1 #define PETSCDM_DLL 2 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 #include <petsc/private/hashseti.h> /*I "petscdmplex.h" I*/ 4 #include <petscsf.h> 5 6 /*@ 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 */ 338 339 /* Side 0 (Top) */ 340 for (vy = 0; vy < faces[1]; vy++) { 341 for (vx = 0; vx < faces[0]; vx++) { 342 voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx; 343 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0]; 344 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 345 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 346 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 347 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 348 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 349 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);CHKERRQ(ierr); 350 iface++; 351 } 352 } 353 354 /* Side 1 (Bottom) */ 355 for (vy = 0; vy < faces[1]; vy++) { 356 for (vx = 0; vx < faces[0]; vx++) { 357 voffset = numFaces + vy*(faces[0]+1) + vx; 358 cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1; 359 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 360 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 361 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 362 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 363 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 364 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);CHKERRQ(ierr); 365 iface++; 366 } 367 } 368 369 /* Side 2 (Front) */ 370 for (vz = 0; vz < faces[2]; vz++) { 371 for (vx = 0; vx < faces[0]; vx++) { 372 voffset = numFaces + vz*vertices[0]*vertices[1] + vx; 373 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1]; 374 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 375 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 376 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 377 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 378 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 379 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);CHKERRQ(ierr); 380 iface++; 381 } 382 } 383 384 /* Side 3 (Back) */ 385 for (vz = 0; vz < faces[2]; vz++) { 386 for (vx = 0; vx < faces[0]; vx++) { 387 voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx; 388 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1; 389 cone[2] = voffset+1; cone[3] = voffset; 390 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 391 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 392 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 393 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 394 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 395 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);CHKERRQ(ierr); 396 iface++; 397 } 398 } 399 400 /* Side 4 (Left) */ 401 for (vz = 0; vz < faces[2]; vz++) { 402 for (vy = 0; vy < faces[1]; vy++) { 403 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0]; 404 cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1]; 405 cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0]; 406 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 407 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 408 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 409 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 410 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[1]+0, 1);CHKERRQ(ierr); 411 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);CHKERRQ(ierr); 412 iface++; 413 } 414 } 415 416 /* Side 5 (Right) */ 417 for (vz = 0; vz < faces[2]; vz++) { 418 for (vy = 0; vy < faces[1]; vy++) { 419 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + faces[0]; 420 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset; 421 cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0]; 422 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 423 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 424 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 425 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 426 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 427 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);CHKERRQ(ierr); 428 iface++; 429 } 430 } 431 } 432 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 433 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 434 /* Build coordinates */ 435 ierr = DMSetCoordinateDim(dm, 3);CHKERRQ(ierr); 436 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 437 ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr); 438 for (v = numFaces; v < numFaces+numVertices; ++v) { 439 ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr); 440 } 441 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 442 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 443 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 444 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 445 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 446 ierr = VecSetBlockSize(coordinates, 3);CHKERRQ(ierr); 447 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 448 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 449 for (vz = 0; vz <= faces[2]; ++vz) { 450 for (vy = 0; vy <= faces[1]; ++vy) { 451 for (vx = 0; vx <= faces[0]; ++vx) { 452 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx; 453 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy; 454 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz; 455 } 456 } 457 } 458 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 459 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 460 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 461 PetscFunctionReturn(0); 462 } 463 464 static PetscErrorCode DMPlexCreateLineMesh_Internal(MPI_Comm comm,PetscInt segments,PetscReal lower,PetscReal upper,DMBoundaryType bd,DM *dm) 465 { 466 PetscInt i,fStart,fEnd,numCells = 0,numVerts = 0; 467 PetscInt numPoints[2],*coneSize,*cones,*coneOrientations; 468 PetscScalar *vertexCoords; 469 PetscReal L,maxCell; 470 PetscBool markerSeparate = PETSC_FALSE; 471 PetscInt markerLeft = 1, faceMarkerLeft = 1; 472 PetscInt markerRight = 1, faceMarkerRight = 2; 473 PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE; 474 PetscMPIInt rank; 475 PetscErrorCode ierr; 476 477 PetscFunctionBegin; 478 PetscValidPointer(dm,4); 479 480 ierr = DMCreate(comm,dm);CHKERRQ(ierr); 481 ierr = DMSetType(*dm,DMPLEX);CHKERRQ(ierr); 482 ierr = DMSetDimension(*dm,1);CHKERRQ(ierr); 483 ierr = DMCreateLabel(*dm,"marker");CHKERRQ(ierr); 484 ierr = DMCreateLabel(*dm,"Face Sets");CHKERRQ(ierr); 485 486 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 487 if (!rank) numCells = segments; 488 if (!rank) numVerts = segments + (wrap ? 0 : 1); 489 490 numPoints[0] = numVerts ; numPoints[1] = numCells; 491 ierr = PetscMalloc4(numCells+numVerts,&coneSize,numCells*2,&cones,numCells+numVerts,&coneOrientations,numVerts,&vertexCoords);CHKERRQ(ierr); 492 ierr = PetscMemzero(coneOrientations,(numCells+numVerts)*sizeof(PetscInt));CHKERRQ(ierr); 493 for (i = 0; i < numCells; ++i) { coneSize[i] = 2; } 494 for (i = 0; i < numVerts; ++i) { coneSize[numCells+i] = 0; } 495 for (i = 0; i < numCells; ++i) { cones[2*i] = numCells + i%numVerts; cones[2*i+1] = numCells + (i+1)%numVerts; } 496 for (i = 0; i < numVerts; ++i) { vertexCoords[i] = lower + (upper-lower)*((PetscReal)i/(PetscReal)numCells); } 497 ierr = DMPlexCreateFromDAG(*dm,1,numPoints,coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 498 ierr = PetscFree4(coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 499 500 ierr = PetscOptionsGetBool(((PetscObject)*dm)->options,((PetscObject)*dm)->prefix,"-dm_plex_separate_marker",&markerSeparate,NULL);CHKERRQ(ierr); 501 if (markerSeparate) { markerLeft = faceMarkerLeft; markerRight = faceMarkerRight;} 502 if (!wrap && !rank) { 503 ierr = DMPlexGetHeightStratum(*dm,1,&fStart,&fEnd);CHKERRQ(ierr); 504 ierr = DMSetLabelValue(*dm,"marker",fStart,markerLeft);CHKERRQ(ierr); 505 ierr = DMSetLabelValue(*dm,"marker",fEnd-1,markerRight);CHKERRQ(ierr); 506 ierr = DMSetLabelValue(*dm,"Face Sets",fStart,faceMarkerLeft);CHKERRQ(ierr); 507 ierr = DMSetLabelValue(*dm,"Face Sets",fEnd-1,faceMarkerRight);CHKERRQ(ierr); 508 } 509 if (wrap) { 510 L = upper - lower; 511 maxCell = (PetscReal)1.1*(L/(PetscReal)PetscMax(1,segments)); 512 ierr = DMSetPeriodicity(*dm,PETSC_TRUE,&maxCell,&L,&bd);CHKERRQ(ierr); 513 } 514 PetscFunctionReturn(0); 515 } 516 517 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) 518 { 519 DM boundary; 520 PetscInt i; 521 PetscErrorCode ierr; 522 523 PetscFunctionBegin; 524 PetscValidPointer(dm, 4); 525 for (i = 0; i < dim; ++i) if (periodicity[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity is not supported for simplex meshes"); 526 ierr = DMCreate(comm, &boundary);CHKERRQ(ierr); 527 PetscValidLogicalCollectiveInt(boundary,dim,2); 528 ierr = DMSetType(boundary, DMPLEX);CHKERRQ(ierr); 529 ierr = DMSetDimension(boundary, dim-1);CHKERRQ(ierr); 530 ierr = DMSetCoordinateDim(boundary, dim);CHKERRQ(ierr); 531 switch (dim) { 532 case 2: ierr = DMPlexCreateSquareBoundary(boundary, lower, upper, faces);CHKERRQ(ierr);break; 533 case 3: ierr = DMPlexCreateCubeBoundary(boundary, lower, upper, faces);CHKERRQ(ierr);break; 534 default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 535 } 536 ierr = DMPlexGenerate(boundary, NULL, interpolate, dm);CHKERRQ(ierr); 537 ierr = DMDestroy(&boundary);CHKERRQ(ierr); 538 PetscFunctionReturn(0); 539 } 540 541 static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ) 542 { 543 DMLabel cutLabel = NULL; 544 PetscInt markerTop = 1, faceMarkerTop = 1; 545 PetscInt markerBottom = 1, faceMarkerBottom = 1; 546 PetscInt markerFront = 1, faceMarkerFront = 1; 547 PetscInt markerBack = 1, faceMarkerBack = 1; 548 PetscInt markerRight = 1, faceMarkerRight = 1; 549 PetscInt markerLeft = 1, faceMarkerLeft = 1; 550 PetscInt dim; 551 PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE; 552 PetscMPIInt rank; 553 PetscErrorCode ierr; 554 555 PetscFunctionBegin; 556 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 557 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 558 ierr = DMCreateLabel(dm,"marker");CHKERRQ(ierr); 559 ierr = DMCreateLabel(dm,"Face Sets");CHKERRQ(ierr); 560 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL);CHKERRQ(ierr); 561 if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST || 562 bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST || 563 bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) { 564 565 if (cutMarker) {ierr = DMCreateLabel(dm, "periodic_cut");CHKERRQ(ierr); ierr = DMGetLabel(dm, "periodic_cut", &cutLabel);CHKERRQ(ierr);} 566 } 567 switch (dim) { 568 case 2: 569 faceMarkerTop = 3; 570 faceMarkerBottom = 1; 571 faceMarkerRight = 2; 572 faceMarkerLeft = 4; 573 break; 574 case 3: 575 faceMarkerBottom = 1; 576 faceMarkerTop = 2; 577 faceMarkerFront = 3; 578 faceMarkerBack = 4; 579 faceMarkerRight = 5; 580 faceMarkerLeft = 6; 581 break; 582 default: 583 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %d not supported",dim); 584 break; 585 } 586 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 587 if (markerSeparate) { 588 markerBottom = faceMarkerBottom; 589 markerTop = faceMarkerTop; 590 markerFront = faceMarkerFront; 591 markerBack = faceMarkerBack; 592 markerRight = faceMarkerRight; 593 markerLeft = faceMarkerLeft; 594 } 595 { 596 const PetscInt numXEdges = !rank ? edges[0] : 0; 597 const PetscInt numYEdges = !rank ? edges[1] : 0; 598 const PetscInt numZEdges = !rank ? edges[2] : 0; 599 const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; 600 const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; 601 const PetscInt numZVertices = !rank ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0; 602 const PetscInt numCells = numXEdges*numYEdges*numZEdges; 603 const PetscInt numXFaces = numYEdges*numZEdges; 604 const PetscInt numYFaces = numXEdges*numZEdges; 605 const PetscInt numZFaces = numXEdges*numYEdges; 606 const PetscInt numTotXFaces = numXVertices*numXFaces; 607 const PetscInt numTotYFaces = numYVertices*numYFaces; 608 const PetscInt numTotZFaces = numZVertices*numZFaces; 609 const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces; 610 const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices; 611 const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices; 612 const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices; 613 const PetscInt numVertices = numXVertices*numYVertices*numZVertices; 614 const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges; 615 const PetscInt firstVertex = (dim == 2) ? numFaces : numCells; 616 const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices; 617 const PetscInt firstYFace = firstXFace + numTotXFaces; 618 const PetscInt firstZFace = firstYFace + numTotYFaces; 619 const PetscInt firstXEdge = numCells + numFaces + numVertices; 620 const PetscInt firstYEdge = firstXEdge + numTotXEdges; 621 const PetscInt firstZEdge = firstYEdge + numTotYEdges; 622 Vec coordinates; 623 PetscSection coordSection; 624 PetscScalar *coords; 625 PetscInt coordSize; 626 PetscInt v, vx, vy, vz; 627 PetscInt c, f, fx, fy, fz, e, ex, ey, ez; 628 629 ierr = DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);CHKERRQ(ierr); 630 for (c = 0; c < numCells; c++) { 631 ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr); 632 } 633 for (f = firstXFace; f < firstXFace+numFaces; ++f) { 634 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 635 } 636 for (e = firstXEdge; e < firstXEdge+numEdges; ++e) { 637 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 638 } 639 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 640 /* Build cells */ 641 for (fz = 0; fz < numZEdges; ++fz) { 642 for (fy = 0; fy < numYEdges; ++fy) { 643 for (fx = 0; fx < numXEdges; ++fx) { 644 PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx; 645 PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 646 PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices); 647 PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 648 PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices); 649 PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 650 PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices); 651 /* B, T, F, K, R, L */ 652 PetscInt ornt[6] = {-4, 0, 0, -1, 0, -4}; /* ??? */ 653 PetscInt cone[6]; 654 655 /* no boundary twisting in 3D */ 656 cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL; 657 ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr); 658 ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr); 659 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 660 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 661 if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 662 } 663 } 664 } 665 /* Build x faces */ 666 for (fz = 0; fz < numZEdges; ++fz) { 667 for (fy = 0; fy < numYEdges; ++fy) { 668 for (fx = 0; fx < numXVertices; ++fx) { 669 PetscInt face = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 670 PetscInt edgeL = firstZEdge + ( fy* numXVertices+fx)*numZEdges + fz; 671 PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz; 672 PetscInt edgeB = firstYEdge + ( fz* numXVertices+fx)*numYEdges + fy; 673 PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy; 674 PetscInt ornt[4] = {0, 0, -2, -2}; 675 PetscInt cone[4]; 676 677 if (dim == 3) { 678 /* markers */ 679 if (bdX != DM_BOUNDARY_PERIODIC) { 680 if (fx == numXVertices-1) { 681 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);CHKERRQ(ierr); 682 ierr = DMSetLabelValue(dm, "marker", face, markerRight);CHKERRQ(ierr); 683 } 684 else if (fx == 0) { 685 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);CHKERRQ(ierr); 686 ierr = DMSetLabelValue(dm, "marker", face, markerLeft);CHKERRQ(ierr); 687 } 688 } 689 } 690 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 691 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 692 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 693 } 694 } 695 } 696 /* Build y faces */ 697 for (fz = 0; fz < numZEdges; ++fz) { 698 for (fx = 0; fx < numXEdges; ++fx) { 699 for (fy = 0; fy < numYVertices; ++fy) { 700 PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 701 PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx )*numZEdges + fz; 702 PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz; 703 PetscInt edgeB = firstXEdge + ( fz *numYVertices+fy)*numXEdges + fx; 704 PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx; 705 PetscInt ornt[4] = {0, 0, -2, -2}; 706 PetscInt cone[4]; 707 708 if (dim == 3) { 709 /* markers */ 710 if (bdY != DM_BOUNDARY_PERIODIC) { 711 if (fy == numYVertices-1) { 712 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);CHKERRQ(ierr); 713 ierr = DMSetLabelValue(dm, "marker", face, markerBack);CHKERRQ(ierr); 714 } 715 else if (fy == 0) { 716 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);CHKERRQ(ierr); 717 ierr = DMSetLabelValue(dm, "marker", face, markerFront);CHKERRQ(ierr); 718 } 719 } 720 } 721 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 722 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 723 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 724 } 725 } 726 } 727 /* Build z faces */ 728 for (fy = 0; fy < numYEdges; ++fy) { 729 for (fx = 0; fx < numXEdges; ++fx) { 730 for (fz = 0; fz < numZVertices; fz++) { 731 PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 732 PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx )*numYEdges + fy; 733 PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy; 734 PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy )*numXEdges + fx; 735 PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx; 736 PetscInt ornt[4] = {0, 0, -2, -2}; 737 PetscInt cone[4]; 738 739 if (dim == 2) { 740 if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -2;} 741 if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;} 742 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 743 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 744 } else { 745 /* markers */ 746 if (bdZ != DM_BOUNDARY_PERIODIC) { 747 if (fz == numZVertices-1) { 748 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);CHKERRQ(ierr); 749 ierr = DMSetLabelValue(dm, "marker", face, markerTop);CHKERRQ(ierr); 750 } 751 else if (fz == 0) { 752 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);CHKERRQ(ierr); 753 ierr = DMSetLabelValue(dm, "marker", face, markerBottom);CHKERRQ(ierr); 754 } 755 } 756 } 757 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 758 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 759 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 760 } 761 } 762 } 763 /* Build Z edges*/ 764 for (vy = 0; vy < numYVertices; vy++) { 765 for (vx = 0; vx < numXVertices; vx++) { 766 for (ez = 0; ez < numZEdges; ez++) { 767 const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez; 768 const PetscInt vertexB = firstVertex + ( ez *numYVertices+vy)*numXVertices + vx; 769 const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx; 770 PetscInt cone[2]; 771 772 if (dim == 3) { 773 if (bdX != DM_BOUNDARY_PERIODIC) { 774 if (vx == numXVertices-1) { 775 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 776 } 777 else if (vx == 0) { 778 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 779 } 780 } 781 if (bdY != DM_BOUNDARY_PERIODIC) { 782 if (vy == numYVertices-1) { 783 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 784 } 785 else if (vy == 0) { 786 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 787 } 788 } 789 } 790 cone[0] = vertexB; cone[1] = vertexT; 791 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 792 } 793 } 794 } 795 /* Build Y edges*/ 796 for (vz = 0; vz < numZVertices; vz++) { 797 for (vx = 0; vx < numXVertices; vx++) { 798 for (ey = 0; ey < numYEdges; ey++) { 799 const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx; 800 const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey; 801 const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx; 802 const PetscInt vertexK = firstVertex + nextv; 803 PetscInt cone[2]; 804 805 cone[0] = vertexF; cone[1] = vertexK; 806 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 807 if (dim == 2) { 808 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 809 if (vx == numXVertices-1) { 810 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);CHKERRQ(ierr); 811 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 812 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 813 if (ey == numYEdges-1) { 814 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 815 } 816 } else if (vx == 0) { 817 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);CHKERRQ(ierr); 818 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 819 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 820 if (ey == numYEdges-1) { 821 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 822 } 823 } 824 } else { 825 if (vx == 0 && cutLabel) { 826 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 827 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 828 if (ey == numYEdges-1) { 829 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 830 } 831 } 832 } 833 } else { 834 if (bdX != DM_BOUNDARY_PERIODIC) { 835 if (vx == numXVertices-1) { 836 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 837 } else if (vx == 0) { 838 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 839 } 840 } 841 if (bdZ != DM_BOUNDARY_PERIODIC) { 842 if (vz == numZVertices-1) { 843 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 844 } else if (vz == 0) { 845 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 846 } 847 } 848 } 849 } 850 } 851 } 852 /* Build X edges*/ 853 for (vz = 0; vz < numZVertices; vz++) { 854 for (vy = 0; vy < numYVertices; vy++) { 855 for (ex = 0; ex < numXEdges; ex++) { 856 const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices; 857 const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex; 858 const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex; 859 const PetscInt vertexR = firstVertex + nextv; 860 PetscInt cone[2]; 861 862 cone[0] = vertexL; cone[1] = vertexR; 863 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 864 if (dim == 2) { 865 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 866 if (vy == numYVertices-1) { 867 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);CHKERRQ(ierr); 868 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 869 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 870 if (ex == numXEdges-1) { 871 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 872 } 873 } else if (vy == 0) { 874 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);CHKERRQ(ierr); 875 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 876 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 877 if (ex == numXEdges-1) { 878 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 879 } 880 } 881 } else { 882 if (vy == 0 && cutLabel) { 883 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 884 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 885 if (ex == numXEdges-1) { 886 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 887 } 888 } 889 } 890 } else { 891 if (bdY != DM_BOUNDARY_PERIODIC) { 892 if (vy == numYVertices-1) { 893 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 894 } 895 else if (vy == 0) { 896 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 897 } 898 } 899 if (bdZ != DM_BOUNDARY_PERIODIC) { 900 if (vz == numZVertices-1) { 901 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 902 } 903 else if (vz == 0) { 904 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 905 } 906 } 907 } 908 } 909 } 910 } 911 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 912 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 913 /* Build coordinates */ 914 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 915 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 916 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 917 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr); 918 for (v = firstVertex; v < firstVertex+numVertices; ++v) { 919 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 920 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 921 } 922 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 923 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 924 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 925 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 926 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 927 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 928 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 929 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 930 for (vz = 0; vz < numZVertices; ++vz) { 931 for (vy = 0; vy < numYVertices; ++vy) { 932 for (vx = 0; vx < numXVertices; ++vx) { 933 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx; 934 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy; 935 if (dim == 3) { 936 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz; 937 } 938 } 939 } 940 } 941 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 942 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 943 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 944 } 945 PetscFunctionReturn(0); 946 } 947 948 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) 949 { 950 PetscInt i; 951 PetscErrorCode ierr; 952 953 PetscFunctionBegin; 954 PetscValidPointer(dm, 7); 955 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 956 PetscValidLogicalCollectiveInt(*dm,dim,2); 957 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 958 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 959 switch (dim) { 960 case 2: {ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], DM_BOUNDARY_NONE);CHKERRQ(ierr);break;} 961 case 3: {ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], periodicity[2]);CHKERRQ(ierr);break;} 962 default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 963 } 964 if (periodicity[0] == DM_BOUNDARY_PERIODIC || periodicity[0] == DM_BOUNDARY_TWIST || 965 periodicity[1] == DM_BOUNDARY_PERIODIC || periodicity[1] == DM_BOUNDARY_TWIST || 966 (dim > 2 && (periodicity[2] == DM_BOUNDARY_PERIODIC || periodicity[2] == DM_BOUNDARY_TWIST))) { 967 PetscReal L[3]; 968 PetscReal maxCell[3]; 969 970 for (i = 0; i < dim; i++) { 971 L[i] = upper[i] - lower[i]; 972 maxCell[i] = 1.1 * (L[i] / PetscMax(1,faces[i])); 973 } 974 ierr = DMSetPeriodicity(*dm,PETSC_TRUE,maxCell,L,periodicity);CHKERRQ(ierr); 975 } 976 if (!interpolate) { 977 DM udm; 978 979 ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr); 980 ierr = DMPlexCopyCoordinates(*dm, udm);CHKERRQ(ierr); 981 ierr = DMDestroy(dm);CHKERRQ(ierr); 982 *dm = udm; 983 } 984 PetscFunctionReturn(0); 985 } 986 987 /*@C 988 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra). 989 990 Collective on MPI_Comm 991 992 Input Parameters: 993 + comm - The communicator for the DM object 994 . dim - The spatial dimension 995 . simplex - PETSC_TRUE for simplices, PETSC_FALSE for tensor cells 996 . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 997 . lower - The lower left corner, or NULL for (0, 0, 0) 998 . upper - The upper right corner, or NULL for (1, 1, 1) 999 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 1000 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1001 1002 Output Parameter: 1003 . dm - The DM object 1004 1005 Options Database Keys: 1006 + -dm_plex_box_lower <x,y,z> - Specify lower-left-bottom coordinates for the box 1007 - -dm_plex_box_upper <x,y,z> - Specify upper-right-top coordinates for the box 1008 1009 Note: Here is the numbering returned for 2 faces in each direction for tensor cells: 1010 $ 10---17---11---18----12 1011 $ | | | 1012 $ | | | 1013 $ 20 2 22 3 24 1014 $ | | | 1015 $ | | | 1016 $ 7---15----8---16----9 1017 $ | | | 1018 $ | | | 1019 $ 19 0 21 1 23 1020 $ | | | 1021 $ | | | 1022 $ 4---13----5---14----6 1023 1024 and for simplicial cells 1025 1026 $ 14----8---15----9----16 1027 $ |\ 5 |\ 7 | 1028 $ | \ | \ | 1029 $ 13 2 14 3 15 1030 $ | 4 \ | 6 \ | 1031 $ | \ | \ | 1032 $ 11----6---12----7----13 1033 $ |\ |\ | 1034 $ | \ 1 | \ 3 | 1035 $ 10 0 11 1 12 1036 $ | 0 \ | 2 \ | 1037 $ | \ | \ | 1038 $ 8----4----9----5----10 1039 1040 Level: beginner 1041 1042 .keywords: DM, create 1043 .seealso: DMPlexCreateFromFile(), DMPlexCreateHexCylinderMesh(), DMSetType(), DMCreate() 1044 @*/ 1045 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) 1046 { 1047 PetscInt fac[3] = {0, 0, 0}; 1048 PetscReal low[3] = {0, 0, 0}; 1049 PetscReal upp[3] = {1, 1, 1}; 1050 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1051 PetscInt i, n; 1052 PetscBool flg; 1053 PetscErrorCode ierr; 1054 1055 PetscFunctionBegin; 1056 n = 3; 1057 ierr = PetscOptionsGetIntArray(NULL, NULL, "-dm_plex_box_faces", fac, &n, &flg);CHKERRQ(ierr); 1058 for (i = 0; i < dim; ++i) fac[i] = faces ? faces[i] : (flg && i < n ? fac[i] : (dim == 1 ? 1 : 4-dim)); 1059 if (lower) for (i = 0; i < dim; ++i) low[i] = lower[i]; 1060 if (upper) for (i = 0; i < dim; ++i) upp[i] = upper[i]; 1061 if (periodicity) for (i = 0; i < dim; ++i) bdt[i] = periodicity[i]; 1062 /* Allow bounds to be specified from the command line */ 1063 n = 3; 1064 ierr = PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_lower", low, &n, &flg);CHKERRQ(ierr); 1065 if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim); 1066 n = 3; 1067 ierr = PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_upper", upp, &n, &flg);CHKERRQ(ierr); 1068 if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim); 1069 1070 if (dim == 1) {ierr = DMPlexCreateLineMesh_Internal(comm, fac[0], low[0], upp[0], bdt[0], dm);CHKERRQ(ierr);} 1071 else if (simplex) {ierr = DMPlexCreateBoxMesh_Simplex_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);CHKERRQ(ierr);} 1072 else {ierr = DMPlexCreateBoxMesh_Tensor_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);CHKERRQ(ierr);} 1073 PetscFunctionReturn(0); 1074 } 1075 1076 /*@ 1077 DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells. 1078 1079 Collective on MPI_Comm 1080 1081 Input Parameters: 1082 + comm - The communicator for the DM object 1083 . faces - Number of faces per dimension, or NULL for (1, 1, 1) 1084 . lower - The lower left corner, or NULL for (0, 0, 0) 1085 . upper - The upper right corner, or NULL for (1, 1, 1) 1086 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 1087 . ordExt - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1088 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1089 1090 Output Parameter: 1091 . dm - The DM object 1092 1093 Level: beginner 1094 1095 .keywords: DM, create 1096 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateWedgeCylinderMesh(), DMPlexExtrude(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1097 @*/ 1098 PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool ordExt, PetscBool interpolate, DM *dm) 1099 { 1100 DM bdm, botdm; 1101 PetscInt i; 1102 PetscInt fac[3] = {0, 0, 0}; 1103 PetscReal low[3] = {0, 0, 0}; 1104 PetscReal upp[3] = {1, 1, 1}; 1105 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1106 PetscErrorCode ierr; 1107 1108 PetscFunctionBegin; 1109 for (i = 0; i < 3; ++i) fac[i] = faces ? (faces[i] > 0 ? faces[i] : 1) : 1; 1110 if (lower) for (i = 0; i < 3; ++i) low[i] = lower[i]; 1111 if (upper) for (i = 0; i < 3; ++i) upp[i] = upper[i]; 1112 if (periodicity) for (i = 0; i < 3; ++i) bdt[i] = periodicity[i]; 1113 for (i = 0; i < 3; ++i) if (bdt[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity not yet supported"); 1114 1115 ierr = DMCreate(comm, &bdm);CHKERRQ(ierr); 1116 ierr = DMSetType(bdm, DMPLEX);CHKERRQ(ierr); 1117 ierr = DMSetDimension(bdm, 1);CHKERRQ(ierr); 1118 ierr = DMSetCoordinateDim(bdm, 2);CHKERRQ(ierr); 1119 ierr = DMPlexCreateSquareBoundary(bdm, low, upp, fac);CHKERRQ(ierr); 1120 ierr = DMPlexGenerate(bdm, NULL, PETSC_FALSE, &botdm);CHKERRQ(ierr); 1121 ierr = DMDestroy(&bdm);CHKERRQ(ierr); 1122 ierr = DMPlexExtrude(botdm, fac[2], upp[2] - low[2], ordExt, interpolate, dm);CHKERRQ(ierr); 1123 if (low[2] != 0.0) { 1124 Vec v; 1125 PetscScalar *x; 1126 PetscInt cDim, n; 1127 1128 ierr = DMGetCoordinatesLocal(*dm, &v);CHKERRQ(ierr); 1129 ierr = VecGetBlockSize(v, &cDim);CHKERRQ(ierr); 1130 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 1131 ierr = VecGetArray(v, &x);CHKERRQ(ierr); 1132 x += cDim; 1133 for (i=0; i<n; i+=cDim) x[i] += low[2]; 1134 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 1135 ierr = DMSetCoordinatesLocal(*dm, v);CHKERRQ(ierr); 1136 } 1137 ierr = DMDestroy(&botdm);CHKERRQ(ierr); 1138 PetscFunctionReturn(0); 1139 } 1140 1141 /*@ 1142 DMPlexExtrude - Creates a (d+1)-D mesh by extruding a d-D mesh in the normal direction using prismatic cells. 1143 1144 Collective on idm 1145 1146 Input Parameters: 1147 + idm - The mesh to be extruted 1148 . layers - The number of layers 1149 . height - The height of the extruded layer 1150 . ordExt - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1151 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1152 1153 Output Parameter: 1154 . dm - The DM object 1155 1156 Notes: The object created is an hybrid mesh, the vertex ordering in the cone of the cell is that of the prismatic cells 1157 1158 Level: advanced 1159 1160 .keywords: DM, create 1161 .seealso: DMPlexCreateWedgeCylinderMesh(), DMPlexCreateWedgeBoxMesh(), DMPlexSetHybridBounds(), DMSetType(), DMCreate() 1162 @*/ 1163 PetscErrorCode DMPlexExtrude(DM idm, PetscInt layers, PetscReal height, PetscBool ordExt, PetscBool interpolate, DM* dm) 1164 { 1165 PetscScalar *coordsB; 1166 const PetscScalar *coordsA; 1167 PetscReal *normals = NULL; 1168 Vec coordinatesA, coordinatesB; 1169 PetscSection coordSectionA, coordSectionB; 1170 PetscInt dim, cDim, cDimB, c, l, v, coordSize, *newCone; 1171 PetscInt cStart, cEnd, vStart, vEnd, cellV, numCells, numVertices; 1172 PetscErrorCode ierr; 1173 1174 PetscFunctionBegin; 1175 PetscValidHeaderSpecific(idm, DM_CLASSID, 1); 1176 PetscValidLogicalCollectiveInt(idm, layers, 2); 1177 PetscValidLogicalCollectiveReal(idm, height, 3); 1178 PetscValidLogicalCollectiveBool(idm, interpolate, 4); 1179 ierr = DMGetDimension(idm, &dim);CHKERRQ(ierr); 1180 if (dim < 1 || dim > 3) SETERRQ1(PetscObjectComm((PetscObject)idm), PETSC_ERR_SUP, "Support for dimension %D not coded", dim); 1181 1182 ierr = DMPlexGetHeightStratum(idm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1183 ierr = DMPlexGetDepthStratum(idm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1184 numCells = (cEnd - cStart)*layers; 1185 numVertices = (vEnd - vStart)*(layers+1); 1186 ierr = DMCreate(PetscObjectComm((PetscObject)idm), dm);CHKERRQ(ierr); 1187 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1188 ierr = DMSetDimension(*dm, dim+1);CHKERRQ(ierr); 1189 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1190 for (c = cStart, cellV = 0; c < cEnd; ++c) { 1191 PetscInt *closure = NULL; 1192 PetscInt closureSize, numCorners = 0; 1193 1194 ierr = DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1195 for (v = 0; v < closureSize*2; v += 2) if ((closure[v] >= vStart) && (closure[v] < vEnd)) numCorners++; 1196 ierr = DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1197 for (l = 0; l < layers; ++l) { 1198 ierr = DMPlexSetConeSize(*dm, ordExt ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart, 2*numCorners);CHKERRQ(ierr); 1199 } 1200 cellV = PetscMax(numCorners,cellV); 1201 } 1202 ierr = DMPlexSetHybridBounds(*dm, 0, PETSC_DETERMINE, PETSC_DETERMINE, PETSC_DETERMINE);CHKERRQ(ierr); 1203 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1204 1205 ierr = DMGetCoordinateDim(idm, &cDim);CHKERRQ(ierr); 1206 if (dim != cDim) { 1207 ierr = PetscCalloc1(cDim*(vEnd - vStart), &normals);CHKERRQ(ierr); 1208 } 1209 ierr = PetscMalloc1(3*cellV,&newCone);CHKERRQ(ierr); 1210 for (c = cStart; c < cEnd; ++c) { 1211 PetscInt *closure = NULL; 1212 PetscInt closureSize, numCorners = 0, l; 1213 PetscReal normal[3] = {0, 0, 0}; 1214 1215 if (normals) { 1216 ierr = DMPlexComputeCellGeometryFVM(idm, c, NULL, NULL, normal);CHKERRQ(ierr); 1217 } 1218 ierr = DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1219 for (v = 0; v < closureSize*2; v += 2) { 1220 if ((closure[v] >= vStart) && (closure[v] < vEnd)) { 1221 PetscInt d; 1222 1223 newCone[numCorners++] = closure[v] - vStart; 1224 if (normals) { for (d = 0; d < cDim; ++d) normals[cDim*(closure[v]-vStart)+d] += normal[d]; } 1225 } 1226 } 1227 switch (numCorners) { 1228 case 4: /* do nothing */ 1229 case 2: /* do nothing */ 1230 break; 1231 case 3: /* from counter-clockwise to wedge ordering */ 1232 l = newCone[1]; 1233 newCone[1] = newCone[2]; 1234 newCone[2] = l; 1235 break; 1236 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_SUP, "Unsupported number of corners: %D", numCorners); 1237 } 1238 ierr = DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1239 for (l = 0; l < layers; ++l) { 1240 PetscInt i; 1241 1242 for (i = 0; i < numCorners; ++i) { 1243 newCone[ numCorners + i] = ordExt ? (layers+1)*newCone[i] + l + numCells : l*(vEnd - vStart) + newCone[i] + numCells; 1244 newCone[2*numCorners + i] = ordExt ? (layers+1)*newCone[i] + l + 1 + numCells : (l+1)*(vEnd - vStart) + newCone[i] + numCells; 1245 } 1246 ierr = DMPlexSetCone(*dm, ordExt ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart, newCone + numCorners);CHKERRQ(ierr); 1247 } 1248 } 1249 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1250 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1251 ierr = PetscFree(newCone);CHKERRQ(ierr); 1252 1253 cDimB = cDim == dim ? cDim+1 : cDim; 1254 ierr = DMGetCoordinateSection(*dm, &coordSectionB);CHKERRQ(ierr); 1255 ierr = PetscSectionSetNumFields(coordSectionB, 1);CHKERRQ(ierr); 1256 ierr = PetscSectionSetFieldComponents(coordSectionB, 0, cDimB);CHKERRQ(ierr); 1257 ierr = PetscSectionSetChart(coordSectionB, numCells, numCells+numVertices);CHKERRQ(ierr); 1258 for (v = numCells; v < numCells+numVertices; ++v) { 1259 ierr = PetscSectionSetDof(coordSectionB, v, cDimB);CHKERRQ(ierr); 1260 ierr = PetscSectionSetFieldDof(coordSectionB, v, 0, cDimB);CHKERRQ(ierr); 1261 } 1262 ierr = PetscSectionSetUp(coordSectionB);CHKERRQ(ierr); 1263 ierr = PetscSectionGetStorageSize(coordSectionB, &coordSize);CHKERRQ(ierr); 1264 ierr = VecCreate(PETSC_COMM_SELF, &coordinatesB);CHKERRQ(ierr); 1265 ierr = PetscObjectSetName((PetscObject) coordinatesB, "coordinates");CHKERRQ(ierr); 1266 ierr = VecSetSizes(coordinatesB, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1267 ierr = VecSetBlockSize(coordinatesB, cDimB);CHKERRQ(ierr); 1268 ierr = VecSetType(coordinatesB,VECSTANDARD);CHKERRQ(ierr); 1269 1270 ierr = DMGetCoordinateSection(idm, &coordSectionA);CHKERRQ(ierr); 1271 ierr = DMGetCoordinatesLocal(idm, &coordinatesA);CHKERRQ(ierr); 1272 ierr = VecGetArray(coordinatesB, &coordsB);CHKERRQ(ierr); 1273 ierr = VecGetArrayRead(coordinatesA, &coordsA);CHKERRQ(ierr); 1274 for (v = vStart; v < vEnd; ++v) { 1275 const PetscScalar *cptr; 1276 PetscReal ones2[2] = { 0., 1.}, ones3[3] = { 0., 0., 1.}; 1277 PetscReal *normal, norm, h = height/layers; 1278 PetscInt offA, d, cDimA = cDim; 1279 1280 normal = normals ? normals + cDimB*(v - vStart) : (cDim > 1 ? ones3 : ones2); 1281 if (normals) { 1282 for (d = 0, norm = 0.0; d < cDimB; ++d) norm += normal[d]*normal[d]; 1283 for (d = 0; d < cDimB; ++d) normal[d] *= 1./PetscSqrtReal(norm); 1284 } 1285 1286 ierr = PetscSectionGetOffset(coordSectionA, v, &offA);CHKERRQ(ierr); 1287 cptr = coordsA + offA; 1288 for (l = 0; l < layers+1; ++l) { 1289 PetscInt offB, d, newV; 1290 1291 newV = ordExt ? (layers+1)*(v -vStart) + l + numCells : (vEnd -vStart)*l + (v -vStart) + numCells; 1292 ierr = PetscSectionGetOffset(coordSectionB, newV, &offB);CHKERRQ(ierr); 1293 for (d = 0; d < cDimA; ++d) { coordsB[offB+d] = cptr[d]; } 1294 for (d = 0; d < cDimB; ++d) { coordsB[offB+d] += l ? normal[d]*h : 0.0; } 1295 cptr = coordsB + offB; 1296 cDimA = cDimB; 1297 } 1298 } 1299 ierr = VecRestoreArrayRead(coordinatesA, &coordsA);CHKERRQ(ierr); 1300 ierr = VecRestoreArray(coordinatesB, &coordsB);CHKERRQ(ierr); 1301 ierr = DMSetCoordinatesLocal(*dm, coordinatesB);CHKERRQ(ierr); 1302 ierr = VecDestroy(&coordinatesB);CHKERRQ(ierr); 1303 ierr = PetscFree(normals);CHKERRQ(ierr); 1304 if (interpolate) { 1305 DM idm; 1306 1307 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1308 ierr = DMPlexCopyCoordinates(*dm, idm);CHKERRQ(ierr); 1309 ierr = DMDestroy(dm);CHKERRQ(ierr); 1310 *dm = idm; 1311 } 1312 PetscFunctionReturn(0); 1313 } 1314 1315 /*@C 1316 DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database. 1317 1318 Logically Collective on DM 1319 1320 Input Parameters: 1321 + dm - the DM context 1322 - prefix - the prefix to prepend to all option names 1323 1324 Notes: 1325 A hyphen (-) must NOT be given at the beginning of the prefix name. 1326 The first character of all runtime options is AUTOMATICALLY the hyphen. 1327 1328 Level: advanced 1329 1330 .seealso: SNESSetFromOptions() 1331 @*/ 1332 PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) 1333 { 1334 DM_Plex *mesh = (DM_Plex *) dm->data; 1335 PetscErrorCode ierr; 1336 1337 PetscFunctionBegin; 1338 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1339 ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);CHKERRQ(ierr); 1340 ierr = PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);CHKERRQ(ierr); 1341 PetscFunctionReturn(0); 1342 } 1343 1344 /*@ 1345 DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. 1346 1347 Collective on MPI_Comm 1348 1349 Input Parameters: 1350 + comm - The communicator for the DM object 1351 . numRefine - The number of regular refinements to the basic 5 cell structure 1352 - periodicZ - The boundary type for the Z direction 1353 1354 Output Parameter: 1355 . dm - The DM object 1356 1357 Note: Here is the output numbering looking from the bottom of the cylinder: 1358 $ 17-----14 1359 $ | | 1360 $ | 2 | 1361 $ | | 1362 $ 17-----8-----7-----14 1363 $ | | | | 1364 $ | 3 | 0 | 1 | 1365 $ | | | | 1366 $ 19-----5-----6-----13 1367 $ | | 1368 $ | 4 | 1369 $ | | 1370 $ 19-----13 1371 $ 1372 $ and up through the top 1373 $ 1374 $ 18-----16 1375 $ | | 1376 $ | 2 | 1377 $ | | 1378 $ 18----10----11-----16 1379 $ | | | | 1380 $ | 3 | 0 | 1 | 1381 $ | | | | 1382 $ 20-----9----12-----15 1383 $ | | 1384 $ | 4 | 1385 $ | | 1386 $ 20-----15 1387 1388 Level: beginner 1389 1390 .keywords: DM, create 1391 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1392 @*/ 1393 PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, PetscInt numRefine, DMBoundaryType periodicZ, DM *dm) 1394 { 1395 const PetscInt dim = 3; 1396 PetscInt numCells, numVertices, r; 1397 PetscMPIInt rank; 1398 PetscErrorCode ierr; 1399 1400 PetscFunctionBegin; 1401 PetscValidPointer(dm, 4); 1402 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1403 if (numRefine < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of refinements %D cannot be negative", numRefine); 1404 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1405 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1406 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1407 /* Create topology */ 1408 { 1409 PetscInt cone[8], c; 1410 1411 numCells = !rank ? 5 : 0; 1412 numVertices = !rank ? 16 : 0; 1413 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1414 numCells *= 3; 1415 numVertices = !rank ? 24 : 0; 1416 } 1417 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1418 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 8);CHKERRQ(ierr);} 1419 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1420 if (!rank) { 1421 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1422 cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16; 1423 cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34; 1424 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1425 cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23; 1426 cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */ 1427 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1428 cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17; 1429 cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38; 1430 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1431 cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15; 1432 cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38; 1433 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1434 cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23; 1435 cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31; 1436 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1437 1438 cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32; 1439 cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20; 1440 ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); 1441 cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36; 1442 cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21; 1443 ierr = DMPlexSetCone(*dm, 6, cone);CHKERRQ(ierr); 1444 cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33; 1445 cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28; 1446 ierr = DMPlexSetCone(*dm, 7, cone);CHKERRQ(ierr); 1447 cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31; 1448 cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28; 1449 ierr = DMPlexSetCone(*dm, 8, cone);CHKERRQ(ierr); 1450 cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36; 1451 cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19; 1452 ierr = DMPlexSetCone(*dm, 9, cone);CHKERRQ(ierr); 1453 1454 cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22; 1455 cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18; 1456 ierr = DMPlexSetCone(*dm, 10, cone);CHKERRQ(ierr); 1457 cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25; 1458 cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17; 1459 ierr = DMPlexSetCone(*dm, 11, cone);CHKERRQ(ierr); 1460 cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21; 1461 cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27; 1462 ierr = DMPlexSetCone(*dm, 12, cone);CHKERRQ(ierr); 1463 cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19; 1464 cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27; 1465 ierr = DMPlexSetCone(*dm, 13, cone);CHKERRQ(ierr); 1466 cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25; 1467 cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15; 1468 ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); 1469 } else { 1470 cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6; 1471 cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10; 1472 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1473 cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13; 1474 cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11; 1475 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1476 cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7; 1477 cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18; 1478 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1479 cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5; 1480 cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18; 1481 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1482 cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13; 1483 cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9; 1484 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1485 } 1486 } 1487 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1488 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1489 } 1490 /* Interpolate */ 1491 { 1492 DM idm; 1493 1494 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1495 ierr = DMDestroy(dm);CHKERRQ(ierr); 1496 *dm = idm; 1497 } 1498 /* Create cube geometry */ 1499 { 1500 Vec coordinates; 1501 PetscSection coordSection; 1502 PetscScalar *coords; 1503 PetscInt coordSize, v; 1504 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1505 const PetscReal ds2 = dis/2.0; 1506 1507 /* Build coordinates */ 1508 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1509 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1510 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1511 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1512 for (v = numCells; v < numCells+numVertices; ++v) { 1513 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1514 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1515 } 1516 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1517 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1518 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1519 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1520 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1521 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1522 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1523 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1524 if (!rank) { 1525 coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0; 1526 coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0; 1527 coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0; 1528 coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0; 1529 coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0; 1530 coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0; 1531 coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0; 1532 coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0; 1533 coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0; 1534 coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0; 1535 coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0; 1536 coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0; 1537 coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0; 1538 coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0; 1539 coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0; 1540 coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0; 1541 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1542 /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5; 1543 /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5; 1544 /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5; 1545 /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5; 1546 /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5; 1547 /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5; 1548 /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5; 1549 /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5; 1550 } 1551 } 1552 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1553 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 1554 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1555 } 1556 /* Create periodicity */ 1557 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1558 PetscReal L[3]; 1559 PetscReal maxCell[3]; 1560 DMBoundaryType bdType[3]; 1561 PetscReal lower[3] = {0.0, 0.0, 0.0}; 1562 PetscReal upper[3] = {1.0, 1.0, 1.5}; 1563 PetscInt i, numZCells = 3; 1564 1565 bdType[0] = DM_BOUNDARY_NONE; 1566 bdType[1] = DM_BOUNDARY_NONE; 1567 bdType[2] = periodicZ; 1568 for (i = 0; i < dim; i++) { 1569 L[i] = upper[i] - lower[i]; 1570 maxCell[i] = 1.1 * (L[i] / numZCells); 1571 } 1572 ierr = DMSetPeriodicity(*dm, PETSC_TRUE, maxCell, L, bdType);CHKERRQ(ierr); 1573 } 1574 /* Refine topology */ 1575 for (r = 0; r < numRefine; ++r) { 1576 DM rdm = NULL; 1577 1578 ierr = DMRefine(*dm, comm, &rdm);CHKERRQ(ierr); 1579 ierr = DMDestroy(dm);CHKERRQ(ierr); 1580 *dm = rdm; 1581 } 1582 /* Remap geometry to cylinder 1583 Interior square: Linear interpolation is correct 1584 The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing 1585 such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance 1586 1587 phi = arctan(y/x) 1588 d_close = sqrt(1/8 + 1/4 sin^2(phi)) 1589 d_far = sqrt(1/2 + sin^2(phi)) 1590 1591 so we remap them using 1592 1593 x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) 1594 y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) 1595 1596 If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. 1597 */ 1598 { 1599 Vec coordinates; 1600 PetscSection coordSection; 1601 PetscScalar *coords; 1602 PetscInt vStart, vEnd, v; 1603 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1604 const PetscReal ds2 = 0.5*dis; 1605 1606 ierr = DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1607 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1608 ierr = DMGetCoordinatesLocal(*dm, &coordinates);CHKERRQ(ierr); 1609 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1610 for (v = vStart; v < vEnd; ++v) { 1611 PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; 1612 PetscInt off; 1613 1614 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 1615 if ((PetscAbsScalar(coords[off+0]) <= ds2) && (PetscAbsScalar(coords[off+1]) <= ds2)) continue; 1616 x = PetscRealPart(coords[off]); 1617 y = PetscRealPart(coords[off+1]); 1618 phi = PetscAtan2Real(y, x); 1619 sinp = PetscSinReal(phi); 1620 cosp = PetscCosReal(phi); 1621 if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) { 1622 dc = PetscAbsReal(ds2/sinp); 1623 df = PetscAbsReal(dis/sinp); 1624 xc = ds2*x/PetscAbsReal(y); 1625 yc = ds2*PetscSignReal(y); 1626 } else { 1627 dc = PetscAbsReal(ds2/cosp); 1628 df = PetscAbsReal(dis/cosp); 1629 xc = ds2*PetscSignReal(x); 1630 yc = ds2*y/PetscAbsReal(x); 1631 } 1632 coords[off+0] = xc + (coords[off+0] - xc)*(1.0 - dc)/(df - dc); 1633 coords[off+1] = yc + (coords[off+1] - yc)*(1.0 - dc)/(df - dc); 1634 } 1635 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1636 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1637 ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); 1638 } 1639 } 1640 PetscFunctionReturn(0); 1641 } 1642 1643 /*@ 1644 DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges. 1645 1646 Collective on MPI_Comm 1647 1648 Input Parameters: 1649 + comm - The communicator for the DM object 1650 . n - The number of wedges around the origin 1651 - interpolate - Create edges and faces 1652 1653 Output Parameter: 1654 . dm - The DM object 1655 1656 Level: beginner 1657 1658 .keywords: DM, create 1659 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1660 @*/ 1661 PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm) 1662 { 1663 const PetscInt dim = 3; 1664 PetscInt numCells, numVertices; 1665 PetscMPIInt rank; 1666 PetscErrorCode ierr; 1667 1668 PetscFunctionBegin; 1669 PetscValidPointer(dm, 3); 1670 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1671 if (n < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n); 1672 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1673 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1674 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1675 /* Create topology */ 1676 { 1677 PetscInt cone[6], c; 1678 1679 numCells = !rank ? n : 0; 1680 numVertices = !rank ? 2*(n+1) : 0; 1681 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1682 ierr = DMPlexSetHybridBounds(*dm, 0, PETSC_DETERMINE, PETSC_DETERMINE, PETSC_DETERMINE);CHKERRQ(ierr); 1683 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 6);CHKERRQ(ierr);} 1684 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1685 for (c = 0; c < numCells; c++) { 1686 cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n; 1687 cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n; 1688 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 1689 } 1690 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1691 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1692 } 1693 /* Interpolate */ 1694 if (interpolate) { 1695 DM idm; 1696 1697 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1698 ierr = DMDestroy(dm);CHKERRQ(ierr); 1699 *dm = idm; 1700 } 1701 /* Create cylinder geometry */ 1702 { 1703 Vec coordinates; 1704 PetscSection coordSection; 1705 PetscScalar *coords; 1706 PetscInt coordSize, v, c; 1707 1708 /* Build coordinates */ 1709 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1710 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1711 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1712 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1713 for (v = numCells; v < numCells+numVertices; ++v) { 1714 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1715 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1716 } 1717 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1718 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1719 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1720 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1721 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1722 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1723 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1724 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1725 for (c = 0; c < numCells; c++) { 1726 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; 1727 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; 1728 } 1729 if (!rank) { 1730 coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0; 1731 coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0; 1732 } 1733 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1734 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 1735 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1736 } 1737 PetscFunctionReturn(0); 1738 } 1739 1740 PETSC_STATIC_INLINE PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1741 { 1742 PetscReal prod = 0.0; 1743 PetscInt i; 1744 for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]); 1745 return PetscSqrtReal(prod); 1746 } 1747 PETSC_STATIC_INLINE PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1748 { 1749 PetscReal prod = 0.0; 1750 PetscInt i; 1751 for (i = 0; i < dim; ++i) prod += x[i]*y[i]; 1752 return prod; 1753 } 1754 1755 /*@ 1756 DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d. 1757 1758 Collective on MPI_Comm 1759 1760 Input Parameters: 1761 . comm - The communicator for the DM object 1762 . dim - The dimension 1763 - simplex - Use simplices, or tensor product cells 1764 1765 Output Parameter: 1766 . dm - The DM object 1767 1768 Level: beginner 1769 1770 .keywords: DM, create 1771 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1772 @*/ 1773 PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *dm) 1774 { 1775 const PetscInt embedDim = dim+1; 1776 PetscSection coordSection; 1777 Vec coordinates; 1778 PetscScalar *coords; 1779 PetscReal *coordsIn; 1780 PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e; 1781 PetscMPIInt rank; 1782 PetscErrorCode ierr; 1783 1784 PetscFunctionBegin; 1785 PetscValidPointer(dm, 4); 1786 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1787 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1788 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1789 ierr = DMSetCoordinateDim(*dm, dim+1);CHKERRQ(ierr); 1790 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) *dm), &rank);CHKERRQ(ierr); 1791 switch (dim) { 1792 case 2: 1793 if (simplex) { 1794 DM idm; 1795 const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI); 1796 const PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)}; 1797 const PetscInt degree = 5; 1798 PetscInt s[3] = {1, 1, 1}; 1799 PetscInt cone[3]; 1800 PetscInt *graph, p, i, j, k; 1801 1802 numCells = !rank ? 20 : 0; 1803 numVerts = !rank ? 12 : 0; 1804 firstVertex = numCells; 1805 /* Use icosahedron, which for a unit sphere has coordinates which are all cyclic permutations of 1806 1807 (0, \pm 1/\phi+1, \pm \phi/\phi+1) 1808 1809 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 1810 length is then given by 2/\phi = 2 * 2.73606 = 5.47214. 1811 */ 1812 /* Construct vertices */ 1813 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 1814 for (p = 0, i = 0; p < embedDim; ++p) { 1815 for (s[1] = -1; s[1] < 2; s[1] += 2) { 1816 for (s[2] = -1; s[2] < 2; s[2] += 2) { 1817 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim]; 1818 ++i; 1819 } 1820 } 1821 } 1822 /* Construct graph */ 1823 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 1824 for (i = 0; i < numVerts; ++i) { 1825 for (j = 0, k = 0; j < numVerts; ++j) { 1826 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 1827 } 1828 if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree); 1829 } 1830 /* Build Topology */ 1831 ierr = DMPlexSetChart(*dm, 0, numCells+numVerts);CHKERRQ(ierr); 1832 for (c = 0; c < numCells; c++) { 1833 ierr = DMPlexSetConeSize(*dm, c, embedDim);CHKERRQ(ierr); 1834 } 1835 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 1836 /* Cells */ 1837 for (i = 0, c = 0; i < numVerts; ++i) { 1838 for (j = 0; j < i; ++j) { 1839 for (k = 0; k < j; ++k) { 1840 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) { 1841 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; 1842 /* Check orientation */ 1843 { 1844 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}}}; 1845 PetscReal normal[3]; 1846 PetscInt e, f; 1847 1848 for (d = 0; d < embedDim; ++d) { 1849 normal[d] = 0.0; 1850 for (e = 0; e < embedDim; ++e) { 1851 for (f = 0; f < embedDim; ++f) { 1852 normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]); 1853 } 1854 } 1855 } 1856 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 1857 } 1858 ierr = DMPlexSetCone(*dm, c++, cone);CHKERRQ(ierr); 1859 } 1860 } 1861 } 1862 } 1863 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1864 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1865 ierr = PetscFree(graph);CHKERRQ(ierr); 1866 /* Interpolate mesh */ 1867 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1868 ierr = DMDestroy(dm);CHKERRQ(ierr); 1869 *dm = idm; 1870 } else { 1871 /* 1872 12-21--13 1873 | | 1874 25 4 24 1875 | | 1876 12-25--9-16--8-24--13 1877 | | | | 1878 23 5 17 0 15 3 22 1879 | | | | 1880 10-20--6-14--7-19--11 1881 | | 1882 20 1 19 1883 | | 1884 10-18--11 1885 | | 1886 23 2 22 1887 | | 1888 12-21--13 1889 */ 1890 const PetscReal dist = 1.0/PetscSqrtReal(3.0); 1891 PetscInt cone[4], ornt[4]; 1892 1893 numCells = !rank ? 6 : 0; 1894 numEdges = !rank ? 12 : 0; 1895 numVerts = !rank ? 8 : 0; 1896 firstVertex = numCells; 1897 firstEdge = numCells + numVerts; 1898 /* Build Topology */ 1899 ierr = DMPlexSetChart(*dm, 0, numCells+numEdges+numVerts);CHKERRQ(ierr); 1900 for (c = 0; c < numCells; c++) { 1901 ierr = DMPlexSetConeSize(*dm, c, 4);CHKERRQ(ierr); 1902 } 1903 for (e = firstEdge; e < firstEdge+numEdges; ++e) { 1904 ierr = DMPlexSetConeSize(*dm, e, 2);CHKERRQ(ierr); 1905 } 1906 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 1907 /* Cell 0 */ 1908 cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17; 1909 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1910 ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0; 1911 ierr = DMPlexSetConeOrientation(*dm, 0, ornt);CHKERRQ(ierr); 1912 /* Cell 1 */ 1913 cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20; 1914 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1915 ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; 1916 ierr = DMPlexSetConeOrientation(*dm, 1, ornt);CHKERRQ(ierr); 1917 /* Cell 2 */ 1918 cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23; 1919 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1920 ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; 1921 ierr = DMPlexSetConeOrientation(*dm, 2, ornt);CHKERRQ(ierr); 1922 /* Cell 3 */ 1923 cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15; 1924 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1925 ornt[0] = -2; ornt[1] = -2; ornt[2] = 0; ornt[3] = -2; 1926 ierr = DMPlexSetConeOrientation(*dm, 3, ornt);CHKERRQ(ierr); 1927 /* Cell 4 */ 1928 cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25; 1929 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1930 ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = 0; 1931 ierr = DMPlexSetConeOrientation(*dm, 4, ornt);CHKERRQ(ierr); 1932 /* Cell 5 */ 1933 cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23; 1934 ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); 1935 ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = -2; 1936 ierr = DMPlexSetConeOrientation(*dm, 5, ornt);CHKERRQ(ierr); 1937 /* Edges */ 1938 cone[0] = 6; cone[1] = 7; 1939 ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); 1940 cone[0] = 7; cone[1] = 8; 1941 ierr = DMPlexSetCone(*dm, 15, cone);CHKERRQ(ierr); 1942 cone[0] = 8; cone[1] = 9; 1943 ierr = DMPlexSetCone(*dm, 16, cone);CHKERRQ(ierr); 1944 cone[0] = 9; cone[1] = 6; 1945 ierr = DMPlexSetCone(*dm, 17, cone);CHKERRQ(ierr); 1946 cone[0] = 10; cone[1] = 11; 1947 ierr = DMPlexSetCone(*dm, 18, cone);CHKERRQ(ierr); 1948 cone[0] = 11; cone[1] = 7; 1949 ierr = DMPlexSetCone(*dm, 19, cone);CHKERRQ(ierr); 1950 cone[0] = 6; cone[1] = 10; 1951 ierr = DMPlexSetCone(*dm, 20, cone);CHKERRQ(ierr); 1952 cone[0] = 12; cone[1] = 13; 1953 ierr = DMPlexSetCone(*dm, 21, cone);CHKERRQ(ierr); 1954 cone[0] = 13; cone[1] = 11; 1955 ierr = DMPlexSetCone(*dm, 22, cone);CHKERRQ(ierr); 1956 cone[0] = 10; cone[1] = 12; 1957 ierr = DMPlexSetCone(*dm, 23, cone);CHKERRQ(ierr); 1958 cone[0] = 13; cone[1] = 8; 1959 ierr = DMPlexSetCone(*dm, 24, cone);CHKERRQ(ierr); 1960 cone[0] = 12; cone[1] = 9; 1961 ierr = DMPlexSetCone(*dm, 25, cone);CHKERRQ(ierr); 1962 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1963 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1964 /* Build coordinates */ 1965 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 1966 coordsIn[0*embedDim+0] = -dist; coordsIn[0*embedDim+1] = dist; coordsIn[0*embedDim+2] = -dist; 1967 coordsIn[1*embedDim+0] = dist; coordsIn[1*embedDim+1] = dist; coordsIn[1*embedDim+2] = -dist; 1968 coordsIn[2*embedDim+0] = dist; coordsIn[2*embedDim+1] = -dist; coordsIn[2*embedDim+2] = -dist; 1969 coordsIn[3*embedDim+0] = -dist; coordsIn[3*embedDim+1] = -dist; coordsIn[3*embedDim+2] = -dist; 1970 coordsIn[4*embedDim+0] = -dist; coordsIn[4*embedDim+1] = dist; coordsIn[4*embedDim+2] = dist; 1971 coordsIn[5*embedDim+0] = dist; coordsIn[5*embedDim+1] = dist; coordsIn[5*embedDim+2] = dist; 1972 coordsIn[6*embedDim+0] = -dist; coordsIn[6*embedDim+1] = -dist; coordsIn[6*embedDim+2] = dist; 1973 coordsIn[7*embedDim+0] = dist; coordsIn[7*embedDim+1] = -dist; coordsIn[7*embedDim+2] = dist; 1974 } 1975 break; 1976 case 3: 1977 if (simplex) { 1978 DM idm; 1979 const PetscReal edgeLen = 1.0/PETSC_PHI; 1980 const PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5}; 1981 const PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0}; 1982 const PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0}; 1983 const PetscInt degree = 12; 1984 PetscInt s[4] = {1, 1, 1}; 1985 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}, 1986 {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}}; 1987 PetscInt cone[4]; 1988 PetscInt *graph, p, i, j, k, l; 1989 1990 numCells = !rank ? 600 : 0; 1991 numVerts = !rank ? 120 : 0; 1992 firstVertex = numCells; 1993 /* Use the 600-cell, which for a unit sphere has coordinates which are 1994 1995 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16 1996 (\pm 1, 0, 0, 0) all cyclic permutations 8 1997 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96 1998 1999 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 2000 length is then given by 1/\phi = 2.73606. 2001 2002 http://buzzard.pugetsound.edu/sage-practice/ch03s03.html 2003 http://mathworld.wolfram.com/600-Cell.html 2004 */ 2005 /* Construct vertices */ 2006 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 2007 i = 0; 2008 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2009 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2010 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2011 for (s[3] = -1; s[3] < 2; s[3] += 2) { 2012 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d]; 2013 ++i; 2014 } 2015 } 2016 } 2017 } 2018 for (p = 0; p < embedDim; ++p) { 2019 s[1] = s[2] = s[3] = 1; 2020 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2021 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim]; 2022 ++i; 2023 } 2024 } 2025 for (p = 0; p < 12; ++p) { 2026 s[3] = 1; 2027 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2028 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2029 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2030 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]]; 2031 ++i; 2032 } 2033 } 2034 } 2035 } 2036 if (i != numVerts) SETERRQ2(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts); 2037 /* Construct graph */ 2038 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 2039 for (i = 0; i < numVerts; ++i) { 2040 for (j = 0, k = 0; j < numVerts; ++j) { 2041 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 2042 } 2043 if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree); 2044 } 2045 /* Build Topology */ 2046 ierr = DMPlexSetChart(*dm, 0, numCells+numVerts);CHKERRQ(ierr); 2047 for (c = 0; c < numCells; c++) { 2048 ierr = DMPlexSetConeSize(*dm, c, embedDim);CHKERRQ(ierr); 2049 } 2050 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 2051 /* Cells */ 2052 for (i = 0, c = 0; i < numVerts; ++i) { 2053 for (j = 0; j < i; ++j) { 2054 for (k = 0; k < j; ++k) { 2055 for (l = 0; l < k; ++l) { 2056 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] && 2057 graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) { 2058 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l; 2059 /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */ 2060 { 2061 const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2062 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}}, 2063 {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}}, 2064 {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}}, 2065 2066 {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}}, 2067 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2068 {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}}, 2069 {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}}, 2070 2071 {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}}, 2072 {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}}, 2073 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2074 {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}, 2075 2076 {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}}, 2077 {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}}, 2078 {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2079 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}}; 2080 PetscReal normal[4]; 2081 PetscInt e, f, g; 2082 2083 for (d = 0; d < embedDim; ++d) { 2084 normal[d] = 0.0; 2085 for (e = 0; e < embedDim; ++e) { 2086 for (f = 0; f < embedDim; ++f) { 2087 for (g = 0; g < embedDim; ++g) { 2088 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]); 2089 } 2090 } 2091 } 2092 } 2093 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 2094 } 2095 ierr = DMPlexSetCone(*dm, c++, cone);CHKERRQ(ierr); 2096 } 2097 } 2098 } 2099 } 2100 } 2101 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 2102 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 2103 ierr = PetscFree(graph);CHKERRQ(ierr); 2104 /* Interpolate mesh */ 2105 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2106 ierr = DMDestroy(dm);CHKERRQ(ierr); 2107 *dm = idm; 2108 break; 2109 } 2110 default: SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim); 2111 } 2112 /* Create coordinates */ 2113 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 2114 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2115 ierr = PetscSectionSetFieldComponents(coordSection, 0, embedDim);CHKERRQ(ierr); 2116 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);CHKERRQ(ierr); 2117 for (v = firstVertex; v < firstVertex+numVerts; ++v) { 2118 ierr = PetscSectionSetDof(coordSection, v, embedDim);CHKERRQ(ierr); 2119 ierr = PetscSectionSetFieldDof(coordSection, v, 0, embedDim);CHKERRQ(ierr); 2120 } 2121 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2122 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2123 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 2124 ierr = VecSetBlockSize(coordinates, embedDim);CHKERRQ(ierr); 2125 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2126 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2127 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2128 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2129 for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];} 2130 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2131 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 2132 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2133 ierr = PetscFree(coordsIn);CHKERRQ(ierr); 2134 PetscFunctionReturn(0); 2135 } 2136 2137 /* External function declarations here */ 2138 extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling); 2139 extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat); 2140 extern PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mat); 2141 extern PetscErrorCode DMCreateDefaultSection_Plex(DM dm); 2142 extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm); 2143 extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J); 2144 extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm); 2145 extern PetscErrorCode DMCreateCoordinateField_Plex(DM dm, DMField *field); 2146 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm); 2147 extern PetscErrorCode DMSetUp_Plex(DM dm); 2148 extern PetscErrorCode DMDestroy_Plex(DM dm); 2149 extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer); 2150 extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer); 2151 extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm); 2152 extern PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm); 2153 static PetscErrorCode DMInitialize_Plex(DM dm); 2154 2155 /* Replace dm with the contents of dmNew 2156 - Share the DM_Plex structure 2157 - Share the coordinates 2158 - Share the SF 2159 */ 2160 static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew) 2161 { 2162 PetscSF sf; 2163 DM coordDM, coarseDM; 2164 Vec coords; 2165 PetscBool isper; 2166 const PetscReal *maxCell, *L; 2167 const DMBoundaryType *bd; 2168 PetscErrorCode ierr; 2169 2170 PetscFunctionBegin; 2171 ierr = DMGetPointSF(dmNew, &sf);CHKERRQ(ierr); 2172 ierr = DMSetPointSF(dm, sf);CHKERRQ(ierr); 2173 ierr = DMGetCoordinateDM(dmNew, &coordDM);CHKERRQ(ierr); 2174 ierr = DMGetCoordinatesLocal(dmNew, &coords);CHKERRQ(ierr); 2175 ierr = DMSetCoordinateDM(dm, coordDM);CHKERRQ(ierr); 2176 ierr = DMSetCoordinatesLocal(dm, coords);CHKERRQ(ierr); 2177 ierr = DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);CHKERRQ(ierr); 2178 ierr = DMSetPeriodicity(dmNew, isper, maxCell, L, bd);CHKERRQ(ierr); 2179 ierr = DMDestroy_Plex(dm);CHKERRQ(ierr); 2180 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 2181 dm->data = dmNew->data; 2182 ((DM_Plex *) dmNew->data)->refct++; 2183 dmNew->labels->refct++; 2184 if (!--(dm->labels->refct)) { 2185 DMLabelLink next = dm->labels->next; 2186 2187 /* destroy the labels */ 2188 while (next) { 2189 DMLabelLink tmp = next->next; 2190 2191 ierr = DMLabelDestroy(&next->label);CHKERRQ(ierr); 2192 ierr = PetscFree(next);CHKERRQ(ierr); 2193 next = tmp; 2194 } 2195 ierr = PetscFree(dm->labels);CHKERRQ(ierr); 2196 } 2197 dm->labels = dmNew->labels; 2198 dm->depthLabel = dmNew->depthLabel; 2199 ierr = DMGetCoarseDM(dmNew,&coarseDM);CHKERRQ(ierr); 2200 ierr = DMSetCoarseDM(dm,coarseDM);CHKERRQ(ierr); 2201 PetscFunctionReturn(0); 2202 } 2203 2204 /* Swap dm with the contents of dmNew 2205 - Swap the DM_Plex structure 2206 - Swap the coordinates 2207 - Swap the point PetscSF 2208 */ 2209 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 2210 { 2211 DM coordDMA, coordDMB; 2212 Vec coordsA, coordsB; 2213 PetscSF sfA, sfB; 2214 void *tmp; 2215 DMLabelLinkList listTmp; 2216 DMLabel depthTmp; 2217 PetscInt tmpI; 2218 PetscErrorCode ierr; 2219 2220 PetscFunctionBegin; 2221 ierr = DMGetPointSF(dmA, &sfA);CHKERRQ(ierr); 2222 ierr = DMGetPointSF(dmB, &sfB);CHKERRQ(ierr); 2223 ierr = PetscObjectReference((PetscObject) sfA);CHKERRQ(ierr); 2224 ierr = DMSetPointSF(dmA, sfB);CHKERRQ(ierr); 2225 ierr = DMSetPointSF(dmB, sfA);CHKERRQ(ierr); 2226 ierr = PetscObjectDereference((PetscObject) sfA);CHKERRQ(ierr); 2227 2228 ierr = DMGetCoordinateDM(dmA, &coordDMA);CHKERRQ(ierr); 2229 ierr = DMGetCoordinateDM(dmB, &coordDMB);CHKERRQ(ierr); 2230 ierr = PetscObjectReference((PetscObject) coordDMA);CHKERRQ(ierr); 2231 ierr = DMSetCoordinateDM(dmA, coordDMB);CHKERRQ(ierr); 2232 ierr = DMSetCoordinateDM(dmB, coordDMA);CHKERRQ(ierr); 2233 ierr = PetscObjectDereference((PetscObject) coordDMA);CHKERRQ(ierr); 2234 2235 ierr = DMGetCoordinatesLocal(dmA, &coordsA);CHKERRQ(ierr); 2236 ierr = DMGetCoordinatesLocal(dmB, &coordsB);CHKERRQ(ierr); 2237 ierr = PetscObjectReference((PetscObject) coordsA);CHKERRQ(ierr); 2238 ierr = DMSetCoordinatesLocal(dmA, coordsB);CHKERRQ(ierr); 2239 ierr = DMSetCoordinatesLocal(dmB, coordsA);CHKERRQ(ierr); 2240 ierr = PetscObjectDereference((PetscObject) coordsA);CHKERRQ(ierr); 2241 2242 tmp = dmA->data; 2243 dmA->data = dmB->data; 2244 dmB->data = tmp; 2245 listTmp = dmA->labels; 2246 dmA->labels = dmB->labels; 2247 dmB->labels = listTmp; 2248 depthTmp = dmA->depthLabel; 2249 dmA->depthLabel = dmB->depthLabel; 2250 dmB->depthLabel = depthTmp; 2251 tmpI = dmA->levelup; 2252 dmA->levelup = dmB->levelup; 2253 dmB->levelup = tmpI; 2254 PetscFunctionReturn(0); 2255 } 2256 2257 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 2258 { 2259 DM_Plex *mesh = (DM_Plex*) dm->data; 2260 PetscErrorCode ierr; 2261 2262 PetscFunctionBegin; 2263 /* Handle viewing */ 2264 ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); 2265 ierr = PetscOptionsInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL);CHKERRQ(ierr); 2266 ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL);CHKERRQ(ierr); 2267 ierr = PetscOptionsInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL);CHKERRQ(ierr); 2268 /* Point Location */ 2269 ierr = PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL);CHKERRQ(ierr); 2270 /* Partitioning and distribution */ 2271 ierr = PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL);CHKERRQ(ierr); 2272 /* Generation and remeshing */ 2273 ierr = PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL);CHKERRQ(ierr); 2274 /* Projection behavior */ 2275 ierr = PetscOptionsInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL);CHKERRQ(ierr); 2276 ierr = PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);CHKERRQ(ierr); 2277 /* Checking structure */ 2278 { 2279 PetscBool flg = PETSC_FALSE, flg2 = PETSC_FALSE; 2280 2281 ierr = PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2282 if (flg && flg2) {ierr = DMPlexCheckSymmetry(dm);CHKERRQ(ierr);} 2283 ierr = PetscOptionsBool("-dm_plex_check_skeleton", "Check that each cell has the correct number of vertices (only for homogeneous simplex or tensor meshes)", "DMPlexCheckSkeleton", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2284 if (flg && flg2) {ierr = DMPlexCheckSkeleton(dm, 0);CHKERRQ(ierr);} 2285 ierr = PetscOptionsBool("-dm_plex_check_faces", "Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type", "DMPlexCheckFaces", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2286 if (flg && flg2) {ierr = DMPlexCheckFaces(dm, 0);CHKERRQ(ierr);} 2287 ierr = PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2288 if (flg && flg2) {ierr = DMPlexCheckGeometry(dm);CHKERRQ(ierr);} 2289 } 2290 2291 ierr = PetscPartitionerSetFromOptions(mesh->partitioner);CHKERRQ(ierr); 2292 PetscFunctionReturn(0); 2293 } 2294 2295 static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 2296 { 2297 PetscInt refine = 0, coarsen = 0, r; 2298 PetscBool isHierarchy; 2299 PetscErrorCode ierr; 2300 2301 PetscFunctionBegin; 2302 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2303 ierr = PetscOptionsHead(PetscOptionsObject,"DMPlex Options");CHKERRQ(ierr); 2304 /* Handle DMPlex refinement */ 2305 ierr = PetscOptionsInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL);CHKERRQ(ierr); 2306 ierr = PetscOptionsInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy);CHKERRQ(ierr); 2307 if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 2308 if (refine && isHierarchy) { 2309 DM *dms, coarseDM; 2310 2311 ierr = DMGetCoarseDM(dm, &coarseDM);CHKERRQ(ierr); 2312 ierr = PetscObjectReference((PetscObject)coarseDM);CHKERRQ(ierr); 2313 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 2314 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 2315 /* Total hack since we do not pass in a pointer */ 2316 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 2317 if (refine == 1) { 2318 ierr = DMSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 2319 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2320 } else { 2321 ierr = DMSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 2322 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2323 ierr = DMSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 2324 ierr = DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);CHKERRQ(ierr); 2325 } 2326 ierr = DMSetCoarseDM(dms[refine-1], coarseDM);CHKERRQ(ierr); 2327 ierr = PetscObjectDereference((PetscObject)coarseDM);CHKERRQ(ierr); 2328 /* Free DMs */ 2329 for (r = 0; r < refine; ++r) { 2330 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2331 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2332 } 2333 ierr = PetscFree(dms);CHKERRQ(ierr); 2334 } else { 2335 for (r = 0; r < refine; ++r) { 2336 DM refinedMesh; 2337 2338 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2339 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);CHKERRQ(ierr); 2340 /* Total hack since we do not pass in a pointer */ 2341 ierr = DMPlexReplace_Static(dm, refinedMesh);CHKERRQ(ierr); 2342 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2343 ierr = DMDestroy(&refinedMesh);CHKERRQ(ierr); 2344 } 2345 } 2346 /* Handle DMPlex coarsening */ 2347 ierr = PetscOptionsInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL);CHKERRQ(ierr); 2348 ierr = PetscOptionsInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy);CHKERRQ(ierr); 2349 if (coarsen && isHierarchy) { 2350 DM *dms; 2351 2352 ierr = PetscMalloc1(coarsen, &dms);CHKERRQ(ierr); 2353 ierr = DMCoarsenHierarchy(dm, coarsen, dms);CHKERRQ(ierr); 2354 /* Free DMs */ 2355 for (r = 0; r < coarsen; ++r) { 2356 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2357 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2358 } 2359 ierr = PetscFree(dms);CHKERRQ(ierr); 2360 } else { 2361 for (r = 0; r < coarsen; ++r) { 2362 DM coarseMesh; 2363 2364 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2365 ierr = DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);CHKERRQ(ierr); 2366 /* Total hack since we do not pass in a pointer */ 2367 ierr = DMPlexReplace_Static(dm, coarseMesh);CHKERRQ(ierr); 2368 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2369 ierr = DMDestroy(&coarseMesh);CHKERRQ(ierr); 2370 } 2371 } 2372 /* Handle */ 2373 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2374 ierr = PetscOptionsTail();CHKERRQ(ierr); 2375 PetscFunctionReturn(0); 2376 } 2377 2378 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 2379 { 2380 PetscErrorCode ierr; 2381 2382 PetscFunctionBegin; 2383 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2384 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 2385 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 2386 ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); 2387 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 2388 ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); 2389 PetscFunctionReturn(0); 2390 } 2391 2392 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 2393 { 2394 PetscErrorCode ierr; 2395 2396 PetscFunctionBegin; 2397 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2398 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 2399 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 2400 PetscFunctionReturn(0); 2401 } 2402 2403 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 2404 { 2405 PetscInt depth, d; 2406 PetscErrorCode ierr; 2407 2408 PetscFunctionBegin; 2409 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2410 if (depth == 1) { 2411 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 2412 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 2413 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 2414 else {*pStart = 0; *pEnd = 0;} 2415 } else { 2416 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 2417 } 2418 PetscFunctionReturn(0); 2419 } 2420 2421 static PetscErrorCode DMGetNeighors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 2422 { 2423 PetscSF sf; 2424 PetscErrorCode ierr; 2425 2426 PetscFunctionBegin; 2427 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 2428 ierr = PetscSFGetRanks(sf, nranks, ranks, NULL, NULL, NULL);CHKERRQ(ierr); 2429 PetscFunctionReturn(0); 2430 } 2431 2432 static PetscErrorCode DMHasCreateInjection_Plex(DM dm, PetscBool *flg) 2433 { 2434 PetscFunctionBegin; 2435 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 2436 PetscValidPointer(flg,2); 2437 *flg = PETSC_TRUE; 2438 PetscFunctionReturn(0); 2439 } 2440 2441 static PetscErrorCode DMInitialize_Plex(DM dm) 2442 { 2443 PetscErrorCode ierr; 2444 2445 PetscFunctionBegin; 2446 dm->ops->view = DMView_Plex; 2447 dm->ops->load = DMLoad_Plex; 2448 dm->ops->setfromoptions = DMSetFromOptions_Plex; 2449 dm->ops->clone = DMClone_Plex; 2450 dm->ops->setup = DMSetUp_Plex; 2451 dm->ops->createdefaultsection = DMCreateDefaultSection_Plex; 2452 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 2453 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 2454 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 2455 dm->ops->getlocaltoglobalmapping = NULL; 2456 dm->ops->createfieldis = NULL; 2457 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 2458 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 2459 dm->ops->getcoloring = NULL; 2460 dm->ops->creatematrix = DMCreateMatrix_Plex; 2461 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 2462 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 2463 dm->ops->getaggregates = NULL; 2464 dm->ops->getinjection = DMCreateInjection_Plex; 2465 dm->ops->hascreateinjection = DMHasCreateInjection_Plex; 2466 dm->ops->refine = DMRefine_Plex; 2467 dm->ops->coarsen = DMCoarsen_Plex; 2468 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 2469 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 2470 dm->ops->adaptlabel = DMAdaptLabel_Plex; 2471 dm->ops->adaptmetric = DMAdaptMetric_Plex; 2472 dm->ops->globaltolocalbegin = NULL; 2473 dm->ops->globaltolocalend = NULL; 2474 dm->ops->localtoglobalbegin = NULL; 2475 dm->ops->localtoglobalend = NULL; 2476 dm->ops->destroy = DMDestroy_Plex; 2477 dm->ops->createsubdm = DMCreateSubDM_Plex; 2478 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 2479 dm->ops->getdimpoints = DMGetDimPoints_Plex; 2480 dm->ops->locatepoints = DMLocatePoints_Plex; 2481 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 2482 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 2483 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 2484 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 2485 dm->ops->computel2diff = DMComputeL2Diff_Plex; 2486 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 2487 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 2488 dm->ops->getneighbors = DMGetNeighors_Plex; 2489 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);CHKERRQ(ierr); 2490 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);CHKERRQ(ierr); 2491 PetscFunctionReturn(0); 2492 } 2493 2494 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 2495 { 2496 DM_Plex *mesh = (DM_Plex *) dm->data; 2497 PetscErrorCode ierr; 2498 2499 PetscFunctionBegin; 2500 mesh->refct++; 2501 (*newdm)->data = mesh; 2502 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 2503 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 2504 PetscFunctionReturn(0); 2505 } 2506 2507 /*MC 2508 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 2509 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 2510 specified by a PetscSection object. Ownership in the global representation is determined by 2511 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 2512 2513 Options Database Keys: 2514 + -dm_plex_hash_location - Use grid hashing for point location 2515 . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes 2516 . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing 2517 . -dm_plex_max_projection_height - Maxmimum mesh point height used to project locally 2518 . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement 2519 . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric 2520 . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices 2521 . -dm_plex_check_faces <celltype> - Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type 2522 . -dm_plex_check_geometry - Check that cells have positive volume 2523 . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ 2524 . -dm_plex_view_scale <num> - Scale the TikZ 2525 - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices 2526 2527 2528 Level: intermediate 2529 2530 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 2531 M*/ 2532 2533 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 2534 { 2535 DM_Plex *mesh; 2536 PetscInt unit, d; 2537 PetscErrorCode ierr; 2538 2539 PetscFunctionBegin; 2540 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2541 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 2542 dm->dim = 0; 2543 dm->data = mesh; 2544 2545 mesh->refct = 1; 2546 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 2547 mesh->maxConeSize = 0; 2548 mesh->cones = NULL; 2549 mesh->coneOrientations = NULL; 2550 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 2551 mesh->maxSupportSize = 0; 2552 mesh->supports = NULL; 2553 mesh->refinementUniform = PETSC_TRUE; 2554 mesh->refinementLimit = -1.0; 2555 2556 mesh->facesTmp = NULL; 2557 2558 mesh->tetgenOpts = NULL; 2559 mesh->triangleOpts = NULL; 2560 ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); 2561 mesh->remeshBd = PETSC_FALSE; 2562 2563 mesh->subpointMap = NULL; 2564 2565 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 2566 2567 mesh->regularRefinement = PETSC_FALSE; 2568 mesh->depthState = -1; 2569 mesh->globalVertexNumbers = NULL; 2570 mesh->globalCellNumbers = NULL; 2571 mesh->anchorSection = NULL; 2572 mesh->anchorIS = NULL; 2573 mesh->createanchors = NULL; 2574 mesh->computeanchormatrix = NULL; 2575 mesh->parentSection = NULL; 2576 mesh->parents = NULL; 2577 mesh->childIDs = NULL; 2578 mesh->childSection = NULL; 2579 mesh->children = NULL; 2580 mesh->referenceTree = NULL; 2581 mesh->getchildsymmetry = NULL; 2582 for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE; 2583 mesh->vtkCellHeight = 0; 2584 mesh->useAnchors = PETSC_FALSE; 2585 2586 mesh->maxProjectionHeight = 0; 2587 2588 mesh->printSetValues = PETSC_FALSE; 2589 mesh->printFEM = 0; 2590 mesh->printTol = 1.0e-10; 2591 2592 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 2593 PetscFunctionReturn(0); 2594 } 2595 2596 /*@ 2597 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 2598 2599 Collective on MPI_Comm 2600 2601 Input Parameter: 2602 . comm - The communicator for the DMPlex object 2603 2604 Output Parameter: 2605 . mesh - The DMPlex object 2606 2607 Level: beginner 2608 2609 .keywords: DMPlex, create 2610 @*/ 2611 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 2612 { 2613 PetscErrorCode ierr; 2614 2615 PetscFunctionBegin; 2616 PetscValidPointer(mesh,2); 2617 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 2618 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 2619 PetscFunctionReturn(0); 2620 } 2621 2622 /* 2623 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 2624 */ 2625 /* TODO: invertCells and spaceDim arguments could be added also to to DMPlexCreateFromCellListParallel(), DMPlexBuildFromCellList_Internal() and DMPlexCreateFromCellList() */ 2626 PetscErrorCode DMPlexBuildFromCellList_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscBool invertCells, PetscSF *sfVert) 2627 { 2628 PetscSF sfPoint; 2629 PetscLayout vLayout; 2630 PetscHSetI vhash; 2631 PetscSFNode *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex; 2632 const PetscInt *vrange; 2633 PetscInt numVerticesAdj, off = 0, *verticesAdj, numVerticesGhost = 0, *localVertex, *cone, c, p, v, g; 2634 PetscMPIInt rank, size; 2635 PetscErrorCode ierr; 2636 2637 PetscFunctionBegin; 2638 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 2639 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); 2640 /* Partition vertices */ 2641 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);CHKERRQ(ierr); 2642 ierr = PetscLayoutSetLocalSize(vLayout, numVertices);CHKERRQ(ierr); 2643 ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr); 2644 ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr); 2645 ierr = PetscLayoutGetRanges(vLayout, &vrange);CHKERRQ(ierr); 2646 /* Count vertices and map them to procs */ 2647 ierr = PetscHSetICreate(&vhash);CHKERRQ(ierr); 2648 for (c = 0; c < numCells; ++c) { 2649 for (p = 0; p < numCorners; ++p) { 2650 ierr = PetscHSetIAdd(vhash, cells[c*numCorners+p]);CHKERRQ(ierr); 2651 } 2652 } 2653 ierr = PetscHSetIGetSize(vhash, &numVerticesAdj);CHKERRQ(ierr); 2654 ierr = PetscMalloc1(numVerticesAdj, &verticesAdj);CHKERRQ(ierr); 2655 ierr = PetscHSetIGetElems(vhash, &off, verticesAdj);CHKERRQ(ierr); 2656 ierr = PetscHSetIDestroy(&vhash);CHKERRQ(ierr); 2657 if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj); 2658 ierr = PetscSortInt(numVerticesAdj, verticesAdj);CHKERRQ(ierr); 2659 ierr = PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);CHKERRQ(ierr); 2660 for (v = 0; v < numVerticesAdj; ++v) { 2661 const PetscInt gv = verticesAdj[v]; 2662 PetscInt vrank; 2663 2664 ierr = PetscFindInt(gv, size+1, vrange, &vrank);CHKERRQ(ierr); 2665 vrank = vrank < 0 ? -(vrank+2) : vrank; 2666 remoteVerticesAdj[v].index = gv - vrange[vrank]; 2667 remoteVerticesAdj[v].rank = vrank; 2668 } 2669 /* Create cones */ 2670 ierr = DMPlexSetChart(dm, 0, numCells+numVerticesAdj);CHKERRQ(ierr); 2671 for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);} 2672 ierr = DMSetUp(dm);CHKERRQ(ierr); 2673 ierr = DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2674 for (c = 0; c < numCells; ++c) { 2675 for (p = 0; p < numCorners; ++p) { 2676 const PetscInt gv = cells[c*numCorners+p]; 2677 PetscInt lv; 2678 2679 ierr = PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);CHKERRQ(ierr); 2680 if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv); 2681 cone[p] = lv+numCells; 2682 } 2683 if (invertCells) { ierr = DMPlexInvertCell_Internal(spaceDim, numCorners, cone);CHKERRQ(ierr); } 2684 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 2685 } 2686 ierr = DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2687 /* Create SF for vertices */ 2688 ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfVert);CHKERRQ(ierr); 2689 ierr = PetscObjectSetName((PetscObject) *sfVert, "Vertex Ownership SF");CHKERRQ(ierr); 2690 ierr = PetscSFSetFromOptions(*sfVert);CHKERRQ(ierr); 2691 ierr = PetscSFSetGraph(*sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);CHKERRQ(ierr); 2692 ierr = PetscFree(verticesAdj);CHKERRQ(ierr); 2693 /* Build pointSF */ 2694 ierr = PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);CHKERRQ(ierr); 2695 for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;} 2696 for (v = 0; v < numVertices; ++v) {vertexOwner[v].index = -1; vertexOwner[v].rank = -1;} 2697 ierr = PetscSFReduceBegin(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 2698 ierr = PetscSFReduceEnd(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 2699 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); 2700 ierr = PetscSFBcastBegin(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 2701 ierr = PetscSFBcastEnd(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 2702 for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost; 2703 ierr = PetscMalloc1(numVerticesGhost, &localVertex);CHKERRQ(ierr); 2704 ierr = PetscMalloc1(numVerticesGhost, &remoteVertex);CHKERRQ(ierr); 2705 for (v = 0, g = 0; v < numVerticesAdj; ++v) { 2706 if (vertexLocal[v].rank != rank) { 2707 localVertex[g] = v+numCells; 2708 remoteVertex[g].index = vertexLocal[v].index; 2709 remoteVertex[g].rank = vertexLocal[v].rank; 2710 ++g; 2711 } 2712 } 2713 ierr = PetscFree2(vertexLocal, vertexOwner);CHKERRQ(ierr); 2714 if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost); 2715 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 2716 ierr = PetscObjectSetName((PetscObject) sfPoint, "point SF");CHKERRQ(ierr); 2717 ierr = PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);CHKERRQ(ierr); 2718 ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr); 2719 /* Fill in the rest of the topology structure */ 2720 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2721 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2722 PetscFunctionReturn(0); 2723 } 2724 2725 /* 2726 This takes as input the coordinates for each owned vertex 2727 */ 2728 PetscErrorCode DMPlexBuildCoordinates_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numV, PetscSF sfVert, const PetscReal vertexCoords[]) 2729 { 2730 PetscSection coordSection; 2731 Vec coordinates; 2732 PetscScalar *coords; 2733 PetscInt numVertices, numVerticesAdj, coordSize, v; 2734 PetscErrorCode ierr; 2735 2736 PetscFunctionBegin; 2737 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 2738 ierr = PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);CHKERRQ(ierr); 2739 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2740 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2741 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 2742 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVerticesAdj);CHKERRQ(ierr); 2743 for (v = numCells; v < numCells+numVerticesAdj; ++v) { 2744 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 2745 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 2746 } 2747 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2748 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2749 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 2750 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 2751 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2752 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2753 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2754 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2755 { 2756 MPI_Datatype coordtype; 2757 2758 /* Need a temp buffer for coords if we have complex/single */ 2759 ierr = MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);CHKERRQ(ierr); 2760 ierr = MPI_Type_commit(&coordtype);CHKERRQ(ierr); 2761 #if defined(PETSC_USE_COMPLEX) 2762 { 2763 PetscScalar *svertexCoords; 2764 PetscInt i; 2765 ierr = PetscMalloc1(numV*spaceDim,&svertexCoords);CHKERRQ(ierr); 2766 for (i=0; i<numV*spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 2767 ierr = PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 2768 ierr = PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 2769 ierr = PetscFree(svertexCoords);CHKERRQ(ierr); 2770 } 2771 #else 2772 ierr = PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 2773 ierr = PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 2774 #endif 2775 ierr = MPI_Type_free(&coordtype);CHKERRQ(ierr); 2776 } 2777 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2778 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2779 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2780 PetscFunctionReturn(0); 2781 } 2782 2783 /*@ 2784 DMPlexCreateFromCellListParallel - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 2785 2786 Input Parameters: 2787 + comm - The communicator 2788 . dim - The topological dimension of the mesh 2789 . numCells - The number of cells owned by this process 2790 . numVertices - The number of vertices owned by this process 2791 . numCorners - The number of vertices for each cell 2792 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 2793 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 2794 . spaceDim - The spatial dimension used for coordinates 2795 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2796 2797 Output Parameter: 2798 + dm - The DM 2799 - vertexSF - Optional, SF describing complete vertex ownership 2800 2801 Note: Two triangles sharing a face 2802 $ 2803 $ 2 2804 $ / | \ 2805 $ / | \ 2806 $ / | \ 2807 $ 0 0 | 1 3 2808 $ \ | / 2809 $ \ | / 2810 $ \ | / 2811 $ 1 2812 would have input 2813 $ numCells = 2, numVertices = 4 2814 $ cells = [0 1 2 1 3 2] 2815 $ 2816 which would result in the DMPlex 2817 $ 2818 $ 4 2819 $ / | \ 2820 $ / | \ 2821 $ / | \ 2822 $ 2 0 | 1 5 2823 $ \ | / 2824 $ \ | / 2825 $ \ | / 2826 $ 3 2827 2828 Level: beginner 2829 2830 .seealso: DMPlexCreateFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate() 2831 @*/ 2832 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) 2833 { 2834 PetscSF sfVert; 2835 PetscErrorCode ierr; 2836 2837 PetscFunctionBegin; 2838 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2839 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2840 PetscValidLogicalCollectiveInt(*dm, dim, 2); 2841 PetscValidLogicalCollectiveInt(*dm, spaceDim, 8); 2842 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 2843 ierr = DMPlexBuildFromCellList_Parallel_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE, &sfVert);CHKERRQ(ierr); 2844 if (interpolate) { 2845 DM idm; 2846 2847 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2848 ierr = DMDestroy(dm);CHKERRQ(ierr); 2849 *dm = idm; 2850 } 2851 ierr = DMPlexBuildCoordinates_Parallel_Internal(*dm, spaceDim, numCells, numVertices, sfVert, vertexCoords);CHKERRQ(ierr); 2852 if (vertexSF) *vertexSF = sfVert; 2853 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 2854 PetscFunctionReturn(0); 2855 } 2856 2857 /* 2858 This takes as input the common mesh generator output, a list of the vertices for each cell 2859 */ 2860 PetscErrorCode DMPlexBuildFromCellList_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscBool invertCells) 2861 { 2862 PetscInt *cone, c, p; 2863 PetscErrorCode ierr; 2864 2865 PetscFunctionBegin; 2866 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 2867 for (c = 0; c < numCells; ++c) { 2868 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 2869 } 2870 ierr = DMSetUp(dm);CHKERRQ(ierr); 2871 ierr = DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2872 for (c = 0; c < numCells; ++c) { 2873 for (p = 0; p < numCorners; ++p) { 2874 cone[p] = cells[c*numCorners+p]+numCells; 2875 } 2876 if (invertCells) { ierr = DMPlexInvertCell_Internal(spaceDim, numCorners, cone);CHKERRQ(ierr); } 2877 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 2878 } 2879 ierr = DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2880 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2881 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2882 PetscFunctionReturn(0); 2883 } 2884 2885 /* 2886 This takes as input the coordinates for each vertex 2887 */ 2888 PetscErrorCode DMPlexBuildCoordinates_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]) 2889 { 2890 PetscSection coordSection; 2891 Vec coordinates; 2892 DM cdm; 2893 PetscScalar *coords; 2894 PetscInt v, d; 2895 PetscErrorCode ierr; 2896 2897 PetscFunctionBegin; 2898 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 2899 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2900 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2901 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 2902 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); 2903 for (v = numCells; v < numCells+numVertices; ++v) { 2904 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 2905 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 2906 } 2907 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2908 2909 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 2910 ierr = DMCreateLocalVector(cdm, &coordinates);CHKERRQ(ierr); 2911 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 2912 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2913 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2914 for (v = 0; v < numVertices; ++v) { 2915 for (d = 0; d < spaceDim; ++d) { 2916 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 2917 } 2918 } 2919 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2920 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2921 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2922 PetscFunctionReturn(0); 2923 } 2924 2925 /*@ 2926 DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 2927 2928 Input Parameters: 2929 + comm - The communicator 2930 . dim - The topological dimension of the mesh 2931 . numCells - The number of cells 2932 . numVertices - The number of vertices 2933 . numCorners - The number of vertices for each cell 2934 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 2935 . cells - An array of numCells*numCorners numbers, the vertices for each cell 2936 . spaceDim - The spatial dimension used for coordinates 2937 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2938 2939 Output Parameter: 2940 . dm - The DM 2941 2942 Note: Two triangles sharing a face 2943 $ 2944 $ 2 2945 $ / | \ 2946 $ / | \ 2947 $ / | \ 2948 $ 0 0 | 1 3 2949 $ \ | / 2950 $ \ | / 2951 $ \ | / 2952 $ 1 2953 would have input 2954 $ numCells = 2, numVertices = 4 2955 $ cells = [0 1 2 1 3 2] 2956 $ 2957 which would result in the DMPlex 2958 $ 2959 $ 4 2960 $ / | \ 2961 $ / | \ 2962 $ / | \ 2963 $ 2 0 | 1 5 2964 $ \ | / 2965 $ \ | / 2966 $ \ | / 2967 $ 3 2968 2969 Level: beginner 2970 2971 .seealso: DMPlexCreateFromDAG(), DMPlexCreate() 2972 @*/ 2973 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) 2974 { 2975 PetscErrorCode ierr; 2976 2977 PetscFunctionBegin; 2978 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2979 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2980 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 2981 ierr = DMPlexBuildFromCellList_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE);CHKERRQ(ierr); 2982 if (interpolate) { 2983 DM idm; 2984 2985 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2986 ierr = DMDestroy(dm);CHKERRQ(ierr); 2987 *dm = idm; 2988 } 2989 ierr = DMPlexBuildCoordinates_Internal(*dm, spaceDim, numCells, numVertices, vertexCoords);CHKERRQ(ierr); 2990 PetscFunctionReturn(0); 2991 } 2992 2993 /*@ 2994 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 2995 2996 Input Parameters: 2997 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 2998 . depth - The depth of the DAG 2999 . numPoints - Array of size depth + 1 containing the number of points at each depth 3000 . coneSize - The cone size of each point 3001 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 3002 . coneOrientations - The orientation of each cone point 3003 - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim() 3004 3005 Output Parameter: 3006 . dm - The DM 3007 3008 Note: Two triangles sharing a face would have input 3009 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 3010 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 3011 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 3012 $ 3013 which would result in the DMPlex 3014 $ 3015 $ 4 3016 $ / | \ 3017 $ / | \ 3018 $ / | \ 3019 $ 2 0 | 1 5 3020 $ \ | / 3021 $ \ | / 3022 $ \ | / 3023 $ 3 3024 $ 3025 $ Notice that all points are numbered consecutively, unlikely DMPlexCreateFromCellList() 3026 3027 Level: advanced 3028 3029 .seealso: DMPlexCreateFromCellList(), DMPlexCreate() 3030 @*/ 3031 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 3032 { 3033 Vec coordinates; 3034 PetscSection coordSection; 3035 PetscScalar *coords; 3036 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 3037 PetscErrorCode ierr; 3038 3039 PetscFunctionBegin; 3040 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3041 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 3042 if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %d cannot be less than intrinsic dimension %d",dimEmbed,dim); 3043 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 3044 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 3045 for (p = pStart; p < pEnd; ++p) { 3046 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 3047 if (firstVertex < 0 && !coneSize[p - pStart]) { 3048 firstVertex = p - pStart; 3049 } 3050 } 3051 if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %d vertices but could not find any", numPoints[0]); 3052 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 3053 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 3054 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 3055 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 3056 } 3057 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3058 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3059 /* Build coordinates */ 3060 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3061 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3062 ierr = PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);CHKERRQ(ierr); 3063 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 3064 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 3065 ierr = PetscSectionSetDof(coordSection, v, dimEmbed);CHKERRQ(ierr); 3066 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);CHKERRQ(ierr); 3067 } 3068 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3069 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3070 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3071 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3072 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3073 ierr = VecSetBlockSize(coordinates, dimEmbed);CHKERRQ(ierr); 3074 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 3075 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3076 for (v = 0; v < numPoints[0]; ++v) { 3077 PetscInt off; 3078 3079 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 3080 for (d = 0; d < dimEmbed; ++d) { 3081 coords[off+d] = vertexCoords[v*dimEmbed+d]; 3082 } 3083 } 3084 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3085 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3086 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3087 PetscFunctionReturn(0); 3088 } 3089 3090 /*@C 3091 DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file. 3092 3093 + comm - The MPI communicator 3094 . filename - Name of the .dat file 3095 - interpolate - Create faces and edges in the mesh 3096 3097 Output Parameter: 3098 . dm - The DM object representing the mesh 3099 3100 Note: The format is the simplest possible: 3101 $ Ne 3102 $ v0 v1 ... vk 3103 $ Nv 3104 $ x y z marker 3105 3106 Level: beginner 3107 3108 .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate() 3109 @*/ 3110 PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3111 { 3112 DMLabel marker; 3113 PetscViewer viewer; 3114 Vec coordinates; 3115 PetscSection coordSection; 3116 PetscScalar *coords; 3117 char line[PETSC_MAX_PATH_LEN]; 3118 PetscInt dim = 3, cdim = 3, coordSize, v, c, d; 3119 PetscMPIInt rank; 3120 int snum, Nv, Nc; 3121 PetscErrorCode ierr; 3122 3123 PetscFunctionBegin; 3124 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 3125 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 3126 ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr); 3127 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 3128 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 3129 if (!rank) { 3130 ierr = PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);CHKERRQ(ierr); 3131 snum = sscanf(line, "%d %d", &Nc, &Nv); 3132 if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3133 } else { 3134 Nc = Nv = 0; 3135 } 3136 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3137 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3138 ierr = DMPlexSetChart(*dm, 0, Nc+Nv);CHKERRQ(ierr); 3139 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3140 ierr = DMSetCoordinateDim(*dm, cdim);CHKERRQ(ierr); 3141 /* Read topology */ 3142 if (!rank) { 3143 PetscInt cone[8], corners = 8; 3144 int vbuf[8], v; 3145 3146 for (c = 0; c < Nc; ++c) {ierr = DMPlexSetConeSize(*dm, c, corners);CHKERRQ(ierr);} 3147 ierr = DMSetUp(*dm);CHKERRQ(ierr); 3148 for (c = 0; c < Nc; ++c) { 3149 ierr = PetscViewerRead(viewer, line, corners, NULL, PETSC_STRING);CHKERRQ(ierr); 3150 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]); 3151 if (snum != corners) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3152 for (v = 0; v < corners; ++v) cone[v] = vbuf[v] + Nc; 3153 /* Hexahedra are inverted */ 3154 { 3155 PetscInt tmp = cone[1]; 3156 cone[1] = cone[3]; 3157 cone[3] = tmp; 3158 } 3159 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 3160 } 3161 } 3162 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 3163 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 3164 /* Read coordinates */ 3165 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 3166 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3167 ierr = PetscSectionSetFieldComponents(coordSection, 0, cdim);CHKERRQ(ierr); 3168 ierr = PetscSectionSetChart(coordSection, Nc, Nc + Nv);CHKERRQ(ierr); 3169 for (v = Nc; v < Nc+Nv; ++v) { 3170 ierr = PetscSectionSetDof(coordSection, v, cdim);CHKERRQ(ierr); 3171 ierr = PetscSectionSetFieldDof(coordSection, v, 0, cdim);CHKERRQ(ierr); 3172 } 3173 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3174 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3175 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3176 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3177 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3178 ierr = VecSetBlockSize(coordinates, cdim);CHKERRQ(ierr); 3179 ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr); 3180 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3181 if (!rank) { 3182 double x[3]; 3183 int val; 3184 3185 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 3186 ierr = DMGetLabel(*dm, "marker", &marker);CHKERRQ(ierr); 3187 for (v = 0; v < Nv; ++v) { 3188 ierr = PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);CHKERRQ(ierr); 3189 snum = sscanf(line, "%lg %lg %lg %d", &x[0], &x[1], &x[2], &val); 3190 if (snum != 4) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3191 for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d]; 3192 if (val) {ierr = DMLabelSetValue(marker, v+Nc, val);CHKERRQ(ierr);} 3193 } 3194 } 3195 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3196 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 3197 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3198 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 3199 if (interpolate) { 3200 DM idm; 3201 DMLabel bdlabel; 3202 3203 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3204 ierr = DMDestroy(dm);CHKERRQ(ierr); 3205 *dm = idm; 3206 3207 ierr = DMGetLabel(*dm, "marker", &bdlabel);CHKERRQ(ierr); 3208 ierr = DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 3209 ierr = DMPlexLabelComplete(*dm, bdlabel);CHKERRQ(ierr); 3210 } 3211 PetscFunctionReturn(0); 3212 } 3213 3214 /*@C 3215 DMPlexCreateFromFile - This takes a filename and produces a DM 3216 3217 Input Parameters: 3218 + comm - The communicator 3219 . filename - A file name 3220 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 3221 3222 Output Parameter: 3223 . dm - The DM 3224 3225 Options Database Keys: 3226 . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5 3227 3228 Level: beginner 3229 3230 .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellList(), DMPlexCreate() 3231 @*/ 3232 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3233 { 3234 const char *extGmsh = ".msh"; 3235 const char *extGmsh2 = ".msh2"; 3236 const char *extGmsh4 = ".msh4"; 3237 const char *extCGNS = ".cgns"; 3238 const char *extExodus = ".exo"; 3239 const char *extGenesis = ".gen"; 3240 const char *extFluent = ".cas"; 3241 const char *extHDF5 = ".h5"; 3242 const char *extMed = ".med"; 3243 const char *extPLY = ".ply"; 3244 const char *extCV = ".dat"; 3245 size_t len; 3246 PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isCV; 3247 PetscMPIInt rank; 3248 PetscErrorCode ierr; 3249 3250 PetscFunctionBegin; 3251 PetscValidPointer(filename, 2); 3252 PetscValidPointer(dm, 4); 3253 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 3254 ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); 3255 if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 3256 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);CHKERRQ(ierr); 3257 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh2, 5, &isGmsh2);CHKERRQ(ierr); 3258 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh4, 5, &isGmsh4);CHKERRQ(ierr); 3259 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);CHKERRQ(ierr); 3260 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);CHKERRQ(ierr); 3261 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);CHKERRQ(ierr); 3262 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);CHKERRQ(ierr); 3263 ierr = PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);CHKERRQ(ierr); 3264 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);CHKERRQ(ierr); 3265 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);CHKERRQ(ierr); 3266 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);CHKERRQ(ierr); 3267 if (isGmsh || isGmsh2 || isGmsh4) { 3268 ierr = DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3269 } else if (isCGNS) { 3270 ierr = DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3271 } else if (isExodus || isGenesis) { 3272 ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3273 } else if (isFluent) { 3274 ierr = DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3275 } else if (isHDF5) { 3276 PetscBool load_hdf5_xdmf = PETSC_FALSE; 3277 PetscViewer viewer; 3278 3279 /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */ 3280 ierr = PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf", 5, &load_hdf5_xdmf);CHKERRQ(ierr); 3281 ierr = PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);CHKERRQ(ierr); 3282 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 3283 ierr = PetscViewerSetType(viewer, PETSCVIEWERHDF5);CHKERRQ(ierr); 3284 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 3285 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 3286 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3287 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3288 if (load_hdf5_xdmf) {ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);CHKERRQ(ierr);} 3289 ierr = DMLoad(*dm, viewer);CHKERRQ(ierr); 3290 if (load_hdf5_xdmf) {ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);} 3291 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 3292 3293 if (interpolate) { 3294 DM idm; 3295 3296 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3297 ierr = DMDestroy(dm);CHKERRQ(ierr); 3298 *dm = idm; 3299 } 3300 } else if (isMed) { 3301 ierr = DMPlexCreateMedFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3302 } else if (isPLY) { 3303 ierr = DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3304 } else if (isCV) { 3305 ierr = DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3306 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 3307 PetscFunctionReturn(0); 3308 } 3309 3310 /*@ 3311 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 3312 3313 Collective on comm 3314 3315 Input Parameters: 3316 + comm - The communicator 3317 . dim - The spatial dimension 3318 - simplex - Flag for simplex, otherwise use a tensor-product cell 3319 3320 Output Parameter: 3321 . refdm - The reference cell 3322 3323 Level: intermediate 3324 3325 .keywords: reference cell 3326 .seealso: 3327 @*/ 3328 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm) 3329 { 3330 DM rdm; 3331 Vec coords; 3332 PetscErrorCode ierr; 3333 3334 PetscFunctionBeginUser; 3335 ierr = DMCreate(comm, &rdm);CHKERRQ(ierr); 3336 ierr = DMSetType(rdm, DMPLEX);CHKERRQ(ierr); 3337 ierr = DMSetDimension(rdm, dim);CHKERRQ(ierr); 3338 switch (dim) { 3339 case 0: 3340 { 3341 PetscInt numPoints[1] = {1}; 3342 PetscInt coneSize[1] = {0}; 3343 PetscInt cones[1] = {0}; 3344 PetscInt coneOrientations[1] = {0}; 3345 PetscScalar vertexCoords[1] = {0.0}; 3346 3347 ierr = DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3348 } 3349 break; 3350 case 1: 3351 { 3352 PetscInt numPoints[2] = {2, 1}; 3353 PetscInt coneSize[3] = {2, 0, 0}; 3354 PetscInt cones[2] = {1, 2}; 3355 PetscInt coneOrientations[2] = {0, 0}; 3356 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 3357 3358 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3359 } 3360 break; 3361 case 2: 3362 if (simplex) { 3363 PetscInt numPoints[2] = {3, 1}; 3364 PetscInt coneSize[4] = {3, 0, 0, 0}; 3365 PetscInt cones[3] = {1, 2, 3}; 3366 PetscInt coneOrientations[3] = {0, 0, 0}; 3367 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 3368 3369 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3370 } else { 3371 PetscInt numPoints[2] = {4, 1}; 3372 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3373 PetscInt cones[4] = {1, 2, 3, 4}; 3374 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3375 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 3376 3377 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3378 } 3379 break; 3380 case 3: 3381 if (simplex) { 3382 PetscInt numPoints[2] = {4, 1}; 3383 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3384 PetscInt cones[4] = {1, 3, 2, 4}; 3385 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3386 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}; 3387 3388 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3389 } else { 3390 PetscInt numPoints[2] = {8, 1}; 3391 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3392 PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8}; 3393 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3394 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, 3395 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3396 3397 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3398 } 3399 break; 3400 default: 3401 SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %d", dim); 3402 } 3403 ierr = DMPlexInterpolate(rdm, refdm);CHKERRQ(ierr); 3404 if (rdm->coordinateDM) { 3405 DM ncdm; 3406 PetscSection cs; 3407 PetscInt pEnd = -1; 3408 3409 ierr = DMGetSection(rdm->coordinateDM, &cs);CHKERRQ(ierr); 3410 if (cs) {ierr = PetscSectionGetChart(cs, NULL, &pEnd);CHKERRQ(ierr);} 3411 if (pEnd >= 0) { 3412 ierr = DMClone(rdm->coordinateDM, &ncdm);CHKERRQ(ierr); 3413 ierr = DMCopyDisc(rdm->coordinateDM, ncdm);CHKERRQ(ierr); 3414 ierr = DMSetSection(ncdm, cs);CHKERRQ(ierr); 3415 ierr = DMSetCoordinateDM(*refdm, ncdm);CHKERRQ(ierr); 3416 ierr = DMDestroy(&ncdm);CHKERRQ(ierr); 3417 } 3418 } 3419 ierr = DMGetCoordinatesLocal(rdm, &coords);CHKERRQ(ierr); 3420 if (coords) { 3421 ierr = DMSetCoordinatesLocal(*refdm, coords);CHKERRQ(ierr); 3422 } else { 3423 ierr = DMGetCoordinates(rdm, &coords);CHKERRQ(ierr); 3424 if (coords) {ierr = DMSetCoordinates(*refdm, coords);CHKERRQ(ierr);} 3425 } 3426 ierr = DMDestroy(&rdm);CHKERRQ(ierr); 3427 PetscFunctionReturn(0); 3428 } 3429