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);CHKERRQ(ierr); 111 ierr = DMPlexSetRefinementLimit(*newdm, refinementLimit);CHKERRQ(ierr); 112 ierr = DMRefine(*newdm, comm, &rdm);CHKERRQ(ierr); 113 ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); 114 ierr = PetscObjectSetName((PetscObject) rdm, name);CHKERRQ(ierr); 115 ierr = DMDestroy(newdm);CHKERRQ(ierr); 116 *newdm = rdm; 117 } 118 if (interpolate) { 119 DM idm; 120 121 ierr = DMPlexInterpolate(*newdm, &idm);CHKERRQ(ierr); 122 ierr = DMDestroy(newdm);CHKERRQ(ierr); 123 *newdm = idm; 124 } 125 { 126 DM refinedMesh = NULL; 127 DM distributedMesh = NULL; 128 129 /* Distribute mesh over processes */ 130 ierr = DMPlexDistribute(*newdm, 0, NULL, &distributedMesh);CHKERRQ(ierr); 131 if (distributedMesh) { 132 ierr = DMDestroy(newdm);CHKERRQ(ierr); 133 *newdm = distributedMesh; 134 } 135 if (refinementUniform) { 136 ierr = DMPlexSetRefinementUniform(*newdm, refinementUniform);CHKERRQ(ierr); 137 ierr = DMRefine(*newdm, comm, &refinedMesh);CHKERRQ(ierr); 138 if (refinedMesh) { 139 ierr = DMDestroy(newdm);CHKERRQ(ierr); 140 *newdm = refinedMesh; 141 } 142 } 143 } 144 PetscFunctionReturn(0); 145 } 146 147 /*@ 148 DMPlexCreateSquareBoundary - Creates a 1D mesh the is the boundary of a square lattice. 149 150 Collective 151 152 Input Parameters: 153 + comm - The communicator for the DM object 154 . lower - The lower left corner coordinates 155 . upper - The upper right corner coordinates 156 - edges - The number of cells in each direction 157 158 Output Parameter: 159 . dm - The DM object 160 161 Note: Here is the numbering returned for 2 cells in each direction: 162 $ 18--5-17--4--16 163 $ | | | 164 $ 6 10 3 165 $ | | | 166 $ 19-11-20--9--15 167 $ | | | 168 $ 7 8 2 169 $ | | | 170 $ 12--0-13--1--14 171 172 Level: beginner 173 174 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate() 175 @*/ 176 PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 177 { 178 const PetscInt numVertices = (edges[0]+1)*(edges[1]+1); 179 const PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1]; 180 PetscInt markerTop = 1; 181 PetscInt markerBottom = 1; 182 PetscInt markerRight = 1; 183 PetscInt markerLeft = 1; 184 PetscBool markerSeparate = PETSC_FALSE; 185 Vec coordinates; 186 PetscSection coordSection; 187 PetscScalar *coords; 188 PetscInt coordSize; 189 PetscMPIInt rank; 190 PetscInt v, vx, vy; 191 PetscErrorCode ierr; 192 193 PetscFunctionBegin; 194 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 195 if (markerSeparate) { 196 markerTop = 3; 197 markerBottom = 1; 198 markerRight = 2; 199 markerLeft = 4; 200 } 201 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 202 if (!rank) { 203 PetscInt e, ex, ey; 204 205 ierr = DMPlexSetChart(dm, 0, numEdges+numVertices);CHKERRQ(ierr); 206 for (e = 0; e < numEdges; ++e) { 207 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 208 } 209 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 210 for (vx = 0; vx <= edges[0]; vx++) { 211 for (ey = 0; ey < edges[1]; ey++) { 212 PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1); 213 PetscInt vertex = ey*(edges[0]+1) + vx + numEdges; 214 PetscInt cone[2]; 215 216 cone[0] = vertex; cone[1] = vertex+edges[0]+1; 217 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 218 if (vx == edges[0]) { 219 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 220 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 221 if (ey == edges[1]-1) { 222 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 223 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerRight);CHKERRQ(ierr); 224 } 225 } else if (vx == 0) { 226 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 227 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 228 if (ey == edges[1]-1) { 229 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 230 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft);CHKERRQ(ierr); 231 } 232 } 233 } 234 } 235 for (vy = 0; vy <= edges[1]; vy++) { 236 for (ex = 0; ex < edges[0]; ex++) { 237 PetscInt edge = vy*edges[0] + ex; 238 PetscInt vertex = vy*(edges[0]+1) + ex + numEdges; 239 PetscInt cone[2]; 240 241 cone[0] = vertex; cone[1] = vertex+1; 242 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 243 if (vy == edges[1]) { 244 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 245 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 246 if (ex == edges[0]-1) { 247 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 248 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerTop);CHKERRQ(ierr); 249 } 250 } else if (vy == 0) { 251 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 252 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 253 if (ex == edges[0]-1) { 254 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 255 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom);CHKERRQ(ierr); 256 } 257 } 258 } 259 } 260 } 261 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 262 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 263 /* Build coordinates */ 264 ierr = DMSetCoordinateDim(dm, 2);CHKERRQ(ierr); 265 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 266 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 267 ierr = PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);CHKERRQ(ierr); 268 ierr = PetscSectionSetFieldComponents(coordSection, 0, 2);CHKERRQ(ierr); 269 for (v = numEdges; v < numEdges+numVertices; ++v) { 270 ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr); 271 ierr = PetscSectionSetFieldDof(coordSection, v, 0, 2);CHKERRQ(ierr); 272 } 273 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 274 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 275 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 276 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 277 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 278 ierr = VecSetBlockSize(coordinates, 2);CHKERRQ(ierr); 279 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 280 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 281 for (vy = 0; vy <= edges[1]; ++vy) { 282 for (vx = 0; vx <= edges[0]; ++vx) { 283 coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx; 284 coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy; 285 } 286 } 287 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 288 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 289 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 290 PetscFunctionReturn(0); 291 } 292 293 /*@ 294 DMPlexCreateCubeBoundary - Creates a 2D mesh that is the boundary of a cubic lattice. 295 296 Collective 297 298 Input Parameters: 299 + comm - The communicator for the DM object 300 . lower - The lower left front corner coordinates 301 . upper - The upper right back corner coordinates 302 - faces - The number of faces in each direction (the same as the number of cells) 303 304 Output Parameter: 305 . dm - The DM object 306 307 Level: beginner 308 309 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMSetType(), DMCreate() 310 @*/ 311 PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) 312 { 313 PetscInt vertices[3], numVertices; 314 PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2]; 315 Vec coordinates; 316 PetscSection coordSection; 317 PetscScalar *coords; 318 PetscInt coordSize; 319 PetscMPIInt rank; 320 PetscInt v, vx, vy, vz; 321 PetscInt voffset, iface=0, cone[4]; 322 PetscErrorCode ierr; 323 324 PetscFunctionBegin; 325 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"); 326 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 327 vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1; 328 numVertices = vertices[0]*vertices[1]*vertices[2]; 329 if (!rank) { 330 PetscInt f; 331 332 ierr = DMPlexSetChart(dm, 0, numFaces+numVertices);CHKERRQ(ierr); 333 for (f = 0; f < numFaces; ++f) { 334 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 335 } 336 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 337 338 /* Side 0 (Top) */ 339 for (vy = 0; vy < faces[1]; vy++) { 340 for (vx = 0; vx < faces[0]; vx++) { 341 voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx; 342 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0]; 343 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 344 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 345 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 346 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 347 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 348 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);CHKERRQ(ierr); 349 iface++; 350 } 351 } 352 353 /* Side 1 (Bottom) */ 354 for (vy = 0; vy < faces[1]; vy++) { 355 for (vx = 0; vx < faces[0]; vx++) { 356 voffset = numFaces + vy*(faces[0]+1) + vx; 357 cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1; 358 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 359 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 360 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 361 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 362 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 363 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);CHKERRQ(ierr); 364 iface++; 365 } 366 } 367 368 /* Side 2 (Front) */ 369 for (vz = 0; vz < faces[2]; vz++) { 370 for (vx = 0; vx < faces[0]; vx++) { 371 voffset = numFaces + vz*vertices[0]*vertices[1] + vx; 372 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1]; 373 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 374 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 375 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 376 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 377 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 378 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);CHKERRQ(ierr); 379 iface++; 380 } 381 } 382 383 /* Side 3 (Back) */ 384 for (vz = 0; vz < faces[2]; vz++) { 385 for (vx = 0; vx < faces[0]; vx++) { 386 voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx; 387 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1; 388 cone[2] = voffset+1; cone[3] = voffset; 389 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 390 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 391 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 392 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 393 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 394 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);CHKERRQ(ierr); 395 iface++; 396 } 397 } 398 399 /* Side 4 (Left) */ 400 for (vz = 0; vz < faces[2]; vz++) { 401 for (vy = 0; vy < faces[1]; vy++) { 402 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0]; 403 cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1]; 404 cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0]; 405 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 406 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 407 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 408 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 409 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[1]+0, 1);CHKERRQ(ierr); 410 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);CHKERRQ(ierr); 411 iface++; 412 } 413 } 414 415 /* Side 5 (Right) */ 416 for (vz = 0; vz < faces[2]; vz++) { 417 for (vy = 0; vy < faces[1]; vy++) { 418 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + faces[0]; 419 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset; 420 cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0]; 421 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 422 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 423 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 424 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 425 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 426 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);CHKERRQ(ierr); 427 iface++; 428 } 429 } 430 } 431 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 432 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 433 /* Build coordinates */ 434 ierr = DMSetCoordinateDim(dm, 3);CHKERRQ(ierr); 435 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 436 ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr); 437 for (v = numFaces; v < numFaces+numVertices; ++v) { 438 ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr); 439 } 440 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 441 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 442 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 443 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 444 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 445 ierr = VecSetBlockSize(coordinates, 3);CHKERRQ(ierr); 446 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 447 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 448 for (vz = 0; vz <= faces[2]; ++vz) { 449 for (vy = 0; vy <= faces[1]; ++vy) { 450 for (vx = 0; vx <= faces[0]; ++vx) { 451 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx; 452 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy; 453 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz; 454 } 455 } 456 } 457 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 458 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 459 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 460 PetscFunctionReturn(0); 461 } 462 463 static PetscErrorCode DMPlexCreateLineMesh_Internal(MPI_Comm comm,PetscInt segments,PetscReal lower,PetscReal upper,DMBoundaryType bd,DM *dm) 464 { 465 PetscInt i,fStart,fEnd,numCells = 0,numVerts = 0; 466 PetscInt numPoints[2],*coneSize,*cones,*coneOrientations; 467 PetscScalar *vertexCoords; 468 PetscReal L,maxCell; 469 PetscBool markerSeparate = PETSC_FALSE; 470 PetscInt markerLeft = 1, faceMarkerLeft = 1; 471 PetscInt markerRight = 1, faceMarkerRight = 2; 472 PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE; 473 PetscMPIInt rank; 474 PetscErrorCode ierr; 475 476 PetscFunctionBegin; 477 PetscValidPointer(dm,4); 478 479 ierr = DMCreate(comm,dm);CHKERRQ(ierr); 480 ierr = DMSetType(*dm,DMPLEX);CHKERRQ(ierr); 481 ierr = DMSetDimension(*dm,1);CHKERRQ(ierr); 482 ierr = DMCreateLabel(*dm,"marker");CHKERRQ(ierr); 483 ierr = DMCreateLabel(*dm,"Face Sets");CHKERRQ(ierr); 484 485 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 486 if (!rank) numCells = segments; 487 if (!rank) numVerts = segments + (wrap ? 0 : 1); 488 489 numPoints[0] = numVerts ; numPoints[1] = numCells; 490 ierr = PetscMalloc4(numCells+numVerts,&coneSize,numCells*2,&cones,numCells+numVerts,&coneOrientations,numVerts,&vertexCoords);CHKERRQ(ierr); 491 ierr = PetscArrayzero(coneOrientations,numCells+numVerts);CHKERRQ(ierr); 492 for (i = 0; i < numCells; ++i) { coneSize[i] = 2; } 493 for (i = 0; i < numVerts; ++i) { coneSize[numCells+i] = 0; } 494 for (i = 0; i < numCells; ++i) { cones[2*i] = numCells + i%numVerts; cones[2*i+1] = numCells + (i+1)%numVerts; } 495 for (i = 0; i < numVerts; ++i) { vertexCoords[i] = lower + (upper-lower)*((PetscReal)i/(PetscReal)numCells); } 496 ierr = DMPlexCreateFromDAG(*dm,1,numPoints,coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 497 ierr = PetscFree4(coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 498 499 ierr = PetscOptionsGetBool(((PetscObject)*dm)->options,((PetscObject)*dm)->prefix,"-dm_plex_separate_marker",&markerSeparate,NULL);CHKERRQ(ierr); 500 if (markerSeparate) { markerLeft = faceMarkerLeft; markerRight = faceMarkerRight;} 501 if (!wrap && !rank) { 502 ierr = DMPlexGetHeightStratum(*dm,1,&fStart,&fEnd);CHKERRQ(ierr); 503 ierr = DMSetLabelValue(*dm,"marker",fStart,markerLeft);CHKERRQ(ierr); 504 ierr = DMSetLabelValue(*dm,"marker",fEnd-1,markerRight);CHKERRQ(ierr); 505 ierr = DMSetLabelValue(*dm,"Face Sets",fStart,faceMarkerLeft);CHKERRQ(ierr); 506 ierr = DMSetLabelValue(*dm,"Face Sets",fEnd-1,faceMarkerRight);CHKERRQ(ierr); 507 } 508 if (wrap) { 509 L = upper - lower; 510 maxCell = (PetscReal)1.1*(L/(PetscReal)PetscMax(1,segments)); 511 ierr = DMSetPeriodicity(*dm,PETSC_TRUE,&maxCell,&L,&bd);CHKERRQ(ierr); 512 } 513 PetscFunctionReturn(0); 514 } 515 516 static PetscErrorCode DMPlexCreateBoxMesh_Simplex_Internal(MPI_Comm comm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate, DM *dm) 517 { 518 DM boundary; 519 PetscInt i; 520 PetscErrorCode ierr; 521 522 PetscFunctionBegin; 523 PetscValidPointer(dm, 4); 524 for (i = 0; i < dim; ++i) if (periodicity[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity is not supported for simplex meshes"); 525 ierr = DMCreate(comm, &boundary);CHKERRQ(ierr); 526 PetscValidLogicalCollectiveInt(boundary,dim,2); 527 ierr = DMSetType(boundary, DMPLEX);CHKERRQ(ierr); 528 ierr = DMSetDimension(boundary, dim-1);CHKERRQ(ierr); 529 ierr = DMSetCoordinateDim(boundary, dim);CHKERRQ(ierr); 530 switch (dim) { 531 case 2: ierr = DMPlexCreateSquareBoundary(boundary, lower, upper, faces);CHKERRQ(ierr);break; 532 case 3: ierr = DMPlexCreateCubeBoundary(boundary, lower, upper, faces);CHKERRQ(ierr);break; 533 default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 534 } 535 ierr = DMPlexGenerate(boundary, NULL, interpolate, dm);CHKERRQ(ierr); 536 ierr = DMDestroy(&boundary);CHKERRQ(ierr); 537 PetscFunctionReturn(0); 538 } 539 540 static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ) 541 { 542 DMLabel cutLabel = NULL; 543 PetscInt markerTop = 1, faceMarkerTop = 1; 544 PetscInt markerBottom = 1, faceMarkerBottom = 1; 545 PetscInt markerFront = 1, faceMarkerFront = 1; 546 PetscInt markerBack = 1, faceMarkerBack = 1; 547 PetscInt markerRight = 1, faceMarkerRight = 1; 548 PetscInt markerLeft = 1, faceMarkerLeft = 1; 549 PetscInt dim; 550 PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE; 551 PetscMPIInt rank; 552 PetscErrorCode ierr; 553 554 PetscFunctionBegin; 555 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 556 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 557 ierr = DMCreateLabel(dm,"marker");CHKERRQ(ierr); 558 ierr = DMCreateLabel(dm,"Face Sets");CHKERRQ(ierr); 559 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL);CHKERRQ(ierr); 560 if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST || 561 bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST || 562 bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) { 563 564 if (cutMarker) {ierr = DMCreateLabel(dm, "periodic_cut");CHKERRQ(ierr); ierr = DMGetLabel(dm, "periodic_cut", &cutLabel);CHKERRQ(ierr);} 565 } 566 switch (dim) { 567 case 2: 568 faceMarkerTop = 3; 569 faceMarkerBottom = 1; 570 faceMarkerRight = 2; 571 faceMarkerLeft = 4; 572 break; 573 case 3: 574 faceMarkerBottom = 1; 575 faceMarkerTop = 2; 576 faceMarkerFront = 3; 577 faceMarkerBack = 4; 578 faceMarkerRight = 5; 579 faceMarkerLeft = 6; 580 break; 581 default: 582 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %d not supported",dim); 583 break; 584 } 585 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 586 if (markerSeparate) { 587 markerBottom = faceMarkerBottom; 588 markerTop = faceMarkerTop; 589 markerFront = faceMarkerFront; 590 markerBack = faceMarkerBack; 591 markerRight = faceMarkerRight; 592 markerLeft = faceMarkerLeft; 593 } 594 { 595 const PetscInt numXEdges = !rank ? edges[0] : 0; 596 const PetscInt numYEdges = !rank ? edges[1] : 0; 597 const PetscInt numZEdges = !rank ? edges[2] : 0; 598 const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; 599 const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; 600 const PetscInt numZVertices = !rank ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0; 601 const PetscInt numCells = numXEdges*numYEdges*numZEdges; 602 const PetscInt numXFaces = numYEdges*numZEdges; 603 const PetscInt numYFaces = numXEdges*numZEdges; 604 const PetscInt numZFaces = numXEdges*numYEdges; 605 const PetscInt numTotXFaces = numXVertices*numXFaces; 606 const PetscInt numTotYFaces = numYVertices*numYFaces; 607 const PetscInt numTotZFaces = numZVertices*numZFaces; 608 const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces; 609 const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices; 610 const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices; 611 const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices; 612 const PetscInt numVertices = numXVertices*numYVertices*numZVertices; 613 const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges; 614 const PetscInt firstVertex = (dim == 2) ? numFaces : numCells; 615 const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices; 616 const PetscInt firstYFace = firstXFace + numTotXFaces; 617 const PetscInt firstZFace = firstYFace + numTotYFaces; 618 const PetscInt firstXEdge = numCells + numFaces + numVertices; 619 const PetscInt firstYEdge = firstXEdge + numTotXEdges; 620 const PetscInt firstZEdge = firstYEdge + numTotYEdges; 621 Vec coordinates; 622 PetscSection coordSection; 623 PetscScalar *coords; 624 PetscInt coordSize; 625 PetscInt v, vx, vy, vz; 626 PetscInt c, f, fx, fy, fz, e, ex, ey, ez; 627 628 ierr = DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);CHKERRQ(ierr); 629 for (c = 0; c < numCells; c++) { 630 ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr); 631 } 632 for (f = firstXFace; f < firstXFace+numFaces; ++f) { 633 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 634 } 635 for (e = firstXEdge; e < firstXEdge+numEdges; ++e) { 636 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 637 } 638 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 639 /* Build cells */ 640 for (fz = 0; fz < numZEdges; ++fz) { 641 for (fy = 0; fy < numYEdges; ++fy) { 642 for (fx = 0; fx < numXEdges; ++fx) { 643 PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx; 644 PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 645 PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices); 646 PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 647 PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices); 648 PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 649 PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices); 650 /* B, T, F, K, R, L */ 651 PetscInt ornt[6] = {-4, 0, 0, -1, 0, -4}; /* ??? */ 652 PetscInt cone[6]; 653 654 /* no boundary twisting in 3D */ 655 cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL; 656 ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr); 657 ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr); 658 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 659 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 660 if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 661 } 662 } 663 } 664 /* Build x faces */ 665 for (fz = 0; fz < numZEdges; ++fz) { 666 for (fy = 0; fy < numYEdges; ++fy) { 667 for (fx = 0; fx < numXVertices; ++fx) { 668 PetscInt face = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 669 PetscInt edgeL = firstZEdge + ( fy* numXVertices+fx)*numZEdges + fz; 670 PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz; 671 PetscInt edgeB = firstYEdge + ( fz* numXVertices+fx)*numYEdges + fy; 672 PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy; 673 PetscInt ornt[4] = {0, 0, -2, -2}; 674 PetscInt cone[4]; 675 676 if (dim == 3) { 677 /* markers */ 678 if (bdX != DM_BOUNDARY_PERIODIC) { 679 if (fx == numXVertices-1) { 680 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);CHKERRQ(ierr); 681 ierr = DMSetLabelValue(dm, "marker", face, markerRight);CHKERRQ(ierr); 682 } 683 else if (fx == 0) { 684 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);CHKERRQ(ierr); 685 ierr = DMSetLabelValue(dm, "marker", face, markerLeft);CHKERRQ(ierr); 686 } 687 } 688 } 689 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 690 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 691 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 692 } 693 } 694 } 695 /* Build y faces */ 696 for (fz = 0; fz < numZEdges; ++fz) { 697 for (fx = 0; fx < numXEdges; ++fx) { 698 for (fy = 0; fy < numYVertices; ++fy) { 699 PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 700 PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx )*numZEdges + fz; 701 PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz; 702 PetscInt edgeB = firstXEdge + ( fz *numYVertices+fy)*numXEdges + fx; 703 PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx; 704 PetscInt ornt[4] = {0, 0, -2, -2}; 705 PetscInt cone[4]; 706 707 if (dim == 3) { 708 /* markers */ 709 if (bdY != DM_BOUNDARY_PERIODIC) { 710 if (fy == numYVertices-1) { 711 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);CHKERRQ(ierr); 712 ierr = DMSetLabelValue(dm, "marker", face, markerBack);CHKERRQ(ierr); 713 } 714 else if (fy == 0) { 715 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);CHKERRQ(ierr); 716 ierr = DMSetLabelValue(dm, "marker", face, markerFront);CHKERRQ(ierr); 717 } 718 } 719 } 720 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 721 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 722 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 723 } 724 } 725 } 726 /* Build z faces */ 727 for (fy = 0; fy < numYEdges; ++fy) { 728 for (fx = 0; fx < numXEdges; ++fx) { 729 for (fz = 0; fz < numZVertices; fz++) { 730 PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 731 PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx )*numYEdges + fy; 732 PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy; 733 PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy )*numXEdges + fx; 734 PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx; 735 PetscInt ornt[4] = {0, 0, -2, -2}; 736 PetscInt cone[4]; 737 738 if (dim == 2) { 739 if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -2;} 740 if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;} 741 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 742 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 743 } else { 744 /* markers */ 745 if (bdZ != DM_BOUNDARY_PERIODIC) { 746 if (fz == numZVertices-1) { 747 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);CHKERRQ(ierr); 748 ierr = DMSetLabelValue(dm, "marker", face, markerTop);CHKERRQ(ierr); 749 } 750 else if (fz == 0) { 751 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);CHKERRQ(ierr); 752 ierr = DMSetLabelValue(dm, "marker", face, markerBottom);CHKERRQ(ierr); 753 } 754 } 755 } 756 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 757 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 758 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 759 } 760 } 761 } 762 /* Build Z edges*/ 763 for (vy = 0; vy < numYVertices; vy++) { 764 for (vx = 0; vx < numXVertices; vx++) { 765 for (ez = 0; ez < numZEdges; ez++) { 766 const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez; 767 const PetscInt vertexB = firstVertex + ( ez *numYVertices+vy)*numXVertices + vx; 768 const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx; 769 PetscInt cone[2]; 770 771 if (dim == 3) { 772 if (bdX != DM_BOUNDARY_PERIODIC) { 773 if (vx == numXVertices-1) { 774 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 775 } 776 else if (vx == 0) { 777 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 778 } 779 } 780 if (bdY != DM_BOUNDARY_PERIODIC) { 781 if (vy == numYVertices-1) { 782 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 783 } 784 else if (vy == 0) { 785 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 786 } 787 } 788 } 789 cone[0] = vertexB; cone[1] = vertexT; 790 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 791 } 792 } 793 } 794 /* Build Y edges*/ 795 for (vz = 0; vz < numZVertices; vz++) { 796 for (vx = 0; vx < numXVertices; vx++) { 797 for (ey = 0; ey < numYEdges; ey++) { 798 const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx; 799 const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey; 800 const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx; 801 const PetscInt vertexK = firstVertex + nextv; 802 PetscInt cone[2]; 803 804 cone[0] = vertexF; cone[1] = vertexK; 805 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 806 if (dim == 2) { 807 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 808 if (vx == numXVertices-1) { 809 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);CHKERRQ(ierr); 810 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 811 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 812 if (ey == numYEdges-1) { 813 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 814 } 815 } else if (vx == 0) { 816 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);CHKERRQ(ierr); 817 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 818 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 819 if (ey == numYEdges-1) { 820 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 821 } 822 } 823 } else { 824 if (vx == 0 && cutLabel) { 825 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 826 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 827 if (ey == numYEdges-1) { 828 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 829 } 830 } 831 } 832 } else { 833 if (bdX != DM_BOUNDARY_PERIODIC) { 834 if (vx == numXVertices-1) { 835 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 836 } else if (vx == 0) { 837 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 838 } 839 } 840 if (bdZ != DM_BOUNDARY_PERIODIC) { 841 if (vz == numZVertices-1) { 842 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 843 } else if (vz == 0) { 844 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 845 } 846 } 847 } 848 } 849 } 850 } 851 /* Build X edges*/ 852 for (vz = 0; vz < numZVertices; vz++) { 853 for (vy = 0; vy < numYVertices; vy++) { 854 for (ex = 0; ex < numXEdges; ex++) { 855 const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices; 856 const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex; 857 const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex; 858 const PetscInt vertexR = firstVertex + nextv; 859 PetscInt cone[2]; 860 861 cone[0] = vertexL; cone[1] = vertexR; 862 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 863 if (dim == 2) { 864 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 865 if (vy == numYVertices-1) { 866 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);CHKERRQ(ierr); 867 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 868 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 869 if (ex == numXEdges-1) { 870 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 871 } 872 } else if (vy == 0) { 873 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);CHKERRQ(ierr); 874 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 875 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 876 if (ex == numXEdges-1) { 877 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 878 } 879 } 880 } else { 881 if (vy == 0 && cutLabel) { 882 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 883 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 884 if (ex == numXEdges-1) { 885 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 886 } 887 } 888 } 889 } else { 890 if (bdY != DM_BOUNDARY_PERIODIC) { 891 if (vy == numYVertices-1) { 892 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 893 } 894 else if (vy == 0) { 895 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 896 } 897 } 898 if (bdZ != DM_BOUNDARY_PERIODIC) { 899 if (vz == numZVertices-1) { 900 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 901 } 902 else if (vz == 0) { 903 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 904 } 905 } 906 } 907 } 908 } 909 } 910 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 911 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 912 /* Build coordinates */ 913 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 914 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 915 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 916 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr); 917 for (v = firstVertex; v < firstVertex+numVertices; ++v) { 918 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 919 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 920 } 921 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 922 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 923 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 924 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 925 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 926 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 927 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 928 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 929 for (vz = 0; vz < numZVertices; ++vz) { 930 for (vy = 0; vy < numYVertices; ++vy) { 931 for (vx = 0; vx < numXVertices; ++vx) { 932 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx; 933 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy; 934 if (dim == 3) { 935 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz; 936 } 937 } 938 } 939 } 940 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 941 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 942 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 943 } 944 PetscFunctionReturn(0); 945 } 946 947 static PetscErrorCode DMPlexCreateBoxMesh_Tensor_Internal(MPI_Comm comm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate, DM *dm) 948 { 949 PetscInt i; 950 PetscErrorCode ierr; 951 952 PetscFunctionBegin; 953 PetscValidPointer(dm, 7); 954 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 955 PetscValidLogicalCollectiveInt(*dm,dim,2); 956 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 957 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 958 switch (dim) { 959 case 2: {ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], DM_BOUNDARY_NONE);CHKERRQ(ierr);break;} 960 case 3: {ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], periodicity[2]);CHKERRQ(ierr);break;} 961 default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 962 } 963 if (periodicity[0] == DM_BOUNDARY_PERIODIC || periodicity[0] == DM_BOUNDARY_TWIST || 964 periodicity[1] == DM_BOUNDARY_PERIODIC || periodicity[1] == DM_BOUNDARY_TWIST || 965 (dim > 2 && (periodicity[2] == DM_BOUNDARY_PERIODIC || periodicity[2] == DM_BOUNDARY_TWIST))) { 966 PetscReal L[3]; 967 PetscReal maxCell[3]; 968 969 for (i = 0; i < dim; i++) { 970 L[i] = upper[i] - lower[i]; 971 maxCell[i] = 1.1 * (L[i] / PetscMax(1,faces[i])); 972 } 973 ierr = DMSetPeriodicity(*dm,PETSC_TRUE,maxCell,L,periodicity);CHKERRQ(ierr); 974 } 975 if (!interpolate) { 976 DM udm; 977 978 ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr); 979 ierr = DMPlexCopyCoordinates(*dm, udm);CHKERRQ(ierr); 980 ierr = DMDestroy(dm);CHKERRQ(ierr); 981 *dm = udm; 982 } 983 PetscFunctionReturn(0); 984 } 985 986 /*@C 987 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra). 988 989 Collective 990 991 Input Parameters: 992 + comm - The communicator for the DM object 993 . dim - The spatial dimension 994 . simplex - PETSC_TRUE for simplices, PETSC_FALSE for tensor cells 995 . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 996 . lower - The lower left corner, or NULL for (0, 0, 0) 997 . upper - The upper right corner, or NULL for (1, 1, 1) 998 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 999 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1000 1001 Output Parameter: 1002 . dm - The DM object 1003 1004 Options Database Keys: 1005 + -dm_plex_box_lower <x,y,z> - Specify lower-left-bottom coordinates for the box 1006 . -dm_plex_box_upper <x,y,z> - Specify upper-right-top coordinates for the box 1007 - -dm_plex_box_faces <m,n,p> - Number of faces in each linear direction 1008 1009 Notes: 1010 The options database keys above take lists of length d in d dimensions. 1011 1012 Here is the numbering returned for 2 faces in each direction for tensor cells: 1013 $ 10---17---11---18----12 1014 $ | | | 1015 $ | | | 1016 $ 20 2 22 3 24 1017 $ | | | 1018 $ | | | 1019 $ 7---15----8---16----9 1020 $ | | | 1021 $ | | | 1022 $ 19 0 21 1 23 1023 $ | | | 1024 $ | | | 1025 $ 4---13----5---14----6 1026 1027 and for simplicial cells 1028 1029 $ 14----8---15----9----16 1030 $ |\ 5 |\ 7 | 1031 $ | \ | \ | 1032 $ 13 2 14 3 15 1033 $ | 4 \ | 6 \ | 1034 $ | \ | \ | 1035 $ 11----6---12----7----13 1036 $ |\ |\ | 1037 $ | \ 1 | \ 3 | 1038 $ 10 0 11 1 12 1039 $ | 0 \ | 2 \ | 1040 $ | \ | \ | 1041 $ 8----4----9----5----10 1042 1043 Level: beginner 1044 1045 .seealso: DMPlexCreateFromFile(), DMPlexCreateHexCylinderMesh(), DMSetType(), DMCreate() 1046 @*/ 1047 PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate, DM *dm) 1048 { 1049 PetscInt fac[3] = {0, 0, 0}; 1050 PetscReal low[3] = {0, 0, 0}; 1051 PetscReal upp[3] = {1, 1, 1}; 1052 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1053 PetscInt i, n; 1054 PetscBool flg; 1055 PetscErrorCode ierr; 1056 1057 PetscFunctionBegin; 1058 n = 3; 1059 ierr = PetscOptionsGetIntArray(NULL, NULL, "-dm_plex_box_faces", fac, &n, &flg);CHKERRQ(ierr); 1060 for (i = 0; i < dim; ++i) fac[i] = faces ? faces[i] : (flg && i < n ? fac[i] : (dim == 1 ? 1 : 4-dim)); 1061 if (lower) for (i = 0; i < dim; ++i) low[i] = lower[i]; 1062 if (upper) for (i = 0; i < dim; ++i) upp[i] = upper[i]; 1063 if (periodicity) for (i = 0; i < dim; ++i) bdt[i] = periodicity[i]; 1064 /* Allow bounds to be specified from the command line */ 1065 n = 3; 1066 ierr = PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_lower", low, &n, &flg);CHKERRQ(ierr); 1067 if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim); 1068 n = 3; 1069 ierr = PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_upper", upp, &n, &flg);CHKERRQ(ierr); 1070 if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim); 1071 1072 if (dim == 1) {ierr = DMPlexCreateLineMesh_Internal(comm, fac[0], low[0], upp[0], bdt[0], dm);CHKERRQ(ierr);} 1073 else if (simplex) {ierr = DMPlexCreateBoxMesh_Simplex_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);CHKERRQ(ierr);} 1074 else {ierr = DMPlexCreateBoxMesh_Tensor_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);CHKERRQ(ierr);} 1075 PetscFunctionReturn(0); 1076 } 1077 1078 /*@ 1079 DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells. 1080 1081 Collective 1082 1083 Input Parameters: 1084 + comm - The communicator for the DM object 1085 . faces - Number of faces per dimension, or NULL for (1, 1, 1) 1086 . lower - The lower left corner, or NULL for (0, 0, 0) 1087 . upper - The upper right corner, or NULL for (1, 1, 1) 1088 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 1089 . orderHeight - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1090 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1091 1092 Output Parameter: 1093 . dm - The DM object 1094 1095 Level: beginner 1096 1097 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateWedgeCylinderMesh(), DMPlexExtrude(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1098 @*/ 1099 PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool orderHeight, PetscBool interpolate, DM *dm) 1100 { 1101 DM bdm, botdm; 1102 PetscInt i; 1103 PetscInt fac[3] = {0, 0, 0}; 1104 PetscReal low[3] = {0, 0, 0}; 1105 PetscReal upp[3] = {1, 1, 1}; 1106 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1107 PetscErrorCode ierr; 1108 1109 PetscFunctionBegin; 1110 for (i = 0; i < 3; ++i) fac[i] = faces ? (faces[i] > 0 ? faces[i] : 1) : 1; 1111 if (lower) for (i = 0; i < 3; ++i) low[i] = lower[i]; 1112 if (upper) for (i = 0; i < 3; ++i) upp[i] = upper[i]; 1113 if (periodicity) for (i = 0; i < 3; ++i) bdt[i] = periodicity[i]; 1114 for (i = 0; i < 3; ++i) if (bdt[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity not yet supported"); 1115 1116 ierr = DMCreate(comm, &bdm);CHKERRQ(ierr); 1117 ierr = DMSetType(bdm, DMPLEX);CHKERRQ(ierr); 1118 ierr = DMSetDimension(bdm, 1);CHKERRQ(ierr); 1119 ierr = DMSetCoordinateDim(bdm, 2);CHKERRQ(ierr); 1120 ierr = DMPlexCreateSquareBoundary(bdm, low, upp, fac);CHKERRQ(ierr); 1121 ierr = DMPlexGenerate(bdm, NULL, PETSC_FALSE, &botdm);CHKERRQ(ierr); 1122 ierr = DMDestroy(&bdm);CHKERRQ(ierr); 1123 ierr = DMPlexExtrude(botdm, fac[2], upp[2] - low[2], orderHeight, NULL, interpolate, dm);CHKERRQ(ierr); 1124 if (low[2] != 0.0) { 1125 Vec v; 1126 PetscScalar *x; 1127 PetscInt cDim, n; 1128 1129 ierr = DMGetCoordinatesLocal(*dm, &v);CHKERRQ(ierr); 1130 ierr = VecGetBlockSize(v, &cDim);CHKERRQ(ierr); 1131 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 1132 ierr = VecGetArray(v, &x);CHKERRQ(ierr); 1133 x += cDim; 1134 for (i=0; i<n; i+=cDim) x[i] += low[2]; 1135 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 1136 ierr = DMSetCoordinatesLocal(*dm, v);CHKERRQ(ierr); 1137 } 1138 ierr = DMDestroy(&botdm);CHKERRQ(ierr); 1139 PetscFunctionReturn(0); 1140 } 1141 1142 /*@C 1143 DMPlexExtrude - Creates a (d+1)-D mesh by extruding a d-D mesh in the normal direction using prismatic cells. 1144 1145 Collective on idm 1146 1147 Input Parameters: 1148 + idm - The mesh to be extruded 1149 . layers - The number of layers, or PETSC_DETERMINE to use the default 1150 . height - The height of the extruded layer, or PETSC_DETERMINE to use the default 1151 . orderHeight - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1152 . extNormal - The normal direction in which the mesh should be extruded, or NULL to extrude using the surface normal 1153 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1154 1155 Output Parameter: 1156 . dm - The DM object 1157 1158 Notes: 1159 The mesh created has prismatic cells, and the vertex ordering in the cone of the cell is that of the tensor prismatic cells. Not currently supported in Fortran. 1160 1161 Options Database Keys: 1162 -dm_plex_extrude_layers <k> - Sets the nubmer of layers k 1163 -dm_plex_extrude_height <h> - Sets the height h of each layer 1164 -dm_plex_extrude_order_height - If true, order cells by height first 1165 -dm_plex_extrude_normal <n0,...,nd> - Sets the normal vector along which to extrude 1166 1167 Level: advanced 1168 1169 .seealso: DMPlexCreateWedgeCylinderMesh(), DMPlexCreateWedgeBoxMesh(), DMSetType(), DMCreate() 1170 @*/ 1171 PetscErrorCode DMPlexExtrude(DM idm, PetscInt layers, PetscReal height, PetscBool orderHeight, const PetscReal extNormal[], PetscBool interpolate, DM* dm) 1172 { 1173 PetscScalar *coordsB; 1174 const PetscScalar *coordsA; 1175 PetscReal *normals = NULL; 1176 PetscReal clNormal[3]; 1177 Vec coordinatesA, coordinatesB; 1178 PetscSection coordSectionA, coordSectionB; 1179 PetscInt dim, cDim, cDimB, c, l, v, coordSize, *newCone; 1180 PetscInt cStart, cEnd, vStart, vEnd, cellV, numCells, numVertices; 1181 const char *prefix; 1182 PetscBool haveCLNormal; 1183 PetscErrorCode ierr; 1184 1185 PetscFunctionBegin; 1186 PetscValidHeaderSpecific(idm, DM_CLASSID, 1); 1187 PetscValidLogicalCollectiveInt(idm, layers, 2); 1188 PetscValidLogicalCollectiveReal(idm, height, 3); 1189 PetscValidLogicalCollectiveBool(idm, interpolate, 4); 1190 ierr = DMGetDimension(idm, &dim);CHKERRQ(ierr); 1191 ierr = DMGetCoordinateDim(idm, &cDim);CHKERRQ(ierr); 1192 cDimB = cDim == dim ? cDim+1 : cDim; 1193 if (dim < 1 || dim > 3) SETERRQ1(PetscObjectComm((PetscObject)idm), PETSC_ERR_SUP, "Support for dimension %D not coded", dim); 1194 1195 ierr = PetscObjectGetOptionsPrefix((PetscObject) idm, &prefix);CHKERRQ(ierr); 1196 if (layers < 0) layers = 1; 1197 ierr = PetscOptionsGetInt(NULL, prefix, "-dm_plex_extrude_layers", &layers, NULL);CHKERRQ(ierr); 1198 if (layers <= 0) SETERRQ1(PetscObjectComm((PetscObject) idm), PETSC_ERR_ARG_OUTOFRANGE, "Number of layers %D must be positive", layers); 1199 if (height < 0.) height = 1.; 1200 ierr = PetscOptionsGetReal(NULL, prefix, "-dm_plex_extrude_height", &height, NULL);CHKERRQ(ierr); 1201 if (height <= 0.) SETERRQ1(PetscObjectComm((PetscObject) idm), PETSC_ERR_ARG_OUTOFRANGE, "Height of layers %g must be positive", (double) height); 1202 ierr = PetscOptionsGetBool(NULL, prefix, "-dm_plex_extrude_order_height", &orderHeight, NULL);CHKERRQ(ierr); 1203 c = 3; 1204 ierr = PetscOptionsGetRealArray(NULL, prefix, "-dm_plex_extrude_normal", clNormal, &c, &haveCLNormal);CHKERRQ(ierr); 1205 if (haveCLNormal && c != cDimB) SETERRQ2(PetscObjectComm((PetscObject)idm), PETSC_ERR_ARG_SIZ, "Input normal has size %D != %D extruded coordinate dimension", c, cDimB); 1206 1207 ierr = DMPlexGetHeightStratum(idm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1208 ierr = DMPlexGetDepthStratum(idm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1209 numCells = (cEnd - cStart)*layers; 1210 numVertices = (vEnd - vStart)*(layers+1); 1211 ierr = DMCreate(PetscObjectComm((PetscObject)idm), dm);CHKERRQ(ierr); 1212 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1213 ierr = DMSetDimension(*dm, dim+1);CHKERRQ(ierr); 1214 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1215 /* Must create the celltype label here so that we do not automatically try to compute the types */ 1216 ierr = DMCreateLabel(*dm, "celltype");CHKERRQ(ierr); 1217 for (c = cStart, cellV = 0; c < cEnd; ++c) { 1218 DMPolytopeType ct, nct; 1219 PetscInt *closure = NULL; 1220 PetscInt closureSize, numCorners = 0; 1221 1222 ierr = DMPlexGetCellType(idm, c, &ct);CHKERRQ(ierr); 1223 switch (ct) { 1224 case DM_POLYTOPE_SEGMENT: nct = DM_POLYTOPE_SEG_PRISM_TENSOR;break; 1225 case DM_POLYTOPE_TRIANGLE: nct = DM_POLYTOPE_TRI_PRISM_TENSOR;break; 1226 case DM_POLYTOPE_QUADRILATERAL: nct = DM_POLYTOPE_QUAD_PRISM_TENSOR;break; 1227 default: nct = DM_POLYTOPE_UNKNOWN; 1228 } 1229 ierr = DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1230 for (v = 0; v < closureSize*2; v += 2) if ((closure[v] >= vStart) && (closure[v] < vEnd)) numCorners++; 1231 ierr = DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1232 for (l = 0; l < layers; ++l) { 1233 const PetscInt cell = orderHeight ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart; 1234 1235 ierr = DMPlexSetConeSize(*dm, cell, 2*numCorners);CHKERRQ(ierr); 1236 ierr = DMPlexSetCellType(*dm, cell, nct);CHKERRQ(ierr); 1237 } 1238 cellV = PetscMax(numCorners,cellV); 1239 } 1240 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1241 1242 if (dim != cDim && !(extNormal || haveCLNormal)) {ierr = PetscCalloc1(cDim*(vEnd - vStart), &normals);CHKERRQ(ierr);} 1243 ierr = PetscMalloc1(3*cellV,&newCone);CHKERRQ(ierr); 1244 for (c = cStart; c < cEnd; ++c) { 1245 PetscInt *closure = NULL; 1246 PetscInt closureSize, numCorners = 0, l; 1247 PetscReal normal[3] = {0, 0, 0}; 1248 1249 if (normals) {ierr = DMPlexComputeCellGeometryFVM(idm, c, NULL, NULL, normal);CHKERRQ(ierr);} 1250 ierr = DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1251 for (v = 0; v < closureSize*2; v += 2) { 1252 if ((closure[v] >= vStart) && (closure[v] < vEnd)) { 1253 PetscInt d; 1254 1255 newCone[numCorners++] = closure[v] - vStart; 1256 if (normals) {for (d = 0; d < cDim; ++d) normals[cDim*(closure[v]-vStart)+d] += normal[d];} 1257 } 1258 } 1259 ierr = DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1260 for (l = 0; l < layers; ++l) { 1261 PetscInt i; 1262 1263 for (i = 0; i < numCorners; ++i) { 1264 newCone[ numCorners + i] = orderHeight ? (layers+1)*newCone[i] + l + numCells : l*(vEnd - vStart) + newCone[i] + numCells; 1265 newCone[2*numCorners + i] = orderHeight ? (layers+1)*newCone[i] + l + 1 + numCells : (l+1)*(vEnd - vStart) + newCone[i] + numCells; 1266 } 1267 ierr = DMPlexSetCone(*dm, orderHeight ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart, newCone + numCorners);CHKERRQ(ierr); 1268 } 1269 } 1270 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1271 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1272 ierr = PetscFree(newCone);CHKERRQ(ierr); 1273 1274 ierr = DMGetCoordinateSection(*dm, &coordSectionB);CHKERRQ(ierr); 1275 ierr = PetscSectionSetNumFields(coordSectionB, 1);CHKERRQ(ierr); 1276 ierr = PetscSectionSetFieldComponents(coordSectionB, 0, cDimB);CHKERRQ(ierr); 1277 ierr = PetscSectionSetChart(coordSectionB, numCells, numCells+numVertices);CHKERRQ(ierr); 1278 for (v = numCells; v < numCells+numVertices; ++v) { 1279 ierr = PetscSectionSetDof(coordSectionB, v, cDimB);CHKERRQ(ierr); 1280 ierr = PetscSectionSetFieldDof(coordSectionB, v, 0, cDimB);CHKERRQ(ierr); 1281 ierr = DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr); 1282 } 1283 ierr = PetscSectionSetUp(coordSectionB);CHKERRQ(ierr); 1284 ierr = PetscSectionGetStorageSize(coordSectionB, &coordSize);CHKERRQ(ierr); 1285 ierr = VecCreate(PETSC_COMM_SELF, &coordinatesB);CHKERRQ(ierr); 1286 ierr = PetscObjectSetName((PetscObject) coordinatesB, "coordinates");CHKERRQ(ierr); 1287 ierr = VecSetSizes(coordinatesB, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1288 ierr = VecSetBlockSize(coordinatesB, cDimB);CHKERRQ(ierr); 1289 ierr = VecSetType(coordinatesB,VECSTANDARD);CHKERRQ(ierr); 1290 1291 ierr = DMGetCoordinateSection(idm, &coordSectionA);CHKERRQ(ierr); 1292 ierr = DMGetCoordinatesLocal(idm, &coordinatesA);CHKERRQ(ierr); 1293 ierr = VecGetArray(coordinatesB, &coordsB);CHKERRQ(ierr); 1294 ierr = VecGetArrayRead(coordinatesA, &coordsA);CHKERRQ(ierr); 1295 for (v = vStart; v < vEnd; ++v) { 1296 const PetscScalar *cptr; 1297 PetscReal ones2[2] = { 0., 1.}, ones3[3] = { 0., 0., 1.}; 1298 PetscReal normal[3]; 1299 PetscReal norm, h = height/layers; 1300 PetscInt offA, d, cDimA = cDim; 1301 1302 if (normals) {for (d = 0; d < cDimB; ++d) normal[d] = normals[cDimB*(v - vStart)+d];} 1303 else if (haveCLNormal) {for (d = 0; d < cDimB; ++d) normal[d] = clNormal[d];} 1304 else if (extNormal) {for (d = 0; d < cDimB; ++d) normal[d] = extNormal[d];} 1305 else if (cDimB == 2) {for (d = 0; d < cDimB; ++d) normal[d] = ones2[d];} 1306 else if (cDimB == 3) {for (d = 0; d < cDimB; ++d) normal[d] = ones3[d];} 1307 else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unable to determine normal for extrusion"); 1308 for (d = 0, norm = 0.0; d < cDimB; ++d) norm += normal[d]*normal[d]; 1309 for (d = 0; d < cDimB; ++d) normal[d] *= 1./PetscSqrtReal(norm); 1310 1311 ierr = PetscSectionGetOffset(coordSectionA, v, &offA);CHKERRQ(ierr); 1312 cptr = coordsA + offA; 1313 for (l = 0; l < layers+1; ++l) { 1314 PetscInt offB, d, newV; 1315 1316 newV = orderHeight ? (layers+1)*(v -vStart) + l + numCells : (vEnd -vStart)*l + (v -vStart) + numCells; 1317 ierr = PetscSectionGetOffset(coordSectionB, newV, &offB);CHKERRQ(ierr); 1318 for (d = 0; d < cDimA; ++d) { coordsB[offB+d] = cptr[d]; } 1319 for (d = 0; d < cDimB; ++d) { coordsB[offB+d] += l ? normal[d]*h : 0.0; } 1320 cptr = coordsB + offB; 1321 cDimA = cDimB; 1322 } 1323 } 1324 ierr = VecRestoreArrayRead(coordinatesA, &coordsA);CHKERRQ(ierr); 1325 ierr = VecRestoreArray(coordinatesB, &coordsB);CHKERRQ(ierr); 1326 ierr = DMSetCoordinatesLocal(*dm, coordinatesB);CHKERRQ(ierr); 1327 ierr = VecDestroy(&coordinatesB);CHKERRQ(ierr); 1328 ierr = PetscFree(normals);CHKERRQ(ierr); 1329 if (interpolate) { 1330 DM idm; 1331 1332 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1333 ierr = DMPlexCopyCoordinates(*dm, idm);CHKERRQ(ierr); 1334 ierr = DMDestroy(dm);CHKERRQ(ierr); 1335 *dm = idm; 1336 } 1337 PetscFunctionReturn(0); 1338 } 1339 1340 /*@C 1341 DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database. 1342 1343 Logically Collective on dm 1344 1345 Input Parameters: 1346 + dm - the DM context 1347 - prefix - the prefix to prepend to all option names 1348 1349 Notes: 1350 A hyphen (-) must NOT be given at the beginning of the prefix name. 1351 The first character of all runtime options is AUTOMATICALLY the hyphen. 1352 1353 Level: advanced 1354 1355 .seealso: SNESSetFromOptions() 1356 @*/ 1357 PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) 1358 { 1359 DM_Plex *mesh = (DM_Plex *) dm->data; 1360 PetscErrorCode ierr; 1361 1362 PetscFunctionBegin; 1363 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1364 ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);CHKERRQ(ierr); 1365 ierr = PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);CHKERRQ(ierr); 1366 PetscFunctionReturn(0); 1367 } 1368 1369 /*@ 1370 DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. 1371 1372 Collective 1373 1374 Input Parameters: 1375 + comm - The communicator for the DM object 1376 . numRefine - The number of regular refinements to the basic 5 cell structure 1377 - periodicZ - The boundary type for the Z direction 1378 1379 Output Parameter: 1380 . dm - The DM object 1381 1382 Note: Here is the output numbering looking from the bottom of the cylinder: 1383 $ 17-----14 1384 $ | | 1385 $ | 2 | 1386 $ | | 1387 $ 17-----8-----7-----14 1388 $ | | | | 1389 $ | 3 | 0 | 1 | 1390 $ | | | | 1391 $ 19-----5-----6-----13 1392 $ | | 1393 $ | 4 | 1394 $ | | 1395 $ 19-----13 1396 $ 1397 $ and up through the top 1398 $ 1399 $ 18-----16 1400 $ | | 1401 $ | 2 | 1402 $ | | 1403 $ 18----10----11-----16 1404 $ | | | | 1405 $ | 3 | 0 | 1 | 1406 $ | | | | 1407 $ 20-----9----12-----15 1408 $ | | 1409 $ | 4 | 1410 $ | | 1411 $ 20-----15 1412 1413 Level: beginner 1414 1415 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1416 @*/ 1417 PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, PetscInt numRefine, DMBoundaryType periodicZ, DM *dm) 1418 { 1419 const PetscInt dim = 3; 1420 PetscInt numCells, numVertices, r; 1421 PetscMPIInt rank; 1422 PetscErrorCode ierr; 1423 1424 PetscFunctionBegin; 1425 PetscValidPointer(dm, 4); 1426 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1427 if (numRefine < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of refinements %D cannot be negative", numRefine); 1428 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1429 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1430 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1431 /* Create topology */ 1432 { 1433 PetscInt cone[8], c; 1434 1435 numCells = !rank ? 5 : 0; 1436 numVertices = !rank ? 16 : 0; 1437 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1438 numCells *= 3; 1439 numVertices = !rank ? 24 : 0; 1440 } 1441 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1442 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 8);CHKERRQ(ierr);} 1443 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1444 if (!rank) { 1445 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1446 cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16; 1447 cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34; 1448 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1449 cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23; 1450 cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */ 1451 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1452 cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17; 1453 cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38; 1454 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1455 cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15; 1456 cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38; 1457 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1458 cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23; 1459 cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31; 1460 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1461 1462 cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32; 1463 cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20; 1464 ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); 1465 cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36; 1466 cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21; 1467 ierr = DMPlexSetCone(*dm, 6, cone);CHKERRQ(ierr); 1468 cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33; 1469 cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28; 1470 ierr = DMPlexSetCone(*dm, 7, cone);CHKERRQ(ierr); 1471 cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31; 1472 cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28; 1473 ierr = DMPlexSetCone(*dm, 8, cone);CHKERRQ(ierr); 1474 cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36; 1475 cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19; 1476 ierr = DMPlexSetCone(*dm, 9, cone);CHKERRQ(ierr); 1477 1478 cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22; 1479 cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18; 1480 ierr = DMPlexSetCone(*dm, 10, cone);CHKERRQ(ierr); 1481 cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25; 1482 cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17; 1483 ierr = DMPlexSetCone(*dm, 11, cone);CHKERRQ(ierr); 1484 cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21; 1485 cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27; 1486 ierr = DMPlexSetCone(*dm, 12, cone);CHKERRQ(ierr); 1487 cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19; 1488 cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27; 1489 ierr = DMPlexSetCone(*dm, 13, cone);CHKERRQ(ierr); 1490 cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25; 1491 cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15; 1492 ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); 1493 } else { 1494 cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6; 1495 cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10; 1496 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1497 cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13; 1498 cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11; 1499 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1500 cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7; 1501 cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18; 1502 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1503 cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5; 1504 cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18; 1505 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1506 cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13; 1507 cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9; 1508 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1509 } 1510 } 1511 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1512 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1513 } 1514 /* Interpolate */ 1515 { 1516 DM idm; 1517 1518 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1519 ierr = DMDestroy(dm);CHKERRQ(ierr); 1520 *dm = idm; 1521 } 1522 /* Create cube geometry */ 1523 { 1524 Vec coordinates; 1525 PetscSection coordSection; 1526 PetscScalar *coords; 1527 PetscInt coordSize, v; 1528 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1529 const PetscReal ds2 = dis/2.0; 1530 1531 /* Build coordinates */ 1532 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1533 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1534 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1535 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1536 for (v = numCells; v < numCells+numVertices; ++v) { 1537 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1538 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1539 } 1540 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1541 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1542 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1543 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1544 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1545 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1546 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1547 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1548 if (!rank) { 1549 coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0; 1550 coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0; 1551 coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0; 1552 coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0; 1553 coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0; 1554 coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0; 1555 coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0; 1556 coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0; 1557 coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0; 1558 coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0; 1559 coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0; 1560 coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0; 1561 coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0; 1562 coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0; 1563 coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0; 1564 coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0; 1565 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1566 /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5; 1567 /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5; 1568 /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5; 1569 /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5; 1570 /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5; 1571 /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5; 1572 /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5; 1573 /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5; 1574 } 1575 } 1576 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1577 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 1578 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1579 } 1580 /* Create periodicity */ 1581 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1582 PetscReal L[3]; 1583 PetscReal maxCell[3]; 1584 DMBoundaryType bdType[3]; 1585 PetscReal lower[3] = {0.0, 0.0, 0.0}; 1586 PetscReal upper[3] = {1.0, 1.0, 1.5}; 1587 PetscInt i, numZCells = 3; 1588 1589 bdType[0] = DM_BOUNDARY_NONE; 1590 bdType[1] = DM_BOUNDARY_NONE; 1591 bdType[2] = periodicZ; 1592 for (i = 0; i < dim; i++) { 1593 L[i] = upper[i] - lower[i]; 1594 maxCell[i] = 1.1 * (L[i] / numZCells); 1595 } 1596 ierr = DMSetPeriodicity(*dm, PETSC_TRUE, maxCell, L, bdType);CHKERRQ(ierr); 1597 } 1598 /* Refine topology */ 1599 for (r = 0; r < numRefine; ++r) { 1600 DM rdm = NULL; 1601 1602 ierr = DMRefine(*dm, comm, &rdm);CHKERRQ(ierr); 1603 ierr = DMDestroy(dm);CHKERRQ(ierr); 1604 *dm = rdm; 1605 } 1606 /* Remap geometry to cylinder 1607 Interior square: Linear interpolation is correct 1608 The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing 1609 such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance 1610 1611 phi = arctan(y/x) 1612 d_close = sqrt(1/8 + 1/4 sin^2(phi)) 1613 d_far = sqrt(1/2 + sin^2(phi)) 1614 1615 so we remap them using 1616 1617 x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) 1618 y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) 1619 1620 If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. 1621 */ 1622 { 1623 Vec coordinates; 1624 PetscSection coordSection; 1625 PetscScalar *coords; 1626 PetscInt vStart, vEnd, v; 1627 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1628 const PetscReal ds2 = 0.5*dis; 1629 1630 ierr = DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1631 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1632 ierr = DMGetCoordinatesLocal(*dm, &coordinates);CHKERRQ(ierr); 1633 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1634 for (v = vStart; v < vEnd; ++v) { 1635 PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; 1636 PetscInt off; 1637 1638 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 1639 if ((PetscAbsScalar(coords[off+0]) <= ds2) && (PetscAbsScalar(coords[off+1]) <= ds2)) continue; 1640 x = PetscRealPart(coords[off]); 1641 y = PetscRealPart(coords[off+1]); 1642 phi = PetscAtan2Real(y, x); 1643 sinp = PetscSinReal(phi); 1644 cosp = PetscCosReal(phi); 1645 if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) { 1646 dc = PetscAbsReal(ds2/sinp); 1647 df = PetscAbsReal(dis/sinp); 1648 xc = ds2*x/PetscAbsReal(y); 1649 yc = ds2*PetscSignReal(y); 1650 } else { 1651 dc = PetscAbsReal(ds2/cosp); 1652 df = PetscAbsReal(dis/cosp); 1653 xc = ds2*PetscSignReal(x); 1654 yc = ds2*y/PetscAbsReal(x); 1655 } 1656 coords[off+0] = xc + (coords[off+0] - xc)*(1.0 - dc)/(df - dc); 1657 coords[off+1] = yc + (coords[off+1] - yc)*(1.0 - dc)/(df - dc); 1658 } 1659 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1660 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1661 ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); 1662 } 1663 } 1664 PetscFunctionReturn(0); 1665 } 1666 1667 /*@ 1668 DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges. 1669 1670 Collective 1671 1672 Input Parameters: 1673 + comm - The communicator for the DM object 1674 . n - The number of wedges around the origin 1675 - interpolate - Create edges and faces 1676 1677 Output Parameter: 1678 . dm - The DM object 1679 1680 Level: beginner 1681 1682 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1683 @*/ 1684 PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm) 1685 { 1686 const PetscInt dim = 3; 1687 PetscInt numCells, numVertices, v; 1688 PetscMPIInt rank; 1689 PetscErrorCode ierr; 1690 1691 PetscFunctionBegin; 1692 PetscValidPointer(dm, 3); 1693 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1694 if (n < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n); 1695 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1696 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1697 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1698 /* Must create the celltype label here so that we do not automatically try to compute the types */ 1699 ierr = DMCreateLabel(*dm, "celltype");CHKERRQ(ierr); 1700 /* Create topology */ 1701 { 1702 PetscInt cone[6], c; 1703 1704 numCells = !rank ? n : 0; 1705 numVertices = !rank ? 2*(n+1) : 0; 1706 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1707 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 6);CHKERRQ(ierr);} 1708 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1709 for (c = 0; c < numCells; c++) { 1710 cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n; 1711 cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n; 1712 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 1713 ierr = DMPlexSetCellType(*dm, c, DM_POLYTOPE_TRI_PRISM_TENSOR);CHKERRQ(ierr); 1714 } 1715 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1716 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1717 } 1718 for (v = numCells; v < numCells+numVertices; ++v) { 1719 ierr = DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr); 1720 } 1721 /* Interpolate */ 1722 if (interpolate) { 1723 DM idm; 1724 1725 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1726 ierr = DMDestroy(dm);CHKERRQ(ierr); 1727 *dm = idm; 1728 } 1729 /* Create cylinder geometry */ 1730 { 1731 Vec coordinates; 1732 PetscSection coordSection; 1733 PetscScalar *coords; 1734 PetscInt coordSize, c; 1735 1736 /* Build coordinates */ 1737 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1738 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1739 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1740 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1741 for (v = numCells; v < numCells+numVertices; ++v) { 1742 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1743 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1744 } 1745 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1746 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1747 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1748 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1749 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1750 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1751 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1752 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1753 for (c = 0; c < numCells; c++) { 1754 coords[(c+0*n)*dim+0] = PetscCosReal(2.0*c*PETSC_PI/n); coords[(c+0*n)*dim+1] = PetscSinReal(2.0*c*PETSC_PI/n); coords[(c+0*n)*dim+2] = 1.0; 1755 coords[(c+1*n)*dim+0] = PetscCosReal(2.0*c*PETSC_PI/n); coords[(c+1*n)*dim+1] = PetscSinReal(2.0*c*PETSC_PI/n); coords[(c+1*n)*dim+2] = 0.0; 1756 } 1757 if (!rank) { 1758 coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0; 1759 coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0; 1760 } 1761 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1762 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 1763 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1764 } 1765 PetscFunctionReturn(0); 1766 } 1767 1768 PETSC_STATIC_INLINE PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1769 { 1770 PetscReal prod = 0.0; 1771 PetscInt i; 1772 for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]); 1773 return PetscSqrtReal(prod); 1774 } 1775 PETSC_STATIC_INLINE PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1776 { 1777 PetscReal prod = 0.0; 1778 PetscInt i; 1779 for (i = 0; i < dim; ++i) prod += x[i]*y[i]; 1780 return prod; 1781 } 1782 1783 /* The first constant is the sphere radius */ 1784 static void snapToSphere(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1785 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1786 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1787 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 1788 { 1789 PetscReal r = PetscRealPart(constants[0]); 1790 PetscReal norm2 = 0.0, fac; 1791 PetscInt n = uOff[1] - uOff[0], d; 1792 1793 for (d = 0; d < n; ++d) norm2 += PetscSqr(PetscRealPart(u[d])); 1794 fac = r/PetscSqrtReal(norm2); 1795 for (d = 0; d < n; ++d) f0[d] = u[d]*fac; 1796 } 1797 1798 /*@ 1799 DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d. 1800 1801 Collective 1802 1803 Input Parameters: 1804 + comm - The communicator for the DM object 1805 . dim - The dimension 1806 . simplex - Use simplices, or tensor product cells 1807 - R - The radius 1808 1809 Output Parameter: 1810 . dm - The DM object 1811 1812 Level: beginner 1813 1814 .seealso: DMPlexCreateBallMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1815 @*/ 1816 PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscReal R, DM *dm) 1817 { 1818 const PetscInt embedDim = dim+1; 1819 PetscSection coordSection; 1820 Vec coordinates; 1821 PetscScalar *coords; 1822 PetscReal *coordsIn; 1823 PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e; 1824 PetscMPIInt rank; 1825 PetscErrorCode ierr; 1826 1827 PetscFunctionBegin; 1828 PetscValidPointer(dm, 4); 1829 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1830 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1831 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1832 ierr = DMSetCoordinateDim(*dm, dim+1);CHKERRQ(ierr); 1833 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) *dm), &rank);CHKERRQ(ierr); 1834 switch (dim) { 1835 case 2: 1836 if (simplex) { 1837 DM idm; 1838 const PetscReal radius = PetscSqrtReal(1 + PETSC_PHI*PETSC_PHI)/(1.0 + PETSC_PHI); 1839 const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI) * (R/radius); 1840 const PetscInt degree = 5; 1841 PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)}; 1842 PetscInt s[3] = {1, 1, 1}; 1843 PetscInt cone[3]; 1844 PetscInt *graph, p, i, j, k; 1845 1846 vertex[0] *= R/radius; vertex[1] *= R/radius; vertex[2] *= R/radius; 1847 numCells = !rank ? 20 : 0; 1848 numVerts = !rank ? 12 : 0; 1849 firstVertex = numCells; 1850 /* Use icosahedron, which for a R-sphere has coordinates which are all cyclic permutations of 1851 1852 (0, \pm 1/\phi+1, \pm \phi/\phi+1) 1853 1854 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 1855 length is then given by 2/(1+\phi) = 2 * 0.38197 = 0.76393. 1856 */ 1857 /* Construct vertices */ 1858 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 1859 if (!rank) { 1860 for (p = 0, i = 0; p < embedDim; ++p) { 1861 for (s[1] = -1; s[1] < 2; s[1] += 2) { 1862 for (s[2] = -1; s[2] < 2; s[2] += 2) { 1863 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim]; 1864 ++i; 1865 } 1866 } 1867 } 1868 } 1869 /* Construct graph */ 1870 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 1871 for (i = 0; i < numVerts; ++i) { 1872 for (j = 0, k = 0; j < numVerts; ++j) { 1873 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 1874 } 1875 if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree); 1876 } 1877 /* Build Topology */ 1878 ierr = DMPlexSetChart(*dm, 0, numCells+numVerts);CHKERRQ(ierr); 1879 for (c = 0; c < numCells; c++) { 1880 ierr = DMPlexSetConeSize(*dm, c, embedDim);CHKERRQ(ierr); 1881 } 1882 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 1883 /* Cells */ 1884 for (i = 0, c = 0; i < numVerts; ++i) { 1885 for (j = 0; j < i; ++j) { 1886 for (k = 0; k < j; ++k) { 1887 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) { 1888 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; 1889 /* Check orientation */ 1890 { 1891 const PetscInt epsilon[3][3][3] = {{{0, 0, 0}, {0, 0, 1}, {0, -1, 0}}, {{0, 0, -1}, {0, 0, 0}, {1, 0, 0}}, {{0, 1, 0}, {-1, 0, 0}, {0, 0, 0}}}; 1892 PetscReal normal[3]; 1893 PetscInt e, f; 1894 1895 for (d = 0; d < embedDim; ++d) { 1896 normal[d] = 0.0; 1897 for (e = 0; e < embedDim; ++e) { 1898 for (f = 0; f < embedDim; ++f) { 1899 normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]); 1900 } 1901 } 1902 } 1903 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 1904 } 1905 ierr = DMPlexSetCone(*dm, c++, cone);CHKERRQ(ierr); 1906 } 1907 } 1908 } 1909 } 1910 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1911 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1912 ierr = PetscFree(graph);CHKERRQ(ierr); 1913 /* Interpolate mesh */ 1914 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1915 ierr = DMDestroy(dm);CHKERRQ(ierr); 1916 *dm = idm; 1917 } else { 1918 /* 1919 12-21--13 1920 | | 1921 25 4 24 1922 | | 1923 12-25--9-16--8-24--13 1924 | | | | 1925 23 5 17 0 15 3 22 1926 | | | | 1927 10-20--6-14--7-19--11 1928 | | 1929 20 1 19 1930 | | 1931 10-18--11 1932 | | 1933 23 2 22 1934 | | 1935 12-21--13 1936 */ 1937 PetscInt cone[4], ornt[4]; 1938 1939 numCells = !rank ? 6 : 0; 1940 numEdges = !rank ? 12 : 0; 1941 numVerts = !rank ? 8 : 0; 1942 firstVertex = numCells; 1943 firstEdge = numCells + numVerts; 1944 /* Build Topology */ 1945 ierr = DMPlexSetChart(*dm, 0, numCells+numEdges+numVerts);CHKERRQ(ierr); 1946 for (c = 0; c < numCells; c++) { 1947 ierr = DMPlexSetConeSize(*dm, c, 4);CHKERRQ(ierr); 1948 } 1949 for (e = firstEdge; e < firstEdge+numEdges; ++e) { 1950 ierr = DMPlexSetConeSize(*dm, e, 2);CHKERRQ(ierr); 1951 } 1952 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 1953 if (!rank) { 1954 /* Cell 0 */ 1955 cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17; 1956 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1957 ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0; 1958 ierr = DMPlexSetConeOrientation(*dm, 0, ornt);CHKERRQ(ierr); 1959 /* Cell 1 */ 1960 cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20; 1961 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1962 ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; 1963 ierr = DMPlexSetConeOrientation(*dm, 1, ornt);CHKERRQ(ierr); 1964 /* Cell 2 */ 1965 cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23; 1966 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1967 ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; 1968 ierr = DMPlexSetConeOrientation(*dm, 2, ornt);CHKERRQ(ierr); 1969 /* Cell 3 */ 1970 cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15; 1971 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1972 ornt[0] = -2; ornt[1] = -2; ornt[2] = 0; ornt[3] = -2; 1973 ierr = DMPlexSetConeOrientation(*dm, 3, ornt);CHKERRQ(ierr); 1974 /* Cell 4 */ 1975 cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25; 1976 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1977 ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = 0; 1978 ierr = DMPlexSetConeOrientation(*dm, 4, ornt);CHKERRQ(ierr); 1979 /* Cell 5 */ 1980 cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23; 1981 ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); 1982 ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = -2; 1983 ierr = DMPlexSetConeOrientation(*dm, 5, ornt);CHKERRQ(ierr); 1984 /* Edges */ 1985 cone[0] = 6; cone[1] = 7; 1986 ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); 1987 cone[0] = 7; cone[1] = 8; 1988 ierr = DMPlexSetCone(*dm, 15, cone);CHKERRQ(ierr); 1989 cone[0] = 8; cone[1] = 9; 1990 ierr = DMPlexSetCone(*dm, 16, cone);CHKERRQ(ierr); 1991 cone[0] = 9; cone[1] = 6; 1992 ierr = DMPlexSetCone(*dm, 17, cone);CHKERRQ(ierr); 1993 cone[0] = 10; cone[1] = 11; 1994 ierr = DMPlexSetCone(*dm, 18, cone);CHKERRQ(ierr); 1995 cone[0] = 11; cone[1] = 7; 1996 ierr = DMPlexSetCone(*dm, 19, cone);CHKERRQ(ierr); 1997 cone[0] = 6; cone[1] = 10; 1998 ierr = DMPlexSetCone(*dm, 20, cone);CHKERRQ(ierr); 1999 cone[0] = 12; cone[1] = 13; 2000 ierr = DMPlexSetCone(*dm, 21, cone);CHKERRQ(ierr); 2001 cone[0] = 13; cone[1] = 11; 2002 ierr = DMPlexSetCone(*dm, 22, cone);CHKERRQ(ierr); 2003 cone[0] = 10; cone[1] = 12; 2004 ierr = DMPlexSetCone(*dm, 23, cone);CHKERRQ(ierr); 2005 cone[0] = 13; cone[1] = 8; 2006 ierr = DMPlexSetCone(*dm, 24, cone);CHKERRQ(ierr); 2007 cone[0] = 12; cone[1] = 9; 2008 ierr = DMPlexSetCone(*dm, 25, cone);CHKERRQ(ierr); 2009 } 2010 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 2011 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 2012 /* Build coordinates */ 2013 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 2014 if (!rank) { 2015 coordsIn[0*embedDim+0] = -R; coordsIn[0*embedDim+1] = R; coordsIn[0*embedDim+2] = -R; 2016 coordsIn[1*embedDim+0] = R; coordsIn[1*embedDim+1] = R; coordsIn[1*embedDim+2] = -R; 2017 coordsIn[2*embedDim+0] = R; coordsIn[2*embedDim+1] = -R; coordsIn[2*embedDim+2] = -R; 2018 coordsIn[3*embedDim+0] = -R; coordsIn[3*embedDim+1] = -R; coordsIn[3*embedDim+2] = -R; 2019 coordsIn[4*embedDim+0] = -R; coordsIn[4*embedDim+1] = R; coordsIn[4*embedDim+2] = R; 2020 coordsIn[5*embedDim+0] = R; coordsIn[5*embedDim+1] = R; coordsIn[5*embedDim+2] = R; 2021 coordsIn[6*embedDim+0] = -R; coordsIn[6*embedDim+1] = -R; coordsIn[6*embedDim+2] = R; 2022 coordsIn[7*embedDim+0] = R; coordsIn[7*embedDim+1] = -R; coordsIn[7*embedDim+2] = R; 2023 } 2024 } 2025 break; 2026 case 3: 2027 if (simplex) { 2028 DM idm; 2029 const PetscReal edgeLen = 1.0/PETSC_PHI; 2030 PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5}; 2031 PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0}; 2032 PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0}; 2033 const PetscInt degree = 12; 2034 PetscInt s[4] = {1, 1, 1}; 2035 PetscInt evenPerm[12][4] = {{0, 1, 2, 3}, {0, 2, 3, 1}, {0, 3, 1, 2}, {1, 0, 3, 2}, {1, 2, 0, 3}, {1, 3, 2, 0}, 2036 {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}}; 2037 PetscInt cone[4]; 2038 PetscInt *graph, p, i, j, k, l; 2039 2040 vertexA[0] *= R; vertexA[1] *= R; vertexA[2] *= R; vertexA[3] *= R; 2041 vertexB[0] *= R; vertexB[1] *= R; vertexB[2] *= R; vertexB[3] *= R; 2042 vertexC[0] *= R; vertexC[1] *= R; vertexC[2] *= R; vertexC[3] *= R; 2043 numCells = !rank ? 600 : 0; 2044 numVerts = !rank ? 120 : 0; 2045 firstVertex = numCells; 2046 /* Use the 600-cell, which for a unit sphere has coordinates which are 2047 2048 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16 2049 (\pm 1, 0, 0, 0) all cyclic permutations 8 2050 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96 2051 2052 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 2053 length is then given by 1/\phi = 0.61803. 2054 2055 http://buzzard.pugetsound.edu/sage-practice/ch03s03.html 2056 http://mathworld.wolfram.com/600-Cell.html 2057 */ 2058 /* Construct vertices */ 2059 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 2060 i = 0; 2061 if (!rank) { 2062 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2063 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2064 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2065 for (s[3] = -1; s[3] < 2; s[3] += 2) { 2066 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d]; 2067 ++i; 2068 } 2069 } 2070 } 2071 } 2072 for (p = 0; p < embedDim; ++p) { 2073 s[1] = s[2] = s[3] = 1; 2074 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2075 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim]; 2076 ++i; 2077 } 2078 } 2079 for (p = 0; p < 12; ++p) { 2080 s[3] = 1; 2081 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2082 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2083 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2084 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]]; 2085 ++i; 2086 } 2087 } 2088 } 2089 } 2090 } 2091 if (i != numVerts) SETERRQ2(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts); 2092 /* Construct graph */ 2093 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 2094 for (i = 0; i < numVerts; ++i) { 2095 for (j = 0, k = 0; j < numVerts; ++j) { 2096 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 2097 } 2098 if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree); 2099 } 2100 /* Build Topology */ 2101 ierr = DMPlexSetChart(*dm, 0, numCells+numVerts);CHKERRQ(ierr); 2102 for (c = 0; c < numCells; c++) { 2103 ierr = DMPlexSetConeSize(*dm, c, embedDim);CHKERRQ(ierr); 2104 } 2105 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 2106 /* Cells */ 2107 if (!rank) { 2108 for (i = 0, c = 0; i < numVerts; ++i) { 2109 for (j = 0; j < i; ++j) { 2110 for (k = 0; k < j; ++k) { 2111 for (l = 0; l < k; ++l) { 2112 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] && 2113 graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) { 2114 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l; 2115 /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */ 2116 { 2117 const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2118 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}}, 2119 {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}}, 2120 {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}}, 2121 2122 {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}}, 2123 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2124 {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}}, 2125 {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}}, 2126 2127 {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}}, 2128 {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}}, 2129 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2130 {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}, 2131 2132 {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}}, 2133 {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}}, 2134 {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2135 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}}; 2136 PetscReal normal[4]; 2137 PetscInt e, f, g; 2138 2139 for (d = 0; d < embedDim; ++d) { 2140 normal[d] = 0.0; 2141 for (e = 0; e < embedDim; ++e) { 2142 for (f = 0; f < embedDim; ++f) { 2143 for (g = 0; g < embedDim; ++g) { 2144 normal[d] += epsilon[d][e][f][g]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f])*(coordsIn[l*embedDim+f] - coordsIn[i*embedDim+f]); 2145 } 2146 } 2147 } 2148 } 2149 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 2150 } 2151 ierr = DMPlexSetCone(*dm, c++, cone);CHKERRQ(ierr); 2152 } 2153 } 2154 } 2155 } 2156 } 2157 } 2158 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 2159 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 2160 ierr = PetscFree(graph);CHKERRQ(ierr); 2161 /* Interpolate mesh */ 2162 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2163 ierr = DMDestroy(dm);CHKERRQ(ierr); 2164 *dm = idm; 2165 break; 2166 } 2167 default: SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim); 2168 } 2169 /* Create coordinates */ 2170 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 2171 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2172 ierr = PetscSectionSetFieldComponents(coordSection, 0, embedDim);CHKERRQ(ierr); 2173 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);CHKERRQ(ierr); 2174 for (v = firstVertex; v < firstVertex+numVerts; ++v) { 2175 ierr = PetscSectionSetDof(coordSection, v, embedDim);CHKERRQ(ierr); 2176 ierr = PetscSectionSetFieldDof(coordSection, v, 0, embedDim);CHKERRQ(ierr); 2177 } 2178 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2179 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2180 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 2181 ierr = VecSetBlockSize(coordinates, embedDim);CHKERRQ(ierr); 2182 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2183 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2184 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2185 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2186 for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];} 2187 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2188 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 2189 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2190 ierr = PetscFree(coordsIn);CHKERRQ(ierr); 2191 /* Create coordinate function space */ 2192 { 2193 DM cdm; 2194 PetscDS cds; 2195 PetscFE fe; 2196 PetscScalar radius = R; 2197 PetscInt dT, dE; 2198 2199 ierr = DMGetCoordinateDM(*dm, &cdm);CHKERRQ(ierr); 2200 ierr = DMGetDimension(*dm, &dT);CHKERRQ(ierr); 2201 ierr = DMGetCoordinateDim(*dm, &dE);CHKERRQ(ierr); 2202 ierr = PetscFECreateLagrange(PETSC_COMM_SELF, dT, dE, PETSC_TRUE, 1, -1, &fe);CHKERRQ(ierr); 2203 ierr = DMSetField(cdm, 0, NULL, (PetscObject) fe);CHKERRQ(ierr); 2204 ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); 2205 ierr = DMCreateDS(cdm);CHKERRQ(ierr); 2206 2207 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 2208 ierr = PetscDSSetConstants(cds, 1, &radius);CHKERRQ(ierr); 2209 } 2210 ((DM_Plex *) (*dm)->data)->coordFunc = snapToSphere; 2211 PetscFunctionReturn(0); 2212 } 2213 2214 /*@ 2215 DMPlexCreateBallMesh - Creates a simplex mesh on the d-dimensional ball, B^d. 2216 2217 Collective 2218 2219 Input Parameters: 2220 + comm - The communicator for the DM object 2221 . dim - The dimension 2222 - R - The radius 2223 2224 Output Parameter: 2225 . dm - The DM object 2226 2227 Options Database Keys: 2228 - bd_dm_refine - This will refine the surface mesh preserving the sphere geometry 2229 2230 Level: beginner 2231 2232 .seealso: DMPlexCreateSphereMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 2233 @*/ 2234 PetscErrorCode DMPlexCreateBallMesh(MPI_Comm comm, PetscInt dim, PetscReal R, DM *dm) 2235 { 2236 DM sdm; 2237 DMLabel bdlabel; 2238 PetscErrorCode ierr; 2239 2240 PetscFunctionBegin; 2241 ierr = DMPlexCreateSphereMesh(comm, dim-1, PETSC_TRUE, R, &sdm);CHKERRQ(ierr); 2242 ierr = PetscObjectSetOptionsPrefix((PetscObject) sdm, "bd_");CHKERRQ(ierr); 2243 ierr = DMSetFromOptions(sdm);CHKERRQ(ierr); 2244 ierr = DMPlexGenerate(sdm, NULL, PETSC_TRUE, dm);CHKERRQ(ierr); 2245 ierr = DMDestroy(&sdm);CHKERRQ(ierr); 2246 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 2247 ierr = DMGetLabel(*dm, "marker", &bdlabel);CHKERRQ(ierr); 2248 ierr = DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 2249 ierr = DMPlexLabelComplete(*dm, bdlabel);CHKERRQ(ierr); 2250 PetscFunctionReturn(0); 2251 } 2252 2253 /* External function declarations here */ 2254 extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling); 2255 extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat); 2256 extern PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mat); 2257 extern PetscErrorCode DMCreateLocalSection_Plex(DM dm); 2258 extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm); 2259 extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J); 2260 extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm); 2261 extern PetscErrorCode DMCreateCoordinateField_Plex(DM dm, DMField *field); 2262 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm); 2263 extern PetscErrorCode DMSetUp_Plex(DM dm); 2264 extern PetscErrorCode DMDestroy_Plex(DM dm); 2265 extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer); 2266 extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer); 2267 extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm); 2268 extern PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm); 2269 static PetscErrorCode DMInitialize_Plex(DM dm); 2270 2271 /* Replace dm with the contents of dmNew 2272 - Share the DM_Plex structure 2273 - Share the coordinates 2274 - Share the SF 2275 */ 2276 static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew) 2277 { 2278 PetscSF sf; 2279 DM coordDM, coarseDM; 2280 DMField coordField; 2281 Vec coords; 2282 PetscBool isper; 2283 const PetscReal *maxCell, *L; 2284 const DMBoundaryType *bd; 2285 PetscErrorCode ierr; 2286 2287 PetscFunctionBegin; 2288 ierr = DMGetPointSF(dmNew, &sf);CHKERRQ(ierr); 2289 ierr = DMSetPointSF(dm, sf);CHKERRQ(ierr); 2290 ierr = DMGetCoordinateDM(dmNew, &coordDM);CHKERRQ(ierr); 2291 ierr = DMGetCoordinatesLocal(dmNew, &coords);CHKERRQ(ierr); 2292 ierr = DMGetCoordinateField(dmNew, &coordField);CHKERRQ(ierr); 2293 ierr = DMSetCoordinateDM(dm, coordDM);CHKERRQ(ierr); 2294 ierr = DMSetCoordinatesLocal(dm, coords);CHKERRQ(ierr); 2295 ierr = DMSetCoordinateField(dm, coordField);CHKERRQ(ierr); 2296 ierr = DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);CHKERRQ(ierr); 2297 ierr = DMSetPeriodicity(dmNew, isper, maxCell, L, bd);CHKERRQ(ierr); 2298 ierr = DMDestroy_Plex(dm);CHKERRQ(ierr); 2299 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 2300 dm->data = dmNew->data; 2301 ((DM_Plex *) dmNew->data)->refct++; 2302 ierr = DMDestroyLabelLinkList_Internal(dm);CHKERRQ(ierr); 2303 ierr = DMCopyLabels(dmNew, dm, PETSC_OWN_POINTER, PETSC_TRUE);CHKERRQ(ierr); 2304 ierr = DMGetCoarseDM(dmNew,&coarseDM);CHKERRQ(ierr); 2305 ierr = DMSetCoarseDM(dm,coarseDM);CHKERRQ(ierr); 2306 PetscFunctionReturn(0); 2307 } 2308 2309 /* Swap dm with the contents of dmNew 2310 - Swap the DM_Plex structure 2311 - Swap the coordinates 2312 - Swap the point PetscSF 2313 */ 2314 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 2315 { 2316 DM coordDMA, coordDMB; 2317 Vec coordsA, coordsB; 2318 PetscSF sfA, sfB; 2319 void *tmp; 2320 DMLabelLink listTmp; 2321 DMLabel depthTmp; 2322 PetscInt tmpI; 2323 PetscErrorCode ierr; 2324 2325 PetscFunctionBegin; 2326 ierr = DMGetPointSF(dmA, &sfA);CHKERRQ(ierr); 2327 ierr = DMGetPointSF(dmB, &sfB);CHKERRQ(ierr); 2328 ierr = PetscObjectReference((PetscObject) sfA);CHKERRQ(ierr); 2329 ierr = DMSetPointSF(dmA, sfB);CHKERRQ(ierr); 2330 ierr = DMSetPointSF(dmB, sfA);CHKERRQ(ierr); 2331 ierr = PetscObjectDereference((PetscObject) sfA);CHKERRQ(ierr); 2332 2333 ierr = DMGetCoordinateDM(dmA, &coordDMA);CHKERRQ(ierr); 2334 ierr = DMGetCoordinateDM(dmB, &coordDMB);CHKERRQ(ierr); 2335 ierr = PetscObjectReference((PetscObject) coordDMA);CHKERRQ(ierr); 2336 ierr = DMSetCoordinateDM(dmA, coordDMB);CHKERRQ(ierr); 2337 ierr = DMSetCoordinateDM(dmB, coordDMA);CHKERRQ(ierr); 2338 ierr = PetscObjectDereference((PetscObject) coordDMA);CHKERRQ(ierr); 2339 2340 ierr = DMGetCoordinatesLocal(dmA, &coordsA);CHKERRQ(ierr); 2341 ierr = DMGetCoordinatesLocal(dmB, &coordsB);CHKERRQ(ierr); 2342 ierr = PetscObjectReference((PetscObject) coordsA);CHKERRQ(ierr); 2343 ierr = DMSetCoordinatesLocal(dmA, coordsB);CHKERRQ(ierr); 2344 ierr = DMSetCoordinatesLocal(dmB, coordsA);CHKERRQ(ierr); 2345 ierr = PetscObjectDereference((PetscObject) coordsA);CHKERRQ(ierr); 2346 2347 tmp = dmA->data; 2348 dmA->data = dmB->data; 2349 dmB->data = tmp; 2350 listTmp = dmA->labels; 2351 dmA->labels = dmB->labels; 2352 dmB->labels = listTmp; 2353 depthTmp = dmA->depthLabel; 2354 dmA->depthLabel = dmB->depthLabel; 2355 dmB->depthLabel = depthTmp; 2356 depthTmp = dmA->celltypeLabel; 2357 dmA->celltypeLabel = dmB->celltypeLabel; 2358 dmB->celltypeLabel = depthTmp; 2359 tmpI = dmA->levelup; 2360 dmA->levelup = dmB->levelup; 2361 dmB->levelup = tmpI; 2362 PetscFunctionReturn(0); 2363 } 2364 2365 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 2366 { 2367 DM_Plex *mesh = (DM_Plex*) dm->data; 2368 PetscBool flg; 2369 PetscErrorCode ierr; 2370 2371 PetscFunctionBegin; 2372 /* Handle viewing */ 2373 ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); 2374 ierr = PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL,0);CHKERRQ(ierr); 2375 ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL);CHKERRQ(ierr); 2376 ierr = PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL,0);CHKERRQ(ierr); 2377 ierr = DMMonitorSetFromOptions(dm, "-dm_plex_monitor_throughput", "Monitor the simulation throughput", "DMPlexMonitorThroughput", DMPlexMonitorThroughput, NULL, &flg);CHKERRQ(ierr); 2378 if (flg) {ierr = PetscLogDefaultBegin();CHKERRQ(ierr);} 2379 /* Point Location */ 2380 ierr = PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL);CHKERRQ(ierr); 2381 /* Partitioning and distribution */ 2382 ierr = PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL);CHKERRQ(ierr); 2383 /* Generation and remeshing */ 2384 ierr = PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL);CHKERRQ(ierr); 2385 /* Projection behavior */ 2386 ierr = PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL,0);CHKERRQ(ierr); 2387 ierr = PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);CHKERRQ(ierr); 2388 ierr = PetscOptionsEnum("-dm_plex_cell_refiner", "Strategy for cell refinment", "ex40.c", DMPlexCellRefinerTypes, (PetscEnum) mesh->cellRefiner, (PetscEnum *) &mesh->cellRefiner, NULL);CHKERRQ(ierr); 2389 /* Checking structure */ 2390 { 2391 PetscBool flg = PETSC_FALSE, flg2 = PETSC_FALSE, all = PETSC_FALSE; 2392 2393 ierr = PetscOptionsBool("-dm_plex_check_all", "Perform all checks", NULL, PETSC_FALSE, &all, &flg2);CHKERRQ(ierr); 2394 ierr = PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2395 if (all || (flg && flg2)) {ierr = DMPlexCheckSymmetry(dm);CHKERRQ(ierr);} 2396 ierr = PetscOptionsBool("-dm_plex_check_skeleton", "Check that each cell has the correct number of vertices (only for homogeneous simplex or tensor meshes)", "DMPlexCheckSkeleton", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2397 if (all || (flg && flg2)) {ierr = DMPlexCheckSkeleton(dm, 0);CHKERRQ(ierr);} 2398 ierr = PetscOptionsBool("-dm_plex_check_faces", "Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type", "DMPlexCheckFaces", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2399 if (all || (flg && flg2)) {ierr = DMPlexCheckFaces(dm, 0);CHKERRQ(ierr);} 2400 ierr = PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2401 if (all || (flg && flg2)) {ierr = DMPlexCheckGeometry(dm);CHKERRQ(ierr);} 2402 ierr = PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2403 if (all || (flg && flg2)) {ierr = DMPlexCheckPointSF(dm);CHKERRQ(ierr);} 2404 ierr = PetscOptionsBool("-dm_plex_check_interface_cones", "Check points on inter-partition interfaces have conforming order of cone points", "DMPlexCheckInterfaceCones", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2405 if (all || (flg && flg2)) {ierr = DMPlexCheckInterfaceCones(dm);CHKERRQ(ierr);} 2406 ierr = PetscOptionsBool("-dm_plex_check_cell_shape", "Check cell shape", "DMPlexCheckCellShape", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2407 if (flg && flg2) {ierr = DMPlexCheckCellShape(dm, PETSC_TRUE, PETSC_DETERMINE);CHKERRQ(ierr);} 2408 } 2409 2410 ierr = PetscPartitionerSetFromOptions(mesh->partitioner);CHKERRQ(ierr); 2411 PetscFunctionReturn(0); 2412 } 2413 2414 static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 2415 { 2416 PetscInt refine = 0, coarsen = 0, r; 2417 PetscBool isHierarchy; 2418 PetscErrorCode ierr; 2419 2420 PetscFunctionBegin; 2421 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2422 ierr = PetscOptionsHead(PetscOptionsObject,"DMPlex Options");CHKERRQ(ierr); 2423 /* Handle DMPlex refinement */ 2424 ierr = PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL,0);CHKERRQ(ierr); 2425 ierr = PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy,0);CHKERRQ(ierr); 2426 if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 2427 if (refine && isHierarchy) { 2428 DM *dms, coarseDM; 2429 2430 ierr = DMGetCoarseDM(dm, &coarseDM);CHKERRQ(ierr); 2431 ierr = PetscObjectReference((PetscObject)coarseDM);CHKERRQ(ierr); 2432 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 2433 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 2434 /* Total hack since we do not pass in a pointer */ 2435 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 2436 if (refine == 1) { 2437 ierr = DMSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 2438 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2439 } else { 2440 ierr = DMSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 2441 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2442 ierr = DMSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 2443 ierr = DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);CHKERRQ(ierr); 2444 } 2445 ierr = DMSetCoarseDM(dms[refine-1], coarseDM);CHKERRQ(ierr); 2446 ierr = PetscObjectDereference((PetscObject)coarseDM);CHKERRQ(ierr); 2447 /* Free DMs */ 2448 for (r = 0; r < refine; ++r) { 2449 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2450 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2451 } 2452 ierr = PetscFree(dms);CHKERRQ(ierr); 2453 } else { 2454 for (r = 0; r < refine; ++r) { 2455 DM refinedMesh; 2456 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 2457 2458 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2459 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);CHKERRQ(ierr); 2460 /* Total hack since we do not pass in a pointer */ 2461 ierr = DMPlexReplace_Static(dm, refinedMesh);CHKERRQ(ierr); 2462 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2463 if (coordFunc) { 2464 ierr = DMPlexRemapGeometry(dm, 0.0, coordFunc);CHKERRQ(ierr); 2465 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 2466 } 2467 ierr = DMDestroy(&refinedMesh);CHKERRQ(ierr); 2468 } 2469 } 2470 /* Handle DMPlex coarsening */ 2471 ierr = PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL,0);CHKERRQ(ierr); 2472 ierr = PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy,0);CHKERRQ(ierr); 2473 if (coarsen && isHierarchy) { 2474 DM *dms; 2475 2476 ierr = PetscMalloc1(coarsen, &dms);CHKERRQ(ierr); 2477 ierr = DMCoarsenHierarchy(dm, coarsen, dms);CHKERRQ(ierr); 2478 /* Free DMs */ 2479 for (r = 0; r < coarsen; ++r) { 2480 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2481 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2482 } 2483 ierr = PetscFree(dms);CHKERRQ(ierr); 2484 } else { 2485 for (r = 0; r < coarsen; ++r) { 2486 DM coarseMesh; 2487 2488 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2489 ierr = DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);CHKERRQ(ierr); 2490 /* Total hack since we do not pass in a pointer */ 2491 ierr = DMPlexReplace_Static(dm, coarseMesh);CHKERRQ(ierr); 2492 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2493 ierr = DMDestroy(&coarseMesh);CHKERRQ(ierr); 2494 } 2495 } 2496 /* Handle */ 2497 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2498 ierr = PetscOptionsTail();CHKERRQ(ierr); 2499 PetscFunctionReturn(0); 2500 } 2501 2502 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 2503 { 2504 PetscErrorCode ierr; 2505 2506 PetscFunctionBegin; 2507 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2508 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 2509 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 2510 ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); 2511 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 2512 ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); 2513 PetscFunctionReturn(0); 2514 } 2515 2516 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 2517 { 2518 PetscErrorCode ierr; 2519 2520 PetscFunctionBegin; 2521 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2522 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 2523 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 2524 PetscFunctionReturn(0); 2525 } 2526 2527 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 2528 { 2529 PetscInt depth, d; 2530 PetscErrorCode ierr; 2531 2532 PetscFunctionBegin; 2533 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2534 if (depth == 1) { 2535 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 2536 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 2537 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 2538 else {*pStart = 0; *pEnd = 0;} 2539 } else { 2540 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 2541 } 2542 PetscFunctionReturn(0); 2543 } 2544 2545 static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 2546 { 2547 PetscSF sf; 2548 PetscInt niranks, njranks, n; 2549 const PetscMPIInt *iranks, *jranks; 2550 DM_Plex *data = (DM_Plex*) dm->data; 2551 PetscErrorCode ierr; 2552 2553 PetscFunctionBegin; 2554 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 2555 if (!data->neighbors) { 2556 ierr = PetscSFGetRootRanks(sf, &njranks, &jranks, NULL, NULL, NULL);CHKERRQ(ierr); 2557 ierr = PetscSFGetLeafRanks(sf, &niranks, &iranks, NULL, NULL);CHKERRQ(ierr); 2558 ierr = PetscMalloc1(njranks + niranks + 1, &data->neighbors);CHKERRQ(ierr); 2559 ierr = PetscArraycpy(data->neighbors + 1, jranks, njranks);CHKERRQ(ierr); 2560 ierr = PetscArraycpy(data->neighbors + njranks + 1, iranks, niranks);CHKERRQ(ierr); 2561 n = njranks + niranks; 2562 ierr = PetscSortRemoveDupsMPIInt(&n, data->neighbors + 1);CHKERRQ(ierr); 2563 /* The following cast should never fail: can't have more neighbors than PETSC_MPI_INT_MAX */ 2564 ierr = PetscMPIIntCast(n, data->neighbors);CHKERRQ(ierr); 2565 } 2566 if (nranks) *nranks = data->neighbors[0]; 2567 if (ranks) { 2568 if (data->neighbors[0]) *ranks = data->neighbors + 1; 2569 else *ranks = NULL; 2570 } 2571 PetscFunctionReturn(0); 2572 } 2573 2574 static PetscErrorCode DMInitialize_Plex(DM dm) 2575 { 2576 PetscErrorCode ierr; 2577 2578 PetscFunctionBegin; 2579 dm->ops->view = DMView_Plex; 2580 dm->ops->load = DMLoad_Plex; 2581 dm->ops->setfromoptions = DMSetFromOptions_Plex; 2582 dm->ops->clone = DMClone_Plex; 2583 dm->ops->setup = DMSetUp_Plex; 2584 dm->ops->createlocalsection = DMCreateLocalSection_Plex; 2585 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 2586 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 2587 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 2588 dm->ops->getlocaltoglobalmapping = NULL; 2589 dm->ops->createfieldis = NULL; 2590 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 2591 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 2592 dm->ops->getcoloring = NULL; 2593 dm->ops->creatematrix = DMCreateMatrix_Plex; 2594 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 2595 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 2596 dm->ops->createinjection = DMCreateInjection_Plex; 2597 dm->ops->refine = DMRefine_Plex; 2598 dm->ops->coarsen = DMCoarsen_Plex; 2599 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 2600 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 2601 dm->ops->adaptlabel = DMAdaptLabel_Plex; 2602 dm->ops->adaptmetric = DMAdaptMetric_Plex; 2603 dm->ops->globaltolocalbegin = NULL; 2604 dm->ops->globaltolocalend = NULL; 2605 dm->ops->localtoglobalbegin = NULL; 2606 dm->ops->localtoglobalend = NULL; 2607 dm->ops->destroy = DMDestroy_Plex; 2608 dm->ops->createsubdm = DMCreateSubDM_Plex; 2609 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 2610 dm->ops->getdimpoints = DMGetDimPoints_Plex; 2611 dm->ops->locatepoints = DMLocatePoints_Plex; 2612 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 2613 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 2614 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 2615 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 2616 dm->ops->projectbdfieldlabellocal = DMProjectBdFieldLabelLocal_Plex; 2617 dm->ops->computel2diff = DMComputeL2Diff_Plex; 2618 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 2619 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 2620 dm->ops->getneighbors = DMGetNeighbors_Plex; 2621 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);CHKERRQ(ierr); 2622 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);CHKERRQ(ierr); 2623 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C",DMCreateNeumannOverlap_Plex);CHKERRQ(ierr); 2624 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex);CHKERRQ(ierr); 2625 PetscFunctionReturn(0); 2626 } 2627 2628 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 2629 { 2630 DM_Plex *mesh = (DM_Plex *) dm->data; 2631 PetscErrorCode ierr; 2632 2633 PetscFunctionBegin; 2634 mesh->refct++; 2635 (*newdm)->data = mesh; 2636 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 2637 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 2638 PetscFunctionReturn(0); 2639 } 2640 2641 /*MC 2642 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 2643 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 2644 specified by a PetscSection object. Ownership in the global representation is determined by 2645 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 2646 2647 Options Database Keys: 2648 + -dm_plex_hash_location - Use grid hashing for point location 2649 . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes 2650 . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing 2651 . -dm_plex_max_projection_height - Maxmimum mesh point height used to project locally 2652 . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement 2653 . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric 2654 . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices 2655 . -dm_plex_check_faces <celltype> - Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type 2656 . -dm_plex_check_geometry - Check that cells have positive volume 2657 . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ 2658 . -dm_plex_view_scale <num> - Scale the TikZ 2659 - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices 2660 2661 2662 Level: intermediate 2663 2664 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 2665 M*/ 2666 2667 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 2668 { 2669 DM_Plex *mesh; 2670 PetscInt unit; 2671 PetscErrorCode ierr; 2672 2673 PetscFunctionBegin; 2674 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2675 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 2676 dm->dim = 0; 2677 dm->data = mesh; 2678 2679 mesh->refct = 1; 2680 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 2681 mesh->maxConeSize = 0; 2682 mesh->cones = NULL; 2683 mesh->coneOrientations = NULL; 2684 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 2685 mesh->maxSupportSize = 0; 2686 mesh->supports = NULL; 2687 mesh->refinementUniform = PETSC_TRUE; 2688 mesh->refinementLimit = -1.0; 2689 mesh->interpolated = DMPLEX_INTERPOLATED_INVALID; 2690 mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID; 2691 2692 mesh->facesTmp = NULL; 2693 2694 mesh->tetgenOpts = NULL; 2695 mesh->triangleOpts = NULL; 2696 ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); 2697 mesh->remeshBd = PETSC_FALSE; 2698 2699 mesh->subpointMap = NULL; 2700 2701 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 2702 2703 mesh->regularRefinement = PETSC_FALSE; 2704 mesh->depthState = -1; 2705 mesh->celltypeState = -1; 2706 mesh->globalVertexNumbers = NULL; 2707 mesh->globalCellNumbers = NULL; 2708 mesh->anchorSection = NULL; 2709 mesh->anchorIS = NULL; 2710 mesh->createanchors = NULL; 2711 mesh->computeanchormatrix = NULL; 2712 mesh->parentSection = NULL; 2713 mesh->parents = NULL; 2714 mesh->childIDs = NULL; 2715 mesh->childSection = NULL; 2716 mesh->children = NULL; 2717 mesh->referenceTree = NULL; 2718 mesh->getchildsymmetry = NULL; 2719 mesh->vtkCellHeight = 0; 2720 mesh->useAnchors = PETSC_FALSE; 2721 2722 mesh->maxProjectionHeight = 0; 2723 2724 mesh->neighbors = NULL; 2725 2726 mesh->printSetValues = PETSC_FALSE; 2727 mesh->printFEM = 0; 2728 mesh->printTol = 1.0e-10; 2729 2730 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 2731 PetscFunctionReturn(0); 2732 } 2733 2734 /*@ 2735 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 2736 2737 Collective 2738 2739 Input Parameter: 2740 . comm - The communicator for the DMPlex object 2741 2742 Output Parameter: 2743 . mesh - The DMPlex object 2744 2745 Level: beginner 2746 2747 @*/ 2748 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 2749 { 2750 PetscErrorCode ierr; 2751 2752 PetscFunctionBegin; 2753 PetscValidPointer(mesh,2); 2754 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 2755 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 2756 PetscFunctionReturn(0); 2757 } 2758 2759 static PetscErrorCode DMPlexInvertCell_Internal(PetscInt dim, PetscInt numCorners, PetscInt cone[]) 2760 { 2761 PetscErrorCode ierr; 2762 2763 PetscFunctionBegin; 2764 if (dim != 3) PetscFunctionReturn(0); 2765 switch (numCorners) { 2766 case 4: ierr = DMPlexInvertCell(DM_POLYTOPE_TETRAHEDRON,cone);CHKERRQ(ierr); break; 2767 case 6: ierr = DMPlexInvertCell(DM_POLYTOPE_TRI_PRISM,cone);CHKERRQ(ierr); break; 2768 case 8: ierr = DMPlexInvertCell(DM_POLYTOPE_HEXAHEDRON,cone);CHKERRQ(ierr); break; 2769 default: break; 2770 } 2771 PetscFunctionReturn(0); 2772 } 2773 2774 /* 2775 This takes as input the common mesh generator output, a list of the vertices for each cell, but vertex numbers are global and an SF is built for them 2776 */ 2777 /* TODO: invertCells and spaceDim arguments could be added also to to DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellList_Internal() and DMPlexCreateFromCellListPetsc() */ 2778 PetscErrorCode DMPlexBuildFromCellList_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[], PetscBool invertCells, PetscSF *sfVert) 2779 { 2780 PetscSF sfPoint; 2781 PetscLayout vLayout; 2782 PetscHSetI vhash; 2783 PetscSFNode *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex; 2784 const PetscInt *vrange; 2785 PetscInt numVerticesAdj, off = 0, *verticesAdj, numVerticesGhost = 0, *localVertex, *cone, c, p, v, g; 2786 PetscMPIInt rank, size; 2787 PetscErrorCode ierr; 2788 2789 PetscFunctionBegin; 2790 ierr = PetscLogEventBegin(DMPLEX_CreateFromCellList,dm,0,0,0);CHKERRQ(ierr); 2791 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 2792 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); 2793 /* Partition vertices */ 2794 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);CHKERRQ(ierr); 2795 ierr = PetscLayoutSetLocalSize(vLayout, numVertices);CHKERRQ(ierr); 2796 ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr); 2797 ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr); 2798 ierr = PetscLayoutGetRanges(vLayout, &vrange);CHKERRQ(ierr); 2799 /* Count vertices and map them to procs */ 2800 ierr = PetscHSetICreate(&vhash);CHKERRQ(ierr); 2801 for (c = 0; c < numCells; ++c) { 2802 for (p = 0; p < numCorners; ++p) { 2803 ierr = PetscHSetIAdd(vhash, cells[c*numCorners+p]);CHKERRQ(ierr); 2804 } 2805 } 2806 ierr = PetscHSetIGetSize(vhash, &numVerticesAdj);CHKERRQ(ierr); 2807 ierr = PetscMalloc1(numVerticesAdj, &verticesAdj);CHKERRQ(ierr); 2808 ierr = PetscHSetIGetElems(vhash, &off, verticesAdj);CHKERRQ(ierr); 2809 ierr = PetscHSetIDestroy(&vhash);CHKERRQ(ierr); 2810 if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj); 2811 ierr = PetscSortInt(numVerticesAdj, verticesAdj);CHKERRQ(ierr); 2812 ierr = PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);CHKERRQ(ierr); 2813 for (v = 0; v < numVerticesAdj; ++v) { 2814 const PetscInt gv = verticesAdj[v]; 2815 PetscInt vrank; 2816 2817 ierr = PetscFindInt(gv, size+1, vrange, &vrank);CHKERRQ(ierr); 2818 vrank = vrank < 0 ? -(vrank+2) : vrank; 2819 remoteVerticesAdj[v].index = gv - vrange[vrank]; 2820 remoteVerticesAdj[v].rank = vrank; 2821 } 2822 /* Create cones */ 2823 ierr = DMPlexSetChart(dm, 0, numCells+numVerticesAdj);CHKERRQ(ierr); 2824 for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);} 2825 ierr = DMSetUp(dm);CHKERRQ(ierr); 2826 ierr = DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2827 for (c = 0; c < numCells; ++c) { 2828 for (p = 0; p < numCorners; ++p) { 2829 const PetscInt gv = cells[c*numCorners+p]; 2830 PetscInt lv; 2831 2832 ierr = PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);CHKERRQ(ierr); 2833 if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv); 2834 cone[p] = lv+numCells; 2835 } 2836 if (invertCells) { ierr = DMPlexInvertCell_Internal(spaceDim, numCorners, cone);CHKERRQ(ierr); } 2837 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 2838 } 2839 ierr = DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2840 /* Create SF for vertices */ 2841 ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfVert);CHKERRQ(ierr); 2842 ierr = PetscObjectSetName((PetscObject) *sfVert, "Vertex Ownership SF");CHKERRQ(ierr); 2843 ierr = PetscSFSetFromOptions(*sfVert);CHKERRQ(ierr); 2844 ierr = PetscSFSetGraph(*sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);CHKERRQ(ierr); 2845 ierr = PetscFree(verticesAdj);CHKERRQ(ierr); 2846 /* Build pointSF */ 2847 ierr = PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);CHKERRQ(ierr); 2848 for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;} 2849 for (v = 0; v < numVertices; ++v) {vertexOwner[v].index = -1; vertexOwner[v].rank = -1;} 2850 ierr = PetscSFReduceBegin(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 2851 ierr = PetscSFReduceEnd(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 2852 for (v = 0; v < numVertices; ++v) if (vertexOwner[v].rank < 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Global vertex %d on rank %d was unclaimed", v + vrange[rank], rank); 2853 ierr = PetscSFBcastBegin(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 2854 ierr = PetscSFBcastEnd(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 2855 for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost; 2856 ierr = PetscMalloc1(numVerticesGhost, &localVertex);CHKERRQ(ierr); 2857 ierr = PetscMalloc1(numVerticesGhost, &remoteVertex);CHKERRQ(ierr); 2858 for (v = 0, g = 0; v < numVerticesAdj; ++v) { 2859 if (vertexLocal[v].rank != rank) { 2860 localVertex[g] = v+numCells; 2861 remoteVertex[g].index = vertexLocal[v].index; 2862 remoteVertex[g].rank = vertexLocal[v].rank; 2863 ++g; 2864 } 2865 } 2866 ierr = PetscFree2(vertexLocal, vertexOwner);CHKERRQ(ierr); 2867 if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost); 2868 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 2869 ierr = PetscObjectSetName((PetscObject) sfPoint, "point SF");CHKERRQ(ierr); 2870 ierr = PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);CHKERRQ(ierr); 2871 ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr); 2872 /* Fill in the rest of the topology structure */ 2873 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2874 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2875 ierr = PetscLogEventEnd(DMPLEX_CreateFromCellList,dm,0,0,0);CHKERRQ(ierr); 2876 PetscFunctionReturn(0); 2877 } 2878 2879 /* 2880 This takes as input the coordinates for each owned vertex 2881 */ 2882 PetscErrorCode DMPlexBuildCoordinates_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numV, PetscSF sfVert, const PetscReal vertexCoords[]) 2883 { 2884 PetscSection coordSection; 2885 Vec coordinates; 2886 PetscScalar *coords; 2887 PetscInt numVertices, numVerticesAdj, coordSize, v; 2888 PetscErrorCode ierr; 2889 2890 PetscFunctionBegin; 2891 ierr = PetscLogEventBegin(DMPLEX_CreateFromCellList_Coordinates,dm,0,0,0);CHKERRQ(ierr); 2892 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 2893 ierr = PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);CHKERRQ(ierr); 2894 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2895 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2896 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 2897 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVerticesAdj);CHKERRQ(ierr); 2898 for (v = numCells; v < numCells+numVerticesAdj; ++v) { 2899 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 2900 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 2901 } 2902 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2903 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2904 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 2905 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 2906 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2907 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2908 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2909 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2910 { 2911 MPI_Datatype coordtype; 2912 2913 /* Need a temp buffer for coords if we have complex/single */ 2914 ierr = MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);CHKERRQ(ierr); 2915 ierr = MPI_Type_commit(&coordtype);CHKERRQ(ierr); 2916 #if defined(PETSC_USE_COMPLEX) 2917 { 2918 PetscScalar *svertexCoords; 2919 PetscInt i; 2920 ierr = PetscMalloc1(numV*spaceDim,&svertexCoords);CHKERRQ(ierr); 2921 for (i=0; i<numV*spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 2922 ierr = PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 2923 ierr = PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 2924 ierr = PetscFree(svertexCoords);CHKERRQ(ierr); 2925 } 2926 #else 2927 ierr = PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 2928 ierr = PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 2929 #endif 2930 ierr = MPI_Type_free(&coordtype);CHKERRQ(ierr); 2931 } 2932 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2933 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2934 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2935 ierr = PetscLogEventEnd(DMPLEX_CreateFromCellList_Coordinates,dm,0,0,0);CHKERRQ(ierr); 2936 PetscFunctionReturn(0); 2937 } 2938 2939 /*@ 2940 DMPlexCreateFromCellListParallelPetsc - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 2941 2942 Input Parameters: 2943 + comm - The communicator 2944 . dim - The topological dimension of the mesh 2945 . numCells - The number of cells owned by this process 2946 . numVertices - The number of vertices owned by this process 2947 . numCorners - The number of vertices for each cell 2948 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 2949 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 2950 . spaceDim - The spatial dimension used for coordinates 2951 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2952 2953 Output Parameter: 2954 + dm - The DM 2955 - vertexSF - Optional, SF describing complete vertex ownership 2956 2957 Note: Two triangles sharing a face 2958 $ 2959 $ 2 2960 $ / | \ 2961 $ / | \ 2962 $ / | \ 2963 $ 0 0 | 1 3 2964 $ \ | / 2965 $ \ | / 2966 $ \ | / 2967 $ 1 2968 would have input 2969 $ numCells = 2, numVertices = 4 2970 $ cells = [0 1 2 1 3 2] 2971 $ 2972 which would result in the DMPlex 2973 $ 2974 $ 4 2975 $ / | \ 2976 $ / | \ 2977 $ / | \ 2978 $ 2 0 | 1 5 2979 $ \ | / 2980 $ \ | / 2981 $ \ | / 2982 $ 3 2983 2984 Level: beginner 2985 2986 .seealso: DMPlexCreateFromCellListPetsc(), DMPlexCreateFromDAG(), DMPlexCreate() 2987 @*/ 2988 PetscErrorCode DMPlexCreateFromCellListParallelPetsc(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, PetscBool interpolate, const PetscInt cells[], PetscInt spaceDim, const PetscReal vertexCoords[], PetscSF *vertexSF, DM *dm) 2989 { 2990 PetscSF sfVert; 2991 PetscErrorCode ierr; 2992 2993 PetscFunctionBegin; 2994 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2995 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2996 PetscValidLogicalCollectiveInt(*dm, dim, 2); 2997 PetscValidLogicalCollectiveInt(*dm, spaceDim, 8); 2998 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 2999 ierr = DMPlexBuildFromCellList_Parallel_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE, &sfVert);CHKERRQ(ierr); 3000 if (interpolate) { 3001 DM idm; 3002 3003 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3004 ierr = DMDestroy(dm);CHKERRQ(ierr); 3005 *dm = idm; 3006 } 3007 ierr = DMPlexBuildCoordinates_Parallel_Internal(*dm, spaceDim, numCells, numVertices, sfVert, vertexCoords);CHKERRQ(ierr); 3008 if (vertexSF) *vertexSF = sfVert; 3009 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 3010 PetscFunctionReturn(0); 3011 } 3012 3013 3014 /*@ 3015 DMPlexCreateFromCellListParallel - Deprecated, use DMPlexCreateFromCellListParallelPetsc() 3016 3017 Level: deprecated 3018 3019 .seealso: DMPlexCreateFromCellListParallelPetsc() 3020 @*/ 3021 PetscErrorCode DMPlexCreateFromCellListParallel(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, PetscBool interpolate, const int cells[], PetscInt spaceDim, const PetscReal vertexCoords[], PetscSF *vertexSF, DM *dm) 3022 { 3023 PetscErrorCode ierr; 3024 PetscInt i; 3025 PetscInt *pintCells; 3026 3027 PetscFunctionBegin; 3028 if (sizeof(int) > sizeof(PetscInt)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Size of int %zd greater than size of PetscInt %zd. Reconfigure PETSc --with-64-bit-indices=1", sizeof(int), sizeof(PetscInt)); 3029 if (sizeof(int) == sizeof(PetscInt)) { 3030 pintCells = (PetscInt *) cells; 3031 } else { 3032 ierr = PetscMalloc1(numCells*numCorners, &pintCells);CHKERRQ(ierr); 3033 for (i = 0; i < numCells*numCorners; i++) { 3034 pintCells[i] = (PetscInt) cells[i]; 3035 } 3036 } 3037 ierr = DMPlexCreateFromCellListParallelPetsc(comm, dim, numCells, numVertices, numCorners, interpolate, pintCells, spaceDim, vertexCoords, vertexSF, dm);CHKERRQ(ierr); 3038 if (sizeof(int) != sizeof(PetscInt)) { 3039 ierr = PetscFree(pintCells);CHKERRQ(ierr); 3040 } 3041 PetscFunctionReturn(0); 3042 } 3043 3044 /* 3045 This takes as input the common mesh generator output, a list of the vertices for each cell 3046 */ 3047 PetscErrorCode DMPlexBuildFromCellList_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[], PetscBool invertCells) 3048 { 3049 PetscInt *cone, c, p; 3050 PetscErrorCode ierr; 3051 3052 PetscFunctionBegin; 3053 ierr = PetscLogEventBegin(DMPLEX_CreateFromCellList,dm,0,0,0);CHKERRQ(ierr); 3054 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 3055 for (c = 0; c < numCells; ++c) { 3056 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 3057 } 3058 ierr = DMSetUp(dm);CHKERRQ(ierr); 3059 ierr = DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 3060 for (c = 0; c < numCells; ++c) { 3061 for (p = 0; p < numCorners; ++p) { 3062 cone[p] = cells[c*numCorners+p]+numCells; 3063 } 3064 if (invertCells) { ierr = DMPlexInvertCell_Internal(spaceDim, numCorners, cone);CHKERRQ(ierr); } 3065 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 3066 } 3067 ierr = DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 3068 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3069 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3070 ierr = PetscLogEventEnd(DMPLEX_CreateFromCellList,dm,0,0,0);CHKERRQ(ierr); 3071 PetscFunctionReturn(0); 3072 } 3073 3074 /* 3075 This takes as input the coordinates for each vertex 3076 */ 3077 PetscErrorCode DMPlexBuildCoordinates_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const PetscReal vertexCoords[]) 3078 { 3079 PetscSection coordSection; 3080 Vec coordinates; 3081 DM cdm; 3082 PetscScalar *coords; 3083 PetscInt v, d; 3084 PetscErrorCode ierr; 3085 3086 PetscFunctionBegin; 3087 ierr = PetscLogEventBegin(DMPLEX_CreateFromCellList_Coordinates,dm,0,0,0);CHKERRQ(ierr); 3088 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 3089 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3090 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3091 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 3092 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); 3093 for (v = numCells; v < numCells+numVertices; ++v) { 3094 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 3095 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 3096 } 3097 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3098 3099 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 3100 ierr = DMCreateLocalVector(cdm, &coordinates);CHKERRQ(ierr); 3101 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 3102 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3103 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3104 for (v = 0; v < numVertices; ++v) { 3105 for (d = 0; d < spaceDim; ++d) { 3106 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 3107 } 3108 } 3109 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3110 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3111 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3112 ierr = PetscLogEventEnd(DMPLEX_CreateFromCellList_Coordinates,dm,0,0,0);CHKERRQ(ierr); 3113 PetscFunctionReturn(0); 3114 } 3115 3116 /*@ 3117 DMPlexCreateFromCellListPetsc - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 3118 3119 Input Parameters: 3120 + comm - The communicator 3121 . dim - The topological dimension of the mesh 3122 . numCells - The number of cells 3123 . numVertices - The number of vertices 3124 . numCorners - The number of vertices for each cell 3125 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 3126 . cells - An array of numCells*numCorners numbers, the vertices for each cell 3127 . spaceDim - The spatial dimension used for coordinates 3128 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3129 3130 Output Parameter: 3131 . dm - The DM 3132 3133 Note: Two triangles sharing a face 3134 $ 3135 $ 2 3136 $ / | \ 3137 $ / | \ 3138 $ / | \ 3139 $ 0 0 | 1 3 3140 $ \ | / 3141 $ \ | / 3142 $ \ | / 3143 $ 1 3144 would have input 3145 $ numCells = 2, numVertices = 4 3146 $ cells = [0 1 2 1 3 2] 3147 $ 3148 which would result in the DMPlex 3149 $ 3150 $ 4 3151 $ / | \ 3152 $ / | \ 3153 $ / | \ 3154 $ 2 0 | 1 5 3155 $ \ | / 3156 $ \ | / 3157 $ \ | / 3158 $ 3 3159 3160 Level: beginner 3161 3162 .seealso: DMPlexCreateFromDAG(), DMPlexCreate() 3163 @*/ 3164 PetscErrorCode DMPlexCreateFromCellListPetsc(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, PetscBool interpolate, const PetscInt cells[], PetscInt spaceDim, const PetscReal vertexCoords[], DM *dm) 3165 { 3166 PetscErrorCode ierr; 3167 3168 PetscFunctionBegin; 3169 if (!dim) SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "This is not appropriate for 0-dimensional meshes. Consider either creating the DM using DMPlexCreateFromDAG(), by hand, or using DMSwarm."); 3170 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3171 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3172 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3173 ierr = DMPlexBuildFromCellList_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE);CHKERRQ(ierr); 3174 if (interpolate) { 3175 DM idm; 3176 3177 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3178 ierr = DMDestroy(dm);CHKERRQ(ierr); 3179 *dm = idm; 3180 } 3181 ierr = DMPlexBuildCoordinates_Internal(*dm, spaceDim, numCells, numVertices, vertexCoords);CHKERRQ(ierr); 3182 PetscFunctionReturn(0); 3183 } 3184 3185 /*@ 3186 DMPlexCreateFromCellList - Deprecated, use DMPlexCreateFromCellListPetsc() 3187 3188 Level: deprecated 3189 3190 .seealso: DMPlexCreateFromCellListPetsc() 3191 @*/ 3192 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) 3193 { 3194 PetscErrorCode ierr; 3195 PetscInt i; 3196 PetscInt *pintCells; 3197 PetscReal *prealVC; 3198 3199 PetscFunctionBegin; 3200 if (sizeof(int) > sizeof(PetscInt)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Size of int %zd greater than size of PetscInt %zd. Reconfigure PETSc --with-64-bit-indices=1", sizeof(int), sizeof(PetscInt)); 3201 if (sizeof(int) == sizeof(PetscInt)) { 3202 pintCells = (PetscInt *) cells; 3203 } else { 3204 ierr = PetscMalloc1(numCells*numCorners, &pintCells);CHKERRQ(ierr); 3205 for (i = 0; i < numCells*numCorners; i++) { 3206 pintCells[i] = (PetscInt) cells[i]; 3207 } 3208 } 3209 if (sizeof(double) > sizeof(PetscReal)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Size of double %zd greater than size of PetscReal %zd. Reconfigure PETSc --with-precision=<higher precision>.", sizeof(double), sizeof(PetscReal)); 3210 if (sizeof(double) == sizeof(PetscReal)) { 3211 prealVC = (PetscReal *) vertexCoords; 3212 } else { 3213 ierr = PetscMalloc1(numVertices*spaceDim, &prealVC);CHKERRQ(ierr); 3214 for (i = 0; i < numVertices*spaceDim; i++) { 3215 prealVC[i] = (PetscReal) vertexCoords[i]; 3216 } 3217 } 3218 ierr = DMPlexCreateFromCellListPetsc(comm, dim, numCells, numVertices, numCorners, interpolate, pintCells, spaceDim, prealVC, dm);CHKERRQ(ierr); 3219 if (sizeof(int) != sizeof(PetscInt)) { 3220 ierr = PetscFree(pintCells);CHKERRQ(ierr); 3221 } 3222 if (sizeof(double) != sizeof(PetscReal)) { 3223 ierr = PetscFree(prealVC);CHKERRQ(ierr); 3224 } 3225 PetscFunctionReturn(0); 3226 } 3227 3228 /*@ 3229 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 3230 3231 Input Parameters: 3232 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 3233 . depth - The depth of the DAG 3234 . numPoints - Array of size depth + 1 containing the number of points at each depth 3235 . coneSize - The cone size of each point 3236 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 3237 . coneOrientations - The orientation of each cone point 3238 - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim() 3239 3240 Output Parameter: 3241 . dm - The DM 3242 3243 Note: Two triangles sharing a face would have input 3244 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 3245 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 3246 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 3247 $ 3248 which would result in the DMPlex 3249 $ 3250 $ 4 3251 $ / | \ 3252 $ / | \ 3253 $ / | \ 3254 $ 2 0 | 1 5 3255 $ \ | / 3256 $ \ | / 3257 $ \ | / 3258 $ 3 3259 $ 3260 $ Notice that all points are numbered consecutively, unlike DMPlexCreateFromCellListPetsc() 3261 3262 Level: advanced 3263 3264 .seealso: DMPlexCreateFromCellListPetsc(), DMPlexCreate() 3265 @*/ 3266 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 3267 { 3268 Vec coordinates; 3269 PetscSection coordSection; 3270 PetscScalar *coords; 3271 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 3272 PetscErrorCode ierr; 3273 3274 PetscFunctionBegin; 3275 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3276 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 3277 if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %d cannot be less than intrinsic dimension %d",dimEmbed,dim); 3278 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 3279 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 3280 for (p = pStart; p < pEnd; ++p) { 3281 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 3282 if (firstVertex < 0 && !coneSize[p - pStart]) { 3283 firstVertex = p - pStart; 3284 } 3285 } 3286 if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %d vertices but could not find any", numPoints[0]); 3287 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 3288 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 3289 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 3290 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 3291 } 3292 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3293 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3294 /* Build coordinates */ 3295 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3296 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3297 ierr = PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);CHKERRQ(ierr); 3298 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 3299 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 3300 ierr = PetscSectionSetDof(coordSection, v, dimEmbed);CHKERRQ(ierr); 3301 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);CHKERRQ(ierr); 3302 } 3303 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3304 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3305 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3306 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3307 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3308 ierr = VecSetBlockSize(coordinates, dimEmbed);CHKERRQ(ierr); 3309 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 3310 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3311 for (v = 0; v < numPoints[0]; ++v) { 3312 PetscInt off; 3313 3314 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 3315 for (d = 0; d < dimEmbed; ++d) { 3316 coords[off+d] = vertexCoords[v*dimEmbed+d]; 3317 } 3318 } 3319 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3320 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3321 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3322 PetscFunctionReturn(0); 3323 } 3324 3325 /*@C 3326 DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file. 3327 3328 + comm - The MPI communicator 3329 . filename - Name of the .dat file 3330 - interpolate - Create faces and edges in the mesh 3331 3332 Output Parameter: 3333 . dm - The DM object representing the mesh 3334 3335 Note: The format is the simplest possible: 3336 $ Ne 3337 $ v0 v1 ... vk 3338 $ Nv 3339 $ x y z marker 3340 3341 Level: beginner 3342 3343 .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate() 3344 @*/ 3345 PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3346 { 3347 DMLabel marker; 3348 PetscViewer viewer; 3349 Vec coordinates; 3350 PetscSection coordSection; 3351 PetscScalar *coords; 3352 char line[PETSC_MAX_PATH_LEN]; 3353 PetscInt dim = 3, cdim = 3, coordSize, v, c, d; 3354 PetscMPIInt rank; 3355 int snum, Nv, Nc; 3356 PetscErrorCode ierr; 3357 3358 PetscFunctionBegin; 3359 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 3360 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 3361 ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr); 3362 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 3363 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 3364 if (!rank) { 3365 ierr = PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);CHKERRQ(ierr); 3366 snum = sscanf(line, "%d %d", &Nc, &Nv); 3367 if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3368 } else { 3369 Nc = Nv = 0; 3370 } 3371 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3372 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3373 ierr = DMPlexSetChart(*dm, 0, Nc+Nv);CHKERRQ(ierr); 3374 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3375 ierr = DMSetCoordinateDim(*dm, cdim);CHKERRQ(ierr); 3376 /* Read topology */ 3377 if (!rank) { 3378 PetscInt cone[8], corners = 8; 3379 int vbuf[8], v; 3380 3381 for (c = 0; c < Nc; ++c) {ierr = DMPlexSetConeSize(*dm, c, corners);CHKERRQ(ierr);} 3382 ierr = DMSetUp(*dm);CHKERRQ(ierr); 3383 for (c = 0; c < Nc; ++c) { 3384 ierr = PetscViewerRead(viewer, line, corners, NULL, PETSC_STRING);CHKERRQ(ierr); 3385 snum = sscanf(line, "%d %d %d %d %d %d %d %d", &vbuf[0], &vbuf[1], &vbuf[2], &vbuf[3], &vbuf[4], &vbuf[5], &vbuf[6], &vbuf[7]); 3386 if (snum != corners) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3387 for (v = 0; v < corners; ++v) cone[v] = vbuf[v] + Nc; 3388 /* Hexahedra are inverted */ 3389 { 3390 PetscInt tmp = cone[1]; 3391 cone[1] = cone[3]; 3392 cone[3] = tmp; 3393 } 3394 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 3395 } 3396 } 3397 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 3398 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 3399 /* Read coordinates */ 3400 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 3401 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3402 ierr = PetscSectionSetFieldComponents(coordSection, 0, cdim);CHKERRQ(ierr); 3403 ierr = PetscSectionSetChart(coordSection, Nc, Nc + Nv);CHKERRQ(ierr); 3404 for (v = Nc; v < Nc+Nv; ++v) { 3405 ierr = PetscSectionSetDof(coordSection, v, cdim);CHKERRQ(ierr); 3406 ierr = PetscSectionSetFieldDof(coordSection, v, 0, cdim);CHKERRQ(ierr); 3407 } 3408 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3409 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3410 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3411 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3412 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3413 ierr = VecSetBlockSize(coordinates, cdim);CHKERRQ(ierr); 3414 ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr); 3415 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3416 if (!rank) { 3417 double x[3]; 3418 int val; 3419 3420 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 3421 ierr = DMGetLabel(*dm, "marker", &marker);CHKERRQ(ierr); 3422 for (v = 0; v < Nv; ++v) { 3423 ierr = PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);CHKERRQ(ierr); 3424 snum = sscanf(line, "%lg %lg %lg %d", &x[0], &x[1], &x[2], &val); 3425 if (snum != 4) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3426 for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d]; 3427 if (val) {ierr = DMLabelSetValue(marker, v+Nc, val);CHKERRQ(ierr);} 3428 } 3429 } 3430 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3431 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 3432 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3433 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 3434 if (interpolate) { 3435 DM idm; 3436 DMLabel bdlabel; 3437 3438 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3439 ierr = DMDestroy(dm);CHKERRQ(ierr); 3440 *dm = idm; 3441 3442 ierr = DMGetLabel(*dm, "marker", &bdlabel);CHKERRQ(ierr); 3443 ierr = DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 3444 ierr = DMPlexLabelComplete(*dm, bdlabel);CHKERRQ(ierr); 3445 } 3446 PetscFunctionReturn(0); 3447 } 3448 3449 /*@C 3450 DMPlexCreateFromFile - This takes a filename and produces a DM 3451 3452 Input Parameters: 3453 + comm - The communicator 3454 . filename - A file name 3455 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 3456 3457 Output Parameter: 3458 . dm - The DM 3459 3460 Options Database Keys: 3461 . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5 3462 3463 Use -dm_plex_create_ prefix to pass options to the internal PetscViewer, e.g. 3464 $ -dm_plex_create_viewer_hdf5_collective 3465 3466 Level: beginner 3467 3468 .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellListPetsc(), DMPlexCreate() 3469 @*/ 3470 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3471 { 3472 const char *extGmsh = ".msh"; 3473 const char *extGmsh2 = ".msh2"; 3474 const char *extGmsh4 = ".msh4"; 3475 const char *extCGNS = ".cgns"; 3476 const char *extExodus = ".exo"; 3477 const char *extGenesis = ".gen"; 3478 const char *extFluent = ".cas"; 3479 const char *extHDF5 = ".h5"; 3480 const char *extMed = ".med"; 3481 const char *extPLY = ".ply"; 3482 const char *extCV = ".dat"; 3483 size_t len; 3484 PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isCV; 3485 PetscMPIInt rank; 3486 PetscErrorCode ierr; 3487 3488 PetscFunctionBegin; 3489 PetscValidCharPointer(filename, 2); 3490 PetscValidPointer(dm, 4); 3491 ierr = DMInitializePackage();CHKERRQ(ierr); 3492 ierr = PetscLogEventBegin(DMPLEX_CreateFromFile,0,0,0,0);CHKERRQ(ierr); 3493 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 3494 ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); 3495 if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 3496 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);CHKERRQ(ierr); 3497 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh2, 5, &isGmsh2);CHKERRQ(ierr); 3498 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh4, 5, &isGmsh4);CHKERRQ(ierr); 3499 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);CHKERRQ(ierr); 3500 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);CHKERRQ(ierr); 3501 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);CHKERRQ(ierr); 3502 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);CHKERRQ(ierr); 3503 ierr = PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);CHKERRQ(ierr); 3504 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);CHKERRQ(ierr); 3505 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);CHKERRQ(ierr); 3506 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);CHKERRQ(ierr); 3507 if (isGmsh || isGmsh2 || isGmsh4) { 3508 ierr = DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3509 } else if (isCGNS) { 3510 ierr = DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3511 } else if (isExodus || isGenesis) { 3512 ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3513 } else if (isFluent) { 3514 ierr = DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3515 } else if (isHDF5) { 3516 PetscBool load_hdf5_xdmf = PETSC_FALSE; 3517 PetscViewer viewer; 3518 3519 /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */ 3520 ierr = PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf", 5, &load_hdf5_xdmf);CHKERRQ(ierr); 3521 ierr = PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);CHKERRQ(ierr); 3522 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 3523 ierr = PetscViewerSetType(viewer, PETSCVIEWERHDF5);CHKERRQ(ierr); 3524 ierr = PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_");CHKERRQ(ierr); 3525 ierr = PetscViewerSetFromOptions(viewer);CHKERRQ(ierr); 3526 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 3527 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 3528 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3529 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3530 if (load_hdf5_xdmf) {ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);CHKERRQ(ierr);} 3531 ierr = DMLoad(*dm, viewer);CHKERRQ(ierr); 3532 if (load_hdf5_xdmf) {ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);} 3533 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 3534 3535 if (interpolate) { 3536 DM idm; 3537 3538 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3539 ierr = DMDestroy(dm);CHKERRQ(ierr); 3540 *dm = idm; 3541 } 3542 } else if (isMed) { 3543 ierr = DMPlexCreateMedFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3544 } else if (isPLY) { 3545 ierr = DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3546 } else if (isCV) { 3547 ierr = DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3548 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 3549 ierr = PetscLogEventEnd(DMPLEX_CreateFromFile,0,0,0,0);CHKERRQ(ierr); 3550 PetscFunctionReturn(0); 3551 } 3552 3553 /*@ 3554 DMPlexCreateReferenceCellByType - Create a DMPLEX with the appropriate FEM reference cell 3555 3556 Collective 3557 3558 Input Parameters: 3559 + comm - The communicator 3560 - ct - The cell type of the reference cell 3561 3562 Output Parameter: 3563 . refdm - The reference cell 3564 3565 Level: intermediate 3566 3567 .seealso: DMPlexCreateReferenceCell(), DMPlexCreateBoxMesh() 3568 @*/ 3569 PetscErrorCode DMPlexCreateReferenceCellByType(MPI_Comm comm, DMPolytopeType ct, DM *refdm) 3570 { 3571 DM rdm; 3572 Vec coords; 3573 PetscErrorCode ierr; 3574 3575 PetscFunctionBegin; 3576 ierr = DMCreate(comm, &rdm);CHKERRQ(ierr); 3577 ierr = DMSetType(rdm, DMPLEX);CHKERRQ(ierr); 3578 switch (ct) { 3579 case DM_POLYTOPE_POINT: 3580 { 3581 PetscInt numPoints[1] = {1}; 3582 PetscInt coneSize[1] = {0}; 3583 PetscInt cones[1] = {0}; 3584 PetscInt coneOrientations[1] = {0}; 3585 PetscScalar vertexCoords[1] = {0.0}; 3586 3587 ierr = DMSetDimension(rdm, 0);CHKERRQ(ierr); 3588 ierr = DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3589 } 3590 break; 3591 case DM_POLYTOPE_SEGMENT: 3592 { 3593 PetscInt numPoints[2] = {2, 1}; 3594 PetscInt coneSize[3] = {2, 0, 0}; 3595 PetscInt cones[2] = {1, 2}; 3596 PetscInt coneOrientations[2] = {0, 0}; 3597 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 3598 3599 ierr = DMSetDimension(rdm, 1);CHKERRQ(ierr); 3600 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3601 } 3602 break; 3603 case DM_POLYTOPE_TRIANGLE: 3604 { 3605 PetscInt numPoints[2] = {3, 1}; 3606 PetscInt coneSize[4] = {3, 0, 0, 0}; 3607 PetscInt cones[3] = {1, 2, 3}; 3608 PetscInt coneOrientations[3] = {0, 0, 0}; 3609 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 3610 3611 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 3612 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3613 } 3614 break; 3615 case DM_POLYTOPE_QUADRILATERAL: 3616 { 3617 PetscInt numPoints[2] = {4, 1}; 3618 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3619 PetscInt cones[4] = {1, 2, 3, 4}; 3620 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3621 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 3622 3623 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 3624 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3625 } 3626 break; 3627 case DM_POLYTOPE_SEG_PRISM_TENSOR: 3628 { 3629 PetscInt numPoints[2] = {4, 1}; 3630 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3631 PetscInt cones[4] = {1, 2, 3, 4}; 3632 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3633 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, 1.0}; 3634 3635 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 3636 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3637 } 3638 break; 3639 case DM_POLYTOPE_TETRAHEDRON: 3640 { 3641 PetscInt numPoints[2] = {4, 1}; 3642 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3643 PetscInt cones[4] = {1, 3, 2, 4}; 3644 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3645 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}; 3646 3647 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3648 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3649 } 3650 break; 3651 case DM_POLYTOPE_HEXAHEDRON: 3652 { 3653 PetscInt numPoints[2] = {8, 1}; 3654 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3655 PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8}; 3656 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3657 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, 3658 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3659 3660 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3661 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3662 } 3663 break; 3664 case DM_POLYTOPE_TRI_PRISM: 3665 { 3666 PetscInt numPoints[2] = {6, 1}; 3667 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3668 PetscInt cones[6] = {1, 3, 2, 4, 5, 6}; 3669 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3670 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 3671 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 3672 3673 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3674 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3675 } 3676 break; 3677 case DM_POLYTOPE_TRI_PRISM_TENSOR: 3678 { 3679 PetscInt numPoints[2] = {6, 1}; 3680 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3681 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 3682 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3683 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 3684 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 3685 3686 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3687 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3688 } 3689 break; 3690 case DM_POLYTOPE_QUAD_PRISM_TENSOR: 3691 { 3692 PetscInt numPoints[2] = {8, 1}; 3693 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3694 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 3695 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3696 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, 3697 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3698 3699 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3700 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3701 } 3702 break; 3703 default: SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for cell type %s", DMPolytopeTypes[ct]); 3704 } 3705 { 3706 PetscInt Nv, v; 3707 3708 /* Must create the celltype label here so that we do not automatically try to compute the types */ 3709 ierr = DMCreateLabel(rdm, "celltype");CHKERRQ(ierr); 3710 ierr = DMPlexSetCellType(rdm, 0, ct);CHKERRQ(ierr); 3711 ierr = DMPlexGetChart(rdm, NULL, &Nv);CHKERRQ(ierr); 3712 for (v = 1; v < Nv; ++v) {ierr = DMPlexSetCellType(rdm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr);} 3713 } 3714 ierr = DMPlexInterpolate(rdm, refdm);CHKERRQ(ierr); 3715 if (rdm->coordinateDM) { 3716 DM ncdm; 3717 PetscSection cs; 3718 PetscInt pEnd = -1; 3719 3720 ierr = DMGetLocalSection(rdm->coordinateDM, &cs);CHKERRQ(ierr); 3721 if (cs) {ierr = PetscSectionGetChart(cs, NULL, &pEnd);CHKERRQ(ierr);} 3722 if (pEnd >= 0) { 3723 ierr = DMClone(*refdm, &ncdm);CHKERRQ(ierr); 3724 ierr = DMCopyDisc(rdm->coordinateDM, ncdm);CHKERRQ(ierr); 3725 ierr = DMSetLocalSection(ncdm, cs);CHKERRQ(ierr); 3726 ierr = DMSetCoordinateDM(*refdm, ncdm);CHKERRQ(ierr); 3727 ierr = DMDestroy(&ncdm);CHKERRQ(ierr); 3728 } 3729 } 3730 ierr = DMGetCoordinatesLocal(rdm, &coords);CHKERRQ(ierr); 3731 if (coords) { 3732 ierr = DMSetCoordinatesLocal(*refdm, coords);CHKERRQ(ierr); 3733 } else { 3734 ierr = DMGetCoordinates(rdm, &coords);CHKERRQ(ierr); 3735 if (coords) {ierr = DMSetCoordinates(*refdm, coords);CHKERRQ(ierr);} 3736 } 3737 ierr = DMDestroy(&rdm);CHKERRQ(ierr); 3738 PetscFunctionReturn(0); 3739 } 3740 3741 /*@ 3742 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 3743 3744 Collective 3745 3746 Input Parameters: 3747 + comm - The communicator 3748 . dim - The spatial dimension 3749 - simplex - Flag for simplex, otherwise use a tensor-product cell 3750 3751 Output Parameter: 3752 . refdm - The reference cell 3753 3754 Level: intermediate 3755 3756 .seealso: DMPlexCreateReferenceCellByType(), DMPlexCreateBoxMesh() 3757 @*/ 3758 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm) 3759 { 3760 PetscErrorCode ierr; 3761 3762 PetscFunctionBeginUser; 3763 switch (dim) { 3764 case 0: ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_POINT, refdm);CHKERRQ(ierr);break; 3765 case 1: ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_SEGMENT, refdm);CHKERRQ(ierr);break; 3766 case 2: 3767 if (simplex) {ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_TRIANGLE, refdm);CHKERRQ(ierr);} 3768 else {ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_QUADRILATERAL, refdm);CHKERRQ(ierr);} 3769 break; 3770 case 3: 3771 if (simplex) {ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_TETRAHEDRON, refdm);CHKERRQ(ierr);} 3772 else {ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_HEXAHEDRON, refdm);CHKERRQ(ierr);} 3773 break; 3774 default: 3775 SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %D", dim); 3776 } 3777 PetscFunctionReturn(0); 3778 } 3779