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