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 2276 ierr = PetscPartitionerSetFromOptions(mesh->partitioner);CHKERRQ(ierr); 2277 PetscFunctionReturn(0); 2278 } 2279 2280 static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 2281 { 2282 PetscInt refine = 0, coarsen = 0, r; 2283 PetscBool isHierarchy; 2284 PetscErrorCode ierr; 2285 2286 PetscFunctionBegin; 2287 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2288 ierr = PetscOptionsHead(PetscOptionsObject,"DMPlex Options");CHKERRQ(ierr); 2289 /* Handle DMPlex refinement */ 2290 ierr = PetscOptionsInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL);CHKERRQ(ierr); 2291 ierr = PetscOptionsInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy);CHKERRQ(ierr); 2292 if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 2293 if (refine && isHierarchy) { 2294 DM *dms, coarseDM; 2295 2296 ierr = DMGetCoarseDM(dm, &coarseDM);CHKERRQ(ierr); 2297 ierr = PetscObjectReference((PetscObject)coarseDM);CHKERRQ(ierr); 2298 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 2299 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 2300 /* Total hack since we do not pass in a pointer */ 2301 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 2302 if (refine == 1) { 2303 ierr = DMSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 2304 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2305 } else { 2306 ierr = DMSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 2307 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2308 ierr = DMSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 2309 ierr = DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);CHKERRQ(ierr); 2310 } 2311 ierr = DMSetCoarseDM(dms[refine-1], coarseDM);CHKERRQ(ierr); 2312 ierr = PetscObjectDereference((PetscObject)coarseDM);CHKERRQ(ierr); 2313 /* Free DMs */ 2314 for (r = 0; r < refine; ++r) { 2315 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2316 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2317 } 2318 ierr = PetscFree(dms);CHKERRQ(ierr); 2319 } else { 2320 for (r = 0; r < refine; ++r) { 2321 DM refinedMesh; 2322 2323 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2324 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);CHKERRQ(ierr); 2325 /* Total hack since we do not pass in a pointer */ 2326 ierr = DMPlexReplace_Static(dm, refinedMesh);CHKERRQ(ierr); 2327 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2328 ierr = DMDestroy(&refinedMesh);CHKERRQ(ierr); 2329 } 2330 } 2331 /* Handle DMPlex coarsening */ 2332 ierr = PetscOptionsInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL);CHKERRQ(ierr); 2333 ierr = PetscOptionsInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy);CHKERRQ(ierr); 2334 if (coarsen && isHierarchy) { 2335 DM *dms; 2336 2337 ierr = PetscMalloc1(coarsen, &dms);CHKERRQ(ierr); 2338 ierr = DMCoarsenHierarchy(dm, coarsen, dms);CHKERRQ(ierr); 2339 /* Free DMs */ 2340 for (r = 0; r < coarsen; ++r) { 2341 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2342 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2343 } 2344 ierr = PetscFree(dms);CHKERRQ(ierr); 2345 } else { 2346 for (r = 0; r < coarsen; ++r) { 2347 DM coarseMesh; 2348 2349 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2350 ierr = DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);CHKERRQ(ierr); 2351 /* Total hack since we do not pass in a pointer */ 2352 ierr = DMPlexReplace_Static(dm, coarseMesh);CHKERRQ(ierr); 2353 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2354 ierr = DMDestroy(&coarseMesh);CHKERRQ(ierr); 2355 } 2356 } 2357 /* Handle */ 2358 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2359 ierr = PetscOptionsTail();CHKERRQ(ierr); 2360 PetscFunctionReturn(0); 2361 } 2362 2363 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 2364 { 2365 PetscErrorCode ierr; 2366 2367 PetscFunctionBegin; 2368 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2369 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 2370 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 2371 ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); 2372 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 2373 ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); 2374 PetscFunctionReturn(0); 2375 } 2376 2377 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 2378 { 2379 PetscErrorCode ierr; 2380 2381 PetscFunctionBegin; 2382 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2383 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 2384 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 2385 PetscFunctionReturn(0); 2386 } 2387 2388 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 2389 { 2390 PetscInt depth, d; 2391 PetscErrorCode ierr; 2392 2393 PetscFunctionBegin; 2394 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2395 if (depth == 1) { 2396 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 2397 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 2398 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 2399 else {*pStart = 0; *pEnd = 0;} 2400 } else { 2401 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 2402 } 2403 PetscFunctionReturn(0); 2404 } 2405 2406 static PetscErrorCode DMGetNeighors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 2407 { 2408 PetscSF sf; 2409 PetscErrorCode ierr; 2410 2411 PetscFunctionBegin; 2412 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 2413 ierr = PetscSFGetRanks(sf, nranks, ranks, NULL, NULL, NULL);CHKERRQ(ierr); 2414 PetscFunctionReturn(0); 2415 } 2416 2417 static PetscErrorCode DMHasCreateInjection_Plex(DM dm, PetscBool *flg) 2418 { 2419 PetscFunctionBegin; 2420 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 2421 PetscValidPointer(flg,2); 2422 *flg = PETSC_TRUE; 2423 PetscFunctionReturn(0); 2424 } 2425 2426 static PetscErrorCode DMInitialize_Plex(DM dm) 2427 { 2428 PetscErrorCode ierr; 2429 2430 PetscFunctionBegin; 2431 dm->ops->view = DMView_Plex; 2432 dm->ops->load = DMLoad_Plex; 2433 dm->ops->setfromoptions = DMSetFromOptions_Plex; 2434 dm->ops->clone = DMClone_Plex; 2435 dm->ops->setup = DMSetUp_Plex; 2436 dm->ops->createdefaultsection = DMCreateDefaultSection_Plex; 2437 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 2438 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 2439 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 2440 dm->ops->getlocaltoglobalmapping = NULL; 2441 dm->ops->createfieldis = NULL; 2442 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 2443 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 2444 dm->ops->getcoloring = NULL; 2445 dm->ops->creatematrix = DMCreateMatrix_Plex; 2446 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 2447 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 2448 dm->ops->getaggregates = NULL; 2449 dm->ops->getinjection = DMCreateInjection_Plex; 2450 dm->ops->hascreateinjection = DMHasCreateInjection_Plex; 2451 dm->ops->refine = DMRefine_Plex; 2452 dm->ops->coarsen = DMCoarsen_Plex; 2453 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 2454 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 2455 dm->ops->adaptlabel = DMAdaptLabel_Plex; 2456 dm->ops->adaptmetric = DMAdaptMetric_Plex; 2457 dm->ops->globaltolocalbegin = NULL; 2458 dm->ops->globaltolocalend = NULL; 2459 dm->ops->localtoglobalbegin = NULL; 2460 dm->ops->localtoglobalend = NULL; 2461 dm->ops->destroy = DMDestroy_Plex; 2462 dm->ops->createsubdm = DMCreateSubDM_Plex; 2463 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 2464 dm->ops->getdimpoints = DMGetDimPoints_Plex; 2465 dm->ops->locatepoints = DMLocatePoints_Plex; 2466 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 2467 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 2468 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 2469 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 2470 dm->ops->computel2diff = DMComputeL2Diff_Plex; 2471 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 2472 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 2473 dm->ops->getneighbors = DMGetNeighors_Plex; 2474 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);CHKERRQ(ierr); 2475 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);CHKERRQ(ierr); 2476 PetscFunctionReturn(0); 2477 } 2478 2479 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 2480 { 2481 DM_Plex *mesh = (DM_Plex *) dm->data; 2482 PetscErrorCode ierr; 2483 2484 PetscFunctionBegin; 2485 mesh->refct++; 2486 (*newdm)->data = mesh; 2487 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 2488 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 2489 PetscFunctionReturn(0); 2490 } 2491 2492 /*MC 2493 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 2494 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 2495 specified by a PetscSection object. Ownership in the global representation is determined by 2496 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 2497 2498 Options Database Keys: 2499 + -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ 2500 . -dm_plex_view_scale <num> - Scale the TikZ 2501 - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices 2502 2503 2504 Level: intermediate 2505 2506 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 2507 M*/ 2508 2509 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 2510 { 2511 DM_Plex *mesh; 2512 PetscInt unit, d; 2513 PetscErrorCode ierr; 2514 2515 PetscFunctionBegin; 2516 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2517 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 2518 dm->dim = 0; 2519 dm->data = mesh; 2520 2521 mesh->refct = 1; 2522 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 2523 mesh->maxConeSize = 0; 2524 mesh->cones = NULL; 2525 mesh->coneOrientations = NULL; 2526 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 2527 mesh->maxSupportSize = 0; 2528 mesh->supports = NULL; 2529 mesh->refinementUniform = PETSC_TRUE; 2530 mesh->refinementLimit = -1.0; 2531 2532 mesh->facesTmp = NULL; 2533 2534 mesh->tetgenOpts = NULL; 2535 mesh->triangleOpts = NULL; 2536 ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); 2537 mesh->remeshBd = PETSC_FALSE; 2538 2539 mesh->subpointMap = NULL; 2540 2541 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 2542 2543 mesh->regularRefinement = PETSC_FALSE; 2544 mesh->depthState = -1; 2545 mesh->globalVertexNumbers = NULL; 2546 mesh->globalCellNumbers = NULL; 2547 mesh->anchorSection = NULL; 2548 mesh->anchorIS = NULL; 2549 mesh->createanchors = NULL; 2550 mesh->computeanchormatrix = NULL; 2551 mesh->parentSection = NULL; 2552 mesh->parents = NULL; 2553 mesh->childIDs = NULL; 2554 mesh->childSection = NULL; 2555 mesh->children = NULL; 2556 mesh->referenceTree = NULL; 2557 mesh->getchildsymmetry = NULL; 2558 for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE; 2559 mesh->vtkCellHeight = 0; 2560 mesh->useAnchors = PETSC_FALSE; 2561 2562 mesh->maxProjectionHeight = 0; 2563 2564 mesh->printSetValues = PETSC_FALSE; 2565 mesh->printFEM = 0; 2566 mesh->printTol = 1.0e-10; 2567 2568 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 2569 PetscFunctionReturn(0); 2570 } 2571 2572 /*@ 2573 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 2574 2575 Collective on MPI_Comm 2576 2577 Input Parameter: 2578 . comm - The communicator for the DMPlex object 2579 2580 Output Parameter: 2581 . mesh - The DMPlex object 2582 2583 Level: beginner 2584 2585 .keywords: DMPlex, create 2586 @*/ 2587 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 2588 { 2589 PetscErrorCode ierr; 2590 2591 PetscFunctionBegin; 2592 PetscValidPointer(mesh,2); 2593 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 2594 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 2595 PetscFunctionReturn(0); 2596 } 2597 2598 /* 2599 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 2600 */ 2601 /* TODO: invertCells and spaceDim arguments could be added also to to DMPlexCreateFromCellListParallel(), DMPlexBuildFromCellList_Internal() and DMPlexCreateFromCellList() */ 2602 PetscErrorCode DMPlexBuildFromCellList_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscBool invertCells, PetscSF *sfVert) 2603 { 2604 PetscSF sfPoint; 2605 PetscLayout vLayout; 2606 PetscHSetI vhash; 2607 PetscSFNode *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex; 2608 const PetscInt *vrange; 2609 PetscInt numVerticesAdj, off = 0, *verticesAdj, numVerticesGhost = 0, *localVertex, *cone, c, p, v, g; 2610 PetscMPIInt rank, size; 2611 PetscErrorCode ierr; 2612 2613 PetscFunctionBegin; 2614 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 2615 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); 2616 /* Partition vertices */ 2617 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);CHKERRQ(ierr); 2618 ierr = PetscLayoutSetLocalSize(vLayout, numVertices);CHKERRQ(ierr); 2619 ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr); 2620 ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr); 2621 ierr = PetscLayoutGetRanges(vLayout, &vrange);CHKERRQ(ierr); 2622 /* Count vertices and map them to procs */ 2623 ierr = PetscHSetICreate(&vhash);CHKERRQ(ierr); 2624 for (c = 0; c < numCells; ++c) { 2625 for (p = 0; p < numCorners; ++p) { 2626 ierr = PetscHSetIAdd(vhash, cells[c*numCorners+p]);CHKERRQ(ierr); 2627 } 2628 } 2629 ierr = PetscHSetIGetSize(vhash, &numVerticesAdj);CHKERRQ(ierr); 2630 ierr = PetscMalloc1(numVerticesAdj, &verticesAdj);CHKERRQ(ierr); 2631 ierr = PetscHSetIGetElems(vhash, &off, verticesAdj);CHKERRQ(ierr); 2632 ierr = PetscHSetIDestroy(&vhash);CHKERRQ(ierr); 2633 if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj); 2634 ierr = PetscSortInt(numVerticesAdj, verticesAdj);CHKERRQ(ierr); 2635 ierr = PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);CHKERRQ(ierr); 2636 for (v = 0; v < numVerticesAdj; ++v) { 2637 const PetscInt gv = verticesAdj[v]; 2638 PetscInt vrank; 2639 2640 ierr = PetscFindInt(gv, size+1, vrange, &vrank);CHKERRQ(ierr); 2641 vrank = vrank < 0 ? -(vrank+2) : vrank; 2642 remoteVerticesAdj[v].index = gv - vrange[vrank]; 2643 remoteVerticesAdj[v].rank = vrank; 2644 } 2645 /* Create cones */ 2646 ierr = DMPlexSetChart(dm, 0, numCells+numVerticesAdj);CHKERRQ(ierr); 2647 for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);} 2648 ierr = DMSetUp(dm);CHKERRQ(ierr); 2649 ierr = DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2650 for (c = 0; c < numCells; ++c) { 2651 for (p = 0; p < numCorners; ++p) { 2652 const PetscInt gv = cells[c*numCorners+p]; 2653 PetscInt lv; 2654 2655 ierr = PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);CHKERRQ(ierr); 2656 if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv); 2657 cone[p] = lv+numCells; 2658 } 2659 if (invertCells) { ierr = DMPlexInvertCell_Internal(spaceDim, numCorners, cone);CHKERRQ(ierr); } 2660 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 2661 } 2662 ierr = DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2663 /* Create SF for vertices */ 2664 ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfVert);CHKERRQ(ierr); 2665 ierr = PetscObjectSetName((PetscObject) *sfVert, "Vertex Ownership SF");CHKERRQ(ierr); 2666 ierr = PetscSFSetFromOptions(*sfVert);CHKERRQ(ierr); 2667 ierr = PetscSFSetGraph(*sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);CHKERRQ(ierr); 2668 ierr = PetscFree(verticesAdj);CHKERRQ(ierr); 2669 /* Build pointSF */ 2670 ierr = PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);CHKERRQ(ierr); 2671 for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;} 2672 for (v = 0; v < numVertices; ++v) {vertexOwner[v].index = -1; vertexOwner[v].rank = -1;} 2673 ierr = PetscSFReduceBegin(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 2674 ierr = PetscSFReduceEnd(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 2675 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); 2676 ierr = PetscSFBcastBegin(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 2677 ierr = PetscSFBcastEnd(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 2678 for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost; 2679 ierr = PetscMalloc1(numVerticesGhost, &localVertex);CHKERRQ(ierr); 2680 ierr = PetscMalloc1(numVerticesGhost, &remoteVertex);CHKERRQ(ierr); 2681 for (v = 0, g = 0; v < numVerticesAdj; ++v) { 2682 if (vertexLocal[v].rank != rank) { 2683 localVertex[g] = v+numCells; 2684 remoteVertex[g].index = vertexLocal[v].index; 2685 remoteVertex[g].rank = vertexLocal[v].rank; 2686 ++g; 2687 } 2688 } 2689 ierr = PetscFree2(vertexLocal, vertexOwner);CHKERRQ(ierr); 2690 if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost); 2691 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 2692 ierr = PetscObjectSetName((PetscObject) sfPoint, "point SF");CHKERRQ(ierr); 2693 ierr = PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);CHKERRQ(ierr); 2694 ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr); 2695 /* Fill in the rest of the topology structure */ 2696 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2697 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2698 PetscFunctionReturn(0); 2699 } 2700 2701 /* 2702 This takes as input the coordinates for each owned vertex 2703 */ 2704 PetscErrorCode DMPlexBuildCoordinates_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numV, PetscSF sfVert, const PetscReal vertexCoords[]) 2705 { 2706 PetscSection coordSection; 2707 Vec coordinates; 2708 PetscScalar *coords; 2709 PetscInt numVertices, numVerticesAdj, coordSize, v; 2710 PetscErrorCode ierr; 2711 2712 PetscFunctionBegin; 2713 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 2714 ierr = PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);CHKERRQ(ierr); 2715 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2716 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2717 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 2718 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVerticesAdj);CHKERRQ(ierr); 2719 for (v = numCells; v < numCells+numVerticesAdj; ++v) { 2720 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 2721 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 2722 } 2723 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2724 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2725 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 2726 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 2727 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2728 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2729 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2730 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2731 { 2732 MPI_Datatype coordtype; 2733 2734 /* Need a temp buffer for coords if we have complex/single */ 2735 ierr = MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);CHKERRQ(ierr); 2736 ierr = MPI_Type_commit(&coordtype);CHKERRQ(ierr); 2737 #if defined(PETSC_USE_COMPLEX) 2738 { 2739 PetscScalar *svertexCoords; 2740 PetscInt i; 2741 ierr = PetscMalloc1(numV*spaceDim,&svertexCoords);CHKERRQ(ierr); 2742 for (i=0; i<numV*spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 2743 ierr = PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 2744 ierr = PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 2745 ierr = PetscFree(svertexCoords);CHKERRQ(ierr); 2746 } 2747 #else 2748 ierr = PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 2749 ierr = PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 2750 #endif 2751 ierr = MPI_Type_free(&coordtype);CHKERRQ(ierr); 2752 } 2753 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2754 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2755 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2756 PetscFunctionReturn(0); 2757 } 2758 2759 /*@C 2760 DMPlexCreateFromCellListParallel - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 2761 2762 Input Parameters: 2763 + comm - The communicator 2764 . dim - The topological dimension of the mesh 2765 . numCells - The number of cells owned by this process 2766 . numVertices - The number of vertices owned by this process 2767 . numCorners - The number of vertices for each cell 2768 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 2769 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 2770 . spaceDim - The spatial dimension used for coordinates 2771 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2772 2773 Output Parameter: 2774 + dm - The DM 2775 - vertexSF - Optional, SF describing complete vertex ownership 2776 2777 Note: Two triangles sharing a face 2778 $ 2779 $ 2 2780 $ / | \ 2781 $ / | \ 2782 $ / | \ 2783 $ 0 0 | 1 3 2784 $ \ | / 2785 $ \ | / 2786 $ \ | / 2787 $ 1 2788 would have input 2789 $ numCells = 2, numVertices = 4 2790 $ cells = [0 1 2 1 3 2] 2791 $ 2792 which would result in the DMPlex 2793 $ 2794 $ 4 2795 $ / | \ 2796 $ / | \ 2797 $ / | \ 2798 $ 2 0 | 1 5 2799 $ \ | / 2800 $ \ | / 2801 $ \ | / 2802 $ 3 2803 2804 Level: beginner 2805 2806 .seealso: DMPlexCreateFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate() 2807 @*/ 2808 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) 2809 { 2810 PetscSF sfVert; 2811 PetscErrorCode ierr; 2812 2813 PetscFunctionBegin; 2814 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2815 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2816 PetscValidLogicalCollectiveInt(*dm, dim, 2); 2817 PetscValidLogicalCollectiveInt(*dm, spaceDim, 8); 2818 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 2819 ierr = DMPlexBuildFromCellList_Parallel_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE, &sfVert);CHKERRQ(ierr); 2820 if (interpolate) { 2821 DM idm; 2822 2823 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2824 ierr = DMDestroy(dm);CHKERRQ(ierr); 2825 *dm = idm; 2826 } 2827 ierr = DMPlexBuildCoordinates_Parallel_Internal(*dm, spaceDim, numCells, numVertices, sfVert, vertexCoords);CHKERRQ(ierr); 2828 if (vertexSF) *vertexSF = sfVert; 2829 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 2830 PetscFunctionReturn(0); 2831 } 2832 2833 /* 2834 This takes as input the common mesh generator output, a list of the vertices for each cell 2835 */ 2836 PetscErrorCode DMPlexBuildFromCellList_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscBool invertCells) 2837 { 2838 PetscInt *cone, c, p; 2839 PetscErrorCode ierr; 2840 2841 PetscFunctionBegin; 2842 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 2843 for (c = 0; c < numCells; ++c) { 2844 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 2845 } 2846 ierr = DMSetUp(dm);CHKERRQ(ierr); 2847 ierr = DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2848 for (c = 0; c < numCells; ++c) { 2849 for (p = 0; p < numCorners; ++p) { 2850 cone[p] = cells[c*numCorners+p]+numCells; 2851 } 2852 if (invertCells) { ierr = DMPlexInvertCell_Internal(spaceDim, numCorners, cone);CHKERRQ(ierr); } 2853 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 2854 } 2855 ierr = DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2856 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2857 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2858 PetscFunctionReturn(0); 2859 } 2860 2861 /* 2862 This takes as input the coordinates for each vertex 2863 */ 2864 PetscErrorCode DMPlexBuildCoordinates_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]) 2865 { 2866 PetscSection coordSection; 2867 Vec coordinates; 2868 DM cdm; 2869 PetscScalar *coords; 2870 PetscInt v, d; 2871 PetscErrorCode ierr; 2872 2873 PetscFunctionBegin; 2874 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 2875 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2876 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2877 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 2878 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); 2879 for (v = numCells; v < numCells+numVertices; ++v) { 2880 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 2881 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 2882 } 2883 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2884 2885 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 2886 ierr = DMCreateLocalVector(cdm, &coordinates);CHKERRQ(ierr); 2887 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 2888 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2889 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2890 for (v = 0; v < numVertices; ++v) { 2891 for (d = 0; d < spaceDim; ++d) { 2892 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 2893 } 2894 } 2895 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2896 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2897 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2898 PetscFunctionReturn(0); 2899 } 2900 2901 /*@C 2902 DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 2903 2904 Input Parameters: 2905 + comm - The communicator 2906 . dim - The topological dimension of the mesh 2907 . numCells - The number of cells 2908 . numVertices - The number of vertices 2909 . numCorners - The number of vertices for each cell 2910 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 2911 . cells - An array of numCells*numCorners numbers, the vertices for each cell 2912 . spaceDim - The spatial dimension used for coordinates 2913 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2914 2915 Output Parameter: 2916 . dm - The DM 2917 2918 Note: Two triangles sharing a face 2919 $ 2920 $ 2 2921 $ / | \ 2922 $ / | \ 2923 $ / | \ 2924 $ 0 0 | 1 3 2925 $ \ | / 2926 $ \ | / 2927 $ \ | / 2928 $ 1 2929 would have input 2930 $ numCells = 2, numVertices = 4 2931 $ cells = [0 1 2 1 3 2] 2932 $ 2933 which would result in the DMPlex 2934 $ 2935 $ 4 2936 $ / | \ 2937 $ / | \ 2938 $ / | \ 2939 $ 2 0 | 1 5 2940 $ \ | / 2941 $ \ | / 2942 $ \ | / 2943 $ 3 2944 2945 Level: beginner 2946 2947 .seealso: DMPlexCreateFromDAG(), DMPlexCreate() 2948 @*/ 2949 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) 2950 { 2951 PetscErrorCode ierr; 2952 2953 PetscFunctionBegin; 2954 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2955 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2956 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 2957 ierr = DMPlexBuildFromCellList_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE);CHKERRQ(ierr); 2958 if (interpolate) { 2959 DM idm; 2960 2961 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2962 ierr = DMDestroy(dm);CHKERRQ(ierr); 2963 *dm = idm; 2964 } 2965 ierr = DMPlexBuildCoordinates_Internal(*dm, spaceDim, numCells, numVertices, vertexCoords);CHKERRQ(ierr); 2966 PetscFunctionReturn(0); 2967 } 2968 2969 /*@ 2970 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 2971 2972 Input Parameters: 2973 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 2974 . depth - The depth of the DAG 2975 . numPoints - Array of size depth + 1 containing the number of points at each depth 2976 . coneSize - The cone size of each point 2977 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 2978 . coneOrientations - The orientation of each cone point 2979 - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim() 2980 2981 Output Parameter: 2982 . dm - The DM 2983 2984 Note: Two triangles sharing a face would have input 2985 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 2986 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 2987 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 2988 $ 2989 which would result in the DMPlex 2990 $ 2991 $ 4 2992 $ / | \ 2993 $ / | \ 2994 $ / | \ 2995 $ 2 0 | 1 5 2996 $ \ | / 2997 $ \ | / 2998 $ \ | / 2999 $ 3 3000 $ 3001 $ Notice that all points are numbered consecutively, unlikely DMPlexCreateFromCellList() 3002 3003 Level: advanced 3004 3005 .seealso: DMPlexCreateFromCellList(), DMPlexCreate() 3006 @*/ 3007 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 3008 { 3009 Vec coordinates; 3010 PetscSection coordSection; 3011 PetscScalar *coords; 3012 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 3013 PetscErrorCode ierr; 3014 3015 PetscFunctionBegin; 3016 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3017 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 3018 if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %d cannot be less than intrinsic dimension %d",dimEmbed,dim); 3019 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 3020 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 3021 for (p = pStart; p < pEnd; ++p) { 3022 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 3023 if (firstVertex < 0 && !coneSize[p - pStart]) { 3024 firstVertex = p - pStart; 3025 } 3026 } 3027 if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %d vertices but could not find any", numPoints[0]); 3028 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 3029 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 3030 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 3031 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 3032 } 3033 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3034 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3035 /* Build coordinates */ 3036 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3037 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3038 ierr = PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);CHKERRQ(ierr); 3039 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 3040 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 3041 ierr = PetscSectionSetDof(coordSection, v, dimEmbed);CHKERRQ(ierr); 3042 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);CHKERRQ(ierr); 3043 } 3044 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3045 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3046 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3047 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3048 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3049 ierr = VecSetBlockSize(coordinates, dimEmbed);CHKERRQ(ierr); 3050 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 3051 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3052 for (v = 0; v < numPoints[0]; ++v) { 3053 PetscInt off; 3054 3055 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 3056 for (d = 0; d < dimEmbed; ++d) { 3057 coords[off+d] = vertexCoords[v*dimEmbed+d]; 3058 } 3059 } 3060 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3061 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3062 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3063 PetscFunctionReturn(0); 3064 } 3065 3066 /*@C 3067 DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file. 3068 3069 + comm - The MPI communicator 3070 . filename - Name of the .dat file 3071 - interpolate - Create faces and edges in the mesh 3072 3073 Output Parameter: 3074 . dm - The DM object representing the mesh 3075 3076 Note: The format is the simplest possible: 3077 $ Ne 3078 $ v0 v1 ... vk 3079 $ Nv 3080 $ x y z marker 3081 3082 Level: beginner 3083 3084 .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate() 3085 @*/ 3086 PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3087 { 3088 DMLabel marker; 3089 PetscViewer viewer; 3090 Vec coordinates; 3091 PetscSection coordSection; 3092 PetscScalar *coords; 3093 char line[PETSC_MAX_PATH_LEN]; 3094 PetscInt dim = 3, cdim = 3, coordSize, v, c, d; 3095 PetscMPIInt rank; 3096 int snum, Nv, Nc; 3097 PetscErrorCode ierr; 3098 3099 PetscFunctionBegin; 3100 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 3101 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 3102 ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr); 3103 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 3104 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 3105 if (!rank) { 3106 ierr = PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);CHKERRQ(ierr); 3107 snum = sscanf(line, "%d %d", &Nc, &Nv); 3108 if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3109 } else { 3110 Nc = Nv = 0; 3111 } 3112 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3113 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3114 ierr = DMPlexSetChart(*dm, 0, Nc+Nv);CHKERRQ(ierr); 3115 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3116 ierr = DMSetCoordinateDim(*dm, cdim);CHKERRQ(ierr); 3117 /* Read topology */ 3118 if (!rank) { 3119 PetscInt cone[8], corners = 8; 3120 int vbuf[8], v; 3121 3122 for (c = 0; c < Nc; ++c) {ierr = DMPlexSetConeSize(*dm, c, corners);CHKERRQ(ierr);} 3123 ierr = DMSetUp(*dm);CHKERRQ(ierr); 3124 for (c = 0; c < Nc; ++c) { 3125 ierr = PetscViewerRead(viewer, line, corners, NULL, PETSC_STRING);CHKERRQ(ierr); 3126 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]); 3127 if (snum != corners) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3128 for (v = 0; v < corners; ++v) cone[v] = vbuf[v] + Nc; 3129 /* Hexahedra are inverted */ 3130 { 3131 PetscInt tmp = cone[1]; 3132 cone[1] = cone[3]; 3133 cone[3] = tmp; 3134 } 3135 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 3136 } 3137 } 3138 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 3139 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 3140 /* Read coordinates */ 3141 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 3142 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3143 ierr = PetscSectionSetFieldComponents(coordSection, 0, cdim);CHKERRQ(ierr); 3144 ierr = PetscSectionSetChart(coordSection, Nc, Nc + Nv);CHKERRQ(ierr); 3145 for (v = Nc; v < Nc+Nv; ++v) { 3146 ierr = PetscSectionSetDof(coordSection, v, cdim);CHKERRQ(ierr); 3147 ierr = PetscSectionSetFieldDof(coordSection, v, 0, cdim);CHKERRQ(ierr); 3148 } 3149 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3150 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3151 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3152 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3153 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3154 ierr = VecSetBlockSize(coordinates, cdim);CHKERRQ(ierr); 3155 ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr); 3156 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3157 if (!rank) { 3158 double x[3]; 3159 int val; 3160 3161 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 3162 ierr = DMGetLabel(*dm, "marker", &marker);CHKERRQ(ierr); 3163 for (v = 0; v < Nv; ++v) { 3164 ierr = PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);CHKERRQ(ierr); 3165 snum = sscanf(line, "%lg %lg %lg %d", &x[0], &x[1], &x[2], &val); 3166 if (snum != 4) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3167 for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d]; 3168 if (val) {ierr = DMLabelSetValue(marker, v+Nc, val);CHKERRQ(ierr);} 3169 } 3170 } 3171 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3172 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 3173 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3174 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 3175 if (interpolate) { 3176 DM idm; 3177 DMLabel bdlabel; 3178 3179 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3180 ierr = DMDestroy(dm);CHKERRQ(ierr); 3181 *dm = idm; 3182 3183 ierr = DMGetLabel(*dm, "marker", &bdlabel);CHKERRQ(ierr); 3184 ierr = DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 3185 ierr = DMPlexLabelComplete(*dm, bdlabel);CHKERRQ(ierr); 3186 } 3187 PetscFunctionReturn(0); 3188 } 3189 3190 /*@C 3191 DMPlexCreateFromFile - This takes a filename and produces a DM 3192 3193 Input Parameters: 3194 + comm - The communicator 3195 . filename - A file name 3196 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 3197 3198 Output Parameter: 3199 . dm - The DM 3200 3201 Options Database Keys: 3202 . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5 3203 3204 Level: beginner 3205 3206 .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellList(), DMPlexCreate() 3207 @*/ 3208 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3209 { 3210 const char *extGmsh = ".msh"; 3211 const char *extCGNS = ".cgns"; 3212 const char *extExodus = ".exo"; 3213 const char *extGenesis = ".gen"; 3214 const char *extFluent = ".cas"; 3215 const char *extHDF5 = ".h5"; 3216 const char *extMed = ".med"; 3217 const char *extPLY = ".ply"; 3218 const char *extCV = ".dat"; 3219 size_t len; 3220 PetscBool isGmsh, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isCV; 3221 PetscMPIInt rank; 3222 PetscErrorCode ierr; 3223 3224 PetscFunctionBegin; 3225 PetscValidPointer(filename, 2); 3226 PetscValidPointer(dm, 4); 3227 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 3228 ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); 3229 if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 3230 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);CHKERRQ(ierr); 3231 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);CHKERRQ(ierr); 3232 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);CHKERRQ(ierr); 3233 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);CHKERRQ(ierr); 3234 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);CHKERRQ(ierr); 3235 ierr = PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);CHKERRQ(ierr); 3236 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);CHKERRQ(ierr); 3237 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);CHKERRQ(ierr); 3238 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);CHKERRQ(ierr); 3239 if (isGmsh) { 3240 ierr = DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3241 } else if (isCGNS) { 3242 ierr = DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3243 } else if (isExodus || isGenesis) { 3244 ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3245 } else if (isFluent) { 3246 ierr = DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3247 } else if (isHDF5) { 3248 PetscBool load_hdf5_xdmf = PETSC_FALSE; 3249 PetscViewer viewer; 3250 3251 ierr = PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);CHKERRQ(ierr); 3252 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 3253 ierr = PetscViewerSetType(viewer, PETSCVIEWERHDF5);CHKERRQ(ierr); 3254 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 3255 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 3256 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3257 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3258 if (load_hdf5_xdmf) {ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);CHKERRQ(ierr);} 3259 ierr = DMLoad(*dm, viewer);CHKERRQ(ierr); 3260 if (load_hdf5_xdmf) {ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);} 3261 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 3262 3263 if (interpolate) { 3264 DM idm; 3265 3266 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3267 ierr = DMDestroy(dm);CHKERRQ(ierr); 3268 *dm = idm; 3269 } 3270 } else if (isMed) { 3271 ierr = DMPlexCreateMedFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3272 } else if (isPLY) { 3273 ierr = DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3274 } else if (isCV) { 3275 ierr = DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3276 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 3277 PetscFunctionReturn(0); 3278 } 3279 3280 /*@ 3281 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 3282 3283 Collective on comm 3284 3285 Input Parameters: 3286 + comm - The communicator 3287 . dim - The spatial dimension 3288 - simplex - Flag for simplex, otherwise use a tensor-product cell 3289 3290 Output Parameter: 3291 . refdm - The reference cell 3292 3293 Level: intermediate 3294 3295 .keywords: reference cell 3296 .seealso: 3297 @*/ 3298 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm) 3299 { 3300 DM rdm; 3301 Vec coords; 3302 PetscErrorCode ierr; 3303 3304 PetscFunctionBeginUser; 3305 ierr = DMCreate(comm, &rdm);CHKERRQ(ierr); 3306 ierr = DMSetType(rdm, DMPLEX);CHKERRQ(ierr); 3307 ierr = DMSetDimension(rdm, dim);CHKERRQ(ierr); 3308 switch (dim) { 3309 case 0: 3310 { 3311 PetscInt numPoints[1] = {1}; 3312 PetscInt coneSize[1] = {0}; 3313 PetscInt cones[1] = {0}; 3314 PetscInt coneOrientations[1] = {0}; 3315 PetscScalar vertexCoords[1] = {0.0}; 3316 3317 ierr = DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3318 } 3319 break; 3320 case 1: 3321 { 3322 PetscInt numPoints[2] = {2, 1}; 3323 PetscInt coneSize[3] = {2, 0, 0}; 3324 PetscInt cones[2] = {1, 2}; 3325 PetscInt coneOrientations[2] = {0, 0}; 3326 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 3327 3328 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3329 } 3330 break; 3331 case 2: 3332 if (simplex) { 3333 PetscInt numPoints[2] = {3, 1}; 3334 PetscInt coneSize[4] = {3, 0, 0, 0}; 3335 PetscInt cones[3] = {1, 2, 3}; 3336 PetscInt coneOrientations[3] = {0, 0, 0}; 3337 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 3338 3339 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3340 } else { 3341 PetscInt numPoints[2] = {4, 1}; 3342 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3343 PetscInt cones[4] = {1, 2, 3, 4}; 3344 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3345 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 3346 3347 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3348 } 3349 break; 3350 case 3: 3351 if (simplex) { 3352 PetscInt numPoints[2] = {4, 1}; 3353 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3354 PetscInt cones[4] = {1, 3, 2, 4}; 3355 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3356 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}; 3357 3358 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3359 } else { 3360 PetscInt numPoints[2] = {8, 1}; 3361 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3362 PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8}; 3363 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3364 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, 3365 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 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 } 3369 break; 3370 default: 3371 SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %d", dim); 3372 } 3373 ierr = DMPlexInterpolate(rdm, refdm);CHKERRQ(ierr); 3374 if (rdm->coordinateDM) { 3375 DM ncdm; 3376 PetscSection cs; 3377 PetscInt pEnd = -1; 3378 3379 ierr = DMGetSection(rdm->coordinateDM, &cs);CHKERRQ(ierr); 3380 if (cs) {ierr = PetscSectionGetChart(cs, NULL, &pEnd);CHKERRQ(ierr);} 3381 if (pEnd >= 0) { 3382 ierr = DMClone(rdm->coordinateDM, &ncdm);CHKERRQ(ierr); 3383 ierr = DMSetSection(ncdm, cs);CHKERRQ(ierr); 3384 ierr = DMSetCoordinateDM(*refdm, ncdm);CHKERRQ(ierr); 3385 ierr = DMDestroy(&ncdm);CHKERRQ(ierr); 3386 } 3387 } 3388 ierr = DMGetCoordinatesLocal(rdm, &coords);CHKERRQ(ierr); 3389 if (coords) { 3390 ierr = DMSetCoordinatesLocal(*refdm, coords);CHKERRQ(ierr); 3391 } else { 3392 ierr = DMGetCoordinates(rdm, &coords);CHKERRQ(ierr); 3393 if (coords) {ierr = DMSetCoordinates(*refdm, coords);CHKERRQ(ierr);} 3394 } 3395 ierr = DMDestroy(&rdm);CHKERRQ(ierr); 3396 PetscFunctionReturn(0); 3397 } 3398