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 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 .seealso: DMSetType(), DMCreate() 25 @*/ 26 PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscBool refinementUniform, PetscReal refinementLimit, DM *newdm) 27 { 28 DM dm; 29 PetscInt p; 30 PetscMPIInt rank; 31 PetscErrorCode ierr; 32 33 PetscFunctionBegin; 34 ierr = DMCreate(comm, &dm);CHKERRQ(ierr); 35 ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr); 36 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 37 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 38 switch (dim) { 39 case 2: 40 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "triangular");CHKERRQ(ierr);} 41 else {ierr = PetscObjectSetName((PetscObject) dm, "quadrilateral");CHKERRQ(ierr);} 42 break; 43 case 3: 44 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "tetrahedral");CHKERRQ(ierr);} 45 else {ierr = PetscObjectSetName((PetscObject) dm, "hexahedral");CHKERRQ(ierr);} 46 break; 47 default: 48 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); 49 } 50 if (rank) { 51 PetscInt numPoints[2] = {0, 0}; 52 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 53 } else { 54 switch (dim) { 55 case 2: 56 if (simplex) { 57 PetscInt numPoints[2] = {4, 2}; 58 PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; 59 PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; 60 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 61 PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5}; 62 PetscInt markerPoints[8] = {2, 1, 3, 1, 4, 1, 5, 1}; 63 64 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 65 for (p = 0; p < 4; ++p) {ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 66 } else { 67 PetscInt numPoints[2] = {6, 2}; 68 PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; 69 PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4}; 70 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 71 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}; 72 73 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 74 } 75 break; 76 case 3: 77 if (simplex) { 78 PetscInt numPoints[2] = {5, 2}; 79 PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; 80 PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; 81 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 82 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}; 83 PetscInt markerPoints[10] = {2, 1, 3, 1, 4, 1, 5, 1, 6, 1}; 84 85 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 86 for (p = 0; p < 5; ++p) {ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 87 } else { 88 PetscInt numPoints[2] = {12, 2}; 89 PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 90 PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8}; 91 PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 92 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, 93 -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5, 94 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5}; 95 96 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 97 } 98 break; 99 default: 100 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); 101 } 102 } 103 *newdm = dm; 104 if (refinementLimit > 0.0) { 105 DM rdm; 106 const char *name; 107 108 ierr = DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);CHKERRQ(ierr); 109 ierr = DMPlexSetRefinementLimit(*newdm, refinementLimit);CHKERRQ(ierr); 110 ierr = DMRefine(*newdm, comm, &rdm);CHKERRQ(ierr); 111 ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); 112 ierr = PetscObjectSetName((PetscObject) rdm, name);CHKERRQ(ierr); 113 ierr = DMDestroy(newdm);CHKERRQ(ierr); 114 *newdm = rdm; 115 } 116 if (interpolate) { 117 DM idm; 118 119 ierr = DMPlexInterpolate(*newdm, &idm);CHKERRQ(ierr); 120 ierr = DMDestroy(newdm);CHKERRQ(ierr); 121 *newdm = idm; 122 } 123 { 124 DM refinedMesh = NULL; 125 DM distributedMesh = NULL; 126 127 /* Distribute mesh over processes */ 128 ierr = DMPlexDistribute(*newdm, 0, NULL, &distributedMesh);CHKERRQ(ierr); 129 if (distributedMesh) { 130 ierr = DMDestroy(newdm);CHKERRQ(ierr); 131 *newdm = distributedMesh; 132 } 133 if (refinementUniform) { 134 ierr = DMPlexSetRefinementUniform(*newdm, refinementUniform);CHKERRQ(ierr); 135 ierr = DMRefine(*newdm, comm, &refinedMesh);CHKERRQ(ierr); 136 if (refinedMesh) { 137 ierr = DMDestroy(newdm);CHKERRQ(ierr); 138 *newdm = refinedMesh; 139 } 140 } 141 } 142 PetscFunctionReturn(0); 143 } 144 145 /*@ 146 DMPlexCreateSquareBoundary - Creates a 1D mesh the is the boundary of a square lattice. 147 148 Collective 149 150 Input Parameters: 151 + comm - The communicator for the DM object 152 . lower - The lower left corner coordinates 153 . upper - The upper right corner coordinates 154 - edges - The number of cells in each direction 155 156 Output Parameter: 157 . dm - The DM object 158 159 Note: Here is the numbering returned for 2 cells in each direction: 160 $ 18--5-17--4--16 161 $ | | | 162 $ 6 10 3 163 $ | | | 164 $ 19-11-20--9--15 165 $ | | | 166 $ 7 8 2 167 $ | | | 168 $ 12--0-13--1--14 169 170 Level: beginner 171 172 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate() 173 @*/ 174 PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 175 { 176 const PetscInt numVertices = (edges[0]+1)*(edges[1]+1); 177 const PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1]; 178 PetscInt markerTop = 1; 179 PetscInt markerBottom = 1; 180 PetscInt markerRight = 1; 181 PetscInt markerLeft = 1; 182 PetscBool markerSeparate = PETSC_FALSE; 183 Vec coordinates; 184 PetscSection coordSection; 185 PetscScalar *coords; 186 PetscInt coordSize; 187 PetscMPIInt rank; 188 PetscInt v, vx, vy; 189 PetscErrorCode ierr; 190 191 PetscFunctionBegin; 192 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 193 if (markerSeparate) { 194 markerTop = 3; 195 markerBottom = 1; 196 markerRight = 2; 197 markerLeft = 4; 198 } 199 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 200 if (!rank) { 201 PetscInt e, ex, ey; 202 203 ierr = DMPlexSetChart(dm, 0, numEdges+numVertices);CHKERRQ(ierr); 204 for (e = 0; e < numEdges; ++e) { 205 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 206 } 207 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 208 for (vx = 0; vx <= edges[0]; vx++) { 209 for (ey = 0; ey < edges[1]; ey++) { 210 PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1); 211 PetscInt vertex = ey*(edges[0]+1) + vx + numEdges; 212 PetscInt cone[2]; 213 214 cone[0] = vertex; cone[1] = vertex+edges[0]+1; 215 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 216 if (vx == edges[0]) { 217 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 218 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 219 if (ey == edges[1]-1) { 220 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 221 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerRight);CHKERRQ(ierr); 222 } 223 } else if (vx == 0) { 224 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 225 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 226 if (ey == edges[1]-1) { 227 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 228 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft);CHKERRQ(ierr); 229 } 230 } 231 } 232 } 233 for (vy = 0; vy <= edges[1]; vy++) { 234 for (ex = 0; ex < edges[0]; ex++) { 235 PetscInt edge = vy*edges[0] + ex; 236 PetscInt vertex = vy*(edges[0]+1) + ex + numEdges; 237 PetscInt cone[2]; 238 239 cone[0] = vertex; cone[1] = vertex+1; 240 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 241 if (vy == edges[1]) { 242 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 243 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 244 if (ex == edges[0]-1) { 245 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 246 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerTop);CHKERRQ(ierr); 247 } 248 } else if (vy == 0) { 249 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 250 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 251 if (ex == edges[0]-1) { 252 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 253 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom);CHKERRQ(ierr); 254 } 255 } 256 } 257 } 258 } 259 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 260 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 261 /* Build coordinates */ 262 ierr = DMSetCoordinateDim(dm, 2);CHKERRQ(ierr); 263 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 264 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 265 ierr = PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);CHKERRQ(ierr); 266 ierr = PetscSectionSetFieldComponents(coordSection, 0, 2);CHKERRQ(ierr); 267 for (v = numEdges; v < numEdges+numVertices; ++v) { 268 ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr); 269 ierr = PetscSectionSetFieldDof(coordSection, v, 0, 2);CHKERRQ(ierr); 270 } 271 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 272 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 273 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 274 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 275 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 276 ierr = VecSetBlockSize(coordinates, 2);CHKERRQ(ierr); 277 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 278 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 279 for (vy = 0; vy <= edges[1]; ++vy) { 280 for (vx = 0; vx <= edges[0]; ++vx) { 281 coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx; 282 coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy; 283 } 284 } 285 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 286 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 287 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 288 PetscFunctionReturn(0); 289 } 290 291 /*@ 292 DMPlexCreateCubeBoundary - Creates a 2D mesh that is the boundary of a cubic lattice. 293 294 Collective 295 296 Input Parameters: 297 + comm - The communicator for the DM object 298 . lower - The lower left front corner coordinates 299 . upper - The upper right back corner coordinates 300 - edges - The number of cells in each direction 301 302 Output Parameter: 303 . dm - The DM object 304 305 Level: beginner 306 307 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMSetType(), DMCreate() 308 @*/ 309 PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) 310 { 311 PetscInt vertices[3], numVertices; 312 PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2]; 313 Vec coordinates; 314 PetscSection coordSection; 315 PetscScalar *coords; 316 PetscInt coordSize; 317 PetscMPIInt rank; 318 PetscInt v, vx, vy, vz; 319 PetscInt voffset, iface=0, cone[4]; 320 PetscErrorCode ierr; 321 322 PetscFunctionBegin; 323 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"); 324 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 325 vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1; 326 numVertices = vertices[0]*vertices[1]*vertices[2]; 327 if (!rank) { 328 PetscInt f; 329 330 ierr = DMPlexSetChart(dm, 0, numFaces+numVertices);CHKERRQ(ierr); 331 for (f = 0; f < numFaces; ++f) { 332 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 333 } 334 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 335 336 /* Side 0 (Top) */ 337 for (vy = 0; vy < faces[1]; vy++) { 338 for (vx = 0; vx < faces[0]; vx++) { 339 voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx; 340 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0]; 341 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 342 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 343 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 344 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 345 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 346 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);CHKERRQ(ierr); 347 iface++; 348 } 349 } 350 351 /* Side 1 (Bottom) */ 352 for (vy = 0; vy < faces[1]; vy++) { 353 for (vx = 0; vx < faces[0]; vx++) { 354 voffset = numFaces + vy*(faces[0]+1) + vx; 355 cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1; 356 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 357 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 358 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 359 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 360 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 361 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);CHKERRQ(ierr); 362 iface++; 363 } 364 } 365 366 /* Side 2 (Front) */ 367 for (vz = 0; vz < faces[2]; vz++) { 368 for (vx = 0; vx < faces[0]; vx++) { 369 voffset = numFaces + vz*vertices[0]*vertices[1] + vx; 370 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1]; 371 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 372 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 373 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 374 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 375 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 376 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);CHKERRQ(ierr); 377 iface++; 378 } 379 } 380 381 /* Side 3 (Back) */ 382 for (vz = 0; vz < faces[2]; vz++) { 383 for (vx = 0; vx < faces[0]; vx++) { 384 voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx; 385 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1; 386 cone[2] = voffset+1; cone[3] = voffset; 387 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 388 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 389 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 390 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 391 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 392 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);CHKERRQ(ierr); 393 iface++; 394 } 395 } 396 397 /* Side 4 (Left) */ 398 for (vz = 0; vz < faces[2]; vz++) { 399 for (vy = 0; vy < faces[1]; vy++) { 400 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0]; 401 cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1]; 402 cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0]; 403 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 404 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 405 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 406 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 407 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[1]+0, 1);CHKERRQ(ierr); 408 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);CHKERRQ(ierr); 409 iface++; 410 } 411 } 412 413 /* Side 5 (Right) */ 414 for (vz = 0; vz < faces[2]; vz++) { 415 for (vy = 0; vy < faces[1]; vy++) { 416 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + faces[0]; 417 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset; 418 cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0]; 419 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 420 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 421 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 422 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 423 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 424 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);CHKERRQ(ierr); 425 iface++; 426 } 427 } 428 } 429 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 430 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 431 /* Build coordinates */ 432 ierr = DMSetCoordinateDim(dm, 3);CHKERRQ(ierr); 433 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 434 ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr); 435 for (v = numFaces; v < numFaces+numVertices; ++v) { 436 ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr); 437 } 438 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 439 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 440 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 441 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 442 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 443 ierr = VecSetBlockSize(coordinates, 3);CHKERRQ(ierr); 444 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 445 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 446 for (vz = 0; vz <= faces[2]; ++vz) { 447 for (vy = 0; vy <= faces[1]; ++vy) { 448 for (vx = 0; vx <= faces[0]; ++vx) { 449 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx; 450 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy; 451 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz; 452 } 453 } 454 } 455 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 456 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 457 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 458 PetscFunctionReturn(0); 459 } 460 461 static PetscErrorCode DMPlexCreateLineMesh_Internal(MPI_Comm comm,PetscInt segments,PetscReal lower,PetscReal upper,DMBoundaryType bd,DM *dm) 462 { 463 PetscInt i,fStart,fEnd,numCells = 0,numVerts = 0; 464 PetscInt numPoints[2],*coneSize,*cones,*coneOrientations; 465 PetscScalar *vertexCoords; 466 PetscReal L,maxCell; 467 PetscBool markerSeparate = PETSC_FALSE; 468 PetscInt markerLeft = 1, faceMarkerLeft = 1; 469 PetscInt markerRight = 1, faceMarkerRight = 2; 470 PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE; 471 PetscMPIInt rank; 472 PetscErrorCode ierr; 473 474 PetscFunctionBegin; 475 PetscValidPointer(dm,4); 476 477 ierr = DMCreate(comm,dm);CHKERRQ(ierr); 478 ierr = DMSetType(*dm,DMPLEX);CHKERRQ(ierr); 479 ierr = DMSetDimension(*dm,1);CHKERRQ(ierr); 480 ierr = DMCreateLabel(*dm,"marker");CHKERRQ(ierr); 481 ierr = DMCreateLabel(*dm,"Face Sets");CHKERRQ(ierr); 482 483 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 484 if (!rank) numCells = segments; 485 if (!rank) numVerts = segments + (wrap ? 0 : 1); 486 487 numPoints[0] = numVerts ; numPoints[1] = numCells; 488 ierr = PetscMalloc4(numCells+numVerts,&coneSize,numCells*2,&cones,numCells+numVerts,&coneOrientations,numVerts,&vertexCoords);CHKERRQ(ierr); 489 ierr = PetscArrayzero(coneOrientations,numCells+numVerts);CHKERRQ(ierr); 490 for (i = 0; i < numCells; ++i) { coneSize[i] = 2; } 491 for (i = 0; i < numVerts; ++i) { coneSize[numCells+i] = 0; } 492 for (i = 0; i < numCells; ++i) { cones[2*i] = numCells + i%numVerts; cones[2*i+1] = numCells + (i+1)%numVerts; } 493 for (i = 0; i < numVerts; ++i) { vertexCoords[i] = lower + (upper-lower)*((PetscReal)i/(PetscReal)numCells); } 494 ierr = DMPlexCreateFromDAG(*dm,1,numPoints,coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 495 ierr = PetscFree4(coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 496 497 ierr = PetscOptionsGetBool(((PetscObject)*dm)->options,((PetscObject)*dm)->prefix,"-dm_plex_separate_marker",&markerSeparate,NULL);CHKERRQ(ierr); 498 if (markerSeparate) { markerLeft = faceMarkerLeft; markerRight = faceMarkerRight;} 499 if (!wrap && !rank) { 500 ierr = DMPlexGetHeightStratum(*dm,1,&fStart,&fEnd);CHKERRQ(ierr); 501 ierr = DMSetLabelValue(*dm,"marker",fStart,markerLeft);CHKERRQ(ierr); 502 ierr = DMSetLabelValue(*dm,"marker",fEnd-1,markerRight);CHKERRQ(ierr); 503 ierr = DMSetLabelValue(*dm,"Face Sets",fStart,faceMarkerLeft);CHKERRQ(ierr); 504 ierr = DMSetLabelValue(*dm,"Face Sets",fEnd-1,faceMarkerRight);CHKERRQ(ierr); 505 } 506 if (wrap) { 507 L = upper - lower; 508 maxCell = (PetscReal)1.1*(L/(PetscReal)PetscMax(1,segments)); 509 ierr = DMSetPeriodicity(*dm,PETSC_TRUE,&maxCell,&L,&bd);CHKERRQ(ierr); 510 } 511 PetscFunctionReturn(0); 512 } 513 514 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) 515 { 516 DM boundary; 517 PetscInt i; 518 PetscErrorCode ierr; 519 520 PetscFunctionBegin; 521 PetscValidPointer(dm, 4); 522 for (i = 0; i < dim; ++i) if (periodicity[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity is not supported for simplex meshes"); 523 ierr = DMCreate(comm, &boundary);CHKERRQ(ierr); 524 PetscValidLogicalCollectiveInt(boundary,dim,2); 525 ierr = DMSetType(boundary, DMPLEX);CHKERRQ(ierr); 526 ierr = DMSetDimension(boundary, dim-1);CHKERRQ(ierr); 527 ierr = DMSetCoordinateDim(boundary, dim);CHKERRQ(ierr); 528 switch (dim) { 529 case 2: ierr = DMPlexCreateSquareBoundary(boundary, lower, upper, faces);CHKERRQ(ierr);break; 530 case 3: ierr = DMPlexCreateCubeBoundary(boundary, lower, upper, faces);CHKERRQ(ierr);break; 531 default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 532 } 533 ierr = DMPlexGenerate(boundary, NULL, interpolate, dm);CHKERRQ(ierr); 534 ierr = DMDestroy(&boundary);CHKERRQ(ierr); 535 PetscFunctionReturn(0); 536 } 537 538 static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ) 539 { 540 DMLabel cutLabel = NULL; 541 PetscInt markerTop = 1, faceMarkerTop = 1; 542 PetscInt markerBottom = 1, faceMarkerBottom = 1; 543 PetscInt markerFront = 1, faceMarkerFront = 1; 544 PetscInt markerBack = 1, faceMarkerBack = 1; 545 PetscInt markerRight = 1, faceMarkerRight = 1; 546 PetscInt markerLeft = 1, faceMarkerLeft = 1; 547 PetscInt dim; 548 PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE; 549 PetscMPIInt rank; 550 PetscErrorCode ierr; 551 552 PetscFunctionBegin; 553 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 554 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 555 ierr = DMCreateLabel(dm,"marker");CHKERRQ(ierr); 556 ierr = DMCreateLabel(dm,"Face Sets");CHKERRQ(ierr); 557 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL);CHKERRQ(ierr); 558 if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST || 559 bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST || 560 bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) { 561 562 if (cutMarker) {ierr = DMCreateLabel(dm, "periodic_cut");CHKERRQ(ierr); ierr = DMGetLabel(dm, "periodic_cut", &cutLabel);CHKERRQ(ierr);} 563 } 564 switch (dim) { 565 case 2: 566 faceMarkerTop = 3; 567 faceMarkerBottom = 1; 568 faceMarkerRight = 2; 569 faceMarkerLeft = 4; 570 break; 571 case 3: 572 faceMarkerBottom = 1; 573 faceMarkerTop = 2; 574 faceMarkerFront = 3; 575 faceMarkerBack = 4; 576 faceMarkerRight = 5; 577 faceMarkerLeft = 6; 578 break; 579 default: 580 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %d not supported",dim); 581 break; 582 } 583 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 584 if (markerSeparate) { 585 markerBottom = faceMarkerBottom; 586 markerTop = faceMarkerTop; 587 markerFront = faceMarkerFront; 588 markerBack = faceMarkerBack; 589 markerRight = faceMarkerRight; 590 markerLeft = faceMarkerLeft; 591 } 592 { 593 const PetscInt numXEdges = !rank ? edges[0] : 0; 594 const PetscInt numYEdges = !rank ? edges[1] : 0; 595 const PetscInt numZEdges = !rank ? edges[2] : 0; 596 const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; 597 const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; 598 const PetscInt numZVertices = !rank ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0; 599 const PetscInt numCells = numXEdges*numYEdges*numZEdges; 600 const PetscInt numXFaces = numYEdges*numZEdges; 601 const PetscInt numYFaces = numXEdges*numZEdges; 602 const PetscInt numZFaces = numXEdges*numYEdges; 603 const PetscInt numTotXFaces = numXVertices*numXFaces; 604 const PetscInt numTotYFaces = numYVertices*numYFaces; 605 const PetscInt numTotZFaces = numZVertices*numZFaces; 606 const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces; 607 const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices; 608 const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices; 609 const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices; 610 const PetscInt numVertices = numXVertices*numYVertices*numZVertices; 611 const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges; 612 const PetscInt firstVertex = (dim == 2) ? numFaces : numCells; 613 const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices; 614 const PetscInt firstYFace = firstXFace + numTotXFaces; 615 const PetscInt firstZFace = firstYFace + numTotYFaces; 616 const PetscInt firstXEdge = numCells + numFaces + numVertices; 617 const PetscInt firstYEdge = firstXEdge + numTotXEdges; 618 const PetscInt firstZEdge = firstYEdge + numTotYEdges; 619 Vec coordinates; 620 PetscSection coordSection; 621 PetscScalar *coords; 622 PetscInt coordSize; 623 PetscInt v, vx, vy, vz; 624 PetscInt c, f, fx, fy, fz, e, ex, ey, ez; 625 626 ierr = DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);CHKERRQ(ierr); 627 for (c = 0; c < numCells; c++) { 628 ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr); 629 } 630 for (f = firstXFace; f < firstXFace+numFaces; ++f) { 631 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 632 } 633 for (e = firstXEdge; e < firstXEdge+numEdges; ++e) { 634 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 635 } 636 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 637 /* Build cells */ 638 for (fz = 0; fz < numZEdges; ++fz) { 639 for (fy = 0; fy < numYEdges; ++fy) { 640 for (fx = 0; fx < numXEdges; ++fx) { 641 PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx; 642 PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 643 PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices); 644 PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 645 PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices); 646 PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 647 PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices); 648 /* B, T, F, K, R, L */ 649 PetscInt ornt[6] = {-4, 0, 0, -1, 0, -4}; /* ??? */ 650 PetscInt cone[6]; 651 652 /* no boundary twisting in 3D */ 653 cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL; 654 ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr); 655 ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr); 656 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 657 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 658 if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 659 } 660 } 661 } 662 /* Build x faces */ 663 for (fz = 0; fz < numZEdges; ++fz) { 664 for (fy = 0; fy < numYEdges; ++fy) { 665 for (fx = 0; fx < numXVertices; ++fx) { 666 PetscInt face = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 667 PetscInt edgeL = firstZEdge + ( fy* numXVertices+fx)*numZEdges + fz; 668 PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz; 669 PetscInt edgeB = firstYEdge + ( fz* numXVertices+fx)*numYEdges + fy; 670 PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy; 671 PetscInt ornt[4] = {0, 0, -2, -2}; 672 PetscInt cone[4]; 673 674 if (dim == 3) { 675 /* markers */ 676 if (bdX != DM_BOUNDARY_PERIODIC) { 677 if (fx == numXVertices-1) { 678 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);CHKERRQ(ierr); 679 ierr = DMSetLabelValue(dm, "marker", face, markerRight);CHKERRQ(ierr); 680 } 681 else if (fx == 0) { 682 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);CHKERRQ(ierr); 683 ierr = DMSetLabelValue(dm, "marker", face, markerLeft);CHKERRQ(ierr); 684 } 685 } 686 } 687 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 688 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 689 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 690 } 691 } 692 } 693 /* Build y faces */ 694 for (fz = 0; fz < numZEdges; ++fz) { 695 for (fx = 0; fx < numXEdges; ++fx) { 696 for (fy = 0; fy < numYVertices; ++fy) { 697 PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 698 PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx )*numZEdges + fz; 699 PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz; 700 PetscInt edgeB = firstXEdge + ( fz *numYVertices+fy)*numXEdges + fx; 701 PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx; 702 PetscInt ornt[4] = {0, 0, -2, -2}; 703 PetscInt cone[4]; 704 705 if (dim == 3) { 706 /* markers */ 707 if (bdY != DM_BOUNDARY_PERIODIC) { 708 if (fy == numYVertices-1) { 709 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);CHKERRQ(ierr); 710 ierr = DMSetLabelValue(dm, "marker", face, markerBack);CHKERRQ(ierr); 711 } 712 else if (fy == 0) { 713 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);CHKERRQ(ierr); 714 ierr = DMSetLabelValue(dm, "marker", face, markerFront);CHKERRQ(ierr); 715 } 716 } 717 } 718 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 719 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 720 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 721 } 722 } 723 } 724 /* Build z faces */ 725 for (fy = 0; fy < numYEdges; ++fy) { 726 for (fx = 0; fx < numXEdges; ++fx) { 727 for (fz = 0; fz < numZVertices; fz++) { 728 PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 729 PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx )*numYEdges + fy; 730 PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy; 731 PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy )*numXEdges + fx; 732 PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx; 733 PetscInt ornt[4] = {0, 0, -2, -2}; 734 PetscInt cone[4]; 735 736 if (dim == 2) { 737 if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -2;} 738 if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;} 739 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 740 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 741 } else { 742 /* markers */ 743 if (bdZ != DM_BOUNDARY_PERIODIC) { 744 if (fz == numZVertices-1) { 745 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);CHKERRQ(ierr); 746 ierr = DMSetLabelValue(dm, "marker", face, markerTop);CHKERRQ(ierr); 747 } 748 else if (fz == 0) { 749 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);CHKERRQ(ierr); 750 ierr = DMSetLabelValue(dm, "marker", face, markerBottom);CHKERRQ(ierr); 751 } 752 } 753 } 754 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 755 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 756 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 757 } 758 } 759 } 760 /* Build Z edges*/ 761 for (vy = 0; vy < numYVertices; vy++) { 762 for (vx = 0; vx < numXVertices; vx++) { 763 for (ez = 0; ez < numZEdges; ez++) { 764 const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez; 765 const PetscInt vertexB = firstVertex + ( ez *numYVertices+vy)*numXVertices + vx; 766 const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx; 767 PetscInt cone[2]; 768 769 if (dim == 3) { 770 if (bdX != DM_BOUNDARY_PERIODIC) { 771 if (vx == numXVertices-1) { 772 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 773 } 774 else if (vx == 0) { 775 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 776 } 777 } 778 if (bdY != DM_BOUNDARY_PERIODIC) { 779 if (vy == numYVertices-1) { 780 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 781 } 782 else if (vy == 0) { 783 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 784 } 785 } 786 } 787 cone[0] = vertexB; cone[1] = vertexT; 788 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 789 } 790 } 791 } 792 /* Build Y edges*/ 793 for (vz = 0; vz < numZVertices; vz++) { 794 for (vx = 0; vx < numXVertices; vx++) { 795 for (ey = 0; ey < numYEdges; ey++) { 796 const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx; 797 const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey; 798 const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx; 799 const PetscInt vertexK = firstVertex + nextv; 800 PetscInt cone[2]; 801 802 cone[0] = vertexF; cone[1] = vertexK; 803 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 804 if (dim == 2) { 805 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 806 if (vx == numXVertices-1) { 807 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);CHKERRQ(ierr); 808 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 809 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 810 if (ey == numYEdges-1) { 811 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 812 } 813 } else if (vx == 0) { 814 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);CHKERRQ(ierr); 815 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 816 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 817 if (ey == numYEdges-1) { 818 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 819 } 820 } 821 } else { 822 if (vx == 0 && cutLabel) { 823 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 824 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 825 if (ey == numYEdges-1) { 826 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 827 } 828 } 829 } 830 } else { 831 if (bdX != DM_BOUNDARY_PERIODIC) { 832 if (vx == numXVertices-1) { 833 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 834 } else if (vx == 0) { 835 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 836 } 837 } 838 if (bdZ != DM_BOUNDARY_PERIODIC) { 839 if (vz == numZVertices-1) { 840 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 841 } else if (vz == 0) { 842 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 843 } 844 } 845 } 846 } 847 } 848 } 849 /* Build X edges*/ 850 for (vz = 0; vz < numZVertices; vz++) { 851 for (vy = 0; vy < numYVertices; vy++) { 852 for (ex = 0; ex < numXEdges; ex++) { 853 const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices; 854 const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex; 855 const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex; 856 const PetscInt vertexR = firstVertex + nextv; 857 PetscInt cone[2]; 858 859 cone[0] = vertexL; cone[1] = vertexR; 860 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 861 if (dim == 2) { 862 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 863 if (vy == numYVertices-1) { 864 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);CHKERRQ(ierr); 865 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 866 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 867 if (ex == numXEdges-1) { 868 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 869 } 870 } else if (vy == 0) { 871 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);CHKERRQ(ierr); 872 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 873 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 874 if (ex == numXEdges-1) { 875 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 876 } 877 } 878 } else { 879 if (vy == 0 && cutLabel) { 880 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 881 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 882 if (ex == numXEdges-1) { 883 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 884 } 885 } 886 } 887 } else { 888 if (bdY != DM_BOUNDARY_PERIODIC) { 889 if (vy == numYVertices-1) { 890 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 891 } 892 else if (vy == 0) { 893 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 894 } 895 } 896 if (bdZ != DM_BOUNDARY_PERIODIC) { 897 if (vz == numZVertices-1) { 898 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 899 } 900 else if (vz == 0) { 901 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 902 } 903 } 904 } 905 } 906 } 907 } 908 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 909 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 910 /* Build coordinates */ 911 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 912 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 913 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 914 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr); 915 for (v = firstVertex; v < firstVertex+numVertices; ++v) { 916 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 917 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 918 } 919 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 920 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 921 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 922 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 923 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 924 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 925 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 926 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 927 for (vz = 0; vz < numZVertices; ++vz) { 928 for (vy = 0; vy < numYVertices; ++vy) { 929 for (vx = 0; vx < numXVertices; ++vx) { 930 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx; 931 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy; 932 if (dim == 3) { 933 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz; 934 } 935 } 936 } 937 } 938 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 939 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 940 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 941 } 942 PetscFunctionReturn(0); 943 } 944 945 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) 946 { 947 PetscInt i; 948 PetscErrorCode ierr; 949 950 PetscFunctionBegin; 951 PetscValidPointer(dm, 7); 952 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 953 PetscValidLogicalCollectiveInt(*dm,dim,2); 954 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 955 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 956 switch (dim) { 957 case 2: {ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], DM_BOUNDARY_NONE);CHKERRQ(ierr);break;} 958 case 3: {ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], periodicity[2]);CHKERRQ(ierr);break;} 959 default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 960 } 961 if (periodicity[0] == DM_BOUNDARY_PERIODIC || periodicity[0] == DM_BOUNDARY_TWIST || 962 periodicity[1] == DM_BOUNDARY_PERIODIC || periodicity[1] == DM_BOUNDARY_TWIST || 963 (dim > 2 && (periodicity[2] == DM_BOUNDARY_PERIODIC || periodicity[2] == DM_BOUNDARY_TWIST))) { 964 PetscReal L[3]; 965 PetscReal maxCell[3]; 966 967 for (i = 0; i < dim; i++) { 968 L[i] = upper[i] - lower[i]; 969 maxCell[i] = 1.1 * (L[i] / PetscMax(1,faces[i])); 970 } 971 ierr = DMSetPeriodicity(*dm,PETSC_TRUE,maxCell,L,periodicity);CHKERRQ(ierr); 972 } 973 if (!interpolate) { 974 DM udm; 975 976 ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr); 977 ierr = DMPlexCopyCoordinates(*dm, udm);CHKERRQ(ierr); 978 ierr = DMDestroy(dm);CHKERRQ(ierr); 979 *dm = udm; 980 } 981 PetscFunctionReturn(0); 982 } 983 984 /*@C 985 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra). 986 987 Collective 988 989 Input Parameters: 990 + comm - The communicator for the DM object 991 . dim - The spatial dimension 992 . simplex - PETSC_TRUE for simplices, PETSC_FALSE for tensor cells 993 . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 994 . lower - The lower left corner, or NULL for (0, 0, 0) 995 . upper - The upper right corner, or NULL for (1, 1, 1) 996 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 997 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 998 999 Output Parameter: 1000 . dm - The DM object 1001 1002 Options Database Keys: 1003 + -dm_plex_box_lower <x,y,z> - Specify lower-left-bottom coordinates for the box 1004 - -dm_plex_box_upper <x,y,z> - Specify upper-right-top coordinates for the box 1005 1006 Note: Here is the numbering returned for 2 faces in each direction for tensor cells: 1007 $ 10---17---11---18----12 1008 $ | | | 1009 $ | | | 1010 $ 20 2 22 3 24 1011 $ | | | 1012 $ | | | 1013 $ 7---15----8---16----9 1014 $ | | | 1015 $ | | | 1016 $ 19 0 21 1 23 1017 $ | | | 1018 $ | | | 1019 $ 4---13----5---14----6 1020 1021 and for simplicial cells 1022 1023 $ 14----8---15----9----16 1024 $ |\ 5 |\ 7 | 1025 $ | \ | \ | 1026 $ 13 2 14 3 15 1027 $ | 4 \ | 6 \ | 1028 $ | \ | \ | 1029 $ 11----6---12----7----13 1030 $ |\ |\ | 1031 $ | \ 1 | \ 3 | 1032 $ 10 0 11 1 12 1033 $ | 0 \ | 2 \ | 1034 $ | \ | \ | 1035 $ 8----4----9----5----10 1036 1037 Level: beginner 1038 1039 .seealso: DMPlexCreateFromFile(), DMPlexCreateHexCylinderMesh(), DMSetType(), DMCreate() 1040 @*/ 1041 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) 1042 { 1043 PetscInt fac[3] = {0, 0, 0}; 1044 PetscReal low[3] = {0, 0, 0}; 1045 PetscReal upp[3] = {1, 1, 1}; 1046 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1047 PetscInt i, n; 1048 PetscBool flg; 1049 PetscErrorCode ierr; 1050 1051 PetscFunctionBegin; 1052 n = 3; 1053 ierr = PetscOptionsGetIntArray(NULL, NULL, "-dm_plex_box_faces", fac, &n, &flg);CHKERRQ(ierr); 1054 for (i = 0; i < dim; ++i) fac[i] = faces ? faces[i] : (flg && i < n ? fac[i] : (dim == 1 ? 1 : 4-dim)); 1055 if (lower) for (i = 0; i < dim; ++i) low[i] = lower[i]; 1056 if (upper) for (i = 0; i < dim; ++i) upp[i] = upper[i]; 1057 if (periodicity) for (i = 0; i < dim; ++i) bdt[i] = periodicity[i]; 1058 /* Allow bounds to be specified from the command line */ 1059 n = 3; 1060 ierr = PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_lower", low, &n, &flg);CHKERRQ(ierr); 1061 if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim); 1062 n = 3; 1063 ierr = PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_upper", upp, &n, &flg);CHKERRQ(ierr); 1064 if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim); 1065 1066 if (dim == 1) {ierr = DMPlexCreateLineMesh_Internal(comm, fac[0], low[0], upp[0], bdt[0], dm);CHKERRQ(ierr);} 1067 else if (simplex) {ierr = DMPlexCreateBoxMesh_Simplex_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);CHKERRQ(ierr);} 1068 else {ierr = DMPlexCreateBoxMesh_Tensor_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);CHKERRQ(ierr);} 1069 PetscFunctionReturn(0); 1070 } 1071 1072 /*@ 1073 DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells. 1074 1075 Collective 1076 1077 Input Parameters: 1078 + comm - The communicator for the DM object 1079 . faces - Number of faces per dimension, or NULL for (1, 1, 1) 1080 . lower - The lower left corner, or NULL for (0, 0, 0) 1081 . upper - The upper right corner, or NULL for (1, 1, 1) 1082 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 1083 . ordExt - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1084 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1085 1086 Output Parameter: 1087 . dm - The DM object 1088 1089 Level: beginner 1090 1091 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateWedgeCylinderMesh(), DMPlexExtrude(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1092 @*/ 1093 PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool ordExt, PetscBool interpolate, DM *dm) 1094 { 1095 DM bdm, botdm; 1096 PetscInt i; 1097 PetscInt fac[3] = {0, 0, 0}; 1098 PetscReal low[3] = {0, 0, 0}; 1099 PetscReal upp[3] = {1, 1, 1}; 1100 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1101 PetscErrorCode ierr; 1102 1103 PetscFunctionBegin; 1104 for (i = 0; i < 3; ++i) fac[i] = faces ? (faces[i] > 0 ? faces[i] : 1) : 1; 1105 if (lower) for (i = 0; i < 3; ++i) low[i] = lower[i]; 1106 if (upper) for (i = 0; i < 3; ++i) upp[i] = upper[i]; 1107 if (periodicity) for (i = 0; i < 3; ++i) bdt[i] = periodicity[i]; 1108 for (i = 0; i < 3; ++i) if (bdt[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity not yet supported"); 1109 1110 ierr = DMCreate(comm, &bdm);CHKERRQ(ierr); 1111 ierr = DMSetType(bdm, DMPLEX);CHKERRQ(ierr); 1112 ierr = DMSetDimension(bdm, 1);CHKERRQ(ierr); 1113 ierr = DMSetCoordinateDim(bdm, 2);CHKERRQ(ierr); 1114 ierr = DMPlexCreateSquareBoundary(bdm, low, upp, fac);CHKERRQ(ierr); 1115 ierr = DMPlexGenerate(bdm, NULL, PETSC_FALSE, &botdm);CHKERRQ(ierr); 1116 ierr = DMDestroy(&bdm);CHKERRQ(ierr); 1117 ierr = DMPlexExtrude(botdm, fac[2], upp[2] - low[2], ordExt, interpolate, dm);CHKERRQ(ierr); 1118 if (low[2] != 0.0) { 1119 Vec v; 1120 PetscScalar *x; 1121 PetscInt cDim, n; 1122 1123 ierr = DMGetCoordinatesLocal(*dm, &v);CHKERRQ(ierr); 1124 ierr = VecGetBlockSize(v, &cDim);CHKERRQ(ierr); 1125 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 1126 ierr = VecGetArray(v, &x);CHKERRQ(ierr); 1127 x += cDim; 1128 for (i=0; i<n; i+=cDim) x[i] += low[2]; 1129 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 1130 ierr = DMSetCoordinatesLocal(*dm, v);CHKERRQ(ierr); 1131 } 1132 ierr = DMDestroy(&botdm);CHKERRQ(ierr); 1133 PetscFunctionReturn(0); 1134 } 1135 1136 /*@ 1137 DMPlexExtrude - Creates a (d+1)-D mesh by extruding a d-D mesh in the normal direction using prismatic cells. 1138 1139 Collective on idm 1140 1141 Input Parameters: 1142 + idm - The mesh to be extruted 1143 . layers - The number of layers 1144 . height - The height of the extruded layer 1145 . ordExt - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1146 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1147 1148 Output Parameter: 1149 . dm - The DM object 1150 1151 Notes: The object created is an hybrid mesh, the vertex ordering in the cone of the cell is that of the prismatic cells 1152 1153 Level: advanced 1154 1155 .seealso: DMPlexCreateWedgeCylinderMesh(), DMPlexCreateWedgeBoxMesh(), DMPlexSetHybridBounds(), DMSetType(), DMCreate() 1156 @*/ 1157 PetscErrorCode DMPlexExtrude(DM idm, PetscInt layers, PetscReal height, PetscBool ordExt, PetscBool interpolate, DM* dm) 1158 { 1159 PetscScalar *coordsB; 1160 const PetscScalar *coordsA; 1161 PetscReal *normals = NULL; 1162 Vec coordinatesA, coordinatesB; 1163 PetscSection coordSectionA, coordSectionB; 1164 PetscInt dim, cDim, cDimB, c, l, v, coordSize, *newCone; 1165 PetscInt cStart, cEnd, vStart, vEnd, cellV, numCells, numVertices; 1166 PetscErrorCode ierr; 1167 1168 PetscFunctionBegin; 1169 PetscValidHeaderSpecific(idm, DM_CLASSID, 1); 1170 PetscValidLogicalCollectiveInt(idm, layers, 2); 1171 PetscValidLogicalCollectiveReal(idm, height, 3); 1172 PetscValidLogicalCollectiveBool(idm, interpolate, 4); 1173 ierr = DMGetDimension(idm, &dim);CHKERRQ(ierr); 1174 if (dim < 1 || dim > 3) SETERRQ1(PetscObjectComm((PetscObject)idm), PETSC_ERR_SUP, "Support for dimension %D not coded", dim); 1175 1176 ierr = DMPlexGetHeightStratum(idm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1177 ierr = DMPlexGetDepthStratum(idm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1178 numCells = (cEnd - cStart)*layers; 1179 numVertices = (vEnd - vStart)*(layers+1); 1180 ierr = DMCreate(PetscObjectComm((PetscObject)idm), dm);CHKERRQ(ierr); 1181 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1182 ierr = DMSetDimension(*dm, dim+1);CHKERRQ(ierr); 1183 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1184 for (c = cStart, cellV = 0; c < cEnd; ++c) { 1185 PetscInt *closure = NULL; 1186 PetscInt closureSize, numCorners = 0; 1187 1188 ierr = DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1189 for (v = 0; v < closureSize*2; v += 2) if ((closure[v] >= vStart) && (closure[v] < vEnd)) numCorners++; 1190 ierr = DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1191 for (l = 0; l < layers; ++l) { 1192 ierr = DMPlexSetConeSize(*dm, ordExt ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart, 2*numCorners);CHKERRQ(ierr); 1193 } 1194 cellV = PetscMax(numCorners,cellV); 1195 } 1196 ierr = DMPlexSetHybridBounds(*dm, 0, PETSC_DETERMINE, PETSC_DETERMINE, PETSC_DETERMINE);CHKERRQ(ierr); 1197 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1198 1199 ierr = DMGetCoordinateDim(idm, &cDim);CHKERRQ(ierr); 1200 if (dim != cDim) { 1201 ierr = PetscCalloc1(cDim*(vEnd - vStart), &normals);CHKERRQ(ierr); 1202 } 1203 ierr = PetscMalloc1(3*cellV,&newCone);CHKERRQ(ierr); 1204 for (c = cStart; c < cEnd; ++c) { 1205 PetscInt *closure = NULL; 1206 PetscInt closureSize, numCorners = 0, l; 1207 PetscReal normal[3] = {0, 0, 0}; 1208 1209 if (normals) { 1210 ierr = DMPlexComputeCellGeometryFVM(idm, c, NULL, NULL, normal);CHKERRQ(ierr); 1211 } 1212 ierr = DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1213 for (v = 0; v < closureSize*2; v += 2) { 1214 if ((closure[v] >= vStart) && (closure[v] < vEnd)) { 1215 PetscInt d; 1216 1217 newCone[numCorners++] = closure[v] - vStart; 1218 if (normals) { for (d = 0; d < cDim; ++d) normals[cDim*(closure[v]-vStart)+d] += normal[d]; } 1219 } 1220 } 1221 switch (numCorners) { 1222 case 4: /* do nothing */ 1223 case 2: /* do nothing */ 1224 break; 1225 case 3: /* from counter-clockwise to wedge ordering */ 1226 l = newCone[1]; 1227 newCone[1] = newCone[2]; 1228 newCone[2] = l; 1229 break; 1230 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_SUP, "Unsupported number of corners: %D", numCorners); 1231 } 1232 ierr = DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1233 for (l = 0; l < layers; ++l) { 1234 PetscInt i; 1235 1236 for (i = 0; i < numCorners; ++i) { 1237 newCone[ numCorners + i] = ordExt ? (layers+1)*newCone[i] + l + numCells : l*(vEnd - vStart) + newCone[i] + numCells; 1238 newCone[2*numCorners + i] = ordExt ? (layers+1)*newCone[i] + l + 1 + numCells : (l+1)*(vEnd - vStart) + newCone[i] + numCells; 1239 } 1240 ierr = DMPlexSetCone(*dm, ordExt ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart, newCone + numCorners);CHKERRQ(ierr); 1241 } 1242 } 1243 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1244 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1245 ierr = PetscFree(newCone);CHKERRQ(ierr); 1246 1247 cDimB = cDim == dim ? cDim+1 : cDim; 1248 ierr = DMGetCoordinateSection(*dm, &coordSectionB);CHKERRQ(ierr); 1249 ierr = PetscSectionSetNumFields(coordSectionB, 1);CHKERRQ(ierr); 1250 ierr = PetscSectionSetFieldComponents(coordSectionB, 0, cDimB);CHKERRQ(ierr); 1251 ierr = PetscSectionSetChart(coordSectionB, numCells, numCells+numVertices);CHKERRQ(ierr); 1252 for (v = numCells; v < numCells+numVertices; ++v) { 1253 ierr = PetscSectionSetDof(coordSectionB, v, cDimB);CHKERRQ(ierr); 1254 ierr = PetscSectionSetFieldDof(coordSectionB, v, 0, cDimB);CHKERRQ(ierr); 1255 } 1256 ierr = PetscSectionSetUp(coordSectionB);CHKERRQ(ierr); 1257 ierr = PetscSectionGetStorageSize(coordSectionB, &coordSize);CHKERRQ(ierr); 1258 ierr = VecCreate(PETSC_COMM_SELF, &coordinatesB);CHKERRQ(ierr); 1259 ierr = PetscObjectSetName((PetscObject) coordinatesB, "coordinates");CHKERRQ(ierr); 1260 ierr = VecSetSizes(coordinatesB, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1261 ierr = VecSetBlockSize(coordinatesB, cDimB);CHKERRQ(ierr); 1262 ierr = VecSetType(coordinatesB,VECSTANDARD);CHKERRQ(ierr); 1263 1264 ierr = DMGetCoordinateSection(idm, &coordSectionA);CHKERRQ(ierr); 1265 ierr = DMGetCoordinatesLocal(idm, &coordinatesA);CHKERRQ(ierr); 1266 ierr = VecGetArray(coordinatesB, &coordsB);CHKERRQ(ierr); 1267 ierr = VecGetArrayRead(coordinatesA, &coordsA);CHKERRQ(ierr); 1268 for (v = vStart; v < vEnd; ++v) { 1269 const PetscScalar *cptr; 1270 PetscReal ones2[2] = { 0., 1.}, ones3[3] = { 0., 0., 1.}; 1271 PetscReal *normal, norm, h = height/layers; 1272 PetscInt offA, d, cDimA = cDim; 1273 1274 normal = normals ? normals + cDimB*(v - vStart) : (cDim > 1 ? ones3 : ones2); 1275 if (normals) { 1276 for (d = 0, norm = 0.0; d < cDimB; ++d) norm += normal[d]*normal[d]; 1277 for (d = 0; d < cDimB; ++d) normal[d] *= 1./PetscSqrtReal(norm); 1278 } 1279 1280 ierr = PetscSectionGetOffset(coordSectionA, v, &offA);CHKERRQ(ierr); 1281 cptr = coordsA + offA; 1282 for (l = 0; l < layers+1; ++l) { 1283 PetscInt offB, d, newV; 1284 1285 newV = ordExt ? (layers+1)*(v -vStart) + l + numCells : (vEnd -vStart)*l + (v -vStart) + numCells; 1286 ierr = PetscSectionGetOffset(coordSectionB, newV, &offB);CHKERRQ(ierr); 1287 for (d = 0; d < cDimA; ++d) { coordsB[offB+d] = cptr[d]; } 1288 for (d = 0; d < cDimB; ++d) { coordsB[offB+d] += l ? normal[d]*h : 0.0; } 1289 cptr = coordsB + offB; 1290 cDimA = cDimB; 1291 } 1292 } 1293 ierr = VecRestoreArrayRead(coordinatesA, &coordsA);CHKERRQ(ierr); 1294 ierr = VecRestoreArray(coordinatesB, &coordsB);CHKERRQ(ierr); 1295 ierr = DMSetCoordinatesLocal(*dm, coordinatesB);CHKERRQ(ierr); 1296 ierr = VecDestroy(&coordinatesB);CHKERRQ(ierr); 1297 ierr = PetscFree(normals);CHKERRQ(ierr); 1298 if (interpolate) { 1299 DM idm; 1300 1301 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1302 ierr = DMPlexCopyCoordinates(*dm, idm);CHKERRQ(ierr); 1303 ierr = DMDestroy(dm);CHKERRQ(ierr); 1304 *dm = idm; 1305 } 1306 PetscFunctionReturn(0); 1307 } 1308 1309 /*@C 1310 DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database. 1311 1312 Logically Collective on dm 1313 1314 Input Parameters: 1315 + dm - the DM context 1316 - prefix - the prefix to prepend to all option names 1317 1318 Notes: 1319 A hyphen (-) must NOT be given at the beginning of the prefix name. 1320 The first character of all runtime options is AUTOMATICALLY the hyphen. 1321 1322 Level: advanced 1323 1324 .seealso: SNESSetFromOptions() 1325 @*/ 1326 PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) 1327 { 1328 DM_Plex *mesh = (DM_Plex *) dm->data; 1329 PetscErrorCode ierr; 1330 1331 PetscFunctionBegin; 1332 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1333 ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);CHKERRQ(ierr); 1334 ierr = PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);CHKERRQ(ierr); 1335 PetscFunctionReturn(0); 1336 } 1337 1338 /*@ 1339 DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. 1340 1341 Collective 1342 1343 Input Parameters: 1344 + comm - The communicator for the DM object 1345 . numRefine - The number of regular refinements to the basic 5 cell structure 1346 - periodicZ - The boundary type for the Z direction 1347 1348 Output Parameter: 1349 . dm - The DM object 1350 1351 Note: Here is the output numbering looking from the bottom of the cylinder: 1352 $ 17-----14 1353 $ | | 1354 $ | 2 | 1355 $ | | 1356 $ 17-----8-----7-----14 1357 $ | | | | 1358 $ | 3 | 0 | 1 | 1359 $ | | | | 1360 $ 19-----5-----6-----13 1361 $ | | 1362 $ | 4 | 1363 $ | | 1364 $ 19-----13 1365 $ 1366 $ and up through the top 1367 $ 1368 $ 18-----16 1369 $ | | 1370 $ | 2 | 1371 $ | | 1372 $ 18----10----11-----16 1373 $ | | | | 1374 $ | 3 | 0 | 1 | 1375 $ | | | | 1376 $ 20-----9----12-----15 1377 $ | | 1378 $ | 4 | 1379 $ | | 1380 $ 20-----15 1381 1382 Level: beginner 1383 1384 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1385 @*/ 1386 PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, PetscInt numRefine, DMBoundaryType periodicZ, DM *dm) 1387 { 1388 const PetscInt dim = 3; 1389 PetscInt numCells, numVertices, r; 1390 PetscMPIInt rank; 1391 PetscErrorCode ierr; 1392 1393 PetscFunctionBegin; 1394 PetscValidPointer(dm, 4); 1395 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1396 if (numRefine < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of refinements %D cannot be negative", numRefine); 1397 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1398 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1399 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1400 /* Create topology */ 1401 { 1402 PetscInt cone[8], c; 1403 1404 numCells = !rank ? 5 : 0; 1405 numVertices = !rank ? 16 : 0; 1406 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1407 numCells *= 3; 1408 numVertices = !rank ? 24 : 0; 1409 } 1410 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1411 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 8);CHKERRQ(ierr);} 1412 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1413 if (!rank) { 1414 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1415 cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16; 1416 cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34; 1417 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1418 cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23; 1419 cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */ 1420 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1421 cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17; 1422 cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38; 1423 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1424 cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15; 1425 cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38; 1426 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1427 cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23; 1428 cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31; 1429 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1430 1431 cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32; 1432 cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20; 1433 ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); 1434 cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36; 1435 cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21; 1436 ierr = DMPlexSetCone(*dm, 6, cone);CHKERRQ(ierr); 1437 cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33; 1438 cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28; 1439 ierr = DMPlexSetCone(*dm, 7, cone);CHKERRQ(ierr); 1440 cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31; 1441 cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28; 1442 ierr = DMPlexSetCone(*dm, 8, cone);CHKERRQ(ierr); 1443 cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36; 1444 cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19; 1445 ierr = DMPlexSetCone(*dm, 9, cone);CHKERRQ(ierr); 1446 1447 cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22; 1448 cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18; 1449 ierr = DMPlexSetCone(*dm, 10, cone);CHKERRQ(ierr); 1450 cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25; 1451 cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17; 1452 ierr = DMPlexSetCone(*dm, 11, cone);CHKERRQ(ierr); 1453 cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21; 1454 cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27; 1455 ierr = DMPlexSetCone(*dm, 12, cone);CHKERRQ(ierr); 1456 cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19; 1457 cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27; 1458 ierr = DMPlexSetCone(*dm, 13, cone);CHKERRQ(ierr); 1459 cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25; 1460 cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15; 1461 ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); 1462 } else { 1463 cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6; 1464 cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10; 1465 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1466 cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13; 1467 cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11; 1468 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1469 cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7; 1470 cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18; 1471 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1472 cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5; 1473 cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18; 1474 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1475 cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13; 1476 cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9; 1477 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1478 } 1479 } 1480 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1481 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1482 } 1483 /* Interpolate */ 1484 { 1485 DM idm; 1486 1487 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1488 ierr = DMDestroy(dm);CHKERRQ(ierr); 1489 *dm = idm; 1490 } 1491 /* Create cube geometry */ 1492 { 1493 Vec coordinates; 1494 PetscSection coordSection; 1495 PetscScalar *coords; 1496 PetscInt coordSize, v; 1497 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1498 const PetscReal ds2 = dis/2.0; 1499 1500 /* Build coordinates */ 1501 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1502 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1503 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1504 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1505 for (v = numCells; v < numCells+numVertices; ++v) { 1506 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1507 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1508 } 1509 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1510 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1511 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1512 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1513 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1514 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1515 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1516 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1517 if (!rank) { 1518 coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0; 1519 coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0; 1520 coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0; 1521 coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0; 1522 coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0; 1523 coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0; 1524 coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0; 1525 coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0; 1526 coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0; 1527 coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0; 1528 coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0; 1529 coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0; 1530 coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0; 1531 coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0; 1532 coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0; 1533 coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0; 1534 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1535 /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5; 1536 /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5; 1537 /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5; 1538 /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5; 1539 /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5; 1540 /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5; 1541 /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5; 1542 /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5; 1543 } 1544 } 1545 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1546 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 1547 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1548 } 1549 /* Create periodicity */ 1550 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1551 PetscReal L[3]; 1552 PetscReal maxCell[3]; 1553 DMBoundaryType bdType[3]; 1554 PetscReal lower[3] = {0.0, 0.0, 0.0}; 1555 PetscReal upper[3] = {1.0, 1.0, 1.5}; 1556 PetscInt i, numZCells = 3; 1557 1558 bdType[0] = DM_BOUNDARY_NONE; 1559 bdType[1] = DM_BOUNDARY_NONE; 1560 bdType[2] = periodicZ; 1561 for (i = 0; i < dim; i++) { 1562 L[i] = upper[i] - lower[i]; 1563 maxCell[i] = 1.1 * (L[i] / numZCells); 1564 } 1565 ierr = DMSetPeriodicity(*dm, PETSC_TRUE, maxCell, L, bdType);CHKERRQ(ierr); 1566 } 1567 /* Refine topology */ 1568 for (r = 0; r < numRefine; ++r) { 1569 DM rdm = NULL; 1570 1571 ierr = DMRefine(*dm, comm, &rdm);CHKERRQ(ierr); 1572 ierr = DMDestroy(dm);CHKERRQ(ierr); 1573 *dm = rdm; 1574 } 1575 /* Remap geometry to cylinder 1576 Interior square: Linear interpolation is correct 1577 The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing 1578 such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance 1579 1580 phi = arctan(y/x) 1581 d_close = sqrt(1/8 + 1/4 sin^2(phi)) 1582 d_far = sqrt(1/2 + sin^2(phi)) 1583 1584 so we remap them using 1585 1586 x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) 1587 y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) 1588 1589 If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. 1590 */ 1591 { 1592 Vec coordinates; 1593 PetscSection coordSection; 1594 PetscScalar *coords; 1595 PetscInt vStart, vEnd, v; 1596 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1597 const PetscReal ds2 = 0.5*dis; 1598 1599 ierr = DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1600 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1601 ierr = DMGetCoordinatesLocal(*dm, &coordinates);CHKERRQ(ierr); 1602 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1603 for (v = vStart; v < vEnd; ++v) { 1604 PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; 1605 PetscInt off; 1606 1607 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 1608 if ((PetscAbsScalar(coords[off+0]) <= ds2) && (PetscAbsScalar(coords[off+1]) <= ds2)) continue; 1609 x = PetscRealPart(coords[off]); 1610 y = PetscRealPart(coords[off+1]); 1611 phi = PetscAtan2Real(y, x); 1612 sinp = PetscSinReal(phi); 1613 cosp = PetscCosReal(phi); 1614 if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) { 1615 dc = PetscAbsReal(ds2/sinp); 1616 df = PetscAbsReal(dis/sinp); 1617 xc = ds2*x/PetscAbsReal(y); 1618 yc = ds2*PetscSignReal(y); 1619 } else { 1620 dc = PetscAbsReal(ds2/cosp); 1621 df = PetscAbsReal(dis/cosp); 1622 xc = ds2*PetscSignReal(x); 1623 yc = ds2*y/PetscAbsReal(x); 1624 } 1625 coords[off+0] = xc + (coords[off+0] - xc)*(1.0 - dc)/(df - dc); 1626 coords[off+1] = yc + (coords[off+1] - yc)*(1.0 - dc)/(df - dc); 1627 } 1628 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1629 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1630 ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); 1631 } 1632 } 1633 PetscFunctionReturn(0); 1634 } 1635 1636 /*@ 1637 DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges. 1638 1639 Collective 1640 1641 Input Parameters: 1642 + comm - The communicator for the DM object 1643 . n - The number of wedges around the origin 1644 - interpolate - Create edges and faces 1645 1646 Output Parameter: 1647 . dm - The DM object 1648 1649 Level: beginner 1650 1651 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1652 @*/ 1653 PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm) 1654 { 1655 const PetscInt dim = 3; 1656 PetscInt numCells, numVertices; 1657 PetscMPIInt rank; 1658 PetscErrorCode ierr; 1659 1660 PetscFunctionBegin; 1661 PetscValidPointer(dm, 3); 1662 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1663 if (n < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n); 1664 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1665 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1666 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1667 /* Create topology */ 1668 { 1669 PetscInt cone[6], c; 1670 1671 numCells = !rank ? n : 0; 1672 numVertices = !rank ? 2*(n+1) : 0; 1673 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1674 ierr = DMPlexSetHybridBounds(*dm, 0, PETSC_DETERMINE, PETSC_DETERMINE, PETSC_DETERMINE);CHKERRQ(ierr); 1675 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 6);CHKERRQ(ierr);} 1676 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1677 for (c = 0; c < numCells; c++) { 1678 cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n; 1679 cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n; 1680 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 1681 } 1682 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1683 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1684 } 1685 /* Interpolate */ 1686 if (interpolate) { 1687 DM idm; 1688 1689 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1690 ierr = DMDestroy(dm);CHKERRQ(ierr); 1691 *dm = idm; 1692 } 1693 /* Create cylinder geometry */ 1694 { 1695 Vec coordinates; 1696 PetscSection coordSection; 1697 PetscScalar *coords; 1698 PetscInt coordSize, v, c; 1699 1700 /* Build coordinates */ 1701 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1702 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1703 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1704 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1705 for (v = numCells; v < numCells+numVertices; ++v) { 1706 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1707 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1708 } 1709 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1710 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1711 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1712 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1713 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1714 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1715 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1716 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1717 for (c = 0; c < numCells; c++) { 1718 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; 1719 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; 1720 } 1721 if (!rank) { 1722 coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0; 1723 coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0; 1724 } 1725 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1726 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 1727 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1728 } 1729 PetscFunctionReturn(0); 1730 } 1731 1732 PETSC_STATIC_INLINE PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1733 { 1734 PetscReal prod = 0.0; 1735 PetscInt i; 1736 for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]); 1737 return PetscSqrtReal(prod); 1738 } 1739 PETSC_STATIC_INLINE PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1740 { 1741 PetscReal prod = 0.0; 1742 PetscInt i; 1743 for (i = 0; i < dim; ++i) prod += x[i]*y[i]; 1744 return prod; 1745 } 1746 1747 /*@ 1748 DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d. 1749 1750 Collective 1751 1752 Input Parameters: 1753 + comm - The communicator for the DM object 1754 . dim - The dimension 1755 - simplex - Use simplices, or tensor product cells 1756 1757 Output Parameter: 1758 . dm - The DM object 1759 1760 Level: beginner 1761 1762 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1763 @*/ 1764 PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *dm) 1765 { 1766 const PetscInt embedDim = dim+1; 1767 PetscSection coordSection; 1768 Vec coordinates; 1769 PetscScalar *coords; 1770 PetscReal *coordsIn; 1771 PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e; 1772 PetscMPIInt rank; 1773 PetscErrorCode ierr; 1774 1775 PetscFunctionBegin; 1776 PetscValidPointer(dm, 4); 1777 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1778 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1779 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1780 ierr = DMSetCoordinateDim(*dm, dim+1);CHKERRQ(ierr); 1781 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) *dm), &rank);CHKERRQ(ierr); 1782 switch (dim) { 1783 case 2: 1784 if (simplex) { 1785 DM idm; 1786 const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI); 1787 const PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)}; 1788 const PetscInt degree = 5; 1789 PetscInt s[3] = {1, 1, 1}; 1790 PetscInt cone[3]; 1791 PetscInt *graph, p, i, j, k; 1792 1793 numCells = !rank ? 20 : 0; 1794 numVerts = !rank ? 12 : 0; 1795 firstVertex = numCells; 1796 /* Use icosahedron, which for a unit sphere has coordinates which are all cyclic permutations of 1797 1798 (0, \pm 1/\phi+1, \pm \phi/\phi+1) 1799 1800 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 1801 length is then given by 2/\phi = 2 * 0.61803 = 1.23606. 1802 */ 1803 /* Construct vertices */ 1804 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 1805 if (!rank) { 1806 for (p = 0, i = 0; p < embedDim; ++p) { 1807 for (s[1] = -1; s[1] < 2; s[1] += 2) { 1808 for (s[2] = -1; s[2] < 2; s[2] += 2) { 1809 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim]; 1810 ++i; 1811 } 1812 } 1813 } 1814 } 1815 /* Construct graph */ 1816 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 1817 for (i = 0; i < numVerts; ++i) { 1818 for (j = 0, k = 0; j < numVerts; ++j) { 1819 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 1820 } 1821 if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree); 1822 } 1823 /* Build Topology */ 1824 ierr = DMPlexSetChart(*dm, 0, numCells+numVerts);CHKERRQ(ierr); 1825 for (c = 0; c < numCells; c++) { 1826 ierr = DMPlexSetConeSize(*dm, c, embedDim);CHKERRQ(ierr); 1827 } 1828 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 1829 /* Cells */ 1830 for (i = 0, c = 0; i < numVerts; ++i) { 1831 for (j = 0; j < i; ++j) { 1832 for (k = 0; k < j; ++k) { 1833 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) { 1834 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; 1835 /* Check orientation */ 1836 { 1837 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}}}; 1838 PetscReal normal[3]; 1839 PetscInt e, f; 1840 1841 for (d = 0; d < embedDim; ++d) { 1842 normal[d] = 0.0; 1843 for (e = 0; e < embedDim; ++e) { 1844 for (f = 0; f < embedDim; ++f) { 1845 normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]); 1846 } 1847 } 1848 } 1849 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 1850 } 1851 ierr = DMPlexSetCone(*dm, c++, cone);CHKERRQ(ierr); 1852 } 1853 } 1854 } 1855 } 1856 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1857 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1858 ierr = PetscFree(graph);CHKERRQ(ierr); 1859 /* Interpolate mesh */ 1860 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1861 ierr = DMDestroy(dm);CHKERRQ(ierr); 1862 *dm = idm; 1863 } else { 1864 /* 1865 12-21--13 1866 | | 1867 25 4 24 1868 | | 1869 12-25--9-16--8-24--13 1870 | | | | 1871 23 5 17 0 15 3 22 1872 | | | | 1873 10-20--6-14--7-19--11 1874 | | 1875 20 1 19 1876 | | 1877 10-18--11 1878 | | 1879 23 2 22 1880 | | 1881 12-21--13 1882 */ 1883 const PetscReal dist = 1.0/PetscSqrtReal(3.0); 1884 PetscInt cone[4], ornt[4]; 1885 1886 numCells = !rank ? 6 : 0; 1887 numEdges = !rank ? 12 : 0; 1888 numVerts = !rank ? 8 : 0; 1889 firstVertex = numCells; 1890 firstEdge = numCells + numVerts; 1891 /* Build Topology */ 1892 ierr = DMPlexSetChart(*dm, 0, numCells+numEdges+numVerts);CHKERRQ(ierr); 1893 for (c = 0; c < numCells; c++) { 1894 ierr = DMPlexSetConeSize(*dm, c, 4);CHKERRQ(ierr); 1895 } 1896 for (e = firstEdge; e < firstEdge+numEdges; ++e) { 1897 ierr = DMPlexSetConeSize(*dm, e, 2);CHKERRQ(ierr); 1898 } 1899 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 1900 if (!rank) { 1901 /* Cell 0 */ 1902 cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17; 1903 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1904 ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0; 1905 ierr = DMPlexSetConeOrientation(*dm, 0, ornt);CHKERRQ(ierr); 1906 /* Cell 1 */ 1907 cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20; 1908 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1909 ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; 1910 ierr = DMPlexSetConeOrientation(*dm, 1, ornt);CHKERRQ(ierr); 1911 /* Cell 2 */ 1912 cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23; 1913 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1914 ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; 1915 ierr = DMPlexSetConeOrientation(*dm, 2, ornt);CHKERRQ(ierr); 1916 /* Cell 3 */ 1917 cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15; 1918 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1919 ornt[0] = -2; ornt[1] = -2; ornt[2] = 0; ornt[3] = -2; 1920 ierr = DMPlexSetConeOrientation(*dm, 3, ornt);CHKERRQ(ierr); 1921 /* Cell 4 */ 1922 cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25; 1923 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1924 ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = 0; 1925 ierr = DMPlexSetConeOrientation(*dm, 4, ornt);CHKERRQ(ierr); 1926 /* Cell 5 */ 1927 cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23; 1928 ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); 1929 ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = -2; 1930 ierr = DMPlexSetConeOrientation(*dm, 5, ornt);CHKERRQ(ierr); 1931 /* Edges */ 1932 cone[0] = 6; cone[1] = 7; 1933 ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); 1934 cone[0] = 7; cone[1] = 8; 1935 ierr = DMPlexSetCone(*dm, 15, cone);CHKERRQ(ierr); 1936 cone[0] = 8; cone[1] = 9; 1937 ierr = DMPlexSetCone(*dm, 16, cone);CHKERRQ(ierr); 1938 cone[0] = 9; cone[1] = 6; 1939 ierr = DMPlexSetCone(*dm, 17, cone);CHKERRQ(ierr); 1940 cone[0] = 10; cone[1] = 11; 1941 ierr = DMPlexSetCone(*dm, 18, cone);CHKERRQ(ierr); 1942 cone[0] = 11; cone[1] = 7; 1943 ierr = DMPlexSetCone(*dm, 19, cone);CHKERRQ(ierr); 1944 cone[0] = 6; cone[1] = 10; 1945 ierr = DMPlexSetCone(*dm, 20, cone);CHKERRQ(ierr); 1946 cone[0] = 12; cone[1] = 13; 1947 ierr = DMPlexSetCone(*dm, 21, cone);CHKERRQ(ierr); 1948 cone[0] = 13; cone[1] = 11; 1949 ierr = DMPlexSetCone(*dm, 22, cone);CHKERRQ(ierr); 1950 cone[0] = 10; cone[1] = 12; 1951 ierr = DMPlexSetCone(*dm, 23, cone);CHKERRQ(ierr); 1952 cone[0] = 13; cone[1] = 8; 1953 ierr = DMPlexSetCone(*dm, 24, cone);CHKERRQ(ierr); 1954 cone[0] = 12; cone[1] = 9; 1955 ierr = DMPlexSetCone(*dm, 25, cone);CHKERRQ(ierr); 1956 } 1957 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1958 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1959 /* Build coordinates */ 1960 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 1961 if (!rank) { 1962 coordsIn[0*embedDim+0] = -dist; coordsIn[0*embedDim+1] = dist; coordsIn[0*embedDim+2] = -dist; 1963 coordsIn[1*embedDim+0] = dist; coordsIn[1*embedDim+1] = dist; coordsIn[1*embedDim+2] = -dist; 1964 coordsIn[2*embedDim+0] = dist; coordsIn[2*embedDim+1] = -dist; coordsIn[2*embedDim+2] = -dist; 1965 coordsIn[3*embedDim+0] = -dist; coordsIn[3*embedDim+1] = -dist; coordsIn[3*embedDim+2] = -dist; 1966 coordsIn[4*embedDim+0] = -dist; coordsIn[4*embedDim+1] = dist; coordsIn[4*embedDim+2] = dist; 1967 coordsIn[5*embedDim+0] = dist; coordsIn[5*embedDim+1] = dist; coordsIn[5*embedDim+2] = dist; 1968 coordsIn[6*embedDim+0] = -dist; coordsIn[6*embedDim+1] = -dist; coordsIn[6*embedDim+2] = dist; 1969 coordsIn[7*embedDim+0] = dist; coordsIn[7*embedDim+1] = -dist; coordsIn[7*embedDim+2] = dist; 1970 } 1971 } 1972 break; 1973 case 3: 1974 if (simplex) { 1975 DM idm; 1976 const PetscReal edgeLen = 1.0/PETSC_PHI; 1977 const PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5}; 1978 const PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0}; 1979 const PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0}; 1980 const PetscInt degree = 12; 1981 PetscInt s[4] = {1, 1, 1}; 1982 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}, 1983 {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}}; 1984 PetscInt cone[4]; 1985 PetscInt *graph, p, i, j, k, l; 1986 1987 numCells = !rank ? 600 : 0; 1988 numVerts = !rank ? 120 : 0; 1989 firstVertex = numCells; 1990 /* Use the 600-cell, which for a unit sphere has coordinates which are 1991 1992 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16 1993 (\pm 1, 0, 0, 0) all cyclic permutations 8 1994 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96 1995 1996 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 1997 length is then given by 1/\phi = 0.61803. 1998 1999 http://buzzard.pugetsound.edu/sage-practice/ch03s03.html 2000 http://mathworld.wolfram.com/600-Cell.html 2001 */ 2002 /* Construct vertices */ 2003 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 2004 i = 0; 2005 if (!rank) { 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 } 2035 if (i != numVerts) SETERRQ2(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts); 2036 /* Construct graph */ 2037 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 2038 for (i = 0; i < numVerts; ++i) { 2039 for (j = 0, k = 0; j < numVerts; ++j) { 2040 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 2041 } 2042 if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree); 2043 } 2044 /* Build Topology */ 2045 ierr = DMPlexSetChart(*dm, 0, numCells+numVerts);CHKERRQ(ierr); 2046 for (c = 0; c < numCells; c++) { 2047 ierr = DMPlexSetConeSize(*dm, c, embedDim);CHKERRQ(ierr); 2048 } 2049 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 2050 /* Cells */ 2051 if (!rank) { 2052 for (i = 0, c = 0; i < numVerts; ++i) { 2053 for (j = 0; j < i; ++j) { 2054 for (k = 0; k < j; ++k) { 2055 for (l = 0; l < k; ++l) { 2056 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] && 2057 graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) { 2058 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l; 2059 /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */ 2060 { 2061 const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2062 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}}, 2063 {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}}, 2064 {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}}, 2065 2066 {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}}, 2067 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2068 {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}}, 2069 {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}}, 2070 2071 {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}}, 2072 {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}}, 2073 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2074 {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}, 2075 2076 {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}}, 2077 {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}}, 2078 {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2079 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}}; 2080 PetscReal normal[4]; 2081 PetscInt e, f, g; 2082 2083 for (d = 0; d < embedDim; ++d) { 2084 normal[d] = 0.0; 2085 for (e = 0; e < embedDim; ++e) { 2086 for (f = 0; f < embedDim; ++f) { 2087 for (g = 0; g < embedDim; ++g) { 2088 normal[d] += epsilon[d][e][f][g]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f])*(coordsIn[l*embedDim+f] - coordsIn[i*embedDim+f]); 2089 } 2090 } 2091 } 2092 } 2093 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 2094 } 2095 ierr = DMPlexSetCone(*dm, c++, cone);CHKERRQ(ierr); 2096 } 2097 } 2098 } 2099 } 2100 } 2101 } 2102 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 2103 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 2104 ierr = PetscFree(graph);CHKERRQ(ierr); 2105 /* Interpolate mesh */ 2106 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2107 ierr = DMDestroy(dm);CHKERRQ(ierr); 2108 *dm = idm; 2109 break; 2110 } 2111 default: SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim); 2112 } 2113 /* Create coordinates */ 2114 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 2115 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2116 ierr = PetscSectionSetFieldComponents(coordSection, 0, embedDim);CHKERRQ(ierr); 2117 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);CHKERRQ(ierr); 2118 for (v = firstVertex; v < firstVertex+numVerts; ++v) { 2119 ierr = PetscSectionSetDof(coordSection, v, embedDim);CHKERRQ(ierr); 2120 ierr = PetscSectionSetFieldDof(coordSection, v, 0, embedDim);CHKERRQ(ierr); 2121 } 2122 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2123 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2124 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 2125 ierr = VecSetBlockSize(coordinates, embedDim);CHKERRQ(ierr); 2126 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2127 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2128 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2129 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2130 for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];} 2131 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2132 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 2133 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2134 ierr = PetscFree(coordsIn);CHKERRQ(ierr); 2135 PetscFunctionReturn(0); 2136 } 2137 2138 /* External function declarations here */ 2139 extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling); 2140 extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat); 2141 extern PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mat); 2142 extern PetscErrorCode DMCreateLocalSection_Plex(DM dm); 2143 extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm); 2144 extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J); 2145 extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm); 2146 extern PetscErrorCode DMCreateCoordinateField_Plex(DM dm, DMField *field); 2147 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm); 2148 extern PetscErrorCode DMSetUp_Plex(DM dm); 2149 extern PetscErrorCode DMDestroy_Plex(DM dm); 2150 extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer); 2151 extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer); 2152 extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm); 2153 extern PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm); 2154 static PetscErrorCode DMInitialize_Plex(DM dm); 2155 2156 /* Replace dm with the contents of dmNew 2157 - Share the DM_Plex structure 2158 - Share the coordinates 2159 - Share the SF 2160 */ 2161 static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew) 2162 { 2163 PetscSF sf; 2164 DM coordDM, coarseDM; 2165 Vec coords; 2166 PetscBool isper; 2167 const PetscReal *maxCell, *L; 2168 const DMBoundaryType *bd; 2169 PetscErrorCode ierr; 2170 2171 PetscFunctionBegin; 2172 ierr = DMGetPointSF(dmNew, &sf);CHKERRQ(ierr); 2173 ierr = DMSetPointSF(dm, sf);CHKERRQ(ierr); 2174 ierr = DMGetCoordinateDM(dmNew, &coordDM);CHKERRQ(ierr); 2175 ierr = DMGetCoordinatesLocal(dmNew, &coords);CHKERRQ(ierr); 2176 ierr = DMSetCoordinateDM(dm, coordDM);CHKERRQ(ierr); 2177 ierr = DMSetCoordinatesLocal(dm, coords);CHKERRQ(ierr); 2178 ierr = DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);CHKERRQ(ierr); 2179 ierr = DMSetPeriodicity(dmNew, isper, maxCell, L, bd);CHKERRQ(ierr); 2180 ierr = DMDestroy_Plex(dm);CHKERRQ(ierr); 2181 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 2182 dm->data = dmNew->data; 2183 ((DM_Plex *) dmNew->data)->refct++; 2184 ierr = DMDestroyLabelLinkList_Internal(dm);CHKERRQ(ierr); 2185 ierr = DMCopyLabels(dmNew, dm, PETSC_OWN_POINTER, PETSC_TRUE);CHKERRQ(ierr); 2186 ierr = DMGetCoarseDM(dmNew,&coarseDM);CHKERRQ(ierr); 2187 ierr = DMSetCoarseDM(dm,coarseDM);CHKERRQ(ierr); 2188 PetscFunctionReturn(0); 2189 } 2190 2191 /* Swap dm with the contents of dmNew 2192 - Swap the DM_Plex structure 2193 - Swap the coordinates 2194 - Swap the point PetscSF 2195 */ 2196 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 2197 { 2198 DM coordDMA, coordDMB; 2199 Vec coordsA, coordsB; 2200 PetscSF sfA, sfB; 2201 void *tmp; 2202 DMLabelLink listTmp; 2203 DMLabel depthTmp; 2204 PetscInt tmpI; 2205 PetscErrorCode ierr; 2206 2207 PetscFunctionBegin; 2208 ierr = DMGetPointSF(dmA, &sfA);CHKERRQ(ierr); 2209 ierr = DMGetPointSF(dmB, &sfB);CHKERRQ(ierr); 2210 ierr = PetscObjectReference((PetscObject) sfA);CHKERRQ(ierr); 2211 ierr = DMSetPointSF(dmA, sfB);CHKERRQ(ierr); 2212 ierr = DMSetPointSF(dmB, sfA);CHKERRQ(ierr); 2213 ierr = PetscObjectDereference((PetscObject) sfA);CHKERRQ(ierr); 2214 2215 ierr = DMGetCoordinateDM(dmA, &coordDMA);CHKERRQ(ierr); 2216 ierr = DMGetCoordinateDM(dmB, &coordDMB);CHKERRQ(ierr); 2217 ierr = PetscObjectReference((PetscObject) coordDMA);CHKERRQ(ierr); 2218 ierr = DMSetCoordinateDM(dmA, coordDMB);CHKERRQ(ierr); 2219 ierr = DMSetCoordinateDM(dmB, coordDMA);CHKERRQ(ierr); 2220 ierr = PetscObjectDereference((PetscObject) coordDMA);CHKERRQ(ierr); 2221 2222 ierr = DMGetCoordinatesLocal(dmA, &coordsA);CHKERRQ(ierr); 2223 ierr = DMGetCoordinatesLocal(dmB, &coordsB);CHKERRQ(ierr); 2224 ierr = PetscObjectReference((PetscObject) coordsA);CHKERRQ(ierr); 2225 ierr = DMSetCoordinatesLocal(dmA, coordsB);CHKERRQ(ierr); 2226 ierr = DMSetCoordinatesLocal(dmB, coordsA);CHKERRQ(ierr); 2227 ierr = PetscObjectDereference((PetscObject) coordsA);CHKERRQ(ierr); 2228 2229 tmp = dmA->data; 2230 dmA->data = dmB->data; 2231 dmB->data = tmp; 2232 listTmp = dmA->labels; 2233 dmA->labels = dmB->labels; 2234 dmB->labels = listTmp; 2235 depthTmp = dmA->depthLabel; 2236 dmA->depthLabel = dmB->depthLabel; 2237 dmB->depthLabel = depthTmp; 2238 tmpI = dmA->levelup; 2239 dmA->levelup = dmB->levelup; 2240 dmB->levelup = tmpI; 2241 PetscFunctionReturn(0); 2242 } 2243 2244 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 2245 { 2246 DM_Plex *mesh = (DM_Plex*) dm->data; 2247 PetscErrorCode ierr; 2248 2249 PetscFunctionBegin; 2250 /* Handle viewing */ 2251 ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); 2252 ierr = PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL,0);CHKERRQ(ierr); 2253 ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL);CHKERRQ(ierr); 2254 ierr = PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL,0);CHKERRQ(ierr); 2255 /* Point Location */ 2256 ierr = PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL);CHKERRQ(ierr); 2257 /* Partitioning and distribution */ 2258 ierr = PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL);CHKERRQ(ierr); 2259 /* Generation and remeshing */ 2260 ierr = PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL);CHKERRQ(ierr); 2261 /* Projection behavior */ 2262 ierr = PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL,0);CHKERRQ(ierr); 2263 ierr = PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);CHKERRQ(ierr); 2264 /* Checking structure */ 2265 { 2266 PetscBool flg = PETSC_FALSE, flg2 = PETSC_FALSE, all = PETSC_FALSE; 2267 2268 ierr = PetscOptionsBool("-dm_plex_check_all", "Perform all checks", NULL, PETSC_FALSE, &all, &flg2);CHKERRQ(ierr); 2269 ierr = PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2270 if (all || (flg && flg2)) {ierr = DMPlexCheckSymmetry(dm);CHKERRQ(ierr);} 2271 ierr = PetscOptionsBool("-dm_plex_check_skeleton", "Check that each cell has the correct number of vertices (only for homogeneous simplex or tensor meshes)", "DMPlexCheckSkeleton", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2272 if (all || (flg && flg2)) {ierr = DMPlexCheckSkeleton(dm, 0);CHKERRQ(ierr);} 2273 ierr = PetscOptionsBool("-dm_plex_check_faces", "Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type", "DMPlexCheckFaces", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2274 if (all || (flg && flg2)) {ierr = DMPlexCheckFaces(dm, 0);CHKERRQ(ierr);} 2275 ierr = PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2276 if (all || (flg && flg2)) {ierr = DMPlexCheckGeometry(dm);CHKERRQ(ierr);} 2277 ierr = PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2278 if (all || (flg && flg2)) {ierr = DMPlexCheckPointSF(dm);CHKERRQ(ierr);} 2279 ierr = PetscOptionsBool("-dm_plex_check_interface_cones", "Check points on inter-partition interfaces have conforming order of cone points", "DMPlexCheckInterfaceCones", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2280 if (all || (flg && flg2)) {ierr = DMPlexCheckInterfaceCones(dm);CHKERRQ(ierr);} 2281 } 2282 2283 ierr = PetscPartitionerSetFromOptions(mesh->partitioner);CHKERRQ(ierr); 2284 PetscFunctionReturn(0); 2285 } 2286 2287 static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 2288 { 2289 PetscInt refine = 0, coarsen = 0, r; 2290 PetscBool isHierarchy; 2291 PetscErrorCode ierr; 2292 2293 PetscFunctionBegin; 2294 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2295 ierr = PetscOptionsHead(PetscOptionsObject,"DMPlex Options");CHKERRQ(ierr); 2296 /* Handle DMPlex refinement */ 2297 ierr = PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL,0);CHKERRQ(ierr); 2298 ierr = PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy,0);CHKERRQ(ierr); 2299 if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 2300 if (refine && isHierarchy) { 2301 DM *dms, coarseDM; 2302 2303 ierr = DMGetCoarseDM(dm, &coarseDM);CHKERRQ(ierr); 2304 ierr = PetscObjectReference((PetscObject)coarseDM);CHKERRQ(ierr); 2305 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 2306 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 2307 /* Total hack since we do not pass in a pointer */ 2308 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 2309 if (refine == 1) { 2310 ierr = DMSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 2311 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2312 } else { 2313 ierr = DMSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 2314 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2315 ierr = DMSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 2316 ierr = DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);CHKERRQ(ierr); 2317 } 2318 ierr = DMSetCoarseDM(dms[refine-1], coarseDM);CHKERRQ(ierr); 2319 ierr = PetscObjectDereference((PetscObject)coarseDM);CHKERRQ(ierr); 2320 /* Free DMs */ 2321 for (r = 0; r < refine; ++r) { 2322 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2323 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2324 } 2325 ierr = PetscFree(dms);CHKERRQ(ierr); 2326 } else { 2327 for (r = 0; r < refine; ++r) { 2328 DM refinedMesh; 2329 2330 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2331 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);CHKERRQ(ierr); 2332 /* Total hack since we do not pass in a pointer */ 2333 ierr = DMPlexReplace_Static(dm, refinedMesh);CHKERRQ(ierr); 2334 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2335 ierr = DMDestroy(&refinedMesh);CHKERRQ(ierr); 2336 } 2337 } 2338 /* Handle DMPlex coarsening */ 2339 ierr = PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL,0);CHKERRQ(ierr); 2340 ierr = PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy,0);CHKERRQ(ierr); 2341 if (coarsen && isHierarchy) { 2342 DM *dms; 2343 2344 ierr = PetscMalloc1(coarsen, &dms);CHKERRQ(ierr); 2345 ierr = DMCoarsenHierarchy(dm, coarsen, dms);CHKERRQ(ierr); 2346 /* Free DMs */ 2347 for (r = 0; r < coarsen; ++r) { 2348 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2349 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2350 } 2351 ierr = PetscFree(dms);CHKERRQ(ierr); 2352 } else { 2353 for (r = 0; r < coarsen; ++r) { 2354 DM coarseMesh; 2355 2356 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2357 ierr = DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);CHKERRQ(ierr); 2358 /* Total hack since we do not pass in a pointer */ 2359 ierr = DMPlexReplace_Static(dm, coarseMesh);CHKERRQ(ierr); 2360 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2361 ierr = DMDestroy(&coarseMesh);CHKERRQ(ierr); 2362 } 2363 } 2364 /* Handle */ 2365 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2366 ierr = PetscOptionsTail();CHKERRQ(ierr); 2367 PetscFunctionReturn(0); 2368 } 2369 2370 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 2371 { 2372 PetscErrorCode ierr; 2373 2374 PetscFunctionBegin; 2375 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2376 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 2377 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 2378 ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); 2379 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 2380 ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); 2381 PetscFunctionReturn(0); 2382 } 2383 2384 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 2385 { 2386 PetscErrorCode ierr; 2387 2388 PetscFunctionBegin; 2389 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2390 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 2391 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 2392 PetscFunctionReturn(0); 2393 } 2394 2395 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 2396 { 2397 PetscInt depth, d; 2398 PetscErrorCode ierr; 2399 2400 PetscFunctionBegin; 2401 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2402 if (depth == 1) { 2403 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 2404 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 2405 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 2406 else {*pStart = 0; *pEnd = 0;} 2407 } else { 2408 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 2409 } 2410 PetscFunctionReturn(0); 2411 } 2412 2413 static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 2414 { 2415 PetscSF sf; 2416 PetscErrorCode ierr; 2417 2418 PetscFunctionBegin; 2419 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 2420 ierr = PetscSFGetRootRanks(sf, nranks, ranks, NULL, NULL, NULL);CHKERRQ(ierr); 2421 PetscFunctionReturn(0); 2422 } 2423 2424 static PetscErrorCode DMInitialize_Plex(DM dm) 2425 { 2426 PetscErrorCode ierr; 2427 2428 PetscFunctionBegin; 2429 dm->ops->view = DMView_Plex; 2430 dm->ops->load = DMLoad_Plex; 2431 dm->ops->setfromoptions = DMSetFromOptions_Plex; 2432 dm->ops->clone = DMClone_Plex; 2433 dm->ops->setup = DMSetUp_Plex; 2434 dm->ops->createlocalsection = DMCreateLocalSection_Plex; 2435 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 2436 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 2437 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 2438 dm->ops->getlocaltoglobalmapping = NULL; 2439 dm->ops->createfieldis = NULL; 2440 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 2441 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 2442 dm->ops->getcoloring = NULL; 2443 dm->ops->creatematrix = DMCreateMatrix_Plex; 2444 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 2445 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 2446 dm->ops->createinjection = DMCreateInjection_Plex; 2447 dm->ops->refine = DMRefine_Plex; 2448 dm->ops->coarsen = DMCoarsen_Plex; 2449 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 2450 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 2451 dm->ops->adaptlabel = DMAdaptLabel_Plex; 2452 dm->ops->adaptmetric = DMAdaptMetric_Plex; 2453 dm->ops->globaltolocalbegin = NULL; 2454 dm->ops->globaltolocalend = NULL; 2455 dm->ops->localtoglobalbegin = NULL; 2456 dm->ops->localtoglobalend = NULL; 2457 dm->ops->destroy = DMDestroy_Plex; 2458 dm->ops->createsubdm = DMCreateSubDM_Plex; 2459 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 2460 dm->ops->getdimpoints = DMGetDimPoints_Plex; 2461 dm->ops->locatepoints = DMLocatePoints_Plex; 2462 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 2463 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 2464 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 2465 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 2466 dm->ops->computel2diff = DMComputeL2Diff_Plex; 2467 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 2468 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 2469 dm->ops->getneighbors = DMGetNeighbors_Plex; 2470 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);CHKERRQ(ierr); 2471 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);CHKERRQ(ierr); 2472 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C",DMCreateNeumannOverlap_Plex);CHKERRQ(ierr); 2473 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex);CHKERRQ(ierr); 2474 PetscFunctionReturn(0); 2475 } 2476 2477 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 2478 { 2479 DM_Plex *mesh = (DM_Plex *) dm->data; 2480 PetscErrorCode ierr; 2481 2482 PetscFunctionBegin; 2483 mesh->refct++; 2484 (*newdm)->data = mesh; 2485 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 2486 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 2487 PetscFunctionReturn(0); 2488 } 2489 2490 /*MC 2491 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 2492 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 2493 specified by a PetscSection object. Ownership in the global representation is determined by 2494 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 2495 2496 Options Database Keys: 2497 + -dm_plex_hash_location - Use grid hashing for point location 2498 . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes 2499 . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing 2500 . -dm_plex_max_projection_height - Maxmimum mesh point height used to project locally 2501 . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement 2502 . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric 2503 . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices 2504 . -dm_plex_check_faces <celltype> - Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type 2505 . -dm_plex_check_geometry - Check that cells have positive volume 2506 . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ 2507 . -dm_plex_view_scale <num> - Scale the TikZ 2508 - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices 2509 2510 2511 Level: intermediate 2512 2513 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 2514 M*/ 2515 2516 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 2517 { 2518 DM_Plex *mesh; 2519 PetscInt unit, d; 2520 PetscErrorCode ierr; 2521 2522 PetscFunctionBegin; 2523 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2524 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 2525 dm->dim = 0; 2526 dm->data = mesh; 2527 2528 mesh->refct = 1; 2529 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 2530 mesh->maxConeSize = 0; 2531 mesh->cones = NULL; 2532 mesh->coneOrientations = NULL; 2533 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 2534 mesh->maxSupportSize = 0; 2535 mesh->supports = NULL; 2536 mesh->refinementUniform = PETSC_TRUE; 2537 mesh->refinementLimit = -1.0; 2538 mesh->ghostCellStart = -1; 2539 mesh->interpolated = DMPLEX_INTERPOLATED_INVALID; 2540 mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID; 2541 2542 mesh->facesTmp = NULL; 2543 2544 mesh->tetgenOpts = NULL; 2545 mesh->triangleOpts = NULL; 2546 ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); 2547 mesh->remeshBd = PETSC_FALSE; 2548 2549 mesh->subpointMap = NULL; 2550 2551 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 2552 2553 mesh->regularRefinement = PETSC_FALSE; 2554 mesh->depthState = -1; 2555 mesh->globalVertexNumbers = NULL; 2556 mesh->globalCellNumbers = NULL; 2557 mesh->anchorSection = NULL; 2558 mesh->anchorIS = NULL; 2559 mesh->createanchors = NULL; 2560 mesh->computeanchormatrix = NULL; 2561 mesh->parentSection = NULL; 2562 mesh->parents = NULL; 2563 mesh->childIDs = NULL; 2564 mesh->childSection = NULL; 2565 mesh->children = NULL; 2566 mesh->referenceTree = NULL; 2567 mesh->getchildsymmetry = NULL; 2568 for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE; 2569 mesh->vtkCellHeight = 0; 2570 mesh->useAnchors = PETSC_FALSE; 2571 2572 mesh->maxProjectionHeight = 0; 2573 2574 mesh->printSetValues = PETSC_FALSE; 2575 mesh->printFEM = 0; 2576 mesh->printTol = 1.0e-10; 2577 2578 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 2579 PetscFunctionReturn(0); 2580 } 2581 2582 /*@ 2583 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 2584 2585 Collective 2586 2587 Input Parameter: 2588 . comm - The communicator for the DMPlex object 2589 2590 Output Parameter: 2591 . mesh - The DMPlex object 2592 2593 Level: beginner 2594 2595 @*/ 2596 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 2597 { 2598 PetscErrorCode ierr; 2599 2600 PetscFunctionBegin; 2601 PetscValidPointer(mesh,2); 2602 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 2603 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 2604 PetscFunctionReturn(0); 2605 } 2606 2607 /* 2608 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 2609 */ 2610 /* TODO: invertCells and spaceDim arguments could be added also to to DMPlexCreateFromCellListParallel(), DMPlexBuildFromCellList_Internal() and DMPlexCreateFromCellList() */ 2611 PetscErrorCode DMPlexBuildFromCellList_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscBool invertCells, PetscSF *sfVert) 2612 { 2613 PetscSF sfPoint; 2614 PetscLayout vLayout; 2615 PetscHSetI vhash; 2616 PetscSFNode *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex; 2617 const PetscInt *vrange; 2618 PetscInt numVerticesAdj, off = 0, *verticesAdj, numVerticesGhost = 0, *localVertex, *cone, c, p, v, g; 2619 PetscMPIInt rank, size; 2620 PetscErrorCode ierr; 2621 2622 PetscFunctionBegin; 2623 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 2624 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); 2625 /* Partition vertices */ 2626 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);CHKERRQ(ierr); 2627 ierr = PetscLayoutSetLocalSize(vLayout, numVertices);CHKERRQ(ierr); 2628 ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr); 2629 ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr); 2630 ierr = PetscLayoutGetRanges(vLayout, &vrange);CHKERRQ(ierr); 2631 /* Count vertices and map them to procs */ 2632 ierr = PetscHSetICreate(&vhash);CHKERRQ(ierr); 2633 for (c = 0; c < numCells; ++c) { 2634 for (p = 0; p < numCorners; ++p) { 2635 ierr = PetscHSetIAdd(vhash, cells[c*numCorners+p]);CHKERRQ(ierr); 2636 } 2637 } 2638 ierr = PetscHSetIGetSize(vhash, &numVerticesAdj);CHKERRQ(ierr); 2639 ierr = PetscMalloc1(numVerticesAdj, &verticesAdj);CHKERRQ(ierr); 2640 ierr = PetscHSetIGetElems(vhash, &off, verticesAdj);CHKERRQ(ierr); 2641 ierr = PetscHSetIDestroy(&vhash);CHKERRQ(ierr); 2642 if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj); 2643 ierr = PetscSortInt(numVerticesAdj, verticesAdj);CHKERRQ(ierr); 2644 ierr = PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);CHKERRQ(ierr); 2645 for (v = 0; v < numVerticesAdj; ++v) { 2646 const PetscInt gv = verticesAdj[v]; 2647 PetscInt vrank; 2648 2649 ierr = PetscFindInt(gv, size+1, vrange, &vrank);CHKERRQ(ierr); 2650 vrank = vrank < 0 ? -(vrank+2) : vrank; 2651 remoteVerticesAdj[v].index = gv - vrange[vrank]; 2652 remoteVerticesAdj[v].rank = vrank; 2653 } 2654 /* Create cones */ 2655 ierr = DMPlexSetChart(dm, 0, numCells+numVerticesAdj);CHKERRQ(ierr); 2656 for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);} 2657 ierr = DMSetUp(dm);CHKERRQ(ierr); 2658 ierr = DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2659 for (c = 0; c < numCells; ++c) { 2660 for (p = 0; p < numCorners; ++p) { 2661 const PetscInt gv = cells[c*numCorners+p]; 2662 PetscInt lv; 2663 2664 ierr = PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);CHKERRQ(ierr); 2665 if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv); 2666 cone[p] = lv+numCells; 2667 } 2668 if (invertCells) { ierr = DMPlexInvertCell_Internal(spaceDim, numCorners, cone);CHKERRQ(ierr); } 2669 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 2670 } 2671 ierr = DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2672 /* Create SF for vertices */ 2673 ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfVert);CHKERRQ(ierr); 2674 ierr = PetscObjectSetName((PetscObject) *sfVert, "Vertex Ownership SF");CHKERRQ(ierr); 2675 ierr = PetscSFSetFromOptions(*sfVert);CHKERRQ(ierr); 2676 ierr = PetscSFSetGraph(*sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);CHKERRQ(ierr); 2677 ierr = PetscFree(verticesAdj);CHKERRQ(ierr); 2678 /* Build pointSF */ 2679 ierr = PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);CHKERRQ(ierr); 2680 for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;} 2681 for (v = 0; v < numVertices; ++v) {vertexOwner[v].index = -1; vertexOwner[v].rank = -1;} 2682 ierr = PetscSFReduceBegin(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 2683 ierr = PetscSFReduceEnd(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 2684 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); 2685 ierr = PetscSFBcastBegin(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 2686 ierr = PetscSFBcastEnd(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 2687 for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost; 2688 ierr = PetscMalloc1(numVerticesGhost, &localVertex);CHKERRQ(ierr); 2689 ierr = PetscMalloc1(numVerticesGhost, &remoteVertex);CHKERRQ(ierr); 2690 for (v = 0, g = 0; v < numVerticesAdj; ++v) { 2691 if (vertexLocal[v].rank != rank) { 2692 localVertex[g] = v+numCells; 2693 remoteVertex[g].index = vertexLocal[v].index; 2694 remoteVertex[g].rank = vertexLocal[v].rank; 2695 ++g; 2696 } 2697 } 2698 ierr = PetscFree2(vertexLocal, vertexOwner);CHKERRQ(ierr); 2699 if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost); 2700 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 2701 ierr = PetscObjectSetName((PetscObject) sfPoint, "point SF");CHKERRQ(ierr); 2702 ierr = PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);CHKERRQ(ierr); 2703 ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr); 2704 /* Fill in the rest of the topology structure */ 2705 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2706 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2707 PetscFunctionReturn(0); 2708 } 2709 2710 /* 2711 This takes as input the coordinates for each owned vertex 2712 */ 2713 PetscErrorCode DMPlexBuildCoordinates_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numV, PetscSF sfVert, const PetscReal vertexCoords[]) 2714 { 2715 PetscSection coordSection; 2716 Vec coordinates; 2717 PetscScalar *coords; 2718 PetscInt numVertices, numVerticesAdj, coordSize, v; 2719 PetscErrorCode ierr; 2720 2721 PetscFunctionBegin; 2722 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 2723 ierr = PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);CHKERRQ(ierr); 2724 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2725 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2726 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 2727 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVerticesAdj);CHKERRQ(ierr); 2728 for (v = numCells; v < numCells+numVerticesAdj; ++v) { 2729 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 2730 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 2731 } 2732 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2733 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2734 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 2735 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 2736 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2737 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2738 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2739 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2740 { 2741 MPI_Datatype coordtype; 2742 2743 /* Need a temp buffer for coords if we have complex/single */ 2744 ierr = MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);CHKERRQ(ierr); 2745 ierr = MPI_Type_commit(&coordtype);CHKERRQ(ierr); 2746 #if defined(PETSC_USE_COMPLEX) 2747 { 2748 PetscScalar *svertexCoords; 2749 PetscInt i; 2750 ierr = PetscMalloc1(numV*spaceDim,&svertexCoords);CHKERRQ(ierr); 2751 for (i=0; i<numV*spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 2752 ierr = PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 2753 ierr = PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 2754 ierr = PetscFree(svertexCoords);CHKERRQ(ierr); 2755 } 2756 #else 2757 ierr = PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 2758 ierr = PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 2759 #endif 2760 ierr = MPI_Type_free(&coordtype);CHKERRQ(ierr); 2761 } 2762 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2763 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2764 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2765 PetscFunctionReturn(0); 2766 } 2767 2768 /*@ 2769 DMPlexCreateFromCellListParallel - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 2770 2771 Input Parameters: 2772 + comm - The communicator 2773 . dim - The topological dimension of the mesh 2774 . numCells - The number of cells owned by this process 2775 . numVertices - The number of vertices owned by this process 2776 . numCorners - The number of vertices for each cell 2777 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 2778 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 2779 . spaceDim - The spatial dimension used for coordinates 2780 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2781 2782 Output Parameter: 2783 + dm - The DM 2784 - vertexSF - Optional, SF describing complete vertex ownership 2785 2786 Note: Two triangles sharing a face 2787 $ 2788 $ 2 2789 $ / | \ 2790 $ / | \ 2791 $ / | \ 2792 $ 0 0 | 1 3 2793 $ \ | / 2794 $ \ | / 2795 $ \ | / 2796 $ 1 2797 would have input 2798 $ numCells = 2, numVertices = 4 2799 $ cells = [0 1 2 1 3 2] 2800 $ 2801 which would result in the DMPlex 2802 $ 2803 $ 4 2804 $ / | \ 2805 $ / | \ 2806 $ / | \ 2807 $ 2 0 | 1 5 2808 $ \ | / 2809 $ \ | / 2810 $ \ | / 2811 $ 3 2812 2813 Level: beginner 2814 2815 .seealso: DMPlexCreateFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate() 2816 @*/ 2817 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) 2818 { 2819 PetscSF sfVert; 2820 PetscErrorCode ierr; 2821 2822 PetscFunctionBegin; 2823 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2824 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2825 PetscValidLogicalCollectiveInt(*dm, dim, 2); 2826 PetscValidLogicalCollectiveInt(*dm, spaceDim, 8); 2827 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 2828 ierr = DMPlexBuildFromCellList_Parallel_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE, &sfVert);CHKERRQ(ierr); 2829 if (interpolate) { 2830 DM idm; 2831 2832 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2833 ierr = DMDestroy(dm);CHKERRQ(ierr); 2834 *dm = idm; 2835 } 2836 ierr = DMPlexBuildCoordinates_Parallel_Internal(*dm, spaceDim, numCells, numVertices, sfVert, vertexCoords);CHKERRQ(ierr); 2837 if (vertexSF) *vertexSF = sfVert; 2838 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 2839 PetscFunctionReturn(0); 2840 } 2841 2842 /* 2843 This takes as input the common mesh generator output, a list of the vertices for each cell 2844 */ 2845 PetscErrorCode DMPlexBuildFromCellList_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscBool invertCells) 2846 { 2847 PetscInt *cone, c, p; 2848 PetscErrorCode ierr; 2849 2850 PetscFunctionBegin; 2851 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 2852 for (c = 0; c < numCells; ++c) { 2853 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 2854 } 2855 ierr = DMSetUp(dm);CHKERRQ(ierr); 2856 ierr = DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2857 for (c = 0; c < numCells; ++c) { 2858 for (p = 0; p < numCorners; ++p) { 2859 cone[p] = cells[c*numCorners+p]+numCells; 2860 } 2861 if (invertCells) { ierr = DMPlexInvertCell_Internal(spaceDim, numCorners, cone);CHKERRQ(ierr); } 2862 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 2863 } 2864 ierr = DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2865 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2866 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2867 PetscFunctionReturn(0); 2868 } 2869 2870 /* 2871 This takes as input the coordinates for each vertex 2872 */ 2873 PetscErrorCode DMPlexBuildCoordinates_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]) 2874 { 2875 PetscSection coordSection; 2876 Vec coordinates; 2877 DM cdm; 2878 PetscScalar *coords; 2879 PetscInt v, d; 2880 PetscErrorCode ierr; 2881 2882 PetscFunctionBegin; 2883 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 2884 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2885 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2886 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 2887 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); 2888 for (v = numCells; v < numCells+numVertices; ++v) { 2889 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 2890 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 2891 } 2892 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2893 2894 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 2895 ierr = DMCreateLocalVector(cdm, &coordinates);CHKERRQ(ierr); 2896 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 2897 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2898 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2899 for (v = 0; v < numVertices; ++v) { 2900 for (d = 0; d < spaceDim; ++d) { 2901 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 2902 } 2903 } 2904 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2905 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2906 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2907 PetscFunctionReturn(0); 2908 } 2909 2910 /*@ 2911 DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 2912 2913 Input Parameters: 2914 + comm - The communicator 2915 . dim - The topological dimension of the mesh 2916 . numCells - The number of cells 2917 . numVertices - The number of vertices 2918 . numCorners - The number of vertices for each cell 2919 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 2920 . cells - An array of numCells*numCorners numbers, the vertices for each cell 2921 . spaceDim - The spatial dimension used for coordinates 2922 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2923 2924 Output Parameter: 2925 . dm - The DM 2926 2927 Note: Two triangles sharing a face 2928 $ 2929 $ 2 2930 $ / | \ 2931 $ / | \ 2932 $ / | \ 2933 $ 0 0 | 1 3 2934 $ \ | / 2935 $ \ | / 2936 $ \ | / 2937 $ 1 2938 would have input 2939 $ numCells = 2, numVertices = 4 2940 $ cells = [0 1 2 1 3 2] 2941 $ 2942 which would result in the DMPlex 2943 $ 2944 $ 4 2945 $ / | \ 2946 $ / | \ 2947 $ / | \ 2948 $ 2 0 | 1 5 2949 $ \ | / 2950 $ \ | / 2951 $ \ | / 2952 $ 3 2953 2954 Level: beginner 2955 2956 .seealso: DMPlexCreateFromDAG(), DMPlexCreate() 2957 @*/ 2958 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) 2959 { 2960 PetscErrorCode ierr; 2961 2962 PetscFunctionBegin; 2963 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2964 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2965 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 2966 ierr = DMPlexBuildFromCellList_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE);CHKERRQ(ierr); 2967 if (interpolate) { 2968 DM idm; 2969 2970 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2971 ierr = DMDestroy(dm);CHKERRQ(ierr); 2972 *dm = idm; 2973 } 2974 ierr = DMPlexBuildCoordinates_Internal(*dm, spaceDim, numCells, numVertices, vertexCoords);CHKERRQ(ierr); 2975 PetscFunctionReturn(0); 2976 } 2977 2978 /*@ 2979 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 2980 2981 Input Parameters: 2982 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 2983 . depth - The depth of the DAG 2984 . numPoints - Array of size depth + 1 containing the number of points at each depth 2985 . coneSize - The cone size of each point 2986 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 2987 . coneOrientations - The orientation of each cone point 2988 - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim() 2989 2990 Output Parameter: 2991 . dm - The DM 2992 2993 Note: Two triangles sharing a face would have input 2994 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 2995 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 2996 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 2997 $ 2998 which would result in the DMPlex 2999 $ 3000 $ 4 3001 $ / | \ 3002 $ / | \ 3003 $ / | \ 3004 $ 2 0 | 1 5 3005 $ \ | / 3006 $ \ | / 3007 $ \ | / 3008 $ 3 3009 $ 3010 $ Notice that all points are numbered consecutively, unlikely DMPlexCreateFromCellList() 3011 3012 Level: advanced 3013 3014 .seealso: DMPlexCreateFromCellList(), DMPlexCreate() 3015 @*/ 3016 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 3017 { 3018 Vec coordinates; 3019 PetscSection coordSection; 3020 PetscScalar *coords; 3021 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 3022 PetscErrorCode ierr; 3023 3024 PetscFunctionBegin; 3025 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3026 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 3027 if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %d cannot be less than intrinsic dimension %d",dimEmbed,dim); 3028 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 3029 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 3030 for (p = pStart; p < pEnd; ++p) { 3031 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 3032 if (firstVertex < 0 && !coneSize[p - pStart]) { 3033 firstVertex = p - pStart; 3034 } 3035 } 3036 if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %d vertices but could not find any", numPoints[0]); 3037 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 3038 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 3039 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 3040 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 3041 } 3042 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3043 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3044 /* Build coordinates */ 3045 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3046 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3047 ierr = PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);CHKERRQ(ierr); 3048 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 3049 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 3050 ierr = PetscSectionSetDof(coordSection, v, dimEmbed);CHKERRQ(ierr); 3051 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);CHKERRQ(ierr); 3052 } 3053 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3054 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3055 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3056 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3057 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3058 ierr = VecSetBlockSize(coordinates, dimEmbed);CHKERRQ(ierr); 3059 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 3060 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3061 for (v = 0; v < numPoints[0]; ++v) { 3062 PetscInt off; 3063 3064 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 3065 for (d = 0; d < dimEmbed; ++d) { 3066 coords[off+d] = vertexCoords[v*dimEmbed+d]; 3067 } 3068 } 3069 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3070 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3071 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3072 PetscFunctionReturn(0); 3073 } 3074 3075 /*@C 3076 DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file. 3077 3078 + comm - The MPI communicator 3079 . filename - Name of the .dat file 3080 - interpolate - Create faces and edges in the mesh 3081 3082 Output Parameter: 3083 . dm - The DM object representing the mesh 3084 3085 Note: The format is the simplest possible: 3086 $ Ne 3087 $ v0 v1 ... vk 3088 $ Nv 3089 $ x y z marker 3090 3091 Level: beginner 3092 3093 .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate() 3094 @*/ 3095 PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3096 { 3097 DMLabel marker; 3098 PetscViewer viewer; 3099 Vec coordinates; 3100 PetscSection coordSection; 3101 PetscScalar *coords; 3102 char line[PETSC_MAX_PATH_LEN]; 3103 PetscInt dim = 3, cdim = 3, coordSize, v, c, d; 3104 PetscMPIInt rank; 3105 int snum, Nv, Nc; 3106 PetscErrorCode ierr; 3107 3108 PetscFunctionBegin; 3109 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 3110 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 3111 ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr); 3112 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 3113 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 3114 if (!rank) { 3115 ierr = PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);CHKERRQ(ierr); 3116 snum = sscanf(line, "%d %d", &Nc, &Nv); 3117 if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3118 } else { 3119 Nc = Nv = 0; 3120 } 3121 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3122 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3123 ierr = DMPlexSetChart(*dm, 0, Nc+Nv);CHKERRQ(ierr); 3124 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3125 ierr = DMSetCoordinateDim(*dm, cdim);CHKERRQ(ierr); 3126 /* Read topology */ 3127 if (!rank) { 3128 PetscInt cone[8], corners = 8; 3129 int vbuf[8], v; 3130 3131 for (c = 0; c < Nc; ++c) {ierr = DMPlexSetConeSize(*dm, c, corners);CHKERRQ(ierr);} 3132 ierr = DMSetUp(*dm);CHKERRQ(ierr); 3133 for (c = 0; c < Nc; ++c) { 3134 ierr = PetscViewerRead(viewer, line, corners, NULL, PETSC_STRING);CHKERRQ(ierr); 3135 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]); 3136 if (snum != corners) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3137 for (v = 0; v < corners; ++v) cone[v] = vbuf[v] + Nc; 3138 /* Hexahedra are inverted */ 3139 { 3140 PetscInt tmp = cone[1]; 3141 cone[1] = cone[3]; 3142 cone[3] = tmp; 3143 } 3144 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 3145 } 3146 } 3147 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 3148 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 3149 /* Read coordinates */ 3150 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 3151 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3152 ierr = PetscSectionSetFieldComponents(coordSection, 0, cdim);CHKERRQ(ierr); 3153 ierr = PetscSectionSetChart(coordSection, Nc, Nc + Nv);CHKERRQ(ierr); 3154 for (v = Nc; v < Nc+Nv; ++v) { 3155 ierr = PetscSectionSetDof(coordSection, v, cdim);CHKERRQ(ierr); 3156 ierr = PetscSectionSetFieldDof(coordSection, v, 0, cdim);CHKERRQ(ierr); 3157 } 3158 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3159 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3160 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3161 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3162 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3163 ierr = VecSetBlockSize(coordinates, cdim);CHKERRQ(ierr); 3164 ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr); 3165 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3166 if (!rank) { 3167 double x[3]; 3168 int val; 3169 3170 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 3171 ierr = DMGetLabel(*dm, "marker", &marker);CHKERRQ(ierr); 3172 for (v = 0; v < Nv; ++v) { 3173 ierr = PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);CHKERRQ(ierr); 3174 snum = sscanf(line, "%lg %lg %lg %d", &x[0], &x[1], &x[2], &val); 3175 if (snum != 4) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3176 for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d]; 3177 if (val) {ierr = DMLabelSetValue(marker, v+Nc, val);CHKERRQ(ierr);} 3178 } 3179 } 3180 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3181 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 3182 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3183 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 3184 if (interpolate) { 3185 DM idm; 3186 DMLabel bdlabel; 3187 3188 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3189 ierr = DMDestroy(dm);CHKERRQ(ierr); 3190 *dm = idm; 3191 3192 ierr = DMGetLabel(*dm, "marker", &bdlabel);CHKERRQ(ierr); 3193 ierr = DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 3194 ierr = DMPlexLabelComplete(*dm, bdlabel);CHKERRQ(ierr); 3195 } 3196 PetscFunctionReturn(0); 3197 } 3198 3199 /*@C 3200 DMPlexCreateFromFile - This takes a filename and produces a DM 3201 3202 Input Parameters: 3203 + comm - The communicator 3204 . filename - A file name 3205 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 3206 3207 Output Parameter: 3208 . dm - The DM 3209 3210 Options Database Keys: 3211 . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5 3212 3213 Use -dm_plex_create_ prefix to pass options to the internal PetscViewer, e.g. 3214 $ -dm_plex_create_viewer_hdf5_collective 3215 3216 Level: beginner 3217 3218 .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellList(), DMPlexCreate() 3219 @*/ 3220 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3221 { 3222 const char *extGmsh = ".msh"; 3223 const char *extGmsh2 = ".msh2"; 3224 const char *extGmsh4 = ".msh4"; 3225 const char *extCGNS = ".cgns"; 3226 const char *extExodus = ".exo"; 3227 const char *extGenesis = ".gen"; 3228 const char *extFluent = ".cas"; 3229 const char *extHDF5 = ".h5"; 3230 const char *extMed = ".med"; 3231 const char *extPLY = ".ply"; 3232 const char *extCV = ".dat"; 3233 size_t len; 3234 PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isCV; 3235 PetscMPIInt rank; 3236 PetscErrorCode ierr; 3237 3238 PetscFunctionBegin; 3239 PetscValidCharPointer(filename, 2); 3240 PetscValidPointer(dm, 4); 3241 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 3242 ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); 3243 if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 3244 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);CHKERRQ(ierr); 3245 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh2, 5, &isGmsh2);CHKERRQ(ierr); 3246 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh4, 5, &isGmsh4);CHKERRQ(ierr); 3247 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);CHKERRQ(ierr); 3248 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);CHKERRQ(ierr); 3249 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);CHKERRQ(ierr); 3250 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);CHKERRQ(ierr); 3251 ierr = PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);CHKERRQ(ierr); 3252 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);CHKERRQ(ierr); 3253 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);CHKERRQ(ierr); 3254 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);CHKERRQ(ierr); 3255 if (isGmsh || isGmsh2 || isGmsh4) { 3256 ierr = DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3257 } else if (isCGNS) { 3258 ierr = DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3259 } else if (isExodus || isGenesis) { 3260 ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3261 } else if (isFluent) { 3262 ierr = DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3263 } else if (isHDF5) { 3264 PetscBool load_hdf5_xdmf = PETSC_FALSE; 3265 PetscViewer viewer; 3266 3267 /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */ 3268 ierr = PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf", 5, &load_hdf5_xdmf);CHKERRQ(ierr); 3269 ierr = PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);CHKERRQ(ierr); 3270 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 3271 ierr = PetscViewerSetType(viewer, PETSCVIEWERHDF5);CHKERRQ(ierr); 3272 ierr = PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_");CHKERRQ(ierr); 3273 ierr = PetscViewerSetFromOptions(viewer);CHKERRQ(ierr); 3274 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 3275 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 3276 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3277 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3278 if (load_hdf5_xdmf) {ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);CHKERRQ(ierr);} 3279 ierr = DMLoad(*dm, viewer);CHKERRQ(ierr); 3280 if (load_hdf5_xdmf) {ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);} 3281 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 3282 3283 if (interpolate) { 3284 DM idm; 3285 3286 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3287 ierr = DMDestroy(dm);CHKERRQ(ierr); 3288 *dm = idm; 3289 } 3290 } else if (isMed) { 3291 ierr = DMPlexCreateMedFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3292 } else if (isPLY) { 3293 ierr = DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3294 } else if (isCV) { 3295 ierr = DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3296 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 3297 PetscFunctionReturn(0); 3298 } 3299 3300 /*@ 3301 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 3302 3303 Collective 3304 3305 Input Parameters: 3306 + comm - The communicator 3307 . dim - The spatial dimension 3308 - simplex - Flag for simplex, otherwise use a tensor-product cell 3309 3310 Output Parameter: 3311 . refdm - The reference cell 3312 3313 Level: intermediate 3314 3315 .seealso: 3316 @*/ 3317 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm) 3318 { 3319 DM rdm; 3320 Vec coords; 3321 PetscErrorCode ierr; 3322 3323 PetscFunctionBeginUser; 3324 ierr = DMCreate(comm, &rdm);CHKERRQ(ierr); 3325 ierr = DMSetType(rdm, DMPLEX);CHKERRQ(ierr); 3326 ierr = DMSetDimension(rdm, dim);CHKERRQ(ierr); 3327 switch (dim) { 3328 case 0: 3329 { 3330 PetscInt numPoints[1] = {1}; 3331 PetscInt coneSize[1] = {0}; 3332 PetscInt cones[1] = {0}; 3333 PetscInt coneOrientations[1] = {0}; 3334 PetscScalar vertexCoords[1] = {0.0}; 3335 3336 ierr = DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3337 } 3338 break; 3339 case 1: 3340 { 3341 PetscInt numPoints[2] = {2, 1}; 3342 PetscInt coneSize[3] = {2, 0, 0}; 3343 PetscInt cones[2] = {1, 2}; 3344 PetscInt coneOrientations[2] = {0, 0}; 3345 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 3346 3347 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3348 } 3349 break; 3350 case 2: 3351 if (simplex) { 3352 PetscInt numPoints[2] = {3, 1}; 3353 PetscInt coneSize[4] = {3, 0, 0, 0}; 3354 PetscInt cones[3] = {1, 2, 3}; 3355 PetscInt coneOrientations[3] = {0, 0, 0}; 3356 PetscScalar vertexCoords[6] = {-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] = {4, 1}; 3361 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3362 PetscInt cones[4] = {1, 2, 3, 4}; 3363 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3364 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 3365 3366 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3367 } 3368 break; 3369 case 3: 3370 if (simplex) { 3371 PetscInt numPoints[2] = {4, 1}; 3372 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3373 PetscInt cones[4] = {1, 3, 2, 4}; 3374 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3375 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}; 3376 3377 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3378 } else { 3379 PetscInt numPoints[2] = {8, 1}; 3380 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3381 PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8}; 3382 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3383 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, 3384 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3385 3386 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3387 } 3388 break; 3389 default: 3390 SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %d", dim); 3391 } 3392 ierr = DMPlexInterpolate(rdm, refdm);CHKERRQ(ierr); 3393 if (rdm->coordinateDM) { 3394 DM ncdm; 3395 PetscSection cs; 3396 PetscInt pEnd = -1; 3397 3398 ierr = DMGetLocalSection(rdm->coordinateDM, &cs);CHKERRQ(ierr); 3399 if (cs) {ierr = PetscSectionGetChart(cs, NULL, &pEnd);CHKERRQ(ierr);} 3400 if (pEnd >= 0) { 3401 ierr = DMClone(*refdm, &ncdm);CHKERRQ(ierr); 3402 ierr = DMCopyDisc(rdm->coordinateDM, ncdm);CHKERRQ(ierr); 3403 ierr = DMSetLocalSection(ncdm, cs);CHKERRQ(ierr); 3404 ierr = DMSetCoordinateDM(*refdm, ncdm);CHKERRQ(ierr); 3405 ierr = DMDestroy(&ncdm);CHKERRQ(ierr); 3406 } 3407 } 3408 ierr = DMGetCoordinatesLocal(rdm, &coords);CHKERRQ(ierr); 3409 if (coords) { 3410 ierr = DMSetCoordinatesLocal(*refdm, coords);CHKERRQ(ierr); 3411 } else { 3412 ierr = DMGetCoordinates(rdm, &coords);CHKERRQ(ierr); 3413 if (coords) {ierr = DMSetCoordinates(*refdm, coords);CHKERRQ(ierr);} 3414 } 3415 ierr = DMDestroy(&rdm);CHKERRQ(ierr); 3416 PetscFunctionReturn(0); 3417 } 3418