1 #define PETSCDM_DLL 2 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 #include <petscdmda.h> 4 #include <petscsf.h> 5 6 /*@ 7 DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement. 8 9 Collective on MPI_Comm 10 11 Input Parameters: 12 + comm - The communicator for the DM object 13 . dim - The spatial dimension 14 . simplex - Flag for simplicial cells, otherwise they are tensor product cells 15 . interpolate - Flag to create intermediate mesh pieces (edges, faces) 16 . refinementUniform - Flag for uniform parallel refinement 17 - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell 18 19 Output Parameter: 20 . dm - The DM object 21 22 Level: beginner 23 24 .keywords: DM, create 25 .seealso: DMSetType(), DMCreate() 26 @*/ 27 PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscBool refinementUniform, PetscReal refinementLimit, DM *newdm) 28 { 29 DM dm; 30 PetscInt p; 31 PetscMPIInt rank; 32 PetscErrorCode ierr; 33 34 PetscFunctionBegin; 35 ierr = DMCreate(comm, &dm);CHKERRQ(ierr); 36 ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr); 37 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 38 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 39 switch (dim) { 40 case 2: 41 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "triangular");CHKERRQ(ierr);} 42 else {ierr = PetscObjectSetName((PetscObject) dm, "quadrilateral");CHKERRQ(ierr);} 43 break; 44 case 3: 45 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "tetrahedral");CHKERRQ(ierr);} 46 else {ierr = PetscObjectSetName((PetscObject) dm, "hexahedral");CHKERRQ(ierr);} 47 break; 48 default: 49 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); 50 } 51 if (rank) { 52 PetscInt numPoints[2] = {0, 0}; 53 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 54 } else { 55 switch (dim) { 56 case 2: 57 if (simplex) { 58 PetscInt numPoints[2] = {4, 2}; 59 PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; 60 PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; 61 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 62 PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5}; 63 PetscInt markerPoints[8] = {2, 1, 3, 1, 4, 1, 5, 1}; 64 65 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 66 for (p = 0; p < 4; ++p) {ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 67 } else { 68 PetscInt numPoints[2] = {6, 2}; 69 PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; 70 PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4}; 71 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 72 PetscScalar vertexCoords[12] = {-1.0, -0.5, 0.0, -0.5, 0.0, 0.5, -1.0, 0.5, 1.0, -0.5, 1.0, 0.5}; 73 74 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 75 } 76 break; 77 case 3: 78 if (simplex) { 79 PetscInt numPoints[2] = {5, 2}; 80 PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; 81 PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; 82 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 83 PetscScalar vertexCoords[15] = {-1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0}; 84 PetscInt markerPoints[10] = {2, 1, 3, 1, 4, 1, 5, 1, 6, 1}; 85 86 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 87 for (p = 0; p < 5; ++p) {ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 88 } else { 89 PetscInt numPoints[2] = {12, 2}; 90 PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 91 PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8}; 92 PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 93 PetscScalar vertexCoords[36] = {-1.0, -0.5, -0.5, -1.0, 0.5, -0.5, 0.0, 0.5, -0.5, 0.0, -0.5, -0.5, 94 -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5, 95 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5}; 96 97 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 98 } 99 break; 100 default: 101 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); 102 } 103 } 104 *newdm = dm; 105 if (refinementLimit > 0.0) { 106 DM rdm; 107 const char *name; 108 109 ierr = DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);CHKERRQ(ierr); 110 ierr = DMPlexSetRefinementLimit(*newdm, refinementLimit);CHKERRQ(ierr); 111 ierr = DMRefine(*newdm, comm, &rdm);CHKERRQ(ierr); 112 ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); 113 ierr = PetscObjectSetName((PetscObject) rdm, name);CHKERRQ(ierr); 114 ierr = DMDestroy(newdm);CHKERRQ(ierr); 115 *newdm = rdm; 116 } 117 if (interpolate) { 118 DM idm; 119 120 ierr = DMPlexInterpolate(*newdm, &idm);CHKERRQ(ierr); 121 ierr = DMDestroy(newdm);CHKERRQ(ierr); 122 *newdm = idm; 123 } 124 { 125 DM refinedMesh = NULL; 126 DM distributedMesh = NULL; 127 128 /* Distribute mesh over processes */ 129 ierr = DMPlexDistribute(*newdm, 0, NULL, &distributedMesh);CHKERRQ(ierr); 130 if (distributedMesh) { 131 ierr = DMDestroy(newdm);CHKERRQ(ierr); 132 *newdm = distributedMesh; 133 } 134 if (refinementUniform) { 135 ierr = DMPlexSetRefinementUniform(*newdm, refinementUniform);CHKERRQ(ierr); 136 ierr = DMRefine(*newdm, comm, &refinedMesh);CHKERRQ(ierr); 137 if (refinedMesh) { 138 ierr = DMDestroy(newdm);CHKERRQ(ierr); 139 *newdm = refinedMesh; 140 } 141 } 142 } 143 PetscFunctionReturn(0); 144 } 145 146 /*@ 147 DMPlexCreateSquareBoundary - Creates a 1D mesh the is the boundary of a square lattice. 148 149 Collective on MPI_Comm 150 151 Input Parameters: 152 + comm - The communicator for the DM object 153 . lower - The lower left corner coordinates 154 . upper - The upper right corner coordinates 155 - edges - The number of cells in each direction 156 157 Output Parameter: 158 . dm - The DM object 159 160 Note: Here is the numbering returned for 2 cells in each direction: 161 $ 18--5-17--4--16 162 $ | | | 163 $ 6 10 3 164 $ | | | 165 $ 19-11-20--9--15 166 $ | | | 167 $ 7 8 2 168 $ | | | 169 $ 12--0-13--1--14 170 171 Level: beginner 172 173 .keywords: DM, create 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 on MPI_Comm 297 298 Input Parameters: 299 + comm - The communicator for the DM object 300 . lower - The lower left front corner coordinates 301 . upper - The upper right back corner coordinates 302 - edges - The number of cells in each direction 303 304 Output Parameter: 305 . dm - The DM object 306 307 Level: beginner 308 309 .keywords: DM, create 310 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMSetType(), DMCreate() 311 @*/ 312 PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) 313 { 314 PetscInt vertices[3], numVertices; 315 PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2]; 316 Vec coordinates; 317 PetscSection coordSection; 318 PetscScalar *coords; 319 PetscInt coordSize; 320 PetscMPIInt rank; 321 PetscInt v, vx, vy, vz; 322 PetscInt voffset, iface=0, cone[4]; 323 PetscErrorCode ierr; 324 325 PetscFunctionBegin; 326 if ((faces[0] < 1) || (faces[1] < 1) || (faces[2] < 1)) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Must have at least 1 face per side"); 327 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 328 vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1; 329 numVertices = vertices[0]*vertices[1]*vertices[2]; 330 if (!rank) { 331 PetscInt f; 332 333 ierr = DMPlexSetChart(dm, 0, numFaces+numVertices);CHKERRQ(ierr); 334 for (f = 0; f < numFaces; ++f) { 335 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 336 } 337 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 338 for (v = 0; v < numFaces+numVertices; ++v) { 339 ierr = DMSetLabelValue(dm, "marker", v, 1);CHKERRQ(ierr); 340 } 341 342 /* Side 0 (Top) */ 343 for (vy = 0; vy < faces[1]; vy++) { 344 for (vx = 0; vx < faces[0]; vx++) { 345 voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx; 346 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0]; 347 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 348 iface++; 349 } 350 } 351 352 /* Side 1 (Bottom) */ 353 for (vy = 0; vy < faces[1]; vy++) { 354 for (vx = 0; vx < faces[0]; vx++) { 355 voffset = numFaces + vy*(faces[0]+1) + vx; 356 cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1; 357 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 358 iface++; 359 } 360 } 361 362 /* Side 2 (Front) */ 363 for (vz = 0; vz < faces[2]; vz++) { 364 for (vx = 0; vx < faces[0]; vx++) { 365 voffset = numFaces + vz*vertices[0]*vertices[1] + vx; 366 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1]; 367 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 368 iface++; 369 } 370 } 371 372 /* Side 3 (Back) */ 373 for (vz = 0; vz < faces[2]; vz++) { 374 for (vx = 0; vx < faces[0]; vx++) { 375 voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx; 376 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1; 377 cone[2] = voffset+1; cone[3] = voffset; 378 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 379 iface++; 380 } 381 } 382 383 /* Side 4 (Left) */ 384 for (vz = 0; vz < faces[2]; vz++) { 385 for (vy = 0; vy < faces[1]; vy++) { 386 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0]; 387 cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1]; 388 cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0]; 389 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 390 iface++; 391 } 392 } 393 394 /* Side 5 (Right) */ 395 for (vz = 0; vz < faces[2]; vz++) { 396 for (vy = 0; vy < faces[1]; vy++) { 397 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + faces[0]; 398 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset; 399 cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0]; 400 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 401 iface++; 402 } 403 } 404 } 405 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 406 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 407 /* Build coordinates */ 408 ierr = DMSetCoordinateDim(dm, 3);CHKERRQ(ierr); 409 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 410 ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr); 411 for (v = numFaces; v < numFaces+numVertices; ++v) { 412 ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr); 413 } 414 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 415 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 416 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 417 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 418 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 419 ierr = VecSetBlockSize(coordinates, 3);CHKERRQ(ierr); 420 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 421 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 422 for (vz = 0; vz <= faces[2]; ++vz) { 423 for (vy = 0; vy <= faces[1]; ++vy) { 424 for (vx = 0; vx <= faces[0]; ++vx) { 425 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx; 426 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy; 427 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz; 428 } 429 } 430 } 431 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 432 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 433 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 434 PetscFunctionReturn(0); 435 } 436 437 static PetscErrorCode DMPlexCreateLineMesh_Internal(MPI_Comm comm,PetscInt segments,PetscReal lower,PetscReal upper,DMBoundaryType bd,DM *dm) 438 { 439 PetscInt i,fStart,fEnd,numCells = 0,numVerts = 0; 440 PetscInt numPoints[2],*coneSize,*cones,*coneOrientations; 441 PetscScalar *vertexCoords; 442 PetscReal L,maxCell; 443 PetscBool markerSeparate = PETSC_FALSE; 444 PetscInt markerLeft = 1, faceMarkerLeft = 1; 445 PetscInt markerRight = 1, faceMarkerRight = 2; 446 PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE; 447 PetscMPIInt rank; 448 PetscErrorCode ierr; 449 450 PetscFunctionBegin; 451 PetscValidPointer(dm,4); 452 453 ierr = DMCreate(comm,dm);CHKERRQ(ierr); 454 ierr = DMSetType(*dm,DMPLEX);CHKERRQ(ierr); 455 ierr = DMSetDimension(*dm,1);CHKERRQ(ierr); 456 ierr = DMCreateLabel(*dm,"marker");CHKERRQ(ierr); 457 ierr = DMCreateLabel(*dm,"Face Sets");CHKERRQ(ierr); 458 459 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 460 if (!rank) numCells = segments; 461 if (!rank) numVerts = segments + (wrap ? 0 : 1); 462 463 numPoints[0] = numVerts ; numPoints[1] = numCells; 464 ierr = PetscMalloc4(numCells+numVerts,&coneSize,numCells*2,&cones,numCells+numVerts,&coneOrientations,numVerts,&vertexCoords);CHKERRQ(ierr); 465 ierr = PetscMemzero(coneOrientations,(numCells+numVerts)*sizeof(PetscInt));CHKERRQ(ierr); 466 for (i = 0; i < numCells; ++i) { coneSize[i] = 2; } 467 for (i = 0; i < numVerts; ++i) { coneSize[numCells+i] = 0; } 468 for (i = 0; i < numCells; ++i) { cones[2*i] = numCells + i%numVerts; cones[2*i+1] = numCells + (i+1)%numVerts; } 469 for (i = 0; i < numVerts; ++i) { vertexCoords[i] = lower + (upper-lower)*((PetscReal)i/(PetscReal)numCells); } 470 ierr = DMPlexCreateFromDAG(*dm,1,numPoints,coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 471 ierr = PetscFree4(coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 472 473 ierr = PetscOptionsGetBool(((PetscObject)*dm)->options,((PetscObject)*dm)->prefix,"-dm_plex_separate_marker",&markerSeparate,NULL);CHKERRQ(ierr); 474 if (markerSeparate) { markerLeft = faceMarkerLeft; markerRight = faceMarkerRight;} 475 if (!wrap && !rank) { 476 ierr = DMPlexGetHeightStratum(*dm,1,&fStart,&fEnd);CHKERRQ(ierr); 477 ierr = DMSetLabelValue(*dm,"marker",fStart,markerLeft);CHKERRQ(ierr); 478 ierr = DMSetLabelValue(*dm,"marker",fEnd-1,markerRight);CHKERRQ(ierr); 479 ierr = DMSetLabelValue(*dm,"Face Sets",fStart,faceMarkerLeft);CHKERRQ(ierr); 480 ierr = DMSetLabelValue(*dm,"Face Sets",fEnd-1,faceMarkerRight);CHKERRQ(ierr); 481 } 482 if (wrap) { 483 L = upper - lower; 484 maxCell = (PetscReal)1.1*(L/(PetscReal)PetscMax(1,segments)); 485 ierr = DMSetPeriodicity(*dm,PETSC_TRUE,&maxCell,&L,&bd);CHKERRQ(ierr); 486 } 487 PetscFunctionReturn(0); 488 } 489 490 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) 491 { 492 DM boundary; 493 PetscInt i; 494 PetscErrorCode ierr; 495 496 PetscFunctionBegin; 497 PetscValidPointer(dm, 4); 498 for (i = 0; i < dim; ++i) if (periodicity[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity is not supported for simplex meshes"); 499 ierr = DMCreate(comm, &boundary);CHKERRQ(ierr); 500 PetscValidLogicalCollectiveInt(boundary,dim,2); 501 ierr = DMSetType(boundary, DMPLEX);CHKERRQ(ierr); 502 ierr = DMSetDimension(boundary, dim-1);CHKERRQ(ierr); 503 ierr = DMSetCoordinateDim(boundary, dim);CHKERRQ(ierr); 504 switch (dim) { 505 case 2: ierr = DMPlexCreateSquareBoundary(boundary, lower, upper, faces);CHKERRQ(ierr);break; 506 case 3: ierr = DMPlexCreateCubeBoundary(boundary, lower, upper, faces);CHKERRQ(ierr);break; 507 default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 508 } 509 ierr = DMPlexGenerate(boundary, NULL, interpolate, dm);CHKERRQ(ierr); 510 ierr = DMDestroy(&boundary);CHKERRQ(ierr); 511 PetscFunctionReturn(0); 512 } 513 514 static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ) 515 { 516 DMLabel cutLabel = NULL; 517 PetscInt markerTop = 1, faceMarkerTop = 1; 518 PetscInt markerBottom = 1, faceMarkerBottom = 1; 519 PetscInt markerFront = 1, faceMarkerFront = 1; 520 PetscInt markerBack = 1, faceMarkerBack = 1; 521 PetscInt markerRight = 1, faceMarkerRight = 1; 522 PetscInt markerLeft = 1, faceMarkerLeft = 1; 523 PetscInt dim; 524 PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE; 525 PetscMPIInt rank; 526 PetscErrorCode ierr; 527 528 PetscFunctionBegin; 529 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 530 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 531 ierr = DMCreateLabel(dm,"marker");CHKERRQ(ierr); 532 ierr = DMCreateLabel(dm,"Face Sets");CHKERRQ(ierr); 533 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL);CHKERRQ(ierr); 534 if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST || 535 bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST || 536 bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) { 537 538 if (cutMarker) {ierr = DMCreateLabel(dm, "periodic_cut");CHKERRQ(ierr); ierr = DMGetLabel(dm, "periodic_cut", &cutLabel);CHKERRQ(ierr);} 539 } 540 switch (dim) { 541 case 2: 542 faceMarkerTop = 3; 543 faceMarkerBottom = 1; 544 faceMarkerRight = 2; 545 faceMarkerLeft = 4; 546 break; 547 case 3: 548 faceMarkerBottom = 1; 549 faceMarkerTop = 2; 550 faceMarkerFront = 3; 551 faceMarkerBack = 4; 552 faceMarkerRight = 5; 553 faceMarkerLeft = 6; 554 break; 555 default: 556 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %d not supported",dim); 557 break; 558 } 559 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 560 if (markerSeparate) { 561 markerBottom = faceMarkerBottom; 562 markerTop = faceMarkerTop; 563 markerFront = faceMarkerFront; 564 markerBack = faceMarkerBack; 565 markerRight = faceMarkerRight; 566 markerLeft = faceMarkerLeft; 567 } 568 { 569 const PetscInt numXEdges = !rank ? edges[0] : 0; 570 const PetscInt numYEdges = !rank ? edges[1] : 0; 571 const PetscInt numZEdges = !rank ? edges[2] : 0; 572 const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; 573 const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; 574 const PetscInt numZVertices = !rank ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0; 575 const PetscInt numCells = numXEdges*numYEdges*numZEdges; 576 const PetscInt numXFaces = numYEdges*numZEdges; 577 const PetscInt numYFaces = numXEdges*numZEdges; 578 const PetscInt numZFaces = numXEdges*numYEdges; 579 const PetscInt numTotXFaces = numXVertices*numXFaces; 580 const PetscInt numTotYFaces = numYVertices*numYFaces; 581 const PetscInt numTotZFaces = numZVertices*numZFaces; 582 const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces; 583 const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices; 584 const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices; 585 const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices; 586 const PetscInt numVertices = numXVertices*numYVertices*numZVertices; 587 const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges; 588 const PetscInt firstVertex = (dim == 2) ? numFaces : numCells; 589 const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices; 590 const PetscInt firstYFace = firstXFace + numTotXFaces; 591 const PetscInt firstZFace = firstYFace + numTotYFaces; 592 const PetscInt firstXEdge = numCells + numFaces + numVertices; 593 const PetscInt firstYEdge = firstXEdge + numTotXEdges; 594 const PetscInt firstZEdge = firstYEdge + numTotYEdges; 595 Vec coordinates; 596 PetscSection coordSection; 597 PetscScalar *coords; 598 PetscInt coordSize; 599 PetscInt v, vx, vy, vz; 600 PetscInt c, f, fx, fy, fz, e, ex, ey, ez; 601 602 ierr = DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);CHKERRQ(ierr); 603 for (c = 0; c < numCells; c++) { 604 ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr); 605 } 606 for (f = firstXFace; f < firstXFace+numFaces; ++f) { 607 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 608 } 609 for (e = firstXEdge; e < firstXEdge+numEdges; ++e) { 610 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 611 } 612 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 613 /* Build cells */ 614 for (fz = 0; fz < numZEdges; ++fz) { 615 for (fy = 0; fy < numYEdges; ++fy) { 616 for (fx = 0; fx < numXEdges; ++fx) { 617 PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx; 618 PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 619 PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices); 620 PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 621 PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices); 622 PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 623 PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices); 624 /* B, T, F, K, R, L */ 625 PetscInt ornt[6] = {-4, 0, 0, -1, 0, -4}; /* ??? */ 626 PetscInt cone[6]; 627 628 /* no boundary twisting in 3D */ 629 cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL; 630 ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr); 631 ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr); 632 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 633 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 634 if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 635 } 636 } 637 } 638 /* Build x faces */ 639 for (fz = 0; fz < numZEdges; ++fz) { 640 for (fy = 0; fy < numYEdges; ++fy) { 641 for (fx = 0; fx < numXVertices; ++fx) { 642 PetscInt face = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 643 PetscInt edgeL = firstZEdge + ( fy* numXVertices+fx)*numZEdges + fz; 644 PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz; 645 PetscInt edgeB = firstYEdge + ( fz* numXVertices+fx)*numYEdges + fy; 646 PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy; 647 PetscInt ornt[4] = {0, 0, -2, -2}; 648 PetscInt cone[4]; 649 650 if (dim == 3) { 651 /* markers */ 652 if (bdX != DM_BOUNDARY_PERIODIC) { 653 if (fx == numXVertices-1) { 654 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);CHKERRQ(ierr); 655 ierr = DMSetLabelValue(dm, "marker", face, markerRight);CHKERRQ(ierr); 656 } 657 else if (fx == 0) { 658 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);CHKERRQ(ierr); 659 ierr = DMSetLabelValue(dm, "marker", face, markerLeft);CHKERRQ(ierr); 660 } 661 } 662 } 663 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 664 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 665 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 666 } 667 } 668 } 669 /* Build y faces */ 670 for (fz = 0; fz < numZEdges; ++fz) { 671 for (fx = 0; fx < numXEdges; ++fx) { 672 for (fy = 0; fy < numYVertices; ++fy) { 673 PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 674 PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx )*numZEdges + fz; 675 PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz; 676 PetscInt edgeB = firstXEdge + ( fz *numYVertices+fy)*numXEdges + fx; 677 PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx; 678 PetscInt ornt[4] = {0, 0, -2, -2}; 679 PetscInt cone[4]; 680 681 if (dim == 3) { 682 /* markers */ 683 if (bdY != DM_BOUNDARY_PERIODIC) { 684 if (fy == numYVertices-1) { 685 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);CHKERRQ(ierr); 686 ierr = DMSetLabelValue(dm, "marker", face, markerBack);CHKERRQ(ierr); 687 } 688 else if (fy == 0) { 689 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);CHKERRQ(ierr); 690 ierr = DMSetLabelValue(dm, "marker", face, markerFront);CHKERRQ(ierr); 691 } 692 } 693 } 694 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 695 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 696 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 697 } 698 } 699 } 700 /* Build z faces */ 701 for (fy = 0; fy < numYEdges; ++fy) { 702 for (fx = 0; fx < numXEdges; ++fx) { 703 for (fz = 0; fz < numZVertices; fz++) { 704 PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 705 PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx )*numYEdges + fy; 706 PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy; 707 PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy )*numXEdges + fx; 708 PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx; 709 PetscInt ornt[4] = {0, 0, -2, -2}; 710 PetscInt cone[4]; 711 712 if (dim == 2) { 713 if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -2;} 714 if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;} 715 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 716 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 717 } else { 718 /* markers */ 719 if (bdZ != DM_BOUNDARY_PERIODIC) { 720 if (fz == numZVertices-1) { 721 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);CHKERRQ(ierr); 722 ierr = DMSetLabelValue(dm, "marker", face, markerTop);CHKERRQ(ierr); 723 } 724 else if (fz == 0) { 725 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);CHKERRQ(ierr); 726 ierr = DMSetLabelValue(dm, "marker", face, markerBottom);CHKERRQ(ierr); 727 } 728 } 729 } 730 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 731 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 732 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 733 } 734 } 735 } 736 /* Build Z edges*/ 737 for (vy = 0; vy < numYVertices; vy++) { 738 for (vx = 0; vx < numXVertices; vx++) { 739 for (ez = 0; ez < numZEdges; ez++) { 740 const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez; 741 const PetscInt vertexB = firstVertex + ( ez *numYVertices+vy)*numXVertices + vx; 742 const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx; 743 PetscInt cone[2]; 744 745 if (dim == 3) { 746 if (bdX != DM_BOUNDARY_PERIODIC) { 747 if (vx == numXVertices-1) { 748 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 749 } 750 else if (vx == 0) { 751 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 752 } 753 } 754 if (bdY != DM_BOUNDARY_PERIODIC) { 755 if (vy == numYVertices-1) { 756 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 757 } 758 else if (vy == 0) { 759 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 760 } 761 } 762 } 763 cone[0] = vertexB; cone[1] = vertexT; 764 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 765 } 766 } 767 } 768 /* Build Y edges*/ 769 for (vz = 0; vz < numZVertices; vz++) { 770 for (vx = 0; vx < numXVertices; vx++) { 771 for (ey = 0; ey < numYEdges; ey++) { 772 const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx; 773 const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey; 774 const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx; 775 const PetscInt vertexK = firstVertex + nextv; 776 PetscInt cone[2]; 777 778 cone[0] = vertexF; cone[1] = vertexK; 779 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 780 if (dim == 2) { 781 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 782 if (vx == numXVertices-1) { 783 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);CHKERRQ(ierr); 784 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 785 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 786 if (ey == numYEdges-1) { 787 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 788 } 789 } else if (vx == 0) { 790 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);CHKERRQ(ierr); 791 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 792 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 793 if (ey == numYEdges-1) { 794 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 795 } 796 } 797 } else { 798 if (vx == 0 && cutLabel) { 799 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 800 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 801 if (ey == numYEdges-1) { 802 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 803 } 804 } 805 } 806 } else { 807 if (bdX != DM_BOUNDARY_PERIODIC) { 808 if (vx == numXVertices-1) { 809 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 810 } else if (vx == 0) { 811 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 812 } 813 } 814 if (bdZ != DM_BOUNDARY_PERIODIC) { 815 if (vz == numZVertices-1) { 816 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 817 } else if (vz == 0) { 818 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 819 } 820 } 821 } 822 } 823 } 824 } 825 /* Build X edges*/ 826 for (vz = 0; vz < numZVertices; vz++) { 827 for (vy = 0; vy < numYVertices; vy++) { 828 for (ex = 0; ex < numXEdges; ex++) { 829 const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices; 830 const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex; 831 const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex; 832 const PetscInt vertexR = firstVertex + nextv; 833 PetscInt cone[2]; 834 835 cone[0] = vertexL; cone[1] = vertexR; 836 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 837 if (dim == 2) { 838 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 839 if (vy == numYVertices-1) { 840 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);CHKERRQ(ierr); 841 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 842 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 843 if (ex == numXEdges-1) { 844 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 845 } 846 } else if (vy == 0) { 847 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);CHKERRQ(ierr); 848 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 849 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 850 if (ex == numXEdges-1) { 851 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 852 } 853 } 854 } else { 855 if (vy == 0 && cutLabel) { 856 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 857 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 858 if (ex == numXEdges-1) { 859 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 860 } 861 } 862 } 863 } else { 864 if (bdY != DM_BOUNDARY_PERIODIC) { 865 if (vy == numYVertices-1) { 866 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 867 } 868 else if (vy == 0) { 869 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 870 } 871 } 872 if (bdZ != DM_BOUNDARY_PERIODIC) { 873 if (vz == numZVertices-1) { 874 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 875 } 876 else if (vz == 0) { 877 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 878 } 879 } 880 } 881 } 882 } 883 } 884 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 885 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 886 /* Build coordinates */ 887 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 888 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 889 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 890 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr); 891 for (v = firstVertex; v < firstVertex+numVertices; ++v) { 892 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 893 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 894 } 895 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 896 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 897 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 898 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 899 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 900 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 901 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 902 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 903 for (vz = 0; vz < numZVertices; ++vz) { 904 for (vy = 0; vy < numYVertices; ++vy) { 905 for (vx = 0; vx < numXVertices; ++vx) { 906 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx; 907 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy; 908 if (dim == 3) { 909 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz; 910 } 911 } 912 } 913 } 914 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 915 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 916 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 917 } 918 PetscFunctionReturn(0); 919 } 920 921 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) 922 { 923 PetscInt i; 924 PetscErrorCode ierr; 925 926 PetscFunctionBegin; 927 PetscValidPointer(dm, 7); 928 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 929 PetscValidLogicalCollectiveInt(*dm,dim,2); 930 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 931 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 932 switch (dim) { 933 case 2: {ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], DM_BOUNDARY_NONE);CHKERRQ(ierr);break;} 934 case 3: {ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], periodicity[2]);CHKERRQ(ierr);break;} 935 default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 936 } 937 if (periodicity[0] == DM_BOUNDARY_PERIODIC || periodicity[0] == DM_BOUNDARY_TWIST || 938 periodicity[1] == DM_BOUNDARY_PERIODIC || periodicity[1] == DM_BOUNDARY_TWIST || 939 (dim > 2 && (periodicity[2] == DM_BOUNDARY_PERIODIC || periodicity[2] == DM_BOUNDARY_TWIST))) { 940 PetscReal L[3]; 941 PetscReal maxCell[3]; 942 943 for (i = 0; i < dim; i++) { 944 L[i] = upper[i] - lower[i]; 945 maxCell[i] = 1.1 * (L[i] / PetscMax(1,faces[i])); 946 } 947 ierr = DMSetPeriodicity(*dm,PETSC_TRUE,maxCell,L,periodicity);CHKERRQ(ierr); 948 } 949 if (!interpolate) { 950 DM udm; 951 952 ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr); 953 ierr = DMPlexCopyCoordinates(*dm, udm);CHKERRQ(ierr); 954 ierr = DMDestroy(dm);CHKERRQ(ierr); 955 *dm = udm; 956 } 957 PetscFunctionReturn(0); 958 } 959 960 /*@C 961 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra). 962 963 Collective on MPI_Comm 964 965 Input Parameters: 966 + comm - The communicator for the DM object 967 . dim - The spatial dimension 968 . simplex - PETSC_TRUE for simplices, PETSC_FALSE for tensor cells 969 . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 970 . lower - The lower left corner, or NULL for (0, 0, 0) 971 . upper - The upper right corner, or NULL for (1, 1, 1) 972 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 973 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 974 975 Output Parameter: 976 . dm - The DM object 977 978 Note: Here is the numbering returned for 2 faces in each direction for tensor cells: 979 $ 10---17---11---18----12 980 $ | | | 981 $ | | | 982 $ 20 2 22 3 24 983 $ | | | 984 $ | | | 985 $ 7---15----8---16----9 986 $ | | | 987 $ | | | 988 $ 19 0 21 1 23 989 $ | | | 990 $ | | | 991 $ 4---13----5---14----6 992 993 and for simplicial cells 994 995 $ 14----8---15----9----16 996 $ |\ 5 |\ 7 | 997 $ | \ | \ | 998 $ 13 2 14 3 15 999 $ | 4 \ | 6 \ | 1000 $ | \ | \ | 1001 $ 11----6---12----7----13 1002 $ |\ |\ | 1003 $ | \ 1 | \ 3 | 1004 $ 10 0 11 1 12 1005 $ | 0 \ | 2 \ | 1006 $ | \ | \ | 1007 $ 8----4----9----5----10 1008 1009 Level: beginner 1010 1011 .keywords: DM, create 1012 .seealso: DMPlexCreateFromFile(), DMPlexCreateHexCylinderMesh(), DMSetType(), DMCreate() 1013 @*/ 1014 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) 1015 { 1016 PetscInt i; 1017 PetscInt fac[3] = {0, 0, 0}; 1018 PetscReal low[3] = {0, 0, 0}; 1019 PetscReal upp[3] = {1, 1, 1}; 1020 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1021 PetscErrorCode ierr; 1022 1023 PetscFunctionBegin; 1024 for (i = 0; i < dim; ++i) fac[i] = faces ? faces[i] : (dim == 1 ? 1 : 4-dim); 1025 if (lower) for (i = 0; i < dim; ++i) low[i] = lower[i]; 1026 if (upper) for (i = 0; i < dim; ++i) upp[i] = upper[i]; 1027 if (periodicity) for (i = 0; i < dim; ++i) bdt[i] = periodicity[i]; 1028 1029 if (dim == 1) {ierr = DMPlexCreateLineMesh_Internal(comm, fac[0], low[0], upp[0], bdt[0], dm);CHKERRQ(ierr);} 1030 else if (simplex) {ierr = DMPlexCreateBoxMesh_Simplex_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);CHKERRQ(ierr);} 1031 else {ierr = DMPlexCreateBoxMesh_Tensor_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);CHKERRQ(ierr);} 1032 PetscFunctionReturn(0); 1033 } 1034 1035 /*@C 1036 DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database. 1037 1038 Logically Collective on DM 1039 1040 Input Parameters: 1041 + dm - the DM context 1042 - prefix - the prefix to prepend to all option names 1043 1044 Notes: 1045 A hyphen (-) must NOT be given at the beginning of the prefix name. 1046 The first character of all runtime options is AUTOMATICALLY the hyphen. 1047 1048 Level: advanced 1049 1050 .seealso: SNESSetFromOptions() 1051 @*/ 1052 PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) 1053 { 1054 DM_Plex *mesh = (DM_Plex *) dm->data; 1055 PetscErrorCode ierr; 1056 1057 PetscFunctionBegin; 1058 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1059 ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);CHKERRQ(ierr); 1060 ierr = PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);CHKERRQ(ierr); 1061 PetscFunctionReturn(0); 1062 } 1063 1064 /*@ 1065 DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. 1066 1067 Collective on MPI_Comm 1068 1069 Input Parameters: 1070 + comm - The communicator for the DM object 1071 . numRefine - The number of regular refinements to the basic 5 cell structure 1072 - periodicZ - The boundary type for the Z direction 1073 1074 Output Parameter: 1075 . dm - The DM object 1076 1077 Note: Here is the output numbering looking from the bottom of the cylinder: 1078 $ 17-----14 1079 $ | | 1080 $ | 2 | 1081 $ | | 1082 $ 17-----8-----7-----14 1083 $ | | | | 1084 $ | 3 | 0 | 1 | 1085 $ | | | | 1086 $ 19-----5-----6-----13 1087 $ | | 1088 $ | 4 | 1089 $ | | 1090 $ 19-----13 1091 $ 1092 $ and up through the top 1093 $ 1094 $ 18-----16 1095 $ | | 1096 $ | 2 | 1097 $ | | 1098 $ 18----10----11-----16 1099 $ | | | | 1100 $ | 3 | 0 | 1 | 1101 $ | | | | 1102 $ 20-----9----12-----15 1103 $ | | 1104 $ | 4 | 1105 $ | | 1106 $ 20-----15 1107 1108 Level: beginner 1109 1110 .keywords: DM, create 1111 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1112 @*/ 1113 PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, PetscInt numRefine, DMBoundaryType periodicZ, DM *dm) 1114 { 1115 const PetscInt dim = 3; 1116 PetscInt numCells, numVertices, r; 1117 PetscMPIInt rank; 1118 PetscErrorCode ierr; 1119 1120 PetscFunctionBegin; 1121 PetscValidPointer(dm, 4); 1122 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1123 if (numRefine < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of refinements %D cannot be negative", numRefine); 1124 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1125 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1126 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1127 /* Create topology */ 1128 { 1129 PetscInt cone[8], c; 1130 1131 numCells = !rank ? 5 : 0; 1132 numVertices = !rank ? 16 : 0; 1133 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1134 numCells *= 3; 1135 numVertices = !rank ? 24 : 0; 1136 } 1137 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1138 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 8);CHKERRQ(ierr);} 1139 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1140 if (!rank) { 1141 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1142 cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16; 1143 cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34; 1144 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1145 cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23; 1146 cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */ 1147 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1148 cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17; 1149 cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38; 1150 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1151 cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15; 1152 cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38; 1153 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1154 cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23; 1155 cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31; 1156 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1157 1158 cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32; 1159 cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20; 1160 ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); 1161 cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36; 1162 cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21; 1163 ierr = DMPlexSetCone(*dm, 6, cone);CHKERRQ(ierr); 1164 cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33; 1165 cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28; 1166 ierr = DMPlexSetCone(*dm, 7, cone);CHKERRQ(ierr); 1167 cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31; 1168 cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28; 1169 ierr = DMPlexSetCone(*dm, 8, cone);CHKERRQ(ierr); 1170 cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36; 1171 cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19; 1172 ierr = DMPlexSetCone(*dm, 9, cone);CHKERRQ(ierr); 1173 1174 cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22; 1175 cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18; 1176 ierr = DMPlexSetCone(*dm, 10, cone);CHKERRQ(ierr); 1177 cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25; 1178 cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17; 1179 ierr = DMPlexSetCone(*dm, 11, cone);CHKERRQ(ierr); 1180 cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21; 1181 cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27; 1182 ierr = DMPlexSetCone(*dm, 12, cone);CHKERRQ(ierr); 1183 cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19; 1184 cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27; 1185 ierr = DMPlexSetCone(*dm, 13, cone);CHKERRQ(ierr); 1186 cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25; 1187 cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15; 1188 ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); 1189 } else { 1190 cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6; 1191 cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10; 1192 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1193 cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13; 1194 cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11; 1195 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1196 cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7; 1197 cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18; 1198 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1199 cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5; 1200 cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18; 1201 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1202 cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13; 1203 cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9; 1204 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1205 } 1206 } 1207 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1208 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1209 } 1210 /* Interpolate */ 1211 { 1212 DM idm; 1213 1214 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1215 ierr = DMDestroy(dm);CHKERRQ(ierr); 1216 *dm = idm; 1217 } 1218 /* Create cube geometry */ 1219 { 1220 Vec coordinates; 1221 PetscSection coordSection; 1222 PetscScalar *coords; 1223 PetscInt coordSize, v; 1224 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1225 const PetscReal ds2 = dis/2.0; 1226 1227 /* Build coordinates */ 1228 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1229 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1230 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1231 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1232 for (v = numCells; v < numCells+numVertices; ++v) { 1233 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1234 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1235 } 1236 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1237 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1238 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1239 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1240 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1241 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1242 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1243 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1244 if (!rank) { 1245 coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0; 1246 coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0; 1247 coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0; 1248 coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0; 1249 coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0; 1250 coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0; 1251 coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0; 1252 coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0; 1253 coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0; 1254 coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0; 1255 coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0; 1256 coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0; 1257 coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0; 1258 coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0; 1259 coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0; 1260 coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0; 1261 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1262 /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5; 1263 /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5; 1264 /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5; 1265 /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5; 1266 /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5; 1267 /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5; 1268 /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5; 1269 /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5; 1270 } 1271 } 1272 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1273 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 1274 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1275 } 1276 /* Create periodicity */ 1277 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1278 PetscReal L[3]; 1279 PetscReal maxCell[3]; 1280 DMBoundaryType bdType[3]; 1281 PetscReal lower[3] = {0.0, 0.0, 0.0}; 1282 PetscReal upper[3] = {1.0, 1.0, 1.5}; 1283 PetscInt i, numZCells = 3; 1284 1285 bdType[0] = DM_BOUNDARY_NONE; 1286 bdType[1] = DM_BOUNDARY_NONE; 1287 bdType[2] = periodicZ; 1288 for (i = 0; i < dim; i++) { 1289 L[i] = upper[i] - lower[i]; 1290 maxCell[i] = 1.1 * (L[i] / numZCells); 1291 } 1292 ierr = DMSetPeriodicity(*dm, PETSC_TRUE, maxCell, L, bdType);CHKERRQ(ierr); 1293 } 1294 /* Refine topology */ 1295 for (r = 0; r < numRefine; ++r) { 1296 DM rdm = NULL; 1297 1298 ierr = DMRefine(*dm, comm, &rdm);CHKERRQ(ierr); 1299 ierr = DMDestroy(dm);CHKERRQ(ierr); 1300 *dm = rdm; 1301 } 1302 /* Remap geometry to cylinder 1303 Interior square: Linear interpolation is correct 1304 The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing 1305 such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance 1306 1307 phi = arctan(y/x) 1308 d_close = sqrt(1/8 + 1/4 sin^2(phi)) 1309 d_far = sqrt(1/2 + sin^2(phi)) 1310 1311 so we remap them using 1312 1313 x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) 1314 y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) 1315 1316 If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. 1317 */ 1318 { 1319 Vec coordinates; 1320 PetscSection coordSection; 1321 PetscScalar *coords; 1322 PetscInt vStart, vEnd, v; 1323 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1324 const PetscReal ds2 = 0.5*dis; 1325 1326 ierr = DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1327 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1328 ierr = DMGetCoordinatesLocal(*dm, &coordinates);CHKERRQ(ierr); 1329 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1330 for (v = vStart; v < vEnd; ++v) { 1331 PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; 1332 PetscInt off; 1333 1334 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 1335 if ((PetscAbsScalar(coords[off+0]) <= ds2) && (PetscAbsScalar(coords[off+1]) <= ds2)) continue; 1336 x = PetscRealPart(coords[off]); 1337 y = PetscRealPart(coords[off+1]); 1338 phi = PetscAtan2Real(y, x); 1339 sinp = PetscSinReal(phi); 1340 cosp = PetscCosReal(phi); 1341 if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) { 1342 dc = PetscAbsReal(ds2/sinp); 1343 df = PetscAbsReal(dis/sinp); 1344 xc = ds2*x/PetscAbsReal(y); 1345 yc = ds2*PetscSignReal(y); 1346 } else { 1347 dc = PetscAbsReal(ds2/cosp); 1348 df = PetscAbsReal(dis/cosp); 1349 xc = ds2*PetscSignReal(x); 1350 yc = ds2*y/PetscAbsReal(x); 1351 } 1352 coords[off+0] = xc + (coords[off+0] - xc)*(1.0 - dc)/(df - dc); 1353 coords[off+1] = yc + (coords[off+1] - yc)*(1.0 - dc)/(df - dc); 1354 } 1355 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1356 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1357 ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); 1358 } 1359 } 1360 PetscFunctionReturn(0); 1361 } 1362 1363 /*@ 1364 DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges. 1365 1366 Collective on MPI_Comm 1367 1368 Input Parameters: 1369 + comm - The communicator for the DM object 1370 . n - The number of wedges around the origin 1371 - interpolate - Create edges and faces 1372 1373 Output Parameter: 1374 . dm - The DM object 1375 1376 Level: beginner 1377 1378 .keywords: DM, create 1379 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1380 @*/ 1381 PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm) 1382 { 1383 const PetscInt dim = 3; 1384 PetscInt numCells, numVertices; 1385 PetscMPIInt rank; 1386 PetscErrorCode ierr; 1387 1388 PetscFunctionBegin; 1389 PetscValidPointer(dm, 3); 1390 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1391 if (n < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n); 1392 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1393 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1394 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1395 /* Create topology */ 1396 { 1397 PetscInt cone[6], c; 1398 1399 numCells = !rank ? n : 0; 1400 numVertices = !rank ? 2*(n+1) : 0; 1401 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1402 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 6);CHKERRQ(ierr);} 1403 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1404 for (c = 0; c < numCells; c++) { 1405 cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n; 1406 cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n; 1407 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 1408 } 1409 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1410 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1411 } 1412 /* Interpolate */ 1413 if (interpolate) { 1414 DM idm; 1415 1416 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1417 ierr = DMDestroy(dm);CHKERRQ(ierr); 1418 *dm = idm; 1419 } 1420 /* Create cylinder geometry */ 1421 { 1422 Vec coordinates; 1423 PetscSection coordSection; 1424 PetscScalar *coords; 1425 PetscInt coordSize, v, c; 1426 1427 /* Build coordinates */ 1428 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1429 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1430 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1431 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1432 for (v = numCells; v < numCells+numVertices; ++v) { 1433 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1434 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1435 } 1436 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1437 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1438 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1439 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1440 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1441 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1442 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1443 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1444 for (c = 0; c < numCells; c++) { 1445 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; 1446 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; 1447 } 1448 if (!rank) { 1449 coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0; 1450 coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0; 1451 } 1452 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1453 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 1454 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1455 } 1456 PetscFunctionReturn(0); 1457 } 1458 1459 PETSC_STATIC_INLINE PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1460 { 1461 PetscReal prod = 0.0; 1462 PetscInt i; 1463 for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]); 1464 return PetscSqrtReal(prod); 1465 } 1466 PETSC_STATIC_INLINE PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1467 { 1468 PetscReal prod = 0.0; 1469 PetscInt i; 1470 for (i = 0; i < dim; ++i) prod += x[i]*y[i]; 1471 return prod; 1472 } 1473 1474 /*@ 1475 DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d. 1476 1477 Collective on MPI_Comm 1478 1479 Input Parameters: 1480 . comm - The communicator for the DM object 1481 . dim - The dimension 1482 - simplex - Use simplices, or tensor product cells 1483 1484 Output Parameter: 1485 . dm - The DM object 1486 1487 Level: beginner 1488 1489 .keywords: DM, create 1490 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1491 @*/ 1492 PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *dm) 1493 { 1494 const PetscInt embedDim = dim+1; 1495 PetscSection coordSection; 1496 Vec coordinates; 1497 PetscScalar *coords; 1498 PetscReal *coordsIn; 1499 PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e; 1500 PetscMPIInt rank; 1501 PetscErrorCode ierr; 1502 1503 PetscFunctionBegin; 1504 PetscValidPointer(dm, 4); 1505 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1506 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1507 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1508 ierr = DMSetCoordinateDim(*dm, dim+1);CHKERRQ(ierr); 1509 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) *dm), &rank);CHKERRQ(ierr); 1510 switch (dim) { 1511 case 2: 1512 if (simplex) { 1513 DM idm; 1514 const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI); 1515 const PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)}; 1516 const PetscInt degree = 5; 1517 PetscInt s[3] = {1, 1, 1}; 1518 PetscInt cone[3]; 1519 PetscInt *graph, p, i, j, k; 1520 1521 numCells = !rank ? 20 : 0; 1522 numVerts = !rank ? 12 : 0; 1523 firstVertex = numCells; 1524 /* Use icosahedron, which for a unit sphere has coordinates which are all cyclic permutations of 1525 1526 (0, \pm 1/\phi+1, \pm \phi/\phi+1) 1527 1528 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 1529 length is then given by 2/\phi = 2 * 2.73606 = 5.47214. 1530 */ 1531 /* Construct vertices */ 1532 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 1533 for (p = 0, i = 0; p < embedDim; ++p) { 1534 for (s[1] = -1; s[1] < 2; s[1] += 2) { 1535 for (s[2] = -1; s[2] < 2; s[2] += 2) { 1536 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim]; 1537 ++i; 1538 } 1539 } 1540 } 1541 /* Construct graph */ 1542 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 1543 for (i = 0; i < numVerts; ++i) { 1544 for (j = 0, k = 0; j < numVerts; ++j) { 1545 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 1546 } 1547 if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree); 1548 } 1549 /* Build Topology */ 1550 ierr = DMPlexSetChart(*dm, 0, numCells+numVerts);CHKERRQ(ierr); 1551 for (c = 0; c < numCells; c++) { 1552 ierr = DMPlexSetConeSize(*dm, c, embedDim);CHKERRQ(ierr); 1553 } 1554 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 1555 /* Cells */ 1556 for (i = 0, c = 0; i < numVerts; ++i) { 1557 for (j = 0; j < i; ++j) { 1558 for (k = 0; k < j; ++k) { 1559 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) { 1560 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; 1561 /* Check orientation */ 1562 { 1563 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}}}; 1564 PetscReal normal[3]; 1565 PetscInt e, f; 1566 1567 for (d = 0; d < embedDim; ++d) { 1568 normal[d] = 0.0; 1569 for (e = 0; e < embedDim; ++e) { 1570 for (f = 0; f < embedDim; ++f) { 1571 normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]); 1572 } 1573 } 1574 } 1575 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 1576 } 1577 ierr = DMPlexSetCone(*dm, c++, cone);CHKERRQ(ierr); 1578 } 1579 } 1580 } 1581 } 1582 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1583 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1584 ierr = PetscFree(graph);CHKERRQ(ierr); 1585 /* Interpolate mesh */ 1586 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1587 ierr = DMDestroy(dm);CHKERRQ(ierr); 1588 *dm = idm; 1589 } else { 1590 /* 1591 12-21--13 1592 | | 1593 25 4 24 1594 | | 1595 12-25--9-16--8-24--13 1596 | | | | 1597 23 5 17 0 15 3 22 1598 | | | | 1599 10-20--6-14--7-19--11 1600 | | 1601 20 1 19 1602 | | 1603 10-18--11 1604 | | 1605 23 2 22 1606 | | 1607 12-21--13 1608 */ 1609 const PetscReal dist = 1.0/PetscSqrtReal(3.0); 1610 PetscInt cone[4], ornt[4]; 1611 1612 numCells = !rank ? 6 : 0; 1613 numEdges = !rank ? 12 : 0; 1614 numVerts = !rank ? 8 : 0; 1615 firstVertex = numCells; 1616 firstEdge = numCells + numVerts; 1617 /* Build Topology */ 1618 ierr = DMPlexSetChart(*dm, 0, numCells+numEdges+numVerts);CHKERRQ(ierr); 1619 for (c = 0; c < numCells; c++) { 1620 ierr = DMPlexSetConeSize(*dm, c, 4);CHKERRQ(ierr); 1621 } 1622 for (e = firstEdge; e < firstEdge+numEdges; ++e) { 1623 ierr = DMPlexSetConeSize(*dm, e, 2);CHKERRQ(ierr); 1624 } 1625 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 1626 /* Cell 0 */ 1627 cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17; 1628 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1629 ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0; 1630 ierr = DMPlexSetConeOrientation(*dm, 0, ornt);CHKERRQ(ierr); 1631 /* Cell 1 */ 1632 cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20; 1633 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1634 ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; 1635 ierr = DMPlexSetConeOrientation(*dm, 1, ornt);CHKERRQ(ierr); 1636 /* Cell 2 */ 1637 cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23; 1638 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1639 ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; 1640 ierr = DMPlexSetConeOrientation(*dm, 2, ornt);CHKERRQ(ierr); 1641 /* Cell 3 */ 1642 cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15; 1643 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1644 ornt[0] = -2; ornt[1] = -2; ornt[2] = 0; ornt[3] = -2; 1645 ierr = DMPlexSetConeOrientation(*dm, 3, ornt);CHKERRQ(ierr); 1646 /* Cell 4 */ 1647 cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25; 1648 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1649 ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = 0; 1650 ierr = DMPlexSetConeOrientation(*dm, 4, ornt);CHKERRQ(ierr); 1651 /* Cell 5 */ 1652 cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23; 1653 ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); 1654 ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = -2; 1655 ierr = DMPlexSetConeOrientation(*dm, 5, ornt);CHKERRQ(ierr); 1656 /* Edges */ 1657 cone[0] = 6; cone[1] = 7; 1658 ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); 1659 cone[0] = 7; cone[1] = 8; 1660 ierr = DMPlexSetCone(*dm, 15, cone);CHKERRQ(ierr); 1661 cone[0] = 8; cone[1] = 9; 1662 ierr = DMPlexSetCone(*dm, 16, cone);CHKERRQ(ierr); 1663 cone[0] = 9; cone[1] = 6; 1664 ierr = DMPlexSetCone(*dm, 17, cone);CHKERRQ(ierr); 1665 cone[0] = 10; cone[1] = 11; 1666 ierr = DMPlexSetCone(*dm, 18, cone);CHKERRQ(ierr); 1667 cone[0] = 11; cone[1] = 7; 1668 ierr = DMPlexSetCone(*dm, 19, cone);CHKERRQ(ierr); 1669 cone[0] = 6; cone[1] = 10; 1670 ierr = DMPlexSetCone(*dm, 20, cone);CHKERRQ(ierr); 1671 cone[0] = 12; cone[1] = 13; 1672 ierr = DMPlexSetCone(*dm, 21, cone);CHKERRQ(ierr); 1673 cone[0] = 13; cone[1] = 11; 1674 ierr = DMPlexSetCone(*dm, 22, cone);CHKERRQ(ierr); 1675 cone[0] = 10; cone[1] = 12; 1676 ierr = DMPlexSetCone(*dm, 23, cone);CHKERRQ(ierr); 1677 cone[0] = 13; cone[1] = 8; 1678 ierr = DMPlexSetCone(*dm, 24, cone);CHKERRQ(ierr); 1679 cone[0] = 12; cone[1] = 9; 1680 ierr = DMPlexSetCone(*dm, 25, cone);CHKERRQ(ierr); 1681 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1682 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1683 /* Build coordinates */ 1684 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 1685 coordsIn[0*embedDim+0] = -dist; coordsIn[0*embedDim+1] = dist; coordsIn[0*embedDim+2] = -dist; 1686 coordsIn[1*embedDim+0] = dist; coordsIn[1*embedDim+1] = dist; coordsIn[1*embedDim+2] = -dist; 1687 coordsIn[2*embedDim+0] = dist; coordsIn[2*embedDim+1] = -dist; coordsIn[2*embedDim+2] = -dist; 1688 coordsIn[3*embedDim+0] = -dist; coordsIn[3*embedDim+1] = -dist; coordsIn[3*embedDim+2] = -dist; 1689 coordsIn[4*embedDim+0] = -dist; coordsIn[4*embedDim+1] = dist; coordsIn[4*embedDim+2] = dist; 1690 coordsIn[5*embedDim+0] = dist; coordsIn[5*embedDim+1] = dist; coordsIn[5*embedDim+2] = dist; 1691 coordsIn[6*embedDim+0] = -dist; coordsIn[6*embedDim+1] = -dist; coordsIn[6*embedDim+2] = dist; 1692 coordsIn[7*embedDim+0] = dist; coordsIn[7*embedDim+1] = -dist; coordsIn[7*embedDim+2] = dist; 1693 } 1694 break; 1695 case 3: 1696 if (simplex) { 1697 DM idm; 1698 const PetscReal edgeLen = 1.0/PETSC_PHI; 1699 const PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5}; 1700 const PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0}; 1701 const PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0}; 1702 const PetscInt degree = 12; 1703 PetscInt s[4] = {1, 1, 1}; 1704 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}, 1705 {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}}; 1706 PetscInt cone[4]; 1707 PetscInt *graph, p, i, j, k, l; 1708 1709 numCells = !rank ? 600 : 0; 1710 numVerts = !rank ? 120 : 0; 1711 firstVertex = numCells; 1712 /* Use the 600-cell, which for a unit sphere has coordinates which are 1713 1714 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16 1715 (\pm 1, 0, 0, 0) all cyclic permutations 8 1716 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96 1717 1718 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 1719 length is then given by 1/\phi = 2.73606. 1720 1721 http://buzzard.pugetsound.edu/sage-practice/ch03s03.html 1722 http://mathworld.wolfram.com/600-Cell.html 1723 */ 1724 /* Construct vertices */ 1725 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 1726 i = 0; 1727 for (s[0] = -1; s[0] < 2; s[0] += 2) { 1728 for (s[1] = -1; s[1] < 2; s[1] += 2) { 1729 for (s[2] = -1; s[2] < 2; s[2] += 2) { 1730 for (s[3] = -1; s[3] < 2; s[3] += 2) { 1731 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d]; 1732 ++i; 1733 } 1734 } 1735 } 1736 } 1737 for (p = 0; p < embedDim; ++p) { 1738 s[1] = s[2] = s[3] = 1; 1739 for (s[0] = -1; s[0] < 2; s[0] += 2) { 1740 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim]; 1741 ++i; 1742 } 1743 } 1744 for (p = 0; p < 12; ++p) { 1745 s[3] = 1; 1746 for (s[0] = -1; s[0] < 2; s[0] += 2) { 1747 for (s[1] = -1; s[1] < 2; s[1] += 2) { 1748 for (s[2] = -1; s[2] < 2; s[2] += 2) { 1749 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]]; 1750 ++i; 1751 } 1752 } 1753 } 1754 } 1755 if (i != numVerts) SETERRQ2(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts); 1756 /* Construct graph */ 1757 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 1758 for (i = 0; i < numVerts; ++i) { 1759 for (j = 0, k = 0; j < numVerts; ++j) { 1760 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 1761 } 1762 if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree); 1763 } 1764 /* Build Topology */ 1765 ierr = DMPlexSetChart(*dm, 0, numCells+numVerts);CHKERRQ(ierr); 1766 for (c = 0; c < numCells; c++) { 1767 ierr = DMPlexSetConeSize(*dm, c, embedDim);CHKERRQ(ierr); 1768 } 1769 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 1770 /* Cells */ 1771 for (i = 0, c = 0; i < numVerts; ++i) { 1772 for (j = 0; j < i; ++j) { 1773 for (k = 0; k < j; ++k) { 1774 for (l = 0; l < k; ++l) { 1775 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] && 1776 graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) { 1777 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l; 1778 /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */ 1779 { 1780 const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 1781 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}}, 1782 {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}}, 1783 {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}}, 1784 1785 {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}}, 1786 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 1787 {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}}, 1788 {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}}, 1789 1790 {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}}, 1791 {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}}, 1792 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 1793 {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}, 1794 1795 {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}}, 1796 {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}}, 1797 {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 1798 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}}; 1799 PetscReal normal[4]; 1800 PetscInt e, f, g; 1801 1802 for (d = 0; d < embedDim; ++d) { 1803 normal[d] = 0.0; 1804 for (e = 0; e < embedDim; ++e) { 1805 for (f = 0; f < embedDim; ++f) { 1806 for (g = 0; g < embedDim; ++g) { 1807 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]); 1808 } 1809 } 1810 } 1811 } 1812 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 1813 } 1814 ierr = DMPlexSetCone(*dm, c++, cone);CHKERRQ(ierr); 1815 } 1816 } 1817 } 1818 } 1819 } 1820 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1821 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1822 ierr = PetscFree(graph);CHKERRQ(ierr); 1823 /* Interpolate mesh */ 1824 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1825 ierr = DMDestroy(dm);CHKERRQ(ierr); 1826 *dm = idm; 1827 break; 1828 } 1829 default: SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim); 1830 } 1831 /* Create coordinates */ 1832 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1833 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1834 ierr = PetscSectionSetFieldComponents(coordSection, 0, embedDim);CHKERRQ(ierr); 1835 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);CHKERRQ(ierr); 1836 for (v = firstVertex; v < firstVertex+numVerts; ++v) { 1837 ierr = PetscSectionSetDof(coordSection, v, embedDim);CHKERRQ(ierr); 1838 ierr = PetscSectionSetFieldDof(coordSection, v, 0, embedDim);CHKERRQ(ierr); 1839 } 1840 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1841 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1842 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1843 ierr = VecSetBlockSize(coordinates, embedDim);CHKERRQ(ierr); 1844 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1845 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1846 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1847 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1848 for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];} 1849 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1850 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 1851 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1852 ierr = PetscFree(coordsIn);CHKERRQ(ierr); 1853 PetscFunctionReturn(0); 1854 } 1855 1856 /* External function declarations here */ 1857 extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling); 1858 extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat); 1859 extern PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mat); 1860 extern PetscErrorCode DMCreateDefaultSection_Plex(DM dm); 1861 extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm); 1862 extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J); 1863 extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm); 1864 extern PetscErrorCode DMCreateCoordinateField_Plex(DM dm, DMField *field); 1865 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm); 1866 extern PetscErrorCode DMSetUp_Plex(DM dm); 1867 extern PetscErrorCode DMDestroy_Plex(DM dm); 1868 extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer); 1869 extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer); 1870 extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm); 1871 extern PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm); 1872 static PetscErrorCode DMInitialize_Plex(DM dm); 1873 1874 /* Replace dm with the contents of dmNew 1875 - Share the DM_Plex structure 1876 - Share the coordinates 1877 - Share the SF 1878 */ 1879 static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew) 1880 { 1881 PetscSF sf; 1882 DM coordDM, coarseDM; 1883 Vec coords; 1884 PetscBool isper; 1885 const PetscReal *maxCell, *L; 1886 const DMBoundaryType *bd; 1887 PetscErrorCode ierr; 1888 1889 PetscFunctionBegin; 1890 ierr = DMGetPointSF(dmNew, &sf);CHKERRQ(ierr); 1891 ierr = DMSetPointSF(dm, sf);CHKERRQ(ierr); 1892 ierr = DMGetCoordinateDM(dmNew, &coordDM);CHKERRQ(ierr); 1893 ierr = DMGetCoordinatesLocal(dmNew, &coords);CHKERRQ(ierr); 1894 ierr = DMSetCoordinateDM(dm, coordDM);CHKERRQ(ierr); 1895 ierr = DMSetCoordinatesLocal(dm, coords);CHKERRQ(ierr); 1896 ierr = DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);CHKERRQ(ierr); 1897 ierr = DMSetPeriodicity(dmNew, isper, maxCell, L, bd);CHKERRQ(ierr); 1898 ierr = DMDestroy_Plex(dm);CHKERRQ(ierr); 1899 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 1900 dm->data = dmNew->data; 1901 ((DM_Plex *) dmNew->data)->refct++; 1902 dmNew->labels->refct++; 1903 if (!--(dm->labels->refct)) { 1904 DMLabelLink next = dm->labels->next; 1905 1906 /* destroy the labels */ 1907 while (next) { 1908 DMLabelLink tmp = next->next; 1909 1910 ierr = DMLabelDestroy(&next->label);CHKERRQ(ierr); 1911 ierr = PetscFree(next);CHKERRQ(ierr); 1912 next = tmp; 1913 } 1914 ierr = PetscFree(dm->labels);CHKERRQ(ierr); 1915 } 1916 dm->labels = dmNew->labels; 1917 dm->depthLabel = dmNew->depthLabel; 1918 ierr = DMGetCoarseDM(dmNew,&coarseDM);CHKERRQ(ierr); 1919 ierr = DMSetCoarseDM(dm,coarseDM);CHKERRQ(ierr); 1920 PetscFunctionReturn(0); 1921 } 1922 1923 /* Swap dm with the contents of dmNew 1924 - Swap the DM_Plex structure 1925 - Swap the coordinates 1926 - Swap the point PetscSF 1927 */ 1928 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 1929 { 1930 DM coordDMA, coordDMB; 1931 Vec coordsA, coordsB; 1932 PetscSF sfA, sfB; 1933 void *tmp; 1934 DMLabelLinkList listTmp; 1935 DMLabel depthTmp; 1936 PetscErrorCode ierr; 1937 1938 PetscFunctionBegin; 1939 ierr = DMGetPointSF(dmA, &sfA);CHKERRQ(ierr); 1940 ierr = DMGetPointSF(dmB, &sfB);CHKERRQ(ierr); 1941 ierr = PetscObjectReference((PetscObject) sfA);CHKERRQ(ierr); 1942 ierr = DMSetPointSF(dmA, sfB);CHKERRQ(ierr); 1943 ierr = DMSetPointSF(dmB, sfA);CHKERRQ(ierr); 1944 ierr = PetscObjectDereference((PetscObject) sfA);CHKERRQ(ierr); 1945 1946 ierr = DMGetCoordinateDM(dmA, &coordDMA);CHKERRQ(ierr); 1947 ierr = DMGetCoordinateDM(dmB, &coordDMB);CHKERRQ(ierr); 1948 ierr = PetscObjectReference((PetscObject) coordDMA);CHKERRQ(ierr); 1949 ierr = DMSetCoordinateDM(dmA, coordDMB);CHKERRQ(ierr); 1950 ierr = DMSetCoordinateDM(dmB, coordDMA);CHKERRQ(ierr); 1951 ierr = PetscObjectDereference((PetscObject) coordDMA);CHKERRQ(ierr); 1952 1953 ierr = DMGetCoordinatesLocal(dmA, &coordsA);CHKERRQ(ierr); 1954 ierr = DMGetCoordinatesLocal(dmB, &coordsB);CHKERRQ(ierr); 1955 ierr = PetscObjectReference((PetscObject) coordsA);CHKERRQ(ierr); 1956 ierr = DMSetCoordinatesLocal(dmA, coordsB);CHKERRQ(ierr); 1957 ierr = DMSetCoordinatesLocal(dmB, coordsA);CHKERRQ(ierr); 1958 ierr = PetscObjectDereference((PetscObject) coordsA);CHKERRQ(ierr); 1959 1960 tmp = dmA->data; 1961 dmA->data = dmB->data; 1962 dmB->data = tmp; 1963 listTmp = dmA->labels; 1964 dmA->labels = dmB->labels; 1965 dmB->labels = listTmp; 1966 depthTmp = dmA->depthLabel; 1967 dmA->depthLabel = dmB->depthLabel; 1968 dmB->depthLabel = depthTmp; 1969 PetscFunctionReturn(0); 1970 } 1971 1972 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 1973 { 1974 DM_Plex *mesh = (DM_Plex*) dm->data; 1975 PetscErrorCode ierr; 1976 1977 PetscFunctionBegin; 1978 /* Handle viewing */ 1979 ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMView", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); 1980 ierr = PetscOptionsInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMView", 0, &mesh->printFEM, NULL);CHKERRQ(ierr); 1981 ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMView", mesh->printTol, &mesh->printTol, NULL);CHKERRQ(ierr); 1982 /* Point Location */ 1983 ierr = PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMView", PETSC_FALSE, &mesh->useHashLocation, NULL);CHKERRQ(ierr); 1984 /* Generation and remeshing */ 1985 ierr = PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMView", PETSC_FALSE, &mesh->remeshBd, NULL);CHKERRQ(ierr); 1986 /* Projection behavior */ 1987 ierr = PetscOptionsInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL);CHKERRQ(ierr); 1988 ierr = PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);CHKERRQ(ierr); 1989 1990 ierr = PetscPartitionerSetFromOptions(mesh->partitioner);CHKERRQ(ierr); 1991 PetscFunctionReturn(0); 1992 } 1993 1994 static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 1995 { 1996 PetscInt refine = 0, coarsen = 0, r; 1997 PetscBool isHierarchy; 1998 PetscErrorCode ierr; 1999 2000 PetscFunctionBegin; 2001 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2002 ierr = PetscOptionsHead(PetscOptionsObject,"DMPlex Options");CHKERRQ(ierr); 2003 /* Handle DMPlex refinement */ 2004 ierr = PetscOptionsInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL);CHKERRQ(ierr); 2005 ierr = PetscOptionsInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy);CHKERRQ(ierr); 2006 if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 2007 if (refine && isHierarchy) { 2008 DM *dms, coarseDM; 2009 2010 ierr = DMGetCoarseDM(dm, &coarseDM);CHKERRQ(ierr); 2011 ierr = PetscObjectReference((PetscObject)coarseDM);CHKERRQ(ierr); 2012 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 2013 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 2014 /* Total hack since we do not pass in a pointer */ 2015 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 2016 if (refine == 1) { 2017 ierr = DMSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 2018 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2019 } else { 2020 ierr = DMSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 2021 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2022 ierr = DMSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 2023 ierr = DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);CHKERRQ(ierr); 2024 } 2025 ierr = DMSetCoarseDM(dms[refine-1], coarseDM);CHKERRQ(ierr); 2026 ierr = PetscObjectDereference((PetscObject)coarseDM);CHKERRQ(ierr); 2027 /* Free DMs */ 2028 for (r = 0; r < refine; ++r) { 2029 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2030 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2031 } 2032 ierr = PetscFree(dms);CHKERRQ(ierr); 2033 } else { 2034 for (r = 0; r < refine; ++r) { 2035 DM refinedMesh; 2036 2037 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2038 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);CHKERRQ(ierr); 2039 /* Total hack since we do not pass in a pointer */ 2040 ierr = DMPlexReplace_Static(dm, refinedMesh);CHKERRQ(ierr); 2041 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2042 ierr = DMDestroy(&refinedMesh);CHKERRQ(ierr); 2043 } 2044 } 2045 /* Handle DMPlex coarsening */ 2046 ierr = PetscOptionsInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL);CHKERRQ(ierr); 2047 ierr = PetscOptionsInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy);CHKERRQ(ierr); 2048 if (coarsen && isHierarchy) { 2049 DM *dms; 2050 2051 ierr = PetscMalloc1(coarsen, &dms);CHKERRQ(ierr); 2052 ierr = DMCoarsenHierarchy(dm, coarsen, dms);CHKERRQ(ierr); 2053 /* Free DMs */ 2054 for (r = 0; r < coarsen; ++r) { 2055 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2056 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2057 } 2058 ierr = PetscFree(dms);CHKERRQ(ierr); 2059 } else { 2060 for (r = 0; r < coarsen; ++r) { 2061 DM coarseMesh; 2062 2063 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2064 ierr = DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);CHKERRQ(ierr); 2065 /* Total hack since we do not pass in a pointer */ 2066 ierr = DMPlexReplace_Static(dm, coarseMesh);CHKERRQ(ierr); 2067 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2068 ierr = DMDestroy(&coarseMesh);CHKERRQ(ierr); 2069 } 2070 } 2071 /* Handle */ 2072 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2073 ierr = PetscOptionsTail();CHKERRQ(ierr); 2074 PetscFunctionReturn(0); 2075 } 2076 2077 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 2078 { 2079 PetscErrorCode ierr; 2080 2081 PetscFunctionBegin; 2082 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2083 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 2084 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 2085 ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); 2086 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 2087 ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); 2088 PetscFunctionReturn(0); 2089 } 2090 2091 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 2092 { 2093 PetscErrorCode ierr; 2094 2095 PetscFunctionBegin; 2096 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2097 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 2098 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 2099 PetscFunctionReturn(0); 2100 } 2101 2102 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 2103 { 2104 PetscInt depth, d; 2105 PetscErrorCode ierr; 2106 2107 PetscFunctionBegin; 2108 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2109 if (depth == 1) { 2110 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 2111 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 2112 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 2113 else {*pStart = 0; *pEnd = 0;} 2114 } else { 2115 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 2116 } 2117 PetscFunctionReturn(0); 2118 } 2119 2120 static PetscErrorCode DMGetNeighors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 2121 { 2122 PetscSF sf; 2123 PetscErrorCode ierr; 2124 2125 PetscFunctionBegin; 2126 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 2127 ierr = PetscSFGetRanks(sf, nranks, ranks, NULL, NULL, NULL);CHKERRQ(ierr); 2128 PetscFunctionReturn(0); 2129 } 2130 2131 static PetscErrorCode DMHasCreateInjection_Plex(DM dm, PetscBool *flg) 2132 { 2133 PetscFunctionBegin; 2134 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 2135 PetscValidPointer(flg,2); 2136 *flg = PETSC_TRUE; 2137 PetscFunctionReturn(0); 2138 } 2139 2140 static PetscErrorCode DMInitialize_Plex(DM dm) 2141 { 2142 PetscErrorCode ierr; 2143 2144 PetscFunctionBegin; 2145 dm->ops->view = DMView_Plex; 2146 dm->ops->load = DMLoad_Plex; 2147 dm->ops->setfromoptions = DMSetFromOptions_Plex; 2148 dm->ops->clone = DMClone_Plex; 2149 dm->ops->setup = DMSetUp_Plex; 2150 dm->ops->createdefaultsection = DMCreateDefaultSection_Plex; 2151 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 2152 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 2153 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 2154 dm->ops->getlocaltoglobalmapping = NULL; 2155 dm->ops->createfieldis = NULL; 2156 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 2157 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 2158 dm->ops->getcoloring = NULL; 2159 dm->ops->creatematrix = DMCreateMatrix_Plex; 2160 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 2161 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 2162 dm->ops->getaggregates = NULL; 2163 dm->ops->getinjection = DMCreateInjection_Plex; 2164 dm->ops->hascreateinjection = DMHasCreateInjection_Plex; 2165 dm->ops->refine = DMRefine_Plex; 2166 dm->ops->coarsen = DMCoarsen_Plex; 2167 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 2168 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 2169 dm->ops->adaptlabel = DMAdaptLabel_Plex; 2170 dm->ops->adaptmetric = DMAdaptMetric_Plex; 2171 dm->ops->globaltolocalbegin = NULL; 2172 dm->ops->globaltolocalend = NULL; 2173 dm->ops->localtoglobalbegin = NULL; 2174 dm->ops->localtoglobalend = NULL; 2175 dm->ops->destroy = DMDestroy_Plex; 2176 dm->ops->createsubdm = DMCreateSubDM_Plex; 2177 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 2178 dm->ops->getdimpoints = DMGetDimPoints_Plex; 2179 dm->ops->locatepoints = DMLocatePoints_Plex; 2180 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 2181 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 2182 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 2183 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 2184 dm->ops->computel2diff = DMComputeL2Diff_Plex; 2185 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 2186 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 2187 dm->ops->getneighbors = DMGetNeighors_Plex; 2188 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);CHKERRQ(ierr); 2189 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);CHKERRQ(ierr); 2190 PetscFunctionReturn(0); 2191 } 2192 2193 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 2194 { 2195 DM_Plex *mesh = (DM_Plex *) dm->data; 2196 PetscErrorCode ierr; 2197 2198 PetscFunctionBegin; 2199 mesh->refct++; 2200 (*newdm)->data = mesh; 2201 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 2202 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 2203 PetscFunctionReturn(0); 2204 } 2205 2206 /*MC 2207 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 2208 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 2209 specified by a PetscSection object. Ownership in the global representation is determined by 2210 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 2211 2212 Level: intermediate 2213 2214 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 2215 M*/ 2216 2217 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 2218 { 2219 DM_Plex *mesh; 2220 PetscInt unit, d; 2221 PetscErrorCode ierr; 2222 2223 PetscFunctionBegin; 2224 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2225 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 2226 dm->dim = 0; 2227 dm->data = mesh; 2228 2229 mesh->refct = 1; 2230 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 2231 mesh->maxConeSize = 0; 2232 mesh->cones = NULL; 2233 mesh->coneOrientations = NULL; 2234 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 2235 mesh->maxSupportSize = 0; 2236 mesh->supports = NULL; 2237 mesh->refinementUniform = PETSC_TRUE; 2238 mesh->refinementLimit = -1.0; 2239 2240 mesh->facesTmp = NULL; 2241 2242 mesh->tetgenOpts = NULL; 2243 mesh->triangleOpts = NULL; 2244 ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); 2245 mesh->remeshBd = PETSC_FALSE; 2246 2247 mesh->subpointMap = NULL; 2248 2249 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 2250 2251 mesh->regularRefinement = PETSC_FALSE; 2252 mesh->depthState = -1; 2253 mesh->globalVertexNumbers = NULL; 2254 mesh->globalCellNumbers = NULL; 2255 mesh->anchorSection = NULL; 2256 mesh->anchorIS = NULL; 2257 mesh->createanchors = NULL; 2258 mesh->computeanchormatrix = NULL; 2259 mesh->parentSection = NULL; 2260 mesh->parents = NULL; 2261 mesh->childIDs = NULL; 2262 mesh->childSection = NULL; 2263 mesh->children = NULL; 2264 mesh->referenceTree = NULL; 2265 mesh->getchildsymmetry = NULL; 2266 for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE; 2267 mesh->vtkCellHeight = 0; 2268 mesh->useAnchors = PETSC_FALSE; 2269 2270 mesh->maxProjectionHeight = 0; 2271 2272 mesh->printSetValues = PETSC_FALSE; 2273 mesh->printFEM = 0; 2274 mesh->printTol = 1.0e-10; 2275 2276 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 2277 PetscFunctionReturn(0); 2278 } 2279 2280 /*@ 2281 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 2282 2283 Collective on MPI_Comm 2284 2285 Input Parameter: 2286 . comm - The communicator for the DMPlex object 2287 2288 Output Parameter: 2289 . mesh - The DMPlex object 2290 2291 Level: beginner 2292 2293 .keywords: DMPlex, create 2294 @*/ 2295 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 2296 { 2297 PetscErrorCode ierr; 2298 2299 PetscFunctionBegin; 2300 PetscValidPointer(mesh,2); 2301 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 2302 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 2303 PetscFunctionReturn(0); 2304 } 2305 2306 /* 2307 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 2308 */ 2309 /* TODO: invertCells and spaceDim arguments could be added also to to DMPlexCreateFromCellListParallel(), DMPlexBuildFromCellList_Internal() and DMPlexCreateFromCellList() */ 2310 PetscErrorCode DMPlexBuildFromCellList_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscBool invertCells, PetscSF *sfVert) 2311 { 2312 PetscSF sfPoint; 2313 PetscLayout vLayout; 2314 PetscHashI vhash; 2315 PetscSFNode *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex; 2316 const PetscInt *vrange; 2317 PetscInt numVerticesAdj, off, *verticesAdj, numVerticesGhost = 0, *localVertex, *cone, c, p, v, g; 2318 PETSC_UNUSED PetscHashIIter ret, iter; 2319 PetscMPIInt rank, size; 2320 PetscErrorCode ierr; 2321 2322 PetscFunctionBegin; 2323 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 2324 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); 2325 /* Partition vertices */ 2326 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);CHKERRQ(ierr); 2327 ierr = PetscLayoutSetLocalSize(vLayout, numVertices);CHKERRQ(ierr); 2328 ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr); 2329 ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr); 2330 ierr = PetscLayoutGetRanges(vLayout, &vrange);CHKERRQ(ierr); 2331 /* Count vertices and map them to procs */ 2332 PetscHashICreate(vhash); 2333 for (c = 0; c < numCells; ++c) { 2334 for (p = 0; p < numCorners; ++p) { 2335 PetscHashIPut(vhash, cells[c*numCorners+p], ret, iter); 2336 } 2337 } 2338 PetscHashISize(vhash, numVerticesAdj); 2339 ierr = PetscMalloc1(numVerticesAdj, &verticesAdj);CHKERRQ(ierr); 2340 off = 0; ierr = PetscHashIGetKeys(vhash, &off, verticesAdj);CHKERRQ(ierr); 2341 if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj); 2342 ierr = PetscSortInt(numVerticesAdj, verticesAdj);CHKERRQ(ierr); 2343 ierr = PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);CHKERRQ(ierr); 2344 for (v = 0; v < numVerticesAdj; ++v) { 2345 const PetscInt gv = verticesAdj[v]; 2346 PetscInt vrank; 2347 2348 ierr = PetscFindInt(gv, size+1, vrange, &vrank);CHKERRQ(ierr); 2349 vrank = vrank < 0 ? -(vrank+2) : vrank; 2350 remoteVerticesAdj[v].index = gv - vrange[vrank]; 2351 remoteVerticesAdj[v].rank = vrank; 2352 } 2353 /* Create cones */ 2354 ierr = DMPlexSetChart(dm, 0, numCells+numVerticesAdj);CHKERRQ(ierr); 2355 for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);} 2356 ierr = DMSetUp(dm);CHKERRQ(ierr); 2357 ierr = DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2358 for (c = 0; c < numCells; ++c) { 2359 for (p = 0; p < numCorners; ++p) { 2360 const PetscInt gv = cells[c*numCorners+p]; 2361 PetscInt lv; 2362 2363 ierr = PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);CHKERRQ(ierr); 2364 if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv); 2365 cone[p] = lv+numCells; 2366 } 2367 if (invertCells) { ierr = DMPlexInvertCell(spaceDim, numCorners, cone);CHKERRQ(ierr); } 2368 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 2369 } 2370 ierr = DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2371 /* Create SF for vertices */ 2372 ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfVert);CHKERRQ(ierr); 2373 ierr = PetscObjectSetName((PetscObject) *sfVert, "Vertex Ownership SF");CHKERRQ(ierr); 2374 ierr = PetscSFSetFromOptions(*sfVert);CHKERRQ(ierr); 2375 ierr = PetscSFSetGraph(*sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);CHKERRQ(ierr); 2376 ierr = PetscFree(verticesAdj);CHKERRQ(ierr); 2377 /* Build pointSF */ 2378 ierr = PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);CHKERRQ(ierr); 2379 for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;} 2380 for (v = 0; v < numVertices; ++v) {vertexOwner[v].index = -1; vertexOwner[v].rank = -1;} 2381 ierr = PetscSFReduceBegin(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 2382 ierr = PetscSFReduceEnd(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 2383 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); 2384 ierr = PetscSFBcastBegin(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 2385 ierr = PetscSFBcastEnd(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 2386 for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost; 2387 ierr = PetscMalloc1(numVerticesGhost, &localVertex);CHKERRQ(ierr); 2388 ierr = PetscMalloc1(numVerticesGhost, &remoteVertex);CHKERRQ(ierr); 2389 for (v = 0, g = 0; v < numVerticesAdj; ++v) { 2390 if (vertexLocal[v].rank != rank) { 2391 localVertex[g] = v+numCells; 2392 remoteVertex[g].index = vertexLocal[v].index; 2393 remoteVertex[g].rank = vertexLocal[v].rank; 2394 ++g; 2395 } 2396 } 2397 ierr = PetscFree2(vertexLocal, vertexOwner);CHKERRQ(ierr); 2398 if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost); 2399 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 2400 ierr = PetscObjectSetName((PetscObject) sfPoint, "point SF");CHKERRQ(ierr); 2401 ierr = PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);CHKERRQ(ierr); 2402 ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr); 2403 PetscHashIDestroy(vhash); 2404 /* Fill in the rest of the topology structure */ 2405 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2406 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2407 PetscFunctionReturn(0); 2408 } 2409 2410 /* 2411 This takes as input the coordinates for each owned vertex 2412 */ 2413 PetscErrorCode DMPlexBuildCoordinates_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numV, PetscSF sfVert, const PetscReal vertexCoords[]) 2414 { 2415 PetscSection coordSection; 2416 Vec coordinates; 2417 PetscScalar *coords; 2418 PetscInt numVertices, numVerticesAdj, coordSize, v; 2419 PetscErrorCode ierr; 2420 2421 PetscFunctionBegin; 2422 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 2423 ierr = PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);CHKERRQ(ierr); 2424 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2425 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2426 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 2427 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVerticesAdj);CHKERRQ(ierr); 2428 for (v = numCells; v < numCells+numVerticesAdj; ++v) { 2429 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 2430 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 2431 } 2432 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2433 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2434 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 2435 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 2436 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2437 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2438 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2439 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2440 { 2441 MPI_Datatype coordtype; 2442 2443 /* Need a temp buffer for coords if we have complex/single */ 2444 ierr = MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);CHKERRQ(ierr); 2445 ierr = MPI_Type_commit(&coordtype);CHKERRQ(ierr); 2446 #if defined(PETSC_USE_COMPLEX) 2447 { 2448 PetscScalar *svertexCoords; 2449 PetscInt i; 2450 ierr = PetscMalloc1(numV*spaceDim,&svertexCoords);CHKERRQ(ierr); 2451 for (i=0; i<numV*spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 2452 ierr = PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 2453 ierr = PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 2454 ierr = PetscFree(svertexCoords);CHKERRQ(ierr); 2455 } 2456 #else 2457 ierr = PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 2458 ierr = PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 2459 #endif 2460 ierr = MPI_Type_free(&coordtype);CHKERRQ(ierr); 2461 } 2462 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2463 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2464 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2465 PetscFunctionReturn(0); 2466 } 2467 2468 /*@C 2469 DMPlexCreateFromCellListParallel - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 2470 2471 Input Parameters: 2472 + comm - The communicator 2473 . dim - The topological dimension of the mesh 2474 . numCells - The number of cells owned by this process 2475 . numVertices - The number of vertices owned by this process 2476 . numCorners - The number of vertices for each cell 2477 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 2478 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 2479 . spaceDim - The spatial dimension used for coordinates 2480 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2481 2482 Output Parameter: 2483 + dm - The DM 2484 - vertexSF - Optional, SF describing complete vertex ownership 2485 2486 Note: Two triangles sharing a face 2487 $ 2488 $ 2 2489 $ / | \ 2490 $ / | \ 2491 $ / | \ 2492 $ 0 0 | 1 3 2493 $ \ | / 2494 $ \ | / 2495 $ \ | / 2496 $ 1 2497 would have input 2498 $ numCells = 2, numVertices = 4 2499 $ cells = [0 1 2 1 3 2] 2500 $ 2501 which would result in the DMPlex 2502 $ 2503 $ 4 2504 $ / | \ 2505 $ / | \ 2506 $ / | \ 2507 $ 2 0 | 1 5 2508 $ \ | / 2509 $ \ | / 2510 $ \ | / 2511 $ 3 2512 2513 Level: beginner 2514 2515 .seealso: DMPlexCreateFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate() 2516 @*/ 2517 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) 2518 { 2519 PetscSF sfVert; 2520 PetscErrorCode ierr; 2521 2522 PetscFunctionBegin; 2523 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2524 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2525 PetscValidLogicalCollectiveInt(*dm, dim, 2); 2526 PetscValidLogicalCollectiveInt(*dm, spaceDim, 8); 2527 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 2528 ierr = DMPlexBuildFromCellList_Parallel_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE, &sfVert);CHKERRQ(ierr); 2529 if (interpolate) { 2530 DM idm; 2531 2532 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2533 ierr = DMDestroy(dm);CHKERRQ(ierr); 2534 *dm = idm; 2535 } 2536 ierr = DMPlexBuildCoordinates_Parallel_Internal(*dm, spaceDim, numCells, numVertices, sfVert, vertexCoords);CHKERRQ(ierr); 2537 if (vertexSF) *vertexSF = sfVert; 2538 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 2539 PetscFunctionReturn(0); 2540 } 2541 2542 /* 2543 This takes as input the common mesh generator output, a list of the vertices for each cell 2544 */ 2545 PetscErrorCode DMPlexBuildFromCellList_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscBool invertCells) 2546 { 2547 PetscInt *cone, c, p; 2548 PetscErrorCode ierr; 2549 2550 PetscFunctionBegin; 2551 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 2552 for (c = 0; c < numCells; ++c) { 2553 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 2554 } 2555 ierr = DMSetUp(dm);CHKERRQ(ierr); 2556 ierr = DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2557 for (c = 0; c < numCells; ++c) { 2558 for (p = 0; p < numCorners; ++p) { 2559 cone[p] = cells[c*numCorners+p]+numCells; 2560 } 2561 if (invertCells) { ierr = DMPlexInvertCell(spaceDim, numCorners, cone);CHKERRQ(ierr); } 2562 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 2563 } 2564 ierr = DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2565 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2566 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2567 PetscFunctionReturn(0); 2568 } 2569 2570 /* 2571 This takes as input the coordinates for each vertex 2572 */ 2573 PetscErrorCode DMPlexBuildCoordinates_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]) 2574 { 2575 PetscSection coordSection; 2576 Vec coordinates; 2577 DM cdm; 2578 PetscScalar *coords; 2579 PetscInt v, d; 2580 PetscErrorCode ierr; 2581 2582 PetscFunctionBegin; 2583 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 2584 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2585 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2586 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 2587 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); 2588 for (v = numCells; v < numCells+numVertices; ++v) { 2589 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 2590 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 2591 } 2592 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2593 2594 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 2595 ierr = DMCreateLocalVector(cdm, &coordinates);CHKERRQ(ierr); 2596 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 2597 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2598 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2599 for (v = 0; v < numVertices; ++v) { 2600 for (d = 0; d < spaceDim; ++d) { 2601 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 2602 } 2603 } 2604 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2605 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2606 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2607 PetscFunctionReturn(0); 2608 } 2609 2610 /*@C 2611 DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 2612 2613 Input Parameters: 2614 + comm - The communicator 2615 . dim - The topological dimension of the mesh 2616 . numCells - The number of cells 2617 . numVertices - The number of vertices 2618 . numCorners - The number of vertices for each cell 2619 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 2620 . cells - An array of numCells*numCorners numbers, the vertices for each cell 2621 . spaceDim - The spatial dimension used for coordinates 2622 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2623 2624 Output Parameter: 2625 . dm - The DM 2626 2627 Note: Two triangles sharing a face 2628 $ 2629 $ 2 2630 $ / | \ 2631 $ / | \ 2632 $ / | \ 2633 $ 0 0 | 1 3 2634 $ \ | / 2635 $ \ | / 2636 $ \ | / 2637 $ 1 2638 would have input 2639 $ numCells = 2, numVertices = 4 2640 $ cells = [0 1 2 1 3 2] 2641 $ 2642 which would result in the DMPlex 2643 $ 2644 $ 4 2645 $ / | \ 2646 $ / | \ 2647 $ / | \ 2648 $ 2 0 | 1 5 2649 $ \ | / 2650 $ \ | / 2651 $ \ | / 2652 $ 3 2653 2654 Level: beginner 2655 2656 .seealso: DMPlexCreateFromDAG(), DMPlexCreate() 2657 @*/ 2658 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) 2659 { 2660 PetscErrorCode ierr; 2661 2662 PetscFunctionBegin; 2663 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2664 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2665 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 2666 ierr = DMPlexBuildFromCellList_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE);CHKERRQ(ierr); 2667 if (interpolate) { 2668 DM idm; 2669 2670 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2671 ierr = DMDestroy(dm);CHKERRQ(ierr); 2672 *dm = idm; 2673 } 2674 ierr = DMPlexBuildCoordinates_Internal(*dm, spaceDim, numCells, numVertices, vertexCoords);CHKERRQ(ierr); 2675 PetscFunctionReturn(0); 2676 } 2677 2678 /*@ 2679 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 2680 2681 Input Parameters: 2682 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 2683 . depth - The depth of the DAG 2684 . numPoints - The number of points at each depth 2685 . coneSize - The cone size of each point 2686 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 2687 . coneOrientations - The orientation of each cone point 2688 - vertexCoords - An array of numVertices*dim numbers, the coordinates of each vertex 2689 2690 Output Parameter: 2691 . dm - The DM 2692 2693 Note: Two triangles sharing a face would have input 2694 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 2695 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 2696 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 2697 $ 2698 which would result in the DMPlex 2699 $ 2700 $ 4 2701 $ / | \ 2702 $ / | \ 2703 $ / | \ 2704 $ 2 0 | 1 5 2705 $ \ | / 2706 $ \ | / 2707 $ \ | / 2708 $ 3 2709 $ 2710 $ Notice that all points are numbered consecutively, unlikely DMPlexCreateFromCellList() 2711 2712 Level: advanced 2713 2714 .seealso: DMPlexCreateFromCellList(), DMPlexCreate() 2715 @*/ 2716 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 2717 { 2718 Vec coordinates; 2719 PetscSection coordSection; 2720 PetscScalar *coords; 2721 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 2722 PetscErrorCode ierr; 2723 2724 PetscFunctionBegin; 2725 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2726 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 2727 if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %d cannot be less than intrinsic dimension %d",dimEmbed,dim); 2728 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 2729 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 2730 for (p = pStart; p < pEnd; ++p) { 2731 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 2732 if (firstVertex < 0 && !coneSize[p - pStart]) { 2733 firstVertex = p - pStart; 2734 } 2735 } 2736 if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %d vertices but could not find any", numPoints[0]); 2737 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 2738 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 2739 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 2740 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 2741 } 2742 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2743 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2744 /* Build coordinates */ 2745 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2746 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2747 ierr = PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);CHKERRQ(ierr); 2748 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 2749 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 2750 ierr = PetscSectionSetDof(coordSection, v, dimEmbed);CHKERRQ(ierr); 2751 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);CHKERRQ(ierr); 2752 } 2753 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2754 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2755 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 2756 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2757 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2758 ierr = VecSetBlockSize(coordinates, dimEmbed);CHKERRQ(ierr); 2759 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2760 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2761 for (v = 0; v < numPoints[0]; ++v) { 2762 PetscInt off; 2763 2764 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 2765 for (d = 0; d < dimEmbed; ++d) { 2766 coords[off+d] = vertexCoords[v*dimEmbed+d]; 2767 } 2768 } 2769 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2770 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2771 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2772 PetscFunctionReturn(0); 2773 } 2774 2775 /*@C 2776 DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file. 2777 2778 + comm - The MPI communicator 2779 . filename - Name of the .dat file 2780 - interpolate - Create faces and edges in the mesh 2781 2782 Output Parameter: 2783 . dm - The DM object representing the mesh 2784 2785 Note: The format is the simplest possible: 2786 $ Ne 2787 $ v0 v1 ... vk 2788 $ Nv 2789 $ x y z marker 2790 2791 Level: beginner 2792 2793 .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate() 2794 @*/ 2795 PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 2796 { 2797 DMLabel marker; 2798 PetscViewer viewer; 2799 Vec coordinates; 2800 PetscSection coordSection; 2801 PetscScalar *coords; 2802 char line[PETSC_MAX_PATH_LEN]; 2803 PetscInt dim = 3, cdim = 3, coordSize, v, c, d; 2804 PetscMPIInt rank; 2805 int snum, Nv, Nc; 2806 PetscErrorCode ierr; 2807 2808 PetscFunctionBegin; 2809 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 2810 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 2811 ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr); 2812 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 2813 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 2814 if (!rank) { 2815 ierr = PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);CHKERRQ(ierr); 2816 snum = sscanf(line, "%d %d", &Nc, &Nv); 2817 if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 2818 } else { 2819 Nc = Nv = 0; 2820 } 2821 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2822 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2823 ierr = DMPlexSetChart(*dm, 0, Nc+Nv);CHKERRQ(ierr); 2824 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 2825 ierr = DMSetCoordinateDim(*dm, cdim);CHKERRQ(ierr); 2826 /* Read topology */ 2827 if (!rank) { 2828 PetscInt cone[8], corners = 8; 2829 int vbuf[8], v; 2830 2831 for (c = 0; c < Nc; ++c) {ierr = DMPlexSetConeSize(*dm, c, corners);CHKERRQ(ierr);} 2832 ierr = DMSetUp(*dm);CHKERRQ(ierr); 2833 for (c = 0; c < Nc; ++c) { 2834 ierr = PetscViewerRead(viewer, line, corners, NULL, PETSC_STRING);CHKERRQ(ierr); 2835 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]); 2836 if (snum != corners) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 2837 for (v = 0; v < corners; ++v) cone[v] = vbuf[v] + Nc; 2838 /* Hexahedra are inverted */ 2839 { 2840 PetscInt tmp = cone[1]; 2841 cone[1] = cone[3]; 2842 cone[3] = tmp; 2843 } 2844 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 2845 } 2846 } 2847 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 2848 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 2849 /* Read coordinates */ 2850 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 2851 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2852 ierr = PetscSectionSetFieldComponents(coordSection, 0, cdim);CHKERRQ(ierr); 2853 ierr = PetscSectionSetChart(coordSection, Nc, Nc + Nv);CHKERRQ(ierr); 2854 for (v = Nc; v < Nc+Nv; ++v) { 2855 ierr = PetscSectionSetDof(coordSection, v, cdim);CHKERRQ(ierr); 2856 ierr = PetscSectionSetFieldDof(coordSection, v, 0, cdim);CHKERRQ(ierr); 2857 } 2858 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2859 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2860 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 2861 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2862 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2863 ierr = VecSetBlockSize(coordinates, cdim);CHKERRQ(ierr); 2864 ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr); 2865 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2866 if (!rank) { 2867 double x[3]; 2868 int val; 2869 2870 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 2871 ierr = DMGetLabel(*dm, "marker", &marker);CHKERRQ(ierr); 2872 for (v = 0; v < Nv; ++v) { 2873 ierr = PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);CHKERRQ(ierr); 2874 snum = sscanf(line, "%lg %lg %lg %d", &x[0], &x[1], &x[2], &val); 2875 if (snum != 4) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 2876 for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d]; 2877 if (val) {ierr = DMLabelSetValue(marker, v+Nc, val);CHKERRQ(ierr);} 2878 } 2879 } 2880 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2881 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 2882 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2883 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 2884 if (interpolate) { 2885 DM idm; 2886 DMLabel bdlabel; 2887 2888 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2889 ierr = DMDestroy(dm);CHKERRQ(ierr); 2890 *dm = idm; 2891 2892 ierr = DMGetLabel(*dm, "marker", &bdlabel);CHKERRQ(ierr); 2893 ierr = DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 2894 ierr = DMPlexLabelComplete(*dm, bdlabel);CHKERRQ(ierr); 2895 } 2896 PetscFunctionReturn(0); 2897 } 2898 2899 /*@C 2900 DMPlexCreateFromFile - This takes a filename and produces a DM 2901 2902 Input Parameters: 2903 + comm - The communicator 2904 . filename - A file name 2905 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 2906 2907 Output Parameter: 2908 . dm - The DM 2909 2910 Level: beginner 2911 2912 .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellList(), DMPlexCreate() 2913 @*/ 2914 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 2915 { 2916 const char *extGmsh = ".msh"; 2917 const char *extCGNS = ".cgns"; 2918 const char *extExodus = ".exo"; 2919 const char *extGenesis = ".gen"; 2920 const char *extFluent = ".cas"; 2921 const char *extHDF5 = ".h5"; 2922 const char *extMed = ".med"; 2923 const char *extPLY = ".ply"; 2924 const char *extCV = ".dat"; 2925 size_t len; 2926 PetscBool isGmsh, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isCV; 2927 PetscMPIInt rank; 2928 PetscErrorCode ierr; 2929 2930 PetscFunctionBegin; 2931 PetscValidPointer(filename, 2); 2932 PetscValidPointer(dm, 4); 2933 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 2934 ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); 2935 if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 2936 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);CHKERRQ(ierr); 2937 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);CHKERRQ(ierr); 2938 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);CHKERRQ(ierr); 2939 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);CHKERRQ(ierr); 2940 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);CHKERRQ(ierr); 2941 ierr = PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);CHKERRQ(ierr); 2942 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);CHKERRQ(ierr); 2943 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);CHKERRQ(ierr); 2944 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);CHKERRQ(ierr); 2945 if (isGmsh) { 2946 ierr = DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2947 } else if (isCGNS) { 2948 ierr = DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2949 } else if (isExodus || isGenesis) { 2950 ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2951 } else if (isFluent) { 2952 ierr = DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2953 } else if (isHDF5) { 2954 PetscBool load_hdf5_xdmf = PETSC_FALSE; 2955 PetscViewer viewer; 2956 2957 ierr = PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);CHKERRQ(ierr); 2958 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 2959 ierr = PetscViewerSetType(viewer, PETSCVIEWERHDF5);CHKERRQ(ierr); 2960 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 2961 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 2962 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2963 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2964 if (load_hdf5_xdmf) {ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);CHKERRQ(ierr);} 2965 ierr = DMLoad(*dm, viewer);CHKERRQ(ierr); 2966 if (load_hdf5_xdmf) {ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);} 2967 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 2968 2969 if (interpolate) { 2970 DM idm; 2971 2972 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2973 ierr = DMDestroy(dm);CHKERRQ(ierr); 2974 *dm = idm; 2975 } 2976 } else if (isMed) { 2977 ierr = DMPlexCreateMedFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2978 } else if (isPLY) { 2979 ierr = DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2980 } else if (isCV) { 2981 ierr = DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2982 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 2983 PetscFunctionReturn(0); 2984 } 2985 2986 /*@ 2987 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 2988 2989 Collective on comm 2990 2991 Input Parameters: 2992 + comm - The communicator 2993 . dim - The spatial dimension 2994 - simplex - Flag for simplex, otherwise use a tensor-product cell 2995 2996 Output Parameter: 2997 . refdm - The reference cell 2998 2999 Level: intermediate 3000 3001 .keywords: reference cell 3002 .seealso: 3003 @*/ 3004 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm) 3005 { 3006 DM rdm; 3007 Vec coords; 3008 PetscErrorCode ierr; 3009 3010 PetscFunctionBeginUser; 3011 ierr = DMCreate(comm, &rdm);CHKERRQ(ierr); 3012 ierr = DMSetType(rdm, DMPLEX);CHKERRQ(ierr); 3013 ierr = DMSetDimension(rdm, dim);CHKERRQ(ierr); 3014 switch (dim) { 3015 case 0: 3016 { 3017 PetscInt numPoints[1] = {1}; 3018 PetscInt coneSize[1] = {0}; 3019 PetscInt cones[1] = {0}; 3020 PetscInt coneOrientations[1] = {0}; 3021 PetscScalar vertexCoords[1] = {0.0}; 3022 3023 ierr = DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3024 } 3025 break; 3026 case 1: 3027 { 3028 PetscInt numPoints[2] = {2, 1}; 3029 PetscInt coneSize[3] = {2, 0, 0}; 3030 PetscInt cones[2] = {1, 2}; 3031 PetscInt coneOrientations[2] = {0, 0}; 3032 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 3033 3034 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3035 } 3036 break; 3037 case 2: 3038 if (simplex) { 3039 PetscInt numPoints[2] = {3, 1}; 3040 PetscInt coneSize[4] = {3, 0, 0, 0}; 3041 PetscInt cones[3] = {1, 2, 3}; 3042 PetscInt coneOrientations[3] = {0, 0, 0}; 3043 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 3044 3045 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3046 } else { 3047 PetscInt numPoints[2] = {4, 1}; 3048 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3049 PetscInt cones[4] = {1, 2, 3, 4}; 3050 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3051 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 3052 3053 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3054 } 3055 break; 3056 case 3: 3057 if (simplex) { 3058 PetscInt numPoints[2] = {4, 1}; 3059 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3060 PetscInt cones[4] = {1, 3, 2, 4}; 3061 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3062 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}; 3063 3064 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3065 } else { 3066 PetscInt numPoints[2] = {8, 1}; 3067 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3068 PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8}; 3069 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3070 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, 3071 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3072 3073 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3074 } 3075 break; 3076 default: 3077 SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %d", dim); 3078 } 3079 ierr = DMPlexInterpolate(rdm, refdm);CHKERRQ(ierr); 3080 if (rdm->coordinateDM) { 3081 DM ncdm; 3082 PetscSection cs; 3083 PetscInt pEnd = -1; 3084 3085 ierr = DMGetDefaultSection(rdm->coordinateDM, &cs);CHKERRQ(ierr); 3086 if (cs) {ierr = PetscSectionGetChart(cs, NULL, &pEnd);CHKERRQ(ierr);} 3087 if (pEnd >= 0) { 3088 ierr = DMClone(rdm->coordinateDM, &ncdm);CHKERRQ(ierr); 3089 ierr = DMSetDefaultSection(ncdm, cs);CHKERRQ(ierr); 3090 ierr = DMSetCoordinateDM(*refdm, ncdm);CHKERRQ(ierr); 3091 ierr = DMDestroy(&ncdm);CHKERRQ(ierr); 3092 } 3093 } 3094 ierr = DMGetCoordinatesLocal(rdm, &coords);CHKERRQ(ierr); 3095 if (coords) { 3096 ierr = DMSetCoordinatesLocal(*refdm, coords);CHKERRQ(ierr); 3097 } else { 3098 ierr = DMGetCoordinates(rdm, &coords);CHKERRQ(ierr); 3099 if (coords) {ierr = DMSetCoordinates(*refdm, coords);CHKERRQ(ierr);} 3100 } 3101 ierr = DMDestroy(&rdm);CHKERRQ(ierr); 3102 PetscFunctionReturn(0); 3103 } 3104